Key: 3 Medline: Authors: Abdulkader N;Brun JL Title: Induction, detection and isolation of temperature-sensitive lethal and/or sterile mutants in nematodes. I. The free-living nematode C. elegans. Citation: Revue de Nematologie 1: 27-37 1978 Type: ARTICLE Genes: Abstract: Applying a series of techniques intended to induce, detect and isolate lethal and/or sterile temperature-sensitive mutants, specific to the self-fertilizing hermaphrodite nematode Caenorhabditis elegans, Bergerac strain, 25 such mutants have been found. Optimal conditions for the application of mutagenic treatment and the detection of such mutations are discussed. ------------------- Key: 5 Medline: Authors: Abi-Rached M;Brun JL Title: Etude ultrastructurale des relations entre ovocytes et rachis au cours de l'ovogenese du nematode C. elegans. Citation: Nematologica 21: 151-162 1975 Type: ARTICLE Genes: Abstract: Before diakinesis, the development of the oocytes of C. elegans takes place in the presence of a specific anatomical structure: the rachis. This is an undivided, anucleated cytoplasmic mass placed in the central part of the ovary. Electron microscopy shows that, at first, in the gonial region, it is made of two branches which infiltrate themselves between the oogonia and then converge in a single axial column. Afterwards, this column will be pushed to the outside of the gonad and will disappear when the great oocyte increase takes place. Until then, the rachis is limited by its own envelope and connects each germinal cell through a pore present in the double layered membrane. The cytoplasmic bridge established between the oogonia and the rachis, the presence of a typical Golgi apparatus and of numerous mitochondria in the rachis strongly suggest that the rachis plays a role in the oocyte ------------------- Key: 6 Medline: Authors: Abi-Rached M;Brun JL Title: Ultrastructural changes in the nuclear and perinuclear regions of the oogonia and primary oocytes of C. elegans, Bergerac strain. Citation: Revue de Nematologie 1: 63-72 1978 Type: ARTICLE Genes: Abstract: Electron microscope studies in and around the nucleus of C. elegans oogonia and primary oocytes showed fibrogranular formations whose presence is not always constant. The nucleolus, very large in the first oogenetic stages, disappeared during early diakinesis. In pachytene and diplotene, it underwent a vacuolization phase in its central part. Perinuclear corpuscules and groups of granules were limited to the vitellogenetic phase of meiotic I prophase: they were localized in the vicinity of the nuclear membrane and nucleolus. The perinuclear formations, detectable as early as germigene, remained until full ooplasmic growth. Their localization at the limit of the nucleus led to their involvement in the exchange processes which took place between the nucleolus and the cytoplasm, by way of the perinucleolar granules and ------------------- Key: 7 Medline: Authors: Abi-Rached M;Brun JL Title: Changes in the synaptonemal complex in the oocyte nucleus in meiotic prophase of C. elegans. Citation: C.R. des Seances de l'Academie des Sciences Serie D 288: 425-428 1979 Type: ARTICLE Genes: Abstract: During oogenesis in the hermaphroditic nematode C. elegans, the synaptonemal complex is not detectable until the homologous chromosomes are at least partly paired (that is until meiotic prophase synapsis). In the pachytene stage, the complex has a typically classic organization. At the separation phase, the complex persists in certain places, in the diplotene stage and even in early diakinesis. These zones which persist during separation of the homologous chromosomes are believed to correspond to chiasma. This interpretation therefore implicates the complex in the recombination mechanism. ------------------- Key: 8 Medline: 78127686 Authors: Albertson DG;Sulston JE;White JG Title: Cell cycling and DNA replication in a mutant blocked in cell division in the nematode C. elegans. Citation: Developmental Biology 63: 165-178 1978 Type: ARTICLE Genes: lin-5 nuc-1 Abstract: The postembryonic development of the nematode Caenorhabditis elegans has been described at the level of individual cell lineages. A mutant of postembryonic development, lin-5 II, causes a failure of postembryonic nuclear and cell divisions. Mitosis in living animals is seen by light microscopy to proceed through prophase and nuclear envelope breakdown, but an abnormal-looking metaphase plate forms in the mutant, after which the interphase nuclear morphology reappears until the next attempted round of division. The precursor cells which give rise to the ventral nerve cord have been studied in lin-5. In the wild type these cells divide asymmetrically to give six descendants (one hypodermal cell and five neurons). In the mutant these precursors accumulate approximately six times the diploid quantity of DNA within a single nucleus, while attempting mitosis up to three times. These polyploid cells display characteristics of cells they would have produced ordinarily. ------------------- Key: 9 Medline: 76269913 Authors: Albertson DG;Thomson JN Title: The pharynx of C. elegans. Citation: Philosophical Transactions of the Royal Society of London 275B: 299-325 1976 Type: ARTICLE Genes: Abstract: The anatomy of the pharynx of Caenorhabditis elegans has been reconstructed from electron micrographs of serial sections. The pharynx is used for pumping food into the gut, and is composed of 34 muscle cells, 9 marginal cells, 9 epithelial cells, 5 gland cells and 20 neurones. Three regions of specialization in the cuticle lining of the pharyngeal lumen may aid in the accumulation of food particles. A basement membrane isolates the pharynx from the rest of the animal, making the pharyngeal nervous system a nearly self-contained unit which is composed primarily of five classes of motor neurones and six classes of interneurones. Three other classes have also been described, which by their morphology appear to be neurosecretory and motor, motor and interneuronal, and lastly one pair that only innervates three of the marginal cells. Some classes of neurone have free endings just under the cuticle lining the lumen of the pharynx, suggesting that these are mechano- or proprio-receptive endings. The connectivity of these neurones has been described at the level of individual synaptic regions, and after combining this information with video taped observations of the pharynx pumping, some interpretations of how these neurones function have been offered. ------------------- Key: 10 Medline: Authors: Ali M;Wahab A;El-Kifel AH Title: Nematodes associated with Coleoptera species in Egypt Part 2. Citation: Parasitologia Hungarica 6: 169-188 1973 Type: ARTICLE Genes: Abstract: ------------------- Key: 11 Medline: Authors: Anderson GL Title: Responses of dauerlarvae of C. elegans (Nematoda: Rhabditidae) to thermal stress and oxygen deprivation. Citation: Canadian Journal of Zoology 56: 1786-1791 1978 Type: ARTICLE Genes: Abstract: Larval forms of the free-living nematode Caenorhabditis elegans possess the ability to enter a developmental stage which is thought to be specialized for survival in harsh environmental conditions, i.e. the dauerlarval stage. In this study the responses of dauerlarvae to thermal stress and oxygen deprivation are investigated. Oxygen consumption of dauerlarvae is less sensitive to temperature change than that of adults, with Q10 values of 1.7 and 2.6 respectively. The upper thermal tolerance limit of dauerlarvae is also different from that of adults; dauerlarvae survive approximately three times longer than adults when exposed to 37C. In addition to differences in thermal tolerance, dauerlarvae surrvive longer under anaerobic conditions than adults, 7 days and 2 days respectively. On recovery from anaerobic stress dauerlarvae exhibit behavior changes which are suggestive of emergence from the dauerlarval stage. The responses of dauerlarvae to thermal stress and oxygen deprivation appear to be important aspects of the specialization for survival ------------------- Key: 12 Medline: Authors: Anderson GL;Dusenbery DB Title: Critical oxygen tension of C. elegans. Citation: Journal of Nematology 9: 253-254 1977 Type: ARTICLE Genes: Abstract: Regulators are able to maintain a stable oxygen consumption, despite variations in ambient tension, down to a characteristically low "critical" oxygen tension. Below this tension, oxygen consumption is a function of ambient oxygen tension. Free-living nematodes are generally reported to have low critical oxygen tensions; i.e., they generally behave as regulators with respect to oxygen consumption. Caenorhabditis briggsae, a commonly studied free-living nematode, behaves as a regulator with a reported critical oxygen tension of 38 mm Hg. A closely related species, Caenorhabditis elegans, is reported to have a much higher critical oxygen tension, approximately 122 mm Hg. Caenorhabditis elegans would, therefore, be an exception to the generalization that free-living nematodes are regulators. The current study was undertaken to re-evaluate the influence of oxygen tension upon oxygen consumption in this species. A more accurate estimate of its critical oxygen tension may be useful in view of the increasing use of the species as an experimental model. ------------------- Key: 14 Medline: Authors: Andrew PA;Nicholas WL Title: Effect of bacteria on dispersal of C. elegans Citation: Nematologica 22: 451-461 1976 Type: ARTICLE Genes: Abstract: The dispersal and behavior of Caenorhabditis elegans in the presence of various species of bacteria were studied on agar plates. Several species proved attractive to the nematode, the proximity of colonies of living bacteria increasing the rate of dispersal of the nematodes, which on contact tended to remain within the colonies feeding on the bacteria. Other species showed little attraction, or proved repellent. Escherichia coli, Pseudomonas fluorescens and P. aeruginosa were attractive as well as supporting growth and reproduction of the nematode. Dead bacteria were unattractive. Bacillus megatherium repelled ------------------- Key: 15 Medline: Authors: Ward S Title: Genetic studies of chemotaxis mutants in nematodes. Citation: Experimental Neurology 48: 58-59 1975 Type: NEWS Genes: Abstract: The precision of neuronal development is programmed genetically. The genes involved must be expressed in an orderly sequence so that their products appear in the right cell at the right time. By studying mutants in which this sequence is altered, it should be possible to dissect the development and recognize the steps controlled by individual genes.... ------------------- Key: 16 Medline: Authors: Babu P Title: Biochemical genetics of C. elegans. Citation: Molecular & General Genetics 135: 39-44 1974 Type: ARTICLE Genes: flu-1 flu-2 flu-3 flu-4 Abstract: A new method of isolating mutants of the free-living nematode Caenorhabditis elegans is described. This method utilizes the fluorescence of the nematode as the phenotype. 15 mutants belonging to four genes obtained using this technique have been characterised. Mutants in two of these genes are shown to have blocks in tryptophan catabolism. It is suggested that this method could be used to obtain mutants corresponding to blocks in other metabolic pathways with fluorescent end products. ------------------- Key: 21 Medline: 72243209 Authors: Beguet B Title: The persistence of processes regulating the level of reproduction in the herm nematode C. elegans, despite parental aging/ Citation: Experimental Gerontology 7: 207-218 1972 Type: ARTICLE Genes: Abstract: Starting with a laboratory strain of C. elegans, a self-fertilizing hermaphrodite nematode, 2 experimental series (Y from young parents and O from old parents) were selectively maintained over 9 consecutive generations. Each series was characterized by the age of the parents from which each generation was derived (5 and 8 days respectively). The differential behaviour of the average fecundity in these two series was studied systematically in each generation. First of all it could be shown that fecundity was significantly reduced in the first 4 generations of the O series. Then, in the 5th generation, the fecundity of the O series returned to a level similar to that of the Y series. The regulation thus demonstrated in C. elegans contrasts with the results obtained in most work on aging, from which it would appear rather to be linked to a disorganization of the homeostatic processes. The regulatory processes noted were identified by means of the comparative analysis of the various lines maintained in individual cultures. Two explanatory hypotheses are put forward to try to link the regulation seen with the selection obtained. ------------------- Key: 22 Medline: Authors: Beguet B Title: Un exemple de derive meiotique chez un nematode libre autofecond C. elegans. Citation: C.R. des Seances de l'Academie des Sciences Serie D 279: 2115-2118 1974 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 23 Medline: Authors: Beguet B Title: Cryoconservation de mutants "femelle-steriles" d'un nematode libre hermaphrodite C. elegans a la temperature de l'azote liquide. Citation: Bulletin de la Societe Zoologique de France 101: 137-137 1976 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 24 Medline: Authors: Beguet B Title: Genetique de la physiologie ovocytaire chez un nematode libre autofecond C. elegans. I. Influence du genotype et selection/ Citation: Genetica 45: 405-424 1975 Type: ARTICLE Genes: Abstract: In the free-living hermaproditic autogamous nematode C. elegans, a strain heterozygous at one locus, which controls size but also has a pleiotropic effect on fecundity, was created artificially. We have studied the inbreeding effects on fecundity and viability for the three genotypes obtained by self-fertilization with controlled cultures submitted to intensive inbreeding. An effect which produced a 10% significant reduction in homozygote wild type fecundity was found. After four generations, the fecundity of homozygous wild type returned to the heterozygous level. The initial reduction in fecundity is caused by the low viability of the homozygous eggs. This is an expression of the genetic load. A hypothesis is suggested concerning the next homozygous generations: the regulatory processes specific to inbreeding would contribute to maintaining the best genetic state. ------------------- Key: 25 Medline: Authors: Beguet B Title: Etude genetique d'un mutant meiotique dominant chez C. elegans, souche Bergerac. Citation: Revue de Nematologie 1: 39-45 1978 Type: ARTICLE Genes: Abstract: In Caenorhabditis elegans, wild-type hermaphrodites produce by self-fertilization hermaphrodites mainly with only a low frequency of males (10*-3). This XO male progeny is produced by nullo-X gametes. A mutant with increased frequency of males was found during a search for ethane-methane-sulfonate induced mutants. This mutation f69 dm is dominant and is located in an autosomal linkage group. Homozygous him/him or heterozygous him/+ hermaphrodite for this mutation gave rise to approximatively 20% males. They also produced 17% sterile hermaphrodites. Such mutants might allow analysis of meiosis in this organism because it reflects some kind of chromosomal abnormality. Probably, X loss occurs by a meiotic nondisjunction mechanism in both gametic lines. ------------------- Key: 26 Medline: 72243208 Authors: Beguet B;Brun JL Title: Influence of parental aging on the reproduction of the F1 generation in a hermaphrodite nematode C. elegans. Citation: Experimental Gerontology 7: 195-206 1972 Type: ARTICLE Genes: Abstract: In the free-living hermaphrodite autogamous nematode C. elegans, parental senescence generally leads to a significant reduction in the number of F2 adults derived from F1 parents. Indeed, this reduction is seen in 70 per cent of lines. It is related to changes in the reproductive mechanisms of the F1 generation, affecting both the physiology of the gonad and the products of the ovotestis: Earlier sexual maturation of the F1 O hermphrodite derived from elderly parents (4 1/4 days instead of 4 1/2 days); A 15 per cent reduction in the number of spermatozoa produced by the F1 O; An increase in the mortality of F2 O eggs, rising to 50 per cent in eggs laid on the last day. These findings suggest that the causes of the reduction of fecundity arise during oogenesis in the F1 O subjects. It is principally the cytoplasm of the ooctye that appears to be affected. Various hypotheses are put forward concerning the way in which this prolonged ------------------- Key: 27 Medline: Authors: Beguet B;Gibert M-A Title: Obtaining a self-fertilizing hermaphrodite mutant with a male copulatory bursa in the free-living nematode C. elegans var. Bergerac. Citation: C.R. des Seances de l'Academie des Sciences Serie D 286: 989-992 1978 Type: ARTICLE Genes: tra-2 Abstract: The ethylmethanesulfonate, acting on larva of the wild type strain of Caenorhabditis elegans, allowed us to isolate a recessive mutant, f70, with an abnormal sexual differentiation. Both the gonad and genital tractus which are phenotypically hermaphrodite and functional and the copulatory bursa which is typical of the rare males (1/1000) usually observed in such a population are found on this self-fertilizing mutant. The mutation threw off the repression of the mitotic division mechanisms in some postembryonic cellular lineages normally blocked in the hermaphrodite wild type. ------------------- Key: 28 Medline: 70112698 Authors: Behme R;Pasternak J Title: DNA base composition of some free living nematode species. Citation: Canadian Journal of Genetics & Cytology 11: 993-1000 1969 Type: ARTICLE Genes: Abstract: The mean base compositions (% GC) of DNA samples from five free-living nematodes were determined by CsCl equilibrium buoyant-density centrifugation and thermal denaturation studies. Both methods gave similar results indicating that there is no extensive replacement of the usual bases in nematode DNA. From the ultracentrifugation studies the % GC content of the DNA of Caenorhabditis briggsae, Turbatrix aceti, Rhabditis (Rhabditis) anomala, Panagrellus redivivus, and Panagrellus silusiae was 36, 40, 42, 44 and 44, respectively. The sample of DNA from T. aceti showed two distinct ultraviolet absorbing bands in a CsCl gradient. The band at 1,688 g/cm3 proved to be a polysaccharide. It gave a distinctive refractive index pattern when viewed with the schlieren optical system, was insensitive to DNase treatment and was removed by a-amylase treatment. On the other hand, the material banding at 1,699 g/cm3 was shown to be DNA. This band produced no disturbance in the refractive index gradient. It was not altered by a-amylase treatment, but it was DNase sensitive. Since P. redivivus and P. silusiae were found to have the same DNA base composition their ability to interbreed was examined. These two forms were cross-fertile and the ------------------- Key: 29 Medline: Authors: Bird AF Title: A method of distinguishing between living and dead nematodes by enzymatically induced fluorescence. Citation: Journal of Nematology 11: 103-105 1979 Type: ARTICLE Genes: Abstract: Since it is sometimes difficult to distinguish between living and dead nematodes, dyes are used, such as New Blue R, Chrysoidin, Eosin-Y, and several fluorochromes, with varied success. A method is described here that is rapid (results in 15 min) and has a mechanism of staining that is understood. The technique was described first by Rotman and Papermaster, working with living mammalian cells, and later by Heslop-Harrison and Heslop-Harrison, working with plant material. It takes advantage of the presence of esterases which hydrolyse nonfluorescent fatty acid esters of fluorescein to yield fluorescein, which accumulates and is detectable by its fluorescence. Since esterases are known to be present in quantity in nematodes, concentrated principally in the nervous system, male spicules, and gut, this technique seemed worth testing as a rapid means of distinguishing between living and dead nematodes. ------------------- Key: 30 Medline: 76207304 Authors: Brenner S Title: The genetics of behaviour. Citation: British Medical Bulletin 29: 269-271 1973 Type: REVIEW Genes: unc-5 unc-30 Abstract: There is growing interest in the study of the genetics of behaviour. No one can doubt that the behaviour patterns of higher organisms are central for their existence and survival and that changes in these patterns have accompanied evolutionary diversification. Micro-organisms pursue a mode of existence close to the molecular level and very little is interposed between the environment and the biochemical machinery of uptake, biosynthesis and replication. The opposite is true of higher organisms, where we find an elaborate apparatus that is responsible for the generation and control of movement, for the detection of food and for mating. Much of this is genetically determined and, particularly in invertebrates, there are complex sequences of behaviour which are not learnt but are programmed by the genes. ------------------- Key: 31 Medline: 74271161 Authors: Brenner S Title: The genetics of Caenorhabditis elegans. Citation: Genetics 77: 71-94 1974 Type: ARTICLE Genes: bli-1 bli-2 bli-3 bli-4 bli-5 dpy-1 dpy-2 dpy-3 dpy-5 dpy-6 dpy-7 dpy-8 dpy-9 dpy-10 dpy-11 dpy-13 dpy-14 dpy-17 dpy-18 lev-1 lon-1 lon-2 rol-1 rol-3 sma-1 sma-2 sma-3 sma-4 sqt-3 unc-1 unc-2 unc-3 unc-4 unc-5 unc-6 unc-7 unc-8 unc-9 unc-10 unc-11 unc-13 unc-14 unc-15 unc-16 unc-17 unc-18 unc-20 unc-23 unc-24 unc-25 unc-26 unc-27 unc-29 unc-30 unc-31 unc-32 unc-33 unc-34 unc-35 unc-36 unc-37 unc-38 unc-39 unc-40 unc-41 unc-42 unc-43 unc-44 unc-45 unc-46 unc-47 unc-49 unc-50 unc-51 unc-53 unc-55 unc-57 unc-58 unc-59 unc-60 unc-61 unc-62 unc-63 unc-64 unc-65 unc-67 unc-68 unc-69 unc-70 unc-71 unc-73 unc-74 unc-75 unc-76 unc-77 vab-1 vab-2 vab-5 Abstract: Methods are described for the isolation, complementation and mapping of mutants of Caenorhabditis elegans, a small free-living nematode worm. About 300 EMS-induced mutants affecting behavior and morphology have been characterized and about one hundred genes have been defined. Mutations in 77 of these alter movement of the animal. Estimates of the induced mutation frequency of both the visible mutants and X chromosome lethals suggest that, just as in Drosophila, the genetic units in C. elegans are large. ------------------- Key: 33 Medline: Authors: Brun J Title: Evolution de la prophase meiotique chez C. elegans Maupas 1900, sous l'influence de temperature elevees. Citation: Bulletin Biologique de la France et de la Belgique 89: 326-346 1955 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 34 Medline: Authors: Brun J Title: Genetic adaptation of C. elegans (Nematoda) to high temperatures. Citation: Science 150: 1467- 1965 Type: ARTICLE Genes: Abstract: When taken directly from a strain kept for several years at 18C in the laboratory, Caenorhabditis elegans cannot reproduce indefinetely at temperatures higher than 22C. By progressive and very slow increments of the breeding temperature, a strain fecund at 24.5C was obtained. ------------------- Key: 36 Medline: Authors: Brun JL Title: L'adaptation aux temperatures elevees chez un nematode C. elegans Maupas 1900. I. L'adaptation et son evolution. Citation: Annales de Biologie Animale, Biochimie, Biophysique 6: 127-158 1966 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans is a Nematode strain of almost exclusively hermaphroditic self-fertilizing animals. Since they are kept individually on an agar medium, it is easy to determine their fertilities. The Bergerac strain experimented upon had been kept for 700 generations at 18C when this investigation was started. Average fertility was 141 progeny per hermaphrodite. Under our experimental conditions, the animals could never be kept on after the 1st generation if they were raised from 18 to 24.5C straight off. But, they could lastingly withstand this temperature if a certain number of generations were previously kept at intervening temperatures, viz. 22, 23, 23.5 and 24. Shortly after the transfers to any one of these intermediate temperatures - or to 24.5C as well - , we noticed a gradual slowing down of fertility; a minimum was reached at the 5th or 6th generation. After this initial stage of sensitiveness, fertility was gradually increased in relation with the duration of breeding. The adaptive modification is very slow. At 23.5C for instance, it is after 100 generations only that a fertility four times greater than that of the first generation transferred is reached. It is only after 1000 generations that the Nematodes can withstand exposure to 24.5C. When a strain has become acclimatized to a higher temperature, it shows an intrinsic fertility greater than that of a strain acclimatized to a lower temperature. This can be observed when 23.5C adapted animals are taken down to 18C: their average fertility (=230) can then be compared with that of the animals kept at 18C throughout (=140). So, both the possible acclimatization to a higher temperature and the fertility at normal or lower temperatures are conditionned by the duration of breeding at a high temperature. Therefore, it appears that acclimatization results from a cumulative effect in the action of temperature. In the second part of this report, we shall see that these conclusions are enforced by the results of our investigations upon the durability of the acclimatization. ------------------- Key: 37 Medline: Authors: Brun JL Title: L'adptation aux temperatures elevees chez un nematode C. elegans Maupas 1900. II. Stabilite et physiologie de l'adaptation. Citation: Annales de Biologie Animale, Biochimie, Biophysique 6: 267-300 1966 Type: ARTICLE Genes: Abstract: From a 'psychrophile' Bergerac stock of C. elegans can be obtained strains genetically adapted to high temperatures (22 to 24.5C). The adaptive processes thus established can be most enduring. This appears in the following way: -a sufficiently heat acclimatized strain taken down to a low temperature (18C) does not recover, after 18 generations, the fertility rate typical of the strain kept at this low temperature throughout. -the same strain, raised again to its acclimatization temperature, always shows a fertility rate higher than that of the strain raised to this temperature for the first time. -the animals, raised again to their acclimatization temperature, quickly recover. Moreover stability depends on: -the magnitude of the alterations in the acclimatization conditions (lowest temperature and duration of breeding at this temperature). -the level of acclimatization to high temperatures of the nematodes. The stabilization of adaptive modifications finally results from a cumulative effect in the action of temperature as well as the adaptation itself. From an investigation at the cell level upon modifications in gametogenesis, we can draw the conclusion that acclimatization makes two differences: 1. the production of the abnormal figures characteristic of the senescence of the ovary is delayed in acclimatized animals. 2. non-acclimatized animals react to high temperatures by blocking meiosis, what acclimatized nematodes no longer do. High temperatures seem to induce a speeding up of the senescence phenomena. It could cumulatively act upon several generations. The acclimatization process seems to result from a new physiological balance showing itself, under constant conditions, in a slowing down of the senescence phenomena. ------------------- Key: 38 Medline: Authors: Brun JL Title: L'adaptation aux temperatures elevees chez un nematode C. elegans Maupas 1900. III. Role des facteurs autres que la temperature/ Citation: Annales de Biologie Animale, Biochimie, Biophysique 6: 439-466 1966 Type: ARTICLE Genes: Abstract: Under experimental conditions, Caenorhabditis elegans stocks kept at 18C could never survive a direct transfer to 24.5C. However, they can bear this temperature if they have been kept for many generations at intermediate temperatures: 22 - 23 - 23.5 and 24C. An experimental analysis entitles us to consider negligible the part played in this adaptation process by the nutritive medium. At intermediate temperatures, fertility increases with the duration of breeding: so does the ability to bear the next higher temperature. On another hand, the stability of the acclimatization appears to depend on the duration of breeding at a given temperature. The longer the nematodes are bred at a high temperature, the stronger the inurement is and the quicker the readaptation. Thus is undisputably defined the fundamental characteristic of the genetic adaptation of Caenorhabditis elegans: the acclimatization results from a cumulative effect in the action of temperature. This effect is very slow; at 23.5C for instance, it was only after 100 generations at least that the fertility of the animals was 4 times what it was in the first generation following the transfer from 23C. It was only after 1081 generations that the nematodes raised from 18C were able to bear 24.5C. If temperature is indeed the determining factor in the setting up and development of adaptive processes, its role may be conceived either as that of a selective agent of pre-adapted forms or as that of an instigator of adaptive modifications. Theoretically, the application of the first hypothesis is limited. As a matter of fact, the strictly autogamous fertilization of this nematode forbids, in a highly heterozygous state, to investigate upon a basis of genetic variability that might be used in order that the acclimatization process be progressively set up. In practice, a number of experimental data led us to think that this effect is almost unconceivable as far as our case is concerned. The most important of these data are: a) At any new-borne temperature, the acclimatization always begins with a short period of sensitization during which fertility decreases before progressively increasing. Now, at the minimum level it reaches, firstly the classes of high fertility are never present; secondly, there are never less than 50 per cent fertile animals. b) A positive selection of begetters is next to inefficient for it may induce either a decrease or an increase in fertility. The action of heat must therefore be considered responsible for the working out of adaptive processes. From this viewpoint, the progressive character of the modifications noticed in fertility, the fact that these modifications seem to take place in the same way at every stage of acclimatization, lead us to think that the corresponding genetic alterations are made of a sequence of stages of little moment distributed throughout the generations under experiment. The whole of our observations lead us to suppose that there is a progressive production of adapted and transmittable cytoplasmic states which would be responsible for the begetting of lineages fertile at high temperatures. ------------------- Key: 39 Medline: Authors: Brun JL Title: Influence des conditions de milieu sur la fecondite de C. elegans a diferentes temperatures. Citation: Nematologica 12: 539-556 1966 Type: ARTICLE Genes: Abstract: When grown under xenic conditions, the fertility of the free living nematode C. elegans is somewhat insensitive to the living part of the oligidic agar-medium. However, the influence of the total concentration of the inert fraction of the medium is important. For a given temperature, there is an ideal concentration, below and above which the fertility decreases significantly. This ideal concentration is much higher at elevated temperatures (23-23.5C) than at 13C. Among the constituents of the agar-medium, only the variations in concentration of the agar seemed to have an effect comparable to that of the total concentration. Variations in mineral salt and organic compound concentration showed no effect. Hence, we are led to hypothesize that changes in concentration of the agar upset the nature of the physiological exchanges between the animal and the medium by completely transforming the physical properties of the nutrient medium in which the nematode lives and reproduces. It appears possible that the increase in concentration of the medium causes a decrease in percentage of the free water of proteins. This dehydration, in turn, could account for an ------------------- Key: 41 Medline: Authors: Brun JL Title: Structure, organisation et variation du materiel genetique du nematode libre hermaphrodite autofecond C. elegans. Citation: Ann. Rep. Univ. CB/Lyon Fr : 68-78 1973 Type: REVIEW Genes: Abstract: ------------------- Key: 42 Medline: Authors: Brun JL;Lebre D Title: Influence of parental aging on the fecundity of 1st generation descendants in a self-fertilizing hermaphrodite nematode: C. elegans. Citation: C.R. des Seances de l'Academie des Sciences Serie D 266: 2149-2152 1968 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 44 Medline: Authors: Bryant C;Nicholas WL;Jantunen R Title: Some aspects of the respiratory metabolism of C. briggsae (Rhabditidae). Citation: Nematologica 13: 197-209 1967 Type: ARTICLE Genes: Abstract: A method is described for the production of large numbers of C. briggsae free from culture medium. Various aspects of the respiratory metabolism of these worms have been examined using a variety of techniques. The respiration of the worms increased rapidly as the amount of oxygen in the gaseous phase of the incubation vessels increased, until a level of 5% O2 was attained. After this no increase was observed. Cyanide in high concentrations and carbon monoxide inhibited respiration. The effect due to carbon monoxide was reduced in daylight. These substances also inhibited the development and reproduction of the worms, but the effect due to carbon monoxide was reversible. Preparations of worms subjected to sonic disruption utilised radioactive succinate, converting it to fumaric, malic, lactic and aspartic acids and to alanine. Spectrophotometric studies of washed homogenates of C. briggsae suggested the presence of pigments similar to a cytochrome b present in parasitic helminths, cytochrome c and traces of cytochrome a. Flavoprotein was detected in the washings. The implications of these results are ------------------- Key: 45 Medline: 69256313 Authors: Buecher EJ;Hansen EL Title: Yeast extract as a supplement to chemically defined medium for axenic culture of C. briggsae. Citation: Experientia 25: 656- 1969 Type: ARTICLE Genes: Abstract: Caenorhabditis briggsae, a free living soil nematode, can be grown axenically in a chemically defined medium if this is supplemented with proteinaceous materials. Only a few such materials, derived from chick embryo, bacteria, and liver have been found to be effective supplements. Since yeast cultures on agar support nematodes in vitro it seemed probable that an effective supplement could also be made from extracts of yeast. ------------------- Key: 46 Medline: Authors: Buecher EJ;Hansen EL Title: Mass culture of axenic nematodes using continuous aeration. Citation: Journal of Nematology 3: 199-200 1971 Type: ARTICLE Genes: Abstract: Biochemical and physiological studies of nematodes often require sufficient material for analysis. Two important limitations of axenic culture methods are the need for proteinaceous components and proper gas exchange. Proteinaceous supplements are tedious to prepare. Suitable gas exchange is obtained by using thin layers of medium, necessitating glassware of considerable size if large populations are desired.... ------------------- Key: 47 Medline: Authors: Buecher EJ;Hansen EL;Gottfried T Title: Yeast ribosomes as a source of growth factor for nematodes. Citation: Nematologica 15: 619-620 1969 Type: ARTICLE Genes: Abstract: There is a current interest in the study of nematodes in axenic (pure) culture. One aspect of these studies is the purification and identification of the proteinaceous growth factor added to the defined medium for maintenance of these cultures. The activation of nematode growth factor isolated from liver has been interpreted as changes in molecular structure of the soluble protein. This postulate appears to be erroneous since treatments used for activation not only cause a portion of the protein to precipitate but, in fact, the biological activity resides in the precipitate rather than in the soluble portion of ------------------- Key: 48 Medline: Authors: Buecher EJ;Hansen EL;Gottfried T Title: A nematode growth factor from baker's yeast. Citation: Journal of Nematology 2: 93-98 1970 Type: ARTICLE Genes: Abstract: An extract prepared from commercially available yeast supported maturation of the free-living nematode Caenorhabditis briggsae. The extract can be used to supplement a chemically defined medium or, after a limited dialysis, as a complete medium. Several biologically active fractions were prepared; those containing larger amounts of ribonucleic acid (RNA) had greater biological activity, the most active being a pellet resuspended after centrifugation at 30,000 X g for 30 min. This fraction could be substituted for serum in a medium which supports the maturation of the animal parasites Trichinella spiralis and Hymenolepis nana. Addition of protamine sulfate decreased the RNA content, leaving inactive protein fractions which could be reactivated by specific treatments that caused protein precipitation. It is postulated that biological activity is associated with protein sedimented with ribosomes. ------------------- Key: 49 Medline: 66132686 Authors: Buecher EJ;Hansen E;Yarwood EA Title: Ficoll activation of a protein essential for maturation of the free-living nematode Caenorhabditis briggsae. Citation: Proc. Society for Experimental Biology & Medicine 121: 390-393 1966 Type: ARTICLE Genes: Abstract: Previous work with axenic culture of the free living nematode, Caenorhabditis briggsae, led to isolation of a heat labile fraction from liver which was essential for maintenance of these cultures in an otherwise chemically defined medium. Subsequently, this fraction has been further separated by chromatography on hydroxylapatite. The globulin recovered has the interesting property of being "activated", that is, certain specific treatments increased the biological activity 30-fold. This phenomenon may have a bearing on the availability of proteinaceous materials in biological systems. This proteinaceous growth factor is present in most animal tissues as well as in bacteria. Preliminary studies show that the material is effective in a wide range of biological systems. ------------------- Key: 50 Medline: Authors: Buecher EJ;Hansen EL;Yarwood EA Title: Growth of nematodes in defined medium containing hemin and supplemented with commercially available proteins. Citation: Nematologica 16: 403-409 1970 Type: ARTICLE Genes: Abstract: It has been shown that several free-living nematodes, the insect parasite Neoaplectana carpocapsae, and the plant parasite Aphelenchus avenae, will grow and reproduce in axenic culture in defined medium containing hemin and supplemented with y-globulin. In addition, other commercially available proteins were tested with Caenorhabditis briggsae and A. avenae. Activity was less than that of liver growth factor. Proper precipitation of the protein was important in determining the effectiveness of the supplements for C. briggsae. Hemin added to growth factor had no stimulatory effect. These results extend the range of proteins suitable as supplements for growing nematodes. ------------------- Key: 51 Medline: Authors: Buecher EJ;Hansen EL;Yarwood EA Title: Cultivation of C. briggsae and Turbatrix aceti with defined proteins. Citation: Journal of Nematology 3: 89-90 1971 Type: ARTICLE Genes: Abstract: Following the report that addition of hemin and cholesterol allowed reproduction of Caenorhabditis briggsae in media containing autoclaved bacteria, we showed that by addition of hemin certain commercially available proteins could be used successfully in the culture medium. We now report that when both hemin and cholesterol are added, certain completely characterized proteins are effective supplements to media for cultivation of C. briggsae and Turbatrix ------------------- Key: 52 Medline: 70042388 Authors: Buecher EJ;Perez-Mendez G;Hansen EL Title: The role of precipitation during activation treatments of growth factor for C. briggsae. Citation: Proc. Society for Experimental Biology & Medicine 132: 724-728 1969 Type: ARTICLE Genes: Abstract: Axenic cultures of Caenorhabditis briggsae, a free living hermaphroditic nematode, have been maintained in chemically defined media supplemented with a proteinaceous growth factor. It has been found that this factor was increased in effectiveness as much as thirtyfold by treatment with a variety of specific processes termed "activation". An explanation for the mechanism of this increase has been sought. It had previously been observed that the complete medium containing Ficoll-activated growth factor lost activity upon filtration suggesting that a partially precipitated material might be of importance in nutrition of the nematode. It had also been observed that when other methods of activation were used there was a noticeable increase in turbidity. We therefore attempted to determine if precipitation in the medium occurred in all activation processes, and if so, whether the precipitated portion of the protein carried the biological activity. The specificity of growth factor from this point of view was examined. ------------------- Key: 53 Medline: 75140489 Authors: Byerly L;Cassada RC;Russell RL Title: Machine for rapidly counting and measuring the size of small nematodes. Citation: Review of Scientific Instruments 46: 517-522 1975 Type: ARTICLE Genes: Abstract: A machine has been developed to accurately count and size large populations of the small nematode Caenorhabditis elegans with minimal effort. Like the related Coulter counter, this machine detects the change in electrical current which a particle (nematode) produces as it passes between two electrodes in a small transducer. Despite the use of alternating current, detailed analysis shows that detection is based primarily on resistance changes. The machine also employs a sheathed-flow system to orient the long thin animals reproducibly in the transducer, so that resistance changes correspond directly to animal size. Accurate, non-destructive measurements of live nematodes which have a 20-fold length-to-width ratio and vary over a 10*3 range in volume can be achieved at a counting rate of 10*3 per minute with 1% coincidence. Sources of measurement errors have been identified and controlled or eliminated. The machine has been calibrated against the optically measured lengths of nematodes in all stages of the life cycle. ------------------- Key: 54 Medline: 76235893 Authors: Byerly L;Cassada RC;Russell RL Title: The life cycle of the nematode C. elegans. I. Wild type growth and reproduction. Citation: Developmental Biology 51: 23-33 1976 Type: ARTICLE Genes: Abstract: The growth and reproduction of the small nematode Caenorhabditis elegans has been studied using an electronic nematode counter recently developed in our laboratory. At 20C, the usual growth temperature, size increases in a smooth sigmoidal manner with time, linear growth being the most rapid around the time of the fourth molt and nearly ceasing by the end of the period of egg-laying. Growth of populations is highly synchronous; the small residual size heterogeneity is maximal at about the time of maximal growth. The four molts do not involve major interruption of growth, but they do entail slight shape changes (elongating upon escape from the old cuticle). Egg-laying begins shortly after the fourth molt, the rate rising rapidly at first, then more gradually to a peak followed by a relatively rapid fall. Comparable measurements at 16 and 25C establish that these are acceptable limit temperatures for work with temperature-sensitive mutants, although egg yield is somewhat reduced and the kinetics of egg-laying are altered at 25C. Developmental chronologies for all three temperatures are presented. ------------------- Key: 55 Medline: 76235894 Authors: Byerly L;Scherer S;Russell RL Title: The life cycle of the nematode C. elegans. II. A simplified method for mutant characterization. Citation: Developmental Biology 51: 34-48 1976 Type: ARTICLE Genes: dpy-10 dpy-13 tax-1 tax-4 Abstract: A simple method for characterizing the development and reproduction of mutant strains of the small nematode Caenorhabditis elegans has been developed. "3-egg" populations of nematode, started with three synchronously laid eggs and allowed to develop undisturbed for about two generations, are measured on the electronic nematode counter, and the resulting size distributions are interpreted by a computer. The computer compares the observed distribution to an expected distribution, generated by assuming the developmental curves previously measured for the wild-type C. elegans; if the distributions do not agree, the computer independently varies scale factors for developmental rate, size, egg-laying rate, and spread until the expected distribution best approximates the observed one. The resulting factors quantify any mutant defect of growth or reproduction, and the poorness of fit tells how greatly the mutant's development differs from that of the wild-type in ways other than those allowed for by the four scale changes. The computer program is shown to be able to fit wild-type C. elegans 3-egg populations grown for various lengths of time at 20C. Three-egg populations of wild-type animals grown at 16 and 25C are fitted by the computer and give altered developmental parameters consistent with those previously measured by more direct means. Nine behavioral and morphological mutants have been analyzed by this method. All show some developmental alterations from the wild-type. Fertility seems to be more adversely affected than growth. One mutant has been studied in more detail to determine the ------------------- Key: 58 Medline: 76044301 Authors: Cassada RC;Russell RL Title: The dauerlarva, a post-embryonic developmental variant of the nematode C. elegans. Citation: Developmental Biology 46: 326-342 1975 Type: ARTICLE Genes: Abstract: In the postembryological development of the free-living nematode Caenorhabditis elegans, a morphologically recognizable, nongrowing stage, called the dauerlarva, may arise. Using synchronous populations and following growth and molting, it has been shown that the dauerlarva is formed by a facultative, reversible arrest at a specific point in the life cycle, the second of four cuticle molts, in response to external conditions. At each molt a normal animal passes through "lethargus", a stage in which feeding and locomotion are transiently arrested. In the dauerlarva stage, feeding is arrested indefinitely and locomotion is markedly reduced. A simple quantitative assay, based on the exceptional resistance of dauerlarvae to sodium dodecyl sulfate (SDS), has been developed to study dauerlarva formation and its reversal. The SDS resistance of dauerlarvae requires both non-feeding and an especially impermeable cuticle. Dauerlarva formation can be efficiently induced by limiting the concentration of bacteria (the food supply), but not by complete starvation. Quantitative recovery to normal development can be induced by transfer to fresh medium with excess bacteria. Simpler stimuli can elicit recovery at slower rates, the principal factors besides nutrition being optimal ionic and osmotic conditions and a noninhibitory concentration of animals. There are identifiable stages in recovery, beginning with a resumption of feeding. The cuticle, ultrastructurally very different from normal cuticle, is shed at the next molt, after which development appears as normal. A temperature-sensitive mutant, which forms dauerlarvae at high temperature despite the presence of abundant food, is described, and the use of dauerlarvae for futher mutant isolation is discussed. ------------------- Key: 60 Medline: Authors: Castillo JM;Kisiel MJ;Zuckerman BM Title: Studies on the effects of 2 procaine preparations on C. briggsae. Citation: Nematologica 21: 401-407 1975 Type: ARTICLE Genes: Abstract: Concentrations below 0.36 mM procaine had no significant effect on several developmental parameters of Caenorhabditis briggsae; growth, fecundity, time of inception of the reproductive period and duration of the reproductive period. In old C. briggsae, significant differences in osmotic fragility occurred to concentrations as low as 0.18 mM. Using cationized ferritin for evaluating membrane negative surface charge, at 33 mM partial lysis of the cuticle surface membrane occurred and negative charge was lost from unlysed areas. At 7.2 mM the negative charge was present in some areas of the membrane but not in others, while at 0.18 mM negative charge density did not differ significantly from that of untreated nematodes. Since the osmotic fragility effect persisted at procaine concentrations which did not affect surface charge, these results suggest two separate modes of action ------------------- Key: 61 Medline: Authors: Cayrol JC;Brun J Title: Etude, a differentes temperatures, de l'activite predatrice de quelques champignons nematophages vis-a-vis du nematode C. elegans/ Citation: Revue de Zoologie Agricole et de Pathologie Vegetale 74: 139-146 1975 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 63 Medline: Authors: Cayrol JC;Dreyfus B Title: Etudes preliminaires sur les relations entre nematodes libres et bacteri es dans le sol. Citation: C.R. des Seances de la Societe Biologie 169: 166-172 1975 Type: ARTICLE Genes: Abstract: At first we have proved that the free-living nematodes are unable to live in axenic conditions without bacteria. Then we have demonstrated that each species of nematode is associated with a typical bacterial complex. It has been later noticed that the nutritious properties of the bacteria greatly change for each species of nematode: some of them give to the animal an abundant food (favourable bacteria). Other provide only a poor food and are not favourable for the nematodes development (tolerant bacteria). Lastly, others are unable to provide the indispensable nutritious factors and the nematodes die (unfavourable bacteria). The formation of a bacterial complex associated with each species of nematode seems in relation with the nutritious properties of the different ------------------- Key: 65 Medline: 80006803 Authors: Chalfie M;Thomson JN Title: Organization of neuronal microtubules in the nematode C. elegans. Citation: Journal of Cell Biology 82: 278-289 1979 Type: ARTICLE Genes: Abstract: We have studied the organization of microtubules in neurons of the nematode Caenorhabditis elegans. Six neurons, which we call the microtubule cells, contain bundles of darkly staining microtubules which can be followed easily in serial-section electron micrographs. Reconstruction of individual microtubules in these cells indicates that most, if not all, microtubules are short compared with the length of the cell process. Average microtubule length varies characteristically with cell type. The arrangement of microtubules gives an overall polarity to each bundle: the distal ends of the microtubules are on the outside of the bundle, whereas the proximal ends are preferentially inside. The distal and proximal ends each have a characteristic appearance indicating that these microtubules may have a polarity of their own. Short microtubules in processes of other neurons in C. elegans ------------------- Key: 66 Medline: 79116354 Authors: Cheng AC;Lu NC;Briggs GM;Stokstad ELR Title: Effect of particulate materials on population growth of the free living nematode C. briggsae. Citation: Proc. Society for Experimental Biology & Medicine 160: 203-207 1979 Type: ARTICLE Genes: Abstract: Recent investigations have shown that ingestion of particulate material has promoted population growth of amoebas and ciliates. The authors have suggested that particulate material in nutrient media induces formation of food vacuoles and thus permits faster uptake of nutrients. Previous work with an axenic culture of free-living nematodes demonstrated that particulate protein stimulates earlier maturation of Caenorhabditis briggsae. However, when polystyrene latex beads were added to the chemically defined medium in place of the particulate protein, no stimulation was observed. Later, Vanfleteren observed larger population increases with acid-precipitated heme and also proposed the idea that acid-precipitated heme can replace the particulate protein. This study of the effects of particulate material on population growth of C. briggsae was prompted by the observation that population growth was greater when the organism was cultured in a turbid medium prepared by the addition of a separately heat-sterilized salt mixture which had become turbid on autoclaving, than when they were cultured in a clear medium prepared by the addition of a separately sterile-filtered salt mixture which remained clear after Millipore filtering. This led to the hypothesis that the particles themselves could stimulate population growth and that the particulate material does not necessarily have to be a protein moiety. Experiments were conducted to examine the effect of various inert particles on population growth, and to determine whether there is any particular size or size range that is most stimulatory. Finally, we wished to see if various particulates could replace casamino acids, which are commonly used in our laboratory as a source of proteinaceous growth factor(s) for the test organism. ------------------- Key: 67 Medline: Authors: Chitwood BG Title: Studies on some physiological functions and morphological characters of Rhabditis (Rhabditidae, Nematoda). Citation: Journal of Morphology 49: 251-275 1930 Type: REVIEW Genes: Abstract: Intravitam stains were used to determine the functions of several organs in two species of nemas (Rhabditis strongyloides and Rhabditis elongata). The organs were also studied in section. From the results obtained it is concluded that the amphids are not excretory in function, but more probably sensory, for definite connections were observed to extend to the nerve ring. No migratory cells, such as those described by Stefanski, were seen. The phasmids stained with all intravitam stains used, but were never observed to secrete. It seems doubtful that they serve as excretory organs. The excretory system was seen to consist of a typical X system. Actual excretion was observed. Deirids were seen for the first time in both species. Oesophageal glands were also described. A study was made of the structure of the intestinal cells, rectal glands, and anal muscles. Attention was called to the fact that there are two kinds of ejaculatory glands, one of which probably serves as a 'cement gland', while the function of the other is still in doubt. ------------------- Key: 69 Medline: 76060401 Authors: Colonna WJ;McFadden BA Title: Isocitrate lyase from parasitic and free living nematodes. Citation: Archives of Biochemistry & Biophysics 170: 608-619 1975 Type: ARTICLE Genes: Abstract: Isocitrate lyase and malate synthase were demonstrated in the soil nematode Caenorhabditis elegans and the isocitrate lyase partially characterized and compared with that from embryos of the hog roundworm Ascaris lumbricoides. Both enzymes have similar pH optima, molecular weights and K(m)s for isocitrate. Isocitrate lyase from A. lumbricoides consists of a single species of pI 6.6; the lyase from C. elegans consists of a major fraction of pI 5.1 and two lesser species of pI 4.4 and 4.1, suggestive of multiple enzymes. Oxalate, a reversible inhibitor, protects isocitrate lyase from both sources against thermal inactivation; protection is better in the case of the Ascaris enzyme. Antibodies to highly purified C. elegans isocitrate lyase inhibit catalysis by the enzyme from either nematode and form precipitin bands in gels with lyase-containing extracts from both organisms, implying common evolutionary ancestry. Isocitrate lyase from C. elegans, unlike that from A. lumbricoides, can be detected in adult forms of the nematode. ------------------- Key: 70 Medline: Authors: Cooper AF;Van Gundy SD Title: Senescence, quiescence, and cryptobiosis. Citation: "Plant Parasitic Nematodes, Volume II. Cytogenetics, Host-Parasite Interactions, and Physiology." Zuckerman BM, Mai WF and Rohde RA (eds), Academic Press, NY. 2: 297-315 1971 Type: REVIEW Genes: Abstract: The words senescence, quiescence, and cryptobiosis describe quantitatively decreasing levels (time rates of change) of metabolic activity which may occur during the aging of an organism. Which mode is operative depends upon the metabolic status and adaptability of the individual and upon the kinds and intensities of environmental stress. Senescence ("normal" aging) is characterized by an average pattern of metabolic activities whereby the life cycle can be completed in a given environment. When the environment balance shifts unfavorably, some organisms experience a metabolic "slowdown" called quiescence: movement slows or ceases, and the normal sequence of life cycle functions is delayed. With further increase or continuation of environmental stress a few biological systems enter cryptobiosis which is a "shutdown" of metabolism to levels not detectable by currently available biochemical methods or physical instrumentation. Structural integrity is maintained (or only slowly declines) and the potential for resumption of quiescence, motility, and even the normal patterns of senescence is retained, often for extended periods of time.... ------------------- Key: 72 Medline: Authors: Cooper AF Jr;Van Gundy SD Title: Metabolism of glycogen and neutral lipids by Aphelenchus avenae and Caenorhabditis sp. in aerobic, microaerobic, and anaerobic environments. Citation: Journal of Nematology 2: 305-315 1970 Type: ARTICLE Genes: Abstract: Starving Aphelenchus avenae survived 3-4 weeks in microaerobic and anaerobic environments, but Caenorhabditis sp. survived less than 80 hr. Aerobically, both nematodes metabolize neutral lipid reserves: there was no microaerobic (<5% 02) or anaerobic neutral lipid catabolism. Early in anaerobiosis both nematodes utilized endogenous glycogen. Caenorhabditis sp. depleted the glycogen and died. A. avenae under oxygen stress longer than 120 hr entered cryptobiosis, during which there was neither measurable O2 uptake nor glycogen or neutral lipid utilization. Only when re-aerated, did A. avenae recover and resume "normal" metabolism. ------------------- Key: 73 Medline: Authors: Cooper AF;Van Gundy SD Title: Ethanol production and utilization by Aphelenchus avenae and Caenorhabditis sp. Citation: Journal of Nematology 3: 205-214 1971 Type: ARTICLE Genes: Abstract: In microaerobic and anaerobic environments the principle glycolytic end-product of A. avenae and Caenorhabditis sp. was lactic acid during the first 12-16 hr, after which it was ethanol. Upon return to aerobiosis, 11C-labeled ethanol in the medium was utilized by the nematodes; 14CO2 and some 14C-labeled glycogen was detected. Total dry weight loss of nonfeeding nematodes was 25% greater in the absence of alcohol than in the presence of ethanol or n-propanol. Physical movement and respiration increased and reproduction was extended by alcohol in the bathing ------------------- Key: 74 Medline: Authors: Cooper AF Jr;Van Gundy SD;Stolzy LH Title: Nematode reproduction in environments of fluctuating aeration. Citation: Journal of Nematology 2: 182-188 1970 Type: ARTICLE Genes: Abstract: Reproduction of Aphelenchus avenae, reared on Rhizoctonia solani growing on steamed wheat seeds and Caenorhabditis sp., reared on a mixed bacterial culture grown on oatmeal, was significantly reduced at 5% oxygen and inhibited at 4% oxygen and below. Aeration ranging from atmospheric air (21%) to 10% oxygen had no effect on reproduction. Close interval (5 days or less) fluctuations between high and low oxygen concentrations, inhibited population buildup of Hemicycliophora arenaria on tomato in soil, and of A. avenae and Caenorhabditis sp. in vitro. In soil tests with H. arenaria exposed to 12 hr of nitrogen every three days (in air) inhibited the rate of buildup compared to controls maintained in continuous air. With the in vitro studies, as little as 4 hr nitrogen every 3 days (stored in air) significantly influenced the population numbers. ------------------- Key: 75 Medline: Authors: Croll NA Title: Components and patterns in the behaviour of the nematode C. elegans. Citation: Journal of Zoology 176: 159-176 1975 Type: ARTICLE Genes: Abstract: The behavioural activities during movement, feeding and defaecation have been recorded and measured in adult females of Caenorhabditis elegans. The postures and components of recognizable wave forms are described. Stress has been laid on the machanism of antagonistic interaction of backward and forward movement, and the rates and characteristics of "spontaneous" and "induced" reversal periods. During feeding, rapid rates of pharyngeal activity are invariably related to low rates of somatic muscle wave propagation. Head oscillations are considered to be separate events not directly linked with feeding or foraging. The combination of certain wave forms, together with other measurements have been used to develop a hypothesis to describe a co-ordinating mechanism to the nematode level of organization. ------------------- Key: 76 Medline: 75185266 Authors: Croll NA Title: Indolealkylamines in the coordination of nematode behavioral activities. Citation: Canadian Journal of Zoology 53: 894-903 1975 Type: ARTICLE Genes: Abstract: Nematode movements result from spontaneous myogenic depolarizations, neuromuscular coordination, and localized hydrostatic changes. These components are integrated into activities which are mutually exclusive or interdependent. Nervous connection is not known between all the organ systems, and the pharynx and female tract are somewhat autonomous. This problem is discussed, as is the limitation of a theory involving only cholinergic transmission. Serotonin, 5-hydroxytryptophan (5HTP), and epinephrine were all found to induce rapid and prolonged contractions in the female vagina/vulva of Caenorhabditis elegans, Aphelenchus avenae, Panagrellus redivivus, and Oswaldocruzia filiformis. It also caused spicule extension in males of P. redivivus. The responses are fully described together with dose-response data and the effect of adult age. The potential significance of indolealkylamines in nematode behavioral coordination is discussed, together with the relevance of anthelmintic formulation and the basis of immunological rejection. ------------------- Key: 77 Medline: Authors: Croll NA Title: When C. elegans (Nematoda: Rhabditidae) bumps into a bead. Citation: Canadian Journal of Zoology 54: 566-570 1976 Type: ARTICLE Genes: Abstract: When C. elegans bumps into a bead, it stops moving, withdraws a short distance, and then resumes forward movement, often in a new direction. This series of events has been analysed in its constituent parts and the features making up the 'stimulus' have been compared numerically with those making up the 'response'. No significant correlations were found that support the interpretation that this is a simple stimulus-response phenomenon. It is argued that the data support an alternative view that when forward movement is interrupted, C. elegans is primed to undergo a short, rapid reversal and that this is not mediated through sensory mechanoreceptors. ------------------- Key: 78 Medline: Authors: Croll NA Title: Behavioral coordination of nematodes. Citation: "The Organization of Nematodes." Croll NA (ed), Academic Press, NY. : 343-364 1976 Type: REVIEW Genes: Abstract: ------------------- Key: 79 Medline: Authors: Croll NA Title: Sensory mechanisms in nematodes. Citation: Annual Review of Phytopathology 15: 75-89 1977 Type: REVIEW Genes: cat-1 cat-2 unc-5 unc-30 Abstract: There have recently been unprecedented advances in our knowledge of senses and responses in nematodes. As this review is being published data on sensory mechanisms in nematodes continue to flood in from laboratories all over the world. Developments have not come directly from electrophysiology, but rather indirectly, through detailed neuroanatomy and through interpretations based on the behavior of the entire organism. Studies of free-living bacteriophagous species Caenorhabditis elegans have led to many of these advances and are the basis for a major part of this review.... ------------------- Key: 80 Medline: Authors: Croll NA;Smith JM Title: Integrated behaviour in the feeding phase of C. elegans (Nematoda). Citation: Journal of Zoology 184: 507-517 1978 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans spends most of its life feeding. When feeding, it moves only short distances but intestinal contents are moved to and fro and thus mixed. The nematodes also defaecate and lay eggs during the feeding phase in bacterial culture. Defaecation is one of a series of events which causes the forward and backward movement of intestinal contents. These rhythmic movements, once initiated, appear to be controlled by a pacemaker and are unrelated to feeding rates. Oviposition is associated with movements of the genital tract and it can occur at any posture and does not influence the rate of other activities. After food-deprivation, C. elegans shows no measureable hunger response on being returned to bacteria. Experiments with excised parts of worms showed that isolated anterior ends will feed both in and out of bacteria and move forward and backward. Isolated posterior halves without a pharynx or circumpharyngeal commissure ------------------- Key: 81 Medline: 78024049 Authors: Croll NA;Smith JM;Zuckerman BM Title: The aging process of the nematode C. elegans in bacterial and axenic culture. Citation: Experimental Aging Research 3: 175-189 1977 Type: ARTICLE Genes: Abstract: While much is known of the morphological and some physiological changes which occur during the aging of Caenorhabditis elegans, little attempt has been made to measure the changes in behavior. Wild type C. elegans (var. Bristol) were cultured axenically, individually observed each day for 15 minutes and their behavioural actions recorded on a multi-channel event recorder or on a video tape recorder of a closed circuit TV. Particular attention was paid to the rate of backwardly directed somatic waves, pharyngeal bulb pulsations, the interval between defecations and oviposition. C. elegans lived significantly longer in axenic culture than in bacteria. A gradual linear decline occurred in the rate of backward waves between maturation (day 4) and death (day 20) for those worms in axenic culture. In striking contrast, the mean maximum rate of pharyngeal bulb pulsations maintained a plateau from day 4 to 18, while the mean interval between defecations doubled from 60 sec (days 4 to 8) to 120 sec (days 10-20). These results are discussed in the context of nematode coordination and the mechanisms of aging. ------------------- Key: 82 Medline: 79086923 Authors: Culotti JG;Russell RL Title: Osmotic avoidance defective mutants of the nematode C. elegans. Citation: Genetics 90: 243-256 1978 Type: ARTICLE Genes: che-1 che-3 daf-10 osm-1 osm-3 osm-5 osm-6 Abstract: A wild-type strain of the nematode Caenorhabditis elegans has been shown to avoid high concentrations of a number of sugars and salts. Individual and population assays for this response were developed and mutants were selected for their inability to avoid high concentrations of fructose or NaCl. Seven nonavoiding mutants representing six complementation groups were isolated and characterized. Genetic studies indicate that the mutants each carry a single recessive mutation responsible for the defective osmotic avoidance behavior. The map locations of the six complementation groups identified by these mutations have been determined. Mutants isolated for their inability to avoid fructose are also unable to avoid NaCl and vice versa. The mutants move normally, exhibit normal touch sensitivity, and, like wild type, follow isotherms in a radial thermal gradient. All of the mutants are at least partially defective in the attraction to sodium chloride exhibited by wild type. None of the mutants is temperature sensitive, and all exhibit defective osmotic avoidance behavior as young L1 larvae. Preliminary anatomical studies indicate selective sensory neuron changes in at ------------------- Key: 83 Medline: Authors: Delavault R Title: La teneur en acide desoxyribonucleique des noyaux sexuels chez un Rhabditis hermaphrodite. Citation: C.R. des Seances de l'Academie des Sciences Serie D 234: 884-885 1952 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 84 Medline: Authors: Delavault R Title: Etude cytologique des acides nucleiques chez un nematode libre (Rhabditis elegans Maupas 1900). Citation: Archiv. Anat. Micro. Morphol. Exp. 41: 41-68 1952 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 85 Medline: Authors: Delavault R Title: Croissance des ovotestis puis des ovaires chez un nematode libre hermaphrodite: C. elegans Maupas 1900. Citation: Bulletin de la Societe Zoologique de France : 321-325 1957 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 86 Medline: Authors: Delavault R Title: Developpement, croissance et fonctionnement des glandes genitales chez les nematodes libres. Citation: Archives de Zoologie Experimentale et Generale 97: 109-208 1959 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 87 Medline: Authors: DeNiro MJ;Epstein S Title: Influence of diet on the distribution of carbon isotopes in animals. Citation: Geochimica et Cosmochimica Acta 42: 495-506 1978 Type: ARTICLE Genes: Abstract: The influence of diet on the distribution of carbon isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant carbon isotopic composition. The isotopic composition of the whole body of an animal reflects the isotopic composition of its diet, but the animal is on average enriched in *13C by about 1% relative to the diet. In three of the four cases examined, the 13C enrichment of the whole body relative to the diet is balanced by a 13C depletion of the respired CO2. The isotopic relationships between the whole bodies of animals and their diets are similar for different species raised on the same diet and for the same species raised on different diets. However, the *13C values of whole bodies of individuals of a species raised on the same diet may differ by up to 2%. The relationship between the 13C/12C ratio of a tissue and the 13C/12C ratio of the diet depends both on the type of tissue and on the nature of the diet. Many of the isotopic relationships among the major biochemical fractions, namely the lipid, carbohydrate and protein fractions, are qualitatively preserved as diet carbon is incorporated into the animal. However, the difference between the *13C values of a biochemical fraction in an animal and in its diet may be as large as 3%. The *13C values of the biochemical components collagen, chitin and the insoluble organic fraction of shells, all of which are often preserved in fossil material, are related to the isotopic composition of the diet. These results indicate that it will be possible to perform dietary analysis based on the determination of the 13C/12C ratio of animal carbon. Analysis of the total animal carbon will in most cases provide a better measure of diet than the analysis of individual tissues, biochemical fractions, or biochemical components. The limits of accuracy of this method will generally restrict its application to situations in which the diet is derived from sources with relatively large differences in their *13C values, such as terrestrial vs aquatic organisms or C3 vs C4 plants. This method should be applicable to fossil ------------------- Key: 88 Medline: 78116013 Authors: Deppe U;Schierenberg E;Cole T;Krieg C;Schmitt D;Yoder B;von Ehrenstein G Title: Cell lineages of embryo of nematode C. elegans. Citation: Proceedings of the National Academy of Sciences USA 75: 376-380 1978 Type: ARTICLE Genes: Abstract: Embryogenesis of the free-living soil nematode Caenorhabditis elegans produces a juvenile having about 550 cells at hatching. We have determined the lineages of 182 cells by tracing the divisions of individual cells in living embryos. An invariant pattern of cleavage divisions of the egg generates a set of stem cells. These stem cells are the founders of six stem cell lineages. Each lineage has its own clock-i.e., an autonomous rhythm of synchronous cell divisions. The rhythms are maintained in spite of extensive cellular rearrangement. The rate and the orientation of the cell divisions of the cell lineages are essentially invariant among individuals. Thus, the destiny of cells seems to depend primarily on their lineage history. The anterior position of the site of origin of the stem cells in the egg relates to the rate of the cell cycle clock, suggesting intracellular preprogramming of the uncleaved egg. We used a technique that allows normal embryogenesis, from the fertilized egg to hatching, outside the parent under a cover glass. Embryogenesis was followed microscopically with Nomarski interference optics and high-resolution vidoe recording. ------------------- Key: 89 Medline: Authors: Deubert KH;Zuckerman BM Title: The histochemical demonstration of cytochrome oxidase in fresh-frozen sections of nematodes. Citation: Nematologica 14: 453-455 1968 Type: ARTICLE Genes: Abstract: Histochemical procedures for the demonstration of cytochrome oxidase in fresh-frozen sections prepared from nematodes are described. ------------------- Key: 90 Medline: 72030103 Authors: Dion M;Brun JL Title: Genetic mapping of the free-living nematode C. elegans Maupas 1900, var. Bergerac. I. Study of two dwarf mutants. Citation: Molecular & General Genetics 112: 133-151 1971 Type: ARTICLE Genes: Abstract: The genetic study of two dwarf and spontaneous mutants of the diploid free-living nematode C. elegans has been realised according to the particular methods imposed by the unbalanced self-fertilizing hermaphroditism usual to this animal by the absence of fertility of the male mutants. By combining crosses of hermaphrodite homozygous dwarfs with exceptional heterozygous males and the study of the progeny by automixis of the hermaphrodite hybrids, it can be shown: 1. Dwarfism in each mutant strain is a recessive and single factor character. 2. Characteristics of the two types of mutants are controlled by two different genes which are independant (phenotype ratio of complementary hermaphrodites progeny: 9N/7n) and not sex-linked. 3. Expression of dwarfness requires that at least one gene should be double recessive. The embryonic determination of dwarfness could correspond to a perturbation of the eutelie characteristic of the nematode. ------------------- Key: 92 Medline: Authors: Dougherty EC Title: Sterile pieces of chick embryo as a medium for the indefinite cultivation of Rhabditis briggsae Dougherty & Nigon, 1949 (Nematoda: Rhabditidae). Citation: Science 111: 2880- 1950 Type: ARTICLE Genes: Abstract: During the past eight months (i.e., since December, 1948) it has been possible to rear successive generations of a rhabditid nematode, Rhabditis briggsae, on sterile pieces of chick embryo. This medium may be termed "axenic" (without strange [life]), inasmuch as the pieces of chick embryo are nonliving. Moreover, in some cases the pieces have been frozen, thawed, and then used; in others they have undergone a certain amount of autolysis before use by reason of being stored at 4C for up to a month's time..... ------------------- Key: 93 Medline: Authors: Dougherty EC Title: The axenic cultivation of Rhabditis briggsae Dougherty & Nigon, 1949 (Nematoda: Rhabditidae) II. Some sources and characteristics of "factor Rb". Citation: Experimental Parasitology 1: 34-45 1951 Type: ARTICLE Genes: Abstract: It is obvious that success in the cultivation in vitro of parasitic helminths would open up important new experimental approaches in the fight against diseases caused by them, but it is also obvious that such cultivation presents many difficulties. The study of free-living forms that can be grown axenically (i.e., free of other living forms) may well provide important clues to the problem of the growing of parasites free from their hosts. Moreover, such free-living forms constitute potentially valuable subjects for experiments on helminth metabolism, with such practical consequences as the testing ------------------- Key: 94 Medline: Authors: Dougherty EC Title: The axenic cultivation of Rhabditis briggsae Dougherty & Nigon, 1949 (Nematoda: Rhabditidae) III. Liver preparation with various supplementations. Citation: Journal of Parasitology 39: 371-380 1953 Type: ARTICLE Genes: Abstract: The axenic cultivation (i.e., growth in the absence of other living organisms) of the free-living soil nematode, Rhabditis briggsae, requires a complex medium including one or more heat-labile, protein-like substances which have been termed "factor Rb". It has been shown that factor Rb can be provided by preparations from liver or chick embryo juice or by human plasma or certain of its fractions. Moreover, it has recently been reported in abstract that a dialysed fraction of buffered aqueous liver extract will support excellent growth of R. briggsae when supplemented with known substances only. The present paper reports the results of recent studies on the nature and properties of factor Rb in liver protein and on various supplementations of certain unheated liver preparations as media for R. briggsae. Aqueous, unheated horse liver extract (hereinafter referred to as LE), prepared by centrifuging liver homogenate and taking supernatant, has been treated in various ways to provide information on the properties of factor Rb. Such preparations have been variously supplemented and tested as media for the axenic cultivation of R. briggsae. The principle supplementation used has been the supernatant (ALE) from autoclaved LE. Both partly and completely defined supplementations have also been employed. From these studies some advance has been made in the direction of a completely defined medium for R. ------------------- Key: 95 Medline: Authors: Dougherty EC Title: The genera of the subfamily Rhabditinae Micolitzky 1922 (Nematoda). Citation: G.S. Thepar Commemoration Volume (Lucknow) : 69-76 1953 Type: ARTICLE Genes: Abstract: ------------------- Key: 96 Medline: Authors: Dougherty EC Title: The genera & species of the subfamily Rhabditinae Micoletzky, 1922(Nematoda): A nomenclatorial analysis-including an addendum on the composition of the family Rhabditidae Orley, 18 Citation: Journal of Helminthology 29: 105-152 1955 Type: REVIEW Genes: Abstract: Osche (1952) has recently published a sorely needed, comprehensive revision of the genus Rhabditis Dujardin [1844] (sensu lato) including detailed study of certain features of the cephalic end, especially of the stoma or mouth cavity. For some time to come his study will surely be the point of departure for morpholigical and systematic work on the group. On the basis principally of the structure of the metastom (a subdivision of the stoma) and of the esophagus, he recognizes some eight subgenera in the genus Rhabditis, which are as follows: Rhabditis Dujardin [1844] (sensu stricto), Choriorhabditis Osche, 1952, Telorhabditis Osche, 1952, Caenorhabditis Osche, 1952, Mesorhabditis Osche, 1952, Teratorhabditis Oshce, 1952, Protorhabditis Osche, 1952, and Parasitorhabditis Fuch, 1937. For all of these save the last he lists the species recognized by him. For a revision of Parasitorhabditis he refers to an unpublished manuscript by Ruhm..... ------------------- Key: 97 Medline: Authors: Dougherty EC Title: Introduction to axenic culture of invertebrate metazoa: A goal*. Citation: Annals of the New York Academy of Sciences 77: 27-54 1959 Type: REVIEW Genes: Abstract: As consulting editor, I saw and now take the opportunity to amalgamate concepts scattered in the papers that follow. My hope also is to bring a certain unity to the heterogeneous studies contributed by the imaginative and resourceful workers who created the program of the conference on which this monograph is based. Axenic cultivation, the rearing of one or more individuals of a single species on a nonliving medium, dominates microbiology. Axenic cultures, usually referred to as "pure cultures", are fundamental to identification of many protists (bacteria, algae, fungi, and protozoa) and to their exploitation in research... ------------------- Key: 98 Medline: Authors: Dougherty EC Title: Cultivation of Aschelminths, especially Rhabditid Citation: "Nematology." Sasser JN and Jenkins WR (eds), University of North Carolina Press, Chapel Hill. : 297-318 1960 Type: REVIEW Genes: Abstract: For the purpose of the present chapter the noun 'cultivation' is to be taken as the maintenance, in the laboratory, of a population of organisms belonging to a desired species through successive generations and subcultures over a prolonged period of time (weeks, months, or years). This is a deliberate restriction of the term. The noun 'culture' is most aptly used for a population within a circumscribed vessel or container (test-tube, Petri dish, U.S. Bureau of Plant Industry watch glass, etc.); it is also used in a looser, more general way (as "in culture") to cover conditions of substantial growth whether or not leading to cultivation in the strict sense ------------------- Key: 100 Medline: Authors: Dougherty EC;Calhoun HG Title: Possible significance of free-living nematodes in genetic research. Citation: Nature 161: 29-29 1948 Type: ARTICLE Genes: Abstract: The free-living nematodes of the sub-order Rhabditina are widespread in the soil and relatively easily cultivable on nutrient agar in the presence of bacteria and have short life-cycles (3-7 days from hatching to sexual maturity), with adult sizes up to 3 mm in length. They offer, in our estimation, certain very interesting possibilities for the study of basic genetic phenomena-morpholical, cytogenetic and physiological. ------------------- Key: 102 Medline: Authors: Dougherty EC;Hansen EL Title: Axenic cultivation of Caenorhabditis briggsae (Nematoda: Rhabditidae). V. Maturation on synthetic media. Citation: Proc. Society for Experimental Biology & Medicine 93: 223-227 1956 Type: ARTICLE Genes: Abstract: The free-living, soil-dwelling, hermaphroditic rhabditid nematode, C. briggsae, can mature under axenic conditions on a variety of media containing ingredients of complex, undefined composition-for example, certain liver fractions, plasma protein fractions, chick embryo juice, and extracts of equine pancreas, thymus, or spleen. Some of these media have also contained a large number of added known substances, but, until recently, all have included at high levels certain of the complex, crude substances mentioned. However, we have recently recorded success in rearing C. briggsae from larva to larva on a defined medium containing only a trace of the standard liver medium used by us in maintenance of stock axenic cultures of this organism. Now we are able to describe limited success following elimination of even this trace, such that C. briggsae can be reported as passing one generation on certain media of synthetic composition. ------------------- Key: 103 Medline: Authors: Dougherty EC;Hansen EL Title: The folic acid requirement and its antagonism by aminopterin in the nematode C. briggsae (Rhabditidae). Citation: Anatomical Record 128: 541-542 1957 Type: ARTICLE Genes: Abstract: Recently we have reported a high folic acid (FA) requirement for C. briggsae (by comparison with many lower organisms) when grown axenically in a simply prepared liver medium: autoclaved liver extract (ALE). It can now be stated that in this medium AF cannot be replaced by biopterin (one form of the "crithidia factor" - viz., 2-amino-4-hydroxy-6-[1,2,3-trihydroxypropyl-(L-erythro)]-pt eridine) or by pABA... ------------------- Key: 104 Medline: Authors: Dougherty EC;Hansen EL;Nicholas WL;Mollett JA;Yarwood EA Title: Axenic cultivation of Caenorhabditis briggsae (Nematoda: Rhabditidae) with unsupplemented and supplemented chemically defined media. Citation: Annals of the New York Academy of Sciences 77: 176-217 1959 Type: REVIEW Genes: Abstract: A detailed summary of methods for axenic cultivation of Caenorhabditis briggsae is given. Results of axenic culture on chemically defined basal media (GM and GS) and on these media supplemented with undefined preparations of horse liver and chick embryos are reported in detail, with a review of the formulation of the GM and GS designs and of the chronology of changes made therein. The best growth so far realized with C. briggsae in axenic culture is suboptimal as compared with growth in the presence of bacteria, and maturation takes longer (4 to 5 days instead of about 3 days at 20C). Suitable media of the GM design give good axenic growth with relatively low levels of complex supplements-Liver Protein Fraction C (LPF-C) and chick embryo extract (CEE), both of which presumably include a protein-linked requirement, Factor Rb. With GM-16 plus CEE or certain GSs plus CEE, requirements have been variously demonstrated for 6 B-vitamins: folic acid, niacinamide, pantothenic acid, pyridoxine, riboflavin, and thiamine; one of these-folic acid-had already been shown to be required. Only niacinamide is also demonstrated as a requirement in the presence of low levels of LPF-C. In the presence of CEE we have tested the essentiality of the other 5 vitamins only by omitting them singly from vitamin mixes added at increased (5 to 50 times GS) levels to media of GM or GS type. Preliminary evidence is given that the ten "rat-essential" amino acids are required. Improvement of nutritional balance with respect to amino acid levels and to relative levels of amino acids in relation to vitamins or salts is discussed as an explanation of differential growth on different media. Possibly the variations of DM-GS so far tested contain unnecessarily high amino acid levels. The definition of nutritional requirements for C. briggsae still presents many ------------------- Key: 105 Medline: Authors: Dougherty EC;Keith DF Title: The axenic cultivation of Rhabditis briggsae Dougherty & Nigon, 1949 (Nematoda: Rhabditidae) IV. Plasma protein fractions with various supplementations. Citation: Journal of Parasitology 39: 381-384 1953 Type: ARTICLE Genes: Abstract: The immediately preceding paper (Dougherty, 1953) has been confined to an account of work with liver as a source of factor Rb. In the present paper we deal with studies using human plasma as a source of this substance (or substances). A preliminary note briefly reporting a part of the results has already appeared (Dougherty, 1951). Whole plasma and its protein fractions and certain subfractions (See Haurowitz, 1950, pp. 148-160) have been tested. These studies throw additional light on the nature of factor Rb. ------------------- Key: 106 Medline: Authors: Dougherty EC;Nigon V Title: The effect of "acriflavine" (a mixture of 2,8-diaminoacridine and 2,8-diamino-10-methyl-acridinium-chloride) on the growth of the nematode C. elegans. Citation: International Congress of Zoology 14: 247-249 1953 Type: ARTICLE Genes: Abstract: "Acriflavine" (in the form of hydrochlorides of its two components) has a remarkable effect on the growth of C. elegans at 13C. It may be readily incorporated in a wide range of concentrations into the peptone-lecithin-mineral agar customarily used by us in rearing this species. Concentrations of 1:250, 1:500, 1:1000, 1:10,000, and 1:100,000 have been tested. Of these, the 1:1000 concentration has proved the most interesting. When adult hermaphrodites are allowed to lay on agar mounds containing acriflavine at 1:1000, larvae hatch from the eggs and grow, but in no case reach maturity if confined strictly to the agar. Moreover, if left 3 or more days on this medium, they fail in most cases to mature when transferred to normal medium. On the latter some have survived immature for over 35 days after transfer, far longer than the usual life expectancy of the normal worm growing with adequate food and without inhibitory substances present..... ------------------- Key: 107 Medline: Authors: Dougherty EC;Raphael JC;Alton CM Title: The axenic cultivation of Rhabditis briggsae I. Experiments with chick embryo juice and chemically defined media/ Citation: Proc. Helminthological Society of Washington 17: 1-10 1950 Type: ARTICLE Genes: Abstract: ------------------- Key: 108 Medline: Authors: Drechsler C Title: A new species of Stylopage preying on nematodes. Citation: Mycologia 28: 241-246 1936 Type: ARTICLE Genes: Abstract: In Zopf's account of tha capture of nematodes by Arthrobotrys oligospora Fres. and Monosporidium repens Zopf were described, apparently for the first time, instances of a biological habit comparable in part to the carnivorous habit of insectivorous flowering plants. More recently nearly a score of additional fungi occurring in soil, in leaf mold, and in solid decaying materials generally, have been found to capture and consume nematodes in large numbers; evidently, indeed, subsisting in nature entirely through such predacious activity. By far most of these fungi are closely related to those dealt with by Zopf, being referable to a group of interrelated genera including Arthrobotrys, Trichothecium, Cephalothecium, Dactylaria, Dactylella and Monacrosporium. The relatively few nematode-capturing forms alien to this hyphomycetous series are conidial phycomycetes belonging to a Zoopagaceae, a family whose known members are mostly destructive to terricolous amoebae, some operating in parasitic, other predacious relationships. Of the few species preying on nematodes, only one, Stylopage hadra Drechsl., has hitherto been described in detail; so that the description offered herein, of a second species of like biological habit, may be of interest even in the absence of pronounced departures in morphology. ------------------- Key: 109 Medline: Authors: Drechsler C Title: Three fungi destructive to free-living terricolous nematodes. Citation: Journal of the Washington Academy of Sciences 30: 240-254 1940 Type: ARTICLE Genes: Abstract: In several earlier papers comparative treatment was accorded to 24 fungi that had been observed to subsist on free-living nematodes infesting old agar cultures started from diseased rootlets or from other decaying vegetable materials. As the agar media employed were of a concentration sufficient to insure a rather firm consistency together with relative freedom from liquid water, the cultures provided approximately terrestrial rather than aquatic conditions, and therefore not only encouraged the multiplication of eelworms mainly terrestrial with respect to source and adaptation, but also permitted development of the similarly terrestrial fungi habitually destructive to them under natural conditions.... ------------------- Key: 110 Medline: Authors: Drechsler C Title: Three new Hyphomycetes preying on free-living terricolous nematodes. Citation: Mycologia 32: 448-470 1940 Type: ARTICLE Genes: Abstract: In an earlier paper was given a comparative account of 18 interrelated mucedinaceous fungi found to subsist habitually on nematodes that they capture by means of vegetative parts variously adapted for prehension. These fungi had come to light in agar cultures started from discolored rootlets or from other affected vegetable materials, and later often further planted with pinches of friable leaf mold. Similar cultures prepared as circumstances permitted during the last few years have revealed 3 additional mucedinaceous forms obviously belonging in the same series as those previously discussed, and like them observed subsisting by the capture of free-living terricolous eelworms. As the forms appear not to have been recorded hitherto in mycological literature, they are described herein as a species new to science. ------------------- Key: 111 Medline: Authors: Drechsler C Title: Some hyphomycetes parasitic on free-living terricolous nematodes. Citation: Phytopathology 31: 773-802 1941 Type: ARTICLE Genes: Abstract: Agar plate cultures, prepared in the isolation of parasitic oomycetes from discolored roots or other decaying plant materials, often permit abundant multiplication of free-living nematodes, which then are frequently destroyed in large numbers by various predaceous and parasitic fungi. As the parasitic manner of attack, wherein infection comes about from germination of affixed or ingested spores, is shared widely among fungi, it is not surprising that the parasitic forms destructive to eelworms are rather diverse in their taxonomic relationships. Thus, while the 3 parasites that I described earlier under the binomials Euryancale sacciospora, Haptoglossa heterospora, and Meristacrum asterospermum, all belong in the Phycomycetes, they are referable to 3 different groups within that class. Ten additional species, similarly parasitic, but, from their septate vegetative mycelium, obviously belonging with the higher rather than with the lower fungi, are described herein. Important or conspicuous differences in the morphology of their conidial apparatus divide these species into 4 catagories, only one of which is represented by more than a single genus. ------------------- Key: 112 Medline: Authors: Drechsler C Title: Three hyphomycetes that capture nematodes in adhesive networks. Citation: Mycologia 36: 138-171 1944 Type: ARTICLE Genes: Abstract: In several previous papers descriptive treatment was given to 22 interrelated hyphomycetes found subsisting by the capture and destruction of eelworms infesting transparent agar plate cultures started from diseased rootlets or from other decaying vegetable materials. Similar treatment is devoted herein to 3 additional fungi of like biological habit and manifestly belonging to the same predaceous series. Capture of eelworms is accomplished, in all 3 fungi, by means of adhesive bail-like hyphal loops, which, as in allied forms, may occur singly, or may be compounded into networks of variable intricacy. Two of the fungi are referred to Arthrobotrys, one being presented as a new variety, while the other is identified with a long-established though somewhat unfamiliar species of that genus. The third fungus is described as a new species of Dactylaria. In relation to a subsidiary spore form apparently connected with the new species, preliminary discussion is devoted to a delicate Trichothecium found producing stalked adhesive knob-cells. ------------------- Key: 113 Medline: Authors: Drechsler C Title: A species of Harposporium invading its nematode host from the stoma. Citation: Bulletin of the Torrey Botanical Club 73: 557-564 1946 Type: ARTICLE Genes: Abstract: In 1874 Lohde briefly described a hyphomycete that he found growing parasitically on numerous eelworms belonging to a species of Anguillula. To this hyphomycete he applied the binomial Harposporium Anguillulae; the generic term then presented for the first time having reference to the crescentically curved, sickle-shaped conidia which the fungus produced terminally on delicate sterigmata arising singley from peculiar round protuberances formed laterally on the hyphal branches or hyphal prolongations that were extended from the multicellular mycelial filaments, from 2 to 4 in number, passing through the animals body.... ------------------- Key: 114 Medline: Authors: Dropkin VH;Lower WR;Acedo J Title: Growth inhibition of C. elegans and Panagrellus redivivus by selected mammalian and insect hormones. Citation: Journal of Nematology 3: 349-355 1971 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans and Panagrellus redivivus were cultured in axenic medium in microwells. The addition of selected steroids and terpenoids to the medium caused quantitative inhibition of numbers of offspring produced per well. Three out of 14 vertebrate sex hormones and analogs, and seven out of 10 insect juvenile hormones and analogs inhibited growth at 25 or 50 micrograms per ml. In addition, two insecticide synergists which mimic juvenile hormones, propyl 2-propynyl phenyl phosphonate and piperonyl butoxide, inhibited growth at 7 ug/ml. Total lipids from Panagrellus and from Nematospiroides dubius were inhibitory. Separation by silicic acid column chromatography yielded active and inactive portions. We concluded that the inhibition observed was non-specific. ------------------- Key: 115 Medline: 73197027 Authors: Dusenbery DB Title: Countercurrent separation: A new method for studying behavior of small aquatic organisms. Citation: Proceedings of the National Academy of Sciences USA 70: 1349-1352 1973 Type: ARTICLE Genes: Abstract: A new method for the analysis of behavior in small free-swimming aquatic organisms is described. In this procedure, called countercurrent separation, a dense solution flows down along the bottom of an inclined chamber while a light solution flows in the opposite direction, upward along the top of the chamber. The attraction of animals (injected into the center of the chamber) to one solution or the other is then determined by observing the proportion of animals that emerges from the chamber in that solution. When used with the nematode Caenorhabditis elegans, it is estimated that the apparatus is equivalent to at least nine theoretical plates. ------------------- Key: 116 Medline: 74143587 Authors: Dusenbery DB Title: Analysis of chemotaxis in the nematode C. elegans by countercurrent separation. Citation: Journal of Experimental Zoology 188: 41-47 1974 Type: ARTICLE Genes: Abstract: C. elegans responds to several common chemicals. Comparisons of pairs of ions at equivalent concentrations indicated orders of attractiveness of: Na+ > K+ > 1/2 Mg++ > 1/2 Ca++. Cl- > 1/2 SO4-- > NO3- > CH3COO-. The least attractive pair of ions, calcium acetate, is attractive, indicating all these ions are attractive. The most attractive pair, sodium chloride, was attractive from a threshold of 0.1 mM to at least 50 mM. The response to NaCl was maximal throughout the temperature range 15 to 25C and the pH range 3.0 to 9.0. Acid was avoided and base was attractive from concentrations of 0.1 to 1 mM. Dissolved CO2 in the concentration range 0.1 to 1 mM was attractive in 10 mM sodium borate buffer, pH 8.8, but avoided in 25 mM potassium phosphate, pH 6.0. All these responses are likely to affect the distribution of C. elegans in nature and they also provide a tool for promising studies in ------------------- Key: 117 Medline: 76026434 Authors: Dusenbery DB Title: The avoidance of D-Tryptophan by the nematode C. elegans. Citation: Journal of Experimental Zoology 193: 413-418 1975 Type: ARTICLE Genes: Abstract: In chemotactic studies employing countercurrent separation the nematode Caenorhabditis elegans was found to avoid D-tryptophan with a threshold in the range 10(-4) to 10(-3) M. There was no response to L-tryptophan up to 10(-2) M although it appeared to partially inhibit the response to D-tryptophan. ------------------- Key: 118 Medline: 76138995 Authors: Dusenbery DB Title: Attraction of the nematode C. elegans to pyridine. Citation: Comparative Biochemistry & Physiology 53C: 1-2 1976 Type: ARTICLE Genes: Abstract: 1. The nematode C. elegans is attracted to pyridine. 2. The threshold is about 0.1 mM. 3. At concentrations above 1 mM the response weakens. 4. No indication of avoidance of high concentrations could be found. ------------------- Key: 119 Medline: Authors: Dusenbery DB Title: Chemotactic behavior of mutants of the nematode C. elegans that are defective in their attraction to NaCl. Citation: Journal of Experimental Zoology 198: 343-352 1976 Type: ARTICLE Genes: tax-1 tax-2 tax-3 tax-4 tax-5 Abstract: Wild-type C. elegans and 16 derivative strains previously selected for defective attraction to NaCl and shown to carry single-gene mutations were tested for their responses to nine chemical stimuli to which the wild-type responds. These were the attractants Na+, Cl-, OH-, cyclic AMP, CO2 in borate buffer, and pyridine and the repellents D-tryptophan, CO2 in phosphate buffer, and acid. All together 563 measurements were performed. Most strains were defective in most responses but responded normally to some chemical stimuli. In a few cases mutant strains avoided a chemical that attracted the wild-type. Analysis of the patterns of defective responses among these mutants indicates that there are probably at least four different receptors. If results previous reported are included, the minimum number of receptors is increased to six. These mutations appear to have rather discrete effects on ------------------- Key: 120 Medline: Authors: Dusenbery DB Title: Chemotactic responses of male C. elegans. Citation: Journal of Nematology 8: 352-355 1976 Type: ARTICLE Genes: lon-2 Abstract: Cultures of C. elegans containing a high proportion of males were subjected to chemotactic tests by using the method of countercurrent separation. The responses of males and hermaphrodites were determined. Both types of worms preferred Na+ over 1/2 Ca++, Cl- over NO3-: they were attracted to NaCl, OH-, cyclic AMP, pyridine, CO2 in borate buffer (pH 8.8); and avoided CO2 in phosphate buffer (pH 6.0), D-tryptophan, and acid. It was thus concluded that male C. elegans have the same chemotactic responses that hermaphrodites of this species are known to have. ------------------- Key: 121 Medline: Authors: Dusenbery DB;Anderson GL;Anderson EA Title: Thermal acclimation more extensive for behavioral parameters than for oxygen consumption in the nematode C. Citation: Journal of Experimental Zoology 206: 191-198 1978 Type: ARTICLE Genes: Abstract: Thermal acclimation in the free-living soil nematode, Caenorhabditis elegans was studied by determining effects of both growth and test temperatures on oxygen consumption and behavior. Growth temperature (15, 20, or 25C) had no significant influence on oxygen consumption in the range 10-30C, although cold-grown worms had higher consumption at 5C. In contrast, measurements of the fraction of worms moving at any instant and of chemotaxic ability both showed nearly complete thermal acclimation (in the sense that activity-temperature relationships were shifted nearly as much as the differences in growth temperature). Measurements of the rates of acclimation using the behavioral assays indicated acclimation is half complete in about two hours. ------------------- Key: 122 Medline: 75168771 Authors: Dusenbery DB;Sheridan RE;Russell RL Title: Chemotaxis-defective mutants of the nematode C. elegans. Citation: Genetics 80: 297-309 1975 Type: ARTICLE Genes: tax-1 tax-2 tax-3 tax-4 tax-5 Abstract: The technique of countercurrent separation has been used to isolate 17 independent chemotaxis-defective mutants of the nematode Caenorhabditis elegans. The mutants, selected to be relatively insensitive to the normally attractive salt NaCl, show varying degrees of residual sensitivity; some are actually weakly repelled by NaCl. The mutants are due to single gene defects, are autosomal and recessive, and identify at least five complementation groups. ------------------- Key: 123 Medline: 78054765 Authors: Edgar RS;Wood WB Title: The nematode C. elegans a new organism for intensive biological study. Citation: Science 198: 1285-1286 1977 Type: NEWS Genes: Abstract: At a recent conference in Woods Hole, Massachusetts, investigators met to discuss the nematode Caenorhabditis elegans. This free-living worm may, according to some workers, become the Escherichia coli or at least the bacteriophage T4 of the animal world. Small (about 1mm in length) and semitransparent, C. elegans provides for research the advantages of a short life cycle (3 days) and a simple anatomy-it contains about 810 nongonadal nuclei. It is both easy to cultivate, on E. coli as a food source, and convenient for genetic analysis. Its genes are carried on five autosomes and a sex chromosome (X), and it has a genome size about 20 times that of E. coli. It generally reproduces as a self-fertilizing hermaphrodite (XX), but occasional males (XO), which arise by nondisjunction, permit sexual reproduction as well.... ------------------- Key: 124 Medline: 79180186 Authors: Emmons SW;Klass MR;Hirsh D Title: Analysis of the constancy of DNA sequences during development and evolution of the nematode C. elegans. Citation: Proceedings of the National Academy of Sciences USA 76: 1333-1337 1979 Type: ARTICLE Genes: Abstract: In order to test for the occurrence of rearrangements in DNA during development and to assess the rate of DNA divergence during evolution, we have compared restriction fragments derived from DNA from four sources: sperm cells and somatic tissues of one strain of the nematode Caenorhabditis elegans, somatic tissues of a second strain of the same species, and whole animals of a closely related species. Restriction fragments were detected by hybridizing radioactive cloned fragments to restriction digests that had been fractionated by size on agarose gels and transferred to nitrocellulose sheets. In this way, approximately 50 BamHI restriction fragments were visualized and compared. Fragments from sperm and somatic DNAs were found to be identical; 15% differed in size between the two strains. Little cross homology was found between the two species. We conclude that, if rearrangements occur in C. elegans DNA during development, they must affect fewer than a few percent of the restriction fragments or restriction sites. The difference found between the two strains and the two species is ------------------- Key: 125 Medline: Authors: Epstein HF;Schachat FH;Wolff JA Title: Molecular genetics of nematode myosin. Citation: "Pathogenesis of the Human Muscular Dystrophies." Rowland LP (ed), Excerpta Medica, Amsterdam. : 460-467 1976 Type: REVIEW Genes: unc-54 Abstract: The genetics of a small, free-living nematode, Caenorhabditis elegans, has been utilized recently to characterize many mutants affecting the development, function and structure of nerve and muscle. A number of mutants induced by ethyl methane sulfonate (EMS) have been discovered and specifically disrupt the myofibrillar elements of body wall muscle cells, leading to paralysis. One of these mutants, E675, produces an abnormal myosin heavy chain in body wall muscles. Several other mutants as well as E675 are the results of mutation within unc-54, a gene on chromosome I.... ------------------- Key: 126 Medline: Authors: Epstein HF;Harris HE;Schachat FH;Suddleson EA;Wolff JA Title: Genetic and molecular studies of nematode myosin. Citation: CSH Conference on Cell Proliferation 3: 203-214 1976 Type: REVIEW Genes: unc-54 Abstract: The organization of any contractile system requires a series of regulated interactions between genes, structural proteins and movement to occur in a precise manner. The goal of our studies is to understand, at least in outline, some of the principles governing these interactions within the muscle cells of the nematode Caenorhabditis elegans. Our approach has been to analyze the consequences of mutations in the unc-54 gene upon the movement of animals, the arrangement of contractile filaments within body wall muscle cells and the molecular properties of myosin. ------------------- Key: 127 Medline: Authors: Epstein HF;Isachsen MM;Suddleson EA Title: Kinetics of movement of normal and mutant nematodes. Citation: Journal of Comparative Physiology A 110: 317-322 1976 Type: ARTICLE Genes: che-2 dpy-10 unc-4 Abstract: The nematode, Caenorhabditis elegans, is strongly attracted towards secretions of Escherichia coli. The movement of a population of nematodes from the center of an agar plate through a gradient of these secretions towards bacteria at the circumference can be represented by a series of first-order rate processes. Normal and mutant strains of various kinds demonstrate marked differences in their rates of movement. This method of kinetic analysis appears to have a useful potential in the characterization of mutants in nerve and muscle as to whether sensory or locomotive machinery is affected and in the isolation of new mutants of these types. ------------------- Key: 128 Medline: 74284321 Authors: Epstein HF;Thomson JN Title: Temperature sensitive mutation affecting myofilament assembly in C. elegans. Citation: Nature 250: 579-580 1974 Type: ARTICLE Genes: unc-45 Abstract: The assembly of contractile and calcium-related regulatory proteins into functioning myofilament arrays within muscle cells and the genetic control of muscle differentiation are still largely unknown processes. Here we present evidence that a particular gene may regulate such lattice assembly in the body wall muscle cells of the nematode Caenorhabditis elegans. A temperature-sensitive mutation in this gene can prevent the appearance of normal myofilament lattices in this muscle without affecting the amounts of major contractile proteins present. The organised or defective adult structures once formed in mutant muscle are stable to changes in temperature. ------------------- Key: 129 Medline: 75116750 Authors: Epstein HF;Waterston RH;Brenner S Title: A mutant affecting the heavy chain of myosin in C. elegans. Citation: Journal of Molecular Biology 90: 291-300 1974 Type: ARTICLE Genes: unc-54 Abstract: A set of non-complementing, closely-linked, ethyl methanesulphonate-induced mutations in Caenorhabditis elegans specifically affects the structure and function of body-wall muscle cells but not the pharyngeal musculature. One of these mutations, e675, is semidominant and results in the production of a new protein of about 203,000 molecular weight in addition to normal myosin at about 210,000 Mr. The abnormal polypeptide chain is structurally very similar to normal myosin heavy chain when maps of iodinated peptides are compared. The E675 mutant shows a clear relation between defective movement, disruption of the body-wall muscle structure, and the molecular defect in the myosin heavy chains. The altered chain is snythesized in heterozygotes, suggesting that the e675 mutation is either in a structural gene for the heavy chain or in a cis acting control element. The hypothesis that there are two classes of myosin heavy chain within the same cells is ------------------- Key: 130 Medline: Authors: Epstein J;Castillo J;Himmelhoch S;Zuckerman BM Title: Ultrastructural studies on C. briggsae. Citation: Journal of Nematology 3: 69-78 1971 Type: ARTICLE Genes: Abstract: A study of the fine structure of Caenorhabditis briggsae revealed several features not previously described in free-living nematodes. These were: chambered walls of the stoma, zonula adherens in the esophagus, daedaloid folds in the inner surface of the uterus and openings in the terminal web of the intestinal epithelium. Other structures observed in these studies were similar to those described from other free-living nematodes. ------------------- Key: 131 Medline: Authors: Epstein J;Gershon D Title: Studies on ageing in nematodes IV. The effect of antioxidants on cellular damage and life span. Citation: Mechanisms of Ageing & Development 1: 257-264 1972 Type: ARTICLE Genes: Abstract: The effect of the antioxidant a-tocopherolquinone (a-TQ) on the free-living nematode Caenorhabditis briggsae was studied. a-TQ was found to prolong markedly the life span of the animals. The 50% survival of treated animals was extended by 11 days to 46 +/- 2 days as compared with 35 +/- 2 days in control populations. a-TQ also caused a marked delay in the appearance of age-pigment in the intestinal tissue of ageing animals and partially prevented its accumulation. A positive correlation between the delay in age-pigment accumulation and the prolongation of life span was shown. The significance of the effect of antioxidant on the life span and cell damage, and the possible role of peroxidation reactions in senescence, are ------------------- Key: 132 Medline: Authors: Epstein J;Himmelhoch S;Gershon D Title: Studies on ageing in nematodes III. Electronmicroscopical studies on age-associated cellular damage. Citation: Mechanisms of Ageing & Development 1: 245-255 1972 Type: ARTICLE Genes: Abstract: The free-living nematode Caenorhabditis briggsae was used as a model for the study of the phenomenon of ageing. Electronmicroscopical examination of cross-sections through animals of different ages revealed severe damage to certain tissues of aged Caenorhabditis briggsae. Progressive age-dependent accumulation of pigment granules containing acid phosphatase activity was demonstrated in the intestinal epithelium of ageing animals. It is suggested that these granules are age-pigment which is the product of peroxidation of cellular constituents. These pigment granules eventually occupy most of the cytoplasmic volume and appear to lead to the breakdown of the entire tissue. At the terminal period of the animal's life, extensive damage to body muscle tissue and nerve complexes is observed. ------------------- Key: 135 Medline: 67135803 Authors: Fatt HV Title: Nutritional requirements for reproduction of a temperature-sensitive nematode, reared in axenic culture. Citation: Proc. Society for Experimental Biology & Medicine 124: 897-903 1967 Type: ARTICLE Genes: Abstract: 1. Temperature-sensitivity in C. elegans Bergerac is a complex system, composed of a combination of factors, i.e., a) the production of an inhibitory factor in response to higher temperatures, and b) nutritional requirements consisting of proper mineral balance and certain vitamins. 2. Temperature-sensitivity can be overcome by growing the worms at 17C in 50% heated liver extract + 30% partially defined (peptone) medium and heat-treating them at 27C for 27 hours in distilled water or in cold blooded Ringers solution. Worms grown in 50% liver extract + water and heat-shocked in distilled water do not reproduce. Deletion and addition of groups of nutrients to the medium indicates that both vitamins and salts are required for protection against heat-shock in distilled water. 3. The need for extra vitamins is eliminated when the worms are grown at 17C in 50% liver extract + water and heat-shocked in Ringers solution. Comparison of the salts in the peptone medium and Ringers solution suggests that either Na+ or (less likely) HCO3- could be responsible for protection against higher temperatures. ------------------- Key: 137 Medline: Authors: Fatt HV;Dougherty EC Title: Genetic control of differential heat tolerance in two strains of the nematode Caenorhabditis elegans. Citation: Science 141: 266-267 1963 Type: ARTICLE Genes: Abstract: Two strains (Bergerac and Bristol) of the nematode Caenorhabditis elegans, with different temperature tolerances, were reared axenically at 23C to 25C. The Bergerac strain is heat sensitive (that is, it is sterile at maturity), whereas the Bristol strain is heat resistant (that is, it matures and reproduces normally). Hybrid hermaphrodites (F1), produced by crossing Bristol males and Bergerac hermaphrodites, are heat tolerant. Heat sensitivity segregates as a simple Mendelian recessive in the F2 and F3 generations. ------------------- Key: 138 Medline: Authors: Fiakpui EZ Title: Some effects of piperazine and methyridine on the free-living nematode C. briggsae (Rhabditidae). Citation: Nematologica 13: 241-255 1967 Type: ARTICLE Genes: Abstract: Some biological effects of methyridine and piperazine on Caenorhabditis briggsae have been investigated using in vitro techniques on intact worms. It has been found that methyridine produces a contracted paralysis which is not reversed in drug-free medium and piperazine produces a flaccid paralysis reversible in drug-free medium. Methyridine and piperazine negate the action of each other competitively. Different types of evidence have been presented and discussed to show that drugs affect the neuromuscular system of C. briggsae, methyridine being a depolarizing agent and piperazine a neuro-muscular junction blocking agent. ------------------- Key: 140 Medline: Authors: Friedman PA;Platzer EG;Eby JE Title: Species differentiation in C. briggsae and C. elegans. Citation: Journal of Nematology 9: 197-203 1977 Type: ARTICLE Genes: Abstract: Identification of five laboratory strains (1-5) of putative Caenorhabditis briggsae was undertaken. Examination of the male bursal ray arrangement, mating tests with males of Caenorhabditis elegans, malate dehydrogenase zymograms, and SDS polyacrylamide electrophoresis demonstrated that strain 4 was C. briggsae and the others were C. elegans. ------------------- Key: 141 Medline: Authors: Fuchs AC Title: Neue parasitische und halbparasitische Nematoden bei Borkenkafern und einige andere Nematoden I. Teil. Citation: Zoologische Jahrbucher - Abt. Zool. Phys. der Tiere 70: 291-380 1937 Type: ARTICLE Genes: Abstract: ------------------- Key: 142 Medline: Authors: Galsky AG;Monoson HL;Williams SA Title: A bioassay for measuring crude nematode extract which induced trap formation in a predaceous fungus. Citation: Nematologica 20: 39-42 1974 Type: ARTICLE Genes: Abstract: A bioassay for quantitatively measuring the ability of a nematode to induce trap formation in a predaceous fungus is described. The bioassay was sensitive to changes in the crude nemin concentration and is specific for the crude nemin. In addition, the bioassay can be performed rapidly and inexpensively. The bioassay provides an important tool that can be used in measuring nematode-predaceous fungus interrelationships. ------------------- Key: 143 Medline: 79063845 Authors: Garcea RL;Schachat F;Epstein HF Title: Coordinate synthesis of two myosins in wild-type and mutant nematode muscle during larval development. Citation: Cell 15: 421-428 1978 Type: ARTICLE Genes: unc-54 Abstract: In this paper we examine the role of two myosins in body-wall muscle cells of the nematode Caenorhabditis elegans. Large populations of nematodes are synchronized, and the synthesis and accumulation of myosin heavy chains and total protein are followed through postmitotic larval development. Growth is exponential with time for both the wild-type N2 and the body-wall muscle-defective mutant E675, with a longer doubling time for the mutant. Utilizing the electrophoretic polymorphism of the E675 myosin heavy chains, we show that distinguishable classes of heavy chains accumulate differentially throughout development. Immunochemical measurements confirm a similar result in N2. Total myosin heavy chain accumulation is also quantitatively similar for the two chains. Myosin heavy chain relative synthetic rates as determined by pulse-labeling are constant throughout development and are equivalent for the two strains. The final fraction of accumulated unc-54 to total heavy chains of approximately 0.63 equals the constant synthetic fraction of approximately 0.62. Since myosin heavy chain accumulation and relative synthesis are equivalent, we conclude that the turnover of heavy chains is also similar in N2 and E675 despite the extensive structural and functional disruption within body-wall muscle cells of the latter strain. Since the accumulated fraction of unc-54 myosin heavy chains reaches a plateau at the constant synthetic fraction, myosin accumulation in the body-wall muscle cells may be attributed to a constant ratio of synthetic rates of the two body-wall myosin species. The coordinate synthesis of two myosins in the same body-wall muscle cells is ------------------- Key: 146 Medline: 70042404 Authors: Ghiselin M Title: The evolution of hermaphroditism among animals. Citation: Quarterly Review of Biology 44: 189-208 1969 Type: REVIEW Genes: Abstract: Possible selective advantages, including some new ones, for hermaphroditism are reviewed. It is proposed that hermaphroditism should evolve under the following conditions: (a) where it is hard to find a mate; (b) where one sex benefits from being larger or smaller than the other; or (c) where there are small, genetically isolated populations. Some conceptual problems and a comparative means of study are discussed. The literature is reviewed to show the conditions under which hermaphroditism may have evolved. It is concluded that all three explanations have some validity. ------------------- Key: 147 Medline: Authors: Golovin E Title: Nabliudeniia nad nematodami (Okonchanie). Citation: Uchenye Zapiski Kazan. 68: 1-50 1901 Type: ARTICLE Genes: Abstract: ------------------- Key: 148 Medline: Authors: Gochnauer MB;McCoy E Title: Responses of a soil nematode. Rhabditis briggsae to antibiotics. Citation: Journal of Experimental Zoology 125: 377-406 1954 Type: ARTICLE Genes: Abstract: The two main phases of research on antibiotics have been their modes of action on bacteria and their toxicity measurements which are necessary to determine toxic properties of the drug and to assay extraneous toxic contaminants contained in the commercial product. If at least a part of the preliminary toxicity screening could be made with an organism that is inexpensive to obtain and easy to culture in the laboratory, yet as sensitive and reliable as the mouse as a test animal, production costs could be reduced considerably. Because Rhabditis briggsae, a free-living soil nematode, can be maintained in the laboratory as inexpensively as bacterial culture, it was chosen as a possible test organism for toxicity studies. To obtain a comprehensive value for toxicity, antibiotics known to have different toxicity levels for higher animals were chosen for this investigation. Listed in order of increasing toxicity they are penicillin, streptomycin, and streptolin. ------------------- Key: 149 Medline: 71116308 Authors: Guerrero J;Silverman PH Title: Ascaris suum: Immune reactions in mice II. Metabolic and somatic antigens from in vitro cultured larvae. Citation: Experimental Parasitology 29: 110-115 1971 Type: ARTICLE Genes: Abstract: The immunologic activity of somatic and metabolic antigens derived solely from in vitro cultured second- and early third-stage Ascaris suum larvae was studied in mice. Eagle's Minimum Essential Medium and Caenorhabditis briggsae medium 75 were used. The results demonstrate for the first time that metabolic and somatic antigens harvested after 12 days from in vitro cultures were capable of inducing resistance to reinfection. The effect on immunity to A. suum in mice of somatic and metabolic antigens from: (1) second- and third-stage in vitro cultured A. suum larvae; (2) metabolic and somatic antigens from third- and fourth-stage A. suum; (3) C. briggsae metabolic antigens; and (4) desalted Haemonchus contortus third-stage larvae exsheathing fluid are described. ------------------- Key: 151 Medline: 76065244 Authors: Haight M;Frim J;Pasternak J;Frey H Title: Freeze-thaw survival of the free-living nematode C. briggsae. Citation: Cryobiology 12: 497-505 1975 Type: ARTICLE Genes: Abstract: For a long time nematodes have been noted for their ability to survive drastic environmental challenges such as severe dessication and low temperatures. The properties that enable a fully differentiated, postembyronic multicellular organism to recover from such treatment are of interest. In addition to the intrinsic need to examine the cryobiological behavior of such a hardy organism, the value of the nematode in other research areas has been described. Therefore, a reliable and successful method for long-term preservation would be an advantage for maintaining diverse stock cultures.... ------------------- Key: 152 Medline: Authors: Hansen EL;Berntzen AK Title: Development of C. briggsae and Hymenolepsis nana in interchanged media. Citation: Journal of Parasitology 55: 1012-1017 1969 Type: ARTICLE Genes: Abstract: Chemically defined media supplemented with proteinaceous growth factos have been developed for axenic culture of Caenorhabditis briggsae and Hymenolepis nana. The chemical compositions of the media and characteristics of the growth factors are compared. Either growth factor was found to be an effective supplement for each organism. The chemically defined portions of the media can be interchanged if suitable adjustments are made in the salts and buffers. It therefore appears possible to develop a single basal medium for both types of organism, and to use the convenience of the C. briggsae bioassay for further isolation and the characterization of growth factors for helminths. ------------------- Key: 153 Medline: Authors: Hansen EL;Buecher EJ Title: Biochemical approach to systematic studies with axenic nematodes. Citation: Journal of Nematology 2: 1-6 1970 Type: ARTICLE Genes: Abstract: The application of biochemical systematics to nematology can provide a much needed tool to resolve problems of taxonomy and phylogeny. These problems are most apparent when the morphological characteristics merge between species, when characteristics occur in the rare form, e.g. male in a hermaphroditic species, or when strains show no morphological differences. Biochemical systematics depends on elucidation of the subtle molecular differences which underlie taxonomic variation. The challenge for the nematologist is to recognize the biochemical processes that can yield information for this differentiation and then to prepare sufficient material for investigation..... ------------------- Key: 154 Medline: 72098726 Authors: Hansen EL;Buecher EJ Title: Effect of insect hormones on nematodes in axenic culture. Citation: Experientia 27: 859-860 1971 Type: ARTICLE Genes: Abstract: Insect juvenile hormones (JH) or JH mimetics have been shown to affect development of nematodes: Trichinella spiralis larvae and fourth stage Phocanema decipiens were inhibited, and abnormal morphology was seen in Heterodera schactii. The effects of insect hormones and analogues on development of several free-living and parasitic nematodes cultured axenically are described in the present paper. ------------------- Key: 155 Medline: Authors: Hansen EL;Buecher EJ;Yarwood EA Title: Development and maturation of C. briggsae in response to growth factor. Citation: Nematologica 10: 623-630 1964 Type: ARTICLE Genes: Abstract: Cultural characteristics of Caenorhabditis briggsae were examined in a medium composed of a chemically defined basal medium and a supplement consisting of a proteinous growth factor. In each of the separate components used as a medium, larvae developed through only one molt. Development was resumed when the medium was restored to completeness. In the complex medium maturation was slower and reproduction somewhat reduced compared with that in monoxenic cultures with E. coli. ------------------- Key: 156 Medline: Authors: Hansen EL;Cryan WS Title: Continuous axenic culture of free-living nematodes. Citation: Nematologica 12: 138-142 1966 Type: ARTICLE Genes: Abstract: A new method for continuous thin film axenic culture of nematodes involving a minimum of handling permits attainment of larger populations and higher proportions of adults than is attained in test tube cultures with identical media. The increase in population may be attributable to improved physiological conditions which enhance gas exchange. These observations suggest that results obtained in test tube cultures have led to an underestimation of the nutritional adequacy of the medium. ------------------- Key: 157 Medline: 72095201 Authors: Hansen EL;Perez-Mendez G;Buecher EJ Title: Glycogen as a supplement in media for axenic cultivation of nematodes. Citation: Proc. Society for Experimental Biology & Medicine 137: 1352-1354 1971 Type: ARTICLE Genes: Abstract: Free-living nematodes have been cultured continuously under axenic conditions for several years. The culture medium consists of a chemically defined portion and an organic supplement. All supplements reported thus far, such as liver growth factor and serum y-globulin are proteinaceous and heat-labile. We now report the use of a polysaccharide, glycogen, as an effective heat-stable ------------------- Key: 158 Medline: 77134682 Authors: Harris H;Tso M-Y W;Epstein HF Title: Actin and myosin-linked calcium regulation in C. elegans. Biochemical and structural properties of native filaments and purified proteins. Citation: Biochemistry 16: 859-865 1977 Type: ARTICLE Genes: Abstract: Calcium regulation of actomyosin activity in the nematode, Caenorhabditis elegans, has been studied with purified proteins and crude thin filaments. Actin and tropomyosin have been purified from C. elegans and shown to be similar in most respects to actin and tropomyosin from rabbit skeletal muscle. The actin comigrates with rabbit actin on polyacrylamide-sodium dodecyl sulfate gel electrophoresis, forms similar filaments and paracrystals, and activates the Mg2+-ATPase of rabbit myosin heads as efficiently as rabbit actin. Nematode tropomyosin has a greater apparent molecular weight (estimated by mobility on polyacrilamide-sodium dodecyl sulfate gels) than the rabbit protein, yet it forms Mg2+-paracrystals with a slightly shorter periodicity. Native thin filaments extracted from nematodes activate rabbit myosin subfragment 1 Mg2+-ATPase in a calcium sensitive manner; the extent of activation is threefold greater in 0.2 mM CaCl2 than in the absence of calcium. This observation suggests that the thin filaments contain components which are functionally equivalent to vertebrate troponins. Calcium is also required for maximal activation of the Mg2+-ATPase of purified nematode myosin and thin filament-linked calcium regulatory systems. The origin of the actin, tropomyosin, and myosin from different tissues and the use of genetic analysis to answer questions about assembly and function in vivo are discussed. ------------------- Key: 159 Medline: 77183614 Authors: Harris HE;Epstein HF Title: Myosin and paramyosin of C. elegans: Biochemical and structural properties of wild-type and mutant proteins. Citation: Cell 10: 709-719 1977 Type: ARTICLE Genes: unc-54 Abstract: Myosin and paramyosin have been purified from the nematode, Caenorhabditis elegans. The properties of the myosin in general resemble those of other myosins. The native molecule is a dimer of heavy (210,000 dalton) polypeptide chains and contains 18,000 and 16,000 dalton light chains. When rapidly precipitated from solution, it forms small, bipolar aggregates, about 150 nm long, consistent with the expected molecular structure of a rigid rod with a globular head region at one end. Its ATPase activity is stimulated by Ca2+ and EDTA. The myosin binds to F actin in a polar and ATP-sensitive manner, and the Mg2+-ATPase is activated by either F actin or nematode thin filaments. Dialysis of myosin to low ionic strength produces very long filaments. When a myosin-paramyosin mixture is dialyzed under the same conditions, co-filaments form which consist of a myosin cortex, surrounding a paramyosin core. Some properties of myosins from the mutants E675 and E190, which have functionally and structurally altered body wall muscles, are compared with those of wild-type myosin. These myosins behave normally in in vitro tests. The implications of these results are discussed in terms of the myosin heavy chain composition. ------------------- Key: 160 Medline: Authors: Hedgecock EM Title: The mating system of C. elegans: Evolutionary equilibrium between self- and cross-fertilization in a facultative hermaphrodite. Citation: American Naturalist 110: 1007-1012 1976 Type: ARTICLE Genes: Abstract: Many hermaphroditic species, including the small soil nematode Caenorhabditis elegans, have an evolutionary option not available to strictly dioecious species or to organisms committed exclusively to monoparental reproduction. The ratio of self-fertilization to cross-fertilization can be adjusted in a nearly continuous fashion to obtain the maximum reproductive potential in a constant or changing environment. In C. elegans, this involves modulating the frequency of male production and the efficiency of their mating. Since a single hermaphrodite produces nearly 300 fertile eggs, whether by selfing or by mating, the advantage of sexual reproduction must be balanced against the dilution of the maternal genetic material which accompanies mating. This paper derives the frequency of male production and the efficiency of mating in C. elegans from a simple deterministic model of a population with discrete generations at approximate equilibrium. Both parameters are experimentally ------------------- Key: 161 Medline: 76078399 Authors: Hedgecock EM;Russell RL Title: Normal and mutant thermotaxis in the nematode C. elegans. Citation: Proceedings of the National Academy of Sciences USA 72: 4061-4065 1975 Type: ARTICLE Genes: tax-1 tax-2 tax-3 tax-4 tax-5 Abstract: When grown at a temperature from 16C to 25C and placed on a thermal gradient, the nematode Caenorhabditis elegans migrates to its growth temperature and then moves isothermally. Behavioral adaptation to a new temperature takes several hours. Starved animals, in contrast, disperse from the growth temperature. Several mutants selected for chemotaxis defects have thermotaxis defects as well; these behaviors depend on some common gene products. New mutants selected directly for thermotaxis defects have unusual phenotypes which suggest mechanims for thermotaxis. ------------------- Key: 162 Medline: 76188534 Authors: Herman RK;Albertson DG;Brenner S Title: Chromosome rearrangements in C. elegans. Citation: Genetics 83: 91-105 1976 Type: ARTICLE Genes: dpy-6 him-1 unc-1 unc-7 mnDp1 mnDp2 mnDp3 mnDp4 mnDp5 Abstract: A method for selecting unlinked duplications of a part of the X chromosome of C. elegans is described. Five such duplications have been identified. One of them, Dp(X;V)1, is translocated to linkage group V, where it suppresses crossing over along the left half of linkage group V. Dp(X;V)1 homozygotes grow slowly and are sterile. The other four duplications are associated with chromosome fragments, as observed cytologically by fluorescence microscopy, and tend to be lost. Their frequency of loss is higher in strains homozygous for a mutation that promotes nondisjunction of X chromosomes. The recombination frequencies between two of these duplications and the X have been measured: the frequencies are at least 50 times less than for X-X recombination in the same region. The duplications may prove useful as balancers of recessive lethal mutations. ------------------- Key: 163 Medline: 78128036 Authors: Herman RK Title: Crossover suppressors and balanced recessive lethals in C. elegans. Citation: Genetics 88: 49-65 1978 Type: ARTICLE Genes: dpy-10 let-19 let-22 let-23 let-24 let-25 let-26 let-27 let-28 let-30 let-31 let-32 unc-4 unc-6 unc-13 unc-24 unc-32 unc-42 mnC1 mnDf71 Abstract: Two dominant suppressors of crossing over have been identified following X-ray treatment of the small nematode C. elegans. They suppress crossing over in linkage group II (LG II) about 100-fold and 50-fold and are both tightly linked to LG II markers. One, called C1, segregates independently of all other linkage groups and is homozygous fertile. The other is a translocation involving LG II and X. The translocation also suppresses crossing over along the right half of X and is homozygous lethal. C1 has been used as a balancer of LG II recessive lethal and sterile mutations induced by EMS. The frequencies of occurrence of lethals and steriles were approximately equal. Fourteen mutations were assigned to complementation groups and mapped. They tended to map in the same region where LG II visibles are clustered. ------------------- Key: 164 Medline: 80025646 Authors: Herman RK;Madl JE;Kari CK Title: Duplications in C. elegans. Citation: Genetics 92: 419-435 1979 Type: ARTICLE Genes: dpy-6 dpy-7 dpy-10 dpy-13 unc-2 unc-6 unc-18 unc-78 mnC1 mnDp1 mnDp2 mnDp8 mnDp9 mnDp10 mnDp25 mnDp26 mnDp27 mnDp30 mnDp31 mnDp32 mnDp33 mnDp34 mnDp35 mnDp36 Abstract: Thirteen chromosomal duplications, all unlinked to their linkage group of origin, have been identified following X-irradiation. Ten are X-chromosome duplications, of which six are half-translocations on three autosomal linkage groups and four are free fragments. Five of the half-translocations are homozygous fertile and two are recognizable cytologically as chromosome satellites, both of which show some mitotic instability. The free-X duplications show varying tendencies for loss. Three appear not to overlap in extent previously identified for free-X duplications. The fourth carries genes from linkage group V, as well as X. Three duplications of a portion of linkage group II were identified and found to be free and quite stable in hyperploids. Some of the free duplications tend to disjoin from the X chromosome in males. New X-chromosome map data are presented. ------------------- Key: 165 Medline: 68199211 Authors: Hieb WF;Rothstein M Title: Sterol requirement for reproduction of a free-living nematode. Citation: Science 160: 778-780 1968 Type: ARTICLE Genes: dpy-7 Abstract: The free-living, hermaphroditic nematode Caenorhabditis briggsae has a nutritional requirement for sterols. It will reproduce indefinitely in a liquid medium containing only bacterial cells (Escherichia coli) and salts if various sterols are present. Several other lipid-soluble materials are ineffective in supporting reproduction. ------------------- Key: 166 Medline: Authors: Hieb WF;Rothstein M Title: Isolation from liver of a heat-stable requirement for reproduction of a free-living nematode. Citation: Archives of Biochemistry & Biophysics 136: 576-578 1970 Type: ARTICLE Genes: Abstract: Free-living nematodes grown in axenic culture require, in addition to a chemically defined medium, a heat-labile "growth factor" which is present in various tissues and bacteria. A purified form of the factor derived from liver extract was reported by Sayre et al to be a discrete protein of high molecular weight which exists in multiple active forms of similar amino acid composition. ------------------- Key: 167 Medline: 70129908 Authors: Hieb WF;Stokstad ELR;Rothstein M Title: Heme requirement for reproduction of a free-living Citation: Science 168: 143-144 1970 Type: ARTICLE Genes: Abstract: The free-living hermaphroditic nematode Caenorhabditis briggsae has a nutritional requirement for heme. The organism can be subcultured repeatedly in a chemically defined axenic medium that contains autoclaved bacterial cells (Escherichia coli) and sterols if a hemeprotein-containing fraction from liver is present. Pure myoglobin, hemoglobin, cytochrome c and hemin, respectively, can substitute effectively for the liver ------------------- Key: 168 Medline: 77099952 Authors: Higgins BJ;Hirsh D Title: Roller mutants of the nematode C. elegans. Citation: Molecular & General Genetics 150: 63-72 1977 Type: ARTICLE Genes: bli-2 dpy-1 dpy-2 dpy-5 dpy-9 dpy-10 dpy-11 dpy-13 lon-2 rol-1 rol-3 Abstract: The wild type nematode, Caenorhabditis elegans, moves in a sinusoidal wave pattern and leaves sinusoidal paths behind it on a bacterial lawn. The nematode crawls on its side on a special cuticular tread that extends straight down the length of its body. Wild type worms also have rows of musculature and a ventral nerve cord that extend straight down the body. Roller mutants rotate around their long axis as they crawl and move in circular paths. Three roller mutants have been studied. Two mutants are left rollers and one is a right roller. The left rollers have left-handed helical treads, body musculatures, and ventral nerve cords whereas these structures are right-handed in the right roller. Double mutants constructed from roller mutants and long mutants indicate that long rollers have helices of the same pitch as normal length rollers. Double mutants constructed from rollers and dumpy mutants that are short and fat indicate dumpy phenotype is epistatic to roller. Double mutants constructed from rollers and blister mutants that have cuticular swelling indicate roller phenotype is epistatic to blister. The results suggest that the roller phenotypes are due to cuticular lesions. Rollers can chemotaxe up a gradient of an attractant by turning off their body muscle movement and continuing their head movements. ------------------- Key: 169 Medline: 78238979 Authors: Himmelhoch S;Zuckerman BM Title: C. briggsae: Aging and the structural turnover of the outer cuticle surface and the intestine. Citation: Experimental Parasitology 45: 208-214 1978 Type: ARTICLE Genes: Abstract: The exposed surface of Caenorhabditis briggsae was examined for the presence of neuraminic acid, hyaluronic acid, and glucuronic acid. None of these molecules was detected. In young nematodes the presence of a surface coat was demonstrated. This surface coat appeared to shrink with age. Ruthenium red staining suggested the presence of acid mucopoly-saccarides on the outer surface. Feeding the nematodes on cationized ferritin enabled visualization of a matrix surrounding the intestinal brush border. Experiments with an inhibitor of acid mucopolysaccharide synthesis suggested that there is no turnover of acid mucopolysaccharides after the final molt of C. briggsae. ------------------- Key: 170 Medline: 77116054 Authors: Himmelhoch S;Kisiel MJ;Zuckerman BM Title: C. briggsae: Electron microscope analysis of changes in negative surface charge density of the outer cuticular membrane. Citation: Experimental Parasitology 41: 118-123 1977 Type: ARTICLE Genes: Abstract: The negative surface charge density of the outer cuticular membrane of Caenorhabditis briggsae was visualized by use of cationized ferritin. When grown axenically in a medium which contained liver extract, the net negative surface charge density was significantly less in nematodes 21-24 days old than in nematodes 6-7 days old. Nematodes grown in heat-treated medium, in which liver enzyme activities were presumably inactivated, did not show lower surface charge densities at 21 days. These findings indicate that the decrease in net negative surface charge was caused by a receptor-destroying enzyme present in the liver extract. The relation of the membrane charge changes observed in vitro to those which might occur in nature is discussed. Further studies showed that the negative charges are evenly distributed over the surface of the nematode except in the tail area, where they are lower. ------------------- Key: 172 Medline: Authors: Hirsh D Title: Patterns of gene expression during development of the nematode C. eleganss. Citation: "Microbiology-1975." Schlessinger D (ed), American Society for Microbiology, Washington DC. : 508-514 1975 Type: REVIEW Genes: Abstract: Much of the discussion in this symposium has addressed the question of how a single cell differentiates into two different daughter cells. Considerable effort is being made to understand the ability of cells to regulate protein synthesis either by temporal regulation at the level of the genome or through the inherent order of assembly of macromolecules, as is seen in the case of T4 bacteriophage late functions. We now turn to consideration of the genetic control of development in an organism which is complex relative to those prokaryotes and unicellular eukaryotes which have been discussed so far. Studies on the development of prokaryotes or simple eukaryotes rely upon the extensive knowledge of how genes are replicated, transcribed, and translated as deciphered over the past 15 years of molecular biology. An alternative approach is required in studying an organism with several cell types and asymmetries in which there is complex development. I have chosen the small nematode Caenorhabditis elegans for studying genetic control of development because it lends itself to detailed morphological studies and because its genetics is now well defined through the elegant work of Brenner...... ------------------- Key: 174 Medline: 76140556 Authors: Hirsh D;Oppenheim D;Klass M Title: Development of the reproductive system of C. elegans. Citation: Developmental Biology 49: 200-219 1976 Type: ARTICLE Genes: Abstract: A morphological study of the growth and the development of the reproductive system of the nematode Caenorhabditis elegans has been carried out. When the first stage larva hatches from the egg it contains four primordial gonadial cells. These cells proliferate and form the entire adult reproductive system, consisting of approximately 2500 nuclei, in 45 h at 25C. Several distinctive morphological features of gonadogenesis and early embryogenesis that are recognizable in the compound microscope can be used to chart the development of the nematode. The mature gonad presents a linear developmental axis both temporally and morphologically of the formation of oocytes, fertilization, and the early stages of embryogenesis. The structure of the adult ovary indicates that the cytoplasm of each newly formed oocyte is derived from a common core of cytoplasm within the multinuclear ovary. ------------------- Key: 175 Medline: 76140557 Authors: Hirsh D;Vanderslice R Title: Temperature-sensitive developmental mutants of C. elegans. Citation: Developmental Biology 49: 220-235 1976 Type: ARTICLE Genes: Abstract: About 200 temperature-sensitive mutants of the nematode Caenorhabditis elegans have been isolated. At restrictive temperature, the mutants are blocked in the reproductive life cycle. They have been placed into six broad categories based on their defective phenotypes. The six categories are: (1) mutants blocked in embryogenesis; (2) mutants defective in gonadogenesis; (3) mutants defective in spermatogenesis; (4) mutants that accumulate at an intermediate growth stage; (5) mutants that produce sterile adult progeny; (6) mutants that have a temperature-sensitive morphological defect that interrupts the reproductive life cycle. The critical times of temperature sensitivity have been measured using temperature-shift experiments. Most of the gonadogenesis and spermatogenesis mutants are temperature sensitive during the period of cellular differentiation rather than proliferation. The temperature responses of the gonadogenesis and zygote-defective mutants indicate a common association between functions in gonadogenesis and early embryogenesis. Many of the mutants placed in different categories share other temperature-sensitive phenotypes upon close examination. This implies that many of the functions required for development are general metabolic reactions under increased demand during ------------------- Key: 176 Medline: 78131001 Authors: Hirsh D;Wood WB;Hecht R;Carr S;Vanderslice R Title: Expression of genes essential for early development in the nematode, C. elegans. Citation: "Molecular Approaches to Eucaryotic Genetic Systems" ICN-UCLA Symposia on Molecular & Cellular Biology, Volume 8. Wilcox G, Abelson J and Fox CF (eds), Academic Press, NY. 8: 347-356 1977 Type: REVIEW Genes: Abstract: Genetic tests for maternal effects have been performed on 25 temperature-sensitive zygote-defective mutants of the nematode Caenorhabditis elegans. For most of the genes defined by these mutants (22 out of 25), maternal expression is sufficient for zygote survival, even if the gene is not expressed in the zygote. Twelve of these 22 genes must be expressed in the mother for zygote survival (strict maternals). For the remaining ten, expression either in the mother or in the zygote is sufficient for survival. One mutant shows a paternal effect in which wild-type sperm cytoplasm appears to rescue mutant zygotes. Maternal effect tests on mutants that block as late as the second larval stage after hatching indicate that in 3 of 11 mutants maternal contributions still can rescue mutant progeny. Temperature shift experiments on the zygote-defective embryos show that all but one of the strict maternal mutants are temperature sensitive only before gastrulation. One of the mutants that can be rescued by gene expression in the zygote is temperature sensitive prior to gastrulation, suggesting that some zygote genes can function in early embryogenesis. ------------------- Key: 177 Medline: Authors: Hitcho PJ;Thorson RE Title: Behavior of free-living and plant-parasitic nematodes in a thermal gradient. Citation: Journal of Parasitology 58: 599-599 1972 Type: ARTICLE Genes: Abstract: Positive thermotactic behavior has been demonstrated in certain parasitic helminths. Unlike most organsims, these parasites did not seek a temperature preferendum, but rather migrated in the gradient until thermal damage and death occurred... ------------------- Key: 178 Medline: 77226072 Authors: Hodgkin JA;Brenner S Title: Mutations causing transformation of sexual phenotype in the nematode C. elegans. Citation: Genetics 86: 275-287 1977 Type: ARTICLE Genes: dpy-21 dpy-22 him-1 lin-4 tra-1 tra-2 tra-3 Abstract: Ten mutations are described that transform genotypic hermaphrodites of the nematode Caenorhabditis elegans into phenotypic males. These fall into three autosomal complementation groups, termed tra-1, tra-2, and tra-3. Two alleles of tra-1 produce almost complete transformation, to a fertile male phenotype; such transformed animals are useful for analyzing sex-linked genes. All alleles of tra-1 and tra-2 are recessive; the one known allele of tra-3 is both recessive and maternal in effect. Where tested, both XX and XXX hermaphrodites are transformed into males, but XO males (true males) are unaffected by these mutations. It is suggested that these genes are actually involved in hermaphrodite development and have no role in male development. ------------------- Key: 179 Medline: Authors: Hodgkin J;Horvitz HR;Brenner S Title: Nondisjunction mutants of the nematode C. elegans. Citation: Genetics 91: 67-94 1979 Type: ARTICLE Genes: dpy-21 him-1 him-2 him-3 him-4 him-5 him-6 him-7 him-8 him-9 unc-86 Abstract: The frequency of males (5AA;XO) among the self progeny of wild-type Caenorhabditis elegans hermaphrodites (5AA;XX) is about one in 500. Fifteen him (for "high incidence of males") mutations have been identified that increase this frequency by a factor of ten to 150, as a result of increased X-chromosome non-disjunction. The mutations define ten complementation groups, which have been mapped: nine are autosomal, and one sex linked. Most of the him mutants are superficially wild type in anatomy and behavior; however, him-4 mutants display gonadal abnormalities, and unc-86 mutants, which have a Him phenotype, exhibit a variety of anatomical and behavioral abnormalities. All the mutants segregate fertile 3X hermaphrodite progeny as well as XO male progeny. Some produce large numbers of inviable zygotes. Mutants in all ten genes produce diplo-X and nullo-X exceptional ova, and in the four strains tested, diplo-X and nullo-X exceptional sperm are produced by 2X "transformed" males. It appears likely that most of the mutants have defects in both gamete lines of the hermaphrodite. XO males of him strains other than him-4 and unc-86 are similar to wild-type males in anatomy and behavior, and all produce equal or almost equal numbers of haplo-X and nullo-X sperm, and no diplo-X sperm. Male fertility is reduced to varying extents in all him mutants. In four of the strains, nondisjunction during oogenesis has been shown to occur at a reductional division, and in three of these strains, abnormalities in recombination have been demonstrated. One mutant also exhibits autosomal nondisjunction, but many of the others probably do not. Therefore, the X chromosome of C. elegans may differ from the autosomes in the machanisms controlling its meiotic behavior. 3X hermaphrodites are shorter and less fertile than 2X hermaphrodites, and they produce many inviable zygotes among their self progeny; these are probably 4X zygotes. Haplo-X and diplo-X ova are produced in 2:1 ratio by 3X hermaphrodites. him mutations are expressed in these animals, increasing the frequency of self-progeny males and 2X hermaphrodites. ------------------- Key: 180 Medline: 75181614 Authors: Johnson CD;Russell RL Title: A rapid, simple radiometric assay for cholinesterase, suitable for multiple determinations. Citation: Analytical Biochemistry 64: 229-238 1975 Type: ARTICLE Genes: Abstract: A rapid and simple radiometric assay for cholinesterase, suitable for multiple determinations, has been developed. (3H-acetyl) choline is enzymatically hydrolyzed in a small reaction volume in a scintillation vial. The released 3H-acetate is then extracted into a toluene-based scintillator added directly to the vial, without removing the reaction volume. The extracted 3H-acetate counts efficiently but the unhydrolyzed 3H-acetylcholine remains unextracted in the small aqueous reaction volume, from which its weak B-particles of decay do not escape to excite the scintillator. The assay is highly reproducible, quite sensitive, and useful for applications in which multiple samples must be quickly assayed. ------------------- Key: 181 Medline: Authors: Hogger CH;Estey RH Title: Cryofracturing for scanning electron microscope observations of internal structures of nematodes. Citation: Journal of Nematology 9: 334-337 1977 Type: ARTICLE Genes: Abstract: Nematodes were prepared for scanning electron microscopy by cryofracturing in ethanol and then by critical-point drying in carbon dioxide. Cross sections of Caenorhabditis briggsae and Xiphinema americanum showed the arrangement of the intestine, ovaries, muscle cells, and some layers of the cuticle. The technique is complementary to transmission electron microscopy and facilitates the interpretation of results from thin sections. ------------------- Key: 182 Medline: Authors: Hogger CH;Estey RH;Kisiel MJ;Zuckerman BM Title: Surface scanning observations of changes in C. briggsae during aging. Citation: Nematologica 23: 213-216 1977 Type: ARTICLE Genes: Abstract: SEM observations of adult Caenorhabditis briggsae females showed differences between young and old nematodes. In young nematodes the cuticle was generally smooth, whereas in old ones it was wrinkled. Deirids were located at the level of the excretory pore in the lateral field. They were distinct in young nematodes but indistinct in old ones. The oral opening was formed by six lips, which were closed in old nematodes and open in young ones. The vulva possessed two semi-circular lips and was bordered by two lateral flaps. These lips were smooth in young specimens and wrinkled in old ones. Cryofractures of old nematodes showed cavities in the intestinal epithelium corresponding to areas in which age pigment granules normally occur. No such cavities were seen in young nematodes. ------------------- Key: 183 Medline: Authors: Honda H Title: Experimental and cytological studies on bisexual and hermaphroditic free-living nematodes with special reference to the problem of sex. Citation: Journal of Morphology 40: 191-233 1925 Type: ARTICLE Genes: Abstract: Hermaphrodite gonads of Rahbditis elegans can be distinguished in early developmental stages, but oogonia cannot be told from spermatogonia. Certain peculiar males show developmental processes approaching those of hermaphrodites. More eggs are produced by a hermaphrodite than there are sperm with which to fertilize them. Such exhausted hermaphrodites may be mated with males and produce fertile eggs, but convincing evidence of cross-fertilization is lacking. Unmated females of Diplogaster serivora live longer than mated ones, but no difference was found in the males. Sexual instinct seems to be lacking in males of R. dolichura and R. elegans. Hermaphrodites mated with males produce many more male offspring than by self-fertilization, but these do not exhibit sexual instincts. Females produced by cross-fertilization are not pure females, nor have they been found at all in R. elegans or R. dolichura. After fertilization in these two species, both polar bodies are fomed and the pronuclei fuse. Sex is determined by the ------------------- Key: 184 Medline: 80077302 Authors: Horvitz HR;Brenner S;Hodgkin J;Herman RK Title: A uniform genetic nomenclature for the nematode C. elegans. Citation: Molecular & General Genetics 175: 129-133 1979 Type: ARTICLE Genes: Abstract: A uniform system of genetic nomenclature for the nematode Caenorhabditis elegans is described. Convenient ways are specified to designate genes, mutations and strains, and to attempt to avoid name duplications. ------------------- Key: 185 Medline: 78148168 Authors: Hosono R Title: Age dependent changes in the behavior of C. elegans on attraction to Escherichia coli. Citation: Experimental Gerontology 13: 31-36 1978 Type: ARTICLE Genes: Abstract: A method to analyze the response of Caenorhabditis elegans to Escherichia coli as food was devised. Age dependency of the response was purchased with this method chronologically. Although the activity of sinusoidal movement and the utilization of bacteria as food began to decrease rapidly in previous to maximum growth, the attraction potency in young adults was maintained ------------------- Key: 186 Medline: 79107291 Authors: Hosono R Title: Sterilization and growth inhibition of C. elegans by 5-fluorodeoxyuridine. Citation: Experimental Gerontology 13: 369-374 1978 Type: ARTICLE Genes: Abstract: Free living nematodes have often been used for the study of ageing as model organisms, because they have a limited number of somatic cells and a short life-span. The study on ageing has been usually carried out with an age-synchronized population of nematodes. For this purpose, the nematode Caenorhabditis elegans seems to be suitable, because its physiological and genetical characters have been most extensively studied among the nematodes. One of the methods for producing the age-synchrony is the use of a specific inhibitor of DNA synthesis. It has been reported that 5-fluorodeoxyuridine (FdUrd) prevents a maturation of reproductive systems without affecting a growth and a life-span of a nematode Turbatrix aceti. This method is convenient for obtaining a small number of synchronously aged worms. However, recently an apparent increase in cell number during the postembryonic development has been observed in other nematodes. Therefore, it is possible that somatic cells in some nematodes are also sensitive to DNA synthesis inhibitors. The effect of FdUrd on the growth and the production of progeny of C. elegans is as yet unknown. For this report, the effect of FdUrd on the life-cycle of C. elegans has been studied with viable or heat-killed ------------------- Key: 187 Medline: Authors: Hosono R Title: Sinusoidal movement of C. elegans in liquid phase. Citation: Zoologica Magazine 87: 191-195 1978 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans propagates sinusoidal waves along the body with much higher frequency in a liquid phase than on an agar plate. The sinusoidal movement in a liquid is rhythmic and its frequency varies depending on ages of the nematode or on temperature in the assay. Mutants with affected musculature, show marked differences in their frequency from wild strains. The process of paralysis by an anesthetic and the recovery from the paralytic state are expressed by an alteration of frequency. This method appears to be a useful means for the characterization of chemicals influencing on the behavior and isolation of a new type of mutant. ------------------- Key: 188 Medline: Authors: Hwang SW Title: Freezing and storage of nematodes in liquid nitrogen. Citation: Nematologica 16: 305-308 1970 Type: ARTICLE Genes: Abstract: Free-living nematodes of the genera Aphelenchoides, Panagrellus, Turbatrix, and Caenorhabditis were successfully frozen in heat-sealed glass ampoules using dimethyl sulfoxide as a protectant. After 6 months storage in liquid nitrogen refrigerator (below -160C), living nematodes were recovered after thawing. The nematodes were slowly cooled to -22 +/- 1C and immediately transferred to liquid nitrogen at -196C. ------------------- Key: 189 Medline: 69225355 Authors: Jakstys BP;Silverman PH Title: Effect of heterologous antibody on Haemonchus contortus development in vitro. Citation: Journal of Parasitology 55: 486-492 1969 Type: ARTICLE Genes: Abstract: Double diffusion tests of sera obtained from rabbits immunized with somatic extracts of the free-living nematodes, Caenorhabditis briggsae and C. elegans, resulted in cross-reactions with metabolic and somatic extracts of the sheep parastic stomach worm, Haemonchus contortus. In vitro culture experiments demonstrated that H. contortus development was retarded by the same heterologous antisera. The possibility of complement playing a role in the heterologous immune cross-reactions is suggested. ------------------- Key: 190 Medline: Authors: Jantunen R Title: Moulting of C. briggsae (Rhabditidae). Citation: Nematologica 10: 419-424 1964 Type: ARTICLE Genes: Abstract: The moulting of Caenorhabditis briggsae was observed under axenic conditions in hanging drop cultures. From these observations, and from a statistical analysis of the dimensions of "sheaths" taken from a mass culture, it is concluded that there are four moults. The process of moulting is described. ------------------- Key: 191 Medline: 79214177 Authors: Johnson K;Hirsh D Title: Patterns of proteins synthesized during development of C. elegans. Citation: Developmental Biology 70: 241-248 1979 Type: ARTICLE Genes: Abstract: Two-dimensional gel electrophoresis has been used to analyze proteins synthesized during postembryonic development of the nematode Caenorhabditis elegans. This organism is favorable for these studies because it has a limited number of cells, it is genetically well-defined, and its development is currently under investigation in several laboratories. 35S-labeled E. coli was used for continuous and pulse labeling of C. elegans during its four juvenile larval stages and as a gravid adult. After continuous labeling or pulse labeling for 1 hr, 600-800 individual spots can be resolved on a 2D gel using fluorography and 2 weeks of exposure. Proteins that represent 0.0017% of the total sample can be detected. Exposure for 12 weeks reveals only 100 additional spots even though the films are not saturated. It therefore appears that the frequency distribution of proteins decreases significantly beyond these 800 most abundant proteins that can be frationated on an O'Farrell gel. When the patterns of pulse-labeled proteins of the five developmental stages were compared, 113 proteins could be seen to undergo modulation at one or more of the developmental stages. A maximum number of changes was seen in the transition from the L4 to the adult stages when 11% of the total spots either appeared, disappeared, or changed in intensity. As controls, different preparations of the same developmental stage were compared and revealed considerable fluctuation, 2.6-4.8%. These fluctuations are presumed to be due to variations in growth conditions during culture of the organism. Continuous label experiments reveal a distinct set of proteins that undergo turnover and/or modification during development. Some of these proteins are absent in only one stage, indicating that stable proteins are also modulated. But nearly all of the proteins seen in a continuous label are also seen in a pulse label indicating that most of the major proteins are ------------------- Key: 192 Medline: Authors: Kermarrec A Title: Recherches sur les ennemis du champignon de couche. I. Zoocenose des composts de champignonniere a Agaricus bisporus Lange/ Citation: Annales de Zoologie - Ecologie Animale 5: 425-464 1973 Type: ARTICLE Genes: Abstract: Investigations on the enemies of the cultivated mushroom. I. Study of the zoocenoses of cultivated composts (Agaricus bisporus Lange). The study of zoocenoses of cultivated composts (Agaricus bisporus Lange) and these of graphical and mathematical tools show up an ecologically "extreme" character of these biotopes according to the nematodes. The analysis of the dynamics of the nematodes fauna reveals successions of species, spatial migrations and escaping behaviours, accompagned by phoresy. The relations between nematodes and the biotical and abiotical phases of the medium are compound and discussed. In particular, animal and especially vegetal predatism allows to envisage the adjusting of biological control methods. ------------------- Key: 193 Medline: 80004565 Authors: Kimble J;Hirsh D Title: The postembryonic cell lineages of the hermaphrodite and male gonads in Caenorhabditis elegans. Citation: Developmental Biology 70: 396-417 1979 Type: ARTICLE Genes: Abstract: The ancestry of the cells in the hermaphrodite and male gonadal somatic structures of C. elegans has been traced from the two gonadal somatic progenitor cells (Z1 and Z4) that are present in the newly hatched larvae of both sexes. The lineages of Z1 and Z4 are essentially invariant. In hermaphrodites, they give rise to a symmetrical group of structures consisting of 143 cells, and in males, they give rise to an asymmetrical group of structures consisting of 56 cells. The male gonad can be distinguished from the hermaphrodite gonad soon after the first division of Z1 and Z4. However, the development of Z1 and Z4 in hermaphrodites shares several features in common with their development in males suggesting that the two programs are controlled by similar mechanisms. In the hermaphrodite lineage, a variability in the positions of two cells is correlated with a variability in the lineages of four cells. This variability suggests that cell-cell interaction may play a more significant role in organisms that develop by invariant lineages than has hitherto been considered. None of the somatic structures (e.g., uterus, spermatheca, vas deferens) develops as a clone of a single cell. Instead, cells that arise early in the Z1-Z4 lineage generally contribute descendants to more than one structure, and individual structures consist of descendants ------------------- Key: 194 Medline: Authors: Kimpinski J Title: Nematodes associated with vegetables in Prince Edward Island Canada. Citation: Plant Disease Reporter 59: 37-39 1975 Type: ARTICLE Genes: Abstract: Twenty-five genera of nematodes were identified in six vegetable crops (carrot, pea, broccoli, rutabaga, Brussels sprouts, cauliflower) at fifty-six locations in Prince Edward Island (P.E.I.). Root lesion nematodes, Pratylenchus penetrans, were found in the soil at all locations and accounted for about 19% of the total nematode fauna. Meloidogyne hapla were recovered in only a few samples in low numbers, as were nematodes in the order Dorylaimida which accounted for about 5% of the total population. Non-stylet bearing nematodes made up 55% of the total and most of these were in two genera, Caenorhabditis spp. and Cephalobus spp. Carrot soils harbored the highest number of root lesion nematodes and pea soils had the least; 4726 and 547/kg of dry soil, respectively. Pea roots, however, had 2647/g dry root of these nematodes. No root lesion or other endoparasitic nematodes were recovered from the tap roots of carrots or from rutabagas. Some carrot and pea fields appeared to have lower than average yields where root lesion nematodes were recovered from soil and roots in very high numbers. ------------------- Key: 196 Medline: 75193113 Authors: Kisiel MJ;Castillo JM;Zuckerman LS;Zuckerman BM;Himmelhoch Title: Studies on ageing Turbatrix aceti. Citation: Mechanisms of Ageing & Development 4: 81-88 1975 Type: ARTICLE Genes: Abstract: Morphologic and physiologic changes which occur during senescence in the free-living nematode Turbatrix aceti are described. With age areas of the interchordal hypodermis containing nerve elements thickened, electron-dense aggregates formed within the pseudocoelom and age pigment granules accumulated within the intestinal epithelium. Specific gravity did not change with age. Old nematodes which had reproduced showed increased osmotic fragility, but this change was not observed in virgin females. The parameters characterizing senescence in T. aceti are compared with those of Caenorhabditis briggsae, another nematode being used as a model to study biological ageing. ------------------- Key: 197 Medline: 77115881 Authors: Kisiel MJ;Deubert KH;Zuckerman BM Title: Biogenic amines in the free-living nematode C. briggsae. Citation: Experimental Aging Research 2: 37-44 1976 Type: ARTICLE Genes: Abstract: Dopamine, epinephrine, norepinephrine and serotonin were demonstrated from homogenates of Caenorhabditis briggsae by two-dimensional thin layer chromatography and the identifications confirmed by gas liquid chromatography. In Vitro studies with 14C precursors of these biogenic amines demonstrate the ability of C. briggsae to synthesize each compound. The results provide required preliminary data for studying the neurophysiology of aging utilizing the nematode as a model. ------------------- Key: 198 Medline: 75039050 Authors: Kisiel MJ;Himmelhoch S;Zuckerman BM Title: C. briggsae: Effects of aminopterin. Citation: Experimental Parasitology 36: 430-438 1974 Type: ARTICLE Genes: Abstract: The characteristic features of senescence developed prematurely in Caenorhabditis briggsae treated with the DNA synthesis inhibitor aminopterin at the minimum dosage which inhibits gonad formation. In addition, aminopterin induced other changes which thus far have not been associated with normal aging of C. briggsae. Interpretations of these results are given based on current knowledge of the mode action of aminopterin and an extant theory of aging. ------------------- Key: 199 Medline: Authors: Kisiel MJ;Nelson B;Zuckerman BM Title: Influence of a growth factor from bacteria on the morphology of C. briggsae. Citation: Nematologica 15: 153-153 1969 Type: ARTICLE Genes: Abstract: Several investigators have reported that nutritional or environmental factors induce morphological variations in the "so-called' bacteriophagous nematodes. For example, Nigon & Dougherty described a morphological mutant of the free-living, self-fertilizing, hermaphroditic nematode Rhabditis (Caenorhabditis) briggsae that ensued following heat-treatment of progeny cultured on bacteria. Also Anderson reported that certain diagnostic features of an Acrobeloides sp., specifically the shape of the labial probolae and tail, varied significantly when the nematodes were grown on bacterial cultures as compared to those grown in soil. The current paper describes a consistent morphological variation in Caenorhabditis briggsae grown axenically on a meridic medium containing a growth factor from a bacterium as compared with nematodes reared on a growth factor from liver extract. ------------------- Key: 200 Medline: Authors: Kisiel MJ;Nelson B;Zuckerman BM Title: Effects of DNA synthesis inhibitors on C. briggsae and Turbatrix aceti. Citation: Nematologica 18: 373-384 1972 Type: ARTICLE Genes: Abstract: The effects of three DNA synthesis inhibitors on axenically grown Caenorhabditis briggsae and Turbatrix aceti were evaluated. Lower dosages of aminopterin sometimes prevented vagina formation and the eggs hatched within the oviduct. Concentrations of aminopterin, 5-fluorodeoxyuridine and hydroxyurea which prevented reproduction, caused significant growth inhibition, prevented maturation past the third larval stage, and reduced longevity. A difference in physiologic state was induced by the inability of aminopterin treated Caenorhabditis briggsae to adjust to osmotic pressures tolerated by untreated nematodes. These studies indicate the difficulties inherent in utilizing age-synchronous nematode cultures produced by the application of DNA ------------------- Key: 202 Medline: Authors: Kisiel MJ;Zuckerman BM Title: Effects of centrophenoxine on the nematode C. briggsae. Citation: Age 1: 17-20 1978 Type: ARTICLE Genes: Abstract: Concentrations below 13.6 mM centrophenoxine in the culture medium had no inhibitory effect on several developmental parameters of Caenorhabditis briggsae: specifically growth, fecundity and longevity. The effects on two parameters which characterize senescence in this nematode, increased osmotic fragility and increased specific gravity, were also evaluated. Above 6.8 mM old nematodes showed significantly less osmotic fragility and reduced specific gravity. Evaluation of the effects on negative charge of the cuticle surface membrane showed that neither 6.8 mM nor 17 mM affected negative surface charge density. Electron microscope studies showed that age-pigment accumulation was significantly retarded by a concentration of 6.8 mM centrophenoxine. It is suggested that the specific gravity effect is correlated with the retardation of lipofuscin accumulation with age. If this proves correct, then specific gravity will be another parameter for measuring the effects of centrophenoxine on aging tissues. This study also demonstrated that the effects of drugs on the retardation of age pigment formation can be visualized in three weeks by utilizing C. briggsae as a model. ------------------- Key: 203 Medline: 78049700 Authors: Klass MR Title: Aging in the nematode C. elegans: Major biological and environmental factors influencing life span. Citation: Mechanisms of Ageing & Development 6: 413-429 1977 Type: ARTICLE Genes: Abstract: The free-living nematode Caenorhabditis elegans is an excellent experimental system for the study of aging. The present study identifies some of the major biological and environmental factors influencing life span as a prelude to more detailed genetic and biochemical analyses. Life span can be altered during any part of the life cycle by a change in either temperature or food concentration. Parental age and parental life span both have relatively small effects on progeny life span. The nematode accumulates fluorescent pigment resembling lipofuscin, and becomes less sensitive to ultra-violet radiation as it ------------------- Key: 204 Medline: 76174434 Authors: Klass M;Hirsh D Title: Nonaging developmental variant of C. elegans. Citation: Nature 260: 523-525 1976 Type: ARTICLE Genes: Abstract: The study of mechanisms affecting the rate of ageing can be facilitated by naturally occurring phenomena, innate to some organisms, that enable the species to retard its ageing rate and extend its life span. Such a phenomenon exists in certain species of nematode. Larval forms of the free-living soil nematode, Caenorhabditis elegans, possess the ability to enter a semi-dormant, quiescent state referred to as the dauer larval stage (German, "enduring" larva). Newly hatched larvae of C. elegans undergo four larval stages (L1-L4) punctuated by moulting. If larvae are starved, they will enter the dauer state during the second larval moult. At this time, the old cuticle is replaced by a special, relatively impermeable cuticle unique to dauer larvae. ------------------- Key: 205 Medline: 77003912 Authors: Klass M;Wolf N;Hirsh D Title: Development of the male reproductive system and sexual transformation in the nematode C. elegans. Citation: Developmental Biology 52: 1-18 1976 Type: ARTICLE Genes: tra-2 Abstract: The small free-living nematode Caenorhabditis elegans is usually found as a hermaphrodite, but occasionally true males appear in the population. This study provides an account of gonadogenesis in the normal male and in a mutant that is a temperature-sensitive sex transformer. Male and hermaphrodite gonads develop from morphologically identical primordia. The small primordial gonad lies on the ventral side of the worm in the coelomic cavity. The gonadial primordium contains four nuclei at parturition. As this primordium develops in a hermaphrodite, it produces a double-armed, mirror symmetrical gonad that produces first sperm and then eggs. In the male, however, this primordium develops into an asymmetrical structure composed of a ventrally located testis, a loop region, a seminal vesicle, and a vas deferens. The male gonad presents a linear sequence of nuclei in successive stages of spermatogenesis with a mitotic region in the testis, followed by clearly distinguishable stages of meiosis throughout the loop region to the seminal vesicle. A temperature-sensitive sex transformer mutant, tsB202, has been isolated. tsB202 carries an autosomal recessive mutation in linkage group II that at restrictive temperature transforms an XX hermaphrodite into a phenotypic male, complete with a normal male gonad and vestigial external genitalia. These transformed males are classified as pseudomales because they do not exhibit mating behavior. Temperature shift experiments have determined the specific temporal sequences of gonadogenesis, oogenesis, and spermatogenesis. Proper manipulation of the temperature regimen causes the production of intersexes. In one intersex, a male gonad complete with sperm, seminal vesical, and vas deferens also contains oocytes. In another intersex produced by the complementary temperature shift, a hermaphrodite-shaped gonad develops that produces only sperm and no oocytes. ------------------- Key: 206 Medline: 79192248 Authors: Klass MR;Wolf N;Hirsh D Title: Further characterization of a temperature-sensitive transformation mutant in C. elegans. Citation: Developmental Biology 69: 329-335 1979 Type: ARTICLE Genes: tra-2 Abstract: The temperature-sensitive sex transformer tra-2(b202)II of the nematode Caenorhabditis elegans causes the tranformation of genotypically hermaphrodite worms into phenotypic males and sterile intersexes at restrictive temperature. In this note, we show that the entire gonad structure is transformed and that oocyte development is autonomous of the form of the gonad and of the presence of a cellular sheath. Four oocyte-specific proteins are present in male intersexes that produce oocytes but are lacking in transformed males and hermaphrodite intersexes ------------------- Key: 207 Medline: Authors: Klefenz HF;Zuckerman BM Title: Review: a comparative analysis of studies of enzyme changes with age, with comments on possible sources of error. Citation: Age 1: 60-67 1978 Type: REVIEW Genes: Abstract: Studies on enzyme changes during aging from rodents, nematodes and tissue culture cells have been reviewed. In the rodent and tissue culture studies, conflicting results on aging of specific enzymes have been reported from several laboratories. These works have been analyzed, with the aim of stressing the different findings and analyzing possible reasons for the discrepancies. With regard to the nematode studies, the authors suggest that the examination of the concept of general failure of protein synthesis mechanisms as a basic cause of cellular senescence requires more rigorous methods than have been utilized in previous studies. ------------------- Key: 208 Medline: Authors: Korner H Title: Die Nematoden-fauna des vergehenden Holzes und ihre Beziehungen zu den Insekten. Citation: Zoolyst 82: 245-353 1954 Type: ARTICLE Genes: Abstract: ------------------- Key: 209 Medline: Authors: Kreis HA Title: Freilebende terristrische Nematoden aus der Umgebung von Peking (China). Citation: Zoologischer Anzeiger 84: 283-294 1929 Type: ARTICLE Genes: Abstract: ------------------- Key: 210 Medline: Authors: Kreis HA Title: A. Freilebende terrestrische Nematoden aus der Umgebung von Peking (China) II. Citation: Zoologischer Anzeiger 87: 67-87 1930 Type: ARTICLE Genes: Abstract: ------------------- Key: 211 Medline: Authors: Kreis HA;Faust EC Title: Two new species of Rhabditis (Rhabditis macrocerca & R. clavopapillata) associated with dogs and monkeys in experimental Strongyloides studies. Citation: Transactions of the American Microscopical Society 52: 162-172 1933 Type: ARTICLE Genes: Abstract: From time to time during our studies on experimental Strongyloides infections, freshly passed stools of dogs have been contaminated with species of Rhabditis. At first it was believed that the contaminations resulted from improper sterilization of the Petri dishes used in collecting the feces, but after this possibility was eliminated the worms appeared with equal consistency. Sterilization of the cages in which the animals were housed also failed to reduce the contamination. Studies were then made of the animals themselves and it was found that the worms were developing in abundance among the perianal hairs, particularly in those dogs which had loose bowel movements. To a lesser extent the hairs of the abdomen, legs and even the face were also discovered to be favorable breeding places for these rhabditids. Thorough cleansing of the dogs externally with cresol solutions reduced the contamination appreciably but did not completely eliminate ------------------- Key: 212 Medline: 78239496 Authors: Krieg C;Cole T;Deppe U;Schierenberg E;Schmitt D;Yoder B;von Ehrenstein G Title: The cellular anatomy of embryos of the nematode C. elegans. Analysis and reconstruction of serial section electron micrographs. Citation: Developmental Biology 65: 193-215 1978 Type: ARTICLE Genes: Abstract: As described from light microscopy, embryogenesis of the free-living soil nematode Caenorhabditis elegans follows a strictly determinate cleavage pattern, producing a newly hatched juvenile with about 550 cells arranged quite predictably. In this communication we present results on the electron microscopy of C. elegans embryos and introduce methods for fixing, embedding, and serially sectioning embryos encased in the egg shell. Fixation at elevated temperature either with osmium tetroxide alone or with glutaraldehyde followed by osmium tetroxide gives reproducible results with embryos in all developmental stages so far tested, from the fertilized egg to hatching. Eighteen wild-type eggs at various stages have been sectioned to date. We have achieved using newly developed procedures for analyzing electron micrographs of serial sections detailed reconstructions of the cellular anatomy of complete embryos of a metazoan organism. Three-dimensional serial section reconstructions were made with a computer system. We characterize and map the 24 cells of an early-stage embryo in this report. Additionally, we can specify the lineage history of all cells of this embryo by matching the reconstructed three-dimensional arrangement of this series to a living embryo at this stage, where cell lineage has been observed with Nomarski optics and analyzed using videotape. In addition, cytoplasmic and nuclear morphological features such as incomplete membranes between sister cells, rounding-off of the cytoplasm, and chromatin condensation patterns have been correlated with cell division. Mapping of such structures presents a new method by which supplementary lineage information can be obtained directly ------------------- Key: 214 Medline: 77119003 Authors: Lewis JA;Hodgkin JA Title: Specific neuroanatomical changes in chemosensory mutants of the nematode C. elegans. Citation: Journal of Comparative Neurology 172: 489-510 1977 Type: ARTICLE Genes: che-1 che-2 che-3 che-5 che-6 che-7 mec-1 mec-2 mor-1 mor-2 unc-7 vab-1 vab-2 vab-3 vab-5 Abstract: Eight of nineteen chemotactic mutants of the nematode, Caenorhabditis elegans have morphological defects in the sensory endings of neurons at the tip of the head. The mutants were obtained as worms swimming away from attractant or found amongst male potency mutants or mutants exhibiting erractic behavior. The nineteen mutants fall into at least twelve complementation groups. Mutants E1034 and E1035, alleles of che-1, show morphological alterations in the sensory endings of amphidial neurons and inner labial type 2 neurons, both prospective chemosensory neurons. Both mutants contain non-complementing ts sterile mutations linked to the chemosensory mutation. E1066 shows abnormalities in all the sheath cells associated with the sensory neurons and in the bundling pattern of the amphidial neurons. E1126 is structurally abnormal only in the sensory endings of inner labial type 2 neurons, supporting a chemosensory role for these neurons. E1033 (che-2) and E1124 (che-3) cause defects in the ciliary structure of all but one type of ciliated sensory neuron in the head. E1062 is grossly defective in head structure and the structure of the male copulatory organ, suggesting these opposite ends of the nematode rich in sensory structures share gene functions in embryogenesis. Our study illustrates the possibilities for genetic dissection of the development of a small set of nerves in a simple ------------------- Key: 215 Medline: 76209326 Authors: Liu A;Rothstein M Title: Nematode biochemistry XV. Enzyme changes related to glycerol excretion in C. briggsae. Citation: Comparative Biochemistry & Physiology 54B: 233-238 1976 Type: ARTICLE Genes: Abstract: 1. In the free-living nematode, Caenorhabditis briggsae, several enzymes involved in glycolysis change markedly in activity when the organism is incubated under different nutritional conditions. 2. Activities of phosphofructokinase and glycerol phosphate dehydrogenase increase sharply in worms incubated in "growth medium". 3. After incubation in buffer, the organisms show higher activities in aldolase, fructose-1,6-diphosphatase and glycerol phosphate dehydrogenase in the reverse direction (glycerol phosphate as substrate). 4. These shifts in enzyme levels can explain the differences in excretion products under both sets of conditions. 5. When C. briggsae is incubated with [2-14C]-acetate in buffer, glucose is the main radioactive product, but trehalose and small amounts of glycerol and fructose are also found; in whole medium, glycerol is most highly labeled, though detectable amounts of glucose and trehalose are present. 6. Extracts of the worms yield similar products in both cases, namely, trehalose and glucose along with small amounts of ribose and glycerol. ------------------- Key: 217 Medline: Authors: Lower WR;Buecher EJ Title: Axenic culturing of nematodes: an easily prepared medium containing yeast extract. Citation: Nematologica 16: 563-566 1970 Type: ARTICLE Genes: Abstract: An aqueous extract from ruptured baker's yeast added as a required supplement to a soy-peptone, Bacto-yeast solution constitutes an easily prepared, inexpensive and stable medium for the axenic culture of some nematodes. Cell walls and unbroken cells were removed by centrifugation and the supernatant was sterilized by filtration. Medium containing the supplement supported growth of three species of free-living nematodes and two species of Neoaplectana, a nematode parasite of insects. ------------------- Key: 218 Medline: 67011548 Authors: Lower WR;Hansen EL;Yarwood EA Title: Assay of a proteinaceous growth factor required for maturation of the free-living nematode, C. briggsae. Citation: Journal of Experimental Zoology 161: 29-36 1966 Type: ARTICLE Genes: Abstract: The time to maturation of a free-living, protandrous, self-fertilizing nematode, Caenorhabditis briggsae, was used to assay preparations of a proteinaceous growth factor and the effects of different treatments. Development was measured as time of the production of F1 offspring against concentration of growth factor. The data were tranformed to the reciprocal of F1 time against logarithm of the dose and analyzed by regression analysis. Estimates were made of the dose of growth factor required for maturation in seven days, and relative potencies were determined for assays whose regression coefficients did not significantly differ from one another. The dose of growth factor required for maturation in seven days fell within range from 8 ug/ml to 28 ug/ml. The methods of treatment for activation of growth factor studied were freezing overnight at -23C, dialysis to low phosphate, and addition of the sucrose polymer, FICOLL. Reproducibility of results was shown for controls made for each experiment and for assays repeated at different times. Inocula of various numbers of larvae per tube, 1 through 30, were compared; significant increase in maturation time occurred when inocula were ------------------- Key: 219 Medline: Authors: Lower WR;Hansen EL;Yarwood EA Title: The use of nematodes cultured axenically on defined medium for biological studies. Citation: American Naturalist 100: 367-370 1966 Type: ARTICLE Genes: Abstract: Nematodes cultured axenically (bacteria free) on defined media represent useful additions to the list of organisms available for genetic studies. Axenic culturing eliminates an important source of confusion, which is present in bacterial cultures: metabolic and other changes in the bacteria themselves. The use of defined instead of crude media allows for more precise analyses of growth and development, and permits determination of the nutrient factors needed. ------------------- Key: 220 Medline: 71292582 Authors: Lower WR;Hansen EL;Yarwood EA Title: Selection for adaptation to increased temperatures in free-living nematodes. Citation: Life Sciences 7: 139-146 1968 Type: ARTICLE Genes: Abstract: Adaptation to high temperature, whether a physiological adaptation of the individual or genetic adaptation of a population, represents one of the adjustments which organisms must make to their environment. The current report represents a time cross-sectional examination of a continuing experiment that deals with the progress in adaptation to high temperature and examination of some of the differences observed. Populations in thin film continuous cultures were incubated at increasing temperatures, and at intervals the reproductive characteristics of individuals were determined. Two species of free-living nematodes were used which differ in their mating system and may differ in their amount of genetic variability: Panagrellus redivivus, a dioecious species, and Caenorhabditis briggsae, a protandrous, self-fertilizing hermaphrodite which produces an occasional male. Populations of P. redivivus may have more genetic variability than populations of C. briggsae. C. briggsae, though largely self-fertilizing, cannot, a priori, be considered highly homozygous, since facultative inbreeding, balanced polymorphism and heterozygote superiority are capable of maintaining genetic variability. ------------------- Key: 223 Medline: 74098203 Authors: Lu NC;Hieb WF;Stokstad ELR Title: Accumulation of formimino-L-glutamic acid in the free-living nematode C. briggsae as related to folic acid Citation: Proc. Society for Experimental Biology & Medicine 145: 67-69 1974 Type: ARTICLE Genes: Abstract: Formimino-L-glutamic acid (FIGLU), which is an intermediate of histidine degradation, is excreted in large amounts in the urine of folic acid deficient rats and humans. Urinary excretion of FIGLU can be raised by increasing the level of dietary histidine in rats. Luhby and Cooperman have used the "histidine load" test for diagnosis of folic acid deficiency in humans. However, very little is known about histidine degradation in folic acid deficiency in lower animals. The present study was conducted with the axenically grown free-living nematode, Caenorhabditis briggsae, which requires folic acid for reproduction. ------------------- Key: 224 Medline: 76176610 Authors: Lu NC;Hieb WF;Stokstad ELR Title: Effect of vitamin B-12 & folate on biosynthesis of methionine from homocysteine in the nematode C. briggsae. Citation: Proc. Society for Experimental Biology & Medicine 151: 701-706 1976 Type: ARTICLE Genes: Abstract: The roles of dietary vitamin B12 and folic acid in methionine biosynthesis from homocysteine were first observed in higher animals. Jukes, Stokstad, and Broquist noted that the growth of vitamin B12-deficient chicks were increased by either methionine or homocysteine and vitamin B12 but not by homocysteine alone. It was also reported that rats were able to utilize homocysteine in lieu of methionine when folic acid or choline was added to the diet. In microorganisms, Escherichia coli is known to possess two alternative pathways for methionine biosynthesis: the vitamin B12-dependent pathway and the vitamin B12-independent one. In the present study, we show evidence that dietary vitamin B12 and folic acid were required for the biosynthesis of methionine from homocysteine in an axenic free-living nematode, Caenorhabditis briggsae. Information related to biochemical nutrition in invertebrates in sparse. Therefore, this study has particular relevance to the fields of comparative nutrition and biochemistry. ------------------- Key: 225 Medline: 78226453 Authors: Lu NC;Hubenberg G Jr;Briggs GM;Stokstad ELR Title: The growth-promoting activity of several lipid-related compounds in the free-living nematode C. briggsae. Citation: Proc. Society for Experimental Biology & Medicine 158: 187-191 1978 Type: ARTICLE Genes: Abstract: During the past decade, much progress has been made in the search of growth factors for the free-living nematode, C. briggsae. In 1968 Hieb and Rothstein showed a sterol requirement in C. briggsae. Hieb, Stokstad and Rothstein further reported a requirement for heme in 1970. These discoveries have led to the use of heme and sterol supplements in a chemically defined medium, the C. briggsae Maintenance Medium (CbMM), for the cultivation of C. briggsae. For many years another unidentified growth factor has been known to be required for C. briggsae. A variety of proteinaceous sources has been used to provide this unidentified growth factor(s), including commercially available products such as soy peptone, egg albumin, and casamino acids, "defined" proteins such as insulin and TMV-protein, and yeast ribosomes. However, attempts at isolating the unidentified growth factor(s) from the proteinaceous sources have not been successful yet. Vanfleteren has recently suggested that an acid-precipitated hemin could replace the proteinaceous growth factor in C. briggsae due to the stimulation of phagocytosis by the precipitates. Also, Pinnock, Shane and Stokstad reported that a dipeptide (leu-phe) can partially replace the growth factor activity of casamino acids (acid hydrolysate of casein). ------------------- Key: 226 Medline: Authors: Lu NC;Newton C;Stokstad ELR Title: The requirement of sterol and various sterol precursors in free-living nematodes. Citation: Nematologica 23: 57-61 1977 Type: ARTICLE Genes: Abstract: The quantitative sterol requirements were studied in C. briggsae, C. elegans (Be), C. elegans (Br), and T. aceti. It was shown that all four nematodes had similar minimal sterol requirements (0.1-2.0 ug/ml) and toxicity appeared in T. aceti at 50 ug/ml. Cholesterol and five precursors were tested for population growth. We found that acetic acid, DL-mevalonic acid lactone, and farnesol did not support population growth; while squalene, lanosterol, and cholesterol supported significant population growth in all four nematodes. Our results suggest that the major metabolic block in the pathway of sterol biosynthesis occurs between the step of farnesol and squalene. ------------------- Key: 228 Medline: Authors: Lyons JM;Keith AD;Thomason IJ Title: Temperature-induced phase transitions in nematode lipids and their influence on respiration. Citation: Journal of Nematology 7: 98-104 1975 Type: ARTICLE Genes: Abstract: Temperature-induced phase transitions estimated by electron spin resonance (ESR) technique were observed in the lipids of several nematode species. In both Meloidogyne javanica and Caenorhabditis elegans, there was a phase transition in their phospholipids from a liquid-crystalline state to a solid gel state at about 10 C. Aphelenchus avenae also had a phase transition, but at about 20 C. With this species, the spin-label motion parameters indicated the transition was from the liquid-crystalline state below 20 C to a more liquid or disordered state above 20 C. Anguina tritici and Meloidogyne hapla, in contrast, had no phase transitions over the entire temperature range studied. Each phase transition detected by ESR was reflected in the respiratory rates of the nematodes, and the temperature of the transition coincides with the environmental adaptation of these species. ------------------- Key: 230 Medline: 79084145 Authors: Mackenzie JM Jr;Garcea RL;Zengel JM;Epstein HF Title: Muscle development in C. elegans mutants exhibiting retarded sarcomere construction. Citation: Cell 15: 751-762 1978 Type: ARTICLE Genes: unc-52 Abstract: We have studied the structural changes within the body-wall muscle cells of Caenorhabditis elegans during postmitotic development. In wildtype, the number of sarcomeres progressively increases, and each sarcomere appears to grow in length and depth continuously during this period. In mature wild-type cells, the anterior-most body-wall muscle cells have 6--7 sarcomeres; the rest have 9--10 sarcomeres per cell. Twelve mutants in the unc-52 II gene exhibit markedly retarded sarcomere construction and progressive paralysis. Several unc-52 mutants, such as the severely paralyzed SU200, produced only 2--3 sarcomeres per body-wall muscle cell, while the other mildly paralyzed unc-52 mutants, such as SU250, build 3--4 sarcomeres per muscle cell. Other structures such as the pharynx and even the noncontractile organelles of the body-wall muscle cells do not appear to be structurally or functionally altered. The unc-52 body-wall sarcomeres become moderately disorganized as they are outstripped by cell growth; sufficient order is preserved, however, so that the majority of thick and thin filaments still interdigitate. The myosin heavy chains of SU200 body-wall muscle fail to accumulate normally, while the pharyngeal myosin heavy chains do not appear to be specifically affected. This biochemical result correlates well with the specificity of morphological changes in the mutant. A model is discussed in which the biochemical and morphological deficits are explained by a simple regulatory mechanism. ------------------- Key: 231 Medline: 79063844 Authors: Mackenzie JM Jr;Schachat F;Epstein HF Title: Immunocytochemical localization of two myosins within the same muscle cells in C. elegans. Citation: Cell 15: 413-419 1978 Type: ARTICLE Genes: unc-54 Abstract: Nematodes synthesize two major classes of myosin heavy chains. These heavy chains associate to form only homodimeric myosin molecules, and these myosin homodimers are antigenically different from one another. The two myosins may be designated unc-54 myosin, since this species is altered in mutants of the unc-54 locus, and non-unc-54 myosin, since this class is not affected in unc-54 mutants. We present here experiments in which specific anti-myosin IgG and anti-unc-54 myosin IgG are used to locate the two myosins within the same body-wall muscle cells of Caenorhabditis elegans. These results are necessary for further evaluation of the possible functions of the two myosin homodimers in the thick filaments of these muscles. Myosin can be localized to all body-wall and pharyngeal muscle cells using anti-myosin antibody. In longitudinal sections of body-wall muscle, the staining with anti-myosin coincides with the birefringence of A bands that contain thick filaments. Anti-unc-54 myosin stains all body-wall A bands uniformly but does not react with the pharynx. This result demonstrates that unc-54 is located exclusively in body-wall muscle cells of the wild-type strain N2. Non-unc-54 myosin is localized with anti-myosin in all body-wall muscle cells of the unc-54 null mutant E190, as expected; however, unc-54 myosin could not be detected by anti-unc-54 myosin antibody in this mutant. Since we can localize unc-54 myosin and non-unc-54 myosin in all body-wall muscle cells of wild-type and E190, respectively, we conclude that the two myosins must be present in the same muscle cells. In addition, since unc-54 myosin is located in all body-wall A bands, at least some sarcomeres must contain both myosins. This conclusion is consistent with the observations of Garcea, Schachat and Epstein that wild-type and E190 synthesize similar amounts of non-unc-54 myosin. Within the limits of resolution of our methods, unc-54 myosin is distributed throughout body-wall A bands. We conclude, therefore, that the majority of thick filaments within these A bands must contain unc-54 myosin along their entire length. Possible roles for unc-54 and non-unc-54 myosins in the assembly and organization of thick filaments are discussed. ------------------- Key: 232 Medline: 78094402 Authors: MacLeod AR;Waterston RH;Brenner S Title: An internal deletion mutant of a myosin heavy chain in C. elegans. Citation: Proceedings of the National Academy of Sciences USA 74: 5336-5340 1977 Type: ARTICLE Genes: unc-54 Abstract: unc-54 I is the structural gene for a myosin heavy chain present in a major fraction of the total myosin of Caenorhabditis elegans. The allele e675, which possesses a normal amount of myosin but fails to assemble thick filaments, has been shown previously to contain a novel heavy chain of molecular weight 2 X 10*5, shorter by 10*4 than the wild-type (N2) unc-54 gene product. The structural alteration of the E675 heavy chain is an internal deletion of 10*4 molecular weight near the COOH terminus of the molecule. This has been determined by mapping the partial digestion products of heavy chain fragments labeled specifically at the NH2 termini. ------------------- Key: 233 Medline: 78007960 Authors: MacLeod AR;Waterston RH;Fishpool RM;Brenner S Title: Identification of the structural gene for a myosin heavy-chain in C. elegans. Citation: Journal of Molecular Biology 114: 133-140 1977 Type: ARTICLE Genes: unc-54 Abstract: Mutants in the unc-54 gene of Caenorhabditis elegans have been characterized by cyanylation and sodium dodecyl sulphate/polyacrylamide gel electrophoresis of the total myosin present in each mutant. In the recessive mutants lacking a major fraction of the total myosin, the high molecular weight doublet of 15 X 10*4 and 14 X 10*4 which dominates the cyanylation pattern of the total wild-type myosin is absent. In the mutant E675, which possesses a novel heavy-chain with a molecular weight of 2 X 10*5, each component of the cyanylation doublet is reduced by 10*4 daltons, indicating that the doublet is derived from partial cleavage of a single polypeptide chain. This suggests that unc-54 is the structural gene for a myosin heavy-chain present in a major fraction of the total ------------------- Key: 235 Medline: Authors: Manning A Title: The place of genetics in the study of behaviour. Citation: "Growing Points in Ethology" Conference, Cambridge, England, 1975. Bateson PPG and Hinde RA (eds), Cambridge University Press, NY. : 327-343 1975 Type: REVIEW Genes: Abstract: Studies in behaviour genetics have covered a wide field: motivation, development, sensory capacities, intelligence, learning, evolution, neuromorphology and neurochemistry have all been approached using genetic techniques, and there are probably others. Whilst it is at present impossible to construct any unities one must accept that many such studies have as their common aim one of the most fundamental problems in biology: how is behavioral potential encoded in genetic terms and expressed in the course of development? The relative enormity of this problem is often matched by its inaccessibilty. It cannot be claimed that there is any agreed view of the way forward and much of the work has frankly to be opportunistic-seizing on some favourable material or a useful new analytical technique to gain a limited objective. Consequently, behaviour genetics often presents a confusing picture of numerous disjointed studies, with ------------------- Key: 236 Medline: Authors: Marks CF Title: Respiration responses of a Caenorhabditis sp. and Aphelencus avenae to the nematicide 1,2-dibromoethane Citation: Journal of Nematology 3: 113-118 1971 Type: ARTICLE Genes: Abstract: The respiration rate of third stage larvae of Caenorhabditis sp. exposed to 0.53 X 10(-2) M EDB was 120% greater than in untreated checks and was highest shortly after the exposure began. Similarly-treated third- and fourth-stage Aphelenchus avenae exhibited no marked respiratory response. Different responses of these animals to EDB probably reflect basic physiological differences ------------------- Key: 237 Medline: Authors: Marks CF;Sorensen O Title: Measurement of nematode respiration with the biological oxygen monitor. Citation: Journal of Nematology 3: 91-92 1971 Type: ARTICLE Genes: Abstract: Cartesian Diver and manometric techniques have frequently been used to measure the respiration rates of nematodes. However, the sensitivity and ease of operation of the polarographic oxygen-sensing equipment currently available offers a technique of great future value to plant nematologists. Our recent experience with the YSI Model 53 Biological Oxygen Monitor (Yellow Springs Instrument Co., Yellow Springs, Ohio 45387) has shown it is quite satisfactory for measuring the respiration rates of a Caenorhabditis sp. and Aphelenchus avenae Bastian...... ------------------- Key: 239 Medline: Authors: Maupas E Title: Modes et formes de reproduction des nematodes. Citation: Archives de Zoologie Experimentale et Generale 8: 463-624 1900 Type: ARTICLE Genes: Abstract: ------------------- Key: 240 Medline: Authors: Maupas E Title: Essais d'hybridisation chez les nematodes. Citation: Bulletin Biologique de la France et de la Belgique 52: 466-498 1918 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 241 Medline: 80047782 Authors: Meneely PM;Herman RK Title: Lethals, steriles and deficiencies in a region of the X chromosome of C. elegans. Citation: Genetics 92: 99-115 1979 Type: ARTICLE Genes: let-1 let-2 let-3 let-4 let-5 let-6 let-7 let-9 let-10 let-11 let-12 let-14 let-16 unc-3 eDf2 mnDf1 mnDf2 mnDf5 mnDf6 mnDf7 mnDf9 mnDf10 mnDf13 mnDf15 mnDf18 mnDf20 mnDf21 Abstract: Twenty-one X-linked recessive lethal and sterile mutations balanced by an unlinked X-chromosome duplication have been identified following EMS treatment of the small nematode, Caenorhabditis elegans. The mutations have been assigned by complementation analysis to 14 genes, four of which have more than one mutant allele. Four mutants, all alleles, are temperature-sensitive embryonic lethals. Twelve mutants, in ten genes, are early larval lethals. Two mutants are maternal-effect lethals; for both, oocytes made by mutant hermaphrodites are rescuable by wild-type sperm. One of the maternal-effect lethals and two larval lethals are allelic. One mutant makes defective sperm. The lethals and steriles have been mapped by recombination and by complementation testing against 19 deficiencies identified after X-ray treatment. The deficiencies divide the region, about 15% of the X-chromosome linkage map, into at least nine segments. The deficiencies have also been used to check the phenotypes of hemizygous lethal and ------------------- Key: 242 Medline: 79100296 Authors: Messner B;Kerstan U Title: The histochemical evidence of peroxidase in invertebrate animals (nematoda and insecta). Citation: Acta Histochemica 62: 244-253 1978 Type: ARTICLE Genes: Abstract: In 15 species of nematodes and 3 species of insects an activity of peroxidase was proofed histochemically in various organs and cells using the benzidine-method. ------------------- Key: 244 Medline: 79089359 Authors: Mitchell DH;Stiles JW;Santelli J;Sanadi DR Title: Synchronous growth and aging of C. elegans in the presence of fluorodeoxyuridine. Citation: Journal of Gerontology 34: 28-36 1979 Type: ARTICLE Genes: Abstract: Fluorodeoxyuridine (FUdR), an inhibitor of DNA synthesis, was examined for its ability to prevent a synchronous population of C. elegans from reproducing without otherwise interfering with the organism's post-maturational development and aging. When a synchronized population was exposed to 400 micrometer FUdR just as the population reached sexual maturity, the FUdR induced complete sterility within five hours by preventing eggs from hatching. Any larvae that hatched from eggs made before the FUdR was added remained small in the presence of FUdR and were easily removed by filtration or sedimentation. FUdR-sterilized adults showed no morphological abnormalities. Age-associated changes seen in controls also occurred in FUdR-treated worms, including atrophy of the gonads, increased pigmentation, sluggishness and increased transparency. Life span was not shortened by FUdR treatment. Our observations suggest that treatment with FUdR under carefully controlled conditions is a reasonable way to maintain synchronously aging populations of C. ------------------- Key: 245 Medline: Authors: Moerman DG;Baillie DL Title: Genetic organization in C. elegans: Fine-structure analysis of the unc-22 gene. Citation: Genetics 91: 95-104 1979 Type: ARTICLE Genes: unc-22 Abstract: Fine-structure analysis of the unc-22 gene of Caenorhabditis elegans has revealed a number of sites that are separable by recombination. Eight new ethyl methanesulfonate-induced recessive mutations of the unc-22 gene have been isolated. Using these new alleles, as well as e66, a number of separable sites have been identified and positioned relative to one another. The map distances obtained are found to be comparable to those associated with intragenic recombination in Drosophila melanogaster, indicating that genetic fine-structure analysis is feasible in Caenorhabditis elegans. Evidence of possible gene conversion is presented. A preliminary estimate of the unc-22 gene size is 2.4 X 10(-2) map units. ------------------- Key: 247 Medline: Authors: Monoson HL;Williams SA Title: Endoparasitic nematode-trapping fungi of Mason State Citation: Mycopathologia et Mycologia Applicata 49: 177-183 1973 Type: ARTICLE Genes: Abstract: An initial survey involving the endoparasitic nematode-trapping fungi of Mason State Forest in Illinois was conducted from 15 May to 26 July 1971. Three endoparasitic forms were isolated from the soil samples collected; one non-endoparasitic form was also isolated. Soil pH's and soil nutrient levels were determined for the investigation period. ------------------- Key: 248 Medline: Authors: Monoson HL;Galsky AG;Stephano RS Title: Studies on the ability of various nematodes to induce trap formation in a nematode-trapping fungus Monacrosporium doedycoides. Citation: Nematologica 20: 96-102 1974 Type: ARTICLE Genes: Abstract: Nemin extracted from five different species of nematodes induced the production of predaceous structures by the nematode-trapping fungus, Monacrosporium doedycoides. Quantitative differences in the ability of the different nematodes to induce trap formation were noted. The RNA synthesis inhibitor 6-methyl purine when applied at the same time with the various nemins completely inhibited trap formation by the fungus. Application of the 6-methyl purine 1 hour after the addition of the various nemins had no effect on the number of traps formed. Two compounds that inhibit normal protein synthesis (5-fluorouracil and p-flourophenylalanine) also exhibited a similar trap inhibition effect. The mechanism of nemin-induced trap formation in M. doedycoides seemd to be at the level of transcription. ------------------- Key: 250 Medline: Authors: Mulvey RH Title: Oogenesis in some free-living nematodes. Citation: "Nematology." Sasser JN and Jenkins WR (eds), University of North Carolina Press, Chapel Hill. : 321-322 1960 Type: REVIEW Genes: Abstract: I would like to introduce my lecture on this subject with a brief consideration of meiosis in the female. The oogonial cells in the anterior part of the ovary in a nematode are small and multiply by mitosis. As they move down the ovary they increase in size with corresponding increase in the size of the nucleus. The chromatin is a single spherical mass located in the center of the nucleus. Eventually the chromatin mass is resolved into individual chromosomes. During prophase of meiosis the homologous chromosomes come together. All diploid cells possess identical chromosomes with the exception of the sex chromosomes and at synapsis these homologous chromosomes pair or come together. Paternal and maternal gametes each contribute a complement of identical chromosomes. ------------------- Key: 251 Medline: 76164376 Authors: Murfitt RR;Vogel K;Sanadi DR Title: Characterization of the mitochondria of the free-living nematode, C. elegans. Citation: Comparative Biochemistry & Physiology 53B: 423-430 1976 Type: ARTICLE Genes: Abstract: 1. Conditions are discussed for obtaining population levels of 200,000/ml in 6 days using axenic cultures of the nematode, Caenorhabditis elegans. Lifespan and growth data under these conditions are presented. 2. An isolation procedure which results in high quality mitochondria is presented, and metabolic data on respiration rates, respiratory control ratios, and ADP:O ratios using various substrates are given. 3. The effects of inhibitors of respiration and ATPase activity and of uncouplers of oxidative phosphorylation are presented. 4. Cytochrome content of the mitochondria as determined from difference spectra is given. No indication of the large amounts of the b type pigment reported in Turbatrix aceti was found. 5. The metabolism and respiratory chain of C. elegans appear to be similar to the classic mammalian systems. The only gross difference noted was the absence of ATPase stimulation by traditional uncouplers of oxidative phosphorylation. In this respect, the C. elegans mitochondria resemble more closely those of Ascaris. ------------------- Key: 252 Medline: 79025333 Authors: Nelson GA;Lew KK;Ward S Title: Intersex, a temperature-sensitive mutant of the nematode C. elegans. Citation: Developmental Biology 66: 386-409 1978 Type: ARTICLE Genes: fem-1 Abstract: A temperature-sensitive mutation, isx-1(hc17), is reported in the nematode Caenorhabditis elegans which alters the sexual phenotypes of both genotypic sexes. At the restrictive temperature, XX animals are functionally female rather than hermaphroditic due to the absence of spermatogenesis, and XO animals develop as intersexes. These intersexes have normal male head and tail structures and exhibit some mating behavior, but possess hermaphrodite-like gonads which produce no sperm and usually contain a few oocytes. An abortive vulva is usually present and evidence is presented which suggests that the formation of the vulva by the hypodermis is induced by the underlying gonad. The direct effects of the mutation are confined to the descendants of four primordial gonad cells. Gametogenesis and gonad sheath development do not seem to be tightly coupled and are shown to differ in their responses to X-chromosome dosage. The interaction of the intersex mutation with mutant alleles of two transformer genes tra-1 and tra-2 is discussed and a model for the action of these genes in gonad development and sex determination is proposed. ------------------- Key: 253 Medline: 78036192 Authors: Neuschulz N Title: Axenic culture of free living nematodes a literature Citation: Zeitschrift fur Versuchstierkunde 19: 241-247 1977 Type: REVIEW Genes: Abstract: In German. ------------------- Key: 254 Medline: Authors: Nicholas WL Title: The cultural and nutritional requirements of free-living nematodes of the genus Rhabditis and related genera. Citation: Technical Bulletin Min. Agric. London 7: 161-168 1959 Type: REVIEW Genes: Abstract: ------------------- Key: 255 Medline: Authors: Nicholas WL Title: The biology of free-living nematodes. Citation: Clarendon Press, Oxford : 1-219 1975 Type: MONOGR Genes: Abstract: ------------------- Key: 256 Medline: Authors: Neuschulz N Title: Axenische Kultivierung freilebender Nematoden. Citation: Wissenschaftliche Zeitschrift der Ernst-Moritz . . . 26: 87-102 1977 Type: ARTICLE Genes: Abstract: The nutritive substratum for axenic nematode cultivation consists of a chemically known basal media and a small supplement of cell or tissue extract. The latter contains an essential growth factor, which has been substituted only recently by sterols, heme and various proteins or glycogen as heme adsorbent. As the population growth in chemically defined media is still insufficient, further research is necessary to clear up the nature of the growth factor. For non-nutritive investigations peptone-yeast-liver-media and other extract mixtures are suitable. Besides giving new research results the present paper contains an historical outline and discusses some points of interest for the selection of test animals. By a detailed description of axenization, inoculation and supplement preparation the paper will also be of use as the first instruction for axenic cultivation of free-living nematodes written in German. ------------------- Key: 257 Medline: Authors: Nicholas WL;Dougherty EC;Hansen EL Title: Axenic cultivation of C. briggsae (Nematoda: Rhabditidae) with chemically undefined supplements; comparative studies with related nematodes. Citation: Annals of the New York Academy of Sciences 77: 218-236 1959 Type: REVIEW Genes: Abstract: This paper is addressed primarily to the unsolved problems of culturing Caenorhabditis briggsae axenically. Included also are some comparative studies of related rhabditid nematodes. ------------------- Key: 258 Medline: Authors: Nicholas WL;Dougherty EC;Hansen EL;Holm-Hansen O;Moses V Title: The incorporation of 14C from sodium acetate-2-14C into the amino acids of the soil-inhabiting nematode, Caenorhabditis briggsae. Citation: Journal of Experimental Biology 37: 435-443 1960 Type: ARTICLE Genes: Abstract: 1. The nematode, Caenorhabditis briggsae, was cultured axenically in a mixture of chick embryo extract, autoclaved liver extract and sodium acetate-2-14C. A protein hydrolysate was prepared from the worms and the eggs which were collected from the cultures. 2. Chromatography and radioautography were carried out in a study of the amino acid composition of the hydrolysate. The following amino acids were found labelled: aspartic acid, glutamic acid, alanine, proline, glycine, serine. Cystein and cystine were oxidized to cysteic acid which was also labelled. The following amino acids were not labelled: arginine, histidine, lysine, methionine, threonine, tyrosine, valine and the combined spot representing phenylalanine, leucine and isoleucine. Tryptophane would have been destroyed by our method of hydrolysis. 3. Since the labelled amino acids are synthesized by the worm, it is suggested, tentatively, that they are not required in an otherwise adequate diet. So far as the unlabelled amino acids are concerned, it is suggested, on the basis of the results of certain culture experiments (published separately) that, with the probable exception of tyrosine, they are essential in the diet of C. briggsae. ------------------- Key: 259 Medline: Authors: Nicholas WL;Grassia A;Viswanathan S Title: The efficiency with which C. briggsae (Rhabditidae) feeds on the bacterium, Escherichia coli. Citation: Nematologica 19: 411-420 1973 Type: ARTICLE Genes: Abstract: The rate of removal of the bacterium E. coli from aqueous suspensions by C. briggsae in feeding has been studied. The decrease in bacteria with time follows a negative exponential equation when bacterial multiplication was restricted and nematode growth was minimal. It was inferred that the feeding activity of the nematodes is maintained at a constant level over a wide range of bacterial concentrations. Other experiments supported the contention that C. briggsae requires dense suspensions of bacteria for the maintenance of cultures and gave estimates of the efficiency of conversion of bacterial protoplasm to worm protoplasm. ------------------- Key: 260 Medline: Authors: Nicholas WL;Hansen EL;Dougherty EC Title: The B-Vitamins required by Caenorhabditis briggsae (Rhabditidae). Citation: Nematologica 8: 129-135 1962 Type: ARTICLE Genes: Abstract: To find which of the B vitamins are required by Caenorhabditis briggsae Dougherty & Nigon, it was cultured axenically in a known medium together with chick embryo extract. The concentration of each vitamin added to the medium was varied, and each was omitted in turn. Omitting thiamine, riboflavin, folic acid, calcium pantothenate, niacinamide and pyridoxine was deleterious. ------------------- Key: 261 Medline: Authors: Nicholas WL;Jantunen R Title: A biotin requirement for C. briggsae (Rhabditidae). Citation: Nematologica 9: 332-336 1963 Type: ARTICLE Genes: Abstract: Caenorhabditis briggsae can be cultured axenically in a biotin-free basal medium supplemented with chick embryo extract. The addition of avidin, which is known to combine with biotin, is inhibiting. The effect of avidin is nullified by the addition of excess biotin. It is concluded that biotin is a vitamin required by C. briggsae. ------------------- Key: 262 Medline: Authors: Nicholas WL;Jantunen R Title: C. briggsae (Rhabditidae) under anaerobic conditions. Citation: Nematologica 10: 409-418 1964 Type: ARTICLE Genes: Abstract: The effect of anaerobic conditions on the eggs, larval stages and adults of C. briggsae was investigated. Anaerobic conditions were produced by exposing the eelworms, in drops of media, to a stream of carefully purified moist N2 or H2. Temperature, the osmotic properties of the media in which the worms were suspended, and pH were considered in designing the experiments. The nematodes were maintained under axenic conditions while anaerobic. It is concluded that swimming is impaired by O2 lack, rapidly leading to complete paralysis. Eelworms recover when returned to aerobic conditions after a short period of paralysis, but after longer periods, of the order of 24 hours, they fail to recover. Eggs survive for several days under anaerobic conditions, but hatching is inhibited until conditions become aerobic. ------------------- Key: 263 Medline: Authors: Nicholas WL;Jantunen R Title: The effect of different concentrations of oxygen and of carbon dioxide on the growth and reproduction of C. briggsae (Rhabditidae). Citation: Nematologica 12: 328-336 1966 Type: ARTICLE Genes: Abstract: The effect of different partial pressures of oxygen on the survival, growth and reproduction of Caenorhabditis briggsae was investigated under axenic conditions. Small volumes of culture medium were inoculated with young larvae, equilibrated with mixtures of oxygen and nitrogen and of oxygen, nitrogen and carbon dioxide, and the development of the cultures followed under the microscope. It was concluded that growth was progressively retarded as the partial pressure of oxygen was reduced below 30 mm Hg and stopped at low levels (below about 1.2 mm HG). The addition of carbon dioxide to the gas mixture probably retarded growth slightly. ------------------- Key: 264 Medline: Authors: Nicholas WL;McEntegart MG Title: A technique for obtaining axenic cultures of rhabditid nematodes. Citation: Journal of Helminthology 31: 135-144 1957 Type: ARTICLE Genes: Abstract: The ultimate purpose of our experiments is to study the nutritional and cultural requirements of free-living nematodes. Before this can be achieved it is essential to develop methods by which the nematodes can be cultured in media free from other organisms, i.e. axenically. Dougherty and Calhoun have reviewed the earlier literature on attempts to obtain axenic cultures of nematodes, and they have developed a method of rendering several species of Rhabditinae axenic. Dougherty and his co-workers have shown that, starting with worms which have been axenized by this method, the growth and reproduction of one species, Caenorhabditis briggsae (=Rhabditis briggsae), can be maintained satisfactorily by subculture in axenic media. However, this method of axenizing the worms is apparently not always equally satisfactory for axenizing other species of Rhabditinae and we have found that it frequently gives unsatisfactory results with the three species which we have worked, see below. ------------------- Key: 265 Medline: Authors: Nicholas WL;Stewart AC Title: The calorific value of C. elegans (Rhabditidae). Citation: Nematologica 24: 45-50 1978 Type: ARTICLE Genes: Abstract: The calorific value of populations of Caenorhabditis elegans was measured by bomb-calorimetry. A value of 27.59 kJ per g ash-free dry weight was obtained (=6,316 calories per g). This value is high, but agrees well with calculations based on previously published analyses of lipid and glycogen reserves in Caenorhabditis sp. It is suggested that when harvested from a rich culture of bacteria Caenorhabditis has substantial lipid reserves accounting for its high calorific value. ------------------- Key: 266 Medline: Authors: Nicholas WL;Viswanathan S Title: A study of the nutrition of C. briggsae (Rhabditidae) fed on Carbon-14 and Phosphorus-32 labelled bacteria. Citation: Nematologica 21: 385-400 1975 Type: ARTICLE Genes: Abstract: Cultures of Caenorhabditis briggsae were fed on Escherichia coli pre-labelled with 14C or 32P. Budgets were constructed to show what proportions of the digested 14C or 32P were retained by the nematode, excreted and, with 14C, respired. A substantial part of the digested C and P appear as soluble metabolites in the medium. Data are also presented on the distribution of 14C and 32P in major tissue fractions of the nematode, and on the rate of loss of radioactivity from nematodes in culture. The percentage of 14C from digested E. coli retained within the nematodes' tissue varied with the substrate used to label E. coli from 17% to 51%. It is suggested that the percentage retained when feeding on E. coli labelled with {14D]NaHCO3, about 20%, in the experiments reported may be a useful criterion in studies of the ecological energetics of baceria-feeding ------------------- Key: 267 Medline: Authors: Nickle WR;Ayre GL Title: C. dolichura in the head glands of the ants Camponotus herculeanus (L.) and Acanthomyops claviger (Roger) in Ontario/ Citation: Proceedings of the Entomological Society of Ontario 96: 96-98 1966 Type: ARTICLE Genes: Abstract: ------------------- Key: 269 Medline: Authors: Nigon V Title: Le determinisme du sexe chez un Nematode libre hermaphrodite Rhabditis dolichura Schneider. Citation: Bulletin de la Societe Zoologique de France 71: 78-86 1947 Type: ARTICLE Genes: Abstract: ------------------- Key: 270 Medline: Authors: Nigon V Title: Effects de la polyploidie chez un nematode libre. Citation: C.R. des Seances de l'Academie des Sciences Serie D 228: 1161-1162 1949 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 271 Medline: Authors: Nigon V Title: Les modalites de la reproduction et le determinisme du sexe chez quelques nematodes libres. Citation: Annales de Sciences Naturelles - Zool. Biol. Anim. 11: 1-132 1949 Type: ARTICLE Genes: Abstract: ------------------- Key: 272 Medline: Authors: Nigon V Title: Contributions a la critique experimentale des theories de la continuite germinale et de la lignee pure. Citation: Acta Biologica Academiae Scientiarum Hungaricae 5: 96-117 1954 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 273 Medline: Authors: Nigon V Title: Developpement et reproduction des nematodes. Citation: "Traite de Zoologie, Tome IV." Grasse PP (ed), Masson et Cie, Paris, France. : 218-294 1965 Type: REVIEW Genes: Abstract: In French. ------------------- Key: 274 Medline: Authors: Nigon V;Arcel R Title: Effets d'une elevation de temperature sur la prophase meiotique d'un nematode libre. Citation: C.R. des Seances de l'Academie des Sciences Serie D 232: 1032-1034 1951 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 275 Medline: Authors: Nigon V;Brun J Title: L'evolution des structures nucleaires dans l'ovogenese de C. elegans Maupas 1900. Citation: Chromosoma 7: 129-169 1955 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 276 Medline: 68040168 Authors: Nigon V;Brun J Title: Genetique et evolution des nematodes libres. Perspectives tirees de l'etude de C. elegans. Citation: Experientia 23: 161-170 1967 Type: REVIEW Genes: Abstract: Free-living nematodes are endowed with a set of properties that make them specially attractive for experimental work. Geneticists and evolutionists may be especially interested in their easy cultivation, great fecundity and polymorphism. As an example, some results are brought concerning Caenorhabditis elegans and related species: (1) Sex determination occurs as the expression of a genic balance involving differences in the number of chromosomes. The alternatives gynogenesis, amphimixis, or auto-heterofecundation take a prominant place in the reproduction processes of these species. (2) Polyploidy may be obtained by heat-shock, giving rise to individuals showing characteristic chromosomal unbalance and variability. (3) C. elegans, which cannot normally be raised at a higher temperature than 22C, has been gradually adapted to temperatures up to 24.5C. This acclimatization implies an adaptive transformation of the ovarian physiology; this effect is obtained after long training, taking more than 1000 generations. Study of the process of acclimatization shows that its genetical basis may be partly of a non-genic nature, partly of a genic type. Hypotheses are developed for explaining this phenomenon and for the understanding of the evolution from free-living to parasitic nematodes. ------------------- Key: 277 Medline: Authors: Nigon V;Dougherty EC Title: Reproduct patterns and attempts at reciprocal crossing of Rhabditis elegans Maupas, 1900, and Rhabditis briggsae Dougherty & Nigon, 1949 (Nematoda: Rhabditidae). Citation: Journal of Experimental Zoology 112: 485-503 1949 Type: ARTICLE Genes: Abstract: For a long time the definition of a species has been the subject of numerous controversies related to the relative weighting that should be accorded to a number of criteria-morphological, ecological, and genetic-that today serve as a guide in the separation of related species. Morphological criteria, the importance of which is evident at the outset, involve, however, some refinement of application in the case of animals in which the anatomy offers only a limited number of possible variations. This is particularly the case with free-living nematodes belonging to the genus Rhabditis, in which the over 100 species named up to the present are differentiated largely on the basis of minimal characters. It was for this reason that early in the 1900's, Maupas ('18), tried to test species differences by attempts at hybridization. Among the experiments performed, several involved hermaphroditic species...... ------------------- Key: 278 Medline: Authors: Nigon V;Dougherty EC Title: A dwarf mutation in a nematode. A morphological mutant of Rhabditis briggsae, a free-living soil nematode. Citation: Journal of Heredity 41: 103-109 1950 Type: ARTICLE Genes: Abstract: 1. A morphological mutant of the self-fertilizing, hermaphroditic, free-living nematode species Rhabditis briggsae Dougherty and Nigon, 1949, is described in detail-the first to be reported in the phylum Nematoda. 2. It is designated micro and affects the gross appearance of the homozygous individuals by a general reduction in size, impairment of the egg-laying mechanism so that the ova are laid so slowly that they accumulate and kill the hermaphroditic parent, and alteration in the structure of the male copulatory bursa. 3. The mutation appeared after heat treatment among descendants of one of a series of isolated hermaphrodites kept at a temperature of 25C for 18 hours during the time of sexual maturation. It is not yet possible to state whether or not a causal mechanism between heat and mutation may exist in these forms. The inheritance of the micro gene is shown to follow a single-factor pattern and to be recessive and not sex-linked. 4. Experiments are described in which micro hermaphrodites have been successfully outcrossed with wild type males. The self-fertilized progeny of the micro parent can be readily distinguished from the cross-fertilized hybrid progeny by the mutant phenotype of the former vs. the wild phenotype of the latter. 5. The theoretical consequences of the production of this mutant are discussed in relation to the general taxonomy of the group, to the phenomenon of eutely (cell-constancy), to the practical usefulness of the micro gene as a chromosome marker and a test of cross-fertilization in linkage and other genetic experiments, and to the general potential importance of free-living nematodes in genetic research. ------------------- Key: 280 Medline: Authors: Nigon V;Guerrier P;Monin H Title: L'Architecture polaire de l'oeuf et les movements des constituants cellulaires au cour des premieres etapes du developpement chez quelques nematodes. Citation: Bulletin Biologique de la France et de la Belgique 94: 132-201 1960 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 281 Medline: Authors: Nolan RA Title: Asteromyces cruciatus from North America. Citation: Mycologia 64: 430-433 1972 Type: ARTICLE Genes: Abstract: The hyphomycete Asteromyces cruciatus F. & Mme Moreau was described without a Latin diagnosis or a designated type. The taxon was validated by Hennebert. The known distribution of this monotypic genus has been limited. F. and Mme Moreau found the fungus in sand dunes at Point du Siege (under Psamma sp.) and between Franceville and Le Home (under Agropyrum sp.) on the Normandy coast of France. Brown found A. cruciatus in open sand in the intertidal zone at Studland, Dorset and Sandwich, Kent, England; and Nicot found it in sand dunes and beach samples at Malo-les-Bains on the North Sea coast of France. ------------------- Key: 282 Medline: Authors: Nonnemacher-Godet J;Dougherty EC Title: Incorporation of tritiated thymidine in the cells of C. briggsae (Nematoda) reared in axenic culture. Citation: Journal of Cell Biology 22: 281-290 1964 Type: ARTICLE Genes: Abstract: In the rhabditid nematode Caenorhabditis briggsae the incorporation of thymidine-H3 has been studied by autoradiography after Feulgen staining, with animals maintained under axenic conditions in a medium of only partly defined composition. Labeling has been followed in adults left in the presence of thymidine-H3 for periods of from 1/2 to 24 hours, as well as in adults reared from larvae in the presence of the tritiated nucleoside. A massive incorporation is found in the nuclei of the gonads and intestine; also a less intense particulate cytoplasmic incorporation is clear in certain cells, especially those of the intestine. In general, all labeling has proved to be sensitive to DNase, but resistant to RNase. The label's stability has been tested by the transfer of adults into a medium containing "cold" thymidine. They remain there for up to 48 hours. A transfer for 24 hours results in a considerable decrease in the intensity of nuclear and cytoplasmic labeling; a stay of 48 hours leads to its complete disappearance from non-dividing (intestinal) as well as dividing (gonadal) nuclei. A phenomenon of DNA turnover is envisaged and discussed as a possible physiological attribute of C. briggsae. ------------------- Key: 283 Medline: 75151562 Authors: O'Farrell PH Title: High-resolution two-dimensional electrophoresis of Citation: Journal of Biological Chemistry 250: 4007-4021 1975 Type: ARTICLE Genes: Abstract: A technique has been developed for the separation of proteins by two-dimensional polyacrylamide gel electrophoresis. Due to its resolution and sensitivity, this technique is a powerful tool for the analysis and detection of proteins from complex biological sources. Proteins are separated according to isoelectric point by isoelectric focusing in the first dimension, and according to molecular weight by sodium dodecyl sulfate electrophoresis in the second dimension. Since these two parameters are unrelated, it is possible to obtain an almost uniform distribution of protein spots across a two-dimensional gel. This technique has resolved 1100 different components from Escherichia coli and should be capable of resolving a maximum of 5000 proteins. A protein containing as little as one disintegration per min of either 14C or 35S can be detected by autoradiography. A protein which constitutes 10-4 to 10-5% of the total protein can be detected and quantified by autoradiography. The reproducibility of the separation is sufficient to permit each spot on one separation to be matched with a spot on a different separation. This technique provides a method for estimation (at the described sensitivities) of the number of proteins made by any biological system. This system can resolve proteins differing in a single charge and consequently can be used in the analysis of in vivo modifications resulting in a change in charge. Proteins whose charge is changed by missense mutations can be identified. A detailed description of the methods as well as the characteristics of this system are presented. ------------------- Key: 284 Medline: Authors: Osche G Title: Systematik und phylogenie der gattung Rhabditis (Nematoda). Citation: Zoologische Jahrbucher - Abteilung Fur Allgemeine Zoologie Und Physiologie Der Tiere 81: 190-280 1952 Type: ARTICLE Genes: Abstract: ------------------- Key: 287 Medline: Authors: Ouazana R Title: A morphological temperature-sensitive mutant of the nematode C. elegans var. Bergerac. Citation: Experientia 34: 170-171 1978 Type: ARTICLE Genes: Abstract: A morphological temperature-sensitive mutant of Caenorhabditis elegans displays 2 overlapping temperature-sensitive periods, both occurring during the post-embryonic development. Data prove that these 2 phenotypes are controlled by the same locus and are not inherited as maternal factors. ------------------- Key: 288 Medline: 75207685 Authors: Ouazana R;Brun JL Title: Intracistronic recombination at a dwarfing locus in the free living self fertilizing nematode C. elegans. Citation: C.R. des Seances de l'Academie des Sciences Serie D 280: 1895-1898 1975 Type: REVIEW Genes: Abstract: In French. ------------------- Key: 289 Medline: Authors: Ouazana R;Brun J Title: Effect of dumpiness on the development and functioning of eutelic and noneutelic organs in the nematode C. elegans. Citation: Genetica 49: 45-52 1978 Type: ARTICLE Genes: Abstract: We analyze, in the wild-type strain of the Bergerac variety of Caenorhabditis elegans and in eight dumpy mutations distributed among the genome, the morphological and physiological characteristics of two organogenetically different organs: -the intestine, a typically eutelic organ (i.e. an organ whose cell number and disposition are theoretically constant), -the ovotestis, a non-eutelic organ. The ovotestis of all mutants can be distinguished from the wild-type by: -reduced fecundity and productivity, -a different distribution for adult progeny according to daily laying, -slowing of gonadic organogenesis during post-embryonic development. Mutants bearing alleles of the same locus (dpy-e) are similar in their gonad development and function, but mutants at other loci may differ in this respect. Several hypotheses concerning the relationship between ovotestis development and function are discussed. As the male phase of its hermaphroditic gonad does not seem to be affected in dumpy mutants, the observed slowing would mainly affect oocyte multiplication and differentiation. We show that intestinal development is independent of dumpiness which does not affect either the number or the positional ------------------- Key: 290 Medline: Authors: Ouazana R;Gibert M-A Title: Cuticular collagen composition of the nematode C. elegans, Bergerac wild-type strain. Citation: C.R. des Seances de l'Academie des Sciences Serie D 288: 911-914 1979 Type: ARTICLE Genes: Abstract: We describe a technique allowing us to isolate the cuticles of Caenorhabditis elegans. The good condition of purification is verified by Electron Microscopy. The amino acid composition of the cuticular collagen, compared with that of Ascaris lumbricoides, shows two important differences only: the first one is the ratio hydroxyproline/proline which is 0,47 for C. elegans but only 0,065 for A. lumbricoides; the second one is the alanine which is near by twice as much for C. elegans. ------------------- Key: 291 Medline: 72135442 Authors: Ozerol NH;Silverman PH Title: Exsheathment phenomenon in the infective-stage larvae of Haemonchus contortus. Citation: Journal of Parasitology 58: 34-44 1972 Type: ARTICLE Genes: Abstract: The nature of exsheathment of 3rd-stage larvae of Haemonchus contortus was investigated further using a new simplified technique for the study of cuticular ring formation. The presence of a second ring on the 2nd-stage larval cuticle, 8 to 9 u from the anterior, is described. Exsheathing activity was observed to occur in 4 consecutive steps on isolated sheaths of H. contortus. Metabolic fluid and somatic extract of Ascaris suum and Caenorhabditis briggsae were investigated for their ability to stimulate exsheathment in H. contortus. Scanning electron microscopy revealed some aspects of the fine structure of cuticle. Exsheathing factor(s) was found to be thermostable, to require no metal ion activation, and to be active over a broad range of pH. Temperature appeared to be an important factor for the exsheathment activity. ------------------- Key: 292 Medline: 76251418 Authors: Pak WL;Pinto LH Title: Genetic approach to the study of the nervous system. Citation: Annual Review of Biophysics & Bioengineering 5: 397-448 Type: REVIEW Genes: Abstract: Beadle & Tatum first showed that single step mutants may be used to elucidate complex physiological processes other than the mechanism of inheritance. These workers used mutants to analyze the biochemical pathways of the fungus Neurospora. It has long been realized that mutants may also be helpful in the study of the nervous system. However, the early approaches relied on spontaneously occurring mutations or on behavioral changes brought about by selective breeding. Benzer proposed that, instead, single step mutations should be induced and appropriate mutants should be screened for use in the study of the nervous system. In the past few years, the technique of induced mutation has been gaining acceptance as potentially one of the most powerful tools available to ------------------- Key: 294 Medline: 76182459 Authors: Patel TR;McFadden BA Title: A simple spectrophotometric method for measurement of nematode populations. Citation: Analytical Biochemistry 70: 447-453 1976 Type: ARTICLE Genes: Abstract: An ordinary spectrophotometer was used to study growth rates and increases in population size of nematodes by optical density measurements of nematodes suspended in 30-40% sucrose (w/v) solutions. The sucrose solution retarded the movement of nematodes in suspension and thereby decreased the fluctuations normally observed in optical density. This method was effectively used to study growth rates and increases in population numbers of a free-living nematode, Caenorhabditis elegans. This procedure was also used to quantitate Ascaris lumbricoides eggs in a given sample. The limitations of this method when employed for establishing total nematode counts in a growing culture by direct spectrophotometric readings are ------------------- Key: 295 Medline: 78018746 Authors: Patel TR;McFadden BA Title: Particulate isocitrate lyase and malate synthase in C. elegans. Citation: Archives of Biochemistry & Biophysics 183: 24-30 1977 Type: ARTICLE Genes: Abstract: Biochemical evidence is presented suggesting the particulate nature of some of the glyoxylate cycle enzymes in the free-living nematode Caenorhabditis elegans. A crude homogenate of freshly grown nematodes was prepared by gentle grinding. Isopycnic sucrose gradient centrifugation of the supernatant fraction obtained by low-speed centrifugation yielded four protein bands. The glyoxylate cycle enzymes, isocitrate lyase and malate synthase, appeared in the lowermost band at a density of 1.25 g/cm3, while the mitochondrial enzymes, fumarase and NADH oxidase, equilibrated at a density of 1.18 g/cm3. The glyoxylate cycle and the mitochondrial enzymes were released differentially from the particulate fraction either by sonic treatment or by treatment with 0.1% Triton X-100. The specific activities of isocitrate lyase and malate synthase in the supernatant fraction obtained after a sonic treatment of the particulate fraction were always higher than those observed in the parent fraction. ------------------- Key: 296 Medline: Authors: Patel TR;McFadden BA Title: Axenic and synchronous cultures of C. elegans. Citation: Nematologica 24: 51-62 1978 Type: ARTICLE Genes: Abstract: A technique to axenize cultures of Caenorhabditis elegans on a large scale is described. This procedure has enabled the isolation of eggs of C. elegans in quantities sufficient to perform biochemical tests. Adults from monoxenic cultures were used to isolate eggs. When egg-bearing worms were suspended for 2-3 hr at 25C n an alkaline (0.4 M) solution of NaOH, the worm cuticle was partially digested, releasing free eggs. The high alkalinity rendered the eggs bacteria-free. Eggs were then isolated from a linear sucrose gradient. Eggs from the least dense band (1.13 g/cm3) hatched within 10-13 hr when resuspended in a liquid medium and yielded a synchronous culture. The hatchability of these eggs ranged from 20-35%. Inhibitory effects of 5-fluorodeoxyuridine and hydroxyurea on freshly hatched (L1 stage) worms are described. Levels of isocitrate lyase were determined in ------------------- Key: 297 Medline: 78107010 Authors: Patel TR;McFadden BA Title: C. elegans and Ascaris suum: Fragmentation of isocitrate lyase in crude extracts. Citation: Experimental Parasitology 44: 72-81 1978 Type: ARTICLE Genes: unc-13 Abstract: It is well known that proteolysis often occurs after rupture of metazoan cells. Thus proteins isolated from extracts may not be representative of their native cellular counterparts. In the present research, extensive proteolysis was observed in crude extracts of the free-living soil nematode Caenorhabditis elegans and the parasitic nematode Ascaris suum. Phenylmethylsulfonyl fluoride (PMSF) reduced the loss in activity of isocitrate lyase (EC 4.1.3.1), fumarase (EC 4.2.1.2), and citrate synthase (EC 4.1.3.7) in extracts of C. elegans but had little or no effect upon loss of malate synthase (EC 4.1.3.2). Catalase (EC 1.11.1.6) was stable. The loss of isocitrate lyase and citrate synthase was less pronounced in extracts of 22-day-old embryos of A. suum. Catalase decayed in these extracts. The addition of PMSF reduced the loss in all three of these activities. Fumarase was stable. The number of active fragments of isocitrate lyase recovered after filtration on Sephadex G-200 increased with the length of storage of crude extracts in the absence of PMSF at 4C. Even in the presence of PMSF five activity peaks were observed after storage of extracts of C. elegans at 4C for 72 hr. The molecular weights of active species ranged between 549,000 and 128,000 for isocitrate lyase in extracts of either C. elegans or A. suum. The 549,000- and 214,000-dalton species of isocitrate lyase from A. suum were much more labile at 50C than the 543,000- and ------------------- Key: 298 Medline: 78190959 Authors: Patel TR;McFadden BA Title: C. elegans and Ascaris suum: Inhibition of isocitrate lyase by itaconate. Citation: Experimental Parasitology 44: 262-268 1978 Type: ARTICLE Genes: Abstract: The largest forms of isocitrate lyase from Caenorhabditis elegans and Ascaris suum of 543,000 and 549,000 daltons, respectively, can be purified from three- to five-fold in excellent yield by pelleting from extracts at 160,000g for 4 hr. Isocitrate lyase in the pellet is much more stable toward proteolysis. Itaconate which both inhibits isocitrate lyase and suppresses the level of this enzyme in bacteria inhibits the partially purified isocitrate lyase from both C. elegans and A. suum. The inhibition is noncompetitive with respect to D(s)-isocitrate at one itaconate concentration. The Ki values at 30C, pH 7.7, are 19 and 7.3 uM for the enzyme from C. elegans and A. suum, respectively. Itaconate inhibits the growth of C. elegans in random axenic as well as monoxenic cultures. At a concentration of 10 mM, itaconate is more effective in the inhibition of random axenic cultures than is oxalate, maleate, or succinate. At 60 mM itaconate, reproduction of C. elegans larvae is completely abolished. ------------------- Key: 299 Medline: Authors: Pertel R Title: Axenic cultivation of two species of rhabditid nematodes on a commercial medium. Citation: Nematologica 10: 343-343 1964 Type: ARTICLE Genes: Abstract: A commercially available crude liver medium capable of supporting the axenic cultivation of Caenorhabditis briggsae and Caenorhabditis elegans has been found. It is Bacto-Liver (manufactured by Difco Laboratories Incorporated) - a desiccated and powdered form of fresh liver that has been found to sustain the growth and reproduction of these species. The medium is prepared by Seitz-filtering a 10% suspension of the powdered liver. ------------------- Key: 302 Medline: 76187597 Authors: Pertel R;Paran N;Mattern CFT Title: C. elegans: Localization of cholinesterase associated with anterior nematode structures. Citation: Experimental Parasitology 39: 401-414 1976 Type: ARTICLE Genes: Abstract: By employing a histochemical procedure on adult nematodes, the base of the Caenorhabditis elegans amphid appears to contain acetylcholinesterase and a nonspecific cholinesterase. Some precipitation was observed in the kinetosome region of the inner labial papilla with acethylthiocholine (AtCh) as substrate but not, in limited observations, in the absence of substrate or with butyrylthiocholine (BtCh). The amphidial tips, the tips of the inner labial papillae, and the lining of the buccal cavity contained substantial reaction product at the ultrastructural level, with or without substrates and inhibitors and therefore cannot be related to the presence of a cholinesterase. ------------------- Key: 303 Medline: 75148966 Authors: Pertel R;Wilson SH Title: Histamine content of the nematode, C. elegans. Citation: Comparative & General Pharmacology 5: 83-85 1974 Type: ARTICLE Genes: Abstract: 1. The histamine contect in axenically grown nematodes was found to be 350 ng. per g. wet weight. 2. Histamine content was determined in extracts from the free-living nematode, Caenorhabditis elegans var. Bristol (strain B1-Pl) by an isotope dilution procedure which obviated error encountered in a conventional fluorescence assay. 3. This is the first report of histamine in the Nematoda. ------------------- Key: 305 Medline: Authors: Pinnock CB;Hieb WF;Stokstad ELR Title: A mass culture bioassay method for C. briggsae using population growth rate as a response parameter. Citation: Nematologica 21: 1-4 1975 Type: ARTICLE Genes: Abstract: A bioassay method for C. briggsae using population growth rate as a response parameter is described in which the nematodes are rotated at 1.0 rpm in 5.0 ml medium in 18 mm tubes on a tissue culture rotator. This method permits higher peak populations of nematodes than a previous mass culture method and also allows nephelometric monitoring of population growth. Population growth rate during the initial phase of growth is an effective index of growth and avoids the variations due to inoculum size and accumulation of metabolites associated with use of direct population counts at fixed time intervals. ------------------- Key: 306 Medline: 75158496 Authors: Pinnock C;Shane B;Stokstad ELR Title: Stimulatory effects of peptides on growth of the free-living nematode C. briggsae. Citation: Proc. Society for Experimental Biology & Medicine 148: 710-713 1975 Type: ARTICLE Genes: Abstract: Recent work on ageing and genetics of higher organisms using nematodes as model systems has focused attention on the need for completely defined axenic culture media for these organsisms. The free-living nematode Caenorhabditis briggsae requires the addition of a proteinaceous factor to a medium containing amino acids, vitamins, minerals, nucleotides, heme and a sterol. Proteins from widely different sources have been found to be active. A recent paper has proposed that such proteins derive their sole activity from facilitation of uptake of the essential nutrient heme, possibly by stimulation of phagocytosis. This theory is supported by the activating effect of precipitation on proteins and on heme itself. The evidence presented, however, has not been supported by experimental work in our own laboratory and we feel alternative modes of action of protein growth factors should be considered. The possibility that such factors may derive their activity from peptide fragments produced by gut hydrolysis was investigated and evidence for this is presented here. Peptides are already known to be of considerable importance in the nutrition of bacteria and mammals, however this is the first indication that they may play a role in the nutrition of invertebrate metazoa. ------------------- Key: 307 Medline: Authors: Pinnock CB;Stokstad ELR Title: The effect of heme source on growth of C. briggsae in peptide and carbohydrate supplemented chemically defined medium. Citation: Nematologica 21: 258-260 1975 Type: ARTICLE Genes: Abstract: A recent paper described the stimulatory effects of mixtures of peptides on population growth of C. briggsae in C. briggsae Maintenance Medium (CbMM) supplemented with B-sitosterol and cytochrome C. We describe here preliminary evidence that the nature of the heme source influences the activity of such supplements, and also that a previously unsuspected class of nutrients, guar gum, can stimulate growth. ------------------- Key: 310 Medline: 79001394 Authors: Popham JD;Webster JM Title: An alternative interpretation of the fine structure of the basal zone of the cuticle of the dauerlarva of the nematode C. elegans (Nematoda). Citation: Canadian Journal of Zoology 56: 1556-1563 1978 Type: ARTICLE Genes: Abstract: The fine structure of the basal zone of the cuticle of the dauerlarva of Caenorhabditis elegans was examined in order to help resolve controversies regarding its structure. The results show that the striated layer in the basal zone consists of two sets of laminae oriented at right angles to each other. One set of laminae consists of longitudinally oriented, alternately thick and thin, osmiophilic strips with the distance between similar strips measuring 19 nm. The other set of laminae consists only of thick strips spaced about 14.5 nm apart which are oriented circumferentially about the larva. It is speculated that the striated layer of the basal zone of the cuticle consists of blocks of protein separated by this apparent network of interconnecting osmiophilic laminae. ------------------- Key: 311 Medline: Authors: Popham JD;Webster JM Title: Aspects of the fine structure of the dauer larva of the nematode C. elegans. Citation: Canadian Journal of Zoology 57: 794-800 1979 Type: ARTICLE Genes: Abstract: Examination of the ultrastructure of the dauer larva of Caenorhabditis elegans showed that cells in the lateral cord and body wall muscle had irregular profiles, few Golgi bodies, and cisternae of endoplasmic reticulum, but they contained abundant lipid and glycogen. These cells and the esophageal cells had mitochondria in the condensed conformation. The intestinal lumen was small and the brush border was so compact that individual microvilli were difficult to discern. Intestinal cells had cytosomes with irregular profiles and unhomogeneous matrices. The striated layer was absent from the cuticle covering the lips and papillae. These ultrastructural features are correlated with the dauer larva's low metabolic rate, its resistance to toxic chemicals and to adverse environmental conditions, and its ability to detect food and to feed soon after exposure to a hospitable environment. ------------------- Key: 312 Medline: Authors: Popham JD;Webster JM Title: The use of osmium mixtures in localizing ions in C. Citation: Nematologica 25: 67-75 1979 Type: ARTICLE Genes: Abstract: Electron microscopy of Caenorhabditis elegans fixed in an aqueous solution of osmium tetroxide mixed with potassium pyroantimonate, silver lactate or lead nitrate revealed the following. Calcium is localised in the median and basal layers of the cuticle, in the myofibrils of the body wall muscle, in mitochondria, and in intestinal cytosomes. Chloride ions are localised in the cortical zone of the cuticle along the apical membrane infoldings of the hypodermal cells and in the ground substance of the cytoplasm and vesicles of intestinal cells. Orthophosphate ions are localised in nucleoli and heterochromatin, in cytosomes of the intestinal cells, in foldings of the external membranes of the hypodermis, and in the intracristal space of mitochondria. Orthophosphates and/or sulphates surround the microvilli of intestinal cells. The results suggest that chloride ion regulation may occur in the hypodermal cells and intestinal cells rather than in the excretory tubules of C. elegans. ------------------- Key: 313 Medline: Authors: Potts FA Title: Notes on the free-living nematodes I. The hermaphrodite species. Citation: Quarterly Journal of Microscopical Science 55: 433-484 1910 Type: REVIEW Genes: Abstract: Orley divided the Nematoda into three groups, roughly corresponding to differences of habitat found in the phylum. (1) Nematozoa embracing all parasitic forms, (2) Rhabditiformae which live free in "decomposing organic substances or in earth saturated with such substances", and (3) Anguillulidae, the rest of the free-living nematodes, found in soil or water. Such a classification, grounded on ecology, pays no attention to the facts of morphology, and is naturally out of place in zoological arrangement, which aims at expressing the relationship of animals by descent. ------------------- Key: 314 Medline: 79114489 Authors: Quinn WG;Gould JL Title: Nerves and genes. Citation: Nature 278: 19-23 1979 Type: REVIEW Genes: Abstract: It is the business of scientists to explain away the magic in the world. The largest coherent body of magic remaining is the behaviour of men and animals. Behavioural geneticists try to construct plausible explanations for behaviour patterns by studying genetic variants. Historically, they have sought to compare inbred strains, or to cross them and examine the progeny. Such comparisons inevitably involve many genetic differences, making the results virtually impossible to interpret. A more recent approach initiated by Delbruck and Benzer has been to generate single-gene mutations which affect behaviour, to analyse the mutants, and to try to infer general principles about how normal behaviour is created. One advantage of such single-gene changes is that now behavioural patterns can be dissected into their component parts. This genetic extension of traditional ethology should have something important to say about how behaviour is organised and regulated, and has been reviewed recently. A more ambitious and potentially more powerful strategy is to examine the effects of single-gene mutations on the ultimate common denominator of behaviour-the physiology of nerve cells and the wiring patterns of neural circuits. This review traces the recent progress of this approach, selecting the work which seems to offer the best prospects ------------------- Key: 315 Medline: Authors: Rammeloo J Title: Harposporium anguillulae Lohde (moniliales), espece nematophage, trouve en Belgique. Citation: Biologisch Jaarboek 41: 180-182 1973 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 316 Medline: Authors: Riddle DL Title: A genetic pathway for dauer larva formation in C. elegans. Citation: Stadler Genetics Symposium 9: 101-120 1977 Type: REVIEW Genes: daf-1 daf-2 daf-3 daf-4 daf-6 daf-7 daf-8 daf-9 daf-10 Abstract: C. elegans is a roundworm, a free-living soil nematode. The dauer larva is a non-feeding, non-growing larval stage which is formed under conditions of starvation. It possesses a relatively impermeable cuticle and differs from all other larval stages in behavior and morphology. Dauer larva formation is a "developmental switch" in the life cycle which offers special advantages for genetic study. A partial genetic pathway for dauer larva formation has been established. Genetic characterization of additional mutants should reveal more details of this pathway. One class of mutants already characterized exhibits morphological alterations in sensory neurons, as determined by electron microscopy. Such mutants are useful for the study of nerve morphogenesis. ------------------- Key: 317 Medline: Authors: Riddle DL Title: The genetics of development and behavior in C. elegans. Citation: Journal of Nematology 10: 1-16 1978 Type: REVIEW Genes: sup-3 unc-40 Abstract: The current genetic research on Caenorhabditis elegans and the application of genetic techniques to the analysis of development and behavior in this animal are reviewed. Some aspects of the work are emphasized more than others and this inevitably reflects the author's own interests and prejudices. An effort was made to point out the advantages that C. elegans offers for certain types of investigations and to point out, in general terms, the relevance of this work to other areas of biological research. ------------------- Key: 318 Medline: 78215868 Authors: Riddle DL;Brenner S Title: Indirect suppression in C. elegans. Citation: Genetics 89: 299-314 1978 Type: ARTICLE Genes: sup-3 unc-1 unc-15 unc-24 unc-41 unc-42 unc-52 unc-87 eDf1 Abstract: Two cases of indirect suppression have been characterized. One case involves suppressors compensating for defects in muscle structure. Nine independent suppressor mutations were judged to lie in a single suppressor gene, sup-3. Suppression is dominant, but dose dependent, and results in improved locomotion, as well as in an increase in the ability of mutant animals to lay eggs. Mutations in six genes known to affect muscle structure were tested for suppression by representative sup-3 mutations. Alleles of three of the six genes are suppressed, two of which are known to code for thick filament proteins. One suppressor allele was identified as a deletion by genetic criteria. A second case of indirect suppression is not associated with muscle defects, but involves two mutant genes producing uncoordinated phenotypes very similar to one another. As in the first case, suppression is domiant but dose dependent and is not allele specific. ------------------- Key: 320 Medline: Authors: Rose AM;Baillie DL Title: The effect of temperature and parental age on recombination and nondisjunction in C. elegans. Citation: Genetics 92: 409-418 1979 Type: ARTICLE Genes: dpy-11 unc-68 Abstract: The effect of temperature and parental age on recombination frequency in C. elegans was studied between pairs of closely linked markers on linkage groups I and IV. In the regions studied, recombination frequency varied threefold over the temperature range 13.5C to 26C. Temperature-shift experiments indicated that a temperature-sensitive recombination event occurs approximately 50 oocytes prior to fertilization. Recombination frequency was observed to decrease with maternal age. The greatest decrease was observed in the first 24 hours of egg production. The frequency of male progeny, a measure of X-chromosome nondisjunction was also studied. This frequency increased with elevated temperature and age of the parent. ------------------- Key: 321 Medline: 80032926 Authors: Rose AM;Baillie DL Title: A mutation in C. elegans that increases recombination frequency more then threefold. Citation: Nature 281: 599-600 1979 Type: ARTICLE Genes: dpy-5 dpy-11 dpy-14 rec-1 unc-13 unc-29 unc-42 unc-43 Abstract: In higher organisms the rate of recombination between genetic loci is presumably responsive to selective pressure. Recently, selective pressures and mutational events that influence recombination have been reviewed. Mutational sites and chromosomal rearrangements that enhance or suppress recombination frequency in specific regions are known, but general mechanisms that enhance recombination have not yet been discovered. We describe here the isolation and characterisation of a strain of the hermaphroditic nematode, Caenorhabditis elegans, that has a recombination frequency at least threefold higher than that found in the wild type. In this strain, rec-1, the number of reciprocal recombination events between linked loci is increased. This is true for all pairs of linked loci studies so far. The high recombination strain behaves as if it carries a classical recessive mutation, although a second mutation exists which can alter the recessive ------------------- Key: 323 Medline: Authors: Rothstein M Title: Nematode biochemistry - III. Excretion products. Citation: Comparative Biochemistry & Physiology 9: 51-59 1963 Type: ARTICLE Genes: Abstract: 1. The free-living nematode, Caenorhabditis briggsae, after incubation with various radioactive substrates, excretes nitrogen chiefly in the form of ammonia and amino acids. No significant amounts of urea, uric acid, allantoin or creatinine are produced. 2. Highly radioactive acidic and neutral components are excreted into the incubation media. 3. The results obtained are in general agreement with the known excretion products of a number of parasitic ------------------- Key: 324 Medline: Authors: Rothstein M Title: Nematode biochemistry - V. Intermediary metabolism and amino acid interconversions in C. briggsae. Citation: Comparative Biochemistry & Physiology 14: 541-552 1965 Type: ARTICLE Genes: Abstract: 1. Formate-C14 is readily incorporated into serine by Caenorhabditis briggsae, presumably by a one-carbon addition to glycine. The reverse reaction (conversion of serine to glycine) appears to take place only to a limited degree. The formate-carbon is also incorporated into glutamate, aspartate and alanine. 2. C(14)O(2) is incorporated, as expected, into the amino acids related to the tricarboxylic acid cycle, probably by way of C02 fixation via malic enzyme. A number of unidentified radioactive acids were also formed, suggesting the existence of additional metabolic pathways. 3. Other findings demonstrated the production of glutamine and asparagine in the incubation medium of worms fed acetate-2-C14; the identification of y-aminobutyric acid in the worms; the conversion of phenylalanine to tryosine, and the inability of the worms to form taurine from labeled acetate or methionine. 4. Products found in the incubation medium of C. briggsae depend upon the substrate and show a direct metabolic relationship to the latter. ------------------- Key: 325 Medline: 71030457 Authors: Rothstein M Title: Nematode biochemistry - IX. Lack of sterol biosynthesis in free-living nematodes. Citation: Comparative Biochemistry & Physiology 27: 309-317 1968 Type: ARTICLE Genes: Abstract: 1. Under axenic conditions, the free-living nematodes, Caenorhabditis briggsae, Turbatrix aceti and Panagrellus redivivus, are unable to synthesize cholesterol from acetate-2-C14 or DL-mevalonate-2-C14. 2. No evidence could be found that sterols other than cholesterol are synthesized by any of the organisms. ------------------- Key: 326 Medline: 70054080 Authors: Rothstein M Title: Nematode biochemistry - X. Excretion of glycerol by free-living nematodes. Citation: Comparative Biochemistry & Physiology 30: 641-648 1969 Type: ARTICLE Genes: Abstract: 1. The free-living nematode, Caenorhabditis briggsae, excretes labeled glycerol as a major product when incubated with acetate-14C in "whole medium". 2. When incubated in water of buffer solution, little or no glycerol is formed, glucose and trehalose being the major products. 3. Turbatrix aceti yields similar results. Panagrellus redivivus shows similar behavior when incubated in water, but in "whole medium" other neutral products, presumably sugars, are formed, in addition to glycerol. ------------------- Key: 327 Medline: Authors: Rothstein M Title: Nematode biochemistry XI, biosynthesis of fatty acids by C. briggsae and Panagrellus redivivus. Citation: International Journal of Biochemistry 1: 422-428 1970 Type: ARTICLE Genes: Abstract: 1. The free-living nematodes, Caenorhabditis briggsae and Panagrellus redivivus, are capable of synthesizing polyunsaturated fatty acids de novo. Acetate-2-14C yields labelled linoleic acid (18:2), linolenic acid (18:3), and C20 fatty acids with up to 5 double bonds. Evidence is presented which shows that these acids are labelled throughout the chain and not formed by simple addition of a labelled 2-carbon unit to pre-existing precursors. 2. Stearate-1-14C and oleate-1-14C are also converted directly to polyunsaturated fatty acids in C. briggsae, providing further proof that oleate can be desaturated to linoleate. Of all the multicellular animals studied so far, only free-living nematodes have this biosynthetic capability. ------------------- Key: 328 Medline: 75057195 Authors: Rothstein M Title: Practical methods for the axenic culture of the free-living nematodes Turbatrix aceti and C. briggsae. Citation: Comparative Biochemistry & Physiology 49B: 669-678 1974 Type: ARTICLE Genes: Abstract: 1. Media are described which are suitable for the axenic culture of large numbers of the free-living nematodes, Turbatrix aceti and Caenorhabditis briggsae. 2. T. aceti grows to a population of over 250,000 worms/ml in 18 days at 30C in a defined basal medium to which is added acetic acid (4%), myoglobin or hemoglobin (500 ug/ml) and cholesterol or other sterols (50 ug/ml). For convenience, a mixture of cholesterol, B-sitosterol and ergosterol is used. 3. C. briggsae grows consistently to over 50,000 worms/ml in 8 days at 20C in the same medium, but without the acetic acid and with the replacement of the amino acids by 4% soy-peptone. Cytochrome c can substitute for myoglobin or hemoglobin. ------------------- Key: 330 Medline: 66161633 Authors: Rothstein M;Cook E Title: Nematode biochemistry - VI. Conditions for axenic culture of Turbatrix aceti, Panagrellus redivivus, Rhabditis anomala and C. briggsae. Citation: Comparative Biochemistry & Physiology 17: 683-692 1966 Type: ARTICLE Genes: Abstract: 1. The small, free-living nematodes, Turbatrix aceti, Rhabditis anomala and Panagrellus redivivus, can be readily grown in axenic culture on a scale suitable for biochemical studies. 2. A number of observations related to the growth requirements of the organisms are reported. 3. An improved yield of Caenorhabditis briggsae has been attained by addition of autoclaved casein to the medium, permitting a reduction in the amount of liver extract required. This procedure also appears to be effective for T. aceti. ------------------- Key: 331 Medline: 89275708 Authors: Rothstein M;Coppens M Title: Nutritional factors and conditions for the axenic culture of free-living nematodes. Citation: Comparative Biochemistry & Physiology 61B: 99-104 1978 Type: ARTICLE Genes: Abstract: 1. Soy-peptone has been fractionated to yield a series of increasingly purified components which sharply increase the populations of Caenorhabditis briggsae and Caenorhabditis elegans when added to the basal medium. The nutritionally active material appears to be a small polypeptide. 2. C. briggsae and C. elegans routinely reach populations of 150,000/ml or greater in 9 days in still culture, starting from an inoculum of only 500 organisms per ml. C. elegans is particularly sensitive to the depth of the medium. However, large populations can be achieved in deep cultures if continuous shaking is carried out. 3. Panagrellus silusiae shows improved populations if the basal medium is supplemented with the nutritional factor from soy-peptone. However, 0.5% acetic acid or 1% ethanol added to the medium serves equally well. There is no additive effect of ethanol and the factor. ------------------- Key: 332 Medline: 66020574 Authors: Rothstein M;Mayoh H Title: Glycine synthesis and isocitrate lyase in the nematode, C. briggsae. Citation: Biochemical and Biophysical Research Communications 14: 43-47 1964 Type: ARTICLE Genes: Abstract: The metabolism of the nematode Caenorhabditis briggsae differs substantially from that expected of an "animal" species. This organism has at least a limited ability to synthesize "essential" amino acids and, although it utilizes the tricarboxylic acid cycle, does not appear to have a typical cytochrome system. This paper presents evidence for the existence of another interesting metabolic feature, namely the presence of the enzyme "isocytrate lyase" and its utilization by C. briggsae to synthesize the amino acid, glycine. The existence of this pathway was first suspected when it was found that the organism excreted glycine as a major radioactive product after ------------------- Key: 333 Medline: Authors: Rothstein M;Mayoh H Title: Nematode biochemistry IV. On isocitrate lyase in C. briggsae. Citation: Archives of Biochemistry & Biophysics 108: 134-142 1964 Type: ARTICLE Genes: Abstract: The small, free-living nematode, Caenorhabditis briggsae, converts aspartic acid-4-C14 to labeled glycine. Evidence is presented which suggests that the mechanism for this conversion involves the formation of isocitrate and its subsequent splitting by isocitrate lyase to yield glyoxalate and hence, glycine. In support of this mechanism, the enzyme "isocitrate lyase" has been demonstrated in sonic extracts of C. briggsae. ------------------- Key: 334 Medline: Authors: Rothstein M;Mayoh H Title: Nematode biochemistry - VIII. Malate synthetase. Citation: Comparative Biochemistry & Physiology 17: 1181-1188 1966 Type: ARTICLE Genes: Abstract: 1. The presence of malate synthetase has been demonstrated in the four small free-living nematodes, Caenorhabditis briggsae, Panagrellus redivivus, Rhabditis anomala and Turbatrix aceti. Since the organisms possess isocitrate lyase, the complete glyoxalate cycle appears to be present. 2. A sensitive procedure for the detection of labeled malate has been employed to confirm unequivocally the presence of this acid as a product of malate synthetase. ------------------- Key: 335 Medline: Authors: Rothstein M;Nicholas WL Title: Culture methods and nutrition of nematodes and Acanthocephala. Citation: "Chemical Zoology, Volume III. Echinodermata, Nematoda, and Acanthocephala." Florkin M and Scheer BT (eds), Academic Press, NY. : 289-328 1969 Type: REVIEW Genes: Abstract: In order to study properly the nutrition and culture of nematodes, it is desirable to establish the organisms in axenic culture. Only in this way can the metabolic abilities of the nematodes be separated from those of coexisting and interacting organisms. One may settle for a mono-axenic culture, but the best way to attain this is to obtain axenic nematodes and then add the second organism or tissue, for example, alfalfa callus tissue for plant parasitic nematodes (Krusberg, 1961). This chapter will devote itself, in the main, to recent work on the culture and nutrition of nematodes, free-living and parasitic, and will refer only in passing to work already thoroughly reviewed (Dougherty et al., 1959; Nicholas, et al., 1959; Dougherty, 1960). ------------------- Key: 336 Medline: Authors: Rothstein M;Tomlinson GA Title: Biosynthesis of amino acids by the nematode C. briggsae. Citation: Biochimica et Biophysica Acta 49: 625-627 1961 Type: ARTICLE Genes: Abstract: We wish to report what we believe to be the first demonstration of the biosynthesis of "essential amino acids" by a multicellular animal species. Axenic cultures of Caenorhabditis briggsae, a small free-living nematode, were grown at 20C in a chemically defined medium supplemented with a heated liver extract. The amino acid moiety of the medium was replaced with soy-peptone. After two weeks, protein which precipitated was solubilized by treatment of the medium with trypsin for approx. 20 h and the worms were then isolated by centrifugation under sterile conditions....... ------------------- Key: 337 Medline: Authors: Rothstein M;Tomlinson GA Title: Nematode biochemistry II. Biosynthesis of amino acids. Citation: Biochimica et Biophysica Acta 63: 471-480 1962 Type: ARTICLE Genes: Abstract: Axenic cultures of the free-living nematode, Caenorhabditis briggsae, were incubated in water for 6 days in the presence of [1-14C]acetate, [2-14C]acetate, [1-14C]glucose and [2-14C]glycine, respectively. From the last three substrates the worms were found to biosynthesize not only the "non-essential" amino acids represented by glutamic acid, aspartic acid, alanine, glycine, serine and arginine, but also the "essential" amino acids, threonine, tyrosine, valine, leucine, isoleucine, histidine and lysine. This appears to be the first report of such syntheses in an animal species. ------------------- Key: 338 Medline: 78131102 Authors: Russell RL;Johnson CD;Rand JB;Scherer S;Zwass MS Title: Mutants of acetylcholine metabolism in the nematode C. elegans. Citation: "Molecular Approaches to Eucaryotic Genetic Systems" ICN-UCLA Symposia on Molecular & Cellular Biology, Volume 8. Wilcox G, Abelson J and Fox CF (eds), Academic Press, NY. 8: 359-371 1977 Type: REVIEW Genes: ace-1 Abstract: Radiochemical assays based on the selective extraction of either substrate or product from an aqueous reaction volume into an organic scintillator have been developed for acetylcholinesterase and choline acetyltransferase. These rapid, convenient assays have made it possible to screen large numbers of mutant lines for potential enzymatic defects. One mutant with a partial acetylcholinesterase defect and two more with choline acetyltransferase defective mutants have been identified. The acetylcholinesterase defective mutant lacks two of the four isozymic forms of acetylcholinesterase found in wild type C. elegans. Behaviorally, it is selectively defective in the propagation of contractile waves in the body region. Of the two mutants with choline acetyltransferase defects, one is remarkabley paralyzed and uncoordinated, while the other is behaviorally nearly normal. ------------------- Key: 339 Medline: Authors: Rutherford TA;Croll NA Title: Wave forms of C. elegans in a chemical attractant and repellent and in thermal gradients. Citation: Journal of Nematology 11: 232-240 1979 Type: ARTICLE Genes: Abstract: The wave forms and activity patterns of Caenorhabditis elegans were examined on agar in the presence of known chemical attractants (NaCl) and repellents (D-tryptophan), and in thermal gradients. Total activity was reduced in both attractants and repellents. Different combinations of transfers between chemicals were investigated. Two thresholds were found for NaCl: 10-3 M NaCl caused reduced activity; 10-5 M NaCl increased reversals. D- or L-tryptophan influenced neither orientation nor the ability of thermally acclimatized individuals to remain at their eccritic temperatures. ------------------- Key: 341 Medline: 68245408 Authors: Sayre FW;Fishler MC;Humphreys GK;Jayko ME Title: Growth factor studies; changes in reactivity of sulfhydryl groups with activation. Citation: Biochimica et Biophysica Acta 160: 63-68 1968 Type: ARTICLE Genes: Abstract: Observed changes in the reactivity of the essential sulfhydryl groups of a protein growth factor correlate with changes in its biological activity. In activated and nonactivated growth factor, the maximal number of sulfhydryl groups reacting with parachloromercuribenzoate was the same; while the spatial arrangement of the sulfhydryl groups appeared to differ, as evidenced by their different rates of chemical reaction. It is believed that these changes in sulfhydryl reactivity reflect structural changes in the protein molecule and that these structural changes are responsible for the observed changes in its biological activity. ------------------- Key: 342 Medline: Authors: Sayre FW;Hansen EL;Starr TJ;Yarwood EA Title: Isolation and partial characterization of a growth-control factor. Citation: Nature 190: 1116-1117 1961 Type: ARTICLE Genes: Abstract: A growth-promoting factor in liver extracts has been reported in work on a chemically defined medium for the axenic cultivation of the nematode, Caenorhabditis briggsae. An active fraction has now been isolated from horse liver by salt precipitation and column chromatography. The purified material emerged from the column as a discrete protein peak.... ------------------- Key: 343 Medline: Authors: Sayre FW;Hansen EL;Yarwood EA Title: Biochemical aspects of the nutrition of Caenorhabditis briggsae. Citation: Experimental Parasitology 13: 98-107 1963 Type: ARTICLE Genes: Abstract: In an attempt to establish a biochemical and biological tool of multiple potential, we have sought to define the absolute and limited nutritional requirements of Caenorhabditis briggsae. The following has thus far been done: (1) a chemically defined basal medium has been obtained, which sustains life and partial growth but not reproduction, (2) certain biological supplements, which enable the organism to reproduce, have been comparatively evaluated, (3) unexplained freeze-activation of one such supplement has been observed, and (4) through the use of analogues, preliminary suggestions have been derived regarding the action of certain metabolites. ------------------- Key: 344 Medline: Authors: Sayre FW;Reiko TL;Sandman RP;Perez-Mendez G Title: Studies of a growth factor: Fractionation studies and amino acid composition of derived fractions. Citation: Archives of Biochemistry & Biophysics 118: 58-72 1967 Type: ARTICLE Genes: Abstract: A protein growth factor for the nematode, Caenorhabditis briggsae, has been shown, by means of electrophoretic and chromatographic separations, to exist in multiple active forms. The amino acid composition of nine of these active fractions has been shown to be essentially identical, although they were of differing specific activities. It is proposed that these active forms have basically the same primary chemical structure and that the major differences between them is their molecular size. Biological specific activity appears to increase as molecular size increases. Maximal biological activity of most of these fractions could be demonstrated only after the protein was subjected to an activation process. Activation is believed to result from a reversible conformational change within the protein molecule. ------------------- Key: 345 Medline: 79063843 Authors: Schachat F;Garcea RL;Epstein HF Title: Myosins exist as homodimers of heavy chains: Demonstration with specific antibody purified by nematode mutant myosin affinity chromatography. Citation: Cell 15: 405-411 1978 Type: ARTICLE Genes: unc-54 Abstract: The body-walls of Caenorhabditis elegans contain two different myosin heavy chains that associate to form at least two species of myosin. To better define the distribution of these heavy chains in myosin molecules, we have characterized the myosin of C. elegans by immunochemical methods. Specific, precipitating anti-myosin antibody has been prepared in rabbits using highly purified nematode myosin as the immunogen. The difference in reactivity of the anti-myosin antibody with wild-type myosin containing both kinds of heavy chains (designated unc-54 and non-unc-54 heavy chains on the basis of genetic specification) and myosin from the mutant E190 that lacks unc-54 heavy chains indicates that there are antigenic differences between myosin molecules containing unc-54 heavy chains and myosin molecules containing only non-unc-54 heavy chains. Antibody specific for the unc-54 myosin determinants has been prepared by immunoadsorption of anti-myosin antibody with E190 myosin. This specific anti-unc-54 myosin antibody precipitates myosin that contains only unc-54 heavy chains. At the limits of resolution of our immunoprecipitation techniques, we could detect no heterodimeric myosin molecules containing both unc-54 and non-unc-54 heavy chains. The body-wall myosins of C. elegans therefore exist only as homodimers of either class of heavy chain. This specific anti-unc-54 myosin antibody promises to be a valuable tool in elucidating the role of two myosins in body-wall muscle and in molecular characterizations of mutant myosins in C. elegans. We report here the use of this antibody to detect antigenic differences between unc-54 myosin from the wild-type and the muscle mutant E675. In conjuction with the original anti-myosin antibody, other studies show that both unc-54 and non-unc-54 myosins exist within the same body-wall muscle cells and that both myosins are coordinately synthesized during muscle development in C. elegans. We discuss the implications of the self-association of unc-54 and non-unc-54 myosin heavy chains into homodimeric myosins within the same body-wall muscles with respect to the assembly of thick filaments and their organization into a regular lattice. ------------------- Key: 346 Medline: 77242494 Authors: Schachat FH;Harris HE;Epstein HF Title: Actin from the nematode, C. elegans, is a single electrofocusing species. Citation: Biochimica et Biophysica Acta 493: 304-309 1977 Type: ARTICLE Genes: Abstract: We have purified actin from wild type Caenorhabditis elegans animals by three procedures: a purification dependent on the ability of actin to form F-actin, affinity chromatography which preferentially binds G-actin, and co-precipitation of an actin-myosin complex by antimyosin antibodies. Each preparation yields a single elecrofocusing species of actin. Comparison of actin from C. elegans embryos and animals reveals that embryos also have the same single electrofocusing species of actin. ------------------- Key: 347 Medline: 77183615 Authors: Schachat FH;Harris HE;Epstein HF Title: Two homogeneous myosins in body-wall muscle of C. elegans. Citation: Cell 10: 721-728 1977 Type: ARTICLE Genes: unc-54 Abstract: Myosin purified from the body-wall muscle-defective mutant E675 of the nematode, Caenorhabditis elegans, has heavy chain polypeptides which can be distinguished on the basis of molecular weight. On SDS-polyacrylamide gels, bands are found at 210,000 and 203,000 daltons. This is in contrast to myosin from the wild-type, N2, which has a single heavy chain band at 210,000 daltons. Both heavy chains of E675 are found in body-wall muscle. When native myosin from E675 is fractionated on hydroxyapatite, it is separated into myosin containing predominantly one or the other molecular weight heavy chain and myosin containing a mixture of the heavy chains. Comparison of the CNBr fragments of myosin that contains predominantly 210,000 dalton heavy chains with those that contains predominantly 203,000 dalton heavy chains reveals multiple differences. These differences are not explained by the difference in molecular weight of the heavy chains, but may be explained if each type of heavy chain is the product of a different structural gene. Furthermore, because there are fractions which exhibit >80% 210,000 or >80% 203,000 dalton heavy chain, there is myosin which is homogeneous for each of the heavy chains. Although N2 myosin has only a single molecular weight heavy chain, it too is fractionated by hydroxyapatite. By comparing the CNBr fragments of different myosin fractions, we show that N2, like E675, has two kinds of heavy chains. E190, a body-wall muscle-defective mutant in the same complementation group as E675, is lacking the myosin heavy chain affected by the e675 mutation. This property has allowed us to determine by co-purification of labeled E190 myosin in the presence of excess, unlabeled E675 myosin that most, if not all, of the myosin that contains two different molecular weight heavy chains is due to the formation of complexes between homogeneous myosins and not to a heterogeneous myosin. ------------------- Key: 348 Medline: 78131223 Authors: Schachat FH;Harris HE;Garcea RL;LaPointe JW;Epstein HF Title: Studies on two body-wall myosins in wild type and mutant nematodes. Citation: "Molecular Approaches to Eucaryotic Genetic Systems" ICN-UCLA Symposia on Molecular & Cellular Biology, Volume 8. Wilcox G, Abelson J and Fox CF (eds), Academic Press, NY. 8: 373-380 1977 Type: REVIEW Genes: unc-54 Abstract: Native myosin purified from the wild-type, N2, and a body-wall defective mutant, E675, of the nematode contains two myosins, each homogeneous for different heavy chains. These myosins can be resolved from one another on hydroxyapatite and, when cleavaged with CNBr, they yield different peptide-fragments. In E190, one of the homogeneous myosins is absent. e190 and e675 are alleles of the same gene, unc-54. The myosin lacking in E190 is the same one affected in E675. This suggests that unc-54 is the structural gene for a myosin heavy chain. In order to determine the role of these different myosins, we plan to use antibodies to locate the myosins on thick filaments from body-wall muscle. Additionally, we are studying the patterns of synthesis and degradation of the two myosins in the wild-type and muscle-defective mutants in order to discover how the observed stoichiometry is maintained. ------------------- Key: 349 Medline: 79062367 Authors: Schachat F;O'Connor DJ;Epstein HF Title: The moderately repetitive DNA sequences of C. elegans do not show short-period interspersion. Citation: Biochimica et Biophysica Acta 520: 688-692 1978 Type: ARTICLE Genes: Abstract: In these studies we show that the moderately repetitive DNA sequences of Caenorhabditis elegans are not arranged in the characteristic short-period interspersion pattern of most eukaryotes. Rather, the moderately repetitive sequences are arranged in long arrays as in Drosophila and Apis. These findings indicate that this type of arrangement is more phylogenetically diverse and hence less exceptional than previously believed. ------------------- Key: 350 Medline: Authors: Schmidt GD;Kuntz RE Title: Nematode parasites of Oceanica. XVIII. Caenorhabditis avicola sp. n. (Rhabditidae) found in a bird from Taiwan. Citation: Proceedings of the Helminthological Society of Washington 39: 189-191 1972 Type: ARTICLE Genes: Abstract: Caenorhabditis avicola sp. n. is described from one male and three female nematodes from the intestine of a plumbeous water redstart, Rhyacornis fuliginosus (Passeriformes, Turdidae), from Taiwan. It is characterized by the extension of the anterior margins of the peloderan bursa into sharp points, giving the male posterior end an arrowheadlike shape in ventral view, and by the spicules, which are 95 u long. It is postulated that the worms were pseudoparasites, possibly symbionts of an insect ingested by the bird. ------------------- Key: 351 Medline: Authors: Schneider A Title: "Monographie der Nematoden" Citation: Berlin : 1-357 1866 Type: MONOGR Genes: Abstract: ------------------- Key: 352 Medline: 77115898 Authors: Searcy DG;Kisiel MJ;Zuckerman BM Title: Age-related increase of cuticle permeability in the nematode C. briggsae. Citation: Experimental Aging Research 2: 293-301 1976 Type: ARTICLE Genes: Abstract: The external cuticular surface of nematodes, which resembles cellular membranes in certain ways, appears to deteriorate with age. For example, when the permeabilities to radioactive water of young and old nematodes were compared, and the data were corrected for the different surface:volume ratios, the older nematodes were significantly more permeable. In both living and dead nematodes, the same rates of water exchange were observed, indicating that the major route of exchange was probably by passive diffusion through the cuticle rather than by active processes such as swallowing or excreting water. ------------------- Key: 353 Medline: Authors: Searcy DG;MacInnis AJ Title: Measurements by DNA renaturation of the genetic basis of parasitic reduction. Citation: Evolution 24: 796-806 1970 Type: ARTICLE Genes: Abstract: It has been suggested that parasitic organisms have a simpler genome than their free-living counterparts. Measurements by reciprocal DNA hybridizations in vitro have shown that the parasitic plant Cuscuta californica has a smaller genome than several closely related autotrophic plants. These studies have the shortcoming of detecting only the hybridization of the highly repetitive sequences of DNA; the non-repetitive sequences react too slowly to hybridize significantly under the conditions used. The size of the genome may also be determined by DNA renaturation. Denatured DNA fragments can be made to renature in vitro, forming a specifically base-paired structure as in native DNA. As predicted theoretically, and as confirmed empirically, the rate of renaturation is inversely related to the molecular weight of the entire DNA molecule of phages and bacteria. The DNA of higher organisms renatures faster than would be predicted from the haploid complement of DNA because of the presence of highly repetitive DNA sequences. However, the rate of renaturation of the slowest reacting components can be used to measure the "kinetic complexity" of an organism, which is a measure of the total number of different sequences in the DNA of an organism. The rate of renaturation of the non-repetitive DNA of higher organisms is much slower than the rate with simpler organisms. Some published experiments have taken 20 days. Therefore we modified the conditions so that significant renaturation can be obtained in a much shorter time. Since there are several different ways to plot the data, we will show why we have used the rate plot suggested by Wetmur and Davidson. Measurements on the rates of renaturation of the plant DNA's show that the parasitic plant Cuscuta has a simpler genome than closely related autotrophic plants; these measurements confirm the results of the earlier hybridization studies. Measuring the rate of renaturation has the added advantage that the size of the genome can be determined in units of molecular weights, thus allowing comparisons between distantly related organisms. Our measurements on parasitic and free-living nematodes and flatworms show that a ------------------- Key: 354 Medline: Authors: Singh RN;Sulston JE Title: Some observations on molting in C. elegans. Citation: Nematologica 24: 63-71 1978 Type: ARTICLE Genes: lin-5 lin-6 Abstract: Moulting of Caenorhabditis elegans has been observed by Nomarski interference contrast microscopy, and by electron microscopy of animals at selected stages. The wild type, cell division mutants and animals in which cells had been ablated by a laser microbeam were examined. The median lateral hypodermis, or "seam", is required for the formation of alae and for dauer larva maturation. During cuticle deposition, large Golgi bodies are seen in the seam cells. The excretory system is not essential for moulting. ------------------- Key: 355 Medline: Authors: Smith RM;Peterson WH;McCoy E Title: Oligomycin, a new antifungal antibiotic. Citation: Antibiotics & Chemotherapy 4: 962-970 1954 Type: ARTICLE Genes: Abstract: Although the majority of antibiotics are of interest because of their activity against bacteria, a vigorous search is underway for antifungal agents. This effort stems from the resistance of many animal and plant pathogens to the known antibiotics. As a result of this effort, there are already about 50 well-defined antibiotics that are more or less active against the filamentous fungi, and because of the active search now in progress, many more such agents will undoubtedly be uncovered in the near future. These antibiotics can be classified into three groups based on the microorganisms that produce them. Among bacteria, the genus Bacillus has so far proved the most fruitful source of antibiotics. Examples of such antibiotics are bacillomycin, fungistatin, mycosubtilin, and toximycin. Those that have been sufficiently purified to judge are of polypeptide nature. Antifungal antibiotics derived from fungi are produced by a number of genera. Examples of such antibiotics are alternaric acid, aspergillic acid, gladiolic acid, glutinosin, griseofulvin, patulin, tricothecin, and viridin. The actinomycetes have yielded the largest number of antifungal agents, among them actinomycin, Actidione, antimycin, ascosin, candicidin, endomycin, fradicin, helixin, Rimocidin, and thiolutin. The antifungal antibiotics have not found widespread use because of inherent toxicity or other unfavorable properties. A few have been tried with some success against the agents of plant disease, and it may be in this and other nonmedical fields that they will have their greatest use. The purpose of this paper is to report a presumably new antifungal antibiotic, oligomycin. ------------------- Key: 356 Medline: Authors: Soos A Title: Rhabditis carpathicus spec. nov. eine neue in Sphagnum-Mooren lebende Nematode/ Citation: Fragmenta Faun. Hungarica 4: 115-119 1941 Type: ARTICLE Genes: Abstract: ------------------- Key: 357 Medline: Authors: Spaull VW Title: Qualitative and quantitative distribution of soil nematodes of Signy Island South Orkney Islands. Citation: British Antarctic Survey Bulletin 33: 177-184 1973 Type: ARTICLE Genes: Abstract: ------------------- Key: 358 Medline: Authors: Starck J Title: Radioautographic study of RNA synthesis in C. elegans (Bergerac variety) oogenesis. Citation: Biology of the Cell 30: 181-182 1977 Type: ARTICLE Genes: Abstract: Each of two ovarian tubes of Caenorhabditis elegans represents an extremely simple organization being totally deprived of follicular or nutrient cells and showing a linear progression of the oocytes. In this organ, syntheses take place with a very high rate. At 18C, two eggs are formed in one hour, and the whole volume of the ovary is transformed into eggs every seven hours. Therefore, the metabolism of RNA in this exceptionally active organ deserves to be better known. Until now, only a cytological study with Unna staining has been devoted to this subject. This preliminary work describes the original method of incubation allowing the use of radioactive precursor for RNA synthesis study. ------------------- Key: 359 Medline: Authors: Stromberg BE;Soulsby EJL Title: Heterologous helminth induced resistance to Ascaris suum in Guinea pigs. Citation: Veterinary Parasitology 3: 169-175 1977 Type: ARTICLE Genes: Abstract: The protection inducing capacity of Toxocara canis, Ancylostoma caninum, Haemonchus cortortus, Caenorhabditis briggsae and Turbatrix aceti given via the mesenteric vein to a challenge infection with Ascaris suum was evaluated. Embryonated eggs and second stage larvae of T. canis and infective larvae of A. caninum were able to induce a statistically significant level of protective immunity, while the other nonrelated helminths were unable to protect against a challenge infection. ------------------- Key: 361 Medline: Authors: Sudhaus W Title: Zur Systematik, Verbreitung, Okologie und Biologie neuer und wenig bekannter Rhabditiden (Nematoda) 2. Teil. Citation: Zool. Jb. Syst. Bd. 101: 417-465 1974 Type: ARTICLE Genes: Abstract: Five new species of the genus Rhabditis are described (Rh. riemanni n. sp., Rh. remanei n. sp., Rh. reciproca n. sp., Rh. blumi n. sp., and Rh. valida n. sp.) belonging to five subgenera (Crustorhabditis, Caenorhabditis, Rhabditis, Cephaloboides, and Pellioditis). The descriptions of four additional species are revised (Rh. ocypodis Chitwood, Rh. scanica Allgen, Rh. plicata Volk, and Rh. bengalensis Timm). The new subgenus Crustorhabditis n. subgen. derives from the paraphyletic subgenus Mesorhabditis. The species of the former group show a transition from living in littoral seaweed deposits to an obligate association with amphibious crabs (Crustacea). Information about the distribution, ecology, biology and ethology of all these species is presented (with two distribution maps, one for Rh. marina for comparison). Supplementary notes are given from Protorhabditis oxyuroides Sudhaus and Rhabditis tripartita von Linstow. ------------------- Key: 362 Medline: Authors: Sukul NC;Croll NA Title: Influence of potential difference and current on the electrotaxis of C. elegans. Citation: Journal of Nematology 10: 314-317 1978 Type: ARTICLE Genes: Abstract: C. elegans responds directionally to a DC current. The response may be to the anode or cathode, depending on the current, potential difference, and ionic concentration of KCl. Tracks of the responding nematodes show that electrotaxes are genuine orientation phenomena. The directional movement is not due to the passive movement of nematodes or to the influence of currents on the muscular physiology; electrotaxes are mediated sensorily. Details of the response are described. ------------------- Key: 363 Medline: 76269912 Authors: Sulston JE Title: Post-embryonic development in the ventral cord of C. elegans. Citation: Philosophical Transactions of the Royal Society of London 275B: 287-298 1976 Type: ARTICLE Genes: nuc-1 Abstract: 56 nerve cells are added to the ventral cord and associated ganglia of Caenorhabditis elegans at about the time of the first larval moult. These cells are produced by the uniform division of 13 neuroblasts followed by a defined pattern of cell deaths. Comparison with the data in the previous paper suggests that there is a relationship between the ancestry of a cell and its function. The significance of programmed cell death is discussed. ------------------- Key: 364 Medline: 74271162 Authors: Sulston JE;Brenner S Title: The DNA of C. elegans. Citation: Genetics 77: 95-104 1974 Type: ARTICLE Genes: Abstract: Chemical analysis and a study of renaturation kinetics show that the nematode, Caenorhabditis elegans, has a haploid DNA content of 8 X 10(7) base pairs (20 times the genome of E. coli). Eighty-three percent of the DNA sequences are unique. The mean base composition is 36% GC; a small component, containing the rRNA cistrons, has a base composition of 51% GC. The haploid genome contains about 300 genes for 4S RNA, 110 for 5S RNA, and 55 for (18 + 28)S RNA. ------------------- Key: 365 Medline: 76025558 Authors: Sulston J;Dew M;Brenner S Title: Dopaminergic neurons in the nematode Caenorhabditis Citation: Journal of Comparative Neurology 163: 215-226 1975 Type: ARTICLE Genes: cat-1 cat-2 cat-3 cat-4 cat-5 flu-4 unc-18 unc-51 Abstract: Dopamine is the putative transmitter of eight neurons in the hermaphrodite form of the nematode Caenorhabditis elegans. These include the cephalic and deirid neurons, which are believed to be mechanosensory. The male has an additional six dopaminergic neurons in the tail. Mutants have been selected which have defects in the formaldehyde induced fluorescence and lack dopamine to varying degrees, but they are not insensitive to touch. The dopaminergic neurons of C. elegans are compared with the homologous neurons in Ascaris lumbricoides. ------------------- Key: 366 Medline: 77116565 Authors: Sulston JE;Horvitz HR Title: Post-embryonic cell lineages of the nematode, Caenorhabditis elegans. Citation: Developmental Biology 56: 110-156 1977 Type: ARTICLE Genes: Abstract: The number of nongonadal nuclei in the free-living soil nematode Caenorhabditis elegans increases from about 550 in the newly hatched larva to about 810 in the mature hermaphrodite and to about 970 in the mature male. The pattern of cell divisions which leads to this increase is essentially invariant among individuals; rigidly determined cell lineages generate a number of progeny cells of strictly specified fates. These lineages range in length ------------------- Key: 367 Medline: Authors: Tattar TA;Stack JP;Zuckerman BM Title: Apparent nondestructive penetration of C. elegans by microelectrodes. Citation: Nematologica 23: 267-269 1977 Type: ARTICLE Genes: Abstract: Free-living nematodes are sometimes used as models for fundamental studies of biological problems such as aging, genetics and behavior. In these it would be advantageous if measured amounts of drugs, nematicides or other substances could be introduced into parts of nematodes. One possibility is injection by a glass microcapillary inserted through the cuticle. However, nematodes have a high turgor pressure and when the body is pierced the nematode usually bursts. We report penetration of Caenorhabditis elegans (Maupas) without apparent harm. ------------------- Key: 368 Medline: 76043799 Authors: Tilby MJ;Moses V Title: Nematode ageing. Automatic maintenance of age synchrony without inhibitors. Citation: Experimental Gerontology 10: 213-223 1975 Type: ARTICLE Genes: Abstract: A technique is described for the continuous growth of an age-synchronized population of Caenrohabditis elegans. After initial isolation of newly hatched individuals from a mixed age culture, synchrony through the reproductive phase was sufficiently well maintained to ensure that over 90% of the post-reproductive population belonged to the original generation. The technique is based on culturing the nematodes on the upper surface of a fine stainless steel mesh through which only larvae, but not adults, are small enough to burrow. It largely overcomes serious disadvantages of the two previously used methods for maintaining synchrony which were based on the use of inhibitors or the manipulation of individual worms. Supplementary techniques are described for the handling and initial synchronization of the worms which are cultured in a sterile completely defined medium. General features of the development and senescence of the worms under our conditions are reported. Mean life span (50% survival) was approx. 58 days and maximum longevity in excess of 80 days. Reproduction lasted from the 5th to about the 26th day of age and its termination coincided with a short period of high mortality. Growth in size of the worms ceased during the reproductive period but recommenced for about 25 days in worms surviving the post-reproductive mortality. ------------------- Key: 369 Medline: Authors: Tiner JD Title: A preliminary in vitro test for anthelminthic activity. Citation: Experimental Parasitology 7: 292-305 1958 Type: ARTICLE Genes: Abstract: The rate of discovery of new anthelmintics has increased but little during the past two decades. The same interval has been characterized by accelerated progress in chemotherapy, and especially by the appearance of various and diverse antibiotics discovered with in vitro screening tests. Lamson and Brown (1936) stated that both in vitro and in vivo anthelmintic tests aid in determining the probable action of chemicals in the host. Subsequently, in vivo tests have been increasingly emphasized by helminthologists, even for the initial evaluation of untried substances. Steward discussed screening methods, and described a preliminary test using rats doubly infected with intestinal and caecal nematodes. Choices of methods by various investigators have been influenced by an assumption that the antinematode activity of phenothiazine is detectable only in vivo, but this assumption is no longer entirely tenable. Anthelmintic tests should be sensitive enough to permit recognition of inhibitors of single vital enzymes. An ideal test would require only minute quantities of chemicals for titration against representative species and stages of the more economically important parasites. The present paper describes a procedure that begins to meet these requirements. It consumes less than 10 mg of each substance, and one operator can process about 100 samples per month. Phenothiazine serves as a standard of reference if developing trichostrongyle nematodes are utilized as test organisms. That chemical is characterized by a general ineffectiveness against members of the nematode subfamily Rhabditinae, together with a high toxicity for embryos and ------------------- Key: 371 Medline: Authors: Tomlinson GA;Rothstein M Title: Nematode Biochemistry I. Culture Methods. Citation: Biochimica et Biophysica Acta 63: 465-470 1962 Type: ARTICLE Genes: Abstract: A simple procedure has been developed by which the nematode Caenorhabditis briggsae can be routinely grown and handled in sufficient numbers for biochemical studies. Culture of the nematode was carried out in media based on either soy-peptone or soy-peptone-yeast extract, both supplemented with liver extract. ------------------- Key: 372 Medline: Authors: Turner RH;Green CD Title: Preparation of biological material for scanning electron microscopy by critical point drying from water miscible solvents. Citation: Journal of Microscopy 97: 357-363 1973 Type: ARTICLE Genes: Abstract: Nematodes and mildew-infected barley leaves when examined in the scanning electron microscope after critical point drying (CPD) from sulphur dioxide (critical temperature 157.7C) showed no obvious physical damage, but the specimens had a surface deposit which was probably heat damaged natural waxes. The nematode Caenorhabditis elegans and clover roots (Trifolium subterraneum) showed no physical or heat damage after CPD from monochlorodifluoromethane (Freon 22, critical temperature 96C). The hyphae and conidia of unfixed mildew on barley were damaged after CPD from Freon 22, probably due to the Freon extracting lipids from the cell walls. Freon 22 was preferred for most specimens as it is cheap, easy to get ------------------- Key: 373 Medline: 76140558 Authors: Vanderslice R;Hirsh D Title: Temperature-sensitive zygote defective mutants of C. elegans. Citation: Developmental Biology 49: 236-249 1976 Type: ARTICLE Genes: zyg-1 zyg-2 zyg-3 Abstract: Three generally complementing temperature-sensitive mutants of Caenorhabditis elegans have been studied. Each of the three mutants has two critical times of temperature sensitivity and two distinct corresponding phenotypes. Exposure to high temperature during gonadogenesis blocks the production of zygotes. Exposure of adults to high temperature interrupts embryogenesis of the zygotes being produced. Each of the mutants carries an autosomal mutation with a maternal effect. These mutants indicate that the individual temperature-sensitive functions are required at least twice during development and that early embryogenesis is dependent on the contribution of these functions from the maternal gonad. ------------------- Key: 374 Medline: Authors: Vanfleteren JR Title: Amino acid requirements of the free-living nematode C. briggsae. Citation: Nematologica 19: 93-99 1973 Type: ARTICLE Genes: Abstract: Washed yeast ribosomes promote growth and reproduction of C. briggsae, even when supplemented to the basal medium at dosages too low to provide the organisms with sufficient amounts of essential amino acids. Hence, a re-investigation of the amino acid requirements of C. briggsae by single and multiple omission of amino acids from the basal medium revealed unambiguously that arginine, histidine, lysine, tryptophan, phenylalanine, methionine, threonine, leucine, isoleucine and valine are not synthesized at levels to permit reproduction; they are called essential amino acids. The requirement for arginine and isoleucine however appears to be less clear-cut. On the contrary, evidence is presented that alanine, asparagine, cysteine, glutamate, glutamine, glycine, proline, serine and tyrosine can be synthesized at adequate levels; they are called non-essential amino acids. In addition it was shown that multiple omission of the non-essential amino acids in not deleterious. This is believed to be an important step towards the development of a minimum essential medium (MEM) for growth and ------------------- Key: 375 Medline: 74132550 Authors: Vanfleteren JR Title: Nematode growth factor. Citation: Nature 248: 255-257 1974 Type: ARTICLE Genes: Abstract: Free-living nematodes, grown axenically in a chemically defined medium, might be of considerable interest as model systems for studying the fundamental aspects of genetics and differentiation of higher organisms. Several species of free-living nematodes have been cultured serially in axenic media. Unfortunately, the chemically defined medium in current use, Caenorhabditis briggsae Maintenance Medium (CbMM), does not support continuous growth unless supplemented with a 'growth factor' that can be derived from various biological sources. ------------------- Key: 376 Medline: Authors: Vanfleteren JR Title: The nature of a nematode growth factor I. Growth and maturation of C. briggsae on ribonucleoprotein particles. Citation: Nematologica 21: 413-424 1975 Type: ARTICLE Genes: Abstract: The biological activity of ribonucleoprotein (RNP) particles from yeast, E. coli, mammalian liver, HeLa cells and pea seedlings on maturation and reproduction of the free-living nematode Caenorhabditis briggsae has been evaluated. RNP particles from yeast, E. coli, mammalian liver and HeLa cells are biologically highly active. The minimum doses permitting maturation and reproduction within 7 days were 3.4, 13, 9.8, and 3.2 ug protein/ml respectively. The addition of haemin chloride at a final concentration of 10 ug/ml did not improve biological activity. RNP particles from E. coli, washed with 1M salt were inactive. Pea seedling particles were inactive, but became active upon addition of haemin chloride to the medium. It is assumed that the activity of RNP preparations is due to a contaminating haem protein. ------------------- Key: 377 Medline: Authors: Vanfleteren JR Title: The nature of a nematode growth factor II. Growth and maturation of C. briggsae on haem proteins. Citation: Nematologica 21: 425-437 1975 Type: ARTICLE Genes: Abstract: The growth promoting activity of cytochrome c, catalase, haemiglobin, myoglobin, horse radish peroxidase, yeast L-lactate dehydrogenase and cytochrome c reductase on maturation and reproduction of Caenorhabditis briggsae has been evaluated. Cytochrome c, catalase, haemiglobin, myoglobin, and horse radish peroxidase were biologically active when properly precipitated. The biological activity of horse radish peroxidase (assayed as the peroxidase-antiperoxidase immunoprecipitate) was greatly increased upon addition of haemin to the medium. This is easily explained on the assumption that much haem could have been split off from the protein during the activation treatment. Yeast L-lactate dehydrogenase and cytochrome c reductase did not contain sufficient amounts of haem after the activation treatment. They were inactive in haemin lacking basal medium, but highly active in basal medium supplemented with haemin. These experiments support the idea that the third and so far unknown component (the other components being sterols and haem) of the growth factor complex is not a protein of particular nature, but rather any convenient vector for the haem component. ------------------- Key: 378 Medline: Authors: Vanfleteren JR Title: The nature of a nematode growth factor. III. Growth and maturation of C. briggsae on protein-haemin Citation: Nematologica 22: 103-112 1976 Type: ARTICLE Genes: Abstract: The growth promoting activity of protein-haemin co-precipitates from ferritin, apoferritin, transferrin, bovine serum albumin, conalbumin and egg white on maturation and reproduction of C. briggsae has been evaluated. Ferritin, apoferritin and transferrin were found to be biologically highly active in the presence of haemin. Bovine serum albumin, conalbumin and egg white were slightly active. Maturation and reproduction of C. briggsae on the coagulates from bovine serum albumin and egg white were nearly independent of the dose administered, probably because the limited availability of haemin from these coagulates permits but slow growth, even in the presence of abundant proteinaceous material. Bovine serum albumin, egg white and conalbumin failed to support continuous growth of C. briggsae. It is supposed that the limited availability of haemin from these coagulates inhibits normal maturation and reproduction of the F1 progeny. These experiments clearly demonstrate the requirement for particulate haem. The requirement for ------------------- Key: 379 Medline: 76257725 Authors: Vanfleteren JR Title: Large scale cultivation of a free-living nematode (C. elegans). Citation: Experientia 32: 1087-1088 1976 Type: ARTICLE Genes: Abstract: A method is presented for the large scale cultivation of the free-living nematode Caenorhabditis elegans, using continuous aeration and agitation in glass ware (stirrer flasks) developed for the continuous culture of suspended cells. With this technique, populations up to 10e9 nematodes may be obtained in a 10 l culture in less than 6 weeks with an inoculum of some 50 worms. Costs can be reduced by using an inexpensive yeast extract, available from the food industry. ------------------- Key: 380 Medline: Authors: Vanfleteren JR Title: Axenic culture of free-living, plant-parasitic, and insect-parasitic nematodes. Citation: Annual Review of Phytopathology 16: 131-157 1978 Type: REVIEW Genes: Abstract: Two excellent reviews, one of them recent, are available on the axenic culture of nematodes. Therefore, the present article is mainly an outline of the present state of nematode culture research and is limited to surveying reports that have a significant bearing on our understanding of nematode growth in axenic culture. The first section covers nutritional requirements with special attention to the material needed for growth and reproduction in repeated subculture. Since nematode nutrition has largely been studied on the free-living nematode Caenorhabditis briggsae, I first scrutinize the dietary requirements of this species and extend our knowledge to other nematodes in axenic culture thereafter. In particular, I demonstrate how a general understanding of the nature of the growth factor emerges from a discriminatory analysis of existing knowledge and I support this concept with experimental evidence; also I attempt to reconcile this concept with some older as well as more recent controversial findings. The next section is devoted to culture methodology and covers some new techniques that render nematodes convenient as model organisms for scientific research. Throughout this review I use the terminology proposed by Dougherty for describing culture conditions with respect to the number of coexisting species and the different degrees of chemical differentiation of the media. The term axenic means free of contaminating organisms and supersedes the less suitable adjectives sterile or aseptic. Monoxenic cultures contain one additional species or tissue (e.g. alfalfa callus tissue), dixenic two and so on. Species that are studied in xenic cultures are reared in interaction with several unidentified organisms. Media that are chemically undefined are called oligidic. Those consisting of a defined basal portion and a less defined supplement are meridic. Holidic media are fully defined and contain ------------------- Key: 381 Medline: 77246411 Authors: Vanfleteren JR;Avau H Title: Selective inhibition of reproduction in aminopterin-treated nematodes. Citation: Experientia 33: 902-904 1977 Type: ARTICLE Genes: Abstract: Aminopterin was applied to the free-living nematode Caenorhabditis briggsae and subsequent growth was recorded. Nematode populations, containing all developmental stages and selected juvenile stages, were exposed to the drug in both growth-promoting and non-promoting media. It is suggested that aminopterin creates a specific requirement for thymine in thymine-free medium. In otherwise growth-promoting medium, aminopterin-induced thymine deficiency will lead to progressively unbalanced growth and maturation and hence to sterility even after removal of the drug. The omission of essential amino acids from the medium during thymine starvation prevents larval growth and results in better reproduction and faster proliferation in animopterin-free medium. The 4 juvenile stages exhibit a different response to thymine starvation created by aminopterin. ------------------- Key: 382 Medline: 89337642 Authors: Vanfleteren JR;Neirynck K;Huylebroeck D Title: Nematode chromosomal proteins-I. Isolation of chromatin and preliminary characterization of the chromosomal proteins of C. elegans. Citation: Comparative Biochemistry & Physiology 62B: 349-354 1979 Type: ARTICLE Genes: Abstract: 1. A procedure is described which gives clean chromatin preparations from the free-living nematode Caenorhabditis elegans. It involves homogenization using glass beads, collection of the precipitate from a low speed centrifugation, removal of cell membranes with Triton X- 100, several washes with 0.14 M NaCl, sucrose density gradient centrifugation, a cycle of extraction and reprecipitation using dilute Tris buffer and 0.14 M NaCl respectively, and final extraction of the purified deoxyribonucleoprotein in 10 mM Tris-HCl (pH 8). 2. Acidic urea gel electrophoresis of the histones from C. elegans yielded 4 main groups which were preliminary identified as H1, H2a (+ H3?), H2b, H4 and moved on the gels in that order of increasing mobility. the coincidence of histone H3 with H2a was putative, but its presence was firmly suggested by the generation of a dimeric form in oxidizing conditions. 3. By SDS-Tris-glycine gel electrophoresis of the non-histone chromosomal proteins of C. elegans, about 18 proteins were distinguished with molecular weights ranging from 15,000 to 100,000 daltons. ------------------- Key: 383 Medline: Authors: Vanfleteren JR;Roets DE Title: The influence of some anthelmintic drugs on the population growth of the free-living nematodes C. briggsae and Turbatrix aceti (Nematoda: Rhabditida). Citation: Nematologica 18: 325-338 1972 Type: ARTICLE Genes: Abstract: Drugs with specific and intensive toxicity to nematodes, termed nematicides, might be suitable for the isolation of nematicide-resistant mutants. For this purpose, several medical anthelmintics, namely ascaridol, bephenium, d-tubocurarine chloride, piperazine adipate, piperazine hydrate, phenothiazine, n-hexylresorcinol, dithiazanine iodide, pyrvinium pamoate and thiabendazole have been tested for their influence on the population growth of Caenorhabditis briggsae and Turbatrix aceti. Ascaridol, bephenium, d-tubocurarine chloride, piperazine adipate, piperazine hydrate, phenothiazine and n-hexylresorcinol were shown to have a small to moderate toxicity. The effect of thiabendazole on population growth of C. briggsae is moderate, but its action on T. aceti is intense. Finally, dithiazanine iodide and pyrvinium pamoate are very toxic to both nematodes. It is concluded that dithiazanine iodide, pyrvinium pamoate and thiabendazole (restricted to T. aceti) might be suitable for the isolation of resistant ------------------- Key: 385 Medline: Authors: von Ehrenstein G Title: A model system for developmental biology and behavioral genetics. Citation: Jahrbuch der Max-Planck-Gesellschaft : 38-60 1973 Type: REVIEW Genes: Abstract: In German. ------------------- Key: 386 Medline: Authors: Wahab A Title: Untersuchungen uber Nematoden in den Drusen des Kopfes der Ameisen (Formicidae). Citation: Zeitschrift fur Morphologie und Oekologie der Tiere 52: 33-92 1962 Type: ARTICLE Genes: Abstract: ------------------- Key: 387 Medline: 73209591 Authors: Ward S Title: Chemotaxis by the nematode C. elegans: Identification of attractants and analysis of the response by use of mutants. Citation: Proceedings of the National Academy of Sciences USA 70: 817-821 1973 Type: ARTICLE Genes: bli-1 bli-4 unc-23 Abstract: The nematode Caenorhabditis elegans is attracted by at least four classes of attractants: by cyclic nucleotides, cAMP and cGMP; by anions, Cl-, Br-, I-; by cations, Na+, Li+, K+, Mg+; and by alkaline pH values. The nematode's behavioral response to gradients of these attractants involves orientation and movement up the gradient, accumulation, and then habituation. Comparison of the tracks of wild-type and mutant animals responding to gradients of attractants indicates that sensory receptors in the head alone mediate the orientation response and that the direction of orientation is determined by the lateral motion of the head. Therefore, the orientation response is ------------------- Key: 388 Medline: Authors: Ward S Title: The use of mutants to analyze the sensory nervous system of C. elegans. Citation: "The Organization of Nematodes." Croll NA (ed), Academic Press, NY. : 365-382 1976 Type: REVIEW Genes: che-1 che-2 che-3 mec-1 sma-1 unc-23 unc-52 Abstract: The isolation of behavioural mutants of an organism can provide a variety of strains that are somehow altered in normal neural function. By physiological, anatomical, and biochemical analysis of such alterations it should be possible to correlate the behavioural defect with an underlying neurological defect. From such correlations, the functional role of the defective elements of the nervous system can be deduced. For such analysis the mutations can be thought of as a dissecting tool used to cut parts of the nervous system to determine the behavioural consequences of such cuts. Pursuit of the underlying defects in behavioural mutants leads rapidly beyond just the analysis of neural function. One is let to ask what kinds of cuts are made by the genetic dissecting tool? What alterations in a nervous system can be introduced by single gene mutations? How did the defective gene product cause such an alteration? Such questions about the genetic specification of the development of the nervous system may also be approached by the study of behavioural mutants. In this chapter, I will first illustrate some of the ways that behavioural mutants of Caenorhabditis elegans can be used to study the function of the sensory nervous sytem and then show how the anatomical analysis of such mutants leads to questions about neural ------------------- Key: 389 Medline: 78079173 Authors: Ward S Title: Invertebrate neurogenetics. Citation: Annual Review of Genetics 11: 415-450 1977 Type: REVIEW Genes: Abstract: In 1967, Benzer demonstrated that phototactic mutants in Drosophila melanogaster could be induced and readily isolated by countercurrent selection. This demonstration stimulated further experimentation in selection and characterization of behavioral mutants in inbred organisms. In the ten years since Benzer's paper, hundreds of mutants altering the nervous system have been identified and studied, not only in Drosophila, but also in nematodes, protozoa, crickets, mice, and other organisms. This review describes recent studies of such mutants and attempts to assess the current status of this genetic approach to neurobiological problems...... ------------------- Key: 390 Medline: Authors: Ward S Title: Use of nematode behavioral mutants for analysis of neural function and development. Citation: "Approaches to the Cell Biology of Neurons" Society for Neuroscience Symposia, Vol. II Sixth Annual Meeting, Toronto, Nov. 1976. Cowan WM and Ferrendelli JA (eds), Society for Neuroscience. : 1-26 1977 Type: REVIEW Genes: che-1 che-2 che-3 mec-1 unc-23 Abstract: The soil nematode Caenorhabditis elegans was selected 11 years ago by Sydney Brenner as an experimental organism suitable for the isolation of many behavioral mutants and small enough for anatomical analysis of such mutants with the electron microscope. Two distinct goals motivated the initial studies of this organism: first, the hope that some of the mutants would have simple anatomical alterations that could be directly correlated with their behavioral defects, allowing the assignment of specific functions to specific neurons, and second, the hope that the detailed analysis of the kinds of alterations induced by individual mutations and the classes of cells affected by given mutations would reveal general features of the genetic program that specifies the development of the organism. Over the past 11 years the number of investigators working on C. elegans has increased to about 75 and is still growing. Nearly 3,000 different mutants have been isolated and different investigators are pursuing their effects on different cells. My own research is in the development of the nervous system. In particular, I would like to learn something about the workings of the complex black box that connects individual genes to the determination of the morphology of developing neurons. Are there gene products whose specific function is to determine the morphology of cells? If so, what are these gene products and how do they act in the developing cell? One would anticipate that mutations in such hypothetical genes would cause specific morphological alterations in cells. Because the morphology of a neuron determines its function, by selecting behavioral mutants altered in the function of the nervous system one might commonly find mutants that alter the morphology of neurons, and some of these might be in specific morphological genes. It is my hope that it will be possible to compare such mutants to the wild type in order to identify the defective gene products and thereby learn something about the role of normal gene products in determining the development of neurons. In this paper I will first summarize the results of several years' work on one specific class of mutants in the nematode, sensory mutants, work performed both in my laboratory and that of my colleagues Jim Lewis and Jonathan Hodgkin. Second, I will discuss frankly some of the difficulties and frustrations we have experienced in trying to interpret the effects of these specific mutants. Some of these difficulties illustrate problems endemic to genetic studies of development. Third, I will describe the more recent work performed in my labortory that is being directed toward genetic analysis of the structure and function of a ------------------- Key: 391 Medline: Authors: Ward S Title: Nematode chemotaxis and chemoreceptors. Citation: "Receptors and Recognition Series B. Taxis and Behavior. Elementary Sensory Systems in Biology." Hazelbauer GL (ed), Halsted Press, Wiley NY. : 141-168 1978 Type: REVIEW Genes: che-1 che-3 unc-23 Abstract: A small sightless worm crawling among particles of soil and decaying vegetation must have a variety of chemical senses to locate bacteria for food and to avoid poisons and predators. What chemicals are sensed? How many different kinds of receptor molecules are there? On which neurons are the receptors located? How sensitive are these neurons? How is the detection of a chemical communicated to the worm's central nervous system and converted into a behavioral response? All of these questions have been addressed in studies of the soil nematode Caenorhabditis elegans. This organism has recently become the subject of intensive genetic, behavioral and anatomical studies. The behavior that has been examined in most detail is chemotaxis. This chapter will review what is known about C. elegans chemotaxis and will present a number of new observations. The results will be interpreted in terms of a specific model of chemoreceptor function. The problem of analysis of central nervous system processing of chemosensory neuron information will be discussed briefly. ------------------- Key: 392 Medline: 80047624 Authors: Ward S;Carrel JS Title: Fertilization and sperm competition in the nematode C. elegans. Citation: Developmental Biology 73: 304-321 1979 Type: ARTICLE Genes: fem-1 fer-1 Abstract: The process of fertilization by hermaphrodite and male sperm is described. In the hermaphrodite fertilization occurs in the spermatheca by the first sperm to contact the oocyte. Other sperm that contact the oocyte are swept into the uterus but they crawl back into the spermatheca to fertilize subsequent oocytes so that every sperm fertilizes an oocyte. Not every oocyte is fertilized because oocytes are made in excess. Fertilization triggers active movement of oocyte cytoplasmic granules. Sperm penetration is not required for this activation because fertilization-defective mutant sperm trigger activation without penetration. When males copulate with hermaphrodites, their sperm is deposited in the uterus beneath the vulva. These sperm crawl up the uterus to the spermatheca where they displace the hermaphrodite sperm from the spermathecal walls and preferentially fertilize the oocytes. This preferential fertilization appears to be due in part to inhibition of hermaphrodite sperm fertility by the male sperm. The male sperm competition ensures male sperm utilization and thus some outcrossing in a population ------------------- Key: 393 Medline: 78149180 Authors: Ward S;Miwa J Title: Characterization of temperature-sensitive, fertilization-defective mutants of the nematode C. elegans. Citation: Genetics 88: 285-303 1978 Type: ARTICLE Genes: che-1 fer-1 Abstract: The isolation and characterization of three Caenorhabditis elegans temperature-sensitive mutants that are defective at fertilization are described. All three are alleles of the gene fer-1. At the restrictive temperature of 25C, mutant hermaphrodites make sperm and oocytes in normal numbers. No oocytes are fertilized, although they pass through the spermatheca and uterus normally. The oocytes can be fertilized by sperm transferred by wild-type males, indicating that the mutant defect is in the sperm. The temperature-sensitive period for the mutants coincides with spermatogenesis. Sperm made by mutants at 25C cannot be distinguished from wild-type sperm by light microscopy. The sperm do contact oocytes in mutant hermaphrodites, but do not fertilize. Mutant sperm appear to be nonmotile. Mutant males are also sterile when grown at 25C. They transfer normal numbers of sperm to hermaphrodites at mating, but these sperm fail to migrate to the spermatheca and are infertile. The phenotype of these mutants is consistent with a primary defect in sperm motility, but the cause of this defect is not known. ------------------- Key: 394 Medline: 75095932 Authors: Ward S;Thomson N;White JG;Brenner S Title: Electron microscopical reconstruction of the anterior sensory anatomy of the nematode C. elegans. Citation: Journal of Comparative Neurology 160: 313-337 1975 Type: ARTICLE Genes: Abstract: The complete structure of the anterior sensory nervous system of the small nematode C. elegans has been determined by reconstruction from serial section electronmicrographs. There are 58 neurons in the tip of the head. Fifty-two of these are arranged in sensilla. These include six inner labial sensilla, six outer labial sensilla, four cephalic sensilla and two amphids. Each sensillum consists of ciliated sensory neurons ending in a channel enclosed by two non-neuronal cells, the sheath and socket cells. The amphidial channel opens to the outside as does that of the inner labial sensilla so that these probably contain chemoreceptive neurons. The endings of the other sensilla are embedded in the cuticle and may be mechanoreceptive. The cell bodies of all neurons lie near the nerve ring and their axons project into the ring or into ventral ganglia. One of the ciliated sensory neurons in each of the six inner labial sensilla makes direct chemical synapses onto a muscle making these sensory-motor neurons. The anatomy of four isogenic animals was compared in detail and found to be largely invariant. The anatomy of juveniles is nearly identical to that of the adult, but males have four additional neuron processes. ------------------- Key: 395 Medline: Authors: Ware RW;Clark D;Crossland K;Russell RL Title: The nerve ring of the nematode C. elegans: Sensory input and motor output. Citation: Journal of Comparative Neurology 162: 71-110 1975 Type: ARTICLE Genes: Abstract: The general organization and structure of the nerve ring, the main mass of central nervous system neuropil, in the small soil nematode Caenorhabditis elegans is described. The nerve ring receives sensory input from the anterior tip of the animal by means of six nerve bundles, all nerve fibers of which have centrally located cell bodies. The anterior sensory structures are classically divided into two types, papillary and amphidial, and are assumed responsible for mechano- and chemoreception, respectively. Papillary fibers enter directly into the nerve ring, whereas amphidial fibers enter the ventral ganglion, a posterior extension of the nerve ring, in a circuitous manner which is not discussed in detail. Of those papillary fibers which project into the nerve ring neuropil, 22 end in easily characterized sensory structures whereas 14 terminate distally near sensory organs but have no function which can be deduced on the basis of comparative morphology. After entering the ring the fibers maintain their identity and do not anastamose with one another. Cell bodies of each papillary sensory neuron have been mapped around the nerve ring. The cephalic musculature is shown to consist of 32 muscle cells which form four longitudinal submedial groups of eight muscles each. Innervation of this musculature occurs wholly within the CNS by means of processes of the muscle cells which are sent centrally. The anterior 16 cephalic muscle cells are innervated by the ring only, in well delimited regions termed muscle plates. The posterior 16 are dually innervated by means of processes sent both to the nerve ring plates and to their nearest medial longitudinal nerve cord. The nerve ring neuropil is characterized as having fibers containing one of four morphologically distinct vesicle types. Gap junction contacts are observed within the main neuropil involving one of these fiber types and within the muscle plate regions among muscle processes, which do not contain vesicles. An evolutionarily primitive sensory-motor synapse within the nerve ring is described from an identified sensory neuron onto an identifed cephalic muscle cell process. Comparisons are made with the nervous system of Ascaris lumbricoides, the only other nematode to be extensively studied, to illustrate the ------------------- Key: 397 Medline: 79032165 Authors: Waterston RH;Brenner S Title: A suppressor mutation in the nematode acting on specific alleles of many genes. Citation: Nature 275: 715-719 1978 Type: ARTICLE Genes: cat-1 dpy-18 nuc-1 sup-5 Abstract: A suppressor mutation has been isolated in Caenorhabditis elegans through reversion analysis of a muscle-defective mutant. The suppressor mutation acts on specific alleles of at least six genes and in one case we have been able to show that it partially restores functional gene product to a mutant otherwise lacking that product. These and other features of the suppressor suggest that it acts at some step in information transfer, perhaps through mechanisms similar to those described previously in microorganisms. ------------------- Key: 398 Medline: 75116749 Authors: Waterston RH;Epstein HF;Brenner S Title: Paramyosin of C. elegans. Citation: Journal of Molecular Biology 90: 285-290 1974 Type: ARTICLE Genes: Abstract: Paramyosin has been isolated from the nematode, Caenorhabditis elegans. Its identity has been established by a variety of criteria, including purification, molecular weight, immunological cross reactivity with known paramyosin and formation of characteristic paracrystals. The presence of paramyosin in both pharyngeal and body-wall musculature was shown by a technique that allows analysis by sodim dodecyl sulphate gels of the protein in a single worm. The possibility of defining the role of paramyosin in the structure and function of the invertebrate muscle through the isolation of mutants in this protein is ------------------- Key: 399 Medline: 78132937 Authors: Waterston RH;Fishpool RM;Brenner S Title: Mutants affecting paramyosin in C. elegans. Citation: Journal of Molecular Biology 117: 679-697 1977 Type: ARTICLE Genes: unc-15 Abstract: Four mutants of Caenorhabditis elegans with abnormal muscle structure are described which are alleles of a single locus unc-15. In one of the mutants, E1214, paramyosin is completely absent from both body-wall and pharyngeal musculature. In the other three mutants paramyosin is present but does not assemble into thick filaments. Instead paramyosin paracrystals are formed in the body-wall muscle cells. Myosin filaments lacking paramyosin cores are present in all four mutants, but these filaments fail to integrate stably into the myofilament lattice. One mutant is temperature-sensitive; all four are semi-dominant in their effect on muscle structure. The hypothesis that unc-15 is the structural gene for paramyosin is discussed. ------------------- Key: 400 Medline: 74297483 Authors: Watson JE;Pinnock CB;Stokstad ELR;Hieb WF Title: A nephelometer for measurement of nematode populations. Citation: Analytical Biochemistry 60: 267-271 1974 Type: ARTICLE Genes: Abstract: A nephelometer for measuring nematode populations is described in which a standard 18 mm culture tube is illuminated from below, and four selenium photocells are placed radially at 90 degrees about the tube. This design minimizes fluctuations in readings due to movement of the nematodes at low population densities. ------------------- Key: 401 Medline: 78114101 Authors: White JG;Albertson DG;Anness MAR Title: Connectivity changes in a class of motoneurone during the development of a nematode. Citation: Nature 271: 764-766 1978 Type: ARTICLE Genes: lin-6 Abstract: The ventral nerve cord of the nematode Caenorhabditis elegans contains a linear array of motoneurones which innervate the body muscles that mediate locomotion. The adult ventral cord has about three times as many cells as that of the first stage larva. The development events that generate the adult complement of cells occur in a period preceding the first larval moult. During this period we find that a class of pre-existing, juvenile motoneurones changes its pattern of connectivity. Neuromuscular junctions are removed from ventral muscles and are reformed onto dorsal muscles. Similarly the dendritic input to these neurones changes over from the dorsal to the ventral side. The structure and connectivity of ventral cord motoneurones in adult hermaphrodites has been determined by serial section reconstruction of electron micrographs. The salient features of the structure are summarised below: ------------------- Key: 402 Medline: 76269914 Authors: White JG;Southgate E;Thomson JN;Brenner S Title: The structure of the ventral nerve cord of C. elegans. Citation: Philosophical Transactions of the Royal Society of London 275B: 327-348 1976 Type: ARTICLE Genes: Abstract: The nervous system of Caenorhabditis elegans is arranged as a series of fibre bundles which run along internal hypodermal ridges. Most of the sensory integration takes place in a ring of nerve fibres which is wrapped round the pharynx in the head. The body muscles in the head are innervated by motor neurones in this nerve ring while those in the lower part of the body are innervated by a set of motor neurones in a longitudinal fibre bundle which joins the nerve ring, the ventral cord. These motor neurones can be put into five classes on the basis of their morphology and synaptic input. At any one point along the cord only one member from each class has neuromuscular junctions. Members of a given class are arranged in a regular linear sequence in the cord and have non-overlapping fields of motor synaptic activity, the transition between fields of adjacent neurones being sharp and well defined. Members of a given class form gap junctions with neighbouring members of the same class but never to motor neurones of another class. Three of the motor neurone classes receive their synaptic input from a set of interneurones coming from the nerve ring. These interneurones can in turn be grouped into four classes and each of the three motor neurone classes receives its synaptic input from a unique combination of interneurone classes. The possible developmental and functional significance of these ------------------- Key: 403 Medline: Authors: Wilson PAG Title: Nematode growth patterns and the moulting cycle: the population growth profile. Citation: Journal of Zoology 179: 135-151 1976 Type: ARTICLE Genes: Abstract: Population growth profiles of Caenorhabditis elegans and Panagrellus redivivus constructed from length frequencies have a number of steps in them coinciding with the number of extrauterine moults. Each step has a constant size in relationship with that of one of the midmoults measured directly. The profiles could only have the shape they do if there are corresponding steps in the true growth curve of individual worms: the fact that previous workers have been unable to detect these steps being due to the limitations of techniques available for the study of synchronous and individual growth curves. Nevertheless, a synchronous system with Trichostrongylus retortaeformis gives qualitative support to the findings from population profiles. The population growth profile is a new tool in the study of environmental effects on moulting, though there are theoretical reasons why the true growth curve cannot be derived from it. Abandonment of the "continuous growth" model for post-embryonic development simplifies the framing of hypotheses to explain ecdysis in nematodes. ------------------- Key: 404 Medline: 78220824 Authors: Wolf N;Hirsh D;McIntosh JR Title: Spermatogenesis in males of the free-living nematode, C. elegans. Citation: Journal of Ultrastructure Research 63: 155-169 1978 Type: ARTICLE Genes: Abstract: We have studied the morphology of spermatogenesis in the free-living nematode Caenorhabditis elegans with the light and electron microscopes. The gonad of the adult male is a single, reflexed cylindrical structure containing all stages of spermatogenesis arranged in a single wave of development. The primary spermatocytes are at the end of the gonad most distal from its opening into the cloaca. In this region, the cells are syncytial, and there is a central core containing cytoplasm common to all the neighboring cells, an organization reminiscent of the ovary in the hermaphrodite. Moving towards the cloaca one encounters the stages of meiotic prophase. At diplotene and diakinesis the cells contain many Golgi complexes. Some of these Golgi complexes are associated with an urn-shaped vesicle with a dark amorphous collar about its neck. Other Golgi complexes are seen next to aggregates of microfilaments. These "fibrous bodies" become enveloped with a flattened vesicle that forms a boundary two membranes thick. After these two structures have grown in size, their membranes fuse to form a composite structure. The membranes at the site of fusion then develop dark-staining thickenings as they fold into convoluted sacs and tubes. At about this time, the cells go through the two meiotic divisions. At telophase II the composite structures and fibrous bodies cluster at the spindle poles and cleavage furrows not only separate the daughter cells, but they also slough off a substantial volume of cytoplasm. In the resulting spermatid the nucleus condenses to form the small mass of dark-staining chromatin characteristic of sperm. The microfilaments of the fibrous bodies now disappear while the membranes of the composite structures continue to fold. The texture of the cytoplasm becomes more dense and now contains numerous slender, wavy tubular elements. A part of each composite structure now fuses with the plasma membrane of the sperm to make an almost spherical invagination of extracellular space partially filled by the tortuous bits of membrane-bound cytoplasm ------------------- Key: 405 Medline: Authors: Wood WB Title: Summary of workshop on nematodes. Citation: "Molecular Approaches to Eucaryotic Genetic Systems" ICN-UCLA Symposia on Molecular & Cellular Biology, Volume 8. Wilcox G, Abelson J and Fox CF (eds), Academic Press, NY. 8: 357-358 1977 Type: NEWS Genes: Abstract: The workshop on nematodes presented current research from four laboratories on the development and physiology of C. elegans. ------------------- Key: 406 Medline: Authors: Wright DJ;Awan FA Title: Acetylcholinesterase activity in the region of the nematode nerve ring: Improved histochemical specificity using ultrasonic pretreatment. Citation: Nematologica 22: 326-331 1976 Type: ARTICLE Genes: Abstract: Panagrellus redivivus, Caenorhabditis elegans, Prionchulus punctatus, Aphelenchus avenae and Ditylenchus dipsaci were stained for cholinesterase activity using the 'direct-colouring' thiocholine method. Enzyme activity was concentrated in the region of the nerve ring in each species. Ultrasonic pretreatment of intact or cut nematodes was found to greatly improve the staining consistency at the nerve ring, and using two substrates (acetylthiocholine and butyrylthiocholine) and three inhibitors (eserine, BW 284C51, and iso-OMPA) this staining was found to be due to acetlycholinesterase (E.C. 3.1.1.7) ------------------- Key: 407 Medline: Authors: Yarwood EA;Hansen EL Title: Dauer larvae of Caenorhabditis briggsae in axenic culture. Citation: Journal of Nematology 1: 184-189 1969 Type: ARTICLE Genes: Abstract: The free-living hermaphroditic nematode, Caenorhabditis briggsae, enters a dauer stage under certain conditions in axenic culture. Dauer larvae differ from directly-developing third-stage larvae in internal structure, size at time of second molt, morphology of second and third cuticles, separation zone of cuticular caps, and survival at 4C and 37C, temperatures fatal to other stages. Males, which occur rarely in liquid medium, may mature under conditions which cause most of the hermaphrodites to go into the dauer stage, resulting in a culture with increased male-to-hermaphrodite ratio. ------------------- Key: 409 Medline: Authors: Zuckerman BM Title: The effects of procaine on aging and development of a nematode. Citation: "Theoretical Aspects of Aging." Rockstein M (ed), Academic Press, NY. : 177-186 1974 Type: REVIEW Genes: Abstract: The free-living nematode, Caenorhaditis briggsae, is being used in our laboratory to study the complex events associated with biological aging. Our approach to this problem involved first the defining of parameters characterizing senescence in this animal, and then evaluating the effects on these aging signs of a drug reported to have a modifying effect on some aspects of the aging processes. Reference in this report to this preparation, Gerovital H3 (2% procaine hydrochloride, 0.16% benzoic acid, 0.14% potassium metabisulfite, buffered to pH 3.3 from Rom-Amer Pharmaceuticals, Ltd., Beverly Hills, California) is by its active ingredient, "Procaine". ------------------- Key: 410 Medline: Authors: Zuckerman BM Title: Nematodes as models for aging studies. Citation: "The Organization of Nematodes." Croll NA (ed), Academic Press, NY. : 211-241 1976 Type: REVIEW Genes: Abstract: ------------------- Key: 411 Medline: 78168994 Authors: Zuckerman BM;Barrett KA Title: Effects of P-chlorophenoxy acetic acid and dimethylaminoethanol on the nematode C. briggsae. Citation: Experimental Aging Research 4: 133-139 1978 Type: ARTICLE Genes: Abstract: Concentrations of 6.8 mM DMAe did not retard age pigment accumulation in Caenorhabditis briggsae. However, when the nematodes were exposed to 6.8 mM PCA + 6.8 mM DMAE combined, the accumulation of age pigment was significantly retarded. A combination of 3.4 mM DMAE + 3.4 mM PCA had no effect on age pigment. It is concluded from this study that PCA and DMAE act in concert to produce the observed effect on age pigment. In respect to this parameter neither molecule was effective alone. The results indicate that the effect of centrophenoxine on age pigment might be enhanced by retarding the hydrolysis of centrophenoxine. The accumulation of electron dense aggregates, thought to be aggregates of cross-linked molecules, was reduced by 6.8 PCA + 6.8 DMAE. It is suggested that centrophenoxine be tested for its ability to remove random, unwanted cross-linkages in higher animals. ------------------- Key: 412 Medline: Authors: Zuckerman BM;Castillo JM;Deubert KH;Gunner HB Title: Studies on a growth supplement for C. briggsae from freeze-dried bacteria. Citation: Nematologica 15: 543-549 1969 Type: ARTICLE Genes: Abstract: Freeze-dried bacteria isolated from Panagrellus redivivus, contained a growth supplement that initially supported rapid growth and reproduction of Caenorhabditis briggsae. However, after four serial subcultures, the nematodes became sluggish and eventually died. Evidence is given that C. briggsae utilizes the bacterial cell as a food source, thereby showing that the bacterium-nematode relation is not one of mutualism. ------------------- Key: 415 Medline: Authors: Zuckerman BM;Himmelhoch S;Kisiel M Title: Fine structure changes in the cuticle of adult C. briggsae with age. Citation: Nematologica 19: 109-112 1973 Type: ARTICLE Genes: Abstract: The cuticle of young, adult Caenorhabditis briggsae contains seven layers. In old nematodes fine structure changes related to aging were observed in two layers. The outer osmiophilic membrane became more defined and in a few cases separated from the external cortical layer. Also, an electron-dense material and electron-dense balls occurred within the fluid-filled layer. The possible significance of these observations is discussed. ------------------- Key: 417 Medline: Authors: Zuckerman BM;Himmelhoch S;Nelson B;Epstein J;Kisiel M Title: Aging in C. briggsae. Citation: Nematologica 17: 478-487 1971 Type: REVIEW Genes: Abstract: Caenorhabditis briggsae was used as a model to study aging of a metazoan under gnotobiotic conditions. At higher temperatures nematodes were shorter-lived and had a shorter generation time. Nematodes moved more slowly as they aged. Physiologic aging was marked by a decreased ability to withstand osmotic stress, a possible increase in the body's internal solute concentration, and increased sensitivity to formaldehyde. These results suggest that the ability to osmoregulate and the permeability of the body wall are altered during senescence. The interchordal hypodermis, as well as the chordal hypodermis, contained fairly abundant structures having biosynthetic activity. During aging mitochondria of the hypodermis degenerated, some areas of the thin hypodermal band thickened and lysosome-like bodies formed in the interchordal hypodermis. Changes in osmoregulatory and excretory mechanisms are probably associated with deterioration of hypodermis organelles. ------------------- Key: 419 Medline: 79191599 Authors: Zuckerman BM;Kahane I;Himmelhoch S Title: C. briggsae and C. elegans: Partial characterization of cuticle surface carbohydrates. Citation: Experimental Parasitology 47: 419-424 1979 Type: ARTICLE Genes: Abstract: The presence of galactose, glucose, mannose, and N-acetylglucosamine on the exposed surface of the nematodes Caenorhabditis briggsae and C. elegans was indicated by specific binding of three iodinated plant lectins. Proteolysis experiments suggested the absence of digestible glycoproteins on the exposed surfaces of the two nematode species. High resolution micrographs of cuticle surface preparations labeled with cationized ferritin indicated that the negative charge-bearing molecules are more densely packed on the nematode surface than on animal plasma membranes. ------------------- Key: 420 Medline: Authors: Zuckerman BM;Nelson B;Kisiel M Title: Specific gravity increase of C. briggsae with age. Citation: Journal of Nematology 4: 261-262 1972 Type: ARTICLE Genes: Abstract: The specific gravity of old Caenorhabditis briggsae was shown to be greater than that of young nematodes. The possible explanations for this age-associated change are discussed. ------------------- Key: 422 Medline: 79136487 Authors: Cortese R;Melton D;Tranquilla T;Smith JD Title: Cloning of nematode tRNA genes and their expression in the frog oocyte. Citation: Nucleic Acids Research 5: 4593-4611 1978 Type: ARTICLE Genes: Abstract: Transfer RNA genes of the nematode Caenorhabditis elegans have been cloned in E. coli using the plasmid Col E1 as vector. The tRNAs coded by 3 hybrid plasmids were purified by hybridisation of labelled nematode tRNA with the plasmid DNAs. Each plasmid appears to code for a single distinct tRNA species. The expression of the cloned DNAs was analysed in vivo by injection into nuclei of Xenopus laevis oocytes. Evidence is presented which suggests that these nematode tRNA genes are accurately transcribed and processed in frog oocytes. Analysis of one hybrid plasmid shows that a 300 base pair DNA fragment contains both the structural gene and those regions required for its transcription in vivo. The results show that cloned eukaryotic DNAs from a heterologous source can be tested for functional gene activity in X. laevis oocytes. ------------------- Key: 424 Medline: Authors: Cassada RC Title: The dauer larva of C. elegans: A specific developmental arrest, inducible environmentally and genetically. Citation: "Developmental Biology: Pattern Formation and Gene Regulation." McMahon DM and Fox CF (eds), WA Benjamin. : 539-547 1975 Type: ARTICLE Genes: Abstract: In the development of the nematode, Caenorhabditis elegans, a recognizable, non-growing stage, the dauerlarva, may arise. It is formed in response to adverse environmental conditions including starvation by an arrest just before the second of four cuticle molts. A quantitative assay for dauerlarva based on their resistance to sodium dodecyl sulfate has been developed. Resistance requires both non-feeding and an especially impermeable cuticle, containing a paracrystalline proteinaceous sheet 1600-1800 A thick. Quantitave, synchronous recovery to normal development can be induced by transfer to fresh medium with excess food; there is a soluble, heat-stable arrest factor in starved cultures. Using the resistance property, mutants have been selected that conditionally (temperature-sensitivity) enter the dauerlarva state even when food is abundant. ------------------- Key: 425 Medline: 80090059 Authors: Melton DA;Cortese R Title: Transcription of cloned tRNA genes and the nuclear partitioning of a tRNA precursor. Citation: Cell 18: 1165-1172 1979 Type: ARTICLE Genes: Abstract: The transcription of transfer RNA genes (tDNAs) and processing of the transcripts have been studied by injecting cloned tDNAs into Xenopus oocyte nuclei. Three main conclusions can be drawn. First, eucaryotic nuclear tRNA genes, but neither procaryotic nor mitochondrial tRNA genes, are expressed in injected oocytes. While both nematode and yeast tDNAs direct the synthesis of authentic tRNAs, neither E. coli tDNA nor human mitochondrial tDNAs support the synthesis of defined tRNAs when injected into oocytes. Second, competition experiments with co-injected 5S genes and inhibition experiments with a-amanitin show that injected tDNAs are transcribed by RNA polymerase III. Third, oocytes injected with a nematode tDNA synthesize a tRNA precursor which is processed post-transcriptionally by removal of a 5' leader sequence. This precursor is found exclusively in the nucleus and is processed in the nucleus before the mature tRNA enters the cytoplasm. ------------------- Key: 426 Medline: 80180014 Authors: Wood WB;Hecht R;Carr S;Vanderslice R;Wolf N;Hirsh D Title: Parental effects and phenotypic characterization of mutations that affect early development in C. elegans. Citation: Developmental Biology 74: 446-469 1980 Type: ARTICLE Genes: emb-7 emb-9 zyg-1 zyg-2 zyg-3 zyg-5 zyg-7 zyg-8 zyg-9 zyg-10 zyg-11 zyg-12 zyg-13 Abstract: Genetic tests for parental effects were performed on 24 temperature-sensitive embryonic-lethal mutants of the nematode Caenorhabditis elegans. For 21 of these mutants, maternal expression of the wild-type allele is sufficient for embryonic survival, regardless of the embryo's genotype. For 11 of these 21 mutants, maternal expression of the wild-type allele is necessary for embryonic survival (strict maternals). For the remaining 10, either maternal or embryonic expression is sufficient for survival (partial maternals). One mutant shows a paternal effect; that is, a wild-type extragenic sperm function appears to rescue homozygous mutant embryos. Similar parental-effect tests were performed on 11 larval-lethal mutants. In 4 mutants, 1 of which blocks as late as the second larval stage after hatching, maternal contributions still can rescue mutant larvae. The remaining 3 embryonic lethals and 8 larval lethals show no parental effects; that is, zygotic expression of the wild-type allele is necessary and sufficient for embryonic survival. Temperature-shift experiments on embryonic-lethal embryos showed that all but 1 of the strict maternal mutants are temperature sensitive only before gastrulation. One of the partial maternal mutants is temperature sensitive prior to gastrulation, suggesting that some zygotic genes can function early in embryogenesis. At the nonpermissive temperature, 7 of the strict maternal mutants either show cleavage abnormalities in early divisions or stop cleavage at less than 100 cells, or both. ------------------- Key: 427 Medline: 81261881 Authors: Rose AM;Baillie DL Title: Genetic organization of the region around unc-15(I), a gene affecting paramyosin in C. elegans. Citation: Genetics 96: 639-648 1980 Type: ARTICLE Genes: dpy-14 dpy-24 let-75 let-77 let-78 let-79 let-80 let-81 let-82 let-83 let-84 let-85 let-86 let-87 let-88 let-89 let-90 mec-8 unc-13 unc-15 unc-29 unc-37 unc-87 Abstract: In the nematode Caenorhabditis elegans mutants in the gene unc-15 (I) affect the muscle protein paramyosin (Waterston, Fishpool and Brenner 1977). We have characterized 20 ethyl methanesulfonate-induced mutations in essential genes closely linked to unc-15. These lethals defined 16 new complementation groups. In the 0.65 map-unit interval around unc-15 defined by dpy-14 and unc-56, seven newly identified genes have been mapped relative to five existing genes. At present, the average distance between genes in this region is approximately 0.05 map units. Two genes, unc-15 and unc-13, are only 0.025 map units apart. Partial fine-structures maps of alleles of these two genes have been constructed. This analysis of unc-15 and genes adjacent to it is the first in a series of genetic and biochemical studies directed towards understanding the control of unc-15 expression. ------------------- Key: 429 Medline: Authors: Kampfe L Title: The consumption of oxygen by nematodes as a characteristic of zootic activity. Citation: Pedobiologica 18: 355-365 1978 Type: ARTICLE Genes: Abstract: The features of respiration in soil-inhabiting nematodes are discussed and some autecological findings on the respiratory rate under normal conditions and those with deviating O2-partial pressure are compiled. Lack of oxygen leads to different reactions by the inhabitants of variable hatitats. They also show a different utilization of their reserve substances. The respiratory quotient differs in the species under consideration, it may change during starvation. Considering the consumption of oxygen the investigations known on the bioenergetic role of nematodes in soil are discussed. Conversions show clues to the catabolism of protein by nematodes per hectare and per year. The values fluctuate between 43 and 250 kg protein ha-1 year-1. The difficulties in these estimations are pointed out. Finally a reference is made to the fact that the respiratory efficiency of nematodes is influenced by the presence of pesticides in the medium. The effects of the new generation of systemic nematicides are particularly interesting because of their relatively small influence on the free-living soil nematodes which is the consequence of the relatively slight immediate efficacy. Herbicides do not seem to be without any effect on the soil nematode ------------------- Key: 430 Medline: Authors: Brun J;Abdulkader N;Abirached M;Beguet B;Gibert M-A;Mounier N;Starck J;Bosch C Title: Controle genetique de la gametogenese et de la differenciation ovocytaire chez C. elegans, souche Citation: Ann. Rep. Univ. CB/Lyon Fr : 25-43 1978 Type: ARTICLE Genes: Abstract: ------------------- Key: 431 Medline: Authors: Hansen EL;Yarwood EA;Nicholas WL;Sayre FW Title: Differential nutritional requirements for reproduction of two strains of Caenorhabditis elegans in axenic culture. Citation: Nematologica 5: 27-31 1959 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans (Maupas) has been maintained in axenic culture for more than three years. Two separate isolations, one in France and one in England, have been made and are here designated as Bergerac strain and Bristol strain respectively. Although morphologically similar and successfully crossed by Nigon, the two strains have shown different cultural requirements. This difference was first observed in 1958, using a supplemented chemically defined medium, and has now been investigated in a wider range of media. ------------------- Key: 432 Medline: 71034132 Authors: Hansen EL;Perez-Mendez G Title: Large scale preparation of liver growth factor for cultivation of nematodes. Citation: Proc. Society for Experimental Biology & Medicine 135: 487-489 1970 Type: ARTICLE Genes: Abstract: Cultivation of metazoa under bacteria-free conditions is valuable for biochemical and nutritional studies and avoids the complexity introduced by associated organisms. For such studies the nematode has particular advantages. Investigation of the nutritional requirements of the free-living nematode Caenorhabditis briggsae led to the development of a chemically defined medium which required addition of a low level of an organic supplement to obtain continued reproduction. One very effective supplement is a partially purified protein designated growth factor (GF). This has been used in the culture of free-living nematodes and parasitic helminths. GF was originally prepared by a slow, laborious, stepwise elution from hydroxylapatite columns. In the present paper a rapid, efficient "batch" technique is described. Using this new method, batches yielding more than 2 g of GF have been prepared easily in a day. ------------------- Key: 433 Medline: Authors: Hirsh D Title: Temperature sensitive maternal effect mutants of early development in C. elegans. Citation: "Determinants of Spatial Organization" Meeting, Society for Developmental Biology, Madison, WI June 1978. Subtelny S and Konigsberg IR (eds), Academic Press, NY. : 149-166 1979 Type: REVIEW Genes: emb-7 emb-9 zyg-1 zyg-2 zyg-3 zyg-7 zyg-8 zyg-9 zyg-10 zyg-12 Abstract: We have isolated temperature sensitive maternal effect mutants in the free-living nematode Caenorhabditis elegans. We use C. elegans for several basic reasons. It is easy to culture in the laboratory and it has a rapid life cycle. The genetics of C. elegans have been elucidated by Brenner and more recently have been refined by the lethal analysis of Herman et. al. Both embryonic and postembryonic development can be observed directly and conveniently on the living worm with Nomarski differential interference optics because egg shell and worm cuticle are transparent. The precise embryonic cell lineages of C. elegans are known from fertilization to the 200 blastomere stage. All of the postembryonic somatic cell lineages are precisely known. It ... ------------------- Key: 434 Medline: Authors: Kunz P;Klingler J Title: A method for direct or microscopic observation and photography of nematode tracks during orientation behaviour studies. Citation: Nematologica 22: 477-479 1976 Type: ARTICLE Genes: Abstract: Considerable progress in the study of orientation behaviour of nematodes was achieved as soon as their tracks could be made visible on agar surfaces from which the free water had evaporated.... ------------------- Key: 435 Medline: Authors: Laskey R;Lawrence P;De Robertis E Title: Genes in development. Citation: Nature 270: 477-478 1977 Type: NEWS Genes: Abstract: Participants in two days of talks held at the Accademia Lincei in Rome-the oldest scientific foundatin in the modern world, tried to tackle the ancient problem of how eggs plus genes produce animals. It was symptomatic of the renewed interest in Drosophila that the whole of the first day was devoted to that fly... ------------------- Key: 436 Medline: Authors: MacLeod AR;Karn J;Waterston RH;Brenner S Title: The unc-54 myosin heavy chain gene of C. elegans: A model system for the study of genetic suppression in higher eukaryotes. Citation: "Nonsense Mutations and tRNA Suppressors" Proc. EMBO Lab Course & Aarhus Univ. 50 Yr. Anniv. Symp. July 1978. Celis CE and Smith JD (eds), Academic Press, London. : 301-312 1979 Type: ARTICLE Genes: unc-54 Abstract: The small free living soil nematode Caenorhabditis elegans, has been the subject of genetical and other studies in this laboratory for several years. Mutants have been isolated in many genes affecting its morphology and behaviour and a considerable amount is now known about its cellular anatomy and development. A subset of mutants with defective movement have severe alterations in the structure of body wall muscle cells. There are 95 muscle cells disposed in four quadrants which run the length of the animal beneath the cuticle. The musculature is obliquely striated and the sarcomeres are oriented parallel to the long axis of the animal. Disruption of the band structure can easily be detected in the living animal by polarized light microscopy and the defects can be more carefully analysed by electron microscopy. Two of the ten genes with altered muscle phenotypes have been shown to specify major structural proteins of muscle; unc-54 codes for a major heavy chain of mysoin, while unc-15 codes for paramyosin, the core protein of the thick filaments. As work with these genes developed, it became evident that it might be possible to use them as models for studying gene-protein relationships in a multicellular higher organism. This notion has been reinforced by the isolation of a large number of suppressors in the organism, some of which suppress specific alleles of the myosin and para-myosin genes. Although the molecular mechanism of these suppressors are unknown, it will be seen that their detailed study can now ------------------- Key: 437 Medline: 80046643 Authors: Popham JD;Webster JM Title: Cadmium toxicity in the free living nematode C. elegans. Citation: Environmental Research 20: 183-191 1979 Type: ARTICLE Genes: Abstract: The effect of cadmium on the fecundity, growth, and fine structure of the free-living nematode Caenorhabditis elegans was studied. High concentrations of cadmium significantly decreased the fecundity and growth of these organisms. Electron microscopy showed that cadmium modifies the structure of the mitochondria in the esophagus and intestine, causes the formation of inclusion bodies in the nucleus of esophageal cells, and alters the morphology of cytosomes in the intestinal cells. The results suggest that the decreased fecundity and growth of cadmium-exposed C. elegans may be due to cadmium interfering with nutrient uptake or assimilation or both. ------------------- Key: 438 Medline: 79010541 Authors: Smith SJ Title: The structural gene for myosin, a closer look. Citation: Nature 272: 495-496 1978 Type: REVIEW Genes: unc-54 Abstract: The humble soild nematode Caenorhabditis elegans has proved a useful tool for the extension of the study of gene-protein relationships from prokaryotic to eukaryotic organisms. A variety of uncoordinated (unc) mutants can be isolated by their behavioral characteristics, and electron micrographs show that such mutations are associated with disorganisation of muscle structure. One such mutant of the unc-54 gene (e675) has a normal amount of myosin but the number of thick filaments (myosin-containing ------------------- Key: 439 Medline: Authors: Sulston JE;Hodgkin J Title: A diet of worms. Citation: Nature 279: 758-759 1979 Type: NEWS Genes: sup-5 sup-7 unc-15 unc-22 unc-54 Abstract: Five years ago Brenner published an extensive genetic characterisation of the small free-living nematode Caenorhabditis elegans. Largely as a result of his pioneering work, this organism has become the subject of many different lines of research. Last May more than 120 researchers met at Cold Spring Harbor to discuss recent findings in C. elegans biology. ------------------- Key: 440 Medline: Authors: von Ehrenstein G;Schierenberg E;Miwa J Title: Cell lineages of wild type and temperature sensitive embryonic arrest mutants of C. elegans. Citation: "Cell Lineage, Stem Cells and Cell Determinations." Le Douarin N (ed), Elsevier, NY. : 49-58 1979 Type: REVIEW Genes: emb-1 emb-2 emb-3 emb-4 emb-5 emb-6 emb-7 emb-8 emb-9 Abstract: Caenorhabditis elegans, a free-living nematode, is the subject of intensive genetic and developmental studies. Embryogenesis in C. elegans, like other nematodes, is strictly determinate and virtually invariant among individuals. The newly hatched juvenile has only about 550 cells arranged quite predictably. Postembryonic development is also quite regular and the number of nongonadal cells increases to only about 810 in the adult hermaphrodite. Here we will summarize results of embryonic cell lineage studies in our laboratory including the wild type and temperature-sensitive embryonic arrest mutants. We will also compare the developmental mechanisms of C. elegans to those of higher animals, and speculate about the possible role of histones in the timing of cell divisions in embryogenesis. ------------------- Key: 442 Medline: 80145768 Authors: Zengel JM;Epstein HF Title: Mutants altering coordinate synthesis of specific myosins during nematode muscle development. Citation: Proceedings of the National Academy of Sciences USA 77: 852-856 1980 Type: ARTICLE Genes: unc-52 unc-54 Abstract: Mutations in the unc-52 gene on linkage group II retard the construction of body-wall muscle sarcomeres during larval development in the nematode Caenorhabditis elegans. Unc-52 mutants show decreased accumulation of myosin heavy chains relative to other polypeptides during larval development, correlating with the structural retardation. Pulse radiolabeling experiments show that decreased synthesis of specific body-wall myosin heavy chains that are encoded by the unc-54 gene on linkage group I is responsible for the defective myosin accumulation. In the wild type, a constant ratio of the synthesis of the unc-54-coded myosin B to myosin A, about 2:1, is maintained during the larval stages in which the synthesis of both myosins increases exponentially and rapid sarcomere growth and addition ensues. During the first 26 hr of larval development, before any structural or behavioral effects of unc-52 mutations are apparent, the synthesis of myosin heavy chains is also normal. By 38 hr, decreased synthesis of myosin B is detected in the unc-52 mutant SU200, when sarcomere growth slows considerably. The effects of mutations in the unc-52 locus are trans acting upon the synthesis of unc-54-coded myosin in a specific set of muscle cells during a defined period of larval development. ------------------- Key: 443 Medline: Authors: Herman RK;Horvitz HR;Riddle DL Title: The nematode Caenorhabditis elegans. Citation: Genetic Maps 1: 183-193 1980 Type: REVIEW Genes: Abstract: ------------------- Key: 444 Medline: Authors: Kimble J;Sulston J;White J Title: Regulative development in the post-embryonic lineages of C. elegans. Citation: "Cell Lineage, Stem Cells and Cell Determinations." Le Douarin N (ed), Elsevier, NY. : 59-68 1979 Type: ARTICLE Genes: lin-1 lin-2 mab-5 Abstract: In many invertebrates, cell lineages are apparently invariant from individual to individual. A given precursor cell follows a specific pattern of cell divisions, and its descendants follow fates that correspond to their respective positions in the lineage tree. Such a reproducible sequence of events provides an excellent system for studying how cells come to pursue particular fates during development. We have been interested to know if a cell's fate is specified by factors intrinsic to the cell, or if it is influenced by interactions between the cell and its environment. C. elegans is a particularly suitable organism for lineage studies because it is transparent throughout its life cycle, and because it consists of relatively few cells. Furthermore, C. elegans is a favorable organism for genetics, so the control of cell lineages can be studied by characterizing mutations that are defective in known lineages. The cell lineages of C. elegans have been described in the embryo to the 182 cell stage and after hatching. Approximately 50 cells resume divisions post-embyronically. In the somatic tissues, the number of cells (or nuclei) is increased from about 550 to about 950 in hermaphrodites and to about 1025 in males. These post-embryonic lineages are essentially invariant from worm to worm. As the worm enlarges and matures sexually, cells (or nuclei) are added to previously existing tissues (hypodermis, muscle, gut, and nervous system), and structures necessary for reproduction are elaborated. The latter include a gonad in both sexes, a vulva in hermaphrodites, and a tail specialized for copulation in males. This paper summarizes the results of laser ablation experiments performed on cells in the post-embryonic lineages of C. elegans. In particular, we focus on those experiments that demonstrate a regulative capacity in the cells of this predominantly invariant system. The post-embyronic lineages have the practical advantage for these studies that they can be traced by direct observation of the cells as they divide and assume their final fate. The regulative response, therefore, can be described at a level of cellular detail that has not been possible in other deletion studies. Our aim in performing these experiments is to infer how cells are controlled during normal development from their behavior in ------------------- Key: 445 Medline: Authors: White JG;Horvitz HR Title: Laser microbeam techniques in biological research. Citation: Electro-Optical Systems Design AUG: 23-24 1979 Type: ARTICLE Genes: Abstract: Microirradiation has been used as a tool for probing cells and subcellular organelles for the last fifty years. It is possible with good, high numerical aperture optics to obtain spot sizes of less than 1 um, which allows microsurgery to be performed at the cellular and subcellular levels. Valuable information has been obtained in this way concerning the functions of various cellular ------------------- Key: 446 Medline: Authors: Hirsh D;Emmons SW;Files JG;Klass MR Title: Stability of the C. elegans genome during development and evolution. Citation: "Eucaryotic Gene Regulation" ICN-UCLA Symposia on Molecular and Cellular Biology, Volume 14. Axel R, Maniatis T and Fox CF (eds), Academic Press, NY. 14: 205-218 1979 Type: ARTICLE Genes: Abstract: Recombinant DNA methods have been used to characterize the genome of Caenorhabditis elegans. To determine if DNA rearrangements occur during somatic differentiation, fifteen randomly cloned Bam H1 fragments of somatic DNA were hybridized to Bam H1 digests of germ and somatic DNA's on Southern filters. In this way, 50 fragments representing 0.3% of the genome were compared and no size differences were detected. The DNA's of two interbreeding strains of C. elegans were also compared to determine the degree of evolutionary divergence. Fifteen percent of the fragments differed between the two strains. However, no differences could be found between the rDNA's. The DNA's of C. elegans and C. briggsae were compared and very little homology could be detected even though these species are morphologically very similar. The fragments that differ in size between the two interbreeding strains are being genetically mapped. These experiments suggest that non-random segregation of chromosomes might be occurring in ------------------- Key: 447 Medline: 80132495 Authors: Nelson GA;Ward S Title: Vesicle fusion, pseudopod extension and amoeboid motility are induced in nematode spermatids by the ionophore monensin. Citation: Cell 19: 457-464 1980 Type: ARTICLE Genes: fer-2 him-5 Abstract: The sodium- and potassium-transporting ionophore monensin induces the maturation of Caenorhabditis elegans spermatids to spermatozoa in vitro. Rearrangement of cytoplasm, fusion of membranous organelles with the plasma membrane and growth of pseudopodia, all characteristic of in vivo spermiogenesis, occur within five minutes after exposure to monensin at concentrations of 0.1-1.0 micronM. This activation is dependent upon external Na+ and K+ ions but not Ca2+ ions. Monensin-activated spermatozoa have normal morphology and normal amoeboid motility. During activation spermatids twitch and rotate prior to pseudopod extension. Analysis of intermediates by transmission and scanning electron microscopy reveals that the sequence of morphogenetic events leading from the spherical spermatid to the polarized spermatozoan involves microvilli rearrangement and membranous organelle fusion, cytoplasmic polarization, then pseudopod extension. ------------------- Key: 448 Medline: 80202192 Authors: Schierenberg E;Miwa J;von Ehrenstein G Title: Cell lineages and developmental defects of temperature-sensitive embryonic arrest mutants in C. elegans. Citation: Developmental Biology 76: 141-159 1980 Type: ARTICLE Genes: emb-1 emb-2 emb-3 emb-4 emb-5 emb-6 emb-7 emb-8 emb-9 Abstract: The cellular phenotypes of 11 temperature-sensitive mutants (emb-1 - emb-9) arresting in embryogenesis in Caenorhabditis elegans are described, including early embryonic cell lineages and developmental defects and the terminal phenotypes at the stage of arrest at the nonpermissive temperature (25C), as well as residual phenotypes at the permissive temperature (16C). By Nomarski microscopy of living embryos, the behavior of individual cells in mutant embryos is compared to that of the same cells in wild-type embryos. All mutants but one (emb-9) have visible defects before the 50-cell stage, even if they arrest much later. Cell proliferation continues in the absence of normal morphogenesis. The terminal phenotype of the late-arresting mutants looks grossly abnormal. The overall rate of cell division is faster than in the wild-type in two mutants, emb-3 and emb-5(hc67), and slower in five mutants, emb-2, emb-4, emb-5(hc61), emb-6 and emb-7. In five of these mutants, emb-3, emb-4, emb-5 (both alleles), and emb-7, the rate and the sequence of divisions of specific cell lines is altered. For all mutants with timing defects, maternal gene expression is at least sufficient. Gastrulation is abnormal in the two emb-5 mutants. A premature division of the intestine precursor cells occurs in close temporal coincidence with the defective execution stage (determined by temperature-shift experiments). The order of migration and division of the intestine precursor cells is reversed in gastrulation, and the cell pattern of the intestine primordium is abnormal. It seems possible that the timing error is responsible for the pattern defect. The cleavage behavior of emb-3 eggs indicates that germ line ------------------- Key: 449 Medline: 80202194 Authors: Miwa J;Schierenberg E;Miwa S;von Ehrenstein G Title: Genetics and mode of expression of temperature-sensitive mutations arresting embryonic development in C. elegans. Citation: Developmental Biology 76: 160-174 1980 Type: ARTICLE Genes: emb-1 emb-2 emb-3 emb-4 emb-5 emb-6 emb-7 emb-8 emb-9 Abstract: Eleven temperature-sensitive mutations causing arrest of embryogenesis in Caenorhabditis elegans have been mapped. The mutations define nine genes (emb-1 to emb-9) on four chromosomes. The functions of six genes seem to be required exclusively for embryogenesis. Mutants in these genes have no other detectable phenotype at the permissive (16C) or nonpermissive (25C) temperature. The function of the other three genes is also required for postembryonic development. As shown by progeny tests for parental effects, for seven genes, maternal gene expression is necessary and sufficient for normal embryogenesis; for one gene, emb-2, either maternal or zygotic expression is sufficient; for one gene, emb-9, zygotic expression is necessary and sufficient. The high proportion of emb genes with maternal expression is consistent with the model of intracellular preprogramming of the egg of C. elegans. Two developmental stages have been defined by temperature-shift experiments: (1) the normal execution stage indicating the time of execution of the normal event at the permissive temperature; (2) the defective execution stage indicating the time of the execution of an irreversible defect at the nonpermissive temperature. The classes of mutants defined by the progeny tests have corresponding stages, but the maternal necessary and sufficient class is subdivided into mutants executing during oogenesis or embryogenesis. ------------------- Key: 450 Medline: 80155174 Authors: Laufer JS;Bazzicalupo P;Wood WB Title: Segregation of developmental potential in early embryos of C. elegans. Citation: Cell 19: 569-577 1980 Type: ARTICLE Genes: Abstract: We have followed the appearance of differentiation markers in cleavage-inhibited and uninhibited early blastomeres of C. elegans and have compared the cleavage patterns of blastomeres in partial and complete embryos. The results indicate that at least some primary differentiation of embryonic cells is determined by internal factors that segregate in early cleavages, whereas patterns of cleavage are dictated by both internally segregating determinants and external cues. ------------------- Key: 451 Medline: Authors: Cryan WS Title: A method for axenizing large numbers of nematodes. Citation: Journal of Parasitology 49: 351-352 1963 Type: ARTICLE Genes: Abstract: Studies with parasitic and free-living nematodes in this laboratory have required large numbers of bacteria-free organisms. A procedure has been developed in which both larval and adult stages free themselves of debris by migrating through paper and glass beads, while the axenizing of concentrated antibiotics followed by prolonged holding in dilute antibiotics is achieved automatically without manipulation of the worms. ------------------- Key: 452 Medline: 81008630 Authors: Pong SS;Wang CC;Fritz LC Title: Studies on the mechanism of action of avermectin B1a: Stimulation of release of GABA from brain synaptosomes. Citation: Journal of Neurochemistry 34: 351-358 1980 Type: ARTICLE Genes: Abstract: Avermectin B1a, a novel macrocyclic lactone antiparasitic agent, causes a marked and sustained increase of gamma-aminobutyric acid from rat brain synaptosomes. A concentration of 8-10 um of avermectin B1a produced the maximal effect (310 +/- 30% of the control), while the half-maximal level was achieved at 2-3 um. The drug also stimulated gamma-aminobutyric acid release (251 +/- 11% of the basal level) from synaptosomes in calcium-free medium, which was 28 +/- 4% lower than that in the 1.8 mm-Ca2+ medium. The compound did not, however, affect the synaptosomal release of glutamate. At the lobster neuromuscular junction, avermectin B1a reduced the input resistance of muscle fibers in control Ringer's solution as well as in Ringer's solution in which Co2+ was substitited for Ca2+. This observation is in accord with the Ca2+ -independent stimulation of gamma-aminobutyric acid release seen with synaptosomes. A good correlation between antiparasitic activity and gamma-aminobutyric acid-releasing activity has been found among various derivatives of avermectin B1a, which suggests that the ability of the drug to release this neurotransmitter may be the basis of its antiparasitic action. ------------------- Key: 453 Medline: 80135165 Authors: Madl JE;Herman RK Title: Polyploids and sex determination in C. elegans. Citation: Genetics 93: 393-402 1979 Type: ARTICLE Genes: mnDp8 mnDp9 mnDp10 mnDp25 mnDp27 mnDp30 Abstract: Tetraploid stocks of Caenorhabditis elegans var. Bristol carrying autosomal and X-linked markers have been produced. Tetraploid hermaphrodites fall into two categories: those that give about 1% male self-progeny and those that give 25 to 40% male self-progeny. The former are basically 4A;4X--four sets of autosomes and four sex chromosomes--and the latter are 4A;3X. Males are 4A;2X. (Diploid hermaphrodites are 2A;2X; males are 2A;1X.) Triploids were produced by crossing tetraploid hermaphrodites and diploid males. Triploids of composition 3A;3X are hermaphrodites; 3A;2X animals are fertile males. Different X-chromosome duplications were added to a 3A;2X chromosome constitution to increase the X-to-autosome ratio. Based on the resulting sexual phenotypes, we conclude that there exists on the C. elegans X chromosome at least three (and perhaps many more) dose- sensitive sites that act cumulatively in determining sex. ------------------- Key: 455 Medline: Authors: Dusenbery DB Title: Responses of nematode C. elegans to controlled chemical stimulation. Citation: Journal of Comparative Physiology 136: 327-331 1980 Type: ARTICLE Genes: Abstract: A new method is described for studying the behavioral responses of nematodes to controlled chemical stimulation. The worm is held by the tail with a suction pipet. Behavior is recorded by an array of light sensors connected to a multichannel recorder. Several types of behavior can be detected in addition to the normal backward propagating waves of about 2 Hz that propel untethered worms forward. The most dramatic of these is the reversal bout, consisting of forward propagating waves of about 0.7 Hz, that propel untethered worms backward. The latter waves are easily distinguished from the former by the large amplitude motion caused by the fact that they contain a sharper bend at the tail. This technique was used to demonstrate that a purely temporal change in chemical stimulation can cause a large change in the probability of occurrence of a reversal bout. These altered probabilities adapt back to the basal level in about one minute. Increased probabilities adapt faster than decreased. Stronger stimulation causes slower adaptation. Since the reversal bout is associated with changes in direction of locomotion, these observations suggest that klinokinesis with adaptation plays a role in the movement of nematodes in chemical gradients. ------------------- Key: 456 Medline: Authors: Dusenbery DB Title: Appetitive response of the nematode C. elegans to oxygen. Citation: Journal of Comparative Physiology 136: 333-336 1980 Type: ARTICLE Genes: Abstract: Using a technique of recording the behavior of individual nematodes during exposure to various solutions, it was demonstrated that C. elegans made more reversal behaviors after transfer to solutions of lower oxygen tension than higher. The response was stronger after the first hour in the apparatus than initially. This change was not dependent on reduced oxygen availability during the initial period. Starvation is the most likely cause of this change. A variety of mutant strains of C. elegans that are defective in response to most known chemotactic stimuli, including two strains that have been shown to be severely abnormal in the ciliated endings of all sensory neurons of the worm's snout, all responded to changes in oxygen tension. This observation suggests that oxygen is sensed internally rather than by specialized receptor cells. ------------------- Key: 457 Medline: 80254943 Authors: Lewis JA Title: Commentary on the uses of small nematode worms. Citation: Neuroscience 5: 961-966 1980 Type: REVIEW Genes: ace-1 ace-2 unc-17 Abstract: Genetics in the study of less complicated organisms like bacteria has been a tremendously powerful way of recognizing individual elements hidden within a process, mutationally tagging them in ways easier to recognize by the biochemist. Identifying the elements used in the construction and function of nervous systems might be easier if genetics were readily applicable. The problem has been that the larger organisms with cells most suitable for impaling with microelectrodes and for obtaining isolated tissue for biochemical studies are the organisms most cumbersome genetically. Smaller, simpler organisms which can be raised rapidly and in the myriad quantity required for genetics usually lack the favorable attributes for study of the nervous system that come with size. One notable exception to this rule is the lowly, single-celled paramecium, which combines physiological accessibility with reasonably good genetics. But otherwise, for those interested in the genetics of multicellular nervous systems, it has been a matter of catch-as-catch-can. The attention of a few scientists has come to rest on the nematode, a worm not too many steps up the evolutionary ------------------- Key: 458 Medline: 80228804 Authors: Gossett LA;Hecht RM Title: A squash technique demonstrating embryonic nuclear cleavage of the nematode C. elegans. Citation: Journal of Histochemistry & Cytochemistry 28: 507-510 1980 Type: ARTICLE Genes: Abstract: A simple squash technique was developed which permits the observation of individual nuclei during embryogenesis of Caenorhabditis elegans. The technique consists of placing several two-cell stage embryos on a subbed slide in a droplet of M-9 salt buffer and incubating them in a sealed humidity chamber at 16.4 degrees C for increasing time intervals. The embryos are then squashed, fixed, and stained with Hoechst 33258. Rate of cleavage at 25.0 degrees C is 1.8 times faster than that at 16.4 degrees C. This yields superimposable growth curves upon correction for temperature. An initial lag in the rate of nuclear cleavage is followed by a burst of cell proliferation, which continues and then slows before 550-580 cells are produced at 4 to 5 hr at 25 degrees C. The squash size increases with cell number and reaches a maximum at about the 400-cell stage when early morphogenesis begins. The second half of embryogenesis is characterized by histogenesis in which the cells are held more tightly together, individual nuclei become less distinct, and the squash size decreases to a minimum as a small worm is ------------------- Key: 459 Medline: Authors: Abdulkader N;Brun JL Title: Caracterist genet et physiol de thermosensibilite du developpement embryon chz un mutant a letalite condition C. elegans/ Citation: Revue de Nematologie 3: 11-19 1980 Type: ARTICLE Genes: Abstract: Genetic physiological studies have been made on a 0.1 M E.M.S.-induced temperature-sensitive (ts) mutation affecting the embryonic development of the hermaphrodite nematode C. elegans, Bergerac strain. This mutation lts is Mendelian monofactorial recessive and autosomal. Using shift up and shift down experiments between permissive (18C) and non permissive (24C) temperatures, and brief heat shock at 24C, it can be seen that the mutant differs from the wild strain by a monophasic temperature-senstive lethal period situated between the 6th (+/- 1/2) and 18th (+/- 1/2) hours of the embryogenesis. During this period (TSP), 4 hours - exposure to the non-permissive temperature (24C) may be sufficient for a complete expression of the mutation, i.e. lethality of all the 1ts nematodes. However, two lethal phases may be observed, according to the TSP time at which embryos are subjected to 24C. In early TSP, the embryos fail to hatch, (= lethal phase I) while in late TSP the L1 normal larvae die before moulting ------------------- Key: 460 Medline: 80164135 Authors: Gandhi S;Santelli J;Mitchell DH;Stiles JW;Sanadi DR Title: A simple method for maintaining large aging populations of C. elegans. Citation: Mechanisms of Ageing & Development 12: 137-150 1980 Type: ARTICLE Genes: Abstract: This paper describes a technique capable of establishing and maintaining large, age-synchronous populations of the nematode Caenorhabditis elegans. The technique has three essential components: a rich chemical medium; a method for producing and harvesting mass quantities of eggs; and 5-fluorodeoxyuridine (FUdR), an inhibitor of DNA synthesis. A culture of worms is filtered through glass wool or a wire screen to isolate young larvae. Eggs laid by these worms after they mature are collected over a period of 4-6 hours and allowed to hatch. A low level of FUdR (25 microM) is added just before the larvae reach maturity. This timing is important to avoid developmental abnormalities. The adults lay eggs in the presence of FUdR but the eggs do not hatch, which maintains the synchrony of the culture. Many aging characteristics appear to be similar in treated and untreated worms, such as the time of cessation of egg production, the appearance of visible and behavioral age-related changes, and the mean lifespan. This system thus seems suitable for large-scale biochemical analysis of certain aspects of aging in C. elegans. ------------------- Key: 461 Medline: 80247148 Authors: Waterston RH;Thomson JN;Brenner S Title: Mutants with altered muscle structure in C. elegans. Citation: Developmental Biology 77: 271-302 1980 Type: ARTICLE Genes: unc-4 unc-11 unc-13 unc-15 unc-18 unc-22 unc-23 unc-26 unc-29 unc-31 unc-32 unc-33 unc-41 unc-42 unc-44 unc-45 unc-51 unc-52 unc-54 unc-60 unc-69 unc-78 unc-82 unc-87 unc-89 unc-90 Abstract: In the small nematode, Caenorhabditis elegans, mutants with disorganized myofilament lattice structure have been identified by polarized light microscopy. Genetic analysis places the mutations in 12 complementation groups which are distributed over the six linkage groups of C. elegans. The phenotypes are described for the mutants from the 9 complementation groups not previously reported on in detail. Most are paralyzed, but some exhibit essentially normal movement; mutants of two loci show changes only in later larval stages and adulthood. Morphological studies show that, in general, all the members of a complementation group show similar changes in muscle structure and that these changes are distinctive for that group. In mutants of several genes, disorganization of the myofilament lattice is general with no one component of the lattice more obviously altered than the others. In mutants of other genes specific structures are prominently altered. In one of the instances where thick filaments appear to be abnormal, double mutants combining mutations in this gene (unc-82 IV) with mutations in the gene for a myosin heavy chain or paramyosin were used to show that the unc-82 gene product probably affects thick filament assembly through its actions on paramyosin. Some possible implications of the morphological features of the mutants as well as the conclusions derived from the genetic studies are discussed. ------------------- Key: 462 Medline: 81004836 Authors: Sulston JE;Albertson DG;Thomson JN Title: The C. elegans male: Postembryonic development of nongonadal structures. Citation: Developmental Biology 78: 542-576 1980 Type: ARTICLE Genes: Abstract: The nongonadal cells in the male nematode Caenorhabditis elegans have been followed through maturation by Nomarski microscopy. Many of the cells are incorporated into the copulatory apparatus, which includes the cloaca, copulatory spicules, sensilla, and musculature. This region has been reconstructed by serial section electron microscopy in order to identify the cell types that arise from known lineages. With the exception of certain bilaterally symmetrical pairs the cells have invariant fates. The development involves a variety of well-defined cell interactions, individual and collective cell movements, cell deaths mediated by designated killers, and the reorganisation of a muscle. The male structures overlie an almost unchanged hermaphrodite tail; their development is more complex than that of the hermaphrodite, and more ------------------- Key: 463 Medline: 81004837 Authors: Sulston JE;White JG Title: Regulation and cell autonomy during postembryonic development of C. elegans. Citation: Developmental Biology 78: 577-597 1980 Type: ARTICLE Genes: Abstract: The role of cell-cell interaction in the postembryonic development of nongonadal tissues in the nematode Caenorhabditis elegans has been explored by selective cell ablation with a laser microbeam. Examples have been found of induction and of regulation in cell lineage and fate. Regulation in which one cell precisely or partially replaces another is seen, but only in certain groups of hypodermal cells which resemble one another closely; cells which are unique are not replaced in this way. The regulation of cell form is more widespread and less ------------------- Key: 464 Medline: 80254944 Authors: Lewis JA;Wu CH;Levine JH;Berg H Title: Levamisole-resistant mutants of the nematode C. elegans appear to lack pharmacological acetylcholine receptors. Citation: Neuroscience 5: 967-989 1980 Type: ARTICLE Genes: ace-1 ace-2 cha-1 lev-1 lev-8 lev-9 lev-10 lev-11 unc-17 unc-18 unc-22 unc-29 unc-30 unc-38 unc-50 unc-51 unc-57 unc-63 unc-68 unc-74 Abstract: The body muscles of the nematode Caenorhabditis elegans contract when the animal is cut in solutions of cholinergic agonists. The pharmacological specificty of the apparent nematode cholinergic receptor is most like a vertebrate nicotinic ganglionic receptor. The anthelmintic levamisole resembles nicotine in its effects and acts directly or indirectly as both a cholinergic agonist and antagonist. Mutants at 7 loci conferring extreme resistance to levamisole respond very poorly to cholinergic agonists effective on the wild type. These mutants all share the same uncoordinated motor behavior and contract like the wild type in response to the noncholinergic muscle agonist ouabain. The uncoordinated motor behavior of the mutants and the resistance to levamisole and cholinergic agonists can be copied by exposing the wild type to the cholinergic blocking agent mecamylamine. Another class of mutants (8 loci, 5 corresponding to loci also producing extremely resistant alleles) possess intermediate resistance to levamisole and cholinergic agonists and behaves pharmacologically and genetically like mutants moderately impaired in the levamisole-senstive function. A third class of mutants (2 loci) with spasmodic muscle twitching is partially resistant to cholinergic agonists and to ouabain and probably represents defects in the muscle-contraction cycle physiologically downstream from the levamisole-sensitive function. Meta-phenyl-substituted derivatives of levamisole retain considerable biological activity and may be useful in the molecular analysis of our mutants. a-bungarotoxin, benzyltrimethylammonium, and 3-quinuclidinyl benzilate, potential probes of cholinergic receptor function, do not show significant activity in our cut worm assay. The nature of the observed cholinergic response and the neuroanatomy of C. elegans suggests that the primary response occurs at muscle synapses. We believe that the physiological defect the extremely resistant mutants share is a severe lack of functional muscle acetylcholine receptors and that most of the wild type function of this molecule is not essential to the life of C. elegans. The ability to obtain such mutants may result from there being more than one pharmacological type of nematode cholinergic muscle receptor and/or from the coexistence of a noncholinergic motor mechanism. More generally, the ease with which levamisole-resistant mutants can be isolated (up to 74 mutants in one gene) makes these mutants a favorable system for understanding how a small group of related genes functions in a simple animal. ------------------- Key: 465 Medline: Authors: Cox GN;Laufer JS;Kusch M;Edgar RS Title: Genetic and phenotypic characterization of roller mutants of C. elegans. Citation: Genetics 95: 317-339 1980 Type: ARTICLE Genes: bli-1 bli-2 dpy-2 dpy-3 dpy-4 dpy-7 dpy-8 dpy-10 dpy-11 rol-1 rol-3 rol-4 rol-6 sqt-1 sqt-2 sqt-3 Abstract: Eighty-eight mutants of C. elegans that display a roller phenotoype (a helically twisted body) have been isolated and characterized genetically and phenotypically. The mutations are located in 14 different genes. Most genes contain a number of alleles. Their distribution among the chromosomes appears nonrandom, with seven of the genes being located on linkage group II, some very closely linked. The phenotypes of the mutants suggest that there are five different classes of genes, each class representing a set of similar phenotypic effects: Left Roller (four genes), Right Roller (one gene), Left Squat (one gene), Right Squat (two genes) and Left Dumpy Roller (six genes). The classes of mutants differ with respect to a number of characteristics that include the developmental stages affected and the types of aberrations observed in cuticle structure. A variety of gene interactions were found, arguing that these genes are involved in a common developmental process. The presence of alterations in cuticle morphology strongly suggests that these genes are active in the formation of the nematode cuticle. ------------------- Key: 466 Medline: Authors: Abdulkader N;Brun J Title: A temperature-sensitive mutant of C. elegans var Bergerac affecting morphological and embryonic development. Citation: Genetica 51: 81-92 1979 Type: ARTICLE Genes: Abstract: Genetic, physiological, morphological and anatomical studies have been made on a 0.1 M EMS-induced temperature sensitive (ts) mutation affecting development and morphology of the hermaphroditic nematode C. elegans, var. Bergerac. The three mutated characters; (1) ts recessive lethality at temperature greater than or equal to 22.5C; (2) ts recessive body length at sublethal temperature 20C; (3) temperature-dependent semi-dominant abnormal tail form, show an absolute linkage. Ts lethal and body length periods are embryonic, monophasic and almost completely overlapping. Animals blocked in the lethal phase, which occurs during the first larval stage, are 'dumpy' with abnormal enlarged anterior regions and zig-zag intestines. The variation of these abnormalities at different permissive (13 and 18C) and restrictive (20, 22.5, 24 and 26C) tempertures shows (1) a decrease in the length of newly-hatched larvae with increased temperature, the decreae being particularly marked between 18 and 20C; (2) an increase in morphological and anatomical abnormalities with temperature. The evolution of the mutated phenotypes with temperature suggests that the activity of the ts genic product, which could take part in the production of the cuticle, decreases gradually with temperature. The origin of the ts genic product and its temperature-sensitivity are discussed in terms of the results of heat shock ------------------- Key: 467 Medline: Authors: Dusenbery DB;Barr J Title: Thermal limits and chemotaxis in mutants of the nematode C. elegans defective in thermotaxis. Citation: Journal of Comparative Physiology 137: 353-356 1980 Type: ARTICLE Genes: Abstract: Four mutant strains of the nematode Caenorhabditis elegans previously isolated as defective in thermotaxis were compared to the wild type in tests of their thermal range of activity and chemotaxis. The cold side of the temperature-activity curves of all four strains were different from wild type. The curves of the two cryophilic strains (EH65 and EH67) were shifted to colder temperatures. The curves of the other two mutant strains were shifted to warmer temperatures. In tests of chemotaxis to a variety of stimuli, strain EH61 made no response to any, EH71 made weak responses to all, and the remaining two strains made responses equal to wild type except for weaker responses to three chemical stimuli. It is concluded that thermotaxis shares specific gene requirements with processes controlling both thermal limits ------------------- Key: 468 Medline: Authors: Hosono R Title: A study of morphology of C. elegans: A mutant of C. elegans with dumpy and temperature-sensitive roller phenotype. Citation: Journal of Experimental Zoology 213: 61-67 1980 Type: ARTICLE Genes: dpy-10 dpy-13 Abstract: The wild-type nematode Caenorhabditis elegans has an elongated and spindle-shaped body, whereas the dumpy mutant has a shorter body with approximately the same diameter. Although the wild-type nematode moves forward by producing sinusoidal waves along the body, the roller mutant moves by rotating the body left or right around its long-body axis. A temperature-sensitive morphological mutant which develops into an adult with dumpy phenotype at 15C, but with roller phenotype at 25C, in addition to dumpy phenotype, was isolated. The dumpy phenotype appeared at the first larval stage and was complete at the fourth larval stage; the roller behavior was also expressed at the fourth larval stage. The heterozygous offspring (F1), produced by crossing the mutant hermaphrodite with wild-type males, were rollers in both hermaphrodites and males. Therefore, the dumpy character is autosomal recessive, and the roller character is dominant in heterozygote but cold-sensitive in homozygote. The dumpy mutation was mapped as allele of dpy-10 gene of linkage group II (LG II). The F2 progeny, produced by self-fertilization of the F1 roller hermaphrodite, segregated to wild, dumpy, and roller animals in a ratio of 1:1:2. An attempt to isolate from the F2 generation the roller mutant which produces no dumpy progeny was entirely unsuccessful. Therefore, the dumpy and the roller phenotypes are produced by closely linked mutations or perhaps by a single mutation. ------------------- Key: 469 Medline: 81004191 Authors: Hosono R;Sato Y;Aizawa SI;Mitsui Y Title: Age-dependent changes in mobility and separation of the nematode C. elegans. Citation: Experimental Gerontology 15: 285-289 1980 Type: ARTICLE Genes: Abstract: It has generally been believed that a senescent state is brought about by the loss of division ability of essential cells or the disappearance of irreplaceable components. Since aging shows considerable individual variations, it is difficult to pursue the problem in any single species. Analysis of population aging have been mainly done by measuring a decrease in the population size. However, the decrease in population size involves not only senescent death but also death due to other changes, and it is not suitable for defining the aging process precisely. Therefore, the study of aging should be carried out in the populations with genetic and environmental similarity, and select several characteristics which are closely related to the senescent process. The nematode Caenorhabditis elegans is easy to handle and it is possible to obtain many individuals with identical genetic background. Information on aging phenotypes of the nematode has been accumulated. But in spite of their identical genetic background in synchronous cultures, individual differences in life span are conspicuous. The maximum life span of wild hermaphrodites at 20C was double the minimum life span in C. elegans. Since aging reflects various biological histories following maturation, individual death has many causes. One way to identify sub-groups is to classify an aged population on the basis of other aging parameters. Previously one of the authors (R.H.) has reported behavioral changes accompanying aging of C. elegans. In this report, we classified the worm population on the basis of difference in movement activity and examined some aging parameters of these fractionated populations. ------------------- Key: 470 Medline: 81033740 Authors: Siddiqui SS;Babu P Title: Genetic mosaics of C. elegans: A tissue-specific fluorescent mutant. Citation: Science 210: 330-332 1980 Type: ARTICLE Genes: flu-3 Abstract: Genetic mosaics can be generated by x-irradiation in the simple nematode Caenorhabditis elegans. A mutation in the gene flu-3 alters the characteristic autofluorescence of intestinal cells under ultraviolet light and can be used as a cell- and tissue-specific marker. Embryos heterozygous for flu-3 give rise to adults with patches of these altered intestinal cells. The previously established intestinal cell lineage in Caenorhabditis elegans and the distribution and sizes of the fluorescent patches are consistent with a somatic segregation of the flu-3 allele. ------------------- Key: 471 Medline: 81054930 Authors: Karn J;Brenner S;Barnett L;Cesareni G Title: Novel bacteriophage lambda cloning vector. Citation: Proceedings of the National Academy of Sciences USA 77: 5172-5176 1980 Type: ARTICLE Genes: unc-54 Abstract: A simple method for generating phage collections representing eukaryotic genomes has been developed by using a novel bacteriophage lambda vector, lambda1059. The phage is a BamH1 substitution vector that accommodates DNA fragments 6-24 kilobases long. Production of recombinants in lambda1059 requires deletion of the lambda red and gamma genes. The recombinants are therefore spi- and may be separated from the spi+ vector phages by plating on strains lysogenic for bacteriophage P2. Random fragments suitable for insertion into lambda1059 are obtained by partial digestion of high molecular weight eukaryotic DNA with Sau3a. This restriction enzyme cleaves at the sequence G-A-T-C and leaves a 5'-tetranucleotide "sticky end." Because G-A-T-C extensions are also produced by BamH1 cleavage, these fragments may be annealed directly to BamH1-cleaved lambda1059. By using these methods, a set of clones covering the entire Caenorhabditis elegans genome was constructed. DNA segments which include the unc-54 myosin heavy chain gene have been isolated from this ------------------- Key: 473 Medline: Authors: von Ehrenstein G;Schierenberg E Title: Cell lineages and development of C. elegans and other nematodes. Citation: "Nematodes as Biological Models, Volume 1: Behavioral and Developmental Models." Zuckerman BM (ed), Academic Press, NY. 1: 1-72 1980 Type: REVIEW Genes: Abstract: Studies on the development of nematodes began about 100 years ago. Nematodes have a unique combination of favorable properties for the microscopic observation of development. These include transparent small eggs and a reproducible cleavage leading to an animal with a constant number of cells and a relatively simple anatomy. Nematodes have been classic models for studying the processes of egg maturation, meiosis, fertilization, zygote formation, and early cleavage... ------------------- Key: 474 Medline: Authors: Zengel JM;Epstein HF Title: Muscle development in C. elegans: A molecular genetic approach. Citation: "Nematodes as Biological Models, Volume 1: Behavioral and Developmental Models." Zuckerman BM (ed), Academic Press, NY. 1: 73-126 1980 Type: REVIEW Genes: Abstract: Muscle contraction is one of the fundamental processes of animal life. Although biochemical, biophysical, and electron microscopic studies have yielded much valuable information about the structure and function of muscle and its component proteins, there are still many unanswered questions. For example, little is known about the molecular basis for gene expression during the development of muscle, the regulation of synthesis and function of muscle proteins, and the in vivo assembly of the myofilament lattice. Progress in answering these types of questions has been hindered in the past by the lack of a system in which one could use biochemical, biophysical, and cytological techniques in analyzing an animal also suitable for genetic and developmental studies of muscle. However, recent work has demonstrated rather convincingly that the nematode, Caenorhabditis elegans, will be very useful for attacking these problems. ------------------- Key: 475 Medline: Authors: Dusenbery DB Title: Behavior of free-living nematodes. Citation: "Nematodes as Biological Models, Volume 1: Behavioral and Developmental Models." Zuckerman BM (ed), Academic Press, NY. 1: 127-158 1980 Type: REVIEW Genes: Abstract: The nematodes form a very important group of animals that have received much less study than deserved. They appear to be nearly as important in human health and agriculture as insects, and yet there are ten times as many entries in Biological Abstracts for the latter. Even from a less ethnocentric point of view, nematodes are significant. Hyman (1951) estimates 500,000 nematode species, which is of the same order as is the number of insect species. In soil, where comparisons have been made, the biomass of the two groups is roughly equal. The great disparity in research effort is simply because nematodes are much less visible to the casual observer. As a consequence of this situation, there is a need for basic biological research on nematodes. Much of the required work could be done on any typical nematode species, and since the free-living microphagous forms are most convenient to work with, they are of great interest. One of the areas in which basic knowledge is lacking for this group is that of behavior. This void is particularly surprising in view of the fact that behavior is presumably one of the more important aspects of parasitic lifestyles. It is also unfortunate from the point of view of basic behavioral biology. Nematodes and their close relatives occupy a unique place in the evolution of the nervous system. They are the only readily studied organisms that have been shown to have a centralized nervous system made up of a specific and countable number of neurons. The nematodes that have been examined have about 200 neurons depending on the species. In contrast, two annelids that have been studied have 10*4 and 10*5 neurons, and an arthropod is estimated to have 10*5 neurons. On the other hand, more primitive nervous systems are apparently not eutelic and often consist of a dispersed nerve net. Thus, it is of general biological interest to determine the behavioral capacities of ------------------- Key: 476 Medline: Authors: Johnson CD;Stretton AOW Title: Neural control of locomotion in Ascaris: anatomy, electrophysiology, and biochemistry. Citation: "Nematodes as Biological Models, Volume 1: Behavioral and Developmental Models." Zuckerman BM (ed), Academic Press, NY. 1: 159-196 1980 Type: REVIEW Genes: Abstract: Locomotory behavior has been investigated in a wide variety of animals, including nematodes. Many studies have concluded that locomotory behavior is under neurogenic control, i.e., during locomotion the coordinated contractions of relevant muscles results from a coordinated firing of motoneurons. Nematodes have long been known to have only a small number of neurons (about 250 in the adult female), an attribute which should make them an attractive simple system in which to examine the control of locomotion. It should be possible, for example, to examine the role of individual neurons in the control of locomotion and also to determine which interactions between neurons are responsible for locomotory behavior. These studies have not been previously attempted primarily because the anatomy of nematode motoneurons had not been determined (a situation recently remedied, see Section IV, B). In the absence of this knowledge, the analysis of nematode locomotion has concentrated on the role of interconnections between muscle cells, and has been dominated by the suggestion that the coordinated contraction of muscle cells results from these interconnections (i.e., myogenic control of locomotion). In these models, the nervous system is relegated to switching the musculature between different patterns of contraction (i.e., directions of wave propagation). This type of organization has been called neurocratic. It is not yet clear whether the control of locomotion in nematodes in neurogenic or myogenic. Our bias (which will be clear) is that it is the nervous system which plays the major role, but the crucial experiments ------------------- Key: 477 Medline: Authors: Willett JD Title: Control mechanisms in nematodes. Citation: "Nematodes as Biological Models, Volume 1: Behavioral and Developmental Models." Zuckerman BM (ed), Academic Press, NY. 1: 197-226 1980 Type: REVIEW Genes: Abstract: Complete information regarding the detailed control mechanisms involved in any specific aspect of nematode physiology or biochemistry is currently not available. There are, however, numerous examples of physiological responses and biochemical changes taking place during the course of the nematode life cycle which will give indications of being under neural and/or hormonal control. In some instances, experimental evidence exists of a particular control system. Though relatively simple in cellular architecture, nematodes possess a number of morphologically and functionally distinct tissues. It is not unreasonable to expect that with this diveristy in tissue function nematodes will be found to possess a system of inter- and intracellular controls not unlike those encountered in higher metazoa. Nematodes display specific behavior in response to both external as well as internal signals. Alterations in its external environment can be detected, recorded, and responded to by the nematode. The response can be reflected in behavioral, physiological, and/or long-term biochemical changes within the organism. Several processes inherent to the nematode life cycle must of necessity reflect the operation of a system of controls. Some experimental evidence concerning the nature of these control systems is available. Neglecting the contol processes involved in embryogenesis and concentrating on postembryonic development and reproduction, there are a number of specific events likely to be under the control of neural and/or hormonal processes... ------------------- Key: 478 Medline: Authors: Herman RK;Horvitz HR Title: Genetic analysis of C. elegans. Citation: "Nematodes as Biological Models, Volume 1: Behavioral and Developmental Models." Zuckerman BM (ed), Academic Press, NY. 1: 227-262 1980 Type: REVIEW Genes: Abstract: Largely through the efforts of Sydney Brenner, many investigators have been attracted to Caenorhabditis elegans as a model organism for asking questions about the genetic basis of eucaryotic development and animal behavior. The philosophy underlying this interest is that of molecular genetics, which has relied heavily on the analysis of single-step mutants to elucidate such genetically controlled processes as metabolic pathways, the regulation of procaryotic gene expression, and the in vivo assembly of bacteriophages. Development and behavior also make use of genetic programs, and it may help to mutate the program steps to discern their nature. At present this seems an enormous undertaking because morphogenesis and behavior, as we now understand them, seem very remote from the genes that control them. Clearly other techniques--physiological, biochemical, anatomical--will be required. But the philosophy behind much C. elegans research is that mutant analysis will ultimately play a valuable role in understanding development and behavior. With this philosophy in mind, the attraction of C. elegans is twofold: suitability for genetic analysis and relative cellular simplicity. The latter feature is reviewed by others in this volume. The purpose of this review is to summarize the current status of the genetics of C. elegans; the applications of genetic analysis to the problems of development and behavior will be left to other reviewers and future work. ------------------- Key: 479 Medline: Authors: Riddle DL Title: Developmental genetics of C. elegans. Citation: "Nematodes as Biological Models, Volume 1: Behavioral and Developmental Models." Zuckerman BM (ed), Academic Press, NY. 1: 263-284 1980 Type: REVIEW Genes: Abstract: Caenorhabditis elegans is widely accepted as an important model organism for the study of animal development and behavior. A dozen new research groups studying this nematode have been established within the past five years. Caenorhabditis elegans offers many advantages for studying a variety of biological processes, but the most important of these advantages is the ability to carry out all types of genetic manipulations. Virtually all of the research utilizing C. elegans relies in some way on its genetics. This research is primarily long term, since much of it is aimed at an understanding of the molecular basis of developmental and behavioral processes. ------------------- Key: 480 Medline: Authors: Siddiqui SS;von Ehrenstein G Title: Biochemical genetics of C. elegans. Citation: "Nematodes as Biological Models, Volume 1: Behavioral and Developmental Models." Zuckerman BM (ed), Academic Press, NY. 1: 285-312 1980 Type: REVIEW Genes: Abstract: In addition to the extensively studied class of mutants with alterations of muscle organization (this volume, Chapter 2), mutants with enzymatic defect are being investigated in Caenorhabditis elegans. This chapter reviews mutants affecting kynurenine hydrolylase, kynureninase, acetylcholinesterase, choline acetyltransferase, and endodeoxyribonuclease. Also included are mutants altered in the metabolism of ------------------- Key: 481 Medline: Authors: Dusenbery DB Title: Chemotactic behavior of mutants of the nematode C. elegans that are defective in osmotic avoidance. Citation: Journal of Comparative Physiology 137: 93-96 1980 Type: ARTICLE Genes: che-3 daf-10 osm-1 osm-5 osm-6 Abstract: Wild-type C. elegans and seven derivative strains previously selected for absence of the wild-type tendency to avoid highly concentrated solutions were tested for responsiveness in 11 assays of chemotaxis, including 6 attractant and 3 repellent stimuli. The two strains altered in the gene osm-1 (P808 and P816) did not respond in any test except, possibly, one or two weak responses. Strain P801 responded to one attractant and two repellents. Strain P802 made moderately strong responses to most stimuli and avoided CO2 in phosphate buffer weakly, if at all, but did respond to the attractants Na+ and Cl-. Conversely, strains P813 and P811 made little if any response to any attractant but did respond to the two strong repellents. Taken together with other results, these findings suggest that the osmotic response has more gene requirements in common with both attractive and repellent chemical stimuli than with thermal or mechanical stimuli. In addition, they indicate that the known chemical stimuli and the osmotic stimulus are probably ------------------- Key: 482 Medline: 81077343 Authors: Kass IS;Wang CC;Walrond JP;Stretton AOW Title: Avermectin B1a, a paralyzing anthelmintic that affects interneurons and inhibitory motoneurons in Ascaris. Citation: Proceedings of the National Academy of Sciences USA 77: 6211-6215 1980 Type: ARTICLE Genes: unc-29 Abstract: Avermectin B1a (AVM) is an antiparasitic agent that paralyzes nematodes without causing hypercontraction or flaccid paralysis. Using selective stimulation techniques, we have shown that AVM blocks transmission between interneuron(s) and excitatory motorneurons in the ventral nerve cord of Ascaris. It also inhibits transmissin between inhibitory motoneurons and muscle but has little effect on excitatory neuromuscular transmission. Picrotoxin can reverse the AVM- induced block of interneuron-excitatory motoneuron transmission but has no effect on the inhibitory motoneuronal synapse in either the presence or absence of AVM. Our results provide an explanation of how AVM may cause paralysis of nematodes. ------------------- Key: 483 Medline: 81054813 Authors: Stinchcomb DT;Thomas M;Kelly J;Selker E;Davis RW Title: Eukaryotic DNA segments capable of autonomous replication in yeast. Citation: Proceedings of the National Academy of Sciences USA 77: 4559-4563 1980 Type: ARTICLE Genes: Abstract: A selective scheme is presented for isolating sequences capable of replicating autonomously in the yeast Saccharomyces cerevisiae. YIp5, a vector that contains the yeast gene ura3, does not transform a ura3 deletion mutant to Ura+. Hybrid YIp5-Escherichia coli DNA molecules also fail to produce transformants. However, collections of molecular hybrids between YIp5 and DNA from any of six eukaryotes tested (S. cerevisiae, Neurospora crassa, Dictyostelium discoideum, Caenorhabditis elegans, Drosophila melanogaster, and Zea mays) do transform the deletion mutant. The Ura+ transformants grow slowly, are unstable under nonselective conditions, and carry transforming DNA as autonomously replicating, supercoiled circular molecules. Such a phenotype is qualitatively identical to that of strains transformed by molecules containing a yeast chromosomal origin of replication. Thus, these DNA hybrid molecules may contain eukaryotic origins of replication. The isolated sequences may be useful in determining the signals controlling DNA replication in yeast and in studying both DNA replication and transformation in other eukaryotic organisms. ------------------- Key: 484 Medline: 81139611 Authors: Lewis JA;Wu CH;Berg H;Levine JH Title: The genetics of levamisole resistance in the nematode C. elegans. Citation: Genetics 95: 905-928 1980 Type: ARTICLE Genes: dpy-4 dpy-13 lev-1 lev-8 lev-9 lev-10 lev-11 sup-5 unc-22 unc-26 unc-29 unc-38 unc-50 unc-51 unc-57 unc-63 unc-68 unc-74 Abstract: We have characterized a small group of genes (13 loci) in the nematode Caenorhabditis elegans that, when mutated, confer resistance to the potent anthelmintic levamisole. Mutants at the 7 loci conferring the most extreme resistance generally possess almost identical visible and pharmacological phenotypes: uncoordinated motor behavior, most severe in early larval life, extreme resistance to cholinergic agonists and sensitivity to hypo-osmotic shock. Mutants with exceptional phenotypes suggest possible functions for several of the resistance loci. The most extreme mutants can readily be selected by their drug resistance (211 mutants, as many as 74 alleles of one gene). The more common resistance loci are likely to be unessential genes, while loci identified by only a few alleles may be essential genes or genes conferring resistance only when mutated in a special way. We propose that these mutants represent a favorable system for understanding how a small group of related genes function in a simple animal. The extreme drug resistance of these mutants makes them useful tools for the genetic manipulation of C. elegans. And, as the most resistant class of mutants might lack pharmacologically functional acetyl-choline receptors (LEWIS et al. 1980), these mutants may also be of some neurobiological significance. ------------------- Key: 485 Medline: 81112143 Authors: Mackenzie JM Jr;Epstein HF Title: Paramyosin is necessary for determination of nematode thick filament length in vivo. Citation: Cell 22: 747-755 1980 Type: ARTICLE Genes: unc-15 Abstract: Nematodes construct thick filaments in body-wall muscle cells using three major protein components: two kinds of myosin and paramyosin. We report the isolation and enrichment of thick filaments from wild type and mutant strains of the nematode, Caenorhabditis elegans, and their examination by electron microscopy. We have compared the morphology and distribution of lengths of isolated filaments from the wild type N2, the unc-15 mutant lacking paramyosin E1214 and the unc-54 mutant lacking specific body-wall mysoin E190. Our studies indicate that very long filaments can be isolated from both N2 and the E190 lacking 60% of the normal amount of myosin and that the mean length of these isolated filaments and filament fragments in these strains is 3.2 and 3.3 um, respectively. However, when similar preparations of thick filaments isolated from E1214 were examined, no long filaments were observed and the mean length was 1.0 um. Most of the E1214 filaments exhibited prominent central bare zones and double tapered ends. The mean length of this normally distributed subpopulation was 1.53 um. For comparison, we determined the in situ length of wild type N2 thick filaments (by polarized light microscopy of body-wall muscle) to be 9.7 um. The diameters of the wild type N2 and the myosin mutant E190 thick filaments were 25 nm uniformly along their length, whereas the paramyosin mutant E1214 filaments showed wider diameters of 32 nm along most of their length. We conclude that functional paramyosin is necessary for the determination of thick filament length and diameter in nematode body-wall muscle cells in vivo. The presence of both body-wall myosins and other myofibrillar components appear insufficient for determination of thick filament structure in these muscles. Both body-wall myosins are unnecessary for the formation of long thick filaments of normal diameter: the presence of one form of myosin, paramyosin and other myofibrillar components is sufficient. We discuss the relevance of these findings to thick filament assembly and myofibrillar organization in general. ------------------- Key: 486 Medline: 81139614 Authors: Greenwald IS;Horvitz HR Title: unc-93(e1500): A behavioral mutant of C. elegans that defines a gene with a wild-type null phenotype. Citation: Genetics 96: 147-164 1980 Type: ARTICLE Genes: daf-2 daf-7 dpy-1 dpy-17 lin-8 lon-1 sup-9 sup-10 unc-3 unc-79 unc-85 unc-93 nDf2 nDf3 nDf4 nDf5 nDf6 nDf7 nDf8 nDf9 mnDf1 mnDf4 mnDf8 nDf10 nDf11 nDf12 nDf13 nDf14 nDf15 mnDf11 mnDf19 Abstract: The uncoordinated, egg-laying-defective mutation, unc-93(e1500) III, of the nematode Caenorhabditis elegans spontaneously reverts to a wild-type phenotype. We describe 102 spontaneous and mutagen-induced revertants that define three loci, two extragenic (sup-9 II and sup- 10 X) and one intragenic. Genetic analysis suggests that e1500 is a rare visible allele that generates a toxic product and that intragenic reversion, resulting from the generation of null alleles of the unc-93 gene, eliminates the toxic product. We propose that the genetic properties of the unc-93 locus, including the spontaneous reversion of the e1500 mutation, indicate that unc-93 may be a member of a multigene family. The extragenic suppressors also appear to arise as the result of elimination of gene activity; these genes may encode regulatory functions or products that interact with the unc-93 gene product. Genes such as unc-93, sup-9 and sup-10 may be useful for genetic manipulations, including the generation of deficiencies and mutagen testing. ------------------- Key: 487 Medline: 81087907 Authors: Mounier N;Brun J Title: A cytogenetical analysis of sterile mutants in C. elegans. Citation: Canadian Journal of Genetics & Cytology 22: 391-403 1980 Type: ARTICLE Genes: Abstract: The regulation of gametogenesis in the hermaphrodite and proterandrous nematode Caenorhabditis elegans is introduced here through the analysis of nonconditional sterile mutants. To investigate the mechanisms which allow the two gametogenetic phases to succeed each other in the same ovotestis, three mutants were studied cytogenetically. Two of the mutants exhibit only the spermatocyte phase and the third shows a greatly reduced and disturbed oogenesis. These three mutations all produce large decreases in ovotestis size and gonocyte number. Each of the three is monofactorial, recessive, autosomal and independent. Homozygous mutant males are also sterile. The gametogenesis phases which could be disturbed by mutation were determined by cytological analysis of the ovotestis of 12 other sterile strains. These phases occur during mitotic divisions of the genital primordium, zygotene chromosome pairing, male meiosis and spermiogenesis, oogenesis induction and oocyte maturation. These steps of gametogenesis need a wild-type genic activity to occur normally. It appears that spermatogenesis and oogenesis are two genetically independent processes, and that oogenesis is rather autonomous and its induction would depend on a hormonal factor. ------------------- Key: 488 Medline: 83077080 Authors: Zengel JM;Epstein HF Title: Identification of genetic elements associated with muscle structure in the nematode C. elegans. Citation: Cell Motility 1: 73-97 1980 Type: ARTICLE Genes: unc-27 unc-45 unc-52 unc-60 unc-78 unc-82 unc-87 unc-89 unc-90 unc-94 unc-95 unc-96 unc-97 unc-98 unc-100 Abstract: A search for new mutants with altered body-wall muscle cell structure has been undertaken in the nematode C elegans. One-hundred seventeen mutants were isolated after mutagenesis with ethyl methanesulfonate or ultraviolet light, enrichment by a motility-requiring test, and screening by polarized light microscopy; 102 of these mutants were in ten previously established genes, whereas 15 mutants permitted the identification of seven new complementation groups in C elegans. Two of the new genes map on linkage group I (unc-94 and unc-95) and four genes are sex linked (unc-96, unc-97, unc-98, and unc-99). One complementation group (unc-100) could not be mapped because of the special characteristics of its cohort mutants. Representative mutants of the mapped genes were examined by polarized light and electron microscopy. All of the mutants exhibit disruptions of the normal A and I band organization of thick and thin filaments. Several of the mutants produce collections of thin filament-like structures. In one of these cases, HE177 demonstrated collections of somewhat wider, intermediate-sized filaments as well, and the HE195 mutant produces paracrystalline aggregates of thin filaments amidst looser arrangements of similar structures. The mutants in newly identified genes, as well as the new mutants in previously established genetic loci, have promise as tools in the study of myofibrillar assembly and function. Among the 22 complementation groups associated with body- wall structure in C elegans, it is likely that some genes code for regulatory and morphogenetic functions in addition to the well- studied structural, contractile, and calcium-associated proteins in muscle. ------------------- Key: 489 Medline: 81177051 Authors: Laufer JS;von Ehrenstein G Title: Nematode development after removal of egg cytoplasm: Absence of localized unbound determinants. Citation: Science 211: 402-404 1981 Type: ARTICLE Genes: Abstract: Embryos of Caenorhabditis elegans develop into fertile adults after cell fragments, containing presumptive cytoplasm of somatic and germ line precursors, are extruded from uncleaved eggs or early blastomeres through laser-induced holes in the eggshells. This suggests that the determinate development of this worm is not dependent on the prelocalization of determinants in specific regions of the egg cytoplasm. ------------------- Key: 490 Medline: Authors: Willett JD;Rahim I;Geist M;Zuckerman BM Title: Cyclic nucleotide exudation by nematodes and the effects on nematode growth, development and longevity. Citation: Age 3: 82-87 1980 Type: ARTICLE Genes: Abstract: The levels of cyclic nucleotides, cAMP and cGMP, in the medium of aging mass cultures of Panagrellus redivivus were determined, respectively, by a protein binding assay and a radioimmunoassay. The amount of cGMP increased as the mass cultures aged while the amount of cAMP remained stable. Since premature death and an inhibition of development have been observed in aging mass cultures, investigators have speculated that a build-up of excretory products in the medium might be toxic to the nematodes and cause abnormal development. To examine this possibility, small cultures containing fixed numbers of the nematode Caenorhabditis elegans were exposed to levels of cGMP analagous to the levels found in aging mass cultures of P. redivivus. Significant increases in growth and longevity occurred with no effect on fecundity, timing or the duration of the reproductive period. It appears then that cGMP is not responsible for the toxic effects observed in mass culture and, in fact, cGMP apparently enhances nematode longevity at concentrations which do not alter development. ------------------- Key: 491 Medline: Authors: Edgar RS Title: The genetics of development in the nematode C. elegans. Citation: "The Molecular Genetics of Development." Leighton T and Loomis WF (eds), Academic Press, NY. : 213-235 1980 Type: REVIEW Genes: osm-3 Abstract: The free-living nematode Caenorhabditis elegans has attracted attention in recent years as an organism for the study of the genetic control of development. This chapter briefly describes the present state of this work. Many of the studies reported on here have not yet been published but have been described in "The Worm Breeder's Gazette", an informal newsletter I edit, and at a C. elegans meeting held at Cold Spring Harbor in May 1979. A previous review of this field was written by Riddle (1978). The use of free-living nematodes in genetic studies was first suggested by Dougherty and Calhoun in 1948. Early studies of C. elegans by Dougherty and co-workers (1959) emphasized methods of axenic cultivation while the sexual cycle was described by Nigon (1949). The present interest in C. elegans, however, was triggered by Sydney Brenner who took up the organism in the late 1960s as a possibly useful organism for the study of the genetic control of the nervous system and of behavior (Brenner, 1973). It was largely due to Brenner (1974) that the present methods of cultivation and of genetic analysis were developed. ------------------- Key: 492 Medline: 81242433 Authors: Emmons SW;Rosenzweig B;Hirsh D Title: Arrangement of repeated sequences in the DNA of the nematode C. elegans. Citation: Journal of Molecular Biology 144: 481-500 1980 Type: ARTICLE Genes: Abstract: The arrangement of repeated sequences in the DNA of the nematode Caenorhabditis elegans has been studied by electron microscopy and reassociation kinetics. Inverted repeats observed in the electron microscope are mostly less than 1000 base-pairs in length and are distributed randomly with an average separation of 33,000 bases. Comparison of the number and distribution of these inverted repeats with the amount of DNA in the foldback fraction isolated by hydroxyapatite chromatography suggests that much of the material in the foldback fraction contains a sequence distinct from the class of inverted repeats observed in the electron microscope. Cot analysis of DNA fragments several thousand nucleotides in length shows that moderately repetitive sequences are interspersed with unique sequences. Most of these interspersed, repeated sequences are a few hundred nucleotides in length, as determined from electron micrographs. DNA sequence arrangement in C. elegans is therefore similar to the arrangement found in most other eukaryotes. ------------------- Key: 493 Medline: 81122166 Authors: Bhat SG;Babu P Title: Mutagen sensitivity of kynureninase mutants of the nematode C. elegans. Citation: Molecular & General Genetics 180: 635-638 1980 Type: ARTICLE Genes: flu-2 Abstract: Mutants in the gene flu-2 of the free-living nematode Caenorhabditis elegans are characterised by an altered autofluorescence of the intestine cells, from the light blue of wild-type to a dull green colour. The properties of flu-2 mutants have been investigated. L- kynureninase activity has been detected in wild-type C. elegans. The flu-2 mutants have markedly reduced kynureninase activity, as predicted earlier from chromatographic analysis of tryptophan catabolites of wild-type and mutant worms. Associated with this enzymatic block, all flu-2 mutants have enhanced sensitivity to ethyl methane sulfonate (EMS) ------------------- Key: 494 Medline: 81139247 Authors: Kimble JE;White JG Title: On the control of germ cell development in C. elegans. Citation: Developmental Biology 81: 208-219 1981 Type: ARTICLE Genes: Abstract: After hatching, the germ line progenitor cells in C. elegans begin to divide mitotically; later, some of the germ line cells enter meiosis and differentiate into gametes. In the adult, mitotic germ cells, or stem cells, are found at one end (the distal end) and meiotic cells occupy the rest of the elongate gonad. Removal of two somatic gonadal cells, the distal tip cells, by laser microsurgery has a dramatic effect on germ cell development. In either sex, this operation leads to the arrest of mitosis and the initiation of meiosis in germ cells. The function of the distal tip cell in the intact animal appears to be the inhibition of meiosis (or stimulation of mitosis) in nearby germ cells. During development, this permits growth and, in the adult, it maintains the germ line stem cell population. A change in the position of the distal tip cell in the gonad at an early point in development is correlated with a change in the axial polarity of the germ line tissue. This suggests that the localization of the distal tip cell's inhibitory activity at the distal end of the gonad establishes the ------------------- Key: 495 Medline: 81261868 Authors: Argon Y;Ward S Title: C. elegans fertilization-defective mutants with abnormal sperm. Citation: Genetics 96: 413-433 1980 Type: ARTICLE Genes: fem-1 fer-1 fer-2 fer-3 fer-4 fer-6 fer-7 eDf1 Abstract: Seven new fertilization-defective mutants of C. elegans have been isolated and characterized; six are temperature sensitive, one is absolute and all are autosomal recessive. One mutation is in a previously described gene, while the other six define six new fer genes that appear to code for sperm-specific functions necessary for normal fertilization. In all fer mutants, both males and hermaphrodites accumulate sperm in near normal numbers. In hermaphrodites, mutant sperm contact the oocytes, but fail to fertilize them. Instead, the sperm are swept into the uterus by the passing oocytes and are expelled when oocytes are laid. Males of two fer mutants do not transfer sperm during copulation, but the other mutant males transfer sperm that fail to move to the spermatheca. Spermatozoa from fer-1 and fer-4 mutants are motility-defective in vitro as well as in vivo, and their pseudopods have an altered morphology. The period of development during which mutant hermaphrodites are temperature sensitive for fertility overlaps the time of sperm development. Some mutants are temperature sensitive throughout the entire period, and others are temperature sensitive during or just prior to spermiogenesis. In fer-4/+ and fer-7/+ males, the fertility of the mutation-bearing sperm is diminished, reducing the transmission ratio. This implies some post-meiotic expression of these genes.--This set of mutants provides a variety of functional and structural alterations in nematode sperm that should help identify and analyze gene products involved in sperm morphogenesis and ------------------- Key: 496 Medline: 81261869 Authors: Horvitz HR;Sulston JE Title: Isolation and genetic characterization of cell-lineage mutants of the nematode C. elegans. Citation: Genetics 96: 435-454 1980 Type: ARTICLE Genes: dpy-18 lin-1 lin-2 lin-3 lin-4 lin-5 lin-6 lin-7 lin-8 lin-9 lon-1 sup-5 sup-7 unc-59 unc-83 unc-84 unc-85 unc-86 Abstract: Twenty-four mutants that alter the normally invariant post-embryonic cell lineages of the nematode Caenorhabditis elegans have been isolated and genetically characterized. In some of these mutants, cell divisions fail that occur in wild-type animals; in other mutants, cells divide that do not normally do so. The mutants differ in the specificities of their defects, so that it is possible to identify mutations that affect some cell lineages but not others. These mutants define 14 complementation groups, which have been mapped. The abnormal phenotype of most of the cell-lineage mutants results from a single recessive mutation; however, the excessive cell divisions characteristic of one strain, CB1322, require the presence of two unlinked recessive mutations. All 24 cell-lineage mutants display incomplete penetrance and/or variable expressivity. Three of the mutants are suppressed by pleiotropic suppressors believed to be specific for null alleles, suggesting that their phenotypes result from the complete absence of gene activity. ------------------- Key: 497 Medline: 81261913 Authors: Meneely PM;Herman RK Title: Suppression and function of X-linked lethal and sterile mutations in C. elegans. Citation: Genetics 97: 65-84 1981 Type: ARTICLE Genes: let-1 let-2 let-3 let-4 let-5 let-6 let-7 let-9 let-10 let-11 let-12 let-14 let-15 let-16 let-18 let-33 let-34 let-35 let-36 let-37 let-38 let-39 let-40 let-41 unc-3 mnDf1 mnDf2 mnDf4 mnDf5 mnDf6 mnDf7 mnDf8 mnDf9 mnDp1 mnDp8 mnDp9 mnDf10 mnDf11 mnDf13 mnDf15 mnDf17 mnDf18 mnDf19 mnDf20 mnDf21 mnDf41 mnDf42 mnDf43 mnDp10 mnDp25 mnDp27 Abstract: We have expanded our collection of recessive lethal and sterile mutants in the region of the X chromosome balanced by mnDp1(X;V), about 15% of the X linkage map, to a total of 54 mutants. The mutations have been mapped with respect to 20 overlapping deficiencies and five X duplications, and they have been assigned to 24 genes by complementation testing. Nine mutants are hermaphrodite- sterile: one of these is a sperm-defect mutant, two have abnormal gonadogenesis and six, in five genes, are maternally influenced mutants, producing inviable zygote progeny. One of the gonadogenesis mutants and two of the maternally influenced mutants are male fertile. All but one of the maternally influenced mutants give cross progeny when mated with wild-type males. Forty-three mutants were tested for suppression by homozygous sup-5 (e1464), which is believed to be specific for null alleles. Ten mutants that were judged by independent criteria not to be null mutants are not suppressed. Nine of the other 33 mutants, in nine genes, are suppressed, five in both heterozygous and homozygous suppressor stocks and four only in homozygous suppressor stocks. ------------------- Key: 498 Medline: 81261882 Authors: Hodgkin J Title: More sex-determination mutants of C. elegans. Citation: Genetics 96: 649-664 1980 Type: ARTICLE Genes: dpy-21 fem-1 her-1 him-5 tra-1 tra-2 tra-3 vab-7 eDf1 eDf2 eDp6 Abstract: Sex determination in Caenorhabditis elegans is controlled by the X chromosome : autosome ratio, i.e. 2A;XX animals are hermaphrodite, and 2A;XO animals are male. A procedure for isolating 2A;XO animals that are transformed in;to hermaphrodites has been developed. Nine mutations causing this transformation have been obtained: eight are recessive, and all of these fall into a new autosomal complementation group, her-1 V. The remaining mutation (her-2) is dominant and has a genetic map location similar to that of tra-1 III. Recessive mutations of tra-1 cause the reverse transformation, transforming 2A;XX animals into males. Therefore, the her-2 mutation may result in constitutive expression of tra-1. Mutations in her-1 are without effect on XX animals, but the her-2 mutation prevents sperm production in both XX and XO animals, in addition to its effect on the sexual phenotype of XO animals. The epistatic relationships between tra and her genes are used to deduce a model for the action of these genes in controlling sex determination. ------------------- Key: 499 Medline: 81148607 Authors: Moerman DG;Baillie DL Title: Formaldehyde mutagenesis in the nematode C. elegans. Citation: Mutation Research 80: 273-279 1981 Type: ARTICLE Genes: dpy-4 let-51 let-53 let-56 let-58 let-59 let-60 unc-5 unc-22 sDf1 sDf2 Abstract: We have found that formaldehyde is capable of inducing mutations in the nematode Caenorhabditis elegans. 4 concentrations of formaldehyde were tested. At a concentration of 1%, formaldehyde is lethal to the nematode, and 0.01% formaldehyde did not induce any mutations in approx. 60 000 tested chromosomes. 2 concentrations of formaldehyde, 0.1% and 0.07%, were found to be mutagenic, inducing both point mutations and deficiencies in the unc-22 region of linkage group IV. 4 of the point mutations have been demonstrated to be alleles of the unc-22 gene and have been mapped within the locus. 2 of the putative deficiencies have been confirmed. Each spans the unc-22 gene and at least 2 other genes in the region. A rough estimate of the forward mutation frequency using 0.1% formaldehyde in this region is 3 X 10(- 5), while for 0.07% ------------------- Key: 500 Medline: 81189438 Authors: Sulston JE;Horvitz HR Title: Abnormal cell lineages in mutants of the nematode C. elegans. Citation: Developmental Biology 82: 41-55 1981 Type: ARTICLE Genes: lin-1 lin-2 lin-3 lin-4 lin-5 lin-6 lin-7 lin-8 lin-9 unc-59 unc-83 unc-84 unc-85 unc-86 Abstract: The phenotypes of cell lineage mutants of the nematode Caenorhabditis elegans are described. The mutants, which define 14 genes, differ in the breadth and nature of their phenotypic defects. Mutants in four genes display very general abnormalities in cell division and may be altered either in cellular maintenance and growth or in the mechanics of cell division and/or DNA replication. Mutants in two genes are specifically defective in the movements and divisions of certain hypodermal nuclei. Mutants in six genes are affected in vulva development in the hermaphrodite and, in some cases, in homologous aspects of sexual maturation in the male; some of these mutants are blocked in vulval cell divisions, wherease others under go extra divisions to generate multiple ectopic pseudovulvae; these genes appear to specify which of two alternative fates is assumed by a set of six cells involved in vulva development. Mutants in two genes produce reiteration in certain cell lineages, i.e., specific cells generate descendants similar to themselves in both their division patterns and the fates of their progeny; these genes may control primary determinative events that occur during the course of a cell lineage. ------------------- Key: 501 Medline: 81237401 Authors: Cassada R;Isnenghi E;Culotti M;von Ehrenstein G Title: Genetic analysis of temperature-sensitive embryogenesis mutants in C. elegans. Citation: Developmental Biology 84: 193-205 1981 Type: ARTICLE Genes: emb-1 emb-2 emb-3 emb-4 emb-5 emb-6 emb-7 emb-8 emb-9 emb-11 emb-12 emb-13 emb-14 emb-15 emb-16 emb-17 emb-18 emb-19 emb-20 emb-21 emb-22 emb-23 emb-24 emb-25 emb-26 emb-27 emb-28 emb-29 emb-30 emb-31 emb-32 emb-33 emb-34 emb-35 let-2 zyg-1 zyg-2 zyg-3 zyg-7 zyg-8 zyg-9 zyg-10 Abstract: A large set of temperature-sensitve (ts) embryonic arrest mutants in the nematode Caenorhabditis elegans has been isolated. Following ethylmethane sulfonate mutagenesis, ts mutants were identified from 10,000 segregated clones by replica plating from 16 to 25C. At least 54 independent ts developmental mutants showed embryonic arrest when the appropriate developmental stage was shifted up. These represent 28% of the independent developmental mutants from 294 ts clones from 155 mutagenized animals. Initial characterization of this subset of emb mutants is reported. Most of them arrest in middle or late embryogenesis with abnormal terminal phenotypes. Additional nonembryonic arrest stages (depending on shift-up regimen) suggest that many emb genes are also required for pre- or postembryonic development. For most of the emb mutants parental gene expression is sufficient for embryonic development at 25C. Based on complementation analysis of 37 new emb mutants together with 32 isolated by other investigators, 25 new emb genes are reported. This brings the total of embryonic arrest genes defined in C. elegans to 54. The new genes have been mapped approximately. In the present set, 10 emb genes map in the middle of linkage group III. The frequency of occurrence of second alleles gives on estimate (by Poisson analysis) for the number of genes required for embryogenesis of about 200. A second estimate is obtained from the fraction of 28% emb mutants among all ts lethal mutants in the screen; for an estimated 2000 essential genes in C. elegans, this corresponds to 560 genes required for embryogenesis. A small subset of highly mutable genes is also described. Results of the present screen for emb mutants are compared to those of others. Several ts mutants gave complex linkage results (apparently not due to double mutations), suggesting chromosome rearrangements. ------------------- Key: 502 Medline: 81189457 Authors: Chalfie M;Sulston J Title: Developmental genetics of the mechanosensory neurons of C. elegans. Citation: Developmental Biology 82: 358-370 1981 Type: ARTICLE Genes: mec-1 mec-2 mec-3 mec-4 mec-5 mec-6 mec-7 mec-8 mec-9 mec-10 mec-12 sup-5 sup-7 unc-86 eDf1 mnDf1 mnDf2 mnDf4 mnDf8 mnDf11 mnDp30 Abstract: Touch sensitivity in the nematode Caenorhabditis elegans is mediated by a set of six sensory neurons, the microtubule cells, of well-characterized anatomy and connectivity. The normal touch response is eliminated when these cells are killed by laser microsurgery. The identification of the microtubule cells as the mediators of touch sensitivity allows us to examine the effects of mutations on the development and differentiation of these cells. Forty-two touch-insensitive mutants have been isolated. These fall into 13 complementation groups. Mutations in five of the complementation groups have recognizable effects on the microtubule cells. These phenotypes include alterations of characteristic cellular ultrastructure, absence of neuronal process growth, and the absence of the cell (either by alterations in the patterns of cell divisions that give rise to the cells or by degeneration or death of existing cells). Because it is likely that we are approaching saturation of genes affecting primarily the microtubule cells, there appear to be relatively few genes that affect the growth and function of this class of cells and no ------------------- Key: 503 Medline: 81216070 Authors: Albert PS;Brown SJ;Riddle DL Title: Sensory control of dauer larva formation in C. elegans. Citation: Journal of Comparative Neurology 198: 435-451 1981 Type: ARTICLE Genes: che-3 daf-1 daf-2 daf-6 daf-10 Abstract: As a sensory response to starvation or overcrowding, Caenorhabditis elegans second-stage larvae may molt into a developmentally arrested state called the dauer larva. When environmental conditions become favorable for growth, dauer larvae mold and resume development. Some mutants unable to form dauer larvae are simultaneously affected in a number of sensory functions, including chemotaxis and mating. The behavior and sensory neuroanatomy of three such mutants, representing three distinct genetic loci, have been determined and compared with wild-type strain. Morphological abnormalities in afferent nerve endings were detected in each mutant. Both amphid and outer labial sensilla are affected in the mutant CB1377 (daf-6)X, while another mutant, CB1387 (daf-10)IV, is abnormal in amphidial cells and in the tips of the cephalic neurons. The most pleitropic mutant, CB1379 (che- 3)I, exhibits gross abnormalities in the tips of virtually all anterior and posterior sensory neurons. The primary structural defect in CB1377 appears to be in the nonneuronal amphidial sheath cells. The disruption of neural organization in CB1377 is much greater in the adult than in the L2 stage. Of all the anterior sense organs examined, only the amphids are morphologically affected in all three mutants. Thus, one or more of the amphidial neurons may mediate the sensory signals for entry into the dauer larva stage in normal animals. Using temperature-sensitive mutants we determined that the same defects which block entry into the dauer stage also prevent recovery of dauer larvae. ------------------- Key: 504 Medline: 81173090 Authors: Riddle DL;Swanson MM;Albert PS Title: Interacting genes in nematode dauer larva formation. Citation: Nature 290: 668-671 1981 Type: ARTICLE Genes: daf-1 daf-2 daf-3 daf-4 daf-5 daf-6 daf-7 daf-8 daf-10 daf-11 daf-12 daf-13 daf-14 daf-16 daf-18 daf-20 Abstract: The dauer larva of Caenorhabditis elegans is a developmentally arrested stage induced by starvation or overcrowding. Mutant genes controlling the ability to form dauer larvae interact in a way which allows them to be ordered in a pathway. Mutant phenotypes suggest that the pathway corresponds to neural processing of environmental stimuli. ------------------- Key: 505 Medline: 81237410 Authors: Swanson MM;Riddle DL Title: Critical periods in the development of the C. elegans dauer larva. Citation: Developmental Biology 84: 27-40 1981 Type: ARTICLE Genes: daf-1 daf-2 daf-4 daf-7 daf-8 daf-10 daf-14 Abstract: The dauer larva of Caenorhabditis elegans is a developmentally arrested stage formed at the second molt under conditions of starvation or overcrowding. It is specialized for long-term survival and dispersal. Dauer-constitutive (daf) mutants form dauer larvae even in an environment favorable for growth. Temperature-sensitive (ts) mutants representing six different genes have been subjected to temperature-shift and -pulse experiments in order to define the times of temperature sensitivity (TSPs). The results for five of the mutants, including one mutant with a maternal effect, show TSPs which bracket the first molt. The exceptional mutant, daf-14, has its TSP within the first larval stage. The TSPs of two mutants, daf-8 and daf-14, exhibit distinct major and minor phases. Temperature-pulse experiments discriminate between alternative interpretations of the temperature-shift data. All the results can be interpreted on the basis of normal and defective execution stages for the ts functions at permissive and restrictive temperatures. ------------------- Key: 506 Medline: 81243723 Authors: Bolanowski MA;Russell RL;Jacobson LA Title: Quantitative measures of aging in the nematode C. elegans. I. Population and longitudinal studies of two behavioral parameters. Citation: Mechanisms of Ageing & Development 15: 279-295 1981 Type: ARTICLE Genes: Abstract: As a first step in the quantitative characterization of senescence in the nematode Caenorhabditis elegans, we have studied movement wave frequency, defecation frequency, and whole-body water efflux as a function of age. Populations of C. elegans, strain N2, were cultured monoxenically on E. coli lawns at 20 degrees C. The median lifespan in such populations was approximately 12 days. Population mean movement wave frequency declined linearly with age (slope = -4.66 waves/minute per day). The decline in population mean defecation frequency (defecations per minute) was multiphasic, consisting of (1) a rapid decline (slope = -0.233 defecations/minute per day) from day 3 to day 6, (2) no apparent trend from day 6 to day 9, and (3) a gradual decline (slope = -0.089 defecations/minute per day) from 9 to day 14. Animals alive on or after day 15 were not observed to defecate. In longitudinal studies, individual animals exhibited linear declines in movement wave frequency and multiphasic declines in defecation frequency. For future population studies, the age- dependent declines in movement and defecation frequency appear sufficiently large and reproducible to a multiparametric description of senescence in C. elegans. One physiological parameter, 3H2O efflux, was found to be age-independent and to consist of two first- order rates. The half-times of the slow and fast efflux rates were approximately 15 and approximately 2.1 minutes, respectively. The two half-times and the fractions of 3H2O exhibiting the two half-times were invariant with ------------------- Key: 507 Medline: 81210196 Authors: Chalfie M;Horvitz HR;Sulston JE Title: Mutations that lead to reiterations in the cell lineages of C. elegans. Citation: Cell 24: 59-69 1981 Type: ARTICLE Genes: lin-4 unc-86 Abstract: Cells in the nematode Caenorhabditis elegans arise from invariant cell lineages. Mutations in two genes, unc-86 and lin-4, alter multiple and mutually exclusive sets of these lineages. In these mutants, particular cells repeat division patterns normally associated with their parental or grandparental progenitors. The effects of unc-86 are highly specific, altering in equivalent ways the lineages of three post-embryonic neuroblasts that in the wild- type undergo similar division patterns. The effects of lin-4 are more varied, resulting in a number of types of lineage reiterations as well as in supernumerary molts and the continued synthesis of larval- specific cuticle. The reiteration of a given cell division or pattern of cell divisions leads to the repeated generation of cells indistinguishable (by both light and electron microscopy) from those produced after the same division or pattern of cell divisions in the wild-type. This correlation between lineage history and cell fate suggests that in C. elegans a particular sequence of cell divisions may be necessary for the generation of a particular cell type. Reiterative lineages, often referred to as stem cell lineages, may be basic to the development of nematodes and other organisms. We suggest that the wild-type unc-86 and lin-4 genes act to modify latent reiterative cell lineages, which are revealed when the activity of one of these genes is eliminated. ------------------- Key: 508 Medline: 81240715 Authors: Hecht RM;Schomer DF;Oro JA;Bartel AH;Hungerford III EV Title: Simple adaptations to extend the range of flow cytometry five orders of magnitude for DNA analysis of uni- and multicell systems. Citation: Journal of Histochemistry & Cytochemistry 29: 771-774 1981 Type: ARTICLE Genes: Abstract: Procedures and instrumentation are described to extend the capability of a cytometry system to record samples that exhibit a wide range of fluorescence such as multicellular systems. The methods employs a log amplifier in combination with a set of neutral density filters that reduces the incident light reaching the photomultiplier tube. With any given filter, signals within an intensity range of 200-fold can be measured; different filters can be used to obtain an extended overall range. Polystyrene fluorescent microspheres and a variety of mithramycin stained biological samples ranging from yeast cells to Paramecium were processed by the system. The relative DNA content of individual multicellular embryos was determined for a heterogeneous population of embryonic stages isolated from the nematode, Caenorhabditis elegans. As part of the evaluation of the procedure, the practical upper limit of range extension was determined. The most intense fluorescent signal was produced when untreated pecan pollen stained with ethidium bromide fluoresced with a factor (8.4 +/- 1.3) x 10*4 more than ethidium bromide stained with E. coli cells. ------------------- Key: 509 Medline: 81220935 Authors: MacLeod AR;Karn J;Brenner S Title: Molecular analysis of the unc-54 myosin heavy-chain gene of C. elegans. Citation: Nature 291: 386-390 1981 Type: ARTICLE Genes: unc-54 Abstract: The properties of a small internal deletion mutant, E675, have been exploited in the molecular cloning of the unc-54 gene. This mutation uniquely identifies unc-54 sequences as molecules of altered length in E675 and provides a genetic and physical marker for the active gene, its messenger RNA and its protein product. ------------------- Key: 510 Medline: 81213193 Authors: Hecht RM;Gossett LA;Jeffery WR Title: Ontogeny of maternal and newly transcribed mRNA analyzed by in situ hybridization during development of C. elegans. Citation: Developmental Biology 83: 374-379 1981 Type: ARTICLE Genes: Abstract: In the present investigation we have examined the titer of poly(A) in squashes prepared from oocytes and variously staged embryos of the nematode Caenorhabditis elegans var. Bristol (N2) by in situ hybridization with a [3H]poly(U) probe. As shown by control experiments in which squashes were treated with dilute alkali and RNase prior to in situ hybridization, this probe interacts specifically with poly(A) sequences which are presumably present in poly(A)+ RNA. Using this method and saturating concentrations of the probe, it was shown that isolated oocytes and embryos up to the 125-cell stage exhibited substantial levels of poly(A) in their cytoplasms but no detectable amounts of this sequence within their nuclei. Nuclear poly(A) was first detected at the 90-cell stage and afterward increased at a linear rate through the 550-cell stage. The titer of total embryonic poly(A) also increased at a linear rate up to larval hatching. The results suggest that the major transcriptional effort for poly(A)+ RNA begins at the 90- to 125-cell stage of C. elegans embryogenesis and that the poly(A)+ RNA present in the cytoplasm prior to this time is primarily of maternal origin. ------------------- Key: 511 Medline: Authors: Cox GN;Kusch M;DeNevi K;Edgar RS Title: Temporal regulation of cuticle synthesis during development of C. elegans. Citation: Developmental Biology 84: 277-285 1981 Type: ARTICLE Genes: fer-1 Abstract: The pattern of cuticle protein synthesis during development of the nematode Caenorhabditis elegans has been studied using NaH(14)CO3. Both pulse-labeling and pulse-chase-labeling experiments indicate that synthesis of cuticle components occurs at high levels during the molting periods and at much reduced rates during the intermolt periods. No such discontinuous pattern is observed for the synthesis of total noncuticle macromolecules during development. The soluble and insoluble proteins of the cuticle, which comprise the inner and outer cuticle layers, respectively, follow similar patterns of synthesis during the two molts examined. At each molt the structural components of the cuticle account for approximately 10% of the total macromolecules labeled by NaH(14)CO3. No evidence is found for reuse of cuticle material between successive developmental stages of C. elegans. ------------------- Key: 512 Medline: Authors: Klass MR;Hirsh D Title: Sperm isolation and biochemical analysis of the major sperm protein from C. elegans. Citation: Developmental Biology 84: 299-312 1981 Type: ARTICLE Genes: him-1 him-8 Abstract: In order to facilitate the biochemical analysis of spermatogenesis in the nematode Caenorhabditis elegans methods have been developed for obtaining large quantities of males and for the isolation of sperm. Males are isolated by a passive filtration method from strains producing high proportions of males and sperm are isolated by physical pressure followed by filtration and differential centrifugation. Biochemical analyses show that sperm contain a major protein component that represents 17% of the total sperm protein. This protein has a molecular weight of 15,600, an isoelectric pH of 8.6, and exists as a dimer. It is shown by immunocytochemical techniques to be a specific product of spermatogenesis. It is localized in the proximal arm of the male gonad and in the sperm of both the male and hermaphrodite but it is not detected in other tissues of the nematode. It is not a nuclear binding protein. Pulse-labeling studies show that this major sperm protein is first synthesized in the proximal arm of the male gonad beginning at 39-42 hr after hatching at 20C. Poly(A) mRNA coding for this protein is first detected in a translatable form just before synthesis of this sperm protein suggesting transcriptional control. ------------------- Key: 513 Medline: 82005153 Authors: Johnson CD;Duckett JG;Culotti JG;Herman RK;Meneely PM;Russell RL Title: An acetylcholinesterase-deficient mutant of the nematode C. elegans. Citation: Genetics 97: 261-279 1981 Type: ARTICLE Genes: ace-1 ace-2 lon-1 mec-4 osm-1 unc-1 unc-3 unc-7 unc-24 unc-64 mnDf4 mnDf8 mnDp1 mnDp8 mnDp9 mnDf41 mnDf42 mnDp25 mnDp27 Abstract: Within a set of five separable molecular forms of acetylcholinesterase found in the nematode Caenorhabditis elegans, previously reported differences in kinetic properties identify two classes, A and B, likely to be under separate genetic control. Using differences between these classes in sensitivity to inactivation by sodium deoxycholate, a screening procedure was devised to search for mutants affected only in class A forms. Among 171 previously isolated behavioral and morphological mutant strains examined by this procedure, one (PR946) proved to be of the expected type, exhibiting a selective deficiency of class A acetylcholinesterase forms. Although originally isolated because of its uncoordinated behavior, this strain was subsequently shown to harbor mutations in two genes; one in the previously identified gene unc-3, accounting for its behavior, and one in a newly identified gene, ace-1, accounting for its selective acetylcholinesterase deficiency. Derivatives homozygous only for the ace-1 mutation also lacked class A acetylcholinesterase forms, but were behaviorally and developmentally indistinguishable from wild type. The gene ace-1 has been mapped near the right end of the X chromosome. Gene dosage experiments suggest that it may be a structural gene for a component of class A acetylcholinesterase forms. ------------------- Key: 514 Medline: 82005154 Authors: Culotti JG;von Ehrenstein G;Culotti MR;Russell RL Title: A second class of acetylcholinesterase-deficient mutants of the nematode C. elegans. Citation: Genetics 97: 281-305 1981 Type: ARTICLE Genes: ace-1 ace-2 unc-11 unc-35 unc-38 unc-57 unc-63 unc-73 unc-74 unc-89 Abstract: In JOHNSON et al. (1981), the Caenorhabditis elegans mutant strain PR1000, homozygous for the ace-1 mutation p1000, is shown to be deficient in the class A subset of acetylcholinesterases, which comprises approximately one-half of the total C. elegans acetylcholinesterase activity. Beginning with this strain, we have isolated 487 new behavioral and morphological mutant strains. Two of these, independently derived, lack approximately 98% of the wild-type acetylcholinesterase activity and share the same specific uncoordinated phenotype; both move forward in a slow and uncoordinated manner, and when mechanically stimulated to induce reversal, both hypercontract and become temporarily paralyzed. In addition to the ace-1 mutation, both strains also harbor recessive mutations in the same newly identified gene, ace-2, which maps to chromosome I and is therefore not linked to ace-1. Gene dosage experiments suggest that ace-2 is a structural gene for the remaining class B acetylcholinesterases, which are not affected by ace-1.--The uncoordinated phenotype of the newly isolated, doubly mutant strains depends on both the ace-1 and ace-2 mutations; homozygosity for either mutation alone produces normally coordinated animals. This result implies functional overlap of the acetylcholinesterases controlled by ace-1 and ace-2, perhaps at common synapses. Consistent with this, light microscopic histochemical staining of permeabilized whole mounts indicates some areas of possible spatial overlap of these acetylcholinesterases (nerve ring, longitudinal nerve cords). In addition, there is at least one area where only ace-2-controlled acetylcholinesterase activity appears (pharyngeo-intestinal ------------------- Key: 515 Medline: 82005155 Authors: Waterston RH Title: A second informational suppressor, sup-7 X, in C. elegans. Citation: Genetics 97: 307-325 1981 Type: ARTICLE Genes: dpy-18 sup-5 sup-7 unc-13 unc-15 unc-52 Abstract: More than 30 independent suppressor mutations have been obtained in the nematode C. elegans through reversion analysis of two unc-13 mutants. Many of the new isolates map to the region of the previously identified informational suppressor, sup-5 III (WATERSTON and BRENNER 1978). Several of the other suppressor mutations map to the left half of the X-linkage group and define a second suppressor gene, sup-7 X. In tests against 40 mutations in six genes, the sup-7(st5) allele was found to suppress to a greater extent the same alleles acted on by sup-5(e1464). Like sup-5(e1464), sup-7(st5) acts on null alleles of the myosin heavy-chain gene unc-54 I (MACLEOD et al. 1977; MACLEOD, WATERSTON and BRENNER 1977) and the putative paramyosin gene unc-15 I (WATERSTON et al. 1977). Chemical analysis of unc-15(e1214); sup- 7(st5) animals show that paramyosin is restored to more than 30% of the wild-type level.--As was observed for sup-5(e1464), suppression by sup-7(st5) is dose dependent and is greater in animals grown at 15 degrees than at 25 degrees. However, associated with this increased suppression is a decreased viability of sup-7(st5) homozygotes. Reversion of the lethality has resulted in the isolation of deficiency mutations that complement st5 lethality, but lack suppressor function. These properties of sup-7(st5) suggest that it, like sup-5(e1464), is an information suppressor of null alleles, and its reversion via deficiencies further narrows the possible explanations of its action. ------------------- Key: 516 Medline: 82078058 Authors: Files JG;Hirsh D Title: Ribosomal DNA of C. elegans. Citation: Journal of Molecular Biology 149: 223-240 1981 Type: ARTICLE Genes: Abstract: We have characterized the organization of the genes encoding for 18 S, 5.8 S and 26 S ribosomal RNAs in the nematode Caenorhabditis elegans. These ribosomal genes, present in about 55 copies per haploid genome, alternate in a repeating tandem array. The repeating unit is only 7000 base-pairs, containing a nontranscribed spacer of no more than 1000 base-pairs. Most of the repeating units have identical restriction maps, but one repeat contains a delection of 2900 base-pairs, which eliminates all or part of the 18 S coding region. We have found no difference in the major ribosomal DNA restriction endonuclease cleavage patterns between two interbreeding strains of C. elegans, but found differences between C. elegans and the closely related Caenorhabditis briggsae. ------------------- Key: 517 Medline: 81239808 Authors: Cox GN;Kusch M;Edgar RS Title: Cuticle of C. elegans: Its isolation and partial characterization. Citation: Journal of Cell Biology 90: 7-17 1981 Type: ARTICLE Genes: fer-1 him-8 Abstract: The adult cuticle of the soil nematode, Caenorhabditis elegans, is a proteinaceous extracellular structure elaborated by the underlying layer of hypodermal cells during the final molt in the animal's life cycle. The cuticle is composed of an outer cortical layer connected by regularly arranged struts to an inner basal layer. The cuticle can be isolated largely intact and free of all cellular material by sonication and treatment with 1% sodium dodecyl sulfate (SDS). Purified cuticles exhibit a negative material in the basal cuticle layer. The cuticle layers differ in their solubility in sulfhydryl reducing agents, susceptibility to various proteolytic enzymes and amino acid composition. The struts, basal layer, and internal cortical layer are composed of collagen proteins that are extensively cross-linked by disulfide bonds. The external cortical layer appears to contain primarily noncollagen proteins that are extensively cross- linked by nonreducible covalent bonds. The collagen proteins extracted from the cuticle with a reducing agent can be separated by SDS-polyacrylamide gel electrophoresis into eight major species differing in apparent molecular weight. ------------------- Key: 518 Medline: 81270494 Authors: Babu P;Brenner S Title: Spectrum of 32P-induced mutants of C. elegans. Citation: Mutation Research 82: 269-273 1981 Type: ARTICLE Genes: unc-17 unc-22 Abstract: Mutants of the free living nematode C. elegans were isolated by using 32P as a mutagen. It is shown that most of these mutants arise from 32P suicide. A comparison of EMS-induced and 32P-induced autosomal recessive mutations shows that there are no large regions of C. elegans genome which are protected from chemical mutagenic action of EMS. ------------------- Key: 520 Medline: Authors: Yeargers E Title: Effect of gamma-radiation on dauer larvae of C. elegans. Citation: Journal of Nematology 13: 235-237 1981 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans is an ideal organism for studying the process of aging. It is easy to culture and has a short lifespan and specific aging symptoms. At 20 C the adult, reproductive stage occurs about 3 d after hatching; 4 d later egg laying ceases and degenerative changes begin. Death occurs about 10 d later. The postdauer lifetime is independent of the duration of the dauer stage of less than 60d; this suggests that dauer larvae do not age. The purpose of this study was to examine the notion that the lack of aging in dauer larvae is due to an intrinsic resistance to environmental stress, specifically ionizing radiation. ------------------- Key: 521 Medline: Authors: Bollinger JA;Willett JD Title: A method for synchrony of adult C. elegans. Citation: Nematologica 26: 491-493 1980 Type: ARTICLE Genes: Abstract: There are two ways of obtaining populations of adults from cultures of nematodes. The first is to treat juveniles with an inhibitor of DNA synthesis or shift them to a higher culture temperature to prevent subsequent reproduction. The second is to separate the adults from juveniles by settling. Inhibitors of DNA synthesis are non-specific and high temperatures may damage the nematodes. Therefore, the second method is preferable. This paper describes a method that uses settling and filtration to obtain synchronized populations of adults in sufficient quantity for life history studies. ------------------- Key: 522 Medline: Authors: Khan FR;McFadden BA Title: A rapid method of synchronizing developmental stages of C. elegans. Citation: Nematologica 26: 280-282 1980 Type: ARTICLE Genes: Abstract: Biochemical studies of the free-living nematode C. elegans require large numbers grown axenically and synchronously. Patel & MacFadden developed a procedure using alkali at 25C to axenize cultures of C. elegans after which eggs were separated into three bands in a sucrose gradient, one of which contained eggs that hatched in 10-13 hrs yielding a synchronous culture. We now report an improvement which is faster, does not require density-gradient sedimentation and markedly increases hatchability. ------------------- Key: 523 Medline: 82028246 Authors: Cox GN;Staprans S;Edgar RS Title: The cuticle of C. elegans. II. Stage-specific changes in ultrastructure and protein composition during postembryonic development. Citation: Developmental Biology 86: 456-470 1981 Type: ARTICLE Genes: daf-2 fer-1 lin-4 lin-14 Abstract: The cuticle of the free-living nematode Caenorhabditis elegans is a proteinaceous extracellular structure that is replaced at each of four postembryonic molts by the underlying hypodermis. The cuticles of the adult and three juvenile stages (L1, Dauer larva, L4) have been compared ultrastructurally and biochemically. Each cuticle has an annulated surface and comprises two main layers, an inner basal layer and an outer cortical layer. The adult cuticle has an additional clear layer which separates the basal and cortical layers and is traversed by regularly arranged columns of electron-dense material. The fine structure of the cortical layer is similar in cuticles from different stages while that of the basal layer is stage specific. Purified cuticles were obtained by sonication and treament with sodium dodecyl sulfate (SDS) and their component proteins solubilized with a sulfhydryl reducing agent. The degree of cuticle solubility is stage specific and the insoluble structures for each cuticle were localized by electron microscopy. Analysis of 35S-labeled soluble cuticle proteins by SDS-polyacrylamide gel electrophoresis yields unique banding patterns for each stage. Most proteins are of high molecular weight (100-200K) and are restricted to particular stages. Sixteen of the nineteen major proteins characterized are specifically degraded by bacterial collagenase. The results indicate that the different molts are not reiterative, but require the integration of both unique and shared gene functions. The potential use of stage-specific cuticle differences to identify and characterize regulatory genes controlling cuticle-type switching during development is discussed. ------------------- Key: 524 Medline: 82028281 Authors: Kimble J Title: Alterations in cell lineage following laser ablation of cells in the somatic gonad of C. elegans. Citation: Developmental Biology 87: 286-300 1981 Type: ARTICLE Genes: Abstract: The postembryonic cell lineage of the somatic gonad is essentially invariant in Caenorhabditis elegans. The two exceptions to this rule of invariance involve a natural ambiguity in the ancestry of certain cells such that each of the two precursor cells assumes one of two alternative fates in a given animal. In this paper, experiments are reported in which laser microsurgery is used to kill individual cells in the developing somatic gonad. Such intervention perturbs the normal environment of the remaining cells; a change observed in the expected behavior of these cells suggests that extrinsic cues may normally play a role in controlling that behavior. Several different lineage alterations have been observed after laser microsurgery in the somatic gonad. These include switches in the type of lineage followed by a given precursor cell, reversals in lineage polarity, duplications of a lineage, and alterations in the number of cells produced in the lineage. The only cases in which cells switch from one lineage type to another involve pairs of cells which exhibit natural ambiguity. In most cases, the interactions inferred from these changes seem to occur between neighboring somatic gonadal cells. In one case, induction of the vulva, the interaction occurs between a single somatic gonadal cell, the anchor cell, and the precursors to the vulva in a neighboring tissue, the hypodermis. The roles of intrinsic and extrinsic cues in ------------------- Key: 525 Medline: 82060653 Authors: Kimble JE Title: Strategies for control of pattern formation in C. elegans. Citation: Philosophical Transactions of the Royal Society of London 295B: 539-551 1981 Type: REVIEW Genes: Abstract: In this paper, strategies for controlling pattern formation in Caenorhabditis elegans are reviewed. The somatic tissues of this small nematode develop, in large part, by invariant cell lineages, whereas the germ-line tissue arises primarily by a variable pattern of divisions. The spatial organization of the germ-line tissue depends on special regulatory cells, the distal tip cells, which appear to influence nearby germ cells to remain in mitosis. In somatic tissues, the problem of specifying that a cell in a particular position assumes a particular fate seems to be controlled by a number of different strategies. These include the production of non-equivalent cells in particular positions of the lineage tree, local interactions between apparently equivalent cells in close contact, and the influence of another special regulatory cell, the anchor cell, over certain neighbouring cells. ------------------- Key: 526 Medline: Authors: Mounier N Title: Location of neurosecretory-like material in C. elegans. Citation: Nematologica 27: 160-166 1981 Type: ARTICLE Genes: Abstract: The distribution of neurosecretory-like material was investigated in C. elegans, var. Bergerac and Bristol by classical histochemical methods. No nerve cells of the anterior nervous system and the cords contained such material but the two gland cells in the excretory system possessed paraldehyde-fuschin positive granules. Fixation in osmium tetroxide and in hot chromic acid were essential before PF treatment. The nature of the granules and their role are discussed. ------------------- Key: 527 Medline: Authors: Russell RL Title: Mutants of neurotransmitter metabolism and action in the nematode C. elegans. Citation: "Genetic Research Strategies in Psychobiology and Psychiatry. Psychobiology and Psychopathology Volume I." Gershon ES, Matthysse S, Breakefield XO and Ciaranello RD (eds), Boxwood Press, Pacific Grove, CA. I: 113-128 1981 Type: REVIEW Genes: ace-2 cat-1 cat-2 cat-3 cat-4 cat-5 cha-1 unc-29 unc-38 unc-40 unc-63 unc-74 unc-86 Abstract: This chapter is in part a review of the work of others and in part a summary of recent results from our own laboratory. It attempts to cover the currently available information on apparent neurotransmitters in the small soil nematode Caenorhabditis elegans, whose advantages of genetic manipulability and cellular simplicity have recently gained it some favor in investigations of genetic control mechanisms in neural development (for review, see Riddle, 1978). Particular attention is given to mutants that affect either the level or the action of apparent neurotransmitters, since it seems likely that such mutants may have the most to offer toward the understanding of human genetic neuropathies. The general features of C. elegans are described briefly at the outset, then each apparent neurotransmitter is considered in turn, and finally a few potential implications for other organisms ------------------- Key: 528 Medline: 82028297 Authors: Sternberg PW;Horvitz HR Title: Gonadal cell lineages of the nematode Panagrellus redivivus and implications for evolution by the modification of cell lineage. Citation: Developmental Biology 88: 147-166 1981 Type: ARTICLE Genes: Abstract: To explore the nature of cell lineage modifications that have occurred during evolution, the gonadal cell lineages of the nematode Panagrellus redivivus have been determined and compared to the known gonadal lineages of Caenorhabditis elegans. Essentially invariant lineages generate the 143 somatic cells of the male gonad and at least 326 somatic cells of the female gonad of P. redivivus. The basic program of gonadogenesis is strikingly similar among both sexes of both species. For example, the early division patterns of the somatic gonad precursors Z1 and Z4 are almost identical. Later division patterns are more divergent and, in a few cases, generate structures that are species specific. In general, similar cell types are produced after similar patterns of cell divisions. Differences among Z1 and Z4 cell lineages appear to reflect phylogenetic modifications of a common developmental program. The nature of these differences suggests that the evolution of cell lineages involves four distinct classes of alterations: switches in the fate of a cell to that normally associated with another cell; reversals in the polarity of the lineage generated by a blast cell; alterations in the number of rounds of cell division; and an "altered segregation" of developmental potential, so that a potential normally associated with one cell instead becomes associated with its sister. A number of cell deaths occur during gonadogenesis in P. redivivus. The death of Z4.pp, a cell that controls the development of the posterior ovary in C. elegans, probably prevents the development of a posterior ovary in P. redivivus and hence is responsible for the gross differences in the morphologies of the gonads of the P. redivivus female and the C. elegans hermaphrodite. As exemplified by the death of Z4.pp, an alteration in the fate of a "regulatory cell" could facilitate rapid and/or discontinous evolutionary ------------------- Key: 529 Medline: 82053219 Authors: Ward S;Argon Y;Nelson GA Title: Sperm morphogenesis in wild-type and fertilization-defective mutants of C. elegans. Citation: Journal of Cell Biology 91: 26-44 1981 Type: ARTICLE Genes: fer-1 fer-2 fer-3 fer-4 fer-6 Abstract: Taking advantage of conditions that allow spermatogenesis in vitro, the timing and sequence of morphological changes leading from the primary spermatocyte to the spermatozoon is described by light and electron microscopy. Together with previous studies, this allows a detailed description of the nuclear, cytoplasmic, and membrane changes occurring during spermatozoan morphogenesis. By comparison with wild type, abnormalities in spermatogenesis leading to aberrant infertile spermatozoa are found in six fertilization-defective (fer) mutants. In fer-1 mutant males, spermatids appear normal, but during spermiogenesis membranous organelles (MO) fail to fuse with the sperm plasma membrane and a short, though motile. pseudopod is formed. In fer-2, fer-3, and fer-4 mutants, spermatids accumulate 48-nm tubules around their nuclei where the centriole and an RNA containing perinuclear halo would normally be. In all three mutants, spermatids still activate to spermatozoa with normal fusion of their MOs, but the pseudopods formed are aberrant in most fer-2 and fer-4 spermatozoa and in some fer-3 spermatozoa. In fer-5 mutant males, spermatozoa do not form. Instead, defective spermatids with crystalline inclusions and abnormal internal laminar membranes accumulate. In fer-6 mutant males, only a few spermatozoa form and these have defective pseudopods. These spermatozoa retain their fibrous bodies, a structure which normally disassembles in the spermatid. The time of appearance of developmental abnormalities in all of these mutants correlates with the temperature-sensitive periods for development of infertility. The observation that each of these mutants has a different and discreet set of morphological defects, a structure which normally disassembles in the spermatid. The time of appearance of developmental abnormalities in all of these mutants correlates with the temperature-sensitive periods for development of infertility. The observation that each of these mutants has a different and discreet set of morphological defects, a structure which normally disassembles in the spermatid. The time of appearance of developmental abnormalities in all of these mutants correlates with the temperature-sensitive periods for development of infertility. The observation that each of these mutants has a different and discreet set of morphological defects shows that the strict sequence of morphogenetic events that occurs during wild-type spermatogenesis cannot arise because each event is dependent on previous events. Instead, spermatozoa, like bacteriophages, must be formed by multiple independent pathways of morphogenesis. ------------------- Key: 530 Medline: 82089292 Authors: Rand JB;Johnson CD Title: A single-vial biphasic liquid extraction assay for choline acetyltransferase using [3H]choline. Citation: Analytical Biochemistry 116: 361-371 1981 Type: ARTICLE Genes: Abstract: A single-vial liquid extraction assay for choline acetyltransferase that uses [3H]choline as the labeled substrate has been devised. [3H]Choline is incubated with an excess of acetyl-CoA in a small reaction vial which also serves as a scintillation vial. After a suitable reaction period, unreacted [3H]choline is quickly and quantitatively converted to phosphoryl-[3H]choline by the addition of an excess of choline kinase. This treatment is followed by the addition of scintillation fluid containing sodium tetraphenylboron after which the vial is capped, shaken, and counted. A two-phase system is produced in which product [3H]acetylcholine is selectively extracted into the scintillation fluid, where it is counted. Phosphoryl-[3H]choline remains in the aqueous phase and is not counted. This assay is rapid, simple, and quite sensitive. In comparison to assays using acetyl-CoA as the labeled substrate, it is less sensitive to interference by other enzymes and thus more suitable for measuring choline acetlytransferase in crude extracts and in the initial stages of purification. Similar single-vial radiometric assays are described for choline kinase and acetyl-CoA hydrolases. ------------------- Key: 531 Medline: Authors: Wright KA;Thomson JN Title: The buccal capsule of C. elegans (Nematoda: Rhabditoidea): An ultrastructural study. Citation: Canadian Journal of Zoology 59: 1952-1961 1981 Type: ARTICLE Genes: Abstract: The buccal cavity of the free-living nematode Caenorhabditis elegans has been analysed by serial section electron microscopy. Whereas the regions classically identified in the rhabditid buccal capsule can be distinguished, the cuticle lining does not constitute separate cuticular plates, but rather, structural-functional differentiations within a cuticle continuous with that of the esophagus. Only the lip region (cheilostom) is lined by body wall cuticle. The prostom cuticle is underlain by two rings of syncytial arcade cytoplasm connected to nine cell bodies. The mesostom cuticle is underlain by the nonmuscular epithelial cells of the esophagus, whereas the cuticle of the metastom and telostom is underlain by esophageal muscle cells m1 and m2. During moulting, buccal cuticle is produced later than body cuticle and its formation is characterized by accumulation of dense granules in both arcade and esophageal cytoplasm. It is concluded that the buccal capsule should be considered as "astomatous" in the terminology of K.A. ------------------- Key: 532 Medline: 82024235 Authors: Ouazana R;Herbage D Title: Biochemical characterization of the cuticle collagen of the nematode C. elegans. Citation: Biochimica et Biophysica Acta 669: 236-243 1981 Type: ARTICLE Genes: Abstract: Proteins of purified cuticles from adults of the small free-living nematode Caenorhabditis elegans are solubilized by reduction in the presence of a strong denaturing agent and then carboxymethylated. As in the large parasitic nematode Ascaris lumbricoides, these soluble proteins appeared to be collagens by their amino acid compositions. C. elegans cuticle collagen is separated into seven major components with different apparent molecular weights by molecular sieve chromatography and sodium dodecyl sulphate-polyacrylamide gel electrophoresis. The two main components, which together account for more than 64% of the total cuticle collagen, were extracted from gel after electrophoresis and analyzed. They differ in their amino acid compositions and would seem to represent genetically distinct collagen chains. The results presented lead to the hypothesis of the presence in this collagen of at least two different chains. ------------------- Key: 533 Medline: 81098344 Authors: Siddiqui SS;Babu P Title: Kynurenine hydroxylase mutants of the nematode C. elegans. Citation: Molecular & General Genetics 179: 21-24 1980 Type: ARTICLE Genes: flu-1 Abstract: The relation of intestinal autofluorescence to tryptophan catabolism in the free-living nematode Caenorhabditis elegans has been investigated. L-Kynurenine hydroxylase (EC 1.14.13.9) activity has been detected in normal (wild-type) individuals. Mutants in the gene flu-1 which are characterized by an altered autofluorescence of the intestine cells, i.e., more intense than wild type and bluish purple instead of light blue have also been examined. They show a markedly reduced activity of kynurenine hydroxylase. The finding supports the previously proposed model for altered fluorescence based on chromatographic identification of tryptophan catabolites ------------------- Key: 534 Medline: 82185819 Authors: Goldstein P;Slaton DE Title: The synaptonemal complexes of C. elegans: Comparison of wild-type and mutant strains and pachytene karyotype analysis of wild-type. Citation: Chromosoma 84: 585-597 1982 Type: ARTICLE Genes: him-8 Abstract: Normal synaptonemal complexes (SCs), consisting of two lateral elements and a central element, are present in wild-type, him-4 and him-8 mutant strains in both hermaphrodites and males of caenorhabditis elegans. Thus, the increase in rate of nondisjunction in the him mutants is not related to aberrant SC morphology. The wild- type hermaphrodite has six SCs, as determined from 3-D reconstruction analysis of serial section from electron microscopy. Thus, n=6 and this confirms early reports based on cytological studies with the light microscope. Only one end of the SC is attached to the nuclear envelope while the other end is free in the nucleoplasm and there is no apparent bouquet formation. Either end of the SC can attach to the nuclear envelope. The pairing behavior of the XX bivalent is normal and occurs synchronously with the autosomes. Electron dense bodies, or knobs, are associated with the SC via the central element and displace the chromatin for a distance of 200 nm. Each pachytene nucleus of the wild-type hermaphrodite has six such structures that are randomly dispersed along the bivalents such that some SCs have one or two knobs while others have none. Their function is unknown. ------------------- Key: 535 Medline: 82145562 Authors: Butler MH;Wall SM;Luehrsen KR;Fox GE;Hecht RM Title: Molecular relationships between closely related strains and species of nematodes. Citation: Journal of Molecular Evolution 18: 18-23 1981 Type: ARTICLE Genes: Abstract: Electrophoretic comparisons have been made for 24 enzymes in the Bergerac and Bristol strains of Caenorhabditis elegans and the related species, Caenorhabditis briggsae. No variation was detected between the two strains of C. elegans. In contrast, the two species, C. elegans and C. briggsae exhibited electrophoretic differences in 22 of 24 enzymes. A consensus 5S rRNA sequence was determined for C. elegans and found to be identical to that from C. briggsae. By analogy with other species with relatively well established fossil records it can be inferred that the time of divergence between the two nematode species is probably in the tens of millions of years. The limited anatomical evolution during a time period in which proteins undergo extensive changes supports the hypothesis that anatomical evolution is not dependent on overall protein ------------------- Key: 536 Medline: 82120291 Authors: Nelson GA;Roberts TM;Ward S Title: C. elegans spermatozoan locomotion: Amoeboid movement with almost no actin. Citation: Journal of Cell Biology 92: 121-131 1982 Type: ARTICLE Genes: fer-2 unc-15 unc-22 unc-23 unc-45 unc-52 unc-60 unc-78 unc-82 unc-87 unc-89 unc-90 Abstract: The pseudopods of Caenorhabditis elegans spermatozoa move actively causing some cells to translocate when the sperm are dissected into a low osmotic strength buffered salts solution. On time-lapse video tapes, pseudopodial projections can be seen moving at 20-45 micrometers/min from the tip to the base of the pseudopod. This movement occurs whether or not the cell is attached to a substrate. Translocation of the cell is dependent on the substrate. Some spermatozoa translocate on acid-washed glass, but a better substrate is prepared by drying an extract of Ascaris uteri (the normal site of nematode sperm motility) onto glass slides. On this substrate more than half the spermatozoa translocate at a velocity (21 micrometers/min) similar to that observed in vivo. Translocating cells attach to the substrate by their pseudopodial projections. They always move toward the pseudopod; changes in direction are caused by changes in pseudopod shape that determine points of detachment and reattachment of the cell to the substrate. Actin comprises less than 0.02% of the proteins in sperm, and myosin is undetectable. No microfilaments are found in the sperm. Immunohistochemistry shows that some actin is localized in patches in the pseudopod. The movement of spermatozoa is unaffected by cytochalasins, however, so there is no evidence that actin participates in locomotion. Fertilization-defective mutants in genes fer-2, fer-4, and fer-6 produce spermatozoa with defective pseudopodial projections, and these spermatozoa are largely immotile. Mutants in the spermatozoa do not translocate. Thus pseudopod movement is correlated with the presence of normal projections. Twelve mutants with defective muscles have spermatozoa with normal movement, so these genes do not specify products needed for both muscle and nonmuscle cell motility. ------------------- Key: 537 Medline: 82120292 Authors: Roberts TM;Ward S Title: Centripetal flow of pseudopodial surface components could propel the amoeboid movement of C. elegans spermatozoa. Citation: Journal of Cell Biology 92: 132-138 1982 Type: ARTICLE Genes: fer-1 fer-2 Abstract: Latex beads and wheat germ agglutinin (WGA) were used to examine the movement of membrane components on amoeboid spermatozoa of Caenorhabditis elegans. The behavior of beads attached to the cell revealed continuous, directed movement from the tip of the pseudopod to its base, but no movement on the cell body. Lectin receptors are also cleared from the pseudopod (4). Blocking preexisting lectin receptors with unlabeled WGA followed by pulse-labeling wih fluorescent WGA showed that new lectin receptors are continuously inserted at the tip of the pseudopod. Like latex beads, these new lectin receptors move continuously over the pseudopod surface to the cell body-pseudopod junction where they are probably internalized. Mutants altering the rate of membrane flow, and eliminating its topographical asymmetry, have been identified. Together with the observation that fluorescent phospholipids are cleared from the pseudopod of developing spermatozoa at the same rate as lectin receptors (25), these results show that there is bulk membrane flow over the pseudopod with assembly at the tip and apparent disassembly at the base. There are no vesicles visible at either the pseudopodial tip or base, so these spermatozoa must have a novel mechanism for insertion and uptake of membrane components. This membrane flow could provide the forward propulsion of spermatozoa attached to a substrate by their pseudopods. ------------------- Key: 538 Medline: 82140057 Authors: Fodor A;Deak P;Kiss I Title: Competition between juvenile hormone antagonist precocene II and juvenile hormone analog: Methoprene in the nematode C. elegans. Citation: General & Comparative Endocrinology 46: 99-109 1982 Type: ARTICLE Genes: che-1 che-2 dpy-11 lev-1 lev-8 lon-2 unc-3 Abstract: Precocene II causes a high adult mortality and a drastic growth reduction of growing Caenorhabditis elegans larvae. Symptoms caused by precocene II were partly reversible by the insect juvenile hormone analog methoprene, suggesting a physiological role of juvenile hormones in nematodes. ------------------- Key: 539 Medline: 82197609 Authors: Ciliberto G;Traboni C;Cortese R Title: Relationship between the two components of the split promoter of eukaryotic tRNA genes. Citation: Proceedings of the National Academy of Sciences USA 79: 1921-1925 1982 Type: ARTICLE Genes: Abstract: Plasmids containing eukaryotic tRNA genes are faithfully transcribed in the nucleus of Xenopus laevis oocytes. It has been established that two separated regions within the coding sequence of a tRNA gene are essential and sufficient for the promotion of transcription. We have constructed a hybrid tRNA gene containing one essential region from tDNA*Leu and the other from tDNA*Pro, both from Caenorhabditis elegans. This hybrid gene is efficiently transcribed, thus showing that the essential regions are independent transcriptional signals regardless of overall regularities of the structure of tRNA genes. We have also constructed mutants of the tRNA*Pro gene in which the distance between the two essential regions is changed; optimal transcription occurs when this distance is about 40-50 nucleotides. ------------------- Key: 540 Medline: 82174562 Authors: Ciliberto G;Castagnoli L;Melton DA;Cortese R Title: Promoter of a eukaryotic tRNApro gene is composed of three noncontiguous regions. Citation: Proceedings of the National Academy of Sciences USA 79: 1195-1199 1982 Type: ARTICLE Genes: Abstract: The 71-base-pair coding sequences of the tRNAPro gene from Caenorhabditis elegans contains all of the information required for transcription and processing in the injected oocytes. Several subclones of the DNA coding for the tRNAPro were constructed, carrying deletions or insertions, or both. Their transcriptional properties lead to the hypothesis that the tRNAPro gene promoter is composed of three discontinuous regions within the coding sequence. ------------------- Key: 541 Medline: 82174639 Authors: Strome S;Wood WB Title: Immunofluorescence visualization of germ-line-specific cytoplasmic granules in embryos, larvae, and adults of C. elegans. Citation: Proceedings of the National Academy of Sciences USA 79: 1558-1562 1982 Type: ARTICLE Genes: Abstract: By using fluorescent antibody staining, we have followed cytoplasmic granules unique to germ-line cells throughout the life cycle of Caenorhabditis elegans. These elements, designated P granules, are segregated exclusively to germ-line precursor cells during early embryogenesis. Prior to mitosis at each of the early cleavages that produce a somatic and germ-line daughter cell, the granules become localized in the region of cytoplasm destined for the germ-line daughter. After the 16-cell stage, the granules appear to be associated with the nuclear envelope. P granules persist in the germ cells throughout the larval and adult stages. The P granules are similar in number, size, and distribution to germ-line-specific structures identified as "germinal plasm" by electron microscopy in C. elegans embryos. ------------------- Key: 542 Medline: 82055726 Authors: Mackenzie JM Jr;Epstein HF Title: Electron microscopy of nematode thick filaments. Citation: Journal of Ultrastructure Research 76: 277-285 1981 Type: ARTICLE Genes: Abstract: Thick filaments have been isolated from the body-wall muscle cells of the nematode Caenorhabditis elegans. Their protein constituents were shown by SDS-polyacrylamide gel electrophoresis to be myosin, paramyosin, several previously unidentified protein bands and small amounts of actin and tropomyosin from contaminating thin filaments. These thick filaments have been studied by electron microscopy using two different methods of preparation: (a) unfixed filaments, negatively stained with uranyl acetate and (b) glutaraldehyde-fixed filaments, critical-point dried and shadowed with platinum-carbon. The latter method has permitted resolution of crossbridges in many different orientations about the cylindrical shaft of the thick filament. These observations support the hypothesis that the myosin crossbridges are flexibly connected to myosin rods within muscle thick filaments. Myosin heads were visualized in individual nematode myosin oligomers. The morphology and dimensions of the myosin heads are very similar to those of the crossbridge in the native filaments. Our results present a direct visual demonstration of the flexible arrangement of crossbridges with respect to the cylindrical backbones of structurally intact thick filaments. ------------------- Key: 543 Medline: Authors: Cassada R;Isnenghi E;Denich K;Radnia K;Schierenberg E;von Ehrenstein G Title: Genetic dissection of embryogenesis in C. elegans. Citation: "Developmental Biology Using Purified Genes" ICN-UCLA Symposia on Molecular and Cellular Biology, Volume 23. Brown DD (ed), Academic Press, NY. 23: 209-227 1981 Type: REVIEW Genes: emb-1 emb-2 emb-3 emb-4 emb-5 emb-6 emb-7 emb-8 emb-9 emb-10 emb-11 emb-12 emb-13 emb-14 emb-15 emb-16 emb-17 emb-18 emb-19 emb-20 emb-21 emb-22 emb-23 emb-24 emb-25 emb-26 emb-27 emb-28 emb-29 emb-30 emb-31 emb-32 emb-33 emb-34 emb-35 let-2 zyg-1 zyg-2 zyg-3 zyg-7 zyg-8 zyg-9 Abstract: The complex process of embryogenesis in the simple nematode Caenorhabditis elegans is invariant from animal to animal. Cell lineages have been studied by direct observation of individual cells in living embryos using Nomarski differential-interference-contrast microscopy. To dissect events genetically involved in embryogenesis, we have isolated a set of 36 recessive temperature-sensitive (ts) mutants in 30 separate emb-genes, which cause arrest of embryonic development. The fraction of emb mutants among total ts lethals and the recurrence frequency (second alleles) allowed two independent estimates of 200-500 genes essential for embryogenesis (of a total of about 2000 essential genes). So far 54 emb genes have been detected, still far from genetic saturation. We have mapped 25 new emb genes (resolution of 1 recombination unit). Surprisingly, 10 emb genes are clustered near gene unc-32 on linkage group III. Higher resolution mapping here, using deletions, is under way. We have tested the mode of expression (the necessity and/or sufficiency for normal embryogenesis) of the wild-type alleles of these 30 genes in the parents and zygote by performing genetic crosses in which a wild-type allele appears in various configurations, and then determining at the restrictive temperature (25C) the effect on the viability of the resulting progeny genotypes. A majority of the emb genes are of maternal-expression-necessary class (18 of 30 genes studied), in agreement with the results from other similar mutants. For 3 genes, neither maternal nor zygotic expression is sufficient (both necessary?). We have also found 2 zygotic-necessary-and-sufficient genes. For 1 gene paternal expression is partially sufficient. The remaining 7 are of the parental-or-zygotic-expression-sufficient class. We have ordered the ts mutants sequentially in development by temperature shift experiments and according to their arrest stage (terminal phenotypes). Their cellular and subcellular properties are being studied to identify the cellular processes defective in the mutants, and ultimately the mechanisms for genetic control of cell behavior in embryogenesis. We are finding a variety of defects in early cell lineages, including the timing of embryonic cell divisions similar to those already described in another set of mutants. ------------------- Key: 544 Medline: Authors: Edgar RS;Cox GN;Kusch M;Politz JC Title: The cuticle of C. elegans. Citation: Journal of Nematology 14: 248-258 1982 Type: REVIEW Genes: lin-4 lin-14 Abstract: The nematode cuticle is among the most complex extracellular structures produced by a living organism. For the last few years the work in our laboratory has been devoted to the study of the cuticle of the free-living nematode, Caenorhabditis elegans. Studies so far largely have been of a descriptive nature, involving attempts to characterize the morphology and composition of the cuticle and to isolate and study mutants altered in genes that control and regulate cuticle formation. Our long-term interest is to understand the genetic control and regulation of complex processes such as cuticle formation. ------------------- Key: 545 Medline: Authors: Ward S;Roberts TM;Nelson GA;Argon Y Title: The development and motility of C. elegans spermatozoa. Citation: Journal of Nematology 14: 259-266 1982 Type: REVIEW Genes: fer-1 fer-2 Abstract: Nematode sperm have puzzled zoologists for nearly a century because they are not flagellated. Their morphology is amoeboid, but there have been only a few descriptions of their actual movement. We have undertaken an intensive examination of the spermatozoa of Caenorhabditis elegans in order to learn how they develop their specialized morphology. This nematode was chosen because it is easily cultured in the laboratory and it has become the subject of detailed studies of its genetics, development, and behavior. In this paper we summarize our recent results which demonstrate that these spermatozoa have a novel mechanism of amoeboid motility. ------------------- Key: 546 Medline: Authors: Wood WB;Laufer JS;Strome S Title: Developmental determinants in embryos of C. elegans. Citation: Journal of Nematology 14: 267-273 1982 Type: REVIEW Genes: Abstract: C. elegans is proving uuseful for the study of cell determination in early embryos. Breeding experiments with embryonic lethal mutants show that abnormal embryogenesis often results from defective gene function in the maternal parent, suggesting that much of the information for normal embryonic development is laid down during oogenesis. Analysis of a gut-specific differentiation marker in cleavage-arrested embryos has provided evidence that the potential for this differentiation behaves as a cell-autonomous internally segregating developmental determinant, which is present at the 2-cell stage onward and is partitioned into the gut precursor cell during early cleavage divisions. Visible prelocalized cytoplasmic granules that segregate with a particular cell lineage have been observed in the embryonic germline precursor cells by fluorescent antibody staining. Whether these granules play a role in germline determina... ------------------- Key: 547 Medline: Authors: Riddle DL Title: Developmental biology of C. elegans: Symposium Citation: Journal of Nematology 14: 238-239 1982 Type: REVIEW Genes: Abstract: Many nematologists do not seem to be interested in nematodes for the nematodes' sake, but instead are concerned primarily with the plants or animals they may parasitize and the economic importance of nematode control. Perhaps as a consequence of this and other factors, nematology has developed along paths which were, in a sense, long ago predetermined by the historical divisions between plant and animal scientists. Obviously, a crucial role for the Society in the development of nematology as a scientific discipline is to bridge the natural gap that has been laid down by historical precedent. ------------------- Key: 548 Medline: Authors: Horvitz HR;Sternberg PW Title: Nematode postembryonic cell lineages. Citation: Journal of Nematology 14: 240-248 1982 Type: REVIEW Genes: Abstract: The complete postembryonic cell lineages of the free-living nematodes Caenorhabditis elegans and Panagrellus redivivus are known. Postembyronic cell divisions lead to substantial increases in the number of cells, and in most cases, in the number of types of cells in the neuronal, muscular, hypodermal, and digestive systems. The patterns of postembryonic cell divisions are essentially invariant and generate a fixed number of progeny cells of strictly specified fates. Cell fates depend upon both lineage history and cell-cell interactions: lineage limits the developmental potential of each cell and, for certain cells, cell-cell interactions specify which of a small number of alternative potential fates is acquired. Relatively simple differences in cell lineage account for some of the striking differences in gross morphology both between sexes and between species. Genetic studies indicate that these cell lineage differences reflect one or a few relatively simple mutational events. Interspecific differences in cell lineage are likely to be good indicators of evolutionary distance and may be helpful in defining taxonomic relationships. Both the techniques utilized in, and the information acquired from, studies of cell lineages in C. elegans and P. redivivus may prove useful to other nematologists. ------------------- Key: 549 Medline: 82176753 Authors: Lew KK;Chritton S;Blumberg PM Title: Biological responsiveness to the phorbol esters and specific binding of 3H phorbol 12, 13-dibutyrate in C. elegans, a manip gen sys/ Citation: Teratogenesis, Carcinogenesis & Mutagenesis 2: 19-30 1982 Type: ARTICLE Genes: Abstract: Because of its suitability for genetic studies, the nematode Caenorhabditis elegans was examined for its responsiveness to the phorbol esters. Phorbol 12-myristate 13-acetate had three effects. It inhibited the increase in animal size during growth; it decreased the yield of progeny; and it caused uncoordinated movement of the adult. The effects on nematode size, progeny yield, and movement were quantitated. Concentrations of phorbol 12-myristate 13-acetate yielding half-maximal responses were 440, 460, and 170 nM, respectively. As was expected from the biological responsiveness of the nematodes, specific, saturable binding of phorbol ester to nematode extracts was found. [3H]phorbol 12,13-dibutyrate bound with a dissociation constant of 26.8 +/- 3.9 nM. At saturation, 5.7 +/- 1.4 pmole/mg protein was bound. ------------------- Key: 550 Medline: 82167789 Authors: Chalfie M;Thomson JN Title: Structural and functional diversity in the neuronal microtubules of C. elegans. Citation: Journal of Cell Biology 93: 15-23 1982 Type: ARTICLE Genes: mec-7 Abstract: Tannic acid fixation reveals differences in the number of protofilaments between microtubules (MTs) in the nematode Caenorhabditis elegans. Most cells have MTs with 11 protofilaments but the six touch receptor neurons (the microtubule cells) have MTs with 15 protofilaments. No 13-protofilament (13-p) MT has been seen. The modified cilia of sensory neurons also possess unusual structures. The cilia contain nine outer doublets with A subfibers of 13 protofilaments and B subfibers of 11 protofilaments and a variable number of inner singlet MTs containing 11 protofilaments. The 15-p MTs but not the 11-p MTs are eliminated by colchicine-treatment or by mutation of the gene mec-7. Concomitantly, touch sensitivity is also lost. However, whereas colchicine treatment leads to the loss of all MTs from the microtubule cells, mutations in mec-7 result in the partial replacement of the 15-p MTs with 11-p MTs. Benzimidazoles (benomyl and nocodazole) have more general effects on C. elegans (slow growth, severe uncoordination, and loss of processes from the ventral cord) but do not affect the 15-p MTs. Benomyl will, however, disrupt the replacement 11-p MTs found in the microtubule cells of mec-7 mutants. The 11-p and 15-p MTs also respond differently to temperature and fixation conditions. It is likely that either type of MT will suffice for the proper outgrowth of the microtubule cell process, but only the 15-p MT can function in the specialized role of sensory transduction of the microtubule ------------------- Key: 551 Medline: Authors: Robertson AMG;Thomson JN Title: Morphology of programmed cell death in the ventral nerve cord of C. elegans larvae. Citation: Journal of Embryology & Experimental Morphology 67: 89-100 1982 Type: ARTICLE Genes: Abstract: In the nematode Caenorhabditis elegans, cells undergoing programmed cell death in the developing ventral nerve cord were identified by Nomarski optics and prepared for ultrastructural study at various times after their birth in mitosis. The sequence of changes observed suggests that the hypodermis recognizes the dying cell before completion of telophase. The dying cell is engulfed and digestion then occurs until all that remains within the hypodermal cytoplasm is a collection of membranous whorls interspersed with condensed chromatin-like remnants. The process shares several features with apoptosis, the mode of programmed cell death observed in vertebrates and insects. The selection of cells for programmed death appears not to involve competition for peripheral targets. ------------------- Key: 552 Medline: 82199429 Authors: Horvitz HR;Chalfie M;Trent C;Sulston JE;Evans PD Title: Serotonin and octopamine in the nematode C. elegans. Citation: Science 216: 1012-1014 1982 Type: ARTICLE Genes: che-3 daf-10 osm-3 unc-86 Abstract: The biogenic amines serotonin and octopamine are present in the nematode Caenorhabditis elegans. Serotonin, detected histochemically in whole mounts, is localized in two pharyngeal neurons that appear to be neurosecretory. Octopamine, identified radioenzymatically in crude extracts, probably is also localized in a few neurons. Exogenous serotonin and octopamine elicit specific and opposite behavioral responses in Caenorhabditis elegans, suggesting that these compounds function physiologically as antagonists. ------------------- Key: 554 Medline: 82211746 Authors: Rosenbluth RE;Baillie DL Title: The genetic analysis of a reciprocal translocation, eT1(III;V), in C. elegans. Citation: Genetics 99: 415-428 1981 Type: ARTICLE Genes: bli-5 dpy-1 dpy-5 dpy-11 dpy-17 dpy-18 sma-2 sma-3 unc-11 unc-13 unc-32 unc-36 unc-42 unc-64 unc-67 eT1 eDf2 Abstract: The Caenorhabditis elegans mutation e873, which results in a recessive uncoordinated phenotype (formerly named Unc-72) and which had been isolated after 32P treatment (Brenner 1974), has now been found to act as a crossover suppressor and to be associated with a translocation between linkage groups (LG's) III and V. The translocation has been named, eT1(III; V); eT1 acts as a dominant crossover suppressor for both the right half of LGIII and the left half of LGV, providing a balancer for a total of 39 map units. The uncoordinated e873 phenotype has been shown to be a consequence of an inactive unc-36III gene. It was possible to demonstrate that, in translocation heterozygotes, eT1 chromosomes marked with either sma-3 or dpy-11 segregate from normal LGIII, while those marked with bli-5, sma-2 or unc-42 segregate from normal LGV. Since bli-5 and sma-2 are normally on LGIII, and dpy-11 is normally on LGV, it is concluded that: (a) eT1 is a reciprocal translocation; (b) there is a breakpoint between sma-3 and sma-2 in LGIII (the region containing unc-36) and one between dpy-11 and unc-42 in LGV; (c) there is no dominant centromere between sma-2 and bli-5 on LGIII, since in eT1 these genes are not linked to a LGIII centromere. Similarly, it is highly unlikely that there is a centromere to the left of dpy-11 on LGV. The new gene order in eT1 was determined by measuring recombination rates between markers in eT1 homozygotes. It is concluded that the new order is: dpy-1 sma-3 (break) dpy-11 unc-60, and bli-5 sma-2 (break) unc-42 unc-51.--This is the first analysis of a C. elegans translocation with respect to reciprocity, breakpoints and new gene order. ------------------- Key: 555 Medline: Authors: Popham JD;Webster JM Title: Ultrastructural changes in C. elegans (Nematoda) caused by toxic levels of mercury and silver. Citation: Ecotoxicology & Environmental Safety 6: 183-189 1982 Type: ARTICLE Genes: Abstract: Mercury toxicity in Caenorhabditis elegans showed as lesions in esophageal muscles and intestinal cells and consisted of degradation of the cytoplasm and the formation of irregularly shaped cytosomes. Specimens intoxicated with silver showed changed cytosomes with a spongy matrix in the intestinal cells and ruffled membranes on the mitochondria of hypodermal cells. General ultrastructural responses reflecting a distress syndrome common to several heavy metals were also noted. The results are discussed with reference to the concept of using free-living nematodes to assist in the diagnosis of the causative toxic heavy metal in a complex. ------------------- Key: 556 Medline: Authors: DeCuyper C;Vanfleteren JR Title: Nutritional alteration of life span in the nematode C. elegans. Citation: Age 5: 42-45 1982 Type: ARTICLE Genes: Abstract: The longevity of the free-living nematode Caenorhabditis elegans was studied under two different nutritional regimes, one axenic and the other monoxenic. Axenic nematodes showed typical sigmoidal survival curves with exceptionally long tailing. Monoxenic worms died off much faster and the maximum life-span in bacterial culture was generally three to four times shorter than that obtained in axenic culture. When nematodes were transferred from axenic to monoxenic culture and vice versa at near adulthood the survival patterns observed were reminiscent of the final medium. These results are in agreement with the hypothesis that worms may die off prematurely in bacterial culture by toxins given off by the bacteria. ------------------- Key: 557 Medline: Authors: Shulkin DJ;Zuckerman BM Title: Spectrofluorometric analysis of the effect of centrophenoxine on lipofuscin accumulation in the nematode C. elegans. Citation: Age 5: 50-53 1982 Type: ARTICLE Genes: Abstract: A 41.3% mean decrease in lipofuscin was found in the nematode Caenorhabditis elegans following treatment of 6.8 mM centrophenoxine for 21 days. It is proposed that the spectrofluorometric technique is a convenient and more accurate method for determining cellular content of lipofuscin than planimetric and histochemical methodologies. This study further demonstrates the similarity of nematode lipofuscin to mammalian age pigment and provides a rapid, inexpensive method for evaluating the effects of pharmaceuticals on age-related lipofuscin ------------------- Key: 558 Medline: 82120290 Authors: Roberts TM;Ward S Title: Membrane flow during nematode spermiogenesis. Citation: Journal of Cell Biology 92: 113-120 1982 Type: ARTICLE Genes: fer-1 fer-15 Abstract: Two distinct types of surface membrane rearrangement occur during the differentiation of Caenorhabditis elegans spermatids into amoeboid spermatozoa. The first, detected by the behavior of latex beads attached to the surface, is a nondirected, intermittent movement of discrete portions of the membrane. This movement starts when spermatids are stimulated to differentiate and stops when a pseudopod is formed. The second type of movement is a directed, continual flow of membrane components from the tip of the pseudopod to its base. Both membrane glycoproteins and fluorescent phospholipids inserted in the membrane flow backward at the same rate, approximately 4 micrometers/min, although their lateral diffusion coefficients in the membrane differ by at least a factor of 5. These observations suggest that pseudopodial membrane movement is due to bulk flow of membrane components away from the tip ------------------- Key: 559 Medline: 82262402 Authors: Ward S;Klass M Title: The location of the major protein in C. elegans sperm and spermatocytes. Citation: Developmental Biology 92: 203-208 1982 Type: ARTICLE Genes: fer-1 fer-2 fer-3 fer-4 fer-6 Abstract: Using an affinity-purified antibody to the major sperm protein (MSP) in Caenorhabditis elegans sperm we have shown by immunofluorescence that the MSP is localized in the fibrous bodies of spermatocytes and early spermatids, in the cytoplasm of late spermatids, and in the pseudopods of spermatozoa. The MSP can also form crystalline inclusions in mutant and wild-type sperm. The function of this protein is still unknown, but its ability to form filaments and its localization in the pseudopod, together with the lack of actin in these sperm suggest that the MSP may be required for amoeboid motility. ------------------- Key: 560 Medline: 82260416 Authors: Chalfie M Title: Microtubule structure in C. elegans neurons. Citation: Cold Spring Harbor Symposia on Quantitative Biology 46: 255-261 1982 Type: REVIEW Genes: mec-7 unc-86 Abstract: Microtubules (MTs) are ubiquitous components of neuronal processes, and although they have been implicated in neurite outgrowth, shape maintenance, axonal transport, and sensory transduction, their function remains unclear. The MTs in the neurons of the nematode Caenorhabditis elegans have unusual structures that permit a comparative approach to the relationship of microtubule structure and function. A set of six touch-receptor neurons (the microtubule cells) contain prominent arrays of large MTs. These MTs have more protofilaments than do MTs in other neurons (15 as opposed to 11), and they respond differently to antimicrotubule drugs, fixation protocols, temperature, and mutation. Studies of C. elegans neurotubules suggest that most MT functions do not require long, continuous MTs or MTs with a specific number of protofilaments. Some functions, however, such as the sensory transduction of the microtubule cells, do require a specific microtubule substructure. A review of these data is presented in this ------------------- Key: 561 Medline: 83025078 Authors: Gossett LA;Hecht RM;Epstein HF Title: Muscle differentiation in normal and cleavage-arrested mutant embryos of C. elegans. Citation: Cell 30: 193-204 1982 Type: ARTICLE Genes: unc-54 zyg-1 Abstract: The differentiation of body-wall muscle cells was studied in the nematode Caenorhabditis elegans. Specific antibodies to myosin and paramyosin, major protein constituents of differentiated muscle, react with mesodermal cells in wild-type embryos towards the end of the first half of embryogenesis. Immunoreactive cells (2-16) first appear in embryos with 400-450 of the 550 cells present at hatching. Such embryos have developed at 25.5 degrees C for 4-4 1/2 hr beyond the two-cell stage. As development proceeds, a maximum of 81 immunoreactive cells forms four columns running anterior-posterior. Each column is composed of two lines of tightly opposed round cells, which then elongate into spindle-shaped cells. Mutant embryos in which cleavage arrests prematurely also generate cells that produce myosin and paramyosin. The initiation of muscle differentiation appears to be independent of the number of cell or nuclear divisions within a lineage or of the proliferation of other cells. These results suggest that the biosynthesis of muscle-specific proteins by nematode embryonic muscle cells is regulated by mechanisms intrinsic to these cells. ------------------- Key: 562 Medline: 83025093 Authors: Hedgecock EM;Thomson JN Title: A gene required for nuclear and mitochondrial attachment in the nematode C. elegans. Citation: Cell 30: 321-330 1982 Type: ARTICLE Genes: anc-1 Abstract: Nuclei occupy characteristic positions in most cells. In Caenorhabditis elegans, nuclei can be observed in living animals. Ordinary movements can distort the cells and displace their nuclei, but the extent of displacement is limited and nuclei return to their resting positions when the muscles relax. We have isolated five mutants in which the nuclei of certain epithelial cells are not elastically anchored but float freely within the cytoplasm. These mutations define a single gene, anc1, on linkage group 1. Mitochondrial positioning, observed by staining live animals with rhodamine 6G, is also disturbed in these cells. Additional defects, including abnormal tonofilaments and inappropriately positioned desmosomes, have been found by electron microscopy. The anc1 product may be a cytoskeletal component of nematode epithelial cells. Although the Anc1 phenotype is fully expressed in the newly hatched larvae, mutants develop and reproduce normally. Despite mispositioning of organelles, cuticle deposition and moulting are essentially normal. These mutations represent the null phenotype of the gene. At least three independent isolates revert spontaneously at high frequency (10(-5) to 10(-4) ). We suggest that anc1 is a member of a family of cytoskeletal genes. ------------------- Key: 563 Medline: 83012962 Authors: Kimble J;Hodgkin J;Smith T;Smith J Title: Suppression of an amber mutation by microinjection of suppressor tRNA in C. elegans. Citation: Nature 299: 456-458 1982 Type: ARTICLE Genes: sup-5 sup-7 tra-3 Abstract: Informational suppression by nonsense suppressor tRNAs has classically been a powerful tool for study of the mechanism of protein synthesis, to obtain conditional mutants and to demonstrate that a gene encodes a given protein product. In the nematode Caenorhabditis elegans, two genetically identified suppressors, sup-5 and sup-7, have recently been shown to be amber suppressor tRNAs. We report here the microinjection of sup-7 tRNA into the gonad of an animal bearing an amber allele of a maternal-effect mutant affecting sex determination (tra-3). We observe phenotypic suppression in the injected parent's offspring. tRNA from wild-type animals does not show this in vivo suppressor activity, and sup-7 tRNA does not cause suppression of a non-amber allele of the same gene. In vivo suppression of an amber mutant by microinjection provides a new means of gene manipulation in C. elegans. ------------------- Key: 564 Medline: 83080421 Authors: Greenwald IS;Horvitz HR Title: Dominant suppressors of a muscle mutant define an essential gene of C. elegans. Citation: Genetics 101: 211-225 1982 Type: ARTICLE Genes: lin-17 sup-5 sup-7 sup-9 sup-10 sup-11 unc-93 Abstract: The sup-11 1 locus of C. elegans was defined by rare dominant suppressors of unc-93(e1500) III, a mutation that affects muscle structure. All ten of these dominant suppressors have a recessive "scrawny" phenotype. Two additional classes of sup-11 alleles were identified. One class, null alleles, was obtained by reversion of the dominant suppressor activity. These null alleles are recessive embryonic lethals, indicating that sup-11 is an essential gene. Members of the second class, rare semidominant revertants of the "scrawny" phenotype, are partial suppressors of unc-93(e1500). The genetic properties of the dominant suppressor mutations suggest that they are rare missense mutations that confer a novel activity to the sup-11 protein. We consider some of the ways that sup-11 alleles might suppress unc-93(e1500), including the possibilities that the altered sup-11 proteins restore function to a protein complex or are modified products of a gene that is a member of an unc-93 ------------------- Key: 565 Medline: 83106425 Authors: Hartman PS;Herman RK Title: Radiation-sensitive mutants of C. elegans. Citation: Genetics 102: 159-178 1982 Type: ARTICLE Genes: flu-2 him-1 him-2 him-3 him-5 him-6 him-7 him-8 him-9 him-10 nuc-1 rad-1 rad-2 rad-3 rad-4 rad-5 rad-6 rad-7 rad-8 rad-9 rec-1 unc-58 Abstract: Nine rad (for abnormal radiation sensitivity) mutants hypersensitive to ultraviolet light were isolated in the small nematode Caenorhabditis elegans. The mutations are recessive to their wild- type alleles, map to four of the six linkage groups in C. elegans and define nine new games named rad-1 through rad-9. Two of the mutants-- rad-1 and rad-2--are very hypersensitive to X rays, and three--rad-2, rad-3 and rad-4--are hypersensitive to methyl methanesulfonate under particular conditions of exposure. The hypersensitivity of these mutants to more than one DNA-damaging agent suggests that they may be abnormal in DNA repair. One mutant--rad-5, a temperature-sensitive sterile mutant--shows an elevated frequency of spontaneous mutation at more than one locus; rad-4, which shows a cold-sensitive embryogenesis, reduces meiotic X-chromosome nondisjunction tenfold and partially suppresses some but not all mutations that increase meiotic X-chromosome nondisjunction; the viability of rad-6 hermaphrodites is half that of rad-6 males at 25 degrees; and newly mature (but not older) rad-8 hermaphrodites produce many inviable embryo progeny. Meiotic recombination frequencies were measured for seven rad mutants and found to be close to ------------------- Key: 566 Medline: 83028183 Authors: Klass M;Dow B;Herndon M Title: Cell-specific transcriptional regulation of the major sperm protein in C. elegans. Citation: Developmental Biology 93: 152-164 1982 Type: ARTICLE Genes: him-8 Abstract: The major protein found in nematode sperm exhibits a distinct pattern of developmental regulation. In the nematode Caenorhabditis elegans, the synthesis of the major sperm protein (15K) begins with the onset of spermatogenesis in both the male and hermaphrodite. Both spermatogenesis and 15K synthesis continue for the life of the male while in the protandrous hermaphrodite the major sperm protein is synthesized only during the fourth larval stage. Inhibitor studies using actinomycin D and a-actinin as well as Northern blot analysis have shown that the primary regulatory mechanism of this gene is at the transcriptional level. Recombinant molecules have been selected bearing the 15K genomic sequence by a positive hybridization translation assay. Using one of these cloned fragments as a probe for in situ hybridization, 15K transcripts have been localized to a specific region of the male gonad. These studies indicate that the gene for the major sperm protein is regulated by a cell-specific transcriptional control mechanism coincidental with the onset of sexual differentiation in the nematode. ------------------- Key: 567 Medline: 83028185 Authors: Sternberg PW;Horvitz HR Title: Postembryonic nongonadal cell lineages of the nematode Panagrellus redivivus: Description and comparison with those of C. elegans. Citation: Developmental Biology 93: 181-205 1982 Type: ARTICLE Genes: Abstract: The postembryonic nongonadal cell lineages of the nematode Panagrellus redivivus are described and compared with those of Caenorhabditis elegans. The newly hatched larvae of P. redivivus females and males and C. elegans hermaphrodites and males are very similar. An almost identical set of blast cells divides postembryonically in P. redivivus and C. elegans to produce similar changes in the neuronal, muscular, hypodermal, and digestive systems. Most of these cell lineages are invariant; however, there is substantial variablility in the number of cell divisions in the relatively extensive lineages of the lateral hypdermis of P. redivivus. Typically, in P. redivivus females, 55 blast cells generate 635 surviving progeny and 29 cell deaths; in P. redivivus males, 59 blast cells generate 758 surviving progeny and 35 cell deaths. The lineages generating the cells of the male tails of P. redivivus and C. elegans are almost identical; thus, the grossly different characteristics of these structures must reflect differences in the morphogenesis of cells equivalent in lineage history. Laser ablation experiments demonstrate that the gonad induces vulva development and that cell-cell interactions are important in specifying the fates of hypodermal precursor cells. The lateral hypodermal lineages provide striking examples of the apparent construction of complex lineages from modular sublineages; one simple pattern of cell divisions and cell fates occurs 70 times in the P. redivivus female. The differences in cell lineage between P. redivivus and C. elegans are relatively minor, and many appear to have involved two types of evolutionary change: the replacement of sublineages, and the modification of sublineages by the four classes of lineage transformations previously proposed based on a comparison of P. redivivus and C. elegans gonadal cell lineages. These types of differences suggest that the genetic programming of cell lineage includes instructions specifying where and when a particular sublineage is utilized, and other instructions specifying ------------------- Key: 568 Medline: Authors: Horvitz HR;Ellis HM;Sternberg PW Title: Programmed cell death in nematode development. Citation: Neuroscience Commentaries 1: 56-65 1982 Type: REVIEW Genes: ced-1 ced-2 ced-3 Abstract: The phenomenon of programmed cell death, which occurs during the normal development of many organisms and is particularly common in neural development, is intriquing. Why should organisms generate cells only to destroy them? We believe that studies of the cell deaths that occur in nematodes have provided some answers to this question. Programmed cell death is a prominent feature of nematode development. For example, the generation of the 816 nongonadal cells of the hermaphroditic free-living nematode Caenorhabditis elegans is accompanied by the generation and death of an additional 131 cells. Most of these deaths appear to involve cells that are neural in character. Neural cell death is similarly common during the development of C. elegans males and during the postembryonic development of both females and males of another nematode species, Panagrellus redivivus. Overall, for both sexes of these two nematode species, approximately 20% of all presumptive neural cells produced undergo ------------------- Key: 569 Medline: 83050944 Authors: Kramer JM;Cox GN;Hirsh D Title: Comparisons of the complete sequences of two collagen genes from C. elegans. Citation: Cell 30: 599-606 1982 Type: ARTICLE Genes: col-1 col-2 col-3 Abstract: Several collagen genes have been isolated from the nematode Caenorhabditis elegans. The complete nucleotide sequences of two of these genes, col-1 and col-2, have been determined. These collagen genes differ from vertebrate collagen genes in that they contain only one or two introns, their triplehelical regions are interrupted by nonhelical amino acid sequences and they are smaller. A high degree of nucleotide and amino acid homology exists between col-1 and col-2. In particular, the regions around cysteines and lysines are most highly conserved. The C. elegans genome contains 50 or more collagen genes, the majority of which probably encode cuticle collagens; col-1 and col-2 apparently are members of this large family of cuticle collagen genes. ------------------- Key: 570 Medline: 82272395 Authors: McLachlan AD;Karn J Title: Periodic charge distributions in the myosin rod amino acid sequence match cross-bridge spacings in muscle. Citation: Nature 299: 226-231 1982 Type: ARTICLE Genes: unc-54 Abstract: The amino acid sequence of the rod portion of nematode myosin, deduced from the sequence of the unc-54 heavy chain gene of Caenorhabditis elegans, is highly repetitive and has the characteristics of an a-helical coiled coil. The molecular surface contains alternate clusters of positive and negative charge. Interactions between charge clusters on adjacent molecules could account for the observed spacings of the myosin cross-bridges in muscle. Calculations also suggest that the N-terminal of the rod is only loosely associated with the thick filament backbone. Bending of the rod near the end of this region could allow the N-terminal section to act as a hinged arm during muscle contraction. ------------------- Key: 571 Medline: 83103105 Authors: Moerman DG;Plurad S;Waterston RH;Baillie DL Title: Mutations in the unc-54 myosin heavy chain gene of C. elegans that alter contractility but not muscle structure. Citation: Cell 29: 773-781 1982 Type: ARTICLE Genes: unc-22 unc-54 Abstract: Reversion analysis of mutants of unc-22 IV, a gene affecting muscle structure and function in Caenorhabditis elegans, led to the isolation of six extragenic dominant suppressors of the "twitching" phenotype of unc-22 mutants. All six suppressors are new alleles of unc-54 I, the major body wall myosin heavy chain gene. Homozygous suppressor strains are slow, stiff and have normal muscle structure, whereas previously identified unc-54 alleles confer flaccid paralysis and drastic reduction in thick filament number and organization. Placement of the three suppressor mutations s74, s77 and s95 on the genetic fine structure map of unc-54 demonstrates that they are clustered near the right end of the map. Since this end of the gene corresponds to the 5' end of the coding sequence, these suppressor mutations probably result in amino acid substitutions in the globular head of the myosin molecule, and should be of value in studies of myosin force ------------------- Key: 572 Medline: Authors: Horvitz HR Title: Factors that influence neural development in nematodes. Citation: "Repair and Regeneration in the Nervous System" Dahlem Workshop Report Series Proceedings, Berlin, 1981. Nicholls JG (ed), Springer-Verlag, NY. 24: 41-55 1982 Type: REVIEW Genes: lin-14 Abstract: Neurons in nematodes are generated by invariant cell lineages. The lineage history of a cell appears to limit its developmental potential, often to a unique fate. Some cells have multiple potential fates; the fate each expresses depends either upon interactions with other cells or upon specific genetically controlled temporal signals. If the principles of neural development in nematodes are similar to those in other organisms, specific conditions involving available cell types and positional and/or temporal cues must be satisfied for neural regeneration to ------------------- Key: 573 Medline: Authors: Epstein HF;Miller DM III;Gossett LA;Hecht RM Title: Immunological studies of myosin isoforms in nematode development. Citation: "Muscle Development: Molecular and Cellular Control." Pearson M and Epstein HF (eds), Cold Spring Harbor Laboratory. : 7-14 1982 Type: REVIEW Genes: Abstract: Much of this meeting is devoted to the study of multi-gene families and the differential expression of various members during muscle development. Structural analysis of myosin and then other muscle proteins by peptide mapping and amino acid sequencing first suggested that these isoforms are the products of different genes. The use of antibodies specific to distinct structural gene products has permitted detailed investigations of myosin structure, biosynthesis and degradation, and cellular location as muscle development proceeds. The small nematode, Caenorhabditis elegans, is a laboratory animal which offers genetic dissection and manipulation as tools in deciphering of gene regulation in terms of specific protein synthesis during muscle development. The examination of specific mutants by protein chemistry and immunochemistry has already proved a powerful comination in many fields. ------------------- Key: 574 Medline: 83105996 Authors: Hecht RM;Wall SM;Schomer DF;Oro JA;Bartel AH Title: DNA replication may be uncoupled from nuclear and cellular division in ts embryonic lethal mutants of C. elegans. Citation: Developmental Biology 94: 183-191 1982 Type: ARTICLE Genes: emb-7 emb-9 zyg-1 zyg-2 zyg-8 zyg-9 zyg-10 zyg-12 Abstract: The nuclear and DNA contents of 18 temperature-sensitive embryonic lethal mutants of Caenorhabditis elegans have been determined at the time of arrest. After each mutant was shifted to restrictive temperature, the embryonic arrest stage was recorded by the number of nuclei counted in embryonic squashes and as DNA nuclear equivalents recorded by flow cytometry. Together the two methods complemented each other and provided qualitative and quantitative information concerning the nuclear number, DNA content, morphological stage of arrest, and presence of anucleate embryonic cells. The arrest stage for most of the embryonic lethal mutants demonstrated their potential to continue nuclear division and DNA replication beyond their respective temperature-sensitive periods. These results suggested that the mutants' primary defect did not reside on a pathway closely coupled to DNA replication or nuclear division. For example, B65 contained up to 650 DNA nuclear equivalents beyond the end of its temperature-sensitive period at the 20- to 30-cell stage. B65 is of additional interest because it continued DNA synthesis beyond the normal 550-cell stage and at the same time failed to progress beyond the morphogenetic period. The presence of enlarged nuclei that contained extra DNA demonstrated that DNA replication was independent of nuclear and cellular division. For example, B1 and B244 arrested with 1 to 50 and 1 to 200 nuclei, respectively. However, they both contained 250 to 400 nuclear equivalents of DNA. Conversely, the presence of embryonic cells without nuclei suggested that cell division may also be independent of nuclear division or nuclear migration. The enlarged nuclear and anucleate embryonic cells were observed only in those mutants requiring a normal parental ------------------- Key: 575 Medline: Authors: Waterston RH;Moerman DG;Baillie DL;Lane TR Title: Mutations affecting myosin heavy chain accumulation and function in the nematode C. elegans. Citation: "Disorders of the Motor Unit." Schotland DM (ed), J. Wiley & Sons. : 747-760 1982 Type: REVIEW Genes: sup-3 unc-22 unc-54 Abstract: The small nematode Caenorhabditis elegans is the subject of intensive investigation into the genetic specification of muscle structure and function. Many mutations affecting muscle structure have been identified, and more than 20 genes have been defined by complementation and recombinational analysis. Biochemical and genetic studies have proved that one of these loci, unc-54 I, is the structural gene for a 210,000-dalton myosin heavy chain in the body-wall musculature. Specific mutations in this gene could help us to understand the role of the myosin heavy chain in the assembly and contraction of muscle. Additional myosin heavy chains, the products of other genes, are present in the body wall and pharyngeal musculature. Alterations in the tissue-specific expression of this family of genes might be useful in studying gene regulation. The classic genetic approaches of reversion and intracistronic recombinational analysis can be applied to these problems in C. elegans because of the ease of handling the large number of animals necessary for systematic application of these methods, and because of the strong phenotype associated with most unc-54 mutations. Reversion analysis can reveal intragenic suppressors of a variety of types and could be especially powerful in the study of the genetic specification of muscle where many gene interactions may be involved. We have, in other work, described allele-specific generalized suppressors in C. elegans that are likely to be informational suppressors. Riddle and Brenner reverted unc-54 mutants and uncovered a gene-specific suppressor, sup-3 V. Part of our current work has been directed toward understanding the molecular basis for sup-3 action on unc-54 mutants. We have also carried out reversion analysis on unc-22 mutants and, surprisingly, have found new alleles of unc-54 that suppress unc-22 expression. In addition, a genetic intracistronic map of the unc-54 gene has been constructed, and we have begun to position these new alleles on this ------------------- Key: 576 Medline: Authors: Fodor A;Deak P Title: Isolation and phenocritical period-analysis of conditional and non-conditional developmental mutants in C. elegans. Citation: Acta Biologica Academiae Scientiarum Hungaricae 32: 229-239 1982 Type: ARTICLE Genes: szT1 Abstract: Forty-five conditional, non-conditional and deletion mutants located on the X chromosome of the nematode Caenorhabditis elegans (C. elegans) were isolated by using a duplication (mnDp1) and a balancer chromosome (szT1). Phenocritical periods of three conditional and two non-conditional mutants were determined; their relation to the actual gene activities is discussed. ------------------- Key: 577 Medline: 83080440 Authors: Herman RK;Kari CK;Hartman PS Title: Dominant X-chromosome nondisjunction mutants of C. elegans. Citation: Genetics 102: 379-400 1982 Type: ARTICLE Genes: mnT2 mnT3 mnT6 mnT7 mnT8 mnT9 mnT10 mnT11 mnDp11 Abstract: Eight dominant X-chromosome nondisjunction mutants have been identified and characterized. Hermaphrodites (XX) heterozygous for any one of the mutations produce 20-35% male (XO) self-progeny compared with the wild-type frequency of 0.2%. Seven of the eight mutants carry X-autosome translocations. Three of these, represented by mnT2, involve linkage group (LG) II and show severe crossover suppression for X-linked markers. The two half-translocations comprising mnT2 are separable and of very unequal size. The smaller one includes the left tip of X and the right end of LGII and can exist as a free duplication, being present in addition to the normal chromosome complement, in either hermaphrodites or males; it has no effect on X nondisjunction. The reciprocal half-translocation of mnT2 includes the bulk of both LGII and X chromosomes; it disjoins regularly from a normal LGII and confers the property of X-chromosome nondisjunction. A fourth translocation, mnT10(V;X), is also reciprocal and consists of half-translocations that recombine with V and X, respectively. Either half-translocation of mnT10 can exist in heterozygous form in the absence of the other to give heterozygous duplication-deficiency animals; the property of X-chromosome nondisjunction is conferred, in homozygotes as well as heterozygotes, solely by one of the half-translocations, which is deficient for the left tip of the X. The final three translocations have X breakpoints near the right end of X and autosomal breakpoints near the right end of LGIV, the left end of LGV and the right end of LGI, respectively. All three are homozygous inviable. Males hemizygous for the X portion of any of the seven translocations are viable and fertile. The final mutant, mn164, maps as a point at or near the left tip of the X and causes X-chromosome nondisjunction in both heterozygotes and homozygotes. In heterozygotes, mn164 promotes equational nondisjunction of itself but not its wild-type allele. The mutants are discussed in light of the holocentric nature of the C. elegans chromosomes. It is proposed that the left end of the X chromosome plays a critical structural role in the segregation of X ------------------- Key: 578 Medline: 82220013 Authors: White JG;Horvitz HR;Sulston JE Title: Neurone differentiation in cell lineage mutants of C. elegans. Citation: Nature 297: 584-587 1982 Type: ARTICLE Genes: lin-5 unc-59 unc-85 Abstract: The nematode Caenorhabditis elegans develops by an essentially invariant sequence of cell divisions leading to an adult complement of 959 somatic cells. In this organism cell fate is correlated with cell lineage, suggesting that genealogy may be a determining factor for the differentiated state of a cell. The study of mutants with altered cell lineages may help elucidate the precise mechanisms by which cell fate is decided. Several cell lineage mutants have been isolated and characterized, some having more and some fewer cell divisions than wild type. We have now investigated the cell types produced by two cell lineage mutants; these mutants exhibit blocks in certain terminal or near terminal cell divisions, which in normal animals generally give rise to daughter cells that differentiate into distinctly different cell types. We find that the blocked cells in the mutants generally exhibit the differentiated characteristics of only one of the two daughter cells that normally would be produced. The differentiated state of the blocked precursors may be due to an intrinsic dominance of one cell type over another in what is essentially a fused cell, and/or it may reveal the state of commitment of the precursor in wild-type ------------------- Key: 579 Medline: 83010290 Authors: Waterston RH;Smith KC;Moerman DG Title: Genetic fine structure analysis of the myosin heavy chain gene unc-54 of C. elegans. Citation: Journal of Molecular Biology 158: 1-15 1982 Type: ARTICLE Genes: let-49 let-50 lev-11 sup-3 sup-5 sup-7 unc-54 Abstract: Taking advantage of the relative ease of detecting single wild-type animals among large numbers of Unc-54 mutant animals, rare intragenic recombinants were recovered between mutations of unc-54 I, the gene coding for the myosin heavy chain of Caenorhabditis elegans body wall musculature. Appropriate closely linked marker mutations were used to improve screening efficiency, to distinguish recombination and conversion events, and to establish the relative order of unc-54 mutations in the gene. From the analysis of more than 400 exceptional chromosomes recovered from tests involving 91 heteroallelic strains, 27 unc-54 mutations have been separated into ten distinct sites. Null mutations, comprising the majority of the mutations studied, are scattered throughout the map with the e1300 and st60 mutations located at the left and right ends, respectively. Three small deficiencies are clustered at an internal site nearer the left end. Two missense mutations lie to the right of these deficiencies. By correlating these results with molecular investigations of specific mutations, we conclude that the 5' end of the coding sequence is at the right end of the gene and is located distally on the chromosome. These correlations also demonstrate that the map includes at least 80% of the structural sequence. The genetic map allows us to infer the approximate location of mutations in the coding sequence, and should aid in the genetic dissection of ------------------- Key: 580 Medline: 82261911 Authors: Hosono R;Mitsui Y;Sato Y;Aizawa S;Miwa J Title: Life span of the wild and mutant nematode C. elegans. Effects of sex, sterilization and temperature. Citation: Experimental Gerontology 17: 163-172 1982 Type: ARTICLE Genes: emb-5 emb-9 Abstract: The survival of Caenorhabditis elegans was studied comparing animals of different sexes, sterilized animals, and animals grown at different temperatures as a prelude to more detailed cytological and genetic analysis of aged nematodes. Temperature-sensitive sterile mutants, animals sterilized by 5-fluorodeoxyuridine treatment, and wild-type males showed little difference in life span from that of wild-type hermaphrodites, although slight changes in P (time of beginning of the dying phase) or T1/2 (half-life of the population in the early dying phase) values were observed. At higher temperatures, P and T1/2 values markedly decreased, indicating a shortened life span. Temperature shift between 16 degrees C and 25 degrees C revealed that an increase in life span always involved low temperatures after the adult phase. High temperature treatment during the growing phase or after the adult phase caused an earlier start of the dying phase, but a downward temperature during the adult phase resulted in a great increase in the half-life of the population (T1/2). The results suggest that the life span of C. elegans is rigidly determined by somatic cells and markedly influenced by the effects of temperature on the cells during the post-mitotic ------------------- Key: 581 Medline: 82260464 Authors: Roberts TM;Ward S Title: Directed membrane flow on the pseudopods of C. elegans spermatozoa. Citation: Cold Spring Harbor Symposia on Quantitative Biology 46: 695-702 1982 Type: REVIEW Genes: fer-1 fer-2 him-5 Abstract: The capping of cross-linked surface receptors on lymphocytes and other cells and the centripetal movement of surface-attached particles on crawling cells are examples of directed surface membrane movement. One possible mechanism for moving membrane components is that cytoskeletal proteins recognize cross-linked surface receptors and drag them through the membrane bilayer to one pole of the cell. Favoring this theory are the localization of actin and/or myosin under capped or mobile cross-linked surface molecules and the biochemical coisolation of actin with capped proteins. Another possibility is that movement results from flow of bulk membrane or membrane lipid between an assembly point at one pole of the cell to a disassembly point elsewhere on the surface. Capping on sessile cells and rearward membrane movement on crawling cells have different functions. The clustering of surface receptors that occurs during capping seems to play a role in the transmission of signals from surface-bound ligands across the membrane. As pointed out by Abercrombie, membrane movement on crawling cells may participate in locomotion. Crawling requires continuous assembly of new cell-substrate contact sites at the leading edge of the cell. Rearward membrane movement would result from this polarized membrane assembly. Thus, it is reasonable that these two types of direct membrane movement could be driven by different mechanisms, with cytoskeletal linkage operating in sessile cells and membrane flow occurring on crawling cells. This notion is supported by studies showing two distinct mechanisms for capping, one occurring spontaneously on motile cells and the other requiring ligand cross-linkage on lymphocytes. Here we examine the surface membrane movements on the amoebid spermatozoon of the free-living nematode Caenorhabditis elegans. This cell exhibits a pronounced morphological asymmetry, with the cellular organelles segregated into a hemispherical cell body (3-4 um dia). The cell forms a single persistent pseudopod, filled with granular cytoplasm, that extends about 4 um. Three features make the C. elegans spermatozoon ideal for studying the crawling movements of metazoan cells. First, differentiation of sessile, spherical spermatids into spermatozoa can be activated in vitro with the monovalent ion ionophore monensin so that the onset of motility can be controlled. Second, the asymmetry of the cell is clearly defined with the cell-body-pseuodopod junction visible both externally and internally. Third, sperm-defective mutants can be isolated, allowing cellular motility to be analyzed genetically. We now report that surface membrane movement on C. elegans spermatozoa occurs exclusively on the pseudopod. This movement comprises centripetal bulk-membrane flow and is not restricted to rearrangement of cross-linked membrane components. Furthermore, surface ------------------- Key: 582 Medline: 82236182 Authors: Khan FR;McFadden BA Title: C. elegans: Decay of isocitrate lyase during larval development. Citation: Experimental Parasitology 54: 47-54 1982 Type: ARTICLE Genes: Abstract: Changes in the levels of isocitrate lyase, malate synthase, catalase, fumarase, and NADP+-isocitrate dehydrogenase have been investigated during larval development of the free-living nematode Caenorhabditis elegans in the presence and absence of Escherichia coli. The specific activities of isocitrate lyase, malate synthase, and catalase are maximal at the time of egg hatching and, thereafter, decline during larval development when larvae feed on E. coli, whereas in the absence of E. coli specific activities of the same enzymes increase for 12 hr and subsequently remain constant. There is, however, no change in specific activity of fumarase or NADP+-isocitrate dehydrogenase during the same developmental period, in either case. Cycloheximide at 100 uM arrests the decline of isocitrate lyase during development of feeding larvae but has no effect upon the appearance of isocitrate lyase during starvation. The latter is true also for 15 mM itaconate. There is inactivation of isocitrate lyase in crude extracts of frozen worms in comparison to that in analogous extracts prepared from freshly harvested nematodes. ------------------- Key: 583 Medline: 83030936 Authors: Miwa J;Tabuse Y;Furusawa M;Yamasaki H Title: Tumor promoters specifically and reversibly disturb development and behavior of C. elegans. Citation: Journal of Cancer Research & Clinical Oncology 104: 81-88 1982 Type: ARTICLE Genes: Abstract: The effect of phorbol ester tumor promoters on the development and behavior of a free-living soil nematode, Caenorhabditis elegans, was studied. When young developing C. elegans were grown on E. coli- seeded agar with low concentrations (0.1 microgram/ml) of 12-0- tetradecanoyl-phorbol-13-acetate or phorbol-12,13-didecanoate, their growth was arrested. These tumor promoters reduced the brood size when gravid adults were treated and caused uncoordinated movement in animals treated at any stage of development. The effects of these tumor promoters on nematode development and behavior were partially reversible. The nonpromoting derivatives phorbol and 4 alpha-phorbol- 12,13-didecanoate showed no effect on the animals. ------------------- Key: 584 Medline: 82236186 Authors: Huang S-P;Tattar TA;Rohde RA;Zuckerman BM Title: C. elegans: Effects of 5-hydroxytryptophan and dopamine on behavior and development. Citation: Experimental Parasitology 54: 72-79 1982 Type: ARTICLE Genes: Abstract: 5-Hydroxytryptophan (5-HTP) was introduced iontophoretically into the vulva region of Caenorhabditis elegans to examine behavioral responses to this putative neurotransmitter. Responses in esophageal basal bulb pulsation and/or vulval contractions occurred. Little relation was observed between dosage and behavioral response. Similar behavioral responses followed topical applications of 5-HTP. An inverse relationship between the rates of esophageal pumping and vulval contraction was recorded following both iontophoretic injection and topical application. Following iontophoretic application, young nematodes resumed body movement sooner than old nematodes did. Growth significantly increased when 5-HTP or dopamine was added to the culture medium, but neither chemical influenced fecundity or life span. ------------------- Key: 585 Medline: 83023040 Authors: Davis BO;Anderson GL;Dusenbery DB Title: Total luminescence spectroscopy of fluorescence changes during aging in C. elegans. Citation: Journal of Biochemistry 21: 4089-4095 1982 Type: ARTICLE Genes: Abstract: Total luminescence spectroscopy was employed to characterize and quantitate age-related changes in fluorescence in the nematode Caenorhabditis elegans, an established model for aging research. The excitation wavelength was varied between 250 and 590 nm in 10-nm increments. At each excitation wavelength, the emission wavelength was varied between 300 and 600 nm. Contour plots of corrected spectra were made. All fluorescence increased severalfold with age, except for that ascribed to tryptophan of soluble protein fractions. This general increase included fluorescence due to flavins, which is not expected to increase with age but has previously been observed to do so in this species. Blue emission peaks that approximated Schiff base product fluorescence were detected in whole aqueous homogenates, chloroform/methanol extracts, and detergent-cleaned cuticle preparations. Age-related increases in emission intensities of these peaks were demonstrated in aqueous homogenates and isolated cuticles. Cuticle preparations, known to be rich in collagenous protein, exhibited a fluorescence peak that approximated the recently described pyridinoline cross-link of vertebrate collagen. This peak, as well as the entire cuticle emission spectrum between 300 and 500 nm, increased dramatically with age. A fluorescence peak tentatively identified as cuticle tyrosine, characteristic of collagenous protein, also increased in older worms. The effectiveness of the spectroscopic technique in distinguishing individual fluorescence peaks in complex mixtures was demonstrated, and the potential of the ------------------- Key: 587 Medline: Authors: Shepherd AM Title: Interpretation of sperm development in nematodes. Citation: Nematologica 27: 122-125 1981 Type: REVIEW Genes: Abstract: With the increased use of the electron microscope to study nematode spermatogenesis and the cytology and physiology of sperm, interpretation of the processes and the terms applied to various stages have not been consistent. ------------------- Key: 588 Medline: 83065222 Authors: Johnson TE;Wood WB Title: Genetic analysis of life-span in C. elegans. Citation: Proceedings of the National Academy of Sciences USA 79: 6603-6607 1982 Type: ARTICLE Genes: Abstract: Crosses between Bristol and Bergerac strains of the self-fertilizing hermaphroditic nematode Caenorhabditis elegans do not show the heterosis effects for life-span that complicate analysis of interstrain crosses with Drosophila or mice. Instead they yield F1 progeny with life-spans similar to those of the parent strains. By analysis of life-span variation among progeny F2 populations from such crosses and by two independent analyses of life-spans among recombinant inbred lines derived from F2 individuals by 18 rounds of self-fertilization, we estimate that the heritability of life-span in C. elegans is between 20% and 50%. Recombinant inbred lines show a range in mean life-spans of 10 days to 31 days compared to life-spans of about 18 days for each of the two parental strains. We conclude that life-span variation in C. elegans has a substantial genetic component and that this organism offers promising opportunities for selective breeding of longer-lived strains and genetic ------------------- Key: 589 Medline: Authors: Ohba K;Ishibashi N Title: Effects of procaine on the development, longevity and fecundity of C. elegans. Citation: Nematologica 27: 275-284 1981 Type: ARTICLE Genes: Abstract: In medium containing 20 mg/ml of procaine-HCl, juvenile development of Caenorhabditis elegans almost ceased, and juveniles entered a dauer-like state. After transfer to procaine-free medium, the nematodes resumed growth and matured in about 4 days. After transfer to drug-free medium the fecundity of the treated nematodes was markedly reduced even by a one-day exposure to the drug, and unlike longevity the decline proceeded stepwise. Procaine-treated nematodes resisted desiccation less but resisted freezing as did juveniles in the dauer state from monoxenic cultures. Under the electron microscope procaine-treated juveniles had empty intestinal lumens but unlike dauer juveniles the morphology of this region had a thick cuticle ------------------- Key: 590 Medline: 83016664 Authors: Golden JW;;Riddle DL Title: A pheromone influences larval development in the nematode C. elegans. Citation: Science 218: 578-580 1982 Type: ARTICLE Genes: Abstract: A Caenorhabditis-specific pheromone and the food supply influence both entry into and exit from a developmentally arrested juvenile stage called the dauer larva. The pheromone increases the frequency of dauer larva formation and inhibits recovery but does not affect adult behavior such as chemotaxis and egg laying. The fatty acid-- like pheromone has been partially purified and characterized by a new bioassay. If similar developmental control mechanisms are used by parasitic nematodes, such mechanisms might be exploited to develop highly selective anthelmintic agents. ------------------- Key: 591 Medline: Authors: Abdulkader N;Gibert M-A;Starck J;Bosch C;Brun J Title: Temperature-sensitive mutations in C. elegans: A sterile mutation affecting oocyte I core relations. Citation: Revue de Nematologie 3: 201-212 1980 Type: ARTICLE Genes: Abstract: ------------------- Key: 592 Medline: 84059034 Authors: Rogalski TM;Moerman DG;Baillie DL Title: Essential genes and deficiencies in the unc-22 IV region of C. elegans. Citation: Genetics 102: 725-736 1982 Type: ARTICLE Genes: let-51 let-52 let-53 let-54 let-55 let-56 let-58 let-59 let-60 let-61 let-63 let-64 let-65 let-66 let-67 unc-22 unc-30 unc-31 unc-43 sDf2 sDf7 sDf8 sDf9 sDf10 Abstract: Five formaldehyde-induced deficiencies that uncover unc-22 IV, a gene affecting muscle structure in the nematode Caenorhabditis elegans were isolated and positioned. The largest deficiency, sDf2, extends in both directions from unc-22 and is approximately 1.0-2.0 map units in length. The other four deficiencies, sDf7, sDf8, sDf9 and sDf10, are all smaller than sDf2 and are located within the region uncovered by this deficiency. Thirty-seven ethyl methane-sulfonate-induced lethal and sterile mutations linked to unc-22 were isolated and tested for complementation with sDf2. Nineteen lethal mutations failed to complement sDf2. Sixteen of these were further positioned by recombination mapping and also by deficiency mapping with sDf7, sDf8, sDf9 and sDf10. These sixteen mutations define 11 new essential genes in this region. Eight of the genes lie in a 0.9-map unit interval to the left of unc-22, whereas the three remaining genes lie in a region of about 0.2 map units to the right of unc-22. We believe that two of the essential genes identified in this study, let-56 and let-52, are the adjacent genes on either side of unc-22. The lethal mutations exhibit a wide range of terminal phenotypes: from first stage larva to sterile ------------------- Key: 593 Medline: Authors: Rinker DL;Bloom JR Title: Phoresy between a mushroom-infesting fly and two free-living nematodes associated with mushroom culture. Citation: Journal of Nematology 14: 599-602 1982 Type: ARTICLE Genes: Abstract: Free-living nematodes are pests of commercial mushroom production. On occasions they contribute significantly to mushroom yield reductions; however, their role in decreased production is not fully understood. Control has been achieved through effective sanitation and good cultural practices. Pasteurization of the old crop has been practiced to kill nematodes in compost and structural framework. Proper preparation of compost, casing soil, and spawn effectively produces nematode-free materials, but despite these precautions, crops are often infested with nematodes. Hussey suggested that nematodes are transported into the houses by mushroom-infesting flies. Members of the Rhabditidae, Diplogasteridae, Chambersiellidae, Cephalobidae, Aphelenchidae, Aphelenchoididae, Cylindrocorporidae, Dorylaimidae, Neotylenchidae, Monochidae, Panagrolaimidae, Plectidae, Strongylidae, and Tylenchidae are reported to have phoretic associations with insects. Thus, the objective of this study was to determine if certain free-living nematode pests of commercial mushrooms could be transported by mushroom ------------------- Key: 594 Medline: Authors: Chitwood DJ;Lusby WR;Lozano R;Thompson MJ;Svoboda JA Title: Sterol metabolism in the nematode C. elegans. Citation: Lipids 19: 500-506 1984 Type: ARTICLE Genes: Abstract: The metabolism of various dietary sterols and the effects of an azasteroid on sitosterol metabolism in the free-living nematode Caenorhabditis elegans was investigated. The major unesterified sterols of C. elegans in media supplemented with sitosterol, cholesterol or desmosterol included 7-dehydrocholesterol (66.5%, 40.5%, 31.2%, respectively), cholesterol (6.7%, 52.3%, 26.9%), lathosterol (4.4%, 3.6%, 1.7%) and 4a-methylcholest-8(14)-en-3B-ol (4.2%, 2.1%, 3.8%). Esterified sterols, representing less than 20% of the total sterols, were somewhat similar except for a significantly higher relative content of 4a-methylcholest-8(14)-en-3B-ol (23.3%, 23.4%, 10.6%). Thus C. elegans not only removes the substituent at C24 of dietary sitosterol but possesses the unusual ability to produce significant quantities of 4a-methylsterols. When C. elegans was propagated in medium supplemented with sitosterol plus 5 ug/ml of 25-azacoprostane hydrochloride, the azasteroid stronly interfered with reproduction and motility of C. elegans and strongly inhibited the delta24-sterol reductase enzyme system; excluding sitosterol, the major free sterols of azacoprostane-treated C. elegans were cholesta-5,7,24-trien-3B-ol (47.9%), desmosterol (9.4%), fucosterol (2.1%) and cholesta-7,24-dien-3B-ol (2.0%). These 4 sterols are likely intermediates in the metabolism ------------------- Key: 596 Medline: 83138965 Authors: Nelson FK;Albert PS;Riddle DL Title: Fine structure of the C. elegans secretory-excretory Citation: Journal of Ultrastructure Research 82: 156-171 1983 Type: ARTICLE Genes: dpy-5 Abstract: The secretory-excretory system of C. elegans, reconstructed from serial-section electron micrographs of larvae, is composed of four cells, the nuclei of which are located on the ventral side of the pharynx and adjacent intestine. (1) The pore cell encloses the terminal one-third of the excretory duct which leads to an excretory pore at the ventral midline. (2) The duct cell surrounds the excretory duct with a lamellar membrane from the origin of the duct at the excretory sinus to the pore cell boundary. (3) A large H- shaped excretory cell extends bilateral canals anteriorly and posteriorly nearly the entire length of the worm. The excretory sinus within the cell body joins the lumena of the canals with the origin of the duct. (4) A binucleate, A-shaped gland cell extends bilateral processes anteriorly from cell bodies located just behind the pharynx. These processes are fused at the anterior tip of the cell, where the cell enters the circumpharyngeal nerve ring. The processes are also joined at the anterior edge of the excretory cell body, where the excretory cell and gland are joined to the duct cell at the origin of the duct. Secretory granules may be concentrated in the gland near this secretory-excretory junction. Although the gland cells of all growing developmental stages stain positively with paraldehyde-fuchsin, the gland of the dauer larva stage (a developmentally arrested third-stage larva) does not stain, nor do glands of starved worms of other stages. Dauer larvae uniquely lack secretory granules, and the gland cytoplasm is displaced by a labyrinth of large, transparent spaces. Exit from the dauer stage results in the return of active secretory morphology in fourth-stage larvae. ------------------- Key: 597 Medline: 83141017 Authors: Hartman PS;Herman RK Title: Somatic damage to the X chromosome of the nematode C. elegans induced by gamma radiation. Citation: Molecular & General Genetics 187: 116-119 1982 Type: ARTICLE Genes: her-1 tra-1 Abstract: Wild-type male embryos and young larvae of the nematode Caenorhabditis elegans were more sensitive than wild-type hermaphrodites to inactivation by gamma rays; wild-type males have one X chromosome per cell (XO), whereas wild-type hermaphrodites have two (XX). Furthermore, after transformation into fertile hermaphrodites by a her-1 mutation, XO animals were more radiosensitive than XX her-1 animals; and XX animals transformed into fertile males by a tra-1 mutation did not show increased radiosensitivity. It is concluded that wild-type males are more radiosensitive than wild-type hermaphrodites because they have one X chromosome rather than two, and the predominant mode of inactivation of XO animals involves damage to the single X chromosome. No sex- specific differences in survival were observed after UV irradiation. ------------------- Key: 598 Medline: 83027644 Authors: Himmelhoch S;Zuckerman BM Title: Xiphinema index and C. elegans: Preparation and molecular labeling of ultrathin frozen sections. Citation: Experimental Parasitology 54: 250-259 1982 Type: ARTICLE Genes: Abstract: A method for the orientation of nematodes for cryoultramicrotomy is described. Comparison of cryosections with sections prepared by conventional electron microscopic procedures showed satisfactory resolution of structural details in frozen sections. Labeling of frozen sections en face was achieved by cationized ferritin and colloidal iron. Actin was localized in cryosections of somatic muscle by immunoferritin labeling. The current study is a practical example of the application potential of cryoultramicrotomy to examination of nematode cytochemistry at a molecular ------------------- Key: 599 Medline: Authors: DeCuyper C;Vanfleteren JR Title: Oxygen consumption during development and aging of the nematode C. elegans. Citation: Comparative Biochemistry & Physiology 73A: 283-289 1982 Type: ARTICLE Genes: Abstract: 1. The oxygen consumption was measured in all four juvenile stages, the reproductive stage and the aged postreprodutive stage of the free-living nematode Caenorhabditis elegans, using the Cartesian diver method. 2. The uptake of oxygen as a function of body weight was VO2 = 1.66 W*0.70 for all stages except the aged stage and VO2 = 1.62 W*0.58 when both first stage juveniles and aged organisms were excluded (VO2 = nl O2/ug hr; W = wet weight). 3. The metabolic rate (VO2/W) was significantly lower in both first stage juveniles and aged adults. This is ascribed to utilization of fat stores by way of the glyoxylate cycle during embryogenesis and early morphogenesis and to a general failure of the metabolic machinery during senescence. 4. A comparison of the actual oxygen consumption with the amount of oxygen available to the nematodes by diffusion through the cuticle showed that the weight-specific coefficient b (0.70 or 0.58) could not be explained by decreasing ability to provide oxygen to body tissues with increasing worm size. 5. It is suggested that ATP dependent activities which occur at the cell surface might greatly determine the magnitude of the weight-specific coefficient in nematodes. ------------------- Key: 600 Medline: 83078557 Authors: Goldstein P Title: The synaptonemal complexes of C. elegans: Pachytene karyotype analysis of male and hermaphrodite wild-type and him mutants. Citation: Chromosoma 86: 577-593 1982 Type: ARTICLE Genes: him-8 Abstract: Only five synaptonemal complexes (SC), representing the 5 autosomes, are present in wild-type, him-4 and him-8, Caenorhabditis elegans males, whereas there are six SCs, accounting for 5 autosomal bivalents and the XX bivalent, in the C. elegans hermaphrodite. The univalent X chromosome of the male is present as a heterochromatic 'X- body' in spermatocyte pachytene nuclei. The XX bivalent in wild-type, him-4 and him-8 hermaphrodites (SC1, 2.5 microns in length) represented 6% of the total karyotype length and a SC of this size is missing from the respective male karyotypes. This corresponds with the fact that the total male karyotype length is only approximately 94% that of the hermaphrodite. Associated with the central element of the SC are structures termed 'SC knobs' that were first described in the wild-type hermaphrodite. The six SC knobs present in the wild- type hermaphrodite oocyte pachytene nuclei and the two SC knobs in the male spermatocyte pachytene nuclei are apparently randomly placed with the exception that they are never found at the ends of the SC. This is also true in him-4 and him-8 in which case there are 3 and zero SC knobs in the hermaphrodites, respectively, and one SC knob each in the male pachytene nuclei. The decrease in number of SC knobs in hermaphrodite to male represents a true sex difference. The presence or absence of the SC knobs may influence the X chromosome nondisjunction process and this effect is not localized to the region of the SC on which the SC knob is located. ------------------- Key: 601 Medline: 83114617 Authors: Rose AM;Baillie DL;Candido EPM;Beckenbach KA;Nelson D Title: The linkage mapping of cloned restriction fragment length differences in C. elegans. Citation: Molecular & General Genetics 188: 286-291 1982 Type: ARTICLE Genes: dpy-5 dpy-10 dpy-11 unc-22 unc-36 Abstract: The genomic DNA of two closely related strains of the nematode, Caenorhabditis elegans, Bristol (N2), and Bergerac (Bo), has different restriction endonuclease sites. Since these two strains interbreed, it is possible to regard the restriction length differences (RFLDs) as mutant variants. The N2 and Bo pattern can be segregated and mapped using classical genetic techniques. Utilizing a number of genetic markers existing in the N2 strain, we have constructed hybrid populations homozygous for either Bristol or Bergerac over a given chromosomal region with random Bristol-Bergerac composition for the remainder of the genome. Genomic restriction digests from these hybrid populations were probed with random cloned fragments of Bristol DNA. In this way, fragments were mapped to genetically well characterized regions of the C. elegans genome. 27 probes which hybridize to a total of 310 Kb of DNA were found to exhibit six restriction fragment differences. Four of these differences have been mapped, providing probes for four different genomic regions. We have combined classical genetics and recombinant DNA technology to construct linkage maps of cloned DNA fragments using restriction length differences. We are pursuing this approach in order to advance the knowledge of the genetic organization of C. elegans and to provide an experimental model for the study of many biological systems. It is hoped that this approach will also provide a practical solution to some difficult problems in nematode strain identification. Furthermore, the characterization of the families of transposable elements responsible for generating many of the RFLDs will undoubtedly contribute to the understanding of the biological significance of these ------------------- Key: 602 Medline: 83129414 Authors: Emmons SW;Yesner L;Ruan K-S;Katzenberg D Title: Evidence for a transposon in C. elegans. Citation: Cell 32: 55-65 1983 Type: ARTICLE Genes: Abstract: The C. elegans genome contains a 1.7 kb repeated DNA sequence (Tc1) that is present in different numbers in various strains. In strain Bristol and 10 other strains analyzed, there are 20 +/- 5 copies of Tc1, and these are located at a nearly constant set of sites in the DNA. In Bergerac, however, there are 200 +/- 50 interspersed copies of Tc1 that have arisen by insertion of Tc1 elements into new genomic sites. The interspersed copies of Tc1 have a conserved, nonpermuted structure. The structure of genomic Tc1 elements was analyzed by the cloning of a single Tc1 element from Bergerac and the comparison of its structure with homologous genomic sequences in Bristol and Bergerac. Tc1 elements at three sites analyzed in Bergerac undergo apparently precise excision from their points of insertion at high frequency. ------------------- Key: 603 Medline: 83078550 Authors: Albertson DG;Thomson JN Title: The kinetochores of C. elegans. Citation: Chromosoma 86: 409-428 1982 Type: ARTICLE Genes: mnDp2 Abstract: Light microscopy of the mitotic chromosomes of Caenorhabditis elegans suggests that non-localized kinetochores are present, since the chromosomes appear as stiff rods 1 to 2 micrometers in length and lack any visible constriction. The holokinetic structure was confirmed by reconstructions of electron micrographs of dividing nuclei in serially sectioned embryos. In prophase the kinetochore appears as an amorphous projection approximately 0.18-0.2 micrometer in diameter in cross section and in longitudinal section it appears to be continuous along the chromatin. At prometaphase and metaphase the kinetochore is a convex plaque covering the poleward face of the chromosome and extending the length of the chromosome. In longitudinal section the kinetochore is a trilaminar structure with electron dense inner and outer layers of 0.02 micrometer, and an electron lucent middle layer of 0.03 micrometer. The inner layer is adjacent to a more electron dense region of chromatin. The kinetochore was also seen as a band extending the length of the chromosome in whole mount preparations of chromosomes stained with ethanolic phosphotungstic acid. Most gamma ray induced chromosome fragments segregate normally in embryonic mitoses, but some fragments display aberrant behavior. Similar behavior was seen in embryos carrying a genetically characterized free duplication. It is suggested that mitotic segregation of small fragments may be inefficient because the probability of attachment of microtubules to the kinetochore is proportional to ------------------- Key: 604 Medline: 83090455 Authors: Kumazaki T;Hori H;Osawa S;Ishii N;Suzuki K Title: The nucleotide sequences of 5S rRNAs from a rotifer, Brachionus plicatilis, and two nematodes, Rhabditis tokai and C. elegans. Citation: Nucleic Acids Research 10: 7001-7004 1982 Type: ARTICLE Genes: Abstract: The nucleotide sequences of 5S rRNAs from a rotifer, Brachionus plicatilis, and two nematodes, Rhabditis tokai and Caenorhabditis elegans have been determined. The rotifer has two 5S rRNA species that are composed of 120 and 121 nucleotides, respectively. The sequences of these two 5S rRNAs are the same except that the latter has an additional base at its 3'-terminus. The 5S rRNAs from the two nematode species are both 119 nucleotides long. The sequence similarity percents are 79% (Brachionus/Rhabditis), 80% (Brachionus/Caenorhabditis), and 95% (Rhabditis/Caenorhabditis) among these three species. Brachionus revealed the highest similarity to Lingula (89%), but not to the nematodes (79%). ------------------- Key: 605 Medline: Authors: Hutzell PA;Krusberg LR Title: Fatty acid compositions of C. elegans and C. briggsae. Citation: Comparative Biochemistry & Physiology 73B: 517-520 1982 Type: ARTICLE Genes: Abstract: 1. Lipid accounted for 19.6 and 22.1% of the dry weight of Caenorhabditis elegans and C. briggsae, respectively. 2. The major portion of the fatty acids of both nematodes contained 18 or 20 carbon atoms. Seventy-eight per cent of the total fatty acid of C. elegans was unsaturated, as was 56% of that of C. briggsae. 3. The same 26 fatty acids occurred in both species; however, relative quantities of certain fatty acids varied. 4. The principal fatty acid fraction in both nematodes was 18:1. Vaccenic acid comprised 44.7 and 74.1% of the total 18:1 of C. briggsae and C. elegans, respectively. ------------------- Key: 606 Medline: 83103971 Authors: Vanfleteren JR Title: Nematode chromosomal proteins II. Fractionation and identification of the histones of C. elegans. Citation: Comparative Biochemistry & Physiology 73B: 709-718 1983 Type: ARTICLE Genes: Abstract: 1. Whole histone of the nematode Caenorhabditis elegans has been fractionated into the five main histone fractions by a combination of techniques including selective extraction, gel filtration, ion- exchange chromatography and electrophoresis. 2. The histones were identified on acid urea gels by a comparison of the electrophoretic profiles with those of calf thymus histone. 3. Acid urea gel electrophoresis of histone fraction H1 revealed one major and several minor bands. 4. At least three of these were most likely derived from H1 degradation, however. 5. Stepwise elution with 0.01 and 0.02 N HCl of the slightly lysine rich histones from carboxymethyl cellulose resolved two subfractions of H2B, designated H2B1 and H2B2 respectively. 6. Both H2B subtypes co-electrophoresed in acid urea gels containing 2.5 and 6.25 M urea. 7. The electrophoretic mobility of H2A was marginally higher at 2.5 M urea and identical with that of H2B1 and H2B2 at 6.25 M urea. 8. Molecular interaction considerably reduced the usefulness of molecular size fractionation of nematode histones. ------------------- Key: 607 Medline: Authors: Spence AM;Malone KMB;Novak MMA;Woods RA Title: The effects of mebendazole on the growth and development of C. elegans. Citation: Canadian Journal of Zoology 60: 2616-2623 1982 Type: ARTICLE Genes: Abstract: Mebendazole inhibits growth, reproductive capacity, and motility of Caenorhabditis elegans. Maximum reduction of length (50%) and volume (80%) was observed at 6.25 ug/mL mebendazole. At this concentration vulva formation was delayed by 18 h and egg production was reduced from 8 eggs/worm per hour to less than 1. The critical period for the effect of mebendazole on length was from 40 to 50 hours after hatching. The drug did not affect the viability of eggs, larvae, or adults. L1 and L2 larvae were motile in the presence of mebendazle (6.25 ug/mL); paralysis became apparent during the L3 and was completed in L4 and adult stages. Paralysed worms coiled into a ring and moved feebly and spasmodically. The first two moults occurred at the same time in control and treated worms, the L3/L4 and L4/adult moults were delayed by less than 1 h in the presence of the drug. Evidence is presented that these observed effects are caused by mebendazole and were not the consequence of partial starvation resulting from paralysis. ------------------- Key: 608 Medline: Authors: Hodgkin J Title: Male phenotypes and mating efficiency in C. elegans. Citation: Genetics 103: 43-64 1983 Type: ARTICLE Genes: ace-1 ace-2 act-1 act-2 act-3 bli-1 bli-2 bli-3 bli-4 bli-5 cat-1 cat-2 cat-4 cha-1 che-1 che-2 che-3 che-5 che-6 che-7 daf-3 daf-5 daf-6 daf-10 daf-12 daf-13 daf-16 daf-18 daf-20 dpy-1 dpy-2 dpy-3 dpy-4 dpy-5 dpy-6 dpy-7 dpy-8 dpy-9 dpy-13 dpy-14 dpy-17 dpy-18 dpy-19 dpy-20 dpy-21 dpy-22 dpy-23 dpy-25 dpy-26 flu-1 flu-2 flu-3 flu-4 him-1 him-2 him-3 him-5 him-6 him-7 him-8 him-9 lev-1 lev-11 lin-1 lin-2 lin-3 lin-4 lin-7 lin-10 lin-15 lin-18 lon-1 lon-2 mab-2 mab-3 mab-4 mab-5 mab-6 mab-7 mab-8 mab-9 mab-10 mec-1 mec-2 mec-3 mec-4 mec-5 mec-6 mec-7 mec-8 mec-9 mec-10 mec-12 mor-1 mor-2 nuc-1 osm-1 osm-3 osm-5 osm-6 rol-1 rol-3 rol-4 rol-6 sma-1 sma-2 sma-3 sma-4 smg-1 sqt-1 sqt-2 sqt-3 unc-1 unc-2 unc-3 unc-4 unc-5 unc-6 unc-7 unc-8 unc-9 unc-10 unc-11 unc-13 unc-14 unc-15 unc-16 unc-17 unc-18 unc-20 unc-22 unc-23 unc-24 unc-25 unc-26 unc-27 unc-29 unc-30 unc-31 unc-32 unc-33 unc-34 unc-35 unc-36 unc-37 unc-38 unc-39 unc-40 unc-41 unc-42 unc-43 unc-44 unc-45 unc-46 unc-47 unc-49 unc-50 unc-51 unc-52 unc-53 unc-54 unc-55 unc-57 unc-58 unc-59 unc-60 unc-61 unc-62 unc-63 unc-64 unc-65 unc-67 unc-68 unc-69 unc-70 unc-71 unc-73 unc-74 unc-75 unc-76 unc-77 unc-78 unc-79 unc-80 unc-81 unc-82 unc-83 unc-84 unc-85 unc-86 unc-87 unc-89 unc-93 unc-94 unc-95 unc-96 unc-97 unc-98 unc-100 unc-103 unc-104 vab-1 vab-2 vab-3 vab-6 vab-7 vab-8 vab-9 vab-10 Abstract: Mating behavior in adult male nematodes can be assayed by mating efficiency, i.e., the number of cross progeny sired by males under standard conditions. Mutant males from 220 strains, representing most known complementation groups of C. elegans, have been examined for mating efficiency and for anatomical abnormalities of the specialized male copulatory organs. These data extend the phenotypic description of these mutants and indicate what anatomical and behavioral components are necessary for the ability to mate successfully. Also, mutants with specific defects in the male were sought by establishing superficially wild-type hermaphrodite stocks after mutagenesis and testing the males segregated by these stocks for mating efficiency. Forty-nine of 1119 stocks yielded abnormal males. Seventeen were characterized in detail and found to be abnormal in sensory behavior (carrying mutations in the genes che-2 or che-3) or male genital anatomy (carrying mutations in one of the genes mab-1 to mab-10). Four of the mab (male abnormal) genes affect specific postembryonic ------------------- Key: 609 Medline: Authors: Hosono R;Hirahara K;Kuno S;Kurihara T Title: Mutants of C. elegans with Dumpy and Rounded head Citation: Journal of Experimental Zoology 224: 135-144 1982 Type: ARTICLE Genes: dpy-1 dpy-20 sma-1 Abstract: Mutations bearing morphological alterations in both head and body are reported in Caenorhabditis elegans. Although most dumpy mutants so far isolated have shorter bodies with normal head form, the mutants presented in this paper have rounded heads in addition to dumpy bodies. On examination with light- and scanning electron microscopes, defects in organs attached to the tip of head were not detected. The mutations were mapped as alleles of the dpy-20 gene on linkage group IV. Segregation of the head abnormality from dumpy body was not detected upon examination of over 10,000 descendants from heterozygous offspring (F1) produced by crossing mutant hermaphrodites with wild-type males. Revertants of dpy-20(cn142) allele were found to be almost wild-type in both head and other body morphology, supporting the possibility that both phenotypes in these alleles have been produced by a single mutation. Genetic analysis of two other revertants are also presented in this ------------------- Key: 610 Medline: 83143266 Authors: Tranquilla TA;Cortese R;Melton D;Smith JD Title: Sequences of four tRNA genes from C. elegans and the expression of C. elegans tRNA Leu (anticodon IAG) in Xenopus oocytes. Citation: Nucleic Acids Research 10: 7919-7934 1982 Type: ARTICLE Genes: Abstract: Four tRNA genes have been identified in cloned segments of Caenorhabditis elegans DNA by tRNA hybridisation and expression after injection into Xenopus laevis oocyte nuclei. From DNA sequencing these are (with DNA anticodon sequences) tRNAAsp (GTC), tRNALeu (AAG), tRNALys (CTT) and tRNAPro (TGG). Their flanking DNA sequences are compared. Two identical tRNALys (CTT) genes from different regions of the genome have quite unrelated 5' flanking sequences. The tRNA synthesised in Xenopus oocytes after injection of the tRNALeu cloned DNA has the modified anticodon IAG. The tRNALeu gene precursor transcript from injected oocytes has short 5' and 3' additional sequences and lacks certain of those modified bases found in the processed tRNA. ------------------- Key: 611 Medline: 83189113 Authors: Files JG;Carr S;Hirsh D Title: Actin gene famly of C. elegans. Citation: Journal of Molecular Biology 164: 355-375 1983 Type: ARTICLE Genes: act-1 act-2 act-3 Abstract: Four actin genes have been isolated from Caenorhabditis elegans that account for all of the major actin hybridization to total genomic DNA. Actin genes I, II and III are clustered within a 12 X 10(3) base region; gene IV is unlinked to the others. All four genes have been sequenced from at least nucleotide -109 to +250. Genes I and III are identical for the first 307 coding nucleotides. Genes I and II differ in 14 positions within the first 250 coding nucleotides; one difference substitutes an aspartic acid for a glutamic acid at codon 5. Genes I and IV differ in 18 positions within the first 259 coding nucleotides without causing any amino acid differences. Genes I, II and III have introns after the first nucleotide of codon 64 and gene IV has an intron between codons 19 and 20. The four nucleotide sequences thus far define two different amino acid sequences. Both of the amino acid sequences resemble vertebrate cytoplasmic actin more than vertebrate muscle actin. A DNA polymorphism between the Bristol and Bergerac strains has been used as a phenotypic marker in genetic crosses to map the cluster of actin genes within a 2% recombination interval on linkage group V between unc-23 and sma-1 in order to begin a molecular genetic analysis of the actin loci. ------------------- Key: 612 Medline: 83189127 Authors: McLachlan AD;Karn J Title: Periodic features in the amino acid sequence of nematode myosin rod. Citation: Journal of Molecular Biology 164: 605-626 1983 Type: ARTICLE Genes: unc-54 Abstract: Properties of the amino acid sequence of the nematode myosin rod region, deduced from cloned DNA, are analysed. The rod sequence of 1117 residues contains a regular region of 1094 residues, which has features typical of an alpha-helical coiled coil, followed by a short non-helical tailpiece at the carboxyl end. The hydrophobic amino acids show the expected seven-residue pattern a, b, c, d, e, f, g, which is modulated by a longer repeat of 28-residue zones. In addition, there are four one-residue insertions, or skip residues, at the ends of zones, at positions 351, 548, 745 and 970. Myosin is considerably less hydrophobic than tropomyosin or alpha-keratin and the outer surface of the coiled coil is covered by clusters of positive and negatively charged amino acid side-chains. Molecular models suggest that the coiled coil is continuous throughout the rod, with an approximately uniform left-handed twist, except for a few turns of helix near each skip region, where the twist flattens out to accommodate the extra residue. Fourier transforms of the amino acid profiles show strong periodicities based on repeats of seven residues (7/2 and 7/3) and 28 residues (especially 28/3 and 28/9). The positive and negative charges each have strong 28/3-residue periodicities that are out of phase with one another. The negative charges also show a 196/9-residue modulation frequency, which may reflect the presence of a 196-residue structural unit in muscle, approximately 2 X 143 A long. The distribution of charged amino acids suggests that electrostatic forces are dominant in forming the thick filament structure. Models that allow regular patterns of interacting charges are restricted and the simplest types are discussed. ------------------- Key: 613 Medline: Authors: Waterston RH;Bolten S;Sive HL;Moerman DG Title: Mutationally altered myosins in C. elegans. Citation: "Muscle Development: Molecular and Cellular Control." Pearson M and Epstein HF (eds), Cold Spring Harbor Laboratory. : 119-127 1982 Type: REVIEW Genes: sup-5 sup-7 unc-54 Abstract: In studies of myogenesis and muscle contraction in Caenorhabditis elegans, more than 20 genes have been found that affect muscle structure. Of these, one gene, unc-54 I, has proved to be especially well suited for a detailed molecular genetic analysis. The unc-54 gene codes for the major myosin heavy chain of the body-wall musculature, with one or more unidentified genes coding for a minor body-wall myosin as well as pharyngeal and other myosins. More than 100 independently isolated mutations have been found for the unc-54 gene, and these have served as the basis for an increasingly sophisticated analysis of the gene and its products. Whereas others have focused on the cloning and sequencing of the gene or the effects of mutants on thick filament formation, our efforts have concentrated on a thorough genetic analysis of the gene. These studies include the isolation of new alleles of unc-54, the construction of a fine-structure map of the gene, and the interpretation of this genetic map in physical terms. ------------------- Key: 614 Medline: 83132844 Authors: Sharrock WJ Title: Yolk proteins of C. elegans. Citation: Developmental Biology 96: 182-188 1983 Type: ARTICLE Genes: Abstract: A group of proteins judged on several criteria to be yolk proteins have been isolated from a homogenate of the nematode Caenorhabditis elegans. Comparison of partial proteolysis fragments indicates that the two bands of a 170,000-dalton doublet (yp170) are closely related; bands observed at 115,000 daltons (yp115) and 88,000 daltons (yp88) appear to be structurally distinct. All three yolk protein species are glycoproteins, as judged by binding of the lectin concanavalin A. The yp170 doublet has been purified by gel filtration in the presence of sodium dodecyl sulfate. An antiserum obtained by immunization with the purified yp170 doublet does not bind either of the two smaller proteins. Staining of C. elegans eggs by indirect immunofluorescence with the anti-yp170 serum indicates a dispersed cytoplasmic location for the antigen throughout embryogenesis, with apparent segregation to the intestine immediately prior to hatching. ------------------- Key: 615 Medline: 83132845 Authors: Kimble J;Sharrock WJ Title: Tissue-specific synthesis of yolk proteins in C. elegans. Citation: Developmental Biology 96: 189-196 1983 Type: ARTICLE Genes: fem-1 fem-2 him-1 him-8 tra-1 tra-2 Abstract: The primary site of yolk protein synthesis in the nematode, Caenorhabditis elegans, has been determined. In animals containing no gonadal cells (obtained by laser ablation of the gonadal precursor cells early in development), yolk proteins are present in abundance. This demonstrates that yolk proteins are made outside the gonad. An examination of proteins present in tissues isolated by dissection, and a comparison of proteins synthesized by isolated tissues incubated in vitro have identified the intestine as the major site of yolk protein synthesis. We propose that yolk proteins are synthesized in the intestine, secreted from the intestine into the body cavity, and taken up from the body cavity by the gonad to reach oocytes. The site of yolk protein synthesis has also been examined in four mutants that have largely male somatic tissues, but a hermaphrodite germ line. Here again, yolk proteins are produced by intestines in a hermaphrodite-specific manner. This suggests that sex determination is coordinately regulated in intestinal and germ line tissues. ------------------- Key: 616 Medline: Authors: Schierenberg E Title: Development of the nematode C. elegans. Citation: "Developmental Biology of Freshwater Invertebrates." Harrison FW and Cowden RR (eds), Alan R. Liss, NY. : 249-281 1982 Type: REVIEW Genes: Abstract: Caenorhabditis elegans is a free-living, nonparasitic nematode. It is a self-fertilizing hermaphrodite. Males arise spontaneously by nondisjunction of X-chromosomes. Of all eukaryotic organisms C. elegans has probably been most extensively studied at the cellular level. Within 12 hours the fertilized egg develops into a young larva with 558 nuclei (560 in the male). During postembryonic development the animal proceeds through four larval stages increasing its number of nuclei to 959 (1,031 in the male) plus some 2,000 germ cells (about 1,000 in the male). The cell lineages from fertilization to adulthood have been completely analyzed in living embryos and animals. This and its well-established genetics (more than 300 genes have been mapped on the six linkage groups) make it a suitable model organism to study problems of gene action and development. Various techniques have been used to interfere with normal development (including laser-induced cell ablations) and to analyze development on the subcellular level (including recombinant DNA technology). The characteristic features of rigidly determined development, the low cell number, and the knowledge of cellular events should make it possible to identify molecular action in situ and relate it to the structure and ------------------- Key: 618 Medline: Authors: Wood WB;Strome S;Laufer JS Title: Localization and determination in embryos of C. elegans. Citation: "Time, Space, and Pattern in Embryonic Development." Jeffery WR and Raff RA (eds), Alan R. Liss, NY. : 221-239 1983 Type: REVIEW Genes: Abstract: More than 100 years ago, early European embryologists had posed the two central questions of animal development: First, how is the sameness of cells and organisms maintained during development and reproduction, and what factors transmit this hereditary information? Second, how do the cells of an embryo become different; what factors dictate that a particular cell at a particular time and position becomes committed to a particular developmental pathway? In the intervening century, we have largely answered the first question, acquiring extensive information about the genetic machinery and how it works. By contrast, we have gained little new understanding of the epigenetic process responsible for temporal and positional control of cell determination in embryos. How this process operates remains a central problem of contemporary ------------------- Key: 619 Medline: Authors: Rosenbluth RE;Cuddeford C;Baillie DL Title: Mutagenesis in Caenorhabditis elegans. I. A rapid eukaryotic mutagen test system using the reciprocal translocation eT1(III;V). Citation: Mutation Research 110: 39-48 1983 Type: ARTICLE Genes: eT1 Abstract: The advantages of developing mutagenicity tests using the nematode, Caenorhabditis elegans, are discussed and an efficient in vivo test for detecting heritable autosomal recessive lethals over 40 map units is described. The test uses the reciprocal translocation, eT1(III;V), as a balancer. Dose-response curves for EMS (0.004-0.06 M) and gamma-radiation (500-3000 R) were obtained. The spontaneous induction frequency for lethal mutations in 40 map units was found to be 0.06%. Mutations could be detected within 10 days and confirmed within another 5 days. From the point of view of C. elegans genetics, the EMS and gamma-ray curves demonstrate that eT1 can be used to test the efficacy of a particular mutagen in this organism. Although the present eT1 protocol simultaneously screens hermaphrodite oocyte and sperm chromosomes, variations of the protocol that screen oocyte and sperm ------------------- Key: 620 Medline: 85040332 Authors: Ambros V;Horvitz HR Title: Heterochronic mutants of the nematode C. elegans. Citation: Science 226: 409-416 1984 Type: ARTICLE Genes: lin-4 lin-14 lin-28 lin-29 Abstract: Mutations in the Caenorhabditis elegans genes lin-14, lin-28, and lin- 29 cause heterochronic developmental defects: the timing of specific developmental events in several tissues is altered relative to the timing of events in other tissues. These defects result from temporal transformations in the fates of specific cells, that is, certain cells express fates normally expressed by cells generated at other developmental stages. The identification and characterization of genes that can be mutated to cause heterochrony support the proposal that heterochrony is a mechanism for phylogenetic change and suggest cellular and genetic bases for heterochronic variation. ------------------- Key: 621 Medline: Authors: Schierenberg E;Cassada R Title: Cell division patterns and cell diversification in the nematode C. elegans. Citation: "Stem Cells, Their Identification and Characterization." Potten CS (ed), Churchill Livingstone. : 73-92 1983 Type: REVIEW Genes: Abstract: ------------------- Key: 622 Medline: 83111132 Authors: Culotti JG;Klein WL Title: Occurrence of muscarinic acetylcholine receptors in wild-type and cholingergic mutants of C. elegans. Citation: Journal of Neuroscience 3: 359-368 1983 Type: ARTICLE Genes: ace-1 ace-2 lev-1 lev-8 lev-9 lev-10 lev-11 unc-13 unc-22 unc-29 unc-38 unc-50 unc-63 unc-68 unc-74 Abstract: Crude homogenates of the nematode worm Caenorhabditis elegans were shown to bind the cholinergic antagonists [3H]N-methylscopolamine and quinuclidinyl benzilate ([3H]QBN) with high affinity. The dissociation constant for [3H]N-methylscopolamine binding determined from equilibrium saturation experiments (KD=3.7 X10*-10 M) was in good agreement with that determined from forward and reverse rate constants (KD=koff/kon=5X10*-10M). These binding sites were blocked sterospecifically by the (+) enantiomer of the muscarinic antagonist benzetimide, as would be expected of true muscarinic receptors. Furthermore, competition experiments with unlabeled cholinergic agonists and antagonists indicate that [3H]QNB and [3H]N-methylscopolamine bind to the same sites in nematode homogenates and that these sites are similar but not identical to muscarinic receptors in vertebrates. The concentration of [3H]N-methylscopolamine and [3H]QNB binding sites in adult populations of wild-type nematodes was approximately 10 fmol/mg of protein. This was approximately 4-fold lower than the concentration of binding sites in young (L1 and L2 stage) juveniles. These stage-specific differences in binding site concentrations parallel differences in acetylcholinesterase activity in larval and adult nematodes. Three methods of elevating cholinergic agonist levels in vivo were attempted in order to determine whether regulation of muscarinic receptors occurs in nematodes as it does in vertebrates. Two methods involved prolonged in vivo inhibition of acetylcholinesterase activlty, while the third method involved in vivo treatment with the potent agonist levamisole. All three methods failed to reveal down regulation of muscarinic receptors, suggesting that this regulatory mechanism may not exist in nematodes. Finally, phenotypic revertants of acetylcholinesterase-deficient double mutants as well as a class of agonist-resistant mutants were screened for possible alterations in [3H]QNB or [3H]N-methylscopolamine binding levels. None of these mutants exhibited gross deficiencies in [3H]QNB or [3H]N-methylscopolamine binding, although partial deficiencies might have gone undetected by the methods used here. Our binding studies show that muscarinic receptors, which mediate a large proportion of cholingeric signaling in advanced vertebrates, are also present in the very ------------------- Key: 623 Medline: Authors: Zuckerman BM;Geist MA Title: Effects of vitamin E on the nematode C. elegans. Citation: Age 6: 1-4 1983 Type: ARTICLE Genes: Abstract: Vitamin E at 200 ug/ml significantly extended the mean lifespan and extended maximum lifespan of the nematode Caenorhabditis elegans when supplied early in the prereproductive stage. At this concentration, vitamin E increased growth, but did not affect fecundity or the length of the reproductive period. The vitamin E effect was not passed from the parents to the progeny. Evaluations of the effects of vitamin E on lipofuscin accumulation were inconclusive. The results are compared to previous studies on C. briggsae and Turbatrix aceti. ------------------- Key: 624 Medline: 83267327 Authors: Wolf N;Priess J;Hirsh D Title: Segregation of germline granules in early embryos of C. elegans: An electron microscopic analysis. Citation: Journal of Embryology & Experimental Morphology 73: 297-306 1983 Type: ARTICLE Genes: Abstract: Using an improved fixation method for electron microscopy, we have found germline granules in Caenorhabditis elegans embryos shortly after fertilization and prior to the first cleavage. They are localized in the egg cytoplasm which becomes segregated into the posterior blastomere at the first cleavage. In the following divisions, the granules continue this pattern of asymmetric segregation and are ultimately segregated into the germline precursor cell. The granules are then symmetrically segregated into the germline cells. ------------------- Key: 625 Medline: 83157610 Authors: Gabius HG;Graupner G;Cramer F Title: Activity patterns of amino acyl-tRNA synthetases, tRNA methylases, arginyltransferase and tubulin-tyrosine ligase. Citation: European Journal of Biochemistry 131: 231-234 1983 Type: ARTICLE Genes: Abstract: As a step in the characterization of development and ageing in the nematode Caenorhabditis elegans, the activities of different groups of enzymes that supposedly exert modulating functions in and after protein synthesis have been determined. From embryonic (E), the four juvenile larval stages (L1-L4) and the gravid adult (A,A+), the selection of defined developmental stages extends to two different preparations of aged nematodes (S10, S12). Some aminoacyl-tRNA synthetase activities remain nearly unchanged in all stages up to the adult, some increase continuously during the larval stages and the remaining activities show stage-specific alterations. Upon ageing all activities except the one for tryptophan decrease sharply, tRNA methylase activities increase from E to L4, decrease from L4 to adult and to aged nematodes with only qualitative alterations in substrate specificity. The activity of tubulin: tyrosine ligase exhibits a parallel pattern, while arginyltransferase activity has a plateau between L2 and L4. The results are consistent with the idea of a modulation of protein synthesis and other cellular processes by quantitative activity changes during ------------------- Key: 626 Medline: Authors: Bazzicalupo P Title: C. elegans - A model system for the study of nematodes. Citation: "Molecular Biology of Parasites." Guardiola J, Luzzato L and Trager W (eds), Raven Press, NY. : 73-92 1983 Type: REVIEW Genes: ace-1 ace-2 flu-1 flu-2 flu-3 flu-4 unc-15 unc-54 Abstract: Nematodes are a very large group of animals. The estimated 500,000 species represent an independent phylum, and a very successful one, since they are found, with the exception of the pelagic and aerial habitats, in every type of environment. The great majority of nematodes are free-living and inhabit in large numbers the top few centimeters of the ocean's bed, fresh water muds, and a variety of soils. In the soil, where it has been measured, their biomass is comparable to that of insects. A few hundred species are extremely important in human health and agriculture because of their parasitic relationship to plants and animals. In humans, parasitic nematodes can cause very severe diseases, such as filariasis and river blindness (Oncocercus)... ------------------- Key: 627 Medline: 83223565 Authors: Hedgecock EM;Sulston JE;Thomson JN Title: Mutations affecting programmed cell deaths in the nematode C. elegans. Citation: Science 220: 1277-1279 1983 Type: ARTICLE Genes: ced-1 ced-2 ced-3 mec-4 nuc-1 Abstract: Mutations in two nonessential genes specifically block the phagocytosis of cells programmed to die during development. With few exceptions, these cells still die, suggesting that, in nematodes, engulfment is not necessary for most programmed deaths. Instead, these deaths appear to occur by cell suicide. ------------------- Key: 628 Medline: 83220736 Authors: Russnak RH;Jones D;Candido EPM Title: Cloning and analysis of cDNA sequences coding for two 16 kilodalton heat shock proteins (hsps) in C. elegans: homology with the small hsps of Drosophila. Citation: Nucleic Acids Research 11: 3187-3205 1983 Type: ARTICLE Genes: Abstract: The nucleotide sequences of two different cDNAs, CEHS48 and CEHS41, coding for the 16,000 dalton heat shock proteins (hsps) of Caenorhabditis elegans have been determined. CEHS48 codes for a polypeptide of 135 amino acids, approximately 15 fewer than the complete protein while CEHS41 is missing approximately 46 amino acids. From nucleotide 113 to the TAA termination signal the extent of homology between the sequences is 91%. Toward the 5' ends, the homology drops to 20% and results in completely divergent amino acid sequences. The 3' noncoding regions are only 30% homologous. Only CEHS48 contains a poly(A) signal and a poly(A) tail, suggesting that CEHS41 has an incomplete 3' end. The region from amino acid 43 to amino acid 115 shows extensive homology with corresponding regions in the four small hsps of Drosophila melanogaster and in mammalian alpha- crystallin. Two-dimensional gel analysis of in vitro synthesized hsp16 reveals the existence of five distinct components of identical molecular weights, but with different isoelectric points. ------------------- Key: 629 Medline: 83223597 Authors: Chalfie M;Thomson JN;Sulston JE Title: Induction of neuronal branching in C. elegans. Citation: Science 221: 61-63 1983 Type: ARTICLE Genes: mab-5 Abstract: The two postembryonic touch receptor neurons in the nematode Caenorhabditis elegans arise from essentially identical cell lineages and have the same ultrastructural features. The cells are found in different positions in the animal, however, and differ in neuronal branching, connectivity, and function. These structural and functional differences are not seen when cells are placed in similar positions by mutation or laser-induced damage. Thus, some, but probably not all, of the differentiated properties of these cells are a consequence of their cellular ------------------- Key: 630 Medline: 83245049 Authors: Hodgkin J Title: Two types of sex determination in a nematode. Citation: Nature 304: 267-268 1983 Type: ARTICLE Genes: fem-1 her-1 sup-7 tra-1 tra-2 tra-3 eDf2 Abstract: Sex in the nematode Caenorhabditis elegans is normally determined by a genic balance mechanism, the ratio of X chromosomes to autosomes, so that XX animals are self-fertilizing hermaphrodites and X0 animals are males. However, recessive mutations of the autosomal gene tra-1 III cause both XX and X0 animals to develop into males, and a linked dominant mutation causes both XX and X0 animals to develop into females. Here I show that these two kinds of mutation are allelic, and that stable mutant strains can be constructed in which sex is determined not by X-chromosome dosage but by the presence or absence of a single active gene. In these strains the autosomes carrying the tra-1 locus are in effect homomorphic Z and W sex chromosomes, and the sexes are homogametic ZZ males and heterogametic ZW females, in contrast to the wild-type arrangement of homogametic XX hermaphrodites and heterogametic X0 males. ------------------- Key: 631 Medline: 83221640 Authors: Liao LW;Rosenzweig B;Hirsh D Title: Analysis of a transposable element in C. elegans. Citation: Proceedings of the National Academy of Sciences USA 80: 3585-3589 1983 Type: ARTICLE Genes: Abstract: A transposable element, designated Tc1, has been characterized in Caenorhabditis elegans. Tc1 is 1.7 kilobases long, has an inverted terminal repeat of less than 100 base pairs, and is repeated as a highly conserved element. The copy number and genomic positions of Tc1 are extremely variable among strains, implying that Tc1 is mobile. However, progeny of interstrain crosses did not show hybrid dysgenic traits that might be due to Tc1 transposition. ------------------- Key: 632 Medline: 83233129 Authors: Tabuse Y;Miwa J Title: A gene involved in action of tumor promoters is identified and mapped in C. elegans. Citation: Carcinogenesis 4: 783-786 1983 Type: ARTICLE Genes: dpy-9 tpa-1 Abstract: We isolated mutants of the nematode Caenorhabditis elegans resistant to 12-O-tetradecanoylphorbol-13-acetate (TPA). The TPA-resistant mutants, although they grew somewhat smaller than normal, reproduced well and behaved normally in TPA; they also did similarly in another phorbol ester tumor promoter, phorbol-12,13-didecanoate (PDD), thus proving they are also resistant to PDD. All the mutations defined by these TPA-resistant mutants were semidominant to the wild-type allele. The 15 independently isolated mutants all fell into the same complementation group, defining a single gene, tpa-1. The gene tpa-1 mapped near the marker gene dpy-9 on chromosome IV. ------------------- Key: 633 Medline: 83210585 Authors: Edwards MK;Wood WB Title: Location of specific messenger RNAs in C. elegans by cytological hybridization. Citation: Developmental Biology 97: 375-390 1983 Type: ARTICLE Genes: Abstract: We have developed an autoradiographic technique for detecting specific Caenorhabditis elegans messenger RNA molecules in situ by hybridization of labeled, cloned DNA probes to fixed tissue sections and squashes of embryos and adults. We report analyses with probes of actin and collagen gene sequences from a C. elegans genomic clone library. Hybridization is RNase sensitive and tissue specific. In adults the actin probe, which recognizes cytoplasmic as well as muscle actin mRNA, hybridizes strongly to muscle and distal gonad (ovary), somewhat less strongly to maturing oocytes, and weakly to intestine. The collagen probe hybridizes weakly to distal gonad and intestine and very strongly to subcuticular tissues, in particular to the hypodermal cells and syncytial cytoplasm of the lateral hypodermal ridges, which are the sites of cuticle synthesis. In embryos, hybridization to squashes indicates that actin message is present at fertilization, decreases during early cleavage, and then increases again during morphogenesis. By contrast, collagen message is absent until the 100-cell stage and then increases rapidly during morphogenesis. The number of cells labeled is consistent with the view that the collagen probe hybridizes to hypodermal precursor cells. We estimate that our present methods can detect messages representing about 0.2% or more of the total mRNA population, and increases in this sensitivity should be possible. Therefore, the cytological hybridization technique should be useful for determining temporal and spatial patterns of specific mRNA distributions during development, at least for abundant and ------------------- Key: 634 Medline: 83235332 Authors: Ward S;Hogan E;Nelson GA Title: The initiation of spermiogenesis in the nematode C. Citation: Developmental Biology 98: 70-79 1983 Type: ARTICLE Genes: fem-1 him-5 Abstract: Spermiogenesis in nematodes involves the activation of sessile spherical spermatids to motile bipolar amoeboid spermatozoa. In Caenorhabditis elegans males spermiogenesis is normally induced by copulation. Spermatids transferred to hermaphrodites as well as some of those left behind in the male become spermatozoa a few minutes after mating. Spermiogenesis can also be induced in vitro by the ionophore monensin (G.A. Nelson and S. Ward, 1980, Cell 19, 457-464) and by weak bases such as triethanolamine. Both triethanolamine and monensin cause a rapid increase in intracellular pH from 7.1 to 7.5 or 8.0. This pH increase precedes the subsequent morphological events of spermiogenesis. Triethanolamine or monensin must be present throughout spermiogenesis for all cells to form pseudopods, but once pseudopods are formed the inducers are unnecessary for subsequent motility. The pH induced spermiogenesis is inhibited by drugs that block mitochondria or glycolysis. Protease treatment can also induce spermiogenesis without increasing intracellular pH, apparently bypassing the pH-dependent steps in activation and the requirement for glycolysis. These results show that the initiation of spermiogenesis in C. elegans, like some steps in egg activation and the initiation of sea urchin sperm motility, can be induced by an increase in intracellular pH, but this pH change can be bypassed by proteolysis. ------------------- Key: 635 Medline: 11813735 Authors: Trent C;Tsung N;Horvitz HR Title: Egg-laying defective mutants of the nematode C. elegans. Citation: Genetics 104: 619-647 1983 Type: ARTICLE Genes: ced-3 daf-1 daf-3 daf-4 daf-5 daf-7 daf-8 daf-14 egl-1 egl-2 egl-3 egl-4 egl-5 egl-6 egl-7 egl-8 egl-9 egl-10 egl-11 egl-12 egl-13 egl-14 egl-15 egl-17 egl-18 egl-19 egl-20 egl-21 egl-23 egl-24 egl-25 egl-26 egl-27 egl-28 egl-29 egl-30 egl-31 egl-32 egl-33 egl-34 egl-35 egl-36 egl-37 egl-39 egl-40 her-1 lin-7 lin-10 lin-11 lin-12 lin-15 lin-17 lin-24 lin-25 lin-26 lin-28 lin-29 lin-31 mec-3 sdc-1 sup-17 tra-2 unc-6 unc-31 unc-40 unc-45 unc-51 unc-53 unc-59 unc-85 unc-86 unc-98 Abstract: We have isolated 144 mutants defective in egg-laying and have characterized 58 of these genetically, behaviorally and pharmacologically. Most of the other mutants proved to be alleles of previously identified genes that affect egg-laying. These 58 mutants define 40 new genes called egl, for egg-laying defective. The egl mutants vary with respect to the severity of their egg-laying defects and the presence of behavioral or morphological pleiotropies. We have defined five categories of mutants based on their responses to the pharmacological agents serotonin and imipramine, which stimulate egg-laying by wild-type hermaphrodites. Mutants in 19 egl genes failed to respond to both serotonin and imipramine and are likely to be defective in the functioning of the vulva or the sex muscles. Four mutants (in four different genes) lay eggs in response to serotonin but not imipramine and appear to be egg-laying defective because of defects in the "hermaphrodite-specific neurons" (HSN's), which provide major neural inputs to the vulval muscles. Three of these four were selected specifically for these drug responses. Alleles of 7 egl genes as well as 4 dauer constitutive (daf) genes lay eggs in response to both serotonin and imipramine. One egl mutant responds to imipramine but not serotonin. The remaining egl mutants show variable or intermediate responses to the drugs. Two of the HSN-defective mutants, egl-1 and her-1(n695), lack HSN cell bodies and appear to be expressing the normally male-specific program of HSN cell death. Whereas egl-1 appears to specifically affect HSN development, n695 has multiple morphological pleiotrophies, displaying partial transformation in the sexual phenotype of many cells and tissues. At least two of the egl mutants appear to be defective in the processing of environmental signals that modulate egg-laying and may define new components of the ------------------- Key: 636 Medline: 83273600 Authors: Karn J;Brenner S;Barnett L Title: Protein structural domains in the C. elegans unc-54 myosin heavy chain gene are not separated by introns. Citation: Proceedings of the National Academy of Sciences USA 80: 4253-4257 1983 Type: ARTICLE Genes: unc-54 Abstract: The 1,966-amino acid unc-54 myosin heavy chain sequence was determined from DNA sequence studies of the cloned gene. The gene is split by eight short introns, 48-561 base pairs long, and appears to lack a "TATA" box at its promoter. The physical map of the gene was aligned with the genetic map by locating two point mutations and three internal deletions: 0.01 map units correspond to approximately 5 kilobases. Comparison of the unc-54 protein sequence with the sequence of a second myosin heavy chain from nematode, indicates that the globular head sequence S-1 is more highly conserved than the alpha-helical coiled-coil rod. Major sites of proteolysis in S-1 are associated with variable sequences that have the characteristics of surface loops. In both genes there is no correlation between the positions of introns and the major protein structural ------------------- Key: 637 Medline: Authors: Johnson TE Title: Aging in C. elegans. Citation: "Review of Biological Research in Aging, Volume 1." Rothstein M, Adler W, Cristofalo V, Finch CE, Florini J and Martin G (eds), Alan R. Liss, NY. 1: 37-49 1983 Type: REVIEW Genes: axe-1 Abstract: In 1974, Sydney Brenner published an elegant paper that described the genetic system of Caenorhabditis elegans and led to its use in research on a wide variety of topics, including aging (Brenner, 1974). Its small size (1mm as an adult) and determinate cell lineage has allowed a description of the entire somatic cell lineage from the one-cell stage to the adult (Sulston and Horvitz, 1977; Deppe et al., 1978; Kimble and Hirsh, 1979; Suslton et al., personal communication). Its ease of culture makes it an organism of choice for studies of various aspects of anatomy and physiology, including muscle formation and function (Zengel and Epstein, 1980; Mackenzie and Epstein, 1980), cuticle formation (Cox et al, 1981), neuroanatomy (Ward et al, 1975; Ware et al, 1975; Sulston et al, 1975), and behavior (Dusenbery, 1980). Several genes have been cloned by recombinant DNA techniques ablation (Kimble, 1981; Laufer and von Ehrenstin, 1981) procedures, as well as most of the modern molecular techniques, are in use. ------------------- Key: 638 Medline: Authors: Yamaguchi Y;Murakami K;Furusawa M;Miwa J Title: Germline-specific antigens identified by monoclonal antibodies in the nematode C. elegans. Citation: Development, Growth & Differentiation 25: 121-131 1983 Type: ARTICLE Genes: Abstract: Of 27 monoclonal antibodies identified to react, by indirect immunofluorescent antibody staining, with specific cells and tissues of the nematode Caenorhabditis elegans, we report here three monoclonal antibodies pertaining to the gonadal tissues. One antibody defines an antigen that is distributed over the entire embryo at earlier development and later becomes unique to the gonad, including mature oocytes. The antigens recognized by the other two are distributed asymmetrically in the posterior region of the fertilized egg's cytoplasm destined to become the germline precursor cell. Each antigen is successively segregated only to the germline precursor cells of the developing embryo and, postembryonically, is uniquely localized around the germline cell nuclei of the larvae and ------------------- Key: 639 Medline: 83284540 Authors: Snutch TP;Baillie DL Title: Alterations in the pattern of gene expression following heat shock in the nematode C. elegans. Citation: Canadian Journal of Biochemistry & Cell Biology 61: 480-487 1983 Type: ARTICLE Genes: Abstract: Exposure of the nematode Caenorhabditis elegans to elevated temperatures induces the preferential synthesis of eight major polypeptides of approximate molecular weights 81 000, 70 000, 41 000, 38 000, 29 000, 19 000, 18 000, and 16 000. In pulse-labelled worms these peptides first appear at 29 degrees C and continue to be synthesized up to lethal temperatures. They are heat inducible at every stage of development. While temperature elevation induces the synthesis of the heat-shock polypeptides, the in vivo synthesis of most other proteins present before heat shock is suppressed. In contrast, in vitro translation of mRNA from heat-shocked worms shows no alteration from the pattern of normal 20 degrees C mRNAs except for the appearance of the heat-shock mRNAs. An in vitro study of RNA from control and heat-shocked dauer larvae shows that this developmental variant possesses little translatable mRNA but, upon heat shock, synthesizes a set of messages corresponding to the heat- shock polypeptides. The low background of this system will be especially useful in the analysis and purification of heat-shock mRNA for molecular cloning experiments. Extensive similarities between the Drosophila and C. elegans heat-shock responses are shown, including homology between the 70-kdalton heat-shock genes ------------------- Key: 640 Medline: 83246543 Authors: Rosenzweig B;Liao LW;Hirsh D Title: Sequence of the C. elegans transposable element Tc1. Citation: Nucleic Acids Research 11: 4201-4209 1983 Type: ARTICLE Genes: Abstract: The complete nucleotide sequence was determined for Tc1, a transposable element in the nematode Caenorhabditis elegans. The 1610- base-pair element terminates in 54-base-pair perfect inverted repeats and is flanked by a 2-base-pair duplication of the target sequence. The Tc1 sequence contains two long open reading frames on the same DNA strand but in different translational reading frames. The positions of transcriptional control sequences suggest that a single transcript is made, which could produce two polypeptides, 273 and 112 amino acids in length. These features, i.e. terminal repeats, target site duplication and open reading frames, make Tc1 similar to transposable elements from other species. ------------------- Key: 641 Medline: 83210028 Authors: Himmelhoch S;Zuckerman BM Title: C. elegans: Characters of negatively charged groups on the cuticle and intestine. Citation: Experimental Parasitology 55: 299-305 1983 Type: ARTICLE Genes: Abstract: Partial characterization of carboxyl, sulfate, and phosphate groups on the Caenorhabditis elegans cuticle and intestinal microvilli was achieved by en face labeling of floating cryosections at two pH levels and specific blockage of sulfate groups by Alcian blue. All negatively charged groups on the cuticle and intestinal microvilli labeled heavily at pH 7.2-7.4. Pretreatment to block sulfate groups followed by ferritin labeling at pH 7.2-7.4 gave a 35% reduction of binding on the cuticle and an 80% reduction in binding on the microvilli. At pH 1.8 or 2.5, only the sulfate groups labeled as shown by the complete abolition of labeling on the cuticle and the microvilli following blockage of the sulfate groups. Molecules with accessible sulfate groups were distributed in clusters throughout the cortical layer of the cuticle, were present in the struts of the median layer but were absent from the basal layer. The advantages of applying molecular probes to cryosections as compared to sections prepared by standard electron microscopical techniques are discussed. ------------------- Key: 642 Medline: 83240682 Authors: Johnson CD;Russell RL Title: Multiple molecular forms of acetylcholinesterase in the nematode C. elegans. Citation: Journal of Neurochemistry 41: 30-46 1983 Type: ARTICLE Genes: ace-1 ace-2 Abstract: Extracts of the nematode Caenorhabditis elegans contain five molecular forms of acetylcholinesterase (AChE) activity that can be separated by a combination of selective solubilization, velocity sedimentation, and ion-exchange chromatography. These are called form IA (5.2s), form IB (4.9s), form II (6.7s), form III (11.3s), and form IV (13.0s). All except form III are present in significant amounts in rapidly prepared extracts and are probably native; form III is probably derived autolytically from form IV. Most of forms IA and IB can be solubilized by repeated extractions without detergent, whereas forms II, III, and IV require detergent for effective solubilization and may therefore be membrane-bound. High salt concentrations are not required for, and do not aid in, the solubilization of these forms. For all forms, molecular weights and frictional ratios have been estimated by a combination of gel permeation chromatography and velocity sedimentations in both H2O and D2O. The molecular weight estimates range from 83,000 to 357,000 and only form II shows extensive asymmetry. The separated forms have been characterized with respect to substrate affinity, substrate specificity, inhibitor sensitivity, thermal inactivation, and detergent sensitivity. Judging by these properties, C. elegans is like other invertebrates in that none of its cholinesterase forms resembles either the "true" or the "pseudo" cholinesterase of vertebrates. However, internal comparison of the C. elegans forms clearly distinguishes forms IA, III, and IV as a group from forms IB and II; the former are therefore designated "class A" forms, the latter "class B" forms. Genetic evidence indicates that separate genes control class A and class B forms, and that these two classes overlap functionally. Several factors, including kinetic properties, molecular asymmetry, molecular size, and solubility, all suggest that a molecular model of the multiple cholinesterase forms observed in vertebrate electric organs probably does not apply in C. elegans. Potential functional roles and subunit structures of the multiple AChE forms within each C. elegans class are ------------------- Key: 643 Medline: Authors: Hirsh D;Files JG;Carr SH Title: Isolation and genetic mapping of the actin genes of C. elegans. Citation: "Muscle Development: Molecular and Cellular Control." Pearson M and Epstein HF (eds), Cold Spring Harbor Laboratory. : 77-86 1982 Type: REVIEW Genes: act-1 act-2 act-3 Abstract: The nematode Caenorhabditis elegans contains a small genome of 8 X 10*7 bp of DNA. The adult animal has 953 somatic cells whose complete embryonic and postembryonic cell lineages are known. Many are muscle cells or cells containing thin filaments. C. elegans is a self-fertilizing hermaphrodite that is convenient for genetic analyses, and a detailed genetic map has been constructed. Approximately 20 muscle genes have been identified on the basis of mutant phenotypes that include uncoordinated behavior and defective muscles. Among these 20 muscle genes, only 2 have been connected with functional gene products; unc-54 codes for a major myosin, and unc-15 codes for paramyosin. No actin gene has been identified in C. elegans. It is possible that one of the known muscle genes codes for actin, but actin loci may be difficult to detect genetically. For example, mutations in actin genes might be lethal or cryptic if multiple, identical genes are present. Nevertheless, the actin genes of C. elegans are important objects of study because actin is an abundant protein in C. elegans, because its synthesis is regulated developmentally in specific cell lineages, and because the genetic manipulation of actin genes seems feasible once these genes are recognized and mapped. We therefore began a search for the actin genes of C. elegans using nongenetic ------------------- Key: 644 Medline: Authors: Karn J;McLachlan AD;Barnett L Title: unc-54 myosin heavy-chain gene of C. elegans: Genetics, sequence, structure. Citation: "Muscle Development: Molecular and Cellular Control." Pearson M and Epstein HF (eds), Cold Spring Harbor Laboratory. : 129-142 1982 Type: REVIEW Genes: unc-15 unc-54 Abstract: The small soil nematode Caenorhabditis elegans is an attractive organism for the molecular study of muscle function and development because of its anatomical simplicity and suitability for genetic and biochemical analysis (Brenner 1974; Sulston and Horvitz 1977). The body-wall musculature of C. elegans is composed of 95 cell disposed in four quadrants, which run the length of the animal beneath the cuticle. The musculature is obliquely striated, and the sarcomeres are oriented parallel to the long axis of the animal. Since these cells represent a large reaction of the animal mass, isolation of contractile proteins is comparatively simple (Epstein et al. 1974; Waterston et al. 1974, 1977a; Harris and Epstein 1977; Mackenzie and Epstein 1980). Mutants affecting the characteristic pattern of motility of C. elegans can be easily identified, and microscopic examination of these "uncoordinated," or unc strains, in the living animal by polarized light microscopy or, more carefully, by electron microscopy has led to the identification of 22 genes that produce altered muscle phenotypes (Waterston et al. 1980; Zengel and Epstein 1980). Of these, two are known to code for major structural proteins of muscle: The unc-54 gene codes for the major heavy chain of myosin (Epstein et al. 1974; MacLeod et al. 1977b), whereas the un-15 gene codes for paramyosin, the core protein of the thick filaments (Waterston et al. 1974; MacLeod et al. 1977a; Harris and Epstein 1977). ------------------- Key: 645 Medline: Authors: Epstein HF;Berman SA;Miller DM III Title: Myosin synthesis and assembly in nematode body-wall muscle. Citation: "Muscle Development: Molecular and Cellular Control." Pearson M and Epstein HF (eds), Cold Spring Harbor Laboratory. : 419-427 1982 Type: REVIEW Genes: unc-15 Abstract: Myosin is the central piece in the protein machinery that produces muscle contraction. In this role, the myosin molecule must serve as an energy-transducing enzyme and as the major building block of the thick filament. In differentiated muscle cells, myosin is constantly being synthesized and assembled into thick filaments. Many issues regarding the processes of myosin synthesis and assembly in muscle remain unresolved. Is the synthesis and assembly of myosin coupled? Are additional protein components required for the assembly of myosin into native thick filaments? Do different myosin isoforms play distinct structural or functional roles within thick filaments? The combined approaches of protein biochemistry, immunology, and electron microscopy have proved useful in establishing our present knowledge concerning the roles of myosin within muscle. The nematode Caenorhabditis elegans offers several experimental advantages in addition to these time-honored methods that may provide further insights concerning the process of myosin synthesis and assembly. This animal has an elegantly simple and well-defined development and anatomy of body-wall muscle cells. Genetic analysis has characterized hundreds of specific mutants in over 20 genes affecting the development, structure, and function of body-wall muscle cells. This genetic approach, in combination with biochemical, immunological, and morphological methods, promises to offer significant ------------------- Key: 646 Medline: 84002251 Authors: Greenwald IS;Sternberg PW;Horvitz HR Title: The lin-12 locus specifies cell fates in C. elegans. Citation: Cell 34: 435-444 1983 Type: ARTICLE Genes: lin-12 sup-7 eT1 mnDp37 Abstract: We describe two classes of mutations in the lin-12 locus of the nematode Caenorhabditis elegans. Ten semidominant mutations (lin- 12[d]) appear to elevate the level of lin-12 activity. Thirty-two recessive alleles (lin-12[0]), including two amber mutations, appear to eliminate gene activity. The lin-12(d) and lin-12(0) mutations result in reciprocal homeotic transformations in the fates of defined cells in several different tissues. Gene dosage studies suggest that a high level of lin-12 activity specifies one cell fate and a low level specifies an alternative fate. Temperature-shift experiments indicate that lin-12 acts at the time cell fate is determined in wild type. We propose that lin-12 functions as a binary switch to control decisions between alternative cell fates during C. elegans development. ------------------- Key: 647 Medline: 84002255 Authors: Miller DM III;Ortiz I;Berliner GC;Epstein HF Title: Differential localization of two myosins within nematode thick filaments. Citation: Cell 34: 477-490 1983 Type: ARTICLE Genes: unc-54 Abstract: The body wall muscle cells of the nematode, Caenorhabditis elegans, contain two unique types of myosin heavy chain, A and B. We have utilized an immunochemical approach to define the structural location of these myosins within body wall muscle thick filaments. By immunofluorescence microscopy, myosin B antibodies label the thick filament-containing A-bands of body wall muscle with the exception of a thin gap at the center of each A-band, and myosin A antibodies react to form a medial fluorescent stripe within each A-band. The complexes of these monoclonal antibodies with isolated thick filaments were negatively stained and studied by electron microscopy. The myosin B antibody reacts with the polar regions of all filaments but does not react with a central 0.9 um zone. The myosin A antibody reacts with a central 1.8 um zone in all filaments but does not react with the polar regions. ------------------- Key: 648 Medline: Authors: Ohba K;Ishibashi N Title: A factor inducing dauer juvenile formation in C. elegans. Citation: Nematologica 28: 318-325 1982 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans were induced to form true dauer juveniles by the material lyophilized from a water solution in which living C. elegans (1 g fresh weight/50 ml distilled water) were incubated for 24 hr at 20C. The material best induced dauer formation at 23C, pH 6.0, 2% agar with 1/8 strength of Sayre et al.'s axenic medium. Overcrowding itself exerted no major effect. First and 2nd stage juveniles most actively secreted the dauer inducing substance into the incubating medium. Neither dauer juveniles nor other nematodes such as Bursaphelenchus xylophilus or Neoaplectana carpocapsae secreted the active substance. ------------------- Key: 649 Medline: 84026513 Authors: Strome S;Wood WB Title: Generation of asymmetry and segregation of germ-line granules in early C. elegans embryos. Citation: Cell 35: 15-25 1983 Type: ARTICLE Genes: emb-27 fem-2 fer-1 zyg-9 Abstract: Germ-line granules in C. elegans embryos (P granules) can be visualized by immunofluorescence microscopy using a monoclonal antibody. In mutant zygotes with abnormal spindle orientations and in wild-type zygotes treated with the microtubule inhibitors nocodazole, colcemid, vinblastine, and griseofulvin, both P-granule segregation to the posterior pole and the concomitant pseudocleavage occur apparently normally, but the normally concurrent migration of the pronuclei is inhibited. Conversely, treatment of wild-type embryos with the microfilament inhibitors cytochalasins D and B inhibits P- granule segregation and pseudocleavage, as well as other manifestations of polarity, without preventing pronuclear migration. The results suggest that P-granule segregation does not require either the spindle or cytoplasmic microtubules, but that this process as well as generation of other asymmetries does require cytoskeletal functions ------------------- Key: 650 Medline: 84062370 Authors: Albert PS;Riddle DL Title: Developmental alterations in sensory neuroanatomy of the C. elegans dauer larva. Citation: Journal of Comparative Neurology 219: 461-481 1983 Type: ARTICLE Genes: Abstract: The anterior sensory ultrastructure of the C. elegans dauer larva was examined in several specimens and compared with that of the second- stage (L2) larva, which immediately precedes the dauer stage. In some instances comparisons were made with L3, postdauer L4, and adult stages. Whereas sensory structures in different nondauer stages closely resemble each other, including the inner labial sensilla, amphids, and deirids. The relative positions of the afferent tips of the two types of inner labial neurons are reversed in the dauer stage compared to the L2 and postdauer L4 stages. Inner labial neuron 1 rather than neuron 2 is more anterior in each of the six sensilla, and neuron 1 has an enlarged tip. The neuron 2 cilia are only one- third as long as those in the L2. Amphidial neurons c, d, g, and i and the amphidial sheath cell are altered in shape or position in the dauer stage. Neurons g and i are displaced posteriorly within the dauer amphidial channel. Neuron d has significantly more microvillar projections than do the d cells in L2, L3, or postdauer L4 larvae. Winglike processes of dauer neuron c form a 200 degrees-240 degrees arc in transverse section, including extensive overlap of the two cells. The arc in an L2 seldom spans more than 100 degrees, and overlap does not occur. While L2 larvae possess two separate bilateral amphidial sheath cells, the left and right sheath cells are often continuous in the dauer larva. Deirid sensory dendrites exhibit a dauer-specific structure and orientation. The tip of each neuron is attached to the body wall cuticle by a substructure not observed in L2 or postdauer L4 stages, and the neurons are oriented parallel to the longitudinal axis of the dauer larva. The deirid sensory terminals are oriented perpendicular to the cuticle in other stages. Reversible alterations in neural structure are discussed in ------------------- Key: 651 Medline: 84010852 Authors: McLachlan AD Title: Analysis of gene duplication repeats in the myosin rod. Citation: Journal of Molecular Biology 169: 15-30 1983 Type: ARTICLE Genes: Abstract: The helical coiled-coil region of the myosin rod in the nematode Caenorhabditis elegans is a repetitive sequence 1094 amino acids long which contains 39 repeats of a 28-residue pattern. The repeats are extremely significant when compared with the statistical distributions expected, first for random sequences, and then for sequences with a typical seven-residue coiled-coil periodicity. New and improved statistical tests are used. The repeats are stronger in the first 350 residues of the rod (fragment S-2) than in the remainder. The corresponding DNA sequence of the unc-54 gene shows the same features, but they are less significant when judged by the number of identical bases than are the amino acid similarities, as measured by Dayhoff scores. The rod sequence shows strong evidence for a longer repeat unit of 196 residues, which may be related to the cross-bridge spacing of 143 A in muscle. ------------------- Key: 652 Medline: Authors: Kenyon CJ Title: Pattern, symmetry and surprises in the development of C. elegans. Citation: Trends in Biochemical Sciences 8: 349-351 1983 Type: REVIEW Genes: Abstract: In the course of metazoan development, the generation of multiple cell types from a single cell requires the repeated creation of daughter cells that differ from one another. This production of non-equivalent daughter cells can be called a developmental decision, or switch. The task of understanding development is that of determining how these switches are arranged in space and time, and then how they operate at a molecular level. ------------------- Key: 653 Medline: 84005467 Authors: Sulston JE;Schierenberg E;White JG;Thomson JN Title: The embryonic cell lineage of the nematode C. elegans. Citation: Developmental Biology 100: 64-119 1983 Type: ARTICLE Genes: Abstract: The embryonic cell lineage of Caenorhabditis elegans has been traced from zygote to newly hatched larva, with the result that the entire cell lineage of this organism is now known. During embryogenesis 671 cells are generated; in the hermaphrodite 113 of these (in the male 111) undergo programmed death and the remainder either differentiate terminally or become postembryonic blast cells. The embryonic lineage is highly invariant, as are the fates of the cells to which it gives rise. In spite of the fixed relationship between cell ancestry and cell fate, the correlation between them lacks much obvious pattern. Thus, although most neurons arise from the embryonic ectoderm, some are produced by the mesoderm and a few are sisters to muscles; again, lineal boundaries do not necessarily coincide with functional boundaries. Nevertheless, cell ablation experiments (as well as previous cell isolation experiments) demonstrate substantial cell autonomy in at least some sections of embryogenesis. We conclude that the cell lineage itself, complex as it is, plays an important role in determining cell fate. We discuss the origin of the repeat units (partial segments) in the body wall, the generation of the various orders of symmetry, the analysis of the lineage in terms of sublineages, and evolutionary implications. ------------------- Key: 654 Medline: 84032491 Authors: Sanford T;Golomb M;Riddle DL Title: RNA polymerase II from wild type and alpha-amanitin-resistant strains of C. elegans. Citation: Journal of Biological Chemistry 258: 12804-12809 1983 Type: ARTICLE Genes: ama-1 let-56 nT1 Abstract: DNA-dependent RNA polymerases I, II, and III have been isolated from the soil nematode, Caenorhabditis elegans, and RNA polymerase II has been partially purified. The sensitivities of these enzymes to alpha- amanitin resemble those of the cognate enzymes from vertebrates. RNA polymerase II from C. elegans is 50% inhibited by 7 ng/ml of the amatoxin and RNA polymerase III by 80 micrograms/ml, whereas RNA polymerase I is insensitive to 500 micrograms/ml. We have obtained mutants of C. elegans which can grow and reproduce in concentrations of alpha-amanitin which arrest development of wild type animals. One of these mutants (DR432) has an altered RNA polymerase II which in partially purified extracts is 150 times less sensitive to the drug than the wild type enzyme. The mutation, ama-1(m130), in DR432 is dominant and maps near dpy-13 on linkage group IV. RNA polymerase II isolated from ama-1/+ heterozygotes contains equal proportions of two components, corresponding in alpha-amanitin sensitivity to the enzymes from DR432 and wild type. Thus, ama-1 appears to affect a subunit of RNA polymerase II. ------------------- Key: 655 Medline: Authors: Roberts TM Title: Crawling C. elegans spermatozoa contact the substrate only by their pseudopods and contain 2-nm filaments. Citation: Cell Motility 3: 333-347 1983 Type: ARTICLE Genes: him-5 Abstract: The locomotion of C. elegans spermatozoa resembles, in many respects, the crawling movements of other eukaryotic cells. However, these sperm contain surprising little actin, which plays no apparent role in this cell's motility. Electron microscopy has revealed that crawling spermatozoa retain a strict morphological polarity so that the organelle-filled cell body is separated from the pseudopod by an array of ctyoplasmic laminar membranes. When sperm crawl only the pseudopod contacts the substrate; the cell body is either pulled behind or carried on top of the rear portion of the pseudopod. Fingerlike projections which extend forward from the leading edge of the psuedopod initiate contact with the substrate. The underside of the pseudopod exhibits areas of close (40 nm separation) membrane-substrate association with intervening areas of wide (up to 300 nm) membrane-substrate gaps. The pseudopod cytoplasm contains 2-nm filaments but no filamentous actin has been observed. These 2-nm filaments were detected in thin sections of crawling cells and in negative-stained remnants of spermatozoa disrupted by either hypotonic buffer or Triton X-100. The filaments are found both free in the cytoplasm and closely associated with the cytoplasmic face of the plasma membrane and are usually oriented along the long axis of the cell. Neither the identity nor the function of these filaments has been established although their location and orientation suggest ------------------- Key: 656 Medline: 84064866 Authors: Burke DJ;Ward S Title: Identification of a large multigene family encoding the major sperm protein of C. elegans. Citation: Journal of Molecular Biology 171: 1-29 1983 Type: ARTICLE Genes: fem-1 him-5 Abstract: DNA fragments corresponding to genes encoding the MSP of Caenorhabditis elegans sperm have been isolated by recombinant DNA techniques. Analyses of individual genomic clones suggest that there are multiple MSP genes that are dispersed in the genome. From restriction enzyme digests of genomic DNA fractionated and hybridized with an MSP complementary DNA probe, there appear to be more than 30 MSP genes in the genome. Despite the occurrence of this large dispersed multigene family, the MSP messenger RNA from both males and hermaphrodites is homogene in size. There are at least three different proteins of identical molecular weight but different isoelectric point that cross-react with anti-MSP antisera. Each protein is a primary translation product with no detectable post- translational modifications, suggesting that at least three of the MSP genes are expressed. ------------------- Key: 657 Medline: 84056432 Authors: Vanfleteren JR;Van Beeumen JJ Title: Nematode chromosomal proteins-III. Some structural properties of the histones of C. elegans. Citation: Comparative Biochemistry & Physiology 76B: 179-184 1983 Type: ARTICLE Genes: Abstract: The histones of Caenorhabditis elegans (Nematoda) have been identified by correlating criteria of electrophoresis and amino acid composition with the five main histones from calf thymus. C. elegans H1(1) consists of at least two subtypes with approximate molecular weights of 20,000 and 18,500 daltons as resolved by SDS polyacrylamide gel electrophoresis. They are some 10% smaller than the two subtypes of calf histone H1. The differences are also corrobated by the amino acid composition of the nematode and calf H1 complements. Nematode H2A resembles calf H2A in chromatographic and electrophoretic properties and in the amino acid composition, although it lacks histidine, which seems to be replaced by lysine. Like calf H2A, it is dimorphic as shown by Triton/acid/urea polyacrylamide gel electrophoresis. The H2B complement from C. elegans consists of two proteins with a molecular weight of approximately 12,500. They can be separated by ion-exchange chromatography, but they are very analogous to each other and to calf H2B in amino acid composition. Each form is also resolved into two more subtypes by Triton/acid/urea polyacrylamide gel electrophoresis. Nematode H3 resembles calf thymus H3 in its electrophoretic behaviour; three subfractions can be distinguished in Triton/acid/urea gels. C. elegans H4 is very similar to calf H4 in its chromatographic, electrophoretic and solubility properties, but differs significantly in composition. The meaning of this difference is discussed with regard to the generally observed stringent conservation of H4 sequences between distantly related species. ------------------- Key: 658 Medline: 84038230 Authors: Klass M;Nguyen PN;Dechavigny A Title: Age correlated changes in the DNA template in the nematode C. elegans. Citation: Mechanisms of Ageing & Development 22: 253-263 1983 Type: ARTICLE Genes: fer-15 Abstract: Analysis of DNA from the nematode Caenorhabditis elegans demonstrated a number of significant age-correlated changes. The number of single- strand breaks as assayed by an in vitro assay procedure using Escherichia coli DNA polymerase I increased significantly with age. There was also an exponential increase in the amount of 5- methylcytosine in C. elegans DNA as the worm matured and aged. Furthermore, DNA isolated from older worms exhibited reduced transcriptional capacity when assayed in a HeLa cell in vitro transcription system. Finally, a biological assay to determine age- correlated changes in the DNA of aging sperm demonstrated a significant reduction in the capacity of the sperm to support zygotic development as the age of the male increased. These findings demonstrated significant age-correlated alterations and modifications occurring in the DNA template of the nematode, and their implications to the aging process are discussed. ------------------- Key: 659 Medline: 84038232 Authors: Klass MR Title: A method for the isolation of longevity mutants in the nematode C. elegans and initial results. Citation: Mechanisms of Ageing & Development 22: 279-286 1983 Type: ARTICLE Genes: fer-15 Abstract: The free-living nematode Caenorhabditis elegans is used as a genetically manipulable experimental system for the study of aging. Utilizing a temperature-sensitive sterile strain with a normal life span, a method is described for the isolation of mutant strains with significantly increased life spans. Eight mutant strains were isolated each having increased life spans. Two mutant strains were spontaneous dauer formers, accounting for their increased longevity. Another was chemotaxis-defective, causing reduced food intake which could account for its increased life span. Five mutants suffered from varying degrees of paralysis affecting their rate of pharyngeal pumping and food ingestion. The high correlation of the decreased rate of food ingestion of these mutants with their increased longevity is interpreted as indicating that the increased longevity is most likely due to reduced caloric intake. These results appear to indicate that specific life span genes are extremely rare or, alternatively, life span is controlled in a polygenic fashion. ------------------- Key: 660 Medline: Authors: Starck J;Gibert M-A;Brun J;Bosch C Title: Ribosomal RNA synthesis and processing during oogenesis of the free living nematode C. elegans. Citation: Comparative Biochemistry & Physiology 75B: 575-580 1983 Type: ARTICLE Genes: Abstract: 1. The pattern of RNA synthesis during oogenesis of Caenorhabditis elegans was examined after in vitro labelling of the extruded gonads by ultrastructural radioautography and gel electrophoresis. 2. Nuclear RNA synthesis was found most active during pachytene stage while cells, in late diakinesis, do not transcribe RNA. 3. Labelled RNA molecules accumulate into the cytoplasm during all stages of oogenesis. 4. Most of these molecules apparently result from the processing of large molecular weight RNA into mature ribosomal RNA components. 5. The ribosomal RNA processing studied in vitro differs however to some extent from that observed in vivo. ------------------- Key: 661 Medline: 83262746 Authors: Isnenghi E;Cassada R;Smith K;Denich K;Radnia K;von Ehrenstein G Title: Maternal effects and temperature-sensitive period of mutations affecting embryogenesis in C. elegans. Citation: Developmental Biology 98: 465-480 1983 Type: ARTICLE Genes: emb-5 emb-6 emb-9 emb-11 emb-12 emb-13 emb-14 emb-15 emb-16 emb-17 emb-18 emb-19 emb-20 emb-21 emb-22 emb-23 emb-24 emb-25 emb-26 emb-27 emb-28 emb-29 emb-30 emb-31 emb-32 emb-33 emb-34 emb-35 let-2 zyg-2 Abstract: We have used standard tests to investigate the nature of gene expression of a new set of temperature-sensitive mutants defining 30 emb genes (essential for embryogenesis) in the nematode Caenorhabditis elegans. The mode of gene expression as determined by progeny tests for parental effects divides the genes into four classes. For 18 genes maternal gene expression is necessary and sufficient for normal embryogenesis; for 2 genes zygotic expression is necessary and sufficient; for 7 genes either maternal or zygotic expression is sufficient; for 3 genes both maternal and zygotic expression are necessary. One mutant displayed partial paternal sufficiency. The results of temperature-shift experiments define two "execution stages," corresponding to the limits of the temperature- sensitive period (TSP), and indicate the nature and the time of action or synthesis of the gene products. Most of the maternally expressed genes have very early execution stages indicating translation before fertilization, but some are temperature sensitive late in embryogenesis. Early execution stages for 2 zygotically necessary genes demonstrate that the zygotic genome can be active in the earliest stages of embryogenesis. All taken together, the mode of gene expression, TSP, and arrest stage (terminal phenotype) allow us to classify functionally and begin to order the genes essential for embryogenesis. The results indicate a preeminent role for maternal genes and gene products in embryogenesis, in agreement with the results of ------------------- Key: 662 Medline: 83296078 Authors: Bolanowski MA;Jacobson LA;Russell RL Title: Quantitative measures of aging in the nematode C. elegans: II. Lysosomal hydrolases as markers of senescence. Citation: Mechanisms of Ageing & Development 21: 295-319 1983 Type: ARTICLE Genes: fer-15 Abstract: In an attempt to provide additional quantitative markers of senescence in the nematode Caenorhabditis elegans, we have identified age-dependent increases in four lysosomal enzymes: acid phosphatase, beta-N-acetyl-D-glucosaminidase, beta-D-glucosidase, and alpha-D- mannosidase. These enzymes were judged to be lysosomal on the basis of their resemblance to analogous mammalian lysosomal enzymes with regard to subcellular fractionation, lectin binding, Km, molecular weights, inhibitor sensitivities, and pH optima. In nematode populations which had a median lifespan of 8.9 +/- 0.7 days and a maximum lifespan of 14-16 days, we observed the following increases in acid hydrolase activities per animal from day 3 (early adulthood) to day 10: (1) up to 2.5-fold for acid phosphatase; (2) 8-fold for beta-N-acetyl-D-glucosaminidase; (3) 9-fold for beta-D-glucosidase; and (4) 4-fold for alpha-D-mannosidase. Three forms of acid phosphatase and two forms of beta-D-glucosidase were separated by ion- exchange chromatography, but in each case only one form of the enzyme was primarily responsible for the age-dependent increase in total activity: acid phosphatase I increased 18-fold, while beta-D- glucosidase I increased 100-fold. By contrast, there were only slight age-dependent changes in choline acetyltransferase, acetylcholinesterase, or alpha-D-glucosidase activities after early adulthood. The age-dependent increases in acid phosphatase, beta-N- acetyl-D-glucosaminidase, beta-D-glucosidase, and alpha-D-mannosidase activities are sufficiently large and reproducible to be useful quantitative markers of senescence in C. elegans. ------------------- Key: 663 Medline: 84170641 Authors: Hartman PS Title: UV irradiation of wild type and radiation-sensitive mutants of the nematode C. elegans: Fertilities, survival, and parental effects. Citation: Photochemistry and Photobiology 39: 169-175 1984 Type: ARTICLE Genes: rad-1 rad-2 rad-3 rad-7 Abstract: Survival after UV irradiation was examined in wild type and four radiation-sensitive (rad) mutants of Caenorhabditis elegans. Synchronous populations were employed to assess radiation sensitivities at different developmental stages. In addition, the effects of irradiation on male and hermaphrodite fertilities were measured. Wild-type sensitivity was maximal early in embryogenesis. Different age-dependent patterns of radiation sensitivity were obtained with the rad mutants. The effects of parental genotype were also tested. A parental wild-type allele was capable of quickly elevating the radiation resistance of embryos derived from homozygous rad hermaphrodites. In a second parental-effect test, homozygous rad embryos displayed greater radiation resistance when derived from heterozygous rather than homozygous hermaphrodites. The results indicate that radiation sensitivity in this metazoan is determined by complex interactions of gene ------------------- Key: 664 Medline: 84132366 Authors: Findeis PM;Barinaga CJ;Willett JD;Farwell SO Title: Age-synchronous culture of C. elegans: Technique and applications. Citation: Experimental Gerontology 18: 263-275 1983 Type: ARTICLE Genes: Abstract: The inclusion of mobility to an age synchrony method and the development of an inexpensive filter device resulted in a natural model aging system without resorting to invasive chemical techniques. Large or small cohorts of nematodes with less than 1% offspring contamination are possible. The filter/mobility method is compared to other methods using the same strain and culture temperature. The applicability of the method is shown with a variety of parameters, and a previously reported parameter of aging in nematodes, i.e., specific gravity, is shown not to be an aging parameter of Caenorhabditis elegans. ------------------- Key: 665 Medline: 84109493 Authors: Meneely PM;Wood WB Title: An autosomal gene that affects X chromosome expression and sex determination in C. elegans. Citation: Genetics 106: 29-44 1984 Type: ARTICLE Genes: dpy-21 her-1 him-5 tra-1 tra-2 tra-3 ctDp1 mnDp1 mnDp8 mnDp9 stDp2 mnDp10 mnDp25 mnDp27 mnDp33 Abstract: Recessive mutant alleles at the autosomal dpy-21 locus of C. elegans cause a dumpy phenotype in XX animals but not in XO animals. This dumpy phenotype is characteristic of X chromosome aneuploids with higher than normal X to autosome ratios and is proposed to result from overexpression of X-linked genes. We have isolated a new dpy-21 allele that also causes partial hermaphroditization of XO males, without causing the dumpy phenotype. All dpy-21 alleles show hermaphroditization effects in XO males that carry a duplication of part of the X chromosome and also partially suppress a transformer (tra-1) mutation that converts XX animals into males. Experiments with a set of X chromosome duplications show that the defects of dpy- 21 mutants can result from interaction with several different regions of the X chromosome. We propose that dpy-21 regulates X chromosome expression and may be involved in interpreting X chromosome dose for the developmental decisions of both sex determination and dosage compensation. ------------------- Key: 666 Medline: Authors: Hodgkin J Title: X chromosome dosage and gene expression in C. elegans: Two unusual dumpy genes. Citation: Molecular & General Genetics 192: 452-458 1983 Type: ARTICLE Genes: dpy-21 dpy-22 dpy-23 dpy-26 emb-26 fem-1 her-1 him-8 sup-5 tra-1 sDf2 Abstract: The phenotypes caused by mutations in two autosomal genes of the nematode Caenorhabditis elegans, dpy-21 V and dpy-26 IV, are markedly affected by X chromosome dosage, independent of sexual phenotype. At high X chromosome to autosome ratio, in 2A:3X animals, these dumpy mutations are lethal; at intermediate ratio, in 2A:2X animals, they cause dumpiness or lethality; at low ration 2A:1X animals they cause neither dumpiness nor lethality. One gene, dpy-26, exhibits a strong maternal effect. Interactions between these genes and two major sex-determining genes her-1 V and tra-1 III have been examined. The dumpy mutations partly suppress the masculinization of tra-1 2A:2X animals and also increases the fertility of most her-1 2A:1X hermaphrodites. It is suggested that these dumpy genes are involved in X chromosome dosage compensation, and in some aspect of sexual differentiation. The dpy-26 gene is compared with a similar Drosophila gene, daughterless. ------------------- Key: 667 Medline: 84109239 Authors: Albertson DG Title: Formation of the first cleavage spindle in nematode Citation: Developmental Biology 101: 61-72 1984 Type: ARTICLE Genes: zyg-9 Abstract: The distribution of microtubules and microtubule organizing centers in the events leading up to the establishment of the first asymmetric cleavage furrow in nematode embryos was followed using indirect immunofluorescence of antibodies to tubulin. Oocytes arrest in meiotic prophase then undergo two meiotic reduction divisions after fertilization. At both of these divisions barrel-shaped spindles were observed. Initially a single microtubule organizing center was seen adjacent to the sperm pronucleus following fertilization in Caenorhabditis elegans, but later two sperm asters were distinguished. These increased in size as the egg pronucleus migrated toward the sperm pronucleus and reached maximum size, with fascicles of microtubules extending to the cortex, once the pronuclei had become juxtaposed. The first cleavage spindle formed following rotation and migration of the juxtaposed pronuclei back toward the center of the embryo. The distribution of microtubules in a temperature-sensitive mutant that fails in both pronuclear migration and rotation was also examined. Asters in the mutant embryos at the nonpermissive temperature contained only short microtubules suggesting that the morphology of the asters is important for directing the movement of the pronuclei. In Panagrellus redivivus sperm asters were not detected by anti-tubulin staining until the female pronucleus had migrated to the centrally placed sperm pronucleus. Asters then increased in size and formed the first cleavage spindle. ------------------- Key: 668 Medline: 84109231 Authors: Schierenberg E Title: Altered cell-division rates after laser-induced cell fusion in nematode embryos. Citation: Developmental Biology 101: 240-245 1984 Type: ARTICLE Genes: Abstract: In embryos of Caenorhabditis elegans adjacent cells belonging to different cell lines have been fused by disrupting the cell membrane between them with a single laser pulse. This leads to cytoplasmic mixing. Synchronous mitoses of the two nuclei result in the direct formation of four cells. Subsequent alteration of the cell cycle rhythm in some specific--but not all--descendants of the fused cells is observed, leading to abnormal cell patterns and often embryonic arrest. ------------------- Key: 669 Medline: 84106814 Authors: Traboni C;Ciliberto G;Cortese R Title: Mutations in box B of the promoter of a eukaryotic tRNApro gene affect rate of transcription, processing, and stability of the transcripts. Citation: Cell 36: 179-187 1984 Type: ARTICLE Genes: Abstract: We have constructed a series of single and double base-pair-substitution mutants in and around the second component (Box B) of the promoter of a tRNA(Pro) gene from C. elegans. Their analysis in in vivo and in vitro transcriptional systems establishes the importance of single nucleotides in the promotion of transcription. Most mutants in the region coding for the T*CG stem-loop show a reduced gene expression associated with lack of processing of the primary transcriptional products; in the oocytes these are rapidly degraded, with a half-life considerably shorter than that of wild-type tRNA molecules. In contrast, mutations in the DNA region coding for anticodon stem-loop do not alter the efficiency of transcription or the processing of the transcripts. ------------------- Key: 670 Medline: Authors: Blonston G Title: To build a worm. Citation: Science 84 5: 63-67 1984 Type: NEWS Genes: Abstract: In a dimly lit laboratory room in Gottingen, West Germany, Einhard Schierenberg bent his long, angular frame over his microscope, watching and counting, recording what he saw on charts and videotapes, hour upon hour, day after day, intermittently for six years. Five hundred miles away in a tiny, starkly equipped cubbyhole in Cambridge, England, John Sulston was doing the same thing, hunched over his microscope, earphones on his head to block any sound that might divert him from the image in his eyepiece. Sometimes he would sit watching all day long, diligently marking in a notebook with his colored pens. Schierenberg and Sulston were learning, cell by cell, how to build a worm. ------------------- Key: 671 Medline: 84206573 Authors: Sulston JE Title: Neuronal cell lineages in the nematode C. elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 48: 443-452 1983 Type: REVIEW Genes: ced-3 unc-86 Abstract: One of the most attractive properties of the small nematode Caenorhabditis elegans is that the divisions, migrations, and deaths of all its cells can be followed continuously in living individuals from conception to maturity. By means of Nomarski differential interference contract microscopy, the entire cell lineage of the animal has been traced and has been related to the anatomy as reconstructed by electron microscopy. The early embryonic lineages were accurately described at the turn of the century, but, dependent as the observations then were upon comparisons between embryos fixed and stained at different ages, they could not be extended to later divisions and cell movements, or to postembryonic development. In the assignments of early embryonic cells to tissues, the findings of these pioneers have broadly been confirmed; in the later lineages, however, an unpredicted complexity of detail has emerged. In this review, my aim will be to summarize the principal findings concerning the ontogeny of the nervous system. Special attention will be paid to the embryonic stage, postembryonic neurogenesis having been recently reviewed by Horvitz. Before proceeding to an examination of the actual data, it is well to ask: Does the lineage have any significance beyond mere cell proliferation? To go some way towards answering this question, a number of cell ablation experiments, in which chosen cells are killed by means of a laser microbeam, have been carried out. Only a small proportion of the technically feasible experiments have been performed, but on the basis of this limited sample it appears that the nematode is highly mosaic in character: With certain well-defined exceptions, killed cells are not replaced from any other source and the differentiation of their neighbors is unaffected. Thus, if a given precursor is killed, subsequent examination of the animal reveals in most cases that all the cells usually derived from that precursor are missing and that all other cells are present. Particular examples of such experiments are described below; for the moment, it is sufficient to note that the general bona fides of the lineage, as an instrument of specific cell ------------------- Key: 672 Medline: 84206575 Authors: Horvitz HR;Sternberg PW;Greenwald IS;Fixsen W;Ellis HM Title: Mutations that affect neural cell lineages and cell fates during the development of the nematode C. elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 48: 453-463 1983 Type: REVIEW Genes: ced-1 ced-2 ced-3 lin-1 lin-4 lin-5 lin-6 lin-8 lin-9 lin-12 lin-14 lin-15 lin-22 lin-26 lin-28 lin-29 lin-32 nuc-1 unc-59 unc-83 unc-84 unc-85 unc-86 Abstract: We have described 19 genes that affect neural cell lineages and cell fates during the development of C. elegans. These genes differ markedly in the nature, breadth, and specificity of their effects. Their only obvious common characteristic is that they all lack specificity for the nervous system, affecting both neural and nonneural development. For some of these genes (lin-5, lin-6, unc-59, unc-85), this nonspecificity probably reflects a general utilization of their products in cellular replication. In contrast, most of these genes appear to be highly specific in their effects, but their specificity is not on the basis of cell type but rather on the basis of some particular aspect of development. Specifically, unc-83 and unc-84 mutations affect certain precursor cells that generate both neural and nonneural descendants; lin-22 and lin-26 mutants lead to the generation of supernumerary neural cells with a concomitant loss of nonneural cells; lin-4, lin-14, lin-28, and lin-29 mutants perturb global aspects of developmental timing, altering the time of appearance (or preventing the appearance) of both neural and nonneural cells; lin-1, lin-8, lin-9, and lin-15 mutations affect the cell lineages of certain nonneuron -producing ectoblasts in hermaphrodites and of homologous neuron-producing ectoblasts in males; lin-12 mutations affect many sets of nonidentical homologs (cells of similar lineage history that express different fates), only some of which are neural; ced-3 mutations prevent all programmed cell deaths, again only some of which are neural. Of these 19 genes, only unc-86 is specific for neural as opposed to nonneural cell lineages. However, some unc-86 mutants are abnormal in chromosome segregation at meiosis, indicating that this gene also may affect nonneural aspects of development. One implication of these observations is that genes (and molecules) involved in neural development are likely to function in nonneural development as well. The genes lin-22, lin-12, unc-86, and ced-3 may play decision-making roles during C. elegans neurogenesis, as mutations in each of these genes cause specific transformations in the fates of particular cells. These genes and others like them may act within a hierarchy to effect decisions at different levels within cell lineages. For example, lin-22 animals display transformations affecting entire postembryonic cell lineages, unc-86 animals are altered at an intermediate level of certain cell lineages, and ced-3 animals are affected only in the ultimate fates of cells produced by terminal cell divisions.(ABSTRACT TRUNCATED AT 400 WORDS) ------------------- Key: 673 Medline: Authors: Zuckerman BM Title: The free-living nematode C. elegans as a rapid screen for compounds to retard aging. Citation: "Intervention in the Aging Process, Part B." Regelson W and Sinex FM (eds), Alan R. Liss, NY. : 275-285 1983 Type: REVIEW Genes: Abstract: The advantages of the free-living nematode Caenrohabditis elegans as a model for pharmacologic, toxicant and anthelmintic testing have become apparent to many companies, and the application of this organism as a primary screen for test compounds or toxic agents has expanded rapidly. It is appropriate to briefly summarize some of this nematode's qualities, to invoke an appreciation of this elegant system. As true of many invertebrate test organisms, C. elegans is small (about 1 mm X 40 u at maturity) and has a short life cycle: reproduction starts on day 3-4, ceases by day 14 and by day 25 it dies. Thus, for aging studies, all the symptoms of senescence are compressed into a short time period. In addition, this nematode has a small, fixed number of cells (about 830 at maturity) and differentiated organ systems: nervous, excretory, muscular, digestive and reproductive. The preceding characteristics are not unique in invertebrate model systems and their enumeration fails to explain the increasing popularity of C. elegans as a test organism. To understand this phenomenon several additional facts must be emphasized. First, the selection of C. elegans for detailed studies on the genetic control and regulation of behavior and developmental processes has fostered a wealth of knowledge on its neuroanatomy, cell lineages, biochemistry and behavior. There is now undoubtedly more accumulated knowledge on C. elegans than on any other multicellular creature. It is also the largest metazoan which can be continuously cultured on a chemically defined medium, and though most studies have proceeded on undefined media or in monoxenic culture (utilizing a bacterium as a food source), this property can be exploited for precise nutritional studies. In regard to aging studies, the question of relevance of aging in the nematode to that in mammals has been answered in respect to some parameters which characterize senescence in humans, and further study will define other features of aging which are common to all metazoa. In practical terms, this means that test which require 24-36 months to rear an aged rat for evaluation of a pharmaceutical, can potentially be accomplished in 21 days using the nematode. The paper emphasizes that the use of the C. elegans system as a primary screen for candidate compounds to intervene in the aging process can save time, effort and money, while ------------------- Key: 674 Medline: Authors: Johnson TE Title: C. elegans: A genetic model for understanding the aging process. Citation: "Intervention in the Aging Process, Part B." Regelson W and Sinex FM (eds), Alan R. Liss, NY. : 287-305 1983 Type: REVIEW Genes: Abstract: The long-term goal of our research is the understanding of the molecular processes that control metazoan aging. We present background material that describes the past difficulties in isolating long-lived mutants and present our results describing the isolation of such long-lived variants. Some of these variants have life spans more than 60% longer than wild types. We point out the genetic advantages of C. elegans which may have made the isolation of these variants possible. We also present indirect data suggesting that, at least for a subclass of these variants, the differences in mean lifespan are ascribable to factors other than those mediated by genetically induced caloric restriction. We discuss the possibility that these factors involve an alteration of what has been termed the "rate of aging". We also discuss the genetic approach to the understanding of senescence. ------------------- Key: 675 Medline: 84133307 Authors: Rand JB;Russell RL Title: Choline acetyltransferase-deficient mutants of the nematode C. elegans. Citation: Genetics 106: 227-248 1984 Type: ARTICLE Genes: ace-1 ace-2 cha-1 unc-17 unc-33 Abstract: We have identified five independent allelic mutations, defining the gene cha-1, that result in decreased choline acetyltransferase (ChAT) activity in Caenorhabditis elegans. Four of the mutant alleles, when homozygous, lead to ChAT reductions of greater than 98%, as well as recessive phenotypes of uncoordinated behavior, small size, slow growth and resistance to cholinesterase inhibitors. Animals homozygous for the fifth allele retain approximately 10% of the wild- type enzyme level; purified enzyme from this mutant has altered Km values for both choline and acetyl-CoA and is more thermolabile than the wild-type enzyme. These qualitative alterations, together with gene dosage data, argue that cha-1 is the structural gene for ChAT. cha-1 has been mapped to the left arm of linkage group IV and is within 0.02 map unit of the gene unc-17, mutant alleles of which lead to all of the phenotypes of cha-1 mutants except for the ChAT deficiency. Extensive complementation studies of cha-1 and unc-17 alleles reveal a complex complementation pattern, suggesting that both loci may be part of a single complex ------------------- Key: 676 Medline: Authors: Goldstein P Title: Triplo-X hermaphrodite of C. elegans: Pachytene karyotype analysis, synaptonemal complexes, and pairing mechanisms. Citation: Canadian Journal of Genetics & Cytology 26: 13-17 1984 Type: ARTICLE Genes: him-4 him-5 him-8 rad-4 mnT6 Abstract: Pairing of the three X chromosomes in the triplo-X strain of Caenorhabditis elegans occurs at pachytene in a two-by-two fashion such that one bivalent and one univalent are formed. The XX bivalent pairs synchronously with the autosomes and the univalent X remains in a similar chromatic state as the rest of the chromosomal complement. Normal tripartite synaptonemal complexes (SC) are formed between all bivalents. The univalent X lacks a SC and an axial core is not observed. The condensation of the univalent X in the triplo-X is different than in the male where the univalent X is heterochromatic. This real difference in condensation states of the chromatin may explain the fact that the univalent X is maintained in the male line yet is easily lost in the triplo-X strain. ------------------- Key: 677 Medline: Authors: Ouazana R;Herbage D;Godet J Title: Some biochemical aspects of the cuticle collagen of the nematode C. elegans. Citation: Comparative Biochemistry & Physiology 77B: 51-56 1984 Type: ARTICLE Genes: Abstract: 1. The collagenous proteins of the Caenorhabditis elegans cuticle exhibit different peptide maps when cleaved with Staphylococcus aureus V8 protease. 2. This result indicates that the cuticle proteins probably represent the products of a family of cuticle collagen genes, rather than the products of the post-translational modification of a small number of proteins. 3. Pepsin treatment of the cuticles solubilized only a low percentage of the proteins. 4. The pepsin resistant material shows an increased content of glycine compared with the purified cuticles and, when solubilized by reducing agents yields proteins of lower molecular weights than those released by non-pepsin-treated cuticles. 5. Reducible covalent cross-links derived from lysine are not present in C. elegans cuticle. ------------------- Key: 678 Medline: 84130170 Authors: Emmons SW;Yesner L Title: High-frequency excision of transposable element Tc1 in the nematode C. elegans is limited to somatic cells. Citation: Cell 36: 599-605 1984 Type: ARTICLE Genes: Abstract: Tc 1 transposable elements in the nematode Caenorhabditis elegans undergo excision at high frequency. We show here that this excision occurs primarily or entirely in the somatic tissues of the organism. Absence of germ-line excision is demonstrated by showing that Tc 1 elements are genetically stable; elements at particular genomic sites, as well as the overall number of elements in the genome, were stably maintained during a year of continuous, nonselective propagation. Somatic excision is demonstrated by showing that empty Tc 1 sites arise during a single generation of growth of a synchronous population and are not inherited by the next generation. These results suggest that excision of Tc 1 elements is under the control of tissue-specific factors. ------------------- Key: 679 Medline: 84191131 Authors: Klass MR;Kinsley S;Lopez LC Title: Isolation and characterization of a sperm-specific gene family in the nematode C. elegans. Citation: Molecular and Cellular Biology 4: 529-537 1984 Type: ARTICLE Genes: Abstract: The major sperm protein (MSP) of the nematode Caenorhabditis elegans is a low-molecular-weight (15,000) basic protein implicated in the pseudopodial movement of mature spermatozoa. Its synthesis occurs in a specific region of the gonad and is regulated at the level of transcription (M. Klass and D. Hirsh, Dev. Biol. 84:299-312, 1981; S. Ward and M. Klass, Dev. Biol. 92:203-208, 1982; Klass et al., Dev. Biol. 93:152-164, 1982). A developmentally regulated gene family has been identified that codes for this MSP. Whole genomic blots, as well as analysis of genomic clone banks, indicate that there are between 15 and 25 copies of the MSP gene in the nematode genome. Southern blot analysis also indicates that there is no rearrangement or amplification within the MSP gene family during development. No evidence was found of methylation at various restriction sites surrounding the MSP gene family, and similarly, no correlation between methylation and expression was observed. Three distinct members of this MSP gene family have been cloned, and their nucleotide sequences have been determined. Differential screening of a cDNA clone bank made from polyadenylated mRNA from adult males yielded 45 male-specific clones, 32 of which were clones of MSP genes. One of these cDNA clones was found to contain the entire nucleotide sequence for the MSP, including part of the 5' leader and all of the 3' trailing sequence. Genomic clones bearing copies of the MSP genes have been isolated. At least one of the members of this gene family is a pseudogene.(ABSTRACT TRUNCATED AT 250 ------------------- Key: 680 Medline: 84144794 Authors: Golden JW;Riddle DL Title: A pheromone-induced developmental switch in C. elegans: Temperature-sensitive mutants reveal a wild-type temperature-dependent process. Citation: Proceedings of the National Academy of Sciences USA 81: 819-823 1984 Type: ARTICLE Genes: daf-1 daf-2 daf-4 daf-7 daf-8 daf-11 daf-14 egl-4 egl-32 egl-40 sup-7 Abstract: Formation of a developmentally arrested dispersal stage called the dauer larva is enhanced by a Caenorhabditis-specific pheromone and is inhibited by increasing amounts of food. Pheromone-induced dauer larva formation of three tested wild-type strains is temperature- dependent, so that an increased percentage of the population forms dauer larvae at 25 degrees C compared to lower temperatures. Dauer- defective mutants fail to respond to added pheromone, and some behavioral mutants affected in thermotaxis or egg-laying also exhibit abnormal responses. Temperature-sensitive (ts) dauer-constitutive mutants form dauer larvae at a restrictive temperature regardless of environmental stimuli. At the permissive temperature (17.5 degrees C), alleles of six out of seven dauer-constitutive genes tested overrespond to the dauer-inducing pheromone. All known mutations in daf-4 (eight alleles) and daf-7 (five alleles) produce a ts dauer- constitutive phenotype. One daf-4 and one daf-7 allele are suppressed by the amber nonsense suppressor, sup-7(st5). At least these two dauer-constitutive mutations are likely to cause production of nonfunctional rather than ts gene products. These mutations appear to indirectly result in a ts phenotype by enhancing the expression of a wild-type ts developmental process. ------------------- Key: 681 Medline: Authors: Ohba K;Ishibashi N Title: A nematode, C. elegans, as a test organism for nematicide evaluation. Citation: Journal of Pesticide Science 9: 91-96 1984 Type: ARTICLE Genes: Abstract: Juveniles of Caenorhabditis elegans were transformed to dumpy in the media containing methomyl (10 ug/ml) or aldoxycarb (500 ug/ml), but not in the media containing methylisothiocyanate (MITC). The dumpy did not recover to its normal structure even after being transferred to fresh medium, but underwent to adulthood with a lower reproduction rate. The progeny from the dumpy forms was normal in structure, however, its reproductivity was as low as one-third of normal ones. Longevity of the dumpy form and its progeny were longer than those of normal worms. Methomyl (1 ug/ml), MITC (1 ug/ml) and aldoxycarb (10 ug/ml) did not suppress population growth, but MITC (10 ug/ml) did for the first two weeks. The population growth was markedly suppressed at 100 ug/ml of methomyl, 20 ug/ml of MITC and 1000 ug/ml of aldoxycarb. ------------------- Key: 682 Medline: Authors: Zuckerman BM;Kahane I Title: C. elegans: Stage specific differences in cuticle surface carbohydrates. Citation: Journal of Nematology 15: 535-538 1983 Type: ARTICLE Genes: Abstract: Stage-specific differences in wheat germ agglutinin (WGA) binding saccharides were demonstrated between the surfaces of eggs, L1 larvae, young adults, and old adults of Caenorhabditis elegans. The WGA binding was to n-acetylglucosamine groups but not to terminally linked n-acetylneuraminic acids. An age-related decrease in WGA binding occurred in adults, supporting previous findings of a decrease in net negative cuticle surface charge during aging. ------------------- Key: 683 Medline: Authors: Munakata N;Morohosh F Title: Effects of alkylating-agents on the nematode, C. elegans. Citation: Journal of Radiation Research 25: 31-31 1984 Type: ARTICLE Genes: Abstract: ------------------- Key: 684 Medline: 84188483 Authors: Blumenthal T;Squire M;Kirtland S;Cane J;Donegan M;Spieth J;Sharrock W Title: Cloning of a yolk protein gene family from C. elegans. Citation: Journal of Molecular Biology 174: 1-18 1984 Type: ARTICLE Genes: Abstract: We have cloned a family of five genes which encode the 170,000 Mr yolk proteins in the nematode Caenorhabditis elegans. The genes and their messenger RNAs are about 5 X 10(3) base-pairs in length. Thus most of the length of each gene is exon, although a few small introns have been discovered. Based on hybridization and restriction mapping experiments, the genes can be subdivided into two subfamilies: YP1- YP2 and YP3-YP4-YP5. Within a subfamily the genes are nearly identical. While most of the genes are not clustered, YP3 and YP4 are tandemly linked. Hybrid-arrest translation experiments demonstrate that the YP3-YP4-YP5 subfamily encodes the yp170A yolk protein, while the YP1-YP2 subfamily encodes the yp170B yolk protein. RNAs homologous to these genes are abundant in the adult hermaphrodite, but missing from larvae and males. Furthermore, RNA isolated from dissected intestines is highly enriched for sequences that hybridize to the genes, whereas RNA from gonad or body wall is nearly devoid of these sequences. Thus, this gene family is apparently expressed only in the intestine of the adult hermaphrodite. ------------------- Key: 685 Medline: Authors: Simpkin KG;Coles GC Title: The use of C. elegans for anthelmintic screening. Citation: Journal of Chemical Technology & Biotechnology 31: 66-69 1981 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans maintained on ampicillin-treated Escherichia coli has been found to be sensitive to the benzimidazole anthelmintics, albendazole, cambendazole, fenbendazole, flubendazole, mebendazole, oxfendazole, oxibendazole, parbendazole, thiabendazole and the non-benzimidazoles, avermectin B1a, bitoscanate, febantel, levamisole, morantel, nitroscanate, oxantel, phenothiazine, pyrantel, pyrvinium pamoate, rafoxanide and stilbazium oxide at concentrations of 50 ug cm-3 or less. It can therefore be used in a high through-put in vitro pre-screen for anthelmintics. It is suggested that C. elegans may also be useful for evaluating the mode of action of drugs and the mechanism of resistance of nematodes to ------------------- Key: 686 Medline: 84159203 Authors: Golden JW;Riddle DL Title: The C. elegans dauer larva: Developmental effects of pheromone, food, and temperature. Citation: Developmental Biology 102: 368-378 1984 Type: ARTICLE Genes: daf-14 Abstract: Three environmental cues influence both the entry into and exit from the developmentally arrested dispersal stage called the dauer larva: a dauer-inducing pheromone, food, and temperature. The pheromone, which is a measure of population density, induces dauer larva formation at the second (L2) molt and inhibits recovery in a dose- dependent manner. Food acts competitively to reduce the frequency of dauer larva formation and to enhance recovery. The pheromone causes a specific extension of the second larval stage, coupled with a transient decrease in the growth rate of the L2. Second-stage larvae grown in the presence of added pheromone are morphologically distinguishable from L2 larvae grown without pheromone. We have named the pre-dauer L2 larva the L2d. Commitment to dauer larva formation can occur at the L2d molt. When L2d larvae are shifted out of pheromone to a lawn of E. coli just before the L2d molt, a few worms complete development into dauer larvae. In contrast, worms are essentially committed to the non-dauer life cycle by the first larval molt if the L1 larvae are not grown in appropriately high levels of pheromone. In the presence of pheromone, the percentage of dauer larva formation is enhanced at higher temperatures within the normal growth range. Temperature down-shifts induce dauer larva recovery. Temperature-shift experiments show that the enhancement of dauer larva formation requires exposure to the higher temperature around the L1 molt. Two sensory mutants defective in thermotaxis are altered in their sensitivity to the dauer-inducing pheromone, but their pheromone response retains temperature dependence. Response of dauer larvae to environmental cues is highly age dependent, with older dauer larvae exhibiting an increased tendency to recover. ------------------- Key: 687 Medline: 84232604 Authors: Gibert M-A;Starck J;Beguet B Title: Role of the gonad cytoplasmic core during oogenesis of the nematode C. elegans. Citation: Biology of the Cell 50: 77-85 1984 Type: ARTICLE Genes: Abstract: In order to elucidate the function of the cytoplasmic core (or rachis: a structure specific of the nematode gonads), we have carried out a cytological study of this structure in the free-living nematode Caenorhabditis elegans, in wild-type and in several mutant strains showing an abnormal gametogenesis. We also performed an ultrastructural radioautographic study of RNA synthesis during oogenesis in order to examine the part played by the rachis in the transport of nutritive substances. Our results evidence for the first time a metabolite transfer from the germ cells to the cytoplasmic core and lead us to assign to the core a trophic role linked to oogenesis. A statistical analysis of silver grain distribution has led us to conclude that there is no accumulation of RNA labelling in any part of the cytoplasmic core. In addition, our studies performed on sterile mutant strains suggest that the cytoplasmic core may have a specific function in oogenesis determination. ------------------- Key: 688 Medline: Authors: Chalfie M Title: Genetic analysis of nematode nerve-cell differentiation. Citation: Bioscience 34: 295-299 1984 Type: ARTICLE Genes: mec-1 mec-3 mec-4 mec-5 mec-7 unc-33 unc-86 Abstract: A small roundworm Caenorhabditis elegans has been the subject of extensive studies on the structure, function, and development of the nervous system. It is the only multicellular organism for which both the cellular anatomy (morphology and connectivity) and cell lineage origin for each of its 302 nerve cells are known. These data and the ability to obtain mutants that are defective in nerve-cell origin, structure, or function allow a detailed examination of the genetic control of nerve-cell production and differentiation. The use of touch-insensitive mutants to study the development of the six touch-receptor neurons of C. elegans is an example of such an analysis. ------------------- Key: 689 Medline: Authors: Denich KTR;Schierenberg E;Isnenghi E;Cassada R Title: Cell-lineage and developmental defects of temperature-sensitive embryonic arrest mutants of the nematode C. elegans. Citation: Roux's Archives of Developmental Biology 193: 164-179 1984 Type: ARTICLE Genes: emb-5 emb-6 emb-9 emb-13 emb-15 emb-16 emb-17 emb-18 emb-21 emb-22 emb-23 emb-24 emb-25 emb-26 emb-27 emb-28 emb-29 emb-30 emb-31 emb-32 emb-33 emb-34 emb-35 let-2 zyg-2 Abstract: The cellular phenotypes are described for 28 temperature-sensitive embryonic arrest mutants in 25 genes in the nematode Caenorhabditis elegans. Cell lineages, and cellular and subcellular properties at the non-permissive tmperature (26C) have been studied by direct observation of individual cells in living embryos using Nomarski microscopy and high-resolution video recordings. The sequence, direction and time of division and the position of the individual cells have been compared to wild-type development up to at least the 100-cell stage (or earlier stage of arrest). Defects are related to the previously reported arrest stage, temperature-sensitive period, and to maternal effects. Most maternal mutants display defects in zygote formation. These include absence of pronuclear fusion or of polar bodies, absence or abnormal position of pseudocleavage or of the first division cleavage, anomalous cytoplasmic streaming, eggshell defects, abnormal cytoplasmic yolk granules, extra (pro)nuclei, endomitosis or arrest at the one-cell stage. During embryogenesis, many mutants show cellular and/or morphological abnormalities, including pseudopodia, blastocoel malformation, prolonged mitosis and membrane reformation, ill-defined membranes, segregation of extra nuclei, and cytoplasmic "plaques" at division. Most mutants display defects in cell lineage features, i.e. slow cell division rate, abnormal division sequence or direction. Three mutants show premature germ-line cell division, one of these also having a supernumerary germ-line division. Nine mutants show defects in the intestinal cell lineage, i.e. in division direction, in timing relative to gastrulation or in intestine anatomy. This survey of the cellular properties of the mutants provides a basis for a more ------------------- Key: 690 Medline: 84188508 Authors: Sharrock WJ Title: Cleavage of two yolk proteins from a precursor in C. elegans. Citation: Journal of Molecular Biology 174: 419-431 1984 Type: ARTICLE Genes: Abstract: Four yolk proteins have been identified previously in the nematode Caenorhabditis elegans. However, only two of these proteins ( yp170A and yp170B ) are found among the products of in vitro translation of nematode RNA. The other two yolk proteins ( yp115 and yp88 ) are apparently cleaved from a precursor polypeptide of approximately 180,000 Mr. This precursor has been identified as an in vitro translation product and as a metabolically unstable polypeptide in vivo. It is bound by immunoglobulin G (IgG) specific for yp115 and by IgG specific for yp88 . The immunoadsorbed material yields the same pattern of fragments on partial digestion with Staphylococcus aureus V8 protease regardless of whether anti- yp115 or anti- yp88 IgG is used in the adsorption. Like the yp170 polypeptides, the yp115 / yp88 precursor is synthesized by the intestine and secreted intact. The precursor is evidently cleaved to yield yp115 and yp88 after secretion from the intestine but independent of the presence of the gonad. Thus, cleavage probably occurs in the body cavity of the nematode. ------------------- Key: 691 Medline: Authors: Brenner S Title: Nematode research. Citation: Trends in Biochemical Sciences 9: 172-172 1984 Type: REVIEW Genes: Abstract: For this 100th issue of TIBS, we were asked to look back at our subjects about eight years to when the journal first appeared and to discuss the important developments since that time. I found myself looking further back and I beg the reader's indulgence for some history that goes back some 21 years to the origins of our work on Caenorhabditis elegans. ------------------- Key: 692 Medline: Authors: Fodor A;Riddle DL;Nelson FK;Golden JW Title: Comparison of a new wild-type Caenorhabditis briggsae with laboratory strains of C. briggsae and C. elegans. Citation: Nematologica 29: 203-217 1983 Type: ARTICLE Genes: Abstract: The hermaphrodite nematode strain G16, isolated from soil in Gujarat, India was identified as Caenorhabditis briggsae by genetic and morphological criteria. By contrast with the Dougherty strain of C. briggsae, in culture since 1944, the behavior of G16 resembles that of the wild-type C. elegans N2. The Gujarat population does not exhibit uncoordinated movement, it produces males which mate efficiently, it exhibits chemotaxis, and it forms dauer larvae in response to crowding or starvation. The G16 animals grow bigger, have a shorter generation time (1.6 days at 25C) and produce larger broods than the Dougherty strain. We conclude that the Dougherty strain has accumulated genetic defects during the years of laboratory cultivation. Genetic analysis using G16-Dougherty hybrids demonstrates that the defects in movements, chemotaxis, and dauer larva formation are all X-linked but genetically separable, while morphological differences in the male copulatory bursa are inherited autosomally. A Caenorhabditis-specific pheromone, which enhances entry into the dauer larva stage, is produced by the N2, G16, and Dougherty strains, but the Dougherty strain does not respond to the pheromone. The new wild-type C. briggsae may be more appropriate than the Dougherty strain for genetic study of C. briggsae or for future comparative ------------------- Key: 693 Medline: 84206965 Authors: Goldstein P Title: Sterile mutants in C. elegans: The synaptonemal complex as an indicator of the stage-specific effect of the mutation. Citation: Cytobios 39: 101-108 1984 Type: ARTICLE Genes: Abstract: Two sterile mutants of Caenorhabditis elegans hermaphrodites have been examined using the electron microscope and serial section analysis. The F4 and F80 mutants were described previously ( Mounier and Brun , 1980), and they were shown to be blocked at the start of oogenesis. In the F4 mutant, normal sperm are produced and the pachytene nuclei contain tripartite synaptonemal complexes (SC) between the homologously paired chromosomes. In the F80 asynaptic mutant, only a few sperm are produced and they have abnormal morphology. Whereas SCs and SC associated structures (termed 'SC knobs') are present in the F4, these structures are absent from the F80 . The mutation in F80 affects gametogenesis prior to the pachytene stage of meiosis and pairing of homologous chromosomes apparently does not occur. The SC knobs may influence the regulation of the disjunction of the chromosomes. For that reason, these structures are now ------------------- Key: 694 Medline: Authors: Yosida TH;Sadaie T;Sadaie Y Title: Somatic and meiotic chromosomes of the small free-living nematode, C. elegans. Citation: Proceedings of the Japan Academy 60B: 54-57 1984 Type: ARTICLE Genes: Abstract: The small free-living nematode, Caenorhabditis elegans, has recently been widely utilized as an attractive organism in molecular biology, since the genetic analysis was carried out by Brenner. In the adult hermaphrodites, only about 800 somatic cells are included in one individual and their cell lineage can easily be recognized in the body. The haploid DNA of this worm was known to be only 20 times as large as that of the genome of the Enterobacteriaceae, Escherichia coli, and also know to have six linkage groups. The meiotic chromosomes stained by the Feulgen method of this nematode have been reported by Nigon and Brun. According to them the haploid number was six in accordance with six linkage groups by genetic analysis. The work of karyotype analysis in this worm by light microscope has not attracted cytogeneticists, because the somatic chromosomes had been shown to be very tiny. Electron microscopic analysis seemed to be necessary for analysis of the somatic chromosomes in this worm as carried out by Goldstein et al and Goldstein. However, the technique for observation of somatic chromosomes in small worms has rapidly developed. By use of this technique we succeeded to observe the chromosomes of the small free-living nematode, C. elegans. In the present paper, the chromosomes of this worm in early embryonic stage of hermaphrodites will be described with special attention to their figures of the somatic and ------------------- Key: 695 Medline: 84255548 Authors: McLachlan AD Title: Structural implications of the myosin amino acid sequence. Citation: Annual Review of Biophysics & Bioengineering 13: 167-189 1984 Type: REVIEW Genes: unc-54 Abstract: Many questions about the action of muscle would be answered if we knew the atomic structures of both myosin and actin. The analysis of complete myosin genes and the sequencing of amino acids are vital steps towards this end. Genetic analysis identifies the different variants of myosin that exist in each animal, and the study of mutants will help to distinguish essential parts of the molecule. New cloned genes with changed functions will soon be constructed. The amino acid sequence places the important active groups and structural units of this very large protein in their correct framework. It also helps to show how the individual molecules form into regular arrays in the thick filaments of muscle. Under the electron miscroscope, individual myosin molecules appear to have long, thin rodlike tails with two globular heads emerging in a forked configuration at one end. Each molecule is a doublet containing two, paired myosin chains. The rod part is approximately 1500 A long and 20 A in diameter, while the heads are elongated, with a diameter of 70 A and length of up to 200 A. The main protein subunit of myosin is called the heavy chain. The unc-54 gene heavy chain from the soil nematode worm Caenorhabditis elegans contains 1966 amino acids (Figures 1 and 2). Figure 1 also shows part of M. Elzinga's chemical sequence from the head of rabbit skeletal muscle for comparison. The rod sequence from nematode alone contains 7-residue and 28-residue repeats, so it is laid out in zones of 28 amino acids with its own local numbering system (1' to 1117') indicated in the rest of this article by primes. Other sequences and special features marked in the Figures are described later. This review concentrates on structural aspects of muscle, excluding chemical kinetics and the dynamics of contraction. We begin with a short account of basic facts. Next we consider the myosin genes and the topography of the active regions in the head. An analysis of regularities in the rod sequence then leads on to questions about thick filaments packing and the mechanical flexibility of the ------------------- Key: 696 Medline: 84261408 Authors: Albertson DG Title: Localization of the ribosomal genes in C. elegans chromosomes by in situ hybridization using biotin-labeled probes. Citation: EMBO Journal 3: 1227-1234 1984 Type: ARTICLE Genes: eDf3 mnT2 sDp1 eDp20 mnT11 mnT12 mnDp10 mnDp11 mnDp35 Abstract: The site of the ribosomal gene cluster on embryonic metaphase chromosomes of Caenorhabditis elegans has been mapped by in situ hybridization using probe DNAs that have been nick-translated to incorporate biotin-labeled UTP. The hybridized probe DNA was detected by a double-layer fluorescent antibody technique. Since chromosomes from wild-type C. elegans embryos are indistinguishable, in situ hybridization was carried out with chromosomes from C. elegans strains carrying cytologically distinct translocation or duplication chromosomes in order to identify the right end of linkage group I as the site of the ribosomal genes. Chromosomes carrying a lethal mutation, let-209 I displayed smaller hybridization signals than wild- type, suggesting that these chromosomes carried a partial deficiency of the ribosomal gene cluster. A duplication of the ribosomal genes, eDp20(I;II) rescued let-209 homozygotes. Chromosomes carrying the alterations in the ribosomal genes were combined with mnT12(IV;X) to facilitate the mapping of genes in C. elegans by in situ hybridization. Linkage groups I and II are then labeled by the distinctive hybridization signals from the ribosomal probes, linkage groups IV and X are together distinguishable morphologically and linkage group V is labeled by hybridization to a 5S gene probe. ------------------- Key: 697 Medline: 84273027 Authors: Fujita H;Ishii N;Suzuki K Title: Effects of 8-methoxypsoralen plus near-ultraviolet light on the nematode C. elegans. Citation: Photochemistry and Photobiology 39: 831-834 1984 Type: ARTICLE Genes: Abstract: Effects of 8-methoxypsoralen plus near-UV light on the nematode Caenorhabditis elegans were studied as a novel example of photosensitized actions at the individual level. Either the eggs or the worms were illuminated with near-UV light in the presence of 8-methoxypsoralen. The treatment decreased hatchability of the eggs depending on light fluence and concentration of the sensitizer. Inhibition of growth and premature death were observed when the larvae in the second stage were illuminated in the presence of 8-methoxypsoralen. When young adults were treated before the beginning of egg-laying, they grew to lay eggs, but the total number of eggs deposited per hermaphrodite was decreased and the life span was shortened. ------------------- Key: 698 Medline: 84223963 Authors: Marx JL Title: C. elegans: Getting to know you. Citation: Science 225: 40-42 1984 Type: REVIEW Genes: lin-12 Abstract: The end of 1983 saw the completion of a major project in developmental biology. All the cell divisions, deaths, and migrations that generate the embryonic, then the larval, and finally the adult forms of the roundworm Caenorhabditis elegans have now been traced. It is the first time the complete cell lineage of an organism of this degree of complexity, one that contains many of the diverse cell types found in all higher animals, has been determined. ------------------- Key: 699 Medline: 85035857 Authors: Rose AM;Baillie DL;Curran J Title: Meiotic pairing behavior of two free duplications of linkage group I in C. elegans. Citation: Molecular & General Genetics 195: 52-56 1984 Type: ARTICLE Genes: sDp1 sDp2 Abstract: In this paper we describe the meiotic pairing behavior of two free duplications in Caenorhabditis elegans. sDp1 is a duplication of approximately 30 map units of the right portion of linkage group I including unc-74 to unc-54. This duplication pairs, recombines, and apparently segregates from one of the normal homologues. A second duplication, sDp2, is a duplication of approximately 15 map units of the left portion of the linkage group. sDp2 was not observed to recombine with the normal homologue but did suppress exchange between the two normal homologues in a sDp2/ ++/ dpy-5 unc-35 heterozygote. Although a number of free duplications have been described previously in Caenorhabditis elegans, none of these have been shown to pair with normal homologues. The meiotic behavior of the duplications described in this paper can be understood assuming the existence in C. elegans chromosomes of pairing sites of the type described in D. melanogaster chromosomes (I. Sandler 1956; Hawley 1980). ------------------- Key: 700 Medline: 85035846 Authors: Snutch TP;Baillie DL Title: A high degree of DNA strain polymorphism associated with the major heat shock gene in C. elegans. Citation: Molecular & General Genetics 195: 329-335 1984 Type: ARTICLE Genes: Abstract: We have searched for sequence variation between the Bristol and Bergerac strains of C. elegans in regions flanking three members of the 70 kilodalton (kd) heat shock peptide (hsp) gene family. No sequence variation was detected in 40 kb of DNA flanking two 70 kd hsp genes which are not stimulated by heat shock. In contrast, analysis of DNA flanking the heat shock inducible 70 kd hsp gene showed an unusually high amount of sequence variation between the two strains. Isolation and restriction map analysis of this gene from both strains revealed that the 5' and 3' flanking regions have diverged by 8.1 and 7.0% in nucleotide sequence, respectively. We have shown that these alterations are not due to large DNA rearrangements and conclude that the majority of sequence difference is the result of point mutations. Our results suggest that the heat shock inducible 70 kd hsp gene region accumulates mutations at a rate 10 to 20 fold higher than other regions of the genome. We propose that the anomalously high accumulation of mutational events is a direct consequence of the special status of the 70 kd hsp gene and its surrounding chromatin domain in the germline of C. elegans. ------------------- Key: 701 Medline: Authors: Strome S;Wood WB Title: Segregation of germ-line-specific antigens during embryogenesis in C. elegans. Citation: "Molecular Aspects of Early Development." Malacinski GM and Klein WH (eds), Plenum Press. : 141-165 1984 Type: REVIEW Genes: emb-27 fer-1 ixs-1 ixs-2 zyg-9 zyg-11 Abstract: Germ cells in a wide variety of invertebrate and vertebrate species contain distinctive cytoplasmic organelles that have been visualized by electron microscopy. The ubiliquity of such structures suggests that they play some role in germ-line determination or differentiation, or both. However, the nature and function of these structures remain unknown. We describe experiments with two types of immunologic probes, rabbit sera and mouse monoclonal antibodies, directed against ctyoplamsic granules that are unique to germ-line cells in the nematode, Caenorhabditis elegans, and that may correspond to the germ-line-specific structures seen by electron microscopy in C. elegans embryos. The antibodies have been used to follow the granules, termed P granules, during early embryonic cleavage stages and throughout larval and adult development. P granules become progressively localized to the germ-line precursor cells during early embryogenesis. We are using conditionally lethal maternal-effect mutations to study this localization process. In addition to providing a rapid assay for P granules in wild-type, mutant, and experimentally maipulated embryos, the antibodies also promise to be useful in biochemically characterizing the granules and in investigating their ------------------- Key: 702 Medline: 84206592 Authors: White JG;Southgate E;Thomson JN;Brenner S Title: Factors that determine connectivity in the nervous system of C. elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 48: 633-640 1983 Type: REVIEW Genes: Abstract: The nervous system of C. elegans is arranged as a collection of process bundles. Processes within bundles are generally unbranched and occupy defined positions relative to their neighbors. Small groups of processes are often closely associated together and run adjacent to one another for relatively long distances. We have defined the set of neurons that have processes adjacent to the processes of a given neuron as the neighborhood of that neuron. Synapses in C. elegans are made en passant between adjacent processes. Of the 1165 pairs of adjacent processes that were analyzed, 520 (45%) had synaptic contacts. The set of neurons that make synaptic contact with a given neuron is therefore, on average, 45% of that neuron's neighborhood. Neurons make synaptic contacts with fewer classes of partners than they have the potential for, as they are limited in their choice of partner to those that inhabit their neighborhood. Some classes of neurons have processes that make abrupt transitions from one neighborhood to another. There is usually some identifiable cue at the transition point, such as the termination of a closely associated process or a discontinuity at the junction of one process bundle with another. Neurons that inhabit more than one neighborhood have a more extended set of synaptic partners than those that are confined to a single ------------------- Key: 703 Medline: 84248050 Authors: Ruan K-S;Emmons SW Title: Extrachromosomal copies of transposon Tc1 in the nematode C. elegans. Citation: Proceedings of the National Academy of Sciences USA 81: 4018-4022 1984 Type: ARTICLE Genes: Abstract: Extrachromosomal copies of the 1.6-kilobase transposable element Tc1 are present at the level of between 0.1 and 1.0 copy per cell in Caenorhabditis elegans strain Bergerac. Extrachromosomal elements were detected and studied using Southern hybridizations employing a Tc1-specific probe. The amount of extrachromosomal Tc1 DNA was roughly constant during development in Bergerac, which has approximately 300 integrated chromosomal copies of Tc1 in its haploid genome. Extrachromosomal Tc1 DNA was not detected in strain Bristol, which has 30 chromosomal copies of Tc1. Three forms of extrachromosomal DNA were detected. The predominant form was a 1.6- kilobase linear molecule with ends corresponding to the ends of an integrated Tc1 element. The other two forms were, respectively, relaxed and supercoiled circular copies of the element. Structural assignments were based on electrophoretic mobility, the results of sedimentation velocity and equilibrium density gradient experiments, and on the sizes of the products produced by treatment of purified extrachromosomal DNA with restriction endonucleases. The suggestion is made that these extrachromosomal transposable elements are the products of excision events known to be occurring at high frequency in somatic cells in Bergerac. ------------------- Key: 704 Medline: 84223935 Authors: Lewin R Title: Why is development so illogical? Citation: Science 224: 1327-1329 1984 Type: NEWS Genes: Abstract: "People thought I was crazy," recalls Sydney Brenner, director of the Medical Research Council's Laboratory of Molecular Biology, Cambridge, England. "Jim Watson said he wouldn't give me a penny to do it. He said I was 20 years ahead of my time." But, with the help of a group of extremely dedicated and inventive associates, Brenner is well on the way with his crazy project. He has transformed the tiny nematode Caenorhabditis elegans into a subject of serious science: more is know about the genetics and development of this 1-millimeter roundworm than about any other multicellular creature. ------------------- Key: 705 Medline: 84223981 Authors: Lewin R Title: The continuing tale of a small worm. Citation: Science 225: 153-156 1984 Type: NEWS Genes: Abstract: "We have a complete description of the whole nervous system in terms of all the neurons and the connections they make." This simple statement, by John White of the Medical Research Council's Laboratory of Molecular Biology, Cambridge, England, sums up a brilliantly conceived and doggedly implemented research effort of more than a decade's duration on the 1-mm-long nematode Caenorhabditis elegans. White is currently contemplating the eventual publication of what amounts to a detailed atlas of this modest worm's nervous system, an opus that threatens to exceed the capacity of even the most accommodating journal. A 500-page monograph is the likely compromise. ------------------- Key: 706 Medline: 84291270 Authors: Nelson FK;Riddle DL Title: Functional study of the C. elegans secretory-excretory system using laser microsurgery. Citation: Journal of Experimental Zoology 231: 45-56 1984 Type: ARTICLE Genes: daf-7 unc-32 Abstract: Individual cells of the Caenorhabditis elegans secretory-excretory system were ablated by laser microbeam in various larval stages. Effects on growth, molting, osmoregulation, fertility, longevity, and dauer larva formation were tested. Single-cell ablations did not prevent subsequent molting, but ablation of the pore cell or the duct cell resulted in the absence of the normal cuticular lining of the excretory duct following a molt. When the pore cell, duct cell, or excretory cell was ablated, the animals filled with fluid within 12- 24 hr and died within a few days, producing very few progeny. Ablation of the excretory gland cell, on the other hand, had no obvious developmental or behavioral effects. Excretory activity was monitored in dauer larvae by observing pulsation of the excretory duct in conditions of differing osmolarity. The rate of pulsation was quite variable over time in conditions of low osmotic strength, but average five- to six-fold higher than that observed in buffered saline. These observations, combined with the effects of laser ablation, lead to the conclusion that one ------------------- Key: 707 Medline: 84259343 Authors: Politz JC;Edgar RS Title: Overlapping stage-specific sets of numerous small collagenous polypeptides are translated in vitro from C. elegans RNA. Citation: Cell 37: 853-860 1984 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans synthesizes four morphologically distinct types of collagenous cuticles during its lifetime. We show that in RNA populations isolated early or late during the L4-to-adult molt, chick and nematode collagen DNAs hybridize strongly to RNAs of about 1.2 kb. Different but overlapping classes of correspondingly small collagenous polypeptides (310-460 residues in length) are translated in vitro from these two populations and from RNA isolated at the L2- to-dauer molt. Over 60 different collagenous translation products are identified. These collagenous polypeptides are smaller than mature cuticle collagens and smaller than most vertebrate collagens. They probably represent cuticle collagen precursors and the primary products of the cuticle collagen genes of C. ------------------- Key: 708 Medline: Authors: Chalfie M Title: Neuronal development in C. elegans. Citation: Trends in Neurosciences 7: 197-202 1984 Type: REVIEW Genes: lin-12 mab-5 mec-1 mec-3 mec-4 mec-5 mec-7 mec-12 unc-33 Abstract: Research on the nematode Caenorhabditis elegans has provided a description of the development and structure of a nervous system at an exceptional level of detail. Both the synaptic connectivity and the cell lineage origin of all of the 302 neurons of the adult hermaphrodite are known. This description serves as the background for studies into the genetic control of neuronal development. Numerous mutations have been isolated that affect the production, differentiation, structure and function of the C. elegans neurons. ------------------- Key: 710 Medline: 84272657 Authors: Anderson P;Brenner S Title: A selection for myosin heavy-chain mutants in the nematode C. elegans. Citation: Proceedings of the National Academy of Sciences USA 81: 4470-4474 1984 Type: ARTICLE Genes: let-49 let-50 let-201 let-202 let-203 let-204 let-205 let-206 let-207 let-208 lev-10 lev-11 unc-54 unc-59 unc-75 eDf3 eDf4 eDf5 eDf6 eDf7 eDf9 eDf10 eDf11 eDf12 eDf13 eDf14 eDf15 eDf16 Abstract: The unc-54 gene of Caenorhabditis elegans encodes an abundant myosin heavy chain protein expressed in body-wall muscle cells. We have designed genetic techniques that select directly for unc-54 mutants. This selection is based upon properties of the unc-54 dominant allele e1152. Mutations that eliminate dominance of e1152 are null alleles of unc-54. Deletions have been identified by their genetic properties. We have defined mutationally a number of essential genes near unc-54, and we have described the genetic fine structure of this region of linkage group I. As much as 27% of the unc-54 mutations induced by the bifunctional alkylating agent 1,2,7,8-diepoxyoctane are multisite deletions. Extrachromosomal free duplications that include unc-54 are also described. ------------------- Key: 711 Medline: Authors: Golden JW;Riddle DL Title: A C. elegans dauer-inducing pheromone and an antagonistic component of the food supply. Citation: Journal of Chemical Ecology 10: 1265-1280 1984 Type: ARTICLE Genes: Abstract: The free-living soil nematode Caenorhabditis elegans forms a nonfeeding dispersal stage at the second molt called the dauer larva when exposed to environmental cues indicating crowding and limited food. An improved bioassay, tenfold more sensitive than that used previously, has been used in the characterization of the two chemical cues which act competitively in controlling this developmental process. The pheromone concentration provides a measure of the population density; it enhances dauer larva formation, and inhibits recovery (exit) from the dauer stage. The pheromone is a family of related molecules which are nonvolative, very stable, and possess physical and chromatographic properties similar to those of hydroxylated fatty acids and bile acids. A food signal, with effects on development opposite those of the pheromone, is produced by bacteria, and is also present in yeast extract. In contrast to the pheromone, the food signal is a labile substance which is neutral and hydrophilic. ------------------- Key: 712 Medline: 85004704 Authors: Herman RK Title: Analysis of genetic mosaics of the nematode C. elegans. Citation: Genetics 108: 165-180 1984 Type: ARTICLE Genes: daf-6 flu-3 osm-1 sup-10 unc-3 unc-93 mnDp1 mnDp2 mnDp3 mnDf41 mnDf42 mnDf43 mnDp12 mnDp14 Abstract: A new method for producing genetic mosaics, which involves the spontaneous somatic loss of free chromosome fragments, is demonstrated. Four genes that affect the behavior of C. elegans were studied in mosaic animals. The analysis is known. Two of the mutant genes affect certain sensory responses and prevent uptake of fluorescein isothiocyanate (FITC) by certain sensory neurons. Mosaic analysis indicated that one of these mutant genes is cell autonomous with respect to its effect on FITC uptake and the other is cell nonautonomous. In the latter case, the genotype of a non-neuronal supporting cell that surrounds the processes of the neurons that normally take up FITC probably is critical. The other two mutant genes affect animal movement. Mosaic analysis indicated that the expression of one of these genes is specific to certain neurons (motor neurons of the ventral and dorsal nerve cords are prime candidates and the expression of the other gene is specific ------------------- Key: 713 Medline: Authors: Starck J Title: Synthesis of oogenesis specific proteins in C. elegans: An approach to the study of vitellogenesis in a nematode. Citation: International Journal of Invert. Repro. & Develop. 7: 149-160 1984 Type: ARTICLE Genes: zyg-1 zyg-2 zyg-3 Abstract: In vivo labeled proteins from the nematode Caenorhabditis elegans were analyzed by SDS-polyacrylamide gel electrophoresis and fluorography. The study was performed in the wild-type strain during development and in several mutants displaying altered gametogenesis or altered embryogenesis. The patterns observed during the last larval stage and the beginning of the adult stage show that the synthesis of the 4 adult-hermaphrodite specific proteins described by Klass is tightly correlated to the onset of oogenesis. This synthesis takes place mainly in the intestine and, to a lesser extent, in the two gonadal arms. This synthesis is also observed in all the mutants studied including those which produce no diakinetic growing oocytes. Furthermore, in mutants, a difference in the labeling intensity of the 4 adult-hermaphrodite specific proteins was observed in relation to the ability to lay eggs. These results suggest that these proteins are yolk proteins. Possible interaction between the control of oogenesis and the control of yolk protein synthesis is ------------------- Key: 714 Medline: 84286385 Authors: Kimble J;Edgar L;Hirsh D Title: Specification of male development in C. elegans: The fem genes. Citation: Developmental Biology 105: 234-239 1984 Type: ARTICLE Genes: fem-1 fem-2 him-8 tra-1 Abstract: Mutation of the gene fem-2 causes feminization of both sexes: hermaphrodites make no sperm, and males produce oocytes in an intersexual somatic gonad. A double mutant harboring ts alleles of both fem-1 (formerly named isx-1; G. A. Nelson, K. K. Lew, and S. Ward, 1978, Dev. Biol. 66, 386-409) and fem-2 causes transformation of XO animals (normally male) into spermless hermaphrodites at restrictive temperature. The phenotypes, temperature-sensitive periods, and maternal effects observed in mutants of each fem gene are found to be similar. It is suggested that the fem genes are centrally involved in specification of male development in Caenorhabditis elegans--both in the germ line of hermaphrodites and in somatic and germ line tissues of ------------------- Key: 715 Medline: 85052462 Authors: Sigurdson DC;Spanier GJ;Herman RK Title: Caenorhabditis elegans deficiency mapping. Citation: Genetics 108: 331-345 1984 Type: ARTICLE Genes: bli-1 dpy-2 dpy-10 emb-27 let-19 let-22 let-23 let-24 let-25 let-26 let-27 let-28 let-29 let-30 let-31 let-236 let-237 let-238 let-239 let-240 let-241 let-242 let-243 let-244 let-245 let-246 let-247 let-248 let-249 let-250 let-251 let-252 let-253 let-254 let-255 let-256 let-257 let-258 let-259 let-260 let-261 let-262 let-263 let-264 let-265 let-266 let-267 let-268 let-269 let-270 let-271 lin-5 lin-29 ooc-1 ooc-2 ooc-3 rol-1 rol-6 spe-1 spe-2 spe-3 sqt-1 tra-2 unc-4 unc-15 unc-104 unc-105 vab-9 zyg-11 mnC1 mnDf12 mnDf14 mnDf16 mnDf22 mnDf24 mnDf25 mnDf26 mnDf27 mnDf28 mnDf29 mnDf30 mnDf31 mnDf32 mnDf33 mnDf35 mnDf36 mnDf37 mnDf38 mnDf39 mnDf40 mnDf44 mnDf45 mnDf46 mnDf47 mnDf48 mnDf49 mnDf50 mnDf51 mnDf52 mnDf53 mnDf54 mnDf55 mnDf56 mnDf57 mnDf58 mnDf59 mnDf60 mnDf61 mnDf62 mnDf63 mnDf64 mnDf65 mnDf66 mnDf67 mnDf68 mnDf69 mnDf70 mnDf71 mnDf73 mnDf74 mnDf75 mnDf76 mnDf77 mnDf78 mnDf80 mnDf81 mnDf83 mnDf84 mnDf85 mnDf86 mnDf87 mnDf88 mnDf89 mnDf90 mnDf91 mnDf92 mnDf93 mnDf94 mnDf95 mnDf96 mnDf97 mnDf98 mnDf99 mnDf100 mnDf101 mnDf103 mnDf104 mnDf105 Abstract: Six schemes were used to identify 80 independent recessive lethal deficiencies of linkage group (LG) II following X-ray treatment of the nematode Caenorhabditis elegans. Complementation tests between the deficiencies and ethyl methanesulfonate-induced recessive visible, lethal and sterile mutations and between different deficiencies were used to characterize the extents of the deficiencies. Deficiency endpoints thus helped to order 36 sites within a region representing about half of the loci on LG II and extending over about 5 map units. New mutations occurring in this region can be assigned to particular segments of the map by complementation tests against a small number of deficiencies; this facilitates the assignment of single-site mutations to particular genes, as we illustrate. Five sperm-defective and five oocyte- defective LG II sterile mutants were identified and mapped. Certain deficiency-by-deficiency complementation tests allowed us to suggest that the phenotypes of null mutations at two loci represented by visible alleles are wild type and that null mutations at a third locus confer a visible phenotype. A segment of LG II that is about 12 map units long and largely devoid of identified loci seems to be greatly favored for crossing over. ------------------- Key: 716 Medline: Authors: Vanfleteren JR Title: Nematodes as nutritional models. Citation: "Nematodes as Biological Models, Volume 2: Aging and Other Model Systems." Zuckerman BM (ed), Academic Press, NY. 2: 47-79 1980 Type: REVIEW Genes: Abstract: The use of nematodes as model organisms for the study of metazoan organization assumes a detailed knowledge of all facets of their biology. This chapter covers the nutritional aspects of the nematode model as revealed by studies on Caenorhabditis briggsae and Caenorhabditis elegans and a few other nematode species that have been established in axenic culture. The term axenic, which means "free of other organisms" was proposed by Dougherty (1960) in preference to other terms such as "sterile", "aseptic", and "pure" that would be rather ambiguous in this respect. Since most of the nematodes under discussion are bacteria feeders and some of them fungal-feeding species, it is essential that axenic culture conditions are rigidly maintained when studying nematode requirements. This chapter appraises the present state of nematode nutrition, and refers particularly to those nematodes that are currently used as model organisms for basic research of behavior, development, and aging. Detailed information on the culture methods and specific diets of these and other nematodes in axenic culture may be found in a previous review. ------------------- Key: 717 Medline: 84041508 Authors: Rosenzweig B;Liao LW;Hirsh D Title: Target sequences for the C. elegans transposable element Tc1. Citation: Nucleic Acids Research 11: 7137-7140 1983 Type: ARTICLE Genes: Abstract: The target sequences for two independent insertions of the transposable element Tc1 from Caenorhabditis elegans show homology. Because both insertions are at palindromic TA/AT sequences, the exact boundaries of Tc1 cannot be distinguished; Tc1 could be 1610 bp and flanked by a 2-bp duplication of the target site or it could be 1612 bp and without target site duplication. The latter possibility implies a novel manner for insertion of a transposable element. ------------------- Key: 718 Medline: Authors: Seymour MK;Wright KA;Doncaster CC Title: The action of the anterior feeding apparatus of C. elegans (Nematoda: Rhabditida). Citation: Journal of Zoological Society of London 201: 527-539 1983 Type: ARTICLE Genes: Abstract: From the analysis of cine film, combined with ultrastructural observations, the anterior feeding structures and their behaviour in the free-living microbivorous nematode Caenorhabditis elegans during ingestion in dense and sparse suspensions of Escherichia coli are described. In dense suspensions bacteria accumulate in the buccal cavity against the three metastomal flaps that nearly close it, and are then swallowed down the three tubular apical expansions of the triradiate oesophageal lumen when the flaps open. Excess medium is then expelled, as the oesophageal lumen closes and traps the swallowed bacteria. The flaps and oesophagus operate by contractions in the seven most anterior oesophageal muscle cells, probably coordinated via proprioceptive nerve endings between the cells. About one million nematode hours are needed to extract 1 g of bacteria from 30 ml of medium. With few or no bacteria, the head moves more, the metastomal flaps do not close and the medium seems to pass in and out of the buccal cavity, probably as part of the widespread exploration phase of food-finding behaviour. Abnormal feeding behaviour, control and functions of the metastomal flaps and associated structures, and control of food intake volume ------------------- Key: 719 Medline: Authors: Ward S Title: Genetic analysis of the sensory nervous system of C. elegans. Citation: Proc. Fifth International Congress on Parasitology 2: 28-31 1982 Type: REVIEW Genes: mec-1 mec-3 mec-7 mec-13 unc-86 Abstract: During the past ten years the nematode Caenorhabditis elegans has been subjected to intensive anatomical, genetic, developmental and behavioral analysis. More than 2500 mutants have been isolated; the complete developmental lineages of all embryonic and post embryonic cells have been determined; and the complete wiring diagram of its 300 neurons has been reconstructed by serial electron microscopy. Although C. elegans is a nonparasitic bacteria eating soil nematode and thus is not a proper subject for a parasitology congress, so much has been learned about this worm that it was elevated to honorary parasite status for this meeting. I will review some examples of how the genetic analysis of this helminth has helped established the function of parts of the sensory nervous system. Since the neuroanatomy of nematodes is so highly conserved these results should apply to parasitic nematodes as well. ------------------- Key: 720 Medline: 85012704 Authors: Rose AM;Snutch TP Title: Isolation of the closed circular form of the transposable element Tc1 in C. elegans. Citation: Nature 311: 485-486 1984 Type: ARTICLE Genes: Abstract: The mobilization of Tc1, a transposable element in the genome of the roundworm Caenorhabditis elegans, has been investigated. Genomic blot hybridization has shown that Tc1 exists in very different numbers in the genomes of two closely related strains of C. elegans: there are -30 copies of Tc1 in the Bristol, whereas in the Bergerac strain there are 200-300. Most of these Tc1 elements are structurally highly conserved although there exists a second form which contains a HindIII restriction site (Tc1 (Hin) form) and comprises -10% of the population. Excision of Tc1 from its chromosomal location in the Bergerac strain is indicated by the presence, on genomic blots, of a minor bind corresponding to the size of the uninserted restriction fragment. Here we describe the recovery of extrachromosomal linear and closed circular copies of Tc1 from the Bergerac strain, presumably a result of Tc1 ------------------- Key: 721 Medline: 85030654 Authors: Roberts TM;Streitmatter G Title: Membrane-substrate contact under the spermatozoon of C. elegans, a crawling cell that lacks filamentous actin. Citation: Journal of Cell Science 69: 117-126 1984 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans spermatozoa use a single, persistent pseudopod to crawl at about 20 micrometers/min but, unlike other types of crawling cells, sperm lack both filamentous actin and myosin. Interference reflection microscopy has revealed that sperm form broad grey areas of contact, analogous to the close contacts that have been described underneath other crawling eukaryotic cells, between their pseudopods and their substrate. Individual sperm change the size, shape and pattern of their substrate attachments as they crawl but we found no correlation between the extent of underside of the cell in contact with the substrate and the velocity of locomotion. Two predominant attachment patterns were observed: (1) a single broad contact extending from the front of the pseudopod nearly to the rear of the cell; and (2) two separate contact sites, one under the front of the pseudopod and one under the cell body. Occasionally, under cells exhibiting the second type of attachment pattern, portions of the anterior contact separated and remained stationary relative to the substrate while the cell moved forward. This observation, as well as the continuous change in shape of the contact areas, suggests that sperm continually form new contacts near the tip of the pseudopod and release these contacts backwards. In extreme cases, sperm were able to crawl with only the front of the pseudopod in contact with the substrate. Therefore, we propose that sperm locomotion depends on the interaction of several key events (traction, propulsion, membrane insertion) occurring at the leading edge of the ------------------- Key: 722 Medline: 85085944 Authors: Cox GN;Kramer JM;Hirsh D Title: Number and organization of collagen genes in C. elegans. Citation: Molecular and Cellular Biology 4: 2389-2395 1984 Type: ARTICLE Genes: col-1 col-2 col-12 col-13 col-16 col-18 col-20 daf-2 Abstract: We analyzed the number and organization of collagen genes in the nematode Caenorhabditis elegans. Genomic Southern blot hybridization experiments and recombinant phage library screenings indicated that C. elegans has between 40 and 150 distinct collagen genes. A large number of recombinant phages containing collagen genes were isolated from C. elegans DNA libraries. Physical mapping studies indicated that most phage contained a single small collagen gene less than 3 kilobases in size. A few phage contained multiple collagen hybridizing regions and may contain a larger collagen gene or several tightly linked small collagen genes. No overlaps were observed between phages containing different collagen genes, implying that the genes are dispersed in the C. elegans genome. Consistent with the small size of most collagen genes, we found that the predominant class of collagen mRNA in C. elegans is 1.2 to 1.4 kilobases in length. Genomic Southern blot experiments under stringent hybridization conditions revealed considerable sequence diversity among collagen genes. Our data suggest that most collagen genes are unique or are present in only a few copies. ------------------- Key: 723 Medline: 85050105 Authors: Lozano R;Chitwood DJ;Lusby WR;Thompson MJ;Svoboda JA;Patterson GW Title: Comparative effects of growth-inhibitors on sterol-metabolism in the nematode C. elegans. Citation: Comparative Biochemistry & Physiology 79C: 21-26 1984 Type: ARTICLE Genes: Abstract: An analogous series of dimethylalkyl compounds, consisting of four amines, an amide, and a phosphonate ester, inhibited motility and reproduction of the nematode Caenorhabditis elegans. Dimethylamines with straight-chain lengths of 12, 14, or 16 carbon atoms were equally active nematicides, causing greater than 80% population growth inhibition at a concentration of 25 ppm. The C12 straight- chain amine and its corresponding amide produced similar inhibition and were much more potent than either the corresponding C12 phosphonate or a C12 branched-chain amine. Inhibition of the delta 24- sterol reductase system was exhibited by all four amines, but not by the amide or phosphonate, in the following order of activity: C12 branched-chain amine greater than C12 straight-chain amine greater than C14 amine greater than C16 amine. The C12 branched amine also blocked the C-24(28)-dehydrogenase system in the conversion of sitosterol to fucosterol, the initial step in sitosterol dealkylation. ------------------- Key: 724 Medline: 85028044 Authors: Doniach T;Hodgkin J Title: A sex-determining gene, fem-1, required for both male and hermaphrodite development in C. elegans. Citation: Developmental Biology 106: 223-235 1984 Type: ARTICLE Genes: dpy-21 dpy-26 fem-1 him-8 mor-2 sup-7 tra-1 tra-2 tra-3 unc-7 Abstract: Sex in the nematode Caenorhabditis elegans is normally determined by the X chromosome to autosome (X:A) ratio, with XX hermaphrodites and XO males. Previous work has shown that a set of at least four autosomal genes (her-1, tra-2, tra-3, and tra-1) is signaled by the X:A ratio and appears to act in a regulatory pathway to determine sex. Twenty-one new recessive alleles of the gene fem-1(IV) (formerly isx-1) have been isolated. Seven of these may be null alleles; one of these is an amber mutation. The other 14 alleles are temperature sensitive. The putative null mutations cause both XO and XX animals to develop as females when the mother as well as the zygote is fem-1(- ). Therefore, fem-1(+) is required (a) for the development of the male body and (b) for spermatogenesis in males and hermaphrodites. In addition, fem-1 shows a maternal effect: wild-type fem-1 product partially rescues the development of fem-1(-) progeny. By analyzing double mutants it has been shown that fem-1(+) is part of the sex- determination pathway and has two distinct functions: (1) in the soma it prevents the action of tra-1, thereby allowing male development to occur, and (2) in the germline it is necessary for spermatogenesis in both sexes. ------------------- Key: 725 Medline: Authors: Lu NC;Cheng AC;Briggs GM Title: A study of mineral requirements in C. elegans. Citation: Nematologica 29: 425-434 1983 Type: ARTICLE Genes: Abstract: The quantities of Mg+2, Na+, K+, Mn+2, Ca+2 and Cu+2 required by the free-living nematode C. elegans were determined. An individual mineral deficieny was developed by deleting the mineral from the basal medium. Quantitative requirements of individual minerals were determined respectively by adding each mineral at various concentrations to the depleted medium. Serial subcultures and biological pre-treated media were used for the development of Mn+2, Ca+2 and Cu+2 deficiencies. It was found that most C. elegans were supported at 73 ug/ml Mg+2, 300 ug/ml Na+, 530 Ug/ml K+, 6.3 ug/ml Mn+2, 1500 ug/ml Ca+2 and 7.2 ug/ml Cu+2. ------------------- Key: 726 Medline: 85036460 Authors: Hartman PS Title: Effects of age and liquid holding on the UV-radiation sensitivities of wild-type and mutant C. elegans dauer larvae. Citation: Mutation Research 132: 95-99 1984 Type: ARTICLE Genes: rad-1 rad-2 rad-3 rad-7 Abstract: The dauer larva is a facultative developmental stage in the life cycle of the nematode Caenorhabditis elegans. Dauer larvae, which can survive under starvation for over 60 days, resume normal development when feeding is resumed. Wild-type (N2) and 4 radiation-sensitive (rad) mutant dauer larvae were tested for their abilities to develop into adults after UV-irradiation. The rad-3 mutant was over 30 times as sensitive as N2; rad-1, rad-2 and rad-7 mutants were not hypersensitive. Irradiation also delayed development in survivors. Wild-type dauer larvae did not differ in radiation sensitivity from 0 through 50 days of age. There was no liquid holding recovery (LHR); that is, survival did not increase when wild-type dauer larvae were held in buffer after irradiation. ------------------- Key: 727 Medline: 85077577 Authors: Moerman DG;Waterston RH Title: Spontaneous unstable unc-22 IV mutations in C. elegans var. Bergerac. Citation: Genetics 108: 859-877 1984 Type: ARTICLE Genes: unc-22 Abstract: This paper describes a mutator system in the nematode Caenorhabditis elegans var. Bergerac for the gene unc-22. Of nine C. elegans and two C. briggsae strains tested only the Bergerac BO strain yielded mutant animals at a high frequency and the unc-22 IV gene is a preferred mutational target. The forward spontaneous mutation frequency at the unc-22 locus in Bergerac BO is about 1 X 10(-4), and most of these spontaneous unc-22 mutations revert at frequencies between 2 X 10(-3) and 2 X 10(-4). Both the forward mutation frequency and the reversion frequency are sensitive to genetic background. Spontaneous unc-22 mutations derived in a Bergerac background and placed in a primarily Bristol background revert at frequencies of less than 10(-6). When reintroduced into a Bergerac/Bristol hybrid background the mutations once again become unstable. The mutator activity could not be localized to a discrete site in the Bergerac genome. Nor did mutator activity require the Bergerac unc-22 gene as a target since the Bristol unc-22 homolog placed in a Bergerac background also showed high mutation frequency. Intragenic mapping of two spontaneous unc-22 alleles, st136 and st137, place both mutations in the central region of the known unc-22 map. However, these mutations probably recombine with one another, suggesting that the unstable mutations can occur in more than one site in unc-22. Examination of the phenotypic effect of these mutations on muscle structure indicates that they are less severe in their effect than a known amber allele. We suggest that this mutator system is polygenic and dispersed over the nematode genome and could represent activity of the transposable element Tc1. ------------------- Key: 728 Medline: 85051729 Authors: Jansson H-B;Jeyaprakash A;Damon RA;Zuckerman BM Title: C. elegans and Panagrellus redivivus: Enzyme-mediated modification of chemotaxis. Citation: Experimental Parasitology 58: 270-277 1984 Type: ARTICLE Genes: che-3 daf-6 Abstract: Treatment with mannosidase or sialidase completely inhibited chemotactic responses of Caenorhabditis elegans wild type, C. elegans mutants CB1377 (daf-6)X and CB1379 (che-3)I, and Panagrellus redivivus to a source of attractants. Trypsin (EC3.4.21.4) caused a partial reduction in the level of chemoresponse. Normal chemotaxis was renewed within 20 hr following exposure to the enzymes. Other enzymes tested had no effect. Experimental and supporting evidence is presented that behavioral modification resulted from functional impairments to receptors located within chemosensory sensilla. ------------------- Key: 729 Medline: 85038599 Authors: Bolten SL;Powell-Abel P;Fischhoff DA;Waterston RH Title: The sup-7(st5) X gene of C. elegans encodes a transfer RNA-Trp-UAG amber suppressor. Citation: Proceedings of the National Academy of Sciences USA 81: 6784-6788 1984 Type: ARTICLE Genes: sup-5 sup-7 stDf1 Abstract: In earlier studies, we identified in Caenorhabditis elegans two informational suppressors sup-5 III and sup-7 X and recently showed that these suppressors acted via an altered tRNA to suppress translational termination at amber (UAG) stop codons. We now show that the sup-7 (st5) suppressor is a tRNATrpUAG amber suppressor. These studies utilized a radiolabeled purified tRNA fraction to identify hybridizing genomic sequences in a phage genomic library. DNA sequence analysis of the hybridizing segment of one clone showed that the probe recognized a tRNATrpUGG sequence. The sup-7 gene was shown to be one of an 11 or 12 member tRNATrp family by Southern blot analysis, taking advantage of an Xba I restriction site induced in the anticodon sequence by the mutational event to suppressor. Sequence analysis of a recombinant lambda clone containing sup-7 gene proved that sup-7(st5) is a tRNATrpUAG. This conclusive proof of the nature of sup7(st5) will permit unambiguous interpretation in genetic applications, and the availability of the cloned sequences may allow the sup-7 gene to be used to select for the reintroduction of DNA into C. elegans. ------------------- Key: 730 Medline: 85054957 Authors: Yarbrough PO;Hecht RM Title: Two isoenzymes of glyceraldehyde-3-phosphate dehydrogenase in C. elegans. Isolation, properties, and immunochemical characterization. Citation: Journal of Biological Chemistry 259: 14711-14720 1984 Type: ARTICLE Genes: Abstract: Two glyceraldehyde-3-phosphate dehydrogenases have been separated and purified from the nematode Caenorhabditis elegans. As defined by starch gel electrophoresis, the faster-migrating isoenzyme, glyceraldehyde-3-phosphate dehydrogenase-2, increases its activity during postembryonic development. In contrast, the slower-migrating isoenzyme, glyceraldehyde-3-phosphate dehydrogenase-1, is enriched in isolated embryos. Both isoenzymes were initially purified by ammonium sulfate fractionation, gel filtration, and NAD+-agarose affinity chromatography. The separation of both isoenzymes as well as their purification to homogeneity was obtained by preparative chromatofocusing. The subunit molecular weight of each isoenzyme is 38,500 +/- 500. A tetrameric native molecular weight of 157,000 +/- 2000 was determined for glyceraldehyde-3-phosphate dehydrogenase-2. Monospecific rabbit polyclonal antibodies were initially raised against the major isoenzyme and subsequently used to characterize both isoenzymes. Staphylococcus aureas V8 protease digests of each isoenzyme were separated electrophoretically and stained immunochemically, providing evidence that the two isoenzymes differed in their amino acid sequences. Developmental immunocytochemical studies suggest that the embryonic-enriched isoenzyme, glyceraldehyde- 3-phosphate dehydrogenase-1, is present in all cells. The second isoenzyme, exhibiting the major activity during postembryonic larval development, may define a body-wall-muscle specific activity which is located within the actin-containing I and A zones of the nematode's ------------------- Key: 731 Medline: 85147624 Authors: Sternberg PW;Horvitz HR Title: The genetic control of cell lineage during nematode development. Citation: Annual Review of Genetics 18: 489-524 1984 Type: ARTICLE Genes: ced-3 ced-4 her-1 lin-12 lin-14 lin-17 lin-22 tra-1 unc-86 Abstract: As recognized by T. H. Morgan, the problems of genetics and development are interwoven: understanding how the genotype of an organism specifies its phenotype requires knowing the fundamental mechanism of gene action, how genes interact to specify the properties of cells, and how cells interact to specify each adult character. We now know that the primary effect of a gene is to encode a protein or RNA product. However, little is known about how the genes of a zygote specify a complex pattern of cell divisions, the generation of diverse cell types, and the arrangement of those cells into specific morphological structures. A "favorable material" (as Morgan put it) for investigating these problems would be a simple organism in which development could be analyzed at the level of single genes and single cells. The small free-living soil nematode Caenorhabditis elegans is such an organism. C. elegans is easily grown and handled in the laboratory and is well suited for both genetic and developmental studies. This nematode consists of only about 1,000 (non-germ) cells, and both its anatomy and its development are essentially invariant. The complete anatomy of C. elegans, including the "wiring diagram" of the nervous system, is known at an ultrastructural level. In addition, the developmental origin of every cell is known since the complete cell lineage from the zygote to the adult has been determined. The genetic properties of C. elegans allow researchers to combine the classical Mendelian approach of Morgan and his coworkers with the approach of modern microbial genetics: C. elegans is diploid but microscopic in size (so large numbers of animals can be handled, up to 10*5 on a single petri dish) and has a very rapid life cycle (an egg matures into a fertile adult within two to four days, depending upon temperature; this adult produces 300-400 progeny over the next few days, resulting in an effective organismal doubling time of about 15 hours). Many aspects of the biology of C. elegans have been reviewed. Here we describe how these features have led to an initial understanding of some of the issues concerning genetics and development that Morgan raised fifty years ago. We review the methods underlying and the results derived form four approaches that have been used to study the genetics of nematode development. The first approach, which takes advantage of the genetic diversity generated by evolution, is to compare the development of related species. For example, simple differences in otherwise identical cell lineages may be the result of one or a few mutational events that occurred during the divergence of two species; the nature of these differences can suggest ways in which genes may control development. The second approach is to identify a large set of mutations that affect particular cell lineages; this approach can indicate the number, types, and specificities of genes that affect particular developmental events. The third approach involves the detailed genetic analyses of genes identified by mutations that alter development; such studies can reveal the wild-type functions of those genes and thereby identify genes that play regulatory roles in development. The fourth approach is to examine the interactions among mutations using studies of extragenic suppression and epistasis; this type of analysis can suggest how genes interact during normal development to ------------------- Key: 732 Medline: 85102733 Authors: Eide D;Anderson P Title: The gene structures of spontaneous mutations affecting a C. elegans myosin heavy chain gene. Citation: Genetics 109: 67-79 1985 Type: ARTICLE Genes: unc-54 unc-105 Abstract: We have isolated spontaneous mutations affecting the unc-54 major myosin heavy chain gene of Caenorhabditis elegans (variety Bristol). Spontaneous unc-54 mutants occur in C. elegans populations at a frequency of approximately 3 X 10(-7). We have studied the gene structure of 65 independent unc-54 mutations using filter-transfer hybridization techniques. Most unc-54 mutations (50 of 65) exhibit no abnormalities detected with these techniques; these mutations are small lesions affecting less than 100 base pairs. Approximately 17% of the mutations (11 of 65) are simple deletions, ranging in size from less than 100 base pairs to greater than 17 kilobases. One isolate contains two separate deletions, each of which affects unc- 54. Two mutants contain tandem genetic duplications that include a portion of unc-54 and extend 8-10 kilobases beyond the 5' terminus of the mRNA. Conspicuously absent from our collection of spontaneous unc- 54 mutations are any resulting from insertion of transposable genetic elements. Such mutants, if they occur, must arise at a frequency of less than 5 X 10(-9). ------------------- Key: 733 Medline: 85102734 Authors: Hartman PS Title: Epistatic interactions of radiation-sensitive (rad) mutants of C. elegans. Citation: Genetics 109: 81-93 1985 Type: ARTICLE Genes: rad-1 rad-2 rad-3 rad-7 Abstract: Six double mutants and a quadruple mutant were derived from four UV radiation-hypersensitive single mutants (rad-1, rad-2, rad-3 and rad- 7). Sensitivities of the 11 strains to UV, gamma-radiation and methyl methanesulfonate (MMS) were compared. Of the six double mutants, only the rad-1;rad-2 and rad-3;rad-7 doubles were no more hypersensitive than the most sensitive single mutant to UV-radiation. Thus, rad-1 and rad-2 define one epistasis group, whereas rad-3 and rad-7 define another. Consistent with this model was the observation that rad-1 and rad-2, but not rad-3 and rad-7, were hypersensitive to gamma- radiation. In addition, none of the multiple mutants was more hypersensitive to gamma-radiation than the most sensitive single rad mutant. No synergistic interactions of the rad mutations with respect to MMS sensitivities were ------------------- Key: 734 Medline: 84173237 Authors: Chitwood DJ;Lusby WR;Lozano R;Thompson MJ;Svoboda JA Title: Novel nuclear methylation of sterols by the nematode C. elegans. Citation: Steroids 42: 311-319 1983 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans possesses a unique sterol methylation pathway not reported to occur in any other organism and also removes the C-24 ethyl group of sitosterol (a plant sterol). This nematode produced substantial quantities of 4 alpha-methyl-5 alpha-cholest-8(14)-en-3 beta-ol and smaller amounts of lophenol from dietary cholesterol, desmosterol or sitosterol. When C. elegans was propagated in media containing sitosterol plus 25-azacoprostane hydrochloride (25-aza-5 beta-cholestane hydrochloride), an inhibitor of delta 24-sterol reductase in insects, its 4 alpha-methylsterol fraction largely consisted of equal amounts of 4 alpha-methyl-5 alpha-cholesta-7,24- dien-3 beta-ol and 4 alpha-methyl-5 alpha-cholesta-8(14),24-dien-3 beta-ol. Thus 25-azacoprostane hydrochloride inhibited both a delta 24-sterol reductase and a delta 7-sterol isomerase ------------------- Key: 735 Medline: 85056972 Authors: Rand JB;Russell RL Title: Properties and partial purification of choline acetyltransferase from the nematode C. elegans. Citation: Journal of Neurochemistry 44: 189-200 1985 Type: ARTICLE Genes: Abstract: We have stabilized and studied choline acetyltransferase from the nematode Caenorhabditis elegans. The enzyme is soluble, and two discrete forms were resolved by gel filtration. The larger of these two forms (MW approximately 154,000) was somewhat unstable and in the presence of 0.5 M NaI was converted to a form indistinguishable from the "native" small form (MW approximately 71,000). We have purified the small form of the enzyme greater than 3,300-fold by a combination of gel filtration, ion-exchange chromatography, and nucleotide affinity chromatography. The purified preparation has a measured specific activity of 3.74 mumol/min/mg protein, and is free of acetylcholinesterase and acetyl-CoA hydrolase activities. The Vmax of the purified enzyme is stimulated by NaCl, with half-maximal stimulation at 80 mM NaCl. The Km for each substrate is also affected by salt, but in different manners from each other and the Vmax; the kinetic parameter Vmax/Km thus changes significantly as a function of the salt concentration. ------------------- Key: 736 Medline: 85084899 Authors: Johnson TE;Mitchell DH;Kline S;Kemal R;Foy J Title: Arresting development arrests aging in the nematode C. elegans. Citation: Mechanisms of Ageing & Development 28: 23-40 1984 Type: ARTICLE Genes: Abstract: Larval development of the nematode, Caenorhabditis elegans, can be arrested by either of two different treatment: (1) complete starvation, or (2) growth in a partially defined culture medium (axenic medium) of strains adapted to bacterial growth. The developmental arrest is complete under total starvation and the starved populations live about 10 days. The developmental block is incomplete in axenic medium; most animals mature but maturation takes 10 times longer than normal. If developmentally arrested cultures are returned to growth on E. coli, both the completely starved and the axenically arrested cultures mature at normal rates. Life-span is prolonged by 1 day for each day of complete starvation; life-span is prolonged by 0.7 days for each day of axenic arrest. These results suggest that aging and development are closely coupled in this system. The results are discussed in terms of previous observations on nutritional deprivation in other invertebrates and caloric restriction in mammals and are interpreted in light of theoretical models of senescence. ------------------- Key: 737 Medline: Authors: Marx JL Title: New clues to developmental timing. Citation: Science 226: 425-426 1984 Type: REVIEW Genes: lin-14 lin-28 lin-29 Abstract: Within the past few years researchers have finally begun to be able to peer inside a hitherto impenetrable black box, namely, the development of complex organisms. The genes that control the commitment of embryonic cells to specific fates are now being found and characterized. A case in point is reported in this issue of Science (p. 409). Victor Ambros of Harvard University and H. Robert Horvitz of Massachusetts Institute of Technology have identified genes that affect the timing of developmental events in the roundworm Caenorhabditis elegans. ------------------- Key: 738 Medline: 85163460 Authors: Eide DJ;Anderson P Title: Novel insertion mutation in C. elegans. Citation: Molecular and Cellular Biology 5: 1-6 1985 Type: ARTICLE Genes: unc-54 Abstract: The mutation e1662 is an allele of the Caenorhabditis elegans unc-54 gene induced with the difunctional alkylating agent 1,2,7,8- diepoxyoctane. unc-54 encodes the major myosin heavy chain isozyme of body wall muscle cells. Filter-transfer hybridization and DNA sequence analysis show that e1662 is an insertion of 288 base pairs of DNA within unc-54. The inserted DNA is identical to a 288-base pair region of unc-54 located ca. 600 base pairs from the insertion site. Thus, e1662 is a displaced duplication. A 14-base pair sequence located at one end of the duplicated segment is found adjacent to the site of insertion. These homologous sequences are juxtaposed head-to- tail by the insertion event. e1662 thus contains a tandem direct repeat extending across one of its junctions. ------------------- Key: 739 Medline: 85086059 Authors: Goldstein P Title: The synaptonemal complexes of C. elegans--Pachytene karyotype analysis of the rad-4 radiation-sensitive mutant. Citation: Mutation Research 129: 337-343 1984 Type: ARTICLE Genes: him-4 him-5 him-8 rad-4 mnT6 Abstract: In the rad-4 mutant of C. elegans there is a specific increase in the number of 'Disjunction Regulator Regions' (DDR) present on the synaptonemal complexes (SC) in pachytene nuclei. These DRRs either promote disjunction or inhibit nondisjunction of the X-chromosome as evidenced by the 10-fold decrease in the rate of X-chromosome nondisjunction as compared to the wild-type. The structure of the tripartite SC is normal, thus, the decrease in the rate of X- chromosome nondisjunction in the rad-4 mutant is not related to the structure of the SC but may be related to the number of DRRs. Other changes are also associated with the sensitivity to irradiation, i.e. the pachytene nuclear morphology is altered such that nuclei and nucleoli are 50% the size of wild-type. In addition, the autosomal: X- chromosome size ratio is reduced in the rad-4 mutant. That there are six SCs confirms n = 6 in this mutant and of these six SCs three can be identified: (1) the XX bivalent, SC No. 1, is the shortest and pairs synchronously with the autosomes; (2) the longest bivalent, SC No. 6, carries the nucleolar organizer region at one extreme end; and (3) SC No. 5 has two DRRs located approximately one micron apart from each other. ------------------- Key: 740 Medline: 85077225 Authors: Hedgecock EM;White JG Title: Polyploid tissues in the nematode C. elegans. Citation: Developmental Biology 107: 128-133 1985 Type: ARTICLE Genes: lin-5 Abstract: During larval development, the number of somatic nuclei in C. elegans hermaphrodites increases from 558 to 959 (J. E. Sulston and H. R. Horvitz, Dev. Biol. 56, 110-156, 1977; J. E. Sulston et al., Dev. Biol. 100, 64-119, 1983). At the same time, the animals increase about 60-fold in volume. We have measured the DNA contents of several classes of nuclei by quantitating the fluorescence of Hoescht 33258 stained DNA (D. G. Albertson et al., Dev. Biol. 63, 165-178, 1978). Probably all embryonic nuclei, including those of neurons, muscles, hypodermis, and intestine, are diploid at hatching. Neurons, muscles, and nondividing hypodermal nuclei remain diploid throughout larval development. The DNA content of the intestinal nuclei doubles at the end of each larval stage, reaching 32C by the adult stage. New hypodermal cells, generated by division of seam cells in the larval stages, undergo an additional round of DNA replication before fusing with the major syncytium (hyp7, Sulston et al., 1983). Thus the larval hyp7 syncytium comprises a fixed number of diploid embryonic nuclei plus an increasing number of tetraploid postembryonic nuclei. Some of the endoreduplications that occur in the intestinal and hypodermal lineages of C. elegans may correspond to nuclear or cellular divisions in another nematode Panagrellus redivivus (P. W. Sternberg and H. R. Horvitz, Dev. Biol. 93, 181-205, 1982). ------------------- Key: 741 Medline: 85134867 Authors: Waterston RH;Hirsh D;Lane TR Title: Dominant mutations affecting muscle structure in C. elegans that map near the actin gene cluster. Citation: Journal of Molecular Biology 180: 473-496 1984 Type: ARTICLE Genes: act-1 act-2 act-3 sup-3 eDf1 mDf1 Abstract: By examining F1 progeny of mutagenized Caenorhabditis elegans larvae, we recovered several dominant mutations which affect muscle structure. Five of these new mutations resulted in phenotypes unlike the previously recognized unc-54 and unc-15 dominant alleles. Mapping studies placed all five mutations in the same small region of linkage group V. Polarized light, fluorescence and electron microscopic studies showed that a prominent feature of the disorganized myofilament lattice is the abnormal placement of thin filaments within the body wall muscle cells. Pharyngeal musculature is also affected by three of the mutations when homozygous. Of the five mutations only three are homozygous viable. All three of these have unusually high intragenic reversion rates either spontaneoulsy (10*-6) or after ethyl methanesulfonate mutagenesis (2x10*-5), suggesting that reversion occurs through loss of function mutations. No unlinked suppressor mutations were found. The dominance of the mutations, the effect on thin filaments and the reversion properties suggested that these new dominant mutations lie in a gene or genes specifying a structural component of the thin filament. The positioning of a set of three actin sequences in the same region led us to speculate that these ------------------- Key: 742 Medline: 85134868 Authors: Landel CP;Krause M;Waterston RH;Hirsh D Title: DNA rearrangements of the actin gene-cluster in C. elegans accompany reversion of 3 muscle mutants. Citation: Journal of Molecular Biology 180: 497-513 1984 Type: ARTICLE Genes: act-1 act-2 act-3 Abstract: We present evidence that associates dominant mutations in Caenorhabditis elegans that disrupt muscle structure and motility with a cluster of three actin genes mapped in the same region of linkage group V. We examined spontaneous and mutagen-induced wild-type revertants of these dominant alleles for alterations in the DNA of the actin gene cluster. Four of 73 revertants contain detectable DNA rearrangements within the cluster of actin genes including an insertion, a deletion and gene fusions. We postulate that these rearrangements inactivate or delete at least one gene in the cluster and consequently the original mutations are within the actin gene cluster. ------------------- Key: 743 Medline: 84123650 Authors: Neigauz BM;Ravin VK Title: The effect of physiologically active substances on life duration of a nematode C. elegans. Citation: Zhurnal Obshchei Biologii 44: 835-841 1983 Type: ARTICLE Genes: Abstract: ------------------- Key: 744 Medline: 85080119 Authors: Strehler EE;Mahdavi V;Periasamy M;Nadal-Ginard B Title: Intron positions are conserved in the 5' end region of myosin heavy-chain genes. Citation: Journal of Biological Chemistry 260: 468-471 1985 Type: ARTICLE Genes: unc-54 Abstract: We have determined the 5' end sequence of the rat embryonic skeletal muscle myosin heavy-chain (MHC) gene comprising the first three amino-terminal coding exons. Comparison with the corresponding regions of the rat ventricular a and the nematode Caenorhabditis elegans unc-54 MHC genes shows that the degree of amino acid sequence conservation increases from the first to the third exon. Intron positions between these exons are maintained in all three genes studied, whereas size and sequence of corresponding introns are highly divergent. In contrast to the rat MHC genes where the coding region is highly split throughout its entire length, only the 5' end region is frequently interrupted by introns in the nematode gene indicating the potential importance of these introns in gene structure and expression. The occurrence of "preferential" intron positions in the MHC genes suggests the existence of a highly split ancestral MHC from which different evolutionary lineages removed and/or added specific sets of ------------------- Key: 745 Medline: 85127928 Authors: Schierenberg E;Wood WB Title: Control of cell-cycle timing in early embryos of C. Citation: Developmental Biology 107: 337-354 1985 Type: ARTICLE Genes: Abstract: A technique has been developed for extruding either substantial amounts of cytoplasm without nuclei or individual nuclei with small amounts of cytoplasm from early embryos of C. elegans after perforating the eggshell with a laser microbeam. This technique, in conjunction with laser-induced cell fusion, has allowed the altering of nuclear/cytoplasmic ratios and the exposing of the nucleus of one cell to cytoplasm from another. Using these approaches the roles of nuclei and cytoplasm in determining the different cell-cycle periods of the several blastomere lineages in early embryos have been examined. It was found that nuclei in a common cytoplasm divide synchronously; enucleated blastomeres retain a cycling period characteristic of their lineage; cycling period is not substantially affected by changes in the ratio of nuclear to cytoplasmic volumes or the DNA content per cell; the period of a cell from one lineage can be substantially altered by introduction of cytoplasm from a cell of another lineage with a different period; and short-term effects of foreign cytoplasm on the timing of the subsequent mitosis differ depending on position of the donor cell in the cell cycle. These results are discussed in connection with models for the action of cytoplasmic factors in controlling cell-cycle timing. ------------------- Key: 746 Medline: 85105075 Authors: Kramer JM;Cox GN;Hirsh D Title: Expression of the C. elegans collagen genes col-1 and col-2 is developmentally regulated. Citation: Journal of Biological Chemistry 260: 1945-1951 1985 Type: ARTICLE Genes: col-1 col-2 Abstract: The total collagen gene expression as well as the specific expression of two sequenced Caenorhabditis elegans collagen genes, col-1 and col- 2, has been investigated. Northern blots of RNA isolated from animals at different developmental stages were probed under conditions that allow cross-hybridization of all collagen sequences. The majority of hybridization is to transcripts of 1.1-1.4 kilobases (kb) in length, with weak hybridization to some larger transcripts. Different size patterns, within the 1.1-1.4-kb ranges, are seen in RNAs from different developmental stages. Gene-specific probes were produced from the C. elegans collagen genes col-1 and col-2, and each was shown to hybridize to a single size transcript in the 1.1-1.4-kb region. The col-1 transcript was found in all the developmental stages examined, but its abundance varied between stages. The col-2 transcript was detected only in a single developmental stage, during formation of the dauer larvae. The 5' and the 3' ends of the col-1 and col-2 transcripts were determined by S1 nuclease digestion experiments. Both genes have the common "TATA" and "CAAT" box sequences preceding the 5' end of their transcripts and there is strong sequence homology in their 5' untranslated regions. Multiple copies of an eight-nucleotide repeat sequence were found upstream from both col-1 and col-2. ------------------- Key: 747 Medline: 85140249 Authors: Chandra HS Title: Sex determination: A hypothesis based on noncoding DNA. Citation: Proceedings of the National Academy of Sciences USA 82: 1165-1169 1985 Type: ARTICLE Genes: dpy-26 her-2 tra-1 Abstract: Certain recent models of sex determination in mammals, Drosphila melanogaster, Caenorhabditis elegans, and snakes are examined in the light of the hypothesis that the relevant genetic regulatory mechanisms are similar and interrelated. The proposed key element in each of these instances is a noncoding DNA sequence, which serves as a high-affinity binding site for a repressor-like molecule regulating the activity of a major "sex-determining" gene. On this basis it is argued that, in several eukaryotes, (i) certain DNA sequences that are sex-determining are noncoding, in the sense that they are not the structural genes of a sex-determining protein; (ii) in some species these noncoding sequences are present in one sex and absent in the other, while in others their copy number or accessibility to regulatory molecules is significantly unequal between the two sexes; and (iii) this inequality determines whether the embryo develops into a male or a female. ------------------- Key: 748 Medline: 85137502 Authors: Cox GN;Hirsh D Title: Stage-specific patterns of collagen gene-expression during development of C. elegans. Citation: Molecular and Cellular Biology 5: 363-372 1985 Type: ARTICLE Genes: col-1 col-2 col-3 col-6 col-7 col-8 col-10 col-11 col-12 col-13 col-14 col-15 col-16 col-17 col-18 col-19 Abstract: Collagens are the major protein components of the Caenorhabditis elegans cuticle and are encoded by a large family of 40 to 150 closely related but nonidentical genes. We have determined temporal patterns of mRNA accumulation for a large number of collagen genes by screening recombinant phages and plasmids containing cloned collagen genes under high stringency conditions with 32P-labeled cDNA preparations specific for eggs or three postembryonic molts. We find that collagen mRNA levels are regulated both temporally and quantitatively during C. elegans development. Most genes studied exhibit one of four patterns of mRNA accumulation which correlate with changes in cuticle morphology and collagen protein composition during development. Our results suggest that, in general, there is a progressive activation of new collagen genes during normal development. ------------------- Key: 749 Medline: Authors: Kenyon CJ Title: Heterochronic mutations of C. elegans--their developmental and evolutionary significance. Citation: Trends in Genetics 1: 2-2 1985 Type: REVIEW Genes: lin-14 lin-28 lin-29 Abstract: V. Ambros and R. Horvitz have identified a set of genes that may control the timing of developmental events in the nematode Caenorhabditis elegans. After hatching, C. elegans proceeds to the adult stage via four juvenile stages, each followed by a molt. Each juvenile stage is characterized by a distinct pattern of cell division and differentiation called an S1, S2, S3 or S4 lineage pattern. Ambros and Horvitz have found that the S1-S4 lineage patterns are modular; that is, a lineage pattern (including hypodermal, neuronal, muscle, and intestinal divisions and differentiations) characteristic of one stage can be expressed at a different stage. Each behaves as a complex lineage cassete that can be inserted into one or more of the available temporal slots. ------------------- Key: 750 Medline: 85155449 Authors: Rosenbluth RE;Cuddeford C;Baillie DL Title: Mutagenesis in Caenorhabditis elegans. II. A spectrum of mutational events induced with 1500 R of gamma-radiation. Citation: Genetics 109: 493-511 1985 Type: ARTICLE Genes: let-326 let-327 let-329 let-331 rol-3 unc-46 unc-62 eT1 sT1 sT2 sT3 sT4 sDp3 sDp4 sDf20 sDf26 sDf27 sDf28 sDf29 sDf30 Abstract: We previously established a gamma-ray dose-response curve for recessive lethal events (lethals) captured over the eT1 balancer. In this paper we analyze the nature of lethal events produced, with a frequency of 0.04 per eT1 region, at a dose of 1500 r. To do so, we developed a protocol that, in the absence of cytogenetics, allows balanced lethals to be analyzed for associated chromosomal rearrangements. A set of 35 lethal strains was chosen for the analysis. Although the dosage was relatively low, a large number of multiple-break events were observed. The fraction of lethals associated with rearrangements was found to be 0.76. Currently most X- and gamma-ray dosages used for mutagenesis in C. elegans are 6000- 8000 r. From our data we conservatively estimated that 43% of rearrangements induced with 8000 r would be accompanied by additional chromosome breaks in the genome. With 1500 r the value was 5%. The 35 lethals studied were derived from 875 screened F1's. Among these lethals there were (1) at least two unc-36 duplications, (2) at least four translocations, (3) at least six deficiencies of chromosome V (these delete about 90% of the unc-60 to unc-42 region) and (4) several unanalyzed rearrangements. Thus, it is possible to recover desired rearrangements at reasonable rates with a dose of only 1500 r. We suggest that the levels of ionizing radiation employed in most published C. elegans studies are excessive and efforts should be made to use reduced levels ------------------- Key: 751 Medline: 85155450 Authors: Cox GN;Carr S;Kramer JM;Hirsh D Title: Genetic mapping of C. elegans collagen genes using DNA polymorphisms as phenotypic markers. Citation: Genetics 109: 513-528 1985 Type: ARTICLE Genes: col-2 col-3 col-4 col-5 col-6 col-8 col-9 Abstract: In Caenorhabditis elegans collagens comprise a dispersed family of 40- 150 genes, the majority of which probably code for collagen proteins found in the animal's cuticle. The conserved (Gly-X-Y)n triple helix coding sequence of collagen genes has facilitated the isolation of a large number of C. elegans collagen genes by recombinant DNA methods. We have begun a study of the chromosomal organization of these genes by screening laboratory strains of C. elegans for DNA polymorphisms in the regions surrounding collagen genes. Polymorphisms near seven genes have been identified and have been used as phenotypic markers in genetic crosses to assign the genes to linkage groups II, III, IV, and X. Four genes are shown by multifactor crosses to map to a 2-3 map unit interval between unc-24 and unc-22 on chromosome IV. ------------------- Key: 752 Medline: Authors: Lozano R;Lusby WR;Chitwood DJ;Svoboda JA Title: Dealkylation of various 24-alkylsterols by the nematode C. elegans. Citation: Lipids 20: 102-107 1985 Type: ARTICLE Genes: Abstract: The metabolism of 4 dietary 24-alkylsterols was investigated in the free-living nematode Caenorhabditis elegans. The major unesterified sterols of C. elegans in media supplemented with either campesterol, 22-dihydrobrassicasterol or stigmasterol included cholesta-5,7-dienol, cholesterol, cholest-7-enol, and 4a-methylcholest-8(14)-enol. Dietary stigmastanol yielded cholest-7-enol, cholestanol, cholest-8(14)-enol, and 4a-methylcholest-8(14)-enol as major unesterified sterols. Esterified sterols comprised less than 22% of the total sterol. Removal of a C-24 ethyl substituent of sterols was neither hindered by the presence of a delta22-bond in the sterol side chain nor was it dependent on unsaturation in ring B of the steroid nucleus. C. elegans reduced a delta22-bond during its metabolism of stigmasterol; it did not introduce a delta5-bond during stigmastanol metabolism. C. elegans was capable of removing a C-24 methyl substituent regardless of it stereochemical orientation. Metabolic processes involving the steroid ring system of cholesterol (C-7 dehydrogenation, delta5-reduction, 4a-methylation, delta8(14)-isomerization) in C. elegans were not hindered by the presence of a 24-methyl group; various 24-methylsterol metabolites from campesterol were detected, mostly 24-methylcholesta-5,7-dienol. In contrast, no 24-ethylsterol metabolites from the dietary ethylsterols were found. More dietary 24-methylsterol remained unmetabolized than did dietary 24-ethylsterol. A 24a-ethyl group and a 24B-methyl group were dealkylated to a greater extent by C. elegans than was a 24a-methyl group, perhaps reflecting the substrate specificity of the dealkylation enzyme system, or suggesting different enzymes ------------------- Key: 753 Medline: 85101872 Authors: Jeyaprakash A;Jansson H-B;Marban-Mendoza N;Zuckerman BM Title: C. elegans: Lectin-mediated modification of chemotaxis. Citation: Experimental Parasitology 59: 90-97 1985 Type: ARTICLE Genes: che-3 daf-6 Abstract: Binding of the lectins concanavalin A (Con A) and limulin to Caenorhabditis elegans wild type resulted in consistent, reproducible, partial inhibition of chemoattraction to sterile filtrates of Escherichia coli. Normal chemotaxis resumed within 8 hr following treatment with these lectins. Competitive displacement of Con A or limulin by flooding with the specific sugars resulted in rapid resumption of normal chemotactic behavior. The experimental protocol for Con A applied to three age groups (newly hatched larvae, young adults, and old adults) showed the same response for all groups tested. Two mutant C. elegans with morphological defects in the cephalic chemosensilla showed the same inhibition of chemotactic response after exposure to Con A, and rapidly resumed normal behavior after competitive displacement of the lectin. Limulin and Con A did not affect nematode growth, development, or longevity, demonstrating that the observed results were not attributable to toxic effects. These results and other experimental evidence support the premise that behavioral modification was caused by functional impairments caused by Con A and limulin to chemoreceptors located on sensory dendrites of the cephalic sensilla. ------------------- Key: 754 Medline: Authors: Hosono R;Kuno S Title: Properties of the unc-52 gene and its related mutations in the nematode C. elegans. Citation: Zoological Science 2: 81-88 1985 Type: ARTICLE Genes: lin-7 unc-52 unc-54 cnDp1 Abstract: The mutations in the unc-52 gene show a stage-dependent uncoordinated (Unc) phenotype and belong to either severely or mildly paralyzed Unc. One recessive allele (cn10) of the unc-52 gene, belonging to one of the most severely paralyzed group, and its revertans are depicted. Isolated as a revertant of the severe allele, unc-52 (cn10) cnDp1 (f) produces two types of progeny; parental severe-type and recovered mild-type Unc. Genetic evidence is presented showing that the property of cnDp1 is brought about by the presence (i.e., mild type) or absence (i.e., severe type) of the free chromosomal fragment containing the unc-52 (cn10) gene. Based on the properties of the strain containing cn Dp1 (f), the role of the unc-52 gene is ------------------- Key: 755 Medline: 85166210 Authors: Eide D;Anderson P Title: Transposition of Tc1 in the nematode C. elegans. Citation: Proceedings of the National Academy of Sciences USA 82: 1756-1760 1985 Type: ARTICLE Genes: unc-15 unc-54 unc-105 Abstract: We have identified a strain of Caenorhabditis elegans in which the transposable element Tc1 is genetically active. Most spontaneous mutations affecting the unc-54 myosin heavy chain gene of C. elegans variety Bergerac are due to insertions of Tc1 within unc-54. The Bergerac genome contains an unusually high number of Tc1 elements, but this is not responsible for transpositional activity. Another variety of C. elegans, strain DH424, contains an equally high number of Tc1 elements, but transpositions are not detected. Tc1 insertion mutations are genetically unstable. They revert to unc-54+ in both germ-line and somatic cells. Germ-line revertants are wild type and contain precise or nearly precise excisions of Tc1. Somatic revertants are genetic mosaics; they contain small patches of revertant muscle tissue in otherwise mutant animals. The pattern of mosaicism often allows us to know when and where during muscle development the excisions occur. Somatic reversion can be over 1000- fold more frequent than germ-line reversion. ------------------- Key: 756 Medline: 85133850 Authors: Okamoto H;Thomson JN Title: Monoclonal antibodies which distinguish certain classes of neuronal and support cells in the nervous tissue of the nematode C. elegans. Citation: Journal of Neuroscience 5: 643-653 1985 Type: ARTICLE Genes: ced-3 Abstract: Monoclonal antibodies were generated using mice immunized with total homogenates of Caenorhabditis elegans adults or early larvae. Two of them were shown to distinguish a certain class of neuronal or supporting cells in the nervous tissue of this animal. Their histological specificities were studied in detail by indirect immunofluorescence on a whole mount preparation of animal head (or tail); for one of the antibodies further analysis was done by immunoelectron microscopy with the aid of a colloidal gold probe. An application of this antibody to a mutant of C. elegans is also described. ------------------- Key: 757 Medline: 85187377 Authors: Lozano R;Lusby WR;Chitwood DJ;Thompson MJ;Svoboda JA Title: Inhibition of C-28 and C-29 phytosterol metabolism by N, N-dimethyldodecanamine in the nematode C. elegans. Citation: Lipids 20: 158-166 1985 Type: ARTICLE Genes: Abstract: Effects on the metabolism of campesterol and stigmasterol in Caenorhabditis elegans were investigated using N,N- dimethyldodecanamine, a known inhibitor of growth, reproduction and the delta 24-sterol reductase of this nematode. 7-Dehydrocholesterol was the predominant sterol (51%) of C. elegans grown in stigmasterol- supplemented media, whereas addition of 25 ppm amine resulted in a large decrease in the relative percentage of 7-dehydrocholesterol (23%) and the accumulation of a substantial proportion (33%) of delta 24-sterols (e.g., cholesta-5,7,24-trienol) and delta 22,24-sterols (e.g., cholesta-5,7,22, 24-tetraenol) but yielded no delta 22- sterols. Dealkylation of stigmasterol by C. elegans proceeded in the presence of the delta 22-bond; reduction of the delta 22-bond occurred prior to delta 24-reduction. Addition of 25 ppm amine to campesterol-supplemented media altered the sterol composition of C. elegans by increasing the percentage of unmetabolized dietary campesterol from 39 to 60%, decreasing the percentage of 7- dehydrocholesterol from 26 to 12%, and causing the accumulation of several delta 24-sterols (6%). C. elegans also was shown to be capable of dealkylating a delta 24 (28)-sterol as it converted 24- methylenecholesterol to mostly 7-dehydrocholesterol. The proposed role of 24-methylenecholesterol as an intermediate between campesterol and 7-dehydrocholesterol was supported by the ------------------- Key: 758 Medline: Authors: Johnson TE Title: Analysis of the biological basis of aging in the nematode with special emphasis on C. elegans. Citation: "Invertebrate Models in Aging Research." Mitchell DH and Johnson TE (eds), CRC Press, Boca Raton, FL. : 59-93 1983 Type: REVIEW Genes: dpy-8 her-1 lon-2 unc-2 unc-15 unc-20 unc-54 unc-78 Abstract: In the preparation of this review, I have made the basic assumption that the desire of the reader is to understand the biological basis of organismic aging. Given this premise, the organism of choice should be one that offers the most immediate hope of arriving at such an understanding. An ideal organism should have a short lifespan; be inexpensive to maintain; be experimentally malleable by a variety of techniques including molecular, morphological, genetic, and biological approaches; and be the object of study in a sufficient number of different laboratories to assure the accumulation of a critical mass of data. The nematode, Caenorhabditis elegans, admirably fulfills all of these basic requirememts. Researchers in the field of aging are faced with a large number of different theories which purport to explain the molecular basis of organismic aging. There are two major reasons for this proliferation of theoretical views. First, aging is an extremely complex phenomenon involving changes in a number of different physiological systems; these physiological changes are often detected, but proof that any one of the changes is responsible for aging is lacking. Second, the focus of a great deal of the research in the field has not been so much on understanding the biological basis of the entire aging process as on understanding one or another of the consequences of this process, particularly in humans and other mammals. The mammalian model systems may often be quite inappropriate for addressing the more basic, long-term questions about the ------------------- Key: 759 Medline: Authors: Klass M Title: Cell-specific gene expression in C. elegans. Citation: "Invertebrate Models in Aging Research." Mitchell DH and Johnson TE (eds), CRC Press, Boca Raton, FL. : 45-58 1984 Type: REVIEW Genes: Abstract: ------------------- Key: 760 Medline: Authors: Curran J;Baillie DL;Webster JM Title: Use of genomic DNA restriction fragment length differences to identify nematode species. Citation: Parasitology 90: 137-144 1985 Type: ARTICLE Genes: Abstract: Restriction endonuclease digestion of genomic DNA generates DNA fragments of unique size, dependent upon the particular base sequence. Following fractionation by agarose gel electrophoresis, repetitive DNA can be visualized as distinct bands in stained gels and the restriction fragment length of such bands used as diagnostic characters. Restriction fragment length differences were detected between species within the genera Trichinella, Caenorhabditis, Romanomermis, Steinernema (syn. Neoaplectana) and Meloidogyne. This technique provides a new tool for the taxonomist, which is independent of phenotypic variation and it enables the rapid and reliable separation of closely related species. ------------------- Key: 761 Medline: 85124602 Authors: Herman RK;Kari CK Title: Muscle-specific expression of a gene affecting acetylcholinesterase in the nematode C. elegans. Citation: Cell 40: 509-514 1985 Type: ARTICLE Genes: ace-1 ace-2 daf-6 sup-10 unc-3 unc-93 mnDp14 Abstract: We have generated C. elegans animals that carry a duplication as a free chromosome fragment bearing an ace-1+ gene in an otherwise homozygous ace-1 ace-2 genetic background. The single ace-1+ gene in these animals is responsible for coordinated animal movement and acetylcholinesterase activity in the regions of the nerve ring and ventral and dorsal nerve cords, as judged by histochemical assay. We have used other genes on the free duplication whose cell-specific expressions have already been elucidated to identify particular genetic mosaics produced by spontaneous somatic loss of the duplication. The analysis of these mosaics has led us to conclude that the synthesis of acetylcholinesterase by muscle cells is primarily responsible for the coordinated movement conferred by the ace-1+ gene. ------------------- Key: 762 Medline: 85205300 Authors: Ferguson EL;Horvitz HR Title: Identification and characterization of 22 genes that affect the vulval cell lineages of the nematode C. elegans. Citation: Genetics 110: 17-72 1985 Type: ARTICLE Genes: let-23 let-60 lin-1 lin-2 lin-3 lin-4 lin-7 lin-8 lin-9 lin-10 lin-11 lin-12 lin-13 lin-15 lin-17 lin-18 lin-24 lin-25 lin-26 lin-31 lin-33 nT1 Abstract: Ninety-five mutants of the nematode Caenorhabditis elegans altered in the cell lineages of the vulva have been isolated on the basis of their displaying one of two phenotypes, Vulvaless or Multivulva. In Vulvaless mutants, which define 12 genes, no vulva is present. In Multivulva mutants, which define ten genes, one or more supernumerary vulva-like protrusions are located along the ventral side of the animal. A single recessive mutation is responsible for the phenotypes of most, but not all, of these strains. Fifteen of these 22 genes are represented by multiple alleles. We have shown by a variety of genetic criteria that mutations that result in a Vulvaless or Multivulva phenotype in six of the 22 genes most likely eliminate gene function. In addition, Vulvaless or Multivulva mutations in seven of the other genes most likely result in a partial reduction of gene function; the absence of the activity of any of these genes probably results in lethality or sterility. Our results suggest that we may have identified most, or all, genes of these two classes. ------------------- Key: 763 Medline: Authors: Ouazana R;Garrone R;Godet J Title: Characterization of morphological and biochemical defects in the cuticle of a dumpy mutant of C. elegans. Citation: Comparative Biochemistry & Physiology 80B: 481-483 1985 Type: ARTICLE Genes: dpy-5 dpy-15 Abstract: 1. In this paper, we describe morphological and biochemical cuticle defects in a dumpy mutant of Caenorhabditis elegans. 2. This mutant, FF31, exhibits major alterations in internal cuticle architecture when compared to the wild-type strain. 3. SDS-polyacrylamide gel electrophoresis of the soluble cuticle proteins of this mutant also reveals differences when compared to the proteins of the wild-type. 4. To minimize the possibility that the morphological and biochemical defects are caused by different mutations, we have isolated a revertant strain, FF102, with normal body shape after EMS mutagenesis on FF31 larvae and we have shown that the morphological and biochemical defects revert as well. 5. This suggests that all the modifications displayed by this mutant are the ------------------- Key: 764 Medline: Authors: Swanson MM;Edgley ML;Riddle DL Title: The nematode Caenorhabditis elegans. Citation: Genetic Maps 3: 286-299 1984 Type: REVIEW Genes: Abstract: ------------------- Key: 765 Medline: 85159849 Authors: Chalfie M;Sulston JE;White JG;Southgate E;Thomson JN;Brenner S Title: The neural circuit for touch sensitivity in C. elegans. Citation: Journal of Neuroscience 5: 956-964 1985 Type: ARTICLE Genes: Abstract: The neural pathways for touch-induced movement in Caenorhabditis elegans contain six touch receptors, five pairs of interneurons, and 69 motor neurons. The syaptic relationships among these cells have been deduced from reconstructions from serial section electron micrographs, and the roles of the cells were assessed by examining the behavior of animals after selective killing of precursors of the cells by laser microsurgery. This analysis revealed that there are two pathways for touch-mediated movement for anterior touch (through the AVD and AVB interneurons) and a single pathway for posterior touch (via the PVC interneurons). The anterior touch circuitry changes in two ways as the animal matures. First, there is the formation of a neural network of touch cells as the three anterior touch cells become coupled by gap junctions. Second, there is the addition of the AVB pathway to the pre-existing AVD pathway. The touch cells also synapse onto many cells that are probably not involved in the generation of movement. Such synapses suggest that stimulation of these receptors may modify a number of behaviors. ------------------- Key: 766 Medline: 85239914 Authors: Golden JW;Riddle DL Title: A gene affecting production of the C. elegans dauer-inducing pheromone. Citation: Molecular & General Genetics 198: 534-536 1985 Type: ARTICLE Genes: daf-22 Abstract: A nematode mutant lacking pheromone activity does not enter the developmentally arrested dispersal stage called the dauer larva unless exogenous pheromone is added to the growth medium, indicating that the pheromone is required for wild-type dauer larva formation. In contrast, a class of temperature-sensitive mutant forms dauer larvae even in the absence of detectable pheromone, indicating that such mutants bypass the normal pheromone requirement. A rapid bioassay of pheromone produced by individual nematodes has been developed for genetic analysis of pheromone ------------------- Key: 767 Medline: 85201409 Authors: Karn J;Dibb NJ;Miller DM Title: Cloning nematode myosin genes. Citation: "Cell and Muscle Motility." Shay JW (ed), Plenum Press. 6: 185-237 1985 Type: REVIEW Genes: Abstract: ------------------- Key: 768 Medline: 83232892 Authors: Wills N;Gesteland RF;Karn J;Barnett L;Bolten S;Waterston RH Title: The genes sup-7 X and sup-5 III of C. elegans suppress amber nonsense mutations via altered transfer RNA. Citation: Cell 33: 575-583 1983 Type: ARTICLE Genes: sup-5 sup-7 unc-54 Abstract: The sup-5 III and sup-7 X suppressors in C. elegans have previously been shown to have many genetic properties in common with tRNA nonsense suppressors of microorganisms. We report here the results of two lines of investigation into the molecular basis of these suppressors. In one, which sought to determine the nature of suppressible alleles, we demonstrate through DNA sequencing studies that a suppressible allele, unc-54(e 1300) I, of the myosin heavy chain gene contains a C leads to T substitution, which changes a glutamine codon to amber terminator at residue 1903. In the other approach, which sought to define the nature of the suppressing activity, we show through in vitro translation studies that tRNA fractions from the suppressor strains, but not wild-type, promote the specific readthrough of amber terminators of three different messenger RNAs. We conclude that sup-5 and sup-7 result in readthrough of amber terminators in vivo through an altered ------------------- Key: 769 Medline: 85258981 Authors: Brown SJ;Riddle DL Title: Gene interactions affecting muscle organization in C. elegans. Citation: Genetics 110: 421-440 1985 Type: ARTICLE Genes: dpy-10 dpy-17 dpy-18 lon-1 sqt-1 sup-3 sup-19 sus-1 unc-15 unc-82 Abstract: Revertants of unc-15(e73)I, a paralyzed mutant with an altered muscle paramyosin, include six dominant and two recessive intragenic unc-15 revertants, two new alleles of the previously identified suppressor gene, sup-3 V, and a new suppressor designated sup-19(m210)V. The recessive intragenic unc-15 revertants exhibit novel alterations in paramyosin paracrystal structure and distribution, and these alterations are modified by interaction with unc-82(e1220)IV, another mutation that affects paramyosin. A strain containing both unc-15 and a mutation in sup-3 V that restores movement was mutagenized, and paralyzed mutants resembling unc-15 were isolated. Twenty mutations that interfere with suppression were divided into three classes (nonmuscle, sus-1, and mutations within sup-3) based on phenotype, genetic map position and dominance. The nonmuscle mutations include dumpy and uncoordinated types that have no obvious direct effect on muscle organization. Two recessive mutations define a new gene, sus-1 III. These mutations modify the unc-15(e73) phenotype to produce a severely paralyzed, dystrophic double mutant that is not suppressed by sup-3. Five semidominant, intragenic sup-3 antisuppressor mutations, one of which occurred spontaneously, restore the wild-type sup-3 phenotype of nonsuppression. However, reversion of these mutants generated no new suppressor alleles of sup-3, suggesting that the sup-3 antisuppressor alleles are not wild type but ------------------- Key: 770 Medline: Authors: Epstein HF;Ortiz I;Berliner GC;Miller DM III Title: Nematode thick-filament structure and assembly. Citation: "Molecular Biology of the Cytoskeleton." Borisy G, Cleveland D and Murphy D (eds), Cold Spring Harbor Laboratory. : 275-286 1985 Type: REVIEW Genes: Abstract: Myosins from slime molds to brain cells show a remarkable commonality of general molecular properties. These characteristics include two globular domains or heads that contain ATPase and actin-binding sites and the fibrous, coiled-coil a-helical rod that interacts with other molecules in assembly. Two heavy chains (m.w. 200,000) contribute to both heads, whereas two kinds of light chains bind to each head. In this paper, we consider striated muscles and their myosins. The phylogenetically distant nematode body-wall muscles and rabbit fast skeletal muscles produce myosin heavy chains, with about 47% of the amino acid sequences in the heads and 37% of the amino acids in the rod being identical (Karn et al. 1984). Myosin heavy chains are therefore highly conserved proteins. Contrasting with the phylogenetic conservation of myosin structure and sequence is the diversity of supramolecular arrangements of myosin assemblies in striated muscles, the so-called thick filaments. The lengths of thick filaments range from 1.55 um in vertebrates, 2-4 um in insect flight muscles, 10 um in the nematode to 40 um in certain mollusks. The average diameters of these filaments range from about 15 nm in vertebrates, 20 nm in insects, 25 nm in nematodes to 50-100 nm in some molluscan muscles. The surface arrangements of the myosin heads also vary in these different species. The lattice arrangements between thick filaments and the interdigitating, actin-containing thin filaments differ in terms of symmetry and thick:thin stoichiometry between these muscles. It appears likely that other protein components of these muscles interact with the very similar myosins to produce this structural diversity. The relatively subtle differences between myosin isoforms may also be important in these interactions. We define isoform in the case of myosin, for example, as a protein that is defined as a myosin by biochemical criteria but that can be distinguished on the basis of intrinsic molecular structure from another myosin within the same organism. In this paper, we describe experiments suggesting that two genetically different isoforms of myosin play distinct roles in concert with other proteins during the assembly of thick filaments in ------------------- Key: 771 Medline: 85131340 Authors: Epstein HF;Miller DM III;Ortiz I;Berliner GC Title: Myosin and paramyosin are organized about a newly identified core structure. Citation: Journal of Cell Biology 100: 904-915 1985 Type: ARTICLE Genes: Abstract: Myosin isoforms A and B are differentially localized to the central and polar regions, respectively, of thick filaments in body wall muscle cells of Caenorhabditis elegans (Miller, D.M. III, I. Ortiz, G.C. Berliner, and H.F. Epstein, 1983, Cell, 34: 477-490). Biochemical and electron microscope studies of KCl-dissociated filaments show that the myosin isoforms occupy a surface domain, paramyosin constitutes an intermediate domain, and a newly identified core structure exists. The diameters of the thick filaments vary significantly from 33.4 nm centrally to 14.0 nm near the ends. The latter value is comparable to the 15.2 nm diameter of the core structures. The internal density of the filament core appears solid medially and hollow at the poles. The differentiation of thick filament structure into supramolecular domains possessing specific substructures of characteristic stabilities suggests a sequential mode for thick filament assembly. In this model, the two myosin isoforms have distinct roles in assembly. The behavior of the myosins, including nucleation of assembly and determination of filament length, depend upon paramyosin and the core structure as well as their intrinsic molecular properties. ------------------- Key: 772 Medline: 85295957 Authors: Russnak RH;Candido EPM Title: Locus encoding a family of small heat-shock genes in C. elegans: Two genes duplicated to form a 3.8-kilobase inverted repeat. Citation: Molecular and Cellular Biology 5: 1268-1278 1985 Type: ARTICLE Genes: Abstract: The genes coding for hsp 16-48, previously identified by cDNA cloning, and for another 16-kilodalton heat shock protein designated hsp16-1 were characterized by DNA sequencing. The two genes were arranged in a head-to-head orientation. Both the coding and flanking regions were located within a 1.9-kilobase module which was duplicated exactly to form a 3.8-kilobase inverted repeat structure. The inverted repeat structure ended in an unusual guanine-plus- cytosine-rich sequence 24 nucleotides in length. The identity of the two modules at the nucleotide sequence level implies that the duplication event may have occurred recently. Alternatively, gene conversion between the two modules could also maintain homology of the two gene pairs. The small heat shock genes of Caenorhabditis elegans contained TATA boxes and heat-inducible promoters, the latter agreeing closely with the Drosophila melanogaster consensus sequence described by Pelham (Cell 30:517-528, 1982). Unlike the homologous D. melanogaster genes, each of these C. elegans genes contained a short intron, the position of which has been conserved in a related murine alpha-crystallin gene. The intron separated variable and conserved regions within the amino acid sequences of the encoded heat shock polypeptides. ------------------- Key: 773 Medline: 85223144 Authors: Morgan PG;Cascorbi HF Title: Effect of anesthetics and a convulsant on normal and mutant C. elegans. Citation: Anesthesiology 62: 738-744 1985 Type: ARTICLE Genes: Abstract: The authors have developed a method for studying the action of volatile anesthetics in Caenorhabditis elegans (C.e.), a free living nematode. C.e. appears to be a useful model for the study of the influence of genetics on susceptibility to anesthetics. This worm has a small, completely defined nervous system, easily manipulated genetics, and a large number of nervous system mutants. Under normal conditions C.e. moves almost constantly. When exposed to anesthetics there is an initial phase of increased locomotion, followed by uncoordinated motion that progresses to immobility. Motion returns quickly when the nematodes are removed from the anesthetic. The authors called loss of locomotion "anesthesia." The ED50S of various anesthetics with C.e. are as follows: methoxyflurane 0.45%, chloroform 1.25%, halothane 2.7%, enflurane 4.2%, isoflurane 5.6%, fluroxene 9.9%. The authors also studied the action of a convulsant, flurothyl, on C.e. Flurothyl has anesthetizing properties in these animals with an ED50 of 8.1%. No convulsant activity was noted. However, mixtures of halothane and flurothyl were antagonistic in their effects, while halothane and enflurane were additive. Furthermore, the authors isolated a mutant strain (HS1) of C.e. that shows altered responses to several anesthetics and a convulsant. HS1 is uncoordinated when not exposed to anesthetics. Like the normal strain (N2) HS1 loses mobility when exposed to anesthetics. The ED50S for various anesthetics in HS1 were as follows: methoxyflurane 0.04%, chloroform 0.52%, halothane 0.85%, isoflurane 4.9%, enflurane 6.0%, fluroxene 10.9%.(ABSTRACT TRUNCATED AT 250 WORDS) ------------------- Key: 774 Medline: 85243050 Authors: Burr AH Title: The photomovement of C. elegans, a nematode which lacks ocelli. Proof that the response is to light not radiant heating. Citation: Photochemistry and Photobiology 41: 577-582 1985 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans adults were tested at constant temperature with 10 s periods of monochromatic light alternated with 20 s dark periods. Stimuli at effective intensities and wavelengths caused an increase in the frequency of ecclitic (phobic, avoidance) responses, which was measured as an increase in the probability of a temporary reversal in direction of movement. For monochromatic stimuli ranging from 420 to 680 nm at a constant 56 picoeinsteins s-1 cm-2, only those at 520-600 nm elicited significant responses. At 540 nm the threshold fluence rate was approximately 30 pE s-1 cm-2. At saturating intensities the mean reversal probability was increased to 0.20 in 10 s from a background level of 0.12, approximately. Because C. elegans lacks ocelli and is very sensitive to temperature, possible sources of radiant heating were considered in detail, including (a) infrared present in the stimuli, (b) absorption of light by the arena, and (c) absorption of light by a nematode pigment. All possible sources were found to cause a negligible temperature rise, on the order of or less than the natural temperature fluctuations inside the worm, 1.5 X 10-6 C. A 2 X 10-4 C temperature rise produced by a 1230 nm infrared stimulus had no significant effect on reversal frequency. It was concluded that the response to illumination must have been to light, and not to temperature changes. Large, + or - 2 C changes from the acclimation temperature caused significant increases in the background frequency of ecclitic responses (a thermoecclisis or thermoklinokinesis). However, neither the threshold nor the saturation level of light-induced responses was ------------------- Key: 775 Medline: 85216652 Authors: Stinchcomb DT;Mello C;Hirsh D Title: C. elegans DNA that directs segregation in yeast cells. Citation: Proceedings of the National Academy of Sciences USA 82: 4167-4171 1985 Type: ARTICLE Genes: Abstract: We have isolated seven DNA fragments from Caenorhabditis elegans that enhance the mitotic segregation of autonomously replicating plasmids in the yeast Saccharomyces cerevisiae. These segregators, designated SEG1-SEG7, behave like isolated yeast chromosomes: they increase the stability and simultaneously lower the copy number of circular plasmids during mitotic growth in yeast. During meiosis, plasmids containing the C. elegans segregators show higher levels of precocious or aberrant disjunction than do plasmids bearing isolated yeast centromeres. Yet one of the segregators improved the meiotic segregation of the parental plasmid. We estimate that there may be as many as 30 segregator sequences in the C. elegans genome, a value that is consistent with the polycentric nature of C. elegans chromosomes. Five of the seven segregators are linked to sequences that are repeated in the worm genome, and four of these five segregators cross-hybridize. Other members of this family of repetitive DNA do not contain segregator function. Segregator sequences may prove useful for probing the structure of centromeres of both C. elegans and S. cerevisiae ------------------- Key: 776 Medline: 85204208 Authors: Jameel S;McFadden BA Title: C. elegans: Purification of isocitrate lyase and the isolation and cell-free translation of poly(A+)RNA. Citation: Experimental Parasitology 59: 337-346 1985 Type: ARTICLE Genes: Abstract: Isocitrate lyase (EC 4.1.3.1) from mixed larval populations of Caenorhabditis elegans was stabilized in crude extracts by centrifugation over a 0.2-0.6 M sucrose gradient for 2.5 hr in a vertical rotor (VTi 50) at 210,000g. The peak fractions from this sucrose gradient showed a half-life of 33 hr at 30 C and 225 hr at 4 C in contrast to 2.5 and 52 hr, respectively, for the crude extract. A purification scheme involving (NH4)2SO4 precipitation and chromatography on Sepharose 6B and diethylaminoethyl-cellulose yielded isocitrate lyase that gave one band after electrophoresis in a sodium dodecyl sulfate-gel polymerized from 12% acrylamide. The purified enzyme with a molecular weight of 250,000 and subunit molecular weight of 61,600, had a specific activity of 2 mumoles glyoxylate formed min-1 mg protein-1, and was obtained in a 4% yield. Isocitrate lyase from C. elegans lost 80-85% of its activity in the precipitation by 33-55% (NH4)2SO4, but this step appeared to be necessary for purification to homogeneity. The use of fast protein liquid chromatography appeared to be promising in that it provided an enzyme preparation that was about 50% pure with a specific activity as high as 3 mumoles glyoxylate formed min-1 mg protein-1. Poly(A+)RNA was isolated from C. elegans and translated in wheat germ cell-free system. Analysis on a 10% sodium dodecyl sulfate- polyacrylamide gel showed varied translation products including one or more 60,000-Da polypeptides. ------------------- Key: 777 Medline: Authors: Schierenberg E;Carlson C;Sidio W Title: Cellular development of a nematode: 3-D computer reconstruction of living embryos. Citation: Roux's Archives of Developmental Biology 194: 61-68 1985 Type: ARTICLE Genes: Abstract: Embryos of the free-living soil nematode Caenorhabditis elegans are capable of developing normally outside the mother; we have monitered this process in isolated embryos by light microscopy and recorded it on video tape. The size and position of each nucleus were entered into a computer at short time intervals from the 2- to 102-cell stages. Models were reconstructed in which nuclei are represented by spheres and assigned different colors and patterns according to lineage membership. Three-dimensional reconstructions aid visualization of the spatial arrangement of nuclei and demonstrate the small degree of positional variance among individuals. The dynamic processes of nuclear growth during the cell cycle, division, migration, and pattern formation can be quantitatively analyzed. Our knowledge of the complete embryonic lineage allows the correlation of nuclear ------------------- Key: 778 Medline: Authors: Meheus L;Vanfleteren JR Title: Nematode chromosomal proteins - IV. The nonhistones of C. elegans. Citation: Comparative Biochemistry & Physiology 81B: 377-383 1985 Type: ARTICLE Genes: Abstract: 1. A method has been developed which yields reasonably clean nuclei from the free-living nematode Caenorhabditis elegans. Nonhistones were prepared from these nuclei by gentle extraction with 2 M NaCl and analyzed by one- and two-dimensional electrophoresis using a nonequilibrium pH gradient electrophoresis in the first dimension after removal of nucleic acids by phenol extraction. 2. The extraction procedure yielded nonhistone chromatin proteins and proteins associated with nuclear RNA and a background of polypeptides derived from the nuclear matrix and pore-lamina complex. 3. Over 40 polypeptides were distinguished on silver stained one-dimensional slab gels. 4. The presence of actin, tropomyosin and tubulin was demonstrated by immunoprobing after transfer of the polypeptides to nitrocellulose. 5. Bands co-migrating with myosin and a-actinin gave no specific reaction when probed with antibodies raised against the respective proteins from vertebrate tissues. 6. Over 200 spots were visible on two-dimensional gels stained with silver nitrate. ------------------- Key: 779 Medline: 85264809 Authors: Dibb NJ;Brown DM;Karn J;Moerman DG;Bolten SL;Waterston RH Title: Sequence analysis of mutations that affect the synthesis, assembly and enzymatic activity of unc-54 myosin heavy chain of C. elegans. Citation: Journal of Molecular Biology 183: 543-551 1985 Type: ARTICLE Genes: unc-54 Abstract: We have sequenced 11 representative mutations of the unc-54 myosin heavy chain gene of Caenorhabditis elegans that affect the synthesis, assembly or enzymatic activity of the encoded myosin heavy chain. Six of the sequenced unc-54 mutations cause premature termination of protein synthesis. Four mutations (e1092, e1115, e1213, e1328) were ochre mutations, one mutation (e903) was a frameshift, which caused premature termination at a nearby UGA terminator, and one mutation (e190) was a deletion that altered the reading frame and caused termination at an ochre codon. Two mutations (e675 and s291) were inphase deletions, which resulted in a shortened myosin rod segment. These aberrant myosins fail to assemble into normal thick filaments. The sequence alterations of the missense mutations (e1152, s74, s95) indicated amino acid residues that are critical for myosin function. The mutation e1152 causes the production of a myosin heavy chain that fails to assemble into thick filaments. It had two adjacent amino acid substitutions at the extreme amino terminus of the rod, indicating a role for subfragment-2 in thick filament assembly. Mutants homozygous for s74 or s95 are very slow-moving, although they make myosin heavy chains that assemble normally. The encoded amino acid substitutions of s95 and s74 are in the 23 X 10(3) Mr and 50 X 10(3) Mr domains of the myosin head, flanking the ATP binding site. The sequenced mutations are distributed throughout the gene in the order predicted from genetic fine-structure mapping experiments. Seven of eight point mutations isolated following ethylmethane sulphonate mutagenesis were G X C to A X T transitions. A single X- ray-induced allele proved to be a deletion of two adjacent thymidine residues. The three deletion mutations were found in a region of the myosin rod with numerous direct and inverted nucleotide sequence repeats, but their origin cannot be accounted for by homologous recombination. Instead, a comparison of the deletion junctions suggests that the deletions arose by a site-specific mechanism. ------------------- Key: 780 Medline: 85234504 Authors: Sanford T;Prenger JP;Golomb M Title: Purification and immunological analysis of RNA polymerase II from C. elegans. Citation: Journal of Biological Chemistry 260: 8064-8069 1985 Type: ARTICLE Genes: ama-1 Abstract: We describe a rapid procedure for obtaining highly purified RNA polymerase II from the nematode Caenorhabditis elegans. The structure of the enzyme was examined by denaturing gel electrophoresis and found to consist of three large polypeptides (molecular weights 200,000, 175,000, and 135,000) and eight smaller polypeptides (molecular weights 29,500, 20,000, 16,000, 15,000, 13,000, 11,500, 10,500, and 9,500). As observed for the analogous enzyme from other organisms, the 175,000 polypeptide (II175) appeared to be a degraded form of the 200,000 polypeptide (II200). The structure of nematode RNA polymerase II closely resembles that of the corresponding enzyme from other animals. Four of its larger subunits shared antigenicity with Drosophila RNA polymerase II. Antibody raised against purified RNA polymerase II reacted with several enzyme subunits in "Western" blots of purified polymerase and impure enzyme fractions. Immunofluorescence staining was used to visualize RNA polymerase II in the nuclei of a nematode squash preparation and the nucleoplasm of cultured ------------------- Key: 781 Medline: 85266434 Authors: Johnson TE;McCaffrey G Title: Programmed aging or error catastrophe? An examination by two-dimensional polyacrylamide gel electrophoresis. Citation: Mechanisms of Ageing & Development 30: 285-297 1985 Type: ARTICLE Genes: fer-15 Abstract: We have examined newly synthesized proteins in the young adult and in older populations of the nematode Caenorhabditis elegans using two- dimensional polyacrylamide gel electrophoresis (2D PAGE). A temperature-sensitive mutant strain, DH26, with a mean life span of about 15 days, under our conditions, was used to block progeny development. Nematodes of several different ages were pulse-labeled for 5 h, in vivo, with 35S-labeled E. coli, A subsequent 30-min chase with unlabeled E. coli served to rid the worms of endogenous labeled E. coli proteins. We resolve 700 or more proteins by 2D PAGE polyacrylamide gel electrophoresis of extracts of young nematodes. The patterns of these proteins are highly reproducible in comparisons of independent repeats of identical experiments. No new major proteins are synthesized at any time during the adult phase (4-22 days) nor are any of the most abundant proteins not made during this period. At our level of detectability (estimated as a satellite spot containing 4% of the amount of label in a major spot) we see no misincorporation of radioactive amino acids into newly synthesized proteins. These data are inconsistent with predictions by any one of several, so called, "error catastrophe" models of senescence and also show that modulation of the highest abundancy classes of ------------------- Key: 782 Medline: 85228243 Authors: Cowan AE;McIntosh JR Title: Mapping the distribution of differentiation potential for intestine, muscle, and hypodermis during early development in C. elegans. Citation: Cell 41: 923-932 1985 Type: ARTICLE Genes: Abstract: We have analyzed the differentiation potential of cells in early embryos of Caenorhabditis elegans by assessing the production of markers for intestinal, muscle, and hypodermal cell differentiation in cleavage-arrested blastomeres. Our results show that differentiation potential does not always segregate during cleavage in a linear fashion, i.e., a blastomere can express a differentiation potential that is absent in its parent blastomere and vice versa. Furthermore, the expression of a particular differentiation program by certain cleavage-arrested blastomeres is an exclusive event in that each cell will express only one program of differentiation, even though it may have the potential to express several. ------------------- Key: 783 Medline: 85269643 Authors: Spieth J;Denison K;Kirtland S;Cane J;Blumenthal T Title: The C. elegans vitellogenin genes: short sequence repeats in the promoter regions and homology to the vertebrate Citation: Nucleic Acids Research 13: 5283-5295 1985 Type: ARTICLE Genes: vit-1 vit-2 vit-3 vit-4 vit-5 vit-6 Abstract: The nematode Caenorhabditis elegans contains a small family of vitellogenin genes which is expressed abundantly, but only in the intestine of the adult hermaphrodite worm. In order to identify possible regulatory elements, we have sequenced the DNA surrounding the 5' ends of five of the six genes. Contained within regions which have largely diverged from one another, two different heptameric sequences are found repeated within the first 200 bp upstream of each of the genes. The first sequence, TGTCAAT, is present as a perfect heptamer at least once upstream of each gene. It is repeated in both orientations four to six times in each 5' flanking region, allowing a one-base mismatch. The second sequence, CTGATAA, is also present as a perfect heptamer in a restricted region upstream of each gene. These two sequence elements may be involved in regulation of the vitellogenin genes. Remarkably, the CTGATAA sequence is present in a similar location in the promoter regions of vertebrate vitellogenin genes. In fact, our data reveal a surprising degree of similarity between the nematode and vertebrate vitellogenins. ------------------- Key: 784 Medline: 85281823 Authors: Baillie DL;Beckenbach KA;Rose AM Title: Cloning within the unc-43 to unc-31 interval (LGIV) of the C. elegans genome using Tc1 linkage selection. Citation: Canadian Journal of Genetics & Cytology 27: 457-466 1985 Type: ARTICLE Genes: unc-22 unc-31 unc-43 Abstract: The region around the twitcher gene, unc-22, flanked by unc-43 on the left and by unc-31 on the right, has been intensively studied in our laboratory over the period of the last 8 years. In this paper we describe the identification and isolation of probes specific for several restriction fragment length differences (RFLDs) which lie within this region. Many RFLDs in Caenorhabditis elegans are caused by the insertion of a transposable element, Tc1. The method we used involved the isolation of Tc1-containing genomic fragments. These were recovered from a lambda gt 10 library of DNA from a specially constructed genetic strain containing the unc-43 to unc-31 interval from the BO strain and the rest of the genome from N2. Because the BO strain is rich in Tc1 insertion sites and the N2 strain has few, the majority of Tc1-bearing genomic fragments in the constructed strain were derived from the unc-22 region. Of nine such Tc1-bearing genomic fragments isolated, six were found which mapped within the region of interest. The 350 kilobases of genomic sequences isolated as a result of these studies are being used to study the molecular organization of this region. The method described here for Tc1 linkage selection is one that is rapid, general, and may be targeted to any genetically characterized region of ------------------- Key: 785 Medline: Authors: Waterston RH;Francis GR Title: Genetic analysis of muscle development in C. elegans. Citation: Trends in Neurosciences 8: 270-276 1985 Type: REVIEW Genes: act-1 act-3 myo-3 sup-3 unc-15 unc-45 unc-54 unc-82 unc-87 Abstract: In Caenorhabditis elegans, mutations in about 25 genes are known to alter the normal lattice structure of nematode muscle, and several of these genes have been shown to encode specific contractile proteins including a myosin heavy chain, paramyosin, and actins. These assignments have served as the basis for further genetic, molecular, and ultrastructural studies of the expression of these genes and the roles of their products in muscle assembly and function. These studies are reviewed here, and discussed in the context of the mechanisms directing the assembly of the contractile apparatus during muscle differentiation and growth. ------------------- Key: 786 Medline: Authors: White JG Title: Neuronal connectivity in C. elegans. Citation: Trends in Neurosciences 8: 277-283 1985 Type: REVIEW Genes: Abstract: The connectivity of all the 302 neurones that make up the nervous system of Caenorhabditis elegans has been deduced from reconstructions of electron micrographs of serial sections. The nervous system is arranged as a collection of bundles of parallel processes. Within these bundles the relatively unbranched processes of neurones run in defined locations making en passant synapses to their neighbours. The low level of mixing within process bundles has the consequence that a given process runs in a restricted neighbourhood and has only relatively few potential synaptic partners. Neurones make synaptic contacts with many of these potential partners however. There is some evidence that neurones will still behave in this way regardless of what neighbourhood they happen to be in. The highly locally connected arrangement of the nervous sytem has consequences for the synaptic circuitry, in that the formation of triangular sub-circuits is favoured. The placement of processes into specific neighbourhoods is therefore a major determinant of connectivity. Placement seems to be achieved both by cell lineage mechanisms, which place specific neurones in appropriate locations, and by the selective fasciculation of outgrowing processes to neighbours with high adhesive affinities. ------------------- Key: 787 Medline: Authors: Hedgecock EM Title: Cell lineage mutants in the nematode C. elegans. Citation: Trends in Neurosciences 8: 288-293 1985 Type: REVIEW Genes: ced-3 ced-4 lin-12 lin-14 lin-17 lin-20 lin-22 tra-1 unc-86 Abstract: Nematodes develop by invariant cell lineages. In many cell lineage mutants, specific precursor cells duplicate sublineages normally made elsewhere in the animal. From such mutants, we can infer how different cell types may be specified in normal development. ------------------- Key: 788 Medline: 86036037 Authors: Hosono R;Kuno S;Midsukami M Title: Temperature-sensitive mutations causing reversible paralysis in C. elegans. Citation: Journal of Experimental Zoology 235: 409-421 1985 Type: ARTICLE Genes: cha-1 mah-2 Abstract: A method has been developed for the isolation of temperature- dependent paralytic mutants of the nematode Caenorhabditis elegans, based on a screening procedure using short-time exposure to 30 degrees C. Of ten mutants isolated, eight lose their motilities between 30 degrees C and 33 degrees C without prominent changes in body forms. The other two strains that are mainly described in this report are accompanied by alterations in body forms. One mutation, cn101, is recessive and an allele of cha-1. The cn101 mutant shows reversible paralysis at 30 degrees, accompanied by a hypercontracted and coiled body form. At the restrictive temperature, the strain is resistant to all tested inhibitors of acetylcholinesterase (AChE). Another mutation, designated mah-2 (cn110), is a sex-linked semidominant that is mapped as 0.6 map units left of dpy-6. The cn110 mutant is rapidly paralyzed at the restrictive temperature and has a straight and rigid body form; the mutant rapidly recovers when the temperature is lowered. No disorganization of the muscle structure was detected by polarized light and electron microscopic inspection. ------------------- Key: 789 Medline: 86001974 Authors: Rose AM;Harris LJ;Mawji NR;Morris WJ Title: Tc1(Hin): a form of the transposable element Tc1 in C. elegans. Citation: Canadian Journal of Biochemistry & Cell Biology 63: 752-756 1985 Type: ARTICLE Genes: Abstract: In this paper we describe the coexistence of two forms of the transposable element Tc1 in the genome of the nematode Caenorhabditis elegans. A copy of the variant form has been isolated from the Bergerac genome and characterized. Restriction mapping and DNA sequencing have shown that a G to T transversion generated a HindIII restriction site to form the variant Tc1(Hin). The presence of this new restriction site makes this variant easily detectable on genomic blot hybridizations. There are approximately 20 copies of Tc1(Hin) amongst the Tc1's present in the Bergerac genome. Bergerac has approximately 250 copies of Tc1 per genome, whereas Bristol has about 30. In the Bristol strain we detected at least one copy Tc1(Hin). The ratio of Tc1(Hin) to total Tc1's is similar in the genomes of Bristol and Bergerac, even though they have markedly different total numbers of Tc1. Our results suggest that a trans-acting change in either the elements or the host genome was responsible for the expansion of Tc1 copy number in the Bergerac genome. ------------------- Key: 790 Medline: 85299178 Authors: Rand JB;Russell RL Title: Molecular basis of drug-resistance mutations in C. elegans. Citation: Psychopharmacology Bulletin 21: 623-630 1985 Type: REVIEW Genes: cha-1 unc-11 unc-13 unc-17 unc-18 unc-29 unc-32 unc-36 unc-63 unc-64 unc-65 unc-102 Abstract: Historically, most knowledge about neurvous system function has been derived from experiments in which the nervous system or one of its components is specifically disrupted, and any resulting functional alteration is analyzed. In all cases, the hope has been that by analysis of the altered function, inferences could be drawn concerning the mechanisms of normal neural function. The traditional methods of creating such perturbations have been through surgical intervention and through the use of drugs to inhibit or mimic the function of interest. In recent years, another method has been developed for analysis of the nervous system: the use of specific mutations to alter particular biochemical or cellular functions. Since different types of perturbations have different relative advantages and suffer from different sets of constraints, a combination of genetic and pharmacological analysis together can be more powerful than either approach by itself. In principle, genetic analysis and pharmacology can be combined in three different ways: a) by using mutations and/or genetic variants to investigate the mechanisms of drug action; b) by using drugs to analyze specific mutations; and c) by using drugs and mutations together to help understand nervous system function.... ------------------- Key: 791 Medline: 86005017 Authors: Tomlinson G;Albuquerque CA;Woods RA Title: The effects of amidantel (Bay d 8815) and its deacylated derivative (Bay d 9216) on C. elegans. Citation: European Journal of Pharmacology 113: 255-262 1985 Type: ARTICLE Genes: Abstract: The paralyzing effects of the anthelmintic drugs amidantel (BAY d 8815) and its deacylated derivative (BAY d 9216) on whole and cut C. elegans were investigated. The minimum effective concentrations with whole worms were 350 and 180 microM, respectively, compared to only 4 microM for another anthelmintic drug, levamisole. After rendering the worms permeable by cutting them at their approximate midsections, the minimum effective concentrations were: amidantel 0.30 microM, deacylated amidantel 0.07 microM and levamisole 0.15 microM. Comparison of the effects produced by amidantel and deacylated amidantel with those produced by levamisole, a known cholinergic agonist, suggested a common mode of action for all three drugs. The drugs were moderately potent inhibitors of both E. electricus and C. elegans acetylcholinesterase but at concentrations too high to account for their abilities to contract cut worms. Their primary mode of action appears to be as agonists at the level of the acetylcholine receptor, a view supported by the observation that their effects may be blocked by the nicotinic antagonists d-tubocurarine and gallamine. ------------------- Key: 792 Medline: 85286029 Authors: Edgar LG;Hirsh D Title: Use of a psoralen-induced phenocopy to study genes controlling spermatogenesis in Caenorhabditis elegans. Citation: Developmental Biology 111: 108-118 1985 Type: ARTICLE Genes: fem-1 fem-2 Abstract: In the nematode Caenorhabditis elegans, spermatogenesis represents one of two alternative developmental pathways open to premeiotic germ cells. At least two genes, fem-1 and fem-2, control the initiation of spermatogenesis in XX (hermaphrodite) worms, and the entire spectrum of male differentiation in XO animals. Low-dose irradiation of worms treated with the light-activated DNA crosslinking drug trimethylpsoralen, at levels that do not affect cell division or growth rates, blocks spermatogenesis in C. elegans hermaphrodites and produces an identical phenotype to that of temperature-sensitive mutations in the fem genes. Psoralen treatment does not, however, produce corresponding phenotypes of these mutants in XO animals. The developmental age for phenocopy production is the same as the hermaphrodite temperature-sensitive period of the two mutants. The effects of pulses of restrictive temperature and psoralen treatment on fem-2 mutant hermaphrodites are additive, suggesting that psoralen crosslinking may reduce the level of the fem-2 gene product. Microbeam experiments localize the target for the psoralen effect to the primary germ cells in the first stage larvae, indicating that a critical step occurs in a small number of precursor cells prior to their commitment ------------------- Key: 793 Medline: 85286032 Authors: Hedgecock EM;Culotti JG;Thomson JN;Perkins LA Title: Axonal guidance mutants of Caenorhabditis elegans identified by filling sensory neurons with fluorescein Citation: Developmental Biology 111: 158-170 1985 Type: ARTICLE Genes: cat-6 che-14 unc-6 unc-33 unc-44 unc-51 unc-76 Abstract: Eight pairs of chemosensory neurons in Caenorhabditis elegans take up fluorescein dyes entering through the chemosensory organs. These are amphid neurons ADF, ASH, ASI, ASJ, ASK, and ADL and phasmid neurons PHA and PHB. When filled with dye, the processes and cell bodies of these neurons can be examined in live animals by fluorescence microscopy. Using this technique, we have identified five genes, unc- 33, unc-44, unc-51, unc-76, and unc-106, that affect the growth of the amphid and phasmid axons. These genes were found to affect the axons of the mechanosensory PDE neurons as well. The unc-33 mutation specifically affects neuronal microtubules. Sensory dendrites in this mutant have a superabundance of microtubules. Moreover, many of these microtubules are abnormal in diameter, and some form hooks or multiple ------------------- Key: 794 Medline: Authors: Hodgkin J Title: Males, hermaphrodites and females: Sex determination in C. elegans. Citation: Trends in Genetics 1: 85-88 1985 Type: REVIEW Genes: fem-1 fem-2 fem-3 her-2 tra-1 tra-2 tra-3 Abstract: Sexual phenotype in Caenorhabditis elegans is determined by a small number of control genes which are organized in a cascade of regulatory interactions. ------------------- Key: 795 Medline: 85264033 Authors: Kolson DL;Russell RL Title: New acetylcholinesterase-deficient mutants of the nematode C. elegans. Citation: Journal of Neurogenetics 2: 69-91 1985 Type: ARTICLE Genes: ace-1 ace-2 Abstract: We have used visual screening for a mutationally induced uncoordinated phenotype, coupled with subsequent enzymatic assay, to isolate 19 new mutations producing acetylcholinesterase (AChE) deficiencies in the nematode Caenorhabditis elegans. At least 13 of these are independent, and all fall within two genes, ace-1 X and ace- 2 I, previously shown to control respectively two kinetically distinct major AChE classes, A and B. Three of the 4 new ace-1 alleles and one of the 15 new ace-2 alleles are apparently leaky; the rest are probably null. For the 3 leaky ace-1 alleles, qualitative changes in the residual class A AChE strongly support the contention that ace-1 is a structural gene. In ace-2;ace-1 mutants, marked reduction in class A and B AChE reveals a third, minor, previously unrecognized AChE class, designated C. ------------------- Key: 796 Medline: 85264034 Authors: Kolson DL;Russell RL Title: A novel class of acetylcholinesterase, revealed by mutations, in the nematode C. elegans. Citation: Journal of Neurogenetics 2: 93-110 1985 Type: ARTICLE Genes: ace-1 ace-2 Abstract: In ace-2;ace-1 double mutants of the nematode C. elegans, where the major acetylcholinesterase (AChE) classes A and B have been eliminated by mutation, the animals are viable and residual AChE activity remains. This residual activity differs markedly from AChE classes A and B; its Km for acetylcholine is 1000-5000-fold lower, its resistance to eserine is 3000-260,000-fold higher, it is markedly more thermolabile, and it can be separated from classes A and B by ion exchange chromatography. It has been designated class C AChE. Class C AChE of indistinguishable properties is also present in wild type C. elegans, at levels approximating those seen in ace-2;ace-1 double mutants, suggesting that it is controlled by a third, as yet unidentified, gene. Amongst other sources examined, class C-like AChE has been detected in another nematode species, Stephanurus dentatus, but not in Drosophila melanogaster, Torpedo californica, or Rattus rattus. ------------------- Key: 797 Medline: Authors: Hodgkin J Title: Novel nematode amber suppressors. Citation: Genetics 111: 287-310 1985 Type: ARTICLE Genes: dpy-18 dpy-20 fem-1 lin-1 lon-1 sup-5 sup-21 sup-22 sup-23 tra-1 tra-2 tra-3 unc-13 unc-24 unc-52 unc-93 Abstract: Nine amber suppressor mutations were isolated in the nematode Caenorhabditis elegans by reverting amber alleles of a sex-determining gene, tra-3. One suppressor maps to a known locus, sup-5 III, but the other eight map to three new loci, sup-21 X (five alleles), sup-22 IV (two alleles) and sup-23 IV (one allele). Amber alleles of tra-3 and of a dumpy gene, dpy-20, were used to measure the efficiency of suppression; the sup-21 and the sup-22 alleles were both shown to be heterogeneous and generally weaker suppressors than sup-5 alleles, which are homogeneous. The spectrum of mutations suppressed by a strong sup-21 allele, e1957, was investigated and compared to the spectra for the amber suppressors sup-5 III and sup-7 X, using amber alleles in 13 assorted genes. Some of the differences between these spectra may be due to limited tissue specificity in sup-21 expression. --Suppression of dpy-20 was used to show that the sex-linked suppressors sup-7 and sup-21 are not dosage compensated in male (XO) relative to hermaphrodite (XX).-- Several uses of amber suppressors are critically discussed: for identifying null mutations, for varying levels of gene activity and for detecting maternal mRNA. ------------------- Key: 798 Medline: Authors: Krause M;Hirsh D Title: Actin gene expression in C. elegans. Citation: "Molecular Biology of the Cytoskeleton." Borisy G, Cleveland D and Murphy D (eds), Cold Spring Harbor Laboratory. : 287-292 1984 Type: REVIEW Genes: act-1 act-2 act-3 act-4 Abstract: The switching on or off of specific genes is a fundamental aspect of cellular differentiation during metazoan development. The molecular events involved in this switching are not yet understood, but they are now subject to analysis with the current technology available in molecular biology. Much of the work directed toward the understanding of developmental gene regulation has focused on the genes encoding the protein actin. Actin is the major thin-filament protein in both muscle and nonmuscle cells. The protein sequences of actins from a variety of tissues in several organisms have been determined, and the actin genes from a number of organisms have been isolated and are currently being studied. This work has revealed that actins are evolutionarily conserved, are encoded in most species by multigene families, and are differentially regulated, both spatially and temporally, during ------------------- Key: 799 Medline: Authors: Bejsovec A;Eide D;Anderson P Title: Genetic techniques for analysis of nematode muscle. Citation: "Molecular Biology of the Cytoskeleton." Borisy G, Cleveland D and Murphy D (eds), Cold Spring Harbor Laboratory. : 267-273 1984 Type: REVIEW Genes: act-1 act-2 act-3 unc-15 unc-22 unc-52 unc-54 unc-60 unc-82 unc-87 unc-89 unc-92 unc-105 Abstract: Current knowledge concerning the protein components of muscle is based largely on biochemical analysis of myofibrillar preparations. Such in vitro studies are limited because direct evidence for the in vivo function of isolated proteins is difficult to obtain. In vitro techniques, futhermore, are restricted often to the study of abundant proteins. Very little is known about minor sarcomeric components or how the sarcomere is assembled overall. Certainly, the assembly and function of a structure as complex as the sarcomere require many more than the dozen or so proteins commonly studied. Genetic techniques provide an alternative approach to the study of muscle. Mutations that cause muscle disfunction define genes required to construct a normal muscle. cell. The nature of mutant defects provides insights into the functions of the wild-type gene products. Genetic analysis is not restricted to the study of abundant proteins. The genes for even low-abundance proteins are subject to mutation, and if a gene product is required for muscle assembly or function, such mutants will be muscle-defective. Macromolecular complexes provide special opportunities for genetic intervention, because gene products that directly interact in the structure can often be identified. Mutational defects that affect one member of an interacting pair of proteins can be compensated by mutations affecting its interacting partner. Not all genes, hwoever, are directly accessible to genetic analysis. For example, genes whose products are essential for cell or organism viability and genes having more than one functional copy present special problems..... ------------------- Key: 800 Medline: Authors: Zuckerman BM;Jansson H-B Title: Nematode chemotaxis and possible mechanisms of host/prey recognition. Citation: Annual Review of Phytopathology 22: 95-113 1984 Type: REVIEW Genes: Abstract: It has long been recognized that free-living nematodes utilize specific recognition mechanisms for finding their hosts or prey in the soil. One of the earliest observations described the attraction of the plant parasitic nematode Meloidogyne incognita to tomato roots grown in sterile petri plates. If nematodes were unable to detect signals emanating from a food source, food finding would be a random, inefficient process. Such is not the case. The general consensus, based on experimental evidence and the morphologic configuration of purported sensory structures located in the cephalic region, is that in nematodes the primary food-finding mechanisms are governed by chemotactic factors emanating from the host or prey. Other stimuli, such as thermal, vibratory, or tactile stimuli, are believed to play a minor role, if any, in food-finding behavior. Once the nematode reaches the potential food source, it faces further barriers before it can commence feeding. For plant nematodes this includes recognition of an area of the root susceptible to attack. For bacteriophagous nematodes, recognizing certain species of bacteria as good food sources is vital, for these nematodes will not grow and reproduce on all bacteria. Molecular recognition of "good" and "bad" bacteria undoubtedly come into play, but here again definitive data are lacking. A larger body of information has accrued concerning the way nematophagous fungi attract and attack their prey. In this association, the role of the chemoattractant is reversed; chemotactic factors given off by the fungus lure the nematode to its death. This review considers the possible molecular mechanisms involved in this relation. Mating is another activity in which the perception of chemotactic factors is critical: specifically, detection of female sex pheromone by the male. The mechanisms of this detection appear to include specific binding of the pheromone by the male, sensory recognition, and an effector response. Progress and ------------------- Key: 801 Medline: 86030225 Authors: Albertson DG Title: Mapping muscle protein genes by in situ hybridization using biotin-labeled probes. Citation: EMBO Journal 4: 2493-2498 1985 Type: ARTICLE Genes: act-1 act-2 act-3 act-4 myo-3 Abstract: The genes coding for the myosin heavy chain isoforms (unc-54, myo-1, myo-2 and myo-3) and the actins (act-1,2,3 and act-4) have been mapped on the embryonic metaphase chromosomes of Caenorhabditis elegans by in situ hybridization. The genes were cloned in a cosmid vector and the entire cosmid was nick translated to incorporate biotin-labeled dUTP. This produced a probe DNA complementary to a 35- 45 kb length of chromosomal DNA. The hybridization signal from the cosmid probe, detected by immunofluorescence, could be easily seen by eye. The clear signals and the specific hybridization of the cosmid probes provided a faster means of mapping these single copy genes than small probes cloned in plasmid or lambda vectors. The myosin heavy chain genes are not clustered. Only unc-54 and myo-1 mapped to the same chromosome; the unc-54 locus is at the extreme right end of linkage group I and myo-1 mapped 40-50% from the left end of linkage group I. Myo-2 mapped to the X, 52-75% from the left end. The myo-3 gene mapped to the middle of linkage group V near the cluster of three actin genes (act-1,2,3). The fourth actin gene, act-4 mapped to 20-35% from the left end of X. ------------------- Key: 802 Medline: Authors: Dusenbery DB Title: Video camera-computer tracking of nematode C. elegans to record behavioral responses. Citation: Journal of Chemical Ecology 11: 1239-1247 1985 Type: ARTICLE Genes: Abstract: A new method is used to analyze responses to changes in the concentration of two chemical stimuli. Nematodes are allowed to move around on the surface of a thin layer of agar across which a stream of air blows to carry volatile stimuli. Darkfield illumination provides high-contrast images of the worms which are acquired by a video camera and fed to a microcomputer which is programmed to simultaneously track and record the movements and changes in direction of as many as 25 animals. The results are reported in real time. The worms respond to an increase in CO2 concentration by decreasing the number moving and increasing the number of changes of direction. Both responses adapt to steady-state levels in about half a minute. This suggests that they respond by changing the probability of initiating a reversal bout. This observation adds a repellent to the class of stimuli that C. elegans responds to by klinokinesis. The responses to changes in oxygen concentration are somewhat different. Movements and changes in direction both decrease when the oxygen concentration falls and increase when the concentration rises. No adaptation is seen within the one-minute time span observed. This observation provides further evidence that the response to oxygen differs from the response to other chemicals and may be sensed internally. These observations demonstrate that computer tracking is a sensitive method of analyzing animal behavior. It is further demonstrated that a significant response can be detected to a relatively weak stimulus in ------------------- Key: 803 Medline: 86041902 Authors: Spieth J;Denison K;Zucker E;Blumenthal T Title: The nucleotide sequence of a nematode vitellogenin gene. Citation: Nucleic Acids Research 13: 7129-7138 1985 Type: ARTICLE Genes: vit-1 vit-2 vit-3 vit-4 vit-5 vit-6 Abstract: The nematode, Caenorhabditis elegans, contains a family of six genes that code for vitellogenins. Here we report the complete nucleotide sequence of one of these genes, vit-5. The gene specifies a mRNA of 4869 nucleotides, including untranslated regions of 9 bases at the 5' end and 51 bases at the 3' end. Vit-5 contains four short introns totalling 218 bp. The predicted vitellogenin, yp170A, has a molecular weight of 186,430. At its N terminus it is clearly related to the vitellogenins of vertebrates. However, the vit-5-encoded protein does not contain a serine-rich sequence related to the vertebrate vitellin, phosvitin. In fact, the amino acid composition of the nematode protein is very similar to that of the vertebrate protein without phosvitin. Vit-5 has a highly asymmetric codon choice dictionary. The favored codons are different from those favored in other organisms, but are characteristic of highly expressed C. elegans genes. The strong selection against rare codons is not as great near the 5' end of the gene; rare codons are 15 times more frequent within the first 54 bp than in the next 4.8 kb. ------------------- Key: 804 Medline: 86111699 Authors: Tanii I;Osafune M;Arata T;Inoue A Title: ATPase characteristics of myosin from nematode C. elegans purified by an improved method. Formation of myosin-phosphate-ADP complex/ Citation: Journal of Biochemistry 98: 1201-1209 1985 Type: ARTICLE Genes: unc-54 Abstract: Myosin was purified rapidly from the nematode Caenorhabditis elegans by an improved method. Crude actomyosin was extracted from the worms at low ionic strength. Paramyosin was removed by repeating the precipitation of myosin filaments in the presence of Mg2+ and the dissolution of them in 0.6 M NaCl. Actin was removed by ultracentrifugation in the presence of Mg-ATP and finally by column chromatography on DEAE-cellulose. This method gave a good yield of myosin (20-30 mg from 50 g wet weight of worms), and its EDTA(K+)-ATPase activity was about 3-fold higher than that of myosin prepared by the method of Harris and Epstein (1979). ATP hydrolysis by nematode myosin showed an initial Pi-burst due to formation of the myosin-phosphate-ADP complex. Tryptophan fluorescence of myosin was enhanced about 8% by ATP. The relationship between the structure and function of myosin is discussed based on the above results and the amino acid sequences of myosins from rabbit skeletal muscle and Caenorhabditis elegans. ------------------- Key: 805 Medline: 86310828 Authors: Stinchcomb DT;Shaw JE;Carr SH;Hirsh D Title: Extrachromosomal DNA transformation of Caenorhabditis elegans. Citation: Molecular and Cellular Biology 5: 3484-3496 1985 Type: ARTICLE Genes: nuc-1 unc-54 Abstract: DNA was introduced into the germ line of the nematode Caenorhabditis elegans by microinjection. Approximately 10% of the injected worms gave rise to transformed progeny. Upon injection, supercoiled molecules formed a high-molecular-weight array predominantly composed of tandem repeats of the injected sequence. Injected linear molecules formed both tandem and inverted repeats as if they had ligated to each other. No worm DNA sequences were required in the injected plasmid for the formation of these high-molecular-weight arrays. Surprisingly, these high-molecular-weight arrays were extrachromosomal and heritable. On average 50% of the progeny of a transformed hermaphrodite still carried the exogenous sequences. In situ hybridization experiments demonstrated that approximately half of the transformed animals carried foreign DNA in all of their cells; the remainder were mosaic animals in which some cells contained the exogenous sequences while others carried no detectable foreign DNA. The presence of mosaic and nonmosaic nematodes in transformed populations may permit detailed analysis of the expression and function of C. elegans genes. ------------------- Key: 806 Medline: Authors: Stinchcomb DT;Shaw JE;Carr SH;Hirsh D Title: Extrachromosomal DNA transformation of C. elegans. Citation: Banbury Report 20: 251-263 1985 Type: ARTICLE Genes: col-1 Abstract: We have recently demonstrated that DNA can be introduced into the germline of the worm by microinjection; 10% of the injected worms give rise to progeny that maintain the foreign DNA. The exogenous DNA is present as a high molecular weight array. The array appears to be created by ligation of linear molecules and/or by recombination between supercoils. This high molecular weight foreign DNA is heritable: on average, 50% of the progeny of a transformed self-fertilizing hermaphrodite will still carry the exogenous sequences. Cytological evidence indicates that the array of foreign sequences is extrachromosomal. In situ hybridization experiments demonstrate that the extrachromosomal sequences can be lost during the growth of the organism giving rise to mosaic animals. Approximately one-half of the transformed animals are mosaic; the remainder carry foreign DNA in all of their cells. Loss of foreign DNA may be due to errors in replication or segregation of the exogenous sequences. No worm DNA sequences are required in the injected plasmid for the formation of these extrachromosomal arrays. To assess expression, we constructed a gene fusion between the 5' and 3' sequences of a C. elegans collagen gene and the bacterial coding sequences for B-glucuronidase (uidA). After injection, the gene fusion is expressed as part of a high molecular weight array. Thus, we may contemplate the use of this unusual mode of transformation to study developmental regulation in C. elegans. ------------------- Key: 807 Medline: 86008476 Authors: Francis GR;Waterston RH Title: Muscle organization in C. elegans: Localization of proteins implicated in thin filament attachment and I-band organization. Citation: Journal of Cell Biology 101: 1532-1549 1985 Type: ARTICLE Genes: sup-12 Abstract: The body wall muscle cells of Caenorhabditis elegans contain an obliquely striated myofibrillar lattice that is associated with the cell membrane through two structures: an M-line analogue in the A- band and a Z-disc analogue, or dense-body, in the I-band. By using a fraction enriched in these structures as an immunogen for hybridoma production, we prepared monoclonal antibodies that identify four components of the I-band as determined by immunofluorescence and Western transfer analysis. A major constituent of the dense-body is a 107,000-D polypeptide that shares determinants with vertebrate alpha- actinin. A second dense-body constituent is a more basic and antigenically distinct 107,000-D polypeptide that is localized to a narrow domain of the dense-body at or subjacent to the plasma membrane. This basic dense-body polypeptide is also found at certain cell boundaries where thin filaments in half-bands terminate at membrane-associated structures termed attachment plaques. A third, unidentified antigen is also found closely apposed to the cell membrane in regions of not only the dense-body and attachment plaque, but also the M-line analogue. Finally, a fourth high molecular weight antigen, composed of two polypeptides of approximately 400,000-D, is localized to the I-band regions surrounding the dense-body. The attachment of the dense-body to the cell surface and the differential localization of the dense-body-associated antigens suggest a model for their organization in which the unidentified antigen is a cell surface component, and the two 107,000-D polypeptides define different cytoplasmic ------------------- Key: 808 Medline: 86284606 Authors: Spieth J;Blumenthal T Title: The C. elegans vitellogenin gene family includes a gene encoding a distantly related protein. Citation: Molecular and Cellular Biology 5: 2495-2501 1985 Type: ARTICLE Genes: vit-1 vit-2 vit-3 vit-4 vit-5 vit-6 Abstract: While the nematode Caenorhabditis elegans is more primitive than most egg-laying organisms, it's vitellogenins, or yolk protein precursors, appear to be more complex. C. elegans oocytes accumulate two major classes of yolk proteins. The first consists of two polypeptides with an Mr of about 170,000 (yp170A and yp170B) encoded by a family of five closely related genes called vit-1 through vit-5. The second class consists of two smaller proteins with Mr values of 115,000 (yp115) and 88,000 (yp88) which are cut from a single precursor. Here we report the cloning and analysis of a single-copy gene (vit-6) that encodes this precursor. The lengths of the gene and its mRNA are about 5 X 10(3) base pairs. Like vit-1 through vit-5, vit-6 is expressed exclusively in adult hermaphrodites. Comparison of portions of the coding sequence indicates that vit-6 is distantly related to the vit-1 through vit-5 gene family. Thus, even though the two classes of yolk proteins are antigenically and physically distinct, they are encoded by a single highly diverged gene family. ------------------- Key: 809 Medline: Authors: Noonan D Title: Beyond the double helix. Citation: Esquire 104: 196-210 1985 Type: NEWS Genes: Abstract: In the end, it is attention to detail that makes all the difference. It's the center fielder's extra two steps to the left, the salesman's memory for names, the lover's phone call, the soldier's clean weapon. It is the thing that separates the men from the boys, and, very often, the living from the dead. Professional success depends on it, regardless of the field. But in big-time genetic research, attention to detail is more than just a good work habit, more than a necessary part of the routine. In big-time genetic research, attention to detail is the very meat and the god of science. It isn't something that's expected; it is simply the way of things. Those in the field, particularly those who lead the field, are slaves to detail. They labor in submerged mines of it, and haul great loads of it up from the bottom of an unseen ocean-the invisible sea of biological phenomena, upon which all living things float. Detail's rule over genetics is total and cruel. Months and even years of work have literally gone down the drain because of the most minor miscalculations. Indeed, perhaps the greatest discovery in the history of the discipline-the double-helix structure of DNA-might have been made by Linus Pauling instead of James D. Watson and Francis H. C. Crick. But Pauling's equations contained a simple mistake in undergraduate-level chemistry, a sin against detail that is now part of the legend. Each of the six scientists singled out here has made his mark by mastering his own particular set of ------------------- Key: 810 Medline: Authors: Goldstein P Title: The synaptonemal complexes of C. elegans: Pachytene karyotype analysis of the Dp 1 mutant and disjunction regulator regions. Citation: Chromosoma 93: 177-182 1985 Type: ARTICLE Genes: Abstract: The duplication mutant Dp1 presents morphological changes of the pachytene nuclei which include enlarged nuclei (58% greater than the wild type (WT)) and increased total length of the synaptonemal complex (SC) complement (32% greater than WT). The size of the nucleolus is similar to that of the wild type. The SC of the XX bivalent is 2.5 um long which is similar to the length in other strains. Genetic analysis (Herman et al. 1976) has shown that a duplicated segment of the X chromosome has been transposed to linkage group V in the Dp1 mutant. The present analysis, however, did not reveal the expected duplication loop in bivalent V of the heterozygous Dp1 strain. There is an average of three "Disjunction Regulator Regions" (DRR) per nucleus and approximately 1% X-chromosome nondisjunction which is consistent with the notion that the presence of DRRs somehow facilitates regular disjunction of the X chromosome. Statistical analysis, based on 9 different strains and 81 nuclei, indicates that there is a good correlation between the frequency of occurrence of X-chromosome nondisjunction and the number of DRRs. ------------------- Key: 811 Medline: 86079537 Authors: Bender W Title: Homeotic gene products as growth factors. Citation: Cell 43: 559-560 1985 Type: REVIEW Genes: lin-12 Abstract: Homeotic genes switch the developmental fates of cells between alternative pathways of development. The title was once reserved for a few loci in the fruit fly Drosophila melanogaster, which, when mutated, produced bizarre transformations of appendages. But as the phenotypic effects of more mutations in various organisms are described at the cellular level, many other genes are being recognized as homeotic switches. The isolation of the DNA for these loci is now uncovering the molecular mechanics of developmental decisions. The DNA sequences for two such homeotic loci -the Notch locus in Drosophila and the lin-12 locus in the soil nematode, Caenorhabditis elegans-are presented in this issue of Cell. There was no reason, until now, to compare these apparently unrelated genes in manifestly unrelated organisms. The surprise is that both loci encode proteins with homologies to epidermal growth factor (EGF). ------------------- Key: 812 Medline: 86079540 Authors: Greenwald I Title: lin-12, a nematode homeotic gene, is homologous to a set of mammalian proteins that includes epidermal growth factor. Citation: Cell 43: 583-590 1985 Type: ARTICLE Genes: lin-12 Abstract: The lin-12 gene of the nematode Caenorhabditis elegans controls certain binary decisions during development. The lin-12 locus was cloned by means of Tc1 transposon tagging: spontaneous lin-12 null alleles were isolated in a genetic background permissive for Tc1 transposition, and seven independently isolated mutations were found to be associated with Tc1 insertion events. All of these Tc1-induced mutations mapped to a single 2.9 kb restriction fragment within a 50 kb region examined. The DNA sequence of this fragment revealed that, although it does not contain the entire gene, it does include three complete exons. These three exons together encode 11 peptide units that are homologous to one another. The repeated peptide motif is also homologous to a set of mammalian proteins that includes epidermal growth factor. ------------------- Key: 813 Medline: 86117931 Authors: Rogalski TM;Baillie DL Title: Genetic organization of the unc-22 IV gene and the adjacent region in C. elegans. Citation: Molecular & General Genetics 201: 409-414 1985 Type: ARTICLE Genes: dpy-20 let-52 let-56 let-59 let-60 let-61 let-63 let-64 let-65 let-66 let-67 let-68 let-69 let-70 let-71 let-72 let-73 let-91 let-92 unc-22 sDf2 sDf7 sDf8 sDf9 sDf10 sDf19 Abstract: The genetic organization of the region immediately adjacent to the unc-22 IV gene in Caenorhabditis elegans has been studied. We have identified twenty essential genes in this interval of approximately 1.5-map units on Linkage Group IV. The mutations that define these genes were positioned by recombination mapping and complementation with several deficiencies. With few exceptions, the positions obtained by these two methods agreed. Eight of the twenty essential genes identified are represented by more than one allele. Three possible internal deletions of the unc-22 gene have been located by intra-genic mapping. In addition, the right end point of a deficiency or an inversion affecting the adjacent genes let-56 and unc-22 has been positioned inside the unc-22 gene. ------------------- Key: 814 Medline: 86056983 Authors: Nelson DW;Honda BM Title: Genes coding for 5S ribosomal RNA of the nematode C. elegans. Citation: Gene 38: 245-251 1985 Type: ARTICLE Genes: Abstract: We have identified a 1-kb genomic sequence that represents the major class of 5S rRNA genes in the nematode Caenorhabditis elegans. This 1- kb sequence is tandemly repeated 110 times in the haploid genome forming a single homogeneous gene family. Other nematode genomic sequences, distinct from the major 1-kb repeat class but homologous to it, may represent dispersed 5S rRNA genes or the ends of a gene cluster. One such fragment shows a restriction fragment length difference between two C. elegans strains. This should allow the genetic analysis of 5S rRNA-coding DNA (5S X rDNA) and its flanking regions in C. elegans. ------------------- Key: 815 Medline: 85256184 Authors: Dusenbery DB Title: Using a microcomputer and video camera to simultaneously track 25 animals. Citation: Computers in Biology & Medicine 15: 169-175 1985 Type: ARTICLE Genes: Abstract: A system that can simultaneously track about 25 animals with the position of each determined once a second is described. The system includes a 6809 microprocessor, OS-9 operating system and application programs written in assembly and BASIC09. The movements and changes in direction of the subjects can be determined and displayed in real time. The system has proven to be valuable in studying the chemotaxis of nematodes and should be applicable to the study of other animals that can be viewed ------------------- Key: 816 Medline: Authors: Hall SS Title: The fate of the egg. Citation: Science 85 : 40-49 1985 Type: NEWS Genes: lin-14 Abstract: The biologists who investigate nature's deepest and longest-running mystery often use the term fate map to describe the startling transformations that lie in store for the fertilized egg. It is one of the more venerable terms in embryology, and one of the most appropriate, too, for destiny and geography indeed intersect within the magnificent speck of DNA and cytoplasm that is an egg on the edge of becoming a organism. In this one cell, the entire genetic bill of lading for an animal, be it fruit fly or human, is stored, waiting to unfold with miraculous precision. It is that process of life unfurling-of cells becoming brain or backbone, of genes selectively flashing on and herding cells toward their certain fates, of tissues aggregating and differentiating toward ever more specific tasks-that both confounds and as surely delights developmental biologists. ------------------- Key: 817 Medline: Authors: Zuckerman BM;Himmelhoch S Title: Nematodes as models to study aging. Citation: "Nematodes as Biological Models, Volume 2: Aging and Other Model Systems." Zuckerman BM (ed), Academic Press, NY. 2: 3-28 1980 Type: REVIEW Genes: Abstract: The use of nematodes as models to study aging is currently attracting wide interest among developmental biologists. The trend is clearly indicated by the large numbers of recent papers on nematode aging cited in these volumes. Because of the rapidly expanding interest in free-living nematodes, a large amount of data has accumulated on all aspects of the biology of these organisms. Certainly there is no other group of multicellular organisms about which so much is known. The question arises, Why the nematode and not another small metazoan chosen as a model? This question was considered in detail in other reviews, and only the principal advantages need be summarized here. Briefly, these include a short life span (about 25 days for Caenorhabditis briggsae), small size, ease of maintainance in axenic or monoxenic culture, the relatively small number of cells that are differentiated into nervous, digestive, reproductive, and muscular systems, and, most important, the rapidly expanding body of information which is now available on the genetics, nutrition, development, and physiology of several species of free-living nematodes. Another critical question often asked by biomedical researchers is the relevance of nematode aging to human senescence. As knowledge of molecular biology grew it rapidly became apparent that certain basic cellular processes proceed along similar paths of all living things. This chapter refers to a number of observations related to the biology and physiology of nematode aging that appear to parallel events associated with mammalian aging. ------------------- Key: 818 Medline: Authors: Rothstein M Title: Effects of aging on enzymes. Citation: "Nematodes as Biological Models, Volume 2: Aging and Other Model Systems." Zuckerman BM (ed), Academic Press, NY. 2: 29-46 1980 Type: REVIEW Genes: Abstract: The practical use of free-living nematodes for aging studies must overcome two problems. Not only must cultures begin with organisms of a similar age, but also reproduction must be prevented, or synchrony will be lost and the aging cultures will become contaminated with newborn orrganisms and will eventually revert to typical "mixed" cultures. The problem of obtaining uniformly small organisms to start cultures has been solved by the use of screens for Turbatrix aceti and the hatching of isolated egg masses for Caenorhabditis elegans. Subsequent reproduction is prevented by the use of the DNA inhibitor fluorodeoxyuridine, or by culturing the organisms at elevated temperatures. Another practical method for aging of T. aceti is the use of a repeated screening process that periodically removes small (young) organisms from the aging cultures. ------------------- Key: 820 Medline: Authors: Samoiloff MR Title: Action of chemical and physical agents on free-living nematodes. Citation: "Nematodes as Biological Models, Volume 2: Aging and Other Model Systems." Zuckerman BM (ed), Academic Press, NY. 2: 81-98 1980 Type: REVIEW Genes: Abstract: During the postembryonic portion of their life cycle, free-living nematodes express a limited repertoire of developmental activities; these include limited cell growth, cell division, programmed cell death, differential gene expression, morphogenesis, and the establishment of positional information. These activities are manifested by the growth of the organism, molting, the development of the reproductive system, and the senescence of the organism. Analyses of postembryonic development in free-living nematodes has used three types of experimental approach to disrupt these processes. Genetic dissection of postembyronic development has been mediated in Caenorhabditis elegans by the establishment of temperature-sensitive, postembryonic-development-arrest mutants, temperature-sensitive gonad-development mutants, and a post-embryonic cell division-deficient mutant. Laser microbeam ablation experiments have demonstrated regions controlling postembryonic growth and molting and the site of the receptors for mating attraction in Panagrellus redivivus, and have been used as a probe for specific cellular function in C. elegans. However, the most widely used method for specifically disrupting normal postembryonic development has been the use of chemical agents that interfere with normal biosynthetic ------------------- Key: 821 Medline: Authors: Bird AF Title: The nematode cuticle and its surface. Citation: "Nematodes as Biological Models, Volume 2: Aging and Other Model Systems." Zuckerman BM (ed), Academic Press, NY. 2: 213-236 1980 Type: REVIEW Genes: Abstract: A number of review articles on the nematode cuticle have been published in the last decade. The most recent of these are those of Bird and Lee and Atkinson. These authors, while emphasizing the complexity and variability of nematode cuticles, support the use of a simplified nomenclature of cuticle structure which divides the cuticle into three regions or zones-namely, cortical, median, and basal. It is obvious that many exceptions to this fundamental pattern occur, and I shall mention some of these below. However, I think that they are adaptations to survival in changing environments, particularly where parasitism is involved. In particular, I propose to consider the structure and functions of the surface or epicuticle of the cortical zone, for it is here that reactions similar to those occurring at cell surfaces and in cell membranes are thought to occur in a wide range of "helminth" organisms. At the moment, particularly for the Nematoda, these ideas require more experimental evidence to establish them as facts. However, the use of sensitive techniques currently employed by membrane physicists and chemists to isolate, label, analyze, measure, and observe interactions taking place in cell membranes have in many instances yet to be used on the nematode cuticle. There is no doubt that the free-living bacterial-feeding nematodes such as those belonging to the genus Caenorhabditis, and in particular C. elegans, are the experimental models of ------------------- Key: 822 Medline: Authors: Wright KA Title: Nematode sense organs. Citation: "Nematodes as Biological Models, Volume 2: Aging and Other Model Systems." Zuckerman BM (ed), Academic Press, NY. 2: 237-295 1980 Type: REVIEW Genes: Abstract: Nematodes have long been recognized to have peripherally located sense organs. These comprise modifications of the cuticle as papillae, pores, or setae associated with an underlying nerve process. However, their generally small size precluded any in-depth understanding of either structure or function. As recently as 1971 a review of nematode anatomy considered the nature and function of nematode sense organs within only three and a half pages. Only 5 years later, McLaren required 70 pages to review the same subject, primarily because of the recent contributions from electron microscopic studies. Although most of these studies were of animal parasites, similar studies of plant-parasitic species followed quickly, and in 1975 two major papers were published dealing with the free-living microbial feeder, Caenorhabditis elegans. This nematode has been extensively studied as a model system to investigate developmental processes, and, since it is small, it has been feasible to reconstruct with great accuracy the total cellular composition of various parts of its anatomy. These studies in turn allow us to reappraise others, especially those of the larger animal parasites where cell identities are often harder to trace. They have also shown that nerves are associated with internal tissues of the body in manners suggesting that they may monitor internal functions or detect external stimuli capable of penetrating body tissues. It therefore seems important to recognize two classes of sensory organs (1) cuticular or peripheral sense organs, and (2) internal sensory ------------------- Key: 823 Medline: Authors: Anderson GL Title: Superoxide dismutase activity in dauerlarvae of C. elegans (Nematoda: Rhabditidae). Citation: Canadian Journal of Zoology 60: 288-291 1982 Type: ARTICLE Genes: Abstract: Dauerlarvae are reportedly adapted to withstand adverse environmental conditions. Current knowledge of the mechanisms underlying the unique characteristics of dauerlarvae is limited. This study characterizes superoxide dismutase (SODase) activity in several developmental stages of Caenorhabditis elegans (originally described by E. Maupas in 1900). Extracts of dauerlarvae have 17.1 units SODase per milligram protein, as compared with 4.3 and 3.8 units per milligram for obligate larvae and young adults, respectively. Since oxygen consumption in dauerlarvae is lower than that of young adults, the ratio of SODase to oxygen consumption is markedly higher in dauerlarvae than in young adults. The elevated SODase might contribute to an increased resistance to a variety of environmental stresses, including radiation. Furthermore, the elevation of this activity relative to metabolic rate could account for the long life-span of dauerlarvae. ------------------- Key: 824 Medline: Authors: Bottjer KP;Weinstein PP;Thompson MJ Title: Effects of an azasteroid on growth, development and reproduction of the free-living nematodes C. briggsae and Panagrellus redivivus. Citation: Comparative Biochemistry & Physiology 82B: 99-106 1985 Type: ARTICLE Genes: Abstract: The azasteroid, 25-azacoprostane (ASA-6), was evaluated for its effects on the growth, development and reproduction of the free- living nematodes, Caenorhabditis briggsae and Panagrellus redivivus. The axenic culture medium for either species of nematode consisted of Caenorhabditis briggsae Maintenance Medium (CbMM): formalin-killed Escherichia coli (1:1) with or without the addition of 5 micrograms cholesterol per ml and/or 25 micrograms ASA-6 per ml medium. All cultures also contained 50 micrograms Tween 80 per ml medium. After two generations of growth in sterol-deficient media, both species displayed a decrease in mean length, a decrease in the percent development to the adult stage and an inhibition of reproductive capability. These effects were more apparent in the sterol-deficient medium containing ASA-6. In the presence of cholesterol and ASA-6, growth and reproduction of C. briggsae, but not of P. redivivus, was inhibited after five generations. Morphologic abnormalities of azasteroid-inhibited worms were similar to those shown by worms cultured in sterol-deficient medium. These results suggest that different species of nematodes may exhibit different responses to azasteroid and that sterol utilization and metabolism may vary between nematode species. In addition, the similarities between the known effects of azasteroid inhibition in insects and those presented in this study on nematodes suggest a similar mechanism of action by the inhibitor in both groups of ------------------- Key: 825 Medline: Authors: Bird AF;Jago MV;Cockrum PA Title: Corynetoxins and nematodes. Citation: Parasitology 91: 169-176 1985 Type: ARTICLE Genes: Abstract: Corynetoxins, the toxic glycolipids produced by Corynebacterium rathayi colonizing bacterial galls induced by the seed gall nematode Anguina agrostis in annual ryegrass (Lolium rigidum), did not affect embryogenesis or larval development of A. agrostis although they did inhibit the rate of egg hatching. Corynetoxins were not toxic to several species of nematode which are parasites of roots nor to various stages of the free-living nematode Caenorhabditis elegans and they did not apper to influence the numbers of C. rathayi that became attached to the surface of the cuticle of infective larvae of A. agrostis. ------------------- Key: 826 Medline: Authors: Lewis JA;Paterson I Title: Preparation of tritium-labelled meta-aminolevamisole of high specific radioactivity by catalytic dehalogenation. Citation: Journal of Labelled Compounds & Radiopharmaceuticals 21: 945-959 1984 Type: ARTICLE Genes: Abstract: We describe the synthesis of tritiated meta-aminolevamisole (MAL) of high specific radioactivity. Unlabelled MAL was iodinated with iodine monochloride in aqueous hydrochloric acid. The major reaction product, L[-]2,3,5,6-tetrahydro-6-(5-amino-2-iodophenyl)imidazo [2,1-b]thiazole, was catalytically dehalogenated with carrier-free tritium gas in methanolic potassium hydroxide over 10% palladium-carbon. After extraction and chromatography, a radioactive species ([3H]-MAL) was identified with the same chromatographic motility as unlabelled MAL. [3H]-MAL possesses the same high biological activity in contracting nematode muscle as authentic unlabelled MAL, co-chromatographs with unlabelled MAL in three different TLC systems and is about 90% radiochemically pure. By bioassay and competitive inhibition studies, the specific radioactivity of [3H]-MAL appears greateer than 15 Ci/mmole and is probably close to 29 Ci/mmole. [3H]-MAL was shown to be useful for detecting a high affinity, saturable binding activity in extracts of the nematode Caenorhabditis elegans. ------------------- Key: 827 Medline: 85054292 Authors: Huang L;Albers-Schonberg G;Monaghan RL;Jakubas K;Pong SS et al. Title: Discovery, production and purification of the Na+, K+ activated ATPase inhibitor L-681,110 from the fermentation broth of Streptomyces sp. MA-5038. Citation: Journal of Antibiotics 37: 970-975 1984 Type: ARTICLE Genes: Abstract: The maximum yield for the production of L-681,110 by Streptomyces sp. Ma-5038 (ATCC 31587) was observed after 5 days' incubation at 28C and pH about 8.3. L-681,110 was isolated from the fermentation broth by acetone extraction of the mycelia, absorption to Amberlite XAD-2 resin and two separations by thin-layer chromatography. The structure of L-681,110 was found to consist of a sixteen-membered lactone with a new type of substitution. The inhibition of ATPase, activity against Caenorhabditis elegans and stimulation of Y-amino-butyric acid release indicate that L-681,110 possesses some characteristics of both oligomycin and avermectin. L-681,110 was also active against tapeworm and ticks in an in vivo assay. ------------------- Key: 828 Medline: 84261454 Authors: Santoro C;Costanzo F;Ciliberto G Title: Inhibition of eukaryotic transfer RNA transcription by potential Z-DNA sequences. Citation: EMBO Journal 3: 1553-1559 1984 Type: ARTICLE Genes: Abstract: The effect of d(CA/TG)n DNA segments on tRNA transcription has been examined. Alternating purine-pyrimidine tracts were cloned at a long distance from, adjacent to, or within the coding sequence of a tRNA*Pro gene from Caenorhabditis elegans and shown to be able to assume the Z-DNA conformation in vitro in physiological salt concentrations. The transcriptional level of these constructs was compared to that of normal tDNA*Pro by micro-injection into Xenopus laevis oocytes. Our results show a strong inhibitory effect by potential Z-DNA sequences only when these are placed in the flanking regions of the gene or when they are located between the elements (Box A and Box B) of the split promoter. Transcription was studied in parallel with supercoiled and linear DNA molecules carrying a d(CA/TG) stretch 124-bp long in front of the tRNA*Pro gene. The results show the same level of inhibition of PolIII transcription regardless of the topological status of the injected DNA. ------------------- Key: 829 Medline: Authors: Wat C-K;Prasad SK;Graham EA;Partington S;Arnason T;Towers GHN;Lam J Title: Photosensitization of invertebrates by natural polyacetylenes. Citation: Biochemical Systematics and Ecology 9: 59-62 1981 Type: ARTICLE Genes: Abstract: Fourteen polyacetylenes or their thiophene derivatives, isolated from species in the Asteraceae were screened for their biological acitivity to mosquito larve (Aedes aegypti), blackfly larvae (Simulium vittatum) and adult nematodes (Caenorhabditis elegans). Toxicity of the compounds was found to be enhanced greatly by irradiation with near-UV radiation or natural sunlight. Only wavelengths less than 400 nm were effective in promoting photosensitization. The results are discussed in relation to herbivore-plant interactions. ------------------- Key: 830 Medline: 82158110 Authors: Certa U;von Ehrenstein G Title: Reversed-phase high-performance liquid chromatography of histones. Citation: Analytical Biochemistry 118: 147-154 1981 Type: ARTICLE Genes: Abstract: Calf thymus histones are separated into the five classical components H1, H2A, H2B, H3, and H4 using reversed-phase high-performance liquid chromatography. This method is fast and sensitive; a single run takes 80 min and protein quantities ranging from 3 ug up to 1 mg can be separated. The primary structure of the proteins is not affected, as demonstrated by peptide mapping and gel electrophoresis. Yeast, nematode, and calf thymus histones are compared to each other and have similar retention times for individual peaks, thus demonstrating the evolutionary stability of these proteins by using this different approach. ------------------- Key: 831 Medline: Authors: Ouazana R Title: Cuticle collagen during the post-embryonic development of the nematode C. elegans: Comparison between 1st stage larvae and adults. Citation: C.R. des Seances de l'Academie des Sciences Serie 3 293: 467-470 1981 Type: ARTICLE Genes: Abstract: ------------------- Key: 832 Medline: Authors: Charnar Y;Brun JL Title: Division and endopolyploidization in intestinal nuclei during postnatal ontogenesis of C. elegans (Nematoda). Citation: Revue de Nematologie 5: 155-160 1982 Type: ARTICLE Genes: Abstract: ------------------- Key: 833 Medline: Authors: Tang C Title: Studies on the plant nematodes in south Fujian, China: 2. The species of Rhabditida. Citation: Acta Zoologica Sinica 28: 157-164 1982 Type: ARTICLE Genes: Abstract: ------------------- Key: 834 Medline: Authors: Hofsten AV;Kahan D;Katznelson R;Bar-el T Title: Digestion of free-living nematodes fed to fish. Citation: Journal of Fish Biology 23: 419-428 1983 Type: ARTICLE Genes: Abstract: Free-living nematodes - Panagrellus sp., Turbatrix aceti, Caenorhabditis elegans and C. briggsae - were each fed to the fish Danio sp. and the process of their digestion, in the fish alimentary canal, was studied by light and electron microscope. Almost no identifiable nematodes were found in the fish gut when the digestion period was 3 h or more, except for buccal capsules of the four studied species, males' spicules of Panagrellus sp. and Turbatrix aceti and egg-capsules of the Caenorhabditis species. These structures could serve as indicators that the nematodes had been preyed on and digested by the fish. Differences in the mode of digestion were noticed between the various species of nematodes studied, after a period of 0.5-1 h, in the fish gut. In Panagrellus sp. and T. aceti disintegration of the soft inner tissues occurred mostly at the anterior or posterior ends of the nematode's body, while in Caenorhabditis the majority of digested nematodes were affected at both ends or evenly along the entire body. Digestion seemed to be initiated mostly at the nematodes' body apertures: mouth, anus or cloaca, and vulva which could be due to a more vulnerable cuticle around those areas. Disintegration proceeded from the soft inner parts to the more resistant cuticle that was finally disintegrated. Of the three layers of cuticle the most resistant were the external cortex and the basal layers. ------------------- Key: 835 Medline: Authors: Kaufman TD;Bloom JR;Lukezic FL Title: Effect of an extract from saprozoic nematode-infested compost on the mycelial growth of Agaricus brunnescens. Citation: Journal of Nematology 15: 567-571 1983 Type: ARTICLE Genes: Abstract: Extracts from compost infested with Caenorhabditis elegans suppressed mycelial growth af Agaricus brunnescens. An extract from uninfested compost also inhibited mycelial growth but to a lesser degree. The critical role of compost bacteria and /or other compost micro-organisms is implicated by these results. ------------------- Key: 836 Medline: 84032722 Authors: Bennet MD;Heslop-Harrison JS;Smith JB;Ward JP Title: DNA density in mitotic and meiotic metaphase chromosomes of plants and animals. Citation: Journal of Cell Science 63: 173-179 1983 Type: ARTICLE Genes: Abstract: Studies of chromosome disposition at metaphase using serial thin-sectioning and three-dimensional reconstruction techniques have produced accurate estimates of the total volume of chromosomes per cell in 15 plant and two animal species. Comparing this character with the 4C DNA amount showed no indication of systematic differences in DNA density between either organisms with widely different (>200-fold) C values or different groups or organisms. For example, there was no significant difference between the density of DNA in somatic metaphase chromosomes of man (0.141 pg/um3) and its mean in 14 angiosperm plant species (0.182 pg/um3), or between four dicotyledons (0.180 pg/um3) and 10 monocotyledons (0.182 pg/um3). However, evidence was found showing that DNA density can vary significantly within a species. Thus, although the total chromosome volume per cell was closely correlated (r>0.97) with 4C DNA amount in somatic and meiotic cells, the density of DNA in metaphase chromosomes was significantly lower in meiocytes (0.131 pg/um3) than in somatic metaphase cells (0.179 ------------------- Key: 837 Medline: Authors: Kaufman TD;Lukezic FL;Bloom JR Title: The effect of free-living nematodes and compost moisture on growth and yield in Agaricus brunnescens. Citation: Canadian Journal of Microbiology 30: 503-506 1984 Type: ARTICLE Genes: Abstract: The responses of four mushroom cultivars ('PSU-310', 'PSU-324', 'PSU-348 and 'PSU-344') exposed to free-living nematode infestations were compared in two experiments by quantitatively determining the amount of mycelium in compost samples using a laccase assay technique. The amount of mycelial production for cultivars 'PSU-310', 'PSU-324' and 'PSU-348 in the control treatments of both studies was similar. While cultivar 'PSU-344' produced less mycelium as shown by laccase production, mycelial production was greatly reduced for all four cultivars exposed to nematode infestations in a high-moisture compost (78%) over the duration of the experiment. The initial compost moisture is implicated as a critical factor influencing the potential damage caused by nematode ------------------- Key: 838 Medline: Authors: Andrassy I Title: C. briggsae: A model of genetics. Citation: Allattani Kozlemenyek 70: 113-116 1983 Type: REVIEW Genes: Abstract: In Hungarian. ------------------- Key: 839 Medline: 84235994 Authors: Traboni C;Ciliberto G;Cortese R Title: A novel method for site-directed mutagenesis: its application to an eukaryotic tRNApro gene promoter. Citation: EMBO Journal 1: 415-420 1982 Type: ARTICLE Genes: Abstract: We present a novel general method for localized mutagenesis. The DNA segment to be mutagenized is inserted in the B-galactosidase gene of a M13-lac vector, generally causing loss of B-galactosidase function by generation of frameshift or nonsense codons. Mutations in the inserted DNA which restore B-galactosidase function are readily detected and analyzed. The application of this method to the promoter of an eukaryotic (Caenorhabditis elegans) tRNA*Pro gene has allowed the isolation of several mutants altered in transcription. ------------------- Key: 840 Medline: Authors: Schiemer F Title: Food dependence and energetics of freeliving nematodes. I. Respiration, growth and reproduction of C. briggsae (Nematoda) at different levels of food supply. Citation: Oecologia 54: 108-121 1982 Type: ARTICLE Genes: Abstract: Some bioenergetic parameters of Caenorhabditis briggsae, a saprophagous nematode, were analysed under different conditions of food availability. Respiration (R) and production rates (P) of experimental animals grown on media of defined bacterial concentrations were measured throughout the life cycle of the species at 20C. Energetics are expressed in the form of instantaneous rates and as cumulative budgets. 1. Food dependence: The food threshold of the species is defined as A (assimilation)=R, P=0. The respiratory level of the species is generally high compared to other nematode species and increases only weakly with food availability. Starvation (food densities below threshold) is expressed in a strong reduction in metabolism within 48 h. The food dependence of biosynthetic processes (body growth and egg production) follows a hyperbolic form, which can be described by the Michaelis-Menten function. The relationship P:R changes drastically with availability of food, e.g. the production efficiency for the period of maximal reproduction is 0% at 2x10*8 cells ml-1 (threshold) and 86% at 10*10 cells ml-1. 2. R and P follow different forms of size dependence in the course of the life cycle. The relationship between R and body weight (W) can be described by an allometric function, e.g. at high food density, R=2.8 W*0.75 (R in nl 02 ind-1 h-1; W in ug fresh weight). Weight-specific production rates vary considerably during the life cycle: +/- constant in the early larval phase (exponential growth, "g"=1.44 day-1 at 10*10 cells ml-1); decreasing in the latter larval phase; peak values shortly after onset of reproduction as a result of both body growth and egg production. 3. Differences in resource allocation at varying food densities are also manifest in cumulative energy budgets, e.g. higher Rcum is necessary to achieve the same body size at lower food densities. Size at maturation and egg size are reduced to a different degree at low food densities, indicating bioenergetical constraint and trade-off between ------------------- Key: 841 Medline: Authors: Schiemer F Title: Food dependence and energetics of freeliving nematodes. II. Life history parameters of C. briggsae (Nematoda) at different levels of food supply. Citation: Oecologia 54: 122-128 1982 Type: ARTICLE Genes: Abstract: The food dependence of larval duration, fecundity and the intrinsic rate of natural increase follow a hyperbolic form, which can for the former be described by the Michaelis-Menten function. Maximal larval duration at 20C is 62 h, maximal fecundity is 153 eggs per female and rmax is 1.136 per day. The lower food threshold is 10*8 E. coli cells ml-1 (=0.06 mg dry weight ml-1) for larval growth and 2x10*8 cells ml-1 for reproduction and "r". 50% of maximal performances (Ks) are attained at 5x10*8 and 7.5x10*8 cells ml-1 respectively. Reproductive effort at dense food is highest immediately after maturation (e.g. 50% of the total eggs produced by a female are laid within 2 days after onset of egg production). At lower food densities the reproductive effort is delayed. Larval mortality increases strongly below 10*9 cells ml-1. The results reported sofar were obtained with E. coli cells which were harvested at the phase of decreasing population growth in batch cultures. With cells from the exponential and the stationary phase, performances are increased and decreased respectively. This is partly due to differences in bacterial biomass per unit cell, partly an expression of the change of nutritive value of bacterial cells with ------------------- Key: 842 Medline: Authors: Ouazana R Title: Structure and chemical composition of the cuticular integument of the nematodes. Citation: Bulletin de la Societe Zoologique de France 107: 419-426 1982 Type: ARTICLE Genes: Abstract: ------------------- Key: 843 Medline: Authors: Fodor A;Deak P Title: C. elegans as genetic model. Citation: Allattani Kozlemenyek 69: 91-98 1983 Type: REVIEW Genes: Abstract: ------------------- Key: 844 Medline: Authors: Anderson RV;Coleman DC Title: Nematode temperature responses: A niche dimension in populations of bacterial-feeding nematodes. Citation: Journal of Nematology 14: 69-76 1982 Type: ARTICLE Genes: Abstract: The optimum tempertures for population development were determined for six species of bacterial-feeding nematodes from among eight temperatures, ranging from 5 to 40 C. Four of the species are cohabiting species. The range of temperatures over which population development occurs (temperature niche breadth) is different for the cohabiting species. This difference may be a means of reducing competition between species, thus increasing temperatures over which habitats can be exploited. ------------------- Key: 845 Medline: Authors: McClure MA;Zuckerman BM Title: Localization of cuticular binding sites of concanavalin A on C. elegans and Meloidogyne incognita. Citation: Journal of Nematology 14: 39-44 1982 Type: ARTICLE Genes: Abstract: Utilizing a Concanavalin A (Con-A)-hemocyanin conjugate, the majority of cuticular Con A binding sites were shown to be localized on the head region of Caenorhabditis elegans and Meliodogyne incognita. Secretions which apparently emanated from the amphids and inner labial papillae did not ------------------- Key: 846 Medline: 84236054 Authors: Dente L;Fasano O;Costanzo F;Traboni C;Ciliberto G;Cortese R Title: A prokaryotic tRNAtyr gene, inactive in Xenopus laevis oocytes, is activated by recombination with an eukaryotic tRNApro gene. Citation: EMBO Journal 1: 817-820 1982 Type: ARTICLE Genes: Abstract: Eukaryotic tDNA promoters are composed of two essential regions contained within the coding sequence (Box A and Box B). Due to the highly conserved structure of prokaryotic and eukaryotic tRNA, most prokaryotic tRNA genes are expected to be active templates in eukaryotic transcriptional systems. In this paper we show that Escherichia coli tDNA Tyr is not transcribed in the nucleus of Xenopus laevis oocytes. By in vitro construction of hybrid molecules between inactive prokaryotic tDNA Tyr from E. coli, and active eukaryotic tDNA Pro from Caenorhabditis elegans, we show that tDNA Tyr can be made into an active gene if its first third, including the Box A region, is replaced by that of the eukaryotic tDNA. These results suggest that an improper Box A sequence is responsible for the inactivity of the E. coli tRNA Tyr gene, and argue against the role of secondary and tertiary DNA conformations in RNA polymerase III transcription. ------------------- Key: 847 Medline: Authors: Neuschulz N;Kampfe L Title: The influence of selected abiotic factors on the population development of axenic cultivated C. briggsae (Nematoda). Citation: Zoologische Jahrbucher - Abt. Sys. Oekol. Geo. Tiere 110: 333-344 1983 Type: ARTICLE Genes: Abstract: ------------------- Key: 848 Medline: Authors: Schiemer F Title: Comparative aspects of food dependence and energetics of freeliving nematodes. Citation: Oikos 41: 32-42 1983 Type: ARTICLE Genes: Abstract: Life history data, population parameter ("r") and energetics obtained at a wide range of food supply are compared for two species of bacterivorous nematodes. Caenorhabditis briggsae (Cb) is representative for saprobic environments. Plectus palustris (Pp) and related species are known from heterogeneous habitats of higher predictability in food supply but lower bacterial biomass. In Cb the larval phase is short and maximal reproduction is attained immediately after maturation. Pp has a longer prereproductive period and a prolonged phase of egg production rates. Considerably higher rmax and production rates in Cb are linked to greater maintenance costs. Its food threshold is shifted to higher food densities compared to Pp. Differences in the functional response, thresholds and maximal performance of various parameters are contrasted with different qualities of food availability (overall density; heterogeneity; predictability) in the respective habitats of the two species. Short term, unpredictable conditions (i.e. saprobic environments) are expoited by species with high production performances and rmax. The high level of standard metabolism sets constraints at conditions of lower food availability. Heterogeneous environments of higher predictability in food supply call for homeostatic abilities: in Pp this is expressed in lower maintenance requirements, endurance of starvation and a prolonged reproductive phase. ------------------- Key: 849 Medline: Authors: Kenyon C Title: Cell lineage and the control of C. elegans development. Citation: Philosophical Transactions of the Royal Society of London 312B: 21-38 1985 Type: ARTICLE Genes: lin-12 lin-32 mab-5 unc-86 Abstract: This paper provides a brief summary of the Caenorhabditis elegans cell lineage, the evidence for both intrinsic and extrinsic cell specification, and experiments that suggest mechanisms for cell differentiation and patterning. ------------------- Key: 850 Medline: Authors: Greenwald I Title: The genetic analysis of cell lineage in C. elegans. Citation: Philosophical Transactions of the Royal Society of London 312B: 129-137 1985 Type: ARTICLE Genes: ced-3 egl-1 lin-12 lin-14 lin-22 unc-86 Abstract: The genetic control of cell lineage has been studied extensively in Caenorhabditis elegans. In this paper, three studies of cell lineage mutants are reviewed: the isolation of mutations affecting vulval cell lineages, and the analysis of two 'control genes', lin-12 and lin-14. In addition, certain logical features of the genetic programme, as inferred from or illuminated by the study of cell lineage mutants, are discussed: the concepts of 'control genes' and developmental subprogrammes, and the organization of the lineage into a hierarchy of binary ------------------- Key: 851 Medline: Authors: Andrassy I Title: A dozen new nematode species from Hungary. Citation: Opuscula Zoologica (Budapest) 19: 3-40 1985 Type: ARTICLE Genes: Abstract: In the present article three new genera and twelve new species of Nematoda are described from Hungary. Seleborca gen. n. (Cephalobidae, Acrobelinae) is similar to Acrobeles but differs from it by the double cuticle and the structure of the lateral field. Hoplorhynchus gen. n. (Hoplolaimidae, Rotylenchinae) is unique among the genera of Hoplolaimidae in the structure of lateral field, in the shape of the tail and in the location of phasmids. Labronemella gen. n. (Qudsianematidae) resembles Lobronema but has a discolaimoid head and a very slender spear. The new species are: Penzancia terricola, Theristus pannonicus, Metateratocephalus gracilicaudatus, Acrobeles canalis, Caenorhabditis cervi, Hoplorhynchus riparius, Ogma danubiale, Ogma castellanum, Trischistoma gracile, Aulolaimus autumnalis, Labronema pusillum and Labronemella labiata spp.n. The genera Penzancia (De Man, 1889) Filipjev, 1918, Acrobeles Linstow, 1877, Trischistoma Cobb, 1913, Tripylina Brzeski, 1963 are redefined and their species listed. To each genus Metateratocephalus Eroshenko, 1973, Acrobeles Linstow, 1877, Seleborca gen.n., Trischistoma Cobb, 1913, Tripylna Brezeski, 1963, Aulolaimus Da Man, 1880 and Labronemella gen. n. a key is ------------------- Key: 852 Medline: Authors: Rosenzweig WD;Premachandran D;Pramer D Title: Role of trap lectins in the specificity of nematode capture by fungi. Citation: Canadian Journal of Microbiology 31: 693-695 1985 Type: ARTICLE Genes: Abstract: Seven adhesive-producing nematode-trapping fungi were tested for their ability to capture nine different nematodes. The nematodes included species that are free living as well as plant and insect parasites. The fungi displayed no selectivity. Each fungus was able to trap and consume all of the different nematodes tested. A study of cuticle surface saccharides of five of the nematodes revealed the presence on all of the nematodes of glucose-mannose and N-acetylgalactosamine residues. L-Fucose residues were not found on any of the nematodes. The involvement of lectins in the capture of prey by nematode-trapping fungi is discussed. ------------------- Key: 853 Medline: Authors: Johnson TE;Simpson VJ Title: Aging studies in C. elegans and other nematodes. Citation: "CRC Handbook of Cell Biology of Aging." Cristofalo VJ (ed), CRC Press, Boca Raton, FL. : 481-495 1985 Type: REVIEW Genes: Abstract: At first sight the inclusion of a chapter on Caenorhabditis elegans in a volume on cell biology may seem unusual. However this nematode has been a superb model system for a number of cell biology studies as well as a useful model of aging. This widespread interest in C. elegans is engendered in large part by its genetic system and its optical clarity in Nomarski phase-contrast optics. Nematodes have long been a system in wide use among experimental gerontologists, and with the introduction of C. elegans by Brenner in 1974, this species has become the nematode of choice for most aging studies. We concentrate primarily on C. elegans in this review although a number of other speices, including Caenorhabditis briggsae, Turbatrix aceti, and Panagrellus redivivus, have been used in aging studies also. Other reviews on aging in C. elegans have appeared recently, including a more detailed review in another volume of this series. ------------------- Key: 854 Medline: Authors: Johnson TE Title: Aging in C. elegans: Update 1984. Citation: "Review of Biological Research in Aging, Volume 2." Rothstein M (ed), Alan R. Liss, NY. 2: 45-60 1985 Type: REVIEW Genes: ced-1 ced-2 ced-3 nuc-1 Abstract: Since the last review in this series, several important projects relating to aging research in Caenorhabditis elegans have been completed. A more detailed review of the field is available. A major focus of research in Caenorhabditis elegans over the last few years has been on development, particularly the cell lineage. The entire cell lineage of the adult hermaphrodite has been described. The genetic loci coding for myosin, for rRNA, for actin, collagen, and oocyte yolk proteins, and a major family of proteins synthesized in the sperm have been isolated using recombinant DNA techniques. A transposable element has been identified, and studies aimed at using this element as a mutagen are underway. A good start has been made in generating an ordered series of overlapping recombinant clones of the entire genome; several labs are developing techniques for transformation of the worm. Aging research has also made progress over the last few years. Single-gene mutants and selectively bred stocks displaying longer lifespans have been isolated. A number of new markers of senescence have been described. Programmed cell death during development of the worm has been a major focus of research, and mutants altering this process have been isolated. There are still a few problems for aging research: there is not a single agreed-upon method of culturing biochemical quantities of worms that also gives lifespans comparable to those of small-scale cultures; and observed differences in aging parameters that are general versus those that are due to culture conditions are still under dispute. Two methods of growth (axenic and monoxenic) are still commonly used, for the most part always in distinct laboratories. All of these findings will be described within. ------------------- Key: 855 Medline: 86214991 Authors: Johnson TE Title: Molecular and genetic analyses of a multivariate system specifying behavior and life span. Citation: Behavior Genetics 16: 221-235 1986 Type: ARTICLE Genes: Abstract: Recombinant inbred (RI) lines have been constructed by crossing the Bristol and Bergerac BO strains of the nematode Caenorhabditis elegans. The F1 hermaphroditic progeny are allowed to self-fertilize for 20 generations, yielding the RI lines. Heritability estimates for several behavioral traits and for life span, as well as both phenotypic and genetic covariance estimates for these traits, have been obtained. Significant heritablility is detected only for forward movement. Large genetic covariances are detected between different behavioral components, corroborating earlier studies based on observations of sterotypical behaviors in nematodes. A strain distribution pattern (SDP) has been generated using genetic loci defined both by mutation and by restriction fragment length polymorphisms. Estimates of the number of loci affecting the life span range from three to six; these estimates were obtained both by classic quantitative techniques and by mapping, using the SDP for these RI lines. Thus, loci specifying life span are distributed throughout the genome rather than localized to any one region. EMS-induced, long-lived (Age) mutants were also examined. In contrast to an earlier report, these mutants ingest normal amounts of food. The age locus of one strain, MK546, segregates independently of a behavioral ------------------- Key: 856 Medline: Authors: Huettel RN Title: Chemical communicators in nematodes. Citation: Journal of Nematology 18: 3-8 1986 Type: REVIEW Genes: Abstract: Chemical signals released by one organism and perceived by another organsism are classified as semiochemicals. Semiochemicals are divided into pheromones, which elicit intraspecific responses, and allelochemics, which elicit interspecific responses. Nematodes utilize and (or) recognize signals from both categroies of semiochemicals. The existence of pheromones, specifically sex and aggregation pheromones, has been demonstrated in numerous plant and animal parasitic and free-living nematodes. Sex pheromones have been isolated and purified from Nippostrongylus brasiliensis and Heterodera glycines, and epidietic pheromones have been shown to be responsible for initiation of dauer juvenile formation in Caenorhabditis elegans. Allelochemics cause interspecific responses in insects and other invertebrates but are only postulated to occur in nematodes. Food-finding behavior of nematodes is almost certainly caused by host-released allelochemic messengers. Understanding of the behavioral responses and the chemical messengers that affect bioregulation of various processes in nematodes will influence future management strategies. ------------------- Key: 857 Medline: Authors: Chitwood DJ;Lozano R;Lusby WR Title: Recent developments in nematode steriod biochemistry. Citation: Journal of Nematology 18: 9-17 1986 Type: REVIEW Genes: Abstract: Current knowledge of steroid nutrition, metabolism, and function in free-living, plant-parasitic and animal-parasitic nematodes is reviewed, with emphasis upon recent investigation of Caenorhabditis elegans. A number of 4-desmethylsterols with a trans-A/B ring configuration can satisfy the steroid nutritional requirement in C. elegans, but sterols with a cis-A/B ring configuration or trans-A/B with a 4-methyl group cannot. C. elegans removes methyl or ethyl substituents at C-24 of the plant sterols sitosterol, campesterol, stigmasterol, stigmastanol, and 24-methylenecholesterol to produce various sterols with structures partially dependent upon that of the dietary sterol. Additional metabolic steps in C. elegans include reduction of delta22- and delta5-bonds, C-7 dehydrogenation, isomerization of a delta7-bond to a delta8(14)-bond, and 4a-methylation. An azasteroid and several long-chain alkyl amines interfere with the dealkylation pathway in C. elegans by inhibiting the delta24-sterol reductase; these compounds also inhibit growth and reproduction in various plant-parasitic and animal-parasitic nematodes. A possible hormonal role for various steroids identified in nematodes is discussed. ------------------- Key: 858 Medline: 86152715 Authors: Byard EH;Sigurdson WJ;Woods RA Title: A hot aldehyde-peroxide fixation method for electron microscopy of the free-living nematode C. elegans. Citation: Stain Technology 61: 33-38 1986 Type: ARTICLE Genes: Abstract: An improved method for the fixation of the third and fourth larval stages and adults of Caenorhabditis elegans has been developed. Worms are placed in a mixture of 1.5% paraformaldehyde and 1.0% glutaraldehyde at pH 7.0 and 70 C and the suspension promptly cooled in a water bath at 20 C for 1 hr. The fixed worms are then immersed in a mixture of 5% glutaraldehyde and hydrogen peroxide at 4 C for 1 hr, stained en bloc in uranyl acetate, and embedded in resin for electron microscopy. The procedure results in superior fixation, particularly of microfilaments and microtubules. The high temperature of the initial fixation straightens the worms and thus facilitates serial sectioning. ------------------- Key: 859 Medline: 86174352 Authors: McGhee JD;Cottrell DA Title: The major gut esterase locus in the nematode C. elegans. Citation: Molecular & General Genetics 202: 30-34 1986 Type: ARTICLE Genes: ges-1 Abstract: Mutations in the major gut esterase of the nematode Caenorhabditis elegans have been induced by ethylmethane sulfonate and detected by isoelectric focusing. The gut esterase locus, denoted ges-1, maps less than 0.3 map units to the right of the unc-60 locus, at the left end of chromosome V. ------------------- Key: 860 Medline: 86120377 Authors: Honda BM;Devlin RH;Nelson DW;Khosla M Title: Transcription of class III genes in cell-free extracts from the nematode C. elegans. Citation: Nucleic Acids Research 14B: 869-881 1986 Type: ARTICLE Genes: ncl-1 Abstract: Using the nematode Caenorhabditis elegans as a model organism, we have prepared cell-free extracts which accurately transcribe cloned homologous 5S RNA genes in vitro. These extracts also transcribe cloned tRNA genes, and actively process the resulting products. Unlike tRNA genes, transcription of 5S DNA shows some species specificity: C. elegans extracts do not transcribe Xenopus 5S RNA genes, nor does a Xenopus extract efficiently transcribe the heterologous nematode 5S DNA. However, addition of limiting amounts of C. elegans fractions permits Xenopus extracts to transcribe nematode 5S RNA genes. This apparent biochemical "complementation" may provide an assay to purify 5S RNA gene-specific factors ------------------- Key: 861 Medline: 86135016 Authors: Goldstein P Title: The synaptonemal complexes of C. elegans: The dominant him mutant mnT6 and pachytene karyotype analysis of the X-autosome translocation. Citation: Chromosoma 93: 256-260 1986 Type: ARTICLE Genes: mnT6 Abstract: The dominant X-autosome heterozygous translocation mutant mnT6 of the nematode Caenorhabditis elegans has an X chromosome that has been reduced in size by 40%, yet the remainder of the bivalent pairs effectively at pachytene and has a synaptonemal complex (SC) that has a normal appearance. Six SCs are present in pachytene nuclei of this mutant which correspond to a haploid value of n = 6. Nondisjunction of the X chromosome occurs at a rate of 37% and there are no 'Disjunction Regulator Regions' (DRR) in this him (high incidence of males) mutant. This is consistent with the notion that DRRs either promote disjunction or inhibit nondisjunction of the X chromosome. Their occurrence in pachytene nuclei is independent of the mechanism responsible for nondisjunction, i.e. point mutations as in him-8 versus chromosomal aberrations as in mnT6. Although an SC is present along the entire length of the X chromosome, crossover suppression is observed in ------------------- Key: 862 Medline: 86165785 Authors: Sebastiano M;D'Alessio M;Bazzicalupo P Title: Beta-glucuronidase mutants of the nematode C. elegans. Citation: Genetics 112: 459-468 1986 Type: ARTICLE Genes: gus-1 Abstract: Using a screening procedure that is based on a histochemical stain for the enzyme beta-glucuronidase, we have isolated several mutants of the nematode Caenorhabditis elegans affected in beta-glucuronidase activity. All of the mutations fall into one complementation group and identify a new gene, gus-1, which has been mapped on the right arm of linkage group I (LG I), 1.1 map units to the left of unc-54. The mutants have no visible phenotype, and their viabilities and fertilities are unaffected. Linked revertants of two of the mutations have been isolated. They restore enzyme activity to almost wild-type levels; the beta-glucuronidase that one of the revertants produces differs from that of the wild type. We propose that gus-1 is the structural locus for ------------------- Key: 863 Medline: Authors: Schierenberg E;Cassada R Title: Der Nematode C. elegans. Citation: Biologie in unserer Zeit 16: 1-7 1986 Type: REVIEW Genes: Abstract: In German. ------------------- Key: 864 Medline: 86202903 Authors: Sigurdson DC;Herman RK;Horton CA;Kari CK;Pratt SE Title: An X-autosome fusion chromosome of C. elegans. Citation: Molecular & General Genetics 202: 212-218 1986 Type: ARTICLE Genes: mnT12 Abstract: The translocation mnT12(IV;X) is a fusion of holocentric chromosomes IV and X, the breakpoints occurring near the left end of IV and the right end of X. Animals homozygous for mnT12 are viable and fertile; they contain five pairs of chromosomes rather than the normal set of six pairs. The mnT12 chromosome is larger than all wild-type chromosomes and thus identifies linkage groups IV and X cytologically. Hermaphrodites heterozygous for mnT12 show high frequency meiotic nondisjunction both between mnT12 and the X chromosome, which results in a high incidence of male self progeny (27% compared to the wild-type incidence of 0.2%), and between mnT12 and chromosome IV, which results in a high incidence of self progeny essentially trisomic for chromosome IV (karyotype IV/mnT12/mnT12). The viability of chromosome IV trisomics has been confirmed by constructing animals trisomic for only normal copies of chromosome IV; these animals are morphologically wild type. Meiotic chromosome disjunction in mnT12 homozygotes appears to be normal, although the frequency of recombination between markers that are normally X-linked is significantly reduced. Males of genotype IV/mnT12/0 are fertile. They can be thought of as having a neo-X(mnT12) neo-Y(normal IV) karyotype since it is possible to maintain a male-hermaphrodite stock of C. elegans consisting of such males and hermaphrodites carrying two neo-X chromosomes and no neo-Y; the organism is thus converted from an XO:XX type of sex determination to an XY:XX system. ------------------- Key: 865 Medline: 86176733 Authors: Ellis RE;Sulston JE;Coulson AR Title: The rDNA of C. elegans: Sequence and structure. Citation: Nucleic Acids Research 14: 2345-2364 1986 Type: ARTICLE Genes: let-209 eDf3 Abstract: We have sequenced one complete rDNA tandem repeat from the nematode C. elegans. By comparative analysis we derive secondary structures for the 18s, 5.8s, and 26s rRNA molecules, and comment on other important features of the sequence. We also present the sequence of a junction between the rDNA and non-ribosomal DNA. Finally, we use our data to quantify the evolutionary relationships among several organisms currently studied in developmental ------------------- Key: 866 Medline: 86133569 Authors: Sternberg PW;Horvitz HR Title: Pattern formation during vulval development in C. elegans. Citation: Cell 44: 761-772 1986 Type: ARTICLE Genes: unc-84 Abstract: Previous studies have shown that the development of the vulva of the C. elegans hermaphrodite involves six multipotential hypodermal cells as well as the gonadal anchor cell, which induces vulval formation. Our further examination of the interactions among these seven cells has led to the following model. Each hypodermal precursor cell becomes determined to adopt one of its three potential fates; each of these fates is to generate a particular cell lineage. In the absence of cellular interactions each precursor cell will generate the nonvulval cell lineage; an inductive signal from the anchor cell is required for a precursor cell to generate either of the two types of vulval cell lineages. The inductive signal is spatially graded, and the potency of the signal specifies which lineage is expressed by each of the tripotential precursor ------------------- Key: 867 Medline: 86137024 Authors: Kemphues KJ;Wolf N;Wood WB;Hirsh D Title: Two loci required for cytoplasmic organization in early embryos of Caenorhabditis elegans. Citation: Developmental Biology 113: 449-460 1986 Type: ARTICLE Genes: zyg-9 zyg-11 Abstract: We have identified five new alleles, including an amber allele, at each of two loci (zyg-11 II and zyg-9 II) previously identified by temperature-sensitive strict maternal-effect lethal mutations. Genetic analysis indicates that each of these genes is expressed specifically during oogenesis and encodes a protein product whose function is required only during embryogenesis. Temperature-pulse experiments suggest that the time of action of both products is during the one-cell stage of embryogenesis. Phenotypic analysis reveals that mutations in both loci lead to disorganization of the cytoplasm in early embryos and to abnormalities in at least one of the meiotic divisions. Mutations at the zyg-9 locus appear to specifically affect microtubule function in one-cell embryos while zyg-11 mutations affect many cytoplasmic ------------------- Key: 868 Medline: Authors: Munakata N;Morohoshi F Title: DNA glycosylase activities in the nematode, C. elegans. Citation: Mutation Research 165: 101-107 1986 Type: ARTICLE Genes: Abstract: DNA glycosylases acting upon uracil- or 3-methyl-adenine-containing DNA have been detected in the sonic extracts of the nematode, Caenorhabditis elegans. 4 types of the extracts were prepared either from asynchronously-growing worms, embryos obtained from gravid hermaphrodites, aseptically-hatched larvae, or dauer larvae. Uracil-DNA glycosylase activity was found in all 4 types of the extracts, and the activity was highest in the embryonic extract. In contrast, 3-methyladenine-DNA glycosylase activity was undetectable in the embryonic extract, while an equal level of activity was found in the other 3 types of extracts. The results substantiate the ubiquity of base-excision repair in various organisms, and suggest that some of the repair functions may be developmentally regulated in multicellular animals. ------------------- Key: 869 Medline: 86165348 Authors: Edgar LG;McGhee JD Title: Embryonic expression of a gut-specific esterase in Caenorhabditis elegans. Citation: Developmental Biology 114: 109-118 1986 Type: ARTICLE Genes: Abstract: We describe an esterase activity that, by the criterion of histochemical staining, is completely localized to the intestine of the nematode Caenorhabditis elegans. Esterase activity appears in the embryonic gut when the embryo contains 4-8 intestinal precursor cells and 100-150 total cells. Esterase activity is abolished by treating early embryos with alpha-amanitin, indicating that expression depends upon transcription by RNA polymerase II within the developing embryo. In partial embryos produced by lysing one blastomere of a two-cell embryo, esterase expression appears only in descendants of the blastomere that normally produces the gut; esterase expression appears independent of the other non-gut blastomere. In early cleavage-stage embryos in which cytokinesis has been blocked by cytochalasin D, esterase expression appears at the normal time and only in cells in the gut lineage; thus neither normal cell division nor normal embryogenesis is required for lineage-specific expression. However, esterase does not appear in cytochalasin D blocked one-cell embryos. These observations confirm the traditional view that C. elegans development is "mosaic," with each cell following a defined independent program of gene expression. ------------------- Key: 870 Medline: 86161670 Authors: Ellis HM;Horvitz HR Title: Genetic control of programmed cell death in the nematode C. elegans. Citation: Cell 44: 817-829 1986 Type: ARTICLE Genes: ced-1 ced-3 ced-4 Abstract: The wild-type functions of the genes ced-3 and ced-4 are required for the initiation of programmed cell deaths in the nematode Caenorhabditis elegans. The reduction or loss of ced-3 or ced-4 function results in a transformation in the fates of cells that normally die; in ced-3 or ced-4 mutants, such cells instead survive and differentiate, adopting fates that in the wild type and associated with other cells. ced-3 and ced-4 mutants appear grossly normal in morphology and behavior, indicating that programmed cell death is not an essential aspect of nematode development. The genes ced-3 and ced-4 define the first known step of a developmental pathway for programmed cell death, suggesting that these genes may be involved in determining which cells die during C. elegans development. ------------------- Key: 871 Medline: Authors: Maruyama K;Hori R Title: Isolation and characterization of metallothionein from nematode C. elegans. Citation: Eisei Kagak 32: 22-27 1986 Type: ARTICLE Genes: Abstract: ------------------- Key: 872 Medline: 86177565 Authors: Goddard JM;Weiland JJ;Capecchi MR Title: Isolation and characterization of C. elegans DNA sequences homologous to the v-abl oncogene. Citation: Proceedings of the National Academy of Sciences USA 83: 2172-2176 1986 Type: ARTICLE Genes: Abstract: DNA sequences homologous to the v-abl oncogene were isolated from a Caenorhabditis elegans genomic library by their ability to hybridize with a v-src probe. The DNA sequence of 2465 nucleotides of one clone was determined. This region corresponds to the 5' protein kinase domain of v-abl plus approximately equal to 375 base pairs toward the 3' end. Four potential introns were identified. The homology between the deduced amino acid sequence of the C. elegans clone and that of the 1.2-kilobase-pair protein kinase region of v-abl is 62%. The tyrosine residue corresponding to the tyrosine that is phosphorylated in the v-src protein is conserved in the C. elegans sequence. When 95 amino acids around this tyrosine were compared with the corresponding sequences of Drosophila c-abl, v-abl, and v-src, the identities were 83%, 79%, and 56%, respectively. Hybridization of the cloned DNA with C. elegans poly(A)+ RNA revealed a major transcript of 4.4 kilobases. ------------------- Key: 873 Medline: 86281690 Authors: Heine U;Blumenthal T Title: Characterization of regions of the C. elegans X chromosome containing vitellogenin genes. Citation: Journal of Molecular Biology 188: 301-312 1986 Type: ARTICLE Genes: uvt-1 uvt-2 uvt-3 uvt-4 uvt-5 uvt-6 uvt-7 vit-1 vit-2 vit-3 vit-4 vit-5 vit-6 Abstract: Caenorhabditis elegans contains a family of vitellogenin genes consisting of five closely related genes (vit-1 to vit-5) coding for 186,000 Mr yolk proteins, and one distantly related gene (vit-6) encoding a 200,000 Mr precursor to two smaller yolk proteins. We demonstrate here that, although vit-1 to vit-5 are not clustered (with the exception of vit-3 and vit-4), they are all on the X chromosome. In contrast, vit-6 is autosomal. The genes are strictly regulated during development: they are activated in the intestine of the hermaphrodite worm, following the last larval molt. In order to determine whether the vit genes are contained within chromosomal domains of similarly regulated genes, we have used the chromosomal "walking" technique to isolate 55,000 to 60,000 base-pairs of DNA surrounding each of the X-linked genes and determined the developmental specificity of nearby genes. In the total of 235,400 base-pairs of cloned DNA, seven genes, in addition to the five vit genes, were found. The average gene spacing is approximately 20,000 base-pairs per gene but is highly variable, ranging from less than 2000 to more than 38,000 base-pairs. The seven newly identified genes, called uvt-1 to uvt-7, specify RNAs varying in size from 500 to 2700 bases. With the exception of uvt-4, all of the genes are developmentally regulated; but the patterns of regulation are quite variable, and all are different from the vitellogenin genes. The vit genes, therefore, are not contained within co-regulated chromosomal domains. We also searched for the presence of repetitive DNA, but only four such sequences were found. ------------------- Key: 874 Medline: 86230107 Authors: Emmons SW;Roberts S;Ruan K-S Title: Evidence in a nematode for regulation of transposon excision by tissue-specific factors. Citation: Molecular & General Genetics 202: 410-415 1986 Type: ARTICLE Genes: Abstract: The transposable element Tc1 in Caenorhabditis elegans undergoes an excision reaction, which can be detected in a Southern hybridization as the appearance of empty chromosomal insertion sites. This excision reaction is under tissue-specific regulation in that it occurs at much higher frequency in somatic cells than in the germ line. We show here that this regulation is likely to be due to the action of tissue- specific factors that either promote excision in somatic tissues or repress it in the germ line. The rate of excision of elements at five distinct chromosomal sites has been measured by a method that avoids ambiguities due to cell division. All these elements are found to undergo excision at closely similar rates during the L1 larval stage. No distinct difference exists among the elements at different sites that would suggest regulation by flanking sequences. ------------------- Key: 875 Medline: 86185142 Authors: Hirsh D;Cox GN;Kramer JM;Stinchcomb D;Jefferson R Title: Structure and expression of the collagen genes of C. elegans. Citation: Annals of the New York Academy of Sciences 460: 163-171 Type: REVIEW Genes: bli-6 col-1 col-2 col-3 dpy-20 let-4 Abstract: The cuticle of the nematode Caenorhabditis elegans is composed of collagen. The cuticle is tough and elastic and protects this soil nematode from its harsh environment. As the nematode grows from a juvenile larva to a sexually mature adult, it molts four times. In addition, under starvation conditions the animal can molt to form a dauer larvae that is capable of surviving in the absence of food but can molt again in the presence of nutrients and reenter the normal life cycle. During each molt, the nematode discards its old cuticle and forms a new one. The cuticles formed during the molts differ morphologically from each other. In addition, the patterns of collagens present seem to differ. The cuticles are synthesized by the underlying syncytial hypodermal cells. Thus, given the complexity in structure and protein composition and the temporal modulation of the formation of the cuticles, there must be a rather complicated and delicate control of the expression of the genes that encode the cuticular components. We began some time ago to try to understand the structure of the collagens, the collagen genes, the arrangement of the genes, and their patterns of expression in C. elegans. The organism is especially suited to these kinds of inquiries. It is easy to handle for biochemical preparations. It has a small genome and its genetics has been extremely well studied, making it amenable to classical genetic methods and to recombinant DNA manipulations. By studying the collagens and the collagen genes of C. elegans, we are able to investigate these components from an organism more primitive than the vertebrates from which most of the current information is derived. Thus, these studies acquire a comparative biochemical and evolutionary aspect. Further, these studies address the structure and expression of multigene families because of the apparently large number of collagen genes. The genetic and biochemical methods available with C. elegans also make it possible to study the control of expression of collagen genes in a detailed molecular manner that is often more difficult with more complicated organisms. ------------------- Key: 876 Medline: 86205944 Authors: Miller DM;Stockdale FE;Karn J Title: Immunological identification of the genes encoding the four myosin heavy chain isoforms of C. elegans. Citation: Proceedings of the National Academy of Sciences USA 83: 2305-2309 1986 Type: ARTICLE Genes: myo-1 myo-2 myo-3 Abstract: The nematode Caenorhabditis elegans produces four distinct myosin heavy chain (MHC) isoforms, A, B, C, and D. The MHC A and MHC B proteins are coordinately expressed in the body wall muscle and are incorporated into different regions of a single kind of thick filament. MHC C and MHC D are exclusively produced in the pharyngeal muscle. Previous studies of mutations that affect MHC B have shown that this isoform is encoded by the unc-54 gene. Three other MHC genes, myo-1, myo-2, and myo-3, were isolated from a C. elegans genomic library by hybridization with fragments of the unc-54 gene. We have now established the MHC isoform encoded by each gene. Restriction fragments from each of these genes were cloned in the plasmid expression vector pUR288, producing fusion proteins between Escherichia coli beta-galactosidase and portions of the MHC rod domains of each gene. The hybrid proteins were screened with a panel of 18 isoform-specific monoclonal antibodies. The results demonstrate that myo-1 encodes MHC D, myo-2 encodes MHC C, and myo-3 encodes MHC A. ------------------- Key: 877 Medline: 86205995 Authors: Moerman DG;Benian GM;Waterston RH Title: Molecular cloning of the muscle gene unc-22 in C. elegans by Tc1 transposon tagging. Citation: Proceedings of the National Academy of Sciences USA 83: 2579-2583 1986 Type: ARTICLE Genes: unc-22 Abstract: The previously described mutator system of Caenorhabditis elegans var. Bergerac has as one of its targets unc-22, a previously uncloned gene on chromosome IV important in assembly and function of the body wall musculature. By assuming that the mutator activity involved transposition of the repetitive element Tc1 into the unc-22 gene we have succeeded both in cloning the unc-22 gene and in demonstrating that Tc1 transposition is the principal basis of the mutator activity in the Bergerac strain. Although germ-line excision of Tc1 is sensitive to genetic background, somatic excision appears to be less so, suggesting that Tc1 movement is controlled differently in germ- line and somatic tissue. The availability of a transposon-based mutator system should aid in the cloning of additional genes in C. elegans, and the particular properties of this Tc1 system may provide information about the control of transposable element activity more ------------------- Key: 878 Medline: 86196252 Authors: Ward S;Roberts TM;Strome S;Pavalko FM;Hogan E Title: Monoclonal antibodies that recognize a polypeptide antigenic determinant shared by multiple C. elegans sperm-specific proteins. Citation: Journal of Cell Biology 102: 1778-1786 1986 Type: ARTICLE Genes: Abstract: Four monoclonal antibodies that are directed against antigens present in sperm and absent from other worm tissues were characterized. Antibody TR20 is directed against the major sperm proteins, a family of small, abundant, cytoplasmic proteins that have been previously described (Klass, M. R., and D. Hirsh, 1981, Dev. Biol., 84:299-312; Burke, D. J., and S. Ward, 1983, J. Mol. Biol., 171:1-29). Three other antibodies, SP56, SP150, and TR11, are all directed against the same set of minor sperm polypeptides that range in size from 29 to 215 kD. More than eight different sperm polypeptides are antigenic by both immunotransfer and immunoprecipitation assays. The three antibodies are different immunoglobulin subclasses, yet they compete with each other for antigen binding so they are directed against the same antigenic determinant on the multiple sperm proteins. This antigenic determinant is sensitive to any of six different proteases, is insensitive to periodate oxidation or N-glycanase digestion, and is detectable on a polypeptide synthesized in vitro. Therefore, the antigenic determinant resides in the polypeptide chain. However, peptide fragments of the proteins are not antigenic, thus the determinant is likely to be dependent on polypeptide conformation. The antigenic determinant shared by these proteins could represent a common structural feature of importance to the localization or cellular specificity of these proteins. ------------------- Key: 879 Medline: 86196253 Authors: Roberts TM;Pavalko FM;Ward S Title: Membrane and cytoplasmic proteins are transported in the same organelle complex during nematode spermatogenesis. Citation: Journal of Cell Biology 102: 1787-1796 1986 Type: ARTICLE Genes: fer-1 him-5 Abstract: During the development of pseudopodial spermatozoa of the nematode, Caenorhabditis elegans, protein synthesis stops before differentiation is completed. Colloidal gold conjugates of monoclonal antibody SP56, which binds to the surface of spermatozoa, and TR20, which recognizes the major sperm cytoplasmic protein (MSP), were used to label thin sections of testes embedded in Lowicryl K4M in order to follow polypeptides from their synthesis early in spermatogenesis to their segregation to specific compartments of the mature cell. Both antigens are synthesized in primary spermatocytes and are assembled into a unique double organelle, the fibrous body-membranous organelle (FB-MO) complex. However, the antigens are localized in different regions of this FB-MO complex. As described in detail, the assembly of proteins into the FB-MO complex allows both membrane and cytoplamsic components to be concentrated in the spermatids after meiosis. Then, the stepwise disassembly of this transient structure ensures delivery of each component to its final destination in the mature spermatozoan: MSP filaments in the fibrous body depolymerize, releasing MSP into the cytoplasm and the membranous organelles fuse with the plasma membrane, delivering SP56 antigen to the surface. ------------------- Key: 881 Medline: Authors: Greenwald I;Martinez-Arias A Title: Programmed cell death in invertebrates. Citation: Trends in Neurosciences 7: 179-181 1984 Type: REVIEW Genes: Abstract: Cell death is a developmental fate that is commonly observed during invertebrate and vertebrate neurogenesis. In many cases, these deaths appear to be 'programmed', i.e. they occur predictably at specific times and places. How such programmed cell deaths are determined and why they occur have long intrigued developmental neurobiologists. Here, we consider some recent papers describing how programmed cell death is incorporated into neural developmental strategies in three invertebrate phyla. ------------------- Key: 882 Medline: Authors: Siddiqui S;Culotti J Title: A neural antigen conserved in different invertebrates. Citation: Annals of the New York Academy of Sciences 435: 341-343 Type: REVIEW Genes: Abstract: Antibodies to neuronal antigens have emerged as valuable markers for molecules central to neural development and function in invertebrates and vertebrates. Such immunological probes have been used for both localizing proteins in cells and for identifying neural antigens by immunoblotting. Antibodies to neural components have the added advantage that they can be used to study the morphology of the nervous system at the level of light microscopy without having to resort to electron microscopy. Such markers could be very useful for the characterization of neuronal growth abnormalities in mutants of the nematode Caenorhabditis elegans since the structure and wiring of every one of its 302 neurons are known. ------------------- Key: 883 Medline: Authors: Fodor A;Deak P Title: The isolation and genetic analysis of a C. elegans translocation (szT1) strain bearing an X-chromosome balancer. Citation: Journal of Genetics 64: 143-157 1985 Type: ARTICLE Genes: szT1 Abstract: A single X-chromosome balancer-bearing C. elegans hermaphrodite, as a founder of a strain (AF1), was isolated directly from F1 progeny of irradiated + dpy-8 unc-3/lon-2 + + hermaphrodites on the basis of the absence of recombinant F2 categories. The balancer chromosome (Bal-X-1) suppresses recombination over a two-thirds section of the X chromosome (between genes dpy-8 and let-2) and is associated with a reciprocal translocation between linkage groups (LG) X and I. Animals homozygous for the translocation (szT1 (X;I)) are nonviable. Hermaphrodites heterozygous for the translocation segregate male self-progeny at a frequency of 0.08-0.12. Bal-X-1 carries the marker mutation lon-2(e678) and can be detected cytologically. This balancer chromosome proved useful for maintaining a number of X-linked lethal mutations and ------------------- Key: 884 Medline: Authors: Ward S Title: Asymmetric localization of gene products during the development of C. elegans spermatozoa. Citation: "Gametogenesis and the Early Embryo." 44th Symposium of the Society for Developmental Biology. Gall JG (ed), Alan R. Liss, NY. : 55-75 1986 Type: REVIEW Genes: fer-1 Abstract: (This is the conclusion from the article.) The results described here show that there are two steps in spermatozoan development that involve highly asymmetric segregation of gene products. When the spermatid buds off the residual body sperm-specific proteins are ensured distribution to the spermatid by their assembly into a transient organelle. Proteins with three different destinations in the final spermatozoa are all transported together in this organelle: a secretory protein in the lumen of the head, a membrane component in the membrane of the body of the organelle, and a cytoplasmic protein, MSP, in the paracrystalline fibrous body. In contrast to these proteins destined for the mature sperm, the cytoplasmic proteins actin and tubulin are specifically excluded from the sperm. In the case of tubulin this is accomplished by segregation of the intact spindle into the residual body. Actin is also segregated in a filamentous form to the residual body. It is possible that the meiotic spindle could be the basis for the segregation of the membranous organelle-fibrous bodies. If there were some attachment between these organelles and the outside of the spindle they might be moved by a mechanism similar to that which moves the chromosomes. Mitochondria are also found collected around the spindle during Drosophila spermatogenesis and are likewise segregated to the maturing spermatid (Fuller, this volume). Once the spermatid has separated from the residual body it has abandoned the machinery that is usually thought to establish and maintain cell shape, microtubules, and microfilaments. Yet the cell can still undergo a major rearrangement of its contents and establish and maintain a stable asymmetric shape. The centriole does not participate in this asymmetry, so there must be some other cytoskeletal determinants in these cells. One candidate is the 2-nm wide filaments that have been found throughout the pseudopod [Roberts, 1983]. The composition and function of these filaments is not yet known, but they may participate in shape determination and motility. The results presented here only begin to hint at answers to the general questions posed in the Introduction. It is our hope that molecular analysis of the defects in mutants such as fer-l will lead to a more explicit description of how specific gene products determine the ------------------- Key: 885 Medline: Authors: Strome S Title: Establishment of asymmetry in early C. elegans embryos: Visualization with antibodies to germ cell components. Citation: "Gametogenesis and the Early Embryo." 44th Symposium of the Society for Developmental Biology. Gall JG (ed), Alan R. Liss, NY. : 77-95 1986 Type: REVIEW Genes: fer-1 zyg-9 Abstract: (This is the conclusion from the article.) C. elegans embryos are particularly well suited to studying the establishment of asymmetry and specification of cell fates. They are visibly asymmetric, and segregation of developmental potential occurs early in embryogenesis. We have generated and continue to generate antibody probes to the components that come together at fertilization, namely, sperm and oocyte components. These probes are useful in three ways: 1) They provide us with landmarks of normal development. 2) They allow us to analyze the defects caused by perturbing embryos mutationally and with drugs. 3) They may be used in microinjection experiments to interfere with specific events and processes in early development. It is hoped that a combined genetic and immunologic approach will allow us to better understand this most important first phase in the development of an adult organism from two fused gametes. ------------------- Key: 886 Medline: Authors: Kimble J;Barton KM;Schedl TB;Rosenquist TA;Austin JA Title: Controls of postembryonic germ line development in C. elegans. Citation: "Gametogenesis and the Early Embryo." 44th Symposium of the Society for Developmental Biology. Gall JG (ed), Alan R. Liss, NY. : 97-110 1986 Type: REVIEW Genes: fem-1 fem-2 fem-3 fog-2 glp-1 her-1 tra-1 tra-2 tra-3 Abstract: (Summary from the back page.) The choice between spermatogenesis and oogenesis is controlled by a small number of switch genes. Most of the somatic sex-determination control genes of C. elegans also function to specify germ line sex. However, these master control genes must be regulated in the hermaphrodite germ line to achieve the production of both male and female gametes in the hermaphrodite, essentially female, soma. We have exploited genetic selections to isolate both dominant and recessive mutations that influence the sex of the hermaphrodite germ line. These selections have uncovered several sex-determination genes that were previously unknown. They also have been useful for isolation of gain-of-function alleles of fem-3, tra-2, and other new sex determination loci. Such gain-of-function alleles provide information critical for understanding the functions of these control loci. The gain-of-function alleles of fem-3 have provided evidence that this locus is of particular import in specification of the male sex. The reciprocal effect on sexual transformation observed for gain-of-function and loss-of-function alleles of fem-3 is supportive of its role as a switch-gene for sex determination. The masculinization phenotype and the late TSP of the gain-of-function alleles are consistent with the idea that the fem-3 gene product must be negatively regulated in the hermaphrodite germ line so that it can be packaged into oocytes for embryogenesis without transforming those oocytes into sperm. A deeper understanding of the pathway of sex-determination control depends on identification of the genes central to the pathway and genetic analysis of several types of alleles of these genes. The genetic selections described above will aid in the identification of new sex-determination genes and in the isolation of multiple alleles of genes central to this pathway. Our focus on the control of germ line sex determination was based on the possibility, since proven to be fact, that tissue-specific controls influence sex in the germ line. Such tissue-specific controls, if present in all tissues, might complicate the analysis of sex determination when viewed at the organismal level. A molecular understanding of sex determination controls in general, and fem-3 function in particular, awaits the biochemical isolation of the sex-determination genes and their products. To this end, the selections described here are being used to isolate alleles of the sex-determination genes caused by insertion of the transposable element, Tc1, for molecular cloning of those genes by transposon tagging. ------------------- Key: 887 Medline: 86163010 Authors: Schierenberg E Title: Cell determination during early embryogenesis of the nematode C. elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 50: 59-68 1985 Type: REVIEW Genes: emb-5 Abstract: Investigations in many different organisms indicate that early embryonic development is controlled essentially by maternal gene products, which are deposited in the unfertilized egg. Nevertheless, how a specific developmental pathway for a cell is determined, including eventual functional differentiation, as well as decisions such as the number of progeny a cell will produce and its final position in the organism remain open questions. Some cases in which determination of cell fate is obviously mediated by differential segregation of cytoplasmic components have been reported for somatic and germ line cells. On the other hand, models for the asymmetric segregation of developmental potential via chromosome lineage have been discussed. The nematode Caenorhabditis elegans is a suitable organism for studying the question of cell determination during development. On the basis of classical studies, nematodes are thought to be the best example of "mosaic" development. Laser-induced cell ablations in embryos of C. elegans, in fact, support the notion that here embryogenesis proceeds essentially in a cell-autonomous way. This concept allows an easier interpretation of experiments, because in the first approximation no intercellular regulation phenomena must be taken into consideration..... ------------------- Key: 888 Medline: 86163024 Authors: Hirsh D;Kemphues KJ;Stinchcomb DT;Jefferson R Title: Genes affecting early development in Caenorhabditis Citation: Cold Spring Harbor Symposia on Quantitative Biology 50: 69-78 1985 Type: REVIEW Genes: par-1 Abstract: We have identified several genes that appear to control the early events in the development of Caenorhabditis elegans. We continue to study them genetically and characterize them morphologically. We describe here three of these genes that appear to be involved in establishing the organization of the embryonic cytoplasm and in positioning the early cleavage furrows. In addition, we review our continuing studies on the characterization of the C. elegans genome, the goal of which has been to facilitate the study of the molecular basis of the role of these genes in early development... ------------------- Key: 889 Medline: 86163049 Authors: Fixsen W;Sternberg P;Ellis H;Horvitz R Title: Genes that affect cell fates during the development of C. elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 50: 99-104 1985 Type: REVIEW Genes: let-23 lin-1 lin-2 lin-3 lin-4 lin-7 lin-8 lin-9 lin-10 lin-11 lin-12 lin-13 lin-14 lin-15 lin-17 lin-22 lin-26 lin-28 lin-31 lin-34 lin-39 unc-86 Abstract: (This is the first 2 paragraphs of the paper.) The development of a multicellular organism involves the generation of many different cell types from a single-celled fertilized egg. An understanding of the molecular mechanisms that cause cells to become different from one another is a fundamental goal of developmental biology. One organism well suited for the study of this problem at the level of single cells and individual cell divisions is the nematode Caenorhabditis elegans. The complete pattern of cell divisions, migrations, and differentiations that occur during the development of C. elegans is known (Sulston and Horvitz 1977; Kimble and Hirsh 1979; Sulston et al. 1980, 1983). Two factors have facilitated the elucidation of this detailed knowledge of C. elegans development: (I) It is relatively easy to observe individual cells in living nematodes directly and continuously, using Nomarski differential interference contrast light microscopy. (2) The C. elegans cell lineage (i.e., the pattern of cell divisions and the fates of the cells generated by those divisions) is essentially invariant. Many cell fates appear to be autonomously (intrinsically) determined during the development of C. elegans; in addition, some cell fates are specified by cell interactions and therefore must be controlled extrinsically (Sulston and Horvitz 197% 1981; Sulston and White 1980; Kimble 1981; Sulston et al. 1983). To understand the molecular basis of the generation of cellular diversity, it will be important to define, isolate, and characterize molecules responsible for both the intrinsic and extrinsic determination of cell fates. We have taken a genetic approach toward the identification of such molecules. Specifically, mutations that cause cells that normally express different cell fates to express instead the same cell fate should define genes (and therefore molecules) that are involved (either intrinsically or extrinsically) ------------------- Key: 890 Medline: 86162975 Authors: Emmons SW;Ruan KS;Levitt A;Yesner L Title: Regulation of Tc1 transposable elements in C. elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 50: 313-320 1985 Type: REVIEW Genes: Abstract: C. elegans strains contain variable numbers of a 1.6-kb transposable genetic element. Activity of this element, which is denoted Tcl, shows regulation at at least two levels. At one level, excision of Tcl elements occurs in somatic cells at a frequency several orders of magnitude higher than in germ cells. Evidence is presented suggesting that this results from regulation at the level of trans-acting functions that are required for excision or that repress excision. At the second level, germ line transposition of Tcl occurs at greater frequency in some strains than in others. The hypothesis is proposed that this is because Tcl is one component of a two-element system, the second element of which differs between strains. Evidence for a second putative transposable element family in C. elegans is presented. This family has properties that suggest a relationship to Tcl. This possibility is currently under investigation. ------------------- Key: 891 Medline: 86163008 Authors: Wood WB;Meneely P;Schedin P;Donahue L Title: Aspects of dosage compensation and sex determination in C. elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 50: 575-583 1985 Type: REVIEW Genes: act-4 dpy-21 dpy-22 dpy-23 dpy-26 dpy-27 dpy-28 her-1 let-1 let-2 lin-2 lin-14 lin-15 tra-1 unc-3 unc-54 Abstract: The nematode Caenorhabditis elegans has two sexes, hermaphrodites and males. Hermaphrodites normally have two X chromosomes (XX or 2X) and males only one (XO or 1X). There is no Y chromosome, and sex is determined by the X/A ratio, i.e., the ratio of X chromosomes to sets of autosomes. The X/A ratio acts to determine sex through a set of at least seven interacting autosomal genes, which have been defined, characterized, and shown to act as a regulatory pathway, primarily by Hodgkin and co-workers. The first gene in the pathway, her-1, acts through five intervening genes to regulate the major switch gene tra-1, whose activity determines somatic sexual development. At an X/A ratio of 1.0, her-1 activity is low and tra-1 acivity is high, leading to hermaphrodite development. At an X/A ratio of 0.5, her-1 activity is high and tra-1 activity is low, leading to male development. Loss-of-function mutations in the her-1 gene transform 1X animals into fertile hermaphrodites and have no effect on 2X hermaphrodites. Loss-of-function mutations in the tra-1 gene transform 2X animals into fertile males and have no effect on 1X males.... ------------------- Key: 892 Medline: 86163009 Authors: Hodgkin J;Doniach T;Shen M Title: Sex determination pathway in the nematode C. elegans: Variations on a theme. Citation: Cold Spring Harbor Symposia on Quantitative Biology 50: 585-594 1985 Type: REVIEW Genes: egl-41 fem-1 fem-2 fem-3 fog-1 fog-2 her-1 lin-2 lin-7 mab-3 mab-9 mog-3 tra-1 tra-2 tra-3 eDf18 eDf19 Abstract: Sex determination in Caenorhabditis elegans is a problem that lends itself to investigation by a "top-down" approach. The primary sex-determining signal, the ratio of X chromosomes to autosomes, is known and can be subjected to experimental manipulation. It has also been possible to identify a set of regulatory genes that respond to this primary signal and act to direct development along one of two alternative developmental pathways. Sexual dimorphism in this animal is extensive, involving sexually specialized differentiation in many different tissues, and thus a variety of events must be controlled correctly in order to achieve normal sexual differentiation. The same set of major regulatory genes appears to be involved in all of these events, but there are additional minor controls that seem to be necessary in some tissues but not in others. The interactions between these various genes have been extensively investigated, in the hope of understanding how the whole process of sexual differentiation is coordinated, and why it is organized in this way. ------------------- Key: 893 Medline: Authors: Waterston RH;Moerman DG;Benian GM;Barstead RJ;Mori I;Francis R Title: Muscle genes and proteins in C. elegans. Citation: "Molecular Biology of Muscle Development." UCLA Symposia on Molecular & Cellular Biology. Emerson C, Fischman D, Nadal-Ginard B and Siddiqui MAQ (eds). 29: 605-617 1986 Type: REVIEW Genes: sup-3 unc-15 unc-22 unc-45 unc-54 unc-82 Abstract: Our efforts to understand the role of each of the muscle genes in C. elegans myogenesis and muscle contraction have followed three different but interrelated approaches. Antibodies have been developed and used to define additional components of C. elegans body wall musculature. Studies of gene interactions have revealed epistatic relationships that help to define the function of some gene products. Transposition of the repetitive element Tc1 into the muscle gene unc-22 has allowed us to clone this gene and begin the dissection of its function in the nematode. ------------------- Key: 894 Medline: Authors: Otsuka AJ Title: sup-3 suppression affects muscle structure and myosin heavy chain accumulation in C. elegans. Citation: "Molecular Biology of Muscle Development." UCLA Symposia on Molecular & Cellular Biology. Emerson C, Fischman D, Nadal-Ginard B and Siddiqui MAQ (eds). 29: 619-628 1986 Type: REVIEW Genes: sup-3 unc-15 unc-54 unc-87 eDf1 Abstract: Suppression of paramyosin mutations by sup-3 has been shown to result in the formation of thick filaments of normal appearance distributed in regions of partially organized muscle lattice structure. In the presence or absence of muscle mutations, sup-3 results in the elevation of MHCA, one of the two known body-wall myosin heavy chains. The correlation of sup-3 mutations with MHCA increase suggests that sup-3 may regulate the expression or accumulation of MHCA. ------------------- Key: 895 Medline: Authors: Miller DM;Maruyama I Title: The sup-3 locus is closely linked to a myosin heavy chain gene in C. elegans. Citation: "Molecular Biology of Muscle Development." UCLA Symposia on Molecular & Cellular Biology. Emerson C, Fischman D, Nadal-Ginard B and Siddiqui MAQ (eds). 29: 629-638 1986 Type: REVIEW Genes: myo-1 myo-2 myo-3 sup-3 unc-15 unc-54 eDf1 Abstract: C. elegans body wall muscle thick filaments are assembled from two different types of myosin heavy chain, MHC A and MHC B. The structural gene for the MHC A protein has been identified from the reaction of bacterial fusion peptides with specific monoclonal antibodies. We have also shown that a mutation in the sup-3 locus that enhances the accumulation of the MHC A protein is closely linked to the MHC A gene. A model of sup-3 action is proposed. ------------------- Key: 896 Medline: Authors: Epstein HF Title: Differential roles of myosin isoforms in filament assembly. Citation: "Molecular Biology of Muscle Development." Emerson C, Fischman D, Nadal-Ginard B and Siddiqui MAQ (eds). 29: 653-666 1986 Type: REVIEW Genes: myo-3 sup-3 unc-15 unc-52 unc-54 Abstract: Wild-type body wall muscle cells of Caenorhabditis elegans produce at a constant ratio two myosin heavy chain isoforms, A and B, that form homodimeric myosins. Electron microscopy of negatively stained complexes of isoform-specific antibodies with isolated thick filaments shows that the surface of the 9.7 =B5m long filament is differentiated with respect to myosin content: a medial 1.8 =B5m zone contains myosin A and two polar 4.4 = =B5m zones contain myosin B. Biochemical and electron microscopic studies show that at 0.45 M KC1, pH 6.35, myosin B and paramyosin are solubilized. The medial all-myosin A region with novel core structures extending in a polar manner remain. These dissociation experiments suggest a sequential model for wild-type thick filament assembly in which myosins A and B would participate in the initiation and termination of assembly, respectively. Analysis of mutant thick filaments clarifies the relationship of the myosin isoforms. CB190 (unc-54 I) thick filaments contain myosin A only and have normal length. CB1214 (unc-15 I) mutants produce no paramyosin, and their thick filaments are composed of a medial myosin region ------------------- Key: 897 Medline: 87064462 Authors: Harris LJ;Rose AM Title: Somatic excision of transposable element Tc1 from the Bristol genome of C. elegans. Citation: Molecular and Cellular Biology 6: 1782-1786 1986 Type: ARTICLE Genes: dpy-5 dpy-14 unc-13 unc-22 unc-54 Abstract: We investigated the ability of the transposable element Tc1 to excise from the genome of the nematode Caenorhabditis elegans var. Bristol N2. Our results show that in the standard lab strain (Bristol), Tc1 excision occurred at a high frequency, comparable to that seen in the closely related Bergerac strain BO. We examined excision in the following way. We used a unique sequence flanking probe (pCeh29) to investigate the excision of Tc1s situated in the same location in both strains. Evidence of high-frequency excision from the genomes of both strains was observed. The Tc1s used in the first approach, although present in the same location in both genomes, were not known to be identical. Thus, a second approach was taken, which involved the genetic manipulation of a BO variant, Tc1(Hin). The ability of this BO Tc1(Hin) to excise was retained after its introduction into the N2 genome. Thus, we conclude that excision of Tc1 from the Bristol genome occurs at a high frequency and is comparable to that of Tc1 excision from the Bergerac genome. We showed that many Tc1 elements in N2 were apparently functionally intact and were capable of somatic excision. Even so, N2 Tc1s were prevented from exhibiting the high level of heritable transposition displayed by BO elements. We suggest that Bristol Tc1 elements have the ability to transpose but that transposition is heavily repressed in the gonadal tissue. ------------------- Key: 898 Medline: 86221667 Authors: Greenwald I;Horvitz HR Title: A visible allele of the muscle gene sup-10 X of C. elegans. Citation: Genetics 113: 63-72 1986 Type: ARTICLE Genes: sup-9 sup-10 sup-11 sup-18 unc-93 Abstract: In this paper, we extend our previous analyses of a set of genes in Caenorhabditis elegans that are involved in muscle structure and function: unc-93 III, sup-9 II, sup-10 X and sup-11 I. We describe an unusual, visible allele of sup-10, examine how this allele interacts genetically with mutations in other genes of this set and propose that the wild-type products of the unc-93 and sup-10 loci may be components of a protein complex. We also describe a new gene of this set, sup-18 III, and the interaction of sup-18 alleles with mutations in the other genes. ------------------- Key: 899 Medline: 86323051 Authors: Vanfleteren JR;Van Bun SM;Delcambe LL;Van Beeumen JJ Title: Multiple forms of histone H2B from the nematode C. elegans. Citation: Biochemical Journal 235: 769-773 1986 Type: ARTICLE Genes: Abstract: The complete amino acid sequence of histone H2B from the nematode Caenorhabditis elegans was determined. The protein as obtained by us is a mixture of multiple forms. Approx. 90% of the molecules consist of a polypeptide chain of 122 amino acids with alanine as N-terminal residue and proline at the second position. In the remaining 10% alanine is lacking and the chain starts with proline. In addition to the heterogeneity of chain length, polymorphism occurs at the positions 7 (Ala/Lys), 14 (Ala/Lys) and 72 (Ala/Ser) of the major chain and at position 6 (Ala/Lys) of the shorter chain. In the N- terminal third of the molecule there is a high degree of sequence homology to the corresponding region in H2B from Drosophila (insect), Patella (mollusc) and Asterias (starfish). In contrast, this part of the molecule differs considerably from mammalian histone H2B. ------------------- Key: 900 Medline: 86229306 Authors: Meheus L;Vanfleteren JR Title: Nuclease digestion of DNA and RNA in nuclei from young adult and senescent C. elegans (Nematoda). Citation: Mechanisms of Ageing & Development 34: 23-34 1986 Type: ARTICLE Genes: Abstract: Nuclei prepared from young adult and senescent Caenorhabditis elegans (Nematoda) were subjected to digestion by micrococcal nuclease and DNaseI. The kinetics of digestion of nuclei by micrococcal nuclease showed no change with age. There was, however, an age-related increase of acid-soluble deoxyribonucleotides released by DNaseI, suggesting that subtle alterations of chromatin conformation occur in aged nematodes. The ratio of nuclear RNA to DNA decreased and the nuclear RNA became more susceptible to enzymatic degradation as the worms grew old. These findings appear to indicate that nuclear RNA is less protected by protein in old nematodes. The decline of the nuclear RNA/DNA ratio with age is in good agreement with the generally accepted idea that there is a reduced level of RNA and protein synthesis in old animals. ------------------- Key: 901 Medline: Authors: Kampfe L;Kreil V;Ullrich H-L Title: Effects of lathyrogenous compounds and of the synergist piperonyl butoxide (PBO) on the free-living nematode species C. briggsae and Rhabditis oxycerca. Citation: Zoologische Jahrbucher - Abt. Zool. Phys. der Tiere 90: 257-271 1986 Type: ARTICLE Genes: Abstract: Some substances produced by Lathyrus species cause disorders of the nervous system and connective tissue in vertebrates. These disorders are known as lathyrism and are characterized by suppression of molecular cross linking in collagenous structures. Several lathyrogenous agents caused restricted motion activity in the free-living nematode species Rhabditis oxycerca and Caenorhabditis briggsae apparently through effects on the nervous system (neurolathyrism). However, the death rate was only slightly increased. Retarded development and reduced reproduction occurred after long-term exposure to isoniazide hydrazinehydrate ane and phenylhydrazine. These effects may be related to disorders in the collagen structure and are comparable to osteolathyrism in vertebrates. Under non-sterile conditions the inhibitory effects of isoniazide and hydrazinchydrate on reproduction and development were markedly diminished, apparently due to microbial degradation of these substances. In combination with thiosemicarbazide the insecticidal synergistic substance piperonyl butoxide (PBO), known as a MfO-inhibitor, primarily restrained reproduction mainly by retarding larval development to such a degree that puberty could not be reached. Under axenic conditions a synergistic effect between PBO and isoniazide was also seen. PBO alone had a distinct nematicidal effect as well. Its synergistic effect is probably due to toxic metabolites ------------------- Key: 902 Medline: 87083575 Authors: Goldstein P Title: The synaptonemal complexes of C. elegans: Pachytene karyotype analysis of hermaphrodites from the recessive him-5 and him-7 mutants. Citation: Journal of Cell Science 82: 119-127 1986 Type: ARTICLE Genes: him-5 him-7 Abstract: The him-5 and him-7 mutants (high incidence of males) of Caenorhabditis elegans both showed increased rates of X chromosome non-disjunction (16% and 3%, respectively) but him-7 also had a high frequency of autosomal non-disjunction (34%). Synaptonemal complex (SC) karyotype analysis revealed a haploid chromosome number of six in each strain. Alterations in him-7 nuclear morphology were observed but there were no aberrations in SC structure that could account for the increased frequency of autosomal non-disjunction. However, the frequency of X-chromosome non-disjunction occurred at predicted rates on the basis of the number of disjunction regulator regions (DRRs) present on the SCs. The observation that the levels of X-chromosome non-disjunction were not influenced by the increase in the frequency of autosomal non-disjunction supports the notion that the X chromosome is subject to separate controls during meiosis. The him-7 mutant is nested within the rad-4 map region on linkage group V, however, SC analysis did not reveal the physical position on the chromosome because of synaptic adjustment. ------------------- Key: 903 Medline: 86220667 Authors: Jansson H-B;Jeyaprakash A;Marban-Mendoza N;Zuckerman BM Title: C. elegans: Comparisons of chemotactic behavior from monoxenic and zxenic culture. Citation: Experimental Parasitology 61: 369-372 1986 Type: ARTICLE Genes: Abstract: Significant differences in chemotactic response of Caenorhabditis elegans were demonstrated for nematodes from monoxenic culture as compared to nematodes from axenic culture. These results support those of a previous study in which large differences in growth, development, behavior, and longevity were shown for C. elegans in comparative assays of the monoxenic and axenic regimes. ------------------- Key: 904 Medline: 86230667 Authors: Goldstein P Title: Nuclear aberrations and loss of synaptonemal complexes in response to diethylstilbestrol (DES) in C. elegans hermaphrodites. Citation: Mutation Research 174: 99-107 1986 Type: ARTICLE Genes: Abstract: In Caenorhabditis elegans, loss of viability and fertility is observed after treatment with DES. The decrease in life span is associated with senescent morphology of meiotic prophase nuclei, such that nuclei from young and old specimens cannot be differentiated. Aging in oocytes at the pachytene stage of meiotic prophase is manifested by nucleo-cytoplasmic aberrations, increased density of the nucleoplasm and cytoplasm and decrease in numbers of mitochondria. Increasing concentrations of DES are characterized by concomitant decrease in fertility and increased production of abnormal gametes. At DES concentrations higher than 1.25 micrograms/ml, synaptonemal complexes (SC) are absent from the nuclei, thus, effective pairing and segregation of homologous chromosomes is not possible. The absence of SCs may be the result of: a premeiotic colchicine-like effect that influences pairing of chromosomes; changes in the structure of the DNA due to DES binding that results in changes in expression of the DNA; and changes in temporal DNA synthesis in response to DES. Since the SC is essential for regulating pairing and subsequent separation of bivalents, the lack of an SC explains the loss of fertility, due to the production of unbalanced gametes, observed in DES-treated specimens. ------------------- Key: 905 Medline: 86251023 Authors: Aamodt EJ;Culotti JG Title: Microtubules and microtubule-associated proteins from the nematode C. elegans: periodic cross-links connect microtubules in vitro. Citation: Journal of Cell Biology 103: 23-31 1986 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans should be an excellent model system in which to study the role of microtubules in mitosis, embryogenesis, morphogenesis, and nerve function. It may be studied by the use of biochemical, genetic, molecular biological, and cell biological approaches. We have purified microtubules and microtubule- associated proteins (MAPs) from C. elegans by the use of the anti- tumor drug taxol (Vallee, R. B., 1982, J. Cell Biol., 92:435-44). Approximately 0.2 mg of microtubules and 0.03 mg of MAPs were isolated from each gram of C. elegans. The C. elegans microtubules were smaller in diameter than bovine microtubules assembled in vitro in the same buffer. They contained primarily 9-11 protofilaments, while the bovine microtubules contained 13 protofilaments. The principal MAP had an apparent molecular weight of 32,000 and the minor MAPs were 30,000, 45,000, 47,000, 50,000, 57,000, and 100,000- 110,000 mol wt as determined by SDS-gel electrophoresis. The microtubules were observed, by electron microscopy of negatively stained preparations, to be connected by stretches of highly periodic cross-links. The cross-links connected the adjacent protofilaments of aligned microtubules, and occurred at a frequency of one cross-link every 7.7 +/- 0.9 nm, or one cross-link per tubulin dimer along the protofilament. The cross-links were removed when the MAPs were extracted from the microtubules with 0.4 M NaCl. The cross-links then re-formed when the microtubules and the MAPs were recombined in a low salt buffer. These results strongly suggest that the cross-links are composed of MAPs. ------------------- Key: 906 Medline: 86275946 Authors: Kusch M;Edgar RS Title: Genetic studies of unusual loci that affect body shape of the nematode C. elegans and may code for cuticle structural proteins. Citation: Genetics 113: 621-639 1986 Type: ARTICLE Genes: rol-8 sqt-1 sqt-2 sqt-3 Abstract: In Caenorhabditis elegans, four loci (sqt-1, sqt-2, sqt-3 and rol-8) in which mutations affect body shape and cuticle morphology have unusual genetic properties. Mutant alleles of sqt-1 can interact to produce animals with a variety of mutant phenotypes: left roller, right roller, dumpy and long. At least three mutant phenotypes are specified by mutations in the sqt-3 locus. Most alleles at these loci are either dominant or cryptic dominant (i.e., are dominant only in certain genetic backgrounds). Most alleles of these loci exhibit codominance. Two putative null alleles of the sqt-1 locus produce a wild-type phenotype. Many alleles of these genes demonstrate unusual intergenic interactions that are not the result of simple epistasis: animals doubly heterozygous for mutations at two loci often display unexpected and unpredictable phenotypes. We suggest that these genetic properties might be expected of genes, such as the collagen genes, the products of which interact to form the animal's cuticle, and which are member genes of a gene family. ------------------- Key: 907 Medline: 87032743 Authors: Klass MR Title: Cell-specific gene expression in the nematode. Citation: International Review of Cytology 102: 1-28 1986 Type: REVIEW Genes: flu-1 flu-2 unc-15 unc-22 unc-54 unc-105 vit-1 vit-2 vit-3 vit-4 vit-5 vit-6 Abstract: The problem of cell-specific gene expression has long been a major concern to developmental biologists. Why and how specific genes are expressed only in certain differentiated cells and not in others are of vital importance. Many well-documented examples of differentiated cell types expressing quantitative and/or qualitative changes in gene expression now exist. For example, Galau et al. (1976) demonstrated that different sets of genes are expressed during development and in different adult tissues of the sea urchin. More recently, Angerer and Davidson (1984) have used in situ hybridization of specific DNA probes to demonstrate the expression of lineage-specific genes long before morphological differentiation. Other examples include the ovalbumin gene, known to be expressed only in hormone-stimulated oviducts, and the globin genes expressed at various developmental stages in differentiating erythrocytes. Many other examples of cell-specific gene expression are known, including the silk moth chorion proteins, the glue proteins in Drosophila, and a-amylase in mammals. Detailed molecular analysis of genes has provided important information on the mechanisms of gene expression. For example, numerous studies have examined the role of chromatin structure as well as the significance of specific sequences in the transcription and translation of eukaryotic genes. Furthermore, studies of the globin, actin, immunoglobulin, histone, and silk moth chorion genes have demonstrated the existence of gene families with suggested importance for the evolution of new functions for old genes. In addition, the detailed study of multigene families has provided vital information on the mechanisms of cell-specific gene expression as seen, for example, in the temporal and spatial regulation of different members of the actin gene family.... ------------------- Key: 908 Medline: Authors: Davis BO;Goode M;Dusenbery DB Title: Laser microbeam studes of role of amphid receptors in chemosensory behavior of the nematode C. elegans. Citation: Journal of Chemical Ecology 12: 1339-1347 1986 Type: ARTICLE Genes: Abstract: Amphid sensilla, historically considered the primary chemosensory structures of nematodes, were found to be necessary for the detection of only one of the six chemical stimuli that were tested. Only the attraction to cAMP was eliminated by damaging the two lateral lips, which bear the amphid sensilla. The inner labial sensilla, one of which occurs on each of the six lips, are probably the primary receptor structures for the other chemical stimuli. Damaging all six lips, which should destroy all anterior chemosensory input, not only eliminated the attraction to sodium and chloride ions, but reversed the nematodes' response to them. Nematodes with all six lips destroyed showed reversal behavior when exposed to these attractants. Nematodes with damage to all six lips appeared to recover much of their normal chemosensory function within 24 hr after treatment. ------------------- Key: 909 Medline: 86283462 Authors: Clokey GV;Jacobson LA Title: The autofluorescent "lipofuscin granules" in the intestinal cells of C. elegans are secondary lysosomes. Citation: Mechanisms of Ageing & Development 35: 79-94 1986 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans contains autofluorescent lipofuscin granules, located exclusively in the 32-34 intestinal cells. Using epifluorescence microscopy on live adult animals, we have shown that fluorescent-labeled exogenous probes are taken up by endocytosis and accumulate within the granules. Macromolecular solutes such as proteins and dextran appear to be taken up by fluid- phase pinocytosis. There is no phagocytosis of latex particles with diameter greater than or equal to 0.25 micron. The granules concentrate the lysosomotropic weak base acridine orange, indicating that they have an acidic internal milieu. These observations imply that the lipofuscin granules in the intestinal cells are secondary lysosomes which remain active recipients of ------------------- Key: 910 Medline: Authors: Woods RA;Malone KMB;Albuquerque CA;Tomlinson G Title: The effects of amidantel (Bay d 8815) and its deacylated derivative (Bay d 9216) on wild-type and resistant mutants of C. elegans. Citation: Canadian Journal of Zoology 64: 1310-1316 1986 Type: ARTICLE Genes: Abstract: The anthelmintic drugs amidantel (BAY d 8815) and its deacylated derivative (BAY d 9216) inhibited the growth of wild-type (N2) Caenorhabditis elegans but had little effect on development or reproductive capacity. Inhibition of growth correlated well with drug-induced paralysis, both becoming maximal at around 1.0 mM concentration of either drug. Egg laying was delayed by about 24 h and the rate of laying was only about 60-70% of the controls. However, the period during which eggs were laid was extended by a similar amount and the total number of eggs laid was the same for the controls and the drug-treated worms. Five drug-resistant mutants ( T(1)14, T(2)2, T(2)6, T(2)16, and T(2)26 ) were isolated following ethylmethanesulphonate mutagenesis. All were shorter than N2 at 96 h on drug-free medium; their growth was not further impaired by either of the anthelmintic drugs. All except T(1)14 exhibited a normal pattern of sexual maturation. Cultures of T(1)14 at 96 h contained many immature worms. This mutant also exhibited the most impaired motility, being severely uncoordinated in liquid suspension. The other mutants could swim normally but were noticeably slower than N2. Genetic analysis indicated that each mutant was the result of a single genetic lesion, that the mutants were recessive, and that there were two genes for amidantel resistance (adt1 and adt2). In vitro studies on representatives of each class ( T(1)14 aand T(2)2 ) indicated a defect in the acetylcholine receptor. T(2)2 mutants showed a moderate decrease in sensitivity towards typical cholinergic agonists as well as the anthelmintic drugs, while T(1)14 mutants were apparently devoid of functional pharmacological acetylcholine receptors. ------------------- Key: 911 Medline: Authors: Politz SM;Politz JC;Edgar RS Title: Small collagenous proteins present during the molt in C. elegans. Citation: Journal of Nematology 18: 303-310 1986 Type: ARTICLE Genes: Abstract: Immunoblotting experiments using antibodies directed against the large collagenous cuticle proteins of Caenorhabditis elegans revealed a small class of collagenous proteins (CP) of apparent molecular weight 38,000-52,000 present during the L4 to adult molt. These CP are smaller than most vertebrate collagens characterized to date and share many characteristics with the small collagenous products translated in vitro from DNA isolated at this molt. C. elegans collagen genes, collagen-coding mRNA, and collagenous in vitro products that have been characterized are also small. Detection of small CP in vivo in C. elegans thus lends further support to the hypothesis that such small collagenous proteins are the primary gene product precursors to the larger collagenous proteins isolated from the C. elegans cuticle. ------------------- Key: 912 Medline: 87060987 Authors: Salvato M;Sulston J;Albertson D;Brenner S Title: A novel calmodulin-like gene from the nematode C. elegans. Citation: Journal of Molecular Biology 190: 281-290 1986 Type: ARTICLE Genes: cal-1 eDp20 mnT12 Abstract: A novel gene from the nematode Caenorhabditis elegans was isolated by hybridization with a human calmodulin complementary DNA probe. This gene, cal-1, is present at one copy per haploid genome. In-situ hybridization of the cloned gene to metaphase chromosomes allowed us to assign it to the nematode linkage group IV. The polypeptide predicted from the sequence of this gene displays structural features of both calmodulin and troponin C. ------------------- Key: 913 Medline: 86272095 Authors: Kenyon C Title: A gene involved in the development of the posterior body region of C. elegans. Citation: Cell 46: 477-487 1986 Type: ARTICLE Genes: him-5 lin-22 mab-5 Abstract: Many regional differences in Caenorhabditis elegans body pattern are generated after hatching. Here I describe a gene, mab-5, that is required for the postembryonic development of nearly all ectodermal and mesodermal features that normally characterize a posterior body region. In addition, this gene is necessary for most cell migrations toward the posterior, but not for cell migrations toward the anterior. mab-5+ activity is cell-autonomous. In animals carrying a mutation in the gene lin-22, increases or decreases in mab-5+ gene dosage produce corresponding increases or decreases in the size of the region in which cells adopt posterior-specific fates. The model that best explains the data is that during postembryonic development, posterior-specific patterns of cell differentiation and cell migration are initiated by graded positional information, and that a common step in the different cellular responses to this information is ------------------- Key: 914 Medline: 86301832 Authors: Park E-C;Horvitz HR Title: Mutations with dominant effects on the behavior and morphology of the nematode C. elegans. Citation: Genetics 113: 821-852 1986 Type: ARTICLE Genes: bli-6 egl-30 egl-36 rol-6 sma-8 unc-1 unc-8 unc-43 unc-58 unc-70 unc-103 unc-105 unc-108 unc-109 Abstract: We have analyzed 31 mutations that have dominant effects on the behavior or morphology of the nematode Caenorhabditis elegans. These mutations appear to define 15 genes. We have studied ten of these genes in some detail and have been led to two notable conclusions. First, loss of gene function for four of these ten genes results in a wild-type phenotype; if these genes represent a random sample from the genome, then we would estimate that null mutations in about half of the genes in C. elegans would result in a nonmutant phenotype. Second, the dominant effects of mutations in nine of these ten genes are caused by novel gene functions, and in all nine cases the novel function is antagonized by the wild-type function. ------------------- Key: 915 Medline: 86301833 Authors: Park E-C;Horvitz HR Title: C. elegans unc-105 mutations affect muscle and are suppressed by other mutations that affect muscle. Citation: Genetics 113: 853-867 1986 Type: ARTICLE Genes: sup-20 unc-22 unc-105 Abstract: Certain mutations in the unc-105 II gene of the nematode Caenorhabditis elegans have dominant effects on morphology and behavior: animals become small, severely hypercontracted and paralyzed. These unc-105 mutants revert both spontaneously and with mutagens at high frequencies to a wild-type phenotype. Most of the reversion events are intragenic, apparently because the null (loss-of- function) phenotype of unc-105 is wild type. One revertant defined an extragenic suppressor locus, sup-20 X. Such suppressor alleles of sup- 20 are rare, and the apparent null phenotype of sup-20 is embryonic lethality. By constructing animals genetically mosaic for sup-20, we have shown that the primary effect of sup-20 is in muscle cells. In addition to mutations in sup-20, other mutations causing muscle defects, such as unc-54 and unc-22 mutations, suppress the hypercontracted phenotype of unc-105. The ease of identifying nonhypercontracted revertants of unc-105 mutants greatly facilitates the isolation of new mutants defective in muscle structure and function. ------------------- Key: 916 Medline: 87001659 Authors: Nelson DW;Honda BM Title: Genetic mapping of the 5S rRNA gene cluster of the nematode C. elegans. Citation: Canadian Journal of Genetics & Cytology 28: 545-553 1986 Type: ARTICLE Genes: rrs-1 Abstract: We have identified a restriction fragment length difference (RFLD) affecting the genomic sequences immediately flanking the 5S rRNA gene cluster in the Bristol and Bergerac strains of the nematode Caenorhabditis elegans. We have used this RFLD as a molecular marker to follow the segregation of the 5S rRNA gene cluster through a series of two- and three-factor interstrain crosses. Our results show that the 5S rRNA gene cluster maps between unc-76 and dpy-21 on the right arm of linkage group V. This genetic localization provides a linkage group V "landmark" with which to localize other cloned sequences by in situ ------------------- Key: 917 Medline: 86224142 Authors: Bartnik E;Osborn M;Weber K Title: Intermediate filaments in muscle and epithelial cells of nematodes. Citation: Journal of Cell Biology 102: 2033-2041 1986 Type: ARTICLE Genes: Abstract: Current concepts of the developmentally controlled multigene family of intermediate filament (IF) proteins expect the origin of their complexity in evolutionary precursors preceding all vertebrate classes. Among invertebrates, however, firm ultrastructural as well as molecular documentation of IFs is restricted to some giant axons and to epithelia of a few molluscs and annelids. As Ascaris lumbricoides is easily dissected into clean tissues, IF expression in this large nematode was analyzed by electron microscopic and biochemical procedures and a monoclonal antibody reacting with all mammalian IF proteins. We document for the first time the presence of IFs in muscle cells of an invertebrate. They occur in three muscle types (irregular striated pharynx muscle, obliquely striated body muscle, uterus smooth muscle). IFs are also found in the epithelia studied (syncytial epidermis, intestine, ovary, testis). Immunoblots on muscles, pharynx, intestine, uterus, and epidermis identify a pair of polypeptides (with apparent molecular masses of 71 and 63 kD) as IF constituents. In vitro reconstitution of filaments was obtained with the proteins purified from body muscles. In the small nematode Ceanorhabditis elegans IF proteins are so far found only in the massive desmosome-anchored tonofilament bundles which traverse a special epithelial cell type, the marginal cells of the pharynx. We speculate that IFs may occur in most but perhaps not all invertebrates and that they may not occur in all cells in large amounts. As electron micrographs of the epidermis of a planaria-a member of the platyhelminthes-reveal IFs, the evolutionary origin of this cytoplasmic structure can be expected either among the lowest metazoa or already in some unicellular eukaryotes. ------------------- Key: 918 Medline: 87064628 Authors: Kay RJ;Boissy RJ;Russnak RH;Candido EPM Title: Efficient transcription of C. elegans heat shock gene pair in mouse fibroblasts dependent on multiple promoter elements which can function bidirectionally/ Citation: Molecular and Cellular Biology 6: 3134-3143 1986 Type: ARTICLE Genes: Abstract: A divergently transcribed pair of Caenorhabditis elegans hsp16 genes was introduced into mouse fibroblasts by stable transfection with vectors containing bovine papillomavirus plasmid maintenance sequences and a selectable gene. The hsp16 genes were transcriptionally inactive in the mouse cells under normal growth conditions and were strongly induced by heat shock or arsenite. In a cell line with 12 copies of the gene pair, there were estimated to be more than 10,000 hsp16 transcripts in each cell after 2 h of heat shock treatment. The hsp16 transcript levels were more than 100 times higher than those of a gene with a herpes simplex virus thymidine kinase gene promoter carried on the same vector. A single heat shock promoter element (HSE) could activate bidirectional transcription of the two hsp16 genes when placed between the two TATA elements, but the transcriptional efficiency was reduced 10-fold relative to that of the wild-type gene pair. Four overlapping HSEs positioned between the two TATA elements resulted in inducible bidirectional transcription at greater than wild-type levels. The number of HSEs can therefore be a major determinant of the promoter strength of heat- inducible genes in mammalian cells. Partial disruption of an alternating purine-pyrimidine sequence between the two hsp16 genes had no significant effect on their transcriptional activity. ------------------- Key: 919 Medline: Authors: Okai Y Title: Possible regulating factors for chromatin-dependent RNA polymerase II reaction in C. elegans. Citation: Zoological Science 3: 97-102 1986 Type: ARTICLE Genes: Abstract: The author found possible regulating factors for chromatin-dependent RNA polymerase II reaction in the homogenate of a nematode, Caenorhabditis elegans (C. elegans). The factors repressed calf thymus DNA-dependent transcription catalyzed by all classes of C. elegans RNA polymerases (I, II and III) at the stage of RNA chain initiation. However, the factors specifically enhanced rat liver chromatin-dependent RNA polymerase II reaction at a high ionic strength. The activities exhibited the apparent molecular weights at more than 100 kDA, 70 kDa and about 30 kDa in Sephadex G-100 column chromatography. The largest activity was converted to 70 kDa activity by endogenous or exogenous proteases and 70 kDa activity was shifted to the 30 kDa activity by a sonication procedure. The factors were characterized to be heat-stable sugar-containing molecules and similar to the factors reported previously by the author from rat liver. ------------------- Key: 920 Medline: Authors: Okai Y Title: A low-molecular-weight inhibitory peptide for DNA-dependent RNA polymerase II reaction in a nematoda, C. elegans. Citation: Zoological Science 3: 103-108 1986 Type: ARTICLE Genes: Abstract: A low-molecular-weight factor for RNA polymerase reaction was found in the homogenate of a nematoda Caenorhabditis elegans. This factor repressed DNA-dependent RNA polymerase II reaction at the stage of RNA chain initiation, but not a-amanitin resistant reactions. The factor was partially purified by ion exchange and gel filtration chromatography and characterized to be a heat-stable peptide. Its molecular weight was estimated to be a few thousand daltons. The factor also inhibited mRNA synthesis of T cell growth factor in lectin-induced lymphocyte activation. The properties of the factor were compared with the factors reported previously. ------------------- Key: 921 Medline: Authors: Russell RL;Jacobson LA Title: Some aspects of aging can be studied easily in nematodes. Citation: "Handbook of the Biology of Aging." Finch CE and Schneider EL (eds), Van Nostrand Reinhold, NY. : 128-145 1985 Type: REVIEW Genes: ace-1 ace-2 ced-1 ced-2 cha-1 flu-1 flu-2 nuc-1 Abstract: Studies of aging in nematodes are based largely on the hope that there are some general mechanisms of aging which can be expeditiously revealed in simple multicellular organisms. Although differing greatly from mammals in size, body plan, and some organ systems, nematodes nontheless strongly resemble other metazoans at the cellular, subcellular, and biochemical levels. Moreover, nematodes do exhibit some rather widespread aging phenomena, such as nutritional prolongation of life span, accumulation of age pigments, and enzyme alterations, and their short life span, cellular simplicity, and genetic manipulability can be real advantages in studying the mechanisms underlying these phenomena. ------------------- Key: 922 Medline: 87031517 Authors: Hodgkin J Title: Sex determination in the nematode C. elegans: analysis of tra-3 suppressors and characterization of fem genes. Citation: Genetics 114: 15-52 1986 Type: ARTICLE Genes: egl-26 fem-1 fem-2 fem-3 her-1 smg-2 tra-1 tra-2 tra-3 Abstract: Mutations of the gene tra-3 result in partial masculinization of XX animals of C. elegans, which are normally hermaphrodites (males are XO). A total of 43 tra-3 revertants (one intragenic, 42 extragenic) have been isolated and analyzed, in the hope of identifying new sex- determination loci. Most (38) of the extra-genic suppressors cause partial or complete feminization of XX and XO animals; the remaining four are weak suppressors. The feminizing suppressors are mostly alleles of known sex-determining genes: tra-1 (11 dominant alleles), tra-2 (one dominant allele), fem-1 (four alleles) and fem-2 (four alleles), but 18 are alleles of a new gene, fem-3. Additional alleles have been isolated for the fem-2 and fem-3 genes, as well as fem-3 deficiencies. Mutations in fem-3 resemble alleles of fem-1 (previously characterized): putative null alleles result in complete feminization of XX and XO animals, transforming them into fertile females. Severe alleles of fem-2 also cause complete feminization of XX animals at all temperatures, but feminization of fem-2 XO animals is temperature-sensitive: complete at 25 degrees, incomplete at 20 degrees. As with fem-1, severe mutations of fem-2 and fem-3 are wholly epistatic to masculinizing alleles of tra-2 and tra-3, and epistatic to tra-1 masculinizing alleles in the germline, but not in the soma. All three fem genes are essential for male development and appear to have a dual role in promoting spermatogenesis and repressing tra-1 activity. All three fem genes exhibit strong maternal effects; the maternal contribution of fem gene products may be inactivated in XX animals by a posttranscriptional mechanism. Maternal contributions of wild-type fem-3 product are necessary for normal XO male development and XX hermaphrodite (as opposed ------------------- Key: 923 Medline: 87031525 Authors: Doniach T Title: Activity of the sex-determining gene tra-2 is modulated to allow spermatogenesis in the C. elegans hermaphrodite. Citation: Genetics 114: 53-76 1986 Type: ARTICLE Genes: tra-2 Abstract: In the nematode C. elegans, there are two sexes, the self-fertilizing hermaphrodite (XX) and the male (XO). The hermaphrodite is essentially a female that makes sperm for a brief period before oogenesis. Sex determination in C. elegans is controlled by a pathway of autosomal regulatory genes, the state of which is determined by the X:A ratio. One of these genes, tra-2, is required for hermaphrodite development, but not for male development, because null mutations in tra-2 masculinize XX animals but have no effect on XO males. Dominant, gain-of-function tra-2 mutations have now been isolated that completely feminize the germline of XX animals so that they make only oocytes and no sperm and, thus, are female. Most of the tra-2(dom) mutations do not correspondingly feminize XO animals, so they do not appear to interfere with control by her-1, a gene thought to negatively regulate tra-2 in XO animals. Thus, these mutations appear to cause gain of tra-2 function in the XX animal only. Dosage studies indicate that 5 of 7 tra-2(dom) alleles are hypomorphic, so they do not simply elevate XX tra-2 activity overall. These properties suggest that in the wild type, tra-2 activity is under two types of control: (1) in males, it is inactivated by her-1 to allow male development to occur, and (2) in hermaphrodites, tra-2 is active but transiently inactivated by another, unknown, regulator to allow hermaphrodite spermatogenesis; this mode of regulation is hindered by the tra-2(dom) mutations, thereby resulting in XX females. ------------------- Key: 924 Medline: 86304576 Authors: Epstein HF;Ortiz I;Mackinnon LAT Title: The alteration of myosin isoform compartmentation in specific mutants of C. elegans. Citation: Journal of Cell Biology 103: 985-993 1986 Type: ARTICLE Genes: sup-3 unc-15 unc-52 unc-54 Abstract: Myosin isoforms A and B are located at the surface of the central and polar regions, respectively, of thick filaments in body muscle cells of Caenorhabditis elegans, whereas paramyosin and a distinct core structure comprise the backbones of these filaments. Thick filaments and related structures were isolated from nematode mutants that have altered thick filament protein compositions. These mutant filaments and their complexes with specific antibodies were studied by electron microscopy to determine the distribution of the two myosins. The compartmentation of the two myosin isoforms in body wall muscle thick filaments depends not only upon the intrinsic properties of the myosins but their interactions with other components such as paramyosin and their relative quantities determined by ------------------- Key: 925 Medline: 86300906 Authors: Schierenberg E;Cole T;Carlson C;Sidio W Title: Computer-aided three-dimensional reconstruction of nematode embryos from EM serial sections (technical note). Citation: Experimental Cell Research 166: 247-252 1986 Type: ARTICLE Genes: Abstract: Embryos of the nematode Caenorhabditis elegans were serially sectioned and photographed in the electron microscope (EM). The micrographs were used to produce three-dimensional (3D) reconstructions. Size and position of each nucleus were entered into a computer, displayed as spheres, and were color-coded to indicate lineage membership. Location in space and position in the cell cycle are generally adequate criteria to identify cells. The reconstructions allow visualization of lineage-related topographic patterns and ultrastructural analysis of ------------------- Key: 926 Medline: 86312928 Authors: Simpson VJ;Johnson TE;Hammen RF Title: C. elegans DNA does not contain 5-methylcytosine at any time during development or aging. Citation: Nucleic Acids Research 14: 6711-6717 1986 Type: ARTICLE Genes: fer-15 Abstract: DNA, isolated from age-synchronous senescent populations of Caenorhabditis elegans has been quantitatively and qualitatively analyzed for the presence of 5-methylcytosine. High performance liquid chromatography on two wild-type and several mutant strains of C. elegans failed to detect any 5-methylcytosine. The restriction endonuclease isoschizomers, HpaII and MspI, were used to digest genomic DNA after CsCl purification and failed to detect any 5' cytosine methylation at any age. We conclude that C. elegans does not contain detectable (0.01 mole percent) levels of 5-methylcytosine. ------------------- Key: 927 Medline: 86301508 Authors: Priess JR;Hirsh DI Title: C. elegans morphogenesis: The role of the cytoskeleton in elongation of the embryo. Citation: Developmental Biology 117: 156-173 1986 Type: ARTICLE Genes: sqt-3 Abstract: During development Caenorhabditis elegans changes from an embryo that is relatively spherical in shape to a long thin worm. This paper provides evidence that the elongation of the body is caused by the outermost layer of embryonic cells, the hypodermis, squeezing the embryo circumferentially. The hypodermal cells surround the embryo and are linked together by cellular junctions. Numerous circumferentially oriented bundles of microfilaments are present at the outer surfaces of the hypodermal cells as the embryo elongates. Elongation is associated with an apparent pressure on the internal cells of the embryo, and cytochalasin D reversibly inhibits both elongation and the increase in pressure. Circumferentially oriented microtubules also are associated with the outer membranes of the hypodermal cells during elongation. Experiments with the microtubule inhibitors colcemid, griseofulvin, and nocodazole suggest that the microtubules function to distribute across the membrane stresses resulting from microfilament contraction, such that the embryo decreases in circumference uniformly during elongation. While the cytoskeletal organization of the hypodermal cells appears to determine the shape of the embryo during elongation, an extracellular cuticle appears to maintain the body shape after elongation. ------------------- Key: 928 Medline: 86304344 Authors: Jones D;Russnak RH;Kay RJ;Candido EPM Title: Structure, expression and evolution of a heat-shock gene locus in C. elegans that is flanked by repetitive elements. Citation: Journal of Biological Chemistry 261: 12006-12015 1986 Type: ARTICLE Genes: Abstract: A locus containing two hsp16 genes in Caenorhabditis elegans has been characterized by DNA sequencing. Each gene encodes a 16-kDa polypeptide which is expressed following heat induction. The two genes, designated hsp16-2 and hsp16-41, are arranged in divergent orientations, and each contains a single intron of 46 and 58 base pairs, respectively. Although both gene transcripts are spliced efficiently in vivo, hsp16-41 corresponds to a previously isolated cDNA which contains an unspliced intron sequence. The 5'-noncoding regions of both genes contain TATA boxes preceded 18 or 19 nucleotides upstream by a heat shock regulatory sequence. The 3'- noncoding regions contain polyadenylation signals (AATAAA) either downstream (hsp16-2) or immediately adjacent (hsp16-41) to a sequence capable of forming a hairpin. This pair of hsp16 genes is flanked by three copies of an approximately 200-bp dispersed repetitive element (two copies on one side and a single one on the other side of the locus) which occurs in at least 70 copies throughout the C. elegans genome, and has been designated CeRep-16. Together with data described previously (Russnak, R. H., and Candido, E. P. M. (1985) Mol. Cell. Biol. 5, 1268-1278), the results presented here define a family of four distinct, related small heat shock protein genes. These are arranged in divergently transcribed pairs at two loci. The hsp16-48/41 genes code for one class of HSP16, 143-amino acid residues long, while the hsp16-1/2 genes encode the other class, which is 2 amino acid residues longer. Thus each locus codes for the two major types of HSP16. The two loci differ in a number of respects, including the presence of a tandem inverted duplication of two heat shock protein genes at one locus, and of repetitive elements at the other. Sequence comparisons allow us to propose a scheme for the evolution of the four genes and reveal conserved features of noncoding regions which may be involved in the regulation of their transcription, RNA processing, or translation. Using locus-specific hybridization probes, we have found that the genes at locus hsp16- 2/41 are expressed at levels approximately 20-40-fold higher than those at locus ------------------- Key: 929 Medline: Authors: Klass MR;Johnson TE Title: C. elegans. Citation: Interdisciplinary Topics in Gerontology 21: 164-187 1985 Type: REVIEW Genes: Abstract: The free-living, self-fertilizing hermaphroditic nematode Caenorhabditis elegans is one of the most promising and well-characterized invertebrate organisms available for the study of aging. The ease of culture and availability of a sophisticated system of genetic analysis together with the ability to grow large quantities of aged worms for biochemical analysis make this an attractive experimental system. C. elegans has recently become the subject of intense study in many areas of biology including genetics, development, muscle structure and function, gene expression, neural development, and aging. Beacuse a fixed number of cells is maintained after maturation, C. elegans is an ideal experimental system for the study of aging of post-mitotic cells. In addition, C. elegans has a transparent body with a simple anatomy that has been characterized in exquisite detail. This multicellular eucaryote develops from a single-celled zygote into a functional larva containing 558 cells comprising muscle, nerve, intestinal, hypodermal and gonadal tissues. The entire somatic cell lineage, from the singel-celled zygote to the adult containing 959 somatic cells, has been recorded. Of greatest import is that C. elegans is a genetically manipulable organism that facilitates the combination of biochemical and mutational analyses. One of the greatest series of aging studies in nematodes was that of Gershon who proposed the use of the nematode Caenorhabditis briggsae as an experimental system for the study of aging and who later described changes in enzymatic activity as well as the accumulation of lipofuszin granules and the effect of antioxidants on life span. C. briggsae and other nematode species have been used in detailed studies describing age-correlated alterations in specific activity of enzymes and protein degradation as well as in many other descriptive and analytical stuudies on aging. None of the species previously used, however, have been as well-characterized as C. elegans either genetically or anatomically. The inception of C. elegans as an experimental system for intense biological study originated with its genetic characterization by Brenner. Since then, C. elegans has been used to study the many biological processes described above including aging. Environmental effects on life span, changes in DNA structure and repair, nematode behavior, genetic recombination frequency, O2 consumption, and lipofuszin accumulation over the life span have also been studied. Mutations affecting life span have been isolated, long-lived strains have been developed using seletive breeding techniques. These studies and pertinent others are reviewed following the general description of ------------------- Key: 930 Medline: Authors: Wood WB;Schierenberg E;Strome S Title: Localization and determination in early embryos of C. elegans. Citation: "Molecular Biology of Development." UCLA Smyposia on Molecular and Cellular Biology, New Series. Davidson EH and Firtel RA (eds), Wiley-Liss, Inc. : 37-49 1984 Type: REVIEW Genes: Abstract: Developmental fates of blastomeres in early C. elegans embryos appear to be governed by internally segregating, cell-autonomous determinants. To ascertain whether previously described gut-lineage dterminants are nuclear or cytoplasmic, laser microsurgery was used to show that exposing the nucleus of a non-gut-precursor cell to gut-precursor cytoplasm can cause the progeny of the resulting hybrid cell to express gut-specific differentiation markers, supporting the view that the determinants are cytoplasmic. In attempts to obtain molecular probes for such determinants, a library of monoclonal antibodies to early embryonic antigens was generated and screened by immunofluorescence microscopy for antibodies reacting with lineage-specific components. Three of the antibodies react with cytoplasmic granules (P granules) that segregate specifically with the germ line in early cleavages and are found uniquely in germ-line cells throughout the life cycle. Experiments on unfertilized eggs, on mutant embryos with defects in early cleavage, and on normal embryos treated with various cytoskeletal inhibitors indicate that P-granule segregation depends upon fertilization and requires the function of actin microfilaments, but is independent of spindle and microtubule functions. Work on the biochemical nature and function of the P granules is in progress. ------------------- Key: 931 Medline: Authors: Cole TS;Schierenberg E Title: Laser microbeam-induced fixation for electronmicroscopy: Visualization of transient developmental features in nematode embryos. Citation: Experientia 42: 1046-1048 1986 Type: ARTICLE Genes: Abstract: In order to study development of embryos of Caenorhabditis elegans at an ultrastructural level, a new method of fixation has been developed. With a laser microbeam coupled to a microscope the impermeable eggshell is punctured to allow penetration of the fixative. At specific stages of embryogenesis further development can be arrested at will under visual control. As fixation occurs instantaneously, transient events (e.g. different phases of mitosis and cytokinesis) can be visualized. ------------------- Key: 932 Medline: 87005569 Authors: Perkins LA;Hedgecock EM;Thomson JN;Culotti JG Title: Mutant sensory cilia in the nematode C. elegans. Citation: Developmental Biology 117: 456-487 1986 Type: ARTICLE Genes: cat-6 che-1 che-2 che-3 che-5 che-6 che-7 che-10 che-11 che-12 che-13 che-14 daf-1 daf-2 daf-3 daf-4 daf-5 daf-6 daf-7 daf-8 daf-9 daf-10 daf-11 daf-12 daf-13 daf-14 daf-15 daf-16 daf-18 daf-19 daf-20 mec-1 mec-8 osm-1 osm-3 osm-5 osm-6 Abstract: Eight classes of chemosensory neurons in C. elegans fill with fluorescein when living animals are placed in a dye solution. Fluorescein enters the neurons through their exposed sensory cilia. Mutations in 14 genes prevent dye uptake and disrupt chemosensory behaviors. Each of these genes affects the ultrastructure of the chemosensory cilia or their accessory cells. In each case, the cilia are shorter or less exposed than normal, suggesting that dye contact is the principal factor under selection. Ten genes affect many or all of the sensory cilia in the head. The daf-19 (m86) mutation eliminates all cilia, leaving only occasional centrioles in the dendrites. The cilia in che-13 (e1805), osm-1 (p808), osm-5 (p813), and osm-6 (p811) mutants have normal transition zones and severely shortened axonemes. Doublet-microtubules, attached to the membrane by Y links, assemble ectopically proximal to the cilia in these mutants. The amphid cilia in che-11 (e1810) are irregular in diameter and contain dark ground material in the middle of the axonemes. Certain mechanocilia are also affected. The amphid cilia in che-10 (e1809) apparently degenerate, leaving dendrites with bulb-shaped endings filled with dark ground material. The mechanocilia lack striated rootlets. Cilia defects have also been found in che-2, che-3, and daf- 10 mutants. The osm-3 (p802) mutation specifically eliminates the distal segment of the amphid cilia. Mutations in three genes affect sensillar support cells. The che-12 (e1812) mutation eliminates matrix material normally secreted by the amphid sheath cell. The che- 14 (e1960) mutation disrupts the joining of the amphid sheath and socket cells to form the receptor channel. A similar defect has been observed in daf-6 mutants. Four additional genes affect specific classes of ciliated sensory neurons. The mec-1 and mec-8 (e398) mutations disrupt the fasciculation of the amphid cilia. The cat-6 (e1861) mutation disrupts the tubular bodies of the CEP mechanocilia. A cryophilic thermotaxis mutant, ttx-1 (p767), lacks fingers on the AFD dendrite, suggesting ------------------- Key: 933 Medline: Authors: Fire A Title: Integrative transformation of C. elegans. Citation: EMBO Journal 5: 2673-2680 1986 Type: ARTICLE Genes: sup-7 Abstract: A technique for introducing exogenouus DNA into the chromosomes of the nematode Caenorhabditis elegans is presented. A cloned C. elegans amber suppressor tRNA gene, sup-7, is used as a selectable marker. The activity of this amber suppressor is selected for by injecting worms which carry an amber termination mutation in a gene (tra-3) whose function is required for fertility. Transient expression of sup-7 is evidenced by the presence of fertile (rescued) animals in the generation after injection. In a fraction of cases, these fertile animals give rise to stable suppressor lines (eight have been characterized so far). Each of the stable suppressor lines carries injected DNA sequences. The suppressor activities have been mapped to chromosomal loci, indicating that the exogenous DNA has integrated into the genome. This technique has been used to introduce a chimeric gene containing a Drosophila heat shock promoter element fused to coding sequences from the Escherichia coli B-galactosidase gene. This chimeric gene functions and is heat inducible in the resulting stably ------------------- Key: 934 Medline: Authors: Coulson A;Sulston J;Brenner S;Karn J Title: Toward a physical map of the genome of the nematode C. elegans. Citation: Proceedings of the National Academy of Sciences USA 83: 7821-7825 1986 Type: ARTICLE Genes: Abstract: A technique for digital characterization and comparison of DNA fragments, using restriction enzymes, is described. The technique is being applied to fragments from the nematode Caenorhabditis elegans (i) to facilitate cross-indexing of clones emanating from different laboratories and (ii) to construct a physical map of the genome. Eight hundred sixty clusters of clones, from 35 to 350 kilobases long and totaling about 60% of the genome, ------------------- Key: 935 Medline: 87310228 Authors: Strome S Title: Asymmetric movements of cytoplasmic components in C. elegans zygotes. Citation: Journal of Embryology & Experimental Morphology 97s: 15-29 1986 Type: ARTICLE Genes: zyg-9 Abstract: One of the central problems facing developmental biologists is understanding how the unicellular zygote develops into a multicellular embryo composed of different tissue types. It is now clear that differentiated cell types differ because they express different sets of genes. However, how cells become instructed to express different sets of genes remains a mystery. One popular model for how cell fates are determined invokes the existence and asymmetric distribution of cytoplasmic 'determinants' of cell fate. According to this model, the developmental programmes of embryonic blastomeres are specified by internal factors that are differentially segregated to different blastomeres during the early cleavages of the zygote. Alternatively, cells may be instructed by extrinsic signals, in which case the positions of the cells in the embryo and cell-cell interactions would be important. Observation and manipulation of embryos that show 'mosaic' development provide indirect support for the cell determinant theory. Individual blastomeres isolated from these embryos divide and express the differentiated phenotyes that they would have expressed in the intact embryo. Conversely removal of individual blastomeres from these embryos leads to juveniles or adults missing the tissues derived from the removed blastomeres. The autonomy of blastomere development suggests that, at least in some embryos, instructions for development are internal and that external cues are not required. Despite many suggestive experiments like those described above, a determinant of cell fate has yet to be identified. Perhaps the strongest candidates are germ granules. These electron-dense structures are found uniquely in germ cells, in almost every metazoan that has been examined. The experiments of Illmensee & Mahowald demonstrated that the cytoplasm containing these germ or polar granules is determinative for the germline of Drosophila, although the structures themselves have not been proven to be the determinants. The questions that need to be answered are: (1) are germ granules required for germ cell development?; (2) do determinants of somatic cell fates exist?; (3) if such determinants exist, what are they composed of?; and (4) how are cytoplasmic components differentially partitioned to different embryonic blastomeres? Basically, how are cell differences ------------------- Key: 936 Medline: 87310240 Authors: Schierenberg E Title: Developmental strategies during early embryogenesis of C. elegans. Citation: Journal of Embryology & Experimental Morphology 97s: 31-44 1986 Type: REVIEW Genes: Abstract: How the complex, multicellular structure of an organism is generated from the information contained in the uncleaved egg is a central question in developmental studies. Nematodes are particularly suitable for studying this question. A unique combination of favourable properties, including transparent eggshell, normal embryogenesis under the microscope outside the mother, small number of cells and rapid reproducible development made nematodes classic models for developmental biologists. In addition to the attractive features mentioned above, the free-living soil nematode Caenorhabditis elegans is also well suited for analysis of the genetic control of development unlike the classically studied parasitic nematode Parascaris equorum (Ascaris megalocephala). Recently cellular and genetic aspects of development have been studied extensively in C. elegans. The pattern of early embryogenesis in Ascaris and C. elegans appears to be typical for nematodes in general and includes the following features. (i) Cells are determined (lose totipotency) very early. The first division of the zygote generates two different cells with restricted developmental potential. (ii) Development proceeds in an essentailly 'mosaic' fashion. The pathway of differentiation is thought to be generally dictated by intrinsic factors, although cases of limited intercellular regulation have been found in later embryos. (iii) From the beginning of embryogenesis a germline is present. The germline is separated early from the soma through a series of unequal cleavages. In C. elegans the early phase of embryogenesis, when the framework for further development is laid down with the sequential formation of five somatic founder cells and the primordial germ cell, takes place within the first hour of cleavage. No indication of newly transcribed mRNA has been detected (as poly(A)+ material) in C. elegans during this early period. Thus, it is assumed that at least these first important steps of development are controlled by maternal gene products. Much of our present view of early development, not only in nematodes, is based on the ingenious work by Boveri. Some of his observations and conclusions are therefore briefly ------------------- Key: 937 Medline: 88007920 Authors: Chalfie M;Dean E;Reilly E;Buck K Title: Mutations affecting microtubule structure in C. elegans. Citation: Journal of Cell Science S5: 257-271 1986 Type: ARTICLE Genes: ben-1 cat-6 che-10 che-11 che-13 daf-10 daf-19 mec-7 mec-12 osm-1 osm-3 osm-5 osm-6 unc-33 Abstract: Three types of microtubules are seen in the neuronal processes of the nematode Caenorhabditis elegans. Single cytoplasmic microtubules of most neurones have 11 protofilaments whereas those of six touch receptor cells have 15 protofilaments. The axonemes of sensory cilia have nine outer doublets with a variable number (up to seven) of singlet microtubules. Mutations in 11 genes affect the appearance of these microtubules. ------------------- Key: 938 Medline: Authors: White JG;Southgate E;Thomson JN;Brenner S Title: The structure of the nervous system of the nematode C. elegans. Citation: Philosophical Transactions of the Royal Society of London 314B: 1-340 1986 Type: ARTICLE Genes: Abstract: The structure and connectivity of the nervous system of the nematode Caenorhabditis elegans has been deduced from reconstructions of electron micrographs of serial sections. The hermaphrodite nervous system has a total complement of 302 neurons, which are arranged in an essentially invariant structure. Neurons with similar morphologies and connectivities have been grouped together into classes; there are 118 such classes. Neurons have simple morphologies with few, if any, branches. Processes from neurons run in defined positions within bundles of parallel processes, synaptic connections being made en passant. Process bundles are arranged longitudinally and circumferentially and are often adjacent to ridges of hypodermis. Neurons are generally highly locally connected, making synaptic connections with many of their neighbours. Muscle cells have arms that run out to process bundles containing motoneuron axons. Here they receive their synaptic input in defined regions along the surface of the bundles, where motoneuron axons reside. Most of the morphologically identifiable synaptic connections in a typical animal are described. These consist of about 5000 chemical synapses, 2000 neuromuscular junctions and 600 gap junctions. ------------------- Key: 939 Medline: 87057675 Authors: Strome S Title: Fluorescence visualization of the distribution of microfilaments in gonads and early embryos of the nematode C. elegans. Citation: Journal of Cell Biology 103: 2241-2252 1986 Type: ARTICLE Genes: Abstract: Several intracellular motility events in the Caenorhabditis elegans zygote (pseudocleavage, the asymmetric meeting of the pronuclei, the segregation of germ line-specific granules, and the generation of an asymmetric spindle) appear to depend on microfilaments (MFs). To investigate how MFs participate in these manifestations of zygotic asymmetry, the distribution of MFs in oocytes and early embryos was examined, using both antibodies to actin and the F-actin-specific probe rhodamine-phalloidin. In early-stage zygotes, MFs are found in a uniform cortical meshwork of fine fibers and dots or foci. In later zygotes, concomitant with the intracellular movements that are thought to be MF mediated, MFs also become asymmetrically rearranged; as the zygote undergoes pseudocleavage and as the germ line granules become localized in the posterior half of the cell, the foci of actin become progressively more concentrated in the anterior hemisphere. The foci remain anterior as the spindle becomes asymmetric and the zygote undergoes its first mitosis, at which time fibers align circumferentially around the zygote where the cleavage furrow will form. A model for how the anterior foci of actin may participate in zygotic motility events is discussed. Phalloidin and anti-actin antibodies have also been used to visualize MFs in the somatic tissues of the adult gonad. The myoepithelial cells that surround maturing oocytes are visibly contractile and contain an unusual array of MF bundles; the MFs run roughly longitudinally from the loop of the gonad to the spermatheca. Myosin thick filaments are distributed along the MFs in a periodic manner suggestive of a sarcomere-like configuration. It is proposed that these actin and myosin filaments interact to cause sheath cell contraction and the movement of oocytes ------------------- Key: 940 Medline: Authors: Riddle DL;Swanson MM Title: The nematode Caenorhabditis elegans. Citation: Genetic Maps 2: 244-258 1982 Type: REVIEW Genes: Abstract: ------------------- Key: 941 Medline: 87051768 Authors: Meyer BJ;Casson LP Title: C. elegans compensates for the difference in X chromosome dosage between the sexes by regulating transcript levels. Citation: Cell 47: 871-881 1986 Type: ARTICLE Genes: dpy-21 dpy-27 dpy-28 Abstract: The primary sex-determining signal in the nematode C. elegans is the ratio of X chromosomes to sets of autosomes (X/A ratio). As a consequence, males (XO; ratio 0.5) and hermaphrodites (XX; ratio 1.0) possess different doses of X-linked genes. Here we demonstrate that C. elegans compensates for this disparity in gene dose by equalizing the levels of X-specific mRNA transcripts in the two sexes. Moreover, we show that mutations in three autosomal genes disrupt the process of dosage compensation. Reduction in the activity of either dpy-21, dpy-27, or dpy-28 results in the overexpression of X-specific genes, 2- to 3-fold above wild-type levels. ------------------- Key: 942 Medline: 87226196 Authors: Jefferson RA;Klass M;Wolf N;Hirsh D Title: Expression of chimeric genes in Caenorhabditis elegans. Citation: Journal of Molecular Biology 193: 41-46 1987 Type: ARTICLE Genes: col-1 Abstract: We have shown the expression of transformed genes in the nematode Caenorhabditis elegans using a new gene fusion system. Vectors consisting of the flanking regions of a collagen gene (col-1) or a major sperm protein gene of C. elegans fused to the Escherichia coli uidA gene, encoding beta-glucuronidase, were microinjected into worms and found to be propagated as high-copy extrachromosomal tandem arrays. We have detected beta-glucuronidase activity in transformed lines, and have shown that the activity is dependent upon the correct reading frame of the construction and on the presence of the worm sequences. The enzyme activity was shown to be encoded by the chimeric beta-glucuronidase gene by co-segregation analysis and by inactivation with specific antisera. Expression is at a very low level, and seems to be constitutive. We have used histochemical techniques to visualize the enzyme activity in embryos. ------------------- Key: 943 Medline: 87163435 Authors: Barton MK;Schedl TB;Kimble J Title: Gain-of-function mutations of fem-3, a sex-determination gene in C. elegans. Citation: Genetics 115: 107-119 1987 Type: ARTICLE Genes: fem-1 fem-2 fem-3 her-1 tra-2 tra-3 Abstract: We have isolated nine gain-of-function (gf) alleles of the sex- determination gene fem-3 as suppressors of feminizing mutations in fem-1 and fem-2. The wild-type fem-3 gene is needed for spermatogenesis in XX self-fertilizing hermaphrodites and for male development in both soma and germ line of XO animals. Loss-of- function alleles of fem-3 transform XX and XO animals into females (spermless hermaphrodites). In contrast, fem-3(gf) alleles masculinize only one tissue, the hermaphrodite germ line. Thus, XX fem-3(gf) mutant animals have a normal hermaphrodite soma, but the germ line produces a vast excess of sperm and no oocytes. All nine fem-3(gf) alleles are temperature sensitive. The temperature- sensitive period is from late L4 to early adult, a period just preceding the first signs of oogenesis. The finding of gain-of- function alleles which confer a phenotype opposite to that of loss-of- function alleles supports the idea that fem-3 plays a critical role in germ-line sex determination. Furthermore, the germ-line specificity of the fem-3(gf) mutant phenotype and the late temperature-sensitive period suggest that, in the wild-type XX hermaphrodite, fem-3 is negatively regulated so that the hermaphrodite stops making sperm and starts making oocytes. Temperature shift experiments also show that, in the germ line, sexual commitment appears to be a continuing process. Spermatogenesis can resume even after oogenesis has begun, and oogenesis can be initiated ------------------- Key: 944 Medline: 87078394 Authors: Villeneuve AM;Meyer BJ Title: sdc-1: A link between sex determination and dosage compensation in C. elegans. Citation: Cell 48: 25-37 1987 Type: ARTICLE Genes: egl-41 fem-1 fem-2 fem-3 her-1 lin-14 lin-15 sdc-1 tra-1 tra-2 tra-3 Abstract: Mutations in the X-linked gene sdc-1 affect both sex determination and X-chromosome dosage compensation in C. elegans, providing evidence that these two pathways share a common step. In XX animals (normally hermaphrodites), sdc-1 mutations cause partial masculinization and elevated levels of X-linked gene expression, an apparent shift of both pathways toward their XO modes of expression. The masculinization occurs through effects on the major sex determination pathway, upstream of all previously identified sex- determining genes. XO animals are apparently unaffected by the sdc-1 mutations. We propose a model in which the wild-type sdc-1 activity is either a component of the primary sex-determining signal (the X/Autosome ratio) or involved in transmitting information about this signal to both the sex determination and dosage ------------------- Key: 945 Medline: 87105951 Authors: Vanfleteren JR;Van Bun SM;Van Beeumen JJ Title: The primary structure of histone H3 from the nematode C. elegans. Citation: Federation of European Biochemical Societies 211: 59-63 Type: ARTICLE Genes: Abstract: The complete amino acid sequence of histone H3 (135 residues) from the nematode Caenorhabditis elegans has been established. Microheterogeneity occurs at positions 96 and 100 of the chain. The sequences of the nematode H3 isoforms are very similar to the major chain of calf thymus H3 with which they show 4 substitutions in total. The major variant has cysteine in position 96. This is the first report of cysteine in this position in H3 from non-mammalian tissue. An exceptional methylation site has been detected at position 79. Various other sites of secondary modification are of a conservative nature. ------------------- Key: 946 Medline: Authors: Chitwood DJ;Lusby WR;Salt TA Title: Sterol metabolism in the nematodes Panagrellus redivivus, Turbatrix aceti and C. elegans. Citation: Comparative Biochemistry & Physiology 86B: 103-107 1987 Type: ARTICLE Genes: Abstract: 1. Panagrellus redivivus, Turbatrix aceti and Caenorhabditis elegans were sterilely propagated in semidefined media containing sitosterol or cholesterol, and sterols were isolated and identifed by capillary gas-liquid chromatography-mass spectometry. 2. Each species was capable of removal of the C-24 ethyl substituent of sitosterol and production of 4a-methylsterols. 3. Other modifications of the sterol nucleus varied among the species, as only T. aceti and C. elegans introduced *7- and *8(14)-bonds significantly. 4. P. redivivus and, to a much lesser extent, T. aceti reduced *5-bonds to produce substantial quantities of cholesterol and 4a-methylcholestanol. ------------------- Key: 947 Medline: 87101171 Authors: Yarbrough PO;Hayden MA;Dunn LA;Vermersch PS;Klass MR;Hecht RM Title: The glyceraldehyde-3-phosphate dehydrogenase gene family in the nematode, C. elegans: isolation and characterization of one of the genes. Citation: Biochimica et Biophysica Acta 908: 21-33 1987 Type: ARTICLE Genes: unc-54 Abstract: The isolation and genomic sequence of one of possibly four glyceraldehyde-3-phosphate dehydrogenase genes in the nematode, Caenorhabditis elegans is presented. The complete nucleotide sequence of the coding as well as the noncoding flanking regions of this gene has been determined. The deduced amino-acid sequence agrees with the sequence of typical glyceraldehyde-3-phosphate dehydrogenase enzymes and its molecular weight of 36,235 agrees with its size determined previously (Yarbrough, P. and Hecht, R. (1984) J. Biol. Chem. 259, 14711-14720). That this isolated gene encodes a nematode glyceraldehyde-3-phosphate dehydrogenase is additionally confirmed by demonstrating its immunoreactivity to an anti-nematode glyceraldehyde- 3-phosphate dehydrogenase antibody after its expression as a fusion protein with dihydrofolate reductase. Codon utilization follows a pattern typical of other expressed nematode genes. The gene is split by two introns that are highly conserved in comparison to other introns observed in C. elegans. The placement of one of these introns is conserved with respect to the chicken glyceraldehyde-3-phosphate dehydrogenase gene. Within the 5' flanking sequence homology to actin and the homology 2 block of the major myosin gene (unc-54) is noted. It is of interest that the 3' flanking region contains a CAAAT box, followed by a TATAAT box, before an open reading frame of a closely linked gene that also contains a small AT-rich intron with the nematode consensus splice junction. ------------------- Key: 948 Medline: 87102871 Authors: Priess JR;Thomson JN Title: Cellular interactions in early C. elegans embryos. Citation: Cell 48: 241-250 1987 Type: ARTICLE Genes: Abstract: In normal development both the anterior and posterior blastomeres in a 2-cell C. elegans embryo produce some descendants that become muscles. We show that cellular interactions appear to be necessary in order for the anterior blastomere to produce these muscles. The anterior blastomere does not produce any muscle descendants after either the posterior blastomere or one of the daughters of the posterior blastomere is removed from the egg. Moreover, we demonstrate that a daughter of the anterior blastomere that normally does not produce muscles appears capable of generating muscles when interchanged with its sister, a cell that normally does produce muscles. Embryos develop normally after these blastomeres are interchanged, suggesting that cellular interactions play a major role in determining the fates of some cells in early embryogenesis. ------------------- Key: 949 Medline: 87184513 Authors: Greenwald I Title: The lin-12 locus of C. elegans. Citation: BioEssays 6: 70-73 1987 Type: REVIEW Genes: lin-12 Abstract: Analysis of the patterns of cell lineage observed during development of the nematode Caenorhabditis elegans, combined with selected cell ablation experiments, has revealed that while many cell fates are autonomously (intrinsically) determined, cell-cell interactions are required for a number of developmental decisions. Earlier genetic analysis of one key gene, lin-12, had shown that this gene controls a number of bi-potential fate decisions involving such cellular interactions. Molecular analysis of this gene is now providing clues to its mode of action in mediating these cell-fate decisions. ------------------- Key: 950 Medline: 87115459 Authors: Lewis JA;Fleming JT;Mclafferty S;Murphy H;Wu C Title: The levamisole receptor, a cholinergic receptor of the nematode C. elegans. Citation: Molecular Pharmacology 31: 185-193 1987 Type: ARTICLE Genes: lev-1 lin-12 unc-74 Abstract: We describe a glass fiber filter binding assay for the levamisole receptor, a putative acetylcholine receptor of the nematode Caenorhabditis elegans, and we show that receptor detected in vitro binds both levamisole derivatives and cholinergic agonists with the pharmacological specificity expected of the physiologically functional nematode receptor. The receptor is detected by the binding of tritiated meta-aminolevamisole ([3H]MAL, 27 Ci/mmol). In extracts of the wild-type nematode, there is a saturable, high affinity binding activity for [3H]MAL (Kd approximately 5-10 nM). Well fed wild-type worms contain as much as 3 fmol of high affinity binding activity per mg of extract protein (0.14 pmol/g of wet weight of worms) and dauer larvae, a special juvenile stage, contain as much as 15 fmol of activity per mg of protein. Specific binding activity per mg of protein is highest in larval stages and decreases severalfold in the adult worm. The rates of formation and dissociation of the [3H]MAL-receptor complex are relatively slow (dissociation half-life, 17 min), in agreement with physiological studies of levamisole on Ascaris muscle strips. Levamisole derivatives and cholinergic agonists have the same relative potencies in inhibiting [3H]MAL binding as they do in causing nematode muscle contraction. Vertebrate cholinergic antagonists do not inhibit [3H]MAL binding, but several antagonists (mecamylamine, alpha-bungarotoxin, and cobra venom) potentiate the binding of [3H]MAL and can be used to demonstrate more clearly the presence of a second, lower affinity binding activity whose ligand-binding affinity is also potentiated by these agents. Both high and low affinity wild-type binding components are missing in the ------------------- Key: 951 Medline: 87172096 Authors: Lozano R;Salt TA;Chitwood DJ;Lusby WR Title: Metabolism of sterols of varying ring unsaturation and methylation by C. elegans. Citation: Lipids 22: 84-87 1987 Type: ARTICLE Genes: Abstract: The metabolism of three dietary 4,4-desmethylsterols and two 4 alpha- methylsterols was investigated in the free-living nematode Caenorhabditis elegans. Dietary cholestanol was converted mostly to lathosterol. Dietary lathosterol, 7-dehydrocholesterol, 4 alpha- methylcholest-7-enol and 4 alpha-methylcholest-8(14)-enol each remained largely unchanged. An absolute requirement for a substantial quantity of 7-dehydrocholesterol in C. elegans did not exist. C. elegans was unable to remove a 4 alpha-methyl group or introduce a double bond at C-5 and also demonstrated the lack of a delta 7- reductase. Its nutritional sterol requirement was satisfied by cholestanol, lathosterol or 7-dehydrocholesterol; growth was comparable to that obtained previously in media containing delta 5- sterols. However, the two 4 alpha-methylsterols appeared to be unsatisfactory sterol nutrients. The possible physiological importance of 4 alpha-methylsterols is discussed briefly. ------------------- Key: 952 Medline: Authors: Chitwood DJ;Lozano R;Lusby WR;Thompson MJ;Svoboda JA Title: Metabolism and function of sterols in nematodes. Citation: "Ecology and Metabolism of Plant Lipids." ACS Symposium Series 325. Fuller G and Nes WE (eds). : 200-217 1987 Type: REVIEW Genes: Abstract: Current knowledge of sterol biochemistry and physiology in nematodes is reviewed. Nematodes possess a nutritional requirement for sterol because they lack the capacity for de novo sterol biosynthesis. The free-living nematode Caenorhabditis elegans has recently been used as a model organism for investigation of nematode sterol metabolism. C. elegans is capable of removal of the C-24 alkyl substituent of plant sterols such as sitosterol and also possesses the remarkable ability to attach a methyl group at C-4 on the sterol nucleus. An azasteroid and several long-chain alkyl amines disrupt the phytosterol dealkylation pathway in C. elegans by inhibiting its *24-sterol reductase. These compounds inhibit growth and reproduction in certain parasitic nematodes and provide model compounds for development of novel nematode control ------------------- Key: 953 Medline: 87174754 Authors: Greenwald I;Coulson A;Sulston J;Priess J Title: Correlation of the physical and genetic maps in the lin-12 region of C. elegans. Citation: Nucleic Acids Research 15: 2295-2307 1987 Type: ARTICLE Genes: lin-12 Abstract: We describe the assembly of a set of overlapping clones from the lin- 12 III chromosomal region that spans approximately 600 kb, and the identification of two restriction fragment length polymorphisms, eP6 and eP7, that flank the lin-12 locus. A comparison of the physical map and the genetic map yields approximate measurements of 930 kb/map unit for the eP6--lin-12 interval and 830 kb/map unit for the lin-12-- eP7 interval. We interpret these values as supporting the proposal that the apparent clustering of genes observed for C. elegans autosomes results from decreased recombination frequency in clusters and not from nonrandom distribution of genes on the ------------------- Key: 954 Medline: Authors: Wolstenholme DR;Macfarlane JL;Okimoto R;Clary DO;Wahleithner JA Title: Bizarre tRNAs inferred from DNA sequences of mitochondrial genomes of nematode worms. Citation: Proceedings of the National Academy of Sciences USA 84: 1324-1328 1987 Type: ARTICLE Genes: Abstract: The complete nucleotide sequence of the mitochondrial DNA (mtDNA) molecule of the parasitic nematode worm Ascaris suum has been determined. This molecule lacks genes for tRNAs of the standard form. Instead, 21 sequences are found that can be folded into structures that resemble tRNAs in which the T psi C arm and variable loop are missing and replaced with a single loop of between 4 and 12 nucleotides. Considerations of various properties of these sequences, including the number, predicted anticodons, conserved nucleotides, direction of transcription, base composition, and relative gene arrangements are consistent with the interpretation that they are genes for a different sort of tRNA. Transfer RNA genes with a similar potential secondary structure are found in mtDNA of the free-living nematode Caenorhabditis elegans, suggesting that this unusual form of tRNA is used by all nematode mitochondria. ------------------- Key: 955 Medline: 87031211 Authors: Bennett KL;Ward S Title: Neither a germ line-specific nor several somatically expressed genes are lost during embryonic chromatin diminution in the nematode Ascaris lumbricoides var. suum. Citation: Developmental Biology 118: 141-147 1986 Type: ARTICLE Genes: Abstract: Ascaris lumbricoides var. suum is a parasitic nematode of pigs. Its embryos undergo chromatin diminution between the third and fifth cleavages, resulting in the loss of about 30% of the DNA from all somatic precursor cells while the germ line DNA stays intact. Most of the eliminated DNA has been shown to be satellite sequences. Theodor Boveri proposed that functions essential only to the germ line might be lost from the soma. We have examined this proposal by cloning a gene encoding the major sperm protein (MSP) using a cloned MSP gene from Caenorhabditis elegans as a probe. The MSP appears to be expressed only in the testis of Ascaris, as it is in Caenorhabditis. Actin and a-tubulin were also cloned to serve as somatically expressed gene controls. By probing Southern blots of somatic and germ line DNA with these cloned genes, it was found that none of them was lost or rearranged during chromatin diminution. Thus at least one germ line-specific gene is neither lost nor rearranged during chromatin diminution. We also found that the two nematode species differ widely in their numbers of both MSP and actin genes. Caenorhabditis has >30 MSP genes, but Ascaris has no more than three; whereas Ascaris has many more actin genes than ------------------- Key: 956 Medline: Authors: Bennett KL;Ward S Title: Chromatin diminution in Ascaris lumbricoides. Citation: "Molecular Strategies of Parasitic Invasion." UCLA Symposia on Molecular and Cellular Biology, New Series. Agabian N, Goodman H and Nogueira N (eds), Alan R. Liss, Inc. : 89-98 1987 Type: REVIEW Genes: Abstract: Ascaris and several other parasitic nematodes undergo chromatin diminution in the somatic cell precursors of the early embryo. In 1910 Boveri hypothesized that the chromatin lost might include genes essential to the function of the germ line. We have cloned a germ line-specific cDNA which codes for the major sperm protein. Using this clone as a probe we found that these genes show no loss or rearrangement of DNA in somatic cells which have undergone chromatin diminution. Actin and a-tubulin genes from Ascaris are also unchanged following diminution. Ascaris and the free-living nematode Caenorhabditis elegans differ substantially in the numbers of actin and major sperm protein genes, in spite of conservation of gene ------------------- Key: 957 Medline: 87144656 Authors: Ferguson EL;Sternberg PW;Horvitz HR Title: A genetic pathway for the specification of the vulval cell lineages of C. elegans. Citation: Nature 326: 259-267 1987 Type: ARTICLE Genes: let-23 let-60 lin-1 lin-2 lin-3 lin-4 lin-7 lin-8 lin-9 lin-10 lin-11 lin-12 lin-13 lin-15 lin-17 lin-18 lin-24 lin-25 lin-26 lin-31 lin-33 Abstract: Twenty-three genes have been assigned to particular steps in a genetic pathway for the specification of the vulval cell lineages of the nematode Caenorhabditis elegans. Mutations in most of these genes cause homoeotic transformations in the fates of individual cells, suggesting that these lineages may be specified by a series of decisions that distinguish between alternative cell fates. Fifteen of the genes function in a system involved in the intracellular response to the extracellular signal that induces vulval formation. ------------------- Key: 958 Medline: 87206215 Authors: Sedensky MM;Meneely PM Title: Genetic analysis of halothane sensitivity in Caenorhabditis elegans. Citation: Science 236: 952-954 1987 Type: ARTICLE Genes: unc-9 unc-79 unc-80 Abstract: The nematode Caenorhabditis elegans appears to be a useful model for studying the action of volatile anesthetics. A mutant strain that is hypersensitive to the widely used anesthetic halothane was described earlier. The mutation is now shown to be an allele of unc-79. Other alleles of unc-79 are also associated with hypersensitivity to halothane. A strain with a mutation in a second gene, unc-80, is also hypersensitive to halothane. Nematodes bearing mutations in both unc- 79 and unc-80 are slightly more sensitive to halothane than those bearing only one of these mutations. Mutations in a third gene, unc- 9, suppress both unc-79 and unc-80. Nematodes bearing the suppressor mutations alone have normal sensitivity to halothane. These results show that sensitivity to halothane can be altered by mutations in several different genes. ------------------- Key: 959 Medline: 88007983 Authors: Hecht RM;Berg-Zabelshansky M;Rao PN;Davis FM Title: Conditional absence of mitosis-specific antigens in a temperature-sensitive embryonic arrest mutant of C. Citation: Journal of Cell Science 87: 305-314 1987 Type: ARTICLE Genes: emb-29 Abstract: A monoclonal antibody, specific to phosphoproteins in mitotic HeLa cells was found to crossreact with a similar set of proteins in embryos of the nematode, Caenorhabditis elegans. In C. elegans, as in mammalian cells, the highly conserved antigenic epitope is associated with a family of high molecular weight polypeptides. The antigenic reactivity of these multiple proteins also depends on their phosphorylation, since antibody binding is reduced after alkaline phosphatase treatment. The antigens are detected at the centrosomes, and in the nuclear region and surrounding cytoplasm of mitotic cells. The significance of these antigens is emphasized by their absence at restrictive temperature in embryos of the temperature-sensitive embryonic-arrest mutant, emb-29V. Furthermore, temperature shift-down experiments suggest that the emb-29 mutation defines a cell division cycle function that affects an essential activity required for ------------------- Key: 960 Medline: 87187629 Authors: Ito K;McGhee JD Title: Parental DNA strands segregate randomly during embryonic development of C. elegans. Citation: Cell 49: 329-336 1987 Type: ARTICLE Genes: fem-2 Abstract: The fate of gamete DNA was followed in the next generation embryos of the nematode C. elegans. Either male worms or spermless hermaphrodites were grown on bromodeoxyuridine-containing E. coli in order to label germ-line DNA. Matings then produced embryos in which only the DNA strands provided by the gametes contained label. This original gamete DNA could be detected during embryonic development by using a fluorescently labeled monoclonal antibody specific to bromodeoxyuridine. Both the number and position of fluorescent spots in the embryo indicate that gamete DNA strands segregate randomly during development. Random segregation of parental DNA strands rules out models of development that invoke chromosome imprinting or immortal DNA strands. ------------------- Key: 961 Medline: 87270639 Authors: Vanfleteren JR;Van Bun SM;Van Beeumen JJ Title: The primary structure of histone H2A from the nematode C. elegans. Citation: Biochemical Journal 243: 297-300 1987 Type: ARTICLE Genes: Abstract: The complete primary structure of histone H2A from the nematode Caenorhabditis elegans was determined. The amino acid chain consists of 126 amino acid residues and has a blocked N-terminus. By comparison with calf thymus histone H2A, the nematode protein shows five deletions, two insertions and 16 substitutions. Most of the changes occur in the N- and C-terminal regions of the molecule, whereas the central part covering the residues 21-120 is quite well conserved. The lysine residues 5, 8 and 10 were found to be partially acetylated. ------------------- Key: 962 Medline: 87221139 Authors: Riddle DL Title: Post-embryonic development in C. elegans. Citation: International Journal for Parasitology 17: 223-231 1987 Type: REVIEW Genes: daf-1 daf-2 daf-3 daf-4 daf-5 daf-6 daf-7 daf-8 daf-9 daf-10 daf-11 daf-12 daf-14 daf-15 daf-16 daf-17 daf-18 daf-20 daf-22 Abstract: The free-living soil nematode, Caenorhabditis elegans, is an animal well-suited for developmental studies owing to its genetic and anatomical simplicity. The structure and life cycle of this one-millimeter-long roundworm make it a particularly attractive laboratory model for the analysis of cell lineages, gene action, morphogenesis and behavior during post-embryonic development. Furthermore, similarities between this nematode and other species that are parasites of plants or animals make it a potentially powerful model for understanding the genetic and physiological basis of parasite development and survival strategies. Both normal and mutant strains of C. elegans can be grown rapidly (3-day life cycle) and in large quantity in the laboratory on bacteria (Escherichia coli) as the food source. This is important for biochemical analyses, and for detection of the rare mutants or genetic recombinants that are often extremely useful in genetic analysis. ------------------- Key: 963 Medline: 87231065 Authors: Kay RJ;Russnak RH;Jones D;Mathias C;Candido EPM Title: Expression of intron-containing C. elegans heat shock genes in mouse cells demonstrates divergence of 3' splice site recognition sequences between nema/ Citation: Nucleic Acids Research 15: 3723-3741 1987 Type: ARTICLE Genes: Abstract: Splicing of a pair of intron-containing heat shock genes from Caenorhabditis elegans has been studied in transfected mouse cells. The hsp16-1 and hsp16-48 genes of C. elegans encode 16,000 Da heat shock polypeptides. Each gene contains a short intron of 52 (hsp16-1) or 55 (hsp16-48) base pairs. When these genes were introduced into mouse cells, they were efficiently induced following heat shock, but splicing of the introns was abnormal. In mouse cells, cleavage of the hsp16 transcripts occurred at the correct 5' splice sites, but the 3' splice sites were located at AG dinucleotides downstream of the correct sites. This aberrant splicing was not solely due to the small size of the C. elegans introns, since a hsp16-1 gene containing an intron enlarged by tandem duplication showed exactly the same splicing pattern. The mouse cells thus seem to be unable to recognize the natural 3' splice sites of the C. elegans transcripts. The efficiency of splicing was greatly reduced under heat shock conditions, and unspliced transcripts accumulated in the nucleus. During a subsequent recovery period at 37 degrees C, these transcripts were spliced and transported to the cytoplasm. ------------------- Key: 964 Medline: 87231900 Authors: Johnson TE Title: Aging can be genetically dissected into component processes using long-lived strains of C. elegans. Citation: Proceedings of the National Academy of Sciences USA 84: 3777-3781 1987 Type: ARTICLE Genes: Abstract: The aging process has been dissected by analysis of genetic variants of the nematode Caenorhabditis elegans. Long-lived recombinant inbred lines were generated; some of these lines have mean and maximum life spans up to 70% longer than wild type. Longer life results from a slowing of the characteristic exponential increase in mortality rate that is typical of aging populations in all species. The length of developmental periods and the length of the reproductive period are unrelated to increased life span. Lengthened life is due entirely to an increase in postreproductive life span. Development, reproduction, and life span are each under independent genetic control. General motor activity decays linearly with chronological age in all genotypes. The decay in general motor activity is correlated with and a predictor of life span, suggesting that both share at least one common rate-determining ------------------- Key: 965 Medline: 87248049 Authors: Hartman PS Title: Caffeine-resistant mutants of C. elegans. Citation: Genetical Research 49: 105-110 1987 Type: ARTICLE Genes: caf-1 caf-2 Abstract: Wild-type Caenorhabditis elegans fails to reach adulthoold if L1 larvae are incubated in the presence of 30 mM or greater concentration of caffeine. Eleven mutants have been isolated in which caffeine has a less pronounced effect on development. The mutations are recessive, define two genes, and have been mapped. The mechanism(s) of resistance is unknown. ------------------- Key: 966 Medline: 88056285 Authors: Ambros V;Horvitz HR Title: The lin-14 locus of C. elegans controls the time of expression of specific postembryonic developmental events. Citation: Genes & Development 1: 398-414 1987 Type: ARTICLE Genes: lin-14 szT1 nDf19 Abstract: The lin-14 locus of Caenorhabditis elegans plays an important role in specifying the normal timing and sequence of developmental events in the lateral hypodermal cell lineages. The results of gene dosage, complementation, and temperature-shift experiments indicate that the fates expressed by cells at successive stages of these cell lineages are specified by the level of lin-14 activity and that lin-14 acts at multiple times during development to control stage-specific choices of cell fate. Our observations suggest that during normal development a reduction in the level of lin-14 gene function causes the sequential expression of stage-specific cell fates. ------------------- Key: 967 Medline: Authors: McGhee JD;Ito K;Edgar LG Title: Lineage-specific gene expression in C. elegans. Citation: "Molecular Approaches to Developmental Biology." UCLA Symposia on Molecular and Cellular Biology, New Series. Firtel RA and Davidson EH (eds), Alan R. Liss, NY. 51: 179-193 1987 Type: REVIEW Genes: ges-1 Abstract: We describe an experimental system in which to study gene-specific segregation mechanisms during early development of C. elegans. A non-specific esterase, of unknown physiological function, has convenient properties as a biochemical marker of differentiation: expression is localized to the gut lineage, is due to transcription during zygotic development and is lineage autonomous. The timing of esterase expression does not depend either on the normal number of rounds of cytokinesis or on the normal number of rounds of DNA replication; thus some other clock mechanism must be invoked. We descrbe experiments suggesting that DNA strands donated by the sperm do not co-segregate during development of the next generation. ------------------- Key: 968 Medline: Authors: Otsuka AJ;Wheaton VI;Hedgecock E Title: Transposon tagging of genes affecting axonal outgrowth in C. elegans. Citation: "Molecular Approaches to Developmental Biology." UCLA Symposia on Molecular and Cellular Biology, New Series. Firtel RA and Davidson EH (eds), Alan R. Liss, NY. 51: 665-671 1987 Type: ARTICLE Genes: unc-6 unc-33 unc-44 unc-51 unc-76 unc-104 Abstract: The neurological development of the nematode Caenorhabditis elegans is being analysed by classical genetic and molecular approaches. Putative transposon insertions have been generated using a mutator strain. The mutations isolated include an allele of the axonal growth gene unc-44 and a mutation in a novel dumpy gene. These alleles are unstable, but the reversion rates and the number of extraneous transposons can be decreased by serial backcrosses to a transposon Tc1 low copy number strain. Hybridization of Tc1 DNA to gel blots of mutant DNA revealed a limited number of transposable elements in addition to the wildtype complement. In the case of the dumpy mutation, the association of a unique Tc1 element with the mutation has been demonstrated by loss of the ------------------- Key: 969 Medline: 87215939 Authors: Krause M;Hirsh D Title: A trans-spliced leader sequence on actin mRNA in C. Citation: Cell 49: 753-761 1987 Type: ARTICLE Genes: act-1 act-2 act-3 act-4 Abstract: While determining the 5' ends of C. elegans actin mRNAs, we have discovered a 22 nucleotide spliced leader sequence. The leader sequence is found on mRNA from three of the four nematode actin genes. The leader also appears to be present on some, but not all, nonactin mRNAs. The actin mRNA leader sequence is identical to the first 22 nucleotides of a novel 100 nucleotide RNA transcribed adjacent, and in the opposite orientation, to the 5S ribosomal gene. The evidence suggests that the actin mRNA leader sequence is acquired from this novel nucleotide transcript by an intermolecular trans- splicing mechanism. ------------------- Key: 970 Medline: 87143876 Authors: Ward S;Klass MR Title: Isolation of nematode major sperm proteins. Citation: Methods in Enzymology 134: 414-420 1986 Type: ARTICLE Genes: Abstract: The spermatozoa of the nematode Caenorhabditis elegans are non-flagellated crawling cells. In spite of their crawling motility they contain almost no actin and no microfilaments or microtubules. The spermatozoa have a single pseudopod protruding from a hemispherical cell body and they appear to propel themselves by insertion of new membrane components at the tip of this pseudopod and flow of these components back to the cell body. When the pseudopod is porperly attached to a substrate this flow propels the cell forward. The molecular mechanism driving this flow is unknown and the molecular basis for maintaining and altering pseudopod shape is unknown. An obvious candidate for participation in either motility or shape determination is the major sperm proteins (MSPs). These proteins are a family of nearly identical small basic proteins which make up about 15% of the total protein in the sperm. They are located in the cytoplasm of both the pseudopod and the cell body. In the parasitic nematode Ascaris lumbricoides a protein similar to C. elegans MSPs is also the most abundant protein in the sperm. MSPs are not detected in any tissue other than testis. In the testis they first appear in primary spermatocytes as an amorphous material associated with the membranes of a transient organelle which serves to transport MSPs to the spermatid. The MSPs subsequently form a semicrystalline array of 4.5 mn fibers in this organelle. After segregatin to the spermatid the MSP fibers disassemble dispersing the MSPs throughout the cytoplasm. During the maturation of spermatids to spermatozoa the MSPs concentrate in the pseudopod cytoplasm although some remain in the cell body. ------------------- Key: 971 Medline: 88011322 Authors: Roberts SB;Sanicola M;Emmons SW;Childs G Title: Molecular characterization of the histone gene family of C. elegans. Citation: Journal of Molecular Biology 196: 27-38 1987 Type: ARTICLE Genes: act-3 col-2 Abstract: The core histone genes (H2A, H2B, H3 and H4) of Caenorhabditis elegans are arranged in approximately 11 dispersed clusters and are not tandemly arrayed in the genome. Three well-characterized genomic clones, which contain histone genes, have one copy of each core histone gene per cluster. One of the clones (lambda Ceh-1) carries one histone cluster surrounded by several thousand base-pairs of non- histone DNA, and another clone (lambda Ceh-3) contains a histone cluster duplication surrounded by non-histone DNA. A third clone (lambda Ceh-2) carries a cluster of core histone genes flanked on one side (12,000 base-pairs away) by a single H2B gene and on the other by non-histone DNA. A fourth cluster (clone BE9) has one copy each of H3 and H4 and two copies each of H2A and H2B. This cluster is also flanked by non-histone DNA. Analysis of cosmid clones which overlap three of the clusters shows that no other histone clusters are closer than 8000 to 60,000 base-pairs, although unidentified non-histone transcription units are present on the flanking regions. Gene order within the histone clusters varies, and histone mRNAs are transcribed from both DNA strands. No H1 sequences are found on these core histone clones. Restriction fragment length polymorphisms between two related nematode strains (Bristol and Bergerac) were used as phenotypic markers in genetic crosses to map one histone cluster to linkage group V and another to linkage group IV. Hybridization of gene-specific probes from sea urchin to C. elegans RNA identifies C. elegans core histone messenger RNAs of sizes similar to sea urchin early stage histone mRNAs (H2A, H2B, H3 and H4). The organization of histone genes in C. elegans resembles the clustering found in most vertebrate organisms and does not resemble the tandem patterns of the early stage histone gene family of sea urchins or the major histone locus of Drosophila. ------------------- Key: 972 Medline: 88024046 Authors: Meheus LA;Van Beeumen JJ;Coomans AV;Vanfleteren JR Title: Age-specific nuclear proteins in the nematode worm C. elegans. Citation: Biochemical Journal 245: 257-261 1987 Type: ARTICLE Genes: Abstract: The nematode worm Caenorhabditis elegans is known to undergo characteristic morphological as well as physiological signs of senescence. Two-dimensional gel electrophoresis shows that alterations also occur in the pattern of the nuclear proteins as a function of age. Non-histone proteins whose level exhibits a steep fall with age are egg-specific and not involved in senescence. However, a distinct set of non-histones accumulates with age and can be considered as senescence markers. Some of these are glycoproteins, as shown by their concanavalin A-binding properties. One age-specific polypeptide, called 'protein S-28', was further characterized by peptide mapping and determination of its N-terminal amino acid ------------------- Key: 973 Medline: 88000636 Authors: McGhee JD Title: Purification and characterization of a carboxylesterase from the intestine of the nematode C. elegans. Citation: Biochemistry 26: 4101-4107 1987 Type: ARTICLE Genes: Abstract: The major intestinal esterase from the nematode Caenorhabditis elegans has been purified to essential homogeneity. Starting from whole worms, the overall purification is 9000-fold with a 10% recovery of activity. The esterase is a single polypeptide chain of Mr 60,000 and is stoichiometrically inhibited by organophosphates. Substrate preferences and inhibition patterns classify the enzyme as a carboxylesterase (EC 3.1.1.1), but the physiological function is unknown. The sequence of 13 amino acid residues at the esterase N- terminus has been determined. This partial sequence shows a surprisingly high degree of similarity to the N-terminal sequence of two carboxylesterases recently isolated from Drosophila mojavensis [Pen, J., van Beeumen, J., & Beintema, J. J. (1986) Biochem. J. 238, 691-699]. ------------------- Key: 974 Medline: 87258247 Authors: Anderson P;Kimble J Title: Molecular biology - genetics of development elucidated by nematodes. Citation: Nature 328: 202-202 1987 Type: REVIEW Genes: Abstract: The molecular mechanisms responsible for development of metazoan pattern and form are largely unknown. Embryos have been described and experimentally manipulated for more than a century, but only in the past few years have some of the genes and proteins that influence, and perhaps govern, development been isolated and scrutinized. These genes, cloned chiefly from the fruitfly Drosophila melanogaster, constitute the 'nuts-and-bolts' of developmental decision-making. The challenge to developmental biologists today is to understand the functions of these genes and to describe them in biochemical terms. Results reported at a recent meeting indicate that some elucidation of development at a molecular level will emerge from investigations of the nematode worm Caenorhabditis elegans. ------------------- Key: 975 Medline: Authors: Howell AM;Gilmour SG;Mancebo RA;Rose AM Title: Genetic analysis of a large autosomal region in C. elegans by the use of a free duplication. Citation: Genetical Research 49: 207-213 1987 Type: ARTICLE Genes: him-1 let-351 let-352 let-353 let-354 let-355 let-356 let-357 let-359 let-360 let-361 let-362 let-363 let-364 let-365 let-366 let-367 let-368 let-369 let-370 let-371 let-372 let-376 let-377 let-378 let-379 let-380 let-381 let-382 let-383 let-384 let-385 let-386 let-387 let-388 let-389 let-390 let-391 let-392 lin-6 sDf4 sDp2 Abstract: In this paper we describe the use of a free duplication, sDp2 (I;f), for the recovery, maintenance, and analysis of mutations defining essential genes in the left third of Linkage Group I of Caenorhabditis elegans. The lethals were induced in a strain of genotype (sDp2)+ / dpy-5 + unc-13 / dpy-5 unc-15 +, using either 12 mM ethylmethane sulphonate or 1500 r of gamma radiation. Lethal mutations linked to the dpy-5 unc-13 chromosome were recognized by the absence of Dpy-5 Unc-13 individuals amongst the self progeny and were maintained by isolating Unc-13 hermaphrodites. These strains-which have two mutant alleles of the essential gene and a wild-type allele on the duplication-are balanced, since crossing-over does not occur between sDp2 and the normal homologues. Using this system we have recovered 58 EMS-induced mutations. These have been charactterized with regard to map position and complementation. Twenty-nine of the EMS-induced mutations lie to the left of dpy-5 and define 20 complementation groups; 21 were to the right and define 17 complementation groups. Among a set of 29 gamma radiation-induced lethal mutations, 17 appear to be single gene mutations or are very small deletions. We estimate that we have identified from one-sixth to one-half of the essential genes in the ------------------- Key: 976 Medline: 87277372 Authors: Kim JS;Rose AM Title: The effect of gamma radiation on recombination frequency in C. elegans. Citation: Genome 29: 457-462 1987 Type: ARTICLE Genes: bli-3 dpy-5 dpy-14 unc-11 unc-13 unc-35 Abstract: We have studied the effect of gamma radiation on recombination frequency for intervals across the cluster of linkage group I in Caenorhabditis elegans. Recombination frequency increased approximately twofold across the dpy-5-unc-13 interval after treatment with 2000 rads (1 rad = 10 mGy) of cobalt 60 gamma radiation. Several factors affecting the magnitude of the increase have been characterized. Recombination frequency increased more with higher doses of radiation. However, the increase in recombination frequency with increasing dose was accompanied by a reduced average number of progeny from radiation-treated individuals. The amount of the increase was affected by meiotic stage, age at the time of treatment (premeiotic), and radiation dose. The increase in recombination was detectable in the B brood and remained elevated for the remainder of egg production. X-chromosome nondisjunction was also increased by radiation treatment. A high frequency of the recombinant progeny produced with radiation treatment were sterile unlike their nonrecombinant siblings. When parameters affecting recombination frequency are held constant during treatment, chromosomal regions of high gene density on the meiotic map increased more (fourfold) than an adjacent region of low gene density (no increase). The greatest increase was across the dpy-14-unc-13 interval near the center of the gene cluster. These results may suggest that the physical length of DNA per map unit is greater within the cluster ------------------- Key: 977 Medline: 87277353 Authors: Herman RK Title: Mosaic analysis of two genes that affect nervous system structure in C. elegans. Citation: Genetics 116: 377-388 1987 Type: ARTICLE Genes: daf-6 mec-4 osm-1 unc-3 unc-93 mnDp7 mnDp21 Abstract: The mutation mec-4(e 1611), identified by M. Chalfie, leads to the degeneration and death of the six neurons, called the microtubule cells, that mediate the response of wild-type animals to light touch. The fates of two of these cells, PLML and PLMR, which are responsible for response to light touch in the tail of the animal, have been monitored in animals mosaic for the mec-4(e 1611) mutation. The results are consistent with the view that the mutation behaves cell autonomously in its killing effect; in particular, none of the neurons that make either chemical synapses or gap junctions to PLML or PLMR is responsible for the deaths of PLML or PLMR. The results of gene dosage and dominance tests suggest that the mec-4(+) gene product, which is required for wild-type microtubule cell function, is altered by the e 1611 mutation into a novel product that kills the microtubule cells. Mutation in the gene unc-3 leads to the derangement of the processes of the motor neurons of the ventral cord. Mosaic analysis strongly suggests that unc-3(+) expression is required only in the motor neurons themselves for normal neuronal development. In particular, the hypodermis surrounding the ventral cord is not the primary focus of unc-3 action (body muscle was excluded in earlier work). Finally, the mosaic analysis supports an earlier suggestion that a sensory defect caused by a daf-6 mutation is localized to a non-neuronal cell called the sheath cell. ------------------- Key: 978 Medline: 88004133 Authors: Hedgecock EM;Culotti JG;Hall DH;Stern BD Title: Genetics of cell and axon migrations in C. elegans. Citation: Development 100: 365-382 1987 Type: REVIEW Genes: dpy-24 egl-5 egl-15 egl-27 egl-43 glp-1 hch-1 lin-12 lin-17 lin-20 lin-21 lin-22 lin-32 mab-5 mig-1 mig-2 mig-4 mig-5 mig-6 mig-7 unc-3 unc-5 unc-6 unc-11 unc-23 unc-30 unc-33 unc-34 unc-39 unc-40 unc-44 unc-51 unc-53 unc-62 unc-71 unc-73 unc-76 vab-8 Abstract: The Caenorhabditis elegans epidermis comprises 78 cells which cover the external surface of the embryo as a single cell layer. These cells secrete the cuticle from their exterior faces and support the body wall muscles and most of the nervous system on their interior faces. The epidermal cells arise by autonomous embryonic cell lineages but show regulative interactions after their assembly into an epithelium. It is believed that the various epidermal cells express different kinds or amounts of surface molecules that govern their mutual assembly and also guide the attachments and migrations of the underlying body muscles and neurones. The first muscles and neurones may in turn express new surface molecules that refine later cell movements. Mutations in some 30 known genes disrupt the movements of cells or axons along the body wall. ------------------- Key: 979 Medline: 87247699 Authors: Schierenberg E Title: Reversal of cellular polarity and early cell-cell interaction in the embryo of C. elegans. Citation: Developmental Biology 122: 452-463 1987 Type: ARTICLE Genes: Abstract: During early embryogenesis of Caenorhabditis elegans the serial stem cell-like cleavages of the germ line cells P0-P3 generate a number of somatic founder cells with different developmental potentials. Observations on partial embryos show that in the first two of these unequal divisions in the germ line the somatic daughter cell comes to lie anterior to the new germ line cell. In the following two, however, the somatic daughter cell comes to lie posterior to the new germ line cell, suggesting a reversal of polarity in the germ line. By the use of a laser microbeam, egg fragments can be extruded from young embryos; the fragments often cleave like partial twins. Depending on whether the fragment is derived from the posterior region of the uncleaved zygote P0 or its daughter P1, the mirror image duplications that are generated are joined at their larger soma- like cells or at their smaller germ line-like cells, respectively. This result is best explained as a reversal of polarity taking place in the germ line cell P2. This notion is strengthened by the finding that partial embryos derived from the posterior region of the P2 cell in late interphase do not undergo stem cell-like (i.e., unequal) cleavages in contrast to those derived from P0 or P1. Finally, an apparent early cell-cell interaction is described which is inconsistent with the classical notion of "mosaic" nematode development: removal of the germline cell P2 results in an altered developmental pattern of its somatic sister cell EMS. A working model is presented linking reversal of polarity and cell-cell interaction and offers an explanation for the ------------------- Key: 980 Medline: 87260980 Authors: Link CD;Graf-Whitsel J;Wood WB Title: Isolation and characterization of a nematode transposable element from Panagrellus redivivus. Citation: Proceedings of the National Academy of Sciences USA 84: 5325-5329 1987 Type: ARTICLE Genes: unc-22 Abstract: We have isolated a transposable element, designatd PAT-1, from the free-living nematode Panagrellus redivivus. P. redivivus strain C15 was found to have a high spontaneous mutation frequency compared to the standard Caenorhabditis elegans laboratory strain N2. To characterize the genetic lesions occurring in spontaneous C15 mutants, we molecularly cloned the homolog of the C. elegans unc-22 gene from wild-type P. redivivus and two strains carrying spontaneous mutations in this gene. One of these mutations resulted from the insertion of a 4.8-kilobase segment of repetitive DNA. This repetitive element (PAT-1) varies in copy number (10-50 copies) and location in different P. redivivus strains and is absent from C. elegans. The element could be useful as a transformation vector for C. elegans. Our approach is a general one that could be used to isolate additional nematode transposons from other ------------------- Key: 981 Medline: 88028515 Authors: Vanfleteren JR;Van Bun SM;Van Beeumen JJ Title: The primary structure of histone H-4 from the nematode C. elegans. Citation: Comparative Biochemistry & Physiology 87B: 847-849 1987 Type: ARTICLE Genes: Abstract: 1. The complete amino acid sequence of histone H4 from the nematode Caenorhabditis elegans has been established. 2. The polypeptide chain consists of 102 amino acids and has a completely alpha-N-blocked serine at residue 1. 3. The sequence differs from vertebrate H4 in position 73 by substitution of cysteine for threonine. 4. Lysine in position 20 is monomethylated. ------------------- Key: 982 Medline: 88036060 Authors: Felsenstein KM;Emmons SW Title: Structure and evolution of a family of interspersed repetitive DNA sequences in C. elegans. Citation: Journal of Molecular Evolution 25: 230-240 1987 Type: ARTICLE Genes: Abstract: The structure of three members of a repetitive DNA family from the genome of the nematode Caenorhabditis elegans has been studied. The three repetitive elements have a similar unitary structure consisting of two 451-bp sequences in inverted orientation separated by 491 bp, 1.5 kb, and 2.5 kb, respectively. The 491-bp sequence separating the inverted 451-bp sequences of the shortest element is found adjacent to one of the repeats in the other two elements as well. The combination of the three sequences we define as the basic repetitive unit. Comparison of the nucleotide sequences of the three elements has allowed the identification of the one most closely resembling the primordial repetitive element. Additionally, a process of co- evolution is evident that results in the introduction of identical sequence changes into both copies of the inverted sequence within a single unit. Possible mechanisms are discussed for the homogenization of these sequences. A direct test of one possible homogenization mechanism, namely homologous recombination between the inverted sequences accompanied by gene conversion, shows that recombination between the inverted repeats does not occur at high frequency. ------------------- Key: 983 Medline: 87287287 Authors: Collins J;Saari B;Anderson P Title: Activation of a transposable element in the germ line but not the soma of C. elegans. Citation: Nature 328: 726-728 1987 Type: ARTICLE Genes: him-1 him-2 him-3 him-4 him-5 him-6 him-7 him-8 mut-2 mut-3 unc-22 unc-54 Abstract: The genetic activity of transposable elements is tightly controlled in many species. Transposons that are relatively quiescent under certain circumstances can excise or transpose at greatly increased rates under other circumstances. For example, 'genomic shock' can activate quiescent maize transposons, 'cytotype' and tissue-specific splicing regulate Drosophila P factors, copy number controls Tn5 transposition in bacteria, and developmental timing affects the production of transposon-like intracisternal A-particles in mouse embryos. The Caenorhabditis elegans transposable element Tc1 is subject to both strain-specific and tissue-specific control. Multiple copies of Tc1 are present in the genome of all C. elegans strains collected from nature. However, these elements are genetically active in only certain isolates. For example, in C. elegans variety Bristol transposition and excision of Tc1 are undetectable, but in variety Bergerac transposition and excision are frequent. Moreover, in variety Bergerac, Tc1 is about 1,000-fold more active in somatic cells than in germ cells. We have investigated the genetic basis for the germ/soma regulation of Tc1 activity. We have isolated mutants that exhibit increased frequencies of Tc1 excision in the germ line. The frequencies of Tc1 excision in the soma are unaltered in these mutants. These mutants also exhibit high frequencies of Tc1 germ-line transposition, and this results in a mutator phenotype. Nearly all mutator-induced mutations are caused by ------------------- Key: 984 Medline: Authors: Ibrahim AM Title: Studies on the bioactivity of diflubenzuron on C. elegans. Citation: Arab Gulf Journal of Scientific Research 5: 113-125 1987 Type: ARTICLE Genes: Abstract: ------------------- Key: 985 Medline: Authors: Herman RK;Shaw JE Title: The transposable genetic element Tc1 in the nematode C. elegans. Citation: Trends in Genetics 3: 222-225 1987 Type: REVIEW Genes: lin-12 unc-22 unc-54 Abstract: Tc1 is a 1.6 kbp DNA sequence present in about 30 copies in some strains of C. elegans and 300 or more copies in other strains. Tc1 elements excise much more frequently in somatic cells than in the germ line. Germ-line transposition of Tc1 has been detected and is under genetic control. Tc1 has become very useful as a tool for cloning C. elegans genes identified soley by mutation. ------------------- Key: 986 Medline: Authors: Proujan B Title: Nematode Resource Available. Citation: Research Resources Reporter (DHHS) 10: 13-14 1986 Type: REVIEW Genes: Abstract: A comprehensive collection of the nematode Caenorhabditis elegans, including strains useful in research and in teaching genetics, is maintained at the Caenorhabditis Genetics Center at the University of Missouri in Columbia, Missouri. ------------------- Key: 987 Medline: 88030641 Authors: Meneely PM;Wood WB Title: Genetic analysis of X-chromosome dosage compensation in C. elegans. Citation: Genetics 117: 25-41 1987 Type: ARTICLE Genes: dpy-21 dpy-22 dpy-23 dpy-26 Abstract: We have shown that the phenotypes resulting from hypomorphic mutations (causing reduction but not complete loss of function) in two X-linked genes can be used as a genetic assay for X-chromosome dosage compensation in Caenorhabditis elegans between males (XO) and hermaphrodites (XX). In addition we show that recessive mutations in two autosomal genes, dpy-21 V and dpy-26 IV, suppress the phenotypes resulting from the X-linked hypomorphic mutations, but not the phenotypes resulting from comparable autosomal hypomorphic mutations. This result strongly suggests that the dpy-21 and dpy-26 mutations cause increased X expression, implying that the normal function of these genes may be to lower the expression of X-linked genes. Recessive mutations in two other dpy genes, dpy-22 X and dpy-23 X, increase the severity of phenotypes resulting from some X-linked hypomorphic mutations, although dpy-23 may affect the phenotypes resulting from the autosomal hypomorphs as well. The mutations in all four of the dpy genes show their effects in both XO and XX animals, although to different degrees. Mutations in 18 other dpy genes do not show these ------------------- Key: 988 Medline: 88015533 Authors: Ruan KS;Emmons SW Title: Precise and imprecise somatic excision of the transposon Tc1 in the nematode C. elegans. Citation: Nucleic Acids Research 15: 6875-6881 1987 Type: ARTICLE Genes: Abstract: Eleven chromosomal products of somatic excision of Tc1 transposable elements have been cloned and sequenced. The cloning method did not involve genetic reversion; therefore the products analyzed should be representative. Six empty religated target sites were from excision of one Tc1 element inserted near actin genes on linkage group V; five were from a second Tc1 element inserted elsewhere on the same linkage group. All six products from the first element were identical in sequence to an empty target site from a second strain, indicating excision had been precise. Two of the products from the second element were also precise, whereas the other three contained four extra nucleotides at the point of excision, indicating an imprecise excision. The four nucleotides are the same in all cases and could represent two terminal nucleotides of the transposon plus a two- nucleotide target site duplication. The difference in the ratio of precise to imprecise excision at the two insertion sites suggests a possible chromosomal position effect on the pathway of Tc1 somatic excision. ------------------- Key: 989 Medline: Authors: Blumenthal T;Zucker-Aprison E Title: Evolution and regulation of vitellogenin genes. Citation: "Molecular Biology of Invertebrate Development." UCLA Symposia on Molecular & Cellular Biology. O'Conner JD (ed). 66: 3-19 1987 Type: REVIEW Genes: vit-1 vit-2 vit-3 vit-4 vit-5 vit-6 Abstract: Vitellogenins of many insects, vertebrates, nematodes and sea urchins are very similar in size and amino acid composition. We have determined the nucleotide sequences of the genes that encode vitellogenins in nematodes (C. elegans) and sea urchins (S. purpuratus), and compared the deduced amino acid sequences to the published sequences of two vertebrate vitellogenins (X. laevis and G. gallus). This comparison demonstrated unequivocally that the nematode and vertebrate proteins are encoded by distant members of a single gene family. The less extensive sequence data available for the sea urchin gene indicates that this, too, may be a member of this family of genes, as may the vitellogenin genes of locust. On the other hand, we were unable to detect any similarity between these genes and the D. melanogaster yolk protein genes. Thus it appears that while nematodes, vertebrates, sea urchins and at least some insects utilize the same family of genes to encode vitellogenins, Drosophila uses a different gene family. All of the vitellogenin genes are regulated in a tissue-specific manner. They are expressed in the intestine in nematodes, in the liver in vertebrates, in the fat body in insects, and in the intestine and gonad in sea urchins. Their production is limited to adult females in all species except sea urchins, in which they are expressed by adults of both sexes. In nematodes we have identified two heptameric sequence elements repeated multiple times in all eleven of the vitellogenin genes sequenced. One of these elements is also present in the vertebrate promoters and has recently been shown to be required for transcriptional activation. All of the 5' ends of the vitellogenin mRNAs of nematodes, vertebrates and locust can be folded into potentially-stable secondary structures. We present evidence that these structures have been strongly selected for and presumably perform some function in regulation of vitellogenin production. ------------------- Key: 990 Medline: Authors: McGhee JD;Ito K;Edgar LG Title: Control of gene expression during development of the C. elegans intestine. Citation: "Molecular Biology of Invertebrate Development." UCLA Symposia on Molecular & Cellular Biology. O'Conner JD (ed). 66: 145-155 1987 Type: REVIEW Genes: ges-1 Abstract: We describe the use of a nonspecific carboxylesterase as a biochemical marker for intestinal differentiation in the nematode C. elegans. In particular, we describe how esterase expression responds to inhibition of embryonic DNA synthesis by aphidicolin. Esterase expression requires a short period of DNA synthesis immediattely after the gut lineage is clonally established. However, the subsequent 2-3 rounds of DNA synthesis, which normally occur before esterase gene transcription, can be inhibited without effect. Thus esterase expression depends neither on reaching the normal DNA:cytoplasmic ration nor on counting the normal number of replication rounds. ------------------- Key: 991 Medline: Authors: Ambros V;Fixsen W Title: Cell lineage variation among nematodes. Citation: "Development as an Evolutionary Process." MBL Lectures in Biology. Raff RA and Raff EC (eds), Alan R. Liss. 8: 139-159 1987 Type: REVIEW Genes: lin-12 lin-14 lin-22 lin-28 lin-29 Abstract: Mutations in genes that control developmental patterns undoubtedly underlie evolutionary change in development. The elucidation of the precise genetic basis of evolutionary change requires the identification and genetic analysis of key genes that control normal developmental patterns of an organism ("developmental control genes"), the analysis of the precise nature of developmental differences between that organism and its related species, and the determination of what changes in these developmental control genes actually cause the observed evolutionary developmental differences. Nematodes offer an excellent opportunity to study the roles of developmental control genes in evolutionary change. The simple anatomy and rapid life cycle of the nematode Caenorhabditis elegans has allowed a detailed analysis of its wild-type development. As a result, the complete cell lineage of C. elegans has been elucidated. This lineage is nearly invariant in the wild type; each cell is formed after a defined lineage history and at a specific time during development. Thus, the developmental defects of mutants can be accurately determined at the level of the fates expressed by specific cells at specific times in development. Through genetic analyses of C. elegans developmental mutants, genes have been identified that play crucial roles in specifying and expressing the normal developmental program. If these genes code for developmental control processes common to different nematode species, then mutations of these genes might underlie interspecific developmental change. Other nematode species can be isolated from the wild and cultured in the laboratory with ease. The relatively simple cellular anatomy of nematodes allows the direct comparison of cell lineages between different species on the level of individual cells and cell divisions. If genes affecting development in C. elegans play evolutionary roles, then developmental differences between species should emerge that parallel, or even are identical to, mutationally induced changes in C. elegans. It should eventually be possible to test directly which genes are responsible for certain evolutionary differences in development by altering ------------------- Key: 992 Medline: 86118694 Authors: Akam M Title: Mediators of cell communication? Citation: Nature 319: 447-447 1986 Type: REVIEW Genes: lin-12 Abstract: The control of development operates at many different levels. In recent months this has become easy to forget, with the nucleus the focus of attention and the DNA-binding properties of the homoeo box taking much of the limelight. Now the sequencing of two other 'controlling' gene, one from insects and the other from nematodes, has revealed homology with mammalian proteins of very different function. The lin-12 gene of Caaenorhabditis elegans, which controls patterns of cell lineage, and the Notch gene of Drosophila, which plays a role in the early development of the nervous system, both encode proteins homologous with epidermal growth factor (EGF) and the structurally related family of mammalian proteins. Other members of this family are all membrane-bound or secreted proteins, suggesting that Notch and lin-12 act at or beyond the cell membrane, perhaps to mediate cell communication. ------------------- Key: 993 Medline: Authors: Riddle DL;Golden JW;Albert PS Title: Role of dauer larvae in survival of C. elegans. Citation: "Vistas on Nematology." Veech JA and Dickson DW (eds), Society of Nematologists, Inc. : 174-179 1987 Type: REVIEW Genes: daf-10 daf-22 egl-4 egl-40 lin-14 lin-28 sqt-2 Abstract: The dauer, or "enduring," larval stage of Caenorhabditis elegans is a form of facultative diapause. Environmental factors act as signals to a receptive developmental stage (the J1 juvenile) resulting in altered physiology and developmental potential, so that a third-stage juvenile can be formed that is specialized for dispersal and long-term survival. Dauer larvae are capable of active movement, but they do not feed. They have a unique morphology and resistance to stress, they are altered in energy metabolism, and they are arrested in development. Dauer larvae survive four to eight times the 3-week life span of animals that have bypassed the dauer stage. The dauer stage itself has been considered to be nonaging, because the duration of the dauer stage does not affect postdauer life span. As far as is known, the consumption of stored energy may be the major factor limiting dauer larva life expectancy. Diapause may be ended in response to conditions improved for growth and reproduction. Developmental commitment to recovery (exit) from the dauer stage occurs within 1 hour after the animal is placed in a fresh environment with food. After 2-3 hours it begins to feed, resumes development, and molts to the J4 stage after ------------------- Key: 994 Medline: Authors: Johnson TE;Foltz NL Title: Aging in C. elegans: Update 1986. Citation: "Review of Biological Research in Aging." Rothstein M (ed), Alan R. Liss, NY. 3: 51-61 1987 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 egl-1 fer-15 lin-12 mut-2 rad-1 rad-2 rad-3 rad-4 rad-5 rad-6 rad-7 unc-22 Abstract: Since the last review in this series [Johnson, 1985], many papers have appeared dealing directly with the aging process in both Caenorhabditis elegans and Turbatrix aceti. We will review this work and also briefly review other areas of C. elegans research that may impact on the study of aging. C. elegans has become a major biological model; four "News" articles in Science [Lewin, 1984a,b; Marx, 1984a,b] and inclusion as one of three developmental genetics models in a recent text [Wilkins, 1986] indicate its importance. Recent work has verified earlier results and has advanced progress toward new goals, such as routine molecular cloning. The aging studies reviewed here, together with new findings from other areas of C. elegans research, lay the groundwork for rapid advances in our understanding of aging in nematodes. Several areas of research in C. elegans have been reviewed recently: the genetic approach to understanding the cell lineage [Sternberg and Horvitz, 1984] and a brief summary of cell lineage mutants [Hedgecock, 1985]. The specification of neuronal development and neural connectivity has been a continuing theme in C. elegans research and reviews of these areas have also appeared [Chalfie, 1984; White, 1985]. A major genetic advance is the development of reliable, if not routine, mosaic analysis [Herman, 1984; Herman and Kari, 1985], which is useful for the genetic analysis of tissue-limited gene expression. Hodgkin [1985] reviews studies on a series of mutants involved in the specification of sex. These include her mutations that cause XO worms (normally males) to develop as hermaphrodites and tra mutations that change XX hermaphrodites into phenotypic males. The work on the structure and development of nematode muscle has been summarized by Waterston and Francis [1985]. A comprehensive review of aging research, containing useful reference material on potential biomarkers, has appeared [Johnson and Simpson, 1985], as well as a review including ------------------- Key: 995 Medline: Authors: Johnson TE Title: Developmentally programmed aging: Future directions. Citation: "Modern Biological Theories of Aging." Warner HR, Sprott RL, Butler RN and Schneider EL (eds), Raven Press, NY. : 63-76 1987 Type: REVIEW Genes: age-1 ced-1 ced-2 ced-3 ced-4 lin-12 nuc-1 Abstract: The concept of developmentally programmed senescence has been outlined by Leonard Hayflick (this volume), and examples from development have been used as exemplars of "developmentally programmed senescence" (Richard Russell, this volume). Unlike development, senescence has probably evolved in the absence of direct selection for increased longevity, perhaps as a direct result of the absence of such selection. (For an excellent review see Charlesworth.) A popular evolutionary model that has received experimental support suggests that senescence may result from pleiotropic effects of selection for adaptive life history characteristics. In the literature on aging, less rigorous arguements have been used to suggest that in human evolution, a delay in the age of senescence has been indirectly selected for by means of so-called longevity assurance or longevity-determinant genes. However, all explanations for the evolution of senescence are theoretical, and, with few exceptions, remain largely untested. Like Dr. Hayflick and Russell, I will assume that by developmental programming we mean genetic specification. I will use a general definition so as not to preclude examples that fail to meet one or more of the rigid criteria defined by Russell (this volume). This less rigid definition of programmed aging is necessary, because unlike development, where genetics has been successfully applied for 50 years, examples of genetic specification of senescent processes are quite few. In the literature on aging, it is still not widely accepted that mutants can alter fundamental patterns of senescent events in well-defined ways. One purpose of this presentation is to outline a few examples. In senescence, large batteries of new genes are not differentially regulated; this is quite unlike development, where many genes are differentially regulated. The molecular etiology of senescence is unknown in almost every instance and, as such, makes the study of aging a fascinating area for inquiry. If senescence is unlike development in lacking differential gene regulation, what are the approaches that are likely to yield useful results in the analysis of senescence and the aging process? The developmental genetic paradigm is a useful, indeed essential, theoretical construct for approaching the aging process in an experimental context. The lack of a suitable model organism in which classical and molecular genetics can be productively combined with other experimental techniques has impeded our understanding of senescence. Despite a general lack of evidence for genetic specification, there are instances where genetic specification is clearly evident; the analysis of mutational events that alter normal senescence in well-defined ways demonstrates this point. These instances also provide experimental models for dissecting the aging ------------------- Key: 996 Medline: Authors: Edgley ML;Riddle DL Title: The nematode Caenorhabditis elegans. Citation: Genetic Maps 4: 351-365 1987 Type: REVIEW Genes: Abstract: ------------------- Key: 997 Medline: Authors: Russell RL Title: Evidence for and against the theory of developmentally programmed aging. Citation: "Modern Biological Theories of Aging." Warner HR, Sprott RL, Butler RN and Schneider EL (eds), Raven Press, NY. : 35-61 1987 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 lin-12 nuc-1 Abstract: To my knowledge, a theory of "developmentally programmed aging" has never been explicitly stated, although the notion that aging has some relationship to development has certainly been proposed many times. In the preceding chapter (36), Dr. Hayflick has made a brief description of the central idea of developmental programming within aging. In order to discuss relevant evidence in this chapter, I would like to propose the following, somewhat more specific and operational definition: The theory of developmentally programmed aging posits that aging involves events controlled in ways recognizably similar to those that operate during development. This definition is perhaps a little less extreme than it might have been, since it uses the phrase "aging involves events" rather than the phrase "aging is caused by events." However, I think it captures most of the usual connotations of "developmentally programmed aging," and it at least has the virtue of testability. Of course, to test the theory, as defined, requires evidence of several sorts. In particular, it requires (a) that we understand how some aging events are controlled, (b) that we understand how some developmental events are controlled, and (c) that we know how to recognize whether there is or is not similarity between the two. A central message of what follows is that we are really only at the beginning of being able to test this theory, although some lines of approach do appear ------------------- Key: 998 Medline: 88035150 Authors: Lewis JA;Elmer JS;Skimming J;McLafferty S;Fleming J;McGee T Title: Cholinergic receptor mutants of the nematode C. elegans. Citation: Journal of Neuroscience 7: 3059-3071 1987 Type: ARTICLE Genes: lev-1 lev-8 lev-9 lev-10 lev-11 unc-22 unc-29 unc-38 unc-50 unc-63 unc-68 unc-74 Abstract: Potential acetylcholine receptor (AChR) mutants of the nematode are selectable by resistance to the neurotoxic drug levamisole, a probable cholinergic agonist. To determine which mutants may have achieved resistance through loss of levamisole receptor function, we have assayed mutant extracts for specific 3H-meta-aminolevamisole binding activity in the presence and absence of mecamylamine. We find that mutants in 3 of the 7 genes associated with extreme levamisole resistance are obviously deficient in saturable specific 3H-meta- aminolevamisole binding activity. Mutants of the 4 other genes have abnormal binding activities that fail to undergo the apparent allosteric activation of saturable specific 3H-meta-aminolevamisole binding activity caused by mecamylamine. Thus, all 7 genes appear to be required to produce a fully functional levamisole receptor. Mutants of several other genes associated only with partial resistance to levamisole have at least grossly normal receptor binding ------------------- Key: 999 Medline: 88112816 Authors: Hodgkin J Title: A genetic analysis of the sex-determining gene, tra-1, in the nematode C. elegans. Citation: Genes & Development 1: 731-745 1987 Type: ARTICLE Genes: tra-1 eDf2 eDp6 Abstract: The normal sexes of Caenorhabditis elegans are the self-fertilizing hermaphrodite (XX) and the male (XO). The autosomal gene tra-1 is a major switch gene controlling sexual phenotype. Mutant phenotypes of 43 loss-of-function (lf) tra-1 alleles and 22 gain-of-function (gf) tra-1 alleles are described and discussed. The tra-1(lf) alleles are recessive and, in general, masculinizing. The most severe mutations (such as seven out of eight identified amber alleles) can transform XX animals into fertile males. These mutations have little effect on XO animals (which are male already) but lead to some abnormalities in XO gonadal development, indicating that tra-1 has functions in normal development of both sexes, although its major function is confined to the XX hermaphrodite. Weaker tra-1(lf) alleles lead to incomplete masculinization of XX animals, resulting in a variety of intersexual phenotypes. the tra-1(gf) alleles are dominant and have an opposite, feminizing effect. Six out of 22 can transform XO animals into fertile females or hermaphrodites, whereas the remainder cause partial feminization. All 22 transform XX animals into fertile females. Limited intragenic mapping indicates that the gene is large and that gf alleles map to a location different from lf alleles. The results suggest that the tra-1 gene has several roles in wild-type sexual development. First, tra-1 activity dictates female, as opposed to male, development in all nongonadal tissues of XX animals. Second, tra-1 activity dictates female development in the somatic gonad of XX animals. Third, a high level of tra-1 activity may act to inhibit spermatogenesis in the XX germ line, thereby assisting the switch from spermatogenesis to oogenesis in the hermaphrodite. These three functions are all feminizing and specific to the XX animal; the gene also has minor functions in the XO animal, which are to assist normal male somatic gonad development and to promote abundant spermatogenesis in males. A low level of both spermatogenesis and oogenesis can occur in the absence of tra-1 activity. Both the function and the regulation of ------------------- Key: 1000 Medline: 88097727 Authors: Keller CI;Calkins J;Hartman PS;Rupert CS Title: UV photobiology of the nematode C. elegans: action spectra, absense of photoreactivation and effects of caffeine. Citation: Photochemistry and Photobiology 46: 483-488 1987 Type: ARTICLE Genes: rad-3 Abstract: Action spectra for UV inactivation of reproduction in Caenorhabditis elegans have been obtained for strains N2 (wild-type) and rad-3 (radiation-sensitive). Use of a dye laser radiation source, providing high intensity in a narrow wavelength band, has permitted more detail (14 wavelenghts between 260 and 320 nm) than available in the spectra for other multicellular organisms. Overall sensitivity of N2 is similar to that of wild-type Escherichia coli; that of rad-3 is 30-fold higher between 265 and 310 nm; relative sensitivity decreases above 310 nm but also seems to increase for irradiation below 265 nm. Tests for photoreactivation and for modification of survival by post-irradiation treatment with caffeine were ------------------- Key: 1001 Medline: 88027014 Authors: Lye RJ;Porter ME;Scholey JM;McIntosh JR Title: Identification of a microtubule-based cytoplasmic motor in the nematode C. elegans. Citation: Cell 51: 309-318 1987 Type: ARTICLE Genes: Abstract: C. elegans contains a microtubule binding protein that resembles both dynein and kinesin. This protein has a MgATPase activity and copurifies on both sucrose gradients and DEAE Sephadex columns with a polypeptide of Mr approximately 400 kd. The ATPase activity is 50% inhibited by 10 microM vanadate, 1 mM N-ethyl maleimide, or 5 mM AMP- PNP; it is enhanced 50% by 0.2% Triton. The 400 kd polypeptide is cleaved at a single site by ultraviolet light in the presence of ATP and vanadate. In these ways, the protein resembles dynein. The protein also promotes ATP-dependent translocation of microtubules or axonemes, "plus" ends trailing. This property is kinesin-like; however, the motility is blocked by 5 microM vanadate, 1 mM N-ethyl maleimide, 0.5 mM ATP-gamma-S, or by ATP-vanadate-UV cleavage of the 400 kd polypeptide, characteristics that differ from kinesin. We propose that this protein is a novel microtubule translocator. ------------------- Key: 1002 Medline: 88084361 Authors: Politz SM;Chin KJ;Herman DL Title: Genetic analysis of adult-specific surface antigenic differences between varieties of the nematode C. elegans. Citation: Genetics 117: 467-476 1987 Type: ARTICLE Genes: lin-4 srf-1 Abstract: We have studied developmental stage-specificity and genetic specification of surface antigens in the nematode Caenorhabditis elegans. Rabbit antisera directed against the adult C. elegans cuticle were used in conjunction with antiserum adsorption experiments to obtain antibody reagents with specificity for the adult surface. Adult-specific antibodies were used to identify several varietal strains of C. elegans that display antigen-negative phenotypes as adults. Genetic mapping results using the surface antigen phenotype as a marker indicated that a single gene (designated srf-1) or cluster of genes on linkage group II determines the adult surface ------------------- Key: 1003 Medline: 88041151 Authors: Donahue LM;Quarantillo BA;Wood WB Title: Molecular analysis of X-chromosome dosage compensation in C. elegans. Citation: Proceedings of the National Academy of Sciences USA 84: 7600-7604 1987 Type: ARTICLE Genes: act-4 dpy-21 dpy-22 myo-2 mnDp10 Abstract: We used a convenient quantitative dot blot assay to measure transcript levels for two X chromosome-linked genes, myo-2 and act-4, in the nematode Caenorhabditis elegans. We show that there is dosage compensation of transcript levels for these two genes between XX hermaphrodites and X0 males and that a mutation in the dpy-21 gene, postulated from genetic analysis to be involved in control of X chromosome expression, can affect these transcript levels in the manner predicted. However, we observe the dpy-21 effects only at some stages of the life cycle and not at others. These results are generally consistent with earlier genetic and molecular evidence. ------------------- Key: 1004 Medline: 88061352 Authors: Hosono R;Sassa T;Kuno S Title: Mutations affecting acetylcholine levels in the nematode C. elegans. Citation: Journal of Neurochemistry 49: 1820-1823 1987 Type: ARTICLE Genes: ace-1 ace-2 cha-1 unc-17 Abstract: Gene cha-1.unc-17 of the nematode Caenorhabditis elegans is a complex gene, consisting of at least two complementation groups. One part (cha-1 region) of the gene encodes the enzyme choline acetyltransferase (ChAT), but the function of the other part (unc-17 region) is still unclear. We measured the ChAT activity and ACh levels of the cha-1 and unc-17 complex gene mutants. We show here that alterations in ACh levels, rather than the ChAT activity, reflect abnormal phenotypes accompanying cha-1.unc-17 mutations, that is, the decreased ACh levels in cha-1 mutations and abnormal accumulation in unc-17 mutations. Our results suggest that the unc-17 region may encode functions necessary for storage and/or release of ACh at the ------------------- Key: 1005 Medline: 88120504 Authors: Goldstein P;Curis M Title: Age-related changes in the meiotic chromosomes of the nematode C. elegans. Citation: Mechanisms of Ageing & Development 40: 115-130 1987 Type: ARTICLE Genes: him-5 Abstract: Comparison of pachytene karyotypes from old and young wild-type hermaphrodites and males and the mutant him-5 were made following three-dimensional reconstruction of serial ultrathin sections. Age- related changes included: (1) differential condensation of chromatin with increased variance in length of chromosomes; and (2) increased variation in nuclear and nucleolar volume along with increased density of the nucleoplasm. Synaptonemal complex (SC) fine structure was not altered in the nuclei from older specimens. Attachment of only one end of the SC to the nuclear envelope (NE), common to all nematodes, was present at all ages in the wild-type hermaphrodite and male, however, clustering of the SC ends was present in nuclei from older him-5 hermaphrodites. Condensed chromatin along the SC formed a continuous mass except in those small regions where the chromatin had a granular appearance and was decondensed. Such regions, termed "Disjunction Regulator Regions" (DRR), have been implicated in the regulation of X-chromosome segregation (Goldstein, P., The synaptonemal complexes of Caenorhabditis elegans: Pachytene karyotype analysis of the Dp 1 mutant and disjunction regulator regions. Chromosoma, 93 (1985) 177-182). In the present study, it was observed that the number of DRRs in the nucleus change with aging. In the wild- type hermaphrodite and male, the rate of X-chromosome non-disjunction increases with age which correlates with a decrease in the number of DRRs to the point where they are absent in older males. In him-5, the DRRs increase in number with advanced age, which correlates with an observed decrease in the rate of X-chromosome non-disjunction. ------------------- Key: 1006 Medline: Authors: Sassa T;Hosono R;Kuno S Title: Choline acetyltransferase from a temperature-sensitive mutant of C. elegans. Citation: Neurochemistry International 11: 323-329 1987 Type: ARTICLE Genes: cha-1 unc-17 Abstract: A temperature dependent paralytic mutant of C. elegans was isolated and mapped to be an allele of the cha-1 gene that has been shown to be the structural gene for acetyl-CoA: choline-O-acetyltransferase (EC 2.3.1.6; ChAT). In crude extracts from the mutant, ChAT activity was present when assayed at a permissive temperature but not detectable at a temperature that provoked abnormal phenotypes. The mutant ChAT was purified to a specific activity of 2.9 nmol of product min-1 per mg of protein at 10C and its enzymatic properties were studied by comparison with the wild-type enzyme. The temperature-sensitivity of the mutant ChAT was so remarkable that no activity was detected over 20C. This inactivation at higher temperature appeared to be partly reversible. The Km values of the mutant enzyme for choline and acetyl-CoA were about twice of those in the wild-type enzyme, but increased 10- to 20-fold in the presence of high salt concentrations. The mutant enzyme was also more sensitive to sulfhydryl reagents. These findings indicate that depending upon changes in the physical environment, the mutant ChAT may lose the normal-conformation leading to inactivation. ------------------- Key: 1007 Medline: 88052863 Authors: Austin J;Kimble J Title: glp-1 is required in the germ line for regulation of the decision between mitosis and meiosis in C. elegans. Citation: Cell 51: 589-599 1987 Type: ARTICLE Genes: glp-1 qDp3 mnDp37 Abstract: In the wild-type C. elegans germ line there are both mitotic and meiotic germ cells. Mutations in glp-1 cause germ cells that would normally divide mitotically to enter meiosis. This mutant phenotype mimics the effect of killing the distal tip cell, a somatic cell that interacts with the germ line to regulate the mitotic/meiotic decision. In addition, wild-type glp-1 product is required maternally for embryogenesis. Temperature-shift experiments indicate that the temporal requirement for glp-1 activity in the germ line is the same as that for distal tip cell regulation. Mosaic analyses suggest that glp-1 is produced in the germ line. We propose that glp-1 acts as part of the receiving mechanism in the interaction between the distal tip cell and germ line. ------------------- Key: 1008 Medline: 88052864 Authors: Priess JR;Schnabel H;Schnabel R Title: The glp-1 locus and cellular interactions in early C. elegans embryos. Citation: Cell 51: 601-611 1987 Type: ARTICLE Genes: glp-1 Abstract: Interactions between the early blastomeres in a C. elegans embryo are required for the specification of certain cell fates. Blastomeres that produce neurons and skin cells when cultured in isolation are induced to also produce pharyngeal cells in intact embryos. We have identified maternal effect lethal mutations that, on the basis of phenotype and temperature-sensitive period, appear to disrupt this inductive interaction. These mutations are all alleles of glp-1, a gene also involved in the control of germ cell proliferation during postembryonic development of C. elegans. ------------------- Key: 1009 Medline: Authors: Hodgkin J;Kondo K;Waterston RH Title: Suppression in the nematode C. elegans. Citation: Trends in Genetics 3: 325-329 1987 Type: REVIEW Genes: daf-1 dpy-20 her-1 lin-12 lin-29 mab-1 mab-11 myo-3 pha-1 sup-3 sup-5 sup-7 sup-10 sup-11 sup-24 sup-28 sup-29 tra-1 tra-2 tra-3 unc-13 unc-15 unc-22 unc-54 unc-93 unc-105 Abstract: Suppressor mutations (both dominant and recessive) are easily obtained in Caenorhabditis elegans, as a result of efficient selection methods and the ability to grow large populations by self-fertilization. Several different genetic phenomena are revealed by the study of suppression. A set of five amber suppressors is being used to analyse a family of tRNA genes. ------------------- Key: 1010 Medline: 88059245 Authors: Hyman AA;White JG Title: Determination of cell division axes in the early embryogenesis of C. elegans. Citation: Journal of Cell Biology 105: 2123-2135 1987 Type: ARTICLE Genes: par-1 Abstract: The establishment of cell division axes was examined in the early embryonic divisions of Caenorhabditis elegans. It has been shown previously that there are two different patterns of cleavage during early embryogenesis. In one set of cells, which undergo predominantly determinative divisions, the division axes are established successively in the same orientation, while division axes in the other set, which divide mainly proliferatively, have an orthogonal pattern of division. We have investigated the establishment of these axes by following the movement of the centrosomes. Centrosome separation follows a reproducible pattern in all cells, and this pattern by itself results in an orthogonal pattern of cleavage. In those cells that divide on the same axis, there is an additional directed rotation of pairs of centrosomes together with the nucleus through well-defined angles. Intact microtubules are required for rotation; rotation is prevented by inhibitors of polymerization and depolymerization of microtubules. We have examined the distribution of microtubules in fixed embryos during rotation. From these and other data we infer that microtubules running from the centrosome to the cortex have a central role in aligning the centrosome-nuclear complex. ------------------- Key: 1011 Medline: 88112750 Authors: DeLong L;Casson LP;Meyer BJ Title: Assessment of X-chromosome dosage compensation in C. elegans by phenotypic analysis of lin-14. Citation: Genetics 117: 657-670 1987 Type: ARTICLE Genes: dpy-21 dpy-22 dpy-26 dpy-27 dpy-28 lin-14 yDp1 nDf19 Abstract: Caenorhabditis elegans compensates for the difference in X chromosome gene dose between males (XO) and hermaphrodites (XX) through a mechanism that equalizes the levels of X-specific mRNA transcripts between the two sexes. We have devised a sensitive and quantitative genetic assay to measure perturbations in X chromosome gene expression caused by mutations that affect this process of dosage compensation. The assay is based on quantitating the precocious alae phenotype caused by a mutation that reduces but does not eliminate the function of the X-linked gene lin-14. We demonstrate that in diploid animals the lin-14 gene is dosage compensated, implying that the normal dosage compensation mechanism in C. elegans lacks the capacity to compensate completely for the additional X chromosome in triplo-X animals. Using the lin-14 assay we compare the effects of mutations in the genes dpy-21, dpy-26, dpy-27, dpy-28, and dpy-22 on X-linked gene expression. Additionally, in the case of dpy-21 we correlate the change in phenotypic expression of lin-14 with a corresponding change in the lin-14 mRNA transcript level. ------------------- Key: 1012 Medline: 88096497 Authors: Plasterk RH Title: Differences between Tc1 elements from the C. elegans strain Bergerac. Citation: Nucleic Acids Research 15: 10050-10050 1987 Type: ARTICLE Genes: unc-22 Abstract: The Tc1 transposable element of C. elegans is 1610 bp long and contains one major ORF, encoding a 273 amino acid protein. All C. elegans strains contain copies of Tc1, though not all strains are active in transposition (e.g. the strain Bristol is inactive). The Bergerac strain shows active transposition of Tc1, and contains approximately 300 copies of Tc1 that seem to have (almost) all the same restriction pattern. ------------------- Key: 1013 Medline: 88162184 Authors: Hodgkin J Title: Sex determination and dosage compensation in C. elegans. Citation: Annual Review of Genetics 21: 133-154 1987 Type: REVIEW Genes: dpy-21 dpy-22 dpy-23 dpy-26 dpy-27 dpy-28 egl-41 egl-48 fem-1 fem-2 fem-3 fog-1 fog-2 her-1 lin-12 lin-28 mab-1 mab-3 mab-5 mab-11 sdc-1 sup-7 sup-21 sup-28 sup-30 sup-31 tra-1 tra-2 tra-3 uxt-2 ctDp1 mDf1 mnDp8 mnDp9 mnDp10 mnDp32 mnDp33 nDf19 stDf5 stDp2 Abstract: This review focuses on sex determination as a problem in developmental biology: on the nature of the primary sex-determining signal; how this signal leads to the very different developmental events that occur in the two sexes; and how the different sexually dimorphic processes are controlled and integrated with other developmental processes. Caenorhabditis elegans is a suitable organism for such studies because its sexual dimorphism is extensive and has been described in minute detail; also, a great deal is known about its genetics. C. elegans presents a problem in evolutionary biology, which is how (and why) this species has developed male and hermaphrodite sexes, but no female sex. There is reason to believe that the hermaphrodite is really a modified female (i.e. a female with the capacity to make a limited number of sperm), and the modification may have been a recent specialization. Understanding the basis of this specialization should be illuminating from both evolutionary and developmental perspectives. More generally, it is likely that developmental processes cannot be understood without some reference to the underlying evolutionary history, and conversely the course of evolution may often have been governed by developmental constraints. Sexuality is an almost universal biological phenomenon, and therefore is particularly appropriate for studying the interplay of evolution and development. Organisms with chromosomal sex-determination mechanisms usually exhibit an additional specialization, which is a compensation mechanism to equalize the expression of most sex-linked genes between the two sexes. C. elegans is no exception, exhibiting a mechanism of the Drosophila type (differential expression) rather than the mammalian type (chromosome inactivation). Since primary sex determination in C. elegans depends on a gene dosage mechansism, the two processes of dosage compensation and sex determination are likely to be interrelated. Both sex determination and dosage compensation have been intensively studied in two other animal systems, Drosophila and the mouse. Nematodes and mammals have little in common, but there are interesting paralles between nematodes and flies, which are organsims as remote from each other in phylogenetic terms as either is from mice. Apparent similarities between C. elegans and ------------------- Key: 1014 Medline: 88087411 Authors: Ardizzi JP;Epstein HF Title: Immunochemical localization of myosin heavy chain isoforms and paramyosin in developmentally and structurally diverse muscle cell types of C. elegans/ Citation: Journal of Cell Biology 105: 2763-2770 1987 Type: ARTICLE Genes: myo-1 myo-2 myo-3 unc-15 unc-54 Abstract: The nematode Caenorhabditis elegans contains two major groups of muscle cells that exhibit organized sarcomeres: the body wall and pharyngeal muscles. Several additional groups of muscle cells of more limited mass and spatial distribution include the vulval muscles of hermaphrodites, the male sex muscles, the anal-intestinal muscles, and the gonadal sheath of the hermaphrodite. These muscle groups do not exhibit sarcomeres and therefore may be considered smooth. Each muscle cell has been shown to have a specific origin in embryonic cell lineages and differentiation, either embryonically or postembryonically (Sulston, J. E., and H. R. Horvitz. 1977. Dev. Biol. 56:110-156; Sulston, J. E., E. Schierenberg, J. White, and J. N. Thomson. 1983. Dev. Biol. 100:64-119). Each muscle type exhibits a unique combination of lineage and onset of differentiation at the cellular level. Biochemically characterized monoclonal antibodies to myosin heavy chains A, B, C, and D and to paramyosin have been used in immunochemical localization experiments. Paramyosin is detected by immunofluorescence in all muscle cells. Myosin heavy chains C and D are limited to the pharyngeal muscle cells, whereas myosin heavy chains A and B are localized not only within the sarcomeres of body wall muscle cells, as reported previously, but to the smooth muscle cells of the minor groups as well. Myosin heavy chains A and B and paramyosin proteins appear to be compatible with functionally and structurally distinct muscle cell types that arise by multiple developmental pathways. ------------------- Key: 1015 Medline: 88080474 Authors: Emmons SW Title: Mechanisms of C. elegans development. Citation: Cell 51: 881-883 1987 Type: REVIEW Genes: glp-1 lin-22 mab-5 Abstract: What are the respective roles in multicellular development of mechansims acting at the level of the cell and mechanisms acting at the level of the cell group? It's an old question, and one that is central to the problem of developmental biology. Even early in this century it had long been debated "whether the character of growth and morphogenesis is a cause or a result of the corresponding activities on the part of the component cells individually considered" (E.B. Wilson, The Cell in Development and Heredity, Macmillan, 1925, p. 1029). The question is now being reexamined in the nematode Caenorhabditis elegans, an organism whose embryonic and postembryonic development are easily observed. Initial studies emphasized the reproducibility and, thus, the apparent cell-autonomy of development in the animal. Little flexibility in cell division patterns or differentiation was found in blastomere isolation experiments or after microsurgery with a laser beam. More recent results, however, demonstrate that cellular interactions are more important. These new results, combined with new molecular techniques that make it possible to isolate genes defined by mutations and to reintroduce cloned genes into the germ line, open the way to a molecular analysis of developmental mechanisms that are likely to be widespread in the animal kingdom. ------------------- Key: 1016 Medline: 88080465 Authors: Avery L;Horvitz HR Title: A cell that dies during wild-type C. elegans development can function as a neuron in a ced-3 mutant. Citation: Cell 51: 1071-1078 1987 Type: ARTICLE Genes: ced-3 Abstract: Mutations in the C. elegans gene ced-3 prevent almost all programmed cell deaths, so that in a ced-3 mutant there are many extra cells. We show that the pharyngeal neuron M4 is essential for feeding in wild- type worms, but in a ced-3 mutant, one of the extra cells, probably MSpaaaaap (the sister of M4), can sometimes take over M4's function. The function of MSpaaaaap, unlike that of M4, is variable and subnormal. One possible explanation is that its fate, being hidden by death and not subject to selection, has drifted randomly during evolution. We suggest that such cells may play roles in the evolution of cell lineage analogous to those played by pseudogenes in the evolution of genomes. ------------------- Key: 1017 Medline: 88055882 Authors: Hill DP;Strome S Title: An analysis of the role of microfilaments in the establishment and maintenance of asymmetry in C. elegans zygotes. Citation: Developmental Biology 125: 75-84 1988 Type: ARTICLE Genes: Abstract: Microfilaments are needed to generate asymmetry during the first cell cycle in Caenorhabditis elegans zygotes. To investigate when and how microfilaments participate in this process, we have "pulsed" zygotes with the microfilament inhibitor cytochalasin D (CD) at different times during the cell cycle. We have shown that microfilaments are only required during a narrow time interval approximately three- quarters of the way through the first cell cycle for the manifestations of asymmetry that occur during and subsequent to this interval. When CD treatment spans this critical time interval, pseudocleavage, pronuclear migration, germ-granule segregation (all of which occur during the interval), and movement of the mitotic spindle to an asymmetric position (which occurs later in the cell cycle) are perturbed. In contrast, embryos briefly treated with CD before or after the critical time interval manifest normal asymmetry. Our results suggest that in C. elegans microfilaments participate in the generation of zygotic asymmetry by providing spatial cues and/or serving as a part of the necessary machinery only during a brief period in the first cell cycle, and are not required to maintain asymmetries that have already been established. ------------------- Key: 1018 Medline: 96209411 Authors: McKim KS;Heschl MFP;Rosenbluth RE;Baillie DL Title: Genetic organization of the unc-60 region in Caenorhabditis elegans. Citation: Genetics 118: 49-59 1988 Type: ARTICLE Genes: egl-2 emb-29 ges-1 let-326 let-336 let-337 let-343 let-405 let-407 let-408 let-409 let-410 let-423 let-426 rol-3 sup-12 unc-34 unc-60 eT1 mDf1 mDf3 nDf18 nDf31 sDf32 sDf33 sDf34 sDf35 Abstract: We have investigated the chromosomal region around unc-60 V, a gene affecting muscle structure, in the nematode Caenorhabditis elegans. The region studied covers 3 map units and lies at the left end of linkage group (LG) V. Compared to the region around dpy-11 (at the center of LGV), the unc-60 region has relatively few visible genes per map unit. We found the same to be true for essential genes. By screening simultaneously for recessive lethals closely linked to either dpy-11 or unc-60, we recovered ethyl methanesulfonate-induced mutations in 10 essential genes near dpy-11 but in only two genes near unc-60. Four deficiency breakpoints were mapped to the unc-60 region. Using recombination and deficiency mapping we established the following gene order: let-336, unc-34, let-326, unc-60, emb-29, let-426. Regarding unc-60 itself, we compared the effect of ten alleles (including five isolated during this study) on hermaphrodite mobility and fecundity. We used intragenic mapping to position eight of these alleles. The results show that these alleles are not distributed uniformly within the gene, but map to two groups approximately 0.012 map unit apart. ------------------- Key: 1019 Medline: 96209412 Authors: Rogalski TM;Riddle DL Title: A C. elegans RNA polymerase II gene, ama-1 IV, and nearby essential genes. Citation: Genetics 118: 61-74 1988 Type: ARTICLE Genes: ama-1 dpy-13 let-273 let-274 let-275 let-276 let-277 let-278 let-279 let-280 let-281 let-282 let-284 let-285 let-286 let-287 let-288 mDf4 mDf5 mDf6 mDf7 mDf8 mDf9 mDp1 Abstract: The amanitin-binding subunit of RNA polymerase II in Caenorhabditis elegans is encoded by the ama-1 gene, located approximately 0.05 map unit to the right of dpy-13. Using the amanitin-resistant ama-1(m118) strain as a parent, we have isolated amanitin-sensitive mutants that carry recessive-lethal ama-1 alleles. Of the six ethyl methanesulfonate-induced mutants examined, two are arrested late in embryogenesis. One of these is a large deficiency, mDf9, but the second may be a novel point mutation. The four other mutants are hypomorphs, and presumbably produce altered RNA polymerase II enzymes with some residual function. Two of these mutants develop into sterile adults at 20C but are arrested as larvae at 25C, and two others are fertile at 20C and sterile at 25C. Temperature-shift experiments performed with the adult sterile mutant, ama-1(m118m238ts), have revealed a temperature-sensitive period that begins late in gonadogenesis and is centered around the initiation of egg-laying. Postembryonic development at 25C is slowed by 30%. By contrast, the amanitin-resistant allele of ama-1 has very little effect on developmental rate or fertility. We have identified 15 essential genes in an interval of 4.5 map units surrounding ama-1, as well as four Y-ray-induced deficiencies and two duplications that include the ama-1 gene. The larger duplication, mDp1, may include the entire left arm of chromosome IV, and it recombines with the normal homologue at a low frequency. The smallest deficiency, mDf10, complements all but three identified genes: let-278, dpy-13 and ama-1, which define an interval of only 0.1 map unit. The terminal phenotype of mDf10 homozygotes is developmental arrest during the first larval stage, suggesting that there is sufficient maternal RNA polymerase II to complete embryonic development. ------------------- Key: 1020 Medline: 96209413 Authors: Friedman DB;Johnson TE Title: A mutation in the age-1 gene in C. elegans lengthens life and reduces hermaphrodite fertility. Citation: Genetics 118: 75-86 1988 Type: ARTICLE Genes: age-1 fer-15 unc-31 Abstract: age-1(hx546) is a recessive mutant allele in Caenorhabditis elegans that results in an increase in mean life span averaging 40% and in maximal life span averaging 60% at 20C; at 25C age-1(hx546) averages a 65% increase in mean life span (25.3 days vs. 15.0 days) and a 110% increase in maximum life span (46.2 days vs. 22.0 days for wild-type hermaphrodites). Mutant males also show extended life spans. age-1(hx546) is associated with a 75% decrease in hermaphrodite self-fertility as compared to the age-1+ allele at 20C. Using two novel strategies for following the segregation of age-1, we present evidence that longer life results from a mutation in a single gene that increases the probability of survival at all chronological ages. The long-life and reduced-fertility phenotypes cosegregate and are tightly linked to fer-15, a locus on linkage group II. age-1(hx546) does not affect the timing of larval molts, the length of embryogenesis, food uptake, movement, or behavior in any way tested. Although age-1(hx546) lowers hermaphrodite self-fertility, it does not markedly affect the length of the reproductive period with all the increase in life expenctancy due to an increase in the length of postreproductive life. In so far as we are aware, this mutant in age-1 is the only instance of a well-characterized genetic locus in which the mutant form results in lengthened life. It is likely that the action of age-1 in lengthening life results not from eliminating a programmed aging function but rather from reduced hermaphrodite self-fertility or from some other unknown metabolic or physiologic alteration. ------------------- Key: 1021 Medline: 88094724 Authors: Sheetz MP Title: Muscle-bound bacteria and weak worms. Citation: Nature 331: 212-212 1988 Type: REVIEW Genes: unc-54 Abstract: For myosin to function properly in muscle, its bipolar filaments must be assembled in ordered arrays. A major problem facing cell biologists is the control of local assembly of the filaments. Within non-muscle cells, the filaments are continually assembling and disassembling according to local signals. In muscle cells, however, myosin must be turning over continuously within a permanent array and, therefore, the cells must be replacing myosin subunits or whole filaments in an organized fashion. Two different approaches have now been applied to find out how this is achieved. The first is a classical genetic approach in which mutants of the nematode worm Caenorhabditis elegans with incorrect myosin assembly are isolated; and the second is by inducing expression of portions of the myosin molecule in bacteria. The differences in the information about myosin filament assembly provided by these two methods offer a nice contrast between genetic and molecular-biology approaches to a cell biology problem. Analysis of mutants reveals behaviours requiring molecular explanations, whereas the expression of pieces of the molecule gives information ------------------- Key: 1022 Medline: 88178853 Authors: Salt TA;Lozano R;Lusby WR;Chitwood DJ;Thompson MJ Title: 24-methyl-23-dehydrocholesterol: A new sterol intermediate in C-24 demethylation from the nematodes Panagrellus redivivus and C. elegans? Citation: Steroids 48: 451-460 1986 Type: ARTICLE Genes: Abstract: Panagrellus redivivus produced 24-methyl-23-dehydrocholesterol as 4.0% of the 4-desmethylsterols when propagated in a medium containing campesterol as the dietary sterol. The re-examination of previous data revealed that Caenorhabditis elegans produced 1.8% 24-methyl-23-dehydrocholesterol when propagated in medium containing campesterol. 24-Methyl-23-dehydrocholesterol was not detected when the nematodes were propagated in medium containing 22-dihydrobrassicasterol or 24-methylenecholesterol. This may be a result of the greater efficiency of dealkylation of the latter two sterols. This is the first report of the natural occurrence of this sterol in a non-photosynthetic organism, and the first report in organisms that dealkylate 24-alkylsterols. ------------------- Key: 1023 Medline: 88172451 Authors: Ward S;Burke DJ;Sulston JE;Coulson AR;Albertson DG;Ammons D;Klass M;Hogan E Title: Genomic organization of major sperm protein genes and pseudogenes in the nematode C. elegans. Citation: Journal of Molecular Biology 199: 1-13 1988 Type: ARTICLE Genes: msp-3 msp-10 msp-19 msp-29 msp-31 msp-32 msp-33 msp-36 msp-38 msp-40 msp-41 msp-45 msp-46 msp-47 msp-49 msp-50 msp-51 msp-52 msp-53 msp-54 msp-56 msp-60 msp-71 msp-74 msp-76 msp-77 msp-78 msp-81 msp-113 msp-142 msp-152 Abstract: The major sperm proteins (MSPs) are a family of closely related, small, basic proteins comprising 15% of the protein in Caenorhabditis elegans sperm. They are encoded by a multigene family of more than 50 genes, including many pseudogenes. MSP gene transcription occurs only in late primary spermatocytes. In order to study the genomic organization of transcribed MSP genes, probes specific for the 3' untranslated regions of sequenced cDNA clones were used to isolate transcribed genes from genomic libraries. These and other clones of MSP genes were located in overlapping cosmid clones by DNA fingerprinting. These cosmids were aligned with the genetic map by overlap with known genes or in-situ hybridization to chromosomes. Of 40 MSP genes identified, 37, including all those known to be transcribed, are organized into six clusters composed of 3 to 13 genes each. Within each cluster, MSP genes are not in tandem but are separated by at least several thousand bases of DNA. Pseudogenes are interspersed among functional genes. Genes with similar 3' untranslated sequences are in the same cluster. The six MSP clusters are confined to only three chromosomal loci; one on the left arm of chromosome II and two near the middle of chromosome IV. Additional sperm-specific genes are located in one cluster of MSP genes on chromosome IV. The multiplicity of MSP genes appears to be a mechanism for enhancing MSP synthesis in spermatocytes, and the loose clustering of genes could be a result of the mechanism of gene duplication or could play a role in regulation. ------------------- Key: 1024 Medline: 88172456 Authors: Klass M;Ammons D;Ward S Title: Conservation in the 5' flanking sequences of transcribed members of the C. elegans major sperm protein gene family. Citation: Journal of Molecular Biology 199: 15-22 1988 Type: ARTICLE Genes: msp-10 msp-19 msp-29 msp-38 msp-56 msp-71 msp-74 msp-113 msp-142 msp-152 Abstract: The major sperm proteins (MSPs) are encoded in the Caenorhabditis genome by a multigene family with more than 50 genes dispersed in small clusters at three chromosomal loci. In spite of their dispersed locations, all of the MSP genes appear to be expressed at the same time exclusively in the testis, indicating co-ordinate temporal and spatial regulation of these dispersed genes. Many of the MSP genes must be transcribed, because RNA hybridization with gene-specific probes showed that individual genes each contribute less than 3% to the total poly(A)+ RNA, and 13 out of 14 sequenced cDNAs came from different genes. Primer extension assays from MSP mRNA showed that most of the MSP mRNAs must be initiated at position -35 from the translation start codon. Extensive similarity was found in the first 100 nucleotides of genomic sequence flanking the start codons of ten MSP genes from different chromosomal locations. All MSP genes contained a consensus ribosome binding site, a consensus TATA homology 27 nucleotides distal to the site of mRNA initiation, and ten highly conserved nucleotides adjacent to the site of initiation. All the MSP genes contained the sequence AGATCT located approximately 65 nucleotides upstream from the transcriptional start, but little or no similarity was found more distal to this. Some of these conserved sequences may be cis-acting control elements that ensure the cell and temporal specificity of transcription of these ------------------- Key: 1025 Medline: 88127123 Authors: Walthall WW;Chalfie M Title: Cell-cell interactions in the guidance of late-developing neurons in C. elegans. Citation: Science 239: 643-645 1988 Type: ARTICLE Genes: mab-5 unc-86 Abstract: The initial outgrowth of developing neuronal processes can be affected by a number of extrinsic interactions. Cell-cell interactions are also important in a later stage of neuronal outgrowth when processes grow into the region of their targets. The correct positioning of the process of a postembryonic sensory neuron, the touch cell AVM of the nematode Caenorhabditis elegans, at its synaptic targets requires the presence of a pair of embryonic interneurons, the BDU cells. These cells receive synapses from AVM but do not participate in the touch reflex circuit. Therefore, the AVM-BDU synapses may be required to stabilize the association between these cells and assist in the guidance of the AVM processes through a mature ------------------- Key: 1026 Medline: 88124940 Authors: Mori I;Benian GM;Moerman DG;Waterston RH Title: Transposable element Tc1 of C. elegans recognizes specific target sequences for integration. Citation: Proceedings of the National Academy of Sciences USA 85: 861-864 1988 Type: ARTICLE Genes: lin-12 unc-15 unc-22 unc-54 Abstract: The frequency of movement of Tc1, a 1.6-kilobase transposable element in the nematode Caenorhabditis elegans, is under genetic control, and Tc1 insertion sites are widely but nonrandomly distributed. The usually high frequency of insertions at multiple sites in the gene unc-22 suggested that this gene might be particularly rich in preferred target sites. To discover the features of Tc1 target sites, we have sequenced the sites of seven independent Tc1 transpositions into unc-22 and three other sites. Our comparison of these and two other sites from the literature indicates that in all cases Tc1 integrates at the dinucleotide T-A when it is flanked both 5' and 3' by particular preferred nucleotides. Our analysis revealed the following consensus target for Tc1 integration: G-A-K-A-T-A-T-G-T, in which K = G or T. This target site sequence specificity has implications both for the mechanism of Tc1 transposition and the use of Tc1 in cloning genes by transposon-tagging. ------------------- Key: 1027 Medline: 88174715 Authors: Eide D;Anderson P Title: Insertion and excision of C. elegans transposable element Tc1. Citation: Molecular and Cellular Biology 8: 737-746 1988 Type: ARTICLE Genes: lin-27 unc-22 unc-54 unc-105 Abstract: The transposable element Tc1 is responsible for most spontaneous mutations that occur in Caenorhabditis elegans variety Bergerac. We investigated the genetic and molecular properties of Tc1 transposition and excision. We show that Tc1 insertion into the unc- 54 myosin heavy-chain gene was strongly site specific. The DNA sequences of independent Tc1 insertion sites were similar to each other, and we present a consensus sequence for Tc1 insertion that describes these similarities. We show that Tc1 excision was usually imprecise. Tc1 excision was imprecise in both germ line and somatic cells. Imprecise excision generated novel unc-54 alleles that had amino acid substitutions, amino acid insertions, and, in certain cases, probably altered mRNA splicing. The DNA sequences remaining after Tc1 somatic excision were the same as those remaining after germ line excision, but the frequency of somatic excision was at least 1,000-fold higher than that of germ line excision. The genetic properties of Tc1 excision, combined with the DNA sequences of the resulting unc-54 alleles, demonstrated that excision was dependent on Tc1 transposition functions in both germ line and somatic cells. Somatic excision was not regulated in the same strain-specific manner as germ-line excision was. In a genetic background where Tc1 transposition and excision in the germ line was not detectable, Tc1 excision in the soma still occurred at high frequency. ------------------- Key: 1028 Medline: 89030329 Authors: Hodgkin J Title: Primary sex determination in the nematode C. elegans. Citation: Development 101s: 5-16 1987 Type: REVIEW Genes: dpy-21 dpy-22 dpy-23 dpy-26 dpy-27 dpy-28 egl-16 fem-1 fem-2 fem-3 fog-2 her-1 him-5 him-8 mab-3 sdc-1 tra-1 tra-2 tra-3 unc-1 unc-7 ctDp1 mDf1 mnDf1 mnDp8 mnDp9 mnDp10 mnDp32 mnDp33 mnT12 nDf19 stDf5 stDp2 Abstract: Most nematodes have XO male/XX female sex determination. C. elegans is anomalous, having XX hermaphrodites rather than females. The hermaphrodite condition appears to result from the modification of a basic male/female sex-determination system, which permits both spermatogenesis and oogenesis to occur within a female soma. This modification is achieved by a germ-line-specific control acting at one step in a cascade of autosomal regulatory genes, which respond to X-chromosome dosage and direct male, female, or hermaphrodite development. Mutations of one of these genes can be used to construct artificial strains with ZZ male/WZ female sex determination. Primary sex determination normally depends on the ratio of X chromosomes to autosomes, as in Drosophila, and there appear to be multiple sites on the X chromosome that contribute to this ratio. Also, as in Drosophila, X-chromosome expression is compensated to equalize gene activity in XX and XO animals. Interactions between dosage compensation and sex determination are described and discussed. ------------------- Key: 1029 Medline: 88122669 Authors: Kiff JE;Moerman DG;Schriefer LA;Waterston RH Title: Transposon-induced deletions in unc-22 of C. elegans associated with almost normal gene activity. Citation: Nature 331: 631-633 1988 Type: ARTICLE Genes: unc-22 Abstract: The unc-22 gene of Caenorhabolitis elegans encodes a protein which is a component of the myosin-containing A-band of the worm's striated body-wall muscle. Among 51 revertants of a transposon-induced mutant, we have identified four which retain a barely detectable mutant phenotype. Molecular analysis shows that three of these have in-frame deletions of 1.0, 1.3 and 2.0 kilobases, whereas the fourth partial revertant and two other apparently complete revertants have small insertions. All these rearrangements involve coding sequence and, in the case of the deletions, result in polypeptides that are shorter than the wild-type protein. The region of the gene containing these rearrangements contains 10 copies of a motif recognized in other regions of the gene (our unpublished data). We suggest that one explanation for the minimally mutant phenotype associated with the deletions is that the size and the repeated nature of the unc-22 protein structure make it relatively tolerant of substitutions or deletions involving one or a small number of repeated motifs. These results could explain why in some human genetic diseases, such as Duchenne's muscular dystrophy, deletions can be associated with only mild forms of the ------------------- Key: 1030 Medline: 88132926 Authors: Sarkis GJ;Kurpiewski MR;Ashcom JD;Jen-Jacobson L;Jacobson Title: Proteases of the nematode C. elegans. Citation: Archives of Biochemistry & Biophysics 261: 80-90 1988 Type: ARTICLE Genes: Abstract: Crude homogenates of the soil nematode Caenorhabditis elegans exhibit strong proteolytic activity at acid pH. Several kinds of enzyme account for much of this activity: cathepsin D, a carboxyl protease which is inhibited by pepstatin and optimally active toward hemoglobin at pH 3; at least two isoelectrically distinct thiol proteases (cathepsins Ce1 and Ce2) which are inhibited by leupeptin and optimally active toward Z-Phe-Arg-7-amino-4-methylcoumarin amide at pH 5; and a thiol-independent leupeptin-insensitive protease (cathepsin Ce3) with optimal activity toward casein at pH 5.5. Cathepsin D is quantitatively most significant for digestion of macromolecular substrates in vitro, since proteolysis is inhibited greater than 95% by pepstatin. Cathepsin D and the leupeptin- sensitive proteases act synergistically, but the relative contribution of the leupeptin-sensitive proteases depends upon the protein ------------------- Key: 1031 Medline: 88185826 Authors: Moerman DG;Benian GM;Barstead RJ;Schriefer LA;Waterston RH Title: Identification and intracellular localization of the unc-22 gene product of C. elegans. Citation: Genes & Development 2: 93-105 1988 Type: ARTICLE Genes: unc-22 Abstract: The unc-22 gene is one of a set of genes identified using classical genetics that affect muscle structure and function in the free-living nematode Caenorhabditis elegans. Since cloning the unc-22 gene by transposon tagging, we have used conventional techniques combined with a set of Tc1 transposon insertion alleles to characterize the gene and its products. The gene extends over more than 20 kb of genomic sequence and produces a transcript of approximately 14 kb. A polyclonal antibody raised against an Escherichia coli beta- galactosidase-unc-22 fusion protein recognizes a polypeptide in nematode extracts that is between 500,000 and 600,000 daltons and labels the muscle A-band in indirect immunofluorescent microscopy. The Tc1-induced alleles have been used at every stage to verify these conclusions. The Tc1 insertions are spread over much of the region that contributes to the mature transcript; in most alleles, Tc1 sequences are incorporated into a composite unc-22-Tc1 transcript. The large protein is either absent or severely reduced in amounts in the mutants. In one case, a truncated polypeptide was also identified. The location of the protein in the A-band, along with earlier genetic data, suggests that the unc-22 product may interact with myosin to regulate its function. ------------------- Key: 1032 Medline: 88151036 Authors: Kemphues KJ;Priess JR;Morton DG;Cheng N Title: Identification of genes required for cytoplasmic localization in early C. elegans embryos. Citation: Cell 52: 311-320 1988 Type: ARTICLE Genes: par-1 par-2 par-3 par-4 Abstract: We have isolated and analyzed eight strict maternal effect mutations identifying four genes, par-1, par-2, par-3, and par-4, required for cytoplasmic localization in early embryos of the nematode C. elegans. Mutations in these genes lead to defects in cleavage patterns, timing of cleavages, and localization of germ line-specific P granules. Four mutations in par-1 and par-4 are fully expressed maternal effect lethal mutations; all embryos from mothers homozygous for these mutations arrest as amorphous masses of differentiated cells but are specifically lacking intestinal cells. Four mutations in par-2, par- 3, and par-4 are incompletely expressed maternal effect lethal mutations and are also grandchildless; some embryos from homozygous mothers survive and grow to become infertile adults due to absence of functional germ cells. We propose that all of these defects result from the failure of a maternally encoded system for intracellular localization in early embryos. ------------------- Key: 1034 Medline: Authors: Sudhaus W Title: Vergleichende untersuchengen zur phylogenie, systematik, okologie, biologie und ethologie der Rhabditidae Citation: Zoologica Stuttgart 125: 1-229 1976 Type: BOOK Genes: Abstract: ------------------- Key: 1035 Medline: 88167394 Authors: Albert PS;Riddle DL Title: Mutants of Caenorhabditis elegans that form dauer-like larvae. Citation: Developmental Biology 126: 270-293 1988 Type: ARTICLE Genes: daf-9 daf-15 Abstract: The development, ultrastructure, and genetics of two mutants that form dauer-like larvae have been characterized. Dauer larva morphogenesis is initiated regardless of environmental stimuli, and it is incomplete or abnormal. The resistance to detergent characteristic of normal dauer larvae is not fully achieved, and the mutants are unable to exit from the dauer-like state of developmental arrest. Mutant life span is not extended beyond the three weeks characteristic of the nondauer life cycle, whereas normal dauer larvae can live for several months. Growth of daf-15(m81)IV, the less dauer-like of the two, is nearly arrested at the second (dauer- specific) molt, but feeding is not completely suppressed. Head shape, cuticle, and intestinal ultrastructure are nondauer, whereas sensory structures (amphid and deirid) and excretory gland morphology are intermediate between that of dauer and nondauer stages. The daf- 9(e1406)X mutant is dauer-like in head shape, cuticle, and deirid ultrastructure, intermediate in amphid and inner labial neuron morphology, and nondauer or abnormal in the intestine. Also, the daf- 9 mutant exhibits abnormalities in the pharyngeal arcade cell processes and pharyngeal g1 gland. Double mutants carrying both daf-9 and daf-15 are more resistant to detergent than either single mutant. Like the single mutants, they cannot complete morphogenesis, and they are unable to exit from the dauer-like stage. Both daf-9 and daf-15 mutations are epistatic to previously described dauer-defective mutations, indicating that these two genes act late in the pathway leading to the dauer larva. The genetic tests and the mutant ultrastructure suggest that the two genes may affect parallel pathways of ------------------- Key: 1036 Medline: 88231813 Authors: Harrington LA;Harley CB Title: Effect of vitamin E on lifespan and reproduction in Caenorhabditis elegans. Citation: Mechanisms of Ageing & Development 43: 71-78 1988 Type: ARTICLE Genes: Abstract: Vitamin E extends the lifespan of many animals, including the nematode Caenorhabditis elegans. Our results confirm previous studies that 200 micrograms/ml vitamin E significantly prolonged C. elegans survival (17-23%, P less than 0.05) when added from hatching to day 3, while continuous exposure, either at hatching or from 4 days prior to hatching, had little additional effect. Treatment with 100 or 400 micrograms/ml vitamin E, or with other antioxidants (80 micrograms/ml vitamin C, either alone or in combination with vitamin E, or 120 micrograms/ml N,N'-diphenyl-1,4-diphenylenediamine (DPPD] did not significantly affect lifespan. All treatments with 200 micrograms/ml vitamin E moderately reduced fecundity (total progeny) and increased the mean day of reproduction. At 400 micrograms/ml, vitamin E had severe effects, while DPPD, vitamin C, and 100 micrograms/ml vitamin E had slight effects on both these parameters of reproduction. These data suggest that vitamin E increases lifespan in C. elegans in part by slowing development in the same manner that metabolic-depressant or mildly cytotoxic drugs increase lifespan, decrease fecundity, and delay the timing of reproduction. ------------------- Key: 1037 Medline: 88284309 Authors: Schedl T;Kimble J Title: fog-2, a germ-line-specific sex determination gene required for hermaphrodite spermatogenesis in C. elegans. Citation: Genetics 119: 43-61 1988 Type: ARTICLE Genes: fem-1 fem-2 fem-3 fog-1 fog-2 her-1 tra-1 tra-2 tra-3 Abstract: This paper describes the isolation and characterization of 16 mutations in the germ-line sex determination gene fog-2 (fog for feminization of the germ line). In the nematode Caenorhabditis elegans there are normally two sexes, self-fertilizing hermaphrodites (XX) and males (XO). Wild-type XX animals are hermaphrodite in the germ line (spermatogenesis followed by oogenesis), and female in the soma. fog-2 loss-of-function mutations transform XX animals into females while XO animals are unaffected. Thus, wild-type fog-2 is necessary for spermatogenesis in hermaphrodites but not males. The fem genes and fog-1 are each essential for specification of spermatogenesis in both XX and XO animals. fog-2 acts as a positive regulator of the fem genes and fog-1. The tra-2 and tra-3 genes act as negative regulators of the fem genes and fog-1 to allow oogenesis. Two models are discussed for how fog-2 might positively regulate the fem genes and fog-1 to permit spermatogenesis; fog-2 may act as a negative regulator of tra-2 and tra-3, or fog-2 may act positively on the fem genes and fog-1 rendering them insensitive to the negative action of tra-2 and tra-3. ------------------- Key: 1038 Medline: Authors: Smith ET;Kelly K;Brown C Title: Aging: Can it be slowed? Citation: Business Week : 58-62 1988 Type: NEWS Genes: age-1 Abstract: "Why do we grow old, get sick, and die?" asks Noel K. Johnson. "We should live forever." Johnson is taking his best shot at it. When he turned 70, he had heart trouble, arthritis, and gout. He drank too much, was 50 pounds over weight. He was in such bad shape that his son suggested he enter a convalescent home. Today, at 88, he's a trim 138 pounds and claims his earlier afflictions have disappeared... ------------------- Key: 1039 Medline: 90166503 Authors: Johnson CD;Rand JB;Herman RK;Stern BD;Russell RL Title: The acetylcholinesterase genes of C. elegans: Identification of a third gene (ace-3) and mosaic mapping of a synthetic lethal phenotype. Citation: Neuron 1: 165-173 1988 Type: ARTICLE Genes: ace-1 ace-2 ace-3 Abstract: In C. elegans, the newly identified ace-3 is the third gene affecting acetylcholinesterase (AChE) activity. ace-3 II specifically affects class C AChE and is unlinked to ace-1 X or ace-2 I, which affect the other two AChE classes (A and B, respectively). Strains homozygous for an ace-3 mutation have no apparent behavioral or developmental defect; ace-1 ace-3 and ace-2 ace-3 double mutants are also nearly wild type. In contrast, ace-1 ace-2 ace-3 triple mutant animals are paralyzed and developmentally arrested; their embryonic development is relatively unimpaired, but they are unable to grow beyond the hatching stage. Based on the analysis of genetic mosaics, we conclude that in the absence of ace-2 and ace-3 function, the expression of ace-1(+) in muscles cells, but not in neurons, is essential for postembyronic development. ------------------- Key: 1040 Medline: 88284325 Authors: Clark DV;Rogalski TM;Donati LM;Baillie DL Title: The unc-22(IV) region of Caenorhabditis elegans: Genetic analysis of lethal mutations. Citation: Genetics 119: 345-353 1988 Type: ARTICLE Genes: let-52 let-56 let-59 let-60 let-61 let-63 let-64 let-65 let-66 let-67 let-68 let-69 let-70 let-71 let-72 let-73 let-91 let-92 let-93 let-96 let-97 let-98 let-99 let-100 let-307 let-308 let-309 let-311 let-312 lin-3 nDf27 nT1 mDf7 sDf2 sDf7 sDf8 sDf9 sDf10 sDf21 sDf22 Abstract: The organization of essential genes in the unc-22 region, defined by the deficiency sDf2 on linkage group IV, has been studied. Using the balancer nT1 (IV;V), which suppresses recombination over 49 map units, 294 lethal mutations on LGIV(right) and LGV(left) were recovered using EMS mutagenesis. Twenty-six of these mutations fell into the unc-22 region. Together with previously isolated lethal mutations, there is now a total of 63 lethal mutations which fall into 31 complementation groups. Mutations were positioned on the map using eight overlapping deficiencies in addition to sDf2. The lethal alleles and deficiencies in the unc-22 region were characterized with respect to their terminal phenotypes. Mapping of these lethal mutations shows that sDf2 deletes a minimum of 1.8 map units and a maximum of 2.5 map units. A minimum estimate of essential gene number for the region using a truncated Poisson calculation is 48. The data indicate a minimum estimate of approximately 3500 essential genes in the Caenorhabditis ------------------- Key: 1041 Medline: 88284326 Authors: Jacobson LA;Jen-Jacobson L;Hawdon JM;Owens GP;Bolanowski MA;Emmons SW;Shah MV;Pollock RA;Conklin DS Title: Identification of a putative structural gene for cathepsin D in Caenorhabditis elegans. Citation: Genetics 119: 355-363 1988 Type: ARTICLE Genes: cad-1 let-257 let-259 jDf1 jDf2 jDf4 jDf5 jDf6 jDf7 jDf8 jDf9 Abstract: Mutants of Caenorhabditis elegans having about 10% of wild-type activity of the aspartyl protease cathepsin D have been isolated by screening. Mutant homozygotes have normal growth rates and no obvious morphological or developmental abnormalities. The mutant gene (cad-1) has been mapped to the right extremity of linkage group II. Heterozygous animals (cad-1/+) show intermediate enzyme levels and animals heterozygous for chromosomal deficiencies of the right extremity of linkage group II have 50% of wild-type activity. Cathepsin D purified from a mutant strain has a lower activity per unit mass of pure enzyme. These data suggest that cad-1 is a structural gene ------------------- Key: 1042 Medline: 88284327 Authors: Meneely PM;Nordstrom KD Title: X chromosome duplications affect a region of the chromosome they do not duplicate in Caenorhabditis elegans. Citation: Genetics 119: 365-375 1988 Type: ARTICLE Genes: dpy-21 dpy-22 dpy-23 stDp2 mnDp25 mnDp33 mnDp57 Abstract: X chromosome duplications have been used previously to vary the dose of specific regions of the X chromosome to study dosage compensation and sex determination in Caenorhabditis elegans. We show here that duplications suppress and X-linked hypomorphic mutation and elevate the level of activity of an X-linked enzyme, although these two genes are located in a region of the X chromosome that is not duplicated. The effects do not depend on the region of the X chromosome duplicated and is stronger in strains with two doses of a duplication than in strains with one dose. This is evidence for a general elevation of X-linked gene expression in strains carrying X- chromosome duplications, consistent with the hypothesis that the duplications titrate a repressor acting on many X-linked genes. ------------------- Key: 1043 Medline: 89146926 Authors: Sternberg PW Title: Control of cell fates within equivalence groups in C. elegans. Citation: Trends in Neurosciences 11: 259-264 1988 Type: REVIEW Genes: let-23 lin-12 lin-15 Abstract: Small groups of multipotent cells share the same set of potential developmental fates, with the fate of each cell specified by cell-cell interactions. Genetic studies in the nematode have identified two pathways that distinguish between two alternative cell fates in such 'equivalence groups'. In a group whose members choose between two fates, only a single pathway operates. In groups whose members choose among three fates, both pathways operate, suggesting that complex decisions might result from the combination of binary decisions. ------------------- Key: 1044 Medline: 88309062 Authors: Strome S;Hill DP Title: Early embryogenesis in Caenorhabditis elegans: The cytoskeleton and spatial organization of the zygote. Citation: BioEssays 8: 145-149 1988 Type: REVIEW Genes: zyg-9 Abstract: Early embryogenesis of Caenorhabditis elegans provides a striking example of the generation of polarity and the partitioning of cytoplasmic factors according to this polarity. Microfilaments (MFs) appear to play a critical role in these processes. By visualizing the distribution of MFs and by studying the consequences of disrupting MFs for short, defined periods during zygote development, we have generated some new ideas about when and how microfilaments function in the zygote. ------------------- Key: 1045 Medline: 88223352 Authors: Edgar LG;McGhee JD Title: DNA synthesis and the control of embryonic gene expression in C. elegans. Citation: Cell 53: 589-599 1988 Type: ARTICLE Genes: ges-1 Abstract: DNA synthesis in each cell lineage of the early C. elegans embryo was measured using microspectrofluorimetry. Aphidicolin was shown to inhibit DNA synthesis almost instantly and completely. Aphidicolin was then used to investigate how DNA synthesis controls expression of two biochemical markers that appear at different times during gut development: gut granules and a carboxylesterase. We show that marker expression is controlled neither by reaching the normal DNA: cytoplasm ratio, by counting the normal number of rounds of DNA synthesis, nor by a simple lengthening of the cell cycle. Instead, expression of both gut markers requires a short period of DNA synthesis in the first cell cycle after the gut has been clonally established. ------------------- Key: 1046 Medline: Authors: Rattray B;Rose AM Title: Increased intragenic recombination and non-disjunction in the Rec-1 strain of Caenorhabditis elegans. Citation: Genetical Research 51: 89-93 1988 Type: ARTICLE Genes: rec-1 Abstract: The Rec-1 strain of Caenorhabditis elegans increases recombination frequency three-fold. In this paper, we have investigated the effect of Rec-1 on the intragenic recombination phenomena of crossing-over and gene conversion. These events were increased two- to three-fold as was X -chromosome non-disjunction. All of the recovered recombinants were independent events, indicating that Rec-1 does not act pre-meiotically. The pattern of recombination in the Rec-1 strain resembles a meiotic pattern more than a radiation expansion. We conclude from this result that the Rec-1 enhancement of recombination is not the result of an increased number of DNA lesions randomly distributed along the chromosome. The increased recombination frequency of Rec-1 was not accompanied by any detrimental effects on growth, progeny number or spontaneous mutation rate. In this regard, the results may have implications for models which propose either selective advantage or disadvantage accompanying increased recombination. ------------------- Key: 1047 Medline: 88235937 Authors: Kenyon C Title: The nematode Caenorhabditis elegans. Citation: Science 240: 1448-1453 1988 Type: REVIEW Genes: ced-3 ced-4 fog-2 glp-1 lin-12 lin-14 lin-29 lin-32 mab-5 mec-3 mec-7 tra-1 tra-2 unc-6 unc-40 unc-86 Abstract: In Caenorhabditis elegans patterns of cell division, differentiation, and morphogenesis can be observed with single-cell resolution in intact, living animals. Mechanisms that determine behaviors of individual cells during development are being dissected by means of genetic, cell biological, and molecular approaches. ------------------- Key: 1048 Medline: 88297155 Authors: Snutch TP;Heschl MFP;Baillie DL Title: The Caenorhabditis elegans hsp70 gene family: a molecular genetic characterization. Citation: Gene 64: 241-255 1988 Type: ARTICLE Genes: Abstract: We have isolated genomic clones representing six distinct members of the Caenorhabditis elegans 70-kDa heat-shock protein gene (hsp70) family. Each member exists as a single copy element in the C. elegans genome. Transcripts of four of the hsp70 genes have been detected by Northern-blot analysis. One member, hsp70C, appears to be a heat- shock-cognate hsp70 gene (hsc70) since its transcription is developmentally regulated and is not increased in response to heat shock. Transcripts of another gene, hsp70A, are abundant in control worms and are also increased (two- to six-fold) upon heat shock. Nucleotide sequencing of genomic and cDNA clones of hsp70A reveals that it is highly homologous to Drosophila and yeast heat-shock- inducible and heat-shock-cognate hsp70 genes. Three DNA elements homologous to the heat-shock promoter, 5'-C--GAA--TTC--G-3' are located upstream from the Hsp70A-coding region. We find that hsp70A contains three introns, one of which is in a similar position with an intron in the Drosophila hsc1 and hsc2 genes. Finally, utilizing strain-specific restriction fragment length differences, we have mapped the chromosomal position of hsp70A to the far right of chromosome IV. ------------------- Key: 1049 Medline: 88311798 Authors: Mercer JG;Munn AE;Rees HH Title: Caenorhabditis elegans: Occurrence and metabolism of ecdysteroids in adults and dauer larvae. Citation: Comparative Biochemistry & Physiology 90B: 261-267 1988 Type: ARTICLE Genes: Abstract: 1. Ecdysteroids were detected in extracts of egg-producing adult Caenorhabditis elegans, in dauer larvae and in dietary bacteria. 2. Similar concentrations of free ecdysteroids were recorded in adults and larvae, although the two life cycle stages differed in their ratio of ecdysone: 20-hydroxyecdysone. 3. Patent adults metabolized [3H]ecdysone into apolar products and putative [3H]ecdysone 22- phosphate. ------------------- Key: 1050 Medline: 88262576 Authors: Bektesh SL;Hirsh DI Title: C. elegans mRNAs acquire a spliced leader through a trans-splicing mechanism. Citation: Nucleic Acids Research 16: 5692-5692 1988 Type: ARTICLE Genes: Abstract: A 22 nt spliced leader (SL) is added to some C. elegans mRNAs by a process of discontinuous RNA synthesis. The SL is synthesized as part of a larger precursor RNA, the leader RNA (LR) which is about 100 nt long. ------------------- Key: 1051 Medline: 88257200 Authors: Epstein HF;Berliner GC;Casey DL;Ortiz I Title: Purified thick filaments from the nematode Caenorhabditis elegans: Evidence for multiple proteins associated with core structures. Citation: Journal of Cell Biology 106: 1985-1995 1988 Type: ARTICLE Genes: unc-15 unc-54 Abstract: The thick filaments of the nematode, Caenorhabditis elegans, arising predominantly from the body-wall muscles, contain two myosin isoforms and paramyosin as their major proteins. The two myosins are located in distinct regions of the surfaces, while paramyosin is located within the backbones of the filaments. Tubular structures constitute the cores of the polar regions, and electron-dense material is present in the cores of the central regions. Biochemical, genetic, and immunological experiments indicate that the two myosins and paramyosin are not necessary core components. The existence of the core suggests, therefore, that additionaal proteins may be associated with thick filaments in C. elegans. To biochemically detect minor associated proteins, a new procedure for the isolation of thick filaments of high purity and structural preservation has been developed. The final step, glycerol gradient centrifugation, yielded fractions that are contaminated by, at most, 1-2% with actin, tropomyosin, or ribosome-associated proteins on the basis of Coomassie Blue staining and electron microscopy. Silver staining and radioautography of gel electrophoretograms of unlabeled (35)S-labeled proteins, respectively, revealed at least 10 additional bands that cosedimented with thick filaments in glycerol gradients. Core structures prepared from wild-type thick filaments contained at least six of these thick filament-associated protein bands. The six proteins also cosedimented with thick filaments purified by gradient centrifugation from CB190 mutants lacking myosin heavy chain B and from CB1214 mutants lacking paramyosin. For these reasons, we propose that the six associated proteins are potential candidates for putative components of core structures in the thick ------------------- Key: 1052 Medline: 88253425 Authors: Way JC;Chalfie M Title: mec-3, a homeobox-containing gene that specifies differentiation of the touch receptor neurons in C. Citation: Cell 54: 5-16 1988 Type: ARTICLE Genes: clr-1 mec-3 mec-4 Abstract: The mec-3 gene is essential for proper differentiation of the set of six touch receptor neurons in C. elegans. In mutants lacking mec-3 activity, the touch receptors express none of their unique differentiated features and appear to be transformed into other types of neurons. We cloned the mec-3 gene by transposon tagging and showed that a mec-3 mutant can be rescued by germ line transformation using a 5.6 kb genomic DNA fragment. In a strain in which transforming mec- 3 DNA is present in about 50 copies per haploid genome, additional cells express a mec-3-dependent phenotype. The putative coding sequence of mec-3 contains a homeobox, suggesting that the mec-3 protein specifies the expression of touch cell differentiation by binding to DNA and regulating transcription of genes that encode the differentiated features of these cells. ------------------- Key: 1053 Medline: 88255847 Authors: Rosenquist TA;Kimble J Title: Molecular cloning and transcript analysis of fem-3, a sex-determination gene in Caenorhabditis elegans. Citation: Genes & Development 2: 606-616 1988 Type: ARTICLE Genes: fem-3 glp-1 Abstract: The fem-3 gene is required for specification of the male fate in the nematode Caenorhabditis elegans: XO males need fem-3 for male differentation in both soma and germ line; XX hermaphrodites need it for the production of sperm. We have cloned fem-3 by transposon tagging. Among eight spontaneous fem-3 mutations generated in a strain in which the transposable element Tc1 is mobile, six contain Tc1 insertions in a 2-kb region of the genome. From this region, we have identified three fem-3 transcripts. Two, 1.7 bk and 1.62 bk, are presented in embryos, and two, 1.62 kb and 1.55 kb, are present in L4s and adults. The fem-3 transcripts are not XO specific; however, in XX adult hermaphrodites, they appear to be limited to the germ line - a tissue involved in male development (both for spermatogenesis and for the maternal contribution of fem-3 to the embyro). The amount of fem-3 RNA in XO embryos is approximately sixfold greater than in XX embryos. The significance of this difference in specifying male development in XO but not in XX embryos is discussed. ------------------- Key: 1054 Medline: 88257847 Authors: Friedman DB;Johnson TE Title: Three mutants that extend both mean and maximum life span of the nematode, Caenorhabditis elegans, define the age-1 Citation: Journal of Gerontology 43: B102-B109 1988 Type: ARTICLE Genes: age-1 fer-15 unc-31 Abstract: Long-lived mutants in the nematode Caenorhabditis elegans have been studied to determine if the mutations responsible for extended life were allelic. Three of four mutant strains studied (MK31, MK542, MK546) contain recessive mutations that significantly lengthen life; MK542 and MK546 consistently fail to complement the long life phenotype of age-1 and are therefore allelic. MK31, although longer lived than wild type, is equivocal, in some cases failing to complement age-1 but not in others. All three long-lived strains have reduced hermaphrodite self-fertility and also fail to complement for this presumed pleiotropic effect of the age-1 mutation. Each of these three strains also contains an independent mutation at unc-31 IV. Since the mutants were isolated in the same mutant hunt (Klass, 1983) using protocols that did not guarantee independence, the mutations cannot be assumed to be independently isolated. ------------------- Key: 1055 Medline: 88289347 Authors: Harris LJ;Baillie DL;Rose AM Title: Sequence identity between an inverted repeat family of transposable elements in Drosophila and Caenorhabditis. Citation: Nucleic Acids Research 16: 5991-5998 1988 Type: ARTICLE Genes: Abstract: The Tc1-like transposable elements, originally described in Caenorhabditis elegans, have a much wider phylogenetic distribution than previously thought. In this paper, we demonstrate that Tc1 shares sequence identity in its open reading frame and terminal repeats with a new transposable element Barney (also known as TCb1- Transposon Caenorhabditis briggsae 1). Barney was detected and isolated by Tc1 hybridization from the closely related nematode species, Caenorhabditis briggsae. The conserved open reading frames of Tc1 and Barney share identity with a structurally similar family of elements named HB found in Drosophila melanogaster, after the introduction of 3 small centrally located deletions in HB1. These reading frames would code for proteins with 30% amino acid identity (42% when conservative changes are included). Tc1, Barney and HB1 contain highly conserved blocks of amino acids which are likely to be in the functional domains of the putative transposase. ------------------- Key: 1056 Medline: 88289374 Authors: Henikoff S;Plasterk RHA Title: Related transposons in C. elegans and D. melanogaster. Citation: Nucleic Acids Research 16: 6234-6234 1988 Type: ARTICLE Genes: Abstract: We have found that the transposable element Tc1 in Caenorhabditis elegans is strikingly similar to a translated sequence found within the Drosophila melanogaster element HB1, a member of the HB family of ------------------- Key: 1057 Medline: 89231492 Authors: Link CD;Ehrenfels CW;Wood WB Title: Mutant expression of male copulatory bursa surface markers in Caenorhabditis elegans. Citation: Development 103: 485-495 1988 Type: ARTICLE Genes: bli-3 bli-5 her-1 him-5 lin-4 lin-14 lin-17 lin-22 lin-28 lin-29 mab-2 mab-3 mab-4 mab-5 mab-6 mab-7 mab-8 mab-9 mab-10 sma-2 sma-4 smg-1 tra-1 tra-2 vab-3 vab-8 Abstract: In a search for molecular markers of male tail morphogenesis in C. elegans, we have detected two surface markers that are specifically observed in the copulatory bursa of adult males and the vulva of adult hermaphrodites. These markers are defined by binding of a monoclonal antibody (Ab117) and the lectin wheat germ agglutinin (WGA) to live intact animals. Expression of these markers is dependent on sex, stage and anterior-posterior position in the animal. Four of ten mutants with specific defects in bursal development show altered expression of one or both markers. Because the WGA marker can be expressed in intersexual animals with very little bursal development, posterior surface expression of this marker can serve as an indication of subtle masculinization of hermaphrodites. The timing of expression of these markers is not affected by heterochronic mutations that cause larval animals to express adult cuticles or adult animals to express larval cuticals, indicating that marker expression can be uncoupled from general cuticle development. Mutant lin-22 males, which have an anterior-to-posterior transformation of cell fates in the lateral hypodermis, ectopically express both markers in a manner consistent with a "posteriorization" of positional information in these animals. These markers should be useful for the isolation and characterization of mutants defective in bursal and vulval development, sex determination and expression of anterior-posterior positional information. ------------------- Key: 1058 Medline: 88246494 Authors: Hartman PS;Simpson VJ;Johnson T;Mitchell D Title: Radiation sensitivity and DNA repair in Caenorhabditis elegans strains with different mean life spans. Citation: Mutation Research 208: 77-82 1988 Type: ARTICLE Genes: Abstract: The sensitivities to three DNA damaging agents (UV and gamma- radiation, methyl methanesulfonate) were measured in four recombinant inbred (RI) strains of Caenorhabditis elegans with mean life spans ranging from 13 to 30.9 days, as well as in the wild-type strains used to derive these RI's. Sensitivities at several stages in the developmental cycle were tested. There were no significant correlations between mean life span and the lethal effects of these 3 agents. Excision of two UV-radiation-induced DNA photoproducts was also measured. Long-lived strains were no more repair competent than shorter-lived strains. These data indicate that DNA repair plays at best a minor role in the aging process of C. elegans. ------------------- Key: 1059 Medline: 88303347 Authors: Zucker-Aprison E;Thomas JD;Blumenthal T Title: C. elegans snRNAs: a model for U4/U6 base pairing. Citation: Nucleic Acids Research 16: 7188-7188 1988 Type: REVIEW Genes: Abstract: Two of the snRNAs involved in pre-mRNA splicing, U4 and U6, are known to interact by base pairing. This has been demonstrated by their presence in a single snRNP particle which can be dissociated by heating and by photochemical cross-linking. We have cloned three U4 and two U6 genes from Caenorhabditis elegans and determined their ------------------- Key: 1060 Medline: 88273146 Authors: Graham RW;Van Doren K;Bektesh S;Candido EPM Title: Maturation of the major ubiquitin gene transcript in Caenorhabditis elegans involves the acquisition of a trans-spliced leader. Citation: Journal of Biological Chemistry 263: 10415-10419 1988 Type: ARTICLE Genes: Abstract: Recently, studies on the 5'-ends of actin mRNAs in the nematode, Caenorhabditis elegans, have demonstrated that three of the four mature actin transcripts contain a 22-nucleotide leader sequence which is acquired by trans-splicing from a novel 100-nucleotide RNA. In the course of our studies of the ubiquitin genes in C. elegans (R. W. Graham and E. P. M. Candido, manuscript in preparation) we were led to the possibility that the major ubiquitin transcript in this organism might also contain a trans-spliced leader sequence. The 5'- noncoding region of the major ubiquitin gene (UbiA) contains a 3'- splice consensus sequence six nucleotides upstream of the initiation codon; however, sequencing of a further 1.6 kilobases upstream failed to reveal the existence of any potential 5'-splice sites in the correct relationship to known promoter elements. Furthermore, S1 and Northern blot analyses using probes complementary to upstream regions failed to detect the ubiquitin transcript. Primer extension experiments on total RNA using an oligonucleotide which hybridized to the ubiquitin transcript downstream of the 3'-splice site demonstrated the existence of a 22-nucleotide leader sequence not present in the ubiquitin gene 5'-region. Thus we show here that the 2500-nucleotide mRNA encoding a polyubiquitin precursor protein contains a 22-nucleotide leader sequence identical to that found in several C. elegans actin mRNAs and which is most likely acquired by a trans-splicing mechanism. In addition we have localized the site of transcript initiation for UbiA by S1 nuclease mapping. ------------------- Key: 1061 Medline: 88333012 Authors: Vahidi H;Curran J;Nelson DW;Webster JM;McClure MA;Honda BM Title: Unusual sequences, homologous to 5S RNA, in ribosomal DNA repeats of the nematode Meloidogyne arenaria. Citation: Journal of Molecular Evolution 27: 222-227 1988 Type: ARTICLE Genes: Abstract: There are sequences homologous to 5S ribosomal RNA in the ribosomal DNA (rDNA) repeats of the plant-parasitic nematode Meloidogyne arenaria. This is surprising, because in all other higher eukaryotes studied to date, the genes for 5S RNA are unlinked to and distinct from a tandem rDNA repeat containing the genes for 18S, 5.8S, and 28S ribosomal RNA. Previously, only prokaryotes and certain "lower eukaryotes" (protozoa and fungi) had been found to have both the larger rRNAs and 5S rRNA represented within a single DNA repeat. This has raised questions on the organization of these repeats in the earliest cell (progenote), and on subsequent evolutionary relationships between pro- and eukaryotes. Evidence is presented for rearrangements and deletions with Meloidogyne rDNA. The unusual life cycles (different levels of ploidy, reproduction by meiotic and mitotic parthenogenesis) of members of this genus might allow rapid fixation of any variants with introduced 5S RNA sequences. The 5S RNA sequences in Meloidogyne rDNA may not be expressed, but their presence raises important questions as to the evolutionary origins and stability of repeat gene families. ------------------- Key: 1062 Medline: 88295128 Authors: Thomas JD;Conrad RC;Blumenthal T Title: The C. elegans trans-spliced leader RNA is bound to Sm and has a trimethlguanosine cap. Citation: Cell 54: 533-539 1988 Type: ARTICLE Genes: Abstract: mRNA splicing in C. elegans is unusual: most introns are very short (approximately 50 bases), and many mRNAs receive a leader by trans- splicing. The donor in trans-splicing is a 94 nucleotide molecule, termed the leader RNA, that contributes its 5' 22 nucleotides to a variety of mRNAs. We show here that C. elegans has the usual snRNAs, which presumably catalyze the splicing reactions. As expected, they are bound to the Sm antigen and have 2,2,7-methylguanosine caps. Remarkably, the trans-spliced leader RNA is also Sm-associated and has this special cap. Hence, a molecule discovered as a substate of splicing has properties of molecules heretofore known only to facilitate splicing of other RNAs. Mature mRNAs that have received the leader evidently lack 2,2,7-methylguanosine caps, suggesting that these caps are removed or altered during ------------------- Key: 1063 Medline: 88307989 Authors: Morgan PG;Sedensky MM;Meneely PM;Cascorbi HF Title: The effect of two genes on anesthetic response in the nematode Caenorhabditis elegans. Citation: Anesthesiology 69: 246-251 1988 Type: ARTICLE Genes: unc-79 Abstract: The authors studied the wild type strain, N2, and three mutant strains of the nematode, Caenorhabditis elegans, in order to measure genetically produced changes in responses to nine volatile anesthetics. They determined the anesthetic ED50s of N2 for thiomethoxyflurane, methoxyflurane, chloroform, halothane, enflurane, isoflurane, fluroxene, flurothyl, and diethylether. The log-log relationship of the oil-gas partition coefficients (O/G) and the ED50s of these agents for N2 yields a straight line with a slope of - .997 with a R2 of .98 over a range of O/G (at 37 degrees C) from 48 to 7230. When the O/Gs are corrected to 22 degrees C, the slope is - .964 with an R2 of .98. This relationship is similar to that found in other animals. Two mutant strains, unc-79 and unc-80, show altered responses to these anesthetics. These strains are two to three times more sensitive than N2 to anesthetics with an O/G greater than that of halothane (220 at 37 degrees C), yet they differ little from N2 in response to anesthetics with lower O/Gs. unc-79 and unc-80 are about 30% more sensitive than N2 to diethylether. The double mutant unc-79; unc-80 is more sensitive to halothane, isoflurane, and fluroxene than is either mutant alone. The authors believe these data indicate an alteration at the site of action of volatile anesthetics in unc-79 and unc-80. They also postulate that the interaction of unc-79 and unc-80 indicate these genes code for enzymes in a common pathway, and that unc-79 precedes unc-80 in ------------------- Key: 1064 Medline: 89127201 Authors: Kondo K;Hodgkin J;Waterston RH Title: Differential expression of five tRNA-TRP-UAG amber suppressors in Caenorhabditis elegans. Citation: Molecular and Cellular Biology 8: 3627-3635 1988 Type: ARTICLE Genes: sup-5 sup-7 sup-24 sup-28 sup-29 unc-13 Abstract: Caenorhabditis elegans has 12 tRNA(UGGTrp) genes as defined by Southern analysis. In order to evaluate the function of the individual members of this multigene family, we sought to recover amber (UAG)-suppressing mutations from reversion experiments with animals carrying amber mutations in a nervous system-affecting gene (unc-13) or a sex-determining gene (tra-3). Revertants were analyzed by Southern blot, exploiting the fact that the CCA to CTA change at the anticodon creates a new XbaI site. Five different members of the tRNATrp gene family were identified as suppressors: sup-7 X, sup-5 III, sup-24 IV, sup-28 X, and sup-29 IV. All five suppressor genes were sequenced and found to encode identical tRNA(UAGTrp) molecules with a single base change (CCA to CTA) at the anticodon compared with their wild-type counterparts. The flanking sequences had only limited homology. The relative expression of these five genes was determined by measuring the efficiencies of suppressers against amber mutations in genes affecting the nervous system, hypodermis, muscle, and sex determination. The results of these cross-suppression tests showed that the five members of the tRNA(Trp) gene family were differentially regulated in a tissue- or development stage-specific manner. ------------------- Key: 1065 Medline: 89127215 Authors: Pulak RA;Anderson P Title: Structures of spontaneous deletions in Caenorhabditis elegans. Citation: Molecular and Cellular Biology 8: 3748-3754 1988 Type: ARTICLE Genes: unc-54 unc-80 Abstract: We have investigated the structural features of spontaneous deletions in Caenorhabditis elegans. We cloned and sequenced the junctions of 16 spontaneous deletions affecting the unc-54 myosin heavy-chain gene and compared their sequences with those of the wild type. We analyzed these sequences in an attempt to identify structural features of the gene that are consistently involved in the spontaneous deletion process. Most deletions (15 of 16) removed a single contiguous region of DNA, with no nucleotides inserted or rearranged at the deletion junctions; one deletion was more complex. unc-54 deletions were small, averaging 600 base pairs in length, and were randomly distributed throughout the gene. Unlike deletions that occur in Escherichia coli, spontaneous unc-54 deletions did not contain statistically significant direct or inverted repeats at or near their termini. Except for their small average size, we have not identified any distinguishing features of their sequence or structure. We discuss these results with regard to the mechanisms for spontaneous deletion in eucaryotic and procaryotic cells. ------------------- Key: 1066 Medline: 88318977 Authors: Coulson A;Waterston R;Kiff J;Sulston J;Kohara Y Title: Genome linking with yeast artificial chromosomes. Citation: Nature 335: 184-186 1988 Type: ARTICLE Genes: lin-14 Abstract: The haploid genome of Caenorhabditis elegans consists of some 80 x 10(6) base pairs of DNA contained in six chromosomes. The large number of interesting loci that have been recognized by mutation, and the accuracy of the genetic map, mean that a physical map of the genome is highly desirable, because it will facilitate the molecular cloning of chosen loci. The first steps towards such a map used a fingerprinting method to link cosmid clones together. This approach reached its practical limit last year, when 90-95% of the genome had been cloned into 17,500 cosmids assembled into some 700 clusters (contigs), but the linking clones needed were either non-existent or extremely rare. Anticipating this, we had planned to link by physical means--probably by hybridization to NotI fragments separated by pulse field gel electrophoresis. NotI recognizes an eight base sequence of GC pairs; thus the fragments should be large enough to bridge regions that clone poorly in cosmids, and, with no selective step involved, would necessarily be fully representative. However, with the availability of a yeast artificial chromosome (YAC) vector, we decided to use this alternative source of large DNA fragments to obtain linkage. The technique involves the ligation of large (50- 1,000 kilobase) genomic fragments into a vector that provides centromeric, telomeric and selective functions; the constructs are then introduced into Saccharomyces cerevisiae, and replicate in the same manner as the host ------------------- Key: 1067 Medline: 89121431 Authors: Trent C;Wood WB;Horvitz HR Title: A novel dominant transformer allele of the sex-determining gene her-1 of Caenorhabditis elegans. Citation: Genetics 120: 145-157 1988 Type: ARTICLE Genes: her-1 nDf31 Abstract: We have characterized a novel dominant allele of the sex-determining gene her-1 of Caenorhabditis elegans. This allele, called n695, results in the incomplete transformation of XX animals into phenotypic males. Previously characterized recessive her-1 alleles transform XO animals into phenotypic hermaphrodites. We have identified five new recessive her-1 mutations as intragenic suppressors of n695. Three of these suppressors are weak, temperature- sensitive alleles. We show that the recessive her-1 mutations are loss-of-function alleles, and that the her-1(n695) mutation results in a gain-of-function at the her-1 locus. The existence of dominant and recessive alleles that cause opposite phenotypic transformations demonstrates that the her-1 gene acts to control sexual identity in C. elegans. ------------------- Key: 1068 Medline: 88331679 Authors: Johnson TE;Hartman PS Title: Radiation effects on life span in Caenorhabditis elegans. Citation: Journal of Gerontology 43: B137-B141 1988 Type: ARTICLE Genes: rad-1 rad-2 rad-3 rad-4 rad-5 rad-6 rad-7 Abstract: Wild-type and radiation-sensitive (Rad) mutants of Caenorhabditis elegans were irradiated using a 137Cs source (2.7 krads/min.) at several developmental stages and subsequently monitored for life span. Acute doses of radiation ranged from 1 krad to 300 krads. All stages required doses above 100 krads to reduce mean life span. Dauers and third stage larvae were more sensitive, and 8-day-old adults were the most resistant. Occasional statistically significant but nonrepeatable increases in survival were observed after intermediate levels of irradiation (10-30 krads). Unirradiated rad-4 and rad-7 had life spans similar to wild-type; all others had a significant reduction in survival. The mutants were about as sensitive as wild-type to the effects of ionizing radiation including occasional moderate life span extensions at intermediate doses. We conclude that the moderate life span extensions sometimes observed after irradiation are likely to be mediated by a means other than the induction of DNA repair enzymes. ------------------- Key: 1069 Medline: Authors: Schierenberg E Title: Vom Ei zum Organismus. Citation: Biologie in unserer Zeit 17: 97-106 1987 Type: REVIEW Genes: Abstract: In German. ------------------- Key: 1070 Medline: Authors: Schierenberg E Title: Localization and segregation of lineage-specific cleavage potential in embryos of Caenorhabditis elegans. Citation: Roux's Archives of Developmental Biology 197: 282-293 1988 Type: ARTICLE Genes: Abstract: Early embrogenesis of the nematode Caenorhabditis elegans is characterized by the continuous visibility of a germline and the stepwise separation of all somatic cells from it. Germline and somatic cells exhibit different cleavage patterns. Typical for the germline is a series of stemcell-like, unequal cleavages generating blastomeres, which differ in size, cell cycle periods, and fate. Typical for members of somatic cell lineages during early development are their equal and synchronous cleavages generating cells of similar appearance. Using a laser microbeam various experiments have been carried out to investigate the conditions that lead to the two different types of cleavage. Development of partial embryos demonstrates that the potential for germlin-like cleavage is localized in the posterior region of the fertilized egg prior to both the formation of pronuclei and the posterior aggregation of germline-specific granules. Experimental alteration of the cleavage plane can result from a switch from unequal to equal cleavage, with an apparent correlation between the orientation of the mitotic spindle and the type of cleavage. Nuclear transfer experiments indicate that nuclei and centrioles are not involved in the decision as to which type of cleavage will be executed. Cytoplasmic transfer from soma-like to germline-like cleaving cells and vice versa does not alter the cleavage type in the recipient cell. But if separation of germline from soma is delayed after the removal of a centrosome, germline-like cleavage may be completely suppressed, all cells thereafter dividing soma-like. ------------------- Key: 1071 Medline: 88334596 Authors: Johnsen RC;Baillie DL Title: Formaldehyde mutagenesis of the eT1 balanced region in C. elegans: Dose-response curve and the analysis of mutational events. Citation: Mutation Research 201: 137-147 1988 Type: ARTICLE Genes: let-336 let-338 let-341 let-342 let-344 let-345 let-346 let-347 let-348 let-349 let-350 let-417 let-418 let-420 let-421 let-422 let-430 let-438 let-447 let-450 lin-40 sDf36 sDf42 sDf44 sDf46 sDf47 sDf50 sDf53 Abstract: In this study we have generated a dose-response curve for the formaldehyde induction of recessive lethal mutations in the eT1(III;V)-balanced region of C. elegans. We have mapped 96 out of 112 formaldehyde-induced lesions to either LGIII or LGV and genetically analyzed 31 lesions that mapped to LGV. Our findings showed that a 4-h treatment with 0.1% formaldehyde gave the best mutation induction frequency with the least side effects. We found that formaldehyde induced putative point mutations, deficiencies and more complex lesions in C. elegans. We isolated 11 putative point mutations, 3 of which defined new genes and 8 were alleles of known genes. One of the new genes, let-450, is currently the left-most known gene on LGV. We also isolated 5 deficiencies. Our formaldehyde- induced lesions increased the number of zones in the eT1-balanced region of LGV from 22 to 34. ------------------- Key: 1072 Medline: 89065351 Authors: Mori I;Moerman DG;Waterston RH Title: Analysis of a mutator activity necessary for germline transposition and excision of Tc1 transposable elements in Caenorhabditis elegans. Citation: Genetics 120: 397-407 1988 Type: ARTICLE Genes: mut-4 mut-5 mut-6 Abstract: The Tc1 transposable element family of the nematode Caenorhabditis elegans consists primarily of 1.6-kb size elements. This uniformity of size is in contrast to P in Drosophila and Ac/Ds in maize. Germline transposition and excision of Tc1 are detectable in the Bergerac (BO) strain, but not in the commonly used Bristol (N2) strain. A previous study suggested that multiple genetic components are responsible for the germline Tc1 activity of the BO strain. To analyze further this mutator activity, we derived hybrid strains between the BO strain and the N2 strain. One of the hybrid strains exhibits a single locus of mutator activity, designated mut-4, which maps to LGI. Two additional mutators, mut-5 II and mut-6 IV, arose spontaneously in mut-4 harboring strains. This spontaneous appearance of mutator activity at new sites suggests that the mutator itself transposes. The single mutator-harboring strains with low Tc1 copy number generated in this study should be useful in investigations of the molecular basis of mutator activity. As a first step toward this goal, we examined the Tc1 elements in these low copy number strains for elements consistently co-segregating with mutator activity. Three possible candidates were identified: none was larger than 1.6 kb. ------------------- Key: 1073 Medline: 89065352 Authors: Rogalski TM;Bullerjahn AME;Riddle DL Title: Lethal and amanitin-resistance mutations in the Caenorhabditis elegans ama-1 and ama-2 genes. Citation: Genetics 120: 409-422 1988 Type: ARTICLE Genes: ama-1 ama-2 dpy-11 sma-1 ctDf1 mDf3 mDf9 mDf10 mDp1 Abstract: Mutants of Caenorhabditis elegans resistant to alpha-amanitin have been isolated at a frequency of about 1.6 x 10(-6) after EMS mutagenesis of the wild-type strain, N2. Four new dominant resistance mutations have been studied genetically. Three are alleles of a previously identified gene, ama-1 IV, encoding the largest subunit of RNA polymerase II. The fourth mutation defines a new gene, ama-2 V. Unlike the ama-1 alleles, the ama-2 mutation exhibits a recessive- lethal phenotype. Growth and reproduction of N2 was inhibited at a concentration of 10 micrograms/ml amanitin, whereas ama-2/+ animals were inhibited at 100 micrograms/ml, and 800 micrograms/ml was required to inhibit growth of ama-1/+ larvae. We have also determined that two reference strains used for genetic mapping, dpy-11(e224)V and sma-1(e30)V, are at least four-fold more sensitive to amanitin that the wild-type strain. Using an amanitin-resistant ama-1(m118) or ama-1(m322) strain as a parent, we have isolated amanitin-sensitive mutants that carry recessive-lethal ama-1 alleles. The frequency of EMS-induced lethal ama-1 mutations is approximately 1.7 x 10(-3), 1000-fold higher than the frequency of amanitin-resistance alleles. Nine of the lethal alleles are apparent null mutations, and they exhibit L1-lethal phenotypes at both 20 degrees and 25 degrees. Six alleles result in partial loss of RNA polymerase II function as determined by their sterile phenotypes at 20 degrees. All but one of these latter mutations exhibit a more severe phenotype at 25 degrees C. We have also selected seven EMS-induced revertants of three different ama-1 lethals. These revertants restore dominant resistance to amanitin. The selection for revertants also produced eight new dominant amanitin resistance alleles on the balancer chromosome, nT1. ------------------- Key: 1074 Medline: 89065353 Authors: Bullerjahn AME;Riddle DL Title: Fine-structure genetics of ama-1, an essential gene encoding the amanitin-binding subunit of RNA polymerase II in Caenorhabditis elegans. Citation: Genetics 120: 423-434 1988 Type: ARTICLE Genes: ama-1 mDp1 Abstract: A fine-structure genetic map has been constructed for ama-1 IV, an essential gene in Caenorhabditis elegans encoding the amanitin- binding subunit of RNA polymerase II. Sixteen EMS-induced recessive- lethal mutations have been positioned in the gene by determining their intragenic recombination frequencies with m118, a mutation that confers dominant resistance to alpha-amanitin. The 16 mutants, all isolated in the ama-1(m118) background, include 13 that are early larval lethals, and three that are mid-larval lethals, at 25 degrees. Six of the mutants exhibit temperature-dependence in the severity of their phenotype. Intragenic recombination between the lethal site and the parental resistance mutation was detected by means of resistance to amanitin. Recombinants were detected at frequencies as low as 2 X 10(-6). The segregation of the closely linked flanking markers, unc- 17 and unc-5, revealed whether the lethal mutation was to the left or the right of m118. By adding the distances between the extreme left and right mutations, the ama-1 gene is estimated to be 0.011 map unit long, with m118 positioned 0.004 map unit from the left-most lethal mutation. To order the lethal mutations with respect to each other, viable heteroallelic strains were constructed using the free duplication, mDp1[unc-17(e113) dpy-13(+) ama-1(+)]. The heteroallelic strains were sensitive to amanitin, and recombination events between the lethal mutations were specifically selected by means of the dominant amanitin resistance encoded on the recombinant chromosome. The segregation of outside markers revealed the left-right order of the lethal mutations. The position of mutations within the gene is nonrandom. Functional domains of the ama-1 gene indicated ------------------- Key: 1075 Medline: 89065354 Authors: L'Hernault SW;Shakes DC;Ward S Title: Developmental genetics of chromosome I spermatogenesis-defective mutants in the nematode Caenorhabditis elegans. Citation: Genetics 120: 435-452 1988 Type: ARTICLE Genes: fer-1 fer-6 fer-7 spe-4 spe-5 spe-8 spe-9 spe-11 spe-12 spe-13 spe-15 Abstract: Mutations affecting Caenorhabditis elegans spermatogenesis can be used to dissect the processes of meiosis and spermatozoan morphological maturation. We have obtained 23 new chromosome I mutations that affect spermatogenesis (spe mutations). These mutations, together with six previously described mutations, identify 11 complementation groups, of which six are defined by multiple alleles. These spe mutations are all recessive and cause normally self-fertile hermaphrodites to produce unfertilized oocytes that can be fertilized by wild-type male sperm. Five chromosome I mutation/deficiency heterozygotes have similar phenotypes to the homozygote showing that the probable null phenotype of these genes is defective sperm. Spermatogenesis is disrupted at different steps by mutations in these genes. The maturation of 1 degree spermatocytes is disrupted by mutations in spe-4 and spe-5. Spermatids from spe-8 and spe-12 mutants develop into normal spermatozoa in males, but not in hermaphrodites. fer-6 spermatids are abnormal, and fer-1 spermatids look normal but subsequently become abnormal spermatozoa. Mutations in five genes (fer-7, spe-9, spe-11, spe-13 and spe-15) allow formation of normal looking motile spermatozoa that appear to be defective in either sperm-spermathecal or sperm-oocyte interactions. ------------------- Key: 1076 Medline: 88327846 Authors: Shen MM;Hodgkin J Title: mab-3, a gene required for sex-specific yolk protein expression and a male-specific lineage in C. elegans. Citation: Cell 54: 1019-1031 1988 Type: ARTICLE Genes: lin-22 mab-3 tra-1 tra-2 Abstract: The gene mab-3 appears to regulate a subset of sex-specific events in C. elegans male development. Mutations in mab-3 have no apparent effect on hermaphrodites, but cause synthesis of yolk proteins and a limited lineage alteration in males. We infer that mab-3 has at least two distinct male-specific functions. First, mab-3 activity prevents yolk protein production by males, without affecting stage or tissue specificity of expression. Second, mab-3 activity is required for expression of the male V ray cell lineage. Epistasis analysis is most consistent with a model in which mab-3 is controlled by tra-1, the last switch gene known to act in the somatic sex determination pathway. We discuss how genes such as mab-3 might generate sexual dimorphism. ------------------- Key: 1077 Medline: 89003045 Authors: Miller LM;Plenefisch JD;Casson LP;Meyer BJ Title: xol-1: A gene that controls the male modes of both sex determination and X chromosome dosage compensation in C. elegans. Citation: Cell 55: 167-183 1988 Type: ARTICLE Genes: dpy-21 dpy-26 dpy-27 dpy-28 fem-1 fem-3 her-1 myo-2 sdc-1 sdc-2 tra-1 tra-2 tra-3 uvt-4 xol-1 uDf1 yDf5 Abstract: Loss-of-function mutations in the X-linked gene xol-1 cause the feminization and death of XO animals (normally males) by shifting the sex determination and dosage compensation pathways toward their hermaphrodite modes. XO-specific lethality most likely results from the reduction in X chromosome expression caused by xol-1 mutations. Mutations in genes required for the hermaphrodite mode of dosage compensation suppress lethality but not feminization, and restore X chromosome expression to nearly wild-type levels. Mutations in genes that control the hermaphrodite modes of both sex determination and dosage compensation fully suppress both defects. These interactions suggest that xol-1 is the earliest-acting gene in the known hierarchy controlling the male/hermaphrodite decision and is perhaps the gene nearest the primary sex-determining signal. We propose that the wild- type xol-1 gene product promotes male development by ensuring that genes (or gene products) directing hermaphrodite sex determination and dosage compensation are inactive in XO animals. Interestingly, in addition to feminizing XO animals, xol-1 mutations further masculinize XX animals already partially masculinized. ------------------- Key: 1078 Medline: 89044874 Authors: Williams PL;Dusenbery DB Title: Using the nematode C. elegans to predict mammalian acute lethality to metallic salts. Citation: Toxicology and Industrial Health 4: 469-478 1988 Type: ARTICLE Genes: Abstract: The acute lethality of the salts of eight metals--HgCl2, BeSO4.4H2O, Al(NO3)3.9H2O, CuCl2.2H2O, ZnCl2, Pb(NO3)2, CdCl2, and Sr(NO3)2--was determined using a type of free-living nematode, Caenorhabditis elegans. The LC50 values were compared to the published mammalian oral LD50 values for salts of the same metals. Within this set of chemicals, C. elegans was found to be a predictor of mammalian acute lethality, generating LC50 values parallel to the rat and mouse LD50 values. The total expenses for this testing are about 10% of the cost for mammalian acute lethality testing. The method is considered to have great promise, but further study is needed. ------------------- Key: 1079 Medline: 89089832 Authors: Pavalko FM;Roberts TM;Holliday LS Title: Relationship between plasma membrane mobility and substrate attachment in the crawling movement of spermatozoa from Caenorhabditis elegans. Citation: Cell Motility and the Cytoskeleton 11: 16-23 1988 Type: ARTICLE Genes: him-5 Abstract: Caenorhabditis elegans sperm are nonflagellated cells that lack actin and myosin yet can form pseudopods to propel themselves over solid substrates. Surface-attached probes such as latex beads, lectins, and antimembrane protein monoclonal antibodies move rearward over the dorsal pseudopod surface of sessile cells. Using monoclonal antibodies against membrane proteins of C. elegans sperm to examine the role of localized membrane assembly and rearward flow in crawling movement, we determined that substrates prepared by coating glass with antimembrane protein antibodies, but not naked glass or other nonmembrane-binding proteins, promote sperm motility. Sperm locomotion is inhibited in a concentration-dependent fashion when cells are bathed with soluble antimembrane protein monoclonal antibodies but not with antimouse Ig antibodies or a monoclonal antibody against a sperm cytoplasmic protein. Our results suggest that C. elegans sperm crawl by gaining traction with substrate- attached ligands via their surface proteins and by using the motor that moves those proteins rearward on unattached cells to pull the entire cell forward. Continuous insertion of new proteins at the front of the cell and their subsequent adhesion to the substrate allows this process to continue. ------------------- Key: 1080 Medline: 88334747 Authors: Yochem J;Weston K;Greenwald I Title: The Caenorhabditis elegans lin-12 gene encodes a transmembrane protein with overall similarity to Drosophila Notch. Citation: Nature 335: 547-550 1988 Type: ARTICLE Genes: lin-12 Abstract: The lin-12 gene seems to control certain binary decisions during Caenorhabditis elegans development, from genetic and anatomical studies of lin-12 mutants that have either elevated or reduced levels of lin-12 activity. We report here the complete DNA sequence of lin- 12: 13.5 kilobases (kb) derived from genomic clones and 4.5 kb from complementary DNA clones. It is of interest that the predicted product is a putative transmembrane protein, given that many of the decisions controlled by lin-12 activity require cell-cell interactions for the correct choice of cell fate. In addition, the predicted lin-12 product may be classified into several regions, based on amino acid sequence similarities to other proteins. These include extensive overall sequence similarity to the Drosophila Notch protein, which also is involved in cell-cell interactions that specify cell fate; a repeated motif found in proteins encoded by the yeast cell-cycle control genes cdc10 (Schizosaccharomyces pombe) and SW16 (Saccharomyces cerevisiae); and a repeated motif exemplified by epidermal growth factor, found in many ------------------- Key: 1081 Medline: 88334748 Authors: Sternberg PW Title: Lateral inhibition during vulval induction in Caenorhabditis elegans. Citation: Nature 335: 551-554 1988 Type: ARTICLE Genes: lin-15 Abstract: During Caenorhabditis elegans vulval induction the anchor cell of the gonad specifies a spatial pattern of three cell types among a set of six multipotent epidermal cells, the vulval precursor cells (VPCs). Previous studies suggested that the anchor cell produces a graded inductive signal which can directly stimulate VPCs away from a ground state (type 3) to become type 1 or type 2 depending on their distance from the anchor cell. Here, we investigate the interactions among VPCs in a mutant, lin-15, in which VPC fates are rendered partially independent of the inductive signal, and show that type 1 cells actively inhibit adjacent cells from also becoming type 1 cells. The fate of each VPC therefore depends on the combined action of two intercellular signals: a graded inductive signal from the anchor cell, and a lateral inhibitory signal from at least some of its neighbours. Pattern formation among the VPCs lin-15 mutant is analogous to the establishment of the pattern of neuroblasts and dermatoblasts during early insect neurogenesis, suggesting that the similarities in inferred molecular structure of the lin-12 and Notch gene products, which are involved in these two instances of pattern formation, might extend to similarities in ------------------- Key: 1082 Medline: 88334750 Authors: Van Doren K;Hirsh D Title: Trans-spliced leader RNA exists as small nuclear ribonucleoprotein particles in Caenorhabditis elegans. Citation: Nature 335: 556-559 1988 Type: ARTICLE Genes: Abstract: Maturation of some messenger RNAs in the nematode Caenorhabditis elegans involves the acquisition of a 22-base leader at their 5' ends. This 22-base leader, called the spliced leader (SL), is derived from the 5' end of a precursor RNA of 90-100 bases, called spliced leader RNA (SL RNA). SL RNA is transcribed from a 1-kilobase DNA repeat which also encodes the 5S ribosomal RNA. A subset of mRNAs in C. elegans acquire SL from SL RNA by a trans-splicing mechanism. SL behaves as a 5' exon in the trans-splicing reaction. Using antisera against the Sm antigen that is associated with small nuclear ribonucleoprotein particles (snRNPs), we precipitated SL RNA from extracts of C. elegans, indicating that it is bound by the Sm antigen in vivo. SL RNA also possesses the unique trimethylguanosine (m32,2,7G) cap characteristic of most small nuclear RNAs. Therefore, SL RNA is a chimaeric molecule, made up of an snRNA attached to a 5' exon and is ------------------- Key: 1083 Medline: 88334751 Authors: Bruzik JP;Van Doren K;Hirsh D;Steitz JA Title: Trans splicing involves a novel form of small nuclear ribonucleoprotein particles. Citation: Nature 335: 559-562 1988 Type: ARTICLE Genes: Abstract: The trans-splicing reaction occurring in trypanosomes and related species as well as in the nematode Caenorhabditis elegans involves the transfer of a 5' exon from a spliced leader transcript (SL RNA) to a precursor messenger RNA transcript with a 3' splice acceptor site. This seems to take place in the same nuclear compartment as normal cis splicing and proceeds through Y-branched intermediates analogous to the lariats formed in cis splicing. The cellular machinery catalysing cis and trans splicing might therefore be expected to share some commponents, particularly in the nematode where some mRNAs are produced by both cis and trans splicing. We generated possible secondary structures for the SL RNAs of several species and found they were remarkably similar although neither nucleotide sequence nor length is conserved. Each contained three stem-loops; strikingly the 5' splice site is adjacent to the turn of the most 5' loop and an Sm-binding consensus sequence is found between the second and third stem-loops. Sm is an antigen associated with small nuclear ribonucleoprotein particles (snRNPs). When incubated in HeLa cell nuclear extracts, SL RNAs become immunoprecipitable by anti-Sm, but not by other autoantibodies directed against proteins of mammalian snRNPs. We propose that SL RNAs have a dual function in the trans splicing process: they consist of a 5' exon covalently linked to an snRNA-like sequence and seem likely to exist as Sm snRNP particles (SL snRNPs) within the cell. Just as the RNA in the U1 snRNP base-pairs with the 5' splice site, rendering it susceptible to attack in the cis-splicing reaction, so might the SL snRNP autonomously activate its own 5' splice site and thereby eliminate the need for a U1-like snRNP in the trans-splicing machinery. ------------------- Key: 1084 Medline: Authors: Vanfleteren JR;Meheus LA Title: Analysis of the chromosomal proteins of Caenorhabditis elegans by two-dimensional electrophoresis, silver staining and immunodetection. Citation: Comparative Biochemistry & Physiology 91B: 103-110 1988 Type: ARTICLE Genes: Abstract: 1. The chromatin proteins of the nematode Caenorhabditis elegans have been analysed by two-dimensional polyacrylamide gel electrophoresis. 2. Several amendations to the original technique are described, which enable good resolution of highly concentrated samples of nuclear protein (up to 600 ug/gel) on silverstained gels. 3. The presence of DNA in the protein sample, though having no adverse effect on the separation of proteins by non-equilibrium pH gradient electrophoresis causes the loss of a considerable amount of basic proteins. 4. However, DNA can be removed prior to electrophoresis by the aquous two-phase procedure of Bidney and Reek with negligible effect on the composition of the protein sample. 5. Several proteins have been localized on the two-dimensional protein maps, that are specifically associated with nuclear RNA, but co-extract with the chromatin proteins. 6. Actin is a major non-histone component, whereas tubulin is ------------------- Key: 1085 Medline: 89064939 Authors: Johnson TE;Conley WL;Keller ML Title: Long-lived lines of Caenorhabditis elegans can be used to establish predictive biomarkers of aging. Citation: Experimental Gerontology 23: 281-295 1988 Type: ARTICLE Genes: Abstract: Long-lived recombinant inbred lines, some of which have mean and maximum life spans up to 70% longer than wild type, were used in these analyses. Longer life results from a slower exponential rate of increase in mortality. General motor activity decreases with chronological age in all genotypes; this decay in general motor activity is a biomarker of aging in that it is a predictor of maximum life span. The aging process has also been dissected into component processes. The length of development and the length of reproduction are unrelated to increased life span; lengthened life is due entirely to an increase in post-reproductive life span. Development, reproduction, and life span are each under independent genetic control. General motor activity and life span share at least one common rate-determining genetic component. ------------------- Key: 1086 Medline: 89149701 Authors: Hevelone J;Hartman PS Title: An endonuclease from Caenorhabditis elegans: Partial purification and characterization. Citation: Biochemical Genetics 26: 447-461 1988 Type: ARTICLE Genes: nuc-1 Abstract: A deoxyribonuclease was partially purified from the free-living nematode Caenorhabditis elegans. The DNase functioned as an endonuclease and introduced both single-strand nicks and double- strand breaks into DNA. The enzyme hydrolyzed double-stranded DNA seven times more rapidly than single-stranded DNA. DNase activity was not affected by the addition of divalent cations below 1 mM but was inhibited at higher ionic concentrations. In addition, the enzyme was not inhibited in the presence of 10 mM EDTA. The enzyme was inhibited by salt concentrations greater than 20 mM. Three independent mutations in the nuc-1 gene were shown to reduce nuclease activity to less than 1% of that seen in wild-type organisms. ------------------- Key: 1087 Medline: 89120211 Authors: Lerner K;Goldstein P Title: Electron microscopic autoradiographic analysis: evidence of RNA transcription along pachytene chromosomes of rad-4, him-4 and wild-type Caenorhabditis elegans. Citation: Cytobios 55: 51-61 1988 Type: ARTICLE Genes: him-4 rad-4 Abstract: Decondensed chromatin regions have been described along the pachytene chromosomes of Caenorhabditis elegans (Goldstein, 1985). Regions of similar appearance, but not in pachytene chromosomes, have been shown to be transcriptionally active in other organisms (Angelier et al., 1979; Nagl, 1985). Incorporation of tritiated-uridine and electron microscopy autoradiography were utilized, in the present study, to determine if RNA transcription occurred along meiotic chromosomes of C. elegans. This study presents new evidence that RNA transcription occurs in highly defined regions along pachytene bivalents. ------------------- Key: 1088 Medline: 88335585 Authors: La Volpe A;Ciaramella M;Bazzicalupo P Title: Structure, evolution and properties of a novel repetitive DNA family in Caenorhabditis elegans. Citation: Nucleic Acids Research 16: 8213-8231 1988 Type: ARTICLE Genes: nuc-1 Abstract: We have identified a moderately repeated DNA sequence in Caenorhabditis elegans present at least at twenty different locations in the genome. Elements of this intermingled repetitive DNA family are made up of tandem subreapeats whose smaller unit is ten base pairs long. The occurrence of single base changes between units is reminiscent of mammalian satellite DNA. Sequence analysis has shown that the consensus of these repeats is identical to the consensus of the heat-shock element (HSE) common to all eukaryotes (C--GAA--TTC-- G). This consensus in our sequences is repeated in tandem with an overlap of four bases (C--GAA--TTC--GAA--TTC...). We studied in detail one cloned element of the family and we were unable to detect transcription in the flanking regions either under normal growth or after heat induction. Nevertheless a 242 bp sequences out of this same element was sufficient, when located on a multicopy plasmid in Saccharomyces cerevisiae, to drive transcription from a downstream gene under heat shock conditions. ------------------- Key: 1089 Medline: 89076229 Authors: Vanfleteren JR;Van Bun SM;Van Beeumen JJ Title: The primary structure of the major isoform (H1.1) of histone H1 from the nematode Caenorhabditis elegans. Citation: Biochemical Journal 255: 647-652 1988 Type: ARTICLE Genes: Abstract: The complete primary structure of the major isoform (H1.1) of histone H1 from the nematode Caenorhabditis elegans was determined. The amino acid chain consists of 207 amino acids and has a blocked N-terminus. The nematode histone shows rather little sequence identity when compared with proteins of the H1 family derived from other organisms. However, the main characteristic features of H1 molecules have been well conserved: a tripartite domain structure consisting of a central hydrophobic core of about 80 residues, flanked by an N-terminal domain which is somewhat acidic at the very N-terminus, but very basic further on, and a long C-terminal domain very rich in lysine, alanine and proline. Several repeat structures, including a twice (with modification)-repeated and well-conserved phosphorylation site, can be recognized in this region. The presence of O-phosphoserine at these sites could not be demonstrated, however. ------------------- Key: 1090 Medline: 89079002 Authors: Bektesh S;Van Doren K;Hirsh D Title: Presence of the Caenorhabditis elegans spliced leader on different mRNAs and in different genera of nematodes. Citation: Genes & Development 2: 1277-1283 1988 Type: ARTICLE Genes: act-1 act-2 act-3 act-4 unc-54 Abstract: Several different mRNAs from Caenorhabditis elegans contain the same 22-nucleotide leader sequence at their 5' ends that is acquired in a trans-splicing reaction. About 10 to 15% of the major proteins are translated from mRNAs that contain the spliced leader, among them two ribosomal proteins, ubiquitin, GAPDH, a heat shock protein (hsp70a), and three actins. The same spliced leader sequence is present in mRNAs isolated from nematodes from several different genera; but it is not present in mRNAs from other organisms. The spliced leader is encoded as a spliced leader (SL) RNA about 100 nucleotides long. The gene for the SL RNA is located in the 5S rDNA repeat in C. elegans; however, this association with the 5S repeat is not preserved in other genera. The 22-nucleotide spliced leader sequence is conserved in three genera of nematodes. ------------------- Key: 1091 Medline: 89079005 Authors: Bejsovec A;Anderson P Title: Myosin heavy chain mutations that disrupt Caenorhabditis elegans thick filament assembly. Citation: Genes & Development 2: 1307-1317 1988 Type: ARTICLE Genes: unc-54 eDf10 Abstract: We have investigated Caenorhabditis elegans mutants in which altered unc-54 myosin heavy-chain protein interferes with assembly of thick myofilaments. These mutants have a dominant, muscle-defective phenotype, because altered myosin heavy-chain B (MHC B), the product of the unc-54 gene, disrupts assembly of wild-type MHC B. The mutant MHC B also interferes with assembly of wild-type myosin heavy-chain A (MHC A), the product of another MHC gene expressed in body-wall muscle cells. Because of disrupted MHC A assembly, dominant unc-54 mutants also exhibit a recessive-lethal phenotype. Dominant unc-54 mutations are missense alleles, and the defects in thick filament assembly result from mutant protein that is of normal molecular weight. Accumulation of mutant MHC B in amounts as little as 2% of wild-type levels is sufficient to disrupt assembly of both wild-type MHC A and MHC B. Dominant unc-54 mutations occur at remarkably high frequency following ethylmethane sulfonate (EMS) mutagenesis; their frequency is approximately equal to that of recessive, loss-of- function mutations. This unusually high gain-of-function frequency implies that many different amino acid substitutions in the myosin heavy-chain B protein can disrupt thick filament assembly. ------------------- Key: 1092 Medline: 89043983 Authors: McCoubrey WK;Nordstrom KD;Meneely PM Title: Microinjected DNA from the X chromosome affects sex determination in Caenorhabditis elegans. Citation: Science 242: 1146-1151 1988 Type: ARTICLE Genes: act-3 act-4 lin-12 mlc-1 mlc-2 myo-2 mnDp8 Abstract: The signal for sex determination in the nematode Caenorhabditis elegans is the ratio of the number of X chromosomes to the number of sets of autosomes (X/A ratio). By previous genetic tests, elements that feminized chromosomal males appeared to be widespread on the X chromosome, but the nature of these elements was not determined. In experiments to define a feminizing element molecularly, cloned sequences were added to chromosomally male embryos by microinjection into the mother. Three different X-chromosome clones, including part of an actin gene, part of a myosin heavy chain gene, and all of two myosin light chain genes, feminize chromosomal males. Both somatic and germline aspects of sex determination are affected. In contrast, about 40 kilobases of nematode autosomal DNA, phage lambda DNA, and plasmid pBR322 DNA do not affect sex determination. A feminizing region was localized to a maximum of 131 base pairs within an intron of the X-linked actin gene; a part of the gene that does not have this region is not feminizing. The results suggest that short, discrete elements found associated with many X-linked genes may act as signals for sex determination in C. elegans. ------------------- Key: 1093 Medline: 89057054 Authors: Coohill T;Marshall T;Schubert W;Nelson G Title: Ultraviolet mutagenesis of radiation-sensitive (rad) mutants of the nematode Caenorhabditis elegans. Citation: Mutation Research 209: 99-106 1988 Type: ARTICLE Genes: rad-1 rad-3 rad-7 Abstract: A mutational tester strain (JP10) of the nematode C. elegans was used to capture recessive lethal mutations in a balanced 300 essential gene autosomal region. The probability of converting a radiation interaction into a lethal mutation was measured in young gravid adults after exposure to fluences of 254-nm ultraviolet radiation (UV) ranging from 0 to 300 Jm-2. Mutation frequencies as high as 5% were observed. In addition, three different radiation-hypersensitive mutations, rad-1, rad-3 and rad-7 were incorporated into the JP10 background genotype, which allowed us to measure mutation frequencies in radiation-sensitive animals. The strain homozygous for rad-3 was hypermutable to UV while strains homozygous for rad-1 and rad-7 were hypomutable. Data showing the effects of UV on larval development and fertility for the rad mutants is also shown and compared for wild- type and JP10 ------------------- Key: 1094 Medline: 89218994 Authors: Cummins C;Anderson P Title: Regulatory myosin light-chain genes of Caenorhabditis elegans. Citation: Molecular and Cellular Biology 8: 5339-5349 1988 Type: ARTICLE Genes: mlc-1 mlc-2 Abstract: We have cloned and analyzed the Caenorhabditis elegans regulatory myosin light-chain genes. C. elegans contains two such genes, which we have designated mlc-1 and mlc-2. The two genes are separated by 2.6 kilobases and are divergently transcribed. We determined the complete nucleotide sequences of both mlc-1 and mlc-2. A single, conservative amino acid substitution distinguishes the sequences of the two proteins. The C. elegans proteins are strongly homologous to regulatory myosin light chains of Drosophila melanogaster and vertebrates and weakly homologous to a superfamily of eucaryotic calcium-binding proteins. Both mlc-1 and mlc-2 encode abundant mRNAs. We mapped the 5' termini of these transcripts by using primer extension sequencing of mRNA templates. mlc-1 mRNAs initiate within conserved hexanucleotides at two different positions, located at -28 and -38 relative to the start of translation. The 5' terminus of mlc- 2 mRNA is not encoded in the 4.8-kilobase genomic region upstream of mlc-2. Rather, mlc-2 mRNA contains at its 5' end a short, untranslated leader sequence that is identical to the trans-spliced leader sequence of three C. elegans actin ------------------- Key: 1095 Medline: 89083500 Authors: Warren T;Pasternak JJ Title: A related moderately repetitive DNA family in the nematodes Ascaris lumbricoides and Panagrellus silusiae. Citation: Nucleic Acids Research 16: 10833-10847 1988 Type: ARTICLE Genes: Abstract: Digestion of genomic DNA from the nematodes Panagrellus silusiae and Ascaris lumbricoides with restriction endonuclease BamH1 releases a 0.7 kilobase (kb) fragment. The 0.7 kb fragment from both nematodes was cloned onto E. coli plasmid pUC19. Using representative clones as DNA hybridization probes, it was found that (i) the BamH1 fragments cross-hybridize; (ii) a ladder-effect with multiples of 0.7 kb was evident in both species after hybridization to genomic DNA and (iii) the genomic copy number of BamH1 elements is 150 and 195 for P. silusiae and A. lumbricoides respectively. DNA sequence analysis of the inserts, AL700-1 and PS700-1, revealed nucleotide blocks with over 85% similarity. No open reading frames are present in either DNA fragment. Neither fragment hybridizes to genomic DNA from Caenorhabditis elegans. Northern blot hybridization indicated that the 0.7 kb element is transcribed into poly (A)- -RNA in P. silusiae; but it is not transcribed in adult Ascaris muscle. Thus, P. silusiae and A. lumbricoides share a homologous, tandemly arrayed, moderately repetitive DNA family. ------------------- Key: 1096 Medline: 89031693 Authors: Sternberg PW;Horvitz HR Title: lin-17 mutations of Caenorhabditis elegans disrupt certain asymmetric cell divisions. Citation: Developmental Biology 130: 67-73 1988 Type: ARTICLE Genes: lin-17 Abstract: The identification of a gene necessary for the asymmetry of cell division would be an important first step toward understanding how sister cells come to differ in their developmental fates. The lin-17 gene of the nematode Caenorhabditis elegans is an excellent candidate for being such a gene. lin-17 mutations cause several blast cells that normally generate sister cells of two distinct types to generate instead sister cells of the same type. Moreover, lin-17 mutations cause sister cells to be equal in size as well as equivalent in developmental fate, suggesting that lin-17 acts at or prior to the asymmetric cell division. The lin-17 gene product is involved in asymmetric cell divisions in a variety of tissues, indicating that lin-17 functions in a general mechanism for the establishment of cellular asymmetry in parent cells. ------------------- Key: 1097 Medline: 89031676 Authors: Spieth J;MacMorris M;Broverman S;Greenspoon S;Blumenthal T Title: Regulated expression of a vitellogenin fusion gene in transgenic nematodes. Citation: Developmental Biology 130: 285-293 1988 Type: ARTICLE Genes: vit-2 vit-6 Abstract: In Caenorhabditis elegans the vitellogenin genes are expressed abundantly in the adult hermaphrodite intestine, but are otherwise silent. In order to begin to understand the mechanisms by which this developmental regulation occurs, we used the transformation procedure developed for C. elegans by A. Fire (EMBO. J., 1986, 5, 2673-2680) to obtain regulated expression of an introduced vitellogenin fusion gene. A plasmid with vit-2 upstream and coding sequences fused to coding and downstream sequences of vit-6 was injected into oocytes and stable transgenic strains were selected. We obtained seven independent strains, in which the plasmid DNA is integrated at a low copy number. All strains synthesize substantial amounts of a novel vitellogenin-like polypeptide of 155 kDa that accumulates in the intestine and pseudocoelom, but is not transported efficiently into oocytes. In two strains examined in detail the fusion gene is expressed with correct sex, tissue, and stage specificity. Thus we have demonstrated that the nematode transgenic system can give proper developmental expression of introduced genes and so can be used to identify DNA regulatory regions. ------------------- Key: 1098 Medline: 89042198 Authors: Wadsworth WG;Riddle DL Title: Acidic intracellular pH shift during Caenorhabditis elegans larval development. Citation: Proceedings of the National Academy of Sciences USA 85: 8435-8438 1988 Type: ARTICLE Genes: daf-2 daf-7 Abstract: During recovery from the developmentally arrested, nonfeeding dauer stage of the nematode Caenorhabditis elegans, metabolic activation is accompanied by a decrease in intracellular pH (pHi). Phosphorus-31 nuclear magnetic resonance (31P NMR) analyses of perchloric acid extracts show that inorganic phosphate predominates in dauer larvae, whereas ATP and other high-energy metabolites are abundant within 6 hr after dauer larvae have been placed in food to initiate development. Although metabolic activation has been associated with an alkaline pHi shift in other organisms, in vivo 31P NMR analysis of recovering dauer larvae shows a pHi decrease from approximately 7.3 to approximately 6.3 within 3 hr after the animals encounter food. This shift occurs before feeding begins, and it coincides with, or soon follows, the developmental commitment to recover from the dauer stage, suggesting that control of pHi may be important in the regulation of larval ------------------- Key: 1099 Medline: Authors: Fields C Title: Domain organization and intron positions in Caenorhabditis elegans collagen genes: The 54-bp module hypothesis revisited. Citation: Journal of Molecular Evolution 28: 55-63 1989 Type: ARTICLE Genes: col-1 col-2 col-6 col-7 col-8 col-14 col-19 Abstract: The amino acid (aa) sequences of the polypeptides encoded by five collagen genes of the nematode Caenorhabditis elegans, col-6, col-7 (partial), col-8, col-14, and col-19, were determined. These collagen polypeptides, as well as those encoded by the previously sequenced C. elegans collagen genes col-1 and col-2, share a common organization into five domains: an amino-terminal leader, a short (30-33 aa) (Gly- X-Y)n domain, a non(Gly-X-Y) spacer, a long (127-132 aa) (Gly-X-Y)n domain, and a short carboxyl-terminal domain. The domain organizations and intron positions of these polypeptides were compared with those of the polypeptides encoded by Drosophila and Strongylocentrotus type IV, and vertebrate types I, II, III, IV, and IX collagen genes; the C. elegans collagen polypeptides are most similar to the vertebrate type IX collagens. It is suggested that the collagen gene family comprises two divergent subfamilies, one of which includes the vertebrate interstitial collagen genes, and the other of which includes the invertebrate collagen genes and the vertebrate type IV and type IX collagen genes. Only the vertebrate interstitial collagen genes display clear evidence of evolution via the tandem duplication of a 54-bp ------------------- Key: 1100 Medline: 89028667 Authors: Kramer JM;Johnson JJ;Edgar RS;Basch C;Roberts S Title: The sqt-1 gene of C. elegans encodes a collagen critical for organismal morphogenesis. Citation: Cell 55: 555-565 1988 Type: ARTICLE Genes: rol-6 sqt-1 mnDf75 mnDf76 mnDf77 mnDf86 Abstract: Different mutations in the sqt-1 gene of C. elegans can lengthen, shorten, or helically twist the entire animal. We have cloned the sqt- 1 gene and have shown that it encodes a collagen. sqt-1 was localized to a 35 kb region of DNA by physical mapping of chromosomal deficiencies. A transposon (Tc1)-induced mutation of sqt-1 was generated and utilized to identify the sqt-1 gene within this 35 kb region. Sequence analysis of the sqt-1 gene shows that it encodes a 32 kd collagen polypeptide that is similar in size and structure to other members of the C. elegans collagen family. The Tc1 insertion mutant has no detectable sqt-1 transcripts, yet it is morphologically normal, indicating that the null phenotype of sqt-1 is wild type. These results demonstrate that collagen mutations can have dramatic effects on organismal morphology. ------------------- Key: 1101 Medline: 89028668 Authors: von Mende N;Bird DMcK;Albert PS;Riddle DL Title: dpy-13: A nematode collage gene that affects body shape. Citation: Cell 55: 567-576 1988 Type: ARTICLE Genes: col-1 col-2 col-33 col-34 dpy-13 mDf4 Abstract: Mutations in the Caenorhabditis elegans dpy-13 (dumpy) gene result in a short, chunky body shape. This gene was tagged by insertion of the Tc1 transposon, and the wild-type gene was cloned by chromosomal walking 11 kb from ama-1, a cloned gene encoding the large subunit of RNA polymerase II. Three transposon insertion sites in dpy-13 are located near the 5' end of a 1.2 kb transcribed region. The EMS- induced reference allele, dpy-13(e184), carries a small deletion near the middle of this gene. The DNA sequence reveals that dpy-13 is a member of the collagen multi-gene family, and it could encode a polypeptide of 302 amino acids. A 146 base pair sequence, encoding amino acids 56-103, is unique in the C. elegans genome, and it hybridizes to a 1 kb mRNA of moderate abundance. ------------------- Key: 1102 Medline: 89187951 Authors: Blumenthal T;Thomas J Title: Cis and trans mRNA splicing in C. elegans. Citation: Trends in Genetics 4: 305-308 1988 Type: REVIEW Genes: Abstract: Nematodes are the only organisms in which both cis- and trans-splicing of nuclear mRNAs are known to occur. Despite some unusual characteristics of introns in C. elegans, the nematode splicing machinery is quite similar to that described in other organisms. Nematodes contain a novel snRNP, the RNA moiety of which donates its 5' end to many different transcripts by trans-splicing. In the course of molecular analysis of developmentally interesting genes in the nematode Caenorhabditis elegans, some intriguing observations have been made regarding RNA splicing. Most interesting is the discovery that some, but not all, actin mRNAs receive a 22-nucleotide leader sequence by trans-splicing. In nematodes, the same mRNAs are substrates for both cis- and trans-splicing. This juxtaposition offers a unique opportunity to study the relationship between these two types of reactions. In this review we summarize some unique characteristics of cis-spliced introns in C. elegans as well as data suggesting that this nematode has a typical array of snRNPs. We describe the discovery of trans-splicing in the actin gene family and summarize results showing that many other mRNAs are also trans-spliced. Finally, observations bearing on the mechanism and function of trans-splicing in C. elegans are considered. ------------------- Key: 1103 Medline: 89056610 Authors: Schaeffer JM;Bergstrom AR Title: Identification of gamma-aminobutyric acid and its binding sites in Caenorhabditis elegans. Citation: Life Sciences 43: 1701-1706 1988 Type: ARTICLE Genes: Abstract: Gamma-aminobutyric acid (GABA), glutamate decarboxylase and GABA-transaminase were identified in the nematode Caenorhabditis elegans. The concentration of GABA in C. elegans (0.14 ug/mg protein) is approximately 10-fold lower than the concentration of GABA in rat brain. Glutamate decarboxylase and GABA-transaminase, the GABA anabolic and catabolic enzymes, are also present in C. elegans. Crude membrane fractions were prepared from C. elegans and used to study specific [3H] GABA binding sites. GABA binds to C. elegans membranes with high affinity (37 nM) and low capacity (Bmax= 2.25 pmol/mg protein). Muscimol is a competitive inhibitor of specific GABA binding with a KI value 120 nM. None of the other GABA agonists or antagonists inhibited greater than 40% of the specific GABA binding at concentrations up to 10 -4M. Thirteen spider venoms were examined as possible GABA agonists or antagonists, the venom from Calilena agelenidae inhibits specific GABA binding with a KI value of 6 nl/ml. These results suggest that GABA has a physiological role as a neurotransmitter in C. elegans. ------------------- Key: 1104 Medline: 89042100 Authors: Takacs AM;Denker JA;Perrine KG;Maroney PA;Nilsen TW Title: A 22-nucleotide spliced leader sequence in the human parasitic nematode Brugia malayi is identical to the trans-spliced leader exon in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 85: 7932-7936 1988 Type: ARTICLE Genes: Abstract: The mRNAs encoding a 63-kDa antigen in the human parasitic nematode Brugia Malayi contain a spliced leader sequence of 22 nucleotides (nt) that is identical to the trans-spliced leader found on certain actin mRNAs in the distantly related nematode Caenorhabditis elegans. The 22-nt sequence does not appear to be encoded near the 63-kDa genes but is present in multiple copies in several locations within the parasite genome, including the 5S rRNA gene repeat. The 5S-linked copies of the 22-nt sequence are transcribed to yield a 109-nt nonpolyadenylated RNA with the 22-nt leader sequence at its 5' end. We suggest that the 22-nt leader is acquired by 63-kDa antigen mRNAs through trans-splicing. These results indicate that trans-splicing is widespread in nematodes and argue for the functional significance of the 22-nt spliced leader exon in nematode mRNA metabolism. ------------------- Key: 1105 Medline: 89070695 Authors: Desai C;Garriga G;McIntire SL;Horvitz HR Title: A genetic pathway for the development of the Caenorhabditis elegans HSN motor neurons. Citation: Nature 336: 638-646 1988 Type: REVIEW Genes: cat-1 cat-4 egl-1 egl-5 egl-10 egl-18 egl-20 egl-27 egl-41 egl-42 egl-43 egl-44 egl-45 egl-46 egl-47 egl-49 egl-50 ham-1 ham-2 ham-3 her-1 mig-1 mig-2 mig-10 mig-12 sem-4 tra-2 unc-6 unc-33 unc-34 unc-40 unc-51 unc-71 unc-73 unc-76 unc-86 Abstract: Thirty-five genes define a pathway for the development of the hermaphrodite-specific neurons (HSNs) in Caenorhabditis elegans. Some of these genes affect only one HSN trait, demonstrating that HSN migration, axonal outgrowth and serotonin expression are mutually independent events in HSN development; others, some of which are regulatory, affect multiple HSN traits. Nearly all are pleiotropic, revealing that the genes specifying HSN development also function in the development of other cell types. ------------------- Key: 1106 Medline: 89051865 Authors: Costa M;Weir M;Coulson A;Sulston J;Kenyon C Title: Posterior pattern formation in C. elegans involves position-specific expression of a gene containing a homeobox. Citation: Cell 55: 747-756 1988 Type: ARTICLE Genes: mab-5 Abstract: During postembryonic development in C. elegans, posterior-specific pattern formation requires the gene mab-5. Within the posterior body region, mab-5 activity controls epidermal, neuronal, and mesodermal cell differentiation, and also the direction of cell migration. Here, we show that mab-5 RNA is localized in the posterior body region, indicating that mab-5 activity is targeted to posterior cells, at least in part, by a mechanism that operates at the level of mab-5 RNA synthesis or stabilization. We also show that mab-5 contains a homeobox similar to that of the Drosophila Antennapedia gene. This suggests that mab-5 influences cell differentiation and cell migration by regulating gene expression, and clearly demonstrates that genes containing homeoboxes influence global aspects of pattern formation in organisms other than Drosophila. ------------------- Key: 1107 Medline: 89051866 Authors: Finney M;Ruvkun G;Horvitz HR Title: The C. elegans cell lineage and differentiation gene unc-86 encodes a protein with a homeodomain and extended similarity to transcription factors. Citation: Cell 55: 757-769 1988 Type: ARTICLE Genes: mec-3 unc-86 Abstract: Mutations in the gene unc-86 affect development of the nematode C. elegans by altering cell lineages and cell differentiation. We molecularly cloned unc-86 by chromosomal walking from linked polymorphic genetic loci, and identified the gene by locating polymorphisms specific for unc-86 alleles. A transcript containing a 467 amino acid open reading frame was inferred from the DNA sequence of a genomic clone. The unc-86 transcript encodes a protein containing a 158 amino acid sequence, referred to as the pou ("pow") domain, which is strikingly similar to sequences found in three mammalian transcription factors. Within this conserved region, there is a homeodomain related to but distinct from homeodomains previously identified in Drosophila and other organisms. These findings suggest that unc-86 encodes a transcription factor, and that the related mammalian transcription factors may function to control cell fates and cell ------------------- Key: 1108 Medline: Authors: Rosenbluth RE;Rogalski TM;Johnsen RC;Addison LM;Baillie DL Title: Genomic organization in Caenorhabditis elegans: deficiency mapping on linkage group V(left). Citation: Genetical Research 52: 105-118 1988 Type: ARTICLE Genes: emb-29 let-326 let-327 let-329 let-330 let-331 let-332 let-334 let-335 let-336 let-337 let-338 let-339 let-340 let-341 let-342 let-343 let-344 let-345 let-346 let-347 let-348 let-349 let-350 let-401 let-402 let-403 let-404 let-405 let-406 let-407 let-408 let-409 let-410 let-411 let-412 let-413 let-414 let-415 let-416 let-417 let-418 let-419 let-420 let-421 let-422 let-423 let-424 let-425 let-426 let-427 let-428 let-429 let-430 let-431 lin-40 rol-3 unc-62 unc-70 sDf31 sDp30 Abstract: In this study we genetically analyse a large autosomal region (23 map units) in Caenorhabditis elegans. The region comprises the left half of linkage group V [LGV(left)] and is recombinationally balanced by the translocation eT1(III;V). We have used rearrangement breakpoints to subdivide the region from the left end of LGV to daf-11 into 23 major zones. Twenty of these zones are balanced by eT1. To establish the zones we examined a total of 110 recessive lethal mutations derived from a variety of screening protocols. The mutations identified 12 deficiencies, 1 duplication, as well as 98 mutations that fell into 59 complementation groups, significantly increasing the number of available genetic sites on LGV. Twenty-six of the latter had more than 1 mutant allele. Significant differences were observed among the alleles of only 6 genes, 3 of which have at least one 'visible' allele. Several deficiencies and 3 alleles of let-336 were demonstrated to affect recombination. The duplication identified in this study is sDp30(V;X). Lethal mutations covered by sDp30 were not suppressed uniformly in hermaphrodites. The basis for this nonuniformity may be related to the mechanism of X chromosome dosage ------------------- Key: 1109 Medline: 89137939 Authors: Kemphues KJ;Kusch M;Wolf N Title: Maternal-effect lethal mutations on linkage group II of Caenorhabditis elegans. Citation: Genetics 120: 977-986 1988 Type: ARTICLE Genes: him-14 let-29 let-237 mel-1 mel-2 mel-3 mel-4 mel-5 mel-6 mel-7 mel-8 mel-9 mel-10 mel-11 mel-12 mel-13 mel-14 mel-15 mel-16 mel-17 mel-18 mel-19 mel-20 mel-21 mel-22 ooc-1 zyg-1 zyg-9 zyg-11 Abstract: We have analyzed a set of linkage group (LG) II maternal-effect lethal mutations in Caenorhabditis elegans isolated by a new screening procedure. Screens of 12,455 F1 progeny from mutagenized adults resulted in the recovery of 54 maternal-effect lethal mutations identifying 29 genes. Of the 54 mutations, 39 are strict maternal-effect mutations defining 17 genes. These 17 genes fall into two classes distinguished by frequency of mutation to strict maternal- effect lethality. The smaller class, comprised of four genes, mutated to strict maternal-effect lethality at a frequency close to 5 X 10(- 4), a rate typical of essential genes in C. elegans. Two of these genes are expressed during oogenesis and required exclusively for embryogenesis (pure maternal genes), one appears to be required specifically for meiosis, and the fourth has a more complex pattern of expression. The other 13 genes were represented by only one or two strict maternal alleles each. Two of these are identical genes previously identified by nonmaternal embryonic lethal mutations. We interpret our results to mean that although many C. elegans genes can mutate to strict maternal-effect lethality, most genes mutate to that phenotype rarely. Pure maternal genes, however, are among a smaller class of genes that mutate to maternal-effect lethality at typical rates. If our interpretation is correct, we are near saturation for pure maternal genes in the region of LG II balanced by mnC1. We conclude that the number of pure maternal genes in C. elegans is small, being probably not much higher than 12. ------------------- Key: 1110 Medline: 89137940 Authors: McKim KS;Howell AM;Rose AM Title: The effects of translocations on recombination frequency in Caenorhabditis elegans. Citation: Genetics 120: 987-1001 1988 Type: ARTICLE Genes: eT1 hDf6 szT1 Abstract: In the nematode Caenorhabditis elegans, recombination suppression in translocation heterozygotes is severe and extensive. We have examined the meiotic properties of two translocations involving chromosome I, szT1(I;X) and hT1(I;V). No recombination was observed in either of these translocation heterozygotes along the left (let-362-unc-13) 17 map units of chromosome I. Using half-translocations as free duplications, we mapped the breakpoints of szT1 and hT1. The boundaries of crossover suppression coincided with the physical breakpoints. We propose that DNA sequences at the right end of chromosome I facilitate pairing and recombination. We use the data from translocations of other chromosomes to map the location of pairing sites on four other chromosomes. hT1 and szT1 differed markedly in their effect on recombination adjacent to the crossover suppressed region. hT1 had no effect on recombination in the adjacent interval. In contrast, the 0.8 map unit interval immediately adjacent to the szT1(I;X) breakpoint on chromosome I increased to 2.5 map units in translocation heterozygotes. This increase occurs in a chromosomal interval which can be expanded by treatment with radiation. These results are consistent with the suggestion that the szT1(I) breakpoint is in a region of DNA in which meiotic recombination is suppressed relative to the genomic average. We propose that DNA sequences disrupted by the szT1 translocation are responsible for determining the frequency of meiotic recombination in the vicinity of the ------------------- Key: 1111 Medline: 89066707 Authors: Krishna P;Kennedy BP;van de Sande JH;McGhee JD Title: Yolk proteins from nematodes, chickens, and frogs bind strongly and preferentially to left-handed Z-DNA. Citation: Journal of Biological Chemistry 263: 19066-19070 1988 Type: ARTICLE Genes: Abstract: Yolk proteins purified from the nematode Caenorhabditis elegans, from the frog Xenopus laevis, and from chicken eggs all have the unexpected property of binding strongly and preferentially to a left-handed Z-DNA probe, brominated poly(dG-dC). We estimate that the nematode proteins bind to Z-DNA with an association constant of at least 10(4) (M-1) and that this association constant is at least 40-50-fold higher than the association constant of B-DNA. Thus yolk proteins have a higher Z-DNA specificity than most of the Z-DNA binding proteins previously isolated from other sources. Although yolk protein binding to Z-DNA is poorly competed by a wide variety of nucleic acids, the interaction is strongly competed by the phospholipids cardiolipin and phosphatidic acid (500-1000-fold better than by the same mass of B-DNA). We suggest that Z-DNA interacts with the yolk protein phospholipid binding site. In general, our results emphasize the danger of using physical properties to infer biological function. In particular, our results should raise questions about the biological relevance of previously isolated Z-DNA binding ------------------- Key: 1112 Medline: 89240946 Authors: Kimble J Title: Genetic control of sex determination in the germ line of Caenorhabditis elegans. Citation: Philosophical Transactions of the Royal Society of London 322: 11-18 1988 Type: REVIEW Genes: fem-1 fem-2 fem-3 fog-1 fog-2 her-1 tra-1 tra-2 tra-3 Abstract: The nematode Caenorhabditis elegans normally exists as one of two sexes: self-fertilizing hermaphrodite or male. Development as hermaphrodite or male requires the differentiation of each tissue in a sex-specific way. In this review, I discuss the genetic control of sex determination in a single tissue of C. elegans: the germ line. Sex determination in the germ line depends on the action of two types of genes:--those that act globally in all tissues to direct male or female development and those that act only in the germ line to specify either spermatogenesis or oogenesis. First, I consider a tissue-specific sex-determining gene, fog-1, which promotes spermatogenesis in the germ line. Second, I consider the regulation of the hermaphrodite pattern of germ-line gametogenesis where first sperm and then oocytes are produced. ------------------- Key: 1113 Medline: 89107987 Authors: Herr W;Sturm RA;Clerc RG;Corcoran LM;Baltimore D;Sharp PA;Ingraham HA;Rosenfeld MG;Finney M;Ruvkun G;Horvitz HR Title: The POU domain: a large conserved region in the mammalian pit-1, oct-1, oct-2 and Caenorhabditis elegans unc-86 gene products. Citation: Genes & Development 2: 1513-1516 1988 Type: REVIEW Genes: unc-86 Abstract: We describe a large, 150- to 160-amino-acid-long region of sequence similarity in the three mammalian proteins Pit-1, Oct-1, and Oct-2 and in the product of the unc-86 gene of the nematode Caenorhabditis elegans called POU (pronounced 'pow'). This domain contains homeobox-related and POU-specific subdomains. The three mammalian proteins have been implicated in transcriptional control, and unc-86 is a cell lineage and cell differentiation gene... ------------------- Key: 1114 Medline: 89137951 Authors: Collins J;Forbes E;Anderson P Title: The Tc3 family of transposable genetic elements in Caenorhabditis elegans. Citation: Genetics 121: 47-55 1989 Type: ARTICLE Genes: mut-2 unc-22 Abstract: We describe genetic and molecular properties of Tc3, a family of transposable elements in Caenorhabditis elegans. About 15 Tc3 elements are present in the genomes of several different wild-type varieties of C. elegans, but Tc3 transposition and excision are not detected in these strains. Tc3 transposition and excision occur at high frequencies, however, in strain TR679, a mutant identified because of its highly active Tc1 elements. In TR679, Tc3 is responsible for several spontaneous mutations affecting the unc-22 gene. Tc3-induced mutations are unstable, and revertants result from precise or nearly precise excision of Tc3. Although Tc3 is very active in TR679, it is not detectably active in several other mutator mutants, all of which exhibit high levels of Tc1 activity. Tc3 is 2.5 kilobases long, and except for sequences near its inverted repeat termini, it is unrelated to Tc1. The termini of Tc3 are inverted repeats of at least 70 base pairs; the terminal 8 nucleotides of Tc3 are identical to 8 of the terminal 9 nucleotides of Tc1. ------------------- Key: 1115 Medline: 89137953 Authors: Plenefisch JD;DeLong L;Meyer BJ Title: Genes that implement the hermaphrodite mode of dosage compensation in Caenorhabditis elegans. Citation: Genetics 121: 57-76 1989 Type: ARTICLE Genes: dpy-21 dpy-22 dpy-26 dpy-27 dpy-28 her-1 sdc-3 yDp1 mnDp37 Abstract: We report a genetic characterization of several essential components of the dosage compensation process in Caenorhabditis elegans. Mutations in the genes dpy-26, dpy-27, dpy-28, and the newly identified gene dpy-29 disrupt dosage compensation, resulting in elevated X-linked gene expression in XX animals and an incompletely penetrant maternal-effect XX-specific lethality. These dpy mutations appear to cause XX animals to express each set of X-linked genes at a level appropriate for XO animals. XO dpy animals are essentially wild type. Both the viability and the level of X-linked gene expression in XX animals carrying mutations in two or more dpy genes are the same as in animals carrying only a single mutation, consistent with the view that these genes act together in a single process (dosage compensation). To define a potential time of action for the gene dpd- 28 we performed reciprocal temperature-shift experiments with a heat sensitive allele. The temperature-sensitive period for lethality begins 5 hr after fertilization at the 300-cell stage and extends to about 9 hr, a point well beyond the end of cell proliferation. This temperature-sensitive period suggests that dosage compensation is functioning in XX animals by mid-embryogenesis, when many zygotically transcribed genes are active. While mutations in the dpy genes have no effect on the sexual phenotype of otherwise wild-type XX or XO animals, they do have a slight feminizing effect on animals whose sex- determination process is already genetically perturbed. The opposite directions of the feminizing effects on sex determination and the masculinizing effects on dosage compensation caused by the dpy mutations are inconsistent with the wild-type dpy genes acting to coordinately control both processes. Instead, the feminizing effects are most likely an indirect consequence of disruptions in dosage compensation caused by the dpy mutations. Based on the cumulative evidence, the likely mechanism of dosage compensation in C. elegans involves reducing X-linked gene expression in XX animals to equal that in XO animals via the action of the dpy genes. ------------------- Key: 1116 Medline: 89187961 Authors: Meyer BJ Title: Primary events in C. elegans sex determination and dosage compensation. Citation: Trends in Genetics 4: 337-342 1988 Type: REVIEW Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-29 fem-1 fem-2 fem-3 fog-2 her-1 sdc-1 sdc-2 tra-1 tra-2 tra-3 xol-1 Abstract: An outline of the complex regulatory gene network that controls all aspects of sexual dimorphism in the nematode C. elegans is now known in considerable detail. This review describes the genes and gene interactions involved in the coordinate control of sex determination and X chromosome dosage compensation in C. elegans. ------------------- Key: 1117 Medline: 89180250 Authors: Sarkis GJ;Ashcom JD;Hawdon JM;Jacobson LA Title: Decline in protease activities with age in the nematode Caenorhabditis elegans. Citation: Mechanisms of Ageing & Development 45: 191-201 1988 Type: ARTICLE Genes: fer-15 Abstract: The activities of 3 lysosomal proteases in the nematode Caenorhabditis elegans are markedly lower in older animals. The aspartyl protease cathepsin D declines about 10-fold from day 3 (early adulthood) to day 11 (near the mean lifespan); this reflects a net decline in the amount of cathepsin D antigen. The specific activity of the thiol protease cathepsin Ce1 declines about 2.5-fold over the same period, and the specific activity of the thiol protease cathepsin Ce2 declines about 8-fold. The activity of a new non- lysosomal protease, designated cathepsin CeX, is invariant with age. The data are consistent with the hypothesis that reduced protease activity in older animals may cause a decline in the rate of protein turnover with age, but do not prove this hypothesis. ------------------- Key: 1118 Medline: 89137941 Authors: Hodgkin J Title: Early worms. Citation: Genetics 121: 1-3 1989 Type: REVIEW Genes: dpy-1 Abstract: Just over 21 years ago, in October of 1967, Sydney Brenner soaked a culture of hermaphroditic nematodes of the species Caenorhabditis elegans in a solution of ethyl methane sulfonate. A week later, examining their F2 descendants, he noticed a short, "dumpy" animal among the long, thin wild-type worms. The dumpy animal was picked to a separate culture plate and allowed to produce self-progeny, which were also dumpy: it was a true-breeding mutant. The new strain was given the name E1. Crosses with the parental wild-type strain showed that the mutant phenotype was due to a single autosomal recessive mutation - in modern nomenclature, allele e1 of the gene dpy-1. ------------------- Key: 1119 Medline: 89181579 Authors: Graham RW;Jones D;Candido EPM Title: UbiA, the major polyubiquitin locus in Caenorhabditis elegans, has unusual structural features and is constitutively expressed. Citation: Molecular and Cellular Biology 9: 268-277 1989 Type: ARTICLE Genes: Abstract: Ubiquitin is a multifunctional 76-amino-acid protein which plays critical roles in many aspects of cellular metabolism. In Caenorhabditis elegans, the major source of ubiquitin RNA is the polyubiquitin locus, UbiA. UbiA is transcribed as a polycistronic mRNA which contains 11 tandem repeats of ubiquitin sequence and possesses a 2-amino-acid carboxy-terminal extension on the final repeat. The UbiA locus possesses several unusual features not seen in the ubiquitin genes of other organisms studied to date. Mature UbiA mRNA acquires a 22-nucleotide leader sequence via a trans-splicing reaction involving a 100-nucleotide splice leader RNA derived from a different chromosome. UbiA is also unique among known polyubiquitin genes in containing four cis-spliced introns within its coding sequence. Thus, UbiA is one of a small class of genes found in higher eucaryotes whose heterogeneous nuclear RNA undergoes both cis and trans splicing. The putative promoter region of UbiA contains a number of potential regulatory elements: (i) a cytosine-rich block, (ii) two sequences resembling the heat shock regulatory element, and (iii) a palindromic sequence with homology to the DNA-binding site of the mammalian steroid hormone receptor. The expression of the UbiA gene has been studied under various heat shock conditions and has been monitored during larval moulting and throughout the major stages of development. These studies indicate that the expression of the UbiA gene is not inducible by acute or chronic heat shock and does not appear to be under nutritional or ------------------- Key: 1120 Medline: 88181885 Authors: Ward S Title: Expression of sperm-specific genes during nematode spermatogenesis. Citation: Annals of the New York Academy of Sciences 513: 128-133 Type: REVIEW Genes: Abstract: Unlike mammalian spermatozoa, the spermatozoa of nematodes and certain crustaceans are nonflagellated, crawling cells. Spermatozoa of the nematode Caenorhabditis elegans are asymmetric cells with a single knobby pseudopod protruding from one side of a hemispherical cell body. The pseudopod appears granular, without organelles, microfilaments, or microtubules, but when examined more carefully, it is found to contain numerous thin filaments, 2-3 nm in diameter. The cell body contains a distinctive membranous organelle fused to the plasma membrane surrounding the cell body and also contains the nucleus and mitochondria. These spermatozoa lack many common cytoplasmic structures and organelles such as microtubules, microfilaments, ribosomes, golgi apparatus, or lysosomes. Our laboratory is interested in the genetic control of the morphogenesis and motility of these spermatozoa. By isolating mutations in genes that are expressed only during spermatogenesis and by identifying the gene products, we can dissect spermatogenesis genetically. In this way we can learn how individual genes control morphogenesis and participate in ------------------- Key: 1121 Medline: 89289124 Authors: Goldstein P;Magnano L Title: Effects of dimethyl sulphoxide on early gametogenesis in Caenorhabditis elegans: ultrastructural aberrations and loss of synaptonemal complexes from pachytene nuclei. Citation: Cytobios 56: 45-57 1988 Type: ARTICLE Genes: Abstract: In Caenorhabditis elegans, loss of viability and fertility was observed after treatment with dimethyl sulphoxide (DMSO). The decrease in life span is associated with senescent morphology of meiotic prophase nuclei, such that nuclei from young and old specimens cannot be differentiated. Aging in oocytes at the pachytene stage of meiotic prophase is characterized by nucleo-cytoplasmic aberrations, increased density of the nucleoplasm and cytoplasm and decrease in numbers of mitochondria (Goldstein and Curis, 1987). Increasing concentrations of DMSO result in decrease in fertility and increased production of abnormal gametes. At DMSO concentrations higher than 5.0%, synaptonemal comlexes (SC) are absent from the nuclei, thus, effective pairing and segregation of homologous chromosomes is not possible. The absence of SCs may be the result of: (1) a premeiotic colchicine-like effect which influences pairing of chromosomes; (2) changes in the structure of the DNA due to DMSO binding that results in changes in expression of the DNA; and (3) changes in temporal DNA synthesis in response to DMSO. Since the SC is essential for regulating pairing and subsequent separation of bivalents, the lack of an SC explains the loss of fertility, due to the production of unbalanced gametes, observed in DMSO treated specimens. ------------------- Key: 1122 Medline: Authors: Atkinson HJ;Isaac RE;Harris PD;Sharpe CM Title: FMRFamide-like immunoreactivity within the nervous system of the nematodes Panagrellus redivivus, Caenorhabditis elegans and Heterodera glycines. Citation: Journal of Zoology 216: 663-671 1988 Type: ARTICLE Genes: Abstract: A polyclonal antiserum raised against the molluscan neuromodulatory peptide Phe-Met-Arg-Phe-amide (FMRFamide) reacts with nervous tissue in the free-living nematodes Panagrellus redivius and Caenorhabditis elegans and in infective juveniles (J2) of the soybean cyst nematode Heterodera glycines. Sectioning of the nematodes was unnecessary but penetration of the antibody was improved by cutting the animals or by use of plasma etching to breach the cuticle before incubation with antiserum. Both procedures required subsequent exposure to detergents or partial digestion with protease K for optimum immunoreactivity. A positive reaction was observed for all three nematodes in the longitudinal nerve cords, nerve ring and ventral and lateral ganglia. Neurones were also visualized in association with the vulva in the free-living species and the spicules of the male P. redivius. In H. glycinees, neurones innervating the pharynx reacted positively, as did two loops of neural tissue on either side of the ventral cord slightly anterior to the anus. Immunoreactivity was also noted in the amphicial pouches of H. glycines after prolonged (15 min) protease treatment. Further work is needed to establish the structure of the peptide antigen localized in these nematodes. ------------------- Key: 1123 Medline: Authors: O'Riordan VB;Burnell AM Title: Intermediary metabolism in the dauer larva of the nematode Caenorhabditis elegans-1. Glycolysis, gluconeogenesis, oxidative phosphorylation and tricarboxylic acid cycle/ Citation: Comparative Biochemistry & Physiology 92B: 233-238 1989 Type: ARTICLE Genes: Abstract: 1. The enzymes involved in glycolysis, gluconeogenesis and the tricarboxylic acid cycle were investigated in the dauer larva of C. elegans and their activities compared with those obtained for the corresponding enzymes in adult C. elegans. 2. The dauer larva possessed a considerable capacity to metabolise glycogen, as evident from the high phosphofructokinase activity relative to adult. 3. Re-synthesis of glycogen was suppressed in the dauer and this was indicated by the relatively low activity of fructose 1,6-bisphosphatase. 4. Relatively high levels of phosphoenolpyruvate-carboxykinase fixation of CO2 to form oxaloacetate were observed in dauer larva. 5. The maximal rate of flux of metabolites through the TCA was reduced 11.6 fold in dauer larvae relative to adults. 6. A three fold reduction in the oxidative capacity of dauer larvae mitochondria relative to that of adults was also observed. 7. These metabolic changes form part of the adaptive response which enables dauer larvae to survive for several months without feeding. ------------------- Key: 1124 Medline: 89178677 Authors: Dibb NJ;Maruyama IN;Krause M;Karn J Title: Sequence analysis of the complete Caenorhabditis elegans myosin heavy chain gene family. Citation: Journal of Molecular Biology 205: 603-613 1989 Type: ARTICLE Genes: myo-1 myo-2 myo-3 unc-54 Abstract: The sequences of three myosin heavy chain (MHC) genes from Caenorhabditis elegans, myo-1, 2 and 3, are presented. These genes, together with unc-54, comprise the entire nematode sacromeric MHC family. Comparison of nematode MHC sequences and sarcomeric, smooth and non-muscle MHCs from other organisms highlights conserved sequence features of the MHC rod believed to be important for thick filament assembly. These include: conservation of sequence differences between individual 28 amino acid repeats; invariant placements of large aromatic residues, such as tryptophan, in the rod sequences; conservation of "weak spots" in the hydrophobic seam; and conservation of non-uniform charge distributions along the length of the rod. The rod sequences of the body wall isoforms A and B are more closely related to each other than to the pharyngeal isoforms C and D, suggesting that structural constraints have been imposed by their location within the same thick filament. We have also identified the major transcriptional start site for gene unc-54. Surprisingly, there are no TATA or other known transcription factor elements immediately upstream from the unc-54 start site, or in the upstream regions of the other genes of the C. ------------------- Key: 1125 Medline: 89162028 Authors: Chalfie M;Au M Title: Genetic control of differentiation of the Caenorhabditis elegans touch receptor neurons. Citation: Science 243: 1027-1033 1989 Type: REVIEW Genes: egl-5 lin-32 mec-4 mec-5 mec-6 mec-8 mec-12 mec-14 mec-15 mec-17 mec-18 Abstract: The genetic control of neuronal differentiation has been studied by examining mutations that affect the development and function of the six touch receptor neurons of the nematode Caenorhabditis elegans. By screening for touch-insensitive mutants, it has been possible to identify 18 genes (represented by 417 mutations) that are required at various stages in the developmental program for touch cell differentiation. Two of the genes are needed for the generation of precursors in the touch cell lineages; without the precursors, touch cells are not made. A third gene, mec-3, specifies the differentiation of the touch cells, probably by acting as a transcription factor. The remaining 15 genes are likely targets of mec-3 action; mutants defective in these genes have nonfunctioning, yet differentiated, touch cells. Some of these latter genes are needed for the formation of cell-specific components of the touch cells, such as a set of microtubules that are only found in these cells. The study of the touch genes should help us understand how touch cell fate is determined, how microtubule form is specified, and, perhaps, how mechanical stimuli are transduced. ------------------- Key: 1126 Medline: 89199379 Authors: Herman RK Title: Mosaic analysis in the nematode Caenorhabditis elegans. Citation: Journal of Neurogenetics 5: 1-24 1989 Type: REVIEW Genes: ace-1 ace-2 ace-3 ced-3 ced-4 daf-6 dpy-17 glp-1 mab-5 mec-4 ncl-1 osm-1 sup-10 sup-20 unc-3 unc-26 unc-30 unc-36 unc-93 unc-105 mnDp7 mnDp14 mnDp26 nDp3 qDp3 sDp3 Abstract: The use of genetic mosaics and chimeras is a well established tool in developmental and behavioral genetics. One aim in work with Drosophila mosaics and mouse chimeras has been to elucidate cell lineages. This application of mosaics is largely unnecessary for the nematode Caenorhabditis elegans because the complete wild-type cell lineage has been worked out directly by Nomarski microscopy of living animals. Mosaics have in some cases provided verification of the correctness and invariance of parts of the wild-type C. elegans cell lineage, and it is conceivable that mosaics could be useful in the clonal analysis of mutant lineages, which may be quite variable. But the major goal of mosaic analysis in C. elegans so far has been to address questions about the cell specificity of gene function. These questions arise in two contexts. In the first case, a mutant gene is known to cause a detectable change in a cellular phenotype. One can then use mosaics to ask whether or not the gene is cell autonomous in its action; if it is not, then an interaction with one or more other cells is involved and one can use mosaics again to ask what other cells might be responsible. In the second case, nothing is known at the cellular level about the consequences of a mutant gene; mutant animals may have been identified by virtue of being deficient for an enzyme, for example, or being inviable or showing aberrant behavior or morphology. The general question in this case is: what is the anatomical focus of action of the gene, i.e., what cell or cells are responsible for the phenotype conferred by the gene? In this review I shall first introduce the method by which all of the C. elegans genetic mosaics to be discussed have been generated, and then I shall review the mosaic analysis of 18 genes, eight that were known at the outset to affect cellular phenotypes and ten that were first studied on the basis of their effects on behavior, overall morphology or some other non-cellular phenotype. The positions on the C. elegans genetic map of the loci to be discussed are indicated in Figure 2. Some discussion of C. elegans cell lineage will be necessary for understanding the mosaic analysis of each gene. The derivation of the early embryonic cleavage products called founder cells and a summary of the numbers and types of cells derived from them are given in Figure 2. For several genes it will also be necessary to discuss aspects of C. elegans nervous system structure and function. ------------------- Key: 1127 Medline: 89137738 Authors: Wadsworth WG;Riddle DL Title: Developmental regulation of energy metabolism in Caenorhabditis elegans. Citation: Developmental Biology 132: 167-173 1989 Type: ARTICLE Genes: daf-2 daf-7 Abstract: Changes in energy metabolism during larval development in Caenorhabditis elegans have been investigated using phosphorus nuclear magnetic resonance (31P NMR). The relative concentrations of ATP, ADP, AMP, sugar phosphates, and other metabolites were observed to change during larval development, producing stage-specific spectra. These spectra are consistent with enzyme assays for isocitrate dehydrogenase and isocitrate lyase, indicating that high activity of the glyoxylate pathway during embryonic development decreases during the first larval (L1) stage, and respiration during the L2, L3, and L4 stages occurs preferentially through the TCA cycle. Metabolic strategies were further studied using mutants that are predisposed to enter the dauer stage, a developmentally arrested third-stage larva formed under conditions of overcrowding and limited food. After the L1 molt, energy metabolism in animals destined to become dauer larvae diverges from that of animals committed to growth. Relative to the L1, the L2 larvae committed to growth exhibit increased isocitrate dehydrogenase activity as well as increases in ATP and other high-energy phosphates, but predauer (L2d) larvae exhibit declining enzyme activities and declining levels of high- energy phosphates. The predominant phosphorus NMR signal in dauer larva extracts corresponds to inorganic phosphate. We conclude that metabolism is regulated during C. elegans larval development, with a major transition apparent after the L1 stage. This transition does not occur in larvae destined to form dauer larvae. ------------------- Key: 1128 Medline: 89232692 Authors: Ruvkun G;Ambros V;Coulson A;Waterston R;Sulston J;Horvitz Title: Molecular genetics of the Caenorhabditis elegans heterochronic gene lin-14. Citation: Genetics 121: 501-516 1989 Type: ARTICLE Genes: lin-14 Abstract: We describe a general strategy for the genetic mapping in parallel of multiple restriction fragment length polymorphism (RFLP) loci. This approach allows the systematic identification for cloning of physical genetic loci within about 100 kb of any gene in Caenorhabditis elegans. We have used this strategy of parallel RFLP mapping to clone the heterochronic gene lin-14, which controls the timing and sequence of many C. elegans postembryonic developmental events. We found that of about 400 polymorphic loci in the C. elegans genome associated with the Tc1 family of repetitive elements, six are within 0.3 map unit of lin-14. The three closest lin-14-linked Tc1-containing restriction fragments were cloned and used to identify by hybridization an 830-kb region of contiguous cloned DNA fragments assembled from cosmid and yeast artificial chromosome libraries. A lin-14 intragenic recombinant that separated a previously cryptic lin- 14 semidominant mutation from a cis-acting lin-14 suppressor mutation was used to map the location of the lin-14 gene to a 25-kb region of this 830-kb contig. DNA probes from this region detected lin-14 allele-specific DNA alterations and a lin-14 mRNA. Two lin-14 semi- dominant alleles, which cause temporally inappropriate lin-14 gene activity and lead to the reiterated expression of specific early developmental events, were shown to delete sequences from the lin-14 gene and mRNA. These deletions may define cis-acting sequences responsible for the temporal ------------------- Key: 1129 Medline: 88257849 Authors: Johnson TE Title: Genetic specification of life span: Processes, problems and potentials. Citation: Journal of Gerontology 43: B87-B92 1988 Type: REVIEW Genes: Abstract: Genetic approaches have been used to gain insights into many complex biological phenomena, but until recently most attempts to use genetic approaches to understand aging or senescence processes in metazoans have met with little success. The first review in this series (Martin and Tucker, 1988) surveyed model organisms used in the genetic analysis of aging; here I will review the analysis of life span and of the aging process by means of genetics. Problems inherent in the genetic analysis of aging will be reviewed first. Successful applications of genetics to the phenomena of aging will next be highlighted. Finally, I will present examples of ways in which both molecular and classical genetic approaches can be fruitfully and realistically applied to the study of the aging processes. Where applicable, misinterpretations and possible future directions will be noted. ------------------- Key: 1130 Medline: Authors: Johnson TE;Friedman DB;Fitzpatrick PA;Conley WL Title: Mutant genes that extend life span. Citation: "Evolution of Longevity in Animals." Woodhead AD and Thompson KH (eds), Plenum Press. : 91-110 1987 Type: REVIEW Genes: age-1 dpy-10 fer-15 unc-4 Abstract: One way to gain an understanding of any biological process is through the use of mutant analysis and selective breeding to generate stocks which have genetic alterations in that process. We have taken just this approach in the analysis of aging... ------------------- Key: 1131 Medline: Authors: Pasternak JJ Title: Molecular biology of nematodes: some recent studies on Panagrellus and Ascaris. Citation: Canadian Journal of Zoology 66: 2591-2599 1988 Type: REVIEW Genes: Abstract: Nematodes have a number of biological attributes that make them amenable for molecular studies. In our laboratory, attention has focused on (i) determining the polypeptide composition of cuticles, (ii) using monoclonal antibodies to identify epitopes among the cuticular proteins, (iii) visualizing the sites of collagenous components within the cuticle of Ascaris by immunolocalization, and (iv) sequencing a moderately repetitive DNA element that is found, with extensive similarity, in the genomes of Ascaris and Panagrellus. The role of these and other molecular studies in understanding the biology of nematodes is discussed. ------------------- Key: 1132 Medline: 89093236 Authors: Sepsenwol S;Ris H;Roberts TM Title: A unique cytoskeleton associated with crawling in the amoeboid sperm of the nematode, Ascaris suum. Citation: Journal of Cell Biology 108: 55-66 1989 Type: ARTICLE Genes: Abstract: Nematode sperm extend pseudopods and pull themselves over substrates. They lack an axoneme or the actin and myosins of other types of motile cells, but their pseuodpods contain abundant major sperm protein (MSP), a family of 14kD polyptptides found exclusively in male gametes. Using high voltage electron microscopy, a unique cytoskeleton was discovered in the pseudopod of in vitro-activated, crawling sperm of the pig intestinal nematode Ascaris suum. It consists of 5-10-nm fuzzy fibers organized into 150-250-nm-thick fiber complexes, which connect to each of the moving pseudopodial membrane projections, villipodia, which in turn make contact with the substrate. Individual fibers in a complex splay out radially from its axis in all directions. The centripetal ends intercalate with fibers from other complexes or terminate in a thickened layer just beneath the pseudopod membrane. Monoclonal antibodies directed against MSP heavily label the fiber complexes as well as individual pseudopodial filaments throughout their length. This represents the first evidence that MSP may be the major filament protein in the Ascaris sperm cytoskeleton. The large fiber complexes can be seen clearly in the pseudopods of live, crawling sperm by computer-enhanced video, differential-interference contrast microscopy, forming the villipodia at the leading edge of the sperm pseudopod. Even before the pseudopod attaches, the entire cytoskeleton and villipodia move continuously rearwards in unison toward the cell body. During crawling, complexes and villipodia in the pseudopod recede at the same speed as the spermatozoon moves forward, both disappearing at the pseuodopod-cell body junction. Sections at this region of high membrane turnover reveal a band of densely packed smooth vesicles with round and tubular profiles, some of which are associated with the pseudopod plasma membrane. The exceptional anatomy, biochemistry, and phenomenology of Ascaris sperm locomoton permit direct study of the involvement of the cytoskeleton ------------------- Key: 1133 Medline: 89252769 Authors: Desai C;Horvitz HR Title: Caenorhabditis elegans mutants defective in the functioning of the motor neurons responsible for egg laying. Citation: Genetics 121: 703-721 1989 Type: ARTICLE Genes: egl-1 egl-5 egl-10 egl-41 egl-42 egl-43 egl-44 egl-45 egl-46 egl-47 egl-49 egl-50 tra-2 unc-86 Abstract: We have isolated and characterized 45 Caenorhabditis elegans mutants presumed to be defective in the functioning of the hermaphrodite- specific neurons (HSNs). Like hermaphrodites that lack the HSN motor neurons, these mutants are egg-laying defective and do not lay eggs in response to exogenous imipramine but do lay eggs in response to exogenous serotonin. Twenty of the 45 mutations define 10 new egl genes; the other 25 mutations are alleles of five previously defined genes, four of which are known to affect the HSNs. Seven mutations in three genes cause the HSNs to die in hermaphrodites, as they normally do in males. These genes appear to be involved in the determination of the sexual phenotype of the HSNs, and one of them (egl-41) is a newly identified gene that may function generally in sex determination. Five of the 15 genes are defined only by mutations that have dominant effects on egg laying. One gene egl(n1108), is defined by a temperature-sensitive allele that has a temperature- sensitive period after HSN development is complete, suggesting that egl(n1108) may be involved in HSN synaptic transmission. Four of the genes are defined by single alleles, which suggests that other such genes remain to be discovered. Mutations in no more than 4 of the 15 genes specifically affect the HSNs, indicating that there are few genes with functions needed only in this single type of ------------------- Key: 1134 Medline: 89252770 Authors: Herman RK;Kari CK Title: Recombination between small X chromosome duplications and the X chromosome in Caenorhabditis elegans. Citation: Genetics 121: 723-737 1989 Type: ARTICLE Genes: him-8 mnDp57 mnDp62 mnDp63 mnDp65 mnDp66 mnDp67 mnDp68 mnDp69 mnDp70 mnDp71 mnDp72 mnDp73 Abstract: Twelve new X chromosome duplications were identified and characterized. Eight are translocated to autosomal sites near four different telomeres, and four are free. Ten include unc-1(+), which in wild type is near the left end of the X chromosome, and two of these, mnDp72(X;IV) and mnDp73(X;f), extend rightward past dpy-3. Both mnDp72 and mnDp73 recombined with the one X chromosome in males in the unc-1-dpy-3 interval at a frequency 15- to 30-fold higher than was observed for X-X recombination in hermaphrodites in the same interval. Recombinant duplications and recombinant X chromosomes were both recovered. Recombination with the X chromosome in the unc-1-dpy- 3 interval was also detected for five other unc-1(+) duplications, even though their right breakpoints lie within the interval. In hermaphrodites, mnDp72 and mnDp73 promoted meiotic X nondisjunction and recombined with an X chromosome in the unc-1-dpy-3 interval at frequencies comparable to that found for X-X recombination; mnDp72(X;IV) also promoted trisomy for chromosome IV. A mutation in him-8 IV was identified that severely reduced recombination between the two X chromosomes in hermaphrodites and between mnDp73 and the X chromosome in males. Recombination between the X chromosome and duplications of either the right end of the X or a region near but not including the left end was rare. We suggest that the X chromosome has one or more elements near its ------------------- Key: 1135 Medline: 89183633 Authors: Weston K;Yochem J;Greenwald I Title: A Caenorhabditis elegans cDNA that encodes a product resembling the rat glutathione S-transferase P subunit. Citation: Nucleic Acids Research 17: 2138-2138 1989 Type: ARTICLE Genes: gst-1 Abstract: Part of a Caenorhabditis elegans gene capable of encoding a glutathione S-transferase subunit was present on a genomic clone that also contains part of the lin-22 gene. The genes are oppositely oriented, and their 3' ends lie within 40 base pairs of each other. ------------------- Key: 1136 Medline: 89356251 Authors: Heschl MFP;Baillie DL Title: Characterization of the hsp70 multigene family of Caenorhabditis elegans. Citation: DNA 8: 233-243 1989 Type: ARTICLE Genes: hsp-3 hsp-6 Abstract: Our laboratory has been characterizing the hsp70 multigene family from the nematode Caenorhabditis elegans as the first step to the genetic characterization of the heat shock response in a relatively simple multicellular eukaryote. Two gene members, hsp-1 and hsp-2ps have already been characterized (Snutch et al., 1988; Heschl and Baillie, 1989). The third gene member, hsp-3, is expressed constitutively and is non-heat inducible; its mRNA is most abundant at the L1 larval stage. The hsp-3 protein (hsp70C) shares a high degree of identity with the rat grp78 protein and has a long, hydrophobic leader sequence. The carboxyl terminus of hsp70C has the putative ER-retention signal, KDEL. The fourth gene member, hsp-6 is expressed constitutively and moderately heat inducible. A partial hsp- 6 protein (hsp70F) sequence shares a higher degree of identity with the Escherichia coli dnaK protein than with eukaryotic hsp70 proteins. The predicted amino-terminal half of the hsp70F polypeptide also contains a long, amphiphilic leader sequence similar to mitochondrial import leader sequences. These two genes encode proteins that potentially cross intracellular membranes. We compared the 5'-flanking DNA from the C. elegans hsp-3 gene to fragment containing enhancer activity from the rat grp78 gene regulatory region (Lin et al., 1986). A 23-nucleotide sequence was conserved between the two promoter regions. This sequence shares approximately 80% identity between these two evolutionary distant organisms. A comparison to other hsp70 genes did not reveal any conservation of this 23-nucleotide sequence. We propose that this sequence may be involved in a unique aspect of the regulation of the C. elegans' grp78-like gene and the rat grp78 gene. ------------------- Key: 1137 Medline: 89159428 Authors: Ruvkun G;Giusto J Title: The Caenorhabditis elegans heterochronic gene lin-14 encodes a nuclear protein that forms a temporal developmental switch. Citation: Nature 338: 313-319 1989 Type: ARTICLE Genes: lin-14 Abstract: During wild-type development, a protein product of the Caenorhabditis elegans heterochronic gene lin-14 is localized to nuclei of specific somatic cells in embryos and early larvae, but is absent in late larvae and adult soma. Gain-of-function lin-14 mutations cause the level of lin-14 protein to remain high throughout development, resulting in developmental reiterations of early cell lineages. The normal down-regulation of the lin-14 nuclear protein level encodes a temporal switch between early and ------------------- Key: 1138 Medline: 89155583 Authors: Aamodt E;Holmgren R;Culotti J Title: The isolation and in situ location of adligin: The microtubule cross-linking protein from Caenorhabditis elegans. Citation: Journal of Cell Biology 108: 955-963 1989 Type: ARTICLE Genes: Abstract: Microtubules isolated from the nematode Caenorhabditis elegans contain long stretches of periodic cross-links formed by microtubule- associated proteins (MAPs). These cross-links are 5.7 nm long, 3 nm wide, and occur at one tubulin dimer (8-nm) intervals along the walls of microtubules (Aamodt, E., and J. Culotti, 1986. J. Cell Biol. 103:23-31). The structural protein of the cross-links was isolated from the MAPs by centrifugation and exclusion chromatography. The cross-links were formed exclusively from the most prevalent MAP, a 32,000 mol wt protein. We suggest the name adligin for this MAP. Adligin eluted from the exclusion column at 33,000 mol wt indicating that it was a monomer in solution. Antibodies were made against the purified adligin and affinity purified. The affinity-purified antibodies were used to locate adligin in situ and to determine its distribution relative to that of tubulin by the use of double label immunofluorescence. The anti-adligin antibodies labeled a fibrous network in the cytoplasm of most cells of C. elegans. Neurons were labeled especially well. This labeling pattern was similar to the labeling pattern obtained with antitubulin, but anti-adligin labeled some granules in the gut that were not labeled with antitubulin. These results suggest that adligin may be part of the interphase microtubule network ------------------- Key: 1139 Medline: 89186920 Authors: Tabuse Y;Nishiwaki K;Miwa J Title: Mutations in a protein kinase C homolog confer phorbol ester resistance on Caenorhabditis elegans. Citation: Science 243: 1713-1716 1989 Type: ARTICLE Genes: tpa-1 Abstract: The tpa-1 gene mediates the action of tumor-promoting phorbol esters in the nematode Caenorhabditis elegans. A genomic fragment that constitutes a portion of the tpa-1 gene was cloned by Tc1 transposon tagging and was used as a probe to screen a nematode complementary DNA library. One of the isolated complementary DNA clones had a nucleotide sequence that predicts a polypeptide of 526 amino acids. The predicted amino acid sequence revealed that the predicted tpa-1 protein sequence is highly similar to protein kinase C molecules from various animals, including ------------------- Key: 1140 Medline: Authors: Barstead RJ;Waterston RH Title: Factors important for sarcomere organization in Caenorhabditis elegans. Citation: "Cellular and Molecular Biology of Muscle Development." UCLA Symposia on Molecular & Cellular Biology. Kedes LH and Stockdale FE (eds). 93: - 1989 Type: REVIEW Genes: Abstract: ------------------- Key: 1141 Medline: 89290335 Authors: Fodor A;Timar T;Kiss I;Hosztafi S;Varga E;Soos J;Sebok P Title: Effects of precocene analogs on the nematode Caenorhabditis remanei (var. Bangaloreiensis). 1. Structure/activity relations. Citation: General & Comparative Endocrinology 74: 18-31 1989 Type: ARTICLE Genes: Abstract: Precocenes (PI and PII) and 114 of their analogs (PAs) were synthetized and tested on C. remanei embryos for their precocene-like (P-like) activities resulting in unusual development at sublethal doses. The P-like activity was quantitated by plotting the probit of the percentage of the developmentally affected survivors against the (log) dose to obtain the EC plot and the half effective concentration (EC50). All five PAs (PI, PII, 7-ethoxy-PII, 7-(prop-2-ynyloxy)-PI, and 6-methoxy-7-(prop-2-ynyloxy)-PII) which exert both antiallatal activity in insects and P-like activity in nematodes are 7-alkoxy-substituted 2,2-dimethylchromenes. Both activities can be enhanced by an additional 6-MeO-substitution or by an asymmetric 6,7-dialkoxy-substitution, on condition that R-7 is longer than R-6. There are many more similarities than dissimilarities in the structural requirements needed for antiallatal and P-like activities. All but three nonantiallatal PAs effective in nematodes are 7-prop-2-ynyloxy-substituted; two are symmetrically 6,7-disubstituted, and one is heterosubstituted (thio-PI). All PAs with antiallatal but without P-like activity are 7-monosubstituted with a relatively long alkoxy group. Certain substitutions favor antiallatal activity and others P-like activity. The severe nematocidal effect of 6,7-methylenedioxy-2,2-dimethylchromene (inert in insects) is not accompanied by P-like activity. The present findings lend some indirect support to the supposition that JH-producing cells and/or JH-dependent function(s) might ------------------- Key: 1142 Medline: 89290336 Authors: Fodor A;Timar T Title: Effects of precocene analogs on the nematode Caenorhabditis remanei (var. Bangaloreiensis). 2. Competitions with a juvenile hormone analog (methoprene). Citation: General & Comparative Endocrinology 74: 32-44 1989 Type: ARTICLE Genes: Abstract: Fourteen 7-alkoxy-2,2-dimethylchromenes were synthetized and studied in JH competition experiments: prococenes (Ps) PI and PII, and synthetic analogs (PAs) including (i) three with both antiallatal and P-like activities: 7-ethoxy-PII (7-EPII); 7-(prop-2-ynyloxy)-2,2-dimethylchromene (PPI); and 6-methoxy-7-(prop-2-yynyloxy)-2,2-dimethylchromene (PPIII); (ii) six without antiallatal activity, exerting P-like activity in nematodes; and (iii) three without either antiallatal or P-like activity, but with a strong nematocidal effect. Within the dose range 8-1000 ug/ml, different concentrations of each PA were applied to nematode growth medium which did or did not contain 1000 ug methoprene (a juvenile hormone analog JHA)/ml. Plates inoculated with Caenorhabditis embryos were incubated and scored for developmentally affected survivors. The JHA did not compete with any PA mentioned as (iii). It competed moderately with some nonantiallatal PAs (8-Me-PPI, 8-MeO-PPI, and 3,4-diCl-PPI) with strong P-like and nematocidal activities. The JHA competed most efficiently with all Ps, antiallatal PAs, and two nonantiallatal PAs (PPII and thio-PI) which exerted severe P-like activities in nematodes. Parameters assumed to be indicators of the P-like (rather than nematocidal) activity of the PAs proved more sensitive to the JHA than those of nematocidal activity. Whether the JH-compensable P-like activity of some PAs can be regarded as a real anti-JH action needs further clarification. ------------------- Key: 1143 Medline: 89236409 Authors: Huang X-Y;Barrios LAM;Vonkhorporn P;Honda S;Albertson DG;Hecht RM Title: Genomic organization of the glyceraldehyde-3-phosphate dehydrogenase gene family of Caenorhabditis elegans. Citation: Journal of Molecular Biology 206: 411-424 1989 Type: ARTICLE Genes: gpd-1 gpd-2 gpd-3 gpd-4 Abstract: Glyceraldehyde-3-phosphate dehydrogenase (GAPDHase) is encoded by four genes designated gpd-1 through gpd-4 in the nematode Caenorhabditis elegans. gpd-1 has been isolated and sequenced, and is shown here to have a nearly identical copy (gpd-4) with respect to coding and regulatory flanking sequence information as well as to the placement of its two introns. Both genes, which are separated by 250,000 to 300,000 base-pairs were assigned to chromosome II by in situ hybridization and physically linked to a DNA polymorphism located near unc-4 on the genetic map. The genes gpd-2 and gpd-3 are also nearly identical with each other but differ from the gpd-1 and gpd-4 pair with respect to the positions of their two introns and a cluster of amino acid changes within the amino-terminal region of the enzyme. Furthermore, one gene from each pair (gpd-4 and gpd-2) exhibits a single amino acid substitution at positions heretofore known to be conserved in all other systems so far examined including the extreme thermophiles. gpd-2 and gpd-3 are organized as a direct tandem repeat separated by only 244 base-pairs. They have been assigned to an 85,200 base-pair contig that maps to the left end of the X chromosome. The absence of gpd-3 from C. elegans var. Bergerac was used as a marker to map the gpd-2,3 gene pair near unc-20. Northern analyses have shown that gpd-1 and gpd-4 are preferentially expressed in embryos, while the expression of gpd-2 and gpd-3 increases during postembryonic development. These analyses indicate that the gpd-1,4 gene pair encodes the minor isoenzyme, GAPDHase-1, present in all cells of the nematode while the other gene pair (gpd- 2,3) encodes the major isoenzyme, GAPDHase-2, preferentially expressed in the bodywall muscle. The G + T-rich and T-rich regions essential for vertebrate ------------------- Key: 1144 Medline: 89195221 Authors: Ambros V Title: A hierarchy of regulatory genes controls a larva-to-adult developmental switch in C. elegans. Citation: Cell 57: 49-57 1989 Type: ARTICLE Genes: lin-4 lin-14 lin-28 lin-29 Abstract: The heterochronic genes lin-4, lin-14, lin-28, and lin-29 control the timing of specific postembryonic developmental events in C. elegans. The experiments described here examine how these four genes interact to control a particular stage-specific event of the lateral hypodermal cell lineages. This event, termed the "larva-to-adult switch" (L/A switch), involves several coordinate changes in the behavior of hypodermal cells at the fourth molt: cessation of cell division, formation of adult (instead of larval) cuticle, cell fusion, and cessation of the molting cycle. The phenotypes of multiply mutant strains suggest a model wherein the L/A switch is controlled by the stage-specific activity of a regulatory hierarchy: At early stages of wild-type development, lin-14 and lin-28 inhibit lin-29 and thus prevent switching. Later, lin-4 inhibits lin-14 and lin-28, allowing activation of lin-29, which in turn triggers the switch in the L4 stage. lin-29 may activate the L/A switch by regulating genes that control cell division, differentiation, and stage-specific gene expression in hypodermal cells. ------------------- Key: 1145 Medline: 89326130 Authors: Khosla M;Honda BM Title: Initiator tRNAMet genes from the nematode Caenorhabditis elegans. Citation: Gene 76: 321-330 1989 Type: ARTICLE Genes: rtm-1 rtm-2 rtm-3 rtm-4 Abstract: Five different members of the initiator tRNAMet gene family have been isolated and characterized from the nematode Caenorhabditis elegans. All five show identical tRNA coding sequences, followed by a block of T residues associated with termination by RNA polymerase III. Nucleotide sequences flanking the tDNAs are completely divergent, except for two distinct members with identical flanking sequences, which may have arisen from a recent gene duplication event. Each tDNA is also flanked by middle-repetitive DNA, but the lack of cross- hybridization to each other suggests that these repetitive sequences have no common functional significance. The tRNAMeti genes do not appear to be closely linked to each other, although in vitro transcription reveals a putative tDNA adjacent to one member. Finally, there are large differences in the extent to which the five genes are transcribed by a homologous C. elegans cell-free extract, suggesting that flanking sequences have a significant effect on transcription by RNA ------------------- Key: 1146 Medline: 89326131 Authors: Cox GN;Fields C;Kramer JM;Rosenzweig B;Hirsh D Title: Sequence comparisons of developmentally regulated collagen genes of Caenorhabditis elegans. Citation: Gene 76: 331-344 1989 Type: ARTICLE Genes: col-1 col-2 col-6 col-7 col-8 col-14 col-19 Abstract: Collagen genes col-6, col-7 (partial), col-8, col-14 and col-19 from the nematode Caenorhabditis elegans were sequenced, and compared to the previously sequenced genes col-1 and col-2. The genes are between 1.0 and 1.2 kb in length, and each includes one or two short introns. The presumptive promoter regions contain sequences similar to the eukaryotic TATA promoter element. Two distinct, conserved sequences were found in the presumptive promoter regions of, respectively, the dauer larva-specific genes col-2 and col-6, and the primarily adult- specific genes col-7 and col-19. The domain structures of the collagen polypeptides are similar: each polypeptide contains two triple-helix forming (Gly-X-Y)n domains, one of 30-33 amino acids (aa), and the other of 127-132 aa. The latter domain is interrupted by one to three short (2-8 aa) non-(Gly-X-Y)n segments that occur at relatively conserved locations in each polypeptide. Sets of cysteine residues flank the (Gly-X-Y)n domains in all of the polypeptides. The genes can be placed into three families based upon amino acid sequence similarities. Genes within a family do not always exhibit similar developmental expression programs, suggesting that structural and regulatory regions of the genes have evolved separately. The codon usage in the genes is highly asymmetrical, with adenine appearing in the third position of 85% of the glycine codons, and 93% of ------------------- Key: 1147 Medline: 89273548 Authors: Schierenberg E Title: Cytoplasmic determination and distribution of developmental potential in the embryo of Caenorhabditis elegans. Citation: BioEssays 10: 99-104 1989 Type: REVIEW Genes: Abstract: Development of the nematode Caenorhabditis elegans has been described completely on a cell-by-cell basis. In an invariant pattern five somatic founder cells and the primordial germ cell are generated within the first hour after the onset of cleavage. Using a laser microbeam for manipulation of individual blastomeres several aspects of early embryogenesis have been investigated, including the expression of cellular polarity, the localization of lineage-specific cleavage potential, the necessity for early cell-cell interaction, and the control of differential cell-cycle timing. The experiments demonstrate the central importance of a correct partitioning of cytoplasmic components during early embryogenesis and suggest a stepwise, binary segregation mechanism associated with the unequal cleavages in the germline. ------------------- Key: 1148 Medline: 89276921 Authors: Rand JB Title: Genetic analysis of the cha-1 - unc-17 gene complex in Caenorhabditis. Citation: Genetics 122: 73-80 1989 Type: ARTICLE Genes: cha-1 unc-17 Abstract: In C. elegans, the gene cha-1 is the structural gene for choline acetyltransferase, the enzyme which synthesizes acetylcholine. cha-1 is a complex gene which includes the previously described unc-17 locus; it has been hypothesized that a single protein is encoded which consists of several discrete structural domains. Mutations of the cha-1-unc-17 locus can be assigned to one of four classes on the basis of phenotype and complementation properties. A fine-structure map of this region has now been obtained by recombinational mapping. It is a large locus, spanning at least 0.035 map unit. On the map, the mutations lie in four contiguous, nonoverlapping regions, corresponding exactly to the different classes as defined by complementation and phenotype. Several new cha-1 mutations are described and mapped in the present study, including temperature- sensitive and lethal alleles. ------------------- Key: 1149 Medline: 89240708 Authors: Levitt A;Emmons SW Title: The Tc2 transposon in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 86: 3232-3236 1989 Type: ARTICLE Genes: mut-4 mut-5 Abstract: A second family of transposons, named Tc2 elements, has been identified in the nematode Caenorhabditis elegans. Tc2 elements are polymorphic in sequence and are present in different numbers in different strains. Like the transposon Tc1, Tc2 is active in the germ line of some C. elegans strains. A high rate of transposition has been observed in the progeny of certain interstrain crosses, where transposition events are frequent enough to be detected in blot hybridization experiments, without the use of a genetic screen. Our data suggest that transposition of Tc1 and Tc2 may be regulated by the same genomic factors. ------------------- Key: 1150 Medline: 89293823 Authors: Roberts SB;Emmons SW;Childs G Title: Nucleotide sequences of Caenorhabditis elegans core histone genes. Genes for different histone classes share common flanking sequence elements. Citation: Journal of Molecular Biology 206: 567-577 1989 Type: ARTICLE Genes: his-1 his-2 his-3 his-4 his-9 his-10 his-11 his-12 his-13 his-14 his-15 his-16 Abstract: We have determined the nucleotide sequence of core histone genes and flanking regions from two of approximately 11 different genomic histone clusters of the nematode Caenorhabditis elegans. Four histone genes from one cluster (H3, H4, H2B, H2A) and two histone genes from another (H4 and H2A) were analyzed. The predicted amino acid sequences of the two H4 and H2A proteins from the two clusters are identical, whereas the nucleotide sequences of the genes have diverged 9% (H2A) and 12% (H4). Flanking sequences, which are mostly not similar, were compared to identify putative regulatory elements. A conserved sequence of 34 base-pairs is present 19 to 42 nucleotides 3' of the termination codon of all the genes. Within the conserved sequence is a 16-base dyad sequence homologous to the one typically found at the 3' end of histone genes from higher eukaryotes. The C. elegans core histone genes are organized as divergently transcribed pairs of H3-H4 and H2A-H2B and contain 5' conserved sequence elements in the shared spacer regions. One of the sequence elements, 5' CTCCNCCTNCCCACCNCANA 3', is located immediately upstream from the canonical TATA homology of each gene. Another sequence element, 5' CTGCGGGGACACATNT 3', is present in the spacer of each heterotypic pair. These two 5' conserved sequences are not present in the promoter region of histone genes from other organisms, where 5' conserved sequences are usually different for each histone class. They are also not found in non-histone genes of C. elegans. These putative regulatory sequences of C. elegans core histone genes are similar to the regulatory elements of both higher and lower eukaryotes. The coding regions of the genes and the 3' regulatory sequences are similar to those of higher eukaryotes, whereas the presence of common 5' sequence elements upstream from genes of different histone classes is similar to histone promoter elements in yeast. ------------------- Key: 1151 Medline: 89276524 Authors: Hosono R;Nishimoto S;Kuno S Title: Alterations of life span in the nematode Caenorhabditis elegans under monoxenic culture conditions. Citation: Experimental Gerontology 24: 251-264 1989 Type: ARTICLE Genes: emb-5 zyg-2 zyg-9 Abstract: The nematode Caenorhabditis elegans was cultured monoxenically with E. coli as a food source and the influence of the bacterial growth conditions on the life span was studied. When bacterial growth was restricted by reducing the concentration of bactopeptone, which was supplied as the energy source in nematode growth medium (NGM), the nematode's life span tended to be prolonged without a marked effect on postembryonic development. The effect of bactopeptone on the life span was clearly observed during the postreproductive period (that is, after the egg-laying stage of the wild-type C. elegans) rather than during the larval to young adult stage. Evidence is presented that this alteration of the life span was not brought about by any factor in the bactopeptone but by the concentration of bacteria. ------------------- Key: 1152 Medline: 89291273 Authors: Strome S Title: Generation of cell diversity during early embryogenesis in the nematode Caenorhabditis elegans. Citation: International Review of Cytology 114: 81-124 1989 Type: REVIEW Genes: glp-1 par-1 par-2 par-3 par-4 zyg-9 Abstract: Caenorhabditis elegans zygotes undergo a series of four differentiative divisions to generate 5 somatic founder cells and a germ-line progenitor cell by the 16- to 24-cell stage of embryogenesis. The pattern of divisions, cell positions, and development of the embryonic cells are invariant from embryo to embryo. Through a combination of embryo manipulation, treatment of embryos with pharmacologic agents, and genetic analysis of maternal- effect embryonic-lethal mutants, researchers in several laboratories have investigated when and how cell differences are generated and cell fates are specified during embryogenesis: 1. Most blastomeres develop in a cell-autonomous manner. They do not need to undergo cell division and they do not require their normal neighbors to express differentiation products characteristic of their lineage. In embryos in which specific cells have been ablated, the fates of neighboring cells do not change to compensate for the missing cells. These observations suggest that most embryonic cells are determined by lineally transmitted internally segregated information. 2. There is at least one clear-cut example of inductive interactions during early development. The anterior daughter of AB gives rise to hypodermis, neurons, pharyngeal muscles, and body wall muscles. Interactions between ABa cells and P1-derived blastomeres are required between the 4- and 28-cell stage for ABa to generate pharyngeal and body wall muscles. ABa appears to be directed to generate hypodermis by internally segregated cues and directed to generate muscle by external cues. 3. Certain of the early internal segregation events require the participation of microfilaments. Disruption of the microfilament array leads to the missegregation of germ granules and of the potential of cells to undergo unequal germ-line-like divisions. Microfilaments may be involved in many other segregation events as well. 4. Several maternal-effect lethal mutants also perturb zygotic segregation events. These par mutants, which divide symmetrically and fail to segregate germ granules, may identify genes whose products interact with microfilaments or otherwise participate in cytoplasmic localization during ------------------- Key: 1153 Medline: 90183787 Authors: Maine EM;Kimble J Title: Identification of genes that interact with glp-1, a gene required for inductive cell interactions in Caenorhabditis elegans. Citation: Development 106: 133-143 1989 Type: ARTICLE Genes: dpy-1 dpy-2 dpy-3 dpy-7 dpy-8 dpy-9 dpy-10 glp-1 sqt-1 Abstract: The glp-1 gene functions in two inductive cellular interactions and in development of the embryonic hypodermis of C. elegans. We have isolated six mutations as recessive suppressors of temperature- sensitive (ts) mutations of glp-1. By mapping and complementation tests, we found that these suppressors are mutations of known dumpy (dpy) genes; dpy genes are required for development of normal body shape. Based on this result, we asked whether mutations previously isolated in screens for mutants defective in body shape could also suppress glp-1(ts). From these tests, we learned that unselected mutations of eight genes required for normal C. elegans morphogenesis, including the four already identified, suppress glp- 1(ts). All of these suppressors rescue all three mutant phenotypes of glp-1(ts) (defects in embryonic induction of pharyngeal tissue, in embryonic hypodermis development, and in induction of germline proliferation). However, they do not rescue putative glp-1 null mutants and therefore do not bypass the requirement for glp-1 in development. In the light of current ideas about the molecular nature of the glp-1 and suppressor gene products, we propose an interaction between the glp-1 protein and components of the extracellular matrix and speculate that this interaction may impose spatial constraints on the decision between mitosis and meiosis in the germline. ------------------- Key: 1154 Medline: 89357450 Authors: Hartman PS;Hevelone J;Dwarakanath V;Mitchell DL Title: Excision repair of UV radiation-induced DNA damage in Caenorhabditis elegans. Citation: Genetics 122: 379-385 1989 Type: ARTICLE Genes: rad-1 rad-2 rad-3 rad-7 Abstract: Radioimmunoassays were used to monitor the removal of antibody- binding sites associated with the two major UV radiation-induced DNA photoproducts [cyclobutane dimers and (6-4) photoproducts]. Unlike with cultured human cells, where (6-4) photoproducts are removed more rapidly than cyclobutane dimers, the kinetics of repair were similar for both lesions. Repair capacity in wild type diminished throughout development. The radioimmunoassays were also employed to confirm the absence of photoreactivation in C. elegans. In addition, three radiation-sensitive mutants (rad-1, rad-2, rad-7) displayed normal repair capacities. An excision defect was much more pronounced in larvae than embryos in the fourth mutant tested (rad-3). This correlates with the hypersensitivity pattern of this mutant and suggests that DNA repair may be developmentally regulated in C. elegans. The mechanism of DNA repair in C. elegans as well as the relationship between the repair of specific photoproducts and UV radiation sensitivity during development are discussed. ------------------- Key: 1155 Medline: Authors: Moerman DG;Waterston RH Title: Mobile elements in Caenorhabditis elegans and other nematodes. Citation: "Mobile DNA." Berg DE and Howe MM (eds), American Society for Microbiology. : 537-556 1989 Type: REVIEW Genes: ced-4 dpy-5 dpy-19 lin-12 mut-2 mut-4 mut-5 sma-1 tra-2 unc-15 unc-22 unc-37 unc-54 unc-105 Abstract: Transposable elements have recently been described in several species: Caenorhabditis elegans, Caenorhabditis briggsae, Ascaris lumbricoides, and Panagrellus redivivus. Because of the intense interest in C. elegans as an experimental organism for developmental genetic studies and the availability of sophisticated genetics, most is know about transposons in this species. This review focuses principally on Tc1 (Tc=transposon) of C. elegans, the best understood element in nematodes. Other elements in C. elegans and also elements in other species of nematodes will be briefly surveyed. The interested reader should also see two recent related reviews. The genome of C. elegans is 8 x 10(7) base pairs (bp) in extent, the smallest known for any metazoan. There are six chromosomes per haploid set, and about 83% of C. elegans DNA behaves as single-copy sequence in renaturation experiments. The repeated sequences are of several types, including functional genes, inverted or "foldback" sequences, and short repeated sequences of a few hundred nucleotides. The global arrangment of these short repeats is of the "short-period-interspersion" or "Xenopus" pattern. Some of the repetitive sequences consist of transposable elements, and at least five distinct families have been identified in C. elegans, Tc1 through Tc5. The sequence of one Tc1 element has been determined and shows that Tc1 resembles bacterial insertion sequence elements with terminal inverted repeats and a central open reading frame. The complete sequences for any members of the other transposon families have not been determined, but the data suggest that Tc2, Tc3, and Tc5 are also insertion sequence-like in structure and that Tc4 is foldbacklike in structure. No "retrotransposon-like" elements have been identified in C. elegans, although such elements have been described in A. ------------------- Key: 1156 Medline: Authors: Zuckerman BM;Dicklow MB;Coles GC;Garcia-E R;Marban-Mendoza Title: Suppression of plant parasitic nematodes in the chinampa agricultural soils. Citation: Journal of Chemical Ecology 15: 1947-1955 1989 Type: ARTICLE Genes: Abstract: Soil from the chinampa agricultrual system in the Valley of Mexico suppressed damage by plant-parasitic nematodes to tomatoes and beans in greenhouse and growth chamber trials. Sterilization of the chinampa soil resulted in a loss of the suppressible effect, thereby indicating that one or more biotic factors were responsible for the low incidence of nematode damage. Nine organisms were isolated from chinampa soil, which showed antinematodal properties in culture. Naturally occurring populations of plant-parasitic nematodes were of lower incidence in chinampa soil than in Chapingo soil. ------------------- Key: 1157 Medline: 89329026 Authors: Kagawa H;Gengyo K;McLachlan AD;Brenner S;Karn J Title: Paramyosin gene (unc-15) of Caenorhabditis elegans. Molecular cloning, nucleotide sequence and models for thick filament structure. Citation: Journal of Molecular Biology 207: 311-333 1989 Type: ARTICLE Genes: unc-15 Abstract: Paramyosin is a major structural component of thick filaments isolated from many invertebrate muscles. The Caenorhabditis elegans paramyosin gene (unc-15) was identified by screening with specific antibodies an "exon-expression" library containing lacZ/nematode gene fusions. Short probes recovered from the library were used to identify bacteriophage lambda and cosmid clones that encompass the entire paramyosin (unc-15) gene. From these clones, numerous subclones containing epitopes reacting with anti-paramyosin sera were obtained, providing strong evidence that the initial cloned fragment was, in fact, derived from the structural gene for paramyosin. The complete nucleotide sequence of a 12 x 10(3) base-pair region spanning the gene was obtained. The gene is composed of ten short exons encoding a protein of 866 [corrected] amino acid residues. Paramyosin is highly similar to residues 267 to 1089 of myosin heavy chain rods. For most of its length, paramyosin appears to form an alpha-helical coiled-coil and shows the expected heptad repeat of hydrophobic amino acid residues and the 28-residue repeat of charged amino acids characteristic of myosin heavy chain rods. However, paramyosin differs from myosin in having non-helical extensions at both the N and C termini and an additional "skip" residue that interrupts the 28-residue repeat. The distribution of charges along the length of the paramyosin rod is also significantly different from that of myosin heavy chain rods. Potential charge-mediated interactions between paramyosin rods and between paramyosin and myosin rods were calculated using a model successfully applied previously to the analysis of the myosin rod sequences. Myosin rods aligned in parallel show optimal charge-charge interactions at multiples of 98 residue staggers (i.e. at axial displacements of multiples of 143 A). Paramyosin rods, in contrast, appear to interact optimally at parallel staggers of 493 residues (i.e. at axial displacements of 720 A) but show only weak interaction peaks at 98 or 296 residues. Similar calculations suggest optimal interactions between paramyosin molecules and myosin rods and in their anti- parallel alignments. The implications of these results for the structure of the bare zone and the assembly of nematode thick filaments are discussed. ------------------- Key: 1158 Medline: 89329036 Authors: Schriefer LA;Waterston RH Title: Phosphorylation of the N-terminal region of Caenorhabditis elegans paramyosin. Citation: Journal of Molecular Biology 207: 451-454 1989 Type: ARTICLE Genes: unc-15 Abstract: Paramyosin from Caenorhabditis elegans was examined for post- translational modification by phosphorylation. Paramyosin purified from populations of mixed-age animals contained 0.7 to 2.0 moles of phosphate per mole of paramyosin. Paramyosin was also phosphorylated in vitro by an endogenous kinase in the particulate fraction. Analysis of the in vitro phosphorylated paramyosin in comparison with the DNA sequence of the unc-15 paramyosin gene of C. elegans shows that serine residues in the non-alpha-helical N-terminal region are the targets of the kinase. The N-terminal region of paramyosin has significant similarity to the non-helical C-terminal region of the two body wall myosin heavy chains of C. elegans. All three regions contain three copies of a Ser-*-Ser-*-Ala motif, the most likely target for phosphorylation in paramyosin, suggesting that these regions may be modified by the same kinase. ------------------- Key: 1159 Medline: 89306577 Authors: Heschl MFP;Baillie DL Title: Identification of a heat-shock pseudogene from Caenorhabditis elegans. Citation: Genome 32: 190-195 1989 Type: ARTICLE Genes: hsp-1 hsp-2ps Abstract: While characterizing the hsp70 gene family from Caenorhabditis elegans we encountered an unusual member of this family. Sequence data reveal that the hsp-2ps gene is a pseudogene of the constitutively expressed, heat-inducible hsp-1 gene. Two stop codons generated near the 5' end of the sequence as well as several frameshift mutations and a large internal deletion confirm the identification of hsp-2ps as a pseudogene. The nucleotide substitution rate of the third codon position was twice that of the first and second codon positions, suggesting that the hsp-2ps gene was nonfunctional since the time of the duplication event. The hsp- 2ps gene duplicates a region of the hsp-1 gene that lies exclusively within the transcribed region and retains the introns. We feel that the hsp-2ps gene was produced by a transpositional duplication event, which occurred approximately 8.5 million ------------------- Key: 1160 Medline: 89255506 Authors: Barstead RJ;Waterston RH Title: The basal component of the nematode dense-body is vinculin. Citation: Journal of Biological Chemistry 264: 10177-10185 1989 Type: ARTICLE Genes: deb-1 Abstract: We have constructed a genomic DNA expression library and screened it with antibodies in order to clone the deb-1 gene from the nematode Caenorhabditis elegans. This gene encodes a protein found at the base of the muscle dense-bodies, structures which attach actin thin filaments to the sarcolemma. We report the complete sequence of the deb-1 gene, its localization on the C. elegans genetic map, and the finding that it encodes a protein with a sequence very similar to chicken vinculin. We also show that the difference in size between this nematode protein and chicken vinculin is due in part to the absence from the nematode sequence of one of the three internal repeats found in the chicken sequence. ------------------- Key: 1161 Medline: 89276710 Authors: Cleavinger PJ;McDowell JW;Bennett KL Title: Transcription in nematodes: Early Ascaris embryos are transcriptionally active. Citation: Developmental Biology 133: 600-604 1989 Type: ARTICLE Genes: Abstract: In this report we analyze early zygotic gene expression in the parasitic nematode Ascaris lumbricoides var. suum. Using synchronous populations of early embryonic stages, nuclei were isolated, and in vitro run-off transcription assays were performed. We find transcriptional activity as early as the 4- to 8-cell stage. The percentage of RNA polymerase II activity, as measured in these assays, is >80% of the total transcription at the 60 cell stage. Furthermore, we show that a specific transcript (actin) can be identified in all early stages tested. ------------------- Key: 1163 Medline: 89306623 Authors: Savage C;Hamelin M;Culotti JG;Coulson A;Albertson DG;Chalfie M Title: mec-7 is a beta-tubulin gene required for the production of 15-protofilament microtubules in Caenorhabditis elegans. Citation: Genes & Development 3: 870-881 1989 Type: ARTICLE Genes: mec-7 uDf1 stDp2 Abstract: In the nematode Caenorhabditis elegans, microtubules with 15 protofilaments are a specialized feature of six touch-receptor neurons; microtubules found in other C. elegans neurons have 11 protofilaments. Mutations in the gene mec-7 result in touch- insensitive animals whose touch cells lack the 15-protofilament microtubules. We have characterized 54 mutations in the mec-7 gene. The absence of mec-7 activity results selectively in the recessive loss of touch sensitivity. Partial loss-of-function alleles result in a partial loss of touch sensitivity. Dominant mutations, which are isolated at an unusually high proportion, may encode abnormal products. We have cloned the mec-7 gene; it encodes a beta-tubulin which is 90-93% identical to vertebrate beta-tubulin. Our results are consistent with the hypothesis that tubulin heterogeneity contributes to the formation of structurally and functionally distinct sets of microtubules. ------------------- Key: 1164 Medline: 89281567 Authors: Nelson GA;Schubert WW;Marshall TM;Benton ER;Benton EV Title: Radiation effects in Caenorhabditis elegans. Mutagenesis by high and low LET ionizing radiation. Citation: Mutation Research 212: 181-192 1989 Type: ARTICLE Genes: eT1 Abstract: The nematode C. elegans was used to measure the effectiveness of high- energy ionized particles in the induction of 3 types of genetic lesions. Recessive lethal mutations in a 40-map unit autosomal region, sterility, and X-chromosome nondisjunction or damage were investigated. Induction rates were measured as a function of linear energy transfer, LET infinity, for 9 ions of atomic number 1-57 accelerated at the BEVALAC accelerator. Linear kinetics were observed for all 3 types of lesions within the dose/fluence ranges tested and varied strongly as a function of particle LET infinity. Relative Biological Effectiveness (RBE) values of up to 4.2 were measured and action cross sections were calculated and compared to mutagenic responses in other systems. ------------------- Key: 1165 Medline: 89350901 Authors: Schaeffer JM;Bergstrom AR;Turner MJ Title: MK-801 is a potent nematocidal agent. Characterization of MK-801 binding sites in Caenorhabditis elegans. Citation: Biochemical Journal 260: 923-926 1989 Type: ARTICLE Genes: Abstract: MK-801, an N-methyl-D-aspartate antagonist in mammalian brain tissue, is a potent nematocidal agent. Specific MK-801 binding sites have been identified and characterized in a membrane fraction prepared from the free-living nematode Caenorhabditis elegans. The high- affinity MK-801 binding site has an apparent dissociation constant, Kd, of 225 nM. Unlike the MK-801 binding site in mammalian tissues, the C. elegans binding site is not effected by glutamate or glycine, and polyamines are potent inhibitors of specific MK-801 binding. ------------------- Key: 1166 Medline: 89276723 Authors: Shakes DC;Ward S Title: Initiation of spermiogenesis in C. elegans: A pharmacological and genetic analysis. Citation: Developmental Biology 134: 189-200 1989 Type: ARTICLE Genes: spe-8 spe-12 Abstract: Spermiogenesis in Caenorhabditis elegans involves the conversion of spherical, sessile spermatids into bipolar, crawling spermatozoa. In males, spermiogenesis is induced by mating, while in hermaphrodites, spermiogenesis occurs before the first oocytes are fertilized. Alternatively, spermiogenesis can be induced in vitro by treatment with monensin triethanolamine, or pronase. Treatment with the calmodulin inhibitors, trifluoperazine, chlorpromazine, or W7, also induces spermiogenesis in vitro with a half maximal effect at 20 microM. Upon initial activation, spermatids extend long, thin spikes and undergo extensive cellular movements. Eventually, a single motile pseudopod forms through the restructuring of one or more of these spikes. These transient spikes can be prolonged in vitro by removing triethanolamine as soon as the spermatids first form spikes. Spermatids from spe-8 and spe-12 spermatogenesis-defective (spe) mutants activate in vivo with male but not hermaphrodite sperm activator. In vitro, the mutant spermatids arrest spermiogenesis at the spike stage when activated with pronase, but form normal spermatozoa if subsequently or initially treated with monensin or triethanolamine. We present a model of spermiogenesis in which the mutant defects and the action of the pharmacological agents are ordered relative to one ------------------- Key: 1167 Medline: 89306584 Authors: Starr T;Howell AM;McDowall J;Peters K;Rose AM Title: Isolation and mapping of DNA probes within the linkage group I gene cluster of Caenorhabditis elegans. Citation: Genome 32: 365-372 1989 Type: ARTICLE Genes: dpy-1 unc-29 sDp2 Abstract: We have isolated probes for DNA polymorphisms across the linkage group I gene cluster in Caenorhabditis elegans, using Tc1-linkage selection. The probes detect strain polymorphism between the wild- type strains of var. Bristol and var. Bergerac. As a result of mapping the sites hP4, hP5, hP6, hP7, hP9, and sPl, more than 1000 kilobases (kb) of cloned cosmid DNA has been positioned on the genetic map. We found there is more DNA per map unit in the center of the gene cluster than expected on the basis of the genomic average. Furthermore, the amount is not constant across the entire region but reaches a peak in the hP9 unc-13 interval. To find the coding regions, we examined DNA cross-homology between two species, Caenorhabditis elegans and Caenorhabditis briggsae. Approximately one- third of the DNA in the hP5 hP9 interval was examined for coding regions and 21 sequences were identified within 318 ------------------- Key: 1168 Medline: Authors: Herman RK Title: Caenorhabditis elegans. Citation: Genome 31: 478-479 1989 Type: NEWS Genes: dpy-13 fem-1 him-6 mec-7 sqt-1 tra-1 eT1 sDp2 Abstract: Eight speakers described current research on the small nematode Caenorhabditis elegans, a popular model for the genetic analyis of animal development and behavior. ------------------- Key: 1169 Medline: 89288324 Authors: Seydoux G;Greenwald I Title: Cell autonomy of lin-12 function in a cell fate decision in C. elegans. Citation: Cell 57: 1237-1245 1989 Type: ARTICLE Genes: lin-12 qDp3 Abstract: The lin-12 gene of C. elegans encodes a predicted transmembrane protein that controls a decision by two cells, Z1.ppp and Z4.aaa, between the anchor cell (AC) and ventral uterine precursor cell (VU) fates. We performed laser ablation experiments to demonstrate that specification of the VU fate of Z1.ppp or Z4.aaa depends on an "AC-to- VU" signal from the presumptive AC. We generated genetic mosaics in which defined cells lacked lin-12 activity. By correlating the fates of Z1.ppp and Z4.aaa with the lin-12 genotype of nearly every cell in these mosaics, we conclude that lin-12 function is VU cell autonomous. We present a model in which lin-12 functions in the receiving mechanism for the "AC-to-VU" signal leading to the specification of the AC and VU fates of Z1.ppp and ------------------- Key: 1170 Medline: 89282774 Authors: Kamb A;Weir M;Rudy B;Varmus H;Kenyon C Title: Identification of genes from pattern formation, tyrosine kinase, and potassium channel families by DNA Citation: Proceedings of the National Academy of Sciences USA 86: 4372-4376 1989 Type: ARTICLE Genes: mab-5 Abstract: The study of gene family members has been aided by the isolation of related genes on the basis of DNA homology. We have adapted the polymerase chain reaction to screen animal genomes very rapidly and reliably for likely gene family members. Using conserved amino acid sequences to design degenerate oligonucleotide primers, we have shown that the genome of the nematode Caenorhabditis elegans contains sequences homologous to many Drosophila genes involved in pattern formation, including the segment polarity gene wingless (vertebrate int-1), and homeobox sequences characteristic of the Antennapedia, engrailed, and paired families. In addition, we have used this method to show that C. elegans contains at least five different sequences homologous to genes in the tyrosine kinase family. Lastly, we have isolated six potassium channel sequences from humans, a result that validates the utility of the method with large genomes and suggests that human potassium channel gene diversity may be extensive. ------------------- Key: 1171 Medline: 89339144 Authors: Nusbaum C;Meyer BJ Title: The Caenorhabditis elegans gene sdc-2 controls sex determination and dosage compensation in XX animals. Citation: Genetics 122: 579-593 1989 Type: ARTICLE Genes: dpy-28 fem-3 her-1 sdc-1 sdc-2 xol-1 Abstract: We have identified a new X-linked gene, sdc-2, that controls the hermaphrodite (XX) modes of both sex determination and X chromosome dosage compensation in Caenorhabditis elegans. Mutations in sdc-2 cause phenotypes that appear to result from a shift of both the sex determination and dosage compensation processes in XX animals to the XO modes of expression. Twenty-eight independent sdc-2 mutations have no apparent effect in XO animals, but cause two distinct phenotypes in XX animals: masculinization, reflecting a defect in sex determination, and lethality or dumpiness, reflecting a disruption in dosage compensation. The dosage compensation defect can be demonstrated directly by showing that sdc-2 mutations cause elevated levels of several X-linked transcripts in XX but not XO animals. While the masculinization is blocked by mutations in sex determining genes required for male development (her-1 and fem-3), the lethality, dumpiness and overexpression of X-linked genes are not, indicating that the effect of sdc-2 mutations on sex determination and dosage compensation are ultimately implemented by two independent pathways. We propose a model in which sdc-2 is involved in the coordinate control of both sex determination and dosage compensation in XX animals and acts in the regulatory hierarchy at a step prior to the ------------------- Key: 1172 Medline: 89322366 Authors: Schaeffer JM;Haines HW Title: Avermectin binding in Caenorhabditis elegans. A two-state model for the avermectin binding site. Citation: Biochemical Pharmacology 38: 2329-2338 1989 Type: ARTICLE Genes: Abstract: Specific binding sites for ivermectin (IVM; 22,23-dihydroavermectin- B1) were identified and characterized in a crude membrane fraction prepared from the nematode, Caenorhabditis elegans (C. elegans). Specific [3H]IVM binding was saturable with an apparent dissociation constant, Kd, of 0.26 nM and a receptor concentration of 3.53 pmol/mg protein. [3H]IVM binding in C. elegans was linear with tissue protein concentration, and optimal binding occurred within a pH range of 7.3 to 7.6. Kinetic analysis of the binding showed that the reaction proceeded by a two-step mechanism. Initially, a rapidly reversible complex was formed and, after additional incubation, this complex was transformed to a much more slowly reversible complex. Stereospecificity of [3H]IVM binding to C. elegans membranes was demonstrated by competition with a series of avermectin derivatives. The in vivo effects of IVM and its derivatives on C. elegans motility were concentration dependent and correlated well with their relative binding affinities. Several putative neurotransmitters including gamma-aminobutyric acid (GABA), carbamyl choline, taurine, glutamate and dopamine were tested and found to have no effect on IVM binding. Specific IVM binding sites were also identified in rat brain; however, the affinity was approximately 100-fold lower than that observed in C. elegans and stereospecificity studies demonstrated structural differences in the two binding sites. These results are the first direct demonstration of a specific IVM binding site in nematodes and thus are important in furthering our understanding of its mode of action. ------------------- Key: 1173 Medline: 89313989 Authors: Sadaie T;Sadaie Y Title: Rad-2-dependent repair of radiation-induced chromosomal aberrations in Caenorhabditis elegans. Citation: Mutation Research 218: 25-31 1989 Type: ARTICLE Genes: rad-2 Abstract: A method involving light microscopy was developed and utilized for the observation of gamma- or ultraviolet-induced aberrations of the chromosomes of Caenorhabditis elegans var. Bristol (N2). Gravid worms were irradiated and the chromosomes were examined in the early embryos derived from eggs fertilized after the irradiation. The frequency of gamma-induced aberrations in the early embryonic cells of C. elegans increased proportionally with the dosage of gamma-rays. It decreased greatly following incubation of the irradiated gravid worms for 2 days. This decrease was blocked by the rad-2 mutation but not by the rad-1 mutation of the same epistasis group. Both mutations make worms sensitive to radiation and chemicals. In addition, the hatchability of eggs laid by the rad-2 mutant after irradiation was restored very quickly as was that of the wild-type strain. Ultraviolet irradiation, on the other hand, induced few aberrations in both the wild-type and rad-1 strains, but it caused an elevated frequency of aberrations in the rad-2 strain. Ultraviolet irradiation strongly blocked the separation of chromosomes of the rad-2 strain. Furthermore, hatchability was very low in eggs laid by ultraviolet- irradiated rad-2 worms. These results suggest the existence of a rad- 2-dependent mechanism for gonadal repair of chromosomal aberrations, including chromosomal non-separation, and indicate that gamma-induced chromosome aberrations are not fatal to the hatching of Caenorhabditis elegans which has holocentric chromosomes. ------------------- Key: 1174 Medline: 89306174 Authors: Shakes DC;Ward S Title: Mutations that disrupt the morphogenesis and localization of a sperm-specific organelle in Caenorhabditis elegans. Citation: Developmental Biology 134: 307-316 1989 Type: ARTICLE Genes: spe-10 unc-22 hcDf1 Abstract: Nematode sperm contain unusual organelles, membranous organelles, which undergo dramatic morphological changes during spermatogenesis. Early in spermatogenesis, the membranous organelle functions to transport sperm specific components to the spermatids; later, during the formation of the crawling spermatozoa, it adds new components to the cell surface as it fuses with the plasma membrane. Genetic analysis of spermatogenesis in the nematode Caenorhabditis elegans has revealed mutations that specifically disrupt the proper cellular localization and morphogenesis of this organelle. In animals homozygous for the either the known deficiency hcDf1 or the probable deficiency h12, the membranes of the membranous organelles are aberrantly covered with ribosomes. A mutation in the spermatogenesis- defective spe-10 gene causes severe defects in the morphogenesis of a fibrous body-membranous organelle complex. In both cases, these mutations also disrupt the proper localization of both nuclei and membranous organelles in haploid spermatids and spermatozoa. ------------------- Key: 1175 Medline: 89366311 Authors: Scott AL;Dinman J;Sussman DJ;Ward S Title: Major sperm protein and actin genes in free-living and parasitic nematodes. Citation: Parasitology 98: 471-478 1989 Type: ARTICLE Genes: msp-3 Abstract: The DNA from a number of free-living and parasitic nematode species was examined to determine the genomic number and distribution of DNA sequences encoding two evolutionarily conserved proteins; the major sperm protein (MSP) and nematode actin. Ascaris and Caenorhabditis MSP cDNA sequences and Ascaris genomic actin sequences were used to probe Southern blots of Eco RI and Hin d III digested nematode DNA. The number of MSP genes varied widely between the 1 MSP gene in Ascaris and the 60 MSP genes in Caenorhabditis. Filarial nematodes appeared to have 1-4 MSP genes while the plant and insect parasitic species showed from 5-12 MSP-hybridizing restriction fragments. Mammalian intestinal parasites showed between 1 and 13 bands hybridizing with the MSP probes. Blots probed to estimate the number of actin genes showed that, with the exception of Ascaris which contains more than 20 germ line sequences that encode actin, all of the nematodes tested had between 3 and 9 bands that hybridized to the Ascaris genomic actin probe. The possible use of highly conserved sequences such as MSP and actin to differentiate between nematode species in diagnostic and taxonomic studies is discussed. ------------------- Key: 1176 Medline: 90014812 Authors: Nilsen TW;Shambaug J;Denker J;Chubb G;Faser C;Putnam L;Bennett K Title: Characterization and expression of a spliced leader RNA in the parasitic nematode Ascaris lumbricoides var. suum. Citation: Molecular and Cellular Biology 9: 3543-3547 1989 Type: REVIEW Genes: Abstract: The parasitic nematode Ascaris spp. contains a 22-nucleotide spliced-leader (SL) sequence identical to the trans-SL previously described in Caenorhabditis elegans and other nematodes. The SL comprises the first 22 nucleotide of a -110-base RNA and is transcribed by RNA polymerase II. The SL RNA contains a trimethylguanosine cap and a consensus Sm binding site. Furthermore, the Ascaris SL RNA has the potential to adopt a secondary structure which is nearly identical to potential secondary structures of similar SL RNAs in C. elegans and Brugia malayi. ------------------- Key: 1177 Medline: 90007535 Authors: Prasad SS;Baillie DL Title: Evolutionarily conserved coding sequences in the dpy-20 - unc-22 region of Caenorhabditis elegans. Citation: Genomics 5: 185-198 1989 Type: ARTICLE Genes: mDf7 sDf2 sDf7 sDf8 sDf9 sDf10 Abstract: Caenorhabditis elegans provides an excellent opportunity to study the organization of a complex genome. The alignment of the genetic and molecular maps over a large stretch of the genome is an essential part of this study. The objective of this paper was the identification and characterization of coding regions in four cosmids containing DNA from the interval between dpy-20 and unc-22 on linkage group IV. These cosmids were characterized with regard to the map position and the developmental patterns of expression of coding sequences. Since an extensive genetic map already exists for this region, this detailed description of the coding sequences in the dpy- 20-unc-22 region will make possible alignment of the molecular and genetic maps for this portion of the C. elegans genome. In this study, we have used interspecies cross-hybridization to localize and identify potential coding elements. We have investigated four cosmids containing approximately 150 kb of C. elegans genome adjacent to the well-characterized muscle gene, unc-22(IV). Fragments subcloned from the four cosmids were hybridized at moderate stringency to the genome of the related species, Caenorhabditis briggsae. In this way nine potential coding regions were identified. Seven of these nine fragments also hybridized to mRNA transcripts on Northern blots. Five of the seven showed maximal hybridization to RNA from L2-stage animals, a pattern that resembles that of actin transcription. It is speculated that the functions of these five may in some way be related to one another, and perhaps also to that of unc-22, which is itself a muscle gene. ------------------- Key: 1178 Medline: 90012207 Authors: Krause M;Wild M;Rosenzweig B;Hirsh D Title: Wild type and mutant actin genes in Caenorhabditis elegans. Citation: Journal of Molecular Biology 208: 381-392 1989 Type: ARTICLE Genes: act-1 act-2 act-3 act-4 Abstract: We have sequenced the four actin genes of Caenorhabditis elegans. These four genes encode typical invertebrate actins and are highly homologous, differing from each other by, at most, three amino acid residues. As a first step toward an understanding of the developmental regulation of this gene set we have also sequenced mutant actin genes. The mutant genes were cloned from two independent revertants of a single dominant actin mutant. For both revertants, reversion was accompanied by an actin gene rearrangement. The accumulation of actin mRNA during development in these two revertants is different from that of wild-type animals. We present here a correlation between actin gene structure and expression in wild-type and mutant animals. The results, suggest that co-ordinate regulation of actin genes is not essential for wild-type muscle function. In addition, it appears that changes in the 3' region of at least one of the actin mRNA may affect its steady-state regulation during development. ------------------- Key: 1179 Medline: 89336787 Authors: Yochem J;Greenwald I Title: glp-1 and lin-12, genes implicated in distinct cell-cell interactions in C. elegans, encode similar transmembrane proteins. Citation: Cell 58: 553-563 1989 Type: ARTICLE Genes: glp-1 lin-12 Abstract: Genomic DNA closely related in sequence to lin-12, a gene that specifies certain cell fates during C. elegans development, was isolated from a C. elegans library by low stringency hybridization. DNA sequencing of genomic and cDNA clones predicts the new sequence to encode an integral membrane protein that shares three repeated amino acid sequence motifs with the lin-12 product and the Drosophila Notch product: an epidermal growth factor-like motif, the "lin- 12/Notch Repeat," and a motif present in two yeast gene products that have cell cycle dependent functions. Austin and Kimble (see accompanying paper) present evidence that this sequence corresponds to glp-1, a gene implicated in cell-cell interactions distinct from those involving lin-12. Possible implications of the predicted structure of the glp-1 product with respect to these cell-cell interactions are discussed. ------------------- Key: 1180 Medline: 89336788 Authors: Austin J;Kimble J Title: Transcript analysis of glp-1 and lin-12, homologous genes required for cell interactions during development of C. elegans. Citation: Cell 58: 565-571 1989 Type: ARTICLE Genes: glp-1 lin-12 Abstract: The glp-1 and lin-12 genes mediate several cell interactions during C. elegans development. We have identified the glp-1 gene in a region about 20 kb from lin-12. In collaboration with Yochem and Greenwald (1989; see accompanying paper), we show that a sequence identified by its similarity to lin-12 is in fact glp-1. We find a single 4.4 kb glp-1 transcript and a distinct 4.6 kb lin-12 transcript. Expression of the glp-1 transcript during development differs from that of lin- 12. As expected from genetic analyses, glp-1 RNA is primarily in the germline while lin-12 RNA is primarily in the soma. Unexpectedly, we find that glp-1 RNA is also expressed in larval somatic tissues and that lin-12 RNA is abundant in early embryos. We suggest that glp-1 and lin-12 may play broader roles in development than previously thought. ------------------- Key: 1181 Medline: 90070197 Authors: Greenwald I Title: Cell-cell interactions that specify certain cell fates in C. elegans development. Citation: Trends in Genetics 5: 237-241 1989 Type: REVIEW Genes: glp-1 lin-12 Abstract: Cell-cell interactions are important for several cell fate decisions during C. elegans development. Two genes, lin-12 and glp-1, encode similar predicted transmembrane proteins that are members of a potentially ubiquitous family of proteins that may mediate intercellular communication. ------------------- Key: 1182 Medline: 90034106 Authors: Ferguson EL;Horvitz HR Title: The multivulva phenotype of certain Caenorhabditis elegans mutants results from defects in two functionally redundant pathways. Citation: Genetics 123: 109-121 1989 Type: ARTICLE Genes: lin-8 lin-9 lin-15 lin-35 lin-36 lin-37 lin-38 Abstract: We previously identified Caenorhabditis elegans mutants in which certain of the six vulval precursor cells adopt fates normally expressed by other vulval precursor cells. These mutants define genes that appear to function in the response to an intercellular signal that induces vulval development. The multivulva (Muv) phenotype of one such mutant, CB1322, results from an interaction between two unlinked mutations, lin-8(n111) II and lin-9(n112) III. In this paper, we identify 18 new mutations, which are alleles of eight genes, that interact with either lin-8(n111) or lin-9(n112) to generate a Muv phenotype. None of these 20 mutations alone causes any vulval cell lineage defects. The "silent Muv" mutations fall into two classes; hermaphrodites carrying a mutation of each class are Muv, while hermaphrodites carrying two mutations of the same class have a wild-type vulval phenotype. Our results indicate that the Muv phenotype of these mutants results from defects in two functionally- redundant pathways, thereby demonstrating that redundancy can occur at the level of gene pathways as well as at the level of gene ------------------- Key: 1183 Medline: 89327580 Authors: Sithigorngul P;Cowden C;Guastella J;Stretton AOW Title: Generation of monoclonal antibodies against a nematode peptide extract: another approach for identifying unknown peptides. Citation: Journal of Comparative Neurology 284: 389-397 1989 Type: ARTICLE Genes: Abstract: Monoclonal antibodies that cross-react with Ascaris neural antigens were generated in mice immunized with a conjugate made with keyhole limpet hemocyanin (KLH) linked to a crude peptide extract from Caenorhabditis elegans. The response to KLH was suppressed by injection of cyclophosphamide 3 days after immunization with a gamma-aminobutyric acid (GABA)-KLH conjugate. Screening of hybridomas was carried out by enzyme-linked immunosorbent assay and whole mount immunocytochemistry. Two similar clones produced antibodies that recognized a small subset of Ascaris neurons. This result suggests that the monoclonal antibody technique might be useful for identifying new neuropeptides since the antibodies can be used for localization of the neuropeptidelike substances and, potentially, for immunoaffinity chromatography. As a by-product of this experiment, monoclonal antibodies that recognize GABA-like immunoreactivity in whole mounts and plastic sections were also obtained. ------------------- Key: 1184 Medline: 89361662 Authors: Siddiqui SS;Aamodt E;Rastinejad F;Culotti J Title: Anti-tubulin monoclonal antibodies that bind to specific neurons in Caenorhabditis elegans. Citation: Journal of Neuroscience 9: 2963-2972 1989 Type: ARTICLE Genes: Abstract: We have identified 2 anti-tubulin monoclonal antibodies that bind to 2 different subpopulations of identified neurons in the simple nervous system of the nematode Caenorhabditis elegans. The antibodies also recognize specific tubulin isotypes from C. elegans that were separated by isoelectric focusing. Antibody 6-11B-1 intensely stained the mechanosensory neurons ALML, ALMR, PLML, PLMR, PVM, and AVM, plus neuron PVR by indirect immunofluorescence, and it bound to 1 of 2 major a-tubulin isotypes separated by isoelectric focusing. The epitope for antibody (Ab) 6-11B-1 is acetylated a-tubulin. Antibody 2-28-33 stained a set of neurons that contain the neurotransmitter GABA. It bound to the 2 major and 1 of the minor B-tubulin isotypes of C. elegans. These results suggest that specific a- and B-tubulin isotypes are greatly enriched in the subsets of neurons recognized by these antibodies. Most (possibly all) of the neurons in each subset are functionally related. The antibodies should allow us to examine whether specific tubulin isotypes have specific functions in these neurons. They may also be useful for examining neuron morphologies in mutants of C. ------------------- Key: 1185 Medline: 89354543 Authors: Sternberg PW;Horvitz HR Title: The combined action of two intercellular signaling pathways specifies three cell fates during vulval induction in C. elegans. Citation: Cell 58: 679-693 1989 Type: ARTICLE Genes: lin-2 lin-3 lin-7 lin-10 lin-12 lin-15 Abstract: Each of the six C. elegans vulval precursor cells (VPCs) has three potential fates (1 degree, 2 degrees, or 3 degrees). The fate of each VPC depends on two types of signals: a graded inductive signal that acts at a distance and a short-range lateral signal among the VPCs. We describe interactions among mutations that cause different misspecifications of VPC fates. Particular combinations of mutations cause all six VPCs to have a single fate independent of their positions. Our results suggest that specification of the three VPC fates is accomplished by two binary decisions, each effected by one of the two signaling pathways. The gene lin-12 acts in the lateral signaling pathway and specifies 2 degrees. The "vulvaless" and "multivulva" genes act in the inductive signaling pathway and specify 1 degree independently of lin-12 and 2 degrees via lin-12. We describe a model for the regulatory circuitry underlying VPC determination that includes a role for lin-12 in both autocrine and paracrine VPC signaling. ------------------- Key: 1186 Medline: 89359510 Authors: Hyman AA Title: Centrosome movement in the early divisions of Caenorhabditis elegans: A cortical site determining Citation: Journal of Cell Biology 109: 1185-1193 1989 Type: ARTICLE Genes: Abstract: In Caenorhabditis elegans embryos, early blastomeres of the P cell lineage divide successively on the same axis. This axis is a consequence of the specific rotational movement of the pair of centrosomes and nucleus (Hyman, A. A., and J. G. White. 1987. J. Cell Biol. 105:2123-2135). A laser has been used to perturb the centrosome movements that determine the pattern of early embryonic divisions. The results support a previously proposed model in which a centrosome rotates towards its correct position by shortening of connections, possibly microtubules, between a centrosome and a defined site on the cortex of the embryo. ------------------- Key: 1187 Medline: 89356269 Authors: Jones D;Dixon DK;Graham RW;Candido EPM Title: Differential regulation of closely related members of the hsp16 gene family in Caenorhabditis elegans. Citation: DNA 8: 481-490 1989 Type: ARTICLE Genes: Abstract: The heat-inducible genes encoding 16-kD heat shock polypeptides in Caenorhabditis elegans are found at two separate loci, one containing the 16-1 and 16-48 genes (locus A), and the other, the 16-2 and 16-41 genes (locus B). Despite the highly conserved structures of these genes and their promoters, the B locus produces up to sevenfold more mRNA during heat induction than does the A locus. Since there are two copies of the 16-1 and 16-48 genes at the A locus, the discrepancy in mRNA production is actually as high as 14:1 on a per gene basis. Measurements of the rate of hsp16 mRNA decay during recovery from a heat shock suggest that this difference is not caused by differential mRNA stability; furthermore, nuclear runon experiments yield rates of transcription for the 16-1/48 locus that are approximately threefold higher than those from the 16-2/41 locus. The higher levels of mRNA from the 16-2/41 locus, particularly at longer induction times, seem to be due to a marked difference in the temporal pattern of mRNA production from the two loci. While both loci are transiently activated by a heat shock, the 16-1 and 16-48 genes of the A locus are down-regulated to a lower transcription rate sooner than the genes from the B locus. ------------------- Key: 1188 Medline: 89387447 Authors: Harris LJ;Rose AM Title: Structural analysis of Tc1 elements in Caenorhabditis elegans var. Bristol (strain N2). Citation: Plasmid 22: 10-21 1989 Type: ARTICLE Genes: Abstract: The transposable element Tc1 in the genome of Caenorhabditis elegans var. Bristol strain N2 is very stable. In order to investigate possible causes of Tc1 immobility in this strain 17 individual isolates have been cloned and characterized with regard to their structure and genomic environment. Ten of 16 elements examined had identical restriction maps, and at least 1 of these (#7) showed a high level of somatic excision. Two of the elements had altered restriction sites, 2 had different internal deletions of about 700 bp, 1 had an 89-bp terminal deletion, and 1 a 54-bp insertion. When DNA sequences flanking the N2 Tc1 elements were used as probes in genomic hybridizations, it was found that most N2 elements are located in regions of repetitive DNA. Furthermore when hybridizations to DNA from N2 and var. Bergerac strain B0 were performed, a major band of the same size was observed in both strains. Two flanking sequences identified strain polymorphic sites hP2(IV) and hP3(IV). In at least one of these cases, a rearranged Tc1 was present in the B0 strain at the same location. The fact that all or most of the Tc1 elements are in the same location in N2 and B0 adds support to the hypothesis that the high copy number B0 strain arose from amplification of Tc1 copies in a N2-like strain. The N2 Tc1 elements are highly conserved; however, intact elements had fewer nucleotide changes than the rearranged elements. These results may indicate that the intact Tc1 elements in N2 are functionally active and subject to ------------------- Key: 1189 Medline: 90108689 Authors: Chisholm AD;Hodgkin J Title: The mab-9 gene controls the fate of B, the major male-specific blast cell in the tail region of Caenorhabditis elegans. Citation: Genes & Development 3: 1413-1423 1989 Type: ARTICLE Genes: lin-12 mab-9 nDf3 Abstract: The internal structures of the tail of male Caenorhabditis elegans nematodes are made by the descendants of four cells (B, Y, F, and U) which divide only in males. These cells are also present in hermaphrodites, where they have minor structural roles in the rectum. Here we show that the gene mab-9 is required for the correct development of two of these male-specific blast cells, B and F. In mutant males, the lineages of B and F resemble those of Y and U, respectively. These abnormal lineages lead to grossly defective male tails. We suggest that in mab-9 males the identities of B and F are transformed into Y and U, their respective anterior neighbors. The case for the F-to-U transformation is less strong than for the B-to-Y transformation because the wild-type lineages of F and U are very similar. Some mab-9 hermaphrodites are constipated as a result of abnormal rectal structure. This may be the result of an analogous fate transformation. mab-9 worms of both sexes are slightly uncoordinated. We propose that the fates of the four rectal cells are initially specified as two pairs (B and Y, F and U) and that the function of mab-9 in both sexes is to differentiate the posterior member of each pair from its anterior neighbor. ------------------- Key: 1190 Medline: 89384901 Authors: Burglin TR;Finney M;Coulson A;Ruvkun G Title: Caenorhabditis elegans has scores of homeobox-containing genes. Citation: Nature 341: 239-243 1989 Type: ARTICLE Genes: ceh-2 ceh-3 ceh-4 ceh-5 ceh-6 ceh-7 ceh-8 ceh-11 ceh-12 ceh-14 unc-86 Abstract: Homoeobox-containing genes control cell identities in particular spatial domains, cell lineages, or cell types during the development of Drosophila and Caenorhabditis elegans, and they probably control similar processes in vertebrates. More than 80 genes with homoeoboxes that have sequence similarities ranging from 25 to 100% have been isolated by genetic means or by DNA hybridization to previously isolated genes. We synthesized 500-2,000-fold degenerate oligonucleotides corresponding to a set of well-conserved eight amino acid sequences from the helix-3 region of the homoeodomain. We screened C. elegans genomic libraries with these probes and identified 49 putative homoeobox-containing loci. DNA sequencing confirmed that eight out of ten selected loci had sequences corresponding to the conserved helix-3 region plus additional flanking sequence similarity. One of these genes contained a sequence corresponding to a complete pou-domain and another was closely related to the homoeobox-containing genes caudal/cdx-1. The putative homoeobox loci were mapped to the physical contig map of C. elegans, allowing the identification of potentially corresponding genes from the correlated genetic map. We estimate that the number of homoeobox- containing genes in C. elegans is at least 60, constituting approximately 1% of the estimated total number of genes. ------------------- Key: 1191 Medline: 90066416 Authors: Bird DM;Riddle DL Title: Molecular cloning and sequencing of ama-1, the gene encoding the largest subunit of Caenorhabditis elegans RNA polymerase II. Citation: Molecular and Cellular Biology 9: 4119-4130 1989 Type: ARTICLE Genes: ama-1 rpc-1 mDf4 Abstract: Two genomic sequences that share homology with Rp11215, the gene encoding the largest subunit of RNA polymerase II in Drosophila melanogaster, have been isolated from the nematode Caenorhabditis elegans. One of these sequences was physically mapped on chromosome IV within a region deleted by the deficiency mDf4, 25 kilobases (kb) from the left deficiency breakpoint. This position corresponds to ama- 1 (resistance to alpha-amanitin), a gene shown previously to encode a subunit of RNA polymerase II. Northern (RNA) blotting and DNA sequencing revealed that ama-1 spans 10 kb, is punctuated by 11 introns, and encodes a 5.9-kb mRNA. A cDNA clone was isolated and partially sequenced to confirm the 3' end and several splice junctions. Analysis of the inferred 1,859-residue ama-1 product showed considerable identity with the largest subunit of RNAP II from other organisms, including the presence of a zinc finger motif near the amino terminus, and a carboxyl-terminal domain of 42 tandemly reiterated heptamers with the consensus Tyr Ser Pro Thr Ser Pro Ser. The latter domain was found to be encoded by four exons. In addition, the sequence oriented ama-1 transcription with respect to the genetic map. The second C. elegans sequence detected with the Drosophila probe, named rpc-1, was found to encode a 4.8-kb transcript and hybridized strongly to the gene encoding the largest subunit of RNA polymerase III from yeast, implicating rpc-1 as encoding the analogous peptide in the nematode. By contrast with ama-1, rpc-1 was not deleted by mDf4 or larger deficiencies examined, indicating that these genes are no closer than 150 kb. Genes flanking ama-1, including two collagen genes, also ------------------- Key: 1192 Medline: 90060702 Authors: Hodgkin J;Papp A;Pulak R;Ambros V;Anderson P Title: A new kind of informational suppression in the nematode Caenorhabditis elegans. Citation: Genetics 123: 301-313 1989 Type: ARTICLE Genes: dpy-5 lin-29 smg-1 smg-2 smg-3 smg-4 smg-5 smg-6 tra-1 tra-2 unc-54 Abstract: Independent reversions of mutations affecting three different Caenorhabditis elegans genes have each yielded representatives of the same set of extragenic suppressors. Mutations at any one of six loci act as allele-specific recessive suppressors of certain allels of unc- 54 (a myosin heavy chain gene), lin-29 (a heterochronic gene), and tra-2 (a sex determination gene). The same mutations also suppress certain alleles of another sex determination gene, tra-1, and of a morphogenetic gene, dpy-5. In addition to their suppression phenotype, the suppressor mutations cause abnormal morphogenesis of the male bursa and the hermaphrodite vulva. We name these genes smg-1 through smg-6 (suppressor with morphogenetic effect on genitalia), in order to distinguish them from mab (male abnormal) genes that can mutate to produce abnormal genitalia but which do not act as suppressors (smg-1 and smg-2 are new names for two previously described genes, mab-1 and mab-11). The patterns of suppression, and the interactions between the different smg genes, are described and discussed. In general, suppression is recessive and incomplete, and at least some of the suppressed mutations are hypomorphic in nature. A suppressible allele of unc-54 contains a deletion in the 3' noncoding region of the gene; the protein coding region of the gene is apparently unaffected. This suggests that the smg suppressors affect a process other than translation, for example mRNA processing, transport, or stability. ------------------- Key: 1193 Medline: 90008929 Authors: Guo X;Kramer JM Title: The two Caenorhabditis elegans basement membrane (type IV) collagen genes are located on separate chromosomes. Citation: Journal of Biological Chemistry 264: 17574-17582 1989 Type: ARTICLE Genes: emb-9 let-2 Abstract: We have identified and characterized the two genes, clb-1 and clb-2, that encode basement membrane collagen (IV) in Caenorhabditis elegans. Both genes encode 5.5-kilobase mRNAs, similar in size to the mammalian and Drosophila type IV collagen gene transcripts but much larger than the cuticle collagen transcripts of C. elegans. The nucleotide sequences of the NC1 regions of both genes were determined. Comparisons of the clb-1 and clb-2 NC1 amino acid sequences with those of mouse and human show that clb-1 shares 72% identity with mammalian alpha 2(IV) and clb-2 shares 63% identity with mammalian alpha 1(IV), suggesting that clb-1 is the alpha 2(IV) homologue and clb-2 is the alpha 1(IV) homologue. The presence of two type IV collagen genes in C. elegans and the mammals, but a single gene in Drosophila, indicates that the primordial type IV collagen gene had already duplicated early in the evolution of the invertebrates and that one of the genes has been subsequently lost from Drosophila. The mouse and human alpha 1(IV) and alpha 2(IV) genes are separated by only about 130 base pairs and are transcribed in opposite directions from overlapping promoters. We show that the C. elegans genes are located on separate chromosomes, clb-1 on X and clb-2 on III, demonstrating that the mammalian arrangement is not a requirement for all type IV collagen genes. We have identified a candidate genetic locus for the clb-2 basement membrane collagen gene, which will allow us to pursue a genetic analysis of basement membrane structure and function in C. elegans. ------------------- Key: 1194 Medline: 90059937 Authors: Fire A;Waterston RH Title: Proper expression of myosin genes in transgenic nematodes. Citation: EMBO Journal 8: 3419-3428 1989 Type: ARTICLE Genes: myo-3 unc-54 Abstract: Caenorhabditis elegans has four genes which encode skeletal myosin heavy chain isoforms. We have re-introduced clones of two of these genes, myo-3 and unc-54 at low copy number into the germline of C. elegans. The resulting loci behave as functional copies of the genes by two genetic criteria: (i) they can result in phenotypic rescue of strains carrying inactivating myo-3 or unc-54 mutations, and (ii) their presence in strains with wild-type copies of the endogenous myosin loci has genetic consequences similar to duplicating the endogenous loci. The re-introduced genes function at a level close to that of the endogenous loci. Monoclonal antibodies specific for the different isoforms have been used to localize the expressed proteins. The re-introduced genes express in precisely the same cell types as the endogenous genes, and the myosin products produced assemble into filament structures as in wild-type. Unexpectedly, we have found in the course of this work that very high copy numbers of the unc-54 gene lead to a disruption of muscle structure which may result from overexpression of the protein product. ------------------- Key: 1195 Medline: 90059938 Authors: Waterston RH Title: The minor myosin heavy chain, mhcA, of Caenorhabditis elegans is necessary for the initiation of thick filament assembly. Citation: EMBO Journal 8: 3429-3436 1989 Type: ARTICLE Genes: myo-3 ctDf1 Abstract: Caenorhabditis elegans body wall muscle has two distinct myosin heavy chain isoforms, mhcA and mhcB. Mutations eliminating the major isoform, mhcB, have previously been shown to yield paralyzed, viable animals. In this paper we show that the minor isoform, mhcA, is essential for viability. We have utilized the known physical map position of the gene encoding mhcA to obtain two recessive lethal mutations that virtually eliminate accumulation of mhcA. The mutations are allelic, and the interactions of these alleles with mutations affecting other thick filament components are consistent with the hypothesis that the new mutations lie in the structural gene for mhcA. The homozygous mutant animals move very little and morphological analysis shows that thick filament assembly is severely impaired. Together with the location of mhcA in the center of the thick filament (Miller et al., 1983), the results suggest that mhcA has a unique role in initiating filament assembly. The homozygous mutations have an unexpected effect on morphogenesis that indicates an interaction between the muscle cells and the hypodermis during development. The resultant phenotype may be useful in the search for additional essential muscle genes. ------------------- Key: 1196 Medline: 90033759 Authors: Hill DP;Shakes DC;Ward S;Strome S Title: A sperm-supplied product essential for initiation of normal embryogenesis in Caenorhabditis elegans is encoded by the paternal-effect embyonic-lethal gene, spe-11. Citation: Developmental Biology 136: 154-166 1989 Type: ARTICLE Genes: spe-11 sDf4 Abstract: Loss-of-function mutations in the spe-11 gene in Caenorhabditis elegans result in a paternal-effect embryonic-lethal phenotype: fertilization of wild-type oocytes by sperm from homozygous spe-11 mutant males leads to abnormal zygotic development, whereas oocytes from homozygous spe-11 hermaphrodites when fertilized by wild-type sperm develop normally. Embryos fertilized by sperm from homozygous spe-11 worms fail to complete meiosis and show defects in eggshell formation, mitotic spindle orientation, and cytokinesis. Genetic analysis suggests that the spe-11 gene is expressed before the completion of spermatogenesis and that the wild-type locus encodes a product that is present in sperm and participates, directly or indirectly, in initiating the correct program of early events in C. elegans embryos. Such an ontogenetic role of the spe-11+ gene product in early embryogenesis distinguishes spe-11 mutations from the two paternal-effect mutations identified in Drosophila, ms(3)K81 and pal, which primarily affect chromosome behavior. Analysis of spe-11 provides the first step toward genetic dissection of the functions of the sperm in early embryogenesis in C. ------------------- Key: 1197 Medline: 90380389 Authors: Avery L;Horvitz HR Title: Pharyngeal pumping continues after laser killing of the pharyngeal nervous system of C. elegans. Citation: Neuron 3: 473-485 1989 Type: ARTICLE Genes: cha-1 Abstract: Using a laser microbeam to kill specific subsets of the pharyngeal nervous system of C. elegans, we found that feeding was accomplished by two separately controlled muscle motions, isthmus peristalsis and pumping. The single neuron M4 was necessary and sufficient for isthmus peristalsis. The MC neurons were necessary for normal stimulation of pumping in response to food, but pumping continued and was functional in MC- worms. The remaining 12 neuron types were also unnecessary for functional pumping. No operation we did, including destruction of the entire pharyngeal nervous system, abolished pumping altogether. When we killed all pharyngeal neurons except M4, the worms were viable and fertile, although retarded and starved. Since feeding is one of the few known essential actions controlled by the nervous system, we suggest that most of the C. elegans nervous system is dispensable in hermaphrodites under laboratory conditions. This may explain the ease with which nervous system mutants are ------------------- Key: 1198 Medline: Authors: Woods RA;Malone KMB;Spence AM;Sigurdson WJ;Byard EH Title: The genetics, ultrastructure, and tubulin polypeptides of mebendazole-resistant mutants of Caenorhabditis elegans. Citation: Canadian Journal of Zoology 67: 2422-2431 1989 Type: ARTICLE Genes: ben-1 Abstract: Mebendazole-resistant mutants of Caenorhabditis elegans were isolated following mutagenesis of the wild-type strain, N2, with ethylmethane sulphonate. The mutants define a single autosomal gene and are allelic to ben-1. They grow, move, and reproduce normally in the presence of mebendazole and are cross-resistant to albendazole, cambendazole, fenbendazole, methylbenzimidazole carbamate, and thiabendazole. Accumulations of membrane-bound, electron-dense material associated with the nervous tissue and associated cells are seen in electron micrographs of L3, L4 and adult stages of N2 grown in the presence of mebendazole, but are not found in the mutants. The electron-dense material appears to be associated with the accessory cells of the neuropil rather than with neurons. The tubulins from wild type, N2, and the mutants were characterised by two-dimensional electrophoresis followed by silver staining and Western blotting with monoclonal antibodies to a- and B-tubulin. A single isotype of a-tubulin is apparent in both N2 and the mutants. One major and three minor B-tubulin isotypes, bt-1 to bt-3, can be discerned in N2; the minor isotype bt-2 is absent in all the mutants. These findings suggest that the isotype bt-2 is the primary site of action of benzimidazole-based drugs in C. elegans. ------------------- Key: 1199 Medline: Authors: Waterston RH Title: Molecular genetic approaches to the study of motility in Caenorhabditis elegans. Citation: "Molecular Genetic Approaches to Protein Structure and Function, Applications to Cell and Developmental Biology." Spudich JA (ed), Alan R. Liss, Inc. : 136-145 1989 Type: REVIEW Genes: Abstract: ------------------- Key: 1200 Medline: Authors: Schierenberg E Title: Mikroskopische Untersuchungen an freilebenden Nematoden. Citation: Mikrokosmos 77: 377-380 1988 Type: REVIEW Genes: Abstract: In German. ------------------- Key: 1201 Medline: Authors: Ohba K;Ishiguro T;Hayashi Y Title: Freeze-thaw survival of the entomogenous nematodes, Steinernema feltiae and S. glaseri in brief comparison with survival of Caenorhabditis elegans and Aphelenchus avenae. Citation: Japanese Journal of Nematology 18: 30-35 1989 Type: ARTICLE Genes: Abstract: Survival in liquid nitrogen was investigated for the infective juveniles of entomogenous nematodes Steinernema feltiae and S. glaseri, dauer juveniles of free-living nematode Caenorhabditis elegans, and adults of mycophagous nematode Aphelenchus avenae. When the frozen nematodes were quickly thawed at 35C, the survival rate was over 90% for S. feltiae, 50% for A. avenae, 30% for C. elegans and less than 1% for S. glaseri. Glycerol was a more effective freeze protectant than dimethyl sulfoxide, however, the latter effectively protected nematodes frozen at -80C. Irrespective of freeze protectants used, survival was always poor for the nematodes thawed slowly at room ------------------- Key: 1202 Medline: 90136497 Authors: Maruyama IN;Miller DM;Brenner S Title: Myosin heavy chain gene amplification as a suppressor mutation in Caenorhabditis elegans. Citation: Molecular & General Genetics 219: 113-118 1989 Type: ARTICLE Genes: myo-3 sup-3 eDf1 Abstract: In the nematode, Caenorhabditis elegans, the body wall muscles contain paramyosin and two different types of myosin heavy chain, MHC A and MHC B. In mutants that do not express MHC B or that express defective paramyosin, muscle structure is disrupted and movement is impaired. Second site mutations in the sup-3 locus partially reverse these defects and are correlated with a 2- to 3-fold increase in the accumulation of the MHC A isoform. The sup-3 mutations occur at a high frequency (10(-4] after ethyl methanesulfonate (EMS) mutagenesis. This is comparable to the average EMS-induced mutation rate per gene in C. elegans. In this paper we show that the sup-3 mutation is an amplification of the structural gene for the MHC A protein, myo-3. We employed genomic Southern hybridization with MHC gene-specific probes in order to measure the copy number of the myo-3 gene relative to that of the MHC B gene, unc-54. We have identified the putative amplification junctions for these sup-3 alleles using a set of cosmid clones which encompass myo-3 region. Although it has been suggested that gene amplification plays an important role in evolution, there are few known cases of gene amplification in the germ line cells of multicellular organisms. The results shown here provide a clear example of a heritable gene amplification event that occurs at a high frequency in the germ line. Similar events may thus represent the initial event in the evolution of new function and in the formation of multigene families. ------------------- Key: 1203 Medline: 90044042 Authors: Benian GM;Kiff JE;Neckelmann N;Moerman DG;Waterston RH Title: Sequence of an unusually large protein implicated in regulation of myosin activity in C. elegans. Citation: Nature 342: 45-50 1989 Type: ARTICLE Genes: unc-22 Abstract: The Caenorhabditis elegans gene unc-22 encodes a very large muscle protein, called twitchin, which consists of a protein kinase domain and several copies of two short motifs. The sequence of twitchin has unexpected similarities to the sequences of proteins of the immunoglobulin superfamily, cell adhesion molecules and vertebrate muscle proteins, including myosin light-chain kinase. These homologies, together with results from earlier genetic and molecular analyses, indicate that twitchin is involved in a novel mechanism of myosin ------------------- Key: 1204 Medline: 90033142 Authors: Nilsen TW Title: Trans-splicing in nematodes. Citation: Experimental Parasitology 69: 413-416 1989 Type: REVIEW Genes: Abstract: ------------------- Key: 1206 Medline: 90273884 Authors: Villeneuve AM;Meyer BJ Title: The regulatory hierarchy controlling sex determination and dosage compensation in Caenorhabditis elegans. Citation: Advances in Genetics. Scandalios JG and Wright TRF (eds), Academic Press, Inc. 27: 117-188 1990 Type: REVIEW Genes: dpy-21 dpy-22 dpy-23 dpy-26 dpy-27 dpy-28 dpy-29 egl-1 egl-14 fem-1 fem-2 fem-3 fog-1 fog-2 her-1 let-2 lin-10 lin-12 lin-14 lin-15 lin-17 mab-3 sdc-1 sdc-2 myo-2 sup-7 sup-21 tra-1 tra-2 tra-3 uvt-4 uxt-1 uxt-2 xol-1 mnDp8 mnDp9 mnDp10 mnDp25 mnDp27 stDp2 Abstract: The decision of an organism to develop either as a male or female (or as a hermaphrodite) poses a variety of intriguing problems, both for the organism confronting this decision and its consequences and for the investigator attempting to understand how such a decision is made and executed. How do cells choose between alternative cell fates? Once an initial decision is made, how do cells subsequently become restricted in developmental potential, committed to a particular fate prior to the time when differentiation takes place? After differentiation occurs, how is the differentiated state maintained? Further, how does the organism ensure that all cells or tissues make the same choice? What aspects of this process involve intercellular communication, and what functions are cell autonomous? What are the mechanisms by which the pertinent intracellular and/or intercellular signals are transduced? What role does the maternally supplied oocyte cytoplasm play in the decisions directed by the zygotic genome? These questions are easily recognized as encompassing many of the central issues common to all fundamental developmental processes. In Caenorhabditis elegans the manner in which sexual dimorphism arises during development adds a further dimension to this already substantial problem. Sexual dimorphism in C. elegans is pervasive, occurring in all tissue types and arising in almost all major branches of the cell lineage. Moreover, the strategies for generating dimorphism are diverse... ------------------- Key: 1207 Medline: 89365002 Authors: Scott AL;Dinman J;Sussman DJ;Yenbutr P;Ward S Title: Major sperm protein genes from Onchocerca volvulus. Citation: Molecular & Biochemical Parasitology 36: 119-126 1989 Type: ARTICLE Genes: msp-3 Abstract: Nematode spermatozoa, unlike their mammalian counterparts, are nonflagellated crawling cells. The pseudopod of these cells contains the major sperm protein (MSP) which comprises more than 15% of the protein in the sperm. MSP is presumed to function as a cytoskeletal element involved in motility. An Ascaris MSP cDNA sequence was used as a probe to identify and isolate Onchocerca volvulus MSP clones from a lambda gt11 genomic library. Two clones, OVGS-1 (765 bp) and OVGS-2 (1765 bp), were characterized by restriction endonuclease mapping and sequence analysis. Both genomic clones contain MSP protein coding regions of 99 and 282 bp separated by an intervening sequence of 153 bp. The genes OVGS-1 and OVGS-2 are 95% similar in nucleotide sequence in the protein coding regions, but only 79% similar in their intron sequences. A number of potential regulatory sequences in the flanking regions and at the exon/intron junctions of the O. volvulus MSP genes are in good agreement with consensus sequences in other eukaryotic cells. The nucleotide sequence of the O. volvulus MSP genes were over 80% similar to the Ascaris MSP cDNA sequence and 79% similar to the Caenorhabditis MSP-3 cDNA. The predicted amino acid sequence of the O. volvulus MSPs were 96% similar to each other, 90-91% similar to Ascaris MSP and 81-82% similar to Caenorhabditis MSP-3. These results offer evidence that the MSP sequences have been highly conserved throughout nematode evolution but are variable in their genomic organization and the presence of ------------------- Key: 1208 Medline: 90128229 Authors: Schedl T;Graham PL;Barton MK;Kimble J Title: Analysis of the role of tra-1 in germline sex determination in the nematode Caenorhabditis elegans. Citation: Genetics 123: 755-769 1989 Type: ARTICLE Genes: fem-3 tra-1 tra-2 tra-3 eDf2 Abstract: In wild-type Caenorhabditis elegans there are two sexes, self- fertilizing hermaphrodites (XX) and males (XO). To investigate the role of tra-1 in controlling sex determination in germline tissue, we have examined germline phenotypes of nine tra-1 loss-of-function (lf) mutations. Previous work has shown that tra-1 is needed for female somatic development as the nongonadal soma of tra-1(lf) XX mutants is masculinized. In contrast, the germline of tra-1(lf) XX and XO animals is often feminized; a brief period of spermatogenesis is followed by oogenesis, rather than the continuous spermatogenesis observed in wild-type males. In addition, abnormal gonadal (germ line and somatic gonad) phenotypes are observed which may reflect defects in development or function of somatic gonad regulatory cells. Analysis of germline feminization and abnormal gonadal phenotypes of the various mutations alone or in trans to a deficiency reveals that they cannot be ordered in an allelic series and they do not converge to a single phenotypic endpoint. These observations lead to the suggestion that tra-1 may produce multiple products and/or is autoregulated. One interpretation of the germline feminization is that tra-1(+) is necessary for continued specification of spermatogenesis in males. We also report the isolation and characterization of tra-1 gain-of-function (gf) mutations with novel phenotypes. These include temperature sensitive, recessive germline feminization, and partial somatic loss-of-function ------------------- Key: 1209 Medline: 90046848 Authors: Huang XY;Hirsh D Title: A second trans-spliced RNA leader sequence in the nematode Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 86: 8640-8644 1989 Type: ARTICLE Genes: gpd-1 gpd-2 gpd-3 gpd-4 msp-142 Abstract: In the nematode Caenorhabditis elegans, the 22-nucleotide RNA sequence called the spliced leader (SL) is trans-spliced from the 100- nucleotide-long SL RNA to some mRNAs. We have identified a trans- spliced leader (SL2) whose sequence differs from that of the original spliced leader (SL1), although both are 22 nucleotides long. By primer-extension sequencing, SL2 but not SL1 was shown to be present at the 5' end of the mRNA encoded by one of the four glyceraldehyde-3- phosphate dehydrogenase genes. The other three glyceraldehyde-3- phosphate dehydrogenase genes encode mRNAs that have the SL1 but not the SL2 sequence at their 5' ends. Therefore, the trans-splicing process can discriminate the transfer of SL1 from that of SL2 in a gene-specific manner. ------------------- Key: 1210 Medline: 90067836 Authors: Nelson DW;Honda BM Title: Two highly conserved transcribed regions in the 5S DNA repeats of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. Citation: Nucleic Acids Research 17: 8657-8667 1989 Type: ARTICLE Genes: Abstract: The 5S RNA genes of Caenorhabditis briggsae consist of approximately 65 copies of a 1 kb repeat unit and 20 copies of a related 0.7 kb repeat unit, organized in separate tandem clusters. DNA sequence comparisons with the 1kb 5S DNA repeat from the closely related nematode C. elegans show that the 5S RNA coding region is perfectly conserved. Both C. briggsae 1 kb and 0.7 kb repeats are also efficiently transcribed in vitro,suggesting that both represent functional 5S RNA genes. Surprisingly, a second block of 118 bp is also perfectly conserved between the 1 kb repeats,and is less well conserved in the 0.7 kb repeat. In C. elegans, this DNA is transcribed to produce and abundant 100 nt transcript (SL RNA) which participates in a trans-splicing process (Krause and Hirsh, Cell 49:753, 1987). This SL RNA region of the C. briggsae 1 kb 5S DNA repeat also appears to be transcribed in vivo, while the corresponding region of the 0.7 kb repeat is not. ------------------- Key: 1211 Medline: 90136718 Authors: Shamansky LM;Pratt D;Boisvenue RJ;Cox GN Title: Cuticle collagen genes of Haemonchus contortus and Caenorhabditis elegans are highly conserved. Citation: Molecular & Biochemical Parasitology 37: 73-86 1989 Type: ARTICLE Genes: col-1 col-2 dpy-13 Abstract: Several genes and partial cDNAs encoding cuticle collagens have been isolated from the sheep parasitic nematode Haemonchus contortus. DNA sequencing and Southern blot hybridization studies reveal that H. contortus collagens comprise a large family of related, but non- identical genes. The genes appear to be dispersed throughout the genome. The predominant size of collagen mRNA in molting worms was found to be between 1.0 and 1.2 kb. The one complete gene that was sequenced contains two short introns and encodes a protein of about 300 amino acids. The predicted protein sequence contain several (Gly- X-Y)n triple helix-coding domains that are interrupted by short stretches of non-helix-coding amino acids. The size of the predicted protein and the organization of the triple-helix coding domains are similar to that of Caenorhabditis elegans collagens. All the H. contortus genes studied show a striking homology to the C. elegans collagen gene subfamily represented by col-1. In particular, the amino acid sequence of the carboxy-terminal non-(Gly-X-Y)n region and the positions of cysteine residues flanking the (Gly-X-Y)n domains were found to be highly conserved in the collagens of these two nematodes. ------------------- Key: 1212 Medline: 90136710 Authors: Kingston IB;Wainwright SM;Cooper D Title: Comparison of collagen gene sequences in Ascaris suum and Caenorhabditis elegans. Citation: Molecular & Biochemical Parasitology 37: 137-146 1989 Type: ARTICLE Genes: col-1 col-2 Abstract: The nucleotide sequences of a 3060-bp fragment containing almost the entire coding sequence of one Ascaris suum collagen gene, and a 3019- bp pair fragment containing the 3' end of another A. suum collagen gene have been determined. The polypeptides encoded by these genes show a striking similarity to two Caenorhabditis elegans cuticular collagens, both in the position of the triple-helical regions and in the position of cysteine residues. The results of Northern blot hybridisation experiments together with dot blot analysis of RNA isolated from different adult worm tissues suggest that one of these genes is expressed in the adult nematode and that it encodes a protein of approximately 30 kDa. ------------------- Key: 1213 Medline: Authors: Matsuno A;Takano-Ohmuro H;Itoh Y;Matsuura T;Shibata M;Nakae H;Kaminuma T;Maruyama K Title: Anti-connectin monoclonal antibodies that react with the unc-22 gene product bind dense bodies of Caenorhabditis (nematode) bodywall muscle cells. Citation: Tissue & Cell 21: 517-524 1989 Type: ARTICLE Genes: unc-22 Abstract: Monoclonal antibodies, 3B9 and 4C9, specific to connectin (also called titin) 3000kDa elastic filamentous protein of vertebrate skeletal muscle, crossreacted with a high molecular weight protein (500 kDa) of the nematode Caenorhabditis elegans. However, its crossreactivity was weak to that of the unc-22 gene deficient mutant. Immunofluorescence showed that the antibodies stained both bodywall and pharynx muscles in the wild type, but only pharynx muscle in the mutant. Immunoelectron microscopy revealed that the antibodies bound to the dense bodies of bodywall muscle cells of the wild type but not to those of the mutants. In the pharynx muscles the localization of the antibodies was not clear in both normal and mutant worms. Moerman, D.G. et al. (Genes & Development 2: 93-105 (1988)) reported that the unc-22 gene product (500 kDa) is located in the A band of the bodywall muscle cells of C. elegans. Taking this information into consideration, it is suggested that the unc-22 gene product may be a filamentous protein linking a dense body and myosin filaments in the bodywall muscles of C. elegans. ------------------- Key: 1214 Medline: 90060325 Authors: Vanfleteren JR;Van Bun SM;Van Beeumen JJ Title: The histones of Caenorhabditis elegans: no evidence of stage-specific isoforms. Citation: FEBS Letters 257: 233-237 1989 Type: REVIEW Genes: Abstract: The nematode Caenorhabditis elegans expresses one species of H2A and one species of H4 molecules, at least two species of H1 (H1.1, H1.2), two species of H2B (H2B.1, H2B.2) and 2-4 species of H3 (H3.1 and H3.3 and an unassigned Ile/Leu microheterogeneity in H3). The study of their primary structures has been completed now and all of them, with the exception of the Ile/Leu microheterogeneity in H3, have been assigned to protein spots on two-dimensional gels. One spot, previously designated H3.2, probably represents C-terminally cleaved H3.1. The relative abundance of the isohistones was essentially the same when derived from either eggs, gravid adults or postreproductive, senescent worms. The degree of post-translational modification, however, particularly acetylation of H2A, H2B and H3 histone species, was reduced ------------------- Key: 1215 Medline: 89377322 Authors: Kimble J;Austin J Title: Genetic control of cellular interactions in Caenorhabditis elegans development. Citation: Ciba Foundation Symposium 144: 212-226 1989 Type: REVIEW Genes: glp-1 lin-12 qDf2 Abstract: During development of the nematode, Caenorhabditis elegans, cell interactions play a significant role in controlling cell fate. Regulatory cells in the somatic gonad control proliferation in the germline and induce formation of the vulva in the hypodermis. In the early embryo, mesodermal cells are induced in a process similar to embryonic induction. In addition, interactions between precursor cells of equivalent developmental potential direct one cell to adopt one fate and the other to adopt a second fate. Two genes have been identified in C. elegans that appear to mediate cell interactions. The glp-1 gene is required for embryonic induction and continued germline proliferation; lin-12 is required for cells of equal developmental potential to adopt different fates. Genetic mosaics indicate that glp-1 may be part of the receiving mechanism in controlling germline proliferation. ------------------- Key: 1216 Medline: 90169466 Authors: Villeneuve AM;Meyer BJ Title: The role of sdc-1 in the sex determination and dosage compensation decisions in Caenorhabditis elegans. Citation: Genetics 124: 91-114 1990 Type: ARTICLE Genes: sdc-1 xol-1 mnDf1 mnDf10 yDf1 mnDp12 mnDp25 Abstract: Our previous work demonstrated that mutations in the X-linked gene sdc-1 disrupt both sex determination and dosage compensation in Caenorhabditis elegans XX animals, suggesting that sdc-1 acts at a step that is shared by the sex determination and dosage compensation pathways prior to their divergence. In this report, we extend our understanding of early events in C. elegans sex determination and dosage compensation and the role played by sdc-1 in these processes. First, our analysis of 14 new sdc-1 alleles suggests that the phenotypes resulting from the lack of sdc-1 function are (1) an incompletely penetrant sexual transformation of XX animals toward the male fate, and (2) increased levels of X-linked gene transcripts in XX animals, correlated with XX-specific morphological defects but not significant XX-specific lethality. Further, all alleles exhibit strong maternal rescue for all phenotypes assayed. Second, temperature-shift experiments suggest that sdc-1 acts during the first half of embryogenesis in determining somatic sexual phenotype, long before sexual differentiation actually takes place, and consistent with our previous proposal that sdc-1 acts at an early step in the regulatory hierarchy controlling the choice of sexual fate. Other temperature-shift experiments suggest that sdc-1 may be involved in establishing but not maintaining the XX mode of dosage compensation. Third, a genetic mosaic analysis of sdc-1 produced an unusual result: the genotypic mosaics failed to display the sdc-1 sexual transformation phenotypes. This result suggests several possible interpretations: (1) sdc-1 is expressed immediately, in the one- or two-celled embryo; (2) sdc-1 acts non-cell-autonomously, such that expression of the gene in either the AB or P1 lineage can supply sdc-1(+) function to cells of the other lineage; (3) the X/A ratio is assessed immediately, in the one- or two-celled embryo; or (4) the X/A signal directs the choice of sexual fate in a non-cell-autonomous fashion. Finally, examination of the classes of sexual phenotypes produced in sdc-1 mutant strains suggests that different cells in the organism may ------------------- Key: 1217 Medline: 90169452 Authors: McKim KS;Rose AM Title: Chromosome I duplications in Caenorhabditis elegans. Citation: Genetics 124: 115-132 1990 Type: ARTICLE Genes: hDf6 hDp2 hDp3 hDp4 hDp5 hDp6 hDp7 hDp8 hDp9 hDp10 hDp11 hDp12 hDp13 hDp14 hDp15 hDp16 hDp17 hDp18 hDp19 hDp20 hDp21 hDp22 hDp23 hDp25 hDp28 hDp29 hDp30 hDp31 hDp32 hDp33 hDp34 hDp35 hDp36 hDp37 hDp38 hDp39 hDp41 hDp42 hDp43 hDp44 hDp45 hDp46 hDp47 hDp48 hDp49 hDp50 hDp51 hDp52 hDp53 hDp54 hDp55 hDp56 hDp57 hDp58 hDp60 hDp61 hDp62 hDp64 hDp65 hDp66 hDp67 hDp68 hDp69 hDp70 hDp71 hDp72 hDp73 hDp74 hDp75 hDp77 szDp1 sDp2 hT2 szT1 Abstract: We have isolated and characterized 76 duplications of chromosome I in the genome of Caenorhabditis elegans. The region studied is the 20 map unit left half of the chromosome. Sixty-two duplications were induced with gamma radiation and 14 arose spontaneously. The latter class was apparently the result of spontaneous breaks within the parental duplication. The majority of duplications behave as if they are free. Three duplications are attached to identifiable sequences from other chromosomes. The duplication breakpoints have been mapped by complementation analysis relative to genes on chromosome I. Nineteen duplication breakpoints and seven deficiency breakpoints divide the left half of the chromosome into 24 regions. We have studied the relationship between duplication size and segregational stability. While size is an important determinant of mitotic stability, it is not the only one. We observed clear exceptions to a size-stability correlation. In addition to size, duplication stability may be influenced by specific sequences or chromosome structure. The majority of the duplications were stable enough to be powerful tools for gene mapping. Therefore the duplications described here will be useful in the genetic characterization of chromosome I and the techniques we have developed can be adapted to other regions of the genome. ------------------- Key: 1218 Medline: Authors: Hosono R;Sassa T;Kuno S Title: Spontaneous mutations of trichlorfon resistance in the nematode, Caenorhabditis elegans. Citation: Zoological Science 6: 697-708 1989 Type: ARTICLE Genes: cha-1 unc-3 unc-10 unc-13 unc-17 unc-18 unc-41 Abstract: Spontaneous trichlorfon-resistant mutations were isolated in Caenorhabditis elegans var. Bergerac and its derived mutator strains. Of these, six uncoordinated mutations were assigned by complementation analysis to the unc-13(cn490), unc-17(cn355), unc-18(cn347), unc-10(cn257), unc-3(cn4146) and unc-41(cn252) genes. Resistance of these mutations to acetylcholinesterase (AChE) inhibitors is partial, with the extent dependent on the mutations. These mutations fall into two classes based on acetylcholine (ACh) levels, that is, the normal ACh levels in unc-10 and unc-3 mutations and the abnormally high ACh levels in unc-13, unc-17, unc-41 and unc-18 mutations. Mutations in the latter gene groups are also accompanied by growth retardation and small body size in adulthood. Double mutants were constructed between the six trichlorfon-resistant strains together with the cha-1*unc-17 complex gene alleles which are also resistant to trichlorfon. All doubles constructed between trichlorfon-resistant strains survived and their properties ------------------- Key: 1219 Medline: Authors: Edgley ML;Riddle DL Title: The nematode Caenorhabditis elegans. Citation: Genetic Maps 5: 3.111-3.133 1990 Type: REVIEW Genes: Abstract: ------------------- Key: 1220 Medline: 90004470 Authors: Goldstein P;Watts M;Aun J Title: Resistance to lethal levels of diethylstilbestrol in the nematode Caenorhabditis elegans. Citation: Cytobios 58: 7-17 1989 Type: ARTICLE Genes: Abstract: Concentrations of diethylstilboestrol (DES) exceeding 100 microM are normally fatal to all living tissues due to inhibition of cell division and other cell processes. However, in Caenorhabditis elegans, with increasing levels of DES, there was an observed decrease in fertility and fecundity (99%), although a small percentage of the population (1%) survived concentrations as high as 400 microM DES. Uptake studies, using tritiated-DES liquid scintillation and ELISA analysis, revealed that uptake exhibited saturation at 100 microM and levels exceeding 100 microM resulted in no further biological response. Thus, ultrastructural morphology and viability of the organism was unchanged after the DES saturation point. ------------------- Key: 1221 Medline: 90104269 Authors: Hawdon JM;Emmons SW;Jacobson LA Title: Regulation of proteinase levels in the nematode Caenorhabditis elegans. Preferential depression by acute or chronic starvation. Citation: Biochemical Journal 264: 161-165 1989 Type: ARTICLE Genes: daf-4 unc-52 Abstract: Acute starvation of the wild-type of the nematode Caenorhabditis elegans depresses the level of cathepsin D by 65% within 4-8 h and the level of the thiol cathepsins Ce1 and Ce2 to about the same extent after 24 h. There is no parallel loss of lysosomal beta- glucosidase or beta-hexosaminidase activities. In strains which are chronically starved as a result of mutations which compromise feeding behaviour (unc-52) or nutrient uptake into the intestinal cells (daf- 4), cathepsin D levels are decreased to about 15% of the level in fully fed wild-type animals. We suggest that the decline in the cathepsin D level results from autodigestion when alternative protein substrates are depleted in the lysosomes. ------------------- Key: 1222 Medline: Authors: Coles GC;Dicklow MB;Zuckerman BM Title: Protein changes associated with the infection of the nematode Caenorhabditis elegans by the nematophagous fungus Drechmeria coniospora. Citation: International Journal for Parasitology 19: 733-736 1989 Type: ARTICLE Genes: Abstract: Protein changes associated with the predation of the nematode Caenorhabditis elegans by the nematophagous fungus Drechmeria coniospora were examined at intervals of 72 h following infection. The disappearance of two high molecular weight proteins in the nematodes by 72 h following infection was demonstrated by SDS gel electrophoresis. Nematode protein was not differentiated from fungus protein by immunoblotting due to high cross-reactivity. Changes in three proteins specifically of fungus origin and one protein of nematode origin were detected at 72 h following infection using serum purified by affinity column chromatography. This study demonstrated for the first time the separation of nematode and fungal proteins from complexes derived from the two organisms. ------------------- Key: 1223 Medline: Authors: Kemphues KJ Title: Caenorhabditis. Citation: "Genes and Embryos." Glover DM and Hames ED (eds), IRL Press, London. : 95-126 1989 Type: REVIEW Genes: glp-1 par-1 par-2 par-3 par-4 par-5 zyg-9 zyg-11 Abstract: Classical embryological studies of nematodes, primarily by Van Beneden and Boveri near the turn of the century, have made lasting contributions to our understanding of embryonic development (1). However, during most of this century, nematodes have been eclipsed as a model system for embryology by organisms with more tractable embryos such as sea urchins, insects, amphibians, birds, and mice. Two features of the free-living soil nematode Caenorhabditis elegans have returned nematodes to a prominent place in embryological investigations: its suitability for genetic analysis and its invariant and completely described cell lineage. These two features, combined with technological advances in microscopy and molecular biology, are providing the opportunity to combine experimental embryology with genetic and molecular analyses of embryonic development at the level of individual cells in a single organism. This chapter focuses on efforts to understand the molecular and cellular events of early development in C. elegans with particular emphasis on events relating to the determination of embryonic cell fates. Extensive coverage of the various contributions that the study of Caenorhabditis has made to our knowledge of developmental biology can be found in ref. 2. ------------------- Key: 1224 Medline: 90108677 Authors: Greenwald I;Moerman DG Title: A feast of worms. Citation: Genes & Development 3: 1269-1271 1989 Type: REVIEW Genes: ces-1 ces-2 emb-9 fem-3 glp-1 let-23 lin-12 lin-14 lin-29 mec-3 mec-7 pal-1 rol-6 sdc-1 spe-11 sqt-1 tra-1 tra-2 unc-15 unc-22 unc-54 unc-79 unc-80 Abstract: The rapid growth of the Caenorhabditis elegans field in recent years reflects the remarkable utility of this nematode for study of diverse biological problems. This organism has many natural attributes. Its anatomy is simple and relatively invariant. Its ease of cultivation, large brood size, and rapid generation of time facilitate genetic analysis; its small genome size facilitates molecular analysis. Although these features have been important to the expansion of this field of study, the deliberate accumulation of basic biological knowledge and techniques-the complete cell lineage and anatomy of wild type, extensive genetic and physical maps, and methods for gene isolation, DNA transformation, and genetic mosaic analysis-has provided the foundation for further progress. The magnitude of this progress was evident at the 1989 Cold Spring Harbor Laboratory C. elegans meeting. In this review, due to limited space, we describe only some of this progress. ------------------- Key: 1225 Medline: Authors: Kemphues KJ Title: Genetic analysis of embryogenesis in Caenorhabditis Citation: "Developmental Genetics of Higher Organisms." Malacinski GM (ed), MacMillan, New York. : 193-219 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1226 Medline: 90032494 Authors: van Kessel WHM;Zaalberg RWB;Seinen W Title: Testing environmental pollutants on soil organisms: A simple assay to investigate toxicity on soil organisms, using CdCl2 and nematodes/ Citation: Ecotoxicology & Environmental Safety 18: 181-190 1989 Type: ARTICLE Genes: Abstract: Juvenile stages of Caenorhabditis elegans (nematoda) were isolated and grown in an axenic medium containing various concentrations of CdCl2. Growth of the organisms was significantly reduced from a level of 1 microM CdCl2. Reproduction of the nematodes was also reduced from that 1 microM exposure level. At levels of 160 and 320 microM, growth was retarded at the early juvenile stages and the organisms did not reach the adult stage and could therefore not reproduce. The test system turned out to be simple and reproducible and is therefore suitable for the investigation of the toxicity of compounds to soil ------------------- Key: 1227 Medline: 90130670 Authors: Pavalko FM;Roberts TM Title: Posttranslational insertion of a membrane protein on Caenorhabditis elegans sperm occurs without de novo protein synthesis. Citation: Journal of Cellular Biochemistry 41: 57-70 1989 Type: ARTICLE Genes: him-5 Abstract: We have examined the mechanism of membrane protein insertion in the ameboid spermatozoa of Caenorhabditis elegans using two monoclonal antibodies which recognize the same set of eight sperm-specific polypeptides. Previous electron microscopic studies demonstrated that these antibodies label surface and cytoplasmic populations of antigen. Cells whose surface antigen had been removed by proteolysis were able to localize new membrane protein insertion at the tips of pseudopodial projections. C. elegans sperm do not contain the protein synthesizing machinery needed for delivery of new membrane to the cell surface. It has, therefore, been of interest to determine how localized membrane assembly occurs. Here we have determined the subcellular location of each of these eight polypeptides. A closely positioned doublet of bands around 97 kD (comprising 40% of the total antigen in sperm) represents surface (larger member of doublet) and cytoplasmic (lower member) forms of protein. Proteolysis of live cells eliminated this surface form from immunoblots but did not affect the cytoplasmic protein. When cells were allowed to reinsert new protein following removal of the enzyme, this surface form was regenerated. Since sperm are unable to synthesize new protein, this higher molecular weight species may arise from a posttranslational modification of proteins in the cytoplasmic pool. We present evidence suggesting that the surface protein is generated from this cytoplasmic pool by addition of fatty acid. Fatty acid acylation would account for both the observed decrease in electrophoretic mobility of the surface form and provide increased hydrophobicity to the ------------------- Key: 1228 Medline: 90078333 Authors: Driscoll M;Dean E;Reilly E;Bergholz E;Chalfie M Title: Genetic and molecular analysis of a Caenorhabditis elegans beta tubulin that conveys benzimidazole sensitivity. Citation: Journal of Cell Biology 109: 2993-3003 1989 Type: ARTICLE Genes: ben-1 tub-1 Abstract: Benzimidazole anti-microtubule drugs, such as benomyl, induce paralysis and slow the growth of the nematode Caenorhabditis elegans. We have identified 28 mutations in C. elegans that confer resistance to benzimidazoles. All resistant mutations map to a single locus, ben- 1. Virtually all these mutations are genetically dominant. Molecular cloning and DNA sequence analysis established that ben-1 encodes a beta-tubulin. Some resistant mutants are completely deleted for the ben-1 gene. Since the deletion strains appear to be fully resistant to the drugs, the ben-1 product appears to be the only benzimidazole- sensitive beta-tubulin in C. elegans. Furthermore, since animals lacking ben-1 are viable and coordinated, the ben-1 beta-tubulin appears to be nonessential for growth and movement. The ben-1 function is likely to be redundant in the nematode genome. ------------------- Key: 1229 Medline: 90098824 Authors: Uitterlinden AG;Slagboom PE;Johnson TE;Vijg J Title: The Caenorhabditis elegans genome contains monomorphic minisatellites and simple sequences. Citation: Nucleic Acids Research 17: 9527-9530 1989 Type: ARTICLE Genes: Abstract: Many species have been shown to contain tandemly repeated short sequence DNA known as minisatellites and simple sequence motifs. Due to allelic variation in the copy number of the repeat unit these loci are usually highly polymorphic. Here we demonstrate the presence of sequences in the genome of the nematode Caenorhabditis elegans which are homologous to two sets of short sequence DNA. However, when two independent strains were compared no polymorphism for these sequences could be detected. ------------------- Key: 1230 Medline: 90146226 Authors: Anderson P Title: Molecular genetics of nematode muscle. Citation: Annual Review of Genetics 23: 507-525 1989 Type: REVIEW Genes: act-1 act-2 act-3 mlc-1 mlc-2 mlc-3 mua-1 mua-2 mua-3 mup-1 mup-2 mup-3 myo-3 unc-15 unc-22 unc-23 unc-45 unc-52 unc-54 unc-60 unc-78 unc-82 unc-89 unc-90 unc-93 unc-94 unc-95 unc-97 unc-105 Abstract: Striated muscle functions universally to generate biological force. It contains two major filament systems, the myosin-containing thick filaments and the actin-containing thin filaments. During contraction, hydrolysis of ATP by a myosin-linked ATPase causes thin filaments to slide past thick filaments, thus shortening the sarcomere and producing tension on the contractile unit. During the past decade or two, the small nematode Caenorhabditis elegans has emerged as an important experimental organism for the study of muscle structure, assembly, and function. Like muscle biologists in general, C. elegans investigators are concerned with the questions: What are the components of striated muscle? How are these components assembled within the cell? How do these components function during the contractile cycle?... ------------------- Key: 1231 Medline: 90089446 Authors: Russell GJ;Lacey E Title: Colchicine binding in the free-living nematode Caenorhabditis elegans. Citation: Biochimica et Biophysica Acta 993: 233-239 1989 Type: ARTICLE Genes: Abstract: The [3H]colchicine-binding activity of a crude supernatant of the free-living nematode Caenorhabditis elegans was resolved into a non- saturable component and a tubulin-specific component after partial purification of tubulin by polylysine affinity chromatography. The two fractions displayed opposing thermal dependencies of [3H]colchicine binding, with non-saturable binding increasing, and tubulin binding decreasing, at 4 degrees C. Binding of [3H]colchicine to C.elegans tubulin at 37 degrees C is a pseudo-first-order rate process with a long equilibration time. The affinity of C. elegans tubulin for [3H]colchicine is relatively low (Ka = 1.7 x 10(5) M(-1)) and is characteristic of the colchicine binding affinities observed for tubulins derived from parasitic nematodes. [3H]Colchicine binding to C. elegans tubulin was inhibited by unlabelled colchicine, podophyllotoxin and mebendazole, and was enhanced by vinblastine. The inhibition of [3H]colchicine binding by mebendazole was 10-fold greater for C. elegans tubulin than for ovine brain tubulin. The inhibition of [3H]colchicine binding to C. elegans tubulin by mebendazole is consistent with the recognised anthelmintic action of the benzimidazole carbamates. These data indicate that C. elegans is a useful model for examining the interactions between microtubule inhibitors and the colchicine binding site of nematode tubulin. ------------------- Key: 1232 Medline: 90094407 Authors: Slice LW;Freedman JH;Rubin CS Title: Purification, characterization, and cDNA cloning of a novel metallothionein-like, cadmium-binding protein from Caenorhabditis elegans. Citation: Journal of Biological Chemistry 265: 256-263 1990 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans adapted for survival in high concentrations of Cd(II) express a heavy metal binding protein designated C. elegans metallothionein-like protein or MT-Ce. This protein was purified to homogeneity and characterized. MT-Ce binds 6 mol of Cd(II)/mol protein. The sequence of 39 amino-terminal residues in MT-Ce was determined. A radiolabeled 41-mer oligonucleotide, designed from the partial MT-Ce sequence, was used in conjunction with sucrose gradient centrifugation to obtain size-fractionated poly(A+) RNA enriched in MT-Ce sequences. Subsequently, cloned cDNAs, corresponding to MT-Ce mRNA sequences, were isolated from a lambda ZapII cDNA library prepared from the enriched template mRNA. cDNA and protein sequence analysis revealed that MT-Ce comprises 62 amino acid residues and has a predicted Mr of 6462. Seventeen of the 18 Cys residues in the nematode cadmium-binding protein are included in Cys-X-Cys and X-Cys- Cys-X motifs that are characteristic of mammalian metallothioneins (MTs). However, the resemblance of MT-Ce to mammalian MTs is superficial. The amino acid sequence of MT-Ce is unique, and neither its putative alpha and beta domains nor its Cys residues can be readily aligned with the corresponding regions of other eukaryotic MTs. This suggests that MT-Ce is an example of convergent evolution. The MT-Ce mRNA level in nematodes that were selected and grown with Cd(II) concentrations that are lethal for wild-type worms, was 55- fold higher than the level of MT-Ce mRNA in wild-type C. elegans. Comparison of the sequences of MT-Ce cDNAs revealed the occurrence of two types of MT-Ce mRNA. Each contains an identical coding region, but the cDNAs diverge markedly in their 5'-untranslated regions. This suggests the possibilities of regulation by alternative splicing and/or the presence of multiple MT-Ce genes encoding a single protein, but controlled by different regulatory ------------------- Key: 1233 Medline: 90106634 Authors: Waring DA;Kenyon C Title: Selective silencing of cell communication influences anteroposterior pattern formation in C. elegans. Citation: Cell 60: 123-131 1990 Type: ARTICLE Genes: lin-22 mab-5 pal-1 Abstract: In C. elegans males, laterally located V cells generate a simple pattern of anterior alae (cuticular ridges) and posterior rays (mating sensilla). We have found that this pattern is generated, at least in part, by the selective interruption of cell-cell interactions. In anterior V cells, lineages leading to the production of alae are induced by cell interactions. These cell interactions are inhibited in specific posterior V cells by the activity of the gene pal-1, which allows these cells to generate rays instead of alae. The activities of cell signals and pal-1 appear to influence V cell fates by determining the state of a developmental switch that involves two homeotic genes, lin-22 and mab-5. ------------------- Key: 1234 Medline: 90106635 Authors: Bejsovec A;Anderson P Title: Functions of the myosin ATP and actin binding sites are required for C. elegans thick filament assembly. Citation: Cell 60: 133-140 1990 Type: ARTICLE Genes: unc-54 Abstract: We have determined the positions and sequences of 31 dominant mutations affecting a C. elegans muscle myosin heavy chain gene. These mutations alter thick filament structure in heterozygotes by interfering with the ability of wild-type myosin to assemble into stable thick filaments. These assembly-disruptive mutations are missense alleles affecting the globular head of myosin. The most strongly dominant alleles alter highly conserved residues of the myosin ATP binding site, indicating that functions of the myosin ATPase are important for thick filament assembly. Other alleles alter the site at which myosin ------------------- Key: 1235 Medline: 90255392 Authors: Austin J;Maine EM;Kimble J Title: Genetics of intercellular signalling in C. elegans. Citation: Development 1989 Supplement : 53-57 1989 Type: REVIEW Genes: dpy-1 dpy-2 dpy-3 dpy-7 dpy-8 dpy-9 dpy-10 glp-1 lin-12 sqt-1 Abstract: Cell-cell interactions play a significant role in controlling cell fate during development of the nematode Caenorhabditis elegans. It has been found that two genes, glp-1 and lin-12, are required for many of these decisions. glp-1 is required for induction of mitotic proliferation in the germline by the somatic distal tip cell and for induction of the anterior pharynx early in embryogenesis. lin-12 is required for the interactions between cells of equivalent developmental potential, which allow them to take on different fates. Comparison of these two genes on a molecular level indicates that they are similar in sequence and organization, suggesting that the mechanisms of these two different sets of cell-cell interactions are similar. ------------------- Key: 1237 Medline: 90152330 Authors: Way JC;Chalfie M Title: The mec-3 gene of Caenorhabditis elegans requires its own product for maintained expression and is expressed in three neuronal cell types. Citation: Genes & Development 3: 1823-1833 1989 Type: ARTICLE Genes: lin-32 mec-3 mec-4 mec-17 unc-86 Abstract: The homeo-box-containing gene mec-3 of the nematode Caenorhabditis elegans, is expressed in several sensory neurons, as assayed by expression of a mec-3-lacZ fusion. These cells are the touch receptors, which mediate the response to gentle touch, and the FLP and PVD neurons. PVD mediates a response to harsh mechanical stimuli, and FLP has an ultrastructure suggestive of a mechanoreceptor, but its function is unknown. mec-3 is necessary for the differentiation of the touch receptors, because in mec-3 mutants, the touch receptors do not function and have none of their distinguishing features. mec-3 is also needed for PVD function: The PVD neurons no longer mediate a response to harsh mechanical stimuli in the mutants. The expression of the mec-3-lacZ fusion, and presumably mec-3 itself, is altered by mutations in several genes originally identified by their effects on touch cell development. unc-86, another homeo-box-containing gene, is necessary for all mec-3-lacZ expression, but also affects several other lineages and cells in which mec-3 is not expressed. mec-3 activity appears to be required for maintained expression of the mec- 3-lacZ fusion in all cells in which it is expressed. In a mec-17 mutant, mec-3-lacZ expression is not maintained in the touch receptors, but is not affected in the FLP and PVD neurons. These findings suggest that combinatorial mechanisms of gene regulation control both the expression of mec-3 itself and its action in promoting the terminal differentiation of various cell types. ------------------- Key: 1238 Medline: 90174908 Authors: Ogg SC;Anderson P;Wickens MP Title: Splicing of a C. elegans myosin pre-mRNA in a human nuclear extract. Citation: Nucleic Acids Research 18: 143-149 1990 Type: ARTICLE Genes: unc-52 Abstract: Splicing of mammalian introns requires that the intron possess at least 80 nucleotides. This length requirement presumably reflects the constraints of accommodating multiple snRNPs simultaneously in the same intron. In the free-living nematode, C. elegans, introns typically are 45 to 55 nucleotides in length. In this report, we determine whether C. elegans introns can obviate the mammalian length requirement by virtue of their structure or sequence. We demonstrate that a 53 nucleotide intron from the unc-54 gene of C. elegans does not undergo splicing in a mammalian (HeLa) nuclear extract. However, insertion of 31 nucleotides of foreign, prokaryotic sequence into the same intron results in efficient splicing. The observed splicing proceeds by the same two-step mechanism observed with mammalian introns, and exploits the same 3' and 5' splice sites as are used in C. elegans. The branch point used lies in the inserted sequence. We conclude that C. elegans splicing components are either fewer in number or smaller than their mammalian counterparts. ------------------- Key: 1239 Medline: 90220497 Authors: Mori I;Moerman DG;Waterston RH Title: Interstrain crosses enhance excision of Tc1 transposable elements in Caenorhabditis elegans. Citation: Molecular & General Genetics 220: 251-255 1990 Type: ARTICLE Genes: mut-5 mut-6 Abstract: We report here an unusual activation of the Tc1 transposable element system in Caenorhabditis elegans. Germline Tc1 activity, as measured by reversion of unc-22::Tc1 alleles, is elevated 50- to 100-fold by certain crosses. For example, unc-22::Tc1 reversion is 1 x 10(-3) in a mut-6 IV strain and less than 1 x 10(-6) in a non-mutator strain, but in the unc-22::Tc1 progeny of a cross between mut-6 hermaphrodites and non-mutator males, reversion is 10(-1). The reciprocal cross does not induce this enhancement of reversion. Results similar to those for mut-6 were obtained using a mut-5 II strain. The mutator hermaphrodite by nonmutator male cross per se is not required for the enhancement of reversion, as mut-5 hermaphrodites x mut-6/+ males also induce unc-22 revertants at an elevated frequency. This reversion enhancement appears to depend on a maternal component inherited from a mutator strain, suggesting that the ------------------- Key: 1240 Medline: 90276229 Authors: Schnabel R;Schnabel H Title: Early determination in the C. elegans embryo: a gene, cib-1, required to specify a set of stem-cell-like Citation: Development 108: 107-119 1990 Type: ARTICLE Genes: cib-1 par-1 par-2 par-3 par-4 sDf4 Abstract: The early somatic blastomeres founding the tissues in the C. elegans embryo are derived in a stem-cell-like lineage from the P cells. We have isolated maternal effect lethal mutations defining the gene cib- 1 in which the P cells, P1-P3, skip a cell cycle and acquire the fates of only their somatic daughters. Therefore, the cib-1 gene is required for the specification of the stem-cell-like fate of these cells. The analysis of the development of these mutants suggests that the clock controlling the cell cycles in the early embryo is directly coupled to the fate of a cell and that there must be another developmental clock that activates the determinative inventory for the early ------------------- Key: 1241 Medline: 90276232 Authors: Hill DP;Strome S Title: Brief cytochalasin-induced disruption of microfilaments during a critical interval in 1-cell C. elegans embryos alters the partitioning of developmental instructions to/ Citation: Development 108: 159-172 1990 Type: ARTICLE Genes: par-3 Abstract: We are investigating the involvement of the microfilament cytoskeleton in the development of early Caenorhabditis elegans embryos. We previously reported that several cytoplasmic movements in the zygote require that the microfilament cytoskeleton remain intact during a narrow time interval approximately three-quarters of the way through the first cell cycle. In this study, we analyze the developmental consequences of brief, cytochalasin D-induced microfilament disruption during the 1-cell stage. Our results indicate that during the first cell cycle microfilaments are important only during the critical time interval for the 2-cell embryo to undergo the correct pattern of subsequent divisions and to initiate the differentiation of at least 4 tissue types. Disruption of microfilaments during the critical interval results in aberrant division and P-granule segregation patterns, generating some embryos that we classify as 'reverse polarity', 'anterior duplication', and 'posterior duplication' embryos. These altered patterns suggest that microfilament disruption during the critical interval leads to the incorrect distribution of developmental instructions responsible for early pattern formation. The strict correlation between unequal division, unequal germ-granule partitioning, and the generation of daughter cells with different cell cycle periods observed in these embryos suggests that the three processes are couppled. We hypothesize that (1) an 'asymmetry determinant', normally located at the posterior end of the zygote, governs asymmetric division, germ-granule segregation, and the segregation of cell cycle timing elements during the first cell cycle, and (2) the integrity or placement of this asymmetry determinant is sensitive to microfilament disruption during the critical time interval. ------------------- Key: 1242 Medline: Authors: Hodgkin J;Chisholm AD;Shen MM Title: Major sex-determining genes and the control of sexual dimorphism in Caenorhabditis elegans. Citation: Genome 31: 625-637 1989 Type: REVIEW Genes: egl-1 egl-5 egl-15 egl-16 egl-17 egl-22 egl-41 fem-1 fem-2 fem-3 fer-15 fog-1 fog-2 gon-1 her-1 him-4 lin-1 lin-2 lin-7 lin-10 lin-12 lin-15 lin-17 lin-22 lin-28 lin-32 mab-3 mab-5 mab-9 pal-2 sdc-1 sdc-2 spe-6 tra-1 tra-2 Abstract: Sex determination in Caenorhabditis elegans involves a cascade of major regulatory genes connecting the primary sex determining signal, X chromosome dosage, to key switch genes, which in turn direct development along either male or female pathways. Animals with one X chromosome (XO) are male, while animals with two X chromosomes (XX) are hermaphrodite; hermaphrodite development occurs because the action of the regulatory genes is modified in the germ line so that both sperm and oocytes are made inside a completely female soma. The regulatory genes are being examined by both genetic and molecular means. We discuss how these major genes, in particular the last switch gene in the cascade, tra-1, might regulate the many different sex-specific events that occur during the development of the hermaphrodite and of the male. ------------------- Key: 1243 Medline: 90215253 Authors: Candido EPM;Jones D;Dixon DK;Graham RW;Russnak RH;Kay RJ Title: Structure, organization, and expression of the 16-kDa heat shock gene family of Caenorhabditis elegans. Citation: Genome 31: 690-697 1989 Type: ARTICLE Genes: Abstract: Exposure of the nematode Caenorhabditis elegans to a heat shock results in the induction of a number of genes not normally expressed in the animals under normal growth conditions. Among these are a family of genes encoding 16 kDa heat shock proteins (hsp16s). The major hsp16 genes have been cloned and characterized, and found to reside at two clusters in the C. elegans genome. One cluster contains two distinct genes, hsp16-1 and hsp16-48, arranged in divergent orientations separated by only 348 base pairs (bp). An identical pair, duplicated and inverted with respect to the first pair, is located 415 bp away. This cluster, located on chromosome V, therefore contains four genes as two identical pairs within less than 4 kilobases of DNA, and the pairs form the arms of a large inverted repeat. A second pair of genes, hsp16-2 and hsp16-41, constitutes a second hsp16 locus with an organization very similar to that of the hsp16-1/48 locus, except that it is not duplicated. Comparisons of the derived amino acid sequences show that hsp16-1 and hsp16-2 form a closely related pair, as do hsp16-41 and hsp16-48. These hsps show extensive sequence identity with the small hsps of Drosophila, as well as with mammalian alpha-crystallins. The coding region of each gene is interrupted by a single intron of approximately 50 bp, in a position homologous to that of the first intron in mouse alpha- crystallin ------------------- Key: 1244 Medline: 90185183 Authors: Liu Z;Ambros V Title: Heterochronic genes control the stage-specific initiation and expression of the dauer larva developmental program in Caenorhabditis elegans. Citation: Genes & Development 3: 2039-2049 1989 Type: ARTICLE Genes: lin-4 lin-14 lin-28 lin-29 Abstract: We report that a stage-specific developmental program, dauer larva formation, is temporally regulated by four heterochronic genes, lin- 4, lin-14, lin-28, and lin-29. The effects of mutations in these four genes on dauer larva formation have revealed that they regulate two different processes of dauer larva formation: (1) a decision specifying the larval stage at which dauer larva development initiates, and (2) the specialized differentiation of hypodermal cells during dauer larva morphogenesis. Epistasis analysis has suggested a model in which lin-4 negatively regulates lin-14, and the resulting temporal decrease in lin-14 activity specifies the stage of dauer larva initiation. Our results further suggest that dauer larva morphogenesis by hypodermal cells requires that lin-28 acts to inhibit lin-29 during early larval stages. ------------------- Key: 1245 Medline: 90138980 Authors: Honda S;Epstein HF Title: Modulation of muscle gene expression in Caenorhabditis elegans: Differential levels of transcripts, mRNAs, and polypeptides from thick filament proteins during/ Citation: Proceedings of the National Academy of Sciences USA 87: 876-880 1990 Type: ARTICLE Genes: myo-3 unc-15 unc-54 Abstract: The body-wall muscle cells of the nematode Caenorhabditis elegans produce thick filaments during embryonic, larval, and adult stages. These thick filaments contain two myosin isoforms, A and B, which assemble into different zones along the 10-microns lengths. Paramyosin, a protein homologous to myosin rods, forms a substratum for the myosins. The three filament proteins are encoded by different genes: myo-3 V (myosin heavy chain A), unc-54 I (myosin heavy chain B), and unc-15 I (paramyosin). The relative expression of these genes has been studied by run-on nuclear transcription in vitro, hybridization of accumulated mRNA, and immunochemical determination of specific polypeptide accumulation. In late larval nematodes (L4), the relative levels of nuclear run-on transcription per mol of probe are 6.4 unc-54:2.4 myo-3:1.0 unc-15. Similarly, the relative levels of immunospecific proteins are 4.5 unc-15:3.1 unc-54:1.0 myo-3. Most strikingly, the relative mRNA amounts are 50.0 unc-54:12.4 unc-15:1.0 myo-3. Thus, the orders of relative abundance and the quantitative relations of expression of the three functionally related genes change from transcriptional activities to final accumulated product of thick filament proteins. Modulation of the expression appears to involve processes affecting accumulation of mRNA and protein. The great difference in accumulation of the mRNAs for the two myosin heavy chain isoforms A and B may be related to the ------------------- Key: 1246 Medline: 90180497 Authors: Hedgecock EM;Culotti JG;Hall DH Title: The unc-5, unc-6, and unc-40 genes guide circumferential migrations of pioneer axons and mesodermal cells on the epidermis in C. elegans. Citation: Neuron 2: 61-85 1990 Type: ARTICLE Genes: unc-5 unc-6 unc-40 Abstract: Three known genes guide circumferential migrations of pioneer axons and mesodermal cells on the nematode body wall. unc-5 affects dorsal migrations, unc-40 primarily affects ventral migrations, and unc-6 affects migrations in both directions. Circumferential movements still occur, but are misdirected whereas longitudinal movements are normal in these mutants. Pioneer growth cones migrating directly on the epidermis are affected; growth cones migrating along established axon fascicles are normal. Thus these genes affect cell guidance and not cell motility per se. We propose that two opposite, adhesive gradients guide circumferential migrations on the epidermis. unc-5, unc-6 and unc-40 may encode these adhesion molecules or their cellular receptors. Neurons have access to the basal lamina and the basolateral surfaces of the epidermis, but mesodermal cells contact only the basal lamina. These genes probably identify molecular cues on the basal lamina that guide mesodermal migrations. The same basal lamina cues, or perhaps related molecules on the epidermal cell surfaces, guide pioneer neurons. ------------------- Key: 1247 Medline: 90172409 Authors: Park Y-S;Kramer JM Title: Tandemly duplicated Caenorhabditis elegans collagen genes differ in their modes of splicing. Citation: Journal of Molecular Biology 211: 395-406 1990 Type: ARTICLE Genes: col-12 col-13 Abstract: Caenorhabditis elegans contains 50 to 150 collagen genes dispersed throughout its genome. We have determined the complete nucleotide sequences of two collagen genes, col-12 and col-13, that are separated by only 1800 bases and are transcribed in the same direction. The 951 nucleotides of their coding regions differ by only five nucleotides (99.5% identity). The amino acid sequences are identical except for two conservative amino acid changes within the putative secretory signal sequences, so the mature forms of the col- 12 and col-13 collagens would be identical. The position and sequence of the intron (52 base-pairs) within the coding region of each gene are perfectly conserved. In contrast to the coding regions and the introns, the 5' and 3' flanking regions show little sequence similarity, col-12 and col-13 are expressed at similar levels at the same developmental stages, and appear to utilize conserved TATA boxes and transcription start sites. The major differences between the genes is that, preceding the initiator ATG, col-12 has a cis-spliced intron, while col-13 is transspliced. Thus, col-12 and col-13 are essentially identical in all aspects except that the col-12 mRNA has a 26-nucleotide cis-spliced leader at the same place where the col-13 mRNA has a 22-nucleotide trans-spliced leader. These results suggest that col-12 and col-13 are derived from a gene duplication and that sequence homology in the coding regions, but not in the flanking regions, has been maintained by gene conversion. The fact that the only significant difference between the two genes is in their modes of splicing suggests that cis and trans-splicing can be interchanged during gene evolution. ------------------- Key: 1248 Medline: Authors: O'Riordan VB;Burnell AM Title: Intermediary metabolism in the dauer larva of the nematode Caenorhabditis elegans - II. The glyoxalate cycle and fatty-acid oxidation. Citation: Comparative Biochemistry & Physiology 95B: 125-130 1990 Type: ARTICLE Genes: Abstract: 1. The activities of the enzymes of the glyoxylate cycle and of the B-oxidation pathway were compared in the dauer larva and the adult stages of C. elegans. 2. The relative rates of NADP isocitrate dehydrogenase (TCA cycle) and isocitrate lyase (glyoxlylate cycle) in adult and dauer larvae indicate the increased importance of the glyoxylate cycle in dauer larvae. 3. High levels of the B-oxidation enxymes acyl-CoA dehydrogenase, enoyl-CoA hydratase and acetyl-CoA acetyltransferase were observed in both adult and dauer fractions, the relative levels of activity being lower in the dauers. 4. These data demonstrate the importance of lipid storage as an energy reserve for the non-feeding dauer larva. ------------------- Key: 1249 Medline: 90165873 Authors: Vanfleteren JR;Van Bun SM;De Baere I;Van Beeumen JJ Title: The primary structure of a minor isoform (H1.2) of histone H1 from the nematode Caenorhabditis elegans. Citation: Biochemical Journal 265: 739-746 1990 Type: ARTICLE Genes: Abstract: The complete amino acid sequence of a minor isoform (H1.2) of histone H1 from the nematode Caenorhabditis elegans was determined. The amino acid chain consists of 190 residues and has a blocked N-terminus. Histone subtype H1.2 is 17 residues shorter than the major isoform H1.1, mainly as the result of deletions of short peptide fragments. Considerable divergence from isoform H1.1 has occurred in the N- terminal domain and the very C-terminus of the molecule, but the central globular domain and most of the C-terminal domain, including two potential phosphorylation sites, have been well conserved. Secondary-structure predictions for both H1 isoforms reveal a high potential for helix formation in the N-terminal region 1-33 of isoform H1.1 whereas the corresponding region in isoform H1.2 has low probability of being found in alpha-helix. No major differences in secondary structure are predicted for other parts of both H1 subtypes. The aberrant conformation of isoform H1.2 may be indicative of a significantly ------------------- Key: 1250 Medline: 90153982 Authors: Lu X;Gross RE;Bagchi S;Rubin CS Title: Cloning, structure, and expression of the gene for a novel regulatory subunit of cAMP-dependent protein kinase in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 265: 3293-3303 1990 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans (C. elegans) expresses the regulatory subunit (R) of cAMP-dependent protein kinase at a level similar to the levels determined for R subunits in mammalian tissues. Approximately 60% of the C. elegans cAMP-binding protein is tightly associated with particulate structures by noncovalent interactions. Ionic detergents or 7 M urea solubilize particulate R. Solubilized and cytosolic R subunits have apparent Mr values of 52,000 and pI values of 5.5. cDNA and genomic DNA encoding a unique C. elegans R subunit were cloned and sequenced. The derived amino acid sequence contains 375 residues; carboxyl-terminal residues 145-375 are 69% identical with mammalian RI. However, residues 44-145 are markedly divergent from the corresponding regions of all other R sequences. This region might provide sufficient structural diversity to adapt a single R subunit for multiple functional roles in C. elegans. Antibodies directed against two epitopes in the deduced amino acid sequence of C. elegans R avidly bound nematode cytosolic and particulate R subunits on Western blots and precipitated dissociated R subunits and R2C2 complexes from solution. Immunofluorescence analysis revealed that the tip of the head, which contains chemosensory and mechanosensory neurons, and the pharyngeal nerve ring were enriched in R. The R subunit concentration is low during early embryogenesis in C. elegans. A sharp increase (approximately 6- fold) in R content begins several hours before the nematodes hatch and peaks during the first larval stage. Developmental regulation of R expression occurs at translational and/or post-translational levels. The 8-kilobase pair C. elegans R gene is divided into 8 exons by introns ranging from 46 to 4300 base pairs. The 5'-flanking region has no TATA box and contains preferred ------------------- Key: 1251 Medline: 90180200 Authors: Rankin CH;Beck CDO;Chiba CM Title: Caenorhabditis elegans: a new model system for the study of learning and memory. Citation: Behavioural Brain Research 37: 89-92 1990 Type: ARTICLE Genes: Abstract: The extensive information on the neuroanatomy, development and genetics of Caenorhabditis (C.) elegans make it an ideal candidate model system for the analysis of the mechanisms underlying learning and memory. A first step in this analysis is the demonstration of the capacity of C. elegans to learn. In these experiments non-associative learning in C. elegans was investigated by observing changes in reversal reflex response amplitude to a mechanical vibratory stimulus. The results from these studies of non-associative learning show that C. elegans is capable of short-term habituation, dishabituation and sensitization, as well as long-term retention of habituation training lasting for at least 24 h. These findings set the stage for detailed developmental, genetic and physiological analyses of learning and memory. ------------------- Key: 1252 Medline: 90185142 Authors: Rosenbluth RE;Johnsen RC;Baillie DL Title: Pairing for recombination in LG V of Caenorhabditis elegans: A model based on recombination in deficiency Citation: Genetics 124: 615-625 1990 Type: ARTICLE Genes: sDf27 sDf28 sDf32 sDf33 sDf34 sDf38 sDf39 sDf40 sDf42 sDf45 sDf50 sDf52 sDf53 sDf74 Abstract: The effect of deficiencies on recombination was studied in Caenorhabditis elegans. Heterozygous deficiencies in the left half of linkage group V [LGV(left)] were shown to inhibit recombination to their right. Fourteen deficiencies, all to the left of unc-46, were analyzed for their effect on recombination along LGV. The deficiencies fell into two groups: 10 "major inhibitors" which reduce recombination to less than 11% of the expected rate between themselves and unc-46; and four "minor inhibitors" which reduce recombination, but to a much lesser extent. All four minor inhibitors delete the left-most known gene on the chromosome, while six of the ten major inhibitors do not (i.e., these are "internal" deficiencies). Where recombination could be measured on both sides of a deficiency, recombination was inhibited to the right but not to the left. In order to explain these results we have erected a model for the manner in which pairing for recombination takes place. In doing so, we identify a new region of LGV, near the left terminus, that is important for the pairing process. ------------------- Key: 1253 Medline: 90192165 Authors: Schukkink RF;Plasterk RHA Title: TcA, the putative transposase of the C. elegans Tc1 transposon, has an N-terminal DNA binding domain. Citation: Nucleic Acids Research 18: 895-900 1990 Type: ARTICLE Genes: Abstract: Tc1 is a transposon present in several copies in the genome of all natural isolates of the nematode C.elegans; it is actively transposing in many strains. In those strains Tc1 insertion is the main cause of spontaneous mutations. The transposon contains one large ORF that we call TcA; we assume that the TcA protein is the transposase of Tc1. We expressed TcA in E.coli, purified the protein and showed that it has a strong affinity for DNA (both single stranded and double stranded). A fusion protein of beta-galactosidase and TcA also exhibits DNA binding; deletion derivatives of this fusion protein were tested for DNA binding. A deletion of 39 amino acids at the N-terminal region of TcA abolishes the DNA binding, whereas a deletion of 108 C-terminal amino acids does not affect DNA binding. This shows that the DNA binding domain of TcA is near the N- terminal region. The DNA binding capacity of TcA supports the assumption that TcA is a transposase of Tc1. ------------------- Key: 1254 Medline: 90169310 Authors: Yuan JY;Horvitz HR Title: The Caenorhabditis elegans genes ced-3 and ced-4 act cell autonomously to cause programmed cell death. Citation: Developmental Biology 138: 33-41 1990 Type: ARTICLE Genes: ced-3 ced-4 dpy-4 dpy-17 unc-26 unc-30 unc-36 nDp3 sDp3 Abstract: Mutations in the genes ced-3 and ced-4 prevent almost all of the programmed cell deaths that occur during Caenorhabditis elegans development. To determine the sites of action of these two genes, we performed genetic mosaic analyses. We generated C. elegans animals that carried a free chromosomal duplication bearing either ced-3(+) or ced-4(+) in an otherwise homozygous ced-3 or ced-4 genetic background. We used other genes on the duplication as markers to identify genetic mosaic animals in which the duplication was present in some but not all cells. The patterns of cell death survivors in these mosaic animals indicated that the products of both ced-3 and ced-4 function within dying cells to cause cell death. ------------------- Key: 1255 Medline: Authors: Siddiqui SS Title: Axonal outgrowth and process placement of sensory lumbar neurons in the nematode Caenorhabditis elegans. Citation: "Neurobiology of Sensory Systems." Singh RN and Strausfeld NJ (eds), Plenum Press. : 241-265 1989 Type: ARTICLE Genes: unc-6 unc-13 unc-33 unc-44 unc-51 unc-53 unc-61 unc-71 unc-73 unc-76 unc-98 Abstract: One of the most remarkable features of the brain is the degree of precision with which neurons are interconnected. As the neural circuitry of the nematode Caenorhabditis elegans has been completely established through serial section electron micrographs, and because the nematode is amenable to genetic analysis, it is an excellent system to study the genetic basis of axonal outgrowth and process placement in the formation of a neural network. Here, I will describe the identification of 11 genes which affect the axonal outgrowth and guidance of five pairs of lumbar neurons in C. elegans. A pair of bilaterally symmetric luumbar ganglia are situated in the tail of C. elegans, each consisting of 12 neurons. We have examined the morphology and pattern of axonal processes of three embryonic (PHA, PHB, and PLM) and two postembryonic (PHC and PVN) lumbar neurons on the wild type and existing uncoordinated (unc) mutants, immunocytochemically. We have earlier shown that antibodies against horseradish peroxidase (HRP) stain PHA, PHB, PHC and PVN neurons, and monoclonal antibodies specific to different tubulin isotypes stain the mechanosensory neuron PLM. A monoclonal antibody TY21, raised against C. elegans crude homogenate is specific for phasmid neurons PHA, and PHB. In the wild type, PHA, PHB, PHC, and PVN send anteriorly directed processes ventrally via the lumbar commissures to targets in the ventral cord; whereas, PLM sends a process anteriorly in a subventral position, sending a branch ventrally to the ventral cord near the vulva. PHA, PHN, PHC, and PLM are bipolar neurons, extend a backward process into the tail spike. Mutations in nine genes (unc-6, unc-13, unc-33, unc-44, unc-51, unc-61, unc-71, unc-73, and unc-98) result in abnormal axonal outgrowth and process placement of PHC, PCN and PLM neurons. Four (unc-6, unc-33, unc-44, and unc-51) of the nine genes identified above, and unc-76 were previously shown to affect the growth of PHA and PHB neurons. Mutants in unc-53, which are apparently normal in the growth of PHA, PHB, PHC, and PVN neurons, and unc-76, harbor defects in PLM axonal outgrowth and guidance. In summary, we have identified a set of 11 genes, which exert overlapping, but distinct effects on the axonal outgrowth and process placement of embryonic (PHA, PHB, and PLM), and postembryonic (PHC and ------------------- Key: 1256 Medline: 90215193 Authors: Thomas JH Title: Genetic analysis of defecation in Caenorhabditis elegans. Citation: Genetics 124: 855-872 1990 Type: ARTICLE Genes: aex-1 aex-2 aex-3 aex-4 aex-5 aex-6 cha-1 dec-1 eat-2 egl-8 exp-1 exp-2 mec-4 mec-5 mec-9 osm-3 osm-5 pbo-1 unc-16 unc-25 unc-33 unc-44 unc-47 unc-89 unc-101 Abstract: Defecation in the nematode Caenorhabditis elegans is achieved by a cyclical stereotyped motor program. The first step in each cycle is contraction of a set of posterior body muscles (pBoc), followed by contraction of a set of anterior body muscles (aBoc), and finally contraction of specialized anal muscles that open the anus and expel intestinal contents (Exp). By testing existing behavioral mutants and screening for new mutants that become constipated due to defects in defecation, I have identified 18 genes that are involved in defecation. Mutations in 16 of these genes affect specific parts of the motor program: mutations in two genes specifically affect the pBoc step; mutations in four genes affect the aBoc step; mutations in four genes affect the Exp step; and mutations in six genes affect both aBoc and Exp. Mutations in two other genes affect the defecation cycle period but have a normal motor program. Sensory inputs that regulate the cycle timing in the wild type are also described. On the basis of the phenotypes of the defecation mutants and of double mutants, I suggest a formal genetic pathway for the control of the ------------------- Key: 1257 Medline: Authors: Tedesco PM;Link CD;Hutchinson EW;Johnson TE Title: Cloning a gene for life-extension in Caenorhabditis Citation: "Molecular Biology of Aging." UCLA Symposia on Molecular and Cellular Biology, New Series. Finch CE and Johnson TE (eds), Wiley-Liss, Inc. 123: 3-17 1990 Type: REVIEW Genes: age-1 Abstract: Single-gene mutants and genetic lines of the simple roundworm Caenorhabditis elegans that have mean life spans of about 35 days as compared with the wild type (20 days) have been developed. One recessive gene, age-1, has been mapped to a well-studied region of linkage group II, affects both males and hermaphrodites, and is responsible for a five-fold decrease in hermaphrodite self-fertility. This gene is being more precisely mapped by means of multi-factor crosses and deficiency analysis. We are currently cloning the age-1 gene using strategies including the construction of congenic strains carrying multiple transposon-mediated RFLPs flanking age-1 and deficiencies ------------------- Key: 1258 Medline: 90262569 Authors: Mitchell DL;Hartman PS Title: The regulation of DNA repair during development. Citation: BioEssays 12: 74-79 1990 Type: REVIEW Genes: rad-1 rad-3 Abstract: DNA repair is important in such phenomena as carcinogenesis and aging. While much is known about DNA repair in single-cell systems such as bacteria, yeast, and cultured mammalian cells, it is necessary to examine DNA repair in a develomental context in order to completely understand its processes in complex metazoa such as man. We present data to support the notion that proliferating cells from organ systems, tumors, and embryos have a greater DNA repair capacity than terminally differentiated, nonproliferating cells. Differential expression of repair genes and accessibility of chromatin to repair enzymes are considered as determinants in the developmental regulation of DNA repair. ------------------- Key: 1259 Medline: 90199879 Authors: Spence AM;Coulson A;Hodgkin J Title: The product of fem-1, a nematode sex-determining gene, contains a motif found in cell cycle control proteins and receptors for cell-cell interactions. Citation: Cell 60: 981-990 1990 Type: ARTICLE Genes: fem-1 Abstract: We report the cloning and sequencing of fem-1, a gene required for sex determination in both germline and somatic tissues in the nematode C. elegans. Clones carrying a 5.5 kb fragment are able to rescue the progeny of a fem-1 mutant when injected into its oocytes. The major fem-1 transcript in both sexes is 2.4 kb and comprises 11 exons. It encodes a soluble, intracellular protein of 656 amino acids that includes near its N-terminus six contiguous copies of a motif found in the products of the cdc10 gene of S. pombe, the SWI6 gene of S. cerevisiae, the Notch gene of Drosophila, and the lin-12 and glp-1 genes of C. ------------------- Key: 1260 Medline: 90202988 Authors: Hu E;Rubin CS Title: Casein kinase II from Caenorhabditis elegans. Properties and developmental regulation; cloning and sequence of cDNA and the gene for the catalytic subunit/ Citation: Journal of Biological Chemistry 265: 5072-5080 1990 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans provides a model system for investigating the structure, function, and regulation of casein kinase II. Cytosols from C. elegans embryos and gravid adults, which contain fertilized eggs and embryos, are enriched in casein kinase II activity; cytosols from newly hatched larva, four subsequent larval stages, and immature adults exhibit casein kinase II levels that are 3-10-fold lower than those observed in embryo cytosol. C. elegans casein kinase II contains alpha (Mr = 42,000) and beta (Mr = 29,000) subunits and has a Stokes radius of 50 nm. The enzyme utilizes ATP and GTP as substrates, is potently inhibited by heparin and undergoes autophosphorylation. Sequence analyses of cloned cDNAs corresponding to the 1.7-kilobase mRNA encoding the alpha (catalytic) subunit of casein kinase II indicate that the alpha polypeptide contains 359 amino acid residues. Variations in the abundance of casein kinase II alpha mRNA are coordinated with changes in enzyme activity during C. elegans development, indicating that alpha subunit expression is controlled at a pretranslational level. However, the magnitude of the developmentally controlled changes in phosphotransferase activity exceeded the corresponding increments in alpha subunit mRNA content. This suggests that translational and/or post-translational mechanisms also play an important role in the developmental regulation of C. elegans casein kinase II activity. The 2.9-kilobase casein kinase II alpha gene is divided into eight exons by intervening sequences ranging from 48 to 457 base pairs in length. The alpha gene promoter contains a TATA box, and a unique transcription start site has been identified. The intron/exon organization of the casein kinase II alpha gene differs markedly from the gene structure of the catalytic subunit of murine cAMP-dependent protein kinase (Chrivia, J. C., Uhler, M. D., and McKnight, G. S. (1988) J. Biol. Chem. 263, 5739- 5744). ------------------- Key: 1261 Medline: 90127264 Authors: Cox GN;Shamansky LM;Boisvenue RJ Title: Haemonchus contortus: Evidence that the 3A3 collagen gene is a member of an evolutionarily conserved family of nematode cuticle collagens. Citation: Experimental Parasitology 70: 175-185 1990 Type: ARTICLE Genes: col-1 Abstract: Rabbit antisera were raised against an 18 amino acid-long peptide that corresponds to the predicted sequence of the carboxy-terminal, nontriple helical region of the Haemonchus contortus 3A3 collagen gene. This sequence is highly conserved and diagnostic for members of the col-1 collagen family, which includes the 3A3 gene. We find that these antisera react predominantly with multiple, high molecular weight (>68 kDa) proteins on Western blots of whole extracts. The number and molecular weights of the reacting proteins vary depending upon the developmental stage of the worms analyzed. All of the reacting proteins are collagenase sensitive. The reacting collagens copurify with cuticles and are released from cuticles by reducing agents. In indirect immunofluorescence assays the antisera react only with the broken edges of isolated cuticles, suggesting that the antisera are reacting with an internal cuticle layer. This layer appears to be circular and to extend throughout the length of the worm. The antisera react on Western blots with multiple, high molecular weight collagens of eight other nematodes examined, representing two classes and several orders. These data provide additional support for the notion that the 3A3 collagen gene, and other members of the col-1 collagen family, encode cuticle collagens. Collagens with this peptide sequence, presumably other members of the col-1 collagen family, appear to be widely distributed in the phylum ------------------- Key: 1262 Medline: 90205857 Authors: Liou RF;Blumenthal T Title: Trans-spliced Caenorhabditis elegans messenger RNAs retain trimethylguanosine caps. Citation: Molecular and Cellular Biology 10: 1764-1768 1990 Type: ARTICLE Genes: act-1 act-2 act-3 act-4 Abstract: The nematode Caenorhabditis elegans has an unusual small nuclear RNA, containing a 100-nucleotide RNA molecule, spliced leader RNA, which donates its 5' 22 nucleotides to a variety of recipient RNAs by a trans-splicing reaction. The spliced leader RNA has a 5' trimethylguanosine (TMG) cap, which becomes the 5' end of trans- spliced mRNAs. We found that mature trans-spliced mRNAs were immunoprecipitable with anti-TMG cap antibodies and that TMG- containing dinucleotides specifically competed with the trans-spliced mRNAs for antibody binding. We also found that these mRNAs retained their TMG caps throughout development and that the TMG-capped mRNAs were polysome associated. Since the large majority of C. elegans mRNAs are not trans-spliced, the addition of the spliced leader and its TMG cap to a limited group of recipient RNAs may create a functionally distinct subset of mRNAs. ------------------- Key: 1263 Medline: 90205858 Authors: Van Doren K;Hirsh D Title: mRNAs that mature through trans-splicing in Caenorhabditis elegans have a trimethylguanosine cap at their 5' termini. Citation: Molecular and Cellular Biology 10: 1769-1772 1990 Type: ARTICLE Genes: Abstract: Approximately 10% of the mRNAs in the nematode Caenorhabditis elegans mature through a trans-splicing mechanism that involves the transfer of a 22-nucleotide spliced leader to the 5' end of the pre-mRNA. The spliced leader RNA exists as a small nuclear ribonucleoprotein particle and has the trimethylguanosine cap that is characteristic of eucaryotic small nuclear RNAs. We found that the trimethylguanosine cap present on the spliced leader RNA was transferred to the pre-mRNA during the trans-splicing reaction. Thereafter, the trimethylguanosine cap was maintained on the mature mRNA. This is the first example of eucaryotic cellular mRNAs possessing a trimethylguanosine cap structure. ------------------- Key: 1264 Medline: 90138897 Authors: Maroney PA;Hannon GJ;Nilsen TW Title: Transcription and cap trimethylation of a nematode spliced leader RNA in a cell-free system. Citation: Proceedings of the National Academy of Sciences USA 87: 709-713 1990 Type: ARTICLE Genes: Abstract: Maturation of a fraction of mRNAs in nematodes involves the acquisition of a common 5' terminal spliced leader sequence derived from a nonpolyadenylylated spliced leader RNA by trans splicing. We have developed a cell-free system prepared from Ascaris lumbricoides embryos that accurately and efficiently synthesized the spliced leader RNA of A. lumbricoides. Transcription of the spliced leader RNA was catalyzed by RNA polymerase II, and the majority of the spliced leader RNAs synthesized in vitro possessed a trimethylguanosine cap structure identical to that found on in vivo-synthesized spliced leader RNA. ------------------- Key: 1265 Medline: 90220522 Authors: Carter PW;Roos JM;Kemphues KJ Title: Molecular analysis of zyg-11, a maternal-effect gene required for early embryogenesis of Caenorhabditis elegans. Citation: Molecular & General Genetics 221: 72-80 1990 Type: ARTICLE Genes: zyg-11 Abstract: The product of the maternally acting gene zyg-11 is required for early embryogenesis of Caenorhabditis elegans. One-cell embryos that lack a functional zyg-11 gene product exhibit an arrest of meiosis at metaphase II, a delay in the formation of pronuclei, unusually vigorous movements of cytoplasm, the formation of multiple pronuclei, incorrect segregation of P granules, and incorrect placement of the first cleavage furrow. We have isolated and sequenced a molecular clone of zyg-11, and shown that microinjection of the cloned DNA can rescue zyg-11 mutations. A transcriptional analysis shows that transcription of the gene is not limited to the female germ-line, despite the strict maternal-effect phenotype of zyg-11 mutations. ------------------- Key: 1266 Medline: 90204554 Authors: Sanicola M;Ward S;Childs G;Emmons SW Title: Identification of a Caenorhabditis elegans histone H1 gene family. Characterization of a family member containing an intron and encoding a poly(A)+ mRNA. Citation: Journal of Molecular Biology 212: 259-268 1990 Type: ARTICLE Genes: fem-1 fem-3 his-24 Abstract: The isolation and properties of a gene encoding a histone H1 protein of Caenorhabditis elegans, his-24, are described. The predicted protein sequence is similar to histone H1 proteins of other eukaryotes. However, the gene structure of his-24 is atypical for a histone H1 gene; it contains an intron and encodes a polyadenylated mRNA. A family of approximately five histone H1 genes is defined by cross-hybridization to his-24. All appear to encode polyadenylated mRNAs. One gene is expressed specifically in male germ cells. These histone H1 genes are dispersed individually in the genome, apart from the previously described clusters of core histone genes (H2A, H2B, H3 and H4), which probably all encode non-polyadenylated mRNAs. This histone gene organization, with clustered core histone genes, encoding non-polyadenylated transcripts, and dispersed, histone H1 genes from which it appears only polyadenylated messages arise, suggests that C. elegans is at a stage of evolution of the histone gene family intermediate between lower eukaryotes (e.g. yeast) and the most advanced forms. ------------------- Key: 1267 Medline: 90264942 Authors: Harris LJ;Prasad S;Rose AM Title: Isolation and sequence analysis of Caenorhabditis briggsae repetititve elements related to the Caenorhabditis elegans transposon Tc1. Citation: Journal of Molecular Evolution 30: 359-369 1990 Type: ARTICLE Genes: Abstract: We have identified two repetitive element families in the genome of the nematode Caenorhabditis briggsae with extensive sequence identity to the Caenorhabditis elegans transposable element Tc1. Five members each of the TCb1 (previously known as Barney) and TCb2 families were isolated by hybridization to a Tc1 probe. Tc1-hybridizing repetitive elements were grouped into either the TCb1 or TCb2 family based on cross-hybridization intensities among the C. briggsae elements. The genomic copy number of the TCb1 family is 15 and the TCb2 family copy number is 33 in the C. briggsae strain G16. The two transposable element families show numerous genomic hybridization pattern differences between two C. briggsae strains, suggestive of transpositional activity. Two members of the TCb1 family, TCb1#5 and TCb1#10, were sequenced. Each of these two elements had suffered an independent single large deletion. TCb1#5 had a 627-bp internal deletion and TCb1#10 had lost 316 bp of one end. The two sequenced TCb1 elements were highly conserved over the sequences they shared. A 1616-bp composite TCb1 element was constructed from TCb1#5 and TCb1#10. The composite TCb1 element has 80-bp terminal inverted repeats with three nucleotide mismatches and two open reading frames (ORFs) on opposite strands. TCb1 and the 1610-bp Tc1 share 58% overall nucleotide sequence identity, and the greatest similarity occurs in their ORF1 and inverted repeat termini. ------------------- Key: 1268 Medline: 90236277 Authors: Clark DV;Johnsen RC;McKim KS;Baillie DL Title: Analysis of lethal mutations induced in a mutator strain that activates transposable elements in Caenorhabditis elegans. Citation: Genome 33: 109-114 1990 Type: ARTICLE Genes: let-448 let-449 lin-40 mut-4 sDf40 sDf41 sDf45 sDf48 sDf49 sDf51 sDf52 Abstract: A screen was conducted for lethal mutations in the nematode Caenorhabditis elegans in a strain containing the mutator mut-4 (st700)I to examine the nature of mutator-induced lethal mutations within two large chromosomal regions comprising a total of 49 map units (linkage group IV (right) and linkage group V (left)). The genetic analysis of 28 lethal mutations has revealed that the mutator locus mut-4(st700)I causes both putative single-gene mutations and deficiencies. We have identified lethal mutations in three different genes, in addition to seven deficiencies. There is a mutational hot spot on linkage group V (left) around the lin-40 locus. Six mutations appear to be alleles of lin-40. In addition, 5 of 7 deficiencies have breakpoints at or very near lin-40. All seven deficiencies delete the left-most known gene on linkage group V (left) and thus appear to delete the tip of the chromosome. This is in contrast to gamma ray and formaldehyde induced deficiencies, which infrequently delete the closest known gene to the tip of a chromosome. ------------------- Key: 1269 Medline: 90221876 Authors: Fields C Title: Information content of Caenorhabditis elegans splice site sequences varies with intron length. Citation: Nucleic Acids Research 18: 1509-1512 1990 Type: ARTICLE Genes: Abstract: A database of sequences of 139 introns from the nematode Caenorhabditis elegans was analyzed using the information measure of Schneider et al. (1986) J. Mol. Biol. 128: 415-431. Statistically significant information is encoded by at least the first 30 nt and last 20 nt of C. elegans introns. Both the quantity and the distribution of information in the 5' splice site sequences differs between the typical short (length less than 75 nt) and rarer long (length greater than 75 nt) introns, with the 5 sites of long introns containing approximately one bit more information. 3' splice site sequences of long and short C. elegans introns differ significantly in the region between -20 and -10 nt. ------------------- Key: 1270 Medline: 90255951 Authors: Barton MK;Kimble J Title: fog-1, a regulatory gene required for specification of spermatogenesis in the germ line of Caenorhabditis elegans. Citation: Genetics 125: 29-39 1990 Type: ARTICLE Genes: fem-3 fog-1 glp-1 qDf3 Abstract: In wild-type Caenorhabditis elegans, the XO male germ line makes only sperm and the XX hermaphrodite germ line makes sperm and then oocytes. In contrast, the germ line of either a male or a hermaphrodite carrying a mutation of the fog-1 (feminization of the germ line) locus is sexually transformed: cells that would normally make sperm differentiate as oocytes. However, the somatic tissues of fog-1 mutants remain unaffected. All fog-1 alleles identified confer the same phenotype. The fog-1 mutations appear to reduce fog-1 function, indicating that the wild-type fog-1 product is required for specification of a germ cell as a spermatocyte. Two lines of evidence indicate that a germ cell is determined for sex at about the same time that it enters meiosis. These include the fog-1 temperature sensitive period, which coincides in each sex with first entry into meiosis, and the phenotype of a fog-1; glp-1 double mutant. Experiments with double mutants show that fog-1 is epistatic to mutations in all other sex-determining genes tested. These results lead to the conclusion that fog-1 acts at the same level as the fem genes at the end of the sex determination pathway to specify germ cells as sperm. ------------------- Key: 1271 Medline: 90263088 Authors: Georgi LL;Albert PS;Riddle DL Title: daf-1, a C. elegans gene controlling dauer larva development, encodes a novel receptor protein kinase. Citation: Cell 61: 635-645 1990 Type: ARTICLE Genes: daf-1 Abstract: The dauer larva is a developmentally arrested, non-feeding dispersal stage normally formed in response to overcrowding and limited food. The daf-1 gene specifies an intermediate step in a hierarchy of genes thought to specify a pathway for neural transduction of environmental cues. Mutations in daf-1 result in constitutive formation of dauer larvae even in abundant food. This gene has been cloned by Tc1- transposon tagging, and it appears to encode a new class of serine/threonine kinase. A daf-1 probe detects a 2.5 kb mRNA of low abundance, and the DNA sequence indicates that the gene encodes a 669 amino acid protein, with a putative transmembrane domain and a C- terminal protein kinase domain most closely related to the cytosolic, raf proto-oncogene family. Hence, the daf-1 product appears to be a cell-surface receptor required for transduction of environmental signals into an appropriate developmental response. ------------------- Key: 1272 Medline: Authors: Johnson TE Title: Caenorhabditis elegans offers the potential for molecular dissection of the aging process. Citation: Handbook of the Biology of Aging. Schneider EL and Rowe JW (eds), Academic Press, Inc. 3: 45-58 1990 Type: REVIEW Genes: age-1 fer-15 Abstract: Nematodes have been used as biological models of aging for some twenty years, and a large number of reviews have appeared both as a chapter in the previous edition of this handbook and in other sources. Major advantages and disadvantages in the use of nematodes as model organisms have been well reviewed. It is clear that for some purposes, such as the identification of genetic variants in length of life, which will be reviewed here, nematodes are an invaluable model. Genetic variants of Caenorhabditis elegans have recently been isolated that have life span extensions of more than 70%; these strains offer an exceptional new avenue for the dissection of aging processes. With the exception of dietary restriction and selectively bred long-lived strains of Drosophila melanogaster, there are no other techniques for lengthening life, thereby allowing the study of associated changes in other physiological systems. This chapter will concentrate on C. elegans and will review the genetic techniques used to study againg as well as methodological advances in other areas of C. elegans genetics. The possibilities for the study of physiological alterations associated with aging through the use of such genetic variants are not yet being widely exploited, leaving open a wide variety of potential research areas. ------------------- Key: 1273 Medline: 90220593 Authors: Kramer JM;French RP;Park E-C;Johnson JJ Title: The Caenorhabditis elegans rol-6 gene, which interacts with the sqt-1 collage gene to determine organismal morphology, encodes a collagen. Citation: Molecular and Cellular Biology 10: 2081-2089 1990 Type: ARTICLE Genes: rol-6 sqt-1 mnDf16 mnDf45 mnDf46 mnDf61 mnDf67 mnDf80 Abstract: The rol-6 gene is one of the more than 40 loci in Caenorhabditis elegans that primarily affect organismal morphology. Certain mutations in the rol-6 gene produce animals that have the right roller phenotype, i.e., they are twisted into a right-handed helix. The rol-6 gene interacts with another gene that affects morphology, sqt-1; a left roller allele of sqt-1 acts as a dominant suppressor of a right roller allele of rol-6. The sqt-1 gene has previously been shown to encode a collagen. We isolated and sequenced the rol-6 gene and found that it also encodes a collagen. The rol-6 gene was identified by physical mapping of overlapping chromosomal deficiencies that cover the gene and by identification of an allele- specific restriction site alteration. The amino acid sequence of the collagen encoded by rol-6 is more similar to that of the sqt-1 collagen than to any of the other ten C. elegans cuticle collagen sequences compared. The locations of cysteine residues flanking the Gly-X-Y repeat regions of rol-6 and sqt-1 are identical, but differ from those in the other collagens. The sequence similarities between rol-6 and sqt-1 indicate that they represent a new collagen subfamily in C. elegans. These findings suggest that these two collagens physically interact, possibly explaining the genetic interaction seen between the rol-6 and sqt-1 genes. ------------------- Key: 1274 Medline: 90337281 Authors: Mains PE;Sulston IA;Wood WB Title: Dominant maternal-effect mutations causing embryonic lethality in Caenorhabditis elegans. Citation: Genetics 125: 351-369 1990 Type: ARTICLE Genes: let-354 mei-1 mel-23 mel-24 mel-25 mel-26 Abstract: We undertook screens for dominant, temperature-sensitive, maternal- effect embryonic-lethal mutations of Caenorhabditis elegans as a way to identify certain classes of genes with early embryonic functions, in particular those that are members of multigene families and those that are required in two copies for normal development. The screens have identified eight mutations, representing six loci. Mutations at three of the loci result in only maternal effects on embryonic viability. Mutations at the remaining three loci cause additional nonmaternal (zygotic) effects, including recessive lethality or sterility and dominant male mating defects. Mutations at five of the loci cause visible pregastrulation defects. Three mutations appear to be allelic with a recessive mutation of let-354. Gene dosage experiments indicate that one mutation may be a loss-of-function allele at a haploin sufficient locus. The other mutations appear to result in gain-of-function "poison" gene products. Most of these become less deleterious as the relative dosage of the corresponding wild-type allele is increased; we show that relative self-progeny viabilities for the relevant hermaphrodite genotypes are generally M/+/+ greater than M/+ greater than M/M/+ greater than M/Df greater than M/M, where M represents the dominant mutant allele. ------------------- Key: 1275 Medline: Authors: Johnson TE Title: A developmental genetic approach to the analysis of aging processes. Citation: "Biomedical Advances in Aging." Goldstein AL (ed), Plenum Press. : 43-48 1990 Type: REVIEW Genes: age-1 fer-15 Abstract: The biological processes collectively called aging are being dissected in our laboratory using classic genetic analyses akin to those used in the dissection of other fundamental biological processes, e.g., development or metabolism. Many pitfalls are inherent in the genetic analysis of components of fitness; many result from effects of inbreeding. These inbreeding effects have been avoided by the use of the small free-living nematode Caenorhabditis elegans. The hermaphroditic life-style of this animal facilitates the analysis of life span and senescence by permitting the direct isolation and genetic analysis of long-lived mutants and recombinant inbred (RI) lines without complications resulting from inbreeding problems. Both approaches to obtaining long-lived genotypes have been used effectively in the analysis of the aging processes of C. elegans and the reader will find a brief summary of ------------------- Key: 1276 Medline: 88170002 Authors: Epstein HF;Ortiz I;Berliner GC Title: Assemblages of multiple thick filaments in nematode Citation: Journal of Muscle Research & Cell Motility 8: 527-536 1987 Type: ARTICLE Genes: unc-15 unc-82 Abstract: A spectrum of thick filament-related structures exhibiting novel structural features is isolated in addition to the normal thick filaments from unc-15 and unc-82 mutants of Caenorhabditis elegans. Many assemblages have multiple myosin-coated filaments extending from both ends of central domains exhibiting paracrystalline paramyosin. The filament ends resemble the polar core structures of native thick filaments. Assemblages with filaments at only one end and short thick filaments that branch are also present. This spectrum of novel structures accumulates at high levels in specific mutants due to alterations in paramyosin or other interacting proteins. The multifilament structures are either alternative assemblages of thick filament proteins and substructures or usually transient nucleation centres active in the assembly of thick filaments which are favoured under mutant conditions. ------------------- Key: 1277 Medline: 90249740 Authors: Kim SK;Horvitz HR Title: The Caenorhabditis elegans gene lin-10 is broadly expressed while required specifically for the determination of vulval cell fates. Citation: Genes & Development 4: 357-371 1990 Type: ARTICLE Genes: lin-10 Abstract: As a first step in a molecular dissection of the pathway controlling the determination of vulval cell fates in Caenorhabditis elegans, we have analyzed the gene lin-10. We show that loss-of-function mutations in this gene specifically prevent the induction of vulval cell lineages and result instead in the expression of hypodermal cell lineages. We isolated a transposon-insertion allele of lin-10 and used it to clone a genomic region that contains the lin-10 locus. The location of lin-10 within this region was determined by identifying a transcript affected by three independent lin-10 mutations and by delimiting the minimal segment of DNA sufficient to rescue the lin-10 mutant phenotype in germ line transformation experiments. The predicted lin-10 protein sequence is not similar to sequences in current data bases, suggesting that lin-10 defines a novel class of gene involved in the specification of cell fates. Although our genetic studies indicate that lin-10 is required specifically for the determination of vulval cell fates, lin-10 transcripts are present in cells other than vulval precursor cells. This result suggests that lin-10 may have a general but redundant role in development, functioning in diverse cell lineages to control cell fates. Alternatively, lin-10 may function specifically in vulval development, in which case lin-10 activity could be regulated at a post-transcriptional level or could have biological consequences only in conjunction with the products of other genes. ------------------- Key: 1278 Medline: 90216721 Authors: Gross RE;Bagchi S;Lu X;Rubin CS Title: Cloning, characterization, and expression of the gene for the catalytic subunit of cAMP-dependent protein kinase in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 265: 6896-6907 1990 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans expresses substantial amounts of several forms (Mr values = 39,000-41,000) of the catalytic subunit (C) of cAMP-dependent protein kinase. Approximately 65% of the total cAMP-dependent phosphotransferase activity is recovered in particulate fractions of homogenates prepared from asynchronous populations of C. elegans. The C subunit is expressed at a low level in cytosolic and particulate compartments during embryogenesis. As the nematodes progress from late embryonic stages to the newly hatched, first larval (L1) stage, C subunit content increases 15- fold. High levels of C subunits are observed in several subsequent larval and adult stages of development. Since the relative abundance of C subunit mRNA changes little with development, it appears that control of C expression is exerted the translational and/or post- translational levels. cDNAs for two types of C have been cloned and sequenced. The derived amino acid sequence of a major isoform (CeCAT alpha, 358 residues) is highly homologous (82% identical) with the murine C alpha subunit. A second, novel C subunit (CeCAT alpha', 374 residues) has a unique 56-residue carboxyl-terminal region that is generated by the alternative splicing of the C pre-mRNA. The splicing process that yields CeCAT alpha' is unusual because it converts the central portion of an apparent 1-kilobase (kb) intron to an exon. The alternative exon introduces the novel carboxyl terminus and a new translation stop signal, while simultaneously converting the coding sequence for 40 carboxyl-terminal residues in CeCAT alpha into 3'- untranslated nucleotides. The 5' end of the C. elegans C subunit mRNA is produced by the trans-splicing of the C gene transcript to a 22- base pair C. elegans leader sequence originally described by Krause, M., and Hirsh, D. [1987) Cell 49, 753-761). The 20-kb C. elegans C gene is divided into seven exons by introns ranging in size from 54 to 8000 bp. The sizes of the C. elegans C subunit gene, cytoplasmic mRNA (2.5 kb), and subunit protein are similar to the sizes of the murine C alpha gene, mRNA, and polypeptide. However, the nematode and murine C genes differ significantly in the organization of their introns ------------------- Key: 1279 Medline: 90231408 Authors: Hodgkin J Title: Sex determination compared in Drosophila and Citation: Nature 344: 721-728 1990 Type: REVIEW Genes: dpy-21 dpy-26 dpy-27 dpy-28 fem-1 fem-2 fem-3 fog-2 glp-1 her-1 lin-12 sdc-1 sdc-2 tra-1 tra-2 tra-3 xol-1 mnDp3 Abstract: Fruitflies and nematodes show many similarities in the general organization of the gene networks that control sexual dimorphism and dosage compensation. In contrast, the underlying molecular mechanisms appear to be very different in these two species. Developmental processes such as sex determination need not be strongly conserved in evolution. ------------------- Key: 1280 Medline: 90222138 Authors: Politz SM;Philipp M;Estevez M;O'Brien PJ;Chin KJ Title: Genes that can be mutated to unmask hidden antigenic determinants in the cuticle of the nematode Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 87: 2901-2905 1990 Type: ARTICLE Genes: srf-1 srf-2 srf-3 Abstract: Rabbit antisera directed against a mixture of proteins solubilized from the wild-type adult Caenorhabditis elegans cuticle were used to isolate mutants, induced by ethyl methanesulfonate treatment, that exhibit alterations in surface antigenicity by immunofluorescence. Genetic mapping and complementation data for four such mutations define two genes, srf-2(I) and srf-3(IV). The mutant phenotypes observed by immunofluorescence appear to result from unmasking of antigenic determinants that are normally hidden in the wild-type cuticle. In support of this hypothesis, surface radioiodination experiments indicate that components labeled on the wild-type surface are missing or less readily labeled on the surface of srf-2 and ------------------- Key: 1281 Medline: 90222150 Authors: Morgan PG;Sedensky M;Meneely PM Title: Multiple sites of action of volatile anesthetics in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 87: 2965-2969 1990 Type: ARTICLE Genes: unc-1 unc-7 unc-9 unc-79 unc-80 Abstract: The mechanism and site(s) of action of volatile anesthetics are unknown. In all organisms studied, volatile anesthetics adhere to the Meyer-Overton relationship--that is, a ln-ln plot of the oil-gas partition coefficients versus the potencies yields a straight line with a slope of -1. This relationship has led to two conclusions about the site of action of volatile anesthetics. (i) It has properties similar to the lipid used to determine the oil-gas partition coefficients. (ii) All volatile anesthetics cause anesthesia by affecting a single site. In Caenorhabditis elegans, we have identified two mutants with altered sensitivities to only some volatile anesthetics. These two mutants, unc-79 and unc-80, confer large increases in sensitivity to very lipid soluble agents but have little or no increases to other agents. In addition, a class of extragenic suppressor mutations exists that suppresses some altered sensitivities but specifically does not suppress the altered sensitivity to diethyl ether. There is much debate concerning the molecular nature of the site(s) of anesthetic action. One point of discussion is whether the site(s) consists of a purely lipid binding site or if protein is involved. The simplest explanation of our observations is that volatile anesthetics cause immobility in C. elegans by specifically interacting with multiple sites. This model is in turn more consistent with involvement of protein at the site(s) of action. ------------------- Key: 1282 Medline: 90253612 Authors: Dixon DK;Jones D;Candido EPM Title: The differentially expressed 16-kD heat shock genes of Caenorhabditis elegans exhibit differential changes in chromatin structure during heat shock. Citation: DNA and Cell Biology 9: 177-191 1990 Type: ARTICLE Genes: Abstract: The 16-kD heat shock genes of Caenorhabditis elegans are encoded by four highly similar genes, arranged as divergently transcribed pairs. In spite of the high level of identity that exists between the HSP16 genes, after 2 hr of heat shock the mRNA from one locus accumulates at 7-14 times the level of that from the other locus. To determine if differential HSP16 gene transcriptional activity contributes to these differences, we examined the chromatin structure of the HSP16 genes in nonshocked embryos and in embryos undergoing both the initial phases of heat shock and after 2 hr of heat shock. To carry out these studies, we developed a nuclei isolation procedure that has allowed us to prepare large amounts of nuclei from C. elegans embryos, larvae, and adults that are essentially free of endogenous nuclease and protease activities and appear to be an excellent substrate for investigating chromatin structure in C. elegans. This procedure has enabled us to report the first observations of C. elegans basic chromatin structure, as well as characterize HSP16 chromatin structure in detail. The data suggest that differential HSP16 RNA accumulation following 2 hr of heat shock appears to be correlated with a change in the chromatin structure of one of the HSP16 loci to a preinduction, ------------------- Key: 1283 Medline: 90231440 Authors: Freyd G;Kim SK;Horvitz HR Title: Novel cysteine-rich motif and homeodomain in the product of the Caenorhabditis elegans cell lineage gene lin-11. Citation: Nature 344: 876-879 1990 Type: ARTICLE Genes: ceh-14 lin-11 mec-3 Abstract: The gene lin-11 is required for the asymmetric division of a vulval precursor cell type in the nematode Caenorhabditis elegans. Putative lin-11 complementary DNAs were sequenced and found to encode a protein that contains both a homeodomain and two tandem copies of a novel cysteine-rich motif: C-X2-C-X17-19-H-X2-C-X2-C-X2-C-X7-11-(C)- X8-C. Two tandem copies of this motif are also present amino-terminal to the homeodomains in the proteins encoded by the genes mec-3, which is required for C. elegans touch neuron differentiation, and isl-1, which encodes a rat insulin I gene enhancer-binding protein. The arrangement of cysteine residues in this motif, referred to as LIM (for lin-11 isl-1 mec-3), suggests that this region is a metal- binding domain. The presence in these three proteins of both a potential metal-binding domain and a homeodomain distinguishes them from previously characterized proteins. ------------------- Key: 1284 Medline: 90301032 Authors: Hirsh D;Huang X-Y Title: Trans-splicing and SL RNAs in C. elegans. Citation: Molecular Biology Reporter 14: 115-115 1990 Type: REVIEW Genes: Abstract: ------------------- Key: 1285 Medline: 90203850 Authors: Avery L;Horvitz HR Title: Effects of starvation and neuroactive drugs on feeding in Caenorhabditis elegans. Citation: Journal of Experimental Zoology 253: 263-270 1990 Type: ARTICLE Genes: cat-1 cat-2 cat-4 cha-1 unc-29 Abstract: Caenorhabditis elegans concentrates its food, bacteria, by pharyngeal pumping. The rate of pumping is affected by the presence of bacteria. Using a new assay that allows measurement of pumping rate in a population of worms suspended in liquid by measuring their uptake of microscopic iron particles, we have confirmed and quantitated this effect. Furthermore, we demonstrated that starvation stimulates pumping. Worms that had been deprived of bacteria for more than 4 hours pumped in the absence of bacteria under conditions in which well-fed worms did not. Furthermore, starved worms responded to lower amounts of bacteria than did fed worms. The assay was also useful for measuring effects of drugs on pumping. Of about 30 chemicals screened, 5 had clear effects. The neurotransmitter serotonin and the serotonin uptake inhibitor imipramine stimulated pumping, while the serotonin antagonist gramine inhibits. Imipramine stimulation is greatly decreased in cat-1 and cat-4 mutants, which have low levels of serotonin. Muscimol, an agonist for the neurotransmitter GABA, and ivermectin, whose site of action may also be the GABA receptor, both inhibit pumping. Qualitative observations suggested a role for acetylcholine in the regulation of pumping. ------------------- Key: 1286 Medline: 90236564 Authors: Enos A;Coles GC Title: Effect of benzimidazole drugs on tubulin in benzimidazole resistant and susceptible strains of Caenorhabditis Citation: International Journal for Parasitology 20: 161-167 1990 Type: ARTICLE Genes: Abstract: An in vitro assay was used to determine efficacy and if side resistance was present to benzimidazole anthelmintics tested against Caenorhabditis elegans after selection with albendazole. Side resistance was present to all the benzimidazoles tested, except for oxibendazole and parbendazole. At a concentration of 1 mM, all of the drugs, except thiabendazole, were effective in killing 100% of the albendazole susceptible worms. Tubulin from albendazole resistant and susceptible C. elegans was isolated and run on polyacrylamide gels. Western blots with anti-tubulin antibody showed that the albendazole resistant strain had an altered tubulin. Electron microscopy of albendazole-treated drug resistant worms showed microtubules throughout the intestinal cells. Microtubules were not observed in albendazole-treated drug susceptible ------------------- Key: 1287 Medline: Authors: Schaeffer JM;White T;Bergstrom AR;Wilson KE;Turner MJ Title: Identification of glutamate-binding sites in Caenorhabditis elegans. Citation: Pesticide Biochemistry & Physiology 36: 220-228 1990 Type: ARTICLE Genes: Abstract: ------------------- Key: 1288 Medline: 90262552 Authors: Imagawa M;Onozawa T;Okumura K;Osada S;Nishihara T;Kondo M Title: Characterization of metallothionein cDNAs induced by cadmium in the nematode Caenorhabditis elegans. Citation: Biochemical Journal 268: 237-240 1990 Type: ARTICLE Genes: Abstract: cDNAs of metallothioneins (MTs) in the nematode Caenorhabditis elegans were characterized. The MT-II clone encodes 62 amino acid residues and the predicted Mr is 6462. The MT-I clone contains an additional 12 residues at the C-terminal end, and the predicted Mr is 7959. There is a considerable similarity between MT-I and MT-II. Both of these proteins are cysteine-rich and, with a few exceptions, show a good alignment of cysteine residues. No obvious sequence relationship in the coding region was discernible between C. elegans MTs and mammalian MTs, aside from Cys-Cys, Cys-Xaa-Cys, and Cys-Xaa- Xaa-Xaa-Cys segments. However, 3'-untranslated region of cDNAs of C. elegans MT-I and -II have some consensus sequences found in mammalian MT cDNAs, suggesting that these regions may have some roles in the regulation of MT-gene expression. ------------------- Key: 1289 Medline: 90243098 Authors: Boswell MV;Morgan PG;Sedensky MM Title: Interaction of GABA and volatile anesthetics in the nematode Caenorhabditis elegans. Citation: FASEB Journal 4: 2506-2510 1990 Type: ARTICLE Genes: unc-9 unc-79 Abstract: The authors tested whether mutant strains of Caenorhabditis elegans with altered sensitivity to volatile anesthetics have altered responses to GABA or GABA-agonists. They determined the ED50s of the wild-type strain N2 and two mutant strains of C. elegans to a GABA- mimetic ivermectin (IVM) and to GABA. unc-79, a strain with increased sensitivity to halothane, was more sensitive than N2 to IVM and GABA. unc-9, a strain that suppresses the increased sensitivity of unc-79 to halothane, was less sensitive than N2 to IVM and GABA. The authors also tested whether doses of GABA or IVM and volatile anesthetics were additive in their effects on C. elegans. Halothane (2.1%) did not shift the ED50 of IVM, but was antagonistic to GABA. Enflurane (4%) was antagonistic to both IVM and GABA. However, ED50s of halothane and enflurane were unchanged in the presence of IVM (35 nM) or GABA (150 mM). The authors conclude that GABA by itself does not appear to mediate halothane or enflurane sensitivity in C. elegans. ------------------- Key: 1290 Medline: 90251437 Authors: Thomas J;Lea K;Zucker-Aprison E;Blumenthal T Title: The spliceosomal snRNAs of Caenorhabditis elegans. Citation: Nucleic Acids Research 18: 2633-2642 1990 Type: ARTICLE Genes: Abstract: Nematodes are the only group of organisms in which both cis- and trans-splicing of nuclear mRNAs are known to occur. Most Caenorhabditis elegans introns are exceptionally short, often only 50 bases long. The consensus donor and acceptor splice site sequences found in other animals are used for both cis- and trans-splicing. In order to identify the machinery required for these splicing events, we have characterized the C. elegans snRNAs. They are similar in sequence and structure to those characterized in other organisms, and several sequence variations discovered in the nematode snRNAs provide support for previously proposed structure models. The C. elegans snRNAs are encoded by gene families. We report here the sequences of many of these genes. We find a highly conserved sequence, the proximal sequence element (PSE), about 65 bp upstream of all 21 snRNA genes thus far sequenced, including the SL RNA genes, which specify the snRNAs that provide the 5' exons in trans-splicing. The sequence of the C. elegans PSE is distinct from PSE's from ------------------- Key: 1291 Medline: Authors: Watabe S;Kantha SS;Hashimoto K;Kagawa H Title: Phosphorylation and immunological cross-reactivity of paramyosin: A comparative study. Citation: Comparative Biochemistry & Physiology 96B: 81-88 1990 Type: ARTICLE Genes: Abstract: 1. Paramyosins isolated from nematode Caenorhabditis elegans, clam Meretrix meretrix and Mercenaria mercenaria, scallop Patinopecten yessoensis, abalone Notohaliotis discus, lobster Homarus vulgaris and sea cucumber Holothuria leucospilata were examined for phosphorylation rate and immunological reactivity against anti-Meretrix a-paramyosin antiserum. 2. A high phosphorylation was only observed with the a-forms of bivalve paramyosins from Meretrix, Mercenaria and Patinopecten. 3. The enzyme-linked immunosorbent assay data also revealed that phosphorylatable paramyosins of catch muscle differed in structure from those of non-catch muscles. ------------------- Key: 1292 Medline: 90273892 Authors: Sternberg PW Title: Genetic control of cell type and pattern formation in Caenorhabditis elegans. Citation: "Advances in Genetics." Scandalios JG and Wright TRF (eds), Academic Press, Inc. 27: 63-116 1990 Type: REVIEW Genes: ced-1 ced-3 ced-4 egl-1 her-1 let-23 lin-2 lin-3 lin-4 lin-5 lin-6 lin-7 lin-8 lin-9 lin-10 lin-11 lin-12 lin-13 lin-14 lin-15 lin-17 lin-18 lin-22 lin-26 lin-28 lin-29 lin-34 mec-1 mec-3 mec-4 mec-5 mec-7 nuc-1 sup-7 tra-1 Abstract: As recognized by T. H. Morgan, the problems of genetics and development are interwoven. Morgan noted that understanding how the genotype of an organism specifies its phenotype would require knowing the fundamental mechanisms of gene action, how genes interact to specify the properties of cells, and how cells interact to specify each adult character. We now have a basic understanding of the primary effects of genes (to encode protein or RNA products). However, little is known about how the genes of a zygote specify a complex pattern of cell divisions, the generation of diverse cell types, and the arrangement of those cells into specific morphological structures. A "favorable material" (as Morgan put it) for investigating these problems would be a simple organism in which development could be analyzed at the level of single genes and single cells. The small free-living soil nematode Caenorhabditis elegans is such an organism... ------------------- Key: 1293 Medline: Authors: Sternberg P;Hill R;Jongeward G;Aroian R;Han M;Mendel J;Holboke A Title: Pattern formation during C. elegans vulval induction. Citation: "Developmental Biology." UCLA Symposia on Molecular and Cellular Biology, New Series. Davidson EH, Ruderman JV and Posakony JW (eds), Wiley-Liss, Inc. 125: 185-196 1990 Type: REVIEW Genes: let-23 let-60 lin-2 lin-3 lin-7 lin-10 lin-12 lin-13 lin-15 mnDf67 Abstract: Induction of the C. elegans vulva is a simple example of pattern formation in which the combined action of two intercellular signals specifies three cell types in a precise spatial pattern. These two signals, a graded inductive signal and a short-range lateral signal, are each mediated by a distinct genetic pathway. To understand how these intercellular signals specify cell type, we are studying, by genetic analysis and molecular cloning, genes whose products are involved in the induction pathway. ------------------- Key: 1294 Medline: 90288421 Authors: Roberts L Title: The worm project. Citation: Science 248: 1310-1313 1990 Type: REVIEW Genes: Abstract: An exhaustive study of the tiny roundworm C. elegans has revealed a wealth of information about development and the brain. And now the effort to decipher the worm's genome is fast becoming the benchmark by which the human genome project will be measured. ------------------- Key: 1295 Medline: 90245646 Authors: Schaller D;Wittmann C;Spicher A;Muller F;Tobler H Title: Cloning and analysis of three new homeobox genes from the nematode Caenorhabditis elegans. Citation: Nucleic Acids Research 18: 2033-2036 1990 Type: ARTICLE Genes: ceh-11 ceh-12 ceh-13 Abstract: Three homeobox-containing genes from the nematode Caenorhabditis elegans are described. Two of them (ceh-11 and ceh-12) were isolated from a genomic library by hybridization at low stringency with the Ascaris lumbricoides homeobox AHB-1. The first clone contains a homeobox defining a new class of homeoboxes (ceh-11). This gene maps on the third chromosome of C. elegans, at the same locus as egl-5, a gene already known to be essential for the determination of specific neurons. In the second clone, sequence analysis revealed the existence of the third helix of a putative homeobox (ceh-12) which is interrupted by an intron located upstream of the codon for the amino acid 45 of the homeodomain. Using the ceh-11 homeobox as a probe, a third homeobox (ceh-13) was isolated from a cDNA library. As ceh-13 belongs to the labial class of homeoboxes, we conclude that, at the time when the nematode lineage diverged from the myriapod-insect and the vertebrate lineages, the duplication which led to the Antp and the labial families of homeoboxes had already taken ------------------- Key: 1296 Medline: 90282703 Authors: Wolinsky E;Way J Title: The behavioral genetics of Caenorhabditis elegans. Citation: Behavior Genetics 20: 169-189 1990 Type: REVIEW Genes: che-3 che-10 daf-6 daf-10 daf-19 deg-1 egl-1 egl-15 egl-17 lev-1 lev-7 lin-32 mec-1 mec-2 mec-3 mec-4 mec-5 mec-6 mec-7 mec-8 mec-9 mec-10 mec-11 mec-12 mec-13 mec-14 mec-15 mec-16 mec-17 unc-3 unc-5 unc-6 unc-15 unc-17 unc-25 unc-29 unc-30 unc-34 unc-38 unc-40 unc-43 unc-44 unc-47 unc-50 unc-51 unc-53 unc-54 unc-55 unc-62 unc-63 unc-71 unc-73 unc-74 unc-76 unc-86 unc-104 Abstract: Caenorhabditis elegans, a small free-living soil nematode, is an ideal organism for the genetic dissection of simple behaviors. Over 150 genes required for normal behavior have been identified. We review here the neural and genetic pathways underlying four of the best-studied C. elegans behaviors: locomotion, response to gentle touch, egg-laying, and chemotaxis. Mutations affecting these behaviors have identified genes which specify neuronal cell lineage, neuronal cell fate, and the formation of cell matrix cues involved in axonal guidance. Molecular analysis of genes required for normal behavior offers the prospect of characterizing functionally important nervous system proteins, regardless of their abundance or biochemical ------------------- Key: 1297 Medline: 90250769 Authors: van der Voorn L;Gebbink M;Plasterk RHA;Ploegh HL Title: Characterization of a G-protein beta subunit gene from the nematode Caenorhabditis elegans. Citation: Journal of Molecular Biology 213: 17-26 1990 Type: ARTICLE Genes: Abstract: The gene encoding the beta-subunit of guanine nucleotide binding regulatory proteins (G-proteins) has been cloned from the nematode Caenorhabditis elegans. The predicted 340 amino acid sequence matches the highly conserved amino acid sequences of previously isolated G- protein beta-subunits from mammals and Drosophila. The coding region of the C. elegans beta-subunit gene, which has been mapped to the C. elegans chromosome II, is interrupted by eight introns. Southern analysis indicates that C. elegans has only one beta-subunit gene. A 2.8 kb (1 kb = 10(3) bases or base-pairs) transcript derived from this gene could be detected. ------------------- Key: 1298 Medline: 90258864 Authors: Zeng W;Alarcon CM;Donelson JE Title: Many transcribed regions of the Onchocerca volvulus genome contain the spliced leader sequence of Caenorhabditis elegans. Citation: Molecular and Cellular Biology 10: 2765-2773 1990 Type: ARTICLE Genes: Abstract: Genomic DNAs of the related parasitic nematodes Onchocerca volvulus and Dirofilariae immitis, and a cDNA library of O. volvulus, were examined for the presence of the 22-nucleotide spliced leader (SL) found at the 5' ends of 10 to 15% of the mRNAs in the free-living nematode Caenorhabditis elegans. As in C. elegans, genes for the SL RNA are linked to the repetitive 5S rRNA genes of O. volvulus and D. immitis, but unlike C. elegans, they are in the same orientation as the 5S rRNA genes within the repeat unit. In O. volvulus the SL sequence is also encoded at more than 30 additional genomic locations and occurs at interior sites within many transcripts. Sequence determinations of four different cDNAs of O. volvulus, each containing an internal copy of the SL within a conserved 25mer, and one corresponding genomic DNA clone indicate that this sequence is not trans spliced onto these RNAs, but is encoded within the genes. The RNAs of two of these cDNAs appear to be developmentally regulated, since they occur in adult O. volvulus but were not detected in the infective L3 stage larvae. In contrast, actin mRNAs are present at all developmental stages, and at least one actin mRNA species contains a trans-spliced 5' SL. The internal locations of the SL in various transcripts and its perfect sequence conservation among parasitic and free-living nematodes argues that it serves specific, and perhaps multiple, functions for these organisms. ------------------- Key: 1299 Medline: 90259089 Authors: Chalfie M;Wolinsky E Title: The identification and suppression of neurodegeneration in Caenorhabditis elegans. Citation: Nature 345: 410-416 1990 Type: ARTICLE Genes: deg-1 mec-4 mec-6 Abstract: The dominant mutation deg-1(u38) results in a toxic gene product that leads to the late-onset degeneration of a small number of neurons in the nematode Caenorhabditis elegans. Both intragenic and extragenic mutations as well as changes in wild-type gene dosage can delay or block the time of onset of the neuronal deaths. The deg-1 gene has been cloned and a partial complementary DNA reveals that the gene encodes a novel protein that may act as a membrane receptor. Because the late-onset loss of specific sets of neurons, often as a result of dominant mutations, is characteristic of several human neurodegenerative diseases, the analysis of the deg-1 gene and its suppressors may provide a means of understanding the mechanisms underlying some of these human diseases. ------------------- Key: 1300 Medline: 90262719 Authors: Li C;Chalfie M Title: Organogenesis in C. elegans: Positioning of neurons and muscles in the egg-laying system. Citation: Neuron 4: 681-695 1990 Type: ARTICLE Genes: egl-1 egl-15 lin-8 lin-9 lin-12 lin-15 lin-17 lin-37 lin-39 Abstract: One of the final stages in the development of egg-laying behavior in the nematode C. elegans is the organization of 8 motor neurons (2 HSN and 6 VC cells) and 8 muscles into a motor system to control the opening of the vulva. Using mutations that disrupt the development of specific components of the egg-laying system and laser microsurgery to ablate selected precursor cells, we have determined that the guidance of the egg-laying neurons and muscles, and in particular the VC neurons and vulval muscles, into the vulval region is dependent on interactions with surrounding epithelial and gonadal tissue and appears to be independent of neuron-neuron and neuron-muscle interactions. The development of the egg-laying system can be described as a series of cell interactions in which certain cells arise through induction and subsequently provide inductive cues themselves. ------------------- Key: 1301 Medline: 90224441 Authors: Fodor A;Deak P;Berenyi M;Timar T;Hosztafi S;Kiss I Title: The antiallatal effects on locusts and lethal effects on nematodes of synthetic precocene-1 derivatives differing at the carbon 7 position. Citation: Acta Biologica Hungarica 40: 255-269 1989 Type: ARTICLE Genes: Abstract: Fourteen precocene-1 (P1) derivatives differing at C-7 were synthetized and tested for their antiallatal activities on Locusta migratoria (in vitro and in vivo) and nematocidal effects on Caenorhaditis elegans. An outstanding antiallatal effect was produced by 7-propargyloxy-P1 in vitro. It caused an elevated rate of mortality when applied in vivo to locusts or nematodes. The antiallatal effect of 7-cyclopentyloxy-P1 was not accompanied by toxicity. Aralkyloxy substitution at C-7 eliminated the precocene activity. ------------------- Key: 1302 Medline: 90255399 Authors: Davidson EH Title: How embryos work: a comparative view of diverse modes of cell fate specification. Citation: Development 108: 365-389 1990 Type: REVIEW Genes: glp-1 lin-12 Abstract: Embryonic processes in the nematode C. elegans, the gastropod mollusc Ilyanassa, the dipteran Drosophila, the echinoid Strongylocentrotus purpuratus, the ascidian Ciona, the anuran Xenopus, the teleost Brachydanio and mouse are compared with respect to a series of parameters such as invariant or variable cleavage, the means by which the embryonic axes are set up, egg anisotropies and reliance on conditional or on autonomous specification processes. A molecular interpretation of these modes of specification of cell fate in the embryo is proposed, in terms of spatial modifications of gene regulatory factors. On this basis, classically defined phenomena such as regluative development and cytoplasmic localization can be interpreted at a mechanistic level, and the enormous differences between different forms of embryogenesis in the Animal Kingdom can be considered within a common mechanistic framework. Differential spatial expression of histospecific genes is considered in terms of the structure of the gene regulatory network that will be required in embryos that utilize cell-cell interaction, autonomous vs conditional specification and maternal spatial information to differing extents. It is concluded that the regulatory architectures according to which the programs of gene expression are organized are special to each form of development, and that common regulatory principles are to be found only at lower levels, such as those at which the control regions of histospecific structural genes operate. ------------------- Key: 1303 Medline: 90340298 Authors: Charest DL;Clark DV;Green ME;Baillie DL Title: Genetic and fine-structure analysis of unc-26(IV) and adjacent regions in Caenorhabditis elegans. Citation: Molecular & General Genetics 221: 459-465 1990 Type: ARTICLE Genes: let-301 let-302 let-313 let-314 let-315 let-316 let-317 let-318 let-319 let-320 let-321 let-322 let-323 let-324 let-325 unc-26 nDf27 sDf21 sDf22 sDf60 Abstract: The genetic organization of unc-26(IV) and adjacent regions was studied in Caenorhabditis elegans. We constructed a fine structure genetic map of unc-26(IV), a gene that affects locomotion and pharyngeal muscle movement but not muscle structure. Eleven alleles were positioned relative to each other recombinationally and were classified according to phenotypic severity. The unc-26 gene spans at least 0.026 map units, which is exceptionally large for a C. elegans gene. All but one allele, e205, are amorphic alleles. Interestingly, e205 is hypomorphic but also suppressible by the amber suppressor sup- 7. Nineteen lethal mutations in the unc-26 region were isolated and characterized. The unc-26 region is subdivided into four zones by five deficiency breakpoints. These mutations fall into 15 complementation groups. The stages of development affected by these mutations were determined. ------------------- Key: 1304 Medline: 90298583 Authors: Manser J;Wood WB Title: Mutations affecting embryonic cell migrations in Caenorhabditis elegans. Citation: Developmental Genetics 11: 49-64 1990 Type: ARTICLE Genes: mig-10 mig-11 unc-39 vab-8 ctDf1 nDf20 Abstract: Four recessive mutations that affect long-range embryonic migration of the two canal-associated neurons (CANs) in C. elegans were isolated and characterized with the goal of identifying genes involved in control of directed cell movement. Mutant animals were identified initially by their "withered" tails, a phenotype associated with abnormal CAN migration; the mutants were then analyzed for abnormal cell migrations by Nomarski microscopy. Based on genetic complementation tests, the mutations were assigned to four different loci, two new (mig-10 III, mig-11 III) and two previously identified (unc-39 V, vab-8 V). Mutations at all four loci affect CAN migration with high to moderate penetrance (the percentage of mutant animals that exhibit the phenotype). In addition, two other bilaterally symmetric pairs of neurons (ALM and HSN), the mesoblast M, and a pair of coelomocyte mother cells are affected by one or more of the mutations, generally with lower penetrance. With the exceptions of HSN and the right coelomocyte mother cell, which occasionally migrate beyond their normal destinations, the cells affected appear to migrate either incompletely or not at all. All the migration phenotypes show incomplete penetrance and variable expressively, although genetic tests suggest that mutations at mig-10 and vab-8 result in complete or nearly complete loss of gene function. The variability in mutant phenotypes allowed tests for interdependence of several of the affected migrations; all those analyzed appeared independent of one another. The possible nature of the mutant defects and possible roles of these four loci in cell migration are ------------------- Key: 1305 Medline: 90337294 Authors: McGhee JD;Birchall JC;Chung MA;Cottrell DA;Edgar LG;Svendsen PC;Ferrari DC Title: Production of null mutants in the major intestinal esterase gene (ges-1) of the nematode Caenorhabditis elegans. Citation: Genetics 125: 505-514 1990 Type: ARTICLE Genes: ges-1 Abstract: The ges-1 gene of the nematode Caenorhabditis elegans codes for a nonspecific carboxylesterase that is expressed only in the intestinal lineage. This esterase has turned out to be a convenient biochemical marker for lineage-specific differentiation. In the present paper, we describe the production of several C. elegans strains that lack detectable activity of the ges-1 esterase. To isolate these ges-1 null strains, we first produced a strain of hermaphrodites in which the wild-type copy of the ges-1 gene was stably balanced over a previously isolated isoelectric focusing allele, ges-1(ca6); this parental strain was then mutagenized with EMS and isoelectric focusing gels were used to identify progeny populations that lacked either ges-1(+) or ges-1(ca6) esterase activity. This method is a straightforward and general approach to obtaining null mutations in any gene that has a biochemical or immunological assay. The ges-1 gene is not essential to worm survival, development or reproduction. Furthermore, lack of the ges-1 product has no obvious effect on the ability of worms (containing either normal or greatly reduced levels of acetylcholinesterases) to survive exposure to esterase inhibitors. The ges-1 gene product provides roughly half of the total esterase activity measured in crude extracts of L1 larvae or mixed worm populations. However, histochemical staining of individual ges-1(0) embryos shows that the ges-1 esterase is the first and essentially the only esterase to be produced during embryonic development, from the midproliferation phase up to at least the twofold stage of morphogenesis. These ges-1(0) strains now allow us to investigate the developmental control of the ges-1 gene by DNA-mediated transformation, in which the ges-1 gene acts as its own ------------------- Key: 1306 Medline: 90309997 Authors: Greenwald I;Seydoux G Title: Analysis of gain-of-function mutations of the lin-12 gene of Caenorhabditis elegans. Citation: Nature 346: 197-199 1990 Type: ARTICLE Genes: lin-12 Abstract: Certain cell fate decisions are specified by cell-cell interactions during the development of the nematode Caenorhabditis elegans. For example, in a wild-type hermaphrodite gonad, two cells, Z1.ppp and Z4.aaa, have the potential to become the anchor cell (AC). Intercellular communication establishes their fates and ensures that only one cell becomes the AC, while the other becomes a ventral uterine precursor cell (VU). One component of this intercellular communication seems to be the 'AC-to-VU' signal from the presumptive AC that causes the other cell to become a VU. Genetic and developmental studies indicated that the lin-12 gene specifies the fates of Z1.ppp and Z4.aaa. Molecular studies suggest that lin-12 directly participates in their communications, perhaps acting as the receptor for the 'AC-to-VU' signal. Here, we report the molecular lesions associated with lin-12 gain-of-function mutations, cell isolation experiments, and genetic studies of an unusual lin-12 allele. These data suggest that self-association of the putative lin- 12-encoded receptor leads to its activation, and that certain gain-of- function mutations result in ligand-independent activation. ------------------- Key: 1307 Medline: 90275614 Authors: Seydoux G;Schedl T;Greenwald I Title: Cell-cell interactions prevent a potential inductive interaction between soma and germline in C. elegans. Citation: Cell 61: 939-951 1990 Type: ARTICLE Genes: glp-1 lin-12 Abstract: In each gonadal arm of wild-type C. elegans hermaphrodites, the somatic distal tip cell (DTC) maintains distal germline nuclei in mitosis, while proximal nuclei enter meiosis. We have identified two conditions under which a proximal somatic cell, the anchor cell (AC), inappropriately maintains proximal germline nuclei in mitosis: when defined somatic gonadal cells have been ablated in wild type, and in lin-12 null mutants. Laser ablations and mosaic analysis indicate that somatic gonadal cells neighboring the AC normally require lin-12 activity to prevent the inappropriate AC-germline interaction. The AC- germline interaction, like the DTC-germline interaction, requires glp- 1 activity. In one model, we propose that the AC sends an intercellular signal intended to interact with the lin-12 product in somatic gonadal cells; when lin-12 activity is absent, the signal interacts instead with the related glp-1 product in germline. Our data illustrate the importance of mechanisms that prevent inappropriate interactions during development. ------------------- Key: 1308 Medline: 91042428 Authors: Babity JM;Starr TVB;Rose AM Title: Tc1 transposition and mutator activity in a Bristol strain of Caenorhabditis elegans. Citation: Molecular & General Genetics 222: 65-70 1990 Type: ARTICLE Genes: dpy-1 dpy-5 dpy-6 dpy-11 dpy-14 rec-1 unc-11 unc-13 unc-15 unc-22 unc-31 Abstract: In most strains of Caenorhabditis elegans with a low copy number of Tc1 transposable elements, germline transposition is rare or undetectable. We have observed low-level Tc1 transposition in the genome of the C. elegans var. Bristol strain KR579 (unc-13[e51]) resulting in an increase in Tc1 copy number and subsequent mutator activity. Examination of genomic blots from KR579 and KR579-derived strains revealed that more Tc1-hybridizing bands were present than in other Bristol strains. A novel Tc1-hybridizing fragment was cloned from a KR579-derived strain. Unique sequence DNA flanking the Tc1 element identified a 1.6 kb restriction fragment length difference between the KR579 and N2 strains consistent with a Tc1 insertion at a new genomic site. The site of insertion of this Tc1 was sequenced and is similar to the published Tc1 insertion site consensus sequence. Several isolates of KR579 were established and maintained on plates for a period of 3 years in order to determine if Tc1 copy number would continue to increase. In one isolate, KR1787, a further increase in Tc1 copy number was observed. Examination of the KR1787 strain has shown that it also exhibits mutator activity as assayed by the spontaneous mutation frequency at the unc-22 (twitcher) locus. The KR579 strain differs from most low copy number strains in that it exhibits low-level transposition which has developed into mutator activity. ------------------- Key: 1309 Medline: 90351457 Authors: Maine EM;Kimble J Title: Genetic control of cell communication in C. elegans development. Citation: BioEssays 12: 265-271 1990 Type: REVIEW Genes: dpy-1 dpy-2 dpy-3 dpy-7 dpy-8 dpy-9 dpy-10 fem-1 glp-1 lin-12 sog-1 sog-2 sog-3 sog-4 sog-5 sqt-1 Abstract: Cell communication is crucial for many aspects of growth and differentiation during the development of the nematode Caenorhabditis elegans. Two genes, glp-1 and lin-12, mediate a number of known cell- cell interactions. Genetic and molecular analyses of these two genes lead to the conclusion that they are structurally and functionally related. We summarize these studies as well as those involving the identification of other genes that interact with glp-1 and/or lin-12. ------------------- Key: 1310 Medline: 90297957 Authors: Hekimi S Title: A neuron-specific antigen in C. elegans allows visualization of the entire nervous system. Citation: Neuron 4: 855-865 1990 Type: ARTICLE Genes: unc-53 Abstract: In the present work, I describe an antiserum that specifically stains all neurons in C. elegans. This probe should facilitate developmental studies in this organism in the same way as anti-horseradish peroxidase has in Drosophila. The antiserum was raised against an 8 amino acid peptide representing part of an insect neuropeptide precursor, but there are no indications that this cross-reactivity reflects evolutionary homology. The antiserum allows the whole nervous system of C. elegans, including all cell bodies and processes, to be brightly stained. The subcellular staining pattern suggests that a cytoskeletal component is recognized. I have also isolated a mutation (e2481) that abolishes staining in all but 7 neurons, the 6 microtubule cells and 1 cell in the tail. Finally, I show that the pattern of staining in the nematode P. redivivus is similar to that seen in animals carrying the e2481 mutation. ------------------- Key: 1311 Medline: 90330950 Authors: Chiba CM;Rankin CH Title: A developmental analysis of spontaneous and reflexive reversals in the nematode Caenorhabditis elegans. Citation: Journal of Neurobiology 21: 543-554 1990 Type: ARTICLE Genes: unc-86 Abstract: Reversals of forward locomotion in the nematode Caenorhabditis elegans are thought to be mediated by a common neural circuit, the touch withdrawal circuit. Despite substantial neuroanatomical changes over post-embryonic development, one reversal behavior, the head- touch withdrawal reflex, does not appear to change over development (Chalfie and Sulston, 1981). The experiments reported here indicate that two other reversal behaviors, spontaneous reversals and the tap reversal reflex to vibratory stimuli, show developmental changes. Young adult animals showed higher frequencies of spontaneous reversals than all other developmental stages, while larval stages differed from adults in their pattern of responses to tap. Although animals of all stages reversed in response to touch, taps elicited both reversals and accelerations of forward movement. In response to single taps, larval stages reversed on approximately half the occasions; young adult and 4-day-old adults almost always reversed. Increasing stimulus magnitudes increased the probability of accelerations at all developmental stages, but larval stages showed fewer reversals and more accelerations than adults. The behavioral changes observed coincide with known periods of neuroanatomical change in the touch withdrawal circuit. The addition of a late- developing sensory neuron, AVM, is implicated in the behavioral differences between juveniles and adults. ------------------- Key: 1312 Medline: 90339500 Authors: Heschl MFP;Baillie DL Title: Functional elements and domains inferred from sequence comparisons of a heat shock gene in two nematodes. Citation: Journal of Molecular Evolution 31: 3-9 1990 Type: ARTICLE Genes: hsp-3 Abstract: Caenorhabditis elegans and Caenorhabditis briggsae are two closely related nematode species that are nearly identical morphologically. Interspecific cross-hybridizing DNA appears to be restricted primarily to coding regions. We compared portions of the hsp-3 homologs, two grp 78-like genes, from C. elegans and C. briggsae and detected regions of DNA identity in the coding region, the 5' flanking DNAs, and the introns. The hsp-3 homologs share approximately 98% and 93% identity at the amino acid and nucleotide levels, respectively. Using the nucleotide substitution rate at the silent third position of the codons, we have estimated a lower limit for the date of divergence between C. elegans and C. briggsae to be approximately 23-32 million years ago. The 5' flanking DNAs and one of the introns contain elements that are highly conserved between C. elegans and C. briggsae. Some of the regions of nucleotide identity in the 5' flanking DNAs correspond to previously detected identities including viral enhancer sequences, a heat shock element, and an element present in the regulatory regions of mammalian grp78 and grp94 genes. We propose that a comparison of C. elegans and C. briggsae sequences will be useful in the detection of potential regulatory and structural elements. ------------------- Key: 1313 Medline: Authors: Johnson TE;Hutchinson EW Title: Aging in Caenorhabditis elegans: update 1988. Citation: Review of Biological Research in Aging 4: 15-27 1990 Type: REVIEW Genes: age-1 fer-1 Abstract: The last few years have marked a transition for aging research in Caenorhabditis elegans. Several new lines of work have appeared, most notable of which is the derivation of long-lived strains obtained both from naturally occurring variation and by mutation. The loss of several workers in the field due to retirement or movement to other areas of research as well as the increasingly competitive nature of funding for fundamental, nonclinical research in aging had led to the loss of several labs that in the past have been among the most productive in the field. Other areas of research with C. elegans have continued to advance, and the physical map of the nematode is more than 95% complete. The background material for studying C. elegans has also become much more accessible as a result of the publication of a book detailing much of the nonaging background material for C. elegans [Wood, 1988]. ------------------- Key: 1314 Medline: Authors: Smith BS;Hodgson-Smith A;Popiel I;Minter DM;James ER Title: Cryopreservation of the entomogenous nematode parasite Steinernema feltiae (= Neoaplectana carpocapsae). Citation: Cryobiology 27: 319-327 1990 Type: ARTICLE Genes: Abstract: Cryopreservation studies were conducted with the J1 juvenile and third stage infective juvenile (IJ) larval stages of the entomogenous parasitic nematode Steinernema feltiae (=Neoaplectana carpocapsae). The main parameters evaluated were (i) tolerance of the organisms to the cryoprotectants methanol, ethanediol, glycerol, and dimethyl sulfoxide; (ii) the incubation temperature and exposure period in cryoprotectant; and (iii) slow cooling (circa 1C min-1) vs rapid cooling (circa 5,100C min-1). The J1 stage was sensitive to all cryoprotectants at >20% (v/v). This sensitivity increased at 22 and 37C. Exsheathed IJ stage organisms tolerated exposure to 50% (v/v) ethanediol or Me2SO and 60% (v/v) methanol or glycerol. A proportion (3.4%) of J1s preincubated in 20% (v/v) methanol for 10 min at 0C survived slow cooling to -35C followed by plunge into liquid nitrogen. Preincubation in 60% (v/v) Me2SO for 45 sec at 0C followed by rapid cooling yielded a higher proportion (12.3%0 of surviving J1s. The infective IJ stage only survived rapid cooling. Preincubation for 20 min at 0C in either 60% (v/v) methanol or 45% glycerol, followed by rapid cooling at 5,100C min-1, yielded 30-34% viable IJs following thawing. These larvae were capable of further growth and development in vitro. The results suggest that the organisms are vitrified during the rapid cooling step. For routine maintenance of strains of S. feltiae and related ------------------- Key: 1315 Medline: 90332442 Authors: Fire A;Kondo K;Waterston R Title: Vectors for low copy transformation of C. elegans. Citation: Nucleic Acids Research 18: 4269-4270 1990 Type: ARTICLE Genes: sup-7 tra-3 Abstract: The amber suppressor gene sup-7 has been used as a selectable marker to introduce cloned DNA at low copy number into C. elegans chromosomes. We describe structure and several characteristics of seven new sup-7 containing transformation vectors. ------------------- Key: 1316 Medline: 90354432 Authors: Sharrock WJ;Sutherlin ME;Leske K;Cheng TK;Kim TY Title: Two distinct yolk lipoprotein complexes from Caenorhabditis elegans. Citation: Journal of Biological Chemistry 265: 14422-14431 1990 Type: ARTICLE Genes: vit-6 Abstract: The four yolk polypeptides of the nematode Caenorhabditis elegans are found in two types of lipoprotein particle: 12 S particles with Mr estimated at 450,000 and 8 S particles with Mr estimated at 250,000. Both types of particle contain approximately 8% phospholipids, 3% triglycerides, and 3% other lipids by mass. All four C. elegans yolk polypeptides can be found in either 12 or 8 S particles, depending upon the conditions of isolation. While the properties of the 12 and 8 S lipoprotein particles are consistent with a dimermonomer relationship, the asymmetric distribution of the yolk polypeptides between 12 and 8 S fractions suggests that at least two different oligomeric lipoprotein complexes are present in C. elegans embryos. In order to clarify the subunit composition of the C. elegans yolk lipoproteins, the patterns of polypeptides retained in immunoaffinity binding procedures by immunoglobulins of different antigenic specificities have been compared. When immunoaffinity binding is performed in the absence of sodium dodecyl sulfate, three C. elegans yolk proteins (yp170A, yp115, and yp88) are retained together by polyclonal immunoglobulins directed against either yp115 or yp88. A monoclonal immunoglobulin also retains these three proteins together. In contrast, a second monoclonal immunoglobulin retains only the fourth yolk protein (yp170B). Aggregate species, evidently reflecting the spontaneous formation of interchain disulfide bonds, indicate that yp170A and yp88 are physically associated, whereas yp170B self- associates in dimers. It is concluded that there are two distinct lipoprotein complexes in C. elegans: the A complex, which consists of yp170A, yp115, and yp88 and is essentially heterodimeric and the B dimer, ------------------- Key: 1317 Medline: 90364408 Authors: Johnson TE Title: Increased life-span of age-1 mutants in Caenorhabditis elegans and lower Gompertz rate of aging. Citation: Science 249: 908-912 1990 Type: ARTICLE Genes: age-1 Abstract: A mutation in the age-1 gene of the nematode Caenorhabditis elegans has been shown to result in a 65 percent increase in mean life-span and a 110 percent increase in maximum life-span at 25 degrees. One of the hallmarks of organismic aging and senescent processes is an exponential acceleration of age-specific mortality rate with chronological age. This exponential acceleration is under genetic control: age-1 mutant hermaphrodites show a 50 percent slower rate of acceleration of mortality with chronological age than wild-type strains. Mutant males also show a lengthening of life and a slowing of the rate of acceleration of mortality, although age-1 mutant males still have significantly shorter life-spans than do hermaphrodites of the same genotype. The slower rates of acceleration of mortality are recessive characteristics of ------------------- Key: 1318 Medline: 91104031 Authors: Greenwald I Title: Genetic and molecular analysis of EGF-related genes in Caenorhabditis elegans. Citation: Molecular Reproduction 27: 73-79 1990 Type: ARTICLE Genes: glp-1 lin-12 Abstract: Caenorhabditis elegans develops from the embryo, through four larval stages that are punctuated by molts, then to adulthood. There are two sexes: hermaphrodites and males. Hermaphrodites may reproduce by self-fertilization or they may mate with males to produce cross-progeny... ------------------- Key: 1319 Medline: Authors: Marx J Title: The nematode as a guide to human brain disease. Citation: Science 249: 985-985 1990 Type: NEWS Genes: ced-3 ced-4 deg-1 Abstract: Can a lowly worm help neurobiologists untangle the pathology of Alzheimer's, Huntington's, Parkinson's, and other human brain diseases? That surprising question kept cropping up at a recent Dahlem conference on degenerative brain disorders. Although progress has been made toward understanding those disorders, conference participants had to conclude that they don't yet know nearly enough about how brain cells die. And that's where the lowly worm may ------------------- Key: 1320 Medline: 91030467 Authors: Heschl MFP;Baillie DL Title: The HSP70 multigene family of Caenorhabditis elegans. Citation: Comparative Biochemistry & Physiology 96B: 633-637 1990 Type: REVIEW Genes: hsp-1 hsp-2ps hsp-3 hsp-4 hsp-6 Abstract: 1. The heat shock response of the nematode Caenorhabditis elegans has been characterized. 2. There are at least nine genes in the hsp70 multigene family of C. elegans. 3. Five of the hsp70 genes have been characterized and assigned to one of at least three hsp70 gene subfamilies. One of the subfamilies consists of an hsp70 protein that has the potential to be translocated into the endoplasmic reticulum and another subfamily consists of a protein that has the potential to be translocated into the mitochondria. 4. The C. elegans hsp70 multigene family has several unique characteristics including introns in the heat inducible hsp70 genes, at least one trans-spliced hsp70 mRNA and two grp78 related genes, one of which is highly heat inducible. 5. The identification and characterization of C. elegans hsp70 multigene family is the basis for a genetic characterization of the regulation and function of a gene family during the development of a multicellular eukaryote. ------------------- Key: 1321 Medline: 91048659 Authors: Williams PL;Dusenbery DB Title: A promising indicator of neurobehavioral toxicity using the nematode Caenorhabditis elegans and computer tracking. Citation: Toxicology and Industrial Health 6: 425-440 1990 Type: ARTICLE Genes: Abstract: A promising screening test for neurotoxicity has been developed using a computer tracking system and a species of nematode, Caenorhabditis elegans. The animals are viewed in dark-field illumination by a video camera interfaced directly to a microcomputer. Several hundred nematodes are tracked simultaneously and rates of locomotion and frequency of change of direction are reported in real time. This system can rapidly obtain reliable data on a variety of behavioral parameters relating to locomotion and response to sensory stimulation. Initial testing has examined the effects of six chemicals on locomotion. Four metals (copper, beryllium, mercury, and lead) and two organophosphate pesticides (malathion and vapona) have been studied. Copper and beryllium were chosen as chemicals that have not been shown to be neurotoxins and the other four chemicals were chosen as substances known to be neurotoxins. Our findings indicate that the rate of movement of exposed nematodes compared to the rate of movement of vehicle controls may prove to be useful as an ------------------- Key: 1322 Medline: 91050994 Authors: Cox GN Title: Molecular biology of the cuticle collagen gene families of Caenorhabditis elegans and Haemonchus contortus. Citation: Acta Tropica 47: 269-281 1990 Type: REVIEW Genes: col-1 col-2 col-6 col-7 col-8 col-12 col-13 col-14 col-19 dpy-13 sqt-1 Abstract: This review is intended primarily to summarize current knowledge of the structure and expression of cuticle collagen genes in the free-living nematode Caenorhabditis elegans. The study of cuticle collagen genes in C. elegans is part of a larger study of the genetic control of cuticle formation in this simple eukaryote. Like other nematodes, C. elegans sheds and replaces its cuticle at each of four postembryonic molts. The cuticle is largely proteinaceous and collagens comprise a major fraction of the structural proteins. Collagens are extracellular structural proteins that have a characteristic repeating structure in which glycine is every third amino acid. This structure is typically abbreviated by (Gly-X-Y)n where X and Y can be any amino acid, but often are proline or hydroxyproline. A large number of morphological mutants with altered cuticles have been identified in C. elegans by genetic analyses, and it is likely that some of these mutations are in genes encoding cuticle structural proteins, such as collagens, or ancillary proteins involved in modification and asssembly of structural proteins within the cuticle... ------------------- Key: 1323 Medline: 91050995 Authors: Kingston IB;Pettitt J Title: Structure and expression of Ascaris suum collagen genes: a comparison with Caenorhabditis elegans. Citation: Acta Tropica 47: 283-287 1990 Type: ARTICLE Genes: col-1 col-2 Abstract: We are interested in the structure and organization of collagen and collagen genes in the parasitic nematode Ascaris suum and in the control of collagen gene expression in Ascaris. In this nematode, as in all others studied, collagens constitute the major component of the extracellular cuticle and ultimately we would like to correlate the expression pattern of Ascaris cuticular collagen genes with the structure of the nematode cuticle. We would also like to see if there is any correlation between differential collagen gene expression and the biology and life-cycle of the parasite. In addition, we are also interested in comparing our data with the more extensive data available on collagen genes in the free living nematode Caenorhabditis elegans. ------------------- Key: 1324 Medline: 90376336 Authors: Kondo K;Makovec B;Waterston RH;Hodgkin J Title: Genetic and molecular analysis of eight tRNAtrp amber suppressors in Caenorhabditis elegans. Citation: Journal of Molecular Biology 215: 7-19 1990 Type: ARTICLE Genes: sup-5 sup-7 sup-21 sup-24 sup-28 sup-29 sup-33 sup-34 Abstract: Over 100 revertants of five different amber mutants were analyzed by Southern blot hybridization using synthetic oligomers as probes to detect a single base change at the anticodon, CCA to CTA (amber), of tRNA(Trp) genes of Caenohrabditis elegans. Of the 12 members of the tRNA(Trp) gene family, a total of eight were converted to amber suppressor alleles. All eight encode identical tRNAs; three of these are new tRNA(Trp) suppressors, sup-21, sup-33 and sup-34. Previous results had suggested that individual suppressor tRNA genes were expressed differentially in a cell-type- or developmental stage- specific manner. To extend these observations to the new genes and to test the specificity of expression against additional genes, cross suppression tests of these eight amber suppressors were carried out against amber mutations in several different genes including genes likely to be expressed in the same cell-type: three nervous system- affecting genes, two muscle structure-affecting genes and two genes presumed to be expressed in hypodermis. Seven out of eight suppressors could be distinguished one from another by the spectrum of their suppression efficiencies. These results also provide further evidence of cell-type-specific patterns of expression in the nervous system, muscle and hypodermis. The suppression pattern of the suppressor against the two muscle-affecting genes, unc-15 and unc-52, suggested that either the suppressors are expressed in a developmental stage-specific manner or that the unc-52 products are expressed in cell-types other than muscle, possibly hypodermis. ------------------- Key: 1325 Medline: Authors: Riddle DL;Georgi LL Title: Advances in research on Caenorhabditis elegans: Application to plant parasitic nematodes. Citation: Annual Review of Phytopathology 28: 247-269 1990 Type: REVIEW Genes: ace-1 ace-2 ace-3 cha-1 daf-1 dpy-13 fog-2 lin-14 lin-32 mab-5 mec-3 mec-7 sqt-1 unc-5 unc-6 unc-17 unc-29 unc-86 Abstract: In the last 20 years a scientific community has evolved to exploit the soil nematode Caenorhabditis elegans as a model system for studying how an animal's genes specify its development and behavior. Initially, a great deal of descriptive work was needed to define these processes, and now the information is being used to design and interpret experiments aimed at understanding the basic mechanisms underlying cellular function. The number of investigators studying this nematode has grown exponentially, so that more than 1000 papers on Caenorhabditis appeared in the literature by the end of 1988. A total of 90 papers were published from 1950-1970, aimed primarily at understanding the growth and physiology of this nematode. By contrast, nearly 100 research papers and reviews were published in 1989 alone, and in the decade ahead more will be learned about C. elegans than all other nematodes combined. The adoption of this organism by Sydney Brenner in 1965 as a laboratory model to study the nervous system was the key development. He trained many of the leading researchers in the field, and his influence is reflected in virtually every aspect of the biology of C. elegans. ------------------- Key: 1326 Medline: 91030489 Authors: Rohrer SP;Evans DV;Bergstrom A Title: A membrane associated glutamate binding protein from Caenorhabditis elegans and Haemonchus contortus. Citation: Comparative Biochemistry & Physiology 95C: 223-228 1990 Type: ARTICLE Genes: Abstract: 1. A glutamate binding protein has been identified in membrane preparations from the free living nematode, Caenorhabditis elegans, and from the parasitic nematode, Haemonchus contortus. 2. This putative glutamate receptor was solubilized with 30 mM octyl-B-glucoside and partially purified by ion exchange and gel filtration chromatography. 3. An 80-fold purification with recovery of 75% of the glutamate binding activity was acheived. 4. The soluble C. elegans binding protein displayed a Kd for glutamate of 0.1 uM, in close agreement with the findings for the membrane associated binding protein. 5. Quisqualate was capable of displacing glutamate from the soluble C. elegans receptor, again in agreement with previous findings for the membrane bound receptor. 6. The fact that a parasitic nematode, Haemonchus contortus, also possesses this putative glutamate receptor, strengthens the case for using C. elegans as a model system for the study of parasitic nematode neuromuscular physiology. ------------------- Key: 1327 Medline: 91060061 Authors: Horvitz HR;Sulston JE Title: Joy of the Worm. Citation: Genetics 126: 287-292 1990 Type: REVIEW Genes: lin-12 lin-14 lin-17 unc-86 Abstract: It has been ten years since we published in Genetics a paper describing the isolation and genetic characterization of cell lineage mutants of the nematode Caenorhabditis elegans (Horvitz and Sulston 1980). We have reviewed elsewhere what has been learned from the study of these and other mutants abnormal in the pattern of cell divisions and cell fates that characterizes C. elegans development (Horvitz 1988, 1990). Here we wish to reflect upon the days of our initial experiments, and to recall our excitement, our visions and our qualms as we elucidated the nematode cell lineage and began exploring methods for its ------------------- Key: 1328 Medline: 91060067 Authors: Baird SE;Emmons SW Title: Properties of a class of genes required for ray morphogenesis in Caenorhabditis elegans. Citation: Genetics 126: 335-344 1990 Type: ARTICLE Genes: dpy-11 dpy-18 ram-1 ram-2 ram-3 ram-4 ram-5 sqt-1 Abstract: We have identified eight mutations that define at least five terminal differentiation genes (ram genes) whose products are required during the extension of the male-specific ray sensilla in Caenorhabditis elegans. ram gene mutations result in morphological abnormalities in the sensory rays but do not appear to interfere with ray functions. A similar ray morphology phenotype was observed in males harboring mutations in three previously defined genes, dpy-11, dpy-18 and sqt- 1, that also affect body shape. One of these genes, sqt-1, is known to encode a collagen. Mutations in different ram genes failed to complement, from which we infer that their gene products functionally interact. For one ram gene, failure to complement was shown to result from haploinsufficiency. Intergenic noncomplementation did not extend to the body morphology genes. The temperature-sensitive periods of both ram and body morphology mutations corresponded to the period of development in which ray extension occurs. We propose that ram gene products act together in a critical interaction between the rays and the cuticle required for wild-type ray morphology. ------------------- Key: 1329 Medline: 91060068 Authors: Venolia L;Waterston RH Title: The unc-45 gene of Caenorhabditis elegans is an essential muscle-affecting gene with maternal expression. Citation: Genetics 126: 345-353 1990 Type: ARTICLE Genes: myo-3 unc-45 unc-54 Abstract: We have isolated three novel alleles of the unc-45 locus in C. elegans, that are recessive lethals. Two of these alleles, when homozygous, result in a nearly total loss of muscle contraction with a concomitant arrest of development and a displacement of muscle cells. The third allele is similar, but showed maternal rescue by a wild-type allele. All previously identified unc-45 alleles were temperature sensitive and, although they produced paralysis of adult animals, all were homozygous viable. Prior genetic studies with these temperature sensitive alleles had suggested that at least one function of the unc-45 gene product was to interact with the major myosin heavy chain isoform, MHC B, of body wall muscles. Our observations of the lethal alleles suggest that the unc-45 product normally interacts with additional muscle components in both the body wall and pharyngeal muscles. In particular, we suggest that the unc- 45 product might interact with all four myosin heavy chains: MHC B; MHC A; and the pharyngeal isoforms, MHC C and MHC D. Maternal rescue of the lethality of the third allele shows that the unc-45 gene product is present in the oocytes, although it may not be necessary until late in development when myofilaments begin to assemble. ------------------- Key: 1330 Medline: 91060069 Authors: Zetka M-C;Rose AM Title: Sex-related differences in crossing over in Caenorhabditis elegans. Citation: Genetics 126: 355-363 1990 Type: ARTICLE Genes: her-1 rec-1 Abstract: In the nematode Caenorhabditis elegans, hermaphrodite recombination has been characterized and is the basis of the genetic map used in this organism. In this study we have examined male recombination on linkage group I and have found it to be approximately one-third less than that observed in the hermaphrodite. This decrease was interval- dependent and nonuniform. We observed less recombination in the male in 5 out of 6 intervals examined, and no observable difference in one interval on the right end of LG I. Hermaphrodite recombination frequencies are the result of recombination in two germlines; oocyte and hermaphrodite spermatocytes. We have measured recombination in the oocyte and have found it to be approximately twofold lower than that calculated for hermaphrodite spermatocytes and not significantly different from the male spermatocyte frequency. Thus, recombination frequencies appear to be a function of gonad physiology rather than the sex of the germline. Evidence from experiments examining the effect of karyotype on recombination in males sexually transformed by the her-1 mutation into XO hermaphrodites (normally XX), suggests the sexual phenotype rather than genotype determines the recombination frequency characteristic of a particular sex. Hermaphrodite recombination is known to be affected by temperature, maternal age, and the rec-1 mutation. We have examined the effect of these parameters on recombination in the male and have found male recombination frequency increased with elevated temperatures and in the presence of Rec-1, and decreased ------------------- Key: 1331 Medline: 90384804 Authors: Cangiano G;Ameer H;Waterston R;La Volpe A Title: Use of repetitive DNA probes as physical mapping strategy in Caenorhabditis elegans. Citation: Nucleic Acids Research 18: 5077-5081 1990 Type: ARTICLE Genes: Abstract: A method for linking genomic sequences cloned in yeast artificial chromosomes (YACs) has been tested using Caenorhabditis elegans as a model system. Yeast clones carrying YACs with repeated sequences were selected from a C. elegans genomic library, total DNA was digested with restriction enzymes, transferred to nylon membranes and probed with a variety of repetitive DNA probes. YAC clones that overlap share common bands with one or more repetitive DNA probes. In 159 YAC clones tested with one restriction enzyme and six probes 28 overlapping clones were detected. The advantages and limitations of this method for construction of YAC physical maps is discussed. ------------------- Key: 1332 Medline: 90381762 Authors: Thomas JH;Stern MJ;Horvitz HR Title: Cell interactions coordinate the development of the C. elegans egg-laying system. Citation: Cell 62: 1041-1052 1990 Type: ARTICLE Genes: dig-1 lin-12 nDf16 Abstract: Egg laying by the nematode Caenorhabditis elegans requires the functioning of the vulva, the gonad, the egg-laying muscles, and the two HSN neurons, which innervate these muscles. By analyzing a newly isolated mutant (dig-1) that displaces the gonad, we discovered that cell interactions coordinate the spatial relationships among the different components of the egg-laying system. First, the gonad induces the formation of the vulva, and vulval induction by dorsal gonads strongly suggests that the inductive signal can act at a distance. Second, the gonad acts at a distance to regulate the migrations of the sex myoblasts that generate the egg-laying musculature. Third, the positions of the axonal branch and synapses of each HSN neuron are displaced correspondingly with the rest of the egg-laying system in dig-1 animals, which suggests that cell interactions also control aspects of HSN development. ------------------- Key: 1333 Medline: Authors: Williams PL;Dusenbery DB Title: Aquatic toxicity testing using the nematode Caenorhabditis elegans. Citation: Environmental Toxicology and Chemistry 9: 1285-1290 1990 Type: ARTICLE Genes: Abstract: A promising aquatic toxicity test has been developed using a species of free-living nematode, Caenorhabditis elegans. The testing was performed with soluble forms of Ag, Hg, Cu, Be, Al, Pb, Cr, As, Tl, Zn, Cd, Ni, Sr and Sb. The LC50 values for 1 to 4 d of exposure were determined and compared to the published invertebrate data. With Caenorhabditis elegans Pb, Cr and Cd were found to have the lowest 96-h LC50 (0.06 mg/L) and Sr had the highest LC50 (465 mg/L). Al the metals except As have a significantly lower 96-h LC50 (from 20 to 15,000 times lower) than 24-h LC50. Comparison with published data for other invertebrates indicated that was more sensitive to Pb, Cr and Be and less sensitive to As than any of the other organisms that have been tested. Given the ease in culturing and the extensive knowledge of the basic biology of Caenorhabditis elegans, coupled with the ecological abundance of nematodes, the method is worthy of further study to determine its usefulness as an aquatic test ------------------- Key: 1334 Medline: Authors: Johnson TE;Friedman DB;Foltz N;Fitzpatrick PA;Shoemaker JE Title: Genetic variants and mutations of Caenorhabditis elegans provide tools for dissecting the aging processes. Citation: "Genetic Effects on Aging II." Harrison DE (ed), The Telford Press, Caldwell, NJ. : 101-127 1990 Type: REVIEW Genes: age-1 fer-15 mnDf91 Abstract: Caenorhabditis elegans is a short-lived species that has been widely used in the genetic dissection of development. This species is becoming important in the genetic analysis of aging because strains with mean life spans more than 70% longer than wild type have been identified both through the use of recombinant inbred lines and by the induction of single-gene mutants. Its unique hermaphroditic mode of reproduction leads to a lack of inbreeding depression and simplifies genetic analyses of quantitative traits such as length of life or behavior. Aging in this organism is composed of at least three independent processes: that specifying length of life, that specifying reproductive senescence, and that specifying senescence of the general motor system. These data suggest that aging is not a unitary process but that many different processes or independent components may be involved in various aspects of aging. Most importantly, an apparent single-gene mutation has been mapped to the middle of linkage group II; this mutation lengthens mean and maximum life span 60-110% and also decreases fertility about five-fold. ------------------- Key: 1335 Medline: Authors: Hartman PS;Mitchell D;Svendsen B-A;Reddy J Title: DNA repair in the nematode Caenorhabditis elegans. Citation: "Molecular Biology of Aging." UCLA Symposia on Molecular and Cellular Biology, New Series. Finch CE and Johnson TE (eds), Wiley-Liss, Inc. 123: 67-79 1990 Type: REVIEW Genes: rad-1 rad-2 rad-3 rad-7 Abstract: Three DNA repair systems (photoreactivation, excision repair and post-replication repair) exist in most organisms. Their status has been examined in the nematode C. elegans. This metazoan is deficient in photoreactivation but possesses efficient excision and post-replication repair systems. The stage-specific variations in hypersensitivity displayed by radiation-sensitive (rad) mutants, as well as the stage-specific excision-repair deficiency displayed by rad-3, indicate that DNA repair is developmentally regulated in this popular model system. In addition, various data suggest that C. elegans may possess novel ------------------- Key: 1336 Medline: Authors: Roberts TM;Sepsenwol S;Ris H Title: Sperm motility in nematodes: Crawling movement without actin. Citation: "The Cell Biology of Fertilization." Schatten H and Schatten G (eds), Academic Press, Inc. : 41-60 1989 Type: REVIEW Genes: Abstract: Sperm motility usually refers to swimming motion propelled by a beating flagellum. In fact, the abundance and availability of flagellated sperm, particularly from sea urchins, have made these cells valuable models for studying all aspects of microtubule-based motility. There are, however, other types of sperm that lack flagella and must use alternative methods to reach oocytes. Among these are the amoeboid sperm of nematodes... ------------------- Key: 1337 Medline: Authors: Roberts TM Title: Nematode sperm as a model for research on cell motility. Citation: "Vistas on Nematology." Veech JA and Dickson DW (eds), Society of Nematologists, Inc. : 440-447 1987 Type: REVIEW Genes: Abstract: Nematode sperm are crawling cells that exhibit a type of locomotion characteristic of an entire class of protozoa as well as numerous embryonic, differentiated, and transformed metazoan cells. Despite considerable variation in morphology and speed of locomotion expressed by these various types of crawling, or amoeboid, cells, there is general agreement that in all cases locomotion is propelled by cytoplasmic contraction involving myosin-induced sliding of actin filaments and regulated, in ways that are not fully understood, by a spectrum of actin-binding proteins. We began to study the motility of sperm of Caenorhabditis elegans hoping to exploit the mutability of this cell in order to analyze the molecular basis of amoeboid movement genetically. Much to our surprise, we discovered that sperm motility is not driven by an actin-based mechanism. Subsequent work, however, has shown that nematode sperm do share many fundamental properties with other amoeboid cells. As a consequence, sperm continue to serve as a profitable model for understanding how cells crawl and, at the same time, have allowed us to examine a new type of cellular motor. ------------------- Key: 1338 Medline: 91054346 Authors: Schaeffer JM;Donatelli MR Title: Characterization of a high-affinity membrane-associated ornithine decarboxylase from the free-living nematode Caenorhabditis elegans. Citation: Biochemical Journal 270: 599-604 1990 Type: ARTICLE Genes: Abstract: Ornithine decarboxylase has been identified and characterized in the free-living nematode Caenorhabditis elegans. Unlike previously described ornithine decarboxylases, the enzyme activity is membrane- associated and remains in the membrane fraction after treatment with high salt, detergents or phosphatidylinositol-specific phospholipase C. Ornithine has an apparent Km value of 2.7 microM for ornithine decarboxylase. The enzyme is competitively inhibited by arginine and lysine with Ki values of 4.0 and 24.4 microM respectively. None of the other naturally occurring amino acids inhibited more than 10% of the enzyme activity at concentrations up to 1 mM. Agmatine, putrescine, spermidine and spermine inhibit ornithine decarboxylase in a non-competitive manner with Ki values of 10, 53.5, 59 and 855 microM respectively. A similar ornithine decarboxylase activity was also identified in membrane preparations from the parasitic nematode Haemonchus contortus. ------------------- Key: 1339 Medline: 91065495 Authors: Howell AM;Rose AM Title: Essential genes in the hDf6 region of chromosome I in Caenorhabditis elegans. Citation: Genetics 126: 583-592 1990 Type: ARTICLE Genes: let-351 let-353 let-354 let-356 let-366 let-373 let-374 let-375 let-501 let-502 let-503 let-504 let-505 let-506 let-507 let-508 let-509 let-510 let-511 hDf6 hDf7 hDp3 hDp5 hDp13 hDp20 hDp22 hDp25 hDp31 hDp32 hDp34 sDf4 sDp2 hT1 Abstract: In this paper we describe the analysis of essential genes in the hDf6 region of chromosome I of Caenorhabditis elegans. Nineteen complementation groups have been identified which are required for the growth, survival or fertility of the organism (essential genes). Since ten of these genes were represented by more than one allele, a Poisson calculation predicts a minimum estimate of 25 essential genes in hDf6. The most mutable gene in this region was let-354 with seventeen alleles. An average mutation rate of 5 x 10(-5) mutations/gene/chromosome screened was calculated for an ethyl methanesulfonate dose of 15 mM. Mutations were recovered by screening for lethal mutations using the duplication sDp2 for recovery. Our analysis shows that duplications are very effective for maintenance and mapping of large numbers of lethal mutations. Approximately 600 lethal mutations were mapped in order to identify the 54 that are in the deficiency hDf6. The hDf6 region appears to have a lower proportion of early arresting mutations than other comparably sized ------------------- Key: 1340 Medline: 91033027 Authors: Fire A;Harrison SW;Dixon D Title: A modular set of lacZ fusion vectors for studying gene expression in Caenorhabditis elegans. Citation: Gene 93: 189-198 1990 Type: ARTICLE Genes: glp-1 myo-2 sup-7 unc-6 unc-54 Abstract: We describe a series of plasmid vectors which contain modular features particularly useful for studying gene expression in eukaryotic systems. The vectors contain the Escherichia coli beta- galactosidase (beta Gal)-encoding region (the lacZ gene) flanked by unique polylinker segments on the 5' and 3' ends, and several combinations of a variety of modules: a selectable marker (an amber suppressor tRNA), a translational initiation region, a synthetic intron segment, the early polyadenylation signal from SV40, and 3' regions from two nematode genes. A segment encoding the nuclear localization peptide from the SV40 T antigen is incorporated into many of the constructs, leading to beta Gal accumulation in nuclei, which can facilitate identification of producing cells in complex tissues. To make functional beta Gal fusions to secreted proteins, we constructed plasmids with an alternate module encoding a synthetic transmembrane domain upstream from lacZ. This domain is designed to stop transfer of secreted proteins across the membrane during secretion, allowing the beta Gal domain of the fusion polypeptide to remain in the cytoplasm and thus function in enzymatic assays. We have used the vectors to analyze expression of several genes in the nematode Caenorhabditis elegans, and have demonstrated in these studies that lacZ can be expressed in a wide variety of different tissues and cell types. These vectors should be useful in studying gene expression both in C. elegans and in other experimental systems. ------------------- Key: 1341 Medline: 91197255 Authors: Meneely PM Title: X-linked gene expression and sex determination in Caenorhabidits elegans. Citation: BioEssays 12: 513-518 1990 Type: REVIEW Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-29 her-1 sdc-1 sdc-2 uxt-2 xol-1 Abstract: The signal for sex determination in the nematode Caenorhabditis elegans is the ratio between the number of X chromosomes and the number of sets of autosomes (the X/A ratio). Animals with an X/A ratio of 0.67 (a triploid with two X chromosomes) or less are males. Animals with an X/A ratio of 0.75 or more are hermaphrodites. Thus, diploid males have one X chromosome and diploid hermaphrodites have two X chromosomes. However, the difference in X-chromosome number between the sexes is not reflected in general levels of X-linked gene expression because of the phenomenon of dosage compensation. In dosage compensation, X-linked gene expression appears to be 'turned down' in 2X animals to the 1X level of expression. An intriguing and unexplained finding is that mutations and X-chromosome duplications that elevate X-linked gene expression also feminize triploid males. One way that this relationship between sex determination and X-linked gene expression may be operating is discussed. ------------------- Key: 1342 Medline: 91042732 Authors: Ishii N;Takahashi K;Tomita S;Keino T;Honda S;Yoshino K;Suzuki K Title: A methyl viologen-sensitive mutant of the nematode Caenorhabditis elegans. Citation: Mutation Research 237: 165-171 1990 Type: ARTICLE Genes: mev-1 Abstract: A methyl viologen (paraquat)-sensitive mutant, mev-1 (LG III), in Caenorhabditis elegans was about 4 times more sensitive to methyl viologen than the wild type. This mutant was also hypersensitive to oxygen. The brood size was about 1/4 that of the wild type. The average life span was determined to be 9.3 days as compared to 14.3 days for the wild type. The activity of superoxide dismutase (SOD), a scavenging enzyme for superoxide anion, was about half the wild-type level. We suggest that oxygen radicals may be involved in the normal aging mechanism in C. elegans. ------------------- Key: 1343 Medline: Authors: Riddle DL Title: Cell lineage. Citation: "McGraw-Hill Yearbook of Science & Technology 1991." Parker SP (ed)), McGraw-Hill. : 55-57 1991 Type: REVIEW Genes: Abstract: ------------------- Key: 1344 Medline: Authors: Epstein HF Title: Modulation of myosin assembly. Citation: "Cellular and Molecular Biology of Muscle Development." UCLA Symposia on Molecular & Cellular Biology. Kedes LH and Stockdale FE (eds). 93: 207-219 1989 Type: REVIEW Genes: myo-3 unc-15 unc-22 unc-45 unc-54 unc-82 unc-87 Abstract: Myosin is assembled into thick filaments of distinct lengths and substructures in phylogenetically and histologically diverse muscles. In these different muscles, specific proteins are associated with myosin in the assembled filaments. In the nematode Caenorhabditis elegans, the major protein component is paramyosin which assembles with two myosin isoforms about a separate core structure. At least six non-myosin proteins are associated with the core structures. Previous models of myosin assembly have emphasized a linear sequence of steps in which myosin molecules themselves are involved in nucleation, elongation and termination of individual filaments. Nematode muscle mutants accumulate assemblages of multiple thich filaments which also appear at low levels in wild-type. The effects of various alterations of myosin myosin levels upon the assembly of the two myosins and the existence of these multi-filament assemblages suggest a possible alternative model for myosin assembly. In this model, a cycle in which multiple thick filaments nucleate from a common structure is driven by synthesis of a ------------------- Key: 1345 Medline: 91081104 Authors: Siddiqui SS Title: Mutations affecting axonal growth and guidance of motor neurons and mechansensory neurons in the nematode Caenorhabditis elegans. Citation: Neuroscience Research 13: S171-S190 1990 Type: ARTICLE Genes: unc-1 unc-5 unc-6 unc-13 unc-25 unc-27 unc-30 unc-33 unc-34 unc-40 unc-44 unc-49 unc-51 unc-53 unc-55 unc-59 unc-61 unc-62 unc-69 unc-71 unc-73 unc-76 unc-85 unc-98 unc-104 Abstract: In the nematode Caenorhabditis elegans, each of its 302 individual neurons is an identified neuron. We have screened more than 100 mutations affecting locomotion in C. elegans immunocytochemically, using monoclonal antibodies that recognize specific subsets of neurons. Mutations in 25 genes affect the axonal outgrowth and guidance of a set of 6 mechanosensory receptor neurons (ALML, ALMR, AVM, PVM, PLML and PLMR). Similarly, mutations in 14 genes alter the axonal growth and process placement of two classes of inhibitory motor neurons (DD and VD). Most of these genes affect both embryonic and postembryonic development of the C. elegans nervous system, and have variable expressivity. Our results suggest that different neuron types are specified by a combination of genes that are activated in different cell types. Molecular characterization of such genes could lead to the identification of molecules critical in axonal outgrowth and guidance in higher ------------------- Key: 1346 Medline: 91045075 Authors: Hawkins NC;McGhee JD Title: Homeobox containing genes in the nematode Caenorhabditis elegans. Citation: Nucleic Acids Research 18: 6101-6106 1990 Type: ARTICLE Genes: ceh-1 ceh-9 ceh-10 ceh-11 Abstract: We designed a unique 36-mer oligonucleotide probe, based on the most highly conserved amino acid sequences of Antennapedia-like homeodomains and the codon bias of Caenorhabditis elegans. This probe was then used to isolate four classes of genes from a C. elegans genomic library. Sequencing reveals that we have isolated three new homeobox genes, designated ceh-1, ceh-9 and ceh-10. The fourth homeobox gene, ceh-11, has recently been described by Schaller et al (Nucleic Acids Res. 18, 2033-2036). The amino acid sequence of ceh-1 is 87% similar to the honeybee H40 homeodomain, 85% similar to the Drosophila NK-1 homeodomain and 82% similar to the chicken CHox3 homeodomain. The sequence ceh-10 appears to be a member of the paired class of homeodomains. The other two sequences, ceh-9 and ceh-11, remain unclassified. Three of the four sequences have at least one intron within the homeobox region. Transcripts of ceh-10 and ceh-11 are present in embryonic RNA but are greatly diminished in later developmental stages. Three of the four new genes have been placed on the C. elegans genomic map. ------------------- Key: 1347 Medline: 91045077 Authors: Okimoto R;Macfarlane JL;Wolstenholme DR Title: Evidence for the frequent use of TTG as the translation initiation codon of mitochondrial protein genes in the nematodes, Ascaris suum and Caenorhabditis elegans. Citation: Nucleic Acids Research 18: 6113-6118 1990 Type: ARTICLE Genes: Abstract: Data obtained from alignments of nucleotide sequences of mitochondrial (mt) DNA molecules of the nematode worms Ascaris suum and Caenorhabditis elegans indicate that in six of the mt-protein genes of A. suum and three of the mt-protein genes of C. elegans TTG is used as the translation initiation codon. Also, GTT seems to be the translation initiation codon of the A. suum COIII gene. All of the five remaining A. suum mt-protein genes appear to begin with ATT and the remaining nine C. elegans mt-protein genes appear to begin with either ATT or ATA. Therefore, in contrast to all other metazoan mtDNAs sequenced so far, it is likely that none of the nematode mt- protein genes use the standard ATG translation initiation codon. Some A. suum and C. elegans mt-protein genes end in T or TA, suggesting that, as found in other metazoan mitochondria, 3'-terminal polyadenylation is occasionally necessary to generate complete translation termination codons in transcripts of nematode mt-protein genes. ------------------- Key: 1348 Medline: Authors: Schnabel H;Schnabel R Title: An organ-specific differentiation gene, pha-1, from Caenorhabditis elegans. Citation: Science 250: 686-688 1990 Type: ARTICLE Genes: pha-1 tra-1 vab-7 eDf20 tDf2 tDf3 Abstract: Embryonic lethal mutation in the nematode Caenorhabditis elegans were generated and screened for phenotypes that suggest regulatory functions in order to identify genes involved in the control of early development. In embryos homozygous for mutations in one such gene, pha-1, the pharynx fails to undergo late differentiation and morphogenesis. Early pharynx development is not affected; thus, pha-1 controls the latter stages of this developmental process. All markers specific for differentiation in various pharyngeal cell types tested are affected, suggesting that pha-1 acts in an organ-specific, rather than cell type-specific, manner. The temperature-sensitive phases of both temperature-sensitive mutations indicate that pha-1 function is required solely during midembryogenesis, shortly before the onset of ------------------- Key: 1349 Medline: Authors: Horvitz HR Title: Genetic control of Caenorhabditis elegans cell lineage. Citation: Harvey Lectures 84: 65-77 1990 Type: REVIEW Genes: lin-10 lin-11 lin-12 lin-17 lin-26 lin-44 unc-86 Abstract: Animal development involves a complex pattern of cell divisions ultimately leading to the generation of a highly diverse complement of cell types. What are the molecular mechanisms responsible for controlling patterns of cell division and for causing cells to become different from one another? To address the problem, my colleagues and I have been examining how genes control cell lineage and cell fate in the nematode Caenorhabditis elegans. The study of C. elegans was pioneered by Sydney Brenner (1973, 1974), who selected this organism because it is highly tractable genetically (e.g., see Herman, 1988)and because it is simple and essentially invariant in its cellular anatomy (the adult hermaphrodite is now known to contain a total of 959 somatic cell nuclei; Sulston and Horvitz, 1977; Kimble and Hirsh, 1979; Sulston et al., 1983). The invariance in C. elegans anatomy reflects a similar invariance in development. For example, the cell lineage of C. elegans is essentially the same in all individuals (Sulston and Horvitz, 1977; Kimble and Hirsh, 1979; Sulston et al., 1983). This cell lineage was determined by direct observation of living nematodes: individual nuclei were watched with the aid of Nomarski optics as they migrated, ------------------- Key: 1350 Medline: 91039310 Authors: Silva IF;Plasterk RH Title: Characterization of a G-protein alpha subunit gene from the nematode Caenorhabditis elegans. Citation: Journal of Molecular Biology 215: 483-487 1990 Type: ARTICLE Genes: gpa-2 Abstract: A gene encoding the alpha-subunit of a guanine nucleotide binding regulatory protein (G-protein) was isolated from a library of genomic Caenorhabditis elegans DNA. The predicted coding region is colinear to related genes from mammals and the 356 amino acid residues show 63% sequence identity to e.g. rat Gi alpha 2. Three of the eight introns within the coding sequence are at exactly the same positions as those in a Drosophila G-protein alpha-subunit gene, and two of these are also conserved in the mammalian homologues. The nematode gene does not encode the cysteine residue that forms the substrate site for pertussis toxin-catalyzed ADP-ribosylation in several G- proteins. In spite of the similarity to mammalian G-protein alpha- subunit genes the gene can not unambiguously be categorized in one of the classes of G-proteins recognized in mammals (G alpha i, o, z, etc.). The position of the gene on the physical map of the animal was determined (chromosome V). The cloning and sequencing of this gene can be the starting point of reverse genetics experiments aimed at the isolation of animals mutated in a G-protein alpha-subunit ------------------- Key: 1351 Medline: 91120717 Authors: Plasterk RHA Title: The ins and outs of transposition. Citation: The New Biologist 2: 787-792 1990 Type: REVIEW Genes: Abstract: DNA rearrangements are responsible for a variety of phenomena in unicellular organisms, such as bacterial or protozoan antigenic variation, yeast mating type switching, and bacterial nitrogen fixation. In multicellular organisms, however, DNA rearrangements do not seem to be a major contributor to cell determination; in fact the only mammalian tissue in which rearrangements play an identified vital role, the immune system, could be viewed as a collection of unicellular organisms. Perhaps in multicellular organisms there are sufficient alternative strategies to determine the fate of cell lineages, and the costs or risks of reshuffling the genome may be too high. Nevertheless, transposons are probably found in all organisms. Why? ------------------- Key: 1352 Medline: 89206775 Authors: Epstein HF Title: Modulation of myosin assembly. Citation: BioEssays 9: 197-200 1988 Type: REVIEW Genes: myo-3 sup-3 unc-15 unc-22 unc-45 unc-54 unc-82 unc-87 Abstract: Myosin self-assembly is generally considered to be the major process in thick filament formation within striated muscles. The biological assembly of myosin into thick filaments is being analysed by genetic dissection as well as biochemical and morphological experiments in the nematode Caenorhabditis elegans. This work shows that the assembly of myosin is modulated by its biosynthesis and interaction with non-myosin proteins. Assemblages which generate multiple nascent thick filaments may play a central role in a catalytic cycle of myosin assembly. ------------------- Key: 1353 Medline: 91065496 Authors: Mains PE;Kemphues KJ;Sprunger SA;Sulston IA;Wood WB Title: Mutations affecting the meiotic and mitotic divisions of the early Caenorhabditis elegans embryo. Citation: Genetics 126: 593-605 1990 Type: ARTICLE Genes: mei-1 mei-2 mel-26 zyg-9 zyg-11 nDf23 Abstract: We describe interactions between maternal-effect lethal mutations in four genes of Caenorhabditis elegans whose products appear to be involved in the meiotic and mitotic divisions of the one-cell embryo. Mitosis is disrupted by two dominant temperature-sensitive gain-of- function maternal-effect lethal mutations, mei-1(ct46) and mel- 26(ct61), and by recessive loss-of-function maternal-effect lethal mutations of zyg-9. The phenotypic defects resulting from these mutations are similar. Doubly mutant combinations show a strong enhancement of the maternal-effect lethality under semipermissive conditions, suggesting that the mutant gene products interact. We isolated 15 dominant suppressors of the gain-of-function mutation mei- 1(ct46). Thirteen of these suppressors are apparently intragenic, but 11 of them suppress in trans as well as cis. Two extragenic suppressors define a new gene, mei-2. The suppressor mutations in these two genes also result in recessive maternal-effect lethality, but with meiotic rather than mitotic defects. Surprisingly, most of these suppressors are also able to suppress mel-26(ct61) in addition to mei-1(ct46). The products of the four genes mei-1, mei-2, zyg-9 and mel-26 could be responsible for some of the specialized features that distinguish the meiotic from the mitotic divisions in the one- cell embryo. ------------------- Key: 1354 Medline: 91169267 Authors: Rogalski TM;Golomb M;Riddle DL Title: Mutant Caenorhabditis elegans RNA polymerase II with a 20,000-fold reduced sensitivity to alpha-amanitin. Citation: Genetics 126: 889-898 1990 Type: ARTICLE Genes: ama-1 Abstract: A doubly mutant ama-1(m118m526) gene results in an RNA polymerase (Rpo) II that is unusually resistant to alpha-amanitin. Rpo II activity in isolated Caenorhabditis elegans cell nuclei is inhibited 50% by alpha-amanitin at a concentration of 150 micrograms/ml, making this enzyme 150 times more resistant to the toxin than Rpo II from the singly mutant allele, ama-1(m118), 20,000 times more resistant than the wild-type Rpo II, and about six times more resistant to amanitin than is Rpo III. It was determined that the SL1 spliced leader precursor is transcribed by Rpo II, and this transcript was used to measure Rpo II activity. The Rpo II activity is unstable in vitro, and the mutant strain has a temperature-sensitive sterile phenotype. The highly resistant double mutant was selected among four million progeny of the mutagenized ama-1(m118) parent by its ability to grow and reproduce in 200 micrograms/ml amanitin in the presence of a permeabilizing agent, Triton X-100. ------------------- Key: 1355 Medline: 91169268 Authors: Han M;Aroian RV;Sternberg PW Title: The let-60 locus controls the switch between vulval and nonvulval cell fates in Caenorhabditis elegans. Citation: Genetics 126: 899-913 1990 Type: ARTICLE Genes: let-23 let-60 lin-1 lin-12 lin-15 sDf8 Abstract: During induction of the Caenorhabditis elegans hermaphrodite vulva by the anchor cell of the gonad, six multipotent vulval precursor cells (VPCs) have two distinct fates: three VPCs generate the vulva and the other three VPCs generate nonspecialized hypodermis. Genes that control the fates of the VPCs in response to the anchor cell signal are defined by mutations that cause all six VPCs to generate vulval tissue (Multivulva or Muv) or that cause all six VPCs to generate hypodermis (Vulvaless or Vul). Seven dominant Vul mutations were isolated as dominant suppressors of a lin-15 Muv mutation. These mutations are dominant alleles of the gene let-60, previously identified only by recessive lethal mutations. Our genetic studies of these dominant Vul recessive lethal mutations, recessive lethal mutations, intragenic revertants of the dominant Vul mutations, and the closely mapping semi-dominant multivulva lin-34 mutations suggest that: (1) loss-of-function mutations of let-60 are recessive lethal at a larval stage, but they also cause a Vul phenotype if the lethality is rescued maternally by a lin-34 gain-of-function mutation. (2) The dominant Vul alleles of let-60 are dominant negative mutations whose gene products compete with wild-type activity. (3) lin-34 semidominant Muv alleles are either gain-of- function mutations of let-60 or gain-of-function mutations of an intimately related gene that elevates let-60 activity. We propose that let-60 activity controls VPC fates. In a wild-type animal, reception by a VPC of inductive signal activates let-60, and it generates into a vulval cell type; in absence of inductive signal, let-60 activity is low and the VPC generates hypodermal cells. Our genetic interaction studies suggest that let-60 acts downstream of let-23 and lin-15 and upstream of lin-1 and lin-12 in the genetic pathway specifying the switch between vulval and nonvulval cell ------------------- Key: 1356 Medline: 91077930 Authors: Han M;Sternberg PW Title: let-60, a gene that specifies cell fates during C. elegans vulval induction, encodes a ras protein. Citation: Cell 63: 921-931 1990 Type: ARTICLE Genes: let-23 let-60 lin-3 Abstract: Genetic analysis previously suggested that the let-60 gene controls the switch between vulval and hypodermal cell fates during C. elegans vulval induction. We have cloned the let-60 gene, and shown that it encodes a gene product identical in 84% of its first 164 amino acids to ras gene products from other vertebrate and invertebrate species. This conservation suggests that the let-60 product contains all the biochemical functions of ras proteins. Extrachromosomal arrays of let- 60 ras DNA cause cell-type misspecification (extra vulval fates) phenotypically opposite to that caused by let-60 ras loss-of-function mutations (no vulval fates), and suppress the vulvaless phenotype of mutations in two other genes necessary for vulval induction. Thus, the level and pattern of let-60 ras expression may be under strict regulation; increase in let-60 ras activity bypasses or reduces the need for upstream genes in the vulval induction pathway. ------------------- Key: 1357 Medline: 91077928 Authors: Finney M;Ruvkun G Title: The unc-86 gene product couples cell lineage and cell identity in C. elegans. Citation: Cell 63: 895-905 1990 Type: ARTICLE Genes: unc-86 Abstract: The C. elegans gene unc-86 is required in several distinct neuroblast lineages for daughter cells to become different from their mothers, and is also required for the specification of particular neural identities. Consistent with the fact that unc-86 encodes a POU domain protein, we find that the unc-86 protein is localized to the nucleus. In the affected lineages, unc-86 protein appears within a few minutes after cell division in the nuclei of those daughter cells that are transformed by unc-86 mutations. Thus, expression of unc-86 protein is dependent on cell lineage. unc-86 protein is not asymmetrically segregated at further divisions. unc-86 protein also appears shortly after cell division in the nuclei of particular identified differentiating neurons; at least some of these neurons are nonfunctional in unc-86 mutants. ------------------- Key: 1358 Medline: 91077929 Authors: Krause M;Fire A;White Harrison S;Priess J;Weintraub H Title: CeMyoD accumulation defines the body wall muscle cell fate during C. elegans embryogenesis. Citation: Cell 63: 907-919 1990 Type: ARTICLE Genes: hlh-1 unc-54 Abstract: We have cloned a gene from the nematode C. elegans that is closely related to the vertebrate MyoD gene family. The nematode gene product, CeMyoD, is a nuclear protein that is expressed specifically in body wall muscle cells. Antibody staining of early embryos shows that CeMyoD accumulates in early blastomeres that will subsequently produce only body wall muscle cells. CeMyoD is not detected in pharyngeal muscle cells or in nonmyogenic lineages. A CeMyoD-beta- galactosidase fusion gene is accurately expressed in myogenic cells that also express CeMyoD. In addition, the beta-galactosidase reporter is expressed as early as the 28 cell stage of embryogenesis in specific blastomeres prior to their clonal commitment to body wall muscle. This early fusion gene activity reveals that part of the specificity for CeMyoD transcription can arise very early in development and that subsequently, negative events may restrict CeMyoD expression in progeny cells not destined to ------------------- Key: 1359 Medline: 91079847 Authors: Walthall WW Title: Metamorphic-like changes in the nervous system of the nematode Caenorhabditis elegans. Citation: Journal of Neurobiology 21: 1085-1091 1990 Type: REVIEW Genes: unc-55 Abstract: During postembryonic development of the nematode Caenorhabditis elegans, one class of embryonic motoneurons, the DD cells, respecifies its pattern of synaptic connections. At the same time, a closely related set of postembryonic motoneurons, the VD cells, complete differentiation and assume a pattern of connections equivalent to the original pattern of the DD cells. These types of changes are reminiscent of changes observed in the nervous systems of animals as they undergo metamorphosis. The DD and VD neurons arise through different lineage mechanisms and in the adult, receive different synaptic inputs and make different outputs. The embryonic DD motoneurons are clonally related to one another; whereas the postembryonic VD motoneurons are produced by a repeated sublineage in which each stem cell generates four or five cell types in addition to the VD cells. In spite of these differences, it has been possible to identify only one gene by mutation that effects one of the two motoneuronal classes. Mutations in the gene unc-55 (unc meaning uncoordinated) cause the VD cells to become essentially identical to the DD cells; thus the unc-55 gene product appears necessary and sufficient to transform homeotically the pattern of synaptic connections of an entire class of motoneuron. ------------------- Key: 1360 Medline: 91043072 Authors: Herman RK;Hedgecock EM Title: Limitation of the size of the vulval primordium of Caenorhabditis elegans by lin-15 expression in surrounding hypodermis. Citation: Nature 348: 169-171 1990 Type: ARTICLE Genes: lin-15 Abstract: In the nematode Caenorhabditis elegans six hypodermal cells, the vulval precursor cells, are each competent to generate vulval cells. Normally only the three nearest precursor cells to the uterine anchor cell generate the vulva (22 nuclei), while the three others fuse with the non-specialized hypodermal syncytium (hyp7) surrounding each precursor cell and covering the body. Without an inductive signal from the anchor cell, all six vulval precursor cells fuse with hyp7 and no vulva is formed. But without activity of the vulval determination gene lin-15(+), all six cells undergo vulval divisions whether the anchor cell is present or not. Using mosaic analysis, we demonstrate here that lin-15(+) expression is necessary in cells other than the vulval precursor cells or the anchor cell, most probably in the hyp7 syncytium. We propose that lin-15(+) is active in hyp7 in order to repress an intrinsic vulval program in the precursor cells. The inductive signal from the anchor cell counteracts this repression for three precursor cells, allowing them to generate vulval cells. Such a two-signal (repressor/derepressor) mechanism may operate in other ------------------- Key: 1361 Medline: 91032565 Authors: Kirby C;Kusch M;Kemphues K Title: Mutations in the par genes of Caenorhabditis elegans affect cytoplasmic reorganization during the first cell cycle. Citation: Developmental Biology 142: 203-215 1990 Type: ARTICLE Genes: par-1 par-2 par-3 par-4 Abstract: A dramatic reorganization of cytoplasm occurs during the first cell cycle in embryos of the nematode, Caenorhabditis elegans. We present here the results of a quantitative study of some of the events during this reorganization in wild-type embryos and in par mutant embryos. The par mutations define a set of genes required for cytoplasmic localization in early embryos. We show that par mutations lead to defects in several events of the reorganization. Mutations in all four of the par genes we studied lead to defects in pseudocleavage and asymmetric redistribution of cortical microfilaments. In addition, some of the par mutations affect streaming of cytoplasm, migration of the pronuclei, and asymmetric shortening of the embryo. We propose that the major function of the par genes might be to orchestrate this initial reorganization of cytoplasm. ------------------- Key: 1362 Medline: 91037556 Authors: Ishii N;Suzuki K Title: X-ray inactivation of Caenorhabditis elegans embryos or larvae. Citation: International Journal of Radiation Biology 58: 827-833 1990 Type: ARTICLE Genes: rad-1 Abstract: The lethal effects of X-irradiation were examined in staged populations of Caenorhabditis elegans embryos or larvae. Radiation resistance decreased slightly throughout the first, proliferative phase of embryogenesis. This might be due to the increase in target size, since most cells in C. elegans are autonomously determined. Animals irradiated in the second half of embryogenesis were about 40-more resistant to the lethal effects of X-rays. This is probably due to the absence of cell divisions during this time. The radiation resistance increased still more with advancing larval stages. A radiation hypersensitive mutant, rad-1, irradiated in the first half of embryogenesis, is about 30-fold more sensitive than wild-type, but in the second half it is the same as ------------------- Key: 1363 Medline: 91058490 Authors: Vanfleteren JR;Evers EAIM;Van de Werken G;Van Beeumen JJ Title: The primary structure of cytochrome c from the nematode Caenorhabditis elegans. Citation: Biochemical Journal 271: 613-620 1990 Type: ARTICLE Genes: Abstract: The complete amino acid sequence of cytochrome c from the nematode Caenorhabditis elegans was determined. The native protein displays the same spectral properties in the oxidized and reduced states as horse heart cytochrome c. The apoprotein consists of 110 amino acid residues and differs from human cytochrome c by 44 substitutions, one internal deletion, five N-terminal additions and two C-terminal additions. One of the substitutions is the replacement of an 'invariant' phenylalanine residue at position 15 by tyrosine. The N-terminal sequence extension contains a short peptide motif, which is highly homologous with a peptide fragment present at the N-terminus of annelid and insect cytochrome c sequences. From the number of amino acid changes and the evolutionary rate of cytochrome c it would appear that nematodes diverged from a line leading to man about 1.4 billion years ago. When similar data based on the amino acid sequences of the histones H1, H2A, H2B and H3 are taken into account, the average estimate is 1.1 +/- 0.1 billion years. ------------------- Key: 1364 Medline: Authors: Chalfie M Title: The differentiation of touch receptor neurons in Caenorhabditis elegans: A case study of genetic and molecular analysis. Citation: American Zoologist 30: 531-543 1990 Type: REVIEW Genes: lin-14 lin-32 mec-1 mec-2 mec-3 mec-4 mec-5 mec-6 mec-7 mec-8 mec-9 mec-12 mec-17 unc-86 Abstract: A set of six touch receptor neurons in the nematode Caenorhabditis elegans allows the animal to respond to a gentle touch stimulus. Since the removal of these cells results in the specific loss of this touch sensitivity, behavioral mutants with this touch-insensitive phenotype can be used to identify and study genes that are required for the development and function of the touch cells. Using our experience with the touch cells as an example, I describe here some of the genetic and molecular approaches that can be used to study neuronal differentation. ------------------- Key: 1365 Medline: Authors: Chitwood DJ;Feldlaufer MF Title: Ecysteroids in axenically propagated Caenorhabditis elegans and culture medium. Citation: Journal of Nematology 22: 598-607 1990 Type: ARTICLE Genes: Abstract: Ecdysteroids (insect molting hormones) from Caenorhabditis elegans were chromatographically purified and quantified by radioimmunoassay. Nematodes from semidefined medium contained the immunoreactive equivalent of 460 pg ecdysone per gram dry weight. Culture medium, however, contained the immunoreactive equivalent of 68 times the quantity within the nematodes. In a defined medium lacking immunoreactivity, C. elegans contained 520 pg ecdysone equivalents per gram dry weight but reproduced slowly. Reproduction of C. elegans in defined medium was enhanced by formulation in agar. Propagation of C. elegans in either agar-based or aqueous defined medium supplemented with [14C]cholesterol of high specific activity failed to result in production of radiolabeled free ecdysteroids or polar or apolar ecdysteroid conjugates. Failure to demonstrate ecdysteroid biosynthesis in C. elegans raises questions about the ecdysteroids identified previously in nematodes being products of endogenous biosynthesis, a necessary condition for these compounds to be nematode ------------------- Key: 1366 Medline: 91061905 Authors: Beitel GJ;Clark SG;Horvitz HR Title: Caenorhabditis elegans ras gene let-60 acts as a switch in the pathway of vulval induction. Citation: Nature 348: 503-509 1990 Type: ARTICLE Genes: let-60 lin-15 sDf8 Abstract: The let-60 gene, an essential ras gene of the nematode Caenorhabditis elegans, acts as a switch in the inductive signalling pathway that initiates vulva formation. Recessive let-60 mutations that cause a vulvaless phenotype prevent let-60 function in response to the inductive signal. These mutations are clustered and define regions necessary either for the activation or for the action of the let-60 ras protein. Dominant let-60 mutations that cause a multivulva phenotype alter codon 13 and activate let-60 in vivo, rendering it independent of the inductive signal. The let-60 gene acts within an extensively defined genetic pathway, and other genes within this pathway seem likely to encode molecules that regulate let-60 function as well as molecules that are targets of let-60 action. ------------------- Key: 1367 Medline: 91080919 Authors: Aroian RV;Koga M;Mendel JE;Ohshima Y;Sternberg PW Title: The let-23 gene necessary for Caenorhabditis elegans vulval induction encodes a tyrosine kinase of the EGF receptor subfamily. Citation: Nature 348: 693-699 1990 Type: ARTICLE Genes: let-23 let-60 Abstract: The let-23 gene is required for induction of the Caenorhabditis elegans vulva. It is shown that let-23 encodes a putative tyrosine kinase of the epidermal growth factor receptor subfamily. Thus, let- 23 might encode the receptor for the inductive signal required for vulval development. Because let-23 acts upstream of let-60 ras in the vulval determination pathway, the identification of the let-23 product provides support for a link in vivo between tyrosine kinase growth factor receptors and ras proteins in a pathway of cell-type determination. ------------------- Key: 1369 Medline: 91097805 Authors: Otsuka AJ;Jeyaprakash A;Garcia-Anoveros J;Tang LZ;Fisk G;Hartshorne T;Franco R;Born T Title: The C. elegans unc-104 gene encodes a putative kinesin heavy chain-like protein. Citation: Neuron 6: 113-122 1991 Type: ARTICLE Genes: unc-104 Abstract: Mutations in the unc-104 gene of the nematode C. elegans result in uncoordinated and slow movement. Transposon insertions in three unc- 104 alleles (e2184, rh1016, and rh1017) were used as physical markers to clone the unc-104 gene. DNA sequence analysis of unc-104 cDNAs revealed an open reading frame capable of encoding a 1584 amino acid protein with similarities to kinesin heavy chain. The similarities are greatest in the amino-terminal ATPase and microtubule-binding domains. Although the primary sequence relatedness to kinesin is weak in the remainder of the molecule, the predicted secondary structure and regional isoelectric points are similar to kinesin heavy chain. ------------------- Key: 1370 Medline: 91301055 Authors: Schauer IE;Wood WB Title: Early C. elegans embryos are transcriptionally active. Citation: Development 110: 1303-1317 1990 Type: ARTICLE Genes: act-3 act-4 her-1 Abstract: We have developed a nucleotide incorporation assay for run-on transcription in C. elegans embryonic extracts as an approach to characterizing early transcription. The incorporation is primarily polymerase II-catalyzed RNA synthesis, producing transcripts of the expected size range for mRNAs. Incorporation is insensitive to inhibitors of reinitiation, indicating that the activity represents primarily elongation of nascent chains initiated prior to extract preparation. The transcripts produced appear to be unprocessed pre- mRNAs. Hybridization of labeled transcripts from extracts of staged embryos to a set of cloned genes suggests that the specificity of the in vitro reaction accurately reflects developmentally regulated in vivo transcription. Comparative analyses of transcription in extracts from various stages indicate that pregastrulation embryos are active transcriptionally and that the level of transcription per nucleus is approximately constant throughout embryogenesis. Furthermore, most embryonically expressed genes are already being transcribed in pregastrulation embryos. We also demonstrate that the labeled embryonic run-on transcripts can be used as probes to screen for sequences transcribed preferentially in pregastrulation embryos. There appears to be only a small set of such sequences, which could represent a previously unsuspected class of embryonically transcribed genes important for early embryogenesis. ------------------- Key: 1371 Medline: Authors: Angier N Title: Life's machinery, seen in a transparent worm. Citation: New York Times, January 8 : B5-B8 1991 Type: NEWS Genes: Abstract: Through a microscope, they look like tiny crystal serpents, curving and slithering across the dish with an almost opiated languor, doubling back on themselves as though discovering their tails for the first time, or bumping up against a neighbor clumsily and then slowly recoiling. Beneath their translucent skin the pulsing muscle cells and nerve fibers are clearly visible, a sight so strange and so exquisite that it is hard to believe these creatures are common roundworms, found in gardens and compost heaps everywhere. And it is harder still to believe that such slippery squiggles of life are fast changing the face of fundamental biology. ------------------- Key: 1372 Medline: Authors: Reape TJ;Burnell AM Title: Dauer larva recovery in Caenorhabditis elegans - I. The effect of mRNA synthesis inhibitors on recovery, growth and pharyngeal pumping. Citation: Comparative Biochemistry & Physiology 98B: 239-243 1991 Type: ARTICLE Genes: Abstract: 1. There are several well-characterized stages in the recovery of dauer larvae, beginning with resumption of pharyngeal pumping and followed by growth of the dauer larvae to normal juvenile diameter. 2. The mRNA synthesis inhibitors actinomycin D and a-amanitin failed to affect these critical components of the recovery process. 3. Polyacrylamide gel electrophoresis revealed the loss of dauer specific bands in the presence of high actinomycin D concentrations, an indication of normal exit from the dauer state. 4. These results indicate that mRNA synthesis is not required for the initial pre-molt period of dauer larva recovery, but failure of the worms to molt in the presence of actinomycin D or a-amanitin suggests that mRNA synthesized during the recovery period is required for the first post-dauer molt. ------------------- Key: 1373 Medline: Authors: Reape TJ;Burnell AM Title: Dauer larva recovery in the nematode Caenorhabditis elegans - II. The effect of inhibitors of protein synthesis on recovery, growth and pharyngeal pumping. Citation: Comparative Biochemistry & Physiology 98B: 245ss-252 1991 Type: ARTICLE Genes: Abstract: 1. The requirement for protein synthesis in the recovery process of the dauer larva of Caenorhabditis elegans was investigated using several protein synthesis inhibitors. 2. Cycloheximide retarded and inhibited the onset of pharyngeal pumping and the onset of SDS sensitivity in dauer larvae placed in fresh medium. It also affected longitudinal growth in recovering larvae. 3. Anisomycin had similar effects to cycloheximide. Puromycin and oxytetracycline also affected longitudinal growth, but they had a milder effect on dauer larva recovery. 4. Both cycloheximide and puromycin inhibited the incorporation of [35S]methionine into protein in recovering dauer larvae, cycloheximide being the more effective drug. 5. Measurement of peptidyl transferase activity suggested that a rapid burst of protein synthesis occurs before the onset of pharyngeal pumping in recovering dauer larvae. 6. Polyacrylamide gel electrophoresis revealed the retention of dauer specific protein bands when 10 mM cycloheximide was present in the recovery medium, indicating that recovery is prevented by the drug. 7. Since protein synthesis, but not mRNA synthesis appears to be obligatory for dauer larva recovery, the dauer larva may represent a developmental state analogous to unfertilized oocytes or to diapausing insect embryos which contain mRNA stores which are translated when stimulated by a suitable activating ------------------- Key: 1374 Medline: 92111171 Authors: Bargmann CI;Thomas JH;Horvitz HR Title: Chemosensory cell function in the behavior and development of Caenorhabditis elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 55: 529-538 1990 Type: REVIEW Genes: aex-3 osm-10 unc-31 Abstract: Chemosensation enables organisms to detect food, predators, potential mates, and other indicators of environmental quality. Organisms ranging in complexity from bacteria to mammals identify chemicals as attractants or repellents and modify their behaviors accordingly. In bacteria, the identity and regulation of chemosensory receptors has been elegantly elucidated. More recently, chemosensory cAMP receptors in the slime mold Dictyostelium discoideum and pheromone receptors in yeast have been identified. Less is known about the molecules and mechanisms of chemosensation in metazoan organisms... ------------------- Key: 1375 Medline: Authors: Donelson JE;Zeng W Title: A comparison of trans-RNA splicing in trypanosomes and nematodes. Citation: Parasitology Today 6: 327-334 1990 Type: REVIEW Genes: Abstract: Many aspects of the biology of kinetoplastids are unique, so it is surprising that they share with nematodes an unusual post-transcriptional process called trans-splicing. During this process, a small conserved RNA sequence is added to the 5' non-translated ends of transcribed RNAs of protein-encoding genes. Trypanosomes and nematodes are the only organisms to date in which these sequences have been described, and the biological significance of trans-splicing remains a mystery but may be of wider occurrence in invertebrates. In this review, John Donelson and Wenlin Zeng compare the process in nematodes and trypanosomes and speculate on its raison d'etre. ------------------- Key: 1376 Medline: 91008709 Authors: Schaeffer JM;Frazier EG;Bergstrom AR;Williamson JM;Liesch JM;Goetz MA Title: Cochlioquinone A, a nematocidal agent which competes for specific [3H]ivermectin binding sites. Citation: The Journal of Antibiotics 43: 1179-1182 1990 Type: ARTICLE Genes: Abstract: Cochlioquinone A, isolated from the fungus Helminthosporium sativum, was found to have nematocidal activity. Cochlioquinone A is a competitive inhibitor of specific [3H]ivermectin binding suggesting that cochlioquinone A and ivermectin interact with the same membrane receptor. ------------------- Key: 1377 Medline: 91058529 Authors: Reape TJ;Burnell AM Title: Enzyme induction in recovering dauer larvae of the nematode Caenorhabditis elegans in response to increasing concentrations of food source in the recovery medium. Citation: Biochemical and Biophysical Research Communications 172: 1013-1021 1990 Type: ARTICLE Genes: Abstract: Exposure of recovering dauer larvae of Caenorhabditis elegans to increasing concentrations of Escherichia coli in the recovery medium produced dramatic increases in the enzymes of intermediary metabolism. There was no significant difference between the rates of development of recovering dauer larvae grown on different concentrations of E. coli. When the activity of several key enzymes was assayed after 12, 22 and 32 hours of recovery in 0.5% w/v E. coli it was found that the activities recorded never reached levels observed at 12 hours for larvae grown on the optimum concentration of E. coli. These results imply that enzymes of intermediary metabolism in the nematode C. elegans are capable of being induced in response to changes in nutrient intake, as previously described for mammals and microorganisms. ------------------- Key: 1378 Medline: 91101727 Authors: Ahringer J;Kimble J Title: Control of the sperm-oocyte switch in Caenorhabditis elegans hermaphrodites by the fem-3 3' untranslated region. Citation: Nature 349: 346-348 1991 Type: ARTICLE Genes: fem-3 Abstract: In the Caenorhabditis elegans hermaphrodite germ line, sperm and then oocytes are made from a common pool of germ-cell precursors. The decision to differentiate as a sperm or an oocyte is regulated by the sex-determining gene, fem-3. Expression of fem-3 in the hermaphrodite germ line directs spermatogenesis and must be negatively regulated to allow the switch to oogenesis. In adult hermaphrodites (which are producing oocytes), most fem-3 RNA is found in the germ line, consistent with both the requirement for fem-3 in hermaphrodite spermatogenesis and the maternal effects of fem-3 on embryonic sex determination. Whereas loss-of-function mutants in fem-3 produce only oocytes, hermaphrodites carrying any of nine fem-3 gain-of-function (gf) mutations make none; instead sperm are produced continuously and in vast excess over wild-type amounts. Genetic analyses suggest that fem-3(gf) mutations have escaped a negative control required for the switch to oogenesis. Here we report that all nine fem-3(gf) mutants carry sequence alterations in the fem-3 3' untranslated region (3' UTR). There is no increase in the steady-state level of fem-3(gf) RNA over wild-type, but there is an increase in the polyadenylation of fem-3(gf) RNA that is coincident with the unregulated fem-3 activity. Results of a titration experiment support the hypothesis that a regulatory factor may bind the fem-3 3' UTR. We speculate that fem-3 RNA is regulated through its 3' UTR by binding a factor that inhibits translation, and discuss the idea that this control may be part of a more general regulation of maternal RNAs. ------------------- Key: 1379 Medline: 91031883 Authors: Bacic A;Kahane I;Zuckerman BM Title: Panagrellus redivivus and Caenorhabditis elegans: Evidence for the absence of sialic acids. Citation: Experimental Parasitology 71: 483-488 1990 Type: ARTICLE Genes: Abstract: Complementary experiments were performed to indicate the presence or absence of sialic acids in axenically cultured Panagrellus redivivus and Caenorhabditis elegans. Competitive displacement experiments with radiolabeled Limax flavus agglutinin demonstrated the presence of sialic acid in nematodes grown in medium which contained liver extract as a growth factor but the absence of sialic acid when heme was substituted for liver extract. This finding suggested that sialic acid present in the liver medium was responsible for conflicting results of other studies. Transmission electron microscopy of thin sections from nematodes labeled with an LFA-ferritin conjugate revealed no label to the surface area of the cephalic chemosensilla. Fluorometric analysis with a modification of the thiobarbituric acid assay was negative for sialic acid. Analyses by gas chromatography- mass spectrometry, sensitive to the high picomole range, were also negative for sialic acid. Taken together the results provide evidence for the absence of sialic acid in P. redivivus and C. elegans using the most sensitive and diagnostic ------------------- Key: 1380 Medline: 91056115 Authors: Hu E;Rubin CS Title: Expression of wild-type and mutated forms of the catalytic (alpha) subunit of Caenorhabditis elegans casein kinase II in Escherichia coli. Citation: Journal of Biological Chemistry 265: 20609-20615 1990 Type: ARTICLE Genes: Abstract: A full-length Caenorhabditis elegans cDNA that encodes the alpha subunit of casein kinase II was inserted into the inducible bacterial expression vector pET3a to generate the plasmid pCK alpha. Escherichia coli DE21 lysozyme S that was transformed with pCK alpha expressed soluble, catalytically active casein kinase II alpha upon induction with isopropyl beta-D-thiogalactopyranoside. The expressed alpha subunit was purified to homogeneity with a 60% yield by chromatography on CM-Sephadex, P-11 phosphocellulose, and heparin- agarose. The Mr values estimated from sodium dodecyl sulfate- polyacrylamide gel electrophoresis (Mr = 42,000) or calculated from hydrodynamic measurements (s20,w = 3.3 S, Stokes radius = 2.8 nm, Mr = 37,000) were similar, thereby indicating that the expressed enzyme is monomeric. The native holoenzyme and the expressed alpha subunit exhibited several similar properties including the utilization of both ATP and GTP as substrates and the susceptibility to inhibition of phosphotransferase activity by low concentrations of heparin. However, the kcat for E. coli-derived alpha was only 9% of the kcat for the native holoenzyme, and catalytic activity was not stimulated by polyamines. Recombinant casein kinase II alpha aggregates at low ionic strength, and the aggregation is partially reversible. A mutant alpha subunit in which Lys74 and Lys75 were substituted by glutamic acid residues was constructed by site-directed mutagenesis. The mutant enzyme was not inhibited by typically effective concentrations of heparin (e.g. IC50 = 0.3 micrograms/ml) because the affinity of modified recombinant casein kinase II Glu-74Glu-75 for heparin decreased approximately 70-fold. Thus, Lys74 and Lys75 are implicated in the heparin binding, inhibitory domain. The successful expression of casein kinase II alpha in E. coli will facilitate the analysis of the structural basis for functional domains in this enzyme. ------------------- Key: 1381 Medline: 91084839 Authors: Greenwald I;Broach JR Title: Cell fates in C. elegans: In medias ras. Citation: Cell 63: 1113-1116 1990 Type: REVIEW Genes: let-60 Abstract: ras proteins play a central role in controlling cell proliferation in a variety of organisms and also appear to mediate specific developmental processes in certain cells. Nonetheless, how ras protein activity is regulated and how ras protein activation yields its biological effect have not been clearly defined in any metazoan. Now, Han and Sternberg (1990a) have found that a ras protein is encoded by the C. elegans let-60 gene. Since powerful classical and molecular genetic methods are available for C. elegans, this finding offers great promise for identifying components of the ras pathway and defining the nature of their interactions in this organism. In addition, the extensive literature on the biochemistry and genetics of ras function in other organisms should greatly facilitate translating genetic analysis of let-60 (Beitel et al., 1990; Han and Sternberg, 1990b) into detailed molecular models of cell fate determination. ------------------- Key: 1382 Medline: 91084848 Authors: Hunter CP;Wood WB Title: The tra-1 gene determines sexual phenotype cell-autonomously in C. elegans. Citation: Cell 63: 1193-1204 1990 Type: ARTICLE Genes: dpy-18 tra-1 ctDp2 ctDp6 eDp6 mnDp37 Abstract: The tra-1 gene plays a central role in C. elegans sex determination. XX animals develop as hermaphrodites when tra-1 is active and as males when it is not. By analyzing a large number of tra-1 genetic mosaics we have shown that, with the expected exception of vulval induction by the hermaphrodite gonad, tra-1 functions cell- autonomously, consistent with a role as an intracellular component of a signaling pathway. Moreover, all the sexual differentiation genes under tra-1 control must also function cell-autonomously. Our results have additional implications for several aspects of postembryonic development, including mechanisms of sex-specific directed cell migrations and the question of an organizer in the male tail. ------------------- Key: 1383 Medline: 91093734 Authors: Hall DH;Russell RL Title: The posterior nervous system of the nematode Caenorhabditis elegans: Serial reconstruction of identified neurons and complete pattern of synaptic interactions. Citation: Journal of Neuroscience 11: 1-22 1991 Type: ARTICLE Genes: Abstract: Serial-section electron microscopy has been used to reconstruct the cellular architecture of the posterior nervous system of the nematode Caenorhabditis elegans. Each of 40 neurons in the tail of the adult hermaphrodite can be reproducibly and unambiguously identified by a set of morphological features, including cell body position, fiber geometry and size, and staining properties. A complete list of synapses has been assembled for 2 isogenic animals, and these lists are compared with a third isogenic animal reconstructed by White et al. (1986). The set of neurons and their pattern of synaptic interactions is simple and reproducible. Most of the cells are involved in sensory transduction or in local signal processing to relay signals via a few interneurons to motoneurons and thence to body muscles. Because the tail neurons are well separated and fairly reproducible in position, the hermaphrodite tail lends itself to laser-ablation studies of sensory processing (cf. Chalfie et al., 1985). Most of the synapses in the tail are concentrated in the preanal ganglion. Among the approximately 150 synapses there, about 85% are dyadic chemical synapses. The dyadic synapses are involved in reproducible patterns that have several interesting features. Most neurons synapse onto a few preferred pairs of target cells, in patterns that suggest a combinatorial model of synapse specification that may be open to genetic analysis. Furthermore, most dyadic contacts A----B,C fit a pattern in which the 2 postsynaptic partners are involved elsewhere in unidirectional synapses B----C. Thus, the dyadic synapse may serve to diverge sensory signals into parallel pathways, which then reconverge. This divergence/reconvergence pattern eventually directs processed sensory signals to the ventral cord interneurons PVCL and PVCR. About 80-90% of the synapses fall into repeated classes of synapses. Many of the remaining synapses are widely scattered and irreproducible from one animal to the next. Some of these contacts may be developmental mistakes reflecting a degree of "noise" in synapse specification (Waddington, 1957). ------------------- Key: 1384 Medline: Authors: Opperman CH;Chang S Title: Effects of aldicarb and fenamiphos on acetylcholinesterase and motility of Caenorhabditis elegans. Citation: Journal of Nematology 23: 20-27 1991 Type: ARTICLE Genes: ace-1 ace-2 Abstract: The ability of Caenorhabditis elegans to recover from exposure to high doses of aldicarb and fenamiphos was examined at the organismal and biochemical levels by determination of movement and acetylcholinesterase activity. Nematodes recovered rapidly from a 24-hour exposure to both compounds at concentrations that caused complete paralysis. Acetylcholinesterase regained nearly full activity after a 24-hour exposure to aldicarb but only 10% activity after exposure to fenamiphos. The nematodes were able to move normally, however, on the limited activity that was regained after fenamiphos treatment. Mutant C. elegans strains deficient in various molecular forms of acetylcholinesterase were utilized to demonstrate that the mechanism of recovery did not involve new synthesis of enzyme. This result was confirmed by experiments on acetylcholinesterase reactivation from live ------------------- Key: 1385 Medline: 91114701 Authors: Okkema PG;Kimble J Title: Molecular analysis of tra-2, a sex determining gene in C. elegans. Citation: EMBO Journal 10: 171-176 1991 Type: ARTICLE Genes: tra-2 Abstract: We have cloned the Caenorhabditis elegans sex determining gene, tra- 2, by transposon tagging. The tra-2 region is delineated by mapping Southern blot differences associated with 11 tra-2 mutations, mutant rescue, and analysis of tra-2 RNAs. The tra-2 gene encodes three transcripts. One transcript, a 1.8 kb RNA, is not detected in animals lacking a germ line, and therefore may be germline specific. Comparison of the two sexes shows that adult hermaphrodites have approximately 15-fold more tra-2 RNA than adult males. In addition, adult hermaphrodites contain 5 kb and 1.8 kb tra-2 RNAs whereas adult males possess 5 kb and 1.9 kb RNAs. A 1.9 kb tra-2 RNA is also found during hermaphrodite larval development, prior to sexual differentiation of the XX germ line. Surprisingly, analysis of tra-2 expression in selected sex determination mutants reveals that the sex specificity of tra-2 RNAs is not dictated by the pathway of sex determination that has been established by genetic experiments. This result can be interpreted in two ways. Either the sex specificity of the tra-2 RNAs is irrelevant to regulation of the sexual phenotype, which seems unlikely, or there is additional complexity within the hierarchy of sex determining genes, such as feedback regulation, which ensures that the tra-2 product corresponds to phenotypic sex. ------------------- Key: 1386 Medline: 91156020 Authors: Hodgkin J Title: Neurobiology - Nematodes in nervous decline. Citation: Nature 349: 564-565 1991 Type: REVIEW Genes: deg-1 mec-4 mec-6 Abstract: Stroking tiny worms with an eyebrow hair might seem an unlikely way to embark on the study of neuronal degeneration, but two reports on touch sensitivity in the nematode Caenorhabditis elegans (one of which appears on page 588 of this issue) provide impressive case studies of the pathological degeneration and death of identified neurons. These studies define two members of a new gene family, called 'degenerins', which can undergo mutation and cause the deterioration of certain nerve cells. The degenerin genes seem to exhibit some phylogenetic conservation and could therefore turn out to be involved in neuronal degeneratin in mammals as well as in nematodes. ------------------- Key: 1387 Medline: 91156026 Authors: Driscoll M;Chalfie M Title: The mec-4 gene is a member of a family of Caenorhabditis elegans genes that can mutate to induce neuronal degeneration. Citation: Nature 349: 588-593 1991 Type: ARTICLE Genes: deg-1 mec-4 Abstract: Three dominant mutations of mec-4, a gene needed for mechanosensation, cause the touch-receptor neurons of Caenorhabditis elegans to degenerate. With deg-1, another C. elegans gene that can mutate to induce neuronal degeneration and that is similar in sequence, mec-4 defines a new gene family. Cross-hybridizing sequences are detectable in other species, raising the possibility that degenerative conditions in other organisms may be caused by mutations in similar genes. All three dominant mec-4 mutations affect the same amino acid. Effects of amino-acid substitutions at this position suggest that steric hindrance may induce the degenerative state. ------------------- Key: 1388 Medline: 91141582 Authors: Guo X;Johnson JJ;Kramer JM Title: Embryonic lethality caused by mutations in basement membrane collagen of C. elegans. Citation: Nature 349: 707-709 1991 Type: ARTICLE Genes: emb-9 Abstract: Basement membranes are specialized forms of extracellular matrix with important functions in development. A major structural component of basement membranes is type IV collagen, a heterotrimer of two alpha 1(IV) and one alpha 2(IV) chains, which forms a complex, polygonal network associated with other basement membrane components. Here we report that the alpha 1(IV) collagen chain of Caenorhabditis elegans is encoded by the genetic locus emb-9. Mutations in emb-9 cause temperature-sensitive lethality during late embryogenesis. We have identified single nucleotide alterations that substitute glutamic acid for glycine in the triple-helical Gly-X-Y repeat region of the alpha 1(IV) collagen in three emb-9 mutant strains. These results are direct evidence that defects in basement membranes can disrupt embryonic development and form a basis for the genetic analysis of basement membrane ------------------- Key: 1389 Medline: 91153658 Authors: Schaller D;Wittman C;Linning R;Spicher A;Muller F;Tobler H Title: Cloning and expression in vitro of a gene encoding tRNA ACG(Arg) from the nematode Caenorhabditis elegans. Citation: Gene 97: 273-276 1991 Type: ARTICLE Genes: ceh-2 ceh-12 dpy-5 rtr-1 sup-7 sup-24 sup-29 Abstract: A gene (rtr-1) coding for the tRNAArgACG has been isolated and characterized from the nematode, Caenorhabditis elegans. The coding portion is not interrupted by an intron and is followed by a track of four thymidines associated with termination by RNA polymerase III. The predicted mature product is 76 nucleotides (nt) long including the CCA tail, and is specific for the most used Arg codon in C. elegans. The gene can be transcribed and processed in a homologous in vitro system. The 82-nt primary transcript begins at the first purine upstream from the mature tRNA 5' end and terminates after the first thymidine of the terminator signal. ------------------- Key: 1390 Medline: Authors: Zuckerman B Title: The nematode Caenorhabditis elegans as a model for rapid evaluation of cellular aging. Citation: Advances in the Biosciences 64: 155-163 1987 Type: REVIEW Genes: Abstract: Data supporting the use of nematodes as a preliminary screen for pharmaceuticals effective in retarding certain degenerative events associated with mammalian aging is presented. Among the criteria are 1. certain indices of cellular aging in nematodes are relevant to mammals; 2. the nematode system produces results in weeks as compared to one to two years for laboratory rats; and 3. the overall cost of nematode research is but a fraction of that required for mammalian studies with similar goals. ------------------- Key: 1391 Medline: Authors: Hooper C Title: Old-aged mutant ninja nematodes' cool anti-age gene. Citation: The Journal of NIH Research 3: 28-28 1991 Type: NEWS Genes: age-1 Abstract: Cowabugna, dudes! Those lean, gene-revealing machines have scored a most totally excellent victory in the battle to understand aging. We are, of course, talking about mutant ninja nematodes here. At a conference on aging in January at Cold Spring Harbor's Banbury Center, Thomas Johnson of the Institute for Behavioral Genetics at the University of Colorado in Boulder brought some dudes and dudettes from Capitol Hill up to date on the latest awesome achievements of the bodacious beasts know as Caenorhabditis elegans. ------------------- Key: 1392 Medline: Authors: Kingston IB Title: Nematode collagen genes. Citation: Parasitology Today 7: 11-15 1991 Type: REVIEW Genes: clb-1 clb-2 col-1 col-2 col-6 col-7 col-8 col-12 col-13 col-14 col-19 dpy-10 dpy-13 glp-1 lin-12 rol-6 sqt-1 Abstract: The collagen genes of nematodes encode proteins that have a diverse range of functions. Among their most abundant products are the cuticular collagens, which include about 80% of the proteins present in the nematode cuticle. The structures of these collagens have been found to be strikingly similar in the free-living and parasitic nematode species studied so far, and the genes that encode them appear to constitute a large multigene family whose expression is subject to developmental regulation. Collagen genes that may have a role in cell-cell interactions and collagen genes that correspond to the vertebrate type IV collagen genes have also been identified and studied in nematodes. ------------------- Key: 1393 Medline: 91173296 Authors: Bargmann CI;Horvitz HR Title: Control of larval development by chemosensory neurons in Caenorhabditis elegans. Citation: Science 251: 1243-1246 1991 Type: ARTICLE Genes: che-2 daf-3 daf-5 daf-6 daf-10 daf-12 daf-16 daf-18 daf-20 daf-22 Abstract: Larval development of the nematode Caenorhabditis elegans is controlled by the activities of four classes of chemosensory neurons. The choice between normal development and development into a specialized larval form called a dauer larva is regulated by competing environmental stimuli: food and a dauer pheromone. When the neuron classes ADF, ASG, ASI, and ASJ are killed, animals develop as dauer larvae regardless of environmental conditions. These neurons might sense food or dauer pheromone, or both, to initiate the specialized differentiation of many cell types that occurs during dauer formation. Entry into and exit from the dauer stage are primarily controlled by different chemosensory neurons. The analysis of mutants defective in dauer formation indicates that the chemosensory neurons are active in the absence of sensory inputs and that dauer pheromone inhibits the ability of these neurons to generate a signal necessary for normal ------------------- Key: 1394 Medline: 91166769 Authors: Epstein HF Title: Genetic analysis of myosin assembly in Caenorhabditis elegans. Citation: Molecular Neurobiology 4: 1-25 1990 Type: REVIEW Genes: myo-3 sup-3 sup-19 sus-1 unc-15 unc-22 unc-45 unc-52 unc-54 unc-82 Abstract: The established observations and unresolved questions in the assembly of myosin are outlined in this article. Much of the background information has been obtained in classical experiments using the myosin and thick filaments from vertebrate skeletal muscle. Current research is concerned with problems of myosin assembly and structure in smooth muscle, a broad spectrum of invertebrate muscles, and eukaryotic cells in general. Many of the general questions concerning myosin assembly have been addressed by a combination of genetic, molecular, and structural approaches in the nematode Caenorhabiditis elegans. Detailed analysis of multiple myosin isoforms has been a prominent aspect of the nematode work. The molecular cloning and determination of the complete sequences of the genes encoding the four isoforms of myosin heavy chain and of the myosin-associated protein paramyosin have been a major landmark. The sequences have permitted a theoretical analysis of myosin rod structure and the interactions of myosin in thick filaments. The development of specific monoclonal antibodies to the individual myosins has led to the delineation of the different locations of the myosins and to their special roles in thick filament structure and assembly. In nematode body-wall muscles, two isoforms, myosins A and B, are located in different regions of each thick filament. Myosin A is located in the central biopolar zones, whereas myosin B is restriced to the flanking polar regions. This specific localization directly implies differential behavior of the two myosins during assembly. Genetic and structural experiments demonstrate that paramyosin and the levels of expression of the two forms are required for the differential assembly. Additional genetic experiments indicate that several other gene products are involved in the assembly of myosin. Structural studies of mutants have uncovered two new structures. A core structure separate from myosin and paramyosin appears to be an integral part of thick filaments. Multifilament assemblages exhibit multiple nascent thick filament-like structures extending from central paramyosin regions. Dominant mutants of myosin that disrupt thick filament assembly are located in the ATP and actin binding sites of the heavy chain. A model for a cycle of reactions in the assembly of myosin into thick filaments is presented. Specific reactions of the two myosin isoforms, paramyosin, and core proteins with multifilament assemblages as ------------------- Key: 1395 Medline: 91125484 Authors: Wood WB Title: Evidence from reversal of handedness in C. elegans embryos for early cell interactions determining cell fates. Citation: Nature 349: 536-538 1991 Type: ARTICLE Genes: glp-1 Abstract: Many animals with overall bilateral symmetry also exhibit some left- right asymmetries with generally invariant handedness. Therefore, the left-right embryonic axis must have a consistent polarity, whose origins and subsequent effects on development are not understood. Caenorhabditis elegans exhibits such left-right asymmetries at all developmental stages. The embryonic cell lineage is asymmetric as well: although the animal is generally bilaterally symmetric, many of its contralaterally analogous cells arise from different lineages on the two sides of the embryo. I accomplished reversal of embryonic handedness by micromanipulation at the 6-cell stage, which resulted in mirror-image but otherwise normal development into healthy, fertile animals with all the usual left-right asymmetries reversed. This result demonstrates that in the 6-cell embryo the pair of anterior (AB) blastomeres on the right is equivalent to the pair on the left, and that the extensive differences in fates between lineally homologous derivatives of these cells on the two sides of the animal must be dictated by cell interactions, most of which are likely to occur early in embryogenesis. ------------------- Key: 1396 Medline: 91187685 Authors: Papp A;Rougvie AE;Ambros V Title: Molecular cloning of lin-29, a heterochronic gene required for the differentiation of hypodermal cells and the cessation of molting in C. elegans. Citation: Nucleic Acids Research 19: 623-630 1991 Type: ARTICLE Genes: lin-29 Abstract: The lin-29 gene product of C.elegans activates a temporal developmental switch for hypodermal cells. Loss-of-function lin-29 mutations result in worms that fail to execute a stage-specific pattern of hypodermal differentiation that includes exist from the cell cycle, repression of larval cuticle genes, activation of adult cuticle genes, and the cessation of molting. Combined genetic and physical mapping of restriction fragment length polymorphisms (RFLPs) was used to identify the lin-29 locus. A probe from the insertion site of a Tc1 (maP1), closely linked and to the left of lin-29 on the genetic map, was used to identify a large set of overlapping cosmid, lambda and yeast artificial chromosome (YAC) clones assembled as part of the C.elegans physical mapping project. Radiolabeled DNA from one YAC clone identified two distinct allele-specific alterations that cosegregated with the lin-29 mutant phenotype in lin-29 intragenic recombinants. lin-29 sequences were severely under-represented in all cosmid and lambda libraries tested, but were readily cloned in a YAC vector, suggesting that the lin-29 region contains sequences incompatible with standard prokaryotic cloning ------------------- Key: 1397 Medline: Authors: Liu ZC;Ambros V Title: Alternative temporal control systems for hypodermal cell differentiation in Caenorhabditis elegans. Citation: Nature 350: 162-165 1991 Type: REVIEW Genes: lin-4 lin-14 lin-28 lin-29 Abstract: In certain multicellular organisms, genetic regulatory systems that specify the timing of cell division, differentiation and morphogenesis must accommodate environmental and physiological contingencies that perturb or arrest development. For example, Caenorhabditis elegans can either develop continuously through four larval stages (L1-L4) or arrest indefinitely as a 'dauer larva' at the second larval (L2) moult, and later resume L3 an dL4 development. At the larva-to-adult (L4) moult of both continuous and 'post-dauer' development, hypodermal cells switch (the 'L/A switch') from a proliferating state to the terminally differentiated state. Four temporal regulators, lin-4, lin-14, lin-28 and lin-29, have been identified in C. elegans by mutations that cause precocious or retarded expression of stage-specific post-embryonic development events, including the L/A switch (refs 3, 8, 9; Fig. 1a). These genes have been organized into a genetic pathway that controls the timing of the L/A switch during continuous development; lin-29 activates the switch and the other heterochronic genes regulate it indirectly by regulating lin-29. We have now examined how proper timing of this event is specified in alternative developmental pathways. In continuously developing lin-4, lin-14 and lin-28 mutants the L/A switch occurs at abnormally early or late moults, but during post-dauer development of the same mutants the L/A switch occurs normally. Thus hypodermal cell differentiation is regulated by separate temporal control systems, depending on the developmental history. ------------------- Key: 1398 Medline: 91347895 Authors: Goh P-Y;Bogaert T Title: Positioning and maintenance of embryonic body wall muscle attachments in C. elegans requires the mup-1 gene. Citation: Development 111: 667-681 1991 Type: ARTICLE Genes: mup-1 Abstract: As part of a general study of genes specifying a pattern of muscle attachments, we identified and genetically characterised mutants in the mup-1 gene. The body wall muscles of early stage mup-1 embryos have a wild-type myofilament pattern but may extend ectopic processes. Later in embryogenesis, some body wall muscles detach from the hypodermis. Genetic analysis suggests that mup-1 has both a maternal and a zygotic component and is not required for postembryonic muscle growth and attachment. mup-1 mutants are suppressed by mutations in several genes that encode extracellular matrix components. We propose that mup-1 may encode a cell surface/extracellular matrix molecule required both for the positioning of body wall muscle attachments in early embryogenesis and the subsequent maintenance of these attachments to the hypodermis until ------------------- Key: 1399 Medline: 91284211 Authors: Savage C;Chalfie M Title: Genetic aspects of microtubule biology in the nematode Caenorhabditis elegans. Citation: Cell Motility and the Cytoskeleton 18: 159-163 1991 Type: REVIEW Genes: ben-1 che-2 che-3 che-13 daf-10 him-3 him-6 lin-5 mec-7 mec-12 osm-1 osm-5 osm-6 tub-1 unc-33 zyg-9 Abstract: Microtubules are required for a variety of cellular processes, including mitosis, meiosis, cell motility, morphogenesis, and, in neurons, neurite outgrowth, axonal transport, and sensory transduction. One approach to the study of microtubule biology is to isolate mutations that disrupt microtubules; these mutations should identify genes and gene products that are important for microtubule structure and/or function. The phenotype resulting from the loss of a particular gene product also gives an indication of the role of that product. Genetic approaches have been particularly useful in the study of microtubules in Drosophila, Aspergillus, and yeast. In this review we summarize genetic and biochemical studies of microtubule function and structure in the nematode Caenorhabditis elegans. ------------------- Key: 1400 Medline: 91172177 Authors: Conrad R;Thomas J;Spieth J;Blumenthal T Title: Insertion of part of an intron into the 5' untranslated region of a Caenorhabditis elegans gene converts it into a trans-spliced gene. Citation: Molecular and Cellular Biology 11: 1921-1926 1991 Type: ARTICLE Genes: act-4 tra-3 sup-7 vit-1 vit-2 vit-5 vit-6 Abstract: In nematodes, the RNA products of some genes are trans-spliced to a 22-nucleotide spliced leader (SL), while the RNA products of other genes are not. In Caenorhabditis elegans, there are two SLs, SL1 and SL2, donated by two distinct small nuclear ribonucleoprotein particles in a process functionally quite similar to nuclear intron removal. We demonstrate here that it is possible to convert a non- trans-spliced gene into a trans-spliced gene by placement of an intron missing only the 5' splice site into the 5' untranslated region. Stable transgenic strains were isolated expressing a gene in which 69 nucleotides of a vit-5 intron, including the 3' splice site, were inserted into the 5' untranslated region of a vit-2/vit-6 fusion gene. The RNA product of this gene was examined by primer extension and PCR amplification. Although the vit-2/vit-6 transgene product is not normally trans-spliced, the majority of transcripts from this altered gene were trans-spliced to SL1. We termed the region of a trans-spliced mRNA precursor between the 5' end and the first 3' splice site an "outron." Our results suggest that if a transcript begins with intronlike sequence followed by a 3' splice site, this alone may constitute an outron and be sufficient to demarcate a transcript as a trans-splice acceptor. These findings leave open the possibility that specific sequences are required to increase the efficiency of trans-splicing. ------------------- Key: 1401 Medline: 91322111 Authors: Lochrie MA;Mendel JE;Sternberg PW;Simon MI Title: Homologous and unique G protein alpha subunits in the nematode Caenorhabditis elegans. Citation: Cell Regulation 2: 135-154 1991 Type: ARTICLE Genes: act-1 act-2 act-3 goa-1 gpa-1 gpa-2 gpa-3 gpb-1 her-1 hsp-16 lin-10 mec-1 unc-13 Abstract: A cDNA corresponding to a known G protein alpha subunit, the alpha subunit of Go (Go alpha), was isolated and sequenced. The predicted amino acid sequence of C. elegans Go alpha is 80-87% identical to other Go alpha sequences. An mRNA that hybridizes to the C. elegans Go alpha cDNA can be detected on Northern blots. A C. elegans protein that crossreacts with antibovine Go alpha antibody can be detected on immunoblots. A cosmid clone containing the C. elegans Go alpha gene (goa-1) was isolated and mapped to chromosome I. The genomic fragments of three other C. elegans G protein alpha subunit genes (gpa-1, gpa-2, and gpa-3) have been isolated using the polymerase chain reaction. The corresponding cosmid clones were isolated and mapped to disperse locations on chromosome V. The sequences of two of the genes, gpa-1 and gpa-3, were determined. The predicted amino acid sequences of gpa-1 and gpa-3 are only 48% identical to each other. Therefore, they are likely to have distinct functions. In addition they are not homologous enough to G protein alpha subunits in other organisms to be classified. Thus C. elegans has G proteins that are identifiable homologues of mammalian G proteins as well as G proteins that appear to be unique to C. elegans. Study of identifiable G proteins in C. elegans may result in a further understanding of their function in other organisms, whereas study of the novel G proteins may provide an understanding of unique aspects of nematode ------------------- Key: 1402 Medline: 91224478 Authors: Prasad SS;Harris LJ;Baillie DL;Rose AM Title: Evolutionarily conserved regions in Caenorhabditis transposable elements deduced by sequence comparison. Citation: Genome 34: 6-12 1991 Type: ARTICLE Genes: Abstract: In this paper we present the sequence of an intact Caenorhabditis briggsae transposable element, Tcb2. Tcb2 is 1606 base pairs in length and contains 80 base pair imperfect terminal repeats and a single open reading frame. We have identified blocks of T-rich repeats in the regions 150-200 and 1421-1476 of this element which are conserved in the Caenorhabditis elegans element Tc1. The sequence conservation of these regions in elements from different Caenorhabditis species suggests that they are of functional importance. A single open reading frame corresponding to the major open reading frame of Tc1 is conserved among Tc1, Tcb1, and Tcb2. Comparison of the first 550 nucleotides of the sequence among the three elements has allowed the evaluation of a model proposing an extension of the major open reading frame. Our data support the suggestion that Tc1 is capable of producing a 335 amino acid protein. A comparison of the sequence coding for the amino and carboxy termini of the 273 amino acid transposase from Caenorhabditis Tc1-like elements and Drosophila HB1 showed different amounts of divergence for each of these regions, indicating that the two functional domains have undergone different amounts of selection. Our data are not compatible with the proposal that Tc1-related sequences have been acquired via horizontal transmission. The divergence of Tc1 from the two C. briggsae elements, Tcb1 and Tcb2, indicated that all three elements have been diverging from each other for approximately the same amount of time as the genomes of the two species. ------------------- Key: 1403 Medline: Authors: Mlot C Title: The education of C. elegans: A well-rounded worm. Citation: Science 252: 1619-1620 1991 Type: NEWS Genes: Abstract: The millimeter-long roundworm Caenorhabditis elegans is amassing a sizable research following. As more and more people have joined teh confederation of research efforts loosely called the worm project (see Science, 15 June 1990, p. 1310), the community's biennial meeting has outgrown the traditional watering hole at Cold Spring Harbor. This year, the researchers moved inland for the Eighth International C. elegans Meeting, held June 1-5 on Lake Mendota at the University of Wisconsin, Madison. More than 500 "worm people" turned out to absorb progress reports on the sequencing of the C. elegans genome, the study of its developmental pathways-and some newer topics as well. ------------------- Key: 1404 Medline: 91301451 Authors: Aroian RV;Sternberg PW Title: Multiple functions of let-23, a Caenorhabditis elegans receptor tyrosine kinase gene required for vulval Citation: Genetics 128: 251-267 1991 Type: ARTICLE Genes: dpy-10 him-5 let-23 lin-2 lin-7 lin-15 rol-6 mnDf61 mnDf67 mnDf68 Abstract: The let-23 gene, which encodes a putative tyrosine kinase of the epidermal growth factor (EGF) receptor subfamily, has multiple functions during Caenorhabditis elegans development. We show that let- 23 function is required for vulval precursor cells (VPCs) to respond to the signal that induces vulval differentiation: a complete loss of let-23 function results in no induction. However, some let-23 mutations that genetically reduce but do not eliminate let-23 function result in VPCs apparently hypersensitive to inductive signal: as many as five of six VPCs can adopt vulval fates, in contrast to the three that normally do. These results suggest that the let-23 receptor tyrosine kinase controls two opposing pathways, one that stimulates vulval differentiation and another that negatively regulates vulval differentiation. Furthermore, analysis of 16 new let-23 mutations indicates that the let-23 kinase functions in at least five tissues. Since various let-23 mutant phenotypes can be obtained independently, the let-23 gene is likely to have tissue- specific functions. ------------------- Key: 1405 Medline: 91301452 Authors: Thomas WK;Wilson AC Title: Mode and tempo of molecular evolution in the nematode Caenorhabditis: cytochrome oxidase II and calmodulin sequences. Citation: Genetics 128: 269-279 1991 Type: ARTICLE Genes: Abstract: Through direct sequencing methods, the mitochondrial gene for cytochrome oxidase subunit two (CO II) and the single-copy nuclear gene for calmodulin were compared among strains of Caenorhabidits elegans and two other Caenorhabditis species (C. remanei and C. briggsae). In addition the CO II sequence was determined from a distantly related nematode, Steinernema intermedii. Among the 11 strains of C. elegans tested, there are four types of CO II gene, arising from two major lineages. Levels of intraspecific difference in the CO II gene are low (less than 2.0%) compared to the extraordinary divergence between congeneric species, which is about 50% when corrected for multiple hits. Concordant with the increase in divergence between taxa is a change in the pattern of substitution from a strong transition bias (24 transitions compared to two transversions) within species to a substitution pattern that appears to reflect the base composition of the mitochondrial genome when more divergent nematodes are compared. The base composition of the Caenorhabditis CO II gene is strongly biased toward A + T at all three positions of codons and appears to constrain the amino acid composition of the protein. Both the CO II and calmodulin genes show extreme conservation of amino acid sequences. When the accumulation of changes at silent sites in the two genes is compared among strains, it becomes evident that the mitochondrial gene is changing faster than the nuclear ------------------- Key: 1406 Medline: 91301453 Authors: Bucher EA;Greenwald I Title: A genetic mosaic screen of essential zygotic genes in Caenorhabditis elegans. Citation: Genetics 128: 281-292 1991 Type: ARTICLE Genes: qDp3 Abstract: We have devised a simple genetic mosaic screen, which circumvents the difficulties posed by phenotypic analysis of early lethal mutants, to analyze essential zygotic genes in Caenorhabditis elegans. The screen attempts to distinguish genes involved in cell type and/or lineage specific processes such as determination, differentiation or morphogenesis from genes involved in general processes such as intermediary metabolism by using the pattern of gene function to classify genes: genes required in one or a subset of early blastomeres may have specific functions, whereas genes required in all early blastomeres may have general functions. We found that 12 of 17 genes examined function in specific early blastomeres, suggesting that many zygotic genes contribute to specific early processes. We discuss the advantages and limitations of this screen, which is applicable to other regions of the C. elegans ------------------- Key: 1407 Medline: 91238524 Authors: Aamodt E Title: Isolation of microtubules, adligin, and other microtubule-associated proteins from Caenorhabditis Citation: Methods in Enzymology 196: 274-284 1991 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans provides a system in which many biological processes involving microtubules, including multicellular processes such as development and nerve function, can be studied in the context of the living animal. The attributes that make C. elegans an attractive system include its simplicity, transparency, ease of cultivation, short life cycle, suitability for genetic analysis, small genome size in a small number of chromosomes, and the wealth of descriptive information now available on the biology of this organism. Caenorhabditis elegans contains several structurally distinct microtubule types, including 11 protofilament microtubules, 13 protofilament microtubules in the A-subfiber of ciliary outer doublet microubules, and 15 protofilament microtubules in some specialized sensory nerve processes that detect touch. Mutants have been identified that lack the tubulin required to form the 15 protofilament microtubules and other mutants show abnormalities in the organization of their microtubules. Microtubules purified by reassembly from C. elegans are composed of between 8 and 13 protofilaments and contain a variety of associated proteins with interesting properties. This chapter covers methods for growing C. elegans in quantities sufficient for biochemical studies and for the isolation of microtubules and microtubule-associated proteins (MAPs) from C. elegans. Detailed information on the biology, growing, and handling of C. elegans is available. ------------------- Key: 1408 Medline: 91192173 Authors: Hockertz MK;Clark-Lewis I;Candido EPM Title: Studies of the small heat shock proteins of Caenorhabditis elegans using anti-peptide antibodies. Citation: FEBS Letters 280: 375-378 1991 Type: ARTICLE Genes: Abstract: Peptides corresponding to selected regions of the 16 kDa small heat shock proteins (hsps) of the nematode C. elegans were synthesized and used to elicit polyclonal antibodies. It was found that these antibodies reacted predominantly with either the 16 kDa or the 18 kDa proteins, suggesting a close structural similarity between these hsps. Western blots of two-dimensional gels revealed extensive heterogeneity in these proteins, probably resulting from post- synthetic modifications. The native structures of both size classes of hsps were found to consist of large complexes of 4-5 x 10(5) Da. ------------------- Key: 1409 Medline: 91218851 Authors: Waring DA;Kenyon C Title: Regulation of cellular responsiveness to inductive signals in the developing C. elegans nervous system. Citation: Nature 350: 712-715 1991 Type: ARTICLE Genes: ceh-3 dpy-17 him-8 lin-22 mab-5 ncl-1 pal-1 unc-31 unc-36 Abstract: In Caenorhabditis elegans, cell-cell communication is required to form a simple pattern of sensory ray neurons and cuticular structures (alae). The C. elegans pal-1 gene initiates one developmental pathway (ray lineages) simply by blocking a cell-cell interaction that induces an alternative pathway. Here we show by mosaic analysis that pal-1+ acts by preventing specific cells from responding to inductive signals. The results indicate that although cell signals play a critical role in generating this pattern, they do not provide spatial information. Instead, signals are sent to many, if not all, of the precursor cells, and the ability to respond is spatially restricted. This patterning strategy thus differs from many well known models for pattern formation in which localized inductive signals influence a subset of cells within a field. We find that pal-1 encodes a homeodomain protein and so is likely to regulate transcription. The pal-1+ protein could block the response to cell signals either by repressing genes involved in signal transduction or by acting directly on downstream genes in a way that neutralizes the effects of the intercellular signals. Genetic experiments indicate that one candidate for such a downstream gene is the Antennapedia-like homeotic selector gene mab-5. ------------------- Key: 1410 Medline: 91195345 Authors: Yuan J;Finney M;Tsung N;Horvitz HR Title: Tc4, a Caenorhabditis elegans transposable element with an unusual foldback structure. Citation: Proceedings of the National Academy of Sciences USA 88: 3334-3338 1991 Type: ARTICLE Genes: ced-4 dpy-17 mut-2 unc-33 unc-79 unc-86 Abstract: We have identified and characterized a family of transposable elements in the nematode Caenorhabditis elegans. The Tc4 transposable element family is present at about 20 copies per haploid genome in the C. elegans Bristol and Bergerac strains. Although Tc4 transposition events have not been observed in these wild-type strains, we have identified Tc4 transposition events in the mut-2 mutant strain TR679, in which the elements Tc1 and Tc3 also transpose at a higher frequency than in the wild type. We determined the sequence of one Tc4 element. This 1.6-kilobase element contains almost perfect inverted terminal repeats of 774 base pairs (bp) with a 57-bp unique internal sequence. Tc4 is a fold-back element, but its long inverted terminal repeats, unlike those of the fold-back elements of other organisms, do not consist of multiple short repeats. In the two cases studied, Tc4 insertion resulted in duplication of a TNA trinucleotide target site. The family of Tc4 elements differs from other C. elegans transposable element families in structure, degree of structural heterogeneity, and target-site specificity. ------------------- Key: 1411 Medline: 91212983 Authors: Aamodt EJ;Chung MA;McGhee JD Title: Spatial control of gut-specific gene expression during Caenorhabditis elegans development. Citation: Science 252: 579-582 1991 Type: ARTICLE Genes: ges-1 rol-6 unc-22 unc-39 Abstract: The nematode Caenorhabditis elegans was transformed with constructs containing upstream deletions of the gut-specific ges-1 carboxylesterase gene. With particular deletions, ges-1 was expressed, not as normally in the gut, but rather in muscle cells of the pharynx (which belong to a sister lineage of the gut) or in body wall muscle and hypodermal cells (which belong to a cousin lineage of the gut). These observations suggest that gut-specific gene expression in C. elegans involves not only gut-specific activators but also multiple repressors that are present in particular nongut lineages. ------------------- Key: 1412 Medline: 91226537 Authors: Nonet ML;Meyer BJ Title: Early aspects of Caenorhabditis elegans sex determination and dosage compensation are regulated by a zinc-finger protein. Citation: Nature 351: 65-68 1991 Type: ARTICLE Genes: act-1 her-1 him-1 let-3 rol-6 sdc-1 sdc-2 sdc-3 mnDf4 mnDf41 mnDp1 Abstract: The sdc-1 gene acts at an early step in the regulatory hierarchy that controls the choice of sexual fate in Caenorhabditis elegans. It functions at a point before the control of sex determination and X- chromosome dosage compensation diverge. Here we report that sdc-1 encodes a protein of 1,203 amino acids containing seven zinc fingers. This protein motif in combination with other genetic and molecular information suggests that sdc-1 is likely to function as an embryonic transcription factor regulating downstream genes involved specifically in the sex determination and dosage compensation pathways, or regulating other genes involved in the coordinate control of both processes. These results enhance our general understanding of sex determination strategies, which are already known to involve transcriptional regulation and alternative RNA splicing in Drosophila melanogaster, DNA rearrangements in Saccharomyces cerevisiae, and transcriptional regulation in mammals. ------------------- Key: 1413 Medline: 91347937 Authors: Chisholm A Title: Control of cell fate in the tail region of C. elegans by the gene egl-5. Citation: Development 111: 921-932 1991 Type: ARTICLE Genes: deg-1 egl-5 mab-5 nDf16 nDf17 nDf20 sDp3 Abstract: The tail region of C. elegans contains a number of blast cell and neuron types that either are found only in the tail, or are different from more anterior homologues. In egl-5 mutants, the fates of many of these tail cells are abnormal or transformed to those of anterior homologues. The affected cells are related only by position and not by ancestry. egl-5 is also required for normal development of the somatic gonad and sex muscles in males. The function of egl-5 in all these tissues is cell autonomous. By genetic mapping, egl-5 lies very close to mab-5, a gene with an analogous role in the immediately anterior body region. egl-5 and mab-5 may constitute a 'mini-cluster' of regional determination genes, similar to those described in other animal phyla. ------------------- Key: 1414 Medline: 91317901 Authors: Nave R;Furst D;Vinkemeier U;Weber K Title: Purification and physical properties of nematode mini-titins and their relation to twitchin. Citation: Journal of Cell Science 98: 491-496 1991 Type: ARTICLE Genes: unc-22 Abstract: We have isolated mini-titin from the nematodes Ascaris lumbricoides and Caenorhabditis elegans under native conditions using a modification in the procedure to prepare this protein from insect muscle. The proteins have an apparent molecular weight of 600,000 and appear in oriented specimens as flexible thin rods with a length around 240-250 nm. The circular dichroism spectrum of the Ascaris protein is dominated by beta-structure. The proteins react with antibodies to insect mini-titin and also with antibodies raised against peptides contained in the sequence predicted for twitchin, the product of the Caenorhabditis elegans unc-22 gene. Antibodies to insect mini-titin decorate the body musculature as well as the pharynx of wild-type C. elegans in immunofluorescence microscopy. In the twitchin mutant E66 only the pharynx is decorated. We conclude that the mini-titins of invertebrate muscles defined earlier by ultrastructural criteria are very likely to be twitchins, i.e. molecules necessary for normal muscle contraction. We discuss the molecular properties of the proteins in the light of the sequence ------------------- Key: 1415 Medline: 91251142 Authors: Spieth J;Nettleton M;Zucker-Aprison E;Lea K;Blumenthal T Title: Vitellogenin motifs conserved in nematodes and vertebrates. Citation: Journal of Molecular Evolution 32: 429-438 1991 Type: ARTICLE Genes: vit-2 vit-3 vit-5 vit-6 Abstract: Caenorhabditis elegans vitellogenins are encoded by a family of six genes, one of which, vit-5, has been previously sequenced and shown to be surprisingly closely related to the vertebrate vitellogenin genes. Here we report an alignment of the amino acid sequences of vitellogenins from frog and chicken with those from three C. elegans genes: vit-5 and two newly sequenced genes, vit-2 and vit-6. The four introns of vit-6 are all in different places from the four introns of vit-5, but three of these eight positions are identical or close to intron locations in the vertebrate vitellogenin genes. The encoded polypeptides have diverged from one another sufficiently to allow us to draw some conclusions about conserved positions. Many cysteine residues have been conserved, suggesting that vitellogenin structure has been maintained over a long evolutionary distance and is dependent upon disulfide bonds. In addition, a 20-residue segment shows conservation between the vertebrate and the nematode vitellogenins. This sequence may play a highly conserved role in vitellogenesis, such as specific recognition by oocytes. On the whole, however, selection may be acting more strongly on amino acid composition and codon usage than on amino acid sequence, as might be expected for abundant storage proteins: The amino acid compositions of vit-2, vit-5, and vit-6 products are remarkably similar, despite the fact that the sequence of the vit-2 protein is only 22% and 50% identical to the sequences of vit-6 and ------------------- Key: 1416 Medline: 92001536 Authors: Trent C;Purnell B;Gavinski S;Hageman J;Chamblin C;Wood WB Title: Sex-specific transcriptional regulation of the C. elegans sex-determining gene her-1. Citation: Mechanisms of Development 34: 43-56 1991 Type: ARTICLE Genes: egl-3 fem-3 her-1 him-8 sdc-1 sdc-2 tra-1 unc-23 eDp3 Abstract: Expression of the sex-determining gene her-1 is required in C. elegans for the normal male development of XO animals. Abnormal expression in XX animals, which normally develop as hermaphrodites, results in aberrant male development. We have isolated a molecular clone of the her-1 gene and have identified two transcripts that are present in XO animals at all stages of development: an abundant 0.8 kb transcript and a less abundant 1.2 kb transcript. In preparations of XX animals, the 0.8 kb transcript was observed only at very low levels in embryos or L1 larvae and the 1.2 kb transcript was not detected. Two gain-of-function her-1 mutations result in high levels of the 1.2 and 0.8 kb transcripts in XX animals. The levels of these transcripts are also elevated in XX animals carrying a loss-of- function mutation in either sdc-1 or sdc-2, consistent with the proposed roles of these genes as negative regulators of her-1. These results demonstrate that expression of the her-1 gene in males and hermaphrodites is controlled at the level of transcript synthesis or accumulation. This mode of regulation contrasts with that found for the Drosophila sex-determining genes, whose sex-specific expression is controlled by differential splicing in males and females. ------------------- Key: 1417 Medline: Authors: Abad P;Tares S;Brugier N;De Guiran G Title: Characterization of the relationships in the pinewood nematode species complex (Bursephalenchus spp.) using a heterologous unc-22 DNA probe from Caenorhabditis elegans/ Citation: Parasitology 102: 303-308 1991 Type: ARTICLE Genes: unc-22 Abstract: Pine wilt is the most serious disease of native pines in Japan and potentially the most important nematode disease of conifers in the world. The pinewood nematode Bursaphelenchus xylophilus was found to be the casual agent. Difficulties arose with respect to the precise identity of some isolates of B. xylophilus and of similar species B. mucronatus and B. fraudulentus. Restriction enzyme analyses of repetitive DNA revealed bands specific for the species B. xylophilus, B. mucronatuus and B. fraudulentus. Hybridization patterns obtained with unc-22 gene of C. elegans, clearly identified B. xylophilus, B. mucronatus and B. fraudulentus as well as the different geographic isolates of these species. Furthermore, it is possible to define the phylogenetic relationships between the different populations constituting the 'pine wood ------------------- Key: 1418 Medline: Authors: Schlicht P;Schierenberg E Title: Altered establishment of cell lineages in the Caenorhabditis elegans embryo after suppression of the first cleavage supports a concentration-dependent decision Citation: Roux's Archives of Developmental Biology 199: 437-448 1991 Type: ARTICLE Genes: Abstract: In the early embryo of Caenorhabditis elegans five somatic cell lineages and a germ cell lineage are established by a series of unequal cleavages in the germline. We suppressed first cleavage by means of cold, mechanical pressure or centrifugation. Thereafter, with the second attempt of the zygote to divide, four blastomeres were generated simultanwously in a tetrapolar cleavage. Cell division pattern, segregation of germline-specific granules, and terminal differentiation of such manipulated embryos were analysed. Instead of six, only from one to five visible cell lineages were established before the germline prematurely aborted from its typical pattern of unequal cleavage. The absence of germline-specific cleavage appears to accompany the abnormal segregation of germline-specific granules. While muscle differentiation was detected even in embryos expressing only one cell lineage, in general, gut differentation became visible only if a separate gut lineage had been generated. We hypothesize that the potential for differential cleavage is lost in manipulated embryos because a cytoplasmic control factor is diminished as a result of the retarded some/germline separation. According to this hypothesis, after manipulation, a concentration-dependent decision mechanism leads to: a reduced number of unequal germline cleavages or even none at all, the establishment of fewer distinct cell lineages, and limited cellular ------------------- Key: 1419 Medline: Authors: White JG;Southgate E;Thomson JN Title: On the nature of undead cells in the nematode Caenorhabditis elegans. Citation: Philosophical Transactions of the Royal Society of London 331: 263-271 1991 Type: ARTICLE Genes: ced-3 Abstract: During the course of normal embryonic and post-embryonic development, 131 cells in a Caenorhabditis elegans hermaphrodite undergo programmed cell death. Loss of function mutations in either of the genes ced-3 or ced-4 abolish cell deaths, enabling these 'undead' cells to survive and be incorporated into the adult with no obvious deleterious consequences. Ultrastructural reconstructions have shown that the undead cells exhibit many differentiated characteristics. Most of the reconstructed cells appear to be neurons wit all the characterisic features associated with such cells, such as processes, synaptic vesicles and pre-synaptic specializations. However, clear morphological differences were seen among the undead neurons, suggesting a diversity of cell type. One of the reconstructed cells was a rectal epithelial cell, which had displaced its lineal sister that normally functions in this role. Removal of the ability to undergo programmed cell death by mutation therefore reveals a diversity of cryptic differentiated states that are acquired by cells that normally are destined to die. ------------------- Key: 1420 Medline: Authors: Grewal PS Title: Influence of bacteria and temperature on the reproduction of Caenorahbditis elegans (Nematoda: Rhabditidae) infesting mushrooms (Agaricus bisporus). Citation: Nematologica 37: 72-82 1991 Type: ARTICLE Genes: Abstract: Ten species of bacteria associated with Caenorhabditis elegans, a saprobic rhabditid nematode infesting cultivated mushroom (Agaricus bisporus), were isolated and identified. In monogenic cultures, five species of bacteria (Acinetobacter calcoaceticus var. anitratus, A. calcoaceticus var. lwoffi, Enterobacter cloacae, Pseudomonas maltophilia and Serratia liquefaciens) sustained the growth and reproduction of C. elegans for several generations. Bacillus cereus and Pseudomonas sp. supported growth and reproduction of the nematode, but resulted in smaller populations. E. amnigenus and P. aeruginosa could support nematode growth and reproduction for the first 2-3 generations; Bacillus sp. could support growth but not reproduction. The reproductive capacity of parthenogenetic female C. elegans varied with temperature and bacterial food source. Cubic equations were fitted to the data on nematode fecundity. Temperature optima for reproduction were estimated. Temperautre significantly affected generation time of the nematode but bacterial species had little effect. The significance of interactions between C. elegans and its associated bacteria in mushroom culture is discussed. ------------------- Key: 1421 Medline: 91232955 Authors: Dreyfus DH;Emmons SW Title: A transposon-related palindromic repetitive sequence from C. elegans. Citation: Nucleic Acids Research 19: 1871-1877 1991 Type: ARTICLE Genes: Abstract: A family of transposon-like sequences in the C. elegans genome is described. This family, termed the Tc6 family, consists mostly of conserved, 1.6 kb elements. Four Tc6 elements or partial elements have been cloned and the DNA sequences of three were determined. One appears to be a complete element of 1603 nucleotides, consisting of a palindrome of 765 nucleotides, with a central, non-palindromic region of 73 nucleotides. Another has an identical structure except for an internal deletion. A third is a partial element terminating at a probable internal restriction site used for cloning. A fourth clone contained portions of the Tc6 sequence juxtaposed to non-Tc6 sequences. All C. elegans strains examined contain 20-30 Tc6 elements. The ends of Tc6 elements are conserved and have sequence similarity to the ends of C. elegans transposons Tc1 and Tc3. The ends of Tc6 elements also have sequence similarity to the heptamer portion of the immunoglobulin and T-cell receptor recombination signal sequence, raising the possibility of wide phylogenetic conservation of the recombination mechanism. Tc6 elements also share sequence motifs with plant-pathogenic viroid RNA's, possibly indicative of a Tc6 RNA replicative phase. ------------------- Key: 1422 Medline: Authors: Grewal PS Title: Effects of Caenorhabditis elegans (Nematoda: Rhabditidae) on the spread of the bacterium Pseudomonas tolaasii in mushrooms (Agaricus bisporus). Citation: Annals of Applied Biology 118: 47-55 1991 Type: ARTICLE Genes: Abstract: The effects of mass-produced saprobic rhabditid nematodes, Caenorhabditis elegans on the spread of the bacterial blotch pathogen, Pseudomonas tolaasii, were studied in mushroom growth chambers. C. elegans significantly reduced the intensity of blotch on sporophores. Repeated isolations of the bacterial flora from the gut of C. elegans recovered from mushroom sporophores duuring cropping, revealed the presence of Pseudomonas fluorescens biovar reactans. All the isolates of P. fluorescens biovar reactans isolated from nematodes were antagonists of P. tolaasii. C. elegans produced much larger populations in monoxenic cultures with P. fluorescens biovar reactans than wit P. tolaasii. It is suggested that as C. elegans selects P. fluorescens biovar reactans rather than P. tolaasii as a food substrate it probably spreads the antagonist in the mushroom crop and may contribute to the ------------------- Key: 1423 Medline: 92120100 Authors: Lambie EJ;Kimble J Title: Two homologous regulatory genes, lin-12 and glp-1, have overlapping functions. Citation: Development 112: 231-240 1991 Type: ARTICLE Genes: glp-1 lag-1 lag-2 lin-12 sDf50 Abstract: Two homologous genes, lin-12 and glp-1, encode transmembrane proteins required for regulatory cell interactions during C. elegans development. Based on their single mutant phenotypes, each gene has been thought to govern a distinct set of cell fates. We show here that lin-12 and glp-1 are functionally redundant during embryogenesis: Unlike either single mutant, the lin-12 glp-1 double mutant dies soon after hatching. Numerous cellular defects can be observed in these Lag (for lin-12 and glp-1) double mutants. Furthermore, we have identified two genes, lag-1 and lag-2, that appear to be required for both lin-12 and glp-1-mediated cell interactions. Strong loss-of-function lag mutants are phenotypically indistinguishable from the lin-12 glp-1 double; weak lag mutants have phenotypes typical of lin-12 and glp-1 single mutants. We speculate that the lin-12 and glp-1 proteins are biochemically interchangeable and that their divergent roles in development may rely largely on differences in gene expression. ------------------- Key: 1424 Medline: 91249390 Authors: Hall DH;Hedgecock EM Title: Kinesin-related gene unc-104 is required for axonal transport of synaptic vesicles in C. elegans. Citation: Cell 65: 837-847 1991 Type: ARTICLE Genes: clr-1 dpy-10 unc-5 unc-104 mnDf30 Abstract: unc-104 encodes a novel kinesin paralog that may act as a microtubule- based motor in the nervous system. Neuronal cell lineages and axonogenesis are normal in unc-104 null mutants, but axons have few synaptic vesicles and make only a few small synapses. By contrast, neuron cell bodies have surfeits of similar vesicles tethered together within the cytoplasm. Based on behavioral and cellular phenotypes, we suggest that UNC-104 is a neuron-specific motor used for anterograde translocation of synaptic vesicles along axonal microtubules. Other membrane-bounded organelles are transported normally. ------------------- Key: 1425 Medline: 91295972 Authors: Stewart HI;Rosenbluth RE;Baillie DL Title: Most ultraviolet irradiation induced mutations in the nematode Caenorhabditis elegans are chromosomal rearrangements. Citation: Mutation Research 249: 37-54 1991 Type: ARTICLE Genes: bli-5 dpy-1 dpy-11 dpy-17 dpy-18 dpy-28 let-326 let-329 let-336 let-349 let-418 let-422 let-426 let-447 let-448 let-458 let-462 lin-40 mel-23 sma-2 sma-3 unc-4 unc-42 unc-46 mnC2 sDf26 sDf32 sDf36 sDf44 sDf70 sDf71 sDf72 sDf73 sDf74 sDf75 sDp3 hT2 sT5 Abstract: In this study we have determined the utility of 254-nm ultraviolet light (UV) as a mutagenic tool in C. elegans. We have demonstrated that irradiation of adult hermaphrodites provides a simple method for the induction of heritable chromosomal rearrangements. A screening protocol was employed that identifies either recessive lethal mutations in the 40 map unit region balanced by the translocation eT1(III;V), or unc-36(III) duplications. Mutations were recovered in 3% of the chromosomes screened after a dose of 120 J/m2. This rate resembles that for 1500 R gamma-ray-induced mutations selected in a similar manner. The mutations were classified either as lethals [mapping to Linkage Group (LG)III or LGV] or as putative unc-36 duplications. In contrast to the majority of UV-induced mutations analysed in microorganisms, we found that a large fraction of the C. elegans UV-induced mutations are not simple intragenic lesions, but are deficiencies for more than one adjacent gene or more complex events. Preliminary evidence for this conclusion came from the high frequency of mutations that had a dominant effect causing reduced numbers of adult progeny. Subsequently 6 out of 9 analysed LGV mutations were found to be deficiencies. Other specific rearrangements also identified were: one translocation, sT5(II;III), and two unc-36 duplications, sDp8 and sDp9. It was concluded that UV irradiation can easily be used as an additional tool for the analysis of C. elegans chromosomes, and that C. elegans should prove to be a useful organism in which to study the mechanisms whereby UV acts as a mutagen in cells of complex eukaryotes. ------------------- Key: 1426 Medline: 92008402 Authors: Johnson TE;Nelson GA Title: Caenorhabditis elegans: A model system for space biology studies. Citation: Experimental Gerontology 26: 299-309 1991 Type: REVIEW Genes: age-1 mev-1 mev-2 mev-3 nuc-1 rad-1 rad-2 rad-3 rad-4 rad-5 rad-6 rad-7 unc-22 unc-31 Abstract: The utility of the nematode Caenorhabditis elegans in studies spanning aspects of development, aging, and radiobiology is reviewed. These topics are interrelated via cellular and DNA repair processes especially in the context of oxidative stress and free-radical metabolism. The relevance of these research topics to problems in space biology is discussed and properties of the space environment are outlined. Exposure to the space-flight environment can induce rapid changes in living systems that are similar to changes occurring during aging; manipulation of these environmental parameters may represent an experimental strategy for studies of development and senscence. The current and future opportunities for such space-flight experimentation are presented. ------------------- Key: 1427 Medline: Authors: Goldberg J Title: Worm mapping. Citation: Discover 12: 22-22 1991 Type: NEWS Genes: Abstract: Undulating under the microscope, its muscle and nerve cells visible within its transparent body, the tiny roundworm Caenorhabditis elegans is normally a creature of surprising grace. But one mutant strain is not elegans at all. It thrashes about in such an uncoordinated fashion that researchers have dubbed the mutant worm "unc"... ------------------- Key: 1428 Medline: 92010949 Authors: Brooks A;Johnson TE Title: Genetic specification of life span and self-fertility in recombinant-inbred strains of Caenorhabditis elegans. Citation: Heredity 67: 19-28 1991 Type: ARTICLE Genes: Abstract: The genetic basis of life-span and age-specific fertility has been analysed using recombinant-inbred strains of the nematode Caenorhabditis elegans. Estimates of narrow-sense heritability range from 0.05 to 0.36 for life span and from 0.36 to 0.49 for total self- fertility. Positive phenotypic and genetic correlations for life span and total fertility were also observed, although in most cases the correlations were not significant. In general, age-specific hermaphrodite fertility was positively correlated with fertility on contiguous days but was negatively correlated with fertility on more distant days. We estimate that a minimum of two to three genes specify each of these traits in this genetic background. Three single- gene markers were used to generate strain distribution patterns, and two of these were found to be linked with loci that specify life span and/or fertility. We also saw evidence for a significant environmental component affecting ------------------- Key: 1429 Medline: 91260871 Authors: Horvitz HR;Sternberg PW Title: Multiple intercellular signaling systems control the development of the Caenorhabditis elegans vulva. Citation: Nature 351: 535-541 1991 Type: REVIEW Genes: dig-1 let-23 let-60 lin-10 lin-11 lin-12 lin-15 lon-1 Abstract: Developmental, genetic and molecular studies indicate that multiple intercellular signalling systems interact to specify the types and spatial patterns of cells generated during the formation of the vulva of the nematode Caenorhabditis elegans. Two classes of evolutionarily conserved transmembrane receptors and a Ras protein function in these signalling systems. The biology of vulval development provides a framework for understanding how cell interactions control the development of animals as diverse as nematodes, insects and mammals. ------------------- Key: 1430 Medline: Authors: Grewal PS;Richardson PN Title: Effects of Caenorhabditis elegans (Nematoda: Rhabditidae) on yield and quality of the cultivated mushroom Agaricus bisporus. Citation: Annals of Applied Biology 118: 381-394 1991 Type: ARTICLE Genes: Abstract: Thirteen species of saprobic rhabditid nematodes (11 genera) were identified from samples of compost and casing material collected from mushroom farms in the British Isles. Caenorhabditis elegans, the most frequently found saprobe, was mass-produced monoxenically and its effects on the cultivated mushroom, Agaricus bisporus (strain U3) were studied. C. elegans did not multiply in well-prepared, pasteurised, spawned compost, whereas casing material proved to be a highly suitable environment for its reproduction. An initial casing inoculum of 10^6 nematodes/crate of compost (7.5 kg), caused a significant reduction in mushroom yield. Losses in total mushroom yields of 11%, 20% and 26% were caused by initial inoculum rates of 10^6 , 10^7 and 2 x 10^7 nematodes/create, respectively. Yields were negativelycorrelated with the initial nematode inoculation level and regression equations were derived. The nematode treatments caused fewer mushrooms to be produced and an absence of the uusual distinctive flushing patterns. C. elegans caused considerable deterioration in mushroom quality and characteristic distortion of mushrooms. Individual sporophores were mis-shapen, notched and had brown or violet coloured grills. Up to 3.8%, 6.7% and 10.8% of total weight and 3.5%, 5.4% and 8% of total numbers of mushrooms were distorted at the three highest nematode inoculum rates tested. Weights and numbers of distorted mushrooms were positively correlated with the initial nematode population. C. elegans commonly colonised ------------------- Key: 1431 Medline: 91269320 Authors: Gengyo-Ando K;Kagawa H Title: Single charge change on the helical surface of the paramyosin rod dramatically disrupts thick filament assembly in Caenorhabditis elegans. Citation: Journal of Molecular Biology 219: 429-441 1991 Type: ARTICLE Genes: myo-3 unc-15 Abstract: Charge interactions between alpha-helical coiled-coil proteins have been postulated to determine the alignment of many filamentous proteins, such as myosin heavy-chain rod, paramyosin and alpha- keratin. Here we determined the sequence changes in nine mutations in the unc-15 paramyosin gene of Caenorhabditis elegans, including one nonsense, four missense, one deletion and three suppressor mutations. These mutation sites were located on a molecular model, constructed by optimizing charge interactions between paramyosin rods. Remarkably, single charge reversals (e.g., glutamic acid to lysine) were found that either disrupted or restored filament assembly in vivo. The positions of the mutations within the paramyosin molecule support the models of paramyosin assembly and further suggest that the C-terminal region containing a cluster of five mutations, and a site interacting with it, play a key role in assembly. One amino acid substitution in this C-terminal region, in which there is a "weak spot", led to a loss of reactivity with one monoclonal anti- paramyosin antibody. The results demonstrate how a single amino acid substitution can alter the assembly properties of ------------------- Key: 1432 Medline: 91266922 Authors: Plasterk RHA Title: The origin of footprints of the Tc1 transposon of Caenorhabditis elegans. Citation: EMBO Journal 10: 1919-1925 1991 Type: ARTICLE Genes: dpy-4 dpy-13 mut-5 mut-6 unc-22 vab-9 Abstract: Mutations caused by the Tc1 transposon in Caenorhabditis elegans can revert by loss of the element. Usually the transposon leaves behind a 'footprint'--a few nucleotides of one or both ends of the transposon. Two possible explanations for the footprints are: (i) imprecise excision or (ii) interrupted repair. Here I report that in a diploid animal having a homozygous Tc1 insertion the reversion frequency is approximately 10(-4), and a Tc1 footprint is found; however when the corresponding sequence on the homologous chromosome is wild-type, the reversion frequency is 100 times higher, and the reverted sequence is precise. Apparently the footprint results from incomplete gene conversion from the homologous chromosome, and not from imprecise excision of Tc1. These results support the following model: Tc1 excision leaves a double-strand DNA break, which can be repaired using the homologous chromosome or sister chromatid as a template. In heterozygotes repair can lead to reversion; in homozygotes Tc1 is copied into the 'empty' site, and only rare interrupted repair leads to reversion, hence the 100-fold lower reversion rate and the footprint. ------------------- Key: 1433 Medline: 92174818 Authors: Ellis RE;Horvitz HR Title: Two C. elegans genes control the programmed deaths of specific cells in the pharynx. Citation: Development 112: 591-603 1991 Type: ARTICLE Genes: ced-1 ced-2 ced-3 ces-1 ces-2 ces-3 ces-4 egl-1 him-5 lin-10 eDf6 nDf23 nDf24 nDf25 nDp4 Abstract: The genes ces-1 and ces-2 control the decisions of two cells in the nematode Caenorhabditis elegans to undergo programmed cell death. Mutations that cause a gain of ces-1 function or a reduction of ces-2 function prevent these cells, the sisters of the two pharyngeal NSM neurons, from dying. These mutations do not affect most other cell deaths. Genetic studies indicate that ces-1 and ces-2 affect the fates of the NSM sisters by regulating the genes required for all programmed cell deaths to occur. ------------------- Key: 1434 Medline: 91287793 Authors: Burglin TR;Ruvkun G;Coulson A;Hawkins NC;McGhee JD;Schaller D;Wittman C;Muller F;Waterston RH Title: Nematode homeobox cluster. Citation: Nature 351: 703-703 1991 Type: REVIEW Genes: ceh-11 ceh-13 ceh-15 mab-5 Abstract: Clusters of Antennapedia-like homeobox genes have been found in Drosophila and in vertebrates (see ref. 2 for review) that show a remarkable similarity of organization and expression. Intriguingly, the order of the homeobox genes along the chromosome corresponds to the order of expression domains along the anterior-posterior axis of the animal. A large-scale screening for homeobox-containing genes in the nematode Caenorhabditis elegans did not initially reveal such clusters. But, as the C. elegans map has been further refined, a previously unmapped small contiguous set of cosmid clones (locus No. 38 in ref. 2) containing two homeobox genes, ceh-13 (ref. 4) and ceh-15 (hom-2/3 in ref. 5; C. Kenyon personal communication) has now been located on chromosome III, to the left of the homeobox genes mab-5 (ref. 6) and ceh-11 (refs 4, 7; see figure). These four genes form a cluster of Antennapedia-like homeobox genes that appear to maintain the same anterior-posterior ordering found in flies and ------------------- Key: 1435 Medline: 91359136 Authors: Siddiqui SS;Culotti JG Title: Examination of neurons in wild type and mutants of Caenorhabditis elegans using antibodies to horseradish peroxidase. Citation: Journal of Neurogenetics 7: 193-211 1991 Type: ARTICLE Genes: lin-4 lin-14 lin-21 mab-5 unc-6 unc-13 unc-18 unc-33 unc-44 unc-51 unc-61 unc-71 unc-73 unc-76 unc-86 unc-98 Abstract: Antibodies to horseradish peroxidase (HRP) recognize 27 of 302 neurons and several non-neuronal cells in adult hermaphrodites of the soil nematode Caenorhabditis elegans and can be used to label these cells for cytological analysis in whole animals. The antibodies bind to the anterior members, but not to the posterior members of a set of mechanosensory neurons in wild type animals. Binding to one of the posterior mechanosensory neurons (PVM) occurs when this neuron migrates to an abnormal anterior position in mab-5 mutant animals, suggesting that expression of the epitope recognized by these antibodies is position dependent or that mab-5 mutations transform PVM into AVM intrinsically. The antibodies were used to characterize morphologies of two pairs of lumbar neurons (PHC and PVN) in uncoordinated mutants representing 95 unc genes. PHC and PVN morphologies were normal in most of the unc mutants examined, however, in mutants of 9 unc genes (unc-6, unc-13, unc-33, unc-44, unc-51, unc-61, unc-71, unc-73, and unc-98), misdirected PHC and/or PVN processes were observed at a high frequency. The morphologies of 2 other lumbar neurons, PHA and PHB, were determined previously in these mutants (Hedgecock et al., 1985). Mutations in most, but not all of these 9 unc genes affect the growth of the embryonic lumbar neurons PHA and PHB differently than they affect the growth of the postembryonic lumbar neurons PHC and PVN, indicating that these neurons require different, but overlapping sets of genes for different stages of ------------------- Key: 1436 Medline: 91288538 Authors: Maruyama IN;Brenner S Title: A phorbol ester/diacylglycerol-binding protein encoded by the unc-13 gene of Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 88: 5729-5733 1991 Type: ARTICLE Genes: dpy-5 lin-10 lin-12 unc-13 unc-15 sDf6 Abstract: Mutations in the unc-13 gene cause diverse defects in the nervous system of the nematode Caenorhabditis elegans. Molecular cloning of the gene and sequencing of the cDNA revealed that the product encodes a protein, 1734 amino acids in length, with a central domain with sequence similarity to the regulatory region of protein kinase C. The domain was expressed in Escherichia coli and shown to bind specifically to a phorbol ester in the presence of calcium; diacylglycerol inhibited the binding in a competitive manner. These findings confirm that the unc-13 gene product has binding sites similar to those of protein kinase C and may be a component of an alternative transduction pathway of the diacylglycerol signal to a different effector function in the nervous system. ------------------- Key: 1437 Medline: 92038958 Authors: Schnabel H;Bauer G;Schnabel R Title: Suppressors of the organ-specific differentiation gene pha-1 of Caenorhabditis elegans. Citation: Genetics 129: 69-77 1991 Type: ARTICLE Genes: dpy-18 dpy-20 pha-1 smg-1 smg-2 sup-7 sup-35 sup-36 sup-37 tra-1 unc-32 vab-7 eDf2 eDf6 eDf20 Abstract: The embryonic lethal gene pha-1 of the nematode Caenorhabditis elegans is required for late differentiation and morphogenesis of the pharynx in the developing embryo. Revertants of two temperature- sensitive alleles of pha-1 were isolated with the aim of obtaining mutations in genes that interact with pha-1. By various methods of mutagenesis, chemical, X-ray, transposon, or by spontaneous reversion, 220 recessive revertants were obtained, defining three complementation groups. The largest, sup-35 on linkage group (LG) III, maps close to but is separable from pha-1. This suppressor can exert its effect either maternally or zygotically to allow survival of pha-1(ts) embryos. The other two, sup-36 and sup-37, are required zygotically and map on LGIV and LGV, respectively. We have not noted a phenotype distinguishing any of the suppressors from wild type except for suppression of pha-1. That suppression is the null phenotype of at least sup-35 is indicated by the high frequency of mutation and by the fact that heterozygotes carrying sup-35 and a deficiency spanning the locus are also able to suppress. Five spontaneous mutations in sup-35 were found to be associated ------------------- Key: 1438 Medline: 92038960 Authors: Ellis RE;Jacobson DM;Horvitz HR Title: Genes required for the engulfment of cell corpses during programmed cell death in Caenorhabditis elegans. Citation: Genetics 129: 79-94 1991 Type: ARTICLE Genes: ced-1 ced-2 ced-5 ced-6 ced-7 ced-8 ced-10 nuc-1 sem-4 nDf17 sDf2 sDf64 uDf1 yDf5 Abstract: After programmed cell death, a cell corpse is engulfed and quickly degraded by a neighboring cell. For degradation to occur, engulfing cells must recognize, phagocytose and digest the corpses of dying cells. Previously, three genes were known to be involved in eliminating cell corpses in the nematode Caenorhabditis elegans: ced- 1, ced-2 and nuc-1. We have identified five new genes that play a role in this process: ced-5, ced-6, ced-7, ced-8 and ced-10. Electron microscopic studies reveal that mutations in each of these genes prevent engulfment, indicating that these genes are needed either for the recognition of corpses by other cells or for the initiation of phagocytosis. Based upon our study of double mutants, these genes can be divided into two sets. Animals with mutations in only one of these sets of genes have relatively few unengulfed cell corpses. By contrast, animals with mutations in both sets of genes have many unengulfed corpses. These observations suggest that these two sets of genes are involved in distinct and partially redundant processes that act in the engulfment of cell corpses. ------------------- Key: 1439 Medline: 92038961 Authors: Peters K;McDowall J;Rose AM Title: Mutations in the bli-4 (I) locus of Caenorhabditis elegans disrupt both adult cuticle and early larval development. Citation: Genetics 129: 95-102 1991 Type: ARTICLE Genes: bli-4 dpy-1 dpy-3 dpy-5 dpy-6 dpy-9 dpy-10 dpy-13 dpy-14 dpy-17 dpy-18 lin-14 lin-29 mut-6 rol-6 sqt-3 hDp16 hDp19 sDp2 Abstract: The bli-4 (I) gene of Caenorhabditis elegans had been previously defined by a single recessive mutation, e937, which disrupts the structure of adult-stage cuticle causing the formation of fluid- filled separations of the cuticle layers, or blisters. We report the identification of 11 new alleles of bli-4, all early larval lethals, including an allele induced by transposon mutagenesis. Nine of the lethal alleles failed to complement the blistered phenotype of e937; two alleles, s90 and h754, complement e937. The complementing alleles arrested development somewhat later than the noncomplementing alleles, which blocked just prior to hatching. We conclude that bli-4 is a complex locus with an essential function late in embryogenesis. We investigated the blistered phenotype of e937 through interactions with other mutations that alter worm morphology or cuticle structure. Recessive and dominant epistasis of several dumpy mutations over the blistered phenotype was observed. Using two heterochronic mutations that alter the developmental stage at which adult cuticle is expressed, we observed that adult worms that lack an adult-stage cuticle could not express blisters. However, late larval worms that expressed the adult cuticle did not express blisters either. It seems likely that the presence of the adult cuticle is necessary, but not sufficient, for blister expression. Blistering resulting from e937 is more severe in trans to null alleles, indicating that e937 is hypomorphic. We postulate that the adult-specific blistering is due to an altered or reduced function of bli-4 gene product in the adult cuticle.(ABSTRACT TRUNCATED ------------------- Key: 1440 Medline: Authors: Schierenberg E Title: Genealogy, geometry and genes: Experimental embryology of Caenorhabditis elegans. Citation: "Experimental Embryology in Aquatic Plants and Animals." Marthy H (ed), Plenum Press, NY. 195: 163-176 1990 Type: REVIEW Genes: Abstract: The free-living nematode Caenorhabditis elegans is a small and unpretentious organism. It may thrive unnoticed in the cabbage patch in your backyard or the flower pot on your balcony. In their natural habitat soil nematodes live in a thin film of water. In the laboratory C. elegans dwells on Petri dishes in the liquid film on the top of an agar layer, but can also be grown in liquid culture. As in other nematodes the liquid-filled body cavity (pseudocoelom) functions as a hydroskeleton. When the worm dries out, the hydroskeleton collapses and the animal inevitably dies. In a loose sense C. elegans may therefore be considered as a kind of aquatic animal. Because of this and because C. elegans is particularly well suited to the study of certain aspects of development, the following chapter is included in this book on Experimental Embryology of Aquatic Organisms. The intention of this contribution is to serve as an introduction and as a reference source rather than as a complete summary of present knowledge in the field. As indicated by the title, the review will focus on embryonic cell lineages, pattern formation in the embryo and the analysis of mutants affecting early ------------------- Key: 1441 Medline: 91317865 Authors: Francis R;Waterston RH Title: Muscle cell attachment in Caenorhabditis elegans. Citation: Journal of Cell Biology 114: 465-479 1991 Type: ARTICLE Genes: Abstract: In the nematode Caenorhabditis elegans, the body wall muscles exert their force on the cuticle to generate locomotion. Interposed between the muscle cells and the cuticle are a basement membrane and a thin hypodermal cell. The latter contains bundles of filaments attached to dense plaques in the hypodermal cell membranes, which together we have called a fibrous organelle. In an effort to define the chain of molecules that anchor the muscle cells to the cuticle we have isolated five mAbs using preparations enriched in these components. Two antibodies define a 200-kD muscle antigen likely to be part of the basement membrane at the muscle/hypodermal interface. Three other antibodies probably identify elements of the fibrous organelles in the adjacent hypodermis. The mAb IFA, which reacts with mammalian intermediate filaments, also recognizes these structures. We suggest that the components recognized by these antibodies are likely to be involved in the transmission of tension from the muscle cell to the ------------------- Key: 1442 Medline: 92037191 Authors: Schedin P;Hunter CP;Wood WB Title: Autonomy and nonautonomy of sex determination in triploid intersex mosaics of C. elegans. Citation: Development 112: 863-879 1991 Type: ARTICLE Genes: fem-2 her-1 mab-3 mab-5 tra-1 vit-1 vit-2 vit-3 vit-4 vit-5 vit-6 mnDp9 mnDp25 Abstract: The primary sex-determining signal in Caenorhabditis elegans is the ratio of X chromosomes to sets of autosomes (X/A ratio), normally 1.0 in hermaphrodites (XX) and 0.5 in males (XO). XX triploids (X/A = 0.67) are males, but if these animals carry a partial duplication of the X chromosome such that X/A approximately equal to 0.7, they develop as intersexes that are sexually mosaic. We have analyzed these mosaics using Nomarski microscopy and in situ hybridization to obtain information on whether sex determination decisions can be made independently in different cells and tissues, and when these commitments are made. The observed patterns of male and female cells in individual animals indicate that sex determination decisions can be influenced by anterior-posterior position and that sex determination decisions can be made as late as the third larval stage of postembryonic development. Although these decisions clearly can be made independently in different lineages, they show substantial biases toward one sex or the other in individual animals. We interpret these results to suggest that sex determination in C. ------------------- Key: 1443 Medline: 92050388 Authors: Hosono R;Kamiya Y Title: Additional genes which result in an elevation of acetylcholine levels by mutations in Caenorhabditis Citation: Neuroscience Letters 128: 243-244 1991 Type: REVIEW Genes: cha-1 unc-3 unc-10 unc-11 unc-13 unc-17 unc-18 unc-41 unc-63 unc-64 Abstract: Four mutant genes (unc-17, unc-18, unc-41 and unc-13) have been identified that result in abnormal accumulation of acetylcholine (ACh). We have now identified 3 more such genes (unc-63, unc-11 and unc-64). In addition to the abnormal accumulation of ACh, mutants in these 7 genes possess common phenotypes in locomotion, resistance to inhibitors of acetylcholinesterase (AChE) and in post-embryonic development. These results suggest that the 7 genes are involved in some related functions. ------------------- Key: 1444 Medline: 92001545 Authors: Schnabel R Title: Cellular interactions involved in the determination of the early C. elegans embryo. Citation: Mechanisms of Development 34: 85-100 1991 Type: ARTICLE Genes: glp-1 mel-21 Abstract: Classical work implied that early nematode embryogenesis is completely mosaic. This view was lately challenged by the demonstration that in C. elegans an early interaction has to occur to induce the production of muscle from a blastomere. Here, early embryonic blastomeres were inactivated by laser microsurgery. The cell lineages of irradiated embryos were compared to those of intact embryos. It is shown that one blastomere, MS, is required for the specification of mesodermal pharyngeal fates and another blastomere, P2, for the specification of hypodermal fates from the descendants of the AB blastomere, whereas the proper specification of the nervous system requires the presence of both. The irradiation of a third blastomere shows that interactions also occur within the ectoderm. I propose that the body plan of the C. elegans embryo may be established by two primary signals followed by secondary interactions. The suggested mechanisms are reminiscent of those involved in amphibian development. ------------------- Key: 1445 Medline: 92045638 Authors: Rankin CH Title: Interactions between two antagonistic reflexes in the nematode Caenorhabditis elegans. Citation: Journal of Comparative Physiology 169A: 59-67 1991 Type: ARTICLE Genes: Abstract: 1. Antagonistic reflexes that use the same final common path cannot be activated simultaneously; as a consequence one reflex often inhibits the expression of the other. Results of experiments with two antagonistic reflexes in Caenorhabditis elegans showed that the reflex inhibition in this simple animal is the same as in more complex organisms. Thus C. elegans can serve as a model system for studying the neural mechanisms underlying these behavioral patterns. 2. In adult C. elegans tail-touch normally elicits forward movement, while tap normally elicits backward movement. When tail-touch is delivered 1 s before a tap, reversals to the tap are inhibited and the magnitude of any reversal that does occur is reduced. 3. The relative magnitude of the 2 stimuli, tail-touch and tap, affects the amount of inhibition observed. 4. The effectiveness of tail-touch as an inhibitory stimulus can be varied as a result of experience. Habituating the response to tail-touch decreased the inhibition of reversal to tap following a tail-touch. 4. The tail-touch induced inhibition of reversal to tap diminishes over an interval of at least 10 s; however, following the inhibition an enhancement of responding to tap is seen. 6. Inhibition of reversal to tap is present in worms of all stages of development including newly hatched worms. ------------------- Key: 1446 Medline: 92076000 Authors: Ruvkun G;Wightman B;Burglin T;Arasu P Title: Dominant gain-of-function mutations that lead to misregulation of the C. elegans heterochronic gene lin-14, and the evolutionary implications of dominant mutations in pattern-for.. Citation: Development S1: 47-54 1991 Type: REVIEW Genes: lin-4 lin-12 lin-14 lin-28 lin-29 Abstract: The heterochronic gene lin-14 controls the temporal sequence of developmental events in the C. elegans postembryonic cell lineage. It encodes a nuclear protein that is normally present in most somatic cells of late embryos and L1 larvae but not in later larval stages or adults. Two lin-14 gain-of-function mutations cause an inappropriately high level of the lin-14 nuclear protein late in development. These mutations delete 3' untranslated sequences from the lin-14 mRNAs and identify a negative regulatory element that controls the formation of the lin-14 protein temporal gradient. The 21 kb lin-14 gene contains 13 exons that are differentially spliced to generate two lin-14 protein products with variable N-terminal regions and a constant C-terminal region. No protein sequence similarity to any proteins in various databases was found. The temporal and cellular expression patterns of lin-14 protein accumulation is altered by the mutations in the heterochronic genes lin-4 and lin-28. The lin-4 gene is required to down-regulate lin-14 protein levels during the mid-L1 stage. The lin-4 gene product could be the trans-acting factor that binds to the negative regulatory element in the lin-14 3' untranslated region. In contrast, the lin-28 gene activity positively regulates lin-14 protein levels during early L1. Thus, these genes act antagonistically to regulate the lin-14 temporal switch. The normal down-regulation of lin-14 within 10 h of hatching is not determined by the passage of time per se, but rather is triggered when feeding induces post-embryonic development. Loss of lin-28 gene activity causes precocious down-regulation of lin-14 protein levels before feeding, whereas loss of lin-4 gene activity does not affect the level of lin-14 protein before feeding. These data suggest that to trigger the lin-14 temporal switch, the lin-4 gene is up-regulated after feeding which in turn down-regulates lin-14 via its 3' untranslated region. We speculate on the evolutionary implications of ------------------- Key: 1447 Medline: 91342618 Authors: Cully DF;Paress PS Title: Solubilization and characterization of a high-affinity ivermectin binding site from Caenorhabditis elegans. Citation: Molecular Pharmacology 40: 326-332 1991 Type: ARTICLE Genes: Abstract: Ivermectin is a member of the avermectin family of compounds that are used to treat helminth and arthropod diseases in humans, domestic animals, and plants. A membrane-bound high affinity ivermectin binding site was extracted from Caenorhabditis elegans with the nonionic detergent 1-O-n-octyl-beta-D-glucopyranoside. The free- living nematode C. elegans is highly sensitive to the avermectins and was used as a model of parasitic nematodes. The membrane-bound and detergent-solubilized ivermectin binding sites are stable and exhibit high affinity binding, with dissociation constants of 0.11 nM and 0.20 nM, respectively. The maximum binding of [3H]ivermectin is 0.54 pmol/mg of membrane protein and 0.66 pmol/mg of detergent-soluble protein. Kinetic analysis of ivermectin binding shows that the ivermectin binding sites form a slowly reversible complex with ivermectin. The rates of dissociation of [3H]ivermectin with the solubilized and membrane-bound binding sites are 0.005 min-1 and 0.006 min-1, respectively. The association rate of the soluble binding site is 0.053 nM-1 min-1, slightly slower than that observed for the membrane-bound site, 0.074 nM-1 min-1. To characterize the ivermectin binding site, competition experiments were performed by inhibiting [3H]ivermectin binding with several avermectin derivatives and the neurotransmitter gamma-aminobutyric acid (GABA). The order of potency was 22,23-dihydroavermectin B1a monosaccharide greater than 22,23-dihydroavermectin B1a aglycone greater than 3,4,8,9,10,11,22,23- octahydro B1 avermectin for both the membrane-bound and NOG-soluble binding sites. GABA did not compete with ivermectin binding, although it has been suggested that ivermectin acts at the GABA-gated chloride channel in some invertebrate systems. Optimum ivermectin binding and assay conditions have been determined. The detergent-soluble ivermectin binding site appears to be negatively charged and has a pl of 4.0 and an apparent Mr in Triton X-100 micelles of 340,000. Detergent solubilization of a high affinity ivermectin binding site will enable the subsequent purification and characterization of a putative site of ivermectin action. ------------------- Key: 1448 Medline: 91340768 Authors: Pettitt J;Kingston IB Title: The complete primary structure of a nematode a2(IV) collagen and the partial structural organization of its Citation: Journal of Biological Chemistry 266: 16149-16156 1991 Type: ARTICLE Genes: Abstract: We have isolated and characterized cDNA and genomic DNA clones which encode an a2(IV) collagen chain from the parasitic nematode Ascaris suum. In addition we have determined, by nucleic acid sequence analysis, the structural organization of approximately two-thirds of the gene. This analysis has shown that the gene contains at least 15 introns, and those that have been characterized range in size from 141 to 854 base pairs. The derived protein sequence contains 1763 amino acids and includes a putative 26-amino acid signal sequence. The collagenous triple-helical region contains 17 interruptions, many of which occur in the same positions as those in the human a1(IV) and a2(IV) chains. Comparison of the genomic DNA sequence with the cDNA sequence has revealed the presence of a sequence within the gene which appears to be an intact and normal exon that is not represented in our cDNA sequence. The presence of this putative exon raises the possibility that the A. suum a2(IV) collagen gene may undergo alternative splicing. ------------------- Key: 1449 Medline: 92139973 Authors: Chitwood DJ;Lusby WR Title: Metabolism of plant sterols by nematodes. Citation: Lipids 26: 619-627 1991 Type: ARTICLE Genes: Abstract: Parasitic nematodes do not biosynthesize sterols de novo and therefore possess a nutritional requirement for sterol, which must be obtained from their hosts. Consequently, the metabolism of phytosterols by plant-parasitic nematodes is an important process with potential for selective exploitation. The sterol compositions of several species of plant-parasitic nematodes were determined by capillary gas chromatography-mass spectrometry and compared with the sterol compositions of their hosts. Saturation of the phytosterol nucleus was the major metabolic transformation performed by the root-knot nematodes Meliodogyne arenaria and M. incognita and the corn root lesion nematode, Pratylenchus agilis. In addition to saturation, the corn cyst nematode, Heterodera zeae, dealkylated its host sterols at C-24. Because free-living nematodes can be cultured in sterol-defined artificial medium, they have been successfully used as model organsisms for investigaion of sterol metabolism in plant-parasitic nematodes. Major pathways of phytosterol metabolism in Caenorhabditis elegans, Turbatrix aceti and Panagrellus redivivus included C-24 dealkylation and 4a-methylation (a pathway unique to nematodes). C. elegans and T. aceti introduced double bonds at C-7, and T. aceti and P. redivivus saturated the sterol nucleus similarly to the plant-parasitic species examined. Several azasteroids and long-chain dimethylalkylamines inhibited growth and development of C. elegans and also the delta24-sterol reductase enzyme system involved in the nematode C-24 dealkylation pathway. ------------------- Key: 1450 Medline: 92099309 Authors: Abad P;Quiles C;Tares S;Piotte C;Castagnone-Sereno P;Abadon M;Dalmasso A Title: Sequences homologous to Tc(s) transposable elements of Caenorhabditis elegans are widely distributed in the phylum Nematoda. Citation: Journal of Molecular Evolution 33: 251-258 1991 Type: ARTICLE Genes: unc-22 Abstract: To have a better understanding of the evolutionary history of mobile elements within the nematodes, we examined the distribution and the conservation of homologues to transposable elements from Caenorhabditis elegans (Tc1, Tc2, Tc3, Tc4, Tc5, and FB1) in 19 nematode species belonging to the class Secernentea. Our results show that Tc1 elements display a distribution restricted to the family Rhabditidae with poor conservation. The Tc2 and FB1 homologous elements have the same patchy distribution within the Rhabditidae. They were only found in Caenorhabditis and in Teratorhabditis. The Tc3 element is widely distributed among nematode species. Tc3 homologous elements are present in the majority of the Rhabditidae but also in two genera within the family Panagrolaimidae, and in Bursaphelenchus, which belongs to the order Aphelenchida. Tc4 and Tc5 homologues show the most limited distribution of all tested elements, being strictly limited to C. elegans. These data indicate that in some cases, the distribution of transposable elements in the nematode cannot be explained by strict vertical transmission. The distribution of Tc3, Tc4, and Tc5 suggests that horizontal transmission may have occurred between reproductively isolated species during their evolutionary history. ------------------- Key: 1451 Medline: 92062034 Authors: Coulson A;Kozono Y;Lutterbach B;Shownkeen R;Sulston J;Waterston R Title: YACs and the C. elegans genome. Citation: BioEssays 13: 413-417 1991 Type: REVIEW Genes: Abstract: During the past decade, it has become apparent that it is within our grasp to understand fully the development and functioning of complex organisms. It is widely accepted that this undertaking must include the elucidation of the genetic blueprint - the genome sequence - of a number of model organisms. As a prelude to the determination of these sequences, clone-based physical maps of the genomes of a number of multicellular animals and plants are being constructed. Yeast artificial chromosome (YAC) vectors, by virtue of their relatively unbiased cloning capabilities and capacity to carry large inserts, have come to play a central role in the construction of these maps. The application of YACs to the physical map of the Caenorhabditis elegans genome has enabled cosmid clone 'islands' to be linked together in an efficient manner. The long-range continuity has improved the linkage between the genetic and physical maps, greatly increasing its utility. Since the genome can be represented by a relatively small number of YACs, it has been possible to make replica filters of genomically ordered YACs available to the ------------------- Key: 1452 Medline: 91342668 Authors: Spieth J;Shim YH;Lea K;Conrad R;Blumenthal T Title: elt-1, an embryonically expressed Caenorhabditis elegans gene homologous to the GATA transcription factor family. Citation: Molecular and Cellular Biology 11: 4651-4659 1991 Type: ARTICLE Genes: elt-1 Abstract: The short, asymmetrical DNA sequence to which the vertebrate GATA family of transcription factors binds is present in some Caenorhabditis elegans gene regulatory regions: it is required for activation of the vitellogenin genes and is also found just 5' of the TATA boxes of tra-2 and the msp genes. In vertebrates GATA-1 is specific to erythroid lineages, whereas GATA-2 and GATA-3 are present in multiple tissues. In an effort to identify the trans-acting factors that may recognize this sequence element in C. elegans, we used a degenerate oligonucleotide to clone a C. elegans homolog to this gene. We call this gene elt-1 (erythrocytelike transcription factor). It is single copy and specifies a 1.75-kb mRNA that is present predominantly, if not exclusively, in embryos. The region of elt-1 encoding two zinc fingers is remarkably similar to the DNA- binding domain of the vertebrate GATA-binding proteins. However, outside of the DNA-binding domains the amino acid sequences are quite divergent. Nevertheless, introns are located at identical or nearly identical positions in elt-1 and the mouse GATA-1 gene. In addition, elt-1 mRNA is trans-spliced to the 22-base untranslated leader, SL1. The DNA upstream of the elt-1 TATA box contains eight copies of the GATA recognition sequence within the first 300 bp, suggesting that elt-1 may be autogenously regulated. Our results suggest that the specialized role of GATA-1 in erythroid gene expression was derived after separation of the nematodes and the line that led to the vertebrates, since C. elegans lacks an erythroid ------------------- Key: 1453 Medline: 91351288 Authors: Mango SE;Maine EM;Kimble J Title: Carboxy-terminal truncation activates glp-1 protein to specify vulval fates in Caenorhabditis elegans. Citation: Nature 352: 811-815 1991 Type: ARTICLE Genes: glp-1 lin-12 smg-1 Abstract: The glp-1 and lin-12 genes encode homologous transmembrane proteins that may act as receptors for cell interactions during development. The glp-1 product is required for induction of germ-line proliferation and for embryogenesis. By contrast, lin-12 mediates somatic cell interactions, including those between the precursor cells that form the vulval hypodermis (VPCs). Here we analyse an unusual allele of glp-1, glp-1(q35), which displays a semidominant multivulva phenotype (Muv), as well as the typical recessive, loss-of- function Glp phenotypes (sterility and embryonic lethality). We find that the effects of glp-1(q35) on VPC development mimic those of dominant lin-12 mutations, even in the absence of lin-12 activity. The glp-1(q35) gene bears a nonsense mutation predicted to eliminate the 122 C-terminal amino acids, including a ProGluSerThr (PEST) sequence thought to destabilize proteins. We suggest that the carboxy terminus bears a negative regulatory domain which normally inactivates glp-1 in the VPCs. We propose that inappropriate glp- 1(q35) activity can substitute for lin-12 to determine vulval fate, perhaps by driving the VPCs to proliferate. ------------------- Key: 1454 Medline: 91348397 Authors: Beh CT;Ferrari DC;Chung MA;McGhee JD Title: An acid phosphatase as a biochemical marker for intestinal development in the nematode Caenorhabditis elegans. Citation: Developmental Biology 147: 133-143 1991 Type: ARTICLE Genes: bli-1 bli-2 clr-1 dpy-10 dpy-11 dpy-13 emb-13 fer-1 ges-1 lon-2 mei-1 mel-26 pho-1 pho-2 pho-3 unc-4 unc-32 unc-52 unc-85 unc-104 mnC1 mnDf30 Abstract: We describe an acid phosphatase enzyme (EC 3.1.3.2) that is localized to the intestine of the nematode Caenorhabditis elegans and that should serve as a convenient biochemical marker for gut differentiation. In adult worms, acid phosphatase activity is located along the edge of the gut lumen in the vicinity of the intestinal brush border. All but the anterior six cells of the intestine stain for phosphatase activity; the nonstaining cells all descend from the Ea(l/r)(a/p)a cells. Acid phosphatase activity is low in oocytes and early embryos but increases substantially when embryos reach late morphogenesis stage; this increase corresponds to the appearance of a major band of acid phosphatase activity detectable on isoelectric focusing gels. We designate this band as the product of the pho-1 gene. The pattern of acid phosphatase expression in several embryonic mutants suggests that pho-1 expression in the developing intestine is lineage autonomous. We induced an isoelectric focusing variant in the pho-1 enzyme and used this to map the pho-1 locus about 1.5 map units to the left of center of chromosome II. We purified the pho-1 enzyme to homogeneity (6500-fold purification; 4% recovery of activity); the pho-1 acid phosphatase is a homodimeric glycoprotein with a subunit molecular weight of 55,000 Da. This paper establishes a new experimental system with which to investigate the molecular basis of lineage-specific gene expression during C. elegans development. ------------------- Key: 1455 Medline: 91282280 Authors: Morgan PG;Sedensky MM;Meneely PM Title: The genetics of response to volatile anesthetics in Caenorhabditis elegans. Citation: Annals of the New York Academy of Sciences 625: 524-531 Type: REVIEW Genes: unc-1 unc-7 unc-9 unc-24 unc-79 unc-80 Abstract: Understanding the molecular basis of behavior is one of the fundamental challenges in biology. We are interested in the molecular nature of the response of the nervous system to volative anesthetics. This response must be governed by the same constraints that govern other aspects of the nervous system. We are using a simple genetic approach to understand this problem. ------------------- Key: 1456 Medline: 91323673 Authors: Sebastiano M;Lassandro F;Bazzicalupo P Title: cut-1, a Caenorhabditis elegans gene coding for a dauer-specific noncollagenous component of the cuticle. Citation: Developmental Biology 146: 519-530 1991 Type: ARTICLE Genes: cut-1 daf-8 sqt-1 mnDf76 mnDf77 Abstract: We have molecularly identified a new gene of Caenorhabditis elegans that codes for a component of the cuticle. The gene has been physically mapped on LGII near the locus sqt-1. The structure and the sequence of the gene have been determined and antisera have been raised against parts of the protein produced as fusions in Escherichia coli. By transcription analysis, and by the use of specific antisera, we have determined that this gene is expressed specifically during dauer larva formation. In extracts of worms completing the dauer transformation the product of this gene migrates in sodium dodecyl sulfate acrylamide gels with an apparent molecular mass of 40 kDa. By immunofluorescence we have determined that it is a component of the cuticles of dauer larvae. It forms a ribbon approximately 2 microns wide running along the lateral lines underneath the alae. Once it is assembled in the cuticle the protein becomes insoluble even in the presence of strong detergents and reducing agents in a manner that is similar to that described for the noncollagenous, insoluble residue of nematode cuticles called cuticlins; therefore, we have named the gene cut-1 for cuticlin 1. cut-1 represents the first gene for a noncollagenous component of C. elegans cuticle that has ------------------- Key: 1457 Medline: 92076822 Authors: Sternberg PW Title: Control of cell lineage and cell fate during nematode development. Citation: "Current Topics in Developmental Biology." Bode HR (ed), Academic Press. 25: 177-225 1991 Type: REVIEW Genes: glp-1 gly-1 let-23 let-60 lin-1 lin-2 lin-3 lin-4 lin-7 lin-8 lin-9 lin-10 lin-11 lin-12 lin-13 lin-14 lin-15 lin-17 lin-18 lin-22 lin-28 lin-29 lin-35 lin-36 lin-37 lin-38 mab-5 mec-3 pal-1 unc-6 unc-86 Abstract: The striking invariance of nematode development has inspired and intrigues developmental biologists for 100 years (e.g., Boveri, 1892; zur Strassen, 1892; Pai, 1928). We now know that this invariant development is the result of both intrinsic and extrinsic controls over cell fate. Highly reproducible cell interactions occur since most cells do not migrate, and are thus always subject to signals from the same neighbors. Some of the very features that make the nematode Caenorhabditis elegans an attractive organism with which to study development - its small cell number and essentially invariant development- make one wonder how relevant studies of this nematode will be to animals whose development is not invariant: To what extent will conclusions based on studies with C. elegans apply to organisms with a large number of cells and variable development? One can answer that nematode development is not wholly invariant. One can also answer this question of relevance by arguing that molecular mechanisms are conserved even if developmental phenomena are not, and what one learns about a particular gene product in one organism can be extended to other organisms. This "model system" argument is certainly meritorious, and the success of yeast molecular genetics in unraveling cell biological problems might well be repeated by C. elegans molecular genetics for problems specific to metazoans. Moreover, since nematodes diverged from the their coelomate relatives prior to the arthropod - chordate split, nematodes afford useful molecular biological comparisons for genes conserved between, for example, insects and mammals. Caenorhabditis elegans will provide such a comparison, given the intensive molecular biological studies driven by the genome-mapping project (Coulson et al., 1986, 1988; reviewed by Robertson, ------------------- Key: 1458 Medline: 91332108 Authors: Barstead RJ;Waterston RH Title: Vinculin is essential for muscle function in the nematode. Citation: Journal of Cell Biology 114: 715-724 1991 Type: ARTICLE Genes: deb-1 myo-3 sup-7 Abstract: Actin filaments in the body wall muscle of the nematode Caenorhabditis elegans are attached to the sarcolemma through vinculin-containing structures called dense bodies, Z-line analogues. To investigate the in vivo function of vinculin, we executed a genetic screen designed to recover mutations in the region of the nematode vinculin gene, deb-1. According to four independent criteria, two of the isolated mutants were shown to be due to alterations in the deb-1 gene. First, antibody staining showed that the mutants had reduced levels of vinculin. Second, the sequence of each mutant gene was altered from that of wild type, with one mutation altering a conserved splice sequence and the other generating a premature amber stop codon. Third, the amber mutant was suppressed by the sup-7 amber suppressor tRNA gene. Finally, injection of a cloned wild type copy of the gene rescued the mutant. Mutant animals lacking vinculin arrested development as L1 larvae. In such animals, embryonic elongation was interrupted at the twofold length, so that the mutants were shorter than wild type animals at the same stage. The mutants were paralyzed and had disorganized muscle, a phenotype consistent with the idea that vinculin is essential for muscle function in the nematode. ------------------- Key: 1459 Medline: 92097210 Authors: Barstead RJ;Kleiman L;Waterston RH Title: Cloning, sequencing, and mapping of an alpha-actinin gene from the nematode Caenorhabditis elegans. Citation: Cell Motility and the Cytoskeleton 20: 69-78 1991 Type: ARTICLE Genes: atn-1 myo-3 ctDf1 eDf1 Abstract: The dense-bodies in the body wall muscle of the nematode Caenorhabditis elegans function to anchor the actin thin filaments to the adjacent sarcolemma. One of the major components of the dense- bodies is the actin-binding protein alpha-actinin. To facilitate a genetic analysis of alpha-actinin, we have cloned a cDNA encoding the nematode protein, identified its position on the nematode physical map, and developed a unique PCR based approach to test the position of the cloned gene relative to known genetic deletions. The peptide sequence deduced from the cDNA shows that, apart from a few exceptional regions, the nematode protein shows strong similarity to other known alpha-actinins. Its position on the genetic map shows that none of the known muscle affecting mutations identified in C. elegans are in this alpha-actinin gene. This gene has been given the name atn-1 (alpha-actinin-1). ------------------- Key: 1460 Medline: 92017961 Authors: Hartman P;Reddy J;Svendsen B-A Title: Does trans-lesion synthesis explain the UV-radiation resistance of DNA synthesis in C. elegans embryos? Citation: Mutation Research-DNA Repair 255: 163-173 1991 Type: ARTICLE Genes: rad-1 rad-2 rad-3 rad-7 Abstract: Over 10-fold larger fluences were required to inhibit both DNA synthesis and cell division in wild-type C. elegans embryos as compared with other model systems or C. elegans rad mutants. In addition, unlike in other organisms, the molecular weight of daughter DNA strands was reduced only after large, superlethal fluences. The molecular weight of nascent DNA fragments exceeded the interdimer distance by up to 19-fold, indicating that C. elegans embryos can replicate through non-instructional lesions. This putative trans- lesion synthetic capability may explain the refractory nature of UV radiation on embryonic DNA synthesis and nuclear division in C. elegans. ------------------- Key: 1461 Medline: Authors: Howells RE;Johnstone I Title: Caenorhabditis elegans: A model for parasitic nematodes. Citation: Parasitology Today 7: 224-226 1991 Type: ARTICLE Genes: dyf-1 lev-1 unc-29 unc-39 Abstract: The free-living nematode Caenorhabditis elegans offers many advantages as an experimental system and extensive similarities in overall structure and development exist between it and parasitic nematodes. The purpose of the meeting held at Broadway, 17-20 February 1991, with the financial support of the Wellcome Trust, was to stimulate interaction between schools of nematologists. ------------------- Key: 1462 Medline: 91375435 Authors: Haack H;Hodgkin J Title: Tests for parental imprinting in the nematode Caenorhabditis elegans. Citation: Molecular & General Genetics 228: 482-485 1991 Type: ARTICLE Genes: him-6 Abstract: The mutation him-6 (e1423) leads to generalized chromosomal nondisjunction during meiosis in oogenesis and spermatogenesis of C. elegans. As a result, gametes nullisomic or disomic for each of the six chromosomes occur at appreciable frequency. Crosses utilizing marked him-6 strains were used to generate and identify exceptional euploid progeny which had received both homologues of a marked autosome either from the male parent or from the female parent. Examples of all ten possible exceptions were identified and found to be viable and fertile. These results (together with previous data for the X chromosome) indicate that major chromosomal imprinting effects do not occur during gametogenesis in this organism. ------------------- Key: 1463 Medline: 91375463 Authors: Arena JP;Liu KK;Paress PS;Cully DF Title: Avermectin-sensitive chloride currents induced by Caenorhabditis elegans RNA in Xenopus oocytes. Citation: Molecular Pharmacology 40: 368-374 1991 Type: ARTICLE Genes: Abstract: Avermectins are a family of potent broad-spectrum anthelmintic compounds, which bind with high affinity to membranes isolated from the free-living nematode Caenorhabditis elegans. Binding of avermectins is thought to modulate chloride channel activity, but the exact mechanism for anthelmintic activity remains to be determined. In this report, the properties of an avermectin-sensitive membrane current were evaluated in Xenopus laevis oocytes that were injected with poly(A)+ RNA from C. elegans. In such oocytes, avermectins increased inward membrane current at a holding potential of -80 mV. An avermectin analog without anthelmintic activity had no effect. Half-maximal activation of current was observed with 90 nM avermectin. The reversal potential for avermectin-sensitive current was -19.3 +/- 1.9 mV, and it shifted with external chloride, as expected for a chloride current. Avermectin increased membrane current in C. elegans-injected oocytes that were also injected with the Ca2+ chelator ethylene glycol bis(beta-aminoethyl ether)- N,N,N',N'-tetraacetic acid. The response to avermectin was greatest in the 1.0-2.5-kilobase class of size-fractionated C. elegans poly(A)+ RNA. Oocytes that responded to avermectin were insensitive to gamma-aminobutyric acid and ------------------- Key: 1464 Medline: 92011787 Authors: Hu E;Rubin CS Title: Casein kinase II from Caenorhabditis elegans. Cloning, characterization, and developmental regulation of the gene encoding the beta subunit. Citation: Journal of Biological Chemistry 266: 19796-19802 1991 Type: ARTICLE Genes: Abstract: Complementary DNAs encoding the beta subunit of casein kinase II (CKII beta) from the nematode Caenorhabditis elegans were cloned and sequenced. The predicted beta subunit polypeptide comprises 234 amino acid residues and has a Mr of 26,452. CKII beta is not homologous with other types of proteins. In synchronously developing C. elegans the abundance of the 1.3-kilobase mRNA for CKII beta varies in parallel with the level of mRNA encoding the catalytic subunit (alpha) of CKII. Thus, the developmental expression of CKII subunits is controlled coordinately and pretranslationally. CKII beta and CKII alpha mRNAs are enriched 5-10-fold in C. elegans embryos relative to their concentrations at several other stages of nematode development. A 3.8-kilobase pair segment of C. elegans DNA that contains the CKII beta gene and an extensive 5'-flanking region was cloned and sequenced. The CKII beta gene is divided into 6 exons by introns ranging from 49 to 533 base pairs in length. The first exon encodes 88 nucleotides of 5'-untranslated mRNA. Exon 2 (72 base pairs) contains the initiator Met codon and only 5 additional codons. Exons 3-6 encode 52, 63, 64, and 49 amino acid residues, respectively. The 5' terminus of CKII beta mRNA is modified post-transcriptionally by trans-splicing with a leader sequence of 22 nucleotides. The CKII beta gene was mapped to a position on C. elegans chromosome 2 that is in close proximity to the lin-11 gene. ------------------- Key: 1465 Medline: 92021020 Authors: Li PM;Reichert J;Freyd G;Horvitz HR;Walsh CT Title: The LIM region of a presumptive Caenorhabditis elegans transcription factor is an iron-sulfur- and zinc-containing metallodomain. Citation: Proceedings of the National Academy of Sciences USA 88: 9210-9213 1991 Type: ARTICLE Genes: lin-11 mec-3 Abstract: The cysteine-rich LIM motif is highly conserved between invertebrates and mammals. This motif shows similarity both to proteins that bind zinc and to ferredoxins, which contain iron-sulfur clusters. Two tandem copies of the LIM motif are found in a number of presumptive transcription factors, including the protein product of the Caenorhabditis elegans cell-lineage gene lin-11. To investigate the possible metal-binding properties of the LIM region of the lin-11 protein, we expressed and purified a 151-amino acid peptide containing the tandem LIM motifs. The purified peptide binds both zinc (two atoms per protein molecule) and iron (as a redox-active iron-sulfur cluster, with four atoms of iron and four atoms of inorganic sulfide per protein molecule). These observations suggest that the LIM motif is a metallodomain that might function in a redox- sensitive regulation of transcription. ------------------- Key: 1466 Medline: 92082452 Authors: Williamson VM;Long M;Theodoris G Title: Isolation of Caenorhabditis elegans mutants lacking alcohol dehydrogenase activity. Citation: Biochemical Genetics 29: 313-323 1991 Type: ARTICLE Genes: Abstract: Alcohol dehydrogenase (ADH) and the genes encoding this enzyme have been studied intensively in a broad range of organisms. Little, however, has been reported on ADH in the free-living nematode Caenorhabditis elegans. Extracts of wild-type C. elegans contain ADH activity and display a single band of activity on a native polyacrylamide gel. Reaction rate for alcohol oxidation is more rapid with higher molecular weight alcohols as substrate than with ethanol. Primary alcohols are preferred to secondary alcohols. C. elegans is sensitive to allyl alcohol, a compound that has been used to select for ADH-null mutants of several organisms. Allyl alcohol-resistant mutant strains were selected from ethylmethanesulfonate (EMS)- mutagenized nematode populations. ADH activity was measured in extracts from eight of these strains and was found to be low or nondetectable. These results form a basis for molecular and genetic characterization of ADH expression in ------------------- Key: 1467 Medline: 92009172 Authors: Wightman B;Burglin TR;Gatto J;Arasu P;Ruvkun G Title: Negative regulatory sequences in the lin-14 3' untranslated region are necessary to generate a temporal switch during Caenorhabditis elegans development. Citation: Genes & Development 5: 1813-1824 1991 Type: ARTICLE Genes: lin-4 lin-14 lin-29 Abstract: The heterchronic gene lin-14 controls the temporal sequence of developmental events in the Caenorhabditis elegans postembryonic cell lineage. It encodes a nuclear protein that normally is present in most somatic cells of late embryos and L1 larvae but is absent at later stages. Two lin-14 gain-of-function mutations delete 3'- untranslated sequences causing an inappropriately high level of the lin-14 nuclear protein late in development. These mutations identify a negative regulatory element that controls the formation of the lin- 14 protein temporal gradient. The 21-kb lin-14 gene is differentially spliced to generate three lin-14 transcripts that encode protein products with variable amino-terminal regions and a constant carboxy- terminal region. The sequence of the gene revealed no protein sequence similarity to any proteins in various data bases. ------------------- Key: 1468 Medline: 92009173 Authors: Arasu P;Wightman B;Ruvkun G Title: Temporal regulation of lin-14 by the antagonistic action of two other heterochronic genes, lin-4 and lin-28. Citation: Genes & Development 5: 1825-1833 1991 Type: ARTICLE Genes: lin-4 lin-14 lin-28 lin-29 Abstract: Heterochronic genes form a regulatory pathway that controls the temporal sequence of the Caenorhabditis elegans postembryonic cell lineage. One of these genes, lin-14, encodes a nuclear protein that constitutes a temporal developmental switch. During wild-type development, lin-14 protein is abundant during early larval stage 1 (L1) to specific L1-specific cell lineages but is nearly undetectable at L2 and later stages to specify L2-specific and later cell lineages. To determine the roles played by other genes in executing this temporal switch, we have analyzed how lin-14 expression is regulated by other heterochronic genes. lin-4 is required to down- regulate lin-14 protein levels during the L1 stage, whereas lin-28 positively regulates lin-14 protein levels. The lin-4 gene product is a candidate for interacting with the negative regulatory element in the 3'-untranslated region of lin-14. lin-29 mutations do not affect lin-14 protein levels, consistent with lin-29 acting downstream of lin-14. Switching off lin-14 expression during the L1 stage is not triggered by the passage of time per se but, rather, is normally dependent on feeding or the feeding-dependent initiation of postembryonic cell division. ------------------- Key: 1469 Medline: 92146253 Authors: Hope IA Title: Promoter trapping in Caenorhabditis elegans. Citation: Development 113: 399-408 1991 Type: ARTICLE Genes: rol-6 Abstract: A screen of gene expression patterns has been developed for the nematode Caenorhabditis elegans. Promoter-reporter gene fusions were constructed in vitro by ligating C. elegans genomic DNA fragments upstream of a lacZ gene. Patterns of beta-galactosidase expression were examined by histochemical staining of C. elegans lines transformed with the constructs. beta-galactosidase expression depended on translational fusion, so constructs were assayed in large pools to expedite detection of the low proportion that were active. Expression in a variety of cell types and temporal patterns was observed with different construct pools. The most striking expression patterns were obtained when the beta-galactosidase activity was localized to subcellular structures by the C. elegans portion of the fusion protein. The active constructs of three selected pools were identified subsequently by an efficient combinatorial procedure. The genomic locations of the DNA fragments from the active constructs were determined and appear to define previously uncharacterized genetic loci. ------------------- Key: 1470 Medline: 92146262 Authors: Fire A;Albertson D;Harrison SW;Moerman DG Title: Production of antisense RNA leads to effective and specific inhibition of gene expression in C. elegans muscle. Citation: Development 113: 503-514 1991 Type: ARTICLE Genes: myo-3 unc-22 unc-54 Abstract: We have used an antisense strategy to effectively disrupt the expression of two genes encoding myofilament proteins present in C. elegans body wall muscles. DNA segments from the unc-22 and unc-54 genes have been placed in reverse orientation in vectors designed to produce RNA in body wall muscles. When the resulting plasmids are injected into oocytes, progeny with defects in muscle function are produced. These animals have phenotypes consistent with reduction and/or elimination of function of the gene to which antisense RNA has been produced: twitching and disorganization of muscle filaments for the unc-22 antisense constructs and lack of muscle tone, slow movement, and egg laying defects for the unc-54 antisense constructs. A fraction of the affected animals transmit the defective-muscle trait to subsequent generations. In these cases the transforming DNA is present at high copy number and cosegregates with the observed muscle defects. We have examined several of the unc-22 antisense plasmid transformed lines to determine the mechanistic basis for the observed phenotypes. The RNA product of the endogenous unc-22 locus is present at normal levels and this RNA is properly spliced in the region homologous to the antisense RNA. No evidence for modification of this RNA by deamination of adensoine to inosine was found. In affected animals the level of protein product from the endogenous unc-22 locus is greatly reduced. Antisense RNA produced from the transforming DNA was detected and was much more abundant than 'sense' RNA from the endogenous locus. These data suggest that the observed phenotypes result from interference with a late step in gene expression, such as transport into the cytoplasm or translation. ------------------- Key: 1471 Medline: 92146263 Authors: Baird SE;Fitch DHA;Kassem IAA;Emmons SW Title: Pattern formation in the nematode epidermis: determination of the arrangement of peripheral sense organs in the C. elegans mail tale. Citation: Development 113: 515-526 1991 Type: ARTICLE Genes: mab-18 mab-20 mab-21 sma-2 sma-3 Abstract: The developmental process that determines the arrangement of ray sensilla in the Caenorhabditis elegans male tail has been studied. It is shown that the adult arrangement of rays is determined by the placement of ray cells at specific sites in the epidermis of the last larval (L4) stage. Placement of ray cells at specific epidermal sites results from the generation of neurons and support cells in the epidermis near to their final positions, and the subsequent refinement of these positions by an active mechanism involving specific cellular associations. Positions of ray cells and adjacent epidermal cells have been studied during ray development by means of indirect immunofluorescence staining with an antibody to a cell junctional antigen. Mutations are described in six genes that alter the adult arrangement of the rays, frequently resulting in fusion of rays. Changes in the adult pattern of rays in mutants appear to result from prior changes in the epidermal positions of ray cells, and for two mutants it is suggested that this may be due to the inappropriate clustering of processes from neurons and support cells of adjacent rays. Development of the wild-type arrangement of rays appears to require the specification of molecular differences between the rays that affect the specificity of ------------------- Key: 1472 Medline: 92029622 Authors: Ofulue EN;Candido EPM Title: Molecular cloning and characterization of the Caenorhabditis elegans elongation factor 2 gene (eft-2). Citation: DNA and Cell Biology 10: 603-611 1991 Type: ARTICLE Genes: eft-2 Abstract: A Caenorhabditis elegans lambda ZAP cDNA library was screened using a fragment amplified from highly conserved regions of the mammalian and Drosophila elongation factor 2 (EF-2). Two types of cDNA clones were obtained, corresponding to two mRNA species with 3'-untranslated regions of 60 and 115 nucleotides, both encoding identical polypeptides. Sequence analysis of these clones and comparisons with hamster and Drosophila EF-2 sequences suggests that they encode C. elegans EF-2. Clone pCef6A, encoding the entire C. elegans EF-2 mRNA sequence including 45 nucleotides of 5'-untranslated region, contains a 2,556-bp open reading frame which predicts a polypeptide of 852 amino acid residues (Mr 94,564). The deduced amino acid sequence is greater than 80% identical to that of mammalian and Drosophila EF-2. Conserved sequence segments shared among a variety of GTP-binding proteins are found in the amino-terminal region. The carboxy-terminal half contains segments unique to EF-2 and its prokaryotic homolog, EF- G, as well as the histidyl residue which is ADP-ribosylated by diphtheria toxin. The C. elegans protein contains a 12-amino-acid insertion between positions 90 and 100, and a 13-amino-acid deletion between positions 237 and 260, relative to hamster EF-2. Partial sequencing of a genomic clone encoding the entire C. elegans EF-2 gene (named eft-2) has so far revealed two introns of 48 and 44 bp following codons Gln-191 and Gln-250, respectively. Southern and Northern blot analyses indicate that eft-2 is a single-copy gene and encodes a 3-kb mRNA species which is present throughout nematode development. ------------------- Key: 1473 Medline: 92118714 Authors: Hodgkin J Title: The interactive worm - Review of the 8th international C. elegans meeeting, June 1-5, 1991, Madison, WI, USA Citation: New Biologist 3: 951-954 1991 Type: REVIEW Genes: egl-5 fem-3 her-1 glp-1 let-23 let-60 lin-3 lin-12 lin-14 lin-39 mab-5 mec-3 odr-1 odr-2 pie-1 sdc-1 sdc-2 sdc-3 skn-1 tra-1 tra-2 unc-4 unc-5 unc-6 unc-25 unc-49 unc-86 unc-104 xol-1 Abstract: The biennial meeting on the nematode Caenorhabditis elegans, which has been held at Cold Spring Harbor on six previous occasions, this year grew too big for the motels of Long Island and moved westward to Madison, where over 500 participants spent 4 packed days discussing recent discoveries and future prospects. Gone are the days when research on this tiny worm seemed like a cottage industry, pursued only by a small group of devotees. However, the holistic approach to the nematode still prevails, as demonstrated by the absence of parallel sessions at the meeting. Genomics, genetics, neurobiology, cell biology, biochemistry, and development remain inextricably interwoven for most of the scientists studying C. elegans. Appropriately enough, biological interactions proved to be a leitmotiv of the 1991 meeting. ------------------- Key: 1474 Medline: 92090695 Authors: Johnsen RC;Baillie DL Title: Genetic analysis of a major segment [LGV(left)] of the genome of Caenorhabditis elegans. Citation: Genetics 129: 735-752 1991 Type: ARTICLE Genes: dpy-11 emb-29 ges-1 let-34 let-60 let-83 let-326 let-329 let-330 let-331 let-332 let-334 let-335 let-337 let-338 let-339 let-340 let-341 let-342 let-343 let-344 let-345 let-346 let-347 let-348 let-349 let-350 let-401 let-402 let-403 let-404 let-405 let-406 let-407 let-408 let-409 let-410 let-411 let-412 let-413 let-414 let-415 let-416 let-417 let-418 let-419 let-421 let-422 let-423 let-424 let-425 let-426 let-428 let-429 let-430 let-431 let-436 let-437 let-438 let-439 let-440 let-441 let-442 let-443 let-444 let-445 let-447 let-448 let-449 let-450 let-452 let-453 let-454 let-455 let-456 let-458 let-459 let-460 let-461 let-462 let-463 let-464 let-466 let-467 let-468 let-469 let-470 let-471 let-472 let-473 let-474 let-475 let-476 let-477 let-478 let-479 let-480 let-481 mec-1 unc-23 unc-46 unc-62 unc-68 unc-70 Abstract: From 10,900 F1 progeny of ethyl methanesulfonate (EMS)-mutagenized Caenorhabditis elegans nematodes, we isolated 194 lethal mutations on the left arm of LGV, a region balanced by the reciprocal translocation of eT1. The analysis of 166 of those mutations resulted in the identification of one deficiency and alleles of 78 genes including 38 new genes, thus increasing the number of identified essential genes to 101. We estimate that there are a minimum of 120 essential genes in this region, which comprises approximately 7% of the recombinational distance, although only about 4.2% of the genes, in C. elegans. We calculate that there are a minimum of 2850 essential genes in the genome. The left arm of LGV has two recombinational gene clusters separated by a high-recombination and/or essential gene-sparse region. One gene in this region, let- 330, is the largest EMS target on the left arm of LGV, with twice as many alleles (16) as the next most EMS-mutable genes, let-332 and rol- 3. Another gene in the sparse region, lin-40, and the region near lin- 40 are major targets for Tc1 mobilization-induced mutagenesis. The analysis of essential genes in large regions should help to define C. elegans in terms of all its genes and aid in the understanding of the relationship of genome structure to genome function. ------------------- Key: 1475 Medline: 92100756 Authors: Hodgkin J;Barnes TM Title: More is not better: brood size and population growth in a self-fertilizing nematode. Citation: Proceedings of the Royal Society of London B 246: 19-24 Type: ARTICLE Genes: fem-3 fog-2 tra-2 tra-3 Abstract: The normal form of the nematode Caenorhabditis elegans is a self- fertilizing hermaphrodite, which produces from the same germ-line tissue first a limited number of sperm and then a larger number of oocytes. Self-progeny brood sizes are determined by the number of sperm, and most of the oocytes remain unfertilized. Therefore it might seem selectively advantageous to increase the number of sperm, and hence the size of the brood. A mutation that leads to a 50% increase in sperm production allows a comparison of population growth rates between the wild type (mean brood 327 progeny) and the mutant (mean brood 499 progeny). Wild-type populations grow faster, as measured by food consumption, indicating that increased brood size is not advantageous. The mutant appears to be at a disadvantage because the additional spermatogenesis leads to a delay in the onset of oogenesis, and hence to an increase in the minimum generation time. In support of the notion of an optimal brood size, it was found that different natural isolates of this species have self-fertilities similar to that of the standard laboratory strain, in the range 250- 350 progeny per worm. ------------------- Key: 1476 Medline: 92051313 Authors: Moerman DG;Kiff JE;Waterston RH Title: Germline excision of the transposable element Tc1 in C. elegans. Citation: Nucleic Acids Research 19: 5669-5672 1991 Type: ARTICLE Genes: mut-6 unc-22 unc-54 Abstract: We have examined eight germline revertants generated by the excision of Tc1 from a site within the unc-22 gene of Caenorhabditis elegans. A rich variety of rearrangements accompanied Tc1 excision at this site, including transposon 'footprints', deletions of sequences flanking the insertion site and direct nontandem duplications of flanking DNA. With only modest modification the double-strand gap repair model for transposition, recently proposed by Engles and coworkers (Cell 62: 515-525 1990), can explain even the most complex of these rearrangements. In light of this model rearrangements of the target site accompanying transposition/excision may not be the end result of imprecise excision of the element. Instead, these rearrangements may be the result of imprecise repair of the double- strand gap by the host replication and repair machinery. Sequences surrounding an insertion site influence the fidelity of gap repair by this machinery. This may lead to a number of possible resolutions of a double-strand gap as documented here for a Tc1 site in ------------------- Key: 1477 Medline: 92146931 Authors: Capowski EE;Martin P;Garvin C;Strome S Title: Identification of grandchildless loci whose products are required for normal germ-line development in the nematode Caenorhabditis elegans. Citation: Genetics 129: 1061-1072 1991 Type: ARTICLE Genes: dpy-11 glp-1 lon-2 mes-1 mes-2 mes-3 mes-4 mes-5 mes-6 par-2 rol-1 unc-2 arDf-1 eDf18 eDf19 itDf2 sDf4 hDp20 sDp2 Abstract: To identify genes that encode maternal components required for development of the germ line in the nematode Caenorhabditis elegans, we have screened for mutations that confer a maternal-effect sterile or "grandchildless" phenotype: homozygous mutant hermaphrodites produced by heterozygous mothers are themselves fertile, but produce sterile progeny. Our screens have identified six loci, defined by 21 mutations. This paper presents genetic and phenotypic characterization of four of the loci. The majority of mutations, those in mes-2, mes-3 and mes-4, affect postembryonic germ-line development; the progeny of mutant mothers undergo apparently normal embryogenesis but develop into agametic adults with 10-1000-fold reductions in number of germ cells. In contrast, mutations in mes-1 cause defects in cytoplasmic partitioning during embryogenesis, and the resulting larvae lack germ-line progenitor cells. Mutations in all of the mes loci primarily affect the germ line, and none disrupt the structural integrity of germ granules. This is in contrast to grandchildless mutations in Drosophila melanogaster, all of which disrupt germ granules and affect abdominal as well ------------------- Key: 1478 Medline: 92201023 Authors: Wood WB;Kershaw D Title: Handed asymmetry, handedness reversal and mechanisms of cell fate determination in nematode embryos. Citation: Ciba Foundation Symposia 162: 143-164 1991 Type: REVIEW Genes: Abstract: Embryos of the nematode Caenorhabditis elegans exhibit left-right asymmetry with an invariant handedness. The embryonic cell lineage is asymmetrical: although the animal is generally bilaterally symmetrical with only a few left-right asymmetries, many of ts contrlaterally analogous cells arise via different lineages on the two sides of the embryo. Larvae and adults also exhibit left-right asymmetries with a handedness that is normally invariant. The frequency of animals with opposite handedness was increased among the progeny of adults exposed to the mutagen ethyl methanesulphonate and among animals that developed from embryos treated in early cleavage with chitinase to destroy the egg shell. Reversal of embryonic handedness was accomplished directly by micormanipulation at the 6-cell stage, resulting in mirror-image but otherwise normal development into healthy, fertile animals with all the usual left-right asymmetries reversed. This demonstrates that (1) the handedness of cell positions in the 6-cell embryo dictates handedness throughout development; (2) at this stage the pair of anterior blastomeres on the right is equivalent to the pair on the left; and (3) the extensive differences in fates of lineally homologous cells on the two sides of the animal must be dictated by cellular interactions, most of which are likely to occur early in embryogenesis and appear to have been conserved in widely diverged nematode species. ------------------- Key: 1479 Medline: 92037560 Authors: Mello CC;Kramer JM;Stinchcomb D;Ambros V Title: Efficient gene transfer in C. elegans: Extrachromosomal maintenance and integration of transforming sequences. Citation: EMBO Journal 10: 3959-3970 1992 Type: ARTICLE Genes: rol-6 sup-7 Abstract: We describe a dominant behavioral marker, rol-6(su-1006), and an efficient microinjection procedure which facilitate the recovery of Caenorhabditis elegans transformants. We use these tools to study the mechanism of C.elegans DNA transformation. By injecting mixtures of genetically marked DNA molecules, we show that large extrachromosomal arrays assemble directly from the injected molecules and that homologous recombination drives array assembly. Appropriately placed double-strand breaks stimulated homologous recombination during array formation. Our data indicate that the size of the assembled transgenic structures determines whether or not they will be maintained extrachromosomally or lost. We show that low copy number extrachromosomal transformation can be achieved by adjusting the relative concentration of DNA molecules in the injection mixture. Integration of the injected DNA, though relatively rare, was reproducibly achieved when single-stranded oligonucleotide was co- injected with the double-stranded DNA. ------------------- Key: 1480 Medline: 92064663 Authors: Hemmer RM;Donkin SG;Chin KJ;Grenache DG;Bhatt H;Politz SM Title: Altered expression of an L1-specific, O-linked cuticle surface glycoprotein in mutants of the nematode Caenorhabditis elegans. Citation: Journal of Cell Biology 115: 1237-1247 1991 Type: ARTICLE Genes: srf-2 srf-3 Abstract: Mouse mAb M38 was used in indirect immunofluorescence experiments to detect a stage-specific antigen on the surface of the first larval stage (L1) of the free-living nematode Caenorhabditis elegans, and to detect alterations in the apparent expression of this antigen in two distinct classes of C. elegans mutants. In previously described srf-2 and srf-3 mutants (Politz S. M., M. T. Philipp, M. Estevez, P.J. O'Brien, and K. J. Chin. 1990. Proc. Natl. Acad. Sci. USA. 87:2901- 2905), the antigen is not detected on the surface of any stage. Conversely, in srf-(yj43) and other similar mutants, the antigen is expressed on the surface of the first through the fourth (L4) larval stages. To understand the molecular basis of these alterations, the antigen was characterized in gel immunoblotting experiments. After SDS-PAGE separation and transfer to nitrocellulose, M38 detected a protein antigen in extracts of wild-type L1 populations. The antigen was sensitive to digestion by Pronase and O-glycanase (endo-alpha-N- acetylgalactosaminidase), suggesting that it is an O-linked glycoprotein. This antigen was not detected in corresponding extracts of wild-type L4s or srf-2 or srf-3 L1s, but was detected in extracts of srf-(yj43) L4s. The antigen-defective phenotype of srf-3 was epistatic to the heterochronic mutant phenotype of srf-(yj43) in immunofluorescence tests of the srf-3 srf-(yj43) double mutant, suggesting that srf-(yj43) causes incorrect regulation of a pathway of antigen formation that requires wild-type srf-3 activity. ------------------- Key: 1481 Medline: 92075268 Authors: Bargmann CI;Horvitz HR Title: Chemosensory neurons with overlapping functions direct chemotaxis to multiple chemicals in C. elegans. Citation: Neuron 7: 729-742 1991 Type: ARTICLE Genes: che-2 lin-17 Abstract: The functions of the 11 classes of exposed chemosensory neurons of C. elegans were tested by killing cells with a laser microbeam. One pair of neurons, the ASE neurons, is uniquely important for chemotaxis: killing the ASE neurons greatly reduced chemotaxis to cAMP, biotin, Cl-, and Na+. Additional chemosensory function is distributed among several other cell types. Thus, 3 pairs of chemosensory neurons (ADF, ASG, and ASI) contribute to a residual response to cAMP, biotin, Cl-, and Na+ after ASE is killed. Chemotaxis to lysine similarly depends on the partly redundant functions of 4 pairs of chemosensory neurons (ASE, ASG, ASI, and ASK). The combined activity of several neuron types that act in parallel might increase the fidelity of chemotaxis. ------------------- Key: 1482 Medline: 92120509 Authors: Vowels JJ;Thomas JH Title: Genetic analysis of chemosensory control of dauer formation in Caenorhabditis elegans. Citation: Genetics 130: 105-123 1992 Type: ARTICLE Genes: che-2 che-3 che-10 che-11 che-13 daf-1 daf-2 daf-3 daf-4 daf-5 daf-6 daf-7 daf-8 daf-9 daf-10 daf-11 daf-12 daf-14 daf-15 daf-16 daf-18 daf-20 daf-22 osm-1 osm-3 osm-5 osm-6 Abstract: Dauer larva formation in Caenorhabditis elegans is controlled by chemosensory cells that respond to environmental cues. Genetic interactions among mutations in 23 genes that affect dauer larva formation were investigated. Mutations in seven genes that cause constitutive dauer formation, and mutations in 16 genes that either block dauer formation or result in the formation of abnormal dauers, were analyzed. Double mutants between dauer-constitutive and dauer- defective mutations were constructed and characterized for their capacity to form dauer larvae. Many of the genes could be interpreted to lie in a simple linear epistasis pathway. Three genes, daf-16, daf- 18 and daf-20, may affect downstream steps in a branched part of the pathway. Three other genes, daf-2, daf-3 and daf-5, displayed partial or complex epistasis interactions that were difficult to interpret as part of a simple linear pathway. Dauer-defective mutations in nine genes cause structurally defective chemosensory cilia, thereby blocking chemosensation. Mutations in all nine of these genes appear to fall at a single step in the epistasis pathway. Dauer-constitutive mutations in one gene, daf-11, were strongly suppressed for dauer formation by mutations in the nine cilium-structure genes. Mutations in the other six dauer-constitutive genes caused dauer formation despite the absence of functional chemosensory endings. These results suggest that daf-11 is directly involved in chemosensory transduction essential for dauer formation, while the other Daf-c genes play roles ------------------- Key: 1483 Medline: 92320587 Authors: Sternberg PW;Horvitz HR Title: Signal transduction during C. elegans vulval induction. Citation: Trends in Genetics 7: 366-371 1991 Type: REVIEW Genes: let-23 let-60 lin-1 lin-15 lin-34 Abstract: Nematode proteins related to the human epidermal growth factor receptor and Ras proteins act in a common pathway to control cell fates in response to an inductive signal. Analysis of these gene products during C. elegans vulval induction allows detailed study of their function in the context of a developing organism. ------------------- Key: 1484 Medline: 92339360 Authors: Stern MJ;Horvitz HR Title: A normally attractive cell interaction is repulsive in 2 C. elegans mesodermal cell migration mutants. Citation: Development 113: 797-803 1991 Type: ARTICLE Genes: dig-1 egl-15 egl-17 Abstract: In wild-type Caenorhabditis elegans hermaphrodites, two bilaterally symmetric sex myoblasts (SMs) migrate anteriorly to flank the precise center of the gonad, where they divide to generate the muscles required for egg laying (J. E. Sulston and H. R. Horvitz (1977) Devl Biol. 56, 110-156). Although this migration is largely independent of the gonad, a signal from the gonad attracts the SMs to their precise final positions (J. H. Thomas, M. J. Stern and H. R. Horvitz (1990) Cell 62, 1041-1052). Here we show that mutations in either of two genes, egl-15 and egl-17, cause the premature termination of the migrations of the SMs. This incomplete migration is caused by the repulsion of the SMs by the same cells in the somatic gonad that are the source of the attractive signal in wild-type animals. ------------------- Key: 1485 Medline: 92084093 Authors: Han M;Sternberg PW Title: Analysis of dominant negative mutations of the Caenorhabditis elegans let-60 ras gene. Citation: Genes & Development 5: 2188-2198 1991 Type: ARTICLE Genes: let-23 let-60 nDp5 Abstract: The let-60 gene of Caenorhabditis elegans controls the choice between vulval and hypodermal differentiation in response to an inductive signal from the gonad. let-60 encodes a ras protein that acts downstream of the let-23 receptor tyrosine kinase in a signal transduction pathway. Dominant-negative mutations of let-60 [let- 60(dn)] cause a reduction of the gene activity in let-60(dn)/+ heterozygotes and a vulva-less mutant phenotype. We have found that nine let-60(dn) mutations cause replacements of conserved residues. Four are in two novel positions; others are in positions known previously to cause dominant-negative mutations in mammalian cells. The locations of these lesions suggest that they disrupt the ability of the ras protein to bind guanine nucleotides. Four let-60(dn) mutant genes were introduced into wild-type animals in the form of extrachromosomal arrays and were found to generate three dominant phenotypes--lethality, vulva-less, or multivulva--depending on gene dose and alleles. The dominant lethality caused by high-dose transgenic let-60(dn) genes suggests a toxic effect of these mutant genes in early development. The dominant-negative effects of these mutations in heterozygotes are likely to be caused by competition between let-60(dn) and let-60(+) protein for a positive regulator. All let-60(dn) mutations interfere with let-60(+) activity, but some alleles have partial constitutive activity, suggesting that the ability to interact with the activator is separable from the ability to exert a physiological effect (stimulation of vulval differentiation). These dn mutations might be useful for interfering with ras-mediated signal transduction pathways ------------------- Key: 1486 Medline: 92084094 Authors: Way JC;Wang L;Run JQ;Wang A Title: The mec-3 gene contains cis-acting elements mediating positive and negative regulation in cells produced by asymmetric cell division in Caenorhabditis elegans. Citation: Genes & Development 5: 2199-2211 1991 Type: ARTICLE Genes: mec-3 unc-86 Abstract: The homeo box-containing genes mec-3 and unc-86 are necessary to specify the fate of a defined set of mechanoreceptors in Caenorhabditis elegans. Previous experiments have shown that mec-3 expression can be divided into two phases: initial synthesis mediated in part by unc-86, and continued synthesis that requires mec-3 itself. We now identify sequences that have been conserved during Caenorhabditis evolution and are necessary for establishment, maintenance, and repression of mec-3 expression. Upstream of the start codon for the mec-3-coding sequence are four segments (regions I-IV) of 71, 29, 28, and 24 bp, which are almost identical between C. elegans and Caenorhabditis vulgarensis. Region I is the only conserved sequence that effects establishment of mec-3 synthesis. Maintenance of mec-3 expression is mediated primarily by region II. Repression appears to be controlled by several segments: Mutation of region III, region IV, and parts of region I in a mec-3-lacZ fusion results in beta-galactosidase expression in some non-mec-3-expressing sisters of mec-3-positive cells. These results indicate that the mec- 3 5' region contains target sequences that mediate a genetic switch between alternative fates expressed by sister cells in a stereotyped cell lineage. ------------------- Key: 1487 Medline: 92232380 Authors: Ellis RE;Yuan J;Horvitz HR Title: Mechanisms and functions of cell death. Citation: Annual Review of Cell Biology 7: 663-698 1991 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-9 ced-10 ces-1 ces-2 deg-1 egl-1 lin-24 lin-33 mec-4 mec-6 Abstract: The processes of cell division and cell death interact to generate the proper numbers and types of cells during development and to maintain this balance in the mature animal. The view that some cells die as a normal part of both development and homeostasis was established more than forty years ago. The precise function that naturally-occurring cell death plays, the manner in which it is regulated, and the mechanisms by which it occurs are currently subjects of intense research. Naturally occurring cell death is found throughuot the animal kingdom. In vertebrates, cell deaths have been observed in almost all tissues and have been studied most extensively in the developing nervous system and in the immune system. Cell death also affects many different tissues during invertebrate development. In nematodes, neurons, muscle cells, epithelial cells, intestinal cells, and gonadal cells all can die during normal development. Both muscle cell death and neuronal cell death have been extensively analyzed in moths. The deaths of muscle pioneer cells and of neurons have been observed in grasshoppers. In leeches, unneeded segmental founder cells die, as do some developing neurons. Naturally-occurring cell death has also been observed in the coelenterate Hydra. For historical reasons many terms have been used to describe naturally-occurring deaths. We refer to these deaths as "programmed cell deaths" to distinguish them from pathological deaths, which are not part of an animal's developmental program and which appear to occur by distinct mechanisms. Because we study cell deaths that occur in the nematode Caenorhabditis elegans, we first describe below what is known about cell death in nematodes. Next, we briefly review studies of cell death in other animals. Finally, we compare these examples and discuss common features that might underlie the functions that cell death serves during development and homeostasis and the mechanisms by which cell death occurs. ------------------- Key: 1488 Medline: Authors: Niebur E;Erdos P Title: Theory of the locomotion of nematodes. Citation: Biophysical Journal 60: 1132-1146 1991 Type: ARTICLE Genes: Abstract: We develop a model of the undulatory locomotion of nematodes, in particular that of Caenorhabditis elegans, based on mechanics. The model takes into account the most important forces acting on a moving worm and allows the computer simulation of a creeping nematode. These forces are produced by the interior pressure in the liquid-filled body cavity, the elasticity of the cuticle, the excitation of certain sets of muscles and the friction between the body and its support. We propose that muscle excitation patterns can be generated by stretch receptor control. By solving numerically the equations of motion of the model of the nematode, we demonstrate that these muscle excitation patterns are suitable for the propulsion of the animal. ------------------- Key: 1489 Medline: 92155864 Authors: Russell GJ;Lacey E Title: Temperature dependent binding of mebendazole to tubulin in benzimidazole-susceptible and -resistant strains of Trichostrongylus colubriformis and Caenorhabditis elegans. Citation: International Journal for Parasitology 21: 927-934 1991 Type: ARTICLE Genes: Abstract: The binding of [3H]mebendazole ([3H]MBZ) to tubulin in benzimidazole- susceptible (BZ-S) and benzimidazole-resistant (BZ-R) strains of Trichostrongylus colubriformis and Caenorhabditis elegans was examined in order to investigate the biochemical changes to tubulin that result in BZ resistance in parasitic and free-living nematodes. In both species the extent of [3H]MBZ binding to tubulin was significantly reduced in the BZ-R strain compared with the BZ-S strain. The decrease in [3H]MBZ binding in the BZ-R strain of each species was the result of a significant reduction in the amount of charcoal stable [3H]MBZ-tubulin complexes and was not related to a change in the association constant of the [3H]MBZ-tubulin interaction. [3H]MBZ binding to tubulin was temperature dependent, reaching maximum levels at 37 degrees C in BZ-S T. colubriformis and 10 degrees C in BZ-R T. colubriformis. Both the BZ-S and BZ-R strains of C. elegans displayed maximum [3H]MBZ binding at 4 degrees C. Resistance ratios derived from the amount of [3H]MBZ binding in the BZ-S and BZ-R strains and in vitro development assays demonstrated that the temperature dependence and extent of drug binding was indicative of BZ resistance status and was species specific in the BZ- S isolates. These results indicate that biochemical differences exist in the binding of benzimidazole carbamates to tubulin in nematode species, and suggest that the susceptibility of the parasitic nematodes to the benzimidazole anthelmintics is the result of a unique high affinity and/or high capacity interaction of benzimidazole carbamates with tubulin. ------------------- Key: 1490 Medline: 92255262 Authors: Lambie EJ;Kimble J Title: Genetic control of cell interactions in nematode development. Citation: Annual Review of Genetics 25: 411-436 1991 Type: REVIEW Genes: dpy-1 dpy-2 dpy-3 dpy-7 dpy-8 dpy-9 dpy-10 glp-1 her-1 lag-1 lag-2 let-23 let-60 let-461 lin-1 lin-2 lin-3 lin-7 lin-8 lin-9 lin-10 lin-12 lin-13 lin-15 lin-34 mab-5 pal-1 sel-3 sqt-1 tra-1 tra-2 Abstract: Cell interactions are vital to the regulation of cell division, differentiation, and pattern formation during the development of most multicellular creatures. The nematode Caenorhabditis elegans is no exception to this rule. Like other metazoans, this small worm relies heavily on cell interactions during development. With the powerful genetics of C. elegans and its relatively simple anatomy, researchers have been able to delineate the genetic mechanisms regulating cell interactions with an unparralleled degree of precision. In addition, as the analysis of cell fate regulation in C. elegans has advanced to the molecular level, it has merged to a remarkable degree with the rapidly expanding field of signal transduction biochemistry, which has been intensively studied in vertebrate cells. The conjunction of these two areas of research is certain to enhance our understanding of the mechanisms, regulation, and evolution of cell interactions during development. In this review, we emphasize those interactions in C. elegans that have been best characterized genetically. These include examples of both induction and lateral signaling. Induction occurs between separate tissues, with one tissue regulating the fate of another, whereas lateral signaling occurs within a single tissue and results in the adoption of distinct fates by cells with equivalent developmental potential. In addition to our discussion of the genetics of these better characterized interactions, we briefly mention other cell interactions and other genetic controls that promise to provide special insight into how cell interactions ------------------- Key: 1491 Medline: 92263525 Authors: Driscoll M;Chalfie M Title: Developmental and abnormal cell death in C. elegans. Citation: Trends in Neurosciences 15: 15-19 1992 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-10 ces-1 ces-2 deg-1 egl-1 lin-24 lin-33 mec-4 mec-6 nuc-1 Abstract: Genetic analysis in Caenorhabditis elegans has identified several genes that function in normal developmental death as well as genes that can mutate to cause inappropriate cell death. The processes whereby some of these abnormal deaths occur depend on genes that participate in normal programmed cell death; others occur by an independent mechanism whereby mutation of members of a gene family leads to cell lysis. Molecular characterization of these 'death' genes in C. elegans is beginning to provide insight into the normal and aberrant mechanisms of cell death. ------------------- Key: 1492 Medline: 92114965 Authors: Salser SJ;Kenyon C Title: Activation of a C. elegans Antennapedia homolog in migrating cells controls their direction of migration. Citation: Nature 355: 255-258 1992 Type: ARTICLE Genes: mab-5 Abstract: Anterior-posterior patterning in insects, vertebrates and nematodes involves members of conserved Antennapedia-class homeobox gene clusters (HOM-C) that are thought to give specific body regions their identities. The effects of these genes on region-specific body structures have been described extensively, particularly in Drosophila, but little is known about how HOM-C genes affect the behaviours of cells that migrate into their domains of function. In Caenorhabditis elegans, the Antennapedia-like HOM-C gene mab-5 not only specifies postembryonic fates of cells in a posterior body region, but also influences the migration of mesodermal and neural cells that move through this region. Here we show that as one neuroblast migrates into this posterior region, it switches on mab-5 gene expression; mab-5 then acts as a developmental switch to control the migratory behaviour of the neuroblast descendants. HOM-C genes can therefore not only direct region-specific patterns of cell division and differentiation, but can also act within migrating cells to programme region-specific ------------------- Key: 1493 Medline: Authors: Politz SM;Philipp M Title: Caenorhabditis elegans as a model for parasitic nematodes - A focus on the cuticle. Citation: Parasitology Today 8: 6-12 1992 Type: REVIEW Genes: col-1 cut-1 cut-2 srf-1 srf-2 srf-3 Abstract: The phylum Nematoda consists of over half a million species of worms that inhabit astoundingly diverse environments. Nematodes can live as obligatory parasites of plants and animals, or alternate a parasitic with a free-living life style. The fact that the vast majority of species are strictly free living often surprises parasitology students, for obviously the highest research priorities in this field have involved parasites of medical, veterinary and agricultural importance. Here Samuel Politz and Mario Philipp contend that some basic questions concerning the biology of the parasite cuticle can be investigated more easily and in greater depth in the free-living nematode Caenorhabditis elegans than in the parasites themselves. ------------------- Key: 1494 Medline: 92155169 Authors: Plasterk RHA;Groenen JTM Title: Targeted alterations of the Caenorhabditis elegans genome by transgene instructed DNA double strand break repair following Tc1 excision. Citation: EMBO Journal 11: 287-290 1992 Type: ARTICLE Genes: unc-22 Abstract: Excision of a Tc1 transposon of Caenorhabditis elegans is thought to leave a DNA double strand break. We report here that sequence polymorphisms in a transgenic DNA template are copied into the corresponding chromosomal gene upon excision of Tc1 from the chromosome. This shows that the double strand DNA break resulting from Tc1 excision is repaired with the extrachromosomal DNA as template and that sequences flanking the break can be replaced by sequences from the transgene. Transgene instructed break repair provides a method for the targeted introduction of precise alterations into the Caenorhabditis elegans genome. ------------------- Key: 1495 Medline: 92294247 Authors: Hartman PS;Marshall A Title: Inactivation of wild-type and rad mutant Caenorhabditis elegans by 8-methoxypsoralen and near ultraviolet Citation: Photochemistry and Photobiology 55: 103-111 1992 Type: ARTICLE Genes: rad-1 rad-2 rad-3 rad-7 Abstract: Survival of wild-type and four radiation-sensitive (rad) mutants of the nematode Caenorhabditis elegans was determined after near-UV irradiation in the presence of 8-methoxypsoralen (8-MOP). Three sets of inactivation profiles were generated for each strain by irradiating synchronous populations of either early embryos, late embryos or first-stage larvae (L1s). Late embryos were consistently the most sensitive. Curiously, none of the four rad mutants were even moderately hypersensitive. Split-dose experiments indicated that DNA- DNA crosslinks were primarily responsible for lethality. Crosslink induction and repair were determined using two different assays. In both cases, little if any repair was observed in wild-type. This lack of repair thus explains why the rad mutants were not hypersensitive to 8-MOP photoinactivation. Since early embryos undergo extensive cell cycling, their resistance to 8-MOP photoinactivation suggests that replication is highly refractory to both monoadducts and crosslinks, as has been demonstrated previously for UV radiation- induced photoproducts (Hartman et al., 1991, Mutat. Res., 255, pp. 163-173). ------------------- Key: 1496 Medline: 92158050 Authors: Hunter CP;Wood WB Title: Evidence from mosaic analysis of the masculinizing gene her-1 for cell interactions in C. elegans sex Citation: Nature 355: 551-555 1992 Type: ARTICLE Genes: her-1 ncl-1 sdc-1 tra-1 tra-2 ctDp8 ctDp11 sDp3 Abstract: Sex in Caenorhabditis elegans is determined by a regulatory cascade of seven interacting autosomal genes controlled by three X-linked genes in response to the X chromosome-to-autosome (X/A) ratio. XX animals (high X/A) develop as self-fertile hermaphrodites, and XO animals (low X/A) develop as males. The activity of the first gene in the sex-determining cascade, her-1, is required for male sexual development. XO her-1 loss-of-function mutants develop as self- fertile hermaphrodites, whereas XX her-1 gain-of-function mutants develop as masculinized intersexes. By genetic mosaic analysis using a fused free duplication linking her-1 to a cell-autonomous marker gene, we show here that her-1 expression in a sexually dimorphic cell is neither necessary nor sufficient for that cell to adopt a male fate. Our results suggest that her-1 is expressed in many, possibly all, cells and that its gene product can function non-autonomously through cell interactions to determine male sexual development. ------------------- Key: 1497 Medline: 92199352 Authors: Stringham EG;Dixon DK;Jones D;Candido EPM Title: Temporal and spatial expression patterns of the small heat shock (hsp-16) genes in transgenic Caenorhabditis elegans. Citation: Molecular Biology of the Cell 3: 221-233 1992 Type: ARTICLE Genes: rol-6 unc-22 Abstract: The expression of the hsp16 gene family in Caenorhabditis elegans has been examined by introducing hsp16-lacZ fusions into the nematode by transformation. Transcription of hsp16-lacZ transgenes was totally heat-shock dependent and resulted in the rapid synthesis of detectable levels of B-galactosidase. Although the two hsp16 gene pairs of C. elegans are highly similar within both their coding and noncoding sequences, quantitative and qualitative differences in the spatial pattern of expression between gene pairs was observed. The hsp16-48 promoter was shown to direct greater expression of B-galactosidase in muscle and hypodermis, whereas the hsp16-41 promoter was more efficient in intestine and pharyngeal tissue. Transgenes that eliminated one promoter from a gene pair were expressed at reduced levels, particularly in postembryonic stages, suggesting that the heat shock elements in the intergenic region of an hsp16 gene pair may act cooperatively to achieve high levels of expression of both genes. Although the hsp16 gene pairs are never constitutively expressed, their heat inducibility is developmentally restricted; they are not heat inducible during gametogenesis or early embryogenesis. The hsp16 genes represent the first fully inducible system in C. elegans to be characterized in detail at the molecular level, and the promoters of these genes should find wide applicability in studies of tissue- and developmentally regulated genes in this experimental organism. ------------------- Key: 1498 Medline: Authors: Nelson GA;Schubert WW;Marshall TM Title: Radiobiological studies with the nematode Caenorhabditis elegans - genetic and developmental effects of high let radiation. Citation: Nuclear Tracks & Radiation Measurements 20: 227-232 1992 Type: ARTICLE Genes: mev-1 nuc-1 rad-1 rad-2 rad-3 rad-4 rad-5 rad-6 rad-7 Abstract: The biological effects of heavy charged particle (HZE) radiation are of particular interest to travellers and planners for long-duration space flights where ixposure levels represent a potential health hazard. The unique feature of HZE radiation is the the structured pattern of its energy deposition in targets. There are many consequences of this feature to biological endpoints when compared with effects of ionizing photons. Dose vs response and dose-rate kinetics may be modified, DNA and cellular repair systems may be altered in their abilities to cope with damage, and the qualitative features of damage may be unique for different ions. The nematode Caenorhabditis elegans is being used to address these and related questions associated with exposure to radiation. HZE-induced mutation, chromosome aberration, cell inactivation and altered organogenesis are discussed along with plans for radiobiological experiments in space. ------------------- Key: 1499 Medline: 92153422 Authors: McIntire SL;Garriga G;White J;Jacobson D;Horvitz HR Title: Genes necessary for directed axonal elongation or fasciculation in C. elegans. Citation: Neuron 8: 307-322 1992 Type: ARTICLE Genes: egl-43 sem-4 unc-5 unc-6 unc-14 unc-33 unc-34 unc-40 unc-43 unc-44 unc-51 unc-71 unc-73 unc-76 eDf2 sDf4 eDf6 Abstract: The outgrowth of single axons through different cellular environments requires distinct sets of genes in the nematode C. elegans. Three genes are required for the pioneering circumferential outgrowth of identified motor neuron axons between the lateral hypodermal cell membrane and the basal lamina. Three other genes are required for the longitudinal outgrowth of these axons along preexisting axon bundles as well as for the fasciculation of axons within these neuron bundles. Five additional genes are required for circumferential outgrowth, longitudinal outgrowth, and fasciculation; mutations in three of these genes disrupt axon ultrastructure, suggesting that they function in axon formation rather than in axon guidance. ------------------- Key: 1500 Medline: 92242574 Authors: Schinkmann K;Li C Title: Localization of FMRFamide-like peptides in Caenorhabditis elegans. Citation: Journal of Comparative Neurology 316: 251-260 1992 Type: ARTICLE Genes: ced-1 ced-2 ced-3 ced-4 egl-1 lin-4 sem-4 srf-3 unc-25 Abstract: The neuropeptide FMRFamide (Phe-Met-Arg-Phe-NH2) is a member of a large family of related peptides that have been found throughout the animal kingdom. By using an antiserum specific for the Arg-Phe-NH2 moiety, we have found that about 10% of the neurons in the nematode Caenorhabditis elegans are immunoreactive. Most of these neurons, which include sensory, motor, and interneurons, were identified on the basis of their number, position, and projection pattern and by analysis of characterized mutants. Neurons that were immunoreactive in hermaphrodite animals were generally also found in males, but each sex had, in addition, sex-specific immunoreactive cells. Staining of hermaphrodite animals from different larval stages suggests that the onset of FMRFamide-like expression is differentially regulated among the cells. We have found a possible neuromodulatory role for the related peptide FLRFamide (Phe-Leu-Arg-Phe-NH2). In an egg-laying assay, FLRFamide by itself was not active but could potentiate a serotonin effect. The FMRFamide-like immunoreactivity was also used as a marker to examine the differentiation of cells that normally undergo programmed cell death. Cells that are destined to die in the Pn.a lineages appear to differentiate and adopt the fate of lineally equivalent ------------------- Key: 1501 Medline: 92168138 Authors: White JG;Southgate E;Thomson JN Title: Mutations in the Caenorhabditis elegans unc-4 gene alter the synaptic input to ventral cord motor neurons. Citation: Nature 355: 838-841 1992 Type: ARTICLE Genes: ham-1 unc-4 Abstract: Identification of the genes orchestrating neurogenesis would greatly enhance our understanding of this process. Genes have been identified that specify neuron type (for example cut and numb in Drosophila and mec-3 in Caenorhabditis elegans) and process guidance (for example, unc-5, unc-6 and unc-40 in C. elegans and the fas-1 gene of Drosophila). We sought genes defining synaptic specificity by identifying mutations that alter synaptic connectivity in the motor circuitry in the nematode C. elegans. We used electron microscopy of serial sections to reconstruct the ventral nerve-cords of uncoordinated (unc) mutants that have distinctive locomotory choreographies. Here we describe the phenotype of mutations in the unc-4 gene in which a locomotory defect is correlated with specific changes in synaptic input to a subset of the excitatory VA motor neurons, normally used in reverse locomotion. The circuitry alterations do not arise because of the inaccessibility of the appropriate synaptic partners, but are a consequence of changes in synaptic specificity. The VA motor neurons with altered synaptic inputs are all lineal sisters of VB motor neurons; the VA motor neurons without VB sisters have essentially the same synaptic inputs as in wild-type animals. The normal function of the wild-type allele of unc-4 may thus be to invoke the appropriate synaptic specificities to VA motor neurons produced in particular developmental contexts. ------------------- Key: 1502 Medline: 92168139 Authors: Miller DM;Shen MM;Shamu CE;Burglin TR;Ruvkun G;Dubois ML;Ghee M;Wilson L Title: C. elegans unc-4 gene encodes a homeodomain protein that determines the pattern of synaptic input to specific motor neurons. Citation: Nature 355: 841-845 1992 Type: ARTICLE Genes: unc-4 eDf21 mnDf14 mnDf16 mnDf24 mnDf25 mnDf26 mnDf56 mnDf59 mnDf60 mnDf61 Abstract: The creation of neural circuits depends on the formation of synapses between specific sets of neurons. Little is known, however, of the molecular mechanisms governing synaptic choice. A mutation in the unc- 4 gene alters the pattern of synaptic input to one class of motor neurons in the Caenorhabditis elegans ventral nerve cord. In unc- 4(e120), the presynaptic partners of VA motor neurons are replaced with interneurons appropriate to motor neurons of the VB class. This change in neural specificity is not accompanied by any detectable effects on neuronal morphology or process extension. We show that the absence of a functional unc-4 gene product accounts for the mutant phenotype. The unc-4 gene encodes a homeodomain protein and thus is likely to function as a transcription factor. The limited effect of the unc-4 null mutation on cell fate may mean that unc-4 regulates the expression of a small number of target genes and that the products of these genes are directly involved in the choice of synaptic partners. ------------------- Key: 1503 Medline: 92168156 Authors: Sulston J;Du Z;Thomas K;Wilson R;Hillier L;Staden R;Halloran N;Green P;Thierry-Mieg J et al. Title: The C. elegans genome sequencing project: a beginning. Citation: Nature 356: 37-41 1992 Type: ARTICLE Genes: lin-9 sup-5 unc-32 Abstract: The long-term goal of this project is the elucidation of the complete sequence of the Caenorhabditis elegans genome. During the first year methods have been developed and a strategy implemented that is amenable to large-scale sequencing. The three cosmids sequenced in this initial phase are surprisingly rich in genes, many of which have mammalian homologues. ------------------- Key: 1504 Medline: 92201635 Authors: Okimoto R;Macfarlane JL;Clary DO;Wolstenholm DR Title: The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Citation: Genetics 130: 471-498 1992 Type: ARTICLE Genes: Abstract: The nucleotide sequences of the mitochondrial DNA (mtDNA) molecules of two nematodes, Caenorhabditis elegans [13,794 nucleotide pairs (ntp)], and Ascaris suum (14,284 ntp) are presented and compared. Each molecule contains the genes for two ribosomal RNAs (s-rRNA and l- rRNA), 22 transfer RNAs (tRNAs) and 12 proteins, all of which are transcribed in the same direction. The protein genes are the same as 12 of the 13 protein genes found in other metazoan mtDNAs: Cyt b, cytochrome b; COI-III, cytochrome c oxidase subunits I-III; ATPase6, Fo ATPase subunit 6; ND1-6 and 4L, NADH dehydrogenase subunits 1-6 and 4L: a gene for ATPase subunit 8, common to other metazoan mtDNAs, has not been identified in nematode mtDNAs. The C. elegans and A. suum mtDNA molecules both include an apparently noncoding sequence that contains runs of AT dinucleotides, and direct and inverted repeats (the AT region: 466 and 886 ntp, respectively). A second, apparently noncoding sequence in the C. elegans and A. suum mtDNA molecules (109 and 117 ntp, respectively) includes a single, hairpin- forming structure. There are only 38 and 89 other intergenic nucleotides in the C. elegans and A. suum mtDNAs, and no introns. Gene arrangements are identical in the C. elegans and A. suum mtDNA molecules except that the AT regions have different relative locations. However, the arrangement of genes in the two nematode mtDNAs differs extensively from gene arrangements in all other sequenced metazoan mtDNAs. Unusual features regarding nematode mitochondrial tRNA genes and mitochondrial protein gene initiation codons, previously described by us, are reviewed. In the C. elegans and A. suum mt-genetic codes, AGA and AGG specify serine, TGA specifies tryptophan and ATA specifies methionine. From considerations of amino acid and nucleotide sequence similarities it appears likely that the C. elegans and A. suum ancestral lines diverged close to the time of divergence of the cow and human ancestral lines, about 80 ------------------- Key: 1505 Medline: 92171874 Authors: Sassa T;Miwa J Title: Purification and characterization of protein kinase C from the nematode Caenorhabditis elegans. Citation: Biochemical Journal 282: 219-223 1992 Type: ARTICLE Genes: tpa-1 Abstract: Protein kinase C (PKC) of Caenorhabditis elegans was identified by enzymatic activity and [3H]phorbol 12,13-dibutyrate binding after DEAE-Sephacel column chromatography of a crude cytosolic extract. Ca(2+)-dependent activation of nematode PKC was observed in the presence of phosphatidylserine. The enzyme was maximally activated by 1,2-dioleoylglycerol or phorbol 12-myristate 13-acetate in the presence of phosphatidylserine and Ca2+. Hydroxyapatite column chromatography showed only one peak of PKC activity with histone H1 and myelin basic protein as substrates. The enzyme was purified to near homogeneity by sequential chromatography on polylysine-agarose and phosphatidylserine affinity columns. The purified protein showed a molecular mass of 79 kDa on SDS/PAGE. The substrate specificity of the C. elegans enzyme was shown to be different from that of mammalian PKCs. Here we describe some of the properties ------------------- Key: 1506 Medline: Authors: Grewal PS;Hand P Title: Effects of bacteria isolated from a saprophagous rhabditid nematode Caenorhabditis elegans on the mycelial growth of Agaricus bisporus. Citation: Journal of Applied Bacteriology 72: 173-179 1992 Type: ARTICLE Genes: Abstract: The effects of 10 species of bacteria isolated from a saprophagous rhabditid nematode Caenorhabditis elegans on mycelial growth of the cultivated mushroom Agaricus bisporus were studied in agar cultures. Bacterial species showed differential effects on the mycelial growth of A. bisporus and the effects also depended upon the mushroom strain (C43, C54 and U3). Bacillus cereus, Bacillus sp. and Enterobacter amnigenus caused significant inhibition in mycelial growth of all three strains of A. bisporus. Pseudomonas aeruginosa, Ps. fluorescens biovar reactans and Ps. maltophilia resulted in a significant increase in mycelial growth of C54 strain. Enterobacter cloacae caused a mean inhibition of about 83% in the linear mycelial extension of the most commonly cultivated mushroom strain U3. Bacillus cereus, Ent. amnigenus and Ent. cloacae produced volatile inhibitory substance(s). This is believed to be the first report about the inhibitory effects of specific bacteria isolated from a saphrophagous nematode on the mycelial growth of A. bisporus. ------------------- Key: 1507 Medline: 92172022 Authors: Schaeffer JM;Blizzard TA;Ondeyka J;Goegelman R;Sinclair PJ;Mrozik H Title: [3H]Paraherquamide binding to Caenorhabditis elegans. Studies on a potent new anthelmintic agent. Citation: Biochemical Pharmacology 43: 679-684 1992 Type: ARTICLE Genes: Abstract: Paraherquamide was identified recently as a potent anthelmintic agent. In this paper we describe the identification and characterization of a specific, high-affinity paraherquamide binding site in a membrane preparation isolated from the free-living nematode, Caenorhabditis elegans. [3H] Paraherquamide bound specifically to C. elegans membranes with an apparent dissociation constant, Kd, of 263 nM. A series of paraherquamide analogs were examined, and their relative affinity for the paraherquamide binding site correlated with their nematocidal activity. Phenothiazines were the only other class of anthelmintics tested which inhibited specific [3H]paraherquamide binding. These results suggest that the anthelmintic activity of paraherquamide and phenothiazine is mediated via an interaction with a common ------------------- Key: 1508 Medline: 92345889 Authors: Wadsworth WG;Hedgecock EM Title: Guidance of neuroblast migrations and axonal projections in Caenorhabditis elegans. Citation: Current Opinion in Neurobiology 2: 36-41 1992 Type: ARTICLE Genes: mec-3 unc-3 unc-5 unc-6 unc-39 unc-40 unc-73 unc-76 unc-86 Abstract: The nematode Caenorhabditis elegans provides an excellent model system in which to study the mechanisms involved in the development of the nervous system. Mutation analyses have now identified several genes that appear to be important in the interaction of neuroblasts and axons with both guidance cues and their target cells. ------------------- Key: 1510 Medline: 92244294 Authors: Ray C;McKerrow JH Title: Gut-specific and developmental expression of a Caenorhabditis elegans cysteine protease gene. Citation: Molecular & Biochemical Parasitology 51: 239-250 1992 Type: ARTICLE Genes: gcp-1 Abstract: A Caenorhabditis elegans cysteine protease gene fragment, amplified by PCR using conserved eukaryotic protease gene sequences as primers, was used as a probe to isolate cDNA and genomic clones. The genomic clone, which had a coding sequence of 987 bp interrupted by 2 small introns, was physically mapped to the middle of linkage group V. The predicted amino acid sequence of the mature C. elegans cysteine protease was homologous to those of other eukaryotic cysteine proteases, particularly to that of the nematode parasite Haemonchus contortus (50%) and to the cathepsin B-like hemoglobinase of the trematode parasite Schistosoma mansoni (54%). The pro region of the C. elegans protease was homologous only to that of the H. contortus enzyme, implying a similar mechanism of protease activation. The C. elegans cysteine protease gene was temporally regulated: abundant 1.1- kb transcripts were detected in larvae and adults, but not in embryos. Transcription also was spatially regulated, occurring only in the intestine. Like the vitellogenin genes, which also are transcribed exclusively in the intestine, the 5' end of the C. elegans cysteine protease gene had at least one copy of each of 2 heptameric sequences which may be transcriptional regulatory elements governing gut-specific ------------------- Key: 1511 Medline: 92037550 Authors: Maroney PA;Hannon GJ;Shambaugh JD;Nilsen TW Title: Intramolecular base pairing between the nematode spliced leader and its 5' splice site is not essential for trans-splicing in vitro. Citation: EMBO Journal 10: 3869-3875 1991 Type: ARTICLE Genes: Abstract: The spliced leader RNAs of both trypanosomes and nematodes can form similar secondary structures where the trans-splice donor site is involved in intramolecular base pairing with the spliced leader sequence. It has been proposed that this base pairing could serve to activate autonomously the SL RNA splice donor site. Here, we have examined exon requirements for trans-splicing in a nematode cell free system. Complete disruption of secondary structure interactions at and around the trans-splice donor site did not affect the ability of the SL RNA to function in trans-splicing. In addition, the highly conserved 22 nt sequence could be productively replaced by artificial exons ranging in size from 2 to 246 nucleotides. These results reinforce the view that the 'intron' portion of the SL RNA functions as an independent Sm snRNP whose role is to deliver exon sequences to the trans-spliceosome. ------------------- Key: 1512 Medline: 83177107 Authors: Blum J;Fridovich I Title: Superoxide, hydrogen peroxide, and oxygen toxicity in two free-living nematode species. Citation: Archives of Biochemistry & Biophysics 222: 35-43 1983 Type: ARTICLE Genes: Abstract: Two species of free-living nematodes, Turbatrix aceti and Caenorhabditis elegans, exhibited a marked sensitivity to 3 atm of 100% O2. Environmental changes in pH and temperature, which altered nematode respiration, resulted in alterations in the survival of these organisms under high pO2. Levels of defensive enzymes such as superoxide dismutase, catalase, glutathione peroxidase, and dianisidine peroxidase were measured in the two species. No changes in the level of superoxide dismutase or catalase activity were induced by exposure of the nematodes to high pO2. Manipulation of these two enzymes was however achieved using the inhibitors 3-amino-1,2,4-triazole and diethyldithiocarbamate. 3-Amino-1,2,4-triazole (20 mM) eliminated >80% of the catalase activity in vivo and diethyldithiocarbamate (5mM) decreased the level of CuZn superoxide dismutase by >70%. Both of these compounds increased teh sensitivity of C. elegans to high pO2 toxicity. Compounds capable of intracellular redox-cycling with O2- -production, such as plumbagin, increased CN- -resistant respiration in the nematodes and imposed an O2-dependent toxicity. These experiments demonstrate the toxicity of intracellular O2- and H2O2 in nematodes and the importance of superoxide dismutase and catalase in providing a defense against these toxic molecules in vivo. ------------------- Key: 1513 Medline: 91128766 Authors: Hodgkin J Title: Sex determination and the generation of sexually dimorphic nervous systems. Citation: Neuron 6: 177-185 1991 Type: REVIEW Genes: ced-3 ced-4 dig-1 egl-1 her-1 fem-1 fem-2 fem-3 mab-3 mab-5 sdc-1 sdc-2 tra-1 tra-2 tra-3 xol-1 Abstract: Most animal species occurr in two different sexual forms, which usually exhibit a substantial degree of dimorphism in behavior. Often the most elaborate patterns of activity displayed by an animal are sex-specific behaviors such as courtship, mating, nest-building, and so forth. A vast literature exists on every aspect of sex-specific behavior, reporting observations on a great variety of different animal types. The questions addressed by these studies reange across the whole of biology, from ethology to crystallography. The present review is concerned with a limited part of this subject, the molecular basis of sex-specific development in the nervous systems, and will focus on systems in which it is becoming possible to define precise genetic and cellular mechanisms. This means concentrating primarily on two invertebrates, the nematode Caenorhabditis elegans and the fruitfly Drosophila melanogaster, and on a few mammalian and avian species. ------------------- Key: 1514 Medline: Authors: Hall DH Title: Freeze-fracture and freeze-etch studies of the nematode Caenorhabditis elegans. Citation: Annals of the New York Academy of Sciences 494: 215-217 Type: REVIEW Genes: Abstract: The freeze-fracture technique offers a unique view of intramembrane particles (IMPs), which derive from large membrane-associated molecules such as gap junctions, receptors, and ion channels. We are particularly interested in the gap junction (gj) and its role in intercellular communication. The anatomy of the soil nematode, C. elegans, has been studied extensively in serial thin sections and gjs have been noted in many cell types. Although gjs vary in frequency and extent, their appearance in sectioned material is rather uniform. The freeze-fracture technique can be used to identify and differentiate gjs according to IMP size, packing density, and preferred fracture face. For instance, in the planarian, Dugesia, this technique revealed three classes of gjs occurring in different tissues. The nematode usually fractures lengthwise; the fracture plane preferentially travels along membranes, splitting the unit membrane into two opposing halves (the P- and E-faces). Many tissues are recognizable: hypodermis, muscle, neurons, nerve cords, intestine, and so forth... ------------------- Key: 1515 Medline: 92148586 Authors: Cox GN Title: Molecular and biochemical aspects of nematode collagens. Citation: Journal of Parasitology 78: 1-15 1992 Type: REVIEW Genes: col-1 col-3 col-6 col-7 col-8 col-12 col-14 col-19 dpy-13 rol-6 sqt-1 Abstract: Collagens are major structural proteins of nematode cuticles and basement membranes (basal laminae). The collagen proteins that form these structures differ in their biochemical and physical properties and are encoded by distinct gene families. Nematode basement membrane collagens are large proteins that show strong homology to basement membrane collagens of vertebrates. There appear to be 2 nonidentical basement membrane collagen genes in nematodes. Cuticle collagens are about one-sixth the size of basement membrane collagens and are encoded by a large family of 20-150 nonidentical genes. Cuticle collagens can be subdivided into 4 families based upon certain structural features in the proteins. The mature, extracellular forms of both types of collagen proteins are extensively cross-linked by disulfide bonds and are largely insoluble in the absence of a thiol-reducing agent. Cuticle collagens are also cross-linked by nonreducible covalent bonds that involve tyrosine residues. The experimental studies that have led to our current understanding of the structures of basement membrane and cuticle collagens are reviewed. Some previous questions about the physical properties of these proteins are reexamined in light of the primary sequence information now available for the ------------------- Key: 1516 Medline: 92258691 Authors: Morton DG;Roos JM;Kemphues KJ Title: par-4, a gene required for cytoplasmic localization and determination of specific cell types in Caenorhabditis elegans embryogenesis. Citation: Genetics 130: 771-790 1992 Type: ARTICLE Genes: dpy-21 par-1 par-2 par-3 par-4 par-5 yDf6 Abstract: Specification of some cell fates in the early Caenorhabditis elegans embryo is mediated by cytoplasmic localization under control of the maternal genome. Using nine newly isolated mutations, and two existing mutations, we have analyzed the role of the maternally expressed gene par-4 in cytoplasmic localization. We recovered seven new par-4 alleles in screens for maternal effect lethal mutations that result in failure to differentiate intestinal cells. Two additional par-4 mutations were identified in noncomplementation screens using strains with a high frequency of transposon mobility. All 11 mutations cause defects early in development of embryos produced by homozygous mutant mothers. Analysis with a deficiency in the region indicates that it33 is a strong loss-of-function mutation. par-4(it33) terminal stage embryos contain many cells, but show no morphogenesis, and are lacking intestinal cells. Temperature shifts with the it57ts allele suggest that the critical period for both intestinal differentiation and embryo viability begins during oogenesis, about 1.5 hr before fertilization, and ends before the four-cell stage. We propose that the primary function of the par-4 gene is to act as part of a maternally encoded system for cytoplasmic localization in the first cell cycle, with par-4 playing a particularly important role in the determination of intestine. Analysis of a par-4; par-2 double mutant suggests that par-4 and ------------------- Key: 1517 Medline: Authors: Grewal PS Title: Relative contribution of nematodes (Caenorhabditis elegans) and bacteria towards the disruption of flushing patterns and losses in yield and quality of mushrooms (Agaricus bisporus). Citation: Annals of Applied Biology 119: 483-499 1991 Type: ARTICLE Genes: Abstract: Laboratory tests of bacteria isolated from the body surface, or from the gut, of a saprophagaous rhabditid nematode Caenorhabditis elegans infesting mushrooms (Agaricus bisporus) showed that some bacteria enhanced nematode reproduction and that others inhibited it. As some bacteria were shown to inhibit mycelial growth of mushrooms, the effects of Acinetobacter calcoaceticus var. anitratus, Enterobacter cloacae and Serratia liquefaciens, either alone or in combination with C. elegans, on the flushing patterns, quality and yield of A. bisporus (strain Horst U3) were studied. Bacteria alone had little effect on flushing patterns whereas C. elegans delayed the onset of mushroom production and significantly disrupted the growth pattern of crops, with mushrooms apppearing more regularly and not within obvious flushes. Inoculation with bacteria resulted in 'browning' of mushrooms that was even more pronounced in C. elegans treatments. Characteristic distortion of sporophores was observed only in the presence of C. elegans. Nematodes commonly colonised sporophores. Bacteria affected the size of nematode populations both on the sporophores and in the casing. Significant yield loss occurred: up to 10% when bacteria were inoculated, up to 27.8% when C. elegans was inoculated, and up to 35% with both bacteria and nematodes. Synergism between C. elegans and A. calcoaceticus var. anitratus was observed; the combination resulted in significantly greater reduction in mushroom yield than any other treatment. It is concluded that bacteria contribute to yield loss and quality deterioration in A. bisporus but that the effects are far greater in the presence of C. elegans. ------------------- Key: 1518 Medline: Authors: Bossinger O;Schierenberg E Title: Transfer and tissue-specific accumulation of cytoplasmic components in embryos of C. elegans and R. dolichura: in vivo analysis with a low-cost signal enhancement device/ Citation: Development 114: 317-330 1992 Type: ARTICLE Genes: Abstract: The pattern of autofluorescence in the two free-living soil nematodes Rahbditis dolichura and Caenorhabditis elegans has been compared. In C. elegans, during later embryogenesis the prospective gut cells develop a typical bluish autofluorescence as seen under UV illumination, whil in Rh. dolichura a strong autofluorescence is already present in the unfertilized egg. Using a new, low-cost signal enhancement device, we have been able to follow in vivo the dramatic change in the pattern of autofluorescence during embryogenesis of Rh. dolichura. Autofluorescent material accumulates progressively in the gut promordium and disappears completely from all other cells. To investigate whether such an accumulation of cytoplasmic components also takes place in the C. elegans embryo, we labeled the cytoplasm of the egg with the fluorescing tracer dyes Lucifer Yellow (LY) or Rhaodamie 6G (R6G). While LY appears to bind to yolk and progressively accumulates in the developing gut primordium, R6G does not show any such binding and remains equally distributed over all cells. Measurements in early and late stages indicate a significant increase in the volume of the gut cells during embryogenesis, while the embryo as a whole does not grow. Moreover, in cleavage-blocked 2-cell stages after development overnight, a reversal of cell size relationship to the benefit of the gut precursor takes place. In summary, our observations suggest a previously unknown massive transfer of yolk components in the nematode embryo from non-gut cells into lysosomes of the gut primordium, where they are futher metabolized during postembryonic development. ------------------- Key: 1519 Medline: 92195405 Authors: Clark SG;Stern MJ;Horvitz HR Title: C. elegans cell signalling gene sem-5 encodes a protein with SH2 and SH3 domains. Citation: Nature 356: 340-344 1992 Type: ARTICLE Genes: clr-1 egl-15 let-23 let-60 lin-15 sem-5 Abstract: The induction of the hermaphrodite vulva and the migration of the sex myoblasts in the nematode Caenorhabditis elegans are both controlled by intercellular signalling. The gonadal anchor cell induces formation of the vulva from nearby hypodermal cells, and a set of somatic gonadal cells attract the migrating sex myoblasts to their final positions. Many genes required for vulval induction have been identified, including the let-23 receptor tyrosine kinase gene and the let-60 ras gene. We report here the identification and characterization of a new gene, sem-5 (sem, sex muscle abnormal), that acts both in vulval induction and in sex myoblast migration. On the basis of its DNA sequence, sem-5 encodes a novel 228-amino-acid protein which consists almost entirely of one SH2 (SH, src homology region) and two SH3 domains. SH2 and SH3 domains are present in many signalling proteins regulated by receptor and non-receptor tyrosine kinases. Mutations that impair sem-5 activity alter residues that are highly conserved among different SH2 and SH3 domains. Our results indicate that the sem-5 gene encodes a novel protein that functions in at least two distinct cell-signalling ------------------- Key: 1520 Medline: 92193858 Authors: Hosono R;Hekimi S;Kamiya Y;Sassa T;Murakami S;Nishiwaki K;Miwa J;Taketo A;Kodaira KI Title: The unc-18 gene encodes a novel protein affecting the kinetics of acetylcholine metabolism in the nematode Caenorhabditis elegans. Citation: Journal of Neurochemistry 58: 1517-1525 1992 Type: ARTICLE Genes: unc-18 Abstract: Genes affecting acetylcholine (ACh) levels without influencing choline acetyltransferase activity have been identified in Caenorhabditis elegans. We have examined one such gene, unc-18. We isolated a transposon-insertion allele for unc-18 and used it to clone a genomic region containing the unc-18 locus. The unc-18 location within this region was determined by rescuing the unc-18 mutant phenotype in a germ-line transformation experiment and identifying transcripts affected by four independent unc-18 mutations. A single-sized poly(A)+ RNA was synthesized from the gene. Expression of the transcript appears to be stage specific: The transcript is found in abundance at the early larval stage but in decreased amounts at the fourth larval and the adult stages. These results show that the unc-18 gene plays a role in development as well as in the kinetics of ACh metabolism. ------------------- Key: 1521 Medline: 92191285 Authors: Bowerman B;Eaton BA;Priess JR Title: skn-1, a maternally expressed gene required to specify the fate of ventral blastomeres in the early C. elegans embryo. Citation: Cell 68: 1061-1075 1992 Type: ARTICLE Genes: act-1 fem-1 fer-1 glp-1 skn-1 srg-1 unc-44 nDf41 mDp1 Abstract: By the 4-cell stage of C. elegans embryogenesis, a ventral blastomere, called EMS, is already committed to producing pharyngeal and intestinal cell types. Recessive, maternal-effect mutations in the gene skn-1 prevent EMS from producing both pharyngeal and intestinal cells. In skn-1 mutant embryos, EMS instead produces hypodermal cells and body wall muscle cells, much like its sister blastomere. Genetic analysis suggests that the skn-1 gene product is also required post-embryonically for development of the intestine. We have cloned and sequenced the skn-1 gene and describe sequence similarities to the basic regions of bZIP transcription factors. We propose that the maternally expressed skn-1 gene product acts to specify the fate of the EMS blastomere. ------------------- Key: 1522 Medline: 92204141 Authors: Clark DV;Baillie DL Title: Genetic analysis and complementation by germ-line transformation of lethal mutations in the unc-22 IV region of Caenorhabditis elegans. Citation: Molecular & General Genetics 232: 97-105 1992 Type: ARTICLE Genes: dpy-20 dpy-26 him-8 let-52 let-56 let-59 let-60 let-61 let-63 let-64 let-65 let-66 let-67 let-68 let-69 let-70 let-71 let-72 let-73 let-91 let-92 let-93 let-96 let-97 let-98 let-99 let-100 let-307 let-308 let-309 let-311 let-312 let-651 let-652 let-653 let-654 let-655 let-656 lin-3 mec-3 par-5 sem-3 unc-22 eDf19 mDf7 nDf27 sDf2 sDf7 sDf8 sDf9 sDf10 sDf19 sDf21 sDf22 sDf60 sDf61 sDf62 sDf63 sDf64 sDf65 sDf67 nT1 Abstract: The subject of this study is the organization of essential genes in the 2 map-unit unc-22 IV region of the Caenorhabditis elegans genome. With the goal of achieving mutational saturation of essential genes in this region, 6491 chromosomes mutagenized with ethyl methanesulfonate (EMS) were screened for the presence of lethal mutations in the unc-22 region. The genetic analysis of 21 lethal mutations in the unc-22 region resulted in the identification of 6 new essential genes, making a total of 36 characterized to date. A minimum of 49 essential genes are estimated to lie in this region. A set of seven formaldehyde-induced deficiencies of unc-22 and surrounding loci were isolated to facilitate the positioning of essential genes on the genetic and physical maps. In order to study essential genes at the molecular level, our approach was to rescue lethal mutations by the injection of genomic DNA in the form of cosmid clones into the germ-line of balanced heterozygotes carrying a lethal mutation. The cosmid clones containing let-56 and let-653 were identified by this method. ------------------- Key: 1523 Medline: 92195311 Authors: MacMorris M;Broverman S;Greenspoon S;Lea K;Madej C;Blumenthal T;Spieth J Title: Regulation of vitellogenin gene expression in transgenic Caenorhabditis elegans - Short sequences required for activation of the vit-2 promoter. Citation: Molecular and Cellular Biology 12: 1652-1662 1992 Type: ARTICLE Genes: mab-3 sup-7 vit-2 vit-6 Abstract: The Caenorhabditis elegans vitellogenin genes are subject to sex-, stage-, and tissue-specific regulation: they are expressed solely in the adult hermaphrodite intestine. Comparative sequence analysis of the DNA immediately upstream of these genes revealed the presence of two repeated heptameric elements, vit promoter element 1 (VPE1) and VPE2. VPE1 has the consensus sequence TGTCAAT, while VPE2, CTGATAA, shares the recognition sequence of the GATA family of transcription factors. We report here a functional analysis of the VPEs within the 5'-flanking region of the vit-2 gene using stable transgenic lines. The 247 upstream bp containing the VPEs was sufficient for high- level, regulated expression. Furthermore, none of the four deletion mutations or eight point mutations tested resulted in expression of the reporter gene in larvae, males, or inappropriate hermaphrodite tissues. Mutation of the VPE1 closest to the TATA box inactivated the promoter, in spite of the fact that four additional close matches to the VPE1 consensus sequence are present within the 5'-flanking 200 bp. Each of these upstream VPE1-like sequences could be mutated without loss of high-level transgene expression, suggesting that if these VPE1 sequences play a role in regulating vit-2, their effects are more subtle. A site-directed mutation in the overlapping VPE1 and VPE2 at -98 was sufficient to inactivate the promoter, indicating that one or both of these VPEs must be present for activation of vit- 2 transcription. Similarly, a small perturbation of the VPE2 at -150 resulted in reduction of fp155 expression, while a more extensive mutation in this element eliminated expression. On the other hand, deletion of this VPE2 and all upstream DNA still permitted correctly regulated expression, although at a very low level, suggesting that this VPE2 performs an important role in activation of vit-2 expression but may not be absolutely required. The results, taken together, demonstrate that both VPE1 and VPE2 are sites for activation of the vit-2 promoter. ------------------- Key: 1524 Medline: 92192288 Authors: Arata Y;Tada S;Ui M Title: Probable occurrence of toxin-susceptible G-proteins in the nematode Caenorhabditis elegans. Citation: FEBS Letters 300: 73-76 1992 Type: ARTICLE Genes: Abstract: Pertussis toxin, islet-activating protein (IAP), and cholera toxin ADP-ribosylated 40 kDa and 45 kDa proteins in membrane preparations from Caenorhabditis elegans. Proteins with the same molecular weights were recognized in the same membranes by an antibody that had been raised against a peptide common to alpha-subunits of mammalian alpha beta gamma-heterotrimeric G proteins. The antibody produced immunoprecipitation with the 40 kDa protein 32P-labeled by IAP. A 35 kDa protein immunochemically indistinguishable from the beta- component of mammalian G proteins was also found in C. elegans membranes. The membranes displayed adenylate cyclase activity which was highly sensitive to forskolin and GTP analogues, whose action was antagonized by GDP beta S. Receptor-coupled regulation of adenylate cyclase thus appears to be mediated by mammalian-type G proteins in C. elegans as well. ------------------- Key: 1525 Medline: 92210636 Authors: Levin JZ;Horvitz HR Title: The Caenorhabditis elegans unc-93 gene encodes a putative transmembrane protein that regulates muscle contraction. Citation: Journal of Cell Biology 117: 143-155 1992 Type: ARTICLE Genes: daf-2 dpy-17 mut-2 sup-9 sup-10 sup-18 unc-54 unc-93 Abstract: unc-93 is one of a set of five interacting genes involved in the regulation or coordination of muscle contraction in Caenorhabditis elegans. Rare altered-function alleles of unc-93 result in sluggish movement and a characteristic "rubber band" uncoordinated phenotype. By contrast, null alleles cause no visibly abnormal phenotype, presumably as a consequence of the functional redundancy of unc-93. To understand better the role of unc-93 in regulating muscle contraction, we have cloned and molecularly characterized this gene. We isolated transposon-insertion alleles and used them to identify the region of DNA encoding the unc-93 protein. Two unc-93 proteins differing at their NH2 termini are potentially encoded by transcripts that differ at their 5' ends. The putative unc-93 proteins are 700 and 705 amino acids in length and have two distinct regions: the NH2 terminal portion of 240 or 245 amino acids is extremely hydrophilic, whereas the rest of the protein has multiple potential membrane- spanning domains. The unc-93 transcripts are low in abundance and the unc-93 gene displays weak codon usage bias, suggesting that the unc- 93 protein is relatively rare. The unc-93 protein has no sequence similarity to proteins listed in current data-bases. Thus, unc-93 is likely to encode a novel membrane-associated muscle protein. We discuss possible roles for the unc-93 protein either as a component of an ion transport system involved in excitation-contraction coupling in muscle or in coordinating muscle contraction between muscle cells by affecting the functioning of gap ------------------- Key: 1526 Medline: 92273960 Authors: Goldstein P;Magnano L;Rojo J Title: Effects of dimethyl sulfone (DMSO2) on early gametogenesis in C. elegans - Ultrastructural aberrations and loss of synaptonemal complexes from pachytene nuclei. Citation: Reproductive Toxicology 6: 149-159 1992 Type: ARTICLE Genes: him-5 him-8 Abstract: The free-living nematode Caenorhabditis elegans has been used extensively for studies in developmental and reproductive genetics. Recently, toxicologic studies have been initiated using specific sex chromosome mutations. In the present study, high incidence of male (him) mutants, him-5 and him-8, were treated with dimethyl sulfone (DMSO2), the primary metabolite of dimethyl sulfoxide (DMSO). In addition to differential effects on X-chromosome nondisjunction, loss of viability and fertility were observed. Much lower concentrations of DMSO2 were required to elicit the same aberrational effects characteristic of DMSO (1); thus, the toxicity of the former was significantly more potent. The observed decrease in life span was associated with senescent morphology of meiotic prophase nuclei, such that nuclei from young and old specimens could not be differentiated. Aging in oocytes at pachytene is characterized by nucleo-cytoplasmic aberrations, increased density of the nucleoplasm and cytoplasm, and decrease in numbers of mitochondria. Increasing concentrations of DMSO2 resulted in a corresponding decrease in fertility and increased production of abnormal gametes. At DMSO2 concentrations higher than 1.0%, synaptonemal complexes (SC) were absent from pachytene nuclei; thus, effective pairing and segregation of homologous chromosomes was prohibited. Since the SC is essential for regulating pairing and subsequent separation of bivalents, the lack of an SC explains the loss of fertility, due to the production of unbalanced ------------------- Key: 1527 Medline: 92229449 Authors: Chen L;Krause M;Draper B;Weintraub H;Fire A Title: Body-wall muscle formation in Caenorhabditis elegans embryos that lack the MyoD homolog hlh-1. Citation: Science 256: 240-243 1992 Type: ARTICLE Genes: deb-1 dpy-25 lin-31 myo-1 myo-2 myo-3 unc-15 unc-22 unc-54 ccDf1 ccDf2 ccDf3 ccDf4 ccDf5 ccDf7 ccDf9 ccDf11 maDf4 Abstract: The myoD family of DNA binding proteins has been implicated in the control of myogenesis in a variety of organisms. Searches for homologs in the nematode Caenorhabditis elegans yielded only one gene, designated hlh-1, expressed in body-wall muscle cells and their precursors. To assess the role of hlh-1 in C. elegans myogenesis, genetic deficiencies spanning the hlh-1 locus were isolated after gamma irradiation. Embryos homozygous for these deficiencies exhibited extensive body-wall muscle differentiation, including expression of several characteristic myofilament proteins and weak contracile behavior. Thus, zygotic hlh-1 expression was not required for body-wall muscle precursors to adopt muscle cell fates. ------------------- Key: 1528 Medline: Authors: McCallum ME;Dusenbery DB Title: Computer tracking as a behavioral GC detector: nematode responses to vapor of hosts roots. Citation: Journal of Chemical Ecology 18: 585-592 1992 Type: ARTICLE Genes: Abstract: ------------------- Key: 1529 Medline: 92220162 Authors: Hengartner MO;Ellis RE;Horvitz HR Title: Caenorhabditis elegans gene ced-9 protects cells from programmed cell death. Citation: Nature 356: 494-499 1992 Type: ARTICLE Genes: ced-1 ced-3 ced-4 ced-5 ced-9 egl-1 nDf40 Abstract: The gene ced-9 of the nematode Caenorhabditis elegans acts to protect cells from programmed cell death. A mutation that abnormally activates ced-9 prevents the cell deaths that occur during normal C. elegans development. Conversely, mutations that inactivate ced-9 cause cells that normally live to undergo programmed cell death; these mutations result in embryonic lethality, indicating that ced-9 function is essential for development. The ced-9 gene functions by negatively regulating the activities of other genes that are required for the process of programmed cell death. ------------------- Key: 1530 Medline: 92153310 Authors: Ofulue EN;Candido EPM Title: Isolation and characterization of eft-1, an elongation factor 2-like gene on chromosome III of Caenorhabditis elegans. Citation: DNA and Cell Biology 11: 71-82 1992 Type: ARTICLE Genes: eft-1 eft-2 ubq-1 Abstract: A gene (eft-1) encoding an elongation factor 2-like protein was isolated from a region adjacent to the polyubiquitin gene, ubq-1, of Caenorhabditis elegans. Sequence analysis of genomic and cDNA clones revealed that the deduced amino acid sequence of the protein (EFT-1) is 38% identical to that of mammalian and Drosophila elongation factor 2 (EF-2). The entire eft-1 gene is approximately 3.8 kb in length and contains 5 exons separated by short introns of 46-75 bp. The 2,547-bp open reading frame predicts a protein of 849 amino acid residues (calculated Mr, 96,151). Conserved sequences shared among a variety of GTP-binding proteins including EF-2 are found in the amino- terminal third of EFT-1. The carboxy-terminal half contains regions with 40-57% similarity (including conservative changes) with segments characteristic of EF-2 and its prokaryotic homolog, EF-G. However, the histidyl residue target for ADP-ribosylation of EF-2 by diphtheria toxin is replaced by tyrosine in EFT-1. Southern and Northern blot analyses indicate that eft-1 is a single-copy gene that is expressed at all stages of nematode development. Amplification of fragments encoding highly conserved regions of EF-2 using the polymerase chain reaction led to the isolation of a fragment encoding the modifiable histidyl residue and which likely represents part of the C. elegans EF-2 gene (eft-2). This suggests that EFT-1 is not the C. elegans homolog of EF-2, but a closely related protein. ------------------- Key: 1531 Medline: 92290112 Authors: Bossinger O;Schierenberg E Title: Cell-cell communication in the embryo of Caenorhabditis elegans. Citation: Developmental Biology 151: 401-409 1992 Type: ARTICLE Genes: Abstract: We have investigated the pattern of cell-cell communication in embryos of the free-living soil nematode Caenorhabditis elegans. For this, we have established a method for microinjection of tracer dyes into individual blastomeres. After iontophoresis of fluorescent dyes of different molecular weights (Lucifer yellow, LY, M(r) 457; rhodamine-labeled dextran, RD, M(r) 4000), we can visualize intercellular communication pathways. The dye-spread of LY, indicating communication via gap junctions, becomes first visible in the late 2-cell stage. From the 4-cell stage onward all cells appear to be well coupled by communication channels, which allow the free diffusion of LY. In contrast, RD remains restricted to the injected cell and its descendants. After the primordial germcell P4 has been generated in the 24-cell stage, dye-spread of LY into this cell and its somatic sister D is delayed. However, the restricted dye-coupling of D is only temporary. After a brief period it joins the somatic compartment. With the beginning of the morphogenesis phase the two existing germline cells (the daughters of P4) are completely uncoupled from the soma, while the latter still forms a single dye- coupling compartment. Only during the second half of embryogenesis different separate somatic communication compartments are established. We followed the pattern of intercellular communication in the alimentary tract and found a progressive restriction into smaller dye-coupling units. Our data are compared to those found in other systems and discussed with respect to cellular determination and differentiation. ------------------- Key: 1532 Medline: 92309975 Authors: Honda S;Matsuo M Title: Lifespan shortening of the nematode Caenorhabditis elegans under higher concentrations of oxygen. Citation: Mechanisms of Ageing & Development 63: 235-246 1992 Type: ARTICLE Genes: mev-1 zyg-9 Abstract: The effects of higher concentrations of atmospheric oxygen on the lifespans of wild type and a temperature-sensitive zyg-9(b244) mutant of the nematode Caenorhabditis elegans were examined. Their mean and maximum lifespans decreased with increasing oxygen concentration. The mean and maximum lifespans of the wild type under 60, 75, and 90% oxygen shrunk by 17 and 10, 31 and 31, and 40 and 41%, respectively, as compared with those under 21% oxygen (normal air). The mean and maximum lifespan of the zyg-9(b244) mutant under 60 and 90% oxygen shrunk by 18 and 22%, and 38 and 39%, respectively, as compared with those under 21% oxygen. The Gompertz analysis of the survival data of the wild type revealed that the exponential Gompertz component, the rate of acceleration of mortality, increased with increasing oxygen concentration: i.e. the ageing was accelerated under higher concentrations of oxygen. Oxygen acts as a lifespan determinant of the nematode. When the animals were exposed to a high concentration of oxygen at the early phase of lifespan, the oxygen-induced lifespan shortening was not observed. This means that oxygen-induced damage leading to lifespan shortening is repaired under 21% oxygen and that the oxygen-induced lifespan shortening does not result from any alteration in development and/or mutation. ------------------- Key: 1533 Medline: 92290129 Authors: Skiba F;Schierenberg E Title: Cell lineages, developmental timing, and spatial pattern formation in embryos of free-living soil nematodes. Citation: Developmental Biology 151: 597-610 1992 Type: ARTICLE Genes: Abstract: From soils of various origins we have isolated a number of nematode strains and cultured them on agar plates. We have analyzed their anatomy, reproduction, and particularly their pattern of embryogenesis. With respect to early cleavage we can define six different classes. The basic scheme of embryogenesis is similar in all strains but considerable differences were observed in detail. Embryogenesis is more than five times longer in the slowest strain than in the fastest. The following general correlation was found: The slower embryogenesis proceeds in a strain, the relatively earlier the cleavage of germline cells occurs. In the fastest strain the primordial germ cell P4 is present at the 24-cell stage, while in the slowest strain it is already generated in the 5-cell stage. We hypothesize that germline cleavages have to occur within a certain time limit to preserve germline quality. The typical reversal of cleavage polarity in the division of the germline cell P2 is absent in the slowest, on other grounds apparently more primitive strain. This results in an unusual spatial arrangement of cells transiently. However, prior to gastrulation as a consequence of compensatory cell migrations (which may indicate the necessity for cell interactions), the pattern becomes very similar to that in the other strains. We propose that a standard cellular configuration is required at the beginning of gastrulation to ensure normal further development. Early cell interactions might be necessary to achieve this standard pattern. In about half of the analyzed strains cellular structures can be marked with an antibody raised against germline-specific granules of Caenorhabditis elegans. Our results do not support the notion that the staining pattern for P granules is a useful indicator for phylogenetic ------------------- Key: 1534 Medline: 92269941 Authors: Goldstein B Title: Induction of gut in Caenorhabditis elegans embryos. Citation: Nature 357: 255-257 1992 Type: ARTICLE Genes: Abstract: Two types of developmental events can cause an embryonic cell to adopt a fate different from that of its neighbours: during a cell division particular contents may be segregated to only one daughter cell and cells may experience different external cues, commonly in the form of inductive cell interactions. Work on development in the nematode Caenorhabditis elegans suggests that most cell fates are specified without a need for cell interactions. In particular, the gut cell lineage of C. elegans has been used as a primary example of specification by differential segregation of determinants. Here I re- examine the role of induction in gut specification by isolating early blastomeres. In C. elegans, the gut derives from all the progeny of a single blastomere (E) of the eight-cell stage. When a gut precursor cell (EMS) is isolated during the first half of the four-cell stage, gut does not differentiate. Gut differentiation is rescued by recombining EMS with its posterior neighbour (P2), but not by recombining EMS with one or both of the other two cells of the four- cell stage. These results demonstrate that P2 induces EMS to form gut in C. elegans. ------------------- Key: 1535 Medline: 92241665 Authors: Stringham EG;Jones D;Candidio EP Title: Expression of the polyubiquitin-encoding gene (ubq-1) in transgenic Caenorhabditis elegans. Citation: Gene 113: 165-173 1992 Type: ARTICLE Genes: rol-6 ubq-1 unc-22 Abstract: The expression of the polyubiquitin-encoding gene (ubq-1) of Caenorhabditis elegans was analysed using transgenic nematode lines carrying translational ubq-1::lacZ fusions. Animals carrying a construct consisting of 938 bp of ubq-1 upstream sequences fused to lacZ (ubq938::lacZ) expressed beta Gal in embryos and in a tissue- general manner in 20% of L1 larvae. Somatic expression in later stages was usually confined to body muscle. Progressively larger deletions extending from the 5' end of ubq938::lacZ did not significantly alter the pattern of expression until 827 bp of sequence had been removed. Thus, sequences upstream from the transcription start point, including a G+C-rich block and a sequence resembling a TATA box (GAATAA), are not required to generate the expression pattern seen with ubq938::lacZ. Moreover, a basal level of expression was maintained in embryos when 903 bp were deleted. These results suggest that the promoter elements required for efficient expression of ubq-1 may reside within the transcribed region of the gene; alternatively, they must lie more than 1.7 kb upstream or 0.8 kb downstream from this region. Polymerase chain reaction analysis indicates that RNA molecules transcribed from the ubq938::lacZ and ubq delta 827::lacZ transgenes are trans-spliced to SL1, as is ubq-1 RNA. ------------------- Key: 1536 Medline: 92205341 Authors: Barinaga M Title: Signals into unknown territory. Citation: Science 255: 1640-1641 1992 Type: REVIEW Genes: sem-5 Abstract: Oncogene researchers and developmental geneticists used to inhabit separate territories, but work on cellular signal transduction pathways is bringing them closer together. ------------------- Key: 1537 Medline: 29195395 Authors: Pawson T Title: Cell signalling. Conviction by genetics. Citation: Nature 356: 285-286 1992 Type: NEWS Genes: clr-1 let-23 sem-5 Abstract: ------------------- Key: 1538 Medline: 92168144 Authors: Little P Title: DNA sequencing. The worm turns and delivers. Citation: Nature 356: 14-15 1992 Type: NEWS Genes: Abstract: Supporters of large DNA sequencing projects will take heart (and find much to learn) from the report by J. Sulston and colleagues that appears on page 37 of this issue. Sulston et al. describe the first results of the Caenorhabditis elegans genome sequencing project, and have come up with not only hitherto unknown genes but also with fresh and biologically relevant information. ------------------- Key: 1539 Medline: Authors: Anderson C;Aldous P Title: Genome project faces commercialization test. Citation: Nature 355: 483-484 1992 Type: NEWS Genes: Abstract: ------------------- Key: 1540 Medline: 92127587 Authors: Greenwald I;Rubin GM Title: Making a difference: the role of cell-cell interactions in establishing separate identities for equivalent cells. Citation: Cell 68: 271-281 1992 Type: REVIEW Genes: glp-1 let-23 let-60 lin-12 Abstract: Equivalent cells have the same set of potential fates and must choose one of the available options. In many cases, the choice is influenced by intercellular signaling events. If the signal originates outside the population of equivalent cells (equivalence group), the signaling process is termed induction. If the signal arises within the equivalence group, the signaling process is termed lateral specification (or lateral inhibition). Cells that do not receive and respond to the signal express a default fate, while cells that receive and respond to the signal express an alternative fate. In this review, we describe in detail one example of each process in Caenorhabditis elegans and Drosophila. In both organisms, powerful methods of genetic analysis and single cell resolution have facilitated the identification of molecules involved in induction and lateral specification, and are beginning to lead to an understanding of the biochemical circuitry that mediates cellular decisions. Common features emerge from a comparison of the worm and fly examples that are immediately applicable to higher organisms. Key components of identified signaling systems have proven to be members of highly conserved gene families, implying that similar molecular mechanisms underlie cell-cell interactions that specify cell fate decisions in all animals. ------------------- Key: 1541 Medline: Authors: Grewal PS;Wright DJ Title: Migration of Caenorhabditis elegans larvae towards bacteria and the nature of the bacterial stimulus. Citation: Fundamental and Applied Nematology 15: 159-166 1992 Type: ARTICLE Genes: Abstract: Chemotaxis by Caenorhabditis elegans larvae to several species of bacteria was studied on agar in specially designed Petri plates. All the bacteria affected the pattern of nematode migration and the degree of this alteration depended on the species of bacteria. Acinetobacter calcoaceticus var. anitratus, Enterobacter amnigenus, E. cloacae, Pseudomonas maltophilia and Serratia liquefaciens were more attractive than Escherichia coli and Pseudomonas fluorescens biovar reactans. Bacillus cereus, B. thuringiensis and Bacillus sp. showed least influence on nematode migration. Younger bacterial colonies (24-48 h old) were more attractive than the older ones (96-192 h old). When killed in-situ by chloroform fumes, bacterial colonies remained attractive to the nematode. Methods were developed to study the nature of the bacterial stimulus and the involvement of both diffusible and/or volatile attractants was found. ------------------- Key: 1542 Medline: 92249658 Authors: Dalley BK;Golomb M Title: Gene expression in the Caenorhabditis elegans dauer larva: developmental regulation of Hsp90 and other genes. Citation: Developmental Biology 151: 80-90 1992 Type: ARTICLE Genes: act-2 act-3 col-1 Abstract: Under conditions unfavorable to growth, the nematode Caenorhabditis elegans enters a developmentally arrested stage, the dauer larva. We have examined gene expression in the dauer larva and during recovery from the dauer stage. Run-on transcription assays with isolated nuclei reveal a depression of general RNA polymerase II transcription to 11-17% of that in other stages. Transcription of individual gene families (including actin, collagen, hsp70, and histone) is similarly depressed relative to actively growing stages. Dauer larvae are, however, capable of being induced for heat shock messages, indicating that they are competent to initiate and elongate transcripts. For most genes surveyed, reduced transcription in dauer larvae correlates with a decrease in message abundance. Hsp70 mRNA, however, is transcribed at lower rates but accumulates at levels comparable to those in other stages. Interestingly, dauer larvae are 15-fold enriched in a mRNA for a C. elegans hsp90 gene. Hsp90 mRNA accumulation is regulated at least in part by differential stability. Dauer larvae thus appear to have a unique pattern of gene expression. Upon placement in food, dauer larvae reenter the developmental pathway as late-stage larvae. Dauer recovery is accompanied by a temporally regulated sequence of gene expression. At least four distinct patterns of gene expression can be distinguished during exit from the dauer stage. Steady-state levels of hsp70 and polyubiquitin mRNA rise sharply within 75 min of recovery before declining by the fourth hour. Actin and histone mRNAs increase steadily following 2-4 hr of recovery, whereas myosin mRNA increases after 10 hr. In contrast, hsp90 mRNA declines sharply within the first 75 min of recovery. Changes in mRNA populations during dauer formation and exit may be ------------------- Key: 1543 Medline: 92306697 Authors: Yamamoto WS;Achacoso TB Title: Scaling up the nervous system of Caenorhabditis elegans: is one ape equal to 33 million worms? Citation: Computer & Biomedical Research 25: 279-291 1992 Type: ARTICLE Genes: Abstract: Although vastly different, both the mammalian brain and the nematode Caenorhabditis elegans' nervous system must contribute critically to assure survival. Two quantitative conditions which place bounds on networks for connectedness and stability are tested on the published neural network of C. elegans and fit. Consideration of networks scaled up to mammalian size and confined between these bounds suggests that perhaps, the entire spectrum of brain size may be built between these bounds. Further consequences of increasing brain size relate to the trade-off between complexity, providing internal resistance to individual damage, and redundancy of population, as survival ------------------- Key: 1544 Medline: 92281548 Authors: Hodgkin J Title: Genetic sex determination mechanisms and evolution. Citation: BioEssays 14: 253-261 1992 Type: REVIEW Genes: fem-1 fem-2 fem-3 fog-2 her-1 sdc-1 sdc-2 tra-1 tra-2 tra-3 xol-1 Abstract: Differnet animal groups exhibit a surprisingly diversity of sex determination systems. Moreover, even systems that are superficially similar may utilize differnet underlying mechanisms. This diversity is illustrated by a comparison of sex determination in three well-studied model organisms: the fruitfly Drosophila melanogaster, the nematode Caenorhabditis elegans, and the mouse. All three animals exhibit male heterogamety, extensive sexual dimorphism and sex chromosome dosage compensation, yet the molecular and cellular processes involved are now known to be quite unrelated. The similarities must have arisen by convergent evolution. Studies of sex determination demonstrates that evolution can produce a variety of solutions to the same basic problems in development. ------------------- Key: 1545 Medline: 92273014 Authors: Rankin CH;Broster BS Title: Factors affecting habituation and recovery from habituation in the nematode Caaenorhabditis elegans. Citation: Behavioral Neuroscience 106: 239-249 1992 Type: ARTICLE Genes: Abstract: In four experiments, the factors that affect the rate of habituation, the degree of habituation, and the rate of recovery from habituation in a simple reflex circuit in Caenorhabditis elegans were investigated. The results showed that habituation was more pronounced and faster, and that recovery from habituation was more rapid, with short interstimulus intervals (ISIs) than with longer ISIs. Rate of recovery differed in animals that had reached asymptotic response levels when compared with animals still in the descending portion of the habituation curve. Once animals reached asymptotic response levels, rate of recovery appeared to be determined by ISI and not by additional stimuli. ------------------- Key: 1546 Medline: 92127585 Authors: Horvitz HR;Herskowitz I Title: Mechanisms of asymmetric cell division: two Bs or not two Bs, that is the question. Citation: Cell 68: 237-255 1992 Type: ARTICLE Genes: glp-1 ham-1 lin-11 lin-12 lin-17 lin-18 lin-26 lin-44 Abstract: How sister cells have different fates is a fundamental aspect of the problem of how cell diversity is generated during development. In principle, sister cells that are different could be produced in two distinct ways. First, polar mother cells could divide to generate daughters that are different from the time they are formed. Alternatively, two identical sisters could be generated and become different as a consequence of some later event. Consideration of these mechansisms raises immediate further questions: What causes a mother cell to be polar? How do initially identical sister cells become different? And in each case, how do initial differences in sister cells lead to their ultimately distinct fates? Answers to these questions would provide important insights into the mechanisms responsible for the control of development. In this review we use the term "asymmetric cell division" to refer to any cell division in which sister cells have different fates... ------------------- Key: 1547 Medline: 92322641 Authors: Henikoff S Title: Detection of Caenorhabditis transposon homologs in diverse organisms. Citation: The New Biologist 4: 382-388 1992 Type: ARTICLE Genes: Abstract: Although transposons that move via DNA intermediates are common in bacteria, invertebrates, and plants, none have been clearly documented in vertebrates and certain other classes of organisms. One such family of transposons includes invertebrate elements related to Caenorhabditis elegans Tc1. Blocks of aligned protein segments derived from this family were used to search a nucleotide sequence databank. Among the relatives detected were known bacterial insertion elements, revealing the ancient origin of the family. Furthermore, a Tc1-like homolog was detected in a catfish, raising the possibility that this valuable tool of C. elegans genetics can be used with vertebrate genomes. This study illustrates the use of multiple protein blocks for detection and evaluation of distant relationships. ------------------- Key: 1548 Medline: 92293173 Authors: Dreyfus DH Title: Evidence suggesting an evolutionary relationship between transposable elements and immune system recombination sequences. Citation: Molecular Immunology 29: 807-810 1992 Type: ARTICLE Genes: Abstract: Sequence similarity between the termini of invertebrate Tc1-like transposable sequences and the signal sequences of the vertebrate immunoglobulin somatic recombination pathway is described. These similarities suggest that the Tc1 transposition pathway may share common sequence-specific binding factors with the immunoglobulin somatic recombination pathway. ------------------- Key: 1549 Medline: Authors: Olson MV Title: Genome sequencing: the lessons from the nematode. Citation: Current Biology 2: 221-223 1992 Type: REVIEW Genes: Abstract: The recent publication of the first results in the effort to sequence the entire nematode genome provides a first look at the type of biological information such projects may be expected to uncover. ------------------- Key: 1550 Medline: Authors: Olson EN;Perry WM Title: MyoD and paradoxes of myogenesis. Citation: Current Biology 2: 35-37 1992 Type: REVIEW Genes: Abstract: When the mammalian skeletal-muscle-specific transcription factors MyoD, myogenin, myf5 and MRF4, were first identified and shown to have the potential to activate myogenesis in nonmyogenic cell types, the molecular basis for establishment of the muscle phenotype seemed satisfyingly simple. These proteins share a 70-amino-acid region of homology that encompass a basic-helix-loop-helix (BHLH) motif that mediates oligomerization and binding to a conserved DNA sequence. That this conserved sequence is associated with most muscle-specific genes, seemed sufficient to explain the mechanism for activation of the set of genetically unlinked genes that is induced during myogenesis... ------------------- Key: 1551 Medline: Authors: Fyrberg E Title: Cytoskeleton: The worm turns to vinculin function. Citation: Current Biology 2: 1-3 1992 Type: REVIEW Genes: deb-1 Abstract: The identification of a mutant nematode that has little muscle function and no vinculin has opened the door to a new approach to understanding adhesion plaque function. ------------------- Key: 1552 Medline: 92189726 Authors: Ruvolo V;Hill JE;Levitt A Title: The Tc2 transposon of Caenorhabditis elegans has the structure of a self-regulated element. Citation: DNA and Cell Biology 11: 111-122 1992 Type: ARTICLE Genes: Abstract: We have analyzed the sequence of the Tc2 transposon of the nematode Caenorhabditis elegans. The Tc2 element is 2,074 bp in length and has perfect inverted terminal repeats of 24 bp. The structure of this element suggests that it may have the capacity to code for a transposase protein and/or for regulatory functions. Three large reading frames on one strand exhibit nonrandom codon usage and may represent exons. The first open coding region is preceded by a potential CAAT box, TATA box, and consensus heat shock sequence. In addition to its inverted terminal repeats, Tc2 has an unusual structural feature: subterminal degenerate direct repeats that are arranged in an irregular overlapping pattern. We have also examined the insertion sites of two Tc2 elements previously identified as the cause of restriction fragment length polymorphisms. Both insertions generated a target site duplication of 2 bp. One element had inserted inside the inverted terminal repeat of another transposon, splitting it into two unequal parts. ------------------- Key: 1553 Medline: 92360913 Authors: Kuwabara PE;Okkema PG;Kimble J Title: tra-2 encodes a membrane-protein and may mediate cell communication in the Caenorhabditis elegans sex determination pathway. Citation: Molecular Biology of the Cell 3: 461-473 1992 Type: ARTICLE Genes: fem-1 fem-2 fem-3 her-1 sdc-1 tra-1 tra-2 Abstract: The Caenorhabditis elegans sex-determining gene, tra-2, promotes female development in XX animals. In this paper we report the cDNA sequence corresponding to a 4.7 kb tra-2 mRNA and show that it is composed of 23 exons, is trans-spliced to SL2, and contains a perfect direct repeat in the 3' untranslated region. This mRNA is predicted to encode a 1475 amino acid protein, named pTra2A, that has a secretory signal and several potential membrane-spanning domains. The molecular analysis of tra-2 loss-of-function mutations supports our open reading frame identification and suggests that the carboxy- terminal domain is important for tra-2 activity. We propose that in XX animals the carboxy-terminal domain of pTra2A negatively regulates the downstream male promoting fem genes. In XO animals, tra-2 is negatively regulated by her-1, which acts cell nonautonomously. Because hydropathy predictions suggest that pTra2A is an integral membrane protein, pTra2A might act as a receptor for the her-1 protein. We propose that in XO animals, the her-1 protein promotes male development by binding and inactivating pTra2A. The role of cell communication in C. elegans sex determination might be to ensure unified sexual development throughout the animal. If so, then regulation of sexual fate by her-1 and tra-2 might provide a general model for the coordination of groups of cells to follow a single cell fate. ------------------- Key: 1554 Medline: 95334841 Authors: Kuwabara PE;Kimble J Title: Molecular genetics of sex determination in C. elegans. Citation: Trends in Genetics 8: 164-168 1992 Type: REVIEW Genes: fem-1 fem-2 fem-3 fog-1 her-1 mab-3 sdc-1 sdc-2 tra-1 tra-2 tra-3 xol-1 Abstract: Sexual fate in the nematode Caenorhabditis elegans is controlled by a group of genetically well-characterized genes. Several of these sex-determining genes have now been analysed at the molecular level. Transcriptional regulation is likely to control both commitment to a single sexual fate and maintenance of that decision; in addition, intercellular signalling appears to coordinate the sexual fates of cells throughout the animal to adopt a single ------------------- Key: 1555 Medline: 92237328 Authors: Rohrer SP;Meinke PT;Hayes EC;Mrozik H;Schaeffe JM Title: Photoaffinity-labeling of avermectin binding-sites from Caenorhabditis elegans and Drosophila melanogaster. Citation: Proceedings of the National Academy of Sciences USA 89: 4168-4172 1992 Type: ARTICLE Genes: Abstract: An azido-avermectin analog [4'' alpha-(4-azidosalicylamido-epsilon- caproylamido-beta-alan ylamido)-4''-deoxyavermectin B1a; azido-AVM] was synthesized and used to photoaffinity label avermectin binding sites present in the membranes of Caenorhabditis elegans and Drosophila melanogaster. Azido-AVM was biologically active and behaved like a competitive inhibitor of [3H]ivermectin binding to C. elegans membranes (Ki = 0.2 nM). Radiolabeled azido-AVM bound specifically and with high affinity to C. elegans membranes (Kd = 0.14 nM) and, upon photoactivation, became covalently linked to three C. elegans polypeptides of 53, 47, and 8 kDa. Photoaffinity labeling of a membrane preparation from D. melanogaster heads resulted in labeling of a single major polypeptide of approximately 47 kDa. The proteins that were covalently tagged in these experiments are believed to be associated with avermectin-sensitive chloride channels present in the neuromuscular systems of C. elegans and D. melanogaster. Azido-AVM did not bind to rat brain membranes and therefore was selective for the nematode and insect ------------------- Key: 1556 Medline: 92348337 Authors: Hirabayashi J;Satoh M;Ohyama Y;Kasai K Title: Purification and characterization of Beta-galactoside-binding proteins from Caenorhabditis elegans. Citation: Journal of Biochemistry 111: 553-555 1992 Type: ARTICLE Genes: Abstract: Two carbohydrate-binding proteins (subunit molecular masses, 32 and 16 kDa, respectively) were isolated for the first time from a nematode, Caenorhabditis elegans. They were specifically extracted with lactose and adsorbed on asialofetuin-Sepharose in the absence of a metal ion. Although these two proteins were co-eluted from a gel filtration column at a position corresponding to an apparent molecular size of 30 kDa under non-denaturing conditions, they could be separated by reversed-phase chromatography. The 32 kDa protein, the main component, was further characterized. Together with its solubility, saccharide specificity and metal independence, some other structural properties, including its amino acid composition, UV spectrum, and partial amino acid sequence, strongly suggested that the 32 kDa protein is a member of a class of soluble beta-galactoside- binding lectins which had previously been only found in vertebrates. ------------------- Key: 1557 Medline: 92293121 Authors: McKim KS;Starr T;Rose AM Title: Genetic and molecular analysis of the dpy-14 region in Caenorhabditis elegans. Citation: Molecular & General Genetics 233: 241-251 1992 Type: ARTICLE Genes: dpy-5 dpy-14 let-75 let-76 let-80 let-81 let-82 let-85 let-86 let-87 let-88 let-89 let-90 let-351 let-383 let-385 let-389 let-392 let-394 let-397 let-398 let-399 let-400 let-520 let-521 let-522 let-523 let-524 let-525 let-527 let-528 let-529 let-534 let-535 let-538 let-539 let-540 let-542 let-543 let-544 let-545 let-605 lin-6 mec-8 sem-4 unc-1 unc-11 unc-13 unc-14 unc-15 unc-29 unc-37 unc-55 unc-87 hDf6 hDf8 hDf9 nDf23 nDf24 nDf25 nDf43 sDf4 sDf5 sDf6 hDp4 hDp13 hDp14 hDp19 hDp33 hDp35 hDp36 hDp39 hDp42 hDp43 hDp50 hDp58 hDp60 hDp62 hDp64 hDp65 hDp70 hDp73 hDp102 nDp4 sDp2 sDp30 szDp1 Abstract: Essential genes have been identified in the 1.5 map unit (m.u.) dpy- 14-unc-29 region of chromosome 1 in Caenorhabditis elegans. Previous work defined nine genes with visible mutant phenotypes and nine genes with lethal mutant phenotypes. In this study, we have identified an additional 28 essential genes with 97 lethal mutations. The mutations were mapped using eleven duplication breakpoints, eight deficiencies and three-factor recombination experiments. Genes required for the early stages of development were common, with 24 of the 37 essential genes having mutant phenotypes arresting at an early larval stage. Most mutants of a gene have the same time of arrest; only four of the 20 essential genes with multiple alleles have alleles with different phenotypes. From the analysis of complementing alleles of let-389, alleles with the same time-of-arrest phenotype were classified as either hypomorphic or amorphic. Mutants of let-605, let-534 and unc- 37 have both uncoordinated and lethal phenotypes, suggesting that these genes are required for the coordination of movement and for viability. The physical and genetic maps in the dpy-14 region were linked by positioning two N2/BO polymorphisms with respect to duplications in the region, and by localizing the right breakpoint of the deficiency hDf8 on the physical map. Using cross-species hybridization to C. briggsae, ten regions of homology have been identified, eight of which are known to be coding regions, based on Northern analysis and/or the isolation of cDNA clones. ------------------- Key: 1558 Medline: 92354885 Authors: Zetka MC;Rose AM Title: The meiotic behavior of an inversion in Caenorhabditis elegans. Citation: Genetics 131: 321-332 1992 Type: ARTICLE Genes: bli-3 bli-4 dpy-3 dpy-5 dpy-11 dpy-18 him-5 let-49 let-50 lev-11 lin-11 lon-2 unc-1 unc-10 unc-11 unc-29 unc-36 unc-42 unc-54 unc-59 unc-75 unc-101 mnC1 hDf11 hDf12 hDp131 hDp132 hIn1 hT2 szT1 Abstract: The rearrangement hIn1(I) was isolated as a crossover suppressor for the right end of linkage group (LG) I. By inducing genetic markers on this crossover suppressor and establishing the gene order in the homozygote, hIn1(I) was demonstrated to be the first genetically proven inversion in Caenorhabditis elegans. hIn1(I) extensively suppresses recombination in heterozygotes in the right arm of chromosome I from unc-75 to unc-54. This suppression is associated with enhancement of recombination in other regions of the chromosome. The enhancement observed maintains the normal distribution of events but does not extend to other chromosomes. The genetic distance of chromosome I in inversion heterozygotes approaches 50 map units (m.u.), approximately equal to one chiasma per meiosis. This value is maintained in hIn1(I)/szT1(I;X) heterozygotes indicating that small homologous regions can pair and recombine efficiently. hIn1(I)/hT2(I;III) heterozygotes share no uninverted homologous regions and segregate randomly, suggesting the importance of chiasma formation in proper segregation of chromosomes. The genetic distance of chromosome I in these heterozygotes is less that 1 m.u., indicating that crossing over can be suppressed along an entire chromosome. Since one of our goals was to develop an efficient balancer for the right end of LGI, the effectiveness of hIn1(I) as a balancer was tested by isolating and maintaining lethal mutations. The meiotic behaviour of hIn1(I) is consistent with other genetic and cytogenetic data suggesting the meiotic chromosomes are monocentric. Rare recombinants bearing duplications and deficiencies of chromosome I were recovered from hIn1(I) heterozygotes, leading to the proposal the inversion was paracentric. ------------------- Key: 1559 Medline: 92344659 Authors: Emmons SW Title: From cell fates to morphology-developmental genetics of the Caenorhabditis elegans male tail. Citation: BioEssays 14: 309-316 1992 Type: REVIEW Genes: egl-5 mab-3 mab-5 mab-9 pal-1 tra-1 Abstract: The C. elegans male tail is being studied as a model to understand how genes specify the form of multicellular animals. Morphogenesis of the specialized male copulatory organ takes place in the last larval stages during male development. Genetic analysis is facilitated because the structure is not necessary for male viability or for strain propagation. Analysis of developmental mutants, isolated in several functional and morphological screens, has begun to reveal how fates of cells are determined in the cell lineages, and how the specification of cell fates affects the morphology of the structure. Cytological studies in wild type and in mutants have been used to study the mechanism of pattern formation in the tail peripheral nervous system. The ultimate goal is to define the entire pathway leading to the male copulatory organ. ------------------- Key: 1560 Medline: 92289695 Authors: Ahringer J;Rosenquist TA;Lawson DN;Kimble J Title: The Caenorhabditis elegans sex determining gene fem-3 is regulated post-transcriptionally. Citation: EMBO Journal 11: 2303-2310 1992 Type: ARTICLE Genes: act-1 fem-2 fem-3 fog-1 fog-2 glp-1 spe-8 tra-1 Abstract: The fem-3 gene of Caenorhabditis elegans is required for male development. Both maternal and zygotic fem-3 activities are required for spermatogenesis in the XX hermaphrodite germline and for male development in somatic and germline tissues XO (male) animals. Here we show that fem-3 RNA is contributed to embryos as a maternal product and that this RNA is degraded early in embryonic development. The poly(A) tail of embryonic fem-3 RNA is substantially longer than that of adult hermaphrodites which indicates that poly(A) tail lengthening probably occurs at or soon after fertilization. During subsequent development, fem-3 poly(A) tails shorten. The amount of fem-3 RNA in XX and XO embryos is equivalent, suggesting sex-specific regulation of maternal fem-3 activity occurs post-transcriptionally. The sequence of fem-3 predicts an open reading frame that could encode a soluble protein; putative fem-3 null mutants truncate this open reading frame. We discuss the implications of these results for the regulation and function of fem-3. ------------------- Key: 1561 Medline: 92300457 Authors: Rosoff ML;Burglin TR;Li C Title: Alternatively spliced transcripts of the flp-1 gene encode distinct FMRFamide-like peptides in Caenorhabditis elegans. Citation: Journal of Neuroscience 12: 2356-2361 1992 Type: ARTICLE Genes: flp-1 vit-4 vit-5 Abstract: We have isolated and characterized several cDNAs and the corresponding genomic region of a gene encoding multiple FMRFamide-like neuropeptides from the nematode Caenorhabditis elegans. The gene, named flp-1, consists of six exons of which four encode FMRFamide-like peptides. The cDNA and genomic sequences revealed that two distinct transcripts are generated by the use of an alternative 3' splice acceptor site between exons 3 and 4. This alternative splice results in the substitution of AGSDPNFLRFG for one of the copies of SADPNFLRFG found in the other translation product. Based on PCR analysis of RNA from mixed-stage animals, both transcripts are expressed. The gene is the first example of a distinct FMRFamide-like peptide being derived from alternative splicing, suggesting a unique role for the substituted ------------------- Key: 1562 Medline: Authors: Vanfleteren JR Title: Cu-Zn superoxide dismutase from Caenorhabditis elegans: purification, properties and isoforms. Citation: Comparative Biochemistry & Physiology B-Comparative Biochemistry 102: 219-229 1992 Type: ARTICLE Genes: age-1 Abstract: 1. Cytosolic superoxide dismutase was purified to homogeneity from Caenorhabditis elegans tissue. The active enzyme had a specific activity of 2660 U/mg protein, a molecular mass of 37.5-40 kDA, and appeared to be composed of 2 subunits of approximately 17 kDA. A subunit molecular mass of 16 kDa was determined for protein unfolded in the absence of reducing agents, suggesting the presence of an intramolecular disulfide bond. 2. The enzyme preparation contained a number of charge isoforms having pI values of 9.0, 8.1 (major fraction), 6.9, and 5.2 (minor fractions). These charge isoforms were also present in freshly made homogenates. 3. No alteration of the electrophoretic pattern was observed in ctyosolic extracts from the mutant strain TJ412 which has a 100% longer life expectancy and which overproduces cytosolic superoxide dismutase. ------------------- Key: 1563 Medline: 92331900 Authors: Williams BD;Schrank B;Huynh C;Shownkeen R;Waterston RH Title: A genetic-mapping system in Caenorhabditis elegans based on polymorphic sequence-tagged sites. Citation: Genetics 131: 609-624 1992 Type: ARTICLE Genes: deb-1 dpy-1 dpy-3 dpy-5 dpy-9 dpy-10 dpy-11 dpy-18 dpy-21 lev-11 rol-9 sqt-2 unc-4 unc-22 unc-23 unc-27 unc-29 unc-45 unc-52 unc-60 unc-75 unc-90 unc-95 unc-101 Abstract: We devised an efficient genetic mapping system in the nematode Caenorhabditis elegans which is based upon the differences in number and location of the transposable element Tc1 between the Bristol and Bergerac strains. Using the nearly completed physical map of the C. elegans genome, we selected 40 widely distributed sites which contain a Tc1 element in the Bergerac strain, but not in the Bristol strain. For each site a polymerase chain reaction assay was designed that can distinguish between the Bergerac Tc1-containing site and the Bristol "empty" site. By combining appropriate assays in a single reaction, one can score multiple sites within single worms. This permits a mutation to be rapidly mapped, first to a linkage group and then to a chromosomal subregion, through analysis of only a small number of progeny from a single interstrain cross. ------------------- Key: 1564 Medline: 92371904 Authors: Novak J;Vanek Z Title: Screening for a new generation of anthelmintic compounds. In vitro selection of the nematode Caenorhabditis elegans for ivermectin resistance. Citation: Folia Microbiologica (Prague) 37: 237-238 1992 Type: ARTICLE Genes: Abstract: Development of resistance to ivermectin in vitro is reported for the first time. Two strains of Caenorhabditis elegans D5 and D6 able to grow on agar plates after treating with up to 3 mg ivermectin per L were selected. The parent strain N2 was extremely sensitive to ivermectin, its growth being inhibited by treatment with 0.1-0.2 mg IVM ------------------- Key: 1565 Medline: 92318259 Authors: Naclerio G;Cangiano G;Coulson A;Levitt A;Ruvolo V;LaVolpe A Title: Molecular and genomic organization of clusters of repetitive DNA sequences in Caenorhabditis elegans. Citation: Journal of Molecular Biology 226: 159-169 1992 Type: ARTICLE Genes: Abstract: Repetitive sequences in Caenorhabditis elegans are interspersed along the holocentric chromosomes. We have physically mapped some of these repetitive families and found that, although the distribution of members of each family is relatively even along the chromosomes, members of more than one family tend to cluster in some locations. We compared the sequence organization of 11 clusters located at known positions on different chromosomes in the N2 strain. These studies allow a comparison between repetitive elements belonging to the same family that are located on the same or on different chromosomes, providing an important tool in the study of genome turnover and ------------------- Key: 1566 Medline: 93250982 Authors: Waterston R;Martin C;Craxton M;Hunyh C;Coulson A;Hillier L;Durbin R;Green P;Shownkeen R;Halloran N Title: A survey of expressed genes in Caenorhabditis elegans. Citation: Nature Genetics 1: 114-123 1992 Type: ARTICLE Genes: Abstract: GENBANK As an adjunct to the genomic sequencing of Caenorhabditis elegans, we have investigated a representative cDNA library of 1,517 clones. A single sequence read has been obtained from the 5' end of each clone, allowing its characterization with respect to the public databases, and the clones are being localized on the genome map. The result is the identification of about 1,200 of the estimated 15,000 genes of C . elegans . More than 30% of the inferred protein sequences have significant similarity to existing sequences in the databases, providing a route towards in vivo analysis of known genes in the nematode. These clones also provide material for assessing the accuracy of predicted exons and splicing patterns and will lead to a more accurate estimate of the total number of genes in the organism than has hitherto ------------------- Key: 1567 Medline: 93250983 Authors: McCombie WR;Adams MD;Kelley JM;Fitzgerald MG;Utterback TR;Khan M;Dubnick M;Kerlavage AR;Venter JC;Fields C Title: Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologs. Citation: Nature Genetics 1: 124-131 1992 Type: ARTICLE Genes: act-1 act-2 act-3 act-4 col-1 col-2 col-6 col-12 col-13 col-14 daf-15 dpy-8 dpy-13 fem-1 let-60 lon-2 myo-1 rad-7 sqt-1 unc-5 unc-15 vit-2 vit-5 Abstract: A database containing mapped partial cDNA sequences from Caenorhabditis elegans will provide a ready starting point for identifying nematode homologues of important human genes and determining their functions in C . elegans . A total of 720 expressed sequence tags (ESTs) have been generated from 585 clones randomly selected from a mixed-stage C . elegans cDNA library. Comparison of these ESTs with sequence databases identified 422 new C . elegans genes, of which 317 are not similar to any sequences in the database. Twenty-six new genes have been mapped by YAC clone hybridization. Members of several gene families, including cuticle collagens, GTP-binding proteins, and RNA helicases were discovered. Many of the new genes are similar to known or potential human disease genes, including CFTR and the LDL receptor. ------------------- Key: 1568 Medline: 92319619 Authors: Naito M;Kohara Y;Kurosawa Y Title: Identification of a homeobox-containing gene located between lin-45 and unc-24 on chromosome IV in the nematode Caenorhabditis elegans. Citation: Nucleic Acids Research 20: 2967-2969 1992 Type: ARTICLE Genes: ceh-3 ceh-13 ceh-15 ceh-19 lin-11 lin-45 mab-5 mec-3 unc-24 Abstract: Using two primers corresponding to helix 1 and helix 3 regions in the homeodomain, we subjected genomic DNA from Caenorhabditis elegans to amplification by the polymerase chain reaction. Sequence analysis of the amplified products revealed a new homeobox-containing gene, designated ceh-19. This gene was located between lin-45 and unc-24 on chromosome IV where no homeogene has previously been ------------------- Key: 1569 Medline: 92331819 Authors: Azzaria M;McGhee JD Title: DNA synthesis in the early embryo of the nematode Ascaris suum. Citation: Developmental Biology 152: 89-93 1992 Type: ARTICLE Genes: Abstract: We have used microspectrofluorimetry to measure the rate of DNA synthesis in the first two embryonic cell cycles of the parasitic nematode Ascaris suum. The S-phase of the early Ascaris cell cycles occupies at most 1 hr; G2 phase is prominent and occupies approximately 11 hr; no G1 phase could be detected. These results contrast with our previous measurements made with embryos of the free-living nematode Caenorhabditis elegans, in which the earliest cell cycles consist of simple alternations between S and M phases. ------------------- Key: 1570 Medline: 92347322 Authors: Hamelin M;Scott IM;Way JC;Culotti JG Title: The mec-7 Beta-tubulin gene of Caenorhabditis elegans is expressed primarily in the touch receptor neurons. Citation: EMBO Journal 11: 2885-2893 1992 Type: ARTICLE Genes: lin-14 lin-32 mec-3 mec-4 mec-7 mec-12 mec-17 rol-6 unc-24 unc-54 unc-86 Abstract: Mutants of the mec-7 beta-tubulin gene of Caenorhabditis elegans lack the large diameter 15-protofilament microtubules normally found only in the set of six touch receptor neurons. Both a mec-7-lacZ reporter gene and affinity-purified anti-mec-7 antibodies were used to show that mec-7 is expressed primarily in the touch neurons. These data are consistent with a possible instructive role for the mec-7 tubulin in determining microtubule protofilament number. The antibodies and the mec-7-lacZ transgene were also used to examine mec-7 expression in mutants affecting the generation, differentiation or maintenance of the touch neurons. Decreased expression was observed in mutants of unc-86 and mec-3, genes that encode transcription factors essential for touch receptor neuron generation and differentiation, respectively. ------------------- Key: 1571 Medline: 92346712 Authors: Zarkower D;Hodgkin J Title: Molecular analysis of the C. elegans sex-determining gene tra-1: a gene encoding 2 zinc finger proteins. Citation: Cell 70: 237-249 1992 Type: ARTICLE Genes: act-1 fer-2 glp-4 him-8 myo-1 pha-1 tra-1 Abstract: The tra-1 gene is the terminal control gene for somatic sex determination in the nematode Caenorhabditis elegans. Here we identify two tra-1 mRNAs: one is a 1.5 kb transcript that peaks in abundance in the second larval stage, and the other is a 5 kb transcript that is present at relatively constant abundance throughout development. Both RNAs occur at similar levels in both sexes, suggesting that regulation of tra-1 is posttranscriptional. Neither RNA is germline restricted. The two RNAs are colinear at their 5' ends: the shorter RNA encodes a protein with two zinc finger motifs, and the longer RNA encodes a protein with five zinc fingers. The identification of eight nonsense mutations confirms that these are authentic tra-1 RNAs and demonstrates that the longer one is essential for tra-1 activity. The transcription pattern reveals that alternative mRNA processing governs the number of zinc fingers in the resulting tra-1 protein. The tra-1 fingers are strikingly similar to those of three other proteins, the products of the human GLI and GLI3 and Drosophila cubitus interruptus Dominant (ciD) genes. ------------------- Key: 1572 Medline: 92348399 Authors: Hirabayashi J;Satoh M;Kasai K Title: Evidence that C. elegans 32kDa Beta-galactoside-binding pritein is homologous to vertebrate Beta-galactoside-binding lectins- cDNA cloning and deduced Citation: Journal of Biological Chemistry 267: 15485-15490 1992 Type: ARTICLE Genes: Abstract: We have cloned a full-length cDNA for a beta-galactoside-binding protein with a relative molecular mass of 32 kDa (32-kDa GBP), recently purified from a nematode, Caenorhabditis elegans (Hirabayashi, J., Satoh, M., Ohyama, Y., and Kasai, K. (1992) J. Biochem. 111, 553-555). The clone contained a single open reading frame encoding 279 amino acids, including the initiator methionine. Significant sequence homology to metal-independent beta-galactoside- binding lectins (25-30% identities), which had previously been found only in vertebrates, was observed. Moreover, the nematode 32-kDa GBP proved to have a unique polypeptide architecture; that is, it is composed of two tandemly repeated homologous domains, each consisting of about 140 amino acids. The internal homology was about 32%. Thus, this protein is constructed with a duplicated fundamental unit which is similar to the subunit of vertebrate 14-kDa lectins. In spite of the extreme phylogenic distance between nematodes and vertebrates (divergence greater than 6 x 10(8) years ago), both of the two repeated domains of the nematode 32-kDa GBP retained most of the amino acid residues conserved in vertebrate lectins. This means that members of the metal-independent animal lectin family are distributed much more widely than had been believed: from nematodes to vertebrates. The implication is that proteins belonging to this family have fundamental roles which are not restricted to vertebrates but are common to almost all animals. ------------------- Key: 1573 Medline: 92350298 Authors: Hill RJ;Sternberg PW Title: The gene lin-3 encodes an inductive signal for vulval development in C. elegans. Citation: Nature 358: 470-476 1992 Type: ARTICLE Genes: dpy-20 him-5 let-23 let-60 lin-3 lin-12 lin-15 mut-6 unc-4 unc-22 unc-31 Abstract: The lin-3 gene is necessary for induction of the Caenorhabditis elegans vulva by the anchor cell. It encodes a molecule similar to epidermal growth factor and to transforming growth factor-alpha and acts through the epidermal growth factor receptor homologue let-23. Expression of lin-3 in the anchor cell stimulates vulval induction; lin-3 may encode the vulval inducing signal. ------------------- Key: 1574 Medline: 93007822 Authors: Peixoto CA;de Souza W Title: Cytochemical characterization of the cuticle of Caenorhabditis elegans. Citation: Journal of Submicroscopic Cytology 24: 425-435 1992 Type: ARTICLE Genes: Abstract: At the ultrastructural level, the Caenorhabditis elegans (Maupas, 1990; Doughert, 1953) cuticle shows the presence of six layers: epicuticle, external cortical, internal cortial, intermediate, fibrous and basal. Two techniques were used for carbohydrate localization: the periodic acid-thiosemiarbazide-silver proteinate (Thiery) and gold-labelled lectins. No labelling was found on the nematode's cuticle. With the ethanolic phosphotungstic acid technique (E-PTA), that detects basic proteins, reaction product was observed in the outer cortical layer, in the cuticle struts and in the dense bodies of the muscle cell. Surface anionic sites of C . elegans were visualized by using cationized ferritin particles, at pH 7.2, and by using colloidal iron hydroxide particles at pH 1.8. Treatments with trypsin and neuraminidase (Vibrio cholerae) did not interfere with the binding of the cationic particles to the nematode's surface. In contrast, treatment with chondroitinase ABC, a specific enzyme for glycosaminoglycans, significantly reduced the binding. ------------------- Key: 1575 Medline: 93075116 Authors: Golden A;Sternberg PW Title: The roles of SH2/SH3 domains in nematode development. Citation: BioEssays 14: 481-484 1992 Type: REVIEW Genes: clr-1 egl-15 let-23 let-60 lin-15 sem-5 Abstract: During the past few years, intensive research has focused on elucidating the function of two polypeptide domains known as SH2 and SH3 (for src homology). These two domains were originally recognized in the non-catalytic regions of non-receptor tyrosine kinases. It was then discovered that a class of cytoplasmic proteins that complex with ligand-stimulated receptor tyrosine kinases contain SH2 and SH3 domains. Among these proteins are the GTPase-activating protein (GAP) of p21 ras, phospholipase C-y, and the 85 kD subunit of ------------------- Key: 1576 Medline: 92387525 Authors: Link CD;Silverman MA;Breen M;Watt KE;Dames SA Title: Characterization of Caenorhabditis elegans lectin-binding mutants. Citation: Genetics 131: 867-881 1992 Type: ARTICLE Genes: glp-1 her-1 lin-12 mec-7 rol-9 srf-2 srf-3 srf-4 srf-5 srf-8 srf-9 unc-6 unc-51 unc-68 ctDf1 mDf3 ozDf1 ozDf2 sDf20 sDf29 sDf35 yDf4 Abstract: We have identified 45 mutants of Caenorhabditis elegans that show ectopic surface binding of the lectins wheat germ agglutinin (WGA) and soybean agglutinin (SBA). These mutations are all recessive and define six genes: srf-2, srf-3, srf-4, srf-5, srf-8 and srf-9. Mutations in these genes fall into two phenotypic classes: srf-2, -3, -5 mutants are grossly wild-type, except for their lectin-binding phenotype; srf-4, -8, -9 mutants have a suite of defects, including uncoordinated movement, abnormal egg laying, and defective copulatory bursae morphogenesis. Characterization of these pleiotropic mutants at the cellular level reveals defects in the migration of the gonadal distal tip cell and in axon morphology. Unexpectedly, the pleiotropic mutations also interact with mutations in the lin-12 gene, which encodes a putative cell surface receptor involved in the control of cell fate. We propose that the underlying defect in the pleiotropic mutations may be in the general processing or secretion of extracellular proteins. ------------------- Key: 1578 Medline: 95099572 Authors: Avery L;Wasserman S Title: Ordering gene function: the interpretation of epistasis in regulatory hierarchies. Citation: Trends in Genetics 8: 312-316 1992 Type: REVIEW Genes: ced-1 ced-3 daf-1 daf-12 her-1 let-23 let-60 lin-4 lin-14 lin-15 tra-1 Abstract: The order of action of genes in a regulatory hierarchy that is governed by a signal can often be determined by the method of epistasis analysis, in which the phenotype of a double mutant is compared with that of single mutants. The epistatic mutation may be in either the upstream or the downstream gene, depending on the nature of the two mutations and the type of regulation. Nevertheless, when the regulatory hierarchy satisfies certain conditions, simple rules allow the position of the epistatic locus in the pathway to be determined without detailed knowledge of the nature of the mutations, the pathway, or the molecular mechanisms of regulation. ------------------- Key: 1579 Medline: 93250989 Authors: Bargmann CI Title: cDNA sequencing: a report from the worm front. Citation: Nature Genetics 1: 79-80 1992 Type: REVIEW Genes: Abstract: Predicting coding regions from genomic sequence is not entirely accurate, and predicting expression patterns of candidate genes is still a fantasy. Both of these concerns can be addressed by analysing expressed sequences (cDNA) in addition to genomic sequences. The genomic sequencing of the nematode Caenorhabditis elegans has begun; in parallel, several groups (including the genomic sequencing participants) are isolating, sequencing and mapping C. elegans cDNA clones. The first results of this endeavor, including the analysis of about 1,600 independent cDNA sequences, appear in this issue. ------------------- Key: 1580 Medline: Authors: Baird SE;Sutherlin ME;Emmons SW Title: Reproductive isolation in Rhabditidae (Nematoda: Secernentea); mechanisms that isolate six species of three genera. Citation: Evolution 46: 585-594 1992 Type: ARTICLE Genes: plg-1 Abstract: We have attempted interspecific hybridizations among six species of rhabditid nematodes: Caenorhabditis elegans, Caenorhabditis briggsae, Caenorhabditis remaiei, Caenorhabditis sp. v, Rhabditis sp., and Pelodera teres. Copulation was observed in all crossed between Caenorhabditis species; however, none resulted in the generation of stable hybrid populations. No copulation was observed in crosses between Caenorhabditis males and Rhabditis or Pelodera females, even when congeneric females were present, suggesting that Caenorhabditis males are able to selectively recognize congeneric females by a short-range stimulus. All pairwise combinations of Caenorhabditis species were isolated to some degree by gametic mechanisms: 7 of 12 combinations were cross infertile and 5 of 12 were cross-fertile but had low brood sizes. In cross-fertile combinations, most hybrid embryos were inviable and arrested prior to gastrulation. Only in crosses of C. briggsae males to C. sp. m females did any hybrids survive embryogenesis. Most of these C. briggsae/C. sp. v hybrids arrested during larval development, and the few that reached adulthood invariably were female. These results are consistent with the presence of at least two lethal factors in the C. briggsae-C. sp. v combination: a maternal lethal factor in the cytoplasm of C. briggsae and a recessive lethal factor ------------------- Key: 1581 Medline: Authors: Schierenberg E;Strome S Title: The establishment of embryonic axes and determination of cell fates in embryos of the nematode Caenorhabditis elegans. Citation: Seminars in Developmental Biology 3: 25-33 1992 Type: ARTICLE Genes: par-2 par-3 Abstract: At the 4-cell stage of the C. elegans embryo, three axes can be defined: anterior-posterior (A-P), dorsal-ventral (D-V), and left-right (L-R). The A-P axis first becomes obvious in the newly fertilized 1-cell embryo. Pronouned cytoplasmic assymmetries arise along the A-P axis during the first cell cycle, after which the zygote undergoes a series of stem cell-like cleavages with an A-P orientation of the mitotic spindle; these cleavages generate several somatic founder cells and a primordial germ cell. The D-V and L-R axes are defined by the direction of spindle rotation as the 2-cell embryo divides into four cells. In contrast to the A-P axis, there do not appear to be cellular asymmetries associated with the D-V and L-R axes, and both axes can easily be reversed by micromanipulation. Thus, with respect to the roles that the embryonic axes serve in cell-fate determination in the early C. elegans embryo, it appears that internally transmitted developmental information is differentially segregated along the A-P axis, but not along the D-V or L-R axes. Instead, D-V and L-R differences in the fates of cells within lineages appear to be dictated by differential ------------------- Key: 1582 Medline: Authors: Priess JR Title: Caenorhabditis elegans morphogenesis. Morphogenesis, An Analysis of the Development of Biological Form. Citation: : 129-142 1992 Type: REVIEW Genes: ced-3 ced-4 glp-1 lin-12 sqt-3 Abstract: Nematodes are generally small animals that superficially resemble miniature earthworms in overall shape. Although the morphology of Caenorhabditis elegans is very simple, the establishment or maintenance of this shape involves a large number of genes. Mutant C. elegans strains have been isolated in which worms are short and fat, abnormally long and thin, twisted into a left or right helix, or covered with irregular lumps. This chapter deals with experiments and observations that suggest how the basic shape of the nematode is first established during embryogenesis and why certain genes may be essential for normal morphogenesis. ------------------- Key: 1584 Medline: 92323546 Authors: Mello CC;Draper BW;Krause M;Weintraub H;Priess JR Title: The pie-1 and mex-1 genes and maternal control of blastomere identity in early C. elegans embryos. Citation: Cell 70: 163-176 1992 Type: ARTICLE Genes: ced-2 glp-1 lin-12 pie-1 rol-1 skn-1 spe-6 unc-25 unc-52 mnC1 eDf2 eDp6 Abstract: During C. elegans embryogenesis an 8-cell stage blastomere, called MS, undergoes a reproducible cleavage pattern, producing pharyngeal cells, body wall muscles, and cell deaths. We show here that maternal- effect mutations in the pie-1 and mex-1 genes cause additional 8-cell stage blastomeres to adopt a fate very similar to that of the wild- type MS blastomere. In pie-1 mutants one additional posterior blastomere adopts an MS-like fate, and in mex-1 mutants four additional anterior blastomeres adopt an MS-like fate. We propose that maternally provided pie-1(+) and mex-1(+) gene products may function in the early embryo to localize or regulate factors that determine the fate of the MS blastomere. ------------------- Key: 1585 Medline: Authors: Roussell DL;Bennett KL Title: Caenorhabditis cDNA encodes an eIF-4A-like protein. Citation: Nucleic Acids Research 20: 3783- 1992 Type: ARTICLE Genes: Abstract: The eukaryotic initiation factor 4A (eIF-4A) is one of the best characterized members of the 'DEAD box' family of RNA helicases. The function of eIF-4A protein within the initiation factor complex includes RNA binding and melting of RNA secondary structures that might interfere with the translation process. The eIF-4A protein also has an RNA-dependent ATPase activity. A modified ATPase B site (DEAD:asp, glu, ala, asp) distinguishes this family of RNA helicases. The DEAD helicase family members are a subgroup of a superfamily of (putative) helicases characterized by six conserved motifs. ------------------- Key: 1586 Medline: 93020601 Authors: Davis RE;Stretton AO Title: Extracellular recordings from the motor nervous system of the nematode, Ascaris suum. Citation: Journal of Comparative Physiology A 171: 17-28 1992 Type: ARTICLE Genes: Abstract: 1. The close association of muscle and neurons in Ascaris suum makes it difficult to determine whether spikes recorded from nerve cords originate in muscle or neurons. We have developed criteria that distinguish muscle and neuronal activity. There are two categories of extracellular spikes. 2. The first category consists of spikes with a wide range of amplitudes, marked by large spikes. These spikes, which can be recorded over lateral muscle and over the dorsal and ventral nerve cords, are abolished when muscle is disrupted or removed, or when curare is applied. Large spikes are relatively infrequent, are correlated with intracellularly recorded events, and respond to polarization of motor neurons, implying that they originate in muscle. 3. The second spike category, small amplitude spikes, is exclusive to the ventral nerve cord, occurs more frequently than large spikes and displays patterned firing. Small spikes are not affected by muscle removal or by curare, and are correlated with motor neuronal postsynaptic potentials, but not with intracellularly recorded muscle events. We infer that they originate in neurons. 4. Low level activity recorded extracellularly over nerve cords may represent muscle activity due to tonic motor neuronal synaptic transmission. It responds to motro neuronal polarization and is ------------------- Key: 1587 Medline: 92378622 Authors: Dey CS;Deitiker PR;Epstein HF Title: Assembly-dependent phosphorylation of myosin and paramyosin of native thick filaments in Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 186: 1528-1532 1992 Type: ARTICLE Genes: Abstract: Phosphorylation of the thick filament proteins myosin and paramyosin was studied in Caenorhabditis elegans. We have incubated partially purified, native thick filaments with [gamma 32P] ATP in the presence of 50-750 mM NaCl, pH 6.5-8.0. Myosin heavy chain and paramyosin were phosphorylatable only upon solubilization at 450 mM and higher NaCl concentrations. Under conditions preserving native structures, no phosphorylation of these proteins occurred. The phosphorylation required Mg2+ but was unaffected by cAMP, cGMP or Ca2+. The specific inhibitor of cAMP and cGMP kinase catalytic subunits, H8, inhibits the activity. Sedimentation experiments show that the kinase may associate with but is not an intrinsic component of thick filaments. In C. elegans, phosphorylation by the thick filament associated activity of myosin and paramyosin is dependent upon the state of their assembly. ------------------- Key: 1588 Medline: Authors: McGhee JD Title: Gut esterase expression in the nematode Caenorhabditis elegans. Citation: Advances in Developmental Biochemistry 1: 169-210 1992 Type: ARTICLE Genes: emb-13 ges-1 Abstract: In the free-living nematode Caenorhabditis elegans, the entire intestine is clonally derived from one cell of the 8-cell embryo. This makes gut an excellent lineage in which to study the early spatial control of gene expression in a "mosaic" embryo. We have used histochemistry to identify a nonspecific carboxylesterase activity that is a convenient biochemical marker for embryonic differentiation. The major gut esterase (the product of the gut esterase #1 or ges-1 gene) has been purified to homogeneity and is a 60,000 dalton single polypeptide enzyme with a serine residue at the active site. The sequence of the cloned gene reveals significant homology with esterases from vertebrates and from insects. The genetic locus of the ges-1 gene has been identified by means of induced isoelectric focusing mutants; these variants have in turn been used in a scheme to generate worms that completely lack ges-1 activity. From an examination of these ges-1 null embryos, we conclude that the ges-1 esterase is essentially the only esterase that is expressed during the first half of embryogenesis. ges-1 activity appears when the developing gut has 4-8 cells and the total embryo has only 100-150 cells. We show that the ges-1 gene is transcribed from the zygotic genome, that ges-1 expression is lineage autonomous, and that, after the embryo has divided once, ges-1 expression is completely independent of cytokinesis. The DNA-polymerase inhibitor aphidicolin was used to show that ges-1 expression depends neither on the nucleus:cytoplasm ratio of the embryo nor on the total number of rounds of DNA synthesis. Rather, ges-1 expression responds in a manner that suggests a "quantal" cell cycle (i.e., a crucial period of DNA synthesis must occur during the cell cycle in which the gut is clonally established). This DNA synthesis somehow confers permission for a set of gut-specific genes to be transcribed up to several hours later. Molecular analysis of ges-1 expression, in which mutated copies of the gene are transformed into the null mutants, is beginning to reveal some of the control circuitry of this simple developmental system. For example, deletions of the 5' flanking region of the ges-1 gene can lead to esterase expression in both sister and cousin lineages, suggesting that spatial control of gene expression during development ------------------- Key: 1589 Medline: Authors: Reape TJ;Burnell AM Title: Dauer larva recovery in the nematode Caenorhabditis elegans-III. The effect of inhibitors of protein and mRNA synthesis on the activity of the enzymes of intermediary Citation: Comparative Biochemistry & Physiology B-Comparative Biochemistry 102B: 241-245 1992 Type: ARTICLE Genes: Abstract: 1. The increase in specific activity of the enzymes of intermediary metabolism which is associated with dauer recovery can be prevented in a rich recovery medium by cycloheximide but not by actinomycin D. 2. This suggests that teh metabolic enzymes investigated are subject to "coarse" control and that de novo synthesis of these enzymes occurs from stored mRNA. 3. However, when the larvae recover in a medium containing a low concentration of food, the regulatory enzymes phosphofructokinase and citrate synthase appear to be subject to "fine" control. ------------------- Key: 1590 Medline: Authors: Hedgecock EM;Hall DH Title: Motor vesicles. Citation: Current Biology 1: 77-79 1992 Type: REVIEW Genes: unc-104 Abstract: Neurons communicate with distant cells by extending axons and dendrites to form chemical synapses or gap junctions (electrotonic synapses). Genesis and maintenance of these long, thin cytoplasmic extensions, collectively termed neurites, pose several problems of intracellular transport. Although some materials are synthezised within neurites, many are made only within the cell body and must then be transported anterograde along the neurite. Each material moves along neurites at a characteristic speed; many sort selectively to either axon or dendrites, and some halt at specific sites along the neurite. Not surprisingly, several distinct transport mechanisms have been identified. Notably, the motor proteins kinesin and cytoplasmic dynein have been implicated in anterograde and retrograde translocation, respectively, of membrane-bound organelles along axonal microtubules. Here we review two recent papers describing the sequence and mutant phenotypes of the unc-104 gene of Caenorhabditis elegans, which encodes such a motor protein. ------------------- Key: 1591 Medline: Authors: Wood WB Title: Introduction to C. elegans biology. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 1-16 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1592 Medline: Authors: Herman RK Title: Genetics. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 17-45 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1593 Medline: Authors: Emmons SW Title: The genome. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 47-79 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1594 Medline: Authors: White J Title: The anatomy. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 81-122 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1595 Medline: Authors: Sulston J Title: Cell lineage. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 123-155 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1596 Medline: Authors: Horvitz HR Title: Genetics of cell lineage. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 157-190 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1597 Medline: Authors: Kimble J;Ward S Title: Germ-line development and fertilization. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 191-213 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1598 Medline: Authors: Wood WB Title: Embryology. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 215-241 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1599 Medline: Authors: Hodgkin J Title: Sexual dimorphism and sex determination. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 243-279 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1600 Medline: Authors: Waterston RH Title: Muscle. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 281-335 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1601 Medline: Authors: Chalfie M;White J Title: The nervous system. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 337-391 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1602 Medline: Authors: Riddle DL Title: The dauer larva. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 393-412 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1603 Medline: Authors: Sulston J;White J Title: Parts list. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 415-431 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1604 Medline: Authors: White J;Southgate E;Durbin R Title: Neuroanatomy. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 433-455 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1605 Medline: Authors: Sulston J;Horvitz HR;Kimble J Title: Cell lineage. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 457-489 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1606 Medline: Authors: Hodgkin J;Edgley M;Riddle DL;Albertson DG Title: Genetics. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 491-584 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1607 Medline: Authors: Sulston J;Hodgkin J Title: Methods. Citation: "The Nematode Caenorhabditis elegans." Wood WB and the Community of C. elegans Researchers (eds), Cold Spring Harbor Laboratory. : 587-606 1988 Type: REVIEW Genes: Abstract: ------------------- Key: 1608 Medline: 92375684 Authors: Iwasaki M;Okumura K;Kondo Y;Tanaka T;Igarashi H Title: cDNA cloning of a novel heterogeneous nuclear ribonucleoprotein gene homolog in Caenorhabditis elegans using hamster prion protein as a hybridization probe. Citation: Nucleic Acids Research 20: 4001-4007 1992 Type: ARTICLE Genes: Abstract: The mammalian prion protein (PrPc) is a cellular protein of unknown function, an altered isoform of which (PrPsc) is a component of the infectious particle (prion) thought to be responsible for spongiform encephalopathies in humans and animals. The evolutionary conservation of the PrP gene has been reported in the genomes of many vertebrates as well as certain invertebrates. In the genome of nematode Caenorhabditis elegans, the sequence capable of hybridizing with the mammalian PrP cDNA probe has been demonstrated, predicting the presence of the PrP gene homologue in C.elegans. In this study, Southern analysis with the hamster PrP cDNA (HaPrP) probe confirmed the previous observation. Moreover, Northern analysis revealed that the sequence is actively transcribed in adult worms. Thus, we screened C.elegans cDNA libraries with the HaPrP probe and isolated a cDNA that hybridizes to the same sequence in C.elegans that hybridized with the HaPrP probe in the Southern and Northern analyses. The deduced amino acid sequence of this cDNA, however, is substantially homologous with heterogeneous nuclear ribonucleoprotein (hnRNP) core proteins rather than mammalian PrPc. The hnRNPs contain the glycine-rich domain in the C-terminal half of the molecule, which also seemed to be in PrPc at the N-terminal half of the molecule. Both of the glycine-rich domains are composed of tracts with high G + C content, indicating that these tracts may due to the hybridizing signals. These results suggest that this cDNA clone is derived from a novel hnRNP gene homologue in C.elegans but not from a predicted PrP ------------------- Key: 1609 Medline: Authors: Kuwabara PE;Kimble J Title: Sex determination in Caenorhabditis elegans. Citation: Journal of Nematology 24: 324-329 1992 Type: ARTICLE Genes: fem-1 fem-2 fem-3 fog-1 fog-2 her-1 mog-1 sdc-1 sdc-2 tra-1 tra-2 tra-3 xol-1 Abstract: In Caenorhabditis elegans, the decision to develop as a hermaphrodite or male is controlled by a cascade of regulatory genes. These genes and other tissue-specific regulatory, genes also control sexual fate in the hermaphrodite germline, which makes sperm first and then oocytes. In this review, we summarize the genetic and molecular characterization of these genes and speculate how they mutually interact to specify sexual fate. ------------------- Key: 1610 Medline: 92381249 Authors: Johnson TE;Lithgow GJ Title: The search for the genetic basis of aging- The identification of gerontogenes in the nematode Caenorhabditis elegans. Citation: Journal of the American Geriatrics Society 40: 936-945 1992 Type: ARTICLE Genes: age-1 dpy-10 unc-4 Abstract: Study of C. elegans has provided much information for gerontologists. The influence of the genome on life span is clearly observable, and at least one gerontogene, age-1, has been defined. Data relating to important evolutionary questions has emerged and will continue to be used in testing current hypotheses. We are using an approach unbiased by theoretical constraints to delineate aging processes simultaneously at the molecular and organismal levels. Much remains to be discovered before fundamental questions posed in this article are answered to a satisfactory degree. The immediate agenda is the identification and isolation of gerontogenes which influence life span in invertebrate models. This work is well in hand and will lead to the unraveling of specific life-span-determining processes. At this point we may be able to predict whether analogous processes also limit life in mammals. If we are fortunate and aging processes exhibit evolutionary conservation, many exciting possibilities await. Molecular tools provided by the invertebrate system can then be used to isolate homologous mammalian gerontogenes that could be subsequently utilized in highly targeted attempts to intervene in mammalian aging. This offers the most direct strategy for identifying life-span prolongation genes in humans. ------------------- Key: 1611 Medline: 93083485 Authors: Kita K;Mizuchi D;Wang H;Takamiya S;Aoki T;Kojima S Title: cDNA sequence of 3 cysteine-rich clusters in the iron-sulfur subunit of complex-II (succinate-ubiquinone oxidoreductase) from Caenorhabditis elegans determined by Citation: Electrophoresis 13: 506-511 1992 Type: ARTICLE Genes: Abstract: Homology probing by using mixed primers for polymerase chain reaction (PCR) and a subsequent sequence analysis by automated DNA sequencer were applied to determine a partial cDNA sequence of the iron-sulfur subunit of complex II (succinate-ubiquinone oxidoreductase). Complex II is a membrane-bound flavoenzyme, which catalyzes the oxidation of succinate to fumarate in the tricarboxylic acid cycle, and it is a component of the mitochondrial and bacterial respiratory chains. In this study, the partial amino acid sequence of iron-sulfur subunits in Caenorhabditis elegans mitochondria was deduced from the DNA sequence obtained from cDNA-PCR. Mixed oligonucleotide primers corresponding to two conserved regions which appear to be the binding site for the prosthetic group were used. The product of PCR was cloned into plasmid vector pUC 119 and the sequence was determined from double strand plasmid DNA by the dideoxy method using of one-day, four-lane type the automated DNA sequencer (DSQ-1, Shimadzu). The PCR product contained 483 nucleotides and its deduced amino acid sequence was highly homologous with that in human liver (68.9%) and that of Escherichia coli sdh B product (50.3%). As expected, striking sequence conservation was found around the three cysteine-rich clusters which have been thought to comprise the iron-sulfur centers of the enzyme. ------------------- Key: 1612 Medline: 92407040 Authors: L'Hernault SW;Arduengo PM Title: Mutation of a putative sperm membrane protein in Caenorhabditis elegans prevents sperm differentiation but not its associated meiotic divisions. Citation: Journal of Cell Biology 119: 55-68 1992 Type: ARTICLE Genes: dpy-5 fem-1 fem-3 gld-1 him-5 lin-10 rol-6 spe-4 spe-10 unc-13 unc-15 sDf5 sDf6 nDp4 Abstract: Spermatogenesis in the nematode Caenorhabditis elegans uses unusual organelles, called the fibrous body-membranous organelle (FB-MO) complexes, to prepackage and deliver macromolecules to spermatids during cytokinesis that accompanies the second meiotic division. Mutations in the spe-4 (spermatogenesis-defective) gene disrupt these organelles and prevent cytokinesis during spermatogenesis, but do not prevent completion of the meiotic nuclear divisions that normally accompany spermatid formation. We report an ultrastructural analysis of spe-4 mutant sperm where the normally close association of the FB's with the MO's and the double layered membrane surrounding the FB's are both defective. The internal membrane structure of the MO's is also disrupted in spe-4 mutant sperm. Although sperm morphogenesis in spe-4 mutants arrests prior to the formation of spermatids, meiosis can apparently be completed so that haploid nuclei reside in an arrested spermatocyte. We have cloned the spe-4 gene in order to understand its role during spermatogenesis and the molecular basis of how mutation of this gene disrupts this process. The spe-4 gene encodes an approximately 1.5-kb mRNA that is expressed during spermatogenesis, and the sequence of this gene suggests that it encodes an integral membrane protein. These data suggest that mutation of an integral membrane protein within FB-MO complexes disrupts morphogenesis and prevents formation of spermatids but does not affect completion of the meiotic nuclear divisions in ------------------- Key: 1613 Medline: Authors: Binder BF;Demilo AB;Kochansk JP;Chitwood DJ Title: Inhibition of Development in Caenorhabditis elegans (Nematoda) by a reduced aromatic schiff base and related compounds. Citation: Journal of Agricultural and Food Chemistry 40: 1475-1477 1992 Type: ARTICLE Genes: Abstract: Insect growth regulators with dissimilar chemical structures possess biological activity in parasitic and free-living nematodes. Certain steroids inhibit growth and reproduction in Caenorhabditis elegans, Nippostrongylus brasiliensis, and Heligmosoides polygyrus (=Nematospiroides dubius). Sesquiterpenoid insect juvenile hormones and their analogs disrupt the development of a wide variety of nematodes, whereas nonterpenoid insect juvenile hormone mimics such as benzimidazoles and methoxyphenyl ethers inhibit egg hatch in the pinewood nematode, Bursaphelenchus xylophilus, and reduce growth in a goat parasite, Haemonchus contortus. The insect anti-juvenile hormone precocene II has biological activity against Caenorhabditis remanei, but its role as a nematode antihormone has not been fully clarified. The impact of these compounds on the hormonal systems in insects is fairly clear; their role as endocrine-active bioregulators in nematodes has not yet ------------------- Key: 1614 Medline: 93061847 Authors: Arena JP;Liu KK;Paress PS;Schaeffer JM;Cully DF Title: Expression of a glutamate-activated chloride current in Xenopus oocytes injected with Caenorhabditis elegans RNA - evidence for modulation by avermectin. Citation: Molecular Brain Research 15: 339-348 1992 Type: ARTICLE Genes: Abstract: Membrane currents were recorded from Xenopus laevis oocytes injected with C . elegans poly(A)+ RNA. In such oocytes glutamate activated an inward membrane current that desensitized in the continued presence of glutamate. Glutamate-receptor agonists quisqualate, kainate, and N-methy-D-asparate were inactive. The reversal potential of the glutamate-sensitive current was -22 mV, and exhibited a strong dependence on external chloride with a 48 mV change for a 10-fold change in chloride. The chloride channel blockers flufenamate and picrotoxin inhibited the glutamate-sensitive current. Ibotenate, a structural analog of glutamate, also activated a picrotoxin-sensitive chloride current. Ibotenate was inactive when current was partially densentized with glutamate, and the responses to low concentrations of glutamate and ibotenate were additive. The anthelmintic/insecticide compound avermectin directly activated the glutamate-sensitive current. In addition, avermectin increased the response to submaximal concentrations of glutamate concentration-response curve to lower concentrations, and slowed the desensitization of glutamate-sensitive current. We propose that the glutmate-sensitive chloride current and the avermectin-sensitive chloride current are mediated via the same channel. ------------------- Key: 1615 Medline: 93051282 Authors: Gilchrist EJ;Moerman DG Title: Mutations in the sup-38 gene of Caenorhabditis elegans suppress muscle-attachment defects in unc-52 mutants. Citation: Genetics 132: 431-442 1992 Type: ARTICLE Genes: dpy-4 dpy-20 let-323 let-324 sup-5 sup-7 sup-38 unc-23 unc-26 unc-52 nDf27 sDf21 sDf23 mnDp34 Abstract: Mutations in the unc-52 locus of Caenorhabditis elegans have been classified into three different groups based on their complex pattern of complementation. These mutations result in progressive paralysis (class 1 mutations) or in lethality (class 2 and 3 mutations). The paralysis exhibited by animals carrying class 1 mutations is caused by disruption of the myofilaments at their points of attachment to the cell membrane in the body wall muscle cells. We have determined that mutations of this class also have an effect on the somatic gonad, and this may be due to a similar disruption in the myoepithelial sheath cells of the uterus, or in the uterine muscle cells. Mutations that suppress the body wall muscle defects of the class 1 unc-52 mutations have been isolated, and they define a new locus, sup-38. Only the muscle disorganization of the Unc-52 mutants is suppressed; the gonad abnormalities are not, and the suppressors do not rescue the lethal phenotype of the class 2 and class 3 mutations. The suppressor mutations on their own exhibit a variable degree of gonad and muscle disorganization. Putative null sup-38 mutations cause maternal-effect lethality which is rescued by a wild-type copy of the locus in the zygote. These loss-of-function mutations have no effect on the body wall muscle structure. ------------------- Key: 1616 Medline: Authors: Grant WN Title: Transformation of Caenorhabditis elegans with genes from parasitic nematodes. Citation: Parasitology Today 8: 344-346 1992 Type: ARTICLE Genes: dpy-13 rol-6 Abstract: Our knowledge of many aspects of the molecular biology of animal parasitic nematodes has rapidly expanded in recent years but the classical genetic analysis of this group of organisms has yet to emerge as a viable discipline. For example, it is not possible to routinely perform crosses between single males and females to examine the genetic basis of even simple phenotypes such as anthelmintic resistance. This has meant that the function of many cloned parasite genes can only be inferred from sequence comparison with genes from other organsims where function is known, or by correlation of DNA polymorphisms linked to the gene with phenotypic differences between strains or individuals. In the absence of classical genetic techniques, a molecular solution is to transform a suitable host with the gene of interest, but what defines a suitable host? Here, Warwick Grant describes recent work that aims to provide such a host. ------------------- Key: 1617 Medline: 95194390 Authors: Plasterk RH Title: Reverse genetics of Caenorhabditis elegans. Citation: BioEssays 14: 629-633 1992 Type: REVIEW Genes: dpy-19 gpa-1 gpa-2 hlh-1 let-2 mlc-2 unc-22 Abstract: It is somewhat ironic that animals that are the prime choice for detailed genetic analysis, such as the fruit fly and the nematode, have thus far been largely refractory to reverse genetic analysis. Their detailed genetic map, and small genome size have made them subjects of ambitious genome analysis projects, but there is still no strategy to introduce desired changes into their genomes by homologous recombination. Some alternative approaches have recently become available; this review describes possibilities and unsolved problems for reverse genetics in the nematode Caenorhabditis elegans. The transposon Tc1 could prove to be very useful for the isolation of knock out mutants, and possibly also for introduction of more subtle alterations. ------------------- Key: 1618 Medline: 93010980 Authors: Johnstone IL;Shafi Y;Barry JD Title: Molecular analysis of mutations in the Caenorhabditis elegans collagen gene dpy-7. Citation: EMBO Journal 11: 3857-3863 1992 Type: ARTICLE Genes: col-1 dpy-2 dpy-7 dpy-10 rol-6 sqt-1 unc-6 unc-18 Abstract: Collagens are a family of proteins contributing to the body structure of eukaryotes. They are encoded by a large and diverse gene family in the nematode Caenorhabditis elegans but by only a few genes in vertebrates. We have studied mutant alleles of the C . elegans dpy-7 gene, one of a large group of genes whose mutant phenotype is altered body form and several of which have previously been shown to encode cuticular collagens. We made use of the C . elegans physical map to screen specifically for collagen genes in the region of the X chromosome to which dpy-7 maps. This yielded a wild-type collagen gene clone which we showed, by microinjection, could repair the dpy-7 mutant phenotype in transgenic animals. We cloned the homologous sequence from four dpy-7 mutant strains and by sequence analysis identified a single mutation in each case. All four mutations result in the substitution of a glycine with a larger residue in the conserved Gly-X-Y collagen domains. Similar substitutions in vertebrate collagens cause the herbicide brittle bone disorder osteogenesis imperfecta. Whereas the human mutations are dominant, the dpy-7 mutations are recessive, and this may reflect different levels of complexity of collagenous macromolecular structures in the two organisms. ------------------- Key: 1619 Medline: 93046629 Authors: Leung-Hagesteijn CY;Spence AM;Stern BD;Zhou YW;Su MW;Hedgecock EM;Culotti JG Title: UNC-5, a transmembrane protein with immunoglobulin and thrombospondin type-1 domains, guides cell and pioneer axon migrations in C. elegans. Citation: Cell 71: 289-299 1992 Type: ARTICLE Genes: dpy-1 dpy-13 ncl-1 unc-5 unc-6 unc-44 sDp3 Abstract: The unc-5 gene is required for guiding pioneering axons and migrating cells along the body wall in C. elegans. In mutants, dorsal migrations are disrupted, but ventral and longitudinal movements are largely unaffected. The gene was tagged for molecular cloning by transposon insertions. Based on genomic and cDNA sequencing, the gene encodes UNC-5, a transmembrane protein of 919 aa. The predicted extracellular N-terminus comprises two immunoglobulin and two thrombospondin type 1 domains. Except for an SH3-like motif, the large intracellular C-terminus is novel. Mosaic analysis shows that unc-5 acts in migrating cells and pioneering neurons. We propose that UNC-5 is a transmembrane receptor expressed on the surface of motile cells and growth cones to guide dorsal movements. ------------------- Key: 1620 Medline: 93045556 Authors: Lewis JA;Berberic S Title: A detergent-solubilized nicotinic acetylcholine receptor of Caenorhabditis elegans. Citation: Brain Research Bulletin 29: 667-674 1992 Type: ARTICLE Genes: unc-29 unc-63 Abstract: We have used a spin column assay to study the detergent-solubilized levamisole receptor, a nicotinic acetylcholine receptor of the nematode Caenorhabditis elegans. The receptor can be successfully solubilized in detergent solutions of Triton X-100, Lubrol PX, or sodium cholate. Centrifugal gel filtration assay using the tritiated ligand [3H]meta-aminolevamisole ([3H]MAL) provides a greater signal and a better signal-to-noise ratio for soluble levamisole receptor binding than either polyethylene glycol precipitation or DEAE filter assay with the same ligand. As for membrane-bound receptor, the detergent-solubilized levamisole receptor consists of more than one affinity state. Detergent solubilization appears to increase the affinity of all states for [3H]MAL (Kd for the highest affinity solubilized [3H]MAL binding state, 41 .+-. 5 pM). Data is presented on the equilibrium binding and the association and dissociation reaction rates of the receptor. The similar relative efficacy with which various compounds inhibit specific [3H]MAL binding and deficiencies in solubilizable high affinity specific [3H]MAL binding in two receptor mutants show that the solubilized receptor is the same nicotinic acetylcholine receptor that is detected by assaying membrane-bound specific [3H]MAL binding. The detergent-solubilized levamisole receptor is stable at 0.degree. to 4.degree. C, making receptor purification feasible. ------------------- Key: 1621 Medline: 93013043 Authors: Bird DM Title: Sequence comparison of the Caenorhabditis elegans dpy-13 and col-14 genes, and their deduced collagen products. Citation: Gene 120: 261-266 1992 Type: ARTICLE Genes: ama-1 ceh-18 col-2 col-6 col-7 col-19 col-34 dpy-13 unc-86 Abstract: A 2232-nucleotide sequence spanning the col-34 gene from the nematode, Caenorhabditis elegans, is presented. This gene, which encodes a collagen protein (Clg), is transcribed from right to left with respect to the genetic map, and convergently with the nearby dpy-13 gene which also encodes a Clg. Both col-34 and dpy-13 have 5'-flanking elements in common with each other and also with other nematode Clg-encoding genes (clg). One element, variants of which are shared by col-7, col-19 and dpy-13, is predicted to be a target for a number of regulatory molecules, possibly including the ceh-18 product, a nematode POU-domain protein. The deduced amino acid sequence of Col-34 has a high degree of homology with the Dpy-13 collagen, although there are significant differences. In particular, one region of Dpy-13, which is predicted to have secondary structure different from Col-34, is altered by the recessive dpy-13(e225) mutation. ------------------- Key: 1622 Medline: 93106371 Authors: Li W;Herman RK;Shaw JE Title: Analysis of the Caenorhabditis elegans axonal guidance and outgrowth gene unc-33. Citation: Genetics 132: 675-689 1992 Type: ARTICLE Genes: cat-6 ced-4 che-14 dpy-13 unc-33 unc-86 Abstract: Mutations in the unc-33 gene of the nematode Caenorhabditis elegans lead to severely uncoordinated movement, abnormalities in the guidance and outgrowth of the axons of many neurons, and a superabundance of microtubules in neuronal processes. We have cloned unc-33 by tagging the gene with the transposable element Tc4. Three unc-33 messages, which are transcribed from a genomic region of at least 10 kb, were identified and characterized. The three messages have common 3' ends and identical reading frames. The largest (3.8-kb) message consists of the 22-nucleotide trans-spliced leader SL1 and 10 exons (I-X); the intermediate-size (3.3-kb) message begins with SL1 spliced to the 5' end of exon V and includes exons V-X; and the smallest (2.8-kb) message begins within exon VII and also includes exons VIII-X. A gamma-ray-induced deletion mutation situated within exon VIII reduces the sizes of all three messages by 0.5 kb. The three putative polypeptides encoded by the three messages overlap in C-terminal sequence but differ by the positions at which their N termini begin; none his significant similarity to any other known protein. A Tc4 insertion in exon VII leads to alterations in splicing that result in three approximately wild-type-size messages: the Tc4 sequence and 28 additional nucleotides are spliced out of the two larger messages; the Tc4 sequence is trans-spliced off the smallest message such that SL1 is added 13 nucleotides upstream of the normal 5' end of the smallest message. ------------------- Key: 1623 Medline: 93096371 Authors: Kamiya Y;Harada S;Yamamoto H;Hosono R Title: Mutations in genes for acetylcholinesterase intensify lethality by acrylamide in Caenorhabditis elegans. Citation: Neuroscience Letters 145: 37-39 1992 Type: ARTICLE Genes: ace-1 ace-2 ace-3 Abstract: Acrylamide inhibits growth and results in death in the nematode Caenorhabditis elegans. The lethargic effect is marked in the mutants defective in genes for acetylcholinesterase (AChE) and the effect is approximately parallel with the decrease in AChE activity by mutations. Although neither the activity nor the localization of the enzyme is affected by acrylamide, the acetylcholine level was significantly elevated. ------------------- Key: 1624 Medline: 93097010 Authors: Anton AH;Berk AI;Nicholls CH Title: The anesthetic effect of alcohols and alkanes in Caenorhabditis elegans. Citation: Research Communications in Chemical Pathology & Phar 78: 69-83 1992 Type: ARTICLE Genes: unc-79 Abstract: In order to help validate the free-living roundworm, C.e. , as a simple model to study the mechanism of general anesthesia, we demonstrated that homologous series of alcohols and alkanes produced a reversible ''anesthetic'' effect in these worms as in other animals. Also, as in other animals, the potency of these compounds was directly related to their respective lipid solubilities within each series. The alcohols were much more potent than the alkanes even though the latter were much more lipid soluble than the alcohols. The cut-off point (a decrease followed by a loss of activity) for these compounds occurred at about C-9 In mice, the alcohols had an effect analogous to that seen in C.e. but the alkanes were inactive after intraperitoneal injection. ------------------- Key: 1625 Medline: 92350294 Authors: Herman RK Title: Inducing concentric worm holes. Citation: Nature 358: 450- 1992 Type: REVIEW Genes: let-23 let-60 lin-3 lin-12 sem-5 Abstract: Induction is the process in development in which the fate of one cell mass is determined by another. A simple example occurs during vulval development in the nematode Caenorhabditis elegans: a gonadal cell called the anchor cell induces three neighbouring cells to embark on a programme of cell division and morphogenesis, which culminates, in a few hours, in the formation of a vulva. On page 470 of this issue, Hill and Sternberg report strong evidence that they have identified the anchor-cell signalling molecule, which they find is a member of the EGF (epidermal growth factor) group of growth factors. ------------------- Key: 1626 Medline: Authors: Hyman AA;Stearns T Title: Spindle positioning and cell polarity. Citation: Current Biology 2: 469-471 1992 Type: REVIEW Genes: Abstract: The ability to establish and maintain a polar organization is a fundamental property of all cells, prokaryotic and eukaryotic alike. In its simplest form, cell polarity is used to coordinate the events of growth and division; most cells grow with distinct morphologies and actively divide their contents. The establishment of polarity requires both that a position in a cell, the polar determinant, be determined in some way, and that this position be communicated to the rest of the cell so that it can respond to the determined polarity. There is abundant evidence that the cytoskeleton is involved in both determining and responding to cell polarity; a particularly clear example of a cytoskeletal response to cell polarity is the positioning of the mitotic spindle prior to cell division. ------------------- Key: 1627 Medline: 92329978 Authors: Smith MJ Title: A C. elegans gene encodes a protein homologous to mammalian calreticulin. Citation: DNA Sequence 2: 235-240 1992 Type: ARTICLE Genes: crt-1 Abstract: The gene encoding a C. elegans homologue of the mammalian reticuloplasmin, calreticulin, was cloned and sequenced and the amino- acid sequence of its product deduced. The coding region of the gene comprises three exons separated by introns of 95 and 55 nucleotides, followed by either 158 or 279 bases of 3' non-coding sequence before putative polyadenylation signals. The precursor protein of 395 residues includes an N-terminal signal sequence of 13 residues. The C- terminus has the ER retention signal HDEL preceded by a polyacidic zone similar to known mammalian calreticulins. The sequence shows a 61% identity with mouse calreticulin, increasing to 82% in the proline-rich region of the molecule. Comparison of the C. elegans sequence with the calreticulin-related antigen RAL-1 of Oncocerca volvulus shows 73% identity, excluding the calreticulin C-terminal region. The sequence of this region differs markedly from RAL-1 where the parasite protein has a polybasic stretch and no ER retention signal. The C. elegans gene described here and designated crt-1 was mapped to a region towards the left-hand end of Chromosome V on the physical map of the genome. Southern blotting of genomic DNA indicates that in C. elegans the calreticulin homologue exists in only one form as the product of a ------------------- Key: 1628 Medline: 92345793 Authors: Schnabel R Title: Early determinative events in Caenorhabditis elegans. Citation: Current Opinion in Genetics & Development 1: 179-184 1991 Type: REVIEW Genes: cib-1 glp-1 par-1 par-2 par-3 Abstract: Classical developmental biology has distinguished two major modes of embryogenesis, determinate and indeterminate. Nematodes have been considered the chief paradigm for determinate and cell-autonomous development, but recent experiments on the early development of Caenorhabditis elegans suggest that most blastomeres of this nematode are, in fact, determined by interactions. ------------------- Key: 1629 Medline: 92345794 Authors: Schedl T Title: The role of cell-cell interactions in postembryonic development of the Caenorhabditis elegans germ line. Citation: Current Opinion in Genetics & Development 1: 185-190 1991 Type: REVIEW Genes: fem-1 fem-2 fem-3 fog-1 fog-2 glp-1 glp-4 her-1 lag-1 lag-2 let-23 lin-12 tra-1 tra-2 tra-3 Abstract: This review addresses the role of cell-cell interactions in the development of the Caenorhabditis elegans germ line: specifically, the relative contributions of germ-line-soma interactions versus autonomous processes are considered. Current knowledge of the interacting cell types and the genes essential for various aspects of germ-line development is discussed. ------------------- Key: 1630 Medline: 92338590 Authors: Hoffman FM;Sternberg PW;Herskowitz I Title: Learning about cancer through invertebrate genetics. Citation: Current Opinion in Genetics & Development 2: 45-52 1992 Type: REVIEW Genes: let-23 let-60 Abstract: Genetic studies in yeast, nematodes and Drosophila are revealing the signal transduction pathways that regulate differentiation and cell proliferation. Some of the critical molecules involved are homologous to proto-oncogenes and others are likely to be analogous to the products of tumor suppressor genes. ------------------- Key: 1631 Medline: 92366726 Authors: Blakely EA Title: Cell inactivation by heavy charged particles. Citation: Radiation and Environmental Biophysics 31: 181-196 1992 Type: REVIEW Genes: Abstract: The inactivation of cells resulting in lethal or aberrant effects by charged particles is of growing interest. Charged particles at extremely high LET are capable of completely eliminating cell-type and cell-line differences in repair capacity. It is still not clear however whether the repair systems are inactivated, or merely that heavy-ion lesions are less repairable. Studies correlating the particle inactivation dose of radioresistant cells with intact DNA analyzed with pulse field gel electrophoresis and other techniques may be useful, but more experiments are also needed to assess the fidelity of repair. For particle irradiations between 40-100 keV/microns there is however evidence for particle-induced activation of specific genes in mammalian cells, and certain repair processes in bacteria. New data are available on the inactivation of developmental processes in several systems including seeds, and cells of the nematode C . elegans . Future experimental and theoretical modeling research emphasis should focus on exploring particle-induced inactivation of endpoints assessing functionality and not just lethality, and on analyzing molecular damage and genetic effects arising in damaged but non-inactivated survivors. The discrete nature of selective types of particle damage as a function of radiation quality indicates the value of accelerated ions as probes of normal and aberrant biological processes. Information obtained from molecular analyses of damage and repair must however be integrated into the context of cellular and tissue ------------------- Key: 1632 Medline: 92363831 Authors: Conder GA;Zielinski RJ;Johnson SS;Kuo MS;Cox DL;Marshall VP;Haber CL;DiRoma PJ;Nelson SJ;Conklin RD; et al Title: Anthelmintic activity of dioxapyrrolomycin. Citation: Journal of Antibiotics 45: 977-983 1992 Type: ARTICLE Genes: Abstract: Dioxapyrrolomycin, pyrrolomycin C , pyrrolomycin D, and piericidin C2 produced by UC 11065 were evaluated as anthelmintics. Assays used to examine these compounds included effects on the free-living nematode Caenorhabditis elegans , ability to clear target nematodes (Haemonchus contortus and Trichostrongylus colubriformis) from jirds, and clearance of Haemonchus contortus from lambs. A crude extract of UC 11065 containing dioxapyrrolomycin, pyrrolomycin C , pyrrolomycin D, and piericidin C2 was active against C . elegans and against H. contortus in the jird. Purified and/or synthetic samples of dioxapyrrolomycin, pyrrolomycin C , pyrrolomycin D, and piericidin C2 were tested in the jird model; only dioxapyrrolomycin exhibited appreciable activity against H. contortus (greater than or equal to 90.9% clearance at 0.33 mg/jird), while none of the compounds showed appreciable activity against T. colubriformis. Dioxapyrrolomycin cleared 99.9% of H. contortus from lambs at 12.5 mg/kg. An in vitro migration study using susceptible and closantel-resistant H. contortus showed there is cross-resistance between dioxapyrrolomycin and closantel. Dioxapyrrolomycin appears to be a narrow-spectrum anthelmintic which works through a closantel-like ------------------- Key: 1633 Medline: Authors: Winter CE Title: The yolk polypeptides of a free-living Rhabditid nematode. Citation: Comparative Biochemistry & Physiology B-Comparative Biochemistry 103: 189-196 1992 Type: ARTICLE Genes: vit-6 Abstract: The yolk proteins of hermaphrodite Dolichorhabditis sp. (Nematoda, Rhabditida) are composed of at least three polypeptides: VT1, VT2 and VT3 with molecular masses of 175.2, 107 and 82 kDa respectively. All three yolk polypeptides make up at least one native protein complex which can be resolved by PAGE. The yolk proteins are glycosylated and can be isolated by chromatography in Con A-Sepharose. Partial chymotryptic hydrolysis shows that VT2 is different from its C . elegans homologue, YP115. The main polypeptides synthesized by whole animals are the yolk components which are actively secreted in the incubation medium. ------------------- Key: 1634 Medline: 93077036 Authors: Lee YH;Huang X-Y;Hirsh D;Fox GE;Hecht RM Title: Conservation of gene organization and trans-splicing in the glyceraldehyde-3-phosphate dehydrogenase-encoding genes of Caenorhabditis briggsae. Citation: Gene 121: 227-235 1992 Type: ARTICLE Genes: gpd-1 gpd-2 gpd-3 gpd-4 vit-2 Abstract: The genes encoding body-wall-specific glyceraldehyde-3-phosphate dehydrogenase from Caenorhabditis briggsae were sequenced and compared to the homologous genes from Caenorhabditis elegans. The direct tandem organization of these genes, gpd-2 and gpd-3, and the size and location of the two introns in each gene are the same in C. elegans and C. briggsae. Primer-extension studies demonstrated that the two genes in C. briggsae are trans-splice differentially with the same splice leader (SL) RNAs as are observed in C. elegans. The gdp-2 gene is trans-spliced with SL1 while gdp-3 is trans-spliced with SL2. Significant sequence conservation was observed within the promoter regions of each species and may indicate those regions responsible for body-wall-muscle-specific gene expression and/or differential trans-splicing. Comparisons of the sequences suggest that the tandem repeat of the genes has been subjected to concerted evolution and that C. briggsae and C. elegans diverged much earlier than would be anticipated based on morphological similarities alone. Finally, an open reading frame found several hundred nucleotides upstream from gpd-2, in both species, appears to be homologous to the ATP synthase subunit, ATPase inhibitor protein, from bovine mitochondria. ------------------- Key: 1635 Medline: 95194349 Authors: Edgar LG Title: Genes controlling specific cell fates in C. elegans Citation: BioEssays 14: 705-708 1992 Type: REVIEW Genes: glp-1 lin-12 mex-1 pie-1 skn-1 Abstract: How does an early embryonic cell become committed to a particular path of development and differentiation? One of the current areas of investigation in invertebrate development concerns the respective roles of maternal and embryonic gene activities in setting up first general, and then specific, patterning in the early stages of embryogenesis. In Drosophila, the principles are becoming clear: localized maternally expressed gene products are used initially to define body axes and broad regional zones in which various combinations of genes are zygotically expresses to further define the emerging pattern of segmentation. In the nematode C. elegans, although the embryonic cell lineage is well understood and there is ample evidence of a high degree of maternal control of cell fates, individual genes that control the processes of asymmetric early cell division and lineage-specific initiation of zygotic gene expression have not until now been identified... ------------------- Key: 1636 Medline: 93075060 Authors: Ahmed S;Maruyama IN;Kozma R;Lee J;Brenner S;Lim L Title: The Caenorhabditis elegans unc-13 gene product is a phospholipid-dependent high-affinity phorbol ester Citation: Biochemical Journal 287: 995-999 1992 Type: ARTICLE Genes: unc-13 Abstract: The Caenorhabditis elegans unc-13 mutant is a member of a class of mutants that have un-coordinated movement. Mutations of the unc-13 gene cause diverse defects in C. elegans, including abnormal neuronal connections and modified synaptic transmission in the nervous system. unc-13 cDNA encodes a protein (UNC-13) of 1734 amino acid residues with a predicted molecular mass of 198 kDa and sequence identity to the C1/C2 regions but not to the catalytic domain of the ubiquitously expressed protein kinase C family [Maruyama & Brenner (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 5729-5733]. To characterize the phorbol ester binding site of the UNC-13 protein, cDNA encoding the C1/C2-like regions (amino acid residues 546-940) was expressed in Escherichia coli and the 43 kDa recombinant protein was purified. Phorbol ester binding to the 43 kDa protein was zinc- and phospholipid-dependent, stereospecific and of high affinity (K(d) 67 nM). UNC-13 specific antisera detected a protein of approx. 190 kDa in wild-type (N2) but not in mutant (e1019) C. elegans cell extracts. We conclude that UNC-13 represents a novel class ------------------- Key: 1637 Medline: 93161939 Authors: Yuan JY;Horvitz HR Title: The Caenorhabditis elegans cell-death gene ced-4 encodes a novel protein and is expressed during the period of extensive programmed cell death. Citation: Development 116: 309-320 1992 Type: ARTICLE Genes: ced-1 ced-3 ced-4 unc-31 Abstract: Mutations in the gene ced-4 block almost all of the programmed cell deaths that normally occur during Caenorhabditis elegans development. We have cloned the ced-4 gene using a ced-4 mutation caused by the insertion of the transposon Tc4. When microinjected into a ced-4 animal, a 4.4 kb DNA fragment derived from the wild-type strain and corresponding to the region of the Tc4 insertion in the mutant ced-4(n1416) rescues the Ced-4 mutant phenotype. The ced-4 gene encodes a 2.2 kb RNA transcript. This mRNA is expressed primarily during embryogenesis, when most programmed cell deaths occur. The Ced-4 protein, as deduced from cDNA and genomic DNA clones, is 549 amino acids in length. Two regions of the putative Ced-4 protein product show some similarity to known calcium-binding ------------------- Key: 1638 Medline: 93161952 Authors: Waring DA;Wrischnik L;Kenyon C Title: Cell signals allow the expression of a preexistent neural pattern in C. elegans. Citation: Development 116: 457-466 1992 Type: ARTICLE Genes: him-5 lin-22 pal-1 mDp1 sDp3 Abstract: In C. elegans, a simple pattern develops within a row of epidermal precursor cells, V1-V6. One cell, V5, gives rise to a neuroblast called the postdeirid neuroblast, while the other V cells produce epidermal cells instead. Here we describe experiments suggesting that in order for V5 to produce the postdeirid it must be in close or direct contact with neighboring V cells. Signaling between V cells is required for the formation of the neuroblast; however, which of the V cells can make a postdeirid is not determined by these signals but rather by the action of the homeotic lin-22 and pal-1 genes. These genes prevent V cells in specific body regions from responding to intercellular signals and producing postdeirids. This is a clear example of cell signals playing a permissive rather than an instructive role in neuroblast induction. ------------------- Key: 1639 Medline: 93161954 Authors: Cowing DW;Kenyon C Title: Expression of the homeotic gene mab-5 during Caenorhabditis elegans embryogenesis. Citation: Development 116: 481-490 1992 Type: ARTICLE Genes: daf-7 dpy-20 dpy-21 egl-5 lon-1 par-1 par-2 par-3 par-4 par-5 rol-4 rol-6 unc-31 unc-37 Abstract: mab-5 is a member of a complex of homeobox-containing genes evolutionarily related to the Antennapedia and bithorax complexes of Drosophila melanogaster. Like the homeotic genes in Drosophila, mab-5 is required in a particular region along the anterior-posterior body axis, and acts during postembryonic development to give cells in this region their characteristic identities. We have used a mab-5-lacZ fusion integrated into the C elegans genome to study the posterior-specific expression of mab-5 during embryogenesis. The mab-5-lacZ fusion was expressed in the posterior of the embryo by 180 minutes after the first cleavage, indicating that the mechanisms responsible for the position-specific expression of mab-5-lacZ act at a relatively early stage of embryogenesis. In embryos homozygous for mutations in the par genes, which disrupt segregation of factors during early cleavages, expression of mab-5-lacZ was no longer localized to the posterior. This suggests that posterior-specific expression of mab-5 depends on the appropriate segregation of developmental factors during early embryogenesis. After extrusion of any blastomere of the four-cell embryo, descendants of the remaining three cells could still express the mab-5-lacZ fusion. In these partial embryos, however, the fusion was often expressed in cells scattered throughout the embryo, suggesting that cell-cell interactions and/or proper positioning of early blastomeres are required for mab-5 expression to be localized to the posterior. ------------------- Key: 1640 Medline: 93040228 Authors: Ishii N;Wadsworth WG;Stern BD;Culotti JG;Hedgecock EM Title: UNC-6, a laminin-related protein, guides cell and pioneer axon migrations in C. elegans. Citation: Neuron 9: 873-881 1992 Type: ARTICLE Genes: dpy-7 lev-9 unc-5 unc-6 Abstract: The unc-6 gene is required for the guidance of pioneer axons and migrating cells along the body wall in C. elegans. In mutants, dorsal and ventral migrations are disrupted, but longitudinal movements are largely unaffected. The gene was tagged for molecular cloning by two independent transposon insertions. Based on genomic and cDNA sequencing, the gene encodes a novel laminin-related protein, UNC-6 (591 amino acids). The N-terminus is homologous to the N-termini (i.e., domains VI, V-1, V-2, and V-3) of laminin subunits, while the C-terminus is a unique domain. We propose that UNC-6 is a component of an extracellular matrix cue that guides dorsoventral ------------------- Key: 1641 Medline: 93090161 Authors: Mah KB;Rankin CH Title: An analysis of behavioral plasticity in male Caenorhabditis elegans. Citation: Behavioral and Neural Biology 58: 211-221 1992 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans is a simple soil-dwelling nematode which has two sexes, hermaphrodite and male. The male C . elegans is differentiated from the hermaphrodite by the presence of 14 sensory structures in the tail. In this study, we compared the behavioral responses of males and hermaphrodites to head-touch and to tap. We hypothesized that the anatomical difference in sensory structures might result in behavioral differences in the reversal response to vibratory stimulation (a tap to the side of the holding dish). In the response to increasing intensities of tap, both sexes showed an increase in response magnitude, with the males showing larger responses than hermaphrodites. In addition, the male was shown to be capable of simple nonassociative learning: it demonstrated habituation and recovery from habituation in a similar manner as the hermaphrodite. Tail-touch-induced inhibition of the reversal response appeared to be similar in males and hermaphrodites. The evidence suggests that the touch withdrawal circuit in hermaphrodites is also present in the male C . elegans , and that the subtle differences in response to tap seen in males may result from the additional sensory receptors of the copulatory bursa of the tail. It seems clear from these studies that these structures do not play a key role in the male worm's ------------------- Key: 1642 Medline: 93107899 Authors: Driscoll M Title: Molecular genetics of cell death in the nematode Caenorhabditis elegans. Citation: Journal of Neurobiology 23: 1327-1351 1992 Type: REVIEW Genes: act-1 ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-9 ced-10 ces-1 ces-2 deg-1 egl-1 lin-24 lin-33 mec-4 mec-6 nuc-1 Abstract: In C. elegans, cell death can be readily studied at the cellular, genetic, and molecular levels. Two types of death have been characterized in this nematode: (1) programmed cell death, which occurs as a normal component in development; and (2) pathological cell death, which occurs aberrantly as a consequence of mutation. Analysis of mutations that disrupt programmed cell death in various ways has defined a genetic pathway for programmed cell death which includes genes that perform such functions as determination of which cells die, the execution of cell death, the engulfment of cell corpses, and the digestion of DNA from dead cells. Molecular analysis is providing insight into the nature of the molecules that function in these aspects of programmed cell death. Characterization of some genes that mutate to induce abnormal cell death has defined a novel gene family called degenerins that encode putative membrane proteins. Dominant alleles of at least two degenerin genes, mec-4 and deg-1, can cause cellular swelling and late onset of neurodegeneration of specific groups of cells. ------------------- Key: 1643 Medline: 93078873 Authors: Van Voorhies WA Title: Production of sperm reduces nematode life-span. Citation: Nature 360: 456-458 1992 Type: ARTICLE Genes: spe-26 Abstract: Sex and death are two fundamental but poorly understood aspects of life. They are often thought to be linked because reproduction requires the diversion of limited resources from somatic growth and maintenance. This diversion of resources in mated animals, often called a cost of reproduction, is usually expressed as a reduction of lifespan in mated animals, although some debate exists on the best way to measure this cost. I report here that in the soil nematode, Caenorhabditis elegans, sex significantly decreases male lifespan without reducing hermaphrodite lifespan. The reduction of mated male lifespan seems to be caused by additional sperm production and not by the physical activity of mating. This conclusion is supported by observations that a mutation reducing sperm production increased mean lifespan by about 65% in both mated males and hermaphrodites. This suggests that spermatogenesis, rather than oogenesis or the physical act of mating, is a major factor reducing lifespan in C . elegans . This contradicts the traditional biological assumption that large oocytes are much costlier to produce ------------------- Key: 1644 Medline: Authors: Schierenberg E;Junkersdorf B Title: The role of eggshell and underlying vitelline membrane for normal pattern formation in the early C. elegans embryo. Citation: Roux's Archives of Developmental Biology 202: 10-16 1992 Type: ARTICLE Genes: Abstract: The embryo of the nematode Caenorhabditis elegans is surrounded by an inconspicuous inner vitelline membrane and a prominent outer chitinous eggshell proper. We demonstrate that the complete removal of the chitinous eggshell does not interfere with successful development to yield a normal worm. The same result can be obtained when the vitelline membrane is penetrated with laser microbeam irradiation of only the eggshell proper, gently enough to permit its resealing after a while. However, when large holes are made into the eggshell the concomitantly penetrated vitelline membrane does not reseal. While early development is quite normal under these conditions, gastrulation is defective in that gut precursor cells do not migrate in properly, eventually leading to embryonic arrest. This suggests a crucial role for pattern formation of the ''micro-environment'' around the embryo preserved by the intact vitelline membrane. Removing both eggshell and vitelline membrane results in a string-like arrangement of founder cells and subsequent grossly abnormal cell patterns. Our experiments support the idea that the prominent eggshell proper just functions as a mechanical protection while the thin vitelline membrane directly or indirectly serves as a necessary control element affecting the positions of cells which to begin with are determined by the orientation of the cleavage spindle. ------------------- Key: 1645 Medline: Authors: Junkersdorf B;Schierenberg E Title: Embryogenesiis in C. elegans after elimination of individual blastomeres or induced alteration of the cell-division order. Citation: Roux's Archives of Developmental Biology 202: 17-22 1992 Type: ARTICLE Genes: Abstract: Our earlier studies on embryonic arrest mutants of C. elegans had indicated that early deviations from the normal temporal and spatial pathway of development lead to monstrous terminal phenotypes with little resemblance to a hatched juvenile. To analyze more directly the roles of different parameters for cellular pattern formation, various experiments with a laser microbeam have now been performed and are described in this and the accompanying paper. By ablating early blastomeres we demonstrate here that the establishment of certain cell lineages is not necessary for the generation of a hatching juvenile. However, no replacement of missing cells was observed in these cases, and the resultant animals lacked those structures which are normally produced by the ablated cells. We found that retardation of cell cycle periods in certain cell lineages and thus a change in the normal order of cell divisions is compatible with development to a hatching juvenile. This is also true when, after irradiation of gut precursor cells, their inward migration is considerably delayed. Our results demonstrate that the invariant pattern of early nematode embryogenesis is not a necessary prerequisite for normal development. Studying parameters necessary for gastrulation we found that after irradiation leading to prolonged cell cycle periods the undivided gut founder cell itself rather than its two daughters moves into the center of the embryo. We removed individual early blastomeres and tested whether the typical inward movement of gut precursors still took place. Our results show that the presence of specific neighboring founder cells is not required, indicating that prospective gut cells reduce their cohesive contacts with adjacent ------------------- Key: 1646 Medline: 93120453 Authors: Kim YK;Valdivia HH;Maryon EB;Anderson P;Coronado R Title: High molecular weight proteins in the nematode C. elegans bind H3-ryanodine and form a large conductance channel. Citation: Biophysical Journal 63: 1379-1384 1992 Type: ARTICLE Genes: Abstract: Single-channel properties of a polypeptide fraction from the nematode Caenorhabditis elegans highly enriched in binding sites were studied in planar bilayers. [H-3]Ryanodine binding sites were purified by sucrose gradient centrifugation of C. elegans microsomes solubilized in CHAPS detergent. The highest [H-3]ryanodine binding activity sedimented at approximately 18% sucrose (wt/vol), and was composed of a major polypeptide with a M(r) of 360,000 and a minor polypeptide with a M(r) of 170,000. The ryanodine-binding polypeptide(s) formed a Ca2+-permeable channel with a permeability ratio P(divalent)/P(monovalent) = 4 and two conductance states of 215 pS and 78 pS in 0.25 M KCl. Ryanodine locked the channel in the 78 pS state and inhibited transitions between the 215 pS and 78 pS states. These data demonstrated the presence of a ryanodine receptor in C. elegans with functional properties comparable to those ------------------- Key: 1647 Medline: 93085750 Authors: Lincke CR;The I;Vangroen M;Borst P Title: The P-glycoprotein gene family of Caenorhabditis elegans--cloning and characterization of genomic and complementary DNA sequences. Citation: Journal of Molecular Biology 228: 701-711 1992 Type: ARTICLE Genes: pgp-1 pgp-2 pgp-3 pgp-4 Abstract: P-glycoproteins, encoded by families of evolutionary conserved genes, can confer a multidrug-resistant phenotype to mammalian tumor cells. To obtain more information on their functions in normal cells we have cloned genomic and complementary DNA sequences of four P-glycoprotein gene homologs of the genetically well-characterized nematode Caenorhabditis elegans, termed pgp-1, pgp-2, pgp-3 and pgp-4, respectively. The genes were physically mapped on chromosome IV (pgp-1), I (pgp-2) and X (pgp-3 and pgp-4). Phenotypic mutants corresponding to these loci have not yet been described. Two of the genes, pgp-1 and pgp-3, were analyzed in detail. They are predicted to encode ATP-binding membrane-spanning proteins of 1321 and 1254 amino acid residues, respectively, with the characteristic features shared by most P-glycoproteins described thus far. Intra-species divergence of P-glycoprotein genes is more pronounced in C . elegans than in mammals. Only 40% of the amino acids of pgp-1 and pgp-3 are identical, in contrast to 77% identity between human MDR1 and MDR3. pgp-1 consists of 14 exons, pgp-3 of 13. The two genes share only one intron position, whereas they share four (pgp-1) and five (pgp-3) intron positions with mammalian P-glycoprotein genes. pgp-1, pgp-2, and pgp-3 are transcribed into low abundance mRNAs in wild-type nematodes. pgp-1 and pgp-3 mRNAs have the trans-spliced leader SL1 at their 5' ends. Arsenite, emetine and actinomycin D drugs did not increase the steady state levels of pgp mRNA, unlike in some mammalian cell types. Heat shock disturbed trans as well as cis-splicing of pgp-1 and led to the accumulation of partially processed pgp-1 RNA. Thus, in C . elegans these genes are not induced in the context of a general stress response, as has been proposed for mammalian P-glycoprotein ------------------- Key: 1648 Medline: Authors: Opperman CH;Chang S Title: Nematode acetylcholinesterases--molecular forms and their potential role in nematode behavior. Citation: Parasitology Today 8: 406-411 1992 Type: REVIEW Genes: ace-1 ace-2 ace-3 Abstract: Nematode movement is reliant upon the somatic musculature that runs longitudinally along the body wall. Neuromuscular synapses occur in the ventral and dorsal cords and employ the excitatory neurotransmitter, acetylcholine (ACh), for modulation of muscle activity. Acetylcholine activity is terminated by hydrolysis by acetylcholinesterase (AChE). Here, Charles Opperman and Stella Chang discuss the molecular forms and potential role of this enzyme. ------------------- Key: 1649 Medline: 93170178 Authors: Beanan MJ;Strome S Title: Characterization of a germ-line proliferation mutation in C. elegans. Citation: Development 116: 755-766 1992 Type: ARTICLE Genes: bli-2 dpy-5 dpy-11 egl-23 fem-3 glp-1 glp-4 him-3 him-5 lev-10 lon-2 skn-1 tra-1 unc-5 unc-32 unc-54 unc-75 Abstract: The C. elegans germ line is generated by extensive proliferation of the two germ-line progenitor cells present in newly hatched larvae. We describe genetic and phenotypic characterization of glp-4, a locus whose product is required for normal proliferation of the germ line. glp-4(bn2ts) mutant worms raised at the restrictive temperature contain approximately 12 germ nuclei, in contrast to the 700-1000 present in wild-type adults. The few germ cells present in sterile glp-4 adults appear to be arrested at prophase of the mitotic cell cycle. This cell-cycle disruption prevents the germ cells from entering meiosis and differentiating, into gametes. Shifting sterile glp-4 worms to the permissive temperature enables their germ cells to undergo extensive proliferation and form gametes, demonstrating that the bn2-induced cell-cycle arrest is reversible and that proliferation and differentiation of germ cells can be uncoupled from development of the somatic gonad. The glp-4(bn2ts) mutation can be used to generate large populations of worms that are severely depleted in germ cells, facilitating determination of whether any gene of interest is expressed in the germ ------------------- Key: 1650 Medline: 93101977 Authors: Hannon GJ;Maroney PA;Yu YT;Hannon GE;Nilsen TW Title: Interaction of U6 snRNA with a sequence required for function of the nematode SL RNA in trans-splicing. Citation: Science 258: 1775-1780 1992 Type: ARTICLE Genes: Abstract: Nematode trans-spliced leader (SL) RNAs are composed of two domains, an exon [the 22-nucleotide spliced leader] and a small nuclear RNA (snRNA)-like sequence. Participation in vitro of the spliced leader RNA in trans-splicing reactions is independent of the exon sequence or size and instead depends on features contained in the snRNA-like domain of the molecule. Chemical modification interference analysis has revealed that two short sequence elements in the snRNA-like domain are necessary for SL RNA activity. These elements are sufficient for such activity because when added to a 72-nucleotide fragment of a nematode U1 snRNA, this hybrid RNA could participate in trans-splicing reactions in vitro. One of the critical sequence elements may function by base-pairing with U6 snRNA, an essential U snRNA for both cis- and trans-splicing. ------------------- Key: 1651 Medline: 93110362 Authors: Vaux DL;Weissman IL;Kim SK Title: Prevention of programmed cell death in Caenorhabditis elegans by human bcl-2. Citation: Science 258: 1955-1957 1992 Type: ARTICLE Genes: ced-1 ced-3 ced-4 ced-9 rol-6 Abstract: Programmed cell death is a physiological process that eliminates unwanted cells. The bcl-2 gene regulates programmed cell death in mammalian cells, but the way it functions is not known. Expression of the human bcl-2 gene in the nematode Caenorhabditis elegans reduced the number of programmed cell deaths, suggesting that the mechanism of programmed cell death controlled by bcl-2 in humans is the same as that in nematodes. ------------------- Key: 1652 Medline: 93078867 Authors: Partridge L;Harvey PH Title: What the sperm count costs. Citation: Nature 360: 415- 1992 Type: REVIEW Genes: Abstract: Dissecting the sex life of the nematode worm Caenorhabditis elegans has already provided surprises for biologists interested in life-history theory. In a report on page 456 of this issue, Van Voorhies throws another spanner in the works by demonstrating that the costs of producing sperm are not as negligible as we might have thought. ------------------- Key: 1653 Medline: Authors: Angier N Title: Production of sperm is found to cut life, in a worm, at least. Citation: New York Times, December 3 : A1-A11 1992 Type: NEWS Genes: Abstract: The simple act of making sperm substantially shortens a male worm's life span, a researcher has discovered in results that overturn accepted biological dogma about the relative cheapness of a male's ejaculation compared with the preciousness of a female's egg. The scientist studying simple but revealing worms called nematodes found that males live much shorter lives than their mates, and he has traced that discrepancy to sperm production. ------------------- Key: 1654 Medline: Authors: Edgar L Title: Embryogenesis in Caenorhabditis elegans. Citation: "Development: The Molecular Genetic Approach." Russo (ed), Springer-Verlag, New York. : 273-294 1992 Type: REVIEW Genes: cib-1 emb-29 glp-1 hlh-1 lin-12 mei-1 mei-2 mel-26 mes-1 mes-2 mes-3 mes-4 mes-5 par-1 par-2 par-3 par-4 par-5 pha-1 spe-11 zen-1 zyg-9 Abstract: Caenorhabditis elegans is a small soil nematode which is currently being extensively studied to discern general principles of how genes control development. The short life cycle, ability to culture in quantities sufficient for biochemical work, well-developed genetics, small cell number for a rather sophisticated animal, and rapidly increasing possibilities for molecular genetics are features that make this species a very productive system ------------------- Key: 1655 Medline: Authors: Ruvkun G Title: Generation of temporal and cell lineage asymmetry during C. elegans development. Citation: "Development: The Molecular Genetic Approach." Russo (ed), Springer-Verlag, New York. : 295-307 1992 Type: REVIEW Genes: let-23 let-60 lin-4 lin-12 lin-14 lin-15 lin-28 lin-29 mec-3 mec-7 unc-86 Abstract: Genetic analysis of C. elegans development has focused on developmental events that take place after hatching, during postembryonic development. After hatching with 558 cells, about 10% of these are blast cells that undergo further cell divisions (Fig. 1) to generate a total of 959 neurons, muscles, intestinal and hypodermal cells in the hermaphrodite and 1031 cells in the male. Like embryonic development (se Edgar, Chap. 19 this Vol.), the pattern of cell division and differentiation during C. elegans postembryonic development is nearly invariant and has been completely described. The cell lineage of wild-type, mutant, or laser-ablated animals can be determined by direct observation of development using Normarski optics. Because most cells during C. elegans postembryonic development generate unique patterns of descendents (though symmetries in the lineage exist), the cell lineage produced by a particular blast cell during development is a signature of that cell's identity. Any changes in cell identity, induce, for example, by laser ablation or neighboring cells or by mutation, can be recognized by a change in the lineage produced by that cell. By laser ablation, it has been shown that in many cases, that patterns of cell lineage executed by particular cells do not depend on their neighbors and instead reflect some intrinsic developmental program. On the other hand, the lineages of particular blast cells, for example, those that generate the hermaphrodite vulva, have been shown by laser ablation experiments to depend on interactions with their neighbors. Thus the pattern of cell divisions and differentiations that normally occur during C. elegans development depends on the ancestry of cells in some cases on their neighbors or positional signals in other cases. Two major goals of developmental genetic analysis in C. elegans have been to explain how genes couple cell lineage information to cell identity and to explain how genes control and mediate cell-cell interactions. As described below, this analysis has revealed molecular mechanisms for the generation of lineage asymmetry and for intercellular signaling that are general to perhaps all metazoans. ------------------- Key: 1656 Medline: Authors: Lambie EJ;Kimble J Title: lin-12 and glp-1: homologous genes with overlapping functions in Caenorhabditis elegans. Citation: "Cell-Cell Interactions in Early Development." 49th Symposium of the Society for Developmental Biology. Gerhart J (ed), Wiley-Liss, New York. : 283-296 1991 Type: REVIEW Genes: glp-1 lag-1 lag-2 lin-12 Abstract: During the development of the nematode, Caenorhabditis elegans, cell fates are determined via a combination of cell-autonomous and cell-nonautonomous mechanisms. The latter, regulative phenomena, require the existence of one or more intercellular signaling pathways. In this review, we consider the function of two genes, lin-12 (lineage abnormal) and glp-1 (germ line proliferation defective), that are required for intercellular signaling during nematode development. ------------------- Key: 1657 Medline: Authors: Sternberg PW;Hill RJ;Chamberlin HM Title: Inductive signalling in C. elegans. Citation: "Evolutionary Conservation of Developmental Mechanisms." Spradling AC (ed), Wiley-Liss, New York. : 141-158 1993 Type: REVIEW Genes: let-23 let-60 lin-3 lin-12 lin-15 Abstract: We now know that the invariance of C. elegans development arises in part from highly reproducible cell interactions. Each cell is formed in an identical position within the developing organism and is therefore susceptible to the same set of intercellular signals. Some of these interactions involve signals among cells of equivalent developmental potential (lateral signalling) while other involve signals between cells of distinct developmental potential (induction). The invariant development and the small cell number of this nematode species allows study of cell interactions at the level of individual cells. Recent molecular evidence indicates that nematodes share many classes of proteins with vertebrates and insects, including proteins involved in signal transduction and transcriptional regulation. Thus, from the point of view of developmental phenomenology and molecular mechanisms, nematodes provide a useful experimental system for the study of general properties of cell signalling. ------------------- Key: 1658 Medline: Authors: Anderson P;Emmons SW;Moerman DG Title: Discovery of Tc1 in the nematode Caenorhabditis elegans. Citation: "The Dynamic Genome." Fedoroff N and Botstein D (eds), Cold Spring Harbor Laboratory Press, New York. : 319-333 Type: REVIEW Genes: Abstract: ------------------- Key: 1659 Medline: Authors: Wood WB;Trent C;Meneely P;Manser J;Burgess S Title: Control of X-chromosome expression and sex determination in embryos of Caenorhabditis elegans. Citation: "Genetic Regulation of Development." Liss, New York. : 191-199 1987 Type: REVIEW Genes: dpy-21 dpy-22 dpy-23 dpy-26 dpy-27 dpy-28 egl-16 her-1 sdc-1 tra-1 Abstract: Work in our laboratory over the past several years has focused on the nature of early determinative decisions in embryos of the free-living nematode Caenorhabditis elegans. Two of these decisions regard determination of sex and determination of the level of X-chromosome expression. C. elegans has two sexes, self-fertilizing hermaphrodites and males. Hermaphrodites normally have two X chromosomes, and males have only one (there is no Y chromosome). Genetic and molecular evidence suggest that C. elegans compensates for this difference in X dosage, not by X inactivation as in mammals, but rather by global regulation of the X chromosome as in Drosophila; that is, X-linked genes are expressed at a higher level per chromosome in 1X than 2X animals, so that levels of X expression are similar in the two sexes. Also as in Drosophila, the primary signal that dictates both sex determination and level of X expression in C. elegans is the ration of the number of X chromosomes to the number of sets of autosomes (X/A ratio) rather than the absolute number of X chromosomes.| ------------------- Key: 1660 Medline: Authors: Blumenthal T;Zucker E;Denison K;Cane J;Spieth J Title: Sequences conserved in the promoter regions of nematode vitellogenin genes. Citation: "Sequence Specificity in Transcription and Translation." Liss, New York. : 125-133 1985 Type: REVIEW Genes: vit-1 vit-2 vit-3 vit-4 vit-5 vit-6 Abstract: Expression of the vitellogenin genes is restricted to the intestine of adult hermaphrodite C. elegans. In order to identify potential cis-acting elements involved in this developmental regualtion, we have sequenced the regions surrounding the 5' ends of five of the six members of this gene family. In addition, we have sequenced several of the promoters from the homologous genes from the related species C. briggsae. Although the various promoters are largely diverged from one another, we have discovered two potential regulatory sequences within the first 250 bp upstream of each of the genes. The first, TGTCAAT, occurs eight times as a perfect heptamer upstream of the five C. elegans genes, at least once per promoter. Allowing a 1 bp mismatch, the element is found in both orientations a total of 27 times, four to six timer per promoter. It is present preferentially at two locations: just upstream of the TATA box and, in the opposite orientation, at position -180. The second sequence, CTGATAA, is also present as a perfect heptamer in a restricted region of each promoter: near position -135. Remarkably, this sequence is also found upstream of the vitellogenin genes of vertebrates. Both sequences have been conserved in the C. briggsae promoters. We hypothesize that these two sequences are involved in the sex-, tissue-, and stage-specific expression of the vitellogenin genes. ------------------- Key: 1661 Medline: 93059220 Authors: Meinke PT;Rohrer SP;Hayes EC;Schaeffer JM;Fisher MH;Mrozik Title: Affinity probes for the avermectin binding proteins. Citation: Journal of Medicinal Chemistry 35: 3879-3884 1992 Type: ARTICLE Genes: Abstract: The design and synthesis of a series of avermectin affinity probes used in the identification and purification of the avermectin binding proteins is described. These modified avermectins fall into two design classes: ligands to covalently modify specific avermectin binding proteins [an I-125-labeled aryl azide photoprobe (15) and a tritiated aziridine analog (6)] and ligands for affinity chromatography applications [three biotinylated compounds (10, 12, and 13) and one resin-bound derivative(9)]. The binding affinities of these compounds for the Caenorhabditis elegans avermectin binding protein is presented as well as their biological activities against C. elegans and Artemia salina. ------------------- Key: 1662 Medline: Authors: Epstein HF;Casey DL;Ortiz I Title: Myofilament Assembly in muscle development of Caenorhabditis elegans. Citation: "Neuromuscular Development and Disease." Kelley AM (ed), Raven Press, New York. : 211-222 1992 Type: REVIEW Genes: deb-1 mup-1 mup-2 mup-3 myo-3 unc-15 unc-22 unc-45 unc-52 unc-54 unc-82 unc-87 unc-89 Abstract: The body wall muscle cells of Caenorhabditis elegans are a developmental system in which questions of gene expression in determination of muscle cell fates and in differentiation to produce functioning myofibrillar contracile units are examined by genetic, molecular, and cellular techniques. These approaches have been singularly useful in understanding the requirements of nonmyosin proteins and activities in the assembly of myosin into thick myofilaments and of membrane and extracellular proteins in the organization of myofilaments into ordered ------------------- Key: 1663 Medline: Authors: Rose AM;McKim KS Title: Meiotic Recombination in Caenorhabditis elegans. Citation: "Mechanisms of Eukaryotic DNA Recombination." Gottesman ME (ed), Academic Press, San Diego. : 113-124 1992 Type: REVIEW Genes: him-2 him-7 him-14 rec-1 mnC1 hDf8 hDp14 mnDp1 sDp1 sDp2 eT1 hT2 mnT2 nT1 sT1 sT2 szT1 Abstract: Meiosis is the process by which eukaryotes reduce their chromosome content by half. During meiosis, the chromosomes undergo two divisions, the first of which involves the organized synapsis of homologous chromosomes. During this division, synapsis predisposes the chromosomes to recombination and proper disjunction. We review here aspects of meiotic recombination under study using the self-fertilizing hermaphroditic nematode Caenorhabditis elegans. Six linkage groups wre identified by Brenner that correlated with the six chromosomes observed by Nigon. Although the behavior of the chromosomes is reported to be holokinetic, we have not needed to invoke any unusual mechanisms to explain their behavior with regard to meiotic recombination. On the contrary, there appears to be a single homolog recognition site localized at or near one end of each of the chromosomes. It is not known whether the homolog recognition site is associated with a centromere, but it is clear that this region is responsible for the initiation of the meiotic phenomena of homolog pairing, recombination, and proper disjunction. ------------------- Key: 1664 Medline: 93099872 Authors: Xue D;Finney M;Ruvkun G;Chalfie M Title: Regulation of the mec-3 gene by the C. elegans homeoproteins UNC-86 and MEC-3. Citation: EMBO Journal 11: 4969-4979 1992 Type: ARTICLE Genes: lin-11 mec-3 mec-4 mec-7 mec-17 rol-6 unc-54 unc-86 Abstract: The mec-3 gene encodes a homeodomain protein with LIM repeats that is required for the specification of touch cell fate in Caenorhabditis elegans. Previous experiments suggested that mec-3 expression requires the product of the unc-86 gene, a POU-type homeoprotein, and mec-3 itself. We have analyzed the control of mec-3 expression by identifying potential cis regulatory elements in the mec-3 gene (by conservation in a related nematode and by DNase I footprinting using unc-86 and mec-3 proteins) and testing their importance by transforming C.elegans with mec-3lacZ fusions in which these sites have been mutagenized in vitro. Both unc-86 and mec-3 proteins bind specifically to the promoter of the mec-3 gene, suggesting that both proteins may be directly involved in the regulation of the mec-3 gene. In addition, the footprint pattern with mec-3 protein is altered in the presence of unc-86 protein. In vivo transformation experiments reveal that some of the binding regions of the two proteins are needed for general positive control and maintenance of mec-3 expression while others have no detectable, unique function. Interestingly, the unc-86 gene appears to be required not only to initiate mec-3 expression but also to maintain it. ------------------- Key: 1665 Medline: Authors: Hotez P;Hawdon J;Schad GA Title: Hookworm larval infectivity, arrest and amphiparatenesis- The Caenorhabditis elegans daf-c paradigm. Citation: Parasitology Today 9: 23-26 1993 Type: REVIEW Genes: daf-1 daf-11 daf-12 daf-22 Abstract: Arrested development dramatically alters the life history of some species of soil-transmitted nematodes and elicits profound variations in the epidemiology of the infections they cause. Here, Peter Hotez, John Hawdon and Gerhard Schad show how an understanding of the cellular and molecular bases of arrested development may lead to new approaches for the control of ancylostomiasis and related ------------------- Key: 1666 Medline: 93107021 Authors: Chen WI;Lim HH;Lim L Title: A new member of the ras superfamily, the rac1 homolog from Caenorhabditis elegans. Citation: Journal of Biological Chemistry 268: 320-324 1993 Type: ARTICLE Genes: cha-1 dpy-4 let-60 Abstract: A new member of the ras superfamily, designated CErac1 has been identified. The CErac1 cDNA clone was isolated from a Caenorhabditis elegans mixed stage library and encodes a protein of 191 amino acids with 82 and 79% identity to human rac1 and rac2 proteins, respectively. The CErac1 cDNA maps to a position on C. elegans chromosome IV in close proximity to cha-1, a choline acetyltransferase gene. The CErac1 cDNA hybridizes to two mRNAs (1.7 and 0.9 kilobases). Their expression is developmentally regulated, that of the more abundant 1.7 kilobases being highest at the embryonic stage and decreasing dramatically during development with 10% of the embryonic level in adult nematodes. The glutathione-S-transferase/CErac1 fusion protein expressed in Escherichia coli binds GTP and exhibits intrinsic GTPase activity. The GTPase activity of the CErac1 protein is stimulated by human n-chimaerin, a GTPase-activating protein for p21 rac1. These data suggest a role of CErac1 in C. elegans early development. The conserved biochemical properties indicate that further characterization of CErac1 by genetic analysis will be helpful in elucidating not only its role in the signal transduction, but also the biological function of its ------------------- Key: 1667 Medline: 93109349 Authors: Aroian RV;Levy AD;Koga M;Ohshima Y;Kramer JM;Sternberg PW Title: Splicing in Caenorhabditis elegans does not require an AG at the 3' splice acceptor site. Citation: Molecular and Cellular Biology 13: 626-637 1993 Type: ARTICLE Genes: act-1 dpy-10 him-5 let-23 rol-6 sqt-1 unc-4 Abstract: The dinucleotide AG, found at the 3' end of virtually all eukaryotic pre-mRNA introns, is thought to be essential for splicing. Reduction-of-function mutations in two Caenorhabditis elegans genes, the receptor tyrosine kinase gene let-23 and the collagen gene dpy-10, both alter the AG at the end of a short (ca. 50-nucleotide) intron to AA. The in vivo effects of these mutations were studied by sequencing polymerase chain reaction-amplified reverse-transcribed RNA isolated from the two mutants. As expected, we find transcripts that splice to a cryptic AG, skip an exon, and retain an unspliced intron. However, we also find significant levels of splicing at the mutated 3' splice site (AA) and at nearby non-AG dinucleotides. Our results indicate that for short C. elegans introns an AG is not required for splicing at either the correct 3' splice site or incorrect sites. Analysis of a splice site mutant involving a longer, 316-nucleotide C elegans intron indicates that an AO is also not required there for splicing. We hypothesize that elements besides the invariant AG, e.g., an A-U-rich region, a UUUC motif, and/or a potential branch point sequence, are directing the selection of the 3' splice site and that in wild-type genes these elements cooperate so that proper splicing occurs. ------------------- Key: 1668 Medline: 93160547 Authors: Way JC;Run JQ;Wang AY Title: Regulation of anterior cell-specific mec-3 expression during asymmetric cell division in C. elegans. Citation: Developmental Dynamics 194: 289-302 1992 Type: ARTICLE Genes: egl-5 egl-27 glp-1 lin-5 lin-12 lin-17 lin-32 mab-5 mec-3 mec-7 mig-1 unc-11 unc-40 unc-53 unc-73 unc-86 vab-8 Abstract: The homeobox-containing mec-3 gene of C. elegans is expressed in 10 mechanosensory neurons and is necessary for these cells to acquire their fate. All the mec-3-expressing cells are anterior daughters from an asymmetric cell division. In this paper, we examine the expression of a mec-3-lacZ fusion in the presence of mutations that may disrupt asymmetric cell division or anterior-posterior positional information, as well as mutations that may specifically alter mec-3 expression. A mutation in lin-17 causes production of additional mec-3-expressing cells and can have its effect on the cell division that produces a mec-3-expressing cell. In a lin-5 mutant, in which postembryonic blast cells do not complete cell division and become polyploid, blast cells that would give rise to mec-3-expressing daughters instead express mec-3 themselves. In a lin-12 glp-1 double mutant, which is disrupted for many cell interactions in which two cells compete for the same fate, mec-3 expression is unaffected. These results are consistent with a model for asymmetric cell division in which the mec-3-expressing cell and its sister are different immediately upon cell division, rather than acquiring differences through later interaction with each other or their surroundings. lin-17 mutant animals also show defects in the position of the PVM cell and the PLM axons. Animals mutant in unc-73 and unc-40, known to have axon outgrowth defects, also show errors in PVM position and a low frequency of additional mec-3-expressing cells, as well as occasional secondary vulval protrusions, a common phenotype of lin-17 animals. Many other mutations have either no effect on mec-3 expression or an effect that can be largely predicted from previously known phenotypes: these include mab-5, mig-1, unc-53, egl-5, lin-32, and egl-27. unc-11 shows an unexpected and specific defect in mec-3 expression in the PVD neurons, but not in the other mec-3-expressing cells. Two mutations that suppress the egg-laying defect of unc-86 have no effect on the mec-3 expression defect in an unc-86 mutant. ------------------- Key: 1669 Medline: 93114600 Authors: Varkey JP;Jansma PL;Minniti AN;Ward S Title: The Caenorhabditis elegans spe-6 gene is required for major sperm protein assembly and shows second site noncomplementation with an unlinked deficiency. Citation: Genetics 133: 79-86 1993 Type: ARTICLE Genes: spe-4 spe-6 spe-7 spe-26 spe-32 eDf2 eDf18 eDf19 Abstract: Caenorhabditis elegans spermatozoa move by crawling. Their motility requires thin cytoskeletal filaments assembled from a unique cytoskeletal protein, the major sperm protein (MSP). During normal sperm development the MSP is segregated to developing sperm by assembly into filaments that form a paracrystalline array in a transient organelle, the fibrous body-membranous organelle. Mutations in the spe-6 gene cause sterility because they lead to defective primary spermatocytes that do not form spermatids. In these mutant spermatocytes the MSP fails to assemble into fibrous body filaments. Instead, the unassembled MSP distributes throughout the cytoplasm and nucleus. Thus, the spe-6 gene product is necessary for normal MSP localization and assembly during sperm development. In addition to their MSP assembly defect, spe-6 mutant spermatocytes arrest meiosis at diakinesis although their spindle pole bodies still replicate and separate. This results in spermatocytes with four half-spindles surrounding condensed, but unsegregated, chromosomes. All four spe-6 alleles, as well as a chromosome III deficiency that deletes the spe-6 gene, fail to complement two small overlapping chromosome IV deficiencies, eDf18 and eDf19. This non-allele-specific second site non-complementation suggests a concentration-dependent interaction between the spe-6 gene product and products of the gene(s) under eDf18 and eDf19, which include a cluster of sperm-specific genes. Since MSP filament assembly is highly concentration-dependent in vitro, the non-complementation might be expected if the sperm-specific gene products under eDf18 and eDf19 were needed together with the spe-6 gene product to promote MSP ------------------- Key: 1670 Medline: 93201998 Authors: Bowerman B;Tax FE;Thomas JH;Priess JR Title: Cell interactions involved in development of the bilaterally symmetrical intestinal valve cells during embryogenesis in Caenorhabditis elegans. Citation: Development 116: 1113-1122 1992 Type: ARTICLE Genes: dpy-13 glp-1 lag-2 let-23 lin-3 lin-12 lin-15 pie-1 skn-1 unc-8 Abstract: We describe two different cell interactions that appear to be required for the proper development of a pair of bilaterally symmetrical cells in Caenorhabditis elegans called the intestinal valve cells. Previous experiments have shown that at the beginning of the 4-cell stage of embryogenesis, two sister blastomeres called ABa and ABp are equivalent in developmental potential. We show that cell interactions between ABp and a neighboring 4-cell-stage blastomere called P2 distinguish the fates of ABa and ABp by inducing descendants of ABp to produce the intestinal valve cells, a cell type not made by ABa. A second cell interaction appears to occur later in embryogenesis when two bilaterally symmetrical descendants of ABp, which both have the potential to produce valve cells, contact each other; production of the valve cells subsequently becomes limited to only one of the two descendants. This second interaction does not occur properly if the two symmetrical descendants of ABp are prevented from contacting each other. Thus the development of the intestinal valve cells appears to require both an early cell interaction that establishes a bilaterally symmetrical pattern of cell fate and a later interaction that breaks the symmetrical cell fate pattern by restricting to only one of two cells the ability to produce ------------------- Key: 1671 Medline: 93181182 Authors: Li W;Shaw JE Title: A variant Tc4 transposable element in the nematode C. elegans could encode a novel protein. Citation: Nucleic Acids Research 21: 59-67 1993 Type: ARTICLE Genes: act-1 mut-2 unc-33 Abstract: A variant C.elegans Tc4 transposable element, TC4-rh1030, has been sequenced and is 3483 bp long. The Tc4 element that had been analyzed previously is 1605 bp long, consists of two 774-bp nearly perfect inverted terminal repeats connected by a 57-bp loop, and lacks significant open reading frames. In Tc4-rh1030, by comparison, a 2343-bp novel sequence is present in place of a 477-bp segment in one of the inverted repeats. The novel sequence of Tc4-rh1030 is present about five times per haploid genome and is invariably associated with Tc4 elements; we have used the designation Tc4v to denote this variant subfamily of Tc4 elements. Sequence analysis of three cDNA clones suggests that a Tc4v element contains at least five exons that could encode a novel basic protein of 537 amino acid residues. On northern blots, a 1.6-kb Tc4v-specific transcript was detected in the mutator strain TR679 but not in the wild-type strain N2; Tc4 elements are known to transpose in TR679 but appear to be quiescent in N2. We have analyzed transcripts produced by an unc-33 gene that has the Tc4-rh1030 insertional mutation in its transcribed region; all or almost all of the Tc4v sequence is frequently spliced out of the mutant unc-33 transcripts, sometimes by means of non-consensus splice acceptor sites. ------------------- Key: 1672 Medline: 93140788 Authors: Rushforth AM;Saari B;Anderson P Title: Site-selected insertion of the transposon Tc1 into a Caenorhabditis elegans myosin light chain gene. Citation: Molecular and Cellular Biology 13: 902-910 1993 Type: ARTICLE Genes: dpy-19 gpa-1 gpa-2 hlh-1 mlc-1 mlc-2 mut-2 pgp-3 unc-13 unc-22 unc-54 Abstract: We used the polymerase chain reaction to detect insertions of the transposon Tc1 into mlc-2, one of two Caenorhabditis elegans regulatory myosin light chain genes. Our goals were to develop a general method to identify mutations in any sequenced gene and to establish the phenotype of mlc-2 loss-of-function mutants. The sensitivity of the polymerase chain reaction allowed us to identify nematode populations containing rare Tc1 insertions into mlc-2. mlc-2::Tc1 mutants were subsequently isolated from these populations by a sib selection procedure. We isolated three mutants with Tc1 insertions within the mlc-2 third exon and a fourth strain with Tc1 inserted in nearby noncoding DNA. To demonstrate the generality of our procedure, we isolated two additional mutants with Tc1 insertions within hlh-1, the C. elegans MyoD homolog. All of these mutants are essentially wild type when homozygous. Despite the fact that certain of these mutants have Tc1 inserted within exons of the target gene, these mutations may not be true null alleles. All three of the mlc-2 mutants contain mlc-2 mRNA in which all or part of Tc1 is spliced from the pre-mRNA, leaving small in-frame insertions or deletions in the mature message. There is a remarkable plasticity in the sites used to splice Tc1 from these mlc-2 pre-mRNAs; certain splice sites used in the mutants are very different from typical eukaryotic splice sites. ------------------- Key: 1673 Medline: Authors: Barker DM Title: Evolution of sperm shortage in a selfing hermaphrodite. Citation: Evolution 46: 1951-1955 1992 Type: ARTICLE Genes: Abstract: In this note I examine the theoretical consequences of a negative correlation between the production of sperm and eggs in a protandrous, selfing hermaphrodite. This trade-off may explain the unusual condition of sperm-limited fecundity that has been described in the nematode Caenorhabditis elegans (Maupas). An enormous amount of work has been done in recent decades on the genetics, development, and neuroanatomy of C. elegans (Wood, 1988). Populations in the lab and in nature consist of self-fertilizing hermaphrodites and rare males. Hermaphrodites are little more than females able to mature sperm in a portion of their ovaries; they are not able to exchange sperm with other hermaphrodites, but they can be inseminated by a male. The physical basis of the trade-off between sperm and egg production is clear... ------------------- Key: 1674 Medline: 93225570 Authors: Wilson DL Title: A comparison of methods for estimating mortality parameters from survival data. Citation: Mechanisms of Ageing & Development 66: 269-281 1993 Type: ARTICLE Genes: Abstract: The Gompertz mortality function, R(m) = R0e(alphat), is frequently used to describe changes in mortality rate (R(m)) with time (t). In this paper, four methods for determining the best fit values of the two parameters, R0 and alpha, are compared. Three of the four methods use the Gompertz mortality function with mortality rate estimates derived from survival data to determine the best fit values for the two parameters. All three confront problems. The fourth method uses the Gompertz survival function, which can be derived from the Gompertz mortality function and which allows one to use survival data directly. It thereby avoids the problems and generally gives the best estimates for the two parameters. The use of the mortality function, with mortality rate estimates, confronts four distinct problems One of these is caused by time intervals when zero organisms die. A second is caused by errors produced in estimating mortality rates from survival data. If too high a proportion of a population die in a given time inter-val, the mortality rate estimates are too low. A third problem is the sensitivity of the mortality-equation-based analyses to values at the end of the survival curve, where scatter in mortality values tends to be greater. A final problem occurs when time intervals greater than one time unit (day, week, year, etc.) are used in the analysis. Such problems with the use of mortality rates to estimate parameter values are revealed when the calculated parameters are used to produce a survival curve, or when known values of R0 and alpha are used to generate survival data. This paper introduces a non-linear regression analysis, using a Simplex algorithm to fit parameters R0 and alpha in the Gompertz Survival function and concludes that it gives more reliable and consistent results with a variety of data than do three methods that use the mortality function. ------------------- Key: 1675 Medline: 93137326 Authors: Strome S Title: Determination of cleavage planes. Citation: Cell 72: 3-6 1993 Type: REVIEW Genes: Abstract: Most biologists appreciate the precision with which the mitotic spindle separates the duplicated chromosomes into two identical sets. Not as many realize that precision in the subsequent cleavage of the cell into two daughter cells is also important. Selection of the proper orientation and placement of the cleavage plane determines the relative positions of the daughter cells and ensures that each will receive the proper complement of cytoplasmic and membrane material, along with a nucleus. ------------------- Key: 1676 Medline: 93170629 Authors: Dalley BK;Rogalski TM;Tullis GE;Riddle DL;Golomb M Title: Posttranscriptional regulation of RNA polymerase-II in Caenorhabditis elegans. Citation: Genetics 133: 237-245 1993 Type: ARTICLE Genes: ama-1 Abstract: To investigate the regulation of RNA polymerase II levels in Caenorhabditis elegans, we have constructed nematode strains having one, two, or three copies of ama-1, the gene for the largest subunit of RNA polymerase II. Steady-state levels of RNA polymerase II polypeptides and solubilized enzyme activity are invariant with gene dosage, indicating regulatory compensation. However, steady-state levels of ama-1 mRNA are directly proportional to gene dosage. These results imply that RNA polymerase II levels in C. elegans are regulated post-transcriptionally. ------------------- Key: 1677 Medline: 93091267 Authors: Kodoyianni V;Maine EM;Kimble J Title: Molecular basis of loss-of-function mutations in the glp-1 gene of Caenorhabditis elegans. Citation: Molecular Biology of the Cell 3: 1199-1213 1992 Type: ARTICLE Genes: dpy-19 fem-1 glp-1 him-5 lin-12 smg-1 unc-32 unc-69 qDf2 qDp2 qDp3 Abstract: The glp-1 gene encodes a membrane protein required for inductive cell interactions during development of the nematode Caenorhabditis elegans. Here we report the molecular characterization of 15 loss-of-function (lf) mutations of glp-1. Two nonsense mutations appear to eliminate glp-1 activity; both truncate the glp-1 protein in its extracellular domain and have a strong loss-of-function phenotype. Twelve missense mutations and one in-frame deletion map to sites within the repeated motifs of the glp-1 protein (10 epidermal growth factor [EGF]-like and 3 LNG repeats extracellularly and 6 cdc10/SWI6, or ankyrin, repeats intracellularly). We find that all three types of repeated motifs are critical to glp-1 function, and two individual EGF-like repeats may have distinct functions. Intriguingly, all four missense mutations in one phenotypic class map to the N-terminal EGF-like repeats and all six missense mutations in a second phenotypic class reside in the intracellular cdc10/SWI6 repeats. These two clusters of mutations may identify functional domains within the glp-1 protein. ------------------- Key: 1678 Medline: 93135894 Authors: McKeown M;Madigan SJ Title: Sex determination and differentiation in invertebrates: Drosophila and Caenorhabditis elegans. Citation: Current Opinion in Cell Biology 4: 948-954 1992 Type: REVIEW Genes: fem-1 fem-2 fem-3 her-1 sdc-1 sdc-2 sdc-3 tra-1 tra-2 tra-3 xol-1 Abstract: Sex determination in flies and worms is controlled by cascades beginning with the X chromosome: autosome ratio and terminating in transcription factors. We are now gaining an understanding of the molecular mechanisms governing the largely post-transcriptional regulation of the intermediate steps in these cascades. ------------------- Key: 1679 Medline: 93135893 Authors: Katz W;Sternberg PW Title: A plethora of intercellular signals during Caenorhabditis elegans development. Citation: Current Opinion in Cell Biology 4: 939-947 1992 Type: REVIEW Genes: egl-15 egl-17 her-1 hsp-15 let-23 let-60 lin-3 lin-15 lin-22 mab-5 ncl-1 pal-1 sdc-1 sdc-2 sem-5 unc-4 unc-5 unc-6 unc-22 unc-34 unc-40 unc-71 unc-76 Abstract: Reproducible cell-cell interactions contribute to the invariance of Caenorhabditis elegans development and allow high resolution study of molecular mechanisms of intercellular signaling. A number of new cell interactions have been discovered in the past year. The power of nematode molecular genetics has been increased through several technical advances and the genome project, and these new approaches are now being successfully applied both to familiar and new signaling mechanisms. ------------------- Key: 1680 Medline: 93101199 Authors: Bruzik JP;Maniatis T Title: Spliced leader RNAs from lower eukaryotes are trans-spliced in mammalian cells. Citation: Nature 360: 692-695 1992 Type: ARTICLE Genes: sem-4 Abstract: EXON sequences present on separate RNA molecules can be joined by trans-splicing in trypanosomatids, Euglena, and in the nematode and trematode worms1-3. Trans-splicing involves an interaction between a 5' splice site present in a spliced leader RNA and a 3' splice site located near the 5' end of pre-messenger RNAs. In vitro trans-splicing of artificial mammalian pre-mRNAs has been reported, but the efficiency of splicing appears to depend on sequence complementarity between the two substrates4-7. There has been speculation that some natural pre-mRNAs can be trans-spliced in mammalian cells in vivo8,9, but alternative interpretations have not been ruled out. Here we show that spliced leader RNAs can be accurately trans-spliced in mammalian cells in vivo and in vitro. Both nematode and mammalian 3' splice sites can function as acceptors for trans-splicing in vivo. These results reveal functional conservation in the splicing machinery between lower eukaryotes and mammals, and they directly demonstrate the potential for trans-splicing in mammalian cells. ------------------- Key: 1681 Medline: 93050174 Authors: Moens L;Vanfleteren J;De Baere I;Jellie AM;Tate W;Trotman CNA Title: Unexpected intron location in non-vertebrate globin genes. Citation: FEBS Letters 312: 105-109 1992 Type: REVIEW Genes: Abstract: The Caenorhabditis elegans and Artemia T4 globin sequences are highly homologous with other invertebrate globins. The intron/exon patterns of their genes display a single intron in the E and G helices respectively. Precoding introns in multirepeat globins are inserted in homologous positions. Comparison of the intron/exon patterns in the known globin gene sequences demonstrates that they are more diverse than first expected but nevertheless can be derived from an ancestral pattern having 3 introns and 4 exons. ------------------- Key: 1683 Medline: Authors: Hodgkin J Title: Sex determination in the nematode Caenorhabditis. Citation: Seminars in Developmental Biology 3: 307-317 1992 Type: REVIEW Genes: dpy-27 egl-1 fem-1 fem-2 fem-3 fog-1 fog-2 her-1 mab-3 sdc-1 sdc-2 tra-1 tra-2 tra-3 xol-1 Abstract: The nematode Caenorhabditis elegans has two natural sexes, the self-fertilizing hermaphrodite (essentially a modified female) and the male. Sex is determined by X chromosome dosage: hermaphrodites are XX, males are XO. This primary signal sets the state of activity for a series of regulatory genes, which are organized hierarchically. The genes at the top of the hierarchy control both sex and dosage compensation; genes acting lower down in the hierarchy control sexual phenotype in both soma and germ-line, but do not affect dosage compensation. Regulation of sexual phenotype is somewhat different between soma and germ line. Many of the genes involved in sex determination have been subjected to molecular analyses. The results indicate that some of the regulatory interactions involve transcriptional controls and others ------------------- Key: 1684 Medline: Authors: Godfray HCJ;Harvey PH Title: More fecund but not so fit. Citation: Nature 354: 190-191 1991 Type: REVIEW Genes: tra-1 Abstract: Populations of the soil nematode Caenorhabditis elegans normally consist almost exclusively of self-fertilizing hermaphrodites. The animal first matures about 300 sperm and then a much larger number of oocytes (eggs). Nearly every sperm is used to fertilize an egg and so the maximum fecundity is around 300. Why doesn't the nematode mature more sperm and thus increase its fecundity? In a paper in the Proceedings of the Royal Society (B246, 19-24; 1991), J. Hodgkin and T.M. Barnes provide both an elegant answer and a rare insight into the mechanistic basis of an important life-history trade-off. ------------------- Key: 1685 Medline: 93013027 Authors: Maruyama IN;Brenner S Title: A selective lambda phage cloning vector with automatic excision of the insert in a plasmid. Citation: Gene 120: 135-141 1992 Type: ARTICLE Genes: mup-2 unc-13 unc-53 Abstract: A bacteriophage lambda cloning vehicle has been constructed for thegeneration of cDNA libraries. The vector has the following properties. (1) Ithas a unique BamHI site engineered into the lambda gam gene. Segments of DNAcan be cloned into this site and clones with an insert can be selected by theirability to grow on an Escherichia coli host lysogenic for phage P2(Spi-phenotype). (2) When the recombinant phage infects a Cre-producing E. colistrain, a site-specific recombination event results in the excision of aplasmid replicon with the cloned insert. (3) Single-stranded DNAs can berecovered by growing helper M13 phages on bacteria harboring such plasmids ------------------- Key: 1686 Medline: 93202469 Authors: Starich TA;Herman RK;Shaw JE Title: Molecular and genetic analysis of unc-7, a Caenorhabditis elegans gene required for coordinated locomotion. Citation: Genetics 133: 527-541 1993 Type: ARTICLE Genes: act-1 daf-6 osm-1 sup-10 unc-3 unc-7 unc-93 unc-33 unc-80 mnDp3 mnDp14 mnDf124 Abstract: Mutations in the Caenorhabditis elegans gene unc-7 confer an uncoordinated phenotype. Wild-type animals trace smooth, sinuous waves as they move; unc-7 mutants make irregular bends or kinks along their bodies, particularly when they move forward. The unc-7 locus has also been implicated in the nematode's response to volatile anesthetics. We have cloned unc-7 by transposon tagging: an unc-7 mutation was correlated with the insertion of the transposon Tc1, and reversion of the mutant phenotype was correlated with loss of the Tc1 element. We have physically mapped the region flanking the sites of Tc1 insertion and identified DNA rearrangements corresponding to eight additional unc-7 alleles. Northern analysis indicates that a 2.7-kb unc-7 message is present in all developmental stages but is most abundant in L1-L3 larvae. The 5' end of the message contains a trans-spliced leader SL1. An 18-kb intron is located upstream of the predicted translational start site of the gene, and DNA breakpoints of four gamma-ray-induced alleles were located within this intron. We determined the sequence of a cDNA corresponding to the unc-7 message. The message may encode a 60-kd protein whose amino acid sequence is unrelated to any other available protein sequence; a transmembrane location for the unc-7 protein is predicted. We predict from our analysis of unc-7 genetic mosaics that the unc-7 gene product is not required in muscle cells for wild-type coordination but is probably required in motor neurons (although a hypodermal role has not been excluded). We speculate that unc-7 may be involved in the function of neuronal ion channels. ------------------- Key: 1687 Medline: 93202470 Authors: Hodgkin J Title: Molecular cloning and duplication of the nematode sex-determining gene tra-1. Citation: Genetics 133: 543-560 1993 Type: ARTICLE Genes: dpy-1 dpy-18 fem-1 fem-2 fem-3 fer-2 her-1 mel-23 pha-1 sdc-2 tra-1 unc-32 unc-47 unc-49 unc-64 unc-119 vab-7 eC1 eDf2 eDf20 eDp6 eDp24 Abstract: The autosomal sex-determining gene tra-1 plays a major role in controlling sexual phenotype in the nematode Caenorhabditis elegans. This gene is the terminal global regulator in a well-characterized cascade of sex-determining genes. It governs all aspects of somatic sexual differentiation, and it also has important functions in governing germ-line differentiation. Previous genetic analyses have led to the characterization of many loss-of-function (masculinizing) and gain-of-function (dominant feminizing) alleles, and to models for the functions and regulation of tra-1, The gene was cloned by identifying linked transposon insertions, about 200 kb away from tra-1. From this starting point a series of YAC, cosmid and phage clones were assembled into a genomic walk covering over 400 kb. Much of this region was found to be unrepresented in the cosmid database that covers most of the C. elegans genome. This deficit is largely or wholly due to the presence of sequences that cannot be cloned in rec+bacterial hosts. The ratio of physical map distances to recombinational map distances in the tra-1 region of the genome appears to be unusually low, indicating considerable local map expansion. The location of tra-1 within the cloned region was determined using a variety of tra-1 mutations that are associated with physical rearrangements of the gene. One of these is a 14-kb deletion, which behaves as a null allele. Another rearrangement, eDp24, is a tandem duplication of 22 kb. Genetic analysis demonstrates that eDp24 carries two incomplete copies of tra-1, and that these copies appear to interact, suggesting some form of negative autoregulation at this locus. Three variant forms of the tra-1 locus have been identified in different natural isolates of C. elegans. ------------------- Key: 1688 Medline: 93155063 Authors: Freedman JH;Slice LW;Dixon D;Fire A;Rubin CS Title: The novel metallothionein genes of Caenorhabditis elegans - structural organization and inducible, cell-specific expression. Citation: Journal of Biological Chemistry 268: 2554-2564 1993 Type: ARTICLE Genes: dpy-29 kin-12 mtl-1 mtl-2 rol-6 unc-76 vmp-2 Abstract: Two genes (mtl-1 and mtl-2) that encode the novel metallothioneins (MTs) of Caenorhabditis elegans (CeMTs) were cloned and characterized. Both genes contain a single intron that interrupts codon 6 and short 3'-untranslated regions. However, their promoter regions are distinctively non-homologous. The mtl-2 promoter contains a TATAA box and a single putative metal regulatory element. These elements are absent in the mtl-1 promoter. Nevertheless, both CeMT1 and CeMT2 mRNAs are induced by cadmium and contain precisely initiated, 5'-untranslated sequences. The inducibility and cell type specificity of metallothionein gene expression were investigated in transgenic C. elegans that carry the lacZ (beta-galactosidase) reporter gene under the control of an mtl-1 or mtl-2 promoter sequence. Upon treatment of transgenic C. elegans with cadmium or heat stress, the mtl-2:lacZ fusion gene is abundantly and exclusively expressed in the intestinal cells of larvae and adult animals. Expression is not detected in the absence of metal or heat shock. In contrast, an mtl-1:lacZ construct is constitutively expressed in the pharynx and induced by cadmium and heat shock in the intestinal cells of C. elegans larvae. The metal-inducible expression of the mt1-1:lacZ gene is attenuated in adult transgenic nematodes. Thus, the activity of each mtl promoter is modulated by metals as well as developmental and ------------------- Key: 1689 Medline: 93173104 Authors: Marra MA;Prasad SS;Baillie DL Title: Molecular analysis of two genes between let-653 and let-56 in the unc-22(IV) region of Caenorhabditis elegans. Citation: Molecular & General Genetics 236: 289-298 1993 Type: ARTICLE Genes: cat-1 cat-4 let-52 let-56 let-653 unc-22 sDf2 sDf9 sDf19 sDf65 Abstract: A previous study of genomic organization described the identification of nine potential coding regions in 150 kb of genomic DNA from the unc-22(IV) region of Caenorhabditis elegans. In this study, we focus on the genomic organization of a small interval of 0.1 map unit bordered on the right by unc-22 and on the left by the left-hand breakpoints of the deficiencies sDf9, sDf19 and sDf65. This small interval at present contains a single mutagenically defined locus, the essential gene let-56. The cosmid C11F2 has previously been used to rescue let-56. Therefore, at least some of C11F2 must reside in the interval. In this paper, we report the characterization of two coding elements that reside on C11F2. Analysis of nucleotide sequence data obtained from cDNAs and cosmid subclones revealed that one of the coding elements closely resembles aromatic amino acid decarboxylases from several species. The other of these coding elements was found to closely resemble a human growth factor activatable Na+/H+ antiporter. Pairs of oligonucleotide primers, predicted from both coding elements, have been used in PCR experiments to position these coding elements between the left breakpoint of sDf19 and the left breakpoint of sDf65, between the essential genes let-653 and let-56. ------------------- Key: 1690 Medline: Authors: Elder D Title: Reiterating mutants of the nematode Caenorhabditis elegans. Citation: Rivista Di Biologia-Biology Forum 85: 461-466 1992 Type: REVIEW Genes: Abstract: Certain mutants of the nematode Caenorhabditis elegans exhibit an abnormal reiteration of specific cell divisions... ------------------- Key: 1691 Medline: 93161411 Authors: Klein RD;Meyer BJ Title: Independent domains of the sdc-3 protein control sex determination and dosage compensation in C. elegans. Citation: Cell 72: 349-364 1993 Type: ARTICLE Genes: dpy-26 dpy-27 dpy-28 fem-1 fem-2 fem-3 her-1 him-5 him-8 sdc-1 sdc-2 sdc-3 tra-1 tra-2 tra-3 unc-76 xol-1 yDf9 yDf11 nT1 Abstract: sdc-3 is an early-acting regulatory gene that controls both sex determination and X chromosome dosage compensation in C. elegans. It is unique among sdc genes in that its sex determination and dosage compensation functions act independently. The molecular analysis reported here demonstrates that separate domains of the Sdc-3 protein control these two developmental processes. Sequence analysis of 16 sdc-3 alleles reveals that the dosage compensation mutations specifically eliminate a pair of zinc finger motifs at the carboxyl terminus of Sdc-3, while the sex determination mutations alter a region with limited homology to the ATP-binding domain of myosin. Null mutations, which disrupt both processes, abort translation of Sdc-3 prior to both domains. Analysis of site-directed changes confirms the functional significance of the two separate regions in sex determination and dosage compensation and reveals that an additional region, undetected by genetic analysis, is also required for proper ------------------- Key: 1692 Medline: 93170661 Authors: Perry MD;Li WQ;Trent C;Robertson B;Fire A;Hageman JM; Wood WB Title: Molecular characterization of the her-1 gene suggests a direct role in cell signaling during Caenorhabditis elegans sex determination. Citation: Genes & Development 7: 216-228 1993 Type: ARTICLE Genes: act-1 fem-1 her-1 him-8 par-1 rol-4 rol-6 tra-1 tra-2 tra-3 unc-37 unc-42 unc-54 unc-61 unc-76 xol-1 Abstract: We have characterized two transcripts from the male-determining her-1 locus in Caenorhabditis elegans. The larger transcript, which appears more important for male development, is predicted to encode a novel 175-amino-acid, cysteine-rich polypeptide with an apparent amino-terminal signal sequence and potential cleavage and glycosylation sites. Expression of a full-length cDNA construct for the larger transcript driven by a body-wall-myosin promoter causes extensive masculinization of all sexually dimorphic tissues in XX (normally hermaphrodite) animals. This activity is dependent on the presence of the her-1 signal sequence or a substitute synthetic signal sequence in the encoded polypeptide. These results suggest that a secreted product of the her-1 gene dictates male development. ------------------- Key: 1694 Medline: 93180781 Authors: Zhen M;Heinlein R;Jones D;Jentsch S;Candido EPM Title: The ubc-2 gene of Caenorhabditis elegans encodes a ubiquitin-conjugating enzyme involved in selective protein degradation. Citation: Molecular and Cellular Biology 13: 1371-1377 1993 Type: ARTICLE Genes: ubc-2 ubc-3 Abstract: The ubiquitin-protein conjugation system is involved in a variety of eukaryotic cell functions, including the degradation of abnormal and short-lived proteins, chromatin structure, cell cycle progression, and DNA repair. The ubiquitination of target proteins is catalyzed by a ubiquitin-activating enzyme (El) and ubiquitin-conjugating enzymes (E2s) and in some cases also requires auxiliary substrate recognition proteins (E3s). Multiple E2s have been found, and these likely possess specificity for different classes of target proteins. Here we report the cloning and characterization of a gene (ubc-2) encoding a ubiquitin-conjugating enzyme which is involved in the selective degradation of abnormal and short-lived proteins in the nematode Caenorhabditis elegans. The nematode ubc-2 gene encodes a 16.7-kDa protein with striking amino acid sequence similarity to Saccharomyces cerevisiae UBC4 and UBC5 and Drosophila UbcD1. When driven by the UBC4 promoter, ubc-2 can functionally substitute for UBC4 in yeast cells; it rescues the slow-growth phenotype of ubc4 ubc5 mutants at normal temperature and restores their ability to grow at elevated temperatures. Western blots (immunoblots) of ubc4 ubc5 yeast cells transformed with ubc-2 reveal a protein of the expected size, which cross-reacts with anti-Drosophila UbcD1 antibody. C elegans ubc-2 is constitutively expressed at all life cycle stages and, unlike yeast UBC4 and UBC5, is not induced by heat shock. Both trans and cis splicing are involved in the maturation of the ubc-2 transcript. These data suggest that yeast UBC4 and UBC5, Drosophila UbcD1, and C. elegans ubc-2 define a highly conserved gene family which plays ------------------- Key: 1695 Medline: 93188021 Authors: Kennedy BP;Aamodt EJ;Allen FL;Chung MA;Heschl MFP;McGhee JD Title: The gut esterase gene (ges-1) from the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. Citation: Journal of Molecular Biology 229: 890-908 1993 Type: ARTICLE Genes: ges-1 hsp-3 hsp-16 mec-3 rol-6 unc-22 Abstract: The ges-1 gene codes for a non-specific carboxylesterase that is normally expressed only in the intestine of the nematode Caenorhabditis elegans. In the current paper, we describe the cloning and characterization of the ges-1 gene from C. elegans, as well as the homologous gene from the nematode Caenorhabditis briggsae. The ges-1 esterases from the two nematodes are 83% identical at the amino acid level and contain regions of significant similarity to insect and mammalian esterases; these conserved regions can be identified with residues believed to be necessary for esterase function. The ges- 1 mRNAs from both C. elegans and C. briggsae are trans-spliced. The coding regions, the codon bias and the splicing signals of the two ges-1 genes are quite similar and most (6/7) of the intron positions are retained precisely. Yet, the flanking sequences of the two ges-1 genes appear to have diverged almost completely. For example, the C. elegans ges-1 5'-flanking region (as well as several introns) contains copies of three different SINE-like sequences, previously identified near the hsp-16 genes, near the unc-22 gene and in a repetitive element CeRep-3; none of these elements are found in the C. briggsae ges-1 gene. We show that: (1) the C. elegans ges-1 gene can be used to transform C. briggsae, whereupon expression of the exogenous ges-1 gene is confined to the C. briggsae intestine; (2) the ges-1 homologue cloned from C. briggsae can be transformed into C. elegans, whereupon it is expressed largely in the C. elegans intestine; and (3) a 5'-deletion of the C. elegans ges-1 gene that we have previously shown to be expressed in the C. elegans pharynx is also expressed in the pharynx of C. briggsae (either in the presence or absence of vector sequences). These results suggest that the ges-1 gene control circuits have been maintained between the two nematode species, despite the divergent 5'-flanking sequences of the gene. This raises the question of the evolutionary distance between C. elegans and C. briggsae and we attempt to estimate the C. elegans-C. briggsae divergence time by analysing the rate of synonymous substitutions in coding regions of ges-1 and six other C. elegans-C. briggsae gene pairs. We propose a new method of analysis, which attempts to remove rate differences found between different genes by extrapolating to zero codon bias.(ABSTRACT TRUNCATED AT 400 WORDS) ------------------- Key: 1696 Medline: 93179861 Authors: Avery L Title: Motor-neuron M3 controls pharyngeal muscle relaxation timing in Caenorhabditis elegans. Citation: Journal of Experimental Biology 175: 283-297 1993 Type: ARTICLE Genes: eat-4 unc-29 unc-31 Abstract: 1. Previous work has shown that 12 of the 14 types of neurons in the Caenorhabditis elegans pharyngeal nervous system are collectively but not individually necessary for the trapping and transport of bacteria. The aim of these experiments was to determine the functions of individual neuron types by laser-killing combinations of neurons and looking at the effects on behavior. ' 2. The motor neuron M3 and the sensory neuron I5 are important in trapping bacteria, as shown by two observations. First, when M3 and I5 are both killed, trapping is inefficient in the isthmus (the middle section of the pharynx). Second, M3 is sufficient in the absence of the other 11 neuron types for normal trapping in the corpus (anterior pharynx). 3. M3 and I5 influence the timing of pharyngeal muscle motions. When M3 is killed, pump duration (the interval from the beginning of pharyngeal contraction to the end of relaxation) increases from 170 to 196 ms. This increase is at least partially due to a slower relaxation. Thus, M3 speeds up relaxation. Pump duration decreases to 159 ms when I5 is killed. When I5 and M3 are both killed, pump durations are long (192 ms), just as when M3 alone is killed. These observations, together with previous electron microscopic work showing synapses from I5 to M3, suggest that I5 slows down relaxation by inhibiting M3. 4. To explain these results, I propose that M3 and I5 promote bacterial trapping by regulating the relative timing of muscle relaxation in different regions of the pharynx. ------------------- Key: 1697 Medline: 93209535 Authors: Prasad SS;Starr TV;Rose AM Title: Molecular characterization in the dpy-14 region identifies the S-adenosylhomocysteine hydrolase gene in Caenorhabditis elegans. Citation: Genome 36: 57-65 1993 Type: ARTICLE Genes: col-4 dpy-14 hsp-70 unc-22 Abstract: The region around dpy-14 on chromosome 1 of Caenorhabditis elegans has been extensively studied genetically, with regard to essential gene organization. This region was one of the first for which cloned DNA was available as a result of restriction fragment length polymorphism mapping. To examine the information content of the cloned DNA in this region, evolutionarily conserved sequences were identified by cross-species hybridization. Ten regions of conservation have been identified and characterized with regard to mRNA abundance and DNA sequence. cDNAs were obtained for seven of these conserved regions and sequence from the cDNAs were used to search the SWISS protein and EMBL nucleotide data banks. Two coding regions shared DNA identities with existing sequences, the opa repeat family of Drosophila and the S-adenosylhomocysteine hydrolase gene. Of the three for which no corresponding cDNA were found, one corresponds to the snRNA U1-1. The other two did not detect transcripts on Northern analysis and are either conserved, but not coding, or code for low abundance transcripts. The density of conserved coding regions in this study was one per 15 kbp of genomic DNA, three times lower than that reported on chromosome 3 by the genome sequencing project. ------------------- Key: 1698 Medline: 93216850 Authors: Krause M;Fire A;White-Harrison S;Weintraub H;Tapscott S Title: Functional conservation of nematode and vertebrate myogenic regulatory factors. Citation: Journal of Cell Science S16: 111-115 1992 Type: REVIEW Genes: hlh-1 Abstract: The Caenorhabditis elegans protein, CeMyoD, is related to the vertebrate myogenic regulatory factors MyoD, myogenin, MRF-4 and Myf-5. Like its vertebrate counterparts, CeMyoD accumulates in the nucleus of striated muscle cells prior to the onset of terminal differentiation. CeMyoD also shares functional similarities with the vertebrate myogenic regulatory factors. Viral LTR driven expression of CeMyoD in mouse 10T1/2 cells can convert this cell line into myoblasts as well as efficiently trans-activate mouse muscle-specific promoters. Furthermore, mouse MyoD expression can activate a CeMyoD-beta-galactosidase reporter construct in a 10T1/2 co-transfection assay. ------------------- Key: 1699 Medline: 93232500 Authors: Honda S;Ishii N;Suzuki K;Matsuo M Title: Oxygen-dependent perturbation of life-span and aging rate in the nematode. Citation: Journal of Gerontology 48: 57B-61 1993 Type: ARTICLE Genes: mev-1 rad-1 rad-2 rad-3 rad-5 rad-6 rad-7 rad-8 rad-9 Abstract: The effects of atmospheric oxygen on the life span and aging rate of the nematode Caenorhabditis elegans were examined. The mean and maximum life spans of both the wild type and mev-1(kn1) mutant, whose cytoplasmic superoxide dismutase activity level is about half of the wild type, were increased and decreased under low and high concentrations of oxygen, respectively. The Gompertz component, a parameter of aging rate, of the wild type was smaller under 1% oxygen than under 2% or more oxygen. Further, the Gompertz component of the mutant increased with an increase in oxygen concentration. These effects of oxygen on the perturbation of life span and aging rate were more pronounced in the mev-1(kn1) mutant than in the wild type. The oxygen-dependent perturbation of life span and aging rate seems to be enhanced by a genetic defect of the mutant in antioxidant defense. A 1% oxygen exposure at the early phase of life span was ineffective for life span extension in the mutant, suggesting that the effect of oxygen concentrations on life span is not secondary to the effects of development and maturation. These results show that changes in oxygen concentration perturb aging rate, and hence oxygen is involved in the specification of life ------------------- Key: 1700 Medline: Authors: Kamiya Y;Harada S;Okoyama S;Yamamoto H;Hosono R Title: Developmental and pharmacological studies of acetylcholinesterase-defective mutants of Caenorhabditis elegans. Citation: Zoological Science 10: 43-51 1993 Type: ARTICLE Genes: ace-1 ace-2 ace-3 Abstract: Three genes (ace-1, ace-2, and ace-3), which code for acetylcholinesterase (class A, B, and C) have been identified in the nematode Caenorhabditis elegans. Here we investigate the developmental and pharmacological properties of mutants retaining only one of distinct classes of acetylcholinesterase. Both class A and B acetylcholinesterases share about one-half of the total enzyme activity throughout development and maximum specific activity at the first larval stage, and are sufficient for maintaining normal acetylcholine levels. Although class B acetylcholinesterase is distributed at the head and the body region as seen in the wild type, the class A enzyme is biased towards the head region. Class C acetylcholinesterase occupies only a few percent of the total activity, is mainly distributed in the body, shows maximum specific activity at the late larval stage and is clearly different in pharmacological response from class A and B acetylcholinesterases. We propose that class B is the major acetylcholinesterase, and that classes A and C are supplementary. ------------------- Key: 1701 Medline: 93209225 Authors: Conrad R;Liou RF;Blumenthal T Title: Conversion of a trans-spliced C. elegans gene into a conventional gene by introduction of a splice donor site. Citation: EMBO Journal 12: 1249-1255 1993 Type: ARTICLE Genes: col-12 rol-6 Abstract: In Caenorhabditis elegans, pre-mRNAs that are trans-spliced are distinguished by the presence of an 'outron', intron-like RNA at the 5' end followed by a splice acceptor. We report that trans-splicing of the rol-6 gene can be completely suppressed simply by introducing a donor site into its 173 nt outron, at a site 50 nt upstream of the trans-splice site, thereby converting rol-6 into a conventional gene with a spliced intron near its 5' end. When the consensus donor site was inserted at sites further upstream it was less effective in replacing trans-splicing with cis-splicing. Surprisingly, the length of the intron was not the important variable, since lengthening of the 50 nt intron to 250 nt did not restore trans-splicing. Apparently the context into which the splice site was introduced determined the efficiency of its use. These results support the conclusion that the sole signal for trans-splicing is the presence of an outron. Clearly, cis- and trans-splice acceptor sites are interchangeable, allowing the possibility of competition between the two types of splicing. ------------------- Key: 1702 Medline: 93197157 Authors: Conrad R;Liou RF;Blumenthal T Title: Functional analysis of a C. elegans trans-splice acceptor. Citation: Nucleic Acids Research 21: 913-919 1993 Type: ARTICLE Genes: gpd-3 rol-6 Abstract: The rol-6 gene is trans-spliced to the 22 nt leader, SL1, 173 nt downstream of the transcription start. We have analyzed splicing in transformants carrying extrachromosomal arrays of rol-6 with mutations in the trans-splice acceptor site. This site is a close match to the consensus, UUUCAG, that is highly conserved in both trans-splice and intron acceptor sites in C.elegans. When the trans-splice site was inactivated by mutating the perfectly-conserved AG, trans-splicing still occurred, but at a cryptic site 20 nt upstream. We tested the frequency with which splicing switched from the normal site to the cryptic site when the pyrimidines at this site were changed to A's. Since most C.elegans 3' splice sites lack an obvious polypyrimidine tract, we hypothesized that these four pyrimidines might play this role, and indeed mutation of these bases caused splicing to switch to the cryptic site. We also demonstrated that a major reason the downstream site is normally favored is because it occurs at a boundary between A + U rich and non-A + U rich RNA. When the RNA between the two splice sites was made less A + U rich, splicing occurred preferentially at the upstream ------------------- Key: 1703 Medline: Authors: Beck CDO;Rankin CH Title: Effects of aging on habituation in the nematode Caenorhabditis elegans. Citation: Behavioural Processes 28: 145-163 1993 Type: ARTICLE Genes: Abstract: The effects of aging on spontaneous locomotor behavior and habituation in a mechanosensory reflex were examined in the nematode Caenorhabditis elegans. Worms were tested at 4 days (at the peak of egg laying), at 7 days (when egg laying ends) and at 12 days post-hatching. Both spontaneous and reflexive movements were smaller in older worms than in younger worms. In addition the magnitude of these movements was related to life span; the shorter an animal's life span, the smaller its reversal movements while still young. Worms at all ages expressed habituation and dishabituation at a 10 s interstimulus interval (ISI); thus even aged worms were capable of non-associative learning. However, older worms showed greater habituation than did 4-day-old worms to stimuli delivered at a 60 s ISI. There was also an age-related change in the recovery from habituation. At days 4 and 7, worms had recovered from habituation by 30 min after training; however, responses of day 12 worms were still significantly smaller than baseline at 30 min after training. Further behavioral tests with normal and mutant worms may help elucidate the nature of the age-related changes in the learning and memory processes of C. elegans and the genetic mechanisms which underlie them. ------------------- Key: 1704 Medline: 93213074 Authors: Bargmann CI Title: Genetic and cellular analysis of behavior in C. elegans. Citation: Annual Review of Neuroscience 16: 47-71 1993 Type: REVIEW Genes: daf-6 daf-10 daf-19 dec-1 cat-1 cat-4 cha-1 che-1 che-2 che-3 che-5 che-6 che-7 che-10 che-11 che-12 che-13 che-14 egl-1 egl-5 egl-8 egl-18 egl-20 egl-27 egl-41 egl-44 egl-45 egl-46 exp-1 exp-2 ham-1 her-1 lin-32 mec-1 mec-2 mec-3 mec-4 mec-5 mec-6 mec-7 mec-8 mec-9 mec-10 mec-12 mec-14 mec-15 mec-17 mec-18 mig-1 mig-2 mig-10 mig-12 osm-1 osm-3 osm-5 osm-6 pbo-1 sem-4 tax-2 tax-3 tax-4 tax-6 tra-2 ttx-1 unc-6 unc-16 unc-25 unc-33 unc-34 unc-40 unc-44 unc-47 unc-51 unc-71 unc-73 unc-76 unc-86 unc-101 Abstract: Behavior arises through the interplay of innate properties of the nervous system, environmental stimuli, and experience. An opportunity to integrate neuronal and genetic approaches to study behavior is provided by the soil nematode Caenorhabditis elegans. C. elegans is attractive for study because of the simplicity and accessibility of its nervous system. The adult hermaphrodite is 1 mm long, and its nervous system is composed of only 302 neurons. The nucleus of each neuron can be identified in live animals by differential interference microscopy, and the cell lineage that gives rise to each of these neurons has been described in its entirety. C. elegans develops to adulthood in about three days at 25C, which facilitates observation of its ------------------- Key: 1705 Medline: 93211935 Authors: Kaplan JM;Horvitz HR Title: A dual mechanosensory and chemosensory neuron in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 90: 2227-2231 1993 Type: ARTICLE Genes: che-2 che-3 che-5 che-7 che-12 che-13 osm-3 osm-6 Abstract: After light touch to its nose, the nematode Caenorhabditis elegans halts forward locomotion and initiates backing. Here we show that three classes of neurons (ASH, FLP, and OLQ) sense touch to the nose and hence are required for this avoidance response. ASH, FLP, and OLQ have sensory endings that contain axonemal cilia. Mutant animals that have defective ciliated sensory endings as well as laser-operated animals that lack ASH, FLP, and OLQ fail to respond to touch to the nose. Together with the previous work of others, these results demonstrate that C. elegans has at least five morphologically distinct classes of mechanosensory neurons. Interestingly, the ASH neuron also acts as a chemosensory neuron; it mediates the avoidance of noxious chemicals. Since ASH possesses both chemosensory and mechanosensory modalities, this neuron might be functionally analogous to vertebrate nociceptors, which ------------------- Key: 1706 Medline: 93203259 Authors: Blaxter ML Title: Cuticle surface proteins of wild-type and mutant Caenorhabditis elegans. Citation: Journal of Biological Chemistry 268: 6600-6609 1993 Type: ARTICLE Genes: dpy-3 him-5 lin-4 rol-6 srf-1 srf-2 srf-3 srf-4 srf-5 srf-8 srf-9 Abstract: The molecular components of the surface of the free-living nematode Caenorhabditis elegans have been identified by surface-specific radioiodination. Four compartments were defined by fractionation of labeled wild type (N2 strain) adult hermaphrodites. Organic solvents extracted cuticular lipids. Homogenization in detergents released a single, non-collagenous, hydrophobic protein. This is not glycosylated and is a heterodimer of 6.5- and 12-kDa subunits. The third compartment, proteins solubilized by reducing agents, included both the cuticular collagens and the heterodimer. Residual material corresponds to the cuticulin fraction. Larval stages showed a similar pattern, except that the dauer larva had an additional 37-kDa detergent-soluble protein. Other species of rhabditid nematodes displayed similar profiles, and comparison with parasitic species suggests that this simple pattern may be primitive in the Nematoda. A C . elegans strain mutant in cuticular collagen (rol-6) had a pattern identical to that of wild type, but another morphological mutant (dpy-3) [corrected from (dpy-6)] and several mutants that differ in surface reactivity to antibody and lectins (srf mutants) also had striking differences in surface labeling patterns. ------------------- Key: 1707 Medline: 93219072 Authors: Cangiano G;La Volpe A Title: Repetitive DNA sequences located in the terminal portion of the Caenorhabditis elegans chromosomes. Citation: Nucleic Acids Research 21: 1133-1139 1993 Type: ARTICLE Genes: Abstract: We describe the distribution along the chromosomes of Caenorhabditis elegans of two repetitive DNA families, RcS5 and Cerep3 and interstitial telomeric sequences. Both families show, among other interesting features, a preferential location in the terminal 30% of the chromosomes. It is known that in these regions of the genome the frequency of recombination is much higher than in the central portion, genes are rarer and sequences important for chromosome disjunction may lie. ------------------- Key: 1708 Medline: 93216087 Authors: DeLong L;Plenefisch JD;Klein RD;Meyer BJ Title: Feedback-control of sex determination by dosage compensation revealed through Caenorhabditis elegans sdc-3 Citation: Genetics 133: 875-896 1993 Type: ARTICLE Genes: dpy-26 dpy-27 dpy-28 her-1 sdc-1 sdc-2 sup-7 sDf21 yDf8 yDf9 yDf10 yDf11 Abstract: In Caenorhabditis elegans, sex determination and dosage compensation are coordinately controlled through a group of genes that respond to the primary sex determination signal. Here we describe a new gene, sdc-3, that also controls these processes. In contrast to previously described genes, the sex determination and dosage compensation activities of sdc-3 are separately mutable, indicating that they function independently. Paradoxically, the sdc-3 null phenotype fails to reveal the role of sdc-3 in sex determination: sdc-3 null mutations that lack both activities disrupt dosage compensation but cause no overt sexual transformation. We demonstrate that the dosage compensation defect of sdc-3 null alleles suppresses their sex determination defect. This self-suppression phenomenon provides a striking example of how a disruption in dosage compensation can affect sexual fate. We propose that the suppression occurs via a feedback mechanism that acts at an early regulatory step in the sex determination pathway to ------------------- Key: 1709 Medline: 93216088 Authors: Avery L Title: The genetics of feeding in Caenorhabditis elegans. Citation: Genetics 133: 897-917 1993 Type: ARTICLE Genes: act-1 act-2 act-3 aex-3 ali-1 bli-4 bli-6 ced-2 cha-1 che-2 daf-2 daf-7 deb-1 dpy-1 dpy-3 dpy-5 dpy-6 dpy-9 dpy-10 dpy-11 dpy-13 dpy-14 dpy-17 dpy-18 dpy-19 dpy-20 eat-1 eat-2 eat-3 eat-4 eat-5 eat-6 eat-7 eat-8 eat-9 eat-10 eat-11 eat-12 eat-13 eat-14 eat-15 eat-16 eat-17 egl-10 egl-15 egl-17 emb-9 fem-2 glp-1 him-5 him-8 let-2 let-59 let-75 let-201 let-202 let-203 lin-1 lin-7 lin-10 lin-11 lin-12 lin-15 lin-45 lon-1 lon-2 mec-4 mec-12 pha-2 pha-3 phm-2 phm-3 ric-2 rol-3 rol-6 sem-3 sma-2 sma-5 sqt-3 sup-10 unc-1 unc-2 unc-3 unc-4 unc-6 unc-8 unc-10 unc-11 unc-13 unc-16 unc-17 unc-18 unc-20 unc-24 unc-26 unc-29 unc-30 unc-31 unc-32 unc-36 unc-44 unc-45 unc-46 unc-52 unc-54 unc-57 unc-58 unc-59 unc-75 unc-76 unc-78 unc-89 unc-93 unc-101 unc-104 unc-101 ctDf1 eDf2 eDf3 eDf4 eDf5 eDf6 eDf9 eDf12 eDf15 eDf16 eDf18 eDf19 jDf1 jDf4 maDf1 mnDf4 mnDf16 mnDf30 mnDf31 mnDf39 mnDf41 mnDf67 mnDf68 mnDf69 mnDf88 mnDf89 mnDf96 nDf19 nDf20 nDf23 nDf24 nDf25 qDf2 qDf3 sDf2 sDf8 sDf10 sDf20 sDf26 sDf27 sDf28 sDf35 sDf60 sDf62 sDf63 sDf64 sDf67 hDp62 qDp3 sDp2 Abstract: The pharynx of Caenorhabditis elegans is a nearly self-contained neuromuscular organ responsible for feeding. To identify genes involved in the development or function of the excitable cells of the pharynx, I screened for worms with visible defects in pharyngeal feeding behavior. Fifty-two mutations identified 35 genes, at least 22 previously unknown. The genes broke down into three broad classes: 2 pha genes, mutations in which caused defects in the shape of the pharynx, 7 phm genes, mutations in which caused defects in the contractile structures of the pharyngeal muscle, and 26 eat genes, mutants in which had abnormal pharyngeal muscle motions, but had normally shaped and normally birefringent pharynxes capable of vigorous contraction. Although the Eat phenotypes were diverse, most resembled those caused by defects in the pharyngeal nervous system. For some of the eat genes there is direct evidence from previous genetic mosaic and pharmacological studies that they do in fact affect nervous system. In eat-5 mutants the motions of the different parts of the pharynx were poorly synchronized. eat-6 and eat-12 mutants failed to relax their pharyngeal muscles properly. These pharyngeal motion defects are most easily explained as resulting from abnormal electrical excitability of the pharyngeal muscle membrane. ------------------- Key: 1710 Medline: 93216089 Authors: Graham PL;Kimble J Title: The mog-1 gene is required for the switch from spermatogenesis to oogenesis in Caenorhabditis elegans. Citation: Genetics 133: 919-931 1993 Type: ARTICLE Genes: fem-1 fem-2 fem-3 fog-1 fog-2 her-1 mog-1 tra-1 tra-2 tra-3 sup-7 qC1 nDf40 qDp3 Abstract: Caenorhabditis elegans hermaphrodites make first sperm, then oocytes. By contrast, animals homozygous for any of six loss-of-function mutations in the gene mog-1 (for masculinization of the germ line) make sperm continuously and do not switch into oogenesis. Therefore, in mog-1 mutants, germ cells that normally would become oocytes are transformed into sperm. By contrast, somatic sexual fates are normal, suggesting that mog-1 plays a germ line-specific role in sex determination. Analyses of double mutants suggest that mog-1 negatively regulates the fem genes and/or fog-1: mog-1;fem and mog-1;fog-1 double mutants all make oocytes rather than sperm. Therefore, we propose that wild-type mog-1 is required in the hermaphrodite germ line for regulation of the switch from spermatogenesis to oogenesis rather than for specification of oogenesis per se. In addition to its role in germ-line sex determination, maternal mog-1 is required for embryogenesis: most progeny of a mog-1;fem or mog-1;fog-1 mother die as embryos. How might the roles of mog-1 in the sperm/oocyte switch and embryogenesis be linked? Previous work showed that fem-3 is regulated post-transcriptionally to achieve the sperm/oocyte switch. We speculate that mog-1 may function in the post-transcriptional regulation of numerous germ-line RNAs, including fem-3. A loss of mog-1 might inappropriately activate fem-3 and thereby abolish the sperm/oocyte switch; its loss might also lead to misregulation of maternal RNAs and thus embryonic death. ------------------- Key: 1711 Medline: 93218750 Authors: Watson A;Smaldon N;Lucke R;Hawkins T Title: The Caenorhabditis elegans genome sequencing project--1st steps in automation. Citation: Nature 362: 569-570 1993 Type: REVIEW Genes: Abstract: The development of automated devices to facilitate high-throughput DNA sequencing is essential to the future success of the large-scale genome projects. Before designing any robotic system it is important to have an appreciation of the scale of operation and the difficulties that this might impose. For example, the completion of the 100-Mb Caenorhabditis elegans genome will require in excess of 10*6 DNA templates, all of which will need to be sequenced, identified and tracked at all times from plaque picking to entry in the database. In an effort to increase the throughput of the C. elegans genome project, we have simultaneously designed a robotic system and developed several biochemical procedures to begin the automation of the shotgun sequencing process. ------------------- Key: 1712 Medline: 93156832 Authors: Chalfie M;Driscoll M;Huang MX Title: Degenerin similarities. Citation: Nature 361: 504- 1993 Type: LETTER Genes: deg-1 mec-4 mec-6 mec-10 Abstract: We were delighted to hear, before publication on 4 February, that Canessa et al. Had identified a gene whose product, arEnaC conveys amiloride sensitivity on Xenopus oocytes and exhibits extensive similarity to two Caenorhabditis elegans genes, deg-1 and emc-4, that can mutate to produce neuronal degeneration. We have called the products of these C. elegans genes degenerins. Here we would like to point out that the similarity extends from our previously published sequences, demonstrating that the mammalian and C. elegans genes are members of the same gene ------------------- Key: 1713 Medline: 93157358 Authors: Vaux DL Title: Toward an understanding of the molecular mechanisms of physiological cell death. Citation: Proceedings of the National Academy of Sciences USA 90: 786-789 1993 Type: REVIEW Genes: ced-3 ced-4 ced-9 nuc-1 Abstract: Cell death is a normal physiological process. Morphological studies have shown that cells that die by physiological mechanisms often undergo characteristic changes termed ''apoptosis'' or ''programmed cell death.'' Recent work has begun to unravel the molecular mechanisms of these deaths and has shown that one of the primary cell-death pathways is conserved throughout much of evolution. In the nematode Caenorhabditis elegans programmed cell deaths are mediated by a mechanism controlled by the ced-9 gene; in mammals apoptosis can often be inhibited by expression of the bcl-2 gene. The ability of the human BCL2 gene to prevent cell deaths in C. elegans strongly suggests that bcl-2 and ced-9 are homologous genes. Although the process of cell death controlled by bcl-2 can occur in many cell types, there appears to be more than one physiological cell-death mechanism. Targets of cytotoxic T cells and cells deprived of growth factor both exhibit changes characteristic of apoptosis, such as DNA degradation. However, bcl-2 expression protects cells from factor withdrawal but fails to prevent cytotoxic T-cell killing. DNA degradation is, thus, not specific for any one cell-death mechanism. The ability of bcl-2 to protect cells from a wide variety of pathological, as well as physiological, stimuli indicates that many triggers can serve to activate the same suicide pathway, even some thought to cause necrosis, and not physiological cell death. ------------------- Key: 1714 Medline: 93136659 Authors: Fleming JT;Tornoe C;Riina HA;Coadwell J;Lewis JA;Sattelle Title: Acetylcholine receptor molecules of the nematode Caenorhabditis elegans. Citation: "Comparative Molecular Neurobiology." Pichon Y (ed), Birkhauser Verlag, Switzerland. 63: 65-80 1993 Type: REVIEW Genes: lev-1 lev-8 lev-9 lev-10 unc-29 unc-38 unc-50 unc-63 unc-74 Abstract: Receptors for acetylcholine are present in nematodes. Studies using physiological and biochemical methods have revealed the existence of nicotinic acetylcholine receptors with a novel pharmacology. Caenorhabditis elegans provides a particularly suitable organsim with which to investigate such receptors using molecular genetic approaches. Mutants resistant to the cholinergic agonist (and anthelmintic drug) levamisole have permitted the isolation of a number of genes, including structural subunits of the nicotinic acetylcholine receptor. The only known viable mutants of nicotinic receptors are those of Caenorhabditis elegans. This organism offers the prospect of studying the developmental and regulatory effects of the loss of a single component of the receptor. Using Caenorhabditis elegans it is possible to select interesting phenotypic mutations by in vivo mutagenesis before determining the causative lesion. Resistance genes other than those encoding structural subunits are of particular interest, as they will encode additional polypeptides closely associated with nicotinic receptor functions. Such proteins are often difficult or impossible to identify using conventional biochemical approaches, whereas genetic selection should permit their identification. ------------------- Key: 1715 Medline: 93203840 Authors: Segerberg MA;Stretton AO Title: Actions of cholinergic drugs in the nematode Ascaris suum - complex pharmacology of muscle and motorneurons. Citation: Journal of General Physiology 101: 271-296 1993 Type: ARTICLE Genes: Abstract: The cholinergic agonists acetylcholine (ACh), nicotine, and pilocarpine produced depolarizations and contractions of muscle of the nematode Ascaris suum. Dose-dependent depolarization and contraction by ACh were suppressed by about two orders of magnitude by 100 muM d-tubocurarine (dTC), a nicotinic antagonist, but only about fivefold by 100 muM N-methyl-scopolamine (NMS), a muscarinic antagonist. NMS itself depolarized both normal and synaptically isolated muscle cells. The muscle depolarizing action of pilocarpine was not consistently antagonized by either NMS or dTC. ACh receptors were detected on motorneuron classes DE1 DE2, DI, and VI as ACh-induced reductions in input resistance. These input resistance changes were reversed by washing in drug-free saline or by application of dTC. NMS applied alone lowered input resistance in DE1, but not in DE2, DI, or VI motorneurons. In contrast to the effect of ACh, the action of NMS in DE1 was not reversed by dTC, suggesting that NMS-sensitive sites may not respond to ACh. Excitatory synaptic responses in muscle evoked by depolarizing current injections into, DE1 and DE2 motorneurons were antagonized by dTC; however, NMS antagonized the synaptic output of only the DE1 and DE3 classes of motorneurons, an effect that was more likely to have been produced by motorneuron conduction failure than by pharmacological blockade of receptor. The concentration of NMS required to produce these changes in muscle polarization and contraction, ACh antagonism, input resistance reduction, and synaptic antagonism was 100 muM, or more than five orders of magnitude higher than the binding affinity for [H-3]NMS in larval Ascaris homogenates and adult Caenorhabditis elegans (Segerberg, M. A. 1989. Ph.D. thesis. University of Wisconsin-Madison, Madison, WI). These results describe a nicotinic-like pharmacology, but muscle and motorneurons also have unusual responses to ------------------- Key: 1716 Medline: 93248060 Authors: Rosoff ML;Doble KE;Price DA;Li C Title: The flp-1 propeptide is processed into multiple, highly similar FMRF amide-like peptides in Caenorhabditis elegans. Citation: Peptides 14: 331-338 1993 Type: ARTICLE Genes: flp-1 Abstract: Previously, we described a gene, flp-1, that encodes seven FMRFamide-like peptides from two alternatively spliced transcripts in the nematode Caenorhabditis elegans. To determine whether all or a subset of the predicted peptides coded for by flp-1 are produced in vivo, we undertook the isolation of FMRFamide-like peptides from C elegans. Six FLRFamide-containing peptides, all contained within the putative translation products of the flp-1 gene, were isolated from extracts of mixed stage animals. By quantitative PCR analysis of RNA from mixed stage animals, we found that the shorter transcript of flp-1 has a higher level of expression than the longer transcript. ------------------- Key: 1717 Medline: 93223702 Authors: Lincke CR;Broeks A;The I;Plasterk RHA;Borst P Title: The expression of two P-glycoprotein (pgp) genes in transgenic Caenorhabditis elegans is confined to intestinal cells. Citation: EMBO Journal 12: 1615-1620 1993 Type: ARTICLE Genes: dpy-5 lin-14 pgp-1 pgp-2 pgp-3 pgp-4 unc-31 Abstract: P-glycoproteins can cause multidrug resistance in mammalian tumor cells by active extrusion of cytotoxic drugs. The natural function of these evolutionarily conserved, membrane-bound ATP binding transport proteins is unknown. In mammals, P-glycoproteins are abundantly present in organs associated with the digestive tract. We have studied the tissue-specific expression of Caenorhabditis elegans P- glycoprotein genes pgp-1 and pgp-3 by transformation of nematodes with pgp-lacZ gene fusion constructs in which the promoter area of the pgp genes was fused to the coding region of lacZ. Expression of pgp-1 and pgp-3, as inferred from pgp-lacZ transgenic nematodes, was confined to the intestinal cells. The expression patterns of both genes were virtually indistinguishable. Quantitative analysis of pgp mRNA levels during development showed that pgp-1, -2, and -3 were expressed throughout the life cycle of C.elegans, albeit with some variation indicating developmental regulation. The expression of P- glycoprotein genes in intestinal cells is an evolutionarily conserved feature of these genes, consistent with the hypothesis that P- glycoproteins provide a mechanism of protection against environmental toxins. ------------------- Key: 1718 Medline: 93207792 Authors: Fire A Title: Histochemical techniques for locating Escherichia coli beta-galactosidase activity in transgenic organisms. Citation: Genetic Analysis-Techniques and Applications 9: 151-158 Type: ARTICLE Genes: Abstract: Escherichia coli beta-galactosidase is a commonly used reporter molecule for analyzing gene expression. Recently, beta-galactosidase fusions have been applied to a variety of eukaryotic systems. The techniques for constructing and introducing beta-galactosidase fusion constructs as well as soluble assays for total enzyme function have been described in detail elsewhere. This article describes histochemical techniques for analyzing organisms that contain a functional beta-galactosidase fusion construct. The object is to determine semiquantitatively which cells are expressing the beta-galactosidase fusion protein, as well as the subcellular localization of the protein. Due to its prevalence in the author's laboratory, Caenorhabditis elegans is used as a canonical organism for the detailed methods described. ------------------- Key: 1719 Medline: 93314568 Authors: Garriga G;Desai C;Horvitz HR Title: Cell interactions control the direction of outgrowth, branching and fasciculation of the HSN axons of Caenorhabditis elegans. Citation: Development 117: 1071-1087 1993 Type: ARTICLE Genes: clr-1 dig-1 egl-15 egl-18 egl-27 egl-43 lin-1 lin-2 lin-3 lin-7 lin-10 lin-11 lin-12 lin-15 lin-39 mig-1 mig-10 sem-2 unc-5 unc-5 unc-14 unc-32 unc-33 unc-34 unc-40 unc-44 unc-51 unc-71 unc-73 unc-76 Abstract: The two serotonergic HSN motor neurons of the nematode Caenorhabditis elegans innervate the vulval muscles and stimulate egg laying by hermaphrodites. By analyzing mutant and laser-operated animals, we find that both epithelial cells of the developing vulva and axons of the ventral nerve cord are required for HSN axonal guidance. Vulval precursor cells help guide the growth cone of the emerging HSN axon to the ventral nerve cord. Vulval cells also cause the two HSN axons to join the ventral nerve cord in two separate fascicles and to defasciculate from the ventral nerve cord and branch at the vulva. The axons of either the PVP or PVQ neurons are also necessary for the HSN axons to run in two separate fascicles within the ventral nerve cord. Our observations indicate that the outgrowth of the HSN axon is controlled in multiple ways by both neuronal and nonneuronal cells. ------------------- Key: 1720 Medline: 93283927 Authors: MacMorris M;Blumenthal T Title: In situ analysis of C. elegans vitellogenin fusion gene expression in integrated transgenic strains - effects of promoter mutations on RNA localization. Citation: Gene Expression 3: 27-36 1993 Type: ARTICLE Genes: glp-4 him-1 him-5 mab-3 sup-7 tra-3 vit-2 vit-5 vit-6 Abstract: Expression of the Caenorhabditis elegans vitellogenin (vit) genes is initiated at the larva-to-adult molt in all of the 30 to 34 nuclei of the hermaphrodite intestine. A series of strains in which DNA carrying a vit fusion gene was integrated at low copy number was analyzed by in situ hybridization to determine whether the transgene showed the same tissue-specific expression. Strains with only 247 bp of 5'-flanking DNA accumulated the mRNA product of the introduced vitellogenin gene only in the adult hermaphrodite intestine, and uniformly in all of the intestinal cells. When similar strains carrying vit fusion genes with promoter modifications were tested, no loss of tissue specificity was observed. Surprisingly, however, strains with modified promoters that resulted in reduced levels of expression displayed a novel pattern of transgene RNA localization within their intestines. Strains with severe promoter defects accumulated the transgene mRNA in the central part of the intestine but lacked the mRNA at both ends. Those with less severe promoter mutations lacked the transgene mRNA only in the most anterior intestinal cells. We hypothesize that genes with altered promoters require higher activator concentrations to express the reporter gene, thus revealing an inherent asymmetry in activator levels, lowest in the anterior cells and highest in the central cells of the intestine. ------------------- Key: 1721 Medline: 93292921 Authors: Clandinin TR;Mains PE Title: Genetic studies of mei-1 gene activity during the transition from meiosis to mitosis in Caenorhabditis Citation: Genetics 134: 199-210 1993 Type: ARTICLE Genes: dpy-5 him-8 lin-10 lin-11 lon-2 mei-1 mei-2 mel-26 unc-13 unc-29 zyg-9 nDf23 gaDp1 Abstract: Genetic evidence suggests that the mei-1 locus of Caenorhabditis elegans encodes a maternal product required for female meiosis. However, a dominant gain-of-function allele, mei-1(ct46), can support normal meiosis but causes defects in subsequent mitotic spindles. Previously identified intragenic suppressors of ct46 lack functional mei-1 activity; null alleles suppress only in cis but other alleles arise frequently and suppress both in cis and in trans. Using a different screen for suppressors of the dominant ct46 defect, the present study describes another type of intragenic mutation that also arises at high frequency. These latter alleles appear to have reduced meiotic activity and retain a weakened dominant effect. Characterization of these alleles in trans-heterozygous combinations with previously identified mei-1 alleles has enabled us to define more clearly the role of the mei-1 gene product during normal embryogenesis. We propose that a certain level of mei-1 activity is required for meiosis but must be eliminated prior to mitosis. The dominant mutation causes mei-1 activity to function at mitosis; intragenic trans-suppressors act in an antimorphic manner to inactivate multimeric mei-1 complexes. We propose that inactivation of meiosis-specific functions may be an essential precondition of mitosis; failure to eliminate such functions may allow ectopic meiotic activity during mitosis and cause embryonic lethality. ------------------- Key: 1722 Medline: 93292923 Authors: Albertson DG Title: Mapping chromosome rearrangement breakpoints to the physical map of Caenorhabditis elegans by fluorescent in situ hybridization. Citation: Genetics 134: 211-219 1993 Type: ARTICLE Genes: gpd-2 gpd-3 dpy-3 lin-18 lon-2 osm-5 pha-1 rol-1 rol-5 sqt-1 tra-1 unc-1 unc-2 unc-4 unc-20 unc-22 unc-50 unc-53 unc-69 unc-78 unc-119 vit-2 vit-3 vit-4 vit-5 eDf2 eDf6 mnDp11 mnDp33 Abstract: A scheme for rapidly mapping chromosome rearrangements relative to the physical map of Caenorhabditis elegans is described that is based on hybridization patterns of cloned DNA on meiotic nuclei, as visualized by fluorescent in situ hybridization. From the nearly complete physical map, DNA clones, in yeast artificial chromosomes (YACs), spanning the rearrangement breakpoint were selected. The purified YAC DNAs were first amplified by degenerate oligonucleotide-primed polymerase chain reaction, then reamplified to incorporate fluorescein dUTP or rhodamine dUTP. The site of hybridization was visualized directly (without the use of antibodies) on meiotic bivalents. This allows chromosome rearrangements to be mapped readily if the duplicated, deficient or translocated regions do not pair with a normal homologous region, because the site or sites of hybridization of the probe on meiotic prophase nuclei will be spatially distinct. The pattern, or number, of hybridization signals from probes from within, or adjacent to, the rearranged region of the genome can be predicted from the genetic constitution of the strain. Characterization of the physical extent of the genetically mapped rearrangements places genetic landmarks on the physical map, and so provides linkage between the two types of map. ------------------- Key: 1723 Medline: 93258816 Authors: Spieth J;Brooke G;Kuersten S;Lea K;Blumenthal T Title: Operons in C. elegans - Polycistronic messenger RNA precursors are processed by transsplicing of SL2 to downstream coding regions. Citation: Cell 73: 521-532 1993 Type: ARTICLE Genes: elt-1 gpd-1 gpd-2 gpd-3 gpd-4 hsp-16 kin-10 kin-13 kup-1 kup-2 lin-15 mai-1 rol-6 tra-1 vit-6 Abstract: The MRNAs of six C. elegans genes are known to be trans-spliced to SL2. We report here that a similarly oriented gene is located 100-300 bp upstream of each. We present evidence that the genes in these clusters are cotranscribed and downstream mRNAs are formed by cleavage at the polyadenylation site and trans-splicing. From one three-gene cluster we isolated cDNA clones representing both polycistronic RNAs and mRNAs polyadenylated at the free 3' end created by trans-splicing, suggesting that polycistronic RNAs can be processed by trans-splicing. Several experiments indicate that SL2 trans-splicing is a consequence of a gene's downstream location in an operon. In particular, when an SL1-accepting gene was moved to a downstream location, its mRNA was trans-spliced largely to SL2. The possible regulatory significance of cotranscription of C. elegans genes is discussed. ------------------- Key: 1724 Medline: 93247635 Authors: Han M;Golden A;Han YM;Sternberg PW Title: C. elegans lin-45 raf gene participates in let-60 RAS-stimulated vulval differentiation. Citation: Nature 363: 133-140 1993 Type: ARTICLE Genes: bli-6 deb-1 dpy-13 dpy-20 let-23 let-60 lin-1 lin-2 lin-3 lin-7 lin-10 lin-15 lin-45 sem-5 unc-24 unc-44 unc-82 Abstract: Vulval differentiation in Caenorhabditis elegans is controlled by intercellular signalling mediated by a receptor tyrosine kinase and a ras gene product. The lin-45 gene encodes a homologue of the raf family of serine/threonine kinases and is necessary for vulval differentiation. The lin-45 raf gene product appears to act downstream of the ras protein in this pathway. A proto-oncogene-mediated signalling pathway may be a common feature of metazoan development. ------------------- Key: 1725 Medline: 93117565 Authors: Mains PE Title: Embryonic development in Caenorhabditis elegans. Citation: "Results and Problems in Cell Differentiation. Early Embryonic Development in Animals." Henning W (ed), Springer-Verlag, Berlin. 18: 49-89 1992 Type: REVIEW Genes: cib-1 emb-29 glp-1 him-14 lin-10 lin-12 mei-1 mei-2 mel-26 par-1 par-2 par-3 par-4 pha-1 spe-11 zyg-1 zyg-9 zyg-11 Abstract: Nematodes were first used to study embryogenesis more than 100 years ago, and this in part led to the concepts of cell-autonomous differentiation and localized cytoplasmic determinants. More recently, the techniques of genetics, experimental and descriptive embryology, and molecular biology have been combined to study the development of the small, free-living nematode Caenorhabditis elegans (Brenner 1974, 1988. This chapter focuses on embryonic development and is intended as a general overview of C. elegans embryogenesis, illustrating the experimental techniques available for this organism and the conclusions that can be drawn. Excellent reviews on postembryonic development (i.e. after hatching) in C. elegans and most other aspects of the worm's development, genetics and biology can be found in Wood (1988a). This book includes extensive appendices detailing techniques and anatomy and includes phenotypic descriptions of all mutants known at the time of publication. Other reviews of C. elegans embryogenesis can be found in Kemphues (1989), Wood (1988b), Schierenberg (1989) and Strome (1989). ------------------- Key: 1726 Medline: Authors: Dicklow MB;Acosta N;Zuckerman BM Title: A novel streptomyces species for controlling plant-parasitic nematodes. Citation: Journal of Chemical Ecology 19: 159-173 1993 Type: ARTICLE Genes: Abstract: A novel species of Steptromyces isolated from nematode suppressive soils in Costa Rica was evaluated for efficacy in controlling plant-parasitic nematodes. This isolate, designated CR-43, was shown to inhibit reproduction of Caenorhabditis elegans in a laboratory assay. Greenhouse trials utilizing three different methods of treatment with CR-43 gave significant reductions of tomato root galling due to Meloidogyne incognita. In a field experiment in Puerto Rico, [West Indies] in soil naturally infested with M. incognita, CR-43-treated pepper showed significant reductions in root galling and significant increases in yield as compared to untreated controls. In a second experiment in Puerto Rico, a significant reduction in tomato root galling and a slight reduction in root galling on pepper occurred. In this trial, yields on both tomato and pepper were higher in CR-43 treatments, but these differences were not statistically significant. In both experiments populations of Rotylenchulus reniformis were reduced by CR-43 treatment. In a field trial on strawberry in Massachusetts, CR-43-treated plants had lower numbers of Pratylenchus penetrans within roots and showed a significant decrease in black root rot disease. Studies on sterile filtrates from CR-43 cultures indicated that a major determinant of CR-43 antinematodal activity was mostly thermostable macromolecules of molecular weight higher than 6000. Culture filtrates of CR-43 exhibited antifungal activity in vitro. ------------------- Key: 1727 Medline: Authors: Bargmann CI Title: Death from natural and unnatural causes. Citation: Current Biology 1: 388-390 1991 Type: REVIEW Genes: ced-3 ced-4 deg-1 her-1 egl-1 lin-14 lin-17 lin-39 mab-5 mec-4 mec-6 tra-2 unc-86 Abstract: Extensive cell death accompanies normal development of both the nervous system and the immune system in vertebrates. A common form of programmed cell death in normal development, called apoptosis, can be initiated in a cell-type-specific fashion by depriving cells of survival factors (for example, sympathetic and sensory neurons that depend on nerve growth factor for survival) or by a lethal stimulus (like glucocorticoid-induced lymphocyte death). Death of a cell by apoptosis requires de novo protein and RNA synthesis, suggesting that an active cell suicide program is being induced. The cell death that occurs in neurodegenerative diseases or brain injury could arise from inappropriate expression of the cell death program, or from the effects of toxic products. Genetic analysis of normal and abnormal cell death may provide insights into the mechanisms for these processes. ------------------- Key: 1728 Medline: Authors: Bargmann CI Title: Nervous system development in Drosophila melanogaster and Caenorhabditis elegans. Citation: "Molecular Genetics of Nervous System Tumors." Levine AJ and Schmidek JJ (eds), Wiley-Liss, New York. : 49-59 1993 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-10 glp-1 let-23 let-60 lin-3 lin-11 lin-12 lin-14 lin-29 mec-3 unc-5 unc-6 unc-34 unc-40 unc-86 Abstract: In the past 10 years, the remarkable discovery has been made that molecular mechanisms of development are conserved among all animals, and that many of the same molecular components appear in signal transduction pathways of all eukaryotes from yeast to man. This mechanistic conservation means that molecules can be studied in the organism in which their properties are most transparent; general principles or specific predictions made from work in one organism can subsequently be explored in other organisms. This chapter reviews aspects of nervous system development that have been studied using genetic approaches in two simple invertebrates, the fruit fly Drosophila melanogaster (herein referred to as Drosophila) and the soil nematode worm Caenorhabditis elegans (C. elegans). The nervous systems of both of these organisms are extremely simple compared to those of mammals.... ------------------- Key: 1729 Medline: 93282858 Authors: Abad P;Cerutti M;Pauron D;Quiles C;Palin B;Devauche G;Dalmasso A Title: Expression and biochemical characterization of the DNA-binding activity of TcA, the putative transposase of Caenorhabditis elegans transposable element Tc1. Citation: Biochemical and Biophysical Research Communications 192: 1445-1452 1993 Type: ARTICLE Genes: Abstract: The TcA protein is one of the proteins essential for Tc1 transposition. In order to study the biochemical parameters of Tc1 transposition mechanism, we used TcA protein overproduced in baculovirus system for DNA binding experiments. We show that, despite its relatively strong non specific affinity for DNA, TcA exhibits a better affinity for its Tc1 specific binding sites. The K0.5 is 3.8 nM for the Tc1 whereas in the same type of experiment the K0.5 is 24 nM for calf thymus DNA. The ratio value between specific and non specific DNA binding activity of the TcA protein was also exhibited by other transposases such as those of the bacteriophage Mu, Tn 10 and the Drosophila P element. This nonspecific DNA binding activity may be involved in determining sites of transposable ------------------- Key: 1730 Medline: 93281578 Authors: Broverman S;MacMorris M;Blumenthal T Title: Alteration of Caenorhabditis elegans gene expression by targeted transformation. Citation: Proceedings of the National Academy of Sciences USA 90: 4359-4363 1993 Type: ARTICLE Genes: dpy-5 dpy-13 lon-1 lon-2 lon-3 sup-7 vit-2 vit-6 Abstract: We have produced strains carrying a synthetic fusion of parts of two vitellogenin genes, vit-2 and vit-6, integrated into the Caenorhabditis elegans genome. In most of the 63 transformant strains, the plasmid sequences are integrated at random locations in the genome. However, in two strains the transgene integrated by homologous recombination into the endogenous vit-2 gene. In both cases the reciprocal exchange between the chromosome and the injected circular plasmid containing a promoter deletion led to switching of the plasmid-borne promoter and the endogenous promoter, with a reduction in vit-2 expression. Thus in nematodes, transforming DNA can integrate by homologous recombination to result in partial inactivation of the chromosomal locus. The simplicity of the event and its reasonably high frequency suggest that gene targeting by homologous recombination should be considered as a method for directed inactivation of C. elegans genes. ------------------- Key: 1731 Medline: 93281621 Authors: Yochem J;Greenwald I Title: A gene for a low density lipoprotein receptor-related protein in the nematode Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 90: 4572-4576 1993 Type: ARTICLE Genes: lin-12 Abstract: A >23-kb gene that encodes a large integral membrane protein with a predicted structure similar to that of the low density lipoprotein (LDL) receptor-related protein (LRP) of mammals has been isolated and sequenced from the free-living nematode Caenorhabditis elegans. The 4753-amino acid predicted C. elegans product shares a nearly identical number and arrangement of amino acid sequence motifs with human LRP, and several exons of the C. elegans LRP gene correspond to exons of related parts of the human LDL receptor gene. The existence of an apparent homolog of LRP in C. elegans offers the possibility of genetic analysis of the in vivo roles of LRP and of the relationship between protein structure and function in a simple model organism. ------------------- Key: 1732 Medline: 93278101 Authors: Chalfie M Title: Homeobox genes in Caenorhabditis elegans. Citation: Current Opinion in Genetics & Development 3: 275-277 1993 Type: REVIEW Genes: lin-11 mab-5 mec-3 mec-4 mec-7 pal-1 unc-4 unc-86 Abstract: It is estimated that approximately 60 homeobox genes occur in the nematode Caenorhabditis elegans. These genes are required for specifying the cell fate of both precursor and terminally differentiated cells. In some cases, highly specific cell functions, such as migration pattern or synaptic connectivity, require the action of these genes. ------------------- Key: 1733 Medline: 93314933 Authors: Avery L;Bargmann CI;Horvitz HR Title: The Caenorhabditis elegans unc-31 gene affects multiple nervous system-controlled functions. Citation: Genetics 134: 455-464 1993 Type: ARTICLE Genes: unc-31 Abstract: We have devised a method for selecting Caenorhabditis elegans mutants that execute feeding motions in the absence of food. One mutation isolated in this way is an allele of the gene unc-31, first discovered by S. Brenner in 1974, because of its effects on locomotion. We find that strong unc-31 mutations cause defects in four functions controlled by the nervous system. Mutant worms are lethargic, feed constitutively, are defective in egg-laying and produce dauer larvae that fail to recover. We discuss two extreme models to explain this pleiotropy: either unc-31 affects one or a few neurons that coordinately control several different functions, or it affects many neurons that independently control different functions. ------------------- Key: 1734 Medline: 93314934 Authors: Johnson TE;Hutchinson EW Title: Absence of strong heterosis for life span and other life history traits in Caenorhabditis elegans. Citation: Genetics 134: 465-474 1993 Type: ARTICLE Genes: Abstract: We have examined crosses between wild-type strains of Caenorhabditis elegans for heterosis effects on life span and other life history traits. Hermaphrodites of all wild strains had similar life expectancies but males of two strains had shorter life spans than hermaphrodites while males of two other strains lived longer than hermaphrodites. F1 hermaphrodite progeny showed no heterosis while some heterosis for longer life span was detected in F1 males. F1 hybrids of crosses between two widely studied wild-type strains, N2 (var. Bristol) and Berg BO (var. Bergerac), were examined for rate of development, hermaphrodite fertility, and behavior; there was no heterosis for these life history traits. Both controlled variation of temperature and uncontrolled environmental variation affected the length of life of all genotypes. Significant G X E effects on life span were observed in comparisons of N2 and Berg BO hermaphrodites, or N2 hermaphrodites and males, or N2 and a Ts mutant strain (DH26). Nevertheless, within an experiment, environmental variation was minimal and life spans were ------------------- Key: 1735 Medline: Authors: Nakae H;Obinata T Title: Immunocytochemical localization of troponin-I and troponin-C in the muscles of Caenorhabditis elegans. Citation: Zoological Science 10: 375-379 1993 Type: ARTICLE Genes: Abstract: Troponin-I (TNI) and troponin-C (TNC) in muscle tissues of a nematode, C. elegans, were investigated using antibodies against the respective troponin-components of Ascaris. Immunoblot analysis demonstrated that these antibodies recognize the troponin components of C elegans that have the same molecular masses as the corresponding troponin components in Ascaris body-wall muscle. In the immunocytochemical staining of the serial cryosections of C. elegans, the anti-TNI antibody stained both the pharyngeal and the body-wall muscles. On the other hand, the anit-TNC antibody reacted with the body-wall muscle but not with the pharyngeal muscle. These results suggest that variants of troponin components exist between the pharyngeal and body-wall muscles, and troponin is involved in the actin-linked regulatory system of C. elegans. ------------------- Key: 1736 Medline: 93279470 Authors: Miller LM;Gallegos ME;Morisseau BA;Kim SK Title: lin-31, a Caenorhabditis elegans HNF-3/fork head transcription factor homolog, specifies three alternative cell fates in vulval development. Citation: Genes & Development 7: 933-947 1993 Type: ARTICLE Genes: bli-2 dpy-3 dpy-20 let-23 let-60 lin-1 lin-2 lin-3 lin-7 lin-8 lin-9 lin-10 lin-13 lin-15 lin-23 lin-31 lin-35 lin-36 lin-37 lin-38 rol-6 sem-5 unc-3 unc-29 unc-30 unc-82 unc-85 nDf3 Abstract: Cell-cell signaling controls the specification of vulval cell fates in Caenorhabditis elegans. Although previous studies have identified genes that function at early steps in the signaling pathway, the late steps are not well understood. Here, we begin to characterize those late events by showing that the lin-31 gene acts near the end of the vulval signaling pathway. We show that lin-31 acts downstream of the ras homolog let-60 and that lin-31 encodes a member of the HNF-3/fork head family of DNA-binding transcription factors. lin-31 regulates how vulval precursor cells choose their fate; in lin-31 mutants, these cells do not properly choose which fate to express and therefore adopt any one of the three possible vulval cell fates in a deregulated fashion. This interesting mutant phenotype suggests mechanisms for how vulval cell fates become determined. ------------------- Key: 1737 Medline: 93277532 Authors: Vanfleteren JR Title: Oxidative stress and aging in Caenorhabditis elegans. Citation: Biochemical Journal 292: 605-608 1993 Type: ARTICLE Genes: age-1 fer-15 Abstract: Mutations in the age-1 gene double both the mean and maximum life span of Caenorhabditis elegans. They also result in an age-specific increase of catalase and Cu/Zn superoxide dismutase activity levels. The higher superoxide dismutase activity levels in age-1 mutants confer hyperresistance to the superoxide-anion-generating drug paraquat. The rate of superoxide anion production by microsome fractions declines linearly with age in age-1(+) worms, but, after an initial decline, is stabilized at a higher level in senescent age-1 mutant nematodes. These results clearly show that oxidative stress resistance and potential life span are correlated in this organism, and they suggest that the natural product of age-1 either directly or indirectly downregulates the activities of ------------------- Key: 1738 Medline: 93273079 Authors: Seydoux G;Savage C;Greenwald I Title: Isolation and characterization of mutations causing abnormal eversion of the vulva in Caenorhabditis elegans. Citation: Developmental Biology 157: 423-436 1993 Type: ARTICLE Genes: bli-2 clr-1 dpy-5 dpy-10 dpy-11 dpy-13 dpy-17 dpy-100 egl-3 egl-9 egl-44 egl-47 glp-1 him-5 let-26 let-242 lin-12 lon-2 sma-1 smg-1 smg-3 smg-4 sqt-3 unc-4 unc-8 unc-13 unc-17 unc-24 unc-26 unc-32 unc-36 unc-41 unc-42 unc-46 unc-85 unc-93 zyg-3 mnC1 mDf1 mnDf83 mnDf89 sDf29 eT1 Abstract: In Caenorhabditis elegans hermaphrodites, morphogenesis of the vulva culminates in a process called vulval eversion, whereby a passageway is made from the uterus through the vulva to the outside of the animal. We have screened for mutations causing abnormal eversion of the vulva (evl mutations) to identify new genes involved in vulval development, and found that evl mutants are relatively common after EMS mutagenesis. We also hoped to identify genes involved in lin-12-mediated cell fate decisions, since lin-12 null mutants have abnormally everted vulvae, but none of the 68 evl mutations recovered in our screen appeared to be good candidates for genes that function with lin-12. Initial genetic and phenotypic analysis of 30 evl mutations revealed that all affect the development of the uterus, but only some affect the vulval precursor cell lineages. We used laser ablation to show that the uterus and anchor cell are important for correct vulval eversion in wild type; the anchor cell is important early in the L3 stage, before the vulval cells have been generated, but not later, when vulval eversion occurs. We conclude that certain evl mutations may influence vulval eversion by primarily affecting the development of the somatic gonad, while others may affect processes required in the ------------------- Key: 1739 Medline: 93285122 Authors: van Luenen HG;Colloms SD;Plasterk RH Title: Mobilization of quiet, endogenous Tc3 transposons of Caenorhabditis elegans by forced expression of Tc3 transposase. Citation: EMBO Journal 12: 2513-2520 1993 Type: ARTICLE Genes: age-1 mev-1 rad-8 Abstract: The commonly studied Caenorhabditis elegans strain Bristol N2 contains approximately 15 copies per genome of the transposon Tc3. However, Tc3 is not active in Bristol N2. Tc3 contains one major open reading frame (Tc3A). We have fused this open reading frame to an inducible promoter and expressed it in a transgenic Bristol N2 line. Tc3A expression resulted in frequent excision and transposition of endogenous Tc3 elements. This shows that the Bristol N2 genome contains Tc3 transposons that are cis proficient for transposition, but are immobile because Tc3A is absent. We demonstrate that recombinant Tc3A binds specifically to the terminal nucleotides of the Tc3 inverted repeat, indicating that Tc3A is the Tc3 transposase. Activation of Tc3 transposition in vivo was accompanied by the appearance of extrachromosomal, linear copies of Tc3. These may be intermediates in Tc3 transposition. ------------------- Key: 1740 Medline: 93353937 Authors: Ishii N;Suzuki N;Hartman PS;Suzuki K Title: The radiation-sensitive mutant rad-8 of Caenorhabditis elegans is hypersensitive to the effects of oxygen on aging and development. Citation: Mechanisms of Ageing & Development 68: 1-10 1993 Type: ARTICLE Genes: age-1 mev-1 rad-8 Abstract: A mutant of rad-8, originally isolated on the basis of its hypersensitivity to ultraviolet radiation, is also hypersensitive to oxygen and methyl viologen, a superoxide-anion generator. Oxygen also retarded development and reduced fecundity in a concentration-dependent fashion in rad-8 but not in wild type. In addition, the mean life span of rad-8 (but not wild type) was progressively shortened when animals were incubated in increasing oxygen concentrations. This cross hypersensitivity to both UV radiation and free radicals provides further evidence that DNA damage may be important ------------------- Key: 1741 Medline: 93286186 Authors: Hird SN;White JG Title: Cortical and cytoplasmic flow polarity in early embryonic cells of Caenorhabditis elegans. Citation: Journal of Cell Biology 121: 1343-1355 1993 Type: ARTICLE Genes: Abstract: We have examined the cortex of Caenorhabditis elegans eggs during pseudocleavage (PC), a period of the first cell cycle which is important for the generation of asymmetry at first cleavage (Strome, S. 1989. Int. Rev. Cytol. 114: 81-123). We have found that directed, actin dependent, cytoplasmic, and cortical flow occurs during this period coincident with a rearrangement of the cortical actin cytoskeleton (Strome, S. 1986. J. Cell Biol. 103: 2241-2252). The flow velocity (4-7 mum/min) is similar to previously determined particle movements driven by cortical actin flows in motile cells. We show that directed flows occur in one of the daughters of the first division that itself divides asymmetrically, but not in its sister that divides symmetrically. The cortical and cytoplasmic events of PC can be mimicked in other cells during cytokinesis by displacing the mitotic apparatus with the microtubule polymerization inhibitor nocodazole. In all cases, the polarity of the resulting cortical and cytoplasmic flows correlates with the position of the attenuated mitotic spindle formed. These cortical flows are also accompanied by a change in the distribution of the cortical actin network. The polarity of this redistribution is similarly correlated with the location of the attenuated spindle. These observations suggest a mechanism for generating polarized flows of cytoplasmic and cortical material during embryonic cleavages. We present a model for the events of PC and suggest how the poles of the mitotic spindle mediate the formation of the contractile ring during cytokinesis in ------------------- Key: 1742 Medline: 93302704 Authors: Nishiwaki K;Sano T;Miwa J Title: emb-5, a gene required for the correct timing of gut precursor cell division during gastrulation in Caenorhabditis elegans, encodes a protein similar to the yeast nuclear protein spt-6. Citation: Molecular & General Genetics 239: 313-322 1993 Type: ARTICLE Genes: dpy-17 emb-5 emb-13 emb-16 emb-23 glp-1 rol-6 unc-79 Abstract: The emb-5 gene is required for the correct timing of division of gut precursor cells during gastrulation in Caenorhabditis elegans. We have now characterized the molecular structure of emb-5. The predicted emb-5-encoded protein (EMB-5) possesses an extremely acidic amino-terminus and overall similarity to the Saccharomyces cerevisiae nuclear protein SPT6, which has been shown to affect the transcription of a variety of genes and suggested to play a role in chromatin assembly or modification. EMB-5 may function in the control of cell cycle timing by modulating chromatin structure and consequently affects morphogenesis of C. elegans. ------------------- Key: 1743 Medline: 93288400 Authors: Shackleford GM;Shivakumar S;Shiue L;Mason J;Kenyon C;Varmus HE Title: Two wnt genes in Caenorhabditis elegans. Citation: Oncogene 8: 1857-1864 1993 Type: ARTICLE Genes: ced-3 col-4 daf-14 daf-15 dpy-10 dpy-13 egl-1 fem-3 gon-1 let-51 let-53 let-55 let-657 let-658 let-659 hlh-1 lin-8 lin-31 lin-42 mab-9 mec-3 sqt-1 sup-9 unc-43 unc-52 wnt-1 wnt-2 Abstract: wnt genes encode secretory glycoproteins that have been implicated in growth control and development in mice, frogs and insects. In this report we examine properties of two wnt genes recently identified in the nematode Caenorhabditis elegans. The first gene, Ce-wnt-1, was previously identified by a polymerase chain reaction-based screen of genomic DNA, and the second, Ce-wnt-2, was fortuitously encountered in a survey of clones in a cDNA library by the Caenorhabditis Genome Project. Full-length or nearly full-length cDNAs representing both mRNAs encode proteins that are similar in length, sequence and functional domains to other Wnt proteins. Primary products of 372 and 362 amino acids begin with a hydrophobic signal peptide, include two potential N-linked glycosylation sites and contain the 22 cysteine residues conserved throughout the wnt family. In contrast to mammalian and insect wnt genes with four or five exons and conserved intron-exon boundaries, Ce-wnt-1 has nine coding exons; only one of the eight identified introns interrupts the coding sequence at a position homologous to an intron position in other wnt genes. The major transcript derived from Ce-wnt-1 is 1.4 kb in length, and the 22 nucleotides at its 5' end are added by a trans-splicing mechanism. Ce-wnt-2 is also expressed via a single major transcript, 1.5 kb in length. Both RNAs are detectable in all larval forms and adults, but they are most abundant at the embryonic stage. Ce-wnt-1 is localized to the left arm of chromosome II and Ce-wnt-2 maps to a ------------------- Key: 1744 Medline: 93293845 Authors: Chen WN;Lim HH;Lim L Title: The CDC42 homologue from Caenorhabditis elegans - Complementation of yeast mutation. Citation: Journal of Biological Chemistry 268: 13280-13285 1993 Type: ARTICLE Genes: act-1 let-60 lin-26 Abstract: A Caenorhabditis elegans cDNA encoding a homologue of the p21 ras-related CDC42, designated as CDC42Ce, was isolated from a nematode mixed stage cDNA library. The encoded protein of 188 amino acid residues has 85% identity to both human G25K and CDC42Hs and 79 and 76% identity to the yeast CDC42Sp and CDC42Sc proteins, respectively. The CDC42Ce cDNA maps to a position on C. elegans chromosome II in close proximity to lin-26, a cell lineage gene. The CDC42Ce cDNA hybridizes to 2- and 1.5-kilobase mRNAs. Their expression is developmentally regulated with highest levels at the embryonic stage, decreasing progressively during development except for an increase of the more abundant 1.5-kilobase mRNA at the L3 stage. The glutathione S-transferase/CDC42Ce fusion protein expressed in Escherichia coli displays both GTP binding and intrinsic GTPase activities. The GTPase activity of CDC42Ce is moderately stimulated by human n-chimaerin, a GTPase-activating protein for the related p21 rac1. The CDC42Ce protein complements the temperature-sensitive lethal mutation cdc42-1 in yeast Saccharomyces cerevisiae. These data suggest that CDC42Ce is the C. elegans homologue of the yeast CDC42. The developmental expression pattern of mRNA and is biochemical properties of its encoded protein which are closely related to CErac1 suggest that the two p21s might be involved in related biological processes. ------------------- Key: 1745 Medline: 94038677 Authors: Chamberlin HM;Sternberg PW Title: Multiple cell interactions are required for fate specification during male spicule development in Caenorhabditis elegans. Citation: Development 118: 297-324 1993 Type: ARTICLE Genes: him-5 lin-12 Abstract: The B blast cell divides postembryonically in C. elegans males to produce 47 progeny that include all of the cells of the copulatory spicules. During the early development of the B lineage, the anterior daughter of B, B.a, generates eight cells. These cells migrate to form four pairs of cells that flank the developing cloaca (ventral, dorsal, and two identical lateral pairs). For each pair, the more anterior cell produces a distinct lineage ('anterior fate') from the posterior cell ('posterior fate'). For the ventral and dorsal pairs, either cell can migrate to the anterior position and produce the anterior lineage, and the other cell migrates posterior and produces the posterior lineage (Sulston and Horvitz, 1977, Dev. Biol. 56, 110-156). The migration is variable, although the resultant fate pattern is invariant. In the two lateral pairs, both the migration and fate pattern are invariant. Using a laser microbeam to selectively ablate neighboring cells we have found that the cells of the lateral pair also respond to positional cues. For all four pairs other male-specific blast cells provide extracellular cues. In general, F and U promote anterior fates, Y promotes some posterior fates, and the B.a progeny promote posterior fates. Several of these cues are redundant. By ablating combinations of cells we have deduced how these signals may act in concert to specify the fates of the B.a progeny. We propose that fate specification in these pairs depends on three general classes of extracellular cues: positional cues, modulators of positional cues, and lateral signals. The B lineage thus provides an opportunity to study with single cell resolution the integration of multiple intercellular ------------------- Key: 1746 Medline: Authors: Donkin SG;Dusenbery DB Title: A soil toxicity test using the nematode Caenorhabditis elegans and an effective method of recovery. Citation: Archives of Environmental Contamination and Toxicology 25: 145-151 1993 Type: ARTICLE Genes: Abstract: A new method for recovering nematodes from soils in an efficient, reproducible, and non-destructive manner has been developed. It was used to conduct short-term soil toxicity tests using the soil-dwelling nematode Caenorhabditis elegans and several different soil types spiked with copper chloride. The recovery method, which involves centrifugation through a colloidal silica suspension, allows the nematodes to be extracted from the soil matrix so that lethality can be assessed. The nematodes are unharmed by the recovery procedure, and both live and dead individuals are recovered with high efficiency (well over 80%), allowing reproducible concentration-response curves to be made after a 24-h exposure. The LC50s for copper were increased about tenfold by the presence of soil, and different soils had significantly different effects on toxicity. Toxicity of copper ion was also influenced by the concentration of sodium chloride and potassium chloride in the test solution, and the presence of bacteria increased the toxicity of copper ion in some soils. The LC50s in soil were close to the LC50 for the 2-week earthworm soil toxicity test, suggesting that a 24-h nematode toxicity test may be comparable to the 2-week earthworm test in ------------------- Key: 1747 Medline: 93351848 Authors: McKim KS;Peters K;Rose AM; Title: Two types of sites required for meiotic chromosome-pairing in Caenorhabditis elegans. Citation: Genetics 134: 749-768 1993 Type: ARTICLE Genes: bli-3 bli-4 dpy-1 dpy-3 dpy-5 dpy-7 dpy-8 dpy-11 dpy-14 dpy-17 dpy-18 let-2 let-201 let-202 let-360 let-362 let-363 let-365 lin-15 unc-1 unc-3 unc-7 unc-11 unc-13 unc-20 unc-29 unc-32 unc-36 unc-40 unc-42 unc-45 unc-54 unc-59 unc-60 unc-63 unc-64 unc-75 unc-101 eDf3 eDf4 eDf6 eDf7 eDf24 hDf9 hDf10 mnDf7 mnDf11 mnDf20 mnDf41 mnDf43 nDf23 nDf24 nDf25 tDf3 hDp4 hDp12 hDp14 hDp31 hDp39 hDp51 hDp56 hDp69 hDp70 hDp101 hDp102 hDp133 hDp134 hDp135 mnDp1 mnDp25 sDp1 sDp2 sDp30 sDp133 szDp1 Abstract: Previous studies have shown that isolated portions of Caenorhabditis elegans chromosomes are not equally capable of meiotic exchange. These results led to the proposal that a homolog recognition region (HRR), defined as the region containing those sequences enabling homologous chromosomes to pair and recombine, is localized near one end of each chromosome. Using translocations and duplications we have localized the chromosome I HRR to the right end. Whereas the other half of chromosome I did not confer any ability for homologs to pair and recombine, deficiencies in this region dominantly suppressed recombination to the middle of the chromosome. These deletions may have disrupted pairing mechanisms that are secondary to and require an HRR. Thus, the processes of pairing and recombination appear to utilize at least two chromosomal elements, the HRR and other pairing sites. For example, terminal sequences from other chromosomes increase the ability of free duplications to recombine with their normal homologs, suggesting that telomere-associated sequences, homologous or nonhomologous, play a role in facilitating meiotic exchange. Recombination can also initiate at internal sites separated from the HRR by chromosome rearrangement, such as deletions of the unc-54 region of chromosome I. When crossing over was suppressed in a region of chromosome I, compensatory increases were observed in other regions. Thus, the presence of the HRR enabled recombination to occur but did not determine the distribution of the crossover events. It seems most likely that there are multiple initiation sites for recombination once homolog recognition has been ------------------- Key: 1748 Medline: 93351849 Authors: L'Hernault SW;Benian GM;Emmons RB Title: Genetic and molecular characterization of the Caenorhabditis elegans spermatogenesis-defective gene Citation: Genetics 134: 769-780 1993 Type: ARTICLE Genes: fem-1 fem-3 him-5 let-52 let-56 rol-6 spe-17 unc-22 unc-54 unc-86 hDf13 hcDf1 sDf8 sDf9 sDf19 sDf83 Abstract: Two self-sterile mutations that define the spermatogenesis-defective gene spe-1 7 have been analyzed. These mutations affect unc-22 and fail to complement each other for both Unc-22 and spermatogenesis defects. Both of these mutations are deficiencies (hcDf1 and hDf13) that affect more than one transcription unit. Genomic DNA adjacent to and including the region deleted by the smaller deficiency (hcDf1) has been sequenced and four mRNAs (including unc-22) have been localized to this sequenced region. The three non unc-22 mRNAs are shown to be sex-specific: a 1.2-kb mRNA that can be detected in sperm-free hermaphrodites and 1.2- and 0.56-kb mRNAs found in males. hDf13 deletes at least 55 kb of chromosome IV, including all of unc-22, both male-specific mRNAs and at least part of the female-specific mRNA. hcDf1, which is approximately 15.6 kb, deletes only the 5' end of unc-22 and the gene that encodes the 0.56-kb male-specific mRNA. The common defect that apparently accounts for the defective sperm in hcDf1 and hDf13 homozygotes is deletion of the spe-17 gene, which encodes the 0. 56-kb mRNA. Strains carrying two copies of either deletion are self-fertile when they are transgenic for any of four extrachromosomal array that include spe-17. We have sequenced two spe-17 cDNAs, and the deduced 142 amino acid protein sequence is highly charged and rich in serine and threonine, but shows no significant homology to any previously determined protein sequence. ------------------- Key: 1749 Medline: Authors: Lu NC;Goetsch KM Title: Carbohydrate requirement of Caenorhabditis elegans and the final development of a chemically defined medium. Citation: Nematologica 39: 303-311 1993 Type: ARTICLE Genes: Abstract: The carbohydrate requirement in the free-living nematode Caenorhabditis elegans was investigated. Glucose, fructose, sucrose, trehalose and glycogen were tested individually at concentrations of 0, 1.3, 6.5, 32.5, and 162.5 mg/ml as the energy source in a chemically defined medium containing C . briggsae Maintenance Medium (CbMM without glucose), 50 .mu.g/ml cytochrome c and 50 .mu.g/ml .beta.-sitosterol. Potassium acetate, used as the energy source in other studies, was not added to the medium. Therefore, carbohydrate was the major energy source for the nematode. At 32.5 mg/ml, glucose was found to support the maximal population at 80,000 nematodes/ml (100%), followed by glycogen (96%) and trehalose (73%). Population was significantly reduced when fructose (46%) or sucrose (26%) was the carbohydrate source. Toxicity was shown at 162.5 mg/ml for four carbohydrates tested, except glycogen. These results suggested that all five carbohydrates can be utilized as energy sources by C . elegans ; however, the degree of utilization of each carbohydate by C . elegans varied. Since glucose was best utilized by the nematode at 32.5 mg/ml, this concentration is recommended for future use in preparation in CbMM. Based on this study, the chemically defined medium that has been used for cultivation of C . elegans can also be modified to: CbMM (1x, with 32.5 mg/ml glucose), 50 .mu./ml cytochrome c and .mu.g/ml .beta.-sitosterol. Glucose (at 32.5 mg/ml) can be used as the major energy source in a chemically defined medium for the axenic cultivation of C . elegans . ------------------- Key: 1750 Medline: 93313960 Authors: Nonet ML;Grundahl K;Meyer BJ;Rand JB Title: Synaptic function is impaired but not eliminated in C. elegans mutants lacking synaptotagmin. Citation: Cell 73: 1291-1305 1993 Type: ARTICLE Genes: dpy-2 dpy-10 egl-27 him-8 let-263 ric-2 rol-6 snt-1 tra-2 unc-17 unc-25 unc-29 unc-38 unc-104 vab-9 mnDf30 mnDf31 mnDf39 mnDf88 mnDf96 mnDf97 mnDf99 mnDf103 mnDf105 mnDf106 Abstract: Synaptotagmin is an abundant synaptic vesicle-associated protein proposed to be involved in calcium-mediated neurotransmitter release. Our molecular and genetic results demonstrate that, although synaptotagmin is required for the proper function of the presynaptic nerve terminal in C. elegans, some neurotransmitter release persists in synaptogamin mutants. In C. elegans neurons, synaptotagmin is localized to regions known to be rich in synapses and appears to be associated with synaptic vesicles. Mutants defective in the synaptotagmin gene, called snt-1, exhibit severe behavioral abnormalities that are characteristic of deficiencies in synaptic function, including severe locomotion, feeding, and defecation defects. The mutants are defective in exocytosis, since they accumulate acetylcholine, and are resistant to cholinesterase inhibitors, but they nevertheless remain sensitive to cholinergic receptor agonists. In spite of these exocytic defects, snt-1 mutants are capable of coordinated motor movements, indicating that the mutants do not have a complete block of neurotransmitter release. ------------------- Key: 1751 Medline: 93307658 Authors: Vos JC;Van Luenen HGAM;Plasterk RHA Title: Characterization of the Caenorhabditis elegans Tc1 transposase in vivo and in vitro. Citation: Genes & Development 7: 1244-1253 1993 Type: ARTICLE Genes: gpa-2 hsp-16 unc-54 Abstract: We have investigated the function of the Tc1A gene of the mobile element Tc1 of Caenorhabditis elegans. Tc1 is a member of a family of transposons found in several animal phyla, such as nematodes, insects, and vertebrates. Two tines of evidence show that Tc1A encodes the transposase of Tc1. First, forced expression of the Tc1A protein in transgenic nematodes results in an enhanced level of transposition of endogenous Tc1 elements. Second, DNase I footprinting and gel retardation assays show that Tc1A binds specifically to the inverted repeats at the ends of the element and that the Tc1A recognition site is located between base pairs 5 and 26 from the ends of Tc1. Functional dissection of the transposase shows the presence of two distinct DNA-binding domains. A site-specific DNA-binding domain is contained within the amino-terminal 63 residues of Tc1A; this region shows sequence similarity to the prokaryotic IS30 transposase. A second, general DNA-binding domain is located between amino acids 71 and 207. Our results suggest that Tc1 is more similar to prokaryotic insertion elements than to eukaryotic transposons such as P elements in Drosophila or Ac and En-1 ------------------- Key: 1752 Medline: 93372377 Authors: Young JM;Hope IA Title: Molecular markers of differentiation in Caenorhabditis elegans obtained by promoter trapping. Citation: Developmental Dynamics 196: 124-132 1993 Type: ARTICLE Genes: Abstract: Differentiation of specific cell types during animal development can be detected by monitoring expression of appropriate genes. For this study, six different beta-galactosidase expression patterns which can be used as differentiation markers in the nematode Caenorhabditis elegans are described. An earlier promoter trap screen identified pools of recombinant plasmids which gave patterns of beta-galactosidase expression when used to transform C. elegans. Each recombinant plasmid contained a random fragment of C. elegans genomic DNA fused upstream of a promoterless lacZ gene. Six of these pools were chosen, and individual pattern-producing plasmids within these pools were identified. The expression patterns have been characterized more thoroughly than in the original screen, thereby providing molecular markers for differentiation of several cell types. Many of the expression patterns involve more than one cell type. The genomic origin of the inserts of active plasmids were determined through localization on the physical genome map. (C) 1993 Wiley-Liss, Inc. ------------------- Key: 1753 Medline: 93251016 Authors: Burglin TR;Ruvkun G Title: New motif in PBX genes. Citation: Nature Genetics 1: 319-320 1992 Type: REVIEW Genes: ceh-20 Abstract: Human pre-B cell acute lymphoblastic leukaemias are associated with a chimaeric gene that is generated from a t(1;19) chromosomal translocation. This fusion joins the regulatory regions of the lymphoid transcription factor gene, E2A, to the C-terminal region, including the homeodomain, of PBX1 (previously called prl). Tow additional human genes (PBX2 and PBX3) with 77-84% identity to PBX1 have been isolated based on sequence similarity. These genes, however, are too closely related to distinguish between recent divergence and conserved essential motifs, if any, outside the homeodomain. Such conserved domains might be revealed by comparing mammalian sequences with those of more evolutionarily distant organisms, such as the expressed sequence tags (ESTs) generated recently in Caenorhabditis elegans. ------------------- Key: 1754 Medline: 94191905 Authors: Albertson DG;Thomson JN Title: Segregation of holocentric chromosomes at meiosis in the nematode, Caenorhabditis elegans. Citation: Chromosome Research 1: 15-26 1993 Type: ARTICLE Genes: mlc-1 mlc-2 unc-22 eDp20 Abstract: The meiotic segregation of the holocentric chromosomes of Caenorhabditis elegans in both spermatogenesis and oogenesis is described. The extended kinetochore typical of the mitotic chromosome could not be differentiated on meiotic bivalents; instead microtubules appeared to project into the chromatin. The meiotic spindles formed during spermatogenesis contain centrioles and asters, while in oogenesis the spindles are acentriolar and barrel shaped. The formation of the acentriolar spindle was studied in fixed specimens by anti-tubulin immunofluorescence. Microtubule arrays were seen first to accumulate in the vicinity of the meiotic chromosomes prior to congression. At later stages, elongated spindle structures up to 13 mu in length were observed parallel to the surface of the embryo. Further development of the spindle appeared to involve its shortening into a barrel shape and rotation so that one spindle pole was opposed to the membrane. By anaphase the pole-to-pole spindle length reached a minimum of 3-4 mu. One end of each chromatid in the meiotic bivalent was labelled by in situ hybridization of a probe DNA to show that in oogenesis the chromatids were associated end-to-end in the bivalent. Furthermore, either the right or the left ends of the homologues could be held in association. At metaphase I the bivalents were oriented axially, such that kinetic activity was restricted to one end of each pair of sister chromatids. At metaphase II the chromosomes were also aligned axially. ------------------- Key: 1755 Medline: Authors: Blaxter ML;Page AP;Rudin W;Maizels RM Title: Nematode surface coats: Actively evading immunity. Citation: Parasitology Today 8: 243-247 1992 Type: REVIEW Genes: Abstract: The classical view of nematode parasites depicts their surface as the epicuticle, the outermost layer of a thick extracellular cuticle. However, many stages and species of nematode have been found to bear an electron-dense outer envelope distinct from and distal to the epicuticle itself. In this review, Mark Blaxter and colleagues summarize some wide-ranging studies in both free-living and parasitic nematodes, and suggest that, in many cases, it is the surface coat rather than the cuticle that displays dynamic properties thought to be involved in immune evasion by parasites. ------------------- Key: 1756 Medline: 93382946 Authors: Sternberg PW;Golden A;Han M Title: Role of a raf proto-oncogene during Caenorhabditis elegans vulval development. Citation: Philosophical Transactions of the Royal Society of London Series B-Biological Sciences 340: 259-265 1993 Type: ARTICLE Genes: deb-1 dpy-20 let-23 let-60 lin-1 lin-2 lin-3 lin-7 lin-10 lin-15 lin-23 lin-45 sem-5 raf-1 unc-44 Abstract: During Caenorhabditis elegans vulval induction, multipotent precursors respond to an inductive signal by generating vulval cells as opposed to non-specialized epidermal cells. Both classical and 'reverse' genetic approaches have revealed that a cascade of nematode homologues of mammalian proto-oncogenes is necessary for induction of the vulva. The inductive signal is a growth factor encoded by the lin-3 gene and its candidate receptor is a tyrosine kinase encoded by the let-23 gene. let-23 acts via a Ras protein encoded by the let-60 gene. A nematode homologue of mammalian raf family protein serine/threonine kinases has been cloned and found to be encoded by the lin-45 gene. Dominant negative lin-45 raf mutants prevent vulval induction. A recessive lin-45 raf mutation prevents the excessive vulval differentiation caused by activated ras, indicating that raf might act downstream of ras during ------------------- Key: 1757 Medline: 93379214 Authors: Shakir MA;Fukishige T;Yasuda H;Miwa J;Siddiqui SS Title: C. elegans osm-3 gene mediating osmotic avoidance-behavior encodes a kinesin-like protein. Citation: Neuroreport 4: 891-894 1993 Type: ARTICLE Genes: osm-3 rol-6 unc-17 unc-104 unc-116 Abstract: IN the nematode Caenorhabditis elegans, mutants in osm-3 gene are known to be defective in osmotic avoidance, chemotaxis and dauer formation behaviours. To study the molecular basis of these pleiotropic defects we have cloned the osm-3 gene by germline transformation of osm-3 (p802) mutants through microinjection of the wild type genomic DNA. Northern analysis reveals a 3.0 kb transcript corresponding to osm-3. DNA sequencing of the transforming 4.3 kb fragment revealed a kinesin heavy chain-like protein, which contains conserved ATPase and microtubule binding domains. Our results are consistent with the previous EM data on osm-3(p802) mutants that show an accumulation of dense matrix material in the amphid sheath cytoplasm and a shortened distal segment of the amphid channel cilium. These data suggest a kinesin-like role of the osm-3 product in axonal transport. ------------------- Key: 1758 Medline: 93323970 Authors: Hamelin M;Zhou YW;Su MW;Scott IM;Culotti JG Title: Expression of the UNC-5 guidance receptor in the touch neurons of C. elegans steers their axons dorsally. Citation: Nature 364: 327-330 1993 Type: ARTICLE Genes: mec-7 unc-5 unc-6 unc-22 Abstract: GROWTH cones in developing nervous systems encounter a sequence of extracellular cues during migration1,2. In theory, a growth cone can navigate by selectively expressing or activating surface receptor(s) that recognize extracellular cues appropriate to each migratory phase. Using the simple Caenorhabditis elegans nervous system, we attempted to demonstrate that path selection by migrating growth cones can be predictably altered by ectopic expression of a single receptor. The unc-5 gene of C. elegans encodes a unique receptor of the immunoglobulin superfamily (UNC-5), required cell-autonomously to guide growth cone and mesodermal cell migrations in a dorsal direction on the epidermis3,4. We report here that the UNC-5 receptor induces dorsally oriented axon trajectories when ectopically expressed in the touch receptor neurons which normally extend pioneer axons longitudinally or ventrally on the epidermis5. These errant trajectories depend on unc-6, which encodes a putative epidermal path cue6, just as normal dorsally oriented axon trajectories do (such as those of certain motor neurons4), suggesting that UNC-5 acts to reorient the touch cell growth cones by using its normal guidance mechanisms. These results support previous evidence that UNC-5 and UNC-6 play instructive roles in guiding growth cone migrations on the epidermis in C elegans4, and indicate that pioneering growth cones, which normally migrate in different directions may use equivalent intracellular signalling mechanisms for ------------------- Key: 1759 Medline: 93323972 Authors: McIntire SL;Jorgensen E;Horvitz HR Title: Genes required for GABA function in Caenorhabditis elegans. Citation: Nature 364: 334-337 1993 Type: ARTICLE Genes: lin-15 unc-25 unc-30 unc-43 unc-46 unc-47 unc-49 Abstract: Gamma-AMINOBUTYRIC acid (GABA) neurotransmission is widespread in vertebrate and invertebrate nervous systems1. Here we use a genetic approach to identify molecules specific to GABA function. On the basis of the known in vivo roles of GABAergic neurons in controlling behaviour of the nematode Caenorhabditis elegans2, we identified mutants defective in GABA-mediated behaviours. Five genes are necessary either for GABAergic neuronal differentiation or for pre- or postsynaptic GABAergic function. The gene unc-30 is required for the differentiation of a specific type of GABAergic neuron, the type-D inhibitory motor neuron. The gene unc-25 is necessary for GABA expression and probably encodes the GABA biosynthetic enzyme glutamic acid decarboxylase. The genes unc-46 and unc-47 seem to be required for normal GABA release. Finally, the gene unc-49 is apparently necessary postsynaptically for the inhibitory effect of GABA on the body muscles and might encode a protein needed for the function of a GABA(A)-like receptor. Some of these genes are likely to encode previously unidentified proteins required for GABA function. ------------------- Key: 1760 Medline: 93323973 Authors: McIntire SL;Jorgensen E;Kaplan J;Horvitz HR Title: The GABAergic nervous system of Caenorhabditis elegans. Citation: Nature 364: 337-341 1993 Type: ARTICLE Genes: egl-5 lin-4 unc-25 Abstract: Gamma-AMINOBUTYRIC acid (GABA) is the most abundant inhibitory neurotransmitter in vertebrates and invertebrates1. GABA receptors are the target of anxiolytic, antiepileptic and antispasmodic drugs2, as well as of commonly used insecticides3. How does a specific neurotransmitter such as GABA control animal behaviour? To answer this question, we identified all neurons that react with antisera raised against the neurotransmitter GABA in the nervous system of the nematode Caenorhabditis elegans. We determined the in vivo functions of 25 of the 26 GABAergic neurons by killing these cells with a laser microbeam in living animals and by characterizing a mutant defective in GABA expression. On the basis of the ultrastructurally defined connectivity of the C. elegans nervous system, we deduced how these GABAergic neurons act to control the body and enteric muscles necessary for different behaviours. Our findings provide evidence that GABA functions as an excitatory as well as an inhibitory neurotransmitter. ------------------- Key: 1761 Medline: 93343906 Authors: Blumenthal T Title: Mammalian cells can trans-splice. But do they? Citation: BioEssays 15: 347-348 1993 Type: REVIEW Genes: act-1 Abstract: In trans-splicing, the pre-mRNA products of two different genes are spliced together to form a single, mature mRNA. In one type of trans-splicing, pre-mRNAs of many different genes receive a single, short leader, called spliced leader or SL. This type of trans-splicing was first discovered in the primitive eukaryotes, the trypanosomes, where it is apparently the only kind of nuclear mRNA splicing. Subsequently, it was discovered in nematodes (round worms), trematodes (flat worms), and euglena. Although this type of trans-splicing has never been found in any of the other well-studied organisms, Bruzik and Maniatis have recently reported that mammalian cells are capable of performing the reaction when they are provided with the appropriate pre-mRNAs. ------------------- Key: 1762 Medline: 93294498 Authors: Stringham EG;Candido EPM Title: Targeted single-cell induction of gene products in Caenorhabditis elegans: A new tool for developmental studies. Citation: Journal of Experimental Zoology 266: 227-233 1993 Type: ARTICLE Genes: mab-5 mec-3 rol-6 unc-6 Abstract: Heat shock promoters have been employed to achieve tightly regulated expression of transformed genes in a wide variety of model systems including tissue culture cells, bacteria, yeast, Drosophila, and more recently Caenorhabditis elegans. Here we investigate the feasibility of using a laser microbeam to induce a sub-lethal heat shock response in individual cells of C. elegans. We demonstrate that in transgenic strains carrying heat shock promoter-lacZ fusions, single cell expression of beta-galactosidase in a variety of cell types of endodermal, mesodermal, or ectodermal origin can be achieved after pulsing with a laser. A tissue-general, inducible promoter can therefore be converted into one of single cell specificity which can be induced rapidly at any point in development, offering unique opportunities to study cell-cell interactions in C. elegans. This technique defines a new approach to generate mosaic animals and may be adaptable to other organisms or ------------------- Key: 1763 Medline: 93324330 Authors: Radice AD;Emmons SW Title: Extrachromosomal circular copies of the transposon Tc1. Citation: Nucleic Acids Research 21: 2663-2667 1993 Type: ARTICLE Genes: Abstract: The 1.6 kb Tc1 transposable element of Caenorhabditis elegans undergoes excision and transposition in the germline. In somatic tissue it is excised at high frequency. Extrachromosomal linear and circular copies of Tc1 have been identified that are likely to be products of somatic and germline excision. In the present study, we have determined the sequences of the sites of circularization in circular extrachromosomal Tc1 molecules. DNA molecules containing these sites were cloned after PCR amplification with primers directed outward from within Tc1. Sequences were obtained with two complete Tc1 ends and one or more intervening copies of the TA dinucleotide, with one complete end and one deleted end, and with two deleted ends. The 24 clones had different structures, indicating the pool of molecules serving as PCR templates was heterogeneous. The predominant circular junction had one or more nucleotides deleted from at least one transposon end. Such a molecule without two complete ends might not be expected to serve as a transposition intermediate. Hence, some extrachromosomal circular Tc1 molecules may result from a deadend excision pathway. ------------------- Key: 1764 Medline: Authors: Kaplan JM Title: Neurodegeneration: Great minds think alike. Citation: Current Biology 3: 285-287 1993 Type: ARTICLE Genes: deg-1 mec-4 mec-6 mec-10 sup-20 unc-105 Abstract: The recently cloned gene for the rat epithelial Na+ channel turns out to be related to nematode genes, mutations in which affect mechanosensation and cause neurodegeneration. ------------------- Key: 1765 Medline: 93306993 Authors: Goldstein P;McCann-Hargrove E;Magnano L Title: Hypervitaminosis E and gametogenesis in Caenorhabditis elegans. Citation: Cytobios 73: 121-133 1993 Type: ARTICLE Genes: Abstract: Expected benefits, i.e. increasing life span and vitality, from ingesting d,1-alpha tocopherol (vitamin E), are not realized using vitamin E acetate (VEA) since the acetate form is only slowly converted to vitamin E in either mammalian or nematode tissues. The resultant accumulation of VEA in the cytosol is toxic, which results in aberrations in nuclear morphology, decreased life span and production of progeny, increased mean reproductive day and general loss of vitality. Incorporation of VEA into membranes results in allosteric changes in membrane structure. Such changes are proportional to increasing concentrations of VEA, thereby inhibiting the attachment of the telomere to the nuclear envelope. Reproductive and chromosomal strategies are compromised such that synaptonemal complexes, normally found during pachytene in oocytes, are rarely present in those nematodes exposed to high concentrations of VEA. The resultant loss of SCs correlates with decreased progeny and the chromosomal aberrations characteristic of hypervitaminosis E. ------------------- Key: 1766 Medline: Authors: Hamelin M;Zhou Y;Su MW;Scott JM;Culotti JG Title: UNC-5 and UNC-6, proteins that steers migrating growth cones in C. elegans. Citation: Journal of Neurochemistry 61: S125- 1993 Type: ARTICLE Genes: unc-5 unc-6 Abstract: The unc-5 and unc-6 genes of C. elegans are required to guide pioneer axon growth cone (GC) and mesodermal cell migrations in a dorsal direction on the epidermis. ------------------- Key: 1767 Medline: 93327429 Authors: Wang BB;Muller-Immergluck MM;Austin J;Robinson NT;Chisholm A;Kenyon C Title: A homeotic gene-cluster patterns the anteroposterior body axis of C. elegans. Citation: Cell 74: 29-42 1993 Type: ARTICLE Genes: ceh-13 ceh-23 egl-5 lin-39 mab-5 Abstract: In insects and vertebrates, clusters of Antennapedia class homeobox (HOM-C) genes specify anteroposterior body pattern. The nematode C. elegans also contains a small cluster of HOM-C genes, one of which has been shown to specify positional identity. Here we show that two additional C. elegans HOM-C genes also specify positional identity and that together these three HOM-C genes function along the anteroposterior axis in the same order as their homologs in other organisms. Thus, HOM-C-based pattern formation has been conserved in nematodes despite the many differences in morphology and embryology that distinguish them from other phyla. Each C. elegans HOM-C gene is responsible for a distinct body region; however, where their domains overlap, two HOM-C genes can act together to specify the fates of individual cells. ------------------- Key: 1768 Medline: 93327430 Authors: Clark SG;Chisholm AD;Horvitz HR Title: Control of cell fates in the central body region of C. elegans by the homeobox gene lin-39. Citation: Cell 74: 43-55 1993 Type: ARTICLE Genes: ced-1 ced-3 egl-5 him-5 him-8 lin-13 lin-39 mab-5 ncl-1 sma-3 unc-36 qDp3 sDp3 Abstract: Cells in the mid-body region of the nematode C. elegans develop differently from their anterior or posterior homologs. The gene lin-39 is required for mid-body region-specific development. In lin-39 mutants, midbody cells express fates characteristic of more anterior or posterior homologs, and the migration of a neuroblast through the mid-body is defective. lin-39 acts cell autonomously in these mid-body cells and in the migrating neuroblast. lin-39 encodes a protein with an Antennapedia class homeodomain, most similar to those of the Drosophila homeotic genes Deformed and Sex combs reduced, and is located in a homeotic gene cluster with two other regional homeotic genes, mab-5 and egl-5. lin-39 and mab-5 function combinatorially in 2 ectodermal cells and have redundant functions in gonad development. ------------------- Key: 1769 Medline: 93314965 Authors: Kloek AP;Sherman DR;Goldberg DE Title: Novel gene structure and evolutionary context of Caenorhabditis elegans globin. Citation: Gene 129: 215-221 1993 Type: ARTICLE Genes: Abstract: Animal and plant globin-encoding genes (Glo) contain two introns in strictly conserved positions. Plant Glo genes possess an additional, centrally located intron. We have determined the cDNA sequence and gene structure of a putative Glo gene from the free-living nematode, Caenorhabditis elegans. The gene encodes a one-domain globin with a single intron, corresponding to the central intron of plant Glo genes. The two introns common to virtually all animal and plant Glo genes are missing. Comparison with the related organisms Trichostrongylus colubriformis, Ascaris suum and Pseudoterranova decipiens, provides evidence of gene duplication, intron loss, and functional divergence within the Glo genes of the nematode phylum. It is now apparent that differential intron loss during evolution has generated Glo genes with a panoply of exon/intron permutations. ------------------- Key: 1770 Medline: 93342494 Authors: Alfonso A;Grundahl K;Duerr JS;Han HP;Rand JB Title: The Caenorhabditis elegans unc-17 gene: A putative vesicular acetylcholine transporter. Citation: Science 261: 617-619 1993 Type: ARTICLE Genes: cha-1 unc-17 unc-104 Abstract: Mutations in the unc-17 gene of the nematode Caenorhabditis elegans produce deficits in neuromuscular function. This gene was cloned and complementary DNAs were sequenced. On the basis of sequence similarity to mammalian vesicular transporters of biogenic amines and of localization to synaptic vesicles of cholinergic neurons in C. elegans, unc-17 likely encodes the vesicular transporter of acetylcholine. Mutations that eliminated all unc-17 gene function were lethal, suggesting that the acetylcholine transporter is essential. Molecular analysis of unc-17 mutations will allow the correlation of specific parts of the gene (and the protein) with observed functional defects. The mutants will also be useful for the isolation of extragenic suppressors, which could identify genes encoding proteins that interact with UNC-17. ------------------- Key: 1771 Medline: 93354437 Authors: Pelham HRB Title: Neurotransmission and secretion. Citation: Nature 364: 582- 1993 Type: LETTER Genes: unc-18 Abstract: Recent discoveries have led to the realization that proteins involved in synaptic transmission have counterparts in the normal secretory pathways of animal cells and yeast, and thus that the basic machinery involved in these disparate processes is similar. Synaptic proteins with homologues elsewhere include rab3a, the syntaxins and the VAMPs/synaptobrevins. I have found an additional similarity between a protein implicated in neurotransmitter release and a yeast SEC gene product, which appears to previously have gone unnoticed. Mutations in the unc-18 gene of the nematode Caenorhabditis elegans result in severe paralysis, and confer partial resistance to an acetylcholinesterase inhibitor. ------------------- Key: 1772 Medline: Authors: Hsu DR;Meyer BJ Title: X chromosome dosage compensation and its relationship to sex determination in C. elegans. Citation: Seminars in Developmental Biology 4: 93-106 1993 Type: REVIEW Genes: act-4 dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 fem-1 fem-2 fem-3 her-1 lin-14 lin-15 mlc-1 mlc-2 myo-2 sdc-1 sdc-2 sdc-3 sup-7 sup-21 tra-1 tra-2 tra-3 unc-54 uvt-4 uxt-1 uxt-2 xol-1 Abstract: A genetic regulatory hierarchy controls all aspects of Caenorhabditis elegans sex determination and X chromosome dosage compensation in response to the primary sex-determining signal, the X/A ratio. Initially, these two processes are coordinately regulated by a group of genes that transmit this primary signal to downstream genes that preferentially control either sex determination or dosage compensation. The relationship between these two processes is complex: not only are they coordinately controlled, a feedback mechanism operates to allow a disruption in dosage compensation to affect sexual fate. We describe our genetic and molecular understanding of the regulatory hierarchy, the feedback control and the dosage ------------------- Key: 1773 Medline: 93387664 Authors: Benian GM;L'Hernault SW;Morris ME Title: Additional sequence complexity in the muscle gene, unc-22, and its encoded protein, twitchin, of Caenorhabditis elegans. Citation: Genetics 134: 1097-1104 1993 Type: ARTICLE Genes: unc-22 hcDf1 Abstract: Null mutations of the Caenorhabditis elegans unc-22 gene cause a pronounced body surface twitch associated with impaired movement and disruption of muscle structure. Partial sequence analysis of unc-22 has previously revealed that its encoded polypeptide, named twitchin, consists of a single protein kinase domain and multiple copies of both an immunoglobulin-like domain and a fibronectin type III-like domain. This paper reports additional DNA sequence information that has revealed the transcription start of unc-22, the N terminus of twitchin, and an explanation for the weak phenotype of a transposon insertion allele. These new data indicate that the unc-22 gene is 18 kb larger than previously reported and has a transcription unit of 38,308 bp. These data add 791 amino acids to the twitchin N terminus for a complete polypeptide size of 6,839 amino acids and a predicted molecular weight of 753,494. This new polypeptide sequence includes four additional copies of the above-mentioned immunoglobulin-like domains and also includes a glycine-rich sequence that might form a flexible hinge. The additional coding sequence reveals that the insertion of the Tc1 transposon, in the unc-22 allele, st139, should disrupt twitchin structure because it is located in an exon. However, cDNA sequencing has revealed that several cryptic splice donors and acceptors adjacent to the Tc1 insertion site are used to splice the transposon out of unc-22(st139) mRNA. One of these splicing events produces a near wild-type mRNA that deletes only six amino acids from twitchin, and this might explain the unusually mild phenotype associated with this mutation. ------------------- Key: 1774 Medline: 93387665 Authors: Thomas JH;Birnby DA;Vowels JJ Title: Evidence for parallel processing of sensory information controlling dauer formation in Caenorhabditis elegans. Citation: Genetics 134: 1105-1117 1993 Type: ARTICLE Genes: che-11 daf-1 daf-3 daf-4 daf-5 daf-7 daf-8 daf-11 daf-14 daf-21 osm-6 unc-42 Abstract: Dauer formation in Caenorhabditis elegans is induced by chemosensation of high levels of a constitutively secreted pheromone. Seven genes defined by mutations that confer a dauer-formation constitutive phenotype (Daf-c) can be congruently divided into two groups by any of three criteria. Group 1 genes (daf-11 and daf-21) are (1) strongly synergistic with group 2 genes for their Daf-c phenotype, (2) incompletely suppressed by dauer-formation defective (Daf-d) mutations in the genes daf-3 and daf-5 and (3) strongly suppressed by Daf-d mutations in nine genes that affect the structure of chemosensory endings. Group 2 genes (daf-1, daf-4, daf-7, daf-8 and daf-14) are (1) strongly synergistic with group 1 genes for their Daf-c phenotype, (2) fully suppressed by Daf-d mutations in daf-3 and daf-5 and (3) not suppressed by Daf-d mutations in the nine genes that affect chemosensory ending structure. Mutations in each group of genes also cause distinct additional behavioral defects. We propose that these two groups of Daf-c genes act in parallel pathways that process sensory information. The two pathways are partially redundant with each other and normally act in concert to ------------------- Key: 1775 Medline: Authors: Kawaii S;Yoshizawa Y;Mizutani J Title: Measurement of intracellular ionized calcium in a free-living soil nematode, Caenorhabditis elegans. Citation: Bioscience Biotechnology and Biochemistry 57: 1115-1118 Type: ARTICLE Genes: Abstract: A calcium chelating fluorescence indicator, fura-2, was used to measure intracellular ionized calcium in Caenorhabditis elegans. The indicator loading process was harmless to the nematode, and completed within 2-3 h. Fura-2 was loaded mainly at its intestinal tract. The effects of DOPA on locomotion and the level of intracellular calcium were investigated and measured by using a microfluorometer. The addition of DOPA temporarily increased [Ca2+]i for several minutes. ------------------- Key: 1776 Medline: 93365259 Authors: Matsuo M Title: Oxygen dependency of life-span in the nematode. Citation: Comparative Biochemistry & Physiology A-Comparative Physiology 105: 653-658 1993 Type: REVIEW Genes: mev-1 rad-1 rad-2 rad-3 rad-4 rad-6 rad-7 rad-8 rad-9 Abstract: 1. The mean and maximum life-spans of both wild type Caenorhabditis elegans and the mev-1(kn1) mutant, whose cytoplasmic superoxide dismutase activity level is about half of the wild type, were increased and decreased under low and high concentrations of oxygen, respectively. 2. The Gompertz component, a parameter of ageing rate, of the wild type was smaller under 1% oxygen than under 2% or more oxygen. Further, the Gompertz component of the mutant increased with an increase in oxygen concentration. 3. The oxygen-dependent modulation of life-span and ageing rate seems to be enhanced by a genetic defect of the mutant in antioxidant defence. ------------------- Key: 1777 Medline: 93354444 Authors: Roehl H;Kimble J Title: Control of cell fate in C. elegans by a glp-1 peptide consisting primarily of ankryin repeats. Citation: Nature 364: 632-635 1993 Type: ARTICLE Genes: dpy-4 glp-1 lin-12 rol-6 Abstract: THE homologous proteins GLP-1 and LIN-12 are required for cell interactions during nematode development1-5. glp-1 and lin-12 are members of a gene family that includes Drosophila Notch and several vertebrate homologues6. The members of this family have a single transmembrane domain and a similar arrangement of repeated amino-acid motifs (see Fig. 1). The mechanism by which proteins in this family function is not understood. One hypothesis is that these proteins are receptors, each with an extracellular domain that binds a ligand and an intracellular domain that influences the activity of downstream cell fate regulators. Here we report that a region of the GLP-1 intracellular domain, consisting primarily of six ankyrin repeats, is sufficient to direct cell fate. The cell fate transformations seen are similar to transformations caused by gain-of-function mutations in either glp-1 or lin-12 and do not rely on endogenous lin-12 or glp-1 activity. We propose that the ankyrin repeat region of GLP-1 is responsible for controlling downstream regulators of cell ------------------- Key: 1778 Medline: 93345021 Authors: Struhl G;Fitzgerald K;Greenwald I Title: Intrinsic activity of the lin-12 and notch intracellular domains in vivo. Citation: Cell 74: 331-345 1993 Type: ARTICLE Genes: glp-1 hsp-70 lin-11 lin-12 Abstract: The lin-12 gene of C. elegans and the Notch gene of D. melanogaster encode structurally related transmembrane proteins that mediate intercellular signaling. We show that truncated forms of these proteins consisting of only the intracellular domains cause cell fate transformations associated with constitutive activity in their respective organisms. This activity does not depend on endogenous gene function. Our results indicate that the intracellular domains of Lin-12 and Notch have intrinsic activity and that the principal role of the extracellular domains in the intact proteins is to regulate this activity. Our results also suggest that equivalent truncated forms of lin-12/Notch family members in vertebrates, including known oncogenes, are similarly active. ------------------- Key: 1779 Medline: 93339574 Authors: Rogalski TM;Williams BD;Mullen GP;Moerman DG Title: Products of the unc-52 gene in Caenorhabditis elegans are homologous to the core protein of the mammalian basement membrane heparan sulfate proteoglycan. Citation: Genes & Development 7: 1471-1484 1993 Type: ARTICLE Genes: unc-52 Abstract: Mutations in the unc-52 gene of Caenorhabditis elegans affect attachment of the myofilament lattice to the muscle cell membrane. Here, we demonstrate that the unc-52 gene encodes a nematode homolog of perlecan, the mammalian basement membrane heparan sulfate proteoglycan. The longest potential open reading frame of this gene encodes a 2482-amino-acid protein with a signal peptide and four domains. The first domain is unique to the unc-52 polypeptide, whereas the three remaining domains contain sequences found in the LDL receptor (domain II) laminin (domain II)) and N-CAM (domain IV). We have identified three alternatively spliced transcripts that encode different carboxy-terminal sequences. The two larger transcripts encode proteins containing all or part of domain IV, whereas the smaller transcript encodes a shortened polypeptide that completely lacks domain IV. We have determined that the disorganized muscle phenotype observed in unc-52(st196) animals is caused by the insertion of a Tc1 transposon into domain IV. Two monoclonal antibodies that recognize an extracellular component of all contractile tissues in C. elegans fail to stain embryos homozygous for a lethal unc-52 allele. We have mapped the epitopes recognized by both monoclonal antibodies to a region of domain IV in the unc-52-encoded ------------------- Key: 1780 Medline: 93323962 Authors: Herman RK Title: Genes make worms behave. Citation: Nature 364: 282-283 1993 Type: REVIEW Genes: unc-25 unc-30 unc-46 unc-47 unc-49 Abstract: Twenty years ago Sydney Brenner described an electrode-less plan for attacking the problems of neural development and physiology in the small nematode Caenorhabditis elegans. He proposed to set the groundwork by reconstructing the entire nervous system of the worm by serial section electron microscopy. Given the resulting wiring diagram, he thought it might be possible to make guesses as to how the nervous system worked. A second aspect of his plan was genetics: single-gene mutants exhibiting aberrant behaviour, such as uncoordinated movement, were to be analysed to address the question of how genes specify development and function of the nervous system. In two papers beginning on page 334 of this issue, McIntire et al. demonstrate that work on Brenner's plan, with a few tricks added over the years, is progressing very nicely. ------------------- Key: 1781 Medline: Authors: McGhee JD;Mains PE Title: Embryonic transcription in Caenorhabditis elegans. Citation: Seminars in Developmental Biology 3: 163-173 1992 Type: REVIEW Genes: ges-1 glp-1 hlh-1 mec-1 pha-1 sdc-1 unc-86 Abstract: The cell lineage of the nematode Caenorhabditis elegans is essentially invariant and many cell fates are autonomous. It seems likely that factors capable of influencing lineage-specific gene expressions are segregated or activated asymmetrically during the early cleavages. The maternal genome provides most of the raw materials for embryogenesis as well as the information required to pattern early cell divisions. Nonetheless, the zygotic genome is transcriptionally active early in embryogenesis and is expressing at least some genes required for future developmental decisions. Several of these zygotically active genes have been analysed; they show complex lineal expression patterns, implying that their regulation may not be as straightforward as initially thought. However, an understanding of the logic governing how different combinations of transcription factors regulate lineage-specific differentiation may be possible in this organism. ------------------- Key: 1782 Medline: 93352698 Authors: Epstein HF;Casey DL;Ortiz I Title: Myosin and paramyosin of Caenorhabditis elegans embryos assemble into nascent structures distinct from thick filaments and multi-filament assemblages. Citation: Journal of Cell Biology 122: 845-858 1993 Type: ARTICLE Genes: unc-15 Abstract: The organization of myosin heavy chains (mhc) A and B and paramyosin (pm) which are the major proteins of thick filaments in adult wild-type Caenorhabditis elegans were studied during embryonic development. As a probe of myosin-paramyosin interaction, the unc-15 mutation e73 which produces a glu342lys charge change in pm and leads to the formation of large paracrystalline multi-filament assemblages was compared to wild type. These three proteins colocalized in wild-type embryos from 300 to 550 min of development after first cleavage at 20-degrees-C on the basis of immunofluorescence microscopy using specific monoclonal antibodies. Linear structures which were diversely oriented around the muscle cell peripheries appeared at 360 min and became progressively more aligned parallel to the embryonic long axis until distinct myofibrils were formed at 550 min. In the mutant, mhc A and pm were colocalized in the linear structures, but became progressively separated until they showed no spatial overlap at the myofibril stage. These results indicate that the linear structures represent nascent assemblies containing myosin and pm in which the proteins interact differently than in wild-type thick filaments of myofibrils. In e73, these nascent structures were distinct from the multifilament assemblages. The overlapping of actin and mhc A in the nascent linear structures suggests their possible structural and functional relationship to the ''stress fiber-like structures'' of cultured vertebrate ------------------- Key: 1783 Medline: 94004604 Authors: Mansell JB;Timms K;Tate WP;Moens L;Trotman CNA Title: Expression of a globin gene in Caenorhabditis elegans. Citation: Biochemistry and Molecular Biology International 30: 643-647 1993 Type: ARTICLE Genes: Abstract: Oligonucleotides related to parts of a globin-like sequence in the genome of Caenorhabditis elegans were used to probe a cDNA library from the same species. A complete globin-like sequence was found in the cDNA, showing that a globin gene appears to be expressed. The hypothetical protein was compatible with the conventional globin fold but may be truncated in the B helix, as in Chironomus globin III. An intron in the codon for residue E3 in the E helix was removed in expression. An initiation codon preceded the globin but the sequence upstream (extending for 30 nucleotides to the vector ligation site) had characteristics both of the code for a protein hydrophobic leader and of a trans-spliced RNA leader. The evidence indicates that C . elegans globin has a single domain, unlike some nematodes that express two tandem globin domains in a continuous translation product, and from its sequence may be predicted to have a high affinity for ------------------- Key: 1784 Medline: 93361462 Authors: Zwaal RR;Broeks A;van Meurs J;Groenen JTM;Plasterk RHA Title: Target-selected gene inactivation in Caenorhabditis elegans by using a frozen transposon insertion mutant bank. Citation: Proceedings of the National Academy of Sciences USA 90: 7431-7435 1993 Type: ARTICLE Genes: ceh-13 ceh-18 gpa-2 gpa-3 pgp-1 Abstract: To understand how genotype determines the phenotype of the animal Caenorhabditis elegans, one ideally needs to know the complete sequence of the genome and the contribution of genes to phenotype, which requires an efficient strategy for reverse genetics. We here report that the Tc1 transposon induces frequent deletions of flanking DNA, apparently resulting from Tc1 excision followed by imprecise DNA repair. We use this to inactivate genes in two steps, (i) We established a frozen library of 5000 nematode lines mutagenized by Tc1 insertion, from which insertion mutants of genes of interest can be recovered. Their address within the library is determined by PCR. (ii) Animals are then screened, again by PCR, to detect derivatives in which Tc1 and 1000-2000 base pairs of Ranking DNA are deleted, and thus a gene of interest is inactivated. We have thus far isolated Tc1 insertions in 16 different genes and obtained deletion derivatives of 6 of ------------------- Key: 1785 Medline: 93351225 Authors: Bowerman B;Draper BW;Mello CC;Priess JR Title: The maternal gene skn-1 encodes a protein that is distributed unequally in early C. elegans embryos. Citation: Cell 74: 443-452 1993 Type: ARTICLE Genes: glp-1 mex-1 par-1 skn-1 pie-1 nDf41 mDp1 Abstract: The autonomous or cell-intrinsic developmental properties of early embryonic blastomeres in nematodes are thought to result from the action of maternally provided determinants. After the first cleavage of the C . elegans embryo, only the posterior blastomere, P1, has a cell-intrinsic ability to produce pharyngeal cells. The product of the maternal gene skn-1 is required for P1 to produce pharyngeal cells. We show here that the Skn-1 protein is nuclear localized and that P1 appears to accumulate markedly higher levels of Skn-1 protein than its sister, the AB blastomere. We have examined the distribution of Skn-1 protein in embryos from mothers with maternal-effect mutations in the genes mex-1, par-1, and pie-1. These results suggest that mex-1(+) and par-1(+) activities are required for the unequal distribution of the Skn-1 protein and that pie-1(+) activity may function to regulate the activity of Skn-1 protein in the descendants of the posterior blastomere P1. ------------------- Key: 1786 Medline: 93351232 Authors: Bargmann CI;Hartwieg E;Horvitz HR Title: Odorant-selective genes and neurons mediate olfaction in C. elegans. Citation: Cell 74: 515-527 1993 Type: ARTICLE Genes: che-1 che-2 odr-1 odr-2 odr-3 odr-4 odr-5 nDf16 nDf32 sDf16 sDf20 Abstract: Olfaction is a versatile and sensitive mechanism for detecting volatile odorants. We show that the nematode C . elegans detects many volatile chemicals, which can be attractants, repellents, or attractants at low concentrations and repellents at high concentrations. Through laser ablation, we have identified chemosensory neurons that detect volatile odorants. Chemotaxis to volatile odorants requires different sensory neurons from chemotaxis to water-soluble attractants, indicating that C . elegans might have senses that correspond to smell and taste, respectively. Single neurons have complex sensory properties, since six distinguishable volatile odorants are sensed by only two types of sensory neurons. Chemotaxis to subsets of volatile odorants is disrupted by mutations in the odr genes, which might be involved in odorant sensation or signal transduction. ------------------- Key: 1787 Medline: 93324367 Authors: Fickett JW;Guigo R Title: Estimation of protein coding density in a corpus of DNA sequence data. Citation: Nucleic Acids Research 21: 2837-2844 1993 Type: ARTICLE Genes: Abstract: A number of experimental methods have been reported for estimating the number of genes in a genome, or the closely related coding density of a genome, defined as the fraction of base pairs in codons. Recently, DNA sequence data representative of the genome as a whole have become available for several organisms, making the problem of estimating coding density amenable to sequence analytic methods. Estimates of coding density for a single genome vary widely, so that methods with characterized error bounds have become increasingly desirable. We present a method to estimate the protein coding density in a corpus of DNA sequence data, in which a 'coding statistic' is calculated for a large number of windows of the sequence under study, and the distribution of the statistic is decomposed into two normal distributions, assumed to be the distributions of the coding statistic in the coding and noncoding fractions of the sequence windows. The accuracy of the method is evaluated using known data and application is made to the yeast chromosome III sequence and to C.elegans cosmid sequences. It can also be applied to fragmentary data, for example a collection of short sequences determined in the course of STS mapping. ------------------- Key: 1788 Medline: 93352881 Authors: Cowden C;Sithigorngul P;Brackley P;Guastella J;Stretton AOW Title: Localization and differential expression of FMRFamide-like immunoreactivity in the nematode Ascaris suum. Citation: Journal of Comparative Neurology 333: 455-468 1993 Type: ARTICLE Genes: Abstract: By immunocytochemical and immunohistochemical methods, FMRF amide-like immunoreactivity (FLI) was localized to many neurons and processes in the Ascaris nervous system, including the head, tail, and lateral lines. Some of these cells were identified; they included sensory neurons, interneurons, and motor neurons. FLI was also present in the pharyngeal neurons and in their varicosities near the surface of the pharynx. By HPLC analysis of extracts, only a subset of the FMRF amide-like peptides (FLPs) expressed in Ascaris heads, and heads from which the pharynx had been removed, were expressed in the pharynx. Furthermore, FLPs appeared to be differentially expressed in female heads and tails and male heads and tails. Acetone and acid methanol differentially extracted subforms of FLI from Ascaris heads and from C . elegans . ------------------- Key: 1790 Medline: 93376490 Authors: Zarkower D;Hodgkin J Title: Zinc fingers in sex determination: only one of the two C. elegans Tra-1 proteins binds DNA in vitro. Citation: Nucleic Acids Research 21: 3691-3698 1993 Type: ARTICLE Genes: mab-3 tra-1 Abstract: GENBANK-M93256 The tra-1 gene of Caenorhabditis elegans is a major developmental regulator that promotes female development. Two mRNAs are expressed from the tra-1 locus as a result of alternative mRNA processing. One mRNA encodes a protein with five zinc fingers and the other a protein with only the first two zinc fingers. We have derived a preferred in vitro DNA binding site for the five finger protein by selection from random oligonucleotides. The two finger protein does not bind to DNA in vitro. Moreover, removal of the first two fingers from the five finger protein does not eliminate binding and has little effect on its preferred binding site. We find that a protein sequence amino-terminal to the finger domain also appears to play a role in DNA binding. ------------------- Key: 1791 Medline: 94010274 Authors: Pilgrim D Title: The genetic and RFLP characterization of the left end of linkage group III in Caenorhabditis elegans. Citation: Genome 36: 712-724 1993 Type: ARTICLE Genes: daf-7 dpy-1 fem-2 mec-12 par-2 tra-3 unc-45 vab-6 Abstract: A genetic approach was taken to identify new transposable element Tc1-dependent polymorphisms on the left end of linkage group III in the nematode Caenorhabditis elegans. The cloning of the genomic DNA surrounding the Tc1 allowed the selection of overlapping clones (from the collection being used to assemble the physical map of the C . elegans genome). A contig of approximately 600-800 kbp in the re-ion has been identified, the genetic map of the region has been refined, and 10 new RFLPs as well as at least four previously characterized genetic loci have been positioned onto the physical map. to the resolution of a few cosmids. This analysis demonstrated the ability to combine physical and genetic mapping for the rapid analysis of large genomic regions (0.5-1 Mbp) in genetically amenable eukaryotes. ------------------- Key: 1792 Medline: 94060446 Authors: Levy AD;Yang J;Kramer JM Title: Molecular and genetic analyses of the Caenorhabditis elegans dpy-2 and dpy-10 collagen genes: A variety of molecular alterations affect organismal morphology. Citation: Molecular Biology of the Cell 4: 803-817 1993 Type: ARTICLE Genes: dpy-2 dpy-10 glp-1 mup-1 rol-6 sqt-1 mnDf39 Abstract: We have identified and cloned the Caenorhabditis elegans dpy-2 and dpy-10 genes and determined that they encode collagens. Genetic data suggested that these genes are important in morphogenesis and possibly other developmental events. These data include the morphologic phenotypes exhibited by mutants, unusual genetic interactions with the sqt-1 collagen gene, and suppression of mutations in the glp-1 and mup-1 genes. The proximity of the dpy-2 and dpy-10 genes (3.5 kilobase) and the structural similarity of their encoded proteins (41% amino acid identity) indicate that dpy-2 and dpy-10 are the result of a gene duplication event. The genes do not, however, appear to be functionally redundant, because a dpy-10 null mutant is not rescued by the dpy-2 gene. In addition, full complementation between dpy-2 and dpy-10 can be demonstrated with all recessive alleles tested in trans. Sequence analysis of several mutant alleles of each gene was performed to determine the nature of the molecular defects that can cause the morphologic phenotypes. Glycine substitutions within the Gly-X-Y portion of the collagens can result in dumpy (Dpy), dumpy, left roller (DLRol), or temperature-sensitive DLRol phenotypes. dpy-10(cn64), a dominant temperature-sensitive DLRol allele, creates an Arg-to-Cys substitution in the amino non-Gly-X-Y portion of the protein. Three dpy-10 alleles contain Tc1 insertions in the coding region of the gene. dpy-10(cg36) (DRLol) creates a nonsense codon near the end of the Gly-X-Y region. The nature of this mutation, combined with genetic data, indicates that DLRol is the null phenotype of dpy-10. The Dpy phenotype results from reduced function of the dpy-10 collagen gene. Our results indicate that a variety of molecular defects in these collagens can result in severe ------------------- Key: 1793 Medline: 93369588 Authors: Xue D;Tu Y;Chalfie M Title: Cooperative interactions between the Caenorhabditis elegans homeoproteins UNC-86 and MEC-3. Citation: Science 261: 1324-1328 1993 Type: ARTICLE Genes: dpy-20 mec-3 mec-4 mec-7 unc-86 Abstract: The POU-type homeodomain protein UNC-86 and the LIM-type homeodomain protein MEC-3, which specify neuronal cell fate in the nematode Caenorhabditis elegans, bind cooperatively as a heterodimer to the mec-3 promoter. Heterodimer formation increases DNA binding stability and, therefore, increases DNA binding specificity. The in vivo significance of this heterodimer formation in neuronal differentiation is suggested by (i) a loss-of-function mec-3 mutation whose product in vitro binds DNA well but forms heterodimers with UNC-86 poorly and (ii) a mec-3 mutation with wild-type function whose product binds DNA poorly but forms heterodimers well. ------------------- Key: 1794 Medline: 94007683 Authors: Sternberg PW;Hill RJ;Jongeward G;Huang LS;Carta L Title: Intercellular signaling during Caenorhabditis elegans vulval induction. Citation: Cold Spring Harbor Symposia on Quantitative Biology 57: 353-362 1993 Type: ARTICLE Genes: her-1 let-23 let-60 lin-2 lin-3 lin-7 lin-8 lin-9 lin-10 lin-12 lin-15 lin-35 lin-36 lin-37 sem-5 sli-1 unc-101 Abstract: The essential invariance of Caenorhabditis elegans development has allowed detailed analysis of the mechanisms of cell fate determination. A variety of studies suggest a major role for cell interactions in specifying cell fates during nematode development. The original observations of natural variability of certain cell fates and the cell fate changes after particular cell ablation experiments indicated that the fates of some cells during later embryonic and postembryonic development depend on cell ------------------- Key: 1795 Medline: 94007684 Authors: Clark SG;Stern MJ;Horvitz HR Title: Genes involved in two Caenorhabditis elegans cell-signaling pathways. Citation: Cold Spring Harbor Symposia on Quantitative Biology 57: 363-373 1993 Type: ARTICLE Genes: clr-1 dig-1 egl-15 egl-17 let-23 let-60 let-341 lin-1 lin-3 lin-15 lin-45 sem-5 Abstract: Cell interactions are responsible for may aspects of animal development. What are the signals, receptors, and signal transduction molecules that function as cells communicate with each other during development? Answers to this question are only beginning to emerge from studies in developmental biology. To what extent are particular intercellular signaling molecules shared among different sets of interacting cells? Are the same signaling molecules and pathways used in different cell types, at different locations, and at different times during development? Or does each group of interacting cells use a unique signaling pathway? Answers to these questions would provide fundamental insights into the molecular basis of animal development. ------------------- Key: 1796 Medline: 94007688 Authors: Kimble J;Crittenden S;Lambie E;Kodoyianni V;Mango S;Troemel E Title: Regulation of induction by GLP1, a localized cell surface receptor in Caenorhabditis elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 57: 401-407 1993 Type: ARTICLE Genes: fem-1 glp-1 lin-12 Abstract: During the development of the nematode Caenorhabditis elegans, cell interactions influence fundamental decisions of growth, differentiation, and pattern formation from early embryogenesis through adulthood. The powerful genetics and cellular simplicity of C. elegans make it an ideal organism to analyze the mechanisms by which cell interactions regulate cell fate. Specific cell interactions can be defined at the levl of individual cells, and genes controlling those interactions can be identified and manipulated both genetically and molecularly. In this paper, we focus on the role of a single gene, glp-1 (for germline proliferation defective), in the control of cell fate by inductive signaling. ------------------- Key: 1797 Medline: 94094745 Authors: Goldstein B Title: Establishment of gut fate in the E lineage of C. elegans: The roles of lineage-dependent mechanisms and cell interactions. Citation: Development 118: 1267-1277 1993 Type: ARTICLE Genes: mex-1 par-1 par-4 pie-1 skn-1 Abstract: The gut of C. elegans derives from all the progeny of the E blastomere, a cell of the eight cell stage. Previous work has shown that gut specification requires an induction during the four cell stage (Goldstein, B. (1992) Nature 357, 255-257). Blastomere isolation and recombination experiments were done to determine which parts of the embryo can respond to gut induction. Normally only the posterior side of the EMS blastomere contacts the inducing cell, P2. When P2 was instead placed in a random position on an isolated EMS, gut consistently differentiated from the daughter of EMS contacting P2, indicating that any side of EMS can respond to gut induction. Additionally, moving P2 around to the opposite side of EMS in an otherwise intact embryo caused EMS's two daughter cells to switch lineage timings, and gut to differentiate from the descendents of what normally would be the MS blastomere. The other cells of the four cell stage, ABa, ABp, and P2, did not form gut when placed in contact with the inducer. To determine whether any other inductions are involved in gut specification, timed blastomere isolations were done at the two and eight cell stages. In the absence of cell contact at the two cell stage, segregation of gut fate proceeded normally at both the two and four cell stages. Gut fate also segregated properly in the absence of cell contact at the eight cell stage. A model is presented for the roles of lineage-dependent mechanisms and cell interactions in establishing gut fate in the E lineage. ------------------- Key: 1798 Medline: 93380647 Authors: Salser SJ;Loer CM;Kenyon C Title: Multiple HOM-C gene interactions specify cell fates in the nematode central nervous system. Citation: Genes & Development 7: 1714-1724 1993 Type: ARTICLE Genes: egl-5 lin-39 mab-5 tra-1 Abstract: Intricate patterns of overlapping HOM-C gene expression along the A/P axis have been observed in many organisms; however, the significance of these patterns in establishing the ultimate fates of individual cells is not well understood. We have examined the expression of the Caenorhabditis elegans Antennapedia homolog mab-5 and its role in specifying cell fates in the posterior of the ventral nerve cord. We find that the pattern of fates specified by mab-5 not only depends on mab-5 expression but also on post-translational interactions with the neighboring HOM-C gene lin-39 and a second, inferred gene activity. Where mab-5 expression overlaps with lin-39 activity, they can interact in two different ways depending on the cell type: They can either effectively neutralize one another where they are both expressed or lin-39 can predominate over mab-5. As observed for Antennapedia in Drosophila, expression of mab-5 itself is repressed by the next most posterior HOM-C gene, egl-5. Thus, a surprising diversity in HOM-C regulatory mechanisms exists within a small set of cells even in a simple organism. ------------------- Key: 1799 Medline: 94040749 Authors: Katsura I Title: In search of new mutants in cell-signaling systems of the nematode Caenorhabditis elegans. Citation: Genetica 88: 137-146 1993 Type: REVIEW Genes: clr-1 daf-1 egl-15 flr-1 flr-2 flr-3 flr-4 flr-5 glp-1 gpa-1 gpa-2 gpb-1 her-1 lag-2 let-23 let-60 let-341 lin-3 lin-12 lin-15 lin-22 mup-1 pal-1 sem-5 sqt-3 tpa-1 tra-2 unc-15 unc-17 unc-52 unc-104 Abstract: Development of multicellular organisms is controlled mainly by cell-signaling systems. In this review I first discuss methods of genetic analysis and properties of mutants of cell-signaling systems in general and in the nematode C. elegans. Then, I describe two of our approaches to isolating new mutants in cell-signaling of C. elegans. The first approach is to select for mutants that have the same visible phenotype as those in known cell-signaling genes. In a survey of larval lethal mutations we found that there are quite a few mutants in which the inner surface of the body wall is detached from the outer surface of the intestine. Some of them map in genes that are known to act in cell-signaling systems in vulval induction or sex myoblast migration, which are not essential to the growth and survival of C. elegans. Therefore, we think many of the mutations of the above phenotype disrupt cell-signaling in an unidentified essential function, and also cell-signaling in the non-essential functions. The second approach is to isolate mutants resistant to a drug expected to disturb cell-signaling. As the drug we have chosen sodium fluoride, which depletes calcium ion, activates G-proteins and inactivates some phosphatases. The mutants are grouped into two classes (three and two genes, respectively) according to degree of fluoride-resistance and growth rate of larvae. Although there is so far no direct evidence that these mutants are related to cell-signaling, they show complex epistasis that can be explained by a model consisting of a cell-signaling pathway. ------------------- Key: 1800 Medline: 94040696 Authors: Levin JZ;Horvitz HR Title: 3 New classes of mutations in the Caenorhabditis elegans muscle gene sup-9. Citation: Genetics 135: 53-70 1993 Type: ARTICLE Genes: dpy-10 dpy-17 lin-15 lin-31 lin-42 sup-9 sup-10 sup-11 sup-18 unc-93 nDf3 Abstract: We are studying five interacting genes involved in the regulation or coordination of muscle contraction in Caenorhabditis elegans. A distinctive ''rubber-band'' muscle-defective phenotype was previously shown to result from rare altered-function mutations in either of two of these genes, unc-93 and sup-10. Null mutations in sup-9, sup-10, sup-18 or unc-93 act as essentially recessive suppressors of these rubber-band mutations. In this work, we identify three new classes of sup-9 alleles: altered-function rubber-band, partial loss-of-function and dominant-suppressor. The existence of rubber-band mutations in sup-9, sup-10 and unc-93 and the suppression of these mutations by null mutations in any of these three genes suggest that these proteins are required at the same step in muscle contraction. Moreover, allele-specific interactions shown by the partial loss-of-function mutations indicate that the products of these interacting genes may physically contact each other in a multiple subunit protein complex. Finally, the phenotypes of double rubber-band mutant combinations suggest that the rubber-band mutations affect a neurogenic rather than a myogenic input in excitation-contraction coupling in ------------------- Key: 1801 Medline: 93374946 Authors: Jones D;Candido EPM Title: Novel ubiquitin-like ribosomal protein fusion genes from the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. Citation: Journal of Biological Chemistry 268: 19545-19551 1993 Type: ARTICLE Genes: ubq-1 Abstract: Among eukaryotes studied to date, homologs of the yeast 76-amino acid ribosomal protein have invariably been found to be cotranslated with ubiquitin. However, in the nematodes Caenorhabditis elegans and Caenorhabditis briggsae, a 70-amino acid domain with only 40% identity to ubiquitin is cotranslated with a homolog of the ribosomal protein. In the nematode ubiquitin-like (UbL) proteins, the nucleotide sequence of the UbL coding region is 92% identical in C. elegans and C. briggsae. The corresponding gene sequence contains a single intron at a location identical to that found in the polyubiquitin gene of C. elegans, further confirming that the ubl genes are evolutionarily related to ubiquitin. The ribosomal protein portion of the UbL polypeptide consists of 93 amino acids and is 68% identical to the human homolog. The ribosomal protein portion of UbL is longer than in other homologs, with the additional sequence being present as a basic carboxyl extension. The ubl gene is constitutively expressed in all life cycle stages of C. elegans. A comparison of the nematode UbL sequences with other ubiquitin-like genes reveals a pattern of sequence conservation, which suggests that the ubiquitin- like ------------------- Key: 1802 Medline: 94033228 Authors: Shakir MA;Miwa J;Siddiqui SS Title: A role of ADF chemosensory neurones in dauer formation behaviour in C. elegans. Citation: Neuroreport 4: 1151-1154 1993 Type: ARTICLE Genes: che-13 daf-10 osm-3 Abstract: IN Caenorhabditis elegans, mutants in osmotic avoidance behaviour (osm), which fail to avoid high concentrations of salts and sugars, have been previously identified. These osm mutants are also defective in dauer larva formation, and fail to take up fluorescein dye in six pairs of amphid neurones (ADF, ADL, ASH, ASI, ASJ, and ASK) and two pairs of phasmid neurones. Analysis of the FITC dye uptake by osm-3 mutants show that seven of the eight osm-3 alleles can take up FITC dyes in one pair of amphid neurones, ADF. Comparison of dauer larva formation behaviour in different osm-3 alleles shows a direct correlation between improved behaviour and FITC dye uptake. Therefore, these allelic strains are useful in defining the role of ADF neurones in dauer larva formation. ------------------- Key: 1803 Medline: 94048946 Authors: Satouchi K;Hirano K;Sakaguchi M;Takehara H;Matsuura F Title: Phospholipids from the free-living nematode Caenorhabditis elegans. Citation: Lipids 28: 837-840 1993 Type: ARTICLE Genes: age-1 Abstract: The phospholipid and the fatty chain compositions of diacyl, alkylacyl and alkenylacyl glycerophospholipids of the free-living nematode, Caenorhabditis elegans, were investigated. The phospholipids were comprised of 54.5% ethanolamine glycerophospholipid (EGP), 32.3% choline glycerophospholipid (CGP), 8.1% sphingomyelin and 5.1% others. The most abundant fatty acid in CGP was eicosapentaenoic acid (20:5n-3). The fatty acids in CGP were more unsaturated than those in EGP. Alkenylacyl and alkylacyl subclasses accounted for 1.0 and 2.6%, respectively, of CGP and 14.0 and 19.6%, respectively. of EGP. At least 80% of the alkenyl and alkyl groups were 18:0 chains and the remaining were odd numbered chains. The potential presence of platelet-activating factor (PAF) was examined by bioassay, but PAF-like activity was not detected in the extracts of this nematode. ------------------- Key: 1804 Medline: 94045621 Authors: Chalfie M Title: Touch receptor development and function in Caenorhabditis elegans. Citation: Journal of Neurobiology 24: 1433-1441 1993 Type: REVIEW Genes: deg-1 lin-32 mec-3 mec-4 mec-6 mec-7 mec-17 unc-86 Abstract: Mutations causing a touch-insensitive phenotype in the nematode Caenorhabditis elegans have been the basis of studies on the specification of neuronal cell fate, inherited neurodegeneration, and the molecular nature of mechanosensory transduction. (C) 1993 John Wiley & sons, Inc. ------------------- Key: 1805 Medline: 94021383 Authors: Amaar YG;Baillie DL Title: Cloning and characterization of the C. elegans histidyl-tRNA synthetase gene. Citation: Nucleic Acids Research 21: 4344-4347 1993 Type: ARTICLE Genes: Abstract: In this paper, we report the cloning and sequencing of the C. elegans histidyl-tRNA synthetase gene. The complete genomic sequence, and most of the cDNA sequence, of this gene is now determined. The gene size including flanking and coding regions is 2230 nucleotides long. Three small introns (45 - 50 bp long) are found to interrupt the open reading frame. The open reading frame translates to 523 amino acids. This putative protein sequence shows extensive homology with the human and yeast histidyl-tRNA the histidyl-tRNA synthetase gene is a single copy gene. Hence, it is very likely that it encodes both the cytoplasmic and the mitochondrial histidyl-tRNA synthetases. It is likely to be trans-spliced since it contains a trans-splice site in its 5' untranslated region. ------------------- Key: 1806 Medline: 94012964 Authors: Sibley MH;Johnson JJ;Mello CC;Kramer JM Title: Genetic identification, sequence, and alternative splicing of the Caenorhabditis elegans alpha2(IV) collagen gene. Citation: Journal of Cell Biology 123: 255-264 1993 Type: ARTICLE Genes: emb-9 fer-1 let-2 rol-6 Abstract: The nematode Caenorhabditis elegans has two type IV collagen genes homologous to the mammalian alpha1(IV) and alpha2(IV) collagen genes. We demonstrate by transgenic rescue of mutant animals that the genetic locus encoding the C elegans alpha2(IV) collagen gene is let-2 on the X chromosome. The most severe effect of mutations in let-2 is temperature-sensitive embryonic lethality. The embryonic lethal phenotype is similar to that seen in animals with mutations in the alpha1(IV) collagen gene, emb-9. The sequence of the entire AC. elegans alpha2(IV) collagen gene is presented. Comparisons with mammalian type IV collagen sequences show high amino acid sequence conservation in the C-terminal NC1 domain and of crosslinking residues (Cys and Lys) in the N-terminal 7S domain. RT-PCR analysis shows that transcripts of the C elegans alpha2(IV) collagen gene are alternatively spliced. Transcripts contain one of two mutually exclusive exons, exon 9 or 10. These exons encode very similar products, differing primarily in the sequence of a 9-10 amino acid Gly-X-Y interruption. The expression of these alternatively spliced alpha2(IV) collagen transcripts is developmentally regulated. In embryos over 90% of the alpha2(IV) collagen mRNA contains exon 9, while larval and adult RNAs contain 80-90% exon 10. This shift in expression of alternative alpha2(IV) collagen transcripts suggests that C elegans embryos may require a different form of alpha2(IV) collagen than do larvae and adults. ------------------- Key: 1807 Medline: 94063479 Authors: Okkema PG;Harrison SW;Plunger V;Aryana A;Fire A Title: Sequence requirements for myosin gene-expression and regulation in Caenorhabditis elegans. Citation: Genetics 135: 385-los a 1993 Type: ARTICLE Genes: ges-1 mlc-1 myo-1 myo-2 myo-3 unc-54 Abstract: Four Caenorhabditis elegans genes encode muscle-type specific myosin heavy chain isoforms: myo-1 and myo-2 are expressed in the pharyngeal muscles; unc-54 and myo-3 are expressed in body wall muscles. We have used transformation-rescue and lacZ fusion assays to determine sequence requirements for regulated myosin gene expression during development. Multiple tissue-specific activation elements are present for all four genes. For each of the four genes, sequences upstream of the coding region are tissue-specific promoters, as shown by their ability to drive expression of a reporter gene (lacZ) in the appropriate muscle type. Each gene contains at least one additional tissue-specific regulatory element, as defined by the ability to enhance expression of a heterologous promoter in the appropriate muscle type. In rescue experiments with unc-54, two further requirements apparently independent of tissue specificity were found: sequences within the 3' non-coding region are essential for activity while an intron near the 5' end augments expression levels. The general intron stimulation is apparently independent of intron sequence, indicating a mechanistic effect of splicing. To further characterize the myosin gene promoters and to examine the types of enhancer sequences in the genome, we have initiated a screen of C. elegans genomic DNA for fragments capable of enhancing the myo-2 promoter. The properties of enhancers recovered from this screen suggest that the promoter is limited to muscle cells in its ability to respond to enhancers. ------------------- Key: 1808 Medline: Authors: Arpagaus M;Richier P;L'Hermite Y;Le Roy F;Berge J;Thierry-Mieg D;Toutant J-P Title: Nematode acetylcholinesterases: Several genes and molecular forms of their products. Citation: "Multidisciplinary Approaches to Cholinesterase Functions." Shafferman A and Velan B (eds), Plenum Press, New York, NY. : 65-74 1992 Type: REVIEW Genes: ace-1 ace-2 ace-3 Abstract: In vertebrates, acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) are polymorphic enzymes presenting both globular and asymmetric forms. In invertebrates, only AChE has been characterized so far that presents a reduced molecular diversity. In insects for example the major molecular form of AChE is an amphiphilic dimeric form attached to the membrane through a glycolipid covalently linked at the C-terminus of each catalytic subunit. This AChE has a substrate specificity intermediate to those of mammalina AChE and BChE. A glycoplipid-anchored 7.5S from has also been observed in the trematode Schistosoma mansoni. Asymmetric forms have never been convincingly reported in invertebrates except in the more evolved animals such as Amphioxius. In the latter case also there is no BChE but AChE presents catalytic properties intermediate to those of vertebrate AChE and BChE. We are now interested in nematode AChE(s) for the following reasons: -several species are agricultural pest and it is important to get further informations on the target of potential nematicides; -it has been shown that at least three different genes code for AChE in Caenorhabditis elegans. It is therefore interesting to see whether the presence of multiple genes results in an increased molecular diversity, to define what are the structural characteristics of each gene product and finally to clone and sequence thee three genes for evolutionary relationships with the other members of the cholinesterase ------------------- Key: 1809 Medline: Authors: Edgley ML;Riddle DL Title: The nematode Caenorhabditis elegans. Citation: "Genetic Maps: Locus Maps of Complex Genomes, Lower Eukaryotes." O'Brien SJ (ed), Cold Spring Harbor Laboratory Press, Plainview, NY. 6: - 1993 Type: REVIEW Genes: Abstract: ------------------- Key: 1810 Medline: Authors: Goldstein P;Huang J-X Title: Trans-generational effects of diethylstilboestrol: spermatogenesis and absence of synaptonemal complexes in the him-8 mutant of Caenorhabditis elegans. Citation: Chromatin 1: 235-249 1992 Type: ARTICLE Genes: him-8 Abstract: This work represents the first comprehensive study of the effects of diethylstilboestrol (DES) on early spermatogenesis through the third generation. Exposure to a DES concentration of 12.5 ug/ml resulted in a significant decrease in the third generation, presumably due to genetic load. In some aspects, the reaction of males and hermaphrodites for DES were similar, such that decreased fecundity and ultrastructral changes were observed in both forms. Ultrastructural analyses demonstrated that the decrease in the number of offspring in him-8 C. elegans was associated with the production of abnormal speratocytes. Males were more sensitive to DES than hermaphrodites. At a DES concentration of 1.25 ug/ml, no morphological changes were observed in hermaphrodites, while nuclear architecture was compromised in males. In addition, at this low DES concentration, synaptonemal complexes were present in the hermaphrodites but absent in males. ------------------- Key: 1811 Medline: 94049685 Authors: Pilgrim DB;Bell JB Title: Expression of a Drosophila melanogaster amber suppressor tRNA(Ser) in Caenorhabditis elegans. Citation: Molecular & General Genetics 241: 26-32 1993 Type: ARTICLE Genes: rol-6 sup-7 tra-3 Abstract: The purpose of this study was to test a cloned amber-suppressing tRNA(Ser) gene derived from Drosophila melanogaster for its ability to produce amber suppression in the nematode Caenorhabditis elegans. To date, all characterized nonsense suppressors in C. elegans have been derived from tRNA(Trp) genes. Suppression was assayed by monitoring the reversal of a mutant tra-3 phenotype among individuals transformed with the cloned Drosophila suppressor gene. An amber allele of tra-3 results in masculinization of XX animals with accompanying sterility. Complete suppression was observed among the transformants. The presence of the heterologous transgene, in both suppressed experimental animals and controls injected with a non-suppressing wild-type Drosophila tRNA(Ser) gene, was verified by PCR amplification of DNA from single worms using primers flanking the tRNA(Ser) gene. Suppression by the heterologous transgene was comparable in quality to that produced by endogenous C. elegans suppressors, and, in frequency as well as quality, to that produced by a transgenic C. elegans tRNA(Trp)-derived suppressor. Thus, a heterologous suppressor gene will function in C. elegans, and it need not be based on tRNA(Trp). ------------------- Key: 1812 Medline: 94080020 Authors: Schwarzbauer JE;Spencer CS Title: The Caenorhabditis elegans homolog of the extracellular calcium-binding protein sparc/osteonectin affects nematode body morphology and mobility. Citation: Molecular Biology of the Cell 4: 941-952 1993 Type: ARTICLE Genes: rol-6 unc-52 unc-54 Abstract: The extracellular matrix-associated protein, SPARC (osteonectin [Secreted Protein Acidic and Rich in Cysteine]), modulates cell adhesion and induces a change in cell morphology. SPARC expression in mammals is developmentally regulated and is highest at sites of extracellular matrix assembly and remodeling such as parietal endoderm and bone. We have isolated cDNA and genomic DNA clones encoding the Caenorhabditis elegans homologue of SPARC. The gene organization is highly conserved, and the proteins encoded by mouse, human, and nematode genes are about 38% identical. SPARC consists of four domains (I-IV) based on predicted secondary structure. Using bacterial fusion proteins containing nematode domain I or the domain IV EF-hand motif, we show that, like the mammalian proteins, both domains bind calcium. In transgenic nematodes expressing a SPARC-lacZ fusion gene, beta-galactosidase staining accumulated in a striated pattern in the more heavily stained muscle cells along the body. Comparison of the pattern of transgene expression to unc-54-lacZ animals demonstrated that SPARC is expressed by body wall and sex muscle cells. Appropriate levels of SPARC are essential for normal C. elegans development and muscle function. Transgenic nematodes overexpressing the wild-type SPARC gene were abnormal. Embryos were deformed, and adult hermaphrodites had vulval protrusions and an uncoordinated (Unc) phenotype with reduced mobility and paralysis. ------------------- Key: 1813 Medline: 94010287 Authors: Pulak R;Anderson P Title: Messenger RNA surveillance by the Caenorhabditis elegans smg genes. Citation: Genes & Development 7: 1885-1897 1993 Type: ARTICLE Genes: act-1 glp-1 lin-29 mlc-1 mlc-2 smg-1 smg-2 smg-3 smg-4 smg-5 smg-6 sup-5 tra-2 tra-3 unc-17 unc-54 Abstract: mRNAs that contain premature stop codons are unstable in most eukaryotes, but the mechanism of their degradation is largely unknown. We demonstrate that functions of the six C. elegans smg genes are necessary for rapid turnover of nonsense mutant mRNAs of the unc-54 myosin heavy chain gene. Nonsense alleles of unc-54 express mRNAs that are unstable in smg(+) genetic backgrounds but have normal or near normal stability in smg(-) backgrounds. smg mutations also stabilize mRNA of unc-54(r293), a small deletion that removes the unc-54 polyadenylation site and expresses an aberrant mRNA. Most unc-54 nonsense mutations are recessive in both smg(+) and smg(-) genetic backgrounds. However, four specific alleles are recessive when smg(+) and dominant when smg(-). These smg-dependent dominant alleles express nonsense mutant polypeptides that disrupt thick filament and/or sarcomere assembly. All four alleles are predicted to express nonsense fragment polypeptides that contain most of the myosin globular head domain without an attached rod segment. By degrading messages that contain premature stop codons, the smg genes eliminate mRNAs that encode potentially toxic protein fragments. We propose that this system of mRNA turnover protects cells from their own errors of transcription, mRNA processing, or mRNA ------------------- Key: 1814 Medline: 94015309 Authors: Hekimi S;Kershaw D Title: Axonal guidance defects in a Caenorhabditis elegans mutant reveal cell-extrinsic determinants of neuronal morphology. Citation: Journal of Neuroscience 13: 4254-4271 1993 Type: ARTICLE Genes: dpy-3 lon-1 unc-6 unc-40 unc-53 Abstract: Mutations in the gene unc-53 of Caenorhabditis elegans result in behavioral and anatomical abnormalities. Immunocytochemistry and electron microscopy revealed neuroanatomical defects in all main longitudinal nervous tracts. Whole tracts were found to be misguided in specific ways suggesting that unc-53 affects pioneering axons. The four lateral microtubule cells (LMs), which are probably pioneering neurons, were examined in greatest detail. In the mutants, the processes of the LMs leave their normal position on the body wall and terminate prematurely. Examination of five unc-53 alleles for penetrance and expressivity of these defects revealed a spatial restriction in the requirement for unc-53. The morphology and positioning of the branch of the posterior lateral microtubule cells (PLMs) were also examined. In wild-type animals, the PLM branches lack the ultrastructural specializations of the main process, which include large microtubules, apposition to the cuticle, and a polarized extracellular matrix (the mantle). Two differences were noted in unc-53 mutants. First, a majority of PLMs branch at random and display an abnormally enlarged branching point and branch cross section. The unusual branch morphologies correlate with branch position, rather than PLM length. Second, the ectopic branches display the specific ultrastructural features characteristic of the main process. Furthermore, after entering the ventral nerve cord, the abnormal branches constantly change position relative to the other processes and the hypodermis, retaining their specialized microtubules throughout, but displaying a mantle only when in direct contact with hypodermis. Taken together, these observations suggest that the differentiated features of the PLMs, including process length, branch position, intracellular branch morphology, and surrounding extracellular matrix, are locally specified by cell-extrinsic cues, some of which ------------------- Key: 1815 Medline: 94060693 Authors: Burglin TR;Ruvkun G Title: The Caenorhabditis elegans homeobox gene-cluster. Citation: Current Opinion in Genetics & Development 3: 615-620 1993 Type: REVIEW Genes: ceh-13 ceh-23 egl-5 lin-39 mab-5 unc-89 Abstract: Understanding of the C. elegans homeobox gene cluster has been significantly expanded since the genes egl-5 and lin-39 have been shown to correspond to homeobox genes in the cluster. Genes of the homeobox cluster not only function as regionally restricted homeotic genes along the anterior-posterior body axis, but also control cell migrations within the affected body regions. ------------------- Key: 1816 Medline: 94079323 Authors: Nilsen TW Title: Transsplicing of nematode premessenger RNA. Citation: Annual Review of Microbiology 47: 413-440 1993 Type: REVIEW Genes: Abstract: In nematodes, many mRNAs contain a common 5' terminal 22-nt sequence. This sequence, the spliced leader (SL), is acquired from a small (approximately 100 nt) SL RNA via trans-splicing. Parallel in vitro and in vivo experiments have begun to clarify both the mechanism and biological role of trans-splicing. In vitro analysis (in cell free extracts) has shown that trans-splicing is remarkably similar to the snRNP mediated removal of intervening sequences from pre-mRNAs (cis-splicing). Additionally, this analysis has suggested a mechanism that may explain how the two substrates of trans-splicing (the SL RNA and pre-mRNA) efficiently associate with one another in the absence of sequence complementarity. In vivo experiments suggest that a major biological function of trans-splicing in nematodes may be to process polycistronic transcription units. Results obtained from the study of both parasitic and free-living species are discussed, and trans-splicing in nematodes is compared and contrasted to the analogous process in trypanosomatid protozoans. ------------------- Key: 1817 Medline: 94022283 Authors: Larsen PL Title: Aging and resistance to oxidative damage in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 90: 8905-8909 1993 Type: ARTICLE Genes: age-1 fer-15 sod-1 Abstract: The dauer larva state and the age-1 mutation, both of which extend life-span in Caenorhabditis elegans, were tested for hyperresistance to cellular damage that may be relevant to aging. The age-1 strain TJ401 displayed hyperresistance to oxidative stress relative to its parental strain. The activities of two enzymes that protect cells from oxidative damage, superoxide dismutase (SOD) and catalase, showed an age-dependent increase in mutant animals, which was not seen in the parental strain. These increases in activities paralleled the time course of the hyperresistance. The results are consistent with the age-1 gene product functioning as a negative regulator of SOD and catalase activities. In wild-type and age-1 dauer larvae, elevated levels of SOD activity, but not of catalase activity, were present when compared with young adults. The common increase in SOD activity prompted cloning the C. elegans Cu/Zn SOD gene. Its position on the physical map of the genome was in the region to which the age-1 gene has been genetically mapped, but it is unlikely that a mutation at the SOD locus confers the Age phenotype. Results support the free radical theory of aging by suggesting that the increased resistance to oxidative stress may be among the causes of increased longevity in both strain TJ401 and in ------------------- Key: 1818 Medline: 94022338 Authors: Patel N;Thierry-Mieg D;Mancillas JR Title: Cloning by insertional mutagenesis of a cDNA encoding Caenorhabditis elegans kinesin heavy chain. Citation: Proceedings of the National Academy of Sciences USA 90: 9181-9185 1993 Type: ARTICLE Genes: unc-104 unc-116 Abstract: An additional genetic locus in Caenohabditis elegans, unc-116, was identified in a screen for mutations resulting in defective locomotion. unc-116 was cloned by use of a transposon insertion mutant and the physical and genetic map of the genome. The cDNA sequence predicts an 815 -amino acid protein. Based upon sequence comparison and secondary structure predictions, unc-116 encodes all three domains of the kinesin heavy chain: the motor, stalk, and tail. While the motor and tail domains have a high degree of identity to the equivalent domains of cloned kinesin heavy chains, the rodII domain of the stalk is significantly shorter than those previously reported and is not predicted to form a coiled-coil alpha-helix. Analysis of mutational defects in two C. elegans genes encoding anterograde motor molecules, unc-116 and unc-104, should provide insight into the in vivo functions of these members of the kinesin heavy chain superfamily. ------------------- Key: 1819 Medline: 94019813 Authors: Estevez M;Attisano L;Wrana JL;Albert PS;Massague J;Riddle Title: The daf-4 gene encodes a bone morphogenetic protein receptor controlling C. elegans dauer larva development. Citation: Nature 365: 644-649 1993 Type: ARTICLE Genes: daf-1 daf-4 rol-6 Abstract: THE bone morphogenetic protein (BMP) family is a conserved group of signalling molecules within the transforming growth factor-beta (TGF-beta) superfamily1,2. This group, including the Drosophila decapentaplegic (dpp) protein and the mammalian BMPs, mediates cellular interactions and tissue differentiation during development3,4 . Here we show that a homologue of human BMPs controls a developmental switch in the life cycle of the free-living soil nematode Caenorhabditis elegans. Starvation and overcrowding induce C elegans to form a developmentally arrested, third-stage dauer larva5. The daf-4 gene, which acts to inhibit dauer larva formation and promote growth, encodes a receptor protein kinase similar to the daf-1, activin and TGF-beta receptor serine/threonine kinases. When expressed in monkey COS cells, the daf-4 receptor binds human BMP-2 and BMP-4. The daf-4 receptor is the first to be identified for any growth factor in the BMP family. ------------------- Key: 1820 Medline: 94012977 Authors: Deitiker PR;Epstein HF Title: Thick filament substructures in Caenorhabditis elegans: Evidence for two populations of paramyosin. Citation: Journal of Cell Biology 123: 303-311 1993 Type: ARTICLE Genes: myo-3 unc-15 unc-22 unc-54 Abstract: The thick filaments of the nematode Caenorhabditis elegans contain two myosin heavy chain isoforms A and B and paramyosin, the products of the myo-3, unc-54, and unc-45 genes, respectively. Dissociation of paramyosin from native thick filaments at pH 6.36 shows a biphasic function with respect to NaCl concentration. Electron microscopy of the remaining structures shows 15-nm core structures that label with monoclonal anti-paramyosin antibody at 72.5-nm intervals. Purified core structures also show 72.5 nm repeats by negative staining. Structural analysis of native thick filaments and dissociated structures suggests that the more dissociable paramyosin is removed radially as well as processively from the filament ends. Minor proteins with masses of 20, 28, and 30 kD cosediment stoichiometrically with paramyosin in purified core structures. ------------------- Key: 1821 Medline: 94000833 Authors: Gengyo-Ando K;Kamiya Y;Yamakawa A;Kodaira K;Nishiwaki K;Miwa J;Hori I;Hosono R Title: The C. elegans unc-18 gene encodes a protein expressed in motor neurons. Citation: Neuron 11: 703-711 1993 Type: ARTICLE Genes: cha-1 unc-13 unc-17 unc-18 unc-104 Abstract: The C. elegans unc-18 gene is required to maintain normal acetylcholine levels. We determined the complete structure of an unc-18 cDNA that encodes a protein of 591 highly charged and hydrophilic amino acids. The protein shows sequence similarity with elements of the secretory pathway in the yeast S. cerevisiae. Antibodies raised against a portion of the unc-18-encoded protein (UNC-18) detected a 68 kd soluble antigen on immunoblots and intensely stained all ventral cord motor neurons in situ. These findings suggest that UNC-18 participates in the axonal transport system and influences the acetylcholine flow in motor ------------------- Key: 1822 Medline: 94022363 Authors: Roussell DL;Bennett KL Title: glh-1, a germ-line putative RNA helicase from Caenorhabditis, has 4 zinc fingers. Citation: Proceedings of the National Academy of Sciences USA 90: 9300-9304 1993 Type: ARTICLE Genes: fem-1 fem-3 glh-1 glp-1 glp-4 let-545 Abstract: We have cloned a family of putative RNA helicases from the free-living nematode Caenorhabditis elegans. One of these, a cDNA that we call glh-1, most closely matches in sequence and expression the previously described germ-line helicases PL10 from mouse and vasa from Drosophila. The amino terminus of the predicted protein of glh-1 contains a set of glycine-rich repeats similar in location and sequence to those in the predicted vasa protein. However, unlike all other putative RNA helicases, glh-1 also contains four retroviral-type zinc ringers. The RNA expression pattern of this Caenorhabditis helicase correlates with the presence of germ-line tissue in the parasitic nematode Ascaris lumbricoides var. suum and with the presence of germ cells in wild type and several germ-line mutants of Caenorhabditis. In the germ-fine mutants glp-4 and glp-1, additional larger species of glh-1 RNA exist, which correspond to different adenylylated forms of the glh-1 transcript; these may be specified by motifs in the 3' untranslated region of glh-1 that are similar to adenylylation control elements and nos response elements. ------------------- Key: 1823 Medline: 94022438 Authors: Lichtsteiner S;Tjian R Title: Cloning and properties of the Caenorhabditis elegans TATA-box-binding protein. Citation: Proceedings of the National Academy of Sciences USA 90: 9673-9677 1993 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans has become an organism of choice for the study of developmental processes at the genetic level. We have undertaken to develop an in vitro system to study transcription in C. elegans. As a first step we report here the cloning of the cDNA encoding the C. elegans TATA-box-binding protein (CeTBP). We used ''touchdown PCR'' to generate a specific DNA probe derived from the C-terminal region conserved in all TBP genes cloned to date. Several clones encoding an extended open reading frame were isolated from a phage lambda cDNA library. The complete amino acid sequence of CeTBP deduced from the cDNA reveals a protein of 37 kDa with an extended sequence similarity in the C-terminal region with all other TBP cDNAs sequenced so far. The N-terminal region of CeTBP (amino acids 1-153), however, does not show any homology with TBPs from other organisms. Interestingly, the N-terminal portion of the molecule contains three short direct repeats. Purified recombinant CeTBP binds specifically to the TATA box sequence, interacts with transcription factors TFIIA and TFIIB, and is able to substitute for the MID basal activity when assayed by in vitro transcription in both HeLa and C. elegans nuclear extracts. CeTBP is therefore a basal transcription factor. ------------------- Key: 1824 Medline: 94006564 Authors: Goodwin EB;Okkema PG;Evans TC;Kimble J Title: Translational regulation of tra-2 by its 3' untranslated region controls sexual identity in C. elegans. Citation: Cell 75: 329-339 1993 Type: ARTICLE Genes: act-1 fem-1 fem-2 fem-3 fog-1 fog-2 glp-1 glp-4 her-1 lin-14 myo-1 tra-2 Abstract: C. elegans hermaphrodites make sperm and then oocytes in an otherwise female animal. Gain-of-function mutations in the sex-determining gene tra-2 (tra-2(gf)) transform hermaphrodites into females (spermless hermaphrodites). The tra-2(gf) mutations map to a perfect direct repeat in the 3' untranslated region; each repeat is called a direct repeat element (DRE). Three experiments demonstrate that DREs repress tra-2 at the translational level. First, tra-2(gf) mRNAs are associated with larger polysomes than are their wild-type counterparts. Second, translation of a reporter RNA is inhibited by DREs. Third, disruption of DREs does not increase tra-2 mRNA levels. An RNA binding activity specifically associates with the DREs. We propose that tra-2 translation is inhibited by association of an RNA binding-factor with the DREs and that this translational control is essential for development of C . elegans as a hermaphrodite/male species. ------------------- Key: 1825 Medline: 94019384 Authors: Morgan WR;Greenwald I Title: Two novel transmembrane protein tyrosine kinases expressed during Caenorhabditis elegans hypodermal development. Citation: Molecular and Cellular Biology 13: 7133-7143 1993 Type: ARTICLE Genes: kin-15 kin-16 let-31 let-240 lin-12 rol-6 mnDf59 mnDf67 Abstract: We describe our characterization of kin-15 and kin-16, a tandem pair of homologous Caenorhabditis elegans genes encoding transmembrane protein tyrosine kinases (PTKs) with an unusual structure: the predicted extracellular domain of each putative gene product is only about 50 amino acids, and there are no potential autophosphorylation sites in the C-terminal domain. Using lacZ fusions, we found that kin-15 and kin-16 both appear to be expressed during postembryonic development in the large hypodermal syncytium (hyp7) around the time that specific hypodermal cells fuse with hyp7. kin-15 and kin-16 were positioned on the genetic and physical maps, but extrachromosomal arrays containing wild-type kin-15 and/or kin-16 genes were unable to complement candidate lethal mutations. The results suggest that kin-15 and kin-16 may be specifically involved in cell-cell interactions regulating cell fusions that generate the hypodermis during postembryonic development. ------------------- Key: 1826 Medline: 94123969 Authors: Miller DM;Niemeyer CJ;Chitkara P Title: Dominant unc-37 mutations suppress the movement defect of a homeodomain mutation in unc-4, a neural specificity gene in Caenorhabditis elegans. Citation: Genetics 135: 741-753 1993 Type: ARTICLE Genes: rol-6 unc-4 unc-24 unc-37 unc-76 hDf8 Abstract: The unc-4 gene of Caenorhabditis elegans encodes a homeodomain protein that defines synaptic input to ventral cord motor neurons. unc-4 mutants are unable to crawl backward because VA motor neurons are miswired with synaptic connections normally reserved for their sister cells, the VB motor neurons. These changes in connectivity are not accompanied by any visible effects upon neuronal morphology, which suggests that unc-4 regulates synaptic specificity but not axonal guidance or outgrowth. In an effort to identify other genes in the unc-4 pathway, we have devised a selection scheme for rare mutations that suppress the Unc-4 phenotype. We have isolated four, dominant, extragenic, allele-specific suppressors of unc-4(e2322ts), a temperature sensitive allele with a point mutation in the unc-4 homeodomain. Our data indicate that these suppressors are gain-of-function mutations in the previously identified unc-37 gene. We show that the loss-of-function mutation unc-37(e262) phenocopies the Unc-4 movement defect but does not prevent unc-4 expression or alter VA motor neuron morphology. These findings suggest that unc-37 functions with unc-4 to specify synaptic input to the VA motor neurons. We propose that unc-37 may be regulated by unc-4. Alternatively, unc-37 may encode a gene product that interacts with the unc-4 homeodomain. ------------------- Key: 1827 Medline: 94123970 Authors: Sundaram M;Greenwald I Title: Genetic and phenotypic studies of hypomorphic lin-12 mutants in Caenorhabditis elegans. Citation: Genetics 135: 755-763 1993 Type: ARTICLE Genes: lin-12 qDp3 Abstract: The lin-12 gene of Caenorhabditis elegans is thought to encode a receptor for intercellular signals that specify certain cell fates during development. We describe several alleles of lin-12 that reduce but do not eliminate lin-12 activity (hypomorphic alleles). These alleles cause a novel egg-laying defective (Egl) phenotype in hermaphrodites as well as incompletely penetrant cell fate transformations seen with high penetrance in lin-12 null mutants. Characterization of the Egl phenotype revealed additional roles of lin-12 in the development of the egg-laying system that were not apparent from studying lin-12 null mutants: lin-12 activity is required for proper early vulval morphogenesis as well as for some unknown later aspect of egg-laying system development. Reversion of the Egl phenotype caused by one lin-12 hypomorphic allele was used to identify potential interacting genes as described in the accompanying paper. ------------------- Key: 1828 Medline: 94123971 Authors: Sundaram M;Greenwald I Title: Suppressors of a lin-12 hypomorph define genes that interact with both lin-12 and glp-1 in Caenorhabditis Citation: Genetics 135: 765-783 1993 Type: ARTICLE Genes: daf-11 dpy-5 egl-10 glp-1 int-3 let-334 let-340 let-409 let-412 let-416 let-433 let-434 let-464 lin-12 rol-3 sel-1 sel-9 sel-10 sel-11 srf-8 srf-9 arDf1 ctDf1 itDf2 mDf1 mDf3 sDf4 sDf35 sDf47 sDf57 sDf71 ctDp11 mnDp26 nDp20 Abstract: The lin-12 gene of Caenorhabditis elegans is thought to encode a receptor which mediates cell-cell interactions required to specify certain cell fates. Reversion of the egg-laying defective phenotype caused by a hypomorphic lin-12 allele identified rare extragenic suppressor mutations in five genes, sel-1, sel-9, sel-10, sel-11 and sel(ar40) (sel = suppressor and/or enhancer of lin-12). Mutations in each of these sel genes suppress defects associated with reduced lin-12 activity, and enhance at least one defect associated with elevated lin-12 activity. None of the sel mutations cause any obvious phenotype in a wild-type background. Gene dosage experiments suggest that sel-1 and sel(ar40) mutations are reduction-of-function mutations, while sel-9 and sel-11 mutations are gain-of-function mutations. sel-1, sel-9, sel-11 and sel(ar40) mutations do not suppress amorphic lin-12 alleles, while sel-10 mutations are able to bypass partially the requirement for lin-12 activity in at least one cell fate decision. sel-1, sel-9, sel-10, sel-11 and sel(ar40) mutations are also able to suppress the maternal-effect lethality caused by a partial loss-of-function allele of glp-1, a gene that is both structurally and functionally related to lin-12. These sel genes may therefore function in both lin-12 and glp-1 ------------------- Key: 1829 Medline: 94244473 Authors: Mitani S;Du H;Hall D;Driscoll M;Chalfie M Title: Combinatorial control of touch receptor neuron expression in Caenorhabditis elegans. Citation: Development 119: 773-783 1993 Type: ARTICLE Genes: ced-3 ced-4 dpy-11 egl-5 egl-44 egl-46 lin-1 lin-3 lin-4 lin-5 lin-7 lin-13 lin-14 lin-15 lin-19 lin-22 lin-26 lin-28 lin-29 lin-30 lin-31 lin-32 lin-33 lin-37 lin-39 lin-44 mab-5 mec-3 mec-4 mec-7 mec-17 sem-4 unc-59 unc-61 unc-86 vab-3 Abstract: Six touch receptor neurons with distinctive morphological features sense gentle touch in Caenorhabditis elegans. Previous studies have identified three genes (lin-32, unc-86 aad mec-3) that regulate touch cell development. However, since other cell types also require these genes, we suspected that other genes help restrict the expression of touch cell characteristics to the six neurons seen in the wild type. To identify such genes, we have examined mutants defective in genes required for the development of other C. elegans cells for changes in the pattern of touch cell-specific features. Mutations in seven genes either reduce (lin-14) or increase (lin-4, egl-44, egl-46, sem-4, ced-3 and ced-4) the number of touch receptorlike cells. The combinatorial action of these genes, all of which are required for the production of many cell types, restrict the number of cells expressing touch receptor characteristics in wild-type animals by acting as positive and negative regulators and by removing cells by programmed ------------------- Key: 1830 Medline: 94061982 Authors: Yuan J;Shaham S;Ledoux S;Ellis HM;Horvitz HR Title: The C. elegans cell death gene ced-3 encodes a protein similar to mammalian interleukin-1B-converting enzyme. Citation: Cell 75: 641-652 1993 Type: ARTICLE Genes: ced-1 ced-3 ced-4 unc-31 Abstract: We have cloned the C. elegans cell death gene ced-3. A ced-3 transcript is most abundant during embryogenesis, the stage during which most programmed cell deaths occur. The predicted CED-3 protein shows similarity to human and murine interleukin-1 beta-converting enzyme and to the product of the mouse nedd-2 gene, which is expressed in the embryonic brain. The sequences of 12 ced-3 mutations as well as the sequences of ced-3 genes from two related nematode species identify sites of potential functional importance. We propose that the CED-3 protein acts as a cysteine protease in the initiation of programmed cell death in C. elegans and that cysteine proteases also function in programmed cell death in mammals. ------------------- Key: 1831 Medline: 94061983 Authors: Miura M;Zhu H;Rotello R;Hartwieg EA;Yuan JY Title: Induction of apoptosis in fibroblasts by IL-1B-converting enzyme, a mammalian homolog of the C. elegans cell death gene ced-3. Citation: Cell 75: 653-660 1993 Type: ARTICLE Genes: ced-3 fem-1 glp-1 hlh-1 lin-12 Abstract: The mammalian interleukin-1 beta-converting enzyme (ICE) has sequence similarity to the C. elegans cell death gene ced-3. We show here that overexpression of the murine ICE (mICE) gene or of the C. elegans ced-3 gene causes Rat-1 cells to undergo programmed cell death. Point mutations in a region homologous between mICE and CED-3 eliminate the ability of mICE and ced-3 to cause cell death. The cell death caused by mICE can be suppressed by overexpression of the crmA gene, a specific inhibitor of ICE, as well as by bcl-2, a mammalian oncogene that can act to prevent programmed cell death. Our results suggest that ICE may function during mammalian development to cause programmed ------------------- Key: 1832 Medline: 94140073 Authors: Ebert RH;Cherkasova VA;Dennis RA;Wu JH;Ruggles S;Perrin TE;Reis RJS Title: Longevity-determining genes in Caenorhabditis elegans: chromosomal mapping of multiple noninteractive loci. Citation: Genetics 135: 1003-1010 1993 Type: ARTICLE Genes: age-1 sod-1 unc-22 unc-54 Abstract: We have used chromosome mapping with polymorphic markers to define genetic components governing life span in the nematode Caenorhabditis elegans. A complex recombinant-inbred population was derived from an interstrain cross, yielding gt 1000 genotypes, each a composite of homozygous segments from the two parental strains. Genotypes were analyzed for the last-surviving 1-5% of worms in aging cohorts, and for young controls, by multiplex polymerase chain reaction using polymorphic markers to distinguish the parental alleles. We identified five regions of the genome at which one parental allele was significantly enriched in long-lived subpopulations. At four of five loci, the same alleles were selected in aging cohorts maintained under two different conditions, implying that these genes determine life span in differing environments. ------------------- Key: 1833 Medline: 94140074 Authors: Maine EM;Kimble J Title: Suppressors of glp-1, a gene required for cell communication during development in Caenorhabditis elegans, define a set of interacting genes. Citation: Genetics 135: 1011-1022 1993 Type: ARTICLE Genes: fem-1 fem-2 fog-1 gld-1 glp-1 lin-12 sel-2 smg-1 sog-1 sog-2 sog-3 sog-4 sog-5 sog-6 sog-7 sog-8 sog-9 sog-10 eDf18 eDf19 nDf11 nDf25 nDp4 ozDf5 sDf35 Abstract: The glp-1 gene is essential for two cell interactions that control cell fate in Caenorhabditis elegans induction of anterior pharynx in the embryo and induction of mitotic proliferation in the germ line. To identify other genes involved in these cell interactions, we have isolated suppressors of two temperature sensitive alleles of glp-1. Each of 14 recessive suppressors rescues both embryonic and germline glp-1(ts) defects. These suppressors are extragenic and define a set of six genes designated sog, for suppressor of glp-1. Suppression of glp-1 is the only obvious phenotype associated with sog mutations. Mutations in different sog genes show allele-specific intergenic noncomplementation, suggesting that the sog gene products may interact. In addition, we have analyzed a semidominant mutation that suppresses only the glp-1 germline phenotype and has a conditional feminized phenotype of its own. None of the suppressors rescues a glp-1 null mutation and therefore they do not bypass a requirement for glp-1. Distal tip cell function remains necessary for germline proliferation in suppressed animals. These suppressor mutations identify genes that may encode other components of the glp-1 mediated cell-signaling pathway or regulate ------------------- Key: 1834 Medline: 94140075 Authors: Lissemore JL;Currie PD;Turk CM;Maine EM Title: Intragenic dominant suppressors of glp-1, a gene essential for cell-signaling in Caenorhabditis elegans, support a role for cdc10/SW16/Ankyrin motifs in GLP-1 function. Citation: Genetics 135: 1023-1034 1993 Type: ARTICLE Genes: glp-1 lin-12 Abstract: The glp-1 gene product mediates cell-cell interactions required for cell fate specification during development in Caenorhabditis elegans. To identify genes that interact with glp-1, we screened for dominant suppressors of two temperature-sensitive glp-1 alleles and recovered 18 mutations that suppress both germline and embryonic glp-1 phenotypes. These dominant suppressors are tightly linked to glp-1 and do not bypass the requirement for a distal tip cell, which is thought to be the source of a signal that is received and transduced by the GLP-1 protein. Using single-strand conformation polymorphism (SSCP) analysis and DNA sequencing, we found that at least 17 suppressors are second-site intragenic revertants. The suppressors, like the original glp-1(ts) mutations, are all located in the cdc10/SW16/ankyrin domain of GLP-1. cdc10/SW16/ankyrin motifs have been shown to mediate specific protein-protein interactions in other polypeptides. We propose that the glp-1(ts) mutations disrupt contact between GLP-1 and an as yet unidentified target protein(s) and that the dominant suppressor mutations restore appropriate protein-protein interactions. ------------------- Key: 1835 Medline: 94140076 Authors: Kramer JM;Johnson JJ Title: Analysis of mutations in the sqt-1 and rol-6 collagen genes of Caenorhabditis elegans. Citation: Genetics 135: 1035-1045 1993 Type: ARTICLE Genes: col-1 col-2 col-6 col-7 col-8 col-12 col-13 col-14 col-19 col-36 col-40 daf-2 dpy-2 dpy-7 dpy-10 dpy-13 glp-1 mup-1 rol-6 sqt-1 mnDf45 mnDf80 Abstract: Different mutations in the sqt-1 and rol-6 collagen genes of Caenorhabditis elegans can cause diverse changes in body morphology and display different genetic attributes. We have determined the nucleotide alterations in 15 mutant alleles of these genes. Three mutations in sqt-1 and one in rol-6 that cause dominant right-handed helical twisting (RRol) of animals are arginine to cysteine replacements. These mutations are all within a short conserved sequence, on the amino terminal side of the Gly-X-Y repeats, that is found in all C. elegans cuticle collagens. A recessive RRol mutation of rol-6 is a replacement of one of the same conserved arginines by histidine. In contrast, three sqt-1 mutations that cause recessive left-handed helical twisting (LRol) are replacements of a conserved carboxy-terminal cysteine residue with either tyrosine or serine. These results suggest that disulfide bonding is important in collagen organization and that a deficit or surplus of disulfides may cause cuticle alterations of opposite handedness. In contrast to other collagens, glycine replacement mutations in the Gly-X-Y repeats of sqt-1 cause very mild phenotypes. Nonsense mutations of both sqt-1 and rol-6 cause nearly, but not totally, wild-type phenotypes. A nonsense mutation in sqt-1 suppresses the phenotype of rol-6 RRol mutations, suggesting that rol-6 collagen function is dependent on the presence of sqt-1 collagen. Mutations of sqt-1 are not suppressed by a rol-6 nonsense mutation, however, indicating that sqt-1 collagen can ------------------- Key: 1836 Medline: 94040732 Authors: Garriga G;Guenther C;Horvitz HR Title: Migrations of the Caenorhabditis elegans HSNs are regulated by egl-43, a gene encoding two zinc finger proteins. Citation: Genes & Development 7: 2097-2109 1993 Type: ARTICLE Genes: egl-5 egl-43 let-242 lin-39 mab-5 mnDf14 mnDf22 mnDf24 mnDf25 mnDf26 mnDf28 mnDf56 mnDf60 Abstract: During embryonic development, the two Caenorhabditis elegans HSN motor neurons migrate from their birthplace in the tail to positions near the middle of the embryo. Here, we demonstrate that of all cells that undergo long-range migrations, only the HSNs are affected in animals that lack function of the egl-43 gene. We also show that egl-43 function is required for normal development of phasmid neurons, which are sensory neurons located in the tail. The egl-43 gene encodes two proteins containing zinc finger motifs that are similar to the zinc fingers of the murine Evi-1 proto-oncoprotein. Our genetic and molecular results suggest that egl-43 encodes two transcription factors and acts to control HSN migration and phasmid neuron development, presumably by regulating other genes that function directly in these processes. ------------------- Key: 1837 Medline: 94067343 Authors: Kenyon C;Chang J;Gensch E;Rudner A;Tabtiang R Title: A C. elegans mutant that lives twice as long as wild type. Citation: Nature 366: 461-464 1993 Type: ARTICLE Genes: daf-2 daf-7 daf-11 daf-14 daf-16 fem-3 spe-26 Abstract: We have found that mutations in the gene daf-2 can cause fertile, active, adult Caenorhabditis elegans hermaphrodites to live more than twice as long as wild type. This lifespan extension, the largest yet reported in any organism, requires the activity of a second gene, daf-16. Both genes also regulate formation of the dauer larva, a developmentally arrested larval form that is induced by crowding and starvation and is very long-lived. Our findings raise the possibility that the longevity of the dauer is not simply a consequence of its arrested growth, but instead results from a regulated lifespan extension mechanism that can be uncoupled from other aspects of dauer formation. daf-2 and daf-16 provide entry points into understanding how lifespan can be extended. ------------------- Key: 1838 Medline: 94067333 Authors: Partridge L;Harvey PH Title: Methuselah among nematodes. Citation: Nature 366: 404-405 1993 Type: REVIEW Genes: daf-2 Abstract: Myth and literature have given human immortality mixed reviews. There is, nonetheless, fairly general agreement that intimations of mortality, in the form of ageing or senescence, are regrettable and should be postponed as long as possible. On page 461 of this issue, Kenyon and co-workers report a mutation of the nematode worm Caenorahbditis elegans that more than doubles its healthy and fertile adult lifespan. ------------------- Key: 1839 Medline: 94080017 Authors: Waddle JA;Cooper JA;Waterston RH Title: The alpha and beta subunits of nematode actin capping protein function in yeast. Citation: Molecular Biology of the Cell 4: 907-917 1993 Type: ARTICLE Genes: cap-1 cap-2 deb-2 unc-4 unc-24 Abstract: We cloned and analyzed two genes, cap-1 and cap-2, which encode the alpha and beta subunits of Caenorhabditis elegans capping protein (CP). The nematode CP subunits are 55% (cap-1) and 66% (cap-2) identical to the chicken CP subunits and 32% (cap-1) and 48% (cap-2) identical to the yeast CP subunits. Purified nematode CP made by expression of both subunits in yeast is functionally similar to chicken skeletal muscle CP in two different actin polymerization assays. The abnormal cell morphology and disorganized actin cytoskeleton of yeast CP null mutants are restored to wild-type by expression of the nematode CP subunits. Expression of the nematode CP alpha or beta subunit is sufficient to restore viability to yeast cap1 sac6 or cap2 sac6 double mutants, respectively. Therefore, despite evolution of the nematode actin cytoskeleton to a state far more complex than that of yeast, one important component can function in both organisms. ------------------- Key: 1840 Medline: 89144971 Authors: Kagawa H;Gengyo K Title: Antigenic sites of the muscle protein, paramyosin, in Caenorhabditis elegans determined with exon-expression plasmid. Citation: Nucleic Acids Symp Ser 19: 81-84 1988 Type: ARTICLE Genes: unc-15 Abstract: Sonicated and restricted DNA fragments from plasmid clones containing the paramyosin gene, unc-15 in C. elegans were recloned into lac-z expression plasmid vectors. Numerous fragments were recovered which encoded paramyosin epitopes. These clones produced fusion protein which cross-reacted with a polyclonal and three monoclonal antibodies. The samples of sonicated fragments were also used for shot gun sequencing of the gene. Sequenced fragments were aligned with a computer analysis. Amino acid sequence of the expressed clones matched exactly to that of the exon. ------------------- Key: 1841 Medline: 89362486 Authors: Zucker-Aprison E;Blumenthal T Title: Potential regulatory elements of nematode vitellogenin genes revealed by interspecies sequence comparison. Citation: Journal of Molecular Evolution 28: 487-496 1989 Type: ARTICLE Genes: uvt-1 vit-1 vit-2 vit-3 vit-4 vit-5 vit-6 Abstract: The nematode, Caenorhabditis elegans, has a six-member gene family encoding vitellogenins, the yolk protein precursors. These genes are expressed exclusively in the intestine of the adult hermaphrodite. Here we report the cloning of all five members of the homologous gene family from another Caenorhabditis species, Caenorhabditis briggsae. Nucleotide sequence analysis of these genes reveals they are about 85% identical to the C. elegans genes in the coding regions. Overall similarity is much reduced in noncoding and flanking regions. However, two repeated heptamers, previously identified in the upstream regions of the C. elegans genes, are largely conserved in both location and sequence in C. briggsae. Conservation of certain of these heptamers suggests that proteins bound at these positions may be especially important to promoter function and/or regulation. Comparative sequence analysis also suggests the possibility that the first 70 bases of the vitellogenin mRNAs can be folded into stable secondary structures. Almost all base differences between the two species occur in sequences predicted to be unpaired, suggesting that the ability to form intrastrand base pairs has been selected during Caenorhabditis evolution. ------------------- Key: 1842 Medline: 85184479 Authors: Hodgkin J Title: Switch genes and sex determination in the nematode C. elegans. Citation: Journal of Embryology & Experimental Morphology 83: 103-117 1984 Type: REVIEW Genes: ced-3 dpy-21 fem-1 fem-2 fem-3 her-1 lin-12 lin-14 lin-28 mab-9 tra-1 tra-2 tra-3 Abstract: The development of the nematode C. elegans is highly invariant, and has been described in great detail. Many developmental mutations have been isolated and analysed; some of these identify switch genes, i.e. genes that control the choice between two developmental alternatives. It appears that the genetic controls of development in this animal are discrete, hierarchical and relatively simple. The control of sexual dimorphism provides an example of how a series of switch genes are organized in a regulatory cascade. ------------------- Key: 1843 Medline: 88296888 Authors: Latchman DS Title: A potential role for U1 RNA genes in gene duplication and conversion events. Citation: FEBS Letters 236: 5-8 1988 Type: ARTICLE Genes: Abstract: A gene encoding U1 snRNA has been identified in Caenorhabditis elegans by homology to the human U1 gene. The gene lies at the boundary of a duplication event also involving the small heat shock protein genes. The possible role of the U1 sequence in mediating the duplication event is discussed. ------------------- Key: 1844 Medline: 92280326 Authors: Bailly F;Gaill F;Mosseri R Title: A dynamical system for biological development: The case of Caenorhabditis elegans. Citation: Acta Biotheoretica 39: 167-184 1991 Type: ARTICLE Genes: Abstract: We show how a simple nonlinear dynamical system (the discrete quadratic iteration on the unit segment) can be the basis for modelling the embryogenesis process. Such an approach, even though being crude, can nevertheless prove to be useful when looking with the two main involved processes: (i) on one hand the cell proliferation under successive divisions; (ii) on the other hand, the differentiation between cell lineages. We illustrate this new approach in the case of Caenrhabditis elegans by looking at the early stages of embryogenesis, up to several hundreds of cells ("lima bean" larval stage). We show how the many results that have been obtained by several groups can be interpreted in terms of values for the parameters controlling the dynamical system. Furthermore, we can extend the model to the cases of genetic mutations. More precisely the teratogenetic and lethal effects are associated with abnormal variation of the control ------------------- Key: 1845 Medline: 88174732 Authors: Felsenstein KM;Emmons SW Title: Nematode repetitive DNA with ARS and segregation function in Saccaromyces cerevisiae. Citation: Molecular and Cellular Biology 8: 875-883 1988 Type: ARTICLE Genes: Abstract: Several members of a repetitive DNA family in the nematode Caenorhabditis elegans have been shown to express ARS and centromeric function in Saccharomyces cerevisiae. The repetitive family, denoted CeRep3, consists of dispersed repeated elements about 1 kilobase in length, present 50 to 100 times in the nematode genome. Three elements were sequenced and found to contain DNA sequences homologous to yeast ARS and CEN consensus sequences. Nematode DNA segments containing these repeats were tested for ARS and CEN (or SEG) function after ligation to shuttle vectors and introduction into yeast cells. Such nematode segments conferred ARS function to the plasmid, as judged by an increased frequency of transformation compared with control plasmids without ARS function. Some, but not all, also conferred to the plasmid increased mitotic stability, increased frequency of 2+:2- segregation in meiosis, and decreased plasmid copy number. These effects are similar to those of yeast centromeric DNA. In view of these results, we suggest that the CeRep3 repetitive family may have replication and centromeric functions in C. elegans. ------------------- Key: 1846 Medline: 91006037 Authors: Okimoto R;Wolstenholme DR Title: A set of tRNAs that lack either the T psi C arm or the dihydrouridine arm: Towards a minimal tRNA adaptor. Citation: EMBO Journal 9: 3405-3411 1990 Type: ARTICLE Genes: Abstract: The mitochondrial DNA (mtDNA) molecules of the nematode worms, Caenorhabditis elegans and Ascaris suum contain 22 putative genes for non-standard forms of tRNAs. The inferred transcripts can be folded into 20 separate structures each resembling a tRNA whose T psi C arm and variable loop are replaced with a simple loop of 6-12 nucleotides. In two further structures [that resemble tRNAs for ser(UCN) and ser(AGN)], the dihydrouridine arm is replaced by a loop of 5-8 nucleotides. By hybridizing mt-tRNA gene-specific oligonucleotide probes to nematode RNAs, we have obtained evidence for transcription of at least nine C.elegans and three A.suum mt-tRNA genes. Each transcript (tRNA) is the exact size predicted from the respective DNA sequence, to which three nucleotides, presumably CCA, have been added following transcription. An exception was C.elegans mt-tRNAasn, most molecules of which had one nucleotide (plus CCA) more than predicted from the gene. The data presented strongly support the conclusion that the functional mt-tRNAs of nematode worms are direct transcripts (with only CCA addition) of the structurally unusual mt-tRNA genes. There is no evidence of trans-splicing or RNA editing to add the sequences missing from these nonstandard tRNAs. We presume, therefore, that the non-standard forms are active in mitochondrial protein ------------------- Key: 1847 Medline: 94132786 Authors: Walthall WW;Li L; Plunkett JA;Hsu CY Title: Changing synaptic specificities in the nervous system of Caenorhabditis elegans: Differentiation of the DD motoneurons. Citation: Journal of Neurobiology 24: 1589-1599 1993 Type: ARTICLE Genes: dpy-18 spe-6 unc-4 unc-25 unc-30 unc-123 Abstract: During postembryonic development, the DD motoneurons in the nematode Caenorhabditis elegans completely reorganize their pattern of synapses. Ablation of a pair of embryonic precursors results in the absence of this entire class of motoneurons. In their absence animals exhibit two developmentally distinct locomotory defects. The transition period from one defect to the other is correlated with the synaptic reorganization of the DD mns. Mutations in a gene (unc-123) have been isolated that exhibit locomotory defects similar to those of the ablated adult animals. Genetic and cellular analyses of one of these alleles suggest that the unc-123 gene product may be involved in the reestablishment of functional synapses in these ------------------- Key: 1848 Medline: 94073964 Authors: Lee RC;Feinbaum RL;Ambros V Title: The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Citation: Cell 75: 843-854 1993 Type: ARTICLE Genes: bli-3 dpy-10 lin-4 lin-14 mnC1 Abstract: lin-4 is essential for the normal temporal control of diverse postembryonic developmental events in C. elegans. lin-4 acts by negatively regulating the level of LIN-14 protein, creating a temporal decrease in LIN-14 protein starting in the first larval stage (L1). We have cloned the C. elegans lin-4 locus by chromosomal walking and transformation rescue. We used the C. elegans clone to isolate the gene from three other Caenorhabditis species; all four Caenorhabditis clones functionally rescue the lin-4 null allele of C. elegans. Comparison of the lin-4 genomic sequence from these four species and site-directed mutagenesis of potential open reading frames indicated that lin-4 does not encode a protein. Two small lin-4 transcripts of approximately 22 and 61 nt were identified in C. elegans and found to contain sequences complementary to a repeated sequence element in the 3' untranslated region (UTR) of lin-14 mRNA, suggesting that lin-4 regulates lin-14 translation via an antisense RNA-RNA ------------------- Key: 1849 Medline: 94073965 Authors: Wightman B;Ha I;Ruvkun G Title: Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Citation: Cell 75: 855-862 1993 Type: ARTICLE Genes: col-10 lin-4 lin-14 myo-1 rol-6 unc-54 Abstract: During C. elegans development, the temporal pattern of many cell lineages is specified by graded activity of the heterochronic gene Lin-14. Here we demonstrate that a temporal gradient in Lin-14 protein is generated posttranscriptionally by multiple elements in the lin-14 3'UTR that are regulated by the heterochronic gene Lin-4. The lin-14 3'UTR is both necessary and sufficient to confer lin-4-mediated posttranscriptional temporal regulation. The function of the lin-14 3'UTR is conserved between C. elegans and C. briggsae. Among the conserved sequences are seven elements that are each complementary to the lin-4 RNAs. A reporter gene bearing three of these elements shows partial temporal gradient activity. These data suggest a molecular mechanism for Lin-14p temporal gradient formation: the lin-4 RNAs base pair to sites in the lin-14 3'UTR to form multiple RNA duplexes that down-regulate ------------------- Key: 1850 Medline: 94010305 Authors: Stone S;Shaw JE Title: A Caenorhabditis elegans act-4-lacZ fusion - Use as a transformation marker and analysis of tissue-specific expression. Citation: Gene 131: 167-173 1993 Type: ARTICLE Genes: act-4 rol-6 smg-2 Abstract: A plasmid vector that serves as a dominant marker for isolating transformed animals in Caenorhabditis elegans has been constructed as a translational fusion of the C. elegans act-4 gene (encoding actin) and the Escherichia coli lacZ gene. This gene fusion can be used as a marker in transformation rescue experiments in any fertile strain of C. elegans. Progeny of animals injected with the act-4=lacZ fusion vector are stained histochemically with XGa1, and transformants turn blue. The internal eggs of stained animals remain viable, allowing recovery of the transformed strain. When the act-4=lacZ vector is co-injected with an unselected plasmid with which it shares some sequence homology, most transformants that are recovered by screening for expression of the act-4=lacZ fusion contain both plasmids. Production of active betaGal in animals transformed with the act-4=lacZ gene fusions appears to be limited to certain tissues. A chimeric gene that contains the 5' and 3' regions of act-4 is expressed strongly in the body-wall muscles, vulval muscles, and spermathecae. Addition of the internal portion of act-4, including the protein-coding region and introns, to this chimeric gene leads to additional lacZ expression in the pharynx. ------------------- Key: 1851 Medline: 94139548 Authors: Fitzgerald K;Wilkinson HA;Greenwald I Title: glp-1 can substitute for lin-12 in specifying cell fate decisions in Caenorhabditis elegans. Citation: Development 119: 1019-1027 1993 Type: ARTICLE Genes: glp-1 lin-11 lin-12 Abstract: Members of the lin-12/Notch gene family encode receptors for intercellular signals and are found throughout the animal kingdom. In many animals, the presence of at least two lin-12/Notch genes raises the issue of the significance of this duplication and divergence. In Caenorhabditis elegans, two lin-12/Notch genes, lin-12 and glp-1, encode proteins that are 50% identical, with different numbers of epidermal growth factor-like motifs in their extracellular domains. Many of the cell fate decisions mediated by lin-12 and glp-1 are distinct. Here, we express glp-1 protein under the control of lin-12 regulatory sequences in animals lacking endogenous lin-12 activity and find that glp-1 can substitute for lin-12 in mediating cell fate decisions. These results imply that the lin-12 and glp-1 proteins are biochemically interchangeable, sharing common ligand and effector proteins, and that the discrete lin-12 and glp-1 mutant phenotypes result from differential gene expression. In addition, these results suggest that the duplicate lin-12/Notch genes found in vertebrates may also be biochemically interchangeable. ------------------- Key: 1852 Medline: 94186037 Authors: Broverman SA;Meneely PM Title: Meiotic mutants that cause a polar decrease in recombination on the X chromosome in Caenorhabditis Citation: Genetics 136: 119-127 1994 Type: ARTICLE Genes: dpy-3 dpy-6 dpy-20 him-1 him-5 him-8 lin-15 lon-2 rad-4 tra-1 unc-1 unc-2 unc-3 unc-9 unc-18 unc-24 ecDf4 mDf7 Abstract: Recessive mutations in three autosomal genes, him-1, him-5 and him-8, cause high levels of X chromosome nondisjunction in hermaphrodites of Caenorhabditis elegans, with no comparable effect on autosomal disjunction. Each of the mutants has reduced levels of X chromosome recombination, correlating with the increase in nondisjunction. However, normal or elevated levels of recombination occur at the end of the X chromosome hypothesized to contain the pairing region (the left end), with recombination levels decreasing in regions approaching the right end. Thus, both the number and the distribution of X chromosome exchange events are altered in these mutants. As a result, the genetic map of the X chromosome in the him mutants exhibits a clustering of genes due to reduced recombination, a feature characteristic of the genetic map of the autosomes in non-mutant animals. We hypothesize that these him genes are needed for some processive event that initiates near the left end of the X chromosome. ------------------- Key: 1853 Medline: 94186038 Authors: Barbazuk WB;Johnsen RC;Baillie DL Title: The generation and genetic analysis of suppressors of lethal mutations in the Caenorhabditis elegans rol-3(V) Citation: Genetics 136: 129-143 1994 Type: ARTICLE Genes: dpy-1 dpy-4 dpy-5 dpy-10 dpy-13 dpy-17 dpy-18 let-456 lin-14 lin-29 mab-3 mab-5 mab-9 rol-3 sma-2 smg-6 srl-1 srl-2 sqt-1 unc-46 sDf57 eT1 Abstract: The Caenorhabditis elegans rol-3(e754) mutation is a member of a general class of mutations affecting gross morphology, presumably through disruption of the nematode cuticle. Adult worms homozygous for rol-3(e754) exhibit rotation about their long axis associated with a left-hand twisted cuticle, musculature, gut and ventral nerve cord. Our laboratory previously isolated 12 recessive lethal alleles of rol-3. All these lethal alleles cause an arrest in development at either early or mid-larval stages, suggesting that the rol-3 gene product performs an essential developmental function. Furthermore, through the use of the heterochronic mutants lin-14 and lin-29, we have established that the expression of rol-3(e754)'s adult specific visible function is not dependent on the presence of an adult cuticle. In an attempt to understand rol-3's developmental role we sought to identify other genes whose products interact with that of rol-3. Toward this end, we generated eight EMS induced and two gamma irradiation-induced recessive suppressors of the temperature sensitive (ts) mid-larval lethal phenotype of rol-3(s1040ts). These suppressors define two complementation groups srl-1 II and srl-2 III; and, while they suppress the rol-3(s1040) lethality, they do not suppress the adult specific visible rolling phenotype. Furthermore, there is a complex genetic interaction between srl-2 and srl-1 such that srl-2(s2506) fails to complement all srl alleles tested. These results suggest that srl-1 and srl-2 may share a common function and, thus, possibly constitute members of the same gene family. Mutations in both srl-1 and srl-2 produce no obvious hermaphrodite phenotypes in the absence of rol-3(s1040ts); however, males homozygous for either srl-1 or srl-2 display aberrant tail morphology. We present evidence suggesting that the members of srl-2 are not allele specific with respect to their suppression of rol-3 lethality, and that rol-3 may act in some way to influence proper posterior morphogenesis. Finally, based on our genetic analysis of rol-3 and the srl mutations, we present a model whereby the wild-type ------------------- Key: 1854 Medline: 94186039 Authors: Katsura I;Kondo K;Amano T;Ishihara T;Kawakami M Title: Isolation, characterization and epistasis of fluoride-resistant mutants of Caenorhabditis elegans. Citation: Genetics 136: 145-154 1994 Type: ARTICLE Genes: ace-1 ace-2 ace-3 cat-4 cat-6 cha-1 che-11 che-12 daf-1 dpy-9 dpy-11 dpy-13 flr-1 flr-2 flr-3 flr-4 flr-5 let-364 lin-1 mut-5 mut-6 osm-6 sma-1 tpa-1 unc-3 unc-7 unc-9 unc-17 unc-23 unc-46 unc-76 unc-84 ctDf1 mnDf4 mnDf12 mnDf19 mnDf20 mnDf21 mnDf43 sDf20 sDf26 sDf30 sDf35 mnDp1 mnDp9 mnDp25 eT1 nT1 Abstract: We have isolated 13 fluoride-resistant mutants of the nematode Caenorhabditis elegans. All the mutations are recessive and mapped to five genes. Mutants in three of the genes (class 1 genes: flr-1 X,flr-3 IV, and flr-4 X) are resistant to 400 mug/ml NaF. Furthermore, they grow twice as slowly as and have smaller brood size than wild-type worms even in the absence of fluoride ion. In contrast, mutants in the other two genes (class 2 genes: flr-2 V and flr-5 V) are only partially resistant to 400 mug/ml NaF, and they have almost normal growth rates and brood sizes in the absence of fluoride ion. Studies on the phenotypes of double mutants showed that class 2 mutations are epistatic to class 1 mutations concerning growth rate and brood size but hypostatic with respect to fluoride resistance. We propose two models that can explain the epistasis. Since fluoride ion depletes calcium ion, inhibits some protein phosphatases and activates trimeric G-proteins, studies on these mutants may lead to discovery of a new signal transduction system that controls the growth of C. elegans. ------------------- Key: 1855 Medline: Authors: Johnson TE;Hutchinson EW;Tedesco PM;Fabian TJ;Brooks A;Lithgow GJ Title: Cloning age-1, a gene that limits the life of C. elegans. Citation: "New Horizons in Aging Science: Proceedings of the Fourth Asia/Oceania Regional Congress of Gerentology." Univ. of Tokyo Press, Tokyo. : - 1992 Type: ARTICLE Genes: age-1 dpy-10 fer-15 unc-4 Abstract: Mutants in the age-1 gene have life spans that are 70% longer than wild type under various environmental conditions. Here we show that the age-1 gene localizes to chromosome 2 near unc-4 and that the increase in life span is separable from a previously associated decrease in fertility. ------------------- Key: 1856 Medline: 94221915 Authors: Sengupta P;Colbert HA;Kimmel BE;Dwyer N;Bargmann CI Title: The cellular and genetic basis of olfactory responses in Caenorhabditis elegans. Citation: CIBA Foundation Symposia 179: 235-250 1993 Type: REVIEW Genes: deg-1 odr-1 odr-2 odr-3 odr-4 odr-5 odr-7 osm-9 Abstract: The small soil nematode Caenorhabditis elegans has only 302 neurons in its entire nervous system, so it is possible to analyse the functions of individual neurons in the animal's behaviour. We are using behavioural, cellular and genetic analyses of chemotactic responses to find out how olfactory behaviour patterns are generated and regulated. Single chemosensory neurons in C. elegans can recognize several different attractive odorants that are distinguished by the animal. Distinct sets of chemosensory neurons detect high and low concentrations of a single odorant. Odorant responses adapt after prolonged exposure to an odorant; this adaptation is odorant specific and reversible. Mutants with defects in odorant responses have been identified. Some genes appear to be necessary for the development or function of particular kinds of sensory neurons. Other genes have effects that suggest that they participate in odorant reception or signal transduction. ------------------- Key: 1857 Medline: 94138074 Authors: Stern MJ;Marenger LE;Daly RJ;Lowenstein EJ;Kokel M;Batzer A;Olivier P;Pawson T; Schlessinger J Title: The human GRB2 and Drosophila drk genes can functionally replace the Caenorhabditis elegans cell signalling gene sem-5. Citation: Molecular Biology of the Cell 4: 1175-1188 1993 Type: ARTICLE Genes: clr-1 let-23 let-60 lin-3 rol-6 sem-5 Abstract: Mutations in the Caenorhabditis elegans gene sem-5 affect cell signaling processes involved in guiding a class of cell migrations and inducing vulval cell fates. The sem-5 sequence encodes a protein comprised almost exclusively of SH2 and SH3 domains (SH, src homology region) that are found together in many signaling proteins and nonreceptor tyrosine kinases. A human protein, GRB2, was identified by its ability to associate with the activated human epidermal growth factor receptor (hEGFR). The GRB2 and Sem-5 proteins share an identical architecture of their SH2 and SH3 domains and 58% amino acid sequence identity. Here we demonstrate that GRB2 and a Drosophila sem-5-like gene Drk can specifically rescue sem-5 mutants. We also show that Sem-5, like GRB2, can bind to the activated hEGFR in vitro. We further correlate the abilities of several mutant variants of GRB2 and Sem-5 to bind to the hEGFR in vitro with their abilities to functionally replace sem-5 in vivo. These data indicate that GRB2 and Drk are functional homologues of Sem-5 and demonstrate the high degree of conservation of both structure and function between signaling systems throughout evolution. ------------------- Key: 1858 Medline: 94089766 Authors: Daigle I;Li C Title: apl-1, a Caenorhabditis elegans gene encoding a protein related to the human beta-amyloid protein-precursor. Citation: Proceedings of the National Academy of Sciences USA 90: 12045-12049 1993 Type: ARTICLE Genes: apl-1 Abstract: The major component of senile plaques found in the brains of Alzheimer disease patients is the beta-amyloid peptide, which is derived from a larger amyloid precursor protein (APP). Recently, a number of APP and APP-related proteins have been identified in different organisms and constitute the family of APP proteins. We have isolated several cDNAs encoding an APP-related protein in the nematode Caenorhabditis elegans and have designated the corresponding gene as apl-1. The apl-1 transcripts undergo two forms of posttranscriptional modification: trans-splicing and alternative polyadenylylation. In vitro translation of an apl-1 cDNA results in a protein of approximately the expected size. Similar to the Drosophila, human, and mouse APP-related proteins, APL-1 does not appear to contain the beta-amyloid peptide. Because APP-related proteins seem to be conserved through evolution, the apl-1 gene from C. elegans should be important for determining the normal function of human APP. ------------------- Key: 1859 Medline: 94087746 Authors: Fukushige T;Yasuda H;Siddiqui SS Title: Molecular cloning and developmental expression of the alpha-2 tubulin gene of Caenorhabditis elegans. Citation: Journal of Molecular Biology 234: 1290-1300 1993 Type: ARTICLE Genes: Abstract: Alpha tubulin isotypes are encoded by at least four genes designated alpha-1 to alpha-4 in the nematode Caenorhabditis elegans. We describe here, molecular cloning of the alpha-2 tubulin gene, located on chromosome I, that encodes a protein of 449 amino acids that has high homology to human, mouse and Drosophila alpha tubulins, but relatively lower homology to the yeast alpha tubulins. The alpha-2 tubulin gene is trans-spliced to the SL1 leader sequence. Northern analysis shows that the gene is increasingly transcribed during the early (L1-L3) larval stages but has a lower level of transcription in L4 L4 larvae, adults, and embryos. Using an alpha-2-lacZ fusion gene expression in transgenic animals, we show that the gene is expressed in a tissue-specific manner in the intestine, pharyngeal muscle cells, and a subset of neurons which include a class of DB and VB motor neurons in the ventral nerve cord, posterior touch receptor neurons, PLML, PLMR, in the lumbar ganglia; PVT in the pre-anal ganglion, and ALA in the dorsal ganglion in the head. Our results support the notion that tubulin structure may contribute to the functional specialization of microtubules. ------------------- Key: 1860 Medline: 94168462 Authors: Sternberg PW Title: Intercellular signaling and signal-transduction in C. elegans. Citation: Annual Review of Genetics 27: 497-521 1993 Type: REVIEW Genes: ace-1 ace-2 ace-3 daf-1 egl-15 egl-17 fem-1 glp-1 her-1 lag-1 lag-2 let-23 let-60 lev-1 lin-1 lin-2 lin-3 lin-7 lin-8 lin-9 lin-10 lin-12 lin-15 lin-45 mab-5 pal-1 sem-5 sli-1 srf-4 srf-8 srf-9 tra-2 unc-5 unc-6 unc-29 unc-38 unc-40 unc-101 Abstract: ------------------- Key: 1861 Medline: 94076040 Authors: Loer CM;Kenyon CJ Title: Serotonin-deficient mutants and male mating-behavior in the nematode Caenorhabditis elegans. Citation: Journal of Neuroscience 13: 5407-5417 1993 Type: ARTICLE Genes: bas-1 cat-1 cat-4 egl-5 lin-22 lin-39 mab-5 pal-1 unc-29 unc-49 Abstract: Defining a behavior that requires the function of specific neurons in the free-living nematode Caenorhabditis elegans can allow one to screen for mutations that disrupt the specification or function of those neurons. We identified serotonin-immunoreactive neurons required for tail curling or "turning" behavior exhibited by C. elegans males during mating. Males mutant in three different genes that reduce serotonin expression, cat-1, cat-4, and bas-1, exhibited defects in turning behavior similar to those of wild-type males in which these neurons were ablated. The turning defect of cat-4 males was rescued by exogenous serotonin, consistent with the idea that their behavioral defect is caused by a lack of serotonin. While the serotonin-deficient mutants we analyzed shared certain behavioral traits, they were blocked for serotonin synthesis at different steps. Analysis of these and additional serotonin-deficient mutants may help us understand how a neuron controls the expression of a ------------------- Key: 1862 Medline: 94190291 Authors: Thomas JH Title: Chemosensory regulation of development in C. elegans. Citation: BioEssays 15: 791-797 1993 Type: REVIEW Genes: che-2 che-3 che-10 che-11 che-13 daf-1 daf-2 daf-3 daf-4 daf-5 daf-6 daf-7 daf-8 daf-10 daf-11 daf-12 daf-14 daf-21 daf-22 lin-17 osm-1 osm-3 osm-5 osm-6 Abstract: The dauer larva is a specialized third-larval stage of Caenorhabditis elegans that is long-lived and resistant to environmental insult. The dauer larva is formed in response to a high external concentration of a constitutively secreted pheromone. Response to the dauer-inducing pheromone of C. elegans is a promising genetic model for metazoan chemosensory transduction. More than 20 genes have been identified that are required for normal pheromone response. The functions of these genes include production of the pheromone, exposure of sensory neuron endings to the environment, structural and functional integrity of those sensory endings, and the capacity of sensory neurons to make appropriate output. Genetic evidence suggests that two partially redundant sensory pathways act in concert to control dauer formation. At least two classes of chemosensory neurons, ADF and ASI, are implicated in the pheromone response. On the basis of on these findings, a speculative model for the pheromone response is proposed. In this model, the neurons ADF and ASI are pheromone sensors that repress dauer formation in the absence of pheromone and derepress dauer formation in response to pheromone. It is currently unclear whether or not the two genetically defined sensory pathways both act in ADF and ------------------- Key: 1863 Medline: Authors: Arena JP Title: Expression of Caenorahbditis elegans messenger RNA in Xenopus oocytes: A model system to study the mechanism of action of avermectins. Citation: Parasitology Today 10: 35-37 1994 Type: REVIEW Genes: Abstract: It has recently been shown that Xenopus oocytes injected with mRNA from the free-living nematode Caenorhabditis elegans express avermectin-sensitive chloride channels(1). Joseph Arena here reviews whet is known about the mechanism of action of avermectin and how these recent results relate to the mechanism in nematodes. ------------------- Key: 1864 Medline: 94088547 Authors: MacMorris M;Spieth J;Madej C;Lea K;Blumenthal T Title: Analysis of the VPE sequences in the Caenorhabditis elegans vit-2 promoter with extrachromosomal tandem array-containing transgenic strains. Citation: Molecular and Cellular Biology 14: 484-491 1994 Type: ARTICLE Genes: rol-6 sup-7 tra-3 vit-2 vit-6 Abstract: The Caenorhabditis elegans vit genes, encoding vitellogenins, are abundantly expressed in the adult hermaphrodite intestine. Two repeated elements, vit promoter element 1 (VPE1 [TGTCAAT]) and VPE2 (CTGATAA), have been identified in the 5' flanking DNA of each of the vit genes of C. elegans and Caenorhabditis briggsae. These elements have previously been shown to be needed for correctly regulated expression of a vit-2/vit-6 fusion gene in low-copy-number, integrated transgenes. Here we extend the analysis of the function of VPE1 and VPE2 by using transgenic lines carrying large, extrachromosomal arrays of the test genes. The results validate the use of such arrays for transgenic analysis of gene regulation in C. elegans, by confirming previous findings showing that the VPE1 at -45 and both VPE2s are sites of activation. Additional experiments now indicate that when the -45 VPE1 is inverted or replaced by a VPE2, nearly total loss of promoter function results, suggesting that the highly conserved -45 VPE1 plays a unique role in vit-2 promoter function. In contrast, single mutations eliminating the three upstream VPE1s are without effect. However, in combination in double and triple mutants, these upstream VPE1 mutations cause drastic reductions in expression levels. The -150 VPE2 can be replaced by a XhoI site (CTCGAG), and the -90 VPE2 can be eliminated, as long as the overlapping VPE1 is left intact, but when these two replacements are combined, activity is lost. Thus, the promoter must have at least one VPE2 and it must have at least two VPE1s, one at -45 and one additional upstream ------------------- Key: 1865 Medline: Authors: Kawaii S;Yoshizawa Y;Mizutani J Title: Two-dimensional analysis of intracellular ionized calcium in a free-living soil nematode, Caenorhabditis elegans. Citation: Bioscience Biotechnology and Biochemistry 57: 2154-2159 Type: ARTICLE Genes: Abstract: Two-dimensional analysis of [Ca2+]i in the intact body of a free-living soil nematode, Caenorhabditis elegans, was done. The effects of DOPA on the level of [Ca2+]i were measured and compared with the data from microspectrofluorometry. DOPA caused a temporal elevation of [Ca2+]i in the intestinal tract. The pattern of [Ca2+]i transient from image analysis accords well with that from microspectrofluorometry. The subcellular distribution of fura-2 in C. elegans was also examined and it was shown that the fluorescence indicator was mainly in the cytosol fraction. ------------------- Key: 1866 Medline: Authors: Gbewonyo K;Rohrer SP;Lister L;Burgess B;Cully D;Buckland B Title: Large-scale cultivation of the free-living nematode Caenorhabditis elegans. Citation: Bio-Technology 12: 51-54 1994 Type: ARTICLE Genes: Abstract: We describe conditions for reproducible large scale cultivation of the free living nematode, Caenorhabditis elegans, and downstream processing of large quantities of this tissue. We were able to grow and harvest 500 grams of purified worms from a 150-liter bioreactor. Cultivation on this scale was accomplished in three steps by using worms from 50 agar plates as inoculum for 4 liters of liquid media. Mature worms from the 4-liter culture were transferred to 20 liters of fresh liquid media. After three days of incubation, the 20-liter culture was used for inoculation of the 150-liter tank. At the time of harvest, a mixture of developmental stages of worms was present. Healthy, motile, egg-laden adults worms appeared to make up the major portion of the population. Membranes prepared from sucrose purified worms were biologically active in an ivermectin binding assay. The affinity of ivermectin (K(d)) and the density of receptors (B(max)) were comparable to values generated using membranes from worms grown on agar plates. The amount of membrane tissue obtained from the 500 gm worm harvest made it feasible to consider purification to homogeneity of a nematode protein such as the ivermectin receptor, which is not abundant in crude homogenates. In addition, RNA isolated from sucrose purified worms was translated in Xenopus oocytes. Several channel proteins expressed from this RNA have been characterized, including a chloride channel sensitive to ivermectin and glutamate. ------------------- Key: 1867 Medline: 94150577 Authors: Wickens M;Takayama K Title: Deviants - or emissaries. Citation: Nature 367: 17-18 1994 Type: REVIEW Genes: fem-3 lin-4 lin-14 tra-2 Abstract: RNA trespasses in what was once thought to be protein's province. The notion that RNAs can be enzymes, binding specifically to ligands, cofactors and substrates, is now commonplace; yet only a few years ago, these were the sacred acts of proteins. History may be about to repeat itself. Regulatory proteins bind to specific sequences in the genes or messenger RNAs they control, and so determine how much a gene is expressed, in what cells, and when. But why should these regulators have to be protein? Why not RNA? We already know, in bacteria, of RNAs that can control gene expression through remarkably sophisticated mechanisms. Now, two reports in Cell not only identify a tiny, repressing RNA in animal cells, but also show that it acts upon a region of mRNA often thought to be barren and insignificant. Although this could be a rare, deviant case, there is the tantalizing possibility that a new family of regulatory RNAs awaits discovery. ------------------- Key: 1868 Medline: 94116859 Authors: Lee J;Jongeward GD;Sternberg PW Title: unc-101, a gene required for many aspects of Caenorhabditis elegans development and behavior, encodes a clathrin-associated protein. Citation: Genes & Development 8: 60-73 1994 Type: ARTICLE Genes: let-23 let-60 lin-2 lin-3 lin-7 lin-10 lin-45 rol-6 sem-5 unc-101 Abstract: Our genetic analysis indicates that the unc-101 gene of Caenorhabditis elegans is required for many aspects of development and behavior, including negative regulation of vulval differentiation. We have cloned unc-101 and found that it encodes a homolog of the mammalian medium chains of clathrin-associated protein complexes located at the trans-Golgi and the plasma membrane, AP47 and AP50, respectively. Therefore, clathrin-mediated events might contribute to the negative regulation of vulval differentiation. Comparison of sequences, including a full-length sequence of a C. elegans AP50 homolog, reveals that UNC-101 is most closely related to AP47. Mouse AP47 and nematode UNC-101 proteins are functionally equivalent as assayed in transgenic nematodes. We have sequenced the mutant alleles of unc-101 identified in various genetic screens and shown that all but one are deletions or nonsense mutations, suggesting that these alleles severely reduce unc-101 function. ------------------- Key: 1869 Medline: 94131269 Authors: Wu Y;Han M Title: Suppression of activated Let-60 Ras protein defines a role of Caenorhabditis elegans Sur-1 MAP kinase in vulval differentiation. Citation: Genes & Development 8: 147-159 1994 Type: ARTICLE Genes: dpy-17 dpy-27 him-5 let-23 let-60 lin-1 lin-3 lin-15 lin-45 rol-6 sur-1 unc-32 unc-79 unc-93 qC1 nDf11 yDf10 sDp3 Abstract: The let-60 ras gene of Caenorhabditis elegans is one of the key players in a signal transduction pathway that controls the choice between vulval and epidermal differentiation in response to extracellular signals. To identify components acting downstream of let-60 ras in the vulval signaling pathway, we have identified a reduction-of-function mutation in the sur-1 gene that completely suppresses the multivulva phenotype of a hyperactive let-60 ras mutation. About 10% of animals homozygous for the sur-1 mutation also display a specific and intriguing vulval cell lineage defect. In addition, the sur-1 mutation results in a cold-sensitive egg-laying defective phenotype and a partial larval lethal phenotype. We have cloned the sur-1 gene by DNA-mediated transformation and have shown that it encodes a protein similar in overall structure to mammalian MAP kinases (ERKs). The functional homology between Sur-1 MAP kinase and mammalian MAP kinases was also demonstrated by the ability of a rat ERK2 kinase to rescue the sur-1 mutant phenotypes. Genetic double-mutant analyses place sur-1 downstream of let-60 ras but upstream of lin-1 in the vulval signaling pathway. Our results provide further evidence for the extreme conservation of Ras-mediated signaling pathway between worms and humans and for the function of MAP kinases in cell signaling processes that control cell differentiation and animal development. ------------------- Key: 1870 Medline: 94131270 Authors: Lackner MR;Kornfeld K;Miller LM;Horvitz HR;Kim SK Title: A MAP kinase homolog, mpk-1, is involved in ras-mediated induction of vulval cell fates in Caenorhabditis elegans. Citation: Genes & Development 8: 160-173 1994 Type: ARTICLE Genes: dpy-17 let-23 let-60 lin-1 lin-15 lin-31 mpk-1 mpk-2 Abstract: During development of the Caenorhabditis elegans hermaphrodite, the gonadal anchor cell induces nearby Pn.p cells to adopt vulval fates. The response to this signal is mediated by a receptor tyrosine kinase signal transduction pathway that has been remarkably well conserved during metazoan evolution. Because mitogen-activated protein (MAP) kinases are activated by receptor tyrosine kinase pathways in vertebrate cells, we hypothesized that C. elegans MAP kinase homologs may play a role in vulval induction. Two C. elegans MAP kinase genes, mpk-1 and mpk-2 (mpk, MAP kinase), were cloned using degenerate oligonucleotide primers and PCR amplification; in parallel, genes involved in vulval induction were identified by screening for mutations that suppress the vulval defects caused by an activated let-60 ras gene. One such suppressor mutation is an allele of mpk-1. We used a new type of mosaic analysis to show that mpk-1 acts cell autonomously in the Pn.p cells. Our results show that mpk-1 plays an important functional role as an activator in ras-mediated cell ------------------- Key: 1871 Medline: 94150625 Authors: Huang M;Chalfie M Title: Gene interactions affecting mechanosensory transduction in Caenorhabditis elegans. Citation: Nature 367: 467-470 1994 Type: ARTICLE Genes: deg-1 kin-9 mec-1 mec-2 mec-3 mec-4 mec-5 mec-6 mec-7 mec-8 mec-9 mec-10 mec-12 mec-14 mec-15 mec-18 Abstract: Genetic screening has identified a group of mec (mechanosensory) genes that are required for the function of a set of six touch-receptor neurons in the nematode Caenorhabditis elegans1,2. Such genes potentially encode components of the mechanosensory apparatus. We have cloned one of these genes, mec-10, which is a member of the degenerin gene family (genes such as mec-4 and deg-1 (refs 3, 4) that can be mutated to cause neurodegeneration). Because components of an amiloride-sensitive sodium channel (alpha, beta and gammarENaC) from rat6-8 share considerable sequence similarity with the C. elegans genes, it is likely that degenerins may function as channel proteins. Here we show that two degenerin homologues (mec-4 and mec-10) are expressed in the same cells, although each provides a unique function. Based on genetic data of mutations affecting mec-10-induced degeneration, we propose that the products of three genes (mec-4, mec-10 and mec-6) form a complex needed for mechanosensation, and that several other mec genes may be important in regulating the putative ------------------- Key: 1872 Medline: 94150626 Authors: Hong K;Driscoll M Title: A transmembrane domain of the putative channel subunit MEC-4 influences mechanotransduction and neurodegeneration in C. elegans. Citation: Nature 367: 470-473 1994 Type: ARTICLE Genes: deg-1 mec-4 mec-6 mec-7 rol-6 Abstract: Aberrant ion channel activity plays a causative role in several human disorders1-3. Inappropriately regulated channel activity also appears to be the basis for neurodegeneration induced by dominant mutations of Caenorhabditis elegans mec-4 (mec-4(d)), a member of the degenerin gene family postulated to encode a subunit of a mechanosensory channel4. The degenerin gene family has been defined by two C. elegans genes, mec-4 and deg-1 (ref. 5), which can mutate to gain-of-function alleles that induce degeneration of specific groups of neurons. A related mammalian gene, rat alpha-rENaC, induces an amiloride-sensitive Na+ current when introduced to Xenopus oocytes6, strongly suggesting that degenerin genes encode ion channel proteins. Deduced amino-acid sequences of the degenerins include two predicted membrane-spanning domains6,7. Here we show that conserved amino acids within the second membrane-spanning domain (MSDII) are critical for MEC-4 activity and that specific substitutions within MSDII, whether encoded in cis or in trans to a mec-4(d) mutation, block or delay the onset of degeneration. Remarkably, MSDII from two other family members, C. elegans deg-1 (ref. 5) and rat alpha-rENaC (ref. 6), can functionally substitute for MEC-4 MSDII in chimaeric proteins. Our results support a structural model for a mechanosensory channel in which multiple MEC-4 subunits are oriented such that MSDII lines the channel pore, and a neurodegeneration model in which aberrant ion flow through ------------------- Key: 1873 Medline: 94150615 Authors: Jentsch TJ Title: Trinity of cation channels. Citation: Nature 367: 412-413 1994 Type: NEWS Genes: deg-1 mec-4 mec-6 mec-7 mec-10 unc-105 Abstract: One of the most satisfying moments in science is when different lines of investigation converge to yield a beautiful picture that opens up new perspectives. This happened last year when expression cloning of an epithelial sodium channel subunit revealed that the DNA encoding it was significantly similar in sequence to that of certain nematode genes, mutations in which lead to insensitivity to touch, neurodegeneration or both. Three reports on pages 463, 467 and 470 of this issue now suggest that at least three distinct subunits are used to build channel complexes in both mammals and the nematode Caenorhabditis elegans. Further, the new work provides insights into the relationship between subunit structure and function, and demonstrates a remarkable degree of functional conservation between vertebrates and invertebrates. ------------------- Key: 1874 Medline: Authors: Baird SE;Fitch DH;Emmons SW Title: Caenorhabditis vulgaris sp.n. (Nematoda: Rhabditidae): A necromenic associate of pill bugs and snails. Citation: Nematologica 40: 1-11 1994 Type: ARTICLE Genes: Abstract: Caenorhabditis vulgaris sp.n. (Nematoda: Rhabditidae), a necromenic associate of pill bugs (Armadillidium vulgare and Armadillidium nasatum) and snails (Oxychilus sp.), is described. C. vulgaris is known from two locations, both in the northeastern United States. It is gonochoristic, with males & females equally abundant. Its associations with pill bugs and snails are as dauer juveniles and appear not to be deleterious to the host animal. These associations are not a requisite part of the C. vulgaris life-cycle; cultures of C. vulgaris can be maintained indefinitely if grown on a bacterial lawn. C. vulgaris can be distinguished from other species of Caenorhabditis based on reproductive, molecular and morphological criteria. ------------------- Key: 1875 Medline: 94135230 Authors: Brooks A;Lithgow GJ;Johnson TE Title: Mortality rates in a genetically heterogeneous population of Caenorhabditis elegans. Citation: Science 263: 668-671 1994 Type: ARTICLE Genes: age-1 fer-15 spe-9 Abstract: Age-specific mortality rates in isogenic populations of the nematode Caenorhabditis elegans increase exponentially throughout life. In genetically heterogeneous populations, age-specific mortality increases exponentially until about 17 days and then remains constant until the last death occurs at about 60 days. This period of constant age-specific mortality results from genetic heterogeneity. Subpopulations differ in mean life-span, but they all exhibit near exponential, albeit different, rates of increase in age-specific mortality. Thus, much of the observed heterogeneity in mortality rates later in life could result from genetic heterogeneity and not from an inherent effect of aging. ------------------- Key: 1876 Medline: 94117490 Authors: Chen WN;Blanc J;Lim L Title: Characterization of a promiscuous GTPase-activating protein that has a Bcr-related domain from Caenorhabditis elegans. Citation: Journal of Biological Chemistry 269: 820-823 1994 Type: ARTICLE Genes: let-60 Abstract: Human breakpoint cluster region (bcr) gene product is a member of a group of GTPase-activating proteins that act exclusively on members of the Ras-related Rho subfamily. A complementary DNA was isolated from Caenorhabditis elegans that encoded a polypeptide of 1438 amino acid residues, CeGA-P, which contains a domain with sequence similarity to the COOH-terminal segment (GTPase-activating protein region) of Bcr and other known GTPase-activating proteins of the Rho subfamily. It also contains a ''pleckstrin homology'' motif, present in many signaling proteins including GTPase-activating proteins and nucleotide exchange factors. The Bcr-like domain of CeGAP exhibited activity not only on members of the C. elegans and human Rho subfamily but surprisingly also on C. elegans Ras protein (let-60), human Ras, and Rab3A. CeGA-P is therefore the first GTPase-activating protein acting on Ras-related proteins across different subfamilies. Together with the presence of the pleckstrin homology motif, our finding suggests a central and integrative role for CeGAP in a signaling pathway common to Ras and related proteins. ------------------- Key: 1877 Medline: Authors: Powers TO;Harris TS;Hyman BC Title: Mitochondrial DNA sequence divergence among Meloidogyne incognita, Romanomermis culicivorax, Ascaris suum, and Caenorhabditis elegans. Citation: Journal of Nematology 25: 564-572 1993 Type: ARTICLE Genes: Abstract: Mitochondrial DNA sequences were obtained from the NADH dehydrogenase subunit 3 (ND3), large rRNA, and cytochrome b genes from Meloidogyne incognita and Romanomermis culicivorax. Both species show considerable genetic distance within these same genes when compared with Caenorhabditis elegans or Ascaris suum, two species previously analyzed. Caenorhabditis, Ascaris, and Meloidogyne were selected as representatives of three subclasses in the nematode class Secernentea: Rhabditia, Spiruria, and Diplogasteria, respectively. Romanomermis served as a representative outgroup of the class Adenophorea. The divergence between the phytoparasitic lineage (represented by Meloidogyne) and the three other species is so great that virtually every variable position in these genes appears to have accumulated multiple mutations, obscuring the phytogenetic information obtainable from these comparisons. The 39 and 42% amino acid similarity between the M. incognita and C. elegans ND3 and cytochrome b coding sequences, respectively, are approximately the same as those of C. elegans-mouse comparisons for the same genes (26 and 44%). This discovery calls into question the feasibility of employing cloned C. elegans probes as reagents to isolate phytoparasitic nematode genes. The genetic distance between the phytoparasitic nematode lineage and C. elegans markedly contrasts with the 79% amino acid similarity between C. elegans and A. suum for the same sequences. The molecular data suggest that Caenorhabditis and Ascaris belong to the ------------------- Key: 1878 Medline: Authors: Middendorf PJ;Dusenbery DB Title: Fluoroacetic acid is a potent and specific inhibitor of reproduction in the nematode Caenorhabditis elegans. Citation: Journal of Nematology 25: 573-577 1993 Type: ARTICLE Genes: Abstract: Fluoroacetic acid is known to lead to inhibition of aconitase and block both the Krebs and glyoxylate cycles. In this study, we discovered it to be a potent and specific inhibitor of reproduction in a bioassay using the nematode Caenorhabditis elegans. Fluoroacetic acid added to the growth medium reduced reproduction in the second generation by 50% at concentrations 3,000 times lower than the concentrations that reduced 24-hour survival by 50%. Four concentrations (2, 4, 8, and 17 mM) of fluoroacetic acid were tested thoroughly. At the two lower concentrations, the survival rates were unaffected, and first-generation reproduction was greatly reduced but not completely eliminated. Survival was reduced at the higher concentrations. Malonate, which inhibits the Krebs cycle, and itaconate, which inhibits the glyoxylate cycle, were tested individually and in combination. The combination did not specifically inhibit reproduction, suggesting another mode of action for fluoroacetic acid. Fluoroacetic acid shows promise as a tool in studies requiring age synchrony. ------------------- Key: 1879 Medline: 95010151 Authors: Riemer D;Dodemont H;Weber K Title: A nuclear lamin of the nematode Caenorhabditis elegans with unusual structural features; cDNA cloning and gene organization. Citation: European Journal of Cell Biology 62: 214-223 1993 Type: ARTICLE Genes: Abstract: This report describes the characterization of the nuclear lamin CeLam-1 of the nematode Caenorhabditis elegans by molecular analysis of the corresponding complete cDNA and gene sequences. The primary structure of CeLam-1, representing only the third non-vertebrate lamin sequence currently known, follows essentially the features displayed by the B-type lamins of vertebrates and Drosophila. The nematode lamin shows, however, some exceptional properties. First, it lacks the SPTR sequence in front of the coil 1a domain which constitutes the major mitotic cdc2 kinase phosphorylation site. Second, two prominent deletions occur in the CeLam-1 sequence. One eliminates 14 amino acid residues from the coil 2 domain. A larger deletion of similar to 25 residues results in the shortest lamin tail domain documented so far. The latter corresponds to a region which varies considerably in sequence from highly acidic in vertebrate B-type lamins to rather basic in Drosophila lamin Dm(o). CeLam-1 is encoded by a single 2.3 kb mRNA which is abundantly expressed in mixed-stage worm populations. The 5'-end of the mRNA is generated by trans-splicing to the SL1 leader sequence. The CeLam-1 gene extending over 2.7 kb is located on chromosome I. The gene is composed of 6 exons and 5 short introns, which all interrupt the coding sequence. Surprisingly, none of the intron positions has a counterpart in either the Drosophila lamin Dm(o) or the vertebrate lamin genes. ------------------- Key: 1880 Medline: 94135249 Authors: Barinaga M Title: Cell Suicide: By ICE, not fire. Citation: Science 263: 754-756 1994 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: Like people, cells die in different ways: accident, murder, old age, even suicide. In fact, cellular suicide isn't just a curiosity, it's necessary for the health of the organism. During embryonic development, for example, it helps weed out superfluous nerve cells, as well as immune cells that might attack and damage the body's own tissues. Like a spy-plane pilot who carries a little vial of poison under his seat in case he's captured, cells carry in their nuclei a genetic program for suicide that can be set in motion, should the cell receive orders to self-destruct. Now, after years of eluding researchers, the genes that carry out the suicide program are coming into the light... ------------------- Key: 1881 Medline: 94135254 Authors: Chalfie M;Tu Y;Euskirchen G;Ward WW;Prasher DC Title: Green fluorescent protein as a marker for gene expression. Citation: Science 263: 802-805 1994 Type: ARTICLE Genes: mec-3 mec-7 rol-6 Abstract: A complementary DNA for the Aequorea victoria green fluorescent protein (GFP) produces a fluorescent product when expressed in prokaryotic (Escherichia coli) or eukaryotic (Caenorhabditis elegans) cells. Because exogenous substrates and cofactors are not required for this fluorescence, GFP expression can be used to monitor gene expression and protein localization in living ------------------- Key: 1882 Medline: 94204018 Authors: Peixoto CA;Desouza W Title: Freeze-fracture characterization of the cuticle of adult and dauer forms of Caenorhabditis elegans. Citation: Parasitology Research 80: 53-57 1994 Type: ARTICLE Genes: daf-2 Abstract: At the ultrastructural level, a trilaminate structure, designated as the epicuticle, is always present on the outermost surface of the nematode Caenorhabditis elegans. The freeze-fracture technique revealed the existence of two fracture faces: an inner face that showed homogeneously distributed particles and an outer fracture face that was almost completely smooth in adult nematodes but appeared delicately granular in the dauer forms. ------------------- Key: 1883 Medline: 94155468 Authors: Graham PL;Schedl T;Kimble J Title: More mog genes that influence the switch from spermatogenesis to oogenesis in the hermaphrodite germ-line of Caenorhabditis elegans. Citation: Developmental Genetics 14: 471-484 1993 Type: ARTICLE Genes: fem-1 fem-2 fem-3 fog-1 fog-2 fog-3 her-1 mog-1 mog-2 mog-3 mog-4 mog-5 mog-6 tra-1 tra-2 tra-3 jDf2 jDf4 maDf4 mnDf89 yDf10 Abstract: The Caenorhabditis elegans XX animal possesses a hermaphrodite germ line, producing first sperm, then oocytes. In this paper, we report the genetic identification of five genes, mog-2, mog-3, mog-4, mog-5, and mog-6, that influence the hermaphrodite switch from spermatogenesis to oogenesis. In mog-2-mog-6 mutants, spermatogenesis continues past the time at which hermaphrodites normally switch into oogenesis and no oocytes are observed. Therefore, in these mutants, germ cells are transformed from a female fate (oocyte) to a male fate (sperm). The fem-3 gene is one of five genes that acts at the end of the germline sex determination pathway to direct spermatogenesis. Analyses of mog;fem-3 double mutants suggest that the mog-2-mog-6 genes act before fem-3; thus these genes may be in a position to negatively regulate fem-3 or one of the other terminal regulators of germline sex determination. Double mutants of fem-3 and any one of the meg mutations make oocytes. Using these double mutants, we show that oocytes from any mog;fem-3 double mutant are defective in their ability to support embryogenesis. This maternal effect lethality indicates that each of the meg genes is required for embryogenesis. The two defects in mog-2-mog-6 mutants are similar to those of mog-1: all six meg genes eliminate the sperm/oocyte switch in hermaphrodites and cause maternal effect lethality. We propose that the mog-2-mog-6 mutations identify genes that act with mog-1 to effect the sperm/oocyte switch. We further speculate that the mog-1-mog-6 mutations all interfere with translational controls of fem-3 and other maternal mRNAs. (C) 1993 ------------------- Key: 1884 Medline: 94200595 Authors: Clark-Maguire S;Mains PE Title: mei-1, a gene required for meiotic spindle formation in Caenorhabditis elegans, is a member of a family of ATPases. Citation: Genetics 136: 533-546 1994 Type: ARTICLE Genes: fem-1 fem-3 glp-1 kin-10 kup-2 lin-10 lin-28 mei-1 mei-2 mel-26 zyg-9 gaD1 Abstract: Meiotic spindle formation in the female germline of Caenorhabditis elegans requires expression of the gene mei-1. We have cloned mei-1 by transformation rescue and found that it resides near a hot spot for recombination, in an area of high gene density. The highest levels of mei-1 mRNA accumulate in the female germline of adult hermaphrodites as well as in fertilized embryos. The message persists for several hours after the protein functions in embryos, implying the need for post-transcriptional regulation. Two alternatively spliced messages are made that would result in proteins that differ internally by three amino acids; the larger of the two mRNAs is preferentially enriched in the female germline. The sequence of mei-1 shows that it is a member of a newly described family of ATPases that share a highly conserved nucleotide-binding site; four dominant negative mutations of mei-1 are found at or near this region. Divergent roles ascribed to this family include membrane function, proteolysis, transcription and cell cycle regulation. ------------------- Key: 1885 Medline: 94171012 Authors: Johnson TE;Tedesco PM;Lithgow GJ Title: Comparing mutants, selective breeding, and transgenics in the dissection of aging processes of Caenorhabditis Citation: Genetica 91: 65-77 1993 Type: ARTICLE Genes: age-1 fer-15 rol-6 mnDf63 mnDf89 mnDf91 mnDf92 Abstract: The genetic analysis of aging processes has matured in the last ten years with reports that long-lived strains of both fruit flies and nematodes have been developed. Several attempts to identify mutants in the fruit fly with increased longevity have failed and the reasons for these failures are analyzed. A major problem in obligate sexual species, such as the fruit fly is the presence of inbreeding depression that makes the analysis of life-history traits in homozygotes very difficult. Nevertheless, several successful genetic analyses of aging in Drosophila suggest that with careful design, fruitful analysis of induced mutants affecting life span is possible. In the nematode Caenorhabditis elegans, mutations in the age-1 gene result in a life extension of some 70%; thus age-1 clearly specifies a process involved in organismic senescence. This gene maps to chromosome II, well separated from a locus (fer-15) which is responsible for a large fertility deficit in the original stocks. There is no trade-off between either rate of development or fertility versus life span associated with the age-1 mutation. Transgenic analyses confirm that the fertility deficit can be corrected by a wild-type fer-15 transformant (transgene); however, the life span of these transformed stocks is affected by the transgenic array in an unpredictable fashion. The molecular nature of the age-1 gene remains unknown and we continue in our efforts to ------------------- Key: 1886 Medline: 94128773 Authors: Johnson TE Title: Genetic influences on aging in mammals and invertebrates. Citation: Aging-Clinical and Experimental Research 5: 299-307 1993 Type: REVIEW Genes: age-1 Abstract: A central theme underlies this review: "Genetics offers an important tool for identifying key molecular events that are involved in specifying biological functions." This approach has been used repeatedly to understand such diverse biological phenomena as oncogenesis, development, and the cell cycle, but has only recently been applied to the analysis of organismic aging and senescence. The power of the genetic approach lies in the ability to integrate phenomena that are displayed at multiple observational levels (i.e., from the molecular to the whole organism), and the power to reveal causal factors that are not dependent upon the prejudice of the investigator. I discuss several areas where genetics has been fruitfully applied to the study of the aging processes: human genes identified by "segmental progeroid" mutations; neurological diseases of the elderly; the limited proliferative life span of human somatic cells in tissue culture; studies on the life span of the mouse; and genetic analysis of life span in shorter-lived metazoans (Drosophila melanogaster and Caenorhabditis elegans), and the yeast Saccaromyces cerevisiae. ------------------- Key: 1887 Medline: 94033620 Authors: Fedon Y;Cousin X;Toutant JP;Thierry-Mieg D;Arpagaus M Title: cDNA sequence, gene structure, and cholinesterase-like domains of an esterase from Caenorhabditis mapped to chromosome V. Citation: DNA Sequence 3: 347-356 1993 Type: ARTICLE Genes: ace-1 ace-2 ace-3 ges-1 Abstract: The structure of an esterase gene from Caenorhabditis elegans has been determined by comparison of the sequences in genomic and cDNA clones. The gene was mapped close to the center of chromosome V (1.7 centimorgans to the left of dpy-11) and is therefore distinct from the gut esterase gene ges-1. It possessed 7 short introns. The 5' splice site of intron 3 presented the sequence GC instead of the usual GT that was found in the other six introns. The cDNA was trans-spliced with the short leader SL1. The open reading frame indicated that a protein of 557 aminoacids was encoded. The deduced aminoacid sequence did not present a signal peptide at the N-terminal but a potential N-myristoylation site (GXXXS) provided that the initiator methionine was removed. This protein should therefore remain intracellular. Comparison of this C. elegans sequence to other protein sequences in databases, as well as the analysis of the secondary structure in the protein showed that it belongs to the subgroup of esterases in the alpha/beta hydrolase fold family. ------------------- Key: 1888 Medline: 94022572 Authors: Martin RJ Title: Neuromuscular transmission in nematode parasites and antinematodal drug action. Citation: Pharmacology & Therapeutics 58: 13-50 1993 Type: ARTICLE Genes: Abstract: Some anthelmintic drugs interfere selectively with nematode neuromuscular transmission. These drugs include: the nicotinic agonists, e.g. levamisole, the gamma-amino butyric acid agonist piperazine, and the avermectins which open Cl- channels. The physiology and pharmacology of neuromuscular transmission in nematodes is reviewed and the actions of antinematodal drugs which interfere with the transmission described. The results of experiments on the large porcine-intestinal nematode parasite, Ascaris suum, form the basis of the account presented but experiments on other nematodes suggest that these observations may be generalized. Results of some experiments on the small free living nematode Caenorhabditis elegans are also included. ------------------- Key: 1889 Medline: 94083732 Authors: Niebur E;Erdos P Title: Theory of the locomotion of nematodes: Control of the somatic motor neurons by interneurons. Citation: Mathematical Biosciences 118: 51-82 1993 Type: REVIEW Genes: Abstract: The only animal of which the complete neural circuitry is known at the submicroscopical level is the nematode Caenorhabditis elegans. This anatomical knowledge is complemented by functional insight from electrophysiological experiments in the related nematode Ascaris lumbricoides, which show that Ascaris motor neurons transmit signals electrotonically and not with unattenuated spikes. We developed a mathematical model for electrotonic neural networks and applied it to the motor nervous system of nematodes. This enabled us to reproduce experimental results in Ascaris quantitatively. In particular, our computed result of the velocity v approximately equal to 6 cm/s of neural excitations in the Ascaris interneurons supports the simple hypothesis that the so-called rapidly moving muscular wave is produced by a neural excitation traveling at the same speed in the interneuron as the muscular wave. In C. elegans, the computed velocity v approximately equal to 8-30 cm/s of signals in the interneurons is much larger than the observed velocity v approximately equal to 0.2 cm/s of the body wave. Therefore, the hypothesis that the muscular wave is produced by a synchronous neural excitation wave cannot hold for C. elegans. We argue that stretch receptor control is the most likely mechanism for the generation of body waves used in the locomotion of C. elegans. Extending the simulation to larger groups of neurons, we found that the neural system of C. elegans can operate purely electrotonically. We demonstrate that the same conclusion cannot be drawn for the nervous system of Ascaris, because in the long (l approximately equal to 30 cm) interneurons the electrotonic signals would be too strongly attenuated. This conclusion is not in contradiction with the experimental findings of electrotonic signal propagation in the motor neurons of Ascaris because the latter are shorter ------------------- Key: 1890 Medline: 94144003 Authors: Thomas JH Title: Thinking about genetic redundancy. Citation: Trends in Genetics 9: 395-399 1993 Type: REVIEW Genes: glp-1 lin-12 Abstract: Partial functional redundancy among genes is frequently observed in a wide range of organisms and processes, but the selective value of such redundancy is not immediately apparent. Any fully redundant function should be evolutionarily unstable; unless selection acts to maintain the redundancy it will tend to be lost by mutational drift. I discuss four possible mechanisms by which selection might act to maintain genetic redundancy. ------------------- Key: 1891 Medline: 94156167 Authors: Schein JE;Marra MA;Benian GM;Fields C;Baillie DL Title: The use of deficiencies to determine essential gene content in the let-56 - unc-22 region of Caenorhabditis elegans. Citation: Genome 36: 1148-1156 1993 Type: ARTICLE Genes: let-52 let-56 let-653 unc-22 sDf2 sDf19 sDf65 sDf83 sDf88 Abstract: We have investigated the possibility of using the polymerase chain reaction to detect deletions of coding elements in the unc-22-let-56 interval on chromosome IV in the nematode Caenorhabditis elegans. Our analysis of approximately 13 kb of genomic sequence immediately to the left of the unc-22 gene resulted in the identification of four possible genes. Partial cDNAs have been identified for three of them. To determine whether any of these coding elements are essential for development, we required a method for the induction and selection of mutations in these elements. Our approach was to identify a set of formaldehyde and gamma radiation induced unc-22 mutations that mapped to the unc-22-let-56 region, and then employ polymerase chain reaction methodology to identify deficiencies that affected one or more of the four identified coding elements. Two small deficiencies were identified in this manner. Characterization of these deficiencies shows that there are no coding elements between unc-22 and let-56 (the nearest mutationally identified gene to the left of unc-22), which are required in development under laboratory conditions. We conclude that the polymerase chain reaction is a practical tool for the detection of deletions of coding elements identified in this region, and that characterization of such deficiencies provides a method for assessing whether or not these ------------------- Key: 1892 Medline: 94119712 Authors: Amaar YG;Baillie DL Title: Cloning and characterization of the C. elegans histidyl-tRNA synthetase gene. Citation: Nucleic Acids Research 21: 6050-6051 1993 Type: CORRECT Genes: Abstract: ------------------- Key: 1893 Medline: 94212446 Authors: Burglin TR Title: A Caenorhabditis elegans prospero homologue defines a novel domain. Citation: Trends in Biochemical Sciences 19: 70-71 1994 Type: LETTER Genes: Abstract: The Drosophila gene prospero (pros) encodes a sequence motif with similarity to homeodomains. This homeodomain motif is highly atypical, since it contains three extra residues between helix 2 and helix 3. Furthermore, some usually highly conserved residues are not conserved (for a comparison of atypical homeodomains see Ref. 4). .. ------------------- Key: 1894 Medline: 94149050 Authors: Williams BD;Waterston RH Title: Genes critical for muscle development and function in Caenorhabditis elegans identified through lethal mutations. Citation: Journal of Cell Biology 124: 475-490 1994 Type: ARTICLE Genes: deb-1 emb-9 hlh-1 let-2 lev-11 mec-8 myo-3 pat-2 pat-3 pat-4 pat-5 pat-6 pat-8 pat-9 pat-10 pat-11 pat-12 tra-2 unc-45 unc-52 unc-82 unc-87 unc-94 unc-112 unc-120 zyg-1 mnDf1 mnDf8 mnDp1 mnDp8 nDf41 stDf7 stDf8 Abstract: By taking advantage of a lethal phenotype characteristic of Caenorhabditis elegans embryos that fail to move, we have identified 13 genes required for muscle assembly and function and discovered a new lethal class of alleles for three previously known muscle-affecting genes. By staining mutant embryos for myosin and actin we have recognized five distinct classes of genes: mutations in four genes disrupt the assembly of thick and thin filaments into the myofilament lattice as well as the polarized location of these components to the sarcolemma. Mutations in another three genes also disrupt thick and thin filament assembly, but allow proper polarization of lattice components based on the myosin heavy chain isoform that we analyzed. Another two classes of genes are defined by mutations with principal effects on thick or thin filament assembly into the lattice, but not both. The final class includes three genes in which mutations cause relatively minor defects in lattice assembly. Failure of certain mutants to stain with antibodies to specific muscle cell antigens suggest that two genes associated with severe disruptions of myofilament lattice assembly may code for components of the basement membrane and the sarcolemma that are concentrated where dense bodies (Z-line analogs) and M-lines attach to the cell membrane. Similar evidence suggests that one of the genes associated with mild effects on lattice assembly may code for tropomyosin. Many of the newly identified genes are likely to play critical roles in muscle development and function. ------------------- Key: 1895 Medline: 94149051 Authors: Hresko MC;Williams BD;Waterston RH Title: Assembly of body wall muscle and muscle cell attachment structures in Caenorhabditis elegans. Citation: Journal of Cell Biology 124: 491-506 1994 Type: ARTICLE Genes: act-1 act-2 act-3 act-4 act-5 deb-1 myo-3 pat-3 unc-52 unc-54 Abstract: C. elegans has four muscle quadrants that are used for locomotion. Contraction is converted to locomotion because muscle cells are anchored to the cuticle (the outer covering of the worm) by a specialized basement membrane and hemidesmosome structures in the hypodermis (a cellular syncytium that covers the worm and secretes the cuticle). To study muscle assembly, we have used antibodies to determine the spatial and temporal distribution of muscle and attachment structure components in wild-type and mutant C. elegans embryos. Myofibrillar components are first observed diffusely distributed in the muscle cells, and are expressed in some dividing cells. Later, the components accumulate at the membrane adjacent to the hypodermis where the sarcomeres will form, showing that the cells have become polarized. Assembly of muscle attachment structures is spatially and temporally coordinated with muscle assembly suggesting that important developmental signals may be passed between muscle and hypodermal cells. Analysis of embryos homozygous for mutations that affect muscle assembly show that muscle components closer to the membrane than the affected protein assemble quite well, while those further from the membrane do not. Our results suggest a model where lattice assembly is initiated at the membrane and the spatial organization of the structural elements of the muscle is dictated by membrane proximal events, not by the filament components themselves. ------------------- Key: 1896 Medline: 94039663 Authors: Maizels RM;Blaxter ML;Selkirk ME Title: Forms and functions of nematode surfaces. Citation: Experimental Parasitology 77: 380-384 1993 Type: REVIEW Genes: cut-1 Abstract: Nematodes possess biologically unusual surfaces. The dominant feature is the cuticle, a collagen-rich extracellular matrix which acts as the exoskeleton and is synthesized in the outermost tissue layer of the organism, the epidermis or hypodermis. The cuticle, which may be 1 um or more in depth, has on its external face a lipid-rich epicuticle which in some species resembles a unit membrane. There may be an additional envelope, loosely attached and distal to the epicuticle, in the form of a surface coat or glycocalyx, or as a thin sheath retained by some larval nematodes from previous developmental stages. The organisation of these components is depicted in Fig. 1. Detailed studies of these structures are now becoming available in both parasitic and free-living nematodes such as Caenorhabditis elegans... ------------------- Key: 1897 Medline: 94173670 Authors: van Luenen HGAM;Plasterk RHA Title: Target site choice of the related transposable elements Tc1 and Tc3 of Caenorhabditis elegans. Citation: Nucleic Acids Research 22: 262-269 1994 Type: ARTICLE Genes: gpa-2 nuc-1 rol-6 unc-22 Abstract: We have investigated the target choice of the related transposable elements Tc1 and Tc3 of the nematode C.elegans. The exact locations of 204 independent Tc1 insertions and 166 Tc3 insertions in an 1 kbp region of the genome were determined. There was no phenotypic selection for the insertions. All insertions were into the sequence TA. Both elements have a strong preference for certain positions in the 1 kbp region. Hot sites for integration are not clustered or regularly spaced. The orientation of the integrated transposon has no effect on the distribution pattern. We tested several explanations for the target site preference. If simple structural features of the DNA (e.g. bends) would mark hot sites, we would expect the patterns of the two related transposons Tc1 and Tc3 to be similar; however we found them to be completely different. Furthermore we found that the sequence at the donor site has no effect on the choice of the new insertion site, because the insertion pattern of a transposon that jumps from a transgenic donor site is identical to the insertion pattern of transposons jumping from endogenous genomic donor sites. The most likely explanation for the target choice is therefore that the primary sequence of the target site is recognized by the transposase. However, alignment of the Tc1 and Tc3 integration sites does not reveal a strong consensus sequence for either transposon. ------------------- Key: 1898 Medline: Authors: Kimble J;Schedl T Title: Developmental Genetics of Caenorhabditis elegans. Citation: "Developmental Genetics of Higher Organisms. A Primer in Developmental Biology." G.M. Malacinski (ed), Macmillan Publishing Company, NY, 1988. : 171-192 1988 Type: REVIEW Genes: ced-3 daf-2 dpy-21 fem-1 fem-2 fem-3 fog-1 fog-2 fog-3 glp-1 her-1 lin-12 lin-14 tra-1 tra-2 tra-3 unc-86 Abstract: The development of a multicellular organism from a single-celled egg involves the coordinated control of many cells and tissues. How are cells specified to develop as one cell type rather than another, in one position rather than another, and at one time rather than another? What is the molecular basis of the spatial and temporal cues necessary to direct development of the organism? The information for this developmental feat is stored in the egg-either in its genome or in products of the maternal genome contributed to that cell. Developmental genetics provides a powerful way to investigate that information. The nematode, Caenorhabditis elegans, has proven to be an excellent model organism for analysis of the genes that control development... ------------------- Key: 1899 Medline: 94151334 Authors: Yandell MD;Edgar LG;Wood WB Title: Trimethylpsoralen induces small deletion mutations in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 91: 1381-1385 1994 Type: ARTICLE Genes: pal-1 unc-22 sDf22 Abstract: To examine the mutagenic spectrum of 4,5',8-trimethylpsoralen (TMP) in Caenorhabditis elegans, we isolated mutations in the unc-22 and pal-1 genes following TMP mutagenesis and analyzed them for restriction fragment length polymorphisms by Southern blot. Eleven of 21 unc-22 mutations exhibited restriction fragment length polymorphisms, 8 of which were deletions of between 0.10 and 15 kb in length. Both of two pal-1 mutations were also small deletions within this size range. Comparison of our results with previous studies on mutagenesis by gamma-rays and x-rays suggests that the mutagenic spectrum of TMP may be similar. TMP should be useful in generating mutations that cause complete loss of function of single genes and that are likely to result in allele-specific DNA ------------------- Key: 1900 Medline: 94148122 Authors: Podbilewicz B;White JG Title: Cell fusions in the developing epithelia of C. elegans. Citation: Developmental Biology 161: 408-424 1994 Type: ARTICLE Genes: Abstract: In this paper we characterize the order of hypodermal cell fusions in the Caenorhabditis elegans hermaphrodite. Somatic cell fusions are part of the developmental program of many tissues in a variety of organisms. The formation and remodeling of tissues and organs can be studied at the cellular level in C . elegans . Here we establish a system for studying cell fusion by characterizing somatic cell fusions during morphogenesis in C . elegans . Fusion is a common cell fate in this nematode; numerous epithelial fusions occur in the hypodermis, vulva, uterus, and excretory gland cells (Sulston et al., 1983. Dev. Biol. 100, 64-119). Some but not all pharyngeal muscles also fuse (Albertson and Thomson, 1976. Philos. Trans. R. Soc. London Ser. B 275, 299-325). We have studied the behavior of epithelial adherens junctions before and during cell-to-cell fusions in embryonic and postembryonic development. Our results define the timing and sequence of short-range migrations followed by fusions that generate syncytia. We have made use of an antibody that stains adherens junctions to study the behavior of hypodermal cells during development. Fusion of specific cells in the hypodermis causes rearrangements of the adherens junctions between cells. Fusion events usually start in the anterior part of embryos or larvae. There is some variation in the specific order in which cells fuse, but the final positions, boundaries, and sizes of syncytia are the same. In some cases fusion causes isolation of a mononucleate cell or group of cells by a surrounding, growing syncytium. Our characterization of the order of cell fusions will provide a basis for the identification of molecular events required for regulated membrane fusion during development. ------------------- Key: 1901 Medline: 94249074 Authors: Wood WB;Edgar LG Title: Patterning in the C. elegans embryo. Citation: Trends in Genetics 10: 49-54 1994 Type: REVIEW Genes: ceh-11 ceh-13 ceh-15 egl-5 glp-1 lag-1 lag-2 lin-12 lin-39 mab-5 mex-1 par-1 par-2 par-3 par-4 par-5 pie-1 skn-1 Abstract: Recent studies reveal preliminary insights into the mechanisms of embryonic patterning in Caenorhabditis elegans. It appears that both embryonic axes and early blastomere fates are determined by a combination of segregating determinants and cell interactions, under the control of maternally expressed genes. Later in embryogenesis, some regional identities are specified by a group of homeotic selector genes homologous to the HOM-C clusters in other animals. Intervening stages of specification, which could link these two classes of genes in a regulatory hierarchy, are beginning to be ------------------- Key: 1902 Medline: 94150718 Authors: Wilson R;Ainscough R;Anderson K;Baynes C;Berks M;Burton J;Connell M;Bonfield J;Copsey T;Cooper J Title: 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans. Citation: Nature 368: 32-38 1994 Type: ARTICLE Genes: ceh-11 ceh-13 ceh-15 ceh-16 ceh-23 dpy-19 egl-5 egl-45 emb-9 glp-1 gst-1 lin-9 lin-12 lin-36 lin-39 mab-5 mig-10 ncc-1 sup-5 tbg-1 unc-32 unc-36 unc-86 unc-116 Abstract: As part of our effort to sequence the 100-megabase (Mb) genome of the nematode Caenorhabditis elegans, we have completed the nucleotide sequence of a contiguous 2,181,032 base pairs in the central gene cluster of chromosome III. Analysis of the finished sequence has indicated an average density of about one gene per five kilobases; comparison with the public sequence databases reveals similarities to previously known genes for about one gene in three. In addition, the genomic sequence contains several intriguing features, including putative gene duplications and a variety of other repeats with potential evolutionary ------------------- Key: 1903 Medline: 94123855 Authors: Pettitt J;Kingston IB Title: Developmentally regulated alternative splicing of a nematode type-IV collagen gene. Citation: Developmental Biology 161: 22-29 1994 Type: ARTICLE Genes: let-2 Abstract: A comparison of the genomic DNA sequence that encodes the Ascaris suum alpha2(IV) collagen chain with the corresponding cDNA sequence led to the identification of a putative exon that was not expressed in the cDNA. The identification of this putative exon raised the possibility that transcripts of the alpha2(IV) gene may undergo alternative splicing. We have used a reverse transcriptase-polymerase chain reaction assay to establish that such alternative splicing does indeed occur. Our results show that the A. suum alpha2(IV) collagen gene produces at least two similar, but not identical, transcripts via the selection of two alternative exons. Furthermore, this alternative splicing appears to be developmentally regulated, suggesting that alternative splicing may be used in order to modify the properties of type IV collagen during nematode development. ------------------- Key: 1904 Medline: 94126074 Authors: Egilmez NK;Reis RJS Title: Age-dependent somatic excision of transposable element Tc1 in Caenorhabditis elegans. Citation: Mutation Research 316: 17-24 1994 Type: ARTICLE Genes: unc-13 unc-22 Abstract: The Tc1 element of the free-living nematode Caenorhabditis elegans is a well characterized transposon that is present in 30-500 copies per haploid genome, depending on the strain. Excision of Tc1 elements, which occurs readily in somatic tissues during larval development, has not previously been examined during aging of adult worms. We have identified a recently inserted Tc1 element in the KR1787 mutator strain of C. elegans and have found that Tc1 somatic excision at that site increases by more than 14-fold during the organism's lifespan. ------------------- Key: 1905 Medline: 94131298 Authors: Levy AD;Kramer JM Title: Identification, sequence and expression patterns of the Caenorhabditis elegans col-36 and col-40 collagen-encoding genes. Citation: Gene 137: 281-285 1993 Type: ARTICLE Genes: act-4 col-6 col-12 col-13 col-14 col-36 col-40 Abstract: The collagen (Col)-encoding gene family in the nematode, Caenorhabditis elegans, consists of 50-150 members. We have undertaken studies of these genes as part of the analysis of the assembly of the cuticle, the nematode's exoskeleton. We present here the complete nucleotide and deduced amino acid sequences of the col-36 and col-40 genes, both located on chromosome II and encoding cuticle Col. Both Col possess the structural properties found in the type of Col that form the cuticle, such as short Gly-Xaa-Yaa interruptions and Cys clusters at conserved sites. On the basis of identical patterns of conserved cysteines, col-36 and col-40 belong to the col-6 cuticle Col family. Semi-quantitative analysis using reverse transcription-PCR demonstrates that the col-36 transcript is present in L1 larvae and at the L1-L2 and L2d-dauer molts. The col-40 transcript is present in L1 larvae and at the L2d-dauer molt. Different members of the col-6 family are structurally related, but have different developmental ------------------- Key: 1906 Medline: Authors: Hope IA Title: Caenorhabditis elegans, the Nematode Worm. Citation: "Embryos. Color Atlas of Development" J. Bard (ed), Wolfe Publishing, London, England. : 55-75 1994 Type: REVIEW Genes: bli-4 dpy-2 her-1 lin-1 lin-12 lin-14 lin-22 lon-2 tra-1 tra-2 unc-5 unc-6 unc-17 unc-40 unc-86 Abstract: The current interest in the nematode Caenorhabditis elegans began approximately 25 years ago when Sidney Brenner selected this species as the most suitable for studies of metazoan development and nervous system. The basis of this selection rested on the anatomical simplicity of nematodes, which nevertheless possess the major differentiated cell types of higher animals, and the tractability of C. elegans to the genetic approach. Over the past two decades or so, progress has been impressive: the cell lineage from egg to adult and the anatomy of the nervous system have been completely described, genetic investigations of numerous developmental problems are co-ordinated within a universally-agreed, systematic nomenclature, a physical map of the C. elegans genome is nearing completion and a project to sequence the entire genome is underway. Furthermore, the number of laboratories seeking to understand the mechanisms controlling animal development through genetic and molecular investigations of C. elegans is rising rapidly as the advantages of this organism become ------------------- Key: 1907 Medline: Authors: Rankin CH Title: Mechanistic questions raised by a behavioral analysis of habituation in Caenorhabditis elegans. Citation: Seminars in the Neurosciences 6: 3-9 1994 Type: ARTICLE Genes: Abstract: In the rush to discover molecular mechanisms of learning we sometimes lose sight of the behavior that we are trying to explain. Habituation is an example: although a 'simple' form of learning, surprisingly little is known about its underlying mechanisms. Although research on Aplysia has identified several possible mechanisms of habituation, there are still unanswered questions. Research on habituation in Caenorhabditis elegans demonstrates how a thorough understanding of the behavior can guide studies of mechanism. In particular, interstimulus interval (ISI) is a key component in determining the dynamics of habituation; no mechanistic explanation is complete without accounting for the effects of different ISIs. ------------------- Key: 1908 Medline: 94203734 Authors: Holden-Dye L; Walker RJ Title: Characterization of identifiable neurones in the head ganglia of the parasitic nematode Ascaris suum: a comparison with central neurones of Caenorhabditis elegans. Citation: Parasitology 108: 81-87 1994 Type: ARTICLE Genes: Abstract: Intracellular recordings have been made from neurones in the head ganglia of Ascaris. The neurones had low resting membrane potentials of -21 +9 mV (n = 78) and a relatively high input resistance (e.g. 25 M-OMEGA for a 100 mu-m cell). In all cases the intracellular location of the recording electrode was verified by injection of the fluorescent marker, 5,6-carboxyfluorescein (CBXF). To ascertain whether or not the low membrane potential was due to impalement damage, the same neurone was recorded from using two microelectrodes. The membrane potential following the first impalement by a 20 M-OMEGA 3 M KCl electrode was -38 mV and following the second impalement by a 80 M-OMEGA CBXF (for subsequent intracellular labelling) electrode was decreased to - 34 mV. Input resistance of these cells was estimated using both single and two electrode intracellular recording techniques and in both cases yielded a relatively high value for the size of cell (e.g. 25 M-OMEGA for a 100 mu-m cell). Neurones labelled by intracellular injection of the fluorescent market 5,6-carboxyfluorescein were morphologically simple and lacked extensive arborizations. The dorsal ganglion is a discrete structure consisting of only 3 neurones. Here we compare the morphological properties of these neurones to those described in the dorsal ganglion of Caenorhabditis elegans. The whole mount preparation of Ascaris ganglia thus provides a useful model to study the functional properties of neurones in nematode central nervous system and presents the possibility to assess central sites of action for anthelmintics. ------------------- Key: 1909 Medline: 94200160 Authors: Austin J;Kenyon C Title: Cell contact regulates neuroblast formation in the Caenorhabditis elegans lateral epidermis. Citation: Development 120: 313-324 1994 Type: ARTICLE Genes: egl-5 glp-1 lag-2 let-23 let-60 lin-3 lin-12 lin-22 lin-39 mab-5 pal-1 Abstract: A single line of epidermal seam cells lies along each side of the nematode C. elegans. During normal development, one of these cells, V5, produces a neuroblast that will give rise to a sensory structure, the postdeirid. If seam cells located either anterior or posterior to V5 are ablated however, this neuroblast formation is blocked. Because of this requirement for the presence of adjacent seam cells, we have asked whether V5's ability to produce a neuroblast depends on direct contact with its seam cell neighbors. We find that direct contact between seam cells is required for commitment to neuroblast production. Seam cells lose and reform their contacts with each other as they go through rounds of cell division during larval development. Signaling required for neuroblast formation occurs when the seam cells make contact after their first round of division. If this contact is prevented, no neuroblast is made; when it is delayed, the time of signaling is also delayed. The characteristics of these signals suggest that a seam cell must be part of a continuous epithelium in order to develop normally and that signaling may occur via a cell recognition/cell adhesion pathway. The effect of seam cell ablations on neuroblast formation is altered in mab-5(-) animals, suggesting that this HOM-C gene is part of the pathway by which seam cell signaling controls the decision to make a postdeirid neuroblast. ------------------- Key: 1910 Medline: 94200170 Authors: Edgar LG;Wolf N;Wood WB Title: Early transcription in Caenorhabditis elegans embryos. Citation: Development 120: 443-451 1994 Type: ARTICLE Genes: emb-29 hlh-1 Abstract: We have analysed early transcription in devitellinized, cultured embryos of the nematode Caenorhabditis elegans by two methods: measurement of [P-32]UTP uptake into TCA-precipitable material and autoradiographic detection of [H-3]UTP labelling both in the presence and absence of a-amanitin. RNA synthesis was first detected at the 8- to 12-cell stage, and alpha-amanitin sensitivity also appeared at this time, during the cleavages establishing the major founder cell lineages. The requirements for maternally supplied versus embryonically produced gene products in early embryogenesis were examined in the same culture system by observing the effects of alpha-amanitin on cell division and the early stereotyped lineage patterns. In the presence of high levels of alpha-amanitin added at varying times from two cells onward, cell division continued until approximately the 100-cell stage and then stopped during a single round of cell division. The characteristic unequal early cleavages, orientation of cleavage planes and lineage-specific timing of early divisions were unaffected by alpha-amanitin in embryos up to 87 cells. These results indicate that embryonic transcription starts well before gastrulation in C. elegans embryos, but that although embryonic transcripts may have important early functions, maternal products can support at least the mechanics of the first 6 to 7 cell cycles. ------------------- Key: 1911 Medline: 94174285 Authors: Schnabel R Title: Autonomy and nonautonomy in cell fate specification of muscle in the Caenorhabditis elegans embryo: A reciprocal induction. Citation: Science 263: 1449-1452 1994 Type: REVIEW Genes: glp-1 Abstract: EMS, a blastomere of the Caenorhabditis elegans embryo, produces body wall muscle cell-autonomously in isolation. Within the embryonic context, however, the specification of body wall muscle derived from EMS depends on inductive interactions between its daughter MS and ABa descendants that are required to overcome inhibitory interactions with other cells. The inductive events between the MS and ABa descendants are reciprocal, specifying subsequent fates in both lineages. Both induction events are blocked by mutations in the gene glp-1, known to encode a Notch-like transmembrane receptor protein. ------------------- Key: 1912 Medline: 94150469 Authors: McKim KS;Matheson C;Marra MA;Wakarchuk MF;Baillie DL Title: The Caenorhabditis elegans unc-60 gene encodes proteins homologous to a family of actin-binding proteins. Citation: Molecular & General Genetics 242: 346-357 1994 Type: ARTICLE Genes: act-1 act-3 daf-11 deb-1 dpy-11 emb-9 ges-1 let-326 let-327 let-330 let-331 let-347 lin-40 myo-3 rol-6 sup-12 unc-22 unc-34 unc-45 unc-46 unc-52 unc-54 unc-60 unc-62 unc-78 unc-94 sDf28 sDf32 sDf33 sDf34 sDf42 sDf56 sDf74 sDf75 Abstract: Mutations in the unc-60 gene of the nematode Caenorhabditis elegans result in paralysis. The thin filaments of the muscle cells are severely disorganized and not bundled with myosin into functional contractile units. Here we report the cloning and sequence of unc-60. Two unc-60 transcripts, 1.3 and 0.7 kb in size, were detected. The transcripts share a single exon encoding only the initial methionine, yet encode proteins with homologous sequences. The predicted protein products are 165 and 152 amino acids in length and their sequences are 38% identical. Both proteins are homologous to a family of actin depolymerizing proteins identified in vertebrate, plant and protozoan systems. We propose that the unc-60 locus encodes proteins that depolymerize growing actin filaments in muscle cells, and that these proteins are required for the assembly of actin filaments into the contractile myofilament lattice of C. elegans muscle, unc-60 has an essential function in development, since one unc-60 allele, s1586, has a recessive lethal phenotype. Our characterization of s1586 has shown that it is a small deletion which disrupts both ------------------- Key: 1913 Medline: 94103905 Authors: Peloquin JJ;Bird DM;Platzer EG Title: Rapid miniprep isolation of mitochondrial DNA from metacestodes, and free-living and parasitic nematodes. Citation: Journal of Parasitology 79: 964-967 1993 Type: ARTICLE Genes: Abstract: A method, based on one to isolate supercoiled plasmid DNA from bacterial cells, has been developed to purify mitochondrial DNA (mtDNA) from cestode and nematode tissue easily and efficiently. Starting with as little as 100 mg of helminth tissue, sufficient mtDNA for electrophoretic analysis was extracted. This DNA was essentially free of nuclear DNA and readily digested by restriction endonucleases. Approximately 20% of the mtDNA in helminth tissue was recovered, which is a significant improvement over previously available techniques. ------------------- Key: 1914 Medline: 94150712 Authors: Oliver S Title: Back to bases in biology. Citation: Nature 368: 14-15 1994 Type: REVIEW Genes: Abstract: On page 32 of this issue, a joint team from the Genome Sequencing Center (St. Louis, USA) and the newly founded Sanger Centre (Hinxton Hall, Cambridge, UK) report a contiguous sequence of over two megabases from chromosome III of the nematode worm, Caenorhabditis elegans. This is the longest contiguous DNA sequence yet determined, and it prompts rumination on how far we have come in the sequencing enterprise, and on how far - and where - we have ------------------- Key: 1915 Medline: 94187845 Authors: Tax FE;Yeargers JJ;Thomas JH Title: Sequence of C. elegans lag-2 reveals a cell-signalling domain shared with Delta and Serrate of Drosophila. Citation: Nature 368: 150-154 1994 Type: ARTICLE Genes: glp-1 lag-1 lag-2 let-330 let-347 let-461 lin-12 lin-40 sDf27 sDf31 sDf34 sDf40 sDf46 sDf49 sDf51 yDp1 Abstract: THE lin-12 and glp-1 genes of Caenorhabditis elegans encode members of the Notch family of transmembrane proteins(1,2). Genetic studies indicate that the lin-12 and glp-1 proteins act as receptors in specific developmental cell interactions(3-6) and that their functions are partially redundant(7). lin-12 glp-1 double mutants display certain embryonic defects not found in either single mutant(7,8). The phenotype of this double mutant is called Lag, and recessive mutations in either of the genes lag-1 or lag-2 can also result in the Lag phenotype(7), indicating that these two genes may participate in the same cell interactions that require lin-12 or glp-1. We report here that lag-2 encodes a predicted transmembrane protein of 402 amino acids. The predicted extracellular region of lag-2 is similar to amino-terminal regions of Delta and Serrate, two Drosophila proteins that are thought to function as ligands for Notch(9-14). The region of similarity includes sequences related to epidermal growth factor (EGF) repeats. We have isolated lag-2(sa37), a dominant allele that shows specific genetic interactions with lin-12. The sa37 mutation causes a Gly-->Asp change in a conserved residue of an EGF motif. Because of its overall structure, its sequence similarity to Delta and Serrate, and its genetic interactions, ne suggest that lag-2 encodes an intercellular signal for the lin-12 and glp-1 receptors. ------------------- Key: 1916 Medline: Authors: Roussell D;Gruidl M;Bennett K Title: Germ-line determination in Caenorhabditis and Ascaris: Will a helicase begin to unravel the mystery? Citation: Parasitology Today 10: 110-113 1994 Type: REVIEW Genes: glh-1 glh-2 let-545 Abstract: How cell lineages are established during development in higher eukaryotes is being addressed by geneticists and by developmental and molecular biologists, in Drosophila melanogaster, a gene corresponding to a germ-line-specific RNA helicase, vasa, has been shown to be a component of the posteriorly localized germ granules of the developing embryo. A putative RNA helicase, glh-1, which appears germ-line specific in its expression, has recently been reported from the free-living nematode Caenorhabditis elegans. Parasitologists studying the nematode Ascaris lumbricoides var. suum have found it to be a useful complement to Caenorhabditis. Deborah Roussell, Michael Gruidl and Karen Bennett predict that Ascaris will be valuable in determining the role played by germ-line helicases in development. ------------------- Key: 1917 Medline: 94147981 Authors: Aroian RV;Lesa GM;Sternberg PW Title: Mutations in the Caenorhabditis elegans let-23 EGFR-like gene define elements important for cell-type specificity and function. Citation: EMBO Journal 13: 360-366 1994 Type: ARTICLE Genes: let-23 mnDf68 Abstract: The Caenorhabditis elegans let-23 gene is a genetically characterized member of the epidermal growth factor receptor (EGFR) tyrosine kinase family. Mutations in let-23 can produce five phenotypes in the nematode. Alleles of let-23 include null alleles, reduction-of-function alleles and alleles that disrupt function in some cell types and not others. We have sequenced some of these mutations to identify sequences and regions important for overall let-23 function and for let-23 function in specific cell types. Our data indicate that in vivo, the receptor's C-terminus can be partitioned into at least three domains that each contribute to receptor function in different cell types. In particular, we find distinct domains that mediate hermaphrodite fertility and vulval induction. Our data also demonstrate for the first time that a single, conserved residue in the ligand binding domain is critical for function in vivo and that mutations in the extracellular cysteines characteristic of the EGFR family can lead to a partial or a complete reduction of receptor function. ------------------- Key: 1918 Medline: 94192901 Authors: Kramer JM Title: Structures and functions of collagens in Caenorhabditis elegans. Citation: FASEB Journal 8: 329-336 1994 Type: REVIEW Genes: clb-1 clb-2 col-1 col-2 col-6 col-8 col-12 col-13 col-14 col-19 col-34 col-35 col-36 col-39 col-40 dpy-2 dpy-7 dpy-10 dpy-13 emb-9 let-2 rol-6 sqt-1 sqt-3 Abstract: Two types of collagens have been identified in Caenorhabditis elegans corresponding to two types of extracellular matrix, the cuticle and basement membranes. Cuticle collagens are encoded by a developmentally regulated family of similar to 100 genes. Mutations in cuticle collagens can produce animals that are longer or shorter than normal and/or that are helically twisted. Mutations in different collagens can cause different morphological abnormalities, as can different mutations in the same collagen. Genetic interactions between collagen genes have been described and may identify collagens that interact to form the cuticle. Two basement membrane (type IV) collagen genes have been identified in C. elegans. They encode proteins similar in structure to vertebrate type IV collagen. One of the genes produces two alternatively spliced forms, one predominantly expressed in embryos and the other in larvae and adults, suggesting that embryonic basement membranes may have unique properties. Most mutations in the type IV genes cause embryonic lethality, indicating that normal basement membranes are required for embryogenesis. Temperature-sensitive mutations have been used to show that type IV collagen function is also required for larval development and adult fertility. ------------------- Key: 1919 Medline: 94179345 Authors: Land M;Islas-Trejo A;Freedman JH;Rubin CS Title: Structure and expression of a novel, neuronal protein kinase C (PKC1B) from Caenorhabditis elegans - PKC1B is expressed selectively in neurons that receive, transmit, Citation: Journal of Biological Chemistry 269: 9234-9244 1994 Type: ARTICLE Genes: kin-13 tpa-1 Abstract: The nematode Caenorhabditis elegans provides an advantageous system for investigating the regulation, expression, and functions of protein kinase C (PKC) isoforms. We cloned and characterized cDNAs encoding a novel C. elegans PKC designated PKC1B. The predicted PKC1B polypeptide contains features characteristic of the nPKC subfamily of PKC isoforms. The levels of PKC1B and its cognate mRNA vary over a 7-fold range during C. elegans postembryonic development. PKC1B protein and mRNA are abundant at the earliest larval stage, but their relative concentrations decrease coordinately in late larvae. Embryos, which are enriched in PKC1B mRNA, contain little PKC1B protein. Thus, PKC1B expression is regulated at a translational or post-translational level during early development. Cells engaged in PKC1B gene transcription were identified in transgenic C. elegans that carry the lacZ gene under the regulation of the PKC1B promoter. Staining for beta galactosidase revealed PKC1B promoter activity exclusively in sensory neurons and interneurons. Immunofluorescence microscopy disclosed that the PKC1B polypeptide is located in the processes (axons and dendrites) and perinuclear regions of similar to 75 neurons that constitute the sensory circuitry of the nematode. The intracellular lo calization of PKC1B and the enzyme's differential solubility in ionic and nonionic detergents suggest that the kinase is associated with membranes and ------------------- Key: 1920 Medline: 94206530 Authors: Raizen DM;Avery L Title: Electrical activity and behavior in the pharynx of Caenorhabditis elegans. Citation: Neuron 12: 483-495 1994 Type: ARTICLE Genes: act-2 eat-4 eat-12 snt-1 unc-25 unc-29 unc-49 Abstract: The pharynx of C. elegans, a model system for neural networks and for membrane excitability, has been chiefly studied by observing its behavior in normal worms, in mutant worms, and in worms lacking pharyngeal neurons. To complement this behavioral approach, we devised a method for recording currents produced by changes in pharyngeal muscle membrane potential. The electrical records, called electropharyngeograms, contain transients caused by pharyngeal muscle action potentials and by inhibitory synaptic transmission between pharyngeal neuron M3 and the muscle. Using the electropharyngeograms, we show that gamma-aminobutyric acid is not likely to be the M3 neurotransmitter, that synaptic transmission is present but abnormal in mutants lacking synaptotagmin, and that worms mutant in the eat-4 gene are defective for M3 function or transmission. ------------------- Key: 1921 Medline: 94170367 Authors: Hengartner MO;Horvitz HR Title: C. elegans cell survival gene ced-9 encodes a functional homolog of the mammalian proto-oncogene bcl-2. Citation: Cell 76: 665-676 1994 Type: ARTICLE Genes: ced-3 ced-4 ced-9 cyt-1 fem-1 hlh-1 sup-7 unc-69 Abstract: The activity of the C. elegans gene ced-9 is required to protect cells that normally survive from undergoing programmed cell death. Here we describe the cloning and molecular characterization of this gene. ced-9 is an element of a polycistronic locus that also contains the gene cyt-1, which encodes a protein similar to cytochrome b(560) of complex II of the mitochondrial respiratory chain. ced-9 encodes a 280 amino acid protein showing sequence and structural similarities to the mammalian proto-oncogene bcl-2. Overexpression of bcl-2 can mimic the protective effect of ced-9 on C. elegans cell death and can prevent the ectopic cell deaths that occur in ced-9 loss-of-function mutants. These results suggest that ced-9 and bcl-2 are homologs and that the molecular mechanism of programmed cell death has been conserved from nematodes to ------------------- Key: 1922 Medline: 94187742 Authors: Yang J;Kramer JM Title: In vitro mutagenesis of Caenorhabditis elegans cuticle collagens identifies a potential subtilisin-like protease cleavage site and demonstrates that carboxyl domain disulfide... Citation: Molecular and Cellular Biology 14: 2722-2730 1994 Type: ARTICLE Genes: bli-4 col-6 col-7 col-8 col-12 col-14 col-35 dpy-2 dpy-7 dpy-10 dpy-13 rol-6 sqt-1 sqt-3 Abstract: The importance of conserved amino acids in the amino and carboxyl non-Gly-X-Y domains of Caenorhabditis elegans cuticle collagens was examined by analyzing site-directed mutations of the sqt-1 and rol-6 collagen genes in transgenic animals. Altered collagen genes on transgenic arrays were shown to produce appropriate phenotypes by injecting in vivo cloned mutant alleles. Equivalent alterations in sqt-1 and rol-6 generally produced the same phenotypes, indicating that conserved amino acids in these two collagens have similar functions. Serine substitutions for either of two conserved carboxyl domain cysteines produced LRol phenotypes. Substitution for both cysteines in sqt-1 also resulted in an LRol phenotype, demonstrating that disulfide bonding is important for normal function but not required for assembly. Arg-1 or Arg-4 to Cys mutations in homology block A (HBA; consensus, 1-RXRRQ-5; in the amino non-Gly-X-Y domain) caused RRol phenotypes, while the same alteration at Arg-3 had no effect, indicating that Arg-3 is functionally different from Arg-1 and Arg-4. Substitutions of Arg-4 with Ser, Leu, or Glu also produced the RRol phenotype, while Lys substitutions for Arg-1 or Arg-4 did not generate any abnormal phenotypes. His substitutions for Arg-1 or Arg-4 caused somewhat less severe RRol phenotypes. Therefore, strong positively charged residues, Arg or Lys, are required at positions 1 and 4 for normal function. The conserved pattern of arginines in HBA matches the cleavage sites of the subtilisin-like endoproteinases. HBA may be a cleavage site for a subtilisin-like protease, and cleavage may be ------------------- Key: 1923 Medline: 94274039 Authors: Malone EA;Thomas JH Title: A screen for nonconditional dauer-constitutive mutations in Caenorhabditis elegans. Citation: Genetics 136: 879-886 1994 Type: ARTICLE Genes: daf-1 daf-2 daf-4 daf-7 daf-8 daf-11 daf-12 daf-14 daf-19 daf-21 daf-28 ozDf2 Abstract: In Caenorhabditis elegans, formation of the developmentally arrested dauer larva is induced by high levels of a constitutively secreted pheromone. Synergy between two groups of incompletely penetrant dauer-constitutive (Daf-c) mutations has recently led to a proposal that these two groups of genes are partially redundant and function in two parallel pathways that regulate dauer formation. A possible weakness in this reasoning is that the mutations used to identify the synergy were specifically obtained as incompletely penetrant mutations. Here we use screens to identify new Daf-c alleles without any requirement for partial penetrance. Nevertheless, 22 of the 25 new mutations are incompletely penetrant mutations in 6 previously identified genes. Among these are mutations in daf-8 and daf-19, genes for which only one mutation had been previously identified. Also included in this group are three daf-1 alleles that do not exhibit the maternal rescue characteristic of other daf-1 alleles. Two of the 25 new mutations are fully penetrant and are alleles of daf-2, the one gene in which a fully penetrant mutation had been found earlier. Finally, one of the 25 new mutations is semidominant, temperature-sensitive, and identifies a new gene, daf-28. The results demonstrate that an incompletely penetrant Daf-c phenotype is characteristic of mutations in most Daf-c genes other than daf-2. This finding strengthens the hypothesis that a branched genetic pathway controls dauer formation. ------------------- Key: 1924 Medline: 94274040 Authors: Villeneuve AM Title: A cis-acting locus that promotes crossing over between X chromosomes in Caenorhabditis elegans. Citation: Genetics 136: 887-902 1994 Type: ARTICLE Genes: meDf2 meDf3 meDf4 meDf5 meDf6 meT1 meT2 mnDf1 mnDp1 mnDp66 mnDp69 nDf19 stDp2 syDf1 yDf5 Abstract: This study reports the characterization of a cis-acting locus on the Caenorhabditis elegans X chromosome that is crucial for promoting normal levels of crossing over specifically between the X homologs and for ensuring their proper disjunction at meiosis 1. The function of this locus is disrupted by the mutation me8, which maps to the extreme left end of the X chromosome within the region previously implicated by studies of X;A translocations and X duplications to contain a meiotic pairing site. Hermaphrodites homozygous for a deletion of the locus (Df/Df) or heterozygous for a deletion and the me8 mutation (me8/Df) exhibit extremely high levels of X chromosome nondisjunction at the reductional division; this is correlated with a sharp decrease in crossing over between the X homologs as evidenced both by reductions in genetic map distances and by the presence of achiasmate chromosomes in cytological preparations of oocyte nuclei. Duplications of the wild-type region that are unlinked to the X chromosome cannot complement the recombination and disjunction defects in trans, indicating that this region must be present in cis to the X chromosome to ensure normal levels of crossing over and proper homolog disjunction. me8 homozygotes exhibit an altered distribution of crossovers along the X chromosome that suggests a defect in processivity along the X chromosome of an event that initiates at the chromosome end. Models are discussed in which the cis-acting locus deleted by the Dfs functions as a meiotic pairing center that recruits trans-acting factors onto the chromosomes to nucleate assembly of a crossover-competent complex between the X homologs. This pairing center might function in the process of homolog recognition, or in the initiation of homologous synapsis. ------------------- Key: 1925 Medline: 94167758 Authors: Goldstein P;Modric T Title: Transgenerational, ultrastructural analysis on the antioxidative effects of tocopherol on early gametogenesis in Caenorhabditis elegans grown in 100% oxygen. Citation: Toxicology and Applied Pharmacology 124: 212-220 1994 Type: ARTICLE Genes: Abstract: The random, free-radical-mediated oxidations of biological molecules result in membrane degradation leading to cellular deterioration (B. Halliwell, Free Radical Res. Commun. 9, 1-32, 1990). External oxygen, prooxidants, and internally produced oxygen free radicals (oxyradicals), interact and alter the nature of biomembranes. Antioxidants, e.g., tocopherol (Vitamin E), inhibit such oxidative damage of free radicals. In the present study, the nematode Caenorhabditis elegans was grown under hyperoxia (100% oxygen) with or without the addition of Vitamin E to the growth media. The nematodes were viable under such conditions for at least eight generations, although fecundity gradually decreased through successive generations, presumably due to genetic load. Vitamin E was also shown to have a protective effect against paraquat, which is a strong, intracellular, oxidizing agent. Ultrastructural observations of early meiosis showed that the formation of synaptonemal complexes was compromised and that the telomeres failed to attach to the nuclear envelope. Those nematodes grown in 100% oxygen with 200 micrograms/ml Vitamin E had normal meiotic structures and normal fecundity. Thus, the presence of enhanced levels of intracellular Vitamin E resulted in protection against oxidative stress during gametogenesis. ------------------- Key: 1926 Medline: 94215492 Authors: Hope IA Title: PES-1 is expressed during early embryogenesis in Caenorhabditis elegans and has homology to the fork head family of transcription factors. Citation: Development 120: 505-514 1994 Type: ARTICLE Genes: pes-1 Abstract: Promoter trapping has identified a gene, pes-1, which is expressed during C . elegans embryogenesis. The beta-galactosidase expression pattern, directed by the pes-1/lacZ fusion through which this gene was cloned, has been determined precisely in terms of the embryonic cell lineage and has three components. One component is in a subset of cells of the AB founder cell lineage during early embryogenesis, suggesting pes-1 may be regulated both by cell autonomous determinants and by intercellular signals. Analysis of cDNA suggests pes-1 has two sites for initiation of transcription and the two transcripts would encode related but distinct proteins. The predicted PES-1 proteins have homology to the fork head family of transcription factors and therefore may have important regulatory roles in early embryogenesis. ------------------- Key: 1927 Medline: 94220063 Authors: Johnstone IL Title: The cuticle of the nematode Caenorhabditis elegans: A complex collagen structure. Citation: BioEssays 16: 171-178 1994 Type: REVIEW Genes: col-1 col-2 col-6 col-8 col-12 col-13 col-14 col-19 col-34 col-36 col-40 dpy-2 dpy-7 dpy-10 dpy-13 rol-6 sqt-1 Abstract: The cuticle of the nematode Caenorhabditis elegans forms the barrier between the animal and its environment. In addition to being a protective layer, it is an exoskeleton which is important in maintaining and defining the normal shape of the nematode, The cuticle is an extracellular matrix consisting predominantly of small collagen-like proteins that are extensively crosslinked. Although it also contains other protein and non-protein compounds that undoubtedly play a significant part in its function, the specific role of collagen in cuticle structure and morphology is considered here. The C. elegans genome contains between 50 and 150 collagen genes, most of which are believed to encode cuticular collagens. Mutations that result in cuticular defects and grossly altered body form have been identified in more than 40 genes. Six of these genes are now known to encode cuticular collagens, a finding that confirms the importance of this group of structural proteins to the formation of the cuticle and the role of the cuticle as an exoskeleton in shaping the worm. It is likely that many more of the genes identified by mutations giving altered body form, will be collagen genes. Mutations in the cuticular collagen genes provide a powerful tool for investigating the mechanisms by which this group of proteins interact to form the nematode ------------------- Key: 1928 Medline: 97283483 Authors: Sakube Y;Ando H;Kagawa H Title: Cloning and mapping of a ryanodine receptor homolog gene of Caenorhabditis elegans. Citation: Annals of the New York Academy of Sciences 707: 540-545 Type: ARTICLE Genes: ryr-1 Abstract: Excitation-contraction coupling is one of the interesting mechanisms to be elucidated from the point of view of calcium signal transduction in muscle contraction. Calcium channel genes were cloned and sequenced as the receptors of dihydropyridine and ryanodine receptor in mammals. Takeshima et al. confirmed that the ryanodine receptor has a molecular mass of 500,000 daltons with a large portion at the N-terminal, which was observed as a foot structure by electron microscopy, and the transmembrane domain at the C-terminal. The molecular architecture of the receptor was close to that of rabbit, mink, and human. The functional loss of the molecule causes malignant hyperthermia of swine. The ryanodine binding site and the channel-forming transmembrane structure were clarified by several other observations. ------------------- Key: 1929 Medline: 94193691 Authors: Arpagaus M;Fedon Y;Cousin X;Chatonnet A;Berge JB;Fournier D;Toutant JP Title: cDNA sequence, gene structure, and in vitro expression of ace-1, the gene encoding acetylcholinesterase of class A in the nematode Caenorhabditis elegans. Citation: Journal of Biological Chemistry 269: 9957-9965 1994 Type: ARTICLE Genes: ace-1 ace-2 ace-3 Abstract: Three genes, ace-1, ace-2, and ace-3, encode three acetylcholinesterase classes (A, B, and C) in the nematode Caenorhabditis elegans. A fragment of genomic DNA was amplified by a polymerase chain reaction (PCR) using degenerate oligonucleotides based on sequences conserved in the cholinesterase family. This fragment mapped to chromosome X at a position that perfectly matched the location of ace-1 previously determined by genetic methods. Comparison of genomic and cDNA sequences showed that the open reading frame was interrupted by eight introns. The product of ace-1 (ACE-1, 620 amino acids) presented 42% identity with Torpedo and human acetylcholinesterases, 41% with human butyrylcholinesterase, and 35% with Drosophila acetylcholinesterase. The overall structure of cholinesterases was conserved in ACE-1 as indicated by the conserved sequence positions of Ser-216, His-468, and Glu-346 (S200, H440, E327 in Torpedo AChE) as components of the catalytic triad, of the six cysteines which form three intrachain disulfide bonds, and of Trp-99(84), a critical side chain in the choline binding site. Spodoptera Sf9 cells were infected by a recombinant baculovirus containing ace-1 cDNA. The secreted enzyme was active and existed as hydrophilic 5 and 11.5 S molecular forms. It hydrolyzed both acetylthiocholine and butyrylthiocholine and was inhibited by acetylthiocholine above 10 mM. ------------------- Key: 1930 Medline: 94208066 Authors: Mello CC;Draper BW;Priess JR Title: The maternal genes apx-1 and glp-1 and establishment of dorsal-ventral polarity in the early C. elegans embryo. Citation: Cell 77: 95-106 1994 Type: ARTICLE Genes: apx-1 bgm-1 glp-1 lag-2 mut-6 skn-1 sDf26 sDf27 sDf31 sDf34 sDf40 sDf41 sDf48 sDf49 sDf51 yDp1 Abstract: The sister blastomeres ABp and ABa are equipotent at the beginning of the 4-cell stage in C. elegans embryos, but soon become committed to different fates. We show that the glp-1 gene, a homolog of the Notch gene of Drosophila, functions in two distinct cell-cell interactions that specify the ABp and ABa fates. These interactions both require maternal expression of glp-1. We show that a second maternal gene, apx-1, functions with glp-1 only in the specification of the ABp fate and that apx-1 can encode a protein homologous to the Delta protein of Drosophila. Our results suggest how interactions mediated by glp-1 and apx-1 contribute to the establishment of the dorsal-ventral axis in the early C. elegans embryo. ------------------- Key: 1931 Medline: 94298752 Authors: Vanfleteren JR;De Vreese A Title: Analysis of the proteins of aging Caenorhabditis elegans by high resolution two-dimensional gel electrophoresis. Citation: Electrophoresis 15: 289-296 1994 Type: ARTICLE Genes: age-1 fer-15 Abstract: The metabolic rate decreases dramatically as a function of age in the nematode worm Caenorhabditis elegans. Superoxide anion production, which is tightly linked to oxygen consumption, and thus to metabolic rate, drops to a 20-fold lower level in 10-day-old, senescent worms, as compared to 4-day-old young adults. In a long-lived mutant strain of the same species metabolic activity is much better preserved. High resolution two-dimensional gel electrophoresis was employed to study alterations in the protein profile, correlating with changes of metabolic activity. Surprisingly, few proteins show age- or age- and strain-specific variations of spot intensity. The abundance of the huge majority of proteins displayed on these gels remains unaltered, irrespective of age and strain differences. These results imply that there are no major age-related alterations of proteins due to faulty protein synthesis or free radical attack, and that age-related changes in the rate of protein synthesis and breakdown must be strictly coordinated throughout the aging process. ------------------- Key: 1932 Medline: 94203792 Authors: Melov S;Hertz GZ;Stormo GD;Johnson TE Title: Detection of deletions in the mitochondrial genome of Caenorhabditis elegans. Citation: Nucleic Acids Research 22: 1075-1078 1994 Type: ARTICLE Genes: Abstract: We have examined an aging population of Caenorhabditis elegans via a PCR assay to determine if deletions in the mitochondrial genome occur in the nematode. We detected eight such deletions, identified the breakpoints of four of these, and discovered direct repeats of 4-8 base pairs at the site of all four deletions. Six of the eight repeats involved in the deletions are located in car immediately adjacent to tRNAs. Without a biochemical bias, the probability of direct repeats being present at all four breakpoints was 4x10(-6). ------------------- Key: 1933 Medline: Authors: Han M;Hall A;McCormick F Title: General Discussion II: Ras-mediated signalling pathway during vulval development in Caenorhabditis elegans. Citation: CIBA Foundation Symposia 176: 215-217 1993 Type: REVIEW Genes: let-23 let-45 let-60 lin-3 sem-5 Abstract: ------------------- Key: 1934 Medline: 94166088 Authors: Hu S-H;Lei JY;Wilce MCJ;Valenzuela MRL;Benian GM;Parker MW;Kemp BE Title: Crystallization and preliminary X-ray analysis of the auto-inhibited twitchin kinase. Citation: Journal of Molecular Biology 236: 1259-1261 1994 Type: ARTICLE Genes: unc-22 Abstract: An auto-inhibited fragment of twitchin kinase (residues 5890 to 6262) has been crystallized by vapor diffusion techniques using polyethylene glycol 4000 as the precipitant at pH 7.25 to 7.5 at 4 degrees C. We have found that MgSO4 and glycerol were essential for large crystal growth. The crystals belong to the orthorhombic space group P2(1)2(1)2, with unit cell dimensions of a = 144.1 A, b = 168.3 A and c = 60.6 A. They are suitable for X-ray analysis and diffract to a resolution of at least 2.8 A. ------------------- Key: 1935 Medline: 94231194 Authors: Jurgens TM;Frazier EG;Schaeffer JM;Jones TE;Zink DL;Borris RP;Nanakorn W;Beck HT;Balick MJ Title: Novel nematocidal agents from Curcuma comosa. Citation: Journal of Natural Products 57: 230-235 1994 Type: ARTICLE Genes: Abstract: Curcuma comosa is a member of the economically important plant family, Zingiberaceae. A methanolic extract of C. comosa was shown to be nematocidal when tested against the free-living nematode Caenorhabditis elegans. Five diphenylheptanoids (1-5), one new and four known, have been isolated and shown to be responsible for the activity. This is the first report of three of these compounds (1, 2, 4) being isolated from a natural source. ------------------- Key: 1936 Medline: 95041320 Authors: Wood WB;Johnson TE Title: Stopping the clock. Citation: Current Biology 4: 151-153 1994 Type: REVIEW Genes: age-1 daf-2 daf-7 daf-11 daf-14 daf-16 fem-3 spe-26 Abstract: Two genes that control dauer formation in the soil nematode Caenorhabditis elegans have direct effects on senescence. ------------------- Key: 1937 Medline: 94210034 Authors: Liu DWC;Thomas JH Title: Regulation of a periodic motor program in C. elegans. Citation: Journal of Neuroscience 14: 1953-1962 1994 Type: ARTICLE Genes: aex-2 dec-8 Abstract: A three-part motor program mediates a defecation every 45 sec in well-fed wild-type Caenorhabditis elegans. Individual worms maintain this 45 sec rhythm with an SD of about 3 sec. We present evidence that the defecation cycle is controlled by an endogenous clock, most likely a neuronal pattern generator. The phase of the behavioral rhythm can be reset like pattern generators in other animals. The rhythm was reset by stimulating a well-characterized neuronal circuit mediating response to light touch. Also, animals that spontaneously stopped feeding interrupted their defecation rhythms. When they resumed feeding these animals reactivated the motor program in phase with the previously established rhythm, indicating that an endogenous clock continues to run even when the behavior is not expressed. Control of the defecation rhythm is independent of expression of the motor program. Most previously isolated mutations that affect the motor program (Thomas, 1990) do not alter the rhythm of the behavior; the motor steps themselves are defective but not the timing of their activation. Laser kills of identified motor neurons that affect particular parts of the motor program also did not change the defecation rhythm. Another sensory stimulus, food, strongly modulates defecation behavior: animals away from food rarely activated the motor program, and food dilution resulted in a graded lengthening of the cycle period. To elucidate further the relationship between feeding and defecation rhythms we studied a mutation, dec-8(sa200), that caused worms to continue to activate the motor program in the absence of food. The mutant did not require the presence of food to activate the motor program, although food made the rhythm more precise. In the presence of food, dec-8(sa200) animals exhibited tandem activations of the defecation motor program; the principal activation was followed by a more variable second activation. Further experiments suggested that the tandem activations of the motor program are not due to the activity of multiple ------------------- Key: 1938 Medline: 94210062 Authors: Alfonso A;Grundahl K;McManus JR;Rand JB Title: Cloning and characterization of the choline acetyltransferase structural gene (cha-1) from C. elegans. Citation: Journal of Neuroscience 14: 2290-2300 1994 Type: ARTICLE Genes: cha-1 unc-17 Abstract: We have cloned the cha-1 gene from Caenorhabditis elegans using the method of transposon tagging. cha-1 is the structural gene for ChAT, the enzyme that synthesizes ACh. Sequence analysis of cDNAs predicts a protein of 71.5 kDa; comparison of the deduced amino acid sequence with ChAT sequences from other species confirms that cha-1 encodes ChAT. Comparison of cDNA and genomic sequences reveals that transcription is from right to left on the genetic map, and that some of the transcripts may result from trans-splicing of the 22-base spliced leader SL1. The cha-1 gene is organized into 11 exons. The first exon contains only untranslated sequences, and is followed by an extremely long intron. The coding sequence of the cha-1 transcript is disrupted by mutations in the cha-1 gene. We have determined the sites of four transposon insertions and the end-points of two deletions that lead to the cha-1 mutant phenotype; one of the deletions appears to eliminate gene function completely. Comparison of the Drosophila, rat, and C. elegans genes reveals conserved motifs and conserved intron sites. ------------------- Key: 1939 Medline: 94217737 Authors: Carr B;Anderson P Title: Imprecise excision of the Caenorhabditis elegans transposon Tc1 creates functional 5' splice sites. Citation: Molecular and Cellular Biology 14: 3426-3433 1994 Type: ARTICLE Genes: smg-2 unc-54 Abstract: Imprecise excision of the Caenorhabditis elegans transposon Tc1 from a specific site of insertion within the unc-54 myosin heavy chain gene generates either wild-type or partial phenotypic revertants. Wild-type revertants and one class of partial revertants contain insertions of four nucleotides in the unc-54 third exon (Tc1 ''footprints''). Such revertants express large amounts of functional unc-54 myosin despite having what would appear to be frameshifting insertions in the unc-54 third exon. We demonstrate that these Tc1 footprints act as efficient 5' splice sites for removal of the unc-54 third intron. Splicing of these new 5' splice sites to the normal third intron splice acceptor removes the Tc1 footprint from the mature mRNA and restores the normal translational reading frame. Partial revertant unc-54(r661), which contains a single nucleotide substitution relative to the wild-type gene, is spliced similarly, except that the use of its new 5' splice site creates a frameshift in the mature mRNA rather than removing one. In all of these revertants, two alternative 5' splice sites are available to remove intron 3. We determined the relative efficiency with which each alternative 5' splice site is used by stabilizing frameshifted mRNAs with smg(-) genetic backgrounds. In all cases, the upstream member of the two alternative sites is used preferentially (>75% utilization). This may reflect an inherent preference of the splicing machinery for the upstream member of two closely spaced 5' splice sites. Creation of new 5' splice sites may be a general characteristic of Tc1 insertion and excision events. ------------------- Key: 1940 Medline: Authors: Cucinotta FA;Wilson JW;Katz R Title: Radiosensitivity parameters for lethal mutagenesis in Caenorhabditis elegans. Citation: Radiation Protection Dosimetry 52: 25-27 1994 Type: ARTICLE Genes: Abstract: For the first time track structure theory has been applied to radiobiological effects in a living organism. Data for lethal mutagenesis in Caenorhabditis elegans, obtained after irradiation with nine different types of ions of atomic number 1-57 and gamma rays have yielded radiosensitivity parameters comparable with those found for the transformation of C3HT10 1/2 cells but remote from those for mammalian cell survival. ------------------- Key: 1941 Medline: 94221636 Authors: Evans TC;Crittenden SL;Kodoyianni V;Kimble J Title: Translational control of maternal glp-1 mRNA establishes an asymmetry in the C. elegans embryo. Citation: Cell 77: 183-194 1994 Type: ARTICLE Genes: glh-1 glp-1 skn-1 Abstract: In C. elegans, the glp-1 gene encodes a membrane receptor that is required for anterior cell fates in the early embryo. We report that GLP-1 protein is focalized to anterior blastomeres in 2- to 28-cell embryos. By contrast, glp-1 mRNA is present in all blastomeres until the 8-cell stage. Furthermore, the glp-1 3' untranslated region can restrict translation of a reporter mRNA to anterior blastomeres. Therefore, the translation of maternal glp-1 mRNA is temporally and spatially regulated in the C. elegans embryo. The regulation of maternal glp-1 mRNA has striking parallels to the regulation of maternal hunchback mRNA in the Drosophila embryo. Thus, the establishment of embryonic asymmetry in diverse organisms may involve conserved mechanisms of maternal mRNA regulation. ------------------- Key: 1942 Medline: 94333774 Authors: Gottlieb S;Ruvkun G Title: daf-2, daf-16 and daf-23: Genetically interacting genes controlling dauer formation in Caenorhabditis elegans. Citation: Genetics 137: 107-120 1994 Type: ARTICLE Genes: che-3 daf-1 daf-2 daf-3 daf-4 daf-5 daf-6 daf-7 daf-8 daf-10 daf-11 daf-12 daf-14 daf-16 daf-18 daf-20 daf-21 daf-23 mnDf87 mnDf90 Abstract: Under conditions of high population density and low food, Caenorhabditis elegans forms an alternative third larval stage, called the dauer stage, which is resistant to desiccation and harsh environments. Genetic analysis of some dauer constitutive (Daf-c) and dauer defective (Daf-d) mutants has revealed a complex pathway that is likely to function in particular neurons and/or responding tissues. Here we analyze the genetic interactions between three genes which comprise a branch of the dauer formation pathway that acts in parallel to or downstream of the other branches of the pathway, the Daf-c genes daf-2 and daf-23 and the Daf-d gene daf-16. Unlike mutations in other Daf-c genes, mutations in both daf-2 and daf-23 cause non-conditional arrest at the dauer stage. Our epistasis analysis suggests that daf-2 and daf-23 are functioning at a similar point in the dauer pathway. First, mutations in daf-2 and daf-23 are epistatic to mutations in the same set of Daf-d genes. Second, daf-2 and daf-23 mutants are suppressed by mutations in daf-16. Mutations in daf-16 do not suppress any of the other Daf-c mutants as efficiently as they suppress daf-2 and daf-23 mutants. Third, double mutants between either daf-2 or daf-23 and several other daf-d mutants exhibit an unusual interaction. Based on these results, we present a model for the function of daf-2, daf-23 and daf-16 in dauer formation. ------------------- Key: 1943 Medline: 94310687 Authors: Salser SJ;Kenyon C Title: Patterning C. elegans: Homeotic cluster genes, cell fates and cell migrations. Citation: Trends in Genetics 10: 159-164 1994 Type: REVIEW Genes: ceh-13 egl-5 lin-39 mab-5 pal-1 Abstract: Despite its simple body form, the nematode C. elegans expresses homeotic cluster genes similar to those of insects and vertebrates in the patterning of many cell types and tissues along the anteroposterior axis. In the ventral nerve cord these genes program spatial patterns of cell death fusion, division and neurotransmitter production; in migrating cells they regulate the direction and extent of movement. Nematode development permits an analysis at the cellular level of how homeotic cluster genes interact to specify cell fates, and how cell behavior can be regulated to assemble an organism. ------------------- Key: 1944 Medline: 94222994 Authors: Ishii N;Suzuki N;Hartman PS; Suzuki K Title: The effects of temperature on the longevity of a radiation-sensitive mutant rad-8 of the nematode Caenorhabditis elegans. Citation: Journal of Gerontology 49: B117-B120 1994 Type: ARTICLE Genes: rad-8 Abstract: The effects of temperature on development and life span were examined in a radiation- and oxygen-hypersensitive mutant (rad-8) of the nematode Caenorhabditis elegans. At temperatures greater than 20 degrees C, the rad-8 mutant developed slightly slower and possessed a life span roughly equivalent to that of the wild type. At 16 degrees C, however, the mutant lived considerably longer than the wild type, with mean life spans of approximately 28 and 21 days, respectively. This lengthened life span was due to slower development. It was also dependent upon oxygen concentration, because the mean life spans of rad-8 and wild type were experimentally identical when reared at 16 degrees C in the presence of 5% rather than atmospheric oxygen. The rad-8 mutant represents an interesting paradox, as its life span can either be shortened or lengthened relative to the wild type, depending on temperature and oxygen concentration. ------------------- Key: 1945 Medline: Authors: Kayne PS Title: Knocking down a pathway to build it up. Citation: Trends in Genetics 10: 145-147 1994 Type: REVIEW Genes: let-23 let-60 lin-1 lin-3 lin-15 lin-45 mpk-1 mpk-2 sem-5 sur-1 Abstract: Recently, a large number of papers, which seem to proliferate almost as rapidly as the cellular events they describe, have charted pathways from the cell surface to the nucleus. Several of these pathways begin with a receptor tyrosine kinase binding its ligand, and subsequently becoming dimerized; they end with the activation of transcription factors in the nucleus. While most of the players involved were initially identified as oncogenes, later research has shown that these pathways are remarkably well conserved in vertebrates, Caenorhabditis elegans, Drosophila melanogaster and yeasts. ------------------- Key: 1946 Medline: 94325629 Authors: Hill RJ;Sternberg PW Title: Cell fate patterning during C. elegans vulval development. Citation: Development 1993 Supplement : 9-18 1993 Type: REVIEW Genes: dig-1 glp-1 let-23 let-60 lin-1 lin-3 lin-12 lin-15 lin-45 sem-5 Abstract: Precursor cells of the vulva of the C. elegans hermaphrodite choose between two vulval cell fates (1 degree and 2 degree ) and a non-vulval epidermal fate (3 degree ) in response to three intercellular signals. An inductive signal produced by the anchor cell induces the vulval precursors to assume the 1 degree and 2 degree vulval fates. This inductive signal is an EGF-like growth factor encoded by the gene lin-3. An inhibitory signal mediated by lin-15, and which may originate from the surrounding epidermis, prevents the vulval precursors from assuming vulval fates in the absence of the inductive signal. A short range lateral signal, which acts through the gene lin-12, regulates the pattern of 1 degree and 2 degree fates assumed by the induced vulval precursors. The combined action of the three signals precisely directs the six vulval precursors to adopt a 3 degree 3 degree 2 degree 1 degree 2 degree 3 degree pattern of fates. The amount of inductive signal produced by the anchor cell appears to determine the number of vulval precursors that assume vulval fates. The three induced vulval precursors most proximal to the anchor cell are proposed to adopt the 2 degree 1 degree 2 degree pattern of fates in response to a gradient of the inductive signal and also in response to lateral signalling that inhibits adjacent vulval precursor cells from both assuming the 1 degree fate. ------------------- Key: 1947 Medline: 94325620 Authors: Goldstein B;Hird SN;White JG Title: Cell polarity in early C. elegans development. Citation: Development 1993 Supplement : 279-287 1993 Type: REVIEW Genes: mex-1 par-1 pie-1 skn-1 Abstract: The polarization of the embryonic axes is a key event in embryogenesis, being one of the earliest manifestations of the shape and form of the organism. The acquisition of polarity by individual blastomeres is one of the earliest indicators of commitment to a particular pathway of differentiation. These phenomena have been studied in the development of C. elegans both at the cellular and organismal level. This review summarizes what is known about how polarity is established in the blastomeres of this organism, how the division axes of polarized cells are determined, and how the embryonic ------------------- Key: 1948 Medline: 94244600 Authors: Sugimoto A;Friesen PD;Rothman JH Title: Baculovirus p35 prevents developmentally programmed cell death and rescues a ced-9 mutant in the nematode Caenorhabditis elegans. Citation: EMBO Journal 13: 2023-2028 1994 Type: ARTICLE Genes: ced-1 ced-3 ced-4 ced-9 Abstract: Programmed cell death, or apoptosis, occurs throughout the course of normal development in most animals and can also be elicited by a number of stimuli such as growth factor deprivation and viral infection. Certain morphological and biochemical characteristics of programmed cell death are similar among different tissues and species. During development of the nematode Caenorhabditis elegans, a single genetic pathway promotes the death of selected cells in a lineally fixed pattern. This pathway appears to be conserved among animal species. The baculovirus p35-encoding gene (p35) is an inhibitor of virus-induced apoptosis in insect cells. Here we demonstrate that expression of p35 in C. elegans prevents death of cells normally programmed to die. This suppression of developmentally programmed cell death results in appearance of extra surviving cells. Expression of p35 can rescue the embryonic lethality of a mutation in ced-9, an endogenous gene homologous to the mammalian apoptotic suppressor bcl-2, whose absence leads to ectopic cell deaths. These results support the hypothesis that viral infection can activate the same cell death pathway as is used during normal development and suggest that baculovirus p35 may act downstream or independently of ced-9 in this pathway. ------------------- Key: 1949 Medline: 94331780 Authors: Huang LS;Tzou P;Sternberg PW Title: The lin-15 locus encodes two negative regulators of Caenorhabditis elegans vulval development. Citation: Molecular Biology of the Cell 5: 395-412 1994 Type: ARTICLE Genes: let-23 let-60 lin-3 lin-8 lin-9 lin-15 lin-36 lin-37 lin-38 lin-45 sem-5 Abstract: During Caenorhabditis elegans vulval development, an inductive signal from the anchor cell stimulates three of the six vulval precursor cells (VPCs) to adopt vulval rather than nonvulval epidermal fates. Genes necessary for this induction include the lin-3 growth factor, the let-23 receptor tyrosine kinase, and let-60 ras. lin-15 is a negative regulator of this inductive pathway. In lin-15 mutant animals, all six VPCs adopt vulval fates, even in the absence of inductive signal. Previous genetic studies suggested that lin-15 is a complex locus with two independently mutable activities, A and B. We have cloned the lin-15 locus by germline transformation and find that it encodes two nonoverlapping transcripts that are transcribed in the same direction. The downstream transcript encodes the lin-15A function; the upstream transcript encodes the lin-15B function. The predicted lin-15A and lin-15B proteins are novel and hydrophilic. We have identified a molecular null allele of lin-15 and have used it to analyze the role of lin-15 in the signaling pathway. We find that lin-15 acts upstream of let-23 and in parallel to the inductive signal. ------------------- Key: 1950 Medline: 94237906 Authors: Land M;Islas-Trejo A;Rubin CS Title: Origin, properties, and regulated expression of multiple mRNAs encoded by the protein kinase C1 gene of Caenorhabditis elegans. Citation: Journal of Biological Chemistry 269: 14820-14827 1994 Type: ARTICLE Genes: kup-1 tpa-1 Abstract: Recently, we cloned and characterized cDNA encoding a novel, protein kinase C (designated PKC1B) from Caenorhabditis elegans. PKC1B (707 amino acid residues) is a developmentally regulated, calcium-independent kinase that is expressed exclusively in sensory neurons and related interneurons. We have now discovered a mechanism by which a second, distinct mRNA (PKC1A mRNA) with increased protein coding potential is generated from the C. elegans PKC1 gene. PKC1A mRNA is produced in a process that involves the utilization of an alternative, distal promoter, the incorporation of two unique exons into the mRNA, and alternative cis/trans splicing. Diversity among PKC1 gene transcripts is increased substantially by trans-splicing. The 5' end of PKC1A mRNA contains an acceptor site that is modified by the addition of either a classical spliced leader sequence 2 or one of four novel spliced leaders. PKC1A mRNA encodes a predicted kinase that contains the entire sequence of PKC1B as well as an N-terminal extension of 56 residues. The extension contains a preponderance of basic amino acids. The levels of transcripts arising from the distal (1A) and proximal (1B) promoters for the PKC1 gene are differentially regulated during C. elegans development. The ratio of 1B mRNA:1A mRNA varies from 40:1 to unity as the nematodes progress from early larval stages to mature adults. The novel exons in the PKC1A structural gene are not contiguous with the PKC1A promoter but are instead positioned downstream from a second gene, kinase upstream gene-1, in the context of a multicistronic operon. PKC1A and kinase upstream gene-1 mRNAs are coordinately expressed in a fixed ratio throughout C. elegans post-embryonic development, suggesting that a shared upstream promoter regulates transcription of both genes. Finally, PKC1A and PKC1B mRNA levels are differentially regulated by phorbol esters in a process that may involve the participation of another PKC isoform that is analogous to mammalian PKC-delta. ------------------- Key: 1951 Medline: 94229336 Authors: Park Y-S;Kramer JM Title: The C. elegans sqt-1 and rol-6 collagen genes are coordinately expressed during development, but not at all stages that display mutant phenotypes. Citation: Developmental Biology 163: 112-124 1994 Type: ARTICLE Genes: col-1 col-2 daf-2 rol-6 sqt-1 mnDf45 mnDf80 Abstract: Mutations in the sqt-1 and rol-6 cuticle collagen genes of Caenorhabditis elegans can cause dramatic alterations in organismal morphology. Genetic interactions and similarities in sequence and mutant phenotypes suggest that the sqt-1 and rol-6 collagen chains may physically interact. We show here that the sqt-1 and rol-6 genes are coordinately expressed during formation of the L2, L3, L4, adult, and L2d stage cuticles. Quantitative analyses indicate that the ratio of the steady-state levels of the sqt-1 and rol-6 mRNAs is approximately 2:1 at each of these stages, consistent with the possibility that they form a single heterotrimeric collagen. Surprisingly, the temporal expression patterns of sqt-1 and rol-6 mRNAs are not completely correlated with the times of appearance of their mutant phenotypes. Both sqt-1 and rol-6 mutant phenotypes appear in L2, L3, L4, adult, and L2d stage animals, and their mRNAs are easily detectable during synthesis of each of these cuticles. However, both sqt-1 and rol-6 mutant animals also display abnormal phenotypes at the dauer stage, but no transcripts from either gene are detected during synthesis of the dauer cuticle. We propose that dauer animals display a mutant phenotype in the absence of mutant collagen because they maintain the abnormal morphology that was generated in the preceding L2d stage. ------------------- Key: 1952 Medline: 94239527 Authors: Hengartner MO;Horvitz HR Title: Activation of C. elegans cell death protein CED-9 by an amino-acid substitution in a domain conserved in Bcl-2. Citation: Nature 369: 318-320 1994 Type: ARTICLE Genes: ced-9 Abstract: The Caenorhabditis elegans gene ced-9 and the human protooncogene bcl-2, both of which protect cells from programmed cell death, are members of the same gene family ced-9 and bcl-2 were discovered because of the effects of dominant gain-of-function mutations. Such hcl-2 mutations, which are commonly found in follicular lymphoma, are translocations that result in overexpression of a normal Bcl-2 protein in B cells. Here we report that, by contrast, the ced-9(n1950) gain-of-function mutation affects the open reading frame of ced-9 and results in a glycine-to-glutamate substitution in a region highly conserved among all ced-9/bcl-2 family members. We conclude that this glycine has an important function in ced-9 regulation, and we suggest that alteration of this glycine in other members of the ced-9/bcl-2 family might lead to oncogenic activation. We also present genetic evidence suggesting that the CED-9 protein might exist in two distinct forms that have opposite effects on cell death. ------------------- Key: 1953 Medline: 94302674 Authors: Ambros V;Moss EG Title: Heterochronic genes and the temporal control of C. elegans development. Citation: Trends in Genetics 10: 123-127 1994 Type: REVIEW Genes: lin-4 lin-14 lin-28 lin-29 lin-46 Abstract: The heterochronic genes of Caenorhabditis elegans encode part of a regulatory system that controls the temporal component of cell fates in development. The genes have been characterized genetically and molecularly, and their study has so far revealed a genetic hierarchy that specifies sequences of developmental events, a novel RNA-mediated mechanism of gene regulation and a reprogramming phenomenon associated with arrested development. ------------------- Key: 1954 Medline: 94298508 Authors: Herman MA;Horvitz HR Title: The Caenorhabditis elegans gene lin-44 controls the polarity of asymmetric cell divisions. Citation: Development 120: 1035-1047 1994 Type: ARTICLE Genes: let-23 let-353 let-503 let-504 let-505 let-506 let-507 lin-17 lin-44 unc-89 hDf6 hDf7 hDp2 hDp7 sDp2 Abstract: The generation and orientation of cellular and organismic polarity are fundamental aspects of development. Mutations in the gene lin-44 of the nematode Caenorhabditis elegans reverse both the relative positions of specific sister cells and the apparent polarities of these cells. Thus, lin-44 mutants appear to generate polar cells but to misorient these cells along the body axis of the animal. We postulate that lin-44 acts to specify the orientation of polar cells. ------------------- Key: 1955 Medline: 94350203 Authors: Meneely PM Title: Sex determination in polyploids of Caenorhabditis elegans. Citation: Genetics 137: 467-481 1994 Type: ARTICLE Genes: dpy-5 dpy-21 dpy-26 dpy-27 dpy-28 sdc-1 sdc-2 xol-1 mnDp8 mnDp9 mnDp10 mnDp25 mnDp27 mnDp33 mnDp57 stDp2 Abstract: In Caenorhabditis elegans triploid animals with two X chromosomes (symbolized 3A;2X) are males. However, these triploid males can be feminized by making them mutant for recessive dosage compensation mutations, by adding X chromosome duplications or by microinjecting particular DNA sequences termed feminizing elements. None of these treatments affects diploid males. This study explores several aspects of these treatments in polyploids. The dosage compensation Mutants exhibit a strong maternal effect, such that reduction of any of the dosage compensation gene functions in the mother leads to sex reversal of 3A;2X animals. Likewise, all X chromosome duplications tested cause both sex reversal and intersexual development of many 3A;2X animals. Microinjected feminizing element DNA does not cause extensive sex reversal, but does result in intersexual development in 3A;2X animals. Neither X chromosome duplications nor microinjected feminizing elements show the extreme maternal effect of the dosage compensation mutants, although there is indirect evidence for a maternal effect of the feminizing elements. In particular, very little feminizing element DNA needs to be microinjected in order to feminize triploid males, far less than what is needed for stable inheritance, implying that feminizing elements can work within the mother's gonad. However, even very high concentrations of microinjected feminizing elements do not affect sex determination in diploid males, suggesting that they are not part of the numerator of the X/A ratio. In addition, no pair of X chromosome duplications feminizes diploid males, suggesting that none of these duplications contains a numerator of the X/A ratio. Instead, I infer that an X-linked locus, as yet undefined, must be present in two copies for hermaphrodite development to ensue or that the two X chromosomes might interact. ------------------- Key: 1956 Medline: 94350204 Authors: Ahnn J;Fire A Title: A screen for genetic loci required for body wall muscle development during embryogenesis in Caenorhabditis elegans. Citation: Genetics 137: 483-498 1994 Type: ARTICLE Genes: ges-1 hlh-1 myo-3 unc-54 arDf1 ccDf1 ctDf1 eDf2 eDf3 eDf4 eDf6 eDf18 eDf19 eDf24 hDf6 hDf8 hDf9 itDf2 mDf4 mDf10 maDf4 mnDf1 mnDf30 mnDf41 mnDf61 mnDf68 mnDf87 mnDf89 mnDf90 mnDf94 mnDf99 mnDf104 nDf16 nDf25 nDf27 nDf40 nDf41 ozDf2 ozDf5 qDf3 rhDf1 sDf2 sDf6 sDf20 sDf26 sDf28 sDf29 sDf30 sDf32 sDf33 sDf34 sDf35 sDf38 sDf39 sDf40 sDf41 sDf42 sDf45 sDf46 sDf48 sDf49 sDf51 sDf52 sDf53 sDf56 sDf72 sDf73 sDf74 sDf75 stDf7 syDf1 tDf1 tDf2 tDf3 tDf4 uDf1 yDf6 yDf8 yDf10 mnT10 Abstract: We have used available chromosomal deficiencies to screen for genetic loci whose zygotic expression is required for formation of body-wall muscle cells during embryogenesis in Caenorhabditis elegans. To test for muscle cell differentiation we have assayed for both contractile function and the expression of muscle-specific structural proteins. Monoclonal antibodies directed against two myosin heavy chain isoforms, the products of the unc-54 and myo-3 genes, were used to detect body-wall muscle differentiation. We have screened 77 deficiencies, covering approximately 72% of the genome. Deficiency homozygotes in most cases stain with antibodies to the body-wall muscle myositis and in many cases muscle contractile function is observed. We have identified two regions showing distinct defects in myosin heavy chain gene expression. Embryos homozygous for deficiencies removing the left tip of chromosome V fail Lo accumulate the myo-3 and unc-54 products, but express antigens characteristic of hypodermal, pharyngeal and neural development. Embryos lacking a large region on chromosome III accumulate the unc-54 product but not the myo-3 product. We conclude that there exist only a small number of loci whose zygotic expression is uniquely required for adoption of a muscle ------------------- Key: 1957 Medline: 94350205 Authors: Storfer-Glazer FA;Wood WB Title: Effects of chromosomal deficiencies on early cleavage patterning and terminal phenotype in Caenorhabditis elegans embryos. Citation: Genetics 137: 499-508 1994 Type: ARTICLE Genes: emb-29 mex-1 pie-1 skn-1 eDf2 mnDf30 mnDf61 mnDf66 mnDf68 mnDf77 mnDf88 mnDf89 mnDf96 mnDf98 nDf17 nDf20 nDf24 nDf27 sDf28 sDf35 stDf1 Abstract: We have analyzed pregastrulation cleavage patterns in Caenorhabditis elegans embryos homozygous for various chromosomal deficiencies. By two different estimates these deficiencies represent between 37 and 49% of the genome, including the entire X chromosome and substantial portions of each of the five autosomes. Among these genomic regions, we find none whose absence causes defects in pregastrulation cleavage patterns. We can conclude that there are at most very few genes whose transcription after fertilization is required for normal early patterning of cell divisions. We also scored terminal phenotypes of the homozygous deficiency embryos for stage of arrest and for expression of three tissue-specific differentiation markers. Based on these phenotypes, we have identified regions of the genome that are required for completion of cell proliferation, expression of gut differentiation and entry into morphogenesis. Somewhat surprisingly, embryos in which cell proliferation is arrested at less than 20% of the normal cell number can nevertheless initiate morphogenesis and undergo elongation to the twofold stage. Our results are consistent with the view that many early events in C. elegans embryogenesis are controlled exclusively by maternally produced gene products. However, they are also consistent with the likely possibility that, at least in some deficiency embryos, although cleavage patterns may be normal, blastomere identities are not. In this respect the early cleavages may differ from later lineages, in which cell division patterns appear to be characteristic of cell identity. ------------------- Key: 1958 Medline: 94374677 Authors: Collins JJ; Anderson P Title: The Tc5 family of transposable elements in Caenorhabditis elegans. Citation: Genetics 137: 771-781 1994 Type: ARTICLE Genes: ced-4 gld-2 mec-7 mut-2 unc-22 unc-33 unc-86 unc-116 Abstract: We have identified Tc5, a new family of transposable genetic elements in the nematode Caenorhabditis elegans. All wild-type varieties of C. elegans that we examined contain 4-6 copies of Tc5 per haploid me, but we did not observe transposition or excision of Tc5 in these strains. Tc5 is active, however, in the mut-2 mutant strain TR679. Of 60 spontaneous unc-22 mutations isolated from strain TR679, three were caused by insertion of Tc5. All three TcS-induced mutations are unstable; revertants result from precise or nearly precise excision of Tc5. Individual Tc5 elements are similar to each other in size and structure. The 3.2-kb element is bounded by inverted terminal repeats of nearly 500 bp. Eight of the ten terminal nucleotides of Tc5 are identical to the corresponding nucleotides of Tc4. Further, both elements recognize the same target site for insertion (CTNAG) and both cause duplication of the central TNA trinucleotide upon insertion. Other than these similarities to Tc4, Tc5 is unrelated to the three other transposon families (Tc1, Tc3 and Tc4) that transpose and excise at high frequency in mut-2 mutant strains. Mechanisms are discussed by which four apparently unrelated transposon families are all affected by the same mut-2 mutation. ------------------- Key: 1959 Medline: 94296359 Authors: Selfors LM;Stern MJ Title: MAP Kinase function in C. elegans. Citation: BioEssays 16: 301-304 1994 Type: ARTICLE Genes: let-23 let-60 lin-3 lin-45 mpk-1 mpk-2 sem-5 sur-1 Abstract: The understanding of how cells communicate is a fundamental issue in developmental biology. Over the past few years it has become increasingly clear that many cell-cell communication mechanisms are evolutionarily conserved. A striking example of this is signalling through mitogen-activated protein kinases (MAP kinases), also known as extracellular signal regulated kinases (ERKs). MAP kinases have been found in yeast, Drosophila, Xenopus and mammals, where they appear to link stimulation by extracellular factors to changes in gene expression. Two papers have recently reported the identification of MAP kinase genes in the nematode Caenorhabditis elegans. Analysis of these genes in C. elegans may lead to a better understanding of MAP kinase function. ------------------- Key: 1960 Medline: 94261444 Authors: Sedensky MM;Hudson SJ;Everson B;Morgan PG Title: Identification of a mariner-like repetitive sequence in C. elegans. Citation: Nucleic Acids Research 22: 1719-1723 1994 Type: ARTICLE Genes: unc-80 Abstract: A repetitive element in C. elegans has been found that bears high homology to the element mariner of Drosophila mauritiana (EMBL accession number X77804). This element is present in about 20 copies in the N2 strain of C. elegans, and appears in roughly equal copy numbers in the related strain BO and in the hybrid strains RW7097 and TR679. There is only one copy of this MLE in three related species of Caenorhabditis. A cDNA of this mariner-like element (MLE) codes for a protein with 58% homology to the Drosophila transposase. The mariner-like element is not mobile in N2. This class of elements has now been described in insects, planaria and nematodes (GenBank accession number M98552 and this report). ------------------- Key: 1961 Medline: 94261450 Authors: Granato M;Schnabel H;Schnabel R Title: pha-1, a selectable marker for gene-transfer in C. elegans. Citation: Nucleic Acids Research 22: 1762-1763 1994 Type: NOTE Genes: pha-1 rol-6 sud-1 Abstract: The nematode C. elegans is a powerful genetic system to study a large spectrum of biological problems. Once mutants with specific defects are identified and phenotypically characterised, a molecular analysis of gene functions is desirable. A standard method for cloning genes in C. elegans is to complement mutants with cloned genomic DNA introduced into the mutant strain by germline transformation. Furthermore, a germline transformation of regulatory gene sequences fused to a reporter gene provides a rapid method to study the temporal and spatial expression of cloned genes, without preparing specific antisera. Germline transformation has also been used to assay the biological activity of in vitro manipulated nucleic acid sequences or to screen systematically for regulatory promoter sequences using a promoter trap approach. ------------------- Key: 1962 Medline: 94307574 Authors: Szekely AA;Woodruff RC;Mahendra R Title: P element mediated germ line transformation of Drosophila melanogaster with the Tc1 transposable DNA element from Caenorhabditis elegans. Citation: Genome 37: 356-366 1994 Type: ARTICLE Genes: unc-54 Abstract: Questions relating to the origin and regulation of mobile genetic elements are currently of considerable interest. Since it is now possible to address more precisely issues concerning the entry, dispersion, and regulation of elements within a virgin genome, one approach that may afford a better understanding of transposable elements in general could be provided by interspecific DNA transformation. Therefore, the Tc1 transposable DNA element from Caenorhabditis elegans was chosen as a proposed invading element of the Drosophila melanogaster genome. The basis for this selection resided in the inherent structural and functional similarities, as well as sequence identities, between the Caenorhabditis element and elements innate to Drosophila (e.g., P, HB1, and Uhu). Initial investigations were carried out to define a clone carrying an intact Tc1 element. This Tc1 element was inserted into a P transposon vector and two P-Tc1-ry+ constructs, differing only in insert orientation, were identified. P element mediated germ line transfer was then used to generate a transformant that was genetically and molecularly identified as containing a single, structurally intact Tc1 element at cytological location 64C4-5 on the third chromosome. The single P((Tc1,ry+)SAS-B insertion was thereafter mobilized by using a P(ry+ DELTA-2-3) element as a transposase source, and the genetic and molecular data suggested that the insertion had been successfully reintegrated to a variety of genomic locations. On the basis of genetic and molecular analyses, the Tc1 element in the P((Tc1,ry+)) transformed stock is not highly unstable in germ line and ------------------- Key: 1963 Medline: Authors: Kawaii S;Yoshizawa Y;Mizutani J Title: Effects of chavicol on intracellular ionized calcium in a free-living soil nematode, Caenorhabditis elegans. Citation: Bioscience Biotechnology and Biochemistry 58: 982-985 1994 Type: NOTE Genes: Abstract: The physiological effects of two phenolic nematocides, chavicol and demethyleugenol, on C. elegans were studied by [Ca2+](i) measurement using a microspectrofluorometer and an image analyzer. Chavicol and demethyleugenol, which had similar effects on the nematodes, caused a significant elevation of [Ca2+](i) in the intestinal tract. The image analysis suggested that these phenolic nematocides caused the destruction of cell membrane and the leakage of cytosol from the intestinal tract into the pseudocoelomic cavity. ------------------- Key: 1964 Medline: Authors: Labouesse M Title: Small is beautiful - Or the promise of a bright animalcule, C. elegans. Citation: M S-Medecine Sciences 10: 337-341 1994 Type: REVIEW Genes: ced-3 ced-4 ced-9 lin-32 mec-3 unc-4 unc-5 unc-6 unc-40 unc-86 Abstract: In French. ------------------- Key: 1965 Medline: 95136788 Authors: Strome S;Garvin C;Paulsen J;Capowski E;Martin P;Beanan M Title: Specification and development of the germline in Caenorhabditis elegans. Citation: CIBA Foundation Symposia 182: 31-45 1994 Type: REVIEW Genes: glh-1 glp-1 glp-4 mes-1 mes-2 mes-3 mes-4 mes-6 pgl-1 Abstract: Maternal-effect sterile (mes) genes encode maternal components that are required for establishment and development of the germline. Five such genes have been identified in the nematode Caenorhabditis elegans. Mutations in one of the genes result in defects in the asymmetric division and cytoplasmic partitioning that generate the primordial germ cell P4 at the 16-24-cell stage of embryogenesis. As a result of these defects, the P4 cell is transformed into a muscle progenitor and mutant embryos develop into sterile adults with extra body muscles. Mutations in the other four mes genes do not affect formation of the germline during embryogenesis, but result in drastically reduced proliferation of the germline during post-embryonic stages and in an absence of gametes in adults. The failure to form gametes may reflect a defect in germline specification or may be a consequence of reduced germline proliferation. We are currently testing these two possibilities. in addition to the mes gene products, wild-type function of the zygotic gene glp-4 is required for normal post-embryonic proliferation of the germline. Germ cells in glp-4 mutant worms are arrested in prophase of the mitotic cell cycle and are unable to enter meiosis and form gametes. Thus, following establishment of the germ lineage in the early embryo, both maternal and zygotic gene products work in concert to promote the extensive proliferation of the germline and to enable germ cells to generate functional gametes. ------------------- Key: 1966 Medline: 95136780 Authors: Ellis RE;Kimble J Title: Control of germ cell differentiation in Caenorhabditis elegans. Citation: CIBA Foundation Symposia 182: 179-188 1994 Type: REVIEW Genes: fem-1 fem-2 fem-3 fog-1 fog-2 fog-3 gld-1 glp-1 her-1 lag-1 laf-1 lag-2 lin-12 mog-1 mog-2 mog-3 mog-4 mog-5 mog-6 sdc-1 sdc-2 sdc-3 tra-1 tra-2 tra-3 Abstract: The germline of Caenorhabditis elegans is organized in a linear fashion-the most distal germ cells remain in mitosis, those in the middle enter meiosis and proximal cells differentiate as sperm or oocytes. Two signal transduction pathways control germ cell fates. The glp-1 gene mediates a signal that promotes mitosis and the genes of the sex determination pathway mediate a signal that determines if germ cells will develop as sperm or oocytes. Information from these pathways acts through terminal regulators to specify cell fate. For example, fog-1 and fog-3 are required to initiate spermatogenesis and gld-1 appears to be required to initiate oogenesis. Study of these terminal regulators suggests that the decisions about sexual identity and mitosis are linked in germ cells. We propose a tripartite interaction that forces germ cells to adopt one of only three fates-mitosis, spermatogenesis or ------------------- Key: 1967 Medline: 94362510 Authors: Giglio M-P;Hunter T;Bannister JV;Bannister WH;Hunter GJ Title: The manganese superoxide dismutase gene of Caenorhabditis elegans. Citation: Biochemistry and Molecular Biology International 33: 37-40 1994 Type: ARTICLE Genes: sod-3 Abstract: We have cloned and sequenced a gene (sod-3) encoding manganese superoxide dismutase from the nematode Caenorhabditis elegans. The protein-coding region spans 943 bp including three intron sequences and encodes a protein of 227 amino acids (M-r = 26367) of which the first 33 amino acids are the presumed mitochondrial-targeting signal peptide. The deduced mature manganese-superoxide dismutase has 194 amino acids ------------------- Key: 1968 Medline: 94362511 Authors: Giglio AM;Hunter T;Bannister JV;Bannister WH;Hunter GJ Title: The copper/zinc superoxide dismutase gene of Caenorhabditis elegans. Citation: Biochemistry and Molecular Biology International 33: 41-44 1994 Type: ARTICLE Genes: age-1 sod-1 Abstract: The nucleotide and deduced amino acid sequences of the copper/zinc superoxide dismutase gene (sod-1) from the nematode Caenorhabditis elegans has been determined. The protein coding region is interrupted by three intron sequences covering 608 bp in total and encodes a protein of 158 amino acids (M-r = 16307). ------------------- Key: 1969 Medline: 94259231 Authors: Stroeher VL;Kennedy BP;Millen KJ;Schroeder DF;Hawkins MG;Goszczyn B;McGhee JD Title: DNA-protein interactions in the Caenorhabditis elegans embryo: Oocyte and embryonic factors that bind to the promoter of the gut-specific ges-1 gene. Citation: Developmental Biology 163: 367-380 1994 Type: ARTICLE Genes: elt-1 fer-1 ges-1 hlh-1 mab-5 pho-1 skn-1 eDf19 mDf7 nDf41 Abstract: We describe an experimental system in which to investigate DNA-protein interactions in the early Caenorhabditis elegans embryo. A homogeneous population of developmentally blocked mid-proliferation stage embryos can be produced by exposure to the deoxynucleotide analog fluorodeoxyuridine. These blocked embryos remain viable for days and express a number of biochemical markers of early differentiation, for example, gut granules, the gut esterase ges-1, and two regulatory genes, mab-5 and hlh-1. Using the techniques of gel mobility shift and DNase I footprinting, we show that nuclear extracts prepared from these embryos contain factors that bind to the 5'-promoter sequences of the C. elegans gut-specific ges-1 gene. In particular, we examine a putative gut "activator" region, which was previously identified by deletion-transformation analysis and which contains two copies of a consensus GATA-factor binding sequence. Factors that bind to double-stranded oligonucleotides containing the ges-1 GATA sequences are present predominantly in nuclear extracts of embryos but are found neither in cytoplasmic nor in nuclear extracts of unfertilized oocytes. Two proteins, of 43 and 60 kDa, can be uv-crosslinked to double-stranded oligonucleotides containing the ges-1 GATA sequences. The sizes of these proteins correspond to the sizes expected for the elt-1 protein and for the skn-1 protein, two regulatory factors present in early C. elegans embryos and possible candidates for ges-1 control. However, we show that homozygous deficiency embryos (mDf7/mDf7 embryos and eDf19/eDf19 embryos, both of which lack the elt-1 gene, and nDf41/Df41 embryos, which have no skn-1 gene), still express the ges-1 esterase. We conclude that neither the elt-1 gene nor the skn-1 gene is necessary zygotically for ges-1 expression. We suggest that neither the elt-1 protein nor the skn-1 protein interacts directly with the ges-1 gene and that the observed binding proteins must correspond to products of other genes. More generally, the present experimental system should allow the biochemical study of any gene expressed during early C. elegans embryogenesis. ------------------- Key: 1970 Medline: 94269631 Authors: Thomas JH Title: The mind of a worm. Citation: Science 264: 1698-1699 1994 Type: REVIEW Genes: cha-1 daf-11 daf-21 dec-8 exp-1 odr-1 odr-2 odr-5 unc-16 Abstract: In 1967, Sydney Brenner isolated the first behavioral mutants of the nematode Caenorhabditis elegans, and in 1970, John White began the systematic reconstruction of its nervous system. This dual approach of genetics coupled with detailed morphological analysis, now enhanced by the tools of molecular biology and electrophysiology, still dominates the study of the function and development of the C. elegans nervous system. Although Brenner's vision of a comprehensive understanding of this simple animal has taken time to mature, findings of the past few years indicate that the tree is bearing fruit. ------------------- Key: 1971 Medline: 94340821 Authors: Schedin P;Jonas P;Wood WB Title: Function of the her-1 gene is required for maintenance of male differentiation in adult tissues of C. elegans. Citation: Developmental Genetics 15: 231-239 1994 Type: ARTICLE Genes: her-1 him-8 sdc-1 sdc-2 sdc-3 vit-5 Abstract: Function of the sex-determining gene her-1 is required in XO embryos of C. elegans to specify male development. Using a temperature-sensitive mutant of her-1, we show that when XO males reared at a permissive temperature are shifted as adults to a nonpermissive temperature, they initiate vitellogenin synthesis in the intestine and oocyte production in the germline. A similar shift has no effect on her-1 (+) males. We conclude that sexual differentiation of the intestine and germline is plastic, requiring her-1 expression throughout adulthood for maintenance of the male state. ------------------- Key: 1972 Medline: 94340822 Authors: Zarkower D;De Bono M;Aronoff R;Hodgkin J Title: Regulatory rearrangements and smg-sensitive alleles of the C. elegans sex-determining gene tra-1. Citation: Developmental Genetics 15: 240-250 1994 Type: ARTICLE Genes: act-1 egl-1 emb-9 fem-1 fem-3 mab-3 mab-5 smg-1 smg-2 smg-4 tra-1 tra-2 eC2 eDp6 eDp24 eDp25 Abstract: The tra-1 gene is the terminal regulator in the sex determination pathway in C. elegans, directing all aspects of somatic sexual differentiation. Recessive loss-of-function (lf) mutations in tra-1 masculinize XX animals (normally somatically female), while dominant gain-of-function mutations feminize X animals (normally male). Most tra-1 (lf) mutations can be fitted into a simple allelic series of somatic masculinization, but a small number of lf alleles do not fit into this series. Here we show that three of these mutations are associated with DNA rearrangements 5' to the coding region. One allele is an inversion that may be subject to a position effect. We also report the isolation of a new class of tra-1 alleles that are responsive to mutations in the smg system of RNA surveillance. We show that two of these express RNAs of aberrant size. We suggest that the smg-sensitive mutations may identify a carboxy-terminal domain required for negative regulation of ------------------- Key: 1973 Medline: 95013416 Authors: Borgonie G;Van Driessche E;Link CD;De Waele D;Coomans A Title: Tissue treatment for whole mount internal lectin staining in the nematodes Caenorhabditis elegans, Panagrolaimus superbus and Acrobeloides maximus. Citation: Histochemistry 101: 379-384 1994 Type: ARTICLE Genes: mec-5 Abstract: Four different fixation schemes, using ten fluorescent-labelled lectins, were investigated for whole mount internal staining of three rhabditid nematodes: Caenorhabditis elegans, Panagrolaimus superbus and Acrobeloides maximus. Acetone-only fixation was found to give strong and reproducible staining, which could be prevented either by periodate treatment of the organisms or by specific inhibitory sugars of the lectins under investigation. Whereas the use of either phosphate or TRIS buffers had no effect on the staining pattern or the fluorescence intensity, the incubation time as well as the in- cubation temperature affected the staining reaction. The best results were obtained upon overnight incubation at 4 degrees C: the lectin staining could be inhibited in all cases, except for the intestinal brush border of C. elegans by the lectin of Lens culinaris. ------------------- Key: 1974 Medline: 94286586 Authors: Levitan DJ;Boyd L;Mello CC;Kemphues KJ;Stinchcomb DT Title: par-2, a gene required for blastomere asymmetry in Caenorhabditis elegans, encodes zinc-finger and ATP-binding motifs. Citation: Proceedings of the National Academy of Sciences USA 91: 6108-6112 1994 Type: ARTICLE Genes: fem-2 glp-1 par-2 Abstract: The par-2 gene of Caenorhabditis elegans functions in early embryogenesis to ensure an asymmetric first cleavage and the segregation of cytoplasmic factors. Both processes appear to be required to generate daughter blastomeres with distinct developmental potential. We isolated an allele of par-2 by using a screen for maternal-effect lethal mutations in a strain known for its high frequency of transposition events. A transposable element was found to be linked to this allele. Sequences flanking the site of transposon insertion were cloned and found to rescue the par-2 mutant phenotype. DNA in the par-2 region hybridized to a 2.3-kb germ-line-enriched mRNA. The cDNA corresponding to this germ-line-enriched message was cloned, sequenced, and used to identify the molecular lesions associated with three par-2 alleles. Sequence analysis of the par-2 cDNA revealed that the predicted protein contained two distinct motifs found in other known proteins: an ATP-binding site and a cysteine-rich motif which identifies the par-2 gene product as a member of a growing class of putative zinc-binding proteins. ------------------- Key: 1975 Medline: 94326660 Authors: Chen LS;Krause M;Sepanski M;Fire A Title: The Caenorhabditis elegans MYOD homolog HLH-1 is essential for proper muscle function and complete morphogenesis. Citation: Development 120: 1631-1641 1994 Type: ARTICLE Genes: dpy-7 hlh-1 myo-2 myo-3 smg-1 sup-5 sup-7 unc-54 ccDf1 ccDf4 ccDf12 ccDf13 ccDf14 Abstract: A family of muscle-specific helix-loop-helix transcription factors (myoD, myogenin, myf-5 and MRF4) has been implicated in the control of vertebrate skeletal myogenesis. Searches for homologues of this family in Caenorhabditis elegans identified a single family member, hlh-1, which is expressed in striated muscles and their clonal precursors. We have isolated a null allele of hlh-1 following chemical mutagenesis. Animals homozygous for the null mutation produce contractile body-wall muscles, although muscle contractions are weak and coordination is defective. In addition to the evident muscle defects, mutant animals fail to complete embryonic elongation and die as larvae or young adults. Ultrastructural analysis of the mutant muscle reveals an apparently normal local lattice of thick and thin filaments, with more global defects in sarcomere organization and muscle cell placement. Mosaic studies using the point mutation and an extrachromosomal transgene indicate that the requirement for hlh-1 is fully zygotic, with no maternal hlh-1 requirement for either muscle development or viability. ------------------- Key: 1976 Medline: 95044103 Authors: Waterston R;Ainscough R;Anderson K;Berks M;Blair D;Connell M;Cooper J;Coulson A;Craxton M;Dear S;Du Z;Durbin... Title: The genome of the nematode Caenorhabditis elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 58: 367-376 1994 Type: ARTICLE Genes: ceh-23 egl-5 mab-5 Abstract: he C. elegans genome project is part of a larger effort to understand how the information encoded in its DNA specifies the biology of this small nematode worm...In this paper we review the construction of the physical map and present a preliminary report on the pilot sequencing project. A more detailed report will be published shortly. ------------------- Key: 1977 Medline: 94299640 Authors: Clark-Maguire S;Mains PE Title: Localization of the mei-1 gene product of Caenorhabditis elegans, a meiotic-specific spindle component. Citation: Journal of Cell Biology 126: 199-209 1994 Type: ARTICLE Genes: fem-1 fem-3 glp-1 mei-1 mei-2 mel-26 zyg-9 gaDp1 Abstract: Genetic evidence suggests that the product of the mei-1 gene of Caenorhabditis elegans is specifically required for meiosis in the female germline. Loss-of-function mei-1 mutations block meiotic spindle formation while a gain-of-function allele instead results in spindle defects during the early mitotic cleavages. In this report, we use immunocytochemistry to examine the localization of the mei-1 product in wild-type and mutant embryos. During metaphase of meiosis I in wild-type embryos, mei-1 protein was found throughout the spindle but was more concentrated toward the poles. At telophase I, mei-1 product colocalized with the chromatin at the spindle poles. The pattern was repeated during meiosis II but no mei-1 product was visible during the subsequent mitotic cleavages. The mei-1 gain-of-function allele resulted in ectopic mei-1 staining in the centers of the microtubule-organizing centers during interphase and in the spindles during the early cleavages. This aberrant localization is probably responsible for the poorly formed and misoriented cleavage spindles characteristic of the mutation. We also examined the localization of mei-1(+) product in the presence of mutations of genes that genetically interact with mei-1 alleles. mei-2 is apparently required to localize mei-1 product to the spindle during meiosis while mel-26 acts as a postmeiotic inhibitor. We conclude that mei-1 encodes a novel spindle component, one that is specialized for the acentriolar meiotic spindles unique to female meiosis. The genes mei-2 and mel-26 are part of a regulatory network that confines mei-1 activity to meiosis. ------------------- Key: 1978 Medline: 95042580 Authors: Gomez-Saladin E;Wilson DL;Dickerson IM Title: Isolation and in situ localization of a cDNA encoding a Kex2-like prohormone convertase in the nematode Caenorhabditis elegans. Citation: Cellular and Molecular Neurobiology 14: 9-25 1994 Type: ARTICLE Genes: bli-4 fer-15 Abstract: 1. A cDNA that encodes a Kex2-like prohormone convertase (PC) containing an active site similar to that of mammalian PC2 has been isolated from C. elegans. Total RNA was isolated from a mixed population of strain BA713 worms. After poly-(A)-selection and reverse transcription, degenerate/nested polymerase chain reactions (PCR) were performed using primers based on conserved regions within the active sites of the known vertebrate and invertebrate endoproteases. 2. Two distinct 300-bp PCR products that shared homologies with the active sites of known Kex2-like endoproteases were isolated. These two PCR products were used to screen a C. elegans cDNA library. 3. The complete cDNA for a Kex2-like endoprotease, designated CELPC2, was isolated and determined to be 2527 bp in length. This size was confirmed by northern analysis. The deduced amino acid sequence for the CELPC2, cDNA is very similar to the known Kex2-like endoproteases, especially at conserved regions within the active sites, but not identical to any one of them. The strongest structural homology was to vertebrate and invertebrate PC2 sequences. 4. In situ hybridization suggests that CELPC2 is synthesized primarily in cells associated with the circumpharyngeal nerve ring and the dorsorectal ganglion. ------------------- Key: 1979 Medline: 94287190 Authors: Sommer RJ;Sternberg PW Title: Changes of induction and competence during the evolution of vulva development in nematodes. Citation: Science 265: 114-118 1994 Type: ARTICLE Genes: Abstract: In Caenorhabditis, the vulva is formed in the central body region from three of six equivalent cells and is induced by the gonad. In some nematodes, however, the vulva is located in the posterior body region. Vulval development has been analyzed in three such genera. The same precursor cells give rise to the vulva in Caenorhabditis and in the posterior vulva species, but in the latter the cells first migrate posteriorly. In two such species, the vulva is not induced by the gonad, but instead relies on intrinsic properties of precursor cells. Thus, evolution of organ position involves changes in induction and competence. ------------------- Key: 1980 Medline: Authors: Nelson GA;Schubert WW;Kazarians GA;Richards GF;Benton EV;Benton ER;Henke R Title: Radiation effects in nematodes: Results from IML-1 experiments. Citation: Advances in Space Research 14: 87-91 1994 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans was exposed to natural space radiation using the ESA Biorack facility aboard Spacelab on International Microgravity Laboratory 1, STS-42. For the major experimental objective dormant animals were suspended in buffer or on agar or immobilized next to CR-39 plastic nuclear track detectors to correlate fluence of HZE particles with genetic events. This configuration was used to isolate mutations in a set of 350 essential genes as well as in the unc-22 structural gene. From flight samples 13 mutants in the unc-22 gene were isolated along with 53 lethal from autosomal regions balanced by a translocation eT1(III;V). Preliminary analysis suggests that mutants from worms corrrelated with specific cosmic ray tracks may have a higher proportion of rearrangements than those isolated from tube cultures on a randomly sampled basis. Flight sample mutation rate was approximately 8-fold higher than ground controls which ------------------- Key: 1981 Medline: 94283388 Authors: Dodemont H;Riemer D;Ledger N;Weber K Title: Eight genes and alternative RNA processing pathways generate an unexpectedly large diversity of cytoplasmic intermediate filament proteins in the nematode Citation: EMBO Journal 13: 2625-2638 1994 Type: ARTICLE Genes: Abstract: Cytoplasmic intermediate filament (IF) proteins of Caenorhabditis elegans are encoded by a dispersed multigene family comprising at least eight genes which map to three linkage groups. Exon sequences and intron patterns define three distinct subfamilies. While all eight IF genes display the long coil 1b subdomain of nuclear lamins, only six genes (a(1)-a(4), b(1) and b(2)) retain a lamin-like tail domain. Two genes (c(1) and c(2)) have acquired entirely novel tail domains. The overall sequence identity of the rod domains is only 29%. The gene structures show a strong drift in number and positions of introns, none of which are common to all genes. Individual genes share only one to four intron locations with the Helix aspersa IF gene, but all eight nematode genes together account for nine of the 10 introns of the gastropod gene. All C.elegans IF genes are transcribed and all except gene c(2) produce trans-spliced mRNAs. Alternatively spliced mRNAs arise from genes a(1), b(2) and c(?)2 through several mechanisms acting at the transcriptional and post-transcriptional levels. These involve the alternative use of distinct promoters, polyadenylation sequences and both cis and trans RNA splice sites. The resulting sequence variations are restricted to the non-helical end domains. Minimally 12 distinct IF proteins are encoded by the various mRNAs. Different abundances in mixed-stage nematode populations suggest cell type- and/or ------------------- Key: 1982 Medline: 94233376 Authors: Parkhurst SM;Meneely PM Title: Sex determination and dosage compensation: Lessons from flies and worms. Citation: Science 264: 924-932 1994 Type: REVIEW Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 fem-1 fem-2 fem-3 fog-1 fog-2 fog-3 her-1 mog-1 sdc-1 sdc-2 sdc-3 tra-1 tra-2 tra-3 xol-1 Abstract: In both Drosophila melanogaster and Caenorhabditis elegans somatic sex determination, germline sex determination, and dosage compensation are controlled by means of a chromosomal signal known as the X:A ratio. A variety of mechanisms are used for establishing and implementing the chromosomal signal, and these do not appear to be similar in the two species. Instead, the study of sex determination and dosage compensation is providing more general lessons about different types of signaling pathways used to control alternative developmental states of cells and organisms. ------------------- Key: 1983 Medline: 95019863 Authors: Hosokawa H;Ishii N;Ishida H;Ichimori K;Nakazawa H;Suzuki K Title: Rapid accumulation of fluorescent material with aging in an oxygen-sensitive mutant mev-1 of Caenorhabditis elegans. Citation: Mechanisms of Ageing & Development 74: 161-170 1994 Type: ARTICLE Genes: mev-1 Abstract: Mutations in mev-1 of the nematode Caenorhabditis elegans render animals hypersensitive to high oxygen concentrations. They also reduce life span. To further understand the effects of mev-1 on aging, accumulation of fluorescent material resembling lipofuscin was measured by biochemical and histological analyses. Fluorescent material accumulated in both wild type and mev-1 animals with increasing age. The mev-1 mutant accumulated more fluorescent material at a greater rate than dose wild type. Furthermore, the accumulation rates depended on concentration of oxygen. Since this phenotype has been widely used as an aging marker, these results validate mev-1's use as a model to study aging. ------------------- Key: 1984 Medline: 95057988 Authors: Schinkmann K;Li C Title: Comparison of two Caenorhabditis genes encoding FMRFamide(Phe-Met-Arg-Phe-NH2)-like peptides. Citation: Molecular Brain Research 24: 238-246 1994 Type: ARTICLE Genes: flp-1 Abstract: We have identified a gene encoding multiple FMRFamide-like peptides in the necromenic nematode Caenorhabditis vulgaris. This gene, Cv-flp-1, shares strong sequence homology in the coding regions with the flp-1 gene from the related free-living soil nematode C. elegans. The predicted neuropeptide precursor proteins differ by only four conservative amino acid changes, none of which affects sequences of the predicted neuropeptides. DNA sequences in the non-coding areas are less conserved, but areas of sequence homology are found in introns and in 3' and 5' non-translated regions, suggesting some functional significance for these conserved regions. In C. vulgaris, as was found in C. elegans, two transcripts are presumably produced as a result of use of an alternative 3' splice acceptor site. Lastly, an antibody specific for the RF-moiety of FMRFamide stains a similar subset of cells in C. elegans and C. vulgaris. These results indicate that the function and regulation of the peptides are likely to be conserved in both species. ------------------- Key: 1985 Medline: 94284514 Authors: Fabian TJ;Johnson TE Title: Production of age-sychronous mass cultures of Caenorhabditis elegans. Citation: Journal of Gerontology 49: B145-B156 1994 Type: ARTICLE Genes: age-1 emb-27 fer-15 glp-4 spe-9 Abstract: Methods are described for culturing large populations of age-synchronous Caenorhabditis elegans throughout the adult life span. Contamination of adult populations by progeny was prevented by constructing double-mutant strains that produce progeny at a frequency of less than .005 per adult at the nonpermissive temperature (25.5 degrees C). Of four double-mutant strains that we have characterized, three have wild-type life spans at 25.5 degrees. The other strain contains a mutant allele, age-1(hx542), that results in an increase in life span of 60% over wild type. All four strains produced sufficient numbers of progeny at the permissive temperature (20 degrees C) to generate populations containing 1-5 x 10(6) nematodes within two weeks. Age-synchronous young adult populations were produced using these strains and have been maintained as adults both in liquid culture and on agar medium. Procedures that reduce E. coli contamination by 30-fold in harvested samples of adults are also described. ------------------- Key: 1986 Medline: 95021520 Authors: Lassandro F;Sebastiano M;Zei F;Bazzicalupo P Title: The role of dityrosine formation in the crosslinking of CUT-2, the product of a second cuticlin gene of Caenorhabditis elegans. Citation: Molecular & Biochemical Parasitology 65: 147-159 1994 Type: ARTICLE Genes: cut-1 cut-2 Abstract: A second cuticlin gene, cut-2, of the nematode Caenorhabditis elegans, has been isolated and its genomic and cDNA sequences determined. The gene codes for a component of cuticlin, the insoluble residue of nematode cuticles. Conceptual translation of cut-2 reveals a 231-amino acid secreted protein which, like CUT-I, begins with a putative signal peptide of 16 residues. The central part of the protein consists of 13 repetitions of a short hydrophobic motif, which is often degenerated with substitutions and deletions. Parts of this motif are present also in CUT-1 (Caenorhabditis elegans) as well as in several protein components of the larval cuticle and of the eggshell layers of various insects (Locusta migratoria, Ceratitis capitata and Drosophila species). These sequence similarities are related to the similar functions of these proteins: they are all components of extracellular insoluble protective layers. Immunolocalisation and transcription analysis suggest that CUT-2 contributes to the cuticles of all larval stages and that it is not stage-specific. Analysis by reverse transcriptase-PCR suggests that transcription is not continuous throughout larval development but occurs in peaks which precede the moults. Dityrosine has been detected in the cuticle of nematodes and of insects; formation of dityrosine bridges may be one of the cross-linking mechanisms contributing to the insolubility of cuticlins. Recombinant, soluble CUT-2 is shown to be an excellent substrate for an in vitro cross-linking reaction, catalysed by horseradish peroxidase in the presence of H2O2, which results in the formation of insoluble, high-molecular weight CUT-2 and of dityrosine. ------------------- Key: 1987 Medline: 95009534 Authors: Hutter H;Schnabel R Title: glp-1 and inductions establishing embryonic axes in C. elegans. Citation: Development 120: 2051-2064 1994 Type: ARTICLE Genes: glp-1 lin-12 Abstract: Two successive inductions specify blastomere identities, that is complex cell lineages and not specific tissues, in a major part of the early C. elegans embryo. The first induction acts along the anterior-posterior axis of the embryo and the second along the left-right axis. During the first induction a specific lineage program is induced in the posterior of the two AB blastomeres present in the four cell embryo. During the second induction, almost ail of the left-right differences of the embryo are specified by interactions between a single signalling blastomere, MS, and the AB blastomeres that surround it. In both cases the inductions break the equivalence of pairs of blastomeres. The inductions correlate with the cell-cell contacts to the inducing blastomeres. The stereotype cleavage pattern of the early embryo results in invariant cell-cell contacts that guarantee the specificity of the inductions. Both inductions are affected in embryos mutant for glp-1 suggesting that in both cases glp-1 is involved in the reception of the signal. ------------------- Key: 1988 Medline: 94322393 Authors: Fan J;Amos LA Title: Kinesin light chain isoforms in Caenorhabditis elegans. Citation: Journal of Molecular Biology 240: 507-512 1994 Type: NOTE Genes: unc-104 unc-116 Abstract: cDNAs for two isoforms of kinesin light chain in Caenorhabditis elegans have been cloned and sequenced; the deduced M(r) values of the polypeptides are 60,338 and 58,938. Surprisingly, two independent cDNA libraries, each derived from worms at mixed stages of development, provided different single isoforms. The two isoforms are apparently derived from a single gene but have differences at both N and C termini of the predicted protein sequences. The sequences are highly homologous to those from other species, except for some minor features that may be related to the shortened form of the kinesin heavy chain, the product of gene unc-116, with which the light chains are assumed to associate. ------------------- Key: 1989 Medline: 94329755 Authors: Jain PT;Chang SH;Gutry PP;Berezesky IK;Trump BF Title: The relationship between Ca2+(i) and cell death using an in vivo model: A study using the ced-1 mutant strain of C. elegans. Citation: Toxicologic Pathology 21: 572-583 1994 Type: ARTICLE Genes: ced-1 Abstract: The ced-1 mutant of the free-living nematode, Caenorhabitis elegans, was used to study cell injury and cell death in relation to changes in intracellular ionized calcium (`Ca2+ïi). This animal, which is being genetically characterized, may prove to be extremely useful for certain toxicologic studies because of its small size, optical transparency, rapid generation time, and the morphologic and genetic data currently available. During the development of this animal, 131 of 1,090 ultimate somatic cells undergo programmed cell death. Using mutagenesis techniques, several genes responsible for this death have been identified. In this study, we have taken advantage of the ced-1 mutant in which dead cells accumulate, as they cannot be phagocytized and removed. Although changes in `Ca2+ïi have been studied in relation to cell injury and cell death, observations have been essentially restricted to in vitro monolayer cultures because of the methodology involved. To study the relationship between changes in `Ca2+ïi and injury in vivo, we selected this animal model for further study and report here the morphological changes following the effects of ionomycin treatment in relation to increases of `Ca2+ïi and cell death as measured using the fluorescent probes Fluo-3/AM and propidium iodide, respectively. The technique of confocal laser scanning microscopy is ideally adapted to such measurements in these living animals, and the results can be readily correlated with those made with Nomarski differential interference contrast microscopy as well as with transmission electron microscopy. The results support previous in vitro observations and show that early increases of `Ca2+ïi accompany early reactions to injury. Furthermore, the results also show that changes in this small invertebrate metazoan parallel those seen in mammalian systems, including human. Thus, the current study indicates that ced-1 C elegans can potentially serve as an in vivo model not only for evaluating the possible temporal relationship of `Ca2+ïi elevation with cell death but also for evaluating the `Ca2+ïi elevation observed in relation to ------------------- Key: 1990 Medline: 95073612 Authors: Clark SG;Lu WX;Horvitz HR Title: The Caenorhabditis elegans locus lin-15, a negative regulator of a tyrosine kinase signaling pathway, encodes two different proteins. Citation: Genetics 137: 987-997 1994 Type: ARTICLE Genes: lin-8 lin-9 lin-15 lin-36 mnDf4 Abstract: The Caenorhabditis elegans locus lin-15 negatively regulates an intercellular signaling process that induces formation of the hermaphrodite vulva. The lin-15 locus controls two separate genetic activities. Mutants that lack both activities have multiple, ectopic pseudo-vulvae resulting from the overproduction of vulval cells, whereas mutants defective in only one lin-15 activity appear wild-type. lin-15 acts non-cell-autonomously to prevent the activation of a receptor tyrosine kinase/ras signaling pathway. We report here the molecular characterization of the lin-15 locus. The two lin-15 activities are encoded by contiguous genomic regions and by two distinct, non-overlapping transcripts that may be processed from a single mRNA precursor by trans-splicing. Based on the DNA sequence, the 719- and 1,440-amino acid lin-15 proteins are not similar to each other or to known proteins. lin-15 multivulva mutants, which are defective in both lin-15 activities, contain deletions and insertions that affect the lin-15 genomic region. ------------------- Key: 1991 Medline: 95073613 Authors: Hsu DR;Meyer BJ Title: The dpy-30 gene encodes an essential component of the Caenorhabditis elegans dosage compensation machinery. Citation: Genetics 137: 999-1018 1994 Type: ARTICLE Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 her-1 lin-14 lin-15 myo-1 myo-2 sdc-1 sdc-2 sdc-3 sup-7 tra-1 xol-1 ctDf1 yDf12 Abstract: The need to regulate X chromosome expression in Caenorhabditis elegans arises as a consequence of the primary sex-determining signal, the X/A ratio (the ratio of X chromosomes to sets of autosomes), which directs 1X/2A animals to develop as males and 2X/2A animals to develop as hermaphrodites. C. elegans possesses a dosage compensation mechanism that equalizes X chromosome expression between the two sexes despite their disparity in X chromosome dosage. Previous genetic analysis led to the identification of four autosomal genes, dpy-21, dpy-26, dpy-27 and dpy-28, whose products are essential in XX animals for proper dosage compensation, but not for sex determination. We report the identification and characterization of dpy-30, an essential component of the dosage compensation machinery. Putative null mutations in dpy-30 disrupt dosage compensation and cause a severe maternal-effect, XX-specific lethality. Rare survivors of the dpy-30 lethality are dumpy and express their X-linked genes at higher than wild-type levels. These dpy-30 mutant phenotypes superficially resemble those caused by mutations in dpy-26, dpy-27 and dpy-28; however, detailed phenotypic analysis reveals important differences that distinguish dpy-30 from these genes. In contrast to the XX-specific lethality caused by mutations in the other dpy genes, the XX-specific lethality caused by dpy-30 mutations is completely penetrant and temperature sensitive. In addition, unlike the other genes, dpy-30 is required for the normal development of XO animals. Although dpy-30 mutations do not significantly affect the viability of XO animals, they do cause them to be developmentally delayed and to possess numerous morphological and behavioral abnormalities. Finally, dpy-30 mutations can dramatically influence the choice of sexual fate in animals with an ambiguous sexual identity, despite having no apparent effect on the sexual phenotype of otherwise wild-type animals. Paradoxically, depending on the genetic background, dpy-30 mutations cause either masculinization or feminization, thus revealing the complex regulatory relationship between the sex determination and dosage compensation processes. The novel phenotypes caused by dpy-30 mutations suggest that in addition to acting in the dosage compensation process, dpy-30 may play a more general ------------------- Key: 1992 Medline: Authors: Barker DM Title: Copulatory plugs and paternity assurance in the nematode Caenorhabditis elegans. Citation: Animal Behaviour 48: 147-156 1994 Type: ARTICLE Genes: plg-1 Abstract: The males of some strains of Caenorhabditis elegans (Maupas) make a copulatory plug and place it over the genital opening of the hermaphrodite after mating. The hypothesis is tested that the plug interferes with the mating attempts of second males and thus functions to protect the paternity of the plugging male that mated first. Two pure-breeding strains, which were genetically identical except at the locus governing the plugging trait, were used in the observations. The paper reports on observations of mating behaviour between males and females (a mutant form of the hermaphrodite), which had mated once and were either plugged or not plugged. The observations provide data on the durations of successive encounters between the male and female before copulation was achieved and on the numbers of those encounters. The results show that the plug does indeed lessen the likelihood of a second mating. The presence of a plug increased the likelihood that a male would lose contact with the female on the first encounter rather than mate with her, increased the duration of the encounter that ended in successful copulation and increased the total encounter time before successful copulation. A quantitative description of C. elegans mating ------------------- Key: 1993 Medline: 95384798 Authors: Lim WA; Richards FM Title: Critical residues in an SH3 domain from Sem-5 suggest a mechanism for proline-rich peptide recognition. Citation: Nature Structural Biology 1: 221-225 1994 Type: ARTICLE Genes: sem-5 Abstract: Src homology 3 (SH3) domains bind specific proline-rich peptide motifs. To identify interactions involved in peptide recognition, we have mutated residues on the putative binding surface of an SH3 domain from the Caenorhabditis elegans protein Sem-5. Among the most critical positions ave three adjacent aromatic residues, which appear to participate in highly stereospecific packing interactions with the ligand. The co-planar arrangement of two of these residues closely matches the periodicity of a poly-proline II (PPII) helix. Thus, a model for recognition has the peptide adopting a PPII helix, with the pyrrolidine rings on one helical face interlocking with the aromatic SH3 residues. ------------------- Key: 1994 Medline: 94261669 Authors: Stadler M;Mayer A;Anke H;Sterner O Title: Fatty acids and other compounds with nematicidal activity from cultures of Basidiomycetes. Citation: Planta Medica 60: 128-132 1994 Type: ARTICLE Genes: Abstract: In a screening for nematicidal activities in cultures of Basidiomycetes, cultures of Pleurotus pulmonarius and Hericium coralloides exhibited toxic effects towards the saprophytic nematode Caenorhabditis elegans. Subsequently S-coriolic acid (1), linoleic acid (2), p-anisaldehyde (3), p-anisyl alcohol (4), 1-(4-methoxyphenyl)-1,2-propanediol (5), and 2-hydroxy-(4'-methoxy)-propiophenone (6) were isolated from submerged cultures of P. pulmonarius. All compounds showed nematicidal activities towards C. elegans. The most active compounds were 1 and 2 with LD-50 values between 5 and 10 ppm. Compounds 1, 4, and 5 have not been previously isolated from higher fungi, 6 is a new natural product. From cultures of H. coralloides, which exhibited both repellant and nematicidal effects, a nematicidal fatty acid mixture was obtained, containing linoleic acid, oleic acid, and palmitic acid as its main components. ------------------- Key: 1995 Medline: 94261212 Authors: Hu S-H;Parker MW;Lei JY;Wilce MCJ;Benian GM;Kemp BE Title: Insights into autoregulation from the crystal structure of twitchin kinase. Citation: Nature 369: 581-584 1994 Type: ARTICLE Genes: unc-22 Abstract: Many protein kinases are self-regulated by an intrasteric mechanism where part of the enzyme's structure directly inhibits the active site. This inhibitory structure is called a pseudosubstrate and specific regulators are required to remove it from the active site to allow substrates access. Removal of the pseudosubstrate sequence from members of the myosin light-chain kinase subfamily, including twitchin kinase, activates them but it is not known whether the pseudosubstrate sequence binds to the active site. Native twitchin is a 753K protein (6,839 residues) located in muscle A-bands of the nematode Caenorhabditis elegans and because of its size has not been easy to study. We have determined the crystal structure, refined to 2.8 A resolution, of a recombinant fragment (residues 5,890 to 6,262) of twitchin kinase that contains the catalytic core and a 60 residue carboxy-terminal tail. The C-terminal tail extends through the active site, wedged between the small and large lobes of the structure and making extensive contacts with the catalytic core which accounts for autoinhibition and provides direct support for the intrasteric mechanism of protein kinase regulation. ------------------- Key: 1996 Medline: Authors: Guven K;Duce JA;de Pomerai DI Title: Evaluation of a stress-inducible transgenic nematode strain for rapid aquatic toxicity testing. Citation: Aquatic Toxicology 29: 119-137 1994 Type: ARTICLE Genes: Abstract: A transgenic strain of the nematode Caenorhabditis elegans which carries a stress-inducible lacZ reporter gene has been evaluated in terms of its response to several environmental toxicants. Optimal sensitivity is obtained by exposing these worms to toxicants at a temperature just below that required for heat induction of the transgene. Under these circumstances, several heavy metals (Cd2+, Zn2+, Hg2+, Mn2+, Sn2+, Ag+) cause dose-dependent transgene expression, which can be monitored as beta-galactosidase enzyme activity or by in situ histochemical staining. A simple assessment procedure has been developed so that staining patterns can be compared between runs. The induced enzyme activity is localised in a single band (of apparent size 170 kD) on Western blots, as shown both by histochemical staining and immunoprobing. Endogenous heat-shock proteins (hsp70) are optimally induced under the same assay conditions, but modest induction is also apparent under control conditions (sub-heat-shock temperatures alone). Our system requires relatively high concentrations (ppm) of metallic ions for clear-cut induction, but is apparently more sensitive to certain organic and organo-metallic compounds (lindane and tributyltin are effective at ppb levels). This system works well within strictly defined assay conditions, but some toxicants are more effective inducers than others (e.g. Cd2+ versus Mn2+), while some give paradoxical dose-response curves possibly due to enzyme poisoning at high toxicant concentrations (e.g. Ag+). However, similar problems are likely to be encountered with any transgenic assay system based on the heat-shock response when used to ------------------- Key: 1997 Medline: 94261187 Authors: Marengere LEM;Songyang Z;Gish GD;Schaller MD;Parsons JT;Stern MJ;Cantley LC;Pawson T Title: SH2 domain specificity and activity modified by a single residue. Citation: Nature 369: 502-505 1994 Type: ARTICLE Genes: sem-5 Abstract: Many intracellular targets of protein-tyrosine kinases possess Src homology 2 (SH2) domains that directly recognize phosphotyrosine-containing sites on autophosphorylated growth factor receptors and cytoplasmic proteins, and thereby mediate the activation of biochemical signalling pathways. SH2 domains possess relatively well conserved residues that form the phosphotyrosine-binding pocket, and more variable residues that are implicated in determining binding specificity by recognition of the three amino acids carboxy-terminal to phosphotyrosine (the +1 to +3 positions). One such residue, occupying the EF1 position of the +3-binding pocket, is a Thr in the SH2 domain of the Src tyrosine kinase, but is predicted to be a Trp in the SH2 domain of the Sem-5/drk/Grb2 adaptor protein. Here we report that changing this residue in the Src SH2 domain from Thr to Trp switches its selectivity to resemble that of the Sem-5/drk/Grb2 SH2 domain. Furthermore, this mutant Src SH2 domain effectively substitutes for the SH2 domain of the Sem-5 protein in activation of the Ras pathway in vivo. These results identify a residue that can modify SH2 selectivity, and indicate that the biological activity of an SH2 domain correlates with its binding specificity. ------------------- Key: 1998 Medline: 95037649 Authors: Eisenmann DM;Kim SK Title: Signal transduction and cell fate specification during Caenorhabditis elegans vulval development. Citation: Current Opinion in Genetics & Development 4: 508-516 1994 Type: REVIEW Genes: kin-15 kin-16 lag-2 let-23 let-60 lin-3 lin-12 lin-15 lin-31 lin-45 mpk-1 mpk-2 sem-5 sur-1 unc-101 Abstract: A receptor tyrosine kinase/Ras signaling pathway controls the specification of vulval cell fates in Caenorhabditis elegans. Recently, C. elegans genes encoding proteins with similarity to mammalian Raf (lin-45), mitogen-activated protein kinase (mpk-1/sur-1), and an HNF-3 transcription factor (lin-31) have been identified and shown to act downstream of let-60 (ras) in this pathway. These genetically identified gene products bridge the gap between signal transduction at the plasma membrane and the control of cell fate specification in the nucleus. ------------------- Key: 1999 Medline: 95037656 Authors: Greenwald I Title: Structure/function studies of lin-12/Notch proteins. Citation: Current Opinion in Genetics & Development 4: 556-562 1994 Type: REVIEW Genes: glp-1 lin-12 Abstract: The lin-12/Notch proteins appear to act as transmembrane receptors for intercellular signals that specify cell fates during animal development. Recent structure/function studies have shown that the lin-12/Notch intracellular domain alone has the intrinsic signal-transducing activity of the intact protein, and that the role of the extracellular domain is to regulate this intrinsic activity. These studies have also suggested that the different lin-12/Notch proteins in a given organism are interchangeable biochemically and have addressed the role of lin-12/Notch genes in development. ------------------- Key: 2000 Medline: 95037657 Authors: Priess JR Title: Establishment of initial asymmetry in early Caenorhabditis elegans embryos. Citation: Current Opinion in Genetics & Development 4: 563-568 1994 Type: REVIEW Genes: apx-1 cap-1 cap-2 glp-1 mex-1 pie-1 skn-1 Abstract: The Caenorhabditis elegans embryo has anterior/posterior, dorsal/ventral and left/right axes that correspond to spatially asymmetric patterns of cell differentiation. Recent studies have provided insight into how the different embryonic axes are determined and have shown that the products of the glp-1, skn-1, cap-1 and cap-2 genes appear to be distributed asymmetrically in the early embryo. These gene products should provide important tools for understanding how asymmetries are established initially in nematode embryogenesis. ------------------- Key: 2001 Medline: 95037659 Authors: Garriga G;Stern MJ Title: Hams and Egls: genetic analysis of cell migration in Caenorhabditis elegans. Citation: Current Opinion in Genetics & Development 4: 575-580 1994 Type: REVIEW Genes: egl-5 egl-15 egl-17 egl-18 egl-20 egl-27 egl-43 ham-1 ham-2 ham-3 lin-39 mab-5 mig-1 mig-2 mig-10 sem-5 unc-34 unc-53 unc-71 unc-73 Abstract: The analysis of mutations that disrupt egg laying by the Caenorhabditis elegans hermaphrodite has identified genes that are required for the long-range migrations of two cell types, the hermaphrodite-specific neurons and the sex myoblasts. Molecular analysis of some of these genes indicates that transcription factors and signal transduction molecules are necessary for the migrations of ------------------- Key: 2002 Medline: 95037660 Authors: Hengartner MO;Horvitz HR Title: Programmed cell death in Caenorhabditis elegans. Citation: Current Opinion in Genetics & Development 4: 581-586 1994 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: Programmed cell death in the nematode Caenorhabditis elegans requires the activities of the genes ced-3 and ced-4 and is antagonized by the activity of the gene ced-9. Cloning of these C. elegans genes has shown that two of them encode proteins with similarity to vertebrate cell death genes and has revealed that nematodes and mammals share a common pathway for programmed cell death. ------------------- Key: 2003 Medline: 95037661 Authors: Culotti JG Title: Axon guidance mechanisms in Caenorhabditis elegans. Citation: Current Opinion in Genetics & Development 4: 587-595 1994 Type: REVIEW Genes: egl-43 mab-5 mec-3 unc-5 unc-6 unc-14 unc-33 unc-34 unc-40 unc-44 unc-51 unc-53 unc-71 unc-73 unc-76 Abstract: Genetics studies have identified an extracellular path cue molecule, UNC-6, and a neuronal receptor, UNC-5, that act to guide migrating pioneer growth cones along the dorsoventral coordinate of the Caenorhabditis elegans body wall. Ectopic expression studies and characterization of mutants have demonstrated directly the instructive action of these molecules, suggesting a molecular model for how they perform their guidance functions. Recent evidence suggests that these and other genetically identified axon guidance molecules are likely to have vertebrate ------------------- Key: 2004 Medline: 94320591 Authors: Sibley MH;Graham PL;von Mende N;Kramer JM Title: Mutations in the alpha2(IV) basement membrane collagen gene of Caenorhabditis elegans produce phenotypes of differing severities. Citation: EMBO Journal 13: 3278-3285 1994 Type: ARTICLE Genes: emb-9 let-2 unc-3 mnDf41 mnDp1 Abstract: Type IV collagen forms a network that provides the major structural support of basement membranes. We have determined the nucleotide alterations and phenotypes of 17 mutant alleles of the Caenorhabditis elegans alpha 2(IV) collagen gene let-2. All 17 mutations are within the triple helical (Gly-X-Y) repeat domain of the molecule. Fifteen of the mutations are replacements of Gly-X-Y repeat glycines with aspartate, glutamate or arginine, and they cause a wide range of phenotypes. The mildest alleles are nearly,wild-type at 15 and 20 degrees C but embryonic lethal at 25 degrees C, while the most severe allele is embryonic lethal at all three temperatures, Mutations resulting in severe phenotypes are generally located in areas of lower calculated thermal stability of the type IV collagen molecule. An alanine to threonine substitution at position X of a Gly-X-Y triplet immediately following an interruption results in a severe phenotype. This mutation is unusual because substitutions at positions X or Y have not generally been found to cause strong phenotypes in C.elegans or human collagens. An intron splice acceptor mutation causes a strict embryonic lethal phenotype, but does not completely abolish gene function. Pairs of independent mutations affect each of three glycines, indicating a non-random distribution of mutations in the molecule. It is suggested that this clustering results because many glycine substitutions may cause dominant lethal or sterile phenotypes. ------------------- Key: 2005 Medline: 94373771 Authors: Ristoratore F;Cermola M;Nola M;Bazzicalupo P;Favre R Title: Ultrastructural immuno-localization of CUT-1 and CUT-2 antigenic sites in the cuticles of the nematode Caenorhabditis elegans. Citation: Journal of Submicroscopic Cytology and Pathology 26: 437-443 1994 Type: ARTICLE Genes: cut-1 cut-2 Abstract: CUT-1 and CUT-2 are two distinct proteins found in cuticlin, the insoluble residue of the cuticles of the nematode Caenorhabditis elegans. They are the products of genes which have been previously characterized molecularly. These proteins have been expressed as recombinant in Escherichia coli and specific antisera have been raised against them. The experiments reported here regard their ultrastructural immuno-gold localization either on purified cuticles or on whole worms of various stages of development of Caenorhabditis elegans. A location in the cortical layer of the isolated cuticles is common to all stages, whereas there is a dauer specific location in the fibrous ribbon underneath the alae. These localizations are compared with immune-labelling obtained using a serum raised against the whole cuticlin residue. CUT-1 and CUT-2 epitopes are easily and specifically lost during ------------------- Key: 2006 Medline: 94316481 Authors: Stenico M;Lloyd AT;Sharp PM Title: Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases. Citation: Nucleic Acids Research 22: 2437-2446 1994 Type: ARTICLE Genes: act-1 act-2 act-3 act-4 ama-1 cal-1 ced-4 ced-9 ceh-3 ceh-19 cha-1 clb-1 clb-2 col-1 col-2 col-6 col-7 col-8 col-13 col-14 col-34 crt-1 cut-1 cyt-1 daf-1 deb-1 deg-1 dpy-7 dpy-13 eft-2 elt-1 fem-1 fem-3 flp-1 ges-1 glp-1 goa-1 gpa-2 gpa-3 gpd-1 gpd-2 gpd-3 gpd-4 gst-1 his-9 his-10 his-11 lin-12 his-12 his-24 hlh-1 hsp-3 hsp-4 kin-15 kin-16 kup-1 let-23 lin-3 lin-10 lin-11 lin-14 lin-39 mab-5 mec-3 mec-4 mec-7 mlc-1 mlc-3 myo-1 myo-2 myo-3 nhe-1 pal-1 rac-1 rbp-1 rol-6 sdc-1 sdc-3 sem-5 spe-4 sqt-1 tra-1 tra-2 unc-4 unc-5 unc-6 unc-7 unc-15 unc-18 unc-22 unc-33 unc-54 unc-86 unc-93 unc-104 vit-2 vit-4 vit-5 vit-6 zyg-11 Abstract: Synonymous codon usage varies considerably among Caenorhabditis elegans genes. Multivariate statistical analyses reveal a single major trend among genes. At one end of the trend lie genes with relatively unbiased codon usage. These genes appear to be lowly expressed, and their patterns of codon usage are consistent with mutational biases influenced by the neighbouring nucleotide. At the other extreme lie genes with extremely biased codon usage. These genes appear to be highly expressed, and their codon usage seems to have been shaped by selection favouring a limited number of translationally optimal codons. Thus, the frequency of these optimal codons in a gene appears to be correlated with the level of gene expression, and may be a useful indicator in the case of genes (or open reading frames) whose expression levels (or even function) are unknown. A second, relatively minor trend among genes is correlated with the frequency of G at synonymously variable sites. It is not yet clear whether this trend reflects variation in base composition (or mutational biases) among regions of the C.elegans genome, or some other factor. Sequence divergence between C.elegans and C.briggsae has also been studied. ------------------- Key: 2007 Medline: 94308769 Authors: Harada S;Hori I;Yamamoto H;Hosono R Title: Mutations in the unc-41 gene cause elevation of acetylcholine levels. Citation: Journal of Neurochemistry 63: 439-446 1994 Type: ARTICLE Genes: ace-3 unc-41 mDf3 nDf31 Abstract: Mutations in the Caenorhabditis elegans unc-41 gene result in an allele-dependent elevation of acetylcholine content. Eight recessive alleles (cn252, e268, e399, e650, e1175, e1199, e1294, and e870) lead to phenotypes including uncoordinated locomotion, slow growth, a small mature body, and resistance to the acetylcholinesterase inhibitors as well as the elevation of acetylcholine content. The remaining two alleles, e554 and e1162, exhibit normal acetylcholine levels but display the short-body phenotype in a semidominant way. To determine the localization of the elevated acetylcholine content, a method for the isolation of synaptic vesicles from C. elegans was established. The elevation of acetylcholine content in the unc-41 mutants is accompanied by the accumulation of synaptic vesicles. We propose that at least one unction of the unc-41 gene relates to the release of neurotransmitters. ------------------- Key: 2008 Medline: Authors: Stringham EG;Candido EPM Title: Transgenic hsp16-lacZ strains of the soil nematode Caenorhabditis elegans as biological monitors of environmental stress. Citation: Environmental Toxicology and Chemistry 13: 1211-1220 1994 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans is a small, free-living hermaphroditic nematode that is widely used for the investigation of basic biological phenomena at the genetic and molecular levels. The hsp16 genes in this system encode a family of stress-inducible 16-kDa proteins. Stable transgenic nematode lines were derived that carry fusions of the hsp 16 genes to the Escherichia coli lacZ reporter gene. These transgenic strains express high levels of beta-galactosidase in the nucleus, in response to a heat shock or to a variety of chemical stressors. Agents tested to date that induce the stress response in these animals include Cd2+, Cu2+, Hg2+, Pb2+, Zn2+, AsO2-, and the herbicide paraquat. Some of these agents yield distinct tissue patterns of stress induction (e.g., Pb2+ in the posterior pharynx, Cd2+ throughout the pharynx, Hg2+ in intestine), suggesting that classification of stress agents in complex mixtures may be a useful feature of this biomonitoring system. Using a soluble beta-galactosidase substrate, an assay was developed that allows the magnitude of the stress response to be measured. Stress reporter gene induction always occurred below the LC50 of the test substance, suggesting that this assay is a more sensitive and rapid indicator of stress than current LC50 assays using Caenorhabditis elegans. ------------------- Key: 2009 Medline: Authors: Clifford R;Francis R;Schedl T Title: Somatic control of germ cell development in Caenorhabditis elegans. Citation: Seminars in Developmental Biology 5: 21-30 1994 Type: REVIEW Genes: fem-1 fem-2 fem-3 fog-1 fog-2 gld-1 glp-1 glp-4 glv-1 her-1 lag-2 let-23 lin-3 lin-12 mes-2 mes-3 mog-1 mup-1 tra-1 tra-2 tra-3 Abstract: Germ cell development in Caenorhabditis elegans involves three processes: a shift from the mitotic to the meiotic cell cycle; the adoption of a male or female sexual identity; and differentiation into a functional gamete. All three aspects of germline development appear to be regulated, at least in part, by the soma. We discuss cell ablation, genetic and molecular studies that have shed light on the nature of the signal transduction systems mediating intracellular communication between germline and somatic tissues of the nematode. ------------------- Key: 2010 Medline: 94330998 Authors: Schaeffer JM;Bergstrom AR;Frazier EG;Underwood D Title: Nematocidal activity of MK-801 analogs and related drugs: Structure-activity relationships. Citation: Biochemical Pharmacology 48: 411-418 1994 Type: ARTICLE Genes: Abstract: A series of dibenzo`a,dïcycloalkenimines were evaluated for their affinity to the (+)-5-methyl-10,11-dihydro-5H-dibenzo`a,dïcyclohepten-5,10- imine (MK-801) binding site in Caenorhabditis elegans membranes and their nematocidal activity. The (+)-MK-801 enantiomer (1) had a higher affinity (K-d = 240 nM) for its specific binding site and was a more potent nematocidal agent than the (-)-MK-801 enantiomer (-1). Ring expansion to form the dibenzo`a,dïcyclooctenimine analogs generally resulted in more potent compounds. The most potent of this series (23) was approximately 7-fold more potent than (+)-MK-801. A good correlation was established between binding affinities and nematocidal activity for all of the analogs that were tested. However, there was no correlation between binding to C. elegans membranes and affinity for mammalian MK-801 binding sites. Other noncompetitive inhibitors of the mammalian N-methyl-D-aspartate site were examined, and a series of diphenylguanidines were identified as patent competitive inhibitors of MK-801 binding to C. elegans membranes, in addition to displaying potent nematocidal activity. The most potent diphienylguanidine analog (24) was approximately 80-fold more potent than (+)-MK-801 in both its affinity for the MK-801 binding site and as a nematocidal agent. Molecular modeling studies support the hypothesis that the diphenylguanidines and MK-801 are binding to the same site and suggest that more potent compounds may be developed by effective modeling of the existing compounds. ------------------- Key: 2011 Medline: 95009545 Authors: Okkema PG;Fire A Title: The Caenorhabditis elegans NK-2 class homeoprotein CEH-22 is involved in combinatorial activation of gene expression in pharyngeal muscle. Citation: Development 120: 2175-2186 1994 Type: ARTICLE Genes: ceh-22 glp-1 myo-1 myo-2 myo-3 Abstract: The pharyngeal muscles of Caenorhabditis elegans are single sarcomere muscles used for feeding. Like vertebrate cardiac and smooth muscles, C. elegans pharyngeal muscle does not express any of the known members of the MyoD family of myogenic factors. To identify mechanisms regulating gene expression in this tissue, we have characterized a pharyngeal muscle-specific enhancer from myo-2, a myosin heavy chain gene expressed exclusively in pharyngeal muscle. Assaying enhancer function in transgenic animals, we identified three subelements, designated A, B and C, that contribute to myo-2 enhancer activity. These subelements are individually inactive; however, any combination of two or more subelements forms a functional enhancer. The B and C subelements have distinct cell type specificities. A duplication of B activates transcription in a subset of pharyngeal muscles (m7, m3, m5 and m7). A duplication of C activates transcription in all pharyngeal cells, muscle and non-muscle. Thus, the activity of the myo-2 enhancer is regulated by a combination of pharyngeal muscle-type-specific and organ-specific signals. Screening a cDNA expression library, we identified a gene encoding an NK-2 class homeodomain protein, CEH-22, that specifically binds a site necessary for activity of the B subelement. CEH-22 protein is first expressed prior to myogenic differentiation and is present in the same subset of pharyngeal muscles in which B is active. Expression continues throughout embryonic and larval development. This expression pattern suggests CEH-22 plays a key role in pharyngeal muscle-specific activity of the myo-2 enhancer. ------------------- Key: 2012 Medline: 95009557 Authors: Mango SE;Thorpe CJ;Martin PR;Chamberlain SH;Bowerman B Title: Two maternal genes, apx-1 and pie-1, are required to distinguish the fates of equivalent blastomeres in the early Caenorhabditis elegans embryo. Citation: Development 120: 2305-2315 1994 Type: ARTICLE Genes: apx-1 glp-1 lag-2 pie-1 sDf70 Abstract: In a 4-cell Caenorhabditis elegans embryo, two sister blastomeres called ABa and ABp are born with equivalent developmental potential, but eventually produce distinct patterns of cell fate. The different fates of ABa and ABp are specified at least in part by inductive interactions with neighboring blastomeres. Previous studies indicate that, at the 4-cell stage, a signal from the posterior-most blastomere, P-2, is required for ABp to produce at least one of its unique cell types. This P-2/ABp interaction depends on glp-1, a putative receptor for intercellular interactions. To investigate this early induction further, we isolated mutants in which ABp developed abnormally. We describe the effects of recessive mutations in apx-1, a maternal gene that appears to be required for P-2 to signal ABp. In embryos from mothers homozygous for mutations in apx-1 (apx-1 embryos), ABp fails to produce its characteristic cell types. Instead, ABp from apx-1 embryos develops more like its sister ABa: it produces ABa-like pharyngeal cells and it recapitulates ABa-like cell lineages. Because mutations in apx-1 affect the development of only the ABp blastomere, we suggest that the wild-type gene encodes a component of the P-2/ABp signalling pathway. To explain the observation that ABp in apx-1 embryos adopts an ABa-like fate, we propose a model in which the P-2 signal is required to break the initial equivalence of ABa and ABp. We performed two independent tests of this model. First, we examined ABp development in pie-1 mutant embryos, in which P-2 adopts the identity of another blastomere. We find that, in pie-1 embryos, ABp fails to produce its characteristic cell types and instead adopts a fate similar to that of ABa. We conclude that the changed identity of P-2 in pie-1 embryos prevents the P-2/ABp interaction. As a second test, we examined ABp development in wild-type embryos after physically removing P-2. These operated embryos produce extra pharyngeal cells, consistent with our proposal that a signal from P-2 breaks the initially equivalent developmental state of ABa and ABp. We discuss the possibility that apx-1 acts as a ligand in this glp-1-dependent signalling pathway. ------------------- Key: 2013 Medline: 95009558 Authors: Waddle JA;Cooper JA;Waterston RH Title: Transient localized accumulation of actin in Caenorhabditis elegans blastomeres with oriented asymmetric divisions. Citation: Development 120: 2317-2328 1994 Type: ARTICLE Genes: par-3 Abstract: During Caenorhabditis elegans embryogenesis, specific cells in the P-1 lineage rotate their duplicated centrosome pair onto the anterior-posterior axis; this rotation is correlated with and necessary for a differential inheritance of cytoplasmic determinants in the daughter cells. Centrosome pair rotation is sensitive to inhibitors of actin and microtubule polymerization and may require microtubule attachment to a specific cortical site. We show that actin and the barbed-end binding protein, capping protein, transiently accumulate at this cortical site, possibly by assembly onto persistent remnants of previous cell divisions. Based on these observations, we propose a model for the molecular basis of centrosome rotation that is consistent with the dependence of rotation on actin filaments and microtubules. ------------------- Key: 2014 Medline: 94342272 Authors: Lei JY;Tang XX;Chambers TC;Pohl J;Benian GM Title: Protein kinase domain of Twitchin has protein kinase activity and an autoinhibitory region. Citation: Journal of Biological Chemistry 269: 21078-21085 1994 Type: ARTICLE Genes: unc-22 Abstract: Twitchin is a 753-kDa polypeptide located in the muscle A-bands of the nematode, Caenorhabditis elegans. It consists of multiple copies of both fibronectin m and immunoglobulin C2 domains and, near the C terminus, a protein kinase domain with greatest homology to the catalytic domains of myosin light chain kinases. We have expressed and purified from Escherichia coil twitchin's protein kinase catalytic core and flanking sequences that do not include fibronectin III and immunoglobulin C2 domains. The protein was shown to phosphorylate a model substrate and to undergo autophosphorylation. The autophosphorylation occurs at a slow rate, attaining a maximum at 3 h with a stoichiometry of about 1.0 mol of phosphate/mol of protein, probably through an intramolecular mechanism. Sequence analysis of proteolytically derived phosphopeptides revealed that autophosphorylation occurred N-terminal to the catalytic core, predominantly at Thr-5910, with possible minor sites at Ser-5912 and/or Ser-5913. This portion of twitchin (residues 5890-6268) was also phosphorylated in vitro by protein kinase C in the absence of calcium and phosphotidylserine, but not by cAMP-dependent protein kinase. By comparing the activities of three twitchin segments, the enzyme appears to be inhibited by the 60-amino acid residues lying just C-terminal to the kinase catalytic core. Thus, Like a number of other protein kinases including myosin Light chain kinases, the twitchin ------------------- Key: 2015 Medline: 94335008 Authors: Alfonso A;Grundahl K;McManus JR;Asbury JM;Rand JB Title: Alternative splicing leads to two cholinergic proteins in Caenorhabditis elegans. Citation: Journal of Molecular Biology 241: 627-630 1994 Type: NOTE Genes: cha-1 unc-17 Abstract: The cha-1 gene of Caenorhabditis elegans encodes choline acetyl-transferase (the acetylcholine synthetic enzyme). The C. elegans unc-17 gene encodes a synaptic vesicle-associated acetylcholine transporter. The two genes thus define sequential biochemical steps in the metabolism of the neurotransmitter acetylcholine. Cloning, sequencing, and molecular analysis of the unc-17 region indicate that cha-1 and unc-17 transcripts share a 5' untranslated exon, and the rest of the unc-17 transcript is nested within the long first intron of cha-1. Thus, two proteins with related functions but with no sequences in common are produced as a result of alternative splicing of a common mRNA precursor. The structure of this transcription unit suggests a novel type of coordinate gene expression, and a temporal processing model is proposed for the regulation of cha-1 and unc-17 expression. ------------------- Key: 2016 Medline: 95095057 Authors: Lundquist EA;Herman RK Title: The mec-8 gene of Caenorhabditis elegans affects muscle and sensory neuron function and interacts with three other genes: unc-52, smu-1 and smu-2. Citation: Genetics 138: 83-101 1994 Type: ARTICLE Genes: mec-8 smu-1 smu-2 unc-52 mnDf111 Abstract: Mutations in the Caenorhabditis elegans gene mec-8 were previously shown to cause defects in mechanosensation and in the structure and dye filling of certain chemosensory neurons. Using noncomplementation screens, we have identified eight new mec-8 alleles and a deficiency that uncovers the locus. Strong mec-8 mutants exhibit an incompletely penetrant cold-sensitive embryonic and larval arrest, which we have correlated with defects in the attachment of body muscle to the hypodermis and cuticle. Mutations in mec-8 strongly enhance the mutant phenotype of unc-52(viable) mutations; double mutants exhibit an unconditional arrest and paralysis at the twofold stage of embryonic elongation, a phenotype characteristic of lethal alleles of unc-52, a gene previously shown to encode a homolog of the core protein of heparan sulfate proteogylcan, found in basement membrane, and to be involved in the anchorage of myofilament lattice to the muscle cell membrane. We have identified and characterized four extragenic recessive suppressors of a mec-8; unc-52(viable) synthetic lethality. The suppressors, which define the genes smu-1 and smu-2, can weakly suppress all mec-8 mutant phenes. They also suppress the muscular dystrophy conferred by an unc-52(viable) mutation. ------------------- Key: 2017 Medline: 97285202 Authors: Lewis E;Sebastiano M;Nola M;Zei F;Lassandro F;Ristoratore F;Cermola M;Favre R;Bazzicalupo P Title: Cuticulin genes of nematodes. Citation: Parasite 1: 57-58 1994 Type: REVIEW Genes: cut-1 cut-2 Abstract: Two genes coding for cuticlin components of Coenorhabditis elegans have been cloned and their structure is described. Recombinant proteins have been produced in E. coli and antibodies raised against them. Nucleic acid and specific antibodies are being used to isolate the homologues from the parasitic species Ascaris lumbricoides and Brugia ------------------- Key: 2018 Medline: 95074289 Authors: Savage C;Xue YZ;Mitani S;Hall D;Zakhary R;Chalfie M Title: Mutations in the Caenorhabditis elegans B-tubulin gene mec-7: effects on microtubule assembly and stability and on tubulin autoregulation. Citation: Journal of Cell Science 107: 2165-2175 1994 Type: ARTICLE Genes: mec-7 Abstract: We have sequenced 45 mutations in mec-7, a beta-tubulin gene required for the production of 15-protofilament microtubules in the nematode Caenorhabditis elegans, and have correlated sequence alterations with mutant phenotypes. The expression patterns of most alleles have also been determined by in situ hybridization and immunocytochemistry. Most (12/16) complete loss-of-function alleles, which are recessive, result from nonsense mutations, insertions, or deletions; three others disrupt a putative GTP-binding domain. Three of the four loss-of-function, missense mutations result in elevated mec-7 message levels, suggesting a defect in tubulin autoregulation that may be attributable to a loss in the ability to form heterodimers. Most (8/9) mild alleles are caused by missense mutations. Two mild alleles appear to increase microtubule stability and lead to the elaboration of ectopic neuronal processes in mec-7-expressing cells. Most (15/23) mutations that cause severe dominant or semidominant phenotypes are clustered into three discrete domains; four others occur in putative GTP-binding regions. Many of these dominant mutations appear to completely ------------------- Key: 2019 Medline: 95103350 Authors: Fire A Title: A four-dimensional digital image archiving system for cell lineage tracing and retrospective embryology. Citation: Computer Applications in the Biosciences 10: 443-447 1994 Type: ARTICLE Genes: Abstract: The paper describes a digital image archiving system for time-lapse microscopy. The system uses an MS-DOS compatible computer to store video images while simultaneously, controlling a stepping motor. In a typical experiment, images might be taken at 30 s intervals in each of 25 consecutive focal planes. A system with 2.5 Gbyte disk capacity can store similar to 18 000 full frame images: 6 h recording at maximum resolution. Once recorded, images series stored on disk can be 'played back' in any order. Generally, images from a single focal plane are displayed consecutively in either forward or reverse time. The focal plane can be shifted during playback, allowing individual cells to be followed as they move between focal planes. To facilitate the annotation and interpretation of the real-time images, a mouse-driven interface allows users to define and follow individual objects (e.g. cells). The recorded image series can be archived inexpensively using standard digital tape backup hardware. In this laboratory, the system has been particularly useful for tracing embryonic cell lineages and cell migrations. Detailed system specifications, including source code, compiled programs, hardware requirements and users manual are available directly from the author or by anonymous FTP (ciw1.ciwemb.edu). ------------------- Key: 2020 Medline: 95065075 Authors: Barnes TM Title: OPUS-A growing family of gap junction proteins? Citation: Trends in Genetics 10: 303-305 1994 Type: REVIEW Genes: unc-7 Abstract: Recently, Krishnan et al. Reported the cloning and sequencing of the Drosophila shaking-B (shakB; alias Passover, or Pas) gene, required for the jump response to an optical stimulus. The predicted gene product was similar to those of both the Drosophila gene lethal (1) optic ganglion reduced [l(1)ogre] and the Caenorhabditis elegans gene unc-7, which together define a new family of evolutionarily conserved proteins that may be membrane-associated. Below I describe three additional members of this family, as identified by sequence homologies. An alignment of all these sequences permits a more informed prediction of the general structure of members of this family. The structure is that of a new type of multipass transmembrane protein. On the basis of the phenotypes of mutant organisms, I suggest that the encoded proteins may be members of a family of invertebrate ------------------- Key: 2021 Medline: 95047345 Authors: Greenstein D;Hird S;Plasterk RHA;Andachi Y;Kohara Y;Wang B;Finney M;Ruvkun G Title: Targeted mutations in the Caenorhabditis elegans POU homeo box gene ceh-18 cause defects in oocyte cell cycle arrest, gonad migration, and epidermal differentiation. Citation: Genes & Development 8: 1935-1948 1994 Type: ARTICLE Genes: ceh-18 fem-1 fem-2 syDf1 Abstract: We used targeted gene inactivation to analyze the function of a Caenorhabditis elegans POU gene, ceh-18, and to dissect its functional domains in vivo. In ceh-18 mutants, oocytes exhibit an incompletely penetrant failure to arrest in diakinesis of meiotic prophase I and instead undergo multiple rounds of DNA replication without cytokinesis. ceh-18 is expressed in the gonadal sheath cells that signal the oocyte, but not in the oocyte. This suggests that ceh-18 affects, directly or indirectly, a sheath cell signal that causes oocytes to maintain diakinesis arrest. ceh-18 also participates in directing gonad migration and in specifying the differentiated phenotypes of epidermal cells during postembryonic development. Analysis of targeted deletions that disrupt half of the POU domain selectively by deleting either the POUhd or the POUsp alone, indicates that each CEH-18 POU subdomain is sufficient for partial activity in vivo. ------------------- Key: 2022 Medline: 95078733 Authors: Lim WA;Fox RO;Richards FM Title: Stability and peptide binding affinity of an SH3 domain from the Caenorhabditis elegans signaling protein SEM-5. Citation: Protein Science 3: 1261-1266 1994 Type: ARTICLE Genes: sem-5 Abstract: We have determined the thermodynamic stability and peptide binding affinity of the carboxy-terminal Src homology 3 (SH3) domain from the Caenorhabditis elegans signal-transduction protein Sem-5. Despite its small size (62 residues) and lack of disulfide bonds, this domain is highly stable to thermal denaturation-at pH 7.3, the protein has a T-m of 73.1 degree C. Interestingly, the protein is not maximally stable at neutral pH, but reaches a maximum at around pH 4.7 (T-m simeq 80 degree C). Increasing ionic strength also stabilizes the protein, suggesting that 1 or more carboxylate ions are involved in a destabilizing electrostatic interaction. By guanidine hydrochloride denaturation, the protein is calculated to have a free energy of unfolding of 4.1 kcal/mol at 25 degree C. We have also characterized binding of the domain to 2 different length proline-rich peptides from the guanine nucleotide exchange factor, Sos, one of Sem-5's likely physiological ligands in cytoplasmic signal transduction. Upon binding, these peptides cause about a 2-fold increase in fluorescence intensity. Both bind with only modest affinities (K-d simeq 30 mu-M), lower than some previous estimates for SH3 domains. By fluorescence, the domain also appears to associate with the homopolymer poly-L-proline in a similar fashion. ------------------- Key: 2023 Medline: 95047297 Authors: McKim KS;Rose AM Title: Spontaneous duplication loss and breakage in Caenorhabditis elegans. Citation: Genome 37: 595-606 1994 Type: ARTICLE Genes: him-3 him-6 him-8 hDp2 hDp3 hDp4 hDp5 hDp6 hDp7 hDp12 hDp14 hDp20 hDp22 hDp23 hDp24 hDp25 hDp26 hDp27 hDp28 hDp29 hDp30 hDp31 hDp59 hDp74 hDp75 hDp76 hDp77 hDp78 hDp79 hDp80 hDp81 hDp82 hDp83 hDp84 hDp85 hDp86 hDp87 hDp88 hDp89 hDp90 hDp91 hDp92 hDp93 hDp94 hDp95 hDp100 sDp2 szDp1 Abstract: Duplications in Caenorhabditis elegans spontaneously delete at frequencies ranging from 10(-4) to 10(-5). We have analyzed the structure and mitotic stability of 33 deleted duplications resulting from spontaneous breakage events. (i) Breakage usually occurred at a variety of sites; that is, there were no hot spots for breakage. An exception was the spontaneous breakage of the X chromosome into which hDp14 was inserted. These breaks were close to or at the site of the chromosome I insertion; therefore, the insertion created a type of fragile site. (ii) Spontaneous duplications often had complex structures. In some cases, their structures were most simply resolved by proposing that the progenitor duplication was a ring chromosome with a superimposed inversion. Most of the proposed ring chromosomes were mitotically unstable, suggesting that ring structures increase the frequency of chromosome loss. (iii) Clusters of spontaneous deletion events were rarely observed, suggesting that the majority of spontaneous breakage events probably occurred during meiosis. (iv) A minority of the spontaneous breakage events were associated with linkage to an autosome. Like free duplications of chromosome I, these linked duplications tended to segregate from the X chromosome in males. (v) Three meiotic mutants, him-3, him-6, and him-8, had no effect on somatic loss of the duplications but did reduce the frequency of breakage events. Given the conclusion that chromosome breakage is a meiotic event, these data are consistent with the function of the three meiotic genes being restricted to meiosis. ------------------- Key: 2024 Medline: 95047302 Authors: Marra MA;Baillie DL Title: Recovery of duplications by drug resistance selection in Caenorhabditis elegans. Citation: Genome 37: 701-705 1994 Type: ARTICLE Genes: let-56 lev-1 unc-22 nT1 sDp10 sDp11 Abstract: We have devised a scheme that facilitates rapid screening for duplications of essential loci. Our scheme takes advantage of the lev-1(x22) mutation, which confers resistance in a recessive fashion to the potent anthelmintic levamisole. We have tested our methodology by recovering two gamma ray induced duplications of let-56, the first essential gene to the left of unc-22. One of the duplications is attached to the fourth chromosome. The other duplication is attached to the X chromosome. This duplication contains a functional copy of the unc-22 gene, as well as functional copies of several essential loci adjacent to unc-22. Results we have obtained during analysis of this duplication are compatible with the notion that the copy of the unc-22 gene located on the duplication is subject to X chromosome dosage compensation. ------------------- Key: 2025 Medline: 95044920 Authors: Labouesse M;Sookhare S;Horvitz HR Title: The Caenorhabditis elegans gene lin-26 is required to specify the fates of hypodermal cells and encodes a presumptive zinc-finger transcription factor. Citation: Development 120: 2359-2368 1994 Type: ARTICLE Genes: lin-26 mnDf88 mnDf97 mnDf105 mnDf106 Abstract: The mutation lin-26(n156) prevents vulva formation in C. elegans by transforming the vulval precursor cells into neurons or neuroblasts. We have isolated and characterized three new lin-26 alleles, which result in embryonic lethality. These mutations cause a few other hypodermal cells to express a neural fate and most hypodermal cells to degenerate. lin-26 encodes a presumptive zinc-finger transcription factor. Our data indicate that lin-26 is required for cells to acquire the hypodermal fate. ------------------- Key: 2026 Medline: 95044936 Authors: Chow KL;Emmons SW Title: HOM-C/Hox genes and four interacting loci determine the morphogenetic properties of single cells in the nematode male tail. Citation: Development 120: 2579-2592 1994 Type: ARTICLE Genes: egl-5 lin-22 mab-5 mab-18 mab-20 mab-21 mab-26 pal-1 qDp3 Abstract: The copulatory structure of the C. elegans male tail includes a set of nine bilaterally symmetrical pairs of sense organs known as rays. Each ray comprises three cells, which are generated by a stereotyped cell sublineage expressed by 18 epidermal ray precursor cells. A pattern formation mechanism in the epidermis guides the specification of morphogenetic differences between the rays necessary for correct organelle assembly at specific positions within the epidermis. Expression of these ray differences was altered in mutations we described previously, resulting in displaced and fused rays. Here we show that two genes of the C. elegans HOM-C/Hox gene complex play a role in the pattern formation mechanism. Increasing or decreasing the gene dosage of mab-5, an Antennapedia homolog, and egl-5, an Abdominal B homolog, results in displacement and fusion of specific rays. These changes are interpreted as anterior or posterior transformations in ray identities. Mutations in the genes previously described are dominant modifiers of these effects. This suggests that these genes act in the same morphogenetic pathway as mab-5 and egl-5. Several lines of evidence, including cell ablation experiments, argue that the identity of each ray is specified cell-autonomously in the terminal cells of the ray lineages. mab-5 and egl-5, therefore, specify the morphogenetic properties of differentiating cells, without change in cell lineage or apparent cell type. Modifier genes may act upstream of mab-5 and egl-5 to regulate their expression. Alternatively, they may act at the same step in the pathway, as cofactors, or they may be target genes. Target genes could include genes specifying cell recognition and ------------------- Key: 2027 Medline: 94379960 Authors: Rohrer SP;Jacobson EB;Hayes EC;Birzin ET;Schaeffer JM Title: Immunoaffinity purification of avermectin-binding proteins from the free-living nematode Caenorhabditis elegans and the fruit-fly Drosophila melanogaster. Citation: Biochemical Journal 302: 339-345 1994 Type: ARTICLE Genes: Abstract: Avermectin-binding proteins from the free-living nematode worm Caenorhabditis elegans and from the fruitfly Drosophila melanogaster were purified to homogeneity via a three-step procedure. The binding proteins were covalently labelled using- a radioactive photoaffinity probe and then partially purified on a Sephacryl S-300 gel-filtration column. The radiolabelled binding proteins were then purified by immunoaffinity chromatography using a monoclonal antibody to avermectin covalently attached to Protein A-Sepharose beads. Three affinity-labelled Drosophila proteins with molecular masses between 45 and 50 kDa were isolated in this way and then separated from each other by electroelution. This three-step protocol provides a rapid technique for receptor purification which may be of use in the purification of other binding proteins. ------------------- Key: 2028 Medline: 95102108 Authors: Runswick MJ;Phillipides A;Lauria G;Walker JE Title: Extension of the mitochondrial transporter super-family: sequences of five members from the nematode worm, Caenorhabditis elegans. Citation: DNA Sequence 4: 281-291 1994 Type: ARTICLE Genes: Abstract: The sequences are presented of cDNAs encoding five related proteins from the nematode worm, Caenorhabditis elegans. Three of them can be recognised as the homologues of the ADP/ATP, phosphate and oxoglutarate/malate carrier proteins that have been found in the inner membranes of mitochondria in other species. These carrier proteins, and the uncoupling protein from the mitochondria in mammalian brown adipose tissue, have common features in their primary and secondary structures, and are members of the same protein super-family. Members of this super-family have polypeptide chains approximately 300 amino acid long that consist of three tandem related sequences of about 100 amino acids. The tandem repeats from the different proteins are inter-related, and each repeat is probably folded into a common secondary structural motif consisting of two hydrophobic stretches of amino acids with the potential to form membrane spanning alpha-helices, linked by an extensive hydrophilic region. The common characteristic features of this family of proteins are also present in sequences of two further proteins, named C1 and C2, encoded in nematode cDNAs, and in tour published protein sequences from various sources. Neither the transport properties nor the subcellular locations of any of this latter group of six proteins are known. Therefore, currently the super-family of mitochondrial carrier proteins has at least ten different members. ------------------- Key: 2029 Medline: 94368872 Authors: Park SM;Koo HS Title: Purification of Caenorhabditis elegans DNA topoisomerase I. Citation: Biochimica et Biophysica Acta 1219: 47-54 1994 Type: ARTICLE Genes: Abstract: DNA topoisomerase I was partially purified from Caenorhabditis elegans worms. The enzyme is a 95 kDa polypeptide and its proteolytically degraded form of 70 kDa was also observed. The enzyme removed not only negative but also positive DNA supercoils. The optimum salt concentration for the DNA relaxation activity was 100 mM KCl, and divalent cations were not required but stimulated the activity. The DNA elaxation activity was weakly sensitive to 125 mu-M camptothecin but was completely inhibited by 125 mu-M berenil. ------------------- Key: 2030 Medline: 95102147 Authors: van der Keyl H;Kim H;Espey R;Oke CV;Edwards MK Title: Caenorhabditis elegans sqt-3 mutants have mutations in the col-1 collagen gene. Citation: Developmental Dynamics 201: 86-94 1994 Type: ARTICLE Genes: col-1 col-2 col-34 col-37 dpy-2 dpy-13 sqt-3 ctDf1 Abstract: sqt-3 mutants of Caenorhabditis elegans form dumpy larvae and adults and display allele-specific defects in locomotion, fertility, and viability. We have determined that the sqt-3 locus encodes COL-1 collagen. We physically mapped the col-1 gene to a cosmid on chromosome V whose position is consistent with the location of the sqt-3 gene. We also observed morphological defects in sqt-3 mutants at stages that correlate with the mRNA expression patterns of col-1. Sequence analysis of the col-1 gene in the three temperature-sensitive mutants revealed that each allele of sqt-3 has a unique missense mutation causing arginine or glutamic acid to replace glycine in a Gly-X-Y triple helical domain. These glycine substitutions may result in longer non-collagenous domains, which may decrease the thermal stability or impart additional flexibility to mutant trimmers. In addition, we describe four corrections to the published sequence of col-1, including one fifteen nucleotide addition that completes a conserved domain in the amino terminal coding region. ------------------- Key: 2031 Medline: 94373809 Authors: Bargmann CI Title: Molecular mechanisms of mechanosensation? Citation: Cell 78: 729-731 1994 Type: REVIEW Genes: mec-1 mec-4 mec-5 mec-6 mec-7 mec-10 mec-12 Abstract: Touch sensation is found in almost all organisms, including unicellular organisms. Yet at a molecular level, it might be the least understood of the senses. Understanding touch is made difficult by the relative inaccessibility of touch sensory neurons. The visual and olfactory organs contain millions of sensory neurons localized in well-defined areas, but the neurons that sense touch are dispersed through the body, typically embedded within other cell types. While this arrangement may be convenient for detecting stimuli at many locations, it is inconvenient for the physiologist or the molecular biologist who is interested in mechanosensation. Fortunately, a recent convergence of genetic, physiological, and molecular approaches has led to the identification of a set of molecules that might function in mechanosensation. ------------------- Key: 2032 Medline: Authors: Bazzicalupo P;Hilliard M;Lewis E;De Riso L;Sebastiano M;Ristoratore F Title: Neurons and genes involved in chemical sensitivity in nematodes. Citation: Parasite 1: 58-60 1994 Type: REVIEW Genes: dyf-1 Abstract: Organelles and neurons of nematodes involved in sensing chemical signals present in the environment are described. Laser ablation of neurons has helped assign them a specific function. Genetic mutational analysis has led to the identification of genes controlling the behavior of the worms and/or some cellular properties of the chemosensory neurons. Some conclusions on the general organization and functioning of chemoreception in nematodes can be drawn. ------------------- Key: 2033 Medline: 95129796 Authors: Vowels JJ;Thomas JH Title: Multiple chemosensory defects in daf-11 and daf-21 mutants of Caenorhabditis elegans. Citation: Genetics 138: 303-316 1994 Type: ARTICLE Genes: che-2 daf-1 daf-3 daf-4 daf-7 daf-8 daf-11 daf-12 daf-14 daf-21 lin-17 osm-3 Abstract: Phenotypic analysis of the daf-11 and daf-21 mutants of Caenorhabditis elegans suggests that they have defects in components shared by processes analogous to vertebrate taste and olfaction. daf-11 and daf-21 mutations were previously shown to cause inappropriate response to the dauer-inducing pheromone. By mutational analysis and by disabling specific chemosensory sensilla with a laser, we show that neurons in the amphid sensilla are required for this pheromone response. Using behavioral assays, we find that daf-11 and daf-21 mutants are not defective in avoidance of certain non-volatile repellents, but are defective in taxis to non-volatile attractants. In addition, both mutants are defective in taxis to volatile attractants detected primarily by the amphid neuron AWC, but respond normally to volatile attractants detected primarily by AWA. We propose that daf-11 and daf-21 mediate sensory transduction for both volatile and non-volatile compounds in specific amphid neurons. ------------------- Key: 2034 Medline: 95129797 Authors: Perry MD;Trent C;Robertson B;Chamblin C; Wood WB Title: Sequenced alleles of the Caenorhabditis elegans sex-determining gene her-1 include a novel class of conditional promoter mutations. Citation: Genetics 138: 317-327 1994 Type: ARTICLE Genes: her-1 Abstract: In the control of Caenorhabditis elegans sex determination, the her-1 gene must normally be activated to allow male development of XO animals and deactivated to allow hermaphrodite development of XX animals. The gene is regulated at the transcriptional level and has two nested male-specific transcripts. The larger of these encodes a small, novel, cysteine-rich protein responsible for masculinizing activity. Of the 32 extant mutant alleles, 30 cause partial or complete loss of masculinizing function (lf), while 2 are gain-of-function (gf) alleles resulting in abnormal masculinization of XX animals. We have identified the DNA sequence changes in each of these 32 alleles. Most affect the protein coding functions of the gene, but six are in the promoter region, including the two gf mutations. These two mutations may define a binding site for negative regulators of her-1. Three of the four remaining promoter mutations are single base changes that cause, surprisingly, temperature-sensitive loss of her-1 function. Such conditional promoter mutations have previously not been found among either prokaryotic or eukaryotic mutants analyzed at the molecular level. ------------------- Key: 2035 Medline: 95014720 Authors: Goetinck S;Waterston RH Title: The Caenorhabditis elegans UNC-87 protein is essential for maintenance, but not assembly, of bodywall muscle. Citation: Journal of Cell Biology 127: 71-78 1994 Type: ARTICLE Genes: unc-54 unc-87 Abstract: Mutations in the unc-87 gene of Caenorhabditis elegans cause disorganization of the myofilament lattice in adult bodywall muscle. In order to assess the organization of specific bodywall muscle components in the absence of the unc-87 gene product, we examined the bodywall muscles of mutant animals using phalloidin and monoclonal antibodies to various muscle proteins. These studies indicated that the bodywall muscle of unc-87 embryos is initially almost wild type in its organization, but at later stages, the muscle becomes severely disorganized. To address the possibility that this disorganization is due to deterioration of the muscle as a result of contraction, we introduced into the unc-87 mutant background a mutation that decreases myosin heavy chain activity but does not substantially affect muscle structure. The improved muscle structure and motility of the double mutants are consistent with the hypothesis that at least part of the disorganization phenotype of unc-87 mutants is a consequence of the wild-type levels of force generated during muscle contraction. These results imply that the role of the unc-87 gene product is not in specifying organization but rather in serving as a structural ------------------- Key: 2036 Medline: 95014721 Authors: Goetinck S;Waterston RH Title: The Caenorhabditis elegans muscle-affecting gene unc-87 encodes a novel thin filament-associated protein. Citation: Journal of Cell Biology 127: 79-93 1994 Type: ARTICLE Genes: act-3 lev-11 unc-87 Abstract: Mutations in the unc-87 gene of Caenorhabditis elegans affect the structure and function of bodywall muscle, resulting in variable paralysis. We cloned the unc-87 gene by taking advantage of a transposon-induced allele of unc-87 and the correspondence of the genetic and physical maps in C. elegans. A genomic clone was isolated that alleviates the mutant phenotype when introduced into unc-87 mutants. Sequence analysis of a corresponding cDNA clone predicts a 357-amino acid, 40-kD protein that is similar to portions of the vertebrate smooth muscle proteins calponin and SM22alpha, the Drosophila muscle protein mp20, the deduced product of the C. elegans cDNA cm7g3, and the rat neuronal protein np25. Analysis of the genomic sequence and of various transcripts represented in a cDNA library suggest that unc-87 mRNAs are subject to alternative splicing. Immunohistochemistry of wildtype and mutant animals with antibodies to an unc-87 fusion protein indicates that the gene product is localized to the I-band of bodywall muscle. Studies of the UNC-87 protein in other muscle mutants suggest that the unc-87 gene product associates with thin filaments, in a manner that does not depend on the presence of the thin filament protein ------------------- Key: 2037 Medline: 95030441 Authors: Morgan PG;Sedensky MM Title: Mutations conferring new patterns of sensitivity to volatile anesthetics in Caenorhabditis elegans. Citation: Anesthesiology 81: 888-898 1994 Type: ARTICLE Genes: unc-1 unc-7 unc-9 unc-24 unc-79 unc-80 mnDf41 Abstract: Background: We previously described the use of the nematode Caenorhabditis elegans as a genetic model for studying the mechanism of action of volatile anesthetics. All previous strains of C. elegans with altered responses to anesthetics have been identified by screening the response to halothane. The current study was designed to identify classes of mutations by screening for alterations in sensitivity to enflurane, isoflurane, and diethylether. Methods: Nematodes were mutated and the resulting mutant strains were screened for immobility in low doses of enflurane, isoflurane, or diethylether. Concentrations of halothane, enflurane, isoflurane, and diethylether that anesthetized 50% of the animals were determined in all mutations. Interactions of some new mutations with previously identified mutations were determined by construction of double mutants. Results: Mutations in six genes were identified and were divided into two classes. One class primarily affected sensitivity to enflurane and isoflurane; a second class affected sensitivity to all of the volatile anesthetics studied. The effects of the latter group ominated the effects of previously identified mutations. Conclusions: The interaction of these mutations indicates that multiple sites of anesthetic action exist and that there are at least three such sites. A pathway for control of ------------------- Key: 2038 Medline: 95148692 Authors: Hengartner MO;Horvitz HR Title: The ins and outs of programmed cell death during C. elegans development. Citation: Philosophical Transactions of the Royal Society of London Series B - Biological Sciences 345: 243-246 1994 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-9 ced-10 ces-1 ces-2 egl-1 nuc-1 Abstract: During the development of the C. elegans hermaphrodite, 131 of the 1090 cells generated undergo programmed cell death. Genetic studies have identified mutations in 14 genes that specifically affect this process. These genes define a genetic pathway for programmed cell death in C. elegans. Two genes, ced-3 and ced-4, are required for cells to undergo programmed cell death, while a third gene, ced-9, protects cells that should live from undergoing programmed cell death. The proteins encoded by ced-3 and ced-9 show significant similarity to proteins that affect programmed cell death in vertebrates, suggesting that the molecular cell death pathway in which ced-3, ced-4, and ced-9 act has been conserved between nematodes and vertebrates. ------------------- Key: 2039 Medline: Authors: Tuck S;Greenwald I Title: Cell interactions and signal transduction in C. elegans development. Citation: "Modern Cell Biology. Growth Factors and Signal Transduction in Development." Nilsen-Hamilton, M (ed); John Wiley and Sons, Inc; New York, NY. 14: 179-197 1994 Type: REVIEW Genes: clr-1 egl-15 egl-17 glp-1 her-1 let-23 let-60 let-341 lin-1 lin-2 lin-3 lin-7 lin-8 lin-9 lin-10 lin-11 lin-12 lin-13 lin-15 lin-17 lin-18 lin-25 lin-31 lin-35 lin-36 lin-37 lin-38 lin-45 sdc-1 sem-5 tra-1 tra-2 Abstract: During the development of any multicellular organism, the behavior of any given cell can be influenced in two ways: by its ancestry, i.e., by the particular pattern of determinants it inherits (lineal programming); or by its environment, i.e., the signals it receives from other cells. In C. elegans, the relative importance of these two factors for the development of any given cell can be examined with an unusually high degree of precision. There are a number of reasons for this, but perhaps the most important is that the cell lineage, the particular pattern of cell divisions and differentiations that occur in development, is known, and is largely the same from animal to animal. Alterations in the lineage, therefore, can be understood in terms of altered developmental decisions of ------------------- Key: 2040 Medline: Authors: Bucher EA;Seydoux G Title: Gastrulation in the nematode Caenorhabditis elegans. Citation: Seminars in Developmental Biology 5: 121-130 1994 Type: REVIEW Genes: emb-5 emb-13 emb-23 emb-31 gut-2 skn-1 zen-1 Abstract: Gastrulation in Caenorhabditis elegans has been described by following the movements of individual nuclei in living embryos by Nomarski microscopy. Gastrulation starts in the 26-cell stage when the two gut precursors, Ea and Ep, move into the blastocoele. The migration of Ea and Ep does not depend on interactions with specific neighboring cells and appears to rely on the earlier fate specification of the E lineage. In particular, the long cell cycle length of Ea and Ep appears important for gastrulation. Later in embryogenesis, the precursors to the germline, muscle and pharynx join the E descendants in the interior. As in other organisms, the movement of gastrulation permit novel cell contacts that are important for the specification of certain cell fates. ------------------- Key: 2041 Medline: 95025972 Authors: Blackwell TK;Bowerman B;Priess JR;Weintraub H Title: Formation of a monomeric DNA binding domain by Skn-1 bZIP and homeodomain elements. Citation: Science 266: 621-628 1994 Type: ARTICLE Genes: hlh-1 skn-1 srg-1 Abstract: Maternally expressed Skn-1 protein is required for the correct specification of certain blastomere fates in early Caenorhabditis elegans embryos. Skn-1 contains a basic region similar to those of basic leucine zipper (bZIP) proteins but, paradoxically, it lacks a leucine zipper dimerization segment. Random sequence selection methods were used to show that Skn-1 binds to specific DNA sequences as a monomer. The Skn-1 basic region lies at the carboxyl terminus of an 85-amino acid domain that binds preferentially to a bZIP half-site and also recognizes adjacent 5' AT-rich sequences in the minor groove, apparently with an amino (NH2)-terminal "arm" related to those of homeodomain proteins. The intervening residues appear to stabilize interaction of these two subdomains with DNA. The Skn-1 DNA binding domain thus represents an alternative strategy for promoting binding of a basic region segment recognition helix to its cognate half-site. The results point to an underlying modularity in subdomains within established DNA binding domains. ------------------- Key: 2042 Medline: 95025967 Authors: Kimble J Title: An ancient molecular mechanism for establishing embryonic polarity. Citation: Science 266: 577-578 1994 Type: REVIEW Genes: glp-1 Abstract: Worms, butterflies, and chimpanzees all have the same body axes-head and tail, front and back, and left and right sides. How are these axes established during development? Is there a single molecular map used by most metazoan embryos or have similar coordinates been achieved during evolution by diverse routes? A comparison of the mechanisms that establish body axes in distantly related organisms can begin to answer this fundamental question. ------------------- Key: 2043 Medline: 95331115 Authors: Chamberlin HM;Sternberg PW Title: The lin-3/let-23 pathway mediates inductive signalling during male spicule development in Caenorhabditis elegans. Citation: Development 120: 2713-2721 1994 Type: ARTICLE Genes: let-23 let-60 lin-3 lin-12 lin-15 lin-45 sem-5 Abstract: During Caenorhabditis elegans male spicule development, four pairs of precursor cells respond to multiple positional cues and establish a pattern of fates that correlates with relative anterior-posterior cell position. One of the extracellular cues is provided by the F and U cells, which promote anterior fates. We show that the genes in the lin-3/let-23 signalling pathway required for hermaphrodite vulval induction also mediate this F/U signal. Reduction-of-function mutations in lin-3, let-23, sem-5, let-60 or lin-45 disrupt hte fate of anterior cells. Likewise, activation of the pathway with ubiquitously produced signal results in posterior cells inappropriately adopting the anterior fates even in the absence of F and U. We have further used this genetic pathway to begin to understand how multiple positional cues are integrated to specify cell fate. We demonstrated that lin-15 acts in spicule development as it does in vulval induction, as a negative regulator of let-23 receptor activity. A second extracellular cue, from Y.p, also acts antagonistically to the lin-3/let-23 pathway. However, this signal is apparently integrated into the lin-3/let-23 pathway at some step after lin-45 raf and is thus functionally distinct from lin-15. We have also investigated the role of lin-12 in forming the anterior/posterior pattern of fates. A lin-12 gain-of-function defect is masked by redundant positional information from F and U. ------------------- Key: 2044 Medline: 95331122 Authors: Seydoux G;Fire A Title: Soma-germline asymmetry in the distributions of embryonic RNAs in Caenorhabditis elegans. Citation: Development 120: 2823-2834 1994 Type: ARTICLE Genes: ama-1 act-1 cey-1 cey-2 crf-2 dpy-30 glp-1 hlh-1 lin-19 ncc-1 par-4 pes-10 skn-1 unc-54 ctDf1 nDf41 mDf4 mnDf90 Abstract: Early embryogenesis in Caenorhabditis elegans is characterized by a series of unequal cleavages that mark the stepwise separation of somatic and germ lineages. We have developed an in situ hybridization protocol to examine the localization of specific maternal and embryonic transcribed messenger RNAs during these early cleavages. We detected three classes of maternal RNAs: RNAs that are maintained in all cells, RNAs that are maintained in germline cells but are lost from somatic cells, and a population of RNAs that are associated with the germline-specific P granules. We observed embryonically transcribed RNAs in somatic cells as early as the 4-cell stage. These transcripts were not detected in germline cells. These observations suggest that mechanisms which distinguish between soma and germline cause asymmetries in mRNA stability and transcription within the first few ------------------- Key: 2045 Medline: 95331129 Authors: Crittenden SL;Troemel ER;Evans TC;Kimble J Title: GLP-1 is localized to the mitotic region of the C. elegans germ line. Citation: Development 120: 2901-2911 1994 Type: ARTICLE Genes: fog-1 gld-1 glp-1 lag-2 lin-12 smg-1 hT2 Abstract: In C. elegans, germline mitosis depends on induction by the somatic distal tip cell (DTC) and on activity of the glp-1 gene. Using antibodies to GLP-1 protein, we have examined GLP-1 on western blots and by immunocytochemistry. GLP-1 is tightly associated with membranes of mitotic germline cells, supporting its identification as an integral membrane protein. Furthermore, GLP-1 is localized within the germ line to the mitotic region, consistent with the model that GLP-1 acts as a membrane receptor for the distal tip cell signal. Unexpectedly, GLP-1 and the zone of mitosis extend further than the DTC processes. We present three models by which the DTC may influence GLP-1 activity and thereby determine the zone of mitosis. The spatial restriction of GLP-1 appears to be controlled at the translational level in hermaphrodites. We suggest that down-regulation of GLP-1 may be required to effect the transition from mitosis into meiosis. ------------------- Key: 2046 Medline: 95331130 Authors: Henderson ST;Gao D;Lambie EJ;Kimble J Title: lag-2 may encode a signaling ligand for the GLP-1 and LIN-12 receptors of C. elegans. Citation: Development 120: 2913-2924 1994 Type: ARTICLE Genes: glp-1 lag-1 lag-2 lin-12 sDf27 sDf40 sDf49 Abstract: The C. elegans lag-2 gene is required for several cell-cell interactions that rely on the receptors GLP-1 and LIN-12. In this paper, we report that lag-2 encodes a putative membrane protein with sequence similarity to Drosophila Delta, a proposed ligand for the Notch receptor. Furthermore, we show that lag-2 promoter drives expression of a reporter protein in the signaling distal tip cell (DTC) of the DTC/germline interaction. By in situ hybridization, we have found that endogenous lag-2 mRNA is present in the DTC but not the germline. One fusion protein, called LAG-2::B-gal(intra), rescues a lag-2 null mutant and can be detected in both DTC and germ line. Taking these results together, we propose that lag-2 may encode a signaling ligand for GLP-1/LIN-12 and that the entire LAG-2 protein may be taken up into the receiving cell during induction by GLP-1 and lateral signaling by ------------------- Key: 2047 Medline: 95331137 Authors: Granato M;Schnabel H;Schnabel R Title: Genesis of an organ: molecular analysis of the pha-1 gene. Citation: Development 120: 3005-3017 1994 Type: ARTICLE Genes: pha-1 eDf20 tDf2 Abstract: The organisation of organ formation is still an unsolved problem. Mutations in the zygotic lethal gene pha-1 affect a late step during organ development in the nematode C. elegans. In mutant embryos all tissues in the pharynx fail to undergo terminal differentiation and morphogenesis. The expression of an early differentiation marker in pharyyngeal muscle precursors is not impaired in mutant embryos, which suggests that pharynx cells still acquire their identity. Therefore the gene defines an organ-specific termianl differentiation function. We cloned and sequenced the pha-1 gene and found that the deduced protein sequence contains features characteristic of the bZIP family of transcription factors. During embryogenesis a transgenic pha-1 reporter contruct is expressed transiently in all pharynx precursor cells at the time when these cells become restricted to form the pharynx organ. A mosaic analysis of the requirement of pha-1 activity during pharynx formation is consistent with the notion that pha-1 acts cell-autonomously in all cells of the pharynx primordium. The data suggest that pha-1 initiates and coordinates programs required for cytodifferentiation and morphogenesis in all cell types of the entire organ on the trascriptional level. We propose that organs are independent developmental units whose ------------------- Key: 2048 Medline: 95331138 Authors: Mango SE;Lambie EJ;Kimble J Title: The pha-4 gene is required to generate the pharyngeal primordium of Caenorhabditis elegans. Citation: Development 120: 3019-3031 1994 Type: ARTICLE Genes: ced-1 ced-4 ced-5 glp-1 mex-1 par-3 pha-1 pha-4 pie-1 skn-1 ozDf2 Abstract: In the 4-cell Caenorhabditis elegans embryo, two blastomeres are destined to generate pharyngeal cells, each by a distinct developmental strategy: one pathway is inductive, while the other is autonomous. Here, we identify the pha-4 locus. In animals lacking pha-4 activity, an early step in pharyngeal organogenesis is blocked: no pharyngeal primordium is formed and differentiated pharyngeal cells are absent. Most other tissues are generated normally in pha-4 mutants, including cells related to pharyngeal cells by cell lineage and position. Thus, pha-4 activity is required to form the pharyngeal primordium. We propose that pha-4 marks a convergence of the inductive and autonomous pathways of pharyngeal development and suggest that establishment of pharyngeal organ identity is a crucial step for pharyngeal ------------------- Key: 2049 Medline: 95021740 Authors: Cully DF;Vassilatis DK;Liu KK;Paress PS;Van der Ploeg LHT;Schaeffer JM;Arena JP Title: Cloning of an avermectin-sensitive glutamate-gated chloride channel from Caenorhabditis elegans. Citation: Nature 371: 707-711 1994 Type: ARTICLE Genes: Abstract: The avermectins are a family of macrocyclic lactones used in the control of nematode and arthropod parasites. Ivermectin (22,23-dihydroavermectin B-1a) is widely used as an anthelmintic in veterinary medicine and is used to treat onchocerciasis or river blindness in humans. Abamectin (avermectin B-1a) is a miticide and insecticide used in crop protection. Avermectins interact with vertebrate and invertebrate GABA receptors and invertebrate glutamate-gated chloride channels the soil nematode Caenorhabditis elegans has served as a useful model to study the mechanism of action of avermectins. A C. elegans messenger RNA expressed in Xenopus oocytes encodes an avermectin-sensitive glutamate-gated chloride channel. To elucidate the structure and properties of this channel, we used Xenopus oocytes for expression cloning of two functional complementary DNAs encoding an avermectin-sensitive glutamate-gated chloride channel. We find that the electrophysiological and structural properties of these proteins indicate that they are new ------------------- Key: 2050 Medline: 95047381 Authors: Ogura K-i;Wicky C;Magnenat L;Tobler H;Mori I;Muller F;Ohshima Y Title: Caenorhabditis elegans unc-51 gene required for axonal elongation encodes a novel serine/threonine kinase. Citation: Genes & Development 8: 2389-2400 1994 Type: ARTICLE Genes: sup-5 sup-7 unc-5 unc-6 unc-51 Abstract: Mutations in the unc-51 gene of the nematode Caenorhabditis elegans result in various abnormalities in axonal elongation and axonal structures. We cloned the unc-51 gene by tagging with the transposon Tc1. The wild-type unc-51 gene, which rescued the mutant phenotypes, encodes a novel serine/threonine kinase of 856 amino acids. Mutation sites were identified in the unc-51 gene of six mutants. A Lys->Met mutation created in vitro in the kinase domain led to the loss of rescuing activity and was dominant negative, indicating that the kinase domain of Unc-51 is essential for the function. Expression of an unc-51/lacZ fusion gene was observed in many neurons at all stages. We propose that protein phosphorylation by the unc-51 product is important for axonal elongation and possibly for axonal ------------------- Key: 2051 Medline: 95042726 Authors: van Luenen HGAM;Colloms SD;Plasterk RHA Title: The mechanism of transposition of Tc3 in C. elegans. Citation: Cell 79: 293-301 1994 Type: ARTICLE Genes: unc-22 Abstract: The Tc3 transposon of C. elegns belongs to a family of inverted repeat DNA transposons, found in many different phyla. We studied the mechanism of Tc3 transposition by expression of Tc3 transposase from a heat-shock promoter in transgenic nematodes. Transposition is accompanied by the appearance of linear extrachromosomal Tc3 DNA. Analysis of the ends of this presumed transposition intermediate shows that the transposon is excised incompletely: the 5' ends of the transposon lack two nucleic acids. The 3' ends coincide with the last nucleotide of the integrated element and cary 3' hydroxyls. The nucleotides that are not coexcised with the transposon remain at the donor site and result in a characteristic footprint. A model is derived for the mechanism of Tc3 jumping that probably applies to the entire family of Tc1/marinier transposable elements. ------------------- Key: 2052 Medline: 95011616 Authors: Wang W;Shakes DC Title: Isolation and sequence analysis of a Caenorhabditis elegans cDNA which encodes a 14-3-3 homologue. Citation: Gene 147: 215-218 1994 Type: ARTICLE Genes: glp-4 unc-22 Abstract: We report the cloning of the Caenorhabditis elegans homologue of a 14-3-3 protein-encoding gene which is located within the unc-22 gene cluster on chromosome IV. Sequence analysis reveals that the cDNA-encoded product is 78% identical to both the Drosophila melanogaster and bovine 14-3-3 proteins. Our cDNA hybridizes to at least three major transcripts of 1.5, 1.35 and 0.9 kb, which are all more abundant in fertile hermaphrodites than in those lacking germ cells. ------------------- Key: 2053 Medline: 95023983 Authors: Sedensky MM;Cascorbi HF;Meinwald J;Radford P;Morgan PG Title: Genetic differences affecting the potency of stereoisomers of halothane. Citation: Proceedings of the National Academy of Sciences USA 91: 10054-10058 1994 Type: ARTICLE Genes: unc-1 unc-7 unc-9 unc-49 unc-79 unc-80 Abstract: The mechanism of action of volatile anesthetics is the subject of some debate. Much of the controversy has centered on whether the site of such actions is purely lipid in nature or may contain a protein target. This report studies the interaction of stereoisomers of halothane on the wild type and on a variety of genetic mutants of Caenorhabditis elegans. The mutants studied have previously been shown to have altered sensitivities to volatile anesthetics. In one mutant, fc34, (R)-halothane `the (+) isomerï was 3 times more potent than its S (-) isomer. Other mutants and wild-type animals displayed more modest differences in sensitivity to the enantiomers. The results indicate that a genetic pathway exists in C. elegans controlling sensitivity to halothane and that both lipid and protein targets may mediate halothane's effects. ------------------- Key: 2054 Medline: Authors: Rose AM;Edgley ML;Baillie DL Title: Genetic Analysis in Caenorhabditis elegans. Citation: "Advances in Molecular Plant Nematology." Lamberti F, De Giorgi and Bird (eds), Plenum Press, New York, NY. : 19-33 1994 Type: REVIEW Genes: Abstract: In order to contribute to the understanding of the organization and function of genes in the genome of Caenorhabditis elegans, we have undertaken a genetic approach. This type of approach relies upon the availability of mutant strains. Although there are many specific applications, in general genetic deduction depends upon the removal of a single component, and subsequent inference from phenotypic alterations as to the function of that component. The biology of C. elegans makes it very amenable to genetic manipulation... ------------------- Key: 2055 Medline: 95063923 Authors: Vaupel J;Johnson TE;Lithgow G;Curtsinger J;Fukui H;Xiu L;Khazaeli A;Pletcher S;Wang J;Muller H;Capra WB;Carey J Title: Rates of mortality in populations of Caenorhabditis Citation: Science 266: 826-828 1994 Type: REVIEW Genes: fer-15 spe-9 Abstract: A. Brooks et al. report that mortality increased exponentially for a cohort of 180,000 nematodes of the species Caenorhabditis elegans of the single genotype TJ1060 [spe-9(hc88) fer-15(b26)]. A closer look at the data reveals that from days 5 through 8 mortality increased at a rate of 0.58 +/- 0.0004, which is more than twice the rate thereafter (0.21 +/- 0.02). Such a "biphasic pattern," with death rates increasing rapidly at younger ages and more slowly at older ages, was also found in a genetically heterogeneous population of 79 recombinant-inbred (RI) strains. ------------------- Key: 2056 Medline: Authors: Nelson GA;Schubert WW;Kazarians GA;Richards DG;Benton EV;Benton ER;Henke R Title: Nematode radiobiology and development in space. Results from IML-1. Citation: Proceedings of the Fifth European Symposium on Life Sciences Research in Space. : 187-191 1994 Type: ARTICLE Genes: Abstract: The International Microgravity Laboratory #1 Spacelab mission was launched on 22-Jan-1992 for an 8-day mission. The Radiat experiment was one of 17 investigations which used the ESA Biorack on IML-1 and it had two objectives. The first objective was to isolate and characterize mutations induced by cosmic rays; the second was to assess the fidelity of development in 0-gravity over two consecutive generations. Two strategies were used to isolate mutations in a set of essential genes or a specific gene and to correlate the genetic events with the passage of charged particles. The results were isolation of 60 lethal mutations whose phenotypes are related to the local pattern of energy deposition. 12 mutations in the unc-22 gene include large deletions as characterized by DNA hybridization studies. Development of nematodes proceeded through two consecutive generations with no obvious defects. Cytoplasmic determinants in embryos, nuclear location and symmetry of cellular anatomy were normal as were Mendelian segregation and recombination of ------------------- Key: 2057 Medline: 95151184 Authors: Kugawa F;Yamamoto H;Osada S;Aoki M;Imagawa M;Nishihara T Title: Metallothionein genes in the nematode Caenorhabditis elegans and metal inducibility in mammalian culture cells. Citation: Biomedical and Environmental Sciences 7: 222-231 1994 Type: ARTICLE Genes: mtl-1 mtl-2 Abstract: Genomic DNAs of methallothionein I and II in Caenorhabditis elegans (CeMT-I and CeMT-II) were isolated by YAC library/polytene filter hybridization followed by subcloning of correspponding cosmid clones. Both genes are mapped at chromosome V. Although the similarities of 5'-flanking regions and coding regions have shown only 55-58%, the introns are split at the same position in both genes, indicating that these two genes are originally from the same gene. While several metal responsive elements are conserved among eukaryotes, only one metal responsive element was found in the promoter region in CeMT-II and not in CeMT-I. Indeed, neither of 5'-flanking regions of CeMT-I nor CeMT-II connected to chloramphenicol acetyltransferase reporter gene is responsive to heavy metals in mammalian culture cells by transient transfection analysis. These results would suggest that the metal regulatory factors in C. elegans might be different from those conserved in invertebrates and vertebrates, although the MTs in C. elegans revealed the similarities to ------------------- Key: 2058 Medline: 95153282 Authors: Tax FE;Thomas JH Title: Cell-cell interactions: Receiving signals in the nematode embryo. Citation: Current Biology 4: 914-916 1994 Type: REVIEW Genes: apx-1 glp-1 Abstract: Two molecules involved in an inductive cell-cell interaction in the C. elegans early embryo have been identified. The apx-1 gene seems to encode the ligand and glp-1 the receptor responsible for the induction. ------------------- Key: 2059 Medline: 95154695 Authors: Sutherlin ME;Emmons SW Title: Selective lineage specification by mab-19 during Caenorhabditis elegans male peripheral sense organ development. Citation: Genetics 138: 675-688 1994 Type: ARTICLE Genes: dpy-5 dpy-13 egl-5 lin-22 lin-32 lon-1 mab-3 mab-5 mab-19 pal-1 rol-6 sma-2 sma-3 smg-2 sqt-1 tra-1 eDp6 eDf2 stDp2 uDf1 Abstract: The action of the gene mab-19 is required for specification of a subset of Caenorhabditis elegans male peripheral sense organ (ray) lineages. Two mab-19 alleles, isolated in screens for ray developmental mutations, resulted in males that lacked the three most posterior rays. Cell lineage alterations of male-specific divisions of the most posterior lateral hypodermal (seam) blast cell, T, resulted in the ray loss phenotype in mab-19 mutant animals. Postembryonic seam lineage defects were limited to male-specific T descendent cell divisions. Embryonic lethality resulted when either mab-19 mutation was placed over a chromosomal deficiency encompassing the mab-19 locus. The earliest detectable defect was aberrant hypodermal cell movements during morphogenesis. From these data, it is inferred that both mab-19 alleles described are hypomorphs, and further reduction of mab-19 function results in embryos that are unable to complete morphogenesis. Thus, mab-19 may play a larger role in developmental regulation of hypodermal cell fate, including sensory ray development in males. Body morphology mutations, passage through the dauer stage, and heat or CdCl2 treatment suppressed mab-19 male phenotypes. A model is presented in which all three types of suppression result in a physiological stress response, which in turn leads to ------------------- Key: 2060 Medline: 95154696 Authors: LaMunyon CW;Ward S Title: Assessing the viability of mutant and manipulated sperm by artificial insemination of Caenorhabditis elegans. Citation: Genetics 138: 689-692 1994 Type: ARTICLE Genes: fem-3 Abstract: We describe a protocol for artificial insemination of Caenorhabditis elegans which we used to evaluate the viability of sperm from different strains and of sperm activated in vitro. Worms can be artificially inseminate with almost 100% success. Both male and hermaphrodite sperm can be used for insemination. Sperm from a sterile hermaphrodite `fem-3(q23ts)ï were found to be viable. As with normal mating, male sperm inseminated into hermaphrodites artificially outcompete the hermaphrodite's own sperm, even though they have not been ejaculated with seminal fluid. Spermatozoa that were activated in vitro from spermatids by the weak base triethanolamine were viable. In contrast, spermatozoa activated in vitro by protease treatment were not. ------------------- Key: 2061 Medline: 95042743 Authors: Chuang P-T;Albertson DG;Meyer BJ Title: DPY-27: A chromosome condensation protein homolog that regulates C. elegans dosage compensation through association with the X chromosome. Citation: Cell 79: 459-474 1994 Type: ARTICLE Genes: dpy-27 him-8 xol-1 Abstract: dpy-27 is an essential dosage compensation gene that acts to reduce expression of both hermaphrodite X chromosomes. The DPY-27 protein becomes specifically localized to the X chromosome of wild-type XX embryos, but remains diffusely distributed throughout the nuclei of male (XO) embryos. In xol-1 mutant XO embryos that activate the XX mode of dosage compensation and die from inappropriately low X chromosome transcript levels, Dpy-27 becomes localized to X. Therefore, sex specificity of the dosage compensation process is regulated at the step of DPY-27 X chromosome localization. DPY-27 exhibits striking similarity to proteins required for assembly and structural maintenance of Xenopus chromosomes in vitro and for segregation of yeast chromosomes in vivo. These findings suggest a link between global regulation of gene expression and higher order chromosome structure. We propose that Dpy-27 implements dosage compensation by condensing the chromatin structure of X in a manner that causes general reduction of X chromosome expression. ------------------- Key: 2062 Medline: 95052329 Authors: Lithgow GJ;White TM;Hinerfeld DA;Johnson TE Title: Thermotolerance of a long-lived mutant of Caenorhabditis elegans. Citation: Journal of Gerontology 49: B270-B276 1994 Type: ARTICLE Genes: age-1 fer-15 Abstract: Age-synchronous cohorts of Caenorhabditis elegans were grown at 20C, then stressed at 30C or 35C. Intrinsic thermotolerance of wild type and age-1 mutant strains was assessed by measuring either progeny production or survival. In addition to increased life span (Age), mutation of age-1 results in a highly significant increased intrinsic thermotolerance (Itt) as measured by survival at 35C. Mean survival of Age strains is approximately 45% longer than that of non-Age strains for both sterile and non-sterile worms. Thermotolerance declines across the life span of both Age and non-Age strains, but Itt was observed at almost all ages. Unstressed age-1 animals showed a consistent and significant fertility deficit. Short thermal stresses can cause a dramatic reduction in progeny production for both Age and non-Age genotypes. Mutants of age-1 showed a small but consistent increased thermotolerance as measured by fertility. We propose that the enhanced ability of Age strains to cope with environmental stress may be mechanistically related to their lower age-specific mortality rates. ------------------- Key: 2063 Medline: 95071320 Authors: Curtis D Title: Translational repression as a conserved mechanism for the regulation of embryonic polarity. Citation: BioEssays 16: 709-711 1994 Type: REVIEW Genes: apx-1 glh-1 glp-1 lag-2 lin-12 skn-1 Abstract: The mechanisms used to establish embryonic polarity are still largely unknown. A recent paper((1)) describes the expression pattern of the gene glp-1, which is required for induction events during development of the nematode Caenorhabditis elegans. Although glg-1 RNA is found throughout the early embryo, Glp-1 protein is only expressed in anterior cells. This negative translational regulation in posterior cells is shown to be mediated through sequences in the glp-1 3'untranslated region (3'UTR). Thus in nematodes, as in Drosophila, translational repression is one mechanism used to establish the embryonic anterior-posterior axis. ------------------- Key: 2064 Medline: Authors: Eddy SR Title: The Caenorhabditis elegans genome project. Citation: "Advances in Molecular Plant Nematology." Lamberti F, De Giorgi and Bird (eds), Plenum Press, New York, NY. : 3-18 1994 Type: REVIEW Genes: Abstract: In the next five years, molecular biology will get its first look at the complete genetic code of a multicellular animal. The Caenorhabditis elegans genome sequencing project, a collaboration between Robert Waterston's group in St. Louis and John Sulston's group in Cambridge, is currently on schedule towards its goal of obtaining the complete sequence of this organism and all its estimated 15,000 to 20,000 genes by 1998. By that time, we should also know the complete genome sequence of a few other organisms as well, including the prokaryote Escherichia coli and the single-celled eukaryote Saccharomyces ------------------- Key: 2065 Medline: Authors: Abad P Title: Transposable Elements in Nematodes. Citation: "Advances in Molecular Plant Nematology." Lamberti F, De Giorgi and Bird (eds), Plenum Press, New York, NY. : 35-54 1994 Type: REVIEW Genes: Abstract: ------------------- Key: 2066 Medline: 95096090 Authors: Chen W;Lim L Title: The Caenorhabditis elegans small GTP-binding protein RhoA is enriched in the nerve ring and sensory neurons during larval development. Citation: Journal of Biological Chemistry 269: 32394-32404 1994 Type: ARTICLE Genes: Abstract: p21 Res has been implicated in vulval differentiation in Caenorhabditis elegans. We now describe the characteristics during nematode development of the related p21 RhoA which has been ascribed a morphological role in mammals. The CeRhoA cDNA isolated in this study encodes a sequence of 192 amino acids residues with 87.6% identity to human RhoA Genomic Southern analysis indicates the presence of a single Rho gene in C. elegans. Its 2-kilobase mRNA is expressed at the highest levels during embryogenesis and decreases gradually thereafter. However, the level of the 24-kDa protein detected by the anti-CeRhoA antibody is high at the larval stages but low in embryos. The glutathione S-transferase/CeRhoA fusion protein expressed in Escherichia coli displays conserved biochemical activities. Unlike its counterpart in mammalian cells which is predominantly cytosolic, most of CeRhoA is associated with the membrane and the cytoskeleton throughout development. Indirect immunofluorescence analysis indicates an ubiquitous expression of CeRhoA throughout development with a particular enrichment at larval stages in the pharyngeal nerve ring and at the tip of the head containing chemosensory and mechanosensory neurons. This suggests a stage specific role for p21 RhoA in mediating the signaling pathway underlying the sensory circuitry in C. elegans post-embryonic development. ------------------- Key: 2067 Medline: 95023204 Authors: Wolstenholme DR;Okimoto R;Macfarlane JL Title: Nucleotide correlations that suggest tertiary interactions in the TV-replacement loop-containing mitochondrial tRNAs of the nematodes, Caenorhabditis elegans and Ascaris suum. Citation: Nucleic Acids Research 22: 4300-4306 1994 Type: ARTICLE Genes: Abstract: In the predicted secondary structures of 20 of the 22 tRNAs encoded in mitochondrial DNA (mtDNA) molecules of the nematodes, Caenorhabditis elegans and Ascaris suum, the T psi C arm and variable loop are replaced with a loop of 6 to 12 nucleotides: the TV-replacement loop. From considerations of patterns of nucleotide correlations in the central regions of these tRNAs, it seems highly likely that tertiary interactions occur within five sets of binary and ternary combinations of nucleotides that correspond in location to nucleotides known to be involved in tertiary interactions in yeast tRNA(Phe) and other standard tRNAs. These observations are consistent with the nematode TV-replacement loop-containing mt-tRNAs being folded into a similar L-shaped functional form to that demonstrated for standard tRNAs, and for the bovine DHU (dihydrouridine) arm replacement-loop-containing mt-tRNA(Ser(AGY)). However, the apparent occurrence in nematode mt-tRNAs of tertiary bonds common to standard tRNAs contrasts with the situation in bovine mt-tRNA(Ser(AGY)) where the functional form is dependent on an almost unique set of tertiary interactions. Because three of the proposed conserved tertiary interactions in the nematode mt-tRNAs involve nucleotides that occur in the variable loop in standard tRNAs, it seems more likely that in nematode mt-tRNAs it is the T psi C arm rather than the variable loop that has undergone the greatest proportional decrease in nucleotide number. ------------------- Key: 2068 Medline: 95106284 Authors: La Volpe A Title: A repetitive DNA family, conserved throughout the evolution of free-living nematodes. Citation: Journal of Molecular Evolution 39: 473-477 1994 Type: ARTICLE Genes: Abstract: This paper concerns the molecular evolution of a tandemly repeated DNA family, RcC9, originally identified in Caenorhabditis elegans. The minimum unit of periodicity of this family is the pentanucleotide `nGAAnï and its complement [nTTCn] recurring several times in alternating tandem arrays. This consensus sequence is identical to that of the heat-shock element (HSE). Multiple HSEs are present in the regulatory regions of heat-inducible genes in a wide range of eukaryotic species; HSEs mediate transcriptional activation through the binding of the heat-shock factor (HSF). I describe some repeated DNA families sharing this same consensus and found in nematode species other than C. elegans. Although the consensus is conserved, the repeated sequence diverged between species to the point that cross-hybridization is abolished. Evolutionary implications will be discussed. ------------------- Key: 2069 Medline: 95014533 Authors: Veijola J;Koivunen P;Annunen P;Pihlajaniemi T;Kivirikko KI Title: Cloning, baculovirus expression, and characterization of the alpha-subunit of prolyl 4-hydroxylase from the nematode Caenorhabditis elegans. Citation: Journal of Biological Chemistry 269: 26746-26753 1994 Type: ARTICLE Genes: Abstract: Prolyl 4-hydroxylase (EC 1.14.11.2) catalyzes the formation of 4-hydroxyproline in collagens. The vertebrate enzyme is an alpha(2) beta(2) tetramer, the beta subunit of which is identical to protein disulfide-isomerase (PDI). We report here on the cloning of the catalytically important alpha subunit from Caenorhabditis elegans. This polypeptide consists of 542 amino acids and a signal peptide of 16 additional residues. The C. elegans alpha subunit is 25 amino acids longer than the human alpha subunit, mainly because of a 32-amino-acid C-terminal extension present only in the former. The overall amino acid sequence identity between these two alpha subunits is 45%, a 127-amino acid region close to the C terminus being especially well conserved. When the C. elegans alpha subunit was expressed together with the human PDI/beta subunit in insect cells by baculovirus vectors, an active prolyl 4-hydroxylase was formed, but surprisingly this C. elegans/human enzyme appeared to be an alpha beta dimer. The specific activity of this C. elegans/human enzyme was comparable with that of the human enzyme, and most of the other catalytic properties were also highly similar. Nevertheless, the C. elegans/human enzyme was not inhibited by poly(L-proline). The data indicate that the multifunctional PDI/beta subunit can form an active prolyl 4-hydroxylase with alpha subunits having marked differences ------------------- Key: 2070 Medline: 95014571 Authors: Jantsch-Plunger V;Fire A Title: Combinatorial structure of a body muscle-specific transcriptional enhancer in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 269: 27021-27028 1994 Type: ARTICLE Genes: glp-1 hlh-1 myo-2 unc-54 Abstract: We describe the dissection of a body muscle-specific enhancer sequence contained within the Caenorhabditis elegans myosin heavy chain gene unc-54. A 90-base pair segment that was sufficient for both enhancer function and tissue specificity was subjected to mutational analysis. Several separated sites within this region were required for activity; mutations in these sites led to dramatic decreases in enhancer activity, while substitutions in the intervening regions had minimal effects on activity. The individual sites appear to function as semi-independent and partially interchangeable enhancer subelements, as seen by our ability to create functional enhancers by constructing novel multimers and combinations. Four different enhancer subelements (designated 0, I, II, and III) were identified in this way. Although partially interchangeable, some differences between these subelements were evident. In particular, concatamers of site III exhibited the highest levels of activity but had a broader tissue specificity than the intact enhancer, including both hypodermal and muscle tissue. The specificity of the intact enhancer thus reflects a combinatorial function of the specificities of the constituent subelements. ------------------- Key: 2071 Medline: 95061402 Authors: Kuwabara PE;Shah S Title: Cloning by synteny: identifying C. briggsae homologues of C. elegans genes. Citation: Nucleic Acids Research 22: 4414-4418 1994 Type: ARTICLE Genes: art-1 ppp-1 sod-1 tra-2 Abstract: Phylogenetic comparisons of gene and protein sequences between related species are often used to identify evolutionarily conserved elements that are important for gene expression, function, or regulation. However, homologues may sometimes be difficult to identify by conventional low stringency hybridisation techniques, if they have undergone substantial sequence divergence. A new approach, cloning by synteny, is described that was used to identify the C. briggsae homologue of the C. elegans sex-determining gene tra-2. We show that four genes tra-2, ppp-1, art-1 and sod-1 are organised in a syntenic cluster and suggest that extensive conservation of gene linkage may exist between C. briggsae and C. elegans. We have also constructed a C. briggsae cDNA library to facilitate characterisation of these genes. Given the rapid progress in the physical mapping and sequencing of the C. elegans genome, cloning by synteny may provide the fastest method for identifying C. briggsae gene homologues, especially for genes encoding novel proteins. ------------------- Key: 2072 Medline: 95059453 Authors: Zorio DAR;Cheng NSN;Blumenthal T;Spieth J Title: Operons as a common form of chromosomal organization in C. elegans. Citation: Nature 372: 270-272 1994 Type: ARTICLE Genes: dom-3 dpy-30 fib-1 gpd-2 gpd-3 kin-10 kin-13 kin-15 kin-16 kup-1 kup-2 lin-15 mai-1 mes-3 rnp-1 rps-16 unc-32 Abstract: Although eukaryotic genes are usually transcribed individually, at least a few Caenorhabditis elegans genes appear to be transcribed polycistronically in clusters resembling bacterial operons. The spliced leader SL2 (ref. 2) is specific for trans-splicing to downstream genes in these operons. In addition, many C. elegans pre-mRNAs are trans-spliced to SL1 (ref. 3) near the 5' end of pre-mRNAs. Because operons have not previously been found in higher eukaryotes, we have investigated how widespread they are in the C. elegans genome. We identified gene clusters using the extensive data generated by the genome project and tested seven for trans-splicing specificity. All were found to fit expectations for polycistronic transcription. In addition, we surveyed reported C. elegans genes for trans-splicing specificity. Both methods indicate that the pre-mRNAs of about 70% of C. elegans genes are trans-spliced and as many as a quarter are transcribed in ------------------- Key: 2073 Medline: 95046896 Authors: Krause M;Harrison SW;Xu SQ;Chen LS;Fire A Title: Elements regulating cell- and stage-specific expression of the C. elegans myoD family homolog hlh-1. Citation: Developmental Biology 166: 133-148 1994 Type: ARTICLE Genes: glp-1 hlh-1 myo-2 Abstract: We investigated the cis-acting sequences regulating expression of the Caenorhabditis elegans gene hlh-1, a homolog of the MyoD family of myogenic regulatory factors. The hlh-1 gene is expressed in mature body wall muscle, in clonal muscle precursors, in a set of early embryonic blastomeres (the MS-granddaughters), and in six glial-like cells called GLRs. The entire natural hlh-1 expression pattern is recapitulated in transgenic animals containing an hlh-1:: lacZ fusion with 5.1 kb of hlh-1 sequences beginning upstream of the coding region and extending into the second exon. Deletions and rearrangements in this 5.1-kb sequence were assayed for their effects on reporter gene expression in transgenic animals. Deletions removing a segment 434-550 bp upstream of the coding region resulted in a loss of all aspects of the expression pattern, suggesting that at least one common regulatory factor is required for all expression. Deletions of other regulatory elements affected distinct aspects of the expression pattern; hence, each expression subpattern exhibits a different set of sequence requirements. Interspecies sequence comparison and lacZ expression constructs with the related nematode Caenorhabditis briggsae indicated that the C. briggsae and C. elegans genes contain equivalent sets of control signals. The results from this work implicate the hlh-1 promoter as an integration point for diverse temporal and spatial control signals. ------------------- Key: 2074 Medline: 95203681 Authors: Akerib CC;Meyer BJ Title: Identification of X chromosome regions in Caenorhabditis elegans that contain sex-determination signal elements. Citation: Genetics 138: 1105-1125 1994 Type: ARTICLE Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 sdc-1 sdc-2 sdc-3 unc-2 unc-9 xol-1 meDf5 meDf6 mnDp8 mnDp10 mnDp57 mnDp66 mnDp73 nDf19 stDp2 yDf13 yDf14 yDp4 yDp5 yDp6 yDp7 yDp8 yDp9 yDp10 yDp11 yDp12 yDp13 yDp14 yDp15 yDp16 Abstract: The primary sex-determination signal of Caenorhabditis elegans is the ratio of X chromosomes to sets of autosomes (X/A ratio). This signal coordinately controls both sex determination and X chromosome dosage compensation. To delineate regions of X that contain counted signal elements, we examined the effect on the X/A ratio of changing the dose of specific regions of X, using duplications in XO animals and deficiencies in XX animals. Based on the mutant phenotypes of genes that are controlled by the signal, we expected that increases (in males) or decreases (in hermaphrodites) in the dose of X chromosome elements could cause sex-specific lethality. We isolated duplications and deficiencies of specific X chromosome regions, using strategies that would permit their recovery regardless of whether they affect the signal. We identified a dose-sensitive region at the left end of X that contains X chromosome signal elements. XX hermaphrodites with only one dose of this region have sex determination and dosage compensation defects, and XO males with two doses are more severely affected and die. The hermaphrodite defects are suppressed by a downstream mutation that forces all animals into the XX mode of sex determination and dosage compensation. The male lethality is suppressed by mutations that force all animals into the XO mode of both processes. We were able to subdivide this region into three smaller regions, each of which contains at least one signal element. We propose that the X chromosome component of the sex-determination signal is the dose of a relatively small number of genes. ------------------- Key: 2075 Medline: 95218112 Authors: Eckenhoff RG;Yang BJ Title: Absence of pressure antagonism of ethanol narcosis in C. elegans. Citation: Neuroreport 6: 77-80 1994 Type: ARTICLE Genes: Abstract: Because hydrostatic pressure can antagonize the behavioral effects of anesthetics in many organisms, we examined whether ethanol-induced immobility of the nematode Caenorhabditis elegans was antagonized by 100 ATA pressure. Nematode mobility was examined at pressures ranging from 1 ATA to 132 ATA, with and without increasing concentrations of ethanol (0-1 M). Pressure >100 ATA alone inhibited movement of the nematode (EP = 111.5 +/- 0.6 ATA), as did increasing concentrations of ethanol (EC = 487 +/- 44 mM). Pressure and ethanol appeared to be additive, and not antagonistic. Because of previous results implicating glycine receptor antagonism as a mechanism of pressure reversal, and our current inability to observe significant behavioral effects of strychnine or glycine inhibition of high affinity strychnine binding, we suggest that an absence of glycine receptors in these organisms is the basis for a lack of pressure antagonism of ethanol ------------------- Key: 2076 Medline: 95059445 Authors: Hirsh D Title: Operons in eukaryotes follow the spliced leader. Citation: Nature 372: 222-223 1994 Type: REVIEW Genes: gpd-2 gpd-3 kin-10 lin-13 lin-15 mai-1 rol-6 Abstract: Many bacterial genes are organized into operons which are transcribed as polycistronic messenger RNAs. By contrast, eukaryotic genes were thought to be regulated individually and transribed as monocistronic mRNAs. Last year, however, a group led by Tom Blumenthal announced the discovery that the nematode Caenorhabditis elegans uses both the prokaryotic and the eukaryotic patterns of gene organization and transcription. Blumenthal and colleagues have now taken this work further (page 270 of this issue). They describe how they have examined the C. elegans genomic database and found that at least a quarter of the genes seem to be organized into operons. ------------------- Key: 2077 Medline: 95061415 Authors: Spikes DA;Kramer J;Bingham PM;Van Doren K Title: SWAP pre-mRNA splicing regulators are a novel, ancient protein family sharing a highly conserved sequence motif with the prp21 family of constitutive splicing proteins. Citation: Nucleic Acids Research 22: 4510-4519 1994 Type: ARTICLE Genes: Abstract: Regulators responsible for the pervasive, nonsex-specific alternative pre-mRNA splicing characteristic of metazoans are almost entirely unknown or uncertain. We describe here a novel family of splicing regulators present throughout metazoans. Specifically, we analyze two nematode (Caenorhabditis elegans) genes. One, CeSWAP, is a cognate of the suppressor-of-white-apricot (DmSWAP) splicing regulator from the arthropod Drosophila. Our results define the ancient, conserved SWAP protein family whose members share a colinearly arrayed series of novel sequence motifs. Further, we describe evidence that the CeSWAP protein autoregulates its levels by feedback control of splicing of its own pre-mRNA analogously to the DmSWAP protein and as expected of a splicing regulator. The second nematode gene, Ceprp21, encodes an abundant nuclear cognate of the constitutive yeast splicing protein, prp21, on the basis of several lines of evidence. Our analysis defines prp21 as a second novel, ancient protein family. One of the motifs conserved in prp21 proteins-designated surp-is shared with SWAP proteins. Several lines of evidence indicate that both new families of surp-containing proteins act at the same (or very similar) step in early prespliceosome assembly. We discuss implications of our results for regulated metazoan pre-mRNA splicing. ------------------- Key: 2078 Medline: 95059481 Authors: Lim WA;Richards FM; Fox RO Title: Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Citation: Nature 372: 375-379 1994 Type: ARTICLE Genes: sem-5 Abstract: The Src-homology-3 (SH3) domains of the Caenorhabditis elegans protein SEM-5 and its human and Drosophila homologues, Grb2 and Drk (refs 1-4), bind proline-rich sequences found in the nucleotide-exchange factor Sos as part of their proposed function linking receptor tyrosine kinase activation to Ras activation(5-7). Here we report the crystal structure at 2.0 Angstrom resolution of the carboxy-terminal SH3 domain from SEM-5 complexed to the mSos-derived amino-acid sequence PPPVPPRRR. The peptide is found to bind in an orientation ('minus') that is precisely opposite to that observed previously ('plus' orientation) in other SH3-peptide complexes(8,9). This novel ability of peptide-recognition proteins to recognize peptides in two distinct modes may play an important role in the signalling specificity of pathways involving SH3 domains. Comparison of this structure with other SH3 complexes reveals how a conserved binding face can be used to recognize peptides in different orientations, and why the Sos peptide binds in this particular orientation. ------------------- Key: 2079 Medline: Authors: von Ehrenstein G;Sulston JE;Schierenberg E;Laufer JS;Cole T Title: Embryonic cell lineages and segregation of developmental potential in Caenorhabditis elegans. Citation: "International Cell Biology 1980-1981", H.G. Schweiger (ed), Springer-Verlag, Berlin Heidelberg. : 519-525 1981 Type: REVIEW Genes: Abstract: Embryogenesis of the nematode Caenorhabditis elegans is determinate and virtually invariant from individual to individual. The fertilized egg develops into an anatomically relatively simple juvenile animal having a constant number of only 550 cells (or nuclei) at hatching. The complete embryonic cell lineage up to the 220-cell stage has been described previously, and some lineages have been followed considerably further. During postembryonic development, the cell number increases to about 950 in mature hermaphrodites (including the 143 of the somatic gonad structures) and to about 1025 in males. These cells arise from about 50 blast cells which resume division after hatching. The lineages of all these cells have been described. ------------------- Key: 2080 Medline: Authors: Schierenberg E Title: Laser-induced cell fusion. Citation: "Cell Fusion", A.E. Sowers (ed), Plenum Press. : 409-418 1987 Type: REVIEW Genes: Abstract: In recent years a number of different techniques have been developed to fuse cells of various origin in order to obtain hybrids with qualities different from each of the original cells. In many cases, one wants to fuse large numbers of cells (e.g. to generate hybridomas), and fusion occurs more or less randomly (e.g. Kohler and Milstein, 1975). With other methods, individual cells have been fused under controlled conditions (e.g., McGrath and Solter, 1984). So far a prerequisite for fusing two preselected cells has been that they must be isolated away ------------------- Key: 2081 Medline: 95106299 Authors: Okimoto R;Macfarlan JL;Wolstenholme DR Title: The mitochondrial rRNA genes of the nematodes Caenorhabditis elegans and Ascaris suum: Consensus secondary-structure models and conserved nucleotide sets for phylogenetic analysis. Citation: Journal of Molecular Evolution 39: 598-613 1994 Type: ARTICLE Genes: Abstract: The small- and large-subunit mitochondrial ribosomal RNA genes (mt-s-rRNA and mt-1-rRNA) of the nematode worms Caenorhabditis elegans and Ascaris suum encode the smallest rRNAs so far reported for metazoa. These size reductions correlate with the previously described, smaller, structurally anomalous mt-tRNAs of C. elegans and A. suum. Using primer extension analysis, the 5' end nucleotides of the mt-s-rRNA and mt-1-rRNA genes were determined to be adjacent to the 3' end nucleotides of the tRNA(Glu) and tRNA(His) genes, respectively. Detailed, consensus secondary-structure models were constructed for the mt-s-rRNA genes and the 3' 64% of mt-1-rRNA genes of the two nematodes. The mt-s-rRNA secondary-structure model bears a remarkable resemblance to the previously defined universal core structure of E. coli 16S rRNA: most of the nucleotides that have been classified as variable or semiconserved in the E. coli model appear to have been eliminated from the C. elegans and A. suum sequences. Also, the secondary structure model constructed for the 3' 64% of the mt-1-rRNA is similar to the corresponding portion of the previously defined E. coli 23S rRNA core secondary structure. The proposed C. elegans/A. suum mt-s-rRNA and mt-1-rRNA models include all of the secondary-structure element-forming sequences that in E. coli rRNAs contain nucleotides important for A-site and P-site (but not E-site) interactions with tRNAs. Sets of apparently homologous sequences within the mt-s-rRNA and mt-1-rRNA core structures, derived by alignment of the C. elegans and A. suum mt-rRNAs to the corresponding mt-rRNAs of other eukaryotes, and E. coli rRNAs were used in maximum-likelihood analyses. The patterns of divergence of metazoan phyla obtained show considerable agreement with the most prevalent metazoan divergence patterns derived ------------------- Key: 2082 Medline: 95089817 Authors: Jin YS;Hoskins R;Horvitz HR Title: Control of type-D GABAergic neuron differentiation by C. elegans UNC-30 homeodomain protein. Citation: Nature 372: 780-783 1994 Type: ARTICLE Genes: unc-30 Abstract: The Caenorhabditis elegans gene unc-30 is required for the development and functioning of the 19 inhibitory GABAergic (gamma-aminobutyric-acid-secreting) type D motor neurons, which control locomotion(1-4). In unc-30 mutants the D neurons lack GABA(2) and have defects in axonal pathfinding and synaptic connections (J. White, personal communication). We report here that unc-30 encodes a homeodomain protein that is present in the nuclei of the D neurons at high levels in young larvae, in which the motor circuitry is formed, and at low levels in older animals. The UNC-30 protein is also present in six non-GABAergic neurons and is absent from the seven non-D-type GABAergic neurons. Ectopic expression of unc-30 induced GABA expression in cells that are normally not GABAergic. We propose that unc-30 functions as a transcriptional regulator within the type D neurons to control their terminal differentiation and that unc-30 is sufficient in some but not all cell types to induce GABA expression. ------------------- Key: 2083 Medline: 95236996 Authors: Moskowitz IPG;Gendreau SB;Rothman JH Title: Combinatorial specification of blastomere identity by glp-1-dependent cellular interactions in the nematode Caenorhabditis elegans. Citation: Development 120: 3325-3338 1994 Type: ARTICLE Genes: glp-1 unc-33 Abstract: Most somatic cells in the nematode Caenorhabditis elegans arise from AB, the anterior blastomere of the 2-cell embryo, While the daughters of AB, ABa and ABp, are equivalent in potential at birth, they adopt different fates as a result of their unique positions, One such difference is that the distribution of epidermal precursors arising from ABp is reversed along the anterior-posterior axis relative to those arising from ABa, We have found that a strong mutation in the glp-1 gene eliminates this ABa/ABp difference, Furthermore, extensive cell lineage analyses showed that ABp adopts an ABa-like fate in this mutant, This suggests that glp-1 acts in a cellular interaction that makes ABp distinct from ABa, One ABp-specific cell type was previously shown to be induced by an interaction with a neighboring cell, P-2. By removing P-2 from early embryos, we have found that the widespread differences between ABa and ABp arise from induction of the entire ABp fate by P-2, Lineage analyses of genetically and physically manipulated embryos further suggest that the identities of the AB great-granddaughters (AB(8) cells) are controlled by three regulatory inputs that act in various combinations. These inputs are: (1) induction of the ABp-specific fate by P-2, (2) a previously described induction of particular AB(8) cells by a cell called MS, and (3) a process that controls whether an AB(8) cell is an epidermal precursor in the absence of either induction, When an AB(8) cell is caused to receive a new combination of these regulatory inputs, its lineage pattern is transformed to resemble the lineage of the wild-type AB(8) cell normally receiving that combination of inputs, These lineage patterns are faithfully reproduced irrespective of position in the embryo, suggesting that each combination of regulatory inputs directs a unique lineage program that is intrinsic ------------------- Key: 2084 Medline: 95091781 Authors: Tsoi SCM;Li SSL Title: The nucleotide and deduced amino-acid sequences of a cDNA encoding lactate dehydrogenase from Caenorhabditis elegans: The evolutionary relationships of lactate dehydrogenases from Citation: Biochemical and Biophysical Research Communications 205: 558-564 1994 Type: ARTICLE Genes: Abstract: The nucleotide and deduced amino-acid sequences of a cDNA encoding L-lactate dehydrogenase (LDH) from nematode, Caenorhabditis elegans, were reported. This first invertebrate LDH sequence of 333 amino acids, including the initiation methionine, exhibits 63% identity with that of the most primitive vertebrate lamprey. The evolutionary relationships among 36 LDH isozymes from mammals, birds, amphibian, fish, nematode, plants, bacteria, mycoplasma and plasmodium were analyzed. The invertebrate nematode LDH is evolutionarily positioned between plant LDH and mammalian testicular LDH-C isozymes. The mammalian LDH-C isozyme appears to have arisen after the invertebrate LDH, but prior to the divergence of vertebrate LDH-A (muscle) and LDH-B (heart) isozymes as described previously. ------------------- Key: 2085 Medline: 95007039 Authors: Sonnhammer EL;Durbin R Title: A workbench for large-scale sequence homology analysis. Citation: Computer Applications in the Biosciences 10: 301-307 1994 Type: ARTICLE Genes: Abstract: When routinely analysing very long stretches of DNA sequences produced by genome sequencing projects, detailed analysis of database search results becomes exceedingly time consuming. To reduce the tedious browsing of large quantities of protein similarities, two programs, MSPcrunch and Blixem, were developed, which assist in processing the results from the database search programs in the BLAST suite. MSPcrunch removes biased composition and redundant matches while keeping weak matches that are consistent with a larger gapped alignment. This makes BLAST searching in practice more sensitive and reduces the risk of overlooking distant similarities. Blixem is a multiple sequence alignment viewer for X-windows which makes it significantly easier to scan and evaluate the matches ratified by MSPcrunch. In Blixem, matches to the translated DNA query sequence are simultaneously aligned in three frames. Also, the distribution of matches over the whole DNA query is displayed. Examples of usage are drawn from 36 C. elegans cosmid clones totalling 1.2 megabases, to which these tools were applied. ------------------- Key: 2086 Medline: 95220657 Authors: Rogalski TM;Gilchrist EJ;Mullen GP;Moerman DG Title: Mutations in the unc-52 gene responsible for body wall muscle defects in adult Caenorhabditis elegans are located in alternatively spliced exons. Citation: Genetics 139: 159-169 1995 Type: ARTICLE Genes: unc-52 mnDp34 Abstract: The unc-52 gene in Caenorhabditis elegans produces several large proteins that function in the basement membrane underlying muscle cells. Mutations in this gene result in defects in myofilament assembly and in the attachment of the myofilament lattice to the muscle cell membrane. The st549 and ut111 alleles of unc-52 produce a lethal (Pat) terminal phenotype whereas the c444, e669, e998, e1012 and e1421 mutations result in viable, paralyzed animals. We have identified the sequence alterations responsible for these mutant phenotypes. The st549 allele has a premature stop codon in exon 7 that should result in the complete elimination of unc-52 gene function, and the ut111 allele has a Tc1 transposon inserted into the second exon of the gene. The five remaining mutations are clustered in a small interval containing three adjacent, alternatively spliced exons (16, 17 and 18). These mutations affect some, but not all of the unc-52-encoded proteins. Thirteen intragenic revertants of the e669, e998, e1012 and e1421 alleles have also been sequenced. The majority of these carry the original mutation plus a G to A transition in the conserved splice acceptor site of the affected exon. This result suggests that reversion of the mutant phenotype in these strains may be the result of exon-skipping. ------------------- Key: 2087 Medline: 95220658 Authors: Starich TA;Herman RK;Kari CK;Yeh W-H;Schackwitz WS;Schuyler MW;Collet J;Thomas JH;Riddle DL Title: Mutations affecting the chemosensory neurons of Caenorhabditis elegans. Citation: Genetics 139: 171-188 1995 Type: ARTICLE Genes: caf-1 caf-2 che-2 che-3 che-10 che-11 che-12 che-13 daf-6 daf-10 daf-11 dyf-1 dyf-2 dyf-3 dyf-4 dyf-5 dyf-6 dyf-7 dyf-8 dyf-9 dyf-10 dyf-11 dyf-12 dyf-13 osm-1 osm-3 osm-5 osm-6 ctDf1 eDf2 eDp6 hDf8 maDf4 mnDf13 mnDf30 mnDf88 mnDf99 mnDf105 mnDf111 nDf19 nDf23 nDf24 nDf25 ozDf2 sDf4 sDf35 stDp2 Abstract: We have identified and characterized 95 mutations that reduce or abolish dye filling of amphid and phasmid neurons and that have little effect on viability, fertility or movement. Twenty-seven mutations occurred spontaneously in strains with a high frequency of transposon insertion. Sixty-eight were isolated after treatment with EMS. All of the mutations result in defects in one or more chemosensory responses, such as chemotaxis to ammonium chloride or formation of dauer larvae under conditions of starvation and overcrowding. Seventy-five of the mutations are alleles of 12 previously defined genes, mutations which were previously shown to lead to defects in amphid ultrastructure. We have assigned 20 mutations to 13 new genes, called dyf-1 through dyf-13. We expect that the genes represented by dye-filling defective mutants are important for the differentiation of amphid and phasmid ------------------- Key: 2088 Medline: Authors: Schierenberg E Title: Embryonic development of the nematode Caenorhabditis elegans. Citation: Film D 1542 des IWF, Gottingen, Publ. Wissenschaftlechen Filmen, Sekt. Biol., Ser. 17, Nr. 13/D 1542. : 1-21 1984 Type: REVIEW Genes: Abstract: Summary of the Film: Embryonic Development of the Nematode Caenorhabditis elegans. A major part of the body cavity of the free-living nematode Caenorhabditis elegans is occupied by oocytes and fertilized eggs. Within about 12 hours the fertilized egg develops into a worm. The transparent eggshell and the ability to develop normal outside the mother allow detailed microscopic observation of cellular development. After fertilization both pronuclei are positioned at opposite poles of the uncleaved egg. They migrate towards each other, fuse and form the zygote. A series of asymmetric divisions results in the formation of 5 "somatic founder cells" and one "primordial germ cell". In addition to the typical synchronous cell divisions within individual cell lines characteristic cell and nuclear migrations during embyrogenesis are shown. Taking the primordial gut cells as an example, formation of an organ is described. Colored computer reconstructions aid a better understanding of cellular topography and document early formation of symmetry within individual cell lines. After the first half of embryonic development nearly all cells are present. During the second half the ball of cells stretch, first muscle contractions occur, gradually a worm is formed. When it hatches, it is about 4x as long as the long axis of the egg shell. ------------------- Key: 2089 Medline: Authors: Mendel J;Simon MI;Sternberg PW Title: Molecular genetics of G protein alpha subunit genes in C. elegans. Citation: Ares Sereno Symp. : 33-41 1994 Type: ARTICLE Genes: goa-1 gpa-1 gpa-2 gpa-3 gqa-1 gsa-1 Abstract: Heterotrimeric G proteins coordinate receptor and effector activity and mediate a variety of cellular and developmental processes. Each of the three components of these G proteins exists in multiple forms in all animals studied. One approach to understanding the function of this diversity of subunit types is to use genetics to determine not only the particular receptors and effectors with which each type of G protein can interact, but also, the role of other cellular components in the specificity or regulation of G-protein-mediated signal transduction. We are using the molecular genetics of Caenorhabditis elegans to study the role of G-protein-mediated signal transduction in development and behavior. ------------------- Key: 2090 Medline: 95094282 Authors: Sengupta P;Colbert HA;Bargmann CI Title: The C. elegans gene odr-7 encodes an olfactory-specific member of the nuclear receptor superfamily. Citation: Cell 79: 971-980 1994 Type: ARTICLE Genes: odr-7 Abstract: Olfactory discrimination is achieved through the action of olfactory neurons with diverse chemical specificities. In C. elegans, at least ten different types of chemosensory neurons respond to different chemicals. The odr-7 gene is required for the function of one pair of chemosensory neurons called AWA neurons. odr-7 null mutants fail to respond to all odorants detected by the AWA neurons, while a missense mutation in odr-7 causes a specific defect in one odorant response. odr-7 encodes a protein with similarity to the DNA-binding domain of the nuclear receptor genes; it is expressed predominantly in the AWA neurons. odr-7 may regulate the expression of olfactory signaling molecules that define a single type of olfactory ------------------- Key: 2091 Medline: 95200524 Authors: Broster BS;Rankin CH Title: Effects of changing interstimulus interval during habituation in Caenorhabditis elegans. Citation: Behavioral Neuroscience 108: 1019-1029 1994 Type: ARTICLE Genes: Abstract: The role of the interstimulus interval (ISI) in habituation in Caenorhabditis elegans was explored by examining the effect of changing the ISI on habituation and on spontaneous recovery from habituation. When habituation stimuli were delivered at variable ISIs with an average of 10 s, recovery was slower than when habituation stimuli were delivered at fixed 10-s intervals. There were no differences in recovery following either fixed or variable stimulation at a 60-s ISI. The effect of shifting to a different ISI during habituation training was also explored. A 60-s ISI affected habituation at a 10-s ISI, but a 10-s ISI did not influence habituation at a 60-s ISI. Therefore, habituation must be viewed as an ongoing equilibrium of a number of cellular processes-some decrementing, some facilitating-that are differentially ------------------- Key: 2092 Medline: 95142800 Authors: Way JC;Wang L;Run JQ;Hung MS Title: Cell polarity and the mechanism of asymmetric cell Citation: BioEssays 16: 925-931 1994 Type: REVIEW Genes: lin-11 lin-17 lin-22 mec-3 unc-73 unc-86 Abstract: During development, one mechanism for generating different cell types is asymmetric cell division, by which a cell divides and contributes different factors to each of its daughter cells. Asymmetric cell division occurs throughout the eukaryotic kingdom, from yeast to humans. Many asymmetric cell divisions occur in a defined orientation. This implies a cellular mechanism for sensing direction, which must ultimately lead to differences in gene expression between two daughter cells. In this review, we describe two classes of molecules: regulatory factors that are differentially expressed upon asymmetric cell division, and components of a signal transduction pathway that may define cell polarity. The lin-11 and mec-3 genes of C. elegans, the Isl-1 gene of mammals and the HO gene of yeast, encode regulatory factors that determine cell type of one daughter after asymmetric cell division. The CDC24 and CDC42 genes of yeast affect both bud positioning and orientation of mating projections, and thus may define a general cellular polarity. We speculate that molecules such as Cdc24 and Cdc42 may regulate expression of genes such as lin-II, mec3, Isl-l and HO upon asymmetric cell ------------------- Key: 2093 Medline: 95200272 Authors: Kramer JM Title: Genetic analysis of extracellular matrix in C. elegans. Citation: Annual Review of Genetics 28: 95-116 1994 Type: REVIEW Genes: bli-4 clb-1 clb-2 col-1 cut-1 daf-2 dpy-2 dpy-5 dpy-7 dpy-10 dpy-13 dpy-20 emb-9 glp-1 her-1 let-2 lin-22 mup-1 pat-3 rol-3 rol-6 sqt-1 sqt-3 srf-1 srf-2 srf-3 srf-4 srf-5 srf-6 srf-8 srf-9 srl-1 srl-2 sup-38 tra-1 unc-5 unc-6 unc-40 unc-52 Abstract: All metazoans possess extracellular matrices (ECM) composed of complex assemblies of molecules with generally well conserved structures and functions. ECM play structural roles, providing scaffolds that organize and strengthen tissues, and instructional roles, influencing differentiation and development. Major ECM components include the collagens, a diverse family of fibrous proteins distinguished by their triple-helical coiled coil structure, other large glycoproteins, such as laminin, fibronectin and nidogen, and proteoglycans, proteins with attached glycosaminoglycan chains. For most ECM components, cell surface receptors have been identified that can mediate interactions between the cell and its ECM. The nematode Caenorhabditis elegans is an excellent system for studies of the structures and functions of ECM components, and their roles in development. C. elegans is the simplest metazoan in which detailed genetic analysis of the ECM can be performed. The complete cell lineage and detailed anatomical structure of the organism have been described. The simple life style of C. elegans allows animals with severe morphological and/or motility defects to survive and, because they are internally self-fertilizing hermaphrodites, even reproduce. These properties can simplify mutational analyses of genes encoding ECM components. Two major forms of ECM have been identified in C. elegans, the cuticle and basement membranes. The cuticle, or exoskeleton, covers the outside of the animal and lines the lumen of the pharynx. Basement membranes cover the pseudocoelomic faces of the pharynx, intestine, gonad, and hypodermis. There is no visible interstitial matrix between the cells within tissues, possibly because nearly all cells are adjacent to the cuticle or a basement membrane. This review focuses on studies of the ECM in C. elegans. The reader is referred to excellent recent reviews concerning related topics: collagens in other nematodes; mutations in human fibrillar collagens; mutations in human type IV collagen; composition ------------------- Key: 2094 Medline: 95098129 Authors: Zhao C;Emmons SW Title: A transcription factor controlling development of peripheral sense organs in C. elegans. Citation: Nature 373: 74-78 1995 Type: ARTICLE Genes: lin-22 lin-32 eT2 Abstract: The basic-helix-loop-helix (bHLH) proteins constitute a class of transcription factors thought to be important in the control of cell-type determination(1). These transcription factors are believed to activate the expression of cell-type-specific genes to generate stable differentiated cell types(2). The expression of bHLH proteins, in turn, is regulated by spatial cues, so that switches in cell type occur in a reproducible pattern(3). We report here that the lin-32 gene of Caenorhabditis elegans, which encodes a bHLH protein of the Drosophila achaete-scute family of transcription factors, is necessary and in some cells sufficient for specification of the neuroblast cell fate. Similarity in the function and structure of the lin-32 protein (LIN-32) to transcription factors of the achaete-scute gene family in Drosophila and vertebrates implies that this class of transcription factors functioned in a primitive ancestral form to specify neuronal cell fate, supporting the proposition that certain basic mechanisms of cell-type determination have been conserved through metazoan evolution(1). ------------------- Key: 2095 Medline: 95094294 Authors: Wilkinson HA;Fitzgerald K;Greenwald I Title: Reciprocal changes in expression of the receptor lin-12 and its ligand lag-2 prior to commitment in a C. elegans cell fate decision. Citation: Cell 79: 1187-1198 1994 Type: ARTICLE Genes: glp-1 lag-2 lin-12 smg-1 Abstract: During development of the C. elegans hermaphrodite gonad, two cells interact with each other, so that one chooses to become the anchor cell (AC) and the other becomes a ventral uterine precursor cell (VU). This interaction is mediated by the receptor LIN-12 and its apparent ligand LAG-2. We show that initially lin-12 and lag-2 are expressed in both cells, but prior to commitment, the expression patterns change in a reciprocal manner, so that lin-12 expression becomes restricted to the presumptive VU and lag-2 expression becomes restricted to the presumptive AC. In addition, lin-12 activity promotes expression of lin-12 and represses expression of lag-2. Furthermore, we show that positive autoregulation of lin-12 transcription in the presumptive VU is mediated by a cis-acting 5' regulatory sequence and is necessary to specify the VU fate. Our results suggest that transcriptional control is a component of the feedback mechanism involved in specifying the AC and VU fates. ------------------- Key: 2096 Medline: 95214658 Authors: De Georgi C;Sialer MF;Lamberti F Title: Formalin-induced infidelity in PCR-amplified DNA fragments. Citation: Molecular and Cellular Probes 8: 459-462 1994 Type: ARTICLE Genes: Abstract: A 643-nucleotide-long fragment of rDNA gene was amplified by PCR in the nematode worm Caenorhabditis elegans. When the experiments were performed by using samples fixed in formalin, artefacts were detected. While the size of the amplified fragment resulted unaffected, very striking differences were seen in the nucleotide sequences of the amplified fragments. Furthermore, in many cases, the PCR reaction failed completely. The results obtained might warn of potential problems, especially when the amount of DNA to be amplified is scarce. ------------------- Key: 2097 Medline: 95131956 Authors: Mori H;Palmer RE;Sternberg PW Title: The identification of a Caenorhabditis elegans homolog of p34(cdc2) kinase. Citation: Molecular & General Genetics 245: 781-786 1994 Type: ARTICLE Genes: ncc-1 Abstract: We have identified a Caenorhabditis elegans homolog of p34(cdc2) kinase. The C. elegans homolog, ncc-1, is similar to 60% identical to p34(cdc2) Of Home sapiens. When expressed from a constitutive yeast promoter, ncc-1 is capable of complementing a conditional lethal mutation in the CDC28 gene of Saccharomyces cerevisiae, indicating that this C. elegans homolog can properly regulate the cell cycle. ------------------- Key: 2098 Medline: 95219445 Authors: Lambie EJ Title: Nematode development: Variations on a vulval theme. Citation: Current Biology 4: 1128-1130 1994 Type: REVIEW Genes: lin-39 Abstract: Comparisons between the cell lineages of different nematode species reveal the flexibility of developmental programs over evolutionary time. ------------------- Key: 2099 Medline: Authors: Jansson HB Title: Adhesion of conidia of Drechmeria coniospora to Caenorhabditis elegans wild type and mutants. Citation: Journal of Nematology 26: 430-435 1994 Type: ARTICLE Genes: che-12 che-14 mec-1 vab-1 Abstract: Adhesion of conidia of the endoparasitic fungus Drechmeria coniospora to the cuticles of the wild type and four different head defective mutants of Caenorhabditis elegans, and subsequent infection, was studied. The conidia adhered around the sensory structures in the head region, vulva, and occasionally to other parts of the cuticle in both mutant and wild type hosts. Infection took place after adhesion to the head region by penetration through the cuticle, and, following adhesion around the vulva, through the natural orifice. Infection was not observed after adhesion to other parts of the cuticle. Adhesion was reduced after treatment of the nematodes with Pronase E. Adhesion returned towards normal again within 2 hours, indicating that the proteinaceous material emanating from the sensory structures was rapidly replaced. ------------------- Key: 2100 Medline: 95112823 Authors: Vos JC;Plasterk RHA Title: Tc1 transposase of Caenorhabditis elegans is an endonuclease with a bipartite DNA binding domain. Citation: EMBO Journal 13: 6125-6132 1994 Type: ARTICLE Genes: Abstract: The Tc1 transposon of Caeitorhabditis elegans is a member of the Tc1/mariner family of mobile elements. These elements have inverted terminal repeats that flank a single transposase gene. Here we show that Tc1 transposase, Tc1A, has a bipartite DNA binding domain related to the paired domain of mammalian and Drosophila genes. Both the DNA binding domain of Tc1A and the DNA binding site in the inverted repeat of Tc1 can be divided into two subdomains. Methylation interference studies demonstrate adjacent minor and major groove contacts at the inner part of the binding site by the N-terminal 68 amino acids of the DNA binding domain. In addition, Tc1A amino acids 69-142 are essential for major groove contacts at the outer part of the binding site. Recombinant Tc1A is found to be able to introduce a single strand nick at the 5' end of the transposon in vitro. Furthermore, Tc1A can mediate a phosphoryl transfer reaction. A mutation in a DDE motif abolishes both endonucleolytic and phosphoryl transfer activities, suggesting that Tc1A carries a catalytic core common to retroviral integrases and IS transposases. ------------------- Key: 2101 Medline: 95113166 Authors: Stern MJ;DeVore DL Title: Extending and connecting signaling pathways in C. elegans. Citation: Developmental Biology 166: 443-459 1994 Type: REVIEW Genes: egl-15 egl-17 glp-1 let-23 let-60 let-341 lin-1 lin-2 lin-3 lin-7 lin-10 lin-12 lin-15 lin-31 lin-45 mpk-1 sem-5 sur-1 unc-6 unc-34 unc-40 unc-71 unc-76 Abstract: The development of the nematode Caenorhabditis elegans is known to depend extensively on reproducible cell-cell interactions. The analysis of many of these signaling events has revealed that, in most cases, the mechanisms that mediate them have been conserved throughout metazoan evolution. Thus, the analysis of signaling pathways in C. elegans can aid in the understanding of signal transduction mechanisms in general. In this review we focus on signaling events that occur during the development of the hermaphrodite egg-laying system. Many of these signaling events occur at approximately the same time and in very close proximity to one another. Following a brief review of the individual signaling systems employed, we analyze the data that have started to address how the specificity among these pathways is maintained and how multiple pathways that affect individual developmental decisions are integrated. These issues are common to all signaling systems and should be instructive in presenting the complexities that are involved in obtaining a global ------------------- Key: 2102 Medline: 95113193 Authors: Gendreau SB;Moskowitz IPG;Terns RM;Rothman JH Title: The potential to differentiate epidermis is unequally distributed in the AB lineage during early embryonic development in C. elegans. Citation: Developmental Biology 166: 770-781 1994 Type: ARTICLE Genes: glp-1 unc-33 Abstract: In the early Caenorhabditis elegans embryo most of the ectoderm arises from the AB blastomere, one of the six founder cells. We report that nonequivalent blastomeres are generated at the third division round in the AB lineage. Each AB granddaughter divides to produce one cell that has the potential to make abundant epidermis and one that instead produces primarily nervous system. This unequal distribution of the potential to make epidermis occurs in an AB granddaughter that is isolated by laser-ablation of all other cells or during the development of an isolated AB blastomere in culture. The fidelity of this event is normally masked by a signal from the MS founder cell, which induces mesoderm in particular AB descendants. When MS induction is prevented by laser cell-ablation or by a mutation in the glp-1 gene, the epidermal fate map of the AB great granddaughters becomes left-right symmetrical. Cell lineage analyses demonstrate that, in fact, the AB lineage becomes entirely left-right symmetrical in the absence of MS induction. This accounts for the extra epidermal cells previously observed in a glp-1 mutant. Our results suggest that epidermal differentiation in the nematode may be controlled by a cell-autonomous mechanism that differentially allocates epidermal potential during AB development and that MS induction generates the left-right asymmetry in the fates of AB descendants in part by overriding this potential. ------------------- Key: 2103 Medline: 95116514 Authors: Kostrouch Z;Kostrouchova M;Rall JE Title: Steroid/thyroid hormone receptor genes in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 92: 156-159 1995 Type: ARTICLE Genes: Abstract: The large family of steroid/thyroid hormone receptor (STR) genes has been extensively studied in vertebrates and insects but little information is available on it in more primitive organisms. All members possess a DNA binding domain of zinc fingers of the C2, C2 type. We have used the polymerase chain reaction with degenerate oligonucleotide primers covering this region to clone three distinct members of this family from the nematode Caenorhabditis elegans. All three belong to the retinoic acid receptor (RAR), thyroid hormone receptor subfamily of genes. The cDNA of one of these clones shows such a high homology to DHR3, an early ecdysone response gene found in Drosophila, and MHR3, identified in Manduca sexta, that we have termed it CHR3. Furthermore, the C-terminal portion of the deduced protein sequence shows a box containing eight identical amino acids among CHR3, DHR3, and MHR3 suggesting an identical specific ligand for these proteins. CNR8 shows homology to NAk1, and CNR14 has homology to both the RAR-gamma 1 gene and to another ecdysone response gene, E78A. Neither of the latter two cDNAs is a clear homologue of any known gene and each is distinctive. All of these genes are expressed varyingly in both larval and adult stages of nematode development as shown by Northern blot analyses. These data demonstrate that the STR family of genes is represented in a nematode whose ancestor appeared well before the branching that gave rise to the Arthropoda ------------------- Key: 2104 Medline: 95121221 Authors: Hodgkin J;Zellan JD;Albertson DG Title: Identification of a candidate primary sex determination locus, fox-1, on the X chromosome of Caenorhabditis Citation: Development 120: 3681-3689 1994 Type: ARTICLE Genes: dpy-26 fox-1 him-8 sdc-2 tra-2 xol-1 eDp26 mnDp57 mnDp73 Abstract: Sex in Caenorhabditis elegans (XX hermaphrodite, XO male) is determined by the X:A ratio, which is the ratio of X chromosome number to autosomal set number. Recent genetic results with X chromosome duplications have suggested that there may be only a small number of major numerator sites on the X chromosome that contribute to this ratio. Mapping of duplication endpoints delimited a region of less than 300 kb, likely to contain one such element, Cosmid clones from this region were tested for numerator activity by constructing transgenic lines carrying extra copies of each tested cosmid, Most cosmid arrays have no effect on the viability of either XX or XO animals, One cosmid array was found to be viable in XX animals, but lethal and feminizing in XO animals, consistent with it containing a major numerator element. Further experiments defined a region of 12-30 kb with apparent numerator activity, which is designated fox-1, 'Feminizing locus On X'. A cDNA clone hybridizing across part of this region encodes a predicted RNA-binding protein. ------------------- Key: 2105 Medline: 95108137 Authors: Stadler M;Dagne E;Anke H Title: Nematicidal activities of two phytoalexins from Taverniera abyssinica. Citation: Planta Medica 60: 550-552 1994 Type: ARTICLE Genes: Abstract: The traditional analgesic and antipyretic Ethiopian drug ''Dingetegna'' is made of dried root material of Taverniera abyssinica A. Rich (Leguminosae). In a screening for nematicidal natural products, ''Dingetegna'' extracts showed strong nematicidal activities towards C. elegans. In the following, medicarpin and 4-hydroxymedicarpin were isolated as nematicidal constituents from the extracts. In a microwell plate assay for nematicidal activity, both compounds exhibited an LDS, of 25 mu g/ml towards C. elegans. Beside these nematicidal effects, weak cytotoxic and antimicrobial activities were observed. In addition, both compounds inhibited oxygen consumption of axenically grown C. elegans, L 1210 cells, and filamentous fungi. Respiration in sensitive bacteria was not affected. In L1210 cells, the incorporation of precursors into macromolecules was affected in the presence of glucose, indicating that inhibition of respiration is not the only target site of the compounds. ------------------- Key: 2106 Medline: 95285750 Authors: Newman AP;White JG;Sternberg PW Title: The Caenorhabditis elegans lin-12 gene mediates induction of ventral uterine specialization by the anchor cell. Citation: Development 121: 263-271 1995 Type: ARTICLE Genes: let-23 lin-3 lin-12 lin-45 mpk-1 sur-1 Abstract: The anchor cell (AC) of the Caenorhabditis elegans gonad has a critical role in the development of a functional egg-laying system, which is accomplished through cell-cell interactions. Lateral inhibitory lin-12-mediated signaling among two bipotential cells causes one to adopt the ventral uterine precursor (VU) cell fate while the other becomes the AC. The AC then induces formation of vulval tissue. We find that the AC also induces a particular ventral uterine intermediate precursor fate (pi) by a mechanism that is genetically and temporally distinct from vulval induction. This process requires lin-12, but unlike previously described lin-12-mediated decisions, signaling is unidirectional, is between dissimilar cells and does not involve lateral inhibition. The pi fates are necessary for egg laying and appear to produce a distinct specialized cell type. Thus, patterning of the ventral uterus by the AC is crucial to the development of a functional egg-laying system. ------------------- Key: 2107 Medline: 95112352 Authors: Rhind NE;Miller LM;Kopczynski JB;Meyer BJ Title: xol-1 acts as an early switch in the C. elegans male/hermaphrodite decision. Citation: Cell 80: 71-82 1995 Type: ARTICLE Genes: dpy-27 dpy-30 him-8 sdc-2 tra-2 xol-1 Abstract: xol-1 is the earliest-acting gene in the known hierarchy that controls C. elegans sex determination and dosage compensation. We show that the primary sex-determining signal (the X/A ratio) directs the choice of sexual fate by regulating xol-1 transcript levels: high xol-1 expression during gastrulation triggers male development, whereas low expression at that time permits hermaphrodite development. Inappropriately high xol-1 expression causes hermaphrodites to activate the male program of development and die from a disruption in dosage compensation. These results demonstrate that xol-1 functions as an early developmental switch to set the choice of sexual fate and suggest that assessment of the X/A ratio occurs only early in embryogenesis to determine sex. Moreover, sdc-2, a gene that must be repressed by xol-1 to ensure male development, may be a direct target of negative regulation by xol-1. ------------------- Key: 2108 Medline: 95208118 Authors: Zetka M;Rose A Title: The genetics of meiosis in Caenorhabditis elegans. Citation: Trends in Genetics 11: 27-31 1995 Type: REVIEW Genes: him-1 him-3 him-5 him-6 him-8 him-14 mei-1 mei-2 rad-4 rec-1 eT1 hIn1 hT2 Abstract: The many features that have made the hermaphroditic nematode Caenorhabditis elegans a good model system for studying development have also attracted investigators to the study of meiosis. Genetic analysis suggests that in C. elegans there are two types of chromosomal sites required for proper meiotic function. The first is needed early in meiosis for recombination and segregation. The second is involved in the mechanisms that establish the normal frequency and distribution of exchange. Genes whose products may interact with these sites have been identified by mutant analysis. Study of these mutations in the nematode is enhancing our general understanding of meiotic ------------------- Key: 2109 Medline: 95127235 Authors: Liu KS;Sternberg PW Title: Sensory regulation of male mating behavior in Caenorhabditis elegans. Citation: Neuron 14: 79-89 1995 Type: ARTICLE Genes: plg-1 Abstract: C. elegans male mating behavior comprises a series of steps: response to contact with the hermaphrodite, backing along her body, turning around her head or tail, location of the vulva, insertion of the two copulatory spicules into the vulva, and sperm transfer. By ablation of male-specific copulatory structures and their associated neurons, we have identified sensory structures and neurons that participate in each of these steps: the sensory rays mediate response to contact and turning; the hook, the postcloacal sensilla and the spicules mediate vulva location; the spicules also mediate insertion and regulate sperm transfer. Generally, successful completion of each step places the male in a position to receive a cue for the next step in the pathway. However, the high degree of sensory regulation allows the male to execute some steps ------------------- Key: 2110 Medline: 95137102 Authors: Talesa V;Culetto E;Schirru N;Bernardi H;Fedon Y;Toutant J-P;Arpagaus M Title: Characterization of a null mutation in ace-1, the gene encoding class A acetylcholinesterase in the nematode Caenorhabditis elegans. Citation: FEBS Letters 357: 265-268 1995 Type: ARTICLE Genes: ace-1 ace-2 ace-3 Abstract: Two genes (ace-1 and ace-2) encode two major classes (A and B) of acetylcholinesterase (AChE) in the nematode Caenorhabditis elegans. A null mutation in ace-1 (allele p1000) suppresses all acetylcholinesterase activity of class A. We have identified an opal mutation TGG (W99)->TGA (Stop) as the only alteration in the mutated gene. This leads to a truncated protein (98 instead of 620 amino acids) with no enzymatic activity. The mutation also reduces the level of ace-1 transcripts to only 10% of that in wild-type animals. This most likely results from a destabilization of mRNA containing the nonsense message. In contrast, compensation of class B by Class A AChE in the null mutant strain ace-2 takes place with unchanged ace-1 mRNA level and enzymatic activity similar to class A AChE. ------------------- Key: 2111 Medline: 95229046 Authors: Cheng NN;Kirby CM;Kemphues KJ Title: Control of cleavage spindle orientation in Caenorhabditis elegans: the role of the genes par-2 and par-3. Citation: Genetics 139: 549-559 1995 Type: ARTICLE Genes: par-2 par-3 sup-7 itDf1 Abstract: Polarized asymmetric divisions play important roles in the development of plants and animals. The first two embryonic cleavages of Caenorhabditis elegans provide an opportunity to study the mechanisms controlling polarized asymmetric divisions. The first cleavage is unequal, producing daughters with different sizes and fates. The daughter blastomeres divide with different orientations at the second cleavage; the anterior blastomere divides equally across the long axis of the egg, whereas the posterior blastomere divides unequally along the long axis. We report here the results of our analysis of the genes par-2 and par-3 with respect to their contribution to the polarity of these divisions. Strong loss-of-function mutations in both genes lead to an equal first cleavage and an altered second cleavage. The par-2 mutations lead to transverse spindle orientations in both blastomeres, whereas par-3 mutations lead to longitudinal spindle orientations in both blastomeres. The spindle orientation defects correlate with defects in centrosome movements during both the first and the second cell cycle. Temperature shift experiments with par-2(it5ts) indicate that the par-2(+) activity is not required after the two-cell stage. Analysis of double mutants shows that par-3 is epistatic to par-2. We propose a model wherein par-2(+) and par-3(+) act in concert during the first cell cycle to affect asymmetric modification of the cytoskeleton. This polar modification leads to different behaviors of centrosomes in the anterior and posterior and leads ultimately to blastomere-specific spindle ------------------- Key: 2112 Medline: 95229047 Authors: Ellis RE;Kimble J Title: The fog-3 gene and regulation of cell fate in the germ line of Caenorhabditis elegans. Citation: Genetics 139: 561-577 1995 Type: ARTICLE Genes: fem-3 fog-1 fog-3 gld-1 tra-2 xol-1 hDp18 hDp62 mnDf111 nDf23 nDf24 nDf25 nDf29 nDp4 qDf3 qDf4 qDf5 qDf6 qDf7 qDf8 qDf9 qDf10 qDf11 qDf12 qDf13 qDf14 qDf15 sDf4 sDp1 tDf3 Abstract: In the nematode Caenorhabditis elegans, germ cells normally adopt one of three fates: mitosis, spermatogenesis or oogenesis. We have identified and characterized the gene fog-3, which is required for germ cells to differentiate as sperm rather than as oocytes. Analysis of double mutants suggests that fog-3 is absolutely required for spermatogenesis and acts at the end of the regulatory hierarchy controlling sex determination of the germ line. By contrast, mutations in fog-3 do not alter the sexual identity of other tissues. We also have characterized the null phenotype of fog-1, another gene required for spermatogenesis; we demonstrate that it too controls the sexual identity of germ cells but not of other tissues. Finally, we have studied the interaction of these two fog genes with gld-1, a gene required for germ cells to undergo oogenesis rather than mitosis. On the basis of these results, we propose that germ-cell fate might be controlled by a set of inhibitory interactions among genes that specify one of three fates: mitosis, spermatogenesis or oogenesis. Such a regulatory network would link the adoption of one germ-cell fate to the suppression of the ------------------- Key: 2113 Medline: 95229048 Authors: Francis R;Barton MK;Kimble J;Schedl T Title: gld-1, a tumor suppressor gene required for oocyte development in Caenorhabditis elegans. Citation: Genetics 139: 579-606 1995 Type: ARTICLE Genes: fem-1 fem-3 fog-1 fog-2 gld-1 nDf24 nDf25 nDp4 ozDf5 Abstract: We have characterized 31 mutations in the gld-1 (defective in germline development) gene of Caenorhabditis elegans. In gld-1 (null) hermaphrodites, oogenesis is abolished and a germline tumor forms where oocyte development would normally occur. By contrast, gld-1 (null) males are unaffected. The hermaphrodite germline tumor appears to derive from germ cells that enter the meiotic pathway normally but then exit pachytene and return to the mitotic cycle. Certain gld-1 partial loss-of-function mutations also abolish oogenesis, but germ cells arrest in pachytene rather than returning to mitosis. Our results indicate that gld-1 is a tumor suppressor gene required for oocyte development. The tumorous phenotype suggests that gld-1(+) may function to negatively regulate proliferation during meiotic prophase and/or act to direct progression through meiotic prophase. We also show that gld-1(+) has an additional nonessential role in germline sex determination: promotion of hermaphrodite spermatogenesis. This function of gld-1 is inferred from a haplo-insufficient phenotype and from the properties of gain-of-function gld-1 mutations that cause alterations in the sexual identity of germ ------------------- Key: 2114 Medline: 95229049 Authors: Francis R;Maine E;Schedl T Title: Analysis of the multiple roles of gld-1 in germline development: interactions with the sex-determination cascade and the glp-1 signaling pathway. Citation: Genetics 139: 607-630 1995 Type: ARTICLE Genes: fem-1 fem-2 fem-3 fog-1 fog-2 fog-3 gld-1 glp-1 her-1 mog-1 tra-1 tra-2 tra-3 Abstract: The Caenorhabditis elegans gene gld-1 is essential for oocyte development; in gld-1 (null) hermaphrodites, a tumor forms where oogenesis would normally occur. We use genetic epistasis analysis to demonstrate that tumor formation is dependent on the sexual fate of the germline. When the germline sex determination pathway is set in the female mode (terminal fem/fog genes inactive), gld-1 (null) germ cells exit meiotic prophase and proliferate to form a tumor, but when the pathway is set in the male mode, they develop into sperm. We conclude that the gld-1 (null) phenotype is cell-type specific and that gld-1(+) acts at the end of the cascade to direct oogenesis. We also use cell ablation and epistasis analysis to examine the dependence of tumor formation on the glp-1 signalling pathway. Although glp-1 activity promotes tumor growth, it is not essential for tumor formation by gld-1 (null) germ cells. These data also reveal that gld-1(+) plays a nonessential (and sex nonspecific) role in regulating germ cell proliferation before their entry into meiosis. Thus gld-1(+) may negatively regulate proliferation at two distinct points in germ cell development: before entry into meiotic prophase in both sexes (nonessential premeiotic gld-1 function) and during meiotic prophase when the sex determination pathway is set in the female mode (essential meiotic gld-1 function). ------------------- Key: 2115 Medline: 95140614 Authors: Colloms SD;van Luenen HGAM;Plasterk RHA Title: DNA binding activities of the Caenorhabditis elegans Tc3 transposase. Citation: Nucleic Acids Research 22: 5548-5554 1994 Type: ARTICLE Genes: Abstract: Tc3 is a member of the Tc1/mariner family of transposable elements. All these elements have terminal inverted repeats, encode related transposases and insert exclusively into TA dinucleotides. We have studied the DNA binding properties of Tc3 transposase and found that an N-terminal domain of 65 amino acids binds specifically to two regions within the 462 bp Tc3 inverted repeat; one region is located at the end of the inverted repeat, the other is located about 180 bp from the end. Methylation interference experiments indicate that this N-terminal DNA binding domain of the Tc3 transposase interacts with nucleotides on one face of the DNA helix over adjacent ------------------- Key: 2116 Medline: 95258075 Authors: Kuramochi T;Hirawake H;Kojima S;Takamiya S;Furushima R;Aoki T;Komuniecki R;Kita K Title: Sequence comparison between the flavoprotein subunit of the fumarate reductase (complex II) of the anaerobic parasitic nematode, Ascaris suum and the succinate dehydrogenase of the Citation: Molecular & Biochemical Parasitology 68: 177-187 1994 Type: ARTICLE Genes: Abstract: Complex II in adult mitochondria of the parasitic nematode, Ascaris suum, exhibits high fumarate reductase activity and plays a key role in the anaerobic electron-transport observed in these organelles. In the present study, cDNAs for the flavoprotein (Fp) subunits of complex II have been isolated, cloned and sequenced from both A. suum and the aerobic, free-living nematode, Caenorhabditis elegans. Additional sequence at the 3' end of the mRNAs was determined by the Rapid Amplification of cDNA Ends (RACE). Nucleotide sequence analysis of the A. suum cDNAs revealed a 22-nucleotide trans-spliced leader sequence characteristic of many nematode mRNAs, an open reading frame of 1935 nucleotides and a 3' untranslated region of 616 nucleotides including a poly(A) tail from a polyadenylation signal (AATAAA). The open reading frame encoded a 645 amino acid sequence, including a 30 amino acid mitochondrial presequence. The amino acid sequences for the Fp subunits from both organisms were very similar, even though the ascarid enzyme functions physiologically as a fumarate reductase and the C. elegans enzyme a succinate dehydrogenase. The ascarid sequence was much less similar to the Escherichia coli fumarate reductase. The sensitivity of other Fp subunits to sulfhydryl reagents appears to reside in a cysteine immediately preceding a conserved arginine in the putative active site. In both nematode sequences, this cysteine is replaced by serine even though the succinate dehydrogenase activity of both enzymes is still sensitive to sulfhydryl inhibition. A cysteine six residues upstream of the serine may be involved in the sulfhydryl sensitivity of the nematode enzymes. Surprisingly, in contrast to succinate dehydrogenase activity, the fumarate reductase activity of the ascarid enzyme was not sensitive to sulfhydryl inhibition, suggesting that the mechanism of the two reactions involves separate catalytic processes. ------------------- Key: 2117 Medline: 95132647 Authors: Britten RJ Title: Active gypsy/Ty3 retrotransposons or retroviruses in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 92: 599-601 1995 Type: ARTICLE Genes: Abstract: A gypsy/Ty3-class retrotransposon (Cer1) is intergrated in the DNA of Caenorhabditis elegans chromosome III. It is 8865 nt in length and has 492-nt long terminal repeats that are identical in DNA sequence. There is an exceptionally long (6819 nt) open reading frame uninterrupted by frameshift mutations in the period since the insertion, which must therefore have been rather recent. Alignment with other gypsy-class elements and with retroviruses indicates that an env gene occupies the 3' 1.2 kb of the open reading frame. A search through GenBank has uncovered two additional gypsy-class elements from C. elegans that are very closely related in DNA sequence to this insert and are transcribed. Since gypsy of Drosophila has been shown to be an infectious element, it is possible that retrovirus-like gypsy elements are active in C. elegans. ------------------- Key: 2118 Medline: 95217177 Authors: Wilkins AS Title: Moving up the hierarchy: A hypothesis on the evolution of a genetic sex determination pathway. Citation: BioEssays 17: 71-77 1995 Type: REVIEW Genes: fem-1 fem-2 fem-3 her-1 sdc-1 sdc-2 sdc-3 tra-1 tra-2 tra-3 xol-1 Abstract: A hypothesis on the evolutionary origin of the genetic pathway of sex determination in the nematode Caenorhabditis elegans is presented here. It is suggested that the pathway arose in steps, driven by frequency-dependent selection for the minority sex at each step, and involving the sequential acquisition of dominant negative, neomorphic genetic switches, each one reversing the action of the previous one. A central implication is that the genetic pathway evolved in reverse order from the final step in the heirarchy up to the first. The possible applicability of the model to the other well-characterized sex determination pathway, that of Drosophila melanogaster, and to sex determination in mammals, is discussed, along with some potential implications for pathway evolution in general. Finally, the specific molecular and population genetic questions that the model raises are described and some ------------------- Key: 2119 Medline: 95134359 Authors: Ting SJY Title: A binary model of repetitive DNA sequence in Caenorhabditis elegans. Citation: DNA and Cell Biology 14: 83-85 1995 Type: ARTICLE Genes: Abstract: A great amount of genomic DNA in multicellular eukaryotic organisms is regarded as junk because it has no real function in protein coding. However, there is growing evidence that noncoding DNA can play a vital role in the regulation of gene expression during development. This indicates that the so-called junk DNA may have essential functions that are yet to be found. A novel binary model of noncoding repetitive DNA sequence is proposed to illustrate its possible structure and implications in genome organization and development. ------------------- Key: 2120 Medline: Authors: Donkin SG;Dusenbery DB Title: Using the Caenorhabditis elegans soil toxicity test to identify factors affecting toxicity of four metal ions in intact soil. Citation: Water, Air and Soil Pollution 78: 359-373 1994 Type: ARTICLE Genes: Abstract: A previously developed soil toxicity test for rapidly determining the toxicity of chemicals to the soil-dwelling nematode Caenorhabditis elegans was used to measure the toxicity of four metals (Zn 2+, Cd 2+, Cu 2+, and Pb 2+) added to four soils common to the southeastern United States. Nematode survival after a 24-hour exposure in the presence of a bacterial food source was assessed. All soils reduced the toxicity of most metal ions compared to solutions without soil. Pb was the most strongly affected, while Cd toxicity was not much influenced by the soils. Correlations between the LC50s and various soil or metal characteristics were determined. No significant correlation was found between LC50s and many soil characteristics commonly cited as having large effects on soil bioavailability of metals. Although sample size was limited, the indication was that bioavailability of metals to nematodes is determined by a complex array of many interacting soil, as well as metal, properties. Comparision of the relative mobilities of these ions in other soils with the relative toxicity measured here suggests that mobility may be a good predictor of toxicity. The C. elegans soil toxicity test is shown to be as sensitive and more rapid than the commonly used earthworm ------------------- Key: 2121 Medline: 95154721 Authors: de Bono M;Zarkower D;Hodgkin J Title: Dominant feminizing mutations implicate protein-protein interactions as the main mode of regulation of the nematode sex-determining gene tra-1. Citation: Genes & Development 9: 155-167 1995 Type: ARTICLE Genes: fem-1 fem-2 fem-3 her-1 tra-1 tra-2 tra-3 Abstract: The tra-1 gene is the terminal global selector of somatic sex in Caenorhabditis elegans: High tra-1 activity elicits female somatic development while low tra-1 activity elicits male development. Previous genetic studies defined a cascade of negatively interacting genes that regulates tra-1 activity in response to the primary sex-determining signal. Here, we investigate the last step in this regulatory cascade, by studying rare gain-of-function (gf) mutations of tra-1 that direct female somatic development irrespective of the upstream sex-determining signal. These mutations appear to abolish negative regulation of tra-1 in male tissues. We identify the lesions associated with 29 of these mutations and find that all affect a short stretch of amino acid residues present in both protein products of the tra-1 gene. Twenty-six alleles are associated with single nonconservative amino acid substitutions. Two alleles affect tra-1 RNA splicing and generate messages that omit part or all of the exon encoding this short stretch. These results suggest that sexual regulation of tra-1 is achieved post-translationally, by an inhibitory protein-protein interaction. The amino acid stretch altered by the tra-1(gf) mutations may define a site of interaction for negative regulators of tra-1. The stretch includes a potential phosphorylation site for glycogen synthase kinase 3 and may be conserved in the human gene GLI3, a homolog of tra-1 identified previously. ------------------- Key: 2122 Medline: 95262956 Authors: Darr D;Fridovich I Title: Adaptation to oxidative stress in young, but not mature or old, Caenorhabditis elegans. Citation: Free Radical Biology and Medicine 18: 195-201 1995 Type: ARTICLE Genes: Abstract: The effect of aging on the ability of Caenorhabditis elegans to adapt to oxidative stress was examined. Oxidative stress was applied with the quinone plumbagin or with hyperoxia, both of which are expected to increase intraorganismal production of O-2(.-) and of H2O2. Young nematodes adapted by increasing their content of superoxide dismutase (SOD) and they survived, whereas older nematodes did not induce superoxide dismutase and suffered loss of viability. It thus appears that, in C. elegans loss of adaptability to oxidative stress, monitored in terms of induction of SOD, is a hallmark of senescence. ------------------- Key: 2123 Medline: 96083332 Authors: Sommer RJ;Carta LK;Sternberg PW Title: The evolution of cell lineage in nematodes. Citation: Development Supplement : 85-95 1994 Type: ARTICLE Genes: ces-1 ces-2 lin-4 lin-14 lin-15 lin-18 lin-28 lin-29 lin-39 lin-44 mab-5 mex-1 skn-1 unc-6 unc-86 Abstract: The invariant development of free-living nematodes combined with the extensive knowledge of Caenorhabditis elegans developmental biology provides an experimental system for an analysis of the evolution of developmental mechanisms. We have collected a number of new nematode species from soil samples. Most are easily cultured and their development can be analyzed at the level of individual cells using techniques standard to Caenorhabditis. So far, we have focused on differences in the development of the vulva among species of the families Rhabditidae and Panagrolaimidae. Preceding vulval development, twelve Pn cells migrate into the ventral cord and divide to produce posterior daughters [Pn.p cells] whose fates vary in a position specific manner [from P1.p anterior to P12.p posterior]. In C. elegans hermaphrodites, P(3-8).p are tripotent and from an equivalence group. These cells can express either of two vulval fates (1 or 2) in response to a signal from the anchor cell of the somatic gonad, or a non-vulval fate (3), resulting in a 3-3-2-1-2-3 pattern of cell fates. Evolutionary differences in vulval development include the number of cells in the vulval equivalence group, the number of 1 cells, the number of progeny generated by each vulval precursor cell, and the position of VPCs before morphogenesis. Examples of three Rhabditidae genera have a posterior vulva in the position of P9-P11 ectoblasts. In Cruznema tripartitum, P(5-7).p form the vulva as in Caenorhabditis, but they migrate posteriorly before dividing. Induction occurs after the gonad grows posteriorly to the position of P(5-7).p cells. In two other species, Mesorhabditis sp. PS 1179 and Teratorhabditis palmarum, we have found changes in induction and competence with respect to their presumably more C. elegans-like ancestor. In Mesorhabditis, P(5-7).p form the vulva after migrating to a posterior position. However, the gonad is not required to specify the pattern of cell fates 3-2-1-2-3. Moreover, the Pn.p cells are not equivalent in their potentials to form the vulva. A regulatory constraint in this family thus forces the same set of precursors to generate the vulva, rather than more appropriately positioned Pn.p cells. ------------------- Key: 2124 Medline: 95154585 Authors: Sommer RJ;Sternberg PW Title: Evolution of cell lineage and pattern formation in the vulval equivalence group of Rhabditid nematodes. Citation: Developmental Biology 167: 61-74 1995 Type: ARTICLE Genes: Abstract: During the formation of the vulva in many nematode hermaphrodites or females, pattern formation, induction, and cell specification can readily be studied at a single-cell level. Nematodes thus allow an evolutionary analysis of developmental processes. We have analyzed cell lineages and pattern formation in the vulva equivalence group of six rhabditid nematodes of the genera Oscheius, Rhabditella, Rhabditoides, Pelodera, and Protorhabditis. The comparison of these species with four previously analyzed species of this family reveals evolutionary modification at several levels. The number of vulva precursor cells (VPCs) differ among species. Of the three particular cell lineages (1 degrees, 2 degrees, and 3 degrees) generated by the vulva precursor cells in Caenorhabditis, two (2 degrees and 3 degrees) are altered, whereas the third lineage (1 degrees) is conserved among the analyzed species. While most vulval lineages are invariant, we observe variability of the 3 degrees lineage in Pelodera with respect to the number of precursor cells adopting this fate and the number of progeny formed. In two species, the 3 degrees lineage generates an asymmetrical set of cells, oriented by the gonad. In Protorhabditis we frequently find animals with an additional or altered set ------------------- Key: 2125 Medline: 95172384 Authors: Tuck S;Greenwald I Title: lin-25, a gene required for vulval induction in Caenorhabditis elegans. Citation: Genes & Development 9: 341-357 1995 Type: ARTICLE Genes: let-60 lin-1 lin-12 lin-15 lin-25 lin-31 lin-45 mpk-1 sup-7 sur-1 arDf1 ctDf1 itDf2 Abstract: During vulval development in the Caenorhabditis elegans hermaphrodite, the fates of six vulval precursor cells (VPCs) are influenced by distinct cell signaling events. In one event, a somatic gonadal cell, the anchor cell, induces the three nearest VPCs to adopt vulval cell fates. In another event, lateral signaling between adjacent VPCs specifies one of two different vulval fates, 1 degrees and 2 degrees. Induction of vulval fates by the anchor cell is mediated by a signal transduction pathway involving let-60 Ras, lin-45 Raf, and mpk-1/sur-1 MAP kinase, whereas lateral signaling is mediated by lin-12. We have shown that the mutant phenotype of lin-25, a gene required for VPC fate specification, results from a defect in vulval induction. Genetic epistasis experiments indicate that lin-25 is required in the inductive signaling pathway downstream of let-60 Ras and the Raf/MAP kinase cascade. A decrease in induction also appears to decrease lateral signaling. We have cloned and sequenced the lin-25 gene and shown that it encodes a novel protein that may be a target of the mpk-1/sur-1 MAPK. ------------------- Key: 2126 Medline: 95268324 Authors: Kayne PS;Sternberg PW Title: Ras pathways in Caenorhabditis elegans. Citation: Current Opinion in Genetics & Development 5: 38-43 1995 Type: REVIEW Genes: let-23 let-60 lin-3 lin-15 lin-45 mpk-1 sem-5 sur-1 unc-101 Abstract: The let-60 ras gene of Caenorhabditis elegans is required for multiple aspects of development. The vulval differentiation pathway is the most intensively studied of these, but the ras pathway has now been shown to also be essential for male spicule development. Using vulval differentiation, molecular genetic techniques are now being used to study structure/function relationships of particular signaling components and to identify new positively and negatively acting proteins of Ras-mediated signaling pathways. Mutations affecting LET-23, a receptor tyrosine kinase homolog, which cause tissue-specific defects have been localized to the carboxyl terminus. SH2 domain specificity has been analyzed through Src/SEM-5 chimeric proteins in transgenic nematodes. A mitogen-activated protein kinase that acts downstream of LET-60 Ras in vulval differentiation has been identified. Negative regulatory genes have been cloned and found to encode novel proteins and a clathrin adaptor protein. ------------------- Key: 2127 Medline: 95286054 Authors: Wong A;Boutis P;Hekimi S Title: Mutations in the clk-1 gene of Caenorhabditis elegans affect developmental and behavioral timing. Citation: Genetics 139: 1247-1259 1995 Type: ARTICLE Genes: clk-1 gro-1 Abstract: We have identified three allelic, maternal-effect mutations that affect developmental and behavioral timing in Caenorhabditis elegans. They result in a mean lengthening of embryonic and postembryonic development, the cell cycle period and life span, as well as the periods of defecation, swimming and pumping cycles. These mutants also display a number of additional phenotypes related to timing. For example, the variability in the length of embryonic development is several times larger in the mutants than in the wild type, resulting in the occasional production of mutant embryos developing more rapidly than the most rapidly developing wild-type embryos. In addition, the duration of embryonic development of the mutants, but not of the wild type, depends on the temperature at which their parents were raised. Finally, individual variations in the severity of distinct mutant phenotypes are correlated in a counterintuitive way. For example, the animals with the shortest embryonic development have the longest defecation cycle and those with the longest embryonic development have the shortest defecation cycle. Most of the features affected by these mutations are believed to be controlled by biological clocks, and we therefore call the gene defined by these mutations clk-1, for "abnormal function of biological clocks". ------------------- Key: 2128 Medline: 95286055 Authors: Shreffler W;Margardino T;Shekdar K;Wolinsky E Title: The unc-8 and sup-40 genes regulate ion channel function in Caenorhabditis elegans motorneurons. Citation: Genetics 139: 1261-1272 1995 Type: ARTICLE Genes: deg-1 mec-4 mec-6 mec-10 mut-2 ndg-4 sup-40 sup-41 unc-8 Abstract: Two Caenorhabditis elegans genes, unc-8 and sup-40, have been newly identified, by genetic criteria, as regulating ion channel function in motorneurons. Two dominant unc-8 alleles cause motorneuron swelling similar to that of other neuronal types in dominant mutants of the deg-1 gene family, which is homologous to a mammalian gene family encoding amiloride-sensitive sodium channel subunits. As for previously identified deg-1 family members, unc-8 dominant mutations are recessively suppressed by mutations in the mec-6 gene, which probably encodes a second type of channel component. An unusual dominant mutation, sup-41(lb125), also co-suppresses unc-8 and deg-1, suggesting the existence of yet another common component of ion channels containing unc-8 or deg-1 subunits. Dominant, transacting, intragenic suppressor mutations have been isolated for both unc-8 and deg-1, consistent with the idea that, like their mammalian homologues, the two gene products function as multimers. The sup-40(lb130) mutation dominantly suppresses unc-8 motorneuron swelling and produces a novel swelling phenotype in hypodermal nuclei. sup-40 may encode an ion channel component or regulator that can correct the osmotic defect caused by abnormal ------------------- Key: 2129 Medline: 95058914 Authors: Radice AD;Bugaj B;Fitch DHA;Emmons SW Title: Widespread occurrence of the Tc1 transposon family: Tc1-like transposons from teleost fish. Citation: Molecular & General Genetics 244: 606-612 1994 Type: ARTICLE Genes: Abstract: We characterized five transposable elements from fish: one from zebrafish (Brachydanio rerio), one from rainbow trout (Salmo gairdneri), and three from Atlantic salmon (Salmo salar). All are closely similar in structure to the Tc1 transposon of the nematode Caenorhabditis elegans. A comparison of 17 Tc1-like transposons from species representing three phyla (nematodes, arthropods, and chordates) showed that these elements make up a highly conserved transposon family. Most are close to 1.7 kb in length, have inverted terminal repeats, have conserved terminal nucleotides, and each contains a single gene encoding similar polypeptides. The phylogenetic relationships of the transposons were reconstructed from the amino acid sequences of the conceptual proteins and from DNA sequences. The elements are highly diverged and have evidently inhabited the genomes of these diverse species for a long time. To account for the data, it is not necessary to invoke recent horizontal transmission. ------------------- Key: 2130 Medline: 95389524 Authors: Hodgkin J Title: Caenorhabditis elegans. Citation: Trends in Genetics: Genetic Nomenclature Guide : 24-25 1995 Type: REVIEW Genes: Abstract: This summary is based on the original proposals for C. elegans nomenclature, plus additional recommendations that have been distributed in the Worm Breeder's Gazette. ------------------- Key: 2131 Medline: 95136528 Authors: Hodgkin J Title: Epigenetics and the maintenance of gene activity states in Caenorhabditis elegans. Citation: Developmental Genetics 15: 471-477 1994 Type: REVIEW Genes: dpy-21 dpy-26 dpy-27 dpy-28 fem-1 fem-2 fem-3 her-1 hlh-1 mec-3 mec-17 sdc-1 sdc-2 sdc-3 tra-1 tra-2 tra-3 xol-1 Abstract: The nematode Caenorhabditis elegans has been the subject of many detailed investigations in developmental biology. Molecular analyses have failed to detect covalent alterations to DNA, such as methylation or rearrangement, during development of C. elegans. Genetic experiments indicate that imprinting of gamete genomes does not occur to any significant extent. The maintenance of gene activity states in this organism may depend predominantly on regulatory gene circuitry. Some possible examples of maintenance circuits are discussed. ------------------- Key: 2132 Medline: 95293375 Authors: Agulnik SI;Bollag RJ;Silver LM Title: Conservation of the T-box gene family from Mus musculus to Caenorhabditis elegans. Citation: Genomics 25: 214-219 1995 Type: ARTICLE Genes: tbx-2 tbx-7 tbx-8 tbx-9 Abstract: Recently, a novel family of genes with a region of homology to the mouse T locus, which is known to play a crucial, and conserved, role in vertebrate development, has been discovered. The region of homology has been named the T-box. The T-box domain of the prototypical T locus product is associated with sequence-specific DNA binding activity. In this report, we have characterized four members of the T-box gene family from the nematode Caenorhabditis elegans. All lie in close proximity to each other in the middle of chromosome III. Homology analysis among all completely sequenced T-box products indicates a larger size for the conserved T-box domain (166 to 203 residues) than previously reported. Phylogenetic analysis suggests that one C. elegans T-box gene may be a direct ortholog of the mouse Tbx2 and Drosophila omb genes. The accumulated data demonstrate the ancient nature of the T-box gene family and suggest the existence of at least three separate T-box-containing genes in a common early metazoan ancestor to nematodes and vertebrates. ------------------- Key: 2133 Medline: 95214542 Authors: Fitch DHA;Bugaj-Gaweda B;Emmons SW Title: 18S Ribosomal RNA gene phylogeny for some Rhabditidae related to Caenorhabditis. Citation: Molecular Biology and Evolution 12: 346-358 1995 Type: ARTICLE Genes: mih-1 Abstract: We have investigated the molecular evolution of the nucleotide sequences of 18S ribosomal RNA genes (18S rDNA) from a set of nematodes in the family Rhabditidae (Nematoda: Secernentea). Our aim was to evaluate the usefulness of this gene for molecular systematics of this family, as well as to establish phylogenetic relationships within a group that has potential for comparative studies of the relationship between development and evolution. We determined the 18S rDNA sequences of nine species of nematodes representing six genera within this family (Caenorhabditis briggsae, C. vulgaris, C. remanei, Rhabditis blumi, Rhabditis sp. br, Rhabditella axei, Pellioditis typica, Teratorhabditis palmarum, and Pelodera strongyloides dermatitica). Using hypothetical models for secondary structure as well as nucleotide similarity, these sequences were aligned with the 18S rDNA sequence published by Ellis et al. for C. elegans and with the partial sequences published by Nadler for eight ascaridoid species. We find that 18S rDNA is likely to be a useful tool to resolve relationships at the intrafamilial level. However, 18S rDNA sequences cannot be used to resolve relationships between taxa as closely related as the Caenorhabditis species. Parsimony, minimum-evolution, and maximum-likelihood methods strongly reject Andrassy's proposed phylogenetic classification based on adult morphological characters but support that of Sudhaus as one alternative of a few possible phylogenies. Distances between genera in this family are about eight times as great as distances between tetrapod classes, suggesting rapid rates of substitution, ancient devergence, or both. ------------------- Key: 2134 Medline: 95173650 Authors: Walthall WW;Plunkett JA Title: Genetic transformation of the synaptic pattern of a motoneuron class in Caenorhabditis elegans. Citation: Journal of Neuroscience 15: 1035-1043 1995 Type: ARTICLE Genes: unc-30 unc-55 Abstract: Caenorhabditis elegans possesses two classes of inhibitory locomotory neurons, the DD and VD motoneurons (mns), and they form complementary components of a cross-inhibitory neuronal network innervating dorsal and ventral body muscles. The DD and VD mns (collectively called the D mns) share a number of morphological and neurochemical features, and mutations in a number of different genes disrupt both cell types in identical ways; however, the DD and VD mns have different lineal origins and different synaptic patterns. Given the number of phenotypic features shared by the D mns, it was of interest to determine what is responsible for the synaptic patterns that distinguish them. An analysis of the locomotory defect along with a genetic epistasis test suggested that unc-55 mutations alter the function of the VD but not the DD mns. Correlated with the defective locomotory behavior of unc-55 mutants was an alteration in the distribution of varicosities, structures associated with presynaptic elements, on the VD mns. The pattern of varicosities of the unc-55 VD mns resembled that of the wild-type DD mns. Moreover, the selective removal of the DD mns revealed that unc-55 VD mns had adopted a functional role appropriate for the DD mns. Thus, unc-55 appears to be involved in producing the synaptic patterns that distinguish the two D mn classes from one another; when the gene is mutated the VD and DD mns become structurally similar and functionally ------------------- Key: 2135 Medline: 95203727 Authors: De Rosi L;Ristoratore F;Sebastiano M;Bazzicalupo P Title: Amphid defective mutant of Caenorhabditis elegans. Citation: Genetica 94: 195-202 1994 Type: ARTICLE Genes: dyf-1 Abstract: Studies are reported on a chemoreception mutant which arose in a mutator strain. The mutant sensory neurons do not stain with fluoresceine isothiocyanate (Dyf phenotype), hence the name, dyf-1, given to the gene it identifies. The gene maps on LGI, 0.4 map units from dpy-5 on the unc-11 side. The response of mutant worms to various repellents has been studied and shown to be partially altered. Other chemoreception based behaviors are less affected. The cilia of the sensory neurons of the amphid are shorter than normal and the primary defect may be in the capacity of the sheath cells to secrete the matrix material that fills the space between cilia in the amphid channel. Progress toward the molecular cloning of the gene is also reported. Relevant results from other laboratories are briefly ------------------- Key: 2136 Medline: 95278511 Authors: Aspbury RA;Fisher MJ;Rees HH Title: Lipid modification of signal-transducing polypeptides in the free-living nematode Caenorhabditis elegans. Citation: Biochemical Society Transactions 23: 3S- 1995 Type: ARTICLE Genes: let-60 Abstract: Studies are reported on a chemoreception mutant which arose in a mutator strain. The mutant sensory neurons do not stain with fluoresceine isothiocyanate (Dyf phenotype), hence the name, dyf-1, given to the gene it identifies. The gene maps on LGI, 0.4 map units from dpy-5 on the unc-11 side. The response of mutant worms to various repellents has been studied and shown to be partially altered. Other chemoreception based behaviors are less affected. The cilia of the sensory neurons of the amphid are shorter than normal and the primary defect may be in the capacity of the sheath cells to secrete the matrix material that fills the space between cilia in the amphid channel. Progress toward the molecular cloning of the gene is also reported. Relevant results from other laboratories are briefly ------------------- Key: 2137 Medline: 95182458 Authors: Kwa MSG;Veenstra JG;Van Dijk W;Roos MH Title: Beta-tubulin genes from the parasitic nematode Haemonchus contortus modulate drug-resistance in Caenorhabditis elegans. Citation: Journal of Molecular Biology 246: 500-510 1995 Type: ARTICLE Genes: ben-1 mec-7 tub-1 Abstract: Resistance to antimitotic chemotherapeutics in pathogenic nematodes, fungi and mammalian cells is closely associated with structural changes in cytoskeletal beta-tubulin. We investigated the possibility of using the well-characterised free-living nematode Caenorhabditis elegans as a model for studying the mechanism of resistance against benzimidazole (BZ) drugs in the parasitic nematode Haemonchus contortus. Functional analysis of a conserved beta-tubulin isotype (tub-1) mutation near GTP-binding domain II, which is linked to BZ resistance, was carried out in C. elegans by heterologous expression of: (1) parasite BZ-sensitive alleles; (2) BZ-resistant alleles; and (3) in vitro mutagenised beta-tubulin gene constructs. The injected heterologous gene constructs were not only stably maintained, but also expressed as shown by reverse transcriptase-polymerase chain reaction analysis. The degree of BZ drug susceptibility of the transformants was assayed and quantified by incubation with both benomyl and thiabendazol. All H. contortus tub-1 constructs, which encoded Phe at position 200, conferred susceptibility to thiabendazole in BZ-resistant C. elegans ben-1 mutants. In contrast, constructs carrying Tyr200 did not alter the BZ drug phenotype. From these experiments we conclude that: (1) C. elegans can be used as an expression host, since injected parasite genes were biologically active; and (2) the single Phe to Tyr mutation at position 200 in beta-tubulin isotype 1 is the cause of BZ resistance in H. ------------------- Key: 2138 Medline: 95290985 Authors: Duggan A;Chalfie M Title: Control of neuronal development in Caenorhabditis elegans. Citation: Current Opinion in Neurology 5: 6-9 1995 Type: REVIEW Genes: ceh-13 egl-5 egl-46 let-23 lin-3 lin-12 lin-32 lin-39 mab-5 mec-3 mec-4 mec-7 unc-4 unc-86 Abstract: Recent research into the development of the nervous system of the nematode Caenorhabditis elegans indicates the importance of multiple cell interactions and combinatorial gene expression. As many of the genes needed for C. elegans neuronal development have counterparts with similar activities in Drosophila melanogaster, the mechanisms of cell specification may be broadly conserved. ------------------- Key: 2139 Medline: 95267055 Authors: Krause M Title: MyoD and myogenesis in C. elegans. Citation: BioEssays 17: 219-228 1995 Type: REVIEW Genes: ceh-22 hlh-1 hlh-2 mex-1 skn-1 Abstract: One of the goals in developmental biology is the identification of key regulatory genes that govern the transition of embryonic cells from a pluripotent potential to a specific, committed cell fate. During vertebrate skeletal myogenesis, this transition is regulated by the MyoD family of genes. C. elegans has muscle analogous to vertebrate skeletal muscle and has a gene (hlh-1) related to the MyoD family. The molecular and genetic characterization of hlh-1 shows that it is very similar to the vertebrate MyoD family in many respects, including its expression pattern and DNA binding activity. The hlh-1 product is required for proper myogenesis, but it is not required for myogenic commitment during embryogenesis in the nematode. The role of this MyoD-related gene in nematode myogenesis is discussed and compared to those of the vertebrate MyoD family. ------------------- Key: 2140 Medline: 95192706 Authors: Marx J Title: Getting a grip on G protein function in C. elegans. Citation: Science 267: 1596-1597 1995 Type: REVIEW Genes: goa-1 Abstract: When it comes to G proteins, cell biologists have amassed a great wealth of material. They have identified nearly 30 of these proteins, which serve as key relays in the pathways that transmit signals from hormones, neurotransmitters, and other cellular regulators from the cell membrane to the interior. And studies with cultured cells have enabled researchers to learn a great deal about the biochemistry of G proteins... ------------------- Key: 2141 Medline: 95192715 Authors: Segalat L;Elkes DA;Kaplan JM Title: Modulation of serotonin-controlled behaviors by G(o) in Caenorhabditis elegans. Citation: Science 267: 1648-1651 1995 Type: ARTICLE Genes: goa-1 sDf6 Abstract: Seven transmembrane receptors and their associated heterotrimeric guanine nucleotide-binding proteins (G proteins) have been proposed to play a key role in modulating the activities of neurons and muscles. The physiological function of the Caenorhabditis elegans G protein G(o) has been genetically characterized. Mutations in the goa-l gene, which encodes an a subunit of G(o) (G alpha(o)), cause behavioral defects similar to those observed in mutants that lack the neurotransmitter serotonin (5-HT), and goa-1 mutants are partially resistant to exogenous 5-HT. Mutant animals that lack G alpha(o) and transgenic animals that overexpress G alpha(o) [goa-l(xs) animals] have reciprocal defects in locomotion, feeding, and egg laying behaviors. In normal animals, all of these behaviors are regulated by 5-HT. These results demonstrate that the level of G(o) activity is a critical determinant of several C. elegans behaviors and suggest that G(o) mediates many of the behavioral effects of 5-HT. ------------------- Key: 2142 Medline: 95192716 Authors: Mendel JE;Korswagen HC;Liu KS;Hajdu-Cronin YM;Simon MI;Plasterk RHA;Sternberg PW Title: Participation of the protein Go in multiple aspects of behavior in C. elegans. Citation: Science 167: 1652-1655 1995 Type: ARTICLE Genes: goa-1 Abstract: The goa-1 gene encoding the alpha subunit of the heterotrimeric guanosine triphosphate-binding protein (G protein) G(o) from Caenorhabditis elegans is expressed in most neurons, and in the muscles involved in egg laying and male mating, Reduction-of-function mutations in goa-1 caused a variety of behavioral defects including hyperactive movement, premature egg laying, and male impotence, Expression of the activated G(o) alpha subunit (G alpha(o)) in transgenic nematodes resulted in lethargic movement, delayed egg laying, and reduced mating efficiency, Induced expression of activated G alpha(o) in adults was sufficient to cause these phenotypes, indicating that G alpha(o) mediates behavior through its role in neuronal function and the functioning of specialized ------------------- Key: 2143 Medline: 95275533 Authors: Roberts TM;Stewart M Title: Nematode sperm locomotion. Citation: Current Opinion in Cell Biology 7: 13-17 1995 Type: REVIEW Genes: Abstract: The simplicity and specialization of the amoeboid motility of nematode sperm can give intriguing insights into the molecular mechanisms underlying movement in more conventional actin-based systems. Amoeboid motility in nematode sperm is based on their major sperm protein. Advances over the past year in understanding the assembly of this protein in vivo and in vitro have underlined the importance of vectorial assembly and filament bundling. In this system, it is possible that these two properties may be sufficient to generate motility that closely resembles that seen in conventional actin-based systems. ------------------- Key: 2144 Medline: Authors: Galas S Title: A model in molecular-genetic of development: The nematode Caenorhabditis elegans. Citation: Bulletin de la Societe Zoologique de France-Evolution et Zoologie 119: 297-308 1995 Type: ARTICLE Genes: Abstract: Introduced in 1965, the Caenorhabditis elegans model is constructed of genetic and molecular techniques, allowing several developmental investigations specific to the model as well as fundamental. The results of the genomic sequencing project of Caenorhabditis elegans will increase the potential of this model. ------------------- Key: 2145 Medline: 95198118 Authors: Wicks SR;Rankin CH Title: Integration of mechanosensory stimuli in Caenorhabditis elegans. Citation: Journal of Neuroscience 15: 2434-2444 1995 Type: ARTICLE Genes: cat-1 cat-2 Abstract: The tap withdrawal reflex in Caenorhabditis elegans demonstrates various forms of nonassociative learning. A first step in determining the cellular mechanisms of this learning is to identify the neuronal circuitry that underlies this reflex. Studies by Chalfie et al. (1985) have defined the touch-circuit that mediates the response to a stimulus related to tap-a light touch. We used the touch circuit as a starting point in the identification of the tap withdrawal circuitry. Here we report the effects of lesions of identified neurons on the tap withdrawal reflex. Ablations of the sensory neurons and interneurons of the touch circuit produce effects on the tap withdrawal response that generally confirm and expand upon the roles of these cells in mechanosensory integration as proposed by Chalfie et al, (1985). However, no role for the LUA interneurons could be identified in the production of the tap withdrawal response. Furthermore, the effects of ablating some neurons outside the touch circuit suggest roles for two of these cells in the integration of the tap withdrawal response. Ablation of either the midline neuron DVA or the PVD neurons resulted in a decrease in both the frequency and magnitude of reversals that were elicited by tap. Additionally, the ablation of either cell decreased the magnitude of accelerations produced by animals in ------------------- Key: 2146 Medline: 95336730 Authors: Yuan J Title: Molecular control of life and death. Citation: Current Opinion in Cell Biology 7: 211-214 1995 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: Recent evidence has shown that two of the three key genes in the programmed cell death pathway of Caenorhabditis elegans, ced-9 (a cell death suppressor) and ced-3 (a cell death inducer), encode proteins that share structural and functional similarities with the mammalian proto-oncogene product Bcl-2 and interleukin-1 beta converting enzyme, respectively. These findings reveal key molecules that control lire and death decisions in vertebrates. ------------------- Key: 2147 Medline: 95268680 Authors: Guven K;Duce JA;de Pomerai DI Title: Calcium moderation of cadmium stress explored using a stress-inducible transgenic strain of Caenorhabditis elegans. Citation: Comparative Biochemistry & Physiology-C: Comparative Pharmacology & Toxicology 110: 61-70 1995 Type: ARTICLE Genes: Abstract: In a transgenic strain of Caenorhabditis elegans carrying a stress-inducible lacZ reporter gene, short-term sublethal exposure to heavy metals activates transgene expression. The transgene response to Cd2+ is strongly inhibited by Ca2+ ions; furthermore, Ca2+ reduces the net accumulation of Cd2+ by worms. Both Ca2+ and a variety of calcium uptake inhibitors (nifedipine, La3+, verapamil) depress the dose response of the transgene to Cd2+. Calcium ionophore (A23187) slightly increases transgene activity in control and Cd2+ treated worms, but has a much larger effect in the case of Mn2+, reflecting its much greater affinity for this ion. ------------------- Key: 2148 Medline: 95309672 Authors: Jongeward GD;Clandinin TR;Sternberg PW Title: sli-1, a negative regulator of let-23-mediated signaling in C. elegans. Citation: Genetics 139: 1553-1566 1995 Type: ARTICLE Genes: let-23 let-60 lin-2 lin-3 lin-7 lin-10 lin-45 sem-5 sli-1 unc-101 meDf3 mnDf67 mnDp68 Abstract: By screening for suppressors of hypomorphic mutations of let-23, a receptor tyrosine kinase necessary for vulval induction in Caenorhabditis elegans, we recovered greater than or equal to 12 mutations defining the sli-1 (suppressor of lineage defect) locus. sli-1 mutations suppress four of five phenotypes associated with hypomorphic alleles of let-23 but do not suppress let-23 null alleles. Thus, a sli-1 mutation does not bypass the requirement for functional let-23 but rather allows more potent LET-SS-dependent signaling. Mutations at the sli-1 locus are otherwise silent with respect to vulval differentiation and cause only a low-penetrance abnormal head phenotype. Mutations at sli-1 also suppress the vulval defects but not other defects associated with mutations of sem-5, whose product likely interacts with LET-23 protein during vulval induction. Mutations at sli-1 suppress lin-2, lin-7 and lin-10 mutations but only partially suppress lin-3 and let-60 mutations and do not suppress a lin-45 mutation. The sli-1 locus displays dosage sensitivity: severe reduction of function alleles of sli-1 are semidominant suppressors; a duplication of the sli-1 (+) region enhances the vulvaless phenotype of hypomorphic mutations of let-23. We propose that sli-1 is a negative regulator that acts at or near the LET-23-mediated step of the vulval induction pathway. Our analysis suggests that let-23 can activate distinct signaling pathways in different tissues: one pathway is required for vulval induction; another pathway is involved in hermaphrodite ------------------- Key: 2149 Medline: 95309673 Authors: Larsen PL;Albert PS;Riddle DL Title: Genes that regulate both development and longevity in Caenorhabditis elegans. Citation: Genetics 139: 1567-1583 1995 Type: ARTICLE Genes: age-1 daf-1 daf-2 daf-3 daf-4 daf-5 daf-7 daf-8 daf-12 daf-14 daf-16 daf-18 daf-19 daf-20 daf-23 fer-15 Abstract: The nematode Caenorhabditis elegans responds to conditions of overcrowding and limited food by arresting development as a dauer larva. Genetic analysis of mutations that alter dauer larva formation (daf mutations) is presented along with an updated genetic pathway for dauer vs. nondauer development. Mutations in the daf-2 and daf-23 genes double adult life span, whereas mutations in four other dauer-constitutive genes positioned in a separate branch of this pathway (daf-1, daf-4, daf-7 and daf-8) do not. The increased life spans are suppressed completely by a daf-16 mutation and partially in a daf-2; daf-18 double mutant. A genetic pathway for determination of adult life span is presented based on the same strains and growth conditions used to characterize Daf phenotypes. Both dauer larva formation and adult life span are affected in daf-2; daf-12 double mutants in an allele-specific manner. Mutations in daf-12 do not extend adult life span, but certain combinations of daf-2 and daf-le mutant alleles nearly quadruple it. This synergistic effect, which does not equivalently extend the fertile period, is the largest genetic extension of life span yet observed in a metazoan. ------------------- Key: 2150 Medline: 95247035 Authors: Wu Y;Han M;Guan KL Title: MEK-2, a Caenorhabditis elegans MAP kinase kinase, functions in Ras-mediated vulval induction and other developmental events. Citation: Genes & Development 9: 742-755 1995 Type: ARTICLE Genes: let-23 let-60 let-537 lin-3 lin-45 mek-1 mek-2 mpk-1 sem-5 sur-1 Abstract: Activated Ras initiates a cascade of sequential phosphorylation events, including the protein kinases Raf, MEK and MAP kinase. The Let-60 Ras-mediated signal transduction pathway controls vulval induction in Caenorhabditis elegans. Both Lin-45 Raf and Sur-1 MAP kinase have been determined to be essential factors during vulval induction; however, the C. elegans mek gene has not been identified. In this paper, we have cloned a C. elegans mek gene, mek-2, and demonstrated that the MEK-2 protein possesses the biochemical properties of MAP kinase kinases: The C. elegans MEK-2 protein can phosphorylate and activate a human MAP kinase (ERK1), and MEK-2 itself can be phosphorylated and activated by immunoprecipitated mammalian Raf. The mek-2 gene plays a key role in the let-60 ras-mediated vulval induction pathway, as loss-of-function mutations in the gene (ku114 and h294) significantly reduce the signal transmitted through Ras. mek-2(ku114) completely suppressed the Multivulva (Muv) phenotype of a hyperactive let-60 ras mutation, and animals homozygous for mek-2(ku114) also displayed a partial larval lethal phenotype. Animals homozygous for mek-2(h294) exhibited a highly penetrant sterile and Vulvaless phenotype. Microinjection of a gain-of-function mek-2 mutation resulted in Muv and other mutant phenotypes, whereas microinjection of a dominant-negative mutation not only suppressed the Muv phenotype of an activated let-60 ras mutation but also caused an egg-laying defective phenotype in otherwise wild type animals. Our results demonstrate that mek-2 acts between lin-45 raf and sur-1/mpk-1 in a signal transduction pathway used in the control of vulval differentiation and other developmental ------------------- Key: 2151 Medline: 95247036 Authors: Kornfeld K;Guan KL;Horvitz HR Title: The Caenorhabditis elegans gene mek-2 is required for vulval induction and encodes a protein similar to the protein kinase MEK. Citation: Genes & Development 9: 756-768 1995 Type: ARTICLE Genes: let-23 let-60 let-537 lin-1 lin-3 lin-15 lin-45 mek-2 mpk-1 sem-5 sur-1 hDp18 hDp62 hDp72 qDf3 tDf3 tDf4 Abstract: An evolutionarily conserved signal transduction pathway that utilizes a receptor tyrosine kinase and a Ras protein mediates the induction of vulval cell fates in the nematode Caenorhabditis elegans. We sought new genes that function in this pathway by screening for suppressors of the Multivulva phenotype caused by a mutation that activates the let-60 ras gene. Seven such sppressor mutations defined a new gene involved in vulval induction. We named this gene mek-2, because its predicted protein product is most similar to MEK, a protein-serine/threonine and tyrosine kinase. mek-2 mutations can be arranged in an allelic series. A probable null mutation eliminated vulval induction, and the strongest mutations alter codons conserved in most or all protein kinases. Our genetic analysis showed that mek-2 functions downstream of let-60 ras and is required for ras-mediated signal transduction in vivo. The MEK-2 protein may interact with the products of the lin-45 raf and mpk-1 MAP kinase genes, which also ------------------- Key: 2152 Medline: 95212512 Authors: Bessho K;Yamada S;Kunitani T;Nakamura T;Hashiguchi T;Tanimoto Y;Harada S;Yamamoto H;Hosono R Title: Biological responses in Caenorhabditis elegans to high magnetic fields. Citation: Experientia 51: 284-288 1995 Type: ARTICLE Genes: ace-1 ace-2 Abstract: Here we describe a device for testing possible influences of high magnetic fields on biological processes, by which alternating-current magnetic stimuli as high as 1.7T can be administered. Experiments with a simple multicellular organism, the nematode Caenorhabditis elegans, revealed that intermittent exposure to the magnetic fields modestly inhibited the animal's reproduction as well as its post-embryonic development, and caused a marked but transient derangement in its locomotory behavior. Available evidence indicates that alternating high magnetic fields can elicit both chronic and acute biological effects, but that the effects may be well tolerated or compensated for by the living organism. ------------------- Key: 2153 Medline: 95250204 Authors: Blumenthal T Title: Transsplicing and polycistronic transcription in Caenorhabditis elegans. Citation: Trends in Genetics 11: 132-136 1995 Type: REVIEW Genes: ced-9 cyt-1 dom-3 dpy-30 fib-1 gpd-2 gpd-3 kin-10 kin-13 kin-15 lin-15 mai-1 mes-3 rnp-1 rol-6 rps-1 rps-16 tra-2 unc-32 Abstract: Caenorhabditis elegans engages in three distinct versions of nuclear pre-mRNA splicing: cis-splicing of introns and two kinds of trans-splicing that result in the addition of two different spliced leaders onto mRNAs. One leader (SL1) is used near the 5' ends of pre-mRNAs while the other (SL2) is used at internal trans-splice sites of polycistronic pre-mRNAs. Here, I consider bow these three types of splicing event are faithfully carried out. ------------------- Key: 2154 Medline: 95230679 Authors: Tabish M;Siddiqui ZK;Nishikawa K;Siddiqui SS Title: Exclusive expression of C. elegans osm-3 kinesin gene in chemosensory neurons open to the external environment. Citation: Journal of Molecular Biology 247: 377-389 1995 Type: ARTICLE Genes: osm-3 unc-104 unc-116 Abstract: In Caenorhabditis elegans three genetic loci osm-3, unc-104 and unc-116 have been identified, which encode anterograde motor kinesin. Here we show that osm-3 encodes a 672 amino acid long kinesin-like protein (KLP) that contains all three functional domains similar to the kinesin heavy chain, including a globular motor region, an alpha-helical coiled-coil rod, and a globular tail region. OSM-3 shows homology in both the motor and rod domains with kinesins from divergent species such as mouse KIF3, and sea urchin KRP95, and also with the rod domains of several non-kinesin proteins, such as myosin, ezrin, outer membrane proteins alpha precursor OMPA, yeast intracellular protein transport USO1, and the rat neurofilament NF-H. Temporal and spatial expression of the osm-3::lacZ fusion gene during development is limited to an exclusive set of 26 chemosensory neurons whose dendritic endings are exposed to the external environment, including six IL2 neurons of the inner labial sensilla, eight pairs of amphid neurons (ADE ADL, ASE, ASG, ASH, ASI, ASJ, ASK) in the head, and two pairs of phasmid neurons (PHA and PHB) in the tail. Our data are consistent with the known structural defects in the amphid and phasmid sensilla in osm-3 mutants and also show the expression of the gene in IL2 neurons. Temporally, the gene is differentially expressed in all three types of chemosensory sensilla. Further work on osm-3, unc-104 and unc-116 mutants should give insight into the in vivo functions of the kinesin family during C. elegans ------------------- Key: 2155 Medline: 95246923 Authors: Rose LS;Lamb ML;Hird SN;Kemphues KJ Title: Pseudocleavage is dispensable for polarity and development in C. elegans embryos. Citation: Developmental Biology 168: 479-489 1995 Type: ARTICLE Genes: nop-1 nDf16 Abstract: The first cleavage of the Caenorhabditis elegans embryo is asymmetrical, producing daughters with different cell fates. During the first cell cycle, P granules, cytoplasmic components that are segregated to the germ-line, are localized to the posterior of the embryo. It has been hypothesized that the asymmetrical behavior of the daughters of the first division results from a similar localization of developmental determinants. A process called pseudocleavage also occurs during the first cell cycle: Anterior cortical contractions culminate in a single partial constriction of the embryo called the pseudocleavage furrow. Coincident with pseudocleavage, there is an anteriorly directed flow of cortical cytoplasm and a posteriorly directed flow of internal cytoplasm. Foci of filamentous cortical actin become asymmetrically distributed into an anterior cap. Roles for these various first cell cycle events in cytoplasmic localization and development have been suggested but remain unclear. We have isolated a maternal effect mutation, nop-1(it142), which abolishes the anterior cortical contractions and the pseudocleavage furrow. In addition, cortical actin foci remain uniformly distributed in most embryos. Despite these defects, cytoplasmic and cortical streaming is present and P granules are localized to the posterior of the embryos. In most embryos from mutant mothers, development proceeds normally and the embryos hatch and grow into fertile adults. We conclude that the pseudocleavage contractions and furrow are dispensable for ------------------- Key: 2156 Medline: 95262567 Authors: Goldstein B Title: An analysis of the response to gut induction in the C. elegans embryo. Citation: Development 121: 1227-1236 1995 Type: ARTICLE Genes: mex-1 pie-1 skn-1 Abstract: Establishment of the gut founder cell (E) in C. elegans involves an interaction between the P2 and the EMS cell at the four cell stage. Here I show that the fate of only one daughter of EMS, the E cell, is affected by this induction. In the absence of the P2-EMS interaction, both E and its sister cell, MS, produce pharyngeal muscle cells and body wall muscle cells, much as MS normally does. By cell manipulations and inhibitor studies, I show first that EMS loses the competence to respond before it divides even once, but P2 presents an inducing signal for at least three cell cycles. Second, induction on one side of the EMS cell usually blocks the other side from responding to a second P2-derived signal. Third, microfilaments and microtubules may be required near the time of the interaction for subsequent gut differentiation. Lastly, cell manipulations in pie-1 mutant embryos, in which the P2 cell is transformed to an EMS-like fate and produces a gut cell lineage, revealed that gut fate is segregated to one of P2's daughters cell-autonomously. The results contrast with previous results from similar experiments on the response to other inductions, and suggest that this induction may generate cell diversity by a different ------------------- Key: 2157 Medline: Authors: Borgonie G;Claeys M;De Waele D;Coomans A Title: In vivo and in vitro characterization of the intestine of fifteen bacteriophagous nematodes (Nematoda: Rhabditia). Citation: Fundamental and Applied Nematology 18: 115-122 1995 Type: ARTICLE Genes: Abstract: The intestine of the fifteen free-living Rhabditida belonging to three different families was studied using three different approaches : i) using three different axenic media, cultivation of all fifteen nematode species was attempted; ii) in vivo analyses were performed by using two vital stains and one fluorescent dye and by comparing staining patterns; iii) in vitro analyses was done using the intestinal markers acid phosphatase, esterase and the lectin of Ricinus communis II. Although the nematodes can be cultured monoxenically on the same bacterium, Escherichia coli, attempts to culture the fifteen nematode species on the same axenic medium failed. Distinct differences are observed between different areas along the intestinal tract by in vivo study using stains. Similar observations were made in vitro using the intestinal marker acid phosphatase and the binding pattern of Ricinus communis II. This was less evident using esterase as a marker, since considerable non-intestinal tissue staining was evident. The data obtained indicate considerable biochemical differences in the intestinal cells between the nematode species, even if the nematode species belong to ------------------- Key: 2158 Medline: Authors: Borgonie G;Claeys M;De Waele D;Coomans A Title: Ultrastructure of the intestine of the bacteriophagous nematodes Caenorhabditis elegans, Panagrolaimus superbus and Acrobeloides maximus (Nematoda: Rhabditida). Citation: Fundamental and Applied Nematology 18: 123-133 1995 Type: ARTICLE Genes: Abstract: The intestine of the three free-living rhabditid nematodes Caenorhabditis elegans, Panagrolaimus superbus and Acrobeloides maximus was studied using transmission electron microscopy of sections made at three locations along the intestine. Between the three nematode species, ultrastructural differences in cellular components are minor. However, two cell types present in all three nematode species are positioned differently along the intestinal tract. Furthermore, two different types of secretions into the intestinal lumen were identified, one only at the anterior intestine, the second present along the entire length of the intestinal lumen. F-actin staining of fifteen whole-mount nematodes revealed the presence of a well developed, cross-shaped intestinal muscle, only present in Cephalobid species. ------------------- Key: 2159 Medline: 95135079 Authors: Walthall WW Title: Repeating patterns of motoneurons in nematodes: The origin of segmentation? Citation: "The Nervous Systems of Invertebrates: An Evolutionary Approach." Breidbach, O. and W. Kutsch (eds), Birkhauser Verlag, Basel, Switzerland, 1995. : 61-75 1995 Type: REVIEW Genes: mab-5 unc-4 unc-5 unc-6 unc-40 unc-55 Abstract: Evolutionarily diverse groups of animals share numerous similarities as individual neurons are assembled into functional neural circuits. One example is the hierarchical sequence of events that individual nerve cells follow during morphological development. In the initial step a presumptive neuron is generated and positioned appropriately. Second, the undifferentiated cell elaborates a growth cone capable of interacting with extrinsic cues and leading the presumptive axonal process as it is guided into areas where potential synaptic targets reside. Finally, the differentiating nerve cell selects among appropriate and inappropriate target cells as it completes the process of selective synaptogenesis. The extracellular matrix molecule laminin provides a second example, this time at the molecular level. Biochemical and genetic studies have shown that this molecule directs process guidance of neurons in vertebrates, annelids, and nematodes. In both examples an interest in neural development has provided a window through which evolutionarily processes have been revealed. The free-living soil nematode Caenorhabditis elegans possesses several features that collectively place it in a rather unique position among metazoans and has allowed genetic and cellular studies to be integrated at the level of identified neurons and neural circuits. This review will focus on developmental studies of C. elegans locomotory neural circuits. General issues that will be addressed are the similarities and differences among different taxa regarding: the relationship between cell lineage and cell fate determination in generating reiterative neural patterns; pioneer cells and the molecular basis for process guidance and finally genetic epigenetic events involved in ------------------- Key: 2160 Medline: 95293228 Authors: Thacker C;Peters K;Srayko M;Rose AM Title: The bli-4 locus of Caenorhabditis elegans encodes structurally distinct kex2/subtilisin-like endoproteases essential for early development and adult morphology. Citation: Genes & Development 9: 956-971 1995 Type: ARTICLE Genes: bli-4 hDf8 sDp2 Abstract: Many secreted proteins are excised from inactive proproteins by cleavage at pairs of basic residues. Recent studies have identified several serine endoproteases that catalyze this cleavage in the secretory pathways of yeast and metazoans. These enzymes belong to the kex2/subtilisin-like family of proprotein convertases. In this paper we describe the molecular characterization of the bli-4 gene from Caenorhabditis elegans, which was shown previously by genetic analysis of lethal mutants to be essential for the normal development of this organism. Sequencing of cDNA and genomic clones has revealed that bli-4 encodes gene products related to the kex2/subtilisin-like family of proprotein convertases. Analysis of bli-4 cDNAs has predicted four protein products, which we have designated blisterases A,B,C, and D. These protein products share a common amino terminus, but differ at the carboxyl termini, and are most likely produced from alternatively spliced transcripts. We have determined the molecular lesions for three bli-4 alleles (h199, h1010, and q508) that result in developmental arrest during late embryogenesis. In each case, the molecular lesions are within exons common to all of the BLI-4 isoforms. The original defining allele of bli-4, e937, is completely viable yet exhibits blistering of the adult cuticle. Molecular analysis of this allele revealed a deletion that removes exon 13, which is unique to blisterase A. No RNA transcript corresponding to exon 13 is detectable in the blistered mutants. These findings suggest that blisterase A is required for the normal function of the adult cuticle. The bli-4 gene is a complex locus as evidenced by the characterization of mutant strains and RNA transcripts. Furthermore, our data show that functional ------------------- Key: 2161 Medline: 95241497 Authors: Hara M;Han M Title: Ras farnesyltransferase inhibitors suppress the phenotype resulting from an inactivated ras mutation in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 92: 3333-3337 1995 Type: ARTICLE Genes: let-23 let-60 lin-1 lin-3 lin-15 lin-45 sem-5 sur-1 Abstract: Attachment of Ras protein to the membrane, which requires farnesylation at its C terminus, is essential for its biological activity. A promising pharmacological approach of antagonizing oncogenic Ras activity is to develop inhibitors of farnesyltransferase. We use Caenorhabditis elegans vulval differentiation, which is controlled by a Ras-mediated signal transduction pathway, as a model system to test previously identified farnesyltransferase inhibitors. We show here that two farnesyltransferase inhibitors, manumycin and gliotoxin, suppress the Multivulva phenotype resulting from an activated let-60 ras mutation, but not the Multivulva phenotype resulting from mutations in the lin-1 gene or the lin-15 gene, which act downstream and upstream of let-60 ras, respectively, in the signaling pathway. These results are consistent with the idea that the suppression of the Multivulva phenotype of let-60 ras by the two inhibitors is specific for Ras protein and that the mutant Ras protein might be more sensitive than wild-type Ras to the farnesyltransferase inhibitors. This work suggests that C. elegans vulval development could be a simple and effective in vivo system for evaluation of farnesyltransferase inhibitors against ------------------- Key: 2162 Medline: 95287401 Authors: Egilmez NK;Ebert RH;Reis RJS Title: Strain evolution in Caenorhabditis elegans: Transposable elements as markers of interstrain evolutionary history. Citation: Journal of Molecular Evolution 40: 372-381 1995 Type: ARTICLE Genes: Abstract: Evolutionary relationships across taxa can be deduced from sequence divergence of proteins, RNA, or DNA; sequences which diverge rapidly, such as those of mitochondrial genes, have been especially useful for comparisons of closely related species, and-within limits-of strains within a species. We have utilized the transposable element Tc1 as a polymorphic marker to evaluate the evolutionary relationships among nine Caenorhabditis elegans strains. For five low-Tc1-copy strains, we compared patterns of restriction fragments hybridizing to a cloned Tc1 probe. Twenty of the 40 Tc1 insertion sites thus characterized were common to all five strains, and so presumably preceded strain divergence; the 20 differential bands were used to construct a maximum-parsimony tree relating these strains. In four high-copy-number stocks (three wild-type strains and a subline), we determined occupancy of 35 individual Tc1 insertion sites by a polymerase chain reaction assay. Surprisingly, the high-copy strains share a common subset of these Tc1 insertions, and the chromosomal distribution of conserved Tc1 sites is ''clustered'' with respect to the other elements tested. These data imply a close evolutionary relationship among the high-copy strains, such that two of these strains appear to have been derived from the highest-copy-number lineage (represented by two stocks) through crossing with a low-Tc1 strain. Abundances of Tc1 elements were also estimated for the four high-copy-number stocks, at similar to 200-500 copies per haploid genome, by quantitative dot-blot hybridization relative to two low-copy strains. annealing with P-32-labeled probes corresponding to full-length Tc1, an oligonucleotide within the Tc1 terminal inverted repeats, and an internal Tc1 oligonucleotide, gave essentially identical results-indicating that Tc1 termini exist in the genome primarily as components of full-length Tc1 elements. A composite evolutionary tree is proposed, based on the locations and numbers of Tc1 elements in these strains, which is consistent with a four-branch intraspecific tree deduced previously by maximum-parsimony analyses of mitochondrial sequence changes; it also serves to elucidate the evolutionary history of transposon mobility. ------------------- Key: 2163 Medline: 95353697 Authors: Garcia-Anoveros J;Ma C;Chalfie M Title: Regulation of Caenorhabditis elegans degenerin proteins by a putative extracellular domain. Citation: Current Biology 5: 441-448 1995 Type: REVIEW Genes: deg-1 mec-4 mec-10 Abstract: Background: Rare, dominant mutations in the degenerin genes of Caenorhabditis elegans (deg-1, mec-4 and mec-10) cause neuronal degeneration. The extensive sequence similarity between degenerins and mammalian genes that encode subunits of the amiloride-sensitive sodium channel from kidney, colon and lung suggests that the C. elegans degenerins form ion channels. As mec-4 and mer-10 are needed for the reception of gentle touch stimuli, they may contribute to a mechanosensory ion channel. All the dominant degeneration-causing mutations in the C. elegans degenerin genes affect equivalent residues in a hydrophobic region that is structurally similar to the H5 domain of several ion channels, and so could form the channel lining. Increased channel activity may underlie the resulting degeneration, in which the affected cells vacuolate and swell. Results: We now demonstrate that a missense change in a predicted extracellular region of the proteins encoded by deg-1 and mec-4 causes cell death similar to that caused by the dominant mutations. The missense mutation lies within a 22 amino-acid region found in all the C. elegans degenerins for which the sequences have been published, but not in the similar mammalian proteins. Deletion of nine amino acids surrounding the mutation site in mec-4 also causes neuronal degeneration. The degeneration-causing mutations in either the predicted pore-lining or the predicted extracellular regions of deg-1 are suppressed by additional, dominantly acting mutations that substitute larger for smaller residues within the channel lining. Conclusions: Our data suggest that the putative extracellular domain negatively regulates degenerin activity, perhaps by gating the channel. As this region is only found in the C. elegans proteins, it may allow more rapid regulation of the nematode channels, which may be needed for them to function in mechanosensation. The suppressor mutations, by adding larger amino acids to the putative pore lining, could prevent degeneration by ------------------- Key: 2164 Medline: 95222415 Authors: Arena JP;Liu KK;Paress PS;Frazier EG;Cully DF;Mrozik H;Schaeffer JM Title: The mechanism of action of avermectins in Caenorhabditis elegans: Correlation between activation of glutamate-sensitive chloride current, membrane binding, and biological activity. Citation: Journal of Parasitology 81: 286-294 1995 Type: ARTICLE Genes: Abstract: Xenopus laevis oocytes were injected with mRNA isolated from the free-living nematode Caenorhabditis elegans and the activation and potentiation of a glutamate-sensitive chloride current by a series of avermectin analogs and milbemycin D were determined. There was a strong correlation between the EC(50) value determined for current activation in oocytes, the LD(95) value for nematocidal activity, and also for the K-i value determined in a [H-3]ivermectin competition binding assay. Four of the analogs were tested for potentiation of glutamate-sensitive current and the rank order for potentiation correlated with the EC(50) for direct activation of current. We conclude that avermectins and milbemycins mediate their nematocidal effects on C. elegans via an interaction with a common receptor molecule, glutamate-gated chloride channels. ------------------- Key: 2165 Medline: Authors: Chen H;Yim T;Fye D;Schatz B Title: Automatic thesaurus generation for an electronic community system. Citation: Journal of the American Society for Information Science 46: 175-193 1995 Type: ARTICLE Genes: Abstract: This research reports an algorithmic approach to the automatic generation of thesauri for electronic community systems. The techniques used included term filtering, automatic indexing, and cluster analysis. The testbed for our research was the Worm Community System, which contains a comprehensive library of specialized community data and literature, currently in use by molecular biologists who study the nematode worm C. elegans. The resulting worm thesaurus included 2709 researchers' names, 798 gene names, 20 experimental methods, and 4302 subject descriptors. On average, each term had about 90 weighted neighboring terms indicating relevant concepts. The thesaurus was developed as an online search aide. We tested the worm thesaurus in an experiment with six worm researchers of varying degrees of expertise and background. The experiment showed that the thesaurus was an excellent "memory-jogging" device and that it supported learning and serendipitous browsing. Despite some occurrences of obvious noise, the system was useful in suggesting relevant concepts for the researchers' queries and it helped improve concept recall. With a simple browsing interface, an automatic thesaurus can become a useful tool for online search and can assist researchers in exploring and traversing a dynamic and complex electronic community system. ------------------- Key: 2166 Medline: 95234319 Authors: Colbert HA;Bargmann CI Title: Odorant-specific adaptation pathways generate olfactory plasticity in C. elegans. Citation: Neuron 14: 803-812 1995 Type: ARTICLE Genes: adp-1 osm-3 osm-9 osm-11 Abstract: Following prolonged exposure to an odorant, C. elegans exhibits a diminished response to the odorant for several hours. This olfactory adaptation is odorant selective; animals can adapt independently to different odorants sensed by a single pair of olfactory neurons, the AWC neurons. The mechanism of olfactory adaptation is genetically complex, with different genes required for adaptation to different odorants. Animals mutant for the gene adp-1 fail to adapt to a subset of AWC-sensed odorants; adp-1 affects a calcium-dependent process required for adaptation. Mutations in another gene, osm-9 affect adaptation to a different but overlapping subset of AWC-sensed odorants. Mutations in adp-1 and osm-9 do not diminish the ability of unadapted animals to respond to odorants, indicating that odorant sensation and odorant ------------------- Key: 2167 Medline: 95234326 Authors: Treinin M;Chalfie M Title: A mutated acetylcholine receptor subunit causes neuronal degeneration in C. elegans. Citation: Neuron 14: 871-877 1995 Type: ARTICLE Genes: deg-3 DnT1 Abstract: Neurotoxicity through abnormal activation of membrane channels is a potential cause of neurodegenerative disease. Here we show that a gain-of-function mutation, deg 3(u662), leads to the degeneration of a small set of neurons in the nematode C. elegans. The deg-3 gene encodes a nicotinic acetylcholine receptor alpha subunit, which in the region of transmembrane domain II is most similar to the neuronal alpha 7 subunits from rat and chicken. The u662 mutation changes a residue in the second transmembrane domain, the domain thought to form the channel pore. A similar change in the equivalent amino acid in the chick protein produces channels that desensitize slowly. Channel hyperactivity may underlie the degenerations seen in the C. elegans deg-3(u662) mutants, since antagonists of nicotinic acetylcholine receptors suppress the deg-3(u662) mutant phenotypes. ------------------- Key: 2168 Medline: 95240736 Authors: Schafer WR;Kenyon CJ Title: A calcium-channel homologue required for adaptation to dopamine and serotonin in Caenorhabditis elegans. Citation: Nature 375: 73-78 1995 Type: ARTICLE Genes: egl-1 unc-2 yDp16 Abstract: Processing and storage of information by the nervous system requires the ability to modulate the response of excitable cells to neurotransmitter. A simple process of this type, known as adaptation or desensitization, occurs when prolonged stimulation triggers processes that attenuate the response to neurotransmitter. Here we report that the Caenorhabditis elegans gene unc-2 is required for adaptation to two neurotransmitters, dopamine and serotonin. A loss-of-function mutation in unc-2 resulted in failure to adapt either to paralysis by dopamine or to stimulation of egg laying by serotonin. In addition, unc-2 mutants displayed behaviours similar to those induced by serotonin treatment. We found that unc-2 encodes a homologue of a voltage-sensitive calcium-channel alpha-1 subunit. Expression of unc-2 occurs in two types of neurons implicated in the control of egg laying, a behaviour regulated by serotonin, Unc-2 appears to be required in modulatory neurons to downregulate the response of the egg-laying muscles to serotonin, We propose that adaptation to serotonin occurs through activation of an Unc-2-dependent calcium influx, which modulates the postsynaptic response to serotonin, perhaps by inhibiting the release of a potentiating neuropeptide. ------------------- Key: 2169 Medline: 95239203 Authors: Laughton DL;Wheeler SV;Lunt GG;Wolstenholme AJ Title: The beta-subunit of Caenorhabditis elegans avermectin receptor responds to glycine and is encoded by chromosome Citation: Journal of Neurochemistry 64: 2354-2357 1995 Type: ARTICLE Genes: Abstract: A full-length cDNA encoding the beta subunit of the recently described avermectin receptor was amplified from Caenorhabditis elegans mRNA. When this cDNA was injected into Xenopus oocytes a dose-dependent response to glycine was observed, together with a smaller response to 1 mM GABA. The EC(50) of the glycine response was similar to that described previously for glutamate (0.38 mM). Hybridisation of the cDNA to polytene filters identified three yeast artificial chromosome clones that gave a positive signal, Y37B3, Y38E5, and Y24C9, all of which are mapped to chromosome 1. Hybridisation to a series of cosmid clones covering this area further mapped the gene encoding this subunit to the region -2,818 to -2,824. ------------------- Key: 2170 Medline: 95272676 Authors: Simske JS;Kim SK Title: Sequential signaling during Caenorhabditis elegans vulval induction. Citation: Nature 375: 142-146 1995 Type: ARTICLE Genes: let-23 lin-3 lin-7 ncl-1 Abstract: During the induction of the Caenorhabditis elegans vulva, cell signalling causes initially equipotent cells to express a reproducible pattern of cell fates(1,2). The position of the anchor cell determines the pattern of vulval precursor cell fates, such that the closest precursor cell (P6.p) expresses the primary cell fate, the next closest cells (P5.p and P7.p) both express the secondary cell fate, and each of the precursor cells located at a distance (P3.p, P4.p and P8.p) express the tertiary cell fate (Fig. 1a)(3-5). We present data indicating that this stereotypical pattern of cell fates can be generated by sequential signals. We identified genetic mosaic animals in which P5.p and P7.p were defective in the anchor-cell signal-transduction pathway and observed that these cells adopted the secondary cell fate, indicating that anchor-cell signal transduction is not required for the expression of the secondary cell fate. These results suggest that the anchor cell induces P6.p to express the primary cell fate, and that P6.p subsequently induces P5.p and P7.p to express the secondary cell fate. ------------------- Key: 2171 Medline: 95256246 Authors: Kazanietz MG;Lewin NE;Bruns JD;Blumberg PM Title: Characterization of the cysteine-rich region of the Caenorhabditis elegans protein Unc-13 as a high affinity phorbal ester receptor. Citation: Journal of Biological Chemistry 270: 10777-10783 1995 Type: ARTICLE Genes: unc-13 Abstract: The Caenorhabditis elegans Unc-13 protein is a novel member of the phorbol ester receptor family having a single cysteine-rich region with high homology to those present in protein kinase C (PKC) isozymes and the chimaerins, We expressed the cysteine-rich region of Unc-13 in Escherichia coli and quantitatively analyzed its interactions with phorbol esters and related analogs, its phospholipid requirements, and its inhibitor sensitivity, [H-3]Phorbol 12,13-dibutyrate [H-3]PDBu bound with high affinity to the cysteine-rich region of Unc-13 (K-d = 1.3 +/- 0.2 nM). This affinity is similar to that of other single cysteine-rich regions from PKC isozymes as well as n-chimaerin, As also described for PKC isozymes and n-chimaerin, Unc-13 bound diacylglycerol with an affinity about 2 orders of magnitude weaker than [H-3]PDBu. Structure activity analysis revealed significant but modest differences between recombinant cysteine-rich regions of Unc-13 and PKC delta. In addition, Unc-13 required slightly higher concentrations of phospholipid for reconstitution of [H-3]PDBu binding. Calphostin C, a compound described as a selective inhibitor of PKC, was also able to inhibit [H-3]PDBu binding to Unc-13, suggesting that this inhibitor is not able to distinguish between different classes of phorbol ester receptors, In conclusion, although our results revealed some differences in ligand and lipid cofactor sensitivities, Unc-13 represents a high affinity cellular target for the phorbol esters as well as for the lipid second messenger diacylglycerol, at least in C. elegans, The use of phorbol esters or some ''specific'' antagonists of PKC does not distinguish between cellular pathways involving different PKC isozymes or novel phorbol ester receptors such as n-chimaerin or Unc-13. ------------------- Key: 2172 Medline: 95333939 Authors: Driscoll M Title: Methods for the study of cell death in the nematode C. elegans. Citation: Methods in Cell Biology 46: 323-353 1995 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-9 ced-10 deg-1 mec-4 mec-10 Abstract: The nematode Caenorhabditis elegans seems so well suited to investigation of genetically specified cell death that one might also suspect that it was designed for this purpose. The complete cell lineage of this nematode has been recorded. Thus, it is well established that of 1090 somatic cells generated during hermaphrodite development, 131 identified cells undergo programmed cell death (PCD) at characteristic times. Because the cuticle of the animal is transparent and individual cells are easily identified, cell deaths can be observed while they occur in the living animal. The ease of observation of specific cells, coupled with the fact that C. elegans is readily amenable to genetic analysis, has allowed mutations to be identified that either disrupt the normal pattern of PCD or cause inappropriate cell death. Molecular analysis of the identified genes is facilitated by the fact that the genetic map has been aligned with the physical map of the C. elegans genome so each chromosome is now nearly completely represented by an overlapping collection of cosmid or YAC clones that include defined genetic loci. In addition, significant progress toward sequencing the genome has been accomplished. Finally, it is possible to construct transgenic animals so the activities of engineered genes can be assayed in vivo. Two types of cell death have been studied in C. elegans. One type is PCD, which occurs as a component of normal development. Genetic studies have led to the elaboration of a genetic pathway for PCD that includes a negative regulator, ced-9 (cell death abnormal), that acts to prevent PCD and two genes, ced-3 and ced-4, that are involved in the execution of the death program. A third group of genes (ced-1, ced-2, ced-5, ced-5, ced-7, ced-8, ced-10) is required for efficient removal of corpses of dead cells. Cells undergoing PCD exhibit stereotypic morphological changes. A second type of cell death studied in C. elegans resembles necrosis and is characterized by swelling and lysis of specific groups of neurons. This pathological cell death can be induced by mutations in a family of genes including deg-1, mec-4 and mec-10 (degeneration and mechanosensory abnormal, respectively). These genes, called degenerin genes, encode subunits of a newly identified class of ion channels. Degeneration appears to occur as a consequence ------------------- Key: 2173 Medline: Authors: Driscoll M Title: Inherited neurodegeneration in C. elegans. Citation: "Neurodegenerative Diseases", Jolles, G and Stultzmann, J.M. (eds), Academic Press, London. : 3-22 1994 Type: REVIEW Genes: deg-1 mec-4 mec-6 mec-10 Abstract: The goal of much research in the field of neurodegeneration is to understand the causes of human degenerative conditions and to design strategies to circumvent degenerative processes. Unfortunately, the complexities of the human system render it difficult to determine the identities of the genes that can mutate to cause degeneration and to decipher the mechanisms involved in degenerative processes, two pressing issues concerning degenerative states. In terms of biochemical investigations of human degenerative conditions, samples of disease tissue are in limited supply and are often available only well after the events critical to onset of degeneration have transpired. Genetic analyses are complicated by small family sizes, the lengthy human reproductive cycle, and the late onset of many degenerative conditions. Cloning efforts are slowed by the large size of the human genome. In vitro experiments must be interpreted with attention to the fact that conditions used in cell culture may be far removed from complex physiological conditions present in vivo. Inherited neurodegenerative conditions have been documented to afflict a broad range of species, including animals as diverse as nematodes, flies and humans. One approach toward elucidating the mechanisms involved in inherited neurodegeneration is to characterize degenerative conditions in simple model systems that are easily manipulated at the molecular and genetic levels. The rationale for this approach is that the mechanisms deciphered and the genes and gene products involved may be conserved enough to significantly advance our understanding of inherited neurodegeneration in humans. Numerous examples of human genes that can substitute for normal gene activities in experimental systems such as the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster fuel the argument that identification of key proteins that participate in neurodegenerative processes in ------------------- Key: 2174 Medline: 95280732 Authors: Schwarzbauer JE;Mussetbi F;Ryan CS Title: Extracellular calcium-binding protein SPARC/Osteonectin in Caenorhabditis elegans. Citation: Methods in Enzymology 245: 257-270 1995 Type: REVIEW Genes: ost-1 Abstract: The nematode Caenorhabditis elegans is an excellent genetic system for dissecting protein function. Beginning with the pioneering work of Brenner numerous mutations have been generated and characterized phenotypically. Ease of culture, transparency, and small size, (fewer than 1000 nongonadal nuclei), have allowed the determination of a complete cell lineage map by direct observation of living nematodes. Colocalizatioin of genetic and physical loci is made possible by an extensive C. elegans genome map. The ability to identify genes corresponding to particular mutations has ad significantly with the development of methods for transformation of mutants with wild-type genes. The ability to introduce mutations into specific genes is now becoming possible by Tc1 transposon insertion of excision. A comprehensive volume describing all aspects of nematode biology is an excellent resource for anyone studying C. elegans, from novice to expert. In addition, The Worm Breeder's Gazette, published quarterly by the Caenorhabditis Genetics Center (CGC, University of Minnesota, St. Paul, MN), contains short research articles and technical notes contributed by members of the nematode community and represents a unique mechanism for keeping abreast of the latest techniques and the most recent results from other laboratories. The CGC, supported by the NIH National Center for Research Resources, also maintains a large collection of normal and mutant strains for distribution on request. ------------------- Key: 2175 Medline: 95278751 Authors: Leroux MR;Candido EPM Title: Molecular analysis of Caenorhabditis elegans tcp-1, a gene encoding a chaperonin protein. Citation: Gene 156: 241-246 1995 Type: ARTICLE Genes: tcp-1 Abstract: A Caenorhabditis elegans (Ce) homologue to the eukaryotic tcp-1 gene (encoding t-complex polypeptide-1) has been mapped, isolated and sequenced. Ce tcp-1 is a single-copy gene located on chromosome II. Nucleotide sequence analysis of the gene reveals the presence of four introns in the coding region and repetitive elements upstream from the start codon. The predicted Ce TCP-1 protein displays more than 60% amino-acid sequence identity to other eukaryotic TCP-1, suggesting a common origin and function for these proteins. The primary tcp-1 transcript undergoes transsplicing to the spliced leader SL1 RNA, in addition to cis-splicing, to yield a single mRNA species of 1.9 kb. Northern blot analysis shows that unlike the evolutionarily related Hsp60 chaperonin genes, tcp-1 is not upregulated at elevated temperatures, but instead appears to be down-regulated. Additionally, the overall level of the tcp-1 transcript is approximately constant throughout the development of the nematode. The Ce chaperonin-containing TCP-1 (CCT) was identified. A protein extract made from Ce embryos was subjected to sucrose gradient fractionation and ATP-agarose chromatography. Western blot analysis of the purified protein fractions, using anti-mouse TCP-1 monoclonal antibody and antibodies raised against Ce TCP-1, reveals that Ce TCP-1 is a 57-kDa protein subunit of a high-molecular-mass complex capable of binding ATP. ------------------- Key: 2176 Medline: 95260864 Authors: Fukushige T;Yasuda H;Siddiqui SS Title: Selective expression of the tba-1 alpha tubulin gene in a set of mechanosensory and motor neurons during the development of Caenorhabditis elegans. Citation: Biochimica et Biophysica Acta-Gene Structure & Expression 1261: 401-416 1995 Type: ARTICLE Genes: tba-1 tba-2 Abstract: In the nematode Caenorhabditis elegans, a monoclonal antibody 3A5 raised against Drosophila alpha tubulins selectively stains the nervous system immuno-cytochemically. Direct screening of a C. elegans cDNA expression library with 3A5 has allowed cloning of the tba-1 (tubulin alpha-1) gene from C. elegans. The corresponding genomic DNA encodes a protein of 449 amino acid residues that has a high homology with the vertebrate a: tubulins but a lower homology with yeast a tubulins. Interestingly, the carboxyl-terminus sequence EEEGEEY (Glu-Glu-Glu-Gly-Glu-Glu-Tyr) of the nematode tba-1 encoded isotype is identical to these residues in human, mouse, rat, pig and chicken alpha-1 tubulin isotypes that are expressed in the brain. Temporal and spatial expression studies of the tba-1 gene using Northern blot analysis and tba-1::lacZ fusion gene expression analysis during embryonic and the postembryonic development of C. elegans reveal that the tba-1 tubulin is preferentially expressed in the nematode nervous system, especially in a set of mechanosensory neurons and a set of ventral cord motor neurons (DA, DB, VA, and VB) during embryonic and postembryonic development. Our results indicate an inter-species conservation of the alpha tubulin carboxyl-terminal domain in functionally related brain specific isotypes from metazoans as divergent as mammals and nematodes. These results also suggest specificity of the individual alpha tubulin isotypes during neural ------------------- Key: 2177 Medline: 95263662 Authors: Goldstein B Title: Cell contacts orient some cell divisions axes in the Caenorhabditis elegans embryo. Citation: Journal of Cell Biology 129: 1071-1080 1995 Type: ARTICLE Genes: Abstract: Cells of the early Caenorhabditis elegans embryo divide in an invariant pattern. Here I show that the division axes of some early cells (EMS and E) are controlled by specific cell-cell contacts (EMS-P-2 or E-P-3 contact). Altering the orientation of contact between these cells alters the axis along which the mitotic spindle is established, and hence the orientation of cell division. Contact-dependent mitotic spindle orientation appears to work by establishing a site of the type described by Hyman and White (1987. J. Cell Biol. 105:2123-2135) in the cortex of the responding cell: one centrosome moves toward the site of cell-cell contact during centrosome rotation in both intact embryos and reoriented cell pairs. The effect is especially apparent when two donor cells are placed on one side of the responding cell: both centrosomes are ''captured,'' pulling the nucleus to one side of the cell. No centrosome rotation occurs in the absence of cell-cell contact, nor in nocodazole-treated cell pairs. The results suggest that some of the cortical sites described by Hyman and White are established cell autonomously (in P-1, P-2, and P-3), and some are established by cell-cell contact (in EMS and E). Additional evidence presented here suggests that in the EMS cell, contact-dependent spindle orientation ensures a cleavage plane that will partition developmental information, received by induction, to one of EMS's daughter cells. ------------------- Key: 2178 Medline: 95263663 Authors: Otsuka AJ;Franco R;Yang B;Shim K-H;Tang LZ;Zhang YY;Boontrakulpoontawee P;Jeyaprakash A;Hedgecock E;Wheaton VI; Title: An ankyrin-related gene (unc-44) is necessary for proper axonal guidance in Caenorhabditis elegans. Citation: Journal of Cell Biology 129: 1081-1092 1995 Type: ARTICLE Genes: mut-2 mut-6 unc-44 Abstract: Caenorhabditis elegans unc-44 mutations result in aberrant axon guidance and fasciculation with inappropriate partners. The unc-44 gene was cloned by transposon tagging, and verified by genetic and molecular analyses of six transposon-induced alleles and their revertants. Nucleotide sequence analyses demonstrated that unc-44 encodes a series of putative ankyrin-related proteins, including AO49 ankyrin (1815 aa, 198.8 kD), AO66 ankyrin (1867 aa, 204 kD), and AO13 ankyrin (less than or equal to 4700 aa, less than or equal to 517 kD). In addition to the major set of similar to 6 kb alternatively spliced transcripts, minor transcripts were observed at similar to 3, 5, 7, and 14 kb. Evidence is provided that mutations in the similar to 14-kb AO13 ankyrin transcript are responsible for the neuronal defects. These molecular studies provide the first evidence that ankyrin-related molecules are required for axonal ------------------- Key: 2179 Medline: 95263667 Authors: Gettner SN;Kenyon C;Reichardt LF Title: Characterization of beta-pat-3 heterodimers, a family of essential integrin receptors in C. elegans. Citation: Journal of Cell Biology 129: 1127-1141 1995 Type: ARTICLE Genes: pat-3 Abstract: Members of the integrin family of cell surface receptors have been shown to mediate a diverse range of cellular functions that require cell-cell or cell-extracellular matrix interactions. We have initiated the characterization of integrin receptors from the nematode Caenorhabditis elegans, an organism in which genetics can be used to study integrin function with single cell resolution. Here we report the cloning of an integrin beta subunit from C. elegans which is shown to rescue the embryonic lethal mutation pat-3(rh54) and is thus named beta pat-3. Analysis of the deduced amino acid sequence revealed that beta pat-3 is more similar to Drosophila integrin beta PS and to vertebrate integrin beta(1) than to other integrin beta subunits. Regions of highest homology are in the RGD-binding region and in the cytoplasmic domain. In addition, the 56 cysteines present in the majority of integrin beta subunits are conserved. A major transcript of similar to 3 kilobase pairs was detected by RNA blot analysis. Immunoblot analysis using a polyclonal antiserum against the cytoplasmic domain showed that beta pat-3 migrates in SDS-PAGE with apparent M(r) of 109 k and 120 k under nonreducing and reducing conditions, respectively. At least nine protein bands with relative molecular weights in the range observed for known integrin alpha subunits coprecipitate with beta pat-3, and at least three of these bands migrate in SDS-PAGE with increased mobility when reduced. This behavior has been observed for a majority of integrin alpha subunits. Immunoprecipitations of beta pat-3 from developmentally staged populations of C elegans showed that the expression of several of these bands changes during development. The monoclonal antibody MH25, which has been postulated to recognize the transmembrane component of the muscle dense body structure (Francis, G. R., and R. H. Waterston. 1985. Muscle organization in Caenorhabditis elegans: localization of proteins implicated in thin filament attachment and I-band organization. J. Cell Biol. 101:1532-1549), was shown to recognize beta pat-3. Finally, immunocytochemical analysis revealed that beta pat-3 is expressed in the embryo and in many cell types postembryonically, including muscle, somatic gonad, and coelomocytes, suggesting multiple roles for integrin heterodimers containing this beta subunit in the developing ------------------- Key: 2180 Medline: 95262626 Authors: Broeks A;Janssen HWRM;Calafat J;Plasterk RHA Title: A P-glycoprotein protects Caenorhabditis elegans against natural toxins. Citation: EMBO Journal 14: 1858-1866 1995 Type: ARTICLE Genes: pgp-1 pgp-3 Abstract: P-glycoproteins can cause resistance of mammalian tumor cells to chemotherapeutic drugs. They belong to an evolutionarily well-conserved family of ATP binding membrane transporters. Four P-glycoprotein gene homologs have been found in the nematode Caenorhabditis elegans; this report describes the functional analysis of two, We found that PGP-3 is expressed in both the apical membrane of the excretory cell and in the apical membrane of intestinal cells, whereas PGP-1 is expressed only in the apical membrane of the intestinal cells and the intestinal valve. By transposon-mediated deletion mutagenesis we generated nematode strains with deleted P-glycoprotein genes and found that the pgp-3 deletion mutant, but not the pgp-1 mutant, is sensitive to both colchicine and chloroquine. Our results suggest that soil nematodes have P-glycoproteins to protect themselves against toxic compounds made by plants and microbes in the rhizosphere. ------------------- Key: 2181 Medline: 95262900 Authors: Varkey JP;Muhlrad PJ;Minniti AN;Do B;Ward S Title: The Caenorhabditis elegans spe-26 gene is necessary to form spermatids and encodes a protein similar to the actin-associated proteins kelch and scruin. Citation: Genes & Development 9: 1074-1086 1995 Type: ARTICLE Genes: mec-3 spe-26 sup-7 eDf18 eDf19 mDf7 sDf2 Abstract: Six independent mutations in the Caenorhabditis elegans spe-26 gene cause sterility in males and hermaphrodites by disrupting spermatogenesis. Spermatocytes in mutants with the most severe alleles fail to complete meiosis and do not form haploid spermatids. Instead, these spermatocytes arrest with missegregated chromosomes and mislocalized actin filaments, endoplasmic reticulum and ribosomes. In spite of this arrest some of the nuclei and the organelles that normally transport sperm-specific components to the spermatid mature as if they were in spermatids. The spe-26 gene is expressed throughout the testis in both spermatogonial cells and spermatocytes. It encodes a 570-amino acid polypeptide, which contains five tandem repeat motifs, each of similar to 50 amino acids. These repeats are similar in sequence to repeats in the Drosophila kelch protein, in the invertebrate sperm protein scruin that cross-links actin filaments, as well as in the mouse and pox virus proteins. The functional importance of these repeat motifs is shown by the fact that five of the spe-26 mutations are in the tandem repeats, and one of the most severe mutations is a substitution in a highly conserved glycine. These results suggest that spe-26 encodes a cytoskeletal protein, perhaps actin binding, which is necessary to segregate the cellular components that form haploid spermatids. ------------------- Key: 2182 Medline: 95287857 Authors: Clark DV;Suleman DS;Beckenbach KA;Gilchrist EJ;Baillie DL Title: Molecular cloning and characterization of the dpy-20 gene of Caenorhabditis elegans. Citation: Molecular & General Genetics 247: 367-378 1995 Type: ARTICLE Genes: col-5 dpy-20 mut-6 nDf27 sDf7 sDf8 sDf9 sDf19 sDf61 sDf65 Abstract: We describe the molecular analysis of the dpy-20 gene in Caenorhabditis elegans. Isolation of genomic sequences was facilitated by the availability of a mutation that resulted from insertion of a Tcl transposable element into the dpy-20 gene. The Tcl insertion site in the m474::Tcl allele was identified and was found to lie within the coding region of dpy-20. Three revertants (two wild-type and one partial revertant) resulted from the excision of this Tcl element. Genomic dpy-20 clones were isolated from a library of wild-type DNA and were found to lie just to the left of the unc-22 locus on the physical map, compatible with the position of dpy-20 on the genetic map. Cosmid DNA containing the dpy-20 gene was successfully used to rescue the mutant phenotype of animals homozygous for another dpy-20 allele, e1282ts. Sequence analysis of the putative dpy-20 homologue in Caenorhabditis briggsae was performed to confirm identification of the coding regions of the C. elegans gene and to identify conserved regulatory regions. Sequence analysis of dpy-20 revealed that it was not similar to other genes encoding known cuticle components such as collagen or cuticulin. The dpy-20 gene product, therefore, identifies a previously unknown type of protein that may be directly or indirectly involved in cuticle function. Northern blot analysis showed that dpy-20 is expressed predominantly in the second larval stage and that the mRNA is not at all abundant. Data from temperature shift studies using the temperature-sensitive allele e1282ts showed that the sensitive period also occurs at approximately the second larval stage. Therefore, expression of dpy-20 mRNA and function of the DPY-20 protein are closely linked temporally. ------------------- Key: 2183 Medline: Authors: Guven K;de Pomerai DI Title: Differential expression of hsp70 proteins in response to heat and cadmium in Caenorhabditis elegans. Citation: Journal of Thermal Biology 20: 355-363 1995 Type: ARTICLE Genes: Abstract: 1. The patterns of HSP70 expression induced in Caenorhabditis elegans by mild (31 degrees C) or severe (34 degrees C) heat shock, and by cadmium ions at 31 degrees C, have been compared with those expressed constitutively ill 20 degrees C controls by 1- and a-dimensional immunoblotting. 2. The 2D spot patterns become more complex with increasing severity of stress (34 degrees C > 31 degrees C + Cd > 31 degrees C > 20 degrees C). 3. A stress-inducible transgene construct is minimally active at 31 degrees C, but is abundantly expressed in the presence of cadmium or at 34 degrees C. 4. Differing degrees or types of stress may differentially induce available hsp70 ------------------- Key: 2184 Medline: 95273182 Authors: Melov S;Lithgow GJ;Fischer DR;Tedesco PM;Johnson TE Title: Increased frequency of deletions in the mitochondrial genome with age of Caenorhabditis elegans. Citation: Nucleic Acids Research 23: 1419-1425 1995 Type: ARTICLE Genes: age-1 fer-15 spe-9 Abstract: We have developed a long-extension-PCR strategy which amplifies approximately half of the mitochondrial genome (6.3 kb) of Caenorhabditis elegans using an individual worm as target. We analyzed three strains over their life span to assess the number of detectable deletions in the mitochondrial genome. Two of these strains are wild-type for life span; while the third is mutant in the age-1 gene, approximately doubling its maximum life span. At the mean life span in wild-type strains, there was a significant difference between the frequency of deletions detected in the mitochondrial genome compared with the mean number of deletions in young animals. In addition, deletions in the mitochondrial genome occur at a significantly lower rate in age-1 mutants as compared with wild type. We cloned and identified the breakpoints of two deletions and found that one of the deletions had a direct repeat of 8 bp at the breakpoint. This is the largest single study (over 900 individual animals) characterizing the frequency of deletions in the mitochondrial genome as a function of age yet carried out. ------------------- Key: 2185 Medline: 95263507 Authors: Waldmann R;Champigny G;Lazdunski M Title: Functional degenerin-containing chimeras identify residues essential for amiloride-sensitive Na+ channel function. Citation: Journal of Biological Chemistry 270: 11735-11737 1995 Type: ARTICLE Genes: mec-4 Abstract: The highly selective, amiloride-sensitive Na+ channel is formed of three homologous subunits termed alpha, beta, and gamma. The three subunits exhibit similarities with Caenorhabditis elegans proteins called degenerins involved in sensory touch transduction and, when mutated, in neurodegeneration. Swelling of neurons observed in neurodegeneration suggests an involvement of ion transport, but the channel function of degenerins has not yet been demonstrated. We used chimeras to study the functional relationship between the epithelial sodium channel and the degenerin Mec-4. Exchange of the hydrophobic domains of the Na+ channel alpha subunit by those of Mec-4 results in a functional ion channel with changed pharmacology for amiloride and benzamil and changed selectivity, conductance, gating, and voltage dependence. All of these differences were also obtained by exchanging Ser-589 and Ser-593 in the second transmembrane region by the corresponding residues of Mec-4, suggesting that these two residues are essential for the ionic pore function of the ------------------- Key: 2186 Medline: 95309110 Authors: Svendsen PC;McGhee JD Title: The C. elegans neuronally expressed homeobox gene ceh-10 is closely related to genes expressed in the vertebrate eye. Citation: Development 121: 1253-1262 1995 Type: ARTICLE Genes: ceh-10 Abstract: We describe the homeobox gene ceh-10 from the nematode Caenorhabditis elegans. The homeodomain of ceh-10 is closely related to the homeodomains of two genes recently cloned from the vertebrate retina, Chx10 from mice and Vsx-1 from goldfish. We show that the sequence conservation extends well beyond the homeodomain and includes a region (named the CVC domain) of roughly 60 amino acids immediately C-terminal to the homeodomain. As assayed in transgenic worms, the promoter region of ceh-10 directs expression of a lacZ reporter gene to a small number of neurons. We draw a parallel between the bipolar cells of the inner nuclear layer of the vertebrate retina, which express Chx10 and Vsx-1, and an interneuron in C. elegans called AIY, which expresses ceh-10. AIY receives synaptic input from a sensory cell, just as do bipolar cells of the vertebrate retina. In C. elegans, the sensory cell AFD is not known to be photosensitive but is known to be thermosensitive; moreover, a cell with similar position in the amphids of other nematodes has been suggested indeed to be photosensitive. Our results emphasize the highly conserved nature of sensory regulatory mechanisms and suggest one way in which photosensitive organelles might have originated in evolution. ------------------- Key: 2187 Medline: 95309136 Authors: Hutter H;Schnabel R Title: Specificaton of anterior-posterior differences within the AB lineage in the C. elegans embryo - A polarising Citation: Development 121: 1559-1568 1995 Type: ARTICLE Genes: Abstract: In a C. elegans embryo the third cleavages of descendants of the anterior blastomere AB of the 2-cell stage create pairs of blastomeres that develop differently. By laser ablation experiments we show that the fates of all the posterior daughters of this division depend on an induction occurring three cleavages before these blastomeres are born. The time of induction precludes a direct effect on cell fate. Alternatively, we suggest that the induction creates a heritable cell polarity which is propagated through several divisions. We suggest a model to demonstrate how a signal could be propagated through several rounds of cell division. An important implication of our observations is that this early induction acts to specify blastomere identity, not tissue type. A detailed lineage analysis revealed that altering the inductive signal alters complex lineage patterns as a whole. The induction described here, together with two inductions described previously can be used to illustrate how the anterior portion of the C. elegans embryo can be successively subdivided into blastomeres with unique ------------------- Key: 2188 Medline: 95292971 Authors: Ahringer J Title: Embryonic tissue differentiation in Caenorhabditis elegans requires dif-1, a gene homologous to mitochondrial solute carriers. Citation: EMBO Journal 14: 2307-2316 1995 Type: ARTICLE Genes: ced-4 dif-1 hlh-1 nDf41 Abstract: The dif-1 gene was identified in a general screen for maternal-effect embryonic lethal (Mel) mutants, dif-1 mutant embryos complete gastrulation and embryonic cell division normally, but then arrest development with only a small amount of tissue differentiation. Either maternal or zygotic dif-1 activity is sufficient for wild-type development. The temperature-sensitive period of a cold-sensitive dif-1 mutant shows that dif-1 activity is essential only for 3 h, corresponding to the major period of embryonic tissue differentiation, and is not required post-embryonically. The results point to a role for dif-1 in the maintenance of tissue differentiation in the developing embryo, but not for its initiation. Cloning and sequencing of the dif-1 gene revealed that its product is homologous to proteins in the mitochondrial carrier family. Although dif-1 activity is required only during embryogenesis, dif-1 RNA is expressed at all stages of development. In situ hybridization to embryos showed that dif-1 RNA is initially present in all cells of the embryo; this most likely corresponds to maternal dif-1 RNA. Later, the presumable zygotic dif-1 RNA is found only in the gut and hypodermis of the embryo. This tissue-specific expression raises the possibility that the dif-1 protein acts non-cell autonomously and that some communication or molecular transport dependent on DIF-1 takes place during embryonic tissue differentiation. dif-1 is the first mitochondrial carrier homologue known to be needed ------------------- Key: 2189 Medline: 95277848 Authors: Guo S;Kemphues KJ Title: par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Citation: Cell 81: 611-620 1995 Type: ARTICLE Genes: par-1 skn-1 Abstract: The first cleavage of C. elegans is asymmetric, generating daughter cells with different sizes, cytoplasmic components, and fates. Mutations in the par-1 gene disrupt this asymmetry. We report here that par-1 encodes a putative Ser/Thr kinase with similarity to kinases from yeasts and mammals, Two strong alleles have mutations in the kinase domain, suggesting that kinase activity is essential for par-1 function. PAR-1 protein is localized to the posterior periphery of the zygote and is distributed in a polar fashion preceding the asymmetric divisions of the germline lineage. Because PAR-1 distribution in the germline correlates with the distribution of germline-specific P granules, it is possible that PAR-1 functions in germline development as well as in ------------------- Key: 2190 Medline: 95305849 Authors: Bowerman B Title: Determinants of blastomere identity in the early C. elegans embryo. Citation: BioEssays 17: 405-414 1995 Type: ARTICLE Genes: apx-1 glp-1 mex-1 pie-1 skn-1 Abstract: Genetic and molecular studies of development in Caenorhabiditis elegans have identified regulators that appear to control pattern formation in the cellularized nematode embryo. Two genes, skn-1 and pie-1, are required for specifying the different identities of two sister blastomeres in a 4-cell embryo, called P2 and EMS. The skn-1 gene encodes a DNA binding protein that may control blastomere development by regulating transcription in EMS and its descendants. ABa and ABp, the other two sisters in a 4-cell embryo, are influenced to develop differently by cell signaling events that require the two genes apx-1 and glp-1. In this review, I summarize evidence that some or all of these genes may encode embryonic determinants of blastomere identity. ------------------- Key: 2191 Medline: 95281224 Authors: Van Etten RA;Debnath J;Zhou H;Casasnovas JM Title: Introduction of a loss-of-function point mutation from the SH3 region of the Caenorhabditis elegans sem-5 gene activates the transforming ability of c-Abl in vivo and abolishes bin Citation: Oncogene 10: 1977-1988 1995 Type: ARTICLE Genes: sem-5 Abstract: We have introduced two loss-of-function point mutations from highly conserved regions of the src homology 3 (SH3) domains of the Caenorhabditis elegans sem-5 gene into the SH3 domain of the murine type IV c-abl tyrosine kinase proto-oncogene. One of the mutations, P131L, activated abl to transform fibroblasts while tbe other, G128R, did not. When combined with independent activating mutations in the c-abl kinase domain or NH,terminus, the G128R mutation blocked transformation by the double mutant, suggesting that the G128R mutant was unable to transform cells for trivial reasons. The c-Abl G128R mutant, like wild type c-Abi protein, was localized to the nucleus and actin cytoskeleton and had normal tyrosine kinase activity in vitro, while the transforming c-Abl P131L protein was localized exclusively to the cytoplasm and exhibited decreased in vitro kinase activity. By real-time biospecific interaction analysis, the wild type Abl SH3 domain bound to two proteins containing proline-rich motifs with dissociation constants of 0.2 and 17 mu M; the G128R mutant bound with 50-fold lower affinity, and no binding was detected by the P131L mutant. Both mutations completely abolished binding of the Abl SH3 domain to proline-rich target proteins in a filter-binding assay, These results suggest that the transforming activity of Abl is regulated in vivo by an inhibitor protein which associates with the ------------------- Key: 2192 Medline: 95333196 Authors: Glasner JD;Kocher TD;Collins JJ Title: Caenorhabditis elegans contains genes encoding two new members of the Zn-containing alcohol dehydrogenase family. Citation: Journal of Molecular Evolution 41: 46-53 1995 Type: ARTICLE Genes: Abstract: We have characterized two cDNA clones from the nematode Caenorhabditis elegans that display similarity to the alcohol dehydrogenase (ADH) gene family. The nucleotide sequences of these cDNAs predict that they encode Zn-containing long-chain ADH enzymes. Phylogenetic analysis suggests that one is most similar to dimeric class III ADHs found in diverse taxa; the other is most similar to the tetrameric forms of ADH previously described only in fungi. ------------------- Key: 2193 Medline: 95301560 Authors: Hawkins MG;McGhee JD Title: elt-2, a second GATA factor from the nematode Caenorhabditis elegans. Citation: Journal of Biological Chemistry 270: 14666-14671 1995 Type: ARTICLE Genes: elt-1 elt-2 ges-1 Abstract: We have previously shown that a tandem pair of (A/T)GATA(A/G) sequences in the promoter region of the Caenorhabditis elegans gut esterase gene (ges-1) controls the tissue specificity of ges-1 expression in vivo. The ges-1 GATA region was used as a probe to screen a C. elegans cDNA expression library, and a gene for a new C. elegans GATA-factor (named elt-2) was isolated. The longest open reading frame in the elt-2 cDNA codes for a protein of M(r) 47,000 with a single zinc finger domain, similar (approximately 75% amino acid identity) to the C-terminal fingers of all other two-fingered GATA factors isolated to date. A similar degree of relatedness is found with the single-finger DNA binding domains of GATA factors identified in invertebrates. An upstream region in the ELT 8 protein with the sequence C-X(2)-C-X(16)-C-X(2)-C has some of the characteristics of a zinc finger domain but is highly diverged from the zinc finger domains of other GATA factors. The elt-2 gene is expressed as an SL1 trans-spliced message, which can be detected at all stages of development except oocytes; however, elt-2 message levels are 5-10-fold higher in embryos than in other stages. The genomic clone for elt-2 has been characterized and mapped near the center of the C. elegans X chromosome. ELT-2 protein, produced by in. vitro transcription-translation, binds to ges-1 GATA-containing oligonucleotides similar to a factor previously identified in C. elegans embryo extracts, both as assayed by electrophoretic migration and by competition with wild type and mutant oligonucleotides. However, there is as yet no ------------------- Key: 2194 Medline: 96120232 Authors: Macrae M;Plasterk RHA;Coffino P Title: The ornithine decarboxylase gene of Caenorhabditis elegans: cloning, mapping and mutagenesis. Citation: Genetics 140: 517-525 1995 Type: ARTICLE Genes: odc-1 ryr-1 nDf32 sDf20 Abstract: The gene (odc-1) encoding ornithine decarboxylase, a key enzyme in polyamine biosynthesis, was cloned and characterized. Two introns interrupt the coding sequence of the gene. The deduced protein contains 422 amino acids and is homologous to ornithine decarboxylases of other eukaryotic species. In vitro translation of a transcript of the cDNA yielded an enzymatically active product. The mRNA is 1.5 kb in size and is formed by trans-splicing to SL1, a common 5' RNA segment. odc-1 maps to the middle of LG V, between dpy-11 and unc-42 and near a breakpoint of the nDf32 deficiency strain. Enzymatic activity is low in starved stage 1 (L1) larva and, after feeding, rises progressively as the worms develop. Targeted gene disruption was used to create a null allele. Homozygous mutants are normally viable and show no apparent defects, with the exception of a somewhat reduced brood size. In vitro assays for ornithine decarboxylase activity, however, show no detectable enzymatic activity, suggesting that ornithine decarboxylase is dispensible for nematode growth ------------------- Key: 2195 Medline: 96120233 Authors: Nguyen M;Alfonso A;Johnson CD;Rand JB Title: Caenorhabditis elegans mutants resistant to inhibitors of acetylcholinesterase. Citation: Genetics 140: 527-535 1995 Type: ARTICLE Genes: cha-1 ric-1 ric-2 ric-3 ric-4 snt-1 unc-10 unc-11 unc-13 unc-17 unc-18 unc-32 unc-36 unc-41 unc-63 unc-64 unc-65 unc-75 unc-104 Abstract: We characterized 18 genes from Caenorhabditis elegans that, when mutated, confer recessive resistance to inhibitors of acetylcholinesterase. These include previously described genes as well as newly identified genes; they encode essential as well as nonessential functions. In the absence of acetylcholinesterase inhibitors, the different mutants display a wide range of behavioral deficits, from mild uncoordination to almost complete paralysis. Measurements of acetylcholine levels in these mutants suggest that some of the genes are involved in presynaptic functions. ------------------- Key: 2196 Medline: Authors: Ishii N;Suzuki K Title: Oxygen sensitive mutants of the nematode Caenorhabditis elegans and aging. Citation: "Oxygen Stress and Tissue Damage", J. Feher, H. Nakazawa, L. Pronai and S. Matsuzaki (eds), Akademiai Kiado, Budapest, Hungary. : 142-151 1994 Type: ARTICLE Genes: mev-1 rad-8 Abstract: It has been proposed that free radicals, especially those of molecular oxygen, may accelerate aging in animals. To investigate the possible role of oxygen free radicals in aging, mutants of the nematode Caenorhabditis elegans were isolated which are hypersensitive to methyl viologen (paraquat) and oxygen. The free-living nematode is an attractive model system for aging research on metazoans. The nematode offers the great advantages of genetic manipulability, short life span, cellular simplicity, and easy cultivation. Investigation of two genes in C. elegans should serve to illuminate the relationship between oxidative damage and aging. A mutation in one of these genes, mev-1, has been shown to reduce Cu/Zn superoxide dismutase activity by 30 to 50% relative to wild-type animals. The life spans of this mutant and a second mutant, rad-8, are significantly shortened in the presence of high oxygen concentration. We suggest that oxygen radicals may be involved in the normal aging in C. elegans. ------------------- Key: 2197 Medline: 95301085 Authors: Liu F;Thatcher JD;Barral JM;Epstein HF Title: Bifunctional glyoxylate cycle protein of Caenorhabditis elegans: A developmentally regulated protein of intestine and muscle. Citation: Developmental Biology 169: 399-414 1995 Type: ARTICLE Genes: ges-1 Abstract: The reaction of an abundant 106-kDa polypeptide with a specific monoclonal antibody has been localized in intestinal and muscle cells of the nematode Caenorhabditis elegans. This protein was first detected in 4-6 cells of the clonal E lineage of 100-cell embryos. This lineage is committed to the intestinal cell fate. The antigen continued to be expressed in the differentiating gut and then appeared in early differentiating body wall muscle cells of 400- to 500-cell embryos. Molecular cloning and sequencing showed that the largest cDNA clone contained 3274 bp and encoded a sequence of 1005 amino acids. The predicted polypeptide of 112,799 MW contains separate domains for the glyoxylate cycle enzymes isocitrate lyase and malate synthase. Their enzymatic activities had been shown previously to be highest in embryos and L1 larvae (Khan, F. R., and McFadden, B. A. (1980). FEBS Lett. 115, 312-314; Khan, F. R., and McFadden, B. A. (1982). Exp. Parasitol. 54, 48-54; Wads-worth, W. G., and Riddle, D. L. (1989). Dev. Biol. 132, 167-173). The domain-specific sequences were shown to be contiguous in genomic DNA and are separated by an intron of 68 bp. A single polypeptide and both enzymatic activities are precipitated by the antibody, and peptide fragments resulting from limited proteolytic digestion contained amino acid sequences which overlap the predicted junctional region. The physical localization of the gene correlates with a small region of the left arm of Linkage Group V to which multiple embryonic ------------------- Key: 2198 Medline: 95379434 Authors: Chitwood DJ;Lusby WR;Thompson MJ;Kochansky JP;Howarth OW Title: The glycosylceramides of the nematode Caenorhabditis elegans contain an unusual, branched-chain sphingoid base. Citation: Lipids 30: 567-573 1995 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans was cultured in semi-defined medium containing yeast extract, soy peptone, glucose, hemoglobin, Tween 80, and sitosterol. Monoglycosylceramides were chromatographically purified from nematode extracts. Their structures were elucidated with mass spectrometry, nuclear magnetic resonance spectroscopy, and analysis of methanolysis products of the parent cerebrosides. The glycosylceramides were unusual in that the only long-chain sphingoid base detected was an iso-branched compound with a C-4 double bond (i.e., 15-methyl-2-aminohexadec-4-en-1,3-diol). Glucose was the only sugar moiety detected. The fatty acids consisted of a series of primarily straight-chain, saturated, 2-hydroxylated C-20-C-26 acids; some iso-branched analogs also occurred. The sphingomyelins of C. elegans were also hydrolyzed, and the same iso-branched C-17 compound was the only sphingoid base detected. This is the first structural analysis of a nematode glycosphingolipid and the first report of an organism in which the long-chain sphingoid bases are entirely iso-branched. ------------------- Key: 2199 Medline: 96044418 Authors: Hartman PS;De Wilde D;Dwarakanath VN Title: Genetic and molecular analyses of UV radiation-induced mutations in the fem-3 gene of Caenorhabditis elegans. Citation: Photochemistry and Photobiology 61: 607-614 1995 Type: ARTICLE Genes: fem-3 rad-1 rad-3 eT1 Abstract: The utility of a new target gene (fem-3) is described for investigating the molecular nature of mutagenesis in the nematode Caenorhabditis elegans. As a principal attribute, this system allows for the selection, maintenance and molecular analysis of any type of mutation that disrupts the gene, including deletions. In this study, 86 mutant strains were isolated, of which 79 proved to have mutations in fem-3. Twenty of these originally tested as homozygous inviable. Homozygous inviability was expected, as Stewart and coworkers had previously observed that, unlike in other organisms, most UV radiation-induced mutations in C. elegans are chromosomal rearrangements of deficiencies (Mutat. Res. 249, 37-54, 1991). However, additional data, including Southern blot analyses on 48 of the strains, indicated that most of the UV radiation-induced fem-3 mutations were not deficiencies, as originally inferred from their homozygous inviability. Instead, the lethals were most likely ''coincident mutations'' in linked, essential genes that were concomitantly induced. As such, they were lost owing to genetic recombination during stock maintenance. As in mammalian cells, yeast and bacteria, the frequency of coincident mutations was much higher than would be predicted by chance. ------------------- Key: 2200 Medline: 95294725 Authors: Arevalo JI;Saz HJ;Nowak T;Larry JP Title: Glycerophosphorylcholine, a component of both Ascaris suum muscle and Caenorhabditis elegans. Citation: Journal of Parasitology 81: 335-340 1995 Type: ARTICLE Genes: Abstract: Studies of the muscle phospholipid metabolism of Ascaris suum suggest an effect of cholinergic drugs on the turnover of phosphatidylcholine and the generation of glycerophosphorylcholine (GPC(@)). P-31-nuclear magnetic resonance (NMR) studies of helminths revealed the presence of a major peak that was assigned to GPC. The primary effect of the cholinergic drugs on the parasites' phosphate profile appeared to be on the level of GPC. In in vivo studies, decreases in internal GPC concentrations occurred prior To any decrease in the concentration of ATP. The importance of these studies relies on the correct identity of this major P-31-NMR resonance. More recently, the identity of this resonance as GPC was questioned by experimental data obtained from C. elegans dauer larvae using the NMR(@) technique. Because studies from our laboratory suggested that phospholipid metabolism may be intimately connected with the parasite's responses to drugs, the identity of the assigned resonance in the P-31-NMR spectrum as GPC in Ascaris suum was reexamined and found to be correct. Similar studies with C. elegans indicate the presence of both GPC and GPE(@). ------------------- Key: 2201 Medline: Authors: Leyns F;Borgonie G;Arnaut G;De Waele D Title: Nematicidal activity of Bacillus thuringiensis isolates. Citation: Fundamental and Applied Nematology 18: 211-218 1995 Type: ARTICLE Genes: Abstract: The nematicidal activity of the spore-crystal mixtures of three Bacillus thuringiensis isolates against hatched juveniles and adults of Caenorhabditis elegans was investigated. Toxicity was determined by adding 50-ul aliquots of the spore-crystal mixtures to microtitre plate wells containing 50-ul aqueous suspensions of 200-400 hatched juveniles and adults of C. elegans. Nematode mortality was observed from 8 hours incubation onwards; after 24 hours incubation no more significant increases in nematode mortality occurred. Nematode mortality varied from about 50 to 60% when the nematicidal activity was tested in distilled water and was usually somewhat higher (but less than 10%) when tested in axenic medium. Toxicity varied between the three isolates. Concentrations of at least 10*8 particles/ml were necessary to cause a nematode mortality higher than 30%. Nematicidal activity was only observed when spore-crystal mixtures from at least 2-day-old cultures, consisting of about 50% of vegetative cells, often containing a spore, and for about 50% of a mixture of spores and crystals, were used. Heating to 75C and higher for 24 hours and autoclaving at 120C for 20 min destroyed the nematicidal activity of all three isolates. Differences in stability of the nematicidal activity were observed between the three isolates. In two isolates the nematicidal activity did not decline after storage at 28C for 15 days; in the third isolate the nematicidal activity declined after storage at 28C for 7 days. Multiple freezing at -20C or -70C and thawing had no effect on the nematicidal activity of two isolates but decreased the nematicidal activity of the third isolate. pH changes resulted in differences in stability of the nematicidal activity between the three isolates. These results may indicate the presence of different toxins. ------------------- Key: 2202 Medline: Authors: Borgonie G;Claeys M;Vanfletteren J;De Waele D;Coomans A Title: Presence of peritrophic-like membranes in the intestine of three bacteriophagous nematodes (Nematoda: Rhabditida). Citation: Fundamental and Applied Nematology 18: 227-233 1995 Type: ARTICLE Genes: Abstract: Ultrastructural analysis shows the presence of membranes originating at the top of the intestinal microvilli, along the entire length of the intestine in the three rhabditid nematodes Caenorhabditis elegans, Panagrolaimus superbus and Acrobeloides maximus. The membranes allow the passage of fluorescein isothiocyanate, methyl red, neutral red and acridine orange, but allow only sparse passage of ferritin molecules. Upon the introduction of a sublethal dose of sodium azide, the intestinal lumen displays an increased secretion of membrane layers. Whole mount staining of the nematodes with the Solanum tuberosum and Triticum vulgare lectins, known to bind with high affinity to chitin, shows only specific binding of Solanum tuberosum lectin to the brush border in all developmental stages of C. elegans, P. superbus and A. maximus. The results reveal the presence of membranes in the intestine of three species of one of the most ancient metazoan phyla, exhibiting morphological and functional characteristics reminiscent of peritrophic membranes in insects. ------------------- Key: 2203 Medline: 95392824 Authors: Maine EM;Lissemore JL;Starmer WT Title: A phylogenetic analysis of vertebrate and invertebrate Notch-related genes. Citation: Molecular Phylogenetics and Evolution 4: 139-149 1995 Type: ARTICLE Genes: glp-1 lin-12 Abstract: Members of the Notch gene family are thought to mediate inductive cell-cell interactions during development of a wide variety of vertebrates and invertebrates. These genes encode transmembrane proteins that appear to act as receptors and contain three repeated sequence motifs. Two of these motifs (an epidermal growth factor-like sequence and a cdc10/SWI6/ankyrin sequence) have been found in a large number of unrelated proteins, while the third motif (a lin-12/Notch/glp-1 sequence) is unique to proteins of the Notch family. We present a phylogenetic analysis of 17 Notch-related genes from eight species that has implications as to the origins and relative functions of these genes in different species. Several independent gene duplications have occurred and at least one such duplication in the vertebrate lineage preceded the avian/mammalian divergence. Signficantly, the overall organizatin of individual members of each internally repeated motif appears to have been conserved among species, suggesting that each repeat plays a unique role in protein function. Yet, where sequence divergence does occur among genes in vertebrate, dipteran, and nematode lineages, it may signify functional differences for ------------------- Key: 2204 Medline: 94361670 Authors: Schwartz LM;Osborne BA Title: Ced-3/ICE: Evolutionarily conserved regulation of cell death. Citation: BioEssays 16: 387-389 1994 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: If treated harshly, any cell can be induced to die. These pathological deaths typically occur by necrosis, a passive process that involves membrane disruption, cellular swelling and ultimately, cellular lysis. Less well appreciated is the observation that many, if not most, of the cells that die during an organism's life, commit suicide. Instead of swelling, these cells become condensed and in most cases, undergo stereotypic changes in their surface and nuclear morphology that has been termed apoptosis . Another feature of most apoptotic deaths, is the double-stranded cleavage of genomic DNA by an endogenous DNAse . Interestingly, not all cells that undergo programmed cell death exhibit these apoptotic ------------------- Key: 2205 Medline: 95006661 Authors: Austin J;Kenyon C Title: Marking time with antisense. Citation: Current Biology 4: 366-369 1994 Type: REVIEW Genes: lin-4 lin-14 Abstract: For development to progress from fertilized egg to complex organism, gene expression must be controlled in both time and space. We have already begun to understand many of the mechanisms that underlie the spatial control of gene expression. But less is known about how gene expression is controlled over time to create the ordered sequence of growth and differentiation that will result in a mature organism. ------------------- Key: 2206 Medline: 95403581 Authors: Kreutzer MA;Richards JP;De Silva-Udawatta MN;Temenak JJ;Knoblich JA;Lehner CF;Bennett KL Title: Caenorhabditis elegans cyclin A- and B-type genes: a cyclin A multigene family, an ancestral cyclin B3 and differential germline expression. Citation: Journal of Cell Science 108: 2415-2424 1995 Type: ARTICLE Genes: fem-1 fem-3 glp-4 him-5 Abstract: We have cloned cDNAs for Caertorhabditis elegans cyclins A1, B and B3. While cyclins A1 and B are most closely related to either A- or B-type cyclins of other species, cyclin B3 is less related to these cyclins. However, this cyclin is most similar to the recently identified chicken cyclin B3. Our identification of a Caenorhabditis homolog demonstrates that cyclin B3 has been conserved in evolution, cyclin A1 is a member of an A-type multigene family; however the cyclin A1 cDNA only recognizes a single band on northern blots, A single-sized RNA is also observed for the cyclin B3 cDNA. In contrast, three different transcripts are observed for the cyclin B cDNA. Based on our analyses using RNAs from germline-defective mutants and from populations enriched for males, one cyclin B transcript is specific to the paternal germline. The two other cyclin B transcripts, as well as the cyclin A1 and cyclin B3 transcripts, are most abundant in the maternal germline and are only present at low levels in other tissues. Moreover, the 3' untranslated regions of each Caenorhabditis cyclin cDNA possess several copies of potential translational control elements shown in Xenopus and Drosophila maternal cyclin mRNAs to function during ------------------- Key: 2207 Medline: 95324810 Authors: Jones AR;Schedl T Title: Mutations in gld-1, a female germ cell-specific tumor suppressor gene in Caenorhabditis elegans, affect a conserved domain also found in Src-associated protein Citation: Genes & Development 9: 1491-1504 1995 Type: ARTICLE Genes: fem-1 fem-3 gld-1 glp-1 nDf24 nDf25 ozDf5 Abstract: The gld-1 gene of Caenorhabditis elegans is a germ-line-specific tumor suppressor gene that is essential for oogenesis. We have cloned the gld-1 gene and find that it encodes two proteins that differ by 3 amino acids. The predicted proteins contain a similar to 170-amino-acid region that we term the GSG domain (GRP33/Sam68/GLD-1), on the basis of significant similarity between GLD-1, GRP33 from shrimp, and the Src-associated protein Sam68 from mouse (also described as GAPap62 from humans). A conserved structural motif called the KH domain is found within the larger GSG domain, suggesting a biochemical function for GLD-1 protein in binding RNA. The importance of the GSG domain to the function of gld-1 in vivo is revealed by mutations that affect 5 different conserved GSG domain residues. These include missense mutations in an absolutely conserved residue of the KH domain that eliminate the tumor suppressor function of gld-1. ------------------- Key: 2208 Medline: Authors: Krause M;Weintraub H Title: CeMyoD expression and myogenesis in C. elegans. Citation: Seminars in Developmental Biology 3: 277-285 1992 Type: REVIEW Genes: hlh-1 mec-7 myo-2 Abstract: Like its vertebrate counterparts, the nematode Caenorhabditis elegans has a myogenic regulatory factor, CeMyoD, that is expressed very early in muscle development. The temporal and spatial pattern of CeMyoD expression, along with its sequence and functional similarities to the vertebrate MyoD family, suggests that it plays an important role in myogenesis also. However, genetic studies show that zygotic CeMyoD is not required for myogenesis in the nematode. This surprising result is leading to a reconsideration of the role of MyoD family members in invertebrate muscle development. ------------------- Key: 2210 Medline: 95361772 Authors: Schnabel R Title: Duels without obvious sense - Counteracting inductions involved in body-wall muscle development in the Caenorhabditis elegans embryo. Citation: Development 121: 2219-2232 1995 Type: ARTICLE Genes: Abstract: During the first four cleavage rounds of the Caenorhabditis elegans embryo, five somatic founder cells AB, MS, E, C and D are born, which later form the tissues of the embryo. The classical criterion for a cell-autonomous specification of a tissue is the capability of primordial cells to produce this tissue in isolation from the remainder of the embryo. By this criterion, the somatic founder cells MS, C and D develop cell-autonomously, Laser ablation experiments, however, reveal that within the embryonic context these blastomeres form a network of duelling cellular interactions. During normal development, the blastomere D inhibits muscle specification in the MS and the C lineage inhibits muscle specification in the D lineage. These inhibitory interactions are counteracted by two activating inductions. As described before the inhibition of body wall muscle in MS is counteracted by an activating signal from the ABa lineage. Body wall muscle in the D lineage is induced by MS descendants, which suppress an inhibitory activity of the C lineage. The interaction between the D and the MS lineage occurs through the C lineage. An interesting feature of these cell-cell interactions is that they do not serve to discriminate between equivalent cells but are permissive or nonpermissive inductions. No evidence was found that the C-derived body wall muscle also depends on an induction, which suggests that possibly three different pathways coexist in the early embryo to specify body wall muscle, two of which are, in different ways, influenced by cell-cell interactions and a third that is autonomous. This work supplies evidence that cells may acquire transient states during embryogenesis that influence the specification of other cells in the embryo. These states, however, may not be reflected in the developmental potentials of the cells themselves. They can only be scored indirectly by their action on the specification of other cells in the embryo. Blastomeres that behave cell-autonomously in isolation are nevertheless subjected to cell-cell interactions in the embryonic context. Why this should be is an intriguing question. The classical notion has been that blastomeres are specified autonomously in nematodes. In recent years, it was established that at least five inductions are required to determine the AB descendants of C. elegans, whereas the P1 descendants have been typically viewed to develop more autonomously. It appears now that inductions also play a major role during the determination of P1-derived ------------------- Key: 2211 Medline: 96063083 Authors: Sternberg PW;Yoon CH;Lee J;Jongeward GD;Kayne PS;Katz WS;Lesa G;Liu J;Golden A;Huang LS;Chamberlin HM Title: Molecular genetics of proto-oncogenes and candidate tumor suppressors in Caenorhabditis elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 59: 155-163 1994 Type: ARTICLE Genes: let-23 let-60 lin-2 lin-3 lin-7 lin-10 lin-12 lin-15 lin-45 mek-1 mpk-1 rok-1 sem-5 sli-1 sur-1 unc-101 Abstract: Analysis of C. elegans vulval differentiation has led to the definition of a signaling pathway involving nematode homologs of mammalian proto-oncogenes. Results of this analysis led to the placement of ras downstream from a receptor tyrosine kinase, placement of SEM-5/GRB-2 upstream of ras, and raf downstream from ras. These results helped set the stage for the biochemical definition of a "universal" tyrosine kinase/ras pathway. Our current efforts use vulval differentiation to identify new genes involved in intercellular signaling and to elucidate their roles with respect to this universal signaling pathway. The current molecular genetics of C. elegans utilizes the powerful self-fertilizing hermaphrodite genetics, facile description of phenotypes at a cellular level, easy construction of transgenic animals, and an advanced genomic map with almost complete ordering of cosmid and YAC clones and more than 6% of genomic sequences as well as partial random cDNA sequence. Here we describe our uses of C. elegans molecular genetics to identify new genes that act in, or regulate, this universal signaling pathway. This pathway mediates several intercellular signaling events during nematode development, including vulval induction in the hermaphrodite (essentially a female that makes sperm as well as oocytes) and spicule development in the male copulatory tail. ------------------- Key: 2212 Medline: 96063106 Authors: Horvitz HR;Shaham S;Hengartner MO Title: The genetics of programmed cell death in the nematode Caenorhabditis elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 59: 377-385 1994 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ces-1 ces-2 egl-1 nuc-1 nDf41 Abstract: Cancerous growth often results from an increased rate of cell proliferation caused by the abnormal activatin of a signal transduction pathway that normally stimulates cell division only in response to growth factor signals; many of the proto-oncogenes that have been characterized function in or respond to such intercellular signaling pathways. Recent findings indicate that cancerous growth also can result from a decreased rate of cell loss. The most striking example is provided by human B-cell follicular ------------------- Key: 2213 Medline: 94040262 Authors: Muimo R;Isaac RE Title: Metabolism of 5-HT in the nematode Caenorhabditis elegans: Identification of a 5-HT N-acetyltransferase that is developmentally regulated. Citation: Biochemical Society Transactions 21: 295S- 1993 Type: ARTICLE Genes: egl-1 egl-5 egl-10 Abstract: It is generally assumed that biogenic amines function as neurotransmitters and/or hormones in nematodes. Histochemcial techniques have been used to demonstrate the existence of aminergic neurons in a variety of nematodes and a number of studies have reported the presence of biogenic amines in extracts of nematode tissues. There is little known about the precise roles and mechanisms of action of many of these putative neurotransmitters in nematodes, apart from serotonin (5-HT), which appears to be an important intercellular signalling molecule in the free-living nematode, Caenorhabditis elegans and the parasitic nematode, Ascaris suum. ------------------- Key: 2214 Medline: 95356816 Authors: Mori I;Ohshima Y Title: Neural regulation of thermotaxis in Caenorhabditis elegans. Citation: Nature 376: 344-348 1995 Type: ARTICLE Genes: tax-2 tax-4 tax-6 ttx-1 ttx-3 unc-86 Abstract: Thermal stimulus is an important environmental factor influencing animal behaviour(1). However, the mechanisms underlying thermosensation and thermal adaptation are poorly understood. The nematode Caenorhabditis elegans can sense a range of environmental temperatures and migrate towards the cultivation temperature on a thermal gradient(2). This modifiable thermotactic response provides an ideal system for studying the cellular and molecular processes involved in thermosensation and thermal information storage. We have identified neurons critical for thermotaxis by killing individual cells in live animals. The results indicate that an amphid sensory neuron, AFD, is a major thermosensory neuron. Some of the genetically defined cryophilic and thermophilic mutant phenotypes were mimicked when amphid interneurons AIY and AIZ, respectively, were killed, indicating that AIY is responsible for thermophilic movement and AIZ for cryophilic movement. We propose a neural model in which regulation of the activities of the two interneurons in opposite directions, depending on the cultivation ------------------- Key: 2215 Medline: 95354196 Authors: Kenyon C Title: A perfect vulva every time: Gradients and signaling cascades in C. elegans. Citation: Cell 82: 171-174 1995 Type: REVIEW Genes: lag-2 let-23 lin-3 lin-12 lin-15 lin-23 lin-25 Abstract: For many years developmental biologists have been trying to learn whether patterning within fields of cells is driven by graded morphogens or by sequential signaling cascades... ------------------- Key: 2216 Medline: 95354211 Authors: Katz WS;Hill RJ;Clandinin TR;Sternberg PW Title: Different levels of the C. elegans growth factor LIN-3 promote distinct vulval precursor fates. Citation: Cell 82: 297-307 1995 Type: ARTICLE Genes: lin-3 lin-11 lin-13 lin-15 Abstract: An invariant spatial pattern of three cell fates (3 degrees-3 degrees 2 degrees-1 degrees-2 degrees-3 degrees) is generated from a field of multipotent precursor cells during C. elegans vulval development. We demonstrate that the epidermal growth factor-like domain of the LIN-3 protein can induce either of two distinct vulval cell fates: a high dose of LIN-3 induces a 1 degrees fate; a lower dose of LIN-3 induces a 2 degrees fate. A high dose of LIN-3 can also induce adjacent vulval precursor cells to assume 1 degrees fates; thus, high levels of LIN-3 can override the lateral signaling that normally inhibits formation of adjacent 1 degrees fates. We propose that the invariant pattern of vulval cell fates is generated by a graded distribution of LIN-3 that promotes different vulval fates according to local concentration and by a lateral signal that reinforces this initial bias. ------------------- Key: 2217 Medline: 95365402 Authors: Lithgow GJ;White TM;Melov S;Johnson TE Title: Thermotolerance and extended life-span conferred by single-gene mutations and induced by thermal stress. Citation: Proceedings of the National Academy of Sciences USA 92: 7540-7544 1995 Type: ARTICLE Genes: age-1 daf-2 daf-4 daf-7 fer-15 spe-26 Abstract: We have discovered that three longevity mutants of the nematode Caenorhabditis elegans also exhibit increased intrinsic thermotolerance (Itt) as young adults. Mutation of the age-1 gene causes not only 65% longer life expectancy but also Itt. The Itt phenotype cosegregates with age-1. Long-lived spe-26 and daf-2 mutants also exhibit Itt. We investigated the relationship between increased thermotolerance and increased life-span by developing conditions for environmental induction of thermotolerance. Such pretreatments at sublethal temperatures induce significant increases in thermotolerance and small but statistically highly significant increases in life expectancy, consistent with a causal connection between these two traits. Thus, when an animal's resistance to stress is increased, by either genetic or environmental manipulation, we also observe an increase in life expectancy. These results suggest that ability to respond to stress limits the life expectancy of C. elegans and might do so in other metazoa as well. ------------------- Key: 2218 Medline: 95401168 Authors: Favre R;Hermann R;Cermola M;Hohenberg H;Muller M;Bazzicalupo P Title: Immuno-gold-labelling of CUT-1, CUT-2 and cuticulin epitopes in Caenorhabditis elegans and Heterorhabditis sp. processed by high pressure freezing and Citation: Journal of Submicroscopic Cytology & Pathology 27: 341-347 1995 Type: ARTICLE Genes: cut-1 cut-2 Abstract: CUT-1 and CUT-2 are two distinct protein components of cuticlin, the insoluble residue of the cuticles of nematodes. In previous experiments of gold-immuno-labelling on sections of chemically fixed Caenorbabditis elegans, CUT-1 and CUT-2 epitopes were specifically lost. Cryo-immobilization of C. elegans under high pressure followed by freeze-substitution, however, resulted in a good preservation of these antigenic sites and of the ultrastructure of the worms. The entomopathogenic nematode Heterorhabditis sp. processed by the same cryopreparation protocol has shown a strong reactivity with anti-sera raised against CUT-1, CUT-2 and against the whole cuticlin residue of C. elegans. The localization of these epitopes was conserved across the two species. ------------------- Key: 2219 Medline: Authors: Maine EM Title: Cell-signaling events regulate vulval development in the nematode, Caenorhabditis elegans. Citation: Seminars in Developmental Biology 2: 295-304 1995 Type: REVIEW Genes: dig-1 let-23 let-60 lin-1 lin-2 lin-3 lin-7 lin-8 lin-9 lin-10 lin-11 lin-12 lin-13 lin-15 lin-17 lin-18 lin-24 lin-25 lin-26 lin-31 lin-33 lin-34 lin-35 lin-36 lin-37 lin-38 Abstract: Several distinct cell-signaling events are responsible for determination of cell fates during vulval development in C. elegans. A gonadal cell, the anchor cell, induces three hypodermal cells to adopt vulval cell fates. This signal overrides an inhibitory influence, probably exerted by the surrounding hypodermal syncytium. Interactions among the induced cells ensure that they will adopt the appropriate vulval fates. The gonad signals proper attachment and innervation of muscle cells to the developing vulva. These cell-signaling events require the function of a number of proteins that share homology to proteins known to act in signal transduction pathways in other organisms. These proteins include (1) a receptor tyrosine kinase, (2) a ras protein, and (3) a transmembrane protein of the epidermal growth factor precursor/low density lipoprotein receptor family. ------------------- Key: 2220 Medline: Authors: Caldicott IM;Larsen PL;Riddle DL Title: Laboratory cultivation of Caenorhabditis elegans and other free-living nematodes. Citation: "Cell Biology: A Laboratory Handbook", Academic Press, Inc. : 389-397 1994 Type: REVIEW Genes: Abstract: Nematodes have been cultured continuously in the laboratory since 1944 when Margaret Briggs Gochnauer isolated and cultured the free-living hermaphroditic species Caenorhabditis briggsae. Work with C. briggsae and other rhabditid nematodes, C. elegans, Rhabditis anomala, and R. pellio, demonstrated the relative ease with which they could be cultured. The culturing techniques described here were developed for C. elegans, but are generally suitable (to varying degrees) for other free-living nematodes. Whereas much of the early work involved axenic culturing, most of these techniques are no longer in common use and are not included here. In the 1970s C. elegans became the predominant research model due to work by Brenner and co-workers on the genetics and development of this species. An adult C. elegans is about 1.5 mm long, and under optimal laboratory conditions has a life cycle of approximately 3 days. There are two sexes, males and self-fertile hermaphrodites, that are readily distinguishable as adults. The animals are transparent throughout the life cycle, permitting observation of cell divisions in living animals using differential interference microscopy. The complete cell lineage and neural circuitry have been determined and a large collection of behavioral and anatomical mutants have been isolated. C. elegans has six developmental stages: egg, four larval stages (L1-L4), and adult. Under starvation conditions or specific manipulations of the culture conditions a developmentally arrested dispersal stage, the dauer larva, can be formed as an alternative third larval stage. Many of the protocols included here and other experimental protocols have been summarized in "The Nematode Caenorhabditis elegans". We also include a previously unpublished method for long-term chemostat cultures of C. elegans. General laboratory culture conditions for nematode parasites of animals have been described, but none of these nematodes can be cultured in the laboratory through more than one life cycle. Marine nematodes and some plant parasites have been cultured xenically or with fungi. Laboratory cultivation of several plant parasites on Arabidopsis thaliana seedlings in agar petri plates has also been reported. ------------------- Key: 2222 Medline: 95401864 Authors: Liu Z;Kirch S;Ambros V Title: The Caenorhabditis elegans heterochronic gene pathway controls stage-specific transcription of collagen genes. Citation: Development 121: 2471-2478 1995 Type: ARTICLE Genes: col-7 col-17 col-19 lin-4 lin-14 lin-28 lin-29 Abstract: In Caenorhabditis elegans, the terminal differentiation of the hypodermal cells occurs at the larval-to-adult molt, and is characterized ill part by the formation of a morphologically distinct adult cuticle, The timing of this event is controlled by a pathway of heterochronic genes that includes the relatively direct regulatory gene, lin-29, and upstream genes lin-4, lin-14 and lin-28. Using northern analysis to detect endogenous collagen mRNA levels and collagen/lacZ reporter constructs to monitor collagen transcriptional activity, we show that the stage-specific switch from larval cuticle to adult cuticle correlates with the transcriptional activation of adult-specific collagen genes and repression of larval-specific collagen genes, Heterochronic mutations that cause precocious formation of adult cuticle also cause precocious transcription of the adult-specific collagen genes, col-7 and col-19; heterochronic mutations that prevent the switch to adult cuticle cause continued expression of the larval collagen gene, col-17, in adults and prevent adult-specific activation of col-7 or col-19. A 235 bp segment of col-19 5' sequences is sufficient to direct the adult-specific expression of a col-19/lacZ reporter gene in hypodermal cells, These findings indicate that the heterochronic gene pathway regulates the timing of hypodermal cell terminal differentiation by regulating larval- and adult-specific gene expression, perhaps by the direct action of lin-29. ------------------- Key: 2223 Medline: 95401866 Authors: Rougvie AE;Ambros V Title: The heterochronic gene lin-29 encodes a zinc finger protein that controls a terminal differentiation event in Caenorhabditis elegans. Citation: Development 121: 2491-2500 1995 Type: ARTICLE Genes: col-17 col-19 lin-4 lin-14 lin-28 lin-29 Abstract: A hierarchy of heterochronic genes, lin-4, lin-14, lin-28 and lin-29, temporally restricts terminal differentiation of Caenorhabitis elegans hypodermal seam cells to the final molt. This terminal differentiation event involves cell cycle exit, cell fusion and the differential regulation of genes expressed in the larval versus adult hypodermis, lin-29 is the most downstream gene in the developmental timing pathway and thus it is the most direct known regulator of these diverse processes, We show that lin-29 encodes a protein with five zinc fingers of the (Cys)(2)-(HiS)(2) class and thus likely controls these processes by regulating transcription in a stage-specific manner, Consistent with this role, a lin-29 fusion protein binds in vitro to the 5' regulatory sequences necessary in vivo for expression of col-19, a collagen gene expressed in the adult hypodermis. lin-29 mRNA is detected in the first larval stage and increases in abundance through subsequent larval stages until the final molt, w hen lin-29 activity is required for terminal differentiation. ------------------- Key: 2224 Medline: 95401869 Authors: Church DL;Guan KL;Lambie EJ Title: Three genes of the MAP kinase cascade, mek-2, mpk-1/sur-1 and let-60 ras, are required for meiotic cell cycle progression in Caenorhabditis elegans. Citation: Development 121: 2525-2535 1995 Type: ARTICLE Genes: let-23 let-60 let-537 lin-1 lin-8 lin-9 lin-12 lin-15 lin-45 mek-2 mpk-1 sur-1 qDf4 sDp2 sDp3 tDf3 tDf4 Abstract: In the germline of Caenorhabditis elegans hermaphrodites, meiotic cell cycle progression occurs in spatially restricted regions, Immediately after leaving the distal mitotic region, germ cells enter meiosis and thereafter remain in the pachytene stage of first meiotic prophase for an extended period, At the dorsoventral gonadal flexure, germ cells exit pachytene and subsequently become arrested in diakinesis, We have found that exit from pachytene is dependent on the function of three members of the MAP kinase signaling cascade, One of these genes, mek-2, is a newly identified C, elegans MEK (MAP kinase kinase), The other two genes, mpk-1/sur-1 (MAP kinase) and let-60 ras, were previously identified based on their roles in vulval induction and are shown here to act in combination with mek-2 to permit exit from pachytene, Through genetic mosaic analysis, we demonstrate that the expression of mpk-1/sur-1 is required within the germline to permit exit from pachytene. ------------------- Key: 2225 Medline: 95401880 Authors: Koga M;Ohshima Y Title: Mosaic analysis of the let-23 gene function in vulval induction of Caenorhabditis elegans. Citation: Development 121: 2655-2666 1995 Type: ARTICLE Genes: let-23 let-60 lin-1 lin-3 lin-12 mpk-1 sDp3 Abstract: The let-23 receptor tyrosine kinase gene is required for vulval induction and larval survival in the nematode Caenorhabditis elegans. We carried out genetic mosaic analyses of the let-23 gene function by using the cloned let-23 and ncl-1 genes. The wild-type let-23 gene was required in a vulval precursor cell to adopt the 1 degrees vulval fate in animals carrying a let-23 vulvaless or lethal chromosomal mutation. In almost all the animals, vulval precursor cells adjacent to a 1 degrees fate cell were induced to the 2 degrees vulval fate regardless of the let-23 genotypes. These findings indicate that the vulval induction signal from an anchor cell induces a vulval precursor cell to adopt the 1 degrees fate through LET-23, and then a 1 degrees fate cell induces adjacent cells to adopt the 2 degrees fate, for which LET-23 is not required. Foci of lethality of the let-23 (mn23) mutation were found in ABal and ABplp lineages. ------------------- Key: 2226 Medline: 95377544 Authors: Fitch DA;Emmons SW Title: Variable cell positions and cell contacts underlie morphological evolution of the rays in the male tails of nematodes related to Caenorhabditis elegans. Citation: Developmental Biology 170: 564-582 1995 Type: ARTICLE Genes: him-5 mih-1 Abstract: As a first step toward understanding their mechanism of morphological evolution, we compare the morphology and development of the male genitalia in 10 species of Rhabditidae, the family of nematodes that includes Caenorhabditis elegans. We describe a number of variable morphological characteristics and focus in particular on the differing arrangements of the caudal papillae or rays within the acellular fan. We analyze the development of the ray cells within the epidermis of the last larval stage and identify changes in cell positions and cell contacts that underlie evolutionary changes in the arrangement of the rays. Epidermal cell positions were determined by means of indirect immunofluorescence staining with a monoclonal antibody directed towards adherens junctions. Similarities between the species in the cellular arrangements during the earliest developmental stages allow us to propose homologies between the rays in different species, Evolutionary changes in the positions and order of homologous rays are correlated with shifts in cell positions during development. The results suggest that genes for cell. recognition or adhesion proteins, or pattern formation genes that regulate cell recognition or adhesion proteins, may be important foci of evolutionary change affecting morphology. (C) 1995 Academic Press, Inc. ------------------- Key: 2227 Medline: 95381043 Authors: Yoon CH;Lee J;Jongeward GD;Sternberg PW Title: Similarity of sli-1, a regulator of vulval development in C. elegans, to the mammalian proto-oncogene c-cbl. Citation: Science 269: 1102-1105 1995 Type: ARTICLE Genes: let-23 let-60 sem-5 sli-1 unc-101 Abstract: Vulval induction during Caenorhabditis elegans development is mediated by LET-23, a homolog of the mammalian epidermal growth factor receptor tyrosine kinase. The sli-1 gene is a negative regulator of LET-23 and is shown here to encode a protein similar to c-Cbl, a mammalian proto-oncoprotein. SLI-1 and c-Cbl share approximately 55 percent amino acid identity over a stretch of 390 residues, which includes a C3HC4 zinc-binding motif known as the RING finger, and multiple consensus binding sites for Src homology 3 (SH3) domains. SLI-1 and c-Cbl may define new class of proteins that modify receptor tyrosine kinase-mediated signal transduction. ------------------- Key: 2228 Medline: 95377553 Authors: Chamberlin HM;Sternberg PW Title: Mutations in the Caenorhabditis elegans gene vab-3 reveal distinct roles in fate specification and unequal cytokinesis in an asymmetric cell division. Citation: Developmental Biology 170: 679-689 1995 Type: ARTICLE Genes: lin-17 lin-44 vab-3 Abstract: Asymmetric cell divisions in which a precursor cell distributes fate potential unequally between the two daughter cells represent one of the major mechanisms for fate specification during development. Such mechanisms suggest at least two distinct cellular activities: factors that act to establish asymmetry in the precursor cell and factors that are distributed or activated unequally and function to make the daughter cells different from each other. In Caenorhabditis elegans, cytokinesis of the first division of the male-specific postembryonic blast cell B is unequal, and the two daughters adopt different fates, Others have observed that the genes lin-17 and lin-44 are required, respectively, to establish and to orient this asymmetric division. Mutations in lin-17 and lin-44 coordinately disrupt cytokinesis and fate specification. We describe the function of the gene vab-3 in the B cell lineage. Mutations in vab-3 disrupt the fate of the anterior daughter of B, B.a. However, unlike lin-17 and lin-44, mutations in vab-3 can disrupt fate without the corresponding disruption of unequal cytokinesis. Analysis of lin-17; vab-3 double mutants suggests that vab-3 acts after lin-17 for B.a fate specification. Double mutant analysis has also identified additional functions of lin-17 in the B lineage subsequent to this first division. (C) ------------------- Key: 2229 Medline: Authors: Nigon V Title: Polyploidie experimentale chez un nematode libre, Rhabditis elegans maupas. Citation: Bulletin Biologique de la France et de la Belgique 95: 187-225 1951 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 2230 Medline: Authors: Abdulkader N;Brun J Title: Isolation of sterile or lethal temperature-sensitive mutants in Caenorhabditis elegans var. Bergerac. Citation: Nematologica 22: 222-226 1976 Type: ARTICLE Genes: Abstract: In the study of the development and reproduction of multicellular organisms, temperature-sensitive mutants -which may be lethal or sterile-offer an interesting experimental approach. The important results of Suzuki (1970) and coworkers on Drosophila demonstrate the value of such experiments. Our approach takes advantage of the conditionality of the phenotypic expression in C. elegans. This expression is realised at 24C but not at 18C... ------------------- Key: 2231 Medline: Authors: Cadet P;Dion M Title: Production of Caenorhabditis elegans mutants under the influence of ethyl-methane-sulfonate (E.M.S.). Citation: Nematologica 19: 117- 1973 Type: ARTICLE Genes: Abstract: Genetic studies of two spontaneous dwarf mutants (n(a) and n(b)) have led Dion and Brun to mark, in C. elegans genome, two of the five autosomes. The use of natural mutants for genetic mapping is, however, unsatisfactory in that they are rare, certainly because of the self-fertilizing reproduction of this free-living nematode; furthermore, most of them appear to be of the n(a) type described by the authors. For these reasons, chemical mutagens have been used, the most efficient being E.M.S. ------------------- Key: 2232 Medline: 95387388 Authors: Sano T;Tabuse Y;Nishiwaki K;Miwa J Title: The tpa-1 gene of Caenorhabditis elegans encodes two proteins similar to Ca2+-independent protein kinase Cs: Evidence by complete genomic and complementary DNA sequences of the tpu Citation: Journal of Molecular Biology 251: 477-485 1995 Type: ARTICLE Genes: tpa-1 Abstract: The gene tpa-1 on chromosome IV of the nematode Caenorhabditis elegans plays a major and definitive role in the adversary action of tumour-promoting phorbol esters, which induce growth arrest and locomotory distress in the animal. The gene was deduced to code for a protein kinase C (PKC) homologue by molecular cloning. We have now sequenced the complete genomic and complementary DNAs for tpa-1 and have analysed their structural features in detail: (1) tpa-1 spans over 20 kb consisting of eleven exons and ten introns; (2) two different-sized mRNAs are generated from the tpa-1 locus; (3) both mRNAs are trans-spliced to the trans-spliced leader SL1; (4) both mRNAs encode PKC isoforms, which are most similar to Ca2+-independent novel PKC theta; (5) the two PKC isoforms differ from each other in that the smaller lacks the amino-terminal region of the larger corresponding to the first four exons and a portion of the fifth exon; and (6) three introns are located at; identical positions in the polypeptide sequences aligned between the C. elegans tpa-1 product and a PKC of the fruit ------------------- Key: 2233 Medline: 95393970 Authors: Lichtsteiner S;Tjian R Title: Synergistic activation of transcription by UNC-86 and MEC-3 in Caenorhabditis elegans embryo extracts. Citation: EMBO Journal 14: 3937-3945 1995 Type: ARTICLE Genes: mec-3 unc-86 Abstract: The nematode Caenorhabditis elegans has been a choice organism for the study of developmental regulation using classical and molecular genetic approaches, Consequently, many genetically defined pathways have been described and numerous regulatory genes have been identified, However, the biochemical and functional properties of these putative transcription factors have remained uncharacterized, partly because C.elegans cell-free transcription reactions have not been developed, Here we describe the in vitro transcriptional activation properties of two C.elegans homeodomain proteins, UNC-86 and MEC-3, in nuclear extracts derived from C.elegans embryos, Whereas the POU homeodomain protein, UNC-86, alone was able to activate transcription of the mec-3 promoter in vitro, the LIM homeodomain protein, MEC-3, failed to bind DNA or activate transcription on its own. However, in the presence of both UNC-86 and MEC-3, we observed cooperative binding to the mec-3 promoter and synergistic activation of transcription in vitro, Protein-protein interaction assays revealed that UNC-86 can bind directly to MEC-3, and in vitro transcription studies indicate that both proteins contain a functional activation domain, Thus, formation of a heteromeric complex containing two activation domains results in a highly potent activator, These studies provide direct functional evidence for coordinated transcriptional activation by two C.elegans DNA binding proteins that have been defined genetically as regulators of gene expression ------------------- Key: 2234 Medline: 95377532 Authors: Egan CR;Chung MA;Allen FL;Heschl MFP;Vanbuski CL;McGhee JD Title: A gut-to-pharynx/tail switch in embryonic expression of the Caenorhabditis elegans ges-1 gene centers on two GATA sequences. Citation: Developmental Biology 170: 397-419 1995 Type: ARTICLE Genes: ceh-22 elt-1 ges-1 par-4 pho-1 skn-1 Abstract: The Caenorhabditis elegans ges-1 gene (gut esterase No. 1) is expressed only in the intestinal lineage, beginning when the developing gut has only four to eight cells. We analyze the sequence requirements for this tissue-specific gene regulation by injecting deleted/mutated constructs of the ges-l gene into a viable ges-l (null) strain of worms and assaying heritably transformed embryos by esterase histochemistry. Many deletion constructs accurately reconstitute the wildtype gut-specific ges-l expression. However, deletions in the neighborhood of 1100 bp upstream of the ges-l ATG abolish ges-l expression in the developing gut, while at the same time activating ges-l expression in cells of the pharynx/tail that appear to belong to the sister lineage of the gut. Deletions of a 36-bp DNA region containing two tandem WGATAR sequences are sufficient to cause this gut-to-pharynx/tail switch in expression pattern. Deletion of either one of the WGATAR sites or deletion of an adjoining downstream region directs ges-l expression only in a restricted set of cells of the anterior gut. The ges-1 GATA region acts like a gut-specific enhancer in that: (i) it restores ges-l gut expression when reinserted elsewhere into the GATA-deleted ges-1 gene; and (ii) multiple copies direct gut expression of an hsp16-lacZ reporter gene. The ges-l GATA-region also acts as the site of the pharynx/tail repression in that reinsertion elsewhere into the GATA-deleted ges-1 construct causes repression of ges-1 in the pharynx/tail. However, multiple copies of the GATA region are not able to repress the heat-induced expression of an hsp16-lacZ reporter gene, suggesting that the pharynx/tail repression mechanism is specific to the ges-l environment. Finally, mutation rather than deletion of the individual GATA sequences suggests that gut activation and pharynx/tail repression may be due to separate factors. We present a molecular model that summarizes these results. The ges-l control circuitry appears surprisingly complex for what might have been expected to be the simplest possible example of a nonessential gene expressed early in a clonal embryonic ------------------- Key: 2235 Medline: 95388139 Authors: Zhang Y;Emmons SW Title: Specification of sense-organ identity by a Caenorhabditis elegans Pax-6 homologue. Citation: Nature 377: 55-59 1995 Type: ARTICLE Genes: mab-18 vab-3 Abstract: The Pax-6 transcription-factor gene, containing a paired domain and a paired-type homeodomain, is conserved in structure and ubiquitously present among Metazoa(1-5). It is required for development of the central nervous system, and is mutated in human aniridia, mouse and rat small eye and Drosophila eyeless(6). We identified the Pax-6 gene of the nematode Caenorhabditis elegans in genetic studies of male tail morphology(7,8). C. elegans Pax-6 encodes at least two independent genetic functions. One, like other Pax-6 genes, contains paired and homeodomains; this constitutes the genetic locus vab-3 (ref. 9). The other, described here, is expressed from an internal promoter and contains only the homeodomain portion; this constitutes the genetic locus mab-18 (ref. 7), The mab-18 form of the gene is expressed in a peripheral sense organ and is necessary for specification of sense-organ identity. Its function in this context could be to regulate the expression of cell recognition and adhesion proteins required for sense-organ ------------------- Key: 2236 Medline: 95388138 Authors: Chisholm AD;Horvitz HR Title: Patterning of the Caenorhabditis elegans head region by the Pax-6 family member vab-3. Citation: Nature 377: 52-55 1995 Type: ARTICLE Genes: mab-18 vab-3 Abstract: The Pax-6 genes are important for eye development in both vertebrates and Drosophila. Mutations in the human PAX6 gene are found in patients with a variety of eye disorders, including aniridia and Peters' anomaly(1-3), and mutations in the Drosophila Pax-6 homologue cause the eyeless phenotype(4). In the nematode Caenorhabditis elegans, vab-3 mutants display many defects in head-region development, including aberrant morphogenesis, transformation of hypodermal (epidermal-like) cell fates to those of posterior homologues, and abnormal specification of neurons, Here we show that vab-3 is a member of the Pax-6 gene family and is expressed in head-region cells, This C. elegans Pax-6 locus can also encode proteins lacking the paired domain(5). Our results suggest: that. a primordial role of the Pax-6 gene family could have been to pattern part of the head region, and that Pax-6 genes subsequently evolved to be more specifically involved in eye ------------------- Key: 2237 Medline: 95395840 Authors: Kagawa H;Sugimoto K;Matsumoto H;Inoue T;Imadzu H;Takuwa K;Sakube Y Title: Genome structure, mapping and expression of the tropomyosin gene tmy-1 of Caenorhabditis elegans. Citation: Journal of Molecular Biology 251: 603-613 1995 Type: ARTICLE Genes: tmy-1 Abstract: The complete tropomyosin gene, designated tmy-1, of Caenorhabditis elegans was recovered by genome walking from a fragment that was obtained by exon-expression cloning using specific cloning using specific anti-tropomyosin antiserum as a probe. The genome structure of the tmy-1 gene has been determined by combining the DNA sequences of cDNA clones with those of the genomic fragments. The single-copy gene spans approximately 13 kb and include 14 exons. Comparison of cDNA and genomic sequences demonstrates that three isoforms are encoded by the gene tiny-1. Homology of the 27 C-terminal amino acid residues to those of Drosophila and vertebrates suggest that these may be the body wall, pharyngeal and non-muscle types. Tissue-specific expression of the tmy-1 gene was determined by microinjection of a promoter/lacZ fusion gene and with immunohistochemistry by using affinity-purified tissue-specific anti-tropomyosins. The 5' end promoter common to CeTMI and CeTMII is expressed in the body wall muscles, vulva, anus muscles and male tail muscles. Control sequences of the 5' end promoter are located 660 to 800 bp upstream of the initial methionine codon. The third isoform, CeTMIII, encoding 256 amino acids residues was expressed in the pharyngeal muscles by the promoter in the third intron. The mRNA of CeTMIII was trans-spliced with SL1 and SL2. These results allow is to solve the question of what is common from this worm to vertebrates, and also what are the cross-species complexities and the tissue-specific differences of tropomyosins. The tmy-1 gene is located on the C. elegans genomic YAC grid near the right end of chromosome I, in the region on the lev-11 ------------------- Key: 2238 Medline: 96042902 Authors: Barnes TM;Kohara Y;Coulson A;Hekimi S Title: Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans. Citation: Genetics 141: 159-179 1995 Type: ARTICLE Genes: Abstract: The genetic map of each Caenorhabditis elegans chromosome has a central gene cluster (less pronounced on the X chromosome) that contains most of the mutationally defined genes. Many linkage group termini also have clusters, though involving fewer loci. We examine the factors shaping the genetic map by analyzing the rate of recombination and gene density across the genome using the positions of cloned genes and random cDNA clones from the physical map. Each chromosome has a central gene-dense region (more diffuse on the X) with discrete boundaries, flanked by gene-poor regions. Only autosomes have reduced rates of recombination in these gene-dense regions. Cluster boundaries appear discrete also by recombination rate, and the boundaries defined by recombination rate and gene density mostly, but not always, coincide. Terminal clusters have greater gene densities than the adjoining arm but similar recombination rates. Thus, unlike in other species, most exchange in C. elegans occurs in gene-poor regions. The recombination rate across each cluster is constant and similar; and cluster size and gene number per chromosome are independent of the physical size of chromosomes. We propose a model of how this genome organization arose. ------------------- Key: 2239 Medline: 96083060 Authors: McGhee JD Title: Cell fate decisions in the early embryo of the nematode Caenorhabditis elegans. Citation: Developmental Genetics 17: 155-166 1995 Type: REVIEW Genes: apx-1 glp-1 mex-1 pie-1 skn-1 Abstract: Embryos of the small free-living nematode Caenorhabditis elegans develop from the one-celled zygote to a 550-cell worm in about 14 hours at room temperature. Embryos are optically transparent and develop in a highly reproducible manner outside of the mother, features that have permitted the entire cell lineage to be described in detail. The resolution that this vast store of information brings to the study of early C. elegans development is remarkable: cell-cell interactions can be described with a spatial resolution of microns and with a temporal resolution of minutes. Studies over the past few years have begun to translate these precise anatomical events into molecular events that determine cell fate.. ------------------- Key: 2240 Medline: Authors: Peixoto CA;Silva LCF;Mourao PAS;de Souza W Title: Collagen and glycosaminoglycans of adult and dauer forms of Caenorhabditis elegans. Citation: Biology of the Cell 19: 1-9 1995 Type: ARTICLE Genes: daf-2 Abstract: Collagen and glycosaminoglycans were identified in the cuticle of adult and dauer forms of the free-living nematode Caenorhabditis elegans using cytochemical techniques. A polyclonal antibody against a synthetic 18 amino-acid peptide that corresponds to the sequence of domain E of the Haemonchus contortus 3A3 collagen gene labeled all cuticular layers of the adult form of C. elegans. Otherwise, a light labeling was observed on dauer larva cuticle. Only the cortical region of the cuticle of the L(1) stage was labeled. These observations confirm previous biochemical studies on the collagen composition on the various development stages of C. elegans. An anti-chondroitin sulfate monoclonal antibody labeled the cortical layers of adult and dauer cuticle. Otherwise, biochemical analysis showed the presence of a glycosaminoglycan in C. elegans which was sensitive to chondroitinase ABC digestion but differed somewhat from the known vertebrate glycosaminoglycans by its electrophoretic ------------------- Key: 2241 Medline: 95377380 Authors: LaMunyon CW;Ward S Title: Sperm precedence in a hermaphroditic nematode (Caenorhabditis elegans) is due to competitive superiority of male sperm. Citation: Experientia 58: 817-823 1995 Type: ARTICLE Genes: fer-1 spe-8 Abstract: When male and hermaphrodite Caenorhabditis elegans mate, the male's sperm outcompete the hermaphrodite's own sperm and fertilize a majority of the offspring. Here, we investigate the mechanism of male sperm precedence. We rule out the possibility that male sperm are stronger and more competitive because they are activated later than hermaphrodite sperm. We also find that a previously known gender difference in sperm activation does not influence sperm competition. Male sperm, rinsed free of seminal fluid, retained the capacity to take precedence after artificial insemination. Therefore, we conclude that male sperm themselves are competitively superior to hermaphrodite sperm. This trait maximizes outcrossing after mating and may increase both genetic diversity and heterozygosity of offspring whose parents, due to self-fertilization, may be highly homozygous. ------------------- Key: 2242 Medline: 95391655 Authors: Kagan RM;Clarke S Title: Protein L-isoaspartyl methyltransferase from the nematode Caenorhabditis elegans: Genomic structure and substrate specificity. Citation: Biochemistry 34: 10794-10806 1995 Type: ARTICLE Genes: pcm-1 Abstract: We identified a protein L-isoaspartate (D-aspartate) O-methyltransferase (EC 2.1.1.77) in the nematode worm Caenorhabditis elegans. The methylation of abnormal L-isoaspartyl residues by this enzyme can lead to their conversion to L-aspartyl residues and represents a protein repair step for polypeptides damaged by spontaneous reactions during the aging process. We show that the levels of this enzyme increase 2-fold in C. elegans in the dauer larval form, a developmental stage where the organism can survive for extended periods of time. Utilizing degenerate oligonucleotide primers derived from conserved amino acid sequences of mammalian, plant, and bacterial L-isoaspartyl methyltransferases and PCR amplification, we made DNA probes that allowed us to obtain cDNA and genomic DNA clones encoding this enzyme in the nematode. The deduced amino acid sequence is 53% identical to the human enzyme and 29% identical to the Escherichia coli enzyme. Overexpression of the cDNA for the C. elegans enzyme in E. coli gave an active product with micromolar K-m values for L-isoaspartyl-containing peptide substrates and for the methyl donor S-adenosyl-L-methionine. No methylation of D-aspartyl-containing peptides was detected under conditions where the human enzyme catalyzed this reaction, suggesting that the ability to methylate D-aspartyl residues in addition to L-isoaspartyl residues was a later evolutionary adaptation of this enzyme. The C. elegans gene for the methyltransferase, designated pcm-l, was mapped to a single site in a 31 kb region in the central portion of chromosome V. The gene is 3.2 kb in length and includes six introns. Although much smaller, its genomic organization is similar to that of the corresponding mouse gene, with identically positioned intron-exon splice junctions at five of seven sites. We propose that this gene plays an important role in facilitating the long term survival of ------------------- Key: 2243 Medline: 96079263 Authors: Pilgrim D;McGregor A;Jackle P;Johnson T;Hansen D Title: The C. elegans sex-determining gene fem-2 encodes a putative protein phosphatase. Citation: Molecular Biology of the Cell 6: 1159-1171 1995 Type: ARTICLE Genes: fem-2 sC1 sDf124 wcDf1 Abstract: The genetic and molecular analysis of genes involved in the regulation of sex determination in Caenorhabditis elegans suggests that the gene fem-2 plays an important role in regulating a pathway transducing a non-cell-autonomous signal to a nuclear transcription factor. The wild-type fem-2 gene was cloned by identifying sequences from the C. elegans physical map that could restore normal Fem-2 function to homozygous mutant fem-2 transgenic animals. cDNA sequences mapping to the minimal rescuing region correspond to an open reading frame with a sequence similar to protein phosphatase 2C enzymes from systems as diverse as yeast, humans, and plants, but the alignments suggest that FEM-2 falls into a separate class of proteins than the canonical homologues. Several fem-2 mutant alleles were sequenced, and the mutations are predicted to cause protein changes consistent with their observed phenotypes, such as missense mutations in conditional alleles, and a nonsense mutation in a predicted null allele. This is the first evidence implicating phosphorylation and/or dephosphorylation as a control mechanism in C. elegans sex ------------------- Key: 2244 Medline: 96100412 Authors: Lewis JA;Fleming JT Title: Basic culture methods. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 3-29 Type: REVIEW Genes: Abstract: The nematode Caenorhabditis elegans is a small, rapidly growing organism that can easily be raised in the laboratory on the bacterium Escherichia coli. Because C. elegans is a self-fertilizing hermaphrodite, it is possible to readily grow large quantities of the organism in swirling liquid cultures and also possible to propagate severely incapacitated mutants. The rapidity of growth and the ability to self-fertilize necessitate special measures to establish a synchronous culture. ------------------- Key: 2245 Medline: 96100413 Authors: Anderson P Title: Mutagenesis. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 31-58 1995 Type: REVIEW Genes: Abstract: Choosing the right mutagen means selecting the right combination of mutagen efficiency and mutagen specificity. For mutagen efficiency, nothing beats EMS. It is extremely potent, it is easy to use, and its mutational specificity is well documented. If mutations other than G/C-->A/T transitions are desired, mutagens other than EMS must be used. Based on initial observations, ENU appears to be as efficient as EMS. Work with other organisms predicts that ENU will yield a wider variety of transitions and transversions than EMS. If this proves to be true, ENU will become an important mutagen for routine genetic analysis. For investigators wanting large multigene deletions, gamma irradiation, UV irradiation, formaldehyde, and DEO are the mutagens of choice. Gamma irradiation yields the highest frequency of events by far, but may also yield more complex rearrangements. Based on limited information, UV irradiation, formaldehyde, and DEO appear to be effective deletion mutagens. Of the three, UV appears to be the most efficient. For investigators wanting small intragenic deletions, TMP appears most effective. TMP is not very potent, but a large proportion of TMP-induced unc-22 mutations are small deletions. Hopefully this will be true of all genes. For investigators wanting other types of genome rearrangements (e.g., translocations, crossover suppressors), gamma irradiation (or possibly X irradiation) is effective. For transposon insertions, mut-2 (especially strain TR679) provides the highest possible frequency of events. Because mut-2 activates several families of transposons, it yields insertions in genes that are poor targets for Tc1. Manipulating a strain with such high frequencies of spontaneous mutations, however, can be problematical (see above). For Tc1-specific events, mut-6 (strain RW7097) is the best choice. It provides frequencies comparable to those of Bergerac, but its Tc1 copy number is much lower. A reasonable strategy for spontaneous mutagenesis is to use TR679 only if mutants are not obtained in strains with lower levels of activity (e.g., MT3126 or RW7097). ------------------- Key: 2246 Medline: 96100414 Authors: Plasterk RHA Title: Reverse genetics: From gene sequence to mutant worm. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 59-80 1995 Type: REVIEW Genes: Abstract: Caenorhabditis elegans is in all likelihood the first metazoan animal whose entire genome will be determined. In addition, a very detailed description of the animal's morphology, development, and physiology is available (see elsewhere in this book, and Wood, 1988). Thus, the complete phenotype and genotype of an animal will be known. What is not known is how genotype determines phenotype; to study this, one needs to establish connections between genome sequence and phenotypes. Much has been done by classic or forward genetics: mutagenesis experiments have identified loci involved in a specific trait. Many of these loci have already been defined at the molecular level, and the genome sequence will certainly aid in the identification of many more. The opposite approach, reverse genetics, becomes naturally more important when more of the genome sequence is determined: Given the sequence of a gene of which nothing else is know, how can the function of that gene be determined? Reverse genetics is more than targeted inactivation. One can study a gene's function by several approaches...| ------------------- Key: 2247 Medline: 96100415 Authors: Williams BD Title: Genetic mapping with polymorphic sequence-tagged sites. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 81-96 1995 Type: REVIEW Genes: Abstract: The number of easily distinguishable mutant phenotypes in Caenorhabditis elegans is relatively small, and this constrains the number of factors that can be followed in standard genetic crosses. Consequently, a new mutation is mapped, first to a chromosome using two-factor data from one or more crosses, and then to a chromosomal subregion by successive three-factor crosses. Mapping would be more efficient if it were possible to score a large number of well-distributed markers in a single cross. The advent of the polymerase chain reaction makes this approach feasible by allowing polymorphic genomic regions to serve as genetic markers that are easily scored in DNA released from individual animals. The only "phenotype" is a band on a gel, so the segregation of many of these markers can be followed in a single cross. Following the terminology proposed by Olsen et al. (1989), we refer to polymorphisms that can be scored by appropriately designed polymerase chain reaction (PCR) assays as polymorphic seqeunce-tagged sites (STSs)... ------------------- Key: 2248 Medline: 96100416 Authors: Huang LS;Sternberg PW Title: Genetic dissection of developmental pathways. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 97-122 1995 Type: REVIEW Genes: Abstract: A major tool of developmental genetics is the ordering of genes in functional pathways. In this chapter, we explain the logic behind constructing pathways, starting from the knowledge of the relevant phenotypes associated with the genes of interest, assuming that careful analysis of the phenotype has been carried out. We discuss the construction and interpretation of phenotypes of double mutants, screening for and analysis of extragenic suppressors, as well as issues regarding complex pathways and genetic redundancy. Avery and Wasserman (1992) have provided a brief theoretical discussion of epistasis analysis; here we explain the more practical aspects of how models of developmental pathways are built in ------------------- Key: 2249 Medline: 96100417 Authors: Herman RK Title: Mosaic analysis. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 123-146 1995 Type: REVIEW Genes: Abstract: Geneticists like to point out that the ultimate test of a proposed function for a gene and its encoded product (or products) in a living organism involves making a mutant and analyzing its phenotype. This is the goal of reverse genetics: a gene is cloned and sequenced, its transcripts and protein coding sequence are analyzed, and a function may be proposed; one must then introduce a mutation in the gene in a living organism to see what the functional consequences are. The analysis of genetic mosaics takes this philosophy a step further. In mosaics, some cells of an individual are genotypically mutant and other cells are genotypically wild type. One then asks what the phenotypic consequences are for the living organism. This is not the same as asking what cells transcribe the gene or in what cells the protein product of the gene is to be found, but rather it is asking in what cells the wild-type gene is needed for a given function... ------------------- Key: 2250 Medline: 96100418 Authors: Edgley ML;Baillie DL;Riddle DL;Rose AM Title: Genetic balancers. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 147-184 1995 Type: REVIEW Genes: Abstract: Genetic balancers are genetic constructs or chromosomal rearrangements that allow lethal or sterile mutations to be stably maintained in heterozygotes. In this chapter we use the term balancer primarily to refer to chromosomal duplications or rearrangements that suppress crossing over. In addition, we define lethal as any mutation that blocks survival or reproduction. Phenotypes associated with lethal mutations in Caenorhabditis elegans range from egg or larval lethality to adult sterility and maternal effect lethality, and can include conditional effects such as temperature sensitivity. The number of essential genes in C. elegans (those identified by lethal mutations) may range as high as 7000 according to genetic estimates. Thus, lethal mutations constitute a rich source of information about basic biological processes in this nematode. ------------------- Key: 2251 Medline: 96100419 Authors: Rand JB;Johnson CD Title: Genetic pharmacology: Interactions between drugs and gene products in Caenorhabditis elegans. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 187-204 1995 Type: REVIEW Genes: Abstract: Compared with other animals, the nematode Caenorhabditis elegans has many advantages for mutant isolation and for genetic analysis. Some of these, for example, small size and rapid growth to high density on inexpensive media, simplify the manipulation of large numbers of animals. Others, such as the lack of a muscle-driven circulatory system and the self-fertilizing hermaphroditic mode of reproduction, enable the survival of strains with genetic defects that would be lethal to more complex animals. Although a few compounds with C. elegans-specific or nematode-specific actions have been described, the vast majority appear to act on targets that are widely distributed in most or all animals, including humans (or even in most or all eukaryotes). As a result, C. elegans has been a popular organism in which to study drug action and there is a substantial body of published work. In this chapter we attempt to extract an underlying feature of this work: the methods that are used in compound-based studies of C. elegans. We present general approaches to evaluating the effects of compounds on C. elegans growth, development, metabolism, and behavior, we discuss strategies for the isolation and analysis of drug-resistant and hypersensitive mutants, and we describe the use of C. elegans for new drug discovery. We also provide, as Table I, a list of some of the compounds already studied in C. elegans, along with one or more references in which information about the detection of compound-specific effects can be found. It is hoped the table will expedite the use of compound-specific mutants as genetic markers... ------------------- Key: 2252 Medline: 96100420 Authors: Gannon TN;Rankin CH Title: Methods of studying behavioral plasticity in Caenorhabditis elegans. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 205-223 1995 Type: REVIEW Genes: Abstract: Behavioral plasticity is the ability of organisms to modify their behavior over time, based on their experience, and is thus critical to the survival of any organism in a changing environment. It allows organisms to adapt to new surroundings and to take better advantage of novel situational variables they may encounter. It is therefore an extremely important ability, and it has attracted much research attention in innumberable organisms and across several disciplines. Much of the research on plasticity has been characterized by an attempt to integrate information and expertise from a number of these different disciplines within selected invertebrate organisms. Researchers from a variety of fields, including psychology, physiology, biochemistry, genetics, neurobiology, and molecular biology, have been uniting in an effort to investigate "simple system" in which these approaches are being combined and focused on the general goal of elucidating the cellular, molecular, and genetic basis of behavioral plasticity. These simple system approaches have led to considerable progress in our understanding of the mechanisms underlying adaptive behaviors. The general strategy of such approaches is to try to identify the genes, molecules, channels, ion currents, cells, and neural circuits underlying some form of plasticity and then determine the precise nature of their respective roles in producing behavior... ------------------- Key: 2253 Medline: 96100421 Authors: Bargmann CI;Avery L Title: Laser killing of cells in Caenorhabditis elegans. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 225-250 1995 Type: REVIEW Genes: Abstract: One way to study cell function is to eliminate the cell and observe subsequent developmental or behavioral abnormalities in the animal. In Caenorhabditis elegans, this is usually accomplished by killing individual cells or groups of cells with a laser microbeam. Laser killing has been used to determine the functions of many mature cell types, including neurons involved in locomotion, feeding, mechanosensation, and chemosensation. These studies have been practical because only a few cell types appear to be absolutely required for viability. Laser ablation can also be sued to ask how cells interact during development. Signaling and inductive interactions between cells can be examined by removing one cell and observing the development of the remaining cells... ------------------- Key: 2254 Medline: 96100422 Authors: Avery L;Raizen D;Lockery S Title: Electrophysiological methods. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 251-269 1995 Type: REVIEW Genes: Abstract: This chapter has two aims. First, we describe one method, the electropharyngeogram (EPG), insufficient detail that a Caenorhabditis elegans researcher unfamiliar with electrophysiological methods could set up the apparatus and get useful results. Second, we describe more generally for researchers familiar with electrophysiological methods how they may be applied to C. elegans. We do not describe methods for electrophysiological investigation of C. elegans sperm. ------------------- Key: 2255 Medline: 96100423 Authors: L'Hernault SW;Roberts TM Title: Cell biology of nematode sperm. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 273-301 1995 Type: REVIEW Genes: Abstract: In this chapter we review methods that have been developed for working with the amoeboid sperm of nematodes. Although the sperm from a number of species have been examined, we confine our discussion to the free-living Caenorhabditis elegans and the pig parasite Ascaris suum. Each of these experimental systems offers the investigator certain strengths and weaknesses, and the type of contemplated experiment determines which is most suitable. Ascaris sperm are more easily obtainable in large quantity and are, therefore, more suited for biochemical studies. Furthermore, the Ascaris sperm is much larger than its C. elegans counterpart, allowing easier light microscopic analyses. The superb genetics and ease in obtaining DNA clones containing desired gene sequences make C. elegans the system of choice for genetic and molecular biological studies. Much evidence indicates that the sperm of these two systems share important similarities, and data obtained in one are frequently applicable to the other. Consequently, although the rest of this volume concerns principally C. elegans, we feel this chapter requires discussion of both C. elegans and Ascaris sperm because much of understanding of amoeboid sperm cell biology has, in fact, been obtained from Ascaris. ------------------- Key: 2256 Medline: 96100424 Authors: Edgar LG Title: Blastomere culture and analysis. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 303-321 1995 Type: REVIEW Genes: Abstract: In studying embryos of many species, methods of fragmenting and culturing embryonic tissues or cells have been useful for addressing questions of blastomere autonomy in early and later embryogenesis, for exposure to drugs or other agents that perturb specific processes, and for direct labeling of DNA or RNA. For Caenorhabditis elegans workers, the small size of the embryo and the impermeability of the chitinous eggshell and inner vitelline membrane have made such experiments difficult. A method of permeabilization and blastomere isolation, a culture system that will support further cellular development and differentiation, and assay methods for assaying the degree of development and its relative normality after experimental manipulation are minimal requirements for a satisfactory C. elegans embryonic culture system. Methods of isolating early blastomeres have included crushing of the eggshell and extrusion, laser ablation of neighboring blastomeres within an itact eggshell, laser puncturing of the eggshell producing extrusion, and digestion of the eggshell followed by shearing or manual stripping of the vitelline membrane. This last method is described in detail below. Permeabilization of complete embryos can be achieved by the same methods; in addition, one-cell embryos within the shell can be permeabilized to certain drugs such as cytochalasin D by gentle pressure on an overlying ------------------- Key: 2257 Medline: 96100425 Authors: Seydoux G;Fire A Title: Whole-mount in situ hybridization for the detection of RNA in Caenorhabditis elegans embryos. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 323-337 1995 Type: REVIEW Genes: Abstract: In situ hybridization to RNA is an effective tool for the analysis of gene expression during development. This technique is particularly important for Caenorhabditis elegans, as isolation of RNA from specific tissues or developmental stages is generally not possible in this organism (see Chapter 20 in this volume). In addition, the availability of the complete cell lineage and the reproducibility of cell positions from one animal to the next allow RNA expression patterns to be analyzed at the level of individual cells. A number of in situ hybridization protocols have been developed for the detection of RNA in squashed, dissected, or sectioned tissues of C. elegans. More recently, protocols using whole-mount preparations of C. elegans have also been described. By preserving the three-dimensional structure of the specimen, whole-mount preparations facilitate the identification of specific cells and the analysis of complex expression patterns. In this chapter, we describe a protocol for detection of RNA in whole-mount C. elegans embryos. This procedure is based on protocols for Drosophila, which make use of highly sensitive digoxigenin-labeled probes... ------------------- Key: 2258 Medline: 96100426 Authors: Albertson DG;Fishpool RM;Birchall PS Title: Fluorescence in situ hybridization for the detection of DNA and RNA. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 339-364 1995 Type: REVIEW Genes: Abstract: Both the localization and distribution of nucleic acid sequences in genomes and in cells can be visualized by hybridization of labeled probe DNAs to cytological preparations of chromosomes or tissues. With the introduction of nonisotopically labeled nucleotides that could be incorporated into cloned DNAs by enzymatic methods in vitro, it became possible to detect the site of hybridization quickly using antibodies that recognized the modifying group on the nucleotides incorporated into the probe DNA. More recently, nucleotides labeled with a fluorescent molecule have been incorporated into probes by invitro enzymatic reactions and the site of hybridization can then be visualized directly. As fluorescence in situ hybridization provides a rapid and high-resolution method for mapping genes, it is being sued increasingly for mapping cloned DNAs to chromosomes and for the ordering of clones in large-scale genome projects. On the other hand, physically mapped clones can also be used to label chromosomes for analysis of such biological processes as chromosome segregation, pairing in meiosis, and interphase nuclear order. Nonisotopic methods of hybridization are also ideally suited to visualization of mRNA distributions in tissues, because the signal can be detected in thick specimens, in contrast to isotopic methods that require thin specimens for detection by autoradiography... ------------------- Key: 2259 Medline: 96100427 Authors: Miller DM;Shakes DC Title: Immunofluorescence microscopy. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 365-394 1995 Type: REVIEW Genes: Abstract: The purpose of this chapter is to provide a practical guide to immunofluorescence microscopy of Caenorhabditis elegans. In this method, fixed tissue is stained with a fluorescently labeled antibody and visualized with the light microscope. The antibody ensures that staining is limited to the location of the antigen, and the microscope provides a magnified image of the fluorescent area. Immunofluorescence microscopy is an especially powerful tool for studies of C. elegans. The identity of each antibody-stained cell can be determined by reference to detailed knowledge of C. elegans anatomy. Because the developmental cell lineage is known, it is also possible to define the timing of antigen expression with great precision. Because of the transparency and small size of the animal, immunofluorescence staining can be clearly observed in whole mounts and does not require ------------------- Key: 2260 Medline: 96100428 Authors: Hall DH Title: Electron microscopy and three-dimensional image reconstruction. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 395-436 1995 Type: REVIEW Genes: Abstract: Although Caenorhabditis elegans was originally chosen as a model organism for cell biology with serial section electron microscopy (EM) methods in mind, these methods have remained a daunting challenge. There is an apocryphal story that Nichol Thomson originally advised Sydney Brenner that C. elegans was unsuitable for electron microscopy and that Brenner should choose another species. Other experienced microscopists have probably shared similar dark thoughts from time to time. Nonetheless, the worm's very small size, simple organization, and cablelike nervous system have permitted Brenner's colleagues to characterize every cell and cell contact in the wild-type animal, potentiating the genetic characterization of cellular development in remarkable detail. We attempt to provide an adequate background for anyone to initiate EM studies of C. elegans. Two decades ago, as the first of Brenner's postdoctoral fellows left his laboratory to establish new worm laboratories, it was standard practice to include an EM component in their studies. Their combined efforts to characterize the adult animal's cell types and the essential steps in its development helped to erect a lovely scaffold of key manuscripts, capped by the description of the "Mind of the Worm" in some 600 micrographs and 175 drawings. Many of these works required technical heroics or suffered long delays before publication. Most people later chose to leave electron microscopy behind in pursuit of molecular quarry. The fruits of their molecular and genetic studies should soon stimulate a renewed flowering of electron microscopy. We hope to smooth your entry or reentry into these techniques. We also summarize our methods for three-dimensional (3D) image reconstruction, based largely on film techniques introduced by John White and Randle Ware. Digital imaging techniques seem poised to make 3D reconstruction more accessible, and may simplify the exchange of morphological data between laboratories. We discuss several computer systems that the C. elegans community could adopt for high-resolution studies of structure and function. In addition, we briefly cover several specialized specimen preparation techniques for electron microscopy, including freeze fracture and electron microscopic immunocytochemistry. ------------------- Key: 2261 Medline: 96100429 Authors: Epstein HF;Liu F Title: Proteins and protein assemblies. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 437-450 1995 Type: REVIEW Genes: Abstract: The ultimate goal of subcellular fractionation and biochemical purification is to better understand the relationships between structure and function of proteins and protein assemblies. Examples of such relationships with respect to specific gene products include the formation of stable complexes, elucidation of catalytic activities, and subcellular localization of the organellar and supramolecular levels. The detailed aspects of such relationships are not always readily predictable from genetic or molecular studies of the gene products or from their cellular localization by immunological methods. Subcellular fractionation and biochemical purification are generally prerequisites to experimental analysis of biochemical mechanisms underlying a biological phenomenon. These approaches can mutually enhance and interact with parallel cellular, genetic, and molecular analyses. To achieve such goals, methods for isolating proteins and protein assemblies must preserve both structural integrity and biological activity. Ideally, both objectives should be met; practically, it may be critical to know which of these conditions is true. In general, specific protocols must be designed for the optimal isolation, purification, and characterization of each specific protein of interest. Additionally, one wishes to achieve as high a yield as possible; however, each step in protein purification generally produces some reduction in yield... ------------------- Key: 2262 Medline: 96100430 Authors: Mello C;Fire A Title: DNA transformation. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 451-482 1995 Type: REVIEW Genes: Abstract: DNA transformation assays in a whole organism provide experimental links between molecular structure and phenotype. Experiments with transgenic Caenorhabditis elegans start in general with the injection of DNA into the adult gonad. Effects on phenotype or gene expression patterns can be analyzed either in F1 progeny derived from the injected animals or in derived transgenic lines. Microinjection of C. elegans was first carried out by Kimble et al. (1982). Stinchcomb et al. (1985) then showed that injected DNA could be maintained for several generations in transgenic lines. The first selective methods for producing and maintaining transgenic lines were reported in 1986 (Fire, 1986). These methods have been considerably improved since then (Mello et al., 1991) , so that assays involving DNA transformation are now a standard part of the experimental repertoire for C. elegans. ------------------- Key: 2263 Medline: 96100431 Authors: Krause M Title: Transcription and translation. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 483-512 1995 Type: REVIEW Genes: Abstract: The genetics of Caenorhabditis elegans provides a convenient experimental entry point into many developmental processes and a powerful tool that can be exploited to characterize interactions among a set of genes regulating a particular pathway. Eventually, though, the study of developmental processes becomes a molecular study of gene regulation. At this level, the determination of the on/off state of a gene requires an understanding of not only its transcriptional state, but also post-transcriptional, translational, and post-translational control mechanisms. Although the vertebrate literature is rich in details of factors that influence these regulatory processes, relatively few of the factors responsible for gene expression in the nematode C. elegans have been characterized. This lag in knowledge reflects both the relatively recent arrival of C. elegans on the list of experimental systems, as well as its general unsuitability for biochemistry. There are no tissue culture cell lines established from C. elegans, and it is difficult to isolate, in large amounts, any homogeneous cell type. Moreover, the impermeable eggshell encasing the embryo and the cuticle encasing the worm make pharmacological studies in intact animals difficult and tedious. Grim as this sounds, progress has been made in C. elegans in the field of gene expression. The sensitivity of techniques has improved and the available molecular tool kit has expanded. The study of individual genes has provided descriptions of several regulatory processes, some general and some gene specific. Our current level of understanding of gene regulation is sufficient to say that C. elegans appears, in general, to be a typical eukaryote. As such, C. elegans is amenable to many of the standard analytical approaches used in other developmental systems. The purpose of this chapter is to review our current state of knowledge of transcription and translation in C. elegans (for a review ------------------- Key: 2264 Medline: 96100432 Authors: Krause M Title: Techniques for analyzing transcription and translation. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 513-529 1995 Type: REVIEW Genes: Abstract: This chapter is devoted to providing information on techniques applicable to studying transcription and translation in Caenorhabditis elegans. These techniques are constantly evolving and being passed among workers, each making improvements or adaptations. None of the techniques discussed below are original, but, rather, have emerged from a variety of sources over the years, making it difficult to trace their origin or give credit to the originators. Although each technique has been used successfully, for each there are alternative methods available in the literature that work equally well. In fact, depending on the available resources, you might find that an alternative technique suits your needs and facilities better than the one described below. For this reason, the procedures discussed below are usually accompanied by one or more references that will allow you to look at other, related methods. Where appropriate, there will also be a discussion of factors to consider when ------------------- Key: 2265 Medline: 96100433 Authors: Coulson A;Huynh C;Kozono Y;Shownkeen R Title: The physical map of the Caenorhabditis elegans genome. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 533-550 1995 Type: REVIEW Genes: Abstract: The clone-based physical map of the 100-Mb Caenorhabditis elegans genome has evolved over a number of years. Although the detection of clone overlaps and construction of the map have of necessity been carried out centrally, it has been essentially a community project. Without the provision of cloned markers and relevant map information by the C. elegans community as a whole, the map would lack the genetic anchor points and coherent structure that make it a viable entity. Currently, the map consists of 13 mapped contigs totaling in excess of 95 Mb and 2 significant unmapped contigs totaling 1.3 Mb. Telomeric clones are not yet in place. The map carries 600 physically mapped loci, of which 262 have genetic map data. With one exception, the physical extents of the remaining gaps are not known. The exception is the remaining gap on linkage group (LG) II. This has been shown to be bridged by a 225-kb Sse83871 fragment. Because the clones constituting the map are a central resource, there is essentially no necessity for individuals to construct cosmid and yeast artificial chromosome (YAC) libraries. Consequently, such protocols are not included here. Similarly, protocols for clone fingerprinting, which forms the basis of the determination of cosmid overlaps and the mapping of clones received from outside sources and has to be a centralized operation, and YAC linkage are not give here. What follows is essentially a "user's guide" to the physical map. Details of map construction are given where required for interpretation of the map as distributed. The physical mapping has been a collaboration between the MRC Laboratory of Molecular Biology, Cambridge, United Kingdom (now at The Sanger Centre, Cambridge, UK) and Washington University School of Medicine, St. Louis, Missouri. Inquiries regarding map interpretation, information, and materials should be addressed to alan@sanger.ac.uk or rw@nematode.wustl.edu. ------------------- Key: 2266 Medline: 96100434 Authors: Favello A;Hillier L;Wilson RK Title: Genomic DNA sequencing methods. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 551-569 1995 Type: REVIEW Genes: Abstract: Sequence analysis of cosmids from C. elegans and other organisms currently is best done using the random or "shotgun" strategy (Wilson et al., 1994). After shearing by sonication, DNA is used to prepare M13 subclone libraries which provide good coverage and high-quality sequence data. The subclones are assembled and the data edited using software tools developed especially for C. elegans genomic sequencing. These same tools facilitate much of the subsequent work to complete both strands of the sequence and resolve any remaining ambiguities. Analysis of the finished sequence is then accomplished using several additional computer tools including Genefinder and ACeDB. Taken together, these methods and tools provide a powerful means for genome analysis in the nematode. ------------------- Key: 2267 Medline: 96100435 Authors: Fulton LL;Hillier L;Wilson RK Title: Large-scale complementary DNA sequencing methods. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 571-582 1995 Type: REVIEW Genes: Abstract: Complementary DNA libraries are useful tools for uncovering genes of interest in C. elegans and finding specific homologies to genes in other organisms (Waterston et al., 1992; McCombie et al., 1992). When working with existing cDNA libraries, be sure to carefully choose which libraries would be most beneficial to the type of research being done. Some libraries may be specific for genes that are present in lower copy numbers, whereas others may be of a more general nature. It is important to fully understand the source and construction of the library you will be working with. Once an appropriate library has been chosen, work may begin to isolate a specific cDNA and sequence it completely or to survey many cDNAs by single-pass DNA sequencing. Whatever the project, it is important to develop a specific strategy for both the sequencing and the organization of the clones being characterized. The strategies and procedures we have outlined in this chapter have proven effective for rapid and comprehensive cDNA ------------------- Key: 2268 Medline: 96100436 Authors: Eeckman FH;Durbin R Title: ACeDB and Macace. Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 583-605 1995 Type: REVIEW Genes: Abstract: ACeDB (A Caenorhabditis elegans Data Base) is a data management and display system that contains a wide range of genomic and other information about C. elegans. This chapter provides an overview of ACeDB for the C. elegans user, focusing in particular on the Macintosh version Macace. Previous reviews of AceDB include those of Thierry-Mieg and Durbin (1992) and Durbin and Thierry-Mieg (1994), which describe the general properties of the whole system, and that by Dunham et al. (1994), which discussed the use of AceDB for physical map data collection and assembly. ACeDB was developed by Jean Thierry-Mieg and Richard Durbin primarily for the C. elegans project, when the genomic sequencing project was just beginning in 1990. The original aim was to create a single database that integrated the genetic and physical maps with both genomic sequence data and the literature references. The forerunner of ACeDB was the program CONTIG9 (Sulston et al., 1988), which was developed to maintain and edit the physical map. CONTIG9 served researchers around the world by providing critical on-line access to the current physical map as it was being constructed (Coulson et al., 1986). This policy of immediate access allowed members of the worm community to see the same data as the people making the map, and proved very successful in maximizing use of the map. The same approach was adopted as a template for ACeDB. These two principles, developing a comprehensive database for all types of genomic and related data and providing public access to the data in the same form as used by the data-collecting laboratories, have continued to underlie developments of ACeDB. Over the last 5 years, a wide range of genome projects relating to other organisms have taken the ACeDB program and used it to develop databases for their own data. ACeDB has been used both in public projects designed to redistribute public data in a coordinated fashion and laboratory-based projects for collecting new data. Others, such as the C. elegans ACeDB, have used the database for both purposes. The reason it has been possible to adapt ACeDB so widely is that its flexible data structure allows new types of objects and new types of information about these objects to be added easily. This chapter describes (1) how to obtain ACeDB and documentation for it, (2) how to access and use the information in ACeDB, and (3) how to use ACeDB as a laboratory-based data managing system. Some of what we discuss is specific to the nematode database, but other information applies to the basic computer software program and, hence, to any database using the ACeDB program. ------------------- Key: 2269 Medline: 96100437 Authors: Shoman LM;Grossman E;Powell K;Jamison C;Schatz BR Title: The Worm Community System, Release 2.0 (WCSr2). Citation: "Methods in Cell Biology. Caenorhabditis elegans: Modern Biological Analysis of an Organism." H.F. Epstein and D.C. Shakes (eds), Academic Press, Inc., San Diego. 48: 607-625 1995 Type: REVIEW Genes: Abstract: The Worm Community System (WCS) is a digital library that contains knowledge about Caenorhabditis elegans, and a software environment that enables the user to interact with the community library across the international computer network, the Internet. The functions of the software environment enable the user to browse, search, and retrieve the existing knowledge of the community. In addition, users may add data and literature to the library for timely dissemination to the research community and for private collaboration with colleagues at local or remote sites. This capacity for dynamically updating information should help to better propagate knowledge across the community. This chapter provides a survey of the system's history, features, and requirements, and describes basic uses of the system. ------------------- Key: 2270 Medline: 95405493 Authors: Hunter CP;Kenyon C Title: Specification of anteroposterior cell fates in Caenorhabditis elegans by Drosophila Hox proteins. Citation: Nature 377: 229-232 1995 Type: ARTICLE Genes: lin-39 mab-5 Abstract: Antennapedia class homeobox (Hox) genes specify cell fates in successive anteroposterior body domains in vertebrates, insects and nematodes(1-3). The DNA-binding homeodomain sequences are very similar between vertebrate and Drosophila Hox proteins, and this similarity allows vertebrate Hox proteins to function in Drosophila(4-7). In contrast, the Caenorhabditis elegans homeodomains are substantially divertent(8). Further, C. elegans differs from both insects and vertebrates in having a non-segmented body as well as a distinctive mode of development that involves asymmetric early cleavages and invariant cell lineages. Here we report that, despite these differences, Drosophila Hox proteins expressed in C. elegans can substitute for C. elegans Hox proteins in the control of three different cell-fate decisions: the regulation of cell migration, the specification of serotonergic neurons, and the specification of a sensory structure. We also show that the specificity of one C. elegans Hox protein is partly determined by two amino acids that have been implicated in sequence-specific DNA binding. Together these findings suggest that factors important for target recognition by specific Hox proteins have been conserved throughout much ------------------- Key: 2271 Medline: 95405499 Authors: Xue D;Horvitz HR Title: Inhibition of the Caenorhabditis elegans cell-death protease CED-3 by a ced-3 cleavage site in baculovirus p35 Citation: Nature 377: 248-251 1995 Type: ARTICLE Genes: ced-3 Abstract: The baculovirus protein p35 inhibits programmed cell death in such diverse animals as insects, nematodes and mammals(1-5). Here we show that p35 protein is a substrate for and inhibitor of the Caenorhabditis elegans cell-death protease CED-3 (refs 6, 7) and a substrate for four CED-3-like vertebrate cysteine protease activities implicated in apoptosis in mammals(7-14). A p35 mutation that greatly reduced p35 activity in vitro as a CED-3 substrate and inhibitor abolished p35 activity in vivo in protecting against cell death in C. elegans. Introduction of the CED-3 cleavage site in p35 into the cowpox virus protein crmA, which inhibits mammalian apoptosis(14-19) but not programmed cell death in C. elegans, caused crmA to block CED3-mediated cell death. These observations suggest that p35 may prevent programmed cell death in C. elegans and other species by acting as a competitive inhibitor of cysteine proteases. ------------------- Key: 2272 Medline: 95395594 Authors: Reiner DJ;Thomas JH Title: Reversal of a muscle response to GABA during C. elegans male development. Citation: Journal of Neuroscience 15: 6094-6102 1995 Type: ARTICLE Genes: aex-1 aex-2 aex-3 aex-4 aex-5 aex-6 egl-2 egl-23 egl-36 exp-1 exp-2 unc-25 unc-30 unc-46 unc-47 unc-49 Abstract: In the C. elegans hermaphrodite the expulsion step of defecation depends on the coordinated contraction of three enteric muscle groups: the anal depressor muscle, the intestinal muscles, and the sphincter muscle. These muscles are activated by excitatory GABA neurotransmission. Mutations in 13 genes that affect activation of these enteric muscles have previously been identified. We show that the larval male defecates by contracting the same set of enteric muscles, and that these contractions require 12 of these 13 genes. However, near the end of the last larval stage, the male anal region undergoes a developmental change, including dramatic hypertrophy of the anal sphincter muscle and the opening of a cloacal canal. We find that this modified sphincter must now relax to permit defecation. In contrast to the larval male, we find that in the adult male only 2 of the 13 genes required for enteric muscle contraction, unc-25 and unc-47, are important for sphincter muscle relaxation, unc-25 and unc-47 are required for the synthesis and utilization of GABA. We also find that two other genes, unc-46 and unc-49, previously implicated in the inhibitory action of GABA on body-wall muscle, are also required for normal adult male sphincter relaxation. In these mutants, failure to relax the sphincter muscle results in a constipated phenotype, and killing the sphincter muscle rescues this phenotype. We also find that a GABA agonist or GABA itself can suppress the adult male sphincter relaxation defect of unc-25 mutants. Thus, we demonstrate that GABA is required for excitation of the hermaphrodite and larval male sphincter muscle, while GABA is required for inhibition of this sphincter muscle in the adult male. We conclude that the morphological changes that take place during the developmental transition from the larval to adult male are accompanied by changes in response of the anal sphincter ------------------- Key: 2273 Medline: 96077266 Authors: Aspbury RA;Fisher MJ;Rees HH Title: Fatty acylation of polypeptides in the free-living nematode Caenorhabditis elegans. Citation: Biochemical Society Transactions 23: 405S- 1995 Type: ARTICLE Genes: Abstract: Modification, by the addition of lipid-derived groups, is an important determinant of the correct expression of a variety of polypeptides involved in signal transduction. Myristic and palmitic acid are the predominant fatty acids attached to proteins in eucaryotes. Myristic acid is normally linked, cotranslationally, via an amide bond to an N-terminal glycine. In contrast, palmitic acid attachment occurs post-translationally via an alkali-labile ester or thioester linkage... ------------------- Key: 2274 Medline: 95394980 Authors: Ross LH;Freedman JH;Rubin CS Title: Structure and expression of novel spliced leader RNA genes in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 270: 22066-22075 1995 Type: ARTICLE Genes: Abstract: Approximately 25% of Caenorhabditis elegans genes are organized as operons. Polycistronic transcripts are converted to monocistronic mRNAs by 3' cleavage/polyadenylation and 5' trans-splicing with untranslated, 5'-terminal exons called spliced leaders, (SLs). The 5' termini of mRNAs encoded by downstream genes in operons are accepters for greater than or equal to 7 recently discovered ''novel'' SLs and a classical SL (SL2). Diversity in SL exons is now partly explained by the discovery and characterization of five novel genes that encode C. elegans SL RNAs. These novel SL RNAs contain a 22- or 23-nucleotide SL followed by conserved splice donor and downstream sequences that are essential for catalysis of trans-splicing reactions. The SL3 alpha, SL4, and SL5 RNA genes are tightly clustered on chromosome III; their 114-nucleotide transcripts deliver three distinct SLs to mRNAs. The SL3 beta and SL3 gamma RNA genes are on chromosome I, but are not tightly linked. SL RNAs 3 alpha, 3 beta, and 3 gamma provide identical 5' leader exons, although their 3' sequences diverge. Transcription of SL 3-5 RNA genes appears to be driven by flanking DNA elements that are homologous with segments of promoters for the C. elegans SL2 RNA and small nuclear RNA genes. RNase protection assays demonstrated that novel SL RNAs are transcribed in vivo and accumulate in the poly(A(-)) RNA pool. SL3 exons are transferred to mRNAs as frequently as SL2 exons. In contrast, SL4 is appended to mRNAs 10% as frequently as SL3. The abundance of SL4 RNA increased 6-fold during postembryonic development, and the SL4 RNA gene promoter is active principally in hypodermal cells. ------------------- Key: 2275 Medline: 96173078 Authors: Fukushige T;Siddiqui SS Title: Effect of the dpy-20 and rol-6 cotransformation markers on alpha-tubulin gene expression in C. elegans transformants. Citation: Transgenic Research 4: 332-340 1995 Type: ARTICLE Genes: dpy-20 rol-6 Abstract: An alpha-1 tubulin::lacZ fusion gene was introduced into the germline of Caenorhabditis; elegans, using either rol-6 or dpy-20 genomic DNA as a cotransformation marker. Distinct patterns in cellular specificity of the alpha-1 tubulin::lacZ fusion gene expression were observed, depending on the cotransformation marker used. For the rol-6 marker, the tubulin fusion gene was expressed in several neurons in the head and tail ganglia and a set of 38-39 ventral cord motor neurons along the body length of the animal during larval and adult development. In contrast, for the dpy-20 marker system, not only were fewer neurons stained in the head and tail region, but also the staining of ventral cord motor neurons was extremely reduced both in number and intensity. The dpy-20 marked-mediated suppression of the alpha-1 tubulin gene expression was observed both in the cis and trans configurations. Similar down-regulation in the ventral cord motor neurons was observed when the alpha-2 tubulin:: lacZ fusion gene construct was tested in these experiments using the dpy-20 marker. In controls, where the tubulin fusion gene was directly injected to obtain transformants without any marker DNA, the cellular staining pattern was close to the fusion gene expression observed with the rol-6 marker DNA. These results underline the importance of the choice of transformation marker system in generation of the transgenic animals, and reveal a down-regulation of the alpha-tubulin fusion gene expression in the ventral cord motor neurons in transgenic animals when the dpy-20 gene ------------------- Key: 2276 Medline: 96004643 Authors: Oosumi T;Garlick B;Belknap WR Title: Identification and characterization of putative transposable DNA elements in solanaceous plants and Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 92: 8886-8890 1995 Type: ARTICLE Genes: ced-3 Abstract: Several families of putative transposable elements (TrEs) in both solanaceous plants and Caenorhabditis elegans have been identified by screening the DNA data base for inverted repeated domains present in multiple copies in the genome, The elements are localized within intron and flanking regions of many genes, These elements consist of two inverted repeats flanking sequences ranging from 5 bp to >500 bp, Identification of multiple elements in which sequence conservation includes both the flanking and internal regions implies that these TrEs are capable of duplicative transposition, Two of the elements were identified in promoter regions of the tomato (Lycopersicon esculentum) polygalacturonase and potato (Solanum tuberosum) Win1 genes, The element in the polygalacturonase promoter spans a known regulatory region. In both cases, ancestral DNA sequences, which represent potential recombination target sequences prior to insertion of the elements, have been cloned from related species, The sequences of the inverted repeated domains in plants and C, elegans show a high degree of phylogenetic conservation, While frequency of the different elements is variable, some are present in very high copy number, A member of a single C, elegans TrE family is observed approximately once every 20 kb in the genome, The abundance of the described TrEs suggests utility in the genomic analysis of these and ------------------- Key: 2277 Medline: 96109599 Authors: Wilkinson HA;Greenwald I Title: Spatial and temporal patterns of lin-12 expression during C. elegans hermaphrodite development. Citation: Genetics 141: 513-526 1995 Type: ARTICLE Genes: lin-12 smg-1 Abstract: The lin-12 gene encodes a receptor that mediates certain cell-cell interactions during Caenorhabditis elegans development. We have examined the expression of a lin-12::lacZ reporter gene in individual cells during the development of C. elegans hermaphrodites. lin-12::lacZ is expressed in a discrete spatial and temporal pattern during development and the lin-12::lacZ reporter gene will provide a useful marker for other studies, particularly of somatic gonadal and vulval development. In general, the cells that express lin-12::lacZ correspond to cells whose fates are known to be altered in lin-12 mutants implying that restriction of lin-12 expression may be an important regulatory mechanism; the exceptions to this statement may reveal the cellular defects that underlie aspects of the lin-12 phenotype that have not been previously explained. For decisions that are not naturally variable, lin-12::lacZ expression does not appear to change before or upon commitment to a cell fate implying that in these cases posttranscriptional regulation of lin-12 activity may control cell fate specification. ------------------- Key: 2278 Medline: 96109600 Authors: Hodgkin J;Albertson DG Title: Isolation of dominant XO-feminizing mutations in Caenorhabditis elegans: New regulatory tra alleles and an X chromosome duplication with implications for primary sex determination. Citation: Genetics 141: 527-542 1995 Type: ARTICLE Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 fem-1 fem-2 fem-3 fox-1 her-1 him-8 sdc-1 sdc-2 sdc-3 tra-1 tra-2 tra-3 xol-1 eDp26 eDp27 mnDp57 mnDp65 mnDp66 mnDp67 mnDp68 mnDp70 mnDp73 Abstract: A strain of Caenorhabditis elegans was constructed that permits selection of dominant or sex-linked mutations that transform XO animals (normally male) into fertile females, using a feminizing mutation, tra-2(e2046gf), which by itself does not sexually transform XO males. Twenty-three mutations were isolated after chemical mutagenesis and found to fall into both expected classes (four dominant tra-1 mutations and eight recessive xol-1 mutations) and novel classes. The novel mutations include 10 second-site mutations of tra-2, which are called eg mutations, for enhanced gain-of-function. The tra-2(gj, eg) alleles lead to complete dominant transformation of XO animals from fertile male into fertile female. Also isolated was a duplication of the left end of the X chromosome, eDp26 which has dominant XO lethal and feminizing properties, unlike all previously isolated duplications of the X chromosome. The properties of eDp26 indicate that it carries copies of one or more numerator elements, which act as part of the primary sex-determination signal, the X:A ratio. The eDp26 duplication is attached to the left tip of the X chromosome in inverted orientation and consequently can be used to generate unstable attached-X chromosomes. ------------------- Key: 2279 Medline: 96109602 Authors: Qiao L;Lissemore JL;Shu P;Smardon A;Gelber MB;Maine EM Title: Enhancers of glp-1, a gene required for cell-signalling in Caenorhabditis elegans, define a set of genes required for germline development. Citation: Genetics 141: 551-569 1995 Type: ARTICLE Genes: ego-1 ego-2 ego-3 ego-4 ego-5 gld-1 glp-1 glp-4 lag-1 lag-2 ooc-4 sog-1 sog-4 eDf1 hDf9 nDf24 nDf25 nDf40 nDf41 nDf42 ozDf5 sDf35 yDf8 Abstract: The distal tip cell (DTC) regulates the proliferation or differentiation choice in the Caenorhabditis elegans germline by an inductive mechanism. Cell signaling requires a putative receptor in the germline, encoded by the glp-1 gene, and a putative signal from the DTC, encoded by the lag-2 gene. Both glp-1 and lag-2 belong to multigene gene families whose members are essential for cell signaling during development of various tissues in insects and vertebrates as well as C. elegans. Relatively little is known about how these pathways regulate cell fate choice. To identify additional genes involved in the glp-1 signaling pathway, we carried out screens for genetic enhancers of glp-1. We recovered mutations in five new genes, named ego (enhancer of glp-1), and two previously identified genes, lag-1 and glp-4, that strongly enhance a weak glp-1 loss-of-function phenotype in the germline. Ego mutations cause multiple phenotypes consistent with the idea that gene activity is required for more than one aspect of germline and, in some cases, somatic development. Based on genetic experiments, glp-1 appears to act upstream of ego-1 and ego-3. We discuss the possible functional relationships among these genes in light of their phenotypes and interactions with glp-1. ------------------- Key: 2280 Medline: 96004884 Authors: Greenbaum NL;Radhakrishnan I;Hirsh D;Patel DJ Title: Determination of the folding topology of the SL1 RNA from Caenorhabditis elegans by multidimensional heteronuclear NMR. Citation: Journal of Molecular Biology 252: 314-327 1995 Type: ARTICLE Genes: Abstract: The process of trans-splicing involves the transfer of a short spliced leader (SL) RNA sequence to a consensus acceptor site on a separate pre-mRNA transcript. In this study, the first stem loop of the SL1 RNA from the nematode Caenorhabditis elegans was examined by homonuclear and heteronuclear NMR. Results of enzymatic cleavage patterns established that the first 36 nucleotides (which includes the splice site and a complementary base-paired region surrounding a nine-nucleotide hairpin loop) remain structurally independent of the rest of the 100-nucleotide full-length transcript. A comparison of exchangeable and non-exchangeable proton chemical shifts in the region of the splice site and loop between the native sequence and a modified 26-nucleotide fragment from which an asymmetric internal loop had been deleted was made. There was no significant difference between the resonance locations of the equivalent protons in the two molecules, establishing that there was no tertiary interaction between the hairpin and internal loops. Full chemical shift assignments of H-1, C-13, and N-15 chemical shifts were obtained for the modified fragment by multidimensional homonuclear and heteronuclear NMR spectroscopy The stem adopts an A-form helix typical of RNA. The A-type helical conformation of the stem appears to continue for the first three nucleotides of the 5' side of the loop, followed by a guanosine residue in a syn conformation about the glycosidic bond. Base stacking is not seen on the 3' side of the loop. There was no evidence for formation of Watson-Crick base-pairs within the loop, but several long distance NOEs indicated cross-loop contacts, indicative of a structured loop. The final loop residues, an adenine which is conserved among all known nematode SL RNA sequences, adopts an extrahelical conformation. ------------------- Key: 2281 Medline: 96038098 Authors: Miller DM;Niemeyer CJ Title: Expression of the unc-4 homeoprotein in Caenorhabditis elegans motor neurons specifies presynaptic input. Citation: Development 121: 2877-2886 1995 Type: ARTICLE Genes: unc-4 Abstract: In the nematode, Caenorhabditis elegans, VA and Vp motor neurons arise from a common precursor cell but adopt different morphologies and synapse with separate sets of interneurons in the ventral nerve cord. A mutation that inactivates the unc-4 homeodomain gene causes VA motor neurons to assume the VB pattern of synaptic input while retaining normal axonal polarity and output; the disconnection of VA motor neurons from their usual presynaptic partners blocks backward locomotion. We show that expression of a functional unc-4-beta-galactosidase chimeric protein in VA motor neurons restores wild-type movement to an unc-4 mutant. We propose that unc-4 controls a differentiated characteristic of the VA motor neurons that distinguishes them from their VB sisters, thus dictating recognition by the appropriate interneurons. Our results show that synaptic choice can be controlled at the level of transcription in the post-synaptic neuron and identify a homeoprotein that defines a subset of cell-specific traits required for this choice. ------------------- Key: 2282 Medline: 96038106 Authors: Strome S;Martin P;Schierenberg E;Paulsen J Title: Transformation of the germ line into muscle in mes-1 mutant embryos of C. elegans. Citation: Development 121: 2961-2972 1995 Type: ARTICLE Genes: mes-1 nDf19 Abstract: Mutations in the maternal-effect sterile gene mes-1 cause the offspring of homozygous mutant mothers to develop into sterile adults, Lineage analysis revealed that mutant offspring are sterile because they fail to form primordial germ cells during embryogenesis, In wild-type embryos, the primordial germ cell P-4 is generated via a series of four unequal stem-cell divisions of the zygote. mes-1 embryos display a premature and progressive loss of polarity in these divisions: P-0 and P-1 undergo apparently normal unequal divisions and cytoplasmic partitioning, but P-2 (in some embryos) and P-3 (in most embryos) display defects in cleavage asymmetry and fail to partition lineage-specific components to only one daughter cell. As an apparent consequence of these defects, P-4 is transformed into a muscle precursor, like its somatic sister cell D, and generates up to 20 body muscle cells instead of germ cells, Our results show that the wild-type mes-1 gene participates in promoting unequal germ-line divisions and asymmetric partitioning events and thus the determination of cell fate in early C. elegans embryos. ------------------- Key: 2283 Medline: 96038109 Authors: Kuwabara PE;Kimble J Title: A predicted membrane protein, TRA-2A, directs hermaphrodite development in Caenorhabditis elegans. Citation: Development 121: 2995-3004 1995 Type: ARTICLE Genes: tra-2 Abstract: The nematode C. elegans naturally develops as either an XO male or XX hermaphrodite, The sex-determining gene, tra-2, promotes hermaphrodite development in XX animals, This gene encodes a predicted membrane protein, named TRA-2A, which has been proposed to provide the primary feminising activity of the tra-2 locus, Here, we show that transgenic TRA-2A driven from a heat shock promoter can fully feminise the somatic tissues of XX tra-2 loss-of-function mutants, which would otherwise develop as male. TRA-2A is thus likely to provide a component of the tra-2 locus that is both necessary and sufficient to promote female somatic development, Transgenic TRA-2A driven by the heat shock promoter can also transform XO animals from male to self-fertile hermaphrodite, This result establishes the role of tra-2 as a developmental switch that controls somatic sexual cell fate, We show that a carboxy-terminal region of TRA-2A, predicted to be intracellular, can partially feminise XX tra-2 loss-of-function mutants and XO tra-2(+) males, We suggest that this intracellular domain of TRA-2A promotes hermaphrodite development by negatively regulating the FEM proteins. ------------------- Key: 2284 Medline: 96018742 Authors: Jones D; Stringham EG;Graham RW;Candido EPM Title: A portable regulatory element directs specific expression of the Caenorhabditis elegans ubiquitin gene ubq-2 in the somatic gonad. Citation: Developmental Biology 171: 60-72 1995 Type: ARTICLE Genes: ubq-1 ubq-2 Abstract: The Caenorhabditis elegans ubq-2 gene encodes a fusion of ubiquitin and a 52-amino-acid ribosomal protein. This single copy gene is both cis- and trans-spliced. It is expressed in all life stages of the worm and its transcript abundance is unaffected by heat stress. Transgenic analysis shows that expression of ubq-2 is regulated by an upstream promoter and a downstream element. The downstream element is required for ubq-2 promoter activity in embryos and in cells of the somatic gonad, including the distal tip cells, sheath cells, spermathecal cells, and cells of the uterus. The gonad-specific activity of the downstream regulator is transferable to a stress gene promoter such that heat-inducible expression of the transgene occurs in the somatic gonad. Stress-inducible beta-galactosidase expression in the gonad does not occur in all life stages, but is initiated late in the second or early in the third larval stage, when differentiation of gonadal tissues begins. Expression of a beta-galactosidase fusion protein from constructs containing the downstream ubq-2 regulator causes abnormalities of the gonad and embryonic lethality. Gonad abnormalities include arrested development and general disorganization. These abnormalities may be related to the overexpression of ubiquitin in the gonad. (C) 1995 Academic Press, Inc. ------------------- Key: 2285 Medline: 96032531 Authors: Levitan D;Greenwald I Title: Facilitation of lin-12-mediated signalling by sel-12, a Caenorhabditis elegans S182 Alzheimer's disease gene. Citation: Nature 377: 351-354 1995 Type: ARTICLE Genes: glp-1 let-60 lin-12 sel-12 Abstract: The lin-12 and glp-1 genes of Caenorhabditis elegans are members of the lin-12/Notch family of receptors for intercellular signals that specify cell fate(1,2). By screening for suppressors of a lin-12 gain-of-function mutation, we identified a new gene, sel-12, which appears to function in receiving cells to facilitate signalling mediated by lin-12 and glp-1. The sel-12 gene encodes a protein with multiple transmembrane domains, and is similar to S182, which has been implicated in early-onset familial Alzheimer's disease(3). The high degree of sequence conservation suggests that the function of the SEL-12 and S182 proteins may also be conserved. ------------------- Key: 2286 Medline: 96018822 Authors: Singh N;Han M Title: sur-2, a novel gene, functions late in the let-60 ras-mediated signaling pathway during Caenorhabditis elegans vulval induction. Citation: Genes & Development 9: 2251-2265 1995 Type: ARTICLE Genes: let-60 let-537 lin-1 lin-12 lin-15 lin-25 lin-31 lin-45 mek-2 mpk-1 sur-1 sur-2 eDf11 eDf13 eDf14 hIn1 Abstract: We describe here a new gene acting downstream of let-60 ras in the vulval signaling pathway of Caenorhabditis elegans. The sur-2 (suppressor of ras) gene is defined by eight mutations identified in a genetic screen for suppressors of the Multivulva phenotype of let-60(n1046), an activated let-60 ras mutation. sur-2 mutations result in pleiotropic, incompletely penetrant phenotypes that include a Vulvaless phenotype in hermaphrodites, defects in development of the male tail, gonadal abnormalities, and larval lethality, indicating a role for the sur-2 gene product in multiple developmental events. Genetic epistasis analyses suggest that sur-2 is required late in the vulval signaling pathway, downstream of let-60 Ras, and is likely to act downstream of the Raf/MAP Kinase cascade. We cloned the sur-2 gene by DNA-mediated transformation and have shown that it encodes a novel protein. We also shaw that a sur-2::lacZ transgene is expressed in the vulval precursor cells at the time of vulval determination. ------------------- Key: 2287 Medline: 96100379 Authors: Koga M;Ohshima Y Title: Drosophila MAP kinase kinase suppresses the vulvaless phenotype of lin-3, let-23 and lin-45 mutations in Caenorhabditis elegans. Citation: Mechanisms of Development 53: 15-22 1995 Type: ARTICLE Genes: let-23 let-60 lin-3 lin-45 mpk-1 sur-1 Abstract: The vulva of the nematode Caenorhabditis elegans develops from the three vulval precursor cells (VPCs) that are induced by a signal from the gonadal anchor cell. This signal is thought to be mediated by a receptor tyrosine kinase (RTK) in the VPCs to a downstream signal transduction pathway. A mitogen-activated protein kinase kinase (MAPKK) has been found to be one of the major components of an RTK pathway in other organisms. We expressed a wild type and an activated cDNA of Dsor1, a Drosophila MAPKK, in each of the three vulvaless mutants lin-3, let-23 and lin-45. The expression of an activated form of Dsor1 in each of the mutants effectively induced a normal, functional vulva, that is, suppressed the vulvaless phenotype. The wild type Dsor1 also suppressed albeit less effectively. These results suggest that a MAPKK is involved in the vulval induction of C. elegans. ------------------- Key: 2288 Medline: 96003623 Authors: Sugimoto A;Hozak RR;Nakashima T;Nishimoto T;Rothman JH Title: dad-1, an endogenous programmed cell death suppressor in Caenorhabditis elegans and vertebrates. Citation: EMBO Journal 14: 4434-4441 1995 Type: ARTICLE Genes: ced-1 dad-1 Abstract: Programmed cell death (apoptosis) is a normally occurring process used to eliminate unnecessary or potentially harmful cells in multicellular organisms. Recent studies demonstrate that the molecular control of this process is conserved phylogenetically in animals. The dad-1 gene, which encodes a novel 113 amino acid protein, was originally identified in a mutant hamster cell line (tsBN7) that undergoes apoptosis at restrictive temperature. We have identified a dad-1 homologue in Caenorhabditis elegans (Ce-dad-1) whose predicted product is >60% identical to vertebrate DAD-1. A search of the sequence databases indicated that DAD-1-like proteins are also expressed in two plant species. Expression of either human dad-1 or Ce-dad-1 under control of a C.elegans heat-shock-inducible promoter resulted in a reduction in the number of programmed cell death corpses visible in C.elegans embryos. Extra surviving cells were present in these animals, indicating that both the human and C.elegans dad-1 genes can suppress developmentally programmed cell death. Ce-dad-1 was found to rescue mutant tsBN7 hamster cells from apoptotic death as efficiently as the vertebrate genes. These results suggest that dad-1, which is necessary for cell survival in a mammalian cell line, is sufficient to suppress some programmed cell death in C.elegans. ------------------- Key: 2289 Medline: 96016170 Authors: Link CD Title: Expression of human beta-amyloid peptide in transgenic Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 92: 9368-9372 1995 Type: ARTICLE Genes: unc-54 Abstract: Transgenic Caenorhabditis elegans nematodes have been engineered to express potentially amyloidic human proteins. These animals contain constructs in which the muscle-specific unc-54 promoter/enhancer of C. elegans drives the expression of the appropriate coding regions derived from human cDNA clones. Animals containing constructs expressing the 42-amino acid beta-amyloid peptide (derived from human amyloid precursor protein cDNA) produce muscle-specific deposits immunoreactive with anti-beta-amyloid polyclonal and monoclonal antibodies. A subset of these deposits also bind the amyloid-specific dye thioflavin S, indicating that these deposits have the tinctural characteristics of classic amyloid, Coexpression of beta-peptide and transthyretin, a protein implicated in preventing the formation of insoluble beta-amyloid, leads to a dramatic reduction in the number of dye-reactive deposits. These results suggest that this invertebrate model may be useful for in vivo investigation of factors that modulate amyloid formation. ------------------- Key: 2290 Medline: 96114101 Authors: Lye RJ;Wilson RK;Waterston RH Title: Genomic structure of a cytoplasmic dynein heavy chain gene from the nematode Caenorhabditis elegans. Citation: Cell Motility and the Cytoskeleton 32: 26-36 1995 Type: ARTICLE Genes: Abstract: We report the cloning and sequencing of genomic DNA encoding a cytoplasmic dynein heavy chain from the nematode Caenorhabditis elegans. In a contiguous stretch of 35,103 bp of DNA from the left arm of linkage group I, we have found a gene that is predicted to encode a protein of 4,568 amino acids. This gene is composed of 15 exons and 14 relatively short introns, and it has significant homology to the other dynein heavy chains in the databases. The deduced molecular mass of the derived polypeptide is 512,624 Da. As with other dynein heavy chains that have been sequenced to date. it contains four GXXGXGK(S/T) motifs that form part of the consensus sequence for nucleotide triphosphate-binding domains. Comparison of axonemal and cytoplasmic dynein heavy chains shows that regions of homology among all dyneins are clustered in the carboxyl terminal two-thirds of the polypeptide, whereas the amino terminal one-third of the heavy chains may contain domains that specify functions that differ between axonemal and cytoplasmic forms of the dynein heavy chain. ------------------- Key: 2291 Medline: 95400912 Authors: Duhon SA;Johnson TE Title: Movement as an index of vitality: Comparing wild type and the age-1 mutant of Caenorhabditis elegans. Citation: Journal of Gerontology 50A: B254-B261 1995 Type: ARTICLE Genes: age-1 fer-15 Abstract: We have asked whether the mutant form of the age-1 gene, which lengthens the life span of the nematode Caenorhabditis elegans up to 70%, also affects tire ability to move during this extended period of life. Both age-1 mutants and wild-type controls display a linear loss of movement as the nematodes age. age-1 mutant strains moved faster early in life when compared with non-Age strains and continued low rates of movement at older ages than did non-Age strains. Movement rates were not, in general, a good predictor of movement rates at any later age or of life span. Cumulative lifetime movements of individuals were highly correlated with, and thus a good predictor of, individual life span. These findings are similar to earlier studies of movement in long-lived recombinant-inbred strains of C. elegans and imply that the physiological process altered by the age-1 mutation results in increased health during later life as monitored by increased ability ------------------- Key: 2292 Medline: 96400911 Authors: Fabian TJ;Johnson TE Title: Identification of genes that are differentially expressed during aging in Caenorhabditis elegans. Citation: Journal of Gerontology 50A: B245-B253 1995 Type: ARTICLE Genes: act-4 age-1 emb-27 fer-15 spe-9 unc-54 vit-2 vit-5 vit-6 Abstract: We isolated cDNA clones of transcripts that undergo change in abundance over the adult life span of the nematode Caenorhabditis elegans. Replicas of a C. elegans cDNA library were probed with cDNA synthesized from poly(A)(+)RNA isolated from young or old nematodes. We identified clones corresponding to nine distinct transcripts that decreased in abundance with age, two distinct transcripts that increased slightly in abundance with age, and one transcript that peaked in abundance during the early to middle part of the adult life span. Six of the twelve transcripts were quantitated as a function of age by means of a dot blot assay using total RNA isolated at several ages from two strains that have wild-type life spalls. All six mRNAs showed similar age-dependent abundance patterns in these two strains. Mutation of the age-1 gene, which lengthens life span, did not appear to alter these patterns. Nucleotide sequence analysis of clone inserts revealed that three of the mRNAs that decreased in abundance with age corresponded to previously identified C. elegans vitellogenin genes. One transcript that showed a small increase in abundance with age appears to encode translation factor EF1-alpha. The other five clones ------------------- Key: 2293 Medline: 96006529 Authors: Herman MA;Vassilieva LL;Horvitz HR;Shaw JE;Herman RK Title: The C. elegans gene lin-44, which controls the polarity of certain asymmetric cell divisions, encodes a Wnt protein and acts cell nonautonomously. Citation: Cell 83: 101-110 1995 Type: ARTICLE Genes: lin-44 ncl-1 sup-7 unc-36 hDf7 Abstract: Mutations in the C. elegans gene lin-44 lead to reversals in the polarity of certain asymmetric cell divisions. We have discovered that lin-44 is a member of the Wnt family of genes, which encode secretory glycoproteins implicated in intercellular signaling. Both in situ hybridization experiments using lin-44 transcripts and experiments using reporter constructs designed to mimic patterns of lin-44 expression indicate that lin-44 is expressed in hypodermal cells at the tip of the tail and posterior to the cells with polarities affected by lin-44 mutations. Our mosaic analysis indicates that lin-44 acts cell nonautonomously. We propose that LIN-44 protein is secreted by tail hypodermal cells and affects the polarity of asymmetric cell divisions that occur more anteriorly in the tail. ------------------- Key: 2294 Medline: 96117779 Authors: Squire MD;Tornoe C;Baylis HA;Fleming JT;Barnard EA;Sattelle DB Title: Molecular cloning and functional co-expression of a Caenorhabditis elegans nicotinic acetylcholine receptor subunit (acr-2). Citation: Receptors and Channels 3: 107-115 1995 Type: ARTICLE Genes: acr-2 unc-38 Abstract: A number of putative nicotinic acetylcholine receptor subunit clones were isolated by screening a lambda library of Caenorhabditis elegans genomic DNA with a probe derived from the Drosophila melanogaster ard gene (a non-alpha nicotinic acetylcholine receptor subunit clone). Studies on one of these loci, acr-2, are described; acr-2 is located between sup-7 and unc-6 on the X chromosome. A full-length cDNA was isolated and sequenced. The cDNA encodes a putative non-alpha subunit of a nicotinic acetylcholine receptor that shows many of the conserved features of vertebrate and invertebrate non-alpha nicotinic acetylcholine receptor subunits. To investigate the functional expression of the subunit, the corresponding cRNA was produced, in vitro, and micro-injected into Xenopus oocytes. When expressed alone acr-2 shows no levamisole-gated channel activity. When co-expressed with a C. elegans a subunit (unc-38), which is itself unable to form functional homo-oligomers, acr-2 contributed to the formation of a functional channel. This is the first functional expression of a nematode nicotinic acetylcholine receptor and supports the interpretation that the differentiation between alpha and non-alpha subunits dates back to the earliest stages of the evolution of the ------------------- Key: 2295 Medline: 96079949 Authors: Conrad R;Lea K;Blumenthal T Title: SL1 trans-splicing specified by AU-rich synthetic RNA inserted at the 5' end of Caenorhabditis elegans pre-mRNA. Citation: RNA 1: 164-170 1995 Type: ARTICLE Genes: vit-2 vit-6 Abstract: In Caenorhabditis elegans, pre-mRNAs of many genes are trans-spliced to one of two spliced leaders, SL1 or SL2. Some of those that receive exclusively SL1 have been characterized as having at their 5' ends outrons, AU-rich sequences similar to introns followed by conventional 3' splice sites. Comparison of outrons from many different SL1-specific C. elegans genes has not revealed the presence of any consensus sequence that might encode SL1-specificity. In order to determine what parameters influence the splicing of SL1, we performed in vivo experiments with synthetic splice sites. Synthetic AU-rich RNA, 51 nt or longer, placed upstream of a consensus 3' splice site resulted in efficient trans-splicing. With all sequences tested, this trans-splicing was specifically to SL1. Thus, no information beyond the presence of AU-rich RNA at least as long as the minimum-length C. elegans intron, followed by a 3' splice site, is required to specify trans-splicing or for strict SL1 specificity. ------------------- Key: 2296 Medline: 96079961 Authors: Van Horn DJ;Eisenberg D;O'Brien CA;Wolin SL Title: Caenorhabditis elegans embryos contain only one major species of Ro RNP. Citation: RNA 1: 293-303 1995 Type: ARTICLE Genes: Abstract: In virtually all vertebrate cells, Ro RNPs consist of the 60-kDa Ro autoantigen bound to one of several small cytoplasmic RNA molecules known as Y RNAs. Because the 60-kDa Ro autoantigen is also found complexed with defective precursors of 5S rRNA in Xenopus oocytes, we have proposed that this protein functions in a quality control, or discard pathway, for 5S RNA biosynthesis (O'Brien CA, Wolin SL, 1994, Genes & Dev 8:2891-2903). The role of the Y RNAs in this pathway is unknown. To begin a genetic analysis of Ro RNP function, we have characterized these particles in the nematode Caenorhabditis elegans. The C. elegans Ro protein is 12 kDa larger than the vertebrate protein; the larger size is due in part to an N-terminal extension and to two insertions in the RNA recognition motif. In contrast to all previously described vertebrate species, the Ro protein appears bound to a single Y RNA in C. elegans. Similar to vertebrate Y RNAs, the C. elegans Y RNA can be folded to form a pyrimidine-rich internal loop and a long stem in which the 5' and 3' ends are base paired. Within the stem is a conserved bulged helix that is proposed to be the binding site of the Ro protein. Interestingly, although the human protein can bind the nematode Y RNA, the C. elegans protein does not bind human Y RNAs. This is the first description of Ro RNPs in an ------------------- Key: 2297 Medline: Authors: Jorgensen EM;Nonet ML Title: Neuromuscular junctions in the nematode C. elegans. Citation: Seminars in Developmental Biology 6: 207-220 1995 Type: REVIEW Genes: ace-1 ace-2 ace-3 cha-1 exp-1 lev-1 lev-8 lev-9 lev-10 rab-3 ric-1 ric-3 ric-4 ric-6 ric-7 snt-1 unc-2 unc-4 unc-6 unc-11 unc-13 unc-17 unc-18 unc-25 unc-26 unc-29 unc-31 unc-32 unc-36 unc-38 unc-41 unc-46 unc-47 unc-49 unc-50 unc-55 unc-63 unc-64 unc-65 unc-75 unc-104 Abstract: The neuromuscular junction serves widely as a model synapse for both the study of synaptic development and synaptic transmission. We are now attempting to understand the molecular events that underlie these processes. One approach to the study of the neuromuscular junction is to analyse mutants of the nematode Caenorhabditis elegans. We review the motor circuit in the worm responsible for locomotion, the development of the C. elegans neuromuscular junction, and the gene products required for the functioning of nematode synapses. This genetic approach has both identified novel components of the neuromuscular junction and has ascertained the in-vivo roles of biochemically-defined components that regulate neuromuscular transmission and development. ------------------- Key: 2298 Medline: 96114505 Authors: Griff IC;Reed RR Title: The genetics of olfaction. Citation: Current Opinion in Genetics & Development 5: 657-661 1995 Type: REVIEW Genes: adp-1 odr-7 osm-1 Abstract: Our understanding of olfaction has progressed rapidly in recent years as a result of the molecular genetic approaches being used to study this sensory system in a variety of model organisms. Considerable success has been achieved in identifying proteins of the mammalian signaling system that are analogous to those present in other sensory systems. More recently, genetic selection of mutations that cause defects in olfactory function in Drosophila melanogaster and Caenorhabditis elegans has led to the identification of additional proteins that play a role in the detection of odorants. The application of genetic, electrophysiologica, and molecular analyses to olfactory function in mammals is also shedding light on the mechanisms that account for sensitivity and specificity in this system. (This review also appears in Current Opinion in Neurobiology 1995, 5:45-460.) ------------------- Key: 2299 Medline: 96003875 Authors: Gao DL;Kimble J Title: APX-1 can substitute for its homolg LAG-2 to direct cell interactions throughout Caenorhabditis elegans development. Citation: Proceedings of the National Academy of Sciences USA 92: 9839-9842 1995 Type: ARTICLE Genes: apx-1 glp-1 lag-2 lin-12 Abstract: The homologous LAG-2 and APX-1 membrane proteins are putative signaling ligands in the GLP-1/LIN-12 signal-transduction pathway in Caenorhabditis elegans, Normally, LAG-2 and APX-1 mediate distinct cell interactions, Here, we demonstrate that APX-1, which normally interacts with GLP-1 in the early embryo, can substitute for LAG-2 throughout development, When expressed under control of the lag-2 promoter, an apx-1 cDNA can completely rescue a lag-2 null mutant, To substitute for LAG-2, APX-1 must be able to interact with both GLP-1 and LIN-12 receptors and Co mediate a variety of cell interactions during development, Therefore, APX-1 and LAG-2 are essentially equivalent in their ability to influence receptor activity, On the basis of this result, we suggest that the existence of multiple-signaling ligands in the LIN-12/GLP-1 signal transduction pathway does not reflect the evolution of functionally distinct proteins but rather the imposition of distinct controls of gene expression upon functionally similar proteins. Finally, we propose that the specification of distinct fell fates by the LIN-12/GLP-1 signal-transduction pathway relies on activities functioning downstream of the ligand and receptor, rather than on specific ligand-receptor interactions. ------------------- Key: 2300 Medline: 96026348 Authors: Hodgkin J;Plasterk RHA;Waterston RH Title: The nematode Caenorhabditis elegans and its genome. Citation: Science 270: 410-414 1995 Type: ARTICLE Genes: Abstract: Over the past two decades, the small soil nematode Caenorhabditis elegans has become established as a major model system for the study of a great variety of problems in biology and medicine. One of its most significant advantages is its simplicity, both in anatomy and in genomic organization. The entire haploid genetic content amounts to 100 million base pairs of DNA, about 1/30 the size of the human value. As a result, C. elegans has also provided a pilot system for the construction of physical maps of larger animal and plant genomes, and subsequently for the complete sequencing of those genomes. By mid-1995, approximately one-fifth of the complete DNA sequence of this animal had been determined. Caenorhabditis elegans provides a test bed not only for the development and application of mapping and sequencing technologies, but also for the interpretation and use of complete sequence information. This article reviews the progress so far toward a realizable goal--the total description of the ------------------- Key: 2301 Medline: 96150966 Authors: Fabian TJ;Johnson TE Title: Total RNA, rRNA and poly(A)+ RNA abundances during aging in Caenorhabditis elegans. Citation: Mechanisms of Ageing & Development 83: 155-170 1995 Type: ARTICLE Genes: age-1 emb-27 fer-15 spe-9 Abstract: This is the second in a series of studies in which we characterize gene expression at the level of RNA during aging in the nematode Caenorhabditis elegans. Here, we quantitatively analyzed total RNA, poly(A)(+) RNA, and ribosomal RNA as a function of chronological age in two different strains (TJ1060 and TJ1061) having wild-type life spans and in a long-lived age-1 mutant strain (TJ1062). In addition, we compared the age-dependent abundance patterns of these RNAs in two different culture environments. Total RNA yield did not show a consistent pattern of age-related changes. However, total RNA yield was significantly higher in all three strains when grown on agar than when grown in liquid. In addition, total RNA yield was significantly lower from strain TJ1061 than from strain TJ1060 and TJ1062. Relative to total RNA, rRNA did not exhibit any consistent differences with age, strain or environment. Poly(A)(+) RNA decreased by 23-43% in old animals from the long-lived strain and one of the wild-type strains: but was not changed in the second wild-type strain. In addition, control experiments to determine the amount of RNA contributed by E. coli bacteria (present in the nematode culture medium as a food source) suggest that the age-1 mutant strain has a lower bacterial infection rate, which may contribute to the increased life span of this strain. ------------------- Key: 2302 Medline: 96017644 Authors: Hsu DR;Chuang P-T;Meyer BJ Title: DPY-30, a nuclear protein essential early in embryogenesis for Caenorhabditis elegans dosage compensation. Citation: Development 121: 3323-3334 1995 Type: ARTICLE Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 rnp-1 sdc-1 sdc-2 sdc-3 xol-1 ctDf1 yDf12 Abstract: DPY-30 is an essential component of the C, elegans dosage compensation machinery that reduces X chromosome transcript levels in hermaphrodites (XX). DPY-30 is required for the sex-specific association of DPY-27 (a chromosome condensation protein homolog) with the hermaphrodite X chromosomes, Loss of dpy-30 activity results in XX-specific lethality, We demonstrate that dpy-30 encodes a novel nuclear protein of 123 amino acids that is present in both hermaphrodites and males (XO) throughout development. DPY-30 itself is not associated with the X chromosomes, nor is its pattern of expression perturbed by mutations in the gene hierarchy that controls dosage compensation, Therefore, DPY-30 is a ubiquitous factor that is likely to promote the hermaphrodite-specific association of DPY-27 with X by affecting the activity of a sex-specific dosage compensation gene. In XO animals, DPY-30 is required for developmental processes other than dosage compensation: coordinated movement, normal body size, correct tail morphology and mating behavior. We demonstrate that rescue of both the XX-specific lethality and the XO-specific morphological defects caused by dpy-30 mutations can be achieved by inducing dpy-30 transcripts either in the mother or in the embryo through the end of gastrulation, dpy-30 appears to be cotranscribed in an operon with a ------------------- Key: 2303 Medline: 96032778 Authors: Williams N Title: How males and females achieve X equality. Citation: Science 269: 1826-1827 1995 Type: REVIEW Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 sdc-1 sdc-2 sdc-3 xol-1 Abstract: Sex has lots of advantages, as the number of species that indulge in it shows. But it also poses a potentially lethal problem. Most species use distinct X and Y sex chromosomes to determine who develops as female and who as male-and the female generally has more copies of the X chromosome than the male. But the X chromosome contains many genes needed equally by males and females, threatening females with what could be a lethal excess of X-chromosome gene products-or males with an equally serious deficiency. Researchers have known for decades that humans and other sexually reproducing species survive because of a correcting mechanism known as "dosage compensation" that equalizes the expression of X-linked genes between the sexes. But only now are they beginning to figure out how ------------------- Key: 2304 Medline: 96032776 Authors: Marx J Title: Tracing how the sexes develop. Citation: Science 269: 1822-1824 1995 Type: REVIEW Genes: fem-1 fem-2 her-1 sdc-1 sdc-2 sdc-3 tra-1 tra-2 tra-3 xol-1 Abstract: The contrasts between the sexes have inspired countless plays, novels, and other creative works. Sex differences inspire a group of developmental biologists, too-but there's a twist. While artists and most of the rest of us are fascinated by the effects of the male-female divide, these biologists are trying to learn how it arises in the first place. Their goal: to trace out the gene pathways that turn an embryo into a male or female. This quest has recently become one of the hottest areas of developmental biology, as two meetings held this year and devoted solely to the subject attest. ------------------- Key: 2305 Medline: 96129272 Authors: Reiner DJ;Weinshenker D;Thomas JH Title: Analysis of dominant mutations affecting muscle excitation in Caenorhabditis elegans. Citation: Genetics 141: 961-976 1995 Type: ARTICLE Genes: act-1 act-2 act-3 aex-2 dpy-2 dpy-21 eat-12 egl-2 egl-4 egl-12 egl-23 egl-30 egl-36 exp-2 exp-3 exp-4 sup-9 sup-10 unc-43 unc-54 unc-58 unc-60 unc-90 unc-93 unc-103 unc-105 unc-110 eDf18 eDf19 mDf7 mnDf1 mnDf104 nDf3 nDf11 nDf19 nDf27 sDf2 sDf23 sDf30 sDf34 Abstract: We examined mutations that disrupt muscle activation in Caenorhabditis elegans. Fifteen of 17 of these genes were identified previously and we describe new mutations in three of them. We also describe mutations in two new genes, exp-3 and exp-4. We assessed the degree of defect in pharyngeal, body-wall, egg-laying, and enteric muscle activation in animals mutant for each gene. Mutations in all 17 genes are semidominant and, in cases that could be tested, appear to be gain-of-function. Based on their phenotypes, the genes fall into three broad categories: mutations in 11 genes cause defective muscle activation, mutations in four genes cause hyperactivated muscle, and mutations in two genes cause defective activation in some muscle types and hyperactivation in others. In all testable cases, the mutations blocked response to pharmacological activators of egg laying, but did not block muscle activation by irradiation with a laser microbeam. The data suggest that these mutations affect muscle excitation, but not the capacity of the muscle fibers to contract. For most of the genes, apparent loss-of-function mutants have a grossly wild-type phenotype. These observations suggest that there is a large group of genes that function in muscle excitation that can be identified primarily by ------------------- Key: 2306 Medline: 96129273 Authors: Maduro M;Pilgrim D Title: Identification and cloning of unc-119, a gene expressed in the Caenorhabditis elegans nervous system. Citation: Genetics 141: 977-988 1995 Type: ARTICLE Genes: daf-7 daf-11 mut-6 unc-119 eDf2 eDf20 tDf2 eDp6 Abstract: A spontaneous mutation affecting locomotion of the nematode Caenorhabditis elegans has been mapped to a new gene, unc-119. Phenotypic characterization of the mutants suggests the defect does not lie in the musculature and that the animals also have defects in feeding behavior and chemosensation. unc-119 has been physically mapped relative to a previously identified chromosomal break in linkage group III, and DNA clones covering the region can rescue the mutant phenotype in transgenic animals. Three more alleles at the locus, with identical phenotypes, have been induced and characterized, all of which are putative null alleles. The predicted UNC-119 protein has no significant similarity to other known proteins. Expression of an unc-119/lacZ fusion in transgenic animals is seen in many neurons, suggesting that the unc-119 mutant phenotype is due to a defect in the nervous system. ------------------- Key: 2307 Medline: 96129274 Authors: Hedgecock EM;Herman RK Title: The ncl-1 gene and genetic mosaics of Caenorhabditis elegans. Citation: Genetics 141: 989-1006 1995 Type: ARTICLE Genes: dpy-1 him-4 him-8 him-10 lin-15 lin-17 ncl-1 nDf16 mnDp14 mnDp30 mnDp84 mnDp86 mnDp89 mnDp90 mnDp91 mnDp92 qDp3 sDp3 Abstract: A ncl-1 mutation results in enlarged nucleoli, which can be detected in nearly all cells of living animals by Nomarski microscopy. Spontaneous mitotic loss of a ncl-1(+)containing free duplication in an otherwise homozygous ncl-1 mutant animal results in mosaicism for ncl-1 expression, and the patterns of mosaicism lead us to conclude that ncl-1 acts cell autonomously. The probability of mitotic loss of the duplication sDp3 is approximately constant over many cell divisions. About 60% of the losses of sDp3 at the first embryonic cell division involve nondisjunction. Frequencies of mitotic loss of different ncl-1(+)-bearing free duplications varied over a 200-fold range. The frequencies of mitotic loss were enhanced by a chromosomal him-10 mutation. We have used ncl-1 as a cell autonomous marker in the mosaic analysis of dpy-1 and lin-37. The focus of action of dpy-1 is in hypodermis. A mutation in lin-37 combined with a mutation in another gene results in a synthetic multivulva phenotype. We show that lin-37 acts cell nonautonomously and propose that it plays a role, along with the previously studied gene lin-15, in the generation of an intercellular signal by hyp7 that represses vulval development. ------------------- Key: 2308 Medline: 96061006 Authors: Maricq AV;Peckol E;Driscoll M;Bargmann CI Title: Mechanosensory signalling in C. elegans mediated by the GLR-1 glutamate receptor. Citation: Nature 378: 78-81 1995 Type: ARTICLE Genes: glr-1 mec-4 Abstract: Neuronal signalling across synapses involves activation of many neurotransmitter receptors on postsynaptic cells. glr-1 encodes a potential glutamate receptor in the nematode Caenorhabditis elegans which is most similar to vertebrate AMPA-type ionotropic glutamate receptors(1). glr-1 is expressed in motor neurons and interneurons, including interneurons implicated in the control of locomotion(2). Here we investigate the contribution of glr-1 to the normal signalling of these neurons, by generating a deletion mutation in glr-1. We find that mutant worms are deficient in their ability to withdraw backwards when mechanically stimulated, but they withdraw normally in response to chemical repellents. The ASH sensory neurons mediate withdrawal responses both to mechanical stimuli and to chemical repellents(3,4), and ASH makes chemical synapses with glr-1-expressing interneurons. Our results suggest that postsynaptic interneurons use different neurotransmitter receptors to process two sensory stimuli detected by one sensory neuron. ------------------- Key: 2309 Medline: 96061007 Authors: Hart AC;Sims S;Kaplan JM Title: Synaptic code for sensory modalities revealed by C. elegans GLR-1 glutamate receptor. Citation: Nature 378: 82-85 1995 Type: ARTICLE Genes: glr-1 Abstract: How does the nervous system encode environmental stimuli as sensory experiences? Both the type (visual, olfactory, gustatory, mechanical or auditory) and the quality of a stimulus (spatial position, intensity or frequency) are represented as a neural code. Here we undertake a genetic analysis of sensory modality coding in Caenorhabditis elegans. The ASH sensory neurons respond to two distinct sensory stimuli (nose touch and osmotic stimuli). A mutation in the glr-1 (glutamate receptor) gene eliminates the response to nose touch but not to osmotic repellents. The predicted GLR-1 protein is roughly 40% identical to mammalian AMPA-class glutamate receptor (GluR) subunits. Analysis of glr-1 expression and genetic mosaics indicates that GLR-1 receptors act in synaptic targets of the ASH neurons. We propose that discrimination between the ASH sensory modalities arises from differential release of ASH neurotransmitters in response to different stimuli. ------------------- Key: 2310 Medline: 96140645 Authors: Saha V;Chaplin T;Gregorini A;Ayton P;Young BD Title: The leukemia-associated-protein (LAP) domain, a cysteine-rich motif, is present in a wide range of proteins, including MLL, AF10, and MLLT6 proteins. Citation: Proceedings of the National Academy of Sciences USA 92: 9737-9741 1995 Type: ARTICLE Genes: Abstract: We have identified and further characterized a Caenorhabditis elegans gene, CEZF, that encodes a protein with substantial homology to the zinc finger and leucine zipper motifs of the human gene products AF10, MLLT6, and BR140. The first part of the zinc finger region of CEZF has strong similarity to the corresponding regions of AF10 (66%) and MLLT6 (64%) at the cDNA level, As this region is structurally different from previously described zinc finger motifs, sequence homology searches were done, Twenty-five other proteins with a similar motif were identified, Because the functional domain of this motif is potentially disrupted in leukemia-associated chromosomal translocations, we propose the name of leukemia-associated protein (LAP) finger. On the basis of these comparisons, the LAP domain consensus sequence is Cys(1)-Xaa(1-2)-Cys(2)-Xaa(9-21)-Cys(3)-Xaa(2-4)-Cys(4)-Xaa (4-5)-His(5)-Xa (2)-Cys(6)-Xaa(12-46)-Cys(7)-Xaa(2)-Cys(8), where subscripted numbers represent the number of amino acid residues, We review the evidence that this motif binds zinc, is the important DNA-binding domain in this group of regulatory proteins, and may be involved in leukemogenesis. ------------------- Key: 2311 Medline: 96017652 Authors: Hutter H;Schnabel R Title: Establishment of left-right asymmetry in the Caenorhabditis elegans embryo: A multistep process involving a series of inductive events. Citation: Development 121: 3417-3424 1995 Type: ARTICLE Genes: Abstract: Bilateral pairs of blastomeres derived from the founder cell AB, the anterior blastomere of the 2-cell stage, in the Caenorhabditis elegans embryo are initially equivalent in their developmental potential. Recently, we showed that an induction at the 12-cell stage by a blastomere called MS is necessary to establish the differences between left and right pairs of blastomeres in the anterior part of the embryo. Further analysis of the process of creating left-right asymmetry reveals that the induction at the 12-cell stage is only the first of a series of inductions establishing the left-right asymmetry of the embryo. We describe here two further inductions that create additional asymmetries in the posterior part of the embryo. One induction occurs at the 24-cell stage among AB descendants themselves. This induction is restricted to the left side of the embryo as a consequence of the fate changes induced by MS at the 12-cell stage. The second induction requires again blastomeres of the MS lineage and also occurs around the 24-cell stage. Together these inductions establish the fate differences observed in the development of left-right pairs of blastomeres in the embryo. ------------------- Key: 2312 Medline: 96026203 Authors: Vanfleteren JR;De Vreese A Title: The gerontogenes age-1 and daf-2 determine metabolic rate potential in aging Caenorhabditis elegans. Citation: FASEB Journal 9: 1355-1361 1995 Type: ARTICLE Genes: age-1 daf-2 fer-15 spe-26 tra-3 Abstract: Mutations in the genes age-1 and daf-2 extend life span of Caenorhabditis elegans by 100 and 200%, respectively, in axenic culture. Adult worms that are mutant in either of these genes have higher metabolic capacities, called metabolic rate potentials, at all ages and the extension of their life expectancies are positively correlated with the increases of metabolic rate potential. The activities of catalase, superoxide dismutase, isocitrate dehydrogenase, isocitrate lyase, and malate synthase are all higher relative to those in worms that are wild type for these genes, but acid phosphatase is down-regulated and alkaline phosphatase activity is lowered to 10% of the activity measured in age-1(+) and daf-2(+) worms. These results suggest that genes that regulate metabolic activity may play central roles in longevity and senescence. ------------------- Key: 2313 Medline: 96027757 Authors: Leggett DS;Jones D;Candido EPM Title: Caenorhabditis elegans UBC-1, a ubiquitin-conjugating enzyme homologous to yeast RAD6/UBC2, contains a novel carboxy-terminal extension that is conserved in nematodes. Citation: DNA and Cell Biology 14: 883-891 1995 Type: ARTICLE Genes: ubc-1 ubc-2 Abstract: The RAD6/UBC2 gene from Saccharomyces cerevisiae encodes a ubiquitin-conjugating enzyme involved in DNA repair, induced mutagenesis, and sporulation, Here we report the isolation and characterization of the Caenorhabditis elegans RAD6 homolog designated ubc-1, Ubc-1 encodes a 21,5-kD protein that shares considerable identity with RAD6 (66%) as well as with other RAD6 homologs, including Schizosaccharomyces pombe rhp6(+) (70%), Drosophila melanogaster Dhr6 (83%), and the two human homologs HHR6A and HHR6B (84% and 83%, respectively), However, UBC-1 is distinct in being the only known RAD6 homolog, other than RAD6 itself, with a carboxy-terminal extension, Analysis of UBC-1 homologs from C, briggsae and Ascaris suum show that the presence of the carboxy-terminal extension is conserved in nematodes, When constitutively expressed from the yeast promoter ADH1, ubc-1 complements the DNA repair functions in a S, cerevisiae rad6 Delta mutant, Surprisingly, ubc-1 fails to complement the sporulation function of RAD6, despite its possession of an acidic carboxy-terminal tail, C, elegans UBC-1 is capable of forming a thiol-ester bond with ubiquitin, but, unlike RAD6, is unable to transfer ubiquitin to histone H2B in vitro, Both cis and trans splicing are involved in the maturation of the ubc-1 transcript. The presence of the SL2 trans-splice leader in the ubc-1 transcript suggests that ubc-1 may be co-transcribed as part of a polycistronic message. ------------------- Key: 2314 Medline: 96028095 Authors: Troemel ER;Chou JH;Dwyer ND;Colbert HA;Bargmann CI Title: Divergent seven transmembrane receptors are candidate chemosensory receptors in C. elegans. Citation: Cell 83: 207-218 1995 Type: ARTICLE Genes: gpa-1 gpa-2 gpa-3 sra-1 sra-2 sra-3 sra-4 sra-5 sra-6 sra-7 sra-8 sra-9 sra-10 sra-11 sra-12 srb-1 srb-2 srb-3 srb-4 srb-5 srb-6 srb-7 srb-8 srb-9 srb-10 srb-11 srd-1 srd-2 sre-1 sre-2 srg-1 srg-2 srg-3 srg-4 srg-5 srg-6 srg-7 srg-8 srg-9 srg-10 srg-11 srg-12 srg-13 sro-1 Abstract: Using their senses of taste and smell, animals recognize a wide variety of chemicals, The nematode C. elegans has only fourteen types of chemosensory neurons, but it responds to dozens of chemicals, because each chemosensory neuron detects several stimuli. Here we describe over 40 highly divergent members of the G protein-coupled receptor family that could contribute to this functional diversity. Most of these candidate receptor genes are in clusters of two to nine similar genes. Eleven of fourteen tested genes appear to be expressed in small subsets of chemosensory neurons. A single type of chemosensory neuron can potentially express at least four different receptor genes. Some of these genes might encode receptors for water-soluble attractants, repellents, and pheromones. ------------------- Key: 2315 Medline: 96036075 Authors: Iwasaki K;Liu DWC;Thomas JH Title: Genes that control a temperature-compensated ultradian clock in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 92: 10317-10321 1995 Type: ARTICLE Genes: dec-1 dec-2 dec-4 dec-7 dec-9 dec-10 dec-11 dec-12 flr-1 flr-3 flr-4 unc-16 mDf7 nDf19 Abstract: Substantial progress has been made in understanding the genetic basis of temperature-compensated circadian clocks. Ultradian rhythms, with a period shorter than 24 h, are at least as widespread as circadian rhythms. We have initiated genetic analysis of defecation behavior, which is controlled by an ultradian clock in Caenorhabditis elegans. The defecation motor program is activated every 45 sec, and this rhythm is temperature compensated. We describe mutations in 12 genes that either shorten or lengthen the cycle period. We find that most of these mutations also disrupt temperature compensation, suggesting that this process is an integral part of the clock. These genes open the way for molecular genetic dissection of this ultradian ------------------- Key: 2316 Medline: 96069739 Authors: Jorgensen EM;Hartwieg E;Schuske K;Nonet ML;Jin Y;Horvitz HR Title: Defective recycling of synaptic vesicles in synaptotagmin mutants of Caenorhabditis elegans. Citation: Nature 378: 196-199 1995 Type: ARTICLE Genes: cha-1 snt-1 unc-104 Abstract: Synaptotagmin, an integral membrane protein of the synaptic vesicle, binds calcium and interacts with proteins of the plasma membrane. These observations suggest several possible functions for synaptotagmin in synaptic vesicle dynamics: it could facilitate exocytosis by promoting calcium-dependent fusion, inhibit exocytosis by preventing fusion, or facilitate endocytosis of synaptic vesicles from the plasma membrane by acting as a receptor for the endocytotic proteins of the clathrin AP2 complex. Here we show that synaptic vesicles are depleted at synaptic terminals in synaptotagmin mutants of the nematode Caenorhabditis elegans. This depletion is not caused by a defect in transport or by increased synaptic vesicle release, but rather by a defect in retrieval of synaptic vesicles from the plasma membrane. Thus we propose that, as well as being involved in exocytosis, synaptotagmin functions in vesicular recycling. ------------------- Key: 2317 Medline: 96069808 Authors: Hengartner MO Title: Life and death decisions: ced-9 and programmed cell death in Caenorhabditis elegans. Citation: Science 270: 931- 1995 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: Programmed cell death (PCD), or apoptosis, is a conserved terminal differentiation program that multicellular organisms have evolved to get rid of cells that are not needed, that are in the way, or that are potentially dangerous. PCD can be equated with cell suicide in the sense that the dying cell plays an active role in promoting its own demise and removal from the organism. ------------------- Key: 2318 Medline: 96042579 Authors: Lynch AS;Briggs D;Hope IA Title: Developmental expression pattern screen for genes predicted in the C. elegans genome sequencing project. Citation: Nature Genetics 11: 309-313 1995 Type: ARTICLE Genes: Abstract: Maximum use should be made of information generated in the genome sequencing projects. Toward this end, we have initiated a genome sequence-based, expression pattern screen of genes predicted from the Caenorhabditis elegans genome sequence data. We examined beta-galactosidase expression patterns in C. elegans lines transformed with lacZ reporter gene fusions constructed using predicted C. elegans gene promoter regions. Of the predicted genes in the cosmids analysed so far, 67% are amenable to the approach and 54% of examined genes yielded a developmental expression pattern. Expression pattern information is being made generally available using computer databases. ------------------- Key: 2319 Medline: 96042580 Authors: Birchall PS;Fishpool RM;Albertson DG Title: Expression patterns of predicted genes from the C. elegans genome sequence visualized by FISH in whole organisms. Citation: Nature Genetics 11: 314-320 1995 Type: ARTICLE Genes: mec-7 msp-3 unc-22 unc-54 vit-6 Abstract: More than 10 megabases of contiguous genome sequence have been submitted to the databases by the Caenorhabditis elegans Genome Sequencing Consortium. To characterize the genes predicted from the sequence, we have developed high resolution FISH for visualization of mRNA distributions in whole animals. The high resolution and sensitivity afforded by the use of directly fluorescently labelled probes and confocal imaging permitted mRNA distributions to be recorded at the cellular and subcellular level. Expression patterns were obtained for 8 out of 10 genes in an initial test set of predicted gene sequences, indicating that FISH is an effective means of characterizing predicted genes in C. elegans. ------------------- Key: 2320 Medline: 96033785 Authors: Weinshenker D;Garriga G;Thomas JH Title: Genetic and pharmacological analysis of neurotransmitters controlling egg laying in C. elegans. Citation: Journal of Neuroscience 15: 6975-6985 1995 Type: ARTICLE Genes: bas-1 cat-4 cha-1 egl-1 egl-2 lin-15 lin-39 unc-17 unc-43 unc-75 Abstract: We have investigated the neurotransmitters used to control egg-laying in C. elegans. Previous studies suggested that 5-HT released by the HSN motor neurons stimulates egg laying, and that tricyclic antidepressants potentiate egg laying by blocking reuptake of 5-HT by the HSN neurons. We report studies of the wild type and a mutant that lacks detectable 5-HT that suggest 5-HT is not required for egg-laying. Furthermore, we find that ACh is required for egg laying in response to 5-HT, suggesting that 5-HT is not sufficient to activate egg laying. The dominant egl-2(n693) mutation, which causes animals to lay eggs in response to tricyclics but not 5-HT, also conflicts with the model for egg laying. Experiments in which the HSN neurons or 5-HT are removed from egl-2 animals indicate that the action of tricyclics cannot be explained by a block of 5-HT reuptake. We find that D-2 family dopamine antagonists can also induce egg laying in egl-2(n693) mutants, and that dopamine inhibits egg laying in the wild type. These results suggest that dominant egl-2 mutations activate an inhibitory dopaminergic pathway that can be blocked by tricyclics and D-2 antagonists. We also find that these drugs stimulate egg laying in mutants lacking 5-HT or the HSN neurons, consistent with a target on the egg-laying muscles. In contrast to tricyclics, fluoxetine and other selective 5-HT reuptake inhibitors appear to be specific for 5-HT reuptake in C. elegans egg laying. ------------------- Key: 2321 Medline: 96041331 Authors: Epstein HF;Lu GY;Deitiker PR;Ortiz I;Schmid MF Title: Preliminary three-dimensional model for nematode thick filament core. Citation: Journal of Structural Biology 115: 163-174 1995 Type: ARTICLE Genes: Abstract: Understanding the structure and the mechanism of assembly of thick filaments have been longstanding problems in the field of muscle biology. Cores which represent the backbones of thick filaments and consist of paramyosin and associated proteins were isolated from the nematode Caenorhabditis elegans. Electron microscopy of negatively stained and frozen hydrated cores was performed, The resulting images were analyzed by computing their Fourier transforms, three-dimensional reconstruction, and by modeling, A preliminary three-dimensional model is proposed in which the paramyosin constitutes an outer sheath of seven subfilaments about a set of inner 54-nm-long tubules which repeat every 72 nm. The subfilaments are not closely packed but require cross-linking by the internal tubules. Each subfilament consists of two strands of paramyosin molecules which are staggered by 72 nm with respect to one another. This stagger introduces a 22-nm gap between consecutive paramyosin molecules in each strand, An offset of the center of the inner tubules relative to the center of the gap of 6 nm was consistent with the images and their transforms. This model suggests that the nonhelical ends of paramyosin and the unpaired gap between adjacent paramyosin molecules contain sites for the interaction with the inner tubular proteins, The molecular interactions at this locus would appear to be critical in the assembly of thick filaments and their regulation. ------------------- Key: 2322 Medline: Authors: Mitani S Title: Genetic regulation of mec-3 expression implicated in the specification of the mechanosensory neuron cell types in Caenorhabditis elegans. Citation: Development, Growth & Differentiation 37: 551-557 1995 Type: ARTICLE Genes: egl-44 egl-46 lin-4 lin-14 lin-32 mec-3 mec-4 mec-7 sem-4 unc-86 Abstract: The mec-3 gene, a member of the LIM-homeodomain transcription factors, is required for touch receptor, FLP and PVD neurons to differentiate in the nematode Caenorhabditis elegans. Stably integrated transgenic strains with mec-3-lacZ fusion were generated by irradiating UV light to an unstable transgenic strain with the extrachromosomal DNA. Expression patterns of the mec-3-lacZ fusion were examined in mutant backgrounds (lin-4, lin-14, egl-44, egl-46 and sem-4 genes) which alter touch receptor-specific gene expression. In the lin-4 mutant background, ectopic mec-3-lacZ positive AVM/PVM-like cells were observed in 9% of the animals. By contrast, in the lin-14 mutant background, mec-3-lacZ staining in AVM/PVM cells was lost in 86% of the animals. In the egl-44 and egl-46 mutant backgrounds, expression pattern was the same as wild-type animals. In the sem-4 mutant background, more than half of the animals (54-69%) had ectopic staining cells in the tail in addition to the wild-type staining pattern. The modes of action of these genetically interacting genes in the differentiation of mechanosensory neurons are proposed. ------------------- Key: 2323 Medline: 96076737 Authors: Peixoto CA;de Souza W Title: Freeze-fracture and deep-etched view of the cuticle of Caenorhabditis elegans. Citation: Tissue & Cell 27: 561-568 1995 Type: ARTICLE Genes: Abstract: At ultrastructural level, the Caenorhabditis elegans (C. elegans) cuticle shows the presence of well-defined layers, one of them is a membrane-like structure designated as epicuticle, always present on the outermost surface of nematodes. Freeze-fracture replicas revealed the existance of two faces of the epicuticle: a inner face containing numerous particles, and a almost smooth outer face. Deep etching replicas confirmed the existance of these two faces of the epicuticle showing in some replicas two particle populations on the outer face of L4 and adult forms of C. elegans. Also a previously unrecognized structure was noted in the cuticle of C. elegans, a matrix composed by network of globular and filamentous structures, leaving in between them spaces, which probably are occupied by water in the living adult and L4 larvae specimen. This network demonstrates either a compact nature or loose nature according to their cuticle location. Deep etching replicas of the adults nematode revealed large spaces between the cortical and basal layers which are regularly interrupted by struts connecting each other by fibers in a particular arrangement. ------------------- Key: 2324 Medline: Authors: Donkin SG;Eiteman MA;Williams PL Title: Toxicity of glucosinolates and their enzymatic decomposition products to Caenorhabditis elegans. Citation: Journal of Nematology 27: 258-262 1995 Type: ARTICLE Genes: Abstract: An aquatic 24-hour lethality test using Caenorhabditis elegans was used to assess toxicity of glucosinolates and their enzymatic breakdown products. In the absence of the enzyme thioglucosidase (myrosinase), allyl glucosinolate (sinigrin) was found to be nontoxic at all concentrations tested, while a freeze-dried, dialyzed water extract of Crambe abyssinica containing 26% 2-hydroxyl 3-butenyl glucosinolate (epi-progoitrin) had a 50% lethal concentration (LC(50)) of 18.5 g/liter. Addition of the enzyme increased the toxicity (LC(50) value) of sinigrin to 0.5 g/liter, but the enzyme had no effect on the toxicity of the C. abyssinica extract. Allyl isothiocyanate and allyl cyanide, two possible breakdown products of sinigrin, had an LC(50) value of 0.04 g/liter and approximately 3 g/liter, respectively. Liquid chromatographic studies showed that a portion of the sinigrin decomposed into allyl isothiocanate. The results indicated that allyl isothiocyanate is nearly three orders of magnitude more toxic to C. elegans than the corresponding glucosinolate, suggesting isothiocyanate formation would improve nematode control from application of glucosinolates. ------------------- Key: 2325 Medline: 95396825 Authors: Logsdon JM;Tyshenko MG;Dixon C;D-Jafari J;Walker VK;Palmer JD Title: Seven newly discovered intron positions in the triose-phosphate isomerase gene: evidence for the introns-late theory. Citation: Proceedings of the National Academy of Sciences USA 92: 8507-8511 1995 Type: ARTICLE Genes: Abstract: The gene encoding the glycolytic enzyme triose-phosphate isomerase (TPI; EC 5.3.1.1) has been central to the long-standing controversy on the origin and evolutionary significance of spliceosomal introns by virtue of its pivotal support for the introns-early view, or exon theory of genes. Putative correlations between intron positions and TPI protein structure have led to the conjecture that the gene was assembled by exon shuffling, and five TPI intron positions are old by the criterion of being conserved between animals and plants. We have sequenced TPI genes from three diverse eukaryotes--the basidiomycete Coprinus cinereus, the nematode Caenorhabditis elegans, and the insect Heliothis virescens--and have found introns at seven novel positions that disrupt previously recognized gene/protein structure correlations. The set of 21 TPI introns now known is consistent with a random model of intron insertion. Twelve of the 21 TPI introns appear to be of recent origin since each is present in but a single examined species. These results, together with their implication that as more TPI genes are sequenced more intron positions will be found, render TPI untenable as a paradigm for the introns-early theory and, instead, support the introns-late view that spliceosomal introns have been inserted into preexisting genes during eukaryotic evolution ------------------- Key: 2326 Medline: 96074776 Authors: Shim YH;Bonner JJ;Blumenthal T Title: Activity of a C. elegans GATA transcription factor, ELT-1, expressed in yeast. Citation: Journal of Molecular Biology 253: 665-676 1995 Type: ARTICLE Genes: elt-1 ges-1 mtl-1 mtl-2 pgp-1 pgp-3 vit-2 Abstract: The GATA motif (WGATAR) is found in the promoter regions of numerous Caenorhabditis elegans genes, including two intestine-specific genes, vit-2 and ges-l, in which it has been shown to be required for promoter function. The protein ELT-1, encoded by a single-copy gene homologous to the GATA family of vertebrate transcription factors, is potentially capable of interacting with this element. In order to determine whether ELT-1 is a transcriptional activator that recognizes this sequence, we have expressed it under the control of the GAL1 promoter in yeast. lacZ driven by the CYC1 promoter lacking an upstream activation sequence (UAS) but containing GATA sequences was used as a reporter. beta-Galactosidase was expressed upon induction only when GATA sequences were present, and expression was increased dramatically by additional binding sites. Deletion analysis demonstrated that the C terminus, containing only one of the two zinc fingers, is sufficient for activation. In addition, the DNA-binding domain and two transactivation regions were identified by fusing these isolated domains to previously defined domains of heterologous transcription factors. While most single base alterations in the GATA core sequence eliminated activity, an A to C change in position four, creating a GATC core, was found to increase activity significantly. The deleted ELT-1 protein containing only the C-terminal Zn finger was sufficient for activation in response to GATA, but both fingers were required for activation at GATC. A variety of sites with non-optimal sequences surrounding the GATA core also were found to be excluded better by the protein containing both Zn fingers. Furthermore, a fusion protein containing the entire ELT-1 DNA binding domain fused to the VP16 activation domain was found to have an even greater preference for the GATC core, as well as the optimal flanking bases. We conclude that, although ELT-1 having only its C-terminal finger is capable of activation in response to the WGATAR site, the presence of the upstream ------------------- Key: 2327 Medline: 96232914 Authors: Berks M Title: The C. elegans genome sequencing project. Citation: Genome Research 5: 99-104 1995 Type: REVIEW Genes: Abstract: Caenorhabditis elegans, a free-living nematode worm, has proved a particularly useful model organism for studying the anatomy, behavior, genetics, and development of a metazoan. It also has one of the smallest genomes of the higher eukaryotes (100 Mb distributed over six chromosomes), making it an ideal candidate for detailed molecular analysis. The C. elegans genome project began over 10 years ago and is a collaberative effort between two laboratories (St. Louis, MO, USA and Cambridge, UK), with the ultimate aim of mapping and sequencing the whole of the 100-Mb genome. The consortium has now completed the sequence of approximately one-fifth of the genome and plans to have sequenced more than half the genome before the end ------------------- Key: 2328 Medline: 96069711 Authors: Jones SJM;Baillie DL Title: Characterization of the let-653 gene in Caenorhabditis elegans. Citation: Molecular & General Genetics 248: 719-726 1995 Type: ARTICLE Genes: let-653 Abstract: A mutation in the let-653 gene of Caenorhabditis elegans results in larval death. The lethal arrest is concurrent with the appearance of a vacuole anterior to the lower pharyngeal bulb. The position of the vacuole is consistent with a dysfunction of the secretory/excretory apparatus. Germline transformation rescue experiments were able to position the let-653 gene to two overlapping cosmid subclones. Sequence data generated from both cDNA and genomic DNA subclones indicated that let-653 encodes a mucin-like protein. Our characterization suggests that a mucin-like protein is essential for effective functioning of the secretory/excretory apparatus within C. elegans. ------------------- Key: 2329 Medline: 96074412 Authors: Hartman P;Childres E;Beyer T Title: Nematode development is inhibited by methyl viologen and high oxygen concentrations at a rate inversely proportional to life span. Citation: Journal of Gerontology 50A: B322-B326 1995 Type: ARTICLE Genes: age-1 mev-1 rad-8 Abstract: Eight strains of C. elegans, including seven recombinant inbred(RI) strains with mean life spans ranging from 10.9 to 28.8 days, were reared under two conditions (95% oxygen or methyl viologen) known to elevate tire concentration of free radicals. Both agents inhibited development, as ascertained by measuring the lengths of animals at regular intervals. The degree of inhibition correlated inversely with mean life span with both agents; that is, development of short-lived strains was inhibited more profoundly than was development of long-lived strains. Thus, al least some of the polygenes which prominently influence aging are the same as those which control resistance to free radicals. These genes likely influence aging and response to oxidative stress in many ways, both direct and indirect. ------------------- Key: 2330 Medline: 96069861 Authors: Lin RL;Thompson S;Priess JR Title: pop-1 encodes an HMG box protein required for the specification of a mesoderm precursor in early C. elegans embryos. Citation: Cell 83: 599-609 1995 Type: ARTICLE Genes: apx-1 glp-1 hlh-1 mex-1 par-1 pie-1 pop-1 skn-1 hDf10 qDf3 qDf4 tDf3 tDf4 Abstract: In C. elegans embryogenesis, the MS blastomere produces predominantly mesodermal cell types, while its sister E generates only endodermal tissue. We show that a maternal gene, pop-1, is essential for the specification of MS fate and that a mutation in pop-1 results in MS adopting an E fate. Previous studies have shown that the maternal gene skn-1 is required for both MS and E development and that skn-1 encodes a transcription factor. We show here that the pop-1 gene encodes a protein with an HMG box similar to the HMG boxes in the vertebrate lymphoid-specific transcriptional regulators TCF-1 and LEF-1. We propose that POP-1 and SKN-1 function together in the early embryo to allow MS-specific differentiation. ------------------- Key: 2331 Medline: 96069862 Authors: DeVore DL;Horvitz HR;Stern MJ Title: An FGF receptor signaling pathway is required for the normal cell migrations of the sex myoblasts in C. elegans hermaphrodites. Citation: Cell 83: 611-620 1995 Type: ARTICLE Genes: clr-1 egl-15 let-60 sem-5 soc-1 soc-2 nDf19 nDf32 Abstract: The sex myoblasts (SMs) in C. elegans hermaphrodites undergo anteriorly directed cell migrations that allow for the proper localization of the egg-laying muscles. These migrations are controlled in part by a signal emanating from gonadal cells that allows the SMs to be attracted to their precise final positions flanking the center of the go nad. Mutations in egl-15 alter the nature of the interaction between the gonad and the SMs, resulting in the posterior displacement of the SMs. Here we show that egl-15 encodes a receptor tyrosine kinase of the fibroblast growth factor receptor (FGFR) subfamily with multiple roles in development. Three genes were identified that behave genetically as activators or mediators of egl-15 activity. One of these genes, sem-5, encodes an adaptor molecule that transduces signals from a variety of receptor tyrosine kinases. Like egl-15 and sem-5, the other two genes may similarly act in FGFR signaling pathways in C, elegans. ------------------- Key: 2332 Medline: 99396904 Authors: Beck CDO;Rankin CH Title: Heat shock disrupts long-term memory consolidation in Caenorhabditis elegans. Citation: Learning & Memory 2: 161-177 1995 Type: ARTICLE Genes: Abstract: Previous work has demonstrated that memory for habituation training is retained for >24 hr in Caenorhabditis elegans. In this study the timing of memory consolidation was investigated by introducing heat shock (32 degrees C, 45 min) either before training, long after training, or during training. It was found that memory consolidation was disrupted by heat shock during training but not before or after training. In addition, heat shock before training failed to induce thermal tolerance to the effects of heat shock during training on long-term memory formation. When brief heat shock (32 degrees C, 15 min) was presented during training at different intervals, the results suggested that a narrow critical period for memory consolidation of habituation may exist. These findings demonstrate that in C. elegans long-term memory for habituation is disrupted by a temporally defined agent, heat shock. Therefore, heat shock can be used as a fine-grained tool to investigate the dynamics of memory ------------------- Key: 2333 Medline: 96069765 Authors: Huang M;Gu G;Ferguson EL;Chalfie M Title: A stomatin-like protein necessary for mechanosensation in C. elegans. Citation: Nature 378: 292-295 1995 Type: ARTICLE Genes: mec-2 mec-3 mec-4 mec-7 mec-10 mec-12 unc-86 Abstract: The mec-2 gene is required for the function of a set of six touch receptor neurons in the nematode Caenorhabditis elegans; mec-2 mutants, which are touch-insensitive, have touch cells that appear morphologically normal(1,2). Gene interaction studies suggest that mec-2 positively regulates the activity of the putative mechanosensory transduction channel (ref. 3 and the present paper), comprised in part of proteins encoded by the two degenerin genes mec-4 and mec-10 (refs 3-5). The central region of the mec-2 protein (MEC-2) is very similar to stomatin, an integral membrane protein (band 7.2b) in human red blood cells that is thought to regulate cation conductance(6). MEC-2-LacZ fusions are distributed along the touch receptor axons. This axonal distribution, which is mediated by the mec-2-specific amino terminus, is disrupted by mutations in mec-12, an alpha-tubulin gene needed for touch cell function. Our results indicate that MEC-2 links the mechanosensory channel and the microtubule cytoskeleton of the touch receptor neurons. Such linkage provides the basis for a mechanism of mechanosensation whereby microtubule displacement leads to channel opening. ------------------- Key: 2334 Medline: 96155601 Authors: Thomas JH Title: Thermosensation: Some like it hot. Citation: Current Biology 5: 1222-1224 1995 Type: REVIEW Genes: tax-2 tax-4 ttx-1 ttx-3 ttx-6 Abstract: The ability of organisms to respond to fluctuating temperatures is ubiquitous but poorly understood. Recent studies of nematodes reveal specific sensory neurons and interneurons that mediate thermotaxis. ------------------- Key: 2335 Medline: 96102808 Authors: Chow KL;Hall DH;Emmons SW Title: The mab-21 gene of Caenorhabditis elegans encodes a novel protein required for choice of alternate cell fates. Citation: Development 121: 3615-3626 1995 Type: ARTICLE Genes: egl-5 emb-1 emb-2 emb-5 emb-7 emb-8 emb-13 emb-32 mab-21 yDf10 sDp3 Abstract: The gene mab-21, which encodes a novel protein of 386 amino acids, is required for the choice of alternate cell fates by several cells in the C. elegans male tail. Three cells descended from the ray 6 precursor cell adopt fates of anterior homologs, and a fourth, lineally unrelated hypodermal cell is transformed into a neuroblast. The affected cells lie together in the lateral tail epidermis, suggesting that mab-21 acts as part of a short-range pattern-formation mechanism. Each of the changes in cell fate brought about by mab-21 mutants can be interpreted as a posterior-to-anterior homeotic transformation, mab-21 mutant males and hermaphrodites have additional pleiotropic phenotypes affecting movement, body shape and fecundity, indicating that mab-21 has functions outside the tail region of males. We show that the three known alleles of mab-21 are hypomorphs of a new gene, Mosaic analysis revealed that mab-21 acts cell autonomously to specify the properties of the sensory ray, but non-autonomously in the hypodermal versus neuroblast cell fate choice. Presence of cell signalling in the choice of the neuroblast fate was confirmed by cell ablation experiments, Mutations in mab-21 were shown previously to be genetic modifiers of the effects of HOM-C/Hox gene mutations on ray identity specification. The results presented here support the conclusion that mab-21 acts as part of a mechanism required for correct cell fate choice, possibly involving the function of HOM-C/Hox genes in several body regions. ------------------- Key: 2336 Medline: 96077128 Authors: Tabuse Y;Sano T;Nishiwaki K;Miwa J Title: Molecular evidence for the direct involvement of a protein kinase C in developmental and behavioural susceptibility to tumour-promoting phorbol esters in Caenorhabditis elegans. Citation: Biochemical Journal 312: 69-74 1995 Type: ARTICLE Genes: tpa-1 unc-13 Abstract: The nematode Caenorhabditis elegans displays developmental and behavioural sensitivity to tumour-promoting phorbol esters. This sensitivity involves the gene tpa-1, which encodes two protein kinase C isoforms, TPA-1A and TPA-1B. Here we report the molecular nature of the sensitivity in this animal. Characterization of transposon Tc1-induced phorbol ester-resistant mutants has revealed that Tc1 was inserted in a region encoding the kinase domain, resulting in the loss of tpa-1 products. Introduction of a genomic DNA containing the entire wild-type tpa-1 locus into a Tc1-inserted mutant restored the sensitivity to tumour promoters, and tpa-1 products were also produced. These results suggest that the function of wild-type TPA-1 is necessary and sufficient for tumour promoters to cause developmental and behavioural sensitivity in C-elegans. ------------------- Key: 2337 Medline: 96074602 Authors: Waterston R;Sulston J Title: The genome of Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 92: 10836-10840 1995 Type: REVIEW Genes: Abstract: The physical map of the 100-Mb Caenorhabditis elegans genome consists of 17,500 cosmids and 3500 yeast artificial chromosomes (YACs). A total of 22.5 Mb has been sequenced, with the remainder expected by 1998. A further 15.5 Mb of unfinished sequence is freely available online: because the areas sequenced so far are relatively gene rich, about half the 13,000 genes can now be scanned. More than a quarter of the genes are represented by expressed sequence tags (ESTs), All information pertaining to the genome is publicly available in the ACeDB data base. ------------------- Key: 2338 Medline: 96069542 Authors: Leroux MR;Candido EPM Title: Characterization of four new tcp-1-related cct genes from the nematode Caenorhabditis elegans. Citation: DNA and Cell Biology 14: 951-960 1995 Type: ARTICLE Genes: cct-1 cct-2 cct-4 cct-5 cct-6 Abstract: In this report we present the sequences of four new cct chaperonin genes from the nematode Caenorhabditis elegans. The four genes, cct-2, cct-4 cct-5, and cct-6 are orthologs of the mouse chaperonin genes Cctb, Cctd, Ccte, and Cctz sharing 66%, 63%, 68%, and 67% deduced amino acid sequence identity, respectively. The C. elegans multigene family includes these four genes as well as cct-1 (tcp-1), and displays 23-35% pairwise predicted amino acid sequence identity between members, and 31-35% identity to the closely related archaebacterial chaperonin TF55. The five C. elegans cct genes are expressed in all life stages (egg, four larval stages, and adult). Members of the multigene family occur as a loosely associated group of three genes on chromosome II, and two widely separated genes on chromosome III. The predicted secondary structures of all five C. elegans CCT deduced protein sequences are nearly identical. Moreover, all chaperonins examined had comparable predicted secondary structures. Algorithmic predictions of the secondary structures of GroEL, Hsp60, and Rubisco submit-binding protein (RuBP) are almost identical, and are very similar to the known GroEL secondary structure. The CCT/TF55 family predicted secondary structures are essentially identical to each other and are also related to GroEL, Hsp60, and RuBP. The most notable difference between the CCT/TF55 and the GroEL/Hsp60/RuBP families is in the presumed polypeptide ------------------- Key: 2339 Medline: 96170774 Authors: Zetka MC;Rose AM Title: Mutant rec-1 eliminates the meiotic pattern of crossing over in Caenorhabditis elegans. Citation: Genetics 141: 1339-1349 1995 Type: ARTICLE Genes: bli-3 dpy-5 dpy-14 him-6 him-14 rec-1 rrn-1 unc-11 unc-13 unc-54 unc-101 eDf4 eDf9 eDf10 eDf24 sDp1 sDp2 Abstract: Meiotic crossovers are not randomly distributed along the chromosome. In Caenorhabditis elegans the central portions of the autosomes have relatively few crossovers compared to the flanking regions. We have measured the frequency of crossing over for several intervals across chromosome lin strains mutant for rec-1. The chromosome is similar to 50 map units in both wild-type and rec-1 homozygotes, however, the distribution of exchanges is very different in rec-1. Map distances expand across the gene cluster and contract near the right end of the chromosome, resulting in a genetic map more consistent with the physical map. Mutations in two other genes, him-6 and him-14, also disrupted the distribution of exchanges. Unlike rec-1, individuals homozygous for him-G and him-14 had an overall reduction in the amount of crossing over accompanied by a high frequency of nondisjunction and reduced egg hatching. In rec-1; him-6 and rec-1; him-14 homozygotes the frequency of crossing over was characteristic of the Him mutant phenotype, whereas the distribution of the reduced number of exchanges was characteristic of the Rec-1 pattern. It appears that these gene products play a role in establishing the meiotic pattern of exchange events. ------------------- Key: 2340 Medline: 96170775 Authors: Hekimi S;Boutis P;Lakowski B Title: Viable maternal-effect mutations that affect the development of the nematode Caenorhabditis elegans. Citation: Genetics 141: 1351-1364 1995 Type: ARTICLE Genes: clk-1 clk-2 clk-3 mad-1 mad-2 mad-3 mal-1 mal-2 mal-3 mal-4 mau-1 mau-2 mau-3 mau-4 mau-5 mau-6 mau-7 mau-8 mud-1 mum-1 mum-2 mum-3 sdc-1 tra-2 arDf1 ctDf1 eDf3 eDf18 eDf19 mDf7 nDf23 nDf24 nDf41 sDf1 sDf28 sDf32 tDf1 Abstract: We carried out a genetic screen for viable maternal-effect mutants to identify genes with a critical function relatively early in development. This type of mutation would not have been identified readily in previous screens for viable mutants and therefore could define previously unidentified genes. We screened 30,000 genomes and identified 41 mutations falling into 24 complementation groups. We genetically mapped these 24 loci; only two of them appear to correspond to previously identified genes. We present a partial phenotypic characterization of the mutants and a quantitative analysis of the degree to which they can be maternally or zygotically rescued. ------------------- Key: 2341 Medline: 96170776 Authors: Raizen DM;Lee RYN;Avery L Title: Interacting genes required for pharyngeal excitation by motor neuron MC in Caenorhabditis elegans. Citation: Genetics 141: 1365-1382 1995 Type: ARTICLE Genes: cha-1 eat-2 eat-6 eat-8 eat-9 eat-18 snt-1 unc-11 unc-13 unc-17 unc-18 unc-25 unc-26 unc-29 unc-41 unc-104 eDf4 eDf6 eDf7 eDf12 eDf16 Abstract: We studied the control of pharyngeal excitation in Caenorhabditis elegans. By laser ablating subsets of the pharyngeal nervous system, we found that the MC neuron type is necessary and probably sufficient for rapid pharyngeal pumping. Electropharyngeograms showed that MC transmits excitatory postsynaptic potentials, suggesting that MC acts as a neurogenic pacemaker for pharyngeal pumping. Mutations in genes required for acetylcholine (ACh) release and an antagonist of the nicotinic ACh receptor (nAChR) reduced pumping rates, suggesting that a nAChR is required for MC transmission. To identify genes required for MC neurotransmission, we screened for mutations that cause slow pumping but no other defects. Mutations in two genes, eat-2 and eat-18, eliminated MC neurotransmission. A gain-of-function eat-18 mutation, ad820sd, and a putative loss-of-function ent-18 mutation, ad1110, both reduced the excitation of pharyngeal muscle in response to the nAChR agonists nicotine and carbachol, suggesting that eat-18 is required for the function of a pharyngeal nAChR. Fourteen recessive mutations in eat-2 fell into five complementation classes. We found allele-specific genetic interactions between eat-2 and eat-18 that correlated with complementation classes of eat-2. We propose that eat-18 and eat-2 function in a multisubunit protein complex involved in the function of a pharyngeal nAChR. ------------------- Key: 2342 Medline: 96170777 Authors: Paulsen JE;Capowski EE;Strome S Title: Phenotypic and molecular analysis of mes-3, a maternal-effect gene required for proliferation and viability of the germ line in C. elegans. Citation: Genetics 141: 1383-1398 1995 Type: ARTICLE Genes: ced-3 ced-4 dom-3 fem-2 fem-3 glp-1 glp-4 mes-3 hDp20 nDp4 sDp2 sDf4 Abstract: mes-3 is one of four maternal-effect sterile genes that encode maternal components required for normal postembryonic development of the germ line in Caenorhabditis elegans. mes-3 mutant mothers produce sterile progeny, which contain few germ cells and no gametes. This terminal phenotype reflects two problems: reduced proliferation of the germ line and germ cell death. Both the appearance of the dying germ cells and the results of genetic tests indicate that germ cells in mes-3 animals undergo a necrotic-like death, not programmed cell death. The few germ cells that appear healthy in mes-3 worms do not differentiate into gametes, even after elimination of the signaling pathway that normally maintains the undifferentiated population of germ cells. Thus, mes-3 encodes a maternally supplied product that is required both for proliferation of the germ line and for maintenance of viable germ cells that are competent to differentiate into gametes. Cloning and molecular characterization of mes-3 revealed that it is the upstream gene in an operon. The genes in the operon display parallel expression patterns; transcripts are present throughout development and are not restricted to germ-line tissue. Both mes-3 and the downstream gene in the operon encode novel proteins. ------------------- Key: 2343 Medline: 96170778 Authors: Dorman JB;Albinder B;Shroyer T;Kenyon C Title: The age-1 and daf-2 genes function in a common pathway to control the lifespan of Caenorhabditis elegans. Citation: Genetics 141: 1399-1406 1995 Type: ARTICLE Genes: age-1 daf-2 daf-12 daf-16 daf-18 daf-20 fer-15 Abstract: Recessive mutations in two genes, daf-2 and age-1, extend the lifespan of Caenorhabditis elegans significantly. The daf-2 gene also regulates formation of an alternative developmental state called the dauer. Here we asked whether these two genes function in the same or different lifespan pathways. We found that the longevity of both age-1 and daf-2 mutants requires the activities of the same two genes, daf-16 and daf-18. In addition, the daf-2(e1370); age-1(hx546) double mutant did not live significantly longer than the daf-2 single mutant. We also found that, like daf-2 mutations, the age-1(hx546) mutation affects certain aspects of dauer formation. These findings suggest that age-1 and daf-2 mutations do act in the same lifespan pathway and extend lifespan by triggering similar if not identical processes. ------------------- Key: 2344 Medline: Authors: Donkin SG;Williams PL Title: Influence of developmental stage, salts and food presence on various end points using Caenorhabditis elegans for aquatic toxicity testing. Citation: Environmental Toxicology and Chemistry 14: 2139-2147 1995 Type: ARTICLE Genes: Abstract: This study used a randomized block design to investigate the importance of several variables in using the free-living soil nematode Caenorhabditis elegans for aquatic toxicity testing. Concentration-response data were obtained on nematodes of various developmental stages exposed to four metals (Cd, Pb, Cu, and Hg) and a water-soluble organic toxicant, sodium pentachlorophenate (PCP), under conditions of varied solvent medium (with or without salts and with or without a bacterial food source). The end points measured were 24- and 96-h mortality LC50 value, as well as development of larval stages to adulthood and evidence of reproduction. The results suggest that nematodes of various ages respond similarly to a given toxicant for all end points measured, although adults cultured from eggs appeared more sensitive than adults cultured from dauer larvae. The most important environmental variable in determining toxicity was the medium in which the tests were conducted. The presence of potassium and sodium salts in the medium significantly (p < 0.05) reduced the toxicity of many test samples. The presence of bacteria had little effect on 24-h tests with salts, but was important in 96-h survival and development. Based on sensitivity and ease of handling, adults cultured from eggs are recommended in both 24-h and 96-h tests. ------------------- Key: 2345 Medline: 96192973 Authors: Sternberg PW;Lesa G;Lee JH;Katz WS;Yoon C;Clandinin TR;Huang LS;Chamberlin HM;Jongeward G Title: LET-23-mediated signal transduction during Caenorhabditis elegans development. Citation: Molecular Reproduction & Development 42: 523-528 1995 Type: REVIEW Genes: let-23 let-60 lin-3 lin-15 lin-45 mpk-1 rok-1 sli-1 sur-1 unc-101 Abstract: We are using Caenorhabditis elegans vulval induction to study intercellular signaling and its regulation. Genes required for vulval induction include the LIN-3 transforming alpha-like growth factor, the LET-23 epidermal growth factor (EGF)-receptor-like transmembrane tyrosine kinase, the SEM-5 adaptor protein, LET-60 Ras, and the LIN-45 Raf serine/threonine kinase. Inactivation of this pathway results in a failure of vulval differentiation, the ''vulvaless'' phenotype. Activation of this pathway either by overexpression of LIN-3, a point mutation in the LET-23 extracellular domain, or hyperactivity of LET-60 Ras results in excessive vulval differentiation, the ''multivulva'' phenotype. In addition to searching for new genes that act positively in this signaling pathway, we have also characterized genes that negatively regulate this inductive signaling pathway. We find that such negative regulators are functionally redundant: mutation of only one of these negative regulators has no effect on vulval differentiation; however, if particular combinations of these genes are inactivated, excessive vulval differentiation occurs. The LIN-15 locus encodes two functionally redundant products, LIN-15A and LIN-15B, that formally act upstream of the LET-23 receptor to prevent its activity in the absence of inductive signal. The LIN-15A and B proteins are novel and unrelated to each other. The unc-101, sli-1, and rok-1 genes encode a distinct set of negative regulators of vulval differentiation. The unc-101 gene encodes an adaptin, proposed to be involved in intracellular protein trafficking. The sli-1 gene encodes a protein with similarity to c-cbl, a mammalian proto-oncogene not previously linked with a tyrosine kinase-Ras-mediated signaling pathway. LlN-3 and LET-23 are required for several aspects of C. elegans development-larval viability, P12 neuroectoblast specification, hermaphrodite vulval induction and fertility, and three inductions during male copulatory spicule development. Fertility and vulval differentiation appear to be mediated by distinct parts of the cytoplasmic tail of LET-23, and by distinct signal transduction ------------------- Key: 2346 Medline: 96097118 Authors: Etemad-Moghadam B;Guo S;Kemphues KJ Title: Asymmetrically distributed PAR-3 protein contributes to cell polarity and spindle alignment in early C. elegans Citation: Cell 83: 743-752 1995 Type: ARTICLE Genes: par-1 par-2 par-3 par-4 par-5 Abstract: The par-3 gene is required for establishing polarity in early C. elegans embryos. Embryos from par-3 homozygous mothers show defects in segregation of cytoplasmic determinants and in positioning of the early cleavage spindles. We report here that the PAR-3 protein is asymmetrically distributed at the periphery of the zygote and asymmetrically dividing blastomeres of the germline lineage. The PAR-3 distribution is roughly the reciprocal of PAR-1, another protein required-for establishing embryonic polarity in C. elegans. Analysis of the distribution of PAR-3 and PAR-1 in other par mutants reveals that par-2 activity is required for proper localization of PAR-3 and that PAR-3 is required for proper localization of PAR-1. In addition, the distribution of the PAR-3 protein correlates with differences in cleavage spindle orientation and suggests a mechanism by which PAR-3 contributes to control of cleavage pattern. ------------------- Key: 2347 Medline: 96099394 Authors: Kelley RL;Kuroda MI Title: Equality for X chromosomes. Citation: Science 270: 1607-1610 1995 Type: REVIEW Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 sdc-1 sdc-2 sdc-3 xol-1 Abstract: In many species, females possess two X chromosomes and males have one X chromosome. This difference is critical for the initial determination of sex. However, the X encodes many functions required equally in males and females; thus, X chromosome expression must be adjusted to compensate for the difference in dosage between the sexes. Distinct dosage compensation mechanisms have evolved in different species. A common theme in the Drosophila melanogaster and Caenorhabditis elegans systems is that a subtle alteration of chromatin structure may impose this modest, but vital adjustment of the X chromosome ------------------- Key: 2348 Medline: 96099401 Authors: Gavin KA;Hidaka M;Stillman B Title: Conserved initiator proteins in eukaryotes. Citation: Science 270: 1667-1671 1995 Type: ARTICLE Genes: Abstract: The origin recognition complex (ORC), a multisubunit protein identified in Saccharomyces cerevisiae, binds to chromosomal replicators and is required for the initiation of cellular DNA replication. complementary DNAs (cDNAs) encoding proteins related to the two largest subunits of ORC were cloned from various eukaryotes. The cDNAs encoding proteins related to S. cerevisiae Orc1p were cloned from the budding yeast Kluyveromyces lactis, the fission yeast Schizosaccharomyces pombe, and human cells. These proteins show similarity to regulators of the S and M phases of the cell cycle. Genetic analysis of orc1(+) from S. pombe reveals that it is essential for cell viability. The cDNAs encoding proteins related to S. cerevisiae Orc2p were cloned from Arabidopsis thaliana, Caenorhabditis elegans, and human cells. The human ORC-related proteins interact in vivo to form a complex. These studies suggest that ORC subunits are conserved and that the role of ORC is a general feature of eukaryotic DNA replication. ------------------- Key: 2349 Medline: 96107321 Authors: Downward J Title: KSR: A novel player in the RAS pathway. Citation: Cell 83: 831-834 1995 Type: REVIEW Genes: ksr-1 let-23 let-60 lin-1 lin-3 lin-15 lin-45 mpk-1 mpk-2 sem-5 sur-1 Abstract: Over the past 5 years or so, developmental geneticists studying the nematode and the fruit fly have provided many new insights into the signaling pathways linking cell surface receptor tyrosine kinases with nuclear transcription factors. A central component in this information transfer mechanism is the RAS protein, a low molecular weight GTP-binding protein that is a proto-oncogene product in mammals; another key player is the RAF kinase, also a proto-oncogene product in mammals, which is directly regulated by RAS and in turn controls the mitogen-activated protein (MAP) kinase cascade. The workings of this system have been elucidated largely through a combination of biochemical studies in mammalian cells and genetic analysis of the formation of the vulva in Caenorhabditis elegans and photoreceptor cells in the Drosophila eye. Until now, the biochemical and genetic apporaches have moved forward fairly much together, such that some chauvinistic biochemists have been able to claim that they have never learned much new from flies or worms. But all that has now been changed by three reports in this issue of Cell characterizing a novel member of this system, KSR-1, that has not been glimpsed in mammals. ------------------- Key: 2350 Medline: 96107328 Authors: Sundaram M;Han M Title: The C. elegans ksr-1 gene encodes a novel Raf-related kinase involved in Ras-mediated signal transduction. Citation: Cell 83: 889-901 1995 Type: ARTICLE Genes: ksr-1 let-23 let-60 let-537 lin-1 lin-3 lin-15 lin-31 lin-45 mek-2 mpk-1 sem-5 sur-1 stDp2 stDf5 stDf6 Abstract: Vulval induction in C. elegans is controlled by a highly conserved signaling pathway similar to the RTK-Ras-MAPK cascade in mammals. By screening for suppressors of the Multivulva phenotype caused by an activated let-60 ras allele, we isolated mutations in a gene, ksr-1, that acts as a positive modifier of vulval induction and is required for at least two other let-60 ras-mediated processes. Although ksr-1 mutations do not perturb vulval induction in an otherwise wild-type background, they have very strong effects on vulval induction in genetic backgrounds where Ras pathway activity is constitutively activated or compromised, suggesting that ksr-1 activity is required for maximal stimulation of vulval fates by the Ras pathway. Genetic epistasis analysis suggests that ksr-1 acts downstream of or in parallel to let-60 ras. We cloned ksr-1 and have shown that it encodes a novel putative protein kinase related to the Raf family of Ser/Thr kinases. ------------------- Key: 2351 Medline: 96107329 Authors: Kornfeld K;Hom DB;Horvitz HR Title: The ksr-1 gene encodes a novel protein kinase involved in Ras-mediated signaling in C. elegans. Citation: Cell 83: 903-913 1995 Type: ARTICLE Genes: ksr-1 let-60 lin-1 lin-15 lin-31 mpk-1 yDf2 Abstract: By screening for mutations that suppress the vulval defects caused by a constitutively active let gb ras gene, we identified six loss-of-function alleles of ksr-1, a novel C. elegans gene. Our genetic analysis showed ksr-1 positively mediates Ras signaling and functions downstream of or in parallel to let-60. In the absence of ksr-1 function, normal Ras signaling is impaired only slightly, suggesting ksr-1 may act to modulate, or in a branch that diverges from, the main signaling pathway. The predicted KSR-1 protein has a protein kinase domain and is most similar to a recently identified Drosophila protein involved in Ras signaling. We propose that the function of ksr-1 is evolutionarily conserved. ------------------- Key: 2352 Medline: 96127909 Authors: Beitel GJ;Tuck S;Greenwald I;Horvitz HR Title: The Caenorhabditis elegans gene lin-1 encodes an ETS-domain protein and defines a branch of the vulval induction pathway. Citation: Genes & Development 9: 3149-3162 1995 Type: ARTICLE Genes: let-60 lin-1 lin-12 mek-2 mpk-1 Abstract: The Caenorhabditis elegans gene lin-1 appears to act after the Ras-Raf-MEK-MAPK signaling cascade that mediates vulval induction. We show that lin-1 is a negative regulator of vulval cell fates and encodes an ETS-domain putative transcription factor containing potential MAPK phosphorylation sites. In lin-1 null mutants, the vulval precursor cells (VPCs) still respond to signaling from the gonadal anchor cell, indicating that lin-1 defines a branch of the inductive signaling pathway. We also provide evidence that the inductive and lateral signaling pathways are integrated to control the 1 degrees and 2 degrees vulval cell fates after the point at which lin-1 acts in the inductive pathway and that VPCs can assess the relative rather than absolute levels of inductive and lateral signaling in determining whether to express the 1 degrees or 2 degrees vulval cell fates. ------------------- Key: 2353 Medline: Authors: Anke H;Stadler M;Mayer A;Sterner O Title: Secondary metabolites with nematicidal and antimicrobial activity from nematophagous fungi and Ascomycetes. Citation: Canadian Journal of Botany S1: S932-S939 1995 Type: ARTICLE Genes: Abstract: Screening of nematode-trapping fungi for antimicrobial and nematicidal activities gave three new antimicrobial metabolites from cultures of five Arthrobotrys strains. The compounds exhibited no nematicidal activities towards Caenorhabditis elegans and Meloidogyne incognita. From trap-forming submerged cultures of Arthrobotrys conoides, linoleic acid was isolated as a nematicidal principle. Its production increased with the number of traps formed in both Arthrobotrys oligospora and Arthrobotrys conoides. Nematoctonus robustus and Nematoctonus concurrens produced pleurotin, dihydropleurotinic acid, and leucopleurotin, metabolites previously isolated from cultures of Hohenbuehelia species, suggesting that the same biosynthetic pathways function in both the teleomorph and anamorph. Several strains of Ascomycetes had nematicidal activities; linoleic acid was responsible for the activity in cultures of a Chlorosplenium species, 14-epicochlioquinone B in cultures of Neobulgaria pura, and two naphthalenes derived from the melanin biosynthetic pathway in Daldinia concentrica. 5-Pentyl-2-furaldehyde, previously known as a metabolite from a Basidiomycete, was produced by an unidentified Australian Ascomycete. More than 30 mostly new metabolites have been isolated from cultures of Lachnum papyraceum, many being chlorinated. Under different conditions the fungus incorporated bromine instead of chlorine. ------------------- Key: 2354 Medline: 96104594 Authors: Rushforth AM;Anderson P Title: Splicing removes the Caenorhabditis elegans transposon Tc1 from most mutant pre-messenger RNAs. Citation: Molecular and Cellular Biology 16: 422-429 1996 Type: ARTICLE Genes: hlh-1 mlc-2 unc-54 Abstract: The transposable element Tc1 is responsible for most spontaneous mutations that occur in many Caenorhabditis elegans strains. We analyzed the abundance and sequence of mRNAs expressed from five different Tc1 insertions within either hlh-1 (a MyoD homolog) or unc-54 (a myosin heavy chain gene). Each of the mutants expresses substantial quantities of mature mRNA in which most or all of Tc1 has been removed by splicing. Such mRNAs contain small insertions of Tc1 sequences and/or deletions of target gene sequences at the resulting spliced junctions. Most of these mutant mRNAs do not contain premature stop codons, and many are translated in frame to produce proteins that are functional in vivo. The number and variety of splice sites used to remove Tc1 from these mutant pre-mRNAs are remarkable. Two-thirds of the Tc1-containing introns removed from hlh-1 and unc-54 lack either the 5'-GU or AG-3' dinucleotides typically found at the termini of eukaryotic introns. We conclude that splicing to remove Tc1 from mutant pre-mRNAs allows many Tc1 insertions to be phenotypically silent. Such mRNA processing may help Tc1 escape negative selection. ------------------- Key: 2355 Medline: 96366414 Authors: Jia Y;Xie GF;Aamodt E Title: pag-3, a Caenorhabditis elegans gene involved in touch neuron gene expression and coordinated movement. Citation: Genetics 142: 141-147 1996 Type: ARTICLE Genes: mec-3 mec-4 mec-7 pag-3 sup-5 unc-5 unc-86 mnDp1 mnDf1 mnDf4 mnDf5 mnDf7 mnDf8 mnDf19 mnDf20 mnDf43 Abstract: Mutations in a newly identified gene, pag-3, cause ectopic expression of touch neuron genes mec-7, mec-7lacZ and mec-4lacZ in the lineal sisters of the ALM touch neurons, the BDU neurons. pag-3 mutants also show a reverse kinker uncoordinated phenotype. The first pag-3 allele was isolated in a screen for mutants with altered immunofluorescence staining patterns. Two additional pag-3 alleles were identified in a noncomplementation screen of 38,000 haploid genomes. All of the pag-3 alleles were recessive to wild type and cause the same phenotypes. Two-factor crosses, deficiency mapping and three-factor crosses located pag-3 to the right arm of the X chromosome between unc-3 and unc-7. Because recessive mutations in pag-3 result in expression of several touch cell specific genes in the BDU neurons, pag-3(+) must directly or indirectly suppress expression of these genes in the BDU neurons. Although pag-3 mutants did not show mec-3lacZ expression in their BDU neurons, expression of mec-7lacZ and mec-4lacZ in the BDU neurons of pag-3 mutants required ------------------- Key: 2356 Medline: 96125320 Authors: Marks NJ;Shaw C;Maule AG;Davis JP;Halton DW;Verhaert P;Geary TG;Thompson DP Title: Isolation of AF2 (KHEYLRFamide) from Caenorhabditis elegans: Evidence for the presence of more than one FMRFamide-related peptide-encoding gene. Citation: Biochemical and Biophysical Research Communications 217: 845-851 1995 Type: ARTICLE Genes: flp-1 Abstract: Numerous FMRF amide-related peptides (FaRPs) have been isolated and sequenced from extracts of free-living and parasitic nematodes. The most abundant FaRP identified in ethanolic/methanolic extracts of the parasitic forms, Ascaris suum and Haemonchus contortus and from the free-living nematode, Panagrellus redivivus, was KHEYLRF amide (AF2). Analysis of the nucleotide sequences of cloned FaRP-precursor genes from C. elegans and, more recently, Caenorhabditis vulgaris identified a series of related FaRPs which did not include AF2. An acid-ethanol extract of Caenorhabditis elegans was screened radioimmunometrically for the presence of FaRPs using a C-terminally directed FaRP antiserum. Approximately 300 pmols of the most abundant immunoreactive peptide was purified to homogeneity and 30 pmols was subjected to Edman degradation analysis and gas-phase sequencing. The unequivocal primary structure of the heptapeptide, Lys-His-Glu-Tyr-Leu-Arg-Phe-NH2 (AF2) was determined following a single gas-phase sequencing run. The molecular mass of the peptide was determined using a time-of-flight mass spectrometer and was found to be 920 (MH(+))(-), which was consistent with the theoretical mass of C-terminally amidated AF2. These results indicate that C. elegans possesses more than one FaRP gene. ------------------- Key: 2357 Medline: 96125168 Authors: Fitzgerald K;Greenwald I Title: Interchangeability of Caenorhabditis elegans DSL proteins and intrinsic signalling activity of their extracellular domains in vivo. Citation: Development 121: 4275-4282 1995 Type: ARTICLE Genes: apx-1 arg-1 glp-1 lag-2 lin-12 smg-1 unc-54 Abstract: Ligands of the Delta/Serrate/lag-2 (DSL) family and their receptors, members of the lin-12/Notch family, mediate cell-cell interactions that specify cell fate in invertebrates and vertebrates. In C. elegans, two DSL genes, lag-2 and apx-1, influence different cell fate decisions during development. Here we show that APX-1 can fully substitute for LAG-2 when expressed under the control of lag-2 regulatory sequences, In addition, we demonstrate that truncated forms lacking the transmembrane and intracellular domains of both LAG-2 and APX-1 can also substitute for endogenous lag-2 activity. Moreover, we provide evidence that these truncated forms are secreted and able to activate LIN-12 and GLP-1 ectopically. Finally, we show that expression of a secreted DSL domain alone may enhance endogenous LAG-2 signalling. Our data suggest ways that activated forms of DSL ligands in other systems may be created. ------------------- Key: 2358 Medline: 96356219 Authors: Morgan PG;Sedensky MM Title: Mutations affecting sensitivity to ethanol in the nematode, Caenorhabditis elegans. Citation: Alcoholism, Clinical & Experimental Research 19: 1423-1429 1995 Type: ARTICLE Genes: unc-1 unc-9 unc-79 Abstract: Mutations in nine genes have been identified in the nematode, Caenorhabditis elegans, which control sensitivity to ethanol. The interaction of these genes has been examined and used to determine a genetic pathway controlling sensitivity to ethanol. The nature of this pathway indicates that ethanol exerts its anesthetic actions at more than one site of action. These results also indicate that ethanol is similar in its effects to the volatile anesthetics, enflurane and isoflurane. ------------------- Key: 2359 Medline: 96133874 Authors: Xu J;Lapham J;Crothers DM Title: Determining RNA solution structure by segmental isotopic labeling and NMR: Application to Caenorhabditis elegans spliced leader RNA 1. Citation: Proceedings of the National Academy of Sciences USA 93: 44-48 1996 Type: ARTICLE Genes: Abstract: Recent developments in multidimensional heteronuclear NMR spectroscopy and large-scale synthesis of uniformly C-13- and N-15-labeled oligonucleotides have greatly improved the prospects for determination of the solution structure of RNA, However, there are circumstances in which it may be advantageous to label only a segment of the entire RNA chain. For example, in a larger RNA molecule the structural question of interest may reside in a localized domain. Labeling only the corresponding nucleotides simplifies the spectrum and resonance assignments because one can filter proton spectra for coupling to C-13 and N-15. Another example is in resolving alternative secondary structure models that are indistinguishable in imino proton connectivities. Here ne report a general method for enzymatic synthesis of quantities of segmentally labeled RNA molecules required for NMR spectroscopy. me use the method to distinguish definitively two competing secondary structure models for the 5' half of Caenorhabditis elegans spliced leader RNA by comparison of the two-dimensional {N-15}H-1 heteronuclear multiple quantum correlation spectrum of the uniformly labeled sample with that of a segmentally labeled sample. The method requires relatively small samples; solutions in the 200-300 mu M concentration range, with a total of 30 nmol or approximate to 40 mu g of RNA in approximate to 150 mu l, give strong NMR signals in a short accumulation time, The method can be adapted to label an internal segment of a larger RNA chain for study of localized structural problems, This definitive approach provides an alternative to the more common enzymatic and chemical footprinting methods for determination of RNA secondary structure. ------------------- Key: 2360 Medline: 95219449 Authors: Davies AM Title: Neural development. Chemoattractants for navigating axons. Citation: Current Biology 4: 1142-1145 1994 Type: REVIEW Genes: unc-5 unc-6 unc-40 Abstract: Newly identified proteins that seem to act as diffusible attractants for circumferentially growing axons in the vertebrate embryonic spinal cord are related to a protein that directs circumferential axon growth in the nematode. ------------------- Key: 2361 Medline: 95232495 Authors: Artavanis-Tsakonas S;Matsuno K;Fortini ME Title: Notch signaling. Citation: Science 268: 225-232 1995 Type: REVIEW Genes: apx-1 glp-1 lag-1 lin-12 Abstract: The Notch/Lin-12/Glp-1 receptor family mediates the specification of numerous cell fates during development in Drosophila and Caenorhabditis elegans. Studies on the expression, mutant phenotypes, and developmental consequences of unregulated receptor activation have implicated these proteins in a general mechanism of local cell signaling, which includes interactions between equivalent cells andbetween different cell types. Genetic approaches in flies and worms have identified putative components of the signaling cascade, including a conserved family of extracellular ligands and two cellular factors that may associate with the Notch Intracellular domain. One factor, the Drosophila Suppressor of Hairless protein, is a DNA-binding protein, which suggests that Notch signaling may involve relatively direct signal transmission from the cell surface to the nucleus. Several vertebrate Notch receptors have also been discovered recently and play important roles in normal development and tumorigenesis. ------------------- Key: 2362 Medline: 96040827 Authors: Chalfie M Title: The differentiation and function of the touch receptor neurons of Caenorhabditis elegans. Citation: Progress in Brain Research 105: 179-182 1995 Type: REVIEW Genes: ced-3 ced-4 egl-44 egl-46 lin-4 lin-14 lin-32 mec-1 mec-2 mec-3 mec-4 mec-5 mec-6 mec-7 mec-8 mec-9 mec-10 mec-12 mec-14 mec-15 mec-18 sem-4 unc-86 Abstract: Research over the last twenty years on the nematode Caenorhabditis elegans has provided a wealth of information on the structure and development of the nervous system of this animal. For example, complete descriptions of the cellular anatomy (including synaptic contacts) and of the lineage derivation of each of the 302 neurons of the adult C. elegans hermaphrodite are known. Moreover, numerous classical and molecular techniques are available to characterize genes that direct the development and function of cells within the nervous system. Research in my laboratory has used these techniques to study a set of six touch receptor neurons. In this chapter I will describe some of the lessons we have learned about how these cells acquire their specific characteristics (and other cells do not) and how the cells function as touch receptors. ------------------- Key: 2363 Medline: Authors: Williams PL;Dusenbery DB Title: Screening test for Neurotoxins using Caenorhabditis Citation: Model Systems in Neurotoxicology: Alternative Approaches to Animal Testing. : 163-170 1987 Type: ARTICLE Genes: Abstract: Each year thousands of new chemicals are developed but the potential societal benefits are often unrealized or delayed due to the lack of toxicological data. In the past, chemicals were introduced into the environment with little or no toxicological testing. This has resulted in many examples where adverse effects to humans were seen only after years of exposure (e.g., asbestos, benzene, vinyl chloride). Because few chemicals are used as pure substances, the toxicity of mixtures is another problem. However, these potential chemical interactions are seldom evaluated. All of the above have increased the need for toxicological testing. To more efficently use higher animal test models, a need exists for quick, reliable, and inexpensive screening tests. Although limited success has been found in the area of mutagenesis and carcinogenesis (e.g., Ames Assay), few (if any) screening tests have been validated in other areas of toxicological interest.... ------------------- Key: 2364 Medline: 96138421 Authors: Roush W Title: Sperm protein makes its mark upon the worm embryo. Citation: Science 271: 33- 1996 Type: REVIEW Genes: spe-11 Abstract: In creatures from worms to people, it takes two sexes to reproduce, but it's often the female who gets stuck with the real work of childbearing. This division of labor is even mirrored in sperm and eggs. The unfertilized eggs of fruit flies, for example, already contain the molecular signals needed to direct one of the first events in embryonic growth, the creation of distinct body segments. The paternal contribution to early development, in contrast, seems paltry. Sperm carries nuclear material and organelles called centrosomes - organizing sites for cell division - that come into play later on, but no biochemical factors that guide early embryogenesis have been traced back to the father. In the January issue of the journal Development, however, molecular biologist Heidi Browning of the University of Colorado and developmental geneticist Susan Strome of Indiana University report that SPE-11, a protein produced only in the sperm of the nematode Caenorhabditis elegans, may play a crucial role during the first few minutes after the embryo is fertilized. ------------------- Key: 2365 Medline: 96067630 Authors: Buck LB Title: Unraveling chemosensory diversity. Citation: Cell 83: 349-352 1995 Type: REVIEW Genes: Abstract: Most animals have the ability to detect, discriminate, and react to chemicals present in their external environment. These include water-soluble molecules, volatile odorants, and pheromones, molecules that are released from animals and elicit fixed behaviors and physiological responses in animals of the same species. In lower organisms, chemosensory stimuli elicit stereotyped responses. In mammals, responses to some stimuli, such as pheromones, are stereotyped while responses to other stimuli are conscious and measured. Each organism is confronted with a complex array of chemicals. How does the nervous system detect the individual components of this array and organize this information so as to achieve a high level of perceptual discrimination and generate a variety of innate responses? Two recent papers in Cell provide insight into the mechanisms used by chemosensory systems to detect and encode sensory stimuli... ------------------- Key: 2366 Medline: 96107552 Authors: Kim SK Title: Tight junctions, membrane-associated guanylate kinases and cell signaling. Citation: Current Opinion in Cell Biology 7: 641-649 1995 Type: REVIEW Genes: let-23 let-60 lin-2 lin-7 lin-10 lin-45 mek-2 mpk-1 sem-5 sur-1 Abstract: Proteins that define a new family, termed membrane-associated guanylate kinases, have recently been identified as structural components of epithelial tight junctions and neuronal synapses, and as cell signaling proteins in Drosophila and Caenorhabditis elegans. in particular, the lin-2 gene has been shown to encode a membrane-associated guanylate kinase and to act in the let-23 receptor tyrosine kinase/let-60 ras signaling pathway that controls vulval induction in C. elegans. The combined data from recent biochemical and genetic analyses of membrane-associated guanylate kinases suggest that certain tight junction proteins can play an important role in cell signaling pathways. One possibility is that asymmetric segregation of signaling receptors to the basolateral membrane domain of polarized epithelial cells is crucial for proper cell signaling, and that membrane-associated guanylate kinases may be required for ------------------- Key: 2367 Medline: 96140632 Authors: Theriot JA Title: Worm sperm and advances in cell locomotion. Citation: Cell 84: 1-4 1996 Type: REVIEW Genes: Abstract: Across the animal kingdom, fertilization requires the encounter between a large stationary egg and small motile sperm. To maximize their likelihood of reaching the egg before their competition, sperm are extraordinarily specialized cells, generally consisting of little more than a haploid nucleus, mitochondria to generate energy, and a highly efficient movement engine. Almost all animal sperm are flagellated and seek the egg by swimming quickly through a liquid environment. Nematodes, however, produce sperm that move by crawling along solid substrates. These roundworm sperm extend pseudopods that look and behave like the actin-rich pseudopods of a wide variety of cells ranging from free-living soil amoebae to human white blood cells. The crawling sperm appear by most criteria to be exploiting classic actin-based cell motility, with one important difference: the sperm contain practically no ------------------- Key: 2368 Medline: 96026349 Authors: Chalfie M;Eddy S;Hengartner MO;Hodgkin J;Kohara Y;Plasterk RHA;Waterston RH;White JG Title: Genome Maps VI. Caenorhabditis elegans. Citation: Science 270: 415-430 1995 Type: CHART Genes: Abstract: The nematode C. elegans is an important model system for studies of development, cell biology, and neurobiology. It has a short life cycle and reproduces by self- and cross-fertilization, which facilitates genetic analysis. Furthermore, C. elegans is transparent, and the fate of individual cells can be reproducibly mapped in the developing organism. This chart shows on the left progress that has been made in mapping and sequencing the genome, and some of the interesting features that have appeared. The map and sequence are tools that can be used to increase our understanding of fundamental biological processes. On the right side of the chart are highlighted some of the paths that can be taken and some examples of the biological questions that can be addressed. ------------------- Key: 2369 Medline: 96004340 Authors: Jones SJ Title: An update and lessons from whole-genome sequencing Citation: Current Opinion in Genetics & Development 5: 349-353 1995 Type: REVIEW Genes: Abstract: A number of prokaryotic and eukaryotic genomes are currently being sequenced. Already, the nucleotide sequences of four yeast chromosomes and of 2.2 Mb from Caenorhabditis elegans have been reported. Human genomic sequences have also been used in comparative studies with both mouse and Fugu rubripes. ------------------- Key: 2370 Medline: 96140645 Authors: Koelle MR;Horvitz HR Title: EGL-10 regulates G protein signaling in the C. elegans nervous system and shares a conserved domain with many mammalian proteins. Citation: Cell 84: 115-125 1996 Type: ARTICLE Genes: egl-10 goa-1 Abstract: pThe frequencies of certain periodic behaviors of the nematode C. elegans are regulated in a dose-dependent manner by the activity of the gene egl-10. These behaviors are modulated oppositely by the activity of the G protein alpha subunit gene goa-1, suggesting that egl-10 may regulate a G protein signaling pathway in a dose-dependent fashion. egl-10 encodes a protein similar to Sst2p, a negative regulator of G protein signaling in yeast. EGL-10 protein is localized in neural processes, where it may function in neurotransmitter signaling. Two previously known and 13 newly identified mammalian genes have similarity to egl-10 and SST2, and we propose that members of this family regulate many G protein signaling pathways. ------------------- Key: 2371 Medline: 96108943 Authors: Davis MW;Somerville D;Lee RYN;Lockery S;Avery L;Fambrough Title: Mutations in the Caenorhabditis elegans Na,K-ATPase alpha-subunit gene, eat-6, disrupt excitable cell function. Citation: Journal of Neuroscience 15: 8408-8418 1995 Type: ARTICLE Genes: eat-6 egl-10 ric-2 snt-1 unc-29 Abstract: We have cloned a Na,K-ATPase alpha-subunit gene from Caenorhabditis elegans and discovered that it is identical to the gene eat-6. eat-6 mutations cause feeble contractions and slow, delayed relaxations of pharyngeal muscle. The resting membrane potential of eat-6 mutant pharynxes is consistently depolarized compared to wild-type. The action potentials are smaller, and the return to resting potential is slower. To explain these abnormalities, we propose that a reduction of Na,K-ATPase activity in eat-6 mutants leads to a reduction of the ion concentration gradients that power membrane potential ------------------- Key: 2372 Medline: 96144279 Authors: Labbe JC;Jannatipour M;Rokeach LA Title: The Caenorhabditis elegans rop-1 gene encodes the homologue of the human 60-kDa Ro autoantigen. Citation: Gene 167: 227-231 1995 Type: ARTICLE Genes: rop-1 Abstract: As a first step toward establishing a genetic system for the elucidation of the cellular role(s) of the Ro ribonucleoproteins (RoRNP), we have cloned the gene encoding the homologue of the human 60-kDa Ro protein (Ro60) in Caenorhabditis elegans (Ce). This Ce gene is present as a single copy and contains a 643-codon open reading frame interrupted by three introns. The encoded protein, Rop1p, shares 40% identity and 63% overall similarity with both the human and amphibian Ro60. Recombinant protein has been produced in Escherichia coli and used to elicit anti-Rop1p antibodies. Immunological analysis indicated that the Ro60 epitopes have been poorly conserved. Gene-fusion expression studies in transgenic nematodes will provide a new avenue of research to shed ------------------- Key: 2373 Medline: 96152242 Authors: Larminie CGC;Johnstone IL Title: Isolation and characterization of four developmentally regulated cathepsin B-like cysteine protease genes from the nematode Caenorhabditis elegans. Citation: DNA and Cell Biology 15: 75-82 1996 Type: ARTICLE Genes: cpr-1 cpr-3 cpr-4 cpr-5 cpr-6 Abstract: Cathepsin B cysteine protease enzymes have been shown to be involved in a variety of different biological processes in eukaryotes, We have isolated and characterized four distinct cathepsin B-like genes from the genetically tractable nematode, Caenorhabditis elegans, This is the first reported finding of a cathepsin B-like multigene family within a nonparasitic metazoan, The four genes possess distinct genomic architectures, with variations in the position, number, and size of introns. The predicted amino acid sequences of the four genes are highly diverged, Phylogenetic analysis indicates the divergence of this multigene family within C. elegans is as great as the interspecies divergence between the vertebrates and nematode cathepsin B-like genes. In addition, each of the four genes described here shows a distinct temporal pattern of expression during C, elegans development. ------------------- Key: 2374 Medline: 96149385 Authors: Savage C;Das P;Finelli AL;Townsend SR;Sun CY;Baird SE;Padgett RW Title: Caenorhabditis elegans genes sma-2, sma-3 and sma-4 define a conserved family of transforming growth factor beta pathway components. Citation: Proceedings of the National Academy of Sciences USA 93: 790-794 1996 Type: ARTICLE Genes: daf-4 him-5 sma-2 sma-3 sma-4 qDp3 Abstract: Although transforming growth factor beta (TGF-beta) superfamily ligands play critical roles in diverse developmental processes, how cells transduce signals from these ligands is still poorly understood, Cell surface receptors for these ligands have been identified, but their cytoplasmic targets are unknown, We have identified three Caenorhabditis elegans genes, sma-2, sma-3, and sma-4, that have mutant phenotypes similar to those of the TGF-beta-like receptor gene daf-4, indicating that they are required for daf-4-mediated developmental processes, We show that sma-2 functions in the same cells as daf-4, consistent with a role in transducing signals from the receptor, These three genes define a protein family, the dwarfins, that includes the Mad gene product, which participates in the decapentaplegic TGF-beta-like pathway in Drosophila [Sekelsky, J. J., Newfeld, S. J., Raftery, L. A., Chartoff, E. H. & Gelbart, W. M. (1995) Genetics 139, 1347-1358], The identification of homologous components of these pathways in distantly related organisms suggests that dwarfins may be universally required for TGF-beta-like signal transduction, In fact, we have isolated highly conserved dwarfins from vertebrates, indicating that these components are not idiosyncratic to invertebrates, These analyses suggest that dwarfins are conserved cytoplasmic ------------------- Key: 2375 Medline: 96140419 Authors: Katz WS;Lesa GM;Yannoukakos D;Clandinin TR;Schlessinger J;Sternberg PW Title: A point mutation in the extracellular domain activated LET-23, the Caenorhabditis elegans epidermal growth factor receptor homolog. Citation: Molecular and Cellular Biology 16: 529-537 1996 Type: ARTICLE Genes: let-23 let-60 lin-2 lin-3 lin-7 lin-10 sem-5 Abstract: The let-23 gene encodes a Caenorhabditis elegans homolog of the epidermal growth factor receptor (EGFR) necessary for vulval development. We have characterized a mutation of let-23 that activates the receptor and downstream signal transduction, leading to excess vulval differentiation. This mutation alters a conserved cysteine residue in the extracellular domain and is the first such point mutation in the EGFR subfamily of tyrosine kinases. Mutation of a different cysteine in the same subdomain causes a strong loss-of-function phenotype, suggesting that cysteines in this region are important for function and nonequivalent. Vulval precursor cells can generate either of two subsets of vulval cells (distinct fates) in response to sa62 activity. The fates produced depended on the copy number of the mutation, suggesting that quantitative differences in receptor activity influence the decision between these two fates. ------------------- Key: 2376 Medline: 96152649 Authors: White J;Strome S Title: Cleavage plane specification in C. elegans: How to divide the spoils. Citation: Cell 84: 195-198 1996 Type: REVIEW Genes: mes-1 par-1 par-2 par-3 par-4 par-5 Abstract: Anyone who has watched an early embryo develop cannot help but be awed by the choreography of the early cleavages. The orientation and timing of cleavage in an animal cell are always such that the cleavage furrow bisects the mitotic apparatus (MA) during telophase, thus ensuring the equal partitioning of daughter chromosomes. In addition, the regulation of cleavage plane orientation is necessary for correct partitioning of localized determinants to specific daughter cells, for optimal positioning of cells in developing embryos, and for morphogenesis in plants, which are not motile. ------------------- Key: 2377 Medline: Authors: Ebina Y;Okada H;Miki T;Shingai R Title: An extraction method of dynamic features in pulsing organs of Caenorhabditis elegans during feeding. Citation: IEICE Transactions on Information and Systems E79D: 82-91 1996 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans during feeding gives good ''moving biological images'', in which motions of several pulsing organs are superposed on its head swing. A powerful method to extract dynamic features is presented. First step is to use a variance picture VAG4 in order to pick up active pixel coordinates of concerned moving objects. Superiority of VAG4 over usual variance picture VAG2 is shown quantitatively by a model of moving particles. Pulsing areas of C. elegans, are exhibited more clearly in VAG4 than VAG2. Second step is use of a new subtraction method to extract main frequency bands. FFT spectra are averaged in active positions where VAG4 is above threshold THVR in the square with 8 X 8 pixels (ONA). The power spectra averaged in the enlarged squares (ELA) are subtracted from those in ONA, in which ELA includes ONA in its centre position. Large peak bands emerge in the subtracted power spectra, The subtraction eliminates the effect of head swing by spatial averagings in ELA. This new emphasizing method is compared to another subtraction method, The characteristic frequency of periodical moving organs coincides well with the values observed by other research groups and our visual estimation of replayed VTR images. Thus the proposed extraction method is verified to work ------------------- Key: 2378 Medline: 96158920 Authors: Wadsworth WG;Bhatt H;Hedgecock EM Title: Neuroglia and pioneer neurons express UNC-6 to provide global and local netrin cues for guiding migrations in C. elegans. Citation: Neuron 16: 35-46 1996 Type: ARTICLE Genes: unc-5 unc-6 unc-40 Abstract: Netrins are laminin-related proteins that guide circumferential migrations on the ectoderm. To understand how netrin cues direct cell movements, we examined the expression of nematode netrin UNC-6 from embryo to adult. UNC-6 is expressed in 12 types of neuroglia and neurons, creating a hierarchy of netrin cues in the developing nervous system. Comparing gene expression pattern with in vivo phenotypes, we suggest how multiple netrin cues, each with a characteristic role, guide cells and axons during development. We also present the molecular analysis of selective loss-of-function and null alleles. The results indicate that the biological activities of netrins are mediated through distinct protein domains. Subtle mutations in domain VI can produce selective defects in both direction- and tissue-specific guidance. EGF-like module V-2 is essential for dorsal guidance activity; we infer this module is important for interactions between UNC-6 and the dorsal guidance receptor UNC-5. ------------------- Key: 2379 Medline: 96158934 Authors: Du H;Gu GQ;William CM;Chalfie M Title: Extracellular proteins needed for C. elegans mechanosensation. Citation: Neuron 16: 183-194 1996 Type: ARTICLE Genes: mec-3 mec-5 mec-9 Abstract: The mec-5 and mec-9 genes encode putative extracellular proteins that allow a set of six touch receptor neurons in C. elegans to respond to gentle touch. MEC-5 is a collagen made by the epidermal cells that surround the touch cells. Mutations causing touch insensitivity affect the Gly-X-Y repeats of this collagen. mec-9 produces two transcripts, the larger of which is expressed in the touch cells and two PVD neurons. This transcript encodes a protein with 5 Kunitz-type protease inhibitor domains, 6 EGF-like repeats (2 of the Ca2+-binding type), and a glutamic acid-rich region. Missense mutations causing touch insensitivity affect both the EGF-like and Kunitz domains. Since mec-9 loss of function mutations dominantly enhance the touch insensitive phenotype of several mec-5 mutations, MEC-5 and MEC-9 may interact. We propose that these proteins provide an extracellular attachment point for the mechanosensory channels of the touch cells. ------------------- Key: 2380 Medline: 96161983 Authors: Hirabayashi J;Ubukata T;Kasai K Title: Purification and molecular characterization of a novel 16-kDa galectin from the nematode Caenorhabditis elegans. Citation: Journal of Biological Chemistry 271: 2497-2505 1996 Type: ARTICLE Genes: Abstract: In our previous study (Hirabayashi, J., Satoh, M., Ohyama, Y., and Kasai, K. (1992) J. Biochem. (Tokyo) 111, 553-555), two beta-galactoside-binding lectins (apparent subunit molecular masses, 16 and 32 kDa, respectively) were identified in the nematode Caenorhabditis elegans. The subsequent study revealed that the 32-kDa lectin is a member of the galectin family. Since the 32-kDa galectin was found to consist of two homologous domains (similar to 16 kDa), 16-kDa lectin was thought to be a degradation product of the 32-kDa galectin. To clarify this, the 16-kDa lectin was purified by an improved procedure employing extraction with a calcium-supplemented buffer. The purified 16-kDa lectin was found to exist as a dimer (similar to 30 kDa) and showed hemagglutinating activity toward trypsinized rabbit erythrocytes, which was inhibited by lactose. Almost the whole sequence of the 16-kDa polypeptide (approximately 95%, 135 amino acids) was determined after digestion with various proteases. Based on the obtained information, a full-length cDNA was cloned with the aid of RNA-polymerase chain reaction. The clone encoded 146 amino acids including initiator methionine (calculated molecular mass, 15,928 Da). Based on these results, it was concluded that the 16-kDa lectin is a novel member of the galectin family, but not a degradation product of the 32-kDa galectin as had previously thought. However, the 16-kDa galectin showed relatively low sequence similarities to both the N-terminal and the C-terminal domains of the 32-kDa galectin (28% and 27% identities, respectively) and to various vertebrate galectins (14-27%). Nonetheless, all of the critical amino acids involved in carbohydrate binding were conserved. These observations suggest that, in spite of phylogenic distance between nematodes and vertebrates, both the 16-kDa and 32-kDa nematode isolectins have conserved essentially the same function(s) as those of vertebrate galectins, probably through recognition of a key disaccharide moiety, ------------------- Key: 2381 Medline: 96422917 Authors: Sommer RJ;Sternberg PW Title: Apoptosis and change of competence limit the size of the vulva equivalence group in Pristionchus pacificus: a genetic analysis. Citation: Current Biology 6: 52-59 1996 Type: ARTICLE Genes: Abstract: Background: To understand how alterations in the molecular mechanisms underlying developmental processes generate a diversity of biological forms, comparative developmental biology can be combined with genetic analysis. The formation of the nematode vulva is one tractable system for such evolutionary developmental analysis, as much is understood about its development in Caenorhabditis elegans. In Caenorhabditis, six of twelve ventral epidermal cells form the 'vulva equivalence group'; although all six cells are competent to adopt vulval cell fates in response to an inductive signal, only three of these cells are induced to form vulval tissue. Results: In some species of the nematode families Rhabditidae, Neodiplogastridae and Panagrolaimidae, the number of cells in the vulva equivalence group is limited by apoptosis and decreased responsiveness to inductive signals (competence). We have initiated a genetic analysis in one of these species, Pristionchus pacificus, to understand the evolution of the specification of ventral epidermal cells that are competent to generate the vulva. A ped-4 mutation restores competence to an incompetent cell. Mutation of either of two other genes of Pristionchus cause two anterior cells that die in wild-type to survive. A ped-5 mutation causes these cells to be competent to respond to inductive signals, expanding the equivalence group. A ped-6 mutation causes these cells to form ectopic, anterior vulva-like invaginations. Conclusions: During nematode evolution, apoptosis and change of competence alter the number and potency of ventral epidermal cells. The phenotypes of Pristionchus mutants suggest that alterations in homeotic gene control of anteroposterior patterning is involved in creating this ------------------- Key: 2382 Medline: 96152204 Authors: Hoskins R;Hajnal AF;Harp SA;Kim SK Title: The C. elegans vulval induction gene lin-2 encodes a member of the MAGUK family of cell junction proteins. Citation: Development 122: 97-111 1996 Type: ARTICLE Genes: let-23 let-60 lin-2 lin-3 Abstract: The lin-2 gene is required for the induction of the Caenorhabditis elegans vulva, Vulval development is initiated by a signal from the anchor cell that is transduced by a receptor tyrosine kinase/Ras pathway. We show that lin-2 acts in the vulval precursor cell P6.p, downstream of lin-3 EGF and upstream of let-60 ras, to allow expression of the 1 degrees cell fate, lin-2 encodes a protein of relative molecular mass 109,000 (LIN-2A) with regions of similarity to CaM kinase II and membrane-associated guanylate kinases. Mutant lin-2 transgenes designed to lack either protein kinase or guanylate kinase activity are functional, indicating that LIN-2A has a structural rather than an enzymatic role in vulval induction. Most or all identified membrane-associated guanylate kinases are components of cell junctions, including vertebrate tight junctions and arthropod septate junctions in epithelia. Thus, LIN-2A may be a component of the cell junctions of the epithelial vulval precursor cells that is required for signaling by the receptor tyrosine kinase LET-23. We propose that LIN-2A is required for the localization of one or more signal transduction proteins (such as LET-23) to either the basal membrane domain or the cell junctions, and that mislocalization of signal transduction proteins in lin-2 mutants interferes with vulval induction. ------------------- Key: 2383 Medline: 96152232 Authors: Browning H;Strome S Title: A sperm-supplied factor required for embryogenesis in C. elegans. Citation: Development 122: 391-404 1996 Type: ARTICLE Genes: fem-2 fem-3 glp-4 spe-11 hDp29 Abstract: The paternal-effect embryonic-lethal gene, spe-11, is required for normal development of early C. elegans embryos, Spe-11 embryos fail to complete meiosis, form a weak eggshell, fail to orient properly the first mitotic spindle, and fail to undergo cytokinesis, Here we report cloning and sequencing of the spe-11 gene, which encodes a novel protein. As predicted by the paternal-effect mutant phenotype, the gene is expressed during spermatogenesis but is not detectable in females undergoing oogenesis, and the protein is present in mature sperm. To investigate whether SPE-11's essential function is during spermatogenesis or whether sperm-delivered SPE-11 functions in the newly fertilized embryo, we engineered animals to supply SPE-11 to the embryo through the oocyte rather than through the sperm, We found that maternal expression is sufficient for embryonic viability, This result demonstrates that SPE-11 is not required during spermatogenesis, and suggests that SPE-11 is a sperm-supplied factor that participates directly in development of the early embryo, In contrast to the many known maternal factors required for embryogenesis, SPE-11 is the first paternally contributed factor to be genetically identified and molecularly characterized. ------------------- Key: 2384 Medline: 96229268 Authors: Geary TG;Bowman JW;Friedman AR;Maule AG;Davis JP;Winterrowd CA;Klein RD;Thompson DP Title: The pharmacology of FMRFamide-related neuropeptides in nematodes: New opportunities for rational anthelmintic discovery? Citation: International Journal for Parasitology 25: 1273-1280 1995 Type: ARTICLE Genes: Abstract: The chemotherapeutic control of helminth parasites is compromised by the limited number of classes of anthelmintic drugs. Discovery of novel anthelmintics is impeded by the lack of novel screening technologies that overcome the difficulties inherent in screens based on whole organism toxicity. The development and implementation of mechanism-based screens for new anthelmintics offers great promise for the revitalization of antiparasitic drug discovery. However, mechanism-based screens must be based on a thorough understanding of the proteins or processes that offer the best chance for selective chemotherapeutic intervention. Basic research on the characterization of nematode FMRF amide-related peptides (FaRPs) has revealed that these peptides are ubiquitously distributed in helminths. Chemical identification of a number of nematode FaRPs has been achieved, and these peptides have potent and profound effects on the nematode neuromuscular system. Physiological processes mediated by nematode FaRPs (and other helminth neuropeptides) offer potential targets for the discovery of novel anthelmintics. ------------------- Key: 2385 Medline: 96152705 Authors: Moerman DG;Hutter H;Mullen GP;Schnabel R Title: Cell autonomous expression of perlecan and plasticity of cell shape in embryonic muscle of Caenorhabditis elegans. Citation: Developmental Biology 173: 228-242 1996 Type: ARTICLE Genes: unc-52 Abstract: Perlecan, a component of the extracellular matrix (ECM), is essential for myofilament formation and muscle attachment in Caenorhabditis elegans. We show here that perlecan is a product of muscle and that it behaves in a cell autonomous fashion. That is, perlecan expressed in an individual muscle cell does not spread beyond the borders of the ECM underlying that cell. Using a polyclonal antibody that recognizes all isoforms of perlecan, we demonstrate that this protein first appears extracellularly at the comma stage (approx. 350 min) of development. We also show that during morphogenesis muscle cells have a heretofore undescribed plasticity of shape. This ability to regulate cell shape allows cells within a muscle quadrant to compensate for missing cells and to form a functional quadrant. A dramatic example of this morphological flexibility can be observed in animals in which the D blastomere has been removed by laser ablation. Such animals, lacking 20 of the 81 embryonic body wall muscle cells, can survive to become viable adult animals indistinguishable from wildtype animals. This demonstrates that the assembly of an embryo via a stereotypic lineage does not preclude a more general regulation during morphogenesis. It appears that embryos are flexible enough to immediately compensate for drastic alterations in tissue composition, a feature of development that may be of general importance during evolution. ------------------- Key: 2386 Medline: 96187862 Authors: Sommer RJ;Sternberg PW Title: Evolution of nematode vulval fate patterning. Citation: Developmental Biology 173: 396-407 1996 Type: REVIEW Genes: Abstract: Nematodes provide a useful experimental system with which to investigate the evolution of development at the cellular, genetic, and molecular levels. Building on an understanding of vulval development in Caenorhabditis elegans, analysis of vulval development has been extended to a number of other species in three families of the Nematode phylum. Changes have occurred in most aspects of vulval development: alteration in the number of cells competent to participate in vulval development by changes in apoptosis; changes in the relative contributions of position-dependent predisposition toward particular fates (prepattern), inductive signaling and lateral signaling; and in the specific lineages generated by vulval precursor cells. Genetic analysis of one species in which only three vulval precursor cells are present identified a mutation that increases the number of vulva precursor cells toward that found in C. elegans. ------------------- Key: 2387 Medline: 96181656 Authors: Youngman S;van Luenen HGAM;Plasterk RHA Title: Rte-1, a retrotransposon-like element in Caenorhabditis elegans. Citation: FEBS Letters 380: 1-7 1996 Type: ARTICLE Genes: prk-1 rte-1 Abstract: We have characterized a retrotransposon-like element (Rte-1) in C. elegans. It was identified while we were sequencing the pim related kinase-1 (prk-1) gene. The element is 3,298 bp long and flanked by a 200 bp direct repeat. 95 bp of the direct repeat are present in the coding region of prk-1. Rte-1 contains an open reading frame, in the opposite orientation of prk-1, potentially encoding 625 amino acids, with similarity to reverse transcriptases. The element is most similar to members of the non-LTR group of retrotransposable elements. There is weak homology of the predicted amino acid sequence of Rte-1 to several reverse transcriptase-like genes identified by the C. elegans genome sequencing consortium, suggesting that there may be a large family of these elements. Southern blots indicate that there are approximately 10-15 additional Rte-1 elements in the C. elegans Bristol N2 genome and a similar number is found in the genomes of two other geographically distinct strains. The insertion pattern of Rte-1 is polymorphic between these strains. ------------------- Key: 2388 Medline: 96422792 Authors: Yuan JY Title: Evolutionary conservation of a genetic pathway of programmed cell death. Citation: Journal of Cellular Biochemistry 60: 4-11 1996 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ces-1 ces-2 nuc-1 Abstract: Genetic analysis of programmed cell death in Caenorhabditis elegans has led to the identification of 13 genes that constitute a developmental pathway of programmed cell death. Two of the three key genes in this pathway, ced-9, a cell death suppressor, and ced-3, a cell death inducer, were found to encode proteins that share structural and functional similarities with the mammalian proto-oncogene product Bcl-2 and interleukin-1 beta converting enzyme, respectively. These results suggest that the genetic pathway of programmed cell death may be evolutionarily conserved from worms to mammals. ------------------- Key: 2389 Medline: Authors: Davis RE Title: Spliced leader RNA trans-splicing in metazoa. Citation: Parasitology Today 12: 33-40 1996 Type: REVIEW Genes: Abstract: Spliced leader trans-splicing is a form of RNA processing originally described and studied in parasitic kinetoplastida. This mechanism of gene expression also occurs in parasitic and free-living metazoa. In this review, Dick Davis describes current knowledge of the distribution, substrates, specificity and functional significance of trans-splicing in metazoa. ------------------- Key: 2390 Medline: 96178489 Authors: Gems D;Riddle DL Title: Longevity in Caenorhabditis elegans reduced by mating but not gamete production. Citation: Nature 379: 723-725 1996 Type: ARTICLE Genes: fer-1 fer-6 fog-2 spe-26 Abstract: Theories of life-history evolution propose that trade-offs occur between fitness components, including longevity and maximal reproduction(1-3). In Drosophila, female lifespan is shortened by increased egg production(4), receipt of male accessory fluid(5) and courting(6), Male lifespan is also reduced by courting and/or mating(7). Here we show that in the nematode Caenorhabditis elegans, mating with males reduces the lifespan of hermaphrodites by a mechanism independent of egg production or receipt of sperm, Conversely, males appear unaffected by mating, Thus, in C. elegans there is no apparent trade-off between longevity and increased egg or sperm production, but there is a substantial cost to hermaphrodites associated with copulation. ------------------- Key: 2391 Medline: 96431849 Authors: Hengartner MO Title: Programmed cell death in invertebrates. Citation: Current Opinion in Genetics & Development 6: 34-38 1996 Type: REVIEW Genes: ced-3 ced-4 ced-9 dad-1 Abstract: Genetic studies of programmed cell death in Caenorhabditis elegans and Drosophila melanogaster have led to the identification of several invertebrate cell death genes. In C. elegans, ced-3 and ced-4 function to kill cells, whereas ced-9 protects cells from death. In Drosophila, the genes reaper and hid act in parallel to promote cell death. Characterization of these genes has revealed that the process of programmed cell death is evolutionarily conserved and has shed light on the molecular nature of the apoptotic machinery. ------------------- Key: 2392 Medline: 96435790 Authors: Hird S Title: Cortical actin movements during the first cell cycle of the Caenorhabditis elegans embryo. Citation: Journal of Cell Science 109: 525-533 1996 Type: ARTICLE Genes: Abstract: The first division of the Caenorhabditis elegans embryo is unequal, generating daughter cells with distinct fates. The differences between the cells are believed to result from the partitioning of cytoplasmic determinants during the first cell cycle. Actin microfilaments play a critical, but poorly defined, role in this event, In this paper, the actin cortex in live embryos is studied during cytoplasmic localisation by fluorescently labelling microfilaments in oocytes and then using in vivo fluorescence microscopy to observe their behaviour. This reveals that there is a concerted movement of cortical actin to the anterior of the embryo at the time cytoplasmic localisation takes place. Furthermore, it is demonstrated that endogenous foci of F-actin are asymmetrically distributed following this event; these structures have previously been seen in fixed cortices, A model for the participation of the actin cytoskeleton in cytoplasmic localisation is presented based on these results. ------------------- Key: 2393 Medline: 96216447 Authors: Hugunin M;Quintal LJ;Mankovich JA;Ghayur T Title: Protease activity of in vitro transcribed and translated Caenorhabditis elegans cell death gene (ced-3) product. Citation: Journal of Biological Chemistry 271: 3517-3522 1996 Type: ARTICLE Genes: ced-3 Abstract: The Caenorhabditis elegans cell death gene, ced-3, encodes one of the two proteins required for apoptosis in this organism. The primary sequence similarities between Ced-3 and the mammalian interleukin-1 beta converting enzyme (ICE) suggest that these two proteins may have functionally similar active sites and that Ced-3 may function as a cysteine protease, Here we report that in vitro transcribed and translated Ced-S protein (p56) underwent rapid processing to smaller fragments. Replacement of the predicted active site cysteine of Ced-3 with serine (C364S) prevented the generation of smaller proteolytic fragments, suggesting that the processing might be an autocatalytic process. Peptide aldehydes with aspartic acid at the P1 position blocked Ced-3 autocatalysis. Furthermore, the protease inhibition profile of Ced-3 was similar to the profile reported for ICE. These functional data demonstrate that Ced-3 is an Asp-dependent cysteine protease with substrate specificity similar to that of ICE. Aurintricarboxylic acid, an inhibitor of apoptosis in mammalian cells, blocked Ced-3 autocatalytic activity, suggesting that an aurintricarboxylic acid-sensitive Ced-3/ICE-related protease might be involved in the apoptosis pathway(s) in mammalian cells. ------------------- Key: 2394 Medline: 96226955 Authors: Jones CA;Hartman PS Title: Replication in UV-irradiated Caenorhabditis elegans Citation: Photochemistry and Photobiology 63: 187-192 1996 Type: ARTICLE Genes: rad-3 Abstract: Replication continues in wild-type (but not rad mutant) Caenorhabditis elegans embryos even after exposure to massive fluences of UV radiation. It is of interest to elucidate the mechanism(s) for this ''damage-resistant'' DNA synthesis. In this study, DNA from unirradiated and UV-irradiated wild-type embryos was examined using the electron microscope. Large fluences of UV radiation (180 J m(-2)) had little effect on either replication bubble size or distances between bubbles in wild-type embryos, indicating that the damage-resistant DNA synthesis was not grossly aberrant. Conversely, UV irradiation significantly decreased center-to-center distances between bubbles in excision-repair-deficient rad-3 embryos. This suggests that the decreased DNA synthesis observed after UV irradiation in rad-3 embryos is due largely to blockage of elongation of DNA synthesis. ------------------- Key: 2395 Medline: 96231889 Authors: Smith H;Campbell WC Title: Effect of ivermectin on Caenorhabditis elegans larvae previously exposed to alcoholic immobilization. Citation: Journal of Parasitology 82: 187-188 1996 Type: ARTICLE Genes: Abstract: First-stage larvae of Caenorhabditis elegans were immersed in 0.15% 1-phenoxy-2-propanol to induce temporary paralysis, including the suppression of pharyngeal pumping. Subsequent addition of ivermectin (to give 50 mu g/ml) induced coiling and prolonged immobilization of such larvae, as also of control larvae (previously immersed only in water). The results suggest that ingestion of drug by means of pharyngeal pumping is not a prerequisite for the uptake of ivermectin at levels sufficient for antinematodal ------------------- Key: 2396 Medline: 96177760 Authors: Sakai T;Koga M;Ohshima Y Title: Genomic structure and 5' regulatory regions of the let-23 gene in the nematode C. elegans. Citation: Journal of Molecular Biology 256: 548-555 1996 Type: ARTICLE Genes: let-23 Abstract: The let-23 gene in the nematode Caenorhabditis elegans encodes a receptor tyrosine kinase and is necessary for the induction of a vulva, survival past the L1 stage, hermaphrodite fertility and for male spicule development. We sequenced the entire let-23 genomic region of over 12 kb. The 5' end of the let-23 mRNA was mapped by sequencing polymerase chain reaction products, and two mRNAs were found which had alternative exons and were probably initiated at different sites. One transcript was trans-spliced to SL1. Expression of either cDNA rescued a let-23 vulvaless mutation in germline transformation. These results suggest that the let-23 gene encodes two proteins of 1323 or 1335 amino acid residues. We prepared various 5' deletion constructs of the let-23 gene, and examined their rescue activities for a let-23 lethal or vulvaless mutation. The results revealed that two regions were required for let-23 expression, one for larval survival and the other for vulva formation. We also cloned and analyzed a let-23 homologue from Caenorhabditis vulgaris. It can encode two proteins of 77% amino acid residue identity with the Let-23 proteins. The 12 kb fragment carrying the C. vulgaris gene rescued the let-23 vulvaless mutation in C. elegans. Seventeen sequences highly conserved between the two species were identified in the 5' upstream region or within an intron. Three of these sequences are contained in the two regions required for let-23 expression, suggesting that they are cis-acting elements for let-23 expression. ------------------- Key: 2397 Medline: 96230436 Authors: Coulson A Title: The Caenorhabditis elegans genome project. Citation: Biochemical Society Transactions 24: 289-291 1996 Type: REVIEW Genes: Abstract: A number of projects are underway that have as their goal the complete analysis and understanding of the genomes of a variety of organisms. The most advanced of these (as of mid-1995) for a multicellular organism is the Caenorhabditis elegans genome project. To date, 20 Mb of the 100 Mb genome has been fully sequenced, and completion is expected in 1998. In addition to providing an invaluable resource for the C. elegans community, and beyond, experience gained from mapping and sequencing of this genome has led to the formulation of a scheme that could produce a coherent, near-complete 'sequence map' of the human genome in a 5 year period. ------------------- Key: 2398 Medline: 97002542 Authors: Shook DR;Brooks A;Johnson TE Title: Mapping quantitative trait loci affecting life history traits in the nematode Caenorhabditis elegans. Citation: Genetics 142: 801-817 1996 Type: ARTICLE Genes: Abstract: We have identified chromosomal regions containing quantitative trait loci (QTLs) specifying life history traits in recombinant-inbred strains of the nematode Caenorhabditis elegans. This approach also allows us to examine epistatic interactions between loci and pleiotropic effects on different traits at specific loci. QTLs for mean life span were identified on chromosomes II (near stP101), IV (stP5) and the X (stP61), and QTLs for fertility were identified on II (maP1), Ill (stP19) and IV (stP51). The QTLs for mean life span accounted for 90% of the genetic component of variance. The loci for mean fertility accounted for 88% of the genetic component of variance. Additional QTLs for temperature-sensitive fertility [II (stP36) and V (stP6)] and internal hatching [IV (stP5)] were also mapped in these crosses. We found evidence for epistatic effects on mean life span between maP1 and bP1 (V), and for epistatic effects on mean fertility between stP36 and stP6, between stP98 (II) and stP192 (V), between maP1 and stP127 (III), between maP1 and stP103 (X), and between stP5 and stP6. Negatively correlated, pleiotropic effects on mean life spall and internal hatching were found ------------------- Key: 2399 Medline: 96159520 Authors: Xie GF;Jia Y;Aamodt E Title: A C. elegans mutant screen based on antibody or histochemical staining. Citation: Genetic Analysis: Biomolecular Engineering 12: 95-100 1995 Type: ARTICLE Genes: ges-1 gus-1 pag-1 pag-3 Abstract: A method has been developed for isolating mutations in Caenorhabditis elegans that alter antibody or histochemical staining patterns. The basis for this method is a new procedure for making C. elegans permeable that does not kill the eggs contained within the uterus of gravid adult hermaphrodites. A mutagenized population of gravid hermaphrodites is made permeable and then stained with either an antibody or a histochemical stain. Animals that stain aberrantly are picked to individual petri plates and the eggs within the uterus of the stained mother hatch and establish a new genetic line. Antibody and histochemical stains are especially useful phenotypes because the staining pattern will usually directly reflect the gene expression pattern of the gene that codes for the antigen or enzyme, This method was used to isolate mutants that alter the expression of a mec-7lacZ fusion gene. Transgenic animals that contained the mec-7lacZ gene integrated into chromosome I were treated with the mutagen ethylmethanesulfonate, allowed to self-fertilize for two generations and then stained with X-gal or antibodies against beta-galactosidase. Gravid animals that stained abnormally were picked to fresh petri plates and their offspring were used to establish new mutant lines. ------------------- Key: 2400 Medline: 96257962 Authors: Schnabel R;Weigner C;Hutter H;Feichtinger R;Schnabel H Title: mex-1 and the general partitioning of cell fate in the early C. elegans embryo. Citation: Mechanisms of Development 54: 133-147 1996 Type: ARTICLE Genes: mel-21 mex-1 par-1 par-2 par-3 par-4 itDf2 mnDf87 mnDf89 Abstract: It is thought that at least some of the initial specification of the five somatic founder cells of the C. elegans embryo occurs cell-autonomously through the segregation of factors during cell divisions. It has been suggested that in embryos from mothers homozygous for mutations in the maternal-effect gene mex-1, four blastomeres of the 8-cell embryo adopt the fate of the MS blastomere. It was proposed that mex-1 functions to localise or regulate factors that determine the fate of this blastomere. Here, a detailed cell lineage analysis of 9 mex-1 mutants reveals that the fates of all somatic founder cells are affected by mutations in this gene. We propose that mex-1, like the par genes, is involved in establishing the initial polarity of the embryo. ------------------- Key: 2401 Medline: 96351572 Authors: Vanfleteren JR;De Vreese A Title: Rate of aerobic metabolism and superoxide production rate potential in the nematode Caenorhabditis elegans. Citation: Journal of Experimental Zoology 274: 93-100 1996 Type: ARTICLE Genes: age-1 fer-15 spe-9 unc-52 unc-54 Abstract: We have monitored oxygen consumption as a measure of the rate of aerobic metabolism during the lifetime of Caenorhabditis elegans. We have also developed a chemiluminescent technique which measures exogenous NADPH-stimulated superoxide anion production by freeze-thawed worms. In this assay light production depends on the combined activities of all of the enzymes involved in superoxide production, both directly and indirectly, thus reflecting their activity levels immediately prior to freeze fixation. We have designated this parameter the superoxide production rate potential. The superoxide production rate potential is controlled by the longevity determining gene age-1 and varies in a life cycle-dependent fashion. The metabolic rate generally follows these fluctuations, but additionally shows specific alterations as a response to environmental factors. Metabolic rate and superoxide production rate potential increase by 1.3- and 3-fold, respectively, in reproducing adults. This increase is not due to the contribution of embryonating eggs, however. Culture conditions have a large effect on metabolic rate, but not on the superoxide production rate potential. The energetic cost of movement, measured as consumed oxygen, is low relative to the costs of maintenance and reproduction. Identical superoxide production rate potentials are scored in paralyzed and ------------------- Key: 2402 Medline: 96260665 Authors: Reis RJS;Ebert RH Title: Genetics of aging: Current animal models. Citation: Experimental Gerontology 31: 69-81 1996 Type: REVIEW Genes: age-1 daf-2 daf-16 mev-1 spe-26 Abstract: Studies are summarized for three organisms-Caenorhabditis elegans, Mus musculus, and Drosophila melanogaster-utilizing three distinct approaches to the identification of longevity-determining genes: the analysis of mutations that affect life span, the use of transgenic animals to assess the effects of specific gene expression on longevity, and selective breeding to identify naturally occurring allelic variations between strains that have differential effects on life span. Correlative studies of age-dependent changes in physiology, or in cellular and molecular constituents, generally cannot discern cause from effect. In contrast, analyses of genetic influences on longevity can permit underlying mechanisms to be reliably inferred; because genotype remains essentially constant throughout life, longevity comparisons of animals differing only in genetic constitution must reflect the effects of genes on long-term survival, Understanding the genetic regulation of life span may thus lead to methods of intervention in age-associated deterioration and disease. ------------------- Key: 2403 Medline: 96189356 Authors: Wightman B;Clark SG;Taskar AM;Forrester WC;Maricq AV;Bargmann CI;Garriga G Title: The C. elegans gene vab-8 guides posteriorly directed axon outgrowth and cell migration. Citation: Development 122: 671-682 1996 Type: ARTICLE Genes: ceh-23 glr-1 him-6 mec-4 unc-76 unc-107 vab-8 ctDf1 Abstract: The assembly of the nervous system in the nematode C. elegans requires the directed migrations of cells and growth cones along the anteroposterior and dorsoventral body axis. We show here that the gene vab-8 is essential for most posteriorly directed migrations of cells and growth cones. Mutations in vab-8 disrupt fourteen of seventeen posteriorly directed migrations, but only two of seventeen anteriorly directed and dorsoventral migrations. For two types of neurons that extend axons both anteriorly and posteriorly, vab-8 mutations disrupt only the growth of the posteriorly directed axon, vab-8 encodes two genetic activities that function in the guidance of different migrations, Our results suggest that most posteriorly directed cell and growth cone migrations are guided by a common mechanism involving the vab-8 gene. ------------------- Key: 2404 Medline: 96351163 Authors: Sengupta P;Bargmann CI Title: Cell fate specification and differentiation in the nervous system of Caenorhabditis elegans. Citation: Developmental Genetics 18: 73-80 1996 Type: REVIEW Genes: egl-5 egl-44 egl-46 lin-26 lin-32 lin-39 mab-5 mec-3 mec-7 sem-4 unc-30 unc-86 Abstract: Neuronal cell fates are specified by a hierarchy of events mediated by cell-intrinsic determinants and cell-cell interactions. The determination of cell fate can be subdivided into three general steps. First, cell fate is restricted by the cell's position in the animal. For example, neurons are specified along the anterior-posterior body axis through the action of the Hox genes lin-39, mab-5, and egl-5. Second, a decision is made to generate a particular cell type, such as the progenitor of a neurogenic lineage as opposed to that of an epidermal lineage. Among the genes that influence this decision is the proneural gene lin-32. Third, characteristics of a particular cell type are specified. For example, in a neurogenic lineage, a decision may be made to generate a specific neuron type such as a sensory or motor neuron. Genes that affect neuronal fate can act in different ways to influence the development of different types of neurons. ------------------- Key: 2405 Medline: 95128842 Authors: Ziegler C Title: Titin-related proteins in invertebrate muscles. Citation: Comparative Biochemistry & Physiology A-Comparative Physiology 109A: 823-833 1994 Type: REVIEW Genes: unc-22 Abstract: The localization of filaments connecting the Z-line and the A-band in insect flight muscles and the identification of very large proteins as their components is reviewed. The characterization of twitchin in the obliquely striated muscles of Caenorhabditis elegans is reported and the deductions made from its amino acid sequence are considered. The characterization of mini-titins in obliquely striated molluscan muscles is compared. The identification of projectin in the muscles of Drosophila melanogaster by anti-twitchin-antibodies, its sequence analysis and the characterization of mini-titins in arthropod and mollusc fast-striated muscles are summarized. The possible biological functions of the different proteins in various invertebrate muscles are discussed. ------------------- Key: 2406 Medline: Authors: Kreeger KY Title: Hot papers: Programmed cell death. Citation: The Scientist 10: 15- 1996 Type: REVIEW Genes: ced-9 Abstract: Biologist H. Robert Horvitz discusses the genetics of cell death in the nematode C. elegans. ------------------- Key: 2407 Medline: 96038997 Authors: Agarwal P;States DJ Title: The Repeat Pattern Toolkit (RPT): Analyzing the structure and evolution of the C. elegans genome. Citation: ISMB 2: 1-9 1994 Type: ARTICLE Genes: Abstract: Over 3.6 million bases of DNA sequence from chromosome III of the C. elegans have been determined. The availability of this extended region of contiguous sequence has allowed us to analyze the nature and prevalence of repetitive sequences in the genome of a eukaryotic organism with a high gene density. We have assembled a Repeat Pattern Toolkit (RPT) to analyze the patterns of repeats occurring in DNA. The tools include identifying significant local alignments (utilizing both two-way and three-way alignments), dividing the set of alignments into connected components (signifying repeat families), computing evolutionary distance between repeat family members, constructing minimum spanning trees from the connected components, and visualizing the evolution of the repeat families. Over 7000 families of repetitive sequences were identified. The size of the families ranged from isolated pairs to over 1600 segments of similar sequence. Approximately 12.3% of the analyzed sequence participates ------------------- Key: 2408 Medline: 96038992 Authors: Veretnik S;Schatz B Title: Pattern discovery in gene regulation; designing an analysis environment. Citation: ISMB 1: 411-419 1993 Type: ARTICLE Genes: Abstract: Interactions that determine cellular fate are exceedingly complex, can take place at different levels of gene regulation and involve a large number of components (such as genes, proteins). 'Wet lab' biology has an inherent difficulty in considering multiple components within one experimental set-up. Thus, the individual experimental results may reflect the behavior of a sub-system and be missing some important information concerning interactions with other components. Computational tools can help in simultaneously analyzing many different pieces of biological knowledge from different data sources. Such tools will aid in comprehending the whole system (cell, organism) as a function of all of its components; this, in turn, will facilitate discovery of the global patterns in genetic regulation. The Worm Community System (WCS) which contains extensive knowledge from many different sources regarding model organism C. elegans, presents a suitable environment for development of the integrated analysis tools. Here we describe a working version of WCS and the strategies employed for the development of the global analysis tools within the System. The present paper deals with the construction of a highly interconnected information space (in the context of the problem) by introducing more sophisticated data objects representing knowledge about genetic regulation. We describe construction of the in-depth objects, development of the analysis tools and discuss the type of analysis feasible within such interconnected space. The analysis tools will serve as an ideal environment for 'dry biology' experimentation and provide a context for 'wet' ------------------- Key: 2409 Medline: 96131081 Authors: Harrop SA;Prociv P;Brindley PJ Title: Amplification and characterization of cysteine proteinase genes from nematodes. Citation: Tropical Medicine & Parasitology 46: 119-122 1995 Type: ARTICLE Genes: Abstract: In order to isolate proteinase genes from parasitic nematodes by polymerase chain reaction (PCR) techniques, we employed a pair of consensus oligonucleotide primers designed to anneal to the active site cysteine (primer ncpC) and asparagine (primer ncpN) coding regions of cysteine proteinases. The primers were biased toward the nucleotide and codon usages of cysteine proteinase genes of nematodes and were based on the consensus nucleotide sequences flanking the active site residues of genes from Haemonchus contortus, Caenorhabditis elegans, and Ostertagia ostertagi. We employed 'touchdown' PCR conditions and were able to amplify novel cysteine proteinase gene fragments from the rodent parasite Strongyloides ratti, the human pathogen S. stercoralis, the canine hookworm Ancylostoma caninum, and from C. elegans. These clones are gene homologs of cathepsin B-like (lysosomal associated) proteases and will facilitate ------------------- Key: 2410 Medline: 96089060 Authors: Worley KC;King KY;Chua S;McCabe ER;Smith RF Title: Identification of new members of a carbohydrate kinase-encoding gene family. Citation: Journal of Computational Biology 2: 451-458 1995 Type: ARTICLE Genes: Abstract: In a sequence database search using the human glycerol kinase-encoding sequence (HUMGLYKINB) as a query, we identified six previously unidentified carbohydrate kinase sequences. Five of the six newly identified sequences appear to be known types of carbohydrate kinases, four are glycerol kinases and one is a gluconokinase. The sixth newly identified sequence, the Caenorhabditis elegans gene, CER08D7.7-CEF59B2.1, shows similarity to the family of carbohydrate kinases including other glycerol kinases, xylulokinases, gluconokinases, ribulokinases, rhamnulokinases, and fucokinases. A phylogenetic comparison of this newly identified Caenorhabditis elegans gene with the other members of the carbohydrate kinase family demonstrated that this sequence cannot be assigned to one of the known classes of carbohydrate kinases. ------------------- Key: 2411 Medline: 96180278 Authors: Benian GM;Tinley TL;Tang X;Borodovsky M Title: The Caenorhabditis elegans gene unc-89, required for muscle M-line assembly, encodes a giant modular protein composed of Ig and signal transduction domains. Citation: Journal of Cell Biology 132: 835-848 1996 Type: ARTICLE Genes: unc-22 unc-54 unc-73 unc-89 eDp23 Abstract: Mutations in the Caenorhabditis elegans gene unc-89 result in nematodes having disorganized muscle structure in which thick filaments are not organized into A-bands, and there are no M-lines (Waterston, R.H., J.N. Thomson, and S. Brenner. 1980. Dev. Biol. 77:271-302). Beginning with a partial cDNA from the C. elegans sequencing project, we have cloned and sequenced the unc-89 gene. An unc-89 allele, st515, was found to contain an 84-bp deletion and a 10-bp duplication, resulting in an in-frame stop codon within predicted unc-89 coding sequence. Analysis of the complete coding sequence for unc-89 predicts a novel 6,632-amino acid polypeptide consisting of sequence motifs which have been implicated in protein-protein interactions. UNC-89 begins with 67 residues of unique sequence, SH3, dbl/CDC24, and PH domains, 7 immunoglobulin (Ig) domains, a putative KSP-containing multiphosphorylation domain, and ends with 46 Ig domains. A polyclonal antiserum raised to a portion of unc-89 encoded sequence reacts to a twitchin-sized polypeptide from wild type, but truncated polypeptides from st515 and from the amber allele e2338. By immunofluorescent microscopy, this antiserum localizes to the middle of A-bands, consistent with UNC-89 being a structural component of the M-line. Previous studies indicate that myofilament lattice assembly begins with positional cues laid down in the basement membrane and muscle cell membrane (Williams, B.D., and R.H. Waterston. 1994. J. Cell Biol. 124:475-490; Hresko, M.C., B.D. Williams, and R.H. Waterston. 1994. J. Cell Biol. 124:491-506). We propose that the intracellular protein UNC-89 responds to these signals, localizes, and then ------------------- Key: 2412 Medline: 96193762 Authors: Euling S;Ambros V Title: Heterochronic genes control cell cycle progress and developmental competence of C. elegans vulva precursor cells. Citation: Cell 84: 667-676 1996 Type: ARTICLE Genes: lin-3 lin-4 lin-10 lin-11 lin-12 lin-14 lin-15 lin-28 Abstract: Heterochronic genes control the timing of vulval development in the C. elegans hermaphrodite. lin-14 or lin-28 loss-of-function mutations cause the vulval precursor cells (VPCs) to enter S phase and to divide one larval stage earlier than in the wild type. A precocious vulva is formed by essentially normal cell lineage patterns, governed by the same intercellular signals as in the wild type. Mutations that prevent the normal developmental down-regulation of lin-14 activity delay or block VPC division and prevent vulval differentiation. A genetic pathway that includes lin-4, lin-14, and lin-28 controls when VPCs complete G1 and also controls when VPCs acquire the competence to respond to the intercellular patterning signals and express vulval fates. ------------------- Key: 2413 Medline: 96173622 Authors: Shaham S;Horvitz HR Title: Developing Caenorhabditis elegans neurons may contain both cell-death protective and killer activities. Citation: Genes & Development 10: 578-591 1996 Type: ARTICLE Genes: ced-1 ced-3 ced-4 ced-9 mec-7 nuc-1 unc-30 Abstract: We developed a method for examining the effects of overexpressing cell-death-related genes in specific Caenorhabditis elegans neurons that normally live. Using this method, we demonstrated that the cell-death genes ced-3 ced-9, and ced-9 all can act cell autonomously to control programmed cell death. Our observations indicate further that not only the protective activity of ced-9 bur also the killer activities of ced-3 and ced-4 are likely to be present in cells that normally lire. We propose that both in C. elegans and in other organisms a competition between antagonistic protective and killer activities determines whether specific cells will live or die. Our results suggest a genetic pathway for programmed cell death in C. elegans in which ced-4 acts upstream of or in parallel to ced-3 and ced-9 negatively regulates the ------------------- Key: 2414 Medline: 96176302 Authors: Myers CD;Goh PY;Allen TS;Bucher EA;Bogaert T Title: Developmental genetic analysis of troponin T mutations in striated and nonstriated muscle cells of Caenorhabditis elegans. Citation: Journal of Cell Biology 132: 1061-1077 1996 Type: ARTICLE Genes: mup-2 mnDp30 stDf1 Abstract: We have been investigating a set of genes, collectively called mups, that are essential to striated body wall muscle cell positioning in Caenorhabditis elegans. Here we report our detailed characterization of the mup-2 locus, which encodes troponin T (TnT), Mutants for a heat-sensitive allele, called mup-2(e2346ts), and for a putative null, called mup-2(up1), are defective for embryonic body wall muscle cell contraction, sarcomere organization, and cell positioning, Characterizations of the beat-sensitive allele demonstrate that mutants are also defective for regulated muscle contraction in larval and adult body wall muscle, defective for function of the nonstriated oviduct myoepithelial sheath, and defective for epidermal morphogenesis, We cloned the mup-2 locus and its corresponding cDNA. The cDNA encodes a predicted 405-amino acid protein homologous to vertebrate and invertebrate TnT and includes an invertebrate-specific COOH-terminal tail. The mup-2 mutations lie within these cDNA sequences: mup-2(up1) is a termination codon near NH2 terminus (Glu94) and mup-2(e2346ts) is a termination codon in the COOH-terminal invertebrate-specific tail (Trp34). TnT is a muscle contractile protein that, in association with the thin filament proteins tropomyosin, troponin I and troponin C, regulates myosin-actin interaction in response to a rise in intracellular Ca2+, Our findings demonstrate multiple essential functions for TnT and provide a basis to investigate the in vivo functions and protein interactions of TnT in striated and nonstriated muscles. ------------------- Key: 2415 Medline: 96178542 Authors: Vos JC;De Baere I;Plasterk RHA Title: Transposase is the only nematode protein required for in vitro transposition of Tc1. Citation: Genes & Development 10: 755-761 1996 Type: ARTICLE Genes: gpa-2 Abstract: The Tc1 element of Caenorhabditis elegans is a member of the most widespread class of DNA transposons known in nature. Here, we describe efficient and precise transposition of Tc1 in a cell-free system. Tc1 appears to jump by a cut-and-paste mechanism of transposition. The terminal 26 bp of the Tc1 terminal repeats together with the flanking TA sequence are sufficient for transposition. The target site choice in vitro is similar to that in vivo. Transposition is achieved with an extract prepared from nuclei of transgenic nematodes that overexpress Tc1 transposase but also by recombinant transposase purified from Escherichia coli. The simple reaction requirements explain why horizontal spread of Tc1/mariner transposons can occur. They also suggest that Tc1 may be a good vector for transgenesis of diverse animal species. ------------------- Key: 2416 Medline: 97021374 Authors: Herman RK Title: Touch sensation in Caenorhabditis elegans. Citation: BioEssays 18: 199-206 1996 Type: REVIEW Genes: deg-1 mec-1 mec-3 mec-4 mec-6 mec-7 mec-10 mec-12 unc-86 Abstract: The nematode G. elegans exhibits a variety of reponses to touch. When specific sets of mechanosensory neurons are killed with a laser, specific touch responses are abolished. Many mutations that result in defective mechanosensation have been identified. Some of the mutations define genes that specify the fate of a set of mechanoreceptors called the touch cells, which mediate response to light touch to the body of the worm. Genes specifying touch cell fate appear to regulate genes that encode touch-cell differentiation proteins, including apparent subunits of a touch-cell-specific ion channel, rare mutant forms of which lead to swelling and lysis of the touch cells. Molecular attachments of the ion channel, both to extracellular matrix components and, intracellularly, to a special large-diameter microtubule, may be required for mechanical gating of the channel. A mechanoreceptor-interneuron-motorneuron reflex circuit for ------------------- Key: 2417 Medline: 96271524 Authors: Herman RK Title: Worm spadework. Citation: Genetics 142: 1065-1068 1996 Type: REVIEW Genes: ncl-1 mnDp1 Abstract: I fell in love with Caenorhabditis elegans in the summer of '72. Our relationship was cemented four years later, 20 years ago now, by the publication of a paper in Genetics on C. elegans chromosome rearrangements (Herman et al. 1976). My pleasant assignment here is to describe the beginning of that work and to relate it to current worm cytogenetics and chromosome mechanics. ------------------- Key: 2418 Medline: 96184950 Authors: Plunkett JA;Simmons RB;Walthall WW Title: Dynamic interactions between nerve and muscle in Caenorhabditis elegans. Citation: Developmental Biology 175: 154-165 1996 Type: ARTICLE Genes: Abstract: Synaptogenesis among developing motoneurons and muscles was examined in the nematode Caenorhabditis elegans. In this animal embryonic precursor cells give rise to regionally localized, contiguous clones of muscle cells that form two dorsal and two ventral sets that run longitudinally along the body wall. Ablation of selected embryonic muscle precursors resulted in gaps in the posterior dorsal muscle quadrants. We compared the morphological development of GABAergic locomotory neurons in the presence and absence of their target muscle cells. The results led to four main conclusions: (1) target muscle cells are not required for the morphological differentiation of the motoneurons; (2) target muscle cells appear to be required for the formation of presynaptic varicosities by the motoneurons; (3) embryonic muscle cells serve as a guide for migrating postembryonic muscle cells and in the absence of these guides the postembryonic muscles often assume ectopic locations; and (4) in the presence of ectopic muscle cells, the GABAergic locomotory neurons sprouted and formed branches that contributed to ectopic neuromuscular junctions. ------------------- Key: 2419 Medline: 96180658 Authors: Roush W Title: Regulating G protein signaling. Citation: Science 271: 1056-1058 1996 Type: REVIEW Genes: egl-10 goa-1 Abstract: As anyone who has ever slept with a snorer, studied in a college dormitory, or lived next door to a pianist knows, tuning out one's surroundings can be a sanity-preserving skill. This ability isn't just limited to humans. Even the simplest cells can mute their own internal communication lines to tune out the racket of chemical noise made by hormones, neurotransmitters, growth factors, and other cell regulators, allowing them to damp down their responses to such stimuli after prolonged exposure. Exactly how cells achieve this "desensitization" is unclear, but in a spate of recent studies, researchers in several laboratories have closed in on one volume control for a key intracellular communication line: the "G proteins" that serve as intermediaries carrying signals from numerous hormones and neurotransmitters to the cell interior. Over the past year, the work has uncovered a large and growing family of proteins that seem to regulate the sensitivity of G protein signaling pathways in organisms ranging from yeast and nematodes to rats and even ------------------- Key: 2420 Medline: 96178462 Authors: Kenyon C Title: Ponce d'elegans: Genetic quest for the fountain of youth. Citation: Cell 84: 501-504 1996 Type: REVIEW Genes: age-1 daf-2 daf-16 daf-18 daf-23 Abstract: The process of aging influences our poetry, our art, our lifestyle, and our happiness, yet we know surprisingly little about it. Genetics has taught us a great deal about gene regulation, development, and the cell cycle. Can it teach us how we age? ------------------- Key: 2421 Medline: 96182650 Authors: Sengupta P;Chou JH;Bargmann CI Title: odr-10 encodes a seven transmembrane domain olfactory receptor required for responses to the odorant diacetyl. Citation: Cell 84: 899-909 1996 Type: ARTICLE Genes: odr-3 odr-7 odr-10 stDf1 syDf1 uDf1 Abstract: Olfactory signaling is initiated by interactions between odorants and olfactory receptors. We show that the C. elegans odr-10 gene is likely to encode a receptor for the odorant diacetyl. odr-10 mutants have a specific defect in chemotaxis to diacetyl, one of several odorants detected by the AWA olfactory neurons. odr-10 encodes a predicted seven transmembrane domain receptor; a green fluorescent protein-tagged Odr-10 protein is localized to the AWA sensory cilia. odr-10 expression is regulated by odr-7, a transcription factor implicated in AWA sensory specification. Expression of odr-10 from a heterologous promoter directs behavioral responses to diacetyl, but not to another odorant detected by the AWA neurons. These results provide functional evidence for a specific interaction between an olfactory receptor protein and its odorant ligand. ------------------- Key: 2422 Medline: 97083094 Authors: Miura M;Yuan JY Title: Mechanisms of programmed cell death in Caenorhabditis elegans and vertebrates. Citation: Current Topics in Developmental Biology 32: 139-174 1996 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ces-1 ces-2 egl-1 lin-22 lin-39 nuc-1 unc-86 Abstract: Programmed cell death is a common phenomenon during animal development. In the early stages of mouse development, soon after the blastomeres differentiate into inner cell mass (ICM) and trophoectoderm, dead cells are observed among the ICM and trophoblast cells. It was estimated that approximately 10% of blastocyst cells die in 95-h postcoitum mouse embryo. Programmed cell death plays a significant role in morphogenesis and histogenesis during animal development. Well-known examples include cell death in chick limb development and during metamorphosis of the tadpole tail. During neural development, as much as 50% of originally generated neurons die. In the immune system, cell death occurs constantly to eliminate cells that may react against self-antigens. Programmed cell death is involved in the generation of specific tissues and organs including kidney, lens epithelial cells, and cartilage cells. Thus, programmed cell death during animal development may be as important as cell proliferation, growth, and differentiation. Although the phenomenon of cell death during development was established in the 1950s, it attracted the attention of only a small group of embryologists. Little was known about the molecular mechanisms of programmed cell death. The important finding that programmed cell death was strictly determined in cell lineage during development of the nematode Caenorhabditis elegans brought up the idea that programmed cell death is genetically controlled as a specific cell differentiation fate. Intensive molecular genetic studies of programmed cell death in C. elegans have recently led to the identification of the central players of programmed cell death. Progress in the studies of molecular mechanisms of cell death strongly suggest that the genes controlling programmed cell death may be evolutionally conserved from worm to mammals. The objective of this chapter is to review genetic and molecular aspects of programmed cell death in C. elegans and vertebrates for insight into common mechanisms regulating this important biological event. ------------------- Key: 2423 Medline: 97088968 Authors: Duhon SA;Murakami S;Johnson TE Title: Direct isolation of longevity mutants in the nematode Caenorhabditis elegans. Citation: Developmental Genetics 18: 144-153 1996 Type: ARTICLE Genes: age-1 daf-7 fer-15 glp-4 spe-9 Abstract: We have isolated several new EMS-induced, long-lived mutants of Caenorhabditis elegans, using a novel screen that eliminates the need for replica plating. Three new alleles of age-1 (z10, z12, and z25) were identified by failure to complement age-1 (hx546) for life span extension; these alleles had life spans ranging from 18.9 to 25.9 days at 25 degrees C, with an average 46% increase in life span. After backcrossing, alleles were examined in a wild-type background for resistance to several environmental stresses: heat (35 degrees C), ultraviolet (UV) light (20 J/m(2)), and hydrogen peroxide (H2O2) (0.5 M) Two replicates of the test of thermotolerance were completed on each strain, giving mean survivals of 842 min (hx546), 810 min (z10), 862 min (z12), and 860 min (z25), compared to 562 min for wild type. All the age-1 alleles were significantly tolerant, compared with wild type (P < 0.001). Two replicates for UV resistance were also completed with mean survivals of 103, 118, 108, and 89 hr, respectively, compared to 72 hr for wild type. One test of hydrogen peroxide resistance has shown that z12 and N2 had a mean survival of 41 hr, while the other age-1 alleles had mean survival of 54 hr (z10), and 62 hr (z25); H2O2 resistance is the only environmental stress that ------------------- Key: 2424 Medline: 96176303 Authors: Creutz CE;Snyder SL;Daigle SN;Redick J Title: Identification, localization, and functional implications of an abundant nematode annexin. Citation: Journal of Cell Biology 132: 1079-1092 1996 Type: ARTICLE Genes: nex-1 nex-2 nex-3 Abstract: Cultures of the nematode C. elegans were examined for the presence of calcium-dependent, phospholipid-binding proteins of the annexin class. A single protein of apparent mass on SDS-polyacrylamide gels of 32 kD was isolated from soluble extracts of nematode cultures on the basis of its ability to bind to phospholipids in a calcium-dependent manner. After verification of the protein as an annexin by peptide sequencing, an antiserum to the protein was prepared and used to isolate a corresponding cDNA from an expression library in phage lambda gt11. The encoded protein, herein referred to as the nex-1 annexin, has a mass of 35 kD and is 36-42% identical in sequence to 10 known mammalian annexins. Several unique modifications were found in the portions of the sequence corresponding to calcium-binding sites. Possible phosphorylation sites in the NH2-terminal domain of the nematode annexin correspond to those of mammalian annexins. The gene for this annexin (nex-1) was physically mapped to chromosome III in the vicinity of the dpy-17 genetic marker. Two other annexin genes (nex-2 and nex-3) were also identified in chromosome III sequences reported by the nematode genomic sequencing project (Sulston, J., Z. Du, K. Thomas, R. Wilson, L. Hillier, R. Staden, N. Halloran, P. Green, J. Thierry-Mieg, L. Qiu, et al. 1992. Nature (Lond.). 356:37-41). The nex-1 annexin was localized in the nematode by immunofluorescence and by electron microscopy using immunogold labeling. The protein is associated with membrane systems of the secretory gland cells of the pharynx, with sites of cuticle formation in the grinder in the pharynx, with yolk granules in oocytes, with the uterine wall and vulva, and with membrane systems in the spermathecal valve. The presence of the annexin in association with the membranes of the spermathecal valve suggests a novel function of the protein in the folding and unfolding of these membranes as eggs pass through the valve. The localizations also indicate roles for the annexin corresponding to those proposed in mammalian systems in membrane trafficking, collagen deposition, and extracellular matrix formation. ------------------- Key: 2425 Medline: Authors: Hedgecock EM;Hall DH Title: Homologies in the neurogenesis of nematodes, arthropods and chordates. Citation: Seminars in the Neurosciences 2: 159-172 1990 Type: REVIEW Genes: cib-1 unc-5 unc-6 unc-40 Abstract: Animals with bilateral symmetry are organized along two body axes, anteroposterior and dorsoventral. Cells of similar type are generally arranged in rows along the anteroposterior axis while adjacent rows form distinct tissues. Many tissues are further specialized by region along the anteroposterior axis. Early in embryogenesis, tissue diversification is organized along an axis of radial symmetry, animal-vegetal, laid down during oogenesis. A symmetry-breaking event during oogenesis, or early embryogenesis, creates two secondary axes, dorsoventral and anteroposterior, that define the bilateral symmetry of the gastrula. The order and fates of the primary tissue divisions (germ line, endoderm, mesoderm, CNS ectoderm, PNS ectoderm, non-neurogenic ectoderm) along the animal-vegetal and dorsoventral axes are evolutionarily conserved. During gastrulation and neurulation, most tissues move into the interior, tucking the 2-dimensional fate map of the blastula into a solid larva. Molecular genetic studies have identified homologies in the developmental mechanisms operating along the animal-vegetal, dorsoventral and anteroposterior axes among diverse phyla. After gastrulation, the orthogonal patterning of the ectoderm is especially evident in neurogenesis. ------------------- Key: 2426 Medline: 96138394 Authors: Dewji NN;Singer SJ Title: Genetic clues to Alzheimer's disease. Citation: Science 271: 159-160 1996 Type: REVIEW Genes: lin-12 sel-12 Abstract: Patients with Alzheimer's disease (AD) exhibit progressive dementia and the gradual formation of extracellular neuritic plaques in the brain, particularly in the hippocampus and adjoining cortex. An important constituent of the neuritic plaques is B-amyloid, or AB, as set of oligopeptides of about 40 to 43 amino acids that are proteolytically derived from a much larger B-amyloid ------------------- Key: 2427 Medline: 96038267 Authors: Tanaka Y;Ohta A;Matsuo M;Sakamoto H Title: Developmental expression pattern of the Caenorhabditis elegans homologue of the Drosophila suppressor of forked gene. Citation: DNA Research 2: 143-146 1995 Type: ARTICLE Genes: Abstract: We cloned and sequenced the cDNA which encodes the Caenorhabditis elegans homologue (suf-1) of the Drosophila suppressor of forked (su(f)) gene product. The amino acid sequence deduced from the suf-1 cDNA shares extensive similarity with the su(f) and the human 77K subunit of the CstF, including the proline residues near the carboxy-terminus. Developmental Northern blot analysis showed that a 2.6-kb suf-1 transcript was expressed constitutively from L1 to young adult stages, suggesting it has a housekeeping function in vivo. Furthermore, this idea is consistent with the recent proposition that su(f) homologues play an essential role as a subunit of the cleavage stimulation factor (CstF) during polyadenylation of mRNA precursors. ------------------- Key: 2428 Medline: 96386245 Authors: Duffy JB;Perrimon N Title: Recent advances in understanding signal transduction pathways in worms and flies. Citation: Current Opinion in Cell Biology 8: 231-238 1996 Type: REVIEW Genes: let-23 let-60 lin-3 lin-7 lin-12 lin-15 lin-45 mek-2 mpk-1 sem-5 sur-1 Abstract: One major challenge in the fields of signal transduction and pattern formation is to understand how multiple signals are integrated to determine cell fates. Two developmental systems, vulval development in Caenorhabditis elegans and axis formation during Drosophila melanogaster oogenesis, require the epidermal growth factor receptor tyrosine kinase and the NOTCH signaling pathways to specify cell fates. Current work in both systems has provided new opportunities to investigate the potential for the cross-talk between these different signaling pathways. ------------------- Key: 2429 Medline: 96402053 Authors: Plasterk RHA Title: Postsequence genetics of Caenorhabditis elegans. Citation: Genome Research 6: 169-175 1996 Type: REVIEW Genes: Abstract: If world oil prices dropped to zero next year, how would it change the world economy? Investments in oil field exploration would lose their value overnight, whereas shares in a factory making environmentally friendly combustion engines might go up. Everybody would feel the need to plan ahead, and many plans would change. In genetics and molecular biology, DNA sequences are the fuel of research, and their prices are falling dramatically. Within 5 years many complete genomes will be sequenced, and sequence data will be like tap water in Amsterdam-essential for life, but too cheap to measure. A project that was perfectly rational 2 years ago will be a total waste of time tomorrow, and projects that seemed impossible will become feasible. The aim of this review is to explore the consequences for biology of the wealth of DNA sequence data now becoming available. Several bacterial genomes have been sequenced already (Fleischmann et al. 1995; Fraser et al. 1995). The first animal to feel these changes will be the nematode Caenorhabditis elegans, and "the worm" will be the focus of this review. The virtues of C. elegans as a model system in biology have recently been sung elsewhere (Hodgkin et al. 1995). In brief, it does everything that makes life interesting (eating, copulating, getting around, and relating to the environment) and manages to do so with only 959 cells, of which 302 form the brain. However, it is likely that much of what is said will apply equally to other species; thus, I hope that the review may also be of some interest outside of the C. elegans community. ------------------- Key: 2430 Medline: 97088967 Authors: Ebert RH;Shammas MA;Sohal BH;Sohal RS;Egilmez NK;Ruggles S;Reis RJS Title: Defining genes that govern longevity in Caenorhabditis elegans. Citation: Developmental Genetics 18: 131-143 1996 Type: ARTICLE Genes: age-1 daf-23 fer-15 sod-1 zyg-9 Abstract: We previously identified five regions on the chromosomal map of Caenorhabditis elegans, containing genes that help specify life span in this species, by comparing the genotypes of young and long-lived progeny from a cross between strains Bristol-N2 and Bergerac-BO [Ebert ef al. (1993): Genetics 135:1003-1010]. Analyses of additional crosses, and of putative polymorphisms for the implicated genes, are necessary to clarify the roles of naturally occurring polymorphic alleles in determining longevity. We therefore carried out a second multigenerational cross, between strains Bristol-N2 and DH424 (both nonmutators at 20 degrees C), to create a different heterogeneous recombinant-inbred population. We again found strong evidence implicating multiple genes, which differ between the parental strains, in the determination of life span. Increased variance of survival, for F-2 and homozygous F-25 worms relative to F-1 hybrids, is consistent with such alleles asserting randomly in the cross progeny. Moreover, chromosome mapping data corroborate the polygenic nature of this quantitative trait. Genotypes of young and very long-lived adult worms from a synchronous F-15 population were determined by polymerase chain reaction, to identify the parental strain of origin for each of 10 polymorphic loci. Two regions, on chromosomes II and IV, each contain at least one gene with allelic differences in associated longevity. A recombinant-inbred Bergerac-BO x Bristol-N2 population, derived from the earlier cross between those strains, was exposed to an acute toxic level of hydrogen peroxide. Genotyping of H2O2-resistant worms implicated at least one of the five chromosomal regions previously identified in the same cross progeny as harboring a longevity-determining gene. Superoxide dismutase and catalase levels, determined for the three parental strains as they aged, confirm the existence of polymorphisms in the corresponding genes (or their regulatory mechanisms) inferred from the chromosome-it mapping data, and are consistent with the hypothesis that increased longevity is conferred by high levels of these enzymes late in life. ------------------- Key: 2431 Medline: Authors: Barstead RJ Title: Molecular biology of Caenorhabditis elegans. Citation: "Encyclopedia of Molecular Biology and Molecular Medicine. Achilles' Cleavage to Cytoskeleton-Plasma Membrane Interactions." Meyers, R.A. (ed). VCH Publishers, Inc., New York, NY. 1: 227-237 1996 Type: REVIEW Genes: egl-44 egl-46 fem-1 fem-2 fem-3 gld-1 her-1 lin-4 lin-14 lin-32 mec-3 rol-6 sem-4 tra-1 tra-2 tra-3 unc-52 unc-86 Abstract: Each year hundreds of students and practicing scientists join in the study of the soil nematode Caenorhabditis elegans. Their reasons for doing so are varied, but at the core these individuals are uniformly impressed by the cohesiveness and generosity of the C. elegans research community, the focused effort to understand every aspect of C. elegans biology, the power and flexibility of the... ------------------- Key: 2432 Medline: Authors: Hengartner M Title: Molecular mechanisms of cell death and aging. Citation: "Encyclopedia of Molecular Biology and Molecular Medicine. Achilles' Cleavage to Cytoskeleton-Plasma Membrane Interactions." Meyers, R.A. (ed). VCH Publishers, Inc., New York, NY. 1: 299-303 1996 Type: REVIEW Genes: Abstract: Naturally occurring or programmed cell deaths, which play important roles in animal development and homeostasis, are observed in a wide variety of tissues in both vertebrates and invertebrates. Such deaths remove cells that might be harmful, are not needed, or have served their purpose. In many tissues, cell death and cell proliferation are precisely balanced, to maintain the proper number of types of cells. Disruption of this balance can result in disease. Both cell death and aging appear to be under genetic control. Identification of the genes involved in these processes promises to greatly enhance our understanding of these phenomena. ------------------- Key: 2433 Medline: 97090525 Authors: Candido EPM;Jones D Title: Transgenic Caenorhabditis elegans strains as biosensors. Citation: Trends in Biotechnology 14: 125-129 1996 Type: ARTICLE Genes: Abstract: Toxicity bioassays rely largely on lethality measurements. Such assays are generally lengthy and expensive, and provide little information on mechanisms of toxicity. A desire to understand the mechanisms by which cells respond to physical and chemical stresses has led to interest in measuring stress proteins as toxicological endpoints. Transgenic strains of the nematode Caenorhabditis elegans that carry a reporter enzyme under control of a stress-inducible promoter have been created. The reporter is easily quantified in intact nematodes, and it responds to a wide range of chemical stressors. Therefore, transgenic C. elegans can provide the basis for a wide range of quick, simple and informative bioassays. ------------------- Key: 2434 Medline: 96205054 Authors: Hird SN;Paulsen JE;Strome S Title: Segregation of germ granules in living Caenorhabditis elegans embryos: cell-type-specific mechanisms for cytoplasmic localization. Citation: Development 122: 1303-1312 1996 Type: ARTICLE Genes: mes-1 pgl-1 Abstract: Germ granules are ribonucleoprotein particles that are thought to function in germline specification in invertebrates and possibly in vertebrates. In Caenorhabditis elegans, these structures, termed P granules, are partitioned to the germline P cells during the early embryonic divisions, By injecting a fluorescently labelled anti-P-granule antibody into the C. elegans germline syncitium, we followed P-granule segregation in live embryos using laser-scanning confocal microscopy. We show that, in early P cells (P-0 and P-1), P-granule partitioning is achieved primarily by their migration through the cytoplasm towards the site of formation of the germline daughter cell. A different mechanism appears to operate in later P cells (P-2 and P-3): P granules associate with the nucleus and move with it toward the site of formation of the germline daughter cell, where they are then deposited, At each division, there is also disassembly or degradation of those P granules that remain in the cytoplasm destined for the somatic daughter cell, Microfilaments, microtubules and the product of the gene mes-1 are required for the normal pattern of P-granule ------------------- Key: 2435 Medline: 96215431 Authors: Kim J;Kim Y-C;Lee JH;Jang YJ;Chung IK;Koo H-S Title: cDNA cloning, expression, and chromosomal localization of Caenorhabditis elegans DNA topoisomerase I. Citation: European Journal of Biochemistry 237: 367-372 1996 Type: ARTICLE Genes: Abstract: By screening Caenorhabditis elegans cDNA libraries, overlapping cDNA clones encoding DNA topoisomerase I were obtained. An open reading frame of 751 amino acids was found in the 3.2-kb cDNA sequence. The open reading frame has 54% and 50% identities to the amino acid sequences of human and Drosophila melanogaster DNA topoisomerases I, respectively. Northern blot analysis showed the presence of an mRNA of 3.4 kb which suggests that the cDNA sequence is close to full length. The 72-kDa C-terminal polypeptide expressed in Escherichia coli cells showed catalytic DNA topoisomerase I activity. The DNA topoisomerase I gene was mapped to position Is of chromosome I by screening polytene YAC plasmid DNAs. ------------------- Key: 2436 Medline: 96200771 Authors: Simske JS;Kaech SM;Harp SA;Kim SK Title: LET-23 receptor localization by the cell junction protein LIN-7 during C. elegans vulval induction. Citation: Cell 85: 195-204 1996 Type: ARTICLE Genes: let-23 lin-2 lin-7 lin-10 lin-45 Abstract: In C. elegans, the anchor cell signal induces Pn.p cells to form the vulva by activating a conserved receptor tyrosine kinase pathway. lin-2 and lin-7 mutants exhibit a vulvaless phenotype similar to the phenotype observed when this signaling pathway is defective. We have found that LIN-7 is a cell junction-associated protein that binds to the LET-23 receptor tyrosine kinase. LET-23 is also localized to the cell junctions, and both LIN-2 and LIN-7 are required for this localization. LET-23 overexpression rescues the lin-2 or lin-7 vulvaless phenotype, suggesting that increased receptor density can compensate for mislocalization. These results suggest that proper localization of LET-23 receptor to the Pn.p cell junctions is required for signaling activity. ------------------- Key: 2437 Medline: Authors: Lints R;Driscoll M Title: Programmed and pathological cell death in Caenorhabditis elegans. Citation: "Cellular Aging and Cell Death." Holbrook NJ, Martin GR and Rockshin RA (eds), Wiley-Liss, New York. : 235-253 1996 Type: REVIEW Genes: age-1 ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ces-1 ces-2 daf-2 daf-16 egl-1 deg-1 lin-24 lin-26 lin-33 mec-4 mec-6 mec-10 nuc-1 spe-26 unc-105 Abstract: In recent years it has come to be appreciated that cells do not die only as a consequence of injury or disease-they can also be genetically directed to undergo death during the normal course of development and homeostasis. Disease states can result if cell death is inappropriately timed, as observed in degenerative disorders, or if cells do not die when they should, as in the case of various malignancies and cancers. Without question, an understanding of the mechanisms of cell death is of key significance to human health. Studies of cell death in both invertebrate and vertebrate systems have revealed that the genetic instructions for the regulation and execution of normal programmed cell death, also referred to as apoptotic death, have been remarkably conserved. Analyses in the simple nematode Caenorhabditis elegans have provided significant insight into the mechanism of programmed cell death. Less is clear about the mechanisms of inappropriate or pathological cell death, but a detailed molecular model of one inherited neurodegenerative condition identified in the nematode is being elaborated that may provide a means of identifying the genetic requirements for pathological cell death. Here we review molecular and genetic characterization of programmed and pathological cell death in C. elegans and consider how similar mechanisms of cell death may influence health and aging of higher organisms. ------------------- Key: 2438 Medline: Authors: Henriksen O Title: The little worm that could. Citation: NCRR Reporter 20: 4-7 1996 Type: REVIEW Genes: Abstract: They don't know how it tastes, but that's one of the few things scientists don't know about the worm. It is 1 millimeter long and contains a mere 959 somatic cells. But, despite the small numbers, Caenorhabditis elegans is unearthing invaluable information about fundamental questions in human biology. Researchers in about 300 laboratories around the world study the worm's genetic makeup and relate gene structure to cellular and bodily functions. And NCRR aids these efforts by supporting three C. elegans resource centers in the United States, Canada and the Netherlands. ------------------- Key: 2439 Medline: 96227720 Authors: Cherniak C Title: Neural component placement. Citation: Trends in Neurosciences 18: 522-527 1995 Type: ARTICLE Genes: Abstract: A range of neuroanatomical results supports the idea that 'save wire' is an organizing principle of brain structure: that the theory of combinatorial optimization of networks applies to the anatomy of the nervous system. In particular, optimization of the placement of components operates at several hierarchical levels in the nervous system, from gross to microscopic anatomy, and from invertebrates to primates. That is, when anatomical positioning of interconnected neural components is treated like a problem of wire minimization in microchip layout, a hypothesis of 'best of all possible brains' is consistent with the observed siting of brains, ganglia, and even somata of individual neurons that minimizes the length of interconnections. In the case of the positioning of ganglia of Caenorhabditis elegans, optimization predictions of one-in-a-million precision can be verified. ------------------- Key: 2440 Medline: 97104909 Authors: Hecht RM;Norman MA;Vu T;Jones W Title: A novel set of uncoordinated mutants in Caenorhabditis elegans uncovered by cold-sensitive mutations. Citation: Genome 39: 459-464 1996 Type: ARTICLE Genes: unc-1 unc-7 unc-9 unc-124 unc-125 unc-126 unc-127 nDf20 Abstract: A set of uncoordinated (Unc) cold-sensitive (cs) mutants was isolated at a stringent condition of 11 degrees C. About half of the 13 independently isolated cs-Unc mutants were alleles of three X-linked Unc mutants that exhibited the ''kinker'' phenotype. The remaining four isolates identified new mutants that exhibited ''kinker,'' ''coiler,'' or severe paralytic phenotypes. The temperature-sensitive period (TSP) for each gene was determined. As a homozygous or heterozygous dominant, unc-125 exhibited a TSP throughout all stages of development. Its severe paralysis was immediately observed upon a shift down to 11 degrees C and reversed upon a shift up to 23 degrees C. The reversible thermolability of the unc-125 gene product indicated that it may function in a multicomponent process involved in neuro-excitation. ------------------- Key: 2441 Medline: 96196478 Authors: Ballivet M;Alloid C;Bertrand S;Bertrand D Title: Nicotinic acetylcholine receptors in the nematode Caenorhabditis elegans. Citation: Journal of Molecular Biology 258: 261-269 1996 Type: ARTICLE Genes: Abstract: Two cDNAs (Ce21 and Ce13) were isolated from a Caenorhabditis elegans library screened with a probe encoding conserved domains of the avian alpha 5 neuronal nicotinic acetylcholine receptor (nAChR). Alignments to all nAChR subunits in the EMBL/Swissprot data base demonstrate that the Ce21 protein most resembles the vertebrate alpha 7 subunit, whereas Ce13 is closest to the ARD subunit of Drosophila. The corresponding genes were isolated and hybridized to YAC grids: Ce21 maps on chromosome V near the his-23 gene, and Ce13 on chromosome I very near or at unc-29. The structure of the Ce21 gene was compared with that of other vertebrate and invertebrate nAChR genes and found to share by far the largest number of conserved splice sites with the vertebrate alpha 7 gene. Upon expression in the Xenopus oocyte system, the Ce21 subunit assembled into a functional homomeric nAChR, whose properties were compared with those of the chicken alpha 7 receptor. The anthelmintic nicotinic agonist levamisole is unable to activate the Ce21 and alpha 7 receptors, but efficiently antagonises their responses to ACh. Both receptors desensitise quickly upon agonist application, are more sensitive to nicotine than to acetylcholine, and are efficiently blocked by dihydro-beta-erythroidine. Unlike the alpha 7 receptor, however, the Ce21 receptor is relatively insensitive to methyllycaconitine and to alpha-bungarotoxin. The similarities in protein sequence, gene structure and physiological properties between alpha 7 and Ce21 suggest a very ancient lineage for the alpha 7 class of nAChR subunits. ------------------- Key: 2442 Medline: Authors: Felix MA;Sternberg PW;De Ley P Title: Sinistral nematode population. Citation: Nature 381: 122- 1996 Type: REVIEW Genes: Abstract: Several animal taxa display a consistent left-right asymmetry of the body plan. In nematodes, dextrality predominates. However, we have now found a nematode species that has sinistral populations. ------------------- Key: 2443 Medline: 96212989 Authors: Winter CE;Penha C;Blumenthal T Title: Comparison of a vitellogenin gene between two distantly related Rhabditid nematode species. Citation: Molecular Biology and Evolution 13: 674-684 1996 Type: ARTICLE Genes: vit-2 vit-5 vit-6 Abstract: Three vitellogenin genes from the free-living nematode Caenorhabditis elegans have previously been characterized at the molecular level. In order to study evolutionary relationships within this poorly understood taxon, we have cloned a vitellogenin gene, CEW1-vit-6 from a distantly related species belonging to the same family as C. elegans. Screening of a genomic library with a probe to total poly(A+) RNA yielded three clones that hybridized more intensely than all others, and all three corresponded to a single gene homologous to C. elegans vit-6. Comparison of CEW1-vit-6 with Ce-vit-6 reveals both strong similarities and surprising differences. Like Ce-vit-6 the gene is about 5 kb long and contains four unusually small introns (38-41 nt), but only one interrupts the gene at the same location as a Ce-vit-6 intron. The promoter region contains five matches to Vitellogenin Promoter Element 1 (VPE1) and no matches to VPE2, both previously shown to be required for vir gene transcription in C. elegans. Codon usage is in general similar to that of the Ce-vir genes, but a few codon biases are quite different. Alignment of the CEW1-vit-6 protein with the Ce-vit-6 and Ce-vit-2 products suggests the existence of two domains which have evolved at different rates. Sequence comparison shows that nematode vitellogenins are much more closely related to vertebrate than to insect vitellogenins. ------------------- Key: 2444 Medline: 96205306 Authors: Lee M;Cheung HT Title: Isolation and characterization of Caenorhabditis elegans extracellular matrix. Citation: Biochemical and Biophysical Research Communications 221: 503-509 1996 Type: ARTICLE Genes: Abstract: The extracellular matrix (ECM) plays an important structural and functional role in multicellular organisms. Because of the similarities between C. elegans and vertebrate development, this nematode could serve as a simplified model to study the biology of the ECM. In this study, a method for extracting mammalian ECM was adapted for the extraction of C. elegans ECM. ECM components from C. elegans were found to be homologous to mammalian ECM by immunoblotting. It was also demonstrated that antibodies generated against C. elegans ECM stained basement membrane-like structures in C. elegans eggs, larvae, and ------------------- Key: 2445 Medline: 96209957 Authors: Waldmann R;Champigny G;Voilley N;Lauritzen I;Lazdunski M Title: The mammalian degenerin MDEG, an amiloride-sensitive cation channel activated by mutations causing neurodegeneration in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 271: 10433-10436 1996 Type: ARTICLE Genes: deg-1 mec-4 mec-10 Abstract: Mutations of the degenerins (deg-1, mec-4, mec-10) are the major known causes of hereditary neurodegeneration in the nematode Caenorhabditis elegans, We cloned a neuronal degenerin (MDEG) from human and rat brain, MDEG is an amiloride sensitive cation channel permeable for Na+, K+, and Li+. This channel is activated by the same mutations which cause neurodegeneration in C. elegans, Like the hyperactive C. elegans degenerin mutants, constitutively active mutants of MDEG cause cell death, suggesting that gain of function of this novel neuronal ion channel might be involved in human forms of neurodegeneration. ------------------- Key: 2446 Medline: 96304589 Authors: Minniti AN;Sadler C;Ward S Title: Genetic and molecular analysis of spe-27, a gene required for spermiogenesis in Caenorhabditis elegans Citation: Genetics 143: 213-223 1996 Type: ARTICLE Genes: fem-1 fem-3 fer-1 spe-27 eDf18 eDf19 mDf4 mDf9 Abstract: Hermaphrodites with mutations in the spe-27 gene are self-sterile, laying only unfertilized eggs; mutant males are fertile. Hermaphrodites make spermatids that fail to activate to crawling spermatozoa so passing oocytes sweep them out of the spermatheca. These spermatids do activate and produce self-progeny if young mutant hermaphrodites are mated by fertile (or sterile) males. Spermatids isolated from either mutant males or hermaphrodites initiate activation in vitro when treated with proteases, but then arrest with spiky membrane projections that resemble those of a normal intermediate in pseudopod formation. These phenotypes are identical to spe-8 and spe-12 mutants. They can be explained if males and hermaphrodites have distinct pathways for spermatid activation, and these three genes are necessary only for the hermaphrodite pathway. Consistent with this model, when spe-27 mutant male spermatids without seminal fluid are artificially inseminated into hermaphrodites, they fail to activate. The Spe-27 gene has been isolated, sequenced and its regulatory regions identified. The sequence predicts a 131 amino acid polypeptide that has no striking structural motifs and no resemblance to known proteins. Two of the mutations in spe-27 alter mRNA splicing; a third mutation is a temperature-sensitive missense mutation. ------------------- Key: 2447 Medline: 96304590 Authors: Run JQ;Steven R;Hung MS;Vanweeghel R;Culotti JG;Way JC Title: Suppressors of the unc-73 gene of Caenorhabditis elegans. Citation: Genetics 143: 225-236 1996 Type: ARTICLE Genes: bli-1 mec-3 sup-7 sup-39 smg-3 smg-4 smg-6 unc-73 mnDf30 mnDf105 Abstract: The unc-73 gene of Caenorhabditis elegans is necessary for proper axon guidance. Animals mutant in this gene are severely uncoordinated and also exhibit defects in cell migration and cell lineages. We have isolated coordinated revertants of unc-73(e936). These fall into three classes: intragenic revertants, extragenic dominant suppressors (sup-39), and a single apparently intragenic mutation that is a dominant suppressor with a linked recessive lethal phenotype. sup-39 mutations cause early embryonic lethality, but escapers have a wild-type movement phenotype as larvae and adults. Gonads of sub-39 mutant animals show a novel defect: normal gonads have a single row of oocytes, but sup-39 gonads often have true rows of oocytes. This result suggests that the mutant gonad is defective in choosing on its surface only a single site from which nuclei will emerge to form oocytes. These results are interpreted in terms of an effect of unc-73 on ------------------- Key: 2448 Medline: 96304591 Authors: Grant B;Greenwald I Title: The Caenorhabditis elegans sel-1 gene, a negative regulator of lin-12 and glp-1, encodes a predicted extracellular protein. Citation: Genetics 143: 237-247 1996 Type: ARTICLE Genes: daf-4 egl-15 glp-1 let-23 lin-3 lin-12 lin-17 sel-1 sqt-3 tra-2 arDf1 Abstract: The Caenorhabditis elegans lin-12 and glp-1 genes encode members of the LIN-12/NOTCH family of receptors. The sel-1 gene was identified as an extragenic suppressor of a lin-12 hypomorphic mutant. We show in this report that the sel-1 null phenotype is wild type, except for an apparent elevation in lin-12 and glp-1 activity in sensitized genetic backgrounds, and that this genetic interaction seems to be lin-12 and glp-1 specific. We also find that sel-1 encodes a predicted extracellular protein, with a domain sharing sequence similarity to predicted proteins from humans and yeast. SEL-1 may interact with the LIN-12 and GLP-1 receptors and/or their respective ligands to down-regulate signaling. ------------------- Key: 2449 Medline: 96323643 Authors: Arata Y;Akimoto Y;Hirabayashi J;Kasai K-I;Hirano H Title: An immunohistochemical study of the 32-kDa galectin (Beta-galactoside-binding lectin) in the nematode Caenorhabditis elegans. Citation: Histochemical Journal 28: 201-207 1996 Type: ARTICLE Genes: Abstract: The localization of the 32-kDa galectin (beta-galactoside-binding lectin) of the nematode Caenorhabditis elegans, which is the first lectin to be found in a nematode, was examined immunohistochemically using an anti-lectin antiserum. The lectin was found to be localized most abundantly in the adult cuticle and also in the terminal bulb of the pharynx. However, it was difficult to locate the galectin in larval animals, though immunochemical experiments suggested its presence. These results suggest that one of the fundamental roles of the galectin may be as a component of the durable outer barrier, as in the case of the morphogenesis of chick ------------------- Key: 2450 Medline: 96337506 Authors: Bossinger O;Schierenberg E Title: The use of fluorescent marker dyes for studying intercellular communication in nematode embryos. Citation: International Journal of Developmental Biology 40: 431-439 1996 Type: ARTICLE Genes: Abstract: As more and more cases of necessary cell-cell interactions are revealed, the classical view of mosaic development in nematodes has to be replaced by a more dynamic picture showing different types of intercellular communication. To investigate the pattern and function of communication pathways between cells, we have developed different techniques to shunt fluorescent marker dyes into embryos and hatched animals and study their distribution in vivo. During embryogenesis we find that for a long time all somatic cells form a single dye-coupling compartment while transfer into the germline is restricted already at an early stage. Considerable variations between species with respect to the size of communication channels and the time during which these are functional are observed and can be correlated to differences in the developmental program. A different kind of intercellular communication can be visualized with the help of fluorescent dyes: a transfer of yolk proteins in two phases of the life cycle, in the adult hermaphrodite from the gut into the maturing germ cells, and in the embryo from non-gut cells into the gut primordium. Cell-cell interactions in the nematode embryo can be inhibited with polysulfated hydrocarbon dyes (e.g. Trypan Blue) which bind strongly to the plasma membrane. In summary our data indicate that fluorescent marker dyes can be helpful tools to identify and understand the role of intercellular communication and transfer processes in nematode development. ------------------- Key: 2451 Medline: 96202467 Authors: Goldstein B;Hird SN Title: Specification of the anteroposterior axis in Caenorhabditis elegans. Citation: Development 122: 1467-1474 1996 Type: ARTICLE Genes: fem-1 fer-1 Abstract: Anteroposterior asymmetries are apparent in C, elegans development before the first cell division, Here we identify the cue that specifies the anteroposterior axis, and investigate how this cue is interpreted to generate initial asymmetry. In C. elegans, the sperm normally enters the egg in an invariant position. We have found that causing fertilisation to occur in the abnormal end of the egg completely reverses the orientation of the anteroposterior axis, but gives otherwise normal development, This result suggests that a component of the sperm normally specifies the anteroposterior axis, We have found that a cytoplasmic rearrangement in the uncleaved zygote is directed by the sperm, suggesting a mechanism by which the sperm may specify the axis. The results additionally reveal that the C. elegans oocyte is constructed with no axis prespecified in the form of asymmetrically localised cytoplasmic determinants. ------------------- Key: 2452 Medline: 96202459 Authors: Christensen S;Kodoyianni V;Bosenberg M;Friedman L;Kimble J Title: lag-1, a gene required for lin-12 and glp-1 signaling in Caenorhabditis elegans, is homologous to human CBF1 and Drosophila Su(H). Citation: Development 122: 1373-1383 1996 Type: ARTICLE Genes: glp-1 lag-1 lag-2 lin-12 smg-1 Abstract: The homologous receptors LIN-12 and GLP-1 mediate diverse cell-signaling events during development of the nematode Caenorhabditis elegans. These two receptors appear to be functionally interchangeable and have sequence similarity to Drosophila Notch, Here we focus on a molecular analysis of the lag-1 gene (lin-12 and glp-1), which plays a central role in LIN-12- and GLP-1-mediated signal transduction, We find that the predicted LAG-1 protein is homologous to two DNA-binding proteins: human C Promoter Binding Factor (CBF1) and Drosophila Suppressor of Hairless (Su(H)). Furthermore, we show that LAG-1 binds specifically to the DNA sequence RTGGGAA, previously identified as a CBF-1/Su(H)-binding site, Finally, we report that the 5' flanking regions and first introns of the lin-12, glp-1 and lag-1 genes are enriched for potential LAG-1-binding sites, We propose that LAG-1 is a transcriptional regulator that serves as a primary link between the LIN-12 and GLP-1 receptors and downstream target genes in C. elegans. In addition, we propose that LAG-1 may be a key component of a positive feedback loop that amplifies activity of the LIN-12/GLP-1 pathway. ------------------- Key: 2453 Medline: 96202484 Authors: Salser SJ;Kenyon C Title: A C. elegans Hox gene switches on, off, on and off again to regulate proliferation, differentiation and morphogenesis. Citation: Development 122: 1651-1661 1996 Type: ARTICLE Genes: egl-5 lin-22 lin-39 mab-5 pal-1 Abstract: Hox genes establish body pattern throughout the animal kingdom, but the role these genes play at the cellular level to modify and shape parts of the body remains a mystery, We find that the C. elegans Antennapedia homolog, mab-5, sequentially programs many independent events within individual cell lineages, In one body region, mab-5 first switches ON in a lineage to stimulate proliferation, then OFF to specify epidermal structures, then ON in just one branch of the lineage to promote neuroblast formation, finally OFF to permit proper sense organ morphology, In a neighboring lineage, continuous mab-5 expression leads to a different pattern of development, Thus, this Hox gene achieves much of its power to diversify the anteroposterior axis through fine spatiotemporal differences in expression coupled with a changing pattern of cellular response. ------------------- Key: 2454 Medline: 96206041 Authors: Xue D;Shaham S;Horvitz HR Title: The Caenorhabditis elegans cell-death protein CED-3 is a cysteine protease with substrate specificities similar to those of the human CPP32 protease. Citation: Genes & Development 10: 1073-1083 1996 Type: ARTICLE Genes: ced-3 Abstract: The Caenorhabditis elegons cell-death gene ced-3 encodes a protein similar to mammalian interleukin-1 beta-converting enzyme (ICE), a cysteine protease implicated in mammalian apoptosis. We show that the full-length CED-3 protein undergoes proteolytic activation to generate a CED-3 cysteine protease and that CED-3 protease activity is required for killing cells by programmed cell death in C. elegans. We developed an easy and general method for the purification of CED-3/ICE-like proteases and used this method to facilitate a comparison of the substrate specificities of four different purified cysteine proteases. We found that in its substrate preferences CED-3 was more similar to the mammalian CPP32 protease than to mammalian ICE or NEDD2/ICH-1 protease. Our results suggest that different mammalian CED-3/ICE-like proteases may have distinct roles in mammalian apoptosis and that CPP32 is a candidate for being a mammalian functional equivalent of CED-3. ------------------- Key: 2455 Medline: 96208609 Authors: Pennisi E Title: Worm genes imply a master clock. Citation: Science 272: 949-950 1996 Type: REVIEW Genes: clk-1 clk-2 clk-3 daf-2 daf-16 Abstract: What's the secret to long life? For the nematode Caenorhabditis elegans, it's slow, easy living, in which all life's events occur in a leisurely rhythm, according to work described on page 1010 of this issue. The new research, by Siegfried Hekimi and Bernard Lakowski of McGill University in Montreal, identifies four genes that, when mutated, can make these worms use energy more efficiently, feed and swim at a slower pace-and live many times their normal life-span. Some of the experimental nematodes lived for almost 2 months, far longer than their ------------------- Key: 2456 Medline: 96208618 Authors: Lakowski B;Hekimi S Title: Determination of life-span in Caenorhabditis elegans by four clock genes. Citation: Science 272: 1010-1013 1996 Type: ARTICLE Genes: clk-1 clk-2 clk-3 daf-2 daf-16 gro-1 Abstract: The nematode worm Caenorhabditis elegans is a model system for the study of the genetic basis of aging. Maternal-effect mutations in four genes-clk-1, clk-2, clk-3, and gro-1-interact genetically to determine both the duration of development and life-span. Analysis of the phenotypes of these mutants suggests the existence of a general physiological clock in the worm. Mutations in certain genes involved in dauer formation (an alternative larval stage induced by adverse conditions in which development is arrested) can also extend life-span, but the life extension of Clock mutants appears to be independent of these genes. The daf-2(e1370) clk-1(e2519) worms, which carry life-span-extending mutations from two different pathways, live nearly five times as long as wild-type ------------------- Key: 2457 Medline: Authors: Grady D Title: A worm's life: Right mutation makes it long but very dull. Citation: New York Times, May 21 : B5-B8 1996 Type: REVIEW Genes: Abstract: Mutant worms that live five times as long as their normal counterparts are yielding clues to the genetic control of life span-and lending new credence to the old idea that one way to live longer might be to live less. ------------------- Key: 2458 Medline: 96202479 Authors: Lundquist EA;Herman RK;Rogalski TM;Mullen GP;Moerman DG;Shaw JE Title: The mec-8 gene of C. elegans encodes a protein with two RNA recognition motifs and regulates alternative splicing of unc-52 transcripts. Citation: Development 122: 1601-1610 1996 Type: ARTICLE Genes: mec-8 unc-52 Abstract: Mutations in the mec-8 gene of Caenorhabditis elegans were previously shown to affect the functions of body wall muscle and mechanosensory and chemosensory neurons, Mutations in mec-8 also strongly enhance the mutant phenotype of specific mutations in unc-52, a gene that encodes, via alternative splicing of pre-mRNA, a set of basement membrane proteins, homologs of perlecan, that are important for body wall muscle assembly and attachment to basement membrane, hypodermis and cuticle, We have cloned mec-8 and found that it encodes a protein with two RNA recognition motifs, characteristic of RNA binding proteins, We have used reverse transcription-PCR and RNase protection experiments to show that mec-8 regulates the accumulation of a specific subset of alternatively spliced unc-52 transcripts, We have also shown with antibodies to UNC-52 that mec-8 affects the abundance of a subset of UNC-52 isoforms. We propose that mec-8 encodes a trans-acting factor that regulates the alternative splicing of the pre-mRNA of unc-52 and one or more additional genes that affect mechanosensory and chemosensory neuron function. ------------------- Key: 2459 Medline: 96224223 Authors: Machaca K;DeFelice LJ;L'Hernault SW Title: A novel chloride channel localizes to Caenorhabditis elegans spermatids and chloride channel blockers induce spermatid differentiation. Citation: Developmental Biology 176: 1-16 1996 Type: ARTICLE Genes: fer-15 him-5 spe-8 spe-12 spe-27 spe-29 Abstract: Caenorhabditis elegans spermatogenesis is especially suited for studies of nonrandom cytoplasmic segregation during cellular differentiation. Spermatocytes separate from an anuclear cytoplasmic core and undergo two sequential divisions. During the second division, intracellular organelles segregate specifically to spermatids as they bud from an anuclear residual body. We have applied patch-clamp techniques in order to investigate membrane protein distribution during these asymmetric divisions. We show that membrane components, as assayed by voltage-dependent ion channel activity, follow a specific distribution pattern during sperm development. Several voltage-sensitive ion channel activities are observed in spermatocytes and residual bodies, but only a single-channel type can be detected in spermatids, indicating that other channel activities are excluded from or inactivated within these cells as they form. The channel that is observed in spermatids is an inward-rectifying chloride channel (Clir), as indicated by its sensitivity to chloride channel inhibitors and Cl-dependent shifts in its conductance. Treatment of spermatids with Cl channel blockers induce their differentiation into spermatozoa, suggesting that Clir plays a role during this developmental step. These studies are the first application of patch-clamp electrophysiology to C. elegans development. ------------------- Key: 2460 Medline: 96224224 Authors: Bossinger O;Schierenberg E Title: Early embryonic induction in C. elegans can be inhibited with polysulfated hydrocarbon dyes. Citation: Developmental Biology 176: 17-21 1996 Type: ARTICLE Genes: Abstract: During embryogenesis of Caenorhabditis elegans cellular interactions are necessary to determine the fate of blastomeres. In one of these interactions, taking place in the 4-cell stage, the germline cell P2 induces longitudinal orientation of the cleavage spindle in the neighboring EMS cell, its asymmetric division, and the establishment of a gut lineage. Application of several polysulfated hydrocarbon dyes (e.g., trypan blue, TB) in the 1- to 4-cell stages inhibits induction of the gut precursor cell. However, dye application from the late 4-cell stage onward does not interfere with gut induction, supporting the earlier finding of a short time window for this interaction. We also tested the effect of TB on the induction of pharyngeal muscle cells by the MS blastomere, which appears to involve a surface receptor-ligand interaction. We found that this process is inhibited as well. These and additional data indicate that polysulfated hydrocarbon dyes are suitable tools to generally interfere with cell-cell interactions in the nematode embryo. ------------------- Key: 2461 Medline: 96220667 Authors: Wadsworth WG;Hedgecock EM Title: Hierarchical guidance cues in the developing nervous system of C. elegans. Citation: BioEssays 18: 355-362 1996 Type: REVIEW Genes: unc-5 unc-6 unc-40 Abstract: During embryogenesis, the basic axon scaffold of the nervous system is formed by special axons that pioneer pathways between groups of cells. To find their way, the pioneer growth cones detect specific cues in their extracellular environment. One of these guidance cues is netrin. Observations and experimental manipulations in vertebrates and nematodes have shown that netrin is a bifunctional guidance cue that can simultaneously attract and repel axons. During the formation of this basic axon scaffold in Caenorhabditis elegans, the netrin UNC-6 is expressed by neuroglia and pioneer neurons, providing hierarchical guidance cues throughout the animal. Each cue has a characteristic role depending on the cell type, its position and the developmental stage. These roles include activities as global, decussation and labeled-pathway cues. This hierarchical model of UNC-6 netrin-mediated guidance suggests a method by which guidance cues can direct formation of basic axon scaffolds in developing nervous systems. ------------------- Key: 2462 Medline: 96206045 Authors: Ahringer J Title: Posterior patterning by the Caenorhabditis elegans even-skipped homolog vab-7. Citation: Genes & Development 10: 1120-1130 1996 Type: ARTICLE Genes: egl-5 mab-5 vab-7 tDf2 Abstract: Patterning of the posterior end in animals is not well understood. Homologs of Drosophila even-skipped (eve) have a similar posterior expression pattern in many animals, and in vertebrates they are linked physically to the ''posterior'' ends of homeotic clusters (HOM-C), suggesting a conserved role in posterior development. However, the function of this posterior expression is not known. Here I show that the Caenorhabditis elegans gene vab-7 encodes an eve homolog that is required for posterior development and expressed in a pattern strikingly similar to that of vertebrate eve genes. Using a four-dimensional recording system, I found that posterior body muscles and the posterior epidermis are patterned abnormally in vab-7 mutants, but commitment to muscle and epidermal fates is normal. furthermore, vab-7 activity is required for the complete expression of the most posterior HOM-C gene egl-5 in muscle cells, supporting the idea that eve homologs may act with the HOM-C to determine posterior cell fates. The conservation of sequence and expression pattern between vab-7 and eve homologs in other animals argues that most eve genes have posterior mesodermal and ectodermal ------------------- Key: 2463 Medline: 96211460 Authors: Zhang HB;Blumenthal T Title: Functional anaylsis of an intron 3' splice site in Caenorhabditis elegans. Citation: RNA 2: 380-388 1996 Type: ARTICLE Genes: act-4 smg-1 smg-2 smg-3 smg-5 vit-2 vit-6 Abstract: Caenorhabditis elegans introns typically lack both branch point and polypyrimidine tract consensus sequences utilized in other organisms for intron recognition. However, most introns have an unusually long, highly conserved consensus, UUUCAG/R, at the 3' splice site. This site can be recognized even when the -1G is changed to A. To determine how the 3' splice site is defined, we tested mutations in the Sequence UUUCAA/A at the 3' splice site of the first intron of a test gene in vivo. Replacement of individual U's with A's or C's compromised splicing. When the sequence UUUCAA/AAG was tested, splicing occurred following both the -1A and the +3G, indicating that both UUUC and the AG contain 3' Splice site information. When the sequence UUUCAA/AAA was tested, all splicing occurred following the -1A, suggesting that the UUUC contains sufficient information in the absence of an AG to specify the location of the splice site. In support of this idea, when point mutations were introduced into the UUUC, unspliced RNAs accumulated. Surprisingly, RNAs containing the mutant intron often contained the second, nonmutated intron as well, suggesting that interference with splicing of one intron can interfere with splicing of a second intron in the same pre-mRNA. The majority of these unspliced RNAs were degraded by the system responsible for degradation of transcripts containing nonsense mutations (smg), even ------------------- Key: 2464 Medline: 97020667 Authors: Culotti JG;Kolodkin AL Title: Functions of netrins and semaphorins in axon guidance. Citation: Current Opinion in Neurology 6: 81-88 1996 Type: REVIEW Genes: unc-5 unc-6 unc-33 unc-40 Abstract: Neuronal growth cones respond to both contact-mediated and chemotropic guidance cues; these cues can be either attractive or repulsive. This past year has seen further characterization of two gene families implicated in long-range chemoattraction and chemorepulsion: the netrins and the semaphorins. Analysis of invertebrate members of these gene families demonstrates in vivo how netrins play multiple roles in axonal guidance in Caenorhabditis elegans, how specific domains of the netrin molecule confer attractive and repulsive guidance cues, and how semaphorins can function to generate neuromuscular specificity. ------------------- Key: 2465 Medline: 96398833 Authors: Garcia-Anoveros J;Corey DP Title: Mechanosensation - Touch at the molecular level. Citation: Current Biology 6: 541-543 1996 Type: REVIEW Genes: let-2 mec-1 mec-2mec-4 mec-5 mec-6 mec-7 mec-9 mec-10 mec-12 mec-14 mec-15 mec-18 sup-20 unc-105 Abstract: The cloning of genes needed for gentle touch sensitivity in the nematode Caenorhabditis elegans has provided new molecular details about a proposed mechanosensory ion channel complex. ------------------- Key: 2466 Medline: 96221161 Authors: Brundage L;Avery L;Katz A;Kim U-J;Mendel JE;Sternberg PW;Simon MI Title: Mutations in a C. elegans G(q)alpha gene disrupt movement, egg laying, and viability. Citation: Neuron 16: 999-1009 1996 Type: ARTICLE Genes: eat-11 egl-30 unc-104 Abstract: We find that C. elegans egl-30 encodes a heterotrimeric G protein alpha subunit more than 80% identical to mammalian G(q) alpha family proteins, and which can function as a G(q) alpha subunit in COS-7 cells. We have identified new egl-30 alleles in a selection for genes involved in the C. elegans acetylcholine response. Two egl-30 alleles specify premature termination of G(q) alpha and are essentially lethal in homozygotes. Animals homozygous for six other egl-30 alleles are viable and fertile, but exhibit delayed egg laying and leave flattened tracks. Overexpression of the wild-type egl-30 gene produces the opposite behavior. Analysis of these mutants suggest that their phenotypes reflect defects in the muscle or neuromuscular junction. ------------------- Key: 2467 Medline: 96220763 Authors: Jones D;Stringham EG;Babich SL;Candido EPM Title: Transgenic strains of the nematode C. elegans in biomonitoring and toxicology: Effects of captan and related compounds on the stress response. Citation: Toxicology 109: 119-127 1996 Type: ARTICLE Genes: Abstract: The fungicide, captan, induces a cellular stress response in the soil nematode Caenorhabditis elegans. Transgenic C. elegans, which produce beta-galactosidase as a surrogate stress protein, reveal that captan-induced stress is localized mainly to muscle cells of the pharynx. The stress response is elicited by captan concentrations above 5 ppm and occurs within five hours of the initial exposure to the fungicide. Higher concentrations of captan, up to the solubility limit, increase the intensity of the response, Adult nematodes are significantly more sensitive to captan than are larvae, Captan also inhibits feeding in C. elegans, and nematodes exposed to captan rapidly cease muscular contractions in the pharynx. Stress induction and feeding inhibition are also caused by the related fungicides, captafol and folpet, but not by the parent compounds, phthalimide and tetrahydrophthalimide. The inhibition of feeding caused by compounds which elicit the cellular stress response may be an important survival mechanism for C. elegans. ------------------- Key: 2468 Medline: 96242097 Authors: Wicks SR;Roehrig CJ;Rankin CH Title: A dynamic network simulation of the nematode tap withdrawal circuit: Predictions concerning synaptic function using behavioral criteria. Citation: Journal of Neuroscience 16: 4017-4031 1996 Type: ARTICLE Genes: Abstract: The nematode tap withdrawal reflex demonstrates several forms of behavioral plasticity. Although the neural connectivity that supports this behavior is identified (Integration of mechanosensory stimuli in Caenorhabditis elegans, Wicks and Rankin, 1995, J Neurosci 15:2434-2444), the neurotransmitter phenotypes, and hence whether the synapses in the circuit are excitatory or inhibitory, remain uncharacterized. Here we use a novel strategy to predict the polarity configuration, i.e., the array of excitatory and inhibitory connections, of the nematode tap withdrawal circuit using an anatomically and physiologically justifiable dynamic network simulation of that circuit. The output of the modeled circuit was optimized to the behavior of animals, which possessed circuits altered by surgical ablation by exhaustively enumerating an array of synaptic signs that constituted the modeled circuit. All possible polarity configurations were then compared, and a statistical analysis was used to determine whether, for a given synaptic class, a particular polarity was associated with a good fit to behavioral data. The results from four related experiments were used to predict the polarities of seven of the nine cell classes of the tap withdrawal circuit. In addition, the model was used to assess possible roles for two novel mechanosensory integration neurons: DVA and PVD. ------------------- Key: 2469 Medline: 96370137 Authors: Biswas SN;Ebina Y;Okada H;Shingai R Title: A phenomenological model describing pharyngeal pulsing in the nematode Caenorhabditis elegans anesthetized by Citation: Research Communications in Molecular Pathology & Pharmacology 92: 233-244 1996 Type: ARTICLE Genes: Abstract: The recovery process of the suppressed pharyngeal pulsation in the nematode has been investigated for several concentrations of a homologous primary alcohol series (CnH2n-1OH, n=1, 2, 3). A mathematical model describing the time course of the recovery process is phenomenologically constructed by using two time constants of delay time t(D) and recovery time tau. The values of t(D) and tau are obtained by fitting the equation to experimental data The obtained values increase with increasing alcohol concentration. To observe the characteristics of t(D) and tau against the alcohol of order n, the inverse of these time constants are computed at 25 v/v% concentration and plotted on a semi-logarithmic scale. The plot curves decrease non-linearly and are dissimilar to the well-known curves illustrating the importance of lipid solubility in the cell membrane in anesthetic phenomena. ------------------- Key: 2470 Medline: Authors: Bossinger O;Wiegner O;Schierenberg E Title: Embryonic gut differentiation in nematodes: Endocytosis of macromolecules and its experimental inhibition. Citation: Roux's Archives of Developmental Biology 205: 494-497 1996 Type: ARTICLE Genes: Abstract: During embryogenesis of Caenorhabditis elegans cytoplasmic components are transferred from non-gut cells into the developing gut primordium and an exo/endocytosis mechanism has been hypothesized (Bossinger and Schierenberg 1992). To test endocytotic activity of the gut primordium, we compared the uptake of different fluorochrome-conjugated marker molecules in two nematode species, C. elegans and Cephalobus spec., which differ in the pattern of early cleavage and cell-cell communication. We found no uptake of dextran (as a marker for pinocytosis) but rapid internalization of 30-fold larger transferrin molecules (as a marker for receptor-coupled endocytosis) into the differentiating gut primordium in both nematodes. The two studied species differ with respect to when this process starts. While the uptake of macromolecules in the fast developing C. elegans is first observed at a stage when essentially all cells of the hatching juvenile have been generated, in the slow developing Cephalobus endocytosis begins during the early proliferation phase when only two gut precursor cells are present. We found that the polysulfated hydrocarbon dye trypan blue and the cationic amphiphilic drug chlorpromazine both inhibit endocytosis ------------------- Key: 2471 Medline: 96251674 Authors: Lai CC;Hong K;Kinnell M;Chalfie M;Driscoll M Title: Sequence and transmembrane topology of MEC-4, an ion channel subunit required for mechanotransduction in Caenorhabditis elegans. Citation: Journal of Cell Biology 133: 1071-1081 1996 Type: ARTICLE Genes: cah-1 deg-1 mec-4 mec-10 Abstract: The process by which mechanical stimuli are converted into cellular responses is poorly understood, in part because key molecules in this mode of signal transduction, the mechanically gated ion channels, have eluded cloning efforts. The Caenorhabditis elegans mec-4 gene encodes a subunit of a candidate mechanosensitive ion channel that plays a critical role in touch recep tion. Comparative sequence analysis of C. elegans and Caenorhabditis briggsae mec-4 genes was used to initiate molecular studies that establish MEC-4 as a 768-amino acid protein that includes two hydrophobic domains theoretically capable of spanning a lipid bilayer. Immunoprecipitation of in vitro translated mec-4 protein with domain-specific anti-MEC-4, antibodies and in vivo characterization of a series of mec-4lacZ fusion proteins both support the hypothesis that MEC-4 crosses the membrane twice, The MEC-4 amino- and carboxy-terminal domains are situated in the cytoplasm and a large domain, which includes three Cys-rich regions, is extracellular. Definition of transmembrane topology defines regions that might interact with the extracellular matrix or cytoskeleton to mediate mechanical signaling. ------------------- Key: 2472 Medline: 96276416 Authors: Page AP;MacNiven K;Hengartner MO Title: Cloning and biochemical characterization of the cyclophilin homologues from the free-living nematode Caenorhabditis elegans. Citation: Biochemical Journal 317: 179-185 1996 Type: ARTICLE Genes: cyp-1 cyp-2 cyp-3 cyp-4 cyp-5 cyp-6 cyp-7 cyp-8 cyp-9 cyp-10 cyp-11 Abstract: Cyclosporin A (CsA) is the most widely used immunosuppressive agent, whose properties are exerted via an interaction with cyclophilin, resulting in down-regulation of signal-transduction events in the T-cell. Cyclophilin is identical with peptidylprolyl cis-trans isomerase (PPI; EC 5.2.1.8), an enzyme which catalyses the isomerization between the two proline conformations in proteins, thereby acting as a catalyst in protein-folding events. Several reports indicate that CsA has potent anti-parasitic activity, effective against both protozoan and helminth species. In order to understand the various biological roles that cyclophilins play we have initiated a study of these proteins in the genetically tractable nematode Caenorhabditis elegans. Here we describe the cloning and characterization of 11 cyclophilin genes (cyp-1 to -11) derived from this nematode; this is currently the greatest number of isoforms described in a single species. Southern blotting and physical mapping indicated that these genes are dispersed throughout the nematode genome. A high degree of conservation exists between several isoforms, which also share characteristics with the ubiquitous isoforms previously described. The remaining isoforms are divergent, having altered CsA-binding domains and additional non-cyclophilin domains, which may impart compartmental specificity. Ten of these isoforms have been expressed in Escherichia coli, and the resultant fusion proteins have been examined biochemically for PPI activity, which they all possess, Isomerase activity is highest in the conserved and lowest in divergent isoforms, perhaps indicating a more specific substrate for the latter. Analysis of the C. elegans cyp genes will provide answers as to the roles played by cyclophilins in protein folding and signal transduction. ------------------- Key: 2473 Medline: 96279828 Authors: Kipreos ET;Lander LE;Wing JP;He WW;Hedgecock EM Title: cul-1 is required for cell cycle exit in C. elegans and identifies a novel gene family. Citation: Cell 85: 829-839 1996 Type: ARTICLE Genes: cul-1 cul-2 cul-3 cul-4 cul-5 lin-14 lin-19 nDf40 Abstract: The gene cul-1 (formerly lin-19) is a negative regulator of the cell cycle in C. elegans. Null mutations cause hyperplasia of all tissues. cul-1 is required for developmentally programmed transitions from the G1 phase of the cell cycle to the G0 phase or the apoptotic pathway. Moreover, the mutant phenotype suggests that G1-to-S phase progression is accelerated, overriding mechanisms for mitotic arrest and producing abnormally small cells. Significantly, diverse aspects of cell fate and differentiation are unaffected in cul-1 mutants. cul-1 represents a conserved family of genes, designated cullins, with at least five members in nematodes, six in humans, and three in budding yeast. ------------------- Key: 2474 Medline: 96301894 Authors: Barnes TM;Jin Y;Horvitz HR;Ruvkun G;Hekimi S Title: The Caenorhabditis elegans behavioral gene unc-24 encodes a bipartite protein similar to both erythrocyte band 7.2 (stomatin) and non-specific lip transfer protein. Citation: Journal of Neurochemistry 67: 46-57 1996 Type: ARTICLE Genes: arf-3 ceh-19 mec-2 unc-24 eDf28 Abstract: We report here the positional cloning and molecular characterization of the unc-24 gene of Caenorhabditis elegans, This gene is required for normal locomotion and interacts with genes that affect the worm's response to volatile anesthetics. The predicted gene product contains a domain similar to part oi two ion channel regulators (the erythrocyte integral membrane protein stomatin and the C. elegans neuronal protein MEC-2) juxtaposed to a domain similar to nonspecific lipid transfer protein (nsLTP; also called sterol carrier protein 2). Sequence analysis suggests that the nsLTP-like domain of UNC-24 provides lipid carrier function and is tethered to the plasma membrane by the stomatin-like domain, which may be regulatory. We postulate that UNC-24 may be involved in lipid transfer between closely apposed membranes. ------------------- Key: 2475 Medline: 96249386 Authors: Baumeister R;Liu Y;Ruvkun G Title: Lineage-specific regulators couple cell lineage asymmetry to the transcription of the Caenorhabditis elegans POU gene unc-86 during neurogenesis. Citation: Genes & Development 10: 1395-1410 1996 Type: ARTICLE Genes: egl-5 ham-1 lin-11 lin-17 lin-32 lin-39 lin-44 mab-5 unc-86 vab-3 Abstract: The POU homeo box gene unc-86 specifies neuroblast and neural identities in the developing Caenorhabditis elegans nervous system. After an asymmetric neuroblast division, unc-86 is expressed in one of two daughter cells in 27 lineage classes that are not obviously related by function or position. We show here that unc-86 transcriptional regulatory regions detect cell lineage asymmetry to activate unc-86 expression in one of two neuroblast daughter cells. Distinct regulatory regions activate unc-86 expression in particular sets of sublineages. Therefore the unc-86 regulatory region integrates distinct cell lineage asymmetry cues to activate unc-86 expression in the many classes of neuroblast cell lineages. In agreement with such lineage-specific regulation of unc-86 asymmetric activation, mutations in lin-11 (LIM homeo box), ham-1, and lin-17 affect the asymmetry of unc-86 expression in particular cell lineages, and mutations in lin-32 (achaete/scute family), vab-3 (Pax-G homolog) and egl-5 (Abd-B homolog) affect the establishment of unc-86 expression in other cell lineages. Homologs of unc-86 and many of these unc-86 regulators have been implicated in control of neurogenesis in vertebrates and invertebrates. These data suggest that unc-86 acts in a phylogenetically conserved pathway that couples neuroblast cell lineage asymmetry to the generation of diverse neural types. ------------------- Key: 2476 Medline: 96251094 Authors: Tabara H;Motohashi T;Kohara Y Title: A multi-well version of in situ hybridization on whole mount embryos of Caenorhabditis elegans. Citation: Nucleic Acids Research 24: 2119-2124 1996 Type: ARTICLE Genes: clb-2 col-3 glp-1 myo-2 unc-54 Abstract: We report an efficient procedure for in situ hybridization with a multi-well format on Caenorhabditis elegans embryos for large scale screening of gene expression patterns in this organism, Each hybridization well contains embryos at various stages throughout embryogenesis. The validity of the method was confirmed through results with control genes whose expression patterns have been reported; glp-1 in very early embryos, myo-2 in pharyngeal muscle and unc-54 in body wall muscle, Several collagen genes and a pepsinogen gene were also examined to establish a set of lineage-specific markers. As a pilot project, we examined similar to 100 unique cDNA species classified by our cDNA project, finding that similar to 10% of the cDNA groups were expressed in specific cells and at specific stages. ------------------- Key: 2477 Medline: Authors: Katz W;Sternberg PW Title: Intercellular signaling in Caenorhabditis elegans vulval pattern formation. Citation: Seminars in Cell & Developmental Biology 7: 175-183 1996 Type: REVIEW Genes: let-23 let-60 lin-2 lin-3 lin-7 lin-10 lin-12 lin-15 lin-45 mab-5 mek-2 mpk-1 sem-5 sli-1 sur-1 Abstract: The six multipotent precursors of the C. elegans vulva generate an invariant pattern of three fates (3 degrees 3 degrees 2 degrees 1 degrees 2 degrees 3 degrees) which determine their future growth and organization. Multiple, partly redundant mechanisms appear necessary to specify this invariant pattern. A key signal here is the EGF-like growth factor LIN-3 which is made by the anchor cell of the gonad and which induces vulval fate according to dose: a high dose promotes a 1 degrees fate; a lower dose promotes a 2 degrees fate. In addition, a lateral signalling pathway promotes 2 degrees fates and prevents adjacent 1 degrees fates. We propose that a gradient of growth factor directly induces a spatially graded pattern of vulval fates, and lateral signalling reinforces this waded induction. ------------------- Key: 2478 Medline: 96258254 Authors: Ferguson KC;Heid PJ;Rothman JH Title: The SL1 trans-spliced leader RNA performs an essential embryonic function in Caenorhabditis elegans that can also be supplied by SL2 RNA. Citation: Genes & Development 10: 1543-1556 1996 Type: ARTICLE Genes: elt-1 ges-1 hlh-1 myo-3 rrs-1 Abstract: Covalent joining of leader RNA exons to pre-mRNAs by trans-splicing has been observed in protists and invertebrates, and can occur in cultured mammalian cells. In the nematode Caenorhabditis elegans, similar to 60% of mRNA species are trans-spliced to the 22-nucleotide SL1 leader, and another similar to 10% of mRNAs receive the 22-nucleotide SL2 leader. We have isolated deletions that remove the rrs-1 cluster, a gene complex that contains similar to 110 tandem copies of a repeat encoding both SL1 RNA and 5S rRNA. An SL1-encoding gene alone rescues the embryonic lethality caused by these deletions. Mutations within the Sm-binding site of SL1 RNA, which is required for trans-splicing, eliminate rescue, suggesting that the ability of the SL1 leader to be trans-spliced is required for its essential activity. We observe pleiotropic defects in embryos lacking SL1 RNA, suggesting that multiple mRNAs may be affected by the absence of an SL1 leader. We found, however, that SL1-receiving messages are expressed without an SL1 leader. Surprisingly, when overexpressed, SL2 RNA, which performs a distinct function from that of SL1 RNA in wild-type animals, can rescue the lethality of embryos lacking SL1 RNA. Moreover, in these mutant embryos, we detect SL2 instead of SL1 leaders on normally SL1-trans-spliced messages; this result suggests that the mechanism that discriminates between SL1 and SL2-trans-splicing may involve competition between SL1 and SL2-specific trans-splicing. Our findings demonstrate that SL1 RNA is essential for embryogenesis in C. elegans and that SL2 RNA can substitute for SL1 RNA in vivo. ------------------- Key: 2479 Medline: 96232293 Authors: Mickey KM;Mello CC;Montgomery MK;Fire A;Priess JR Title: An inductive interaction in 4-cell stage C. elegans embryos involves APX-1 expression in the signalling cell. Citation: Development 122: 1791-1798 1996 Type: ARTICLE Genes: apx-1 glp-1 pie-1 Abstract: During the 4-cell stage of C. elegans embryogenesis, the P-2 blastomere provides a signal that allows two initially equivalent sister blastomeres, called ABa and ABp, to adopt different fates. Preventing P-2 signalling in wild-type embryos results in defects in ABp development that are similar to those caused by mutations in the glp-1 and apx-1 genes, which are homologs of the Drosophila genes Notch and Delta, respectively. Previous studies have shown that GLP-1 protein is expressed in 4-cell stage embryos in both ABa and ABp. In this report, we show that APX-1 protein is expressed in the P-2 blastomere and that a temperature-sensitive apx-1 mutant has a temperature-sensitive period between the 4-cell and 8-cell stages. We propose that APX-1 is part or all of the P-2 signal that induces ABp to adopt a fate different than ABa. ------------------- Key: 2480 Medline: 96391183 Authors: Wang L;Way JC Title: Activation of the mec-3 promoter in two classes of stereotyped lineages in Caenorhabditis elegans. Citation: Mechanisms of Development 56: 165-181 1996 Type: ARTICLE Genes: ced-3 ced-4 mec-3 mec-4 unc-86 Abstract: The mec-3 gene of Caenorhabditis elegans encodes a homeodomain protein and is expressed in one of two cells upon asymmetric cell division. As a result of asymmetric mec-3 expression, the two sister cells express different fates, so mec-3 is a likely target for the machinery that mediates asymmetric cell division. The unc-86 gene encodes a homeodomain protein of the POU family, which activates mec-3 by binding to its promoter. The ten mec3-expressing cells are a subset of the anterior daughters of UNC-86-containing cells. Posterior daughters of UNC-86-containing cells do not express mec-3, even though the UNC-86 protein is distributed into both daughter cells. Lineages that express the unc-86 and mec-3 genes can be grouped into two types: in Type I lineages, UNC-86 protein is first made in the immediate parent of the terminal mec-3-expressing cell, while in Type II lineages, UNC-86 is first made in the grandparent of the terminal mec-3-expressing cell. The purpose of experiments presented here is to understand the relationship between the mec-3 expression patterns in each type of lineage, and to determine the fundamental activity pattern of the mec-3 promoter. We find that in the Type I V5.pa lineage, mec-3-lacZ is first synthesized in the terminal PVDR neuron, one cell division after unc-86 is expressed. mec-3 expression in PVDR can occur by transcriptional regulation alone; segregation of the mec-3 RNA or protein is not required to explain the asymmetric expression of mec-3. In the Type: II Q lineage, the mec-3 promoter activity can be detected in the immediate anterior daughter of the first unc-86-expressing cell, but when this cell divides, mec-3 is expressed in only one of its daughters at later times. It seems likely that, in the short-lived immediate anterior daughter cell in Type II lineages, mec-3 product does not accumulate to levels that can influence subsequent events. Our results suggest that the mec-3 promoter is activated in ------------------- Key: 2481 Medline: 96391184 Authors: Wang LL;Way JC Title: Promoter sequences for the establishment of mec-3 expression in the nematode Caenorhabditis elegans. Citation: Mechanisms of Development 56: 183-196 1996 Type: ARTICLE Genes: ced-3 mec-3 unc-86 Abstract: In certain stereotyped lineages of Caenorhabditis elegans, the mec-3 gene is transcribed in neurons that are anterior daughters of cells containing the UNC-86 protein. UNC-86 binds to the mec-3 promoter and is necessary for transcription activation, but this protein is present in many cells that do not transcribe mec-3, including the posterior sister and parent cells of the mec-3-expressing neurons. To understand how the mec-3 promoter directs transcription in only a subset of cells that contain UNC-86, we have compared sequences within the promoter that are bound by UNC-86 in vitro with sequences that are necessary for early transcription of mec-3 in vivo. We find that upstream of the mec-3 start codon are two blocks of sequence that are each sufficient to generate the cellular pattern of mec-3 transcription. The proximal sequence includes three previously identified short regions that have been conserved in nematode evolution and each contains one high-affinity UNC-86 binding site. The recognition consensus sequence for UNC-86 is CATnnn(T)/(A)AAT, which is identical to the recognition sequence for the UNC-86-related mammalian transcription factor Brn-3. Adjacent to the UNC-86 recognition site is an additional sequence that is important for establishment of mec-3 expression and is presumably recognized by an unidentified ------------------- Key: 2482 Medline: 96270583 Authors: Gu GQ;Caldwell GA;Chalfie M Title: Genetic interactions affecting touch sensitivity in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 93: 6577-6582 1996 Type: ARTICLE Genes: mec-1 mec-2 mec-4 mec-5 mec-6 mec-7 mec-8 mec-9 mec-10 mec-12 mec-14 mec-15 mec-18 mnDf29 nDf16 nDf31 sDf20 stDf5 yDf1 Abstract: At least 13 genes (mec-1, mec-2, mec-4-10, mec-22, mec-14, mec-15, and mec-18) are needed for the response to gentle touch by 6 touch receptor neurons in the nematode Caenorhabditis elegans. Several, otherwise recessive alleles of some of these genes act as dominant enhancer mutations of temperature-sensitive alleles of mec-1, mec-5, mec-6, mec-12, and mec-15. Screens for additional dominant enhancers of mec-4 and mec-5 yielded mutations in previously known genes, In addition, some mec-7 alleles showed allele-specific, dominant suppression of the mec-15 touch-insensitive (Mec) phenotype. The dominant enhancement and suppression exhibited by these mutations suggest that the products of several touch genes interact, These results are consistent with a model, supported by the known sequences of these genes, that almost all of the ouch function genes contribute to the mechanosensory apparatus. ------------------- Key: 2483 Medline: 96275596 Authors: Hubbard EJA;Dong Q;Greenwald I Title: Evidence for physical and functional association between EMB-5 and LIN-12 in Caenorhabditis elegans. Citation: Science 273: 112-115 1996 Type: ARTICLE Genes: apx-1 emb-5 glp-1 lag-1 lag-2 lin-12 sDp3 Abstract: The Caenorhabditis elegans LIN-12 and GLP-1 proteins are members of the LIN-12/Notch family of receptors for intercellular signals that specify cell fate. Evidence presented here suggests that the intracellular domains of LIN-12 and GLP-1-interact with the C. elegans EMB-5 protein and that the emb-5 gene functions in the same pathway as the lin-12 and glp-1 genes. EMB-5 is similar in sequence to a yeast protein that controls chromatin structure. Hence, a direct consequence of LIN-12 or GLP-1 activation may be an alteration of chromatin structure that produces changes in transcriptional activity. ------------------- Key: 2484 Medline: 96400916 Authors: Miller LM;Waring DA;Kim SK Title: Mosaic analysis using a ncl-1(+) extrachromosomal array reveals that lin-31 acts in the Pn.p cells during Caenorhabditis elegans vulval development. Citation: Genetics 143: 1181-1191 1996 Type: ARTICLE Genes: lin-31 ncl-1 unc-29 Abstract: We describe a genetic mosaic analysis procedure in which Caenorhabditis elegans mosaics are generated by spontaneous loss of an extrachromosomal array. This technique allows almost any C. elegans gene that can be used in germline transformation experiments to be used in mosaic analysis experiments. We identified a cosmid clone that rescues the mutant phenotype of ncl-1, so that this cell-autonomous marker could be used to analyze mosaic animals. To determine the sites of action for unc-29 and lin-31, an extrachromosomal array was constructed containing the ncl-1(+) cosmid linked to lin-31(+) and unc-29(+) cosmids. This array is mitotically unstable and can be lost to produce a clone of mutant cells. The specific cell division at which the extrachromosomal array had been lost was deduced by scoring the Nd phenotypes of individual cells in genetic mosaics. The Unc-29 and Lin-31 phenotypes were then scored in these animals to determine in which cells these genes are required. This analysis showed that unc-29, which encodes a subunit of the acetylcholine receptor, acts in the body muscle cells. Furthermore, lin-31, which specifies cell fates during vulval induction and encodes a putative transcription factor similar to HNF-3/fork head, acts in the Pn.p cells. ------------------- Key: 2485 Medline: 96400917 Authors: Malone EA;Inoue T;Thomas JH Title: Genetic analysis of the roles of daf-28 and age-1 in regulating Caenorhabditis elegans dauer formation. Citation: Genetics 143: 1193-1205 1996 Type: ARTICLE Genes: aex-3 age-1 che-2 che-3 che-11 che-13 daf-1 daf-2 daf-3 daf-4 daf-5 daf-6 daf-7 daf-8 daf-10 daf-11 daf-12 daf-14 daf-16 daf-18 daf-21 daf-22 daf-23 daf-28 egl-4 egl-32 osm-1 osm-3 osm-5 osm-6 unc-3 unc-13 unc-31 unc-58 unc-64 Abstract: Based on environmental cues, the nervous system of Caenorhabditis elegans regulates for mation of the dauer larva, an alternative larval form specialized for long-term survival under harsh conditions. Mutations that cause constitutive or defective dauer formation (Daf-c or Daf-d) have been identified and the genes ordered in a branched pathway. Most Daf-c mutations also affect recovery from the dauer stage. The semi-dominant mutation daf-28(sa191) is Daf-c but has no apparent effect on dauer recovery. We use this unique aspect of daf-28(sa191) to characterize the effects of several Daf-d and synthetic Daf-c mutations on dauer recovery. We present double mutant analysis that indicates that daf-28(sa191) acts at a novel point downstream in the genetic pathway for dauer formation. We also show that daf-28(sa191) causes a modest increase (12-13%) in life span. The phenotypes and genetic interactions of daf-28(sa191) are most similar to those of daf-2 and daf-23 mutations, which also cause a dramatic increase in life span. We present mapping and complementation data that suggest that daf-23 is the same gene as age-1, identified previously by mutations that extend life span. We find that age-1 alleles are also Daf-c at 27 degrees. ------------------- Key: 2486 Medline: 96400918 Authors: Murakami S;Johnson TE Title: A genetic pathway conferring life extension and reistance to UV stress in Caenorhabditis elegans. Citation: Genetics 143: 1207-1218 1996 Type: ARTICLE Genes: age-1 clk-1 daf-2 daf-3 daf-4 daf-7 daf-16 daf-18 daf-23 daf-28 fer-15 let-60 spe-26 Abstract: A variety of mechanisms have been proposed to explain the extension of adult life span (Age) seen in several mutants in Caenorhabditis elegans (age-1: an altered aging rate; daf-2 and daf-23: activation of a dauer-specific longevity program; spe-26: reduced fertility; clk-1: an altered biological clock). Using an assay for ultraviolet (UV) resistance in young adult hermaphrodites (survival after UV irradiation), we observed that all these Age mutants show increased resistance to UV. Moreover, mutations in daf-16 suppressed the UV resistance as well as the increased longevity of all the Age mutants. In contrast to the multiple mechanisms initially proposed, these results suggest that a single, daf-16-dependent pathway, specifies both extended life span and increased UV resistance. The mutations in daf-16 did not alter the reduced fertility of spe-26 and interestingly a daf-16 mutant is more fertile than wild type. We propose that life span and some aspects of stress resistance are jointly negatively regulated by a set of gerontogenes (genes whose alteration causes life extension) in C. elegans. ------------------- Key: 2487 Medline: 96400919 Authors: Schafer WR;Sanchez BM;Kenyon CJ Title: Genes affecting sensitivity to serotonin in Caenorhabditis elegans. Citation: Genetics 143: 1219-1230 1996 Type: ARTICLE Genes: cha-1 egl-1 egl-19 snt-1 unc-2 unc-8 unc-9 unc-10 unc-20 unc-25 unc-35 unc-36 unc-43 unc-75 unc-77 Abstract: Regulating the response of a postsynaptic cell to neurotransmitter is an important mechanism for controlling synaptic strength, a process critical to learning. We have begun to define and characterize genes that may control sensitivity to the neurotransmitter serotonin in the nematode Caenorhabditis elegans by identifying serotonin-hypersensitive mutants. We reported previously that mutations in the gene unc-2 which encodes a putative calcium channel subunit, result in hypersensitivity to serotonin. Here we report that mutants defective in the unc-36 gene, which encodes a homologue of a calcium channel auxiliary subunit, are also serotonin-hypersensitive. Moreover, the unc-36 gene appears to be required in the same cells as unc-2 for control of the same behaviors. Mutations in several other genes, including unc-8, unc-10, unc-20, unc-35, unc-75, unc-77, and snt-1 also result in hypersensitivity to serotonin. Several of these mutations have previously been shown to confer resistance to acetylcholinesterase inhibitors, suggesting that they may affect acetylcholine release. Moreover, we found that mutations that decrease acetylcholine synthesis cause defective egg-laying and serotonin hypersensitivity. Thus, acetylcholine appears to negatively regulate the response to serotonin and may participate in the process of serotonin desensitization. ------------------- Key: 2488 Medline: 96275587 Authors: Lithgow GJ;Kirkwood TBL Title: Mechanisms and evolution of aging. Citation: Science 273: 80- 1996 Type: REVIEW Genes: age-1 clk-1 daf-2 daf-16 daf-23 daf-28 spe-26 Abstract: Single-gene mutations that extend the life-span of the worm Caenorhabditis elegans dramatically demonstrate the genetic basis of aging and may eventually lead to the elucidation of aging mechanisms. At the same time, evolution theory provides a powerful insight into the genetic basis of aging, and recent experiments are allowing these ideas to be tested and refined. ------------------- Key: 2489 Medline: 96320415 Authors: Corey DP;Garcia-Anoveros J Title: Mechanosensation and the DEG/ENaC ion channels. Citation: Science 273: 323-324 1996 Type: REVIEW Genes: deg-1 let-2 mec-1 mec-2 mec-4 mec-5 mec-6 mec-7 mec-9 mec-10 mec-12 unc-8 unc-105 Abstract: Mechanosensation-the transformation of mechanical stimuli into electrochemical signals-is ubiquitous in animals; it includes the senses of hearing, balance, touch, proprioception, as well as cellular functions such as volume regulation. The molecular basis of mechanosensitivity has been hard to discern because mechanosensitive organs are small and their constituent proteins are scarce. Recent genetic studies in the nematode Caenorhabditis elegans have revealed a dozen candidate proteins for mediating the sense of touch, in the process defining a new superfamily of ion channel proteins. A report in this issue now describes two interacting genes (unc-105 and let-2) expressed by C. elegans muscle that may be involved in the muscle's response to stretch; unc-105 is a new member of this channel superfamily and let-2 encodes ------------------- Key: 2490 Medline: 96279656 Authors: Liu J;Schrank B;Waterston RH Title: Interaction between a putative mechanosensory membrane channel and a collagen. Citation: Science 273: 361-364 1996 Type: ARTICLE Genes: deg-1 let-2 mec-4 mec-10 sup-20 unc-105 Abstract: The degenerin family of proteins in Caenorhabditis elegans is homologous to subunits of the mammalian amiloride-sensitive epithelial sodium channels. Mutations in nematode degenerins cause cell death, probably because of defects in channel function. Genetic evidence was obtained that the unc-105 gene product represents a degenerin homolog affecting C. elegans muscles and that this putative channel interacts with type IV collagen in the extracellular matrix underlying the muscle cell. This interaction may serve as a mechanism of stretch-activated muscle contraction, and this system could provide a molecular model for the activation of mechanosensitive ion ------------------- Key: 2491 Medline: 96304263 Authors: Schnabel R Title: Pattern formation: Regional specification in the early C. elegans embryo. Citation: BioEssays 18: 591-594 1996 Type: REVIEW Genes: apx-1 cib-1 glp-1 mex-1 pie-1 Abstract: Recent findings suggest that C. elegans, albeit displaying an invariant cell lineage for embryonic development, uses the same basic strategy for embryogenesis as other organisms. The early embryo is regionalised by cell-cell interactions. ------------------- Key: 2492 Medline: 96281657 Authors: Felix MA;Sternberg PW Title: Symmetry breakage in the development of one-armed gonads in nematodes. Citation: Development 122: 2129-2142 1996 Type: ARTICLE Genes: Abstract: Whereas the hermaphrodite gonad of Caenorhabditis elegans has two symmetric arms (didelphy), the female/hermaphrodite gonad of many nematode species features a single anterior arm (monodelphy). We examined how gonadal cell lineages and intercellular signalling evolve to generate these diverse structures. In C. elegans, the two arms develop symmetrically from two somatic precursor cells, Z1 (anterior) and Z4 (posterior). Each first gives rise to one distal tip cell (which promotes arm growth and germ line proliferation), two ovary precursors and three uterine precursors in the center of the developing gonad. In monodelphic species, Z1 and Z4 have different fates. The first visible asymmetry between them is in the relative timing of their divisions, followed by asymmetric cell movements. The putative posterior distal tip cell is then eliminated in all but one species by programmed cell death. In some species the posterior ovary precursors form a small vestigial posterior arm, the post-vulval sac; in other species, they stay undivided, or die. In Cephalobus sp. PS1197, the specific fate of Z4 progeny is induced by Z1 (or its daughters). In the uterus in C. elegans, symmetric lateral signalling between Z1.ppp and Z4.aaa renders them equally likely to become the anchor cell, which links the uterus to the vulva. In the different monodelphic species, anchor cell specification is biased, or fully fixed, to a descendant of either Z1 or Z4. Replacement regulation upon anchor cell ablation is conserved in some species, but lost in others, leading to a mosaic-type development. Differentiation between Z1 and Z4 is thus manifested at this later stage in the breakage of symmetry of cell interactions in the ventral uterus. ------------------- Key: 2493 Medline: 96281653 Authors: Kuwabara PE Title: A novel regulatory mutation in the C. elegans sex determination gene tra-2 defines a candidate ligand/receptor interaction site. Citation: Development 122: 2089-2098 1996 Type: ARTICLE Genes: dpy-26 fem-3 her-1 myo-1 tra-2 tra-3 Abstract: Sex determination in the nematode C. elegans is dependent on cell-to-cell communication, which appears to be mediated by the predicted membrane protein TRA-2A and the secreted protein HER-1. In XO males, HER-I is hypothesised to function as a repressive ligand that inactivates the TRA-2A receptor. In XX animals, HER-1 is absent and TRA-2A promotes hermaphrodite development by negatively regulating the FEM proteins. This paper describes the molecular and genetic characterisation of a novel class of feminising mutations called tra-2(eg), for enhanced gain-of-function. In XX animals, mutant tra-2(eg) activity promotes entirely normal hermaphrodite development. However, the tra-2(eg) mutations generate an XO-specific gain-of-function phenotype, because they transform XO mutants from male into hermaphrodite. Therefore, the tra-2(eg) mutations identify a major regulatory site, which may be the TRA-2A/HER-1 interaction site. All ten tra-2(eg) mutations encode identical missense changes in a predicted extracellular domain of TRA-2A, named the EG site. It is proposed that the tra-2(eg) mutation encodes a TRA-2A protein that functions constitutively in XO animals, because it is defective in HER-I binding. Phenotypic characterisation of sexually transformed XO tra-2(eg) hermaphrodites reveals that their fertility is strongly affected by dosage compensation mutations, suggesting that dosage compensation plays a role in normal gametogenesis. ------------------- Key: 2494 Medline: 96281648 Authors: Shelton CA;Bowerman B Title: Time-dependent responses to glp-1-mediated inductions in early C. elegans embryos. Citation: Development 122: 2043-2050 1996 Type: ARTICLE Genes: apx-1 apx-3 glp-1 skn-1 Abstract: In an embryo of the nematode Caenorhabditis elegans, two blastomeres at the 4-cell stage, ABa and ABp, are born with equivalent developmental potential. Subsequently, interactions with the P-2 blastomere at the 4-cell stage and the MS blastomere at the 12-cell stage generate differences in developmental fate among descendants of ABa and ABp. We have reproduced these inductions in vitro using embryonic blastomeres isolated in cell-culture medium. We show that during these inductions only the responding AB descendants require the activity of the glp-1 gene, which is similar in sequence to Drosophila Notch, supporting models in which GLP-1 protein acts as a receptor for both the P-2 and MS signals. We also show that P-2 signaling requires the activity of the apx-1 gene, similar in sequence to Drosophila Delta, and that MS signaling requires the putative transcription factor SKN-1. We present evidence that the primary factor determining the different responses to these two signals is the age of the AB descendants, not the identity of the signaling cell or ligand. Therefore, we suggest that time-dependent changes in factors within AB descendants are responsible for their different responses to inductive signals that use a common ------------------- Key: 2495 Medline: 96275675 Authors: Roush W Title: Divide and confer: How worm embryo cells specialize. Citation: Science 272: 1871- 1996 Type: REVIEW Genes: apx-1 glp-1 mom-2 par-1 par-2 par-3 par-4 par-5 par-6 Abstract: The one-cell animal embryo, or zygote, faces a daunting engineering task: implementing the architectural plans inscribed in its DNS for building a complex, multicelled body. So, like any sensible construction supervisor, the zygote swiftly divides the project into manageable chunks, assigning some of its progeny to build only gut, for example, and other to make only muscle or skin. Just how each early embryonic cell gets its orders is understood only for the fruit fly Drosophila melanogaster-an achievement that helped win 1995's Nobel Prize in medicine for three developmental biologists. Now, however, the communication lines governing embryonic development are emerging in another animal beloved of developmental researchers: the tiny worm known as Caenorhabditis elegans. ------------------- Key: 2496 Medline: 96275588 Authors: Jazwinski SM Title: Longevity, genes and aging. Citation: Science 273: 54-58 1996 Type: REVIEW Genes: age-1 clk-1 clk-2 clk-3 daf-2 daf-12 daf-16 daf-18 daf-23 gro-1 spe-26 Abstract: Until recently, biogerontology was a backwater of biology, but progress in the qualitative and quantitative genetic analysis of longevity has led to a revolution in aging research. This research has revealed that extended longevity is frequently associated with enhanced metabolic capacity and response to stress. Moreover, it suggests that there are multiple mechanisms of aging. Because of its complexity, the aging process takes us into the realm of integrative biology, and thus, biogerontology should prove instrumental in deciphering the functional and regulatory circuitry of the sequenced genome. ------------------- Key: 2497 Medline: 96267598 Authors: Wicky C;Rose AM Title: The role of chromosome ends during meiosis in Caenorhabditis elegans. Citation: BioEssays 18: 447-452 1996 Type: REVIEW Genes: him-1 him-5 him-8 eT1 hIn1 Abstract: Chromosome ends have been implicated in the meiotic processes of the nematode Caenorhabditis elegans. Cytological observations have shown that chromosome ends attach to the nuclear membrane and adopt kinetochore functions. In this organism, centromeric activity is highly regulated, switching from multiple spindle attachments all along the chromosome during mitotic division to a single attachment during meiosis. C. elegans chromosomes are functionally monocentric during meiosis. Earlier genetic studies demonstrated that the terminal regions of the chromosomes are not equivalent in their meiotic potentials. There are asymmetries in the abilities of the ends to recombine when duplicated or deleted. In addition, mutations in single genes have been identified that mimic the meiotic effects of a terminal truncation of the X chromosome. The recent cloning and characterization of the C. elegans telomeres has provided a starting point for the study of chromosomal elements mediating the meiotic ------------------- Key: 2498 Medline: 96267600 Authors: Sundaram M;Han M Title: Control and integration of cell signaling pathways during C. elegans vulval development. Citation: BioEssays 18: 473-480 1996 Type: REVIEW Genes: ksr-1 lag-2 let-23 let-60 let-537 lin-1 lin-2 lin-3 lin-7 lin-10 lin-12 lin-15 lin-25 lin-31 lin-37 lin-45 mek-2 mpk-1 sem-5 sli-1 sur-1 sur-2 unc-101 Abstract: Vulval development in the Caenorhabditis elegans hermaphrodite represents a simple, genetically tractable system for studying how cell signaling events control cell fate decisions. Current models suggest that proper specification of vulval cell fates relies on the integration of multiple signaling systems, including one that involves a receptor tyrosine kinase (RTK)-->Ras-->mitogen activated protein kinase (MAPK) cascade and one that involves a LIN-12/Notch family receptor. In this review, we first discuss how genetic strategies are being used to identify and analyze components that control vulval cell fate decisions. We then describe the different signaling systems that have been elucidated and how they relate to one another. Finally, we highlight several recently characterized genes that encode positive regulators, negative regulators or potential targets of the RTK-->Ras-->MAPK cascade involved in vulval ------------------- Key: 2499 Medline: 96241569 Authors: Martin GM;Austad SN;Johnson TE Title: Genetic analysis of ageing: Role of oxidative damage and environmental stresses. Citation: Nature Genetics 13: 25-34 1996 Type: REVIEW Genes: age-1 clk-1 daf-2 daf-12 daf-16 daf-23 daf-28 spe-10 spe-26 Abstract: Evolutionary theory predicts substantial interspecific and intraspecific differences in the proximal mechanisms of ageing. Our goal here is to seek evidence for common ('public') mechanisms among diverse organisms amenable to genetic analysis. Oxidative damage is a candidate for such a public mechanism of ageing. Long-lived strains are relatively resistant to different environmental stresses. The extent to which these stresses produce oxidative damage remains to be established. ------------------- Key: 2500 Medline: Authors: Johnson TE;Lithgow GJ;Murakami S;Duhon SA;Shook DR Title: Genetics of aging and longevity in lower organisms. Citation: "Cellular Aging and Cell Death." Holbrook NJ, Martin GR and Rockshin RA (eds), Wiley-Liss, New York. : 1-17 1996 Type: REVIEW Genes: age-1 daf-1 daf-2 daf-4 daf-7 daf-12 daf-16 daf-23 daf-28 fer-15 rad-8 spe-26 Abstract: Species with short life spans have been the primary targets for studies into the genetic basis of the aging process(es). Almost all genetic studies of aging and longevity have been performed on invertebrates. Invertebrates often have very short life spans, and this fact, together with the excellent genetic systems available for some yeasts, Drosophila melanogaster, and the nematode Caenorhabditis elegans, make them almost the only choice for studying the genetics of aging. The mouse, with its 2-year life span, is an exception to this rule; several genetic studies, including the analysis of short-lived mice, have been performed and used in an attempt to infer causal relationships. The mouse is the focus of a recent NIA initiative on mammalian models of aging. Recently human "marker association" studies, where longevity is shown to be associated with defined regions of the human genome by characterizing molecular markers at certain candidate loci, have started to appear. Genetic approaches have been used also to identify the processes causing replicative senescence in human tissue culture. Two fundamentally distinct but overlapping questions have been the focus of genetic studies. What are the molecular mechanisms limiting life span? How does the process of evolution lead to aging and senescence? Although the answer to the latter question has been obtained to the satisfaction of most in the field, studies into the molecular basis continue. The details of the mechanisms leading to senescence and aging have not been forthcoming. ------------------- Key: 2501 Medline: 96283621 Authors: Zhen M;Schein JE;Baillie DL;Candido EPM Title: An essential ubiquitin-conjugating enzyme with tissue and developmental specificity in the nematode Caenorhabditis elegans. Citation: EMBO Journal 15: 3229-3237 1996 Type: ARTICLE Genes: let-70 ubc-2 Abstract: The ubc-2 gene in Caenorhabditis elegans encodes a ubiquitin-conjugating enzyme (E2) homologous to yeast UBC4 and UBC5. UBC4 and UBC5 are individually dispensable class I E2 enzymes involved in the degradation of short-lived and abnormal proteins. Transgenic analysis using ubc-2-lacZ fusions and in situ immunofluorescence indicate that ubc-2 is abundantly expressed in most tissues of embryos and early larvae, but becomes specific to the nervous system in L4 larvae and adults. This suggests that the functions of this type of E2 are developmentally regulated in C.elegans. This hypothesis is supported by antisense analysis, which shows that blocking the expression of ubc-2 has a more severe effect in early developmental stages than in later stages. Through complementation of previously identified essential genes in the vicinity of ubc-2, we demonstrate that ubc-2 corresponds to let-70, a gene essential for C.elegans larval development. One let-70(ubc-2) allele contains a His75-->Tyr substitution, while another has an altered splice donor site. ------------------- Key: 2502 Medline: 96279144 Authors: Etter A;Cully DF;Schaeffer JM;Liu KK;Arena JP Title: An amino acid substitution in the pore region of a glutamate-gated chloride channel enables the coupling of ligand binding to channel gating. Citation: Journal of Biological Chemistry 271: 16035-16039 1996 Type: ARTICLE Genes: Abstract: Many of the subunits of ligand-gated ion channels respond poorly, if at all, when expressed as homomeric channels in Xenopus oocytes, This lack of a ligand response has been thought to result from poor surface expression, poor assembly, or lack of an agonist binding domain. The Caenorhabditis elegans glutamate-gated chloride channel subunit GluCl beta responds to glutamate as a homomeric channel while the GluCl alpha subunit is insensitive. A chimera between GluCl alpha and GluCl beta was used to suggest that major determinants for glutamate binding are present on the GluCl alpha N terminus, Amino acid substitutions in the presumed pore of GluCl alpha conferred direct glutamate gating indicating that GluCl alpha is deficient in coupling of ligand binding to channel gating. Heteromeric channels of GluCl alpha+beta may differ from the prototypic muscle nicotinic acetylcholine receptor in that they have the potential to bind ligand to all of the subunits forming the channel. ------------------- Key: 2503 Medline: 96300322 Authors: Cowing D;Kenyon C Title: Correct Hox gene expression established independently of position in Caenorhabditis elegans. Citation: Nature 382: 353-356 1996 Type: ARTICLE Genes: mab-5 Abstract: The Hox genes are expressed in a conserved sequence of spatial domains along the anteroposterior (A/P) body axes of many organisms(1). In Drosophila, position-specific signals located along the A/P axis establish the pattern of Hox gene expression(2-4). In the nematode Caenorhabditis elegans, it is not known how the pattern of Hox gene expression is established, C. elegans uses lineal control mechanisms and local cell interactions to specify early blastomere identities(5,6). However, many cells expressing the same Hox gene are unrelated by lineage, suggesting that, as in Drosophila, domains of Hox gene expression may be defined by cell-extrinsic A/P positional signals. To test this, we have investigated whether posterior mesodermal and ectodermal cells will express their normal posterior Hox gene when they are mispositioned in the anterior. Surprisingly, we find that correct Hox gene expression does not depend on cell position, but is highly correlated with cell lineage, Thus, although the most striking feature of Hox gene expression is its positional specificity, in C. elegans the pattern is achieved, at least in part, by a lineage-specific control system that ------------------- Key: 2504 Medline: 97015887 Authors: Gaudet J;VanderElst I;Spence AM Title: Post-transcriptional regulation of sex determination in Caenorhabditis elegans: Widespread expression of the sex-determining gene fem-1 in both sexes. Citation: Molecular Biology of the Cell 7: 1107-1121 1996 Type: ARTICLE Genes: fem-1 fem-2 fem-3 glp-1 glp-4 tra-2 Abstract: The fem-1 gene of C. elegans is one of three genes required for all aspects of male development in the nematode. Cur rent models of sex determination propose that the products of the fem genes act in a novel signal-transduction pathway and that their activity is regulated primarily at the post-translational level in somatic tissues. We analyzed the expression of fem-1 to determine whether it revealed any additional levels of regulation. Both XX hermaphrodites and XO males express fem-1 at approximately constant levels throughout development. Somatic tissues in hermaphrodites adopt female fates, but they nonetheless express fem-2 mRNA and FEM-1 protein, suggesting that the regulation of fem-1 activity is post-transcriptional and probably post-translational. A compact promoter directs functional expression of fem-1 transgenes, as assayed by their masculinizing activity in fem-1 mutants. Activity also requires any two or more introns, suggesting that splicing may enhance fem-1 expression. The minimal noncoding sequences required for activity of fem-1 transgenes suffice to direct expression of a fem-1::lacZ reporter gene in all somatic tissues in both sexes. Many fem-1 transgenes, including those that rescue male somatic development in fem-1 mutants, paradoxically feminize the germline. We suggest that they do so by interfering with the germline expression of the endogenous fem-1 gene. ------------------- Key: 2505 Medline: 96310865 Authors: Starich TA;Lee RYN;Panzarella C;Avery L;Shaw JE Title: eat-5 and unc-7 represent a multigene family in Caenorhabditis elegans involved in cell-cell coupling. Citation: Journal of Cell Biology 134: 537-548 1996 Type: ARTICLE Genes: eat-5 unc-7 Abstract: The Drosophila melanogaster genes Passover and I(1)ogre and the Caenorhabditis elegans gene unc-7 define a gene family whose function is not known. We have isolated and characterized the C. elegans gene eat-5, which is required for synchronized pharyngeal muscle contractions, and find that it is a new member of this family. Simultaneous electrical and video recordings reveal that in eat-5 mutants, action potentials of muscles in the anterior and posterior pharynx are unsynchronized. Injection of carboxyfluorescein into muscles of the posterior pharynx demonstrates that all pharyngeal muscles are dye-coupled in wild-type animals; in eat-5 mutants, however, muscles of the anterior pharynx are no longer dye-coupled to posterior pharyngeal muscles. We show that a gene fusion of eat-5 to the green fluorescent protein is expressed in pharyngeal muscles. unc-7 and eat-5 are two of at least sixteen members of this family in C. elegans as determined by database searches and PCR-based screens. The amino acid sequences of five of these members in C. elegans have been deduced from cDNA sequences. Polypeptides of the family are predicted to have four transmembrane domains with cytoplasmic amino and carboxyl termini. We have constructed fusions of one of these polypeptides with P-galactosidase and with green fluorescent protein. The fusion proteins appear to be localized in a punctate pattern at or near plasma membranes. We speculate that this gene family is required for the formation of gap junctions. ------------------- Key: 2506 Medline: 96310865 Authors: Guo S;Kemphues KJ Title: A non-muscle myosin required for embryonic polarity in Caenorhabditis elegans. Citation: Nature 382: 455-458 1996 Type: ARTICLE Genes: nmy-1 nmy-2 par-1 par-2 par-3 Abstract: Daughter cells with distinct fates can arise through intrinsically asymmetrical divisions'. Before such divisions, factors crucial for determining cell fates become asymmetrically localized in the mother cell(2,3). In Caenorhabditis elegans, PAR proteins are required for the early asymmetrical divisions that establish embryonic polarity(4,8), and are asymmetrically localized in early blastomeres(9,10), although the mechanism of their distribution is not known. Here we report the identification in C. elegans of a nonmuscle myosin II heavy chain (designated NMY-2) by means of its interaction with the PAR-1 protein, a putative Ser/Thr protein kinase. Furthermore, injections of nmy-2 antisense RNA into ovaries of adult worms cause embryonic partitioning defects and lead to mislocalization of PAR proteins. We therefore conclude that NMY-2 is required for establishing cellular polarity in C. elegans embryos. ------------------- Key: 2507 Medline: 96302239 Authors: McDermott JB;Aamodt S;Aamodt E Title: ptl-1, a Caenorhabditis elegans gene whose products are homologous to the tau microtubule-associated proteins. Citation: Biochemistry 35: 9415-9423 1996 Type: ARTICLE Genes: ptl-1 Abstract: The tau microtubule-associated proteins are axonal proteins that have been implicated in axonal outgrowth, microtubule spacing, and microtubule bundling. Moreover, tau is the major structural component of the paired helical filaments present in the brains of Alzheimer's disease patients. The Caenorhabditis elegans Genome Sequencing Consortium identified a genomic sequence with homology to the repeat region of tau. PCR, Northern analyses, and cDNA sequencing were used here to identify transcripts containing the tau homology region. The gene that encodes these transcripts was named ptl-1 for protein with E-like repeats. The ptl-1 transcript, like mammalian tau transcripts, is alternatively spliced to produce messages that encode proteins with variable numbers of repeats. The predicted ptl-1 products have strong sequence homology to tau over the repeat region and are similar to tau in several other important respects including size, amino acid content, charge distribution, predicted secondary structure, hydrophobicity, and flexibility. Both proteins contain several potential glycosylation sites and numerous phosphorylation sites. Bacterially expressed PTL-1 bound to microtubules in vitro. These results show that tau-like proteins evolved early and suggests that they may be present in many different phyla. C. elegans is a powerful system amenable to genetic, molecular, and cellular analysis in which to study the functions of this important ------------------- Key: 2508 Medline: Authors: Abdul Kader N;Cote MG Title: Isolation, identification and characterization of some strains of Caenorhabditis elegans (Maupas, 1900) from Quebec. Citation: Fundamental and Applied Nematology 19: 381-389 1996 Type: ARTICLE Genes: Abstract: 93 strains of the free-living soil nematode, Caenorhabditis elegans, have been isolated from soil and organic decaying matter of different sites in Quebec. Species were identified based on morphological characteristics and mating with the standard British laboratory strain Bristol (N2). The biological characteristics of six strains selected from four sites have been determined (egg-adult generation time, viability, length and fecundity at four different temperatures). Preliminary study of the sensitivity of these strains to four toxicants (diphenylamine, pentachlorophenol, 4-chlorobiphenyl and 2,2'-dichlorobiphenyl) brought out differences among them. ------------------- Key: 2509 Medline: Authors: Borgonie G;Claeys M;Leyns F;Arnaut G;De Waele D;Coomans A Title: Effect of nematicidal Bacillus thuringiensis strains on free-living nematodes. 1. Light microscopic observations, species and biological stage specificity and identification of res Citation: Fundamental and Applied Nematology 19: 391-398 1996 Type: ARTICLE Genes: Abstract: Light-microscopic observations of the toxic action of Bacillus thuringiensis spore/crystals reveals that, in Caenorhabditis elegans, the intestine is destroyed in two stages over a period of 24 h. The anterior ring of four cells is the first and foremost target. Observations indicate that the intestine is the only tissue being destroyed. Screening of fourteen additional rhabditid nematode species against three nematicidal B. thuringiensis strains active against C. elegans, resulted in only one additional sensitive nematode species, and indicates a high species specificity of the nematicidal factor. However, in contrast to insect-specific B. thuringiensis toxins, the nematicidal toxin exhibits low developmental stage specificity against C. elegans; all developmental stages, including adult nematodes are sensitive. Moreover, sensitivity increases as development proceeds. Using ethyl methyl sulfonate induced mutagenesis two mutants of C. elegans have been recovered, exhibiting reduced sensitivity of up to 50 % against one of the nematicidal strains. Moreover, one of the mutants exhibited cross-resistance to a second nematicidal B. thuringiensis strain against which it was not screened. Preliminary data indicate that the reduced sensitivity in the mutants is not due to reduced pharyngeal pumping activity. ------------------- Key: 2510 Medline: 96304327 Authors: Kloek AP;McCarter JP;Setterquist RA;Schedl T;Goldberg DE Title: Caenorhabditis globin genes: Rapid intronic divergence contrasts with conservation of silent exonic sites. Citation: Journal of Molecular Evolution 43: 101-108 1996 Type: ARTICLE Genes: Abstract: Globin genes from the Caenorhabditis species briggsae and remanei were identified and compared with a previously described C. elegans globin gene. The encoded globins share between 86% and 93% amino acid identity, with most of the changes in or just before the putative B helix. C. remanei was found to have two globin alleles, Crg1-1 and Crg1-2. The coding sequence for each is interrupted by a single intron in the same position. The exons of the two genes are only 1% divergent at the nucleotide level and encode identical polypeptides. In contrast, intron sequence divergence is 16% and numerous insertions and deletions have significantly altered the size and content of both introns. Genetic crosses show that Crg1-1 and Crg1-2 segregate as alleles. Homozygous lines for each allele were constructed and northern analysis confirmed the expression of both alleles. These data reveal an unusual situation wherein two alleles encoding identical proteins have diverged much more rapidly in their introns than the silent sites of their coding sequences, suggesting multiple gene ------------------- Key: 2511 Medline: 96304317 Authors: Oosumi T;Garlick B;Belknap WR Title: Identification of putative nonautonomous transposable elements associated with several transposon families in Caenorhabditis elegans. Citation: Journal of Molecular Evolution 43: 11-18 1996 Type: ARTICLE Genes: Abstract: Putative nonautonomous transposable elements related to the autonomous transposons Tc1, Tc2, Tc5, and mariner were identified in the C. elegans database by computational analysis. These elements are found throughout the C. elegans genome and are defined by terminal inverted repeats with regions of sequence similarity, or identity, to the autonomous transposons. Similarity between loci containing related nonautonomous elements ends at, or near, the boundaries of the terminal inverted repeats. In most cases the terminal inverted repeats of the putative nonautonomous transposable elements are flanked by potential target-site duplications consistent with the associated autonomous elements. The nonautonomous elements identified vary considerably in size (from 100 bp to 1.5 kb in length) and copy number in the available database and are localized to introns and flanking regions of a wide variety of C. elegans genes. ------------------- Key: 2512 Medline: 96312960 Authors: Johnstone IL;Barry JD Title: Temporal reiteration of a precise gene expression pattern during nematode development. Citation: EMBO Journal 15: 3633-3639 1996 Type: ARTICLE Genes: ama-1 col-1 col-12 col-14 dpy-7 dpy-13 sqt-1 Abstract: The nematode Caenorhabditis elegans is contained within a multifunctional exoskeleton, the cuticle, that contains a large number of distinct collagens. As the nematode proceeds from the egg through four larval stages to the adult, transition between larval stages is marked by synthesis of a new cuticle and subsequent moulting of the old one. This is a cyclically repeated developmental event, frequently described as the moulting cycle. We have examined the temporal expression of a group of six genes encoding distinct cuticular collagens. As expected, mRNA abundance for each of the six genes tested is found to oscillate, peaking once during each larval stage. Unexpectedly, the periods of abundance for each gene do not coincide, different genes being expressed at different times relative to one another within the moulting cycle. We detect a programme of temporally distinct waves of collagen gene expression, the precise pattern of which is repeated during each of the four larval stages. This multiphasic pattern of oscillating cuticular collagen gene expression indicates an unexpected complexity of temporal control during the nematode moulting cycle and has implications for collagen trimerization and cuticle synthesis. ------------------- Key: 2513 Medline: 97008248 Authors: Benecke M;Epplen JT;Schierenberg E Title: (GTG)(5) allows the distinction between different isolates of the nematode Caenorhabditis elegans. Citation: Electrophoresis 17: 1194- 1996 Type: ARTICLE Genes: Abstract: We have not been able to distinguish different isolates from the nematode Caenorhabditis elegans by morphological means. However, they differ on the molecular level and strains from several geographic regions can be identified with the help of ''genetic fingerprints'' using the oligonucleotide probe (GTG)(5). ------------------- Key: 2514 Medline: 96320556 Authors: Morris JZ;Tissenbaum HA;Ruvkun G Title: A phosphatidylinositol-3-OH kinase family member regulating longevity and diapause in Caenorhabditis elegans. Citation: Nature 382: 536-539 1996 Type: ARTICLE Genes: age-1 daf-23 mnDf75 mnDf76 mnDf86 mnDf90 Abstract: A pheromone-induced neurosecretory pathway in Caenorhabditis elegans triggers developmental arrest and an increase in longevity at the dauer diapause stage. The gene age-1 is required for non-dauer development and normal senescence. age-1 encodes a homologue of mammalian phosphatidylinositol-3-OH kinase (PI(3)K) catalytic subunits. Lack of both maternal and zygotic age-1 activity causes dauer formation, whereas animals with maternal but not zygotic age-1 activity develop as non-dauers that live more than twice as long as normal. These data suggest that phosphatidylinositol signalling mediated by AGE-1 protein controls lifespan and the dauer diapause decision. ------------------- Key: 2515 Medline: 96320559 Authors: Metzstein MM;Hengartner MO;Tsung N;Ellis RE;Horvitz HR Title: Transcriptional regulator of programmed cell death encoded by Caenorhabditis elegans gene ces-2. Citation: Nature 382: 545-547 1996 Type: ARTICLE Genes: ces-1 ces-2 eDf9 eDf13 Abstract: The ces (for cell-death specification) genes of the nematode Caenorhabditis elegans the cell-death fate of individual cell types and are candidates for being the regulators of an evolutionarily conserved general pathway of programmed cell death(1-4). Here we present what we believe is the first molecular characterization of a ces gene. We cloned the gene ces-2, which is required to activate programmed cell death in the sister cells of the serotoninergic neurosecretory motor (NSM) neurons, and found that ces-2 encodes a basic region leucine-zipper (bZIP) transcription factor. The CES-2 protein is most similar to members of the PAR (proline- and acid-rich) subfamily of bZIP proteins and has DNA-binding specificity like that of PAR-family proteins. An oncogenic form of the mammalian PAR-family protein, hepatic leukaemia factor (HLF), is reported to effect programmed cell death in mammalian cells(5). On the basis of these observations, we suggest that some CES-2/PAR family transcription factors are evolutionarily conserved regulators of programmed cell ------------------- Key: 2516 Medline: 96319723 Authors: Shaham S;Horvitz HR Title: An alternatively spliced C. elegans ced-4 RNA encodes a novel cell death inhibitor. Citation: Cell 86: 201-208 1996 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: The C. elegans gene ced-4 is essential for programmed cell death. We report that ced-4 encodes two transcripts and that whereas the major transcript can cause programmed cell death, the minor transcript can act oppositely and prevent programmed cell death, thus defining a novel class of cell death inhibitors. That ced-4 has both cell-killing and cell-protective functions is consistent with previous genetic studies. Our results suggest that the dual protective and killer functions of the C. elegans bcl-2-like gene ced-9 are mediated by inhibition of the killer and protective ced-4 functions, respectively. We propose that a balance between opposing ced-4 functions influences the decision of a cell to live or to die by programmed cell death and that both ced-9 and ced-4 protective functions are required to prevent programmed ------------------- Key: 2517 Medline: 97017658 Authors: Wicks SR;Rankin CH Title: Recovery from habituation in Caenorhabditis elegans is dependent on interstimulus interval and not habituation kinetics. Citation: Behavioral Neuroscience 110: 840-844 1996 Type: ARTICLE Genes: Abstract: The habituation of the tap withdrawal reflex of Caenorhabditis elegans was assessed to determine whether the kinetics of recovery from habituation were dependent on the interstimulus interval (ISI) used during habituation training, or alternately, on the rate and asymptotic level of habituation produced at a given ISI. Two groups of intact animals were trained at either a 10-s (CON10) or a 60-s (CON60) ISI. Laser ablation was used to alter the habituation kinetics in one further group of animals (PLM10), independent of ISI. Although the PLM10 animals trained at a 10-s ISI habituated like CON60 worms, the recovery from habituation of the PLM10 animals very closely resembled the recovery of the CON10 worms. Thus recovery kinetics are dictated by consequences of a given ISI, which do not impact upon habituation rate and asymptote. This suggests the recruitment of multiple ISI-dependent processes during habituation in C. elegans. ------------------- Key: 2518 Medline: 96326306 Authors: Basson M;Horvitz HR Title: The Caenorhabditis elegans gene sem-4 controls neuronal and mesodermal cell development and encodes a zinc finger protein. Citation: Genes & Development 10: 1953-1965 1996 Type: ARTICLE Genes: let-389 let-400 let-520 mec-3 sem-4 hDf8 nDf43 hDp58 hDp62 sDp2 Abstract: Neuronal and mesodermal cell types are generated in separate cell lineages during the larval development of Caenorhabditis elegans. Here we demonstrate that the gene sem-4 is required in both types of lineages for the normal development of neuronal and mesodermal cell types. The sem-4 gene encodes a protein containing seven zinc finger motifs of the C2H2 class, four of which are arranged in two pairs widely separated in the primary sequence of the protein. These pairs of zinc fingers are similar to pairs of zinc fingers in the protein encoded by the Drosophila homeotic gene spalt and in the human transcription factor PRDII-BF1. Analysis of sem-4 alleles suggests that different zinc fingers in the SEM-4 protein may function differentially in neuronal and mesodermal cell types. We propose that sem-4 interacts with different transcription factors in different cell types to control the transcription of genes that function in the processes of neuronal and mesodermal cell development. ------------------- Key: 2519 Medline: 96326675 Authors: Iwasaki K;McCarter J;Francis R;Schedl T Title: emo-1, a Caenorhabditis elegans Sec61p * homologue, is required for oocyte development and ovulation. Citation: Journal of Cell Biology 134: 699-714 1996 Type: ARTICLE Genes: emo-1 fem-1 fem-3 glp-4 ncl-1 ctDf1 ctDp11 sDf35 stDf4 Abstract: emo-1(oz1) is a member of a class of hermaphrodite sterile mutations in Caenorhabditis elegans that produce endomitotic oocytes in the gonad arm. Oocytes in emo-1(oz1) mutants exhibit multiple defects during oogenesis, After meiotic maturation, ovulation fails, trapping oocytes in the gonad arm where they become endomitotic. emo-1 encodes a homologue of the Sec61p gamma subunit, a protein necessary for translocation of secretory and transmembrane proteins into the endoplasmic reticulum of yeast and mammalian cells. A putative emo-1 null mutation, oz151, displays embryonic lethality. The oz1 sterile mutation is a transposable element insertion into the emo-1 3' untranslated region that almost completely eliminates germline mRNA accumulation. Genetic mosaic analysis using the oz1 allele indicates that emo-1(+) expression in germ cells is required for fertility. The J67 monoclonal antibody, which recognizes an oocyte surface antigen (Strome, S. 1986. In Gametogenesis and the Early Embryo, J.G. Gall, editor, Alan R. Liss, Inc., New York. 77-95.), does not stain oz1 oocytes, a finding consistent with defective protein transport in the mutant. We propose that the emo-1 gene product acts in the transport of secreted and transmembrane proteins in C. elegans oocytes, and is necessary for both oogenesis and the coupling of ovulation ------------------- Key: 2520 Medline: 96312929 Authors: Euling S;Ambros V Title: Reversal of cell fate determination in Caenorhabditis elegans vulval development. Citation: Development 122: 2507-2515 1996 Type: ARTICLE Genes: lin-3 lin-10 lin-11 lin-12 lin-14 lin-28 Abstract: In Caenorhabditis elegans, the fates of the multipotent vulval precursor cells (VPCs) are specified by intercellular signals. The VPCs divide in the third larval stage (L3) of the wild type, producing progeny of determined cell types. In lin-28 mutants, vulva development is similar to wild-type vulva development except that it occurs precociously, in the second larval stage (L2). Consequently, when lin-28 hermaphrodites temporarily arrest development at the end of L2 in the dauer larva stage, they have partially developed vulvae consisting of VPC progeny. During post-dauer development, these otherwise determined VPC progeny become reprogrammed back to the multipotent, signal-sensitive state of VPCs. Our results indicate that VPC fate determination by intercellular signals is reversible by dauer larva ------------------- Key: 2521 Medline: 96312930 Authors: Bettinger JC;Lee K;Rougvie AE Title: Stage-specific accumulation of the terminal differentiation factor LIN-29 during Caenorhabditis elegans development. Citation: Development 122: 2517-2527 1996 Type: ARTICLE Genes: lin-4 lin-14 lin-28 lin-29 lin-42 Abstract: The Caenorhabditis elegans gene lin-29 is required for the terminal differentiation of the lateral hypodermal seam cells during the larval-to-adult molt. We find that lin-29 protein accumulates in the nuclei of these cells, consistent with its predicted role as a zinc finger transcription factor. The earliest detectable LIN-29 accumulation in seam cell nuclei is during the last larval stage (L4), following the final seam cell division, which occurs during the L3-to-L4 molt. LIN-29 accumulates in all hypodermal nuclei during the L4 stage. The time of LIN-29 appearance in the hypodermis is controlled by the heterochronic gene pathway: LIN-29 accumulates in the hypodermis abnormally early, during the third larval stage, in loss-of-function lin-14, lin-28 and lin-42 mutants, and fails to accumulate in hypodermis of lin-4 mutants. LIN-29 also accumulates stage-specifically in the nuclei of a variety of non-hypodermal cells during development. Its accumulation is dependent upon the upstream heterochronic genes in some, but not all, of these non-hypodermal cells. ------------------- Key: 2522 Medline: 96322833 Authors: Morgan PG;Usiak MF;Sedensky MM Title: Genetic differences affecting the potency of stereoisomers of isoflurane. Citation: Anesthesiology 85: 385-392 1996 Type: ARTICLE Genes: unc-1 unc-7 unc-9 unc-49 unc-79 unc-80 Abstract: Background: In previous studies, researchers demonstrated the ability of a variety of organisms and in vitro sites of anesthetic action to distinguish between stereoisomers of isoflurane or halothane. However, it was not shown whether organisms with differing sensitivities to stereoisomers of one volatile anesthetic are able to distinguish between stereoisomers of another. In this study, the responses of mutants of Caenorbabditis elegans to stereoisomers of isoflurane were determined for comparison to previous results in halothane. Methods: Mutant strains of C. elegans were isolated and grown by standard techniques. The EC(50)s (the effective concentrations of anesthetia at which 50% of the animals are immobilized for 10 s) of stereoisomers of isoflurane and the racemate were determined in wild type and mutant strains of C. elegans. Results: Wild type C. elegans and strains with high EC(50)s of the racemate were more sensitive to the (+) isomer of isoflurane by approximately 30%. The racemate showed a EC(50)s similar to the less potent isomer, the (-) form. In the strains with low EC(50)s, one strain showed no ability to differentiate between the stereoisomers, whereas two showed a 60% difference between the (+) and (-) forms. Conclusions: The ability to distinguish between stereoisomers of isoflurane is associated with genetic loci separate from those that distinguish between stereoisomers of halothane. These results are consistent with multiple sites of action for these anesthetics. ------------------- Key: 2523 Medline: 97009558 Authors: Moulder GL;Huang MM;Waterston RH;Barstead RJ Title: Talin requires beta-integrin, but not vinculin, for its assembly into focal adhesion-like structures in the nematode Caenorhabditis elegans. Citation: Molecular Biology of the Cell 7: 1181-119 1996 Type: ARTICLE Genes: deb-1 pat-3 nDp5 sDp3 Abstract: In cultured cells, the 230-kDa protein talin is found at discrete plasma membrane foci known as focal adhesions, sites that anchor the intracellular actin cytoskeleton to the extracellular matrix. The regulated assembly of focal adhesions influences the direction of cell migrations or the reorientation of cell shapes. Biochemical studies of talin have shown that it binds to the proteins integrin, vinculin, and actin in vitro. To understand the function of talin in vivo and to correlate its in vitro and in vivo biochemical properties, various genetic approaches have been adopted. With the intention of using genetics in the study of talin, we identified a homologue to mouse talin in a genetic model system, the nematode Caenorhabditis elegans. C. elegans talin is 39% identical and 59% similar to mouse talin. In wild-type adult C. elegans, talin colocalizes with integrin, vinculin, and alpha-actinin in the focal adhesion-like structures found in the body-wall muscle. By examining the organization of talin in two different C. elegans mutant strains that do not make either beta-integrin or vinculin, we were able to determine that talin does not require vinculin for its initial organization at the membrane, but that it depends critically on the presence of integrin for its initial ------------------- Key: 2524 Medline: 96186805 Authors: Johnson KA;Quiocho FA Title: Twitching worms catch S100. Citation: Nature 380: 585-587 1996 Type: REVIEW Genes: unc-22 Abstract: Springtime finds hopeful anglers baiting hungry fish with twitching worms, both live and artificial. Fish prefer the large annelids, but Kemp and coworkers have knotted on their lines the small, alluring nematode Caenorhabditis elegans, which twitches spasmodically when the aptly named protein twitchin goes missing from its muscle cells. And they've caught a big one! On page 636 of this issue, these authors report that the giant protein kinase twitchin, which has a relative molecular mass of 750K and is found in nematode muscle cells, and the protein S100A1(2), a member of the S100 family of calcium-binding proteins, make up a third new calcium-regulated system in muscle which may be of great importance in organizing muscle structure and maintaining its resting tension. They show that a fragment of twitchin containing the autoinhibited kinase domain is specifically activated in a calcium-dependent and zinc-enhanced manner by S100A1(2), but not by the S100B(2) isoform with which it shares 60 percent homology.... ------------------- Key: 2525 Medline: 96361359 Authors: Zwaal RR;Ahringer J;van Luenen HGAM;Rushforth A;Anderson P;Plasterk RHA Title: G proteins are required for spatial orientation of early cell cleavages in C. elegans embryos. Citation: Cell 86: 619-629 1996 Type: ARTICLE Genes: gpb-1 mut-2 Abstract: Heterotrimeric G proteins are signal-transducing molecules activated by seven transmembrane domain receptors. In C. elegans, gpb-1 encodes the sole G beta subunit; therefore, its inactivation should affect all heterotrimeric G protein signaling. When maternal but no zygotic gpb-1 protein (GPB-1) is present, development proceeds until the first larval stage, but these larvae show little muscle activity and die soon after hatching. When, however, the maternal contribution of GPB-1 is also reduced, spindle orientations in early cell divisions are randomized. Cell positions in these embryos are consequently abnormal, and the embryos die with the normal number of cells and well-differentiated but abnormally distributed tissues. These results indicate that maternal G proteins are important for orientation of early cell division axes, possibly by coupling a membrane signal to centrosome position. ------------------- Key: 2526 Medline: 96345667 Authors: Seydoux G;Mello CC;Pettitt J;Wood WB;Priess JR;Fire A Title: Repression of gene expression in the embryonic germ lineage of C. elegans. Citation: Nature 382: 713-716 1996 Type: ARTICLE Genes: cey-1 cey-2 crf-2 cul-1 hlh-1 lin-19 nhr-2 pes-10 pes-11 pes-12 pie-1 skn-1 vet-1 vet-2 vet-4 vet-5 vet-6 Abstract: The distinction between soma and germline was recognized more than a century ago: somatic cells form the body of an organism, whereas germ cells serve to produce future generations'. In Caenorhabditis elegans, the separation of soma and germline occurs through a series of asymmetrical divisions, in which embryonic germline blastomeres divide unequally to produce one somatic daughter and one germline daughter(2). Here we show that after each asymmetrical division, embryonically transcribed RNAs are detected in somatic, but not germline, blastomeres. This asymmetry depends on the activity of the germline-specific factor, PIE-1. In the absence of PIE-1, embryonically transcribed RNAs are detected in both somatic and germline blastomeres. Furthermore, ectopic expression of PIE-1 in somatic blastomeres can significantly reduce the accumulation of new transcripts in these cells. Taken together, these results suggest that germ-cell fate depends on an inhibitory mechanism that blocks new gene expression in the early embryonic germ lineage. ------------------- Key: 2527 Medline: 96345666 Authors: Mello CC;Schubert C;Draper B;Zhang W;Lobel R;Priess JR Title: The PIE-1 protein and germline specification in C. elegans embryos. Citation: Nature 382: 710-712 1996 Type: ARTICLE Genes: pie-1 skn-1 Abstract: Totipotent germline blastomeres in Caenorhabditis elegans contain, but do not respond to, factors that promote somatic differentiation in other embryonic cells(1,2). Mutations in the maternal gene pie-1 result in the germline blastomeres adopting somatic cell fates(3). Here we show that pie-1 encodes a nuclear protein, PIE-1, that is localized to the germline blastomeres throughout early development. During division of each germline blastomere, PIE-1 initially associates with both centrosomes of the mitotic spindle. However, PIE-1 rapidly disappears from the centrosome destined for the somatic daughter, and persists in the centrosome of the daughter that becomes the next germline blastomere. The PIE-1 protein contains potential zinc-finger motifs also found in the mammalian growth-factor response protein TIS-11/NUP475 (refs 4-7). The localization and genetic properties of pie-1 provide an example of a repressor-based mechanism for preserving pluripotency within a stem cell lineage. ------------------- Key: 2528 Medline: 96320546 Authors: Thompson CB Title: A fate worse than death. Citation: Nature 382: 492-493 1996 Type: REVIEW Genes: ced-3 ces-1 ces-2 Abstract: During the development of many, if not all, complex organisms, specific cells are marked out for elimination in a process known as programmed cell death, or apoptosis, a form of cell suicide. For example, during the development of the hermaphrodite nematode worm Caenorhabditis elegans, 131 of the 1,090 cells produced are genetically destined to die. Drosophila embryos without the necessary genes to execute this death programme do not survive. In vertebrates, failure to delete malformed or potentially autoreactive immune cells during development can eventually lead to autoimmunity or leukaemia. So too much or too little cell death threatens the whole organism. ------------------- Key: 2529 Medline: 96300312 Authors: Emmons SW Title: Simple worms, complex genes. Citation: Nature 382: 301-302 1996 Type: REVIEW Genes: mab-5 egl-5 Abstract: Classical results in experimental embryology established long ago that cells of the developing animal have a regional identity. They can be characterized not only as 'skin', 'nerve' and 'bone', but also as 'arm' and 'leg'. But how cells know what body region they belong to, and what to do there, is not known. Results reported in this issue and in Development describe unexpected properties of a key player, one of the Hox genes-the dynamic, lineage-based regulation of a Hox gene in the nematode Caenorhabditis elegans is at odds with a traditional view of Hox genes as relatively fixed markers of regional ------------------- Key: 2530 Medline: Authors: Sommer RJ;Sternberg PW Title: Using nematode vulva development to model the evolution of developmental systems. Citation: "Molecular Zoology: Advances, Strategies; and Protocols." Ferraris JD and SR Palumbi (eds); Wiley-Liss, Inc., New York, NY. : 209-220 1996 Type: REVIEW Genes: lon-1 Abstract: In the nematode model organism Caenorhabditis elegans developmental processes can be anaylzed at various levels. The invariance of cell lineage allows a high-resolution morphological description of development and an experimental approach by ablation of individual cells. Isolation and characterization of genetic mutations reveal the basis of the genetic program underlying particular developmental processes. DNA-mediated transformation can be used to anaylze the function of cloned genes and thus finally generate also a molecular understanding of the process under investigation. Evolutionary approaches to development are rare and so far consist only of a subset of techniques used in the reference model system. By using the complete set of techniques from the model organism, including genetics, in related but morphologically distinct species, one can get a detailed comparison of a developmental process. Here we describe our attempt to establish the techniques known in the model organism Caenorhabditis of the Rhabditidae in other free-living nematodes, including Pristionchus pacificus of the ------------------- Key: 2531 Medline: 96386370 Authors: Guo S;Kemphues KJ Title: Molecular genetics of asymmetric cleavage in the early Caenorhabditis elegans embryo. Citation: Current Opinion in Genetics & Development 6: 408-415 1996 Type: REVIEW Genes: glp-1 mes-1 mex-1 nop-1 par-1 par-2 par-3 par-4 par-5 par-6 pop-1 skn-1 Abstract: Asymmetric cleavage plays an important role in Caenorhabditis elegans embryogenesis. In addition to generating cellular diversity, several early asymmetric cleavages contribute to the spatial organization of the embryo. Genetic and molecular analyses of several genes, including six par genes and the mex-1 and mes-1 genes, together with experimental embryological studies, have provided insights into mechanisms controlling polarity and spindle orientations during these cleavages. In particular, these studies focus attention on microfilament-based motility and changing protein distributions at the cell cortex. ------------------- Key: 2532 Medline: Authors: Zetka MC;Muller F Title: Telomeres in nematodes. Citation: Seminars in Cell & Developmental Biology 7: 59-64 1996 Type: REVIEW Genes: Abstract: Nematode telomeres show the same highly conserved structural features which are observed in other organisms. Cytological and genetic analyses revealed that nematode telomeres are involved in important meiotic processes, such as the attachment of chromosomes to the nuclear envelope, the pairing of homologues, the initiation of synapsis and kinetochore activity during meiosis. The early development of some nematode species is marked by the process of chromatin diminution, which involves developmentally-programmed chromosomal breakage, DNA degradation and new telomere formation in all presomatic cells. This large-scale chromosomal healing is mechanistically related to the healing of spontaneous chromosome breaks and is suggestive of the presence of telomere activity. The diversity present in terms of genome organization and chromosome behaviour makes nematodes an excellent system for the study of metazoan ------------------- Key: 2533 Medline: 96209822 Authors: Kessin RH;Gunderson GG;Zaydfudim V;Grimson M Title: How cellular slime molds evade nematodes. Citation: Proceedings of the National Academy of Sciences USA 93: 4857-4861 1996 Type: ARTICLE Genes: Abstract: We have found a predator-prey association between the social amoeba Dictyostelium discoideum and the free soil living nematode Caenorhabditis elegans. C. elegans feeds on the amoebae and multiplies indefinitely when amoebae are the sole food source. In an environment created from soil, D. discoideum grows and develops, but not in the presence of C. elegans. During development, C. elegans feeds on amoebae until they aggregate and synthesize an extracellular matrix called the slime sheath. After the sheath forms, the aggregate and slug are protected. Adult nematodes ingest Dictyostelium spores, which pass through the gut of the worm without loss of structure and remain viable. Nematodes kill the amoebae but disperse the spores. The sheath that is constructed when the social amoebae aggregate and the spore coats of the individual cells may protect against this predator. Individual amoebae may also protect themselves by secreting compounds that repel ------------------- Key: 2534 Medline: 96352697 Authors: Hartman P;Goldstein P;Algarra M;Hubbard D;Mabery J Title: The nematode Caenorhabditis elegans is up to 39 times more sensitive to gamma radiation generated from Cs137 than from Co60. Citation: Mutation Research-DNA Repair 363: 201-208 1996 Type: ARTICLE Genes: him-5 rad-1 Abstract: Survival after gamma irradiation (generated from either a Cs-137 or Co-60 source) was determined for two strains of the nematode Caenorhabditis elegans. Animals were between 1.3 and 39 times more sensitive to cesium than to cobalt. The magnitude of this differential sensitivity was dependent upon the strain, developmental stage and sex tested. Several control experiments eliminated trivial explanations for this difference. Since cobalt- and cesium-generated gamma particles have nearly identical energy depositions, the differential sensitivity likely reflects different mechanisms of processing the slightly different spectra of DNA damage induced by these two radiations. Sex-specific differences in radiation sensitivity were also noted and were likely due to the fact that males possess a single X chromosome rather than two, ------------------- Key: 2535 Medline: 96392352 Authors: Wicky C;Villeneuve AM;Lauper N;Codourey L;Tobler H;Muller F Title: Telomeric repeats (TTAGGC)(n) are sufficient for chromosome capping function in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 93: 8983-8988 1996 Type: ARTICLE Genes: Abstract: Telomeres are specialized structures located at the ends of linear eukaryotic chromosomes that ensure their complete replication and protect them from fusion and degradation, We report here the characterization of the telomeres of the nematode Caenorhabditis elegans, We show that the chromosomes terminate in 4-9 kb of tandem repeats of the sequence TTAGGC, Furthermore, we have isolated clones corresponding to 11 of the 12 C. elegans telomeres, Their subtelomeric sequences are all different from each other, demonstrating that the terminal TTAGGC repeats are sufficient for general chromosomal capping functions, Finally, we demonstrate that the me8 meiotic mutant, which is defective in X chromosome crossing over and segregation, bears a terminal deficiency that was healed by the addition of telomeric repeats, presumably by the activity of a telomerase enzyme. The 11 cloned telomeres represent an important advance for the completion of the physical map and for the determination of the entire sequence of the C. elegans genome. ------------------- Key: 2536 Medline: 96354907 Authors: Maryon EB;Coronado R;Anderson P Title: unc-68 encodes a ryanodine receptor involved in regulating C. elegans body-wall muscle contraction. Citation: Journal of Cell Biology 134: 885-893 1996 Type: ARTICLE Genes: ryr-1 unc-68 nDf18 nDf32 rDf1 rDf2 sDf20 Abstract: Striated muscle contraction is elicited by the release of stored calcium ions through ryanodine receptor channels in the sarcoplasmic reticulum. ryr-1 is a C. elegans ryanodine receptor homologue that is expressed in body-wall muscle cells used for locomotion. Using genetic methods, we show that ryr-1 is the previously identified locus unc-68. First, transposon-induced deletions within ryr-1 are alleles of unc-68. Second, transformation of unc-68 mutants with ryr-1 genomic DNA results in rescue of the Unc phenotype. unc-68 mutants move poorly, exhibiting an incomplete flaccid paralysis, yet have normal muscle ultrastructure. The mutants are insensitive to the paralytic effects of ryanodine, and lack detectable ryanodine-binding activity. The Unc-68 phenotype suggests that ryanodine receptors are not essential for excitation-contraction coupling in nematodes, but act to amplify a (calcium) signal that is sufficient for ------------------- Key: 2537 Medline: 96332462 Authors: Veijola J;Annunen P;Koivunen P;Page AP;Pihlajaniemi T;Kivirikko KI Title: Baculovirus expression of two protein disulphide isomerase isoforms from Caenorhabditis elegans and characterization of prolyl 4-hydroxylases containing one of these Citation: Biochemical Journal 317: 721-729 1996 Type: ARTICLE Genes: Abstract: Protein disulphide isomerase (PDI; EC 5.3.4.1) is a multifunctional polypeptide that is identical to the beta subunit of prolyl 4-hydroxylases. We report here on the cloning and expression of the Caenorhabditis elegans PDI/beta polypeptide and its isoform. The overall amino acid sequence identity and similarity between the processed human and C. elegans PDI/beta polypeptides are 61% and 85% respectively, and those between the C. elegans PDI/beta polypeptide and the PDI isoform 46 % and 73 %. The isoform differs from the PDI/beta and ERp60 polypeptides in that its N-terminal thioredoxin-like domain has an unusual catalytic site sequence -CVHC-. Expression studies in insect cells demonstrated that the C. elegans PDI/beta polypeptide forms an active prolyl 4-hydroxylase alpha(2) beta(2) tetramer with the human a subunit and an alpha beta dimer with the C. elegans a subunit, whereas the C. elegans PDI isoform formed no prolyl 4-hydroxylase with either ct, subunit. Removal of the 32-residue C-terminal extension from the C. elegans alpha subunit totally eliminated alpha beta dimer formation. The C. elegans PDI/beta polypeptide formed less prolyl 4-hydroxylase with both the human and C. elegans alpha subunits than did the human PDI/beta polypeptide, being particularly ineffective with the C. elegans a subunit. Experiments with hybrid polypeptides in which the C-terminal regions had been exchanged between the human and C. elegans PDI/beta polypeptides indicated that differences in the C-terminal region are one reason, but not the only one, for the differences in prolyl 4-hydroxylase formation between the human and C. elegans PDI/beta polypeptides. The catalytic properties of the C. elegans prolyl 4-hydroxylase alpha beta dimer were very similar to those of the vertebrate type II prolyl 4-hydroxylase tetramer, including the K-m for the hydroxylation of long polypeptide substrates. ------------------- Key: 2538 Medline: Authors: Bossinger O;Schierenberg E Title: Cell-cell communication in nematode embyros: differences between Cephalobus spec. and Caenorhabditis elegans. Citation: Dev Genes Evol 206: 25-34 1996 Type: ARTICLE Genes: Abstract: During early nematode embryogenesis a series of asymmetric cleavages in the germ line generates several somatic founder cells and a primordial germ cell. We have found previously that the two soil nematodes Cephalobus spec. and Caenorhabditis elegans express considerable differences in the order of events and spatial arrangement of cells during early embryogenesis. With the help of microinjected fluorescent marker dyes, we show here that these dissimilarities partner major differences in the pattern of intercellular communication. Whilst in C. elegans all early blastomeres become dye-coupled simultaneously, in Cephalobus communication is established progressively in the sequence in which cells are born. In addition, in Cephalobus but not C. elegans, sequential lucifer yellow accumulation indicates stepwise changes in the state of early blastomeres: if injected into the uncleaved zygote, for example, the dye becomes equally distributed to all cells at first but rapid ly accumulates in a single blastomere in the 4-cell stage. We speculate that such a redistribution mechanism may be involved in the differential segregation of cytoplasmic components to individual blastomeres. The most dramatic difference between the two species was found with respect to the transfer of high molecular weight molecules. In contrast to C. elegans, in Cephalobus not only small lucifer dyes but also high molecular weight dextrans can diffuse along specific pathways between early somatic cells indicating the presence of large communication channels. However, a transfer of dextran into or out of germ line cells never takes place. The origin of these channels as midbodies of previous mitoses and their potential role for normal development is discussed. Tissue-specific dye-coupling compartments in the slow developing Cephalobus are established in the same order but at a considerably earlier developmental stage than in C. elegans suggesting that this process may depend more on parameters like available time for transcription rather than the number of cell cycles ------------------- Key: 2539 Medline: 97015112 Authors: Hishida R;Ishihara T;Kondo K;Katsura I Title: hch-1, a gene required for normal hatching and normal migration of a neuroblast in C. elegans, encodes a protein related to TOLLIOD and BMP-1. Citation: EMBO Journal 15: 4111-4122 1996 Type: ARTICLE Genes: hch-1 toh-1 toh-2 mnDf21 Abstract: Proteins of the tolloid/bone morphogenetic protein (BMP)-1 family play important roles in the differentiation of cell fates, Among those proteins are BMP-1, which plays a role in cartilage and bone formation in mammals, the TOLLOID protein, which is required for the establishment of the dorsoventral axis of Drosophila embryos and BP10/SpAN, which are thought to act in the morphogenesis of sea urchins, These proteins have some properties in common, First, they contain the astacin metalloprotease domain, the CUB domain and the epidermal growth factor-like domain, Second, they are expressed in embryos at stages expected for their role in cell differentiation. Third, at least BMP-1 and TOLLOID are thought to interact with proteins of the transforming growth factor-beta family. We report that the hch-1 gene of the nematode Caenorhabditis elegans encodes a tolloid/BMP-1 family protein, The protein has the characteristic domains common to the tolloid/BMP-1 family, Like other members of the family, it is expressed in embryos, However, the phenotype of hch-1 mutants shows that it is required for normal hatching and normal migration of a post-embryonic neuroblast. Furthermore, in spite of its expression in embryogenesis, it is not required for the viability of embryos, These results show new functions of the tolloid/BMP-1 family proteins and give insight into their evolution. ------------------- Key: 2540 Medline: 96382465 Authors: Newman AP;Sternberg PW Title: Coordinated morphogenesis of epithelia during development of the Caenorhabditis elegans uterine-vulva connection. Citation: Proceedings of the National Academy of Sciences USA 93: 9329-9333 1996 Type: ARTICLE Genes: ksr-1 lag-2 let-23 let-60 lin-1 lin-3 lin-11 lin-12 lin-15 lin-25 lin-31 lin-45 mek-2 mpk-1 sem-5 sur-2 Abstract: Development of the nematode egg-laying system requires the formation of a connection between the uterine lumen acid the developing vulval lumen, thus allowing a passage for eggs and sperm. This relatively simple process serves as a model for certain aspects of organogenesis. Such a connection demands that cells in both tissues become specialized to participate in the connection, and that the specialized cells are brought in register, A single cell, the anchor cell, acts to induce and to organize specialization of the epidermal and uterine epithelia, and registrates these tissues, The inductions act via evolutionarily conserved intercellular signaling pathways. The anchor cell induces the vulva from ventral epithelial cells via the LIN-3 growth factor and LET-23 transmembrane tyrosine kinase. It then induces surrounding uterine intermediate precursors via the receptor LIN-12, a founding member of the Notch family of receptors, Both signaling pathways are used multiple times during development of Caenorhabditis elegans, The outcome of the signaling is context-dependent. Both inductions are reciprocated, After the anchor cell has induced the vulva, it stretches toward the induced vulval cells. After the anchor cell has induced specialized uterine intermediate precursor cells, it fuses ------------------- Key: 2541 Medline: 97141231 Authors: Kobayashi H;Ishii N;Nagaoka S Title: Bioprocessing in microgravity: free flow electrophoresis of C. elegans DNA. Citation: Journal of Biotechnology 47: 367-376 1996 Type: ARTICLE Genes: Abstract: Free flow electrophoresis of a nematode C. elegans DNA was carried out on the space shuttle flight STS65/Colombia. During the processes of the experiment, the house keeping data of the FFEU and the electrophoretic migration profiles were monitored at POCC (Payload Operations Control Center) of MSFC (Marshall Space Flight Center, Alabama) according to the real-time down-link system. The three dimensional electropherogram (3DEP) on the basis of the down-linked data showed some trouble with the apparatus but three sequential experiments indicated this disturbance of the apparatus is rather preferably stable. Comparing post-flight analyses of the DNA component fractionated, that is, amplification by PCR method, it revealed that the DNAs were separated approximately into two peaks: one of them contained seven-fold higher content of DNA estimated by a sod-4 gene probe than an unc-6 gene probe. These results suggested that this separation technique could be still more effective for the separation of biological macromolecules such as DNA, and the efficiency of separation of the free flow electrophoresis under ------------------- Key: 2542 Medline: 97008550 Authors: Hope IA;Albertson DG;Martinelli SD;Lynch AS;Sonnhammer E;Durbin R Title: The C. elegans expression pattern database - A beginning. Citation: Trends in Genetics 12: 370-371 1996 Type: ARTICLE Genes: Abstract: Several different biological aspects of the nematode worm, Caenorhabditis elegans, have been thoroughly described. Embryonic and postembryonic development have been described precisely at the cellular level with unique names for each somatic cell (959 in the hermaphrodite and 1031 in the male) created during an individual's lifetime. There is an ordered set of DNA clones covering almost the entire genome and soon the whole genome will have been sequenced. There will then be complete descriptions of this species at both a light microscope level and a molecular genetic level. However, if we are to understand how the one-dimensional genetic information directs the four-dimensional development of the living animal, these two levels of description need to be interconnected. One form of connection is through the genetic map; gene function within the organism is inferred from mutant phenotype. Another more direct connection is through descriptions of when and ------------------- Key: 2543 Medline: 96397419 Authors: Sawa H;Lobel L;Horvitz HR Title: The Caenorhabditis elegans gene lin-17, which is required for certain asymmetric cell divisions, encodes a putative seven-transmembrane protein similar to the Drosophila Frizzled p Citation: Genes & Development 10: 2189-2197 1996 Type: ARTICLE Genes: lin-17 lin-44 Abstract: Mutations in the gene lin-17 result in the disruption of a variety of asymmetric cell divisions in Caenorhabditis elegans. We have found that lin-17 encodes a protein with seven putative transmembrane domains. The LIN-17 protein is most similar to the Drosophila Frizzled protein and its vertebrate homologs. Studies using a lin-17-green fluorescent protein translational fusion indicate that lin-17 is expressed in mother cells before asymmetric cell divisions and in both daughter cells after the divisions. Our results suggest that lin-17 encodes a receptor that regulates the polarities of cells undergoing asymmetric cell divisions and raise the possibility that the LIN-17 protein acts as a receptor for the Wnt protein LIN-44, which also controls asymmetric cell divisions. ------------------- Key: 2544 Medline: 96421643 Authors: Chen W;Chen S;Yap SF;Lim L Title: The Caenorhabditis elegans p21-activated kinase (CePAK) colocalizes with CeRac1 and CDC42Ce at hypodermal cell boundaries during embryo elongation. Citation: Journal of Biological Chemistry 271: 26362-26368 1996 Type: ARTICLE Genes: Abstract: The p21-activated kinase (PAK) is a downstream target of Rac and CDC42, members of the Ras-related Rho subfamily, that mediates signaling pathway leading to cytoskeletal reorganization. To investigate its function in Caenorhabditis elegans development, we have isolated the cDNA coding for the p21-activated kinase homologue (CePAK) from a C. elegarts embryonic cDNA library, This 2.35-kilobase pair cDNA encodes a polypeptide of 572 amino acid residues, with the highly conserved N-terminal p21-binding and the C-terminal kinase domains, Similar to its mammalian and Drosophila counterparts, the CePAK protein expressed in E. coli exhibits binding activity toward GTP-bound CeRac1 and CDC42Ce. Polyclonal antibodies raised against the recombinant CePAK recognize a specific 70-kDa protein from embryonic extracts that displays CeRac1/CDC42Ce-binding and kinase activities, Immunofluorescence analysis indicates that CePAK is specifically expressed at the hypodermal cell boundaries during embryonic body elongation, which involves dramatic cytoskeletal reorganization. Interestingly, CeRac1 and CDC42Ce are found at the same location, which might point to their common involvement in hypodermal cell fusion, a crucial morphogenetic event for nematode development. ------------------- Key: 2545 Medline: 96359191 Authors: Tomlinson MG;Wright MD Title: A new transmembrane 4 superfamily molecule in the nematode, Caenorhabditis elegans. Citation: Journal of Molecular Evolution 43: 312-314 1996 Type: REVIEW Genes: Abstract: Transmembrane 4 superfamily (TM4SF) molecules are predominantly mammalian cell surface glycoproteins that are thought to transduce signals mediating cell development, activation, and motility. Analysis of the Genpept sequence database reveals YKK8, a novel member of the TM4SF in the nematode, Caenorhabditis elegans. YKK8 is a putative 27.4-kDa protein encoded by a gene on chromosome III of the C. elegans genome. The assignment of YKK8 to the TM4SF is justified by three criteria: statistical comparison of protein sequences, conserved TM4SF protein sequence motifs, and conserved TM4SF intron/exon boundaries in the genomic sequence. The discovery of a TM4SF molecule in the nematode extends this superfamily to a more primitive branch of the phylogenetic tree and suggests a fundamental role for TM4SF molecules in biology. ------------------- Key: 2546 Medline: 97039669 Authors: Radice AD;Lustigman S Title: Cloning and characterization of cDNAs encoding putative glutamate transporters from Caenorhabditis elegans and Onchocerca volvulus. Citation: Molecular & Biochemical Parasitology 80: 41-53 1996 Type: ARTICLE Genes: glt-1 Abstract: We report the identification and partial characterization of cDNAs encoding for putative glutamate transporters from the free-living nematode Caenorhabditis elegans and the filarial parasite Onchocerca volvulus. Glutamate transporters can be used as reliable markers for identifying cells and neurons that synaptically release glutamate and aspartate. An amplified PCR fragment containing a highly conserved amino acid heptamer found in all vertebrate glutamate transporters was used to screen a C. elegans cDNA library. Two full-length cDNA sequences from C. elegans were deduced from the isolated cDNA clones and RT-PCR products with the splice leader. The two C. elegans cDNA sequences differ by only 97 nucleotides at the 5' end. The C. elegans glutamate transporter gene glt-1 spans at least 2.9 kb of chromosomal DNA and possesses nine exons and eight introns. Primers directed to the CeGlt cDNA were used with O. volvulus first-strand cDNA to amplify and isolate the O. volvulus cDNA homolog. The C. elegans and O. volvulus glutamate transporters are 98% identical over 492 amino acids to each other and 52 to 58% identical to the mammalian glutamate transporters. Antibodies generated against partial coding regions of the C. elegans glutamate transporter recognized a protein of approximately 66 kDa in C. elegans and O. volvulus protein extracts. ------------------- Key: 2547 Medline: 96391883 Authors: Kaplan JM Title: Sensory signaling in Caenorhabditis elegans. Citation: Current Opinion in Neurology 6: 494-499 1996 Type: REVIEW Genes: glr-1 odr-3 odr-7 odr-10 Abstract: The simple anatomy, behavior, and genetics of the nematode Caenorhabditis elegans make it an attractive organism for studying sensory circuits and their functions in vivo. Recent advances in our understanding of C. elegans sensory signaling stem from work on topographic maps, chemosensory receptors, modality coding, and the integration of antagonistic sensory inputs. ------------------- Key: 2548 Medline: 97042339 Authors: Barnes TM;Hodgkin J Title: The tra-3 sex determination gene of Caenorhabditis elegans encodes a member of the calpain regulatory protease family. Citation: EMBO Journal 15: 4477-4484 1996 Type: ARTICLE Genes: fem-1 fem-2 fem-3 her-1 sdc-1 sdc-3 tra-1 tra-2 tra-3 Abstract: The Caenorhabditis elegans sex determination gene tra-3 is required for the correct sexual development of the soma and germ line in hermaphrodites, while being fully dispensable in males. Genetic analysis of tra3 has suggested that its product may act as a potentiator of another sex determination gene, tra-2. Molecular analysis reported here reveals that the predicted tra-3 gene product is a member of the calpain family of calcium-regulated cytosolic proteases, though it lacks the calcium binding regulatory domain. Calpains are regulatory processing proteases, exhibiting marked substrate specificity, and mutations in the p94 isoform underlie the human hereditary condition limb-girdle muscular dystrophy type 2A. The molecular identity of TRA-3 is consistent with previous genetic analysis which suggested that tra3 plays a very selective modulatory role and is required in very small amounts. Based on these observations and new genetic data, we suggest a refinement of the position of tra-3 within the sex determination cascade and discuss possible mechanisms ------------------- Key: 2549 Medline: 96340934 Authors: Mannen H;Li SSL Title: The lactate dehydrogenase gene from nematode Caenorhabditis elegans contains only two of six introns conserved in the protein-encoding sequence of LDH genes from bird and mammals. Citation: Biochemistry and Molecular Biology International 37: 1057-1061 1996 Type: ARTICLE Genes: Abstract: The protein-encoding region of L-lactate dehydrogenase (LDH) gene from nematode, Caenorhabditis elegans, was amplified by polymerase-chain-reaction from total genomic DNA and its nucleotide sequence determined. A comparison of this genomic sequence with the published sequence of nematode LDH cDNA reveals the presence of two introns of 57 and 47 nucleotides at codon no. 82 and 279-280, respectively. The positions of the two introns present in this invertebrate LDH gene correspond to the second and sixth introns of vertebrate LDH genes. The protein-coding sequence of human LDH-A (muscle),LDH-B (heart) and LDH-C (testis), mouse LDH-A, and duck LDH-B genes has previously been shown to be interrupted by six introns at the ------------------- Key: 2550 Medline: 96421973 Authors: Chin-Sang ID;Spence AM Title: Caenorhabditis elegans sex-determining protein FEM-2 is a protein phosphatase that promotes male development and interacts directly with FEM-3. Citation: Genes & Development 10: 2314-2325 1996 Type: ARTICLE Genes: fem-1 fem-2 fem-3 Abstract: Male sexual development in the nematode Caenorhabditis elegans requires the genes fem-1, fem-2 and fem-3. The current model of sex determination portrays the FEM proteins as components of a novel signal transduction pathway, but the mechanisms involved in signaling through the pathway are not understood. We report the isolation of fem-2 cDNAs in a yeast two-hybrid screen for clones encoding proteins that interact with FEM-3. Association of FEM-3 and FEM-2 in two independent in vitro binding assays substantiates the interaction detected in the two-hybrid system. FEM-2 is related in sequence to protein serine/threonine phosphatases of Type 2C (PP2C). We demonstrate that FEM-2 exhibits magnesium-dependent casein phosphatase activity, typical of PP2C, in vitro. Point mutations that abolish the casein phosphatase activity of FEM-2 without affecting its FEM-3-binding activity reduce severely its ability to rescue male development in fem-2 mutant nematodes. These results suggest that protein phosphorylation regulates sex determination in C. elegans. ------------------- Key: 2551 Medline: 96379720 Authors: Labouesse M;Hartwieg E;Horvitz HR Title: The Caenorhabditis elegans LIN-26 protein is required to specify and/or maintain all non-neuornal ectodermal cell fates. Citation: Development 122: 2579-2588 1996 Type: ARTICLE Genes: lin-26 Abstract: The C. elegans gene lin-26, which encodes a presumptive zinc-finger transcription factor, is required for hypodermal cells to acquire their proper fates. Here we show that lin-26 is expressed not only in all hypodermal cells but also in all glial-like cells. During asymmetric cell divisions that generate a neuronal cell and a non-neuronal cell, LIN-26 protein is symmetrically segregated and then lost from the neuronal cell. Expression in glial-like cells (socket and sheath cells) is biologically important, as some of these neuronal support cells die or seem sometimes to be transformed to neuron-like cells in embryos homozygous for strong loss-of-function mutations. In addition, most of these glial-like cells are structurally and functionally defective in animals carrying the weak loss-of-function mutation lin-26(n156). lin-26 mutant phenotypes and expression patterns together suggest that lin-26 is required to specify and/or maintain the fates not only of hypodermal cells but also of all other non-neuronal ectodermal cells in C. elegans. We speculate that lin-26 ------------------- Key: 2552 Medline: 96379743 Authors: Sundaram M;Yochem J;Han M Title: A Ras-mediated signal transduction pathway is involved in the control of sex myoblast migration in Caenorhabditis elegans. Citation: Development 122: 2823-2833 1996 Type: ARTICLE Genes: dig-1 egl-15 egl-17 ksr-1 let-23 let-60 let-537 lin-1 lin-3 lin-31 lin-45 mek-2 mpk-1 sem-5 sur-1 Abstract: Sex myoblast migration in the Caenorhabditis elegans hermaphrodite represents a simple, genetically amenable model system for studying how cell migration is regulated during development. Two separable components of sex myoblast guidance have been described: a gonad-independent mechanism sufficient for the initial anterior migration to the mid-body region, and a gonad-dependent mechanism required for precise final positioning (J. H. Thomas, M. J. Stern and H. R. Horvitz (1990) Cell 62, 1041-1052). Here, we demonstrate a role for a Ras-mediated signal transduction pathway in controlling sex myoblast migration. Loss-of-function mutations in let-60 ras, ksr-1, lin-45 raf, let-537/mek-2 or sur-1/mpk-1 cause defects in sex myoblast final positions that resemble those seen in gonad-ablated animals, while constitutively active let-60 ras (G13E) transgenes allow fairly precise positioning to occur in the absence of the gonad. A mosaic analysis demonstrated that let-60 ras is required within the sex myoblasts to control proper positioning. Our results suggest that gonadal signals normally stimulate let-60 ras activity in the sex myoblasts, thereby making them competent to sense or respond to positional cues that determine the precise endpoint of migration. let-60 ms may have additional roles in sex myoblast guidance as well. Finally, we have also investigated genetic interactions between let-60 ras and other genes important for sex myoblast migration, including egl-15, which encodes a fibroblast growth factor receptor tyrosine kinase (D. L. DeVore, H. R. Horvitz and M. J. Stern (1995) Cell 83, 611-623). Since mutations reducing Ras pathway activity cause a different phenotype than those reducing egl-15 activity and since constitutive Ras activity only partially suppresses the migration defects of egl-15 mutants, we argue that let-60 ms and egl-15 do not act together in a ------------------- Key: 2553 Medline: Authors: Borgonie G;Claeys M;Leyns F;Arnaut G;De Waele D;Coomans A Title: Effect of nematicidal Bacillus thuringiensis strains on free-living nematodes. 2. Ultrastructural analysis of the intoxication process in Caenorhabditis elegans. Citation: Fundamental and Applied Nematology 19: 407-414 1996 Type: ARTICLE Genes: Abstract: Transmission electron microscopy is used to describe the intoxication in Caenorhabditis elegans, feeding on toxic spore/crystals of Bacillus thuringiensis. The toxin acts directly against the intestine, first by affecting the anteriormost ring of four intestinal cells. Over a period of 12 hours, these cells lose much of their volume, the microvilli regress slowly, several cell organelles undergo dramatic change and are ultimately destroyed. No rupture of the apical intestinal cell membrane is observed. Non-intestinal tissues seem unaffected. This study indicates considerable ultrastructural differences in the mode of action between the nematicidal toxin and the insecticidal crystal toxins from B. thuringiensis. ------------------- Key: 2554 Medline: Authors: Van Voorhies WA Title: Bergmann size clines: A simple explanation for their occurrence in ectotherms. Citation: Evolution 50: 1259-1264 1996 Type: ARTICLE Genes: Abstract: In general ectothermic organisms grow larger at both lower temperatures and higher latitudes. Adult size in the soil nematode Caenorhabditis elegans reared at 10C was approximately 33% greater than worms grown at 25C. Nematode egg size and fish red blood cell size showed similar size increases at lower temperatures. These results indicate that body size differences in many ectotherms may simply be a consequence of developmental processes that cause cells to grow larger at lower temperatures. This would provide a general explanation for the increased size of ectotherms at lower temperatures ------------------- Key: 2555 Medline: 97061205 Authors: Suzuki N;Inokuma K;Yasuda K;Ishii N Title: Cloning, sequencing and mapping of a manganese superoxidedismutase gene of the nematode Caenorhabditis elegans. Citation: DNA Research 3: 171-174 1996 Type: ARTICLE Genes: sod-2 sod-3 Abstract: We have cloned, sequenced and mapped a gene (sod-2) encoding manganese superoxide dismutase [EC 1.15.1.1] from the nematode Caenorhabditis elegans. The sod-2 was mapped to chromosome I by hybridization with a YAC polytene filter. The protein-coding region spans 1129 base pairs including 4 introns and encodes a protein of 221 amino acids (aa) (Mr = 24536) of which the first 24 aa are the presumed mitochondrial-targeting signal peptide. The gene sequence of sod-2 was slightly different from an isoform, ------------------- Key: 2556 Medline: Authors: Kushibiki Y;Ishii N;Yanase S;Nakazawa H Title: Molecular cloning of oxygen-inducible genes in Caenorhabditis elegans by RT-PCR differential display. Citation: Pathophysiology 3: 107-110 1996 Type: ARTICLE Genes: oxi-1 sod-1 Abstract: To investigate the genetic response to oxidative stress in eukaryotic cells, we have applied the method RT-PCR differential display to the small, free-living nematode Caenorhabditis elegans (C. elegans) which was cultured under atmospheric or high oxygen concentrations. As a result, a new gene was cloned whose expression increased at high oxygen concentration. ------------------- Key: 2557 Medline: 97069944 Authors: Grauso M;Culetto E;Berge J-B;Toutant J-P;Arpagaus M Title: Sequence comparison of ACE-1, the gene encoding acetylcholinesterase of class A, in the two nematodes Caenorhabditis elegans and Caenorhabditis briggsae. Citation: DNA Sequence 6: 217-227 1996 Type: ARTICLE Genes: ace-1 Abstract: The ace-1 gene, which encodes acetylcholinesterase of class A, has been cloned and sequenced in C. briggsae and compared to its homologue in C. elegans. Both genes present an open reading frame of 1860 nucleotides. The percentage of identity are 80% and 95% at the nucleotide and amino acid levels respectively. All residues characteristic of an acetylcholinesterase are found in conserved positions in C. briggsae ACE-1. The deduced C-terminus is hydrophilic, thus resembling the catalytic peptide T of vertebrate cholinesterases. Codon usage in both ace-1 genes appears to be lowly biased. This may indicate that these genes are lowly expressed. The splicing sites of the eight introns of ace-1 in C. elegans are conserved in C. briggsae, but introns are shorter in C. briggsae. No homology was found between intronic sequences in both species, except for the consensus border sequences. ------------------- Key: 2558 Medline: 97080778 Authors: Benian GM;Tang X;Tinley TL Title: Twitchin and related giant IG superfamily members of C. elegans and other invertebrates. Citation: Advanced Biophysics 33: 183-197 1996 Type: REVIEW Genes: unc-22 unc-89 Abstract: During the past 7 years, it has become apparent that the myofilament lattice of invertebrates possess very large (>700,000 Da) polypeptides consisting primarily of immunoglobulin (Ig) and fibronectin type III (FnIII) domains. The founding member of this group was C. elegans twitchin, encoded by the mutationally defined gene unc-22. Twitchin, located in the thick filament containing A-bands, functions both in regulating muscle contraction, and in the final stages of sarcomere assembly. Genetic analysis of unc-22 provided important clues as to the function of twitchin before the gene was cloned and sequenced. The sequence provided the first example of an intracellular protein which belonged to the Ig superfamily. Although the substrate for nematode twitchin is not known, it has been shown to be autoinhibited by 60 amino acid residues lying just C-terminal to the kinase catalytic core. The structural basis for this autoinhibition has been determined by solving the crystal structure of twitchin kinase. Similar proteins have been discovered in honeybees, Lethocerus, scallop, Drosophila, and Aplysia. The similar protein in Drosophil, called projectin, is present in two isoforms, encoded by a single gene. A smaller polypeptide is located in the I-bands of asynchronous muscles, and a larger polypeptide is located in the A-bands of synchronous muscles. Both isoforms appear to have protein kinase activity. Homozygous mutations in the projectin gene result in embryonic or larval lethality, indicating an essential role in muscle ------------------- Key: 2559 Medline: 97044451 Authors: de Bono M;Hodgkin J Title: Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences. Citation: Genetics 144: 587-595 1996 Type: ARTICLE Genes: tra-1 Abstract: The tra-1 gene is a terminal regulator of somatic sex in Caenorhabditis elegans: high tra-1 activity elicits female development, low tra-l activity elicits male development. To investigate the function and evolution of tra-l, we examined the tra-l gene from the closely related nematode C. briggsae. Ce-tra-1 and Cb-tra-1 are unusually divergent. Each gene generates two transcripts, but only one of these is present in both species. This common transcript encodes TRA-1A, which shows only 44% amino acid identity between the species, a figure much lower than that for previously compared genes. A Cb-tra-1 transgene rescues many tissues of tra-1(null) mutants of C. elegans but not the somatic gonad or germ line. This transgene also causes nongonadal feminization of XO animals, indicating incorrect sexual regulation. Alignment of Ce-TRA-1A and Cb-TRA-1A defines several conserved regions likely to be important for tra-1 function. The phenotypic differences between Ce-tra-l(null) mutants rescued by Cb-tra-1 transgenes and wild-type C. elegans indicate significant divergence of regulatory regions. These molecular and functional studies suggest that evolution of sex determination in nematodes is rapid and genetically complex. ------------------- Key: 2560 Medline: 97044452 Authors: Kuwabara PE Title: Interspecies comparison reveals evolution of control regions in the nematode sex-determining gene tra-2. Citation: Genetics 144: 597-607 1996 Type: ARTICLE Genes: tra-2 Abstract: The Caenorhabditis elegans sex-determining gene tra-2 promotes female development and expresses 4.7-, 1.9- and 1.8kb mRNAs. The 4.7-kb mRNA encodes the major feminizing activity of the locus, a predicted membrane receptor that mediates cell-to-cell communication, named TRA-2A. The tra-2 gene was characterized from a close relative, C. briggsae. The Cb-tra-2 gene expresses only a 4.7-kb mRNA and alternatively spliced variants, which encode TRA-2A homologues. The Cb-TRA-2A and Ce-TRA-2A sequences are highly diverged, sharing only $3% identity, although their hydropathy profiles remain remarkably similar. Three potential regulatory sites of Ce-Cra-2 activity were previously identified by analyzing tra-2(eg), tra-2(gf), and tra-2(mx) mutations. Two of these sites, the EG site and MX region, are conserved in Cb-tra-2. By contrast, the two direct repeat elements in the Ce-tra-2 3' untranslated region, which are disrupted in tra-(gf) mutants, are absent. Injection of Cb-tra-2 antisense RNA into C. briggsae mimics the Ce-tra-2 loss-of-function phenotype. Thus, antisense RNA permits studies of gene activity in nematodes that lack extensive genetics. ------------------- Key: 2561 Medline: 97044453 Authors: Browning H;Berkowitz L;Madej C;Paulson JE;Zolan ME;Strome S Title: Macrorestriction analysis of Caenorhabditis elegans genomic DNA. Citation: Genetics 144: 609-619 1996 Type: ARTICLE Genes: dpy-5 let-352 let-362 let-363 let-371 lin-29 mes-1 mes-3 spe-11 unc-38 unc-52 hDf6 hDp24 hDp29 hDp31 hDp76 Abstract: The usefulness of genomic physical maps is greatly enhanced by linkage of the physical map with the genetic map. We describe a ''macrorestriction mapping'' procedure for Caenorhabditis elegans that we have applied to this endeavor. High molecular weight, genomic DNA is digested with infrequently cutting restriction enzymes and size-fractionated by pulsed field gel electrophoresis. Southern blots of the gels are probed with clones from the C. elegans physical map. This procedure allows the construction of restriction maps covering several hundred kilobases and the detection of polymorphic restriction fragments using probes that map several hundred kilobases away. We describe several applications of this technique. (1) We determined that the amount of DNA in a previously uncloned region is <220 kb. (2) We mapped the mes-l gene to a cosmid, by detecting polymorphic restriction fragments associated with a deletion allele of the gene. The 25-kb deletion was initially detected using as a probe sequences located similar to 400 kb away from the gene. (3) We mapped the molecular endpoint of the deficiency hDf6, and determined that three spontaneously derived duplications in the unc-38-dpy-5 region have very complex molecular structures, containing internal rearrangements and deletions. ------------------- Key: 2562 Medline: 96394689 Authors: Wang W;Shakes DC Title: Molecular evolution of the 14-3-3 protein family. Citation: Journal of Molecular Evolution 43: 384-398 1996 Type: ARTICLE Genes: ftt-1 ftt-2 Abstract: Members of the highly conserved and ubiquitous 14-3-3 protein family modulate a wide variety of cellular processes. To determine the evolutionary relationships among specific 14-3-3 proteins in different plant, animal, and fungal species and to initiate a predictive analysis of isoform-specific differences in light of the latest functional and structural studies of 14-3-3, multiple alignments were constructed from forty-six 14-3-3 sequences retrieved from the GenBank and SwissProt databases and a newly identified second 14-3-3 gene from Caenorhabditis elegans. The alignment revealed five highly conserved sequence blocks. Blocks 2-5 correlate well with the alpha helices 3, 5, 7, and 9 which form the proposed internal binding domain in the three-dimensional structure model of the functioning dimer. Amino acid differences within the functional and structural domains of plant and animal 14-3-3 proteins were identified which may account for functional diversity amongst isoforms. Protein phylogenic trees were constructed using both the maximum parsimony and neighbor joining methods of the PHYLIP(3.5c) package; 14-3-3 proteins from Entamoeba histolytica, an amitochondrial protozoa, were employed as an outgroup in our analysis. Epsilon isoforms from the animal lineage form a distinct grouping in both trees, which suggests an early divergence from the other animal isoforms. Epsilons were found to be more similar to yeast and plant isoforms than other animal isoforms at numerous amino acid positions, and thus epsilon may have retained functional characteristics of the ancestral protein. The known invertebrate proteins group with the nonepsilon mammalian isoforms. Most of the current 14-3-3 isoform diversity probably arose through independent duplication events after the divergence of the major eukaryotic kingdoms. Divergence of the seven mammalian isoforms beta, zeta, gamma, eta, epsilon, tau, and sigma (stratifin/HME1) occurred before the divergence of mammalian and perhaps before the divergence of vertebrate species. A possible ------------------- Key: 2563 Medline: Authors: Brownlee DJA;Fairweather I;Holden-Dye L;Walker RJ Title: Nematode neuropeptides: Localization, isolation and functions. Citation: Parasitology Today 12: 343-351 1996 Type: REVIEW Genes: flp-1 flp-2 flp-3 flp-4 Abstract: Historically, peptidergic substances (in the form of neurosecretions) were linked to moulting in nematodes. More recently, there has been a renewal of interest in nematode neurobiology, initially triggered by studies demonstrating the localization of peptide immunoreactivities to the nervous system. Here, David Brownlee, Ian Fairweather, Lindy Holden-Dye and Robert Walker will review progress on the isolation of nematode neuropeptides and efforts to unravel their physiological actions and inactivation mechanisms. Future avenues for research are suggested and the potential exploitation of peptidergic pathways in future therapeutic strategies ------------------- Key: 2564 Medline: 96427384 Authors: Fukushige T;Schroeder DF;Allen FL;Goszczynski B;McGhee JD Title: Modulation of gene expression in the embryonic digestive tract of C. elegans. Citation: Developmental Biology 178: 276-288 1996 Type: ARTICLE Genes: ges-1 mex-1 pha-4 pie-1 pop-1 skn-1 Abstract: The Caenorhabditis elegans digestive tract is composed of four distinct modules derived from separate cell lineages: anterior pharynx from the ABa lineage, posterior pharynx from the MS lineage, gut from tile E lineage, and rectum from the ABp lineage. The C. elegans gut esterase gene (ges-1) is normally expressed in the embryonic gut or E lineage. However, expression of ges-1 can be switched into cells of the embryonic pharynx and tail by virtue of deleting a tandem pair of WGATAR sites in the ges-1 promoter, Here, we use both laser ablation experiments and genetic analysis to show that cells expressing the WGATAR-deleted ges-1 transgene belong to all three nongut lineages of the digestive tract: ABa, MS, and ABp. We also show that the molecular size and spatial distribution of ges-1 mRNA transcripts produced by either the WGATAR-deleted ges-1 transgene or the undeleted ges-l control transgene appear correctly regulated, suggesting that the spatial switch in ges-1 expression occurs at the level of transcription initiation. We further show that both the WGATAR-deleted and the undeleted ges-1 transgenes respond appropriately to mutations in a series of maternal effect genes (skn-1, mex-1, pie-1, and pop-1) that alter early blastomere fate. Moreover, the pharynx/tail expression of the WGATAR-deleted ges-1 transgene is abolished by mutations in the zygotic gene pha-4. Finally, we use imprecise transposon excision to produce two independent C, elegans strains with 1- to 2-kb deletions that remove the tandem WGATAR sites from the promoter of the endogenous chromosomal I gene: in both of these strains, ges-1 is not expressed in the embryonic gut but is expressed in cells of the embryonic pharynx; pharynx expression is weak but incontrovertible, Overall, our results validate previous transgenic analysis of ges-1 control and show further that ges-1 appears to be regulated in a system-specific, rather than a lineage-specific, manner. The multiple facets of ges-l expression provide an opportunity to investigate how a multicomponent organ system such as the digestive tract is established from ------------------- Key: 2565 Medline: 96427385 Authors: Azzaria M;Goszczynski B;Chung MA;Kalb JM;McGhee JD Title: A fork head/HNF-3 homolog expressed in the pharynx and intestine of the Caenorhabditis elegans embryo. Citation: Developmental Biology 178: 289-303 1996 Type: ARTICLE Genes: fkh-1 lin-31 pes-1 Abstract: We have cloned a member of the fork head/HNF-3 family of transcription factors from the nematode Caenorhabditis elegans. Within the predicted DNA binding domain, this gene, called Ce-Fkh-1, is 75-78% identical to the Drosophila fork head and rat liver HNF-3 alpha, beta, and gamma genes. Ce-Fkh-1 mRNA is highly enriched in embryos. The Ce-Fh-1 gene produces three major transcripts: the longest mRNA retains its original 5'-end but two shorter mRNAs are trans-spliced at the beginning of exons 2 and 3, respectively. In situ hybridization and transgenic Ce-Fkh-1::lacZ reporter constructs indicate that the Ce-Fh-1 gene is expressed in both pharynx and intestine of the embryo, beginning at the midproliferation stage. A second phase of Ce-Fh-1 expression occurs in cells of the larval somatic gonad. The pharynx-gut expression of Ce-Fkh-1 in the C. elegans embryo is compared with expression of fork head throughout the gut of Drosophila embryos and with expression of HNF-3 (alpha beta gamma) in the endoderm of mammalian embryos. Such conserved patterns of gene expression point to universal features of gastrulation and of digestive tract formation. ------------------- Key: 2566 Medline: 96427387 Authors: Agostoni E;Albertson D;Wittmann C;Hill F;Tobler H;Muller F Title: cec-1, a soma-specific chromobox-containing gene in C. elegans. Citation: Developmental Biology 178: 316-326 1996 Type: ARTICLE Genes: cec-1 Abstract: The chrome domain is a phylogenetically conserved sequence motif which was identified as a region of homology between the repressor protein Pc and the heterochromatin constitutive protein HP1 of Drosophila. The specific function of the chromo domain is not yet understood, but it seems to be required for protein-protein interactions in chromatin-associated complexes. Here, we present a new chromobox-containing gene from Caenorhabditis elegans (cec-1). It encodes a nuclear protein that is present in all somatic cells from the 50- to 80-cell stage on throughout development and in adult animals. No cec-1 protein was detected in the cells of early embryos, in germ cells, and in their precursor cells Z2 and Z3. cec-1 mRNA, however, is already present in all the blastomeres of early embryos. Immunolocalization experiments revealed a homogeneous distribution of CEC-1 within interphase nuclei, while during mitosis CEC-1 seems to dissociate from the condensing chromosomes. The expression pattern of the cec-1 gene suggests that it may represent a new regulatory gene in C. elegans. ------------------- Key: 2567 Medline: 96427398 Authors: Powell-Coffman JA;Knight J;Wood WB Title: Onset of C. elegans gastrulation is blocked by inhibition of embryonic transcription with an RNA polymerase antisense RNA. Citation: Developmental Biology 178: 472-483 1996 Type: ARTICLE Genes: ama-1 emb-16 her-1 vet-6 Abstract: Cleavage and gastrulation initiation in Caenorhabditis elegans embryos are characterized by an invariant temporal and spatial pattern of cell divisions and cell movements. Although bulk embryonic transcription does not begin until gastrulation onset, some transcription can be detected as early as the 4-cell stage. To determine whether any early transcripts are required for normal cleavage-stage patterning, we blocked transcription in embryos by injecting hermaphrodite parental gonads with RNA antisense to the ama-1 gene, which encodes the large subunit of RNA polymerase II. This treatment no prevented the expression of a reporter gene driven by an early embryonic promoter but did not detectably perturb the maternally controlled segregation of the germ line P granules or the pattern of cell division through the first four cleavages. in the fifth cell cycle, however, the two endodermal precursor (E) cells divided early and abnormally and failed to initiate gastrulation. The embryos arrested between the sixth and seventh cell cycles with less than 100 cells. These results indicate that embryonically transcribed gene products are required for gastrulation initiation. They also demonstrate the efficacy of a method for blocking embryonic transcription that may be useful in other organisms. ------------------- Key: 2568 Medline: Authors: Terrill WF;Dusenbery DB Title: Threshold chemosensitivity and hypothetical chemoreceptor function of the nematode Caenorhabditis elegans. Citation: Journal of Chemical Ecology 22: 1463-1475 1996 Type: ARTICLE Genes: Abstract: The behavioral responses by the nematode Caenorhabditis elegans to 12 organic compounds was explored using tethered nematode and computer tracking methods. Results indicate that the nematode is attracted to acetone, diethyl ether, isoamyl acetate, isoamyl alcohol, 2,4-pentanedione, and n-propanol. No responses were detected to acetaldehyde, acetylcholine, ethanol, formaldehyde, i-propanol, and valerate. Isoamyl acetate and acetone were found to be the most potent attractants eliciting minimal responses at concentrations near 10(-10) M. The geometry and charge distribution of a single hypothetical receptor that would interact with all the compounds that elicited a response and none of the compounds that failed to elicit a response is explored. ------------------- Key: 2569 Medline: 97065632 Authors: Ingham PW Title: Has the quest for a Wnt receptor finally frizzled out? Citation: Trends in Genetics 12: 382-384 1996 Type: REVIEW Genes: Abstract: In the 15 years since they were first discovered, Wnt proteins have emerged as one of the pre-eminent families of signalling molecules in animal development. Everything, from axis specification to kidney development, from the polarity of a mouse limb to the polarity of a nematode cell division, apparently depends one way or another on the activity of these secreted factors. Yet, while the discovery and characterization of Wnt genes has continued apace, progress in discovering how Wnt signals are received and interpreted has been rather less impressive. When confronted with their failure to identify a receptor, Wnt aficionados are quick to point to the notorious difficulty in obtaining soluble forms of these proteins as the principal obstacle to their progress. Recognizing this problem, Roel Nusse took the inspired step of switching to Drosophila to study Wnt signalling. The reasoning was simple: if only a Wnt gene could be discovered in the fly, it should be relatively trivial to use the sophisticated genetics of Drosophila to identify mutations in the reception pathway. Now, some 10 years later, genetic analysis has, indeed, led Nusse and his colleagues to a putative Wnt receptor-but the route has been rather less direct than might originally have been anticipated. ------------------- Key: 2570 Medline: 97027423 Authors: Crowder CM;Shebester LD;Schedl T Title: Behavioral effects of volatile anesthetics in Caenorhabditis elegans. Citation: Anesthesiology 85: 901-912 1996 Type: ARTICLE Genes: dpy-11 fog-2 unc-51 Abstract: Background: The nematode Caenorbabditis elegans offers many advantages as a model organism for studying volatile anesthetic action It has a simple, web-understood nervous system; it allows the researcher to do forward genetics; and its genome will soon be completely sequenced. C. elegans is immobilized by volatile anesthetics only at high concentrations and with an unusually slow time course. Here other behavioral dysfunctions are considered as anesthetic endpoints in C. elegans. Methods: The potency of halothane for disrupting eight different behaviors was determined by logistic regression of concentration and response data. Other volatile anesthetics were also tested for some behaviors. Established protocols were used for behavioral endpoints that, except for pharyngeal pumping, were set as complete disruption of the behavior. Time courses were measured for rapid behaviors. Recovery from exposure to 1 or 4 vol% halothane was determined for mating, chemotaxis, and gross movement. All experiments were performed at 20 to 22 degrees C. Results: The median effective concentration values for halothane inhibition of mating (0.30 vol% - 0.21 mM), chemotaxis (0.34 vol% - 0.24 mM), and coordinated movement (0.32 vol% - 0.23 mM) were similar to the human minimum alveolar concentration (MAC; 0.21 mM). in contrast, halothane produced immobility with a median effective concentration of 3.65 vol% (2.6 mM). Other behaviors had intermediate sensitivities. Halothane's effects reached steady-state in 10 min for all behaviors tested except immobility, which required 2 h. Recovery was complete after exposure to 1 vol% halothane but was significantly reduced after exposure to immobilizing concentrations. Conclusions: Volatile anesthetics selectively disrupt C. elegans behavior. The potency, time course, and recovery characteristics of halothane's effects on three behaviors are similar to its anesthetic properties in vertebrates. The affected nervous system molecules may express structural moths similar to those on vertebrate anesthetic ------------------- Key: 2571 Medline: 97015075 Authors: Chan SS-Y;Zheng H;Su M-W;Wilk R;Killeen MT;Hedgecock EM;Culotti JG Title: UNC-40, a C. elegans homolog of DCC (deleted in colorectal cancer), is required in motile cells responding to UNC-6 netrin cues. Citation: Cell 87: 187-195 1996 Type: ARTICLE Genes: unc-5 unc-6 unc-40 Abstract: UNC-6 netrin, a laminin-related protein secreted from neuroglia and neurons along the ventral midline, orients migrating cells and pioneering growth cones on the nematode epidermis. UNC-5, a cell surface protein expressed on motile cells and pioneer axons, orients movements away from UNC-6 sources. UNC-40, a homolog of the cell surface proteins DCC (Deleted in Colorectal Cancer) and neogenin, is also expressed on motile cells and pioneer neurons. UNC-40 acts cell autonomously to orient movement toward UNC-6 sources. For cells coexpressing UNC-5, it helps orient movement away from UNC-6 sources. Finally, UNC-40 helps determine the dorsoventral position of cells undergoing purely longitudinal migrations. Together with the recent report that DCC is a netrin receptor in vertebrates, our results suggest that UNC-40 is a component of UNC-6 receptors on motile cells. ------------------- Key: 2572 Medline: 97015077 Authors: Draper BW;Mello CC;Bowerman B;Hardin J;Priess JR Title: MEX-3 is a KH domain protein that regulates blastomere identity in early C. elegans embryos. Citation: Cell 87: 205-216 1996 Type: ARTICLE Genes: apx-1 glp-1 mex-3 pal-1 par-1 pie-1 skn-1 hDf10 Abstract: After the first division of the C. elegans embryo, the posterior blastomere can produce numerous muscles while the anterior blastomere cannot. We show here that maternal-effect lethal mutations in the gene mex-3 cause descendants of the anterior blastomere to produce muscles by a pattern of development similar to that of a descendant of the wild-type posterior blastomere. mex-3 encodes a probable RNA-binding protein that is distributed unequally in early embryos and that is a component of germline-specific granules called P granules. We propose that MEX-3 contributes to anterior-posterior asymmetry by regulating one or more mRNAs involved in specifying the fate of the posterior blastomere. ------------------- Key: 2573 Medline: 97015078 Authors: Hunter CP;Kenyon C Title: Spatial and temporal controls target pal-1 blastomere-specification activity to a single blastomere lineage in C. elegans embryos. Citation: Cell 87: 217-226 1996 Type: ARTICLE Genes: mex-3 pal-1 par-1 pie-1 skn-1 smg-3 vab-7 Abstract: The early asymmetric cleavages of Caenorhabditis elegans embryos produce blastomeres with distinct developmental potentials. Here, we show that the caudal-like homeodomain protein PAL-1 is required to specify the somatic identity of one posterior blastomere in the 4 cell embryo. We find that pal-1 activity is sequentially restricted to this blastomere. First, at the 4 cell stage, it is translated only in the two posterior blastomeres. Then, its function is restricted to one of these blastomeres. This second targeting step is dependent on the activities of the posteriorly localized SKN-1 and asymmetrically segregated PIE-1 proteins. We propose that the segregation of PIE-1, combined with the temporal decay of SKN-1, targets pal-1 activity to this posterior lineage, thus coupling the regulation of this conserved posterior patterning gene to asymmetric cell cleavages. ------------------- Key: 2574 Medline: 97045823 Authors: Bigot Y;Auge-Gouillou C;Periquet G Title: Computer analyses reveal a hobo-like element in the nematode Caenorhabditis elegans, which presents a conserved transposase domain common with the Tc1-Mariner transposon family. Citation: Gene 174: 265-271 1996 Type: ARTICLE Genes: Abstract: The present report describes the use of computer analyses to reveal a hobo-like element in the genome of Caenorhabditis elegans. This hobo-like sequence is 3039 bp long, contains two inverted terminal repeats of 25-27 bp and probably does not encoded a functional transposase. Sequence comparisons suggest that each transposase of hobo elements probably has a D(D/S)E motif. Thus the transposases of the hAT superfamily of transposons appear to be close to the other transposases and intregrases. ------------------- Key: 2575 Medline: 97094001 Authors: Sassa T;Ogawa H;Kimoto M;Hosono R Title: The synaptic protein UNC-18 is phosphorylated by protein kinase C. Citation: Neurochemistry International 29: 543-552 1996 Type: ARTICLE Genes: unc-18 Abstract: The C. elegans unc-18 encoded protein UNC-18 is implicated in the interactions between synaptic vesicles and presynaptic plasma membrane. To further characterize the neural protein, we investigated the phosphorylation in vitro of the protein expressed in Spodoptera frugiperda Sf21 cells. The UNC-18 protein is selectively phosphorylated by protein kinase C (PKC) but not by casein kinase II and cyclic AMP-dependent protein kinase. The presumed phosphorylation sites determined by manual Edman degradation were serine-2, serine-322, threonine-462 and serine-515, of which the last is highly conserved as a consensus phosphorylation site for PKC in Drosophila and the mammalian homologue. Phosphorylated UNC-18 extracted from C. elegans was also detected, indicating that it has a physiological role in intact nerve terminals. Therefore, the phosphorylation by PKC may play a physiological role in the regulation. ------------------- Key: 2576 Medline: Authors: Sommer RJ;Carta LK;Kim SY;Sternberg PW Title: Morphological, genetic and molecular description of Pristionchus pacificus sp. n. (Nematoda: Citation: Fundamental and Applied Nematology 19: 511-521 1996 Type: ARTICLE Genes: let-60 Abstract: We describe a new free-living hermaphroditic nematode, Pristionchus pacificus sp. n. (Neodiplogastridae) that will be useful for genetic, developmental and molecular biological studies. P. pacificus sp. n. has six chromosomes, a three day generation time and is easily cultured. Forty-eight morphological mutations are described indicating the genetic accessibility. Molecular studies have been initiated with the generation of a genomic and a cDNA library and the cloning of the homologue of the Caenorhabditis elegans let-60 ras gene. ------------------- Key: 2577 Medline: 97066809 Authors: Barinaga M Title: Mutant mice and worms help solve mysteries of olfaction. Citation: Science 274: 500-501 1996 Type: REVIEW Genes: Abstract: Geoffrey Gold, a physiologist at the Monell Chemical Senses Center in Philadelphia, had wanted for years to put to rest a nagging question: How do odors trigger olfactory neurons to fire off action potentials to the brain? The dogma for the past 5 years had been that odors fall into two catagories, each of which acts via a different inracellular messenger molecule. But Gold believed this view was wrong, and that all odors work by increasing the production of the intracellular messenger cyclic AMP (cAMP). One day last spring, Gold got a phone call out of the blue from neurobiologist John Ngai, at the University of California (UC), Berkeley, offering the possibility of answering this question. "It was my dream come true," says Gold. ...... ------------------- Key: 2578 Medline: 97040380 Authors: Lithgow G Title: Invertebrate gerontology: the age mutations of Caenorhabditis elegans. Citation: BioEssays 18: 809-815 1996 Type: REVIEW Genes: age-1 clk-1 daf-2 daf-23 daf-28 rad-8 spe-26 Abstract: Ageing is a complex phenomenon which remains a major challenge to modern biology. Although the evolutionary biology of ageing is well understood, the mechanisms that limit lifespan are unknown. The isolation and analysis of single-gene mutations which extend lifespan (Age mutations) is likely to reveal processes which influence ageing. Caenorhabditis elegans is the only metazoan in which Age mutations have been identified. The Age mutations not only prolong life, but also confer a complex array of other phenotypes. Some of these phenotypes provide clues to the evolutionary origins of these genes while others allude to mechanisms of lifespan-extension, Many of the Age genes interact and share a second common phenotype, that of stress resistance. Rather than invertebrate ageing being determined by a 'clock mechanism', a picture is emerging of ageing as a non-adaptive process determined, in part, by resistance to intrinsic stress mediated by stress-response ------------------- Key: 2579 Medline: 96393179 Authors: Hamill OP;McBride DW Title: A supramolecular complex underlying touch sensitivity. Citation: Trends in Neurosciences 19: 258-261 1996 Type: REVIEW Genes: deg-1 mec-1 mec-2 mec-4 mec-5 mec-6 mec-7 mec-9 mec-10 mec-12 Abstract: Touch sensitivity in humans is dependent on highly specialized cutaneous nerve endings encapsulated in elaborate cellular structures such as the Pacinian, Ruffini and Meissner's corpuscles. Although the details of the encapsulations vary, the common theme involves the nerve endings making intimate mechanical linkages with the collagen-fiber networks contained within each capsule. Presumably, it is these external linkages with the membrane that serve to transmit and focus mechanical energy onto the mechanotransducers located in the nerve endings, and thus contribute to their low threshold and high mechanosensitivity. Extracellular mechanical linkages are also a feature of specific touch sensors in lower invertebrates, and thus appear to have evolved early in the animal kingdom. Indeed, it seems wherever high mechanosensitivity is required external mechanical linkages are present. In contrast, pain sensation, which is characterized by high threshold and low mechanosensitivity, is mediated by naked or free nerve endings, which lack elaborate external structures. Despite the existence of detailed ultrastructural information, the general inaccessibility of vertebrate touch and pain receptors has hampered studies on the molecules and molecular interactions underlying mechanotransduction in these cells. However, recent molecular-genetic analysis of touch-insensitive mutants in the tiny, free-swimming round worm, Caenorhabditis elegans, carried out by Martin Chalfie and colleagues, has begun to reveal detailed information on the molecular machinery of mechanotransduction. This information should provide useful clues and general principles for unravelling the molecular mechanisms underlying our own sensations of touch and pain. ------------------- Key: 2580 Medline: 97094610 Authors: Seydoux G Title: Mechanisms of translational control in early development. Citation: Current Opinion in Genetics & Development 6: 555-561 1996 Type: REVIEW Genes: fem-3 glp-1 pal-1 tra-2 Abstract: Oocytes accumulate a dowry of maternal mRNAs in preparation for embryogenesis. These maternal transcripts are kept dormant until late oogenesis or early embryogenesis when their translation is activated. In recent years, three types of translational control acting on maternal mRNAs have emerged: translational activation by cytoplasmic polyadenylation, translational activation by RNA localization, and regulated translational repression. In each case, translational control depends on the binding of trans-acting factor to sequences in the 3' untranslated region (3' UTR). Identification of these trans-acting factors is beginning to shed light on the molecular mechanisms that mediate translational control. ------------------- Key: 2581 Medline: 97053807 Authors: Boyd L;Guo S;Levitan D;Stinchcomb DT;Kemphues KJ Title: PAR-2 is asymmetrically distributed and promotes association of P granules and PAR-1 with the cortex in C. elegans embryos. Citation: Development 122: 3075-3084 1996 Type: ARTICLE Genes: par-1 par-2 par-3 par-4 Abstract: The par genes participate in the process of establishing cellular asymmetries during the first cell cycle of Caenorhabditis elegans development. The par-2 gene is required for the unequal first cleavage and for asymmetries in cell cycle length and spindle orientation in the two resulting daughter cells. We have found that the PAR-2 protein is present in adult gonads and early embryos. In gonads, the protein is uniformly distributed at the cell cortex, and this subcellular localization depends on microfilaments. In the one-cell embryo, PAR-2 is localized to the posterior cortex and is partitioned into the posterior daughter, P-1, at the first cleavage, PAR-2 exhibits a similar asymmetric cortical localization in P-1, P-2, and P-3, the asymmetrically dividing blastomeres of germ line lineage. This distribution in embryos is very similar to that of PAR-1 protein. By analyzing the distribution of the PAR-2 protein in various par mutant backgrounds we found that proper asymmetric distribution of PAR-2 depends upon par-3 activity but not upon par-1 or par-4. par-2 activity is required for proper cortical localization of PAR-1 and this effect requires wild-type par-3 gene activity. We also find that, although par-2 activity is not required for posterior localization of P granules at the one-cell stage, it is required for proper cortical association of P granules in P-1. ------------------- Key: 2582 Medline: 97053811 Authors: Harris J;Honigberg L;Robinson N;Kenyon C Title: Neuronal cell migration in C. elegans: regulation of Hox gene expression and cell position. Citation: Development 122: 3117-3131 1996 Type: ARTICLE Genes: egl-20 lin-17 lin-39 mab-5 mig-1 mig-13 mig-14 eDf19 jDf1 jDf2 jDf4 tDf3 tDf4 Abstract: In C, elegans, the Hox gene mab-5, which specifies the fates of cells in the posterior body region, has been shown to direct the migrations of certain cells within its domain of function, mab-5 expression switches on in the neuroblast QL as it migrates into the posterior body region, mab-5 activity is then required for the descendants of QL to migrate to posterior rather than anterior positions. What information activates Hox gene expression during this cell migration? How are these cells subsequently guided to their final positions? We address these questions by describing four genes, egl-20, mig-14, mig-1 and lin-17, that are required to activate expression of mab-5 during migration of the QL neuroblast. We find that two of these genes, egl-20 and mig-14, also act in a mab-5-independent way to determine the final stopping points of the migrating Q descendants. The Q descendants do not migrate toward any obvious physical targets in wild-type or mutant animals. Therefore, these genes appear to be part of a system that positions the migrating Q descendants along the ------------------- Key: 2583 Medline: 97053812 Authors: Watts JL;Etemad-Moghadam B;Guo S;Boyd L;Draper BW;Mello CC;Priess JR;Kemphues KJ Title: par-6, a gene involved in the establishment of asymmetry in early C. elegans embryos, mediates the asymmetric localization of PAR-3. Citation: Development 122: 3133-3140 1996 Type: ARTICLE Genes: par-1 par-2 par-3 par-6 skn-1 hDf15 hDf16 hDf17 Abstract: The generation of asymmetry in the one-cell embryo of Caenorhabditis elegans is necessary to establish the anterior-posterior axis and to ensure the proper identity of early blastomeres. Maternal-effect lethal mutations with a partitioning defective phenotype (pal) have identified several genes involved in this process. We have identified a new gene, par-6, which acts in conjunction with other par genes to properly localize cytoplasmic components in the early embryo. The early phenotypes of par-6 embryos include the generation of equal-sized blastomeres, improper localization of P granules and SKN-1 protein, and abnormal second division cleavage patterns. Overall, this phenotype is very similar to that caused by mutations in a previously described gene, par-3. The probable basis for this similarity is revealed by our genetic and immunolocalization results; par-6 acts through par-3 by localizing or maintaining the PAR-3 protein at the cell periphery. In addition, we find that loss-of-function par-6 mutations act as dominant bypass suppressors of loss-of-function mutations in par-2. ------------------- Key: 2584 Medline: 97048185 Authors: Coburn CM;Bargmann CI Title: A putative cyclic nucleotide-gated channel is required for sensory development and function in C. elegans. Citation: Neuron 17: 695-706 1996 Type: ARTICLE Genes: odr-7 tax-2 tax-4 Abstract: In vertebrate visual and olfactory systems, a cyclic nucleotide-gated channel couples receptor activation to electrical activity of the sensory neurons. The Caenorhabditis elegans tax-2 gene is required for some farms of olfaction, for chemosensation of salts, and for thermosensation. We show here that tax-2 encodes a predicted subunit of a cyclic nucleotide-gated channel that is expressed in olfactory, gustatory, and thermosensory neurons, implicating this channel in multiple sensory modalities. Some sensory neurons display axon outgrowth defects in tax-2 mutants. Thus, the channel has an unexpected role in sensory neuron development in addition to its role in sensation. Consistent with this proposed dual function, a Tax-2::GFP fusion protein is present both in sensory cilia and in sensory axons. ------------------- Key: 2585 Medline: 97048186 Authors: Komatsu H;Mori I;Rhee J-S;Akaike N;Ohshima Y Title: Mutations in a cyclic nucleotide-gated channel lead to abnormal thermosensation and chemosensation in C. elegans. Citation: Neuron 17: 707-718 1996 Type: ARTICLE Genes: tax-2 tax-4 unc-31 Abstract: The C. elegans tax-4 mutants are abnormal in multiple sensory behaviors: they fail to respond to temperature or to water-soluble or volatile chemical attractants. We show that the predicted tax-4 gene product is highly homologous to vertebrate cyclic nucleotide-gated channels. Tax-4 protein expressed in cultured cells functions as a cyclic nucleotide-gated channel. The green fluorescent protein (GFP)-tagged functional Tax-4 protein is expressed in thermosensory, gustatory, and olfactory neurons mediating all the sensory behaviors affected by the tax-4 mutations. The Tax4::GFP fusion is partly localized at the sensory endings of these neurons. The results suggest that a cyclic nucleotide-gated channel is required for thermosensation and chemosensation and that cGMP is an important intracellular messenger in C. elegans sensory transduction. ------------------- Key: 2586 Medline: 97048187 Authors: Schackwitz WS;Inoue T;Thomas JH Title: Chemosensory neurons function in parallel to mediate a pheromone response in C. elegans. Citation: Neuron 17: 719-728 1996 Type: ARTICLE Genes: age-1 daf-1 daf-2 daf-3 daf-4 daf-5 daf-6 daf-7 daf-8 daf-11 daf-12 daf-14 daf-16 daf-21 daf-22 lin-15 Abstract: Formation of the C. elegans dauer larva is repressed by the chemosensory neurons ADF, ASI, and ASG. Mutant analysis has defined two parallel genetic pathways that control dauer formation. By killing neurons in these mutants, we show that mutations in one of these genetic pathways disrupt dauer repression by ADF, ASI, and ASG. One gene in this pathway is daf-7, which encodes a TGF beta-related protein. We find that daf-7::GFP fusions are expressed specifically in ASI and that expression is regulated by dauer-inducing sensory stimuli. We also show that a different chemosensory neuron, ASJ, functions in parallel to these neurons to induce dauer formation. Mutations in the second genetic pathway activate dauer formation in an ASJ-dependent manner. Thus, the genetic redundancy in this process is reflected at the neuronal level. ------------------- Key: 2587 Medline: 96421662 Authors: Gengyo-Ando K;Kitayama H;Mukaida M;Ikawa Y Title: A murine neural-specific homolog corrects cholinergic defects in Caenorhabditis elegans unc-18 mutants. Citation: Journal of Neuroscience 16: 6695-6702 1996 Type: ARTICLE Genes: rol-6 unc-18 unc-47 Abstract: Caenorhabditis elegans UNC-18 protein, homologous to yeast Sec1p, is important in neurotransmitter release, because the unc-18 mutation leads to severe paralysis and presynaptic acetylcholine (ACh) accumulation. To examine the functional conservation in mammals, we tried to isolate unc-18 isoforms from mouse and human brain cDNA libraries and obtained two classes of isoforms-neural genes and ubiquitous genes. Neural genes were identical to Munc-18 (also known as n-Sec1 or rbSec1), identified in rat and bovine brains as a syntaxin-binding protein. According to ''Munc-18'' terminology, we call the neural genes Munc-18-1 and the ubiquitous genes Munc-18-3. These mammalian isoforms exhibit 58% (Munc-18-1) and 42-43% (Munc-18-3) amino acid sequence identity with UNC-18. Next, we constructed transgenic unc-18 mutants to test biological activity of mouse Munc-18-1 and Munc-18-3 under the control of C. elegans unc-18 promoter. Munc-18-1 compensates for severe locomotion disability and cholinergic defects, e.g., abnormal sensitivities to cholinesterase inhibitors and cholinergic receptor agonists in unc-18 mutants, but Munc-18-3 fails. These data suggest that Munc-18-1 and C. elegans unc-18 may play positive roles in ACh release and that the molecular mechanism of neuronal regulated secretion has been partially conserved from nematodes to ------------------- Key: 2588 Medline: 97051960 Authors: Hoppe PE;Waterston RH Title: Hydrophobicity variations along the surface of the coiled-coil rod may mediate striated muscle myosin assembly in Caenorhabditis elegans. Citation: Journal of Cell Biology 135: 371-382 1996 Type: ARTICLE Genes: myo-3 unc-54 eDf1 Abstract: Caenorhabditis elegans body wall muscle contains two isoforms of myosin heavy chain, MHC A and MHC B, that differ in their ability to initiate thick filament assembly. Whereas mutant animals that lack the major isoform, MHC B, have fewer thick filaments, mutant animals that lack the minor isoform, MHC A, contain no normal thick filaments. MHC A, but not MHC B, is present at the center of the bipolar thick filament where initiation of assembly is thought to occur (Miller, D.M., I. Ortiz, G.C. Berliner, and H.F. Epstein. 1983. Cell. 34:477-490). We mapped the sequences that confer A-specific function by constructing chimeric myosins and testing them in vivo. We have identified two distinct regions of the MHC A rod that are sufficient in chimeric myosins for filament initiation function. Within these regions, MHC A displays a more hydrophobic rod surface, making it more similar to paramyosin, which forms the thick filament core. We propose that these regions play an important role in filament initiation, perhaps mediating close contacts between MHC A and paramyosin in an antiparallel arrangement at the filament center. Furthermore, our analysis revealed that all striated muscle myosins show a characteristic variation in surface hydrophobicity along the length of the rod that may play an important role in driving assembly and determining the stagger at which dimers associate. ------------------- Key: 2589 Medline: 97057252 Authors: Grenache DG;Caldicott I;Albert PS;Riddle DL;Politz SM Title: Environmental induction and genetic control of surface antigen switching in the nematode Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 93: 12388-12393 1996 Type: ARTICLE Genes: daf-1 daf-2 daf-3 daf-4 daf-5 daf-6 daf-7 daf-8 daf-11 daf-12 daf-14 srf-2 srf-6 mnDf30 mnDf31 mnDf61 mnDf68 Abstract: Nematodes can alter their surface coat protein compositions at the molts between developmental stages or in response to environmental changes; such surface alterations may enable parasitic nematodes to evade host immune defenses during the course of infection. Surface antigen switching mechanisms are presently unknown. In a genetic study of surface antigen switching, we have used a monoclonal antibody M37, that recognizes a surface antigen on the first larval stage of the free-living nematode Caenorhabditis elegans, We demonstrate that wild-type C. elegans can be induced to display the M37 antigen on a later larval stage by altering the growth conditions, Mutations that result in nonconditional display of this antigen on all four larval stages fall into two classes. One class defines the new gene srf-6 II. The other mutations are in previously identified dauer-constitutive genes involved in transducing environmental signals that modulate formation of the dauer larva, a developmentally arrested dispersal stage. Although surface antigen switching is affected by some of the genes that control dauer formation, these two processes can be blocked separately by specific mutations or induced separately by environmental factors, Based on these results, the mechanisms of nematode surface antigen switching can now be ------------------- Key: 2590 Medline: 97057288 Authors: Miller KG;Alfonso A;Nguyen M;Crowell JA;Johnson CD;Rand JB Title: A genetic selection for Caenorhabditis elegans synaptic transmission mutants. Citation: Proceedings of the National Academy of Sciences USA 93: 12593-12598 1996 Type: ARTICLE Genes: aex-3 cha-1 egl-10 egl-30 ric-1 ric-3 ric-4 ric-8 snt-1 unc-2 unc-10 unc-11 unc-13 unc-17 unc-18 unc-25 unc-26 unc-29 unc-31 unc-41 unc-64 unc-75 unc-104 Abstract: We have isolated 165 Caenorhabditis elegans mutants, representing 21 genes, that are resistant to inhibitors of cholinesterase (Ric mutants), Since mutations in 20 of the genes appear not to affect acetylcholine reception, we suggest that reduced acetylcholine release contributes to the Ric phenotype of most Ric mutants, Mutations in 15 of the genes lead to defects in a gamma-aminobutyric acid-dependent behavior; these genes are likely to encode proteins with general, rather than cholinergic-specific, roles in synaptic transmission. Ten of the genes have been cloned, Seven encode homologs of proteins that function in the synaptic vesicle cycle: two encode cholinergic-specific proteins, while five encode general presynaptic proteins. Two other Ric genes encode homologs of G-protein signaling molecules. Our assessment of synaptic function in Ric mutants, combined with the homologies of some Ric mutants to presynaptic proteins, suggests that the analysis of Ric genes will continue to yield insights into the regulation and functioning of synapses. ------------------- Key: 2591 Medline: 97043380 Authors: Wicks SR;Rankin CH Title: The integration of antagonistic reflexes revealed by laser ablation of identified neurons determines habituation kinetics of the Caenorhabditis elegans tap withdrawal response. Citation: Journal of Comparative Physiology A 179: 675-685 1996 Type: ARTICLE Genes: Abstract: Previously, we described the circuitry that underlies the tap withdrawal response of the nematode Caenorhabditis elegans. In response to a light mechanosensory stimulus a worm will withdraw, usually by initiating backward locomotion, but occasionally with increased forward locomotion. The form of an animal's response is a product of the balance between two antagonistic reflexes. backward locomotion (reversals) triggered by anterior mechanosensory input and forward locomotion (accelerations) triggered by posterior mechanosensory input. During habituation of this reflex, the frequency of forward and backward locomotion in response to tap is modulated by both experience and interstimulus interval; reversals are more frequent early in a habituation series and at longer Inter stimulus intervals. Single-cell laser microsurgery was used to study each of the subcomponents of the intact behavior during habituation training. Groups of intact or laser-ablated worms were habituated at either a 10-s or a 60-s inter stimulus interval and the kinetics of habituation in each group was analyzed. We demonstrate that each component of the behavior habituates and does so with kinetics that are consistent with the decrement observed in the intact ------------------- Key: 2592 Medline: 97099745 Authors: Driscoll M Title: Cell death in C. elegans: Molecular insights into mechanisms conserved between nematodes and mammals. Citation: Brain Pathology 6: 411-425 1996 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ces-1 ces-2 dad-1 deg-1 deg-3 mec-4 mec-10 nuc-1 unc-8 Abstract: As is the case for most metazoans, C. elegans cells have the potential to undergo developmental cell death (programmed cell death) or a necrotic-like death in response to cell injury. Analysis of mutations that disrupt the reproducible pattern of cell death that occurs during C. elegans development has defined a genetic pathway for programmed cell death. This program involves the activities of certain genes, such as ces-1 and the ces-2 bZIP transcription faster, which regulate the life/death decision in specific subsets of cells, ced-9, a Bcl-2 family member, acts globally to negatively regulate the activities of ced-4S (which promotes cell death) and ced-4L, which promotes cell life. ced-3 encodes a member of the ICE cysteine protease family that is essential for execution of all programmed cell deaths. Once cells die, corpses are phagocytized and consumed in what appear to be at least two parallel pathways that require the activities of ced-1, ced-6, ced-7 and ced-2, ced-5, ced-10. Degradation of corpse DNA requires the product of the nuc-1 gene. Degenerative cell death, characterized by cell swelling, can be induced by different cell injuries including that conferred by mutant degenerin ion channels (encoded by deg-1, mec-4, mec-10 and unc-8) and by expression of human beta-amyloid peptide. Remarkable parallels between nematode and mammalian death programs ------------------- Key: 2593 Medline: 97094002 Authors: Ogawa H;Hayashi N;Hori I;Kobayashi T;Hosono R Title: Expression, purification and characterization of recombinant C. elegans UNC-18. Citation: Neurochemistry International 29: 553-563 1996 Type: ARTICLE Genes: unc-18 Abstract: The Caenorhabditis elegans unc-18-encoded protein (UNC-18) is implicated in the processes of vesicle targeting, docking, and/or fusion. To further characterize the properties of this important neural protein, we expressed it at a high level in Spodoptera frugiperda Sf21 cells using a baculovirus expressing system. A cDNA containing the coding sequence for UNC-18 was inserted into the transfer vector pBlueBac to yield the recombinant virus pAcNPV/unc-18. At maximal expression, the recombinant virus produces a protein of 67 kDa, which constitutes about one third of total cell protein. The UNC-18 protein was highly purified and its biochemical and functional properties were assessed. The protein is globular with an isoelectric point of 6.95. Circular dichroism spectroscopy indicated that the alpha-helix and beta-sheet account for 10.0 and 59.0%, respectively. Immunolabeling the Sf21 cells expressing UNC-18 showed that the expressed UNC-18 is predominantly localized in the cytoplasm as a soluble monomer. The protein is phosphorylated by protein kinase C and binds to the recombinant C. elegans syntaxin in vitro. These findings suggest that in vesicle traffic UNC-18 is a regulator factor associated with the plasma membrane through syntaxin, although intrinsically cytoplasmic. ------------------- Key: 2594 Medline: 97051702 Authors: Tornoe C;Holden-Dye L;Garland C;Abramson SN;Fleming JT;Sattelle DB Title: Lophotoxin-insensitive nematode nicotinic acetylcholine receptors. Citation: Journal of Experimental Biology 199: 2161-2168 1996 Type: ARTICLE Genes: Abstract: Nematode nicotinic acetylcholine receptors (nAChRs) are molecular targets of several anthelmintic drugs, Studies to date on Caenorhabditis elegans and Ascaris suum have demonstrated atypical pharmacology with respect to nAChR antagonists, including the finding that kappa-bungarotoxin is a more effective antagonist than alpha-bungarotoxin on Ascaris muscle nAChRs. Lophotoxin and its naturally occurring analogue bipinnatin B block all vertebrate and invertebrate nAChRs so far examined, In the present study, the effects on nematode nAChRs of bipinnatin B have been examined, The Ascaris suum muscle cell nAChR was found to be insensitive to 30 mu moll(-1) bipinnatin B, a concentration that is highly effective on other nAChRs, To our knowledge, this is the first demonstration of a nAChR that is insensitive to one of the lophotoxins. Xenopus laevis oocytes injected with C. elegans polyadenylated, poly(A)(+), mRNA also expressed bipinnatin-B-insensitive levamisole responses, which were, however, blocked by the nAChR antagonist mecamylamine (10 mu moll(-1)). In contrast to the findings for nematode receptors, bipinnatin B (30 mu moll(-1)) was effective in blocking mouse muscle nAChRs expressed in Xenopus laevis oocytes and native insect nAChRs, A possible explanation for insensitivity of certain nematode nAChRs to lophotoxins is advanced based on the sequence of an alpha-like C. elegans nAChR subunit in which tyrosine-190 (numbering based on the Torpedo californica sequence), a residue known to be critical for lophotoxin binding in vertebrate nAChRs, is replaced by a proline residue. ------------------- Key: 2595 Medline: 97053593 Authors: Tessier-Lavigne M;Goodman CS Title: The molecular biology of axon guidance. Citation: Science 274: 1123-1133 1996 Type: REVIEW Genes: unc-5 unc-6 unc-40 Abstract: Neuronal growth cones navigate over long distances along specific pathways to find their correct targets. The mechanisms and molecules that direct this pathfinding are the topics of this review. Growth cones appear to be guided by at least four different mechanisms: contact attraction, chemoattraction, contact repulsion, and chemorepulsion. Evidence is accumulating that these mechanisms act simultaneously and in a coordinated manner to direct pathfinding and that they are mediated by mechanistically and evolutionarily conserved ------------------- Key: 2596 Medline: 97147794 Authors: Orsulic S;Peifer M Title: Cell-cell signaling: Wingless lands at last. Citation: Current Biology 6: 1363-1367 1996 Type: REVIEW Genes: lin-17 lin-44 Abstract: A novel class of receptor - the Frizzled family - has been identified and the members shown to be receptors for Wingless and its homologs, the Wnts, which mediate key cell-cell interactions during the development of fruitflies and vertebrates, respectively. ------------------- Key: 2597 Medline: 97088512 Authors: Tanaka T;Ikita K;Ashida T;Motoyama Y;Yamaguchi Y;Satouchi K Title: Effects of growth temperature on the fatty acid composition of the free-living nematode Caenorhabditis elegans. Citation: Lipids 31: 1173-1178 1996 Type: ARTICLE Genes: Abstract: The effects of growth temperature on the fatty acid compositions of the phosphatidylcholine (PC), phosphatidylethanolamine (PE), and total lipid (TL) fractions of the free-living nematode Caenorhabditis elegans were investigated. A reduction in growth temperature from 25 to 15 degrees C caused the proportions of eicosapentaenoic acid (20:5n-3) to increase from 23.6 to 32.5% in the PC, from 7.4 to 10.8% in the PE, and from 12.9 to 19.9% in the TL fractions. Conversely, the levels of dihomo-gamma-linolenic acid (20:3n-6) and arachidonic acid (20:4n-6) in these phospholipid fractions and the TL fraction both decreased with decreasing growth temperature. Analysis of the positional distribution of fatty acids in the PC fraction revealed that the change in the composition of C-20 polyunsaturated fatty acid was obvious in position sn-2. Lowering the growth temperature induced an increase in the level of the diacyl subclass of PE from 58% at 25 degrees C to 71% at 75 degrees C, with a concomitant decrease in the levels of the alkylacyl and alkenylacyl subclass of PE or C. elegans. These changes observed in the phospholipids of C. elegans might be one mechanism for adaptation to low temperature. ------------------- Key: 2598 Medline: 97080626 Authors: Yamamoto K;Honda S;Ishii N Title: Properties of an oxygen-sensitive mutant mev-3 of the nematode Caenorhabditis elegans. Citation: Mutation Research-Fundamental and Molecular Mechanisms of Mutagenesis 358: 1-6 1996 Type: ARTICLE Genes: mev-1 mev-2 mev-3 Abstract: A spontaneous mutant of meu-3 of the nematode Caenorhabditis elegans was isolated on the basis of its resistance to methyl viologen, which generates superoxide radicals. Contrary to expectation, the mutant proved hypersensitive to oxygen. Oxygen retarded development and reduced fecundity in a concentration-dependent fashion in meu-3 but not in wild-type. In addition, the mean life span of meu-3 (but not wild-type) was progressively shortened when animals were incubated under 70% oxygen. ------------------- Key: 2599 Medline: 97079197 Authors: Kawano T;Takuwa K;Nakajima T Title: Molecular cloning of a cDNA for the glutamate transporter of the nematode Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 228: 415-420 1996 Type: ARTICLE Genes: Abstract: We cloned a cDNA for the glutamate transporter of the nematode Caenorhabditis elegans. The nucleotide sequence and Northern blotting indicated that the glutamate transporter gene is transcribed as a polycistronic mRNA in C. elegans and that subsequent trans-splicing yields two distinct monocistronic mRNAs for the glutamate transporter and the ATP synthase c subunit, respectively. The yields of these monocistronic mRNAs were quite different, suggesting that glutamate transport in C. elegans is regulated in the posttranscriptional phase. The glutamate transporter of C. elegans shows about 50-60% sequence similarity with those of mammals. This is the first description of invertebrate glutamate transporters. ------------------- Key: 2600 Medline: 97067238 Authors: Ren PF;Lim C-S;Johnsen R;Albert PS;Pilgrim D;Riddle DL Title: Control of C. elegans larval development by neuronal expression of a TGF-Beta homolog. Citation: Science 274: 1389-1391 1996 Type: ARTICLE Genes: daf-1 daf-4 daf-7 daf-8 sup-7 Abstract: The Caenorhabditis elegans dauer larva is specialized for dispersal without growth and is formed under conditions of overcrowding and limited food. The daf-7 gene, required for transducing environmental cues that support continuous development with plentiful food, encodes a transforming growth factor-beta (TGF-beta) superfamily member. A daf-7 reporter construct is expressed in the ASI chemosensory neurons. Dauer-inducing pheromone inhibits daf-7 expression and promotes dauer formation, whereas food reactivates daf-7 expression and promotes recovery from the dauer state. When the food/pheromone ratio is high, the level of daf-7 mRNA peaks during the L1 larval stage, when commitment to non-dauer development is made. ------------------- Key: 2601 Medline: 97092319 Authors: Goedert M;Baur CP;Ahringer J;Jakes R;Hasegawa M;Spillantini MG;Smith MJ;Hill F Title: PTL-1, a microtubule-associated protein with tau-like repeats from the nematode Caenorhabditis elegans. Citation: Journal of Cell Science 109: 2661-2672 1996 Type: ARTICLE Genes: ptl-1 Abstract: Tau, MAP2 and MAP4 are structural microtubule-associated proteins (MAPs) that promote the assembly and stability of microtubules. They share three or four imperfect tandem repeats of an amino acid motif, which is involved in the binding to microtubules. All sequences to date containing this motif are of mammalian origin. We report here the cloning and functional characterisation of a new member of this family of proteins from the nematode Caenorhabditis elegans. This protein exists as two isoforms of 413 and 453 amino acids with four or five tandem repeats that are 50% identical to the tau/MAP2/MAP4 repeats. Both isoforms bind to microtubules and promote microtubule assembly, with the five-repeat isoform being more effective at promoting assembly than the four-repeat isoform. When expressed in COS cells, the five-repeat isoform co-localises with microtubules and induces the formation of microtubule bundles, whereas its expression in Sf9 cells leads to the extension of long unipolar processes. In view of its length, amino acid sequence and functional characteristics, we have named this invertebrate structural MAP 'Protein with Tau-Like Repeats' (PTL-1). In C. elegans PTL-1 is expressed in two places known to require microtubule function. It is first seen in the embryonic epidermis, when circumferentially oriented microtubules help to distribute forces generated during elongation. Later, it is found in mechanosensory neurons which contain unusual 15 protofilament microtubules required for the response to touch. These findings indicate that MAPs of the tau/MAP2/MAP4 family are found throughout much of the animal kingdom, where they may play a role in specialised processes requiring microtubules. ------------------- Key: 2602 Medline: 96302570 Authors: Ochoa C;Rodriguez J;Lopez Garcia ML;Ramon Martinez A;Mercedes Martinez M Title: Anthelmintic activity of 6,7-diaryl-pteridines. Citation: Arzneimittel-Forschung 46: 643-648 1993 Type: ARTICLE Genes: Abstract: In a search for new anthelmintic compounds, some 6,7-diaryl-pteridines were synthesized from the corresponding diaminopyrimidines and aromatic aldehydes. Their anthelmintic activity was tested in vitro against Caenorhabditis elegans and Heligmosomoides polygyrus and in vivo against Trichinella spiralis. Structure-activity relationships are discussed. ------------------- Key: 2603 Medline: 96350752 Authors: Tsipouras A;Adefarati AA;Tkacz JS;Frazier EG;Rohrer SP;Birzin E;Rosegay A;Zink DL;Goetz MA;Singh SB;Schaeffer J Title: Ophiobolin M and analogues, noncompetitive inhibitors of ivermectin binding with nematocidal activity. Citation: Bioorganic & Medicinal Chemistry 4: 531-536 1996 Type: ARTICLE Genes: Abstract: A series of ophiobolins were isolated from a fungal extract based on their nematocidal activity. These compounds are non-competitive inhibitors of ivermectin binding to membranes prepared from the free-living nematode, Caenorhabditis elegans, with an inhibition constant of 15 microM. The ophiobolins which were most potent in the biological assays, ophiobolin C and ophiobolin M, were also the most potent compounds when evaluated in a C. elegans motility assay. These data suggest that the nematocidal activity of the ophiobolins is mediated via an interaction with the ivermectin binding site. The isolation, structure and biological activity of ophiobolins have been described. ------------------- Key: 2604 Medline: 97100937 Authors: Drescher U Title: Netrins find their receptor. Citation: Nature 384: 416-417 1996 Type: REVIEW Genes: unc-5 unc-6 unc-40 Abstract: What guides migrating nerve axons to their correct targets during development? This is one of the basic issues in developmental neurobiology, and chemoattraction has long been thought to be involved. A tangible answer began to emerge with the demonstration that explants of rat spinal floorplate promoted the outgrowth of axons from commissural neurons, and caused these axons to turn. Subsequently, the specific factors concerned in axon turning were identified. These factors, called netrin-1 and netrin-2, are phlogenetically conserved molecules related to the product of the unc-6 gene in Caenorhabditis elegans. ------------------- Key: 2605 Medline: 97094382 Authors: Lieb JD;Capowski EE;Meneely P;Meyer BJ Title: DPY-26, a link between dosage compensation and meiotic chromosome segregation in the nematode. Citation: Science 274: 1732-1736 1996 Type: ARTICLE Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 sdc-1 sdc-2 sdc-3 xol-1 Abstract: The DPY-26 protein is required in the nematode Caenorhabditis elegans for X-chromosome dosage compensation as well as for proper meiotic chromosome segregation. DPY-26 was shown to mediate both processes through its association with chromosomes. in somatic cells, DPY-26 associates specifically with hermaphrodite X chromosomes to reduce their transcript levels, in germ cells, DPY-26 associates with all meiotic chromosomes to mediate its role in chromosome segregation. The X-specific localization of DPY-26 requires two dosage compensation proteins (DPY-27 and DPY-30) and two proteins that coordinately control both sex determination and dosage compensation (SDC-2 and ------------------- Key: 2606 Medline: 97094383 Authors: Chuang P-T;Lieb JD;Meyer BJ Title: Sex-specific assembly of a dosage compensation complex on the nematode X chromosome. Citation: Science 274: 1736-1739 1996 Type: ARTICLE Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 sdc-1 sdc-2 sdc-3 xol-1 Abstract: In nematodes, flies, and mammals, dosage compensation equalizes X-chromosome gene expression between the sexes through chromosome-wide regulatory mechanisms that function in one sex to adjust the levels of X-linked transcripts. Here, a dosage compensation complex was identified in the nematode Caenorhabditis elegans that reduces transcript levels from the two X chromosomes in hermaphrodites, This complex contains at least four proteins, including products of the dosage compensation genes dpy-26 and dpy-27. Specific localization of the complex to the hermaphrodite X chromosomes is conferred by XX-specific regulatory genes that coordinately control both sex determination and dosage compensation. ------------------- Key: 2607 Medline: 97108745 Authors: Guenther C;Garriga G Title: Asymmetric distribution of the C. elegans HAM-1 protein in neuroblasts enables daughter cells to adopt distinct fates. Citation: Development 122: 3509-3518 1996 Type: ARTICLE Genes: ced-3 ced-4 egl-1 egl-43 ham-1 lin-26 unc-86 sDf22 Abstract: One mechanism of generating cellular diversity is to distribute developmental potential asymmetrically to daughter cells at mitosis. Two observations described in this report suggest that the C. elegans HAM-1 protein functions in dividing neuroblasts to produce daughter cells that adopt distinct fates. First, HAM-1 is asymmetrically distributed to the periphery of certain mitotic cells, ensuring that it will be inherited by only one daughter cell. Second, ham-1 mutations disrupt the asymmetric divisions of five neuroblasts. In one of these divisions, loss of ham-1 function causes the daughter cell that does not inherit HAM-1 to adopt the fate of the daughter cell that normally inherits HAM-1. We propose that asymmetric distribution of HAM-1 enables daughter cell to adopt distinct fates. ------------------- Key: 2608 Medline: 97108756 Authors: Newman AP;White JG;Sternberg PW Title: Morphogenesis of the C. elegans hermaphrodite uterus. Citation: Development 122: 3617-3626 1996 Type: ARTICLE Genes: Abstract: We have undertaken electron micrographic reconstruction of the Caenorhabditis elegans hermaphrodite uterus and determined the correspondence between cells defined by their lineage history and differentiated cell types. In this organ, many cells do not move during morphogenesis and the cell lineage may function to put cells where they are needed. Differentiated uterine cell types include the toroidal ut cells that make structural epithelium, and specialized utse and uv cells that make the connection between the uterus and the vulva. A cell fate decision in which the anchor cell (AC) induces adjacent ventral uterine intermediate precursor cells to adopt the pi fate, rather than the ground state rho, has profound consequences for terminal differentiation: all pi progeny are directly involved in making the uterine-vulval connection whereas all rho progeny contribute to ut toroids or the uterine-spermathecal valve. In addition to specifying certain uterine cell fates, the AC also induces the vulva. Its multiple inductions thereby function to coordinate the connection of an internal to an external epithelium. The AC induces the pi cells and ultimately fuses with a subset of their progeny. This is an example of reciprocal cell-cell interaction that can be studied at single cell resolution. The AC is thus a transitory cell type that plays a pivotal role in organizing the morphogenesis of the uterine-vulval connection. ------------------- Key: 2609 Medline: 97115885 Authors: Ha I;Wightman B;Ruvkun G Title: A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient formation. Citation: Genes & Development 10: 3041-3050 1996 Type: ARTICLE Genes: lin-4 lin-14 Abstract: The Caenorhabditis elegans heterochronic gene lin-14 generates a temporal gradient of the LIN-14 proteins to control stage-specific patterns of cell lineage during development. Down-regulation of LIN-14 is mediated by the lin-14 3' untranslated region (UTR), which bears seven sites that are complementary to the regulatory lin-4 RNA. Here we report molecular and genetic evidence that RNA duplexes between the lin-4 and lin-14 RNAs form in vivo and are necessary for LIN-14 temporal gradient generation. lin-4 RNA binds in vitro to a lin-14 mRNA bearing the seven lin-4 complementary sites but not to a lin-14 mRNA bearing point mutations in these sites. In vivo, the lin-4 complementary regions are necessary for lin-14 3' UTR-mediated temporal gradient formation. Based on lin-14 3' UTR sequence comparisons between C. elegans and C. briggsae, four of the seven lin-4/lin-14 RNA duplexes are predicted to bulge a lin-4 residue, and three sites are predicted to form nonbulged RNA duplexes. Reporter genes bearing multimerized bulged C lin-4 sites show almost wild-type temporal gradient formation, whereas those bearing multimerized nonbulged lin-4 binding sites do not form a temporal gradient. Paradoxically, lin-4 RNA binds in vitro to nonbulged lin-14 RNA more avidly than to the nonbulged lin-14 RNA. This suggests that a specific secondary structure of lin-4/lin-14 RNA duplex that may be recognized by an accessory protein, rather than an RNA duplex per se, is required in vivo for the generation of ------------------- Key: 2610 Medline: 97105935 Authors: Jones AR;Francis R;Schedl T Title: GLD-1, a cytoplasmic protein essential for oocyte differentiation, shows stage- and sex-specific expression during Caenorhabditis elegans germline development. Citation: Developmental Biology 180: 165-183 1996 Type: ARTICLE Genes: cey-2 fog-1 gld-1 mes-6 mex-3 spe-4 spe-11 spe-26 sst-20 Abstract: GLD-1, a putative RNA binding protein, is essential for oocyte development in Caenorhabditis elegans. A gld-1 null mutation abolishes hermaphrodite oogenesis and confers a tumorous germline phenotype in which presumptive female germ cells exit the meiotic pathway and return to the mitotic cell cycle. Here we demonstrate that gld-l(null) germ lines express female-specific, but not male-specific, molecular markers, indicating that gld-l acts downstream of sexual fate specification to regulate oocyte differentiation. Immunolocalization studies identify GLD-1 as a cytoplasmic germline protein that displays differential accumulation during germline development. first, germ cells that are in the mitotic cell cycle contain low levels of GLD-1 that likely reflect a nonessential gld-l function (negative regulation of proliferation in the mitotic germ line) revealed in previous genetic studies. Second, entry of presumptive oocytes into the meiotic pathway is accompanied by a strong increase in GLD-1 expression/accumulation. GLD-1 levels are high through the pachytene stage but fall to background as germ cells exit pachytene and complete oogenesis. The meiotic prophase accumulation pattern is consistent with GLD-l's essential role in oocyte differentiation, which may be to repress the translation of a subset of maternal RNAs synthesized during early oogenesis until late oogenesis ------------------- Key: 2611 Medline: 97098482 Authors: Gruidl ME;Smith PA;Kuznicki KA;McCrone JS;Kirchner J;Roussell DL;Strome S;Bennett KL Title: Multiple potential germ-line helicases are components of the germ-line-specific P granules of Caenorhabditis Citation: Proceedings of the National Academy of Sciences USA 93: 13837-13842 1996 Type: ARTICLE Genes: glh-1 glh-2 Abstract: Two components of the germ-line-specific P granules of the nematode Caenorhabditis elegans have been identified using polyclonal antibodies specific for each. Both components are putative germ-line RNA helicases (GLHs) that contain CCHC zinc fingers of the type found in the RNA-binding nucleocapsid proteins of retroviruses. The predicted GLH-1 protein has four CCHC fingers; GLH-2 has six. Both GLH proteins localize in the P granules at all stages of germ-line development. However, the two glh genes display different patterns of RNA and protein accumulation in the germ lines of hermaphrodites and males. Injection of antisense glh-1 or glh-2 RNA into wild-type worms causes some offspring to develop into sterile adults, suggesting that either or both genes are required for normal germ-line development. As these very similar glh genes physically map within several hundred kilobases of one another, it seems likely that they represent a fairlyrecent gene duplication event. ------------------- Key: 2612 Medline: 97093151 Authors: Wei A;Jegla T;Salkoff L Title: Eight potassium channel families revealed by the C. elegans genome project. Citation: Neuropharmacology 35: 805-829 1996 Type: ARTICLE Genes: Abstract: The wealth of accumulating data from the Caenorhabditis elegans genome sequencing project has rapidly accelerated the discovery of novel potassium channel genes and now places within reach the possibility of describing the total complement of potassium channels used by an individual species. Using annotated GenBank sequences, BLAST searches of unfinished sequences and degenerate oligonucleotide polymerase chain reaction (PCR) screens, we have identified and compiled genes for 38 C. elegans potassium channel and two cyclic nucleotide-gated cation channel subunits, representing eight conserved multigene families. Novel families of potassium channel genes were revealed, as well as conserved homologues of all known vertebrate families. Two separate families represent C. elegans homologues for human potassium channels recently implicated in hereditary long QT arrhythmias. Of particular note is an exceptionally large class of at least 23 genes with a novel subunit structure having two tandem 'P' domains; these channels may form as dimers in contrast to all other potassium channel types which form as tetramers. The 40 potassium channel genes are evenly distributed on all six C. elegans chromosomes, with the exception of three instances of gene clustering on the fifth and X chromosomes. ------------------- Key: 2613 Medline: 97092712 Authors: Li X;Greenwald I Title: Membrane topology of the C. elegans SEL-12 presenilin. Citation: Neuron 17: 1015-1021 1996 Type: ARTICLE Genes: sel-12 Abstract: Mutant presenilins cause Alzheimer's disease. Presenilins have multiple hydrophobic regions that could theoretically span a membrane, and a knowledge of the membrane topology is crucial for deducing,the mechanism of presenilin function. By analyzing the activity of beta-galactosidase hybrid proteins expressed in C. elegans, we show that the C. elegans SEL-12 presenilin has eight transmembrane domains and that there is a cleavage site after the sixth transmembrane domain. We examine the presenilin sequence in view of the predicted topology and discuss possible mechanisms for presenilin function. ------------------- Key: 2614 Medline: 97142132 Authors: Zhu X;Joh K;Hori K Title: Nucleotide sequence of ribosomal protein L3 cDNA and the exon-intron structure of L3 gene in the nematode, Caenorhabditis elegans. Citation: DNA Sequence 6: 299-302 1996 Type: ARTICLE Genes: Abstract: A cDNA and a gene encoding the nematode (C. elegans) ribosomal protein L3 have been cloned and sequenced. The nearly full-length cDNA is 1255 bp in size except for the poly (A) tail. The encoded protein consists of 401 amino acids and has calculated molecular weight of 45,657 daltons. The gene sequence determined is 1649 bp and consists of four exons. The sequence of the nematode protein shows high homology to other eukaryotic proteins. ------------------- Key: 2615 Medline: 97094732 Authors: Linder B;Jin Z;Freedman JH;Rubin CS Title: Molecular characterization of a novel, developmentally regulated small embryonic chaperone from Caenorhabditis elegans. Citation: Journal of Biological Chemistry 271: 30158-30166 1996 Type: ARTICLE Genes: sec-1 Abstract: Low molecular weight chaperones inhibit protein aggregation and facilitate refolding of partially denatured polypeptides in cells subjected to physical and chemical stresses. The nematode Caenorhabditis elegans provides a system amenable for investigations on roles for chaperone proteins in normal homeostasis and development, We characterized a C. elegans gene and cDNAs that encode a novel, small embryonic chaperone-like protein (SEC-1) that is composed of 159 amino acids, The central core of SEC-1 (residues 45-126) is similar to 40% identical with a corresponding segment of mammalian Hsp27 and alpha B crystallin, Expression of SEC-1 in Escherichia coli confers thermotolerance on the bacterium. SEC-1 mRNA is evident only in C. elegans oocytes and developing embryos. Translation and accumulation of SEC-1 protein is temporally coupled with a prolonged burst of intense protein synthesis and rapid mitogenesis during early embryogenesis. As the rate of protein synthesis decreases during late embryogenesis, levels of SEC-1 and its cognate mRNA decline precipitously. Induction/deinduction of SEC-1 is precisely regulated by intrinsic developmental factors rather than extrinsic stresses, In vivo injection of C. elegans oocytes with antisense oligonucleotides that complement the 5'-end of SEC-1 mRNA arrests nematode development at an early stage after fertilization, Thus, SEC-1 appears to be adapted to perform essential functions in early ------------------- Key: 2616 Medline: Authors: Borgonie G;Claeys M;Leyns F;Arnaut G;De Waele D;Coomans A Title: Effect of a nematicidal Bacillus thuringiensis strain on free-living nematodes. 3. Characterization of the intoxication process. Citation: Fundamental and Applied Nematology 19: 523-528 1996 Type: ARTICLE Genes: Abstract: The toxicity of Bacillus thuringiensis is temperature sensitive. Incubation of Caenorhabditis elegans with nematicidal B. thuringiensis strains at 16, 20, and 25 degrees C shows that toxicity decreases as temperature declines. At 16 degrees C, toxicity is completely lost, while it is maximal at 25 degrees C. Toxicity is pH sensitive and is significantly reduced when nematodes are incubated with the weak bases NH4Cl, chloroquine, acridine orange, methyl red, and neutral red. Based on these results, we proposed the hypothesis that the nematicidal factor is effectively internalized into the intestinal cells, a sharp deviation from the insecticidal B. thuringiensis toxins acting at the level of the brush border membrane. Although the absence of purified toxins prevents a more definitive elucidation of the mode of action, the results of this third and final part of this series of publications convincingly indicate that nematicidal B. thuringiensis do not hold the same promise as a biological control agent as the insecticidal B. ------------------- Key: 2617 Medline: Authors: Lambie EJ Title: Cell-cell communication: Receptor function at the junction. Citation: Current Biology 6: 1089-1091 1996 Type: REVIEW Genes: let-23 let-60 lin-2 lin-3 lin-7 lin-10 lin-15 lin-37 sem-5 sli-1 unc-101 Abstract: Proteins associated with epithelial cell junctions regulate receptor tyrosine kinase activity by maintaining the basolateral localization of the receptor molecules. ------------------- Key: 2618 Medline: 97109807 Authors: Wood WB;Bergmann D;Florance A Title: Maternal effect of low temperature on handedness determination in C. elegans embryos. Citation: Developmental Genetics 19: 222-230 1996 Type: ARTICLE Genes: unc-4 Abstract: C. elegans embryos, larvae, and adults exhibit several left-right asymmetries with an invariant dextral handedness, which first becomes evident in the embryo at the 6-cell stage. Reversed (sinistral) handedness was not observed among > 10,000 N2 adults reared at 16 degrees C or 20 degrees C under standard conditions. However, among the progeny of adults reproducing at 10 degrees C, the frequency of animals with sinistral handedness was increased to similar to 0.5%. Cold pulse experiments indicated that the critical period for this increase was in early oogenesis, several hours before the first appearance of left-right asymmetry in the embryo. Hermaphrodites reared at 10 degrees C and mated with males reared at 20 degrees C produced sinistral outcross as well as sinistral self-progeny, indicating that the low temperature effect on oocytes was sufficient to cause reversals. Increased frequency of reversal was also observed among animals developed from embryos lacking the egg shell. Possible mechanisms for the control of embryonic handedness are discussed in the context of these results, including the hypothesis that handedness could be dictated by the ------------------- Key: 2619 Medline: 97102795 Authors: Broeks A;Gerrard B;Allikmets R;Dean M;Plasterk RHA Title: Homologues of the human multidrug resistance genes MRP and MDR contribute to heavy metal resistance in the soil nematode Caenorhabditis elegans. Citation: EMBO Journal 15: 6132-6143 1996 Type: ARTICLE Genes: mrp-1 mrp-2 mrp-3 mrp-4 pgp-1 pgp-2 pgp-3 Abstract: Acquired resistance of mammalian cells to multiple chemotherapeutic drugs can result from enhanced expression of the multidrug resistance-associated protein (MRP), which belongs to the ABC transporter superfamily, ABC transporters play a role in the protection of organisms against exogenous toxins by cellular detoxification processes, We have identified four MRP homologues in the soil nematode Caenorhabditis elegans, and we have studied one member, mrp-1, in detail, Using an mrp::lacZ gene fusion, mrp-1 expression was found in cells of the pharynx, the pharynx-intestinal valve and the anterior intestinal cells, the rectum-intestinal valve and the epithelial cells of the vulva, Targeted inactivation of mrp-1 resulted in increased sensitivity to the heavy metal ions cadmium and arsenite, to which wild-type worms are highly tolerant. The most pronounced effect of the mrp-1 mutation is on the ability of animals to recover from temporary exposure to high concentrations of heavy metals, Nematodes were found to be hypersensitive to heavy metals when both the MRP homologue, mrp-1, and a member of the P-glycoprotein (Pgp) gene family, pgp-1, were deleted, We conclude that nematodes have multiple proteins, homologues of mammalian proteins involved in the cellular resistance to chemotherapeutic drugs, that protect them against heavy ------------------- Key: 2620 Medline: 97123987 Authors: Fong S;Hamill SJ;Proctor M;Freund SMV;Benian GM;Chothia C;Bycroft M;Clarke J Title: Structure and stability of an immunoglobulin superfamily domain from twitchin, a muscle protein of the nematode Caenorhabditis elegans. Citation: Journal of Molecular Biology 264: 624-639 1996 Type: ARTICLE Genes: Abstract: The NMR solution structure of an immunoglobulin superfamily module of twitchin (Ig 18') has been determined and the kinetic and equilibrium folding behaviour characterised. Thirty molecular coordinates were calculated using a hybrid distance geometry-simulated annealing protocol based on 1207 distance and 48 dihedral restraints. The atomic rms distributions about the mean coordinate for the ensemble of structures is 0.55(+/- 0.09) Angstrom for backbone atoms and 1.10(+/- 0.08) Angstrom for all heavy atoms. The protein has a topology very similar to that of telokin and the titin Ig domains and thus it falls into the I set of the immunoglobulin superfamily. The close agreement between the predicted and observed structures of Ig 18' demonstrates clearly that the I set profile can be applied in the structure prediction of immunoglobulin-like domains of diverse modular proteins. Folding studies reveal that the protein has relatively low thermodynamic stability, Delta G(U-F)(H2O) = 4.0 kcal mol(-1) at physiological pH. Unfolding studies suggest that the protein has considerable kinetic stability, the half life of the unfolding is greater than 40 minutes in the absence of denaturant. ------------------- Key: 2621 Medline: 97128321 Authors: Masson J-Y;Tremblay S;Ramotar D Title: The Caenorhabditis elegans gene CeAPN-1 encodes a homolog of Escherichia coli and yeast apurinic/apyrimidinic endonuclease. Citation: Gene 179: 291-293 1996 Type: ARTICLE Genes: apn-1 Abstract: The Saccharomyces cerevisiae APN1 gene, encoding the bifunctional DNA repair enzyme apurinic/apyrimidinic (AP) endonuclease/3'-repair diesterase, was used as a probe to isolate a gene homolog, CeAPN1, from a Caenorhabditis elegans cDNA library. The CeAPN1 gene is predicted to encode a protein 30 kDa in size, which shares 40.4% and 44.9% identity at the amino acid level with, respectively, S. cerevisiae Apn1 and Escherichia coli endonuclease IV. We suggest that CeApn1 protein is a member of the endonuclease IV family of DNA repair enzymes. ------------------- Key: 2622 Medline: Authors: Scott AL Title: Nematode sperm. Citation: Parasitology Today 12: 425-430 1996 Type: REVIEW Genes: Abstract: Parasitic nematode infections remain a major public health problem in many parts of the world. Because most of the current strategies aimed at controlling parasitic nematode infections have met with only limited success, it may be time to consider alternative approaches. An aspect of nematode biology that has drawn little attention as a target for control is the reproductive process. Although there are numerous facets of the overall reproductive biology of nematodes that hold potential as targets for intervention, Alan Scott here focuses on the male reproductive system, and outlines some of the known unique processes and characteristics of sperm formation and sperm function that could be exploited to block fertilization. ------------------- Key: 2623 Medline: 97148206 Authors: Blumenthal T;Spieth J Title: Gene structure and organization in Caenorhabditis elegans. Citation: Current Opinion in Genetics & Development 6: 692-698 1996 Type: REVIEW Genes: Abstract: The sequencing of the 100 Mb Caenorhabditis elegans genome - containing 14000 genes - is about 50% complete. One of its most interesting features is its compactness; introns and intergenic distances are unusually small and, surprisingly, about 25% of genes are contained in polycistronic transcription units (operons) with only about 100 bp between genes. ------------------- Key: 2624 Medline: 97401889 Authors: Osborne BA Title: Cell death in vertebrates: lessons from the worm. Citation: Trends in Genetics 12: 489-491 1996 Type: REVIEW Genes: ced-3 ced-4 ced-9 ces-1 ces-2 Abstract: Several years ago, Horvitz and Sulston demonstrated that it is the fate of 131 cells to die during development of the small nematode, Caenorhabditis elegans. The recognition that these particular cells are destined to die at exactly the same time in each and every worm suggested that the control and, perhaps, even the elements of this program were genetically determined. From these beginnings, the still-unfolding genetics of cell death has emerged. During the past 10 years, classical genetic approaches have identified loci in worms that either positively or negatively regulate cell death during development. Recently, some of the genes encoded by these loci have been cloned and sequenced. The results from these studies, coupled with experiments directed at identifying the events that regulate mammalian cell death, have led to the important observation that, in many instances, genes that control cell death in worms are conserved structurally and functionally between nematodes and vertebrates. ------------------- Key: 2625 Medline: Authors: You SJ;Dochoi J;Cho NJ Title: Ligand-binding properties of muscarinic acetylcholine receptors in Caenorhabditis elegans. Citation: Journal of Biochemistry and Molecular Biology 29: 525-529 1996 Type: ARTICLE Genes: Abstract: ------------------- Key: 2626 Medline: 97125048 Authors: Podbilewicz B Title: ADM-1, a protein with metalloprotease- and disintegrin-like domains, is expressed in syncytial organs, sperm, and sheath cells of sensory organs in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 7: 1877-1893 1996 Type: ARTICLE Genes: adm-1 Abstract: A search was carried out for homologues of possible fusogenic proteins to study their function in a genetically tractable animal. The isolation, molecular, and cellular characterization of the Caenorhabditis elegans adm-1 gene (a disintegrin and metalloprotease domain) are described. A glycoprotein analogous to viral fusion proteins has been identified on the surface of guinea pig sperm (PH-30/fertilin) and is implicated in sperm-egg fusion. adm-l is the first reported invertebrate gene related to PH-30 and a family of proteins containing snake venom disintegrin- and metalloprotease-like domains. ADM-1 shows a domain organization identical to PH-30. It contains prepro, metalloprotease, disintegrin, cysteine rich with putative fusion peptide, epidermal growth factor-like repeat, transmembrane, and cytoplasmic domains. Antibodies which recognize ADM-1 protein in immunoblots were generated. Using immunofluorescence and in situ hybridization, the products of adm-1 have been detected in specific cells during different stages of development. The localization of ADM-1 to the plasma membrane of embryonic cells and to the sheath cells of sensory organs suggests a function in cell adhesion. ADM-1 expression in the hypodermis, pharynx, vulva, and mature sperm is consistent with a putative role in somatic and gamete cell fusions. ------------------- Key: 2627 Medline: 97121448 Authors: Korswagen HC;Durbin RM;Smits MT;Plasterk RHA Title: Transposon Tc1-derived, sequence-tagged sites in Caenorhabditis elegans as markers for gene mapping. Citation: Proceedings of the National Academy of Sciences USA 93: 14680-14685 1996 Type: ARTICLE Genes: dpy-17 egl-5 gpa-2 him-5 him-8 prk-2 sma-1 unc-13 unc-36 Abstract: We present an approach to map large numbers of Tc1 transposon insertions in the genome of Cacnorhabditis elegans. Strains have been described that contain up to 500 polymorphic Tc1 insertions, From these we hare cloned and shotgun sequenced over 2000 Tc1 flanks, resulting in an estimated set of 400 or more distinct Tc1 insertion alleles. Alignment of these sequences revealed a weak Tc1 insertion site consensus sequence that was symmetric around the invariant TA target site and reads CAYATATRTG. The Tc1 flanking sequences were compared with 40 Mbp of a C. elegans genome sequence, We found 151 insertions within the sequenced area, a density of approximate to 1 Tc1 insertion in every 265 kb. As the rest of the C. elegans genome sequence is obtained remaining Tc1 alleles will fall into place, These mapped Tc1 insertions can serve two functions: (i) insertions in or near genes can be used to isolate deletion derivatives that have that gene mutated: and (ii) they represent a dense collection of polymorphic sequence-tagged sites, We demonstrate a strategy to use these Tc1 sequence-tagged sites in fine-mapping mutations. ------------------- Key: 2628 Medline: 97121494 Authors: Levitan D;Doyle TG;Brousseau D;Lee MK;Thinakaran G;Slunt HH;Sisodia SS;Greenwald I Title: Assessment of normal and mutant human presenilin function in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 93: 14940-14944 1996 Type: ARTICLE Genes: lin-12 sel-12 Abstract: We provide evidence that normal human presenilins can substitute for Caenorhabditis elegans SEL-12 protein in functional assays in vivo. In addition, six familial Alzheimer disease-linked mutant human presenilins were tested and found to have reduced ability to rescue the sel-12 mutant phenotype, suggesting that they have lower than normal presenilin activity. A human presenilin 1 deletion variant that fails to be proteolytically processed and a mutant SEL-12 protein that lacks the C terminus display considerable activity in this assay, suggesting that neither presenilin proteolysis nor the C terminus is absolutely required for normal presenilin function. We also show that sel-12 is expressed in most neural and nonneural cell types in all developmental stages. The reduced activity of mutant presenilins and as yet unknown gain-of-function properties may be a contributing factor in the development of Alzheimer disease. ------------------- Key: 2629 Medline: 97129047 Authors: Baines AJ Title: Caenorhabditis elegans LIN-2A and mammalian neuronal CASK are prototypical members of a subfamily of MAGUKS (membrane-associated guanylate kinases) characterized by a common kin... Citation: Biochemical Journal 320: 694-696 1996 Type: ARTICLE Genes: lin-2 Abstract: The MAGUKs are a family of membrane-associated guanylate kinases characterized by a common set of domains that bind polypeptide and nucleotide ligands. These domains are a guanylate kinase-like (GUK) domain, an SH3 domain, and one to three copies of a structure known as a PDZ or DHR domain. The PDZ/DHR domain was defined by homology with the Drosophila tumour suppressor discs-large (DLG), the post-synaptic density protein PSD-95 and the tight-junction protein Z0-1, and has recently been defined as a domain for binding polypeptide ligands. The three domain types that define MAGUKs are therefore all ligand-binding domains specialized either for binding polypeptides (PDZ, SH3) or nucleotides (GUK)... ------------------- Key: 2630 Medline: 97128830 Authors: Chen WN;Yap SF;Lim L Title: Isolation of the gene coding for Caenorhabditis elegans Rac2 homologue, a Ras-related small GTP-binding protein. Citation: Gene 180: 217-219 1996 Type: ARTICLE Genes: Abstract: When screening a Caenorhabditis elegans genomic library using the human Rac1 cDNA as probe, a hybridizing fragment of 2.7 kb was isolated which contained four exons with high sequence similarity to CeRac1, coding for the nematode homologue of the Ras-related small GTP-binding protein Rad. The putative translational product of 195 amino acids (aa) from the exons displayed 88% identity to the sequence of CeRac1. Interestingly, three alterations were found in the N-terminal 'effector domain' (residues 22-45) which hitherto was identical among all known Rac p21s, suggesting that CeRac2 might have different targets/functions for nematode development. Additionally, an insertion of 4 aa was found in the hypervariable region at the C terminus of ------------------- Key: 2631 Medline: 97137091 Authors: Cline TW;Meyer BJ Title: Vive la difference: Males vs females in flies vs worms. Citation: Annual Review of Genetics 30: 637-702 1996 Type: REVIEW Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 fem-1 fem-2 fem-3 fog-1 fog-2 fog-3 fox-1 gld-1 her-1 mes-2 mes-3 mes-4 mes-6 mog-1 sdc-1 sdc-2 sdc-3 sex-1 tra-1 tra-2 tra-3 xol-1 yDf17 yDf19 yDf20 Abstract: For 600 million years, the two best-understood metazoan species, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, have developed independent strategies for solving a biological problem faced by essentially an metazoans: how to generate two sexes in the proper proportions. The genetic program for sexual dimorphism has been a major focus of research in these two organisms almost from the moment they were chosen for study, and it may now be the best-understood general aspect of their development. In this review, we compare and contrast the strategies used for sex determination (including dosage compensation) between ''the fly'' and ''the worm'' and the way this understanding has come about. Although no overlap has been found among the molecules used by flies and worms to achieve sex determination, striking similarities have been found in the genetic strategies used by these two species to differentiate their sexes. ------------------- Key: 2632 Medline: 97149282 Authors: Maduro M;Pilgrim D Title: Conservation of function and expression of unc-119 from two Caenorhabditis species despite divergence of non-coding Citation: Gene 183: 77-85 1996 Type: ARTICLE Genes: unc-119 Abstract: The Caenorhabditis briggsae homologue of the Caenorhabditis elegans neuronal gene unc-119 has been cloned by low-stringency hybridization. Genomic clones containing the C. briggsae gene are able to completely rescue the unc-119 phenotype in transgenic C. elegans mutants. The open reading frame (ORF) of the predicted C. briggsae cDNA is 90% identical to that of C. elegans. Although the splice donor and acceptor sites are conserved, the untranslated regions, and the introns, differ greatly. For this gene, the average intron size in C. elegans is over 600 base pairs (bp); in C. briggsae it is only 113 bp. Their upstream control regions share limited sequence similarities; however, reporter gene fusions of the two species show strongly similar expression in C. elegans. These results are consistent with the maintenance not only of the function of the unc-119 gene but also the transcriptional control of the gene through tens of ------------------- Key: 2633 Medline: Authors: Sudhaus W;Kiontke K Title: Phylogeny of Rhabditis subgenus Caenorhabditis (Rhabditidae, Nematoda). Citation: Journal of Zoological Systematics & Evolutionary Research 34: 217-233 1996 Type: ARTICLE Genes: Abstract: A phylogenetic analysis was conducted using morphological characters. Eleven of the 18 Caenorhabditis-species described were investigated. The polarity for character transformations was established and a cladogram and the character set of the stem species reconstructed. There are two possible positions for R. plicata. It was not possible to resolve the phylogenetic relationship of the Elegans-group, which consists of seven species, including the four best-known Caenorhabditis-species. Transformation series of characters, e.g. the structure of the precloacal lip, are presented. The evolution of a pharyngeal sleeve is discussed. For the terms caudal papilla, bursal papilla and ray are given precise definitions. Two individual rays are specified as 'anterior dorsal' and 'posterior dorsal'. We present here a new case of a Rhabditis with 10 pairs of bursal papillae where one pair (no. 10) is the phasmids. Information on the geographical distribution and the ecology of the Caenorhabditis-species is given. The markedly different ecological niches of these Species must be derived from a way of life in the stem species in patchily distributed decomposing organic material which necessitated a phoretic phase with waving behaviour of the dauer juveniles. ------------------- Key: 2634 Medline: 97146485 Authors: Liu FZ;Thatcher JD;Epstein HF Title: Induction of glyoxylate cycle expression in Caenorhabditis elegans - A fasting response throughout larval development. Citation: Biochemistry 36: 255-260 1997 Type: ARTICLE Genes: lin-4 lin-14 Abstract: The mRNA and the bifunctional protein for the two glyoxylate cycle (GC) enzymes, isocitrate lyase and malate synthase, are expressed in a tissue- and stage-specific pattern in Caenorhabditis elegans, Since expression of the two enzymes for the carbon-conserving glyoxylate cycle is regulated by the availability of carbon sources in microorganisms, we have studied the bifunctional GCP gene expression under fasting conditions and in certain mutants of C. elegans in order to understand possible mechanisms regulating its expression during nematode development. The GCP mRNA and protein levels were elevated in early larvae which were never fed, a result consistent with previous enzyme activity measurements [Khan, F. R., & McFadden, B. A. (1982) Exp. Parasitol. 54, 48-54]. However, larvae of later stages also expressed higher levels of GCP mRNA and protein when they were shifted from normal to fasting growing conditions. The GCP expression appeared to be regulated primarily at the transcriptional level throughout development. Although the expression of both the GCP gene and lin-14 peaks at about the same time during development and are induced by fasting, the regulation of the GCP gene is independent of the heterochronic lin-14 control mechanism of postembryonic lineages, as demonstrated by the fact that there was no significant change of the GCP at both mRNA and protein levels in the heterochronic lin-4 (If) and lin-14 (gf) mutants compared to the wild type. ------------------- Key: 2635 Medline: 97164723 Authors: Moskowitz IPG;Rothman JH Title: lin-12 and glp-1 are required zygotically for early embryonic cellular interactions and are regulated by maternal GLP-1 signaling in Caenorhabditis elegans. Citation: Development 122: 4105-4117 1996 Type: ARTICLE Genes: glp-1 lag-1 lag-2 lin-12 smg-1 Abstract: Cell-cell interactions mediated by LIN-12 and GLP-1, members of the LNG (LIN-12, Notch, GLP-1) family of receptors, are required to specify numerous cell fates during development of the nematode Caenorhabditis elegans. Maternally expressed GLP-1 participates in two of at least four sequential inductive interactions that specify the fates of early embryonic descendants of the AB founder cell. We report that GLP-1 and LIN-12, and apparently their ligand, LAG-2, as well as a downstream component, LAG-1, are required in the latter two inductions. We find that LAG-2 is expressed in the signaling cells and LIN-12 is expressed in cells receiving the inductions, consistent with their proposed roles as ligand and receptor, respectively. Furthermore, we report that maternal GLP-1 activity is required (1) to repress early zygotic lag-2 expression and (2) to activate zygotic lin-12 expression in the early embryo. The patterning of both receptor and ligand expression by maternal GLP-1 signaling establishes competence for the zygotic LNG-mediated cellular interactions and localizes these interactions to the appropriate cells. We propose that activation of maternal GLP-1 regulates zygotic lin-12 and lag-2 expression by a regulatory mechanism analogous to that described for the ------------------- Key: 2636 Medline: 97164727 Authors: Pettitt J;Wood WB;Plasterk RHA Title: cdh-3, a gene encoding a member of the cadherin superfamily, functions in epithelial cell morphogenesis in Caenorhabditis elegans. Citation: Development 122: 4149-4157 1996 Type: ARTICLE Genes: cdh-3 mut-2 nDf16 Abstract: Several genes that encode members of the cadherin superfamily have been identified in Caenorhabditis elegans. Based on the roles of cadherins in vertebrates and Drosophila, it is expected that they function in the control of epithelial morphogenesis, an event which is poorly understood at the molecular level in C. elegans. Reporter genes under the control of upstream sequences from one of b these genes, cdh-3, are expressed in developing epithelial cells, but also in a number of neuroectodermal cells that extend processes along some of these epithelial cells. We generated a loss-of-function mutation in cdh-3 by transpose son-mediated deletion mutagenesis. This mutation affects the morphogenesis of a single cell, hyp10, which forms the tip of the nematode tail. The lack of detectable defects associated with the other cells expressing cdh-3 reporter constructs hints at the existence of other genes that can compensate for cdh-3 loss of function. ------------------- Key: 2637 Medline: 97144416 Authors: LaMunyon CW;Ward S Title: Increased competitiveness of nematode sperm bearing the male X chromosome. Citation: Proceedings of the National Academy of Sciences USA 94: 185-189 1997 Type: ARTICLE Genes: cby-3 cby-4 mih-3 Abstract: Male offspring, which cannot reproduce independently, represent a cost of sexual reproduction. This cost is eliminated by the production of hermaphroditic offspring in the self-fertilizing nematode Caenarhabditis briggsae. However, these hermaphrodites can outcross by mating with males. Half the sperm received from males contain no sex chromosome and therefore give rise to male progeny. Mating with males should thus impose the cost of making male offspring. We found that male sperm took immediate precedence over hermaphrodite sperm, resulting in maximized outcrossing, but the appearance of male progeny was delayed after mating. This delay is caused by the male X-bearing sperm outcompeting their nullo-X counterparts. The competitive advantage of X-bearing sperm over nullo-X sperm is limited to sperm from males; it did not occur in a mutant hermaphrodite that produces both types of sperm. The chromosomal effect on sperm competitiveness in C. briggsae, which has not been observed in other species, suggests that the X chromosome has evolved a form of meiotic drive, selfishly increasing the competitiveness of sperm that bear it over those that do not. Thus, the multiple levels of sperm competitiveness found in C. briggsae maximize outcrossing after mating while delaying the cost of making male offspring. ------------------- Key: 2638 Medline: 97157491 Authors: Roehl H;Bosenberg M;Blelloch R;Kimble J Title: Roles of the RAM and ANK domains in signaling by the C. elegans GLP-1 receptor. Citation: EMBO Journal 15: 7002-7012 1996 Type: ARTICLE Genes: fem-1 glp-1 lag-1 lin-12 Abstract: In Caenorhabditis elegans, the GLP-1 receptor acts with a downstream transcriptional regulator, LAG-1, to mediate intercellular signaling, GLP-1 and LAG-1 are homologs of Drosophila Notch and Su(H) respectively. Here, we investigate the functions of two regions of the GLP-1 intracellular domain: the ANK repeat domain, which includes six cdc10/ankyrin repeats plus flanking amino acids, and the RAM domain, which spans similar to 60 amino acids just inside the transmembrane domain. First, we demonstrate that both ANK and RAM domains interact with the LAG-1 transcription factor. The interaction between the ANK domain and LAG-1 is only observed in nematodes by a co-focalization assay and, therefore, may be either direct or indirect. By contrast, the interaction between the RAM domain and LAG-1 is likely to be direct, since it is observed by co-precipitation of the protein in vitro as well as by yeast two-hybrid experiments. Second, we demonstrate that the RAM domain, when expressed in nematodes without a functional ANK repeat domain, does not mimic the unregulated receptor in directing cell fates or interfere with signaling by endogenous components. Finally, we show in yeast that the ANK repeats are strong transcriptional activators. Furthermore, missense mutations that eliminate receptor activity also abolish transcriptional activation by the GLP-1 ANK repeats in yeast. We speculate that one possible function for the ANK repeat domain is to act as a transcriptional co-activator ------------------- Key: 2639 Medline: Authors: Chen H;Ng TD;Martinez J;Schatz BR Title: A concept space approach to addressing the vocabulary problem in scientific information retrieval: An experiment on the Worm Community System. Citation: Journal of the American Society for Information Science 48: 17-31 1997 Type: ARTICLE Genes: Abstract: This research presents an algorithmic approach to addressing the vocabulary problem in scientific information retrieval and information sharing, using the molecular biology domain as an example. We first present a literature review of cognitive studies related to the vocabulary problem and vocabulary-based search aids(thesauri) and then discuss techniques for building robust and domain-specific thesauri to assist in cross-domain scientific information retrieval. Using a variation of the automatic thesaurus generation techniques, which we refer to as the concept space approach, we recently conducted an experiment in the molecular biology domain in which we created a C. elegans worm thesaurus of 7,657 worm-specific terms and a Drosophila fly thesaurus of 15,626 terms. About 30% of these terms overlapped, which created vocabulary paths from one subject domain to the other. Based on a cognitive study of term association involving four biologists, we found that a large percentage (59.6-85.6%) of the terms suggested by the subjects were identified in the conjoined fly-worm thesaurus. However, we found only a small percentage( 8.4-18.1%) of the associations suggested by the subjects in the thesaurus. In a follow-up document retrieval study involving eight fly biologists, an actual worm database (Worm Community System), and the conjoined flyworm thesaurus, subjects were able to find more relevant documents (an increase from about 9 documents to 20) and to improve the document recall level (from 32.41 to 65.28%) when using the thesaurus, although the precision level did not improve significantly. Implications of adopting the concept space approach for addressing the vocabulary problem in Internet and digital libraries applications are ------------------- Key: 2640 Medline: 97147299 Authors: Polani PE Title: Developmental asymmetries in experimental animals. Citation: Neurosciences & Biobehavioral Reviews 20: 645-649 1996 Type: REVIEW Genes: Abstract: The early embryo orients to the antero-posterior axis and differentiates along this, and the dorso-ventral and lateral axes. From Drosophila melanogaster, detailed knowledge has accrued of how segmentation and dorso-ventral differentiation proceed, and of their genic control, mostly by selector and homeobox (Hox) genes. The study of the control of lateral differentiation, instead, has been largely neglected. Yet handed asymmetry (the ''obvious'' asymmetries of, for example, heart, lung, anatomical features of the nervous system, etc.) is basic and, possibly, universal. In the mouse, two genes control this: the iv gene which, when mutated, leads to random, in the place of biased, asymmetry and so to random situs inversus viscerum; and the inv mutation which, by contrast, results in 100% situs inversus. Both mutants act as autosomal recessives. Human situs inversus is heterogeneous and may be akin to that produced by the murine iv gene. In spite of situs inversus, there is no shift of hand preference; but there is no information on other lateralization, e.g. of language or of dermatoglyphic patterns. Handed asymmetry is known in Drosophila, but there is no information on its control. In the experimental nematode, Caenorhabditis elegans, asymmetry arises when differently programmed cells arrange themselves to the two body sides, and is present already at the six-cell stage; and even the major sensory neurons chains along the body axis are distributed unequally on the two sides of the worm. Experimentally, by embryonic micro-manipulation or the use of chemical mutagens, the normal and invariate direction of handed asymmetry can be reversed. ------------------- Key: 2641 Medline: 97176149 Authors: Baylis HA;Sattelle DB;Lane NJ Title: Genetic analysis of cholinergic nerve terminal function in invertebrates. Citation: Journal of Neurocytology 25: 747-762 1996 Type: ARTICLE Genes: ace-1 ace-2 ace-3 acr-2 acr-3 cha-1 deg-3 lev-1 lev-8 lev-9 lev-10 rab-3 ric-4 snb-1 snt-1 unc-11 unc-13 unc-17 unc-18 unc-26 unc-29 unc-38 unc-41 unc-50 unc-63 unc-64 unc-74 unc-75 unc-104 Abstract: Genetic analysis of nerve terminal function is proving fruitful and studies on invertebrates are making a substantial impact. In this survey, particular emphasis has been placed on cholinergic chemical synaptic transmission. The advanced genetics of Drosophila melanogaster and Caenorhabditis elegans with their rich diversity of behavioural and biochemical mutants is providing new insights into the functions of key molecular components of synapses. A 'space-invader' mutant of Periplaneta americana permits investigations of competition between neurons during synaptogenesis and its impact on neurotransmitter release. The growing importance of the C. elegans genome as a major research resource is emphasized in this survey. ------------------- Key: 2642 Medline: 97175008 Authors: Heierhorst J;Tang X;Lei JY;Probst WC;Weiss KR;Kemp BE;Benian GM Title: Substrate specificity and inhibitor sensitivity of Ca2+/S100-dependent twitchin kinases. Citation: European Journal of Biochemistry 242: 454-459 1996 Type: ARTICLE Genes: Abstract: Myosin-associated giant protein kinases of the titin/twitchin-like superfamily have previously been implicated in the regulation of muscle function, based on genetic and physiological studies. We find that recombinant constitutively active Caenorhabditis elegans and Aplysia twitchin kinase fragments differ in their catalytic activities and peptide-substrate specificities, as well as in their sensitivities to the naphthalene sulfonamide inhibitors 1-(5-chloronaphthalenesulfonyl)-1H-hexahydro-1,4-diazepine (ML-7) and 1-(5-iodonaphthalenesulfonyl)-1H-hexahydro-1,4-diazepine (ML-9). The constitutively active Aplysia twitchin kinase fragment has a remarkably high activity (V-max > 100 mu mol . min(-1) . mg(-1)) towards some substrate peptides. The autoinhibited forms of these twitchin kinases can be activated in a Ca2+-dependent manner by the dimeric form of the S100A1 protein (S100A1(2)). The twitchin kinase S100A1(2)-binding site can also bind Ca2+/calmodulin but neither kinase is activated by calmodulin. The data provide a functional basis for the ongoing crystallographic study of twitchin kinase fragments. ------------------- Key: 2643 Medline: 97157471 Authors: Kobe B;Heierhorst J;Feil SC;Parker MW;Benian GM;Weiss KR;Kemp BE Title: Giant protein kinases: domain interactions and structural basis of autoregulation. Citation: EMBO Journal 15: 6810-6821 1996 Type: ARTICLE Genes: unc-22 Abstract: The myosin-associated giant protein kinases twitchin and titin are composed predominantly of fibronectin- and immunoglobulin-like modules. We report the crystal structures of two autoinhibited twitchin kinase fragments, one from Aplysia and a larger fragment from Caenorhabditis elegans containing an additional C-terminal immunoglobulin-like domain. The structure of the longer fragment shoes that the immunoglobulin domain contacts the protein kinase domain on the opposite side from the catalytic cleft, laterally exposing potential myosin binding residues. Together, the structures reveal the cooperative interactions between the autoregulatory region and the residues from the catalytic domain involved in protein substrate binding, ATP binding, catalysis and the activation loop, and explain the differences between the observed autoinhibitory mechanism and the one found in the structure of calmodulin-dependent kinase I. ------------------- Key: 2644 Medline: 97166032 Authors: McCarter J;Bartlett B;Dang T;Schedl T Title: Soma-germ cell interactions in Caenorhabditis elegans: Multiple events of hermaphrodite germline development require the somatic sheath and spermathecal lineages. Citation: Developmental Biology 181: 121-143 1997 Type: ARTICLE Genes: ced-3 ceh-18 emo-1 fem-3 fog-1 fog-2 fog-3 glp-1 her-1 let-60 mup-2 ncl-1 tra-2 unc-54 Abstract: Germ cells complete multiple events to form functional oocytes and sperm. In the Caenorhabditis elegans hermaphrodite, germ cells develop in proximity to the somatic gonad sheath and spermathecal cells. We present evidence from cellular laser ablation studies indicating that cells of the somatic sheath and spermathecal lineages play critical roles in four events of hermaphrodite germline development. (1) Cells of the sheath and spermathecal lineage support germline proliferation; ablation of sheath/spermathecal precursor cells reduces mitotic proliferation. (2) These cells also play a role in the exit of germ cells from the pachytene stage of meiotic prophase and/or gamete differentiation; ablation can result in undifferentiated germ cells arrested in pachytene. (3) Proximal sheath and distal spermatheca cells are required for ovulation of the oocyte. During wild-type ovulation, the mature oocyte is expelled from the gonad arm by contraction of the proximal myoepithelial sheath and dilation of the distal spermatheca. Ablation of these cells traps mature oocytes in the gonad arm where they endomitotically replicate their DNA (the Emo phenotype). (4) Cells of the sheath and spermathecal lineage also appear to promote the male germ cell fate since ablation of one sheath/spermathecal precursor cell can feminize the hermaphrodite germ line. These somatic ablation-induced germline phenotypes demonstrate that the somatic gonad is required for multiple events in C. elegans germline development. Further, these results suggest that soma to germline cell-cell interactions in C. elegans are physiological in character (i.e., contraction during ovulation) as well as regulatory. ------------------- Key: 2645 Medline: 97155929 Authors: Khanna N;Cressman CP;Tatara CP;Williams PL Title: Tolerance of the nematode Caenorhabditis elegans to pH, salinity and hardness in aquatic media. Citation: Archives of Environmental Contamination and Toxicology 32: 110-114 1997 Type: ARTICLE Genes: Abstract: The toxicity of many chemicals depends on the physical conditions of the test environment, and any change or adjustment made to the tests can alter the results. Therefore it is important to establish the sensitivity of the test organism over a range of test conditions to determine when it is necessary to make adjustment and to what extent. In this study, we establish the tolerance range of the nematode Caenorhabditis elegans for pH, salinity and hardness using 24- (without food source) and 96-h (with food source) aquatic toxicity tests. The tests were performed in two media: K-medium and moderately hard reconstituted water (MHRW). C. elegans has high tolerance under these test conditions. In K-medium worms survived a pH range of 3.1 to 11.9 for 24 h and 3.2 to 11.8 for 96 h without significant (p>0.05) lethality. In MHRW the pH range was 3.4 to 11.9 for 24 h and 3.4 to 11.7 for 96 h. Salinity tolerance tests were approximated with NaCl and KCl individually. Up to 15.46 g/L NaCl and 11.51 g/L KCl were tolerated by C. elegans in K-medium without significant lethality (p>0.05). In MHRW higher salt concentrations were tolerated; about 20.5 g/L NaCl and 18.85 g/L KCl did not show any adverse effect compared to control. Hardness tolerance was tested by adding NaHCO3. The nematode could tolerate 0.236 to 0.246 g/L of NaHCO3. The high tolerance of C. elegans to these test conditions (pH, salinity, and hardness) allows more versatility than other organisms commonly used in aquatic toxicity tests. It also allows the monitoring of effluents and receiving waters from freshwater or estuarine sources without ------------------- Key: 2646 Medline: 97163389 Authors: Tavernarakis N;Shreffler W;Wang S;Driscoll M Title: unc-8, a DEG/ENaC family member, encodes a subunit of a candidate mechanically gated channel that modulates C. elegans locomotion. Citation: Neuron 18: 107-119 1997 Type: ARTICLE Genes: deg-1 del-1 mec-4 mec-6 mec-10 unc-8 unc-105 Abstract: Mechanically gated ion channels are important modulators of coordinated movement, yet little is known of their molecular properties. We report that C. elegans unc-8, originally identified by gain-of-function mutations that induce neuronal swelling and severe uncoordination, encodes a DEG/ENaC family member homologous to subunits of a candidate mechanically gated ion channel. unc-8 is expressed in several sensory neurons, interneurons, and motor neurons. unc-8 null mutants exhibit previously unrecognized but striking defects in the amplitude and wavelength of sinusoidal tracks inscribed as they move through an E. coli lawn. We hypothesize that UNC-8 channels could modulate coordinated movement in response to body stretch. del-1, a second DEG/ENaC family member coexpressed with unc-8 in a subset of motor neurons, might also participate in a channel that contributes to nematode ------------------- Key: 2647 Medline: 97158724 Authors: Sommer RJ Title: Evolutionary changes of developmental mechanisms in the absence of cell lineage alterations during vulva formation in the Diplogastridae (Nematoda). Citation: Development 124: 243-251 1997 Type: ARTICLE Genes: Abstract: The origin of novelty is one of the least understood evolutionary phenomena. One approach to study evolutionary novelty comes from developmental biology. During developmental cell fate specification of the nematode Pristionchus pacificus (Diplogastridae), five cell fates can be distinguished within a group of twelve ventral epidermal cells. The differentiation pattern of individual cells includes programmed cell death, cell fusion and vulval differentiation after induction by the gonad. A cell lineage comparison among species of seven different genera of the Diplogastridae indicates that the differentiation pattern of ventral epidermal cells is highly conserved. Despite this morphological conservation, cell ablation experiments indicate many independent alterations of underlying mechanisms of cell fate specification. Cell fusion and individual cell competence change during evolution as well as the differentiation property in response to inductive signaling. These results suggest that developmental mechanisms, some of which are redundantly involved in vulval fate specification of the genetic model organism Caenorhabditis elegans, can evolve without concomitant morphological change. ------------------- Key: 2648 Medline: 97158725 Authors: Felix MA;Sternberg PW Title: Two nested gonadal inductions of the vulva in nematodes. Citation: Development 124: 253-259 1997 Type: ARTICLE Genes: Abstract: How do intercellular signals that pattern cell fates vary in evolution? During nematode vulva development, precursor cells acquire one of three fates in a pattern centered around the gonadal anchor cell. Non-vulval fates are at the periphery, outer and inner vulval fates are towards the center. In Caenorhabditis elegans, the three fates are specified around the same time by an induction by the anchor cell and lateral signaling between the vulva precursor cells. We find that, in three other nematode species (Panagrolaimus, Oscheius and Rhabditella spp.) spanning two families, the centered pattern is obtained by two temporally distinct gonadal inductions. The first induction specifies vulval fates; the second induction specifies the inner vulval fates in a subset of the precursors' daughters. This evolutionary change in the spatiotemporal connectivity of cell interactions allows centering of the pattern between two precursors in ------------------- Key: 2649 Medline: 97169851 Authors: Kadyk LC;Lambie EJ;Kimble J Title: glp-3 is required for mitosis and meiosis in the Caenorhabditis elegans germ line. Citation: Genetics 145: 111-121 1997 Type: ARTICLE Genes: fem-3 fog-1 gld-1 glp-1 glp-3 glp-4 nDf16 sDf127 Abstract: The germ line is the only tissue in Caenorhabditis elegans in which a stem cell population continues to divide mitotically throughout life; hence the cell cycles of the germ line and the soma are regulated differently. Here we report the genetic and phenotypic characterization of the glp-3 gene. In animals homozygous for each of five recessive loss-of-function alleles, germ cells in both hermaphrodites and males fail to progress through mitosis and meiosis, but somatic cells appear to divide normally. Germ cells in animals grown at 15 degrees appear by DAPI staining to be uniformly arrested at the G2/M transition with <20 germ cells per gonad on average, suggesting a checkpoint-mediated arrest. In contrast, germ cells in mutant animals grown at 25 degrees frequently proliferate slowly during adulthood, eventually forming small germ lines with several hundred germ cells. Nevertheless, cells in these small germ lines never undergo meiosis. Double mutant analysis with mutations in other genes affecting germ cell proliferation supports the idea that glp-3 may encode a gene product that is required for the mitotic and meiotic cell cycles in the C. elegans germ line. ------------------- Key: 2650 Medline: 97222101 Authors: Guthrie S Title: Axon guidance: Netrin receptors are revealed. Citation: Current Biology 7: R6-R9 1997 Type: REVIEW Genes: unc-5 unc-6 unc-40 Abstract: Netrins are molecules that guide growing axons and that are strikingly similar in sequence and in function in flies, nematodes and vertebrates. Now, members of a family of netrin receptors have been identified in all three animal groups and shown to have crucial, conserved roles in axon navigation. ------------------- Key: 2651 Medline: 97071641 Authors: Johnson TE;Lithgow GJ;Murakami S Title: Hypothesis: Interventions that increase the response to stress offer the potential for effective life prolongation and increased health. Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 51: B392-B395 1996 Type: ARTICLE Genes: age-1 clk-1 daf-2 daf-16 daf-23 spe-26 Abstract: In the last decade it has become evident that many laboratory manipulations, both genetic and environmental, can lend to significant life extension. All or almost all of the observed life-extension phenotypes are associated with increased resistance and/or ability to respond to environmental stress. These observations show dramatically that life span is not maximized. We suggest that latent within many species - perhaps even humans - is the ability for large increases of life expectancy. The striking correlation between the increased stress resistance of oil long-lived mutants in C. elegans and other species and the increased resistance of dietary restricted rodents to environmental toxins is consistent with an evolutionary conservation of a life-span maintenance/environmental stress resistance program. We suggest that it may be possible to develop methods for life extension in mammals, including humans, using relatively straightforward manipulations, such as drug treatments. It should be obvious that these findings have tremendous implications for human society at large, and we suggest that the implications of these findings should be explored. ------------------- Key: 2652 Medline: 97154530 Authors: Zorio DAR;Lea K;Blumenthal T Title: Cloning of Caenorhabditis U2AF(65): an alternatively spliced RNA containing a novel exon. Citation: Molecular and Cellular Biology 17: 946-953 1997 Type: ARTICLE Genes: rab-18 uaf-1 Abstract: The U2 small nuclear ribonucleoprotein particle (snRNP) auxiliary factor, U2AF, is an essential splicing factor required for recognition of the polypyrimidine tract and subsequent U2 snRNP assembly at the branch point. Because Caenorhabditis elegans introns lack both polypyrimidine tract and branch point consensus Sequences but have a very highly conserved UUUUCAG/R consensus at their 3' splice sites, we hypothesized that U2AF might serve to recognize this sequence and thus promote intron recognition in C. elegans. Here we report the cloning of the gene for the large subunit of U2AF, uaf-1. Three classes of cDNA were identified. In the most abundant class the open reading frame is similar to that for the U2AF(65) from mammals and flies. The remaining two classes result from an alternative splicing event in which an exon containing an in-frame stop codon is inserted near the beginning of the second RNA recognition motif. However, this alternative mRNA is apparently not translated. Interestingly, the inserted exon contains 10 matches to the 3' splice site consensus. To determine whether this feature is conserved, we sequenced uaf-1 from the related nematode Caenorhabditis briggsae, It is composed of six exons, including an alternatively spliced third exon interrupting the gene at the same location as in C. elegans. uaf-1 is contained in an operon with the rab-18 gene in both species. Although the alternative exons from the two species are not highly conserved and would not encode related polypeptides, the C. briggsae alternative exon has 18 matches to the 3' splice site consensus. We hypothesize that the array of 3' splice site-like sequences in the pre-mRNA and alternatively spliced exon may have a regulatory role. The alternatively spliced RNA accumulates at high levels following starvation, suggesting that this RNA may represent an adaption for reducing U2AF(65) levels when pre-mRNA levels ------------------- Key: 2653 Medline: 97153022 Authors: Tang Z;Okamoto T;Boontrakulpoontawee P;Katada T;Otsuka AJ;Lisanti MP Title: Identification, sequence, and expression of an invertebrate caveolin gene family from the nematode Caenorhabditis elegans - Implications for the molecular evolution of mammalian... Citation: Journal of Biological Chemistry 272: 2437-2445 1997 Type: ARTICLE Genes: cav-1 cav-2 Abstract: Caveolae are vesicular organelles that represent an appendage of the plasma membrane. Caveolin, a 21-24-kDa integral membrane protein, is a principal component of caveolae membranes in vivo. Caveolin has been proposed to function as a plasma membrane scaffolding protein to organize and concentrate signaling molecules within caveolae, including heterotrimeric G proteins (alpha and beta gamma subunits), In this regard, caveolin interacts directly with G(alpha) subunits and can functionally regulate their activity. To date, three cDNAs encoding four subtypes of caveolin have been described in vertebrates. However, evidence for the existence of caveolin proteins in less complex organisms has been lacking. Here, we report the identification, cDNA sequence and genomic organization of the first invertebrate caveolin gene, Cav(ce) (for caveolin from Caenorhabditis elegans). The Cav(ce) gene, located on chromosome TV, consists of two exons interrupted by a 125-nucleotide intron sequence, The region of Cav(ce) that is strictly homologous to mammalian caveolins is encoded by a single exon in Cav(ce). This suggests that mammalian caveolins may have evolved from the second exon of Cav(ce). Cav(ce) is roughly equally related to all three known mammalian caveolins and, thus, could represent a common ancestor. Remarkably, the invertebrate Cav(ce) protein behaves like mammalian caveolins: (i) Cav(ce) forms a high molecular mass oligomer, (ii) assumes a cytoplasmic membrane orientation, and (iii) interacts with G proteins. A 20-residue peptide encoding the predicted Gr protein binding region of Cav(ce) possesses "GDP dissociation inhibitor like activity" with the same potency as described earlier for mammalian caveolin-1. Thus, caveolin appears to be structurally and functionally conserved from worms to man. In addition, we find that there are at least two caveolin-related genes expressed in C. elegans, defining an invertebrate caveolin gene family. ------------------- Key: 2654 Medline: 97167645 Authors: Crittenden SL;Rudel D;Binder J;Evans TC;Kimble J Title: Genes required for GLP-1 asymmetry in the early Caenorhabditis elegans embryo. Citation: Developmental Biology 181: 36-46 1997 Type: ARTICLE Genes: apx-1 emb-1 emb-3 emb-4 emb-5 emb-6 emb-7 emb-8 emb-11 emb-12 emb-13 emb-16 emb-18 emb-20 emb-21 emb-23 emb-25 emb-26 emb-27 emb-30 emb-31 emb-33 glp-1 mex-1 par-1 par-2 par-3 par-4 par-5 par-6 pie-1 skn-1 zyg-1 zyg-2 zyg-8 Abstract: The translation of maternal glp-1 mRNA is regulated both temporally and spatially in the early Caenorhabditis elegans embryo (T. e. Evans, S. L. Crittenden, V. Kodoyianni, and J. Kimble, Cell 77, 183-194, 1994). To investigate the control of embryonic glp-1 expression, we have examined the distribution of GLP-1 protein in selected maternal effect mutants that affect pattern or fate in the early embryo. We find that mutants that disrupt anterior-posterior asymmetry in the early embryo (par-1-par-6, emb-8, Par(q537)) disrupt the spatial but not temporal control of GLP-1 expression: GLP-1 is observed at the normal stage of embryogenesis in par-like mutants; however, it is uniformity distributed, In contrast mutants that alter blastomere identity (skn-1, pie-1, mex-1, apx-1) do not affect the normal GLP-1 pattern, We conclude that genes controlling the asymmetry of cellular components, including P granules, also control GLP-1 asymmetry ill the early embryo. The finding that mutants that disrupt anterior-posterior asymmetry translate GLP-1 in all blastomeres suggests that loss of embryonic asymmetry ------------------- Key: 2655 Medline: 97228555 Authors: Chen EB;Branda CS;Stern MJ Title: Genetic enhancers of sem-5 define components of the gonad-independent guidance mechanism controlling sex myoblast migration in Caenorhabditis elegans Citation: Developmental Biology 182: 88-100 1997 Type: ARTICLE Genes: clr-1 egl-15 egl-17 ksr-1 let-60 let-341 lin-45 mek-2 mpk-1 sem-5 unc-53 unc-71 unc-73 eDf2 Abstract: The migrations of the sex myoblasts in Caenorhabditis elegans hermaphrodites involve two guidance mechanisms: a gonad-dependent attraction that confers precise positioning of the sex myoblasts and a gonad-independent mechanism that is sufficient for coarse positioning in the absence of the gonad (Thomas et al., 1990). Here we show that mutations in unc-53, unc-71, and unc-73 disrupt sex myoblast positioning in the absence of the gonad, while they do not affect positioning in the presence of the gonad. Thus, mutations in these genes appear to compromise the gonad-independent mechanism without affecting motility or the gonad-dependent attraction. Mutations in sem-5 confer dramatic sex myoblast positioning defects in double mutant combinations with unc-53, unc-71, or unc-73 mutations, even in the presence of the gonad. This suggests that sem-5 is required for the gonad-dependent attractive mechanism. Mutations in let-60 ras and let-341 also confer sex myoblast migration defects in an unc-53 background, implicating these genes in gonad-dependent positioning as well. ------------------- Key: 2656 Medline: 97228560 Authors: Clandinin TR;Katz WS;Sternberg PW Title: Caenorhabditis elegans HOM-C genes regulate the response of vulval precursor cells to inductive signal. Citation: Developmental Biology 182: 150-161 1997 Type: ARTICLE Genes: let-23 let-60 lin-1 lin-2 lin-3 lin-7 lin-12 lin-39 mab-5 Abstract: Factors that determine the competence of cells to respond to extracellular cues are not well. understood. We demonstrate that two HOM-C transcription factors have antagonistic roles in determining the ability of Caenorhabditis elegans vulval precursor cells (VPCs) to respond to the inductive signal from the anchor cell of the somatic gonad. The vulva develops from a subset of ectodermal vulval precursor cells distributed along the anteroposterior axis. Vulval patterning depends on both a localized inductive signal, the LIN-3 growth factor, and lateral signaling between induced VPCs. One HOM-C gene, the Antp homolog mab-5, is expressed in the posterior two VPCs. By examining the response of single VPCs to controlled doses of inductive signal in wild-type and in mab-5 mutant animals, we demonstrate that mab-5 reduces the competence of these two cells. Moreover, a gain-of-function allele of mab-5 that causes ectopic expression of MAB-5 in all VPCs reduces the sensitivity of all VPCs to inductive signal. Additional experiments suggest that another HOM-C gene, the Scr homolog lin-39, is required for VPCs in wild-type animals to respond to activation of inductive signal. Genetic epistasis tests are consistent with models in which lin-39 acts downstream of the RAS pathway to regulate response to inductive signal. We propose that the spatial pattern of HOM-C gene expression may enhance the precision ------------------- Key: 2657 Medline: 97199162 Authors: Guarente L Title: What makes us tick? Citation: Science 275: 943-944 1997 Type: REVIEW Genes: clk-1 Abstract: What determines how long an animal can live? Some have argued that the life-span of a species is limited by a fixed total metabolic potential that is consumed over a lifetime. This follows from the observation that smaller animals have faster metabolic rates and generally shorter life-spans. Consistent with this idea, rats or mice that have existed on a diet reduced in calories live longer than animals that were allowed to eat as much as they liked. A corollary of this view is that the "clock" that times aging might be cumulative damage that is generated by toxic by-products of metabolism, such as oxygen radicals. Others have suggested that life-span may be genetically determined and that these genetic factors override any simple metabolic readout. This could explain why bats and mice, mammals of roughly the same size, have life-spans that differ by a factor of 5 to 10. This view also suggests that the clock is a genetic program set at a different rate in each species. The cloning and sequencing of the clk-1 gene of Caenorhabditis elegans reported in this issue, along with recent findings discussed below, suggests how ------------------- Key: 2658 Medline: 97172561 Authors: Ewbank JJ;Barnes TM;Lakowski B;Lussier M;Bussey H;Hekimi S Title: Structural and functional conservation of the Caenorhabditis elegans timing gene clk-1. Citation: Science 275: 980-983 1997 Type: ARTICLE Genes: clk-1 toc-1 Abstract: Mutations in the Caenorhabditis elegans gene clk-1 affect biological timing and extend longevity. The gene clk-1 was identified, and the cloned gene complemented the clk-1 phenotypes and restored normal longevity. The CLK-1 protein was found to be conserved among eukaryotes, including humans, and structurally similar to the yeast metabolic regulator Cat5p (also called Coq7p). These proteins contain a tandem duplication of a core 82-residue domain. clk-1 complemented the phenotype of cat5/coq7 null mutants, demonstrating that clk-1 and CAT5/COQ7 share biochemical function and that clk-1 acts at the level of cellular physiology. ------------------- Key: 2659 Medline: 97198186 Authors: Goldstein B;Freeman G Title: Axis specification in animal development. Citation: BioEssays 19: 105-116 1997 Type: REVIEW Genes: Abstract: Axis specification is the first step in defining specific regions of the developing embryo. Embryos exploit asymmetries, either pre-existing in the egg or triggered by external cues, to establish embryonic axes. The axial information is then used to generate regional differences within the embryo. In this review, we discuss experiments in animals which address three questions: whether the unfertilized egg is constructed with pre-determined axes, what cues are used to specify the embryonic axes, and how these cues are interpreted to generate the initial regional differences within the embryo. Based on mapping the data onto an animal phylogeny, we then propose a scenario for how this primary developmental decision occurred in ancestral metazoans. ------------------- Key: 2660 Medline: 97195705 Authors: Grant B;Greenwald I Title: Structure, function, and expression of SEL-1, a negative regulator of LIN-12 and GLP-1 in C. elegans. Citation: Development 124: 637-644 1997 Type: ARTICLE Genes: glp-1 lin-12 mtl-2 myo-3 sel-1 Abstract: Previous work indicated that sel-1 functions as a negative regulator of lin-12 activity, and predicted that SEL-1 is a secreted or membrane associated protein. In this study, we describe cell ablation experiments that suggest sel-1 mutations elevate lin-12 activity cell autonomously. We also use transgenic approaches to demonstrate that the predicted signal sequence of SEL-1 can direct secretion and is important for function, while a C-terminal hydrophobic region is not required for SEL-1 function. In addition, by analyzing SEL-1 localization using specific antisera we find that SEL-1 is localized intracellularly, with a punctate staining pattern suggestive of membrane bound vesicles. We incorporate these observations, and new information about a related yeast gene, into a proposal for a possible mechanism for SEL-1 function in LIN-12 turnover. ------------------- Key: 2661 Medline: 97195715 Authors: Guedes S;Priess JR Title: The C. elegans MEX-1 protein is present in germline blastomeres and is a P granule component. Citation: Development 124: 731-739 1997 Type: ARTICLE Genes: mex-1 pal-1 pes-10 pie-1 skn-1 Abstract: In the nematode Caenorhabditis elegans, germ cells arise from early embryonic cells called germline blastomeres. Cytoplasmic structures called P granules are present in the fertilized egg and are segregated into each of the germline blastomeres during the first few cleavages of the embryo. Mutations in the maternally expressed gene mex-1 disrupt the segregation of P granules, prevent the formation of germ cells, and cause inappropriate patterns of somatic cell differentiation. We have cloned the mex-1 gene and determined the distribution pattern of the mex-1 gene products. The MEX-1 protein contains two copies of an unusual 'finger' domain also found in the PIE-1 protein of C. elegans. PIE-1 has been shown to be expressed in germline blastomeres, and is a component of P granules. We show here that MEX-1 also is present in germline blastomeres and is a P granule component, although MEX-1 is a cytoplasmic protein while PIE-1 is present in both the nucleus and cytoplasm. We further show that MEX-1 is required to restrict PIE-1 expression and activity to the germline blastomeres during the early embryonic cleavages. ------------------- Key: 2662 Medline: 97195717 Authors: Goodwin EB;Hofstra K;Hurney CA;Mango S;Kimble J Title: A genetic pathway for regulation of tra-2 translation. Citation: Development 124: 749-758 1997 Type: ARTICLE Genes: fem-1 fem-2 fem-3 fog-1 fog-2 fog-3 her-1 laf-1 tra-1 tra-2 tra-3 saDf1 Abstract: In Caenorhabditis elegans, the tra-2 sex-determining gene is regulated at the translational level by two 28 nt direct repeat elements (DREs) located in its 3' untranslated region (3'UTR). DRF is a factor that binds the DREs and may be a trans-acting translational regulator of tra-2. Here we identify two genes that are required for the normal pattern of translational control. A newly identified gene, called laf-1, is required for translational repression by the tra-2 3'UTR. In addition, the sex-determining gene, tra-3, appears to promote female development by freeing tra-2 from laf-1 repression. Finally, we show that DRF activity correlates with translational repression of tra-2 during development and that tra-3 regulates DRF activity. We suggest that tra-3 may promote female development by releasing tra-2 from translation repression by laf-1 and that translational control is important for proper sex determination - both in the early embryo and during ------------------- Key: 2663 Medline: 97177114 Authors: Spector MS;Desnoyers S;Hoeppner DJ;Hengartner MO Title: Interaction between the C. elegans cell-death regulators CED-9 and CED-4. Citation: Nature 385: 653-656 1997 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: Programmed cell death (apoptosis) is an evolutionarily conserved process used by multicellular organisms to eliminate cells that are not needed or are potentially detrimental to the organism(1,2). Members of the Bcl-2 family of mammalian proteins are intimately involved in the regulation of apoptosis, but, their precise mechanism of action remains unresolved(3-5). In Caenorhabditis elegans, the Bcl-2 homologue CED-9 prevents cell death by antagonizing the death-promoting activities of CED-3, a member of the Caspase family of death proteases, and of CED-4, a protein with no known mammalian homologue(6-9). Here we show that CED-9 interacts physically with CED-4. Mutations that reduce or eliminate CED-9 activity also disrupt its ability to bind CED-4, suggesting that this interaction is important for CED-9 function. Thus, CED-9 might control C. elegans cell death by binding to and regulating CED-4 activity. We propose that mammalian Bcl-2 family members might control apoptosis in a similar way through interaction and regulation of CED-4 homologues or analogues. ------------------- Key: 2664 Medline: 97177103 Authors: Schnabel R;Schnabel H Title: Hox genes misled by local environments. Citation: Nature 385: 588-589 1997 Type: REVIEW Genes: mab-5 Abstract: Cowing and Kenyon raise an important issue concerning Hox genes by suggesting that these genes may not only be expressed according to position but also according to cell lineage. This suggestion is based on two experiments in which the so-called M cell and two hypodermal V6 cells were manipulated to express a Hox gene, mab-5, outside the posterior region of the Caenorhabditis elegans embryo. Here we propose a less radical interpretation of these ------------------- Key: 2665 Medline: Authors: Riddle DL;Blumenthal T;Meyer BJ;Priess JR Title: Introduction to C. elegans. Citation: "C. elegans II" DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 1-22 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2666 Medline: Authors: Waterston RH;Sulston JE;Coulson AR Title: The Genome. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 23-45 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2667 Medline: Authors: Albertson DG;Rose AM;Villeneuve AM Title: Chromosome Organization, Mitosis, and Meiosis. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 47-78 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2668 Medline: Authors: Johnsen RC;Baillie DL Title: Mutation Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 79-95 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2669 Medline: Authors: Plasterk RHA;van Luenen HGAM Title: Transposons Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 97-116 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2670 Medline: Authors: Blumenthal T;Steward K Title: RNA Processing and Gene Structure. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 117-145 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2671 Medline: Authors: McGhee JD;Krause MW Title: Transcription Factors and Transcriptional Regulation. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 147-184 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2672 Medline: Authors: Anderson P;Kimble J Title: mRNA and Translation. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 185-208 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2673 Medline: Authors: Meyer BJ Title: Sex Determination and X Chromosome Dosage Compensation. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 209-240 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2674 Medline: Authors: Schedl T Title: Developmental Genetics of the Germ Line. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 241-269 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2675 Medline: Authors: L'Hernault SWL Title: Spermatogenesis Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 271-294 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2676 Medline: Authors: Emmons SW;Sternberg PW Title: Male Development and Mating Behavior. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 295-334 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2677 Medline: Authors: Kemphues KJ;Strome S Title: Fertilization and Establishment of Polarity in the Embryo. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 335-359 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2678 Medline: Authors: Schnabel R;Priess JR Title: Specification of Cell Fates in the Early Embryo. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 361-382 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2679 Medline: Authors: Hengartner MO Title: Cell Death. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 383-415 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2680 Medline: Authors: Moerman DG;Fire A Title: Muscle: Structure, Function, and Development. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 417-470 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2681 Medline: Authors: Kramer JM Title: Extracellular Matrix. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 471-500 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2682 Medline: Authors: Ambros V Title: Heterochronic Genes. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 501-518 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2683 Medline: Authors: Greenwald I Title: Development of the Vulva. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 519-541 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2684 Medline: Authors: Ruvkun G Title: Patterning the Nervous System. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 543-581 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2685 Medline: Authors: Antebi A;Norris CE;Hedgecock EM;Garriga G Title: Cell and Growth Cone Migrations. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 583-609 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2686 Medline: Authors: Rand JB;Nonet ML Title: Synaptic Transmission. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 611-643 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2687 Medline: Authors: Driscoll M;Kaplan J Title: Mechanotransduction. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 645-677 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2688 Medline: Authors: Avery L;Thomas JH Title: Feeding and Defecation. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 679-716 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2689 Medline: Authors: Bargmann CI;Mori I Title: Chemotaxis and Thermotaxis. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 717-737 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2690 Medline: Authors: Riddle DL;Albert PS Title: Genetic and Environmental Regulation of Dauer Larva Development. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 739-768 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2691 Medline: Authors: Jorgensen EM;Rankin C Title: Neural Plasticity. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 769-790 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2692 Medline: Authors: Kenyon C Title: Environmental Factors and Gene Activities that Influence Life Span. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 791-813 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2693 Medline: Authors: Fitch DHA;Thomas WK Title: Evolution. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 815-850 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2694 Medline: Authors: Blaxter M;Bird D Title: Parasitic Nematodes. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 851-878 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2695 Medline: Authors: Hodgkin J Title: Appendix 1. Genetics. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 881-1047 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2696 Medline: Authors: Rand JB;Nonet ML Title: Appendix 2. Neurotransmitter Assignments for Specific Neurons. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 1049-1052 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2697 Medline: Authors: Sharp PM;Bradnam KR Title: Appendix 3. Codon Usage in C. elegans. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 1053-1057 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2698 Medline: Authors: Edgley ML;Turner CA;Riddle DL Title: On-line C. elegans Resources. Citation: "C. elegans II." DL Riddle, T Blumenthal, BJ Meyer and JR Priess (eds), Cold Spring Harbor Laboratory Press. II: 1059-1062 1997 Type: REVIEW Genes: Abstract: ------------------- Key: 2699 Medline: 97163541 Authors: Coulier F;Pontarotti P;Roubin R;Hartung H;Goldfarb M;Birnbaum D Title: Of worms and men: An evolutionary perspective on the fibroblast growth factor (FGF) and FGF receptor families. Citation: Journal of Molecular Evolution 44: 43-56 1997 Type: ARTICLE Genes: Abstract: FGFs (fibroblast growth factors) play major roles in a number of developmental processes. Recent studies of several human disorders, and concurrent analysis of gene knock-out and properties of the corresponding recombinant proteins have shown that FGFs and their receptors are prominently involved in the development of the skeletal system in mammals. We have compared the sequences of the nine known mammalian FGFs, FGFs from other vertebrates, and three additional sequences that we extracted from existing databases: two human FGF sequences that we tentatively designated FGF10 and FGF11, and an FGF sequence from Caenorhabditis elegans. Similarly, we have compared the sequences of the four FGF receptor paralogs found in chordates with four non-chordate FGF receptors, including one recently identified in C. elegans. Comparison of FGF and FGF receptor sequences in vertebrates and nonvertebrates shows that the FGF and FGF receptor families have evolved through phases of gene duplications, one of which may have coincided with the emergence of vertebrates, in relation with their new system of body scaffold. ------------------- Key: 2700 Medline: Authors: Gonczy P;Hyman AA Title: Cortical domains and the mechanisms of asymmetric cell division. Citation: Trends in Cell Biology 6: 382-387 1996 Type: REVIEW Genes: par-1 par-2 par-3 Abstract: Asymmetric cell divisions are central to the generation of cell-fate diversity because factors that are present in a mother cell and distributed unequally at cell division can generate distinct daughters. The process of asymmetric cell division can be described as consisting of three steps: setting up an asymmetric cue in the mother cell, localizing factors with respect to this cue, and positioning the plane of cell division so that localized factors are partitioned asymmetrically between daughters. This review describes how specialized cortical domains play a key role in each of these steps and discusses our current understanding of the molecular nature of cortical domains and the mechanisms by which they may orchestrate asymmetric ------------------- Key: 2701 Medline: Authors: Keeling PJ;Logsdon JM Title: Highly divergent Caenorhabditis and Saccharomyces tubulins evolved recently from genes encoding gamma-tubulin. Citation: Trends in Cell Biology 6: 375- 1996 Type: REVIEW Genes: Abstract: The tubulin gene family consists of three types, the well-known a- and B-tubulins and the more recently discovered y-tubulin. However, genome-sequencing projects of Caenorhabditis elegans and Saccharomyces cerivisiae have revealed recently two tubulin genes eash so divergent from any known tubulin that they prompted a proposal to classify these as representatives of new families, the delta- and epsilon-tubulin, respectively, a reclassification implicit in the analysis of tubulin structure and function published recently in this journal. However, substantial evidence is accumulating from the distribution, function and phylogeny of these genes for a contrasting argument that really they are rapidly evolving orthologues of y-tubulin. ------------------- Key: 2702 Medline: Authors: Burns RG Title: Reply: Defining the gamma-, delta- and epsilon-tubulins. Citation: Trends in Cell Biology 6: 376- 1996 Type: REVIEW Genes: Abstract: Keeling and Logsdon propose that the y-like sequences from Caenorhabditis elegans and Saccharomyces cerevisiae are bona fide y-tubulins that have undergone rapid evolutionary divergence. Indeed, genetic and localization studies with the yeast epsilon-tubulin (encoded by the TUB4 gene) reveal striking similarities to the bona fide y-tubulins, whereas there is no apparent human analogue to the C. elegans delta-tubulin among the 60 available human y-tubulin expressed-sequence tags. (ESTs). ------------------- Key: 2703 Medline: 97208473 Authors: Kornfeld K Title: Vulval development in Caenorhabditis elegans. Citation: Trends in Genetics 13: 55-61 1997 Type: REVIEW Genes: ksr-1 lag-1 lag-2 let-23 let-60 let-341 let-537 lin-1 lin-2 lin-3 lin-7 lin-8 lin-9 lin-10 lin-12 lin-15 lin-25 lin-31 lin-35 lin-36 lin-37 lin-38 lin-45 mek-2 mpk-1 sem-5 sli-1 sur-1 sur-2 unc-101 Abstract: Ever since the cell lineage of the nematode Caenorhabditis elegans was shown to be nearly invariant, investigators have tried to understand the mechanisms that control these precise patterns of cell divisions and cell fates. Important insights have come from analyzing the cells that form the hermaphrodite valva a specialized hypodermal passageway used for egg laying and sperm entry. Early experiments showed that the invariant pattern of vulval cell fates requires highly reproducible intercellular signals. This review describes recent experiments that have begun to characterize molecules that mediate these signals and explore the relationships between different signaling pathways. Many of these molecules and signaling Pathways have been conserved during evolution suggesting mechanisms used to establish patterns of cell fates during vulval development have also been conserved. ------------------- Key: 2704 Medline: 97188621 Authors: Bauer MKA;Wesselborg S;Schulze-Osthoff K Title: The Caenorhabditis elegans death protein Ced-4 contains a motif with similarity to the mammalian 'death effector domain'. Citation: FEBS Letters 402: 256-258 1997 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: In the nematode Caenorhabditis elegans apoptosis is tightly regulated by a hierarchical set of genes. Two of these, ced-3 and ced-9, possess mammalian homologues encoding executional ICE proteases and inhibitory Bcl-2-related proteins, respectively. The function of a third key player, ced-4, is however completely unknown and no mammalian counterparts have been identified. Here me report that Ced-4 protein contains a structural region with similarity to the mammalian death effector domain which has previously been demonstrated to act as an important protein interaction motif in the signaling pathway of the mammalian surface receptor Fas (APO-1, CD95). Based on this finding and previously described genetic experiments, we propose that Ced-4, similar to the mammalian proteins FADD and FLICE, may possess a function as an adaptor protein in invertebrate apoptotic pathways. ------------------- Key: 2705 Medline: 97201078 Authors: Parise G;Bazzicalupo P Title: Assembly of nematode cuticle: role of hydrophobic interactions in CUT-2 cross-linking. Citation: Biochimica et Biophysica Acta - Protein Structure & Molecular Enzymology 1337: 295-301 1997 Type: ARTICLE Genes: cut-2 Abstract: CUT-2 is a component of cuticlin, the highly cross-linked, insoluble residue of the cuticle of the nematode Caenorhabditis elegans. A recombinant fragment of CUT-2, produced in E. coli, can be cross-linked in vitro by horse radish peroxidase via dityrosine formation to give large molecular species [1]. In this paper it is shown that the formation of CUT-2 polymers is greatly favoured over that of CUT-2 oligomers as no low molecular weight intermediates, dimers or trimers can be detected even when the cross-linking reaction is slowed or interrupted before completion. This suggests that recombinant CUT-2 forms large non-covalent complexes that are the only competent substrate for cross-linking. The inhibition of cross-linking by urea and the behavior of recombinant CUT-2 in size-exclusion chromatography under a variety of conditions suggest that hydrophobic interactions are important in the formation and stabilization of these complexes. The complexes are excellent substrates for cross-linking but react poorly with free tyrosine. In contrast, a soluble recombinant CUT-2 is a poor substrate for cross-linking but can efficiently react with free ------------------- Key: 2706 Medline: 96385431 Authors: Firestein S Title: Olfaction: Scents and sensibility. Citation: Current Biology 6: 666-667 1996 Type: REVIEW Genes: odr-3 odr-10 Abstract: Expression of a receptor protein has, for the first time, been definitively correlated with sensitivity to a particular odorant. This receptor, expressed in the nematode Caenorhabditis elegans, appears to be distinct from the putative vertebrate odorant receptors. ------------------- Key: 2707 Medline: 97207845 Authors: Zwaal RR;Mendel JE;Sternberg PW;Plasterk RHA Title: Two neuronal G proteins are involved in chemosensation of the Caenorhabditis elegans dauer-inducing pheromone. Citation: Genetics 145: 715-727 1997 Type: ARTICLE Genes: che-3 che-13 daf-1 daf-5 daf-8 daf-11 daf-13 gpa-2 gpa-3 Abstract: Caenorhabditis elegans uses chemosensation to determine its course of development. Young larvae can arrest as dauer larvae in response to increasing population density, which they measure by a nematode-excreted pheromone, and decreasing food supply. Dauer larvae can resume development in response to a decrease in pheromone and increase in food concentration. We show here that two novel G protein alpha subunits (GPA-2 and GPA-3) show promoter activity in subsets of chemosensory neurons and are involved in the decision to form dauer larvae primarily through the response to dauer pheromone. Dominant activating mutations in these G proteins result in constitutive, pheromone-independent dauer formation, whereas inactivation results in reduced sensitivity to pheromone, and, under certain conditions, an alteration in the response to food. Interactions between gpa-2, gpa-3 and other genes controlling dauer formation suggest that these G proteins may act in parallel to regulate the neuronal decision making that precedes dauer formation. ------------------- Key: 2708 Medline: 97224391 Authors: Marks NJ;Maule AG;Geary TG;Thompson DP;Davis JP;Halton DW;Verhaert P;Shaw C Title: APEASFIRFamide, a novel FMRFamide-related decapeptide from Caenorhabditis elegans: structure and myoactivity. Citation: Biochemical and Biophysical Research Communications 231: 591-595 1997 Type: ARTICLE Genes: flp-1 Abstract: To date, 9 FMRF amide-related peptides (FaRPs) have been identified in Caenorhabditis elegans. Eight of these peptides are encoded on the flp-1 gene. However, AF2 (KHEYLRF amide) which was not co-encoded was the most abundant FaRP identified in ethanolic extracts. Further radioimmunometrical screening of acidified ethanol extracts of C. elegans has revealed the presence of other novel FaRPs, which are not encoded on the flp-l gene. One of these peptides has been isolated by sequential rpHPLC and subjected to Edman degradation analysis and gas-phase sequencing and the unequivocal primary structure of the decapeptide Ala-Pro-Glu-Ala-Ser-Pro-Phe-Ile-Arg-Phe-NH2 was determined following a single gas-phase sequencing run. The molecular mass of the peptide was found to be 1133.7 Ha, determined using a time-of-flight mass spectrometer. Synthetic replicates of this peptide were found to induce a profound relaxation of both dorsal and ventral somatic muscle-strip preparations of Ascaris suum with a threshold for activity of 10 nM. The inhibitory response was not dependent on the presence of nerve cords, indicating a post-synaptic site-of-action. The relaxation was Ca++- and Cl--independent but was abolished in high-KI medium and could be distinguished from those of other inhibitory nematode FaRPs, including PF1 (SDPNFLRFamide)and PF1 (KPNFIRF amide). ------------------- Key: 2709 Medline: Authors: Chalfie M Title: A molecular model for mechanosensation in Caenorhabditis elegans. Citation: Biological Bulletin 192: 125- 1997 Type: ARTICLE Genes: mec-1 mec-2 mec-4 mec-6 mec-9 mec-10 mec-12 Abstract: Sensory signaling by chemicals and light are fairly well understood in molecular terms, but the molecules needed for molecular signaling, which underlies the senses of touch, hearing, and balance, are not known. By analyzing the genes needed for mechanosensation in the nematode Caenorhabditis elegans, we hope to gain this molecular ------------------- Key: 2710 Medline: 97215250 Authors: Olde B;McCombie WR Title: Molecular cloning and functional expression of a serotonin receptor from Caenorhabditis elegans. Citation: Journal of Molecular Neuroscience 8: 53-62 1997 Type: ARTICLE Genes: Abstract: A cDNA encoding a serotonin receptor has been isolated from a Caenorhabditis elegans mixed stage cDNA library. The nematode serotonin receptor, designated 5HT-Ce, was permanently expressed in murine Ltk- cells, where it mediates adenylate cyclase attenuation. Sequence analysis and the pharmacological profiles demonstrate its relatedness not only to Drosophila and Lymnae 5HT receptors but also to mammalian 5HT1a receptors. The 5HT-Ce gene does not map close to the position of any known serotonergic mutations.e 1133.7 Ha, determined using a time-of-flight mass spectrometer. Synthetic replicates of this peptide were found to induce a profound relaxation of both dorsal and ventral somatic muscle-strip preparations of Ascaris suum with a threshold for activity of 10 nM. The inhibitory response was not dependent on the presence of nerve cords, indicating a post-synaptic site-of-action. The relaxation was Ca++- and Cl--independent but was abolished in high-KI medium and could be distinguished from those of other inhibitory nematode FaRPs, including PF1 (SDPNFLRFamide)and PF1 (KPNFIRF amide). ------------------- Key: 2711 Medline: 97178317 Authors: Hall DH;Gu G;Garcia-Anoveros J;Gong L;Chalfie M;Driscoll M Title: Neuropathology of degenerative cell death in Caenorhabditis elegans. Citation: Journal of Neuroscience 17: 1033-1045 1997 Type: ARTICLE Genes: ced-3 ced-4 deg-1 mec-4 Abstract: In Caenorhabditis elegans necrosis-like neuronal death is induced by gain-of-function (gf) mutations in two genes, mec-4 and deg-1, that encode proteins similar to subunits of the vertebrate amiloride-sensitive epithelial Na+ channel. We have determined the progress of cellular pathology in dying neurons via light and electron microscopy. The first detectable abnormality is an infolding of the plasma membrane and the production of small electron-dense whorls. Later, cytoplasmic vacuoles and larger membranous whorls form, and the cell swells. More slowly, chromatin aggregates and the nucleus invaginates. Mitochondria and Golgi are not dramatically affected until the final stages of cell death when organelles, and sometimes the cells themselves, lyse. Certain cells, including some muscle cells in deg-1 animals, express the abnormal gene products and display a few membrane abnormalities but do not die. These cells either express the mutant genes at lower levels, lack other proteins needed to form inappropriately functioning channels, or are better able to compensate for the toxic effects of the channels. Overall, the ultrastructural changes in these deaths suggest that enhanced membrane cycling precedes vacuolation and cell swelling. The pathology of mec-4(gf) and deg-1(gf) cells shares features with that of genetic disorders with alterations in channel subunits, such as hypokalemic periodic paralysis in humans and the weaver mouse, and with degenerative conditions, e.g., acute excitotoxic death. The initial pathology in all of these conditions may reflect attempts by affected cells ------------------- Key: 2712 Medline: Authors: Felix MA Title: One worm, 959 cells and 13,000 genes. Citation: M S-Medecine Sciences 13: 156-165 1997 Type: REVIEW Genes: glp-1 ksr-1 lag-2 let-23 let-60 lin-1 lin-3 lin-12 lin-31 lin-39 lin-45 mek-2 par-1 sem-5 skn-1 sli-1 sur-1 Abstract: The molecular pathways specifying cell fates during development are identified in the nematode Caeno-rhabditis elegans by the combination of genetic and molecular methods. For example, the differentiation of vulval precursor cells is induced by a signal similar to mammalian EGF, sent by the anchor cell of the gonad. This signal is received by a tyrosine kinase receptor and transmitted to the transcription factors in the nucleus through a very conserved molecular cascade. In mammals many components of this cascade, like Ras, are proto-oncogenes. At the cellular level, the reproducibility of C. elegans development and the possibility to selectively kill cells with a laser, allow the description of development in terms of cell interactions land asymmetric divisions. These developmental mechanisms can be ,compared in other nematode species: whereas molecular cascades are very conserved (even as far as mammals), modes of cell specification vary extensively (among nematodes). ------------------- Key: 2713 Medline: 97180670 Authors: Chinnaiyan AM;O'Rourke K;Lane BR;Dixit VM Title: Interaction of CED-4 with CED-3 and CED-9: A molecular framework for cell death. Citation: Science 275: 1122-1126 1997 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: Previous genetic studies of the nematode Caenorhabditis elegans identified three important components of the cell death machinery. CED-3 and CED-4 function to kill cells, whereas CED-9 protects cells from death. Here CED-9 and its mammalian homolog Bcl-x(L) (a member of the Bcl-2 family of cell death regulators) were both found to interact with and inhibit the function of CED-4. In addition, analysis revealed that CED-4 can simultaneously interact with CED-3 and its mammalian counterparts interleukin-1 beta-converting enzyme (ICE) and FLICE. Thus, CED-4 plays a central role in the cell death pathway, biochemically linking CED-9 and the Bcl-2 family to CED3 and the ICE family of pro-apoptotic cysteine proteases. ------------------- Key: 2714 Medline: 97180671 Authors: Wu D;Wallen HD;Nunez G Title: Interaction and regulation of subcellular localization of CED-4 by CED-9. Citation: Science 275: 1126-1129 1997 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: The Caenorhabditis elegans survival gene ced-9 regulates ced-4 activity and inhibits is cell death, but the mechanism by which this occurs is unknown. Through a genetic screen for CED-4-binding proteins, CED-9 was identified as an interacting partner of CED-4. CED-9, but not loss-of-function mutants, associated specifically with CED-4 in yeast or mammalian cells. The CED-9 protein localized primarily to intracellular membranes and the perinuclear region, whereas CED-4 Was distributed in the cytosol. Expression of CED-9, but not a mutant lacking the carboxy-terminal hydrophobic domain, targeted CED-4 from the cytosol to intracellular membranes in mammalian cells. Thus, the actions of CED-4 and CED-9 are directly linked, which could provide the basis for the regulation of programmed cell death in C. elegans. ------------------- Key: 2715 Medline: 97191303 Authors: Jacobson MD;Weil M;Raff MC Title: Programmed cell death in animal development. Citation: Cell 88: 347-354 1997 Type: REVIEW Genes: ced-3 ced-9 Abstract: Programmed cell death (PCD) occurs during the development of all animals that have been studied, but only recently has its molecular basis been discovered. In this review, we briefly consider some of the main events in the history of PCD in animal development. We then summarize what has been learned about the molecular mechanism of PCD and some of the intracellular proteins that control it. We next discuss the functions of PCD in development and how PCD is regulated during development by signals from other cells. Finally, we consider what the evolutionary origins of PCD ------------------- Key: 2716 Medline: 97188435 Authors: Spychalla JP;Kinney AJ;Browse J Title: Identification of an animal omega-3 fatty acid desaturase by heterologous expression in Arabidopsis. Citation: Proceedings of the National Academy of Sciences USA 94: 1142-1147 1997 Type: ARTICLE Genes: fat-1 Abstract: In animals, fatty acid desaturases catalyze key reactions in the synthesis of arachidonic acid and other polyunsaturated fatty acids, A search of the Caenorhabditis elegans DNA databases, using the sequences of Arabidopsis genes, identified several putative desaturases. Here we describe the characterization of the first of these genes,fat-1. The predicted protein encoded by a fat-1 cDNA showed 32-35% identity with both FAD2 and FAD3 of Arabidopsis. When expressed in transgenic plants,fat-1 resulted in a 90% increase in the proportion of alpha-linolenic acid in root lipids, Wild-type Arabidopsis incorporated omega-6 fatty acids (Delta 8,11,14-20:3 and Delta 5,8,11,14-20:4) into membrane lipids but did not desaturate them. By contrast, fat-1 transgenic plants efficiently desaturated both of these fatty acids to the corresponding omega-3 products. These findings indicate that the C. elegans fat-1 gene encodes the first animal representative of a class of glycero-lipid desaturases that have previously been characterized in plants and cyanobacteria. The FAT-1 protein is an omega-3 fatty acyl desaturase that recognizes a range of 18- and 20-carbon ------------------- Key: 2717 Medline: 97178665 Authors: Kolodziej PA Title: DCC's function takes shape in the nervous system. Citation: Current Opinion in Genetics & Development 7: 87-92 1997 Type: ARTICLE Genes: unc-5 unc-6 unc-40 Abstract: Deleted in colorectal cancer (DCC), a candidate tumor-suppressor gene, has recently been found to encode a netrin receptor required for axon guidance in vitro. Mutations in Caenorhabditis elegans and Drosophila genes encoding DCC-related proteins affect axon guidance, and these phenotypes resemble those of mutations in netrin genes. Netrins and their DCC-related receptors thus play an evolutionarily conserved role in midline guidance, and DCC may be required more generally for cellular morphogenesis. ------------------- Key: 2718 Medline: 96399718 Authors: Greenbaum NL;Radhakrishnan I;Patel DJ;Hirsh D Title: Solution structure of the donor site of a trans-splicing RNA. Citation: Structure 4: 725-733 1996 Type: ARTICLE Genes: Abstract: BACKGROUND: RNA splicing is both ubiquitous and essential for the maturation of precursor mRNA molecules in eukaryotes. The process of trans-splicing involves the transfer of a short spliced leader (SL) RNA sequence to a consensus acceptor site on a separate pre-mRNA transcript. In Caenorhabditis elegans, a majority of pre-mRNA transcripts receive the 22-nucleotide SL from the SL1 RNA. Very little is known about the various roles that RNA structures play in the complex conformational rearrangements and reactions involved in premRNA splicing. RESULTS: We have determined the solution structure of a domain of the first stem loop of the SL1 RNA of C. elegans, using homonuclear and heteronuclear NMR techniques; this domain contains the splice-donor site and a nine-nucleotide hairpin loop. In solution, the SL1 RNA fragment adopts a stem-loop structure: nucleotides in the stem region form a classical A-type helix while nucleotides in the hairpin loop specify a novel conformation that includes a helix, that extends for the first three residues; a syn guanosine nucleotide at the turn region; and an extrahelical adenine that defines a pocket with nucleotides at the base of the loop. CONCLUSION: The proximity of this pocket to the splice donor site, combined with the observation that the nucleotides in this motif are conserved among all nematode SL RNAs, suggests that this pocket may provide a recognition site for a protein or RNA molecule in the ------------------- Key: 2719 Medline: 97043535 Authors: Staddon JER;Higa JJ Title: Multiple time scales in simple habituation. Citation: Psychological Review 103: 720-733 1996 Type: REVIEW Genes: Abstract: Habituation is the waning of a reflex response to repeated stimulation. Habituation to closely spaced stimuli is faster and more complete than to widely spaced stimuli, but recovery is also more rapid (rate sensitivity). We show that a 2-unit, cascaded-integrator dynamic model can explain in detail an extensive data set on rate-sensitive habituation in the nematode Caenorhabditis elegans. Many apparently complex properties of habituation and learning dynamics may reflect interactions among a small number of processes with different time scales. ------------------- Key: 2720 Medline: 97209464 Authors: Kuersten S;Lea K;MacMorris M;Spieth J;Blumenthal T Title: Relationship between 3' end formation and SL2-specific trans-splicing in polycistronic Caenorhabditis elegans pre-mRNA processing. Citation: RNA 3: 269-278 1997 Type: ARTICLE Genes: gpd-2 gpd-3 mai-1 Abstract: About 25% of the genes in the nematode Caenorhabditis elegans are in operons, polycistronic transcription units in which the genes are only 100-400 bp apart. The operon pre-mRNAs are processed into monocistronic mRNAs by a combination of cleavage and polyadenylation at the 3' end of the upstream mRNA and SL2 trans-splicing at the 5' end of the downstream mRNA. To determine whether 3' end formation and SL2 trans-splicing are coupled mechanistically, we tested a gpd-2/gpd-3 operon construct driven by a C. elegans heat shock promoter, and measured the effects of inhibition of 3' end formation and/or trans-splicing on the processing of the polycistronic RNA in vivo. The results indicate that proper 3' end formation of the upstream mRNA in an operon is required for SL2-specificity of downstream mRNA trans-splicing. In contrast, trans-splicing of the downstream mRNA is not necessary for correct 3' end formation of the upstream mRNA. In addition, shortening the distance between the 5' cap and the AAUAAA of gpd-2 (the upstream gene) decreases the efficiency of 3' end formation and is accompanied by a replacement of SL2 with SL1 at the trans-splice site of gpd-3, the downstream gene. These results indicate that SL2 frans-splicing, in C. elegans, is coupled mechanistically to 3' end formation in the processing of polycistronic ------------------- Key: 2721 Medline: 97209425 Authors: Garcia-Anoveros J;Corey DP Title: The molecules of mechanosensation. Citation: Annual Review of Neuroscience 20: 567-594 1997 Type: REVIEW Genes: deg-1 let-2 lin-32 mec-1 mec-2 mec-3 mec-4 mec-5 mec-6 mec-7 mec-8 mec-9 mec-10 mec-12 mec-14 mec-15 mec-17 mec-18 sup-20 unc-8 unc-86 unc-105 Abstract: Mechanosensation, the transduction of mechanical forces into a cellular electrochemical signal, enables living organisms to detect touch; vibrations, such as sound; accelerations, including gravity; body movements; and changes in cellular volume and shape. Ion channels directly activated by mechanical tension are thought to mediate mechanosensation in many systems. Only one channel has been cloned that is unequivocably mechanically gated: the MscL channel in bacteria. Genetic screens for touch-insensitive nematodes or flies promise to identify the proteins that constitute a mechanosensory apparatus in eukaryotes. In Caenorhabditis elegans, the mec genes thus identified encode molecules for a candidate structure, which includes a ''degenerin'' channel tethered to specialized extracellular and intracellular structural proteins. In hair cells of the inner ear, evidence suggests that an extracellular tip link pulls on a channel, which attached intracellularly to actin via a tension-regulating myosin 1 beta. The channel and the tip link have not been cloned. Because degenerins and MscL homologs have not been found outside of nematodes and prokaryotes, respectively, and because intracellular and extracellular accessory structures apparently differ among organs and species, it may be that mechanosensory channel complexes evolved ------------------- Key: 2722 Medline: 97223383 Authors: Inoue T;Yatsuki H;Kusakabe T;Joh K;Takasaki Y;Nikoh N;Miyata T;Hori K Title: Caenorhabditis elegans has two isozymic forms, CE-1 and CE-2, of fructose-1,6-bisphosphate aldolase which are encoded by different genes. Citation: Archives of Biochemistry & Biophysics 339: 226-234 1997 Type: ARTICLE Genes: Abstract: Two distinct types of cDNAs for fructose-1,6-bisphosphate (FBP) aldolase, Ce-1 and Ce-2, have been isolated from nematode Caenorhabditis elegans, and the respective recombinant aldolase isozymes, CE-1 and CE2, have been purified and characterized. The Ce-1 and Ce-2 are 1282 and 1248 bp in total length, respectively, and both have an open reading frame of 1098 bp, which encodes 366 amino acid residues. The entire amino acid sequences deduced from Ce-1 and Ce-2 show a high degree of identity to one another and to those of vertebrate and invertebrate aldolases. The highest sequence diversity was found in the carboxyl-terminal region that corresponds to one of the isozyme group-specific sequences of vertebrate aldolase isozymes that play a role in determining isozyme-specific functions. Southern blot analysis suggests that CE-1 and CE-2 are encoded by different genes. Concerning general or kinetic properties, CE-2 is quite different from CE-1. CE-1 exhibits unique characteristics which are not identical to any aldolase isozymes previously reported, whereas CE-2 is similar to vertebrate aldolase C. These results suggest that CE-2 might preserve the properties of a progenitor aldolase with a moderate preference for FBP over fructose 1-phosphate (F1P) as a substrate, whereas CE-1 evolved to act as an intrinsic enzyme that exhibits a much broader substrate specificity than does CE-2. ------------------- Key: 2723 Medline: 97204389 Authors: Isaac RE;MacGregor D;Coates D Title: Metabolism and inactivation of neurotransmitters in nematodes. Citation: Parasitology 113: S157-S173 1996 Type: REVIEW Genes: ace-1 ace-2 ace-3 Abstract: The nematode nervous system employs many of the same neurotransmitters as are found in higher animals. The inactivation of neurotransmitters is absolutely essential for the correct functioning of the nervous system. In this article we discuss the various mechanisms used generally in animal nervous systems for synaptic inactivation of neurotransmitters and review the evidence for similar mechanisms operating in parasitic and free-living nematodes. The sequencing of the entire Caenorhabditis elegans genome means that the sequence of nematode genes can be accessed from the C. elegans database (ACeDB) and this wealth of information together with the increasing knowledge of the genetics of this free-living nematode will have great impact on all aspects of nematode neurobiology. The review will provide an insight into how this information may be exploited to identify and characterize target proteins for the development of novel anti-nematode ------------------- Key: 2724 Medline: 97204390 Authors: Fleming JT;Baylis HA;Sattelle DB;Lewis JA Title: Molecular cloning and in vitro expression of C. elegans and parasitic nematode ionotropic receptors. Citation: Parasitology 113: S175-S190 1996 Type: ARTICLE Genes: acr-2 acr-3 deg-3 glr-1 itr-1 lev-1 lev-9 lin-15 mec-4 unc-25 unc-29 unc-30 unc-38 unc-43 unc-47 unc-49 unc-68 Abstract: The free living nematode, C. elegans is understood at a level of detail equalled by few other organisms, and much of the cell biology and sequence information is proving of considerable utility in the study of parasitic nematodes. Already, C. elegans provides a convenient vehicle for investigating anthelmintic drug action and resistance mechanisms. Among the ionotropic receptors, with their important roles in the behaviour and development of the organism, are targets for anthelmintics. The subunits of nicotinic acetylcholine receptors of C. elegans form a large and diverse multigene family. Members of this family are among the 11 genes associated with resistance to the anthelmintic drug levamisole. ------------------- Key: 2725 Medline: Authors: Traunspurger W;Haitzer M;Hoss S;Beier S;Ahlf W;Steinberg C Title: Ecotoxicological assessment of aquatic sediments with Caenorhabditis elegans (Nematoda) - A method for testing liquid medium and whole-sediment samples. Citation: Environmental Toxicology and Chemistry 16: 245-250 1997 Type: ARTICLE Genes: Abstract: We present a method using the free-living nematode Caenorhabditis elegans (Maupas, 1899) to assess toxicity in liquid medium and whole-sediment setups. Test duration is 72 h; endpoints are body length, number of eggs inside worms, percentage of gravid worms, and number of offspring per worm. The effect of CdCl2 on C. elegans in liquid-phase exposures is described as an example. Results from a field study with polluted sediments from the River Elbe (Germany) suggest that nematodes may be useful organisms in assessing toxicity of sediments in the whole phase. ------------------- Key: 2726 Medline: 97195483 Authors: Wissmann A;Ingles J;McGhee JD;Mains PE Title: Caenorhabditis elegans LET-502 is related to Rho-binding kinases and human myotonic dystrophy kinase and interacts genetically with a homolog of the regulatory subunit of smooth... Citation: Genes & Development 11: 409-422 1997 Type: ARTICLE Genes: let-354 let-502 mel-11 unc-38 hDf6 mnDf16 mnDf61 mnDf68 Abstract: We have identified two genes associated with the hypodermal cell shape changes that occur during elongation of the Caenorhabditis elegans embryo. The first gene, called let-502, encodes a protein with high similarity to Rho-binding Ser/Thr kinases and to human myotonic dystrophy kinase (DM-kinase). Strong mutations in let-502 block embryonic elongation, and let-502 reporter constructs are expressed in hypodermal cells at the elongation stage of development. The second gene, mel-11, was identified by mutations that act as extragenic suppressors of let-502. mel-11 encodes a protein similar to the 110- to 133-kD regulatory subunits of vertebrate smooth muscle myosin-associated phosphatase (PP-1M). We suggest that the LET-502 kinase and the MEL-11 phosphatase subunit act in a pathway linking a signal generated by the small GTP-binding protein Rho to a myosin-based hypodermal contractile system that drives embryonic elongation. LET-502 may directly regulate the activity of the MEL-11 containing phosphatase complex and the similarity between LET-502 and DM-kinase suggests a similar function for DM-kinase. ------------------- Key: 2727 Medline: 97235812 Authors: Sommer RJ Title: Evolution and development - the nematode vulva as a case study. Citation: BioEssays 19: 225-231 1997 Type: REVIEW Genes: lin-3 lin-12 lin-39 Abstract: To understand how morphological characters change during evolution, we need insight into the evolution of developmental processes. Comparative developmental approaches that make use of our fundamental understanding of development in certain model organisms have been initiated for different animal systems and flowering plants. Nematodes provide a useful experimental system with which to investigate the genetic and molecular alterations underlying evolutionary changes of cell fate specification in development, by comparing different species to the genetic model system Caenorhabditis elegans. In this review, I will first discuss the different types of evolutionary alterations seen at the cellular level by focusing mainly on the analysis of vulva development in different species. The observed alterations involve changes in cell lineage, cell migration and cell death, as well as induction and cell competence. I then describe a genetic approach in the nematode Pristionchus pacificus that might identify those genetic and molecular processes that cause evolutionary changes of cell fate specification. ------------------- Key: 2728 Medline: 97207010 Authors: Moss EG;Lee RC;Ambros V Title: The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Citation: Cell 88: 637-646 1997 Type: ARTICLE Genes: ceh-6 lin-4 lin-14 lin-28 mei-1 nDp4 Abstract: Mutations in the heterochronic gene lin-28 of C. elegans cause precocious development where diverse events specific to the second larval stage are skipped. lin-28 encodes a cytoplasmic protein with a cold shock domain and retroviral-type (CCHC) zinc finger motifs, consistent with a role for LIN-28 in posttranscriptional regulation. The 3'UTR of lin-28 contains a conserved element that is complementary to the 22 nt regulatory RNA product of lin-4 and that resembles seven such elements in the 3'UTR of the heterochronic gene lin-14. Both lin-4 activity and the lin-4-complementaty element (LCE) are necessary for stage-specific regulation of lin-28. Deleting the LCE produces a dominant gain-of-function allele that causes a retarded phenotype, indicating that lin-28 activity is a switch that controls choices of stage-specific fates. ------------------- Key: 2729 Medline: 97201364 Authors: Golstein P Title: Controlling cell death. Citation: Science 275: 1081-1082 1997 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: In many situations-both normal and pathological-cells die as a result of an orderly, stereotyped cascade of cellular events. On pages 1122, 1126, 1129, and 1132 of this issue, four reports describe the molecular basis of crucial steps in this cascade. The importance of understanding the basis of this programmed cell death was spectacularly demonstrated recently through the rescue with cell death inhibitors of mice undergoing acute liver destruction. Programmed cell death is genetically determined, as demonstrated in the nematode Caenorhabditis elegans. Cell death occuring during development of this worm involves the molecules CED-3 and CED-4, which are necessary for cell death to occur, and CED-9, which protects cells from ------------------- Key: 2730 Medline: 97195700 Authors: Berry LW;Westlund B;Schedl T Title: Germ-line tumor formation caused by activation of glp-1, a Caenorhabditis elegans member of the Notch family of receptors. Citation: Development 124: 925-936 1997 Type: ARTICLE Genes: glp-1 lag-1 lag-2 Abstract: Caenorhabditis elegans germ-line proliferation is controlled by an inductive interaction between the somatic distal tip cell and the germ line, GLP-1, a member of the Notch family of transmembrane receptors, is required continuously in the germ line to transduce the proliferative signal, In the absence of GLP-1, all proliferative germ cells exit the mitotic cell cycle and enter meiotic prophase, We have characterized an activating mutation in glp-1, oz112gf, that has the opposite phenotype, Homozygous glp-1(oz112gf) hermaphrodites and males have a completely tumorous germ line in which germ cells never leave the mitotic cycle, In glp-1(oz112gf) heterozygotes, germ-line polarity is established correctly, but as adults age, the distal proliferative population expands leading to a late-onset tumorous phenotype, The mutant receptor is constitutively active, promoting proliferation in the absence of ligand, The normal distal-proximal spatial restriction of GLP-1 expression is lost in tumorous and late-onset tumorous animals; ectopically proliferating germ cells contain membrane-associated GLP-1, The correlation between proliferation and expression, both in wild-type where glp-1 signalling is limited by localized ligand and in glp-1(oz112gf) where signalling is ligand-independent, suggests that glp-1 signalling positively regulates GLP-1 expression, In addition to germ-line defects, glp-1(oz112gf) causes inappropriate vulval cell fate specification, A missense mutation in a conserved extracellular residue, Ser642, adjacent to the transmembrane domain, is sufficient to confer the glp-1(oz112gf) mutant phenotypes. Two mammalian Notch family members, TAN-I and int-3, are proto-oncogenes. Thus, activating mutations in both invertebrate and vertebrate ------------------- Key: 2731 Medline: Authors: Burns RG;Farrell KW Title: Getting to the heart of B-tubulin. Citation: Trends in Cell Biology 6: 297-303 1996 Type: REVIEW Genes: mec-7 Abstract: Cellular microtubules assemble and disassemble at a variety of rates and frequencies, and these properties contribute directly to the cell-cycle-associated rearrangements of the microtubule cytoskeleton and to the molecular basis of mitosis. The kinetics of assembly/disassembly are governed, in part, by the hydrolysis of GTP bound to the B-tubulin nucleotide-binding site. The B-tubulin GTP-binding site, therefore, lies at the heart of microtubule assembly-disassembly kinetics, and the elucidation of its structure is central to an understanding of the cellular behaviour of microtubules. Unfortunately, the crystallographic structure of B-tubulin is not yet available. In this review, we describe the progress being made using mutagenesis and biochemical studies to understand the structure of this unusual GTP-binding site. ------------------- Key: 2732 Medline: 97218908 Authors: Iwasaki K;Thomas JH Title: Genetics in rhythm. Citation: Trends in Genetics 13: 111-115 1997 Type: REVIEW Genes: clk-1 dec-1 dec-2 dec-4 dec-7 dec-9 dec-10 dec-11 dec-12 flr-1 flr-3 flr-4 unc-16 Abstract: Rhythmic phenomena are widespread in biology. Genetic analysis of 24 hour circadian rhythms has a long history, and recent studies of circadian clock genes in Drosophila and Neurospora provide insight into clock mechanisms, including rhythm generation, clock setting by external signals and temperature compensation of rhythm. Faster biological rhythms, called ultradian rhythms, vary widely in periodicity and are likely to be generated by diverse mechanism. In animals, ultradian rhythms are important in many neuromuscular systems, such as heartbeat, peristalsis and breathing. Recent progress has been made in the genetic analysis of heartbeat in humans and an ultradian rhythm controlling defecation in Caenorhabditis elegans. ------------------- Key: 2733 Medline: 97197843 Authors: Islas-Trejo A;Land M;Tcherepanova I;Freedman JH;Rubin CS Title: Structure and expression of the Caenorhabditis elegans protein kinase C2 gene - Origins and regulated expression of a family of Ca2+-activated protein kinase C isoforms. Citation: Journal of Biological Chemistry 272: 6629-6640 1997 Type: ARTICLE Genes: pkc-2 Abstract: The molecular and cellular basis for concerted Ca2+/lipid signaling in Caenorhabditis elegans was investigated, A unique gene (pkc-2) and cognate cDNAs that encode six Ca2+/diacylglycerol-stimulated PKC2 isoenzymes were characterized, PKC2 polypeptides (680-717 amino acid residues) share identical catalytic, Ca2+-binding, diacylglycerol-activation and pseudosubstrate domains, However, sequences of the N- and C-terminal regions of the kinases diverge, PKC2 diversity is partly due to differential activation of transcription by distinct promoters, Each promoter precedes an adjacent exon that encodes 5'-untranslated RNA, an initiator AUG codon and a unique open reading frame. PKC2 mRNAs also incorporate one of two 3'-terminal exons via alternative splicing. Cells that are capable of receiving and propagating signals carried by Ca2+/diacylglycerol were identified by assessing activities of pkc-2 gene promoters in transgenic C. elegans and visualizing the distribution of PKC2 polypeptides via immunofluorescence. Highly-selective expression of certain PKC2 isoforms was observed in distinct subsets of neurons, intestinal and muscle cells, A low level of PKC2 isoforms is observed in embryos, When L1 larvae hatch and interact with the external environment PKC2 content increases 10-fold. Although 77- and 78-kDa PKC2 isoforms are evident throughout post-embryonic development, an 81-kDa isoform appears to be adapted for function in L1 and L2 larvae. ------------------- Key: 2734 Medline: 97239618 Authors: Schierenberg E Title: Specification of cell-by-cell development in the early embryonic stages of Caenorhabditis elegans. Citation: Naturwissenschaften 84: 55-64 1997 Type: REVIEW Genes: apx-1 glp-1 mes-1 mex-1 par-1 pie-1 pop-1 skn-1 Abstract: Embryogenesis of the nematode Caenorhabditis elegans has been described completely on a cell-by-cell basis and found to be essentially invariant. With this knowledge in hands, micromanipulated embryos and mutants have been analyzed for cell lineage defects and the distribution of specific gene products. The results challenge the classical view of cell-autonomous development in nematodes and indicate that the early embryo of C. elegans is a highly dynamic system. A network of inductive events between neighboring cells is being revealed, which is necessary to assign different developmental programs to blastomeres. In those cases where molecules involved in these cell-cell interactions have been identified, homologies to cell surface receptors, ligands and transcription factors found in other systems have become obvious. ------------------- Key: 2735 Medline: 97199435 Authors: Lambie EJ Title: Nematode Development: Evolutionary detours of a pivotal cell. Citation: Current Biology 7: R160-R163 1997 Type: REVIEW Genes: lag-2 let-23 lin-3 lin-12 lin-15 Abstract: The anchor cell plays a central role in organizing the reproductive structures of the nematode Caenorhabditis elegans. Recent studies show that significant alterations in the origin, function and fate of this key regulatory cell have occurred during the course of nematode evolution. ------------------- Key: 2736 Medline: 97220022 Authors: Gilleard JS;Barry JD;Johnstone IL Title: cis regulatory requirements for hypodermal cell-specific expression of the Caenorhabditis elegans cuticle collagen gene dpy-7. Citation: Molecular and Cellular Biology 17: 2301-2311 1997 Type: ARTICLE Genes: dpy-7 Abstract: The Caenorhabditis elegans cuticle collagens are encoded by a multigene family of between 50 and 100 members and are the major component of the nematode cuticular exoskeleton. They are synthesized in the hypodermis prior to secretion and incorporation into the cuticle and exhibit complex patterns of spatial and temporal expression. We have investigated the cis regulatory requirements for tissue- and stage-specific expression of the cuticle collagen gene dpy-7 and have identified a compact regulatory element which is sufficient to specify hypodermal cell reporter gene expression. This element appears to be a true tissue-specific promoter element, since it encompasses the dpy-7 transcription initiation sites and functions in an orientation-dependent manner. We have also shown, by interspecies transformation experiments, that the dpy-7 cis regulatory elements are functionally conserved between C, elegans and C, briggsae, and comparative sequence analysis supports the importance of the regulatory sequence that we have identified by reporter gene analysis. All of our data suggest that the spatial expression of the dpy-7 cuticle collagen gene is established essentially by a small tissue-specific promoter element and does not require upstream activator or repressor elements. In addition, we have found the DPY-7 polypeptide is very highly conserved between the two species and that the C, briggsae polypeptide can function appropriately within the C, elegans cuticle. This finding suggests a remarkably high level of conservation of individual cuticle components, and ------------------- Key: 2737 Medline: 97228737 Authors: Tavernarakis N;Driscoll M Title: Molecular modeling of mechanotransduction in the nematode Caenorhabditis elegans. Citation: Annual Review of Physiology 59: 659-689 1997 Type: REVIEW Genes: deg-1 del-1 let-2 mec-1 mec-2 mec-3 mec-4 mec-5 mec-6 mec-7 mec-8 mec-9 mec-10 mec-12 mec-14 mec-15 mec-17 mec-18 sup-20 unc-8 unc-86 unc-105 Abstract: Genetic and molecular studies of touch avoidance in the nematode Caenorhabditis elegans have resulted in a molecular model for a mechanotransducing complex. mec-4 and mec-10 encode proteins hypothesized to be subunits of a mechanically gated ion channel that are related to subunits of the vertebrate amiloride-sensitive epithelial Na+ channel. Products of mec-5, a novel collagen, and mec-9, a protein that includes multiple Kunitz-type protease inhibitor repeats and EGF repeats, may interact with the channel in the extracellular matrix. Inside the cell, specialized 15-protofilament microtubules composed of mec-12 alpha-tubulin and mec-7 beta-tubulin may be linked to the mechanosensitive channel by stomatin-homologous MEC-2. MEC-4 and MEC-10 are members of a large family of C. elegans proteins, the degenerins. Two other degenerins, UNC-8 and DEL-1, are candidate components of a stretch-sensitive channel in motor neurons. Implications for advancing understanding of mechanotransduction in other systems are discussed. ------------------- Key: 2738 Medline: Authors: Borgonie G;Van Driessche E;Link CD;Claeys M;De Waele D;Coomans A Title: Internal lectin binding patterns in the nematodes Caenorhabditis elegans, Panagrolaimus superbus and Acrobeloides maximus. Citation: Fundamental and Applied Nematology 20: 173-186 1996 Type: ARTICLE Genes: Abstract: Using ten different lectins, the binding patterns were studied in three free-living nematodes: Caenorhabditis elegans, Panagrolaimus superbus, and Acrobeliodes maximus. Although all the nematode tissues showed binding by one or more of the lectins used, considerable differences were noticed between the three nematode species. Yolk, four of the coelomocytes, and the oocytes bind most often with the lectins used. Although the intestinal brush border interacts with a lot of foreign materials, it stained only with few lectins. The lectin binding pattern of the yolk indicated that, at the time of incorporation of the yolk in embryos or shortly thereafter, a processing of the yolk occurs resulting in changes in lectin-binding characteristics of the yolk protein. ------------------- Key: 2739 Medline: 97154517 Authors: Nam K;Lee G;Trambley J;Devine SE;Boeke JD Title: Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation. Citation: Molecular and Cellular Biology 17: 809-818 1997 Type: ARTICLE Genes: Abstract: The cDNAs and genes encoding the intron lariat-debranching enzyme were isolated from the nematode Caenorhabditis elegans and the fission yeast Schizosaccharomyces pombe based on their homology with the Saccharomyces cerevisiae gene. The cDNAs were shown to be functional in an interspecific complementation experiment; they can complement an S. cerevisiae dbr1 null mutant. About 2.5% of budding yeast S. cerevisiae genes have introns, and the accumulation of excised introns in a dbr1 null mutant has little effect on cell growth. In contrast, many S. pombe genes contain introns, and often multiple introns per gene, so that S. pombe is estimated to contain approximately 40 times as many introns as S. cerevisiae. The S. pombe dbr1 gene was disrupted and shown to be nonessential. Like the S. cerevisiae mutant, the S. pombe null mutant accumulated introns to high levels, indicating that intron lariat debranching represents a rate-limiting step in intron degradation in both species. Unlike the S. cerevisiae mutant, the S. pombe dbr1::leu1+ mutant had a severe growth defect and exhibited an aberrant elongated cell shape in addition to an intron accumulation phenotype. The growth defect of the S. pombe dbr1::leu1+ strain suggests that debranching activity is critical for efficient intron RNA degradation and that blocking this pathway interferes with cell growth. ------------------- Key: 2740 Medline: 97061613 Authors: Le T;Saier MH Title: Phylogenetic characterization of the epithelial Na+ channel (ENaC) family. Citation: Molecular Membrane Biology 13: 149-157 1996 Type: ARTICLE Genes: Abstract: Twenty-one sequenced protein members of the epithelial Na+ channel (ENaC) family have been identified and characterized in terms of their sizes, hydropathy profiles, sequence similarities and phylogenies. These proteins derive from mammals, the frog Xenopus laevis and the worm Caenorhabditis elegans. The eleven sequenced vertebrate proteins fall into four subfamilies designated alpha, beta, gamma and delta. The 10 C. elegans proteins do not cluster with the vertebrate proteins, and they all proved to be distantly related to each other. Nonetheless, the 21 ENaC proteins exhibit the same apparent topology, each with two transmembrane spanning segments separated by a large extracellular loop. All but two ENaC proteins possess highly conserved extracellular domains containing numerous conserved cysteine residues as well as adjacent C-terminal amphipathic transmembrane spanning segments, postulated to contribute to the formation of the hydrophillic pores of these oligomeric channel protein complexes. It is proposed that the well-conserved extracellular domains serve as receptors to control the activities of the channels. A topological model for the ENaC family proteins is ------------------- Key: 2741 Medline: 97225970 Authors: Burdine RD;Chen EB;Kwok SF;Stern MJ Title: egl-17 encodes an invertebrate fibroblast growth factor family member required specifically for sex myoblast migration in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 94: 2433-2437 1997 Type: ARTICLE Genes: clr-1 egl-15 egl-17 Abstract: The proper guidance of the Caenorhabditis elegans hermaphrodite sex myoblasts (SMs) requires the genes egl-15 and egl-17, egl-15 has been shown to encode the C, elegans orthologue of the fibroblast growth factor receptor (FGFR). Here we clone egl-17 and show it to be a member of the fibroblast growth factor (FGF) family, one of the first functional invertebrate FGFs known, egl-17 shares homology with other FGF members, conserving the key residues required to form the distinctive tertiary structure common to FGFs, Genetic and molecular evidence demonstrates that the SM migration defect seen in egl-17 mutant animals represents complete loss of egl-17 function, While mutations in egl-17 affect only SM migration, mutations in egl-15 can result in larval arrest, scrawny body morphology, and the ability to suppress mutations in clr-1. We propose that EGL-17 (FGF) acts as a ligand for EGL-15 (FGFR) specifically during SM migration and that another ligand(s) activates EGL-15 for its other functions. ------------------- Key: 2742 Medline: 97228157 Authors: Sze JY;Liu Y;Ruvkun G Title: VP16-activation of the C. elegans neural specification transcription factor UNC-86 suppresses mutations in downstream genes and causes defects in neural migration and axon outgrowt Citation: Development 124: 1159-1168 1997 Type: ARTICLE Genes: mec-3 mec-7 unc-86 Abstract: The POU homeobox gene unc-86 specifies many neuroblast and neural fates in the developing C. elegans nervous system. Genes regulated by unc-86 are mostly unknown. Here we describe a genetic strategy for the identification of downstream pathways regulated by unc-86. We activate UNC-86 transcription activity by inserting the VP16 activation domain into an unc-86 genomic clone that bears all regulatory sequences necessary for normal expression in C. elegans. unc-86/VP16 complements unc-86 mutations in the specification of neuroblast and neural cell fates, but displays novel genetic activities: it can suppress non-null mutations in the downstream genes mec-3 and mec-7 that are necessary for mechanosensory neuron differentiation and function. These data suggest that UNC-86/VP16 increases the expression of mec-3 and mec-7 to compensate for the decreased activities of mutant MEC-3 or MEC-7 proteins. The suppression of mutations in downstream genes by an activated upstream transcription factor should be a general strategy for the identification of genes in transcriptional cascades. unc-86/VP16 also causes neural migration and pathfinding defects and novel behavioral defects. Thus, increased or unregulated expression of genes downstream of unc-86 can confer novel neural phenotypes suggestive of roles for unc-86-regulated genes in neural pathfinding and function. Genetic suppression of these unc-86/VP16 phenotypes may identify the unc-86 downstream genes that mediate these events in neurogenesis. ------------------- Key: 2743 Medline: 97209477 Authors: Davis TL;Meyer BJ Title: SDC-3 coordinates the assembly of a dosage compensation complex on the nematode X chromosome. Citation: Development 124: 1019-1031 1997 Type: ARTICLE Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 her-1 him-8 pes-1 sdc-1 sdc-2 sdc-3 xol-1 Abstract: X chromosome expression in C. elegans is controlled by a chromosome-wide regulatory process called dosage compensation that specifically reduces by half the level of transcripts made from each hermaphrodite X chromosome. This process equalizes X expression between the sexes (XX hermaphrodites and XO males), despite their two-fold difference in X chromosome dose, and thereby prevents sex-specific lethality. Dosage compensation is achieved by a protein complex that associates with X in a sex-specific fashion to modulate gene expression. SDC-3, a protein that coordinately controls both sex determination and dosage compensation, activates dosage compensation by directing the dosage compensation protein complex to the hermaphrodite X chromosomes. We show that SDC-3 coordinates this assembly through its own sex-specific association with X. SDC-3 in turn requires other members of the dosage compensation gene hierarchy for its stability and its X localization. In addition, SDC-3 requires its own zinc finger motifs and an amino-terminal region for its X association. Our experiments suggest the possible involvement of zinc finger motifs in X chromosome recognition and the aminoterminal region in interactions ------------------- Key: 2744 Medline: Authors: Anderson ARA;Young IM;Sleeman BD;Griffiths BS;Robertson WM Title: Nematode movement along a chemical gradient in a structurally heterogeneous environment. 1. Experiment. Citation: Fundamental and Applied Nematology 20: 157-163 1997 Type: ARTICLE Genes: Abstract: The interaction between soil structural heterogeneity and chemical gradients, and their effect on the movement of free-living nematodes was investigated. Four experimental treatments were used. These consisted of a nematode (Caenorhabditis elegans) on a homogeneous layer of nutrient agar in a Petri dish, with or without a localised bacterial food source (Escherichia coli) acting as an attractant. Structural heterogeneity was then introduced by adding a monolayer of sand grains onto both of the homogeneous treatments. AU trails were recorded using time-lapse video, and subsequently digitised prior to analysis. Turning angle distributions and the fractal dimension of the trails were calculated for each treatment. There was a statistically significant effect (P less than or equal to 0.01) of all treatments on the movement of the nematode. In the presence of the attractant, nematode movement was more linear and directed towards the bacterial source. Structural heterogeneity caused the nematode to have more linear movement compared to a homogeneous environment. The fractal dimension of the nematode trails was significantly higher (P less than or equal to 0.01) for the treatment without structure or bacteria, than for the other treatments. The results, for the first time, quantify the degree to which nematodes carry out random foraging type behaviour in a homogeneous environment and produce more directed non-random movement in the presence of attractant. Finally, when structure is present the foraging strategy becomes more of an avoidance strategy, allowing the nematode to escape structural traps, such as ''dead-end'' pores, and then continue to react to attractant gradients. ------------------- Key: 2745 Medline: 97252154 Authors: Emmons SW Title: Worms as an evolutionary model. Citation: Trends in Genetics 13: 131-134 1997 Type: REVIEW Genes: lin-12 Abstract: Focused studies on model organisms with favorable features have been important for advancing many areas of biology. Nematodes have been a successful model for analyzing development. Can they also be used to study evolution? Paul Sternberg and his present and former colleagues are attempting to answer this question by studying variation of that well-described little structure, the nematode vulva. Their efforts have been well rewarded. Two recent publications extend a series of papers showing a surprising degree of evolutionary variability in vulval development among species. Could it be that comparison of nematode species will prove to be as powerful for penetrating the intimate mechanisms of evolutionary change as analysis of mutant nematodes has been to understanding mechanisms of development? ------------------- Key: 2746 Medline: 97254921 Authors: Yuan JY Title: Genetic control of cellular suicide. Citation: Reproductive Toxicology 11: 377-384 1997 Type: REVIEW Genes: ced-3 ced-9 ces-1 ces-2 Abstract: Genetic analysis of programmed cell death in C. elegans has led to the identification of two genes, ced-9, a cell death suppressor, and ced-3, a cell death inducer, that play critical roles in regulating programmed cell death. The ced-9 and ced-3 genes were found to encode proteins that share structural and functional similarities with the mammalian proto-oncogene product Bcl-2 and interleukin-1 beta converting enzyme (ICE), respectively, Multiple members of the Bcl-2 family and the ICE family have been identified in vertebrates, These results suggest that the mechanism of apoptosis in vertebrates may be evolved from a much simpler version of a similar pathway in primitive ------------------- Key: 2747 Medline: 97224222 Authors: Mutwakil MHAZ;Reader JP;Holdich DM;Smithurst PR;Candido EPM;Jones D;Stringham EG;de Pomerai DI Title: Use of stress-inducible transgenic nematodes as biomarkers of heavy metal pollution in water samples from an English river system. Citation: Archives of Environmental Contamination and Toxicology 32: 146-153 1997 Type: ARTICLE Genes: Abstract: Transgenic strains of the nematode Caenorhabditis elegans, which carry stress-inducible lacZ reporter genes, are measurably stressed by exposure to heavy metals in aqueous solution. This stress response can be quantified, using enzymatic assays for the reporter gene-product (Escherichia coil beta-galactosidase), or estimated approximately by in situ staining for beta-galactosidase in exposed worms. Stress responses to heavy metals have been demonstrated both in laboratory tests using Cd2+ or Hg2+, and also in water samples taken from a metal-polluted river system in southwest England. The River Carnon flows through an area with an ancient mining history, principally for Sn, but also for Cu and other metals; As, Cd, Al, Mn, and Zn, as well as large amounts of Fe, are all present in these ore bodies. Four sites in the Carnon river basin were compared with respect to their macroinvertebrate diversity, physical and chemical characteristics (including the concentrations of As, Cd, Al, Cu, Mn, Zn, and Fe). Transgenic worms were exposed to water samples from these four sites, and also to a 0.33% (v/v) dilution of metal-laden minewater from the principal local mine (Wheal Jane). Transgene expression was induced in all five cases, though markedly less so for the least polluted of the sites (which also supported a richer macroinvertebrate fauna). Two different transgenic strains were tested in this study; strain PC72 (using a homologous hsp16 promoter) is slightly more sensitive to most metal-containing water samples than strain CB4027 (using a heterologous Drosophila hsp70 promoter). Both transgenic strains and two different assay methods gave essentially similar results. These findings demonstrate that transgenic nematodes could provide a rapid and simple assessment of aquatic pollution, in that the transgene response is inducible by mixtures of dissolved metals at concentrations actually encountered in metal-polluted watercourses. ------------------- Key: 2748 Medline: 97268124 Authors: Kagawa H;Takuwa K;Sakube Y Title: Mutations and expressions of the tropomyosin gene and the troponin C gene of Caenorhabditis elegans. Citation: Cell Structure and Function 22: 213-218 1997 Type: ARTICLE Genes: act-1 act-2 act-3 act-4 act-5 eat-12 egl-19 kra-1 lev-1 lev-11 mcl-1 mcl-2 mcl-3 mup-2 myo-1 myo-2 myo-3 pat-10 ryr-1 tmy-1 tnc-1 tni-1 tni-2 unc-15 unc-29 unc-38 unc-54 unc-68 Abstract: How does muscle gene mutation affect the muscle structure and function of an animal? Mutant animals of the tropomyosin and troponin C genes of Caenorhabditis elegans show Pat (paralyzed, arrested elongation at twofold) phenotypes together with abnormal muscle filament assembly. We present evidence that the mutation sites of lev-11 gene was in the tropomyosin gene, tmy-1 and that of pat-10 was in the troponin C gene, tnc-l, of the worm, respectively. The lev-11 (st557) mutation occurred at the splice donor site of exon 1 and results in translation termination. Although the gene product from heterozygous (+/st557) animal was not detected, our result could be the reason for the Pat phenotype of this mutation. The lev-11(x12) mutation, isolated as an allele of levamisole resistance, occurred in exon 7 and results in amino acid substitution at 234 from Glu to Lys. This substitution give a charge change from - to + at this point which is common in three isoforms. There may be functional importance of this region for molecular interaction of the tropomyosin. Mutation site of pat10(st575) was Asp64 to Asn and Trp153 to termination in the troponin C. The first mutation site was in the second calcium binding site and the second mutation raised the deletion of H helix in the troponin C. Both might affect the calcium binding or the retaining of the conformation for its function. Results presented here will be useful to understand the interaction site between the tropomyosin and troponin complex. ------------------- Key: 2749 Medline: 97280790 Authors: Sakube Y;Ando H;Kagawa H Title: An abnormal ketamine response in mutants defective in the ryanodine receptor gene ryr-1 (unc-68) of Caenorhabditis elegans. Citation: Journal of Molecular Biology 267: 849-864 1997 Type: ARTICLE Genes: kra-1 ryr-1 unc-22 unc-50 unc-68 unc-74 nDf18 nDf32 sDf20 sDf26 sDf36 Abstract: To characterize excitation-contraction coupling in Caenorhabditis elegans, we applied two approaches. First, we isolated a mutant having abnormal responses to ketamine, an anesthetic in vertebrates. The novel mutation unc-68(kh30) (isolated as kra-1(kh30)), exhibited strict ketamine-dependent convulsions followed by paralysis. Second, we cloned the C. elegans ryanodine receptor gene ryr-1 that is located near the center of chromosome V. ryr-1 consists of 46 exons, which encode a predicted protein of 5071 amino acid residues that is homologous to Drosophila and vertebrate ryanodine receptors. ryr-1 promoter/lacZ plasmids were expressed in body-wall and pharyngeal muscles. Non-muscle cell expression may be seen with a truncated promoter. In addition, we show that the unc-68/kra-1(kh30) mutation is a Ser1444 Asn substitution at a putative protein kinase C phosphorylation site in ryr-1, and that unc-68(e540) contains a splice acceptor mutation that create's a premature stop codon in the ryr-1 gene. We confirmed that unc-68(e540) is a mutation in ryr-1 by injecting the complete ryr-1 gene into unc-68(e540) animals and recovering wildtype progeny. Results presented here will be useful in studying the structure and function of ryanodine receptors in excitation-contraction coupling and in understanding the evolution of ryanodine receptor tissue specificity. ------------------- Key: 2750 Medline: 97306058 Authors: Tanaka Y;Ohta A;Terashima K;Sakamoto H Title: Polycistronic expression and RNA-binding specificity of the C. elegans homologue of the spliceosome-associated protein SAP49. Citation: Journal of Biochemistry 121: 739-745 1997 Type: ARTICLE Genes: mai-1 Abstract: Splicing of mRNA precursors (pre-mRNAs) occurs in a multimolecular complex, termed spliceosome, which is comprised of pre-mRNA, small nuclear ribonucleoprotein particles (snRNPs), and other protein factors including spliceosome-associated proteins (SAPs), SAP49 is thought to be a subunit of the essential splicing factor SF3b and is involved in U2 snRNP function in mammalian cells, We have isolated a Caenorhabditis elegans cDNA encoding an RNA-binding protein with two RNA recognition motifs (RRMs) which shows extensive similarity to the human SAP49, The primary transcript for this C. elegans SAP49 homologue (cSAP49) seems to contain at least two additional cistrons and can be processed into three different mature mRNAs by trans-splicing. The cSAP49 mRNA, like other mRNAs in the same polycistronic unit, is expressed in most of the developmental stages, consistent with its putative essential function for mRNA splicing, By means of an in vitro RNA selection system, we demonstrate that cSAP49 possesses specific RNA-binding activity which resides in its second RRM. ------------------- Key: 2751 Medline: 97250552 Authors: Bloom L;Horvitz HR Title: The Caenorhabditis elegans gene unc-76 and its human homologs define a new gene family involved in axonal outgrowth and fasciculation. Citation: Proceedings of the National Academy of Sciences USA 94: 3414-3419 1997 Type: ARTICLE Genes: smg-1 unc-76 yDf8 Abstract: The gene unc-76 (unc, uncoordinated) is necessary for normal axonal bundling and elongation within axon bundles in the nematode Caenorhabditis elegans. The UNC-76 protein and two human homologs identified as expressed sequence tags are not similar to previously characterized proteins and thus represent a new protein family. At least one of these human homologs can function in C. elegans, suggesting that it, like UNC-76, acts in axonal outgrowth. We propose that the UNC-76 protein, which is found in cell bodies and processes of all neurons throughout development, either has a structural role in the formation and maintenance of axonal bundles or transduces signals to the intracellular machinery that regulates axonal extension and adhesion. ------------------- Key: 2752 Medline: 97280059 Authors: Gerdt S;Lochnit G;Dennis RD;Geyer R Title: Isolation and structural analysis of three neutral glycosphingolipids from a mixed population of Caenorhabditis elegans (Nematoda, Rhabditida). Citation: Glycobiology 7: 265-275 1997 Type: ARTICLE Genes: Abstract: The free-living nematode, Caenorhabditis elegans, has been proposed and analyzed as a prototypic model for parasitic nematodes, In order to study whether there is a structural basis for the proposed analogy with respect to nematode glycoconjugates, me have analyzed Caenorhabditis elegans glycosphingolipids. Three, simple neutral glycosphingolipid components of the neutral glycolipid fraction were isolated by high-performance liquid chromatography, Structural analysis was performed by methylation analysis, exoglycosidase cleavage, matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry, and ceramide analysis. The chemical structures have been determined as Glc beta 1Cer, Man beta 4Glc beta 1Cer and GlcNAc beta 3Man beta 4Glc beta 1Cer; that are characterized as belonging to the arthroseries of protostomial glycosphingolipids. The ceramide moiety of the parent glycosphingolipid-ceramide monohexoside was dominated by 2-hydroxy fatty acids, and a d17:1 sphingoid-base with an iso- or anteiso-branched chain, The chemical composition of the three glycosphingolipids from Caenorhabditis elegans displayed close structural coincidence with the equivalent structures from the porcine parasitic nematode, Ascaris suum (G.Lochnit, R,D. Dennis, U.Zahringer, and R,Geyer, Glycoconjugate J., 1997), in support of this organism as a prototypic glycosphingolipid model for parasitic nematodes. ------------------- Key: 2753 Medline: 97250270 Authors: Chen J-S;Sappington TW;Raikhel AS Title: Extensive sequence conservation among insect, nematode, and vertebrate vitellogenins reveals ancient common ancestry. Citation: Journal of Molecular Evolution 44: 440-451 1997 Type: ARTICLE Genes: Abstract: The eggs of most oviparous animals are provisioned with a class of protein called vitellogenin (Vg) which is stored as the major component of yolk. Until recently, deduced amino acid sequences were available only from vertebrate and nematode Vgs, which proved to be homologous. The sequences of several insect Vgs are now known, but early attempts at pairwise alignments with vertebrate and nematode Vgs have been problematic, leading to conflicting conclusions about how closely insect Vgs are related to the others. In this paper we demonstrate that insect VE sequences can be confidently aligned with one another along their entire lengths and with multiple vertebrate and nematode Vg sequences along most of their spans. Although divergence is high, conservation among insect, vertebrate, and nematode Vg sequences is widespread with a preponderance of glycine, proline, and cysteine residues among strictly conserved amino acids, establishing conclusively that Vgs from the three phyla are homologous. Areas of least-certain alignment are primarily in and around insect and vertebrate polyserine domains which are not homologous. Phylogenetic reconstructions of Vgs based on sequence identities indicate that the insect lineage is the most diverged and that the mammalian serum protein, apolipoprotein B-100, arose from a Vg ancestor after the ------------------- Key: 2754 Medline: 97244087 Authors: Johnson TE Title: Genetic influences on aging. Citation: Experimental Gerontology 32: 11-22 1997 Type: REVIEW Genes: age-1 daf-1 daf-2 daf-4 daf-7 daf-12 daf-16 daf-23 daf-28 spe-26 Abstract: Genetics is an important tool for identifying key molecular events that are involved in specifying biological functions. Genetic approaches have been used repeatedly to understand diverse biological phenomena: oncogenesis, development, and the cell cycle, but have only recently been applied to the analysis of organismic aging and senescence. The power of the genetic approach stems from two facts. First, genetic analyses allow the integration of phenomena that are analyzed at many levels of observation from the molecule to the intact organism, and second, genetics has the real power to reveal causality by factors that are not dependent upon the prejudice of the investigator. I discuss several areas where genetics has been fruitfully applied to the study of the aging process: human genes identified by "segmental progeroid" mutations, neurological diseases of the elderly, the limited proliferative life span of human somatic cells in tissue culture, studies on the life span of the mouse and genetic analysis of life span in shorter lived metazoans (Drosophila melanogaster and Caenorhabditis elegans), and ------------------- Key: 2755 Medline: 97204387 Authors: Maule AG;Bowman JW;Thompson DP;Marks NJ;Friedman AR;Geary Title: FMRFamide-related peptides (FaRPs) in nematodes: occurrence and neuromuscular physiology. Citation: Parasitology 113: S119-S135 1996 Type: ARTICLE Genes: flp-1 flp-2 flp-3 flp-4 flp-5 flp-6 flp-7 flp-8 flp-9 Abstract: The occurrence of classical neurotransmitter molecules and numerous peptidic messenger molecules in nematode nervous systems indicate that although structurally simple, nematode nervous systems are chemically complex. Thus far, studies oh one nematode neuropeptide family, namely the FMRFamide-related peptides (FaRPs), have revealed an unexpected variety of neuropeptide structures in both free-living and parasitic species. To date 23 nematode FaRPs have been structurally characterized including 12 from Ascaris suum, 8 from Caenorhabditis elegans, 5 from Panagrellus redivivus and 1 from Haemonchus contortus. Ten FaRP-encoding genes have been identified in Caenorhabditis elegans. However, the full complement of nematode neuronal messengers has yet to be described und unidentified nematode FaRPs await detection. Preliminary characterization of the actions of nematode neuropeptides on the somatic musculature and neurones of A. suum has revealed that these peptidic messengers have potent and complex effects. Identified complexities include the biphasic effects of KNEFIRFamide/KHEYLRFamide (AF1/2; relaxation of tone followed by oscillatory contractile activity) and KPNFIRFamide (PF4; rapid relaxation of tone followed by an increase in tone), the diverse actions of KSAYMRFamide (AF8 or PF3; relaxes dorsal muscles and contracts ventral muscles) and the apparent coupling of the relaxatory effects of SDPNFLRFamide/SADPNFLRFamide (PF1/PF2) to nitric oxide release. Indeed, all of the nematode FaRPs which have been tested on somatic muscle strips of A. suum have actions which are clearly physiologically distinguishable. Although we are a very long way from understanding how the actions of these peptides are coordinated, not only with those of each other but also with those of the classical transmitter molecules, to control nematode behaviour, their abundance coupled with their diversity of structure and function indicates a hitherto unidentified sophistication to nematode ------------------- Key: 2756 Medline: 97204393 Authors: Thompson DP;Klein RD;Geary TG Title: Prospects for rational approaches to anthelmintic Citation: Parasitology 113: S217-S238 1996 Type: REVIEW Genes: che-3 mec-4 unc-2 unc-38 Abstract: Rational approaches to anthelmintic discovery include the design of screens for compounds directed at specific proteins in helminths that are pharmacologically distinguishable from their vertebrate homologues. The existence of several anthelmintics that selectively target the neuromusculature of helminths (e.g. levamisole, ivermectin, praziquantel, metrifonate), together with recent basic research in helminth physiology, have contributed to the recognition that neurobiology distinguishes these organisms from their vertebrate hosts. In this survey, we focus on mechanism-based screening and its application to anthelmintic discovery, with particular emphasis on targets in the neuromusculature of helminths. Few of these proteins have been exploited in chemotherapy. However, recent studies in comparative pharmacology and molecular biology, including the C. elegans genome project, have provided insights on potential new targets and, in some cases, molecular probes useful for their incorporation ------------------- Key: 2757 Medline: 97204392 Authors: Sangster N Title: Pharmacology of anthelmintic resistance. Citation: Parasitology 113: S201-S216 1996 Type: ARTICLE Genes: Abstract: Anthelmintic resistance has compromised the control of nematode parasites in several animal-based industries. Studies of resistance have not only improved our understanding of this phenomenon but also shed light on physiological systems of parasitic helminths. In addition, research on molecular aspects of anthelmintic resistance may provide selectable markers for use in future transfection studies with helminths. Several anthelmintics act on helminth neuromuscular systems. Drugs such as levamisole are cholinergic agonists and, based on pharmacological studies, levamisole-resistant nematodes appear to have altered acetylcholine receptors. It is likely that anticholinesterase anthelmintics share cross resistance with levamisole. Ivermectin appears to be a glutamate agonist. In vitro studies of ivermectin-resistant nematodes suggest that IVM receptors are located on pharyngeal and somatic muscle. The free-living nematode Caenorhabditis elegans may provide a model for anthelmintic resistance. It has been useful in cloning drug receptors from parasites but differences between its life history and habitat compared with parasitic nematodes may limit its usefulness for studying resistance in these parasites. ------------------- Key: 2759 Medline: 97271897 Authors: Leonardo ED;Hinck L;Masu M;Keino-Masu K;Ackerman SL;Tessier-Lavigne M Title: Vertebrate homologues of C. elegans UNC-5 are candidate netrin receptors. Citation: Nature 386: 833-838 1997 Type: ARTICLE Genes: unc-5 Abstract: In the developing nervous system, migrating cells and axons are guided to their targets by cues in the extracellular environment. The netrins are a family of phylogenetically conserved guidance cues that can function as diffusible attractants and repellents for different classes of cells and axons(1-10). In vertebrates, insects and nematodes, members of the DCC subfamily of the immunoglobulin superfamily have been implicated as receptors that are involved in migration towards netrin sources(6,11-13,15). The mechanisms that direct migration away from netrin sources (presumed repulsions) are less well understood. In Caenorhabditis elegans, the transmembrane protein UNC-5 (ref. 14) has been implicated in these responses, as loss of unc-5 function causes migration defects(16,17) and ectopic expression of unc-5 in some neurons can redirect their axons away from a netrin source(18). Whether UNC-5 is a netrin receptor or simply an accessory to such a receptor has not, however, been defined. We now report the identification of two vertebrate homologues of UNC-5 which, with UNC-5 and the product of the mouse rostral cerebellar malformation gene (rcm)(19), define a new subfamily of the immunoglobulin superfamily, and whose messenger RNAs show prominent expression in various classes of differentiating neurons. We provide evidence that these two UNC-5 homologues, as well as the rcm gene product, are netrin-binding proteins, supporting the hypothesis that UNC-5 and its relatives are netrin receptors. ------------------- Key: 2760 Medline: Authors: Mutwakil MHAZ;Steele TJG;Lowe KC;de Pomerai DI Title: Surfactant stimulation of growth in the nematode Caenorhabditis elegans. Citation: Enzyme & Microbial Technology 20: 462-470 1997 Type: ARTICLE Genes: Abstract: Size fractionation has been used to isolate L1/L2 larvae from mixed cultures of the nematode, Caenorhabditis elegans. Worm lengths have been compared during growth in synchronized liquid and agar cultures. Supplementation of liquid S medium with 10 ppm surfactant (Pluronics F-68, F-127, F-38, L-35; Tween-20 or Triton X-100) promoted a significant stimulation of growth over three clays in all cases. Because of possible poor nutrition and/or aeration in liquid culture, experiments were repeated using the same surfactants in standard NGM agar. Four surfactants again stimulated worm growth significantly whereas two (Tween-20 and Pluronic F-68) did not. Differences between these surfactants were also demonstrated with respect to: (i) toxicity; (ii) induction of stress responses in a transgenic hsp/reporter strain; and (iii) stimulation of amino acid incorporation into soluble protein both initially and after 41 h of surfactant treatment. These surfactants, and in particular, Pluronic F-127, are potentially valuable as culture supplements for enhancing nematode larval growth. Possible mechanisms for growth promotion by surfactants are discussed in light of the fixed somatic cell lineage and the fact that Pluronic F-127 did not speed up maturation from L4 larvae into egg-bearing ------------------- Key: 2761 Medline: 97263500 Authors: Irmler M;Hoffman K;Vaux D;Tschopp J Title: Direct physical interaction between the Caenorhabditis elegans death proteins CED-3 and CED-4. Citation: FEBS Letters 406: 189-190 1997 Type: ARTICLE Genes: ced-3 ced-4 Abstract: The two genes CED-4 and CED-3 (the nematode homologue of interleukin-1 beta converting enzyme, ICE) of Caenorhabditis elegans are implicated in the control of cell death, but the mechanism by which this occurs is unknown, Here we provide evidence that CED-3 and CED-3 both contain sequences with homology to a domain present in RAIDD and the prodomain of certain ICE-like proteases (caspases). This domain is known to establish an interaction between RAIDD and these caspases. Similarly, CED-4 was found to interact with CED-3. Thus, the activity of the death protease CED-3 appears to be controlled by ------------------- Key: 2762 Medline: 97260554 Authors: Wicks SR;Rankin CH Title: Effects of tap withdrawal response habituation on other withdrawal behaviors - The localization of habituation in the nematode Caenorhabditis elegans. Citation: Behavioral Neurosciences 111: 342-353 1997 Type: ARTICLE Genes: Abstract: Four experiments were conducted to identify the possible loci of habituation of the nematode tap withdrawal response (TWR) by characterizing the effects of TWR habituation on other nonmechanosensory withdrawal behaviors that are mediated by overlapping sets of neurons. Experiments 1-2 established behavioral and anatomical relationships between spontaneous and tap-induced backward locomotion in the worm. Experiment 3 demonstrated that habituation of the TWR affected neither the magnitude nor frequency of spontaneous reversal activity. Experiment 4 extended this result to an evoked response: Habituation of the TWR had no effect on reversals evoked by a thermal stimulus. These studies, which show that the loci of change associated with habituation of the TWR are presynaptic to the interneurons and motor neurons that control locomotion, probably distributed among the mechanosensory neurons, illustrate that a complete understanding of plasticity requires a knowledge of both the anatomical and molecular substrates ------------------- Key: 2763 Medline: 97260555 Authors: Wen JYM;Kumar N;Morrison G;Rambaldini G;Runciman S;Rousseau J;van der Kooy D Title: Mutations that prevent associative learning in C. elegans. Citation: Behavioral Neurosciences 111: 354-368 1997 Type: ARTICLE Genes: lrn-1 lrn-2 Abstract: The nematode Caenorhabditis elegans offers a promising system for the reductionist study of learning and memory. in this article, classical conditioning in C. elegans is demonstrated with a variety of associative learning assays. These assays allowed for the isolation and behavioral characterization of 2 mutant C. elegans lines impaired in associative learning. Both lines show no short-term or long-term associative conditioning; however, they appear relatively normal in tests of nonassociative learning and sensorimotor function. In combination with the well-described genetics and neuroanatomy of C. elegans, the isolation of mutants selectively, yet completely, blocked in associative learning provides the basis for an effective characterization of the cellular and molecular aspects of associative learning. ------------------- Key: 2764 Medline: 97265405 Authors: Yochem J;Sundaram M;Han M Title: Ras is required for a limited number of cell fates and not for general proliferation in Caenorhabditis elegans. Citation: Molecular and Cellular Biology 17: 2716-2722 1997 Type: ARTICLE Genes: let-23 let-60 ncl-1 Abstract: Experiments with mammalian tissue culture cells have implicated the small GTPase Ras in the control of cellular proliferation. Evidence is presented here that this is not the case for a living animal, the nematode Caenorhabditis elegans: proliferation late in embryogenesis and throughout the four larval stages is not noticeably affected in animals lacking Ras in various parts of their cell lineages. Instead, genetic mosaic analysis of the let-60 gene suggests that Ras is required only, at least later in development (a maternal effect cannot be excluded), for establishment of a few temporally and spatially distinct cell fates. Only one of these, the duct cell fate, appears to be essential for viability. ------------------- Key: 2765 Medline: 97250735 Authors: Wood WB;Streit A;Li W Title: Dosage compensation: X-repress yourself. Citation: Current Biology 7: R227-R230 1997 Type: REVIEW Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 her-1 sdc-1 sdc-2 sdc-3 xol-1 Abstract: Dosage compensation in Caenorhabditis elegans involves the sex-specific recruitment to the X chromosome of a protein complex, the nature of which suggests that there are mechanistic links between chromosome segregation and global transcriptional regulation. ------------------- Key: 2766 Medline: 97287863 Authors: Manser J;Roonprapunt C;Margolis B Title: C. elegans cell migration gene mig-10 shares similarities with a family of SH2 domain proteins and acts cell nonautonomously in excretory canal development. Citation: Developmental Biology 184: 150-164 1997 Type: ARTICLE Genes: mig-10 sDp3 Abstract: The mig-10 gene of Caenorhabditis elegans is required for the long-range anteroposterior migration of embryonic neurons CAN, ALM, and HSN and proper development of the excretory canals. Here, we report the cloning and initial molecular characterization of mig-10. The predicted MIG-10 proteins share a large region of similarity with a recently identified family of mammalian SH2 domain proteins, Grb7 and Grb10. We call this region of similarity the GM region (for Grb and Mig). MIG-10 proteins do not contain an SH2 domain, but share with the Grbs a pleckstrin homology (PII) domain and proline-rich regions, features commonly found in signal transduction proteins. The functions of Grb7 and Grb10 are unknown, but Grb7 is overexpressed in certain breast cancers, where it is bound to the growth factor receptor HER2, while Grb10 has been implicated in insulin signaling. We also report the isolation of a new mig-10(e2527) allele, as well as the molecular characterization of e2527 (splice acceptor mutation) and the canonical ct41 (amber) allele. finally, we report the results of a genetic mosaic analysis which reveal that mig-10 acts cell nonautonomously in the development of the excretory canals and suggest a possible focus for mig-10 activity within descendants of the AB cell lineage. Elucidation of the role of mig-10 in C. elegans development should lead to a better understanding of cell migration and may shed light on the function of a family of SH2 domain proteins apparently involved in signal transduction and ------------------- Key: 2767 Medline: 97268117 Authors: Liu F;Barral JM;Bauer CC;Ortiz I;Cook RG;Schmid MF;Epstein HF Title: Assemblases and coupling proteins in thick filament assembly. Citation: Cell Structure and Function 22: 155-162 1997 Type: ARTICLE Genes: myo-3 unc-15 unc-45 unc-54 unc-82 Abstract: Thick filaments are stable assemblies of myosin that are characteristic of specific muscle types from both vertebrates and invertebrates. In general, their structure and assembly require remarkably precise determination of lengths and diameters, structural differentiation and nonequivalence of myosins, a high degree of inelasticity and rigidity, and dynamic regulation of assembly and disassembly in response to both extracellular and intracellular signals. Directed assembly of myosin in which additional proteins function in key roles, therefore, is more likely to be significant than the simple self assembly of myosin into thick filaments. The nematode Caenorhabditis elegans permits a wide spectrum of biochemical, genetic, molecular and structural approaches to be applied to the experimental testing of this hypothesis. Biochemical analysis of C. elegans thick filaments reveals that paramyosin, a homologue of the myosin rod that is the unique product of a single genetic locus, exists as two populations which differ by post-translational modification. The major paramyosin species interacts with the two genetically specified myosin heavy chain isoforms. The minor paramyosin species is organized within the cores of the thick filaments, where it is associated stoichiometrically with three recently identified proteins P20, P28 and P30. These proteins have now been characterized molecularly and contain unique, novel amino acid sequences. Structural analysis of the core shows that seven paramyosin subfilaments are crosslinked by additional internal proteins into a highly rigid tubule. P20, P28 and P30 are proposed to couple the paramyosin subfilaments together into the core tubule during filament assembly. Mutants that affect paramyosin assembly are being characterized for alterations in the core proteins. A fourth protein has been identified recently as the product of the unc-45 gene. Computational analysis of this gene's DNA suggests that the predicted protein may exhibit protein phosphatase and chaperone activities. Genetic analysis shows that three classes of specific unc-45 mutant proteins differentially interact with the two myosins during thick filament assembly. The unc-45 protein is proposed to be a myosin assemblase, a protein catalyst of thick filament ------------------- Key: 2768 Medline: 97296386 Authors: Bun-ya M;Maebuchi M;Hashimoto T;Yokota S;Kamiryo T Title: A second isoform of 3-ketoacyl-CoA thiolase found in Caenorhabditis elegans, which is similar to sterol carrier protein x but lacks the sequence of sterol carrier protein 2. Citation: European Journal of Biochemistry 245: 252-259 1997 Type: ARTICLE Genes: Abstract: We cloned a full-length cDNA of the nematode Caenorhabditis elegans that encodes a 44-kDa protein (P-44, 412 residues) similar to sterol carrier protein x (SCPx). Mammalian SCPx is a bipartite protein: its 404-residue N-terminal and 143-residue C-terminal domains are similar to 3-ketoacyl-CoA thiolase and identical to the precursor of sterol carrier protein 2 (SCP2; also termed non-specific lipid-transfer protein), respectively. P-44 has 56% sequence identity to the thiolase domain of SCPx but lacks the SCP2 sequence. Northern blot analysis revealed only a single mRNA species of 1.4 kb, which agrees well with the length of the cDNA (1371 bp), making it improbable that alternative splicing produces an SCPx-like fusion protein. The sequence similarities of P-44 to conventional thiolases an lesser than that to SCPx. Purified recombinant P-44 cleaved long-chain 3-ketoacyl-CoAs (C8-16) in a thiolytic manner by the ping-pong bi-bi reaction mechanism. The inhibition of P-44 by acetyl-CoA was competitive with CoA and non-competitive with 3-ketooctanoyl-CoA. This pattern of inhibition is shared with SCPx but not with conventional 3-ketoacyl-CoA thiolase, which is inhibited uncompetitively with respect to 3-ketoacyl-CoA. From these results, we concluded that nematode P-44 and mammalian SCPx constitute a second isoform of thiolase, which we propose to term type-II 3-ketoacyl-CoA thiolase. ------------------- Key: 2769 Medline: 97250743 Authors: James C;Gschmeissner S;Fraser A;Evan GI Title: CED-4 induces chromatin condensation in Schizosaccharomyces pombe and is inhibited by direct physical association with CED-9. Citation: Current Biology 7: 246-252 1997 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: Background: Three principal genes are involved in developmental programmed cell death (PCD) in the nematode worm Caenorhabditis elegans. The ced-3 and ced-4 genes are both required for each PCD, whereas ced-9 acts to prevent the death-promoting actions of these genes in cells that are destined to survive, Vertebrate homologues of both ced-3 and ced-9 have been identified as the genes encoding the caspase cysteine proteases and the Bcl-2 family, respectively. In contrast, no vertebrate homologue of ced-4 is known. The CED-3/caspases are important effectors of apoptosis that are presumed to act by cleaving specific target substrates. However, the molecular functions of the CED-9/Bcl-2 and CED-4 proteins are unknown. The unicellular yeast Schizosaccharomyces pombe shares many general cellular properties with metazoa, but has no identified cell suicide machinery. We have therefore used S. pombe as a naive model cell system in which to examine the biological effects of cell-death proteins. Results: Induction of wild-type ced-4 expression in S. pombe resulted in rapid focal chromatin condensation and lethality, Mutation of the putative nucleotide-binding P-loop motif of CED-4 (K165Q) eliminated the lethal phenotype. Immunolocalization of CED-4 to the condensed chromatin suggested that the phenotype may result from an intrinsic activity of CED-4. Co-expression of ced-9 prevented CED-4-induced chromatin condensation and lethality, and caused the relocalization of CED-4 to endoplasmic reticulum and outer mitochondrial membranes. A direct interaction between CED-4 and CED-9 was confirmed by yeast two-hybrid analysis. Conclusions: Using S. pombe as a model system in which to assay CED-4 function, we have identified a potential direct role for CED-4 in chromatin condensation. Chromatin condensation is a ubiquitous feature of metazoan apoptosis that has yet to be linked to an effector. The CED-9-mediated rescue of CED-4-induced lethality in this system and the interaction of the two proteins in the yeast two-hybrid analysis suggest that ------------------- Key: 2770 Medline: 97281700 Authors: Hodgkin J;Doniach T Title: Natural variation and copulatory plug formation in Caenorhabditis elegans. Citation: Genetics 146: 149-164 1997 Type: ARTICLE Genes: cal-1 gro-1 gro-2 gro-3 let-551 mab-23 plg-1 rtw-5 tra-1 tra-3 zyg-12 Abstract: Most of the available natural isolates of the nematode Caenorhabditis elegans have been examined and compared with the standard laboratory wild type (Bristol N2). Molecular markers, in particular transposon restriction fragment length polymorphisms, were used to assign these isolates to 22 different races, for which brood size and spontaneous male frequency were determined. Several distinctive traits were observed in some of these races. One example is mab-23, in a race from Vancouver, which leads to severe distortion of male genitalia and prevents male mating. Another is gro-1, segregating in a Californian race, which is associated with Slow growth, heat resistance and longevity. Many races differ from N2 in carrying a dominant allele at the plg-1 locus, causing copulatory plug formation by males. Properties and possible advantages of the plugging trait have been investigated. The dominant plg-1 allele does not lead to increased male mating efficiency, but males from a Stanford race (CB4855), in which the plugging trait was first observed, are much more virile than N2 males. Crosses between N2 and CB4855 indicate that the higher virility is due to multiple factors. Size differences between N2 and CB4855 are ------------------- Key: 2771 Medline: 97281701 Authors: Gatewood BK;Bucher EA Title: The mup-4 locus in Caenorhabditis elegans is essential for hypodermal integrity, organismal morphogenesis and embryonic body wall muscle position. Citation: Genetics 146: 165-183 1997 Type: ARTICLE Genes: mua-3 mup-1 mup-4 nDf16 nDf20 sDf127 sDf135 Abstract: mup-4 is a member of a set of genes essential for correct embryonic body wall muscle cell positions in Caenorhabditis elegans. The mup-4 phenotype is variably expressed and three discrete arrest phenotypes arise during the phase of embryonic development when the worm elongates from a ball of cells to its worm shape (organismal morphogenesis). Mutants representing two of the phenotypic classes arrest without successful completion of elongation. Mutants of the third phenotypic class arrest after completion of elongation. Mutants that arrest after elongation display profound dorsal and ventral body wall muscle cell position abnormalities and a characteristic kinked body shape (the Mup phenotype) due to the muscle cell position abnormalities. Significantly, genetic mosaic analysis of mup-4 mutants demonstrates that mup-4 gene function is essential in the AB lineage, which generates most of the hypodermis (epidermis), a tissue with which muscle interacts. Consistent with the genetic mosaic data, phenotypic characterizations reveal that mutants have defects in hypodermal integrity and morphology. Our analyses support the conclusion that mup-4 is essential for hypodermal function and that this function is necessary for organismal morphogenesis and for the maintenance of body ------------------- Key: 2772 Medline: 97281702 Authors: Terns RM;Kroll-Conner P;Zhu J;Chung S;Rothman JH Title: A deficiency screen for zygotic loci required for establishment and patterning of the epidermis in Caenorhabditis elegans. Citation: Genetics 146: 185-206 1997 Type: ARTICLE Genes: hDf6 hDf8 sDf6 hDf9 nDf3 nDf6 eDf1 tDf3 ozDf5 ccDf5 maDf4 mnDf88 mnDf109 mnDf63 mnDf89 wcDf1 sDf121 nDf40 eDf19 mDf7 sDf2 sDf60 sDf45 sDf26 sDf35 nDf42 ctDf1 itDf2 yDf4 mnDf1 qDf3 nDf23 nDf30 eDf9 ccDf1 mnDf30 sDf124 rhDf1 nDf17 mDf5 eDf18 nDf27 sDf23 sDf33 arDf1 yDf8 ozDf2 syDf1 uDf1 stDf5 nDf19 hDf10 nDf25 nDf24 eDf3 stDf7 eDf2 nDf41 Abstract: To identify genomic regions required for establishment and patterning of the epidermis, we screened 58 deficiencies that collectively delete at least similar to 67% of the Caenorhabditis elegans genome. The epidermal pattern of deficiency homozygous embryos was analyzed by examining expression of a marker specific for one of the three major epidermal cell types, the seam cells. The organization of the epidermis and internal organs was also analyzed using a monoclonal antibody specific for epithelial adherens junctions. While seven deficiencies had no apparent effect on seam cell production, 21 were found to result in subnormal, and five in excess numbers of these cells. An additional 23 deficiencies blocked expression of the seam cell marker, in some cases without preventing cell proliferation. Two deficiencies result in multinucleate seam cells. Deficiencies were also identified that result in subnormal numbers of epidermal cells, hyperfusion of epidermal cells into a large syncytium, or aberrant epidermal differentiation. Finally, analysis of internal epithelia revealed deficiencies that cause defects in formation of internal organs, including circularization of the intestine and bifurcation of the pharynx lumen. This study reveals that many regions of the C. elegans genome are required zygotically for patterning of the epidermis and other epithelia. ------------------- Key: 2773 Medline: 97281703 Authors: Chanal P;Labouesse M Title: A screen for genetic loci required for hypodermal cell and glial-like cell development during Caenorhabditis elegans embryogenesis. Citation: Genetics 146: 207-226 1997 Type: ARTICLE Genes: ale-1 ces-1 elt-1 emb-29 lin-26 hDf10 tDf3 qDf3 qDf4 hDf6 hDf8 ozDf5 mnDf111 hDf9 qDf5 qDf7 qDf8 qDf9 qDf10 hDf15 hDf16 hDf17 eDf3 eDf4 eDf24 nDf3 ccDf1 maDf4 mnDf30 mnDf88 mcDf1 mnDf106 mnDf100 mnDf104 mnDf68 mnDf67 mnDf61 mnDf29 mnDf59 mnDf57 mnDf83 mnDf90 mnDf87 mnDf89 sDf124 nDf11 sDf121 nDf16 nDf20 sDf110 nDf40 tDf1 ctDf3 ctDf2 mDf5 mDf4 stDf7 nDf41 eDf19 eDf18 mDf7 sDf2 sDf60 nDf27 sDf23 sDf45 sDf40 sDf33 sDf34 sDf72 sDf74 sDf75 sDf50 sDf27 sDf20 sDf30 sDf35 ctDf1 yDf12 nDf42 itDf2 yDf8 yDf6 ozDf2 meDf6 syDf1 uDf1 stDf5 nDf19 mnDf1 mnDf20 mnDf2 mnDf41 Abstract: The Caenorhabditis elegans lin-26 gene is expressed in all nonneuronal ectodermal cells. To identify genes required to specify the fates of ectodermal cells, we have conducted screens designed to identify loci whose zygotic function would be required for normal lin-26 expression. First, we examined 90 deficiencies covering 75% of the genome; second, we examined the progeny of 3600 genomes after EMS mutagenesis. We identified six loci that appear to be required for normal lin-26 expression. We argue that the deficiency eDf19 deletes a gene involved in specifying hypodermal cell fates. The genes emb-29 (previously known) and ale-1 (newly found) could be involved in a cell cycle function and/or in specifying the fates of some precursors within different lineages that generate hypodermal cells and nonectodermal cells. We argue that the overlapping deficiencies qDf7, qDf8 and qDf9 delete a gene required to limit the number of nonneuronal ectodermal cells. We suggest that the deficiencies ozDf2, itDf2 and nDf42 delete genes required, directly or indirectly, to repress lin-2G expression in cells that normally do not express lin-26. We discuss the implications of these findings concerning the generation of the ectoderm. ------------------- Key: 2774 Medline: 97281704 Authors: Kelly WG;Xu SQ;Montgomery MK;Fire A Title: Distinct requirements for somatic and germline expression of a generally expressed Caenorhabditis elegans gene. Citation: Genetics 146: 227-238 1997 Type: ARTICLE Genes: cap-2 let-852 let-853 let-854 let-855 let-856 let-857 let-858 mnDf77 mnDf87 mnDf90 Abstract: In screening for embryonic-lethal mutations in Caenorhabditis elegans, we defined an essential gene (let-858) that encodes a nuclear protein rich in acidic and basic residues. We have named this product nucampholin. Closely homologous sequences in yeast, plants, and mammals demonstrate strong evolutionary conservation in eukaryotes. Nucampholin resides in all nuclei of C. elegans and is essential in early development and in differentiating tissue. Antisense-mediated depletion of LET-858 activity in early embryos causes a lethal phenotype similar to characterized treatments blocking embryonic gene expression. Using transgene-rescue, we demonstrated the additional requirement for let-858 in the larval germline. The broad requirements allowed investigation of soma-germline differences in gene expression. When introduced into standard transgene arrays, let-858 (like many other C. elegans genes) functions well in soma but poorly in germline. We observed incremental silencing of simple let-858 arrays in the first few generations following transformation and hypothesized that silencing might reflect recognition of arrays as repetitive or heterochromatin-like. To give the transgene a more physiological context, we included an excess of random genomic fragments with the injected DNA. The resulting transgenes show robust expression in both germline and soma. Our results suggest the possibility of concerted mechanisms for silencing unwanted germline expression of ------------------- Key: 2775 Medline: 97268654 Authors: Keightley PD;Caballero A Title: Genomic mutation rates for lifetime reproductive output and lifespan in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 94: 3823-3827 1997 Type: ARTICLE Genes: Abstract: Theory concerning the evolution of sex and recombination and mutation load relies on information on rates and distributions of effects of deleterious mutations. Direct information on the genomic mutation rate in Drosophila implies that an accumulation of mildly deleterious mutations reduces viability of populations by at least 1% per generation. We carried out an experiment to measure the deleterious mutation rate in Caenorhabditis elegans, in which independent sublines were maintained with one hermaphrodite parent per generation, conditions that minimize the opportunity for natural selection and lead to random fixation of deleterious mutations. After 60 generations of mutation accumulation, negligible changes in mean reproductive output and lifespan occurred, but the genetic variance increased at rates typical for life history traits in other species. The estimated deleterious mutation rate per haploid genome for fitness, U, was 0.0026, a figure two orders of magnitude smaller than previously measured for viability in Drosophila. ------------------- Key: 2776 Medline: 97282461 Authors: Iwasaki K;Staunton J;Saifee O;Nonet M;Thomas JH Title: aex-3 encodes a novel regulator of presynaptic activity in C. elegans. Citation: Neuron 18: 613-622 1997 Type: ARTICLE Genes: aex-3 lev-1 rab-3 snt-1 unc-31 unc-64 Abstract: C. elegans aex-3 mutations cause pleiotropic behavioral defects that are suggestive of reduced synaptic transmission. aex-3 mutations also show strong genetic interactions with mutations in unc-31 and unc-64, two other genes implicated in synaptic transmission. Physiological and pharmacological studies indicate that aex-3 defects are presynaptic. In aex-3 mutants, the synaptic vesicle-associated RAB-3 protein aberrantly accumulates in neuronal cell bodies and is reduced in synapse-rich axons. This localization defect is specific to RAB-3, since other synaptic proteins are localized normally in aex-3 mutants. aex-3 encodes a 1409 amino acid protein with strong homology to DENN, a human protein of unknown function. In C. elegans, aex-3 is expressed in all or nearly all neurons. These results suggest that AEX-3 is a novel regulator of presynaptic activity that interacts with RAB-3 to regulate synaptic vesicle release. ------------------- Key: 2777 Medline: 97295299 Authors: Bini L;Heid H;Liberatori S;Geier G;Pallini V;Zwilling R Title: Two-dimensional gel electrophoresis of Caenorhabditis elegans homogenates and identification of protein spots by microsequencing. Citation: Electrophoresis 18: 557-562 1997 Type: ARTICLE Genes: Abstract: Employing isoelectric focusing on immobilized pH gradients followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) we have obtained a map of C. elegans proteins, from a mixed culture containing all developmental stages, presenting over 2000 spots within the window of isoelectric points (pr) 3.5-9 and a molecular mass of 10-200 kDa. Edman microsequencing yielded successful results in 12 out of 24 analyzed spots. All but one of the N-terminal sequences retrieved C. elegans sequences in cosmid and/or expressed sequence tag clones. Structurally related protein sequences found in data banks included enzymes in energy metabolism (cytochrome oxydase, ATP synthase, enolase), a fatty acid-binding protein, a translationally controlled tumor protein, an unknown C. elegans protein, an acidic ribosomal protein, a titin-like protein, a G-protein beta chain, cyclophilin, and cathepsin D. Experimental determination of N-termini allowed us to define sites of signal cleavage providing further information on the physiological role of the newly found C. elegans proteins. This report demonstrates the possibility of two-dimensional gel electrophoresis and Edman microsequencing in the elucidation of C. elegans proteome. ------------------- Key: 2778 Medline: 97278856 Authors: Schnabel R;Hutter H;Moerman D;Schnabel H Title: Assessing normal embryogenesis in Caenorhabditis elegans using a 4D microscope: Variability of development and regional specification. Citation: Developmental Biology 184: 234-265 1997 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans is renowned for its invariant embryogenesis. This pattern of development is in apparent contrast to other organisms from Drosophila to higher vertebrates. With the aid of a 4D microscope system (multifocal, time-lapse video recording system) which permits the extensive documentation and analysis of cell divisions, cell positions, and migrations in single embryos we have analyzed normal embryogenesis of C. elegans. The instrumentation reveals a naturally occurring variability in cell division timing, cell positioning, and cell-cell contacts which could not have been detected by the direct observation used earlier (Sulston et al., 1983, Dev. Biol. 100, 64-119). Embryos are very flexible and produce an essentially invariant premorphogenetic stage from variable earlier stages. An analysis of the distribution of the descendants of the early founder blastomeres at the premorphogenetic stage shows that these establish discrete regions in the embryo, a process involving a considerable amount of cell movement, which again varies in different embryos. Only cell fate assignment remains invariant. However, as shown earlier, this is not due to an autonomous invariant specification of cell fates but due to the fact that cell-cell interactions occur very early when the topology of blastomeres in the embryo is still sufficiently precise to ensure reproducible patterns of inductions. A new concept that founder blastomeres produce embryonic regions in the embryo can explain the striking complexity of the lineage per se and also the complicated asymmetric lineage patterns by which the bilateral symmetry of the embryo is established. Many cells, including bilateral homologs, were apparently chosen for a specific fate solely by their position in the embryo, irrespectively of the lineage descent by which the cells are created. We postulate that the production of regions by cell-cell interactions is the pivotal principle guiding the embryogenesis of C. elegans and that the embryogenesis of the worm follows the same basic principles as embryogenesis ------------------- Key: 2779 Medline: 97278860 Authors: Sluder AE;Lindblom T;Ruvkun G Title: The Caenorhabditis elegans orphan nuclear hormone receptor gene nhr-2 functions in early embryonic development. Citation: Developmental Biology 184: 303-319 1997 Type: ARTICLE Genes: emb-10 emb-14 emb-17 emb-19 emb-20 fem-2 glp-1 let-367 let-376 let-377 let-378 let-379 let-388 let-393 let-395 let-530 let-531 let-532 let-603 mes-6 myo-1 nhr-2 zyg-2 hDp12 hDp13 hDp15 hDp16 hDp37 sDp2 Abstract: We have identified a Caenorhabditis elegans gene, nhr-2 that is a member of the nuclear hormone receptor superfamily of transcription factors and defines a new subclass of the superfamily. nhr-2 messenger RNA is expressed in the maternal germline and during the first half of embryogenesis. Zygotic expression of nhr-2 begins by the 16-cell stage, making it one of the earliest genes known to be transcribed in the embryo. Immunolocalization detects NHR-2 protein in embryonic nuclei as early as the 2-cell stage. The protein is present in every nucleus until the 16- to 20-cell stage. Subsequently, expression continues in many, but not all, cell lineages, becoming progressively restricted to the anterior and dorsal regions of the embryo and disappearing during the initial stages of morphogenesis. Disruption of nhr-2 function with antisense RNA results in embryonic and early larval arrest, indicating that the gene has an essential function in embryonic development. nhr-2 does not correspond to known mutations mapped to the same genetic interval, and will provide an entry point for further study of a heretofore uncharacterized zygotic gene regulatory pathway. ------------------- Key: 2780 Medline: 97278866 Authors: Costa M;Draper BW;Priess JR Title: The role of actin filaments in patterning the Caenorhabditis elegans cuticle. Citation: Developmental Biology 184: 373-384 1997 Type: ARTICLE Genes: Abstract: Nematodes are covered by a cuticle with a prominent pattern of circumferentially oriented, parallel furrows. We report here that the pattern of furrows on the first larval cuticle of Caenorhabditis elegans, which is secreted during embryogenesis, is coincident with a pattern of submembranous actin filament bundles in the epithelial cells that secrete the cuticle. We propose that the pattern of cortical actin filaments biases the growth of the epithelial cell membranes, creating a furrowed surface template for deposition of the first cuticle layer. This layer then detaches from the epithelial cell surface as additional, nonpatterned components of the cuticle are secreted. Furrows are present on the surfaces of each of the four larval cuticles in C. elegans and the adult cuticle. We show that similar ordered arrays of actin filaments appear during each of the postembryonic molts when new cuticles are synthesized. Our analysis suggests that conditions or mutations that affect the pattern of cuticle furrows might cause primary defects in the cytoskeletal organization of the epithelial cells that ------------------- Key: 2781 Medline: 97277118 Authors: Wickens M;Anderson P;Jackson RJ Title: Life and death in the cytoplasm: messages from the 3' end. Citation: Current Opinion in Genetics & Development 7: 220-232 1997 Type: REVIEW Genes: smg-1 smg-2 smg-3 smg-4 smg-5 smg-6 smg-7 Abstract: The cytoplasmic life of an mRNA revolves around the regulation of its localization, translation and stability. Interactions between the two ends of the mRNA may integrate translation and mRNA turnover. Regulatory elements in the region between the termination codon and poly(A) tail - in the 3' untranslated region - have been identified in a wide variety of systems, as have been some of the key players with which these elements interact. ------------------- Key: 2782 Medline: 97277125 Authors: Smeal T;Guarente L Title: Mechanisms of cellular senescence. Citation: Current Opinion in Genetics & Development 7: 281-287 1997 Type: REVIEW Genes: age-1 clk-1 daf-1 daf-2 daf-3 daf-4 daf-5 daf-7 daf-8 daf-11 daf-12 daf-14 daf-16 daf-21 daf-22 daf-23 gro-1 Abstract: Aging is a near universal process, yet the molecular mechanisms that underlie cellular senescence have remained elusive. Recent progress in determining the roles of various genetic influences in controlling the rate of cellular aging has made this an exciting time in aging research. Genetic screens designed to isolate long-lived mutants in Saccharomyces cerevisiae and Caenorhabditis elegans have implicated factors involved in transcriptional silencing and the dauer pathway in the control of aging. The gene responsible for Werner's syndrome, a disease with symptoms of premature aging, was isolated and found to be a member of the RecQ subfamily of DNA helicases. The regulation of telomere length and its role in senescence and cellular immortalization has been found to be more complex than expected. In C. elegans, mutations have been isolated in maternal-effect genes that presumably control its biological clocks and can dramatically extend its lifespan. Indeed, aging research within the past year has implicated a variety of mechanisms ranging from the control of gene expression, stress resistance, and DNA metabolism to the overall 'rate of living'. ------------------- Key: 2783 Medline: 97050121 Authors: Simpson VJ;Johnson TE Title: Genetic models in the study of anesthetic drug action. Citation: International Review of Neurobiology 39: 223-241 1996 Type: REVIEW Genes: unc-9 unc-79 Abstract: This chapter reviews the use of genetic models in the study of anesthetic drug action. Genetic model systems provide a novel approach to understanding mechanisms of anesthetic drug action. Many models have been derived using selection processes that emphasize differential drug sensitivity, producing animal lines that differ in their CNS drug response. Studies of vertebrate (rodent) and invertebrate (Drosophila, Caenorhabditis elegans) animal model systems are covered. The review discusses studies employing lines derived from spontaneous and induced mutagenic processes, selectively bred lines, and inbred lines possessing inherent differential drug sensitivities. The primary focus of included studies is the general anesthetic drugs that are commonly used in the clinical setting. These are drugs such as the inhalational agents (halothane, enflurane, isoflurane, nitrous oxide) and the intravenous induction agents (propofol and diazepam). Rodent lines with differential sensitivity to opiates are also discussed. Finally, an approach to identifying and isolating the genes that control anesthetic sensitivity is discussed in a section on mapping quantitative trait loci (QTL) in recombinant inbred lines. ------------------- Key: 2784 Medline: Authors: Fitch DHA Title: Evolution of male tail development in Rhabditid nematodes related to Caenorhabditis elegans. Citation: Systematic Biology 46: 145-179 1997 Type: ARTICLE Genes: Abstract: The evolutionary pathway that has led to male tails of diverse morphology among species of the nematode family Rhabditidae was reconstructed. This family includes the well-studied model species Caenorhabditis elegans. By relating the steps of male tail morphological evolution to the phenotypic changes brought about by developmental mutations induced experimentally in C. elegans, the goal is to identify genes responsible for morphological evolution. The varying morphological characters of the male tails of several rhabditid species have been described previously (Fitch and Emmons, 1995, Dev. Biol. 170:564-582). The developmental events preceding differentiation of the adult structures have also been analyzed; in many cases the origins of varying adult morphological characters were traced to differences during ontogeny. In the present work, the evolutionary changes producing these differences were reconstructed in the context of the four possible phylogenies supported independently by sequences of 18S ribosomal RNA genes (rDNA). Two or more alternative states were defined for 36 developmental and adult morphological characters. These characters alone do not provide sufficient data to resolve most species relationships; however, when combined with the rDNA characters, they provide stronger support for one of the four rDNA phylogenies. Assuming a model of ordered transformations for multistate developmental characters generally results in greater resolution. Transformations between character states can be assigned unequivocally by parsimony to unambiguous branches for most of the characters. Correlations are thereby revealed for some of the developmental characters, indicating a probability of a shared developmental or genetic regulatory pathway. Four of the un equivocal character state changes on unambiguously supported branches closely resemble the phenotypic changes brought about by known mutations in C. elegans. These mutations define genes that are known to act in genetic regulatory hierarchies controlling pattern formation differentiation, and morphogenesis. Although these studies are still at an early stage, these results strongly suggest that parallel studies of developmental mutants in C. elegans and of morphological and developmental evolution among related nematodes will help define genetic changes underlying the evolution of form. ------------------- Key: 2785 Medline: 97284769 Authors: Leroux MR;Ma BJ;Batelier G;Melki R;Candido EPM Title: Unique structural features of a novel class of small heat shock proteins. Citation: Journal of Biological Chemistry 272: 12847-12853 1997 Type: ARTICLE Genes: Abstract: Small heat shock proteins (smHSPs) and alpha-crystallins constitute a family of related molecular chaperones that exhibit striking variability in size, ranging from 16 to 43 kDa. Structural studies on these proteins have been hampered by their tendency to form large, often dynamic and heterogeneous oligomeric complexes. Here we describe the structure and expression of HSP12.6, a member of a novel class of smHSPs from the nematode Caenorhabditis elegans. Like other members of its class, HSP12.6 possesses a conserved Lu-crystallin domain but has the shortest N- and C-terminal regions of any known smHSP. Expression of HSP12.6 is limited to the first larval stage of C. elegans and is not significantly up regulated by a wide range of stressors. Unlike other smHSPs, HSP12.6 does not form large oligomeric complexes in vivo. HSP12.6 was produced in Escherichia coil as a soluble protein and purified. Cross-linking and sedimentation velocity analyses indicate that the recombinant HSP12.6 is monomeric, making it an ideal candidate for structure determination. Interestingly, HSP12.6 does not function as a molecular chaperone in vitro, since it is unable to prevent the thermally induced aggregation of a test substrate. The structural and functional implications of these findings are discussed. ------------------- Key: 2786 Medline: 97316786 Authors: Thien CBF;Langdon WY Title: EGF receptor binding and transformation by v-cbl is ablated by the introduction of a loss-of-function mutation from the Caenorhabditis elegans sli-1 gene. Citation: Oncogene 14: 2239-2249 1997 Type: ARTICLE Genes: let-23 sli-1 Abstract: The 120 kD product of the c-cbl oncogene is rapidly tyrosine phosphorylated and recruited to the EGF receptor following ligand binding. Cbl's oncogenic potential is activated by a large carboxy-terminal truncation that generated v-cbl and removes the Ring finger and proline-rich SH3-binding domains. Here we show that this truncation reveals a novel and highly conserved domain that can interact directly with the EGF receptor in a phosphorylation dependent manner. Furthermore we demonstrate that the v-cbl domain is not utilized by c-cbl for recruitment to the receptor since this binding property is not evident in c-cbl constructs with proline domain deletions, and it is only revealed following deletion of the Ring finger. We also analyse a loss-of-function mutation from the C. elegans homologue, sli-1, and show that the corresponding mutation in v-cbl ablates transformation and EGF receptor association. Thus our findings provide further evidence that v-cbl possesses a novel and evolutionarily conserved phospho-tyrosine binding domain and that the dual capability of EGF receptor binding by cbl involves two distinct mechanisms. In addition these findings raise the possibility that v-cbl may transform by competing with c-cbl for phosphorylated binding sites on ------------------- Key: 2787 Medline: 97294066 Authors: Devine SE;Chissoe SL;Eby Y;Wilson RK;Boeke JD Title: A transposon-based strategy for sequencing repetitive DNA in eukaryotic genomes. Citation: Genome Research 7: 551-563 1997 Type: ARTICLE Genes: Abstract: Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using integrated artificial transposons and automated fluorescent sequencing. Mapping and assembly tools represent important components of this strategy and facilitate sequence assembly in complex regions. We have applied the strategy to several cosmid assembly gaps resulting from repetitive DNA and have accurately recovered the sequences of these regions. Analysis of these regions revealed six novel transposon-like repetitive elements, IR-1, IR-2, IR-3, IR-4, IR-5, and TR-1. Each of these elements represents a middle-repetitive DNA family in C. elegans containing at least 3-140 copies per genome. Copies of IR-l, IR-2, IR-4, and IR-5 are located on ail (or most) of the six nematode chromosomes, whereas IR-3 is predominantly located on chromosome X. These elements are almost exclusively interspersed between predicted genes or within the predicted introns of these genes, with the exception of a single IR-S element, which is located within a predicted exon. IR-1, IR-2, and IR-3 are flanked by short sequence duplications resembling the target site duplications of transposons. We have established a website database (http://www.welch.jhu.edu/similar to devine/RepDNAdb.html) to track and cross-reference these transposon-like repetitive elements that contains detailed information on individual element copies and provides links to appropriate GenBank records. This set or tools may be used to sequence, track, and study repetitive DNA in model organisms and ------------------- Key: 2788 Medline: Authors: Anderson ARA;Sleeman BD;Young IM;Griffiths BS Title: Nematode movement along a chemical gradient in a structurally heterogeneous environment. 2. Theory. Citation: Fundamental and Applied Nematology 20: 165-172 1997 Type: ARTICLE Genes: Abstract: The effects of structural heterogeneity on both chemical diffusion and nematode movement are examined with the development of a theoretical model. The model considers three factors affecting nematode movement: soil structure, nematode foraging strategy and chemotaxis. Using a continuous model, we develop a discrete system which allows nematode trails to be simulated in any of the four experimental conditions given by Anderson et al (1997). We show that structural heterogeneity causes mixed levels of attractant concentration over small areas as well as "fingering" of the attractant. Soil structural heterogeneity also restricts the foraging strategy of the nematode which then becomes a strategy to avoid structural "traps". The effect of localised increases in structural density is shown to increase significantly "fingering" of the attractant. ------------------- Key: 2789 Medline: 97303231 Authors: Li H;Avery L;Denk H;Hess GP Title: Identification of chemical synapses in the pharynx of Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 94: 5912-5916 1997 Type: ARTICLE Genes: eat-4 Abstract: The rhythmic contraction of the Caenorhabditis elegans pharynx is unique in that the network of 12 neurons, including two M3 neurons, that regulate the contraction is known. The neurotransmitters secreted by these cells, and the target cells responding to these chemical signals, are not known. Here, we describe an approach to obtain this missing information and use the M3 cells as an example. Electrical recordings (electropharyngeograms) were used in conjunction with temporally and spatially defined application of neurotransmitters via photolysis of inactive, photolabile precursors. To illustrate the technique we used pharyngeal preparations in which the two M3 neurons are intact and preparations in which they were removed by laser irradiation. Removal of M3 neurons results in the loss of the small negative peaks in the electropharyngeograms and an increase in time during which the pharynx remains contracted. We demonstrate that the application of glutamate by photolysis of caged glutamate to a pharynx from which the two M3 neurons were removed produces effects similar to those observed before removal of the M3 neurons. In control experiments, photolytic release from photolabile precursors of carbamoylcholine, a stable and well characterized analog of acetylcholine, or of gamma-aminobutyric acid, from photolabile precursors did not have this effect. The response depended on the amount of glutamate released. By reducing the size of the photolytic beam, glutamate was released at several different locations of the pharynx. Two areas of the pharynx mainly respond to the application of glutamate; one corresponds to the pm4 muscle cells in the metacorpus, and the other to the junction between muscle cells pm5 in the ------------------- Key: 2790 Medline: Authors: Hirabayashi J;Arata Y;Kasai K Title: Galectins from the nematode Caenorhabditis elegans and the genome project. Citation: Trends in Glycoscience and Glycotechnology 9: 113-122 1997 Type: REVIEW Genes: Abstract: The finding of Caenorhabditis elegans galectin (32 kDa) demonstrated, for the first time, the presence of the "tandem-repeat type" of galectin, which consists of two homologous domains (ca. 16 kDa). Its N- and C-terminal half domains show relatively low sequence similarity to each other (ca. 30% identity), though most (but not all) of the amino acids involved in the carbohydrate binding are conserved. The nematode 32-kDa galectin shows strong hemagglutinating activity, but its saccharide specificity is rather complex. The individual half domains have considerably distinct features in the binding to asialofetuin-agarose. Though endogenous ligand for them is not known, these observations imply that the 32-kDa nematode galectin functions as a possible "heterobifunctional cross-linker". Since this galectin is localized most abundantly in the adult cuticle, it possibly plays a role in the formation of tight and insoluble epidermal layers. A recently isolated novel nematode galectin (16 kDa) forms a non-covalent dimer, and exhibits significant hemagglutinating activity, which is inhibitable by lactose. The current progress in the C. elegans genome project has revealed the presence of a number of galectin-related genes, and at least four other tandem-repeat-type galectins (40-75% identical to the 32-kDa galectin) have been proved to be expressed. Two closely related genes encoding CRDs (carbohydrate-recognition domains) having a somewhat longer C-terminal tail have also been predicted. Because the complete genome sequence of C. elegans (1 x 108 bp) will be obtained in the near future, galectin research utilizing this model animal will hopefully provide us with new concepts about both the biological and evolutionary significance of multivalent galectin-carbohydrate ------------------- Key: 2791 Medline: 97318766 Authors: Achanzar WE;Ward S Title: A nematode gene required for sperm vesicle fusion. Citation: Journal of Cell Science 110: 1073-1081 1997 Type: ARTICLE Genes: fer-1 him-5 Abstract: During maturation of spermatids to motile spermatozoa in Caenorhabditis elegans, large vesicles called membranous organelles (MOs) fuse with the spermatid plasma membrane. Mutations in the gene fer-l cause abnormal spermatozoa in which the MOs do not fuse, although they abut the plasma membrane normally. Here we describe the fer-1 gene, which we found to be approximately 8.6 kb in length and to encode a 6.2 kb transcript whose expression is limited to the primary spermatocytes, the cells in which the MOs form. fer-l is predicted to encode a 235 kDa protein which is highly charged except for a putative transmembrane domain near the C terminus. We identified the mutations associated with five fer-1 alleles, all of which are missense mutations causing single amino acid changes. FER-1 is not similar to any characterized proteins in sequence databases, nor does it contain known functional motifs other than the predicted transmembrane domain. The C-terminal transmembrane domain makes FER-1 resemble some viral fusion proteins, suggesting it may play a direct role in MO-plasma membrane fusion. FER-1 does show significant sequence similarity to several predicted human proteins of unknown function. Two of the identified fer-l mutations are located in regions of similarity between FER-1 and two of these predicted proteins. This strengthens the biological significance of these similarities and suggests these regions of similarity represent functionally important domains of FER-I and the human proteins. ------------------- Key: 2792 Medline: Authors: Hekimi S Title: A cellular and psychological clock sets the pace of life of the nematode Caenorhabditis elegans. Citation: M S-Medecine Sciences 13: 474-482 1997 Type: REVIEW Genes: clk-1 clk-2 clk-3 gro-1 Abstract: Many developmental and behavioral features of living organisms appear to be precisely timed by internal mechanisms which are referred to as ''biological clocks''. In the nematode Caenorhabditis elegans four maternal-effect genes which appear to be required for the function of several distinct biological clocks have been identified. The consequences of mutations in the gene clk-1 have been studied in most detail. These mutations result in a mean lengthening of embryonic and post-embryonic development, the cell cycle period and life span, as well as the periods of behavioral cycles such as the defecation, swimming and pumping cycles. This review focuses on the hypothesis that the phenotype of genes like clk-1 reveals the existence of a central mechanism involved in synchronizing the activities of a variety of organismal features. ------------------- Key: 2793 Medline: 97315111 Authors: Wang W;Shakes DC Title: Expression patterns and transcript processing of ftt-1 and ftt-2, two C. elegans 14-3-3 homologues. Citation: Journal of Molecular Biology 268: 619-630 1997 Type: ARTICLE Genes: fem-2 ftt-1 ftt-2 glp-4 mog-1 Abstract: A wide diversity of biological functions have been attributed to the highly conserved and ubiquitous 14-3-3 protein family. Yet how much of this diversity is inherent in the basic structure of 14-3-3 and how much is due to isoform specific functions is not yet fully understood. Here, two Caenorhabditis elegans 14-3-3 isoforms whose protein sequences are 90% similar were found to differ significantly in both their genomic structure and expression patterns. The two genes, ftt-1 (IV) (fourteen-three-three) and ftt-2 (X), differ in both the position and sequence of their introns, Since the various intron/exon boundaries respect neither functional nor structural protein motifs, the introns appear to be relatively recent evolutionary additions. ftt-1(IV) encodes three germline enhanced transcripts, two of which are related through the differential use of alternative poly(A) addition sites. RNA in situ hybridization studies reveal high levels of ftt-1 throughout the gonad with particularly high levels in the distal arm. In contrast, ftt-2 (X) encodes a single transcript which is expressed somatically. In embryos, high levels of ftt-1 transcripts appear to be maternally supplied, whereas ftt-2 is expressed as an early zygotic transcript whose expression pattern later localizes to the posterior region of post-proliferative embryos. These expression pattern differences between ftt-1 and ftt-2 suggest that these two 14-3-3 isoforms perform distinct biological roles within the worm. ------------------- Key: 2794 Medline: 97311751 Authors: Lesa GM;Sternberg PW Title: Positive and negative tissue-specific signaling by a nematode epidermal growth factor receptor. Citation: Molecular Biology of the Cell 8: 779-793 1997 Type: ARTICLE Genes: let-23 let-60 sem-5 Abstract: The major determinants of receptor tyrosine kinase (RTK) signaling specificity have been proposed to be Src homology 2 (SH2) binding sites, phosphotyrosine-containing oligopeptides in the cytoplasmic domain of the receptor. The Caenorhabditis elegans epidermal growth factor receptor homologue LET-23 has multiple functions during development and has eight potential SH2-binding sites in a region carboxyl terminal to its kinase domain. By analyzing transgenic nematodes for three distinct LET-23 functions, we show that six of eight potential sites function in vivo and that they are required for most, but not all, of LET-23 activity. A single site is necessary and sufficient to promote wild-type fertility. Three other sites activate the RAS pathway and are involved only in viability and vulval differentiation. A fifth site is promiscuous and can mediate all three LET-23 functions. An additional site mediates tissue-specific negative regulation. Putative SH2 binding sites are thus key effectors of both cell-specific and negative regulation in an intact organism. We suggest two distinct mechanisms for tissue-specific RTK-mediated signaling. A positive mechanism would promote RTK function through effectors present only in certain cell types. A negative mechanism would inhibit RTK function through tissue-specific negative regulators. ------------------- Key: 2795 Medline: 97307788 Authors: Forrester WC;Garriga G Title: Genes necessary for C. elegans cell and growth cone migrations. Citation: Development 124: 1831-1843 1997 Type: ARTICLE Genes: cam-1 cam-2 ceh-10 ceh-23 epi-1 fam-1 fam-2 ina-1 mig-2 syc-1 syc-2 syc-3 unc-34 unc-73 vab-8 Abstract: The migrations of cells and growth cones contribute to form and pattern during metazoan development. To study the mechanisms that regulate cell motility, we have screened for C. elegans mutants defective in the posteriorly directed migrations of the canal-associated neurons (CANs). Here we describe 14 genes necessary for CAN cell migration. Our characterization of the mutants has led to three conclusions. First, the mutations define three gene classes: genes necessary for cell fate specification, genes necessary for multiple cell migrations and a single gene necessary for final positioning of migrating cells. Second, cell interactions between the CAN and HSN, a neuron that migrates anteriorly to a position adjacent to the CAN, control the final destination of the HSN cell body. Third, C. elegans larval development requires the CANs, In the absence of CAN function, larvae arrest development, with excess fluid accumulating in their pseudocoeloms. This phenotype may reflect a role of the CANs in osmoregulation. ------------------- Key: 2796 Medline: 97277006 Authors: Aroian RV;Field C;Pruliere G;Kenyon C;Alberts BM Title: Isolation of actin-associated proteins from Caenorhabditis elegans oocytes and their localization in the early embryo. Citation: EMBO Journal 16: 1541-1549 1997 Type: ARTICLE Genes: fer-1 par-3 Abstract: The actin cytoskeleton plays an important, but poorly understood, role in the development of multicellular organisms. To help illuminate this role, we used actin filament affinity chromatography to isolate actin binding proteins from large quantities of Caenorhabditis elegans oocytes. To examine how these proteins might be involved in early development, we prepared antibodies against some of them and determined their distribution in fixed embryos. Three of these proteins co-localize with different subsets of the embryonic actin cytoskeleton. One co-localizes with actin to all cell cortices. The second oscillates between the nucleus and cortex in a cell-cycle-dependent manner. The third is asymmetrically enriched at the anterior cortex of one-cell embryos, showing a temporal and spatial localization suggestive of a function in generating developmental asymmetry. We conclude that biochemistry is a feasible and useful approach in the study of early C. elegans development, and that the embryonic actin cytoskeleton is regulated in a complex fashion in order to carry out multiple, simultaneous functions. ------------------- Key: 2797 Medline: 97316897 Authors: Gomez-Saladin E;Luebke AE;Wilson DL;Dickerson IM Title: Isolation of a cDNA encoding a Kex2-like endoprotease with homology to furin from the nematode Caenorhabditis elegans. Citation: DNA and Cell Biology 16: 663-669 1997 Type: ARTICLE Genes: bli-4 Abstract: A cDNA was isolated from the nematode Caenorhabditis elegans that encodes an endoprotease which is a member of the Kex2 family of serine endoproteases. Degenerate oligonucleotide primers were designed based on conserved regions within the active sites of known Kex2-like endoproteases, and were used for reverse transcription-polymerase chain reaction (RT-PCR) of poly(A)(+)RNA isolated from C. elegans. A PCR product was isolated that had homology to the active sites of known furin endoproteases, and was used as a probe to screen a C. elegans cDNA library. A Kex2-like endoprotease (CelfurPC) which encoded a 692-amino-acid preproendoprotease, was identified. The deduced amino acid sequence for the catalytic domain of CelfurPC is homologous to the known Ked-like endoproteases, with strongest structural homology to the furin/PACE4 family. However, all furins and PACE4 proteins contain a characteristic cysteine-rich domain, and all furins contain a transmembrane domain, neither of which is present in the CelfurPC protein. CelfurPC may thus ------------------- Key: 2798 Medline: 97307776 Authors: Pflugrad A;Meir JY-J;Barnes TM;Miller DM Title: The Groucho-like transcription factor UNC-37 functions with the neural specificity gene unc-4 to govern motor neuron identity in C. elegans. Citation: Development 124: 1699-1709 1997 Type: ARTICLE Genes: unc-4 unc-24 unc-37 Abstract: Groucho and Tup1 are members of a conserved family of WD repeat proteins that interact with specific transcription factors to repress target genes. Here we show that mutations in WD domains of the Groucho-like protein, UNC-37, affect a motor neuron trait that also depends on UNC-4, a homeodomain protein that controls neuronal specificity in Caenorhabditis elegans. In unc-4 mutants, VA motor neurons assume the pattern of synaptic input normally reserved for their lineal sister cells, the VB motor neurons; the loss of normal input to the VAs produces a distinctive backward movement defect. Substitution of a conserved residue (H to Y) in the fifth WD repeat in unc-37 (e262) phenocopies the Unc-4 movement defect. Conversely, an amino acid change (E to K) in the sixth WD repeat of UNC-37 is a strong suppressor of unc-37(e262) and of specific unc-4 missense mutations. We have previously shown that UNC-4 expression in the VA motor neurons specifies the wild-type pattern of presynaptic input. Here we demonstrate that UNC-37 is also expressed in the VAs and that unc-37 activity in these neurons is sufficient to restore normal movement to unc-37(e262) animals. We propose that UNC-37 and UNC-4 function together to prevent expression of genes that define the VB pattern of synaptic inputs and thereby generate connections specific to the VA motor neurons. In addition, we show that the WD repeat domains of UNC-37 and of the human homolog, TLE1, are functionally interchangeable in VA motor neurons which suggests that this highly conserved protein domain may also specify motor neuron identity and synaptic choice in more complex nervous ------------------- Key: 2799 Medline: Authors: Herman RK Title: The worm returns. Citation: Science 276: 1656- 1997 Type: REVIEW Genes: Abstract: When I began working on the small nematode Caenorhabditis elegans in the early '70s, not long after Sydney Brenner had chosen it as a model organism for studying animal development and behavior, one could read most of the essentials then published about the creature in an afternoon. As more people joined the worm community and wrote papers that demanded attention, newcomers and interested spectators faced an ever bigger job trying to familiarize themselves with the field. In 1988, a book, The Nematode Caenorhabditis elegans, came to the rescue. "Worm I" reviewed the worm's genome, anatomy, embryology, sex determination, muscle development, and behavior, among other things. Appendixes contained a list of all 959 somatic hermaphrodite cells and their lineages, a list of 774 mapped genes and mutant phenotypes, and a compilation of laboratory methods. "Worm I" has aged gracefully but is irrevocably stuck at 1988. Enter "Worm II". ------------------- Key: 2800 Medline: 97313248 Authors: Jia Y;Xie G;McDermott JB;Aamodt E Title: The C. elegans gene pag-3 is homologous to the zinc finger proto-oncogene gfi-1. Citation: Development 124: 2063-2073 1997 Type: ARTICLE Genes: daf-6 mec-2 mec-3 mec-4 mec-7 mec-9 osm-1 pag-3 sup-10 unc-93 mnDf5 mnDf7 mnDf20 mnDp14 Abstract: Mutations in the Caenorhabditis elegans gene pag-3 result in misexpression of touch receptor-specific genes in the BDU interneurons and in motility defects. We cloned pag-3 and found that the gene encodes a C2H2-type zinc finger protein related to the mammalian GFI-1 protein. Sequencing of the three pag-3 alleles showed that two apparent null alleles encode a nonsense mutation before the zinc fingers and a missense mutation in the fourth zinc finger that changes a coordinating histidine to a tyrosine. The third allele contains a nonsense mutation in the N-terminal region but is not a null allele. Northern analysis showed that a single pag-3 transcript of about 1.6 kb is present in embryos and L1, L2 and L3 larvae. pag-3 message levels were about twofold higher in pag-3 mutants than in wild-type animals, which suggested that pag-3 may negatively regulate its own expression. pag-3lacZ fusion genes were expressed in the BDU interneurons, the touch neurons, 11 VA and 11 VB ventral cord motor neurons, two AVF interneurons and in unidentified neurons of the retrovesicular ganglion. The BDU neurons and the ALM touch neurons are lineal sister cells in the AB.a lineage and the VA and VB motor neurons are lineal sister cells in the AB.p lineage. The VA motor neurons are required for backward movement and the VB motor neurons are required for forward movement. Mosaic analysis showed that the wildtype pag-3 gene is required in the AB.p lineage for coordinated movement and in the AB.a lineage to suppress touch neuron gene expression in the BDU neurons. Because pag-3 is expressed in both the BDU neurons and in the touch neurons, another protein(s) not expressed in the touch neurons may interact with pag-3 to repress touch neuron gene expression in the BDU neurons. Alternatively, another protein in the touch receptor cells may inactivate PAG-3 and allow expression of the touch receptor program. These results show that pag-3 is a temporally regulated gene that is expressed early in development and functions in multiple types of neurons. They also strongly suggest that the PAG-3 protein is a DNA-binding protein with properties similar to ------------------- Key: 2801 Medline: 97330686 Authors: Seydoux G;Dunn MA Title: Transcriptionally repressed germ cells lack a subpopulation of phosphorylated RNA polymerase II in early embryos of Caenorhabditis elegans and Drosophila melanogaster. Citation: Development 124: 2191-2201 1997 Type: ARTICLE Genes: ama-1 pes-10 pie-1 Abstract: Early embryonic germ cells in C. elegans and D. melanogaster fail to express many messenger RNAs expressed in somatic cells. In contrast, we find that ribosomal RNAs are expressed in both cell types. We show that this deficiency in mRNA production correlates with the absence of a specific phosphoepitope on the carboxyterminal domain of RNA polymerase II. In both C. elegans and Drosophila embryos, this phosphoepitope appears in somatic nuclei coincident with the onset of embryonic transcription, but remains absent from germ cells until these cells associate with the gut primordium during gastrulation. In contrast, a second distinct RNA polymerase II phosphoepitope is present continuously in both somatic and germ cells. The germ-line-specific factor PIE-1 is required to block mRNA production in the germ lineage of early C. elegans embryos (Seydoux, G., Mello, C. C., Pettitt, J., Wood, W.B., Priess, J. R. and Fire, A. (1996) Nature 382, 713-716). We show here that PIE-I is also required for the germ-line-specific pattern of RNA polymerase II phosphorylation. These observations link inhibition of mRNA production in embryonic germ cells to a specific modification in the phosphorylation pattern of RNA polymerase II and suggest that repression of RNA polymerase II activity may be part of an evolutionarily conserved mechanism that distinguishes germ line from soma during early embryogenesis. In addition, these studies also suggest that different phosphorylated isoforms of RNA ------------------- Key: 2802 Medline: 97329533 Authors: Royal DC;Royal MA;Wessels D;L'Hernault S;Soll DR Title: Quantitative analysis of Caenorhabditis elegans sperm motility and how it is affected by mutants spe-11 and unc-54. Citation: Cell Motility and the Cytoskeleton 37: 98-110 1997 Type: ARTICLE Genes: dpy-5 him-5 spe-11 unc-54 Abstract: The sperm of Caenorhabditis elegans translocate in a fashion similar to sperm of Ascaris suum even though their pseudopods are longer, more plastic in shaper and Form multiple expansion zones around their perimeter. Mutants in spe-11 form primary spermatocytes with a defective perinuclear region, but the resulting spermatozoa fan still crawl and fertilize eggs. However. the resultant zygotes die due to the absence of sperm-supplied spe-11. Computer-assisted analysis of translocating spe-11 sperm reveals a novel defect in the dynamic morphology of their pseudopods. A similar anal sis of the C. elegans mutant unc-54, which lacks the most abundant isoform of myosin II, reveals no defect in sperm motility, as expected, since C. elegans sperm have substituted the protein MSP for actin in the process of pseudopod expansion. These results reveal an unexpected defect in the dynamic morphology of pseudopods of spe-11 sperm. This defect, however, does not significantly affect crawling velocity, and it demonstrates how computer-assisted motion analysis systems cim reveal subtle behavioral phenotypes in C. elegans mutant ------------------- Key: 2803 Medline: 98014459 Authors: Arata Y;Hirabayashi J;Kasai K Title: The two lectin domains of the tandem-repeat 32-kDa galectin of the nematode Caenorhabditis elegans have different binding properties. Studies with recombinant protein. Citation: Journal of Biochemistry 121: 1002-1009 1997 Type: ARTICLE Genes: Abstract: Some properties of recombinant proteins derived from the 32-kDa galectin isolated from the nematode Caenorhabditis elegans, which lectin is composed of two tandemly repeated homologous domains [Hirabayashi et al. (1992) J. Biol, Chem. 267, 15485], were studied in order to elucidate the function of this unique polypeptide architecture. We expressed the whole molecule (N32), the N-terminal lectin domain (Nh), and the C-terminal lectin domain (Ch) in Escherichia coli using the expression vector pET21a. All of the recombinant proteins were bound by asialofetuin-Sepharose. CD spectra of the recombinant proteins indicated all of them to be rich in beta-structure and properly refolded. Gel filtration on an HPLC column suggested that all of them existed as monomers. Neither Nh nor Ch seemed to form dimers, in contrast to vertebrate proto-type galectins. Only N32 showed hemagglutination activity towards trypsinized rabbit erythrocytes. Comparison of the affinity of N32, Nh, and Ch for asialofetuin-Sepharose by frontal affinity chromatography [Kasai et al, (1986) J. Chromatogr. 376, 33] showed that Ch has 7-fold weaker affinity than N32, and Nh proved to have still weaker affinity. Since the Asn residue in the CRD (carbohydrate recognition domain), which is conserved in all other galectins, is substituted by Ser in the case of Nh, these data suggest that the two CRDs in this tandem-repeat galectin have different sugar binding properties and that the 32-kDa galectin may serve as a ------------------- Key: 2804 Medline: 98014484 Authors: Sambongi Y;Wakabayashi T;Yoshimizu T;Omote H;Oka T;Futai M Title: Caenorhabditis elegans cDNA for a Menkes/Wilson disease gene homologue and its function in a yeast CCC2 gene deletion mutant. Citation: Journal of Biochemistry 121: 1169-1175 1997 Type: ARTICLE Genes: cua-1 Abstract: The full-length cDNA coding for a putative copper transporting P-type ATPase (Cu2+-ATPase) was cloned from Caenorhabditis elegans, The putative Cu2+-ATPase is a 1,238-amino acid protein, and highly homologous to the Menkes and Wilson disease gene products mutations of which are responsible for human defects of copper metabolism, The Saccharomyces cerevisiae mutant with a disrupted CCC2 gene (yeast Menkes/Wilson disease gene homologue) was rescued by the cDNA for the C. elegans Cu2+-ATPase but not by the cDNA with an Asp-786 (an invariant phosphorylation site) to Asn mutation, suggesting that the C. elegans Cu2+-ATPase functions as a copper transporter in yeast, The expressed C. elegans protein was detected in yeast vacuolar membranes by immunofluorescence microscopy. The yeast expression system may facilitate further studies on copper transporting P-type ATPases. ------------------- Key: 2806 Medline: 97321871 Authors: Kawano T;Takuwa K;Nakajima T Title: Structure and activity of a new form of the glutamate transporter of the nematode Caenorhabditis elegans. Citation: Bioscience Biotechnology and Biochemistry 61: 927-929 1997 Type: ARTICLE Genes: Abstract: A Caenorhabditis elegans cDNA for a glutamate transporter was cloned and examined in this study. The predicted protein is 11 residues shorter at the N-terminus than Ceglut-1, which we previously reported, The protein, when expressed in Xenopus laevis oocytes, showed much higher glutamate transport activity than Ceglut-1, suggesting that the N-terminal sequence is critical in glutamate transport. ------------------- Key: 2807 Medline: 97333109 Authors: Morrison GE;van der Kooy D Title: Cold shock before associative conditioning blocks memory retrieval, but cold shock after conditioning blocks memory retention in Caenorhabditis elegans. Citation: Behavioral Neuroscience 111: 564-578 1997 Type: ARTICLE Genes: Abstract: The effects of cooling on associative learning and memory processes in Caenorhabditis elegans were investigated by giving the worms cold shock at various times before or after conditioning. A pretraining cold shock in the 30 min immediately before conditioning and a postraining cold shock in the 30 min immediately after conditioning both disrupted learning and memory processes tested a short time after conditioning. However, if tested 3 hr after conditioning, worms given a pretraining cold shock demonstrated learned preferences, whereas worms given a posttraining cold shock still had memory deficits. These results suggest that the effects of cold shock on associative learning and memory can be dissociated into effects on memory retrieval and memory retention. ------------------- Key: 2808 Medline: 97335833 Authors: Laughton DL;Lunt GG;Wolstenholme AJ Title: Reporter gene constructs suggest that the Caenorhabditis elegans avermectin receptor beta-subunit is expressed solely in the pharynx. Citation: Journal of Experimental Biology 200: 1509-1514 1997 Type: ARTICLE Genes: Abstract: Gene promoter/LacZ reporter constructs were made in order to analyse the expression of the beta-subunit of the Caenorhabditis elegans glutamate-gated Cl- channel (Glu-Cl) receptor. Southern blot analysis of the C. elegans cosmid C35E8 identified a 4kbp EcoRI fragment which contained the 5' portion of the Glu-Cl beta coding sequence together with 5' flanking sequences. This was subcloned and used as the template for polymerase chain reaction (PCR) amplification of a DIVA fragment encoding the first 24 amino acid residues of Glu-Cl beta together with 1.4 kbp of 5' genomic sequence. The fragment was subcloned into the LacZ expression vector pPD22.11 to form a translational reporter fusion. After injection of the construct into worms, six stably transformed lines were established and assayed for beta-galactosidase activity. Stained nuclei were observed in the pharyngeal metacorpus in adults and in all larval stages, and stained nuclei were seen in many embryos undergoing morphogenesis. Additional stained nuclei towards the terminal bulb of the pharynx were observed in larval stages. These results provide further evidence that the Glu-Cl receptor mediates the glutamatergic inhibition of pharyngeal muscle via the M3 motor neurone and point to inhibition of pharyngeal pumping as a major mode of action for avermectins. ------------------- Key: 2809 Medline: 97344078 Authors: Takagi T;Moore CR;Diehn F;Buratowski S Title: An RNA 5'-triphosphatase related to the protein tyrosine phosphatases. Citation: Cell 89: 867-873 1997 Type: ARTICLE Genes: cel-1 Abstract: mRNA capping requires the sequential action of three enzymatic activities: RNA triphosphatase, guanylyltransferase, and methyltransferase. Here we characterize a gene (GEL-I) believed to encode the C., elegans capping enzyme. CEL-1 has a C-terminal domain containing motifs found in yeast and vaccinia virus capping enzyme guanylyltransferases. The N-terminal domain of CEL-1 has RNA tri phosphatase activity. Surprisingly, this domain does not resemble the vaccinia virus capping enzyme but does have significant sequence similarity to the protein tyrosine phosphatase (PTP) enzyme family. However, CEL-1 has no detectable PTP activity. The mechanism of the RNA triphosphatase is similar to that of PTPs: the active site contains a conserved nucleophilic cysteine required for activity. These results broaden the superfamily of PTP-like phosphatases to include enzymes with RNA substrates. ------------------- Key: 2810 Medline: 97389256 Authors: Chou JH;Troemel ER;Sengupta P;Colbert HA;Tong L;Tobin DM;Roayaie K;Crump JG;Dwyer ND;Bargmann CI Title: Olfactory recognition and discrimination in Caenorhabditis elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 61: 157-164 1996 Type: REVIEW Genes: glr-1 odr-1 odr-3 odr-7 odr-10 osm-3 osm-9 Abstract: An animal generates appropriate behavioral responses to a stimulus based on the intrinsic qualities of the stimulus, the context in which it appears, and the animal's previous experience. Olfactory stimuli elicit responses that are often reproducible across different individuals in a species: Many animals display characteristic behaviors in response to the smell of members of their species, food sources, or dangerous conditions. Other sensory modalities can also evoke innate responses, but in the olfactory system, odorants that elicit distinct behaviors are differentiated at the first step of sensory detection by the olfactory receptor neurons. Therefore, the neuronal circuitry responsible for different behaviors can be traced starting from the initial sensory events. Our studies have focused on olfaction and chemosensation in the nematode Caenorhabditis elegans. Chemosensation is the richest mechanism C. elegans has for interacting with its environment, both in the number of different stimuli that are recognized and in the variety of different responses that can be elicited. Virtually all behaviors in C. elegans are modulated by chemical cues. Individual molecules can be attractants or repellents, or they can regulate egg-laying, feeding, or movement. In addition, pheromone cues control development of the animal and mating behavior between males and hermaphrodites. How are these chemical cues recognized and discriminated from one another? The answer to this question lies partly in the biochemical mechanisms that recognize individual odorants, and partly in the neuronal circuitry that drives particular ------------------- Key: 2811 Medline: 97321285 Authors: Eisenmann DM;Kim SK Title: Mechanism of activation of the Caenorhabditis elegans ras homologue let-60 by a novel, temperature-sensitive, gain-of-function mutation. Citation: Genetics 146: 553-565 1997 Type: ARTICLE Genes: gap-1 let-23 let-60 lin-2 lin-3 mpk-1 stDf8 Abstract: The Caenorhabditis elegans let-60 gene encodes a Ras protein that mediates induction of the hermaphrpdite vulva. To better understand how mutations constitutively activate Ras and cause unregulated cell division, we have characterized ga89, a temperature-sensitive, gain-of-function mutation in let-60 ras. At 25 degrees, ga89 increases let-60 activity resulting in a multivulva phenotype. At 15 degrees, ga89 decreases let-60 activity resulting in a vulvaless phenotype in let-60(ga89)/Df animals. The ga89 mutation causes a leucine (L) to phenylalanine (F) substitution at amino acid 19, a residue conserved in all Ras proteins. We introduced the L19F change into human H-Ras protein and found that the in vitro GTPase activity of H-Ras became temperature-dependent. Genetic experiments suggest that LET-60(L19F) interacts with GAP and GNEF, since mutations that decrease GAP and GNEF activity affect the multivulva phenotype of let-60(ga89) animals. These results suggest that the L19F mutation primarily affects the intrinsic rate of GTP hydrolysis by Ras, and that this effect may be sufficient to account for the activated-Ras phenotype caused by let-60(ga89). Our results suggest that a mutation in a human ras gene analogous to ga89 might contribute to ------------------- Key: 2812 Medline: 97321286 Authors: Machaca K;L'Hernault SW Title: The Caenorhabditis elegans spe-5 gene is required for morphogenesis of a sperm-specific organelle and is associated with an inherent cold-sensitive phenotype. Citation: Genetics 146: 567-581 1997 Type: ARTICLE Genes: spe-5 hDf6 hDp2 hDp20 hDp22 hDp29 stDf4 Abstract: The nonrandom segregation of organelles to the appropriate compartment during asymmetric cellular division is observed in many developing systems. Caenorhabditis elegans spermatogenesis is an excellent system to address this issue genetically. The proper progression of spermatogenesis requires specialized intracellular organelles, the fibrous body-membranous organelle complexes (FB-MOs). The FB-MOs play a critical role in cytoplasmic partitioning during the asymmetric cellular division associated with sperm meiosis II. Here we show that spe-5 mutants contain defective, vacuolated FB-MOs and usually arrest spermatogenesis at the spermatocyte stage. Occasionally, spe-5 mutants containing defective FB-MOs will form spermatids that are capable of differentiating into functional spermatozoa. These spe-5 spermatids exhibit an incomplete penetrance for tubulin mis-segregation during the second meiotic division. In addition to morphological and FB-MO segregation defects, all six spe-5 mutants are cold-sensitive, exhibiting a more penetrant sterile phenotype at 16 degrees than 25 degrees. This cold sensitivity could be an inherent property of FB-MO ------------------- Key: 2813 Medline: 97311085 Authors: Graham PL;Johnson JJ;Wang S;Sibley MH;Gupta MC;Kramer JM Title: Type IV collagen is detectable in most, but not all, basement membranes of Caenorhabditis elegans and assembles on tissues that do not express it. Citation: Journal of Cell Biology 137: 1171-1183 1997 Type: ARTICLE Genes: emb-9 let-2 unc-54 Abstract: Type IV collagen in Caenorhabditis elegans is produced by two essential genes, emb-9 and let-2, which encode alpha 1- and alpha 2-like chains, respectively. The distribution of EMB-9 and LET-2 chains has been characterized using chain-specific antisera. The chains colocalize, suggesting that they may function in a single heterotrimeric collagen molecule. Type IV collagen is detected in all basement membranes except those on the pseudocoelomic face of body wall muscle and on the regions of the hypodermis between body wall muscle quadrants, indicating that there are major structural differences between some basement membranes in C. elegans. Using lacZ/green fluorescent protein (GFP) reporter constructs, both type IV collagen genes were shown to be expressed in the same cells, primarily body wall muscles, and some somatic cells of the gonad. Although the pharynx and intestine are covered with basement membranes that contain type IV collagen, these tissues do not express either type IV collagen gene. Using an epitope-tagged emb-9 construct, we show that type IV collagen made in body wall muscle cells can assemble into the pharyngeal, intestinal, and gonadal basement membranes. Additionally, we show that expression of functional type IV collagen only in body wall muscle cells is sufficient for C. elegans to complete development and be partially fertile. Since type IV collagen secreted from muscle cells only assembles into some of the basement membranes that it has access to, there must be a mechanism regulating its assembly. We propose that interaction with a cell surface-associated molecule(s) is required to facilitate type IV collagen assembly. ------------------- Key: 2814 Medline: 97311086 Authors: Gupta MC;Graham PL;Kramer JM Title: Characterization of alpha1(IV) collagen mutations in Caenorhabditis elegans and the effects of alpha1 and alpha2(IV) mutations on type IV collagen distribution. Citation: Journal of Cell Biology 137: 1185-1196 1997 Type: ARTICLE Genes: emb-9 let-2 unc-3 unc-54 Abstract: Type IV collagen is a major component of basement membranes. We have characterized 11 mutations in emb-9, the alpha 1(IV) collagen gene of Caenorhabditis elegans, that result in a spectrum of phenotypes. Five are substitutions of glycines in the Gly-X-Y domain and cause semidominant, temperature-sensitive lethality at the twofold stage of embryogenesis. One is a glycine substitution that causes recessive, non-temperature-sensitive larval lethality. Three putative null alleles, two nonsense mutations and a deletion, all cause recessive, non-temperature-sensitive lethality at the threefold stage of embryogenesis. The less severe null phenotype indicates that glycine substitution containing mutant chains dominantly interfere with the function of other molecules. The emb-9 null mutants do not stain with anti-EMB-9 antisera and show intracellular accumulation of the alpha 2(IV) chain, LET-2, indicating that LET-2 assembly and/or secretion requires EMB-9. Glycine substitutions in either EMB-9 or LET-2 cause intracellular accumulation of both chains. The degree of intracellular accumulation differs depending on the allele and temperature and correlates with the severity of the phenotype. Temperature sensitivity appears to result from reduced assembly/secretion of type IV collagen, not defective function in the basement membrane. Because the dominant interference of glycine substitution mutations is maximal when type IV collagen secretion is totally blocked, this interference appears to occur intracellularly, rather than in the basement membrane. We suggest that the nature of dominant interference caused by mutations in type IV collagen is different than that caused by mutations in fibrillar collagens. ------------------- Key: 2815 Medline: 97318858 Authors: Choudhury BK;Li SSL Title: Identification and characterization of the SMT3 cDNA and gene from Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 234: 788-791 1997 Type: ARTICLE Genes: Abstract: SMT3 gene from nematode, Caenorhabditis elegans, was identified and sequenced. The nematode SMT3 gene codes for a homolog to the yeast SMT3, suppressor of MIF2 mutation in a centromere protein gene. Further, nematode SMT3 cDNA was amplified by polymerase chain reaction from a cDNA library and its nucleotide sequence determined. A comparison of the SMT3 genomic and cDNA sequences established that the protein-encoding sequence is interrupted by two introns of 56 and 50 bp at codon Nos. 22-23 and 56, respectively. The sequence of 91 amino acids deduced from the nematode SMT3 nucleotide sequence exhibited 42 and 47% identity to the yeast and human SMT3 protein sequences, respectively, The evolutionary relationships of SMT3 proteins from human, nematode, Arabidopsis, rice, and yeast were analyzed. ------------------- Key: 2816 Medline: Authors: Wade N Title: Dainty worm tells secrets of the human genetic code. Citation: The New York Times, June 24 : B9-B12 1997 Type: REVIEW Genes: Abstract: Early this month, nearly a thousand biologists met here to discuss the affairs of a speck of protoplasm with a grandiloquent name, a barely visible, almost transparent worm called Caenorhabditis elegans. The worm holds the same secrets of life as other animals, but may be the first to yield them, an event that would deeply influence biology and medicine.... ------------------- Key: 2817 Medline: Authors: Baldwin JG;Giblin-Davis RM;Eddleman CD;Williams DS;Vida JT;Thomas WK Title: The buccal capsule of Aduncospiculum halicti (Nemata: Diplogasterina): an ultrastructural and molecular phylogenetic study. Citation: Canadian Journal of Zoology 75: 407-423 1997 Type: ARTICLE Genes: Abstract: The buccal capsule of Aduncospiculum halicti (Diplogasterina) is compared with that of Zeldia punctata (Cephalobina) and Caenorhabditis elegans (Rhabditina). Characters are mapped on an independent DNA-based phylogenetic tree (inferred from RNA polymerase II and rDNA sequences) to test evolutionary hypotheses. Irrespective of dimorphism, the buccal capsule wall of A. halicti consists of an anterior to posterior series of six cuticular structures classically termed rhabdions. These are defined according to their internal differentiations, discontinuities in profiles, and underlying tissues. Homologies of rhabdions 1 and 2 in A. halicti are proposed on the basis of position and association with adjacent tissues, consistent with those of Cephalobina and Rhabditina. Rhabdion 3 is associated with radial epithelial cells as is the mesorhabdion in C. elegans; this contrasts with Z. punctata, where a rhabdion in a similar position is associated with radial muscle cells. Dorsal and subventral teeth in A. halicti comprise rhabdions 4 and 5; this may be homologous with a corresponding region in Z. punctata but contrasts with C. elegans, where the corresponding region consists of a single metarhabdion. These characters, when mapped on the sequence-based tree, suggest that A. halicti and Diplogasterina share with C. elegans and other Rhabditina derived characters, including a mesorhabdion associated with epithelial cells, but retain some apparently primitive features shared with Cephalobina. ------------------- Key: 2818 Medline: 97303168 Authors: Pal S;Lo MC;Schmidt D;Pelczer I;Thurber S;Walker S Title: Skn-1 - Evidence for a bipartite recognition helix in DNA binding. Citation: Proceedings of the National Academy of Sciences USA 94: 5556-5561 1997 Type: ARTICLE Genes: skn-1 Abstract: Skn-1 is a maternally expressed transcription factor that specifies the fate of certain blastomeres early in the development of Caenorhabditis elegans. This transcription factor contains a basic region, but it binds to DNA as a monomer. Because other transcription factors containing basic regions bind as dimers, this finding implied that Skn represents a new DNA recognition motif. It has been proposed that the basic region helix of Skn is stabilized for binding by tertiary contacts to other parts of the protein. We have tested this proposal by carrying out circular dichroism (CD) and NMR experiments on the Skn domain and five truncated proteins. Our results have shown that the basic region of Skn is unstructured in solution and does not contact other parts of the protein; like other basic region peptides, it folds into a helix only upon binding specifically to DNA. However, there is a stably folded helical module in the Skn domain, and one of the helices in this module terminates immediately before the start of the basic region. This pre-organized helix contains a surface rich in basic amino acids, and we propose that this helix contacts the DNA distal to the basic region proper, providing an extra long helical recognition surface which helps to stabilize monomeric binding. Homology between the Skn domain and several basic-region leucine zipper (bZIP) domains raises the possibility that the affinity and perhaps the specificity of DNA binding by bZIP proteins can be modulated by incorporating a stably folded helical segment that contacts ------------------- Key: 2819 Medline: 97303186 Authors: Radisky DC;Snyder WB;Emr SD;Kaplan J Title: Characterization of VPS41, a gene required for vacuolar trafficking and high-affinity iron transport in yeast. Citation: Proceedings of the National Academy of Sciences USA 94: 5662-5666 1997 Type: ARTICLE Genes: Abstract: Mutations in the yeast gene VPS41 give rise to poor growth on low iron medium, severe alterations in vacuolar morphology, and cause the missorting of membranous and soluble vacuolar proteins. Our studies predict that VPS41 encodes a hydrophilic protein of 992 amino acids that contains no obvious signal sequence or hydrophobic domains. The deduced Vps41p sequence contains a domain rich in glutamic and aspartic residues, as well as a domain with resemblance to a region of clathrin heavy chain. We have also identified and sequenced putative VPS41 homologues from Caenorhabditis elegnns, plants, and humans. The VPS41 homologues (but not the yeast VPS41 itself) contain a conserved cysteine-rich RING-H2 zinc finger at their COOH termini. Biochemical experiments suggest that VPS41 functions in post-Golgi protein processing: the deletion mutant exhibits defective high affinity transport due to impaired Fet3p activity and also exhibits defects in the processing and sorting of multiple vacuolar hydrolases. ------------------- Key: 2820 Medline: 97338254 Authors: Peixoto CA;Kramer JM;de Souza W Title: Caenorhabditis elegans cuticle: A description of new elements of the fibrous layer. Citation: Journal of Parasitology 83: 368-372 1997 Type: ARTICLE Genes: Abstract: At The ultrastructural level, the Caenorhabdits elegans cuticle shows the presence of well defined layers; 1 of them is the fibrous layer composed by 2, strands of fibers that meet each other at a 60 degrees angle and resembling a fish-bone pattern. In this paper, we describe new elements of the fibrous layer When thin sections were obtained at a very low angle, i.e., almost tangential, fibers of wavy appearance could be observed. Those elements were 300 nm in length and 20 nm thick and were Linked to each other by delicate dots. Deep-etched replicas of C. elegens revealed more details of the arrangement of new elements in the fibrous layer. The wavy fibers were organized in S-sided, honeycomblike figures. Each pentagonal fiber was 145 nm across and was composed of tightly packed globular structures arranged linearly. ------------------- Key: 2821 Medline: 97332697 Authors: Baude EJ;Arora VK;Yu S;Garbers DL;Wedel BJ Title: The cloning of a Caenorhabditis elegans guanylyl cyclase and the construction of a ligand-sensitive mammalian/nematode chimeric receptor. Citation: Journal of Biological Chemistry 272: 16035-16039 1997 Type: ARTICLE Genes: Abstract: Substantial guanylyl cyclase activity was detected in membrane fractions prepared from Caenorhabditis elegans (100 pmol cGMP/min/mg at 20 degrees C or 500 pmol cGMP/min/mg art 37 degrees C), suggesting the potential existence of orphan cyclase receptors in the nematode, Using degenerate primers, a cDNA clone encoding a putative membrane form of the enzyme (GCY-X-1) was obtained, The apparent cyclase was most closely related to the mammalian natriuretic peptide receptor family, and retained cysteine residues conserved within the extracellular domain of the mammalian receptors, Expression of the cDNA in COS-7 cells resulted in low, but detectable guanylyl cyclase activity (about 2-fold above vector alone), The extracellular and protein kinase homology domain of the mammalian receptor (GC-B) for C-type natriuretic peptide (CNP) was fused to the catalytic domain of GCY-X, and expressed in COS-7 cells to determine whether ligand dependent regulation would now be obtained. The resulting chimeric protein (GC-BX1) was active, and CNP elevated cGMP in a concentration-dependent manner, Subsequently, a search of the genome data base demonstrated the existence of at least 29 different genes From C. elegans that align closely with the catalytic domain of GCY-X-1, and thus an equally large number of different regulatory ligands may exist. ------------------- Key: 2822 Medline: Authors: Gaugler R;Wilson M;Shearer P Title: Field release and environmental fate of a transgenic entomopathogenic nematode. Citation: Biological Control 9: 75-80 1997 Type: ARTICLE Genes: Abstract: A strain of the entomopathogenic nematode Heterorhabditis bacteriophora, genetically enhanced for thermotolerance by introduction of a heat-shock protein gene from the free-living nematode Caenorhabditis elegans, was released in turfgrass field microplots in the spring, summer, and fall of 1996. As predicted, transgenic and wildtype strains did not differ in their ability to persist. We document the regulatory procedures at the federal, state, university, and local levels needed before held release, none of which posed any significant difficulties. Our risk assessment study supports the regulatory view that the transgenic nematode strain is an unlikely environmental threat. Subsequent regulatory reviews in the United States appear likely to continue to be decided on a case-by-case basis according to organism phenotype rather than the techniques used to generate them. This is the first report of a nonmicrobial, genetically engineered insect natural enemy being released into the environment. ------------------- Key: 2823 Medline: 96398943 Authors: Burglin TR Title: Warthog and Groundhog, novel families related to Hedgehog. Citation: Current Biology 6: 1047-1050 1996 Type: REVIEW Genes: Abstract: Cell-cell signalling is one of the fundamental mechanisms by which different cell fates are generated during development. One group of signalling molecules, encoded by the Drosophila gene hedgehog and its vertebrate orthologues, has been shown to play important roles during development of flies and vertebrates. Searching through the Caenorhabditis elegans genome, a major fraction of which as now been sequenced, reveals several sequences with similarities to hedgehog genes. The similarity is restricted to the carboxyl terminus of the Hedgehog proteins, which is surprising given that the amino-terminal part, which provides the biologically active signal, is more highly conserved between fly and vertebrate Hedgehogs. The carboxyl terminus is a distinct domain that has autoproteolytic activity and cleaves Hedgehog into a protease domain and a signalling part, and it is thought to regulate the release of the amino-terminal signal. ------------------- Key: 2824 Medline: 97347238 Authors: Korswagen HC;Park J-H;Ohshima Y;Plasterk RHA Title: An activating mutation in a Caenorhabditis elegans G(s) protein induces neural degeneration. Citation: Genes & Development 11: 1493-1503 1997 Type: ARTICLE Genes: ced-3 ced-4 clr-1 deg-1 egl-1 egl-19 egl-30 gpb-1 gsa-1 mec-4 mec-6 mec-10 sgs-1 sgs-2 unc-2 unc-8 unc-36 unc-105 Abstract: Heterotrimeric guanine nucleotide-binding proteins (G proteins) act as signal-transducing molecules that connect serpentine-transmembrane receptors to a variety of intracellular effectors. We characterized a Caenorhabditis elegans G(s) gene, gsa-l, which encodes a G(s) alpha-subunit (G alpha(s)) that is expressed throughout the nervous system and in muscle cells. gsa-l is an essential gene; a loss-of-function mutation in gsa-l results in lethality at the first stage of larval development. Partial (mosaic) loss of G alpha(s) expression or overexpression of the protein results in reciprocal defects in movement and egg-laying, suggesting a role for G alpha(s) in the regulation of these behaviors. Expression of a constitutively active form of G alpha(s) from an inducible promotor results in hypercontraction of body-wall muscle cells and vacuolization and degeneration of neurons within hours of induction. Neurons that are susceptible to the degeneration induced by activated G alpha(s) are predominantly motoneurons located within the ventral nerve cord. Phenotypic analysis shows that the induced neural degeneration is not the result of programmed cell death but is probably caused by the activation of ion channels. A genetic suppressor of activated G alpha(s) was isolated that identifies a putative downstream target of G(s) ------------------- Key: 2825 Medline: Authors: Sengupta P Title: Cellular and molecular analyses of olfactory behavior in C. elegans. Citation: Seminars in Cell & Developmental Biology 8: 153-161 1997 Type: REVIEW Genes: adp-1 odr-7 odr-10 osm-9 sra-1 sra-2 sra-3 sra-4 sra-5 sra-6 sra-7 sra-8 sra-9 sra-10 sra-11 srb-6 srd-1 sre-1 srg-1 srg-2 srg-3 srg-4 srg-5 srg-6 srg-7 srg-8 srg-9 srg-12 srg-13 sro-1 Abstract: C. elegans responds to and discriminates among a large number of volatile and water-soluble chemicals using a few defined chemosensory neurons. The functions of individual sensory neurons have been defined by cell killing experiments, and genes required for responses to subsets of chemicals have been identified. C. elegans has several large families of putative chemosensory receptor genes, and one of these genes has been demonstrated to encode a receptor for a specific odorant. Current work is aimed at identifying additional components of chemosensory neuron development and function. ------------------- Key: 2826 Medline: 97330685 Authors: Krause M;Park M;Zhang J-M;Yuan J;Harfe B;Xu S-Q;Greenwald I;Cole M;Paterson B;Fire A Title: A C. elegans E/Daughterless bHLH protein marks neuronal but not striated muscle development. Citation: Development 124: 2179-2189 1997 Type: ARTICLE Genes: hlh-1 hlh-2 hlh-3 Abstract: The E proteins of mammals, and the related Daughterless (DA) protein of Drosophila, are ubiquitously expressed helix-loop-helix (HLH) transcription factors that play a role in many developmental processes. We report here the characterization of a related C. elegans protein, CeE/DA, which has a dynamic and restricted distribution during development. CeE/DA is present embryonically in neuronal precursors, some of which are marked by promoter activity of a newly described Achaete-scute-like gene hlh-3. In contrast, we have been unable to detect CeE/DA in CeMyoD-positive striated muscle cells. In vitro gel mobility shift analysis detects dimerization of CeE/DA with HLH-3 while efficient interaction of CeE/DA with CeMyoD is not seen. These studies suggest multiple roles for CeE/DA in C. elegans development and provide evidence that both common and alternative strategies have evolved for the use of related HLH proteins in controlling cell fates in different species. ------------------- Key: 2827 Medline: 97360135 Authors: Nicoll M;Akerib CC;Meyer BJ Title: X-chromosome-counting mechanisms that determine nematode sex. Citation: Nature 388: 200-204 1997 Type: ARTICLE Genes: fox-1 him-5 xol-1 meDf5 meDf6 mnDp66 yDf17 yDf19 yDf20 yDp13 yDp14 Abstract: Sex is determined in Caenorhabditis elegans by an X-chromosome-counting mechanism that reliably distinguishes the twofold difference in X-chromosome dose between males (1X) and hermaphrodites (2X)(1,2). This small quantitative difference is translated into the 'on/off' response of the target gene, xol-1, a switch that specifies the male fate when active and the hermaphrodite fate when inactive(3). Specific regions of X contain counted signal elements whose combined dose sets the activity of xol-1 (ref. 4). Here we ascribe the dose effects of one region to a discrete, protein-encoding gene, fox-1. We demonstrate that the dose-sensitive signal elements on chromosome X control xol-1 through two different molecular mechanisms. One involves the transcriptional repression of xol-1 in XX animals. The other uses the putative RNA-binding protein encoded by fox-1 to reduce the level of xol-1 protein. These two mechanisms of repression act together to ensure the fidelity of the X-chromosome counting process. ------------------- Key: 2828 Medline: 97373066 Authors: Ahringer J Title: Turn to the worm! Citation: Current Opinion in Genetics & Development 7: 410-415 1997 Type: REVIEW Genes: ced-4 ces-2 mrp-2 sel-12 sma-4 vab-3 Abstract: Caenorhabditis elegans will be the first multicellular animal to have its entire genome sequenced. This is not just good news for those currently working in the field, but also for those trying to understand the biology of more complex animals, including humans. C. elegans is a relatively simple animal that is amenable to studies of genetics and developmental processes that are common to all animals, making this an attractive model in which to study basic processes that are altered in human disease. Powerful forward and reverse genetics mean that virtually any gene of interest can be studied at the functional level. ------------------- Key: 2829 Medline: 97374451 Authors: McDowall JS;Rose AM Title: Genetic analysis of sterile mutants in the dpy-5 unc-13 (I) genomic region of Caenorhabditis elegans. Citation: Molecular & General Genetics 255: 60-77 1997 Type: ARTICLE Genes: bli-4 dpy-5 dpy-14 gld-1 glp-1 glp-4 let-75 let-86 let-355 let-367 let-370 let-376 let-377 let-378 let-379 let-380 let-381 let-382 let-383 let-384 let-385 let-386 let-387 let-388 let-389 let-390 let-391 let-392 let-393 let-394 let-395 let-396 let-397 let-398 let-399 let-400 let-512 let-513 let-514 let-520 let-521 let-522 let-523 let-524 let-525 let-527 let-528 let-529 let-530 let-531 let-532 let-534 let-539 let-542 let-543 let-544 let-545 let-599 let-601 let-602 let-603 let-604 let-605 let-606 let-607 let-608 let-610 let-611 unc-13 unc-37 hDf8 hDp12 hDp13 hDp14 hDp15 hDp16 hDp17 hDp18 hDp19 hDp31 hDp32 hDp33 hDp35 hDp36 hDp37 hDp39 hDp41 hDp43 hDp48 hDp50 hDp54 hDp56 hDp57 hDp58 hDp60 hDp61 hDp64 hDp72 sDf4 sDp2 Abstract: Essential genes were identified in the 1.5-map unit dpy-5 unc-13 region of chromosome I in the Caenorhabditis elegans genome by rescuing lethal mutations using the duplication sDp2. In this paper, we report the mapping and complementation testing of lethal mutations, 45 of which identify 18 new, essential genes. This analysis brings the number of essential genes defined by the sDp2 rescue of lethal mutants to 97; 64 of these map between dpy-5 and unc-13. 61% of these essential genes are identified by more than one allele. Positioning of the mutations was done using the breakpoints of six duplications. The mutant phenotypes of 14 loci essential for fertility were characterized by Nomarski microscopy and DAPI staining. None of the mutants were rescued by wild-type male sperm. The cytological data showed that four genes produced mutants with defects in gonadogenesis, let-395, let-603, let-605 and let-610. Mutations in seven genes, let-355, let-367, let-384, let-513, let-544, let-545 and let-606, affected germ cell proliferation or gametogenesis. Mutants for the remaining three genes, let-370, let-599 and let-604: produced eggs that failed to develop or hatch, thereby acting as maternal effect lethals. We observed a nonrandom distribution of arrest phenotypes with regard to ------------------- Key: 2830 Medline: 97374452 Authors: McDowall JS;Rose A Title: Alignment of the genetic and physical maps in the dpy-5 bli-4 (I) region of C. elegans by serial cosmid rescue of lethal mutations. Citation: Molecular & General Genetics 255: 78-95 1997 Type: ARTICLE Genes: bli-4 dpy-5 dpy-14 let-355 let-367 let-370 let-376 let-377 let-378 let-379 let-380 let-381 let-382 let-384 let-386 let-387 let-388 let-390 let-391 let-393 let-395 let-396 let-512 let-513 let-514 let-530 let-531 let-532 let-599 let-601 let-602 let-604 let-606 let-607 let-608 let-610 let-611 unc-11 unc-13 hDp12 hDp13 hDp14 hDp15 hDp16 hDp17 hDp18 hDp31 hDp32 hDp37 hDp41 hDp48 hDp57 hDp61 hDp71 sDp2 sDf4 Abstract: Lethal mutations in the 0.5 map unit region between dpy-5 and bli-4 on chromosome I in Caenorhabditis elegans were serially rescued using cosmid-containing transgenic strains. All the lethal mutations analyzed came from a set of 495 EMS-induced. sDpr2-rescued lethals described previously. Germline transformation with cosmid DNA was used to create 25 transgenic strains bearing heritable extrachromosomal arrays. These arrays were used as small duplications for the fine-scale mapping of essential genes, via the rescue of lethal mutations. Lethal mutations in 13 essential genes have been phenotypically rescued, allowing the alignment of the genetic and physical maps in this region. Extrachromosomal arrays were found to be transmitted 2- to 7-fold less frequently in oocytes than in hermaphrodite sperm for 12 of the 16 arrays that were examined. Three of these strains showed a subsequent 4- to 13-fold increase in array stability in oocytes. This phenomenon may be influenced by cosmid sequences. Early mitotic loss of the arrays was observed in all 17 transgenic strains examined, suggesting that loss of the array can occur at any time during development when cell divisions are occurring. As a result of this work, 13 of the essential loci positioned between dpy-5 and bli-4 are anchored to the physical map, thereby providing links between the physical and genetic maps on average every 85 ------------------- Key: 2831 Medline: 97354526 Authors: Shreffler W;Wolinsky E Title: Genes controlling ion permeability in both motorneurons and muscle. Citation: Behavior Genetics 27: 211-221 1997 Type: ARTICLE Genes: deg-1 enu-2 mec-6 ndg-4 sup-40 sup-41 sup-42 sup-43 unc-8 unc-105 maDf2 Abstract: Genetic data suggest that unc-8 is a member of the epithelial sodium channel (ENaC) gene family (Shreffler et al., 1995). Consistent with this idea, cosmid R13A1, containing an ENaC homolog, can restore normal locomotion to unc-8 mutants after germline transformation. To identify other genes encoding proteins that regulate ENaC function, extragenic unc-8 suppressor and enhancer mutations were sought. This report describes two new unc-8 suppressor mutations, sup-42(lb88)X and sup-43(lb141) II, and an enhancer mutation, enu-2(lb140) III. sup-43(lb141) and enu-2(lb140), cause vacuoles within body wall muscle, similar in appearance to those of unc-105(n490) II mutants, consistent with their proposed role in ENaC function. Single and double mutant phenotypes observed in this and previous work suggest that sodium channels in different tissues utilize an overlapping set of gene products: at least six in motorneurons, unc-8, mec-6, and sup-40-43, and at least five in muscle, sup-43, unc-8, enu-2, unc-105, and ------------------- Key: 2832 Medline: 97389486 Authors: Rand JB Title: What makes the worm squirm? Citation: Molecular Psychiatry 2: 293-295 1997 Type: ARTICLE Genes: cha-1 egl-30 snt-1 unc-2 unc-13 unc-17 unc-18 Abstract: In the simple, 302-cell nervous system of the soil nematode C. elegans, genetic selection for toxin-resistance was used to isolate mutants with specific defects in synaptic neurotransmission, making it possible to characterize already-known molecules and to identify new components of the machinery required for the release of synaptic ------------------- Key: 2833 Medline: 97366392 Authors: Sonnhammer ELL;Eddy SR;Durbin R Title: Pfam - A comprehensive database of protein domain families based on seed alignments. Citation: Proteins 28: 405-420 1997 Type: ARTICLE Genes: Abstract: Databases of multiple sequence alignments are a valuable aid to protein sequence classification and analysis, One of the main challenges when constructing such a database is to simultaneously satisfy the conflicting demands of completeness on the one hand and quality of alignment and domain definitions on the other, The latter properties are best dealt with by manual approaches, whereas completeness in practice is only amenable to automatic methods, Herein we present a database based on hidden Markov model profiles (HMMs), which combines high quality and completeness, Our database, Pfam, consists of parts A and B, Pfam-A is curated and contains well-characterized protein domain families with high quality alignments, which are maintained by using manually checked seed alignments and HMMs to find and align all members, Pfam-B contains sequence families that were generated automatically by applying the Domainer algorithm to cluster and align the remaining protein sequences after removal of Pfam-A domains. By using Pfam, a large number of previously unannotated proteins from the Caenorhabditis elegans genome project were classified, We have also identified many novel family memberships in known proteins, including new kazal, Fibronectin type III, and response regulator receiver domains, Pfam-A families have permanent accession numbers and form a library of HMMs available for searching and automatic annotation of new ------------------- Key: 2834 Medline: 97397023 Authors: Kagan RM;McFadden HJ;McFadden PN;O'Connor C;Clarke S Title: Molecular phylogenetics of a protein repair methyltransferase. Citation: Comparative Biochemistry & Physiology B-Comparative Biochemistry 117: 379-385 1997 Type: ARTICLE Genes: pcm-1 Abstract: Protein-L-isoaspartyl (D-aspartyl) O-methyltransferase (E.C. 2.1.1.71) is a well-conserved and widely distributed protein repair enzyme that methylates isomerized or racemized aspartyl residues in age-damaged proteins. We exploited the availability of protein sequences from 10 diverse animal, plant and bacterial taxa to construct a phylogenetic tree and determine the rates of amino acid substitution for this enzyme. We used a likelihood ratio rest to show that this enzyme fulfills the conditions for a molecular crock. We found that the rate of substitution is 0.39 amino, acid substitutions per site per 10(9) years and remains relatively constant from bacteria to humans. We argue that this degree of sequence conservation may result from the functional constraints necessitated by the requirement to specifically recognize altered aspartyl but nor normal aspartyl residues in proteins. Relative rate analysis of the Caenorhabditis elegans sequence suggests that the amino acid substitution rate in the nematode lineage may be higher than that in other lineages and that the divergence of nematodes may have been a more recent event than suggested by previous analysis. ------------------- Key: 2835 Medline: 97367723 Authors: Vanfleteren JR;De Vreese A Title: Modulation of kinase activities in dauers and in long-lived mutants of Caenorhabditis elegans. Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 52: B212-B216 1997 Type: ARTICLE Genes: age-1 daf-2 daf-7 daf-12 daf-23 fer-15 Abstract: Mutant alleles of the genes age-1 and daf-2 that lengthen life span (Age phenotype) of Caenorhabditis elegans cause higher protein kinase (PKA, PKC, PTK) activity levels in senescing worms relative to wild-type. Elevated levels of PKA and PTK were also present in dauer larvae, developmentally arrested juveniles specialized for long-term survival, relative to L3 larvae, the alternative developmental stage. PKC activity was downregulated in dauers of a non-Age control strain and in age-1 mutant dauers, compared to L3 larvae, but similar activities were measured in dauers and L3 larvae of a daf-2 mutant strain. Thus, age-1 and daf-2 mutant worms may express distinct elements of a dauer-specific survival program during adult life. ------------------- Key: 2836 Medline: 97362354 Authors: Seshagiri S;Miller LK Title: Caenorhabditis elegans CED-4 stimulates CED-3 processing and CED-3-induced apoptosis. Citation: Current Biology 7: 455-460 1997 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: Background: Programmed cell death or apoptosis is a key feature of normal development, tissue homeostasis and disease progression in metazoans. Genetic studies in the nematode C. elegans have identified three key genes involved in apoptosis, ced-3, ced-4 and ced-9. Expression of ced-3 and ced-4 is required for the induction of cell death, whereas expression of ced-9 is necessary to inhibit cell death. The precise mechanism by which these genes influence the life or death decision of a cell is not known. In this study, we have expressed the genes in an insect cell line to explore their role in the apoptotic pathway. Results: Go-expression of ced-4 with ced-3 in insect cells stimulated both the induction and the level of CED-3-mediated apoptosis. Stimulation of CED-3-dependent apoptosis by CED-4 was accompanied by accelerated processing of CED-3, which was dependent on the presence of a wild-type CED-3 pro-domain and a conserved lysine residue within a putative ATP/GTP-binding motif of CED-4. Go-expression of ced-9 with ced-4 and ced-3 inhibited the ability of CED-4 to stimulate CED-3 processing and CED-9-dependent apoptosis, Although a temperature-sensitive CED-9 mutant was unable to block CED-4 activity and failed to associate with CED-4, a deletion mutant of CED-9 lacking the carboxy-terminal hydrophobic domain could associate with CED-4 and block CED-4 activity.Conclusions: Our results establish a role for CED-4 in the processing of CED-3 and the stimulation of CED-3-induced apoptosis, Furthermore, we show that CED-9 achieves its anti-apoptotic effect by associating with CED-4 and blocking the ability ------------------- Key: 2837 Medline: 97359971 Authors: Wightman B;Baran R;Garriga G Title: Genes that guide growth cones along the C. elegans ventral nerve cord. Citation: Development 124: 2571-2580 1997 Type: ARTICLE Genes: enu-1 fax-1 unc-3 unc-30 unc-42 unc-83 unc-84 unc-115 Abstract: During nervous system development, growth cone pioneering and fasciculation contribute to nerve bundle structure, Pioneer growth cones initially navigate along neuroglia to establish an axon scaffold that guides later extending growth cones. In C. elegans, the growth cone of the PVPR neuron pioneers the left ventral nerve cord bundle, providing a path for the embryonic extensions of the PVQL and AVKR growth cones, Later during larval development, the HSNL growth cone follows cues in the left ventral nerve cord bundle provided by the PVPR and PVQL axons. Here we show that mutations in the genes enu-l, fax-1, unc-3, unc-30, unc-42 and unc-115 disrupt pathfinding of growth cones along the left ventral nerve cord bundle, Our results indicate that unc-3 and unc-30 function in ventral nerve cord pioneering and that enu-1, fax-1, unc-42 and unc-115 function in recognition of the PVPR and PVQL axons by the AVKR and HSNL growth cones. ------------------- Key: 2838 Medline: 97386028 Authors: Hedgecock EM;Norris CR Title: Netrins evoke mixed reactions in motile cells. Citation: Trends in Genetics 13: 251-253 1997 Type: REVIEW Genes: unc-5 unc-6 unc-40 Abstract: Like a molecular bulletin board, the extracellular matrix allows indirect communication between cells during development. For posting messages, soluble molecules from various sources are incorporated into more-or-less stable, matrix polymers surrounding tissues and individual cells. Integrins and other cell surface receptors tether these components and coordinate their assembly. Later, for reading messages, cells can express receptors for particular matrix components. In particular, motile cells and axons use matrix cues originating from path or target cells to control their direction and extent of migration. ------------------- Key: 2839 Medline: 97250547 Authors: Yu S;Avery L;Baude E;Garbers DL Title: Guanylyl cyclase expression in specific sensory neurons: A new family of chemosensory receptors. Citation: Proceedings of the National Academy of Sciences USA 94: 3384-3387 1997 Type: ARTICLE Genes: gcy-1 gcy-2 gcy-3 gcy-4 gcy-5 gcy-6 gcy-7 gcy-8 gcy-9 gcy-10 gcy-11 gcy-12 gcy-13 gcy-14 gcy-31 gcy-32 gcy-33 Abstract: A guanylyl cyclase (GC-D) was recently shown to be expressed in a subclass of neurons within the neuroepithelim of the rat, but given that only a single cyclase was discovered, whether it represents an odorant/pheromone receptor as has been suggested for the large family of seven-transmembrane receptors remains unclear. Through cloning and expression of cDNA we now demonstrate that at least 29 genomic or cDNA sequences found in Caenorhabditis elegans represent guanylyl cyclases. Many of the membrane forms retain cysteine residues conserved within the extracellular, ligand-binding domain of known cyclase receptors. Of eight orphan cyclase receptor::GFP (green fluroescence protein) fusion constructs for which signals were obtained, all were expressed in specific sensory neurons. Furthermore, a cyclase/GFP fusion protein (GCY-10/GFP) was principally expressed in the sensory cilium, suggesting these cyclases function as primary chemosensory receptors. For the first time, we also found that chemosensory neurons (ASE), known to be bilaterally symmetric, demonstrate absolute right or left sidedness with respect to the expression of three different cyclases. Thus, the guanylyl cyclases represent an unexpectedly large and new family of sensory neuron receptors that may complement the 7-transmembrane family of ------------------- Key: 2840 Medline: 97238870 Authors: Lubas WA;Frank DW;Krause M;Hanover JA Title: O-Linked GlcNAc transferase is a conserved nucleocytoplasmic protein containing tetratricopeptide Citation: Journal of Biological Chemistry 272: 9316-9324 1997 Type: ARTICLE Genes: Abstract: O-Linked GlcNAc addition and phosphorylation may compete for sites on nuclear pore proteins and transcription factors. We sequenced O-linked GlcNAc transferase from rabbit blood and identified the homologous Caenorhabditis elegans transferase gene on chromosome III. We then isolated C. elegans and human cDNAs encoding the transferase. The enzymes from the two species appear to be highly conserved; both contain multiple tetratricopeptide repeats and nuclear localization sequences. The C. elegans transferase accumulated in the nucleus and in perinuclear aggregates in overexpressing transgenic lines. O-Linked GlcNAc transferase activity was also elevated in HeLa cells transfected with the human cDNA. At least four human transcripts were observed in the tissues examined ranging in size from 4.4 to 9.3 kilobase pairs. The two largest transcripts (7.9 and 9.3 kilobase pairs) were enriched at least 12-fold in the pancreas. Based on its substrate specificity and molecular features, we propose that O-linked GlcNAc transferase is part of a glucose-responsive pathway previously implicated in the pathogenesis of ------------------- Key: 2841 Medline: 97289688 Authors: Ryazanov AG;Ward MD;Mendola CE;Pavur KS;Dorovkov MV;Wiedmann M;Erdjument-Bromage H;Tempst P;Parmer TG;Prostko CR;Germino FJ;Hait WN Title: Identification of a new class of protein kinases represented by eukaryotic elongation factor-2 kinase. Citation: Proceedings of the National Academy of Sciences USA 94: 4884-4889 1997 Type: ARTICLE Genes: Abstract: The several hundred members of the eukaryotic protein kinase superfamily characterized to date share a similar catalytic domain structure, consisting of 12 conserved subdomains. Here we report the existence and wide occurrence in eukaryotes of a protein kinase with a completely different structure. We cloned and sequenced the human, mouse, rat, and Caenorhabditis elegans eukaryotic elongation factor-2 kinase (eEF-2 kinase) and found that with the exception of the ATP-binding site, they do not contain any sequence motifs characteristic of the eukaryotic protein kinase superfamily. Comparison of different eEF-2 kinase sequences reveals a highly conserved region of approximately 200 amino acids which was found to be homologous to the catalytic domain of the recently described myosin heavy chain kinase A (MHCK A) from Dictyostelium. This suggests that eEF-2 kinase and MHCK A are members of a new class of protein kinases with a novel ------------------- Key: 2842 Medline: 97388498 Authors: Williams-Masson EM;Malik AN;Hardin J Title: An actin-mediated two-step mechanism is required for ventral enclosure of the C. elegans hypodermis. Citation: Development 124: 2889-2901 1997 Type: ARTICLE Genes: Abstract: The epiboly of the Caenorhabditis elegans hypodermis involves the bilateral spreading of a thin epithelial sheet from the dorsal side around the embryo to meet at the ventral midline in a process known as ventral enclosure. We present evidence that ventral enclosure occurs in two major steps. The initial migration of the hypodermis is led by a quartet of cells, which exhibit protrusive activity at their medial tips and are required to pull the hypodermis around the equator of the embryo. These cells display actin-rich filopodia and treatment with cytochalasin D immediately halts ventral enclosure, as does laser inactivation of all four cells. Once the quartet of cells has migrated around the equator of the embryo and approaches the ventral midline, the remainder of the leading edge becomes visible on the ventral surface and exhibits a localization of actin microfilaments along the free edges of the cells, forming an actin ring. Cytochalasin D and laser inactivation block ventral enclosure at this later stage as well and, based upon phalloidin staining, we propose that the second half of enclosure is dependent upon a purse string mechanism, in which the actin ring contracts and pulls together the edges of the hypodermal sheet at the ventral midline. The ventral cells then form junctions with their contralateral ------------------- Key: 2843 Medline: 97367948 Authors: Page BD;Zhang W;Steward K;Blumenthal T;Priess JR Title: ELT-1, a GATA-like transcription factor, is required for epidermal cell fates in Caenorhabditis elegans embryos. Citation: Genes & Development 11: 1651-1661 1997 Type: ARTICLE Genes: elt-1 lin-26 mex-3 eDf18 eDf19 mDf7 Abstract: Epidermal cells are generated during Caenorhabditis elegans embryogenesis by several distinct lineage patterns. These patterns are controlled by maternal genes that determine the identities of early embryonic blastomeres. We show that the embryonically expressed gene elt-1, which was shown previously to encode a GATA-like transcription factor, is required for the production of epidermal cells by each of these lineages. Depending on their lineage history, cells that become epidermal in wild-type embryos become either neurons or muscle cells in elt-1 mutant embryos. The ELT-1 protein is expressed in epidermal cells and in their precursors. We propose that elt-1 functions at an early step in the specification of epidermal cell fates. ------------------- Key: 2844 Medline: 97388497 Authors: Wrischnik LA;Kenyon CJ Title: The role of lin-22, a hairy/Enhancer of split homolog, in patterning the peripheral nervous system of C. elegans. Citation: Development 124: 2875-2888 1997 Type: ARTICLE Genes: egl-5 lin-22 lin-32 lin-39 mab-5 pal-1 Abstract: In C. elegans, six lateral epidermal stem cells, the seam cells V1-V6, are located in a row along the anterior-posterior (A/P) body axis. Anterior seam cells (V1-V4) undergo a fairly simple sequence of stem cell divisions and generate only epidermal cells. Posterior seam cells (VS and V6) undergo a more complicated sequence of cell divisions that include additional rounds of stem cell proliferation and the production of neural as well as epidermal cells. In the wild type, activity of the gene lin-22 allows V1-V4 to generate their normal epidermal lineages rather than V5-like lineages. lin-22 activity is also required to prevent additional neurons from being produced by one branch of the VS lineage. We find that the lin-22 gene exhibits homology to the Drosophila gene hairy and that lin-22 activity represses neural development within the VS lineage by blocking expression of the posterior-specific Hox gene mab-5 in specific cells. In addition, in order to prevent anterior V cells from generating VS-like lineages, wild-type lin-22 gene activity must inhibit (directly or indirectly) at least five downstream regulatory gene activities. In anterior body regions, lin-22(+) inhibits expression of the Hox gene mab-5. It also inhibits the activity of the achaete-scute homolog lin-32 and an unidentified gene that we postulate regulates stem cell division. Each of these three genes is required for the expression of a different piece of the ectopic VS-like lineages generated in lin-22 mutants. In addition, lin-22 activity prevents two other hox genes, lin-39 and egl-5, from acquiring new activities within their normal domains of function along the A/P body axis. Some, but not all, of the patterning activities of lin-22 in C. elegans resemble those of hairy in Drosophila. ------------------- Key: 2845 Medline: 97384993 Authors: Ogura K-i;Shirakawa M;Barnes TM;Hekimi S;Ohshima Y Title: The UNC-14 protein required for axonal elongation and guidance in Caenorhabditis elegans interacts with the serine/threonine kinase UNC-51. Citation: Genes & Development 11: 1801-1811 1997 Type: ARTICLE Genes: unc-14 unc-51 Abstract: Certain unc mutants in the nematode Caenorhabditis elegans, such as unc-14 and unc-51, show abnormal axonal elongation and axonal structures. We cloned the unc-51 gene previously and predicted that it encodes a novel serine/threonine protein kinase. In this study, we precisely localized the activity to rescue an unc-14 mutation. Also, we identified four cDNA clones encoded by the unc-14 rescuing region, in screens for proteins that bind to UNC-51 using a yeast two-hybrid system. A mutation site in the cDNA was identified for each of the six unc-14 mutants, establishing that the unc-14 gene was cloned. The unc-14 gene encodes a novel protein of 665 amino acids, and is coexpressed with the unc-51 gene in the cell bodies and axons of almost all neurons including DD/VD and hermaphrodite-specific neurons. Another clone recovered in the two-hybrid screen encodes a carboxy-terminal region of UNC-51. Analysis using the yeast two-hybrid system suggested that a central region of UNC-14 bound to a carboxy-terminal region of UNC-51, and that the UNC-51 carboxy-terminal region oligomerized. In in vitro binding studies using recombinant fusion proteins, UNC-14 interacted with UNC-51 directly. We propose that UNC-51 protein kinase acts as an oligomer, and that UNC-14 is a regulator of UNC-51, in axonal elongation and guidance. ------------------- Key: 2846 Medline: 97388283 Authors: Wedel BJ;Garbers DL Title: New insights on the functions of the guanylyl cyclase receptors. Citation: FEBS Letters 410: 29-33 1997 Type: ARTICLE Genes: gcy-6 gcy-7 gcy-8 gcy-33 Abstract: The discovery of at least 29 genes encoding putative guanylyl cyclases in Caenorhabditis elegans has raised the question as to whether there are numerous receptors yet to be discovered in the mammal, The nematode, however, not only seems ideal to study guanylyl cyclase receptor localization and function, given the large variety of isoforms, but also leads to possible identification of ligands for orphan guanylyl cyclases by the use of genetic and behavioral assays, A recent powerful approach to describe the function of different guanylyl cyclase isoforms in mammals has been the disruption of the corresponding genes in the mouse, A salt resistant elevation of blood pressure, which corresponds to the phenotype of 50% of all human patients with essential hypertension, is observed in mice lacking the GC-A-receptor. Mice missing the GC-C receptor have been shown to be resistant to STa, an E. coli heat-stable enterotoxin, which is largely responsible for travellers ------------------- Key: 2847 Medline: 97400619 Authors: Kimura KD;Tissenbaum HA;Liu Y;Ruvkun G Title: daf-2, an insulin receptor-like gene that regulates longevity and diapause in Caenorhabditis elegans. Citation: Science 277: 942-946 1997 Type: ARTICLE Genes: age-1 daf-1 daf-2 daf-3 daf-4 daf-7 daf-8 daf-14 daf-16 Abstract: A C. elegans neurosecretory signaling system regulates whether animals enter the reproductive life cycle or arrest development at the long-lived dauer diapause stage. daf-2, a key gene in the genetic pathway that mediates this endocrine signaling, encodes an insulin receptor family member. Decreases in DAF-2 signaling induce metabolic and developmental changes, as in mammalian metabolic control by the insulin receptor. Decreased DAF-2 signaling also causes an increase in life-span. Life-span regulation by insulin-like metabolic control is analogous to mammalian longevity enhancement induced by caloric restriction, suggesting a general link between metabolism, diapause, and longevity. ------------------- Key: 2848 Medline: 97392700 Authors: Khan MLA;Gogonea CB;Siddiqui ZK;Ali MY;Kikuno R;Nishikawa K;Siddiqui SS Title: Molecular cloning and expression of the Caenorhabditis elegans klp-3, an ortholog of C terminus motor kinesins Kar3 and ncd. Citation: Journal of Molecular Biology 270: 627-639 1997 Type: ARTICLE Genes: eat-3 emb-21 emb-27 exp-1 him-14 klp-3 let-24 let-236 let-237 let-238 mel-1 mel-3 mel-8 mel-9 mel-10 mel-11 Abstract: Common to all eukaryotes, kinesins are cytoskeletal motor proteins that mediate intracellular transport on microtubule tracks, using ATP hydrolysis. A Caenorhabditis elegans cDNA clone corresponding to the klp-3 gene, encoding a novel kinesin, was isolated, and mapped on LGII. Northern blot analysis using the klp-3 cDNA probe reveals a 1.9 kb mRNA that is transcribed at a low level during development. Temporal and spatial expression of the klp-3::lacZ fusion gene is limited to the marginal cells in the pharynx, and a group of muscle cells in the posterior gut region. The nucleotide sequence of klp-3 has been deduced from the cDNA and nematode genome sequencing consortium data. Conceptual translation of the klp-3 gene reveals a kinesin-like protein with its conserved motor domain containing the ATP binding and microtubule binding sites located in the C terminus. KLP-3 shares extensive homology with the yeast Kar3 and Drosophila ncd kinesins, which have previously been shown to mediate chromosomal movement and segregation during meiosis and mitosis. Overexpression of the klp-3 gene partially rescues the lethal phenotype of the maternal lethal him-14 ts(it44) mutants at non-permissive temperatures, and reduces the incidence of males caused by non-disjunction of the X-chromosome. Similarly, expression of a klp-3 antisense RNA, under the control of a heat shock promoter, causes embryonic arrest, dead eggs and polyploid cells in transgenic Lines, suggesting a critical role for the klp-3 function in chromosome segregation. Further analysis of the klp-3 gene in C. elegans may elucidate diverse functions of ------------------- Key: 2849 Medline: 97388438 Authors: Elkes DA;Cardozo DL;Madison J;Kaplan JM Title: EGL-36 Shaw channels regulate C. elegans egg-laying muscle activity. Citation: Neuron 19: 165-174 1997 Type: ARTICLE Genes: egl-36 Abstract: The C. elegans egl-36 gene encodes a Shaw-type potassium channel that regulates egg-laying behavior. Gain of function [egl-36(gf)] and dominant negative [egl-36(dn)] mutations in egl-36 cause reciprocal defects in egg laying. An egl-36::gfp reporter is expressed in the egg-laying muscles and in a few other tissues. Expression of an egl-36(gf) cDNA in the egg-laying muscles causes behavioral defects similar to those observed in egl-36(gf) mutants. Gain of function EGL-36 subunits form channels that are active at more negative potentials than wild-type channels. The egl-36(gf) alleles correspond to missense mutations in an amino terminal subunit assembly domain (E138K) and in the S6 transmembrane domain (P435S), neither of which were previously implicated in the voltage dependence of channel activation. Altogether, these results suggest that EGL-36 channels regulate the excitability of the egg-laying muscles. ------------------- Key: 2850 Medline: 97388429 Authors: Baum PD;Garriga G Title: Neuronal migrations and axon fasciculation are disrupted in ina-1 integrin mutants. Citation: Neuron 19: 51-62 1997 Type: ARTICLE Genes: ina-1 pat-3 Abstract: Integrins are heterodimeric cell surface receptors implicated in cell adhesion and signaling. Our analysis of C. elegans ina-1 alpha integrin mutants provides the first genetic evidence that migrating neurons require integrins. Mosaic analysis and expression studies show that ina-1 acts autonomously in cells to promote their migrations. Although axons generally extend to their normal targets in ina-1 mutants, bundling of axons into fascicles is defective, defining a previously unrecognized role for integrins. In addition to these neuronal phenotypes, ina-1 mutants also display many morphogenetic defects. Finally, we show that the C. elegans INA-1 alpha integrin subunit associates with the PAT-3 beta subunit in vivo, suggesting that these proteins function together in cell migration, axon fasciculation, and morphogenesis. ------------------- Key: 2851 Medline: 97388437 Authors: Johnstone DB;Wei A;Butler A;Salkoff L;Thomas JH Title: Behavioral defects in C. elegans egl-36 mutants result from potassium channels shifted in voltage-dependence of activation. Citation: Neuron 19: 151-164 1997 Type: ARTICLE Genes: egl-36 shw-1 nDf19 Abstract: Mutations in the C. elegans egl-36 gene result in defective excitation of egg-laying and enteric muscles. Dominant gain-of-function alleles inhibit enteric and egg-laying muscle contraction, whereas a putative null mutation has no observed phenotype. egl-36 encodes a Shaw-type (Kv3) voltage-dependent potassium channel subunit. In Xenopus oocytes, wild-type egl-36 expresses noninactivating channels with slow activation kinetics. One gain-of-function mutation causes a single amino acid substitution in S6, and the other causes a substitution in the cytoplasmic amino terminal domain. Both mutant alleles produce channels dramatically shifted in their midpoints of activation toward hyperpolarized voltages. An egl-36::gfp fusion is expressed in egg-laying muscles and in a pair of enteric muscle motor neurons. The mutant egl-36 phenotypes can thus be explained by expression in these cells of potassium channels that are inappropriately opened at hyperpolarized potentials, causing decreased excitability due to increased potassium conductance. ------------------- Key: 2852 Medline: 97398150 Authors: Gilleard JS;Henderson DK;Ulla N Title: Conservation of the Caenorhabditis elegans cuticle collagen gene col-12 in Caenorhabditis briggsae. Citation: Gene 193: 181-186 1997 Type: ARTICLE Genes: col-12 col-13 Abstract: The functional importance of the majority of Caenorhabditis elegans cuticle collagen genes is unknown. We have identified, cloned and sequenced the Caenorhabditis briggsae homologue of the C. elegans gene col-12, a cuticle collagen for which no mutants have yet been identified. Homology in the flanking sequence has allowed us to unambiguously identify this gene as the col-12 homologue, as opposed to some other closely related member of this large multigene family. The whole of the predicted polypeptide is highly conserved (94.9% identical), including those regions not yet shown by mutational analysis to be important for C. elegans cuticle collagen function. These include the whole of the N-terminal non-Gly-X-Y domain and the X and Y positions of the Gly-X-Y domain. This may be a consequence of the requirement of cuticle collagens to participate in intermolecular interactions throughout the full length of the polypeptide. There is increasing evidence to suggest that conservation between C. elegans and C. briggsae is confined to functionally significant sequence. Hence, the conservation of col-12 between these two species provides evidence that this member of the cuticle collagen family has a ------------------- Key: 2853 Medline: 97368349 Authors: van Swinderen B;Shook DR;Ebert RH;Cherkasova VA;Johnson TE;Reis RJS;Crowder CM Title: Quantitative trait loci controlling halothane sensitivity in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 94: 8232-8237 1997 Type: ARTICLE Genes: Abstract: Genetic analysis is an essential tool for defining the molecular mechanisms whereby volatile anesthetics (VA) disrupt nervous system function. However, the degree of natural variation of the genetic determinants of VA sensitivity has not been determined nor have mutagenesis approaches been very successful at isolating significantly resistant mutant strains. Thus, a quantitative genetic approach was taken toward these goals. Recombinant-inbred strains derived from two evolutionarily distinct lineages of the nematode Caenorhabditis elegans were tested for sensitivity to clinically relevant concentrations (0.3-0.5 mM) of the VA halothane. The halothane sensitivities of coordinated movement and male mating behavior were highly variant among the recombinant-inbred strains with a range of EC50 values of 13- and 4-fold, respectively. Both traits were highly heritable (H-2 = 0.82, 0.87, respectively). Several strains were found to be significantly resistant to halothane when compared with the wild-type strain N2. A major locus or loci mapping to the middle of chromosome V accounted for more than 40% of the phenotypic variance for both traits. Five weaker loci, four of which interact, explained most of the remaining variance. None of the halothane-sensitivity quantitative trait loci significantly affected behavior in the absence of halothane or halothane's potency for C. elegans immobilization, which requires 5-fold higher drug concentrations. Thus, the quantitative trait loci are unlikely to result from differences in halothane-independent (native) behavior or differences in halothane metabolism or permeability. Rather, these loci mag code for targets and/or downstream effecters of halothane in the C. elegans nervous system or for modifiers of such gene products. ------------------- Key: 2854 Medline: Authors: Bird DM;Kaloshian I;Molinari S Title: Promoter structure of the RNA polymerase II large subunit gene in Caenorhabditis elegans and C. briggsae. Citation: Journal of Nematology 29: 144-152 1997 Type: ARTICLE Genes: ama-1 col-34 dpy-13 Abstract: The 5'-end of the Caenorhabditis elegans ama-1 gene transcript, which encodes the largest subunit of RNA polymerase II, was cloned. Sequencing revealed that the message is trans-spliced. To characterize the Ce-ama-1 promoter, DNA sequence spanning 3 kb upstream from the initiation codon was determined. Typical elements, such as TATA and Sp1 sites, were absent. The homologue of ama-1 in C. briggsae, Cb-ama-1, was isolated and its 5' flanking sequence compared with that of Ce-ama-1, revealing only limited similarity, although both sequences included a potential initiator-class transcriptional regulator and phased repeats of an AT(3)C motif. The latter elements are postulated to facilitate DNA bending and may play a role in transcription regulation. ------------------- Key: 2855 Medline: 97398133 Authors: Watanabe Y;Kita K;Ueda T;Watanabe K Title: cDNA sequence of a translational elongation factor Ts homologue from Caenorhabditis elegans: Mitochondrial factor-specific features found in the nematode homologue peptide. Citation: Biochimica et Biophysica Acta - Gene Structure & Expression 1353: 7-12 1997 Type: ARTICLE Genes: Abstract: The cDNA for a homologue of elongation factor Ts which probably functions in mitochondria has been sequenced from a nematode Caenorhabditis elegans. The deduced amino acid sequence (316 amino acids long) has a possible transit peptide sequence at the amino terminus and several common specific features for mammalian mitochondrial EF-Ts. The amino acid identities in the protein from C. elegans compared with those of bovine mitochondria and Eschericia coli are 29.5% and 24.0%, respectively. The C. elegans sequence was classified as a long EF-Ts (ca. 280 amino acids long) similar to peptides from mammalian mitochondria and eubacteria other than Thermus and cyanobacteria (except Spirulina platensis), rather than short EF-Ts (ca. 200 amino acids long) as those of Thermus, cyanobacteria and ------------------- Key: 2856 Medline: 97331842 Authors: Gbewonyo K;Rohrer SP;Buckland BC Title: Bioreactor cultivation of the nematode Caenorhabditis elegans - Large-scale production of biologically-active drug receptors for pharmaceutical research. Citation: Biotechnology & Genetic Engineering Reviews 14: 37-49 1997 Type: REVIEW Genes: Abstract: There is growing interest within the biotechnology community in the study of nematodes, particularly the free-living nematode Caenorhabditis elegans. The fascination of scientists with C. elegans for both basic and applied research is due to the convergence of a number of current trends in modern biology. The selection of the free-living nematode C. elegans as a model organism for elucidating the genetics and developmental biology of multicellular organisms has led to an explosion in biochemical knowledge about C. elegans. The hallmarks of the concerted research efforts on C. elegans over the last 3 decades are summarized in Table 1. ------------------- Key: 2857 Medline: Authors: Cressman CP;Williams PL Title: Reference toxicants for toxicity testing using Caenorhabditis elegans in aquatic media. Citation: "Environmental Toxicology and Risk Assessment: Modeling and Risk Assessment.", Dwyer FJ, TR Doane and ML Hinman, Eds., American Society for Testing and Materials, Standard Technical Publication 1317. 6: 518-532 1997 Type: ARTICLE Genes: sup-7 unc-54 Abstract: Caenorhabditis elegans aquatic toxicity assays were standardized with five common reference toxicants: CdCl2, NaCl, KCl, sodium lauryl sulfate (SLS), and sodium pentachlorophenate (PCP). Aquatic toxicity testing was conducted in 3 media: a standard C. elegans medium; EPA moderately hard reconstituted water; and EPA moderately hard mineral water. Test duration in each medium was 24h without a food source, and 24h and 48h with Escherichia coli strain OP50 as a food source. Each test was replicated three times with each replicate having 6 wells per concentration, 10 worms per well. LC50 values were calculated using probit analysis. The average LC50s for each set of replicants were compared to assess sensitivity and reproducibility of the data, identifying expected variation between replicate tests. These reference toxicants increase the database for C. elegans and provide ------------------- Key: 2858 Medline: 99385004 Authors: Colbert HA;Bargmann CI Title: Environmental signals modulate olfactory acuity, discrimination, and memory in Caenorhabditis elegans. Citation: Learning & Memory 4: 179-191 1997 Type: ARTICLE Genes: adp-1 Abstract: Caenorhabditis elegans uses a variety of attractive olfactory cues to detect food. We show here that the responses to olfactory cues are regulated in a dynamic way by behavioral context and the animal's previous experience. Prolonged exposure to an odorant leads to a decreased response to that odorant, a form of behavioral plasticity called olfactory adaptation. We show that starvation can increase the extent of olfactory adaptation to the odorant benzaldehyde; this effect of starvation persists for several hours after the animals have been returned to food. The effect of starvation is antagonized by exogenous serotonin, which induces many of the same behavioral responses in C. elegans as are induced by food. Starvation also inhibits recovery from adaptation to a different odorant, 2-methylpyrazine, thus enhancing olfactory memory. In addition to its effects on adaptation, starvation modulates olfactory discrimination in C. elegans; starved animals discriminate more classes of odorants than fed animals. Increased olfactory discrimination is also seen in the adaptation-defective mutant adp-1(ky20). These various forms of behavioral plasticity enhance the ability of starved animals to respond to novel, potentially informative odorants. ------------------- Key: 2859 Medline: 97370024 Authors: Chissoe SL;Marra MA;Hillier L;Brinkman R;Wilson RK;Waterston RH Title: Representation of cloned genomic sequences in two sequencing vectors: Correlation of DNA sequence and subclone distribution. Citation: Nucleic Acids Research 25: 2960-2966 1997 Type: ARTICLE Genes: Abstract: Representation of subcloned Caenorhabditis elegans and human DNA sequences in both M13 and pUC sequencing vectors was determined in the context of large scale genomic sequencing. In many cases, regions of subclone under-representation correlated with the occurrence of repeat sequences, and in some cases the under-representation was orientation specific, Factors which affected subclone representation included the nature and complexity of the repeat sequence, as well as the length of the repeat region, in some but not ail cases, notable differences between the M13 and pUC subclone distributions existed. However, in all regions lacking one type of subclone (either M13 or pUC), an alternate subclone was identified in at least one orientation. This suggests that complementary use of M13 and pUC subclones would provide the most comprehensive subclone coverage of a given ------------------- Key: 2860 Medline: 97368239 Authors: Fleming JT;Squire MD;Barnes TM;Tornoe C;Matsuda K;Ahnn J;Fire A;Sulston JE;Barnard EA;Sattelle DB;Lewis JA Title: Caenorhabditis elegans levamisole resistance genes lev-1, unc-29, and unc-38 encode functional nicotinic acetylcholine receptor subunits. Citation: Journal of Neuroscience 17: 5843-5857 1997 Type: ARTICLE Genes: Abstract: We show that three of the eleven genes of the nematode Caenorhabditis elegans that mediate resistance to the nematocide levamisole and to other cholinergic agonists encode nicotinic acetylcholine receptor (nAChR) subunits. unc-38 encodes an alpha subunit while lev-1 and unc-29 encode non-alpha subunits. The nematode nAChR subunits show conservation of many mammalian nAChR sequence features, implying an ancient evolutionary origin of nAChR proteins. Expression in Xenopus oocytes of combinations of these subunits that include the unc-38 alpha subunit results in levamisole-induced currents that are suppressed by the nAChR antagonists mecamylamine, neosurugatoxin, and d-tubocurarine but not alpha-bungarotoxin. The mutant phenotypes reveal that unc-38 and unc-29 subunits are necessary for nAChR function, whereas the lev-1 subunit is not. An UNC-29-GFP fusion shows that UNC-29 is expressed in body and head muscles. Two dominant mutations of lev-1 result in a single amino acid substitution or addition in or near transmembrane domain 2, a, region important to ion channel conductance and desensitization. The identification of viable nAChR mutants in C. elegans provides an advantageous system in which receptor expression and synaptic targeting can be manipulated and studied in vivo. ------------------- Key: 2861 Medline: 97410303 Authors: Vaux DL Title: CED-4 - The third horseman of apoptosis. Citation: Cell 90: 389-390 1997 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: The remarkable conservation of physiological cell death mechanisms from nematodes to humans has allowed the genetic pathways of programmed cell death determined in Caenorhabditis elegans to act as a framework for understanding the biology of apoptosis in mammalian cells. However, it has been unclear whether the C. elegans cell death gene ced-4 would have a parallel in mammalian cell death. In this issue of Cell, Zou et al. (1997) report the biochemical identification of a human cell death protein whose sequence resembles the nematode protein CED-4, providing a spectacular demonstration of the combined power of genetic analysis of a simple organism with biochemistry of mammalian cells. ------------------- Key: 2862 Medline: 97411154 Authors: Bohm H;Brinkmann V;Drab M;Henske A;Kurzchalia TV Title: Mammalian homologues of C. elegans PAR-1 are asymmetrically localized in epithelial cells and may influence their polarity. Citation: Current Biology 7: 603-606 1997 Type: ARTICLE Genes: par-1 par-3 Abstract: The establishment of polarity in the embryo is fundamental for the correct development of am organism [1]. The first cleavage of the Caenorhabditis elegans embryo is asymmetric with certain cytoplasmic components being distributed unequally between the daughter cells [2-4]. Using a genetic screen, Kemphues and co-workers have identified six par genes (partition-defective) [5,6], which are involved in the process of asymmetric division. One of these genes encodes a highly conserved protein, PAR-1, which is a serine/threonine kinase that localizes asymmetrically to the posterior part of the zygote and to those blastocysts that give rise to the germ line [7-9]. We reasoned that the mammalian homologue of PAR-1 (mPAR-1) might be involved in the process of polarization of epithelial cells, which consist of apical and basolateral membrane domains. We found that mPAR-1 was expressed in a wide variety of epithelial tissues and cell lines and was associated with the cellular cortex. In polarized epithelial cells, mPAR-1 was asymmetrically localized to the lateral domain. A fusion protein lacking the kinase domain had the same localization as the full-length protein but its prolonged expression acted in a dominant-negative fashion: lateral adhesion of the transfected cells to neighbouring cells was diminished, resulting in the former cells being 'squeezed out' from the monoIayer. Moreover, the polarity of these cells was disturbed resulting in mislocalization of E cadherin. Thus, in the C. elegans embryo and in epithelial cells, polarity appears to be governed by similar ------------------- Key: 2863 Medline: 97422869 Authors: Agulnik SI;Ruvinsky I;Silver LM Title: Three novel T-box genes in Caenorhabditis elegans. Citation: Genome 40: 458-464 1997 Type: ARTICLE Genes: tbx-2 tbx-7 tbx-8 tbx-9 tbx-11 tbx-12 tbx-17 Abstract: The T-box gene family consists of members that share a unique DNA binding domain. The best characterized T-box gene, Brachyury or T, encodes a transcription factor that plays an important role in early vertebrate development. Seven other recently described mouse T-box genes are also expressed during development. In the nematode Caenorhabditis elegans, four T-box genes have been characterized to date. In this study, we describe three new C. elegans T-box genes, named Ce-tbx-II, Ce-tbx-12, and Ce-tbx-17. Ce-tbx-Il and Ce-tbx-17 were uncovered through the sequencing efforts of the C. elegans Genome Project. Ce-tbx-12 was uncovered through degenerate PCR analysis of C. elegans genomic DNA. Ce-tbx-11 and Ce-tbx-17 are located in close proximity to the four other previously described T-box genes in the central region of chromosome m. In contrast, Ce-tbx-12 maps alone to chromosome II. Phylogenetic analysis of all known T-box domain sequences provides evidence of an ancient origin for this gene ------------------- Key: 2864 Medline: 97417487 Authors: Park J-H;Ohshima S;Tani T;Ohshima Y Title: Structure and expression of the gsa-1 gene encoding a G protein alpha(s) subunit in C. elegans. Citation: Gene 194: 183-190 1997 Type: ARTICLE Genes: gsa-1 Abstract: The heterotrimeric guanine nucleotide-binding proteins (G proteins) act as switches in the signal transduction from cell surface receptors to a variety of effecters. Among them, Gs proteins stimulate adenylate cyclase activities and regulate ion channels in mammals. We identified the gsa-1 gene encoding a G protein alpha subunit in the nematode Caenorhabditis elegans. The predicted product conisists of 375 amino acid residues, 66% of which are identical with those of a mammalian Gs(alpha) subunit. The gsa-1 gene was physically mapped near the left end of chromosome I. A gsa-1/lacZ fusion gene was expressed in many cells in embryos, larvae and adults, including neurons, body wall muscle cells and muscle cells of the pharynx and the vulva. The results presents a basis for genetic studies of the gsa-1 gene. ------------------- Key: 2865 Medline: 97425419 Authors: Wellerdieck C;Oles M;Pott L;Korsching S;Gisselmann G;Hatt H Title: Functional expression of odorant receptors of the zebrafish Danio rerio and of the nematode C. elegans in HEK293 cells. Citation: Chemical Senses 22: 467-476 1997 Type: ARTICLE Genes: odr-10 Abstract: Odorant receptors of zebrafish and C. elegans were functionally expressed in vertebrate kidney cells (HEK293) using the eucaryotic expression vector pSMyc. Receptor-encoding cDNA cloned into this vector was expressed as a fusion protein with the N-terminal membrane import sequence of the guinea-pig serotonin receptor followed by a myc tag. Immunocytochemical evidence indicates that this strategy directs a protein with the predicted immunoreactivity and approximate molecular weight to the plasma membrane. Fish food extract (TetraMin) evoked a transient increase in intracellular [Ca2+] in HEK293 cells transiently transfected with plasmids containing cDNA for three fish odorant receptors and converted to stable cell lines. The effect of the extract was concentration dependent and limited to the fraction of the extract <5 kDa. Pretreating the transfected cells with the PLC inhibitor U73122 reduced the odor-evoked signal. Fish food extract also evoked a transient increase in intracellular [Ca2+] in HEK293 cells transiently transfected with plasmids containing cDNA for single fish odorant receptors. Diacetyl evoked a transient increase in intracellular [Ca2+] in HEK293 cells transiently transfected with plasmids encoding the cDNA of ODR10, an odorant receptor of C. elegans suggested in other work to be specific for diacetyl. These results strongly imply that odorant receptors can be functionally expressed in HEK293 cells using this novel expression protocol. ------------------- Key: 2866 Medline: Authors: Roberts TM;Stewart M Title: Nematode sperm: Ameboid movement without actin. Citation: Trends in Cell Biology 7: 368-373 1997 Type: REVIEW Genes: Abstract: Nematodes produce amoeboid sperm that crawl over surfaces in a manner reminiscent of many actin-rich cells. However, These sperm contain no F-actin, and their motility is powered by a dynamic filament system composed of polymers of the 14-kDa major sperm protein (MSP). These simple cells use this unique motility apparatus exclusively for locomotion. Recent studies have capitalized on this feature to explore the key structural properties of MSP related to its role in motility and to reconstitute the motility apparatus both in vivo and in vitro. This review discusses how these investigations have laid the foundation for understanding the physical basis of amoeboid movement by identifying the mechanistic properties shared by the MSP-based machinery and the more familiar actin-based ------------------- Key: 2867 Medline: 97461074 Authors: Hengartner MO Title: Genetic control of programmed cell death and aging in the nematode Caenorhabditis elegans. Citation: Experimental Gerontology 32: 363-374 1997 Type: REVIEW Genes: age-1 ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-9 ced-10 clk-1 clk-2 clk-3 dad-1 daf-2 daf-12 daf-16 daf-18 daf-23 gro-1 nuc-1 spe-26 Abstract: The nematode Caenorhabditis elegans has been used extensively as a model system for the study of basic biological processes. In this species, apoptosis and aging are both under genetic control. Molecular studies have shown that the death machinery that kills C. elegans cells has remained conserved through evolution and also functions to promote apoptotic death in mammalian cells. At least some of the genes that affect C. elegans life span are also evolutionarily conserved; whether the vertebrate homologs of these genes also influence life span remains to be determined. Although a large number of mutations have been isolated that affect either apoptosis or aging in C. elegans, there is so far no evidence that the genetic pathways that control these processes might overlap. ------------------- Key: 2868 Medline: 97432712 Authors: Labouesse M Title: Deficiency screen based on the monoclonal antibody MH27 to identify genetic loci required for morphogenesis of the Caenorhabditis elegans embryo. Citation: Developmental Dynamics 210: 19-32 1997 Type: ARTICLE Genes: lin-26 ccDf1 ctDf1 ctDf2 ctDf3 eDf3 eDf4 eDf18 eDf19 eDf24 hDf6 hDf8 hDf9 hDf10 hDf15 hDf16 hDf17 itDf2 mDf4 mDf5 mDf7 maDf4 mcDf1 meDf6 mnDf1 mnDf2 mnDf20 mnDf29 mnDf30 mnDf41 mnDf57 mnDf59 mnDf61 mnDf67 mnDf68 mnDf83 mnDf87 mnDf88 mnDf89 mnDf90 mnDf100 mnDf104 mnDf106 mnDf111 nDf3 nDf11 nDf16 nDf19 nDf20 nDf25 nDf27 nDf40 nDf41 nDf42 ozDf2 ozDf5 qDf3 qDf4 qDf5 qDf7 qDf8 qDf9 qDf10 qDf16 sDf2 sDf4 sDf6 sDf20 sDf23 sDf27 sDf30 sDf33 sDf34 sDf35 sDf40 sDf45 sDf50 sDf60 sDf72 sDf74 sDf75 sDf110 sDf121 sDf124 stDf5 stDf7 syDf1 tDf3 uDf1 yDf6 yDf8 yDf12 Abstract: The monoclonal antibody MH27 recognizes an adherens junction protein present around hypodermal cells in the pharynx and the intestine. By using this antibody and an antiserum against the LIN-26 protein, which is present in hypodermal and glial-like cells, I have examined the morphogenesis of the embryo in embryos homozygous for 91 chromosomal deficiencies that cover approximately 74% of the Caenorhabditis elegans genome. Most deficiencies were found to affect both the morphogenesis of the embryo and the organogenesis of the pharynx. By contrast, the intestine was generally normal. I have classified deficiencies according to their hypodermal staining abnormalities. I identified a few deficiencies that appeared to affect more specifically anterior-directed migration of hypodermal cells or extension of the margins of ventral hypodermal cells, integrity of hypodermal membranes, elongation of the embryo, and hypodermal cell fusions. This work opens the way for a genetic analysis of ------------------- Key: 2869 Medline: 97433068 Authors: Han M Title: Gut reaction to Wnt signaling in worms. Citation: Cell 90: 581-584 1997 Type: REVIEW Genes: apr-1 apx-1 glp-1 lin-17 lin-44 mom-1 mom-2 mom-3 mom-4 mom-5 pop-1 wrm-1 Abstract: The demonstrations in two papers in this issue of Cell (Rocheleau et al., 1997; Thorpe et al., 1997) of the involvement of a Wnt pathway in very early embryogenesis in Caenorhabditis elegans provides another significant step toward the ambitious but realistic goal of understanding all the basic strategies used to control embryogenesis in this model organism. At the same time, they challenge some of the prevailing models of Wnt signaling, suggesting that interactions among Wnt pathway components may vary in different developmental processes. With these papers, as well as the earlier reports on Wnt pathway genes lin-44, lin-17, and pop-1 (Herman et al., 1995; Lin et al., 1995; Harris et al., 1996; Sawa et al., 1996) and new studies on Wnt pahtway genes reported in recent meetings, worm breeders have become a significant force in the army of Wnt researchers. They have also illustrated how different systems can provide important new complementary insights. ------------------- Key: 2870 Medline: 97433080 Authors: Thorpe CJ;Schlesinger A;Carter JC;Bowerman B Title: Wnt signaling polarizes an early C. elegans blastomere to distinguish endoderm from mesoderm. Citation: Cell 90: 695-705 1997 Type: ARTICLE Genes: mom-1 mom-2 mom-3 mom-4 mom-5 pie-1 pop-1 pos-1 skn-1 Abstract: A polarizing signal induces endoderm production by a 4-cell stage blastomere in C. elegans called EMS. We identified 16 mutations in five genes, mom-1 through mom-5, required for EMS to produce endoderm. mom-1, mom-2, and mom-3 are required in the signaling cell, P-2, while mom-4 is required in EMS. P-2 signaling downregulates an HMG domain protein, POP-1, in one EMS daughter. The sequence of mom-2 predicts that it encodes a member of the Wnt family of secreted glycoproteins, which in other systems activate HMG domain proteins. Defective mitotic spindle orientations in mom mutant embryos indicate that Wnt signaling influences cytoskeletal polarity in blastomeres throughout the early embryo. ------------------- Key: 2871 Medline: 97433081 Authors: Rocheleau CE;Downs WD;Lin R;Wittmann C;Bei Y;Cha Y-H;Ali M;Priess JR;Mello CC Title: Wnt signaling and an APC-related gene specify endoderm in early C. elegans embryos. Citation: Cell 90: 707-716 1997 Type: ARTICLE Genes: apr-1 hmp-2 mom-1 mom-2 mom-5 pop-1 skn-1 wrm-1 mDf3 mnDf111 nDf9 nDf24 qDf6 sDf53 Abstract: In a 4-cell stage C. elegans embryo, signaling by the P-2 blastomere induces anterior-posterior polarity in the adjacent EMS blastomere, leading to endoderm formation. We have taken genetic and reverse genetic approaches toward understanding the molecular basis for this induction. These studies have identified a set of genes with sequence similarity to genes that have been shown to be, or are implicated in, Wnt/Wingless signaling pathways in other systems. The C. elegans genes described here are related to wnt/wingless,porcupine, frizzled, beta-catenin/armadillo, and the human adenomatous polyposis coil gene, APC. We present evidence that there may be partially redundant inputs into endoderm specification and that a subset of these genes appear also to function in determining cytoskeletal polarity in certain early blastomeres. ------------------- Key: 2872 Medline: 97407937 Authors: Wu DY;Wallen HD;Inohara N;Nunez G Title: Interaction and regulation of the Caenorhabditis elegans death protease CED-3 by CED-4 and CED-9. Citation: Journal of Biological Chemistry 272: 21449-21454 1997 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: In the nematode Caenorhabditis elegans, three genes, ced-3, ced-4, and ced-9, play critical roles in the induction and execution of the death pathway. Genetic studies have suggested that ced-9 controls programmed cell death by regulating ced-4 and ced-3. However, the mechanism by which CED-9 controls the activities of CED-4 and the cysteine protease CED-3, the effector arm of the cell-death pathway, remains poorly understood. Immunoprecipitation analysis demonstrates that CED-9 forms a multimeric protein complex with CED-4, and CED-3 in vivo. Expression of wild-type CED-4 promotes the ability of CED-3 to induce apoptosis in mammalian cells, which is inhibited by CED-9. The pro-apoptotic activity of CED-4 requires the expression of a functional CED-3 protease. Significantly, loss-of-function CED-4 mutants are impaired in their ability to promote CED-3-mediated apoptosis. Expression of CED-4 enhances the proteolytic activation of CED-3. We also show that CED-9 inhibits the formation of p13 and p15, two cleavage products of CED-3 associated with its proteolytic activation in vivo. Moreover, CED-9 inhibits the enzymatic activity of CED-3 promoted by CED-4. Thus, these results provide evidence that CED-4 and CED-9 regulate the activity of CED-3 through physical interactions, which may provide a molecular basis for the control of programmed cell death in ------------------- Key: 2873 Medline: 97454305 Authors: Maurer P;Sasaki T;Mann K;Gohring W;Schwarzbauer JE;Timpl R Title: Structural and functional characterization of the extracellular calcium-binding protein BM-40/secreted protein, acidic, rich in cysteine/osteonectin from the nematode C. elegans. Citation: European Journal of Biochemistry 248: 209-216 1997 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans BM-40 (positions 19-264) and its extracellular calcium-binding domain (positions 139-264) were obtained in recombinant form from human kidney cells using an episomal expression vector. The purified proteins showed single bands of 33 kDa [BM-40-(19-264)-peptide] or 14 kDa [BM-40-(139-264)-peptide] on electrophoresis, contained internal disulfide bonds and alpha helices and were relatively resistant to matrix metalloproteinases. Hexosamine analysis indicated substitution by one N-linked and two O-linked oligosaccharides and recombinant BM-40 was indistinguishable in its immunological epitopes from nematode tissue-derived BM-40, suggesting that it was obtained in native form. Both recombinant C. elegans proteins showed a distinct binding activity for human collagens I and IV in solid-phase and surface-plasmon-resonance assays with an affinity (K-d = 1-2 mu M), comparable to that of mammalian BM-40. However, calcium-binding studies revealed only a low-affinity site (K-d = 6.2 mM) and failed to show the characteristic conformational change upon addition of EDTA. These and a few other differences are apparently due to two extra disulfide bonds and two deletions/insertions in C. elegans BM-40 and can be partly interpreted from the X-ray structure of a large part of human BM-40. The immunological assays available and the predictions of the location of the collagen-binding epitope should facilitate a molecular and genetic approach to understand the function of BM-40 in the development of C. elegans. ------------------- Key: 2874 Medline: 97420754 Authors: Evans D;Zorio D;MacMorris M;Winter CE;Lea K;Blumenthal T Title: Operons and SL2 trans-splicing exist in nematodes outside the genus Caenorhabditis. Citation: Proceedings of the National Academy of Sciences USA 94: 9751-9756 1997 Type: ARTICLE Genes: rpl-29 rrp-1 Abstract: The genomes of most eukaryotes are composed of genes arranged on the chromosomes without regard to function, with each gene transcribed from a promoter at its 5' end. However, the genome of the free-living nematode Caenorhabditis elegans contains numerous polycistronic clusters similar to bacterial operons in which the genes are transcribed sequentially from a single promoter at the 5' end of the cluster. The resulting polycistronic pre-mRNAs are processed into monocistronic mRNAs by conventional 3' end formation, cleavage, and polyadenylation, accompanied by trans-splicing with a specialized spliced leader (SL), SL2. To determine whether this mode of gene organization and expression, apparently unique among the animals, occurs in other species, we have investigated genes in a distantly related free-living rhabditid nematode in the genus Dolichorhabditis (strain CEW1). We have identified both SL1 and SL2 RNAs in this species. In addition, we have sequenced a Dolichorhabditis genomic region containing a gene cluster with all of the characteristics of the C. elegans operons. We show that the downstream gene is trans-spliced to SL2. We also present evidence that suggests that these two genes are also clustered in the C. elegans and Caenorhabditis briggsae genomes. Thus, it appears that the arrangement of genes in operons pre-dates the divergence of the genus Caenorhabditis from the other genera in the family ------------------- Key: 2875 Medline: 97420760 Authors: Morrison M;Harris KS;Roth MB Title: smg mutants affect the expression of alternatively spliced SR protein mRNAs in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 94: 9782-9785 1997 Type: ARTICLE Genes: emb-14 smg-1 smg-2 smg-3 smg-4 smg-5 smg-6 Abstract: The expression of alternatively spliced mRNAs from genes is an ubiquitous phenomenon in metazoa. A screen for trans-acting factors that alter the expression of alternatively spliced mRNAs reveals that the smg genes of Caenorhabditis elegans participate in this process. smg genes have been proposed to function in degradation of nonsense mutant mRNAs. Here we show that smg genes affect normal gene expression by modulating the levels of alternatively spliced SRp20 and SRp30b mRNAs. These SR genes contain alternatively spliced exons that introduce upstream stop codons. The effect of smg genes on SR transcripts is specific, because the gene encoding the catalytic subunit of the cAMP-dependent protein kinase, which also contains an alternatively spliced exon that introduces upstream stop codon, is not effected in a smg background. These results suggest that the levels of alternatively spliced mRNAs may, in part, be regulated by ------------------- Key: 2876 Medline: 97436751 Authors: Hobert O;Mori I;Yamashita Y;Honda H;Ohshima Y;Liu Y;Ruvkun Title: Regulation of interneuron function in the C. elegans thermoregulatory pathway by the ttx-3 LIM homeobox gene. Citation: Neuron 19: 345-357 1997 Type: ARTICLE Genes: daf-7 sra-11 tax-4 ttx-3 unc-86 maDf1 nDf19 Abstract: Neural pathways, which couple temperature-sensing neurons to motor and autonomic outputs, allow animals to navigate away from and adjust metabolism rates in response to the temperature extremes often encountered. ttx-3 is required for the specification of the AIY interneuron in the C. elegans neural pathway that mediates thermoregulation. ttx-3 null mutant animals exhibit the same thermotactic behavioral defect as that seen with laser ablation of AIY in wild type, suggesting that AIY does not signal in this mutant. ttx-3 encodes a LIM homeodomain protein. A ttx-3-GFP fusion gene is expressed specifically in the adult AIY interneuron pair, which connects to thermosensory neurons. In ttx-3 mutant animals, the AIY interneuron is generated but exhibits patterns of abnormal axonal outgrowth. Thus, the TTX-3 LIM homeodomain protein is likely to regulate the expression of target genes required late in AIY differentiation for the function of this interneuron in the thermoregulatory pathway. The ttx-3-dependent thermosensory pathway also couples to the temperature-modulated dauer neuroendocrine signaling pathway, showing that ttx-3 specifies AIY thermosensory information processing of both motor and autonomic outputs. ------------------- Key: 2877 Medline: Authors: Schnabel R Title: Why does a nematode have an invariant cell lineage? Citation: Seminars in Cell & Developmental Biology 8: 341-349 1997 Type: REVIEW Genes: glp-1 mex-1 pha-1 pie-1 Abstract: C. elegans is renowned for its invariant embryogenesis and functions as a major paradigm for a mode of development coupled to an invariant lineage. Recent work, however, suggests that the embryogenesis of the nematode is much more flexible than anticipated. The invariant premorphogenetic stage is formed from variable earlier stages through a sorting of cells. Cells do not act as individuals but already early in embryogenesis a regionalization of the embryo occurs. Cells are diversified by a binary specification of 'abstract' blastomere (regional) identities. The determination of tissues may thus be a very late event. It appears that C. elegans, although assigning cell fates in an invariant lineage pattern, uses the same strategies and mechanisms for embryogenesis as organisms with variable lineages. ------------------- Key: 2878 Medline: 97442351 Authors: Zipkin ID;Kindt RM;Kenyon CJ Title: Role of a new Rho family member in cell migration and axon guidance in C. elegans. Citation: Cell 90: 883-894 1997 Type: ARTICLE Genes: mig-2 unc-73 Abstract: Rho family GTPases are thought to regulate actin-dependent processes, but their functions in vivo are still poorly understood. We have investigated the function of a new, widely expressed Rho family member in C. elegans by analyzing mutations in the endogenous gene. Activated and null alleles all inhibit cell migration, demonstrating that this protein is required for cell migration in vivo. Only a small subset of the migrations inhibited by activating mutations are inhibited by null mutations, suggesting that considerable functional redundancy exists within this system. Our findings support this conclusion and show that mig-2 functions redundantly with another pathway to regulate nuclear migration. Surprisingly, activated alleles also cause misguided axon growth, suggesting that Rho family GTPases may couple guidance cues to process ------------------- Key: 2879 Medline: 98049909 Authors: Wolstenholme AJ Title: Glutamate-gated Cl- channels in Caenorhabditis elegans and parasitic nematodes. Citation: Biochemical Society Transactions 25: 830-834 1997 Type: ARTICLE Genes: avr-15 Abstract: Excitatory ionotropic and metabotropic glutamate receptors are found throughout the animal kingdom, but inhibitory ionotropic glutamate receptors seem to be confined to invertebrates. Molecular studies on all invertebrate receptors have lagged far behind those of their mammalian counterparts, but recently interest in the glutamate-gated Cl- channels (Glu-Cl) has been greatly stimulated by the discovery that, at least in Caenorhabditis elegans, these molecules act as the receptor for, and probable site of action of, the avermectins, a family of potent anthelminthics, insecticides and acaricides. ------------------- Key: 2880 Medline: 97434225 Authors: Jansen G;Hazendonk E;Thijssen KL;Plasterk RHA Title: Reverse genetics by chemical mutagenesis in Caenorhabditis elegans. Citation: Nature Genetics 17: 119-121 1997 Type: ARTICLE Genes: gpa-4 gpa-6 gpa-7 gpa-8 gpa-10 gpa-11 gpa-14 gpa-15 gpb-2 prk-2 Abstract: Traditional reverse genetics on yeast, mice and other organisms a uses homologous recombination with transgenic DNA to interrupt a target gene. Here we report that target-selected gene inactivation can be achieved in Caenorhabditis elegans with the use of chemical mutagens, We use PCR to selectively visualize deletions in genes of interest; the method is sensitive enough to permit detection of a single mutant among more than 15,000 wild types. A permanent frozen mutant collection of more than a million mutagenized animals has been established, and deletion mutants of several G-protein genes were isolated from it. The approach is suitable to be scaled up for systematic inactivation of all 17,000 C. elegans genes. Because it requires no transgenesis or cell culturing, it may also be applicable to small organisms usually considered to be outside the realm of reverse genetics (for example, other nematodes and insects), Any sequenced gene in any organism that can be handled in Very large numbers can possibly be targeted in this way. ------------------- Key: 2881 Medline: 96137292 Authors: Plasterk RHA Title: The Tc1/Mariner transposon family. Citation: Current Topics in Microbiology and Immunology 204: 125-143 1996 Type: REVIEW Genes: mut-2 mut-4 mut-5 mut-6 Abstract: In many animals the main cause of mutations is transposon insertion. This is true, e.g., for strains of the nematode species C. elegans. It is not true for humans, where only relatively few cases have been reported of germline mutations caused by new transposon insertions, and where base-pair substitutions, frameshifts and errors in replication of nucleotide repeats are more common. Caenorhabditis elegans is a free-living nematode that can be found in the soil anywhere in the world. All C. elegans strains analyzed to date contain several copies of the transposable element Tc1. Insertion of Tc1 is the main cause of gene inactivation in the strain Bergerac. Since discovery of the Tc1 element, related elements have been found in the same species, and elements discovered in other species were also found to be homologous to Tc1.... ------------------- Key: 2882 Medline: Authors: Peter ME;Medema JP;Krammer PH Title: Does the Caenorhabditis elegans protein CED-4 contain a region of homology to the mammalian death effector domain? Citation: Cell Death and Differentiation 4: 523-525 1997 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: The elucidatin of the apoptosis pathway in the nematode C. elegans has been helpful to understand apoptosis signaling pathways in higher eukaryotes. In the worm three genes ced-3, -4 and -9 are involved in regulating the execution of apoptosis during development. Ced-3 codes for a protease homologous to the caspase family. CED-3 activity is negatively regulated by CED-9 which is homologous both structurally and functionally to Bcl-2 and other Bcl-2 family members such as Bcl-xL. To exert its function CED-9 requires the presence of CED-4, another apoptosis promoting factor.... ------------------- Key: 2883 Medline: 97446281 Authors: Baldwin JG;Frisse LM;Vida JT;Eddleman CD;Thomas WK Title: An evolutionary framework for the study of developmental evolution in a set of nematodes related to Caenorhabditis elegans. Citation: Molecular Phylogenetics and Evolution 8: 249-259 1997 Type: ARTICLE Genes: Abstract: Nematodes are known to be a useful system for studies of comparative development. Here we perform a molecular phylogenetic analysis to allow for the independent interpretation of the developmental and morphological changes observed among a selected set of nematode species. Our molecular phylogenetic analysis is based on coding regions of the genes for RNA polymerase II, the small subunit rRNA and an expansion segment of the large subunit rRNA. Sequences were compared from five species in the family (Rhabditidae) that includes the developmental model organism Caenorhabditis elegans and from an outgroup taxon Aduncospiculum halicti (Diplogasterina). The phylogenetic analysis does not support the monophyly of the subfamily Mesorhabditinae and identifies the unnamed strain PS1010 as a sister taxon of C. elegans despite its morphologically divergent buccal capsule. On the basis of the inferred framework, we can begin to interpret the evolution of vulval development and of morphological differences among these nematode species. ------------------- Key: 2884 Medline: 97453231 Authors: Henderson ST;Gao D;Christensen S;Kimble J Title: Functional domains of LAG-2, a putative signaling ligand for LIN-12 and GLP-1 receptors in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 8: 1751-1762 1997 Type: ARTICLE Genes: apx-1 glp-1 lag-2 lin-12 smg-1 Abstract: The LAG-2 membrane protein is a putative signaling ligand for the LIN-12 and GLP-1 receptors of Caenorhabditis elegans. LAG-2, like its Drosophila homologues Delta and Serrate, acts in a conserved signal transduction pathway to regulate cell fates during development. In this article, we investigate the functional domains of LAG-2. For the most part, mutants were constructed in vitro and assayed for activity in transgenic animals. We find a functional role for all major regions except one. Within the extracellular domain, the N-terminal region, which bears no known motif, and the DSL domain are both required. By contrast, the region bearing epidermal growth factor-like repeats can be deleted with no apparent reduction in rescuing activity. The intracellular region is not required for activity but instead plays a role in down-regulating LAG-2 function. Finally, membrane association is critical for mutant ------------------- Key: 2885 Medline: Authors: Traunspurger W;Bergtold M;Goedkoop W Title: The effects of nematodes on bacterial activity and abundance in a freshwater sediment. Citation: Oecologia 112: 118-122 1997 Type: ARTICLE Genes: Abstract: The effects of natural nematode communities on bacterial activity and abundance were investigated in a microcosm study. Nematodes were added at different densities to a freshwater sediment and bacterial parameters were measured after 1, 5, 9, and 17 days. Significant effects of nematode density on bacterial activity were noted on day 5. No long-term changes in bacterial activity were recorded. Bacterial abundance displayed an overall decrease in both treatments and controls. In a second experiment, the effect of nematode feeding-type on bacterial activity was studied. Microcosms were incubated with 100 individuals of a fungus-feeding (Aphelenchus avenae) or a bacteria-feeding nematode species (Caenorhabditis elegans) respectively, and bacterial activity was determined after 0, 1, 2, 4, and 7 days. Significant time and feeding-type effects were found, with consistently higher bacterial activity estimates in treatments with bacteria-feeding nematodes. These results suggest that grazing affects bacterial activity, and indicate that grazing by nematodes may be more important in stimulating bacterial activity than bioturbation or excretion. Combining these results, we conclude that natural nematode communities may have an impact on bacterial activity, and that the magnitude of this impact depends on the proportion of actively feeding bactivores within the community. ------------------- Key: 2886 Medline: Authors: Hoss S;Haitzer M;Traunspurger W;Gratzer H;Ahlf W;Steinberg Title: Influence of particle size distribution and content of organic matter on the toxicity of copper in sediment bioassays using Caenorhabditis elegans (Nematoda). Citation: Water, Air & Soil Pollution 99: 689-695 1997 Type: ARTICLE Genes: Abstract: The influence of particle size distribution and organic matter on the toxicity of copper was investigated using the nematode Caenorhabditis elegans as testorganism. Sediments taken at various depths from three lakes of different trophic status and artificial sediments were spiked with sublethal concentrations of CuSO4. After an exposure of 72 h to spiked sediment or liquid medium, body length of the nematodes was determined. Both artificial and natural sediments reduced the effect of copper, with natural sediments being more effective. In natural sediments worms grew normally at concentrations of copper up to 63.5 mg/L, whereas in artificial sediments body length was reduced at concentrations of 11.3 mg Cu/L or higher. Body length was positively correlated with content of fine particles and organic matter, indicating that particle size distribution and organic matter are determinant factors for the ecotoxicology of sediments. ------------------- Key: 2887 Medline: Authors: Schlak I;Eizinger A;Sommer RJ Title: High rate of restriction fragment length polymorphisms between two populations of the nematode Pristionchus pacificus (Diplogastridae). Citation: Journal of Zoological Systematis and Evolutionary Research 35: 137-142 1997 Type: ARTICLE Genes: dpy-1 dpy-3 dpy-18 let-60 lin-39 mab-5 unc-1 Abstract: Pristionchus pacificus (Diplogastridae, Nematoda) has recently been described as a 'satellite' organism for a functional comparative approach, because genetic, molecular and cell-biological tools can be used in a way similar to the genetic model organism Caenorhabditis elegnns. This study describes the analysis of two previously isolated strains of P. pacificus for the occurrence of restriction fragment length polymorphisms (RFLPs). In all, 14 of 17 randomly chosen cDNA clones give polymorphisms after hybridization to EcoRI digested genomic DNA of the populations from California and Washington. This polymorphism is much higher than polymorphism found among different strains in C. elegans. Therefore, this study compares most of the nucleotide sequence of the Ppa-let-60/ras gene between the two strains. No base-pair substitutions were found between these two sequences within the coding regions. However, within the untranslated regions, four base-pair substitutions in introns and the deletion of three base-pairs in the 5' sequence and in intron 4 have been observed. Since the two strains interbreed, RFLPs can be used as molecular markers for future chromosomal walking and gene cloning. ------------------- Key: 2888 Medline: Authors: Ottilie S;Wang Y;Banks S;Chang J;Vigna NJ;Weeks S;Armstrong RC;Fritz LC;Oltersdorf T Title: Mutational analysis of the interacting cell death regulators CED-9 and CED-4. Citation: Cell Death and Differentiation 4: 526-533 1997 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: The genes ced-3, ced-4 and ced-9 are central components in the cell death pathway of the nematode C, elegans. Ced-9, which functions to inhibit cell death, is homologous to the Bcl-2 family of mammalian anti-apoptotic genes. The ced-3 gene encodes a protein homologous to the caspases, a family of cysteine proteases involved in the execution of programmed cell death. It has recently been demonstrated that CED-4, an inducer of apoptosis for which no mammalian equivalent has been reported, can interact with CED-9 and Bcl-x(L). Here we confirm that CED-9 and CED-4 interact and using a series of deletion mutants, demonstrate that only short N-terminal deletions are tolerated in each molecule without loss-of-interaction. Two loss-of-function point mutations in different regions of CED-4 also lead to a significant loss of interaction suggesting further that the relevant interaction domains are not short linear sequences, but rather, are formed by more complex structural determinants in each molecule. Furthermore, we demonstrate that CED-4 not only interacts with Bcl-X-L but also with its homologue, Bcl-2, and that the unstructured loop region present in Bcl-x(L) and Bcl-2 can regulate the CED-4 interaction. Lastly, we show that a BH3 peptide that can inhibit Bcl-2 family interactions also inhibits the interaction between Bcl-x(L) and CED-4. ------------------- Key: 2889 Medline: 97447798 Authors: Carroll AS;Gilbert DE;Liu XY;Cheung JW;Michnowicz JE;Wagner G;Ellenberger TE;Blackwell TK Title: SKN-1 domain folding and basic region monomer stabilization upon DNA binding. Citation: Genes & Development 11: 2227-2238 1997 Type: ARTICLE Genes: skn-1 Abstract: The SKN-1 transcription factor specifies early embryonic cell fates in Caenorhabditis elegans. SKN-1 binds DNA at high affinity as a monomer, by means of a basic region like those of basic-leucine zipper (bZIP) proteins, which bind DNA only as dimers. We have investigated how the SKN-1 DNA-binding domain (the Skn domain) promotes stable binding of a basic region monomer to DNA. A flexible arm at the Skn domain amino terminus binds in the minor groove, but a support segment adjacent to the carboxy-terminal basic region can independently stabilize basic region-DNA binding. Off DNA, the basic region and arm are unfolded and, surprisingly, the support segment forms a molten globule of four alpha-helices. On binding DNA, the Skn domain adopts a tertiary structure in which the basic region helix extends directly from a support segment alpha-helix, which is required for binding. The remainder of the support segment anchors this uninterrupted helix on DNA, but leaves the basic region exposed in the major groove. This is similar to how the bZIP basic region extends from the leucine zipper, indicating that positioning and cooperative stability provided by helix extension are conserved mechanisms that promote binding of ------------------- Key: 2890 Medline: 97469386 Authors: Zdinak LA;Greenberg IB;Szewczyk NJ;Barmada SJ;Cardamone-Raynor M;Hartman JJ;Jacobson LA Title: Transgene-coded chimeric proteins as reporters of intracellular proteolysis: Starvation-induced catabolism of a lacZ fusion protein in muscle cells of Caenorhabditis elegans. Citation: Journal of Cellular Biochemistry 67: 143-153 1997 Type: ARTICLE Genes: Abstract: The product of an integrated transgene provides a convenient and cell-specific reporter of intracellular protein catabolism in 103 muscle cells of the nematode Caenorhabditis elegans. The transgene is an in-frame fusion of a 5'-region of the C. elegans unc-54 (muscle myosin heavy-chain) gene to the lacZ gene of Escherichia coli [Fire and Waterston (1989): EMBO J 8:3419-3428], encoding a 146-kDa fusion polypeptide that forms active beta-galactosidase tetramers. The protein is stable in vivo in well-fed animals, but upon removal of the food source it is inactivated exponentially (t(1/2) = 17 h) following an initial lag of 8 h. The same rate constant (but no lag) is observed in animals starved in the presence of cycloheximide, implying that inactivation is catalyzed by pre-existing proteases. Both the 146-kDa fusion polypeptide (t(1/2) = 13 h) and a major 116-kDa intermediate (t(1/2) = 7 h) undergo exponential physical degradation alter a lag oi 8 h. Degradation ic thus paradoxically faster than inactivation, and a number oi characteristic immunoreactive degradation intermediates, some less than one-third the size of the parent polypeptide, are found in affinity-purified (active) protein. Some of these intermediates are conjugated to ubiquitin. We infer that the initial proteolytic cleavages occur in the cytosol, possibly by a ubiquitin-mediated proteolytic pathway and do not necessarily inactivate the fusion protein tetramer. ------------------- Key: 2891 Medline: Authors: Desjardins P;Ledoux S Title: The nematode Caenorhabditis elegans as a model system to study neuronal cell death. Citation: "Neuromethods". J Poirier (ed). Humana Press Inc. 29: 255-277 1997 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-10 ces-1 ces-2 deg-1 egl-1 mec-4 nuc-1 Abstract: Normal development and homeostasis result from a tenuous balance between cell proliferation and cell death. Disruption of this balance, in favor of cell death in particular, could easily lead to pathological states in postmitotic organs such as the adult brain. For example, many neurodegenerative disorders are characterized by the premature death of specific subsets of neurons, which gives rise to their full clinical spectra. Although a complete understanding of the selective cell degeneration in these conditions is still lacking, recent observations suggest that it may occur through apoptosis, a gene-directed type of cell death. In many cases, cell death by apoptosis requires an active role by the dying cells, because apoptosis is most often significantly blocked or delayed by inhibitors of RNA or protein synthesis. This genetic regulation of apoptosis offers a potential for therapeutic intervention and further assessment of apoptotic mechanisms in manifestations of neuropathology is warranted. However, employing conventional molecular and biochemical approaches, attempts to determine the genetic machinery responsible for specifying which cells live and which cells die have not always been successful in vertebrate systems. One organism in which programmed cell death (PCD), a physiological counterpart of apoptosis, has been extensively examined is the nematode Caenorhabditis ------------------- Key: 2892 Medline: 97439883 Authors: Clark SG;Shurland D-L;Meyerowitz EM;Bargmann CI;Van der Bliek AM Title: A dynamin GTPase mutation causes a rapid and reversible temperature-inducible locomotion defect in C. elegans. Citation: Proceedings of the National Academy of Sciences USA 94: 10438-10443 1997 Type: ARTICLE Genes: cha-1 dyn-1 let-15 let-18 let-38 let-40 mnDf1 mnDf4 mnDf8 mnDf43 Abstract: Drosophila shibire and its mammalian homologue dynamin regulate an early step in endocytosis. We identified a Caenorhabditis elegans dynamin gene, dyn-1, based upon hybridization to the Drosophila gene. The dyn-1 RNA transcripts are trans-spliced to the spliced leader 1 and undergo alternative splicing to code for either an 830- or 838-amino acid protein. These dyn-1 proteins are highly similar in amino acid sequence, structure, and size to the Drosophila and mammalian dynamins: they contain an N-terminal GTPase, a pleckstrin homology domain, and a C-terminal proline-rich domain. We isolated a recessive temperature-sensitive dyn-1 mutant containing an alteration within the GTPase domain that becomes uncoordinated when shifted to high temperature and that recovers when returned to lower temperatures, similar to D. shibire mutants. When maintained at higher temperatures, dyn-1 mutants become constipated, egg-laying defective, and produce progeny that die during embryogenesi., Using a dyn-1::lacZ gene fusion, a high level of dynamin expression was observed in motor neurons, intestine, and pharyngeal muscle. Our results suggest that dyn-1 function is required during development and for normal locomotion. ------------------- Key: 2893 Medline: 97454726 Authors: Sternberg PW;Felix MA Title: Evolution of cell lineage. Citation: Current Opinion in Genetics & Development 7: 543-550 1997 Type: REVIEW Genes: let-23 lin-3 lin-12 lin-39 mab-5 Abstract: Description of cell lineages has intrigued developmental biologists for over a century. The description of the complete cell lineage of Caenorhabditis elegans, coupled with intensive molecular and genetic analysis, has honored the promise of resolving the genetic basis of cell lineage. The invariance of the cell lineage is now understood to stem from highly reproducible intercellular signaling processes with contributions, at least in some cases, from asymmetric segregation at cell division. We discuss advances in the past year concerning how invariant cell lineages evolve in nematodes, mollusks, and ascidians. ------------------- Key: 2894 Medline: 97477490 Authors: Eizinger A;Sommer RJ Title: The homeotic gene lin-39 and the evolution of nematode epidermal cell fates. Citation: Science 278: 452-455 1997 Type: ARTICLE Genes: lin-39 Abstract: The fate of ventral epidermal cells differs among nematode species. Nonvulval cells fuse with the epidermis in Caenorhabditis elegans, whereas the homologous cells undergo apoptosis in Pristionchus pacificus. The homeotic gene lin-39 is involved in the regulation of these epidermal cell fates. in Caenorhabditis, lin-39 prevents cell fusion of potential vulval cells and specifies the vulva equivalence group. Pristionchus vulvaless mutants that displayed apoptosis of the vulval precursor cells were isolated, and point mutations in lin-39 were identified. Thus, the evolution of these epidermal cell fates is driven by different intrinsic properties of homologous cells. ------------------- Key: 2895 Medline: Authors: Hunt P Title: Wriggling into the next millennium. C. elegans II. Citation: Trends in Genetics 13: 420- 1997 Type: REVIEW Genes: Abstract: Caenorhabditis elegans first became a 'serious' model organism after Brenner's publication of The Genetics of Caenorhabditis elegans. Since then a wealth of knowledge has been acquired regarding this rather simple metazoan animal. Evolution might have been programmed to develop C. elegans for the benefit of biological science. The transparency and invariant cell lineage of C. elegans makes it a desirable organism for cell biology research. Similarly, its large brood size and small generation interval make it an extremely useful organism for the geneticist. Additionally, C. elegans research benefits greatly from the efforts of pioneer reseachers who compiled the complete cell lineage diagram, the neuronal 'wiring' diagram, the physical genetic map (derived from an almost coniguous array of cosmids and YACs covering all six chromosomes) and finally an extensive catalogue of cDNA and almost complete genomic sequences. Murphy's Law prevails however, and C. elegans researchers are cursed with an organism for which no in vitro cell culture system exists, in which gene knockout technology is laborious at best and in which single-cell electrophysiology has only recently become possible. The book C. elegans II is part of the Cold Spring Harbor Laboratory monograph series, as was its precursor, The Nematode Caenorhabditis elegans. The book is more than an update of the previous one and includes chapters concerning a number of areas of C. elegans research only in their infancy in 1988.... ------------------- Key: 2896 Medline: 97328896 Authors: Olasode BJ Title: Dying by default, the biology of apoptosis: A review. Citation: East African Medical Journal 74: 108-111 1997 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: Apoptosis differs from necrosis in that no inflammatory changes occur. The understanding of apoptosis was greatly improved by the discovery of a natural model of apoptosis in Caenorhabditis elegans, a nematode worm. The study of this worm led to the discovery of two sets of genes, the prosuicide genes and the antisuicide genes which control apoptosis. Apoptosis is an active process that involves w activation of specific enzymes. The understanding of the molecular biology of apoptosis may in future lead to the availability of a potent weapon to use against cancer and to modify cell death that occurs in the neurodegenerative disorders. ------------------- Key: 2897 Medline: 97317676 Authors: Padgett RW;Savage C;Das P Title: Genetic and biochemical analysis of TGF beta signal transduction. Citation: Cytokine and Growth Factor Reviews 8: 1-9 1997 Type: REVIEW Genes: daf-1 daf-4 daf-7 sma-2 sma-3 sma-4 tre-1 Abstract: TGF beta-like ligands are involved in many different developmental processes that pattern a variety of tissues in invertebrates and vertebrates. In the last few years, rapid progress has been made toward elucidating the developmental roles of the TGF beta-like pathways and identifying the novel components involved in transducing their signals, particularly the newly discovered Smads. This rapid progress has been the result of a synergy between classical genetic approaches and biochemical approaches, and this combined approach is likely to propel future understanding of the signaling pathway used by TGF ------------------- Key: 2898 Medline: 97476311 Authors: De Stasio E;Lephoto C;Azuma L;Holst C;Stanislaus D;Uttam J Title: Characterization of revertants of unc-93(e1500) in Caenorhabditis elegans induced by N-ethyl-N-nitrosourea. Citation: Genetics 147: 597-608 1997 Type: ARTICLE Genes: sup-9 sup-10 sup-11 unc-93 Abstract: Phenotypic reversion of the rubber-hand, muscle-defective phenotype conferred by unc-93(e1500) aas used to determine the utility of N-ethyl-N-nitrosourea (ENU) as a mutagen for genetic research in Caenorhabditis elegans. In this system, ENU produces revertants at a frequency of 3 x 10(-4), equivalent to that of the commonly used mutagen, EMS. The gene identity of 154 ENU-induced revertants shows that the distribution of alleles between three possible suppressor genes differs from that induced by EMS. A higher percentage of revertants are alleles of unc-93 and many fewer are alleles of sup-9 and sup-10. Three revertants complement the three known suppressor genes; they may therefore identify a new gene product(s) involved in this system of excitation-contraction coupling in C. elegans. Molecular characterization of putative unc-93 null alleles reveals that the base changes induced by ENU are quite different from those induced by EMS; specifically we see an increased frequency of A/T --> G/C transitions. The frequency of ENU-induced intragenic deletions is found to be 13%. We suggest that ENU, at concentrations below 5 mM, will be a superior mutagen for studies of protein function in C. elegans. ------------------- Key: 2899 Medline: 97450964 Authors: Oka T;Yamamoto R;Futai M Title: Three vha genes encode proteolipids of Caenorhabditis elegans vacuolar-type ATPase - Gene structures and preferential expression in an H-shaped excretory cell and rectal cells. Citation: Journal of Biological Chemistry 272: 24387-24392 1997 Type: ARTICLE Genes: vha-1 vha-2 vha-4 Abstract: The proteolipids of the vacuolar-type H+-ATPase (V-ATPase) are major components of the integral membrane sector. The vha-l and vha-2 (vacuolar type H+-ATPase) genes in Caenorhabditis elegans encode putative 16-kDa proteolipids and are tandemly localized on chromosome III. The vha-2 gene has three exons, whereas vha-l has no introns, The deduced amino acid sequences of the two genes exhibit about 60% identity with the homologues from yeast, mouse, and cow. The mRNAs of both vha genes are trans-spliced to spliced leaders, suggesting that these genes constitute a polycistronic transcriptional unit. The vha-4 gene consists of four exons and is very similar to the yeast VMA16 gene that codes for the 23-kDa proteolipid. This is the first example of three distinct V-ATPase proteolipids being identified in higher eukaryotes. Northern blot and transgenic analyses show that the three vha genes may be highly expressed in the II-shaped excretory cell, rectum, and a pair of cells posterior to the anus, These results suggest that the V-ATPase activity may be important for exporting toxic compounds or metabolic wastes in this organism. ------------------- Key: 2900 Medline: 97451001 Authors: Leroux MR;Melki R;Gordon B;Batelier G;Candido EPM Title: Structure-function studies on small heat shock protein oligomeric assembly and interaction with unfolded polypeptides. Citation: Journal of Biological Chemistry 272: 24646-24656 1997 Type: ARTICLE Genes: Abstract: The small heat shock protein (smHSP) and alpha-crystallin genes encode a family of 12-43-kDa proteins which assemble into large multimeric structures, function as chaperones by preventing protein aggregation, and contain a conserved region termed the alpha-crystallin domain. Here we report on the structural and functional characterization of Caenorhabditis elegans HSP16-2, a 16-kDa smRSP produced only under stress conditions. A combination of sedimentation velocity, size exclusion chromatography, and cross-linking analyses on wild-type HSP16-2 and five derivatives demonstrate that the N-terminal domain but not most of the the C-terminal extension which follows the alpha-crystallin domain is essential for the oligomerization of the smHSP into high molecular weight complexes. The N terminus of HSP16-2 is found to be buried within complexes which can accommodate at least an additional 4-kDa of heterologous sequence per subunit. Studies on the interaction of HSP16-2 with fluorescently-labeled and radiolabeled actin and tubulin reveal that this smHSP possesses a high affinity for unfolded intermediates which form early on the aggregation pathway, but has no apparent substrate specificity. Furthermore, both wild-type and C-terminally-truncated HSP16-2 can function as molecular chaperones by suppressing the thermally-induced aggregation of citrate synthase. Taken together our data on HSP16-2 and a unique 12.6-kDa smHSP we have recently characterized demonstrate that multimerization is a prerequisite for the interaction of ------------------- Key: 2901 Medline: 97474792 Authors: Janke DL;Schein JE;Ha T;Franz NW;O'Neil NJ;Vatcher GP;Stewart HI;Kuervers LM;Baillie DL;Rose AM Title: Interpreting a sequenced genome: Toward a cosmid transgenic library of Caenorhabditis elegans. Citation: Genome Research 7: 974-985 1997 Type: ARTICLE Genes: let-713 let-716 let-721 let-725 let-756 let-767 let-774 mel-27 mel-32 rol-6 sDf127 sDp8 Abstract: We have generated a library of transgenic Caenorhabditis elegans strains that carry sequenced cosmids from the genome of the nematode. Each strain carries an extrachromosomal array containing a single cosmid, sequenced by the C. elegans Genome Sequencing Consortium, and a dominate Rol-6 marker. More than 500 transgenic strains representing 250 cosmids have been constructed. Collectively, these strains contain approximately 8 Mb of sequence data, or similar to 8% of the C. elegans genome. The transgenic strains are being used to rescue mutant phenotypes, resulting in a high-resolution map alignment of the genetic, physical, and DNA sequence maps of the nematode. We have chosen the region of chromosome III deleted by sDf127 and not covered by the duplication sDp8(III;I) as a starting point for a systematic correlation of mutant phenotypes with nucleotide sequence. In this defined region, we have identified 10 new essential genes whose mutant phenotypes range From developmental arrest at early larva, to maternal effect lethal. To date, 8 of these 10 essential genes have been rescued. In this region, these rescues represent similar to 10% of the genes predicted by GENEFINDER and considerably enhance the map alignment. Furthermore, this alignment facilitates future efforts to physically position and clone other genes in the ------------------- Key: 2902 Medline: 97465947 Authors: Ketting RF;Fischer SEJ;Plasterk RHA Title: Target choice determinants of the Tc1 transposon of Caenorhabditis elegans. Citation: Nucleic Acids Research 25: 4041-4047 1997 Type: ARTICLE Genes: gpa-2 Abstract: The Tc1 transposon of Caenorhabditis elegans always integrates into the sequence TA, but some TA sites are preferred to others. We investigated a TA target site from the gpa-2 gene of C.elegans that was previously found to be preferred (hot) for Tc1 integration in vivo. This site with its immediate flanks was cloned into a plasmid, and remained hot in vitro, showing that sequences immediately adjacent to the TA dinucleotide determine this target choice. Further deletion mapping and mutagenesis showed that a 4 bp sequence on one side of the TA is sufficient to make a site hot; this sequence nicely fits the previously identified Tc1 consensus sequence for integration. In addition, we found a second type of hot site: this site is only preferred for integration when the target DNA is supercoiled, not when it is relaxed. Excision frequencies were relatively independent of the flanking sequences. The distribution of Tc1 insertions into a plasmid was similar when we used nuclear extracts or purified Tc1 transposase in vitro, showing that the Tc1 transposase is the protein responsible for the target choice. ------------------- Key: 2903 Medline: 97465948 Authors: Rezsohazy R;van Luenen HGAM;Durbin RM;Plasterk RHA Title: Tc7, a Tc1-hitch hiking transposon in Caenorhabditis elegans. Citation: Nucleic Acids Research 25: 4048-4054 1997 Type: ARTICLE Genes: gpa-1 mut-6 Abstract: We have found a novel transposon in the genome of Caenorhabditis elegans. Tc7 is a 921 bp element, made up of two 345 bp inverted repeats separated by a unique, internal sequence. Tc7 does not contain an open reading frame. The outer 38 bp of the inverted repeat show 36 matches with the outer 38 bp of Tc1. This region of Tc1 contains the Tc1-transposase binding site. Furthermore, Tc7 is flanked by TA dinucleotides, just like Tc1, which presumably correspond to the target duplication generated upon integration. Since Tc7 does not encode its own transposase but contains the Tc1-transposase binding site at its extremities, we tested the ability of Tc7 to jump upon forced expression of Tc1 transposase in somatic cells. Under these conditions Tc7 jumps at a frequency similar to Tc1. The target site choice of Tc7 is identical to that of Tc1. These data suggest that Tc7 shares with Tc1 all the sequences minimally required to parasitize upon the Tc1 transposition machinery. The genomic distribution of Tc7 shows a striking clustering on the X chromosome where two thirds of the elements (20 out of 33) are located. Related transposons in C.elegans do not show this asymmetric ------------------- Key: 2904 Medline: 97446017 Authors: Aspbury RA;Fisher MJ;Rees HH;Clegg RA Title: N-myristoylation of the catalytic subunit of cAMP-dependent protein kinase in the free-living nematode Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 238: 523-527 1997 Type: ARTICLE Genes: Abstract: N-Myristoylation of the catalytic subunit (C-subunit) of cAMP-dependent protein kinase is widespread in animal cells. Some invertebrates express non-myristoylated isoforms of C-subunit but these co-exist with at least one myristoylated isoform. The generality of this observation implies an indispensable function for myristoylated C-subunit, but notwithstanding this, neither of the C-subunit isoforms hitherto described in C. elegans is apparently N-myristoylated. In light of this anomaly, the myristoylation status of the C-subunit has been examined in adult C. elegans. Evidence is presented for the presence of an N-myristoylated isoform. ------------------- Key: 2905 Medline: 97467192 Authors: Baker JP;Titus MA Title: A family of unconventional myosins from the nematode Caenorhabditis elegans. Citation: Journal of Molecular Biology 272: 523-535 1997 Type: ARTICLE Genes: hum-1 hum-2 hum-3 hum-4 hum-5 hum-6 nmy-1 Abstract: The unconventional myosins are a superfamily of actin-based motor proteins that are expressed in a wide range of cell types and organisms. Thirteen classes of unconventional myosin have been defined, and current efforts are focused on elucidating their individual functions in vivo. Here, we report the identification of a family of unconventional myosin genes in Caenorhabditis elegans. The hum-1, hum-2, hum-3 and hum-6 (heavy chain of an unconventional myosin) genes encode members of myosin classes I, V, VI and VII, respectively. The hum-4 gene encodes a high molecular mass myosin (ca 307 kDa) that is one of the most highly divergent myosins, and is the founding and only known member of class XII. The physical position of each hurst gene has been determined. The hum-1, hum-2 and hum-3 genes have been mapped by extrapolation near previously uncharacterized mutations, several of which are lethal, identifying potentially essential unconventional myosin genes in C. elegans. ------------------- Key: 2906 Medline: 97476274 Authors: Arata Y;Hirabayashi J;Kasai K Title: Structure of the 32 kDa galectin gene of the nematode Caenorhabditis elegans. Citation: Journal of Biological Chemistry 272: 26669-26677 1997 Type: ARTICLE Genes: Abstract: Galectins are a family of soluble beta-galacto side-binding lectins distributed in both vertebrates and invertebrates and, more recently, found also in fungus. The 32-kDa galectin isolated from the nematode Caenorhabditis elegans (Hirabayashi, J., Satoh, M., and Kasai, K. (1992) J. Biol. Chem. 267, 15485-15490) was the first ''tandem repeat-type'' galectin, containing two homologous carbohydrate-binding sites. Here, we report the structure of the nematode 32-kDa galectin gene. Physical mapping by yeast artificial chromosome polytene filter hybridization revealed that the 32-kDa galectin gene is located on chromosome II. Analysis of the transcript (1.4 kilobases) showed the presence at its 5'-end of a 22-nucleotide trans-spliced leader sequence (SL1). The entire genomic structure spanning >5 kilobase pairs (kbp), including the 5'-noncoding region, two intervening sequences (introns 1 and 2), and the 3'-noncoding region, was completely determined by the combination of genomic polymerase chain reaction and conventional colony hybridization. Intron 1 was relatively long (2.4 kbp) and was found to be inserted after the ninth codon (TAG) from the initiation codon. This position proved to be almost homologous to the conserved first intron insertion position in the vertebrate galectin genes (i.e. genes of mammalian galectin-1, -2, and -3 and chick 14-kDa galectin). On the other hand, intron 2 was much shorter (0.6 kbp), and it was inserted into the central region of the second carbohydrate-binding site. Although such an insertion pattern has never been observed in the vertebrate galectin genes, it seems to be common in C. elegans tandem repeat-type galectin genes, as predicted by the C. elegans genome project (Coulson, A., and the C. elegans Genome Consortium (1996) Biochem, Sec. Trans, 24, 289-291). Based on extensive sequence comparison, the origin and molecular evolution of the tandem repeat-type ------------------- Key: 2907 Medline: 97475691 Authors: Coissac E;Maillier E;Netter P Title: A comparative study of duplications in bacteria and eukaryotes: The importance of telomeres. Citation: Molecular Biology and Evolution 14: 1062-1074 1997 Type: REVIEW Genes: Abstract: The genomes of three bacteria (Haemophilus influenzae, Mycoplasma genitalium, and Escherichia coli) and two eukaryotes (Saccharomyces cerevisiae and Caenorhabditis elegans) were compared. The distribution of their putative open reading frames (ORFs) was studied, and several conclusions were drawn: (1) All of these genomes, even the smallest, exhibit a significant proportion (7%-30%) of duplicated ORFs. This proportion is a function of genome size and appears unrelated to the bacteria/eukaryote division. (2) Some of these ORFs constitute families of up 20 or more members. (3) The levels of sequence similarity within these families are highly variable and their distribution is different among bacteria and eukaryotes. (4) In yeast, there are topological relationships between members of the same family. The paired ORFs are frequently in the same orientation with regard to their respective telomeres and located at comparable distances from them. ------------------- Key: 2908 Medline: 97429937 Authors: Chinnaiyan AM;Chaudhary D;O'Rourke K;Koonin EV;Dixit VM Title: Role of CED-4 in the activation of CED-3. Citation: Nature 388: 728-729 1997 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: Genetic analyses of the nematode Caenorhabditis elegans have identified three core components of the cell-death apparatus. CED-3 and CED-4 promote, whereas CED-9 inhibits cell death. Recent studies indicate that CED-4 might interact independently with CED-3 and CED-9, forming the crux of a multicomponent death complex. But except for its role as an adaptor molecule, little is known about CED-4 function. A clue came with the observation that mutation of the phosphate-binding loop (P-loop) of CED-4 disrupts its ability to induce chromatin condensation in yeast. Further, a P-loop mutant of CED-4 (CED-4K165R) fails to process CED-3 in vivo, both in insect and mammalian cells (unpublished). We now confirm that CED-4 induces CED-3 activation and subsequent apoptosis, and that the process requires binding of ATP. ------------------- Key: 2909 Medline: 97429944 Authors: Hengartner MO Title: Apoptosis. CED-4 is a stranger no more. Citation: Nature 388: 714-715 1997 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: The nematode worm Caenorhabditis elegans has been used with great success to identify the basic components of the machinery underlying apoptosis (programmed cell death). Indeed, of the three key cell death genes that have been identified in C. elegans, two - ced-3 and ced-9 - have mammalian homologues that also function in apoptosis. But the sequence of the third gene, ced-4, revealed no obvious mammalian homologue, and precious little in terms of possible mechanism of action. A flurry of activity has changed that. A paper by Zou et al., published earlier this month in Cell, provides a homologue. And work by Chinnaiyan et al. (page 728 of this issue) and by Seshagiri and Miller in Current Biology lays down some choreography for the part that CED-4 protein plays in the molecular ------------------- Key: 2910 Medline: 97400619 Authors: Roush W Title: Worm longevity gene cloned. Citation: Science 277: 897-898 1997 Type: REVIEW Genes: daf-2 daf-23 Abstract: A gene that helps control the life-span of the nematode C. elegans encodes the worm version of the insulin receptor, thereby providing a possible link between aging and glucose metabolism. ------------------- Key: 2911 Medline: 98007977 Authors: McIntire SL;Reimer RJ;Schuske K;Edwards RH;Jorgensen EM Title: Identification and characterization of the vesicular GABA transporter. Citation: Nature 389: 870-876 1997 Type: ARTICLE Genes: unc-47 unc-104 Abstract: Synaptic transmission involves the regulated exocytosis of vesicles filled with neurotransmitter. Classical transmitters are synthesized in the cytoplasm, and so must be transported into synaptic vesicles. Although the vesicular transporters for monoamines and acetylcholine have been identified, the proteins responsible for packaging the primary inhibitory and excitatory transmitters, gamma-aminobutyric acid (GABA) and glutamate remain unknown(1,2) Studies in the nematode Caenorhabditis elegans have implicated the gene unc-47 in the release of GABA(3). Here we show that the sequence of unc-47 predicts a protein with ten transmembrane domains, that the gene is expressed by GABA neurons, and that the protein colocalizes,vith synaptic vesicles. Further, a rat homologue of unc-47 is expressed by central GABA neurons and confers vesicular GABA transport in transfected cells with kinetics and substrate specificity similar to those previously reported for synaptic vesicles from the brain. Comparison of this vesicular GABA transporter (VGAT) with a vesicular transporter for monoamines shows that there are differences in the bioenergetic dependence of transport, and these presumably account for the differences in structure. Thus VGAT is the first of a new family of neurotransmitter transporters. ------------------- Key: 2912 Medline: 98026882 Authors: Lee RYN;Lobel L;Hengartner M;Horvitz HR;Avery L Title: Mutations in the alpha1 subunit of an L-type voltage-activated Ca2+ channel cause myotonia in Caenorhabditis elegans. Citation: EMBO Journal 16: 6066-6076 1997 Type: ARTICLE Genes: eat-12 egl-19 pat-5 Abstract: The control of excitable cell action potentials is central to animal behavior. We show that the egl-19 gene plays a pivotal role in regulating muscle excitation and contraction in the nematode Caenorhabditis elegans and encodes the alpha I subunit of a homologue of vertebrate L-type voltage-activated Ca2+ channels. Semidominant, gain-of-function mutations in egl-19 cause myotonia: mutant muscle action potentials are prolonged and the relaxation delayed. Partial loss-of-function mutations cause slow muscle depolarization and feeble contraction. The most severe loss-of-function mutants lack muscle contraction and die as embryos. We localized two myotonic mutations in the sixth membrane-spanning domain of the first repeat (IS6) region, which has been shown to be responsible for voltage-dependent inactivation. A third myotonic mutation implicates IIIS4, a region involved in sensing plasma-membrane voltage change, in the inactivation ------------------- Key: 2913 Medline: 97454714 Authors: Baker JC;Harland RM Title: From receptor to nucleus: the Smad pathway. Citation: Current Opinion in Genetics & Development 7: 467-473 1997 Type: REVIEW Genes: daf-4 sma-2 sma-3 sma-4 Abstract: The transforming growth factor-beta (TGF-beta) superfamily plays a central role in the specification and patterning of cells in the early embryo. Several years ago, the TGF-betas were shown to signal through serine/threonine receptor kinases. Now, with the identification of Smad proteins, we can trace the TGF-beta signal transduction pathway from the receptors into the nucleus. ------------------- Key: 2914 Medline: 98013175 Authors: Ogg S;Paradis S;Gottlieb S;Patterson GI;Lee L;Tissenbaum HA;Ruvkun G Title: The Fork head transcription factor DAF-16 transduces insulin-like metabolic and longevity signals in C. elegans. Citation: Nature 389: 994-999 1997 Type: ARTICLE Genes: age-1 daf-2 daf-3 daf-7 daf-16 Abstract: In mammals, insulin signalling regulates glucose transport together with the expression and activity of various metabolic enzymes. In the nematode Caenorhabditis elegans, a related pathway regulates metabolism, development and longevity(1,2). Wild-type animals enter the developmentally arrested dauer stage in response to high levels of a secreted pheromone(3), accumulating large amounts of fat in their intestines and hypodermis. Mutants in DAF-2 (a homologue of the mammalian insulin receptor) and AGE-1 (a homologue of the catalytic subunit of mammalian phosphatidylinositol 3-OH kinase) arrest development at the dauer stage(3), Moreover, animals bearing weak or temperature-sensitive mutations in daf-2 and age-1 can develop reproductively, but nevertheless show increased energy storage and longevity(1,2,4,5). Here we show that null mutations in daf-16 suppress the effects of mutations in daf-2 or age-1; lack of daf-16 bypasses the need for this insulin receptor-like signalling pathway. The principal role of DAF-2/AGE-1 signalling is thus to antagonize DAF-16. daf-16 is widely expressed and encodes three members of the Fork head family of transcription factors, The DAF-2 pathway acts synergistically with the pathway activated by a nematode TGF-beta-type signal, DAF-7, suggesting that DAF-16 cooperates with nematode SMAD proteins in regulating the transcription of key metabolic and developmental control genes. The probable human orthologues of DAF-16, FKHR and AFX, may also act downstream of insulin signalling and cooperate with TGF-beta effecters in mediating metabolic regulation. These ------------------- Key: 2915 Medline: 97477374 Authors: Patterson GI;Koweek A;Wong A;Liu Y;Ruvkun G Title: The DAF-3 Smad protein antagonizes TGF-beta-related receptor signaling in the Caenorhabditis elegans dauer Citation: Genes & Development 11: 2679-2690 1997 Type: ARTICLE Genes: daf-1 daf-2 daf-3 daf-4 daf-7 daf-8 daf-14 mgDf90 Abstract: Signals from TGF-beta superfamily receptors are transduced to the nucleus by Smad proteins, which transcriptionally activate target genes. In Caenorhabditis elegans, defects in a TGF-beta-related pathway cause a reversible developmental arrest and metabolic shift at the dauer larval stage. Null mutations in daf-3 suppress mutations in genes encoding this TGF-beta signal, its receptors, and associated Smad signal transduction proteins. daf-3 encodes a Smad protein that is most closely related to mammalian DPC4, and is expressed throughout development in many of the tissues that are remodeled during dauer development. DAF-4, the type II TGF-beta receptor in this pathway, is also expressed in remodeled tissues. These data suggest that the DAF-7 signal from sensory neurons acts as a neuroendocrine signal throughout the body to directly regulate developmental and metabolic shifts in tissues that are remodeled during dauer formation. A full-length functional DAF-3/GFP fusion protein is predominantly cytoplasmic, and this localization is independent of activity of the upstream TGF-beta-related pathway. However, this fusion protein is associated with chromosomes in mitotic cells, suggesting that DAF-3 binds DNA directly or indirectly. DAF-3 transgenes also interfere with dauer formation, perhaps attributable to a dosage effect. A truncated DAF-3/GFP fusion protein that is predominantly nuclear interferes with dauer formation, implying a role for DAF-3 in the nucleus. These data suggest that DAF-7 signal transduction antagonizes or modifies DAF-3 Smad activity in the nucleus to induce reproductive development; when DAF-7 signals are disabled, unmodified DAF-3 Smad activity mediates dauer arrest and its associated metabolic shift. Therefore, daf-3 is unique in that it is ------------------- Key: 2916 Medline: 97477377 Authors: Hajnal A;Whitfield CW;Kim SK Title: Inhibition of Caenorhabditis elegans vulval induction by gap-1 and by let-23 receptor tyrosine kinase. Citation: Genes & Development 11: 2715-2728 1997 Type: ARTICLE Genes: gap-1 ksr-1 let-23 let-60 lin-2 lin-3 lin-7 lin-8 lin-9 lin-10 lin-15 lin-45 mek-2 mpk-1 sem-5 Abstract: During induction of the Caenorhabditis elegans hermaphrodite vulva, a signal from the anchor cell activates the LET-23 epidermal growth factor receptor (EGFR)/LET-60 Ras/MPK-1 MAP kinase signaling pathway in the vulval precursor cells. We have characterized two mechanisms that limit the extent of vulval induction. First, we found that gap-1 may directly inhibit the LET-60 Ras signaling pathway. We identified the gap-1 gene in a genetic screen for inhibitors of vulval induction. gap-1 is predicted to encode a protein similar to GTPase-activating proteins that likely functions to inhibit the signaling activity of LET-60 Ras. A loss-of-function mutation in gap-1 suppresses the vulvaless phenotype of mutations in the let-60 ras signaling pathway, but a gap-1 single mutant does not exhibit excess vulval induction. Second, we found that let-23 EGFR prevents vulval induction in a cell-nonautonomous manner, in addition to its cell-autonomous role in activating the let-60 ras/mpk-1 signaling pathway. Using genetic mosaic analysis, we show that let-23 activity in the vulval precursor cell closest to the anchor cell (P6.p) prevents induction of vulval precursor cells further away from the anchor cell (P3.p, P4.p, and P8.p). This result suggests that LET-23 in proximal vulval precursor cells might bind and sequester the inductive signal LIN-3 EGF, thereby preventing ------------------- Key: 2917 Medline: 98004220 Authors: Troemel ER;Kimmel BE;Bargmann CI Title: Reprogramming chemotaxis responses: Sensory neurons define olfactory preferences in C. elegans. Citation: Cell 91: 161-169 1997 Type: ARTICLE Genes: mec-4 odr-3 odr-7 odr-10 osm-9 str-1 tax-2 tax-4 Abstract: Different olfactory cues elicit distinct behaviors such as attraction, avoidance, feeding, or mating. In the nematode C. elegans, these cues are sensed by a small number of olfactory neurons, each of which expresses several different odorant receptors. The type of behavioral response elicited by an odorant could be specified by the olfactory receptor or by the olfactory neuron in which the receptor is activated. The attractive odorant diacetyl is detected by the receptor protein ODR-10, which is normally expressed in the AWA olfactory neurons. The repulsive odorant 2-nonanone is detected by the AWB olfactory neurons. Transgenic animals that express ODR-10 in AWB rather than AWA avoid diacetyl, while maintaining qualitatively normal responses to other attractive and repulsive odorants. Animals that express ODR-10 simultaneously in AWA and AWB have a defective response to diacetyl, possibly because of conflicting olfactory inputs. Thus, an animal's preference for an odor is defined by the sensory neurons that express a given odorant receptor ------------------- Key: 2918 Medline: 97477426 Authors: Nonet ML;Staunton J;Kilgard MP;Fergestad T;Hartwieg E;Horvitz HR;Jorgensen EM;Meyer BJ Title: C. elegans rab-3 mutant synapses exhibit impaired function and are partially depleted of vesicles. Citation: Journal of Neuroscience 17: 8061-8073 1997 Type: ARTICLE Genes: aex-3 rab-3 snt-1 unc-104 ccDf4 ccDf5 maDf4 Abstract: Rab molecules regulate vesicular trafficking in many different exocytic and endocytic transport pathways in eukaryotic cells. In neurons, rab3 has been proposed to play a crucial role in regulating synaptic vesicle release. To elucidate the role of rab3 in synaptic transmission, we isolated and characterized Caenorhabditis elegans rab-3 mutants. Similar to the mouse rab3A mutants, these mutants survived and exhibited only mild behavioral abnormalities. In contrast to the mouse mutants, synaptic transmission was perturbed in these animals. Extracellular electrophysiological recordings revealed that synaptic transmission in the pharyngeal nervous system was impaired. Furthermore, rab-3 animals were resistant to the acetylcholinesterase inhibitor aldicarb, suggesting that cholinergic transmission was generally depressed. Last, synaptic vesicle populations were redistributed in rab-3 mutants. In motor neurons, vesicle populations at synapses were depleted to 40% of normal levels, whereas in intersynaptic regions of the axon, vesicle populations were elevated. On the basis of the morphological defects at neuromuscular junctions, we postulate that RAB-3 may regulate recruitment of vesicles to the activezone or sequestration of vesicles near release sites. ------------------- Key: 2919 Medline: 97459988 Authors: van Pouderoyen G;Ketting RF;Perrakis A;Plasterk RHA;Sixma Title: Crystal structure of the specific DNA-binding domain of Tc3 transposase of C. elegans in complex with transposon DNA. Citation: EMBO Journal 16: 6044-6054 1997 Type: ARTICLE Genes: Abstract: The crystal structure of the complex between the N-terminal DNA-binding domain of Tc3 transposase and an oligomer of transposon DNA has been determined. The specific DNA-binding domain contains three a-helices, of which two form a helix-turn-helix (HTH) motif. The recognition of transposon DNA by the transposase is mediated through base-specific contacts and complementarity between protein and sequence-dependent deformations of the DNA. The HTH motif makes four base-specific contacts with the major groove, and the N-terminus makes three base-specific contacts with the minor groove. The DNA oligomer adopts a non-linear B-DNA conformation, made possible by a stretch of seven G:C base pairs at one end and a TATA sequence towards the other end. Extensive contacts (seven salt bridges and 16 hydrogen bonds) of the protein with the DNA backbone allow the protein to probe and recognize the sequence-dependent DNA deformation. The DNA-binding domain forms a dimer in the crystals. Each monomer binds a separate transposon end, implying that the dimer plays a role in synapsis, necessary for the simultaneous cleavage ------------------- Key: 2920 Medline: 97459972 Authors: Dent JA;Davis MW;Avery L Title: avr-15 encodes a chloride channel subunit that mediates inhibitory glutamatergic neurotransmission and ivermectin sensitivity in Caenorhabditis elegans. Citation: EMBO Journal 16: 5867-5879 1997 Type: ARTICLE Genes: avr-15 eat-4 myo-2 nDf42 Abstract: Ivermectin is a widely used anthelmintic drug whose nematocidal mechanism is incompletely understood. We have used Caenorhabditis elegans as a model system to understand ivermectin's effects. We found that the M3 neurons of the C. elegans pharynx form fast inhibitory glutamatergic neuromuscular synapses. avr-15, a gene that confers ivermectin sensitivity on worms, is necessary postsynaptically for a functional M3 synapse and for the hyperpolarizing effect of glutamate on pharyngeal muscle. avr-15 encodes two alternatively spliced channel subunits that share ligand binding and transmembrane domains and are members of the family of glutamate-gated chloride channel subunits. An avr-15-encoded subunit forms a homomeric channel that is ivermectin-sensitive and glutamate-gated. These results indicate that: (i) an ivermectin-sensitive chloride channel mediates fast inhibitory glutamatergic neuromuscular transmission; and (ii) a nematocidal property of ivermectin derives from its activity as an agonist of glutamate-gated chloride channels in essential excitable cells such as those of the pharynx. ------------------- Key: 2921 Medline: 98043402 Authors: Sun AY;Lambie EJ Title: gon-2, a gene required for gonadogenesis in Caenorhabditis elegans. Citation: Genetics 147: 1077-1089 1997 Type: ARTICLE Genes: gon-2 pes-1 smg-2 dxDf1 nDf23 nDf24 nDf25 nDp5 Abstract: The gonad of the Caenorhabditis elegans hermaphrodite is generated by the postembryonic divisions of two somatic precursors, Z1 and Z4, and two germline precursors, Z2 and Z3. These cells begin division midway through the first larval stage. By the end of the fourth larval stage, Z1 and Z4 produce 143 descendants, while Z2 and Z3 give rise to similar to 1000 descendants. The divisions of Z2 and Z3 are dependent on signals produced by ZI and Z4, but not vice versa. We have characterized the properties of five loss-of-function alleles of a newly described gene, which we call gon-2. In gon-2 mutants, gonadogenesis is severely impaired; in some animals, none of the gonad progenitors undergo any postembryonic divisions. Mutations in gon-2 have a partial maternal effect: either maternal or zygotic expression is sufficient to prevent the severe gonadogenesis defects. By cell lineage analysis, we found that the primary defect in gon-2 mutants is a delay (sometimes a complete block) in the onset and continuation of gonadal divisions. The results of upshift experiments using a temperature-sensitive allele suggest that zygotic expression of gon-2 begins early in embryogenesis, before the birth of Z1 and Z4. The results of downshift experiments suggest that Z1 and Z4 can generate the full complement of gonadal tissues even even gon-2 function is inhibited until the end of the second larval stage. Thus, gon-2 activity is probably not required for the specification of gonadal cell fates, but appears to he generally required for gonadal cell divisions. ------------------- Key: 2922 Medline: 98033260 Authors: Bowerman B;Ingram MK;Hunter CP Title: The maternal par genes and the segregation of cell fate specification activities in early Caenorhabditis elegans embryos. Citation: Development 124: 3815-3826 1997 Type: ARTICLE Genes: glp-1 mex-3 pal-1 par-1 par-2 par-3 par-4 skn-1 mDp1 Abstract: After fertilization in C. elegans, activities encoded by the maternally expressed par genes appear to establish cellular and embryonic polarity. Loss-of-function mutations in the par genes disrupt anterior-posterior (a-p) asymmetries in early embryos and result in highly abnormal patterns of cell fate. Little is known about how the early asymmetry defects are related to the cell fate patterning defects in par mutant embryos, or about how the par gene products affect the localization and activities of developmental regulators known to specify the cell fate patterns made by individual blastomeres. Examples of such regulators of blastomere identity include the maternal proteins MEX-3 and GLP-1, expressed at high levels anteriorly, and SKN-1 and PAL-1, expressed at high levels posteriorly in early embryos. To better define par gene functions, we examined the expression patterns of MEX-3, PAL-1 and SKN-1, and we analyzed mex-3, pal-1, skn-1 and glp-1 activities in par mutant embryos. We have found that mutational inactivation of each par gene results in a unique phenotype, but in no case do we observe a complete loss of a-p asymmetry. We conclude that no one par gene is required for all a-p asymmetry and we suggest that, in some cases, the par genes act independently of each other to control cell fate patterning and polarity. Finally, we discuss the implications of our findings for understanding how the initial establishment of polarity in the zygote by the par gene products leads to the proper localization of more specifically acting regulators of blastomere identity. ------------------- Key: 2923 Medline: 98033265 Authors: Ahringer J Title: Maternal control of a zygotic patterning gene in Caenorhabditis elegans. Citation: Development 124: 3865-3869 1997 Type: ARTICLE Genes: apx-1 glp-1 mex-3 pal-1 pie-1 skn-1 vab-7 sDp3 Abstract: The transition from maternal to zygotic gene control is a key process in embryogenesis. Although many maternal effect genes have been studied in the C. elegans embryo, how their activities lead to the positional expression of zygotic patterning genes has not yet been established. Evidence is presented showing that expression of the zygotic patterning gene vab-7 does not depend on cell position or cell contacts, but rather on the production of a C blastomere. Furthermore, pal-1, a caudal homologue with maternal product necessary for the proper development of the C blastomere, is both necessary and sufficient for vab-7 expression. This provides a link between maternal gene activity and zygotic patterning gene expression in C, elegans. The results suggest that zygotic patterning genes might be generally controlled at the level of blastomere fate and not by position. ------------------- Key: 2924 Medline: 98040546 Authors: Chamberlin HM;Palmer RE;Newman AP;Sternberg PW;Baillie DL;Thomas JH Title: The PAX gene egl-38 mediates developmental patterning in Caenorhabditis elegans. Citation: Development 124: 3919-3928 1997 Type: ARTICLE Genes: egl-38 eDf19 mDf7 Abstract: Mutations in the C. elegans gene egl-38 result in a discrete set of defects in developmental pattern formation. In the developing egg-laying system of egl-38 mutant hermaphrodites, the identity of four uterine cells is disrupted and they adopt the fate of their neighbor cells. Likewise, the identity of two rectal epithelial cells in the male tail is disrupted and one of these cells adopts the fate of its neighbor cell. Genetic analysis suggests that the egl-38 functions in the tail and the egg-laying system are partially separable, as different egl-38 mutations can preferentially disrupt the different functions. We have cloned egl-38 and shown that it is a member of the PAX family of genes, which encode transcription factors implicated in a variety of developmental patterning events. The predicted EGL-38 protein is most similar to the mammalian class of proteins that includes PAX2, PAX5 and PAX8. The sequence of egl-38 mutant DNA indicates that the tissue-preferential defects of egl-38 mutations result from substitutions in the DNA-binding paired domain of the EGL-38 protein. egl-38 thus provides the first molecular genetic insight into two specific patterning events that occur during C. elegans development and also provides the opportunity to investigate the in vivo functions of this class of PAX ------------------- Key: 2925 Medline: 98040550 Authors: Okkema PG;Ha E;Haun C;Chen W;Fire A Title: The Caenorhabditis elegans NK-2 homeobox gene ceh-22 activates pharyngeal muscle gene expression in combination with pha-1 and is required for normal pharyngeal development. Citation: Development 124: 3965-3973 1997 Type: ARTICLE Genes: ceh-22 myo-1 myo-2 pha-1 unc-54 ctDf1 mDf1 nDf42 sDf29 Abstract: Pharyngeal muscle development in the nematode Caenorhabditis elegans appears to share similarities with cardiac muscle development in other species. We have previously described CEH-22, an NK-2 class homeodomain transcription factor similar to Drosophila tinman and vertebrate Nkx2-5, which is expressed exclusively in the pharyngeal muscles. In vitro, CEH-22 binds the enhancer from myo-2, a pharyngeal muscle-specific myosin heavy chain gene. In this paper, we examine the role CEH-22 plays in pharyngeal muscle development and gene activation by (a) ectopically expressing ceh-22 in transgenic C. elegans and (b) examining the phenotype of a ceh-22 loss-of-function mutant. These experiments indicate that CEH-22 is an activator of myo-2 expression and that it is required for normal pharyngeal muscle development. However, ceh-22 is necessary for neither formation of the pharyngeal muscles, nor for myo-2 expression. Our data suggest parallel and potentially compensating pathways contribute to pharyngeal muscle differentiation. We also examine the relationship between ceh-22 and the pharyngeal organ-specific differentiation gene pha-1. Mutations in ceh-22 and pha-1 have strongly synergistic effects on pharyngeal muscle gene expression; in addition, a pha-1 mutation enhances the lethal phenotype caused by a mutation in ceh-22. Wild-type pha-1 is not required for the onset of ceh-22 expression but it appears necessary for maintained expression of ------------------- Key: 2926 Medline: 98348621 Authors: Selimi F;Mariani J;Martinou JC Title: Caenorhabditis elegans and mammalian neuronal death. Citation: Revue Neurologique 153: 478-483 1997 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: The development of the nervous system implies not only the generation of neurons, but also their death. This neuronal death can occur through several mechanisms, one of them being apoptosis. This type of cell death seems to be also implicated in some neurodegenerative diseases. The study of the nematode Caenorhabditis elegans has led to the discovery of several genes controlling apoptosis in neurons. Two of them, the pro-apoptotic ced3 and the anti-apoptotic ced9, have mammalian homologs. The mammalian homologs to Ced9 form the Bcl-2 family and can be either pro-apoptotic or anti-apoptotic. Some of them, Bcl-2, Bcl-x, and Bax have been shown to be involved in neuronal death during development and in some pathological situations. The first mammalian homolog of Ced3 to be described was the Interleukin-1b Converting Enzyme (ICE). Since then, many other homologs of the porteases Ced3 and ICE have been discovered constituting the Caspases family. These Cysteinyl Aspartate Specific Proteases are pro-apoptotic in many different systems. Several studies using viral or peptidic inhibitors of the Caspases have demonstrated their role in neuronal death in vitro. In vivo, CPP32, a member of the Caspases family, has been shown to be clearly involved in the development of the nervous system. Finally the analysis of apoptosis in Caenorhabditis elegans has led to the discovery of two families of genes involved in the cascade of events inducing neuronal death in mammals. Indeed, the Caspases seem to be controlled by the Bcl-2 family as Ced3 is by ------------------- Key: 2927 Medline: 98019100 Authors: Otterson GA;Kaye FJ Title: A 'core ATPase', Hsp70-like structure is conserved in human, rat, and C. elegans STCH proteins. Citation: Gene 199: 287-292 1997 Type: ARTICLE Genes: Abstract: We have identified the rat and Caenorhabditis elegans homologues of a 'core ATPase'-encoding Hsp70-like gene, designated Stch. We observed that the human, rat, and C. elegans Stch genes have conserved a stop codon immediately distal to the sequence encoding the Hsp70 ATPase domain. This results in the functional equivalent of an N-terminal, proteolytically cleaved fragment of Hsc70/BiP. Each homologue contains a hydrophobic signal sequence, demonstrates striking identity within the Hsp70 ATPase domain, and retains a similar C-terminal sequence (STCH specific cluster III) that is unique among Hsp70 proteins and which truncates the peptide binding domain. In addition, we have identified an internal 35-aa region that is homologous to the minimal sequence of the Hip chaperone co-factor that is required for direct binding to the ATPase domain of Hsp70. Adjacent to this region, the rat and human STCH protein sequences diverge within a short internal 'insertion' sequence that interrupts the ATPase subdomain between the phosphate-2 and adenosine ATP-binding sites. We have also demonstrated that both human and rat Stch are constitutively produced and are induced by the calcium ionophore A23187, but not by heat shock. The recognition that the truncated 'core ATPase' structure of the STCH molecule is conserved in human, rat, and C. elegans tissues suggests an important role for this unique member of the membrane-bound Hsp70 family. ------------------- Key: 2928 Medline: 97465808 Authors: Leggett DS;Candido EPM Title: Biochemical characterization of Caenorhabditis elegans UBC-1: self-association and auto-ubiquitination of a RAD6-like ubiquitin-conjugating enzyme in vitro. Citation: Biochemical Journal 327: 357-361 1997 Type: ARTICLE Genes: ubc-1 Abstract: The Caenorhabditis elegans ubiquitin-conjugating enzyme UBC-1 is distinct from other RAD6 homologues in possessing a C-terminal tail 40 amino acid residues long [Legett, Jones and Candido (1995) DNA Cell Biol. 14, 883-891]. Such extensions from the core catalytic domain have been found in a subset of known conjugating enzymes, where they have been shown to have diverse roles including target recognition, membrane attachment and sporulation. In the present study we used mutagenesis in vitro to examine the role of the tail in specific aspects of UBC-1 structure and activity. Cross-linking experiments with purified recombinant UBC-1 reveal that it forms dimers and probably tetramers. The acidic tail of UBC-1 has an important role in this interaction because deletions of the tail significantly decrease, but do not abolish, this self-association. Ubiquitin conjugation assays show that, in addition to accepting a thiol-bound ubiquitin at its active site, UBC-1 is stably mono-ubiquitinated. Deletion analysis and site-directed mutagenesis localize the site of ubiquitination to Lys-162 in the tail. These findings demonstrate that the C-terminal tail of UBC-1 is important both for its quaternary structure and post-translational modification in vitro. ------------------- Key: 2929 Medline: Authors: Cangelosi A;Parisi D Title: A neural network model of Caenorhabditis elegans: The circuit of touch sensitivity. Citation: Neural Processing Letters 6: 91-98 1997 Type: ARTICLE Genes: Abstract: The paper presents a neural network model of the touch sensitivity circuit of the nematode Caenorhabditis elegans. We describe a series of simulations in which neural networks are trained, using a genetic algorithm, to reproduce the habituation of the nematode's touch sensitive behavior. A lesion study of the network allows to make a direct comparison between the fine functioning of the model and the data collected in real organisms. The model accords well with the known neurobiological data and it suggests some hypotheses about the functioning of the neural circuit and of single neurons. ------------------- Key: 2930 Medline: 97477445 Authors: Colbert HA;Smith TL;Bargmann CI Title: OSM-9, a novel protein with structural similarity to channels, is required for olfaction, mechanosensation, and olfactory adaptation in Caenorhabditis elegans. Citation: Journal of Neuroscience 17: 8259-8269 1997 Type: ARTICLE Genes: osm-9 tax-2 tax-4 Abstract: Although cyclic nucleotide-gated channels mediate sensory transduction in olfaction and vision, other forms of sensory transduction are independent of these channels. Caenorhabditis elegans cyclic nucleotide-gated channel mutants respond normally to some olfactory stimuli and to osmotic stimuli, suggesting that these chemosensory responses use an alternative sensory transduction pathway. One gene that may act in this pathway is osm-9, which is required for each of these responses as well as a mechanosensory response to nose touch. osm-9 encodes a protein with ankyrin repeats and multiple predicted transmembrane domains that has limited similarity to the Drosophila phototransduction channels transient receptor potential (TRP) and TRP-like (TRPL). The sequence of OSM-9 and other TRP-like genes reveals a previously unsuspected diversity of mammalian and invertebrate genes in this family. osm-9 is required for the activity of the predicted G-protein-coupled odorant receptor ODR-10, which acts in the AWA olfactory neurons; its similarity to other G-protein-regulated transduction channels suggests that OSM-9 is involved in AWA signaling. osm-9::GFP fusion genes are expressed in a subset of chemosensory, mechanosensory, and osmosensory neurons. osm-9 also affects olfactory adaptation within neurons that require the cyclic nucleotide-gated channel for olfaction; in these neurons, the gene has a regulatory function and not a primary role in sensory transduction. ------------------- Key: 2931 Medline: 98004541 Authors: Zhang Y;Chou JH;Bradley J;Bargmann CI;Zinn K Title: The Caenorhabditis elegans seven-transmembrane protein ODR-10 functions as an odorant receptor in mammalian cells. Citation: Proceedings of the National Academy of Sciences USA 94: 12162-12167 1997 Type: ARTICLE Genes: odr-10 Abstract: The nematode Caenorhabditis elegans exhibits behavioral responses to many volatile odorants. Chemotaxis toward one such odorant, diacetyl (butanedione), requires the function of a seven-transmembrane receptor protein encoded by the odr-10 gene. To determine directly whether ODR-10 protein is an odorant receptor, it is necessary to express the protein in a heterologous system and show that it responds to diacetyl by activation of a G protein signaling pathway. Here we demonstrate that human cells expressing ODR-10 on their surfaces exhibit a transient elevation in intracellular Ca2+ levels after diaectyl application. Volatile compounds that differ from diacetyl only by the addition of a methyl group (2,3-pentanedione) or the absence of a keto group (butanone) are not ODR-10 agonists. Behavioral responses to these compounds are not dependent on odr-10 function, so ODR-10 specificity in human cells resembles irt vivo specificity. The apparent affinity of ODR-10 for diacetyl observed in human cells is consistent with the diacetyl concentration ranges that allow efficient nematode chemotaxis. ODR-10 expressed in human cells also responds to two anionic compounds, pyruvate and citrate, which are metabolic precursors used for diacetyl production by certain bacterial species. Ca2+ elevation in response to ODR-10 activation is due to release from intracellular stores. ------------------- Key: 2932 Medline: 98004548 Authors: Li X;Greenwald I Title: HOP-1, a Caenorhabditis elegans presenilin, appears to be functionally redundant with SEL-12 presenilin and to facilitate LIN-12 and GLP-1 signaling. Citation: Proceedings of the National Academy of Sciences USA 94: 12204-12209 1997 Type: ARTICLE Genes: glp-1 hop-1 lin-12 sel-12 Abstract: Mutant presenilins have been found to cause Alzheimer disease, Here, we describe the identification and characterization of HOP-1, a Caenorhabditis elegans presenilin that displays much more lower sequence identity with human presenilins than does the other C. elegans presenilin, SEL-12. Despite considerable divergence, HOP-1 appears to be a bona fide presenilin, because HOP-1 can rescue the egg-laying defect caused by mutations in sel-12 when hop-1 is expressed under the control of sel-12 regulatory sequences. HOP-I also has the essential topological characteristics of the other presenilins. Reducing hop-1 activity in a sel-12 mutant background causes synthetic lethality and terminal phenotypes associated with reducing the function of the C. elegans lin-12 and glp-1 genes. These observations suggest that hop-1 is functionally redundant with sel-12 and underscore the intimate connection between presenilin activity and LIN-12/Notch activity inferred from genetic studies in C. ------------------- Key: 2933 Medline: 98026906 Authors: Jan E;Yoon JW;Walterhouse D;Iannaccone P;Goodwin EB Title: Conservation of the C. elegans tra-2 3' UTR translational control. Citation: EMBO Journal 16: 6301-6313 1997 Type: ARTICLE Genes: fem-1 fem-2 fem-3 fog-1 her-1 laf-1 tra-1 tra-2 tra-3 Abstract: The Caenorhabditis elegans sex-determination gene, tra-2, is translationally regulated by two 28 nt elements (DREs) located in the 3'UTR that bind a factor called DRF. This regulation requires the laf-1 gene activity. We demonstrate that the nematode Caenorhabditis briggsae tra-2 gene and the human oncogene GLI are translationally regulated by elements that sire functionally equivalent to DREs. Here, we rename the DREs to TGEs (tra-2 and GLI elements). Similarly to the C. elegans tra-2 TGEs, the C. briggsae tra-2 and GLI TGEs repress translation of a reporter transgene in a laf-1 dependent manner. Furthermore, they regulate poly(A) tail length and bind DRF. We also find that the C. elegans TGEs control translation and poly(A) tail length in C. briggsae and rodent cells. Moreover, these same organisms contain a factor that specifically associates with the C. elegans TGEs. These findings are consistent with the TGE control being present in C. briggsae and rodent cells. Three lines of evidence indicate that C. briggsae tra-2 and GLI are translationally controlled in vivo by TGEs. First, like C. elegans tra-2 TGEs, the C. briggsae tra-2 and GLI TGEs control translation and poly(A) tail lengths in C. briggsae and rodent cells, respectively. Second, the same factor in C. briggsae and mammalian cells that binds to the C. elegans tra-2 TGEs binds the C. briggsae tra-2 and GLI TGEs. Third, deletion of the GLI TGF increases GLI's ability to transform cells. These findings suggest that TGE control is ------------------- Key: 2934 Medline: 98343909 Authors: Baumeister R;Leimer U;Zweckbronner I;Jakubek C;Grunberg J;Haass C Title: Human presenilin-I, but not familial Alzheimer's disease (FAD) mutants, facilitate Caenorhabditis elegans Notch signalling independently of proteolytic processing. Citation: Genes and Function 1: 149-159 1997 Type: ARTICLE Genes: lin-12 sel-12 spe-4 Abstract: The majority of cases with familial Alzheimer's desease (FAD) are linked to mutations of the presenilin (PS) genes. These genes show considerable sequence similarity to the sel-12 gene of Caenorhabditis elegans, which has been postulated to function in the facilitated signalling by lin-12 and glp-1. In order to analyse the functional conservation of the presenilins, we introduced the human PS-1 cDNA, as well as clinicl deletion mutant proteins, into sel-12 mutant animals and tested their potential to rescue the egg-laying defect. Human PS-1 expressed from the sel-12 promoter fully rescued the sel-12 phenotype, whereas two missense mutations, C410Y and A246E, identified in pedigrees with FAD, exhibited a strongly decreased rescuing activity. The large hydrophilic loop and transmembrane domain 7 are required for the biological activity of PS-1. PS-1 protein was proteolytically cleaved in C. elegans as it is in human cells. A PS-1 splice variant (FAD mutation ?exon9) that does not undergo proteolytic cleavage also substituted for sel-12. The conservation of function of human PS-1 and C. elegans sel-12 suggests that presenilin proteins are required, directly or indirectly, for the proper operation of the Notch signalling pathway. FAD-associated mutant proteins tested showed different rescuing activities, indicating that they might affect different functional or regulatory aspects of PS-1. Proteolytic processing is not a prerequisite for PS-1 ------------------- Key: 2935 Medline: 98028757 Authors: Lin K;Dorman JB;Rodan A;Kenyon C Title: daf-16: An HNF-3/forkhead family member that can function to double the life-span of Caenorhabditis elegans. Citation: Science 278: 1319-1322 1997 Type: ARTICLE Genes: daf-2 daf-16 Abstract: The wild-type Caenorhabditis elegans nematode ages rapidly, undergoing development, senescence, and death in less than 3 weeks. In contrast, mutants with reduced activity of the gene daf-2 a homolog of the insulin and insulin-like growth factor receptors, age more slowly than normal and live more than twice as long. These mutants are active and fully fertile and have normal metabolic rates. The life-span extension caused by daf-2 mutations requires the activity of the gene daf-16. daf-16 appears to play a unique role in life-span regulation and encodes a member of the hepatocyte nuclear factor 3 (HNF-3)/forkhead family of transcriptional regulators. In humans, insulin down-regulates the expression of certain genes by antagonizing the activity of HNF-3, raising the possibility that aspects of this regulatory system have been conserved. ------------------- Key: 2936 Medline: 98019243 Authors: Hunter T;Bannister WH;Hunter GJ Title: Cloning, expression and characterization of two manganese superoxide dismutases from Caenorhabditis elegans. Citation: Journal of Biological Chemistry 272: 28652-28659 1997 Type: ARTICLE Genes: age-1 mev-1 rad-8 sod-2 sod-3 Abstract: Two genes encoding manganese superoxide dismutase (sod-2 and sod-3) have been identified in the nematode Caenorhabditis elegans. Each gene is composed of five exons, and intron positions are identical; however, intron sizes and sequences are not the same. The predicted protein sequences are 86.3% homologous (91.8% conservative), and the cDNAs are only 75.2% homologous. Both deduced protein sequences contain the expected N-terminal mitochondrial transit peptides. Reverse transcriptase polymerase chain reaction analysis shows that both genes are expressed under normal growth conditions and that their RNA transcripts are trans-spliced to the SL-1 leader sequence. The latter result together with Northern blot analysis indicate that both genes have mono-cistronic transcripts. The sod-3 gene was mapped to chromosome X, and the location of sod-2 was confirmed to be chromosome I. Polymerase chain reaction was used to amplify the cDNA regions encoding the predicted mature manganese superoxide dismutase proteins and each was cloned and expressed to high levels in Escherichia coli cells deficient in cytosolic superoxide dismutases. Both proteins were shown to be active in E. coli, providing similar protection against methyl viologen-induced oxidative stress. The expressed enzymes, which were not inhibited by hydrogen peroxide or cyanide, are dimeric, show quite different electrophoretic mobilities and isoelectric points, but exhibit comparable specific ------------------- Key: 2937 Medline: 97478541 Authors: Burglin TR Title: Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals. Citation: Nucleic Acids Research 25: 4173-4180 1997 Type: ARTICLE Genes: ceh-25 Abstract: A new Caenorhabditis elegans homeobox gene, ceh-25, is described that belongs to the TALE superclass of atypical homeodomains which are characterized by three extra residues between helix 1 and helix 2. ORF and PCR analysis revealed a novel type of alternative splicing within the homeobox. The alternative splicing occurs such that two different homeodomains can be generated, which differ in their first 25 amino acids, ceh-25 is an orthologue of the vertebrate Meis genes and it shares a new conserved domain of 130 amino acids with them. A thorough analysis of all TALE homeobox genes was performed and a new classification is presented. Four TALE classes are identified in animals: PBC, MEIS, TGIF and IRO (Iroquois); two types in fungi: the mating type genes (M-ATYP) and the CUP genes; and two types in plants: KNOX and BEL. The IRO class has a new conserved motif downstream of the homeodomain. For the KNOX class, a conserved domain, the KNOX domain, was defined upstream of the homeodomain. Comparison of the KNOX domain and the MEIS domain shows significant sequence similarity revealing the existence of an archetypal group of homeobox genes that encode two associated conserved domains. Thus TALE homeobox genes-were already present in the common ancestor of plants, fungi and animals and represent a branch distinct from the typical homeobox genes. ------------------- Key: 2938 Medline: 98043868 Authors: Bettinger JC;Euling S;Rougvie AE Title: The terminal differentiation factor LIN-29 is required for proper vulval morphogenesis and egg laying in Caenorhabditis elegans. Citation: Development 124: 4333-4342 1997 Type: ARTICLE Genes: lin-3 lin-14 lin-29 Abstract: Caenorhabditis elegans vulval development culminates during exit from the L4-to-adult molt with the formation of an opening through the adult hypodermis and cuticle that is used for egg laying and mating, Vulva formation requires the heterochronic gene lin-29, which triggers hypodermal cell terminal differentiation during the final molt. lin-29 mutants are unable to lay eggs or mate because no vulval opening forms; instead, a protrusion forms at the site of the vulva, We demonstrate through analysis of genetic mosaics that lin-29 is absolutely required in a small subset of lateral hypodermal seam cells, adjacent to the vulva, for wild-type vulva formation and egg laying. However, lin-29 function is not strictly limited to the lateral hypodermis. First, LIN-29 accumulates in many non-hypodermal cells with known roles in vulva formation or egg laying, Second, animals homozygous for one lin-29 allele, ga94, have the vulval defect and cannot lay eggs, despite having a terminally differentiated adult lateral hypodermis, Finally, vulval morphogenesis and egg laying requires lin-29 activity within the EMS lineage, a lineage that does not generate hypodermal cells. ------------------- Key: 2939 Medline: 98019168 Authors: Zhu J;Hill RJ;Heid PJ;Fukuyama M;Sugimoto A;Priess JR;Rothman JH Title: end-1 encodes an apparent GATA factor that specifies the endoderm precursor in Caenorhabditis elegans embryos. Citation: Genes & Development 11: 2883-2896 1997 Type: ARTICLE Genes: end-1 ges-1 lin-26 pie-1 pop-1 skn-1 arDf1 itDf2 nDf42 wDf3 wDf4 yDf8 yDf9 zuDf2 Abstract: The endoderm in the nematode Caenorhabditis elegans is clonally derived from the E founder cell. We identified a single genomic region (the endoderm-determining region, or EDR) that is required for the production of the entire C. elegans endoderm. In embryos lacking the EDR, the E cell gives rise to ectoderm and mesoderm instead of endoderm and appears to adopt the fate of its cousin, the C founder cell. end-1, a gene from the EDR, restores endoderm production in EDR deficiency homozygotes. end-1 transcripts are first detectable specifically in the E cell, consistent with a direct role for end-1 in endoderm development. The END-1 protein is an apparent zinc finger-containing GATA transcription factor. As GATA factors have been implicated in endoderm development in other animals, our findings suggest that endoderm may be specified by molecularly conserved mechanisms in triploblastic animals. We propose that end-1, the first zygotic gene known to be involved in the specification of germ layer and founder cell identity in C. elegans, may link maternal genes that regulate the establishment of the endoderm to downstream genes responsible for endoderm differentiation. ------------------- Key: 2940 Medline: 98056598 Authors: Meneely PM Title: The chromosomal signal for sex determination in Caenorhabditis elegans. Citation: BioEssays 19: 945-948 1997 Type: REVIEW Genes: fox-1 xol-1 Abstract: In Caenorhabditis elegans, sex is determined by the number of X chromosomes which, in turn, determines the expression of the X-linked gene xol-1. Recent work((1)) has shown that xol-1 expression is controlled by least two distinct regulatory mechanisms, one transcriptional and another post-transcriptional. The transcriptional regulator is a repressor acting in XX embryos; although the specific gene has not been identified, the chromosome region has been defined. A previously defined regulator of xol-1, known as fox-1, maps to a different region of the X chromosome and works post-transcriptionally, consistent with the identification of the fox-1 gene product as a putative RNA binding protein((2)). ------------------- Key: 2941 Medline: 98043855 Authors: Wittmann C;Bossinger O;Goldstein B;Fleischmann M;Kohler R;Brunschwig K;Tobler H;Muller F Title: The expression of the C. elegans labial-like Hox gene ceh-13 during early embryogenesis relies on cell fate and on anteroposterior cell polarity. Citation: Development 124: 4193-4200 1997 Type: ARTICLE Genes: ceh-13 mab-5 pop-1 skn-1 Abstract: Clusters of homeobox-containing HOM-C/hox genes determine the morphology of animal body plans and body parts and are thought to mediate positional information. Here, we describe the onset of embryonic expression of ceh-13, the Caenorhabditis elegans orthologue of the Drosophila labial gene, which is the earliest gene of the C. elegans Hox gene cluster to be activated in C. elegans development. At the beginning of gastrulation, ceh-13 is asymmetrically expressed in posterior daughters of anteroposterior divisions, first in the posterior daughter of the intestinal precursor cell E and then in all posterior daughters of the AB descendants ABxxx. In this paper, we present evidence that supports position-independent activation of ceh-13 during early C. elegans embryogenesis, which integrates cell fate determinants and cell polarity cues. Our findings imply that mechanisms other than cell-extrinsic anteroposterior positional signals play an important role in the activation and regulation of the C. ------------------- Key: 2942 Medline: 98044024 Authors: Bowerman B Title: The worm keeps turning. Citation: Nature 390: 228-229 1997 Type: REVIEW Genes: lit-1 Abstract: Who scapes the lurking sepent's mortal sting? Not he that sets his foot upon her back. Even the smallest of worms will turn, when trodden on. ------------------- Key: 2943 Medline: 98044041 Authors: Xue D;Horvitz HR Title: Caenorhabditis elegans CED-9 protein is a bifunctional cell-death inhibitor. Citation: Nature 390: 305-308 1997 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: The Caenorhabditis elegans gene ced-9 prevents cells from undergoing programmed cell death and encodes a protein similar to the mammalian cell-death inhibitor Bcl-2 (refs 1-7). We show here that the CED-9 protein is a substrate for the C. elegans cell-death protease CED-3 (refs 8, 9), which is a member of a family of cysteine proteases first defined by CED-3 and human interleukin-1 beta converting enzyme (ICE)(10-12). CED-9 can be cleaved by CED-3 at two sites near its amino terminus, and the presence of at least one of these sites is important for complete protection by CED-9 against cell death. Cleavage of CED-9 by CED-3 generates a carboxy-terminal product that resembles Bcl-2 in sequence and in function. Bcl-2 and the baculovirus protein p35, which inhibits cell death in different species through a mechanism that depends on the presence of its cleavage site for the CED-3/ICE family of proteases(9,13-17), inhibit cell death additively in C. elegans, Our results indicate that CED-9 prevents programmed cell death in C. elegans through two distinct mechanisms: first, CED-9 may, by analogy with p35 (refs 9, 17), directly inhibit the CED-3 protease by an interaction involving the CED-3 cleavage sites in CED-9; second, CED-9 may directly or indirectly inhibit CED-3 by means of a protective mechanism similar to that used by mammalian ------------------- Key: 2944 Medline: 98016212 Authors: Hitchcock DR;Black MC;Williams PL Title: Investigations into using the nematode Caenorhabditis elegans for municipal and industrial wastewater toxicity testing. Citation: Archives of Environmental Contamination and Toxicology 33: 252-260 1997 Type: ARTICLE Genes: Abstract: This investigative study assesses the ease and usefulness of the nematode Caenorhabditis elegans for identifying contributors to effluent toxicity within an industrial and municipal wastewater treatment plant (WWTP) system. Several different types of industries, including fiberglass manufacturing, paper packaging, and yarn dyeing, discharge effluent into the municipal wastewater treatment plant, which in turn discharges into a local creek. A major objective of this study was to identify primary sources of toxicity throughout the system with a nematode toxicity test. Twenty-four-hour composite water samples were taken periodically over a ten-month period at five strategic points within the system: (1) at the point of discharge at each of the three industries, (2) at the combined industrial influent of the wastewater treatment plant, (3) at the effluent of the WWTP (4) upstream of the WWTP discharge, and (5) downstream of the WWTP discharge. Samples were analyzed for basic water chemistry. and each sample was tested for whole effluent toxicity using a 72-h nematode test with mortality as the end point. Results suggest that interactions between the wastewaters of certain industries may increase the overall nematode toxicity in the wastewater treatment facility's composite influent and effluent. Nematode mortality trends indicate relatively high toxicity levels in wastewater entering the WWTP from contributing industries. High WWTP influent toxicity may potentially be due to varying flow rate ratios of industrial discharges, release of varying toxic constituents in wastewaters, and toxic interactions between chemical constituents of industrial wastewaters. The evaluation of toxicity within the treatment system may pinpoint locations where pollution prevention strategies may be implemented to reduce overall toxicity at the point ------------------- Key: 2945 Medline: 98072437 Authors: Laughton DL;Lunt GG;Wolstenholme AJ Title: Alternative splicing of a Caenorhabditis elegans gene produces two novel inhibitory amino acid receptor subunits with identical ligand binding domains but different ion channels. Citation: Gene 201: 119-125 1997 Type: ARTICLE Genes: gbr-2 Abstract: Two full-length cDNAs, gbr-2A and gbr-2B, encoding inhibitory amino acid receptor subunits have been amplified and cloned from Caenorhabditis elegans mRNA. The 5' 732 bp of the two cDNAs, encoding 237 amino acids, are identical. The 3' 758 bp of the gbr-2B cDNA are present within the 3' untranslated region of the gbr-2A clone. As a result, the two cDNAs are predicted to encode subunits which share a common extracellular N-terminal sequence of 237 amino acids, but different, though closely related, C-terminal sequences which include four predicted membrane-spanning regions. A search of the EMBL database revealed that the sequences of the two subunits are most closely related to the alpha-subunit of the C. elegans avermectin receptor. Northern blot analysis showed the presence of two related mRNAs of approximately 2.2 and 1.5 kb in a developmentally mixed population of C. elegans. The genomic DNA sequence confirms that both mRNAs were transcribed from the same gene, gbr-2, suggesting that the closely related 3' sequences have arisen as a result of a partial gene duplication event. We propose that C. elegans is utilising alternative splicing to generate receptor subunits with identical extracellular, ligand-binding domains but different transmembrane, channel forming domains. ------------------- Key: 2946 Medline: 98044038 Authors: Kaletta T;Schnabel H;Schnabel R Title: Binary specification of the embryonic lineage in Caenorhabditis elegans. Citation: Nature 390: 294-298 1997 Type: ARTICLE Genes: lit-1 pop-1 tDf5 tDf6 ctDf2 Abstract: In Caenorhabditis elegans, the early embryo contains five somatic founder cells (known as AB, MS, E, C and D) which give rise to very different lineages. Two simply produce twenty intestinal (E) or muscle (D) cells each, whereas the remainder produce a total of 518 cells which collectively contribute in a complex pattern to a variety of tissues(1). A central problem in embryonic development is to understand how the developmental potential of blastomeres is restricted to permit the terminal expression of such complex differentiation patterns. Here we identify a gene, lit-1, that appears to play a central role in controlling the asymmetry of cell division during embryogenesis in C. elegans. Mutants in lit-1 suggest that its product controls up to six consecutive binary snitches which cause one of the two equivalent cells produced at each cleavage to assume a posterior fate. Most blastomere identities in C, elegans may therefore stem from a process of stepwise binary diversification. ------------------- Key: 2947 Medline: Authors: Silverman MA;Blaxter ML;Link CD Title: Biochemical analysis of Caenorhabditis elegans surface mutants. Citation: Journal of Nematology 29: 296-305 1997 Type: ARTICLE Genes: srf-2 srf-3 srf-4 srf-5 srf-8 srf-9 Abstract: A collection of Caenorhabditis elegans mutants that show ectopic surface lectin binding (Srf mutants) was analyzed to determine the biochemical basis for this phenotype. This analysis involved selective removal or labeling of surface components, specific labeling of surface glycans, and fractionation of total protein with subsequent detection of wheat germ agglutinin (WGA) binding proteins. Wild-type and mutant nematodes showed no differences in their profiles of extractable surface glycoproteins or total WGA-binding proteins, suggesting that the ectopic lectin binding does not result from the novel expression of surface glycans. Instead, these results support a model in which ectopic lectin binding results from an unmasking of glycosylated components present in the insoluble cuticle matrix of wild-type animals. To explain the multiple internal defects found in some surface mutants, we propose that these mutants have a basic defect in protein processing. This defect would interfere with the expression of the postulated masking protein(s), as well as other proteins required for normal development. ------------------- Key: 2948 Medline: 98046953 Authors: Kuwabara PE Title: Worming your way through the genome. Citation: Trends in Genetics 13: 455-460 1997 Type: REVIEW Genes: abl-1 daf-12 dec-10 dyf-6 egl-36 lin-12 sel-12 sem-5 tra-2 vab-3 Abstract: The 100 Mb sequence of the nematode Caenorhabditis elegans genome will be completed In 1998. More than 10000 predicted genes have been identified to date, so it should come as no surprise to find a C. elegans homologue of your favourite gene in current databases. For some investigators, the discovery of a C. elegans homologue represents a unique opportunity to adopt a genetic approach and to take advantage of the extensive repertoire of c. elegans gene characterization and manipulation fools. RNA injection provides a quick and efficient method for obtaining clues about wild-type gene function. Reverse genetic approaches also make it feasible to screen de novo for mutations in specific gene sequences. This review highlights the resources available for analysing a C. elegans homologue, starting from the gene sequence and proceeding to the biological function. ------------------- Key: 2949 Medline: 98054147 Authors: Zhang B;Gallegos M;Puoti A;Durkin E;Fields S;Kimble J;Wickens MP Title: A conserved RNA-binding protein that regulates sexual fates in the C. elegans hermaphrodite germ line. Citation: Nature 390: 477-484 1997 Type: ARTICLE Genes: fbf-1 fbf-2 fem-3 fog-2 her-1 Abstract: The nematode Caenorhabditis elegans has two sexes, males and hermaphrodites. Hermaphrodites initially produce sperm but switch to producing oocytes. This switch appears to be controlled by the 3' untranslated region of fem-3 messenger RNA. We have now identified a binding factor (FBF) which is a cytoplasmic protein that binds specifically to the regulatory region of fem-3 3'UTR and mediates the sperm/oocyte switch. The RNA-binding domain of FBF consists of a stretch of eight tandem repeats and two short flanking regions. This structural element is conserved in several proteins Including Drosophila Pumilio, a regulatory protein that controls pattern formation in the fly by binding to a 3'UTR. We propose that FBF and Pumilio are members of a widespread family of sequence-specific RNA-binding ------------------- Key: 2950 Medline: 98041503 Authors: Barnes TM;Hekimi S Title: The Caenorhabditis elegans avermectin resistance and anesthetic response gene unc-9 encodes a member of a protein family implicated in electrical coupling of Citation: Journal of Neurochemistry 69: 2251-2260 1997 Type: ARTICLE Genes: eat-5 opu-1 opu-2 opu-3 opu-4 opu-5 opu-6 opu-7 opu-8 opu-9 opu-10 opu-11 opu-12 opu-13 opu-14 opu-15 opu-16 opu-17 opu-18 opu-19 opu-20 opu-21 unc-7 unc-9 unc-124 Abstract: Mutations in the unc-9 gene of the nematode Caenorhabditis elegans cause abnormal forward locomotion and an egg-retention phenotype. unc-9 mutations also reduce the worms' sensitivity to avermectin and block a form of hypersensitivity to volatile anesthetics. We report here the cloning and molecular characterization of unc-9 and show that it encodes a member of the OPUS family of proteins that is 56% identical to another OPUS protein, UNC-7. It is significant that unc-9 mutants share all phenotypes with unc-7 mutants. Mutants in another gene, unc-124, also share all tested phenotypes with unc-9 mutants, including identical locomotory and egg-laying defects, suggesting that multiple genes are required for the same biochemical function. OPUS proteins are implicated in the function of invertebrate gap junctions, and, based on a new alignment including 24 members from C. elegans, we present a refined model for the structure of OPUS proteins suggesting that oligomers could form a hydrophilic pore. We also show that alteration of highly conserved proline residues in UNC-9 reads to a cold sensitivity that likely affects a step in protein expression rather than function. Finally, we speculate on the basis of the avermectin resistance and anesthetic response phenotypes. ------------------- Key: 2951 Medline: 97136774 Authors: Keynes R;Cook GMW Title: Axons turn as netrins find their receptor. Citation: Neuron 17: 1031-1034 1996 Type: REVIEW Genes: unc-5 unc-6 unc-40 Abstract: The idea of chemoattraction as a guiding mechanism for growing axons was originally suggested by Ramon y Cajal as a result of earlier work on leucocytes. Discussing the ventral navigation of commissural axons toward the midline floor plate in the developing spinal cord, he wrote: "...The oblique direction assumed by these axons would be explained if chemoattractants produced by the ventral half of the neuroepithelium were stronger than those produced by the rest of the epithelium...a sufficiently extended period of chemoattractant secretion by the floor plate could explain the relatively long period of time over which the ventral commissure is formed". Chemoattraction is well established at the molecular level in leucocyte biology, but good evidence was lacking in the vertebrate nervous system until collagen gels were used to assay for chemoattractants, allowing the purification and cloning of netrins. The homology then revealed between netrins and UNC-6, a laminin-related protein required for circumferential dorsal and ventral migrations of axons in the body wall of Caenorhabditis elegans, further suggested that netrins may provide highly conserved midline guidance cues for axons, operating in organisms ranging from nematode worms to higher vertebrates. This appealing view is now amply confirmed with an impressive group of studies using worms, flies, and rodents to analyze neural development in the face of netrin loss- and gain-of-function, and the story has simultaneously taken a significant step forward with the identification of the ------------------- Key: 2952 Medline: Authors: Kemphues K;Mello C Title: Antisense RNA injection in Caenorhabditis elegans. Citation: Trends in Cell Biology 7: 462- 1997 Type: REVIEW Genes: nmy-2 par-1 Abstract: Antisense knockout techniques are also being used in worm embryos to inactivate transcripts and look at the effects. This method was pioneered by Su Guo and Ken Kemphues in 1995, initially to verify that the clone they had isolated corresponded to the par-1 gene, and now has been used by a large number of groups studying a variety of different genes. ------------------- Key: 2953 Medline: 96000456 Authors: Burns RG Title: Identification of two new members of the tubulin family. Citation: Cell Motility and the Cytoskeleton 31: 255-258 1995 Type: REVIEW Genes: The tubulin family has been considered to have two members, the alpha and beta tubulins, which interact to form the heterodimers which in turn assemble to form the eukaryotic microtubules. A third member, gamma tubulin, was identified in 1989 and has since been shown to be specifically localized at Microtubule Organizing Centers and has been implicated in the nucleation of microtubules in vivo. Comparisons of individual alpha, beta and gamma tubulin sequences within the three subfamilies yield homologies of 65-100% identity. By contrast, comparisons between the three subfamilies typically yield homologies of only 30-40% identity. The Caenorhabditis and yeast genome projects have recently identified two putative gamma Abstract: The tubilin family has been considered to have two members, the a- and B-tubulins, which interact to form the heterodimers which in turn assemble to form the eukaryotic microtubules. A third member, y-tubulin, was identified in 1989 and has since been shown to be specifically localized in Microtubule Organizing Centers and has been implicated in the nucleation of microtubules in vivo. Comparisons of individual a-, B-, and y-tubulin sequences within the three subfamilies yield homologies of 65-100% identity. By contrast, comparisons between the three subfamilies typically yield homologies of only about 30-40% identity. The Caenorhabditis and yeast genome projects have recently identified two putative y-tubulin sequences. Analysis of these sequences, however, shows that they are significantly different from those of bona fide y-tubulins... ------------------- Key: 2954 Medline: Authors: Tatara CP;Newman MC;McCloskey JT;Williams PL Title: Predicting relative metal toxicity with ion characteristics: Caenorhabditis elegans LC50. Citation: Aquatic Toxicology 39: 279-290 1997 Type: ARTICLE Genes: Abstract: Quantitative Structure Activity Relationships (QSAR) predict relative toxicity of a family of chemicals from fundamental and surrogate molecular qualities. Most QSARs are developed for organic toxicants, with inorganic toxicants (metals) being under-represented. Successful predictive models for relative toxicity of divalent metal ions using ion characteristics have been produced using Microtox(R), a 15 min microbial bioassay. The present study extends this approach to longer exposure durations (24 h), and a more complex organism (metazoan). Twenty-four hour LC50s (expressed as total metal concentration) for the free-living soil nematode, C. elegans were determined for Ca, Cd, Cu, Hg, Mg, Mn, Ni, Pb, and Zn in an aqueous medium. Relative metal toxicity was predicted with least squares linear regression and several ion characteristics. Toxicity was most effectively predicted (r(2) = 0.89) with \ log k(OH) \ (where K-OH is the first hydrolysis constant), which reflects a metal ion's tendency to bind to intermediate ligands such as biochemical functional groups with O donor atoms. The best fitting model was obtained using LC50 metameters based on total metal concentration, indicating that the identification of the bioactive species of metals can be ambiguous, and does not necessarily aid in the prediction of relative metal toxicity with ion characteristics. The modelling of relative metal toxicity using ion characteristics was successful for 24 h exposure durations using this more complex organism. ------------------- Key: 2955 Medline: 99001276 Authors: Easton DM Title: Gompertz growth in number dead confirms medflies and nematodes show excess oldster survival. Citation: Experimental Gerontology 32: 719-726 1997 Type: ARTICLE Genes: Abstract: A recent report (Easton, 1995) showed that, at least for Mediterranean fruit flies, a Gompertz growth equation based on the increase in number of individuals that die is a better predictor of survival data than is the classical Gompertz survivorship model based on the decrease in number that survive (analysis of medfly data of Carey et al., 1992). In the growth model, the rate of increase of the number dead (i.e., the death rate) decreases exponentially with age. The poor fit of the classical model predicts ''excess survival'' of older members, but, when the scale of the better-fitting growth model is increased 2400 x, such excess is now also evident as a small but distinctly separate cohort of the medfly subjects. The smaller population appears to be about 0.01% of the larger, and the death rate decreases about one-fourth as fast. Survival of the nematode C. elegans (Brooks et al., 1994) is also better predicted by the growth model, which also shows excess survival of the worms at great age. ------------------- Key: 2956 Medline: 98058780 Authors: Harbinder S;Tavernarakis N;Herndon LA;Kinnell M;Xu SQ;Fire A;Driscoll M Title: Genetically targeted cell disruption in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 94: 13128-13133 1997 Type: ARTICLE Genes: del-2 mec-4 mec-6 mec-7 myo-2 unc-4 unc-8 unc-54 Abstract: The elimination of identified cells is a powerful tool for investigating development and system function. Here we report on genetically mediated cell disruption effected by the toxic Caenorhabditis elegans mec-4(d) allele, We found that ectopic expression of mec-4(d) in the nematode causes dysfunction of a wide range of nerve, muscle, and hypodermal cells, mec-4(d)-mediated toxicity is dependent on the activity of a second gene, mec-6, rendering cell disruption conditionally dependent on genetic background. We describe a set of mec-4(d) vectors that facilitate construction of cell-specific disruption reagents and note that genetic cell disruption can be used for functional analyses of specific neurons or neuronal classes, for confirmation of neuronal circuitry, for generation of nematode populations lacking defined classes of functional cells, and for genetic screens. We suggest that mec-4(d) and/or related genes may be effective general tools for cell inactivation that could be used toward similar ------------------- Key: 2957 Medline: 98068840 Authors: Page AP Title: Cyclophilin and protein disulfide isomerase genes are co-transcribed in a functionally related manner in Caenorhabditis elegans. Citation: DNA and Cell Biology 16: 1335-1343 1997 Type: ARTICLE Genes: cyp-9 pdi-1 Abstract: The ubiquitous enzymes peptidlyl prolyl cis-trans isomerase (PPI, EC 5.2.1.8) and protein disulfide isomerase (PDI, EC 5.3.4.1) are important rate-limiting catalysts of protein-folding events in the cell. In the free-living nematode Caenorhabditis elegans, two genes encoding these enzymes (cyp-9 and pdi-1, respectively) are clustered together on chromosome Ln. In work described elsewhere, the encoded enzymes have been expressed as recombinant proteins and have been determined to possess in vitro PPI and PDI activity. Taken together, this organization of the two genes and the related functions of their transcripts indicate that they may be cotranscribed as a polycistronic unit, similar to bacterial operons. This study details the very close linkage of pdi-1 and cyp-9, which are in the same orientation. pdi-1 is the upstream gene, and the putative polyadenylation cleavage signal of this gene is separated from the trans-splice acceptor site of cyp-9 by only 103 bp. pdi-1 is trans-spliced by the ubiquitous nematode trans-spliced leader SL1, whereas cyp-9 was found to be predominantly trans-spliced by the ''operon-specific'' trans-spliced leader SL2. Similar trends in relative transcript abundance were demonstrated with synchronously produced mRNA for both genes during larval development, supporting the contention that the genes are co-expressed. Finally, reporter gene analysis provides strong evidence that both genes are controlled by a single upstream regulatory element, which directs expression of both enzymes in the hypodermal cells that ------------------- Key: 2958 Medline: 98072487 Authors: Mitenko NL;Eisner JR;Swiston JR;Mains PE Title: A limited number of Caenorhabditis elegans genes are readily mutable to dominant, temperature-sensitive maternal-effect embryonic lethality. Citation: Genetics 147: 1665-1674 1997 Type: ARTICLE Genes: let-354 mei-1 mel-23 mel-24 mel-25 mel-26 mel-43 mel-44 mel-45 ctDf3 eDf18 eDf19 nDf40 sDf35 tDf7 Abstract: Dominant gain-of-function mutations can give unique insights into the study of gene function. In addition, gain-of-function mutations, unlike loss-of-function alleles, are not biased against the identification of genetically redundant loci. To identify novel genetic functions active during Caenorhabditis elegans embryogenesis, we have collected a set of dominant temperature-sensitive maternal-effect embryonic lethal mutations. In a previous screen, we isolated eight such mutations, distributed among six genes. In the present study, we describe eight new dominant mutations that identify only three additional genes, yielding a total of 16 dominant mutations found in nine genes. Therefore, it appears that a limited number of C. elegans genes mutate to this phenotype at appreciable frequencies. Five of the genes that we identified by dominant mutations have loss-of-function alleles. Two of these genes may lack loss-of-function phenotypes, indicating that they are nonessential and so may represent redundant loci. Loss-of-function mutations of three other genes are associated with recessive lethality, indicating ------------------- Key: 2959 Medline: 98072488 Authors: Tax FE;Thomas JH;Ferguson EL;Horvitz HR Title: Identification and characterization of genes that interact with lin-12 in Caenorhabditis elegans. Citation: Genetics 147: 1675-1695 1997 Type: ARTICLE Genes: glp-1 lag-2 lin-12 sel-4 sel-5 sel-6 sel-7 sel-8 sup-17 mnDf1 mnDf5 mnDf7 mnDf9 mnDf10 mnDf11 mnDf19 nDf3 nDf23 nDf24 nDf25 nDf29 nDf30 sDf20 sDf26 sDf27 sDf28 sDf31 sDf32 sDf33 sDf34 sDf40 sDf41 sDf46 sDf8 sDf49 sDf51 sDf70 yDf10 yDp1 Abstract: We identified and characterized 14 extragenic mutations that suppressed the dominant egg-laying defect of certain lin-12 gain-of-function mutations. These suppressors defined seven genes: sup-17, lag-2 sel-4, sel-5, sel-6, sel-7 and sel-8. Mutations in six of the genes are recessive suppressors, whereas the two mutations that define the seventh gene, lag-2 are semi-dominant suppressors. These suppressor mutations were able to suppress other lin-12 gain-of-function mutations. The suppressor mutations arose at a very low frequency per gene, 10-50 times below the typical loss-of-function mutation frequency. The suppressor mutations in sup-17 and lag-2 were shown to be rare non-null alleles, and we present evidence that null mutations in these two genes cause lethality. Temperature-shift studies for two suppressor genes, sup-17 and lag-2, suggest that both genes act at approximately the same time as lin-12 in specifying a cell fate. Suppressor alleles of six of these genes enhanced a temperature-sensitive loss-of-function allele of glp-1, a gene related to lin-12 in structure and function. Our analysis of these suppressors suggests that the majority of these genes are part of a shared lin-12/glp-1 signal transduction pathway, or act to regulate the ------------------- Key: 2960 Medline: Authors: Beck CDO;Rankin CH Title: Long-term habituation is produced by distributed training at long ISIs and not by massed training or short ISIs in Caenorhabditis elegans. Citation: Animal Learning & Behavior 25: 446-457 1997 Type: ARTICLE Genes: Abstract: To begin an investigation of the cellular processes that underlie long-term memory in the nematode Caenorhabditis elegans, it is first necessary to determine that C. elegans is capable of retention over 24 h, and to investigate the factors that may influence the expression of long-term memory. In the present study, the effects of stimuli number, interstimulus interval (ISI), and training procedure on longterm retention of habituation were tested in C. elegans. At a long (60-sec) ISI, distributed training sessions produced long-term habituation retained for 24 h, whereas massed training sessions or training with few stimuli did not. When training was performed at a short (10-sec) ISI, long-term habituation was not detectable with testing at either a 10- or a 60-sec ISI. The long-term habituation observed after distributed training sessions at a 60-sec ISI was consistently expressed when the training procedures were varied. Thus it is clear that C. elegans can reliably express long-term retention for distributed training sessions at a 60-sec ISI, making the system a candidate for further investigations into the cellular processes supporting memory. ------------------- Key: 2961 Medline: Authors: Wade N Title: A worm and a computer help illuminate diabetes. Citation: The New York Times, December 30 : B13-B14 1997 Type: REVIEW Genes: daf-2 daf-16 Abstract: His tall figure bent over a computer screen in his laboratory at the Massachusetts General Hospital, Dr. Gary Ruvkun rummages through a distant genetic data base for matches to a gene he believes is involved in diabetes. ?You learn how to read these as they are ratcheting by,? he says, while lines of data streak up his screen. ?I think MTV is good training.? ------------------- Key: 2962 Medline: 98058705 Authors: Peter ME;Heufelder AE;Hengartner MO Title: Advances in apoptosis research. Citation: Proceedings of the National Academy of Sciences USA 94: 12736-12737 1997 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: Apoptosis, also called programmed cell death, has attracted great attention in recent years. After its discovery by Carl Vogt in 1842, apoptosis research was dormant for more than a century. Its rediscovery in the second half of this century, and the coining of the term apoptosis in 1972 by Kerr, Wyllie, and Currie, ignited an unparalleled interest in this field of science. The number of publications related to apoptosis has been growing exponentially every year ever since. This is mainly due to three major advances, two of which have been made recently and one that is currently seen. First, studies with the small nematode Caenorhabditis elegans have identified a number of apoptosis regulating genes-the first evidence that cell death is an active process under genetic control. Many of these genes have mammalian homologs that, like their worm counterparts, seem to regulate mammalian apoptosis. Second, elucidation of the signal transduction pathways of apoptosis has lead especially to the identification of specific death signaling molecules such as a new family of cysteine proteases, the caspases. Third, it has now become clear that many diseases are characterized by dysregulation of apoptotic programs. Many of these programs involve a family of receptors and their ligands, the death receptor/ligand family. The hope now is to interfere with apoptosis regulation in these systems and to develop new ------------------- Key: 2963 Medline: 98086466 Authors: Kim SK Title: Polarized signaling: basolateral receptor localization in epithelial cells by PDZ-containing proteins. Citation: Current Opinion in Cell Biology 9: 853-859 1997 Type: REVIEW Genes: let-23 lin-2 lin-3 lin-7 lin-10 Abstract: Extracellular signals are normally presented to one surface of epithelial cells and to one end of neurons, and so neuronal and epithelial cell signaling is inherently polarized. Another aspect of signaling polarity is that receptors are often asymmetrically distributed on the surfaces of polarized cells, Recent evidence from studies of Caenorhabditis elegans shows that signaling polarity plays an important role in development. The underlying mesoderm induces the overlying ectoderm to form the vulva, and asymmetric distribution of the signal receptor on the basolateral surface of the epithelium is crucial for this signaling. In neurons, the localization of neurotransmitter receptors and ion channels at synapses allows neurons to be exquisitely sensitive to synaptic inputs. Exciting recent reports suggest that receptor localization to neuronal synapses and the basolateral membrane domains of epithelia may involve a common molecular mechanism involving localization by PDZ-containing proteins. ------------------- Key: 2964 Medline: 98088688 Authors: Wen C;Metzstein MM;Greenwald I Title: SUP-17, a Caenorhabditis elegans ADAM protein related to Drosophila KUZBANIAN, and its role in LIN-12/NOTCH signalling. Citation: Development 124: 4759-4767 1997 Type: ARTICLE Genes: lin-12 sup-17 Abstract: LIN-12/NOTCH proteins mediate cell-cell interactions that specify cell fates, Previous work suggested that sup-17 facilitates lin-12 signalling in Caenorhabditis elegans, Here, we show that sup-17 encodes a member of the ADAM family of metalloproteases. SUP-17 is highly similar to Drosophila KUZBANIAN, which functions in Drosophila neurogenesis, and the vertebrate ADAM10 protein, Furthermore, we show by genetic analysis that the extracellular domain of LIN-12 appears to be necessary for sup-17 to facilitate lin-12 signalling and that sup-17 does not act downstream of lin-12, Finally, we show by cell ablation experiments that sup-17 can act cell autonomously to facilitate lin-12 activity, We discuss the implications of our observations for LIN-12/NOTCH signalling and how our results complement and extend results obtained from genetic analysis of kuz in Drosophila. ------------------- Key: 2965 Medline: 98070945 Authors: Rose KL;Winfrey VP;Hoffman LH;Hall DH;Furuta T;Greenstein D Title: The POU gene ceh-18 promotes gonadal sheath cell differentiation and function required for meiotic maturation and ovulation in Caenorhabditis elegans. Citation: Developmental Biology 192: 59-77 1997 Type: ARTICLE Genes: ceh-18 hlh-1 mup-2 myo-3 unc-54 unc-89 Abstract: In Caenorhabditis elegans, specialized contractile myoepithelial cells of the somatic gonad, the gonadal sheath cells, are closely apposed to oocytes and are required for normal meiotic maturation and ovulation. Previously we found that mutations in the ceh-18 gene, which encodes a POU-class homeoprotein expressed in sheath cells, result in oocyte defects. To determine the basis for these oocyte defects, we have used time-lapse video Nomarski microscopy to observe meiotic maturation, ovulation, and early embryogenesis in ceh-18 mutants. In ceh-18 mutants sheath cell contractions are weaker, less frequent, and uncoordinated throughout the sequence of ovulation events, and ovulation is defective. Defective ovulation can result in the formation of endomitotic oocytes in the gonad, the formation of haploid embryos, and reversals in embryonic polarity. ceh-18 mutant oocytes exhibit defects prior to nuclear envelope breakdown, suggesting that they are physiologically different from the wild type. We observed delays in meiotic maturation, as well as maturation out of the normal spatial and temporal sequence, suggesting that proximal sheath cells directly or indirectly promote and spatially restrict meiotic maturation. Analysis of sheath cell differentiation in ceh-18 mutants using antibodies to proteins of the contractile apparatus reveals that although contractile proteins are expressed, the sheath cells appear disorganized. Transmission electron microscopy reveals that ceh-18 mutant sheath cells are morphologically irregular and only loosely cover oocytes. Taken together, these observations indicate that ceh-18 is a crucial determinant of sheath cell differentiation, a function required for ------------------- Key: 2966 Medline: 98051191 Authors: Hubbard EJA;Wu G;Kitajewski J;Greenwald I Title: sel-10, a negative regulator of lin-12 activity in Caenorhabditis elegans, encodes a member of the CDC4 family of proteins. Citation: Genes & Development 11: 3182-3193 1997 Type: ARTICLE Genes: lin-12 sel-10 nDf42 Abstract: Mutations that influence lin-12 activity in Caenorhabditis elegans may identify conserved factors that regulate tile activity of lin-12/Notch proteins. We describe genetic evidence indicating that sel-10 is a negative regulator of lin-12/Notch-mediated signaling in C, elegans. Sequence analysis shows that SEL-10 is a member of the CDC4 family of proteins and has a potential human ortholog. Coimmunoprecipitation data indicate that C. Elegans SEL-10 complexes with LIN-12 and with murine Notch4. We propose that SEL-10 promotes the ubiquitin-mediated turnover of LIN-12/Notch proteins, and discuss potential roles for the regulation of a lin-12/Notch activity by sel-10 in cell fate decisions and tumorigenesis. ------------------- Key: 2967 Medline: 98119177 Authors: Mori I;Ohshima Y Title: Molecular neurogenetics of chemotaxis and thermotaxis in the nematode Caenorhabditis elegans. Citation: BioEssays 19: 1055-1064 1997 Type: REVIEW Genes: che-1 che-2 che-3 che-6 che-7 che-10 che-11 che-12 che-13 che-14 daf-6 daf-10 daf-11 daf-21 dyf-1 dyf-2 dyf-3 dyf-4 dyf-5 dyf-6 dyf-7 dyf-8 dyf-8 dyf-9 dyf-10 dyf-11 dyf-12 dyf-13 odr-1 odr-2 odr-3 odr-4 odr-5 odr-7 odr-10 osm-1 osm-3 osm-5 osm-6 tax-2 tax-4 tax-6 ttx-1 ttx-2 ttx-3 sra-7 sra-9 srg-2 srg-8 Abstract: Chemotaxis and thermotaxis in Caenorhabditis elegans are based on the chemical senses (smell and taste) and the thermal sense, respectively, which are important for the life of the animal. Laser ablation experiments have allowed identification of sensory neurons and some interneurons required for these senses. Many mutants that exhibit various abnormalies have been isolated and analyzed. These studies have predicted novel signaling pathways whose components include a putative odorant specific transmembrane receptor (ODR-10) and a cyclic nucleotide-gated channel (TAX-4/TAX-2) functioning in taste and thermosensation as well as in smell. The emerging picture of the mechanisms of sensory transduction in C. elegans seems to be basically similar to what is known of visual and olfactory sensory transduction in vertebrates. Thus, molecular and cellular analyses of chemotaxis and thermotaxis in C. elegans have proved useful and will continue to provide significant implications for the ------------------- Key: 2968 Medline: 98090064 Authors: Takagi S;Benard C;Pak J;Livingstone D;Hekimi S Title: Cellular and axonal migrations are misguided along both body axes in the maternal-effect mau-2 mutants of Caenorhabditis elegans. Citation: Development 124: 5115-5126 1997 Type: ARTICLE Genes: che-3 dpy-5 mau-2 mec-7 unc-31 nDf24 Abstract: We have characterized the mau-2 mutants of Caenorhabditis elegans and found that migrating cells and axons are mispositioned along both the antero-posterior and dorsoventral body axes. This is in contrast to previously characterized guidance mutations in Caenorhabditis and in Drosophila, which have been found to be axis-specific. Two observations suggest that mau-2 acts very early during development: most behavioral phenotypes of man-2 can be rescued by a maternal effect, and variations in expressivity involve an entire body side at a time. The possibility that mau-2 is involved in the spatial organization of guidance cues encoded by other genes is ------------------- Key: 2969 Medline: 98086477 Authors: Sonnhammer ELL;Durbin R Title: Analysis of protein domain families in Caenorhabditis elegans. Citation: Genomics 46: 200-216 1997 Type: ARTICLE Genes: Abstract: The Caenorhabditis elegans genome sequencing project has completed over half of this nematode's 100-Mb genome. Proteins predicted in the finished sequence have been compiled and released in the database Wormpep. Presented here is a comprehensive analysis of protein domain families in Wormpep 11, which comprises 7299 proteins. The relative abundance of common protein domain families was counted by comparing all Wormpep proteins to the Pfam collection of protein families, which is based on recognition by hidden Markov models. This analysis also identified a number of previously unannotated domains. To investigate new apparently nematode-specific protein families, Wormpep was clustered into domain families on the basis of sequence similarity using the Domainer program. The largest clusters that lacked clear homology to proteins outside Nematoda were analyzed in further detail, after which some could be assigned a putative function. We compared all proteins in Wormpep 11 to proteins in the human, Saccharomyces cerevisiae, and Haemophilus influenzae genomes. Among the results are the estimation that over two-thirds of the currently known human proteins are likely to have a homologue in the whole C. elegans genome and that a significant number of proteins are well conserved between C. elegans and H. influenzae, that are not found in S. cerevisiae. ------------------- Key: 2970 Medline: 98105120 Authors: Slack F;Ruvkun G Title: Temporal pattern formation by heterochronic genes. Citation: Annual Review of Genetics 31: 611-634 1997 Type: REVIEW Genes: daf-12 egl-35 let-7 lin-4 lin-14 lin-28 lin-29 lin-41 lin-42 lin-46 Abstract: Heterochrony describes the phylogenetic variation in the relative timing of major developmental events. Such heterochronic variation has been noted across phylogeny, including closely related species, suggesting that particular genetic loci control global aspects of developmental timing, and that variation at those loci may play important roles in evolutionary change. Genetic analyses of heterochronic mutations in the nematode Caenorhabditis elegans reveal that control of temporal patterning is analogous to the dedicated genetic pathways that control the patterning of the spatial axes in Drosophila and other metazoans. These pathways generate graded or binary levels of regulatory factors that pattern particular axes of the developing animal. C. elegans heterochronic genes constitute a regulatory cascade that both generates a temporal decrease in the level of the LIN-14 and LIN-28 proteins and responds to the changes in these gene activities to coordinate the temporal sequence of many cell fates as the animal develops. The temporal regulation of lin-14 and lin-28 gene activities is posttranscriptional and mediated by the antisense RNA product of the lin-4 gene. Hormonal control of developmental timing is a common theme throughout phylogeny. Heterochronic genes that involve hormonal signaling have been identified in vertebrates as well as C. ------------------- Key: 2971 Medline: 98105079 Authors: Wood WB Title: Left-right asymmetry in animal development. Citation: Annual Review of Cell and Developmental Biology 13: 53-82 1997 Type: REVIEW Genes: Abstract: Most animal species exhibit left-right asymmetry in their body plans and show a strong bias for one handedness over the other. The mechanism of handedness choice, recognized as an intriguing problem over a century ago, is still a mystery. However, from recent advances in understanding when and how asymmetry arises in both invertebrates and vertebrates, developmental pathways for establishment and maintenance of left-right differences are beginning to take shape, and speculations can be made on the initial choice mechanism. ------------------- Key: 2972 Medline: 98105088 Authors: Kimble J;Simpson P Title: The LIN-12/Notch signaling pathway and its regulation. Citation: Annual Review of Cell and Developmental Biology 13: 333-361 1997 Type: REVIEW Genes: apx-1 ego-1 ego-2 ego-3 ego-4 ego-5 ego-6 ego-7 ego-8 ego-9 ego-10 emb-5 glp-1 glp-4 lag-1 lag-2 lin-12 sel-1 sel-9 sel-10 sel-11 sel-12 sog-1 sog-2 sog-3 sog-4 sog-5 sog-6 sog-7 sog-8 sog-9 sog-10 Abstract: Notch, LIN-12, and GLP-1 are receptors that mediate a broad range of cell interactions during Drosophila and nematode development. Signaling by these receptors relies on a conserved pathway with three core components: DSL ligand, LNG receptor, and a CSL effector that links the receptor to its transcriptional response. Although key functional regions have been identified in each class of proteins, the mechanism for signal transduction is not yet understood. Diverse regulatory mechanisms influence signaling by the LIN-12/Notch pathway. Inductive signaling relies on the synthesis of ligand and receptor in distinct but neighboring cells. By contrast lateral signaling leads to the transformation of equivalent cells that express both ligand and receptor into nonequivalent cells that express either ligand or receptor. This transformation appears to rely on regulatory feedback loops within the LIN-12/Notch pathway. In addition, the pathway can be regulated by intrinsic factors that are asymmetrically segregated during cell division or by extrinsic cues via other signaling pathways. Specificity in the pathway does not appear to reside in the particular ligand or receptor used for a given cell-cell interaction. The existence of multiple ligands and receptors may have evolved from the stringent demands placed upon the regulation of genes encoding them. ------------------- Key: 2973 Medline: 97450618 Authors: Cooper JA;Hayman W;Reed C;Kagawa H;Good MF;Saul A Title: Mapping of conformational B cell epitopes within alpha-helical coiled coil proteins. Citation: Molecular Immunology 34: 433-440 1997 Type: ARTICLE Genes: unc-15 Abstract: An approach to mapping antigenic B cell epitopes within alpha-helical coiled coil proteins has been developed and applied to two proteins: Streptococcal M protein and C. elegans paramyosin protein UNC-15. Overlapping peptides derived from an alpha-helical coiled coil conformational epitope were embedded between helical flanking peptides derived from the completely unrelated GCN4 leucine zipper peptide. The resulting chimeric peptides exhibited helical propensity. Chimeric peptides were tested for antigenicity (recognition by antibody) or immunogenicity (production of appropriate antibody response). A conformational epitope within the Streptococcal M protein recognised by three mAbs spanned 12 residues. Analysis of chimeric peptides based on C. elegans UNC-15 has enabled fine mapping of the minimal B cell epitope recognised by monoclonal antibody NE1-6B2 to seven non-contiguous residues (spanning 15 residues); the footprint of contact residues involved in antibody recognition being restricted to the hydrophilic face of the helix and covering five helical turns. This chimeric peptide epitope when coupled to diphtheria toxoid was highly immunogenic in mice and antisera recognised the conformationally dependent native peptide epitope. This approach has the potential to map conformational epitopes and design minimal epitopes for use as vaccine candidates. ------------------- Key: 2974 Medline: 98070331 Authors: Cadigan KM;Nusse R Title: Wnt signaling: a common theme in animal development. Citation: Genes & Development 11: 3286-3305 1997 Type: REVIEW Genes: apr-1 egl-20 lin-17 lin-44 mom-1 mom-2 mom-5 pop-1 wrm-1 Abstract: Wnt proteins are now recognized as one of the major families of developmentally important signaling molecules, with mutations in Wnt genes displaying remarkable phenotypes in the mouse, Caenorhabditis elegans, and Drosophila. Among functions provided by Wnt proteins are such intriguing processes as embryonic induction, the generation of cell polarity, and the specification of cell fate. Until recently, our knowledge of the molecular mechanism of Wnt signaling was very limited, but over the past year, several major gaps have been filled. These include the identification of cell-surface receptors and a novel mechanism of relaying the signal to the cell nucleus. In addition, several components of Wnt signaling are implicated in the genesis of human cancer. These insights have come from different corners of the animal kingdom and have converged on a common pathway. At this junction in this rapidly evolving field, we review our current understanding of Wnt function and signaling mechanisms, doing so in a comparative approach. We have put emphasis on the latest findings, highlighting novelty and underscoring questions that remain. For additional literature, we refer to several previous reviews (McMahon 1992; Nusse and Varmus 1992; Klingensmith and Nusse 1994; Miller and Moon 1996; Moon et al 1997). We have limited the number of references, particularly the tables. Fully referenced forms of these tables can be found on the Wnt homepage (http://www.leland.standford.edu/~rnusse/wntwindow.html). ------------------- Key: 2975 Medline: 98109894 Authors: Hekimi S;Lakowski B;Barnes TM;Ewbank JJ Title: Molecular genetics of life span in C. elegans: how much does it teach us? Citation: Trends in Genetics 14: 14-20 1998 Type: REVIEW Genes: age-1 clk-1 clk-2 clk-3 daf-2 daf-16 daf-28 gro-1 Abstract: Several loci have been identified in the nematode worm Caenorhabditis elegans that, when mutated, can increase life span. Three of these genes, age-1, daf-2 and clk-1, have note been cloned. Mutations in these three genes are highly pleiotropic and affect many aspects of worm development and behaviour. age-1 and daf-2 act in the same genetic pathway and have similar effects on the worm. age-1 encodes a homologue of the p110 subunit of phosphatidylinositol 3-kinase and daf-2 encodes an insulin receptor family member. clk-1 encodes a protein of unknown biochemical function similar to the yeast metabolic regulator Cat5p/Coq7p. The implications of these findings for our understanding of organismal ageing are discussed. ------------------- Key: 2976 Medline: 98109890 Authors: Marra MA;Hillier L;Waterston RH Title: Expressed sequence tags - ESTablishing bridges between genomes. Citation: Trends in Genetics 14: 4-7 1998 Type: REVIEW Genes: Abstract: On 1 August 1997, US Vice President Gore officially announced the creation of a new World Wide Web database which aims to provide powerful new resources to researchers investigating the molecular basis of cancer... ------------------- Key: 2977 Medline: 98087404 Authors: Che S;Weil MM;Etkin LD;Epstein HF;Kuang J Title: Molecular cloning of a splice variant of Caenorhabditis elegans YNK1, a putative element in signal transduction. Citation: Biochemicia et Biophysica Acta - Gene Structure and Expression 1354: 231-240 1997 Type: ARTICLE Genes: Abstract: YNK1 is a 98.3-kDa protein whose sequence was originally deduced from a genomic sequence in Caenorhabditis elegans. It was recently found that YNK1 is homologous to three different proteins implicated in signal transduction, suggesting that YNK1 is a signal transduction protein. In this report we describe the isolation of a full-length cDNA that encodes a splice variant of YNK1, designated YNK1a. We also present evidence that both YNK1 and YNK1a transcripts exist in vivo. Furthermore, using an antibody raised against a YNK1a recombinant protein, we demonstrate that the YNK1 protein is expressed in vivo throughout ------------------- Key: 2978 Medline: 98133876 Authors: Forrester WC;Perens E;Zallen JA;Garriga G Title: Identification of Caenorhabditis elegans genes required for neuronal differentiation and migration. Citation: Genetics 148: 151-165 1998 Type: ARTICLE Genes: cam-1 cam-2 ceh-10 epi-1 fam-1 fam-2 ina-1 mig-2 syc-1 syc-2 syc-3 unc-34 unc-73 vab-8 eDf3 mnDf1 mnDf16 qDf3 sDf23 sDf121 yDf10 Abstract: To understand the mechanisms that guide migrating cells, we have been studying the embryonic migrations of the C. elegans canal-associated neurons (CANs). Here, we describe two screens used to identify genes involved in CAN migration. First, we screened for mutants: that died as clear larvae (Clr) or had withered tails (Wit), phenotypes displayed by animals lacking normal CAN function. Second, we screened directly for mutants with missing or misplaced CANs. We isolated and characterized 30 mutants that defined 14 genes necessary for CAN migration. We found that one of the genes, ceh-10, specifies CAN fate. ceh-10 had been defined molecularly as encoding a homeodomain protein expressed in the CANs. Mutations that reduce ceh-10 function result in Wit animals with CANs that are partially defective in their migrations. Mutations that eliminate ceh-10 function result in Clr animals with CANs that fail to migrate or express CEH-23, a CAN differentiation marker. Null mutants also fail to express CEH-10, suggesting that CEH-10 regulates its own expression. Finally we found that ceh-10 is necessary for the differentiation of AIY and RMED, two additional cells that express CEH-10. ------------------- Key: 2979 Medline: 98133877 Authors: Garvin C;Holdeman R;Strome S Title: The phenotype of mes-2, mes-3, mes-4 and mes-6, maternal-effect genes required for survival of the germline in Caenorhabditis elegans, is sensitive to chromosome dosage. Citation: Genetics 148: 167-185 1998 Type: ARTICLE Genes: ced-4 dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 fem-1 fem-2 fem-3 fog-1 glp-1 glp-4 her-1 him-8 mes-2 mes-3 mes-4 mes-6 sdc-1 sdc-2 sdc-3 tra-1 tra-2 tra-3 xol-1 hDp20 Abstract: Mutations in mes-2, mes-3, mes-4, and mes-6 result in maternal-effect sterility: hermaphrodite offspring of mes/mes mothers are sterile because of underproliferation and death of the germ cells, as well as an absence of gametes. Mutant germ cells do not undergo programmed cell death, but instead undergo a necrotic-type death, and their general poor health apparently prevents surviving germ cells from forming gametes. Male offspring of mes mothers display a significantly less severe germline phenotype than their hermaphrodite siblings, and males are often fertile, This differential response of hermaphrodite and male offspring to the absence of mes(+) product is a result of their different X chromosome compositions; regardless of their sexual phenotype, XX worms display a more severe germline phenotype than XO worms, and XXX worms display the most severe phenotype. The sensitivity of the mutant phenotype to chromosome dosage, along with the similarity of two MES proteins to chromatin-associated regulators of gene expression in Drosophila, suggest that the essential role of the mes genes is in control of gene expression in the germline. An additional, nonessential role of the mes genes in the soma is suggested by the surprising finding that mutations in the mes genes, like mutations in dosage compensation genes, feminize animals whose male sexual identity is somewhat ambiguous. We hypothesize that the mes genes encode maternally supplied regulators of chromatin structure and gene expression in the germline and perhaps in somatic cells of the early embryo, and that at least some of their targets are on the X chromosomes. ------------------- Key: 2980 Medline: 98133878 Authors: Collet J;Spike CA;Lundquist EA;Shaw JE;Herman RK Title: Analysis of osm-6, a gene that affects sensory cilium structure and sensory neuron function in Caenorhabditis elegans. Citation: Genetics 148: 187-200 1998 Type: ARTICLE Genes: che-2 che-3 che-11 che-13 daf-10 daf-19 osm-1 osm-3 osm-5 osm-6 sup-5 Abstract: Mutation in the Caenorhabditis elegans gene osm-6 was previously shown to result in defects in the ultrastructure of sensory cilia and defects in chemosensory and mechanosensory behaviors. We have cloned osm-6 by transposon tagging and transformation rescue and have identified molecular lesions associated with five osm-6 mutations. The osm-6 gene encodes a protein that is 40% identical in amino acid sequence to a predicted mammalian protein of unknown function. We fused osm-6 with the gene for green fluorescent protein (GFP); the fusion gene rescued the osm-6 mutant phenotype and showed accumulation of GFP in ciliated sensory neurons exclusively. The OSM-6::GFP protein was localized to cytoplasm, including processes and dendritic endings where sensory cilia are situated. Mutations in other genes known to cause ciliary defects led to changes in the appearance of OSM-6::GFP in dendritic endings or, in the case of daf-19, reduced OSM-6::GFP accumulation. We conclude from an analysis of genetic mosaics that osm-6 acts cell autonomously in ------------------- Key: 2981 Medline: Authors: Dennis JL;Mutwakil MHAZ;Lowe KC;de Pomerai DI Title: Effects of metal ions in combination with a non-ionic surfactant on stress responses in a transgenic nematode. Citation: Aquatic Toxicology 40: 37-50 1997 Type: ARTICLE Genes: Abstract: Exposure to metal ions induces a stress response by activating beta-galactosidase expression in a strain of transgenic nematode (Caenorhabditis elegans strain PC72) carrying an E. coli lacZ gene under the control of an hsp16 heat-shock promoter sequence. This system can also be activated by several organic toxicants, and low beta-galactosidase activities are induced in worms exposed to non-ionic Pluronic surfactants. These surfactants have been shown to stimulate worm growth, possibly through enhanced nutrient uptake via membrane pores created by surfactant action. This paper demonstrates that, in the presence of one such surfactant (Pluronic F-127 at 10 ppm throughout), the stress response of transgenic worms to several metal ions (Cd2+, Hg2+, Cu2+, Mn2+ and Zn2+) is markedly enhanced (by 1.5- to four-fold). This enhancement diminishes at high concentrations of Cd2+, possibly due to increased mortality. A three-way ANOVA confirms that both metal concentration and the presence of surfactant have extremely significant effects on beta-galactosidase induction, and that there are significant interactions between these factors (generally, the surfactant effect is more pronounced at higher metal concentrations). However, the ANOVA also reveals highly significant variations between repeat runs under the same test conditions, although the trends attributable to metal dose or to surfactant are present consistently in all runs. In situ histochemical staining shows that beta-galactosidase is expressed throughout worms treated with metal plus surfactant, in contrast to the localised pharyngeal staining characteristic of worms treated with metal alone. This suggests that Pluronic F-127 may facilitate metal entry into tissues which do not normally display a strong stress response. Tentative support for this is provided by the observation that worms treated with Pluronic F-127 (10 ppm) accumulate slightly (ca. 10%) more Cu2+ or Zn2+ during the standard exposure period than do control worms exposed to metal only. Thus metal ions are significantly more toxic to C. elegans when combined with a non-ionic surfactant, itself present at sub-toxic (indeed, growth promoting) ------------------- Key: 2982 Medline: 98070521 Authors: Vassilatis DK;Arena JP;Plasterk RHA;Wilkinson HA;Schaeffer JM;Cully DF;Van der Ploeg LHT Title: Genetic and biochemical evidence for a novel avermectin-sensitive chloride channel in Caenorhabditis elegans - Isolation and characterization. Citation: Journal of Biological Chemistry 272: 33167-33174 1997 Type: ARTICLE Genes: Abstract: Avermectins are a class of macrocyclic lactones that is widely used in crop protection and to treat helminth infections in man and animals. Two complementary DNAs (GluCl alpha and GluCl beta) encoding chloride channels that are gated by avermectin and glutamate, respectively, were isolated from Caenorhabditis elegans. To study the role of these subunits in conferring avermectin sensitivity we isolated a mutant C. elegans strain with a Tc1 transposable element insertion that functionally inactivated the GluCl alpha gene (GluCl alpha::Tc1). GluCl alpha::Tc1 animals exhibit a normal phenotype including typical avermectin sensitivity, Xenopus oocytes expressing GluCl alpha::Tc1 strain mRNA elicited reduced amplitude avermectin and glutamate-dependent chloride currents. Avermectin binding assays in GluCl alpha::Tc1 strain membranes showed the presence of high affinity binding sites, with a reduced B-max. These experiments suggest that GluCl alpha is a target for avermectin and that additional glutamate-gated and avermectin-sensitive chloride channel subunits exist in C. elegans. We isolated a cDNA (GluCl alpha 2) encoding a chloride channel that shares 75% amino acid identity with GluCl alpha. This subunit forms homomeric channels that are gated irreversibly by avermectin and reversibly by glutamate, GluCl alpha 2 coassembles with GluCl beta to form heteromeric channels that are gated by both ligands. The presence of subunits related to GluCl alpha may explain the low level and rarity of target site involvement in resistance to the avermectin ------------------- Key: 2983 Medline: Authors: Martinelli SD;Brown CG;Durbin R Title: Gene expression and development databases for C. elegans. Citation: Seminars in Cell & Developmental Biology 8: 459-467 1997 Type: REVIEW Genes: Abstract: The nematode worm C. elegans, with its transparent body, is an excellent vehicle for studying developmental gene expression during embryogenesis and throughout its short life. Expression data from in-situ hybridization, immunolocalization and reporter constructs have been put into the ACeDB database, which is used to store and disseminate most types of C. elegans data, and is also widely used for genome-sequencing projects. In the database, the gene-expression patterns are linked to genes, sequences, cells, organs and the developmental stage in which expression occurs. An accessory program 'Angler' can be used to browse sectional Nomarski images of the worm embryo during early development, and to relate these images to overlaid cell lineage data and 3-D schematic views of cell positions. ------------------- Key: 2984 Medline: 97468988 Authors: Rand JB;Duerr JS;Frisby DL Title: Neurogenetics of synaptic transmission in Caenorhabditis elegans. Citation: Advances in Pharmacology 42: 940-944 1998 Type: REVIEW Genes: cat-1 cha-1 unc-17 Abstract: The nematode Caenorhabditis elegans has a number of advantages for the analysis of synaptic molecules. These include ease of manipulation, a simple nervous system, and powerful tools for the analysis of mutants and genes. Genetically, C. elegans is advantageous because of its short generation tiem (3 days), its prolific progeny yield (280 per parent), its small size (1.5 mm long), and its ease of laboratory culture (on E. coli lawns on agar Petri dishes). There are now thousands of mutants strains of C. elegans, exhibiting a wide variety of behavioral, morphological, and developmental phenotypes, and hundreds of genes have now been mapped on the animals' six linkage groups. Cellularly, C. elegans is remarkably simple. At hatching, there are 550 somatic cells, and over the course of the next 48 h, this number increases to produce an adult total of 959 somatic cells. The adult contains 302 neurons, and reproducibility of neuron structure and connectivity has been demonstrated by serial section electron microscopy for most portions of the nervous system. Molecular biology using this organism is simplified by its relatively small genome size of 10*8 bp, the availability of a transposon for gene cloning, and the near completion of the physical map and sequence of the entire genome. ------------------- Key: 2985 Medline: 98096382 Authors: Leroux MR;Candido EPM Title: Subunit characterization of the Caenorhabditis chaperonin containing TCP-1 and expression pattern of the gene encoding CCT-1. Citation: Biochemical and Biophysical Research Communications 241: 687-692 1997 Type: ARTICLE Genes: cct-1 Abstract: The chaperonin containing TCP-1 (CCT) from the free-living nematode Caenorhabditis elegans was purified and shown to contain at least seven subunit species ranging from 52-65 kDa. SDS gel electrophoresis and Western blot analyses with antibodies against C. elegans CCT-1 and CCT-5 and an antibody which recognizes a conserved region in vertebrate CCT subunits confirm that the subunit compositions of CCTs from distantly related organisms (C. elegans and bovine species) are remarkably similar. Surprisingly, the co-purified HSP60 chaperonin present in the C. elegans CCT preparation has the greatest binding activity for denatured actin. Expression of a reporter gene under the control of the C. elegans cct-1 promoter is found to be mainly restricted to neuronal and muscle tissues, an observation which is consistent with the participation of CCT in actin and tubulin folding. ------------------- Key: 2986 Medline: 98075105 Authors: Nonet ML;Saifee O;Zhao H;Rand JB;Wei L Title: Synaptic transmission deficits in Caenorhabditis elegans synaptobrevin mutants. Citation: Journal of Neuroscience 18: 70-80 1998 Type: ARTICLE Genes: rab-3 snt-1 unc-104 ccDf4 ccDf5 maDf4 Abstract: Synaptobrevins are vesicle-associated proteins implicated in neurotransmitter release by both biochemical studies and perturbation experiments that use botulinum toxins. To test these models in vivo, we have isolated and characterized the first synaptobrevin mutants in metazoans and show that neurotransmission is severely disrupted in mutant animals. Mutants lacking snb-1 die just after completing embryogenesis. The dying animals retain some capability for movement, although they are extremely uncoordinated and incapable of feeding. We also have isolated and characterized several hypomorphic snb-1 mutants. Although fully viable, these mutants exhibit a variety of behavioral abnormalities that are consistent with a general defect in the efficacy of synaptic transmission. The viable mutants are resistant to the acetylcholinesterase inhibitor aldicarb, indicating that cholinergic transmission is impaired. Extracellular recordings from pharyngeal muscle also demonstrate severe defects in synaptic transmission in the mutants. The molecular lesions in the hypomorphic alleles reside on the hydrophobic face of a proposed amphipathic-helical region implicated biochemically in interacting with the t-SNAREs syntaxin and SNAP-25. Finally, we demonstrate that double mutants lacking both the v-SNAREs synaptotagmin and snb-1 are phenotypically similar to snb-1 mutants and less severe than syntaxin mutants. Our work demonstrates that synaptobrevin is essential for viability and is required for functional synaptic transmission. However, our analysis also suggests that transmitter release is not completely eliminated by removal of either one or both v-SNAREs. ------------------- Key: 2987 Medline: 98096357 Authors: Kagan RM;Niewmierzycka A;Clarke S Title: Targeted gene disruption of the Caenorhabditis elegans L-isoaspartyl protein repair methyltransferase impairs survival of dauer stage nematodes. Citation: Archives of Biochemistry & Biophysics 348: 320-328 1997 Type: ARTICLE Genes: pcm-1 Abstract: The methylation of abnormal L-isoaspartyl residues by protein L-isoaspartate (D-aspartate) D-methyltransferase (EC 2.1.1.77) can lead to their conversion to L-aspartyl residues'. For polypeptides damaged by spontaneous reactions that generate L-isoaspartyl residues, these steps represent a protein repair pathway that can limit the accumulation of potentially detrimental proteins in the aging process. We report here the construction and the characterization of an animal model deficient iii this methyltransferase. We utilized Tc1-transposon-mediated mutagenesis in the nematode Caenorhabditis elegans to construct a homozygous excision mutant lacking exons 2-5 of the pcm-l gene encoding this enzyme. Nematodes carrying this deletion exhibited no detectable L-isoaspartyl methyltransferase activity. These worms demonstrated normal morphology and behavior and adult mutant nematodes exhibited a normal lifespan. However, the survival pf dauer-phase mutants was diminished by 3.5-fold relative to wild-type dauers after 50 days in the dauer phase. The fitness of the pcm-l deletion nematodes was reduced by about 16% relative to that of wild-type nematodes as measured by the ability of these mutants to compete reproductively against a wild-type population. We found that the absence of the functional methyltransferase gene leads to a modest accumulation of altered protein substrates in aged dauer worms. However in the viable fraction of these dauer worms, no differences were seen in the levels of altered substrate proteins in the parent and methyl-transferase-deficient worms, suggesting that the enzyme in wild-type cells does not efficiently catalyze the ------------------- Key: 2988 Medline: 98089170 Authors: Raz F;van Luenen HGAM;Schaerringer B;Plasterk RHA;Driever W Title: Transposition of the nematode Caenorhabditis elegans Tc3 element in the zebrafish Danio rerio. Citation: Current Biology 8: 82-88 1997 Type: ARTICLE Genes: Abstract: Background: Transposable elements of the Tc1/mariner family are found in many species of the animal kingdom. It has been suggested that the widespread distribution of this transposon family resulted from horizontal transmission among different species. Results: To test the ability of Tc1/mariner to cross species barriers, as well as to develop molecular genetic tools for studying zebrafish development, we determined the ability of the Tc3 transposon, a member of the Tc1/mariner family, to function in zebrafish. Tc3 transposons carrying sequences encoding the green fluorescent protein (GFP) were able to integrate in the fish genome by transposition. Integrated transposons expressed the GFP marker after germline transmission, and were capable of being mobilized upon introduction of transposase protein in trans. Conclusions: Our findings support models of horizontal transmission of Tc1/mariner elements between species. The work also establishes the basis for a novel method of transposon-mediated genetic transformation and for transposon-mediated genetic screens in zebrafish and other organisms. ------------------- Key: 2989 Medline: 98086293 Authors: Wu SL;Staudinger J;Olson EN;Rubin CS Title: Structure, expression and properties of an atypical protein kinase C (PKC3) from Caenorhabditis elegans: PKC3 is required for the normal progression of embryogenesis and viabil... Citation: Journal of Biological Chemistry 273: 1130-1143 1998 Type: ARTICLE Genes: pkc-3 Abstract: Little is known about differential expression, functions, regulation, and targeting of ''atypical'' protein kinase C (aPKC) isoenzymes in vivo. We have cloned and characterized a novel cDNA that encodes a Caenorhabditis elegans aPKC (PKC3) composed of 597 amino acids. In post-embryonic animals, a 647 base pair segment of promoter/enhancer DNA directs transcription of the 3.6-kilobase pair pkc-3 gene and coordinates accumulation of PKC3 protein in similar to 85 muscle, epithelial, and hypodermal cells. These cells are incorporated into tissues involved in feeding, digestion, excretion, and reproduction. Mammalian aPKCs promote mitogenesis and survival of cultured cells. In contrast, C. elegans PKC3 accumulates in non-dividing, terminally differentiated cells that will not undergo apoptosis. Thus, aPKCs may control cell functions that are independent of cell cycle progression and programmed cell death. PKC3 is also expressed during embryogenesis. Ablation of PKC3 function by microinjection of antisense RNA into oocytes yields disorganized, developmentally arrested embryos. Thus, PKC3 is essential for viability. PKC3 is enriched in particulate fractions of disrupted embryos and larvae. Immunofluorescence microscopy revealed that PKC3 accumulates near cortical actin cytoskeleton/plasma membrane at the apical surface of intestinal cells and in embryonic cells. A candidate anchoring/targeting protein, which binds PKC3 in vitro, has ------------------- Key: 2990 Medline: 98113183 Authors: Ogawa H;Harada S;Sassa T;Yamamoto H;Hosono R Title: Functional properties of the unc-64 gene encoding a Caenorhabditis elegans syntaxin. Citation: Journal of Biological Chemistry 273: 2192-2198 1998 Type: ARTICLE Genes: unc-18 unc-64 Abstract: Phenotypes of Caenorhabditis elegans unc-18 and unc-64 gene mutations are similar. While unc-18 is known to be essential for normal synaptic transmission (Hosono, R., Hekimi, S., Kamiya, Y., Sassa, T., Murakami, S., Nishiwaki, S., Miwa, J., Taketo, A, and Kodaira, K.-I. (1992) J. Neurochem. 58, 1517-1525), the function of unc-64 remains unclear. Here we describe the cloning, and the molecular and genetic characterization of the unc-64 gene, especially in relation to unc-18. unc-64 encodes a protein (C. elegans syntaxin) showing sequence and structural similarities to mammalian syntaxin 1A. From unc-64, at least three types of poly(A)(+) RNA are transcribed, which encode two types of syntaxin that differ in the deduced transmembrane domain. In gene expression, unc-64 closely resembles unc-18, that is, both are expressed in neural cells, especially in motor neurons and neurons constituting head ganglions. C. elegans syntaxin binds to UNC-18 with high affinity. The unc-64 (e246) mutation producing a mild phenotype causes an Ala --> Val conversion in the conserved COOH-terminal region in mammalian syntaxin 1A or Drosophila syntaxin-1A whose site is included in three types of transcripts. The binding of the mutant C. elegans syntaxin tb UNC-18 is greatly reduced, indicating the mutation site contributes to the ------------------- Key: 2991 Medline: 98121107 Authors: Dickson B Title: Axon guidance: A roundabout way of avoiding the midline. Citation: Nature 391: 442-443 1998 Type: REVIEW Genes: sax-3 Abstract: Bilaterally symmetrical animals must be able to integrate sensory inputs and coordinate motor control on both sides of the body. Thus, many neurons in the central nervous system (CNS) project their axons to the opposite side of the body, whereas others project axons that remain on the same side. In the latest issues of Cell and Neuron, the groups of Corey Goodman, Guy Tear, Marc Tessier-Lavigne and Cori Bargmann report that, from worms and flies to rats and humans, a common mechanism determines which axons cross the midline and which do not. ------------------- Key: 2992 Medline: Authors: Mikola J;Setala H Title: No evidence of trophic cascades in an experimental microbial-based soil food web. Citation: Ecology 79: 153-164 1998 Type: ARTICLE Genes: Abstract: Trophic-dynamic theories predict the biomass and productivity of trophic levels to be partially top-down regulated in food webs, and that the top-down regulation will manifest itself as cascading trophic interactions. We tested the two principal predictions deduced from these theories: trophic cascades of(1)biomass regulation and (2) productivity regulation occur in food webs. We created three food webs with either one, two, or three trophic levels in soil microcosms containing a sterilized mixture of leaf litter and humus. Twenty species of bacteria and fungi formed the first trophic level, a bacterivorous nematode (Caenorhabditis elegans) and a fungivorous nematode (Aphelenchoides sp.) the second level, and a predatory nematode (Prionchulus punctatus) the third level. We sampled the microcosms destructively four times during a 5-mo experiment for estimations of the biomass of each of the trophic levels. CO2 evolution was analyzed once or twice a week,; and NH4+-N concentration in the soil was measured at the end of the experiment. Glucose was added to the microcosms every second week to provide energy for the microbes. The biomass of microbivores was clearly regulated by the predator. The abundance of bacteria was not affected by the food chain length, and the abundance of fungi was higher in the presence of nematodes than in the pure microbial community. Net mineralization of N and C was highest in the food chains with two trophic levels, at an intermediate level in the presence of predators, and lowest in the pure microbial communities. Microbial production (estimated on the basis of microbial respiration) was higher in the food webs with two and three trophic levels than when the microbes were growing alone. Whether the biomass of the second trophic level was reduced by the predator or not had no effect on microbial biomass or microbial productivity. Therefore, although the microbivore biomass and mineralization of both C and N were regulated by the predator, our experiment did not provide evidence of cascading trophic interactions regulating the microbial biomass and productivity in decomposer food webs. The facts that microbes were able to compensate totally for the consumed biomass by increasing their turnover rate and that the microbes did not behave as a uniform trophic level prevented a trophic cascade of biomass regulation from occurring in our soil food web. Similarly, since microbial productivity did not depend on the biomass at the second trophic level, neither did a trophic cascade of productivity regulation take place. ------------------- Key: 2993 Medline: 98113342 Authors: de Vet ECJM;Prinsen HCMT;van den Bosch H Title: Nucleotide sequence of a cDNA clone encoding a Caenorhabditis elegans homolog of mammalian alkyl-dihydroxyacetonephosphate synthase: Evolutionary switching of peroxisomal target... Citation: Biochemical and Biophysical Research Communications 242: 277-281 1998 Type: ARTICLE Genes: Abstract: The nucleotide sequence is reported of a cDNA clone encoding a Caenorhabditis elegans homolog of guinea pig and human alkyl-dihydroxyacetonephosphate synthase. The open reading frame encodes a protein of 597 amino acids which shows extensive homology with the mammalian enzymes (52% identical and about 76% similar in the overlapping region). In contrast to the mammalian enzymes, which carry a consensus peroxisomal targeting signal type 2 in a cleavable N-terminal presequence, this Caenorhabditis elegans homolog carries a consensus peroxisomal targeting signal type 1 (CKL) at its C-terminus. Expression of this protein in an in vitro transcription/translation system yielded a 65 kDa protein. Recombinant aenorhabditis elegans alkyl-DHAP synthase expressed in the yeast Pichia pastoris was enzymatically active. ------------------- Key: 2994 Medline: 98121106 Authors: Hengartner MO Title: Apoptosis: Death cycle and Swiss army knives. Citation: Nature 391: 441-442 1998 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: Cytochrome c leads a double life. When a cell is called on to commit apoptotic suicide, cytochrome c relocalizes from the mitochondria to the cytosol. There, it helps to activate the foot-soldiers of apoptosis - the death proteases known as caspases. How cytochrome c escapes from the mitochondria is still a matter of debate, but it is clear that certain elements within the apoptotic regulatory hierarchy do not condone such behavior. In particular, overexpression of the cell-death suppressors Bcl-2 and Bcl-xL prevents the release of cytochrome c, suggesting that these proteins act upstream of cytochrome c in the pathway to death. However, on pages 449 and 496 of this issue, Zhivotovsky et al. and Rosse et al. show that Bcl-2 can also protect cells downstream of cytochrome c release, forcing a re-evaluation of this newly acquired dogma. ------------------- Key: 2995 Medline: 98107655 Authors: Li L;Linning RM;Kondo K;Honda BM Title: Differential expression of individual suppressor tRNA(Trp) gene family members in vitro and in vivo in the nematode Caenorhabditis elegans. Citation: Molecular and Cellular Biology 18: 703-709 1998 Type: ARTICLE Genes: sup-5 sup-7 sup-24 sup-28 sup-29 Abstract: Eight different amber suppressor tRNA (suptRNA) mutations in the nematode Caenorhabditis elegans have been isolated; all are derived from members of the tRNA(Trp) gene family (K. Kondo, B. Makovec, R. H. Waterston, and J. Hodgkin, J. Mel. Biol, 215:7-19, 1990), Genetic assays of suppressor activity suggested that individual tRNA genes were differentially expressed, probably in a tissue-or developmental stage-specific manner, We have now examined the expression of representative members of this gene family both in vitro, using transcription in embryonic cell extracts, and in vivo, by assaying suppression of an amber-mutated lacZ reporter gene In animals carrying different suptRNA mutations, Individual wild-type tRNA(Trp) genes and their amber-suppressing counterparts appear to be transcribed and processed identically in vitro, suggesting that the behavior of suptRNAs should reflect wild-type tRNA expression, The levels of transcription of different suptRNA genes closely parallel the extent of genetic suppression in vivo. The results suggest that differential expression of tRNA genes is most likely at the transcriptional rather than the posttranscriptional level and that 5' flanking sequences play a role in vitro, and probably in vivo as well. Using suppression of a lacZ(Am) reporter gene as a more direct assay of suptRNA activity in individual cell types, we have again observed differential expression which correlates with genetic and in vitro transcription results, This provides a model system to more extensively study the basis for differential expression of ------------------- Key: 2996 Medline: 98119530 Authors: Roayaie K;Crump JG;Sagasti A;Bargmann CI Title: The G-alpha protein ODR-3 mediates olfactory and nociceptive function and controls cilium morphogenesis in C. elegans olfactory neurons. Citation: Neuron 20: 55-67 1998 Type: ARTICLE Genes: daf-11 gpa-2 odr-3 odr-10 osm-9 tax-2 tax-4 arDf1 ctDf1 nDf42 Abstract: The G(i)/G(o)-like G alpha protein ODR-3 is strongly and selectively implicated in the function of C. elegans olfactory and nociceptive neurons. Either loss of odr-3 function or overexpression of odr-3 causes severe olfactory defects, and odr-3 function is essential in the ASH neurons that sense noxious chemical and mechanical stimuli. In the nociceptive neurons, ODR-3 may interact with OSM-9, a channel similar to the mammalian capsaicin receptor implicated in pain sensation; in AWC olfactory neurons, ODR-3 may interact with another signal transduction pathway. ODR-3 exhibits an unexpected ability to regulate morphogenesis of the olfactory cilia. In odr-3 null mutants, the fan-like AWC cilia take on a filamentous morphology like normal AWA cilia, whereas ODR-3 overexpression in AWA transforms its filamentous cilia into ------------------- Key: 2997 Medline: 98117250 Authors: Zallen JA;Yi BA;Bargmann CI Title: The conserved immunoglobulin superfamily member SAX-3/Robo directs multiple aspects of axon guidance in C. elegans. Citation: Cell 92: 217-227 1998 Type: ARTICLE Genes: sax-3 mnDp57 Abstract: The C. elegans sax-3 gene encodes a predicted transmembrane protein with five immunoglobulin domains and three fibronectin type III repeats that is closely related to Drosophila Robe. Mutations in sax-3 lead to repeated midline crossing by ventral cord axons that normally do not cross the midline after they join the ventral cord, a phenotype similar to that of robe mutants. sax-3 is also required for guidance of some axons to the ventral cord, implicating this gene in two different types of guidance events. A sax-3:GFP fusion gene is expressed in developing neurons during axon outgrowth, and sax-3 function is required at the time of axon guidance, suggesting that this gene mediates cell interactions during guidance decisions. ------------------- Key: 2998 Medline: 98117251 Authors: Lin RL;Hill RJ;Priess JR Title: POP-1 and anterior-posterior fate decisions in C. elegans embryos. Citation: Cell 92: 229-239 1998 Type: ARTICLE Genes: apr-1 glp-1 mom-2 pop-1 Abstract: Blastomeres in C. elegans embryos execute lineage programs wherein the fate of a cell is correlated reproducibly with the division sequence by which that cell is born. We provide evidence that the pop-1 gene functions to link anterior-posterior cell divisions with cell fate decisions. Each anterior cell resulting from an anterior-posterior division appears to have a higher level of nuclear POP-1 protein than does its posterior sister. Genes in the C. elegans Wnt pathway are required for this inequality in POP-1 levels. We show that loss of pop-1(+) activity leads to several types of anterior cells adopting the fates of their posterior sisters. These results suggest a mechanism for the invariance of blastomere lineages. ------------------- Key: 2999 Medline: 98117254 Authors: Lieb JD;Albrecht MR;Chuang P-T;Meyer BJ Title: MIX-1: an essential component of the C. elegans mitotic machinery executes X chromosome dosage compensation. Citation: Cell 92: 265-277 1998 Type: ARTICLE Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 let-29 mix-1 sdc-1 sdc-2 xol-1 Abstract: We show that a functional component of the C. elegans mitotic machinery regulates X chromosome gene expression. This protein, MIX-1, is a member of the dosage compensation complex that associates specifically with hermaphrodite X chromosomes to reduce their gene expression during interphase. MIX-1 also associates with all mitotic chromosomes to ensure their proper segregation. Both dosage compensation and mitosis are severely disrupted by mix-1 mutations. MIX-1 belongs to the SMC protein family required for mitotic chromosome condensation and segregation in yeast and frogs. Thus, an essential, conserved component of mitotic chromosomes has been recruited to the dosage compensation process. Rather than dosage compensation and mitosis being achieved by two separate sets of related genes, these two processes share an identical component, indicating a common mechanism for establishing higher order chromosome structure and proper X chromosome gene expression. ------------------- Key: 3000 Medline: 98140704 Authors: Raymond CS;Shamu CE;Shen MM;Seifert KJ;Hirsch B;Hodgkin J;Zarkower D Title: Evidence for evolutionary conservation of sex-determining genes. Citation: Nature 391: 691-695 1998 Type: ARTICLE Genes: mab-3 tra-1 eDf21 mnDf27 eDp6 Abstract: Most metazoans occur as two sexes. Surprisingly, molecular analyses have hitherto indicated that sex-determining mechanisms differ completely between phyla. Here we present evidence to the contrary. We have isolated the male sexual regulatory gene mab-3 (ref. 1) from the nematode Caenorhabditis elegans and found that it is related to the Drosophila melanogaster sexual regulatory gene doublesex (dsx)(2). Both genes encode proteins with a DNA-binding motif(3) that we have named the 'DM domain'. Both genes control sex-specific neuroblast differentiation and yolk protein gene transcription; dsx controls other sexually dimorphic features as well. The form of DSX that is found in males can direct male-specific neuroblast differentiation in C. elegans. This structural and functional similarity between phyla suggests a common evolutionary origin of at least some aspects of sexual regulation. We have identified a human gene, DMT1, that encodes a protein with a DM domain and find that DMT1 is expressed only in testis. DMT1 maps to the distal short arm of chromosome 9, a location implicated in human XY sex reversal(4). Proteins with DM domains may therefore also ------------------- Key: 3001 Medline: 98123162 Authors: Ono S;Benian GM Title: Two Caenorhabditis elegans actin depolymerizing factor/cofilin proteins, encoded by the unc-60 gene, differentially regulate actin filament dynamics. Citation: Journal of Biological Chemistry 273: 3778-3783 1998 Type: ARTICLE Genes: unc-60 Abstract: The Caenorhabditis elegans unc-60 gene encodes two actin depolymerizing factor/cofilin proteins which are implicated in the regulation of actin filament assembly in body wall muscle. We examined the interaction of recombinant UNC-60A and B proteins with actin and found that they differentially regulate actin filament dynamics. Co-pelleting assays with F-actin showed that UNC-60A depolymerized but did not remain bound to F-actin, whereas UNC-60B bound to but did not depolymerize F-actin. In the pH range of 6.8-8.0, the apparent activities of UNC-60A and B did not change although UNC-60A showed greater actin-depolymerizing activity at higher pH. These activities were further confirmed by a light scattering assay and electron microscopy. The effects of these proteins on actin polymerization were quite different. UNC-60A inhibited polymerization in a concentration dependent manner. On the other hand, UNC-60B strongly inhibited the nucleation process but accelerated the following elongation step, However, an excess amount of UNC-60B increased the amount of unpolymerized actin. These results indicate that UNC-60A depolymerizes actin filaments and inhibits actin polymerization, whereas UNC-60B strongly binds to F-actin without depolymerizing it and, through binding to G-actin, changes the rate of actin polymerization depending on the UNC-60B:actin ratio. These data suggest that the two UNC-60 isoforms play differential ------------------- Key: 3002 Medline: 98106179 Authors: Liu F;Bauer CC;Ortiz I;Cook RG;Schmid MF;Epstein HF Title: Beta-filagenin, a newly identified protein coassembling with myosin and paramyosin in Caenorhabditis elegans. Citation: Journal of Cell Biology 140: 347-353 1998 Type: ARTICLE Genes: unc-15 Abstract: Muscle thick filaments are stable assemblies of myosin and associated proteins whose dimensions are precisely regulated. The mechanisms underlying the stability and regulation of the assembly are not understood. As an approach to these problems, we have studied the core proteins that, together with paramyosin, form the core structure of the thick filament backbone in the nematode Caenorhabditis elegans. We obtained partial peptide sequences from one of the core proteins, beta-filagenin, and then identified a gene that encodes a novel protein of 201-amino acid residues from databases using these sequences. beta-Filagenin has a calculated isoelectric point at 10.61 and a high percentage of aromatic amino acids. Secondary structure algorithms predict that it consists of four beta-strands but no alpha-helices. Western blotting using an affinity-purified antibody showed that beta-filagenin was associated with the cores. beta-Filagenin was localized by immunofluorescence microscopy to the A bands of body-wall muscles, but not the pharynx. beta-filagenin assembled with the myosin homologue paramyosin into the tubular cores of wild-type nematodes at a periodicity matching the 72-nm repeats of paramyosin, as revealed by immunoelectron microscopy. In CB1214 mutants where paramyosin is absent, beta-filagenin assembled with myosin to form abnormal tubular filaments with a periodicity identical to wild type. These results verify that beta-filagenin is a core protein that coassembles with either myosin or paramyosin in C. elegans to form tubular filaments. ------------------- Key: 3003 Medline: 98062457 Authors: Sonnhammer ELL;Eddy SR;Birney E;Bateman A;Durbin R Title: Pfam: multiple sequence alignments and HMM-profiles of protein domains. Citation: Nucleic Acids Research 26: 320-322 1998 Type: ARTICLE Genes: Abstract: Pfam contains multiple alignments and hidden Markov model based profiles (HMM-profiles) of complete protein domains. The definition of domain boundaries, family members and alignment is done semi-automatically based on expert knowledge, sequence similarity, other protein family databases and the ability of HMM-profiles to correctly identify and align the members. Release 2.0 of Pfam contains 527 manually verified families which are available for browsing and on-line searching via the World Wide Web in the UK at http://www.sanger.ac.uk/Pfam/ and in the US at http://genome.wustl.edu/Pfam/Pfam 2.0 matches one or more domains in 50% of Swissprot-34 sequences, and 25% of a large sample of predicted proteins from the Caenorhabditis elegans genome. ------------------- Key: 3004 Medline: 98087502 Authors: Marcel V;Palacios LG;Pertuy C;Masson P;Fournier D Title: Two invertebrate acetylcholinesterases show activation followed by inhibition with substrate concentration. Citation: Biochemical Journal 329: 329-334 1998 Type: ARTICLE Genes: Abstract: In vertebrates there are two cholinesterases, with differences in catalytic behaviour with respect to substrate concentration: butyrylcholinesterase displays an increased activity at low substrate concentrations, whereas acetylcholinesterase displays inhibition by excess substrate. In two invertebrates, Drosophila melanogaster and Caenorhabditis elegans, we found cholinesterases that showed both kinetic complexities: substrate activation at low substrate concentrations followed by inhibition at higher concentrations. These triphasic kinetics can be explained by the presence of two enzymes with different kinetic behaviours or more probably by the existence of a single enzyme regulated by the substrate concentration. ------------------- Key: 3005 Medline: 98146058 Authors: Fire A;Xu S;Montgomery MK;Kostas SA;Driver SE;Mello CC Title: Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Citation: Nature 391: 806-811 1998 Type: ARTICLE Genes: fem-1 hlh-1 mex-3 myo-3 unc-22 unc-54 Abstract: Experimental introduction of RNA into cells can be used in certain biological systems to interfere with function of an endogenous gene(1,2). Such effects have been proposed io result from a simple antisense mechanism that depends on hybridization between the injected RNA and endogenous messenger RNA transcripts, RNA interference has been used in the nematode Caenorhabditis elegans to manipulate gene expression(3,4). Here we investigate the requirements for structure and delivery of the interfering RNA. To our surprise, we found that double-stranded RNA was substantially more effective at producing interference than was either strand individually. After injection into adult animals, purified single strands had at most a modest effect, whereas double-stranded mixtures caused potent and specific interference. The effects of this interference were evident in bath the injected animals and their progeny. Only a few molecules of injected double-stranded RNA were required per affected cell, arguing against stochiometric interference with endogenous mRNA and suggesting that there could be a catalytic or amplification component in the interference process. ------------------- Key: 3006 Medline: 98139525 Authors: Gutch MJ;Flint AJ;Keller J;Tonks NK;Hengartner MO Title: The Caenorhabditis elegans SH2 domain-containing protein tyrosine phosphatase PTP-2 participates in signal transduction during oogenesis and vulval development. Citation: Genes & Development 12: 571-585 1998 Type: ARTICLE Genes: let-23 let-60 let-537 lin-3 lin-15 lin-45 mek-2 mpk-1 ptp-2 sem-5 sur-1 maDf4 Abstract: Src homology-2 (SH2) domain-containing protein tyrosine phosphatases (SHPs) have been identified as either positive or negative regulators of signaling events downstream of receptor protein tyrosine kinases (R-PTKs). We describe here our characterization of ptp-2, a Caenorhabditis elegans gene that encodes a 668-amino-acid SHP. We isolated a recessive ptp-2 loss-of-function allele, op194, that lacks the conserved protein tyrosine phosphatase catalytic domain by screening for transposon-mediated deletion mutations. Homozygous ptp-2(op194) hermaphrodites exhibit a completely penetrant zygotic semisterile/maternal effect lethal phenotype, characterized by the presence of abnormally large oocytes in the zygotic semisterile animals. These phenotypes indicate that PTP-2 activity is essential for proper oogenesis. Gain-of-function let-GO ras alleles rescued the defects associated with ptp-2(op194), suggesting that LET-GO Ras acts downstream of, or in parallel to, PTP-2 during oogenesis. Although ptp-2 function is not required for normal vulval development, ptp-2(op194) altered significantly the vulval phenotypes caused by mutations in several genes of the inductive signaling pathway. The penetrance of the multivulva phenotype caused by loss-of-function mutations in lin-15, and gain-of-function mutations in let-23 or let-60 ras, was reduced by ptp-2(op194). Moreover, ptp-2(op194) increased the penetrance of the vulvaless phenotype conferred by a weak loss-of-function sem-5 allele. Taken together, our genetic data positions PTP-2 activity downstream of LET-23 in the vulval induction signaling pathway. Although PTP-2 functions to transmit a requisite signal during oogenesis, PTP-2 function during C. elegans vulval cell differentiation appears to be directed at regulating the overall strength of the inductive signal, which may contribute to the quantitative differences in signaling required for the proper specification of the 1 degrees, 2 degrees, and 3 degrees vulval cell fates. ------------------- Key: 3007 Medline: 98146197 Authors: Maloof JN;Kenyon C Title: The Hox gene lin-39 is required during C. elegans vulval induction to select the outcome of Ras signaling. Citation: Development 125: 181-190 1998 Type: ARTICLE Genes: dig-1 let-60 lin-1 lin-3 lin-15 lin-39 mab-5 pry-1 Abstract: The Ras signaling pathway specifies a variety of cell fates in many organisms. However, little is known about the genes that function downstream of the conserved signaling cassette, or what imparts the specificity necessary to cause Ras activation to trigger different responses in different tissues. In C. elegans, activation of the Ras pathway induces cells in the central body region to generate the vulva, Vulval induction takes place in the domain of the Hox gene lin-39. We have found that lin-39 is absolutely required for Ras signaling to induce vulval development, During vulval induction, the Ras pathway, together with basal lin-39 activity, up-regulates lin-39 expression in vulval precursor cells. We find that if lin-39 function is absent at this time, no vulval cell divisions occur. Furthermore, if lin-39 is replaced with the posterior Hox gene mab-5, then posterior structures are induced instead of a vulva. Our findings suggest that in addition to permitting vulval cell divisions to occur. lin-39 is also required to specify the outcome of Ras signaling by selectively activating vulva-specific genes. ------------------- Key: 3008 Medline: 98186262 Authors: Tissenbaum HA;Ruvkun G Title: An insulin-like signaling pathway affects both longevity and reproduction in Caenorhabditis elegans. Citation: Genetics 148: 703-717 1998 Type: ARTICLE Genes: age-1 daf-2 daf-16 Abstract: utations in daf-2 and age-1 cause a dramatic increase in longevity as well as developmental arrest at the dauer diapause stage in Caenorhabditis elegans. daf-2 and age-1 encode components of an insulin-like signaling pathway. Both daf-2 and age-1 act at a similar point in the genetic epistasis pathway for dauer arrest and longevity and regulate the activity of the daf-16 gene. Mutations in daf-16 cause a dauer-defective phenotype and are epistatic to the diapause arrest and life span extension phenotypes of daf-2 and age-1 mutants. Here we show that mutations in this pathway also affect fertility and embryonic development. Weak daf-2 alleles, and maternally rescued age-1 alleles that cause life span extension but do not arrest at the dauer stage, also reduce fertility and viability. We find that age-1(hx546) has reduced both maternal and zygotic age-1 activity. daf-16 mutations suppress all of the daf-2 and age-1 phenotypes, including dauer arrest, life span extension, reduced fertility, and viability defects. These data show that insulin signaling, mediated by DAF-2 through the AGE-1 phosphatidylinositol-3-OH kinase, regulates reproduction and embryonic development, as well as dauer diapause and life span, and that DAF-16 transduces these signals. The regulation of fertility, life span, and metabolism by an insulin-like signaling pathway is similar to the endocrine regulation of metabolism and fertility by mammalian insulin ------------------- Key: 3009 Medline: 98069708 Authors: Madi A;Punyiczki M;Fesus L Title: Lessons to learn from the cell death and heat shock genes of Caenorhabditis elegans. Citation: Acta Biologica Hungarica 48: 303-318 1997 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-9 ced-10 ces-1 ces-2 dad-1 let-70 nuc-1 tcp-1 ubc-1 ubc-2 Abstract: The nematode Caenorrhabditis elegans is an applicable experimental system for simulation of complex biochemical processes of mammalian cells and tissues. The genetic pathway of programmed cell death (PCD) has been partially clarified in the nematode. Analysis of cell death genes of C. elegans led to the conclusion that PCD is conserved in the animal kingdom. Our intention is to study the role of tissue transglutaminase and heat shock proteins in the process of PCD. Tissue transglutaminase is often observed to be induced and activated during the molecular mechanism of PCD. The connection between the heat shock proteins and PCD is not well understood, but it is clear that many apoptosis inducers lead to increased synthesis of heat shock proteins and production of heat shock proteins is coupled with the appearance of apoptosis in numerous experimental systems. Our preliminary observations made by studying cell death mutants of C. elegans we suggest that transglutaminase and heat shock proteins are involved in the death program of the nematode. ------------------- Key: 3010 Medline: 98108031 Authors: Goldstein B;Frisse LM;Thomas WK Title: Embryonic axis specification in nematodes: evolution of the first step in development. Citation: Current Biology 8: 157-160 1998 Type: ARTICLE Genes: Abstract: In 1828, von Baer proposed that the early stages of development must be the most conserved [1]. Others have since countered that the middle stages of development are the most conserved [2]. To address whether the earliest step in pattern formation can evolve, we have examined how asymmetry along the antero-posterior (AP) axis is generated in various nematode species. AP asymmetry is specified in Caenorhabditis elegans at fertilization by the sperm, which directs a cytoplasmic rearrangement that segregates critical factors such as the P granules to one side of the uncleaved embryo [3,4]. We found that AP asymmetry is generated differently in another nematode species: the sperm is not used to specify AP asymmetry, there are no signs of cytoplasmic movements, and P granules are segregated differently. Despite these differences, development from the two-cell stage is remarkably similar in the two species, We have reconstructed the evolutionary history of these mechanisms by analyzing the development of 30 nematode species and mapping the results onto a molecular phylogeny of the nematodes [5]. The results suggest that a new mechanism for axis specification evolved in an ancestor of some of the relatives of C. elegans. We conclude that this fundamental step in development can evolve without affecting other aspects of development. ------------------- Key: 3011 Medline: 98147660 Authors: Peixoto CA;de Melo JV;Kramer JM;de Souza W Title: Ultrastructural analyses of the Caenorhabditis elegans rol-6(su1006) mutant, which produces abnormal cuticle collagen. Citation: Journal of Parasitology 84: 45-49 1998 Type: ARTICLE Genes: rol-6 sqt-1 Abstract: Roller mutants of Caenorhabditis elegans rotate around their long axis and move in circular paths. Isolation and sequence of the rol-6 gene of C. elegans have shown that it encodes a cuticle collagen. In this paper, we describe the morphological alterations seen in the cuticle of the right roller mutant rol-6 (su1006) at the ultrastructural level. Deep-etched replica analyses showed that the honeycomb elements, fibers organized in a pentagonal fashion above the fishbone fibrous layer, completely fill the intermediate layer, which is observed to be largely empty spaces in the wild-type strain. The honeycomb fibers appear to connect the cortical and basal regions of the mutant cuticle. These fibers are Likely to be involved in generating the helical twist of the mutant animals. Deep-etched replicas also revealed a delicate network of filaments on the nematode surface. ------------------- Key: 3012 Medline: 98147691 Authors: Patel MR;Campbell WC Title: Inhibitory effect of chlorpromazine on nematode eggs and larvae. Citation: Journal of Parasitology 84: 191-192 1998 Type: ARTICLE Genes: Abstract: Chlorpromazine inhibited the hatching of eggs of the parasitic nematode Haemonchus contortus and the free-living nematode Caenorhabditis elegans. In both species, hatching occurred st a concentration of 100 mu g/ml but was almost totally blocked at 400 mu g/ml. In the case of C. elegans, the effect was shown to be reversible by removal of chlorpromazine after exposure of the eggs to the drug for 1 hr. Caenorhabditis elegans larvae that hatched in a chlorpromazine concentration of 100 mu g/ml were killed, but those that hatched in a concentration of 6.25 mu g/ml were not. Taken together with data published by others, these observations indicate that the first-stage larva of C. elegans is less sensitive to chlorpromazine than is the adult worm. ------------------- Key: 3013 Medline: 98173782 Authors: Aspbury RA;Fisher MJ;Rees HH Title: Fatty acylation of polypeptides in the nematode Caenorhabditis elegans. Citation: Biochimica et Biophysica Acta-Protein Structure & Molecular Enzymology 1382: 111-119 1998 Type: ARTICLE Genes: Abstract: Covalent modification of eucaryotic proteins, involving addition of fatty acyl groups, is a widespread phenomenon. Here we describe the occurrence of this form of covalent modification in the free-living nematode, Caenorhabditis elegans. Following incubation in the presence of either [H-3]-myristic acid or [H-3]-palmitic acid, specific C. elegans polypeptides became labelled. Chemical analysis revealed that following incubation of C. elegans with [H-3]-myristic acid, polypeptides became labelled with myristoyl, palmitoyl or stearoyl moieties; after incubation with [H-3]-palmitic acid, palmitoyl or stearoyl moieties were incorporated into polypeptides. Fatty acyl groups were linked to target polypeptides, predominantly through alkali-labile thioester or ester linkages and acid-labile amide linkages. Where myristoylation involved an amide linkage, the modified amino acid was usually glycine. Preliminary immunological evidence indicated that heterotrimeric GTP-binding protein alpha subunit(s) are possible target(s) for acylation in C. elegans. ------------------- Key: 3014 Medline: 98141870 Authors: Colavita A;Culotti JG Title: Suppressors of ectopic UNC-5 growth cone steering identify eight genes involved in axon guidance in Caenorhabditis elegans. Citation: Developmental Biology 194: 72-85 1998 Type: ARTICLE Genes: pag-1 seu-1 seu-2 seu-3 unc-5 unc-6 unc-34 unc-40 unc-44 unc-129 eDf18 nDf32 sDf34 stDf8 Abstract: The UNC-5 guidance receptor, in response to the UNC-6/netrin path cue, orients growing axons in a dorsal direction along the epidermis of Caenorhabditis elegans. When ectopically expressed in the touch neurons, which normally extend ventrally or longitudinally, UNC-5 is able to reorient their axons toward the dorsal side in an UNC-6-dependent manner. This forms the basis of a genetic screen to identify other mutations that, like unc-6 mutations, suppress unc-5-induced growth cone guidance. These mutations may identify new components required for pioneer axon guidance by unc-5. In this paper, we describe eight genes that are required for ectopic unc-5-induced growth cone steering. Mutations in four of these identify the previously known axon guidance genes unc-6, unc-40, unc-34, and unc-44 and mutations in four others identify the novel genes unc-129, seu-2, and seu-3. Several of these mutations cause axon guidance defects similar to those found in unc-5 mutants. We propose that some or all of these genes may function in a developmentally important ------------------- Key: 3015 Medline: 98165396 Authors: Harfe BD;Fire A Title: Muscle and nerve-specific regulation of a novel NK-2 class homeodomain factor in Caenorhabditis elegans. Citation: Development 125: 421-429 1998 Type: ARTICLE Genes: ceh-22 ceh-24 myo-2 pes-10 Abstract: We have identified a new Caenorhabditis elegans NK-2 class homeobox gene, designated ceh-24. Distinct cis-acting elements generate a complex neuronal and mesodermal expression pattern. A promoter-proximal enhancer mediates expression in a single pharyngeal muscle, the donut-shaped m8 cell at the posterior end of the pharynx. A second mesodermal enhancer is active in a set of eight nonstriated vulval muscles used in egg laying. Activation in the egg laying muscles requires an 'NdE-box' consensus motif (CATATG) which is related to, but distinct from, the standard E-box motif bound by the MyoD family of transcriptional activators. Ectodermal expression of ceh-24 is limited to a subset of sublateral motor neurons in the head of the animal; this activity requires a cis-acting activator element that is distinct from the control elements for pharyngeal and vulval muscle expression, Activation of ceh-24 in each of the three cell types coincides with the onset of differentiation. Using a set of transposon-induced null mutations, we show that ceh-24 is not essential for the formation of any of these cells. Although ceh-24 mutants have no evident defects under laboratory conditions, the pattern of ceh-24 activity is apparently important for Rhabditid nematodes: the related species C, briggsae contains a close homologue of C, elegans ceh-24 including a highly conserved and functionally equivalent set of cis-acting control signals. ------------------- Key: 3016 Medline: 98146203 Authors: Coburn CM;Mori I;Ohshima Y;Bargmann CI Title: A cyclic nucleotide-gated channel inhibits sensory axon outgrowth in larval and adult Caenorhabditis elegans: a distinct pathway for maintenance of sensory axon structure. Citation: Development 125: 249-258 1998 Type: ARTICLE Genes: daf-1 daf-2 daf-4 daf-7 daf-8 daf-11 daf-12 daf-14 daf-21 tax-2 tax-4 Abstract: The tax-2 and tax-4 genes of C, elegans encode two subunits of a cyclic nucleotide-gated channel that is required for chemosensation, thermosensation and normal axon outgrowth of some sensory neurons. Here we show that, in tax-2 and tax-4 mutants, young larvae have superficially normal axons, but axon outgrowth resumes in inappropriate regions in late larval stages. Using a temperature-sensitive mutation in tax-2, we find that tax-2 activity is required during the adult stage to preserve normal axon morphology. These results indicate that tax-2 and tax-4 are required for the maintenance of correct axon structure, and reveal an unexpected plasticity that allows C. elegans axons to be remodeled long after their initial connections have been established. TAX-2 and TAX-4 have been proposed to form a transduction channel for chemosensation and thermosensation, and tax-2 activity is required in the adult stage for normal chemotaxis to NaCl and odorants. Animals mutant for the daf-11 gene have axon phenotypes that are similar to those of tax-2 and tax 4 mutants; this axon phenotype also has a late time of action, daf-11 regulates a developmental process called dauer larva formation that is controlled by sensory stimuli, and tax-2 and tax-4 can either stimulate or inhibit dauer larva ------------------- Key: 3017 Medline: 98150857 Authors: Clandinin TR;DeModena JA;Sternberg PW Title: Inositol trisphospate mediates a Ras-independent response to LET-23 receptor tyrosine kinase activation in C. Citation: Cell 92: 523-533 1998 Type: ARTICLE Genes: itr-1 let-23 let-60 lfe-1 lfe-2 lin-1 lin-3 sDf4 stDf7 Abstract: Activity of LET-23, the C. elegans homolog of the epidermal growth factor receptor, is required in multiple tissues. RAS activation is necessary and sufficient for certain LET-23 functions. We show that an inositol trisphosphate receptor can act as a PAS-independent, tissue-specific positive effector of LET-23. Moreover, an inositol trisphosphate kinase negatively regulates this transduction pathway. Signals transduced by LET-23 control ovulation through changes in spermathecal dilation, possibly dependent upon calcium release regulated by both IP3 and IP4. Our results demonstrate that one mechanism by which receptor tyrosine kinases can evoke tissue-specific responses is through activation of distinct signal transduction cascades in different tissues. ------------------- Key: 3018 Medline: 98173565 Authors: Hitchcock DR;Law SE;Wu J;Williams PL Title: Determining toxicity trends in the ozonation of synthetic dye wastewaters using the nematode Caenorhabditis elegans. Citation: Archives of Environmental Contamination and Toxicology 34: 259-264 1998 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans was used in 72-h toxicity tests to evaluate the influence of ozonation on the toxicity of three synthetic azo dye wastewaters (two reactive dyes and one acid-based dye). The two reactive dye wastewaters contained high concentrations of NaCl (89-112 g/L) in addition to potentially toxic dye components. To determine the contribution of NaCl to toxicity, simulated dye wastewater samples with and without NaCl were tested. Samples were collected at various times during ozonation (t = 0, 8, 32, 64 min); nematodes were exposed to the samples for 72 h. The influence of ozonation on toxicity varied between dye wastewater types. For the acid-based dye wastewater, toxicity increased as duration of ozonation increased. For the reactive dyes without NaCl, toxicity did not appear to be influenced by ozonation. For the reactive dyes with NaCl, mortality was 100% with or without ozonation. Range-finding experiments with NaCl in water and NaCl in dye wastewaters suggested an additive toxic interaction between NaCl and the dyes in wastewater to the nematodes. The duration of ozonation for acid-based dyes and the relatively high NaCl concentrations for the reactive dyes appear to influence effluent toxicity in the ozonated dye wastewaters. ------------------- Key: 3019 Medline: 98220112 Authors: Burglin TR;Lobos E;Blaxter ML Title: Caenorhabditis elegans as a model for parasitic nematodes. Citation: International Journal for Parasitology 28: 395-411 1998 Type: REVIEW Genes: age-1 ben-1 cut-1 cut-2 daf-1 daf-2 daf-3 daf-4 daf-5 daf-6 daf-7 daf-8 daf-10 daf-11 daf-12 daf-14 daf-16 daf-21 daf-22 daf-23 gpa-2 gpa-3 Abstract: Caenorhabditis elegans has become a popular model system for genetic and molecular research, since it is easy to maintain and has a very fast life-cycle. Its genome is small and a virtually complete physical map in the form of cosmids and YAC clones exists. Thus it was chosen as a model system by the Genome Project for sequencing, and it is expected that by 1998 the complete sequence (100 million bp) will be available. The accumulated wealth of information about C. elegans should be a boon for nematode parasitologists, as many aspects of gene regulation and function can be studied in this simple model system. A large array of techniques is available to study many aspects of C. elegans biology. In combination with genome projects for parasitic nematodes, conserved genes can be identified rapidly. We expect many new areas of fertile research that will lead to new insights in helminth parasitology, which are based not only on the information gained from C. elegans per se, but also from its use as a ------------------- Key: 3020 Medline: 98165343 Authors: George SE;Simokat K;Hardin J;Chisholm AD Title: The VAB-1 Eph receptor tyrosine kinase functions in neural and epithelial morphogenesis in C. elegans. Citation: Cell 92: 633-643 1998 Type: ARTICLE Genes: vab-1 ccDf4 maDf4 Abstract: Mutations in the C. elegans vab-1 gene disrupt the coordinated movements of cells during two periods of embryogenesis. vab-1 mutants are defective in the movement of neuroblasts during closure of the ventral gastrulation cleft and in the movements of epidermal cells during ventral enclosure of the embryo by the epidermis. We show that vab-1 encodes a receptor tyrosine kinase of the Eph family. Disruption of the kinase domain of VAB-1 causes weak mutant phenotypes, indicating that VAB-1 may have both kinase-dependent and kinase-independent activities. VAB-1 is expressed in neurons during epidermal enclosure and is required in these cells for normal epidermal morphogenesis, demonstrating that cell-cell interactions are required between neurons and epidermal cells for epidermal morphogenesis. ------------------- Key: 3021 Medline: 98165778 Authors: Vatcher GP;Thacker CM;Kaletta T;Schnabel H;Schnabel R;Baillie DL Title: Serine hydroxymethyltransferase is maternally essential in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 273: 6066-6073 1998 Type: ARTICLE Genes: let-713 let-721 let-725 let-756 mel-32 Abstract: The mel-32 gene in the free living soil nematode Caenorhabditis elegans encodes a serine hydroxymethyltransferase (SHMT) isoform. Seventeen ethylmethanesulfonate (EMS)-induced mutant alleles of mel-32(SHMT) have been generated, each of which causes a recessive maternal effect lethal phenotype. Animals homozygous for the SHMT mutations have no observable mutant phenotype, but their offspring display an embryonic lethal phenotype. The Mel-32 phenotype has been rescued with a transgenic array containing only mel-32(SHMT) genomic DNA. Heteroduplex analysis of the 17 alleles allowed 14 of the mutations to be positioned to small regions, Subsequent sequence analysis has shown that 16 of the alleles alter highly conserved amino acids, while one allele introduces a stop codon that truncates two thirds of the predicted protein, mel-32(SHMT) has a 55-60% identity at the amino acid level with both isoforms of SHMT found in yeast and humans and a 50% identity with the Escherichia coli isoform. The C. elegans mel-32 mutation represents the first case where SHMT has been shown to be an essential ------------------- Key: 3022 Medline: 98165800 Authors: Shibatohge M;Kariya K;Liao Y;Hu CD;Watari Y;Goshima M;Shima F;Kataoka T Title: Identification of PLC210, a Caenorhabditis elegans phospholipase C, as a putative effector of Ras. Citation: Journal of Biological Chemistry 273: 6218-6222 1998 Type: ARTICLE Genes: ceh-14 lin-1 ttx-3 unc-86 Abstract: Mammalian Ras proteins regulate multiple effecters including Raf, Ral guanine nucleotide dissociation stimulator (RalGDS), and phosphoinositide 3-kinase. In the nematode Caenorhabditis elegans, LIN-45 Raf has been identified by genetic analyses as an effector of LET-60 Ras. To search for other effecters in C. elegans, we performed a yeast two-hybrid screening for LET-60-binding proteins. The screening identified two cDNA clones encoding a phosphoinositide-specific phospholipase C (PI-PLC) with a predicted molecular mass of 210 kDa, designated PLC210, PLC210 possesses two additional functional domains unseen in any known PI-PLCs. One is the C-terminal Ras-associating domain bearing a structural homology with those of RalGDS and AF-6. This domain, which could be narrowed down to 100 amino acid residues, associated in vitro with human Ha-Ras in a GTP-dependent manner and competed with yeast adenylyl cyclase for binding Ha-Ras. The binding was abolished by specific mutations within the effector region of Ha-Ras. The other functional domain is the N-terminal CDC25-like domain, which possesses a structural homology to guanine nucleotide exchange proteins for Ras. These results strongly suggest that PLC210 belongs to a novel class of PI-PLC, which is a putative effector of Ras. ------------------- Key: 3023 Medline: 98169548 Authors: Felix MA;Sternberg PW Title: A gonad-derived survival signal for vulval precursor cells in two nematode species. Citation: Current Biology 8: 287-290 1998 Type: ARTICLE Genes: lin-39 Abstract: Intercellular cell survival signals play a major role in animal development [1]. In the nematode Caenorhabditis elegans, however, the stereotyped cell deaths that occur reproducibly during development are regulated in a cell-autonomous fashion (or, in a few cases, by a death-inducing signal) [2]. We show here the existence of a cell-survival signal acting on the vulval precursor cells in two nematodes, Turbatrix aceti and Halicephalobus sp. JB128. In C. elegans [3], as in many other nematode species [4-7], ablation of the gonad causes ail vulval precursor cells to adopt a default epidermal fate: a gonadal signal is required for the induction of vulval fates. In the nematodes T. aceti and Halicephalobus sp. JB128, however, we found that ablation of the gonad in the L1 larval stage caused all vulval precursor cells to undergo programed cell death. Thus, in intact Turbatrix and Halicephalobus, a survival signal from the gonad prevents activation of the cell-death program in vulval precursor cells. Our results demonstrate the existence of intercellular cell-survival signals in nematodes and uncover an evolutionary variation in the role of the gonad in nematode vulval development. ------------------- Key: 3024 Medline: 98191576 Authors: Bargmann CI;Kaplan JM Title: Signal transduction in the Caenorhabditis elegans nervous system. Citation: Annual Review of Neuroscience 21: 279-308 1998 Type: REVIEW Genes: avr-15 cha-1 daf-1 daf-4 daf-7 daf-8 daf-11 daf-14 deg-1 deg-3 eat-2 eat-5 eat-11 eat-18 egl-10 egl-30 glr-1 goa-1 gpa-2 gpa-3 gpb-1 gsa-1 lev-1 mec-4 mec-5 mec-6 mec-7 mec-9 mec-10 odr-10 osm-9 tax-2 tax-4 unc-2 unc-7 unc-8 unc-11 unc-13 unc-17 unc-18 unc-29 unc-38 unc-49 unc-50 unc-63 unc-74 unc-105 Abstract: Caenorhabditis elegans interacts with its environment by sensing chemicals, touch, and temperature; genetic analysis of each of these responses has led to the identification of candidate signaling molecules within sensory neurons. A molecular model for touch sensation has emerged from studies of the mechanosensory response; the receptors and signal transduction mechanisms in olfactory neurons are being elucidated; and an unusual neuroendocrine role for a TGF-beta-related peptide in chemosensory neurons has been discovered. Presynaptic and postsynaptic components of neuronal synapses have been identified in behavioral and pharmacological mutant screens. Mutations have been found in multiple classes of nicotinic acetylcholine receptor genes, excitatory and inhibitory glutamate receptor genes, and candidate gap junction genes, allowing their function to be studied in vivo. Different G-protein signaling pathways have characteristic effects on behavior, neuronal degeneration, and embryonic development. ------------------- Key: 3025 Medline: 98151395 Authors: Hobert O;D'Alberti T;Liu Y;Ruvkun G Title: Control of neural development and function in a thermoregulatory network by the LIM homeobox gene lin-11. Citation: Journal of Neuroscience 18: 2084-2096 1998 Type: ARTICLE Genes: let-60 lin-45 Abstract: We show here that the lin-11 LIM homeobox gene is expressed in nine classes of head, ventral cord, and tail neurons and functions at a late step in the development of a subset of these neurons. In a lin-11 null mutant, all lin-11-expressing neurons are generated. Several of these neurons, however, exhibit neuroanatomical as well as functional defects. In the lateral head ganglion, lin-11 functions in a neural network that regulates thermosensory behavior. It is expressed in the AIZ interneuron that processes high temperature input and is required for the function of AIZ in the thermoregulatory neural network. Another LIM homeobox gene, ttx-3, functions in the antagonistic thermoregulatory interneuron AIY (Hobert et al., 1997). Thus, distinct LIM genes specify the functions of functionally related antagonistic interneurons within a neural network dedicated for thermoregulatory processes. Both ttx-3 and lin-11 expression are maintained throughout adulthood, suggesting that these LIM homeobox genes play a role in the functional maintenance of this neural circuit. We propose that particular LIM homeobox genes specify the distinct features of functionally related neurons that generate patterned behaviors. ------------------- Key: 3026 Medline: 98260694 Authors: Puoti A;Gallegos M;Zhang B;Wickens MP;Kimble J Title: Controls of cell fate and pattern by 3' untranslated regions: The Caenorhabditis elegans sperm/oocyte decision. Citation: Cold Spring Harbor Symposia on Quantitative Biology 62: 19-24 1997 Type: REVIEW Genes: fbf-1 fbf-2 fem-1 fem-2 fem-3 fog-2 her-1 laf-1 mog-1 mog-5 tra-2 tra-3 Abstract: Most multicellular organisms comprise numerous cell types organized into complex tissues and organs. How are distinct cell types governed to adopt tissue- and organ-specific patterns? We have approached this fundamental problem in the germ line of the nematode Caenorhabditis elegans. Specifically, we have investigated the molecular controls specifying the pattern of gamete differentiation in hermaphrodites. ------------------- Key: 3027 Medline: 98188103 Authors: Steven R;Kubiseski TJ;Zheng H;Kulkarni S;Mancillas J;Morales AR;Hogue CWV;Pawson T;Culotti J Title: UNC-73 activates the Rac GTPase and is required for cell and growth cone migrations in C. elegans. Citation: Cell 92: 785-795 1998 Type: ARTICLE Genes: mec-4 mec-7 unc-73 Abstract: unc-73 is required for cell migrations and axon guidance in C. elegans and encodes overlapping isoforms of 283 and 189 kDa that are closely related to the vertebrate Trio and Kalirin proteins, respectively. UNC-73A contains, in order, eight spectrin-like repeats, a Dbl/Pleckstrin homology (DH/PH) element, an SH3-like domain, a second DH/PH element, an immunoglobulin domain, and a fibronectin type ill domain. UNC-73B terminates just downstream of the SH3-like domain. The first DR/PH element specifically activates the Rac GTPase in vitro and stimulates actin polymerization when expressed in Rat2 cells. Both functions are eliminated by introducing the S1216F mutation of unc-73(rh40) into this DH domain. Our results suggest that UNC-73 acts cell autonomously in a protein complex to regulate actin dynamics during cell and growth cone ------------------- Key: 3028 Medline: 98169459 Authors: Powell-Coffman JA;Bradfield CA;Wood WB Title: Caenorhabditis elegans orthologs of the aryl hydrocarbon receptor and its heterodimerization partner with the aryl hydrocarbon receptor nuclear translocator. Citation: Proceedings of the National Academy of Sciences USA 95: 2844-2849 1998 Type: ARTICLE Genes: aha-1 ahr-1 Abstract: The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor, until now described only in vertebrates, that mediates many of the carcinogenic and teratogenic effects of certain environmental pollutants. Here, we describe orthologs of AHR and its dimerization partner AHR nuclear translocator (ARNT) in the nematode Caenorhabditis elegans, encoded by the genes ahr-1 and aha-1, respectively. The corresponding proteins, AHR-1 and AHA-1, share biochemical properties with their mammalian cognates. Specifically, AHR-1 forms a tight association with HSP90, and AHR-1 and AHA-1 interact to bind DNA fragments containing the mammalian xenobiotic response element with sequence specificity. Yeast expression studies indicate that C. elegans AHR-1, like vertebrate AHR, requires some form of post-translational activation. Moreover, this requirement depends on the presence of the domains predicted to mediate binding of HSP90 and ligand. Preliminary experiments suggest that if AHR-1 is ligand-activated, its spectrum of ligands is different from that of the mammalian receptor: C. elegans AHR-1 is not photoaffinity labeled by a dioxin analog, and it is not activated by beta-naphthoflavone in the yeast system. The discovery of these genes in a simple, genetically tractable invertebrate should allow elucidation of AHR-1 function and identification of its endogenous regulators. ------------------- Key: 3029 Medline: 98185721 Authors: Burr AHJ;Gans C Title: Mechanical significance of obliquely striated architecture in nematode muscle. Citation: Biological Bulletin 194: 1-6 1998 Type: REVIEW Genes: lin-39 Abstract: In certain invertebrate muscles, adjacent narrow columns of sarcomeres are displaced along the fiber axis, providing an obliquely striated myofilament pattern in certain section planes. Although this architecture is described in many phyla and has been the subject of much discussion (1-12), its mechanical significance has yet to be resolved. In nematodes, where ultrastructural details of the obliquely striated muscle have long been known (12-19), another unique and prominent feature is the attachment of every sarcomere to the plasmalemma and basal lamina via dense bodies (Z-disc analogs). Unfortunately the importance of this feature to the transmission of the contractile force to the cuticle is not understood outside the Caenorhabditis elegans literature: it was overlooked in recent reviews covering obliquely striated muscle (9-11). Her-e we consider transmission of force and oblique striation together. We compare the contractile architecture in C. elegans with that in the more complex muscle type of larger nematodes. Both types are designed to transmit the force of contraction laterally to the cuticle rather than longitudinally to the muscle ends. In the second type, folding of the contractile structure around an inward extension of the basal lamina enables a higher number of sarcomeres to be linked to cuticle per unit length. We suggest that the mechanical significance of the oblique arrangement of sarcomeres in both types is that it distributes rite force application sites of the sarcomeres more evenly over the basal lamina and cuticle. With this muscle architecture, smooth bending of the nematode body tube would be possible, and kinking would be prevented. ------------------- Key: 3030 Medline: 98223394 Authors: Ikenishi K Title: Germ plasm in Caenorhabditis elegans, Drosophila and Xenopus. Citation: Development, Growth & Differentiation 40: 1-10 1998 Type: REVIEW Genes: glh-1 glh-2 mex-1 mex-3 par-1 pie-1 Abstract: Special cytoplasm, called germ plasm, that is essential for the differentiation of germ cells is localized in a particular region of Caenorhabditis elegans, Drosophila and Xenopus eggs. The mode of founder cell formation of germline, the origin and behavior of the germline granules, and the molecules localized in germline cells are compared in these organisms. The common characteristics of the organisms are mainly as follows. First, the founder cells of germline are established before the initiation of gastrulation. Second, the germline granules or their derivatives are always present in germline cells or germ cells throughout the life cycle in embryos, larvae, and adults. Lastly, among the proteins localized in the germ plasm, only Vasa protein or its homolog is detected in the germline cells or germ cells throughout the life cycle. As the protein of vasa homolog has been reported to be also localized in the germline-specific structure or nuage in some of the organisms without the germ plasm, the possibility that the mechanism for differentiation of primordial germ cells is basically common in all organisms with or without the germ plasm is discussed. ------------------- Key: 3031 Medline: Authors: Njoku CJ;Zeng L;Asuzu IU;Oberlies NH;McLaughlin JL Title: Oleanolic acid, a bioactive component of the leaves of Ocimum gratissumum (Laciaceae). Citation: International Journal of Pharmacognosy 35: 134-137 1997 Type: ARTICLE Genes: Abstract: Bioactivity-guided fractionation of the leaves of Ocimum gratissimum L. (Lamiaceae), using the brine shrimp lethality test, led to the isolation of oleanolic acid. Oleanolic acid showed bioactivity against a panel of six human solid tumor lines, the nematode Caenorhabditis elegans and yellow fever mosquito larvae Aedes Aegypti. Details of the isolation and bioactivities are described. ------------------- Key: 3032 Medline: 98149727 Authors: Napier JA;Hey SJ;Lacey DJ;Shewry PR Title: Identification of a Caenorhabditis elegans delta(6)-fatty-acid-desaturase by heterologous expression in Saccharomyces cerevisiae. Citation: Biochemical Journal 330: 611-614 1998 Type: ARTICLE Genes: Abstract: We identified a cDNA expressed sequence tag from an animal (the nematode worm Caenorhabditis elegans) that showed weak similarity to a higher-plant microsomal Delta(6)-desaturase. A full-length cDNA clone was isolated and expressed in the yeast Saccharomyces cerevisiae. This demonstrated that the protein encoded by the C. elegans cDNA was that of a fatty acid Delta(6)-desaturase, as determined by the accumulation of gamma-linolenic acid. The C. elegans Delta(6)-desaturase contained an N-terminal cytochrome b(5) domain, indicating that it had a similar structure to that of the higher-plant Delta(6)-desaturase. The C. elegans Delta(6)-desaturase mapped to cosmid W08D2, a region of chromosome III. This is the first example of a Delta(6)-desaturase isolated from an animal and also the first example of an animal desaturase containing a ------------------- Key: 3033 Medline: 98201713 Authors: Lee MH;Jang YJ;Koo H Title: Alternative splicing in the Caenorhabditis elegans DNA topoisomerase I gene. Citation: Biochimica et Biophysica Acta-Gene Structure and Expression 1396: 207-214 1998 Type: ARTICLE Genes: Abstract: 5'-end cDNA fragments of the Caenorhabditis elegans DNA topoisomerase I gene were obtained by rapid amplification of the cDNA ends from C. elegans mRNAs. The presence of a SL1 sequence at the 5'-terminus of the cDNA sequence suggested trans-splicing of the pre-mRNA. By comparing the complete cDNA sequence with the genomic lambda DNA clones, the gene structure composed of five exons was established. Alternative splicing deleting the second exon was observed in the cDNA fragments obtained by a gene-specific reverse transcription followed by polymerase chain reactions. The shorter mRNA missing the second exon was expressed at all the developmental stages, while the full-length mRNA was present only in embryos. ------------------- Key: 3034 Medline: 98198570 Authors: Grauso M;Culetto E;Combes D;Fedon Y;Toutant J;Arpagaus M Title: Existence of four acetylcholinesterase genes in the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. Citation: FEBS Letters 424: 279-284 1998 Type: ARTICLE Genes: ace-1 ace-2 ace-3 Abstract: Three genes, ace-1, ace-2 and ace-3, respectively located on chromosomes X, I and II, were reported to encode acetylcholinesterases (AChEs) of classes A, B and C in the nematode Caenorhabditis elegans. We have previously cloned and sequenced ace-1 in the two related species C, elegans and C, briggsae. We report here partial sequences of ace-2 (encoding class B) and of two other ace sequences located in close proximity on chromosome II in C, elegans and C, briggsae. These two sequences are provisionally named ace-x and ace-y, because it is not possible at the moment to establish which of these two genes corresponds to ace-3. Ace-x acid ace-y are transcribed in vivo as shown by RT-PCR and they are likely to be included in a single operon. ------------------- Key: 3035 Medline: 98290544 Authors: Fujii M;Ishii N;Jogushi A;Yasuda K;Ayusawa D Title: A novel superoxide dismutase gene encoding membrane-bound and extracellular isoforms by alternative splicing in Caenorhabditis elegans. Citation: DNA Research 5: 25-30 1998 Type: ARTICLE Genes: mev-1 Abstract: Regulation of ribosome synthesis is an essential aspect of growth control. Thus far, little is known about the factors that control and coordinate these processes. We show here that the Caenorhabditis elegans gene ncl-1 encodes a zinc finger protein and may be a repressor of RNA polymerase I and III transcription and an inhibitor of cell growth. Loss of function mutations in ncl-1, previously shown to result in enlarged nucleoli. result in increased rates of rRNA and 5S RNA transcription and enlarged cells. Furthermore, ncl-1 adult worms are larger, have more protein, and have twice as much rRNA as wild-type worms. Localization studies show that the level of NCL-1 protein is independently regulated in different cells of the embryo. In wild-type embryos, cells with the largest nucleoli have the lowest level of NCL-1 protein. Based on these results we propose that ncl-1 is a repressor of ribosome synthesis and cell growth. ------------------- Key: 3036 Medline: 98208032 Authors: Wu YC;Horvitz HR Title: C. elegans phagocytosis and cell migration protein CED-5 is similar to human DOCK180. Citation: Nature 392: 501-504 1998 Type: ARTICLE Genes: ced-5 sDf2 Abstract: During programmed cell death, cell corpses are rapidly engulfed(1). This engulfment process involves the recognition and subsequent phagocytosis of cell corpses by engulfing cells(1-4). How cell corpses are engulfed is largely unknown. Here we report that ced-5, a gene that is required for cell-corpse engulfment in the nematode Caenorhabditis elegan(5), encodes a protein that is similar to the human protein DOCK180 and the Drosophila melanogaster protein Myoblast City (MBC), both of which have been implicated in the extension of cell surfaces(6). ced-5 mutants are defective not only in the engulfment of cell corpses but also in the migrations of two specific gonadal cells, the distal tip cells. The expression of human DOCK180 in C. elegans rescued the cell-migration defect of a ced-5 mutant. We present evidence that ced-5 functions in engulfing cells during the engulfment of cell corpses. We suggest that ced-5 acts in the extension of the surface of an engulfing cell around a dying cell during programmed cell death. We name this new family of proteins that function in the extension of cell surfaces the CDM (for CED-5, DOCK180 and MBC) family. ------------------- Key: 3037 Medline: Authors: Schierenberg E;Wiegner O;Bossinger O;Skiba F;Kutzowitz M Title: Pattern formation and cell specification in nematode embryos: A theme with considerable variations. Citation: Zoology-Analysis of Complex Systems 100: 320-327 1997 Type: ARTICLE Genes: Abstract: The pattern of cellular development of the free-living nematode Caenorhabditis elegans has been described completely. For comparison we have begun to study the early embryogenesis of other nematodes to ask how much variation occurs in a group of animals, all with a very similar phenotype. We found one family, Cephalobidae, with a number of specific features, indicating that even for closely related taxa a similar terminal structure does not necessarily imply the same developmental strategies. In particular, we looked for mechanisms of cell specification. Besides studying cell lineages, spatial pattern formation and tissue-specific differentiation, we manipulated embryos with the help of a laser microbeam coupled to a microscope; through a hole shot in the eggshell we added drugs or removed blastomeres. On the one hand C. elegans embryogenesis makes use to a large extent of maternal gene products unequally segregated into early blastomeres. On the other hand early cell-cell interactions in the form of receptor/ligand-mediated inductions play an important role. In contrast, in Cephalobus, the best studied representative of Cephalobid nematodes, embryogenesis appears to rely to a much lesser extent on maternal inheritance but requires massive early transcription, and in addition, inhibitory interactions between blastomeres of similar developmental potential seem to be involved. ------------------- Key: 3038 Medline: 98195352 Authors: Berger AJ;Hart AC;Kaplan JM Title: G-alpha(s)-induced neurodegeneration in Caenorhabditis elegans. Citation: Journal of Neuroscience 18: 2871-2880 1998 Type: ARTICLE Genes: acy-1 ced-3 ced-4 deg-1 eat-4 egl-19 glr-1 mec-6 mec-7 odr-1 odr-7 osm-3 snt-1 tax-2 tax-4 unc-2 unc-8 unc-36 Abstract: We describe a genetic model for neurodegeneration in the nematode Caenorhabditis elegans. Constitutive activation of the GTP-binding protein G alpha(s) induces neurodegeneration. Neuron loss occurs in two phases whereby affected cells undergo a swelling response in young larvae and subsequently die sometime during larval development. Different neural cell types vary greatly in their susceptibility to G alpha(s)-induced cytotoxicity, ranging from 0 to 88% of cells affected. Mutations that prevent programmed cell death do not prevent G alpha(s)-induced killing, suggesting that these deaths do not occur by apoptosis. Mutations in three genes protect against G alpha(s)-induced cell deaths. The acy-1 gene is absolutely required for neurodegeneration, and the predicted ACY-1 protein is highly similar (40% identical) to mammalian adenylyl cyclases. Thus, G(s)-induced neurodegeneration is mediated by the second messenger cAMP. Mutations in the unc-36 and eat-4 genes are partially neuroprotective, which indicates that endogenous signaling modulates the severity of the neurotoxic effects of G alpha(s). These experiments define an intracellular signaling cascade that triggers a necrotic form of neurodegeneration. ------------------- Key: 3039 Medline: 98206469 Authors: Singson A;Mercer KB;L'Hernault SW Title: The C. elegans spe-9 gene encodes a sperm transmembrane protein that contains EGF-like repeats and is required for fertilization. Citation: Cell 93: 71-79 1998 Type: ARTICLE Genes: fem-1 spe-9 dxDf2 hDf17 Abstract: In the nematode worm C. elegans, individuals with mutations in the spe-g gene produce spermatozoa with wild-type morphology and motility that cannot fertilize oocytes even after contact between gametes. Therefore, disruption of spe9 function affects either gamete recognition, adhesion, signaling, and/or fusion; The spe-g gene encodes a sperm transmembrane protein with an extracellular domain that contains ten epidermal growth factor-like repeats. A common feature of proteins that include epidermal growth factor-like motifs is their involvement in extracellular functions such as adhesive and ligand-receptor interactions. Additionally, the overall structure of the predicted SPE-9 protein is similar to that of ligands for the Notch/LIN-12/GLP-1 family of transmembrane receptors. These results suggest that SPE-9 functions in the specialized cell-cell interactions required for ------------------- Key: 3040 Medline: Authors: Goodwin EB;Evans TC Title: Translational control of development in C. elegans. Citation: Seminars in Cell & Developmental Biology 8: 551-559 1997 Type: REVIEW Genes: apx-1 fem-3 gld-1 glp-1 laf-1 lin-4 lin-14 lin-28 mex-1 mex-3 pal-1 pie-1 skn-1 tra-1 tra-2 tra-3 Abstract: Translational control by the 3'untranslated reg-ions (3'UTRs) of mRNAs contributes to important events throughout the development of C. elegans. In oocytes and early embryos, maternal mRNAs are controlled by 3'UTR elements to restrict translation of their protein products to specific blastomeres. Localized translation is probably critical for specifying blastomere identity. In both germline and somatic cells, mRNAs from sex determining genes are translationally repressed by 3'UTR controls. These controls balance the activities that specific male and female cell fates. During larval development, the temporal sequence of cell lineages requires 3'UTR-mediated regulation of heterochronic genes by a small non-protein coding RNA. We review what is known about these translational control mechanisms in C. elegans. This overview illustrates that translational control by 3'UTR elements is a powerful mechanism for regulating the expression of multiple gene products in diverse cell types ------------------- Key: 3041 Medline: 98233641 Authors: Wood WB Title: Handed asymmetry in nematodes. Citation: Seminars in Cell & Developmental Biology 9: 53-60 1998 Type: REVIEW Genes: glp-1 lag-1 lag-2 lin-12 spn-1 Abstract: Like most animals, C. elegans and other nematodes exhibit several internal left-right asymmetries with an essentially invariant (dextral) handedness. Handedness is established in early cleavage, resulting in a markedly left-right-asymmetric embryo on which bilateral symmetry must be superimposed later in embryogenesis. Some of the asymmetric cell interactions that accomplish this have been identified, but the mechanism that initially establishes dextral rather than sinistral handedness is not understood, in C. elegans or any other embryo. Analysis of mutations that result in reversal of handedness, such as spn-l in C. elegans, should help elucidate this process. A model involving centriolar segregation is proposed as a possible mechanism for handedness choice. ------------------- Key: 3042 Medline: 98192620 Authors: Hagen FK;Nehrke K Title: cDNA cloning and expression of a family of UDP-N-acetyl-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase sequence homologs from Caenorhabditis elegans. Citation: Journal of Biological Chemistry 273: 8268-8277 1998 Type: ARTICLE Genes: gly-3 gly-4 gly-5 gly-6 gly-7 gly-8 gly-9 Abstract: The initiation of mucin-type O-glycosylation is catalyzed by a family of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (ppGaNTase) (EC 2.4.1.41), By screening two mixed-stage Caenorhabditis elegans cDNA libraries, a total of 11 distinct sequence homologs of the ppGaNTase gene family were cloned, sequenced, and expressed as truncated recombinant proteins (gly-3, gly-4, gly-5a, gly3-5b, gly-5c, gly-6a, gly-6b, gly-6c, gly-7, gly-8, and gly-9), All clones encoded type II membrane proteins that shaped 60-80% amino acid sequence similarity with the catalytic domain of mammalian ppGaNTase enzymes, Two sets of cDNA clones (gly-5 and gly-6) contained variants that appeared to be produced by alternative message processing. gly-6c contained a reading frameshift and premature termination codon in the C-terminal lectin-libe domain found in most other ppGaNTase proteins, and a second clone (gly-8) racked the typical C-terminal region completely, Homogenates of nematodes and immunopurified. preparations of the recombinant GLY proteins demonstrated that worms express functional ppGaNTase enzymes (GLY-3, GLY-4, GLY-SA, GLY-5B, and GLY-5C), which can O-glycosylate mammalian apomucin peptide sequences in vitro. In addition to demonstrating the existence of ppGaNTase enzymes in a nematode organism, the substantial diversity of these isoforms in C. elegans suggests that mucin O-glycosylation is catalyzed by a complex gene family, which is conserved among ------------------- Key: 3043 Medline: 98139555 Authors: Hisahara S;Kanuka H;Shoji S;Yoshikawa S;Okano H;Miura M Title: Caenorhabditis elegans anti-apoptotic gene ced-9 prevents ced-3-induced cell death in Drosophila cells. Citation: Journal of Cell Science 111: 667-673 1998 Type: ARTICLE Genes: ced-3 ced-9 Abstract: ced-9, a member of the bcl-2 gene family in Caenorhabditis elegans plays a central roles in preventing cell death in norms. Overexpression of human bcl-2 can partially prevent cell death in C. elegans. However, it remains to be elucidated whether ced-9 can regulate cell death when expressed in other organisms. We demonstrated that the CED-9 protein is co-localized with BCL-2 in COS cells and Drosophila Schneider's L2 (SL2) cells, suggesting that the site of CED-9 action is located to specific cytoplasmic compartments. Overexpression of ced-9 only poorly protected cells from the death induced by ced-3 in HeLa cells, but ced-9 significantly reduced the cell death induced by ced-3 in Drosophila SL2 cells. Furthermore, apoptosis of SL2 cells that was induced by a Drosophila cell-death gene, reaper, was shown to be partially prevented by ced-9, bcl-2 and bcl-xL. These results suggest that the signaling pathway that is required for the anti-apoptotic function of bcl-2 family members, including ced-9, is conserved in Drosophila cells. In addition, SL2 cells provide a unique systems for dissecting the main machinery of cell death. ------------------- Key: 3044 Medline: 98177161 Authors: Frank DJ;Roth MB Title: ncl-1 is required for the regulation of cell size and ribosomal RNA synthesis in Caenorhabditis elegans. Citation: Journal of Cell Biology 140: 1321-1329 1998 Type: ARTICLE Genes: clr-1 ncl-1 Abstract: Regulation of ribosome synthesis is an essential aspect of growth control. Thus far, little is known about the factors that control and coordinate these processes. We show here that the Caenorhabditis elegans gene ncl-1 encodes a zinc finger protein and may be a repressor of RNA polymerase I and III transcription and an inhibitor of cell growth. Loss of function mutations in ncl-1, previously shown to result in enlarged nucleoli. result in increased rates of rRNA and 5S RNA transcription and enlarged cells. Furthermore, ncl-1 adult worms are larger, have more protein, and have twice as much rRNA as wild-type worms. Localization studies show that the level of NCL-1 protein is independently regulated in different cells of the embryo. In wild-type embryos, cells with the largest nucleoli have the lowest level of NCL-1 protein. Based on these results we propose that ncl-1 is a repressor of ribosome synthesis and cell growth. ------------------- Key: 3045 Medline: 98130568 Authors: Burdine RD;Branda CS;Stern MJ Title: EGL-17(FGF) expression coordinates the attraction of the migrating sex myoblasts with vulval induction in C. Citation: Development 125: 1083-1093 1998 Type: ARTICLE Genes: dig-1 egl-15 egl-17 let-23 let-60 lin-12 lin-15 lin-39 Abstract: During the development of the egg-laying system in Caenorhabditis elegans hermaphrodites, central gonadal cells organize the alignment of the vulva with the sex myoblasts, the progenitors of the egg-laying muscles. A fibroblast growth factor [EGL-17(FGF)] and an FGF receptor [EGL-15(FGFR)] are involved in the gonadal signals that guide the migrations of the sex myoblasts. Here we show that EGL-17(FGF) can act as an instructive guidance cue to direct the sex myoblasts to their final destinations. We find that egl-17 reporter constructs are expressed in the primary vulval cell and that EGL-17(FGF) expression in this cell correlates with the precise positioning of the sex myoblasts. We postulate that EGL-17(FGF) helps to coordinate the development of a functional egg-laying system, linking vulval induction with proper sex myoblast ------------------- Key: 3046 Medline: 98198486 Authors: Costa M;Raich W;Agbunag C;Leung B;Hardin J;Priess JR Title: A putative catenin-cadherin system mediates morphogenesis of the Caenorhabditis elegans embryo. Citation: Journal of Cell Biology 141: 297-308 1998 Type: ARTICLE Genes: bar-1 cdh-3 hmp-1 hmp-2 hmr-1 wrm-1 ctDf1 eDf3 eDf4 eDf6 eDf9 eDf11 eDf12 eDf13 eDf14 eDf15 eDf16 Abstract: During morphogenesis of the Caenorhabditis elegans embryo, hypodermal (or epidermal) cells migrate to enclose the embryo in an epithelium and, subsequently, change shape coordinately to elongate the body (Priess, J.R., and D.I. Hirsh. 1986, Dev. Biol. 117:156-173, Williams-Masson, E.M., A.N. Malik, and J. Hardin. 1997, Development [Camb.]. 124:2889-2901). We have isolated mutants defective in morphogenesis that identify three genes required for both cell migration during body enclosure and cell shape change during body elongation. Analyses of hmp-1, hmp-2, and hmr-1 mutants suggest that products of these genes anchor contractile actin filament bundles at the adherens junctions between hypodermal cells and, thereby, transmit the force of bundle contraction into cell shape change. The protein products of all three genes localize to hypodermal adherens junctions in embryos. The sequences of the predicted HMP-1, HMP-2, and HMR-1 proteins are related to the cell adhesion proteins alpha-catenin, beta-catenin/Armadillo, and classical cadherin, respectively. This putative catenin-cadherin system is not essential for general cell adhesion in the C. elegans embryo, but rather mediates specific aspects of morphogenetic cell shape change and cytoskeletal ------------------- Key: 3047 Medline: 98217368 Authors: Kuwabara PE Title: Gametogenesis - Keeping the male element under control. Citation: Current Biology 8: R278-R281 1998 Type: REVIEW Genes: fbf-1 fbf-2 fem-3 mog-1 mog-2 mog-3 mog-4 mog-5 mog-6 Abstract: Caenorhabditis elegans hermaphrodites switch from making sperm to oocytes. This switch involves repression of fem-3 mRNA, mediated by a protein that binds RNA through a conserved motif; a similar motif mediates RNA binding by the Drosophila pattern-regulatory protein Pumilio. ------------------- Key: 3048 Medline: 98181063 Authors: Tawe WN;Eschbach ML;Walter RD;Henkle-Duhrsen K Title: Identification of stress-responsive genes in Caenorhabditis elegans using RT-PCR differential display. Citation: Nucleic Acids Research 26: 1621-1627 1998 Type: ARTICLE Genes: col-12 sod-1 sod-3 Abstract: In order to identify genes that are differentially expressed as a consequence of oxidative stress due to paraquat we used the differential display technique to compare mRNA expression patterns in Caenorhabditis elegans. A C.elegans mixed stage worm population and-a homogeneous larval population were treated with 100 mM paraquat, in parallel with controls. Induction of four cDNA fragments, designated L-1, M-47, M-96 and M-132, was confirmed by Northern blot analysis with RNA from stressed and unstressed worm populations. A 40-fold increase in the steady-state mRNA level in the larval population was observed for the L-1/M-47 gene, which encodes the detoxification enzyme glutathione S-transferase. A potential stress-responsive transcription factor (M-132) with C2H2-type zinc finger motifs and an N-terminal leucine zipper domain was identified. The M-96 gene encodes a novel stress-responsive protein. Since paraquat is known to generate superoxide radicals in vivo, the response of the C.elegans superoxide dismutase (SOD) genes to paraquat was also investigated in this study. The steady-state mRNA levels of the manganese-type and the copper/zinc-type SODs increased 2-fold in the larval population in response to paraquat, whereas mixed stage populations did not show any apparent increase in the levels of these SOD mRNAs. ------------------- Key: 3049 Medline: 98202524 Authors: Dent JA;Han M Title: Post-embryonic expression pattern of C. elegans let-60 ras reporter constructs. Citation: Mechanisms of Development 72: 179-182 1998 Type: ARTICLE Genes: let-60 Abstract: let-60 ras plays roles in the differentiation of several C. elegans tissues (Yochem, J., Sundaram, M., Han, M., 1997. Ras is required for a limited number of cell fates and not for general proliferation in Caenorhabditis elegans. Mel. Cell. Biol. 17, 2716-2722). To understand the transcriptional regulation of ras and to identify new functions for ras in development, we examined expression patterns of let-60::lacZ and let-60::GFP reporter constructs in C. elegans hermaphrodites. Fusion constructs were expressed in vulval precursor cells, sex myoblasts and in cell lineages of the somatic gonad, germline cells (GFP construct only), hypodermis, muscle and nervous system. ------------------- Key: 3050 Medline: 98198452 Authors: Shi Y;Mello C Title: A CBP/p300 homolog specifies multiple differentiation pathways in Caenorhabditis elegans. Citation: Genes & Development 12: 943-955 1998 Type: ARTICLE Genes: cbp-1 hda-1 hda-2 hda-3 pal-1 rba-1 rba-2 skn-1 Abstract: Mammalian p300 and CBP are related transcriptional cofactors that possess histone acetyltransferase activity. Inactivation of CBP/p300 is critical for adenovirus E1A to induce oncogenic transformation and to inhibit differentiation, suggesting that these proteins are likely to play a role in cell growth and differentiation. Here we show that a Caenorhabditis elegans gene closely related to CBP/p300, referred to as cbp-1, is required during early embryogenesis to specify several major differentiation pathways. Inhibition of cbp-1 expression causes developmental arrest of C. elegans embryos with no evidence of body morphogenesis but with nearly twice the normal complement of embryonic cells. Mesodermal, endodermal, and hypodermal cells appear to be completely absent in most embryos, however, all of the embryos exhibit evidence of neuronal differentiation. Our analysis of this phenotype suggests a critical role for CBP-1 in promoting all non-neuronal pathways of somatic differentiation in the C. elegans embryo. In contrast, we show that C. elegans genes related to components of a conserved mammalian histone deacetylase, appear to have a role in repressing somatic differentiation. Our findings suggest a model in which CBP-1 may activate transcription and differentiation in C. elegans by directly or indirectly antagonizing a repressive effect of histone deacetylase. ------------------- Key: 3051 Medline: 98208523 Authors: Xie HY;Hirsh D Title: In vivo function of mutated spliced leader RNAs in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 95: 4235-4240 1998 Type: ARTICLE Genes: ges-1 rrs-1 Abstract: The role of spliced leader RNA (SL RNA) in trans-splicing in Caenorhabditis elegans has been studied through a combination of in vitro mutagenesis and in vivo complementation of rrs-1 mutant nematodes, which lack endogenous SL1 RNA. Three classes of mutant SL1 RNAs have been found-those that rescue the lethal phenotype at low concentration of transforming DNA, those that rescue at high but not low concentration, and those that do not rescue at all. These studies showed that some mutations in the otherwise highly conserved 22-nt spliced leader are tolerated for splicing and post-splicing events. A longer spliced leader also can be tolerated but only when present in high copy number. Changes in the first 16 nucleotides result in the appearance of no SL RNA, consistent with the in vitro studies by others showing that the SL1 RNA promoter partly resides within the spliced leader sequence. ------------------- Key: 3052 Medline: 98231079 Authors: Goldstein P Title: The synaptonemal complexes of the nematode Caenorhabditis elegans: gametic response to retinol. Citation: Cytobios 91: 53-67 1997 Type: ARTICLE Genes: Abstract: Retinol (RO) is essential for normal gene expression and progression of gametogenesis. Excessive amounts of RO in the diet results in the condition termed 'hypervitaminosis A' which severely affects gametogenesis. In the present work, the nematode Caenorhabditis elegans was grown in different concentrations of RO for up to seven generations. Decreased fecundity was positively correlated with increasing concentrations of RO with successive generations. Decreased nuclear volume was positively correlated with increasing RO concentration for each generation. Abnormal chromosome condensation was present along the bivalent and the lengths of the synaptonemal complexes (SC) were consistently longer than in the wild-type. Increasing RO concentration was also negatively correlated with the presence of SCs. The presence of disjunction regulator regions (DRR), which are decondensed regions of chromatin along the bivalent which occur in specific numbers, was negatively correlated with increasing RO concentration. By the third generation, DRRs were no longer observed in any of the organisms. This study shows that high levels of retinol in the diet affect gene expression, via changes in chromosome structure, and interferes with gamete production by inhibiting the pairing ------------------- Key: 3053 Medline: 98011424 Authors: Sharief FS;Tsoi SCM;Li SSL Title: cDNA cloning and genomic organization of Enhancer of split groucho gene from nematode Caenorhabditis elegans. Citation: Biochemistry and Molecular Biology International 43: 327-337 1997 Type: ARTICLE Genes: Abstract: This first genomic Enhancer of split groucho (ESG) gene and its full length complementary DNA (cDNA) from nematode C. elegans were cloned and sequenced via homology with the corresponding Drosophila groucho cDNA. The cDNA of 2.1-Kb encodes a protein of 612 amino acids, and the nematode ESG protein is the smallest and most different in structure compared to all ESG related proteins. The gene isolated is 4,246-bp in size, including 1,219-bp promoter region. A putative TATA-box at position -1166, two consensus sequence of ACTGG, characteristic of leader binding protein-1 (LBP-1) binding motifs at position -563 and -211 and nine CAAT boxes were found in the promoter region of ESG gene. The protein-coding sequence is interrupted by five introns. The length of introns 1 to 5 is 52, 252, 87, 53 and 518 bp, respectively. The overall structural relationships of the ESG-related proteins among human, mouse, rat, Xenopus, Drosophila and nematode were also analyzed. ------------------- Key: 3054 Medline: 98221190 Authors: Jankowska-Anyszka M;Lamphear BJ;Aamodt EJ;Harrington T;Darzynkiewicz E;Stolarski R;Rhoads RE Title: Multiple isoforms of eukaryotic protein synthesis initiation factor 4E in Caenorhabditis elegans can distinguish between mono- and trimethylated messenger RNA Citation: Journal of Biological Chemistry 273: 10538-10542 1998 Type: ARTICLE Genes: ife-1 ife-2 ife-3 Abstract: The rate-limiting step for cap dependent translation initiation in eukaryotes is recruitment of mRNA to the ribosome, An early event in this process is recognition of the m(7)GTP-containing cap structure at the 5'-end of the mRNA by initiation factor eIF4E, In the nematode Caenorhabditis elegans, mRNAs from 70% of the genes contain a different cap structure, m(3)(2,2,7)GTP. This cap structure is poorly recognized by mammalian elF4E, suggesting that C, elegans may possess a specialized form of elF4E that can recognize m(3)(2,2,7)GTP. Analysis of the C. elegans genomic sequence data base revealed the presence of three elF4E-like genes, here named ife-1, ife-2, and ife-3, cDNAs for these three eIF4E isoforms were cloned and sequenced. Isoform-specific antibodies were prepared from synthetic peptides based on nonhomologous regions of the three proteins. All three eIF4E isoforms were detected in extracts of C. elegans and were retained on m(7)GTP-Sepharose. One eIF4E isoform, IFE-1, was also retained on m,2 2 7GTP-Sepharose. Furthermore, binding of IFE-1 and IFE-2 to m(7)GTP-Sepharose was inhibited by m(3)(2,2,7)GTP. These results suggest that IFE-1 and IFE-2 bind both m(7)GTP- and m(3)(2,2,7)GTP-containing mRNA cap structures, although with different affinities. In conjunction with IFE-3, these eIF4E isoforms would permit cap-dependent recruitment of all C. elegans mRNAs to the ribosome. ------------------- Key: 3055 Medline: Authors: Borgonie G;Van Driessche E;Coomans A Title: Lectins in nematology: An overview. Citation: "Lectins: Biology, Biochemistry, Clinical Biochemistry". E Van Driessche, P Rouge, S Beeckmans and TC Bog-Hansen (eds). Textop, Hellerup. 11: 337-345 1996 Type: REVIEW Genes: Abstract: Applications of, and investigations on lectins in nematology reflect the existing classification of nematodes according to their life-styles, i.e. free-living, plant-parasitic and animal-parasitic. In animal-parasitic nematodes, lectins have predominately been used to study the cuticle and its interaction between nematode and host. In plant-parasitic nematodes, investigations on the cuticle and amphid exudates have been predominant. Nematode-plant interactions on the other hand have attracted only minor attention. Ironically, however, the free-living nematodes in general, and the widely used model system Caenorhabditis elegans in particular, have been used very little for study of lectins, in spite of the many advantages offered by this organism as a genetic and an experimental model system. ------------------- Key: 3056 Medline: Authors: Bernt U;Junkersdorf B;Londershausen M;Harder A;Schierenberg E Title: Effects of anthelminthics with different modes of action on the behavior and development of Caenorhabditis elegans. Citation: Fundamental and Applied Nematology 21: 251-263 1998 Type: ARTICLE Genes: Abstract: The anthelminthic effects of four substances known to have different modes of action - two well-established nematicides (ivermectin, mebendazole) and two compounds presently in development (annonin, PF 1022)-were evaluated from the results of in vitro and in vivo tests with four different parasitic nematodes. To determine to what extent the test results also apply to free-living nematodes, the effects of the same drugs on locomotion, reproduction, development, and cellular structures of the well-studied free-living species Caenorhabditis elegans were analysed in detail. The role of culture conditions, exposure time necessary for induction of defects, and reversibility of drug effects were also studied. Each of the tested substances induces a specific defect pattern. Our data indicate that it is necessary to combine results from different tests in order to obtain a comprehensive picture of the anthelminthic effects of a substance and hence of its potential suitability as a nematicide. ------------------- Key: 3057 Medline: 98217375 Authors: Duret L;Guex N;Peitsch MC;Bairoch A Title: New insulin-like proteins with atypical disulfide bond pattern characterized in Caenorhabditis elegans by comparative sequence analysis and homology modeling. Citation: Genome Research 8: 348-353 1998 Type: ARTICLE Genes: daf-2 Abstract: We have identified three new families of insulin homologs in Caenorhabditis elegans. In two of these families, concerted mutations suggest that an additional disulfide bond links B and A domains, and that the A-domain internal disulfide bond is substituted by a hydrophobic interaction. Homology modeling remarkably confirms these predictions and shows that despite this atypical disulfide bond pattern and the absence of C-like peptide, all these proteins may adopt the same fold as the insulin. Interestingly, whereas we identified 10 insulin-like peptides, only one insulin-like-receptor (daf-2) has been found. We propose that these insulin-related peptides may correspond to different activators or inhibitors of the daf-2 insulin-regulating pathway. ------------------- Key: 3058 Medline: 98240915 Authors: Wolf FW;Hung M;Wightman B;Way J;Garriga G Title: vab-8 is a key regulator of posteriorly directed migrations in C. elegans and encodes a novel protein with kinesin motor similarity. Citation: Neuron 20: 655-666 1998 Type: ARTICLE Genes: mec-3 pat-3 unc-5 unc-6 vab-8 Abstract: Nervous system assembly requires the directed migrations of cells and axon growth cones along the dorsoventral and anteroposterior axes. Although guidance mechanisms for dorsoventral migrations are conserved from nematodes to mammals, mechanisms for anteroposterior migrations are unknown. In C. elegans, the gene vab-8, which specifically functions in posteriorly directed migrations, encodes two isoforms of a novel intracellular protein that act cell-autonomously in different migrations. VAB-8L, which contains a domain similar to kinesin-like motors, functions in all vab-8-dependent axon growth cone migrations. VAB-8S, which lacks this N-terminal domain, functions in a subset of vab-8-dependent cell migrations. Continuous expression of VAB-8L in the ALM mechanosensory neuron, which normally requires vab-8 early in its development for posteriorly directed cell migration, redirects its anteriorly projecting axon posteriorly. We propose that regulation of vab-8 activity is a mechanism for controlling the direction of cell and axon growth cone migrations. ------------------- Key: 3059 Medline: 98240923 Authors: Goodman MB;Hall DH;Avery L;Lockery SR Title: Active currents regulate sensitivity and dynamic range in C. elegans neurons. Citation: Neuron 20: 763-772 1998 Type: ARTICLE Genes: Abstract: Little is known about the physiology of neurons in Caenorhabditis elegans. Using new techniques for in situ patch-clamp recording in C. elegans, we analyzed the electrical properties of an identified sensory neuron (ASER) across four developmental stages and 42 unidentified neurons at one stage. We find that ASER is nearly isopotential and fails to generate classical Na+ action potentials. Rather, ASER displays a high sensitivity to input currents coupled to a depolarization-dependent reduction in sensitivity that may endow ASER with a wide dynamic range. Voltage clamp revealed depolarization-activated K+ and Ca2+ currents that contribute to high sensitivity near the zero-current potential. The depolarization-dependent reduction in sensitivity can be attributed to activation of K+ current at voltages where it dominates the net membrane current. The voltage dependence of membrane current was similar in all neurons examined, suggesting that C. elegans neurons ------------------- Key: 3060 Medline: 98204779 Authors: Iino Y;Yamamoto M Title: Expression pattern of the C. elegans p21-activated protein kinase, CePAK. Citation: Biochemical and Biophysical Research Communications 245: 177-184 1998 Type: ARTICLE Genes: Abstract: The C. elegans p21-activated protein kinase (CePAK) has a high amino-acid sequence similarity to mammalian PAKs. Tissue specificity of the expression of CePAK was examined using lacZ and GFP reporters. This analysis indicated that CePAK is expressed mainly in pharyngeal muscles, the CAN neurons, and motor neurons in the ventral nerve cord, as well as several cells in the tail region and the distal tip cells. The CePAK::GFP fusion protein was preferentially localized to the cell surface in pharyngeal muscles. ------------------- Key: 3061 Medline: 98136475 Authors: Bowerman B Title: Maternal control of pattern formation in early Caenorhabditis elegans embryos. Citation: Current Topics in Developmental Biology 39: 73-117 1998 Type: REVIEW Genes: aph-2 apx-1 glp-1 let-99 mes-1 mex-1 mex-3 mom-1 mom-2 mom-3 mom-4 mom-5 pal-1 par-1 par-2 par-3 par-4 par-5 par-6 pie-1 pop-1 pos-1 skn-1 Abstract: Genetic screens for recessive, maternal-effect, embryonic-lethal mutations have identified about 25 genes that control early steps of pattern formation in the nematode Caenorhabditis elegans. These maternal genes are discussed as belonging to one of three groups. The par group genes establish and maintain polarity in the one-cell zygote in response to sperm entry, defining an anterior/posterior body axis at least in part through interactions with the cyto-skeleton mediated by cortically localized proteins. Blastomere identity group genes act down-stream of the par group to specify the identities of individual embryonic cells, or blastomeres, using both cell autonomous and non-cell autonomous mechanisms. Requirements for the blastomere identity genes are consistent with previous studies suggesting that early asymmetric cleavages in the C. elegans embryo generate six "founder" cells that account for much of the C. elegans body plan. Intermediate group genes, most recently identified, may link the establishment of polarity in the zygote by par group genes to the localization of blastomere identity group gene functions. This review summarizes the known requirements for the members of each group, although it seems clear that additional regulatory genes controlling pattern formation in the early embryo have yet to be identified. An emerging challenge is to link the function of the genes in these three groups into interacting pathways that can account for the specification of the six founder cell identities in the early embryo, five of which produce somatic cell types and one of which produces the germline. ------------------- Key: 3062 Medline: 98293310 Authors: Zeke T;Gergely P;Dombradi V Title: The catalytic subunits of Ser/Thr protein phosphatases from Caenorhabditis elegans. Citation: Comparative Biochemistry & Physiology B-Biochemistry & Molecular Biology 119: 317-324 1998 Type: ARTICLE Genes: Abstract: The catalytic activities of protein phosphatase 1, 2A, 2B, and 2C were detected in crude extracts of Caenorhabditis elegans with different phosphoprotein substrates and specific inhibitors or activators. The enzymological properties of protein phosphatase 2B as well as those of the catalytic subunits of protein phosphatase 1 and protein phosphatase 2A were determined after partial purification. Gene fragments encoding the catalytic subunits of the protein phosphatase 1-2A-2B superfamily were amplified by polymerase chain reaction and were identified by DNA sequencing. Besides the homologs of protein phosphatase 1, 2B, and X, five protein phosphatase 1-type sequences and four novel protein phosphatase sequences were found. Our data, together with the results of the C. elegans genome project, suggest that this nematode contains an extensive family of Ser/Thr specific protein phosphatases including several up to now biochemically uncharacterized members. ------------------- Key: 3063 Medline: 98250061 Authors: Dwyer ND;Troemel ER;Sengupta P;Bargmann CI Title: Odorant receptor localization to olfactory cilia is mediated by ODR-4, a novel membrane-associated protein. Citation: Cell 93: 455-466 1998 Type: ARTICLE Genes: che-3 odr-3 odr-4 odr-8 odr-10 srd-1 srg-2 tax-2 nDf16 Abstract: Seven transmembrane domain receptors can be localized to different parts of the plasma membrane or to different intracellular compartments in a receptor-specific and cell type-specific fashion. We show here that the C. elegans genes odr-4 and odr-8 are required for localization of a subset of seven transmembrane domain odorant receptors to the cilia of olfactory neurons. Other cilia-signaling proteins, including ion channels, a G alpha protein, and even other receptor types, are localized via an odr-4/odr-8-independent pathway. odr-4 encodes a novel membrane protein that is expressed exclusively on intracellular membranes of chemosensory neurons, where it acts cell-autonomously to facilitate odorant receptor folding or localization. ------------------- Key: 3064 Medline: 98146383 Authors: Antebi A;Culotti JG;Hedgecock EM Title: daf-12 regulates developmental age and the dauer alternative in Caenorhabditis elegans. Citation: Development 125: 1191-1205 1998 Type: ARTICLE Genes: daf-12 lin-4 lin-14 lin-28 lin-29 mig-7 mig-8 stDf1 uDf1 Abstract: From egg through adult, C. elegans has six life stages including an option for dauer formation and diapause at larval stage L3 in adverse environments. Somatic cells throughout the organism make consistent choices and advance in unison, suggesting a mechanism of coordinate regulation at these stage transitions. Earlier studies showed that daf-12, which encodes a nuclear receptor (W. Yeh, 1991, Doctoral Thesis. University of Missouri-Columbia), regulates dauer formation; epistasis experiments placed daf-12 near the end of the dauer signaling pathway. Here we describe novel daf-12 alleles that reveal a general role in advancing L3 stage programs. In these mutants, somatic cells repeat L2-specific cellular programs of division and migration at the L3 stage; epistasis experiments place daf-12 between lin-14 and lin-28 Within the heterochronic pathway. We propose daf-12 and other heterochronic genes provide cellular memories of chronological stage for selecting stage-appropriate developmental programs. Endocrine factors could coordinate these stage transitions and specify developmental alternatives. ------------------- Key: 3065 Medline: 98146397 Authors: Rose LS;Kemphues K Title: The let-99 gene is required for proper spindle orientation during cleavage of the C. elegans embryo. Citation: Development 125: 1337-1346 1998 Type: ARTICLE Genes: gpb-1 let-99 par-1 par-2 par-3 eDf19 sDf2 sDf21 sDf22 sDf62 Abstract: The orientation of cell division is a critical aspect of development, In 2-cell C, elegans embryos, the spindle in the posterior cell is aligned along the long axis of the embryo and contributes to the unequal partitioning of cytoplasm, while the spindle in the anterior cell is oriented transverse to the long axis. Differing spindle alignments arise from blastomere-specific rotations of the nuclear-centrosome complex at prophase. We have found that mutations in the maternally expressed gene let-99 affect spindle orientation in all cells during the first three cleavages. During these divisions, the nuclear-centrosome complex appears unstable in position. In addition, in almost half of the mutant embryos, there are reversals of the normal pattern of spindle orientations at second cleavage: the spindle of the anterior cell is aligned with the long ax-is of the embryo and nuclear rotation fails in the posterior cell causing the spindle to form transverse to the long axis. In most of the remaining embryos, spindles in both cells are transverse at second cleavage. The distributions of several asymmetrically localized proteins, including P granules and PAR-3, are normal in early let-99 embryos, but are perturbed by the abnormal cell division orientations at second cleavage. The accumulation of actin and actin capping protein, which marks the site involved in nuclear rotation in 2-cell wild-type embryos, is abnormal but is not reversed in let-99 mutant embryos. Based on these data, we conclude that let-99(+) is required for the proper orientation of spindles after the establishment of polarity, and we postulate that let-99(+) plays a role in interactions between the astral microtubules and the cortical ------------------- Key: 3066 Medline: Authors: Tabuse Y;Sano T;Nishiwaki K;Miwa J Title: Molecular analysis of the tpa-1 gene and its role in the development and behavior of Caenorhabditis elegans. Citation: NEC Research & Development 39: 118-126 1998 Type: ARTICLE Genes: tpa-1 Abstract: Protein kinase C (PKC) is now known to be a key enzyme in intracellular signaling pathways which mediate various physiological functions in diverse eukaryotic organisms from yeast to humans. The tpa-1 gene was identified as a target of tumor-promoting phorbol esters; which cause developmental and behavioral defects in the nematode Caenorhabditis elegans (C. elegans). Molecular cloning of the tpa-l gene revealed that it encodes two PKC isoforms, TPA-1A and TPA-1B. Further molecular genetic analysis showed that the tpa-l gene product is necessary for C. elegans to be sensitive to phorbol esters. This report reviews the identification and molecular analyses of the tpa-l gene of C. elegans. ------------------- Key: 3067 Medline: 98226769 Authors: Haun C;Alexander J;Stainier DY;Okkema PG Title: Rescue of Caenorhabditis elegans pharyngeal development by a vertebrate heart specification gene. Citation: Proceedings of the National Academy of Sciences USA 95: 5072-5075 1998 Type: ARTICLE Genes: ceh-22 myo-3 Abstract: Development of pharyngeal muscle in nematodes and cardiac muscle in vertebrates and insects involves the related homeobox genes ceh-22, nkx2.5, and tinman, respectively. To determine whether the nematode and vertebrate genes perform similar functions, we examined activity of the zebrafish nkx2.5 gene in transgenic Caenorhabditis elegans. Here, we report that ectopic expression of nkx2.5 in C. elegans body wall muscle can directly activate expression of both the endogenous myo-2 gene, a ceh-22 target normally expressed only in pharyngeal muscle, and a synthetic reporter construct controlled by a multimerized CEH-22 binding site. nkx2.5 also efficiently rescues a ceh-22 mutant when expressed in pharyngeal muscle. Together, these results indicate that nkx2.5 and ceh-22 provide a single conserved molecular function. Further, they suggest that an evolutionarily conserved mechanism underlies heart development in vertebrates and insects and pharyngeal development in nematodes. ------------------- Key: 3068 Medline: 98252808 Authors: Kalb JM;Lau KK;Goszczynski B;Fukushige T;Moons D;Okkema P;McGhee JD Title: pha-4 is Ce-fkh-1, a for head/HNF-3a,B,y homolog that functions in organogenesis of the C. elegans pharynx. Citation: Development 125: 2171-2180 1998 Type: ARTICLE Genes: ceh-22 elt-1 elt-2 fkh-1 ges-1 glp-1 mex-1 myo-2 pha-1 pha-4 pie-1 pop-1 skn-1 Abstract: The C. elegans Ce-fkh-1 gene has been cloned on the basis of its sequence similarity to the winged-helix DNA binding domain of the Drosophila fork head and mammalian HNF3 alpha,beta,gamma genes, and mutations in the zygotically active pha-1 gene have been shown to block formation of the pharynx (and rectum) at an early stage in embryogenesis. In the present paper, we show that Ce-fkh-1 and pha-4 are the same gene. We show that PHA-4 protein is present in nuclei of essentially all pharyngeal cells, of all five cell types. PHA-4 protein first appears close to the point at which a cell lineage will produce only pharyngeal cells, independently of cell type. We show that PHA-4 binds directly to a 'pan-pharyngeal enhancer element' previously identified in the promoter of the pharyngeal myosin myo-2 gene; in transgenic embryos, ectopic PHA-4 activates ectopic myo-2 expression. We also show that ectopic PHA-4 can activate ectopic expression of the ceh-22 gene, a pharyngeal-specific NK-2-type homeodomain protein previously shown to bind a muscle-specific enhancer near the PHA-4 binding site in the myo-2 promoter. We propose that it is the combination of pha-4 and regulatory molecules such as ceh-22 that produces the specific gene expression patterns during pharynx development. Overall, pha-4 can be described as an 'organ identity factor', completely necessary for organ formation, present in all cells of the organ from the earliest stages, capable of integrating upstream developmental pathways (in this case, the two distinct pathways that produce the anterior and posterior pharynx) and participating directly in the transcriptional regulation of organ specific genes. Finally, we note that the distribution of PHA-4 protein in C. elegans embryos is remarkably similar to the distribution of the fork head protein in Drosophila embryos: high levels in the foregut/pharynx and hindgut/rectum; low levels in the gut proper. Moreover, we show that pha-4 expression in the C. elegans gut is regulated by elt-2, a C. elegans gut-specific GATA-factor and possible homolog of the Drosophila gene serpent, which influences fork head expression in the fly gut. Overall, our results provide evidence for a highly conserved pathway regulating formation of the digestive tract in all ------------------- Key: 3069 Medline: 98260020 Authors: Villatte F;Marcel V;Estrada-Mondaca S;Fournier D Title: Engineering sensitive acetylcholinesterase for detection of organophospate and carbamate insecticides. Citation: Biosensors & Bioelectronics 13: 157-164 1998 Type: ARTICLE Genes: Abstract: High quantities of various acetylcholinesterases can now be produced following in vitro expression and it is possible to use them as biosensors to detect organophosphates and carbamates insecticides. In order to check the potentialities of acetylcholinesterase from various sources, we have studied enzyme from bovine erythrocyte, Electrophorus electricus, Drosophila melanogaster, Torpedo californica and Caenorhabditis elegans. It appears that insect acetylcholinesterase is more susceptible to a broad range of organophosphates and carbamates insecticides than the other tested enzymes. D. melanogaster is 8-fold more sensitive than E. electricus enzyme and this sensitivity has been increased to 12-fold by introducing a mutation at position 408. ------------------- Key: 3070 Medline: 98170981 Authors: Finn JT;Krautwurst D;Schroeder JE;Chen TY;Reed RR;Yau KW Title: Functional co-assembly among subunits of cyclic-nucleotide-activated, nonselective cation channels, and across species from nematode to human. Citation: Biophysical Journal 74: 1333-1345 1998 Type: ARTICLE Genes: tax-4 Abstract: Cyclic-nucleotide-activated, nonselective cation channels have a central role in sensory transduction. They are most likely tetramers, composed of two subunits (alpha and beta or 1 and 2), with the former, but not the latter, being able to form homomeric cyclic-nucleotide-activated channels. Identified members of this channel family now include, in vertebrates, the rod and cone channels mediating visual transduction and the channel mediating olfactory transduction, each apparently with distinct alpha- and beta-subunits. Homologous channels have also been identified in Drosophila melanogaster and Caenorhabditis elegans. By co-expressing any combination of two alpha-subunits, or alpha- and beta-subunits, of this channel family in HEK 293 cells, we have found that they can all co-assemble functionally with each other, including those from fly and nematode. This finding suggests that the subunit members so far identified form a remarkably homogeneous and conserved group, functionally and evolutionarily, with no subfamilies yet identified. The ability to cross-assemble allows these subunits to potentially generate a diversity of heteromeric channels, each with properties specifically suited to a particular ------------------- Key: 3071 Medline: 98260725 Authors: Kenyon CJ;Austin J;Costa M;Cowing DW;Harris JM;Honigberg L;Hunter CP;Maloof JN;Muller-Immergluck MM;Salser SJ;Waring DA; Wang BB; Wrischnik LA Title: The dance of the Hox genes - Patterning the anteroposterior body axis of Caenorhabditis elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 62: 293-305 1998 Type: REVIEW Genes: ceh-13 egl-5 lin-1 lin-22 lin-39 mab-5 pal-1 Abstract: Hox mutations are fascinating. Like magic, they can turn antennae into legs or create extra wings. What makes these genes so talented? How can they make such high-level decisions? Are there simple rules that can explain the effects they have on the development of individual cells? Do the genes act multiple times during the development of a tissue to micromanage individual cell fate decisions, or can they act relatively early to initiate developmental programs that run independently of their further input? ------------------- Key: 3072 Medline: 98260731 Authors: Herman T;Horvitz HR Title: Mutations that perturb vulval invagination in C. elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 62: 353-360 1997 Type: ARTICLE Genes: lin-12 sqv-1 sqv-2 sqv-3 sqv-4 sqv-5 sqv-6 sqv-7 sqv-8 Abstract: During development, animals undergo dramatic changes in patterning as a result of the movement and shaping of epithelial cell layers. Sheets of epithelial cells fold, branch, spread, and detach from or fuse with one another to generate the three-dimensional topology of an embryo. One example of such a morphogenetic process is epithelial invagination, which generates tubular structures from flat epithelia. To invaginate, a flat sheet of epithelial cells bends and moves inward, its apical surface facing the concave side of the depression. During sea urchin and Drosophila gastrulation, an epithelium bends inward about a point to form the digestive tract. The result is a tube that is perpendicular to the original sheet. In contrast, vertebrate neurulation, which forms the spinal cord and brain, is initiated by the invagination of a sheet that bends along a line and results in a tube that is parallel to the original sheet.... ------------------- Key: 3073 Medline: 98241501 Authors: Wada K;Sato H;Kinoh H;Kajita M;Yamamoto H;Seiki M Title: Cloning of three Caenorhabditis elegans genes potentially encoding novel matrix metalloproteinases. Citation: Gene 211: 57-62 1998 Type: ARTICLE Genes: Abstract: Three genes potentially encoding novel matrix metalloproteinases (MMPs) were identified by sequence similarity searching of Caenorhabditis elegans genome database, and cDNAs for these MMPs were cloned. The predicted gene products (MMP-C31, -H19 and -Y19) display a similar domain organization to human MMPs. MMP-H19 and -Y19 are unique in that they have an RXKR motif between the propeptide and catalytic domains that is a furin-like cleavage site, and conserved only in stromelysin-3 and membrane-type MMPs. The amino acid sequence homology with MMP-1/human interstitial collagenase at the catalytic domain is 45%, 34% and 23% for MMP-C31, -H19 and -Y19, respectively. Recombinant proteins of C. elegans MMPs cleaved an MMP peptide substrate with efficiency proportional to their amino acid homology with human MMPs. Digestion of gelatin was observed only with MMP-C31. Enzyme activity of MMP-C31 and -H19 was inhibited by human tissue inhibitor of MMPs (TIMP)-1, TIMP-2 and synthetic MMP inhibitors, BB94 and CT543, indicating that the catalytic sites of these C. elegans MMPs are structurally closely related with those of mammalian MMPs. ------------------- Key: 3074 Medline: 98316625 Authors: Madi A;Punyiczki M;Di Rao M;Piacentini M;Fesus L Title: Biochemical characterization and localization of transglutaminase in wild-type and cell-death mutants of the nematode Caenorahbditis elegans. Citation: European Journal of Biochemistry 253: 583-590 1998 Type: ARTICLE Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-9 ced-10 nuc-1 Abstract: Transglutaminase activity was characterized in extracts of the nematode Caenorhabditis elegans using a microtiter plate method, and found to be Ca2+-dependent, optimal at pH 8.0, and to be inhibited by EGTA, ammonia, iodoacetamide and GTP. Monoclonal and polyclonal antibodies raised against human tissue transglutaminase also inhibited the activity and detected a 61-kDa protein from the worm lysate. Constitutive expression of the enzyme in the wild-type intestinal cells was revealed by immunohistochemistry. Potential protein substrates for the enzyme were found in worm lysates using a biotin-labelled amine substrate. There is a basal level of protein-bound epsilon(gamma-glutamyl)lysine cross-links, characteristic of transglutaminase activity, formed in situ in adult wild-type animals. Developmental studies have revealed that the enzyme activity is highest in adult animals, and relatively higher in L1 larvae than in other larval stages. As compared to wild types, lower transglutaminase activity has been measured in lysates of ced-3, ced-4 and ced-9 mutants. Cross-link levels were also low in ced-4 and ced-9 mutants. By contrast, the crosslink content was high in several phagocytosis mutants. The highest concentration was found in the ced-5; ced-7 double phagocytosis mutants which carry an extra number of dead cells during their lifespan. In accordance with this finding, several transglutaminase-immunopositive cells were found in both the embryos and in the head of these double phagocytosis mutants. The results suggest that a transglutaminase is involved in, or related to, the death program of cells in C. elegans and the expression and crosslinking activity of the enzyme may be perturbed in some ced mutants. ------------------- Key: 3075 Medline: 98273328 Authors: Lucchesi JC Title: Dosage compensation in flies and worms: The ups and downs of X-chromosome regulation. Citation: Current Opinion in Genetics & Development 8: 179-184 1998 Type: REVIEW Genes: dpy-26 dpy-27 dpy-30 mix-1 sdc-2 sdc-3 xol-1 Abstract: Dosage compensation ensures that individuals with a single X chromosome have the same amount of most X-linked gene products as those with two. In Drosophila, this equalization is achieved by a two-fold enhancement of the lever of transcription of the X in males (XY) relative to each X chromosome in females (XX). In Caenorhabditis, equalization of X-linked gene products between hermaphrodites (XX) and males (XO) is achieved by decreasing the activity of genes in the former. These two different solutions to the common problem of unequal dosage of X-linked genes in different sexes provide invaluable paradigms for the study of gene regulation at the level of ------------------- Key: 3076 Medline: 98297412 Authors: Daniells C;Duce I;Thomas D;Sewell P;Tattersall J;de Pomerai D Title: Transgenic nematodes as biomonitors of microwave-induced stress. Citation: Mutation Research-Fundamental & Molecular Mechanisms of Mutagenesis 399: 55-64 1998 Type: ARTICLE Genes: Abstract: Transgenic nematodes (Caenorhabditis elegans strain PC72), carrying a stress-inducible reporter gene(Escherichia coli P-galactosidase) under the control of a C. elegans hsp16 heat-shock promoter, have been used to monitor toxicant responses both in water and soil. Because these transgenic nematodes respond both to heat and toxic chemicals by synthesising an easily detectable reporter product, they afford a useful preliminary screen for stress responses (whether thermal or non-thermal) induced by microwave radiation or other electromagnetic fields. We have used a transverse electromagnetic (TEM) cell fed from one end by a source and terminated at the other end by a matched load. Most studies were conducted using a frequency of 750 MHz, at a nominal power setting of 27 dBm. The TEM cell was held in an incubator at 25 degrees C inside a shielded room; corresponding controls were shielded and placed in the same 25 degrees C incubator; additional baseline controls were held at 15 degrees C (worm growth temperature). Stress responses were measured in terms of P-galactosidase (reporter) induction above control levels. The time-course of response to continuous microwave radiation showed significant differences from 25 degrees C controls both at 2 and 16 h, but not at 4 or 8 h. Using a 5 x 5 multiwell plate array exposed for 2 h, the 25 microwaved samples showed highly significant responses compared with a similar control array. The wells most strongly affected were those in the rows closest to the source, whereas the most distant row did not rise above control levels, suggesting a shadow effect. These differential responses are difficult to reconcile with general heating effects, although localised power absorption affords a possible explanation. Experiments in which the frequency and/or power settings were varied suggested a greater response at 21 than at 27 dBm, both at 750 and 300 Mhz, although extremely variable responses were observed at 24 dBm and 750 MHz. Thus, lower power levels tended, if anything, to induce larger responses (with the above-mentioned exception), which is opposite to the trend anticipated for any simple heating effect. These results are reproducible and data acquisition is both rapid and simple. The evidence accrued to date suggests that microwave radiation causes measurable stress to transgenic nematodes, presumably reflecting increased levels of protein damage within cells (the common signal thought to trigger hsp gene induction). The response levels observed are comparable to those observed with moderate concentrations (ppm) of metal ions such as Zn2+ and Cu2+. We conclude that this approach deserves further and more detailed investigation, but that it has already demonstrated clear biological effects of microwave radiation in terms of the activation of cellular stress ------------------- Key: 3077 Medline: 98265964 Authors: Conradt B;Horvitz HR Title: The C. elegans protein EGL-1 is required for programmed cell death and interacts with the Bcl-2-like protein CED-9. Citation: Cell 93: 519-529 1998 Type: ARTICLE Genes: ced-3 ced-4 ced-9 ces-1 ces-2 egl-1 itDf2 lwDf2 nDf42 yDf8 yDf11 zuDf2 Abstract: Gain-of-function mutations in the Caenorhabditis elegans gene egl-1 cause the HSN neurons to undergo programmed cell death. By contrast, a loss-of-function egl-1 mutation prevents most if not all somatic programmed cell deaths. The egl-1 gene negatively regulates the ced-9 gene, which protects against cell death and is a member of the bcl-2 family. The EGL-1 protein contains a nine amino acid region similar to the Bcl-2 homology region 3 (BH3) domain but does not contain a BH1, BH2, or BH4 domain, suggesting that EGL-1 may be a member of a family of cell death activators that includes the mammalian proteins Bik, Bid, Harakiri, and Bad. The EGL-1 and CED-9 proteins interact physically. We propose that EGL-1 activates programmed cell death by binding to and directly inhibiting the activity of CED-9, perhaps by releasing the cell death activator CED-4 from a CED-9/CED-4-containing protein complex. ------------------- Key: 3078 Medline: 98265968 Authors: Tan PB;Lackner MR;Kim SK Title: MAP kinase signaling specificity mediated by the LIN-1 Ets/LIN-31 WH transcription factor complex during C. elegans vulval induction. Citation: Cell 93: 569-580 1998 Type: ARTICLE Genes: let-23 lin-1 lin-7 lin-31 mpk-1 Abstract: The let-23 receptor/mpk-1 MAP kinase signaling pathway induces the vulva in C. elegans. We show that MPK-1 directly regulates both the LIN-31 winged-helix and the LIN-1 Ets transcription factors to specify the vulval cell fate, lin-31 and lin-1 act genetically downstream of mpk-1, and both proteins can be directly phosphorylated by MAP kinase. LIN-31 binds to LIN-1, and the LIN-1/LIN-31 complex inhibits vulval induction. Phosphorylation of LIN-31 by MPK-1 disrupts the LIN-1/LIN-31 complex, relieving vulval inhibition. Phosphorylated LIN-31 may also act as a transcriptional activator, promoting vulval cell fates. LIN-31 is a vulval-specific effector of MPK-1, while LIN-1 acts as a general effector. The partnership of tissue-specific and general effecters may confer specificity onto commonly used signaling pathways, creating distinct tissue-specific outcomes. ------------------- Key: 3079 Medline: Authors: Morse TM;Ferree TC;Lockery SR Title: Robust spatial navigation in a robot inspired by chemotaxis in Caenorhabditis elegans. Citation: Adaptive Behavior 6: 393-410 1998 Type: ARTICLE Genes: Abstract: We report on the design and implementation of an autonomous robot that performs phototaxis under the control of a simulated neural network. The mechanical configuration of the robot and its neural network controller are patterned after those believed to produce chemotaxis in the nematode Caenorhabditis elegans. The network is first optimized to produce phototaxis in a simulated nematode-like robot and then is tested on a real robot. We find that both the simulated and real robot perform reliably, making nearly identical trajectories for similar environments and similar starting conditions. Furthermore, their performance is robust to significant perturbations of the robot's locomotion parameters. Finally, we discuss the implicit computational rule that this network uses to control phototaxis. This makes the results intuitive and improves our intuition about control of tactic behavior in two dimensions. ------------------- Key: 3080 Medline: 98269564 Authors: Baylis HA;Matsuda K;Squire MD;Fleming JT;Harvey RJ;Darlison MG;Barnard EA;Sattelle DB Title: ACR-3, A Caenorhabditis elegans nicotinic acetylcholine receptor subunit - Molecular cloning and functional expression. Citation: Receptors and Channels 5: 149-158 1997 Type: ARTICLE Genes: acr-2 acr-3 lev-1 unc-29 unc-38 Abstract: The molecular cloning and functional co-expression of a novel nicotinic acetylcholine receptor (nAChR) non-alpha subunit gene, acr-3, is described. Previously we determined the sequence and demonstrated the functional co-expression of acr-2, a nAChR non-alpha subunit gene from Caenorhabditis elegans. Analysis of the acr-2 genomic DNA revealed the existence of another potential nAChR subunit gene, acr-3, in the same orientation, only 281bp downstream of acr-2. A cDNA containing the entire acr-3 coding sequence was isolated by RT-PCR and sequenced. The predicted protein contains the conserved features typical of nAChR non-alpha subunits and most closely resembles other invertebrate nAChR non-alpha polypeptides, Unusually, the highly conserved glycine residue (equivalent to residue 240 in the Torpedo alpha subunit) upstream of transmembrane domain 2 (m(2)) is replaced by a serine residue in ACR-3. When acr-3 cDNA was injected alone into Xenopus oocytes no levamisole-gated channel activity was observed. However when co-expressed with a C. elegans alpha subunit (UNC-38), ACR-3 contributed to the formation of levamisole-gated channels. The response of this hetero-oligomer to levamisole (100 mu M) was reduced by the nAChR antagonists mecamylamine(1 mu M) and d-tubocurarine (10 mu M). ------------------- Key: 3081 Medline: 98190051 Authors: Kostrouchova M;Krause M;Kostrouch Z;Rall JE Title: CHR3: A Caenorhabditis elegans orphan nuclear hormone receptor required for proper epidermal development and molting. Citation: Development 125: 1617-1626 1998 Type: ARTICLE Genes: lin-26 nhr-23 Abstract: CHR3 is a Caenorhabditis elegans orphan nuclear hormone receptor highly homologous to Drosophila DHR3, an ecdysone-inducible gene product involved in metamorphosis, Related vertebrate factors include RORalpha/RZRalpha, RZRbeta and RevErb, Gel-shift studies show that CHR3 can bind the DRS-type hormone response sequence. CHR3 is a nuclear protein present in all blastomeres during early embryogenesis. During morphogenesis, both CHR3 protein and zygotically active reporter genes are detectable in epidermal cells and their precursors, Inhibition of the gene encoding CHR3 results in several larval defects associated with abnormal epidermal cell function, including molting and body size regulation, suggesting that CHR3 is an essential epidermal factor required for proper postembryonic development. ------------------- Key: 3082 Medline: 98252828 Authors: Kokel M;Borland CZ;DeLong L;Horvitz HR;Stern MJ Title: clr-1 encodes a receptor tyrosine phosphatase that negatively regulates an FGF receptor signaling pathway in Caenorhabditis elegans. Citation: Genes & Development 12: 1425-1437 1998 Type: ARTICLE Genes: clr-1 egl-15 maDf4 Abstract: Receptor tyrosine phosphatases have been implicated in playing important roles in cell signaling events by their ability to regulate the level of protein tyrosine phosphorylation. Although the catalytic activity of their phosphatase domains has been well established, the biological roles of these molecules are, for the most part, not well understood. Here we show that the Caenorhabditis elegans protein CLR-1 (CLeaR) is a receptor tyrosine phosphatase (RTP) with a complex extracellular region and two intracellular phosphatase domains. Mutations in clr-l result in a dramatic Clr phenotype that we have used to study the physiological requirements for the CLR-1 RTP. We show that the phosphatase activity of the membrane-proximal domain is essential for the in vivo function of CLR-1. By contrast, we present evidence that the membrane-distal domain is not required to prevent the Clr phenotype in vivo. The Clr phenotype of clr-1 mutants is mimicked by activation of the EGL-15 fibroblast growth factor receptor (FGFR) and is suppressed by mutations that reduce or eliminate the activity of egl-15. Our data strongly indicate that CLR-1 attenuates the action of an FGFR-mediated signaling pathway by dephosphorylation. ------------------- Key: 3083 Medline: 98171471 Authors: Prasad BC;Ye B;Zackhary R;Schrader K;Seydoux G;Reed RR Title: unc-3, a gene required for axonal guidance in Caenorhabditis elegans, encodes a member of the O/E family of transcription factors. Citation: Development 125: 1561-1568 1998 Type: ARTICLE Genes: srd-1 unc-3 unc-4 Abstract: The expression of specialized signal transduction components in mammalian olfactory neurons is thought to be regulated by the O/E (Olf-1/EBF) family of transcription factors, The O/E proteins are expressed in cells of the olfactory neuronal lineage throughout development and are also expressed transiently in neurons in the developing nervous system during embryogenesis. We have identified a C. elegans homologue of the mammalian O/E proteins, which displays greater than 80% similarity over 350 amino acids. Like its mammalian homologues, CeO/E is expressed in certain chemosensory neurons (ASI amphid neurons) throughout development and is also expressed transiently in developing motor neurons when these cells undergo axonal outgrowth. We demonstrate that CeO/E is the product of the unc-3 gene, mutations in which cause defects in the axonal outgrowth of motor neurons, as well as defects in dauer formation, a process requiring chemosensory inputs. These observations suggest that the O/E family of transcription factors play a central and evolutionarily conserved role in the expression of proteins essential for axonal pathfinding and/or neuronal differentiation in both sensory and motor ------------------- Key: 3084 Medline: 98248686 Authors: Robertson HM Title: Two large families of chemoreceptor genes in the nematodes Caenorhabditis elegans and C. briggsae reveal extensive gene duplication, diversification, movement, and intron Citation: Genome Research 8: 449-463 1998 Type: ARTICLE Genes: odr-10 Abstract: The str family of genes encoding seven-transmembrane C-protein-coupled or serpentine receptors related to the ODR-10 diacetyl chemoreceptor is very large, with at least 197 members in the Caenorhabditis elegans genome. The closely related stl family has 43 genes, and both families are distantly related to the srd family with 55 genes. Analysis of the structures of these genes indicates that a third of them are clearly or likely pseudogenes, Preliminary surveys of other candidate chemoreceptor Families indicates that as many as 800 genes and pseudogenes or 6% of the genome might encode 550 functional chemoreceptors constituting 4% of the C. elegans protein complement. Phylogenetic analyses of the sa and stl families, and comparisons with a few orthologs in Caenorhabditis briggsae, reveal ongoing processes of gene duplication, diversification, and movement. The reconstructed ancestral gene structures for these two families have eight introns each, four of which are homologous. Mapping of intron distributions on the phylogenetic tree reveals that each intron has been lost many times independently. Most of these introns were lost individually, which might best be explained by precise in-frame deletions involving nonhomologous recombination between short direct repeats at their termini. ------------------- Key: 3085 Medline: 98280930 Authors: Hayashizaki S;Iino Y;Yamamoto M Title: Characterization of the C. elegans gap-2 gene encoding a novel Ras-GTPase activating protein and its possible role in larval development. Citation: Genes to Cells 3: 189-202 1998 Type: ARTICLE Genes: egl-15 let-23 let-60 lin-2 lin-3 lin-7 lin-10 lin-45 gap-2 Abstract: Background: The Ras signalling pathway plays several important roles in the development of the nematode Caenorhabditis elegans. So far, two types of Ras-GTPase activating proteins (Ras-GAPs) have been identified in this organism. To aid the study of the regulation and function of the Ras pathway, we set out to isolate a new GAP gene from C. elegans by transcomplementation of the fission yeats gap1 mutant. Results: We isolated a C. elegans cDNA that encoded a protein which was similar to, but not exactly homologous with mammalian p120 Ras-GAP. This gene, named gap-2, generated at least nine distinct mRNA species through transcription from different promoters and subsequent alternative splicing involving 25 exons. These isoforms were differentially expressed among tissues. A deletion of gap-2 caused no obvious phenotype by itself, but a loss of gap-2 function could suppress larval lethality in both let-23 and let-60 reduction-of-function mutants, in which the Ras activity was lowered. Conclusions: C. elegans gap-2 encodes a novel Ras-GAP, which is similar to vertebrate p120 but which may constitute a new GAP subfamily. gap-2 mRNA isoforms arise by an unusually extensive variation in initiation sites and associated alternative splicing, and each isoform may play a distinct role in specific tissues. GAP-2 appears to function as a negative regulator of LET-60 Ras during ------------------- Key: 3086 Medline: 98269102 Authors: Lin X;Hengartner MO;Kolesnick R Title: Caenorhabditis elegans contains two distinct acid sphingomyelinases. Citation: Journal of Biological Chemistry 273: 14374-14379 1998 Type: ARTICLE Genes: asm-1 asm-2 Abstract: Mounting evidence supports a role for acid sphingomyelinase (ASM) in cellular stress signaling. Only murine and human sphingomyelinases have been defined at the molecular level. These enzymes are the products of a conserved gene and at the amino acid level share 82% identity. In this study, we show that the nematode Caenorhabditis elegans possesses two ASMs, termed ASM-1 and ASM-2 encoded by two distinct genes, but lacks detectable neutral sphingomyelinase activity. The C. elegans ASMs are about 30% identical with each other and with the human and murine enzymes. The conserved regions include a saposin-like domain, proline-rich domain, and a putative signal peptide. In addition, 16 cysteines distributed throughout the molecules, and selected glycosylation sites, are conserved. The expression of these genes in C. elegans is regulated during development Asm-l is preferentially expressed in the embryo, whereas asm-2 is predominantly expressed in postembryonic stages. When transfected as Flag-tagged proteins into COS-7 cells, ASM-P is found almost entirely in a secreted form whereas only 20% of ASM-2 is secreted. Only the secreted forms display enzymatic activity. Furthermore, ASM-S requires addition of Zn2+ to be fully active, whereas ASM-B is active in the absence of cation. C. elegans is the first organism to display two ASMs. This finding suggests the existence of an ASM gene family. ------------------- Key: 3087 Medline: 98269136 Authors: Angelo R;Rubin CS Title: Molecular characterization of an anchor protein (AKAP(CE)) that binds the RI subunit (R(CE)) of type I protein kinase A from Caenorhabditis elegans. Citation: Journal of Biological Chemistry 273: 14633-14643 1998 Type: ARTICLE Genes: kap-1 Abstract: Classical A kinase anchor proteins (AKAPs) preferentially tether type II protein kinase A (PKAII) isoforms to sites in the cytoskeleton and organelles. It is not known if distinct proteins selectively sequester regulatory (R) subunits of type I PKAs, thereby diversifying functions of these critical enzymes. In Caenorhabditis elegans, a single type I PKA mediates all aspects of cAMP signaling. We have discovered a cDNA that encodes a binding protein (AKAP(CE)) for the regulatory subunit (R-CE) of C. elegans PKAI(CE). AKAP(CE) is a novel, highly acidic RING finger protein composed of 1,280 amino acids. It binds RI-like R-CE with high affinity and neither RII alpha nor RII beta competitively inhibits formation of AKAP(CE).R-CE complexes. The R-CE-binding site was mapped to a segment of 20 amino acids in an N-terminal region of AKAP(CE). Several hydrophobic residues in the binding site align with essential Leu and Re residues in the RII-selective tethering domain of prototypic mammalian AKAPs. However, the R-CE-binding region in AKAP(CE) diverges sharply from consensus RII-binding sites by inclusion of three aromatic amino acids, exclusion of a highly conserved Leu or Ile at position 8 and replacement of C-terminal hydrophobic amino acids with basic residues. AKAP(CE). R-CE complexes accumulate in intact cells. ------------------- Key: 3088 Medline: 98290451 Authors: Rupert PB;Daughdrill GW;Bowerman B;Matthews BW Title: A new DNA-binding motif in the SKN-1 binding domain DNA complex. Citation: Nature Structural Biology 5: 484-491 1998 Type: ARTICLE Genes: skn-1 Abstract: The DNA-binding domain of Skn-1, a developmental transcription factor that specifies mesoderm in C. elegans, is shown by X-ray crystallography to have a novel fold in which a compact, monomeric, four-helix unit organizes two DNA-contact elements. At the C-terminus, a helix extends from the domain to occupy the major groove of DNA in a manner similar to bZip proteins. Skn-1, however, lacks the leucine zipper found in all bZips. Additional contacts with the DNA are made by a short basic segment at the N-terminus of the domain, reminiscent of the 'homeodomain arm'. ------------------- Key: 3089 Medline: 98284457 Authors: Hashmi S;Hashmi G;Glazer I;Gaugler R Title: Thermal response of Heterorhabditis bacteriophora transformed with the Caenorhabditis elegans hsp70 encoding gene. Citation: Journal of Experimental Zoology 281: 164-170 1998 Type: ARTICLE Genes: Abstract: A heat-shock response is induced when cells are exposed to temperatures slightly higher than their optimal physiological temperature. This response is based on the synthesis of heat-shock proteins encoded by the heat-shock genes. A correlation between the increased thermotolerance and production of 70-kDa heat-shock protein (hsp70) has been observed in many organisms. We tested this hypothesis by transferring a Caenorhabditis elegans heat-inducible hsp70 A-encoding gene into the entomopathogenic nematodes Heterorhabditis bacteriophora Hp88. Successful transformation of the gene was confirmed by Southern blot hybridization and polymerase chain reaction. Our blot studies showed that the transgenic nematodes contained five to ten copies per genome of the introduced hsp 70 A gene. hsp 70 mRNA transcripts were detected in both wildtype and transgenic nematodes. Transcripts increased severalfold in transgenic nematodes upon heat shock. Infective juveniles of both transgenic and wild-type nematodes that exposed to a sublethal heat treatment (35 degrees C) for 2 h followed by a normally lethal heat treatment (40 degrees C) for 1 h. More than 90% of transgenic nematodes survived heat treatment, compared to 2% to 3% of the wild-type strain. Our observations establish that overexpression of hsp70 A gene resulted an enhanced thermotolerance in the transgenic nematodes. The transgenic nematodes displayed normal growth and development. ------------------- Key: 3090 Medline: 98297349 Authors: Liu QA;Hengartner MO Title: Candidate adaptor protein CED-6 promotes the engulfment of apoptotic cells in C. elegans. Citation: Cell 93: 961-972 1998 Type: ARTICLE Genes: ced-1 ced-2 ced-5 ced-6 ced-7 ced-10 Abstract: The rapid engulfment (phagocytosis) of cells undergoing programmed cell death (apoptosis) is a fundamental biological process that is not well understood. Here we report the cloning and functional characterization of ced-6, a gene specifically required for the engulfment of apoptotic cells in the nematode C. elegans. The CED-6 protein contains a phosphotyrosine binding domain at its N terminus and a proline/serine-rich region in its C-terminal half. Genetic mosaic analysis demonstrates that ced-6 acts within engulfing cells. We also show that ced-6 can promote the engulfment of cells at both early and late stages of apoptosis. Our data suggest that CED-6 is an adaptor molecule acting in a signal transduction pathway that specifically mediates the recognition and engulfment of apoptotic cells. ------------------- Key: 3091 Medline: 98297348 Authors: Wu Y;Horvitz HR Title: The C. elegans cell corpse engulfment gene ced-7 encodes a protein similar to ABC transporters. Citation: Cell 93: 951-960 1998 Type: ARTICLE Genes: ced-1 ced-2 ced-5 ced-6 ced-7 ced-10 Abstract: The C. elegans gene ced-7 functions in the engulfment of cell corpses during programmed cell death. We report that the CED-7 protein has sequence similarity to ABC transporters, is broadly expressed during embryogenesis, and is localized to the plasma membrane. Mosaic analysis revealed that ced-7 functions in both dying cells and engulfing cells during the engulfment process. We propose that CED-7 functions to translocate molecules that mediate homotypic adhesion between the cell surfaces of the dying and engulfing cells. Like CED-7, the mammalian ABC transporter ABC1 has been implicated in the engulfment of cell corpses, suggesting that CED-7 and ABC1 may be functionally similar and that the molecular mechanism underlying cell corpse engulfment during programmed cell death may be conserved from nematodes to mammals. ------------------- Key: 3092 Medline: 98335467 Authors: Padgett RW;Das P;Krishna S Title: TGF-B signaling, Smads, and tumor suppressors. Citation: BioEssays 20: 382-391 1998 Type: REVIEW Genes: daf-1 daf-4 daf-7 sma-2 sma-3 sma-4 Abstract: The transforming growth factor-beta (TGF-beta) superfamily is used throughout animal development for regulating the growth and patterning of many tissue types. During the past few years, rapid progress has been made in deciphering how TGF-beta signals are transduced from outside the cell to the nucleus. This progress is based on biochemical studies in vertebrate systems and a combination of genetic studies in Drosophila and Caenorhabditis elegans. These studies have identified a novel family of signaling proteins, the Smad family. Smads can act positively and be phosphorylated by TGF-beta-like receptors or can act negatively and prevent activation of the positively acting group. The positively acting Smads translocate to the nucleus, bind DNA, and act as transcriptional activators. Thus, genetic and biochemical studies suggest a very simple signaling pathway, in which Smads are the primary downstream ------------------- Key: 3093 Medline: 98220369 Authors: Kadyk LC;Kimble J Title: Genetic regulation of entry into meiosis in Caenorhabditis elegans. Citation: Development 125: 1803-1813 1998 Type: ARTICLE Genes: gld-1 gld-2 glp-1 lag-1 let-606 hDf8 nDf25 sDf4 qDf16 Abstract: The Caenorhabditis elegans germline is composed of mitotically dividing cells at the distal end that give rise to meiotic cells more proximally. Specification of the distal region as mitotic relies on induction by the somatic distal tip tell and the glp-1 signal transduction pathway. However, the genetic control over the transition from mitosis to meiosis is not understood. In this paper, we report the identification of a gene, gld-2, that has at least two functions in germline development. First, gld-2 is required for normal progression through meiotic prophase, Second, gld-2 promotes entry into meiosis from the mitotic cell cycle. With respect to this second function, gld-2 appears to be functionally redundant with a previously described gene, gld-1 (Francis, R.,, Barton, M., K.,, Kimble, J., and Schedl, T. (1995) Genetics 139, 579-606). Germ cells in gld-1(phi) and gld-2 single mutants enter meiosis at the normal time, but germ cells in gld-2 gld-1(phi) double mutants do not enter meiosis. Instead, the double mutant germline is mitotic throughout and forms a large tumor. We suggest that gld-1 and gld-2 define two independent regulatory pathways, each of which can be sufficient for entry into meiosis. Epistasis analyses show that gld-2 and gld-2 work downstream of the glp-1 signal transduction pathway. Therefore, we hypothesize that glp-1 promotes proliferation by inhibiting the meiosis-promoting functions of gld-1 and gld-2. ------------------- Key: 3094 Medline: 98237708 Authors: McKeown C;Praitis V;Austin J Title: sma-1 encodes a B(H)-spectrin homolog required for Caenorhabditis elegans morphogenesis. Citation: Development 125: 2087-2098 1998 Type: ARTICLE Genes: Abstract: Morphogenesis transforms the C, elegans embryo from a ball of cells into a vermiform larva. During this transformation, the embryo increases fourfold in length; present data indicates this elongation results from contraction of the epidermal actin cytoskeleton, In sma-l mutants, the extent of embryonic elongation is decreased and the resulting sma-l larvae, although viable, are shorter than normal. we find that sma-lr mutants elongate for the same length of time as wild-type embryos, but at a decreased rate. The sma-l mutants we have isolated vary in phenotypic severity, with the most severe alleles showing the greatest decrease in elongation rate. The sma-1 gene encodes a homolog of beta(H)-spectrin, a novel beta-spectrin isoform first identified in Drosophila, sma-l RNA is expressed in epithelial tissues in the C. elegans embryo: in the embryonic epidermis at the start of morphogenesis and subsequently in the developing pharynx, intestine and excretory cell, In Drosophila, beta(H)-spectrin associates with the apical plasma membrane of epithelial cells; beta-spectrin is found at the lateral membrane. We propose that SMA-I is a component of an apical membrane skeletonic n the C. elegans embryonic epidermis that determines the rate of elongation during ------------------- Key: 3095 Medline: 98146044 Authors: Wagner RW;Sun L Title: Double-stranded RNA poses puzzle. Citation: Nature 391: 744-745 1998 Type: REVIEW Genes: mex-3 unc-22 Abstract: The human genome is predicted to contain between 50,000 and 100,000 genes. To work out what these genes do, an array of techniques is needed to evaluate the protein-protein interactions and biochemical pathways of any gene product. The nematode worm Caenorhabditis elegans is an excellent system for such studies because of its well-understood genetics and development, evolutionary conservation to human genes, small genome size and relatively short life cycle. The 100-megabase-pair genome will be completely sequenced this year, and a total of 17,000 genes have been predicted, many with human counterparts. Approaches used to manipulate gene expression in C. elegans include transposon-mediated deletion, antisense inhibition and direct isolation of deletions after mutagenesis. Although these methods have proved useful, limitations still exist. ------------------- Key: 3096 Medline: 98208527 Authors: Hill F;Loakes D;Brown DM Title: Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases. Citation: Proceedings of the National Academy of Sciences USA 95: 4258-4263 1998 Type: ARTICLE Genes: Abstract: A universal base that is capable of substituting for any of the four natural bases in DNA would be of great utility in both mutagenesis and recombinant DNA experiments. This paper describes the properties of oligonucleotides incorporating two degenerate bases, the pyrimidine base 6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one and the purine base N6-methoxy-2,6-diaminopurine, designated P and K, respectively. An equimolar mixture of the analogues P and K (called M) acts, in primers, as a universal base. The thermal stability of oligonucleotide duplexes were only slightly reduced when natural bases were replaced by P or K. Templates containing the modified bases were copied by Taq polymerase; P behaved as thymine in 60% of copying events and as cytosine in 40%, whereas K behaved as if it were guanine (13%) or adenine (87%). The dUTPase gene of Caenorhabditis elegans, which we found to contain three nonidentical homologous repeats, was used as a model system to test the use of these bases in primers for DNA synthesis. A pair of oligodeoxyribonucleotides, each 20 residues long and containing an equimolar mixture of P and K at six positions, primed with high specificity both T7 DNA polymerase in sequencing reactions and Taq polymerase in PCRs; no nonspecific amplification was obtained on genomic DNA of C. elegans. Use of P and K can significantly reduce the complexity of degenerate oligonucleotide mixtures, and when used together, P and K can act as a ------------------- Key: 3097 Medline: 98201627 Authors: Yoshida E;Nakajima T;Murakami K;Fukamizu A Title: Identification of N-terminal minimal transactivation domain of CBP, p300 and Caenorhabditis elegans homologues. Citation: Gene 208: 307-314 1998 Type: ARTICLE Genes: Abstract: CBP/p300 is a multidomain transcriptional cofactor that acts in junction with other factors to regulate transcription. To elucidate the domain function of CBP, we fused its dissected fragments to Gal4 DNA-binding domain and transfected the deletion mutants into several lines. First, we found that the minimal transactivation domain (MTD) at the N-terminal portion maps to between 344 and 451 aa, and shows activity in a cell-type dependent manner. Second, we cloned C. elegans homologues corresponding to the MTD by RT-PCR and identified the three related products, two of which exhibited weak transcriptional activity. Finally, by means of the yeast two hybrid screening using MTD as a bait, we cloned hypoxia-inducible factor (HIF) 1a and Stat2 cDNAs. These results suggested a functional role of MTD located at the N-terminal region of CBP/p300 in connecting to transcriptional factors. ------------------- Key: 3098 Medline: 98326318 Authors: Cassata G;Kagoshima H;Pretot RF;Aspock G;Niklaus G;Burglin TR Title: Rapid expression screening of Caenorhabditis elegans homeobox open reading frames using a two-step polymerase chain reaction promotor-gfp reporter construction Citation: Gene 212: 127-135 1998 Type: ARTICLE Genes: ceh-14 ceh-20 ceh-21 ceh-33 ceh-34 ceh-38 ceh-39 Abstract: In this paper a description is given of the expression pattern of the Caenorhabditis elegans homeobox gene ceh-38 using GFP reporter constructs, which were generated using a two-step polymerase chain reaction (PCR) procedure. This method allows fast analysis of genes of interest by looking at their expression in vivo using their putative promoter region to control the expression of a reporter gene. In this case the method was applied to screen C elegans homeobox-containing genes to identify those that are expressed in the head and nervous system. The C elegans genome project has made rapid progress, and more than 79 megabases of genomic data with several thousand open reading frames are available. This information can be used to design primers from putative promoter regions, which are amplified using long-range PCR. The long-range PCR product is then directly joined to the vector in a long-range Fill-in PCR. Since many genome projects are advancing rapidly, this approach should also be applicable for other model systems, and the method lends itself to automation, since no gel-purification steps are necessary. ceh-38 is a member of the ONECUT class of homeobox genes. Expression of ceh-38 starts during embryogenesis. In larvae and adults, expression was seen in many different types of tissues, such as the pharynx, gut, hypodermis and many nerve cells. ------------------- Key: 3099 Medline: 98270892 Authors: Matthews LR;Carter P;Thierry-Mieg D;Kemphues K Title: ZYG-9, a Caenorhabditis elegans protein required for microtubule organization and function, is a component of meiotic and mitotic spindle poles. Citation: Journal of Cell Biology 141: 1159-1168 1998 Type: ARTICLE Genes: mei-1 par-1 zyg-9 zyg-11 mnDf104 Abstract: We describe the molecular characterization of zyg-9, a maternally acting gene essential for microtubule organization and function in early Caenorhabditis elegans embryos. Defects in zyg-9 mutants suggest that the zyg-9 product functions in the organization of the meiotic spindle and the formation of long microtubules. One-cell zyg-9 embryos exhibit both meiotic and mitotic spindle defects. Meiotic spindles are disorganized, pronuclear migration fails, and the mitotic apparatus forms at the posterior, orients incorrectly, and contains unusually short microtubules. We find that zyg-9 encodes a component of the meiotic and mitotic spindle poles. In addition to the strong staining of spindle poles, we consistently detect staining in the region of the kinetochore microtubules at metaphase and early anaphase in mitotic spindles. The ZYG-9 signal at the mitotic centrosomes is not reduced by nocodazole treatment, indicating that ZYG-9 localization to the mitotic centrosomes is not dependent upon long astral microtubules, Interestingly, in embryos lacking an organized meiotic spindle, produced either by nocodazole treatment or mutations in the mei-1 gene, ZYG-9 forms a halo around the meiotic chromosomes. The protein sequence shows partial similarity to a small set of proteins that also localize to spindle poles, suggesting a ------------------- Key: 3100 Medline: Authors: de Chadarevian S Title: Of Worms and programmes - Caenorhabditis elegans and the study of development. Citation: Studies of History & Philosophy of Science 29C: 81-105 1998 Type: REVIEW Genes: Abstract: In 1963, just a year after the researchers of the Medical Research Council (MRC) Unit of Molecular Biology in Cambridge, joined by some other research groups, has moved from various scattered and makeshift buildings in the courtyard of the Physics Department to a lavishly funded four-storey laboratory, B. Lush, the Principal Medical Officer of the MRC, came to inquire about their plans for future expansion. He indicated that the MRC wished to build the laboratory up to what the principal researchers considered its 'final size' until their retirement, which meant planning ahead for at least 15 years. This surprising move was doubtless prompted by the recent award of the Nobel Prize to three members of the laboratory, Max Perutz, John Kendrew and Francis Crick, for their work on the molecular structure of proteins and nucleic acids. The triple award had propelled the new Laboratory of Molecular Biology into the limelight, and the MRC was interested in securing optimal research conditions for this prestigious group of researchers. ------------------- Key: 3101 Medline: 98278941 Authors: Saifee O;Wei L;Nonet ML Title: The Caenorhabditis elegans unc-64 locus encodes a syntaxin that interacts genetically with synaptobrevin. Citation: Molecular Biology of the Cell 9: 1235-1252 1998 Type: ARTICLE Genes: aex-3 snb-1 unc-64 eDf2 Abstract: We describe the molecular cloning and characterization of the unc-64 locus of Caenorhabditis elegans, unc-64 expresses three transcripts, each encoding a molecule with 63-64% identity to human syntaxin 1A, a membrane-anchored protein involved in synaptic vesicle fusion. Interestingly, the alternative forms of syntaxin differ only in their C-terminal hydrophobic membrane anchors. The forms are differentially expressed in neuronal and secretory tissues; genetic evidence suggests that these forms are not functionally equivalent. A complete loss-of-function mutation in unc-64 results in a worm that completes embryogenesis, but arrests development shortly thereafter as a paralyzed L1 larva, presumably as a consequence of neuronal dysfunction. The severity of the neuronal phenotypes of C. elegans syntaxin mutants appears comparable to those of Drosophila syntaxin mutants. However, nematode syntaxin appears not to be required for embryonic development, for secretion of cuticle from the hypodermis, or for the function of muscle, in contrast to Drosophila syntaxin, which appears to be required in all cells. Less severe viable unc-64 mutants exhibit a variety of behavioral defects and show strong resistance to the acetylcholinesterase inhibitor aldicarb. Extracellular physiological recordings from pharyngeal muscle of hypomorphic mutants show alterations in the kinetics of transmitter release. The lesions in the hypomorphic alleles map to the hydrophobic face of the H3 coiled-coil domain of syntaxin, a domain that in vitro mediates physical interactions with similar coiled-coil domains in SNAP-25 and synaptobrevin. Furthermore, the unc-64 syntaxin mutants exhibit allele-specific genetic interactions with mutants carrying lesions in the coiled-coil domain of synaptobrevin, providing in vivo evidence for the significance of these domains in regulating synaptic ------------------- Key: 3102 Medline: 98307385 Authors: Seshagiri S;Chang W;Miller LK Title: Mutational analysis of Caenorhabditis elegans CED-4. Citation: FEBS Letters 428: 71-74 1998 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: Much of our knowledge concerning the genetics that regulate cell death has come from the studies of cell death during the development of the nematode Caenorhabditis elegans. Of the 14 genes identified as components of nematode cell death pathways, two genes, ced-3 and ced-4, are required to promote cell death and a third, ced-9, blocks cell death. Recent studies show CED-4 to be an activator of CED-3 and CED-9 to be an inhibitor of CED-4. Two published sequence alignments suggest that CED-4 contains a death effector domain (DED), a protein sequence motif present in other death signaling proteins like Fadd and Flice; one study suggests a DED sequence similarity near the N-terminus while the other found sequence similarity near the C-terminus of CED-4. Using mutational analysis we have tested the functional significance of the conserved residues found within the putative DEDs of CED-4. Mutations in two conserved residues within the putative N-terminal DED of CED-4 affected its function, while mutations in the conserved residues within the putative C-terminal DED had no effect on CED-4 function. Our results do not support the presence of a DED in the C-terminus of CED-4 and suggest a potential role for the N-terminus in CED-4 function, possibly as a DED or as a CARD (caspase recruitment domain). We also found that CED-9 associated with all the CED-4 mutants and inhibited the activity of all the active-CED-4 mutants. ------------------- Key: 3103 Medline: 98294913 Authors: Brockhaus M;Grunberg J;Rohrig S;Loetscher H;Wittenburg N;Baumeister R;Jacobsen H;Haass C Title: Caspase-mediated cleavage is not required for the activity of presenilins in amyloidogenesis and NOTCH signaling. Citation: NeuroReport 9: 1481-1486 1998 Type: ARTICLE Genes: sel-12 Abstract: The Alzheimer's disease (AD) associated presenilin (PS) proteins are proteolytically processed. One of the processing pathways involves cleavage by caspases. Pharmocological inhibition of caspases is currently being discussed as a treatment for a variety of neurodegenerative diseases, including AD. We therefore inhibited caspase mediated processing of PS-1 and PS-2 in cells transfected with wt and mutant PS by mutagenizing the substrate recognition site or by using specific peptide aldehydes known to block caspases. We found that the inhibition of caspase mediated processing of PS proteins does not decrease its amyloidogenic activity. PS cDNA constructs with mutations in the caspase cleavage site are biologically active in Caenorhabditis elegans such as the wt human PS proteins, demonstrating that caspase-mediated cleavage is not required for the physiological PS function in NOTCH signaling. ------------------- Key: 3104 Medline: 98283905 Authors: Cryns V;Yuan J Title: Proteases to die for. Citation: Genes & Development 12: 1551-1570 1998 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: Apoptosis or programmed cell death (PCD) is a genetically regulated, cellular suicide mechanism that plays a crucial role in development and in the defense of homeostasis. Cells respond to a variety of disparate signals by committing suicide through a series of dramatic but remarkably uniform events. Morphologically, cells undergoing apoptosis demonstrate nuclear/cytoplasmic condensation and membrane protrusions. These initial changes are followed by fragmentation of the nuclear contents and subsequent encapsulation of these fragments into "apoptotic bodies" that are quickly and unobtrusively consumed by adjacent cells, thereby leaving little trace of the apoptotic cell's prior existence. Biochemically, apoptotic cells are characterized by reduction in the mitochondrial transmembrane potential, intracellular acidification, production of reactive oxygen species, externalization of phosphatidylserine residues in membrane bilayers, selective proteolysis of a subset of cellular proteins, and degradation of DNA into internucleosomal fragments. These characteristic manifestations of apoptosis reflect the activation of an intrinsic cell death apparatus that has been exquisitely conserved during evolution. At the core of this death apparatus is a novel family of proteases related to the Caenorhabditis elegans cell death gene product CED-3, the so-called caspases (cysteine proteases with aspartate-specificity), that are universal effectors of apoptotic cell death. Although several features of these pro-apoptotic proteases have been summarized previously, the present review will focus on recent insights into (1) the regulation of caspases (both positively and negatively) by other components of the cell death apparatus; and (2) the mechanisms by which caspase activation leads to the demise of the cell. ------------------- Key: 3105 Medline: 98294656 Authors: Mohler WA;White JG Title: Steroe-4-D reconstruction and animation from living fluorescent specimens. Citation: Biotechniques 24: 1006- 1998 Type: ARTICLE Genes: Abstract: We present a novel approach to the viewing and analysis of 4-dimensional (4-D) data sets recorded from live fluorescent samples. With stereo-4-D reconstructions, the observer manipulates a rotatable projection of the full 3-dimensional (3-D) specimen while simultaneously controlling animation of the recording forward or backward in time. The result is a unique lifelike perspective on the development of an entire living subject. Here, we apply this technique to the observation of the cell membranes of developing Caenorhabditis elegans. Embryos labeled with the vital plasma membrane probe FM(TM) 4-64 were imaged by multiphoton laser scanning fluorescence microscopy, yielding 4-D data sets of entire embryos over several hours of development. Stereo 4-D and standard focal-plane 4-D viewing of these novel time-lapse recordings provide the observer with detail at both the subcellular and whole-animal level from a single data set and produce a unique record of the lineage, cell shape changes, cell contacts and morphogenetic dynamics that make up embryogenesis. The procedures by which stereo-4-D reconstructions are created and viewed rely on public domain software running on a personal computer and should therefore be accessible by a general audience. Data output utilizes the versatile and well-supported QuickTime(TM) animation format. Additional features allow for stereo-4-D reconstruction of isolated 3-D volumes of interest from ------------------- Key: 3106 Medline: Authors: Jang YJ;Park H;Lee J;Koo HS Title: Developmental regulation of Caenorhabditis elegans DNA topoisomerase I expression. Citation: Journal of Biochemistry and Molecular Biology 31: 249-253 1998 Type: ARTICLE Genes: Abstract: The developmental regulation of Caenorhabditis elegans DNA topoisomerase I expression was examined using synchronized Caenorhabditis elegans cultures. Variations of the relative mRNA and protein levels of the enzyme during their development were measured by Northern and Western analyses, respectively. The mRNA level was the highest at the embryonic stage, decreasing rapidly to the one tenth level at the L1 stage, and then increasing by a few fold at the L4 and young adult stages. The protein level was the highest at the L1 stage, with gradual decreasing at the following stages until it showed a slight increase at the young adult stage. Based on our results of the expressional regulation, the possible roles of DNA topoisomerase I in the development of C. elegans are discussed. ------------------- Key: 3107 Medline: Authors: Young IM;Griffiths BS;Robertson WM;McNicol JW Title: Nematode (Caenorhabditis elegans) movement in sand as affected by particle size, moisture and the presence of bacteria (Escherichia coli). Citation: European Journal of Soil Science 49: 237-241 1998 Type: ARTICLE Genes: Abstract: The movement of bacterial-feeding nematodes (Caenorhabditis elegans) through sand was investigated using a range of sand sizes, equilibrated at a range of matric potentials, in the presence or absence of an attractant source (Escherichia coli) at the distal end of a column. In the presence of E. coli there was significantly greater movement of the nematode population towards the E. coli population, and the extent of the movement depended on the matric potential of the sand. Over time, an increasing proportion of the C. elegans population responded to the presence of the E. coli. The processes controlling these effects are discussed with respect to taxis and kinesis mechanisms of the nematode population, and with regard to the diffusive characteristics of the physical structure of ------------------- Key: 3108 Medline: Authors: Venette RC;Ferris H Title: Influence of bacterial type and density of population growth of bacterial-feeding nematodes. Citation: Soil Biology & Biochemistry 30: 949-960 1998 Type: ARTICLE Genes: Abstract: The contribution of bacterial-feeding nematodes to litter decomposition and nutrient mineralization depends, in part, on the abundance of particular nematode species Population dynamics will be constrained by edaphic factors, food availability and food quality. We report the population growth rates for six nematode species as affected by different bacterial isolates and by changes in food supply. Populations of Caenorhabditis elegans grew faster than any other nematode-bacterium combination when Bacillus polymyxa was supplied as food (lambda = 12.26 d(-1)). Caenorhabditis elegans also exhibited the greatest variation in population growth rate across the set of bacteria investigated. Acrobeloides bolenheimeri, A. buetschlii, Bursilla labiata, C. elegans, Cephalobus persegnis, and Rhabditis cucumeris did not develop or reproduce when fed Streptomyces halstedii scabies. Within the range of food concentrations considered, the six nematode species approached their respective maximal population growth rate between 10(4) and 10(5) colony forming-units (CFUs) per nematode. Populations stopped growing when food concentrations declined to 10(3)-10(4) CFUs per nematode. Between 10(3) and 10(6) CFUs per nematode, variation in population growth rate due to changes in food supply was greatest for C. elegans and was least for A. buetschlii. ------------------- Key: 3109 Medline: 98284030 Authors: Selfors LM;Schutzman JL;Borland CZ;Stern MJ Title: soc-2 encodes a leucine-rich repeat protein implicated in fibroblast growth factor receptor signaling. Citation: Proceedings of the National Academy of Sciences USA 95: 6903-6908 1998 Type: ARTICLE Genes: clr-1 egl-15 sem-5 soc-1 soc-2 mDf4 Abstract: Activation of fibroblast growth factor (FGF) receptors elicits diverse cellular responses including growth, mitogenesis, migration, and differentiation. The intracellular signaling pathways that mediate these important processes are not well understood. In Caenorhabditis elegans, suppressors of clr-1 identify genes, termed soc genes, that potentially mediate or activate signaling through the EGL-15 FGF receptor. We demonstrate that three soc genes, soc-1, soc-2, and sem-5, suppress the activity of an activated form of the EGL-15 FGF receptor, consistent with the soc genes functioning downstream of EGL-15. We show that soc-2 encodes a protein composed almost entirely of leucine-rich repeats, a domain implicated in protein-protein interactions. We identified a putative human homolog, SHOC-2, which is 54% identical to SOC-2. We find that shoc-2 maps to 10q25, shoc-2 mRNA is expressed in all tissues assayed, and SHOC-2 protein is cytoplasmically localized. Within the leucine-rich repeats of both SOC-2 and SHOC-2 are two YXNX motifs that are potential tyrosine-phosphorylated docking sites for the SEM-5/GRB2 Src homology 2 domain. However, phosphorylation of these residues is not required for SOC-2 function in vivo, and SHOC-2 is not observed to be tyrosine phosphorylated in response to FGF stimulation. We conclude that this genetic system has allowed for the identification of a conserved gene implicated in mediating FGF receptor signaling in C. elegans. ------------------- Key: 3110 Medline: 98284066 Authors: Li X;Greenwald I Title: Additional evidence for an eight-transmembrane-domain topology for Caenorhabditis elegans and human presenilins. Citation: Proceedings of the National Academy of Sciences USA 95: 7109-7114 1998 Type: ARTICLE Genes: lin-12 sel-12 Abstract: Presenilins have been implicated in the genesis of Alzheimer's disease and in facilitating LIN-12/Notch activity during development. All presenilins have multiple hydrophobic regions that could theoretically span a membrane, and a description of the membrane topology is a crucial step toward deducing the mechanism of presenilin function. Previously we proposed an eight-transmembrane-domain model for presenilin, based on studies of the Caenorhabditis elegans SEL-12 presenilin. Here, we describe experiments that support the view that two of the hydrophobic regions of SEL-12 function as the seventh and eighth transmembrane domains. Furthermore, we have shown that human presenilin 1 behaves like SEL-12 presenilin when analyzed by our methods. Our results provide additional experimental support for the eight-transmembrane-domain model of presenilin topology. ------------------- Key: 3111 Medline: 98321612 Authors: Muckenthaler M;Gunkel N;Frishman D;Cyrklaff A;Tomancak P;Hentze MW Title: Iron-regulatory protein-1 (IRP-1) is highly conserved in two invertebrate species - Characterization of IRP-1 homologues in Drosophila melanogaster and Caenorhabditis Citation: European Journal of Biochemistry 254: 230-237 1998 Type: ARTICLE Genes: irp-1 Abstract: Iron-regulatory protein-1 (IRP-1) plays a dual role as a regulatory RNA-binding protein and as a cytoplasmic aconitase. When bound to iron-responsive elements ORE), IRP-1 post-transcriptionally regulates the expression of mRNAs involved in iron metabolism. IRP have been cloned from several vertebrate species. Using a degenerate-primer PCR strategy and the screening of data bases, we now identify the homologues of IRP-1 in two invertebrate species, Drosophila melanogaster and Caenorhabditis elegans. Comparative sequence analysis shows that these invertebrate IRP are closely related to vertebrate IRP, and that the amino acid residues that have been implicated in aconitase function are particularly highly conserved, suggesting that invertebrate IRP may function as cytoplasmic aconitases. Antibodies raised against recombinant human IRP-1 immunoprecipitate the Drosophila homologue expressed from the cloned cDNA. In contrast to vertebrates, two IRP-1 homologues (Drosophila IRP-1A and Drosophila IRP-1B), displaying 86% identity to each other, are expressed in D. melanogaster: Both of these homologues are distinct from vertebrate IRP-2. In contrast to vhe mammalian system where the two IRP (IRP-1 and IRP-2) are differentially expressed, Drosophila IRP-1A and Drosophila IRP-1B are not preferentially expressed in specific organs. The localization of Drosophila IRP-1A to position 94C1-8 and of Drosophila IRP-1B to position 86B3-6 on the right arm of chromosome 3 and the availability of an IRP-1 cDNA from C. elegans will facilitate a genetic analysis of the IRE/IRP system, thus opening a new avenue to explore this regulatory network. ------------------- Key: 3112 Medline: 98278919 Authors: Schouten GJ;Van Luenen HGAM;Verra NCV;Valerio D;Plasterk Title: Transposon Tc1 of the nematode Caenorhabditis elegans jumps in human cells. Citation: Nucleic Acids Research 26: 3013-3017 1998 Type: ARTICLE Genes: Abstract: The transposon Tc1 of the nematode Caenorhabditis elegans is a member of the widespread family of Tc1/mariner transposons, The distribution pattern of virtually identical transposons among insect species that diverged 200 million years ago suggested horizontal transfer of the elements between species. This hypothesis gained experimental support when it was shown that Tc1 and later also mariner transposons could be made to jump in vitro, with their transposase as the only protein required. Later it was shown that mariner transposons from one fruit fly species can jump in other fruit fly species and in a protozoan and, recently, that a Tc1-like transposon from the nematode jumps in fish cells and that a fish Tc1-like transposon jumps in human cells. Here we show that the Tc1 element from the nematode jumps in human cells. This provides further support for the horizontal spread hypothesis. Furthermore, it suggests that Tc1 can be used as vehicle for DNA integration in human gene therapy. ------------------- Key: 3113 Medline: 98312416 Authors: Smith HE;Ward S Title: Identification of protein-protein interactions of the major sperm protein (MSP) of Caenorhabditis elegans. Citation: Journal of Molecular Biology 279: 605-619 1998 Type: ARTICLE Genes: msp-3 msp-10 msp-33 msp-38 msp-49 msp-55 msp-63 msp-77 msp-142 msp-152 Abstract: In nematodes, sperm are amoeboid cells that crawl via an extended pseudopod. Unlike those in other crawling cells, this pseudopod contains little or no actin; instead, it utilizes the major sperm protein (MSP). In vivo and in vitvo studies of Ascaris suum MSP have demonstrated that motility occurs via the regulated assembly and disassembly of MSP filaments. Filaments composed of MSP dimers are thought to provide the motive force. We have employed the yeast two-hybrid system to investigate MSP-MSP interactions and provide insights into the process of MSP filament formation. Fusions of the Caenorhabditis elegans msp-142 gene to both the lexA DNA binding domain (LEXA-MSP) and a transcriptional activation domain (AD-MSP) interact to drive expression of a lacZ reporter construct. A library of AD-MSP mutants was generated via mutagenic PCR and screened for clones that fail to interact with LEXA-MSP. Single missense mutations were identified and mapped to the crystal structure of A. suum MSP. Two classes of mutations predicted from the structure were recovered: changes in residues critical for the overall fold of the protein, and changes in residues in the dimerization interface. Multiple additional mutations were obtained in the two carboxy-terminal beta strands, a region not predicted to be involved in protein folding or dimer formation. Size fractionation of bacterially expressed MSPs indicates that mutations in this region do not abolish dimer formation. A number of compensating mutations that restore the interaction also map to this region. The data suggest that the carboxy-terminal beta strands are directly involved in ------------------- Key: 3114 Medline: 98288271 Authors: Champigny G;Voilley N;Waldmann R;Lazdunski M Title: Mutations causing neurodegeneration in Caenorhabditis elegans drastically alter the pH sensitivity and inactivation of the mammalian H+-gated Na+ channel MDEG1. Citation: Journal of Biological Chemistry 273: 15418-15422 1998 Type: ARTICLE Genes: deg-1 mec-4 Abstract: The mammalian degenerin MDEG1 belongs to the nematode degenerin/epithelial Na+ channel superfamily. It is constitutively activated by the same mutations that cause gain-of-function of the Caenorhabditis elegans degenerins and neurodegeneration. ASIC and DRASIC, which were recently cloned, are structural homologues of MDEG1 and behave as H+-gated cation channels, MDEG1 is also a H+-activated Na+ channel, but it differs from ASIC in its lower pH sensitivity and slower kinetics, In addition to the generation of a constitutive current, mutations in MDEG1 also alter the properties of the H+-gated current. Replacement of Gly-430 in MDEG1 by bulkier amino acids, such as Val, Phe, or Thr, drastically increases the H+ sensitivity of the channel (half-maximal pH (pH(m)) similar to 4.4 for MDEG1, pH(m) similar to 6.7 for the different mutants). Furthermore, these replacements completely suppress the inactivation observed with the wild-type channel and increase the sensitivity of the H+-gated channel to blockade by amiloride by a factor of 10 without modification of its conductance and ionic selectivity. These results as well as those obtained with other mutants clearly indicate that the region surrounding Gly-430, situated just before the second transmembrane segment, is essential for pH sensitivity and gating. ------------------- Key: 3115 Medline: 98310262 Authors: Lithgow GJ Title: Aging mechanisms from nematodes to mammals. Citation: Nutrition 14: 522-524 1998 Type: ARTICLE Genes: age-1 clk-1 daf-2 daf-28 Abstract: A recent flurry of activity has signaled the maturing of molecular gerontology. During the 1970s and 1980s, while many complex biological processes were being described and explained at the molecular level, the science of aging seemed to lag somewhat behind. Although the complexityof aging processes remains daunting to the experimentalist, research on aging is on the increase and the molecular processes which determine organismal lifespan are emerging. ------------------- Key: 3116 Medline: 98264854 Authors: Fei Y;Fujita T;Lapp DF;Ganapathy V;Leibach FH Title: Two oligopeptide transporters from Caenorhabditis elegans: Molecular cloning and functional expression. Citation: Biochemical Journal 332: 565-572 1998 Type: ARTICLE Genes: Abstract: Two novel oligopeptide transporter cDNA clones, CPTA and CPTB, were identified by screening a Caenorhabditis elegans cDNA library using homology hybridization. The transporter proteins deduced from the cDNAs possess multiple transmembrane domains and reveal a moderate similarity to their mammalian counterparts in amino acid sequences. CPTA and CPTB, when expressed in Xenopus laevis oocytes and studied by both radiotracer flux and microelectrode voltage-clamp protocol, displayed a saturable electrogenic transport activity driven by a proton gradient with an overlapping broad spectrum of substrate specificity. Both transporters recognize di-, tri- and tetra-peptides including phenylalanylmethionylarginylphenylalaninamide (FMRFamide) and N-acetylaspartylglutamate, members of a large neuropeptide family commonly found throughout the animal kingdom. Kinetic analysis, however, revealed that CPTA and CPTB differed in their affinity for the peptide substrates, the former being a high-affinity type and the latter a low-affinity type. CPTA and CPTB are encoded by two distinct genes localized on separate chromosomes and are expressed during the whole life span of the organism. ------------------- Key: 3117 Medline: 98319455 Authors: Aleshin VV;Kedrova OS;Milyutina IA;Vladychenskaya NS;Petrov NB Title: Secondary structure of some elements of 18S rRNA suggests that strongylid and a part of rhabditid nematodes are monophyletic. Citation: FEBS Letters 429: 4-8 1998 Type: ARTICLE Genes: Abstract: Analysis of the secondary structure of 18S rRNA molecules in nematodes revealed some new traits in the secondary structure peculiar to their hairpin 17, Some of them are characteristic of all the nematodes, whereas others are characteristic exclusively of the order Rhabditida. The loss of a nucleotide pair in the highly conservative region of hairpin 17 distinguishes 18S rRNA of tire Strongylida and some species of the Rhabditida from other nematodes and, moreover, from all other organisms. Hence, it is possible to regard the Strongylida and a part of the Rhabditida including Caenorhabditis elegans as a nem monophyletic taxon. ------------------- Key: 3118 Medline: Authors: Lee DG;Shin JY;Ahnn J Title: A screen for genetic loci on the X chromosome required for body-wall muscle development during embryogenesis in Caenorhabditis elegans. Citation: Korean Journal of Biological Sciences 1: 355-361 1997 Type: ARTICLE Genes: meDf6 mnDf5 mnDf7 mnDf10 mnDf13 mnDf42 nDf19 stDf5 szT1 Abstract: We have screened available chromosomal deficiencies on the X chromosome for genetic loci whose zygotic expression is required for body-wall muscle development during embryogenesis in Caenorhabditis elegans. Previously, it had been reported that no sign of muscle development was detected in nullo-X embryos arrested at an early stage of embryogenesis. Based on this observation, it has been suggested that genetic loci exist on the X chromosome whose zygotic expression is essential for body-wall muscle formation. In order to identify such myogenic loci, 9 chromosomal deficiencies covering approximately 45% of the X chromosome have been tested. Homozygous embryos from these deficiency strains were collected and terminal phenotypes of arrested embryos were observed by Nomarski microscopy. As a secondary assay, monoclonal antibodies against two myosin heavy chain (MHC) isoforms, the products of the myo-3 and unc-54 genes, were used to detect body-wall muscle differentiation. All the homozygous deficiency embryos were positively stained with both MHC antibodies and muscle twitching movement was observed in most cases. Combined with previously analyzed deficiencies, our deficiency screen has covered approximately 70% of the X chromosome. We conclude that the regions covered by the available deficiencies on the X chromosome do not include any myogenic locus required for body-wall muscle formation. Alternatively, the possibility that nullo-X embryo may not form body-wall muscle due to a general failure to differentiate during embryogenesis remains to be tested. ------------------- Key: 3119 Medline: 98315098 Authors: Abrahante JE;Miller EA;Rougvie AE Title: Identification of heterochronic mutants in Caenorhabditis elegans: Temporal misexpression of a collagen::Green Fluorescent Protein fusion gene. Citation: Genetics 149: 1335-1351 1998 Type: ARTICLE Genes: col-19 lin-4 lin-14 lin-28 lin-29 lin-42 lin-58 ccDf11 yDf4 yDf8 Abstract: The heterochronic genes lin-4, lin-14, lin-28, and lin-29 specify the timing of lateral hypodermal seam cell terminal differentiation in Caenorhabditis elegans. We devised a screen to identify additional genes involved in this developmental timing mechanism based on identification of mutants that exhibit temporal misexpression from the col-19 promoter, a downstream target of the heterochronic gene pathway. We fused the col-19 promoter to the green fluorescent protein gene (gfp) and demonstrated that hypodermal expression of the fusion gene is adult-specific in wild-type animals and temporally regulated by the heterochronic gene pathway. We generated a transgenic strain in which the col-19::gfp fusion construct is not expressed because of mutation of lin-4 which prevents seam cell terminal differentiation. We have identified and characterized 26 mutations that restore col-19::gfp expression in the lin 4 mutant background. Most of the mutations also restore other aspects of the seam cell terminal differentiation program that are defective in lin-4 mutant animals. Twelve mutations are alleles of three previously identified genes known to be required for proper timing of hypodermal terminal differentiation. Among these are four new alleles of lin-42, a heterochronic gene for which a single allele had been described previously. Two mutations define a new gene, lin-58. When separated from lin-4, the lin-58 mutations cause precocious seam cell terminal differentiation and thus define a new member of the heterochronic gene pathway. ------------------- Key: 3120 Medline: 98315096 Authors: O'Connell KF;Leys CM;White JG Title: A genetic screen for temperature-sensitive cell-division mutants of Caenorhabditis elegans. Citation: Genetics 149: 1303-1321 1998 Type: ARTICLE Genes: abc-1 cyk-2 slo-1 spd-1 spd-2 spd-3 stu-9 stu-9 stu-10 stu-11 stu-12 stu-13 stu-14 stu-15 stu-16 stu-17 stu-18 stu-19 zyg-1 ctDf1 hDf10 mDf7 maDf4 mnDf68 mnDf89 nDf24 nDf25 nDf40 nDf41 nDf42 qDf7 sDf23 Abstract: A novel screen to isolate conditional cell-division mutants in Caenorhabditis elegans has been developed. The screen is based on the phenotypes associated with existing cell-division mutations: some disrupt postembryonic divisions and affect formation of the gonad and Ventral nerve cord-resulting in sterile, uncoordinated animals-while others affect embryonic divisions and result in lethality. We obtained 19 conditional mutants that displayed these phenotypes when shifted to the restrictive temperature at the appropriate developmental stage. Eighteen of these mutations have been mapped; 17 proved to be single alleles of newly identified genes, while 1 proved to be an allele of a previously identified gene. Genetic tests on the embryonic lethal phenotypes indicated that for 13 genes, embryogenesis required maternal expression, while for 6, zygotic expression could suffice. In all cases, maternal expression of wild-type activity was found to be largely sufficient for embryogenesis. Cytological analysis revealed that 10 mutants possessed embryonic cell-division defects, including failure to properly segregate DNA, failure to assemble a mitotic spindle, late cytokinesis defects, prolonged cell cycles, and improperly oriented mitotic spindles. We conclude that this approach can be used to identify mutations that affect various aspects of ------------------- Key: 3121 Medline: 98315097 Authors: Yochem J;Gu T;Han M Title: A new marker for mosaic analysis in Caenorhabditis elegans indicates a fusion between hpy6 and hyp7, two major components of hypodermis. Citation: Genetics 149: 1323-1334 1998 Type: ARTICLE Genes: ncl-1 sur-5 unc-36 Abstract: A fusion of the sur-5 protein to the green fluorescent protein containing a nuclear localization signal is demonstrated as a marker for genetic mosaic analysis in the nematode Caenorhabditis elegans. Because of an extensive accumulation of bright fluorescence in many nuclei, normal growth plates, each containing hundreds of worms, can be rapidly screened with a dissecting microscope for rare mosaic individuals. As the marker carl also be used to detect transgenic worms, the construction of strains for mosaic analyses can be minimized. In the course of examining rare mosaic animals, an unexpected pattern of fluorescence was noticed for hyp6, a syncytial component of the hypodermis, which indicated that the marker may sen-e as a means of assessing cellular fusions during development. Immunofluorescent staining of adherens junctions confirmed a postembryonic fusion of hyp6 with hyp7, the major syncytium of the hypodermis. ------------------- Key: 3122 Medline: 98315099 Authors: Hansen D;Pilgrim D Title: Molecular evolution of a sex determination protein: FEM-2 (PP2C) in Caenorhabditis. Citation: Genetics 149: 1353-1362 1998 Type: ARTICLE Genes: fem-2 Abstract: Somatic sex determination in Caenorhabditis elegans involves a signal transduction pathway linking a membrane receptor to a transcription factor. The fem-2 gene is central to this pathway, producing a protein phosphatase (FEM-2) of the type 2C (PP2C). FEM-2 contains a long amino terminus that is absent in canonical PP2C enzymes. The function of this domain is difficult to predict, since it shows no sequence similarity to any other known proteins or motifs. Here we report the cloning of the fem-2 homologue from Caenorhabditis briggsae (Cb-fem-2). The sequence identity is much higher than that observed for other C. briggsae homologues of C. elegans sex determination proteins. However, this level is not uniform across the entire lengths of the proteins; it is much lower in the amino termini. Thus, the two domains of the same protein are evolving at different rates, suggesting that they have different functional constraints. Consistent with this, Cb-FEM-2 is able to replace some, but not all, of the Ce-FEM-2 in vivo function. We show that removal of the amino terminus from Ce-FEM-2 has no effect on its in vitro phosphatase activity, or its ability to replace the in vivo function of a yeast PP2C enzyme, but that it is necessary for proper FEM-2 function in worms. This demonstrates that the amino terminus is not an extended catalytic domain or a direct negative regulator of phosphatase activity. ------------------- Key: 3123 Medline: 98301430 Authors: Greenwald I Title: LIN-12/Notch signaling: lessons from worms and flies. Citation: Genes & Development 12: 1751-1762 1998 Type: REVIEW Genes: apx-1 emb-5 glp-1 hop-1 lag-1 lag-2 lin-12 sel-1 sel-10 sel-12 sup-17 Abstract: LIN-12/Notch proteins function as receptors for intercellular signals during development. Many aspects of LIN-12/Notch-mediated signaling have been elucidated through studies of cell-cell interactions that occur during Caenorhabditis elegans and Drosophila melanogaster development. The basic prinicles that operate in these lower organisms have also been shown to apply to vertebrates (for review, see Gridley 1997). Molecular features defined in lower organisms have also been shown to be conserved in vertebrates, including components of the signaling and signal transduction systems (for review, see Weinmaster 1997). The focus of this paper is on what has been learned about LIN-12/Notch proteins in development is given, using different model cell fate decisions to illustrate various features. A discussion of the mechanism of LIN-12/Notch signal transduction follows, including new in vivo evidence that favors the direct participation of the intracellular domain of LIN-12/Notch proteins in regulating target gene expression. Finally, other influences on LIN-12/Notch activity are discussed, particularly protein turnover and protein processing. ------------------- Key: 3124 Medline: 98311671 Authors: Mushegian AR;Garey JR;Martin J;Liu LX Title: Large-scale taxonomic profiling of eukaryotic model organisms - A comparison of orthologous proteins encoded by the human, fly, nematode and yeast genomes. Citation: Genome Research 8: 590-598 1998 Type: ARTICLE Genes: Abstract: Comparisons of DNA and protein sequences between humans and model organisms, including the yeast Saccharomyces cerevisiae, the nematode Caenorhabditis elegans, and the Fruit fly Drosophila melanogaster, are a significant source of information about the function of human genes and proteins in both normal and disease states. Important questions regarding cross-species sequence comparison remain unanswered, including (1) the fraction of the metabolic, signaling, and regulatory pathways that is shared by humans and the various model organisms; and (2) the validity of functional inferences based on sequence homology. We addressed these questions by analyzing the available fractions of human, fly, nematode, and yeast genomes for orthologous protein-coding genes, applying strict criteria to distinguish between candidate orthologous and paralogous proteins. Forty-two quartets of proteins could be identified as candidate orthologs. Twenty-four Drosophila protein sequences were more similar to their human orthologs than the corresponding nematode proteins. Analysis of sequence substitutions and evolutionary distances in this data set revealed that most C. elegans genes are evolving more rapidly than Drosophila genes, suggesting that unequal evolutionary rates may contribute to the differences in similarity to human protein sequences. The available fraction of Drosophila proteins appears to lack representatives of many protein families and domains, reflecting the relative paucity of genomic data From this species. ------------------- Key: 3125 Medline: 98296098 Authors: Aspbury RA;Prescott MC;Fisher MJ;Rees HH Title: Isoprenylation of polypeptides in the nematode Caenorhabditis elegans. Citation: Biochemicia et Biophysica Acta - Lipids and Lipid Metabolism 1392: 265-275 1998 Type: ARTICLE Genes: let-60 Abstract: Covalent modification of eucaryotic proteins, involving addition of isoprenyl groups, is a widespread phenomenon. Here we provide direct evidence for this form of covalent modification in the free-living nematode, Caenorhabditis elegans. Following incubation in the presence of [H-3]mevalonolactone, specific C. elegans polypeptides became labelled in both aqueous and detergent (Triton X-114)-enriched extracts. Chemical and CC-MS analysis of modifying groups, cleaved from C. elegans polypeptides, revealed that geranylgeranylation and, to a lesser extent, farnesylation of target polypeptides occurred. Immunoblot analysis provided preliminary evidence that the ras-like let-60 polypeptide was a target for isoprenylation in C. elegans. ------------------- Key: 3126 Medline: 98318242 Authors: Garcia-Anoveros J;Garcia JA;Liu JD;Corey DP Title: The nematode degenerin UNC-105 forms ion channels that are activated by degeneration- or hypercontraction-causing mutations. Citation: Neuron 20: 1231-1241 1998 Type: ARTICLE Genes: deg-1 del-1 mec-4 mec-10 unc-8 unc-105 Abstract: Nematode degenerins have been implicated in touch sensitivity and other forms of mechanosensation. Certain mutations in several degenerin genes cause the swelling, vacuolation, and death of neurons, and other mutations in the muscle degenerin gene unc-105 cause hypercontraction. Here, we confirm that unc-105 encodes an ion channel and show that it is constitutively active when mutated. These mutations disrupt different regions of the channel and have different effects on its gating. The UNC-105 channels are permeable to small monovalent cations but show voltage-dependent block by Ca2+ and Mg2+. Amiloride also produces voltage-dependent block, consistent with a single binding site 65% into the electric field. Mammalian cells expressing the mutant channels accumulate membranous whorls and multicompartment vacuoles, hallmarks of degenerin-induced cell death across species. ------------------- Key: 3127 Medline: 98348961 Authors: Biswas SN;Murata T;Ebina Y;Okada H;Miki T Title: A method for motion compensation of a moving nematode Caenorhabditis elegans and its application to frequency analysis of pharyngeal pulsation. Citation: Journal of Biotechnology 61: 175-189 1998 Type: ARTICLE Genes: Abstract: A new sequential image processing method for motion compensation of a moving object with stringy shape has been developed for estimating the pharyngeal pulsation of the nematode Caenorhabditis elegans under several environmental conditions. The method is based on the pixel data transfer on a new image frame while changing the boundary shape and the position but preserving the conformation of the inner structure of an object. All digitized image frames of C. elegans were first converted to motion-compensated images to arrange the pulsation site in the same region of the every transformed frame. The pulsation site was then automatically detected by determining the pixels where the temporal brightness variation was much larger than that of the other pixels. Finally, the pulsation frequency was determined by the Fourier analysis. The validity of our method has been confirmed by analyzing various test data, and the method has been applied for detecting the pharyngeal pulsation frequencies of C. elegans on some environmental conditions, i.e. feed bacteria-free/rich, doping of nerve inactivating ethyl-alcohol and nerve stimulant neurochemical substance of serotonin. The motion compensation method automatically provided reasonable pulsation frequencies which were found to be comparable to those obtained by manual counting. Thus the method is useful for systematic investigations on the variation of pharyngeal pulsation associated with the activity change of ------------------- Key: 3128 Medline: 98324116 Authors: Knight JK;Wood WB Title: Gastrulation initiation in Caenorhabditis elegans requires the function of a gad-1, which encodes a protein with WD repeats. Citation: Developmental Biology 198: 253-265 1998 Type: ARTICLE Genes: gad-1 nDf18 sDf26 Abstract: Gastrulation in Caenorhabditis elegans is normally initiated by inward migration of the two gut precursor (E) cells at the 26-cell stage. A strong loss-of-function, temperature-sensitive, embryonic lethal mutation in the maternally required gene gad-1 (gastrulation defective) prevents gastrulation initiation. In embryos from homozygous mutant gad-1 (ct226) hermaphrodites reared at 25 degrees C, the E cells divide early with abnormal spindle orientations and fail to migrate into the embryo, and no subsequent gastrulation movements occur. These embryos continue to develop and differentiate the major cell types, but they undergo little morphogenesis. The temperature-sensitive period of the mutant is during early embryogenesis, prior to gastrulation onset. The predicted translation product of the cloned gad-1 gene includes six P-transducin-related repeats of the WD motif, which has been implicated in protein-protein interactions. The ct226 mutation alters a conserved residue in one of these repeats. Injection of gad-1 antisense RNA into wild-type hermaphrodites mimics the mutant phenotype in progeny embryos. We conclude that the gad-1 gene product is required for initiation of gastrulation in C. elegans. ------------------- Key: 3129 Medline: 98324119 Authors: Fukushige T;Hawkins MG;McGhee JD Title: The GATA-factor elt-2 is essential for formation of the Caenorhabditis elegans intestine. Citation: Developmental Biology 198: 286-302 1998 Type: ARTICLE Genes: elt-1 elt-2 elt-3 end-1 ges-1 mex-1 nob-1 pie-1 pop-1 skn-1 itDf2 eDp6 yDp12 Abstract: The Caenorhabditis elegans elt-2 gene encodes a single-finger GATA factor, previously cloned by virtue of its binding to a tandem pair of GATA sites that control the gut-specific ges-l esterase gene. In the present paper, we show that elt-2 expression is completely gut specific, beginning when the embryonic gut has only two cells (one cell cycle prior to ges-l expression) and continuing in every cell of the gut throughout the life of the worm. When elt-2 is expressed ectopically using a transgenic heat-shock construct, the endogenous ges-l gene is now expressed in most if not all cells of the embryo; several other gut markers (including a transgenic elt-2-promoter::lacZ reporter construct designed to test for elt-2 autoregulation) are also expressed ectopically in the same experiment. These effects are specific in that two other C. elegans GATA factors (elt-1 and elt-3) do not cause ectopic gut gene expression. An imprecise transposon excision was identified that removes the entire elt-2 coding region. Homozygous elt-2 null mutants die at the L1 larval stage with an apparent malformation or degeneration of gut cells. Although the loss of elt-2 function has major consequences for later gut morphogenesis and function, mutant embryos still express ges-1. We suggest that elt-2 is part of a redundant network of genes that controls embryonic gut development; other factors may be able to compensate for elt-2 loss in the earlier stages of gut development but not in later stages. We discuss whether elements of this regulatory network may be conserved in all ------------------- Key: 3130 Medline: 98315482 Authors: Jungblut B;Sommer RJ Title: The Pristionchus pacificus mab-5 gene is involved in the regulation of ventral epidermal cell fates. Citation: Current Biology 8: 775-778 1998 Type: ARTICLE Genes: mab-5 Abstract: One system that can be used to study the evolution of gene function is the nematode vulva. In Caenorhabditis elegans, the vulva is formed from three of the six multipotent precursors P(3-8).p [1]. Comparison of vulval development between C. elegans and Pristionchus pacificus has revealed that, during evolution, there have been changes in the specification of cell fate for certain vulval cells [2]. For example, the cell P8.p is a vulval precursor cell (VPC) in C. elegans, but is incompetent to adopt vulval fate in P. pacificus. We have used a genetic approach to study the evolution of cell fate specification and have isolated P. pacificus mutants with a second vulva-like structure in the posterior region resulting from the ectopic differentiation of P8,p. Genetic and molecular analysis indicated that point mutations in the Hox cluster gene mab-5 of P. pacificus cause this multivulval phenotype. Further cell ablation studies revealed that the differentiation of P8.p is independent of gonadal signaling. In C. elegans, mab-5 also acts in P8,p specification, but mab-5 mutant animals do not develop an ectopic vulva. Thus, the effect of a mab-5 mutation differs between species, indicating that alterations in the intrinsic properties of P8,p and corresponding changes in the functional specificity of mab-5 have occurred during evolution. ------------------- Key: 3131 Medline: 98264665 Authors: Rajan TV Title: A hypothesis for the tissue specificity of nematode parasites. Citation: Experimental Parasitology 89: 140-142 1998 Type: REVIEW Genes: daf-1 daf-4 daf-7 daf-8 Abstract: Recent work from Riddle and coworkers has shown that in the free-living soil nematode, Caenorhabditis elegans, the decision to become a developmentally arrested, dispersal form known as the dauer ("enduring") larva is controlled, at least in part, by transcription of a wild-type allele at the daf-7 locus. daf-7 mutants are "constitutive dauers." Using this model as a general paradigm for nematode development, I propose that many nematode parasites behave as though they were daf-7 mutants. This will ensure developmental arrest at the L3 stage. I further propose that these organisms obtain the daf-7 gene product required for reentry into the developmental pathway from the mammalian host and that their tissue localization is dictated by the daf-7 homologue that is uniquely recognized ------------------- Key: 3132 Medline: 98316610 Authors: Hodgkin J Title: Seven types of pleiotropy. Citation: International Journal of Developmental Biology 42: 501-505 1998 Type: REVIEW Genes: ced-9 cha-1 gpb-1 mec-3 sdc-3 unc-17 unc-86 Abstract: Pleiotropy, a situation in which a single gene influences multiple phenotypic tra its, can arise in a variety of ways. This paper discusses possible underlying mechanisms and proposes a classification of the various phenomena ------------------- Key: 3133 Medline: 98337190 Authors: Sieburth DS;Sun Q;Han M Title: SUR-8, a conserved Ras-binding protein with leucine-rich repeats, positively regulates Ras-mediated signaling in C. elegans. Citation: Cell 94: 119-130 1998 Type: ARTICLE Genes: ksr-1 let-23 let-60 lin-1 lin-3 lin-15 lin-45 mek-2 mpk-1 sur-8 mDf4 mDp1 Abstract: We describe the identification and characterization of a novel gene, sur-8, that positively regulates Ras-mediated signal transduction during C. elegans Vulval development. Reduction of sur-8 function suppresses an activated ras mutation and dramatically enhances phenotypes of mpk-1 MAP kinase and ksr-1 mutations, while increase of sur-8 dosage enhances an activated ras mutation. sur-8 appears to act downstream of or in parallel to ras but upstream of raf. sur-8 encodes a conserved protein that is composed predominantly of leucine-rich repeats. The SUR-8 protein interacts directly with Ras but not with the Ras(P34G) mutant protein, suggesting that SURd may mediate its effects through Ras binding. A structural and functional SUR-8 homolog in humans specifically binds K-Ras and N-Ras but not H-Ras in vitro. ------------------- Key: 3134 Medline: 98315073 Authors: Horner MA;Quintin S;Domeier ME;Kimble J;Labouesse M;Mango Title: pha-4, an HNF-3 homolog, specifies pharyngeal organ identity in Caenorhabditis elegans. Citation: Genes & Development 12: 1947-1952 1998 Type: ARTICLE Genes: lin-26 pha-4 Abstract: To build complex organs, embryos have evolved mechanisms that integrate the development of cells unrelated to one another by cell type or ancestry. Here we show that the pha-4 locus establishes organ identity for the Caenorhabditis elegans pharynx. In pha-4 mutants, pharyngeal cells are transformed into ectoderm. Conversely, ectopic pha-4 expression produces excess pharyngeal cells, pha-4 encodes an HNF-3 homolog selectively expressed in the nascent digestive tract, including all pharynx precursors at the time they are restricted to a pharyngeal fate. We suggest that pha-4 is a key component of a transcription-based mechanism to endow cells with pharyngeal organ identity. ------------------- Key: 3135 Medline: 98252823 Authors: Jiang LI;Sternberg PW Title: Interactions of EGF, Wnt and Hom-C genes specify the P12 neuroectoblast fate in C. elegans. Citation: Development 125: 2337-2347 1998 Type: ARTICLE Genes: egl-5 let-23 let-60 lin-3 lin-15 lin-17 lin-44 sem-5 Abstract: We investigate how temporal and spatial interactions between multiple intercellular and intracellular factors specify the fate of a single cell in Caerhorhabditis elegans. P12, which is a ventral cord neuroectoblast, divides postembryonicaIly to generate neurons and a unique epidermal cell. Three classes of proteins are involved in the specification of P12 fate: the LIN-3/LET-23 epidermal growth factor signaling pathway, a Wnt protein LIN-44 and its candidate receptor LIN-17, and a homeotic gene product EGL-5, We show that LIN-3 is an inductive signal sufficient to promote the P12 fate, and the conserved EGF signaling pathway is utilized for P12 fate specification; egl-5 is a downstream target of the lin-3/let-23 pathway in specifying P12 fate; and LIN-44 and LIN-17 act synergistically with lin-3 in the specification of the P12 fate. The Wnt pathway may function early in development to regulate the competence of the cells to respond to the LIN-3 inductive ------------------- Key: 3136 Medline: 98357242 Authors: Yoshimizu T;Omote H;Wakabayashi T;Sambongi Y;Futai M Title: Essential cys-pro-cys motif of Caenorhabditis elegans copper transport ATPase. Citation: Bioscience Biotechnology and Biochemistry 62: 1258-1260 Type: ARTICLE Genes: cua-1 Abstract: Caenorhabditis elegans putative copper ATPase (CUA-1) had been functionally expressed in a yeast Delta ccc2 mutant (copper ATPase gene disruptant). We found that CUA-1 with Cys-Pro-Cys to Cys-Pro-Ala mutation could not rescue the yeast Delta ccc2 mutant, suggesting that the carboxyl terminal cysteine residue in the conserved Cys-Pro-Cys motif is essential for copper transport. ------------------- Key: 3137 Medline: 98315075 Authors: Satyal SH;Chen D;Fox SG;Kramer JM;Morimoto RI Title: Negative regulation of the heat shock transcriptional response by HSBP1. Citation: Genes & Development 12: 1962-1974 1998 Type: ARTICLE Genes: hsb-1 Abstract: In response to stress, heat shock factor 1 (HSP1) acquires rapid DNA binding and transient transcriptional activity while undergoing conformational transition from an inert non-DNA-binding monomer to active functional trimers. Attenuation of the inducible transcriptional response occurs during heat shock or upon recovery at non-stress conditions and involves dissociation of the HSF1 trimer and loss of activity. We have used the hydrophobic repeats of the HSF1 trimerization domain in the yeast two-hybrid protein interaction assay to identify heat shock factor binding protein 1 (HSBP1), a novel, conserved, 76-amino-acid protein that contains two extended arrays of hydrophobic repeats that interact with the HSF1 heptad repeats. HSBP1 is nuclear-localized and interacts in vivo with the active trimeric state of HSF1 that appears during heat shack. During attenuation of HSF1 to the inert monomer, HSBP1 associates with Hsp70. HSBP1 negatively affects HSF1 DNA-binding activity, and overexpression of HSBP1 in mammalian cells represses the transactivation activity of HSF1. To establish a biological role for HSBP1, the homologous Caenorhabditis elegans protein was overexpressed in body wall muscle cells and was shown to block activation of the heat shock response from a heat shock promoter-reporter construct. Alteration in the level of HSBP1 expression in C. elegans has severe effects on survival of the animals after thermal and chemical stress, consistent with a role for HSBP1 as a negative regulator of the heat shock response. ------------------- Key: 3138 Medline: 98274207 Authors: Harfe BD;Branda CS;Krause M;Stern MJ;Fire A Title: MyoD and the specification of muscle and non-muscle fates during postembryonic development of the C. elegans Citation: Development 125: 2479-2488 1998 Type: ARTICLE Genes: ceh-24 egl-15 hlh-1 hlh-8 lin-12 myo-3 sup-5 Abstract: Basic-helix-loop helix factors of the myoD/myf5/myogenin/MRF4 family have been implicated in acquisition and elaboration of muscle cell fates. Here we describe both myogenic and non-myogenic roles for the Caenorhabditis elegans member of this family (CeMyoD) in postembryonic mesodermal patterning. The postembryonic mesodermal lineage in C, elegans provides a paradigm for many of the issues in mesodermal fate specification: a single mesoblast ('M') divides to generate 14 striated muscles, 16 non-striated muscles, and two non-muscle cells. To study CeMyoD function in the M lineage, we needed to circumvent an embryonic requirement for the protein. Two approaches were used: (1) isolation of mutants that decrease CeMyoD levels while retaining viability, and (2) analysis of genetic mosaics that had lost CeMyoD in the M lineage. With either manipulation, we observed a series of cell-fate transformations affecting a subset of both striated muscles and non-muscle cells. In place of these normal fates, the affected lineages produced a number of myoblast-like cells that initially failed to differentiate, instead swelling to acquire a resemblance to sex myoblast (M-lineage-derived precursors to non-striated uterine and vulval muscles). Like normal ses myoblasts, the ectopic myoblast-like cells were capable of migration and proliferation followed by differentiation of progeny cells into vulval and uterine muscle, Our results demonstrate a cell-intrinsic contribution of CeMyoD to specification of both non-muscle and muscle fates. ------------------- Key: 3139 Medline: 98350209 Authors: Colavita A;Krishna S;Zheng H;Padgett RW;Culotti JG Title: Pioneer axon guidance by UNC-129, a C. elegans TGF-B. Citation: Science 281: 706-709 1998 Type: ARTICLE Genes: unc-5 unc-6 unc-40 unc-129 Abstract: The unc-129 gene, like the unc-6 netrin gene, is required to guide pioneer motoraxons along the dorsoventral axis of Caenorhabditis elegans. unc-129 encodes a member of the transforming growth factor-beta (TGF-beta) superfamily of secreted signaling molecules and is expressed in dorsal, but not ventral, rows of body wall muscles. Ectopic expression of UNC-129 from ventral body wall muscle disrupts growth cone and cell migrations that normally occur along the dorsoventral axis. Thus, UNC-129 mediates expression of dorsoventral polarity information required for axon guidance and guided cell migrations in C. elegans. ------------------- Key: 3140 Medline: 98341277 Authors: Montgomery MK;Fire A Title: Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression. Citation: Trends in Genetics 14: 255-258 1998 Type: ARTICLE Genes: unc-22 Abstract: Many fundamental natural processes have been uncovered not by preplanned scientific enquiry, but serendipitously by engineers and scientists who observed unexpected consequences of their manipulations. Biologists routinely use engineering to manipulate the expression of specific genes and, thus, understand (or benefit from) their function. Sometimes we wish to make a particular gene silent; at other times we want the genes to 'talk' more loudly. ------------------- Key: 3141 Medline: 98342106 Authors: Marks NJ;Maule AG;Geary TG;Thompson DP;Li C;Halton DW;Shaw Title: KSAYMRFamide (PF3/AF8) is present in the free-living nematode, Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 248: 422-425 1998 Type: ARTICLE Genes: flp-1 flp-6 Abstract: To date, seven FMRFamide-related peptides (FaRPs) have been structurally characterized from C. elegans, of which one is structurally identical to the parasitic nematode peptide AF2 (KHEYLRFamide). The other six FaRPs have so far been identified in free-living forms only. in the present study an additional FaRP was isolated and structurally characterized from an ethanolic extract of C. elegans. The extract was screened using a C-terminally directed FaRP antiserum, and the FMRFamide-immunoreactive peptide purified to homogeneity using HPLC. Approximately 80 pmol of the peptide was subjected to Edman degradation and the unequivocal primary structure of the K-7-amide, KSAYMRFamide (PF3/AF8) was determined following a single gas-phase sequencing run. The molecular mass of the peptide was determined using a MALDI-TOF mass spectrometer and was found to be 919 (MH+), which is in agreement with the theoretical mass of C-terminally amidated PF3. A new flp-gene, designated flp-6, has recently been identified which encodes six copies of KSAYMRFamide (PF3/AF8). ------------------- Key: 3142 Medline: 98336261 Authors: Gu T;Orita S;Han M Title: Caenorhabditis elegans SUR-5, a novel but conserved protein, negatively regulates LRT-60 ras activity during vulval induction. Citation: Molecular and Cellular Biology 18: 4556-4564 1998 Type: ARTICLE Genes: let-23 let-60 lin-3 lin-8 lin-9 lin-10 lin-15 lin-45 mpk-1 sem-5 sur-1 sur-5 unc-119 Abstract: The let-60 ras gene acts in a signal transduction pathway to control vulval differentiation in Caenorhabditis elegans. By screening suppressors of a dominant negative let-60 ras allele, we isolated three loss-of-function mutations in the sur-5 gene which appear to act as negative regulators of let-60 ras during vulval induction. sur-5 mutations do not cause an obvious mutant phenotype of their own, and they appear to specifically suppress only one of the two groups of let-60 ras dominant negative mutations, suggesting that the gene may be involved in a specific aspect of Ras activation. Consistent with its negative function, overexpressing sur-5 from an extragenic array partially suppresses the Multivulva phenotype of an activated let-60 ras mutation and causes synergistic phenotypes,vith a lin-45 raf mutation. We have cloned sur-5 and shown that it encodes a novel pro tein. We have also identified a potential mammalian SUR-5 homolog that is about 35% identical to the worm protein. SUR-5 also has some sequence similarity to acetyl coenzyme A synthetases and is predicted to contain ATP/GTP and AMP binding sites. Our results suggest that sur-5 gene function may be ------------------- Key: 3143 Medline: 98274204 Authors: Kelly WG;Fire A Title: Chromatin silencing and the maintenance of a functional germline in Caenorhabditis elegans. Citation: Development 125: 2451-2456 1998 Type: ARTICLE Genes: mes-2 mes-3 mes-4 mes-6 let-858 Abstract: The germline of the nematode Caenorhabditis elegans exhibits a remarkable ability to specifically silence transgenic DNA. We have shown that this silencing mechanism is disrupted in animals mutant for the maternal effect sterile genes mes-2, mes-3, mes-4 and mes-6, The proteins encoded by mes-2 and mes-6 have been shown to be related to the Polycomb Group of transcriptional repressors (Holdeman, R., Nehrt, S. and Strome, S. (1998). Development 125, 2457-2467; Korf, I., Fan, F. and Strome, S. (1998), Development 125, 2469-2478). These results suggest that a genetic silencing process is essential for sustained germline function, and that this silencing is mediated, at least in part, by Polycomb Group proteins. ------------------- Key: 3144 Medline: 98274205 Authors: Holdeman R;Nehrt S;Strome S Title: MES-2, a maternal protein essential for viability of the germline in Caenorhabditis elegans, is homologous to Drosophila polycomb group protein. Citation: Development 125: 2457-2467 1998 Type: ARTICLE Genes: fem-2 fem-3 glp-4 mes-2 mes-3 mes-4 mes-6 eDf18 eDf19 Abstract: A unique and essential feature of germ cells is their immortality. In Caenorhabditis elegans, germline immortality requires the maternal contribution from four genes, mes-2, mes-3, mes-4 and mes-6. We report here that mes-2 encodes a protein similar to the Drosophila Polycomb group protein, Enhancer of zeste, and in the accompanying paper that mes-6 encodes another Polycomb group protein. The Polycomb group is responsible for maintaining proper patterns of expression of the homeotic and other genes in Drosophila. It is thought that Polycomb group proteins form heteromeric complexes and control gene expression by altering chromatin conformation of target genes. As predicted from its similarity to a Polycomb group protein, MES-2 localizes to nuclei. MES-2 is found in germline nuclei in larval and adult worms and in all nuclei in early embryos. By the end of embryogenesis, MES-2 is detected primarily in the two primordial germ cells. The correct distribution of MES-2 requires the wild-type functions of mes-3 and mes-6. We hypothesize that mes-2 encodes a maternal regulator of gene expression in the early germline; its function is essential for normal early ------------------- Key: 3145 Medline: 98274206 Authors: Korf I;Fan YA;Strome S Title: The polycomb group in Caenorhabditis elegans and maternal control of germline development. Citation: Development 125: 2469-2478 1998 Type: ARTICLE Genes: mes-2 mes-3 mes-4 mes-6 eDf18 Abstract: Four Caenorhabditis elegans genes, mes-2, mes-3, mes-4 and mes-6, are essential for normal proliferation and viability of the germline. Mutations in these genes cause a maternal-effect sterile (i.e. mes) or grandchildless phenotype. We report that the mes-6 gene is in an unusual operon, the second example of this type of operon in C, elegans, and encodes the nematode homolog of Extra sex combs, a WD-40 protein in the Polycomb group in Drosophila. mes-2 encodes another Polycomb group protein (see paper by Holdeman, R., Nehrt, S. and Strome, S. (1998), Development 125, 2457-2467). Consistent with the known role of Polycomb group proteins in regulating gene expression, MES-6 is a nuclear protein. It is enriched in the germline of larvae and adults and is present in all nuclei of early embryos. Molecular epistasis results predict that the MES proteins, like Polycomb group proteins in Drosophila, function as a complex to regulate gene expression. Database searches reveal that there are considerably fewer Polycomb group genes in C. elegans than in Drosophila or vertebrates, and our studies suggest that their primary function is in controlling gene expression in the germline and ensuring the survival and proliferation of that tissue. ------------------- Key: 3146 Medline: Authors: Adachi H;Fujiwara Y;Ishii N Title: Effects of oxygen on protein carbonyl and aging in Caenorhabditis elegans mutants with long (age-1) and short (mev-1) life spans. Citation: Journal of Gerontology Series A-Biological Sciences & Medical Sciences 53: B240-B244 1998 Type: ARTICLE Genes: age-1 mev-1 Abstract: Protein carbonyl accumulation is an indicator of oxidative damage during aging. The relationship between oxidative stress and protein carbonylation during aging was studied by using a long (age-1) and a short (mev-1) life span mutant of Caenorhabditis elegans. Protein carbonyl concentrations were similar in young adults of both mutants and wild type; however, the subsequent age-dependent accumulation was different with the genotype. The mev-1 mutant (with 50% superoxide dismutase activity) accumulated protein carbonyl at a faster rate than did wild type, whereas the age-1 mutant exhibited no obvious increase except a significant accumulation at the end of extended life span. Exposure to 70% oxygen between the ages of 4 and 11 days caused a far greater accumulation of carbonyl in mev-l than in wildtype, but not in age-1. In addition, rates of aging were enhanced by oxygen ill a concentration-dependent fashion. The age-1 mutant was more resistant to, but mev-1 was more sensitive to, such oxygen enhancements of aging than was wild type. These results provide further evidence that oxidative damage is one of the major causal factors for aging in C. elegans, and that the age-1 and mer-l genes govern resistance to oxidative ------------------- Key: 3147 Medline: 98316341 Authors: Chaudhary D;O'Rourke K;Chinnaiyan AM;Dixit VM Title: The death inhibitory molecules CED-9 and CED-4L use a common mechanism to inhibit the CED-3 death protease. Citation: Journal of Biological Chemistry 273: 17708-17712 1998 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: The apoptotic machinery of Caenorhabditis elegans includes three core interacting components: CED-3, CED-4, and CED-9, CED-3 is a death protease composed of a prodomain and a protease domain. CED-4 is a P-loop-containing, nucleotide-binding molecule that complexes with the single polypeptide zymogen form of CED-3, promoting its activation by autoprocessing, CED-9 blocks death by complexing with CED-4 and suppressing its ability to promote CED-3 activation. A naturally occurring alternatively spliced form of CED-4 that contains an insertion within the nucleotide-binding region (CED-4L) functions as a dominant negative inhibitor of CED-3 processing and attenuates cell death. Domain mapping studies revealed that distinct regions within CED-4 bind to the CED-3 prodomain and protease domain. Importantly, the CED-4 P-loop was involved in prodomain binding. Disruption of P-loop geometry because of mutation of a critical lysine (K165R) or insertional inactivation (CED-4L) abolished prodomain binding. Regardless, K165R and CED-4L still retained CED-3 binding through the protease domain but were unable to initiate CED-3 processing. Therefore, the P-loop-prodomain interaction is critical for triggering CED-4-mediated CED-3 processing. Underscoring the importance of this interaction was the finding that CED-9 contacted the P-loop and selectively inhibited its interaction with the CED-3 prodomain. These results provide a simple mechanism for how CED-9 functions to block CED-4-mediated CED-3 processing and cell death. ------------------- Key: 3148 Medline: 98364616 Authors: Blumenthal T Title: Gene clusters and polycistronic transcription in Citation: BioEssays 20: 480-487 1998 Type: REVIEW Genes: cha-1 deg-3 des-2 gpd-2 gpd-3 lin-15 unc-17 Abstract: Sometimes genes are arranged nonrandomly on the chromosomes of eukaryotes. This review considers instances of gene clusters in which two genes or more are expressed from a single promoter. This includes cases in which a polycistronic pre-mRNA is processed to make monocistronic mRNAs in nematodes, as well as isolated examples of polycistronic mRNAs found in mammals, flies, and perhaps plants. ------------------- Key: 3149 Medline: 98349315 Authors: Strauss E Title: How embryos shape up. Citation: Science 281: 166-167 1998 Type: REVIEW Genes: Abstract: About 800 biologists gathered at Stanford University from 20 to 25 June for the 57th annual meeting of the Society for Developmental Biology. Study organisms ranged from flies to mice to plants, but there was plenty of common ground, including a new pathway by which signaling molecules can shape the early embryo and a new gene that helps specify right from left. ------------------- Key: 3150 Medline: 98369627 Authors: Shima Y;Tada Y;Furuki M;Hara Y;Ohta H Title: A missense mutation of the gene for Na+, K+ -ATPase a-subunit causes abnormal feeding behavior in Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 248: 778-782 1998 Type: ARTICLE Genes: eat-6 Abstract: The Na+,K+-ATPase activity of membranes from a behavioral mutant of C. elegans was found to be about one-third that of the wild-type. The levels of mRNA and polypeptide of Na+,K+-ATPase alpha-subunit in the mutant were as high as those in the wild-type, but the level of the phosphorylated intermediate of the Na+,K+-ATPase in the mutant worm was 80% lower than that in the wild-type. A single predicted amino acid replacement (Leu to Phe) was found in a highly conserved region in the alpha-subunit that is involved in the formation of phosphorylated intermediate. The abnormal feeding behavior of the mutant worm may be attributed to this missense mutation. ------------------- Key: 3151 Medline: 98361329 Authors: Waggoner LE;Zhou GT;Schafer RW;Schafer WR Title: Control of alternative behavioral states by serotonin in Caenorhabditis elegans. Citation: Neuron 21: 203-214 1998 Type: ARTICLE Genes: bas-1 cat-4 cha-1 daf-7 egl-1 egl-3 egl-4 egl-7 egl-10 egl-11 egl-12 egl-19 egl-21 egl-24 egl-30 mab-5 tpa-1 Abstract: Serotonin has been implicated in the regulation of a wide range of brain functions involving alternative behavioral states, including the control of mood, aggression, sex, and sleep. Here, we report that in the nematode Caenorhabditis elegans, serotonin controls a switch between two distinct, on/off states of egg-laying behavior. Through quantitative analysis of the temporal pattern of egg-laying events, we determined that egg laying can be modeled as a novel random process, in which animals fluctuate between discrete behavioral states: an active state, during which eggs are laid in clusters, and an inactive state, during which eggs are retained. Single-cell ablation experiments indicate that two pairs of motor neurons, HSNL/HSNR and VC4/VC5, can induce the active phase by releasing serotonin. These neurons also release acetylcholine, which appears to trigger individual egg-laying events within the active phase. Genetic experiments suggest that determination of the behavioral states observed for C. elegans egg laying may be mediated through protein kinase C-dependent (PKC-dependent) modulation of voltage-gated calcium ------------------- Key: 3152 Medline: 98337936 Authors: Lo MC;Ha S;Pelczer I;Pal S;Walker S Title: The solution structure of the DNA-binding domain of Skn-1. Citation: Proceedings of the National Academy of Sciences USA 95: 8455-8460 1998 Type: ARTICLE Genes: skn-1 Abstract: Skn-1 is a maternally expressed transcription factor that specifies the fate of certain blastomeres early in the development of Caenorhabditis elegans. It has been reported that the DNA-binding domain is a molten globule and that the structure cannot be defined because there are no long-range nuclear Overhauser effects (NOEs). Working with short Skn domain fragments and using C-13-labeled proteins, we have been able to identify 28 long-range NOEs that establish a tertiary fold for the Skn domain. The internal region of the Skn domain consists of three stable helices and one conformationally labile helix organized into a nascent helix-turn-helix-turn-helix-turn-helix motif. The N and C termini of the Skn domain are unstructured and emerge from the same end of the folded domain. This structure is consistent with biochemical data on binding of the Skn domain to DNA, which shows that the N and C termini bind in the adjacent minor and major grooves from the same face of the DNA helix. The NMR solution structure of the Skn domain should be useful for developing a complete understanding of the DNA recognition event, including any conformational changes that take place upon binding. ------------------- Key: 3153 Medline: 98337965 Authors: Hirsch D;Stahl A;Lodish HF Title: A family of fatty acid transporters conserved from mycobacterium to man. Citation: Proceedings of the National Academy of Sciences USA 95: 8625-8629 1998 Type: ARTICLE Genes: Abstract: Long chain fatty acids (LCFAs) are an important source of energy for most organisms. They also function as blood hormones, regulating key metabolic functions such as hepatic glucose production, Although LCFAs can diffuse through the hydrophobic core of the plasma membrane into cells, this nonspecific transport cannot account for the high affinity and specific transport of LCFAs exhibited by cells such as cardiac muscle, hepatocytes, and adipocytes. Transport of LCFAs across the plasma membrane is facilitated by fatty acid transport protein (FATP), a plasma membrane protein that increases LCFA uptake when expressed in cultured mammalian cells [Schaffer, J. E. & Lodish, H. F. (1994) Cell 79, 427-436]. Here, we report the identification of four novel murine FATPs, one of which is expressed exclusively in liver and another only in liver and kidney. Both genes increase fatty acid uptake when expressed in mammalian cells. All five murine FATPs have homologues in humans in addition to a sixth FATP gene. FATPs are found in such diverse organisms as Fugu rubripes, Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae, and Mycobacterium tuberculosis. The function of the FATP gene family is conserved throughout evolution as the C. elegans and mycobacterial FATPs facilitate LCFA uptake when overexpressed in COS cells or Escherichia coli, respectively. The identification of this evolutionary conserved fatty acid trans porter family will allow us to gain a better understanding of the mechanisms whereby LCFAs traverse the lipid bilayer as well as yield insight into the control of energy homeostasis and its dysregulation in diseases such as diabetes and obesity. ------------------- Key: 3154 Medline: 98337986 Authors: Pekarsky Y;Campiglio M;Siprashvili Z;Druck T;Sedkov Y;Tillib S;Draganescu A;Wermuth P;Rothman JH;Huebner K;Buchberg AM;Mazo A;Brenner C;Croce CM Title: Nitrilase and FHIT homologs are encoded as fusion proteins in Drosophila melanogaster and Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 95: 8744-8749 1998 Type: ARTICLE Genes: Abstract: The tumor suppressor gene FHIT encompasses the common human chromosomal fragile site at 3p14.2 and numerous cancer cell biallelic deletions. To study Fhit function we cloned and characterized FHIT genes from Drosophila melanogaster and Caenorhabditis elegans. Both genes code for fusion proteins in which the Fhit domain is fused with a novel domain showing homology to bacterial and plant nitrilases; the D. melanogaster fusion protein exhibited diadenosine triphosphate (ApppA) hydrolase activity expected of an authentic Fhit homolog. In. human and mouse, the nitrilase homologs and Fhit are encoded by two different genes: FHIT and NIT1, localized on chromosomes 3 and 1 in human, and 14 and 1 in mouse, respectively. We cloned and characterized human and murine NIT1 genes and determined their exon-intron structure, patterns of expression, and alternative processing of their mRNAs. The tissue specificity of expression of murine Fhit and Nit1 genes was nearly identical. Because fusion proteins with dual or triple enzymatic activities have been found to carry out specific steps in a given biochemical or biosynthetic pathway, we postulate that Fhit and Nit1 likewise collaborate in a biochemical or cellular pathway in ------------------- Key: 3155 Medline: 98337989 Authors: Rajaram S;Sedensky MM;Morgan PG Title: unc-1: A stomatin homologue controls sensitivity to volative anesthetics in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 95: 8761-8766 1998 Type: ARTICLE Genes: unc-1 unc-79 Abstract: To identify sites of action of volatile anesthetics, we are studying genes in a functional pathway that controls sensitivity to volatile anesthetics in the nematode Caenorhabditis elegans. The unc-1 gene occupies a central position in this pathway. Different alleles of unc-1 have unique effects on sensitivity to the different volatile anesthetics. UNC-1 shows extensive homology to human stomatin, an integral membrane protein thought to regulate an associated ion channel. We postulate that UNC-1 has a direct effect on anesthetic sensitivity in C. elegans and may represent a molecular target for volatile anesthetics. ------------------- Key: 3156 Medline: 98333235 Authors: Walker GA;Walker DW;Lithgow GJ Title: Genes that determine both thermotolerance and rate of aging in Caenorhabditis elegans. Citation: Annals of the New York Academy of Sciences 851: 444-449 Type: ARTICLE Genes: age-1 daf-2 spe-26 Abstract: Caenorhabditis elegans is an excellent experimental system for the genetic dissection of complex processes such as development, cell death, and aging. This organism may now prove informative in the analysis of stress response. Single-gene mutations that confer increased tolerance to a range of acute extrinsic stresses and also increase lifespan in nonstress conditions have been identified. C. elegans is a free-living, self-fertilizing nematode that can be maintained in large, synchronous populations in the laboratory with ease on simple growth media. The hermaphroditic form will at low frequency give rise to males, which facilitates genetic crosses. An alternative larval form called the dauer ("enduring") larvae is formed from first-stage larvae (L1) during overcrowding or starvation. Some of the genes that control dauer formation during development also determine lifespan and stress tolerance in the adult. ------------------- Key: 3157 Medline: 98379992 Authors: Ishii N;Fujii M;Hartman PS;Tsuda M;Yasuda K;Senoo-Matsuda N;Yanase S;Ayusawa D;Suzuki K Title: A mutation in succinate dehydrogenase cytochrome b causes oxidative stress and ageing in nematodes. Citation: Nature 394: 694-697 1998 Type: ARTICLE Genes: ced-9 cyt-1 mev-1 Abstract: Much attention has focused on the aetiology of oxidative damage in cellular and organismal ageing(1-4). Especially toxic are the reactive oxygen byproducts of respiration and other biological processes(5). A mev-1(kn1) mutant of Caenorhabditis elegans has been found to be hypersensitive to raised oxygen concentrations(6,7). Unlike the wild type, its lifespan decreases dramatically as oxygen concentrations are increased from 1 tee 60% (ref. 7). Strains bearing this mutation accumulate markers of ageing (such as fluorescent materials and protein carbonyls) faster than the wild type(8,9). We show here that mev-1 encodes a subunit of the enzyme succinate dehydrogenase cytochrome b, which is a component of complex II of the mitochondrial electron transport chain. We found that the ability of complex II to catalyse electron transport from succinate to ubiquinone is compromised in mev-l animals. This may cause an indirect increase in superoxide levels, which in turn leads to oxygen hypersensitivity and premature ageing. Our results indicate that mev-1 governs the rate of ageing by modulating the cellular response to ------------------- Key: 3158 Medline: 98352130 Authors: Nelson LS;Kim K;Memmott JE;Li C Title: FMRFamide-related gene family in the nematode, Caenorhabditis elegans. Citation: Molecular Brain Research 58: 103-111 1998 Type: ARTICLE Genes: flp-1 flp-2 flp-3 flp-4 flp-5 flp-6 flp-7 flp-8 flp-9 flp-10 flp-11 flp-12 flp-13 flp-14 Abstract: Many organisms, including mammals, use short peptides as neurotransmitters. The family of FMRFamide (Phe-Met-Arg-Phe-NH2)-like neuropeptides, which all share an -RFamide sequence at their C-termini, has been shown to have diverse functions, including neuromodulation and stimulation or inhibition of muscle contraction. In the nematode, Caenorhabditis elegans, FMRFamide-like peptides (FaRPs) are expressed in approximately 10% of the neurons, including motor, sensory, and intemeurons that are involved in movement, feeding, defecation, and reproduction. At least 14 genes, designated flp-1 through flp-14, encode FaRPs in C. elegans. Here, we present data that all 14 flp genes are transcribed in C. elegans, and several of these genes are alternatively spliced. Each flp gene encodes a different set of FaRPs, yielding a predicted total of 44 distinct FaRPs. Using staged RNA for reverse-transcription/polymerase chain reactions (RT/PCR), we determined that most flp genes are expressed throughout development. These results suggest that a complex family of FaRPs have varied roles through all stages of development ------------------- Key: 3159 Medline: 98295134 Authors: Thomas JH;Inoue T Title: Methuselah meets diabetes. Citation: BioEssays 20: 113-115 1998 Type: REVIEW Genes: age-1 daf-2 daf-16 Abstract: Mutations in the daf-2 and age-1 genes cause constitutive dauer larva formation and double adult life span in C, elegans. Their effect on life span has excited considerable interest and their effect on dauer formation has facilitated rapid progress in their genetic and molecular analysis. Two recent papers(12,13) report that daf-2 encodes a member of the insulin-receptor family and that age-1 encodes a PI3 kinase subunit, a second-messenger producing enzyme known to act downstream of the mammalian insulin receptor. These findings provide the first mechanistic insight into the well-established link between ------------------- Key: 3160 Medline: 98356017 Authors: Jacobs D;Beitel GJ;Clark SG;Horvitz HR;Kornfeld K Title: Gain-of-function mutations in the Caenorhabditis elegans lin-1 ETS gene identify a C-terminal regulatory domain phosphorylated by ERK MAP kinase. Citation: Genetics 149: 1809-1822 1998 Type: ARTICLE Genes: let-60 lin-1 lin-15 lin-31 mek-2 mpk-1 smg-1 mDp1 Abstract: Genetic analysis of lin-1 loss-of-function mutations suggests that lin-1 controls multiple cell-fate decisions during Caernorhabditis elegans development and is negatively regulated by a conserved receptor tyrosine kinase-Ras-ERK mitogen-activated protein (MAP) kinase signal transduction pathway. LIN-1 protein contains an ETS domain and presumably regulates transcription. We identified and characterized six gain-of-function mutations that define a new class of lin-1 allele. These lin-1 alleles appeared to be constitutively active and unresponsive to negative regulation. Each allele has a single-base change that affects the predicted C terminus of LIN-1, suggesting this region is required for negative regulation. The C terminus of LIN-1 was a high-affinity substrate for Erk2 in vitro, suggesting that LIN-1 is directly regulated by ERK MAP kinase. Because mpk-1 ERK MAP kinase controls at least one cell-fate decision that does not require lin-1, our results suggest that MPK-1 contributes to the specificity of this receptor tyrosine kinase-Ras-MAP kinase signal transduction pathway by phosphorylating different proteins in different developmental contexts. These lin-1 mutations all affect a four-amino-acid motif, FQFP, that is conserved in vertebrate and Drosophila ETS proteins that are also phosphorylated by ERK MAP kinase. This sequence may be a ------------------- Key: 3161 Medline: 98324891 Authors: Macrea M;Kramer DL;Coffino P Title: Developmental effect of polyamine depletion in Caenorhabditis elegans. Citation: Biochemical Journal 333: 309-315 1998 Type: ARTICLE Genes: odc-1 Abstract: Ornithine decarboxylase (ODC) catalyses the conversion of ornithine to putrescine, an obligate precursor to the polyamines spermidine and spermine. We reported previously that homozygous odc-1 (pc13) worms have no detectable ODC activity. Despite their inability to make polyamines, these mutant worms appear normal, but with a slight reduction in total brood size, when grown in complex medium that presumably contains polyamines. We now show that when ODC-deficient worms are transferred to polyamine-free medium, they show a strong phenotype. odc-1 worms have two different fates, depending upon the developmental stage at which polyamines are removed. If the polyamines are removed at the L1 larval stage, the mutant animals develop into adult hermaphrodites that produce very few or no eggs. In contrast, if mutant larvae at the later L4 stage of development are transferred to polyamine-deficient medium, they develop and lay eggs normally. However, approx. 90% of the eggs yield embryos that, although well differentiated, arrest at early stage 3. Either maternal or zygotic expression of ODC provides partial rescue of embryonic lethality. Supplementing deficient medium with the polyamine spermidine allows ODC-deficient worms to develop as on complex medium. Together, these findings suggest that ODC activity is most critically required during oogenesis and embryogenesis and, furthermore, that exogenous polyamines can override the requirement for ODC activity. ------------------- Key: 3162 Medline: Authors: Tatara CP;Newman MC;McCloskey JT;Williams PL Title: Use of ion characteristics to predict relative toxicity of mono-, di- and trivalent metal ions: Caenorhabditis elegans LC50. Citation: Aquatic Toxicology 42: 255-269 1998 Type: ARTICLE Genes: Abstract: Predictive models for relative toxicity of divalent metal ions using ion characteristics have been produced with both Microtox(R), a 15 min microbial bioassay, and the 24 h Caenorhabditis elegans bioassay. Relative toxicity of mono-, di- and trivalent metal ions has also been successfully modeled using ion characteristics with the Microtox(R) bioassay. This study extends this approach to include longer exposure durations (24 h) and a more complex organism (metazoan). Twenty-four-hour LC50s (expressed as total and free ion concentrations) for the free-living soil nematode, C. elegans, were determined for Li: Na, Mg, K, Ca, Cr, Mn, Fe, Co, Ni, Cu, Zn, Sr, Cd, Cs, Ba, La, and Pb in an aqueous medium. Relative metal toxicity was predicted with least squares linear regression and several ion characteristics. Toxicity was most effectively predicted (r(2) = 0.85) with a two-variable model containing \log K-OH\ (where K-OH is the first hydrolysis constant) and chi(m)(2)r (the covalent index). The first hydrolysis constant reflects a metal ion's tendency to bind to intermediate ligands such as biochemical groups with O donor atoms, while X(m)(2)r reflects binding to soft ligands such as those with S donor atoms. The use of LC50s based on free ion concentrations did not significantly improve model fit. The results of this study are consistent with earlier models generated with Microtox(R) data, with the exception of barium, which was much more toxic to C. elegans than would be predicted from the model. We conclude that, with thoughtful application, ion characteristics can be used to predict the relative toxicity of metal ions that ------------------- Key: 3163 Medline: 98359830 Authors: Raich WB;Moran AN;Rothman JH;Hardin J Title: Cytokinesis and midzone microtubule organization in Caenorhabditis elegans require the kinesin-like protein ZEN-4. Citation: Molecular Biology of the Cell 9: 2037-2049 1998 Type: ARTICLE Genes: zen-4 nDf41 stDf7 Abstract: Members of the MKLP1 subfamily of kinesin motor proteins localize to the equatorial region of the spindle midzone and are capable of bundling antiparallel microtubules in vitro. Despite these intriguing characteristics, it is unclear what role these kinesins play in dividing cells, particularly within the context of a developing embryo. Here, we report the identification of a null allele of zen-4, an MKLP1 homologue in the nematode Caenorhabditis elegans, and demonstrate that ZEN-4 is essential for cytokinesis. Embryos deprived of ZEN-4 form multinucleate single-celled embryos as they continue to cycle through mitosis but fail to complete cell division. Initiation of the cytokinetic furrow occurs at the normal time and place, but furrow propagation halts prematurely. Timelapse recordings and microtubule staining reveal that the cytokinesis defect is preceded by the dissociation of the midzone microtubules. We show that ZEN-4 protein localizes to the spindle midzone during anaphase and persists at the midbody region throughout cytokinesis. We propose that ZEN-4 directly cross-links the midzone microtubules and suggest that these microtubules are required for the ------------------- Key: 3164 Medline: 98322255 Authors: Ashcroft NR;Kosinski ME;Wickramasinghe D;Donovan PJ;Golden Title: The four cdc25 genes from the nematode Caenorhabditis elegans. Citation: Gene 214: 59-66 1998 Type: ARTICLE Genes: Abstract: During eukaryotic evolution, multicellular organisms have evolved multiple members of gene families that may display unique, partially overlapping, or redundant functions during development. More than 75% of the C. elegans genome has been sequenced, which represents approximately 95% of the coding sequences. This provides a unique opportunity to identify most, if not all, of the members of a given gene family. We have searched the C. elegans genome database for members of a key family of cell cycle regulators, the CDC25 phosphatases, and have identified four genes. The four C. elegans genes represent a larger family within a single organism than has been reported so far in Drosophila, mice and humans. An amino acid comparison revealed a high degree of similarity and identity within the phosphatase domain. This analysis also identified an expanded consensus sequence that can be used to discover new members of the CDC25 phosphatase family. However, the four C. elegans sequences display a few novel amino acid substitutions in the residues surrounding the invariant catalytic motif CX5R. These data demonstrate the value of genome database searching for identifying new members of known gene families, understanding genetic diversity, and for studying gene structure. ------------------- Key: 3165 Medline: 98392177 Authors: Chen EB;Stern MJ Title: Understanding cell migration guidance: lessons from sex myoblast migration in C. elegans. Citation: Trends in Genetics 14: 322-327 1998 Type: REVIEW Genes: dig-1 egl-15 egl-17 let-60 sem-5 unc-53 unc-71 unc-73 Abstract: Studies of sex myoblast (SM) migration in the nematode Caenorhabditis elegans have shown that multiple guidance mechanisms cooperate to ensure the accurate and reproducible targeting of the SMs. Many issues arise in the analysis of SM migration, including the action of multiple guidance mechanisms, redundant sources of guidance information, the multiple uses of molecular components, and whether factors affect cell fate determination events or the guidance mechanisms themselves. These issues are common to many cell migration events and make the analysis of SM migration instructive to our general understanding of how cell migrations are controlled. ------------------- Key: 3166 Medline: 98372445 Authors: Dernburg AF;McDonald K;Moulder G;Barstead R;Dresser M;Villeneuve AM Title: Meiotic recombination in C. elegans initiates by a conserved mechanism and is dispensable for homologous chromosome synapsis. Citation: Cell 94: 387-398 1998 Type: ARTICLE Genes: spo-11 Abstract: Chromosome segregation at meiosis I depends on pairing and crossing-over between homologs. In most eukaryotes, pairing culminates with formation of the proteinaceous synaptonemal complex (SC). In budding yeast, recombination initiates through double-strand DNA breaks (DSBs) and is thought to be essential for SC formation. Here, we examine whether this mechanism for initiating meiotic recombination is conserved, and we test the dependence of homologous chromosome synapsis on recombination in C. elegans. We find that a homolog of the yeast DSB-generating enzyme, Spo11p, is required for meiotic exchange in this metazoan, and that radiation-induced breaks partially alleviate this dependence. Thus, initiation of recombination by DSBs is apparently conserved. However, homologous synapsis is independent of recombination in the nematode, since it occurs normally in a C. elegans spo-11 null mutant. ------------------- Key: 3167 Medline: 98311662 Authors: Swan KA;Severson AF;Carter JC;Martin PR;Schnabel H;Schnabel R;Bowerman B Title: cyk-1 : A C. elegans FH gene required for a late step in embryonic cytokinesis. Citation: Journal of Cell Science 111: 2017-2027 1998 Type: ARTICLE Genes: cyk-1 nmy-2 nDf16 Abstract: A maternally expressed Caenorhabditis elegans gene called cyk-1 is required for polar body extrusion during meiosis and for a late step in cytokinesis during embryonic mitosis. Other microfilament- and microtubule-dependent processes appear normal in cyk-1 mutant embryos, indicating that cyk-1 regulates a specific subset of cytoskeletal functions. Because cytokinesis initiates normally and cleavage furrows ingress extensively in cyk-1 mutant embryos, we propose that the wild-type cyk-1 gene is required for a late step in cytokinesis. Cleavage furrows regress after completion of mitosis in cyk-1 mutants, leaving multiple nuclei in a single cell. Positional cloning and sequence analysis of the cyk-1 gene reveal that it encodes an FH protein, a newly defined family of proteins that appear to interact with the cytoskeleton during cytokinesis and in the regulation of cell polarity. Consistent with cyk-1 function being required for a late step in embryonic cytokinesis, we show that the CYK-1 protein colocalizes with actin microfilaments as a ring at the leading edge of the cleavage furrow, but only after extensive furrow ingression. We discuss our findings in the context of other studies suggesting that FH genes in yeast and insects function early in cytokinesis to assemble a ------------------- Key: 3168 Medline: 98301408 Authors: Chihade JW;Hayashibara K;Shiba K;Schimmel P Title: Strong selective pressure to use G:U to mark an RNA acceptor stem for alanine. Citation: Biochemistry 37: 9193-9202 1998 Type: ARTICLE Genes: Abstract: The identity of alanine tRNAs is dependent on a G:U base pair at the 3:70 position of the acceptor helix. This system of molecular recognition is widely distributed from bacteria to human-cell cytoplasm. In contrast, some mitochondrial alanine acceptor helices are markedly different and contain nucleotides known to block aminoacylation by a nonmitochondrial enzyme. Thus, acceptor helix recognition may differ in these systems and may not depend on G:U. Here we report an example of a Caenorhabditis elegans mitochondrial system where the G:U pair is preserved but where proximal nucleotides known to block charging by a nonmitochondrial enzyme are also present. We show that, as expected, the mitochondrial substrate is not charged by the bacterial enzyme. In contrast, the cloned mitochondrial enzyme charged both mitochondrial and bacterial microhelices. Strikingly, charging of each required the G:U pair. Thus, G:U recognition persists even with an acceptor helix context that inactivates nonmitochondrial systems. The results suggest strong selective pressure to use G:U in a variety of contexts to mark an acceptor stem for alanine. Separate experiments also demonstrate that, at least for the mitochondrial enzyme, helix instability or irregularity is ------------------- Key: 3169 Medline: 98337839 Authors: den Boer BGW;Sookhareea S;Dufourcq P;Labouesse M Title: A tissue-specific knock-out stategy reveals that lin-26 is required for the formation of the somatic gonad epithelium in Caenorhabditis elegans. Citation: Development 125: 3213-3224 1998 Type: ARTICLE Genes: lin-26 Abstract: The Caenorhabditis elegans LIN-26 protein is required to specify and/or maintain the fates of all non-neuronal ectodermal cells. Here we show that lin-26 is expressed until the somatic gonad primordium stage in all cells of the somatic gonad, except in distal tip cells, and later in all uterine cells. To determine if lin-26 functions in the somatic gonad, we have generated gonad-specific lin-26 alleles obtained by integration of lin-26 promoter deletion derivatives into a lin-26 null mutant background. In this way. we rescued the lethal phenotype imparted by lin-26 null mutations and uncovered a highly penetrant sterile phenotype. Specifically, the strongest of these new alleles was characterized by the absence of lin-26 expression in the somatic gonad, the presence of endomitotic oocytes, decreased germline proliferation, a protruding vulva and a less penetrant absence of gonad arms, Lineage analysis of mutant somatic gonads and examination of several markers expressed in the spermatheca, sheath cells, distal tip cells and the uterus, suggest that LIN-26 is required in sheath, spermatheca and uterine precursors, and in uterine cells. We conclude that lin-26 performs a similar function in the non-neuronal ectoderm and the somatic gonad, a mesoderm derivative, and we speculate that lin-26 is required to express epithelial characteristics. ------------------- Key: 3170 Medline: 98399424 Authors: Newman-Smith ED;Rothman J Title: The maternal-to-zygotic transition in embryonic patterning of Caenorhabditis elegans. Citation: Current Opinion in Genetics & Development 8: 472-480 1998 Type: REVIEW Genes: ama-1 apr-1 ceh-13 ceh-22 eel-1 elt-1 elt-2 end-1 end-2 end-3 ges-1 hnl-1 lag-1 lag-2 lin-12 lin-26 pal-1 pha-1 pha-4 pop-1 pie-1 skn-1 vab-7 wrm-1 Abstract: Maternal factors,laid down in the oocyte regulate blastomere identities in the early Caenorhabditis elegans embryo by activating zygotic patterning genes and restricting their expression to the appropriate lineages. A number of early-acting zygotic genes:that specify various cell fates have been identified recently and their temporal and spatial regulation by maternal factors has begun to be ------------------- Key: 3171 Medline: Authors: Hengartner M Title: Apoptosis: Death by crowd control. Citation: Science 281: 1298-1299 1998 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: Animals use apoptosis, or programmed cell death, to eliminate extraneous or dangerous cells. The muscle of this controlled cellular deconstruction is provided by the caspase family of cysteine proteases, which cleave key targets in the cell. Caspases normally exist in cells as inactive proenzymes; proteolytic processing at a few specific sites unleashes their latent enzymatic activity and triggers cell destruction. ------------------- Key: 3172 Medline: Authors: Yang XL;Chang HY;Baltimore D Title: Essential role of CED-4 oligomerization in CED-3 activation and apoptosis. Citation: Science 281: 1355-1357 1998 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: Control of the activation of apoptosis is important both in development and in protection against cancer. In the classic genetic model Caenorhabditis elegans, the pro-apoptotic protein CED-4 activates the CED-3 caspase and is inhibited by the Bcl-2-like protein CED-9. Both processes are mediated by protein-protein interaction. Facilitating the proximity of CED-3 zymogen molecules was found to induce caspase activation and cell death. CED-4 protein oligomerized in cells and in vitro. This oligomerization induced CED-3 proximity and competed with CED-4:CED-9 interaction. Mutations that abolished CED-4 oligomerization inactivated its ability to activate CED-3. Thus, the mechanism of control is that CED-3 in CED-3:CED-4 complexes is activated by CED-4 oligomerization, which is inhibited by binding of CED-9 to CED-4. ------------------- Key: 3173 Medline: 98382502 Authors: Paradis S;Ruvkun G Title: Caenorhabditis elegans Akt/PKB transduces insulin receptor-like signals from AGE-1 PI3 kinase to the DAF-16 transcription factor. Citation: Genes & Development 12: 2488-2498 1998 Type: ARTICLE Genes: age-1 akt-1 akt-2 daf-2 daf-3 daf-16 Abstract: A neurosecretory pathway regulates a reversible developmental arrest and metabolic shift at the Caenorhabditis elegans dauer larval stage, Defects in an insulin-like signaling pathway cause arrest at the dauer stage. We show here that two C. elegans Akt/PKB homologs, akr-l and akt-2, transduce insulin receptor-like signals that inhibit dauer arrest and that AKT-1 and AKT-2 signaling are indispensable for insulin receptor-like signaling in C. elegans, A loss-of-function mutation in the Pork head transcription factor DAF-16 relieves the requirement far Akt/PKB signaling, which indicates that AKT-1 and AKT-2 function primarily to antagonize DAF-16. This is the first evidence that the major target of Akt/PKB signaling is a transcription factor. An activating mutation in akt-1, revealed by a genetic screen, as well as increased dosage of wild-type akt-1 relieves the requirement for signaling from AGE-1 PI3K, which acts downstream of the DAF-2 insulin/IGF-1 receptor homolog. This demonstrates that Akt/PKB activity is not necessarily dependent on AGE-1 PI3K activity. akt-1 and akt-2 are expressed in overlapping patterns In the nervous system and in tissues that are remodeled during dauer formation. ------------------- Key: 3174 Medline: 98382513 Authors: Harfe BD;Vaz Gomes A;Kenyon C;Liu J;Krause M;Fire A Title: Analysis of a Caenorhabditis elegans Twist homolog identifies conserved and divergent aspects of mesodermal patterning. Citation: Genes & Development 12: 2623-2635 1998 Type: ARTICLE Genes: ceh-24 egl-5 egl-15 hlh-1 hlh-2 hlh-8 lin-39 mab-5 myo-2 myo-3 Abstract: Mesodermal development is a multistep process in which cells become increasingly specialized to form specific tissue types. In Drosophila and mammals, proper segregation and patterning of the mesoderm involves the bHLH factor Twist. We investigated the activity of a Twist-related factor, CeTwist, during Caenorhabditis elegans mesoderm development. Embryonic mesoderm in C. elegans derives from a number of distinct founder cells that are specified during the early lineages! in contrast, a single blast cell (M) is responsible for all nongonadal mesoderm formation during postembryonic development. Using immunofluorescence and reporter fusions, we determined the activity pattern of the gene encoding CeTwist. No activity was observed during specification of mesodermal lineages in the early embryo; instead, the gene was active within the M lineage and in a number of mesodermal cells with nonstriated muscle fates. A role for CeTwist in postembryonic mesodermal cell fate specification was indicated by ectopic expression and genetic interference assays. These experiments showed that CeTwist was responsible for activating two target genes normally expressed in specific subsets of nonstriated muscles derived from the M lineage. In vitro and in vivo assays suggested that CeTwist cooperates with the C. elegans E/Daughterless homolog in directly activating these targets. The two target genes that we have studied, ceh-24 and eg1-15, encode an NK-2 class homeodomain and an FGF receptor (FGFR) homolog, respectively. Twist activates FGFR and NK-homeodomain target genes during mesodermal patterning of Drosophila and similar target interactions have been proposed to modulate mesenchymal growth during closure of the vertebrate skull. These results suggest the possibility that a conserved pathway may be used for diverse functions in mesodermal specification. ------------------- Key: 3175 Medline: 98370926 Authors: Tenenhaus C;Schubert C;Seydoux G Title: Genetic requirements for PIE-1 localization and inhibition of gene expression in the embryonic germ lineage of Caenorhabditis elegans. Citation: Developmental Biology 200: 212-224 1998 Type: ARTICLE Genes: apx-1 cib-1 emb-1 emb-3 emb-4 emb-5 emb-6 emb-7 emb-8 emb-11 emb-12 emb-13 emb-16 emb-18 emb-20 emb-21 emb-23 emb-25 emb-26 emb-27 emb-30 emb-31 emb-33 fem-1 fem-3 glp-4 mes-1 mes-2 mes-3 mes-6 mex-1 mex-3 par-1 par-2 par-3 par-4 par-6 pie-1 pop-1 skn-1 zyg-1 zyg-2 zyg-9 Abstract: In early Caenorhabditis elegans embryos, production of new mRNAs is inhibited in the germ lineage. This inhibition requires the germline factor PIE-1, and correlates with the absence in germline blastomeres of a phosphoepitope on RNA polymerase II (RNAPII-H5). We show that PIE-1 is uniformly distributed in oocytes and newly fertilized eggs, and becomes localized asymmetrically in the late one-cell stage. To begin to dissect the mechanisms required for PIE-1 localization and inhibition of RNAPII-H5 expression, we have examined the distribution of PIE-1 and RNAPII-H5 in maternal-effect mutants that disrupt embryonic development. We find that mutants that disrupt the asymmetric divisions of germline blastomeres mislocalize PIE-1, and activate RNAPII-H5 expression in the germ lineage. In contrast, mutants that alter somatic cell identities do not affect PIE-1 localization or RNAPII-H5 expression. Our observations suggest that PIE-1 represses mRNA transcription in each germline blastomere in a concentration-dependent manner. We also show that in wild-type, and in mutants where PIE-1 is mislocalized, the cellular and subcellular distribution of PIE-1 remarkably parallels that of the P granules, suggesting that the localizations of these two germline components are ------------------- Key: 3176 Medline: 98441866 Authors: Hodgkin J;Herman RK Title: Changing styles in C. elegans genetics. Citation: Trends in Genetics 14: 352-357 1998 Type: REVIEW Genes: Abstract: The past 30 years have taken the nematode Caenorhabditis elegans from obscurity, as a nondescript member of a large but unglamorous invertebrate phylum, to a position as one of the major model organisms. This year, it will acquire a particular celebrity as the owner of the first animal genome to be sequenced in its entirety. In this review we consider the ways in which genetical investigations of this species have begun to change and what some of the consequences of the completion of the sequence are likely ------------------- Key: 3177 Medline: 98393573 Authors: Lackner MR;Kim SK Title: Genetic analysis of the Caenorhabditis elegans MAP kinase gene mpk-1. Citation: Genetics 150: 103-117 1998 Type: ARTICLE Genes: let-60 lin-1 lin-3 lin-12 lin-15 lin-25 lin-31 lin-45 mek-2 mpk-1 sur-2 sDp3 Abstract: The Caenorhabditis elegans mpk-1 gene encodes a MAP kinase protein that plays an important role in Ras-mediated induction of vulval cell fates. We show that mutations that eliminate mpk-1 activity result in a highly penetrant, vulvaless phenotype. A double mutant containing a gain-of-function mpk-1 mutation and a gain-of-function mek mutation (MEK phosphorylates and activates MPK-1) exhibits a multivulva phenotype. These results suggest that mpk-1 may transduce most or all of the anchor cell signal. Epistasis analysis suggests that mpk-1 acts downstream of mek-2 (encodes a MEK homolog) and upstream of lin-1 (encodes an Ets transcription factor) in the anchor cell signaling pathway. Finally, mpk-1 may act together with let-60 ras in multiple developmental processes, as mpk-1 mutants exhibit nearly the same range of developmental phenotypes as let-60 ras mutants. ------------------- Key: 3178 Medline: 98393574 Authors: Dow RM;Mains PE Title: Genetic and molecular characterization of the Caenorhabditis elegans gene, mel-26, a postmeiotic negative regulator of MEI-1, a meiotic-specific spindle component. Citation: Genetics 150: 119-128 1998 Type: ARTICLE Genes: fem-1 fem-3 glp-1 mei-1 mei-2 mel-26 nDf23 Abstract: We have previously described the gene mei-1, which encodes an essential component of the Caenorhabditis elegans meiotic spindle. When ectopically expressed after the completion of meiosis, mei-1 protein disrupts the function of the mitotic cleavage spindles. In this article, we describe the cloning and the further genetic characterization of mel-26, a postmeiotic negative regulator of mei-1. mel-26 was originally identified by a gain-of-function mutation. We have reverted this mutation to a loss-of-function allele, which has recessive phenotypes identical to the dominant defects of its gain-of-function parent. Both the dominant and recessive mutations of mel-26 result in mei-1 protein ectopically localized in mitotic spindles and centrosomes, leading to small and misoriented cleavage spindles. The loss-of-function mutation was used to clone mel-26 by transformation rescue. As suggested by genetic results indicating that mel-26 is required only maternally, mel-26 mRNA was expressed predominantly in the female germline. The gene encodes a protein that includes the BTB motif, ------------------- Key: 3179 Medline: 98393575 Authors: Gems D;Sutton AJ;Sundermeyer ML;Albert PS;King KV;Edgley ML;Larsen PL;Riddle DL Title: Two pleiotropic classes of daf-2 mutation affect larval arrest, adult behavior, reproduction and longevity in Caenorhabditis elegans. Citation: Genetics 150: 129-155 1998 Type: ARTICLE Genes: age-1 daf-2 daf-12 daf-16 mDf12 Abstract: The nematode Caenorhabditis elegans responds to overcrowding and scarcity of food by arresting development as a dauer larva, a nonfeeding, long-lived, stress-resistant, alternative third-larval stage. Previous work has shown that mutations in the genes daf-2 (encoding a member of the insulin receptor family) and age-1 (encoding a PI 3-kinase) result in constitutive formation of dauer larvae (Daf-c), increased adult longevity (Age), and increased intrinsic thermotolerance (Itt). Some daf-2 mutants have additional developmental, behavioral, and reproductive defects. We have characterized in detail 15 temperature-sensitive and 1 nonconditional daf-2 allele to investigate the extent of daf-2 mutant defects and to examine whether specific mutant traits correlate with each other. The greatest longevity seen in daf-2 mutant adults was approximately three times that of wild type. The temperature-sensitive daf-2 mutants fell into two overlapping classes, including eight class 1 mutants, which are Daf-c, Age, and Itt, and exhibit low levels of L1 arrest at 25.5 degrees. Seven class 2 mutants also exhibit the class I defects as well as some or all of the following: reduced adult motility, abnormal adult body and gonad morphology, high levels of embryonic and L1 arrest, production of progeny late in life, and reduced brood size. The strengths of the Daf-c, Age, and Itt phenotypes largely correlated with each other but not with the strength of class 2-specific defects. This suggests that the DAF-2 receptor is bifunctional. Examination of the null phenotype revealed a maternally rescued egg, L1 lethal component, and a nonconditional Daf-c component. With respect to the Daf-c phenotype, the dauer-defective (Daf-d) mutation daf-12(m20) was epistatic to daf-2 class 1 alleles but not the severe class 2 alleles tested. All daf-2 mutant defects were suppressed by the daf-d mutation daf-16(m26). Our findings suggest a new model for daf-2, age-1, daf-12 and daf-16 ------------------- Key: 3180 Medline: Authors: Takagi T;Taylor GS;Kusakabe T;Charbonneau H;Buratowski S Title: A protein tyrosine phospatase-like protein from baculovirus has RNA 5'-triphosphatase and diphosphatase activities. Citation: Proceedings of the National Academy of Sciences USA 95: 9808-9812 1998 Type: ARTICLE Genes: Abstract: The superfamily of protein tyrosine phosphatases (PTPs) includes at least one enzyme with an RNA substrate. We recently showed that the RNA triphosphatase domain of the Caenorhabditis elegans mRNA capping enzyme is related to the PTP enzyme family by sequence similarity and mechanism. The PTP most similar in sequence to the capping enzyme triphosphatase is BVP, a dual-specificity PTP encoded by the Autographa californica nuclear polyhedrosis virus. Although BW previously has been shown to have modest tyrosine and serine/threonine phosphatase activity, we find that it is much more potent as an RNA 5'-phosphatase. BVP sequentially removes gamma and beta phosphates from the 5' end of triphosphate-terminated RNA, leaving a 5'-monophosphate end. The activity was specific for polynucleotides; nucleotide triphosphates were not hydrolyzed. A mutant protein in which the active site cysteine was replaced with serine was inactive. Three other dual-specificity PTPs (VH1, VHR, and Cdc14) did not exhibit detectable RNA phosphatase activity. Therefore, capping enzyme and BW are members of a distinct PTP-like subfamily ------------------- Key: 3181 Medline: 98342252 Authors: DeBose-Boyd RA;Kwame Nyame A;Cummings RD Title: Molecular cloning and characterization of an alpha1,3 fucosyltransferase, CEFT-1, from Caenorhabditis elegans. Citation: Glycobiology 8: 905-917 1998 Type: ARTICLE Genes: Abstract: We report on the identification, molecular cloning, and characterization of an alpha 1,3 fucosyltransferase (alpha 1,3FT) expressed by the nematode, Caenorhabditis elegans. Although C. elegans glycoconjugates do not express the Lewis x antigen Gal beta 1-->4[Fuc alpha 1-->3]GlcNAc beta-->R, detergent extracts of adult C,elegans contain an al,3FT that can fucosylate both nonsialylated and sialylated acceptor glycans to generate the Le(X) and sialyl Le(X) antigens, as well as the lacdiNAc-containing acceptor GalNAc beta 1-->4GlcNAc beta 1-->R to generate GalNAc beta 1-->4 [Fuc alpha 1-->3]GlcNAc beta 1-->R. A search of the C. elegans genome database revealed the existence of a gene with 20-23% overall identity to all five cloned human alpha 1,3FTs. The putative cDNA for the C,elegans alpha 1,3FT (CEFT-1) was amplified by PCR from a cDNA lambda ZAP library, cloned, and sequenced. COS7 cells transiently transfected with cDNA encoding CEFT-1 express the Le(X), but not sLe(X) antigen. The CEFT-1 in the transfected cell extracts can synthesize Le(X), but not sialyl Le(X), using exogenous accepters. A second fucosyltransferase activity was detected in extracts of C,elegans that transfers Fuc in alpha 1,2 linkage to Gal specifically on type-1 chains. The discovery of alpha-fucosyltransferases in C. elegans opens the possibility of using this well-characterized nematode as a model system for studying the role of fucosylated glycans in the development and survival of C,elegans and possibly ------------------- Key: 3182 Medline: Authors: Napier JA;Hey SJ;Lacey DJ;Shewry PR Title: Identification of a Caenorhabditis elegans triangle(6)-fatty-acid-desaturase by heterologous expression in Saccharomyces cerivisiae. Citation: Biochemical Journal 333: 847- 1998 Type: ARTICLE Genes: Abstract: ------------------- Key: 3183 Medline: Authors: Wade N Title: Can social behavior of man be glimpsed in a lowly worm? Citation: The New York Times, September 8 : B9- 1998 Type: REVIEW Genes: Abstract: Does behavior have a genetic basis? People may find the idea unwelcome, at least as applied to their own conduct, but genes that govern behaviors in animals are beginning to come to light, the most spectacular of them in an article in the current issue of Cell. The gene governs sociability and feeding behavior in a microscopic roundworm, a favorite laboratory organism chosen for its ease of study and its relative simplicity. ------------------- Key: 3184 Medline: Authors: Phelan P;Bacon JP;Davies JA;Stebbings LA;Todman M;Avery L;Baines RA;Barnes TM;Ford C;Hekimi S;Lee R;Shaw JE;Sta Title: Innexins: a family of invertebrate gap-junction proteins. Citation: Trends in Genetics 14: 348-349 1998 Type: REVIEW Genes: eat-5 unc-7 Abstract: In vertebrates, intercellular communication via gap junctions is mediated by the connexin family of molecules, which is made up of at least 13 members. These proteins, which have four transmembrane domains and intracellular C- and N-termini, oligomerize to form hemichannels. Oligomers in the adjacent membranes of two closely apposed cells 'dock' to form intercellular channels, through which ions and small molecules move. ------------------- Key: 3185 Medline: 98412649 Authors: Thomas JH Title: Social life and the single nucleotide: Foraging behavior in C. elegans. Citation: Cell 94: 549-550 1998 Type: REVIEW Genes: npr-1 Abstract: Since the rise of the field of sociobiology, the study of the biological basis of social behavior, scientists have striven to assign genetic origins for a variety of social behaviors. There have been a number of highly publicized and often controversial studies of the basis of human social behavoirs such as sexual orientation and religion. Less trumpeted by the popular press, there have been a number of more credible advances in the genetic analysis of complex behavioral traits. Two papers in the past year, one in this issue of Cell (de Bono and Bargmann, 1998), have established two interesting cases of a molecular basis for complex behaviors that are arguably relevant to social interactions in natural populations. Both have to do with food foraging strategies, one in Drosophila and one in C. ------------------- Key: 3186 Medline: 98412659 Authors: Kawasaki I;Shim Y-H;Kirchner J;Kaminker J;Wood WB;Strome S Title: PGL-1, a predicted RNA-binding component of germ granules, is essential for fertility in C. elegans. Citation: Cell 94: 635-645 1998 Type: ARTICLE Genes: fem-2 glh-1 glp-4 pgl-1 eDf18 eDf19 mDf9 nDf41 sDf2 Abstract: Germ cells are distinct from somatic cells in their immortality, totipotency, and ability to undergo meiosis. Candidates for components that guide the unique germline program are the distinctive granules observed in germ cells of many species. We show that a component of germ granules is essential for fertility in C. elegans and that its primary function is in germline proliferation. This role has been revealed by molecular and genetic analyses of pgl-1. PGL-1 is a predicted RNA-binding protein that is present on germ granules at all stages of development. Elimination of PGL-1 results in defective germ granules and sterility. Interestingly, PGL-1 function is required for fertility only at elevated temperatures, suggesting that germline development is inherently sensitive to ------------------- Key: 3187 Medline: 98412663 Authors: de Bono M;Bargmann CI Title: Natural variation in a neuropeptide Y receptor homolog modifies social behavior and food response in C. elegans. Citation: Cell 94: 679-689 1998 Type: ARTICLE Genes: goa-1 npr-1 npr-2 unc-25 unc-29 syDf1 Abstract: Natural isolates of C. elegans exhibit either solitary or social feeding behavior. Solitary foragers move slowly on a bacterial lawn and disperse across it,while social foragers move rapidly on bacteria and aggregate together. A loss-of-function mutation in the npr-1 gene, which encodes a predicted G protein-coupled receptor similar to neuropeptide Y receptors, causes a solitary strain to take on social behavior. Two isoforms of NPR-1 that differ at a single residue occur in the wild. One isoform, NPR-1 215F, is found exclusively in social strains, while the other isoform, NPR-1 215V, is found exclusively in solitary strains. An NPR-1 215V transgene can induce solitary feeding behavior in a wild social strain. Thus, isoforms of a putative neuropeptide receptor generate natural variation in C. elegans feeding behavior. ------------------- Key: 3188 Medline: 98392856 Authors: Lindberg I;Tu B;Muller L;Dickerson IM Title: Cloning and functional analysis of C. elegans 7B2. Citation: DNA and Cell Biology 17: 727-734 1998 Type: ARTICLE Genes: Abstract: The neuroendocrine protein 7B2 is a binding protein for the prohormone convertase 2 (PC2) and is required for the intracellular conversion of proPC2 to active PC2. Both full-length 7B2 and its carboxy-terminal 31-residue peptide (CT peptide) are capable of potent inhibition of PC2; the 7B2 protein thus regulates both the biosynthesis and the activity of PC2. Vertebrate 7B2s are highly conserved (92%-97% homology), and thus, species comparison has not been informative in assessing the crucial protein domains responsible for bioactivity. We here report the cloning of the Caenorhabditis elegans 7B2 protein. Although weakly conserved with the vertebrate sequences (23% similarity with mouse 7B2), C. elegans 7B2 contains the signature PPNPCP motif as well as a highly conserved heptapeptide within the CT peptide. In in vitro assays, C. elegans 7B2 possessed significant inhibitory activity against recombinant vertebrate PC2 (IC50 130 nhl), and in two functional tests, the amino-terminal domain of C. elegans 7B2 facilitated the activation of proPC2. We conclude that despite low amino acid conservation overall, both functional domains within 7B2 have been conserved between the C. elegans and the vertebrate proteins. ------------------- Key: 3189 Medline: 98380271 Authors: Gregoire FM;Chomiki N;Kachinskas D;Warden CH Title: Cloning and developmental regulation of a novel member of the insulin-like gene family in Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications. 249: 385-390 1998 Type: ARTICLE Genes: daf-2 ilp-1 Abstract: Aging, metabolism and fat accumulation in Caenorhabditis elegans (C. elegans) are influenced by mutations in DAF-2, a putative insulin-like receptor. Ten putative insulin-like genes have been recently identified from the C. elegans genome database. However, it is unclear if these genes are orthologues of human insulin since they lack the C-peptide dibasic amino acid proteolysis sites. We have identified and measured mRNA expression during development of two novel members of the C. elegans insulin-like gene family. We also report the sequence characterization and gene structure for one of these, the insulin-like protein-1 (ILP1). We focused on ILP1 characterization because it has structural features consistent with its being a candidate insulin ligand for the OAF-a insulin-like receptor. For example, ILP1 has a putative C-peptide flanked by dibasic amino acids, exhibits conserved cysteine residues that could provide disulfide bonds between the A and B chains, and has two introns. Northern blot analysis revealed that ILP1 mRNA is expressed at very high levels in embryos and is downregulated very early during postnatal development, suggesting that it may influence embryonic development, but not Dauer formation. We also identified a novel insulin-like growth factor-1-like protein (T28B8/IGF-I) that exhibits a very different developmental expression profile than ILP1. Our results are consistent with the hypothesis that members of the unusually large and complex C. elegans insulin-like protein family exhibit complex and ------------------- Key: 3190 Medline: 98435850 Authors: Yuan J;Tirabassi RS;Bush AB;Cole MD Title: The C. elegans MDL-1 and MXL-1 proteins can functionally substitute for vertebrate MAD and MAX. Citation: Oncogene 17: 1109-1118 1998 Type: ARTICLE Genes: mdl-1 mxl-1 unc-119 Abstract: The genes of the myc/max/mad family play an important role in controlling cell proliferation and differentiation. We have identified the first homologues of the mad and max genes in the nematode C. elegans, which we have named mdl-1 and mxl-1 respectively. Like the vertebrate MAD proteins, MDL-1 binds an E-box DNA sequence (CACGTG) when dimerized with MXL-1. However, unlike vertebrate MAX, MXL-1 can not form homodimers and bind to DNA alone. Promoter fusions to a GFP reporter suggest that these genes are coexpressed in posterior intestinal and post-mitotic neuronal cells during larval development. The coexpression in the posterior intestinal cells occurs before their final division at the end of the L1 stage and persists afterwards, demonstrating that mad and max expression can be correlated directly to the cell cycle state of an individual cell type. These data also show that mxl-1 is an obligate partner for mdl-1 in vivo and in vitro and indicate that these genes may play an important role in post-embryonic development. Finally, MDL-1 can suppress activated c-MYC/RAS-induced focus formation in a rat embryo fibroblast transformation assay. Like the vertebrate MAD protein, MDL-1 activity in suppressing transformation is dependent on a functional SIN3 interaction domain. ------------------- Key: 3191 Medline: 98408881 Authors: Hallam SJ;Jin Y Title: lin-14 regulates the timing of synaptic remodelling in Caenorhabditis elegans. Citation: Nature 395: 78-82 1998 Type: ARTICLE Genes: lin-6 lin-14 unc-25 Abstract: In the nematode Caenorhabditis elegans six GABAergic motor neurons, known as DDs(1,2), remodel their patterns of synaptic connectivity during larval development(3). DD remodelling involves a complete reversal of the direction of information now within nerve processes without marked changes in process morphology. We used a marker localized in vivo to DD presynaptic zones to analyse how the timing of DD remodelling is controlled. In wild-type animals, DDs remodel their synaptic outputs within a 3-5-hour period at the end of the first larval stage. We show that the heterochronic gene lin-14, which controls the timing of stage-specific cell lineages(4,5), regulates the timing of DD synaptic output remodelling. In lin-14 loss-of-function mutants, DDs remodel precociously. The degree of precocious remodelling is correlated with the level of lin-14 activity. Expression of lin-14(+) in the DDs of lin-14-null mutants rescues the precocious remodelling, indicating that lin-14 can act cell-autonomously. Consistent with this hypothesis, LIN-14 protein levels decrease in the DDs before remodelling. Our observations reveal a role of heterochronic genes in non-dividing cells, and provide an example of cell-autonomous respecification of neuronal ------------------- Key: 3193 Medline: 98404277 Authors: Nelson LS;Rosoff ML;Li C Title: Disruption of a neuropeptide gene, flp-1, causes multiple behavioral defects in Caenorhabditis elegans. Citation: Science 281: 1686-1690 1998 Type: ARTICLE Genes: egl-30 flp-1 goa-1 gpb-1 Abstract: Neuropeptides serve as important signaling molecules in the nervous system. The FMRFamide (Phe-Met-Arg-Phe-amide)-related neuropeptide gene family in the nematode Caenorhabditis elegans is composed of at Least 18 genes that may encode 53 distinct FMRFamide-related peptides. Disruption of one of these genes, flp-1, causes numerous behavioral defects, including uncoordination, hyperactivity, and insensitivity to high osmolarity. Conversely, overexpression of flp-1 results in the reciprocal phenotypes. On the basis of epistasis analysis, flp-1 gene products appear to signal upstream of a G protein-coupled second messenger system. These results demonstrate that varying the levels of FLP-1 neuropeptides can profoundly affect behavior and that members of this large neuropeptide gene family are not functionally redundant in C. elegans. ------------------- Key: 3194 Medline: 98416049 Authors: Kokke BPA;Leroux MR;Candido EPM;Boelens WC;de Jong WW Title: Caenorhabditis elegans small heat-shock proteins Hsp12.2 and Hsp12.3 form tetramers and have no chaperone-like Citation: FEBS Letters 433: 228-232 1998 Type: ARTICLE Genes: Abstract: Four 12.2-12.6 kDa small heat-shock proteins (sHSPs) of Caenorhabditis elegans are the smallest known members of the sHSP family. They essentially comprise the characteristic C-terminal 'alpha-crystallin domain' of the sHSPs, having a very short N-terminal region, and lacking a C-terminal tail. Recombinant Hsp12.2 and 12.3 are characterized here. Far-UV CD spectra reveal, as for other sHSPs, predominantly a beta-sheet structure. By gel permeation and crosslinking, they are the first sHSPs shown to occur as tetramers, rather than forming the usual large multimeric complexes. Exceptionally, too, both appear devoid of in vitro chaperone-like abilities. This supports the notion that tetramers are the building blocks of sHSP complexes, and that higher multimer formation, mediated through the N-terminal domains, is a prerequisite for chaperone-like activity. ------------------- Key: 3195 Medline: 98380481 Authors: Oka T;Yamamoto R;Futai M Title: Multiple genes for vacuolar-type ATPase proteolipids in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 273: 22570-22576 1998 Type: ARTICLE Genes: vha-1 vha-2 vha-3 vha-4 vha-11 Abstract: In the vacuolar-type Hf-ATPase (V-ATPase), highly hydrophobic subunits known as the proteolipids are components of the integral membrane V-0 sector. Previously, we described the identification of three different proteolipid genes in Caenorhabditis elegans (Oka, T., Yamamoto, R., and Futai, M. (1997) J. Biol. Chem. 272, 24387-24392): vha-l and vha-2 encoded 16-kDa subunits, and vha-4, a 23-kDa isoform. me report here that a third 16-kDa gene, vha-3, has been identified on chromosome IV. This is the first example in which four proteolipid genes have been found in a single organism, vha-2 and vha-3 exhibited 85% nucleotide identity within the open reading frames which encoded the identical amino acid sequence. Northern blot analysis indicated that all four genes were expressed in a similar pattern during the worm life cycle; however, studies with transgenic worms indicated that the vha-3 gene was expressed differently from other proteolipid genes in a cell-specific manner. These results implied that the isoforms of the proteolipids may be related to functional differences of V-ATPases in various cell types. Another new gene, vha-11, contained seven exons and was found to be located immediately downstream of vha-3. The two genes constitute a single transcriptional unit. The VHA-11 protein had 384 amino acids and shared strong sequence similarities with the C subunit, a component of the peripheral V-1 sector of the V-ATPase, from yeast, bovine, and human. Expression of the Dha-II cDNA complemented a null mutation of VMA5, the yeast C subunit gene, thus demonstrating that vha-11 was the functional C subunit of ------------------- Key: 3196 Medline: 98397136 Authors: Lundquist EA;Herman RK;Shaw JE;Bargmann CI Title: UNC-115, a conserved protein with predicted LIM and acting-binding domains, mediates axon guidance in C. elegans. Citation: Neuron 21: 385-392 1998 Type: ARTICLE Genes: osm-6 unc-115 nDf19 Abstract: Axon guidance receptors modulate the growth cone cytoskeleton through signaling pathways that are not well understood. Here, we describe the C. elegans unc-115 gene, which encodes a candidate cytoskeletal linker protein that acts in axon guidance, unc-115 mutants have defects in a subset of axons, particularly as the affected axons change environments during outgrowth. The unc-115 gene encodes a putative actin-binding protein that is similar to the human actin-binding protein abLIM/limatin; it has a villin headpiece domain and three LIM domains that could mediate protein interactions. unc-115 is expressed in neurons during their development and is required cell-autonomously in certain neurons for normal axon guidance. We propose that UNC-115 modulates the growth cone actin cytoskeleton in response to signals received by growth cone receptors. ------------------- Key: 3197 Medline: 98409254 Authors: Nishiwaki K;Miwa J Title: Mutations in genes encoding extracellular matrix proteins suppress the emb-5 gastrulation defect in Caenorhabditis elegans. Citation: Molecular & General Genetics 259: 2-12 1998 Type: ARTICLE Genes: dpy-1 dpy-2 dpy-3 dpy-5 dpy-6 dpy-7 dpy-8 dpy-9 dpy-10 dpy-11 dpy-13 dpy-17 dpy-18 emb-5 glp-1 lon-2 mup-1 sqt-1 unc-52 Abstract: The second division of the gut precursor E cells is lethally accelerated during Caenorhabditis elegans gastrulation by mutations in the emb-5 gene, which encodes a presumed nuclear protein. We have isolated suppressor mutations of the temperature-sensitive allele emb-5(hc61), screened for them among dpy and other mutations routinely used as genetic markers, and identified eight emb-5 suppressor genes. Of these eight suppressor genes, at least four encode extracellular matrix proteins, i.e., three collagens and one proteoglycan. The suppression of the emb-5 gastrulation defect seemed to require the maternal expression of the suppressors. Phenotypically, the suppressors by themselves slowed down early embryonic cell divisions and corrected the abnormal cell-division sequence of emb-5 mutant embryos, We propose an indirect stress-response mechanism to be the main cause of the suppression because: (1) none of these suppressors is specific, either to particular temperature-sensitive emb-5 alleles or to the emb-5 gene; (2) suppressible alleles of genes, reported here or elsewhere, are temperature sensitive or weak; (3) the suppression is not Strong but marginal (4) the suppression itself shows some degree of temperature dependency; and (5) none of the extracellular matrix proteins identified here is known to be expressed in oocytes or early embryos, despite the present observation ------------------- Key: 3198 Medline: 98399412 Authors: Lu B;Jan LY;Jan Y Title: Asymmetric cell division: lessons from flies and worms. Citation: Current Opinion in Genetics & Development 8: 392-399 1998 Type: REVIEW Genes: glp-1 lef-1 lit-1 mex-1 mex-3 mom-1 mom-2 mom-3 mom-4 mom-4 pal-1 par-1 par-2 par-3 pie-1 pop-1 skn-1 wrm-1 Abstract: Insights into the mechanisms of asymmetric cell division have recently been obtained from studies in genetically amenable systems such as Drosophila and Caenorhabditis elegans. These studies have emphasized the importance of cortically localized polarity organizing molecules, adapter molecules, and the actin cytoskeleton in controlling unequal segregation of cell-fate determinants and spindle orientation. The control of asymmetric cell divisions by Wnt signaling in C. elegans and Frizzled signaling in Drosophila reveals additional mechanisms for modulating cellular polarity and suggests that there are some similarities between the two systems. ------------------- Key: 3199 Medline: Authors: Lee J;Ahnn J Title: Isolation and characterization of lethal mutation near the unc-29 (LG I) region of Caenorhabditis elegans. Citation: Korean Journal of Biological Sciences 2: 123-131 1998 Type: ARTICLE Genes: deg-1 deg-3 mec-4 myo-3 nob-3 unc-29 nDf23 nDf29 Abstract: The unc-29 region of the chromosome I of Caenorhabditis elegans has been mutagenized in order to obtain lethal mutations. In this screen, the uncoordinated phenotype of unc-29(e193) mutant was used to identify any lethal mutations closely linked to the unc-29 gene, which encodes a subunit of nicotinic acetylcholine receptors. We have isolated six independent mutations (jh1 to jh6) out of approximately 5,200 ethyl methanesulfonate (EMS) treated haploids. Four of the six mutations demonstrated embryonic lethal phenotypes, while the other two showed embryonic and larval lethal phenotypes. Terminal phenotypes observed in two mutatins (jh1 and jh2) indicated developmental defects specific to posterior part of embryos which appeared similar to the phenotypes observed in nob (no back end) mutants. Another mutation (jh4) resulted in an interesting phenotype of body-wall muscle degeneration at larval stage. These mutations were mapped by using three-factor crosses and deficiency mutants in this region. Here we report genetic analysis and characterization of these lethal ------------------- Key: 3200 Medline: 98384323 Authors: Eisenmann DM;Maloof JN;Simske JS;Kenyon C;Kim SK Title: The B-catenin homolog BAR-1 and LET-60 Ras coordinately regulate the Hox gene lin-39 during Caenorhabditis elegans vulval development. Citation: Development 125: 3667-3680 1998 Type: ARTICLE Genes: bar-1 hmp-1 let-23 let-60 lin-1 lin-31 lin-39 mab-5 mpk-1 wrm-1 uDf1 Abstract: In C. elegans, the epithelial Pn.p cells adopt either a vulval precursor cell fate or fuse with the surrounding hypodermis (the F fate). Our results suggest that a Wnt signal transduced through a pathway involving the beta-catenin homolog BAR-1 controls whether P3.p through P8.p adopt the vulval precursor cell fate. In bar-1 mutants, P3.p through P8.p can adopt F fates instead of vulval precursor cell fates. The Wnt/bar-1 signaling pathway acts by regulating the expression of the Hox gene lin-39, since bar-1 is required for LIN-39 expression and forced lin-39 expression rescues the bar-1 mutant phenotype. LIN-39 activity is also regulated by the anchor cell signal/let-23 receptor tyrosine kinase/let-60 Ras signaling pathway. Our genetic and molecular experiments show that the vulval precursor cells can integrate the input from the BAR-1 and LET-60 Ras signaling pathways by coordinately regulating activity of the common target ------------------- Key: 3201 Medline: 98384315 Authors: Hong Y;Roy R;Ambros V Title: Developmental regulation of a cyclin-dependent kinase inhibitor controls postembryonic cell cycle progression in Caenorhabditis elegans. Citation: Development 125: 3585-3597 1998 Type: ARTICLE Genes: cki-1 cki-2 cul-1 daf-7 egl-17 glp-1 gon-2 lag-2 lin-4 lin-12 lin-14 lin-29 Abstract: C. elegans cki-1 encodes a member of the CIP/KIP family of cyclin-dependent kinase inhibitors, and functions to link postembryonic developmental programs to cell cycle progression. The expression pattern of cki-1::GFP suggests that cki-1 is developmentally regulated in blast cells coincident with G(1), and in differentiating cells. Ectopic expression of CKI-1 can prematurely arrest cells in G1, while reducing cki-1 activity by RNA-mediated interference (RNAi) causes extra larval cell divisions, suggesting a role for cki-1 in the developmental control of G(1)/S. cki-1 activity is required for the suspension of cell cycling that occurs in dauer larvae and starved L1 larvae in response to environmental signals. In vulva precursor cells (VPCs), a pathway of heterochronic genes acts via cki-1 to maintain VPCs in G(1) during the L2 stage. ------------------- Key: 3202 Medline: Authors: Bredt DS Title: Sorting out genes that regulate epithelial and neuronal polarity. Citation: Cell 94: 691-694 1998 Type: REVIEW Genes: glr-1 let-23 lin-2 lin-3 lin-7 lin-10 Abstract: Muscle contraction is controlled by motor neurons, which are activated by glutamate release in spinal cord. This stimulus triggers action potentials that are propagated down long motor neuron axons to mediate acetylcholine release at distant neuromuscular junctions. This vectorial signaling in a motor neuron requires polarized sorting of proteins to appropriate neuronal domains. Neurotransmitter receptors for glutamate must be targeted to dendrites, while proteins that mediate synthesis and release of acetylcholine are shuttled down axons. Many nonneuronal cells are also polarized, but the two polarized faces are typically much closer than in neurons. For example, intestinal epithelial cells have an apical surface that faces the lumen of the gut and a basolateral surface that contacts the underlying basement membrane. Uptake of nutrients by epithelial cells requires that transporters for glucose and amino acids are expressed selectively at the apical membrane and that Na+/K+ ATPases, which set up ionic gradients essential for resorption, are expressed at the basolateral membrane. Understanding the basis for cellular polarity is important as defects in protein sorting underlie several common human disorders including cystic fibrosis and polycystic kidney disease. ------------------- Key: 3203 Medline: 98337829 Authors: Levitan D;Greenwald I Title: LIN-12 protein expression and localization during vulval development in C. elegans. Citation: Development 125: 3101-3109 1998 Type: ARTICLE Genes: let-60 lin-2 lin-3 lin-7 lin-12 Abstract: We have used a LIN-12::GFP fusion protein to examine LIN-12 accumulation during cell fate decisions important for vulval development. During the naturally variable anchor cell (AC)/ventral uterine precursor cell (VU) decision of the somatic gonad, a transcription-based feedback mechanism biases two equivalent cells so that one becomes the AC while the other becomes a VU. LIN-12::GFP accumulation reflects lin-12 transcription: LIN-12::GFP is initially present in both cells, but disappears from the presumptive AC and becomes restricted to the presumptive VU. During vulval precursor cell (VPC) fate determination, six equipotential cells uniformly transcribe lin-12 and have invariant fates that are specified by multiple cell-cell interactions. The pattern of LIN-12::GFP accumulation in VPCs and in the VPC lineages is dynamic and does not always reflect lin-12 transcription. In particular, LIN-12::GFP is expressed initially in all sig VPCs, but appears to be reduced specifically in P6.p as a consequence of the activation of the Ras pathway by an EGF-like inductive signal from the AC. We propose that downregulation of LIN-12 stability or translation in response to inductive signalling helps impose a bias on lateral signalling and contributes to the invariant pattern of VPC fates. ------------------- Key: 3204 Medline: 98377490 Authors: Lockery SR;Goodman MB Title: Tight-seal whole-cell patch clamping of Caenorhabditis elegans neurons. Citation: Methods in Enzymology 293: 201-217 1998 Type: REVIEW Genes: Abstract: The nematode Caenorhabditis elegans is widely used to study the relationship between genes, neurons, and behavior. The adult hermaphrodite has a compact nervous system of only 302 neurons and the synaptic connections between these cells have been described completely. The neural circuits for many of its behaviors have been delineated. In addition, more than 350 genes affecting behavior have been identified. Caenorhabditis elegans represents a formidable challenge for electrophysiology, however. The animals are only 0.25-1.2 mm long and the cell bodies of C. elegans neurons are typically 2 um in diameter. In addition, the body is protected by a tough, pressurized cuticle that explodes when dissected. The electrical properties of individual neurons in C. elegans, therefore, are largely unknown. Here we present a reliable method for making tight-seal, whole-cell patch-clamp recordings from intact neurons in C. elegans at all larval stages. By combining this technique with cell-specific expression of green fluorescent protein (GFP), whole-cell recordings can be made from identified neurons. Thus, it is now possible to describe the electrical properties of particular neurons and to find out how these properties are altered by mutations affecting neuronal development and behavior. ------------------- Key: 3205 Medline: 98401146 Authors: Oates AC;Wollberg P;Achen MG;Wilks AF Title: Sampling the genomic pool of protein tyrosine kinase genes using the polymerase chain reaction with genomic DNA. Citation: Biochemical and Biophysical Research Communications 249: 660-667 1998 Type: ARTICLE Genes: Abstract: The polymerase chain reaction (PCR), with cDNA as template, has been widely used to identify members of protein families from many species. A major limitation of using cDNA in PCR is that detection of a family member is dependent on temporal and spatial patterns of gene expression. To circumvent this restriction, and in order to develop a technique that is broadly applicable we have tested the use of genomic DNA as PCR template to identify members of protein families in an expression-independent manner. This test involved amplification of DNA encoding protein tyrosine kinase (PTR) genes from the genomes of three animal species that are well known developmental models; namely, the mouse Mus musculus, the fruit fly Drosophila melanogaster, and the nematode worm Caenorhabditis elegans. Ten PTK genes were identified from the mouse, 13 from the fruit fly, and 13 from the nematode worm. Among these kinases were 13 members of the PTR family that had not been reported previously. Selected PTKs from this screen were shown to be expressed during development, demonstrating that the amplified fragments did not arise from pseudogenes. This approach will be useful for the identification of many novel members of gene families in organisms of agricultural, medical, developmental and evolutionary significance and for analysis of gene families from any species, or biological sample whose habitat precludes the isolation of mRNA. Furthermore, as a tool to hasten the discovery of members of gene families that are of particular interest, this method offers an opportunity to sample the genome for new members irrespective of their ------------------- Key: 3206 Medline: 98248696 Authors: McMurray AA;Sulston JE;Quail MA Title: Short-insert libraries as a method of problem solving in genome sequencing. Citation: Genome Research 8: 562-566 1998 Type: ARTICLE Genes: Abstract: As the Human Genome Project moves into its sequencing phase, a serious problem has arisen. The same problem has been increasingly vexing in the closing phase of the Caenorhabditis elegans project. The difficulty lies in sequencing efficiently through certain regions in which the templates (DNA substrates for the sequencing process) form complex folded secondary structures that are inaccessible to the enzymes. The solution, however, is simply to break them up. Specifically, the offending fragments are sonicated heavily and recloned, as much smaller fragments, into pUC vector. The sequences obtained from the resulting library can subsequently be assembled, free from the effects of secondary structure, to produce high-quality, complete sequence. Because of the success and simplicity of this procedure, we have begun to use it for the sequencing of all regions in which standard primer walking has been at all difficult. ------------------- Key: 3207 Medline: 98393546 Authors: Korswagen HC;van der Linden AM;Plasterk RHA Title: G protein hyperactivation of the Caenorhabditis elegans adenylyl cyclase SGS-1 induces neuronal degeneration. Citation: EMBO Journal 17: 5059-5065 1998 Type: ARTICLE Genes: acy-2 sgs-1 nDf17 sDf121 Abstract: Expression of a constitutively activated version of the heterotrimeric G protein alpha-subunit G alpha(s) results in the swelling and vacuolization of a specific subset of ventral nerve cord motoneurons of Caenorhabditis elegans. A second site modifier (sgs-1) that completely suppresses this neuronal degeneration has been isolated. sgs-1 was cloned and was shown to encode an adenylyl cyclase which is most similar to mammalian adenylyl cyclase type IX, Mutations in sgs-1 change residues that are conserved among different adenylyl cyclases. These mutations are located in the two catalytic domains and in the first multiple transmembrane spanning region of the predicted protein. An sgs-1 reporter construct shows a general neuronal expression pattern, demonstrating that sgs-1 is expressed in the neurons that are susceptible to activated G alpha(s)-induced cell death, A second C.elegans adenylyl cyclase gene (acy-2) was analyzed as well, In contrast to sgs-1, acy-2 shows a restricted expression pattern and loss of acy-2 function results in early larval lethality. These results suggest that SGS-1 is a target of G alpha(s) signaling in motoneurons, whereas an interaction of G alpha(s) with ACY-2, probably in the canal-associated neurons, is required for viability. ------------------- Key: 3208 Medline: 98426744 Authors: Vanfleteren JR;Braeckman BP;Roelens I;De Vreese A Title: Age-specific modulation of light production potential, and alkaline phosphatase and protein tyrosine kinase activities in various age mutants of Caenorhabditis elegans. Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 53: B380-B390 1998 Type: ARTICLE Genes: age-1 daf-2 daf-12 fer-15 Abstract: Previous work has shown that reduction-of-function mutations in the genes daf-2 and age-1 can increase adult life (Age phenotype) of Caenorhabditis elegans and that certain daf-12 alleles considerably amplify this effect in daf-2; daf-12 doubles. We have measured the light production potential (LPP) and alkaline phosphatase (ALP) and protein tyrosine kinase (PTK) activity levels as suitable biochemical markers to further investigate genetic interactions between these genes. The light production assay measures superoxide anion production by freeze-thawed worms in assay medium containing sufficient amounts of nicotineamide adenine dinucleotide, reduced form (NADH) and nicotineamide adenine dinucleotide phosphate, reduce form (NADPH) to drive the chemiluminescent reaction at maximal speed, and 5 mM cyanide to fully repress cytosolic superoxide dismutase (SOD). This assay thus provides an estimate of the maximum output of the metabolic pathways involved at the instant of freeze-fixation, and under the conditions of the assay. LPP and PTK activities decreased similarly in daf-12(m20), and a control strain that had wild-type alleles of daf-12, age-1, and daf-2. The age-dependent decrease of LPP and PTK was reduced in age-1(hx542) and age-1(hx542); daf-2(e1370), and virtually absent in daf-2(e1370) and daf-2(e1370); daf-12(m20) mutant worms. ALP activity increased with age in non-Age genotypes and showed little, if any, age-dependent alteration in daf-2(e1370) and daf-2(e1370); daf-12(m20) mutant worms. Mutation in both age-1 and daf-2 caused no stronger phenotype than a single mutation as estimated by LPP, PTK, and ALP. We propose that (a) daf-2 is the major effector of metabolic activity during adult life, (b) daf-2 downregulates metabolic activity with increasing age, and (c) daf-12 stimulates oxygen consumption independently of ------------------- Key: 3209 Medline: 99069613 Authors: Title: C. elegans sequencing project nears finish. Citation: Human Genome News 9: 16- 1998 Type: REVIEW Genes: Abstract: The 97-megabase genomic sequence of the nematode Caenorhabditis elegans reveals over 19,000 genes. More than 40 percent of the predicted protein products find significant matches in other organisms. There is a variety of repeated sequences, both local and dispersed. The distinctive distribution of some repeats and highly conserved genes provides evidence for a regional organization of the chromosomes. ------------------- Key: 3210 Medline: 98421815 Authors: Fay DS;Fluet A;Johnson CJ;Link CD Title: In vivo aggregation of beta-amyloid peptide variants. Citation: Journal of Neurochemistry 71: 1616-1625 1998 Type: ARTICLE Genes: mtl-2 rol-6 unc-54 Abstract: Transgenic Caenorhabditis elegans animals have been engineered to express wild-type and single-amino acid variants of a long form of human beta-amyloid peptide (A beta 1-42). These animals express high levels (similar to 300 ng of A beta/mg of total protein) of apparently full-length peptide, as determined by quantitative immunoblot. Expression of wild-type A beta in these animals leads to rapid production of amyloid deposits reactive with Congo red and thioflavin S. This model system has been used to examine the effect of Leu(17)Pro, Leu(17)Val, Ala(30)- Pro, Met(35)Cys, and Met(35)Leu substitutions on the in vivo production of amyloid deposits. We find that the Leu(17)Pro and Met(35)Cys substitutions completely block the formation of thioflavin S-reactive deposits, implicating these as key residues for in vivo amyloid formation. We have also constructed transgenic strains expressing a novel A beta variant, the single-chain dimer. Animals expressing high levels of this variant also fail to produce thioflavin S-reactive deposits. ------------------- Key: 3211 Medline: 98414621 Authors: Han JH;Wallen HD;Nunez G;White E Title: E1B 19,000-molecular-weight protein interacts with and inhibits CED-4-dependent, FLICE-mediated apoptosis. Citation: Molecular and Cellular Biology 18: 6052-6062 1998 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: Genetic studies of the nematode Caenorhabditis (C. elegans) have identified several important components of the cell death pathway, most notably CED-3, CED-4, and CED-9. CED-4 directly interacts with the Bcl-2 homologue CED-9 (or the mammalian Bcl-2 family member Bcl-x(L)) and the caspase CED-3 (or the mammalian caspases ICE and FLICE). This trimolecular complex of CED-4, CED-3, and CED-9 is functional in that CED-9 inhibits CED-4 from activating CED-3 and thereby inhibits apoptosis in heterologous systems. The E1B 19,000-molecular weight protein (E1B 19K) is a potent apoptosis inhibitor and the adenovirus homologue of Bcl-2-related apoptosis inhibitors. Since E1B 19K and Bcl-X-L, have functional similarity, we determined if E1B 19K interacts with CED-4 and regulates CED-4-dependent caspase activation, Binding analysis indicated that E1B 19K interacts with CED-4 in a Saccharomyces cerevisiae two-hybrid assay, in vitro, and in mammalian cell lysates. The subcellular localization pattern of CED-4 was dramatically changed by E1B 19K, supporting the theory of a functional interaction between CED-4 and E1B 19K. Whereas expression of CED-4 alone could not induce cell death, coexpression of CED-4 and FLICE augmented cell death induction by FLICE, which was blocked by expression of E1B 19K. Even though E1B 19K did not prevent FLICE-induced apoptosis, it did inhibit CED-4-dependent, FLICE-mediated apoptosis, which suggested that CED-4 was required for E1B 19K to block FLICE activation. Thus, E1B 19K functions through interacting with CED-4, and presumably a mammalian homologue of CED-4, to inhibit caspase activation and apoptosis. ------------------- Key: 3212 Medline: Authors: Freeman MN;Marse TJ;Williams PL Title: Establishment of quality assurance procedures for aquatic toxicity testing with the nematode Caenorhabditis elegans. Citation: "Environmental Toxicology and Risk Assessment, ASTM STP 1333". EE Little, AJ DeLonay and BM Greenberg, eds. American Society for Testing and Materials, West Conshohocken, PA 7: 45-59 1998 Type: ARTICLE Genes: Abstract: In this study initial data were generated to develop laboratory control charts for aquatic toxicity testing using the nematode Caenorhabditis elegans. Tests were performed using two reference toxicants: CdCl2 and CuCl2. All tests were performed for 24 h without a food source and for 48 h with a food source in a commonly used nematode aquatic medium. Each test was replicated 6 times with each replicate having 6 wells per concentration with 10 +/- 1 worms per well. Probit analysis was used to estimate LC50 values for each test. The data were used to construct a mean laboratory control chart for each reference toxicant. The coefficient of variation (CV) for three of the four reference toxicant tests was less than 20%, which demonstrates an excellent degree of reproducibility. These CV values are well within suggested standards for determination of organism sensitivity and overall test system credibility. A standardized procedure for performing 24 h and 48 h aquatic toxicity studies with C. elegans is ------------------- Key: 3213 Medline: Authors: Marin I;Baker BS Title: The evolutionary dynamics of sex determination. Citation: Science 281: 1990-1994 1998 Type: REVIEW Genes: mab-3 sdc-2 tra-1 tra-2 xol-1 Abstract: There is substantial cytogenetic data indicating that the process of sex determination can evolve relatively rapidly. However, recent molecular studies on the evolution of the regulatory genes that control sex determination in the insect Drosophila melanogaster, the nematode Caenorhabditis elegans, and mammals suggest that, although certain sex determination regulatory genes have evolved relatively rapidly, other sex determination regulatory genes are quite conserved. Thus, studies of the evolution of sex determination, a process that appears to have elements that, undergo substantial evolutionary change and others that may be conserved, could provide substantial insights into the kinds of forces that both drive and constrain the evolution of developmental hierarchies. ------------------- Key: 3214 Medline: 98424244 Authors: Rongo C;Whitfield CW;Rodal A;Kim SK;Kaplan JM Title: LIN-10 is a shared component of the polarized protein localization pathways in neurons and epithelia. Citation: Cell 94: 751-759 1998 Type: ARTICLE Genes: eat-4 glr-1 let-23 lin-2 lin-7 lin-10 mec-3 osm-10 unc-104 Abstract: We tested the model that neurons and epithelial cells use a shared mechanism for polarized protein sorting by comparing the pathways for localizing basolateral and postsynaptic proteins in C. elegans. GLR-1 glutamate receptors are localized to postsynaptic elements of central synapses and, when ectopically expressed, to basolateral membranes of epithelial cells. Proper localization of GLR-1 in both neurons and epithelia requires the PDZ protein LIN-10, defining LIN-10 as a shared component of the basolateral and postsynaptic localization pathways. Changing the GLR-1 carboxyterminal sequence from a group I PDZ-binding consensus (-TAV) to a group II consensus (-FYV) restores GLR-1 synaptic localization in lin-10 mutants. Thus, these interneurons utilize at least two separate postsynaptic localization pathways. ------------------- Key: 3215 Medline: 98424245 Authors: Kaech SM;Whitfield CW;Kim SK Title: The LIN-2/LIN-7/LIN-10 complex mediates basolateral membrane localization of the C. elegans EGF receptor LET-23 in vulval epithelial cells. Citation: Cell 94: 761-771 1998 Type: ARTICLE Genes: let-23 lin-2 lin-7 lin-10 Abstract: In C. elegans, the LET-23 receptor tyrosine kinase is localized to the basolateral membranes of polarized vulval epithelial cells. lin-2, lin-7, and lin-10 are required for basolateral localization of LET-23, since LET-23 is mislocalized to the apical membrane in lin-2 lin-7, and lin-10 mutants. Yeast two-hybrid, in vitro binding, and in vivo coimmunoprecipitation experiments show that LIN-2, LIN-7, and LIN-10 form a protein complex. Furthermore, compensatory mutations in lin-7 and let-23 exhibit allele-specific suppression of apical mislocalization and signaling-defective phenotypes. These results present a mechanism for basolateral localization of LET-23 receptor tyrosine kinase by direct binding to the LIN-2/LIN-7/LIN-10 complex. Each of the binding interactions within this complex is conserved, suggesting that this complex may also mediate basolateral localization in mammals. ------------------- Key: 3216 Medline: Authors: Rommel C;Hafen E Title: Ras - a versatile cellular switch. Citation: Current Opinion in Genetics & Development 8: 412-418 1998 Type: REVIEW Genes: lin-39 mab-5 Abstract: The small GTP-binding p21 Ras protein plays a central role in the regulation of diverse cellular processes in invertebrates and vertebrates. Ras controls the specification of vulval or tail structures in the nematode Caenorhabditis elegans, the specification of neuronal and non-neuronal cell fates in Drosophila, and the choice between proliferation and differentiation in PC12 cells, to name just a few examples. Furthermore, Ras proteins play a critical role in oncogenesis. In some cases p21 Ras appears to even control opposing pathways regulating cell growth and cell arrest and even cell death within the same cell. A variety of extracellular stimuli activate Ras by inducing exchange of Ras-bound GDP for GTP, a process that is facilitated by exchange factors such as son-of-sevenless. The binding of GTP to Ras triggers a conformational change whereby its effector domain, a loop of eight invariably conserved amino acids, is exposed. How can this simple change control a plethora of developmental and physiological precesses in different cells in vertebrates and invertebrates? Biochemical, genetic and structural studies have begun to shed light onto how Ras can pull so many strings attached to diverse cellular responses. Three broad concepts have emerged. Different effects of Ras activation can originate from first, the activation of parallel effector pathways, second, quantitatively different levels and duration of Ras activity and third, different cellular contexts that determine how the Ras signal is interpreted. After describing the two best known effector molecules of Ras, the protein Raf and the lipid kinase PI(3)K, we discuss how these three different models might account for the ------------------- Key: 3217 Medline: 98399418 Authors: Gumbiner BM Title: Propagation and localization of Wnt signaling. Citation: Current Opinion in Genetics & Development 8: 430-435 1998 Type: REVIEW Genes: apr-1 mom-2 pop-1 wrm-1 Abstract: The Wnt signaling pathway has commanded a great deal of attention lately because of its impact on many different areas of biology. Wnt signaling is associated with cell-fate determination in embryos, cell adhesion, and the genesis of cancer. The outlines of the Wnt signal transduction pathway were first uncovered by a genetic analysis of wingless signaling during the development of segmental polarity in Drosophila and extended through studies of embryonic axis formation in Xenopus. The signal transduction pathways in these two model organisms exhibit remarkable similarities, leading to a common overview of the pathway. The APC (adenomatous polyposis coli) tumor suppressor protein and a novel protein called axin were discovered independently and subsequently linked to the B-catenin and Wnt signaling pathway by experimentation. The convergence of research efforts in these areas has promoted very rapid progress in our understanding of the Wnt signal transduction pathway, which has been thoroughly described in several recent excellent reviews. The goal of this article is to consider, and draw attention to, some important but often overlooked issues about how Wnt signals are localized within cells and propagated through tissues. Several studies in Drosophila, Caenorhabditis elegans, and Xenopus embryos have examined how Wnt signaling mediates long-range patterning events and the establishment of embryonic polarity. They have shown that cellular mechanisms mediating transport and localization of Wnt signaling components are essential for the proper propagation and distribution of Wnt signals through ------------------- Key: 3218 Medline: 99006267 Authors: Arpagaus M;Combes D;Culetto E;Grauso M;Fedon Y;Romani R;Toutant JP Title: Four acetylcholinesterase genes in the nematode Caenorhabditis elegans. Citation: Journal of Physiology-Paris 92: 363-367 1998 Type: ARTICLE Genes: ace-1 ace-2 ace-3 ace-4 Abstract: Whereas a single gene encodes acetylcholinesterase (AChE) in vertebrates and most insect species, four distinct genes have been cloned and characterized in the nematode Caenorhabditis elegans. We found that ace-1 (mapped to chromosome X) is prominently expressed in muscle cells whereas ace-2 (located on chromosome I) is mainly expressed in neurons. Ace-x and ace-y genes are located in close proximity on chromosome II where they are separated by only a few hundred base pairs. The role of these two genes is still unknown. ------------------- Key: 3219 Medline: 98426229 Authors: Take-Uchi M;Kawakami M;Ishihara T;Amano T;Kondo K;Katsura I Title: An ion channel of the degenerin/epithelial sodium channel superfamily controls the defecation rhythm in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 95: 11775-11780 1998 Type: ARTICLE Genes: flr-1 flr-2 flr-5 unc-3 Abstract: Ultradian rhythms are widespread phenomena found in various biological organisms. A typical example is the defecation behavior of the nematode Caenorhabditis elegans, which repeats at about 45-sec intervals. To elucidate the mechanism, we studied flr-1 mutants, which show very short defecation cycle periods. The mutations also affect some food-related functions, including growth rate, the expulsion step of defecation behavior, and the regulation of the dauer larva (a nonfeeding, special third-stage larva) formation in the unc-3 (Olf-1/EBF homolog) background. The flr-1 gene encodes a novel ion channel belonging to the DEG/ENaC (C. elegans degenerin and mammalian epithelial sodium channel) superfamily. A flr-1::GFP (green fluorescent protein) fusion gene that can rescue the flr-1 mutant phenotypes is expressed only in the intestine from embryos to adults. These results suggest that FLR-1 may be a component of an intestinal regulatory system that controls the defecation rhythm as well as other ------------------- Key: 3220 Medline: 98426152 Authors: Nelson DW;Linning RM;Davison PJ;Honda BM Title: 5'-flanking sequences required for efficient transcription in vitro of 5S RNA genes, in the related nematodes Caenorhabditis elegans and Caenorhabditis briggsae. Citation: Gene 218: 9-16 1998 Type: ARTICLE Genes: Abstract: In the nematode C. elegans, we had previously observed apparent species specificity in 5S RNA transcription. We have now undertaken a further study of 5S RNA gene transcription in this organism and in the related nematode, C briggsae; the latter was chosen because it might show evolutionarily conserved, functionally important features. Deletion mutagenesis and transcription in vitro followed by more precise replacements of short blocks of 5' sequence show that a short, TATA-like sequence at -25 is essential for efficient transcription in vitro of the 1.0-kb C. elegans 5S DNA repeat, and of both C. briggsae 0.7- and 1.0-kb 5S DNA repeats. Internal sequences within the 5S RNA gene appear to be required and can compete for limiting transcription components, whereas 5' flanking sequences do not. These observations suggest that the process of 5S RNA transcription is similar in these nematodes and other higher eukaryotes. ------------------- Key: 3221 Medline: 99441478 Authors: Mohler WA;Simske JS;Williams-Masson EM;Hardin JD;White JG Title: Dynamics and ultrastructure of developmental cell fusions in the Caenorhabditis elegans hypodermis. Citation: Current Biology 8: 1087-1090 1998 Type: ARTICLE Genes: Abstract: Cell fusions produce multinucleate syncytia that are crucial to the structure of essential tissues in many organisms [1-5]. In humans the entire musculature, much of the placenta, and key cells in bones and blood are derived from cell fusion. Yet the developmental fusion of cell membranes has never been directly observed and is poorly understood. Similarity between viral fusion proteins and recently discovered cellular proteins implies that both cell-cell and virus-cell fusion may occur by a similar mechanism [6-8]. Paradoxically, however, fusion of enveloped viruses with cells involves an opening originating as a single pore [9-11], whereas electron microscopy studies of cell-cell fusion describe simultaneous breakdown of large areas of membrane [12,13]. Here, we have shown that developmental cell fusion is indeed consistent with initiation by a viruslike, pore-forming mechanism. We examined live cell fusions in the epithelia of Caenorhabditis elegans embryos by a new method that integrates multiphoton, confocal, and electron microscopy. The fusion aperture always originated at a single point restricted to the apical adherens junction and widened slowly as a radial wavefront. The fusing membranes dispersed by vesiculation, rather than simple unfolding of the conjoined double bilayer. Thus, in these cells fusion appears to require two specialized sequential processes: formation of a unique primary pore and expansion of the opening by radial internalization of the interacting cell ------------------- Key: 3222 Medline: 98441479 Authors: Murakami S;Johnson TE Title: Life extension and stress resistance in Caenorhabditis elegans modulated by the tkr-1 gene. Citation: Current Biology 8: 1091-1094 1998 Type: ARTICLE Genes: age-1 clk-1 daf-2 spe-26 tkr-1 tkr-2 Abstract: The nematode Caenorhabditis elegans is widely used to study aging, development, behavior and other basic metazoan processes [1-3]. The only mutants directly identified on the basis of their extended longevity in any metazoan have been isolated in C. elegans [4,5]. All life extension mutants (Age mutants) previously identified in C, elegans result from hypo-morphic or nullo-morphic mutations. We have identified a new class of gerontogene (a gene whose alteration causes life extension) that increases life span when overexpressed. The first gene in this class has been designated tyrosine kinase receptor-1 (tkr-1); it encodes a putative receptor tyrosine kinase. Overexpression of tkr-1 in transgenics increases longevity 40-100% (average 65%), confers increased resistance to heat and ultraviolet (UV) irradiation in transgenic nematodes, and does not alter development or fertility. Unlike previously identified gerontogenes, tkr-1 positively modulates stress resistance and longevity. These results further support the positive relationship between increased stress resistance and increased longevity seen in all previously studied longevity mutants. This transgenic system is an effective means for identifying overexpression gerontogenes. ------------------- Key: 3223 Medline: 99012915 Authors: Tabara H;Grishok A;Mello CC Title: RNAi in C. elegans - Soaking in the genome sequence. Citation: Science 282: 430-431 1998 Type: ARTICLE Genes: pos-1 Abstract: The completion of the Caenorhabditis elegans genome sequence represents a major milestone in a journey initiated by Sydney Brenner some 30 years ago. The goal then as now was to discover how genetic information specifies the development, anatomy, and behavior of a simple animal. Bringing the full potential of the genome sequence to bear on this goal will require facile new reverse genetic tools for converting sequence information into functional information. Here, we briefly describe progress toward understanding and using one such tool termed "RNA interference" or "RNAi". ------------------- Key: 3224 Medline: 98453614 Authors: Zinn K Title: Receptor tyrosine phosphatases: The worm clears the Citation: Current Biology 8: R725-R726 1998 Type: REVIEW Genes: clr-1 egl-15 egl-17 sem-5 soc-2 Abstract: Recent work on the Caenorhabditis elegans clr-1 gene shows that the receptor tyrosine phosphatase that it encodes negatively regulates a receptor tyrosine kinase related to mammalian fibroblast growth factor receptors. This opens up a promising system for investigating receptor tyrosine phosphatase function. ------------------- Key: 3225 Medline: 98453597 Authors: Skop AR;White JG Title: The dynactin complex is required for cleavage plane specification in early Caenorhabditis elegans embryos. Citation: Current Biology 8: 1110-1116 1998 Type: ARTICLE Genes: dnc-1 dnc-2 Abstract: Background: During metazoan development, cell diversity arises primarily from asymmetric cell divisions which are executed in two phases: segregation of cytoplasmic factors and positioning of the mitotic spindle - and hence the cleavage plane - relative to the axis of segregation. When polarized cells divide, spindle alignment probably occurs through the capture and subsequent shortening of astral microtubules by a site in the cortex. Results: Here, we report that dynactin, the dynein-activator complex, is localized at cortical microtubule attachment sites and is necessary for mitotic spindle alignment in early Caenorhabditis elegans embryos. Using RNA interference techniques, we eliminated expression in early embryos of dnc-1 (the ortholog of the vertebrate gene for p150(Glued)) and dnc-2 (the ortholog of the vertebrate gene for p50/Dynamitin). In both cases, misalignment of mitotic spindles occurred, demonstrating that two components of the dynactin complex, DNC-1 and DNC-2, are necessary to align the spindle. Conclusions: Dynactin complexes may serve as a tether for dynein at the cortex and allow dynein to produce forces on the astral microtubules required for mitotic spindle alignment. ------------------- Key: 3226 Medline: 98453602 Authors: Powers J;Bossinger O;Rose D;Strome S;Saxton W Title: A nematode kinesin required for cleavage furrow Citation: Current Biology 8: 1133-1136 1998 Type: ARTICLE Genes: air-1 zen-4 Abstract: Dividing cells need to coordinate the separation of chromosomes with the formation of a cleavage plane. There is evidence that microtubule bundles in the interzone region of the anaphase spindle somehow control both the location and the assembly of the cleavage furrow [1-3]. A microtubule motor that concentrates in the interzone, MKLP1, has previously been implicated in the assembly of both the metaphase spindle and the cleavage furrow [4-6]. To gain insight into mechanisms that might underlie interdependence of the spindle and the cleavage furrow, we used RNA-mediated interference (RNAi) to study the effects of eliminating MKLP1 from Caenorhabditis elegans embryos. Surprisingly, in MKLP1(RNAi) embryos, spindle formation appears normal until late anaphase. Microtubule bundles form in the spindle interzone and the cleavage furrow assembles; anaphase and cleavage furrow ingression initially appear normal. The interzone bundles do not gather into a stable midbody, however, and furrow contraction always fails before complete closure. This sequence of relatively normal mitosis and a late failure of cytokinesis continues for many cell cycles. These and additional results suggest that the interzone microtubule bundles need MKLP1 to encourage the advance and stable ------------------- Key: 3227 Medline: Authors: Kimble J;Henderson S;Crittenden S Title: Notch/LIN-12 signaling: transduction by regulated protein slicing. Citation: Trends in Biochemical Sciences 23: 353-357 1998 Type: REVIEW Genes: apx-1 glp-1 lag-1 lag-2 lin-12 sel-12 sup-17 Abstract: Intercellular signaling through the Notch/LIN-12 transmembrane receptors regulates growth and differentiation during animal development. Moreover, defects in the conserved Notch/LIN-12 pathway are linked to human diseases. Here, we review models for two key steps in Notch/LIN-12 signaling: ligand-mediated activation of the receptor and receptor-mediated activation of transcription. Ligand binding appears to permit proteolysis of the receptor; as a result, the receptor's intracellular domain can enter the nucleus and function as a transcriptional ------------------- Key: 3228 Medline: 98384317 Authors: Tabuse Y;Izumi Y;Piano F;Kemphues KJ;Miwa J;Ohno S Title: Atypical protein kinase C cooperates with PAR-3 to establish embryonic polarity in Caenorhabditis elegans. Citation: Development 125: 3607-3614 1998 Type: ARTICLE Genes: par-2 par-3 par-5 par-6 pkc-3 tpa-1 Abstract: Asymmetric cell divisions, critically important to specify cell types in the development of multicellular organisms, require polarized distribution of cytoplasmic components and the proper alignment of the mitotic apparatus. In Caenorhabditis elegans, the maternally expressed protein, PAR-3, is localized to one pole of asymmetrically dividing blastomeres and is required for these asymmetric divisions. In this paper, we report that an atypical protein kinase C (PKC-3) is essential for proper asymmetric cell divisions and co-localizes with PAR-3. Embryos depleted of PKC-3 by RNA interference die showing Par-like phenotypes including defects in early asymmetric divisions and mislocalized germline-specific granules (P granules). The defective phenotypes of PKC-3-depleted embryos are similar to those exhibited by mutants for par-3 and another par gene, par-6. Direct interaction of PKC-3 with PAR-3 is shown by in vitro binding analysis. This result is reinforced by the observation that PKC-3 and PAR-3 co-localize in vivo. Furthermore, PKC-3 and PAR-3 show mutual dependence on each other and on three of the other par genes for their localization. We conclude that PKC-3 plays an indispensable role in establishing embryonic polarity through interaction with PAR-3. ------------------- Key: 3229 Medline: Authors: Bird DM;Opperman CH Title: Caenorhabditis elegans: A genetic guide to parasitic nematode biology. Citation: Journal of Nematology 30: 299-308 1998 Type: ARTICLE Genes: asp-1 asp-2 Abstract: The advent of parasite genome sequencing projects, as well as an increase in biology-directed gene discovery, promises to reveal genes encoding many of the key molecules required for nematode-host interactions. However, distinguishing parasitism genes from those merely required for nematode viability remains a substantial challenge. Although this will ultimately require a functional test in the host or parasite, the free-living nematode Caenorhabditis elegans can be exploited as a heterologous system to determine function of candidate parasitism genes. Studies of C. elegans also have revealed genetic networks, such as the dauer pathway, that may also be important adaptations for parasitism. As a more directed means of identifying parasitism traits, we developed classical genetics for Heterodera glycines and have used this approach to map genes conferring host resistance-breaking phenotypes. It is likely that the C. elegans and H. glycines genomes will be at least partially syntenic, thus permitting predictive physical mapping of H. glycines genes of interest. ------------------- Key: 3230 Medline: 98440631 Authors: Jayanthi LD;Apparsundaram S;Malone MD;Ward E;Miller DM;Eppler M;Blakely RD Title: The Caenorhabditis elegans gene T23G5.5 encodes an antidepressant- and cocaine-sensitive dopamine transporter. Citation: Molecular Pharmacology 54: 601-609 1998 Type: ARTICLE Genes: Abstract: A small subset of neurons in the nematode Caenorhabditis elegans utilizes the catecholamine dopamine (DA) as a neurotransmitter to control or modulate movement and egg-laying. Disruption of DA-mediated behaviors represents a potentially powerful strategy to identify genes that are likely to participate in dopaminergic systems in man. In vertebrates, extracellular DA is inactivated by presynaptic DA transport proteins (DATs) that are also major targets of addictive agents, including amphetamines and cocaine. We used oligonucleotides derived from the C. elegans genomic locus T23G5.5 to isolate and characterize T23G5.5 cDNAs. Our studies predict that mRNAs from this locus encode a 615-amino-acid polypeptide with twelve stretches of hydrophobicity suitable for transmembrane domains, similar to that found in vertebrate catecholamine transporters. The inferred translation product bears highest identity (43-47%) to catecholamine (DA, norepinephrine, epinephrine) transporters within the GAT1/NET gene family and possesses conserved residues implicated in amine substrate recognition. Consistent with these findings, HeLa cells transfected with the C. elegans cDNA exhibit saturable and high affinity DA transport (K-m = 1.2 mu M) that is dependent on extracellular Na+ and Cl- and blocked by inhibitors of mammalian catecholamine transporters, including norepinephrine transporter- and DAT-selective antagonists, tricyclic antidepressants, and the nonselective amine transporter antagonists cocaine and D-amphetamine. These studies validate the T23G5.5 locus as encoding a functional catecholamine transporter, providing important comparative sequence information for catecholamine transporter structure/function studies and a path to identify regulators of dopaminergic signaling via genetic or pharmacologic manipulation of C. elegans cDNA in ------------------- Key: 3231 Medline: 98384316 Authors: Levitan D Title: Effects of SEL-12 presenilin on LIN-12 localization and function in Caenorhabditis elegans. Citation: Development 125: 3599-3606 1998 Type: ARTICLE Genes: daf-1 daf-4 daf-7 daf-8 daf-14 egl-15 lam-1 let-23 lin-3 lin-12 lin-17 sma-6 unc-6 mnDp68 Abstract: Presenilins have been implicated in the development of Alzheimer's disease and in facilitating LIN-12/Notch activity. Here, we use genetic methods to explore the relationship between C. elegans LIN-12 and SEL-12 presenilin. Reducing sel-12 activity can suppress the effects of elevated lin-12 activity when LIN-12 is activated by missense mutations but not when LIN-12 is activated by removal of the extracellular and transmembrane domains. These results suggest that SEL-12 does not function downstream of activated LIN-12. An active SEL-12::GFP hybrid protein accumulates in the perinuclear region of the vulval precursor cells (VPCs) of living hermaphrodites, consistent with a localization in endoplasmic reticulum/Golgi membranes; when sel-12 activity is reduced, less LIN-12 protein accumulates in the plasma membranes of the VPCs. Together with the genetic interactions between lin-12 and sel-12, these observations suggest a role for SEL-12 in LIN-12 processing or trafficking. However, SEL-12 does not appear to be a general factor that influences membrane protein activity, since reducing sel-12 activity does not suppress or enhance hypomorphic mutations in other genes encoding membrane proteins. We discuss potential parallels for the role of SEL-12/presenilin in facilitating LIN-12/Notch activity and in amyloid precursor protein (APP) processing. ------------------- Key: 3232 Medline: 98437367 Authors: Britton C;McKerrow JH;Johnstone IL Title: Regulation of the Caenorhabditis elegans gut cysteine protease gene cpr-1: Requirement for GATA motifs. Citation: Journal of Molecular Biology 283: 15-27 1998 Type: ARTICLE Genes: cpr-1 cpr-3 cpr-4 cpr-5 cpr-6 gcp-1 glp-1 lin-4 lin-14 lin-28 lin-29 myo-2 pes-10 Abstract: Expression of the Caenorhabditis elegans cysteine protease gene cpr-1 is regulated both spatially and temporally. In situ hybridisation and Northern blot analysis have shown that this gene is expressed exclusively in gut cells of all developmental stages except the embryo. We now show by transgenic transformation with cpr-1/lac Z reporter gene constructs that a sequence contained within the cpr-1 5' flanking region can direct this spatial and temporal expression. Deletion analysis of the cpr-1 promoter indicates that as little as 212 bp of upstream sequence is sufficient for this expression, although more upstream sequence may be involved in quantitative regulation of expression. Mutation of two GATA-like sequence elements at positions -51 and -147 upstream of the transcription start site ablates all expression, indicating an essential role in cpr-l regulation. A concatemer of the cpr-1 -147 GATA motif placed upstream of minimal promoter/lac Z reporter gene constructs results in strong reporter gene expression in gut cells of larval stages and also in embryos. Weak expression is also detected in hypodermal cells. This pattern is reversed in the adult stage with strong expression in hypodermal cells and weaker expression in gut cells. Our findings suggest that spatial and temporal regulation of the cpr-1 gene is complex and involves activation by a GATA-like transcription factor. ------------------- Key: 3233 Medline: 98437350 Authors: Izumi Y;Hirose T;Tamai Y;Hirai S;Nagashima Y;Fujimoto T;Tabuse Y;Kemphues KJ;Ohno S Title: An atypical PKC directly associates and colocalizes at the epithelial tight junction with ASIP, a mammalian homologue of Caenorhabditis elegans polarity protein PAR-3. Citation: Journal of Cell Biology 143: 95-106 1998 Type: ARTICLE Genes: par-1 par-3 Abstract: Cell polarity is fundamental to differentiation and function of most cells. Studies in mammalian epithelial cells have revealed that the establishment and maintenance of cell polarity depends upon cell adhesion, signaling networks, the cytoskeleton, and protein transport. Atypical protein kinase C (PKC) isotypes PKC zeta and PKC lambda have been implicated in signaling through lipid metabolites including phosphatidylinositol 3-phosphates, but their physiological role remains elusive. In the present study we report the identification of a protein, ASIP (atypical PKC isotype-specific interacting protein), that binds to aPKCs, and show that it colocalizes with PKC lambda to the cell junctional complex in cultured epithelial MD CKII cells and rat intestinal epithelia. In addition, immunoelectron microscopy revealed that ASIP localizes to tight junctions in intestinal epithelial cells. Furthermore, ASIP shows significant sequence similarity to Caenorhabditis elegans PAR-3. PAR-3 protein is localized to the anterior periphery of the one-cell embryo, and is required for the establishment of cell polarity in early embryos. ASIP and PAR-3 share three PDZ domains, and can both bind to aPKCs. Taken together, our results suggest a role for a protein complex containing ASIP and aPKC in the establishment and/or maintenance of epithelial cell polarity. The evolutionary conservation of the protein complex and its asymmetric distribution in polarized cells from worm embryo to mammalian-differentiated cells may mean that the complex functions generally in the organization of cellular asymmetry. ------------------- Key: 3234 Medline: Authors: Culotti JG;Merz DC Title: DCC and netrins. Citation: Current Opinion in Cell Biology 10: 609-613 1998 Type: REVIEW Genes: seu-1 seu-2 seu-3 unc-5 unc-6 unc-34 unc-40 unc-44 unc-129 Abstract: Recent advances highlight the versatility and complexity of this highly conserved axon and cell migration guidance system. Characterization of netrin mutant phenotypes in worm, fly and mouse all suggest that netrins play local as well as long-range roles in guidance. Evidence from multiple sources also indicates that the netrin receptor DCC can mediate both attractive and repulsive responses to ------------------- Key: 3235 Medline: 98431933 Authors: Holtzman EJ;Kumar S;Faaland CA;Warner F;Logue PJ;Erickson SJ;Ricken G;Waldman J;Kumar S;Dunham PB Title: Cloning, characterization, and gene organization of K-Cl cotransporter from pig and human kidney and C. elegans. Citation: American Journal of Physiology - Renal Fluid & Electrolyte Physiology 44: F550-F564 1998 Type: ARTICLE Genes: Abstract: We isolated and characterized the cDNAs far the human, pig, and Caenorhabditis elegans K-CI cotransporters. The pig and human homologs are 94% identical and contain 1,085 and 1,086 amino acids, respectively. The deduced protein of the C. elegans K-CI cotransporter clone (CE-KCC1) contains 1,003 amino acids. The mammalian K-CI cotransporters share similar to 45% similarity with CE-KCC1. Hydropathy analyses of the three clones indicate typical KCC topology patterns with 12 transmembrane segments, large extracellular loops between transmembrane domains 5 and 6 (unique to KCC), and large COOH-terminal domains. Human KCC1 is widely expressed among various tissues. This KCC1 gene spans 23 kb and is organized in 24 exons, whereas the CE-KCC1 gene spans 3.5 kb and contains ID exons. Transiently and stably transfected human embryonic kidney cells (HEK-293) expressing the human, pig, and C. elegans K-Cl cotransporter fulfilled two (pig) or five (human and C. elegans) criteria for increased expression of the K-Cl cotransporter. The criteria employed were basal K-CI cotransport; stimulation of cotransport by swelling, N-ethylmaleimide, staurosporine, and reduced cell Mg concentration; and secondary stimulation of Na-K-CI ------------------- Key: 3236 Medline: Authors: Schaffner KF Title: Genes, behavior, and developmental emergentism: one process, indivisible? Citation: Philosophy of Science 65: 209-252 1998 Type: ARTICLE Genes: Abstract: The question of the influence of genes on behavior raises difficult philosophical and social issues. In this paper I delineate what I call the Developmentalist Challenge (DC) to assertions of genetic influence on behavior, and then examine the DC through an in-depth analysis of the behavioral genetics of the nematode, C. elegans, with some briefer references to work on Drosophila. I argue that eight ''rules'' relating genes and behavior through environmentally-influenced and tangled neural nets capture the results of developmental and behavioral studies on the nematode. Some elements of the DC are found to be sound and others are criticized. The essay concludes by examining the relations of this study to Kitcher's antireductionist arguments and Bechtel and Richardson's decomposition and localization heuristics. Some implications for human behavioral genetics are also briefly considered. ------------------- Key: 3237 Medline: Authors: Gilbert SF;Jorgensen EM Title: Wormwholes: A commentary on Schaffner, K.F. Genes, behavior, and developmental emergentism. Citation: Philosophy of Science 65: 259-266 1998 Type: ARTICLE Genes: odr-10 Abstract: Although Caenorhabditis elegans was chosen and modified to be an organism that would facilitate a reductionist program for neurogenetics, recent research has provided evidence for properties that are emergent from the neurons. While neurogenetic advances have been made using C. elegans which may be useful in explaining human neurobiology, there are severe limitations on C. elegans to explain any significant human behavior. ------------------- Key: 3238 Medline: Authors: Schaffner KF Title: Model organisms and behavioral genetics: A rejoinder. Citation: Philosophy of Science 65: 276-288 1998 Type: ARTICLE Genes: Abstract: In this rejoinder to the three preceding comments, I provide some additional philosophical warrant for the biomedical sciences' focus on model organisms. I then relate the inquiries on model systems to the concept of 'deep homology', and indicate that the issues that appear to divide my commentators and myself are in part empirical ones. I cite recent work on model organisms, and especially C. elegans that supports my views. Finally, I briefly readdress some of the issues raised by Developmental Systems Theory. ------------------- Key: 3239 Medline: 98402551 Authors: Maryon EB;Saari B;Anderson P Title: Muscle-specific functions of ryanodine receptor channels in Caenorhabditis elegans. Citation: Journal of Cell Science 111: 2885-2895 1998 Type: ARTICLE Genes: myo-3 unc-68 Abstract: Ryanodine receptor channels regulate contraction of striated muscle hy gating the release of calcium ions from the sarcoplasmic reticulum. Ryanodine receptors are expressed in excitable and non-excitable cells of numerous species, including the nematode C. elegans. Unlike vertebrates, which have at least three ryanodine receptor genes, C. elegans has a single gene encoded by the unc-68 locus. We show that unc-68 is expressed in most muscle cells, and that the phenotypic defects exhibited by unc-68 null mutants result from the loss of unc-68 function in pharyngeal and body-wall muscle cells. The loss of unc-68 function in the isthmus and terminal bulb muscles of the pharynx causes a reduction in growth rate and brood size. unc-68 null mutants exhibit defective pharyngeal pumping (feeding) and have abnormal vacuoles in the terminal bulb of the pharynx. unc-68 is required in body-wall muscle cells for normal motility. We show that UNC-68 is localized in body-wall muscle cells to flattened vesicular sacs positioned between the apical plasma membrane and the myofilament lattice. In unc-68 mutants, the vesicles are enlarged and densely stained. The flattened vesicles in body-wall muscle cells thus represent the C. elegans sarcoplasmic reticulum. Morphological and behavioral phenotypes of unc-68 mutants suggest that intracellular calcium release is not essential for excitation-contraction ------------------- Key: 3240 Medline: Authors: Winand NJ;Panzer JA;Kolodner RD Title: Cloning and characterization of the human and Caenorhabditis elegans homologs of the Saccharomyces Citation: Genomics 53: 69-80 1998 Type: ARTICLE Genes: Abstract: In Saccharomyces cerevisiae the MSH5 gene encoding a MutS homolog was identified as a gene required for meiotic crossing over. To understand the role of MSH5 in higher eukaryotes, we have identified both the human and the Caenorhabditis elegans MSH5 genes. The human and C. elegans MSH5 predicted amino acid sequences share, respectively, 25.3 and 22.0% identity with the S. cerevisiae MSH5 amino acid sequence. The human MSH5 gene consists of 25 exons and spans at least 12 kb of genomic DNA, while the C. elegans gene comprises 17 exons distributed over at least 5.8 kb. Radiation hybrid mapping studies indicate that the human gene is located at 6p22.3-p21.3. Northern blot analysis demonstrates that human MSH5 is expressed to some extent in all tissues, but that particularly high levels of expression occur in testis, thymus, and other tissues of the immune system. Two-hybrid interaction analysis demonstrates that the human MSH4 and MSH5 proteins interact as observed for S. cerevisiae MSH4 and MSH5. ------------------- Key: 3241 Medline: 98447643 Authors: Baset HA;Ford-Hutchinson AW;O'Neill GP Title: Molecular cloning and functional expression of a Caenorhabditis elegans aminopeptidase structurally related to mammalian leukotriene A(4) hydrolases. Citation: Journal of Biological Chemistry 273: 27978-27987 1998 Type: ARTICLE Genes: Abstract: In a search of the Caenorhabditis elegans DNA data base, an expressed sequence tag of 327 base pairs (termed cm0lc7) with strong homology to the human leukotriene A(4) (LTA(4)) hydrolase was found. The use of cm0lc7 as a probe, together with conventional hybridization screening and anchored polymerase chain reaction techniques resulted in the cloning of the full-length 2.1 kilobase pair C. elegans LTA(4) hydrolase-like homologue, termed aminopeptidase-1 (AP-1). The AP-1 cDNA was expressed transiently as an epitope-tagged recombinant protein in COS-7 mammalian cells, purified using an anti-epitope antibody affinity resin, and tested for LTA(4) hydrolase and aminopeptidase activities. Despite the strong homology between the human LTA(4) hydrolase and C. elegans AP-1(63% similarity and 45% identity at the amino acid level), reverse-phase high pressure liquid chromatography and radioimmunoassay for LTB4 production revealed the inability of the C. elegans AP-1 to use LTA(4) as a substrate. In contrast, the C. elegans AP-1 was an efficient aminopeptidase, as demonstrated by its ability to hydrolyze a variety of amino acid p-nitroanilide derivatives. The aminopeptidase activity of C, elegans AP-1 resembled that of the human LTA(4) hydrolase/aminopeptidase enzyme with a preference for arginyl-p-nitroanilide as a substrate. Hydrolysis of the amide bond of arginyl p-nitroanilide was inhibited by bestatin with an IC50 of 2.6 +/- 1.2 mu M. The bifunctionality of the mammalian LTA(4) hydrolase is still poorly understood, as the physiological substrate for its aminopeptidase activity is yet to be discovered. Our results support the idea that the enzyme originally functioned as an aminopeptidase in lower metazoa and then developed LTA(4) hydrolase activity in more evolved ------------------- Key: 3242 Medline: 98449787 Authors: Favre R;Cermola M;Nunes CP;Hermann R;Muller M;Bazzicalupo P Title: Immuno-cross-reactivity of CUT-1 and cuticlin epitopes between Ascaris lumbricoides, Caenorhabditis elegans, and Heterorhabditis. Citation: Journal of Structural Biology 123: 1-7 1998 Type: ARTICLE Genes: cut-1 cut-2 Abstract: Cuticlin is the insoluble residue of nematode cuticle. It has been proved that cuticlin and CUT-1-like epitopes are conserved between the free-living Caenorhabditis elegans and the entomopathogenic nematode Heterorhabditis sp. The cloning of a cut-1 homologous gene from the animal intestinal parasite Ascaris lumbricoides has allowed us to extend the study of immuno-cross-reactivity at the ultrastructural level to this important species. Antibodies against recombinant CUT-1 protein and against cuticlin from Ascaris as well as from C. elegans were used for immuno-labeling ultrathin sections of high-pressure cryoprocessed worms. All the antisera used showed the same specific pattern of localization on sections of C. elegans of Heterorhabditis dauer larvae, and of Ascaris larvae in mature eggs. It was also shown that sera raised against the cuticlin residue contain anti-CUT-1 antibodies. CUT-1-like proteins are thus possibly important components in the immune response of hosts to invading nematodes. The results presented support the use of C. elegans as a model for the study of vertebrate parasitic nematodes. ------------------- Key: 3243 Medline: 99005181 Authors: Wood WB Title: Aging of C. elegans - Mosaics and mechanisms. Citation: Cell 95: 147-150 1998 Type: REVIEW Genes: age-1 clk-1 daf-2 daf-16 daf-23 eat-2 Abstract: Many changes occur as an animal ages. To name a few, proteins become modified and cross-linked, somatic mutations accumulate, stress resistance decreases, and the probability of death increases. One reason for these changes is thought to be oxidative damage to macromolecules and lipid membranes, caused by superoxides and other free-radicals resulting from aerobic metabolism. In the somatic cells, this damage can be partially but never completely counteracted by mechanisms for elimination of free radicals as well as turnover and repair of ------------------- Key: 3244 Medline: 99005188 Authors: Apfeld J;Kenyon C Title: Cell nonautonomy of C. elgans DAF-2 function in the regulation of diapause and life span. Citation: Cell 95: 199-210 1998 Type: ARTICLE Genes: age-1 daf-2 daf-7 daf-12 daf-16 ncl-1 sDp3 Abstract: The insulin/IGF receptor homolog DAF-2 regulates the aging in C. elegans. Decreasing daf-2 activity causes fertile adults to remain active much longer than normal and to live more than twice as long. A more severe decrease in daf-2 function causes young larvae to enter a state of diapause rather than progressing to adulthood. We have asked which cells require daf-2 gene activity in order for the animal to develop to adulthood and to age normally. We found that daf-a functions cell nonautonomously in both processes. Our findings imply that the life span of C. elegans is determined by a signaling cascade in which the DAF-2 receptor acts in multiple cell lineages to regulate the production or activity of a secondary signal (or signals), which, in turn, controls the growth and longevity of individual tissues in the animal. ------------------- Key: 3245 Medline: Authors: Walhout M;Endoh H;Thierry-Mieg N;Wong W;Vidal M Title: Insights from model systems: A model of elegance. Citation: American Journal of Human Genetics 63: 955-961 1998 Type: ARTICLE Genes: Abstract: Since Sydney Brenner wrote this statement in a visionary research proposal addressed to Max Perutz 35 years ago, an enormous amount of information has been gathered on the biology of the nematode Caenorhabditis elegans ("the worm"), both fulfilling his predictions and exceeding his original expectations. Researchers have identified every cell in the worm and have described all the lineages by which these cells are formed... ------------------- Key: 3247 Medline: Authors: Gregory SG;Soderlund CA;Coulson A Title: Contig assembly by fingerprinting. Citation: "Practical Approach Series, 184. Genome Mapping." Oxford University Press, Oxford, England. : 227-254 1997 Type: REVIEW Genes: Abstract: A previous chapter in this series (1) described, primarily, the physical mapping of the 100 Mb Caenorhabditis elegans genome by fingerprinting of cosmid clones, and the linking of the contigs thus derived by YAC hybridization. At that time, the primary function of the map was to enhance the molecular genetics of the organism by facilitating the cloning of known genes, and to serve as an archive for genomic information. However, a clonal physical map - even with good alignment to the genetic map - carries only a tiny proportion of the information present in the genome. Consequently, the current objective of the C. elegans genome project (2) is to establish of the entire genomic sequence. The bacterial clone map, although incomplete by virtue of the uncloneability of regions of the genome in cosmid vectors (a factor which we shall discuss later in this chapter), has proved a sound basis for the systematic sequence analysis. The sevenfold cosmid coverage has a resolution sufficient to enable the selection of a subset of cosmids for sequencing such that, on average, each clone contributes 30 kb of unique sequence to the whole. Sequencing projects based on bacterial clone maps (3-5) of a number of other genomes of a range of sizes are also well advanced, in particular Saccharomyces cerevisiae (15 Mb; complete), Schizosaccharomyces pombe (15Mb), and Drosohpila melanogaster (150 Mb). Although it has recently been demonstrated that small bacterial genomes can be sequenced by direct shotgun sequence analysis of the entire genome with no prior mapping (6), the ability to interrelate and map clone sets, whether derived by random selection of in a directed manner, is still the most convenient route to the sequence analysis of larger genomes. ------------------- Key: 3248 Medline: 98301764 Authors: Ebrahimi FAW;Chess A Title: Olfactory G proteins: Simple and complex signal transduction. Citation: Current Biology 8: R431-R433 1998 Type: REVIEW Genes: odr-3 Abstract: In both vertebrates and invertebrates, olfactory perception is mediated by G-protein-coupled receptors. Recent work, in both mouse and Caenorhabditis elegans, sheds light on the role of specific G proteins in olfactory signal transduction, neuronal morphology and axon guidance. ------------------- Key: 3249 Medline: Authors: Lannoy VJ;Burglin TR;Rousseau GG;Lemaigre FP Title: Isoformsof hepatocyte nuclear factor-6 differ in DNA-binding properties, contain a bifunctional homeodomain, and define the new ONECUT class of homeodomain proteins. Citation: Journal of Biological Chemistry 273: 13552-13562 1998 Type: ARTICLE Genes: ceh-21 ceh-38 ceh-39 Abstract: Hepatocyte nuclear factor-6 (HNF-6) contains a single cut domain and a homeodomain characterized by a phenylalanine at position 48 and a methionine at position 50. We describe here two isoforms of HNF-6 which differ by the linker that separates these domains. Both isoforms stimulated transcription. The affinity of HNF-6 alpha and HNF-6 beta for DNA differed, depending on the target sequence. Binding of HNF-6 to DNA involved the cut domain and the homeodomain, but the latter was not required for binding to a subset of sites. Mutations of the F48M50 dyad that did not affect DNA binding reduced the transcriptional stimulation of constructs that do not require the homeodomain for DNA binding, but did not affect the stimulation of constructs that do require the homeodomain, Comparative trees of mammalian, Drosophila, and Caenorhabditis elegans proteins showed that HNF-6 defines a new class, which we call ONECUT, of homeodomain proteins. C. elegans proteins of this class bound to HNF-6 DNA targets. Thus, depending on their sequence, these targets determine for HNF-6 at least two modes of DNA binding, which hinge on the homeodomain and on the linker that separates it from the cut domain, and two modes of transcriptional stimulation, which hinge on the ------------------- Key: 3250 Medline: Authors: Zhou GT;Schafer WR;Schafer RW Title: A three-state biological point process model and its parameter estimation. Citation: IEEE Transactions on Signal Processing 46: 2698-2707 1998 Type: ARTICLE Genes: Abstract: The Poisson random process is widely used to describe experiments involving discrete arrival data. However, for creating models of egg-laying behavior in recent neural biology studies on the nematode C. elegans, we have found that homogeneous Poisson processes are inadequate to capture the measured temporal patterns. We present here a novel three-state model that effectively represents the measured temporal patterns and that correlates well with the cellular and molecular mechanisms that are known to be responsible for the measured behavior. Although the model involves a combination of two Poisson processes, it is surprisingly tractable. We derive closed-form expressions for the probabilistic and statistical properties of the model and present a maximum likelihood method to estimate its parameters. Both simulated and experimental results are illustrated. The experiments with measured data show that the egg-laying patterns fit the three-state model very well. The model also may be applicable in quantifying the link between other neural processes and behaviors or in other situations where discrete events occur in clusters. ------------------- Key: 3251 Medline: 98399912 Authors: Sommer RJ;Eizinger A;Lee KZ;Jungblut B;Bubeck A;Schlak I Title: The Pristionchus Hox gene Ppa-lin-39 inhibits programmed cell death to specify the vulva equivalence group and is not required during vulval induction. Citation: Development 125: 3865-3873 1998 Type: ARTICLE Genes: ced-3 ced-4 lin-39 Abstract: In the two nematode species Caenorhabditis elegans and Pristionchus pacificus the vulva equivalence group in the central body region is specified by the Hox gene lin-39. C. elegans lin-39 mutants are vulvaless and the vulval precursor cells fuse with the surrounding hypodermis, whereas in P. pacificus lin-39 mutants the vulval precursor cells die by apoptosis. Mechanistically, LIN-39 might inhibit non-vulval fate (cell fusion in C. elegans, apoptosis in P. pacificus), promote vulval fate or do both. To study the mechanism of lin-39 function, we isolated P. pacificus cell death mutants and identified mutations in ced-3. Surprisingly, P. pacificus ced-3; lin-39 double mutants farm a functional vulva in the absence of LIN-39 activity. Thus, in P. pacificus lin-39 specifies the vulva equivalence group by inhibiting programmed cell death. Furthermore, these data reveal an important difference in a later function of lin-39 between the two species. In C. elegans, LIN-39 specifies vulval cell fates in response to inductive RAS signaling, and in P. pacificus LIN-39 is not required for vulval induction. Thus, the comparative analysis indicates that lin-39 has distinct functions in both species although the gene is acting in a homologous developmental system. ------------------- Key: 3252 Medline: 99020255 Authors: Page AP;Winter AD Title: A divergent multi-domain cyclophilin is highly conserved between parasitic and free-living nematode species and is important in larval muscle development. Citation: Molecular & Biochemical Parasitology 95: 215-227 1998 Type: ARTICLE Genes: ama-1 cyp-4 Abstract: A divergent multi-domain cyclophilin from the filarial nematodes Brugia malayi, Onchocerca volvulus and Dirofilaria immitis has a highly conserved orthologue in the free-living nematodes Caenorhabditis elegans and C. briggsae. Cyclophilins are the receptors for the immunosuppressive and anti-parasitic agent cyclosporin A and additionally these ubiquitously expressed proteins have protein folding capabilities, and exhibit proline isomerase activity. These divergent nematode cyclophilins (CYP-4 isoforms) are three domain proteins, which share 63-88% identity and have highly conserved differences present in their functionally important cyclosporin A binding and proline isomerase domains. This unusual class of nematode cyclophilins has been studied in the model nematode C. elegans, revealing a unique temporal and spatial expression pattern. The cyp-4 transcript is most abundantly expressed in the early larval stages and is expressed exclusively in the body-wall striated muscle cells. An important functional role was established for this divergent enzyme, as specific double-stranded RNA interference experiments resulted in progeny with a phenotypically lumpy appearance. This morphological defect was predominantly expressed in the early larval stages and is consistent with an effect on body-wall muscle cell development. This study has established that this highly conserved family of nematode cyclophilins has a tissue-specific, functional role in early larval development and supports the use of C. elegans as a model for the study of orthologues in the experimentally less amenable parasitic nematodes. ------------------- Key: 3253 Medline: 99038805 Authors: LaMunyon CW;Ward S Title: Larger sperm outcompete smaller sperm in the nematode Caenorhabditis elegans. Citation: Proceedings of the Royal Society of London B 265: 1997-2002 1998 Type: ARTICLE Genes: dpy-20 him-5 spe-8 spe-12 Abstract: Sperm competition is generally thought to drive the evolution of sperm miniaturization. Males gain advantage by transferring more sperm, which they produce by dividing limited resources into ever smaller cells. Here, we describe the opposite effect of size on the competitiveness of amoeboid sperm in the hermaphroditic nematode Caenorhabditis elegans. Larger sperm crawled faster and displaced smaller sperm, taking precedence at fertilization. Larger sperm took longer to produce, however, and so were more costly than smaller sperm. Our results provide evidence of a mechanism to support recent theoretical and comparative studies that suggest sperm competition can favour not small, but large sperm. ------------------- Key: 3254 Medline: 99439544 Authors: Power RS;David HE;Mutwakil MHAZ;Fletcher K;Daniells C;Nowell MA;Dennis JL;Martinelli A;Wiseman R;Wharf E;de Title: Stress-inducible transgenic nematodes as biomonitors of soil and water pollution. Citation: Journal of Biosciences 23: 513-526 1998 Type: ARTICLE Genes: Abstract: This paper reviews the current status of nematodes with stress-inducible transgenes as biosensors responsive a range of external stressors, e.g., soil or water pollution, microwave radiation or immunological attack. Transgenic Caenorhabditis elegans carrying reporter genes under heat shock promoter control express reporter products only under stressful conditions. Although relatively insensitive to single metal ions, these worms respond to complex mixtures present in metal-contaminated watercourses and to laboratory mixtures containing similar constituents, but not to any of their components singly at comparable concentrations. Responses to metal mixtures are enhanced by a non-ionic surfactant, Pluronic F-127. Metals taken up by food bacteria and insoluble metal carbonates can also evoke stress responses, both in soil and aqueous media. However, high concentrations of added metals are needed to induce clear-cut responses in soil, owing to metal sorption onto clays and organic matter. Transgenic worms are also stressed by exposure to microwave radiation; pulsed signals generate responses that diminish markedly with distance from the source. Finally, stress responses are inducible by anti-epicuticle antisera and complement, suggesting that immune attack can also activate the heat shock system. The development of rapid microplate toxicity assays based on transgenic nematodes is discussed. ------------------- Key: 3255 Medline: Authors: Mohler WA;White JG Title: Multiphoton laser scanning microscopy for four-dimensional analysis of Caenorhabditis elegans embryonic development. Citation: Optics Express 3: 325-331 1998 Type: ARTICLE Genes: Abstract: Multiphoton laser scanning microscopy (MPLSM) enables the production of long timelapse recordings from live fluorescent specimens. 1047- and 900-nm excitation were used to image both a vital fluorescent membrane probe, FM 4-64, and a modified green fluorescent protein (GFP) in live Caenorhabditis elegans embryos. Automated four-dimensional (4D) data collection yielded individual recordings comprising thousands of images, each allowing analysis of all of the cell divisions, contacts, migrations, and fusions that occur during a span of several ------------------- Key: 3256 Medline: 99037465 Authors: Metzstein MM;Stanfield GM;Horvitz HR Title: Genetics of programmed cell death in C. elegans: past, present and future. Citation: Trends in Genetics 14: 410-416 1998 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-9 ced-10 ces-1 ces-2 egl-1 nuc-1 Abstract: Genetic studies of the nematode Caenorhabditis elegans hale defined a variety of single-gene mutations that have specific effects on programmed cell death. Analyses of the genes defined by these mutations have revealed that cell death is an active process that requires gene function in cells that die. Specific genes are required not only to cause cell death but also to protect cells from dying. Gene interaction studies have defined a genetic pathway for the execution phase of programmed cell death in C. elegans. Molecular and biochemical findings are consistent with the pathway proposed from these genetic studies and have also revealed that the protein products of certain cell-death genes interact directly. This pathway appears to be conserved among organisms ns diverse as nematodes and humans. Important questions remain to be answered about programmed cell cell death in C. elegans. For example, how does a cell decide to die? How is cell death initiated? What are the mechanisms of action of the cell-death protector and killer genes? What genes lie downstream of the cell-death execution pathway? The conservation of the central cell-death pathway suggests that additional genetic analyses of programmed cell death in C. elegans will help answer these questions, not only for this nematode but also for other organisms, including ourselves. ------------------- Key: 3257 Medline: 99007272 Authors: Lakowski B;Hekimi S Title: The genetics of caloric restriction in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 95: 13091-13096 1998 Type: ARTICLE Genes: age-1 clk-1 clk-2 clk-3 daf-2 daf-16 daf-28 eat-1 eat-2 eat-3 eat-5 eat-6 eat-7 eat-10 eat-12 eat-13 eat-18 egl-19 gro-1 unc-2 unc-10 unc-11 unc-15 unc-17 unc-18 unc-20 unc-24 unc-25 unc-26 unc-30 unc-32 unc-36 unc-37 unc-46 unc-47 unc-54 unc-57 unc-75 unc-78 unc-79 unc-80 unc-104 Abstract: Low caloric intake (caloric restriction) can lengthen the life span of a wide range of animals and possibly even of humans. To understand better how caloric restriction lengthens life span, we used genetic methods and criteria to investigate its mechanism of action in the nematode Caenorhabditis elegans. Mutations in many genes (eat genes) result in partial starvation of the worm by disrupting the function of the pharynx, the feeding organ. We found that most eat mutations significantly lengthen life span (by up to 50%). In C. elegans, mutations in a number of other genes that can extend life span have been found. Two genetically distinct mechanisms of life span extension are known: a mechanism involving genes that regulate dauer formation (age-1, daf-2, daf-Id, and daf-28) and a mechanism involving genes that affect the rate of development and behavior (clk-1, clk-2, clk-3, and gro-1). We find that the long life of eat-2 mutants does not require the activity of DAF-16 and that eat-2; daf-2 double mutants live even longer than extremely long-lived daf-2 mutants. These findings demonstrate that food restriction lengthens life span by a mechanism distinct from that of dauer-formation mutants. In contrast, we find that food restriction does not further increase the life span of long-lived clk-1 mutants, suggesting that clk-1 and caloric restriction affect similar processes. ------------------- Key: 3258 Medline: 99016085 Authors: Adames KA;Gawne J;Wicky C;Muller F;Rose AM Title: Mapping a telomere using the translocation eT1(III;V) in Caenorhabditis elegans. Citation: Genetics 150: 1059-1066 1998 Type: ARTICLE Genes: bli-4 dpy-18 sup-5 unc-46 unc-60 eT1 hT1 Abstract: In Caenorhabditis elegans, individuals heterozygous for a reciprocal translocation produce reduced numbers of viable progeny. The proposed explanation is that the segregational pattern generates aneuploid progeny. In this article, we have examined the genotype of arrested embryonic classes. Using appropriate primers in PCR amplifications, we identified one class of arrested embryo, which could be readily recognized by its distinctive spot phenotype. The corresponding aneuploid genotype was expected to he lacking the left portion of chromosome V, from the eT1 breakpoint to the left (unc-60) end. The phenotype of the homozygotes lacking this DNA was a stage 2 embryonic arrest with a dark spot coinciding with the location in wild-type embryos of birefringent gut granules. Unlike induced events, this deletion results from meiotic segregation patterns, eliminating complexity associated with unknown material that may have been added to the end of a broken chromosome. We have used the arrested embryos, lacking chromosome V left sequences, to map a telomere probe. Unique sequences adjacent to the telomeric repeats in the clone cTel3 were missing in the arrested spot embryo. The result was confirmed by examining aneuploid segregants from a second translocation, hT1(I;V). Thus, we concluded that the telomere represented by clone cTel3 maps to the left end of chromosome V. In this analysis, we have shown that reciprocal translocations can be used to generate segregational aneuploids. These aneuploids are deleted for terminal sequences at the noncrossover ends of the C. elegans autosomes. ------------------- Key: 3259 Medline: 99016086 Authors: Rushforth AM;White CC;Anderson P Title: Functions of the Caenorhabditis elegans regulatory myosin light-chain genes mlc-1 and mlc-2. Citation: Genetics 150: 1067-1077 1998 Type: ARTICLE Genes: mlc-1 mlc-2 mut-2 sdc-3 sup-10 mnDp1 Abstract: Caenorhabditis elegans contains two muscle regulatory myosin light chain genes, mlc-1 and mlc-2. To determine their in vivo roles, we identified deletions that eliminate each gene individually and both genes in combination. Functions of mlc-1 are redundant to those of mlc-2 in both body-wall and pharyngeal muscle. mlc-1(0) mutants are wild type, but mlc-1(0) mlc-2(0) double mutants arrest as incompletely elongated L1 larvae, having both pharyngeal and body-wall muscle defects. Transgenic copies of either mlc-1(+) or mlc-2(+) rescue all defects of mlc-1(0) mlc-2(0) double mutants, mlc-2 is redundant to mlc-1 in body-wall muscle, but mlc-2 performs a nearly essential role in the pharynx. Approximately 90% of mlc-2(0) hermaphrodites arrest as L1 larvae due to pharyngeal muscle defects. Lethality of mlc-2(0) mutants is sex specific, with mlc-2(0) males being essentially wild type. Four observations suggest that hermaphrodite-specific lethality of mlc-2(0) mutants results from insufficient expression of the X-linked mlc-1(+) gene in the pharynx. First, mlc-1(0) mlc-2(0) double mutants are fully penetrant L1 lethals in both hermaphrodites and males. Second, in situ localization of mlc mRNAs demonstrates that both mlc-1 and mk-2 are expressed in the pharynx. Third, transgenic copies of either mlc-1(+) or mlc-2(+) rescue the pharyngeal defects of mlc-1(0) mlc-2(0) hermaphrodites. Fourth, a mutation of the dosage compensation gene sdc-3 suppresses hermaphrodite-specific lethality of mlc-2(0) mutants. ------------------- Key: 3260 Medline: 98400798 Authors: Walker GA;Walker DW;Lithgow GJ Title: A relationship between thermotolerance and longevity in Caenorhabditis elegans. Citation: Journal of Investigative Dermatology 3: 6-10 1998 Type: ARTICLE Genes: age-1 clk-1 clk-2 clk-3 daf-2 daf-12 daf-16 daf-28 gro-1 spe-26 Abstract: Studies of aging in the nematode Caenorhabditis elegans have revealed a relationship between stress resistance and the rate of aging: Mutations which extend mean and maximum life-span also confer resistance to thermal stress. We review the molecular genetics of aging in C. elegans and introduce methods for obtaining novel mutants which display altered aging rates. We present the use of the "surrogate" phenotype of thermotolerance to develop a selection for novel mutations which slow aging. ------------------- Key: 3261 Medline: Authors: Sternberg PW;Alberola-Ila J Title: Conspiracy theory: RAS and RAF do not act alone. Citation: Cell 95: 447-450 1998 Type: REVIEW Genes: ksr-1 mek-1 sem-5 soc-2 sur-8 Abstract: In the early 1990s, genetic analysis in Drosophila melanogaster and C. elegans helped define a signaling pathway from cell surface receptors to the nucleus. Cel surface receptors with intrinsic tyrosine kinase activity (receptor tyrosine kinases or RTKs) respond to peptide ligands, growth factors, and inductive signals in development. Activation of RTKs often leads to activation of RAS, which in its GTP-bound state activates effectors, the proteins that exert its biological effect. The identification of SOS (Son of sevenless) as a guanine nucleotide exchange factor of RAS, and the adaptor protein GRB2 (in mammals)/SEM-5(in C. elegans)/DRK(in Drosophila), coupled with the finding that these two proteins act downstream of RTKs and upstream of RAS, allowed the biochemical linking of RTKs to RAS activation... ------------------- Key: 3262 Medline: 99039502 Authors: Carmi I;Kopczynski JB;Meyer BJ Title: The nuclear hormone receptor SEX-1 is an X-chromosome signal that determines nematode sex. Citation: Nature 396: 168-173 1998 Type: ARTICLE Genes: fox-1 sex-1 xol-1 nDf19 stDp2 Abstract: Organisms in many phyla determine sexual fate by distinguishing one X chromosome from two. Here we use the model organism Caenorhabditis elegans to dissect such an X-chromosome-counting mechanism in molecular detail. In this nematode, several genes on the X chromosome called X signal elements communicate X-chromosome dose by controlling the activity of the sex-determination gene xol-1 (refs 1, 2), xol-1 specifies male (XO) fate when active and hermaphrodite (XX) fate when inactive(3,4). The only X signal element described so far represses xol-1 post-transcriptionally, but xol-1 is repressed in XX animals by transcriptional and post-transcriptional mechanisms(2). Here we identify a nuclear-hormone-receptor homologue, SEX-1, that regulates the transcription of xol-1. We show that sex-1 is vital to X-chromosome counting: changing sex-1 gene dose in XX or XO embryos causes sexual transformation and death from inadequate dosage compensation (the hermaphrodite-specific process that equalizes X-gene expression between the sexes(5)). The SEX-1 protein acts directly on xol-1, associating with its promoter in vivo and repressing xol-1 transcription in XX embryos. Thus, xol-1 is the direct molecular target of the primary sex-determination signal, and the dose of a nuclear hormone receptor helps to communicate X-chromosome number ------------------- Key: 3263 Medline: 99039493 Authors: Swain A;Lovell-Badge R Title: Too much sex is bad for males. Citation: Nature 396: 115-117 1998 Type: REVIEW Genes: fox-1 sex-1 xol-1 Abstract: Many species rely on chromosome-based systems-such as one X versus two X chromosomes-to trigger the differences between males and females. To do this they must find ways to count the sex chromosomes and to activate the process of dosage compensation, which corrects the imbalance of sex-linked genes. A paper by Carmi, Kopczynski and Meyer on page 168 of this issue brings us closer to understand chromosome counting in the nematode worm Caenorhabditis elegans. The authors have identified an X-linked gene that encodes a protein related to nuclear-hormone receptors. This protein, SEX-1, represses the transcription of xol-1, the pivotal gene involved in both dosage compensation and sex determination. ------------------- Key: 3264 Medline: 99019563 Authors: Timmons L;Fire A Title: Specific interference by ingested dsRNA. Citation: Nature 395: 854- 1998 Type: ARTICLE Genes: fem-1 unc-22 Abstract: A genetic interference phenomenon in the nematode Caenorhabditis elegans has been described in which expression of an individual gene can be specifically reduced by microinjecting a corresponding fragment of double-stranded (ds) RNA. One striking feature of this process is a spreading effect: intereference in a broad region of the animal is observed following the injection of dsRNA into the extracellular body cavity. Here we show that C. elegans can respond in a gene-specific manner to dsRNA encountered in the environment. C. elegans normally feed on bacteria, ingesting and grinding them in the pharynx and subsequently absorbing bacterial contents in the gut. We find that Escherichia coli bacteria expressing dsRNA can confer specific interference effects on the nematode larvae that fed on them. ------------------- Key: 3265 Medline: 98407966 Authors: Duggan A;Ma C;Chalfie M Title: Regulation of touch receptor differentiation by the Caenorhabditis elegans mec-3 and unc-86 genes. Citation: Development 125: 4107-4119 1998 Type: ARTICLE Genes: mec-3 mec-4 mec-7 unc-86 Abstract: The nematode Caenorhabditis elegans possesses six morphologically similar neurons that are responsible for sensing gentle touch to the body. Previous genetic studies identified genes that are necessary for the production and differentiation of these touch cells. In particular, unc-86 encodes a POU-type homeodomain protein needed for the production of the touch cells, while mec-3 encodes a LIM-type homeodomain protein needed for the differentiation of the touch cells. Molecular studies showed that MEC-3 and UNC-86 bind cooperatively to sites in the mec-3 promoter and can synergistically activate transcription from it in vitro. Here we show that UNC-86::MEC-3 hetero-oligomer-binding sites are also found in the promoters of two presumed targets of mec-3, the mec-4 and mec-7 genes, that are necessary for the function of the touch cells. These sites, which are well-conserved in the related nematode C. briggsae, are required for promoter activity. When one of the binding sites is cloned into a heterologous promoter, expression is found in the touch cells and two to four other cells that express mec-3 and unc-86. These data support a model in which touch-cell differentiation is specified, in part, by the UNC-86::MEC-3 hetero-oligomer and not by MEC-3 alone. Ectopic expression of mec-3, driven by a heat-shock promoter, also supports this hypothesis: the acquisition of touch-cell characteristics by several additional cells under these conditions required unc-86. Since the touch-cell lineages express UNC-86 before MEC-3, MEC-3 appears to modify the activity of UNC-86, leading to touch-cell-specific gene expression. Because both UNC-86 and MEC-3 have activation domains, the formation of the hetero-oligomer may create a strong activator. In the modification of UNC-86 function by MEC-3 in the touch cells, these studies provide an example of how the sequential activation of transcription factors can determine cell fate within particular cell lineages. ------------------- Key: 3266 Medline: Authors: Eddy SR Title: Multiple-alignment and -sequence searches. Citation: Trends Guide to Bioinformatics Supp: 15-18 1998 Type: REVIEW Genes: Abstract: Comparisons of multiple sequences can reveal gene functions that are not clear from simple sequence homologies. The important parameters in multiple alignment and multiple-sequence-based searches, using an example from Caenorhabditis elegans are described. ------------------- Key: 3267 Medline: 98430518 Authors: Mitchell A Title: Behavioral genetics. Worming out social secrets. Citation: Nature 395: 327- 1998 Type: REVIEW Genes: flp-1 npr-1 Abstract: Some species of the nematode worm (Caenorhabditis elegans) are sociable diners, clumping together to share a meal, yet others are more solitary. Why? According to a report by de Bono and Bargmann, these differences can be explained by a change of just one amino acid in a putative neuropeptide receptor. ------------------- Key: 3268 Medline: 98400253 Authors: Bashir R;Britton S;Strachan T;Keers S;Vafiadaki E;Lako M;Richard I;Marchand S;Bourg N;Argov Z;Sadeh M;Mahjneh I;Marconi G;Passos-Bueno MR;Moreira E de S;Zatz M;Beckmann JS;Bushby K Title: A gene related to Caenorhabditis elegans spermatogenesis factor fer-1 is mutated in limb-girdle muscular dystrophy type 2B. Citation: Nature Genetics 20: 37-42 1998 Type: ARTICLE Genes: fer-1 Abstract: The limb-girdle muscular dystrophies are a genetically heterogeneous group of inherited progressive muscle disorders that affect mainly the proximal musculature, with evidence for at least three autosomal dominant and eight autosomal recessive loci. The latter mostly involve mutations in genes encoding components of the dystrophin-associated complex; another form is caused by mutations in the gene for the muscle-specific protease calpain 3. Using a positional cloning approach, we have identified the gene for a form of limb-girdle muscular dystrophy that we previously mapped to chromosome 2p13 (LGMD2B). This gene shows no homology to any known mammalian gene, but its predicted product is related to the C. elegans spermatogenesis factor fer-1. We have identified two homozygous frameshift mutations in this gene, resulting in muscular dystrophy of either proximal or distal onset in nine families. The proposed name 'dysferlin' combines the role of the gene in producing muscular dystrophy with its C. elegans homology. ------------------- Key: 3269 Medline: 98406128 Authors: Ouyang YB;Moore KL Title: Molecular cloning and expression of human and mouse tyrosylprotein sulfotransferase-2 and a tyrosylprotein sulfotransferase homologue in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 273: 24770-24774 1998 Type: ARTICLE Genes: Abstract: Tyrosine O-sulfation, a common post-translational modification in eukaryotes, is mediated by Golgi enzymes that catalyze the transfer of the sulfuryl group from 3'-phosphoadenosine 5'-phosphosulfate to tyrosine residues in polypeptides. We recently isolated cDNAs encoding human and mouse tyrosylprotein sulfotransferase-1 (Ouyang, Y. B., Lane, W. S., and Moore, K. L. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 2896-2901). Here we report the isolation of cDNAs encoding a second tyrosylprotein sulfotransferase (TPST), designated TPST-2. The human and mouse TPST-2 cDNAs predict type II transmembrane proteins of 377 and 376 amino acid residues, respectively. The cDNAs encode functional N-glycosylated enzymes when expressed in mammalian cells. In addition, preliminary analysis indicates that TPST-1 and TPST-2 have distinct specificities toward peptide substrates. The human TPST-2 gene is on chromosome 22q12.1, and the mouse gene is in the central region of chromosome 5. We have also identified a cDNA that encodes a TPST in the nematode Caenorhabditis elegans that maps to the right arm of chromosome III. Thus, we have identified two new members of a class of membrane-bound sulfotransferases that catalyze tyrosine O-sulfation. These enzymes may catalyze tyrosine O-sulfation of a variety of protein substrates involved in diverse physiologic functions. ------------------- Key: 3270 Medline: 98406126 Authors: Fiermonte G;Palmieri L;Dolce V;Lasorsa FM;Palmieri F;Runswick MJ;Walker JE Title: The sequence, bacterial expression, and functional reconstitution of the rat mitochondrial dicarboxylate transporter cloned via distant homologs in yeast and Caenorhabditis elegans Citation: Journal of Biological Chemistry 273: 24754-24759 1998 Type: ARTICLE Genes: Abstract: he dicarboxylate carrier (DIC) belongs to a family of transport proteins found in the inner mitochondrial membranes. The biochemical properties of the mammalian protein have been characterized, but the protein is not abundant. It is difficult to purify and had not been sequenced. We have used the sequence of the distantly related yeast DIC to identify a related protein encoded in the genome of Caenorhabditis elegans. Then, related murine expressed sequence tags were identified with the worm sequence, and the murine sequence was used to isolate the cDNA for the rat homolog. The sequences of the worm and rat proteins have features characteristic of the family of mitochondrial transport proteins. Both proteins were expressed in bacteria and reconstituted into phospholipid vesicles where their transport characteristics closely resembled those of whole rat mitochondria and of the rat DIC reconstituted into vesicles. As expected from the role of the DIC in gluconeogenesis and ureogenesis, its transcripts were detected in rat liver and kidney, but unexpectedly, they were also detected in rat heart and brain tissues where the protein may fulfill other roles, possibly in supplying substrates to the Krebs cycle. ------------------- Key: 3271 Medline: 99016053 Authors: Gallegos M;Ahringer J;Crittenden S;Kimble J Title: Repression by the 3' UTR of fem-3, a sex-determining gene, relies on a ubiquitous mog-dependent control in Caenorhabditis elegans. Citation: EMBO Journal 17: 6337-6347 1998 Type: ARTICLE Genes: fem-3 fog-1 gld-1 glp-1 glp-4 lag-2 mog-1 mog-2 mog-3 mog-4 mog-5 mog-6 tra-2 unc-17 Abstract: The fem-3 sex-determining gene is repressed post-transcriptionally via a regulatory element in its 3' untranslated region (UTR) to achieve the switch from spermatogenesis to oogenesis in the Caenorhabditis elegans hermaphrodite germ line. In this paper, we investigate the fem-3 3' UTR control in somatic tissues using transgenic reporter assays, and we also identify six genes essential for this control. First, we find that a reporter transgene bearing a wild-type fem-3 3' UTR is repressed in somatic tissues, whereas one bearing a mutant fem-3 3' UTR is derepressed, Moreover, control by mutant 3' UTRs is temperature sensitive as predicted from the temperature sensitivity of the fem-3 gain-of-function (gf) mutations. Secondly, we find a fem-3 3' UTR RNA-binding activity in somatic tissues, in addition to the previously reported germline-specific binding by FBF. Thirdly, we find that each of six genes, mog-1-mog-6, is required for repression by the fem-3 3' UTR. Therefore, the mog genes not only affect the sperm/oocyte switch in the germ line, but also function in somatic tissues. We suggest that the mog genes may encode components of a ubiquitous machinery that is used for fem-3 3' UTR-mediated repression and the ------------------- Key: 3272 Medline: 99016219 Authors: Dolinski C;Borgonie G;Schnabel R;Baldwin JG Title: Buccal capsule development as a consideration for phylogenetic analysis of Rhabditida (Nemata). Citation: Development Genes & Evolution 208: 495-503 1998 Type: ARTICLE Genes: Abstract: Bacterial feeding nematodes in the order Rhabditida including Zeldia punctata (Cephalobidae) and Caenorhabditis elegans (Rhabditidae) differ profoundly in the buccal capsule parts and associated cells. We carried out a range of tests to determine which buccal capsule parts and cells are evolutionarily homologous between the representative species of the two families. Tests included reconstruction of the buccal capsule and procorpus with transmission electron microscopy (TEM), nuclei position and morphology using 4,6-diamidino-2phenylindole (DAPI) staining, and cell lineage using four dimensional (4D) microscopy. The lining of the buccal capsule of Z. punctata and additional Cephalobidae includes four sets of muscular radial cells, ma, mb, me and md, in contrast to C. elegans and additional Rhabditidae, which has two sets of epithelial cells (el, e3) and two sets of muscle cells (ml, m2). Cell lineage of a nematode closely related to Z. punctata, Cephalobus cubaensis, supports the hypothesis that in cephalobids the el and e3 cells become hypodermal cells or are programmed to die. Our findings contradict all previous hypotheses of buccal capsule homology, and suggest instead that ma and mb in Z. punctata are homologous to mi and m2 in C. elegans respectively. We also hypothesize that ma and mb could be homologous to primary and secondary sets of stylet-protractor muscle cells in the plant parasitic Tylenchida. ------------------- Key: 3273 Medline: 99043116 Authors: Sternberg PW;Han M Title: Genetics of RAS signaling in C. elegans. Citation: Trends in Genetics 14: 466-472 1998 Type: REVIEW Genes: egl-15 egl-17 gap-1 ksr-1 let-23 let-60 let-341 lin-1 lin-2 lin-3 lin-7 lin-10 lin-15 lin-25 lin-31 lin-39 lin-45 mab-5 mek-2 mpk-1 sem-5 sli-1 soc-2 sur-2 sur-5 sur-8 unc-101 Abstract: Genetic analysis of the RAS function in Caenorhabditis elegans has trot only clarified the functional relationship of signal transduction proteins, but also led to the discovery of new proteins involved positively or negatively in RAS signaling. the stereotyped development of C. elegans has allowed many of the functions of RAS to be elucidated at the level of fates of individual cells. ------------------- Key: 3274 Medline: 99039769 Authors: Yasuda M;D'Sa-Eipper C;Gong X;Chinnadurai G Title: Regulation of apoptosis by a Caenorhabditis elegans BNIP3 homolog. Citation: Oncogene 17: 2525-2530 1998 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: We have identified a C. elegans protein, ceBNIP3, homologous to the human BCL-2/EIB-19K interacting BCL-2 family pro-apoptotic protein BNIP3. In transiently transfected mammalian cells, ceBNIP3 complexes with CED-9, the worm homolog of BCL-2. CeBNIP3 also efficiently heterodimerizes with the cell death protease proCED-3 by direct binding via the prodomain. Transfection of ceBNIP3 and CED-3 results in enhanced proteolytic processing of the CED-3 zymogen and in cooperative induction of apoptosis. Coexpression of CED-9 suppresses the cooperative cell death induced by ceBNIP3 and CED-3. In cells coexpressing CED-9, ceBNIP3 and CED-3, all three proteins exist as a ternary complex suggesting that CED-9 may suppress cooperative apoptosis induced by CED-3 and ceBNIP3 by simultaneous complex formation with CED-3 and ceBNIP3. Our results suggest that ceBNIP3 may be a novel component of the C. elegans apoptosis paradigm and may initiate apoptosis by recruiting CED-3 to mitochondria and other cytoplasmic ------------------- Key: 3275 Medline: 99019718 Authors: Labrousse AM;Shurland DL;van der Bliek AM Title: Contribution of the GTPase domain to the subcellular localization of dynamin in the nematode Caenorhabditis elegans. Citation: Molecular Biology of the Cell 9: 3227-3239 1998 Type: ARTICLE Genes: dyn-1 mec-7 unc-104 Abstract: Caenorhabditis elegans dynamin is expressed at high levels in neurons and at lower levels in other cell types, consistent with the important role that dynamin plays in the recycling of synaptic vesicles. Indirect immunofluorescence showed that dynamin is concentrated along the dorsal and ventral nerve cords and in the synapse-rich nerve ring. Green fluorescent protein (GFP) fused to the N terminus of dynamin is localized to synapse-rich regions. Furthermore, this chimera was detected along the apical membrane of intestinal cells, in spermathecae, and in coelomocytes. Dynamin localization was not affected by disrupting axonal transport of synaptic vesicles in the unc-104 (kinesin) mutant. To investigate the alternative mechanisms that dynamin might use for translocation to the synapse, we systematically tested the localization of different protein domains by fusion to GFP. Localization of each chimera was measured in one specific neuron, the ALM. The GTPase, a middle domain, and the putative coiled coil each contribute to synaptic localization. Surprisingly, the pleckstrin homology domain and the proline-rich domain, which are known to bind to coated-pit constituents, did not contribute to synaptic localization. The GFP-GTPase chimera was most strongly localized, although the GTPase domain has no known interactions with proteins other than with dynamin itself. Our results suggest that different dynamin domains contribute to axonal transport and the sequestration of a ------------------- Key: 3276 Medline: 12572603 Authors: Marin I;Plata-Rengifo P;Labrador M;Fontdevila A Title: Evolutionary relationships among the members of an ancient class of non-LTR retrotransposons found in the nematode Caenorhabditis elegans. Citation: Molecular Biology and Evolution 15: 1390-1402 1998 Type: ARTICLE Genes: Abstract: We took advantage of the massive amount of sequence information generated by the Caenorhabditis elegans genome project to perform a comprehensive analysis of a group of over 100 related sequences that has allowed us to describe two new C. elegans non-LTR retrotransposons. We named them Sam and Frodo. We also determined that several highly divergent subfamilies of both elements exist in C. elegans. It is likely that several master copies have been active at the same time in C. elegans, although only a few copies of both Sam and Frodo have characteristics that are compatible with them being active today. We discuss whether it is more appropriate under these circumstances to define only 2 elements corresponding to the most divergent groups of sequences or up to 16, considering each subfamily a different element. The C. elegans elements are related to other previously described non-LTR retrotransposons (CRI, found in different vertebrates; SR1, from the trematode Schistosoma; Q and T1, from the mosquito Anopheles). All of these elements, according to the analysis of their reverse transcriptases, form a monophyletic cluster that we call the ''T1/CR1 subgroup.'' Elements of this subgroup are thus ancient components of the genome of animal species. However, we discuss the possibility that these elements may occasionally be horizontally transmitted. ------------------- Key: 3277 Medline: 12572608 Authors: Gotoh O Title: Divergent structures of Caenorhabditis elegans cytochrome P450 genes suggest the frequent loss and gain of introns during the evolution of nematodes. Citation: Molecular Biology and Evolution 15: 1447-1459 1998 Type: ARTICLE Genes: Abstract: The Caenorhabditis elegans genome contains more than 60 cytochrome P450 (CYP) genes. The exon-intron organizations of all of the available and potentially active C. elegans CYP genes were inferred by a newly developed program for predicting protein-coding exons based on the alignment of a genomic DNA sequence and a protein profile. From the predicted amino acid sequences, all of the C. elegans CYP genes except one were classified into three groups, which were closely related to the mammalian drug-metabolizing P450 gene families CYP2, CYP3, and CYP3. The gene structures were strikingly divergent within each group; 20, 10, and 5 unique gene organizations were identified among 40, is, and 5 genes in the CYP2-, CYP3-, and CYP4-related groups, respectively. The degrees of divergence in gene organization were strongly correlated with those in the amino acid sequences of encoding proteins, and the minimum rate of change in an intron insertion site was estimated to be about 90 times less frequent than amino acid substitutions. Parsimonious analyses suggested that frequent loss and gain of introns has occurred during the evolution of CYP genes in each froup after the divergence of nematodes, arthropods, and deuterostomia. Few. if any, incidents of intron sliding were evident, and a model that did not allow intron insertions was highly inconsistent with the observations. All of these findings are explained better by the intron-late view than by the intron-early ------------------- Key: 3278 Medline: 99045239 Authors: Schmid MF;Epstein HF Title: Muscle thick filaments are rigid coupled tubules, not flexible ropes. Citation: Cell Motility & the Cytoskeleton 41: 195-201 1998 Type: ARTICLE Genes: Abstract: Understanding the structures of thick filaments and their relation to muscle contraction has been an important problem in muscle biology. The flexural rigidity of natural thick filaments isolated from Caenorhabditis elegans as determined by statistical analysis of their electron microscopic images shows that they are considerably more rigid (persistence length = 263 mu m) than similarly analyzed synthetic actin filaments (6 mu m) or duplex DNA (0.05 mu m), which are known to be helical ropes. Indeed, cores of C. elegans thick filaments, having only 11% of the mass per unit length of intact thick filaments, are quite rigid (85 mu m) compared with the thick filaments. Cores comprise the backbones of the thick filaments and are composed of tubules containing seven subfilaments cross-linked by non-myosin proteins. Microtubules reconstituted from rubulin and microtubule-associated proteins are nearly as rigid (55 mu m) as the cores. We propose a model of coupled tubules as the structural basis for the observed rigidity of natural thick filaments and other linear structures such as microtubules. A similar model was recently presented for microtubules [Felgner et al., 1997]. This coupled tubule model may also explain the differences in flexural rigidity between natural rabbit skeletal muscle thick filaments (27 mu m) or synthetic thick filaments reconstituted from myosin and myosin binding protein C (36 mu m) and those reconstituted from purified myosin (9 mu m). The more flexible myosin structures may be helical ropes like F-actin or DNA, whereas the more rigid muscle or synthetic thick filaments which contain myosin and myosin binding protein C may be constructed of subfilaments coupled into tubules as in C. elegans cores. The observed thick filament rigidity is necessary for the incompressibility and lack of flexure observed with thick filaments in contracting skeletal ------------------- Key: 3279 Medline: Authors: Pilgrim D Title: Caenorhabditis elegans. Citation: "Encyclopedia of Reproduction". E Knobil and J.D. Neill (eds). Academic Press, Inc. 1: 449-457 1999 Type: REVIEW Genes: dpy-26 dpy-27 dpy-28 dpy-30 fem-1 fem-2 fem-3 fog-1 fog-2 fog-3 her-1 laf-1 mog-1 sdc-1 sdc-2 sdc-3 tra-1 tra-2 tra-3 xol-1 Abstract: Caenorhabditis elegans is a free-living soil nematode, about 1 mm in length, that is found around the world. It is currently a common laboratory model for many aspects of cellular, developmental, and molecular biology. Its popularity comes from its transparency (allowing all nuclei to be followed in living animals at all stages of development), its anatomical simplicity (1000 cells), its small genome (100 Mbp), an invariant somatic cell lineage, ease of laboratory culture, rapid generation time, and a mode of reproduction which facilitates classical genetic analysis. An interested beginner needs only a petri plate, some Escherichia coli, and a stereo dissecting microscope to begin study of this fascinating creature. ------------------- Key: 3280 Medline: 99039341 Authors: Vanfleteren JR;De Vreese A;Braeckman BP Title: Two-parameter logistic and Weibull equations provide better fits to survival data from isogenic populations of Caenorhabditis elegans in axenic culture than does the Gompertz model. Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 53: B393-B403 1998 Type: ARTICLE Genes: age-1 daf-2 daf-12 fer-15 spe-9 Abstract: We have fitted Gompertz, Weibull, and two- and three-parameter logistic equations to suvival data obtained from 77 cohorts of Caenorhabditis elegans in axenic culture. Statistical analysis showed that the fitting ability was in the order three-parameter logistic > two-parameter logistic = Weibull > Gompertz Pooled data were better fit by the logistic equations, which tended to perform equally well as population size increased, suggesting that the third parameter is likely to be biologically irrelevant. Considering restraints imposed by the small population sizes used, we simply conclude that the two-parameter logistic and Weibull mortality models for axenically grown C. elegans generally provided good fits to the data, whereas the Gompertz model was inappropriate in many cases. The survival curves of several short- and long-lived mutant strains could be predicted by adjusting only the logistic curve parameter that defines mean life span. We conclude that life expectancy is genetically determined. The life span-altering mutations reported in this study define a novel mean life span, but do not appear to fundamentally alter the aging process. ------------------- Key: 3281 Medline: Authors: Manton K Title: Commentary. Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 53: B404-B405 1998 Type: REVIEW Genes: Abstract: The set of analyses reported in the article by Vanfleteren and colleagues represents a type of statistical investigation of experimental data that has been sorely lacking in the biology of aging studies. In particular, instead of assuming that a Gompertz-type hazard function a priori explains the dynamics of biological sensescence, Vanfleteren and colleagues fit a number of different hazard models to data on the survival of C. elegans from 77 experiments and assessed both the adequacy of the emperical fit and the biological interpretability of model parameter estimates. ------------------- Key: 3282 Medline: Authors: Wilson DL Title: Commentary - Survival of C. elegans in axenic culture. Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 53: B406- 1998 Type: REVIEW Genes: Abstract: Vanfleteren and colleagues present an interesting example of environmental conditions altering the kinetics of survival. Most previous studies of survival in C. elegans have used abundant bacteria as a food source. Such studies have found that the Gompertz function (exponential growth in mortality rate with age) gives a relatively good fit to survival curves, but that there is some deceleration in the rate of growth of mortality later in the life span. Yulong Yang and I have completed dozens of studies of small populations of the wild-type strain, N2, as well as strains TJ401, TJ411, TJ412,and BA713 in the presence of abundant bacteria in liquid or on agar. Survival curves were better fit by Gompertz more often than by Weibull or logistic functions (unpublished observations). ------------------- Key: 3283 Medline: Authors: Braeckman BP;De Vreese A;Vanfleteren JR Title: Authors response to commentaries on "Two-parameter logistic and Weibull equations provide better fits to survival-data from isogenic populations of Caenorhabditis elegans in axenic culture than does.. Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 53: B407-B408 1998 Type: REVIEW Genes: Abstract: Although the classical Gompertz model ha been the standard for over a century, recent research has shown definitely that this model often fails to predict survival at old ages. Also our analyses reported in this article showed that the Weibull and 2-parameter (2-p) logistic functions provide better fits to the extremes of the survival curves of C. elegans in axenic culture. As a commentator argues, individual differences in the Gompertz dynamics of aging processes can generate a 2-p logistic survival curve for the entire population... ------------------- Key: 3284 Medline: 98413140 Authors: Keating HH;White JG Title: Centrosome dynamics in early embryos of Caenorhabditis elegans. Citation: Journal of Cell Science 111: 3027-3033 1998 Type: ARTICLE Genes: par-1 par-2 par-3 Abstract: The early Caenorhabditis elegans embryo divides with a stereotyped pattern of cleavages to produce cells that vary in developmental potential. Differences in cleavage plane orientation arise between the anterior and posterior cells of the 2-cell embryo as a result of asymmetries in centrosome positioning. Mechanisms that position centrosomes are thought to involve interactions between microtubules and the cortex, however, these mechanisms remain poorly defined, Interestingly, in the early embryo the shape of the centrosome predicts its subsequent movement. We have used rhodamine-tubulin and live imaging techniques to study the development of asymmetries in centrosome morphology and positioning. In contrast to studies using fixed embryos, our images provide a detailed characterization of the dynamics of centrosome flattening. In addition, our observations of centrosome behavior in vivo challenge previous assumptions regarding centrosome separation by illustrating that centrosome flattening and daughter centrosome separation are distinct processes, and by revealing that nascent daughter centrosomes may become separated from the nucleus. Finally, we provide evidence that the midbody specifies a region of the cortex that directs rotational alignment of the centrosome-nucleus complex and that the process is likely to involve multiple interactions between microtubules and the cortex; the process of alignment involves oscillations and overshoots, suggesting a multiplicity of cortical sites that interact ------------------- Key: 3285 Medline: 99042123 Authors: Fitzgerald MC;Schwarzbauer JE Title: Importance of the basement membrane protein SPARC for viability and fertility in Caenorhabditis elegans. Citation: Current Biology 8: 1285-1288 1998 Type: ARTICLE Genes: ost-1 Abstract: The basement membrane is a specialized extracellular matrix located at epithelial-mesenchymal boundaries that supports cell adhesion, migration, and proliferation; it is highly conserved between invertebrates and vertebrates [1,2]. One of its component proteins, SPARC (osteonectin/BM-40), binds calcium and collagens, and can modulate cell-matrix interactions, so altering cell shape, growth, and differentiation [3-5]. The tissue distribution of a secreted fusion protein containing SPARC and green fluorescent protein (GFP) was analyzed in Caenorhabditis elegans. The protein localized to most basement membranes along body wall and sex muscles, and was also deposited around the pharynx and the gonad, in the spermatheca and at the distal tip cells. The contributions of SPARC to C. elegans development were determined using RNA interference, which accurately phenocopies loss-of-function defects [6-8]. A reduction in the amount of SPARC protein resulted in embryonic or larval lethality in a significant proportion of progeny. Those that survived developed a 'clear' phenotype characterized by a lack of gut granules, which made the animals appear transparent, plus small size, and sterility or reduced fecundity. No significant morphological abnormalities were observed, indicating that SPARC plays a regulatory rather than structural role in modulating cell-matrix interactions during normal ------------------- Key: 3286 Medline: Authors: Wade N Title: Animal's genetic program decoded, in a science first. Citation: The New York Times, December 11 : A1-A26 1998 Type: REVIEW Genes: Abstract: Biologists have for the first time deciphered the full genetic programming of an animal, a landmark achievement both in its own right and as a milestone toward understanding the human genome. ------------------- Key: 3287 Medline: 99059458 Authors: Michaelson LV;Napier JA;Lewis M;Griffiths G;Lazarus CM;Stobart AK Title: Functional identification of a fatty acid delta-5 desaturase gene from Caenorhabditis elegans. Citation: FEBS Letters 439: 215-218 1998 Type: ARTICLE Genes: Abstract: We have identified a cDNA from the nematode worm Caenorhabditis elegans that encodes a fatty acid Delta(5) desaturase, Saccharomyces cerevisiae expressing the full-length cDNA was able to convert di-homo-gamma-linolenic acid to arachidonic acid, thus confirming Delta(5) desaturation. The 1341 hp Delta(5) desaturase sequence contained an N-terminal cytochrome b(5) domain and was located within a kilobase of the C. elegans Delta(6) desaturase on chromosome IV. With an amino acid identity of 45% it is possible that one of these genes arose from the other by gene duplication. This is the first example of a Delta(5) desaturase gene isolated from an ------------------- Key: 3288 Medline: 99041962 Authors: Liao VHC;Freedman JH Title: Cadmium-regulated genes from the nematode Caenorhabditis elegans - Identification and cloning of new cadmium-responsive genes by differential display. Citation: Journal of Biological Chemistry 273: 31962-31970 1998 Type: ARTICLE Genes: mtl-1 mtl-2 Abstract: The transition metal cadmium is a pervasive and persistent environmental contaminant that has been shown to be both a human toxicant and carcinogen. To inhibit cadmium-induced damage, cells respond by increasing the expression of genes encoding stress-response proteins. In most cases, the mechanism by which cadmium affects the expression of these genes remains unknown. It has been demonstrated in several instances that cadmium activates gene transcription through signal transduction pathways, mediated by protein kinase C, cAMP-dependent protein kinase, or calmodulin. A codicil is that cadmium should influence the expression of numerous genes. To investigate the ability of cadmium to affect gene transcription, the differential display technique was used to analyze gene expression in the nematode Caenorhabditis elegans. Forty-nine cDNAs whose steady-state levels of expression change 2-6-fold in response to cadmium exposure were identified. The nucleotide sequences of the majority of the differentially expressed cDNAs are identical to those of C. elegans cosmids, yeast artificial chromosomes, expressed sequence tags, or predicted genes. The translated amino acid sequences of several clones are identical to C. elegans metallothionein-l, HSP70, collagens, and rRNAs. In addition, C. elegans homologues of pyruvate carboxylase, DNA gyrase, P-adrenergic receptor kinase, and human hypothetical protein KIAA0174 were identified. The translated amino acid sequences of the remaining differentially expressed cDNAs encode novel proteins. ------------------- Key: 3289 Medline: 99058858 Authors: Bergmann DC;Crew JR;Kramer JM;Wood WB Title: Cuticle chirality and body handedness in Caenorhabditis elegans. Citation: Developmental Genetics 23: 164-174 1998 Type: ARTICLE Genes: rol-4 rol-6 rol-8 rol-9 spn-1 sqt-1 Abstract: Caenorhabditis elegans adult animals exhibit an inherent chirality of fiber orientation in the basal layer of the cuticle, as well as a naturally invariant but experimentally reversible handedness in the left-right (L-R) asymmetry of the body plan. We have examined the relationship between cuticle chirality and body handedness in normal and L-R reversed animals, using Roller (Rol) mutants and transmission electron microscopy to monitor cuticle properties. Rot phenotypes, several of which have been shown to result from mutations in cuticle collagen genes, are characterized by an invariant, allele-specific handedness in their direction of rolling. We show for several alleles that this direction is not affected by L-R reversal of the body plan. We further show, by electron microscopy, that the chiral orientation of cuticle Fibers in animals with normal cuticle is not reversed by L-R body-plan reversal. We conclude that cuticle chirality must be established independently of body-plan handedness. The cues that establish cuticle chirality are still unknown, as are the causes for different rolling directions in different Roller mutants. We discuss the question of how cuticle chirality maintains its independence, and how the orientations of the fiber layers may be determined. ------------------- Key: 3290 Medline: 99066932 Authors: Qin L;Smant G;Stokkermans J;Bakker J;Schots A;Helder J Title: Cloning of a trans-spliced glyceraldehyde-3-phosphate-dehydrogenase gene from the potato cyst nematode Globodera rostochiensis and expression of its putative promoter region in Caenorhabditis elegans. Citation: Molecular & Biochemical Parasitology 96: 59-67 1998 Type: ARTICLE Genes: gpd-1 gpd-2 gpd-3 gpd-4 Abstract: Reverse genetics to determine the relative importance of individual pathogenicity factors of the potato cyst nematode Globodera rostochiensis depends, apart from an efficient transformation protocol for this obligatory plant parasite, on the availability of an efficient promoter. PCR-based cloning was used to isolate a cDNA encoding glyceraldehyde-3-phosphate-dehydrogenase (GAPDH, a crucial enzyme in glycolysis and gluconeogenesis; this gene was designated gpd) and its 5'-flanking region. The cDNA includes 1047 nucleotides encoding an open reading frame that shows high homology with GAPDHs from Caenorhabditis elegans and other species. Analysis of the 745 bp 5'-flanking region of the gpd gene showed no homology with a similar region in C. elegans. In this region several eukaryotic promoter elements are present. 5' Rapid amplification of cDNA ends revealed this gene was trans-spliced with a SL1 spliced leader. The 5'-flanking region of the gpd gene was fused to green fluorescent protein reporter gene and microinjected into the gonads of C. elegans. Green fluorescent protein expression, under the transcriptional control of the 5'-flanking region of gpd, was mainly observed in body wall muscles of transgenic animals. This putative promoter region of GAPDH could be a valuable tool to drive gene expression in transgenic G. rostochiensis and other related plant-parasitic nematode species. ------------------- Key: 3291 Medline: 99065757 Authors: Wajant H;Muhlenbeck F;Scheurich P Title: Identification of a TRAF (TNF Receptor-Associated Factor) gene in Caenorhabditis elegans. Citation: Journal of Molecular Evolution 47: 656-662 1998 Type: ARTICLE Genes: Abstract: Many members of the tumor necrosis factor (TNF) receptor superfamily and the interleukin-l (IZ-I) receptor engage intracellular signaling pathways including the nuclear factor kappa B (NF-kappa B)-, c-jun N-terminal kinase (JNK)-, and extracellular signal-regulated kinase (ERK) pathways by direct or indirect interaction with TNF receptor-associated factor (TRAF) molecules. To date, six mammalian members of the TRAF family have been identified. Searching public databases with a sequence pattern comprising 19 conserved amino acid residues derived from the carboxyl-terminal part of the TRAF homology domain, we found significant sequence homologies to a stretch of genomic DNA from Caenorhabditis elegans which encodes 1 of 12 exons of a putative protein. The sequence of this putative protein shows up to 29% sequence identity to the mammalian TRAFs and is therefore designated C. elegans TRAF (CeTRAF). The CeTRAF molecule has an aminoterminal RING finger motif followed by four zinc finger structures and a carboxyl-terminal TRAF domain, a composition which is also found in most of the mammalian TRAFs. Reverse transcription-PCR and sequencing analysis of the respective amplicon clearly demonstrates that CeTRAF is in fact transcribed in C. elegans. The existence of a member of the TRAF family in C. elegans provides strong evidence for evolutionary conserved pathways linking cell surface receptors to activation of JNK, ERK, and NF-kappa B. ------------------- Key: 3292 Medline: 99077259 Authors: Wakabayashi T;Nakamura N;Sambongi Y;Wada Y;Oka T;Futai M Title: Identification of the copper chaperone, CUC-1, in Caenorhabditis elegans: tissue specific co-expression with the copper transporting ATPase, CUA-1. Citation: FEBS Letters 440: 141-146 1998 Type: ARTICLE Genes: cua-1 cuc-1 Abstract: A cDNA encoding a putative copper chaperone protein, CUC-1, was cloned from Caenorhabditis elegans. CUC-1 had the characteristic motifs of MTCXXC and KKTGK, and showed 49.3 and 39.1% sequence identity with yeast Atx1p and human HAH1, respectively. Expression of CUC-1 cDNA complemented a null atx1 mutant, the yeast copper chaperone gene, thus demonstrating that CUC-1 is a functional copper chaperone. Studies with transgenic worms indicated that cuc-1 and cua-1, which encodes the copper transporting ATPase, are expressed together in intestinal cells of adult and hypodermal cells in the larvae. cua-1 was also expressed in pharyngeal muscle but cuc-1 was not. These results suggest that CUC-1 and CUA-1 constitute a copper trafficking pathway similar to the yeast counterparts in intestinal and hypodermal cells, and CUA-1 may have a different function in pharyngeal muscle. ------------------- Key: 3293 Medline: Authors: Hartman PS;Nelson GA Title: Processing of DNA damage in the nematode Caenorhabditis elegans. Citation: "DNA Damage and Repair: DNA Repair in Prokaryotes and Lower Eukaryotes." JA Nickoloff and MF Hoekstra (eds). Humana Press, Inc., Totowa, NJ. 1: 557-576 1996 Type: REVIEW Genes: age-1 ced-9 mev-1 nuc-1 rad-1 rad-2 rad-3 rad-4 rad-5 rad-6 rad-7 rad-8 rad-9 rec-1 sod-1 sod-2 sod-3 sod-4 Abstract: The free-living nematode Caenorhabditis elegans has emerged rapidly as an organism with which to study many basic biological phenomena, particularly those related to development. This can ben evidenced numerically in many ways; for example, the number of presentations at the biennial C. elegans meeting has increased over sevenfold, from 80 in 1979 to 569 in 1995. In addition to numerous review articles, several books are devoted to this nematode, its attributes and various foci of interest. The three preliminary attributes that have rendered C. elegans a popular model system are overviewed briefly in the following three sections. The attributes that have rendered C. elegans popular with developmental biologists have also been exploited to examine specific areas in radiation biology, DNA repair, and mutagenesis. Several of the basic DNA repair pathways operative in C. elegans have been elucidated. Also, a number of biological end points such as survival and mutagenesis, have been examined so as to address the various mechanisms by which C. elegans accommodates DNA damage. Central to these efforts has been the isolation and characterization of radiation-sensitive (rad) mutants that modify various biological responses. In particular, these studies provide insights into damage processing, particularly as related to development and ------------------- Key: 3294 Medline: 99054747 Authors: McArdle K;Allen TS;Bucher EA Title: Ca2+-dependent muscle dysfunction caused by mutation of the Caenorhabditis elegans troponin T-1 gene. Citation: Journal of Cell Biology 143: 1201-1213 1998 Type: ARTICLE Genes: deb-1 egl-19 mup-2 myo-3 pat-5 pat-10 unc-52 mnDp34 stDf1 Abstract: We have investigated the functions of troponin T (CeTnT-1) in Caenorhabditis elegans embryonic body wall muscle. TnT tethers troponin I (TnI) and troponin C (TnC) to the thin filament via tropomyosin (Tm), and TnT/Tm regulates the activation and inhibition of myosin-actin interaction in response to changes in intracellular [Ca2+]. Loss of CeTnT-1 function causes aberrant muscle trembling and tearing of muscle cells from their exoskeletal attachment sites (Myers, C.D., P.-Y, Goh, T. StC. Alien, E.A. Bucher, and T. Bogaert, 1996. J. Cell Biol, 132:1061-1077). We hypothesized that muscle tearing is a consequence of excessive force generation resulting from defective tethering of Tn complex proteins, Biochemical studies suggest that such defective tethering would result in either (a) Ca2+-independent activation, due to lack of Tn complex binding and consequent lack of inhibition, or (b) delayed reestablishment of TnI/TnC binding to the thin filament after Ca2+ activation and consequent abnormal duration of force. Analyses of animals doubly mutant for CeTnT-1 and for genes required for Ca2+ signaling support that CeTnT-1 phenotypes are dependent on Ca2+ signaling, thus supporting the second model and providing new in vivo evidence that full inhibition of thin filaments in low ------------------- Key: 3295 Medline: 99054748 Authors: Barral JM;Bauer CC;Ortiz I;Epstein HF Title: unc-45 mutations in Caenorhabditis elegans implicate a CRO1/She4p-like domain in myosin assembly. Citation: Journal of Cell Biology 143: 1215-1225 1998 Type: ARTICLE Genes: unc-45 Abstract: The Caenorhabditis elegans unc-45 locus has been proposed to encode a protein machine for myosin assembly. The UNC-45 protein is predicted to contain an NH2-terminal domain with three tetratricopeptide repeat motifs, a unique central region, and a COOH-terminal domain homologous to CRO1 and She4p. CRO1 and She4p are fungal proteins required for the segregation of other molecules in budding, endocytosis, and septation. Three mutations that lead to temperature-sensitive (ts) alleles have been localized to conserved residues within the CRO1/She4p-like domain, and two lethal alleles were found to result from stop codon mutations in the central region that would prevent translation of the COOH-terminal domain. Electron microscopy shows that thick filament accumulation in vivo is decreased by similar to 50% in the CB286 ts mutant grown at the restrictive temperature. The thick filaments that assemble have abnormal structure. Immunofluorescence and immunoelectron microscopy show that myosins A and B are scrambled, in contrast to their assembly into distinct regions at the permissive temperature and in wild type. This abnormal structure correlates with the high degree of instability of the filaments in vitro as reflected by their extremely low yields and shortened lengths upon isolation. These results implicate the UNC-45 CRO1/She4p-like region in the assembly of myosin isoforms in C. elegans and suggest a possible common mechanism for the function of this UCS (UNC-45/CRO1/She4p) protein family. ------------------- Key: 3296 Medline: 99082915 Authors: Pennisi E Title: Worming secrets from C. elegans genome. Citation: Science 282: 1972-1974 1998 Type: REVIEW Genes: Abstract: The near completion of the sequence of the C. elegans genome should provide researchers with a gold mine of information on topics ranging from evolution to gene ------------------- Key: 3297 Medline: 99069613 Authors: C. elegans Sequencing Consortium Title: Genome sequence of the nematode Caenorhabditis elegans: A platform for investigating biology. Citation: Science 282: 2012-2018 1998 Type: REVIEW Genes: Abstract: See also CGC #3344 and CGC #3456. The 97-megabase genomic sequence of the nematode Caenorhabditis elegans reveals over 19,000 genes. More than 40 percent of the predicted protein products find significant matches in other organisms. There is a variety of repeated sequences, both local and dispersed. The distinctive distribution of some repeats and highly conserved genes provides evidence for a regional organization of the chromosomes. ------------------- Key: 3298 Medline: 99069614 Authors: Clarke ND;Berg JM Title: Zinc fingers in Caenorhabditis elegans: Finding families and probing pathways. Citation: Science 282: 2018-2022 1998 Type: REVIEW Genes: elt-1 lin-31 mab-3 tra-1 Abstract: More than 3 percent of the protein sequences inferred from the Caenorhabditis elegans genome contain sequence motifs characteristic of zinc-binding structural domains, and of these more than half are believed to be sequence-specific DNA-binding proteins. The distribution of these zinc-binding domains among the genomes of various organisms offers insights into the role of zinc-binding proteins in evolution. In addition, the complete genome sequence of C. elegans provides an opportunity to analyze, and perhaps predict, pathways of transcriptional regulation. ------------------- Key: 3299 Medline: 99069615 Authors: Chervitz SA;Aravind L;Sherlock G;Ball CA;Koonin EV;Dwight SS;Harris MA;Dolinski K;Mohr S;Smith T;Weng S;Cherry JM;Botstein D Title: Comparison of the complete protein sets of worm and yeast: Orthology and divergence. Citation: Science 282: 2022-2028 1998 Type: REVIEW Genes: let-60 ncc-1 Abstract: Comparative analysis of predicted protein sequences encoded by the genomes of Caenorhabditis elegans and Saccharomyces cerevisiae suggests that most of the core biological functions are carried out by orthologous proteins (proteins of different species that can be traced back to a common ancestor) that occur in comparable numbers. The specialized processes of signal transduction and regulatory control that are unique to the multicellular worm appear to use novel proteins, many of which re-use conserved domains. Major expansion of the number of some of these domains seen in the worm may have contributed to the advent of multicellularity. The proteins conserved in yeast and worm are likely to have orthologs throughout eukaryotes; in contrast, the proteins unique to the worm may well define ------------------- Key: 3300 Medline: 99069616 Authors: Bargmann CI Title: Neurobiology of the Caenorhabditis elegans genome. Citation: Science 282: 2028-2033 1998 Type: REVIEW Genes: cha-1 deg-3 eat-5 eat-12 egl-10 egl-19 egl-36 glr-1 let-23 lev-1 lin-2 lin-7 lin-10 mec-2 npr-1 odr-10 osm-9 pat-5 rab-3 tax-2 tax-4 unc-2 unc-7 unc-9 unc-17 unc-18 unc-24 unc-29 unc-38 unc-47 unc-68 Abstract: Neurotransmitter receptors, neurotransmitter synthesis and release pathways, and heterotrimeric GTP-binding protein (G protein)-coupled second messenger pathways are highly conserved between Caenorhabditis elegans and mammals, but gap junctions and chemosensory receptors have independent origins in vertebrates and nematodes. Most ion channels are similar to vertebrate channels but there are no predicted voltage-activated sodium channels. The C. elegans genome encodes at least 80 potassium channels, 90 neurotransmitter-gated ion channels, 50 peptide receptors, and up to 1000 orphan receptors that may be chemoreceptors. For many gene families, C. elegans has both conventional members and divergent outliers with weak homology to known genes; these outliers may provide insights into previously unknown functions of conserved protein families. ------------------- Key: 3301 Medline: 99069617 Authors: Ruvkun G;Hobert O Title: The taxonomy of developmental control in Caenorhabditis elegans. Citation: Science 282: 2033-2041 1998 Type: REVIEW Genes: ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ceh-13 daf-2 daf-4 daf-7 dbl-1 egl-1 egl-5 egl-15 egl-17 hmp-2 kin-15 kin-16 lag-2 let-23 lin-4 lin-12 lin-39 mab-5 mes-2 mes-6 nhr-23 tra-1 tra-2 tra-3 unc-4 unc-129 vab-1 vab-7 Abstract: The Caenorhabditis elegans genome sequence was surveyed for transcription factor and signaling gene families that have been shown to regulate development in a variety of species. About 10 to 25 percent of the genes in most of the gene families already have been genetically analyzed in C. elegans, about half of the genes detect probable orthologs in other species, and about 10 to 25 percent of the genes are, at present, unique to C. elegans. Caenorhabditis elegans is also missing genes that are found in vertebrates and other invertebrates. Thus the genome sequence reveals universals in developmental control that are the legacy of metazoan complexity before the Cambrian explosion, as well as genes that have been more recently invented or lost in particular phylogenetic lineages. ------------------- Key: 3302 Medline: 99069618 Authors: Blaxter M Title: Caenorhabditis elegans is a nematode. Citation: Science 282: 2041-2046 1998 Type: REVIEW Genes: Abstract: See CGC #3345 and CGC #3457. Caenorhabditis elegans is a rhabditid nematode. What relevance does this have for the interpretation of the complete genome sequence, and how will it affect the exploitation of the sequence for scientific and social ends? Nematodes are only distantly related to humans and other animal groups; will this limit the universality of the C. elegans story? Many nematodes are parasites; can knowledge of the C. elegans sequence aid in the prevention and treatment of disease? ------------------- Key: 3303 Medline: 99077285 Authors: Cali BM;Anderson P Title: mRNA surveillance mitigates genetic dominance in Caenorhabditis elegans. Citation: Molecular & General Genetics 260: 176-184 1998 Type: ARTICLE Genes: dpy-15 dpy-17 smg-1 smg-6 unc-1 unc-6 unc-20 unc-54 unc-70 Abstract: Nonsense mutant mRNAs are unstable in all eucaryotes tested, a phenomenon termed nonsense-mediated mRNA decay (NMD) or mRNA surveillance. Functions of the seven sung genes are required for mRNA surveillance in Caenorhabditis elegans. In Smg(+) genetic backgrounds, nonsense-mutant mRNAs are unstable, while in Smg(-) backgrounds such mRNAs are stable. Previous work has demonstrated that the elevated level of nonsense-mutant mRNAs in Smg(-) animals can influence the phenotypic effects of heterozygous nonsense mutations. Certain nonsense alleles of a muscle myosin heavy chain gene are recessive in Smg(+) backgrounds but strongly dominant in Smg(-) backgrounds. Such alleles probably express disruptive myosin polypeptide fragments whose abundance is elevated in sung mutants due to elevation of mRNA levels. We report here that mutations in a variety of C. elegans genes are strongly dominant in Smg(-), but recessive or only weakly dominant in Smg(+) backgrounds. We isolated 32 dominant visible mutations in a Smg(-) genetic background and tested whether their dominance requires a functional NMD system. The dominance of 21 of these mutations is influenced by NMD. We demonstrate, furthermore, that in the case of myosin, the dominant-negative effects of nonsense alleles are likely to be due to expression of N-terminal nonsense-fragment polypeptides, not to mistranslation of the nonsense codons. mRNA surveillance, therefore, may mitigate potentially deleterious effects of many heterozygous germline and somatic nonsense or frameshift mutations. We also provide evidence that smg-6, a gene previously identified as being required for NMD, performs essential function(s) in ------------------- Key: 3304 Medline: 99077298 Authors: Stewart HI;O'Neil NJ;Janke DJ;Franz NW;Chamberlin HM;Howell AM;Gilchrist EJ;Ha TT;Kuervers LM;Vatcher GP Title: Lethal mutations defining 112 complementation groups in a 4.5 mb sequenced region of Caenorhabditis elegans chromosome III. Citation: Molecular & General Genetics 260: 280-288 1998 Type: ARTICLE Genes: let-700 let-702 let-704 let-706 let-707 let-709 let-710 let-711 let-712 let-713 let-714 let-715 let-716 let-717 let-718 let-719 let-721 let-722 let-724 let-725 let-727 let-728 let-729 let-732 let-733 let-734 let-736 let-737 let-738 let-739 let-740 let-741 let-743 let-746 let-747 let-748 let-750 let-752 let-753 let-754 let-755 let-756 let-758 let-759 let-760 let-761 let-763 let-764 let-765 let-766 let-767 let-768 let-769 let-771 let-774 let-775 let-776 let-777 let-778 let-780 let-782 let-783 let-784 let-786 let-789 let-791 let-792 let-793 let-794 let-795 let-796 let-797 let-798 let-799 let-809 let-810 let-812 let-813 let-814 let-815 let-816 let-817 let-818 let-819 let-820 let-821 let-822 let-823 let-824 let-825 let-826 let-827 let-828 let-829 let-730 let-831 let-832 let-834 let-835 let-836 let-837 let-838 let-839 let-840 let-841 let-842 let-843 let-844 mel-31 mel-33 mup-4 sDf121 sDf125 sDf127 sDf128 sDf130 sDf135 Abstract: The central gene cluster of chromosome III was one of the first regions to be sequenced by the Caenorhabditis elegans genome project. We have performed an essential gene analysis on the left part of this cluster, in the region around dpy-17III balanced by the duplication sDp3. We isolated 151 essential gene mutations and characterized them with regard to their arrest stages. To facilitate positioning of these mutations, we generated six new deficiencies that, together with preexisting chromosomal rearrangements, subdivide the region into 14 zones. The 151 mutations were mapped into these zones. They define 112 genes, of which 110 were previously unidentified. Thirteen of the zones have been anchored to the physical sequence by polymerase chain reaction deficiency mapping. Of the 112 essential genes mapped, 105 are within these 13 zones. They span 4.2 Mb of nucleotide sequence. From the nucleotide sequence data, 920 genes are predicted. From a Poisson distribution of our mutations, we predict that 234 of the genes will be essential genes. Thus, the 105 genes constitute 45% of the estimated number of essential genes in the physically defined zones and between 2 and 5% of all essential genes in C. elegans. ------------------- Key: 3305 Medline: 99077299 Authors: Rinaldo C;Ederle S;Rocco V;LaVolpe A Title: The Caenorhabditis elegans Rad51 homolog is transcribed into two alternative messenger-RNAs potentially encoding proteins of different sizes. Citation: Molecular & General Genetics 260: 289-294 1998 Type: ARTICLE Genes: nuc-1 Abstract: In prokaryotes, the RecA protein plays a pivotal role in homologous recombination, catalyzing the transfer of a single DNA strand into an homologous molecule. Structural homologs of the bacterial RecA protein, called Rad51, have been found in different eukaryotes (from yeast to man), suggesting a certain level of conservation in recombination pathways among living organisms. We have cloned the homolog of RAD51 in Caenorhabditis elegans. The CeRAD51 gene is transcribed into two alternative mRNAs and potentially codes for two proteins of 395 and 357 amino acids in length, respectively. We discuss the evolutionary implications of these findings. ------------------- Key: 3306 Medline: 99077301 Authors: Hope IA;Arnold JM;McCarroll D;Jun G;Krupa AP;Herbert R Title: Promoter trapping identifies real genes in C. elegans. Citation: Molecular & General Genetics 260: 300-308 1998 Type: ARTICLE Genes: pes-1 pes-2 vet-4 vha-1 vha-2 vha-3 Abstract: Promoter trapping involved screening uncharacterized fragments of C. elegans genomic DNA for C. elegans promoter activity. By sequencing the ends of these DNA fragments and locating their genomic origin using the available genome sequence data, promoter trapping has now been shown to identify real promoters of real genes, exactly as anticipated. Developmental expression patterns have thereby been linked to gene sequence, allowing further inferences on gene function to be drawn. Some expression patterns generated by promoter trapping include subcellular details. Localization to the surface of particular cells or even particular aspects of the cell surface was found to be consistent with the genes, now associated with these patterns, encoding membrane-spanning proteins. Data on gene expression patterns are easier to generate and characterize than mutant phenotypes and may provide the best means of interpreting the large quantity of sequence data currently being generated in genome projects. ------------------- Key: 3307 Medline: 99057913 Authors: del Peso L;Gonzalez VM;Nunez G Title: Caenorhabditis elegans Egl-1 disrupts the interaction of CED-9 with CED-4 and promotes CED-3 activation. Citation: Journal of Biological Chemistry 273: 33495-33500 1998 Type: ARTICLE Genes: ced-3 ced-4 ced-9 egl-1 Abstract: In the nematode Caenorhabditis elegans, programmed cell death is implemented by the protease CED-3 whose activity is inhibited by CED-9 through physical associations with the regulator CED-4. The product of a recently described gene, egl-1, binds to and inhibits CED-9. In the present studies, we have addressed the molecular mechanism by which EGL-1 regulates CED-9 function and promotes cell death. Expression of CED-4 and CED-3 resulted in decreased survival and apoptosis of mammalian cells, activities that could be inhibited by CED-9. Importantly, this protective effect of CED-9 was antagonized by EGL-1. Immunoprecipitation analysis showed that EGL-1 binding to CED-9 disrupts the association between CED-4 and CED-9, an activity that required the BH3 motif of EGL-1. Consistent with these results, expression of EGL-1 promoted CED-4-dependent processing of CED-3, and this activity of EGL-1 was mediated through inhibition of CED-9. In mammalian cells, CED-9 is known to target the subcellular localization of CED-4 from the cytosol to intracellular membranes. Expression of EGL-1 resulted in redistribution of CED-4 from intracellulal membranes, where it co-localized with CED-9, to the cytoplasm, providing further evidence that EGL-1 regulates CED-4 through CED-9. Finally, the levels of EGL-1 were greatly enhanced by coexpression of CED-9 in both mammalian cells and in a cell-free system, suggesting a. role for CED-9 in the expression and/or stabilization. of EGL-1. These studies provide a mechanism for how EGL-1 functions to antagonize ------------------- Key: 3308 Medline: 99248571 Authors: Crittenden SL;Kimble J Title: Confocal methods for Caenorhabditis elegans. Citation: "Methods in Molecular Biology: Confocal Microscopy Methods and Protocols". S Paddock (ed). Humana Press, Inc. Totowa, NJ. 122: 141-151 1998 Type: REVIEW Genes: Abstract: The use of antibodies to visualize the distribution and subcellular localization of gene products powerfully complements genetic and molecular analysis of gene function in Caenorhabditis elegans. Double and triple staining protocols are particularly useful for several reasons. First, colonization of proteins either within tissues or at a subcellular level can be examined. Second, costaining with stage-specific or tissue-specific markers can define the timing and tissue specificity of antigen expression. For these types of studies it is useful to be able to collect data from multiple fluorescence wavelengths simultaneously. A confocal microscope equipped with a krypton/argon laser can simultaneously detect up to three different antigens. Using a confocal microscope it is also possible to collect a series of optical sections through a sample that allows observation of changes in distribution of the antigen in different focal planes of the tissue or ------------------- Key: 3309 Medline: 99082676 Authors: Chalfie M;Jorgensen EM Title: C. elegans neuroscience: genetics to genome. Citation: Trends in Genetics 14: 506-512 1998 Type: REVIEW Genes: cha-1 deg-1 eat-5 lin-12 mec-3 mec-4 odr-10 sel-12 snb-1 unc-4 unc-7 unc-9 unc-13 unc-17 unc-18 unc-30 unc-47 unc-51 unc-54 unc-86 Abstract: From their earliest experiments, researchers using Caenorhabditis elegans have been interested in the role of genes in the development and function of the nervous system. As the C. elegans Genome Project completes the genomic sequence, we review the accomplishments of these researchers and the impact that the Genome Project has had on their research. We also speculate on future directions in this research that are enabled by the efforts of the Genome Project. ------------------- Key: 3310 Medline: Authors: Hodgkin J;Horvitz HR;Jasny BR;Kimble J Title: C. elegans: sequence to biology. Citation: Science 282: 2011- 1998 Type: REVIEW Genes: Abstract: This special issue of Science celebrates a landmark in biology: determination of the essentially complete DNA sequence of an animal genome. The animal is a small invertebrate, the nematode (or roundworm) Caenorhabditis elegans, and the sequence consists of about 97 million base pairs of DNA, approximately one-thirtieth the number in the human genome. Nonetheless, the information content is enormous - eight times that of the budding yeast Saccharomyces cerevisiae, the only other eukaryote with a sequenced genome. ------------------- Key: 3311 Medline: 99084263 Authors: Mills DK;Hartman PS Title: Lethal consequences of simulated solar radiation on the nematode Caenorhabditis elegans in the presence and absence of photosensitizers. Citation: Photochemistry and Photobiology 68: 816-823 1998 Type: ARTICLE Genes: rad-1 rad-2 rad-3 rad-7 Abstract: The partial destruction of the earth's protective ozone layer has raised concerns about the impact of increased UV radiation on the earth's biological systems. In this study, polychromatic light sources were employed to observe the biological responses of the soil nematode Caenorhabditis elegans to simulated solar UV. Using various filter combinations, action spectra were constructed that approximated those generated previously with monochromatic radiation. In both cases, a mutant strain (rad-3) progressively lost its hypersensitivity as shorter wavelengths were filtered out. In addition, both wild type and radiation-sensitive (rad) mutants were irradiated with several combinations of filtered light sources in the presence and absence of two exogenous photosensitizers (ethidium bromide and bromodeoxyuridine). Treatment with either of the introduced photosensitizers increased photosensitivity to solar UV. Solar UV also induced a fluence-dependent reduction in fertility in wild-type animals. These experiments extend previous data and substantially expand our understanding of the biological responses of C. elegans to solar radiation. ------------------- Key: 3312 Medline: 99063799 Authors: Pilgrim D Title: CeRep25B forms chromosome-specific minisatellite arrays in Caenorhabditis elegans. Citation: Genome Research 8: 1192-1201 1998 Type: ARTICLE Genes: fem-2 unc-45 Abstract: With the completion of the Genome Sequencing Project, it is now possible to rapidly and accurately determine the frequency and position of a particular repeat sequence in the Caenorhabditis elegans genome. Several repeat sequences with a variety of characteristics have been examined and with few exceptions they show a near-random distribution throughout the genome. We characterized several genes near the left end of Chromosome III in the C. elegans genome, and found a 24-bp minisatellite repeat sequence present in the introns of two unrelated genes. This prompted a search of the databank for other occurrences of this sequence. Multiple copy arrays of this repeat are all located on the same autosome and fall in two clusters: one near the left end, and one in the central region separated by similar to 10 Mb. There are >200 copies of this repeat on the chromosome. This euchromatic repeat sequence seems unrelated to gene expression, is absent from homologous sites in a related species, is unstable in Escherichia coli, and is polymorphic between different wild isolates of C. elegans. Most CeRep25B units in the array match the consensus sequence very well, suggesting that either this repeat originated quite recently or its sequence is functionally constrained. Although chromosome-specific repeat sequences have been reported previously in many organisms, such sequences are usually structural and heterochromatic (e.g., centromeric alpha-satellite) or on the mammalian sex chromosomes. This report describes the first confirmed instance from a whole genome sequencing project of an autosomal euchromatic chromosome-specific minisatellite repeat. ------------------- Key: 3313 Medline: 99108927 Authors: Wodarz A;Nusse R Title: Mechanisms of Wnt signaling in development. Citation: Annual Review of Cell & Developmental Biology 14: 59-88 Type: REVIEW Genes: apr-1 lin-17 lin-44 mom-1 mom-2 mom-5 pop-1 wrm-1 Abstract: Wnt genes encode a large family of secreted, cysteine-rich proteins that play key roles as intercellular signaling molecules in development. Genetic studies in Drosophila and Caenorhabditis elegans, ectopic gene expression in Xenopus, and gene knockouts in the mouse have demonstrated the involvement of Wnts in processes as diverse as segmentation, CNS patterning, and control of asymmetric cell divisions. The transduction of Wnt signals between cells proceeds in a complex series of events including post-translational modification and secretion of Wnts, binding to transmembrane receptors, activation of cytoplasmic effecters, and, finally, transcriptional regulation of target genes. Over the past two years our understanding of Wnt signaling has been substantially improved by the identification of Frizzled proteins as cell surface receptors for Wnts and by the finding that beta-catenin, a component downstream of the receptor, can translocate to the nucleus and function as a transcriptional activator. Here we review recent data that ------------------- Key: 3314 Medline: Authors: Mikola J;Setala H Title: Interplay of omnivory, energy channels and C availability in a microbial-based soil food web. Citation: Biology & Fertility of Soils 28: 212-218 1999 Type: ARTICLE Genes: Abstract: To study the effects of omnivory on the structure and function of soil food webs and on the control of trophic-level biomasses in soil, two food webs were established in microcosms. The first one contained fungi, bacteria, a fungivorous nematode (Aphelanchoides saprophilus) and a bacterivorous nematode (Caenorhabditis elegans), and the second one fungi, bacteria, the fungivore and an omnivorous nematode (Mesodiplogaster sp.) feeding on both bacteria and the fungivore. Half of the replicates of each food web received additional glucose. The microcosms were sampled destructively at 5, 9, 13 and 19 weeks to estimate the biomass of microbes and nematodes and the soil NH4+-N concentration. The evolution of CO2 was measured to assess microbial respiration. Microbial respiration was increased and soil NH4+-N concentration decreased by the addition of glucose, whereas neither was affected by the food-web structure. Supplementary energy increased the biomass of fungi and the fungivore, but decreased the biomass of bacteria, the bacterivore and the omnivore. The omnivore achieved greater biomass than the bacterivore and reduced the bacterial biomass less than the bacterivore. The biomass of the fungivore was smaller in the presence of the omnivore than in the presence of the bacterivore at three sampling occasions. Fungal biomass was not affected by food-web structure. The results show that the effects of the omnivore were restricted to its resources, whereas more remote organisms and soil processes were not substantially influenced. The results also indicate that the presence of an omnivore does not necessarily alter the control of populations as compared with a food web containing distinct trophic levels, and that the fungal and bacterial channels may respond differently to changes in energy supply. ------------------- Key: 3315 Medline: 33077975 Authors: Williams C;Xu L;Blumenthal T Title: SL1 trans splicing and 3'-end formation in a novel class of Caenorhabditis elegans operon. Citation: Molecular and Cellular Biology 19: 376-383 1999 Type: ARTICLE Genes: ced-9 cks-1 cyt-1 gpd-2 gpd-3 mes-6 Abstract: Many Caenorhabditis elegans genes exist in operons in which polycistronic precursors are processed by cleavage at the 3' ends of upstream genes and trans splicing 100 to 400 nucleotides away, at the 5' ends of downstream genes, to generate monocistronic messages. Of the two spliced leaders, SL1 is trans spliced to the 5' ends of upstream genes, whereas SL2 is reserved for downstream genes in operons. However, there are isolated examples of what appears to be a different sort of operon, in which trans splicing is exclusively to SL1 and there is no intercistronic region; the polyadenylation signal is only a few base pairs upstream of the trans-splice site. We have analyzed the processing of an operon of this type by inserting the central part of mes-6/cks-1 into an SL2-type operon. In this novel context, cks-1 is trans spliced only to SL1, and mes-6 3'-end formation occurs normally, demonstrating that this unique mode of processing is indeed intrinsic to this kind of operon, which we herein designate "SL1-type." An exceptionally long polypyrimidine tract found in the 3' untranslated regions of the three known SL1-type operons is shown to be required for the accumulation of both upstream and downstream mRNAs. Mutations of the trans-splice and poly(A) signals indicate that the two processes are independent and in competition, presumably due to their close proximity, raising the possibility that production of upstream and downstream ------------------- Key: 3316 Medline: 99078028 Authors: Liu Y;Hengartner MO;Herr W Title: Selected elements of herpes simplex virus accessory factor HCF are highly conserved in Caenorhabditis elegans. Citation: Molecular and Cellular Biology 19: 909-915 1999 Type: ARTICLE Genes: hcf-1 Abstract: HCF is a mammalian nuclear protein that undergoes proteolytic processing and is required for cell proliferation. During productive herpes simplex virus (HSV) infection, the viral transactivator VP16 associates with HCF to initiate HSV gene transcription. Here, we show that the worm Caenorhabditis elegans possesses a functional homolog of mammalian HCF that can associate with and activate the viral protein VP16. The pattern of sequence conservation, however, is uneven. Sequences required for mammalian HCF processing are not present in C. elegans HCF. Furthermore, not all elements of mammalian HCF that are required for promoting cell proliferation are conserved. Nevertheless, unexpectedly, C. elegans HCF can promote mammalian cell proliferation because a region of HCF that is conserved can promote mammalian cell proliferation better than its human counterpart. These results suggest that HCF possesses a highly conserved role in metazoan cell proliferation which is targeted by VP16 to regulate HSV infection. The precise mechanisms, however, by which HCF functions in mammals and worms appear to differ. ------------------- Key: 3317 Medline: 99071313 Authors: Zhou HM;Walthall WW Title: UNC-55, an orphan nuclear hormone receptor, orchestrates synaptic specificity among two classes of motor neurons in Caenorhabditis elegans. Citation: Journal of Neuroscience 18: 10438-10444 1998 Type: ARTICLE Genes: unc-30 unc-55 nDf24 nDf25 Abstract: Loss of UNC-55 function in the nematode Caenorhabditis elegans causes one motor neuron class, the ventral D (VD) motor neurons, to adopt the synaptic pattern of another motor neuron class, the dorsal D (DD) motor neurons. Here we show that unc-55 encodes a member of the nuclear hormone receptor gene family that is similar to the vertebrate chicken ovalbumin upstream promoter transcription factors. Although the VD and DD motor neuron classes arise from different lineages at different developmental stages, they share a number of structural and functional features that appear to be the product of identical genetic programs. UNC-55 is expressed in the VD but not the DD motor neurons to modify this genetic program and to create the synaptic pattern that distinguishes the two motor neuron classes from one another. ------------------- Key: 3318 Medline: 99101145 Authors: Lee YS;Park YS;Chang DJ;Hwang JM;Min CK;Kaang BK;Cho NJ Title: Cloning and expression of a G protein-linked acetylcholine receptor from Caenorhabditis elegans. Citation: Journal of Neurochemistry 72: 58-65 1999 Type: ARTICLE Genes: gar-1 Abstract: We have isolated a cDNA clone from the nematode Caenorhabditis elegans that encodes a protein of greatest sequence similarity to muscarinic acetylcholine receptors. This gene codes for a polypeptide of 682 amino acids containing seven putative transmembrane domains. The amino acid identities, excluding a highly variable middle portion of the third intracellular loop, to the human m1-m5 receptors are 28-34%. When this cloned receptor was coexpressed with a G protein-gated inwardly rectifying K+ channel (GIRK1) in Xenopus oocyte, acetylcholine was able to elicit the GIRK current. This acetylcholine-induced current was substantially inhibited by the muscarinic antagonist atropine in a reversible manner. However, another muscarinic agonist oxotremorine and antagonists scopolamine and pirenzepine had little or negligible effects on this receptor. Taken together, these results suggest that the cloned gene encodes a G protein-linked acetylcholine receptor that is most similar to but pharmacologically distinct from muscarinic acetylcholine ------------------- Key: 3319 Medline: 99101175 Authors: Etter A;Cully DF;Liu KK;Reiss B;Vassilatis DK;Schaeffer JM;Arena JP Title: Picrotoxin blockade of invertebrate glutamate-gated chloride channels: Subunit dependence and evidence for binding within the pore. Citation: Journal of Neurochemistry 72: 318-326 1999 Type: ARTICLE Genes: Abstract: Glutamate-gated chloride channels have been described in nematodes, insects, crustaceans, and mollusks. Subunits from the nematode and insect channels have been cloned and are phylogenetically related to the GABA and glycine ligand-gated chloride channels. Ligand-gated chloride channels are blocked with variable potency by the nonselective blocker picrotoxin. The first two subunits of the glutamate-gated chloride channel family, GluCl alpha and GluCl beta, were cloned from the free living nematode Caenorhabditis elegans. In this study, we analyze the blockade of these novel channels by picrotoxin. In vitro synthesized GluCl alpha and GluCl beta RNAs were injected individually or coinjected into Xenopus oocytes. The EC50 values for picrotoxin block of homomeric GluCl alpha and GluCl beta were 59 mu M and 77 nM, respectively. Picrotoxin block of homomeric GluCl beta channels was promoted during activation of membrane current with glutamate. In addition, recovery from picrotoxin block was faster during current activation by glutamate. A chimeric channel between the N-terminal extracellular domain of GluCl alpha and the C-terminal membrane-spanning domain of GluCl beta localized the higher affinity picrotoxin binding site to the membrane-spanning domains of GluCl beta. A point mutation within the M2 membrane-spanning domain of GluCl beta reduced picrotoxin sensitivity >10,000-fold. We conclude that picrotoxin blocks GluCl channels by binding to a site accessible when the channel is open. ------------------- Key: 3320 Medline: 99069487 Authors: Schumacher JM;Golden A;Donovan PJ Title: AIR-2: An Aurora/Ip11-related protein kinase associated with chromosomes and midbody microtubules is required for polar body extrusion and cytokinesis in C. elegans embyros. Citation: Journal of Cell Biology 143: 1635-1646 1998 Type: ARTICLE Genes: air-1 air-2 tra-2 Abstract: An emerging family of kinases related to the Drosophila Aurora and budding yeast Ipl1 proteins has been implicated in chromosome segregation and mitotic spindle formation in a number of organisms. Unlike other Aurora/Ipl1-related kinases, the Caenorhabditis elegans orthologue, AIR-2, is associated with meiotic and mitotic chromosomes. AIR-2 is initially localized to the chromosomes of the most mature prophase I-arrested oocyte residing next to the spermatheca. This localization is dependent on the presence of sperm in the spermatheca. After fertilization, AIR-2 remains associated with chromosomes during each meiotic division. However, during both meiotic anaphases, AIR-2 is present between the separating chromosomes. AIR-2 also remains associated with both extruded polar bodies. In the embryo, AIR-2 is found on metaphase chromosomes, moves to midbody microtubules at anaphase, and then persists at the cytokinesis remnant. Disruption of AIR-2 expression by RNA-mediated interference produces entire broods of one-cell embryos that have executed multiple cell cycles in the complete absence of cytokinesis. The embryos accumulate large amounts of DNA and microtubule asters. Polar bodies are not extruded, but remain in the embryo where they continue to replicate. The cytokinesis defect appears to be late in the cell cycle because transient cleavage furrows initiate at the proper location, but regress before the division is complete. Additionally, staining with a marker of midbody microtubules revealed that at least some of the components of the midbody are not well localized in the absence of AIR-2 activity. Our results suggest that during each meiotic and mitotic division, AIR-2 may coordinate the congression of metaphase chromosomes with the subsequent events of polar body extrusion and cytokinesis. ------------------- Key: 3321 Medline: 99069210 Authors: Hawkins N;Garriga G Title: Asymmetric cell division: from A to Z. Citation: Genes & Development 12: 3625-3638 1998 Type: REVIEW Genes: apr-1 ham-1 lin-17 lin-44 mom-1 mom-2 mom-3 mom-4 mom-5 pop-1 unc-86 wrm-1 Abstract: Cell divisions producing two daughter cells that adopt distinct fates are defined as asymmetric. In all organisms, ranging from bacteria to mammals, in which development has been studied extensively, asymmetric cell divisions generate cell diversity. Asymmetric cell divisions can be achieved by either intrinsic or extrinsic mechanisms. Intrinsic mechanisms involve the preferential segregation of cell fate determinants to one of two daughter cells during mitosis. Asymmetrically segregated factors that bind cell fate determinants and orient the mitotic spindle may also be necessary to ensure the faithful segregation of determinants into only one daughter cell. Extrinsic mechanisms involve cell-cell communication. In metazoans, a dividing's cell's social contex provides a wealth of positional information and opportunity for cell-cell interactions. Interactions between daughter cells or between a daughter cell and other nearby cells could specify daughter cell fate. Interaction between a progenitor cell and its environment can also influence cell polarity by directing spindle orientation and the asymmetric distribution of developmental potential to daughter cells. Recent studies have indicated that a combination of intrinsic and extrinsic mechanisms specify distinct daughter cell fates during asymmetric cell divisions. We focus on asymmetric cell divisions that occur during the development of the Caenorhabditis elegans and Drosophila nervous system. Although we touch upon asymmetric cell divisions in the early C. elegans embryo, ------------------- Key: 3322 Medline: 99069124 Authors: Wiegner O;Schierenberg E Title: Specification of gut cell fate differs significantly between the nematodes Acrobeloides nanus and Caenorhabditis Citation: Developmental Biology 204: 3-14 1998 Type: ARTICLE Genes: Abstract: The classic view of a strictly cell-autonomous development in nematode embryos has been overturned in recent years with the demonstration of various inductive interactions during early development of Caenorhabditis elegans. To examine how conserved the pattern of embryonic cell specification is among nematodes, we have begun to study the pattern in other species after selective elimination of certain early blastomeres. Here we report considerable differences in specification of the gut lineage between C. elegans and Acrobeloides nanus, another free-living soil nematode belonging to the same order. In C. elegans none of the early blastomeres is by itself able to establish a gut lineage for which an inductive interaction between the somatic EMS cell and its germline sister P-2 is required. In contrast, in A. nanus all blastomeres of the 3-cell stage carry the potential to generate gut cells. Our data suggest that repressive interactions take place among blastomeres to ensure that under normal conditions only one of them executes the gut fate. Thus, in related species of nematodes with a very conserved morphology, the assignment of cell fate during early embryogenesis appears to involve quite different strategies. ------------------- Key: 3323 Medline: 99069142 Authors: Kuwabara PE;Okkema PG;Kimble J Title: Germ-line regulation of the Caenorhabditis elegans sex-determining gene tra-2. Citation: Developmental Biology 204: 251-262 1998 Type: ARTICLE Genes: fem-1 fem-3 fog-2 mor-2 tra-2 Abstract: The Caenorhabditis elegans sex-determining gene tra-2 promotes female development of the XX hermaphrodite soma and germ line. We previously showed that a 4.7-kb tra-2 mRNA, which encodes the membrane protein TRA-2A, provides the primary feminizing activity of the tra-2 locus. This paper focuses on the germ-line activity and regulation of tra-2. First, we characterize a 1.8-kb tra-2 mRNA, which is hermaphrodite-specific and germ-line-dependent. This mRNA encodes TRA-2B, a protein identical to a predicted intracellular domain of TRA-2A. We show that the 1.8-kb mRNA is oocyte-specific, suggesting that it is involved in germ-line or embryonic sex determination. Second, we identify a tra-2 maternal effect on breed size that may be associated with the 1.8-kb mRNA. Third, we investigate seven dominant tra-2(mx) (for mixed character) mutations that sexually transform hermaphrodites to females by eliminating hermaphrodite spermatogenesis. Each of the tra-2(mx) mutants possesses a nonconserved missense change in a 22-amino-acid region common to bath TRA-2A and TRA-2B, called the MX region. We propose that the MX region mediates a posttranslational regulation of tra-2 essential for the onset of hermaphrodite spermatogenesis. Finally, we discuss aspects of tra-2 function and regulation that are specific to the unusual control of cell fate in the hermaphrodite germ line. ------------------- Key: 3324 Medline: 99069143 Authors: Williams-Masson EM;Heid PJ;Lavin CA;Hardin J Title: The cellular mechanism of epithelial rearrangement during morphogenesis of the Caenorhabditis elegans dorsal hypodermis. Citation: Developmental Biology 204: 263-276 1998 Type: ARTICLE Genes: die-1 Abstract: The mechanism by which epithelial cells rearrange is a process that is central to epithelial morphogenesis, yet remains poorly understood. We have investigated epithelial cell rearrangement in the dorsal hypodermis of the Caenorhabditis elegans embryo, in which two rows of epithelial cells rearrange in a morphogenetic process known as dorsal intercalation. The intercalating cells extend basal protrusions which squeeze between their opposing neighbors beneath their adherens junctions. As the intercalating cells move forward, these protruding tips become broader in the anterior-posterior and dorsoventral dimensions, effectively "plowing through" the adherens junctions and forcing an opening for the remainder of the intercalating cell to insert between the contralateral cells. These cell movements are dependent upon intact cytoarchitecture, since the pharmacological disruption of microtubules or actin filaments blocks cell rearrangement. The cells appear to intercalate independently of immediately adjacent neighboring hypodermal cells because dorsal intercalation is not blocked by the ablation of the progenitors for either half of the lateral hypodermal cells or the posterior half of the dorsal hypodermis. This is the first case in which the protrusive mechanism underlying epithelial cell rearrangement has been characterized, and we propose a model describing how epithelial cells rearrange within the confines of an epithelial monolayer, and discuss the mechanisms that may be guiding these directed cell movements. ------------------- Key: 3325 Medline: 98453399 Authors: Schumacher JM;Ashcroft N;Donovan PJ;Golden A Title: A highly conserved centrosomal kinaase, AIR-1, is required for accurate cell cycle progression and segregation of developmental factors in Caenorhabditis elegans embyros. Citation: Development 125: 4391-4402 1998 Type: ARTICLE Genes: air-1 air-2 pie-1 Abstract: S. cerevisiae Ipl1, Drosophila Aurora, and the mammalian centrosomal protein IAK-1 define a new subfamily of serine/threonine kinases that regulate chromosome segregation and mitotic spindle dynamics. Mutations in ipl1 and aurora result in the generation of severely aneuploid cells and, in the case of aurora, monopolar spindles arising from a failure in centrosome separation. Here we show that a related, essential protein from C. elegans, AIR-1 (Aurora/Ipl1 related), is localized to mitotic centrosomes. Disruption of AIR-1 protein expression in C. elegans embryos results in severe aneuploidy and embryonic lethality. Unlike aurora mutants, this aneuploidy does not arise from a failure in centrosome separation. Bipolar spindles are formed in the absence of AIR-1, but they appear to be disorganized and are nucleated by abnormal-looking centrosomes. In addition to its requirement during mitosis, AIR-1 may regulate microtubule-based developmental processes as well. Our data suggests AIR-1 plays a role in P-granule segregation and the association of the germline factor PIE-1 with ------------------- Key: 3326 Medline: 99092382 Authors: Fujita M;Kawano T;Terashima K;Tanaka Y;Sakamoto H Title: Expression of spliceosome-associated protein 49 is required for early embryogenesis in Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 253: 80-84 1998 Type: ARTICLE Genes: mom-2 Abstract: Spliceosome-associated protein 49 (SAP 49) is a subunit of the splicing factor SF3b, which is involved in 3' splice site recognition in pre-mRNA splicing. Here we show the Caenorhabditis elegans SAP 49 gene is located in a gene cluster that is transcribed polycistronically with three other upstream genes. Transgenic analysis of expression of the gene cluster under the control of its native promoter revealed that in spite of its predicted essential function for all cells, the C. elegans SAP 49 expression is limited to specific cells in both larval and adult stages. When the endogenous SAP 49 expression was inhibited by microinjection of an antisense RNA, embryos laid by the injected worms ceased to develop at a specific stage of early embryogenesis, indicating that SAP 49 plays an essential role in the development of C. elegans. These results raise the possibility that SAP 49 is a cell-specific, not constitutive, splicing factor. ------------------- Key: 3327 Medline: 99072547 Authors: van Swinderen B;Galifianakis A;Crowder CM Title: Common genetic determinants of halothane and isoflurane potencies in Caenorhabditis elegans. Citation: Anesthesiology 89: 1509-1517 1998 Type: ARTICLE Genes: Abstract: Background: Genetics provides a may to evaluate anesthetic action simultaneously at the molecular and behavioral levels. Results from strains that differ in anesthetic sensitivity have been mixed in their support of unitary theories of anesthesia. Here the authors use the previously demonstrated large variation of halothane sensitivities in Caenorhabditis elegans recombinant inbred strains to assess the similarities of the determinants of halothane action with those of another volatile anesthetic, Isoflurane. Methods: The recombinant inbred strains, constructed from two evolutionarily distinct C. elegans lineages, were phenotyped. A coordination assay on agar quantified the sensitivity to the volatile anesthetics; median effective concentrations (EC(50)s) were calculated by nonlinear regression of concentration-response data and were correlated between the drugs for those strains tested in common. Genetic loci were identified by statistical association between EC(50)s and chromosomal markers. Results: The recombinant inbred strains varied dramatically in sensitivity to halothane and isoflurane, with a 10-fold range in EC(50)s. Heritability estimates for each drug were imprecise but altogether high ( 49-80%). Halothane and isoflurane EC(50)s were significantly correlated (r = 0.71, P < 10(-9)). Genetic loci controlling sensitivity were found for both volatile anesthetics; the most significant determinant colocalized on chromosome V. A smaller recombinant inbred strain study of ethanol-induced immobility segregated different genetic effects that did not correlate with sensitivity to either halothane or isoflurane. Conclusions: The genetic determinants driving the large variation in anesthetic sensitivity in these C elegans recombinant inbred strains are very similar for halothane and isoflurane sensitivity. ------------------- Key: 3328 Medline: 99088030 Authors: Zhu J;Fukushige T;McGhee JD;Rothman JH Title: Reprogramming of early embryonic blastomeres into endodermal progenitors by a Caenorhabditis elegans GATA Citation: Genes & Development 12: 3809-3814 1998 Type: ARTICLE Genes: elt-1 elt-2 end-1 end-3 lin-26 skn-1 wrm-1 Abstract: The END-1 GATA factor has been implicated in specifying endoderm in Caenorhabditis elegans and is the earliest known zygotic protein expressed in the lineage of E, the clonal endoderm progenitor. We report that ubiquitous end-1 expression during a critical period in embryogenesis causes all non-endodermal lineages to produce endoderm instead of ectoderm and/or mesoderm. END-1 expression bypasses the requirement for maternal SKN-1 and the maternal Wnt signaling pathway in endoderm formation. This suggests that a primary function of these maternal factors is to regulate zygotic end-1 expression, which is then sufficient to initiate the entire program for endoderm development. ------------------- Key: 3329 Medline: 99091056 Authors: Lu X;Horvitz HR Title: lin-35 and lin-53, Two genes that antagonize a C. elegans Ras pathway, encode proteins similar to Rb and its binding protein RbAp48. Citation: Cell 95: 981-991 1998 Type: ARTICLE Genes: col-10 hda-1 hda-2 hda-3 let-23 let-60 lin-2 lin-3 lin-7 lin-10 lin-15 lin-35 lin-45 lin-53 mpk-1 sem-5 qDf9 Abstract: The Ras signaling pathway for vulval induction in Caenorhabditis elegans is antagonized by the activity of the synthetic multivulva (synMuv) genes, which define two functionally redundant pathways. We have characterized two genes in one of these pathways. lin-35 encodes a protein similar to the tumor suppressor Rb and the closely related proteins p107 and p130. lin-53 encodes a protein similar to RbAp48, a mammalian protein that binds Rb. In mammals, Rb and related proteins act as regulators of E2F transcription factors, and RbAp48 may act with such proteins as a transcriptional corepressor. We propose that LIN-35 and LIN-53 antagonize the Ras signaling pathway in C. elegans by repressing transcription in the vulval precursor cells of genes required for the expression of vulval cell fates. ------------------- Key: 3330 Medline: 99026070 Authors: Nilsson L;Li X;Tiensuu T;Auty R;Greenwald I;Tuck S Title: Caenorhabditis elegans lin-25: cellular focus, protein expression and requirement for sur-2 during induction of vulval fates. Citation: Development 125: 4809-4819 1998 Type: ARTICLE Genes: let-23 let-60 lin-3 lin-10 lin-12 lin-15 lin-25 lin-39 mpk-1 sur-2 ctDp11 Abstract: Induction of vulval fates in the C. elegans hermaphrodite is mediated by a signal transduction pathway involving Pas and MAP kinase. Previous genetic analysis has suggested that tno potential targets of this pathway in the vulva precursor cells are two novel proteins, LIN-25 and SUR-2. In this report, we describe further studies of lin-25. The results of a genetic mosaic analysis together with those of experiments in which lin-25 was expressed under the control of an heterologous promoter suggest that the major focus of lin-25 during vulva induction is the vulva precursor cells themselves. We have generated antisera to LIN-25 and used these to analyse the pattern of protein expression. LIN-25 is present in all six precursor cells prior to and during vulva induction but later becomes restricted to cells of the vulval lineages. Mutations in genes in the Ras/MAP kinase pathway do not affect the pattern of expression but the accumulation of LIN-25 is reduced in the absence of sur-2. Overexpression of LIN-25 does not rescue sur-2 mutant defects suggesting that LIN-25 and SUR-2 may function together. LIN-25 is also expressed in the lateral hypodermis. Overexpression of LIN-25 disrupts lateral hypodermal cell fusion, suggesting that lin-25 may play a role in regulating cell fusions in C. elegans. ------------------- Key: 3331 Medline: 99030269 Authors: Schroeder DF;McGhee JD Title: Anterior-posterior patterning within the Caenorhabditis elegans endoderm. Citation: Development 125: 4877-4887 1998 Type: ARTICLE Genes: ceh-13 ges-1 lin-39 mab-5 pha-4 pie-1 pop-1 skn-1 nDf16 Abstract: The endoderm of higher organisms is extensively patterned along the anterior/posterior axis. Although the endoderm (gut or E lineage) of the nematode Caenorhabditis elegans appears to be a simple uniform tube, cells in the anterior gut show several molecular and anatomical differences from cells in the posterior gut. In particular, the gut esterase ges-l gene, which is normally expressed in all cells of the endoderm, is expressed only in the anterior-most gut cells when certain sequences in the ges-1 promoter are deleted. Using such a deleted ges-1 transgene as a biochemical marker of differentiation, we have investigated the basis of anterior-posterior gut patterning in C. elegans. Although homeotic genes are involved in endoderm patterning in other organisms, we show that anterior gut markers are expressed normally in C. elegans embryos lacking genes of the homeotic cluster. Although signalling from the mesoderm is involved in endoderm patterning in other organisms, we show that ablation of all non-gut blastomeres from the C. elegans embryo does not affect anterior gut marker expression; furthermore, ectopic guts produced by genetic transformation express anterior gut markers generally in the expected location and in the expected number of cells. We conclude that anterior gut fate requires no specific cell-cell contact but rather is produced autonomously within the E lineage. Cytochalasin D blocking experiments fully support this conclusion. Finally, the HMG protein POP-1, a downstream component of the Wnt signalling pathway, has recently been shown to be important in many anterior/posterior fate decisions during C. elegans embryogenesis (Lin, R,, Hill, R, J, and Priess, J, R, (1998) Cell 92, 229-239). When RNA-mediated interference is used to eliminate pop-1 function from the embryo, gut is still produced but anterior gut marker expression is abolished. We suggest that the C. elegans endoderm is patterned by elements of the Wnt/pop-1 signalling pathway acting autonomously within the E lineage. ------------------- Key: 3332 Medline: Authors: Patel MR Title: Effects of ivermectin on eggs and first-stage larvae of nematodes. Citation: Bios 68: 152-162 1997 Type: ARTICLE Genes: Abstract: Isolated eggs of the free-living nematode Caenorhabditis elegans and parasitic nematode Haemonchus contortus were tested for susceptibility to ivermectin, a proven antiparasitic agent. Ivermectin inhibited hatching of C. elegans eggs at the highest concentration tested (400 ug/ml). At an intermediate concentration (100 ug/ml), hatching was permitted, but all of the newly hatched first-stage larvae were killed by the drug. At lower concentrations (25 ug/ml and 6.25 ug/ml), the drug permitted hatching and survival of more than 85% of the first-stage larvae. The control eggs and first-stage larvae displayed a similarly high viability. A replicate experiment using the parasitic nematode H. contortus showed similar results, but a somewhat greater sensitivity to the drug. At the highest level tested (400 ug/ml), the eggs did not embryonate and so did not hatch. At 100 ug/ml, they embryonated but did not hatch. At a concentration of 25 ug/ml, hatching was slightly inhibited in comparison to the controls and motility of the newly hatched first-stage larvae was judged to be impaired. Eggs exposed to the lowest concentration (6.25 ug/ml), like the control eggs, had a hatching rate of greater than 85%, with no locomotor impairment. Thiabendazole, used as a positive control, caused complete blockade of embryonation. ------------------- Key: 3333 Medline: Authors: Johnson TE;Shook DR Title: Identification and mapping of genes determining longevity. Citation: "Between Zeus and the Salmon: The Biodemography of Longevity". K W Wachter and CE Finch (eds). National Academy Press, Washington, D.C. : 108-126 1997 Type: REVIEW Genes: age-1 clk-1 clk-2 clk-3 daf-2 daf-12 daf-16 daf-23 gro-1 rad-8 spe-26 Abstract: The world of modern biology is unified by genetics. Genetic approaches have the ability to transcend species and provide cross-links between fields for several reasons. First, is the fact that all species are evolutionarily related. Thus, distinct species have similar gene function, and DNA sequence homology can be found between even distantly related species. Indeed, DNA sequence homology is used as a metric device to determine evolutionary relationships among species. Second, molecular genetic manipulation changes both the genotype and phenotype of an organism. Such manipulations represent an extremely fine-scale tool for dissection of the underlying biochemistry, physiology, anatomy, and development of an individual species. Because virtually any gene can be manipulated at will in many species, a dedicated approach can lead to an unraveling of the relationship between genotype and phenotype for almost any gene in these ------------------- Key: 3334 Medline: Authors: Mikola J Title: Effects of microbivore species composition and basal resource enrichment on trophic-level biomasses in an experimental microbial-based soil food web. Citation: Oecologia 117: 396-403 1998 Type: ARTICLE Genes: Abstract: Previous theoretical and empirical evidence suggests that species composition within trophic levels may profoundly affect the response of trophic-level biomasses to enhanced basal resources. To test whether species composition of microbivorous nematodes has such an effect in microbial-based soil food webs, I created three microcosm food webs, consisting of bacteria, fungi, bacterial-feeding nematodes (Acrobeloides tricornus. Caenorhabditis elegans), fungal-feeding nematodes (Aphelenchus avenae, Aphelenchoides sp.) and a predatory nematode (Prionchulus punctatus). The food webs differed in species composition at the second trophic level: food web A included A. tricornus and Aph. avenae. food web B included C. elegans and Aphelenchoides sp., and food web AB included all four species. I increased basal resources by adding glucose to half of the replicates of each food web, and sampled microcosms destructively four times during a 22-week experiment to estimate the biomass of organisms at each trophic level. Microbivore species composition significantly affected bacterivore and fungivore biomass but not bacterial, fungal or predator biomass. Greatest bacterivore and fungivore biomass was found in food web A. intermediate biomass in food web AB, and smallest biomass in food web B. Basal resource addition increased the biomass of microbes and microbivores but did not affect predator biomass. Importantly, microbivore species composition did not significantly modify the effect of additional resources on trophic-level biomasses. The presence of a competitor reduced the biomass of A. tricornus and Aph. avenae, in that the biomass of these species was less in food web AB than in food web A, whereas the biomass of C. elegans and Aphelenchoides sp, was not affected by their potential competitors. The biomass of Aph. avenae increased with additional resources in the absence of the competitor only, while the biomass of A. tricornus and Aphelenchoides sp. increased also in the presence of their competitors. The results imply that microbivore species composition may determine the second-level biomass in simple microbe-nematode food webs, but may not significantly affect biomass at other levels or modify the response of trophic-level biomasses to enhanced basal resources. The study also shows that even if the role of predation in a food web is diminished, the positive response of organisms to increased resource availability ------------------- Key: 3335 Medline: 99069219 Authors: Cox DN;Chao A;Baker J;Chang L;Qiao D;Lin H Title: A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal. Citation: Genes & Development 12: 3715-3727 1998 Type: ARTICLE Genes: prg-1 prg-2 Abstract: Germ-line stem cells (GSCs) serve as the source for gametogenesis in diverse organisms. We cloned and characterized the Drosophila piwi gene and showed that it is required for the asymmetric division of GSCs to produce and maintain a daughter GSC but is not essential for the further differentiation of the committed daughter cell. Genetic mosaic and RNA in situ analyses suggest that piwi expression in adjacent somatic cells regulates GSC division. piwi encodes a highly basic novel protein, well conserved during evolution. We isolated piwi homologs in Caenorhabditis elegans and humans and also identified Arabidopsis piwi-like genes known to be required for meristem cell maintenance. Decreasing C. elegans piwi expression reduces the proliferation of GSC-equivalent cells. Thus, piwi represents a novel class of genes required for GSC division in diverse organisms. ------------------- Key: 3336 Medline: 99087426 Authors: Li N;Baehr W Title: Expression and characterization of human PDE delta and its Caenorhabditis elegans ortholog CE delta. Citation: FEBS Letters 440: 454-457 1998 Type: ARTICLE Genes: unc-119 Abstract: Cyclic GMP phosphodiesterase (PDE) is rod photoreceptor dish membrane-associated via C-terminal lipid tails. PDE delta, a recently identified subunit, was shown to disrupt PDE/membrane interaction under physiological conditions, without affecting PDE catalytic activity. We found that a PDE delta ortholog from the eyeless nematode Caenorhabditis elegans (termed CE delta) solubilizes bovine PDE in vitro with an EC50 very similar to PDE delta. Immobilized PDE delta and CE delta both bind, in addition to bovine PDE, an N-terminal fragment of human retinitis pigmentosa GTPase regulator, but not rhodopsin kinase and Ran binding protein 1. The results suggest that PDE delta and CE delta may regulate membrane binding of a variety of proteins in photoreceptors and other tissues. ------------------- Key: 3337 Medline: 99136797 Authors: Jazwinski SM Title: Genetics of longevity. Citation: Experimental Gerontology 33: 773-783 1998 Type: REVIEW Genes: age-1 clk-1 daf-2 daf-16 daf-23 Abstract: Recent studies on the genetics of aging in the yeast Saccharomyces cerevisiae, the roundworm Caenorhabditis elegans, and the fruit fly Drosophila melanogaster have converged revealing the central role of metabolic capacity and resistance to stress in determining life span. Signal transduction has emerged from these studies as an important molecular mechanism underlying longevity. In their broad features, the results obtained in these genetic models are applicable to the dietary restriction paradigm in mammals, suggesting a general significance. It will be of interest to determine whether many of the molecular details will also pertain. The examination of centenarian populations for the frequency of certain alleles of pertinent genes may provide insights into the relevance of the conclusions of studies in invertebrates to human aging. These population genetic studies can be augmented by mechanistic studies in transgenic mice. ------------------- Key: 3338 Medline: 99080040 Authors: Treinin M;Gillo B;Liebman L;Chalfie M Title: Two functionally dependent acetylcholine subunits are encoded in a single Caenorhabditis elegans operon. Citation: Proceedings of the National Academy of Sciences USA 95: 15492-15495 1998 Type: ARTICLE Genes: deg-1 deg-3 des-2 Abstract: The deg-3 gene from the nematode Caenorhabditis elegans encodes an alpha subunit of a nicotinic acetylcholine receptor that was first identified by a dominant allele, u662, which produced neuronal degeneration. Because deg-3 cDNAs contain the SL2 trans-spliced leader, we suggested that deg-3 was transcribed as part of a C. elegans operon. Here we show that des-2, a gene in which mutations suppress deg-3(u662), is the upstream gene in that operon. The des-2 gene also encodes an alpha subunit of a nicotinic acetylcholine receptor. As expected for genes whose mRNAs are formed from a single transcript, both genes have similar expression patterns. This coexpression is functionally important because (i) des-2 is needed for the deg-3(u662) degenerations in vivo; (ii) an acetylcholine-gated channel is formed in Xenopus oocytes when both subunits are expressed but not when either is expressed alone; and (iii) channel activity, albeit apparently altered from that of the wild-type channel, results from the expression of a u662-type mutant subunit but, again, only when the wild-type DES-2 subunit is present. Thus, the operon structure appears to regulate the coordinate expression of two channel subunits. ------------------- Key: 3339 Medline: 99080042 Authors: Montgomery MK;Xu SQ;Fire A Title: RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 95: 15502-15507 1998 Type: ARTICLE Genes: cey-2 dpy-20 fem-1 lin-15 mex-3 pes-10 rol-6 smg-3 unc-22 unc-54 Abstract: Introduction of exogenous double-stranded RNA (dsRNA) into Caenorhabditis elegans has been shown to specifically and potently disrupt the activity of genes containing homologous sequences. In this study we present evidence that the primary interference effects of dsRNA are posttranscriptional. First, we examined the primary DNA sequence after dsRNA-mediated interference and found no evidence for alterations. Second, we found that dsRNA-mediated interference with the upstream gene in a polar operon had no effect on the activity of the downstream gene; this finding argues against an effect on initiation or elongation of transcription. Third, we observed by in situ hybridization that dsRNA-mediated interference produced a substantial, although not complete, reduction in accumulation of nascent transcripts in the nucleus, while cytoplasmic accumulation of transcripts was virtually eliminated. These results indicate that the endogenous mRNA is the target for interference and suggest a mechanism that degrades the targeted RNA before translation can occur. This mechanism is not dependent on the SMG system, an mRNA surveillance system in C. elegans responsible for targeting and destroying aberrant messages. We suggest a model of how dsRNA might function in a catalytic mechanism to target homologous mRNAs for ------------------- Key: 3340 Medline: 99080092 Authors: Wu G;Hubbard EJA;Kitajewski JK;Greenwald I Title: Evidence for functional and physical association between Caenorhabditis elegans SEL-10, a Cdc4p-related protein, and SEL-12 presenilin. Citation: Proceedings of the National Academy of Sciences USA 95: 15787-15791 1998 Type: ARTICLE Genes: hop-1 lin-12 sel-10 sel-12 Abstract: Mutations in either of two human presenilin genes (PSI and PS2) cause Alzheimer's disease. Here we describe genetic and physical interactions between Caenorhabditis elegans SEL-10, a member of the Cdc4p family of proteins, and SEL-12, a C. elegans presenilin. We show that loss of sel-10 activity can suppress the egg-laying defective phenotype associated with reducing sel-12 activity, and that SEL-10 can physically complex with SEL-12. Proteins of the Cdc4p family have been shown to target proteins for ubiquitin-mediated turnover. The functional and physical interaction between sel-10 and sel-12 therefore offers an approach to understanding how presenilin levels are ------------------- Key: 3341 Medline: 99077700 Authors: Zhang Y;Ferreira HB;Greenstein D;Chisholm A;Emmons SW Title: Regulated nuclear entry of the C. elegans Pax-6 transcription factor. Citation: Mechanisms of Development 78: 179-187 1998 Type: ARTICLE Genes: mab-18 vab-3 Abstract: It is shown that the C. elegans Pax-6 locus encodes two protein isoforms. One contains a Paired DNA binding domain as well as a homeodomain; the other consists only of the carboxy-terminal portion of the locus encoding the homeodomain. These two isoforms are expressed in a variety of postembryonic cell lineages. In one set of lineages, nuclear localization of a homeodomain-only form (MAB-18 isoform) appears to be under temporal and spatial control. Nuclear localization of MAB-18 is correlated with the genetic requirement for mab-18 and with activation of a reporter gene driven by a mab-18 promoter. Reporter gene expression is dependent on mab-18 gene activity. It is hypothesized that a positive feedback loop is activated by regulated nuclear entry. ------------------- Key: 3342 Medline: 99074291 Authors: Shaham S Title: Identification of multiple Caenorhabditis elegans caspases and their potential roles in proteolytic cascades. Citation: Journal of Biological Chemistry 273: 35109-35117 1998 Type: ARTICLE Genes: ced-3 csp-1 csp-2 csp-3 Abstract: Proteases of the caspase family play a central role in the execution of programmed cell death in all metazoans examined. The Caenorhabditis elegans caspase CED-3 is essential for programmed cell death in this organism. Three additional C. elegans caspase-related genes, csp-l (caspase homolog-(1) under bar), which encodes the csp-1A, csp-1B, and csp-1C RNA species; csp-2, which encodes the csp-2A and csp-2B RNA species; and csp-3 are identified. CSP-1A, CSP-1B, CSP-2A, and CSP-BB proteins are similar in sequence to caspase proproteins. CSP-1C is similar only to large caspase subunits, and CSP-3 is similar only to small caspase subunits. CSP-IB can be activated to become a cysteine protease by processing at internal aspartate residues. Activated CSP-IB can cleave the CSP-1B, CED-3, and CSP-BE proproteins, and activated CED-3 can cleave the CED-3 and CSP-2B proproteins. Inhibitor and synthetic substrate studies further suggest that activated CSP-1B and activated CED-3 have different substrate specificities. These results suggest that C. elegans encodes several caspases that might act in proteolytic cascades to regulate processes such as programmed cell death. ------------------- Key: 3343 Medline: 99061552 Authors: Kuwahara M;Ishibashi K;Gu Y;Terada Y;Kohara Y;Marumo F;Sasaki S Title: A water channel of the nematode C. elegans and its implications for channel selectivity of MIP proteins. Citation: American Journal of Physiology - Cell Physiology 44: C1459-C1464 1998 Type: ARTICLE Genes: Abstract: A genome project focusing on the nematode Caenorhabditis elegans has demonstrated the presence of eight cDNAs belonging to the major intrinsic protein superfamily. We functionally characterized one of these cDNAs named C01G6.1. Injection of C01G6.1 cRNA increased the osmotic water permeability (P-f) of Xenopus oocytes 11-fold and the urea permeability 4.5-fold but failed to increase the glycerol permeability. It has been speculated that the MIP family may be separated into two large subfamilies based on the presence or absence of two segments of extra amino acid residues (similar to 15 amino acids) at the second and third extracellular loops. Because C01G6.1 (designated AQP-CE1), AQP3, and glycerol facilitator (GlpF) all have these two segments, we replaced the segments of AQP-CE1 with those of AQP3 and GlpF to identify their roles. The functional characteristics of these mutants were principally Similar to that of wild-type AQP-CE1, although the values of Pc and urea permeability were decreased by 39-74% and 28-65%, respectively. These results suggest that the two segments of extra amino acid residues may not contribute to channel selectivity or formation of the route ------------------- Key: 3345 Medline: Authors: Blaxter M Title: Caenorhabditis elegans is a nematode (correction). Citation: Science 283: 35- 1999 Type: ARTICLE Genes: Abstract: ------------------- Key: 3346 Medline: 99113826 Authors: Plasterk RHA Title: Hershey heaven and Caenorhabditis elegans. Citation: Nature Genetics 21: 63-64 1999 Type: REVIEW Genes: Abstract: One of the founders of molecular biology, Al Hershey, proffered a vision of heaven, in which one would come into the lab every morning knowing what experiment to do, knowing that it was going to work and knowing that the results would be important. Whether the authors of the Caenorhabditis elegans genome project, published recently in Science felt they had ascended into heaven while performing this gigantic piece of work is unclear, but the project seems to fulfill Hershey's criteria. ------------------- Key: 3347 Medline: 99102962 Authors: Ogg S;Ruvkun G Title: The C. elegnas PTEN homolog, DAF-18, acts in the insulin receptor-like metabolic signaling pathway. Citation: Molecular Cell 2: 887-893 1998 Type: ARTICLE Genes: age-1 akt-1 akt-2 daf-2 daf-16 daf-18 Abstract: An insulin-like signaling pathway, From the DAF-2 receptor, the AGE-I phosphoinositide 3-kinase, and the AKT-1/AKT-2 serine/threonine kinases to the DAF-16 Fork head transcription factor, regulates the metabolism, development, and life span of Caenorhabditis elegans. Inhibition of daf-18 gene activity bypasses the normal requirement for AGE-I and partially bypasses the need for DAF-P signaling. The suppression of age-1 mutations by a daf-18 mutation depends an AKT-1/AKT-2 signaling, showing that DAF-18 acts between AGE-1 and the AKT input to DAF-16 transcriptional regulation. daf-18 encodes a homolog of the human turner suppressor PTEN (MMAC1/TEP1), which has 3-phosphatase activity toward phosphatidylinositol 3,4,5-trisphosphate (PIP3). DAF-18 PTEN may normally limit AKT-1 and AKT-2 activation by decreasing PIP3, levels. The action of daf-18 in this metabolic control pathway suggests that mammalian PTEN may modulate insulin signaling and may be variant in diabetic: pedigrees. ------------------- Key: 3348 Medline: 9870940 Authors: Duerr JS;Frisby DL;Gaskin J;Duke A;Asermely K;Huddleston D;Eiden LE;Rand JB Title: The cat-1 gene of Caenorhabditis elegans encodes a vesicular monoamine transporter required for specific monoamine-dependent behaviors. Citation: Journal of Neuroscience 19: 72-84 1999 Type: ARTICLE Genes: cat-1 egl-6 egl-13 egl-14 unc-104 Abstract: We have identified the Caenorhabditis elegans homolog of the mammalian vesicular monoamine transporters (VMATs); it is 47% identical to human VMAT1 and 49% identical to human VMAT2. C. elegans VMAT is associated with synaptic vesicles in similar to 25 neurons, including ail of the cells reported to contain dopamine and serotonin, plus a few others. When C. elegans VMAT is expressed in mammalian cells, it has serotonin and dopamine transport activity; norepinephrine, tyramine, octopamine, and histamine also have high affinity for the transportee The pharmacological profile of C. elegans VMAT is closer to mammalian VMAT2 than VMAT1. The C. elegans VMAT gene is cat-1; cat-1 knock-outs are totally deficient for VMAT immunostaining and for dopamine-mediated sensory behaviors, yet they are viable and grow relatively well. The cat-1 mutant phenotypes can be rescued by C. elegans VMAT constructs and also (at least partially) by human VMAT1 or VMAT2 transgenes. It therefore appears that the function of amine neurotransmitters can be completely dependent on their loading into synaptic vesicles. ------------------- Key: 3349 Medline: 9870947 Authors: Lee RYN;Sawin ER;Chalfie M;Horvitz HR;Avery L Title: EAT-4, a homolog of a mammalian sodium-dependent inorganic phosphate cotransporter, is necessary for glutamatergic neurotransmission in Caenorhabditis elegans. Citation: Journal of Neuroscience 19: 159-167 1999 Type: ARTICLE Genes: eat-4 glr-1 Abstract: The Caenorhabditis elegans gene eat-4 affects multiple glutamatergic neurotransmission pathways. We find that eat-4 encodes a protein similar in sequence to a mammalian brain-specific sodium-dependent inorganic phosphate cotransporter I (BNPI). Like BNPI in the rat CNS, eat-4 is expressed predominantly in a specific subset of neurons, including several proposed to be glutamatergic. Loss-of-function mutations in eat-4 cause defective glutamatergic chemical transmission but appear to have little effect on other functions of neurons. Our data suggest that phosphate ions imported into glutamatergic neurons through transporters such as EAT-4 and BNPI are required specifically for glutamatergic neurotransmission. ------------------- Key: 3350 Medline: 99098940 Authors: Jin Y;Jorgensen E;Hartwieg E;Horvitz HR Title: The Caenorhabditis elegans gene unc-25 encodes glutamic acid decarboxylase and is required for synaptic transmission but not synaptic development. Citation: Journal of Neuroscience 19: 539-548 1999 Type: ARTICLE Genes: unc-25 Abstract: The neurotransmitter GABA has been proposed to play a role during nervous system development. We show that the Caenorhabditis elegans gene unc-25 encodes glutamic acid decarboxylase (GAD), the GABA biosynthetic enzyme. unc-25 is expressed specifically in GABAergic neurons. Null mutations in unc-25 eliminate the UNC-25 protein or alter amino acids conserved in all known GADs, result in a complete lack of GABA, and cause defects in all GABA-mediated behaviors. In unc-25 mutants the GABAergic neurons have normal axonal trajectories and synaptic connectivity, and the size and shape of synaptic vesicles are normal. The number of synaptic Vesicles at GABAergic neuromuscular junctions is slightly increased. Cholinergic ventral nerve cord neurons, which innervate the same muscles as GABAergic ventral cord neurons, have normal morphology, connectivity, and synaptic vesicles. We conclude that GAD activity and GABA are not necessary for the development or maintenance of neuromuscular junctions ------------------- Key: 3351 Medline: 99038173 Authors: Arduengo PM;Appleberry OK;Chuang P;L'Hernault SW Title: The presenilin protein family member SPE-4 localizes to an ER/Golgi derived organelle and is required for proper cytoplasmic partitioning during Caenorhabditis elegans spermatogenesis. Citation: Journal of Cell Science 111: 3645-3654 1998 Type: ARTICLE Genes: hop-1 sel-12 spe-4 sup-7 sup-21 sup-24 sup-28 sDf5 Abstract: During Caenorhabditis elegans spermatogenesis, asymmetric partitioning of cellular components principally occurs via ER/Golgi-derived organelles, named fibrous body-membranous organelles. In C. elegans spe-4 mutants, morphogenesis of fibrous body-membranous organelle complexes is defective and spermatogenesis arrests at an unusual cellular stage with four haploid nuclei within a common cytoplasm. The spe-4 encoded integral membrane protein is a diverged member of the presenilin family implicated in early onset Alzheimer's disease. Specific antisera were used to show that SPE-4 resides within the fibrous body-membranous organelles membranes during wild-type spermatogenesis. Several spe-4 recessive mutants were examined for SPE-4 immunoreactivity and a deletion mutant lacks detectable SPE-4 while either of two missense mutants synthesize and localize immunoreactive SPE-4 within their fibrous body-membranous organelles. One of these missense mutations is located within a motif that is common to all presenilins. spe-4 mutants were also examined for other partitioning defects and tubulin was found to accumulate in unusual deposits close to the plasma membrane. These results suggest that wild-type SPE-4 is required for proper localization of macromolecules that are subject to ------------------- Key: 3352 Medline: 99085022 Authors: Chen S;Zhou SH;Sarkar M;Spence AM;Schachter H Title: Expression of three Caenorhabditis elegans N-acetylglucosaminyltransferase I genes during development. Citation: Journal of Biological Chemistry 274: 288-297 1999 Type: ARTICLE Genes: gly-12 gly-13 gly-14 Abstract: UDP-N-acetylglucosamine:alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I (GnT I) is a key enzyme in the synthesis of Asn-linked complex and hybrid glycans. Studies on mice with a null mutation in the GnT I gene have indicated that N-glycans play critical roles in mammalian morphogenesis. This paper presents studies on N-glycans during the development of the nematode Caenorhabditis elegans, We have cloned cDNAs for three predicted C. elegans genes homologous to mammalian GnT I (designated gly-12, gly-13, and gly-14), All three cDNAs encode proteins (467, 449, and 437 amino acids, respectively) with the domain structure typical of previously cloned Golgi-type glycosyltransferases. Expression in both insect cells and transgenic worms showed that gly-12 and gly-14, but not gly-13, encode active GnT I. All three genes were expressed throughout worm development (embryo, larval stages L1-L4, and adult worms). The gly-12 and gly-13 promoters were expressed from embryogenesis to adulthood in many tissues. The gly-14 promoter was expressed only in gut cells from L1 to adult developmental stages. Transgenic worms that overexpress any one of the three genes show no obvious phenotypic defects. The data indicate that C. elegans is a suitable model for further study of the role of complex N-glycans in ------------------- Key: 3353 Medline: 99097342 Authors: Dean FB;Lian L;O'Donnell M Title: cDNA cloning and gene mapping of human homologs for Schizosaccharomyces pombe rad17, rad1 and hus1 and cloning of homologs from mouse, Caenorhabditis elegans and Drosophila melanogaster. Citation: Genomics 54: 424-436 1998 Type: ARTICLE Genes: hpr-1 Abstract: Mutations in DNA repair/cell cycle checkpoint genes can lead to the development of cancer. The cloning of human homologs of yeast DNA repair/cell cycle checkpoint genes should yield candidates for human tumor suppressor genes as well as identifying potential targets for cancer therapy. The Schizosaccharomyces pombe genes rad17, rad1, and hus1 have been identified as playing roles in DNA repair and cell cycle checkpoint control pathways. We have cloned the cDNA for the human homolog of S. pombe rad17, RAD17, which localizes to chromosomal location 5q13 by fluorescence in situ hybridization and radiation hybrid mapping; the cDNA for the human homolog of S. pombe rad1, RAD1, which maps to 5p14-p13.2; and the cDNA for the human homolog of S. pombe hus1, HUS1, which maps to 7p13-p12. The human gene loci have previously been identified as regions containing tumor suppressor genes. In addition, we report the cloning of the cDNAs for genes related to S. pombe rad17, rad9, rad1, and hus1 from mouse, Caenorhabditis elegans, and Drosophila melanogaster. These include Rad17 and Rad9 from D. melanogaster, hpr-17 and hpr-l from C. elegans, and RAD1 and HUS1 from mouse. The identification of homologs of the S. pombe rad checkpoint genes from mammals, arthropods, and nematodes indicates that this cell cycle checkpoint pathway is conserved throughout eukaryotes. ------------------- Key: 3354 Medline: 99091901 Authors: Jiang JC;Kirchman PA;Zagulski M;Hunt J;Jazwinski SM Title: Homologs of the yeast longevity gene LAG1 in Caenorhabditis elegans and human. Citation: Genome Research 8: 1259-1272 1998 Type: ARTICLE Genes: gdf-1 lag-1 uog-1 Abstract: LAG1 is a longevity gene, the first such gene to be identified and cloned from the yeast Saccharomyces cerevisiae. A close homolog of this gene, which we call LAC1, has been found in the yeast genome. We have cloned the human homolog of LAG1 with the ultimate,ooal of examining its possible function in human aging. In the process, we have also cloned a homolog from the nematode worm Caenorhabditis elegans. Both of these homologs, LAG1Hs and LAG1Ce-1 functionally complemented the lethality of a lag1 Delta lac1 Delta double deletion, despite low overall sequence similarity to the yeast proteins. The proteins shared a short sequence, the Lag1 motif, and a similar transmembrane domain profile. Another, more distant human homolog, TRAM, which lacks this motif, did not complement. LAG1Hs also restored the life span of the double deletion, demonstrating that it functions in establishing the longevity phenotype in yeast. LAG1Hs mapped to 19p12, and it was expressed in only three tissues: brain, skeletal muscle, and testis. This gene possesses a trinucleotide (CTG) repeat within exon 1. This and its expression profile raise the possibility that it may be involved in neurodegenerative disease. This possibility suggests at least one way in which LAG1Hs might be involved in human ------------------- Key: 3355 Medline: 99091905 Authors: Stein LD;Thierry-Mieg J Title: Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases. Citation: Genome Research 8: 1308-1315 1998 Type: ARTICLE Genes: Abstract: Much of the world's genomic data are available to the community through networked databases that are accessed via Web interfaces. Although this paradigm provides browse-level access and has greatly facilitated linking between databases, it does not provide any convenient mechanism for programmatically fetching and intergrating data from diverse databases. We have created a library and an application programming interface (API) named AcePerl that provides simple, direct access to ACEDB databases from the Perl programming language. With this library, programmers and computer-savvy biologists can write software to pose complex queries on local and remote ACEDB databases, retrieve the data, integrate the results, and move data objects from one database to another. In addition, a set of Web scripts running on top of AcePerl provides Web-based browsing of any local or remote ACEDB database. AcePerl and the AceBrowser Web browser run on Unix systems and are available under a license that allows for unrestricted use and redistribution. Both packages can be downloaded from URL http://stein.cshl.org/AcePerl. A Microsoft Windows port of AcePerl is in the planning ------------------- Key: 3356 Medline: 99094910 Authors: Jan E;Motzny CK;Graves LE;Goodwin EB Title: The STAR protein, GLD-1, is a translational regulator of sexual identity in Caenorhabditis elegans. Citation: EMBO Journal 18: 258-269 1998 Type: ARTICLE Genes: fem-1 fem-2 fem-3 fog-1 fog-2 fog-3 gld-1 her-1 laf-1 tra-1 tra-2 tra-3 Abstract: The Caenorhabditis elegans sex determination gene, tra-2, is translationally regulated by elements in the 3'-untranslated region called TGEs, TGEs govern the translation of mRNAs in both invertebrates and vertebrates, indicating that this is a highly conserved mechanism for controlling gene activity. A factor called DRF, found in worm extracts binds the TGEs and may be a repressor of translation. Using the yeast three-hybrid screen and RNA gel shift analysis, we have found that the protein GLD-1, a germline-specific protein and a member of the STAR family of RNA-binding proteins, specifically binds to the TGEs. GLD-1 is essential for oogenesis, and is also necessary for spermatogenesis and inhibition of germ cell proliferation. Several lines of evidence demonstrate that GLD-1 is a translational repressor acting through the TGEs to repress tra-2 translation. GLD-1 can repress the translation of reporter RNAs via the TGEs both in vitro and iii vivo, and is required to maintain low TRA-2A protein levels in the germline. Genetic analysis indicates that GLD-1 acts upstream of the TGE control. Finally, we show that endogenous GLD-1 is a component of DRF. The conservation of the TGE control and the STAR family suggests that at least a subset of STAR proteins may work through the TGEs to ------------------- Key: 3357 Medline: 99059682 Authors: Da'Dara AA;Walter RD Title: Molecular and biochemical characterization of S-adenosylmethionine decarboxylase from the free-living nematode Caenorhabditis elegans. Citation: Biochemical Journal 336: 545-550 1998 Type: ARTICLE Genes: Abstract: S-Adenosylmethionine decarboxylase (SAMDC) is a major regulatory enzyme in the polyamine biosynthesis and is considered a potentially important drug target for the chemotherapy of proliferative and parasitic diseases. To study regulatory mechanisms which are involved in the expression of SAMDC of the free-living nematode Caenorhabditis elegans, we have isolated the SAMDC gene and cDNA. Genomic Southern-blot analysis suggests that the C. elegans SAMDC is encoded by a single-copy gene which spans 3.9 kb and consists of six exons and five introns. The first two introns are located in the 5'-untranslated region (UTR). Analyses of the 5'-flanking region of the gene revealed several consensus sequences for the binding of different transcription factors such as CBP, AP2, cMyb, VPE2 and others. The C. elegans SAMDC mRNA possesses an open reading frame (ORF) which encodes a polypeptide of 368 amino acids corresponding to a SAMDC proenzyme with a calculated molecular mass of 42,141 Da. The active form of the C. elegans SAMDC is a heterotetramer, consisting of two subunits of 32 and 10 kDa derived from cleavage of the pro-enzyme. The SAMDC mRNA has an unusually long 5'-UTR of 477 nucleotides. This region has a small ORF which could encode a putative peptide of 17 residues. Moreover, the C. elegans SAMDC mRNA is trans-spliced with the 22 nucleotides spliced leader sequence at the 5'-end. ------------------- Key: 3358 Medline: 99156232 Authors: Takanami T;Sato S;Ishihara T;Katsura I;Takahashi H;Higashitani A Title: Characterization of a Caenorhabditis elegans recA-like gene Ce-rdh-1 involved in meiotic recombination. Citation: DNA Research 5: 373-377 1998 Type: ARTICLE Genes: mei-1 mei-2 rdh-1 Abstract: A recA-like gene was identified in the Caenorhabditis elegans genome project database. The putative product of the gene, termed Ce-rdh-1 (C. elegans RAD51 and DMC1/LIM15 homolog 1), consists of 357 amino acid residues. The predicted amino acid sequence of Ce-rdh-1 showed 46-60% identity to both RAD51 type and DMC1/LIM15 type genes in several eukaryote species. The results of RNAi (RNA-mediated interference) indicates that repression of Ce-rdh-1 blocked chromosome condensation of six bivalents and dissociation of chiasmata in oocytes of F1 progeny. Oogenesis did not proceed to the diakinesis stage. Accordingly, all the eggs produced (F2) died in early stages. These results suggest that Ce-rdh-1 participates in ------------------- Key: 3359 Medline: 9874786 Authors: Kanuka H;Hisahara S;Sawamoto K;Shoji S;Okano H;Miura M Title: Proapoptotic activity of Caenorhabditis elegans CED-4 protein in Drosophila: Implicated mechanisms for caspase activation. Citation: Proceedings of the National Academy of Sciences USA 96: 145-150 1999 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: CED-4 protein plays an important role in the induction of programmed cell death in Caenorhabditis elegans through the activation of caspases. However, the precise mechanisms by which it activates caspases remain unknown. To investigate the conservation of CED-4 function in evolution, transgenic Drosophila lines that express CED-4 in the compound eye were generated. Ectopic expression of CED-4 in the eyes induced massive apoptotic cell death through caspase activation. An ATP-binding site (P-loop) mutation in CED-4 (K165R) causes a loss of function in its ability to activate Drosophila caspase, and an ATPase inhibitor blocks the CED-4-dependent caspase activity in Drosophila S2 cells. Immunoprecipitation analysis showed that both CED-4 and CED-4 (K165R) bind directly to Drosophila caspase drICE, and the overexpression of CED-4 (K165R) inhibits CED-4-, ecdysone-, or cycloheximide-dependent caspase activation in S2 cells. Furthermore, CED-4 (K165R) partially prevented cell death induced by CED-4 in Drosophila compound eyes. Thus, CED-4 function is evolutionarily conserved in Drosophila, and the molecular mechanisms by which CED-4 activates caspases might require ATP binding and direct interaction with the caspases. ------------------- Key: 3360 Medline: 9874792 Authors: Faber PW;Alter JR;MacDonald ME;Hart AC Title: Polyglutamine-mediated dysfunction and apoptotic death of a Caenorhabditis elegans sensory neuron. Citation: Proceedings of the National Academy of Sciences USA 96: 179-184 1999 Type: ARTICLE Genes: ced-3 osm-10 Abstract: The effect of expressing human huntingtin fragments containing polyglutamine (polyQ) tracts of varying lengths was assessed in Caenorhabditis elegans ASH sensory neurons in young and old animals. Expression of a huntingtin fragment containing a polyQ tract of 150 residues (Htn-Q150) led to progressive ASH neurodegeneration but did not cause cell death. Progressive cell death and enhanced neurodegeneration were observed in ASH neurons that coexpressed Htn-Q150 and a subthreshold dose of a toxic OSM-10::green fluorescent protein (OSM-10::GFP) fusion protein. Htn-Q150 huntingtin protein fragments formed protein aggregates in ASH neurons, and the number of ASH neurons containing aggregates increased as animals aged. ASH neuronal cell death required ced-3 caspase function, indicating that the observed cell death is apoptotic Of interest, ced-3 played a critical role in Htn-Q150-mediated neurodegeneration but not in OSM10::GFP-mediated ASH neurodegeneration. ced-3 function was important but not essential for the formation of protein aggregates. Finally, behavioral assays indicated that ASH neurons, coexpressing Htn-Q150 and OSM10::GFP, were functionally impaired at 3 days before the detection of neurodegeneration, cell death, and protein aggregates. ------------------- Key: 3361 Medline: 99102422 Authors: Hobert O;Moerman DG;Clark KA;Beckerle MC;Ruvkun G Title: A conserved LIM protein that affects muscular adherens junction integrity and mechanosensory function in Caenorhabditis elegans. Citation: Journal of Cell Biology 144: 45-57 1999 Type: ARTICLE Genes: mec-2 pin-2 unc-97 Abstract: We describe here the molecular and functional characterization of the Caenorhabditis elegans unc-97 gene, whose gene product constitutes a novel component of muscular adherens junctions. UNC-97 and homologues from several other species define the PINCH family, a family of LIM proteins whose modular composition of five LIM domains implicates them as potential adapter molecules. unc-97 expression is restricted to tissue types that attach to the hypodermis, specifically body wall muscles, vulval muscles, and mechanosensory neurons. In body wall muscles, the UNC-97 protein colocalizes with the beta-integrin PAT-3 to the focal adhesion-like attachment sites of muscles. Partial and complete loss-of-function studies demonstrate that UNC-97 affects the structural integrity of the integrin containing muscle adherens junctions and contributes to the mechanosensory functions of touch neurons. The expression of a Drosophila homologue of unc-97 in two integrin containing cell types, muscles, and muscle-attached epidermal cells, suggests that unc-97 function in adherens junction assembly and stability has been conserved across phylogeny. In addition to its localization to adherens junctions UNC-97 can also be detected in the nucleus, suggesting multiple functions for ------------------- Key: 3362 Medline: 99091552 Authors: Vassilieva LL;Lynch M Title: The rate of spontaneous mutation for life-history traits in Caenorhabditis elegans. Citation: Genetics 151: 119-129 1999 Type: ARTICLE Genes: Abstract: Spontaneous mutations were accumulated in 100 replicate lines of Caenorhabditis elegans over a period of similar to 50 generations. Periodic assays of these lines and comparison to a frozen control suggest that the deleterious mutation rate for typical life-history characters in this species is at least 0.05 per diploid genome per generation, with the average mutational effect on the order of 14% or less in the homozygous state and the average mutational heritability similar to 0.0034. While the average mutation rate per character and the average mutational heritability for this species are somewhat lower than previous estimates for Drosophila, these differences can be reconciled to a large extent when the biological differences between these species are taken into consideration. ------------------- Key: 3363 Medline: 99091553 Authors: Molin L;Schnabel H;Kaletta T;Feichtinger R;Hope IA;Schnabel R Title: Complexity of developmental control: Analysis of embryonic cell lineage specification in Caenorhabditis elegans using pes-1 as an early marker. Citation: Genetics 151: 131-141 1999 Type: ARTICLE Genes: apx-1 arm-1 arm-2 arm-4 arm-5 arm-6 arm-7 arm-8 arm-9 emb-40 emb-46 emb-47 emb-48 emb-49 emb-50 emb-52 emb-53 emb-57 emb-60 emb-61 emb-62 emb-67 emb-85 glp-1 inx-1 lit-1 mar-1 mel-11 mel-14 mel-18 mel-20 mel-32 mod-1 mod-2 mod-3 mod-4 mod-5 mod-6 mod-7 mod-8 par-1 pes-1 pie-1 skn-1 sud-1 Abstract: In the early Caenorhabditis elegans embryo five somatic founder cells are born during the first cleavages. The first of these founder cells, named AB, gives rise to 389 of the 558 nuclei present in the hatching larva. Very few genes directly involved in the specification of the AB lineage have been identified so far. Here we describe a screen of a large collection of maternal-effect embryonic lethal mutations for their effect on the early expression of a pes-1::lacZ fusion gene. This fusion gene is expressed in a characteristic pattern in 14 of the 32 AB descendants present shortly after the initiation of gastrulation. Of the 37 mutations in 36 genes suspected to be required specifically during development, 12 alter the expression of the pes-1::lacZ marker construct. The gene expression pattern alterations are of four types: reduction of expression, variable expression, ectopic expression in addition to the normal pattern, and reduction of the normal pattern together with ectopic expression. We estimate that similar to 100 maternal functions are required to establish the pes-1 expression pattern in the early embryo. ------------------- Key: 3364 Medline: 19872955 Authors: Labbe JC;Hekimi S;Rokeach LA Title: The levels of the RoRNP-associated Y RNA are dependent upon the presence of ROP-1, the Caenorhabditis elegans Ro60 protein. Citation: Genetics 151: 143-150 1999 Type: ARTICLE Genes: glp-1 rop-1 yrn-1 Abstract: The Ro ribonucleoproteins (RoRNP) consist of at least one major protein of 60 kD, Ro60, and one small associated RNA, designated Y RNA. Although RoRNP have been found in all vertebrate species examined so far, their function remains unknown. The Caenorhabditis elegans rop-1 gene previously has been identified as encoding a Ro60 homologue. We report here the phenotypic characterization of a C. elegans strain in which rop-1 has been disrupted. This is the first report regarding the inactivation of a major RoRNP constituent in any organism. The rop-1 mutant warms display no visible defects. However, at the molecular level, the disruption of rop-1 results in a dramatic decrease in the levels of the ROP-1-associated RNA (CeY RNA). Moreover, transgenic expression of wild-type rop-1 partially rescues the levels of CeY RNA. Considering that transgenes are poorly expressed in the germline, the fact that the rescue is only partial is most likely related to the high abundance of the CeY RNA in the adult germline and in embryos. The developmental expression pattern and localization of CeY RNA suggest a role for this molecule during embryogenesis. We conclude that, under laboratory culture conditions, ROP-1 does not play a crucial role in C. elegans. ------------------- Key: 3365 Medline: 99132635 Authors: Watari Y;Kariya K;Shibatohge M;Liao Y;Hu CD;Goshima M;Tamada M;Kikuchi A;Kataoka T Title: Identification of Ce-AF-6, a novel Caenorhabditis elegans protein, as a putative Ras effector. Citation: Gene 224: 53-58 1998 Type: ARTICLE Genes: let-60 lin-45 Abstract: Mammalian Ras proteins associate with multiple effecters, including Raf, Ral guanine nucleotide dissociation stimulator, phosphoinositide 3-kinase and AF-6. In the nematode Caenorhabditis elegans, LIN-45/Raf has been identified genetically as an effector of LET-60/Ras. To search for other effecters in C. elegans, we carried out a yeast two-hybrid screening for LET-60-associating proteins. The screening identified a novel protein, designated Ce-AF-6, which exhibited a strong structural homology with human AF-6, rat Afadin and Drosophila melanogaster Canoe and possessed both the Ras-associating (RA) domain and the PSD-95/D1gA/ZO-1 (PDZ) domain. Ce-AF-6 associated with human Ha-Ras in a GTP-dependent manner, with an efficiency comparable to that of human Raf-1 Ras-binding domain. When the effects of mutations of the Ras effector region residues were examined for associations with various effecters, Ce-AF-6 was found to possess a distinct and the most rigorous requirement for the effector region residues. These results strongly suggest that Ce-AF-6 is a putative effector of Ras that possesses a distinct recognition mechanism for association with Ras. ------------------- Key: 3366 Medline: 9989496 Authors: Mahajan-Miklos S;Tan MW;Rahme LG;Ausubel FM Title: Molecular mechanisms of bacterial virulence elucidated using a Pseudomonas aeruginosa Caenorhabditis elegans pathogenesis model. Citation: Cell 96: 47-56 1999 Type: ARTICLE Genes: age-1 mev-1 pgp-1 pgp-3 rad-8 Abstract: The human opportunistic pathogen Pseudomonas aeruginosa strain PA14 kills Caenorhabditis elegans. Using systematic mutagenesis of PA14 to identify mutants that fail to kill C. elegans and a C. elegans mutant that lacks P-glycoproteins, we identified phenazines, secreted P. aeruginosa pigments, as one of the mediators of killing. Analysis of C. elegans mutants with altered responses to oxidative stress suggests that phenazines exert their toxic effects on C. elegans through the generation of reactive oxygen species. Finally, we show that phenazines and other P. aeruginosa factors required for C. elegans killing are also required for pathogenesis in plants and mice, illustrating that this model tackles the dual challenges of identifying bacterial virulence factors as well as host ------------------- Key: 3367 Medline: Authors: Takayama S;Xie Z;Reed JC Title: An evolutionarily conserved family of Hsp70/Hsc70 molecular chaperone regulators. Citation: Journal of Biological Chemistry 274: 781-786 1999 Type: ARTICLE Genes: Abstract: Heat Shock Protein 70 kDa (Hsp70) family molecular chaperones play critical roles in protein folding and trafficking in all eukaryotic cells, The mechanisms by which Hsp70 family chaperones are regulated, however, are only partly understood. BAG-1 binds the ATPase domains of Hsp70 and Hsc70, modulating their chaperone activity and functioning as a competitive antagonist of the co-chaperone Hip. We describe the identification of a family of BAG-1-related proteins from humans (BAG-2, BAG-3, BAG-4, BAG-5), the invertebrate Caenorhabditis elegans (BAG-I, BAG-a), and the fission yeast Schizosaccharomyces pombe (BAG-1A, BAG-1B). These proteins all contain a conserved similar to 45-amino acid region near their C termini (the BAG domain) that binds Hsc70/Hsp70, but they differ widely in their N-terminal domains. The human BAG-1, BAG-2, and BAG-3 proteins bind with high affinity (K-D congruent to 1-10 nM) to the ATPase domain of Hsc70 and inhibit its chaperone activity in a Hip-repressible manner. The findings suggest opportunities for specification and diversification of Hsp70/ Hsc70 chaperone functions through interactions with various BAG-family proteins. ------------------- Key: 3368 Medline: Authors: Sokolowski MB Title: Genes for normal behavioral variation: Recent clues from flies and worms. Citation: Neuron 21: 463-466 1998 Type: REVIEW Genes: npr-1 Abstract: The question of how genes contribute to normal individual differences in behavior has captured our imagination for more than a century. Several fundamental questions come to mind. How do genes and their proteins act in the nervous system and in response to the environment in order to cause individual differences in behavior? Do genetic differences between natural variants arise from alterations in the structural or regulatory region of a gene? Can we predict which genes for behavior, identified by mutant analysis in the laboratory, will have natural allelic variation? Three groundbreaking studies (Osborne et al., 1997; Sawyer et al., 1997; de Bono and Bargmann, 1998) published in the past year demonstrate that we now have the knowledge and technological capability to address these questions empirically. Each study has successfully identified a single major gene for a given behavior and, with the aid of transgenic animals, shown that its gene product is responsible for naturally occurring individual differences ------------------- Key: 3369 Medline: Authors: Walsh S;Anderson M;Cartinhour SW Title: ACEDB: A database for genome information. Citation: Methods of Biochemical Analysis: Bioinformatics: A practical guide to the analysis of genes and proteins. AD Baxevanis and BF Francis Ouellette (eds). Wiley & Sons, Inc., New York, NY : 299-318 1998 Type: REVIEW Genes: Abstract: ------------------- Key: 3370 Medline: Authors: Baker ME Title: Evolution of mammalian 11-beta- and 17-beta-hydroxysteroid dehydrogenases-type 2 and retinol dehydrogenases from ancestors in Caenorhabditis elegans and evidence for horizontal transfer of a eukaryo.. Citation: Journal of Steroid Biochemistry & Molecular Biology 66: 355-363 1998 Type: ARTICLE Genes: Abstract: Physiological responses due to steroid hormones and retinoids are regulated by their cognate receptors and dehydrogenases. The origins of either regulatory mechanism are not fully understood. Here we examine the origins of the human 11-beta-hydroxysteroid dehydrogenase-type 2, which regulates access of glucocorticoids to cells, and 17-beta-hydroxysteroid dehydrogenase-type 2, which regulates access of androgens and estrogens to cells. Sequence comparisons trace their ancestry to homologs in Caenorhabditis elegans. These C. elegans proteins most closely resemble mammalian all-trans and 11-cis-retinol dehydrogenases. The similarity is sufficient -37% to 43% identity to suggest that one or more of the C. elegans homologs metabolizes a retinoid. Receptors for retinoids, but not for androgens, estrogens or glucocorticoids have been identified in C. elegans, suggesting that retinoid-mediated gene transcription is more ancient than that for adrenal and sex steroids. We propose that the hydroxysteroid dehydrogenase-type 2 mechanism for regulating the androgen, estrogen and glucocorticoid concentrations in mammals descended from that for regulating retinoid concentrations. Interestingly, E. coli contains a protein with strong sequence similarity to mammalian retinol dehydrogenases. Sequence comparisons and phylogenetic analysis indicate that the E. coli protein may be an example of horizontal transfer from a eukaryote ------------------- Key: 3371 Medline: 99102119 Authors: McCarter J;Bartlett B;Dang T;Schedl T Title: On the control of oocyte meiotic maturation and ovulation in Caenorhabditis elegans. Citation: Developmental Biology 205: 111-128 1999 Type: ARTICLE Genes: fem-3 fer-1 fer-3 fog-1 fog-2 fog-3 gld-1 glp-4 spe-4 Abstract: Prior to fertilization, oocytes undergo meiotic maturation (cell cycle progression) and ovulation (expulsion from the ovary). To begin the study of these processes in Caenorhabditis elegans, we have defined a time line of germline and somatic events by video microscopy. As the oocyte matures, its nuclear envelope breaks down and its cell cortex rearranges. Immediately thereafter, the oocyte is ovulated by increasing contraction of the myoepithelial gonadal sheath and relaxation of the distal spermatheca. By systematically altering the germ cell contents of the hermaphrodite using mutant strains, we have uncovered evidence of four cell-cell interactions that regulate maturation and ovulation. (1) Both spermatids and spermatozoa induce oocyte maturation. In animals with a feminized germline, maturation is inhibited and oocytes arrest in diakinesis. The introduction of sperm by mating restores maturation. (2) Sperm also directly promote sheath contraction. In animals with a feminized or tumorous germline, contractions are infrequent, whereas in animals with a masculinized germline or with sperm introduced by mating, contractions are frequent. (3 and 4) The maturing oocyte both induces spermathecal dilation and modulates sheath contractions at ovulation; dilation of the distal spermatheca and sharp increases in sheath contraction rates are only observed in the presence of a maturing oocyte. ------------------- Key: 3372 Medline: Authors: Westlund B;Berry LW;Schedl T Title: Regulation of germline proliferation in Caenorhabditis elegans. Citation: "Advances in Developmental Biology". JAI Press, Inc. 5: 43-80 1997 Type: REVIEW Genes: apx-1 arg-1 dpy-1 dpy-2 dpy-3 dpy-7 dpy-8 dpy-9 dpy-10 ego-1 ego-3 ego-4 ego-5 emb-5 fem-1 fem-2 fem-3 fog-1 fog-3 gld-1 glp-1 glp-4 lag-1 lag-2 let-42 let-60 lin-12 mes-3 mpk-1 sel-1 sel-9 sel-10 sel-11 sel-12 sog-1 sog-2 sog-3 sog-4 sog-5 sog-6 sog-10 sqt-1 sur-1 Abstract: Germline development is unique within Caenorhabditis elegans for a number of reasons. First, the germline is the only organ whose cells undergo meiotic development. Second, in contrast to the essentially invariant cell lineages of the C. elegans soma, germ cells divide a variable number of times. Finally, a subset of germ cells remain in a mitotic, undifferentiated state throughout the lifetime of the animal: they serve as a stem cell population for the germ line. Thus, one important decision germ cells face is whether to remain mitotic or enter meiotic prophase. A large body of work has focused on elucidating the molecular mechanism underlying this process. Taken together, these data demonstrate that the GLP-1 signaling pathway is crucial for the mitosis verses meiosis decision. Here we discuss in detail what is known about this pathway in the C. elegans germ line. Since GLP-1 is a Notch homolog and the Notch signaling pathway appears to be conserved from nematodes to mammals, we also summarize some of the findings that have come from studies on other Notch family members, their ligands, and downstream effectors. In addition, several genes have been characterized that do not appear to be involved directly in the mitosis verses meiosis decision, but when mutated display ectopic proliferation or reduced proliferation defects. We describe their mutant phenotypes as well as any known interactions ------------------- Key: 3373 Medline: 99063674 Authors: Scharfe C;Zaccaria P;Hoertnagel K;Jaksch M;Klopstock T;Lill R;Prokisch H;Gerbitz KD;Mewes HW;Meitinger T Title: MITOP: database for mitochondria-related proteins, genes and diseases. Citation: Nucleic Acids Research 27: 153-155 1999 Type: ARTICLE Genes: Abstract: The MITOP database http://websvr.mips.biochem. mpg.de/proj/medgen/mitop/ consolidates information on both nuclear- and mitochondrial-encoded genes and their proteins. The five species files-Saccharomyces cerevisiae, Mus musculus Caenorhabditis elegans, Neurospora crassa and Homo sapiens-include annotated data derived from a variety of online resources and the literature. A wide spectrum of search facilities is given in the interelated sections 'Gene catalogues', 'Protein catalogues', 'Homologies', 'Pathways and metabolism', and 'Human disease catalogue' including extensive references and hyperlinks for each entry. Precomputed FASTA searches using all the MITOP yeast protein entries and a list of the best EST hits with graphical cluster alignments related to the yeast reference sequence are presented. The MITOP orthologue tables with cross-listing to all the protein entries for each species in the database facilitate investigations into interspecies homology. A program (MITOPROT) is available to identify mitochondrial targeting sequences and graphical depictions of several important mitochondrial processes are included. The 'Human disease catalogue' lists a total of 101 disorders related to mitochondrial protein abnormalities, sorted by clinical criteria and age of onset. ------------------- Key: 3374 Medline: 99140101 Authors: van Swinderen B;Galifianakis A;Crowder CM Title: A quantitative genetic approach towards volatile anesthetic mechanisms in C. elegans. Citation: Toxicology Letters 101: 309-317 1998 Type: ARTICLE Genes: Abstract: Quantitative genetics is the study of the heritability of continuous traits such as height or IQ. Quantitative trait loci (QTLs) represent the genes that are responsible for these quantitative traits. Sensitivity to the volatile anesthetic halothane is a genetically controlled quantitative trait in the nematode C. elegans. The QTLs that are responsible for the 12-fold range in halothane EC50 in these strains map to a few places with at least one major effect locus on chromosome V. Congenic strains for chromosome V confirmed these loci and offer the means to finely map them for positional cloning. ------------------- Key: 3375 Medline: 99140104 Authors: Kayser B;Rajaram S;Thomas S;Morgan PG;Sedensky MM Title: Control of anesthetic response in C. elegans. Citation: Toxicology Letters 101: 339-346 1998 Type: ARTICLE Genes: gas-1 unc-1 unc-79 Abstract: We describe the use of the animal model C. elegans to understand how the volatile anesthetics work at the molecular level. Mutations in several different genes can profoundly change the behavior of this animal under volatile anesthetics. Protein products of two of these genes are discussed. One gene is an integral membrane protein thought to regulate ion channels. The other is a subunit of the first protein complex of the electron ------------------- Key: 3376 Medline: 99110956 Authors: Tan MW;Mahajan-Miklos S;Ausubel FM Title: Killing of Caenorhabditis elegans by Pseudomonas aeruginosa used to model mammalian bacterial pathogenesis. Citation: Proceedings of the National Academy of Sciences USA 96: 715-720 1999 Type: ARTICLE Genes: eat-1 fer-1 him-8 Abstract: We show that a single clinical isolate of the human opportunistic pathogen Pseudomonas aeruginosa (strain PA14),which previously was shown to be pathogenic in mice and plants, also kills Caenorhabditis elegans. The rate of PA14-mediated killing of C. elegans depends on the composition of the agar medium on which PA14 is grown. When PA14 is grown on minimal medium, killing occurs over the course of several days and is referred to as "slow" killing. When PA14 is groan on high-osmolarity medium, killing occurs over the course of several hours and is referred to as "fast" killing. Several lines of evidence, including the fact that heat-killed bacteria are still capable of fast but not slow killing of C. elegans, indicate that fast and slow killing occur by distinct mechanisms. Slow killing involves an infection-like process and correlates with the accumulation of PA14 within worm intestines. Among 10 PA14 virulence-related mutants that had been shown previously to affect pathogenicity in plants and mice, 6 were less effective in killing C. elegans under both fast- and slow-killing conditions, indicating a high degree of commonalty among the P. aeruginosa factors required for pathogenicity in disparate eukaryotic hosts. Thus, we show that a C. elegans pathogenicity model that is genetically tractable from the perspectives of both host and pathogen can be used to model mammalian bacterial ------------------- Key: 3377 Medline: 99123854 Authors: Slack F;Ruvkun G Title: Heterochronic genes in development and evolution. Citation: Biological Bulletin 195: 375-376 1998 Type: REVIEW Genes: let-7 lin-4 lin-14 lin-28 lin-29 Abstract: Heterochrony is an evolutionary term that describes the comparatively common phylogenetic variation between species in the relative timing of developmental events. Heterochronic variation has also been induced by mutation to identify genes that regulate the timing of developmental events. ------------------- Key: 3378 Medline: 99121219 Authors: Marks NJ;Maule AG;Li C;Nelson LS;Thompson DP;Alexander-Bowman S;Geary TG;Halton DW;Verhaert P;Shaw C Title: Isolation, pharmacology and gene organization of KPSFVRFamide: A neuropeptide from Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 254: 222-230 1999 Type: ARTICLE Genes: flp-9 Abstract: To date, 53 peptides with C-terminal RFamides have been identified by the genome sequencing project in the nematode, Caenorhabditis elegans. In this study the FMRFamide-related peptide (FaRP) KPSFVRFamide (879.90 Da [MH](+)) was structurally characterized from extracts of the nematode, Caenorhabditis elegans. Two copies of KPSFVRFamide are encoded by a gene designated flp-9. RT-PCR identified a single cDNA product which was confirmed as flp-9 by sequence determination. Flp-9 cDNA was isolated from larval stages of C. elegans but was not detected-in adult worms, indicating that its expression is may be developmentally regulated. KPSFVRFamide displays sequence homology to the nematode peptide, KPNFIRFamide (PF4). The physiological effects of KPSFVRFamide, PF4 and the chimeras, KPNFVRFamide and KPSFIRFamide, were measured on body wall muscle and the vagina vera of the parasitic nematode, Ascaris suum. KPNFVRFamide and KPNFIRFamide had Cl--dependent inhibitory activity on innervated and denervated muscle-preparations, whereas KPSFVRFamide and KPSFIRFamide did not elicit a detectable physiological effect. Although all 4 peptides had inhibitory effects on the vagina vera, KPSFVRFamide and KPSFIRFamide (threshold, greater than or equal to 0.1 mu M) were less potent than KPNFVRFamide and KPNFIRFamide (threshold, greater than or ------------------- Key: 3379 Medline: 99127451 Authors: Rose LS;Kemphues KJ Title: Early patterning of the C. elegans embryo. Citation: Annual Review of Genetics 32: 521-545 1998 Type: REVIEW Genes: apr-1 apx-1 ceh-13 elt-1 end-1 glp-1 gpb-1 let-99 lit-1 mes-1 mex-1 mex-3 mom-1 mom-2 mom-3 mom-4 mom-5 pal-1 par-1 par-2 par-3 par-4 par-5 par-6 pie-1 pkc-3 pop-1 skn-1 vab-7 wrm-1 Abstract: Studies of about 20 maternally expressed genes are providing an understanding of mechanisms of patterning and cell-fate determination in the early Caenorhabditis elegans embryo. The analyses have revealed that fates of the early blastomeres are specified by a combination of intrinsically asymmetric cell divisions and two types of cell-cell interactions: inductions and polarizing interactions. In this review we summarize the current level of understanding of the molecular mechanisms underlying these processes in the specification of cell fates in the pregastrulation embryo. ------------------- Key: 3380 Medline: 99123855 Authors: Hobert O;Ruvkun G Title: A common theme for LIM homeobox gene function across phylogeny? Citation: Biological Bulletin 195: 377-380 1998 Type: REVIEW Genes: ceh-13 lim-4 lim-6 lim-7 lin-11 mec-3 ttx-3 Abstract: The identification of the molecular components of the developmental neurogenic programs in different organisms has revealed an astounding degree of conservation across phylogeny, suggesting that the basic mechanisms of neural development have also been conserved in evolution. One class of conserved neural regulatory genes, the LIM homeobox genes, encode transcription factors with two Zn-finger-like LIM domains and a DNA-binding homeodomain. Vertebrate members of this class have been implicated in neurogenesis by correlative expression evidence: e.g., the combinatorial expression of LIM homeobox genes in the vertebrate spinal cord suggested a "LIM-code" for specific motorneuronal targeting choices. Genetic analysis in Drosophila also demonstrated their essential role in axon pathfinding and the determination of neurotransmitter identity. The genome of the nematode Caenorhabditis elegans is almost completely sequenced, thus allowing the analysis of complete gene families in a metazoan organism. C. elegans contains seven LIM homeobox genes. Almost all C. elegans LIM homeobox genes fall into subclasses that are defined by the presence of similar genes from arthropods and vertebrates, suggesting a common origin for different subclasses of LIM homeobox genes. ------------------- Key: 3381 Medline: 99156055 Authors: Liu J;Zhou GQ;Strasby KB Title: Caenorhabditis elegans ZC376.5 encodes a tRNA(m(2)(2)G(26))dimethyltransferase in which (246)arginine is important for the enzyme activity. Citation: Gene 226: 73-81 1999 Type: ARTICLE Genes: Abstract: It has been estimated that eukaryotes carry more than 50 genes for tRNA modifying enzymes. Of the few so far identified most come from yeast, a lower eukaryote. In Saccharomyces cerevisiae, the TRM1 gene is a nuclear gene encoding the tRNA(m(2)(2)G(26)) dimethyltransferase, which catalyses the formation of the N-2, N-2-dimethylguanosine at position 26 in tRNA. We have isolated and characterized the corresponding gene ZC376.5 in Caenorhabditis elegans. Via RT-PCR the cDNA sequence of the full length ZC376.5 has now been cloned, expressed in Escherichia coli and demonstrated to encode a tRNA(m(2)(2)G(26)) dimethyltransferase that produces dimethyl-G(26) in vivo and in vitro with tRNA from yeast and bacteria as substrates. This is the first example of a complete gene sequence coding for a tRNA modifying enzyme from a multicellular organism. A point mutation in exon IV in the C. elegans genome sequence coding for the tRNA(m(2)(2)G(26))methyltransferase that substituted arginine246 for glycine eliminated the modification activity. Exchanging the corresponding lysine residue in the yeast Trm1p for alanine caused a severe loss of activity, indicating that the identity of the amino acid at ------------------- Key: 3382 Medline: 99054964 Authors: Tabara H;Hill RJ;Mello CC;Priess JR;Kohara Y Title: pos-1 encodes a cytoplasmic zinc-finger protein essential for germline specification in C. elegans. Citation: Development 126: 1-11 1999 Type: ARTICLE Genes: ama-1 apx-1 mex-1 pes-2 pie-1 pos-1 sDf35 Abstract: Germ cells arise during early C. elegans embryogenesis from an invariant sequence of asymmetric divisions that separate germ cell precursors from somatic precursors. We show that maternal-effect lethal mutations in the gene pos-1 cause germ cell precursors to inappropriately adopt somatic cell fates. During early embryogenesis, pos-1 mRNA and POS-1 protein are present predominantly in the germ precursors. POS-1 is a novel protein with two copies of a CCCH finger motif previously described in the germline proteins PIE-1 and MEX-1 in C. elegans, and in the mammalian TIS11/Nup475/TTP protein. However, mutations in pos-1 cause several defects in the development of the germline blastomeres that are distinct from those caused by mutations in pie-1 or mex-1. The earliest defect detected in pos-1 mutants is the failure to express APX-1 protein from maternally provided apx-1 mRNA, suggesting that POS-1 may have an important role in regulating the expression of maternal mRNAs in germline blastomeres. ------------------- Key: 3383 Medline: 99054967 Authors: Maloof JN;Whangbo J;Harris JM;Jongeward GD;Kenyon C Title: A Wnt signaling pathway controls Hox gene expression and neuroblast migration in C. elegans. Citation: Development 126: 37-49 1999 Type: ARTICLE Genes: bar-1 egl-5 egl-20 lin-17 lin-22 lin-39 mab-5 mig-1 mig-14 pry-1 Abstract: The specification of body pattern along the anteroposterior (A/P) body axis is achieved largely by the actions of conserved clusters of Hox genes. Limiting expression of these genes to localized regional domains and controlling the precise patterns of expression within those domains is critically important for normal patterning. Here we report that egl-20, a C. elegans gene required to activate expression of the Hox gene mab-5 in the migratory neuroblast QL, encodes a member of the Wnt family of secreted glycoproteins. We have found that a second Wnt pathway gene, bar-1, which encodes a beta-catenin/Armadillo-like protein, is also required for activation of mab-5 expression in QL. In addition, we describe the gene pry-1, which is required to limit expression of the Hox genes lin-39, mab-5 and egl-5 to their correct local domains. We find that egl-20, pry-1 and bar-1 all function in a linear genetic pathway with conserved Wnt signaling components suggesting that a conserved Wnt pathway activates expression of mab-5 in the migratory neuroblast QL. Moreover, we find that members of this Wnt signaling system play a major role in both the general and fine-scale control of Hox gene expression in ------------------- Key: 3384 Medline: 99054972 Authors: Thatcher JD;Haun C;Okkema PG Title: The DAF-3 Smad binds DNA and respresses gene expression in the Caenorhabditis elegans pharynx. Citation: Development 126: 97-107 1999 Type: ARTICLE Genes: daf-1 daf-3 daf-4 daf-5 daf-7 daf-8 daf-14 myo-2 Abstract: Gene expression in the pharyngeal muscles of Caenorhabditis elegans is controlled in part by organ-specific signals, which in the myo-2 gene target a short DNA sequence termed the C subelement. To identify genes contributing to these signals, we performed a yeast one-hybrid screen for cDNAs encoding factors that bind the C subelement. One clone recovered was from daf-3, which encodes a Smad most closely related to vertebrate Smad4. We demonstrated that DAF-3 binds C subelement DNA directly and specifically using gel mobility shift and DNase1 protection assays. Mutation of any base in the sequence GTCTG interfered with binding in the gel mobility shift assay, demonstrating that this pentanucleotide is a core recognition sequence for DAF-3 binding. daf-3 is known to promote formation of dauer larvae and this activity is negatively regulated by TGF beta-like signaling. To determine how daf-3 affects C subelement enhancer activity in vivo, we examined expression a gfp reporter controlled by a concatenated C subelement oligonucleotide in daf-3 mutants and other mutants affecting the TGF beta-like signaling pathway controlling dauer formation. Our results demonstrate that wild-type daf-3 can repress C subelement enhancer activity during larval development and, like its dauer-promoting activity, daf-3's repressor activity is negatively regulated by TGF beta-like signaling. We have examined expression of this gfp reporter in dauer larvae and have observed no daf-3-dependent repression of C activity. These results suggest daf-3 directly regulates pharyngeal gene expression during non-dauer development. ------------------- Key: 3385 Medline: 99054975 Authors: Hung TJ;Kemphues KJ Title: PAR-6 is a conserved PDZ domain-containing protein that colocalizes with PAR-3 in Caenorhabditis elegans embryos. Citation: Development 126: 127-135 1999 Type: ARTICLE Genes: par-1 par-2 par-3 par-4 par-5 par-6 pkc-3 hDf15 Abstract: The par genes are required to establish polarity in the Caenorhabditis elegans embryo. Mutations in two of these genes, par-3 and par-6, exhibit similar phenotypes. A third gene, pkc-3, gives a similar phenotype when the protein is depleted by RNA interference. PAR-3 and PKC-3 protein are colocalized to the anterior periphery of asymmetrically dividing cells of the germline lineage and the peripheral localizations of both proteins depends upon the activity of par-6. Here we report the molecular cloning of par-6 and the immunolocalization of PAR-6 protein. We found that par-6 encodes a PDZ-domain-containing protein and has homologues in mammals and flies. Moreover, we discovered that PAR-6 colocalizes with PAR-3 and that par-3 and pkc-3 activity are required for the peripheral localization of PAR-6. The localization of both PAR-3 and PAR-6 proteins is affected identically by mutations in the par-2, par-4 and par-5 genes. The co-dependence of PAR-3, PAR-6 and PKC-3 for peripheral localization and the overlap in their distributions lead us to propose that they act in a protein complex. ------------------- Key: 3386 Medline: 99054979 Authors: Hanna-Rose W;Han M Title: COG-2, a Sox domain protein necessary for establishing a functional vulval-uterine connection in Caenorhabditis elegans. Citation: Development 126: 169-179 1999 Type: ARTICLE Genes: cdh-3 cog-2 lin-11 Abstract: In screens for mutants defective in vulval morphogenesis, multiple mutants were isolated in which the uterus and the vulva fail to make a proper connection. We describe five alleles that define the gene cog-2, for connection of gonad defective. To form a functional connection between the vulva and the uterus, the anchor cell must fuse with the multinucleate uterine seam cell, derived from uterine cells that adopt a pi lineage. In cog-2 mutants, the anchor cell does not fuse to the uterine seam cell and, instead, remains at the apex of the vulva, blocking the connection between the vulval and uterine lumens, resulting in an egg-laying defective phenotype. According to lineage analysis and expression assays for two pi-cell-specific markers, induction of the pi fate occurs normally in cog-2 mutants. We have cloned cog-2 and shown that it encodes a Sox family transcription factor that is expressed in the pi lineage. Thus, it appears that COG-2 is a transcription factor that regulates a late-stage aspect of uterine seam cell differentiation that specifically affects anchor cell-uterine seam cell fusion. ------------------- Key: 3387 Medline: 99117288 Authors: Watts JL;Browse J Title: Isolation and characterization of a delta(5)-fatty acid desaturase from Caenorhabditis elegans. Citation: Archives of Biochemistry & Biophysics 362: 175-182 1999 Type: ARTICLE Genes: fat-3 fat-4 Abstract: Arachidonic acid and eicosapentaenoic acid are important precursors for the production of prostaglandins and other hormone-like eicosanoid molecules. These fatty acids are synthesized by animals by elongating and desaturating precursor fatty acids such as linoleic acid (18:2 Delta(9,12)) and alpha-linolenic acid (18:3 Delta(9,12,15)). We have identified a Delta(5) fatty acid desaturase gene (fat-4) from the nematode Caenorhabditis elegans. We have expressed this gene product in Saccharomyces cerevisiae and demonstrate that it readily converts di-homo-gamma-linolenic acid (20:3 Delta(8,11,14)) to arachidonic acid (20:4 Delta(5,8,11,14)). The FAT-4 Delta(5)-desaturase also acts on a number of other substrates, including fatty acids that do not contain a ------------------- Key: 3388 Medline: Authors: Gilgenkrantz S Title: Sex determination - Same pathways for nematodes and mice. Citation: M S-Medecine Sciences 15: 127-128 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3389 Medline: 99126430 Authors: Cali BM;Kuchma SL;Latham J;Anderson P Title: smg-7 is required for mRNA surveillance in Caenorhabditis elegans. Citation: Genetics 151: 605-616 1999 Type: ARTICLE Genes: dpy-5 lin-45 smg-1 smg-2 smg-3 smg-4 smg-5 smg-6 smg-7 tra-2 unc-54 nDf41 rDf3 stDf7 stDf8 rT1 Abstract: Eukaryotic mRNAs that contain premature stop codons are degraded more rapidly than their wild-type counterparts, a phenomenon termed "nonsense-mediated mRNA decay" (NMD) or "mRNA surveillance." Functions of sh previously described Caenorhabditis elegans genes, smg-1 through smg-6, are required for NMD. Whereas nonsense mutant mRNAs are unstable in smg(+) genetic backgrounds, such mRNAs have normal stability in smg(-) backgrounds. Previous screens for smg mutations have likely not identified all genes involved in NMD, but efforts to identify additional smg genes are limited by the fact that almost 90% of sing mutations identified in genome-wide screens are alleles of smg-1, smg-2, or smg-5. We describe a modified screen for smg mutations that precludes isolating alleles of smg-1, sm-2, and smg-5. Using this screen, we have identified and cloned smg-7, a previously uncharacterized gene that we show is required for NMD. smg-7 is predicted to encode a novel protein that contains an acidic carboxyl terminus and two probable tetratricopeptide repeats. We provide evidence that smg-7 is cotranscribed with the previously characterized gene lin-45 and show that null alleles of smg-7 confer a temperature-sensitive defect in NMD. ------------------- Key: 3390 Medline: 99126431 Authors: Skipper M;Milne CA;Hodgkin J Title: Genetic and molecular analysis of fox-1, a numerator element involved in Caenorhabditis elegans primary sex determination. Citation: Genetics 151: 617-631 1999 Type: ARTICLE Genes: fem-1 fox-1 her-1 him-8 tra-1 tra-2 tra-3 xol-1 meDf6 eDp26 yDp13 Abstract: fox-1 was previously identified as a candidate numerator element based on its overexpression phenotype. FOX-1 is an RRM-type RNA-binding protein, which can bind RNAs in vitro. Western analysis detects FOX-1 throughout development. fox-1::lacZ comes on ubiquitously early during embryogenesis. Postembryonically, fox-1::lacZ is expressed ses specifically in a subset of cells in the head and tail. We describe a Tc1-derived deletion allele [fox-1(Delta)] that removes the RRM domain, fox-1(Delta) confers no phenotype in XXs, but can rescue XO-specific lethality and feminization caused by duplications of the left end of the X. fox-1(Delta) synergizes with putative numerators, resulting in abnormal XX development. Genetic analysis indicated that fox-1(Delta) leads to a slight increase in xol-1 activity, while fox-1(gf) leads to partial loss of xol-1 activity, and xol-1 is epistatic to fox-1. RNase protection experiments revealed increased levels of the 2.2-kb xol-1 message in fox-1(Delta) animals, and reduced levels in fox-1(gf) animals. Additionally, fox-1(Delta) impairs male mating efficiency, which, we propose, represents another function of fox-1, independent of xol-1 and its role in sex determination. ------------------- Key: 3391 Medline: 99124693 Authors: Batchelder C;Dunn MA;Choy B;Suh Y;Cassie C;Shim EY;Shin TH;Mello C;Seydoux G;Blackwell TK Title: Transcriptional repression by the Caenorhabditis elegans germ-line protein PIE-1. Citation: Genes & Development 13: 202-212 1999 Type: ARTICLE Genes: pie-1 pos-1 Abstract: In the early Caenorhabditis elegans embryo, maternally expressed PIE-1 protein is required in germ-line blastomeres to inhibit somatic differentiation, maintain an absence of mRNA transcription, and block phosphorylation of the RNA polymerase II large subunit (Pol II) carboxy-terminal domain (CTD). We have determined that PIE-1 can function as a transcriptional repressor in cell culture assays. By fusing PIE-1 sequences to the yeast GAL4 DNA-binding domain, we have identified a PIE-1 repression domain that appears to inhibit the transcriptional machinery directly. A sequence element that is required for this repressor activity is similar to the Pol II CTD heptapeptide repeat, suggesting that the PIE-I repression domain might target a protein complex that can bind the CTD. An alteration of this sequence element that blocks repression also impairs the ability of a transgene to rescue a pie-1 mutation, suggesting that this repressor activity may be important for PIE-1 function in vivo. ------------------- Key: 3392 Medline: 99117349 Authors: Fay DS;Stanley HM;Han M;Wood WB Title: A Caenorhabditis elegans homologue of hunchback is required for late stages of development but not early embryonic patterning. Citation: Developmental Biology 205: 240-253 1999 Type: ARTICLE Genes: fem-2 glp-4 hbl-1 lin-26 Abstract: We have cloned a Caenorhabditis elegans homologue of the Drosophila gap gene hunchback (hb) and have designated it hbl-1 (hunchback-like). hbl-1 encodes a predicted 982-amino-acid protein, containing two putative zinc-finger domains similar to those of Drosophila Hunchback. The gene is transcribed embryonically, but unlike the maternally expressed Drosophila hb, its mRNA is not detected in C. elegans oocytes. A hbl-1::gfp reporter is expressed primarily in ectodermal cells during embryonic and larval development. Double-stranded RNA-interference (RNAi) was used to indicate hbl-1 loss-of-function phenotypes. Progeny of hbl-1(RNAi) hermaphrodites exhibit a range of defects; the most severely affected progeny arrest as partially elongated embryos or as hatching, misshapen L1 larvae. Animals that survive to adulthood exhibit variably dumpy (Dpy), uncoordinated (Unc), and egg-laying defective (Egl) phenotypes, as well as defects in vulval morphology (Pvl). Abnormal organization of hypodermal cells and expression of a hypodermal marker in hbl-1(RNAi) animals suggests that most of the phenotypes observed could be due to improper specification of hypodermal cells. The pattern of hbl-1 expression is similar to that reported for the leech hunchback homologue Lzf-2, suggesting that these proteins may have similar biological functions in diverse species with cellular embryos. ------------------- Key: 3393 Medline: 9914419 Authors: Kagoshima H;Cassata G;Burglin TR Title: A Caenorhabditis elegans homeobox gene expressed in the male tail, a link between pattern formation and sexual dimorphism? Citation: Development Genes & Evolution 209: 59-62 1999 Type: ARTICLE Genes: ceh-7 egl-5 him-8 mab-5 xol-1 Abstract: ceh-7 is a small Caenorhabditis elegans homeobox gene. We have shown that this gene is transcribed. Examination of the expression pattern of ceh-7 using reporter constructs revealed that it is expressed in a few cells of the male tail, which form a ring around the rectum. The most posterior member of the C. elegans Hox cluster, egl-5, an Abd-B homologue, has previously been shown to be required for the proper development of several blast cells in the male tail. We have examined the expression of ceh-7 in mutant backgrounds of egl-5 and also mab-5, an Antp/Ubx/Abd-A homologue. We find that ceh-7 is not expressed in egl-5 mutants, but is still expressed in mab-5 mutants. ------------------- Key: 3394 Medline: 99135634 Authors: Kayser EB;Morgan PG;Sedensky MM Title: GAS-1: A mitochondrial protein controls sensitivity to volatile anesthetics in the nematode Caenorhabditis Citation: Anesthesiology 90: 545-554 1999 Type: ARTICLE Genes: gas-1 let-3 let-10 let-11 let-14 let-15 let-16 let-18 let-33 let-35 let-36 let-37 let-38 let-39 let-40 let-41 lin-15 unc-3 unc-7 mnDf1 mnDp1 Abstract: Background: Mutations in several genes of Caenorhabditis elegans confer altered sensitivities to volatile anesthetics. A mutation in one gene, gas-1(fc21), causes animals to be immobilized at lower concentrations of all volatile anesthetics than in the wild-type, and it does not depend on mutations in other genes to control anesthetic sensitivity. gas-1 confers different sensitivities to stereoisomers of isoflurane, and thus may be a direct target for volatile anesthetics. The authors have cloned and characterized the gas-1 gene and the mutant allele fc21. Methods: Genetic techniques for nematodes were as previously described. Polymerase chain reaction, sequencing, and other molecular biology techniques were performed by standard methods. Mutant rescue was done by injecting DNA fragments into the gonad of mutant animals and scoring the offspring for loss of the mutant phenotype. Results: The gas-1 gene was cloned and identified. The protein GAS-1 is a homologue of the 49-kDa (TP) subunit of the mitochondrial NADH:ubiquinone-oxidoreductase (complex I of the respiratory chain). gas-1(fc21) is a missense mutation replacing a strictly conserved arginine with lysine. Conclusions: The function of the 49-kDa (IP) subunit of complex I is unknown. The finding that mutations in complex I increase sensitivity of C. elegans to volatile anesthetics may implicate this physiologic process in the determination of anesthetic sensitivity. The hypersensitivity of animals with a mutation in the gas-1 gene may be caused by a direct anesthetic effect on a mitochondrial protein or secondary effects at other sites ------------------- Key: 3395 Medline: 20184292 Authors: Bessou C;Giugia JB;Franks CJ;Holden-Dye L;Segalat L Title: Mutations in the Caenorhabditis elegans dystrophin-like gene dys-1 lead to hyperactivity and suggest a link with cholinergic transmission. Citation: Neurogenetics 2: 61-72 1998 Type: ARTICLE Genes: dys-1 myo-3 phm-2 snb-1 hDf17 Abstract: Mutations in the human dystrophin gene cause Duchenne muscular dystrophy, a common neuromuscular disease leading to a progressive necrosis of muscle cells. The etiology of this necrosis has not been clearly established, and the cellular function of the dystrophin protein is still unknown. We report here the identification of a dystrophin-like gene (named dys-1) in the nematode Caenorhabditis elegans. Loss-of-function mutations of the dys-1 gene make animals hyperactive and slightly hypercontracted. Surprisingly, the dys-1 mutants have apparently normal muscle cells. Based on reporter gene analysis and heterologous promoter expression, the site of action of the dys-1 gene seems to be in muscles. A chimeric transgene in which the C-terminal end of the protein has been replaced by the human dystrophin sequence is able to partly suppress the phenotype of the dys-1 mutants, showing that both proteins share some functional similarity. Finally, the dys-1 mutants are hypersensitive to acetylcholine and to the acetylcholinesterase inhibitor aldicarb, suggesting that dys-1 mutations affect cholinergic transmission. This study provides the first functional link between the dystrophin family of proteins and cholinergic transmission. ------------------- Key: 3396 Medline: Authors: Larminie CG;White RJ Title: Identification of putative BRF homologue in the genome of Caenorhabditis elegans. Citation: DNA Sequence 9: 49-58 1998 Type: ARTICLE Genes: Abstract: We have identified a putative gene within the Caenorhabditis elegans genome which has the potential to encode a protein homologous to BRF, an RNA polymerase III general transcription factor. The predicted protein shares very similar overall structure with human and yeast BRF. In particular, its N-terminal half comprises a zinc-ribbon motif and a TR domain which is also present in the cyclin box. The C. elegans protein is more similar to human BRF than to the yeast BRF proteins, as would be expected from an evolutionary standpoint. Alignment of the C. elegans protein with the four known BRF proteins reveals two blocks conserved between all five sequences within the diverged C-terminal region. Profile searches using these regions suggest that they may contain evolutionarily conserved motifs. These comparisons provide insight into the structure and function of an important transcription ------------------- Key: 3397 Medline: Authors: Rand JB;Duerr JS;Frisby DL Title: Using Caenorhabditis elegans to study vesicular transport. Citation: Methods in Enzymology 296: 529-547 1998 Type: REVIEW Genes: cat-1 cha-1 glr-1 pha-1 unc-17 unc-25 unc-47 Abstract: In this chapter, we explore ways in which studies using the nematode Caenorhabditis elegans can add to our knowledge of vesicular transporters and vesicular transport. We discuss four general areas where the use of C. elegans offers advantages over other approaches: the use of C. elegans mutants to determine cellular and behavioral requirements for transporter function, the use of C. elegans for structure-function studies of vesicular transporters, the use of antibodies and mutants to explore protein targeting, and the use of C. elegans genetics to identify interacting genes and proteins. These studies rely on the strengths of C. elegans as a research organism: a simple nervous system in which all cells are identified and synaptic connectivity is known and reproducible; a large collection of mutants and powerful methods of genetic analysis; simple methods for the generation and analysis of transgenic animals; and a number of relatively straightforward quantifiable behaviors. Thus, the major uses of C. elegans in this field are for analysis of the functional (i.e., behavioral) role(s) of transporters, and the analysis of cellular and subcellular localization of these proteins. We conclude this chapter with a brief discussion of plasma membrane transporters of C. elegans. Although little research has been performed to date on these proteins in C. elegans, apparent homologs of the mammalian genes have been identified by the C. elegans Genome Sequencing Project and by other investigators. We explain how the strategies and methods described in this chapter can be applied to this ------------------- Key: 3398 Medline: Authors: Kuwabara PE Title: Developmental genetics of Caenorhabditis elegans sex determination. Citation: Current Topics in Developmental Biology 41: 99-132 1999 Type: REVIEW Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 fbf-1 fbf-2 fem-1 fem-2 fem-3 fog-1 fog-2 fog-3 fox-1 her-1 laf-1 mog-1 mog-2 mog-3 mog-4 mog-5 mog-6 sdc-1 sdc-2 sdc-3 tra-1 tra-2 tra-3 xol-1 eDp26 mnDp73 Abstract: The nematode Caenorhabditis elegans has two naturally occurring sexes: a self-fertile XX hermaphrodite that first produces sperm, then oocytes, and an XO male. The primary determinant of sex is the X:A ratio, the number of X chromosomes to sets of autosomes. The X:A ratio regulates not only sex determination, but also dosage compensation. In the intervening years since the identification of the X:A ratio, most of the key regulatory genes that respond to the X:A ratio have been genetically identified and ordered into regulatory hierarchies. Advances have also been made in identifying the X chromosome numerator elements of the X:A ratio. This review highlights the genetic, molecular, and biochemical approaches that have led to an understanding of how these genes interact to control sex determination and dosage compensation. The review also discusses the differences between the control of sexual cell fate in the soma and germ line of C. elegans and addresses the role of germ-line-specific regulation in controlling the sperm-oocyte decision in the hermaphrodite germ line. Finally, strategies that take advantage of the availability of the entire C. elegans genome sequence, which is expected to be completed in 1998, are discussed for identifying hitherto unidentified genes that may play a role in the control of sexual cell fate. ------------------- Key: 3399 Medline: 99094885 Authors: Yochem J;Tuck S;Greenwald I;Han M Title: A gp330/megalin-related protein is required in the major epidermis of Caenorhabditis elegans for completion of molting. Citation: Development 126: 597-606 1999 Type: ARTICLE Genes: lrp-1 nDf24 ozDf4 nDp4 Abstract: A genetic analysis of a gp330/megalin-related protein, LRP-1, has been undertaken in Caenorhabditis elegans. Consistent with megalin's being essential for development of mice, likely null mutations reveal that this large member of the low density lipoprotein receptor family is also essential for growth and development of this nematode. The mutations confer a striking defect, an inability to shed and degrade all of the old cuticle at each of the larval molts. The mutations also cause an arrest of growth usually at the molt from the third to the fourth larval stage. Genetic mosaic analysis suggests that the lrp-1 gene functions in the major epidermal syncytium hyp7, a polarized epithelium that secretes cuticle from its apical surface. Staining of whole mounts with specific monoclonal antibodies reveals that the protein as expressed on the apical surface of hyp7, Sterol starvation can phenocopy the lrp-1 mutations, suggesting that LRP-1 is a receptor for sterols that must be endocytosed by hyp7. These observations indicate that LRP-1 is related to megalin not only structurally but also functionally. ------------------- Key: 3400 Medline: 9847239 Authors: Krishna S;Maduzia LL;Padgett RW Title: Specificity of TGFB signaling is cnferred by distinct type I receptors and their associated SMAD proteins in Caenorhabditis elegans. Citation: Development 126: 251-260 1999 Type: ARTICLE Genes: daf-1 daf-4 sma-2 sma-3 sma-4 sma-6 mnDf30 mnDf96 Abstract: In C. elegans, the TGF beta-like type II receptor daf-4 is required for two distinct signaling pathways. In association with the type I receptor daf-1, it functions in the dauer pathway. In addition, it is also required for body size determination and male tail patterning, roles which do not require daf-1. In an effort to determine how two different signals are transmitted through daf-4, we looked for other potential signaling partners for DAF-4. We have cloned and characterized a novel type I receptor and show that it is encoded by sma-6, Mutations in sma-6 generate the reduced body size (Sma) and abnormal mail tail (Mab) phenotypes identical to those observed in daf-4 and sma-2, sma-3, sma-4 mutants (C. elegans Smads), indicating that they function in a common signaling pathway. However, mutations in sma-6, sma-2, sma-3, or sma-4 do not produce constitutive dauers, which demonstrates that the unique biological functions of daf-4 are mediated by distinct type I receptors functioning in parallel pathways. We propose that the C. elegans model for TGF beta-like signaling, in which distinct type I receptors determine specificity, may be a general mechanism of achieving specificity in other organisms. These findings distinguish between the manner in which signaling specificity is achieved in TGF beta-like pathways and receptor tyrosine-kinase (RTK) pathways. ------------------- Key: 3401 Medline: 99065495 Authors: Suzuki Y;Yandell MD;Roy PJ;Krishna S;Savage-Dunn C;Ross RM;Padgett RW;Wood WB Title: A BMP homolog acts as a dose-dependent regulator of body size and male tail patterning in Caenorhabditis elegans. Citation: Development 126: 241-250 1999 Type: ARTICLE Genes: daf-4 dbl-1 him-5 him-8 sma-2 sma-3 sma-4 sma-6 sDf20 Abstract: We cloned the dbl-1 gene, a C. elegans homolog of Drosophila decapentaptegic and vertebrate BMP genes. Loss-of-function mutations in dbl-1 cause reduced body size and defective male copulatory structures. Conversely, dbl-1 overexpression causes markedly increased body size and partly complementary male tail phenotypes, indicating that DBL-1 acts as a dose-dependent regulator of these processes. Evidence from genetic interactions indicates that these effects are mediated by a Smad signaling pathway, for which DBL-1 is a previously unidentified ligand, Our study of the dbl-1 expression pattern suggests a role for neuronal cells in global size regulation as well ------------------- Key: 3402 Medline: 99119367 Authors: Ashcroft NR;Srayko M;Kosinski ME;Mains PE;Golden A Title: RNA-mediated interference of a cdc25 homolog in Caenorhabditis elegans results in defects in the embryonic cortical membrane, meiosis, and mitosis. Citation: Developmental Biology 206: 15-32 1999 Type: ARTICLE Genes: fem-1 fem-3 glp-1 nop-1 Abstract: The CDC25 dual-specificity phosphatase family has been shown to play a key role in cell cycle regulation. The phosphatase activity of CDC25 drives the cell cycle by removing inhibitory phosphates from cyclin-dependent kinase/cyclin complexes. Although the regulation of CDC25 phosphatase activity has been elucidated both biochemically and genetically in other systems, the role of this enzyme during development is not well understood. To examine the expression pattern and function of CDC25 in Caenorhabditis elegans, we characterized a cdc25 homolog, cdc-25.1, during early embryonic development. The CDC-25.1 protein localizes to oocytes, embryonic nuclei, and embryonic cortical membranes. When the expression of CDC-25.1 was disrupted by RNA-mediated interference, the anterior cortical membrane of fertilized eggs became very fluid during meiosis and subsequent mitotic cell cycles. Mispositioning of the meiotic spindle, defects in polar body extrusion and chromosome segregation, and abnormal cleavage furrows were also observed. We conclude that CDC-25.1 is required for a very early developmental process-the proper completion of meiosis prior to embryogenesis. ------------------- Key: 3403 Medline: 99143069 Authors: Euling S;Bettinger JC;Rougvie AE Title: The LIN-29 transcription factor is required for proper morphogenesis of the Caenorhabditis elegans male tail. Citation: Developmental Biology 206: 142-156 1999 Type: ARTICLE Genes: him-5 lin-4 lin-14 lin-28 lin-29 ncl-1 Abstract: The Caenorhabditis elegans gene lin-29 encodes a zinc-finger transcription factor that is required for hypodermal cell terminal differentiation and proper vulva morphogenesis. Here we demonstrate that lin-29 is also required in males for productive mating. We show that lin-29 males can perform the early mating behaviors including response to hermaphrodite contact and vulva location, but they do not perform the subsequent steps of vulva attachment via spicule insertion and sperm transfer. Consistent with this observation, we found that lin-29 mutant spicules are on average 43% shorter than wild-type spicules while other male mating structures appear unaltered. In lin-29 mutants, spicule development goes awry after the generation of spicule cells, when spicule morphogenesis occurs in wild-type males. We show that LIN-29 accumulates in many cells of the wild-type male tail, including those that form the spicules. We demonstrate, through analysis of genetic mosaics, that the formation of wild-type-length spicules requires lin-29(+) in the AB.p lineage, the lineage that gives rise to the spicules and other male copulatory structures. Our mosaic analysis also reveals a role for lin-29(+) in the Pi lineage, which mainly produces sex muscles, cells of the ------------------- Key: 3404 Medline: 10081163 Authors: LaMunyon CW;Ward S Title: Evolution of sperm size in nematodes: sperm competition favours larger sperm. Citation: Proceedings of the Royal Society of London B 266: 263-267 1999 Type: ARTICLE Genes: Abstract: In the free-living rhabditid nematode Caenorhabditis elegans, sperm size is a determinant of sperm competitiveness. Larger sperm crawl faster and physically displace smaller sperm to take fertilization priority but not without a cost: larger sperm are produced at a slower rate. Here, we investigate the evolution of sperm size in the family Rhabditidae by comparing sperm among 19 species, seven of which are hermaphroditic (self-fertile hermaphrodites and males), the rest being gonochoristic (females and males). We found that sperm size differed significantly with reproductive mode: males of gonochoristic species had significantly larger sperm than did males of the hermaphroditic species. Because males compose 50% of the populations of gonochoristic species but are rare in hermaphroditic species, the risk of male-male sperm competition is greater in gonochoristic species. Larger sperm have thus evolved in species with a greater risk of sperm competition. Our results support recent studies contending that sperm size may increase in response to sperm competition. ------------------- Key: 3405 Medline: 99128346 Authors: Herman T;Hartwieg E;Horvitz HR Title: sqv mutants of Caenorhabditis elegans are defective in vulval epithelial invagination. Citation: Proceedings of the National Academy of Sciences USA 96: 968-973 1999 Type: ARTICLE Genes: lin-12 sqv-1 sqv-2 sqv-3 sqv-4 sqv-5 sqv-6 sqv-7 sqv-8 mnDf29 mnDf30 nDf40 Abstract: By screening for mutations that perturb the invagination of the vulva of the Caenorhabditis elegans hermaphrodite, we have isolated 25 mutations that define eight genes. We have named these genes sqv-1 to sqv-8 (squashed vulva). All 25 mutations cause the same vulval defect, an apparent partial collapse of the vulval invagination and an elongation of the central vulval cells. Most sqv mutations also cause an oocyte or somatic gonad defect that results in hermaphrodite sterility, and some sqv mutations cause maternal-effect lethality. We propose that the sqv genes affect a pathway common to vulval invagination, oocyte development, and embryogenesis. ------------------- Key: 3406 Medline: 99128347 Authors: Herman T;Horvitz HR Title: Three proteins involved in Caenorhabditis elegans vulval invagination are similar to components of a glycosylation pathway. Citation: Proceedings of the National Academy of Sciences USA 96: 974-979 1999 Type: ARTICLE Genes: sqv-3 sqv-7 sqv-8 unc-104 Abstract: We have molecularly analyzed three genes, sqv-3, sqv-7: and sqv-8, that are required for wild-type vulval invagination in Caenarhabditis elegans. The predicted SQV-8 protein is similar in sequence to two mammalian beta(1,3)-glucuronyltransferases, one of which adds glucuronic acid to protein-linked galactose-beta(1,4)-N-acetylglucosamine. SQV-3 is similar to a family of glycosyltransferases that includes vertebrate beta(1,4)-galactosyltransferases, which create galactose-beta(1,4) -N-acetylglucosamine linkages. One model is therefore that SQV-8 uses a SQV-3 product as a substrate. SQV-7 is similar to members of a family of nucleotide-sugar transporters. The sqv genes therefore are likely to encode components of a conserved glycosylation pathway that assembles a C. elegans carbohydrate moiety, the absence of which perturbs vulval invagination. ------------------- Key: 3407 Medline: 99134356 Authors: Kraev A;Kraev N;Carafoli E Title: Identification and functional expression of the plasma membrane calcium ATPase gene family from Caenorhabditis elegans. Citation: Journal of Biological Chemistry 274: 4254-4258 1999 Type: ARTICLE Genes: mca-1 mca-2 mca-3 Abstract: Calcium-pumping ATPases are an essential component of the intracellular calcium homeostasis system and have been characterized in a large variety of species and cell types. In mammalian genomes, these proteins are encoded by gene families whose individual members feature complex: tissue-specific expression and alternative splicing. ale the search for a less complex system that is more amenable to genetic manipulation, we have identified a family of three genes (mca-1, mca-2, rand mca-3) encoding putative calcium ATPases in the Caenorhabditis elegans Genome Project data and completed their transcript structure. In this work, we report the cloning and functional expression of the mca-l gene, which encodes a calcium-stimulated ATPase whose features resemble those of the plasma membrane calcium adenosine triphosphatase family of mammalian cells and appears to be regulated by a multipartite promoter. ------------------- Key: 3408 Medline: 99165800 Authors: Hart AC;Kass J;Shapiro JE;Kaplan JM Title: Distinct signaling pathways mediate touch and osmosensory responses in a polymodal sensory neuron. Citation: Journal of Neuroscience 19: 1952-1958 1999 Type: ARTICLE Genes: deg-1 eat-4 eos-1 eos-2 mec-2 mec-4 mec-5 mec-6 mec-8 mec-9 mec-10 osm-3 osm-9 osm-10 srb-6 sre-1 unc-8 nDf16 Abstract: The Caenorhabditis elegans ASH sensory neurons mediate responses to nose touch, hyperosmolarity, and volatile repellent chemicals. We show here that distinct signaling pathways mediate the responses to touch and hyperosmolarity. ASH neurons distinguish between these stimuli because habituation to nose touch has no effect on the response to high osmolarity or volatile chemicals (1-octanol). Mutations in osm-10 eliminate the response to hyperosmolarity but have no effect on responses to nose touch or to volatile repellents. OSM-10 is a novel cytosolic protein expressed in ASH and three other classes of sensory neurons. Mutations in two other osmosensory-defective genes, eos-1 and eos-2, interact genetically with osm-10. Our analysis suggests that nose touch sensitivity and osmosensation occur via distinct signaling pathways in ASH and that OSM-10 is required for ------------------- Key: 3409 Medline: 99147024 Authors: Ferguson KC;Rothman JH Title: Alterations in the conserved SL1 trans-spliced leader of Caenorhabditis elegans demonstrate flexibility in length and sequence requirements in vivo. Citation: Molecular and Cellular Biology 19: 1892-1900 1999 Type: ARTICLE Genes: rrs-1 wDf1 Abstract: Approximately 70% of mRNAs in Caenorhabditis elegans are trans spliced to conserved 21- to 23-nucleotide leader RNAs. While the function of SL1, the major C. elegans trans-spliced leader, is unknown, SL1 RNA, which contains this leader, is essential for embryogenesis. Efforts to characterize In vivo requirements of the SL1 leader sequence have been severely constrained by the essential role of the corresponding DNA sequences in SL1 RNA transcription. We devised a heterologous expression system that circumvents this problem, making it possible to probe the length and sequence requirements of the SL1 leader without interfering with its transcription. We report that expression of SL1 from a U2 snRNA promoter rescues mutants lacking the SL1-encoding genes and that the essential embryonic function of SL1 is retained when approximately one-third of the leader sequence and/or the length of the leader is significantly altered. In contrast, although all mutant SL1 RNAs were well expressed, more severe alterations eliminate this essential embryonic function. The one nan-rescuing mutant leader tested was never detected on messages, demonstrating that part of the leader sequence is essential for trans splicing in vivo. Thus, in spite of the high degree of SL1 sequence conservation, its length, primary sequence, and composition are not critical parameters of its essential embryonic function. However, particular nucleotides in the leader are essential for the in vivo function of the SL1 RNA, perhaps for its assembly into a functional snRNP or for the trans-splicing reaction. ------------------- Key: 3410 Medline: 99147053 Authors: Puoti A;Kimble J Title: The Caenorhabditis elegans sex determination gene mog-1 encodes a member of the DEAH-box protein family. Citation: Molecular and Cellular Biology 19: 2189-2197 1999 Type: ARTICLE Genes: act-1 fbf-1 fbf-2 fem-3 lag-1 mog-1 smg-1 Abstract: In the Caenorhabditis elegans hermaphrodite germ line, the sex-determining gene fem-3 is repressed posttranscriptionally to arrest spermatogenesis and permit oogenesis. This repression requires a cis-acting regulatory element in the fem-3 3' untranslated region; the FBF protein, which binds to this element; and at least six mog genes. In this paper, we report the molecular characterization of mog-1 as well as additional phenotypic characterization of this gene. The mog-1 gene encodes a member of the DEAH-box family. Three mog-1 alleles possess premature stop codons and are likely to be null alleles, and one is a missense mutation and is likely to retain residual activity. mog-1 mRNA is expressed in both germ line and somatic tissues and appears to be ubiquitous. The MOG-1 DEAH-box protein is most closely related to proteins essential for splicing in the yeast Saccharomyces cerevisiae, but splicing appears to occur normally in a mog-1-null mutant. In addition to its involvement in the sperm oocyte switch and control of fem-3, zygotic mog-1 is required for robust germ line proliferation and for normal growth during development. We suggest that mog-1 plays a broader role in RNA regulation than previously considered. ------------------- Key: 3411 Medline: 99120531 Authors: Barth JL;Argraves KM;Roark EF;Little CD;Argraves WS Title: Identification of chicken and C. elegans fibulin-1 homologs and characterization of the C. elegans fibulin-1 gene. Citation: Matrix Biology 17: 635-646 1998 Type: ARTICLE Genes: Abstract: Fibulin-1, a member of the emerging family of fibulin proteins, is a component of elastic extracellular matrix fibers, basement membranes and blood. Homologs of fibulin-1 have been described in man, mouse and zebrafish. In this study, we describe the isolation and sequencing of chicken fibulin-1C and D cDNA variants. We also describe identification of a C. elegans cDNA encoding fibulin-1D and cosmids containing the C. elegans fibulin-1 gene. Using the cDNA, RT-PCR and computer-based analysis of genomic sequences, the exon/intron organization of the C. elegans fibulin-1 gene was determined. The C. elegans fibulin-1 gene is located on chromosome IV is approximately 6 kb in length, contains 16 exons and encodes fibulin-1C and D variants. Comparative analysis of the deduced amino acid sequences of nematode and chicken fibulin-1 variants with other known vertebrate fibulin-1 polypeptides showed that the number and organization of structural modules are identical. The results of this study indicate that the structure of the fibulin-1 protein has remained highly conserved over a large period of evolution, suggestive of ------------------- Key: 3412 Medline: 99161002 Authors: Yasuda K;Adachi H;Fujiwara Y;Ishii N Title: Protein carbonyl accumulation in aging dauer formation-defective (daf) mutants of Caenorhabditis Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 54: B47-B51 1999 Type: ARTICLE Genes: age-1 daf-2 daf-12 daf-16 Abstract: It is known that a dauer-constitutive gene, daf-2, controls both larval development and adult life span irt Caenorhabditis elegans. The increased life span caused by the daf-2 mutation can be enhanced by a daf-12 mutation and suppressed by a daf-16 mutation. In order to determine the correlation between longevity and oxidative stress in these mutants, protein carbonyl (a good indicator of oxidative damage during aging) was measured. Mean life spans of these mutants were in the order of daf-16 < daf-2;daf-16 congruent to wild type < daf-2 < daf-2;daf-12. Accumulations of protein carbonyl in these wild-type and daf mutants were in a mirror image of the order of their life spans. These results strongly support the notion that oxidative damage is one of the major causal factors for life-span determination in C. elegans. ------------------- Key: 3413 Medline: Authors: Goto S Title: Commentary on "Protein carbonyl accumulation in aging dauer formation-defective (daf) mutants of Caenorhabditis elegans". Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 54: B52-B53 1999 Type: REVIEW Genes: age-1 daf-2 daf-12 daf-16 mev-1 Abstract: In recent years, oxidative damage to macromolecules has gained popularity as the basis of the molecular mechanism of aging. Martin proposes oxidative damage to macromolecules as one of the major public mechanisms of aging. Interest in modifications of protein by reactive oxygen species in aging was apparently introduced by Stadtman. Although various types of oxidative modifications can occur in proteins, carbonyl residues believed to be generated by metal catalyzed reaction or otherwise introduced by lysine, arginine and/or proline residues in vivo are often used as a marker of direct or ------------------- Key: 3414 Medline: 99104240 Authors: Fukushige T;Siddiqui ZK;Chou M;Culotti JG;Gogonea CB;Siddiqui SS;Hamelin M Title: MEC-12, an alpha-tubulin required for touch sensitivity in C. elegans. Citation: Journal of Cell Science 112: 395-403 1999 Type: ARTICLE Genes: mec-7 mec-12 tba-1 tba-2 Abstract: mec-12 is one of a dozen genes required for touch receptor neuron function in Caenorhabditis elegans, Some mec-12 mutants (mechanosensory-defective) lack the large-diameter microtubules that are characteristic of these neurons (15 protofilaments, as opposed to 11). Mutants of mec-7, a beta-tubulin encoding gene, have a similar phenotype, We have identified the nature of mec-12 by germline transformation rescue and characterization of a point mutation. Sequence analysis of the mec-12 encoded product (MEC-12) indicates that it corresponds to a novel C.elegans alpha-tubulin, MEC-12 is the only identified C. elegans alpha-tubulin that contains a lysine at position 40, a known site of post-translational acetylation. Some mec-12 mutations eliminate microtubule acetylation as assayed immunocytochemically; phenotypic rescue using a MEC-12 variant lacking the lysine-40 showed that acetylation is not required for MEC-12 activity. Although functionally needed only in the touch neurons, mec-12 is expressed in several other neuron types. These results support the notion that tubulin isotype diversity contributes to the formation of distinct classes of microtubules; 15-protofilament microtubule assembly requires MEC-12 alpha-tubulin and MEC-7 beta-tubulin, which are both highly expressed in the touch receptor neurons. MEC-12 is the first reported alpha-tubulin isotype that appears to be required in a single class of neuronal microtubules. ------------------- Key: 3415 Medline: Authors: Haitzer M;Burnison BK;Hoss S;Traunspurger W;Steinberg CE Title: Effects of quantity, quality, and contact time of dissolved organic matter on bioconcentration of benzo[a]pyrene in the nematode Caenorhabditis elegans. Citation: Environmental Toxicology and Chemistry 18: 459-465 1999 Type: ARTICLE Genes: glp-1 Abstract: Quantity and quality of dissolved organic matter (DOM) and the lime allowed for DOM to interact with organic contaminants can influence their bioavailability. We studied the effect of natural aquatic DOM that had been in contact with benzo[a]pyrene (B[a]P) for 1 to 12 d on the bioconcentration of B[a]P in the nematode Caenorhabditis elegans. Dissolved organic matter quality and quantity was varied by using DOM from three different sources, each in three different concentrations. A model, based on the assumption that only freely dissolved B[a]P is bioavailable, was employed to estimate "biologically determined" partition coefficients [K-p(biol.)]. Expressing the data for each combination of DOM source and contact time in a single K-p (biol.) value allowed a direct comparison of the effects of different DOM qualities and contact times. Our results show that the effect of DOM from a specific source was dependent on DOM quantity, but we also observed a distinct effect of DOM quality (represented by different sampling locations) on the bioconcentration of B[a]P. Contact time had no significant influence for the effects of two DOM sources on the bioconcentration of B[a]P. However, the third DOM source was significantly more effective with increased contact time, leading to lower B[a]P bioconcentration in the nematodes. ------------------- Key: 3416 Medline: 99148134 Authors: Sluder AE;Mathews SW;Hough D;Yin VP;Maina CV Title: The nuclear receptor superfamily has undergone extensive proliferation and diversification in nematodes. Citation: Genome Research 9: 103-120 1999 Type: ARTICLE Genes: daf-12 fax-1 nhr-1 nhr-2 nhr-3 nhr-4 nhr-5 nhr-6 nhr-7 nhr-8 nhr-8 nhr-10 nhr-11 nhr-12 nhr-13 nhr-14 nhr-15 nhr-16 nhr-17 nhr-18 nhr-20 nhr-21 nhr-22 nhr-23 nhr-24 nhr-25 nhr-28 nhr-31 nhr-34 nhr-35 nhr-40 nhr-41 nhr-42 nhr-43 nhr-44 nhr-45 nhr-46 nhr-47 nhr-48 nhr-49 nhr-50 nhr-51 nhr-52 nhr-53 nhr-54 nhr-55 nhr-56 nhr-57 nhr-58 nhr-59 nhr-60 nhr-61 nhr-62 nhr-63 nhr-64 nhr-65 nhr-66 nhr-67 odr-7 sex-1 unc-55 Abstract: The nuclear receptor (NR) superfamily is the most abundant class of transcriptional regulators encoded in the Caenorhabditis elegans genome, with >200 predicted genes revealed by the screens and analysis of genomic sequence reported here. This is the largest number of NR genes yet described from a single species, although our analysis of available genomic sequence from the related nematode Caenorhabditis briggsae indicates that it also has a large number. Existing data demonstrate expression for 25% of the C. elegans NR sequences. Sequence conservation and statistical arguments suggest that the majority represent functional genes. An analysis of these genes based on the DNA-binding domain motif revealed that several NR classes conserved in both vertebrates and insects are also represented among the nematode genes, consistent with the existence of ancient NR classes shared among most, and perhaps all, metazoans. None of the nematode NR sequences, however, are distinct from those currently known in other phyla, and reveal a previously unobserved diversity within the NR superfamily. In C. elegans, extensive proliferation and diversification of NR sequences have occurred on chromosome V, accounting for > 50% of the predicted NR genes. ------------------- Key: 3417 Medline: 99029264 Authors: Plasterk RHA Title: The year of the worm. Citation: BioEssays 21: 105-109 1999 Type: REVIEW Genes: Abstract: Developmental biology has almost come full circle. Initially aimed at description at the organismal level, in the last 25 years it has zoomed in on individual genes that are involved in specific steps in development. Now, complete genome sequences are becoming available-and to gain a full understanding of the relevance of the complete genome, experimental developmental biology will hold centre stage again, but now armed with large genome databases, and with a new set of refined genetic tools. The first multicellular organism to be sequenced is the nematode C. elegans. This review aims to recognise some new avenues in C. elegans experimental biology that are opened by the ------------------- Key: 3418 Medline: 99160530 Authors: Nguyen CQ;Hall DH;Yang Y;Fitch DHA Title: Morphogenesis of the Caenorhabditis elegans male tail tip. Citation: Developmental Biology 207: 86-106 1999 Type: ARTICLE Genes: lep-1 let-7 lin-44 mab-3 mab-19 sup-17 tra-1 unc-101 Abstract: Using electron microscopy and immunofluorescent labeling of adherens junctions, we have reconstructed the changes in cell architecture and intercellular associations that occur during morphogenesis of the nematode male tail tip. During late postembryonic development, the Caenorhabditis elegans male rail is reshaped to form a copulatory structure. The most posterior hypodermal cells in the tail define a specialized, sexually dimorphic compartment in which cells fuse and retract in the male, changing their shape from a tapered cone to a blunt dome, Developmental profiles using electron microscopy and immunofluorescent staining suggest that cell fusions are initiated at or adjacent to adherens junctions. Anterior portions of the tail tip cells show the first evidence of retractions and fusions, consistent with our hypothesis that an anterior event triggers these morphogenetic events. Available mutations that interfere with morphogenesis implicate particular regulatory pathways and suggest loci at which evolutionary changes could have produced morphological diversity. ------------------- Key: 3419 Medline: 10051655 Authors: Tan MW;Rahme LG;Sternberg JA;Tompkins RG;Ausubel FM Title: Pseudomonas aeruginosa killing of Caenorhabditis elegans used to identify P. aeruginosa virulence factors. Citation: Proceedings of the National Academy of Sciences USA 96: 2408-2413 1999 Type: ARTICLE Genes: Abstract: We reported recently that the human opportunistic pathogen Pseudomonas aeruginosa strain PA14 kills Caenorhabditis elegans and that many P. aeruginosa virulence factors (genes) required for maximum virulence in mouse patho genicity are also required for maximum killing of C. elegans. Here we report that among eight P. aeruginosa PA14 TnphoA mutants isolated that exhibited reduced killing of C. elegans, at least five also exhibited reduced virulence in mice. Three of the TnphoA mutants corresponded to the known virulence-related genes lasR, gacA, and lemA. Three of the mutants corresponded to known genes (aefA from Escherichia coli, psfP from Azotobacter vinelandii, and mtrR from Neisseria gonorrhoeae) that had not been shown previously to play a role in pathogenesis, and two of the mutants contained TnphoA inserted into novel sequences. These data indicate that the killing of C. elegans by P. aeruginosa can be exploited to identify novel P. aeruginosa virulence factors important far mammalian pathogenesis. ------------------- Key: 3420 Medline: 99162631 Authors: van Swinderen B;Saifee O;Shebester L;Roberson R;Nonet ML;Crowder CM Title: A neomorphic syntaxin mutation blocks volatile-anesthetic action in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 96: 2479-2484 1999 Type: ARTICLE Genes: aex-3 rab-3 ric-4 snb-1 unc-64 Abstract: The molecular mechanisms underlying general anesthesia are unknown. For volatile general anesthetics (VAs), indirect evidence for both lipid and protein targets has been found. However, no in vivo data have implicated clearly any particular lipid or protein in the control of sensitivity to clinical concentrations of VAs. Genetics provides one approach toward identifying these mechanisms, but genes strongly regulating sensitivity to clinical concentrations of VAs have not been identified. By screening existing mutants of the nematode Caenorhabditis elegans, we found that a mutation in the neuronal syntaxin gene dominantly conferred resistance to the VAs isoflurane and halothane. By contrast, other mutations in syntaxin and in the syntaxin-binding proteins synaptobrevin and SNAP-25 produced VA hypersensitivity. The syntaxin allelic variation was striking, particularly for isoflurane, where a 33 fold range of sensitivities aas seen. Both the resistant and hypersensitive mutations decrease synaptic transmission; thus, the indirect effect of reducing neurotransmission does not explain the VA resistance. As assessed by pharmacological criteria, halothane and isoflurane themselves reduced cholinergic transmission, and the presynaptic anesthetic effect was blocked by the resistant syntaxin mutation. A single gene mutation conferring high-lever resistance to VAs is inconsistent with nonspecific membrane-perturbation theories of anesthesia. The genetic and pharmacological data suggest that the resistant syntaxin mutant directly blocks VA binding to or efficacy against presynaptic targets that mediate anesthetic behavioral effects. Syntaxin and syntaxin-binding proteins are candidate anesthetic targets. ------------------- Key: 3421 Medline: 99162634 Authors: Westlund B;Parry D;Clover R;Basson M;Johnson CD Title: Reverse genetic analysis of Caenorhabditis elegans presenilins reveals redundant but unequal roles for sel-12 and hop-1 in Notch-pathway signaling. Citation: Proceedings of the National Academy of Sciences USA 96: 2497-2502 1999 Type: ARTICLE Genes: glp-1 hop-1 lin-12 sel-12 hDf7 Abstract: Mutations in the human presenilin genes PS1 and PS2 cause early-onset Alzheimer's disease. Studies in Caenorhabditis elegans and in mice indicate that one function of presenilin genes is to facilitate Notch-pathway signaling. Notably, mutations in the C. elegans presenilin gene sel-12 reduce signaling through an activated version of the Notch receptor LIN-12. To investigate the function of a second C. elegans presenilin gene hop-1 and to examine possible genetic interactions between hop-1 and sel-12, we used a reverse genetic strategy to isolate deletion alleles of both loci. Animals bearing both hop-1 and sel-12 deletions displayed new phenotypes not observed in animals bearing either single deletion. These new phenotypes-germ-line proliferation defects, maternal-effect embryonic lethality, and somatic gonad defects-resemble those resulting from a reduction in signaling through the C. elegans Notch receptors GLP-1 and LIN-12. Thus SEL-12 and HOP-1 appear to function redundantly in promoting Notch-pathway signaling. Phenotypic analyses of hop-1 and sel-12 single and double mutant animals suggest that sel-12 provides more presenilin function than does hop-1. ------------------- Key: 3422 Medline: 99158743 Authors: Baum PD;Guenther C;Frank CA;Pham BV;Garriga G Title: The Caenorhabditis elegans gene ham-2 links Hox patterning to migration of the HSN neuron. Citation: Genes & Development 13: 472-483 1999 Type: ARTICLE Genes: ced-1 ced-3 egl-5 egl-43 ham-2 lin-26 unc-86 Abstract: The Caenorhabditis elegans HSN motor neurons permit genetic analysis of neuronal development at single-cell resolution. The egl-5 Hox gene, which patterns the posterior of the embryo, is required for both early (embryonic) and late (larval) development of the HSN. Here we show that ham-2 encodes a zinc finger protein that acts downstream of egl-5 to direct HSN cell migration, an early differentiation event. We also demonstrate that the EGL-43 zinc finger protein, also required for HSN migration, is expressed in the HSN specifically during its migration. In an egl-5 mutant background, the HSN still expresses EGL-43, but expression is no longer down-regulated at the end of the cell's migration. Finally, we find a new role in early HSN differentiation for UNC-86, a POU homeodomain transcription factor shown previously to act downstream of egl-5 in the regulation of late HSN differentiation. In an unc-86; ham-2 double mutant the HSNs are defective in EGL-43 down-regulation, an egl-5-like phenotype that is absent in either single mutant. Thus, in the HSN, a Hox gene, egl-5, regulates cell fate by activating the transcription of genes encoding the transcription factors HAM-2 and UNC-86 that in turn individually control some differentiation events and combinatorially affect others. ------------------- Key: 3423 Medline: 99196567 Authors: Venolia L;Ao W;Kim S;Kim C;Pilgrim D Title: unc-45 gene of Canorhabditis elegans encodes a muscle-specific tetratricopeptide repeat-containing Citation: Cell Motility & the Cytoskeleton 42: 163-177 1999 Type: ARTICLE Genes: unc-45 Abstract: The unc-45 gene of the nematode, Caenorhabditis elegans, is essential for muscle organization and embryonic development. Genetic evidence suggests the unc-45 gene product controls muscle thick filament assembly. We report here on the determination of the gene's chromosomal location and the isolation and sequencing of its cDNA. The amino terminus of the predicted unc-45 protein contains three tandem repeats that belong in the tetratricopeptide repeat family. Tetratricopeptide motifs have been shown to be involved in protein interactions, and some of the closest homologues have chaperone-like activity. The carboxy terminus of the protein has homology with the related fungal proteins, CRO1 and She4p, which have been postulated to play a role in assembly of or interactions with a cytoplasmic myosin. We have also determined the sequence of the homologous gene from C. briggsae, which demonstrates a high level of conservation. We show that the unc-45 gene promoter can drive reporter gene expression, which is limited to muscle tissues (pharyngeal, body wall, vulval, and anal muscles), consistent with a role for the unc-45 gene in muscle development or function. ------------------- Key: 3424 Medline: Authors: Kohra S;Tominaga N;Mitsui Y;Takao Y;Ishibashi Y;Arizono K Title: Determination of a screening system of endocrine disruptors by the induction of vitellogenin mRNA in C. elegans larvae. Citation: Japanese Journal of Toxicology & Environmental Health 45: P37- 1999 Type: ARTICLE Genes: Abstract: In this study we investigated the possibility of detection of estrogenic activity of chemical materials, based on a model using vitellogenin (VTG), the egg yolk protein precursor synthesized by female oviparous animals, mRNA expression in Caenorhabditis elegans hermaphrodites. ------------------- Key: 3425 Medline: 99200102 Authors: Mongan NP;Baylis HA;Adcock C;Smith GR;Sansom MSP;Sattelle Title: An extensive and diverse gene family of nicotinic acetylcholine receptor alpha subunits in Caenorhabditis elegans. Citation: Receptors & Channels 6: 213-+ 1998 Type: ARTICLE Genes: acr-2 acr-3 acr-4 acr-5 acr-6 acr-7 acr-8 acr-9 acr-10 acr-11 acr-12 acr-13 acr-14 acr-15 acr-16 deg-3 lev-1 unc-29 unc-38 Abstract: Using reverse transcription-polymerase chain reactions the transcription of eight novel candidate nicotinic acetylcholine receptor (nAChR) a subunit genes has been demonstrated in the nematode Caenorhabditis elegans. Together with five other ct subunit genes described elsewhere by ourselves (unc-38) and other workers (deg-3, acr-4, Ce21 and nci 6), this is now the largest known family of nAChR a subunit genes in a single species. By homology we have identified four groups of cu subunits, DEG-3-like; ACR-16[Ce21]-like; UNC-38-like and ACR-8-like, Five C, elegans nAChR a subunits contain a modification in loop C of the ACh binding site in which the normally conserved Tyr-x-Cys-Cys, is replaced by a distinct motif (Tyr-x-x-Cys-Cys). Variation is also found in the channel lining M2 regions, including the replacement in four subunits of the highly conserved leucine at the 9' position by valine and most notably, the replacement in all ACR-S-like subunits of the highly conserved glutamic acid at the -1' position by histidine. Restrained molecular dynamics simulations have been used to generate homo-pentameric M2 helix bundle models for ct subunits and possible functional implications examined. The calculated electrostatic potential energy profile for the M2 region of ACR-S differs strikingly from that of ACR-16[Ce21] largely due to the presence of histidine at the -1' position, suggesting a possible perturbation of nAChR channel action permeability in the presence of this subunit type. ------------------- Key: 3426 Medline: 10049576 Authors: Ferreira HB;Zhang Y;Zhao C;Emmons SW Title: Patterning of Caenorhabditis elegans posterior structures by the Abdominal-B homolog, egl-5. Citation: Developmental Biology 207: 215-228 1999 Type: ARTICLE Genes: egl-5 lin-32 lin-39 mab-5 Abstract: The Caenorhabditis elegans body axis, like that of other animals, is patterned by the action of Hox genes. In order to examine the function of one C. elegans Hox gene in depth, we determined the postembryonic expression pattern of egl-5, the C. elegans member of the Abdominal-B Hox gene paralog group, by means of whole-mount staining with a polyclonal antibody. A major site of egl-5 expression and function is in the epithelium joining the posterior digestive tract with the external epidermis. Patterning this region and its derived structures is a conserved function of Abd-B paralog group genes in other animals. Cells that initiate egl-5 expression during embryogenesis are clustered around the presumptive anus. Expression is initiated postembryonically in four additional mesodermal and ectodermal cell lineages or tissues. Once initiated in a lineage, egl-5 expression continues throughout development, suggesting that the action of egl-5 can be regarded as defining a positional cell identity. A variety of cross-regulatory interactions between egl-5 and the next more anterior Hox gene, mab-5, help define the expression domains of their respective gene products. In its expression in a localized body region, function as a marker of positional cell identity, and interactions with another Hox gene, egl-5 resembles Hox genes of other animals. This suggests that C. elegans, in spite of its small cell number and reproducible fell lineages, may not differ greatly from other animals in the way it employs Hox genes for regional specification during development. ------------------- Key: 3427 Medline: 99112958 Authors: Sharma-Kishore R;White JG;Southgate E;Podbilewicz B Title: Formation of the vulva in Caenorhabditis elegans: a paradigm for organogenesis. Citation: Development 126: 691-699 1999 Type: ARTICLE Genes: lin-3 lin-12 Abstract: The genes involved in the inductive interactions that specify cell fates in the vulva of Caenorhabditis elegans are known in some detail. However, little is known about the morphogenesis of this organ. Using a combination of cell biological and anatomical approaches, we have determined a complete morphogenetic pathway of cellular events that lead to the formation of the vulva. These events include reproducible cell divisions, migrations, remodeling of adherens junctions, cell fusions and muscle attachments. In the course of these events, an epithelial channel comprising a stack of 7 toroidal cells is formed that connects the internal epithelium of the uterus with the external body epithelium, forming the vulva. Vulval muscles attach to the epithelial channel and the whole structure everts during the final molt. The mature vulva has rotational, two-fold symmetry. Using laser microsurgery, we found that the two halves of the vulva ------------------- Key: 3428 Medline: 99112968 Authors: Hunter CP;Harris JM;Maloof JN;Kenyon C Title: Hox gene expression in a single Caenorhabditis elegans cell is regulated by a caudal homolog and intercellular signals that inhibit Wnt signaling. Citation: Development 126: 805-814 1999 Type: ARTICLE Genes: bar-1 egl-20 lin-17 mab-5 pal-1 Abstract: In Caenorhabditis elegans males, a row of epidermal precursor cells called seam cells generates a pattern of cuticular alae in anterior body regions and neural sensilla called rays in the posterior. The Hox gene mab-5 is required for two posterior seam cells, V5 and V6, to generate rays. In mab-5 mutant males, V5 and V6 do not generate sensory ray lineages but instead generate lineages that lead to alae. Here we show that two independent regulatory pathways can activate mab-5 expression in the V cells. First, the caudal homolog pal-1 turns on mab-5 in V6 during embryogenesis. Second, a Writ signaling pathway is capable of activating mab-5 in the V cells during postembryonic development; however, during normal development Wnt signaling is inhibited by signals from neighboring V cells. The inhibition of this Wnt signaling pathway by lateral signals between the V cells limits the number of rays in the animal and also determines the position of the boundary between alae and rays. ------------------- Key: 3429 Medline: 99175344 Authors: Chang C;Newman AP;Sternberg PW Title: Reciprocal EGF signaling back to the uterus from the induced C. elegans vulva coordinates morphogenesis of Citation: Current Biology 9: 237-246 1999 Type: ARTICLE Genes: egl-38 gap-1 lag-2 let-23 let-60 lin-1 lin-3 lin-12 lin-45 sli-1 Abstract: Background: Reciprocal signaling between distinct tissues is a general feature of organogenesis. Despite the identification of developmental processes in which coordination requires reciprocal signaling, little is known regarding the underlying molecular details. Here, we use the development of the uterine-vulval connection in the nematode Caenorhabditis elegans as a model system to study reciprocal signaling. Results: In C. elegans, development of the uterine-vulval connection requires the specification of uterine uv1 cells and morphogenesis of 1 degrees-derived vulval cells. LIN-3, an epidermal growth factor (EGF) family protein, is first produced by the gonadal anchor cell to induce vulval precursor cells to generate vulval tissue. We have shown that lin-3 is also expressed in the 1 degrees vulval lineage after vulval induction and that the 1 degrees vulva is necessary to induce the uv1 uterine cell fate. Using genetic and cell biological analyses, we found that the specification of uterine uv1 cells is dependent on EGF signaling from cells of the 1 degrees vulval lineages to a subset of ventral uterine cells of the gonad. RAS and RAF are necessary for this signaling. We also found that EGL-38, a member of the PAX family of proteins, is necessary for transcription of lin-3 in the vulva but not in the anchor cell. A let-23 mutation that confers ligand-independent activity bypasses the requirement for EGL-38 in specification of the uv1 cell fate. Conclusions: We have shown how relatively simple EGF signals can be used reciprocally to specify the uterine-vulval connection during C, elegans development. ------------------- Key: 3430 Medline: 99165616 Authors: Komatsu H;Jin YH;L'Etoile N;Mori I;Bargmann CI;Akaike N;Ohshima Y Title: Functional reconstitution of a heteromeric cyclic nucleotide-gated channel of Caenorhabditis elegans in cultured cells. Citation: Brain Research 821: 160-168 1999 Type: ARTICLE Genes: tax-2 tax-4 Abstract: The tax-4 and tax-2 genes of Caenorhabditis elegans are essential for normal olfaction, gustation, and thermosensation, suggesting that they have a role in sensory transduction. The predicted products of these genes are similar to the cyclic nucleotide-gated (CNG) channel subunits used in vertebrate vision and olfaction: TAX-4 is highly related to those ct subunits, while TAX-2 is most closely related to the beta subunits of the rod phototransduction channels. TAX-4 has previously been shown to form a highly sensitive cGMP-gated channel when expressed in human HEK293 cells. Here we show that TAX-4 and TAX-2 form a heteromeric channel when expressed in HEK293 cells, but TAX-2 does not form a channel on its own. Since these genes are expressed in the same neurons, most of the native channels in C. elegans are Likely to be hetero-oligomers of TAX-4 and TAX-2 subunits, with TAX-4 as the or subunit and TAX-2 acting as a modifying beta subunit. The heteromeric TAX-4/TAX-2 channel is 25-fold less sensitive to cGMP than the TAX-4 channel, but it remains highly selective for cGMP over cAMP. The heteromeric channel and the TAX-4 homomeric channel differ in their blockage by divalent cations and in their single channel properties. These results suggest that cGMP is used as the second messenger during sensory signal transduction in C. elegans, and that distinct roles for alpha and beta subunits of CNG channels are conserved in vertebrate and ------------------- Key: 3431 Medline: Authors: Pennisi E Title: Genome secrets of C. elegans. Citation: Recherche : 40-43 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3432 Medline: 99196474 Authors: Hamdan FF;Ungrin MD;Abramovitz M;Ribeiro P Title: Characterization of a novel serotonin receptor from Caenorhabditis elegans: Cloning and expression of two splice variants. Citation: Journal of Neurochemistry 72: 1372-1383 1999 Type: ARTICLE Genes: Abstract: Serotonin [5-hydroxytryptamine (5-HT)] modulates feeding activity, egg-laying, and mating behavior in the free-living nematode, Caenorhabditis elegans. We have cloned a novel receptor cDNA from C. elegans (5-HT2Ce)that has high sequence homology with 5-HT2 receptors from other species. When transiently expressed in COS-7 cells, 5-HT2Ce exhibited 5-HT binding activity and activated Ca2+-mediated signaling in a manner analogous to other 5-HT2 receptors. However, 5-HT2Ce displayed unusual pharmacological properties, which resembled both 5-HT2 and 5-HT1-like receptors but did not correlate well with any of the known 5-HT2 subtypes. Two splice variants of 5-HT2Ce that differ by 48 id-terminal amino acids were identified. The two isoforms were found to have virtually identical binding and signaling properties but differed in their levels of mRNA expression, with the longer variant being four times more abundant than the shorter species in all developmental stages tested. Taken together, the results describe two variants of a novel C. elegans 5-HT receptor, which has some of the properties of the 5-HT2 family but whose pharmacological profile does not conform to any known class ------------------- Key: 3433 Medline: Authors: Haitzer M;Hoss S;Traunspurger W;Steinberg C Title: Relationship between concentration of dissolved organic matter (DOM) and the effect of DOM on the bioconcentration of benzo[a]pyrene. Citation: Aquatic Toxicology 45: 147-158 1999 Type: ARTICLE Genes: glp-1 Abstract: Dissolved organic matter (DOM) from five different origins decreased the bioconcentration of benzo[a]pyrene (BaP) in the nematode, Caenorhabditis elegans. The decrease became more pronounced with increasing concentrations of DOM, but the effect per mg l(-1) DOC was largest at low levels of DOM, indicating the lack of a simple direct relationship between DOM concentration and the bioconcentration factor (BCF). We tested the hypothesis that the quantitative relationship between DOM concentration and BCF can be described by a theoretically derived equation based on the assumption that only freely dissolved contaminants ape bioavailable (BCF = control BCF x 1/(1 + partition coefficient x DOM concentration)). This equation was used in non-linear regression procedures to fit curves to the experimental data. The resulting regression curves for data from this study (correlation coefficients (r(2)) ranging from 0.80 to 0.94), and for data from the literature (r(2) ranging from 0.62 to 1.00), showed that the model equation was able to correctly describe the relationship between DOM concentration and BCF. The slope of each curve resulted from the 'biologically determined' partition coefficient (K-DOC) that had been estimated by the regression procedure. Thus, the data set for each DOM source was reduced to a single K-DOC value (range: 20 +/- 4 x 10(4) to 49 +/- 6 x 10(4) l kg(-1) DOC (mean +/- S.E.), which allowed to compare different types of DOM, regarding their ability to reduce the bioconcentration of BaP. A comparison of 6,,, values showed that there were clear differences between the effects of DOM from different sources. In summary, we conclude that distinct effects of DOM on the bioconcentration of contaminants can occur at environmentally representative concentrations of DOM, but only for combinations of very hydrophobic contaminants (e.g. BaP) and DOM with a high binding capacity. ------------------- Key: 3434 Medline: Authors: Chalfie M Title: Genome sequencing: The worm revealed. Citation: Nature 396: 620-621 1998 Type: REVIEW Genes: Abstract: In 1983, John Sulston and Alan Coulson began to construct a complete physical map of the genome of the nematode worm Caenorhabditis elegans, and started what became known as the C. elegans Genome Project. At the time, several people wondered why John, who had just described all of the cell divisions in C. elegans (the cell lineage), was interested in this project rather than in a more 'biological' problem. He replied by joking that he had a "weakness for grandiose, meaningless projects". In 1989, as the physical map approached completion, the Genome Project, now including Bob Waterston and his group, embarked on the even more ambitious goal of obtaining the complete genomic sequence ------------------- Key: 3435 Medline: 99117130 Authors: Banyai L;Patthy L Title: Amoebapore homologs of Caenorhabditis elegans. Citation: Biochimica et Biophysica Acta 1429: 259-264 1998 Type: ARTICLE Genes: Abstract: It is shown that the Caenorhabditis elegans genome contains several distantly related members of the gene family of saposin-like proteins. The putative products of genes T07C4.4, T08A9.7A, T08A9.7B, T08A9.8, T08A9.9, T08A9.10 are similar to the amoebapores of Entamoeba histolytica, granulysin of cytotoxic T lymphocytes and a putative amoebapore-related protein of the liver fluke Fasciola hepatica inasmuch as they consist of only a single saposin-like domain and a secretory signal peptide. The saposin-like domain of protein T07C4.4, which is most closely related to NK-lysin and granulysin, has been expressed in Escherichia coli and the recombinant protein was shown to have a circular dichroism spectrum consistent with the helix bundle structure characteristic of saposin-like domains. Recombinant T07C4.4 protein was found to have antibacterial activity, suggesting that these amoebapore homologs may play a role in antibacterial mechanisms of C. elegans. ------------------- Key: 3436 Medline: 10077613 Authors: Gil EB;Link EM;Liu LX;Johnson CD;Lees JA Title: Regulation of the insulin-like developmental pathway of Caenorhabditis elegans by a homolog of the PTEN tumor suppressor gene. Citation: Proceedings of the National Academy of Sciences USA 96: 2925-2930 1999 Type: ARTICLE Genes: age-1 akt-1 akt-2 daf-2 daf-16 daf-18 Abstract: The human PTEN tumor suppressor gene is mutated in a wide variety of sporadic tumors. To determine the function of PTEN in vivo we have studied a PTEN homolog in Caenorhabditis elegans. We have generated a strong loss-of function allele of the PTEN homolog and shown that the deficient strain is unable to enter dauer diapause. An insulin-like phosphatidylinositol 3-OH kinase (PI3'K) signaling pathway regulates dauer-stage entry. Mutations in either the daf-2 insulin receptor-like (IRL) gene or the age-1 encoded PI3'K catalytic subunit homolog cause constitutive dauer formation and also affect the life span, brood size, and metabolism of nondauer animals. Strikingly, loss-of-function mutations in the age-1 PI3'K and daf-2 IRL genes are suppressed by loss-of-function mutations in the PTEN homolog, we establish that the PTEN homolog is encoded by daf-18, a previously uncloned gene that has been shown to interact genetically with the DAF-2 IRL AGE-1 PI3'K signaling pathway, This interaction provides clear genetic evidence that PTEN acts to antagonize PI3'K function in vivo. Given the conservation of the PI3'K signaling pathway between C. elegans and mammals, the analysis of daf-18 PTEN mutant nematodes should shed light on the role of human PTEN in the etiology of metabolic disease, aging, and ------------------- Key: 3437 Medline: 99182492 Authors: Kophengnavong T;Carroll AS;Blackwell TK Title: The SKN-1 amino-terminal arm is a DNA specificity segment. Citation: Molecular and Cellular Biology 19: 3039-3050 1999 Type: ARTICLE Genes: skn-1 Abstract: The Caenorhabditis elegans SKN-1 protein binds DNA through a basic region like those of bZIP proteins and through a flexible amino-terminal arm segment similar to those with which numerous helix-turn-helix proteins bind to bases in the minor groove. A recent X-ray crystallographic structure suggests that the SKN-1 aminoterminal arm provides only nonspecific DNA binding. In this study, however, we demonstrate that this segment mediates recognition of an AT-rich element that is part of the preferred SKN-1 binding site and thereby significantly increases the sequence specificity with which SKN-1 binds DNA. Mutagenesis experiments show that multiple amino acid residues within the arm are involved in binding. These residues provide binding affinity through distinct but partially redundant interactions and enhance specificity by discriminating against alternate sites. The AT-rich element minor groove is important for binding of the arm, which appears to affect DNA conformation in this region. This conformational effect does not seem to involve DNA bending, however, because the arm does not appear to affect a modest DNA bend that is induced by SKN-1. The data illustrate an example of how a small, flexible protein segment can make an important contribution to DNA binding specificity through multiple interactions and mechanisms. ------------------- Key: 3438 Medline: 10087299 Authors: Fletcher CF;Jenkins NA;Copeland NG;Chaudhry AZ;Gronostajski RM Title: Exon structure of the nuclear factor I DNA-binding domain from C. elegans to mammals. Citation: Mammalian Genome 10: 390-396 1999 Type: ARTICLE Genes: nfi-1 Abstract: The Nuclear Factor I (NFI) family of DNA-binding proteins is essential for adenovirus DNA replication and the transcription of many cellular genes. Mammals have four genes encoding NFI. proteins, C. elegans has only a single NFI gene, and prokaryotes have none. To assess the relationship between members of this unusually small family of transcription/replication factors, we mapped the chromosomal locations of the four murine NFI genes and analyzed the exons encoding the DNA-binding domains of the mouse, Amphioxus, and C. elegans NFI genes. The four murine NFI genes are on Chrs 4 (Nfia and Nfib), 8 (Nfix), and 10 (Nfic), suggesting early duplication of the genes and dispersal throughout the genome. The DNA-binding domains of all four NFI genes are encoded by large (532 bp) exons with identical splice acceptor and donor sites in each. In contrast, the C. elegans nfi-1 gene has four phased introns interrupting this DNA-binding, domain-encoding exon, and the last exon extends 213 bp past the splice site used in all four murine genes. In addition, the introns present in C. elegans nfi-1 are missing from the NFI genes of Amphioxus and all mammaliam genomes examined. This analysis of the exon structure of the C. elegans and murine NFI genes indicates that the murine genes were probably generated by duplication of a C. elegans-like ancestral gene, but that significant changes have occurred in the genomic organization of either the C. elegans or murine NFI genes during evolution. ------------------- Key: 3439 Medline: 99196980 Authors: Wilm T;Demel P;Koop HU;Schnabel H;Schnabel R Title: Ballistic transformation of Caenorhabditis elegans. Citation: Gene 229: 31-35 1999 Type: ARTICLE Genes: ceh-13 pha-1 rol-6 sud-1 Abstract: A novel method to transform the nematode Caenorhabditis elegans is described. DNA coprecipitated with gold particles is shot at worms by means of a helium beam. Transformed worms are either identified by a dominant visible marker or selected by a conditional lethal system. ------------------- Key: 3440 Medline: Authors: Bourne HR;Wrischnik L;Kenyon C Title: Some signal developments. Citation: Nature 348: 678-679 1990 Type: REVIEW Genes: let-23 let-60 lin-3 lin-15 Abstract: What molecular signalling machines tell a precursor cell to develop into a specialized structure? In one case, described in three papers, including that by Aroian et al. on page 693 of this issue, these machines turn out to be a receptor tyrosine kinase and a ras protein. ------------------- Key: 3441 Medline: Authors: Ash C Title: Romancing the genome. Citation: Parasitology Today 8: 149- 1992 Type: REVIEW Genes: Abstract: Like particle physics, biology is now a big expensive business, and like CERN, the genome projects alternately provoke admiration and detraction. Some feel that it would be more valuable to go for specific genes of interest rather than fill databases with sequences of junk DNA. The detractors would also say that the costs entailed, the limited intellectual and practical payback, and the ethical worries are too big to justify. But like the mythological juggernaut, once started it won't stop and it is indisputable that exciting information will come out of these efforts. Like some of the best discoveries many will be unexpected and have repercussions of immense value. This is indisputable on statistical grounds alone; the Caenorhabditis elegans genome is estimated to contain tens of thousands of genes. However, genome projects cannot be justified by serendipity and they do have obvious immediate value for tracing the genes involved in cancer and other inheritable disorders, and indeed for the multiple technological spin-offs. The C. elegans genome project is already bearing luscious fruit, of the 34 genes reported so far some of which have sequence similarity with genes such as glutathione reductase, an immunogenic protein from Trichostrongylus colubriformis, acetyl-CoA acetyltransferase and various other enzymes, growth factors and signal transducing components. Up-to-date cDNA data will be published by John Sulston and his colleagues in the early issues of Nature Genetics, due out this month. ------------------- Key: 3442 Medline: Authors: Epstein HF;Fischman DA Title: Molecular analysis of protein assembly in muscle development. Citation: Science 251: 1039-1044 1991 Type: REVIEW Genes: act-1 act-2 act-3 myo-1 myo-2 myo-3 unc-15 unc-45 unc-54 unc-82 Abstract: The challenge presented by myofibril assembly in striated muscle is to understand the molecular mechanisms by which its protein components are arranged at each level of organization. Recent advances in the genetics and cell biology of muscle development have shown that in vivo assembly of the myofilaments requires a complex array of structural and associated proteins and that organization of whole sarcomeres occurs initially at the cell membrane. These studies have been complemented by in vitro analyses of the renaturation, polymerization, and three-dimensional structure of the purified proteins. ------------------- Key: 3443 Medline: Authors: Robertson M Title: Homoeo boxes, POU proteins and the limits to promiscuity. Citation: Nature 336: 522-524 1988 Type: REVIEW Genes: unc-86 Abstract: The recent characterization of four proteins, three of them known mammalian transcriptional activators, may do much to diminish the lingering mystique of the homoeo domain and at the same time to focus attention on the role of protein-protein interactions in differential gene expression. The four protein are Oct-2, which is produced in B lymphocytes where it binds to a conserved octamer sequence and activates immunoglobulin genes; Pit-1, which is synthesized in pituitary cells and implicated in the activation of growth-hormone and prolactin genes; unc-86, which has a genetically defined role in the differentiation of specific nematode neural cells; and Oct-1, a ubiquitous mammalian transcriptional activator of small nuclear RNA and histone H2B genes that also acts through a conserved octamer motif. ------------------- Key: 3444 Medline: Authors: Ruvkun G;Finney M Title: Regulation of transcription and cell identity by POU domain proteins. Citation: Cell 64: 475-478 1991 Type: REVIEW Genes: ceh-6 mec-3 unc-86 Abstract: The POU domain is a 150-160 amino acid region consisting of a 75-82 amino acid POU-specific domain, a shot variable linker region, and a 60 amino acid POU homeodomain. Originally found in three mammalian transcription factors and a Caenorhabditis elegans developmental control gene, this dmain has been identified in a growing number of genes. Research on the POU proteins ahs focused on their regulatory roles during development and the dissection of their functional domains to establish how they bind particular DNA sequences and activate transcription of distinct sets of genes. The pituitary-specific transcription factor Pit-1/GHF-1, the ubiquitous transcription factor Oct-1, and the predominantly B cell transcription factor Oct-2 have been the major subjects of biochemical dissection, while the developmental roles of Pit-1/GHF-1 and the C. elegans cell lineage control gene unc-86 have been established by a combination of expression ------------------- Key: 3445 Medline: Authors: Robertson M Title: Developmental decisions and pattern formation. Citation: Nature 335: 494-495 1988 Type: REVIEW Genes: lin-12 lin-15 Abstract: The classical view of embryogenesis in the nematode worm Caenorhabditis elegans has been that developmental decisions are almost entirely dictated by lineage, with little if any contribution from the cellular interactions that are thought to be crucial to the formation of the body pattern in other organisms. (A distinction that Sydney Brenner used to characterize as European versus American - Europeans being defined by their ancestry and Americans by their neighbors.) The notion of a pre-programmed cell-autonomous progression from egg to adult would seem consistent with the remarkable invariance of the worm body plan; but recent research has increasingly eroded the peculiar position of worms in the annals of embryology; and two papers on pages 547 and 551 of this issue illustrate how invariance may be achieved in one critical feature of nematode morphology by a combination of two cellular interactions that together decide the fate of the vulval ------------------- Key: 3446 Medline: Authors: Kenyon C;Kamb A Title: Cellular dialogs during development. Citation: Cell 58: 607-608 1989 Type: REVIEW Genes: glp-1 lin-12 Abstract: Cell-cell communication is one of the basic strategies used in metazoan development. Recent work has identified a (so far) small family of molecules that play central roles in different cell signaling pathways. This family was originally defined by the C. elegans gene lin-12 and the Drosophila gene Notch, and now has been shown to include the glp-1 gene from C. elegans. The products of all three genes share several structural features, including a predicted membrane-spanning domain and regions of homology in the extracellular and cytoplasmic domains. The identification of a family of proteins that participate in cell-cell interactions during development raises questions that are now under investigation. First, what are the biological roles of these proteins, and how are they integrated into different signaling systems to produce specific cellular patterns? Second, how do these proteins function mechanistically, and what is the significance of their structural similarity? ------------------- Key: 3447 Medline: Authors: Horvitz HR Title: Neuronal cell lineages in the nematode Caenorhabditis elegans. Citation: "Development in the Nervous System", Garrod and Feldman (eds). Cambridge University Press. : 331-346 1981 Type: REVIEW Genes: lin-5 lin-6 mab-5 nuc-1 unc-59 unc-83 unc-84 unc-85 unc-86 Abstract: A neuron can be characterized by its morphology, transmitter (s?), receptor(s) and the nature of its synaptic contacts (chemical or electrical; excitatory or inhibitory; number and distribution of synapses; identity of the cells to which it is presynaptic or postsynaptic). It is clear that according to such criteria nervous sytems consist of neurons of many distinct types. The origin of neuronal diversity is unknown. Both how such diversity is generated during development and how the relevant developmental programme is encoded in the genome remain to ------------------- Key: 3449 Medline: Authors: Sharp PA Title: RNAi and double-strand RNA. Citation: Genes & Development 13: 139-141 1999 Type: REVIEW Genes: lin-15 Abstract: Double-strand RNA (dsRNA) is a signal for gene-specific silencing of expression in a number of organisms. This phenomenon was demonstrated recently in Caenorhabditis elegans when dsRNA was injected into the worm and the corresponding gene products disappeared from both the somatic cells of the organism as well as in its F1 progeny. This RNA interference, RNAi, has been generalized to many genes in C. elegans. ds-RNA can also suppress expression of specific genes in plants, a component of the phenomenon called cosuppression. Two recent reports document dsRNA-mediated interference with expression of specific genes in other organisms. Double-strand RNA produced gene-specific phenotypes in Trypanosoma brucei and, very recently, dsRNA-mediated interference was demonstrated in Drosophila. Thus, the RNAi phenomenon is likely to be a general mechanism for gene regulation and may be critical for many developmental and antiviral processes. ------------------- Key: 3450 Medline: 99128194 Authors: Herman MA;Ch'ng Q;Hettenbach SM;Ratliff T;Kenyon C;Herman Title: EGL-27 is similar to a metastasis-associated factor and controls cell polarity and cell migration in C. elegans. Citation: Development 126: 1055-1064 1999 Type: ARTICLE Genes: egl-20 egl-27 lin-17 lin-44 mab-5 mnDf30 mnDf96 Abstract: Mutations in the C. elegans gene egl-27 cause defects in cell polarity and cell migration: the polarity of the asymmetric T cell division is disrupted and the descendants of the migratory QL neuroblast migrate incorrectly because they fail to express the Hox gene mab-5. Both of these processes are known to be controlled by Wnt pathways. Mosaic analysis indicates that egl-27 function is required in the T cell for proper cell polarity. We cloned egl-27 and discovered that a domain of the predicted EGL-27 protein has similarity to Mta1, a mammalian factor overexpressed in metastatic cells. Overlaps in the phenotypes of egl-27 and Wnt pathway mutants suggest that the EGL-27 protein interacts with Wnt signaling pathways in ------------------- Key: 3451 Medline: 99128190 Authors: Gumienny TL;Lambie E;Hartwieg E;Horvitz HR;Hengartner MO Title: Genetic control of programmed cell death in the Caenorhabditis elegans hermaphrodite germline. Citation: Development 126: 1011-1022 1999 Type: ARTICLE Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-9 ced-10 ces-1 ces-2 egl-1 fog-1 gld-1 glp-4 her-1 let-60 lin-45 mek-2 mog-1 mpk-1 nuc-1 sdc-1 tra-1 eDp6 nDp4 Abstract: Development of the nematode Caenorhabditis elegans is highly reproducible and the fate of every somatic cell has been reported. We describe here a previously uncharacterized cell fate in C. elegans: we show that germ cells, which in hermaphrodites can differentiate into sperm and oocytes, also undergo apoptotic cell death. In adult hermaphrodites, over 300 germ cells die, using the same apoptotic execution machinery (ced-3, ced-4 and ced-9) as the previously described 131 somatic cell deaths. However, this machinery is activated by a distinct pathway, as loss of egl-1 function, which inhibits somatic cell death, does not affect germ cell apoptosis. Germ cell death requires ras/MAPK pathway activation and is used to maintain germline homeostasis. We suggest that apoptosis eliminates excess germ cells that acted as nurse cells to provide cytoplasmic components to maturing oocytes. ------------------- Key: 3452 Medline: 99128178 Authors: Yi W;Zarkower D Title: Similarity of DNA binding and transcriptional regulation by Caenorhabditis elegans MAB-3 and Drosophila melanogaster DSX suggests conservation of sex determining mechanisms. Citation: Development 126: 873-881 1999 Type: ARTICLE Genes: mab-3 vit-1 vit-2 vit-3 vit-4 vit-5 vit-6 Abstract: Although most animals occur in two sexes, the molecular pathways they employ to control sexual development vary considerably. The only known molecular similarity between phyla in sex determination is between two genes, mab-3 from C. elegans, and doublesex (dsx) from Drosophila. Both genes contain a DNA binding motif called a DM domain and they regulate similar aspects of sexual development, including yolk protein synthesis and peripheral nervous system differentiation. Here we show that MAB-3, like the DSX proteins, is a direct regulator of yolk protein gene transcription. We show that despite containing different numbers of DM domains MAB-3 and DSX bind to similar DNA sequences, mab-3 mutations deregulate vitellogenin synthesis at the level of transcription, resulting in expression in both sexes, and the vitellogenin genes have potential MAB-3 binding sites upstream of their transcriptional start sites, MAB-3 binds to a site in the vit-2 promoter in vitro, and this site is required in vivo to prevent transcription of a vit-2 reporter construct in males, suggesting that MAB-3 is a direct repressor of vitellogenin transcription. This is the first direct link between the sex determination regulatory pathway and sex-specific structural genes in C. elegans, and it suggests that nematodes and insects use at least some of the same mechanisms to control sexual development. ------------------- Key: 3453 Medline: 10197987 Authors: Jiang LI;Sternberg PW Title: An HMG1-like protein facilitates Wnt signaling in Caenorhabditis elegans. Citation: Genes & Development 13: 877-889 1999 Type: ARTICLE Genes: bar-1 gpa-1 let-2 lin-12 lin-17 lin-44 pop-1 son-1 nDf16 nDf20 nDf21 sDf125 sDf127 sDf135 Abstract: We show that during Caenorhabditis elegans male spicule development, the specification of a glial versus neuronal cell fate in a canonical neurogenic sublineage is dependent on Wnt signaling. Inactivation of a Wnt signaling pathway mediated by the Wnt receptor LIN-17 transforms the SPD sheath cell into its sister, the SPD neuron. We discovered a new mutant, son-1, that displays this same cell fate transformation. The son-1 mutation enhances the phenotypes of reduction-of-function lin-17 mutants in several developmental processes, including vulva development, somatic gonad development, and male tail patterning. son-1 encodes an HMG1/2-like DNA-binding protein and is localized in all cell nuclei through development as revealed by a GFP reporter construct. Disruption of son-1 function by RNA-mediated interference results in the same spicule defect as caused by overexpression of POP-1, a TCF/LEF class HMG protein known to act downstream of the Wnt signaling pathway. Our results provide in vivo evidence for the functional involvement of an HMG1/2-like protein, SON-1, in Wnt signaling. The sequence nonspecific HMG protein SON-1 and the sequence specific HMG protein POP-1 might both act in the Wnt responding cells to regulate gene transcription in opposite directions. ------------------- Key: 3454 Medline: 10021351 Authors: Morita K;Chow KC;Ueno N Title: Regulation of body length and male tail ray pattern formation of Caenorhabditis elegans by a member of the TGF-B family. Citation: Development 126: 1337-1347 1999 Type: ARTICLE Genes: cet-1 daf-1 daf-3 daf-4 daf-7 daf-8 daf-14 him-5 lon-1 lon-2 mab-21 sma-2 sma-3 sma-4 sma-6 Abstract: We have identified a new member of the TGF-beta superfamily, CET-1, from Caenorhabditis elegans, which is expressed in the ventral nerve cord and other neurons, cet-1 null mutants have shortened bodies and male tail abnormal phenotype resembling sma mutants, suggesting cet-1, sma-2, sma-3 and sma-l share a common pathway. Overexpression experiments demonstrated that cet-1 function requires wild-type srna genes. Interestingly, CET-1 appears to affect body length in a dose-dependent manner. Heterozygotes for cet-1 displayed body lengths ranging between null mutant and wild type, and overexpression of CET-1 in wild-type worms elongated body length close to ion mutants. In male sensory ray patterning, lack of cet-1 function results in ray fusions, Epistasis analysis revealed that mab-21 lies downstream and is negatively regulated by the cet-1/sma pathway in the male tail. Our results show that cet-1 controls diverse biological processes during C. elegans development probably through ------------------- Key: 3455 Medline: 99221869 Authors: Prasad BC;Reed RR Title: Chemosensation molecular mechanisms in worms and mammals. Citation: Trends in Genetics 15: 150-153 1999 Type: REVIEW Genes: daf-11 odr-1 odr-4 odr-10 osm-9 tax-2 tax-4 Abstract: Communication with the environment and other animals through chemical cues is an essential process for the survival of many multicellular organisms. Specialized signal transduction pathways are employed in chemodetection and the transformation of information into the electrical signals that elicit behaviors. In organisms as diverse as mice and nematodes, similar molecules are involved in the odorant signaling pathways. Studying the mechanisms of signal transduction in these two systems using biochemical, molecular and genetic approaches has elucidated pathways for odor perception and the roles of specific proteins and second messenger molecules in the signaling cascades. ------------------- Key: 3456 Medline: Authors: C. elegans Sequencing Consortium Title: Genome sequence of the nematode C. elegans: A platform for investigating biology (correction). Citation: Science 283: 2103- 1999 Type: ARTICLE Genes: Abstract: ------------------- Key: 3457 Medline: Authors: Blaxter M Title: Caenorhabditis elegans is a nematode (correction). Citation: Science 283: 2103- 1999 Type: ARTICLE Genes: Abstract: ------------------- Key: 3458 Medline: 99198480 Authors: C. elegans Genome Consortium Title: How the worm was won - The C. elegans genome sequencing project. Citation: Trends in Genetics 15: 51-58 1999 Type: REVIEW Genes: Abstract: The genome sequence of the free-living nematode Caenorhabiditis elegans is nearly complete, with resolution of the final difficult regions expected over the next few months. This will represent the first genome of a multicellular organism to be sequenced to completion. The genome is approximately 97 Mb in total, and encodes more than 19 099 proteins, considerably more than expected before sequencing began. The sequencing project - a collaboration between the Genome Sequencing Center in St Louis and the Sanger Centre in Hinxton - has lasted eight years, with the majority of the sequence generated in the past four years. Analysis of the genome sequence is just beginning and represents an effort that will undoubtedly last more than another decade. However, some interesting findings are already apparent, indicating that the scope of the project, the approach taken, and the usefulness of having the genetic blueprint for this small organism have been well worth the effort. ------------------- Key: 3459 Medline: 99221868 Authors: Tan PBO;Kim SK Title: Signaling specificity - The RTK/RAS/MPK kinase pathway in metazoans. Citation: Trends in Genetics 15: 145-149 1999 Type: REVIEW Genes: let-23 lfe-1 lfe-2 lin-1 lin-31 Abstract: The molecular basis by which commonly used signaling pathways are able to elicit tissue-specific responses in multicellular organisms is an important yet poorly understood problem. In this review, we use the receptor tyrosine kinase (RTK)/RAS/MAP kinase signaling cascade as a model to discuss various hypotheses that have been proposed to explain signaling specificity. Specificity can arise at the level of the receptor, through the modulation of signaling kinetics, through the interaction of different signaling pathways, and at the level of downstream signaling components. Mechanisms of specificity used by the RTK/RAS/MAP kinase signaling pathway might apply to other signaling pathways as well, and might help explain how multicellular organisms are able to generate tissues of diverse forms and functions from a small set of common signaling pathways. ------------------- Key: 3460 Medline: Authors: Kura T Title: Caenorhabditis and the cost of sex. Citation: Trends in Ecology & Evolution 14: 33- 1999 Type: REVIEW Genes: Abstract: In a recent TREE news & comment, Gadagkar made some useful comments on LaMunyon and Ward's interesting study on sexual reproduction in nematodes. I think, however, that he - and LaMunyon and Ward - have confused the benefits of sex for species or demes with those for individuals or genes. ------------------- Key: 3461 Medline: Authors: Gadagkar R Title: Caenorhabditis and the cost of sex - Reply. Citation: Trends in Ecology & Evolution 14: 33-34 1999 Type: REVIEW Genes: Abstract: In a recent TREE news & comment, Gadagkar made some useful comments on LaMunyon and Ward's interesting study on sexual reproduction in nematodes. I think, however, that he - and LaMunyon and Ward - have confused the benefits of sex for species or demes with those for individuals or genes. For females and hermaphrodites (but not for species or demes), `the twofold cost of sexual reproduction or producing males' in Maynard Smith's sense implies the cost of producing offspring that have only half of the hermaphrodite parent's genome set - not directly that of producing males. An offspring of a hermaphrodite Caenorhabditis briggsae inherits half, not more, of each parental genome set. The hermaphrodite parent still pays the two fold cost of sexual reproduction in the same way as ------------------- Key: 3462 Medline: 99243925 Authors: Silverman PH Title: C. elegans as a model. Citation: Science 284: 261- 1999 Type: REVIEW Genes: Abstract: Elizabeth Pennisi, in her excellent commentary "Worming secrets from the C. elegans" (News Focus, 11 Dec 1998, p.1972), states that "The first person to sense that the worm might take on such a prominent role in biology was molecular biologist Sydney Brenner." I am sure that Brenner would wish to acknowledge the role that Ellsworth C. Dougherty played in this matter. Dougherty originally described in 1949, "[a] new species of the free-living nematode genus Rhabditis of interest in comparative physiology and genetics". ------------------- Key: 3463 Medline: 99213657 Authors: Zorio DAR;Blumenthal T Title: U2AF(35) is encoded by an essential gene clustered in an operon with RRM/cyclophilin in Caenorhabditis elegans. Citation: RNA 5: 487-494 1999 Type: ARTICLE Genes: cyp-13 uaf-1 uaf-2 Abstract: In most species the 3' splice site is recognized initially by an interaction between the two-subunit splicing factor USAF with the polypyrimidine (poly(Y)) tract that results in recruitment of the U2 snRNP to the branch-point consensus just upstream. In contrast, in Caenorhabditis elegans, both the poly(Y) tract and the branch-point consensus sequences are missing, apparently replaced by the highly conserved U(4)CAG/R 3' splice site consensus. Nevertheless C. elegans U2AF(65) is very similar to its mammalian and fly counterparts and may recognize the 3' splice site consensus. Here we report the cloning of the C. elegans U2AF(35) gene, uaf-2. We show that it lacks an identifiable RS domain, which, in flies, has been shown to play a role in RNA binding, but it contains an extended glycine-rich stretch at its C-terminus. uaf-2 is in an operon with cyp-13, a gene that encodes a cyclophilin with an RRM domain at its N-terminus. We demonstrate by RNA interference that both U2AF genes, uaf-1 (which encodes U2AF(65)) and uaf-2, are required for viability, whereas ------------------- Key: 3464 Medline: 99223242 Authors: Sambongi Y;Nagae T;Liu Y;Yoshimizu T;Takeda K;Wada Y;Futai Title: Sensing of cadmium and copper ions by externally exposed ADL, ASE, and ASH neurons elicits avoidance response in Caenorhabditis elegans. Citation: Neuroreport 10: 753-757 1999 Type: ARTICLE Genes: che-2 osm-3 Abstract: We developed a quantitative assay for Caenorhabditis elegans avoidance behavior. This was then used to demonstrate that the worm moved away from toxic concentrations of Cd2+ and Cu2+, but not Ni2+, all ions that prevented development from larval to adult stages. Mutants that have structural defects in ciliated neurons (che-2 and osm-3) as well as worms with three laser-operated neurons (ADL, ASE, and ASH), showed no avoidance behavior from Cd2+ and Cu2+. These results suggest that the avoidance from Cd2+ and Cu2+ are mediated through multiple neural pathways including ADL, ASE, and ASH neurons. We hypothesize that the three sensing neurons provide increased accuracy of the sensory response and a ------------------- Key: 3465 Medline: 99206612 Authors: Jansen G;Thijssen KL;Werner P;van der Horst M;Hazendonk E;Plasterk RHA Title: The complete family of genes encoding G proteins of Caenorhabditis elegans. Citation: Nature Genetics 21: 414-419 1999 Type: ARTICLE Genes: egl-30 goa-1 gpa-1 gpa-2 gpa-3 gpa-4 gpa-5 gpa-6 gpa-7 gpa-8 gpa-9 gpa-10 gpa-11 gpa-12 gpa-13 gpa-14 gpa-15 gpa-16 gsa-1 odr-3 Abstract: Caenorhabditis elegans is the first animal whose genomic sequence has been determined(1). One of the new possibilities in post-sequence genetics is the analysis of complete gene families at once. We studied the family of heterotrimeric G proteins(2). C. elegans has 20 G alpha, 2 G beta and 2 G gamma genes. There is 1 homologue of each of the 4 mammalian classes of G alpha genes, G(i)/G(o)alpha, G(s)alpha, G(q)alpha and G(12)alpha, and there are 16 new alpha genes. Although the conserved G alpha subunits are expressed in many neurons and muscle cells(3-7), GFP fusions indicate that 14 new G alpha genes are expressed almost exclusively in a small subset of the chemosensory neurons of C. elegans(8,9). We generated loss-of-function alleles using target-selected gene inactivation(10,11). None of the amphid-expressed genes are essential for viability, and only four show any detectable phenotype (chemotaxis defects), suggesting extensive functional redundancy. On the basis of functional analysis, the 20 genes encoding G alpha proteins can be divided into two groups: those that encode subunits affecting muscle activity (homologues of G(i)/G(o)alpha G(s)alpha and G(q); refs 3-6), and those (14 new genes) that encode proteins ------------------- Key: 3466 Medline: 9950681 Authors: Signor D;Wedaman KP;Rose LS;Scholey JM Title: Two heteromeric kinesin complexes in chemosensory neurons and sensory cilia of Caenorhabditis elegans. Citation: Molecular Biology of the Cell 10: 345-360 1999 Type: ARTICLE Genes: osm-3 Abstract: Chemosensation in the nervous system of the nematode Caenorhabditis elegans depends on sensory cilia, whose assembly and maintenance requires the transport of components such as axonemal proteins and signal transduction machinery to their site of incorporation into ciliary structures. Members of the heteromeric kinesin family of microtubule motors are prime candidates for playing key roles in these transport events. Here we describe the molecular characterization and partial purification of two heteromeric kinesin complexes from C. elegans, heterotrimeric CeKinesin-II and dimeric CeOsm-3. Transgenic worms expressing green fluorescent protein driven by endogenous heteromeric kinesin promoters reveal that both CeKinesin-II and CeOsm-3 are expressed in amphid, inner labial, and phasmid chemosensory neurons. Additionally, immunolocalization experiments on fixed worms show an intense concentration of CeKinesin-II and CeOsm-S polypeptides in the ciliated endings of these chemosensory neurons and a punctate localization pattern in the corresponding cell bodies and dendrites. These results, together with the phenotypes of known mutants in the pathway of sensory ciliary assembly, suggest that CeKinesin-II and CeOsm-3 drive the transport of ciliary components required for sequential steps in the assembly of ------------------- Key: 3467 Medline: 99228471 Authors: Ren XC;Kim S;Fox E;Hedgecock EM;Wadsworth WG Title: Role of netrin UNC-6 in patterning the longitudinal nerves of Caenorhabditis elegans. Citation: Journal of Neurobiology 39: 107-118 1999 Type: ARTICLE Genes: unc-5 unc-6 unc-40 Abstract: The nervous system of Caenorhabditis elegans comprises circumferential and longitudinal axon tracts. Netrin UNC-6 is required for the guidance of circumferential axon migrations and is expressed by ventral neuroglia and neurons in temporally and spatially regulated patterns. Migrating axons mediate the UNC-6 signal through the UNC-5 and UNC-40 receptors, It is thought that UNC-6 is secreted and becomes associated with basement membranes and cell surfaces to form gradients that direct circumferentially migrating axons toward or away from the ventral UNC-6 sources. Little is known about the effects of UNC-6 on longitudinally migrating axons. In unc-6, unc-5, and unc-40 null mutants, some longitudinal nerves are dorsally or ventrally misdirected. Furthermore, the organization of axons are disrupted within nerves. We show that cells ectopically expressing UNC-6 can redirect the migrations of some neighboring longitudinal axons, suggesting that the gradients postulated to direct circumferential migration also help specify the dorsoventral positions of these longitudinal nerves. We also manipulated the temporal and spatial expression pattern of UNC-6 by two different means. First, me removed the PVT midline neuron which expresses UNC-6 for a short time during axon outgrowths. Second, we expressed UNC-6 uniformly in the nervous system throughout development. The results suggest that changing UNC-6 expression patterns modify the distribution of the cue by providing new localized sources. This new guidance information is critical for organizing the axons of ------------------- Key: 3468 Medline: Authors: de Gives PM;Davies KG;Morgan M;Behnke JM Title: Attachment tests of Pasteuria penetrans to the cuticle of plant and animal parasitic nematodes, free living nematodes and srf mutants of Caenorhabditis elegans. Citation: Journal of Helminthology 73: 67-71 1999 Type: ARTICLE Genes: srf-2 srf-3 srf-5 Abstract: Populations of Pasteuria penetrans isolated from root-knot nematodes (Meloidogyne spp.) and cyst nematodes (Heterodeua spp.) were tested for their ability to adhere to a limited selection of sheathed and exsheathed animal parasitic nematodes, free living nematodes, including Caenorhabditis elegans wild type and several srf mutants, and plant parasitic nematodes. The attachment of spores of Pasteuria was restricted and no spores were observed adhering to any of the animal parasitic nematodes either with or without their sheath or to any of the free living nematodes including C. elegans and the srf mutants. All spore attachment was restricted to plant parasitic nematodes; however, spores isolated from cyst nematodes showed the ability to adhere to other genera of plant parasitic nematodes which was not the case with spores isolated from root-knot nematodes. The results are discussed in relationship to cuticular heterogeneity. ------------------- Key: 3469 Medline: 99187129 Authors: Gonczy P;Schnabel H;Kaletta T;Amores AD;Hyman T;Schnabel R Title: Dissection of cell division processes in the one cell stage Caenorhabditis elegans embryo by mutational analysis. Citation: Journal of Cell Biology 144: 927-946 1999 Type: ARTICLE Genes: apo-1 apo-2 apo-3 apo-4 csg-1 csg-2 csg-3 csg-4 csg-5 csg-6 csg-7 csg-8 cta-1 cta-2 cta-3 cta-4 cta-5 cyk-1 cyk-2 cyk-3 faf-1 let-725 let-733 let-748 let-771 mel-27 mel-28 nup-1 nup-2 par-3 pna-1 pna-2 pna-3 pnm-1 pnm-2 pnm-3 pnm-4 pnm-5 pnm-6 rot-1 rot-2 rot-3 sas-1 sas-2 sas-3 zyg-8 zyg-9 zyg-11 nDf16 nDf20 nDf40 sDf110 sDf121 sDf125 tDf2 tDf5 tDf6 tDf7 tDf9 Abstract: To identify novel components required for cell division processes in complex eukaryotes, we have undertaken an extensive mutational analysis in the one cell stage Caenorhabditis elegans embryo. The large size and optical properties of this cell permit observation of cell division processes with great detail in live specimens by simple differential interference contrast (DIC) microscopy. We have screened an extensive collection of maternal-effect embryonic lethal mutations on chromosome III with time-lapse DIC video microscopy. Using this assay, we have identified 48 mutations in 34 loci which are required for specific cell division processes in the one cell stage embryo. We show that mutations fall into distinct phenotypic classes which correspond, among others, to the processes of pronuclear migration, rotation of centrosomes ansi associated pronuclei, spin die assembly, chromosome segregation, anaphase spindle positioning, and cytokinesis. We have further analyzed pronuclear migration mutants by indirect immunofluorescence microscopy using antibodies against tubulin and ZYG-9, a centrosomal marker. This analysis revealed that two pronuclear migration loci are required for generating normal microtubule arrays and four for centrosome separation. All 34 loci have been mapped by deficiencies to distinct regions of chromosome III, thus paving the way for their rapid molecular characterization. Our work contributes to establishing the one cell stage C. elegans embryo as a powerful metazoan model system for dissecting cell division processes. ------------------- Key: 3470 Medline: 10209096 Authors: Fraser AG;James C;Evan GI;Hengartner MO Title: Caenorhabditis elegans inhibitor of apoptosis protein (IAP) homologue BIR-1 plays a conserved role in cytokinesis. Citation: Current Biology 9: 292-301 1999 Type: ARTICLE Genes: bir-1 bir-2 ced-3 ced-4 ced-9 cyk-1 egl-1 Abstract: Background: Inhibitor of apoptosis proteins (IAPs) suppress apoptotic cell death in several model systems and are highly conserved between insects and mammals. All IAPs contain at least one copy of the similar to 70 amino-acid baculovirus IAP repeat (BIR), and this domain is essential for the anti-apoptotic activity of the IAPs. Both the marked structural diversity of IAPs and the identification of BIR-containing proteins (BIRPs) in yeast, however, have led to the suggestion that: BIRPs might play roles in other, as yet unidentified, cellular processes besides apoptosis. Survivin, a human BIRP, is upregulated 40-fold at G2-M phase and binds to mitotic spindles, although its role at the spindle is still unclear. Results: We have identified and characterised two Caenorhabditis elegans BIRPs, BIR-1 and BIR-2; these proteins are the only BIRPs in C. elegans. The bir-1 gene is highly expressed during embryogenesis with detectable expression throughout other stages of development; bir-2 expression is detectable only in adults and embryos. Overexpression of bir-1 was unable to inhibit developmentally occurring cell death in C. elegans and inhibition of bir-1 expression did not increase cell death. Instead, embryos lacking bir-1 were unable to complete cytokinesis and they became multinucleate. This cytokinesis defect could be partially suppressed by transgenic expression of survivin, the mammalian BIRP most structurally related to BIR-1,suggesting a conserved role for BIRPs in the regulation of cytokinesis. Conclusions: BIR-1, a C. elegans BIRP, is probably not involved in the general regulation of apoptosis but is required for embryonic cytokinesis. We suggest that BIRPs may regulate cytoskeletal changes in diverse biological processes including cytokinesis and apoptosis. ------------------- Key: 3471 Medline: 10209098 Authors: Rouault JP;Kuwabara PE;Sinilnikova OM;Duret L;Thierry-Mieg D;Billaud M Title: Regulation of dauer larva development in Caenorhabditis elegans by daf-18, a homologue of the tumour suppressor PTEN. Citation: Current Biology 9: 329-332 1999 Type: ARTICLE Genes: age-1 daf-2 daf-16 daf-18 tra-2 Abstract: The tumour suppressor gene PTEN (also called MMAC1 or TEP1) is somatically mutated in a variety of cancer types [1-4]. In addition, germline mutation of PTEN is responsible for two dominantly inherited, related cancer syndromes called Cowden disease and Bannayan-Ruvalcaba-Riley syndrome [4]. PTEN encodes a dual-specificity phosphatase that inhibits cell spreading and migration partly by inhibiting integrin-mediated signalling [5-7]. Furthermore, PTEN regulates the levels of phosphatidylinositol 3,4,5-trisphosphate (PIP3) by specifically dephosphorylating position 3 on the inositol ring [8]. We report here that the dauer formation gene daf-18 is the Caenorhabditis elegans homologue of PTEN. DAF-18 is a component of the insulin-like signalling pathway controlling entry into diapause and adult longevity that is regulated by the DAF-2 receptor tyrosine kinase and the AGE-1 PI 3-kinase [9]. Others have shown that mutation of daf-18 suppresses the life extension and constitutive dauer formation associated with daf-2 or age-1 mutants. Similarly. we show that inactivation of daf-18 by RNA mediated interference mimics this suppression, and that a wild-type daf-18 transgene rescues the dauer defect. These results indicate that PTEN/DAF-18 antagonizes the DAF-2-AGE-1 pathway, perhaps by catalyzing dephosphorylation of the PIP3 generated by AGE-1. These data further support the notion that mutations of PTEN contribute to the development of human neoplasia through an ------------------- Key: 3472 Medline: Authors: Casey D Title: International team delivers C. elegans sequence. Citation: Human Genome News 10: 8- 1999 Type: REVIEW Genes: Abstract: For the first time, scientists have the nearly complete genetic instructions for an animal that, like humans, has a nervous system, digests food, and reproduces sexually. The 97-million-base genome of the tiny roundworm Caenorhabditis elegans was deciphered by an international team led by Robert Waterston and John Sulston. The work was reported in a special issue of the journal Science (December 11, 1998) that featured six articles describing the history and significance of the accomplishment and some early sequence-analysis results. ------------------- Key: 3473 Medline: Authors: Bignone FA Title: Coupled map lattices dynamics on a variable space for the study of development: A general discussion on Caenorhabditis elegans. Citation: Theoretical Computer Science 217: 157-172 1999 Type: ARTICLE Genes: Abstract: The implementation of models to simulate dynamical aspects of biological systems, particularly in the study of replication and development, has to take into account that gene-gene interactions and cell-cell interactions take place in a space of variable structure and size. In this paper, we discuss the possibility of a detailed reconstruction olf cellular dynamics during early stages of development with coupled map lattices or formalizations of Lindenmayer grammars. ------------------- Key: 3474 Medline: 10097120 Authors: MacMorris MA;Zorio DAR;Blumenthal T Title: An exon that prevents transport of a mature mRNA. Citation: Proceedings of the National Academy of Sciences USA 96: 3813-3818 1999 Type: ARTICLE Genes: rol-6 smg-2 uaf-1 uaf-2 vit-2 vit-6 Abstract: In Caenorhabditis elegans, pre-mRNA for the essential splicing factor U2AF(65) sometimes is spliced to produce an RNA that includes an extra 216-bp internal exon, exon 3, Inclusion of exon 3 inserts an in-frame stop codon, yet this RNA is not subject to SMG-mediated RNA surveillance. To test whether exon 3 causes RNA to remain nuclear and thereby escape decay, we inserted it into the 3' untranslated region of a gfp reporter gene. Although exon 3 did not affect accumulation or processing of the mRNA, it dramatically suppressed expression of green fluorescent protein (GFP), We showed by in situ hybridization that exon 3-containing gfp RNA is retained in the nucleus, Intriguingly, exon 3 contains 10 matches to the 8-bp 3' splice-site consensus. We hypothesized that U2AF might recognize this octamer and thereby prevent export. This idea is supported by RNA interference experiments in which reduced levels of U2AF resulted in a small burst of gfp ------------------- Key: 3475 Medline: 10202142 Authors: Felkai S;Ewbank JJ;Lemieux J;Labbe JC;Brown GG;Hekimi S Title: CLK-1 controls respiration, behavior and aging in the nematode Caenorhabditis elegans. Citation: EMBO Journal 18: 1783-1792 1999 Type: ARTICLE Genes: clk-1 Abstract: Mutations in the clk-1 gene of the nematode Caenorhabditis elegans result in an average slowing of a variety of developmental and physiological processes, including the cell cycle, embryogenesis, post-embryonic growth, rhythmic behaviors and aging. In yeast, a CLK-1 homologue is absolutely required for ubiquinone biosynthesis and thus respiration. Here we show that CLK-1 is fully active when fused to green fluorescent protein and is found in the mitochondria of all somatic cells. The activity of mutant mitochondria, however, is only very slightly impaired, as measured ill vivo by a dye-uptake assay, and in vitro by the activity of succinate cytochrome c reductase. Overexpression of CLK-1 activity in mild-type worms can increase mitochondrial activity, accelerate behavioral rates during aging acid shorten life span, indicating that clk-1 regulates and controls these processes. These observations also provide strong genetic evidence that mitochondria are causally involved in aging. Furthermore, the reduced respiration of the long-lived clk-1 mutants suggests that longevity is promoted by the age-dependent decrease in mitochondrial function that is observed in most ------------------- Key: 3476 Medline: Authors: Goff SP Title: Genetic control of programmed cell death in the nematode Caenorhabditis elegans - Introduction. Citation: Cancer Research 59: 1701S- 1999 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ces-1 ces-2 egl-1 nuc-1 Abstract: It is an honor and a great pleasure to introduce Dr. Robert Horvitz to you as the 1998 recipient of the Alfred Sloan Prize of the General Motors Cancer Research Foundation. Let me begin by telling you a little bit about Bob's ------------------- Key: 3477 Medline: 99211440 Authors: Horvitz HR Title: Genetic control of programmed cell death in the nematode Caenorhabditis elegans. Citation: Cancer Research 59: 1702S-1706S 1999 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ces-1 ces-2 egl-1 nuc-1 Abstract: Studies of the development of the nematode Caenorhabditis elegans established that programmed cell death involves specific genes and proteins and that those genes and proteins act within the cells that die. This finding revealed that cell death is a fundamental and active biological process, much like cell division and cell differentiation. The characterization of genes responsible for programmed cell death in C. elegans has defined a molecular genetic pathway. This pathway is conserved evolutionarily and provides a basis for understanding programmed cell death in more complex organisms, including humans. Knowledge of the mechanisms of programmed fell death should help lead to new methods for the diagnosis and treatment of human diseases characterized by too many or too few cell deaths, including cancer. ------------------- Key: 3478 Medline: 10092511 Authors: Mencinger M;Aman P Title: Characterization of TFG in Mus musculus and Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 257: 67-73 1999 Type: ARTICLE Genes: Abstract: TFG was discovered as a fusion partner of NTRK1 in human papillary thyroid carcinoma. We assembled the mouse TFG cDNA from EST sequences and 5' end RACE product, identified full coding length TFG EST clones in pig (c17b07) and Schistosoma mansoni (SMNAS62), and analyzed the genomic structure of TFG in Caenorhabditis elegans (Y63D3A). The protein sequences of mouse, pig, and S. mansoni TFG are highly homologous to human TFG. The C. elegans sequence has diverged, but its predicted secondary structure is remarkably conserved. Human, mouse, and C. elegans TFG contain a putative trimeric N-terminal coiled-coil domain, glycosylation, myristylation, and phosphorylation sites, and SH2- and SH3-binding motifs. The SH2-binding motif is absent in C. elegans TFG. The expression of TFG does not vary among 7, 11, 15, and 19 day mouse embryonal stages. Pn situ hybridization with a TFG probe in 10, 5-day whole mouse embryos showed preferential staining of the limb buds, branchial arches, nasal processes, and brain, and weak staining of the primitive spinal cord and dorsal root ------------------- Key: 3479 Medline: 99194563 Authors: Goshima M;Kariya K;Yamawaki-Kataoka Y;Okada T;Shibatohge M;Shima F;Fujimoto E;Kataoka T Title: Characterization of a novel Ras-binding protein Ce-FLI-1 comprising leucine-rich repeats and gelsolin-like domains. Citation: Biochemical and Biophysical Research Communications 257: 111-116 1999 Type: ARTICLE Genes: fli-1 Abstract: Ras proteins are conserved from yeasts to mammals and implicated in regulation of the actin cytoskeleton. The flightless-1 (fli-1) gene of Drosophila melanogaster and its homologs in Caenorhabditis elegans and humans encode proteins (FLI-1) comprising a fusion of a leucine-rich repeats (LRRs) domain and a gelsolin-like domain. This LRRs domain is highly homologous to those of three proteins involved in Ras-mediated signaling; Saccharomyces cerevisiae adenylyl cyclase, C. elegans SUR-8, and mammalian RSP-1. Here we report that the LRRs domain of C. elegans FLI-1 (Ce-FLI-1) associates directly with Has (K-d = 11 nM) and, when overexpressed, suppresses the heat shock sensitive phenotype of yeast cells bearing the activated RAS2 gene (RAS2(Val-19)). Further, the gelsolin-like domain of Ce-FLI-1 is shown to possess a Ca2+-independent G-actin-binding activity as well as F-actin-binding and -severing activities. FLI-1 may be involved in regulation of the actin cytoskeleton through Has. ------------------- Key: 3480 Medline: Authors: Boman HG Title: The evolution of C. elegans was a coevolution. Citation: ASM News 65: 187- 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3481 Medline: Authors: Nigon V Title: La gametogenese d'un nematode tetraploide obtenu par voie experimentale. Citation: Bull Soc Hist Natl Toulouse 86: 195-200 1951 Type: ARTICLE Genes: Abstract: In French. ------------------- Key: 3482 Medline: Authors: Khan FR;McFadden BA Title: Embyrogenesis and the glyoxylate cycle. Citation: FEBS Letters 115: 312-314 1980 Type: ARTICLE Genes: Abstract: The key catalysts of the glyoxylate cycle, isocitrate lyase and malate synthase, have been investigated in a variety of tissues. In general, the biological assimilation of acetate units or the conversion of fatty acids to carbohydrates requires function of glyoxylate cycle. For example, the function of this cycle is required for conversion of fat to carbohydrate during germination of fat-rich seedlings. Moreover, the specific activities of isocitrate lyase and malate synthase are highest in second-stage larvae of the nematode Ascaris lumbricoides at a time when the conversion of lipid to carbohydrate is maximal. The presence of isocitrate lyase and malate synthase has also been reported in several other nematodes including a number of free-living forms. Although in recent years scattered information has been published on the biochemistry of larval development of free-living nematodes such as Trubatrix aceti and Caenorhabditis elegans, information about the basic biochemistry is still sketchy. For example, nothing is known about the function of glyoxylate cycle enzymes during embryogenesis, although the presence of high levels of isocitrate lyase in early post-embryonic states of C. elegans implies that this enzyme functions during embyrogenesis. We now present evidence which supports the function of the glyoxylate cycle during embyrogenesis of C. elegans. As far as we know, this is the first report implicating the occurrence of the glyoxylate cycle in any embryonic animal tissue. ------------------- Key: 3483 Medline: Authors: Lewis JA;Fleming JT;Bird D Title: Cloning nematode acetylcholine receptor genes. Citation: "Neurotox '91: Molecular Basis of Drug and Pesticide Action", IR Duce (ed). SCI, Elsevier Applied Science, London. : 155-164 1991 Type: REVIEW Genes: lev-1 unc-29 unc-38 unc-50 unc-63 unc-74 Abstract: Recombinant DNA technology has made it possible to clone receptors from many organisms by cross-hybridization or by the polymerase chain reaction. It may be difficult, though, to establish the functional importance of any clone obtained. We describe the cloning of nematode acetylcholine receptor genes by selection for resistance to levamisole, a scheme providing assurance that the clones obtained are functionally related... ------------------- Key: 3484 Medline: Authors: Kidd VJ Title: Proteolytic activities that mediate apoptosis. Citation: Annual Review of Physiology 60: 533-573 1998 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: Since the discovery that cells can activate their own suicide program, investigators have attempted to determine whether the events that are associated with this form of cell death are genetically determined. The discovery that the ced-3 gene of Caenorhabditis elegans encodes a cysteine protease essential for developmentally regulated apoptosis ignited interest in this area of research. As a result, we now know that cell death is specified by a number of genes and that this biologic process contributes significantly to development, tumorigenesis, and autoimmune disease. In this review I summarize what is currently known about signaling pathways involved in apoptosis, with particular emphasis on the function of the cysteine proteases known as caspases. However, there is also evidence that protease-independent cell death pathways exist. Is there a relationship between these two distinct mechanisms? If so, how do they communicate? Finally, even though the involvement of tumor necrosis factor/nerve growth factor family of receptors and cysteine proteases has been elegantly established as a component of many apoptotic signaling pathways, what happens downstream of these initial events? Why are only a selected group of cellular proteins-many nuclear-the targets of these proteases? Are nuclear events essential for apoptosis in vivo? Are the cellular genes that encode products involved in apoptotic signaling frequent targets of mutation/alteration during tumorigenesis? These are only a few questions that may be answered in the next ten years. ------------------- Key: 3485 Medline: Authors: Cully DF;Wilkinson H;Vassilatis DK;Etter A;Arena JP Title: Molecular biology and electrophysiology of glutamate-gated chloride channels of invertebrates. Citation: Parasitology 113: S191-S200 1996 Type: REVIEW Genes: avr-15 Abstract: In this chapter we summarize the available data on a novel class of ligand-gated anion channels that are gated by the neurotransmitter glutamate. Glutamate is classically thought to be a stimulatory neurotransmitter, however, studies in invertebrates have proven that glutamate also functions as an inhibitory ligand. The bulk of studies conducted in vivo have been on insects and crustaceans, where glutamate was first postulated to act on H-receptors resulting from hyperpolarizing response to glutamate. Recently, glutamate-gated chloride channels have been cloned from several nematodes and Drosophila. The pharmacology and electrophysiological properties of these channels have been studied by expression in Xenopus oocytes. Studies on the cloned channels demonstrate that the invertebrate glutamate-gated chloride channels are the H-receptors and represent important targets for the antiparasitic avermectins. ------------------- Key: 3486 Medline: Authors: Guarente L;Ruvkun G;Amasino R Title: Aging, life span, and senescence. Citation: Proceedings of the National Academy of Sciences USA 95: 11034-11036 1998 Type: REVIEW Genes: age-1 daf-2 daf-16 Abstract: Research in the field of aging recently has entered a new era. Model systems have begun to provide insight into cellular, molecular, and organismal changes that are related intimately to aging. One important approach has been the identification of genes that determine the life span of an organism. The very existence of genes that when mutated can extend life span suggests that one or a few processes may be critical in aging and that a slowing of these processes may slow aging itself. ------------------- Key: 3487 Medline: Authors: Leonardo ED;Hinck L;Masu M;Keino-Masu K;Fazeli A;Stoeckli ET;Ackerman SL;Weinberg RA;Tessier-Lavigne M Title: Guidance of developing axons by netrin-1 and its receptors. Citation: Cold Spring Harbor Symposia on Quantitative Biology 62: 467-478 1997 Type: REVIEW Genes: unc-5 unc-6 unc-40 Abstract: The establishment of neuronal connections involves the accurate guidance of developing axons to their targets through the combined actions of attractive and repulsive cues in the extracellular environment. Accumulating evidence has indicated the importance of long-range mechanisms for axon guidance, involving diffusible chemoattractants secreted by target cells that attract axons to their targets, and diffusible chemorepellents secreted by non-target cells that generate exclusion zones which axons avoid. Two recently identified families of guidance molecules, the netrins and semaphorins, can function as diffusible attractants or repellents for developing axons, but the receptors and signal transduction mechanisms through which they produce their effects are ------------------- Key: 3488 Medline: Authors: Thomas CF;White JG Title: Four-dimensional imaging: the exploration of space and Citation: Trends in Biotechnology 16: 175-182 1998 Type: ARTICLE Genes: Abstract: The process of studying dynamic three-dimensional samples has a long history in biological research. Recent advances in hardware and software have made it easier to visualise and record interior detail from multiple focal planes of three-dimensional samples as they change over time (four-dimensional imaging). Once captured, it is possible to watch these events repeatedly and to analyse them in numerous ways. This article discusses the history and the hardware necessary to perform 4D experiments, the various techniques that make 4D imaging possible, and the applications and various options for 4D-image analysis. ------------------- Key: 3489 Medline: Authors: Civetta A;Singh RS Title: Sex-related genes, directional sexual selection, and speciation. Citation: Molecular Biology and Evolution 15: 901-909 1998 Type: ARTICLE Genes: ace-1 ced-9 cyt-1 ges-1 mec-4 Abstract: Reproductive isolation and speciation can result from the establishment of either premating or postmating barriers that restrict gene flow between populations. Recent studies of speciation have been dominated by a molecular approach to dissect the genetic basis of hybrid male sterility, a specific form of postmating reproductive isolation. However, relatively little attention has been paid to the evolution of genes involved in premating isolation and genes generally involved in other sex-related functions (e.g., mating behavior, fertilization, spermatogenesis, sex determination). We have assembled DNA sequences from 51 nuclear genes and classified them based on their functional characteristics. The proportion of nonsynonymous to synonymous nucleotide substitutions were compared between Drosophila melanogaster, Drosophila simulans, and Drosophila pseudoobscura, as well as between Caenorhabditis elegans and Caenorhabditis briggsae. We found a high ratio of nonsynonymous to synonymous substitutions for sex-related genes (i.e., genes involved in mating behavior, fertilization, spermatogenesis, or sex determination). The results suggest that directional sexual selection has shaped the evolution of sex-related genes and that these changes have more likely occurred during the early stages of speciation. It is possible that directional selection becomes relaxed after reproductive isolation has been completed between more distantly related species (e.g., D. melanogaster and D. pseudoobscura). However, a saturation in the number of nucleotide substitutions since the time of species separation may mask any sign of directional selection between more distantly related species. ------------------- Key: 3490 Medline: Authors: Gadagkar R Title: How to gain the benefits of sexual reproduction without paying the cost: a worm shows the way. Citation: Trends in Ecology & Evolution 13: 220-221 1998 Type: REVIEW Genes: Abstract: Sexual reproduction is perhaps the greatest of all evolutionary puzzles. It's a puzzle because sexually reproducing species pay the cost of spending half their resources (over and above what is needed for vegetative growth) in producing males, whereas parthogenetic species utilize all their resources meant for reproduction in producing only females (or hermaphrodites) like themselves. This twofold cost of sexual reproduction is sometimes referred to as the twofold cost of producing males. Three advantages of sexual reproduction that might offset this cost have been proposed. Genetic recombination and cross fertilization permit sexually reproducing species to (1) bring together, in the same individual, mutations arising in different individuals; (2) generate genetic variability and thus adapt to changing environments; and (3) shuffle their genes in every generation and thus keep parasites at bay. While evolutionary biologists are busy testing their favourite ideas for offsetting the twofold cost of producing males, recent work by Craig LaMunyon and Samuel Ward shows that a nematode, Caenorhabditis briggsae, appears to have found a way of gaining the benefits of sexual reproduction without paying the cost of producing ------------------- Key: 3491 Medline: 99342687 Authors: Waldmann R;Lazdunski M Title: H+-gated cation channels: neuronal acid sensors in the NaC/DEG family of ion channels. Citation: Current Opinion in Neurobiology 8: 418-424 1998 Type: REVIEW Genes: deg-1 del-1 mec-4 mec-10 unc-8 unc-105 Abstract: Ion channels in the amiloride-sensitive Na+ channel/degenerin (NaC/DEG) family of cation channels have very diverse functions. They can be constitutively active (e.g. the epithelial Na+ channel), gated by a ligand (e.g. the peptide-gated channel FaNaC or H+-gated cation channels [ASICs]) or possibly activated by stretch (degenerins of Caenorhabditis elegans). Despite this functional diversity, the heterologous expressed channels share the following properties: permeability to Na+, inhibition by the diuretic amiloride and no voltage gating. This review will focus on recent advances in this ion channel family, with special emphasis on H+-gated cation channels. ------------------- Key: 3492 Medline: Authors: Jacobson MD Title: Programmed cell death: a missing link is found. Citation: Trends in Cell Biology 7: 467-469 1997 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: The evolutionary conservation of programmed cell death (PCD) in animals has meant that genetic studies in worms can illuminate PCD in higher organisms. Genetic analysis in the nematode worm C. elegans has provided a conceptual framework involving, at is heart, three genes: two of these, ced-3 and ced-4, are both required for PCD in the worm, whereas another, ced-9, inhibits the action of ced-3 and ced-4 in surviving cells. Mammalian homologues have been identified for ced-3, which encodes a caspase, and for ced-9, which is related to the cell-death suppressor bcl-2, but, until now, no vertebrate homologue had been found for ced-4. Unfortunately, the sequence of CED-4 gave few clues to how this protein works. Earlier this year, several groups reported physical interactions between CED-9, CED-4 and CED-3 proteins, with CED-4 as a linker in a protein complex. The finding of an indirect interaction between the Bcl-2-related protein Bcl-X(L) and some human caspases, through an unknown intermediate protein, suggested that the same physical interaction might occur in mammalian cells via a CED-4 homologue. Indeed, the remarkable evolutionary conservation between CED-3 and caspases, and between CED-9 and Bcl-2-related proteins, suggests that there must be CED-4 homologues in vertebrates. Zou et al. have now identified a human CED-4 homologue, and findings from this group, along with those of others, provide important clues to how CED-4 and its relatives might work. ------------------- Key: 3493 Medline: Authors: Serra-Pages C;Medley QG;Tan M;Hart A;Streuli M Title: Liprins, a family of LAR transmembrane protein-tyrosine phosphatase-interacting proteins. Citation: Journal of Biological Chemistry 273: 15611-15620 1998 Type: ARTICLE Genes: Abstract: LAR family transmembrane protein-tyrosine phosphatases function in axon guidance and mammary gland development. In cultured cells, LAR binds to the intracellular, coiled coil LAB-interacting protein at discrete ends of focal adhesions, implicating these proteins in the regulation of cell-matrix interactions. We describe seven LAB-interacting protein-like genes in humans and Caenorhabditis elegans that form the liprin gene family, Based on sequence similarities and binding characteristics, liprins are subdivided into alpha-type and beta-type liprins. The C-terminal, non-coiled coil regions of alpha-liprins bind to the membrane-distal phosphatase domains of LAR family members, as well as to the C-terminal, non-coiled coil region of beta-liprins. Both alpha- and beta-liprins homodimerize via their N-terminal, coiled coil regions. Liprins are thus multivalent proteins that potentially form complex structures. Some liprins have broad mRNA tissue distributions, whereas others are predominately expressed in the brain. Go-expression studies indicate that liprin-alpha 2 alters LAR cellular localization and induces LAR clustering. We propose that liprins function to localize LAR family tyrosine phosphatases at specific sites on the plasma membrane, possibly regulating their interaction with the extracellular environment and their ------------------- Key: 3494 Medline: Authors: Jolodar A;Miller DJ Title: Identification of a novel family of non-lysosomal aspartic proteases in nematodes. Citation: Biochimica et Biophysica Acta 1382: 13-16 1998 Type: REVIEW Genes: Abstract: A protein encoded by cDNAs from the human parasite Onchocerca volvulus and its homologs from Caenorhabditis elegans and Ancyclostoma caninum define a family of aspartic proteases that are most closely related to cathepsins D, but differ from them in lacking the N-glycosylation site known to be required for lysosomal targeting. The nematode proteins have a potential N-glycosylation site at the same position as mammalian cathepsins E and in common with these have atypically long N-terminal extensions. The literature implies that cathepsins E may be secreted, and adult female O. volvulus are known to secrete a specific inhibitor of aspartic proteases; we therefore predict that the protease is ------------------- Key: 3495 Medline: Authors: Thomas JB Title: Axon guidance: Crossing the midline. Citation: Current Biology 8: R102-R104 1998 Type: REVIEW Genes: sax-3 Abstract: Neurons that connect the two sides of the nervous system project their axons across the midline. New studies provide evidence for a conserved gatekeeping mechanism that controls this midline crossing. ------------------- Key: 3496 Medline: 99233384 Authors: Yang Y;Wilson DL Title: Characterization of a life-extending mutation in age-2, a new aging gene in Caenorhabditis elegans. Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 54: B137-B142 1999 Type: ARTICLE Genes: age-1 age-2 clk-1 clk-2 clk-3 daf-2 daf-12 daf-16 gro-1 spe-26 Abstract: We have generated a life-extending mutation, yw23, tl Caenorhabditis elegans The mutation is in what appears to be a new aging gene, which we have designated age-2. When homozygous, yw23 produces an increase of mean and maximum life span of about 20% over that of the wild-type strain, N2. Strain HG23 [age-2(yw23)] was obtained by screening for longer life spans among 430 lines of nematodes two generations after exposure to the mutagen ethylmethanesulfonate. Strain HG231 [age-2(yw23)] was obtained after a single oat-crossing of HG23 to NZ. When compared with N2, HG231 exhibits normal motility, slightly higher swimming rates, reduced fertility (especially at higher temperatures), somewhat longer development times, and a slightly larger size at the time of first egg laying. A Gompertz analysis suggests that HG231 extends life span by reducing the initial mortality rate. In generic crosses, yw23 complements other known aging mutants in C. elegans genes-age-1, daf-2, spe-26, clk-1, clk-2, clk-3, and gro-1. A double-mutant strain, HG284, combining mutations in age-1 and age-2, fires longer than animals with individual mutations in either age-1 or age-2, and exhibits a longer life span at 25 degrees C than at 20 degrees C. ------------------- Key: 3497 Medline: 99214262 Authors: Semple C;Wolfe KH Title: Gene duplication and gene conversion in the Caenorhabditis elegans genome. Citation: Journal of Molecular Evolution 48: 555-564 1999 Type: ARTICLE Genes: Abstract: A comprehensive analysis of duplication and gene conversion for 7394 Caenorhabditis elegans genes (about half the expected total for the genome) is presented. Of the genes examined, 40% are involved in duplicated gene pairs. Intrachromosomal or cis gene duplications occur approximately two times more often than expected. In general the closer the members of duplicated gene pairs are, the more likely it is that gene orientation is conserved. Gene conversion events are detectable between only 2% of the duplicated pairs. Even given the excesses of cis duplications, there is an excess of gene conversion events between cis duplicated pairs on every chromosome except the X chromosome. The relative rates of cis and trans gene conversion and the negative correlation between conversion frequency and DNA sequence divergence for unconverted regions of converted pairs are consistent with previous experimental studies in yeast. Three recent, regional duplications, each spanning three genes are described. All three have already undergone substantial deletions spanning hundreds of base pairs. The relative rates of duplication and deletion may contribute to the compactness of the C. elegans genome. ------------------- Key: 3498 Medline: 99187058 Authors: Tabish M;Clegg RA;Rees HH;Fisher MJ Title: Organization and alternative splicing of the Caenorhabditis elegans cAMP-dependent protein kinase catalytic-subunit gene (kin-1). Citation: Biochemical Journal 339: 209-216 1999 Type: ARTICLE Genes: kin-1 Abstract: The cAMP-dependent protein kinase (protein kinase A, PK-A) is multifunctional in nature, with key roles in the control of diverse aspects of eukaryotic cellular activity. In the case of the free-living nematode, Caenorhabditis elegans, a gene encoding the PK-A catalytic subunit has been identified and two isoforms of this subunit, arising from a C-terminal alternative-splicing event, have been characterized [Gross, Bagchi, Lu and Rubin (1990) J. Biol. Chem. 265, 6896-6907]. Here we report the occurrence of N-terminal alternative-splicing events that, in addition to generating a multiplicity of non-myristoylatable isoforms, also generate the myristoylated variant(s) of the catalytic subunit that we have recently characterized [Aspbury, Fisher, Rees and Clegg (1997) Biochem. Biophys. Res. Commun. 238, 523-527]. The gene spans more than 36 kb and is divided into a total of 13 exons. Each of the mature transcripts contains only 7 exons. In addition to the already characterized exon 1, the 5'-untranslated region and first intron actually contain 5 other exons, any one of which may be alternatively spliced on to exon 2 at the 5' end of the pre-mRNA. This N-terminal alternative splicing occurs in combination with either of the already characterized C-terminal alternative exons. Thus, C. elegans expresses at least 12 different isoforms of the catalytic subunit of PK-A. The significance of this unprecedented structural diversity in the family of PK-A catalytic subunits is discussed. ------------------- Key: 3499 Medline: Authors: Shin JY;Kim SJ;Ahnn J Title: Analysis of flectin-like gene expression in Caenorhabditis elegans using germ-line transformation. Citation: Korean Journal of Biological Sciences 2: 377-382 1998 Type: ARTICLE Genes: Abstract: Flectin is a new extracellular matrix protein identified from the eye extract of the chick embryo. Homologous proteins were found in many other vertebrates suggesting that flectin may be an evolutionarily conserved protein. A flectin-like gene (ZK783.4) was found in Caenorhabditis elegans genome data base, showing approximately 40% similarity (20% identity) to chick flectin. In order to study the function of the flectin-like gene in C. elegans, reporter genes fused with this gene were expressed in germ-line transformed transgenic animals. A green fluorescent protein was expressed in various neurons, hypodermis and distal tip cells from the early embryonic stage throughout larval and adult stages. Interestingly, strong expression was observed in neuronal cells and hypodermal cells which compose the ectodermal tissue during early embryogenesis. These observations suggest that the flectin-like protein may be important for the development of hypodermis and neurons. In addition, a majority of cells expressing the reporter gene are migrating cells during development. Here, we summarize our observation of a flectin-like gene expression and speculate on a possible function of the flectin-like gene in C. elegans. ------------------- Key: 3500 Medline: 99156610 Authors: Geary TG;Thompson DP;Klein RD Title: Mechanism-based screening: discovery of the next generation of anthelmintics depends on more basic research. Citation: International Journal for Parasitology 29: 105-112 1999 Type: ARTICLE Genes: Abstract: The therapeutic arsenal for the control of helminth infections contains only a few chemical classes. The development and spread of resistance has eroded the utility of most currently available anthelmintics, at least for some indications, and is a constant threat to further reduce the options for treatment. Discovery and development of novel anthelmintic templates is strategically necessary to preserve the economic and health advantages now gained through chemotherapy. As the costs of development escalate, the question of how best to discover new drugs becomes paramount. Although random screening in infected animals led to the discovery of all currently available anthelmintics, cost constraints and a perception of diminishing returns require new approaches. Taking a cue from drug discovery programmes for human illnesses, we suggest that mechanism-based screening will provide the next generation of anthelmintic molecules. Critical to success in this venture will be the exploitation of the Caenorhabditis elegans genome through bioinformatics and genetic technologies. The greatest obstacle to success in this endeavour is the paucity of information available about the molecular physiology of helminths, making the choice of a discovery target a risky proposition. ------------------- Key: 3501 Medline: Authors: Gartner A;Hengartner MO Title: Genetic approaches to programmed cell death in C. elegans. Citation: "When Cells Die: A Comprehensive Evaluation of Apoptosis and Programmed Cell Death", RA Lockshin, Z Zakeri and JL Tilly (eds). Wiley-Liss, Inc. New York. : 131-146 1998 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-9 ced-10 ces-1 ces-2 egl-1 nuc-1 Abstract: Programmed cell death is a common cell fate in most if not all multicellular organisms. Apoptosis, which will be used as a synonym for programmed cell death throughout this chapter, occurs extensively during development as well as during later life. The development of the nematode worm Caenorhabditis elegans provides a good example of the extensive use of programmed cell death. ------------------- Key: 3502 Medline: Authors: Royal D;Driscoll M Title: Neuronal cell death in C. elegans. Citation: "Cell Death and Diseases of the Nervous System", VE Koliatsos and RR Ratan (eds). Humana Press, Inc. Totowa, New Jersey. : 123-144 1999 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ces-1 ces-2 dad-1 deg-1 egl-1 lin-24 lin-33 mec-4 mec-10 nuc-1 unc-8 unc-105 Abstract: The biochemical mechanisms involved in the regulation and execution of developmental cell death are strikingly conserved from nematodes to humans. As a consequence, powerful genetic approaches to the dissection of the developmental cell death pathway in the nematode Caenorhabditis elegans (referred to as programmed cell death) have provided insights into rules that govern cellular life/death decisions, the process by which cells die, and the elimination of cell corpses that are relevant to understanding similar processes in higher organisms. As is the case for most metazoans, C. elegans neurons can also undergo a necrotic-like death when injured. Study of the basic biology of degenerative cell death in nematodes may thus also extend understanding of mechanisms of aberrant cell death in higher organisms. Here we first review the features of the nematode experimental system and then discuss current understanding of both developmental and degenerative cell death mechanisms in C. elegans. ------------------- Key: 3503 Medline: 9847421 Authors: Kitano H;Hamahashi S;Luke S Title: The perfect C. elegans project: An initial report. Citation: Artificial Life 4: 141-156 1998 Type: REVIEW Genes: Abstract: The soil nematode Caenorhabditis Elegans (C. elegans) is the most investigated of all multicellular organisms. Since the proposal to use it as a model organism, a series of research projects have been undertaken, investigating various aspects of this organism. As a result, the complete cell lineage, neural circuitry, and various genes and their functions have been identified. The complete C. elegans DNA sequencing and gene expression mapping for each cell at different times during embryogenesis will be identified in a few years. Given the abundance of collected data, we believe that the time is ripe to introduce synthetic models of C. elegans to further enhance our understanding of the underlying principles of its development and behavior. For this reason, we have started the Perfect C. elegans Project, which aims to produce ultimately a complete synthetic model of C. elegans' cellular structure and function. This article describes the goal, the approach, and the initial results of the project. ------------------- Key: 3504 Medline: 99218306 Authors: Duret L;Mouchiroud D Title: Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Citation: Proceedings of the National Academy of Sciences USA 96: 4482-4487 1999 Type: ARTICLE Genes: Abstract: We measured the expression pattern and analyzed codon usage in 8,133, 1,550, and 2,917 genes, respectively, from Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana. In those three species, we observed a clear correlation between codon usage and gene expression levels and showed that this correlation is not due to a mutational bias. This provides direct evidence for selection on silent sites in those three distantly related multicellular eukaryotes. Surprisingly, there is a strong negative correlation between codon usage and protein length. This effect is not due to a smaller size of highly expressed proteins. Thus, for a same-expression pattern, the selective pressure on codon usage appears to be lower in genes encoding long rather than short proteins. This puzzling observation is not predicted by any of the current models of selection on codon usage and thus raises the question of how translation efficiency affects fitness in multicellular organisms. ------------------- Key: 3505 Medline: 99187045 Authors: Chen W;Komuniecki PR;Komuniecki R Title: Nematode pyruvate dehydrogenase kinases: role of the C-terminus in binding to the dihydrolipoyl transacetylase core of the pyruvate dehydrogenase complex. Citation: Biochemical Journal 339: 103-109 1999 Type: ARTICLE Genes: Abstract: Pyruvate dehydrogenase kinases (PDKs) from the anaerobic parasitic nematode Ascaris suum and the free-living nematode Caenorhabditis elegans were functionally expressed with hexahistidine tags at their N-termini and purified to apparent homogeneity. Both recombinant PDKs (rPDKs) were dimers, were not autophosphorylated and exhibited similar specific activities with the A. suum pyruvate dehydrogenase (El) as substrate. In addition, the activities of both PDKs were activated by incubation with PDK-depleted A. suum muscle pyruvate dehydrogenase complex (PDC) and were stimulated by NADH and acetyl-CoA. However, the recombinant A. suum PDK (rAPDK) required higher NADH/NAD(+) ratios for half-maximal stimulation than the recombinant C. elegans PDK (rCPDK) or values reported for mammalian PDKs, as might be predicted by the more reduced microaerobic mitochondrial environment of the APDK. Limited tryptic digestion of both rPDKs yielded stable fragments truncated at the C-termini (trPDKs). The trPDKs retained their dimeric structure and exhibited substantial PDK activity with the A. suum El as substrate, but PDK activity was not activated by incubation with PDK-depleted A, suum PDC or stimulated by elevated NADH/NAD(+) or acetyl-CoA/CoA ratios. Direct-binding assays demonstrated that increasing amounts of rCPDK bound to the A. suum PDK-depleted PDC. No additional rCPDK binding was observed at ratios greater than 20 mol of rCPDK/mol of PDC. In contrast, the truncated rCPDK (trCPDK) did not exhibit significant binding to the PDC. Similarly, a truncated form of rCPDK, rCPDK(1-334), generated by mutagenesis, exhibited properties similar to those observed for trCPDK. These results suggest that the C-terminus of the PDK is not required for subunit association of the homodimer or catalysis, but instead seems to be involved in the binding of the PDKs to the dihydrolipoyl transacetylase core of the complex. ------------------- Key: 3506 Medline: 10227290 Authors: Orozco JT;Wedaman KP;Signor D;Brown S;Rose L;Scholey JM Title: Movement of motor and cargo along cilia. Citation: Nature 398: 674- 1999 Type: REVIEW Genes: odr-10 osm-6 Abstract: Intraflagellar transport (IFT) is important in the formation and maintenance of many cilia, such as the motile cilia that drive the swimming of cells and embryos, the nodal cilia that generate left-right asymmetry in vertebrate embryos, and the sensory cilia that detect sensory stimuli in some animals. The heterotrimeric kinesin-II motor protein drives the anterograde transport of macromolecular complexes, called rafts, along microtubule tracks from the base of the cilium to its distal tip, whereas cytoplasmic dynein moves the rafts back in the retrograde direction. We have used fluorescence microscopy to visualize for the first time the intracellular transport of a motor and its cargo in vivo. We observed the anterograde movement of green fluorescent protein (GFP)-labelled kinesin-II motors and IFT rafts within sensory cilia on chemosensory neurons in living ------------------- Key: 3507 Medline: 99225675 Authors: Thacker C;Marra MA;Jones A;Baillie DL;Rose AM Title: Functional genomics in Caenorhabditis elegans: An approach involving comparisons of sequences from related nematodes. Citation: Genome Research 9: 348-359 1999 Type: ARTICLE Genes: bli-4 Abstract: Comparative genomic analysis was used to investigate the gene structure of the bli-4 locus from two related Caenorhabditis species, C. elegans and C. briggsae. In C. elegans, bli-4 is a complex gene encoding a member of the kex2/subtilisin-like family of proprotein convertases. Genomic sequence comparisons coupled with RT-PCR analysis identified five additional coding exons that had not been identified previously using standard recombinant DNA techniques. The C. briggsae gene was able to rescue both viable blistered and developmentally arrested mutants of C. elegans bli-4, demonstrating functional conservation. In addition, deletion analysis of conserved sequences outside of coding regions, combined with phenotypic rescue experiments, identified regulatory elements that alter the expression of the bli-4 gene. These results demonstrate the utility of genomic sequence comparisons of homologous genes in related species as an effective tool with which to dissect the functional information of complex genes. ------------------- Key: 3508 Medline: 99169096 Authors: Brunschwig K;Wittmann C;Schnabel R;Burglin TR;Tobler H;Muller F Title: Anterior organization of the Caenorhabditis elegans embryo by the labial-like Hox gene ceh-13. Citation: Development 126: 1537-1546 1999 Type: ARTICLE Genes: ceh-13 egl-5 lin-39 mab-5 unc-119 nDf16 Abstract: The Caenorhabditis elegans lin-39, mab-5 and egl-5 Hox genes specify cell fates along the anterior-posterior body axis of the nematode during postembryonic development, but little is known about Hox gene functions during embryogenesis. Here, we show that the C. elegans labial-like gene ceh-13 is expressed in cells of many different tissues and lineages and that the rostral boundary of its expression domain is anterior to those of the other Hox genes. By transposon-mediated mutagenesis, we isolated a zygotic recessive ceh-13 loss-of-function allele, sw1, that exhibits an embryonic sublethal phenotype. Lineage analyses and immunostainings revealed defects in the organization of the anterior lateral epidermis and anterior body wall muscle cells. The epidermal and mesodermal identity of these cells, however, is correctly specified. ceh-13(sw1) mutant embryos also show fusion and adhesion defects in ectodermal cells. This suggests that ceh-13 plays a role in the anterior organization of the C. elegans embryo and is involved in ------------------- Key: 3509 Medline: 99169097 Authors: Hobert O;Tessmar K;Ruvkun G Title: The Caenorhabditis elegans lim-6 LIM homeobox regulates neurite outgrowth and function of particular GABAergic neurons. Citation: Development 126: 1547-1562 1999 Type: ARTICLE Genes: aex-2 daf-7 glr-1 lim-6 sem-4 unc-25 unc-30 unc-33 unc-47 unc-73 unc-76 Abstract: We describe here the functional analysis of the C, elegans LIM homeobox gene lim-6, the ortholog of the mammalian Lmx-1a and b genes that regulate limb, CNS, kidney and eye development. lim-6 is expressed in a small number of sensory-, inter- and motorneurons, in epithelial cells of the uterus and in the excretory system. Loss of lim-6 function affects late events in the differentiation of two classes of GABAergic motorneurons which control rhythmic enteric muscle contraction. lim-6 is required to specify the correct axon morphology of these neurons and also regulates expression of glutamic acid decarboxylase, the rate limiting enzyme of GABA synthesis in these neurons. Moreover, lim-6 gene activity and GABA signaling regulate neuroendocrine outputs of the nervous system. In the chemosensory system lim-6 regulates the asymmetric expression of a probable chemosensory receptor. lim-6 is also required in epithelial cells for uterine morphogenesis. We compare the function of lim-6 to those of other LIM homeobox genes in C. elegans and suggest that LIM homeobox genes share the common theme of controlling terminal neural differentiation steps that when disrupted lead to specific neuroanatomical and neural function ------------------- Key: 3510 Medline: 99227123 Authors: Wilson MA;Hoch RV;Ashcroft NR;Kosinski ME;Golden A Title: A Caenorhabditis elegans wee1 homolog is expressed in a temporally and spatially restricted pattern during embryonic development. Citation: Biochimica et Biophysica Acta - Gene Structure & Expression 1445: 99-109 1999 Type: ARTICLE Genes: fem-1 mex-1 mex-3 pop-1 wee-1 Abstract: A wee1 homolog, wee-1.1, is expressed in both a temporally and spatially restricted pattern during early Caenorhabditis elegans embryogenesis, and is undetectable throughout the remainder of embryogenesis. The wee-1.1 message appears to be zygotically expressed in the somatic founder cell E of the 12-cell embryo. This expression disappears when the E blastomere divides for the first time. The wee-1.1 message then appears transiently in the nuclei of the eight great-granddaughter cells of the AB somatic founder cell, just before these cells divide in the 16-cell embryo. Following this division, the wee-1.1 mRNA is no longer detectable throughout the remainder of embryogenesis. The expression of wee-1.1 in the E blastomere and in the AB progeny appears to be restricted to nuclei in prophase and metaphase of the cell cycle. Analysis of the wee-1.1 mRNA expression pattern in maternal-effect lethal mutants suggests that this expression pattern is restricted to cells of the E and AB fates in the early embryo. This mRNA expression pattern is restricted to a 10-15-min span of embryonic development and may be regulating the timing of crucial cell divisions at ------------------- Key: 3511 Medline: 99227113 Authors: Wu X;Fei YJ;Huang W;Chancy C;Leibach FH;Ganapathy V Title: Identity of the F52F12.1 gene product in Caenorhabditis elegans as an organic cation transporter. Citation: Biochimica et Biophysica Acta - Biomembranes 1418: 239-244 1999 Type: ARTICLE Genes: Abstract: We describe here the cloning and functional characterization of an organic cation transporter from Caenorhabditis elegans (CeOCT1). The CeOCT1 cDNA is 1826 bp long and codes for a protein of 568 amino acids. The oct1 gene is similar to 3.2 kb in size and consists of 12 exons. The location of this gene corresponds to the F52F12.1 gene locus on chromosome I. The predicted protein contains 12 putative transmembrane domains. It exhibits significant homology to mammalian OCTs. When expressed in mammalian cells, CeOCT1 induces the transport of the prototypical organic cation tetraethylammonium. The Michaelis-Menten constant for this substrate is 80 +/- 16 mu M. The substrate specificity of CeOCT1 is broad. This represents the first report on the cloning and functional characteristics of an organic cation transporter from C. ------------------- Key: 3512 Medline: 10190976 Authors: Niewmierzycka A;Clarke S Title: Do damaged proteins accumulate in Caenorhabditis elegans L-isoaspartate methyltransferase (pcm-1) deletion mutants? Citation: Archives of Biochemistry & Biophysics 364: 209-218 1999 Type: ARTICLE Genes: pcm-1 Abstract: The protein L-isoaspartate (D-aspartate) O-methyltransferase (E.C. 2.1.1.77) can initiate the conversion of isomerized and racemized aspartyl residues to their normal L-aspartyl forms and has therefore been hypothesized to function as a repair enzyme, responsible for helping to Limit the accumulation of damaged proteins in aging organisms. In this study, the effect of a disruption in the pcm-l gene encoding the L-isoaspartyl methyltransferase was investigated in the nematode Caenorhabditis elegans. It was found that damaged proteins recognized by this enzyme accumulated to significant levels during long-term incubation of bothpcm-1(+) andpcm-1(-) nematodes in a specialized larval stage called the dauer. The L-isoaspartyl methyltransferase-deficient mutants accumulated about twice the level of damaged proteins as the control nematodes during dauer aging. The mutants also accumulated higher levels of damage when both strains were incubated at 30 degrees C for up to 3 days. However, when nonviable nematodes were removed in a Percoll separation, similar levels of damage were measured between the two strains following both dauer aging and 30 degrees C incubation. Both strains were able to effectively eliminate damaged proteins recognized by the methyltransferase after recovery from dauer. Characterization of the methyl-accepting polypeptide substrates which accumulate in aged dauers revealed that although substrates of all molecular weights are present, the majority of substrates are peptides not precipitated by acetone. These results suggest that protein degradation, rather than repair, may be the major mechanism by which C. elegans eliminates damaged proteins containing L-isoaspartyl residues. ------------------- Key: 3513 Medline: 99234093 Authors: Vatcher GP;Barbazuk WB;O'Neil NJ;Marra MA;Ha T;Baillie DL Title: Identification and characterization of a serine hydroxymethyltransferase isoform in Caenorhabditis Citation: Gene 230: 137-144 1999 Type: ARTICLE Genes: mel-32 Abstract: In the nematode Caenorhabditis elegans, the maternal effect lethal gene mel-32 encodes a serine hydroxymethyltransferase isoform. Since interspecies DNA comparison is a valuable tool for identifying sequences that have been conserved because of their functional importance or role in regulating gene activity, mel-32(SHMT) genomic DNA from C. elegans was used to screen a genomic library from the closely related nematode Caenorhabditis briggsae. The C. briggsae genomic clone identified fully rescues the Mel-32 phenotype in C. elegans, indicating functional and regulatory conservation. Computer analysis reveals that CbMEL-32(SHMT) is 92% identical (97% similar) to CeMEL-32(SHMT) at the amino acid level over the entire length of the protein (484 amino acids), whereas the coding DNA is 82.5% identical (over 1455 nucleotides). Several highly conserved noncoding regions upstream and downstream of the mel-32(SHMT) gene reveal potential regulatory sites that may bind ------------------- Key: 3514 Medline: 99234108 Authors: Page AP Title: A highly conserved nematode protein folding operon in Caenorhabditis elegans and Caenorhabditis briggsae. Citation: Gene 230: 267-275 1999 Type: ARTICLE Genes: cyp-9 pdi-1 Abstract: In the free-living model nematode, Caenorhabditis elegans, a protein-folding co-transcribed gene pair has previously been described. The degree and form of trans-splicing, orientation and spacing of the genes, and the co-ordinate co-expression of protein folding catalysts in the nematode's hypodermis indicated this to be a functionally important operon. This gene pair has now been cloned and compared in the related organism Caenorhabditis briggsae to identify evolutionarily conserved, functionally important features. The corresponding C. briggsae gene pair was found to share the operon-specific features, including sequence homology blocks in the upstream 5' flanking regions. The intergenic regions were not conserved. The homology block closest to the translational initiation codon of the upstream gene was found to contain a known Ceanorhabbitis promoter element site, and map therefore be an important cis-regulatory region directing the hypodermis-specific expression of this operon gene of C. elegans. This study also provides further confirmation of the high degree of chromosomal synteny between these nematode species. ------------------- Key: 3515 Medline: 10191044 Authors: Gilleard JS;Shafi Y;Barry JD;McGhee JD Title: ELT-3: A Caenorhabditis elegans GATA factor expressed in the embryonic epidermis during morphogenesis. Citation: Developmental Biology 208: 265-280 1999 Type: ARTICLE Genes: elt-1 elt-2 elt-3 lin-26 Abstract: We have identified a gene encoding a new member of the Caenorhabditis elegans GATA transcription factor family, elt-3. The predicted ELT-3 polypeptide contains a single GATA-type zinc finger (C-X-2-C-X-17-C-X-2-C) along with a conserved adjacent basic region, elt-3 mRNA is present in all stages of C. elegans development but is most abundant in embryos. Reporter gene analysis and antibody staining show that elt-3 is first expressed in the dorsal and ventral hypodermal cells, and in hypodermal cells of the head and tail, immediately after the final embryonic cell division that gives rise to these cells. No expression is seen in the lateral hypodermal (seam) cells. elt-3 expression is maintained at a constant level in the epidermis until the 2 1/2-fold stage of development, after which reporter gene expression declines to a low level and endogenous protein can no longer be detected by specific antibody. A second phase of elt-3 expression in cells immediately anterior and posterior to the gut begins in pretzel-stage embryos, elt-1 and lin-26 are two genes known to be important in specification and maintenance of hypodermal cell fates. We have found that elt-1 is required for the formation of most, but not all, elt-3-expressing cells. In contrast, lin-26 function does not appear necessary for elt-3 expression. Finally, we have characterised the candidate homologue of elt-3 in the nematode Caenorhabditis briggsae. Many features of the elt-3 genomic and transcript structure are conserved between the two species, suggesting that elt-3 is likely to perform an evolutionarily significant function during ------------------- Key: 3516 Medline: 99208649 Authors: Zhang JM;Chen LS;Krause M;Fire A;Paterson BM Title: Evolutionary conservation of MyoD function and differential utilization of E proteins. Citation: Developmental Biology 208: 465-472 1999 Type: ARTICLE Genes: hlh-1 Abstract: The formation of striated muscle in both vertebrates and invertebrates involves the activity of the MyoD family of basic-helix-loop-helix (bHLH) transcription factors. The high degree of evolutionary conservation of MyoD-related proteins, both in the sequence of their bHLH domains and in their general developmental expression patterns, suggests that these factors are also conserved at the level of function. We have addressed this directly using MyoD and E protein factors from vertebrates, Drosophila, and Caenorhabditis elegans. Various MyoD and E factor combinations were tested for their ability to interact in vitro and to function in vivo in the myogenic conversion of 10T1/2 mouse fibroblasts. We found that the ability of different homo- and heterodimers to bind DNA in vitro was an accurate measure of biological activity in vivo. A second assessment of conserved function comes from the ability of these factors to rescue a C. elegans hlh-1 (CeMyoD) null mutation. We found that both Drosophila and chicken MyoD-related factors were able to rescue a C. elegans CeMyoD loss-of-function mutation. These results demonstrate a remarkable degree of functional conservation of these myogenic factors despite differences in E-protein interactions. ------------------- Key: 3517 Medline: 10208747 Authors: Wissmann A;Ingles J;Mains PE Title: The Caenorhabditis elegans mel-11 myosin phosphatase regulatory subunit affects tissue contraction in the somatic gonad and the embryonic epidermis and genetically interacts with the Rac signaling pat Citation: Developmental Biology 209: 111-127 1999 Type: ARTICLE Genes: fem-1 glp-1 let-502 mel-11 mig-2 sup-39 unc-73 mnDf16 Abstract: Caenorhabditis elegans embryonic elongation is driven by cell shape changes that cause a contraction of the epidermal cell layer enclosing the embryo. We have previously shown that this process requires a Rho-associated kinase (LET-502) and is opposed by the activity of a myosin phosphatase regulatory subunit (MEL-11). We now extend our characterization and show that mel-11 activity is required both in the epidermis during embryonic elongation and in the spermatheca of the adult somatic gonad. let-502 and mel-11 reporter gene constructs show reciprocal expression patterns in the embryonic epidermis and the spermatheca, and mutations of the two genes have opposite effects in these two tissues. These results are consistent with let-502 and mel-11 mediating tissue contraction and relaxation, respectively. We also find that mel-11 embryonic inviability is genetically enhanced by mutations in a Rac signaling pathway, suggesting that Rac potentiates or acts in parallel with the activity of the myosin phosphatase complex. Since Rho has been implicated in promoting cellular contraction, our results support a mechanism by which epithelial morphogenesis is regulated by the counteracting activities ------------------- Key: 3518 Medline: Authors: Wilson M;Xin W;Hashmi S;Gaugler R Title: Risk assessment and fitness of a transgenic entomopathogenic nematode. Citation: Biological Control 15: 81-87 1999 Type: ARTICLE Genes: Abstract: A strain of the entomopathogenic nematode, Heterorhabditis bacteriophora, was transformed by the addition of a heat-shock protein gene (hsp70A) from the free-living nematode Caenorhabditis elegans. Laboratory experiments with wild-type and transgenic nematodes were done at 16, 25, 30, and 37 degrees C to investigate infectivity, reproductive capacity, and survival in water. Heat-shocked transgenic nematodes tones subjected to a heat shock that is lethal to wild-type nematodes) were included in experiments to determine if this treatment caused sublethal damage. We found no significant differences in the ability of wildtype, transgenic, and heat-shocked-transgenic nematodes to infect or to reproduce in last-instar Galleria mellonella larvae or to survive at these temperatures. We compared the ability of wild-type and transgenic nematodes to infect and kill 11 species of invertebrates, representing groups known to be susceptible and nonsusceptible to wild-type nematodes. Transformation caused no detectable change in virulence of nematodes to any test invertebrates. Transgenic and wild-type nematodes were also injected interperitoneally into mice and transgenic nematodes were fed by injection to mice without mouse mortality or changes in growth rate. We conclude that genetic engineering has provided a precise method to alter the heat shock tolerance of H. bacteriophora without affecting other important life history characteristics and that the transgenic nematode is unlikely to pose any threat to the environment if released on a wide scale. ------------------- Key: 3519 Medline: 10331608 Authors: Shtang S;Perry MD;Percy ME Title: Search for a Caenorhabditis elegans FMR1 homologue: Identification of a new putative RNA-binding protein (PRP-1) that hybridizes to the mouse FMR1 double K homology Citation: American Journal of Medical Genetics 84: 283-285 1999 Type: ARTICLE Genes: Abstract: A mixed stage lambda gt10 Caenorhabditis elegans cDNA library was screened with a probe derived by polymerase chain reaction from the double K homology (KH) domain of mouse FMR1 cDNA, a region that is highly conserved in the human, mouse, chicken, and frog FMR1 proteins. Four positively hybridizing cDNAs were cloned and characterized by sequencing, The overlapping sequences map to cosmid R119 from C. elegans linkage group (chromosome) I, and encode a novel proline-, polyglutamine-, and RGG box-rich putative RNA-binding protein. While the cDNA has two regions with similarity to the mouse double KH domain probe at the nucleotide level, there is no significant similarity of the amino acid sequence with human FMR1, FXR1 or FXR2, nor with KH amino acid motifs, The Rile protein, therefore, does not represent an FMR1 homologue. ------------------- Key: 3520 Medline: 99257469 Authors: Eizinger A;Jungblut B;Sommer RJ Title: Evolutionary change in the functional specificity of genes. Citation: Trends in Genetics 15: 197-202 1999 Type: REVIEW Genes: bar-1 let-23 let-60 lin-1 lin-3 lin-31 lin-39 lin-45 mab-5 mpk-1 Abstract: Species throughout the animal kingdom share not only housekeeping but also many key regulatory genes. Nonetheless, species differ from one another developmentally and thus, also morphologically. One of the general aims of comparative developmental genetics is to understand how similar molecules can generate the known diversity of biological form. Here, we argue that gene function can change in different ways during the evolution of developmental processes. Genes can be recruited to serve completely new functions in a new regulatory linkage (co-option), they can change their molecular specificity while remaining in the original (homologous) developmental program and can, at the same time, retain other functions. We describe evidence for such evolutionary patterns based on the comparison of loss-of-function mutations of homologous genes of the two free-living nematodes Caenorhabditis elegans and Pristionchus pacificus. Ultimately, it is the interplay of conservation and change of the specificity of genes and genetic networks that generates developmental novelty over evolutionary time. ------------------- Key: 3521 Medline: 10101123 Authors: Peckol EL;Zallen JA;Yarrow JC;Bargmann CI Title: Sensory activity affects sensory axon development in C. elegans. Citation: Development 126: 1891-1902 1999 Type: ARTICLE Genes: ceh-23 che-3 che-11 che-14 daf-6 daf-19 eat-6 egl-19 gcy-5 gcy-7 glr-1 osm-1 osm-5 osm-6 snt-1 sra-6 str-1 str-3 tax-2 tax-4 unc-13 unc-18 unc-31 unc-36 unc-104 Abstract: The simple nervous system of the nematode C. elegans consists of 302 neurons with highly reproducible morphologies, suggesting a hard-wired program of axon guidance. Surprisingly, we show here that sensory activity shapes sensory axon morphology in C. elegans. A class of mutants with deformed sensory cilia at their dendrite endings have extra axon branches, suggesting that sensory deprivation disrupts axon outgrowth. Mutations that alter calcium channels or membrane potential cause similar defects. Cell-specific perturbations of sensory activity can cause cell-autonomous changes in axon morphology, Although the sensory axons initially reach their targets in the embryo, the mutations that alter sensory activity cause extra axon growth late in development. Thus, perturbations of activity affect the maintenance of sensory axon morphology after an initial pattern of innervation is established. This system provides a genetically tractable model for identifying molecular mechanisms linking neuronal activity to nervous system structure. ------------------- Key: 3522 Medline: 99203444 Authors: Ambros V Title: Cell cycle-dependent sequencing of cell fate decisions in Caenorhabditis elegans vulva precursor cells. Citation: Development 126: 1947-1956 1999 Type: ARTICLE Genes: egl-17 lin-12 lin-15 Abstract: In Caenorhabditis elegans, the fates of the six multipotent vulva precursor cells (VPCs) are specified by extracellular signals. One VPC expresses the primary (1 degrees) fate in response to a Ras-mediated inductive signal from the gonad. The two VPCs flanking the 1 degrees cell each express secondary (2 degrees) fates in response to lin-12-mediated lateral signaling. The remaining three VPCs each adopt the non-vulval tertiary (3 degrees) fate. Here I describe experiments examining how the selection of these vulval fates is affected by cell cycle arrest and cell cycle-restricted lin-12 activity. The results suggest that lin-12 participates in two developmental decisions separable by cell cycle phase: lin-12 must act prior to the end of VPC S phase to influence a 1 degrees versus 2 degrees cell fate choice, but must act after VPC S phase to influence a 3 degrees versus 2 degrees cell fate choice. Coupling developmental decisions to cell cycle transitions may provide a mechanism for prioritizing or ordering choices of cell fates for multipotential cells. ------------------- Key: 3523 Medline: 99203451 Authors: Wu D;Chen PJ;Chen S;Hu Y;Nunez G;Ellis RE Title: C. elegans MAC-1, an essential member of the AAA family of ATPases, can bind CED-4 and prevent cell death. Citation: Development 126: 2021-2031 1999 Type: ARTICLE Genes: ced-3 ced-4 ced-9 mac-1 Abstract: In the nematode Caenorhabditis elegans, CED-4 plays a central role in the regulation of programmed cell death. To identify proteins with essential or pleiotropic activities that might also regulate cell death, we used the yeast two-hybrid system to screen for CED-4-binding proteins. We identified MAC-1, a member of the AAA family of ATPases that is similar to Smallminded of Drosophila. Immunoprecipitation studies confirm that MAC-1 interacts with CED-4, and also with Apaf-1, the mammalian homologue of CED-4, Furthermore, MAC-1 can form a multi-protein complex that also includes CED-3 or CED-9, A MAC-1 transgene under the control of a heat shock promoter prevents some natural cell deaths in C. elegans, and this protection is enhanced in a ced-9(n1950sd)/+ genetic background. We observe a similar effect in mammalian cells, where expression of MAC-1 can prevent CED-4 and CED-3 from inducing apoptosis, Finally, mac1 is an essential gene, since inactivation by RNA-mediated interference causes worms to arrest early in larval development. This arrest is similar to that observed in Smallminded mutants, but is not related to the ability of MAC-1 to bind CED-4, since it still occurs in ced-3 or ced-4 null mutants. These results suggest that MAC-1 identifies a new class of proteins that are essential for development, and which might regulate cell death in specific circumstances. ------------------- Key: 3524 Medline: 99289097 Authors: Irie M;Hata Y;Deguchi M;Ide N;Hirao K;Yao I;Nishioka H;Takai Y Title: Isolation and characterization of mammalian homologues of Caenrhabditis elegans lin-7: localization at cell-cell junctions. Citation: Oncogene 18: 2811-2817 1999 Type: ARTICLE Genes: let-23 lin-2 lin-7 lin-10 Abstract: In Caenorhabditis elegans, the vulval induction is mediated by the let-23 receptor tyrosine kinase (RTK)/ Ras signaling pathway. The precise localization of the let-23 RTK at the epithelial junctions is essential for the vulval induction, and requires three genes including lin-2, -7, and -10. The mammalian homologue of lin-2 has been identified as a protein interacting with a neuronal adhesion molecule, neurexin, and named CASK. CASK has recently been reported to interact with syndecans and an actin-binding protein, band 4.1, at epithelial and synaptic junctions, and to play central roles in the formation of cell-cell junctions. The product of C. elegans lin-7 directly interacts with let-23 RTK and localize it at epithelial junctions. Here, we report three rat homologues of lin-7 ubiquitously expressed in various tissues, These homologues are accumulated at the junctional complex region in cultured Madin-Darby canine kidney cells, and are also localized at the synaptic junctions in neurons. The mammalian homologues of lin-7 may be implicated in the formation of cell-cell junctions. ------------------- Key: 3525 Medline: 10340480 Authors: Cho JH;Eom SH;Ahnn J Title: Analysis of calsequestrin gene expression using green fluorescent protein in Caenorhabditis elegans. Citation: Molecules & Cells 9: 230-234 1999 Type: ARTICLE Genes: csq-1 Abstract: The calsequestrin gene of Caenorhabditis elegans is expressed in body-wall muscle cells during muscle development. In order to study the body-wall muscle specific regulation of the calsequestrin gene expression, approximately 2 kb upstream sequences of the calsequestrin gene were analyzed. Transcriptional fusion constructs utilizing green fluorescent protein as a reporter gene were made and microinjected to produce germ-line transformed transgenic C. elegans. The expression of green fluorescent protein was observed in the body-wall muscles of live transgenic animals under fluorescence microscopy. Deletion analyses of upstream sequences have revealed a putative promoter sequence and a regulatory element which appeared to enhance reporter gene expression. Both sequence elements are juxtaposed to constitute a 260 bp regulatory region approximately 260 bp upstream from the putative translational initiation codon. Several possible binding sites for transcription factors were identified including the sites for Wi and NF-W2, a muscle specific zinc finger transcription factor, and an ubiquitous enhancer binding protein, respectively. Interestingly, this region also contains a 20 bp sequence element identical to those found in the mouse dystrophin gene, which suggests a possible role of this regulatory region in muscle specific gene regulation. ------------------- Key: 3526 Medline: 10220328 Authors: Pierce DW;Hom-Booher N;Otsuka AJ;Vale RD Title: Single-molecule behavior of monomeric and heteromeric kinesins. Citation: Biochemistry 38: 5412-5421 1999 Type: ARTICLE Genes: unc-104 Abstract: Conventional kinesin is capable of long-range, processive movement along microtubules, a property that has been assumed to be important for its role in membrane transport. Here we have investigated whether the Caenorhabditis elegans monomeric kinesin unc104 and the sea urchin heteromeric kinesin KRP85/95, two other members of the kinesin superfamily that function in membrane transport, are also processive. Both motors were fused to green fluorescent protein, and the fusion proteins were tested for processive ability using a single-molecule fluorescence imaging microscope. Neither unc104-GFP nor KRP85/95-GFP exhibited processive movement (detection limit similar to 40 nm), although both motors were functional in multiple motor microtubule gliding assays (upsilon = 1760 +/- 540 and 202 +/- 37 nm/s, respectively). Moreover, the ATP turnover rates (5.5 and 3.1 ATPs per motor domain per second, respectively) are too low to give rise to the observed microtubule gliding velocities, if only a single motor were driving transport with an 8 nm step per ATPase cycle. Instead, the results suggest that these motors have low duty cycles and that high processivity may not be required for efficient vesicle transport. Conventional kinesin's unusual processivity may be required for efficient transport of protein complexes that cannot carry ------------------- Key: 3527 Medline: 99266878 Authors: Taub J;Lau JF;Ma C;Hahn JH;Hoque R;Rothblatt J;Chalfie M Title: A cytosolic catalase is needed to extend adult lifespan in C. elegans daf-C and clk-1 mutants. Citation: Nature 399: 162-166 1999 Type: ARTICLE Genes: age-1 clk-1 ctl-1 ctl-2 daf-2 daf-12 daf-16 daf-23 fer-15 Abstract: The dauer larva is an alternative larval stage in Caenorhabditis elegans which allows animals to survive through periods of low food availability. Well-fed worms live for about three weeks, but dauer larvae can live for at least two months without affecting post-dauer lifespan(1). Mutations in daf-2 and age-1, which produce a dauer constitutive (Daf-C) phenotype, and in clk-1, which are believed to slow metabolism, markedly increase adult lifespan(2). Here we show that a ctl-1 mutation reduces adult lifespan in otherwise wild-type animals and eliminates the daf-c and clk-1-mediated extension of adult lifespan. ctl-1 encodes an unusual cytosolic catalase; a second gene, ctl-2, encodes a peroxisomal catalase. ctl-1 messenger RNA is increased in dauer larvae and adults with the daf-c mutations. We suggest that the ctl-1 catalase is needed during periods of starvation, as in the dauer larva, and that its misexpression in daf-c and clk-1 adults extends lifespan. Cytosolic catalase may have evolved to protect nematodes from oxidative damage produced during prolonged dormancy before reproductive maturity, or it may represent a general mechanism for permitting organisms to cope with the metabolic changes that accompany starvation. ------------------- Key: 3528 Medline: 99270321 Authors: Page AP;Winter AD Title: Expression pattern and functional significance of a divergent nematode cyclophilin in Caenorhabditis elegans. Citation: Molecular & Biochemical Parasitology 99: 301-306 1999 Type: ARTICLE Genes: cyp-8 Abstract: Proline isomerases (PPI) of the cyclophilin (CYP) class are found in all organisms examined. These common enzymes catalyse the slow rate-limiting praline isomerisation of numerous proline-rich proteins including collagens [1,2], RNAse [3], transferring [4], rhodopsin [5] and the HIV1 gag polyprotein [6]. As indicated by their nomenclature, these protein catalysts are identical to the receptor for the immunosuppressive agent cyclosporine (CsA) [7]. Many different isoforms of these enzymes exist and can be classified on the basis of their sub-cellular localization, conservation of their CsA-binding residues and the presence of additional flanking non-CYP domains [8]. In the free-living model nematode Caenorhabditis elegans 11 cyp genes are expressed, and these belong to either conserved type A,B, or C or divergent, type D subclasses [8]. Many parasites posses CYPs predominantly of the conserved A-C class, while type D forms have only been described to date in the parasitic filarial nematodes [9-11]. These receptors are being studied in parasites to elucidate the as yet unresolved anti-parasitic effects that CsA impart; including widespread anti-nematode effects [9-12]. ------------------- Key: 3529 Medline: 10225951 Authors: Ono S;Baillie DL;Benian GM Title: UNC-60B, an ADF/cofilin family protein, is required for proper assembly of actin into myofibrils in Caenorhabditis elegans body wall muscle. Citation: Journal of Cell Biology 145: 491-502 1999 Type: ARTICLE Genes: unc-60 Abstract: The Caenorhabditis elegans unc-60 gene encodes two functionally distinct isoforms of ADF/cofilin that are implicated in myofibril assembly. Here, we show that one of the gene products, UNC-60B, is specifically required for proper assembly of actin into myofibrils. We found that all homozygous viable unc-60 mutations resided in the unc-60B coding region, indicating that UNC-60B is responsible for the Unc-60 phenotype. Wild-type UNC-60B had F-actin binding, partial actin depolymerizing, and weak F-actin severing activities in vitro. However, mutations in UNC-60B caused various alterations in these activities. Three missense mutations resulted in weaker F-actin binding and actin depolymerizing activities and complete loss of severing activity. The r398 mutation truncated three residues from the COOH terminus and resulted in the loss of severing activity and greater actin depolymerizing activity. The s1307 mutation in a putative actin-binding helix caused greater activity in actin-depolymerizing and severing. Using a specific antibody for UNC-60B, we found varying protein levels of UNC-60B in mutant animals, and that UNC-60B was expressed in embryonic muscles. Regardless of these various molecular phenotypes, actin was not properly assembled into embryonic myofibrils in all unc-60 mutants to similar extents. We conclude that precise control of actin filament dynamics by UNC-60B is required for proper integration of actin into myofibrils. ------------------- Key: 3530 Medline: 99242576 Authors: Singson A;Hill KL;L'Hernault SW Title: Sperm competition in the absence of fertilization in Caenorhabditis elegans. Citation: Genetics 152: 201-208 1999 Type: ARTICLE Genes: fer-1 fer-14 him-5 spe-8 spe-9 spe-13 sDp2 Abstract: Hermaphrodite self-fertilization is the primary mode of reproduction in the nematode Caenorhabditis elegans. However, when a hermaphrodite is crossed with a male, nearly all of the oocytes are fertilized by male-derived sperm. This sperm precedence during reproduction is due to the competitive superiority of male-derived sperm and results in a functional suppression of hermaphrodite self-fertility. In this study, mutant males that inseminate fertilization-defective sperm were used to reveal that sperm competition within a hermaphrodite does not require successful fertilization. However, sperm competition does require normal sperm motility. Additionally, sperm competition is not an absolute process because oocytes not fertilized by male-derived sperm can sometimes be fertilized by hermaphrodite-derived sperm. These results indicate that outcrossed progeny result from a wild-type cross because male-derived sperm are competitively superior and hermaphrodite-derived sperm become unavailable to oocytes. The sperm competition assays described in this study will be useful in further classifying the large number of currently identified mutations that alter sperm function and development in C. elegans. ------------------- Key: 3531 Medline: 99242577 Authors: Nance J;Minniti AN;Sadler C;Ward S Title: spe-12 encodes a sperm cell surface protein that promotes spermiogenesis in Caenorhabditis elegans. Citation: Genetics 152: 209-220 1999 Type: ARTICLE Genes: fem-1 fem-3 fer-1 spe-8 spe-12 spe-27 spe-29 nDf24 nDf25 Abstract: During spermiogenesis, Caenorhabditis elegans spermatids activate and mature into crawling spermatozoa without synthesizing new proteins. Mutations in the spe-12 gene block spermatid activation, rendering normally self-fertile hermaphrodites sterile. Mutant males, however, are fertile. Surprisingly, when mutant hermaphrodites mate with a male, their self-spermatids activate and form functional spermatozoa, presumably due to contact with male seminal fluid. Here we show that, in addition to its essential role in normal activation of hermaphrodite-derived spermatids, SPE-12 also plays a supplementary but nonessential role in mating-induced activation. We have identified the spe-12 gene, which encodes a novel protein containing a single transmembrane domain. spe-12 mRNA is expressed in the sperm-producing germ line and the protein localizes to the spermatid cell surface. We propose that SPE-12 functions downstream of both hermaphrodite- and male-derived activation signals in a spermatid signaling pathway that initiates spermiogenesis. ------------------- Key: 3532 Medline: 99242578 Authors: Dufourq P;Chanal P;Vicaire S;Camut E;Quintin S;den Boer BGW;Bosher JM;Labouesse M Title: lir-2, lir-1 and lin-26 encode a new class of zinc-finger proteins and are organized in two overlapping operons both in Caenorhabditis elegans and in Caenorhabditis briggsae. Citation: Genetics 152: 221-235 1999 Type: ARTICLE Genes: lin-26 lir-1 lir-2 lir-3 Abstract: lin-26 which encodes a unique Zn-finger protein, is required for differentiation of nonneuronal ectodermal cells in Caenorhabditis elegans. Here, we show that the two genes located immediately upstream of lin-26 encode LIN-26-like Zn-finger proteins; hence their names are lir-1 and lir-2 (lin-26 related). lir-2, lir-1, and lin-26 generate several isoforms by alternative splicing and/or trans-splicing at different positions. On the basis of their trans-splicing pattern, their intergenic distances, and their expression, we suggest that lir-2, lir-1, and lin-26 form two overlapping transcriptional operons. The first operon, which is expressed in virtually all cells, includes lir-2 and long lir-1 isoforms. The second operon, which is expressed in the nonneuronal ectoderm, includes short lir-1 isoforms, starting at exon 2 and lin-26. This unusual genomic organization has been conserved in C. briggsae, as shown by cloning the C. briggsae lir-2 lir-1, and lin-26 homologs. Particularly striking is the sequence conservation throughout the first lir-1 intron, which is very long in both species. Structural conservation is functionally meaningful as C. briggsae lin-26 is also expressed in the nonneuronal ectoderm and can complement a C. elegans lin-26 null mutation. ------------------- Key: 3533 Medline: 99242579 Authors: Li W;Streit A;Robertson B;Wood WB Title: Evidence for multiple promoter elements orchestrating male-specific regulation of the her-1 gene in Caenorhabditis elegans. Citation: Genetics 152: 237-248 1999 Type: ARTICLE Genes: fem-2 her-1 xol-1 Abstract: The sex-determining gene her-1 is required for male development in Caenorhabditis elegans. In XO males, two her-1 mRNAs, her-la and her-lb, are transcribed from two separate promoters: P1, located in the 5'-flanking region, and P2, located in the large second intron. In XX hermaphrodites, accumulation of both her-1 transcripts is repressed by the sdc genes, which in turn are negatively regulated by the xol-1 gene. When introduced into a xol-1(y9) background, transgenic arrays, including 3.4 kb of her-1 intron 2 sequence (P2), result in phenotypes that mimic those of sdc(lf) mutants, including suppression of XO lethality and masculinization of both XX and XO animals. The masculinization, but not the suppression of XO lethality, is dependent on endogenous her-1 activity. These effects could therefore result from sequestration (titration) of sdc gene products by sequences in the arrays, causing derepression of her-1 (masculinizing effect) and disruption of the dosage compensation machinery (allowing survival of XO animals). We used these effects as an assay in a deletion analysis of the two her-1 promoter regions to define potential cis-regulatory sites required for the putative titration. Several regions in P2 contributed to these effects. P1 was effective only in combination with certain P2 sequences and only if a particular P1 site previously implicated in her-1 repression was intact. These results suggest that normal repression of transcription from P1 in XX animals may involve cooperative interaction with sequences in the P2 region. In experiments to test for a possible role of the her-lb transcript in regulation of sdc genes, no ------------------- Key: 3534 Medline: 99264511 Authors: Braeckman BP;Houthoofd K;De Vreese A;Vanfletern JR Title: Apparent uncoupling of energy production and consumption in long-lived Clk mutants of Caenorhabditis elegans. Citation: Current Biology 9: 493-496 1999 Type: ARTICLE Genes: age-1 clk-1 daf-2 daf-16 gro-1 Abstract: Clk mutants of Caenorhabditis elegans are characterised by an overall slow down of temporal processes and increase in life span. It was hypothesised that Clk mutations slow down the pace of many cellular functions and lower the rate of energy metabolism, possibly resulting in slower production of reactive oxygen species which in turn could result in slower ageing [1-3]. We tested this hypothesis by measuring respiration rates, light production capacities [4] (a measure of metabolic potential) and ATP levels in various strains harbouring mutant alleles of the Clk genes clk-1 and gro-1 and of three other genes that interact with the Clk genes. We found a mild reduction of oxygen consumption rates but little alteration of metabolic capacities in the single Clk mutants during the first 4-5 days of their adult lives, relative to the wild-type strain. This difference tended to fade away with increasing age, however, and aged Clk mutants eventually retained higher metabolic capacities than the wild-type control strain N2. These profiles are suggestive of physiological time being retarded, relative to chronological time in Clk mutants. Ageing clk-7 and gro-1 mutants also retained substantially elevated ATP levels relative to the N2 strain, and the simultaneous presence of mutations in daf-2 or age-1 - genes that affect longevity - boosted this effect. Thus, energy production and consumption appear to be uncoupled in these mutants. Mutation in the transcription factor daf-16 suppressed the Age and ATP phenotypes, but not the reduction of respiration rate imparted by mutation in clk-1. ------------------- Key: 3535 Medline: 99151289 Authors: Zwilling R Title: Preparing 2-D protein extracts from Caenorhabditis elegans. Citation: Methods in Molecular Biology 112: 43-48 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3536 Medline: Authors: Felix MA Title: Evolution of developmental mechanisms in nematodes. Citation: Journal of Experimental Zoology 285: 3-18 1999 Type: REVIEW Genes: lag-2 let-23 lin-3 lin-12 lin-39 mab-5 Abstract: The recent findings that key developmental genes are conserved across animal phyla have led to descriptions of evolutionary change in development based on the recruitment of these few molecules. This approach, however, encounters problems in assigning homology across long evolutionary distances. By contrast, reproducibility of the cell lineage of free-living soil nematodes (order Rhabditida) and conservation of larval blast cells across nematode species permit evolutionary comparisons of developmental mechanisms among nematodes at the cellular level. Such comparative studies uncover an unexpected flexibility of developmental mechanisms: Large evolutionary differences have been described between invariant and noninvariant lineages, in the cellular mechanisms specifying a given cell (for instance, the gonadal anchor cell), in the subcellular events leading to asymmetric divisions (for instance, the first division of the egg), and in redundant networks of cell interactions (for instance, those specifying the centered pattern of vulva precursor fates). Interestingly, redundancy of developmental mechanisms favored by selective pressure allows in turn for evolution of these mechanisms. Such evolutionary changes in developmental mechanisms specifying cell fates can occur in the absence of obvious morphological change, which rather correlates with evolution of cell fates per se: death, division, migration, and differentiation (for instance, in the reduction of the posterior gonadal arm in monodelphic species or in change in vulva position). ------------------- Key: 3537 Medline: 99186856 Authors: Brownlee DJA;Fairweather I Title: Exploring the neurotransmitter labyrinth in nematodes. Citation: Trends in Neurosciences 22: 16-24 1999 Type: REVIEW Genes: ace-1 ace-2 ace-21 ace-311 acr-2 acr-3 avr-15 bas-1 cat-1 cat-2 cat-3 cat-4 cat-5 cha-1 che-3 daf-10 deg-3 egl-44 egl-46 flp-1 flp-2 flp-3 flp-4 flp-5 flp-6 flp-7 flp-8 flp-9 flp-10 flp-11 flp-12 flp-13 flp-14 glr-1 glt-1 goa-1 lev-1 osm-3 unc-17 unc-29 unc-30 unc-38 unc-47 unc-49 unc-50 unc-63 unc-74 Abstract: Nematodes include both free-living species such as Caenorhabditis elegans and major parasites of humans, livestock and plants. The apparent simplicity and uniformity of their nervous system belies a rich diversity of putative signalling molecules, particularly neuropeptides. This new appreciation stems largely from the genome-sequencing project with C. elegans, which is due to be completed by the end of 1998. The project has provided additional insights into other aspects of nematode neurobiology, as have studies on the mechanism of action of anthelmintics. Here, progress on the identification, localization, synthesis and physiological actions of transmitters identified in nematodes is explored. ------------------- Key: 3538 Medline: 99227312 Authors: Moghal N;Sternberg PW Title: Multiple positive and negative regulators of signaling by the EGF-receptor. Citation: Current Opinion in Cell Biology 11: 190-196 1999 Type: REVIEW Genes: age-1 gap-1 gap-2 let-23 let-60 lin-2 lin-3 lin-7 lin-10 lin-45 ptp-2 sem-5 sli-1 unc-101 Abstract: Signaling via the epidermal growth factor (EGF)-receptor family is subject to regulation and modulation by multiple ligands, effectors and negative regulators, as well as regulation by heterodimerization between family members and crosstalk between heterologous signaling pathways. Besides serving as a paradigm for receptor tyrosine kinases in general, this family is crucial for development and is often mutated or amplified in human tumors. ------------------- Key: 3539 Medline: 99336519 Authors: Yanase S;Ishi N Title: Cloning of the oxidative stress-responsive genes in Caenorhabditis elegans. Citation: Journal of Radiation Research 40: 39-47 1999 Type: ARTICLE Genes: oxi-1 sod-1 sod-3 Abstract: Defense systems against free radicals and reactive oxygen species minimize the lethal and mutagenic consequences of these destructive agents. To investigate the genetic response to oxidative stress in a eukaryote, we cloned and characterized oxidative stress-responsive genes by comparing gene expression in the free-living nematode Caenorhabditis elegans under atmospheric conditions;md high oxygen concentrations using a method of RNA arbitrarily primed polymerase chain reaction method (RAP-PCR). We identified four genes whose expression levels increase under high oxygen. These encoded 18 s, 5.8 s and 26 s rRNAs, 16 kDa heat shock proteins (hsp16-1 and 16-48) and a vacuolar ATPase G subunit. In addition, we also established that oxi-1, an oxidative stress-responsive gene we previously cloned, encodes a family of proteins related to human E6-AP ubiquitin-protein ligase. The similarity between human and nematode was 54% in one conserved amino ------------------- Key: 3540 Medline: 99179222 Authors: Lo CW Title: Genes, gene knockouts, and mutations in the analysis of gap junctions. Citation: Developmental Genetics 24: 1-4 1999 Type: REVIEW Genes: Abstract: Gap junctions are cell junctions found between most cells and tissues. They contain membrane channels that mediate the cell-to-cell diffusion of ions, metabolites, and small cell signaling molecules. Cell-cell communication mediated by gap junctions has been proposed to have a variety of functions, including roles in regulating events in development, cell differentiation, and cell growth and proliferation. The analysis of these possibilities has been confounded by the fact that there are over a dozen connexin genes encoding polypeptides that make up vertebrate gap junctions. This complexity, coupled with the fact that most cells express multiple connexin isotypes, likely explains why recent studies using reverse genetic and genetic approaches to disrupt connexin gene function have yielded only limited insights into the physiological roles of gap junctions. Nevertheless, studies in vivo and in vitro together have provided evidence for gap junctions being involved in the regulation of cell metabolism, growth, and differentiation in restricted cell and tissue types. Surprisingly, studies in invertebrates suggest that their gap junctions are encoded not by connexins, but by a family of proteins referred to as innexins. Analysis of various Drosophila and C. elegans mutants suggest that innexins may be functional homologs to the connexins. However, whether innexins are the elusive invertebrate gap junction proteins or, rather, accessory proteins that facilitate gap junction formation remains an open question. Given the rapid progress being made in the cloning and functional analysis of gap junctions in many diverse species, confusion and difficulties with nomenclature are coming to a head in this rapidly expanding field. It may be timely to form a Nomenclature Committee to establish a uniform classification scheme for naming gap junction proteins. ------------------- Key: 3541 Medline: 10021378 Authors: Anderton BH Title: Alzheimer's disease: clues from flies and worms. Citation: Current Biology 9: R106-R109 1999 Type: REVIEW Genes: Abstract: Presenilin mutations give rise to familial Alzheimer's disease and result in elevated production of amyloid beta peptide. Recent evidence that presenilins act in developmental signalling pathways may be the key to understanding how senile plaques, neurofibrillary tangles and apoptosis are all biochemically linked. ------------------- Key: 3542 Medline: Authors: Hekimi S;Garcia M Title: Les mecanismes genetiques du vieillissement. Citation: M S-Medecine Sciences 15: 392-396 1999 Type: REVIEW Genes: age-1 clk-1 daf-2 daf-16 eat-2 Abstract: In French. ------------------- Key: 3543 Medline: 99255704 Authors: Yanase S;Hartman PS;Ito A;Ishii N Title: Oxidative stress pretreatment increases the X-radiation resistance of the nematode Caenorhabditis elegans. Citation: Mutation Research-Fundamental & Molecular Mechanisms of Mutagenesis 426: 31-39 1999 Type: ARTICLE Genes: mev-1 rad-1 rad-2 rad-8 sod-1 sod-3 Abstract: Pre-exposure of wild-type Caenorhabditis elegans to oxygen conferred a protective effect against the lethality imposed by subsequent X-irradiation. In contrast, two mutants (rad-1 and rad-2) that are UV and ionizing radiation hypersensitive but not oxygen sensitive, did not exhibit this adaptive response. To explore the molecular basis of protection, the expression of several key genes was examined using Northern blot analyses to measure mRNA levels. In the wild-type, expression of the heat shuck protein genes, hsp16-1 and hsp16-48, increased dramatically after incubation under high oxygen. Expression of two superoxide dismutase genes (sod-1 and sod-3) was relatively unaffected. Unlike the wild-type, the basal levels of these four genes were significantly lower in the rad-1 and rad-2 mutants under atmospheric conditions. These genes were partially induced in response to oxidative stress. These data suggest that at least a portion of the hypersensitive phenotype of rad-1 and rad-2 may be attributed to ------------------- Key: 3544 Medline: 10337485 Authors: Miller DM;Desai NS;Hardin DC;Piston DW;Patterson GH;Fleenor J;Xu S;Fire A Title: Two-color GFP expression system for C. elegans. Citation: Biotechniques 26: 914-921 1999 Type: ARTICLE Genes: del-1 dpy-20 lin-15 myo-3 unc-4 unc-54 Abstract: We describe the use of modified versions of the Aequora victoria green fluorescent protein (GFP) to simultaneously follow the expression and distribution of two different proteins in the nematode, Caenorhabditis elegans. A cyan-colored GFP derivative, designated CFP, contains amino acid (aa) substitutions Y66W, N1461, M153T and V163A relative to the original GFP sequence and is similar to the previously reported "W7" form. A yellow-shifted GFP derivative, designated YFP, contains aa substitutions S65G, V68A, S72A and T203Y and is similar to the previously described "10C" variant. Coding regions for CFP and YFP were constructed in the context of a high-activity C. elegans expression sr stem. Previously characterized promoters and localization signals have been used to express CFP and YFP in C. elegans. Filter sets designed to distinguish YFP and CFP fluorescence spectra allow ed visualization of the two distinct forms of GFP in neurons and in muscle cells. A series of expression vectors carrying CFP and YFP have been constructed and are being made available to the scientific community. ------------------- Key: 3545 Medline: 99284352 Authors: Morrison GE;Wen JYM;Runciman S;van der Kooy D Title: Olfactory associative learning in Caenorhabditis elegans is impaired in lrn-1 and lrn-2 mutants. Citation: Behavioral Neuroscience 113: 358-367 1999 Type: ARTICLE Genes: lrn-1 lrn-2 odr-10 Abstract: The C. elegans mutants, lrn-1 and lrn-2, are impaired in associative learning using conditioned taste cues. Both mutants are defective in associative learning about appetitive and aversive events, indicating that lrn-1 and lrn-2 exert effects across motivational boundaries. In a new olfactory associative learning paradigm, in which wild type worms learn to avoid a previously attractive diacetyl odor after it has been paired with an aversive acetic acid solution, lrn-1 and lrn-2 are impaired. Although defective in associative learning using a conditioned olfactory cue, nonassociative learning (habituation and dishabituation) using this same olfactory cue is unaffected. The discovery that lrn-1 and lrn-2 are defective in associative learning with both taste and olfactory cues may suggest that associative learning in different sensory modalities converges on a common genetic pathway in C. elegans that is subserved by lrn-1 and lrn-2. ------------------- Key: 3546 Medline: 99208620 Authors: Lissemore JL;Starmer WT Title: Phylogenetic analysis of vertebrate and invertebrate Delta/Serrate/LAG-2 (DSL) proteins. Citation: Molecular Phylogenetics and Evolution 11: 308-319 1999 Type: ARTICLE Genes: apx-1 arg-1 lag-2 Abstract: Delta/Serrate/LAG-2 (DSL) proteins are putative transmembrane signaling molecules that regulate cell differentiation in metazoans. DSL proteins are characterized by the presence of a motif unique to these proteins, the DSL motif, and a variable number of tandemly repeated copies of an epidermal growth factor-like (EGF) motif. We have completed a phylogenetic analysis of 15 DSL proteins from eight species. Our findings reveal that at least one gene duplication occurred prior to the divergence of the Drosophila melanogaster and vertebrate lineages, with subsequent duplications in vertebrates. The three known Caenorhabditis elegans proteins likely arose by two independent duplications in the nematode lineage. Analysis of EGF repeats suggests that EGF 2 has been conserved among DSL proteins in vertebrates and D. melanogaster. The sequences of two EGF repeats have been perfectly conserved in vertebrate orthologs: EGF 2 in Delta and EGF 15 in Jagged/Serrate. Finally, the linear order of EGF repeats has been conserved in the vertebrate Jagged/Serrate orthologs and vertebrate Delta orthologs. ------------------- Key: 3547 Medline: 99267413 Authors: Frontali C;Pizzi E Title: Similarity in oligonucleotide usage in introns and intergenic regions contributes to long-range correlation in the Caenorhabditis elegans genome. Citation: Gene 232: 87-95 1999 Type: ARTICLE Genes: Abstract: A method is presented which allows detection of a sequence correlation effect not related to patchiness in base composition or to preferences in codon usage. Recurrence plots providing local views of oligonucleotide recurrence regimen show that introns and intergenic regions are often characterised by a highly recurrent use of oligonucleotides. By window analysis it is possible to score a long sequence for the recurrence of a given subset of oligos while filtering away the effects of short-range correlations. Long-range exploration of chromosome III from Caenorhabditis elegans reveals that consistent use of recurrent oligonucleotides in introns and intergenic regions generates a correlation effect that extends over ------------------- Key: 3548 Medline: 99284521 Authors: Woollard A;Hodgkin J Title: Stu-7/air-2 is a C. elegans aurora homologue essential for chromosome segregation during embryonic and post-embryonic development. Citation: Mechanisms of Development 82: 95-108 1999 Type: ARTICLE Genes: air-2 let-514 let-603 smg-2 stu-7 Abstract: We have isolated a new sterile uncoordinated C. elegans mutant, stu-7, which is defective in post-embryonic cell divisions in a regionally-specific fashion. The anterior of the worm is relatively unaffected whereas the mid-body and/or posterior are markedly thin, often resulting in worms having a central 'waist'. We have cloned stu-7 and found that it encodes a member of the recently expanding aurora sub-family of serine/threonine kinases. Elimination of maternal as well as zygotic stu-7 expression reveals that stn-7 is essential for mitosis from the first embryonic cell cycle onwards and is required for chromosome segregation though not for centrosome separation or for setting up a bipolar spindle. Multicopy expression of stu-7 also causes mitotic defects, suggesting that the level of this protein must be tightly controlled in order to maintain genetic stability during development. ------------------- Key: 3549 Medline: 20184296 Authors: Gieseler K;Bessou C;Segalat L Title: Dystrobrevin- and dystrophin-like mutants display similar phenotypes in the nematode Caenorhabditis elegans. Citation: Neurogenetics 2: 87-90 1999 Type: ARTICLE Genes: dyb-1 dys-1 Abstract: Dystrophin, the protein disrupted in Duchenne muscular dystrophy, forms a transmembrane complex with dystrophin-associated proteins. Dystrobrevins, proteins showing homology to the C-terminal end of dystrophin, and whose function is unknown, are part of the dystrophin complex. We report there that, in the nematode Caenorhabditis elegans, animals carrying mutations in either the dystrophin-like gene dys-1 or the dystrobrevin-like gene dyb-1 display similar behavioral and pharmacological phenotypes consistent with an alteration of cholinergic signalling. These findings suggest that: (1) dystrobrevin and dystrophin are functionaly related and (2) their disruption impairs cholinergic signalling. ------------------- Key: 3550 Medline: 99272645 Authors: Morse DP;Bass BL Title: Long RNA hairpins that contain inosine are present in Caenorhabditis elegans poly(A)+ RNA. Citation: Proceedings of the National Academy of Sciences USA 96: 6048-6053 1999 Type: ARTICLE Genes: Abstract: Adenosine deaminases that act on RNA (ADARs) are RNA-editing enzymes that convert adenosine to inosine within double-stranded RNA. In the 12 years since the discovery of ADARs only a few natural substrates have been identified. These substrates were found by chance, when genomically encoded adenosines were identified as guanosines in cDNAs. To advance our understanding of the biological roles of ADARs, we developed a method for systematically identifying ADAR substrates. In our first application of the method, we identified five additional substrates in Caenorhabditis elegans. Four of those substrates are mRNAs edited in untranslated regions, and one is a noncoding RNA edited throughout its length. The edited regions are predicted to form long hairpin structures, and one of the RNAs encodes POP-1, a protein ------------------- Key: 3551 Medline: 99287319 Authors: Hsin H;Kenyon C Title: Signals from the reproductive system regulate the lifespan of C. elegans. Citation: Nature 399: 362-366 1999 Type: ARTICLE Genes: daf-2 daf-12 daf-16 Abstract: Understanding hew the ageing process is regulated is a fascinating and fundamental problem in biology. Here we demonstrate that signals from the reproductive system influence the Lifespan of the nematode Cacnorhabditis elegans. If the cells that give rise to the germ line are killed with a laser microbeam, the lifespan of the animal is extended. Our findings suggest that germline signals act by modulating the activity of an insulin/IGF-1 (insulin-like growth factor) pathway that is known to regulate the ageing of this organism. Mutants with reduced activity of the insulin/IGF-1-receptor homologue DAF-2 have been shown to live twice as long as normal(1-3), and their longevity requires the activity of DAF-16, a member of the forkhead/winged-helix family of transcriptional regulators(1,2,4,5). We find that, in order for germline ablation to extend lifespan, DAF-16 is required, as well as a putative nuclear hormone receptor, DAF-12 (refs 6, 7). In addition, our findings suggest that signals from the somatic gonad also influence ageing, and that this effect requires DAF-2 activity. Together, our findings imply that the C. elegans insulin/IGF-1 system integrates multiple signals to define the animal's rate of ageing. This study demonstrates an inherent relationship between the reproductive state of this animal and its lifespan, and may have implications for the co-evolution of reproductive ------------------- Key: 3552 Medline: 99300219 Authors: Whisstock JC;Irving JA;Bottomley SP;Pike RN;Lesk AM Title: Serpins in the Caenorhabditis elegans genome. Citation: Proteins 36: 31-41 1999 Type: ARTICLE Genes: Abstract: Data mining in genome sequences can identify distant homologues of known protein families, and is most powerful if solved structures are available to reveal the three-dimensional implications of very dissimilar sequences. Here we describe putative serpin sequences identified with very high statistical significance in the Caenorhabditis elegans genome. When mapped onto vertebrate serpins such as alpha(1)-antitrypsin, they suggest novel structural features. Some appear complete, some show extensive deletions, and others appear to contain only the C-terminal part of the known serpin fold, probably in partnership with N-terminal regions that have conformations unlike those of known serpins. The observation of such striking sequence similarity, in proteins that must have significantly different overall structures, substantially extends the structural characteristics of the serpin family ------------------- Key: 3553 Medline: 10379837 Authors: Ono S Title: Purification and biochemical characterization of actin from Caenorhabditis elegans - Its difference from rabbit muscle actin in the interaction with nematode ADF/cofilin. Citation: Cell Motility and the Cytoskeleton 43: 128-136 1999 Type: ARTICLE Genes: act-1 act-2 act-3 act-4 act-5 unc-60 Abstract: Biochemical analysis of cytoskeletal proteins of the nematode Caenorhabditis elegans can be combined with a vast resource of genetic information in order to understand the regulation and function of the cytoskeleton in vivo. Here, I report an improved and efficient method to purify actin from wild-type C. elegans and characterization of its biochemical propel ties. The purified actin was highly pure and free of several known actin-binding proteins. G-actin was polymerized into F-actin in a similar kinetic process to rabbit muscle actin. G-actin interacted with bovine DNase I and inhibited its activity. However, UNC-60B, an isoform of ADF/cofilin in C. elegans, showed a marked dt polymerizing activity on C. elegans actin but not on rabbit muscle actin. The results indicate that C. elegans actin shares common biochemical properties with rabbit muscle actin, while actin-binding proteins can interact with C. elegans actin in a distinct manner from rabbit muscle ------------------- Key: 3554 Medline: 99225469 Authors: Boxem M;Srinivasan DG;van den Heuvel S Title: The Caenorhabditis elegans gene ncc-1 encodes a cdc2-related kinase required for M phase in meiotic and mitotic cell divisions, but not for S phase. Citation: Development 126: 2227-2239 1999 Type: ARTICLE Genes: cdk-5 ncc-1 pct-1 ctDp6 qDp3 Abstract: We have identified six protein kinases that belong to the family of cdc-related kinases in Caenorhabditis elegans. Results from RNA interference experiments indicate that at least one of these kinases is required for cell-cycle progression during meiosis and mitosis. This kinase, encoded by the nec-1 gene, is closely related to human Cdk1/Cdc2, Cdk2 and Cdk3 and yeast CDC28/cdc2(+). We addressed whether nec-l acts to promote passage through a single transition or multiple transitions in the cell cycle, analogous to Cdks in vertebrates or yeasts, respectively. We isolated five recessive ncc-1 mutations in a genetic screen for mutants that resemble larval arrested ncc-1(RNAi) animals. Our results indicate that maternal ncc-1 product is sufficient for embryogenesis, and that zygotic expression is required for cell divisions during larval development. Cells that form the postembryonic lineages in wild-type animals do not enter mitosis in ncc-1 mutants, as indicated by lack of chromosome condensation and nuclear envelope breakdown. However, progression through Gr and S phase appears unaffected, as revealed by expression of ribonucleotide reductase, incorporation of BrdU and DNA quantitation. Our results indicate that C. elegans uses multiple Cdks to regulate cell-cycle transitions and that ncc-1 is the C. elegans ortholog of Cdk1/Cdc2 in other metazoans, required for M phase in ------------------- Key: 3555 Medline: 99225470 Authors: Baran R;Aronoff R;Garriga G Title: The C. elegans homeodomain gene unc-42 regulates chemosensory and glutamate receptor expression. Citation: Development 126: 2241-2251 1999 Type: ARTICLE Genes: glr-1 sra-6 srb-6 unc-42 ctDp11 sDf29 Abstract: Genes that specify cell fate can influence multiple aspects of neuronal differentiation, including axon guidance, target selection and synapse formation. Mutations in the unc-42 gene disrupt axon guidance along the C. elegans ventral nerve cord and cause distinct functional defects in sensory-locomotory neural circuits. Here we show that unc-42 encodes a novel homeodomain protein that specifies the fate of three classes of neurons in the Caenorhabditis elegans nervous system: the ASH polymodal sensory neurons, the AVA, AVD and AVE interneurons that mediate repulsive sensory stimuli to the nematode head and anterior body, and a subset of motor neurons that innervate head and body-wall muscles. unc-42 is required for the expression of cell-surface receptors that are essential for the mature function of these neurons. In mutant animals, the ASH sensory neurons fail to express SRA-6 and SRB-6, putative chemosensory receptors. The AVA, AVD and AVE interneurons and RME and RMD motor neurons of unc-42 mutants similarly fail to express the GLR-1 glutamate receptor. These results show that unc-42 performs an essential role in defining neuron identity and contributes to the establishment of neural circuits in C. elegans by regulating the transcription of glutamate and chemosensory receptor genes. ------------------- Key: 3556 Medline: 99303092 Authors: Blelloch R;Kimble J Title: Control of organ shape by a secreted metalloprotease in the nematode Caenorhabditis elegans. Citation: Nature 399: 586-590 1999 Type: ARTICLE Genes: gon-1 lag-2 smg-1 unc-54 Abstract: The molecular controls governing organ shape are poorly understood. In the nematode Caenorhabditis elegans, the gonad acquires a U-shape by the directed migration of a specialized 'leader' cell, which is located at the tip of the growing gonadal 'arm'(1). The gon-1 gene is essential for gonadal morphogenesis: in gon-1 mutants, no arm elongation occurs and somatic gonadal structures are severely malformed(2). Here we report that gon-1 encodes a secreted protein with a metalloprotease domain and multiple thrombospondin type-1-like repeats. This motif architecture is typical of a small family of genes that include bovine procollagen I N-protease (P1NP), which cleaves collagen(3), and murine ADAMTS-1, the expression of which correlates with tumour cell progression(4). We find that gon-1 is expressed in two sites, leader cells and muscle, and that expression in each site has a unique role in forming the gonad. We speculate that GON-1 controls morphogenesis by remodelling basement membranes and that regulation of its activity is crucial for achieving organ shape. ------------------- Key: 3557 Medline: 99294856 Authors: Dawes HE;Berlin DS;Lapidus DM;Nusbaum C;Davis TL;Meyer BJ Title: Dosage compensation proteins targeted to X chromosomes by a determinant of hermaphrodite fate. Citation: Science 284: 1800-1804 1999 Type: ARTICLE Genes: dpy-26 dpy-27 dpy-28 dpy-30 her-1 sdc-1 sdc-2 sdc-3 Abstract: In many organisms, master control genes coordinately regulate sex-specific aspects of development. SDC-2 was shown to induce hermaphrodite sexual differentiation and activate X chromosome dosage compensation in Caenorhabditis elegans, To control these distinct processes, SDC-2 acts as a strong gene-specific repressor and a weaker chromosome-wide repressor. To initiate hermaphrodite development, SDC-2 associates with the promoter of the male sex-determining gene her-1 to repress its transcription. To activate dosage compensation, SDC-2 triggers assembly of a specialized protein complex exclusively on hermaphrodite X chromosomes to reduce gene expression by half. SDC-2 can Localize to X chromosomes without other components of the dosage compensation complex, suggesting that SDC-2 targets dosage compensation machinery to X chromosomes. ------------------- Key: 3558 Medline: 99287313 Authors: Riddle DL Title: Ageing - A message from the gonads. Citation: Nature 399: 308-309 1999 Type: REVIEW Genes: ctl-1 daf-2 daf-12 daf-16 Abstract: Animal evolution is commonly viewed as producing diverse, environmentally adapted bodies to propagate the germ line. The evolutionary theory of ageing suggests that genetic limits to lifespan may be inadvertent consequences of evolutionary selection for maximizing that propagation. In other words, trade-offs occur that favour reproductive success over post-reproductive longevity; lifespan should be inversely correlated with fecundity when progeny production diverts resources from the maintenance of somatic (non-reproductive) cells. The germ line contains all the genetic information to specify the soma. But it is also possible that there are other, environmentally modulated instructions for life history that the germ line conveys to the soma to maximize reproduction. ------------------- Key: 3559 Medline: Authors: Legouis R;Quintin S;Labouesse M Title: Complete sequence of the C. elegans genome: The worm's Citation: M S-Medecine Sciences 15: 695-700 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3560 Medline: 99296847 Authors: Sassa T;Harada S;Ogawa H;Rand JB;Maruyama IN;Hosono R Title: Regulation of the UNC-18 Caenorhabditis elegans syntaxin complex by UNC-13. Citation: Journal of Neuroscience 19: 4772-4777 1999 Type: ARTICLE Genes: unc-13 unc-18 unc-64 Abstract: The Caenorhabditis elegans unc-13, unc-18, and unc-64 genes are required for normal synaptic transmission. The UNC-18 protein binds to the unc-64 gene product C. elegans syntaxin (Ce syntaxin). However, it is not clear how this protein complex is regulated. We show that UNC-13 transiently interacts with the UNC-18-Ce syntaxin complex, resulting in rapid displacement of UNC-18 from the complex. Genetic and biochemical evidence is presented that UNC-13 contributes to the modulation of the interaction between UNC-18 and Ce syntaxin. ------------------- Key: 3561 Medline: 99332770 Authors: Ferree TC;Lockery SR Title: Computational rules for chemotaxis in the nematode C. elegans. Citation: Journal of Computational Neuroscience 6: 263-277 1999 Type: ARTICLE Genes: unc-23 Abstract: We derive a linear neural network model of the chemotaxis control circuit in the nematode Caenorhabditis elegans and demonstrate that this model is capable of producing nematodelike chemotaxis. By expanding the analytic solution for the network output in time-derivatives of the network input, we extract simple computational rules that reveal how the model network controls chemotaxis. Based on these rules we find that optimized linear networks typically control chemotaxis by computing the first time-derivative of the chemical concentration and modulating the body turning rate in response to this derivative. We argue that this is consistent with behavioral studies and a plausible mechanism for at least one component of chemotaxis in real ------------------- Key: 3562 Medline: 99388959 Authors: Schimpf J;Sames K;Zwilling R Title: Proteoglycan distribution pattern during aging in the nematode Caenorhabditis elegans: An ultrastructural histochemical study. Citation: Histochemical Journal 31: 285-292 1999 Type: ARTICLE Genes: Abstract: Glycosaminoglycans are important constituents of the extracellular matrix of vertebrates, where distinct changes in their distribution pattern occur during aging. However, little is known about their changes in the nematode Caenorhabditis elegans, which ages extremely rapidly compared to mammals. The presence of glycosaminoglycans was analysed in cross-sections of all organs of the nematode, in three different age groups (60, 144, 228 h), using the electron-dense dye Cuprolinic Blue in conjunction with the critical electrolyte concentration method and specific glycosaminoglycan degrading enzymes. The nematodes (strain DH 26) were grown at 25.5 degrees C. The results indicate the presence of an organ-specific distribution pattern. Chondroitin-4-sulphate and/or chondroitin-6-sulphate are present in the epicuticula. Chondroitin-4-sulphate and/or chondroitin-6-sulphate and dermatan sulphate are detected in the mesocuticula. If stained by conventional methods the mesocuticula shows an empty fissure, which is filled by chondroitin sulphates and dermatan sulphate as shown by Cuprolinic Blue staining and enzymes. Heparan sulphate is found in the terminal web of intestinal cells while dermatan sulphate is revealed in the central cores of microvilli. An unknown polyanion staining at high electrolyte concentrations is observed in the gonads. Age-related changes do not impair the composition of the glycosaminoglycan fraction. In conclusion an unexpected highly differentiated pattern of glycosaminoglycans with high stability during aging exists. ------------------- Key: 3563 Medline: Authors: Amano S;Kitamura K;Hosono R Title: Hierarchy of habituation induced by mechanical stimuli in Caenorhabditis elegans. Citation: Zoological Science 16: 423-429 1999 Type: ARTICLE Genes: Abstract: C. elegans becomes habituated to repetitive mechanical stimuli. We compared the habituated states induced by three types of mechanical stimuli: touch on the head (head-touch), touch on the anterior body (body-touch), and mechanical tapping of the Petri dish, all of which evoke backward movement. The habituation patterns were similar, but differed in retention period and/or the rate of recovery. We found a hierarchy between the habituated states induced by the three types of mechanical stimuli in the decreasing order of head-touch, body-touch, and tap stimulus. Evidence is presented that the hierarchy is brought out by the magnitude of stimuli rather than by independent neural pathways. ------------------- Key: 3564 Medline: Authors: Blaxter ML;Robertson WM Title: The Cuticle. Citation: "The Physiology and Biochemistry of Free-living and Plant-parasitic Nematodes", RN Perry and DJ Wright (eds). CAB International. : 25-48 1998 Type: REVIEW Genes: bli-4 col-1 col-6 col-8 cut-1 cut-2 cut-3 dpy-7 dpy-10 rol-6 sqt-1 srf-2 srf-3 srf-4 srf-5 srf-8 srf-9 Abstract: The nematode cuticle, like the endo- and exo-skeletons of other animals, is much more than just an inert structure against which muscles can act during locomotion. The cuticle performs complex roles in organismal physiology, protection from the environment, nutrition and excretion. Cuticle composition and structure reflects this complexity. In this chapter we review briefly the ultrastructure of the cuticle and examine the biochemistry and genetics of the components of nematode cuticles. We also discuss the cuticle as a dynamic structure, both over the lifetime of the nematode (through the moults) and on shorter ------------------- Key: 3565 Medline: Authors: Blaxter M;Liu L Title: Nematode spliced leaders - Ubiquity, evolution and utility. Citation: International Journal for Parasitology 26: 1025-1033 1996 Type: REVIEW Genes: Abstract: Most nematode messenger RNAs (mRNAs) have at their 5' end a common 22 nucleotide leader sequence, the trans-spliced leader or SL1. The presence of this leader on some but not all mRNAs raises several questions: What is the role of the spliced leader in mRNA maturation, stability and translation? Why do some genes have a spliced leader and others not? What is the evolutionary origin of this trans-splicing mechanism? Recently, additional trans-spliced leaders (SL2, 3, 4, 5) have been described. What roles do these variants play in nematode gene expression? While definitive answers to these questions remain elusive, it is clear that the spliced leader will significantly facilitate the cloning and sequence analysis of most nematode mRNAs. ------------------- Key: 3566 Medline: 99287744 Authors: Whitfield CW;Benard C;Barnes T;Hekimi S;Kim SK Title: Basolateral localization of the Caenorhabditis elegans epidermal growth factor receptor in epithelial cells by the PDZ protein LIN-10. Citation: Molecular Biology of the Cell 10: 2087-2100 1999 Type: ARTICLE Genes: ceh-8 let-23 lin-1 lin-2 lin-7 lin-10 lin-31 mei-1 unc-15 unc-29 nDf23 Abstract: In Caenorhabditis elegans, the EGF receptor (encoded by let-23) is localized to the basolateral membrane domain of the epithelial vulval precursor cells, where it acts through a conserved Ras/MAP kinase signaling pathway to induce vulval differentiation lin-10 acts in LET-23 receptor tyrosine kinase basolateral localization, because lin-10 mutations result in mislocalization of LET-23 to the apical membrane domain and cause a signaling defective (vulvaless) phenotype. We demonstrate that the previous molecular identification of lin-10 was incorrect, and we identify a new gene corresponding to the lin-10 genetic locus. lin-10 encodes a protein with regions of similarity to mammalian X11/mint proteins, containing a phosphotyrosine-binding and two PDZ domains. A nonsense lin-10 allele that truncates both PDZ domains only partially reduces lin-10 gene activity, suggesting that these protein interaction domains are not essential for LIN-10 function in vulval induction. Immunocytochemical experiments show that LIN-10 is expressed in vulval epithelial cells and in neurons. LIN-10 is present at low levels in the cytoplasm and at the plasma membrane and at high levels at or near the Golgi. LIN-10 may function in secretion of LET-23 to the basolateral membrane domain, or it may be involved in tethering LET-23 at the basolateral ------------------- Key: 3567 Medline: Authors: Gimenez-Pardo C;Vazquez-Lopez C;de Armas-Serra C;Rodriquez-Caabeiro F Title: Proteolytic activity in Caenorhabditis elegans: soluble and insoluble fractions. Citation: Journal of Helminthology 73: 123-127 1999 Type: ARTICLE Genes: Abstract: Proteolytic activities of soluble and insoluble fractions of the free-living soil nematode Caenorhabditis elegans were measured across a range of substrates, temperatures and pH conditions. Several protease inhibitors were also tested under these conditions. Results of these studies indicate that proteolytic activity is present in cytosolic (CF) and non-cytosolic (NCF) fractions of C. elegans extracts at every condition of pH, temperature and buffer assayed. On the other hand, the use of different protease inhibitors demonstrated the existence of exo and endoproteases types in CF as well as NCF. Moreover our results show that the use of two protease inhibitor mixed types proposed by several authors are not enough to avoid this lytic activity when homogenates of this nematode are employed in biochemical assays. ------------------- Key: 3568 Medline: 10364160 Authors: Paradis S;Ailion M;Toker A;Thomas JH;Ruvkun G Title: A PDK1 homolog is necessary and sufficient to transduce AGE-1 PI3 kinase signals that regulate diapause in Caenorhabditis elegans. Citation: Genes & Development 13: 1438-1452 1999 Type: ARTICLE Genes: age-1 akt-1 akt-2 daf-2 daf-5 daf-12 daf-16 osm-6 pdk-1 Abstract: An insulin receptor-like signaling pathway regulates Caenorhabditis elegans metabolism, development, and longevity. Inactivation of the insulin receptor homolog DAF-2, the AGE-1 PI3K, or the AKT-1 and AKT-2 kinases causes a developmental arrest at the dauer stage. A null mutation in the daf-16 Fork head transcription factor alleviates the requirement for signaling through this pathway. We show here that a loss-of-function mutation in pdk-1, the C. elegans homolog of the mammalian Akt/PKB kinase PDK1, results in constitutive arrest at the dauer stage and increased life span; these phenotypes are suppressed by a loss of function mutation in daf-16. An activating mutation in pdk-1 or overexpression of wild-type pdk-1 relieves the requirement for AGE-1 PI3K signaling. Therefore, pdk-1 activity is both necessary and sufficient to propagate AGE-1 PI3K signals in the DAF-2 insulin receptor-like signaling pathway. The activating mutation in pdk-1 requires akt-1 and akt-2 gene activity in order to suppress the dauer arrest phenotype of age-1. This indicates that the major function of C. elegans PDK1 is to transduce signals from AGE-1 to AKT-1 and AKT-2. The activating pdk-1 mutation is located in a conserved region of the kinase domain; the equivalent amino acid substitution in human PDK1 activates its kinase activity to ------------------- Key: 3569 Medline: 99292685 Authors: Mehra A;Gaudet J;Heck L;Kuwabara PE;Spence AM Title: Negative regulation of male development in Caenorhabditis elegans by a protein-protein interaction between TRA-2A and FEM-3. Citation: Genes & Development 13: 1453-1463 1999 Type: ARTICLE Genes: fem-1 fem-2 fem-3 her-1 tra-2 Abstract: The tra-2 gene of the nematode Caenorhabditis elegans encodes a predicted membrane protein, TRA-2A, that promotes XX hermaphrodite development. Genetic analysis suggests that tra-2 is a negative regulator of three genes that are required for male development: fem-l, fem-2, and fem-3. We report that the carboxy-terminal region of TRA-2A interacts specifically with FEM-3 in the yeast two-hybrid system and in vitro. Consistent with the idea that FEM-3 is a target of negative regulation, we find that excess FEM-3 can overcome the feminizing effect of tra-2 and cause widespread masculinization of XX somatic tissues. In turn, we show that the masculinizing effects of excess FEM-3 can be suppressed by overproduction of the carboxy-terminal domain of TRA-2A. A FEM-3 fragment that retains TRA-2A-binding activity can masculinize fem-3(+) animals, but not fem-3 mutants, suggesting that it is possible to release and to activate endogenous FEM-3 by titrating TRA-2A. We propose that TRA-2A prevents male development by interacting directly with FEM-3 and that a balance between the opposing activities of TRA-2A and FEM-3 determines sex-specific cell fates in somatic tissues. When the balance favors FEM-3, it acts through or with the other FEM ------------------- Key: 3570 Medline: 99308631 Authors: Rocheleau CE;Yasuda J;Shin TH;Lin R;Sawa H;Okano H;Priess JR;Davis RJ;Mello CC Title: WRM-1 activates the LIT-1 protein kinase to transduce anterior posterior polarity signals in C. elegans. Citation: Cell 97: 717-726 1999 Type: ARTICLE Genes: apr-1 lin-17 lin-44 lit-1 mom-2 mom-5 pop-1 wrm-1 Abstract: During C. elegans development, Wnt/WG signaling is required for differences in cell fate between sister cells born from anterior/posterior divisions. A beta-catenin-related gene, wrm-1, and the lit-1 gene are effecters of this signaling pathway and appear to downregulate the activity of POP-1, a TCF/LEF-related protein, in posterior daughter cells. We show here that lit-1 encodes a serine/threonine protein kinase homolog related to the Drosophila tissue polarity protein Nemo. We demonstrate that the WRM-1 protein binds to LIT-1 in vivo and that WRM-1 can activate the LIT-1 protein kinase when coexpressed in vertebrate tissue culture cells. This activation leads to phosphorylation of POP-1 and to apparent changes in its subcellular-localization. Our findings provide evidence for novel regulatory avenues for an evolutionarily conserved ------------------- Key: 3571 Medline: 99293043 Authors: Gladyshev VN;Krause M;Xu XM;Korotkov KV;Kryukov GV;Sun QA;Lee BJ;Wootton JC;Hatfield DL Title: Selenocysteine-containing thioredoxin reductase in C. elegans. Citation: Biochemical and Biophysical Research Communications 259: 244-249 1999 Type: ARTICLE Genes: Abstract: Mammalian thioredoxin reductases contain a TGA-encoded C-terminal penultimate selenocysteine (Sec) residue, and show little homology to bacterial, yeast, and plant thioredoxin reductases. Here we show that the nematode, Caenorhabditis elegans, contains two homologs related to the mammalian thioredoxin reductase family. The gene. for one of these homologs contains a cysteine codon in place of TGA, and its product, designated TR-S, was previously suggested to function as thioredoxin reductase. The other gene contains TGA and its product is designated TR-Se. This Sec-containing thioredoxin reductase lacks a canonical Sec insertion sequence element in the 3'-untranslated area of the gene. TR-Se shows greater sequence similarity to mammalian thioredoxin reductase isozymes TR1 and TR2, whereas TR-S is more similar to TR3. TR-Se was identified as a thioredoxin reductase selenoprotein by labeling C. elegans with Se-75 and characterizing the resulting Se-75-labeled protein by affinity and other column chromatography and gel-eleetrophoresis. TR-Se was expressed in Escherichia coli as a selenoprotein when a bacterial SECIS element was introduced downstream of the Sec TGA codon. The data show that TR-Se is the major naturally occurring selenoprotein in C. elegans, and suggest an important role for selenium and the thioredoxin system in ------------------- Key: 3572 Medline: 99307420 Authors: Ailion M;Inoue T;Weaver CI;Holdcraft RW;Thomas JH Title: Neurosecretory control of aging in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 96: 7394-7397 1999 Type: ARTICLE Genes: daf-2 daf-5 daf-16 snb-1 snt-1 unc-11 unc-13 unc-31 unc-64 Abstract: See CGC #3687 for correction. In the nematode Caenorhabditis elegans, an insulin receptor signaling pathway regulates adult life span and developmental arrest at the dauer lar,al stage. Here ne show that the unc-64 and unc-31 genes also function in this pathway. These tno genes are involved in mediating Ca2+-regulated secretion, Mutations in unc-64 and unc-31 increase adult life span and cause constitutive dauer formation. Both phenotypes are suppressed by; mutations in daf-16, which also suppresses other mutations in this pathway. We present evidence that the site of action of unc-64 is neuronal, suggesting that a neurosecretory signal regulates life span and dauer formation. ------------------- Key: 3573 Medline: 10377431 Authors: Mihaylova VT;Borland CZ;Manjarrez L;Stern MJ;Sun H Title: The PTEN tumor suppressor homolog in Caenorhabditis elegans regulates longevity and dauer formation in an insulin receptor-like signaling pathway. Citation: Proceedings of the National Academy of Sciences USA 96: 7427-7432 1999 Type: ARTICLE Genes: age-1 daf-2 daf-18 Abstract: Inactivation of the tumor suppressor PTEN gene is found in a variety of human cancers and in cancer predisposition syndromes. Recently, PTEN protein has been shown to possess phosphatase activity on phosphatidylinositol 3,4,5-trisphosphate, a product of phosphatidylinositol 3-kinase. We have identified a homolog of PTEN in Caenorhabditis elegans and have found that it corresponds to the daf-18 gene, which had been defined by a single, phenotypically weak allele, daf-18(e1375). By analyzing an allele, daf-18(nr2037), which bears a deletion of the catalytic portion of CePTEN/DAF-18, we have shown that mutation in daf-18 can completely suppress the dauer-constitutive phenotype caused by inactivation of daf-2 or age-1, which encode an insulin receptor-like molecule and the catalytic subunit of phosphatidylinositol 3-kinase, respectively. In addition, daf-18(nr2037) dramatically shortens lifespan, both in a wild-type background and in a daf-2 mutant background that normally prolongs lifespan. The lifespan in a daf-18(nr2037) mutant can be restored to essentially that of wild type when combined with a daf-2 mutation. Our studies provide genetic evidence that in C. elegans, the PTEN homolog DAF-18 functions as a negative regulator of the DAF-2 and AGE-1 signaling pathway consistent with the notion that DAF-U acts a phosphatidylinositol 3,4,5-trisphosphate phosphatase in vivo. Furthermore, our studies have uncovered a longevity-promoting activity of the PTEN homolog in C. elegans. ------------------- Key: 3574 Medline: 10391246 Authors: Meneghini MD;Ishitani T;Carter JC;Hisamoto N;Ninomiya-Tsuji J;Thorpe CJ;Hamill DR;Matsumoto K;Bowerman B Title: MAP kinase and Wnt pathways converge to downregulate an HMG-domain repressor in Caenorhabditis elegans. Citation: Nature 399: 793-797 1999 Type: ARTICLE Genes: lit-1 mom-1 mom-2 mom-4 pop-1 tap-1 Abstract: The signalling protein Wnt regulates transcription factors containing high-mobility-group (HMG) domains to direct decisions on cell fate during animal development(1). In Caenorhabditis elegans, the HMG-domain-containing repressor POP-1 distinguishes the fates of anterior daughter cells from their posterior sisters throughout development(2,3), and Wnt signalling downregulates POP-1 activity in one posterior daughter cell called E (refs 2, 4, 5). Here we show that the genes mom-4 and lit-1 are also required to downregulate POP-1, not only in E but also in other posterior daughter cells. Consistent with action in a common pathway, mom-4 and lit-1 exhibit similar mutant phenotypes and encode components of the mitogen-activated protein kinase (MAPK) pathway that are homologous to vertebrate transforming-growth-factor-beta-activated kinase (TAK1) and NEMO-like kinase (NLK), respectively. Furthermore, MOM-4 and TAK1 bind related proteins that promote their kinase activities. We conclude that: a MAPK-related pathway cooperates with Wnt signal transduction to downregulate POP-1 activity. These functions are likely to be conserved in vertebrates, as TAK1 and NLK can downregulate HMG-domain-containing ------------------- Key: 3575 Medline: 99318132 Authors: Graves LE;Segal S;Goodwin EB Title: TRA-1 regulates the cellular distribution of the tra-2 mRNA in C. elegans. Citation: Nature 399: 802-805 1999 Type: ARTICLE Genes: ppp-1 tra-1 tra-2 Abstract: The GLI protein family is involved in several key developmental processes in both vertebrates and invertebrates. The Drosophila GLI protein, Cubitus interuptus (Ci), regulates segment polarity and wing and leg development. In vertebrates, the GLI proteins control neural, lung, bone and gut development(1). In the nematode Caenorhabditis elegans, the GLI family member TRA-1 is necessary for normal sexual development(2,3). GLI, Ci and TRA-1 each contain five zinc-finger domains and bind the identical DNA sequence. Previous analyses are consistent with these proteins being transcription factors(4,5). Here we show that TRA-1 can act post-transcriptionally to govern gene activity. Our results indicate that the binding of TRA-1 to the 3' untranslated region of tra-2 regulates the export of tra-2 messenger RNA from the nucleus. The fact that TRA-1 is part of a conserved family of proteins raises the possibility that GLI family members are both transcriptional and post-transcriptional regulators of gene expression. ------------------- Key: 3576 Medline: 99307327 Authors: Bamber BA;Beg AA;Twyman RE;Jorgensen EM Title: The Caenorhabditis elegans unc-49 locus encodes multiple subunits of a heteromultimeric GABA receptor. Citation: Journal of Neuroscience 19: 5348-5359 1999 Type: ARTICLE Genes: unc-49 Abstract: Ionotropic GABA receptors generally require the products of three subunit genes. By contrast, the GABA receptor needed for locomotion in Caenorhabditis elegans requires only the unc-49 gene. We cloned unc-49 and demonstrated that it possesses an unusual overlapping gene structure. unc-49 contains a single copy of a GABA receptor N terminus, followed by three tandem copies of a GABA receptor C terminus. Using a single promoter, unc-49 generates three distinct GABA(A) receptor-like subunits by splicing the N terminus to each of the three C-terminal repeats. This organization suggests that the three UNC-49 subunits (UNC-49A, UNC-49B, and UNC-49C) are coordinately rescued and therefore might coassemble to form a heteromultimeric GABA receptor. Surprisingly, only UNC-49B and UNC-49C are expressed at high levels, whereas UNC-49A expression is barely detectable. Green fluorescent protein-tagged UNC-49B and UNC-49C subunits are coexpressed in muscle cells and are colocalized to synaptic regions. UNC-49B and UNC-49C also coassemble efficiently in Xenopus oocytes and HEK-293 cells to form a heteromeric GABA receptor. Together these data argue that UNC-49B and UNC-49C coassemble at the C. elegans neuromuscular junction. Thus, C. elegans is able to encode a heteromeric GABA receptor with a single locus. ------------------- Key: 3577 Medline: 99296609 Authors: Wen C;Greenwald I Title: p24 proteins and quality control of LIN-12 and GLP-1 trafficking in Caenorhabditis elegans. Citation: Journal of Cell Biology 145: 1165-1175 1999 Type: ARTICLE Genes: glp-1 lin-12 sel-9 Abstract: Mutations in the Caenorhabditis elegans sel-9 gene elevate the activity of lin-12 and glp-1, which encode members of the LIN-12/NOTCH family of receptors. Sequence analyis indicates SEL-9 is one of several C. elegans p24 proteins. Allele-specific genetic interactions suggest that reducing sel-9 activity increases the activity of mutations altering the extracellular domains of LIN-12 or GLP-1. Reducing sel-9 activity restores the trafficking to the plasma membrane of a mutant GLP-1 protein that would otherwise accumulate within the cell. Our results suggest a role for SEL-9 and other p24 proteins in the negative regulation of transport of LIN-12 and GLP-1 to the cell surface, and favor a role for p24 proteins in a quality control mechanism for endoplasmic reticulum-Golgi transport. ------------------- Key: 3578 Medline: 99244701 Authors: Solari F;Bateman A;Ahringer J Title: The Caenorhabditis elegans genes egl-27 and egr-1 are similar to MTA1, a member of a chromatin regulatory complex, and are redundantly required for embryonic Citation: Development 126: 2483-2494 1999 Type: ARTICLE Genes: egl-27 egr-1 hlh-8 lin-39 lin-44 mab-5 vab-7 maDf4 mnDf30 mnDf39 mnDf61 mnDf68 mnDf88 mnDf96 Abstract: We show here that two functionally redundant Caenorhabditis elegans genes, egl-27 and egr-1, have a fundamental role in embryonic patterning. When both are inactivated, cells in essentially all regions of the embryo fail to be properly organised. Tissue determination and differentiation are unaffected and many zygotic patterning genes are expressed normally, including HOX genes. However, hlh-8, a target of the HOX gene mab-5, is not expressed. egl-27 and egr-1 are members of a gene family that includes MTA1, a human gene with elevated expression in metastatic carcinomas. MTA1 is a component of a protein complex with histone deacetylase and nucleosome remodelling activities. We propose that EGL-27 and EGR-1 function as part of a chromatin regulatory complex required for the function of regional patterning ------------------- Key: 3579 Medline: 10373307 Authors: Jiang LI;Sternberg PW Title: Socket cells mediate spicule morphogenesis in Caenorhabditis elegans males. Citation: Developmental Biology 211: 88-99 1999 Type: ARTICLE Genes: dpy-17 egl-17 gpa-1 lin-48 sma-2 sma-3 sma-4 sma-6 Abstract: Caenorhabditis elegans male spicule morphogenesis requires the coordinated cellular behaviors of several types of cells. We found that. the spicule neurons and sheath cells, although important for spicule function, are dispensable for spicule morphology. In contrast, the spicule socket cells are essential for both spicule elongation and formation of spicule cuticle. The socket cells are not only necessary bur also sufficient to produce spicule cuticle. This functional aspect of socket cells is genetically separable from their function in mediating spicule elongation: elongated spicules with defective spicule cuticle can be formed. During spicule morphogenesis, the expression of an egl-17::GFP reporter gene is found in the spicule socket cells and its expression appears to be regulated in the socket cells. Mutants defective in TGP-beta signaling display a crumpled spicules phenotype as a result of failure of socket cell movement during spicule morphogenesis. These observations suggest that both the FGF and the TGF-beta signaling pathways might be involved in ------------------- Key: 3580 Medline: Authors: Bertrandy S;Burlet P;Clermont O;Huber C;Fondrat C;Thierry-Mieg D;Munnich A;Lefebvre S Title: The RNA-binding properties of SMN: deletion analysis of the zebrafish orthologue defines domains conserved in Citation: Human Molecular Genetics 8: 775-782 1999 Type: ARTICLE Genes: Abstract: Spinal muscular atrophy (SMA) is a common autosomal recessive disorder that results in the degeneration of spinal motor neurons. SMA is caused by alterations of the survival motor neuron (SMN) gene which encodes a novel protein of hitherto unclear function. The SMN protein associates with ribonucleoprotein particles involved in RNA processing and exhibits an RNA-binding capacity. We have isolated the zebrafish Danio rerio and nematode Caenorhabditis elegans orthologues and have found that the RNA-binding capacity is conserved across species. Purified recombinant SMN proteins from both species showed selectivity to poly(G) homopolymer RNA in vitro, similar to that of the human protein. Studying deletions of the zebrafish SMN protein, we defined a RNA-binding element in exon 2a, which is highly conserved across species, and revealed that its binding activity is modulated by protein domains encoded by exon 2b and exon 3. Finally, the deleted recombinant zebrafish protein mimicking an SMA frameshift mutation showed a dramatic change in vitro in the formation of the RNA-protein complexes. These observations indicate that the RNA-binding capacity of SMN is an evolutionarily conserved function and further support the view that defects in RNA metabolism most likely account for the pathogenesis of SMA. ------------------- Key: 3581 Medline: 99307512 Authors: Hunter CP Title: Genetics: A touch of elegance with RNAi. Citation: Current Biology 9: R440-R442 1999 Type: REVIEW Genes: lin-15 unc-22 Abstract: RNA-mediated gene interference (RNAi), a rapid, convenient tool for inhibiting gene function in Caenorhabditis elegans, has recently been shown to work in other ------------------- Key: 3582 Medline: 99332723 Authors: Jones D;Candido EPM Title: Feeding is inhibited by sublethal concentrations of toxicants and by heat stress in the nematode Caenorhabditis elegans: Relationship to the cellular stress response. Citation: Journal of Experimental Zoology 284: 147-157 1999 Type: ARTICLE Genes: che-2 che-3 dyf-7 dyf-8 mec-2 osm-1 osm-5 osm-6 Abstract: We report that the free-living nematode Caenorhabditis elegans can respond to a variety of stressors (compounds known to induce the production of cellular stress proteins in model biological systems), by ceasing pharyngeal pumping. This phenomenon results in both a reduction in intake of the stressor and a cessation of feeding. The effect of stressors can therefore be conveniently assayed by monitoring the decrease in the density of the bacterial food in liquid cultures of nematodes. A great range of stressors induced this response including alcohols, heavy metals, sulfhydryl-reactive compounds, salicylate, and heat. For several of these stressors, inhibition of pharyngeal pumping occurred at stressor concentrations below the threshold required for the induction of the 16-kDa heat shock proteins. Salicylate, which did not induce 16-kDa heat shock proteins at any concentration, nevertheless inhibited pharyngeal pumping. Heat was also inhibitory, at a temperature where 16-kDa heat shock protein production was near maximal. Some compounds caused only a partial inhibition of feeding while with others the effect was complete. Upon removal of the stressor, the nematodes resumed pharyngeal pumping with a residual inhibitory effect that depended on the concentration and type of stressor that had been applied. A number of C. elegans neurosensory mutant strains also exhibited a cessation of pharyngeal pumping when exposed to stressors suggesting that the mechanism underlying this inhibition was not entirely neurosensory and may be intrinsic to the pharynx. In C. elegans and other invertebrates, stress-induced inhibition of feeding may be an important survival mechanism that limits the intake of toxic solutes. ------------------- Key: 3583 Medline: 99294710 Authors: Feinbaum R;Ambros V Title: The timing of lin-14 RNA accumulation controls the timing of postembryonic developmental events in Caenorhabditis elegans. Citation: Developmental Biology 210: 87-95 1999 Type: ARTICLE Genes: col-19 lin-4 lin-14 lin-28 Abstract: The lin-4 gene encodes a small RNA that is required to translationally repress lin-14 toward the end of the first larval stage of Caenorhabditis elegans development. To determine if the timing of LIN-14 protein down-regulation depends on the temporal profile of lin-4 RNA level, we analyzed the stage-specificity of lin-4 RNA expression during wild-type development and examined the phenotypes of transgenic worms that overexpress lin-4 RNA during the first larval stage. We found that lin-4 RNA first becomes detectable at approximately 12 h of wild-type larval development and rapidly accumulates to nearly maximum levels by 16 h. This profile of lin-4 RNA accumulation corresponded to the timing of LIN-14 protein down-regulation. Transgenic strains that express elevated levels of lin-4 RNA prior to 12 h of development display reduced levels of LIN-14 protein and precocious phenotypes consistent with abnormally early loss of lin-14 activity. These results indicate that the temporal profile of lin-4 RNA accumulation specifies the timing of LIN-14 down-regulation and thereby controls the timing of ------------------- Key: 3584 Medline: 99427622 Authors: Hansen D;Pilgrim D Title: Sex and the single worm: sex determination in the nematode C. elegans. Citation: Mechanisms of Development 83: 3-15 1999 Type: REVIEW Genes: fbf-1 fem-1 fem-2 fem-3 fog-1 fog-2 fog-3 fox-1 gld-1 her-1 laf-1 mab-3 mog-1 mog-2 mog-3 mog-4 mog-5 mog-6 sdc-1 sdc-2 sdc-3 sex-1 tra-1 tra-2 tra-3 xol-1 Abstract: The study of sex determination in model organisms has been especially fruitful in increasing our understanding of developmental biology, gene regulation and evolutionary mechanisms. The free living nematode, Caenorhabditis elegans, can develop as one of two sexes; male or self-fertilizing hermaphrodite. Here we discuss the progress toward a genetic and molecular understanding of that decision. Numerous genetic loci have been identified that affect sexual fate, and epistasis analysis of these genes has led to a model of a regulatory hierarchy with stepwise negative interactions. It is becoming evident that many of the genes have numerous levels of regulation. We also discuss the apparent rapid rate of evolution that many of the sex determination proteins have undergone. Protein sequences of homologues from closely related species are more divergent than homologues of proteins involved in other developmental processes. Rapid evolution of sex determination genes may be a common theme throughout the animal kingdom. ------------------- Key: 3585 Medline: 99372354 Authors: Hartman PS;Ishii N Title: Isolating mutants of the nematode Caenorhabditis elegans that are hypersensitive to DNA-damaging agents. Citation: DNA Repair Protocols: Eukaryotic Systems 113: 11-16 1999 Type: REVIEW Genes: mev-1 mev-2 Abstract: The nematode Caenorhabditis elegans has gained widespread popularity for use in addressing many biological problems, particularly those relating to development (for brief topical reviews, see 1-5; for comprehensive treatises, see 6-10). This can be attributed to both inherent properties of the organism as well as the collegiality extant within the "worm community". With respect to the former, C. elegans is extremely east to grow in the laboratory (animals are typically propagated on agar-filled Petri dishes seeded with the bacterium Escherichia coli) and possesses a short generation time (3 d at 20C). The system is genetically robust, with the availability of thousands of mutants as well as the existence of a physical map whose sequencing (over 82 Mb finished at present) is scheduled for completion in 1999. Developmental studies have been advantaged by the animal's transparent nature, facilitating complete elucidation of C. elegans' largely invariant cell ------------------- Key: 3586 Medline: Authors: Salkoff L;Kunkel MT;Wang ZW;Butler A;Yuan A;Nonet M;Wei A Title: The impact of the Caenorhabditis elegans genome project on potassium channel biology. Citation: Current Topics in Membranes 46: 9-+ 1999 Type: REVIEW Genes: egl-36 tax-2 tax-4 Abstract: The DNA sequence data produced by the Caenorhabditis elegans genome sequencing project has revealed a large extended family of potassium channels, the outlines of which are conserved with vertebrates. This initial peek into the nearly complete library of potassium channels from a single 'simple' organism has revealed a number and complexity of potassium channel types that surpassed expectations. The vast majority of potassium channel types revealed by expressed sequence tags (EST) sequencing projects from many vertebrate and invertebrate animals fit within the outlines of families present in C. elegans. Thus, the broad picture of potassium channel families in C. elegans may represent family relationships conserved among most vertebrate and invertebrate animals. This conservation implies that the electrical lives of cell from most metazoans have similar requirements and are similarly diverse. Furthermore, the fact that the structures and possible biophysical properties of many distinct potassium channel types are conserved implies that specific functional roles of potassium channels may be conserved, as well. Studies now underway to reveal the tissue channels in C. elegans could reveal such conserved roles. These studies may be a guide to similar studies in higher ------------------- Key: 3587 Medline: 99311611 Authors: Kuroda MI;Kelley RL Title: Sex and repression. Citation: Science 284: 1787-1788 1999 Type: REVIEW Genes: her-1 sdc-1 sdc-2 sdc-3 xol-1 Abstract: Remarkable progress have been made in identifying proteins that are involved in the behavior of who chromosomes. Two of these areas of inquiry converged recently with the surprising discovery that subunits of a large protein complex required for dosage compensation in nematodes are related to, or actually shared with, the mitotic chromosome condensation and segregation machinery (the 13S condensing) originally identified in frogs and yeast (1-4). Dosage compensation in nematodes is a mechanism of partial transcriptional repression that occurs in hermaphrodites (XX genotype) to achieve a total level of X-linked gene expression that is equivalent to that in males (XO genotype) (5). Presumable, the common players in dosage compensation and chromosome condensation participate in mechanistically similar function in their respective complexes, suggesting that dosage compensation may be mediated through organization of inhibitory chromosomal packaging. Although each of these chromosome-wide processes involve large protein complexes assembled on chromosomes, dosage compensation is remarkable in its exquisite specificity for the X chromosome. On page 1800, in this issue of Science, Dawes and colleagues (6) identify the SDC-2 protein in the nematode Caenorhabditis elegans as the critical targeting factor that assembles shared and dosage compensation-specific subunits on the hermaphrodite X chromosomes. ------------------- Key: 3588 Medline: 10472184 Authors: Mano I;Driscoll M Title: DEG/ENaC channels: a touchy superfamily that watches its salt. Citation: BioEssays 21: 568-578 1999 Type: REVIEW Genes: deg-1 del-1 flr-1 mec-2 mec-4 mec-5 mec-7 mec-9 mec-10 mec-12 unc-1 unc-8 unc-105 Abstract: To the surprise of many, studies of molecular mechanisms of touch transduction and analyses of epithelial Na+ transport have converged to define a new class of ion channel subunits. Based on the names of the first two identified subfamilies, the Caenorhabditis elegans degenerins and the vertebrate epithelial amiloride-sensitive Na+ channel, this ion channel class is called the DEG/ENaC superfamily. Members of the DEG/ENaC superfamily have been found in nematodes, flies, snails, and vertebrates. Family members share common topology, such that they span the membrane twice and have intracellular N- and C-termini; a large extracellular loop includes a conserved cysteine-rich region. DEG/ENaC channels have been implicated a broad spectrum of cellular functions, including mechano-sensation, proprioception, pain sensation, gametogenesis, and epithelial Na+ transport. These channels exhibit diverse gating properties, ranging from near constitutive opening to rapid inactivation. We discuss working understanding of DEG/ENaC functions, channel properties, structure/activity correlations and possible evolutionary relationship to other channel classes. ------------------- Key: 3589 Medline: Authors: Hong K;Hinck L;Nishiyama M;Poo MM;Tessier-Lavigne M;Stein E Title: A ligand-gated association between cytoplasmic domains of UNC5 and DCC family receptors converts netrin-induced growth cone attraction to repulsion. Citation: Cell 97: 927-941 1999 Type: ARTICLE Genes: unc-5 unc-6 unc-40 Abstract: Netrins are bifunctional: they attract some axons and repel others. Netrin receptors of the Deleted in Colorectal Cancer (DCC) family are implicated in attraction and those of the UNC5 family in repulsion, but genetic evidence also suggests involvement of the DCC protein UNC-40 in some cases of repulsion. To test whether these proteins form a receptor complex for repulsion, we studied the attractive responses of Xenopus spinal axons to netrin-1, which are mediated by DCC. Vie show that attraction is converted to repulsion by expression of UNC5 proteins in these cells, that this repulsion requires DCC function, that the UNC5 cytoplasmic domain is sufficient to effect the conversion, and that repulsion can be initiated by netrin-1 binding to either UNC5 or DCC. The isolated cytoplasmic domains of DCC and UNC5 proteins interact directly, but this interaction is repressed in the context of the full-length proteins. We provide evidence that netrin-1 triggers the formation of a receptor complex of DCC: and UNC5 proteins and simultaneously derepresses the interaction between their cytoplasmic domains, thereby converting DCC-mediated attraction to UNC5/DCC-mediated repulsion. ------------------- Key: 3590 Medline: 10559886 Authors: Scheel J;Srinivasan J;Honnert U;Henske A;Kurzchalia TV Title: Involvement of caveolin-1 in meiotic cell-cycle progression in Caenorhabditis elegans. Citation: Nature Cell Biology 1: 127-129 1999 Type: ARTICLE Genes: cav-1 cav-2 let-60 mek-2 mpk-1 Abstract: Small invaginations called caveolae are present on the surface of many cells and are a form of glycosphingolipid- and cholesterol-enriched microdomains or rafts in the plasma membrane. The main component of the caveolar coat is caveolin-1 (refs 3,4), a membrane protein of relative molecular mass (Mr) 21,000 (21K), which binds cholesterol and can form high-molecular-mass homo-oligomers resistant to sodium dodecyl sulphate (SDS). Caveolin-1 has been implicated in signal transduction, but its function remains unclear; whereas overactivation of the p42/44 MAP-kinase cascade was observed after downregulation of caveolin-1 (ref. 8), integrin-mediated activation of the Ras/extracellular-signal regulated kinase (ERK) pathway or conversion of prostate cancer cells to an androgen-insensitive phenotype required expression of caveolin-1. To resolve the function of caveolin-1 in intact animals, we analysed caveolin-1 and glycosphingolipid/cholesterol-enriched rafts during the development of the nematode Caenorhabditis elegans. We show that C. elegans caveolin-1 (CAV-1) is expressed in the adult germ line and during embryonic development, and that CAV-1 is essential for Ras/MAP-kinase-dependent progression through the meiotic cell cycle. The function of CAV-1 is dependent on its association with cholesterol-rich membrane microdomains, providing a link between the membrane composition of germ cells and meiotic progression. Our results demonstrate that caveolin-1 and cholesterol-rich microdomains have an essential role in signal transduction in vivo and suggest a model for meiotic progression in the C. elegans germ line. ------------------- Key: 3591 Medline: Authors: Guan KL;Han M Title: A G-protein signaling network mediated by an RGS protein. Citation: Genes & Development 13: 1763-1767 1999 Type: ARTICLE Genes: eat-16 egl-10 egl-30 goa-1 sag-1 Abstract: A wide variety of extracellular stimuli induce signal transduction through receptors coupled to heterotrimeric G proteins, which consist of alpha, beta, and gamma subunits (Gilman 1987). The G alpha subunit has guanine nucleotide binding and GTP hydrolysis activities. Based on function and amino acid sequence homology, the Galpha, G alph i/o, G alpha q, and G alpha 12 (Simon et al. 1991; Hepler and Gilman 1992). As exemplified by the responsiveness of our five senses to environmental stimuli, signaling mediated by trimeric G proteins is often extremely rapid and transient. A key step in achieving such a raid response is the ability of the G alpha subunit to switch between it GDP- and GTP-bound forms. The nucleotide binding state of G alpha is regulated at both the GDP dissociation and GTP hydrolysis steps. Stimulation of receptors by agonists leads to a conformational change in the receptors which can function as a guanine nucleotide exchange factor to stimulate a rapid dissociation of GDP from the inactive G alpha. The nucleotide-free G alpha is then available to bind GTP, leading to the dissociation of G alpha from the G beta gamma heterodimer. Both the G alpha and G beat gamma subunits can interact with and regulate downstream effectors that include adenylyl cyclase, phospholipase C, and ion channels (Gilman 1987; Birnbaumer 1992). ------------------- Key: 3592 Medline: 99350321 Authors: Hajdu-Cronin YM;Chen WJ;Patikoglou G;Koelle MR;Sternberg PW Title: Antagonism between G(o)a and G(q)a in Caenorhabditis elegans: the RGS protein EAT-16 is necessary for G(o)a signaling and regulates G(q)a activity. Citation: Genes & Development 13: 1780-1793 1999 Type: ARTICLE Genes: eat-16 egl-30 goa-1 sag-1 meDf6 qDf9 yDp13 Abstract: To elucidate the cellular role of the heterotrimeric G protein G(o), we have taken a molecular genetic approach in Caenorhabditis elegans. We screened for suppressors of activated GOA-1 (G(o)alpha) that do not simply decrease its expression and found mutations in only two genes, sag-1 and eat-16. Animals defective in either gene display a hyperactive phenotype similar to that of goa-1 loss-of-function mutants. Double-mutant analysis indicates that both sag-1 and eat-16 act downstream of, or parallel to, G(o)alpha and negatively regulate EGL-30 (G(q)alpha) signaling. eat-16 encodes a regulator of G protein signaling (RGS) most similar to the mammalian RGS7 and RGS9 proteins and can inhibit endogenous mammalian G(q)/G(11) in COS-7 cells. Animals defective in both sag-1 and eat-16 are inviable, but reducing function in eg1-30 restores viability, indicating that the lethality of the eat-16; sag-1 double mutant is due to excessive G(q)alpha activity. Analysis of these mutations indicates that the G(o) and G(q) pathways function antagonistically in C. elegans, and that G(o)alpha. negatively regulates the G(q) pathway, possibly via EAT-16 or SAG-1. We propose that a major cellular role of G(o) is to antagonize signaling by G(q). ------------------- Key: 3593 Medline: 99350322 Authors: Sagasti A;Hobert O;Troemel ER;Ruvkun G;Bargmann CI Title: Alternative olfactory neuron fates are specified by the LIM homeobox gene lim-4. Citation: Genes & Development 13: 1794-1806 1999 Type: ARTICLE Genes: ceh-14 lim-4 lim-6 lim-7 lin-11 mec-3 odr-3 odr-7 odr-10 str-1 str-2 ttx-3 Abstract: The Caenorhabditis elegans AWA, AWB, and AWC olfactory neurons are each required for the recognition of a specific subset of volatile odorants. lim-4 mutants express an AWC reporter gene inappropriately in the AWE olfactory neurons and fail to express an AWE reporter gene. The AWE cells are morphologically transformed toward an AWC fate in lim-4 mutants, adopting cilia and axon morphologies characteristic of AWC. AWE function is also transformed in these mutants: Rather than mediating the repulsive behavioral responses appropriate for AWE, the AWE neurons mediate attractive responses, like AWC. LIM-4 is a predicted LIM homeobox gene that is expressed in AWE and a few other head neurons. Ectopic expression of LIM-4 in the AWC neuron pair is sufficient to force those cells to adopt an AWE fate. The AWA nuclear hormone receptor ODR-7 described previously also represses AWC genes, as well as inducing AWA genes. We propose that the LIM-4 and ODR-7 transcription factors function to diversify C. elegans olfactory neuron identities, driving them from an AWC-like state into alternative fates. ------------------- Key: 3594 Medline: 10412978 Authors: Sym M;Robinson N;Kenyon C Title: MIG-13 positions migrating cells along the anteroposterior body axis of C. elegans. Citation: Cell 98: 26-36 1999 Type: ARTICLE Genes: egl-20 lin-39 mab-5 mig-13 syDf1 Abstract: The C. elegans Q neuroblasts and their descendants migrate along the anteroposterior (A/P) body axis to positions that are not associated with any obvious landmarks. We find that a novel protein, MIG-13, is required to position these cells correctly. MIG-13 is a transmembrane protein whose expression is restricted to the anterior and central body regions by Hox gene activity. MIG-13 functions non-cell autonomously within these regions to promote migration toward the anterior: loss of mig-13 activity shifts the Q descendants toward the posterior, whereas increasing the level of MIG-13 shifts them anteriorly in a dose-dependent manner. Our findings suggest that MIG-13 is a component of a global A/P migration system, and that the level of MIG-13 determines where along the body axis these migrating cells stop. ------------------- Key: 3595 Medline: 99318131 Authors: Ishitani T;Ninomiya-Tsuji J;Nagai SI;Nishita M;Meneghini M;Barker N;Waterman M;Bowerman B;Clevers H;Shibuya H;Matsumoto K Title: The TAK1-NLK-MAPK-related pathway antagonizes signalling between B-catenin and transcription factor TCF. Citation: Nature 399: 798-802 1999 Type: ARTICLE Genes: lit-1 mom-2 mom-4 mom-5 pop-1 tap-1 wrm-1 Abstract: The Wnt signalling pathway regulates many developmental processes through a complex of beta-catenin and the T-cell factor/lymphoid enhancer factor (TCF/LEF) family of high-mobility-group transcription factors. Wnt stabilizes cytosolic beta-catenin, which then binds to TCF and activates gene transcription. This signalling cascade is conserved in vertebrates, Drosophila and Caenorhabditis elegans. In C. elegans, the proteins MOM-4 and LIT-1 regulate Wnt signalling to polarize responding cells during embryogenesis. MOM-4 and LIT-1 are homologous to TAK1 (a kinase activated by transforming growth factor-beta) mitogen-activated protein-kinase-kinase kinase (MAP3K) and MAP kinase (MAPK)-related NEMO-like kinase (NLK), respectively, in mammalian cells. These results raise the possibility that TAK1 and NLK are also involved in Wnt signalling in mammalian cells. Here we show that TAK1 activation stimulates NLK activity and downregulates transcriptional activation mediated by beta-catenin and TCF. Injection of NLK suppresses the induction of axis duplication by microinjected beta-catenin in Xenopus embryos. NLK phosphorylates TCF/LE ------------------- Key: 3596 Medline: 10559891 Authors: Sternberg PW;Schmid SL Title: Caveolin, cholesterol and Ras signalling. Citation: Nature Cell Biology 1: E35-E37 1999 Type: REVIEW Genes: cav-1 Abstract: Studies on the role of cholesterol- and caveolin-rich membrane microdomains in localizing Ras to the plasma membrane and enabling its signalling activity reveal intriguing differences both between mammalian H-Ras and K-Ras and between requirements for Ras signalling in mammalian and nematode cells. ------------------- Key: 3597 Medline: 99318835 Authors: Carmi I;Meyer BJ Title: The primary sex determination signal of Caenorhabditis elegans. Citation: Genetics 152: 990-1015 1999 Type: ARTICLE Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 fem-1 fem-2 fem-3 fox-1 her-1 mix-1 sdc-1 sdc-2 sdc-3 sex-1 tra-1 tra-2 tra-3 xol-1 meDf5 meDf6 yDf17 yDf19 yDf20 mnDp66 stDp2 yDp13 yDp14 Abstract: An X chromosome counting process determines sex in Caenorhabditis elegans. The dose of X chromosomes is translated into sexual fate by a set of X-linked genes that together control the activity of the sex-determination and dosage-compensation switch gene, xol-1. The double dose of X elements in XX animals represses xol-1 expression, promoting the hermaphrodite fate, while the single dose of X elements in XO animals permits high xol-1 expression at two levels, transcriptional and post-transcriptional. The two molecularly characterized elements include an RNA binding protein and a nuclear hormone receptor homolog. Here we explore the roles of the two mechanisms of xol-1 repression and further investigate how the combined dose of X signal elements ensures correct, sex-specific expression of xol-1. By studying the effects of increases and decreases in X signal element dose on male and hermaphrodite fate, we demonstrate that signal elements repress xol-1 cumulatively, such that full repression of xol-1 in XX animals results from the combined effect of individual elements. Complete transformation from the hermaphrodite to the male fate requires a decrease in the dose of all four elements, from two copies to one. We show that both mechanisms of xol-1 repression are essential and act synergistically to keep xol-1 levels low in XX animals. However, increasing repression by one mechanism can compensate for loss of the other, demonstrating that each mechanism can exert significant xol-1 repression on its own. Finally, we present evidence suggesting that xol-1 activity can be set at intermediate levels in response to ------------------- Key: 3598 Medline: 99318834 Authors: Nishiwaki K Title: Mutations affecting symmetrical migration of distal tip cells in Caenorhabditis elegans. Citation: Genetics 152: 985-997 1999 Type: ARTICLE Genes: mig-14 mig-17 mig-18 mig-19 mig-20 vab-3 arDf1 ctDf1 eDf2 nDf19 tDf8 Abstract: The rotational symmetry of the Caenorhabditis elegans gonad arms is generated by the symmetrical migration of two distal tip cells (DTCs), located on the anterior and posterior ends of the gonad primordium. Mutations that cause asymmetrical migration of the two DTCs were isolated. All seven mutations were recessive and assigned to six different complementation groups. vab-3(k121) and vab-3(k143) affected anterior DTC migration more frequently than posterior, although null mutants showed no bias. The other five mutations, mig-14(k124), mig-17(k113), mig-18(k140), mig-19(142), and mig-20(k148), affected posterior DTC migration more frequently than anterior. These observations imply that the migration of each DTC is regulated differently. mg-14 and mig-19 also affected the migration of other cells in the posterior body region. Four distinct types of DTC migration abnormalities were defined on the basis of the mutant phenotypes. vab-3; mig-14 double mutants exhibited the types of DTC migration defects seen for vab-3 single mutants. Combination of mig-17 and mig-18 or mig-19, which are characterized by the same types of posterior DTC migration defects, exhibited strong enhancement of anterior DTC migration defects, suggesting that they affect the same of parallel pathways regulating ------------------- Key: 3599 Medline: 99284766 Authors: Hobert O;Ruvkun G Title: Pax genes in Caenorhabditis elegans - A new twist. Citation: Trends in Genetics 15: 214-216 1999 Type: ARTICLE Genes: egl-38 vab-3 Abstract: The Pax genes encode transcription factors that control a wide variety of developmental events in taxa as diverse as vertebrates, arthopods and nematodes. These genes are characterized by the presence of a highly conserved DNA-binding domain, the Paired domain. Based on sequence similarities within the Paired domain, as well as the presence or absence of additional motifs (such as the homeodomain or octapeptide), PAX proteins can be subdivided into specific families. ------------------- Key: 3600 Medline: 10397769 Authors: Nonet ML;Holgado AM;Brewer F;Serpe CJ;Norbeck BA;Holleran J;Wei L;Hartwieg E;Jorgensen EM;Alfonso A Title: UNC-11, a Caenorhabditis elegans AP180 homologue, regulates the size and protein composition of synaptic vesicles. Citation: Molecular Biology of the Cell 10: 2343-2360 1999 Type: ARTICLE Genes: unc-11 unc-104 Abstract: See CGC #3688 for correction. The unc-11 gene of Caenorhabditis elegans encodes multiple isoforms of a protein homologous to the mammalian brain-specific clathrin-adaptor protein AP180. The UNC-11 protein is expressed at high levels in the nervous system and at lower levels in other tissues. Ln neurons, UNC-11 is enriched at presynaptic terminals but is also present in cell bodies. unc-11 mutants are defective in two aspects of synaptic vesicle biogenesis. First, the SNARE protein synaptobrevin is mislocalized, no longer being exclusively localized to synaptic vesicles. The reduction of synaptobrevin at synaptic vesicles is the probable cause of the reduced neurotransmitter release observed in these mutants. Second, unc-11 mutants accumulate large vesicles at synapses. We propose that the UNC-11 protein mediates two functions during synaptic vesicle biogenesis: it recruits synaptobrevin to synaptic vesicle membranes and it regulates the size of the budded vesicle during clathrin coat assembly. ------------------- Key: 3601 Medline: 99360023 Authors: Renukappa T;Roos G;Klaiber I;Vogler B;Kraus W Title: Application of high-performance liquid chromatography coupled to nuclear magnetic resonance spectrometry, mass spectrometry and bioassay for the determination of active saponins from Bacopa monniera W Citation: Journal of Chromatography 847: 109-116 1999 Type: ARTICLE Genes: Abstract: Reversed-phase high-performance liquid chromatographic separation coupled to (structurally informative) spectroscopic methods Like NMR and MS and an efficient bioassay have been used to determine the active compounds from a crude fraction of Bacopa monniera. The fraction containing a mixture of saponins with closely related structures was found to show a significant anthelmintic activity against Caenorhabditis elegans (used as a model test organism for determining anthelmintic activity). The activity was correlated to two dammarane type triterpenoidal saponins containing at least three sugar units. The optimization of separation for 1 mg of the crude sample on column and the sensitivity of on-flow one- and two-dimensional NMR experiments to the high-molecular-mass compounds (M-r 890-930) has been demonstrated. ------------------- Key: 3602 Medline: 10341209 Authors: Daigle SN;Creutz CE Title: Transcription, biochemistry and localization of nematode annexins. Citation: Journal of Cell Science 112: 1901-1913 1999 Type: ARTICLE Genes: nex-1 nex-2 nex-3 nex-4 Abstract: The transcription of three annexin genes in the nematode, Caenorhabditis elegans, was detected by reverse transcriptase/polymerase chain reaction amplification of messenger RNAs, The highest level of expression was from the nex-1 gene, with lower levels detected for the nex-2 and nex-3 genes. The expression of nex-1 was reduced in the Dauer larval stage relative to the other annexins, correlating with the absence of the spermathecal valves, a major site of nex-1 protein localization. Recombinant nex-1 protein was expressed in yeast, isolated by calcium-dependent binding to acidic phospholipids, and its membrane binding and aggregating activities characterized using bovine chromaffin granules as a representative intracellular substrate. Binding to granule membranes was promoted by calcium with half-maximal binding seen at 630 mu M calcium. Chromaffin granule aggregation was similarly promoted by the nex-1 protein at 630 mu M calcium. This low sensitivity to calcium suggests the annexin can only be activated in vivo near the plasma membrane or other sources of calcium, Sequences including the nex-1 promoter were fused to the gene for green fluorescent protein and this construct was introduced into nematodes by microinjection. Examination of transgenic offspring revealed specific nex-1 promoter activity in the pharynx, the hypodermal cells, the vulva, and the spermathecal valve, locations in which the annexin may function in collagen secretion/deposition and membrane-membrane interactions. A sensitive anti-nex-1 antibody labelled with rhodamine was injected into body cavities of the nematode but did not detect extracellular nex-1 protein. Therefore, this annexin is apparently cytosolic and may function on the cytoplasmic side of the plasma membrane of the spermathecal valve to chaperon the folding of this membrane during the opening and closing of the valve. ------------------- Key: 3603 Medline: Authors: Roehrig C;Rankin CH Title: Dymods: A framework for modularizing dynamical neuronal structures. Citation: Neurocomputing 26-7: 831-836 1999 Type: ARTICLE Genes: Abstract: We present an informal framework for modularizing dynamical systems so that they can be recombined to form larger dynamical structures. We use this framework to give a cellular account of how network dynamics might be responsible for the maintenance of reversal locomotion in the nematode C. elegans. Three nonlinear dynamical modules were constructed using physiologically realistic cellular models and they were assembled to form the complete circuit. Finally, we present a real-time, distributed implementation framework that allows dynamical modules to be implemented independently an multiple computer systems and easily interconnected. ------------------- Key: 3604 Medline: 99332308 Authors: Terami H;Williams BD;Kitamura S;Sakube Y;Matsumoto S;Doi S;Obinata T;Kagawa H Title: Genomic organization, expression, and analysis of the troponin C gene pat-10 of Caenorhabditis elegans. Citation: Journal of Cell Biology 146: 193-202 1999 Type: ARTICLE Genes: hlh-1 pat-10 tnc-1 Abstract: We have cloned and characterized the troponin C gene, pat-10 of the nematode Caenorhabditis elegans. At the amino acid level nematode troponin C is most similar to troponin C of Drosophila (45% identity) and cardiac troponin C of vertebrates. Expression studies demonstrate that this troponin is expressed in body wall muscle throughout the life of the animal. Later, vulval muscles and anal muscles also express this troponin C isoform. The structural gene for this troponin is pat-10 and mutations in this gene lead to animals that arrest as twofold paralyzed embryos late in development. We have sequenced two of the mutations in pat-10 and both had identical two mutations in the gene; one changes D64 to N and the other changes W153 to a termination site. The missense alteration affects a calcium-binding site and eliminates calcium binding, whereas the second mutation eliminates binding to troponin I. These combined biochemical and in vivo studies of mutant animals demonstrate that this troponin is essential for proper muscle function during development. ------------------- Key: 3605 Medline: 99326500 Authors: Agostoni E;Gobessi S;Brancolini C;Schneider C Title: Identification and characterization of a new member of the gas3/PMP22 gene family in C. elegans. Citation: Gene 234: 267-274 1999 Type: ARTICLE Genes: Abstract: The Gas3/PMP22 protein family is characterized by tetraspan transmembrane proteins. The gas3/PMP22 gene is highly expressed in Schwann cells of the peripheral nervous system, and different alterations of this gene are associated with hereditary demyelinating neuropathies, such as the Charcot-Marie-Tooth type 1A, the Dejerine-Sottas syndrome and the Hereditary Liability to Pressure Palsies (HNPP). Here, we report on the identification of at least one member of the Gas3/PMP22 family in the nematode C. elegans (C01C10.1b). C01C10.1b shares 36% of identical amino acids with the human Gas3/PMP22 and is characterized by four hydrophobic putative transmembrane domains. It lacks the typical N-linked glycosylation consensus in the first extracellular loop. C01C10.1b is transcribed as an operon downstream to the gene C01C10. In, which encodes for a putative tetraspan protein with less conserved homology with the Gas3/PMP22 family. Interestingly, C01C10.1a contains three N-glycosylation sites at the C-terminus. Both genes are expressed in different nematode developmental stages and in the adults. The characterization of one member of the gas3/PMP22 family in C. elegans gives the opportunity to use this model organism to investigate the role of gas3/PMP22 in the regulation of cell proliferation and differentiation and its relation to the hereditary neurodegenerative diseases in humans. ------------------- Key: 3606 Medline: 99359386 Authors: Tanaka T;Izuwa S;Tanaka K;Yamamoto D;Takimoto T;Matsuura F;Satouchi K Title: Biosynthesis of 1,2-dieicosapentaenoyl-sn-glycero-3-phosphocholine in Caenorhabditis elegans. Citation: European Journal of Biochemistry 263: 189-194 1999 Type: ARTICLE Genes: Abstract: Previously, we showed that lowering the growth temperature increased the level of eicosapentaenoic acid (EPA) in the phosphatidylcholine (PtdCho) of Caenorhabditis elegans. In this study, we investigated the molecular species composition of PtdCho of C. elegans, with an emphasis on EPA-containing species. C. elegans contained a substantial amount of 1,2-dipolyunsaturated fatty acid-containing PtdCho (1,2-diPUFA-PtdCho) species, such as arachidonic acid/EPA and EPA/EPA, which are unusual phospholipids in higher animals. The EPA/EPA-PtdCho content was significantly increased in C. elegans grown at a low temperature. To examine the possibility that the acyltransferase activity involved in the remodeling of phospholipids accounts for the production of 1,2-diPUFA-PtdCho, we investigated the substrate specificity of this enzyme in C. elegans and found that it did not exhibit a preference for saturated fatty acid for acylation to the sn-l position of PtdCho. The efficacy of the esterification of EPA to the sn-l position was almost equal to that of stearic acid. The lack of preference for a saturated fatty acid for acylation to the sn-l position of PtdCho is thought to result in the existence of the unusual ------------------- Key: 3607 Medline: 99321749 Authors: Kawasaki M;Hisamoto N;Iino Y;Yamamoto M;Ninomiya-Tsuji J;Matsumoto K Title: A Caenorhabditis elegans JNK signal transduction pathway regulates coordinated movement via type-D GABAergic motor neurons. Citation: EMBO Journal 18: 3604-3615 1999 Type: ARTICLE Genes: jkk-1 jnk-1 unc-25 Abstract: The c-Jun N-terminal kinase (JNK) of the MAP kinase superfamily is activated in response to a variety of cellular stresses and is involved in apoptosis in neurons. However, the roles of the JNK signaling pathway in the nervous system are unknown. The genes for the Caenorhabditis elegans homolog of JNK, JNK-1, and its direct activator, JRK-1, were isolated based on their abilities to function in the Hog1 MAP kinase pathway in yeast. JKK-1 is a member of the MAP kinase kinase superfamily and functions as a specific activator of JNK. Both jnk-1 and jkk-1 are expressed in most neurons. jkk-1 null mutant animals exhibit defects in locomotion that can be rescued by the conditional expression of JKK-1 in mutant adults, suggesting that the defect is not due to a developmental error. Furthermore, ectopic expression of JKK-1 in type-D motor neurons is sufficient to rescue the movement defect. Thus, the C.elegans JNK pathway functions in type-D GABAergic motor neurons and thereby modulates ------------------- Key: 3608 Medline: 10421575 Authors: Jantsch-Plunger V;Glotzer M Title: Depletion of syntaxins in the early Caenorhabditis elegans embryo reveals a role for membrane fusion events in cytokinesis. Citation: Current Biology 9: 738-745 1999 Type: ARTICLE Genes: syn-1 syn-2 syn-3 syn-4 unc-64 Abstract: Background: During cytokinesis, the plasma membrane of the parent cell is resolved into the two plasma membranes of the daughter cells. Membrane fusion events mediated by the machinery that participates in intracellular vesicle trafficking might contribute to this process. Two classes of molecules that are required for membrane fusion are the t-SNAREs and the v-SNAREs. The t-SNAREs (syntaxins) comprise a multi-gene family that has been suggested to mediate, at least in part, selective membrane fusion events in the cell. Results: We have analyzed the genome of Caenorhabditis elegans and identified eight syntaxin genes. RNA-mediated interference (RNAi) was used to produce embryos deficient in individual syntaxins and these embryos were phenotypically characterized. Embryos deficient in one syntaxin, Syn-4, became multinucleate because of defects in karyomere fusion and cytokinesis. Syn-4, localized both to ingressing cleavage furrows and to punctate structures surrounding nuclei as they reformed during interphase. Conclusions: Our analyses indicate; that both cytokinesis and reformation of the nuclear envelope are dependent on SNARE-mediated membrane fusion. ------------------- Key: 3609 Medline: 99333383 Authors: Fujita M;Kawano T;Ohta A;Sakamoto H Title: Neuronal expression of a Caenorhabditis elegans elav-like gene and the effect of its ectopic expression. Citation: Biochemical and Biophysical Research Communications 260: 646-652 1999 Type: ARTICLE Genes: elr-1 myo-2 Abstract: We examined the expression of a Caenorhabditis elegans (C. elegans) elav-like gene, which we designated elr-1. The elr-1 gene encodes a predicted 456-amino-acid protein containing three putative RNA-binding domains and belongs to the ELAV family, which is functionally involved in neuronal differentiation. Northern blot analysis suggested that the levels of elr-1 mRNA are regulated developmentally. A elr-1::gfp reporter gene under the control of the elr-1 promoter was expressed specifically in the ring ganglia near the nerve ring, the ventral nerve cord (VNC),and the pre-anal and lumbar ganglia. In the VNC, GFP-positive cells were shown to be acetylcholine-producing motor neurons which increased in number as development proceeded, suggesting that elr-1 is expressed in mature neurons. Ectopic expression of ELR-1 protein at the L4 larval and adult stages, but not earlier stages, caused irreversible death, accompanied by uncoordinated movement (Unc), clear (Clr), and egg-laying defective (Egl) phenotypes, which are often observed in mutants with neuronal defects. These results suggest that ELR-1 may have important functions in specific mature neuron in C. ------------------- Key: 3610 Medline: 99342707 Authors: Wang ZW;Kunkel MT;Wei A;Butler A;Salkoff L Title: Genomic organization of nematode 4TM K+ channels. Citation: Annals of the New York Academy of Sciences 868: 286-303 Type: ARTICLE Genes: Abstract: As many as 50 genes in the C. elegans genome may encode K+ channels belonging to the novel structural class of two-pore (4TM) channels. Many 4TM channels can be grouped into channel subfamilies. We analyzed 4TM channels in C. elegans using methods made possible by having complete genomic sequence. Two genes were chosen for comprehensive analysis, n2P16 and n2P17. By comparing the pattern of conservation in genomic DNA sequences between C. elegans and a closely related species, C. briggsae, we were able to identify all coding regions and predict the gene structure for these two genes. Given the extent of the 4TM channel family, we were surprised to discover that n2P17 produced at least six alternative transcripts encoding a constant central region and variable amino- and carboxyl-termini. Blocks of highly conserved DNA sequences in noncoding regions were also apparent and most likely confer important regulatory functions. The interspecies comparison of the deduced channel proteins revealed that the extracellular loop between M1 and P1 is an apparent hot spot for evolutionary change in both channels. This contrasts with the membrane-spanning domains that are highly conserved. Analysis of intron positions for 36 channels revealed that introns are frequently present at an identical position within the pore region, but very few are located in membrane-spanning domains. ------------------- Key: 3611 Medline: 10409742 Authors: Stewart S;Sundaram M;Zhang YP;Lee JY;Han M;Guan KL Title: Kinase suppressor of Ras forms a multiprotein signaling complex and modulates MEK localization. Citation: Molecular and Cellular Biology 19: 5523-5534 1999 Type: ARTICLE Genes: ksr-1 let-60 mek-1 mek-2 Abstract: Genetic screens for modifiers of activated Ras phenotypes have identified a novel protein, kinase suppressor of Ras (KSR), which shares significant sequence homology with Raf family protein kinases. Studies using Drosophila melanogaster and Caenorhabditis elegans predict that KSR positively regulates Ras signaling; however, the function of mammalian KSR is not well understood. We show here that two predicted kinase-dead mutants of KSR retain the ability to complement ksr-1 loss-of-function alleles in C. elegans, suggesting that KSR may have physiological, kinase-independent functions. Furthermore, we observe that murine KSR forms a multimolecular signaling complex in human embryonic kidney 293T cells composed of HSP90, HSP70, HSP68, p50(CDC37), MEK1, MEK2 14-3-3, and several other, unidentified proteins. Treatment of cells with geldanamycin, an inhibitor of HSP90, decreases the half-life of KSR, suggesting that HSPs may serve to stabilize KSR Both nematode and mammalian KSRs are capable of binding to MEKs, and three-point mutants of KSR, corresponding to C. elegans loss-of-function alleles, are specifically compromised in MEK binding. KSR did not alter MEK activity or activation. However, KSR-MEK binding shifts the apparent molecular mass of MEK from 44 to >700 kDa, and this results in the appearance of MEK in membrane-associated fractions. Together, these results suggest that KSR may act as a scaffolding protein for the Ras-mitogen-activated protein kinase pathway. ------------------- Key: 3612 Medline: 99347893 Authors: Mayraz G;Shamir R Title: Construction of physical maps from oligonucleotide fingerprints data. Citation: Journal of Computational Biology 6: 237-252 1999 Type: ARTICLE Genes: Abstract: A new algorithm for the construction of physical maps from hybridization fingerprints of short oligonucleotide probes has been developed. Extensive simulations in high-noise scenarios show that the algorithm produces an essentially completely correct map in over 95% of trials. Tests for the influence of specific experimental parameters demonstrate that the algorithm is robust to both false positive and false negative experimental errors. The algorithm was also tested in simulations using real DNA sequences of C. elegans, E. coli, S. cerevisiae, and H. sapiens. To overcome the non-randomness of probe frequencies in these sequences, probes were preselected based on sequence statistics and a screening process of the hybridization data was developed. With these modifications, the algorithm produced very encouraging results. ------------------- Key: 3613 Medline: 10403845 Authors: Tao W;Walke DW;Morgan JI Title: Oligomerized Ced-4 kills budding yeast through a caspase-independent mechanism. Citation: Biochemical and Biophysical Research Communications 260: 799-805 1999 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: In Caenorhabdtis elegans, Ced-3, Ced-4, and Ced-9 are components of a cell suicide program. Ced-4 facilitates the proteolytic activation of the caspase, Ced-3, while Ced-9 opposes Ced-3/Ced-4 killing. To examine the interactions among these proteins they were expressed in Saccharomyces cerevisiae. Ced-3 and Ced-4 were lethal when expressed alone, revealing an intrinsic Ced-4 killing activity. Coexpression of Ced-9 blocked Ced-3- and Ced-4-induced killing, showing Ced-9 can independently antagonize the action of both proteins. Ced-3- but not Ced-4-toxicity was attenuated by coexpression of the caspase inhibitors, CrmA and p35. Thus, besides its Ced-3- and Ced-9-dependent action in C. elegans, Ced-4 has an additional Ced-9-dependent, Ced-3-independent killing mechanism in yeast. Two-hybrid analysis confirmed that Ced-4 formed heteromers with Ced-9. In addition, Ced-4 formed homomers and mutation of its nucleoside triphosphate binding motif eliminated both homomerization and cell killing. We suggest the caspase-independent lethality of Ced-4 in yeast is mediated by a Ced-4 homomer. ------------------- Key: 3614 Medline: Authors: Bamburg JR;McGough A;Ono S Title: Putting a new twist on actin: ADF/cofilins modulate actin dynamics. Citation: Trends in Cell Biology 9: 364-370 1999 Type: REVIEW Genes: sup-12 unc-60 Abstract: The actin-depolymerizing factor (ADF)/cofilins are a family of essential actin regulatory proteins, ubiquitous among eukaryotes, that enhance the turnover of actin by regulating the rate constants of polymerization and depolmerization at filament ends, changing the twist of the filament and severing actin filaments. Genetic and cell-biological studies have shown that an ADF/cofilin is required to drive the high turnover of the actin cytoskeleton observed in vivo. The activity of ADF/cofilin is regulated by a variety of mechanisms, including specific phosphorylation and dephosphorylation. This review addresses aspects of ADF/cofilin structure, dynamic, ------------------- Key: 3615 Medline: Authors: Vancoppenolle B;Borgonie G;Coomans A Title: Generation time of some free-living nematodes cultured at three temperatures. Citation: Nematology 1: 15-18 1999 Type: ARTICLE Genes: Abstract: Generation times of 21 species of free-living nematodes were determined at three different temperatures. All 21 species are Secernentea, including Cephalobina, Rhabditina, and Diplogastrida, and can be cultured in laboratory conditions. Considerable differences in generation time and optimal temperatures were found among species and ------------------- Key: 3616 Medline: 99310810 Authors: Landesman Y;White TW;Starich TA;Shaw JE;Goodenough DA;Paul DL Title: Innexin-3 forms connexin-like intercellular channels. Citation: Journal of Cell Science 112: 2391-2396 1999 Type: ARTICLE Genes: eat-5 inx-3 Abstract: Innexins comprise a large family of genes that are believed to encode invertebrate gap junction channel-forming proteins. However, only two Drosophila innexins have been directly tested for the ability to form intercellular channels and only one of those was active. Here we tested the ability of Caenorhabditis elegans family members INX-3 and EAT-5 to form intercellular channels between paired Xenopus oocytes. We show that expression of INX-3 but not EAT-5, induces electrical coupling between the oocyte pairs. In addition, analysis of INX-3 voltage and pH gating reveals a striking degree of conservation in the functional properties of connexin and innnexin channels, These data strongly support the idea that innexin genes encode intercellular channels. ------------------- Key: 3617 Medline: 99350222 Authors: Hall DH;Winfrey VP;Blaeuer G;Hoffman LH;Furuta T;Rose KL;Hobert O;Greenstein D Title: Ultrastructural features of the adult hermaphrodite gonad of Caenorhabditis elegans: Relations between the germ line and soma. Citation: Developmental Biology 212: 101-123 1999 Type: ARTICLE Genes: ceh-18 eat-5 epi-1 epi-2 glp-1 lag-2 let-23 lfe-1 lfe-2 lim-7 pat-2 pat-3 unc-7 unc-52 vit-2 Abstract: Genetic and embryological experiments have established the Caenorhabditis elegans adult hermaphrodite gonad as a paradigm for studying the control of germline development and the role of soma-germline interactions. We describe ultrastructural features relating to essential germline events and the soma-germline interactions upon which they depend, as revealed by electron and fluorescence microscopy. Gap junctions were observed between oocytes and proximal gonadal sheath cells that contract to ovulate the oocyte. These gap junctions must be evanescent since individual oocytes lose contact with sheath cells when they are ovulated. In addition, proximal sheath cells are coupled to each other by gap junctions. Within proximal sheath cells, actin/myosin bundles are anchored to the plasma membrane at plaque-like structures we have termed hemi-adherens junctions, which in turn are closely associated with the gonadal basal lamina. Gap junctions and hemi-adherens junctions are likely to function in the coordinated series of contractions required to ovulate the mature oocyte. Proximal sheath cells are fenestrated with multiple small pores forming conduits from the gonadal basal lamina to the surface of the oocyte, passing through the sheath eel. In most instances where pores occur, extracellular yolk particles penetrate the gonadal basal lamina to directly touch the underlying oocytes. Membrane-bounded yolk granules were generally not found in the sheath cytoplasm by either electron microscopy or fluorescence microscopy. Electron microscopic immunocytochemistry was used to confirm and characterize the appearance of yolk protein in cytoplasmic organelles within the oocyte and in free particles in the pseudocoelom. The primary route of yolk transport apparently proceeds from the intestine into the pseudocoelom, then through sheath pores to the surface of the oocyte, where endocytosis occurs. Scanning electron microscopy was used to directly visualize the distal tip cell which extends tentacle-like processes that directly contact distal germ cells. These distal tip cell processes are likely to play a critical role in promoting germline mitosis. Scanning electron microscopy also revealed thin filopodia extending from the distal sheath cells. Distal sheath filopodia were also visualized using a green fluorescent protein reporter gene fusion and confocal ------------------- Key: 3618 Medline: 99350215 Authors: Wang M;Sternberg PW Title: Competence and commitment of Caenorhabditis elegans vulval precursor cells. Citation: Developmental Biology 212: 12-24 1999 Type: ARTICLE Genes: egl-17 lin-3 lin-12 Abstract: Multipotent Caenorhabditis elegans vulval precursor cells (VPCs) choose among three fates (1 degrees, 2 degrees, and 3 degrees) in response to two intercellular signals: the EGF family growth factor LIN-3 induces 1 degrees fates at high levels and 2 degrees fates at low levels; and a signal via the receptor LIN-12 induces 2 degrees fates. If the level of LIN-3 signal is reduced by a lin-3 hypomorphic mutation, the daughters of the WC closest to the anchor cell (AC), P6.p, are induced by the AC. By expressing LIN-3 as a function of time in LIN-3-deficient animals, we find that both VPCs and the daughters of VPCs are competent to respond to LIN-3, and VPC daughters lose competence after fusing with the hypodermis. We also demonstrate that the daughters of VPCs specified to be 2 degrees can respond to LIN-3, indicating that 2 degrees VPCs are not irreversibly committed. We propose that maintenance of WC competence after the first cell cycle and the prioritization of the 1 degrees fate help ensure that P6.p will become 1 degrees. This mechanism of competence regulation might have been maintained from ancestral nematode species that used induction both before and after VPC division and serves to maximize the probability that a functional vulva is formed. ------------------- Key: 3619 Medline: 10414952 Authors: Eastman C;Horvitz HR;Jin Y Title: Coordinated transcriptional regulation of the unc-25 glutamic acid decarboxylase and the unc-47 GABA vesicular transporter by the Caenorhabditis elegans UNC-30 homeodomain protein. Citation: Journal of Neuroscience 19: 6225-6234 1999 Type: ARTICLE Genes: Abstract: An important aspect of the specification of neuronal fate is the choice of neurotransmitter. In Caenorhabditis elegans the neurotransmitter GABA is synthesized by the UNC-25 glutamic acid decarboxylase (GAD) and packaged into synaptic vesicles by the UNC-47 transporter. Both unc-25 and unc-47 are expressed in 26 GABAergic neurons of five different types. Previously, we have identified that the unc-30 homeobox gene controls the fate of 19 type D GABAergic neurons. We report here that the UNC-30 homeodomain protein transcriptionally regulates the expression of unc-25 and unc-47 in the 19 type D neurons. UNC-30 bound to the unc-25 and unc-47 promoters sequence-specifically. Mutations in the UNC-30 binding sites of the unc-25 and unc-47 promoters abolished the expression of reporter genes in the D neurons. The ectopic expression of UNC-30 induced the ectopic expression of reporter genes driven by the wild-type unc-25 and unc-47 promoters. Our data establish a mechanism for cell type-specific transcriptional coregulation of genes required for the synthesis and packaging of the ------------------- Key: 3620 Medline: 99370052 Authors: Culetto E;Combes D;Fedon Y;Roig A;Toutant JP;Arpagaus M Title: Structure and promoter activity of the 5' flanking region of ace-1, the gene encoding acetylcholinesterase of class A in Caenorhabditis elegans. Citation: Journal of Molecular Biology 290: 951-966 1999 Type: ARTICLE Genes: ace-1 ace-2 ceh-22 hlh-1 Abstract: We report the structure and the functional activity of the promoter region of ace-1, the gene encoding acetylcholinesterase of class A in the nematode Caenorhabditis elegans. We found that ace-1 was trans-spliced to the SL1 spliced leader and that transcription was initiated at a cluster of multiple starts. There was neither a TATA nor a CAAT box at consensus distances from these starts. Interspecies sequence comparison of the 5' regions of ace-1 in C. elegans and in the related nematode Caenorhabditis briggsae identified four blocks of conserved sequences located within a sequence of 2.4 kilobases upstream from the initiator ATG. In vitro expression of CAT reporter genes in mammalian cells allowed the determination of a minimal promoter in the first 288 nucleotides. In phenotype rescue experiments in vivo, the ace-1 gene containing 2.4 kilobases of 5' flanking region of either C. elegans or C. briggsae was found to restore a coordinated mobility to the uncoordinated double mutants ace-1(-); ace-2(-) of C. elegans. This showed that the ace-1 promoter was contained in 2.4 kilobases of the 5' region, and indicated that cis-regulatory elements as well as coding sequences of ace-1 were functionally conserved between the two nematode species. The pattern of ace-1expression was established through microinjection of Green Fluorescent Protein reporter gene constructs and showed a major mesodermal expression. Deletion analysis showed that two of the four blocks of conserved sequences act as tissue-specific activators. The distal block is a mesodermal enhancer responsible for the expression in body wall muscle cells, anal sphincter and vulval muscle cells. Another block of conserved sequence directs expression in pharyngeal muscle cells pm5 and three pairs of cephalic sensory neurons. ------------------- Key: 3621 Medline: 99348283 Authors: Buettner C;Harney JW;Berry MJ Title: The Caeorhabditis elegans homologue of thioredoxin reductase contains a selenocysteine insertion sequence (SECIS) element that differs from mammalin SECIS elements but directs selenocysteine incorpora Citation: Journal of Biological Chemistry 274: 21598-21602 1999 Type: ARTICLE Genes: Abstract: Thioredoxin reductases (TRR) serve critical roles in maintaining cellular redox states. Two isoforms of TRR have been identified in mammals: both contain a penultimate selenocysteine residue that is essential for catalytic activity. A search of the genome of the invertebrate, Caenorhabditis elegans, reveals a gene highly homologous to mammalian TRR, with a TGA selenocysteine codon at the corresponding position. A selenocysteyl-tRNA was identified in this organism several years ago, but no selenoproteins have been identified experimentally. Herein we report the first identification of a C. elegans selenoprotein. By Se-75 labeling of C. elegans, one major band was identified, which migrated with the predicted mobility of the C. elegans TRR homologue. Western analysis with an antibody against human TRR provides strong evidence for identification of the C. elegans selenoprotein as a member of the TRR family. The 3'-untranslated region of this gene contains a selenocysteine insertion sequence (SECIS) element that deviates at one position from the previously invariant consensus "AUGA." Nonetheless, this element functions to direct selenocysteine incorporation in mammalian cells, suggesting conservation of the factors recognizing SECIS elements from worm to man. ------------------- Key: 3622 Medline: 99362791 Authors: Labouesse M;Mango SE Title: Patterning the C. elegans embryo - Moving beyond the cell lineage. Citation: Trends in Genetics 15: 307-313 1999 Type: REVIEW Genes: ceh-13 ceh-22 elt-1 elt-2 end-1 ges-1 hlh-1 hlh-2 lin-26 lit-1 myo-2 par-1 par-2 par-3 par-4 par-5 par-6 pha-1 pha-4 pop-1 skn-1 vab-7 Abstract: The Caenorhabditis elegans embryo undergoes a series of stereotyped cell cleavages that generates the organs and tissues necessary for an animal to survive. Here we review two models of embryonic patterning, one that is lineage-based, and one that focuses on domains of organ and tissue precursors. Our evolving view of C. elegans embryogenesis suggests that this animal develops by mechanisms that are qualitatively similar to those used by other animals. ------------------- Key: 3623 Medline: 99375914 Authors: de Gives PM;Davies KG;Clark SJ;Behnke JM Title: Predatory behaviour of trapping fungi against srf mutants of Caenorhabditis elegans and different plant and animal parasitic nematodes. Citation: Parasitology 119: 95-104 1999 Type: ARTICLE Genes: srf-2 srf-3 srf-5 Abstract: The initial infection process of nematode-trapping fungi is based on an interaction between the trapping structure of the fungus and the surface of the nematode cuticle. A bioassay was designed to investigate the predatory response of several isolates of nematode-trapping fungi against 3 mutants of Caenorhabditis elegans (AT6, AT10 and CL261), which have been reported to differ in the reaction of their cuticle to antibodies and lectins. The bioassay was also applied to infective larvae of animal (Haemonchus contortus, Teladorsagia (Ostertagia) circumcincta and Trichostrongylus axei) and plant (Meloidogyne spp.) parasitic nematodes. Differences in trapping ability were most marked in the first 24 h, and were density dependent. Although the isolate of Arthrobotrys responded very rapidly in the first 24 h, Duddingtonia flagrans was generally the most effective isolate and Monacrosporium responded relatively poorly throughout all experiments. All the fungi tested trapped the srf mutants of C. elegans more efficiently than the wild type, and there were differences between the different srf mutants of C. elegans. Differences in trapping ability were also observed between different isolates of D. flagrans; similarly, differences in trapping behaviour were observed not only amongst the different species of plant-parasitic nematodes, but also between the sheathed and exsheathed larvae of the ------------------- Key: 3624 Medline: 99357846 Authors: Shelton CA;Carter JC;Ellis GC;Bowerman B Title: The nonmuscle myosin regulatory light chain gene mlc-4 is required for cytokinesis, anterior-posterior polarity, and body morphology during Caenorhabditis elegans Citation: Journal of Cell Biology 146: 439-451 1999 Type: ARTICLE Genes: let-502 mlc-1 mlc-2 mlc-4 nmy-2 par-1 par-2 par-3 Abstract: Using RNA-mediated genetic interference in a phenotypic screen, we identified a conserved nonmuscle myosin II regulatory light chain gene in Caenorhabditis elegans, which we name mlc-4. Maternally supplied mlc-4 function is required for cytokinesis during both meiosis and mitosis and for establishment of anterior-posterior (a-p) asymmetries after fertilization. Reducing the function of mlc-4 or nmy-2, a nonmuscle myosin II gene, also leads to a loss of polarized cytoplasmic flow in the C. elegans zygote, supporting models in which cytoplasmic flow may be required to establish a-p differences. Germline P granule localization at the time of cytoplasmic flow is also lost in these embryos, although P granules do become localized to the posterior pole after the first mitosis. This result suggests that a mechanism other than cytoplasmic flow or mIc-4/nmy-2 activity can generate some a-p asymmetries in the C. elegans zygote. By isolating a deletion allele, we show that removing zygotic mlc-4 function results in an elongation phenotype during embryogenesis. An mlc-4/green fluorescent protein transgene is expressed in lateral rows of hypodermal cells and these cells fail to properly change shape in mlc-4 mutant animals during elongation. ------------------- Key: 3625 Medline: 99357789 Authors: Eto K;Takahashi N;Kimura Y;Masuho Y;Arai K;Muramatsu M;Tokumitsu H Title: Ca2+/calmodulin-dependent protein kinase cascade in Caenorhabditis elegans - Implication in transcriptional activation. Citation: Journal of Biological Chemistry 274: 22556-22562 1999 Type: ARTICLE Genes: Abstract: We have recently demonstrated that Caenorhabditis elegans Ca2+/calmodulin-dependent protein kinase kinase (CeCaM-KK) can activate mammalian CaM-kinase IV in vitro (Tokumitsu, H., Takahashi, N., Eto, K., Yano, S., Soderling, T.R., and Muramatsu, M. (1999) J. Biol. Chem. 274, 15803-15810). In the present study, we have identified and cloned a target CaM-kinase for CaM-KK in C. elegans, CeCaM-kinase I (CecaM-KI), which has approximately 60% identity to mammalian CaM-KI. Ce-CaM-KI has 348 amino acid residues with an apparent molecular mass of 40 kDa, which is activated by Ce-CaM-KK through phosphorylation of Thr(179) in a Ca2+/CaM-dependent manner, resulting in a 30-fold decrease in the K-m of CeCaM-KI for its peptide substrate. Unlike mammalian CaM-RI, CeCaM-KI is mainly localized in the nucleus of transfected cells because the NH2-terminal six residues ((PLFKRR7)-P-2) contain a functional nuclear localization signal. We have also demonstrated that CeCaM-KK and CecaM-KI reconstituted a signaling pathway that mediates Ca2+-dependent phosphorylation of cAMP response element-binding protein (CREB) and CRE-dependent transcriptional activation in transfected cells, consistent with nuclear localization of Ce-CaM-KI. These results suggest that the CaM-KK/CaM-KI cascade is conserved in C. elegans and is functionally operated both in vitro and in intact cells, and it may be involved in Ca2+-dependent nuclear events such as transcriptional activation through phosphorylation of CREB. ------------------- Key: 3626 Medline: 99350221 Authors: Baird SE;Ellazar SA Title: TGFB-like signaling and spicule development in Caenorhabditis elegans. Citation: Developmental Biology 212: 93-100 1999 Type: ARTICLE Genes: daf-4 dbl-1 egl-5 lin-31 sma-2 sma-3 sma-4 Abstract: A TGF beta-like signal is required for spicule development in Caenorhabditis elegans males. This signal appears to originate in the male-specific musculature and is required for the migrations of cells within the proctodeum The migrations of these cells form cellular molds, the spicule traces, in which the cuticle of the spicules is secreted. Mutations in daf-4 sma-2, sma-3, and sma-4, which disrupt TGF beta-like signaling, result in aberrant migrations and morphologically abnormal spicules. daf-4, and hence the TGF beta-like signal, is required prior to or during cell migrations. Therefore, the TGF beta-like signal may act to prime the migrating cells or as a guidance cue. Mutations in lin-31 result in identical cell migration and spicule morphology defects. Thus, lin-31, which encodes a "winged helix" protein (Miller ef al., Genes Dev. 7, 933-947, 1993), may be a component of this TGF beta-like signaling ------------------- Key: 3627 Medline: 99307069 Authors: Montell DJ Title: The genetics of cell migration in Drosophila melanogaster and Caenorhabditis elegans development. Citation: Development 126: 3035-3046 1999 Type: REVIEW Genes: cam-1 cam-2 ced-5 ceh-10 egl-5 egl-15 egl-17 egl-20 egl-27 egl-43 ham-2 hch-1 ina-1 lin-17 lin-39 mab-5 mig-1 mig-2 mig-10 mig-14 sem-5 unc-5 unc-6 unc-40 unc-73 unc-86 vab-8 Abstract: Cell migrations are found throughout the animal kingdom and are among the most dramatic and complex of cellular behaviors. Historically, the mechanics of cell migration have been studied primarily in vitro, where cells can be readily viewed and manipulated. However, genetic approaches in relatively simple model organisms are yielding additional insights into the molecular mechanisms underlying cell movements and their regulation during development. This review will focus on these simple model systems where we understand some of the signaling and receptor molecules that stimulate and guide cell movements. The chemotactic guidance factor encoded by the Caenorhabditis elegans unc-6 locus, whose mammalian homolog is Netrin, is perhaps the best known of the cell migration guidance factors. In addition, receptor tyrosine kinases (RTKs), and FGF receptors in particular, have emerged as key mediators of cell migration in vivo, confirming the importance of molecules that were initially identified and studied in cell culture. Somewhat surprisingly, screens for mutations that affect primordial germ cell migration in Drosophila have revealed that enzymes involved in lipid metabolism play a role in guiding cell migration in vivo, possibly by producing and/or degrading lipid chemoattractants or chemorepellents. Cell adhesion molecules, such as integrins, have been extensively characterized with respect to their contribution to cell migration in vitro and genetic evidence now supports a role for these receptors in certain instances in vivo as well. The role for non-muscle myosin in cell motility was controversial, but has now been demonstrated genetically, at least in some cell types. Currently the best characterized link between membrane receptor signaling and regulation of the actin cytoskeleton is that provided by the Rho family of small GTPases. Members of this family are clearly essential for the migrations of some cells; however, key questions remain concerning how chemoattractant and chemorepellent signals are integrated within the cell and transduced to the cytoskeleton to produce directed cell migration. New types of genetic ------------------- Key: 3628 Medline: 99307080 Authors: Malone CJ;Fixsen WD;Horvitz HR;Han M Title: UNC-84 localizes to the nuclear envelope and is required for nuclear migration and anchoring during C. elegans development. Citation: Development 126: 3171-3181 1999 Type: ARTICLE Genes: anc-1 unc-40 unc-83 unc-84 mnDp9 mnDp26 Abstract: Nuclear migrations are essential for metazoan development. Two nuclear migrations that occur during C. elegans development require the function of the unc-84 gene. unc-84 mutants are also defective in the anchoring of nuclei within the hypodermal syncytium and in the migrations of the two distal tip cells of the gonad. Complementation analyses of 17 unc-84 alleles defined two genetically separable functions. Both functions are required for nuclear and distal tip cell migrations, but only one is required for nuclear anchorage. The DNA lesions associated with these 17 mutations indicate that the two genetically defined functions correspond to two distinct regions of the UNC-84 protein. The UNC-84 protein has a predicted transmembrane domain and a C-terminal region with similarity to the S, pombe spindle pole body protein Sad1 and to two predicted mammalian proteins. Analysis of a green fluorescent protein reporter indicated that UNC-84 is widely expressed and localized to the nuclear envelope. We propose that UNC-84 functions to facilitate a nuclear-centrosomal interaction required for nuclear ------------------- Key: 3629 Medline: 99401034 Authors: Morton DB;Hudson ML;Waters E;O'Shea M Title: Soluble guanylyl cyclases in Caenorhabditis elegans: NO is not the answer. Citation: Current Biology 9: R546-R547 1999 Type: REVIEW Genes: Abstract: Guanylyl cyclases (GCs), the enzymes that synthesize cyclic GMP (cGMP), have classically been divided into two groups: receptor GCs and soluble GCs. Receptor GCs are integral membrane proteins such as the retinal guanylyl cyclases and the atrial natriuretic peptide receptors. Soluble GCs are heterodimeric proteins consisting of an alpha and a beta subunit that bind a heme group and are activated by nitric oxide (NO). The recent publication of the Caenorhabditis elegans genomic sequence has revealed an unexpected abundance of GCs. ------------------- Key: 3630 Medline: 99385784 Authors: Hodgkin J Title: Sex, cell death, and the genome of C. elegans. Citation: Cell 98: 277-280 1999 Type: REVIEW Genes: ced-3 ced-4 ced-9 ces-1 ces-2 egl-1 fem-1 fem-2 fem-3 fox-1 her-1 mab-3 sdc-1 sdc-2 sdc-3 sex-1 tra-1 tra-2 tra-3 xol-1 Abstract: Cell death in universally important in development, not the least in the nervous system, but little is known about how the programmed cell deaths of cells and neurons are ultimately controlled. Much of the understanding of cell death has come from research on the nematode Caenorhabditis elegans (reviewed by Metzstein et al., 1998). Conradt and Horvitz (1999 [this issue of Cell]) now extend this work to provide a satisfyingly complete explanation for the sex-specific death of one particular neuron type in this animal. In so doing, they link up two extensively studied regulatory pathways in C. elegans, one controlling sexual phenotype, and one controlling cell death. ------------------- Key: 3631 Medline: 10458607 Authors: Conradt B;Horvitz HR Title: The TRA-1A sex determination protein of C. elegans regulates sexually dimorphic cell deaths by repressing the egl-1 cell death activator gene. Citation: Cell 98: 317-327 1999 Type: ARTICLE Genes: ced-3 ced-4 ced-9 egl-1 tra-1 Abstract: The hermaphrodite-specific neurons (HSNs) of the nematode Caenorhabditis elegans are generated embryonically in both hermaphrodites and males but undergo programmed cell death in males. The gene egl-1 encodes a BH3-containing cell death activator that is required for programmed cell death in C. elegans. Gain-of-function (gf) mutations in egl-1 cause the inappropriate programmed cell death of the HSNs in hermaphrodites. These mutations lie 5.6 kb downstream of the egl-1 transcription unit and disrupt the binding of the TRA-1A zinc finger protein, the terminal global regulator of somatic sexual fate. This disruption results in the activation of the egl-1 gene in the HSNs not only in males but also in hermaphrodites. Our findings suggest that in hermaphrodites TRA-1A represses egl-1 transcription in the HSNs to prevent these neurons from undergoing programmed cell death. ------------------- Key: 3632 Medline: 99396709 Authors: Thomas JH;Horvitz HR Title: The C. elegans gene lin-36 acts cell autonomously in the lin-35 Rb pathway. Citation: Development 126: 3449-3459 1999 Type: ARTICLE Genes: let-23 lin-2 lin-3 lin-7 lin-8 lin-9 lin-10 lin-15 lin-35 lin-36 lin-37 lin-51 lin-52 lin-53 lin-55 nDf20 Abstract: The Caenorhabditis elegans gene lin-36 acts to antagonize Ras-mediated vulval induction in a pathway that includes genes with products similar to the mammalian retinoblastoma (Rb) protein and the Rb-binding protein p48. We report that lin-36 encodes a novel protein of 962 amino acids. We demonstrate that lin-36 functions in and is expressed in the vulval precursor cells, establishing that the lin-36 pathway is involved in intercellular signaling. We also report that the lin-36 pathway and/or another pathway that is functionally redundant with the lin-36 pathway antagonize a ligand-independent activity of the receptor tyrosine kinase/Ras vulval induction pathway. ------------------- Key: 3633 Medline: 99396693 Authors: Seydoux G;Strome S Title: Launching the germline in Caenorhabditis elegans: regulation of gene expression in early germ cells. Citation: Development 126: 3275-3283 1999 Type: REVIEW Genes: apx-1 gld-1 glh-1 glh-2 mes-2 mes-3 mes-4 mes-6 mex-1 mex-3 pgl-1 pie-1 pos-1 skn-1 Abstract: One hundred years after Weismann's seminal observations, the mechanisms that distinguish the germline from the soma still remain poorly understood. This review describes recent studies in Caenorhabditis elegans, which suggest that germ cells utilize unique mechanisms to regulate gene expression. In particular, mechanisms that repress the production of mRNAs appear to be essential to maintain germ cell fate and viability. ------------------- Key: 3634 Medline: 99383323 Authors: Ashton FT;Li J;Schad GA Title: Chemo- and thermosensory neurons: structure and function in animal parasitic nematodes. Citation: Veterinary Parasitology 84: 297-316 1999 Type: ARTICLE Genes: Abstract: Nematode parasites of warm-blooded hosts use chemical and thermal signals in host-finding and in the subsequent resumption of development. The free-living nematode Caenorhabditis elegans is a useful model for investigating the chemo- and thermosensory neurons of such parasites, because the functions of its amphidial neurons are well known from laser microbeam ablation studies. The neurons found in the amphidial channel detect aqueous chemoattractants and repellants; the wing cells-flattened amphidial neurons-detect volatile odorants. The finger cells-digitiform amphidial neurons-are the primary thermoreceptors. Two neuron classes, named ADF and ASI, control entry into the environmentally resistant resting and dispersal dauer larval stage, while the paired ASJ neurons control exit from this stage. Skin-penetrating nematode parasites, i.e. the dog hookworm Ancylostoma caninum, and the threadworm, Strongyloides stercoralis, use thermal and chemical signals for host-finding, while the passively ingested sheep stomach worm, Haemonchus contortus, uses environmental signals to position itself for ingestion. Amphidial neurons presumably recognize these signals. In all species, resumption of development, on entering a host, is probably triggered by host signals also perceived by amphidial neurons. In the amphids of the A. caninum infective larva, there are wing- and finger-cell neurons, as well as neurons ending in cilia-like dendritic processes, some of which presumably recognize a sequence of signals that stimulate these larvae to attach to suitable hosts. The functions of these neurons can be postulated, based on the known functions of their homologs in C. elegans. The threadworm, S. stercoralis, has a complex life cycle. After leaving the host, soil-dwelling larvae may develop either to infective larvae (the life-stage equivalent of dauer larvae) or to free-living adults. As with the dauer larva of C. elegans, two neuron classes control this developmental switch. Amphidial neurons control chemotaxis to a skin extract, and a highly modified amphidial neuron, the lamellar cell, appears to be the primary thermoreceptor, in addition to having chemosensory function. The stomach worm, Haemonchus contortus, depends on ingestion by a grazing host. Once ingested, the infective larva is exposed to profound environmental changes in the rumen. These changes stimulate resumption of development in this species. We hypothesize that resumption of development is under the control of the ASJ neuronal pair. Identification of the neurons that control the infective process could provide the basis for entirely new approaches to parasite control involving interference with development at the time and place of initial host-contact. ------------------- Key: 3635 Medline: 99370682 Authors: Saffman EE;Lasko P Title: Germline development in vertebrates and invertebrates. Citation: Cellular & Molecular Life Sciences 55: 1141-1163 1999 Type: REVIEW Genes: glh-1 glh-2 glh-3 let-858 mes-1 mes-2 mes-3 mes-4 mes-6 mex-1 par-1 par-2 par-3 par-4 pgl-1 pie-1 pos-1 Abstract: In all animals information is passed from parent to offspring via the germline, which segregates from the soma early in development and undergoes a complex developmental program to give rise to the adult gametes. Many aspects of germline development have been conserved throughout the animal kingdom. Here we review the unique properties of germ cells, the initial determination of germ cell fates, the maintenance of germ cell identity, the migration of germ cells to the somatic gonadal primordia and the proliferation of germ cells during development invertebrates and invertebrates. Similarities in germline development in such diverse organisms as Drosophila melanogaster, Caenorhabditis elegans, Xenopus laevis and Mus musculus will be highlighted. ------------------- Key: 3636 Medline: Authors: Plasterk RHA;Izsvak Z;Ivics Z Title: Resident aliens - The Tc1/mariner superfamily of transposable elements. Citation: Trends in Genetics 15: 326-332 1999 Type: REVIEW Genes: Abstract: Transgenic technology is currently applied to several animal species of agricultural or medical importance, such as fish, cattle, mosquitos and parasitic worms. However, the repertoire of genetic tools used for molecular analyses of mice and Drosophila is not always applicable to other species. For example, while retroviral enhancer-trap experiments in mice can be based on embryonic stem (ES) cell technology, this is not currently an option with other animals. Similarly, the germline transformation of Drosophila depends on the use of the P-element transposon, which does not jump in other genera. This article analyses the main characteristics of Tc1/mariner transposable elements, examines some of the factors that have contributed to their evolutionary success, and describes their potential, as well as their limitations, for transgenesis and insertional mutagenesis in diverse ------------------- Key: 3637 Medline: 99346338 Authors: Sigrist CB;Sommer RJ Title: Vulva formation in Pristionchus pacificus relies on continuous gonadal induction. Citation: Development Genes & Evolution 209: 451-459 1999 Type: ARTICLE Genes: let-60 lin-39 vul-1 vul-2 vul-3 vul-4 Abstract: One of the best known features of vulva development in Caenorhabditis elegans is the induction of vulval precursor cells by the gonadal anchor cell. Induction is crucial for the initiation of pattern formation within the C. elegans vulva equivalence group, and it is therefore surprising to find that this aspect of vulva formation, in particular, varies greatly among nematodes. In some species which form vulvae in the posterior body region, no gonadal signal is necessary for vulva induction. In other nematodes, such as Panngrolaimus, Oscheius, and Rhabditella, vulva formation depends on two temporally distinct gonadal inductions which specify the different cell fates. Here we report our analysis of vulva induction in Pristionchus pacificus, a species which has recently been used as a genetic system to analyze the evolution of vulva development. Cell ablation studies in P. pacificus show that another mode of vulva induction exists. P. pacificus vulva formation depends on a continuous gonadal induction that starts several hours after hatching and continues until the birth of the anchor cell, some 20 h later. Mutations defective in gonadal induction result in the absence of vulva differentiation, suggesting that only one signaling system is involved in the gonadal-epidermal interaction. This new mode adds further to the great variety of gonadal inductions among nematode species. ------------------- Key: 3638 Medline: 99352432 Authors: Ohmachi M;Sugimoto A;Iino Y;Yamamoto M Title: kel-1, a novel kelch-related gene in Caenorhabditis elegans, is expressed in pharyngeal gland cells and is required for the feeding process. Citation: Genes to Cells 4: 325-337 1999 Type: ARTICLE Genes: kel-1 spe-26 Abstract: BACKGROUND: Kelch-related proteins constitute an expanding family, members of which carry two conserved motifs named the BTB/POZ and the kelch repeat domains. The best-characterized member, Drosophila Kelch, constitutes the ring canals in the egg chamber in association with actin. However, physiological and biochemical functions of the members of this family remain largely uncharacterized. RESULTS: We identified the kel-1 gene encoding a Kelch-related protein in the nematode Caenorhabditis elegans. The deduced KEL-1 protein had 618 amino acid residues and was most similar to Drosophila Kelch. Loss of kel-1 function caused growth arrest at an early larval stage, most likely at the beginning of L2. The kel-1 deletion mutant appeared normal in morphology, movement and pumping action for the initial two to three days after hatching, but it failed to convey foods effectively to intestine and could hardly increase in body size. Analyses using immunostaining and reporter gene expression indicated that kel-1 was expressed almost exclusively in the g1 pharyngeal gland cells during late embryogenesis and at all developmental stages thereafter. CONCLUSIONS: C. elegans KEL-1 protein is essential for the larval development, probably performing a function required for feeding in the pharyngeal g1 gland cells, which are supposed to secrete materials aiding digestion. ------------------- Key: 3639 Medline: Authors: Sommer RJ;Sigrist CB;Grandien K;Jungblut B;Eizinger A;Adamis H;Schlak I Title: A phylogenetic interpretation of nematode vulval Citation: Invertebrate Reproduction and Development 36: 57-65 1999 Type: ARTICLE Genes: lin-39 Abstract: Over the last few years vulva development in nematodes has been used as a model system to study the evolution of developmental processes by carrying out cell lineage and cell ablation studies in various nematodes. Furthermore, a genetic and molecular analysis of vulva development has been initiated in Pristionchus pacificus. Evolutionary interpretation of these comparative developmental studies requires a phylogenetic understanding of nematodes. Recently, a molecular phylogeny for the phylum Nematoda has been published. Here, we place the comparative data of vulva development onto this phylogeny of nematodes to infer the direction of evolutionary change. ------------------- Key: 3640 Medline: 99357718 Authors: Honda Y;Honda S Title: The daf-2 gene network for longevity regulates oxidative stress resistance and Mn-superoxide dismutase gene expression in Caenorhabditis elegans. Citation: FASEB Journal 13: 1385-1393 1999 Type: ARTICLE Genes: age-1 clk-1 daf-1 daf-2 daf-7 daf-11 daf-16 daf-18 fer-15 sod-1 sod-2 sod-3 spe-26 Abstract: Longevity is regulated by the daf-2 gene network in Caenorhabditis elegans. Mutations in the daf-2 gene, which encodes a member of the insulin receptor family, confer the life extension (Age) phenotype and the constitutive dauer (a growth-arrested larval form specialized for dispersal) formation phenotype. The Age phenotype is mutually potentiated by two life extension mutations in the daf-2 gene and the clk-1 gene, a homologue of yeast CAT5/COQ7 known to regulate ubiquinone biosynthesis. In this study, we demonstrated that the daf-2 mutation also conferred an oxidative stress resistance (Oxr) phenotype, which was also enhanced by the clk-1 mutation. Similar to the Age phenotype, the Oxr phenotype was regulated by the genetic pathway of insulin-like signaling from daf-2 to the daf-16 gene, a homologue of the HNF-3/forkhead transcription factor. These findings led us to examine whether the insulin-like signaling pathway regulates the gene expression of antioxidant defense enzymes. We found that the mRNA level of the sod-3 gene, which encodes Mn-superoxide dismutase (SOD), was much higher in daf-2 mutants than in the wild type. Moreover, th ------------------- Key: 3641 Medline: 10476681 Authors: Nonet ML Title: Visualization of synaptic specializations in live C. elegans with synaptic vesicle protein-GFP fusions. Citation: Journal of Neuroscience Methods 89: 33-40 1999 Type: ARTICLE Genes: mec-7 snb-1 sng-1 unc-4 unc-11 unc-64 unc-104 Abstract: Synaptic specializations are difficult to visualize at the light microscope level in living preparations. To circumvent this problem, synaptic vesicle proteins were fused to green fluorescent protein (GFP) and expressed in C. elegans neurons. C. elegans synaptobrevin-GFP and synaptogyrin-GFP fusion proteins were observed to target to synaptic sites. This localization allowed the visualization of synaptic specializations in living animals with light microscopy. Restricted expression of synaptobrevin-GFP fusions in subsets of neurons enables the visualization of individual presynaptic varicosities. The cell biology underlying the sorting of synaptic vesicle proteins, trafficking of vesicles to terminals, and the development of presynaptic specializations is now more amenable to forward genetic analysis using these synaptic markers. ------------------- Key: 3642 Medline: 99365365 Authors: Lim YS;Mallapur S;Kao G;Ren XC;Wadsworth WG Title: Netrin UNC-6 and the regulation of branching and extension of motoneuron axons from the ventral nerve cord of Caenorhabditis elegans. Citation: Journal of Neuroscience 19: 7048-7056 1999 Type: ARTICLE Genes: glr-1 unc-5 unc-6 unc-40 unc-104 unc-119 unc-129 Abstract: In the Caenorhabditis elegans embryo, some ventral midline motoneurons extend a process circumferentially to the dorsal midline and a process longitudinally along ventral nerve cord interneurons. Circumferential migrations are guided by netrin UNC-6, which repels motoneuron axons dorsally. Although the motoneuron cell bodies and the longitudinal axons are positioned along UNC-6-expressing interneurons in the ventral nerve cord, the circumferential processes extend only from the motoneuron cell bodies and from defined locations along some longitudinal axons. This implies a mechanism regulates motoneuron branching of UNC-6-responsive processes. We show that expression of unc-6 Delta C, which encodes UNC-6 without domain C, partially rescues circumferential migration defects in unc-6 null animals. This activity depends on the netrin receptors UNC-5 and UNC-40. These results indicate that UNC-6 Delta C can provide the circumferential guidance functions of UNC-6. Furthermore, we show that expression of unc-6 Delta C causes motoneuron branching and the extension of processes from abnormal positions along the ventral nerve cord. This activity is also UNC-5- and UNC-40-dependent, We propose that local interactions mediated by domain C regulate motoneuron branching and ------------------- Key: 3643 Medline: 99373339 Authors: Hresko MC;Schriefer LA;Shrimankar P;Waterston RH Title: Myotactin, a novel hypodermal protein involved in muscle-cell adhesion in Caenorhabditis elegans. Citation: Journal of Cell Biology 146: 659-672 1999 Type: ARTICLE Genes: let-805 Abstract: In C. elegans, assembly of hypodermal hemidesmosome-like structures called fibrous organelles is temporally and spatially coordinated with the assembly of the muscle contractile apparatus, suggesting that signals are exchanged between these cell types to position fibrous organelles correctly. Myotactin, a protein recognized by monoclonal antibody MH46, is a candidate for such a signaling molecule. The antigen, although expressed by hypodermis, first reflects the pattern of muscle elements and only later reflects the pattern of fibrous organelles. Confocal microscopy shows that in adult worms myotactin and fibrous organelles show coincident localization. Further, cell ablation studies show the bodywall muscle cells are necessary for normal myotactin distribution. To investigate myotactin's role in muscle-hypodermal signaling, we characterized the myotactin locus molecularry and genetically. Myotactin is a novel transmembrane protein of similar to 500 kd. The extracellular domain contains at least 32 fibronectin type III repeats and the cytoplasmic domain contains unique sequence. In mutants lacking myotactin, muscle cells detach when embryonic muscle contraction begins. Later in development fibrous organelles become delocalized and are not restricted to regions of the hypodermis previously contacted by muscle. These results suggest myotactin helps maintain the association between the muscle contractile apparatus and hypodermal fibrous organelles. ------------------- Key: 3644 Medline: 99359428 Authors: Streit A;Li WQ;Robertson B;Schein J;Kamal IH;Marra M;Wood Title: Homologs of the Caenorhabditis elegans masculinizing gene her-1 in C. briggsae and the filarial parasite Brugia malayi. Citation: Genetics 152: 1573-1584 1999 Type: ARTICLE Genes: her-1 him-8 mih-3 Abstract: The masculinizing gene her-1 in Caenorhabditis elegans (Ce-her-1) encodes a novel protein, HER-1A, which is required for male development. To identify conserved elements in her-1 we have cloned and characterized two homologous nematode genes: one by synteny from the closely related free-living species C. briggsae (Cb-her-1) and the other, starting with a fortuitously identified expressed sequence tag, from the distantly related parasite Brugia malayi (Bm-her-1). The overall sequence identities of the predicted gene products with Ce-HER-1A are only 57% for Cb-HER-1, which is considerably lower than has been found for most homologous briggsae genes, and 35% for Bm-HER-1. However, conserved residues are found throughout both proteins, and like Ce-HER-1A, both have putative N-terminal signal sequences. Ce-her-1 produces a larger masculinizing transcript (her-1a) and a smaller transcript of unknown function (her-1b); both are present essentially only in males. By contrast, Cb-her-1 appears to produce only one transcript, corresponding to her-1a; it is enriched in males but present also in hermaphrodites. Injection of dsRNA transcribed from Cb-her-1 into C briggsae hermaphrodites (RNA interference) caused XO animals to develop into partially fertile hermaphrodites. Introducing a Cb-her-1 construct as a transgene under control of the C. elegans unc54 myosin heavy chain promoter caused strong masculinization of both C briggsae and C. elegans hermaphrodites. Introduction of a similar Bm-her-1 construct into C. elegans caused only very weak, if any, masculinization. We conclude that in spite of considerable divergence the Cb gene is likely to be a functional ortholog of Ce-her-1, while the function of the distantly related Bm gene remains uncertain. ------------------- Key: 3645 Medline: 10444600 Authors: Schlesinger A;Shelton CA;Maloof JN;Meneghini M;Bowerman B Title: Wnt pathway components orient a mitotic spindle in the early Caenorhabditis elegans embryo without requiring gene transcription in the responding cell. Citation: Genes & Development 13: 2028-2038 1999 Type: ARTICLE Genes: ama-1 apr-1 gsk-3 mom-1 mom-2 mom-3 mom-4 mom-5 pes-10 pop-1 wrm-1 Abstract: In a four-cell-stage Caenorhabditis elegans embryo, Wnt signaling polarizes an endoderm precursor called EMS. The polarization of this cell orients its mitotic spindle in addition to inducing endodermal fate in one daughter cell. Reducing the function of Wnt pathway genes, including a newly identified GSK-3 beta homolog called gsk-3, disrupts endoderm induction, whereas only a subset of these genes is required for proper EMS mitotic spindle orientation. Wnt pathway genes thought to act downstream of gsk-3 appear not to be required for spindle orientation, suggesting that gsk-3 represents a branch point in the control of endoderm induction and spindle orientation. Orientation of the mitotic spindle does not require gene transcription in EMS, suggesting that Wnt signaling may directly target the cytoskeleton in a responding cell. ------------------- Key: 3646 Medline: 99365296 Authors: Villard L;Fontes M;Ewbank JJ Title: Characterization of xnp-1, a Caenorhabditis elegans gene similar to the human XNP/ATR-X gene. Citation: Gene 236: 13-19 1999 Type: ARTICLE Genes: xnp-1 Abstract: We report the characterization of a new Caenorhabditis elegans gene, xnp-1, that encodes the closest known non-mammalian relative of the human XNP/ATR-X protein. Mutations in the corresponding gene lead to mental retardation in humans. The nematode gene is composed of 10 exons, and we show that a 4.3 kb transcript is produced from the xnp-1 locus. The 1359 residue XNP-1 protein is 33.6% identical and 52.2% similar to the human XNP/ATR-X protein. In two regions of more than 250 amino acids, the proteins display 70% identity. The human and nematode proteins are putative DNA helicases and contain the seven characteristic domains of this family of proteins. In addition to the fact that similar proteins are encoded by the nematode and human gene, they share a partially identical genomic structure. These data indicate that xnp-1 and XNP/ATR-X have diverged from the same ancestral DNA helicase gene and may therefore have conserved similar ------------------- Key: 3647 Medline: 10501036 Authors: Felix MA;Hill RJ;Schwarz H;Sternberg PW;Sudhaus W;Sommer RJ Title: Pristionchus pacificus, a nematode with only three juvenile stages, displays major heterochronic changes relative to Caenorhabditis elegans. Citation: Proceedings of the Royal Society of London B 266: 1617-1621 1999 Type: ARTICLE Genes: Abstract: The nematode Pristionchus pacificus (Diplogastridae) has been described as a satellite organism for a functional comparative approach to the model organism Caenorhabditis elegans because genetic, molecular, and cell-biological tools can be used in a similar way in both species. Here we show that P. pacificus has three juvenile stages, instead of the usual four found in other nematodes. Embryogenesis is lengthened and many developmental events that take place during the first juvenile stage in C. elegans occur during late embryogenesis in P pacificus. Video imaging and transmission electron microscopy revealed no embryonic moult. The timing of later developmental events relative to the moults differs between P. pacificus and C. elegans. In addition, the post-embryonic blast-cell divisions display a specific change in timing between the two species, resulting in heterochrony between different cell lineages, such as vulval and gonadal lineages. Developmental events appear to come into register during the last larval stage. Thus, differences in developmental timing between P. pacificus and C. elegans represent a deep heterochronic change. We designate the thre ------------------- Key: 3648 Medline: 99384262 Authors: Page MF;Carr B;Anders KR;Grimson A;Anderson P Title: SMG-2 is a phosphorylated protein required for mRNA surveillance in Caenorhabditis elegans and related to Upf1p of yeast. Citation: Molecular and Cellular Biology 19: 5943-5951 1999 Type: ARTICLE Genes: smg-1 smg-2 smg-3 smg-4 smg-5 smg-6 smg-7 unc-54 Abstract: mRNAs that contain premature stop codons are selectively degraded in all eukaryotes tested, a phenomenon termed "nonsense-mediated mRNA decay" (NMD) or "mRNA surveillance." NMD may function to eliminate aberrant mRNAs so that they are not translated, because such mRNAs might encode deleterious polypeptide fragments. In both yeasts and nematodes, NMD is a nonessential system. Mutations affecting three yeast UPF genes or seven nematode smg genes eliminate NMD. We report here the molecular analysis of smg-2 of Caenorhabditis elegans. smg-2 is homologous to UPF1 of yeast and to RENT1 (also called HUPF1), a human gene likely involved in NMD. The striking conservation of SMG-2, Upf1p, and RENT1/HUPF1 in both sequence and function suggests that NMD is an ancient system, predating the divergence of most eukaryotes. Despite similarities in the sequences of SMG-2 and Upf1p, expression of Upf1p in C. elegans does not rescue smg-2 mutants. We have prepared anti-SMG-2 polyclonal antibodies and identified SMG-2 on Western blots. SMG-2 is phosphorylated, and mutations of the six other smg genes influence the state of SMG- ------------------- Key: 3649 Medline: Authors: Jewitt N;Anthony P;Lowe KC;de Pomerai DI Title: Oxygenated perfluorocarbon promotes nematode growth and stress-sensitivity in a two-phase liquid culture system. Citation: Enzyme & Microbial Technology 25: 349-356 1999 Type: ARTICLE Genes: Abstract: The nematode, Caenorhabditis elegans, can be grown in liquid culture media supplemented with bacteria as a food source, but growth is limited primarily by lack of oxygen. A novel two-phase liquid culture system has been developed in which the nematodes were grown at an interface between a lower layer of perfluorocarbon and an upper layer of aqueous S medium containing bacteria. By using degassed perfluorodecalin, nematode growth over 3 days was slightly less than in S medium controls above a plastic substrate; however, this difference in growth rate was barely significant over five replica runs. By using oxygen-saturated perfluorodecalin, growth over 3 days was significantly enhanced, as compared both to S-medium controls and to cultures over degassed perfluorodecalin. This much larger effect is attributable to improved oxygenation at the interface on which the worms move. Measurements with an oxygen electrode suggest that dissolved oxygen concentrations were greatly depleted in both the perfluorocarbon and aqueous layers after 24 h. However, during standard 7-h toxicity tests in aqueous media, an underlying layer of oxygenated perfluorocarbo ------------------- Key: 3650 Medline: 99396696 Authors: Ch'ng Q;Kenyon C Title: egl-27 generates anteroposterior patterns of cell fusion in C. elegans by regulating Hox gene expression and Hox protein function. Citation: Development 126: 3303-3312 1999 Type: ARTICLE Genes: egl-5 egl-27 lin-39 mab-5 tra-1 Abstract: Hox genes pattern the fates of the ventral ectodermal Pn,p cells that lie along the anteroposterior (A/P) body axis of C. elegans. In these cells, the Hox genes are expressed in sequential overlapping domains where they control the ability of each Pn,p cell to fuse with the surrounding syncytial epidermis. The activities of Hox proteins are sex-specific in this tissue, resulting in sex-specific patterns of cell fusion: in hermaphrodites, the mid-body cells remain unfused, whereas in males, alternating domains of syncytial and unfused cells develop. We have found that the gene egl-27, which encodes a C. elegans homologue of a chromatin regulatory factor, specifies these patterns by regulating both Hox gene expression and Hox protein function. In egl-27 mutants, the expression domains of Hox genes in these cells are shifted posteriorly, suggesting that egl-27 influences A/P positional information. In addition, egl-27 controls Hox protein function in the Pn,p cells in two ways: in hermaphrodites it inhibits MAB-5 activity, whereas in males it permits a combinatorial interaction between LIN-39 and MAB-5. Thus, by selectively modifying the activities of Hox proteins, egl-2 ------------------- Key: 3651 Medline: 10449352 Authors: Bowerman B;Shelton CA Title: Cell polarity in the early Caenorhabditis elegans embryo. Citation: Current Opinion in Genetics & Development 9: 390-395 1999 Type: ARTICLE Genes: lit-1 mes-1 mom-1 mom-2 mom-3 mom-4 mom-5 par-1 par-2 par-3 par-4 par-6 pop-1 spe-11 Abstract: Beginning with the first mitotic division in a Caenorhabditis elegans embryo, asymmetric cleavages establish much of the body plan. Although they share a common axis of polarity, at least three kinds of asymmetric cell division occur: two are under intrinsic control, while a third requires an inductive signal and may operate repeatedly throughout development. ------------------- Key: 3652 Medline: 10449355 Authors: Branda CS;Stern MJ Title: Cell migration and axon growth cone guidance in Caenorhabditis elegans. Citation: Current Opinion in Genetics & Development 9: 479-484 1999 Type: REVIEW Genes: bar-1 egl-17 egl-20 egl-27 lin-17 mab-5 mig-1 mig-2 mig-5 mig-14 pry-1 sax-3 unc-5 unc-6 unc-40 unc-73 unc-115 unc-129 vab-8 Abstract: In the past year, several new components involved in cell migration and axon guidance have been identified by genetic analysis in Caenorhabditis elegans, taking us a step closer to being able to trace the pathways which mediate these processes. The completion of the C. elegans genome sequencing project has provided us with the knowledge of the full spectrum of genes that might be involved in cell migration and axon guidance, and can facilitate the analysis of components that have been shown to be important for these processes in other systems. ------------------- Key: 3653 Medline: 99404618 Authors: Forrester WC;Dell M;Perens E;Garriga G Title: A C. elegans Ror receptor tyrosine kinase regulates cell motility and asymmetric cell division. Citation: Nature 400: 881-885 1999 Type: ARTICLE Genes: cam-1 Abstract: Ror kinases are a family of orphan receptors with tyrosine kinase activity that are related to muscle specific kinase (MuSK), a receptor tyrosine kinase that assembles acetylcholine receptors at the neuromuscular junction(1,2). Although the functions of Ror kinases are unknown, similarities between Ror and MuSK kinases have led to speculation that Ror kinases regulate synaptic development. Here we show that the Caenorhabditis elegans gene cam-1 encodes a member of the Ror kinase family that guides migrating cells and orients the polarity of asymmetric cell divisions and axon outgrowth. We find that tyrosine kinase activity is required for some of the functions of CAM-1, but not for its role in cell migration. CAM-1 is expressed in cells that require its function, and acts cell autonomously in migrating neurons. Overexpression and loss of cam-1 function result in reciprocal cell-migration phenotypes, indicating that levels of CAM-1 influence the final positions of migrating cells. Our results raise the possibility that Ror kinases regulate cell motility and asymmetric cell division in organisms as diverse as nematodes and mammals. ------------------- Key: 3654 Medline: 99412487 Authors: Davies EK;Peters AD;Keightley PD Title: High frequency of cryptic deleterious mutations in Caenorhabditis elegans. Citation: Science 285: 1748-1751 1999 Type: ARTICLE Genes: unc-22 Abstract: Deleterious mutations with very small phenotypic effects could be important for several evolutionary phenomena, but the extent of their contribution has been unknown. Fitness effects of induced mutations in Lines of Caenorhabditis elegans were measured using a system for which the number of deleterious point mutations in the DNA can be estimated. In fitness assays, only about 4 percent of the deleterious mutations fixed in each Line were detectable. The remaining 96 percent, though cryptic, are significant for mutation Load and, potentially, for the evolution of sex. ------------------- Key: 3655 Medline: 99417954 Authors: Choy RKM;Thomas JH Title: Fluoxetine-resistant mutants in C. elegans define a novel family of transmembrane proteins. Citation: Molecular Cell 4: 143-152 1999 Type: ARTICLE Genes: cat-1 cat-4 cha-1 lev-1 ndg-4 nrf-1 nrf-2 nrf-3 nrf-4 nrf-5 nrf-6 unc-17 unc-29 unc-31 unc-38 Abstract: Fluoxetine (Prozac) is an antidepressant that is thought to act by blocking presynaptic reuptake of the neurotransmitter serotonin. Despite widespread clinical use of fluoxetine, direct evidence for this mechanism has been difficult to obtain in vivo. We have determined that fluoxetine has an additional neuromuscular effect on C. elegans that is distinct from inhibition of serotonin reuptake. By screening for mutants resistant to this effect, we have identified seven genes. We report that two of these genes are homologous to each other and define a novel gene family that encodes over a dozen multipass transmembrane proteins. Our findings may have clinical implications for the mechanism of action of fluoxetine. ------------------- Key: 3656 Medline: 99417967 Authors: Shin TH;Yasuda J;Rocheleau CE;Lin R;Soto M;Bei Y;Davis RJ;Mello CC Title: MOM-4, a MAP kinase kinase kinase-related protein, activates WRM-1/LIT-1 kinase to transduce anterior/posterior polarity in C. elegans. Citation: Molecular Cell 4: 275-280 1999 Type: ARTICLE Genes: apr-1 lit-1 mom-2 mom-4 mom-5 pop-1 hDf9 nDf24 nDf25 nDf29 qDf9 qDf10 mnDf111 Abstract: In C. elegans, a Wnt/WG-like signaling pathway downregulates the TCF/LEF-related protein, POP-1, to specify posterior cell fates. Effecters of this signaling pathway include a beta-catenin homolog, WRM-1, and a conserved protein kinase, LIT-1. WRM-1 and LIT-1 form a kinase complex that can directly phosphorylate POP-1, but how signaling activates WRM-1/LIT-1 kinase is not yet known. Here we show that mom-4, a genetically defined effector of polarity signaling, encodes a MAP kinase kinase kinase-related protein that stimulates the WRM-1/LIT-1-dependent phosphorylation of POP-1. LIT-1 kinase activity requires a conserved residue analogous to an activating phosphorylation site in other kinases, including MAP kinases. These findings suggest that anterior/posterior polarity signaling in C. elegans may ------------------- Key: 3657 Medline: 99421657 Authors: Maebuchi M;Togo SH;Yokota S;Ghenea S;Bun-ya M;Kamiryo T;Kawahara A Title: Type-II 3-oxoacyl-CoA thiolase of the nematode Caenorhabditis elegans is located in peroxisomes, highly expressed during larval stages and induced by clofibrate. Citation: European Journal of Biochemistry 264: 509-515 1999 Type: ARTICLE Genes: Abstract: We examined the expression and localization of type-II 3-oxoacyl-CoA thiolase in the nematode Caenorhabditis elegans. Type-II thiolase acts on 3-oxoacyl-CoA esters with a methyl group at the alpha carbon, whereas conventional thiolases do not. Mammalian type-II thiolase, which is also termed sterol carrier protein x (SCPx) or SCP2/3-oxoacyl-CoA thiolase, is located in the peroxisomes and involved in phytanic acid degradation and most probably in bile acid synthesis. The nematode enzyme lacks the SCP2 domain, which carries the peroxisomal-targeting signal, but produces bile acids in a cell-free system. Northern and Western blot analyses demonstrated that C. elegans expressed type-II thiolase throughout its life cycle, especially during the larval stages, and that the expression was significantly enhanced by the addition of clofibrate at 5 mM or more to the culture medium. Whole-mount in situ hybridization and immunostaining of L4 larvae revealed that the enzyme was mainly expressed in intestinal cells, which are multifunctional like many of the cell types in C. elegans. Subcellular fractionation and indirect immunoelectron microscopy of the nematode detected the enzyme in the matrix of peroxisomes. These results indicate the fundamental homology between mammalian SCPx and the nematode enzyme regardless of whether the SCP2 part is fused, suggesting their common physiological roles. ------------------- Key: 3658 Medline: 99401014 Authors: Gems D Title: Nematode ageing: Putting metabolic theories to the test. Citation: Current Biology 9: R614-R616 1999 Type: ARTICLE Genes: age-1 clk-1 ctl-1 daf-2 daf-16 gro-1 sod-1 Abstract: The increased life span caused by certain mutations in the nematode Caenorhabditis elegans has been interpreted in terms of two metabolic theories of ageing: the oxidative damage theory and the rate of living theory. New findings support the former, but not the latter interpretation. ------------------- Key: 3659 Medline: 99391570 Authors: Wilkie TM Title: G proteins, chemosensory perception, and the C. elegans genome project: An attractive story. Citation: BioEssays 21: 713-717 1999 Type: REVIEW Genes: eat-16 egl-10 egl-30 goa-1 gpa-1 gpa-2 gpa-3 gpa-5 gpa-6 gpa-7 gpa-12 gpb-1 gsa-1 odr-1 odr-3 odr-10 tax-2 tax-4 Abstract: Heterotrimeric G proteins, consisting of alpha, beta, and gamma subunits, couple ligand-bound seven transmembrane domain receptors to the regulation of effector proteins and production of intracellular second messengers. G protein signaling mediates the perception of environmental cues in all higher eukaryotic organisms, including yeast, Dictyostelium, plants, and animals. The nematode Caenorhabditis elegans is the first animal to have complete descriptions of its cellular anatomy, cell lineage, neuronal wiring diagram, and genomic sequence. In a recent paper, Jansen et al.((1)) used sequence searches of the C. elegans genome database to identify all heterotrimeric G protein genes (20 G alpha, 2 G beta, 2 G gamma). C. elegans encodes one ortholog of each of the four Got classes found in metazoans and 16 new G alpha genes. The orthologous genes are widely expressed, whereas 14 of the divergent Ga genes are almost exclusively expressed in sensory neurons where they may regulate perception and chemotaxis. ------------------- Key: 3660 Medline: 99415361 Authors: Guven K;Power RS;Avramide S;Allender R;de Pomerai DI Title: The toxicity of dithiocarbamate fungicides to soil nematodes, assessed using a stress-inducible transgenic strain of Caenorhabditis elegans. Citation: Journal of Biochem Molecular Toxicology 13: 324-333 1999 Type: ARTICLE Genes: Abstract: The dithiocarbamate fungicides maneb and mancozeb induce a short-term stress response in a transgeneic Caenorhabditis elegans (PC72) strain carrying a reporter lacZ gene under the control of a homologous heat shock (hsp16) promoter. This response can be readily monitered as induced B-galactosidase activity, either by in situ staining or by a quantitative fluorometric enzyme assay. Particularly strong responses are induced by mancozeb (three- to fivefold above controls at 500 ug mL-1), causing acute toxicity at concentrations comparable to those recommended for field application (2 mg mL-1). Although much of this fungicide is adsorbed by soil, sufficient (ca. 6%) enters the soil water compartment to cuase mild stress in the transgenic worm assay. Among possible metabolites from mancozeb breakdown, neither Mn2+ nor ethylenethiourea (ETU) is particularly toxic even at 10% of the optimum mancozeb dosage. Stress responses to a range of other pesticides are also reported, and in several cases it is clear that a nontarget soil species (here, transgenic C. elegans) may be sensitive to low-level contamination. ------------------- Key: 3661 Medline: 99398734 Authors: Wittenburg N;Baumeister R Title: Thermal avoidance in Caenorhabditis elegans: An approach to the study of nociception. Citation: Proceedings of the National Academy of Sciences USA 96: 10477-10482 1999 Type: ARTICLE Genes: ace-1 ace-2 ace-3 avr-15 cat-1 cat-2 cat-4 cat-6 cha-1 che-3 che-13 daf-6 daf-10 daf-19 eat-4 flp-1 glr-1 goa-1 lin-11 npr-1 osm-1 osm-3 osm-5 osm-6 osm-9 tax-2 tax-4 ttx-1 ttx-3 unc-25 unc-47 unc-49 unc-86 vab-3 Abstract: Upon perception of a noxious stimulus, an organism executes defense mechanisms, such as escape responses. The molecular basis of these mechanisms is poorly understood. In this paper we show that upon exposure to noxious temperature, Caenorhabditis elegans reacts by a withdrawal reflex. To analyze this thermal avoidance behavior, we developed a laser-based assay to quantify the response. The escape reflex can be observed in 98% of the adult animals, but is not executed in animals in diapause. The thermal avoidance response differs significantly from the thermotaxis behavior that is based on the perception of physiological temperature. It involves different neurons and is influenced by mutations in distinct genes. As in mammals, the strength of the thermal avoidance response is increased by application of capsaicin, the pungent ingredient in chili peppers. We find that thermal avoidance is strongly reduced in mutants affecting the neural transmission modulated by glutamate and neuropeptides as well as in mutants affecting the structure and function of sensory neurons. We suggest that the study of this nociceptive behavior in C. elegans can be used to understand the genetic and molecular basis of thermal nociception. ------------------- Key: 3662 Medline: 99377169 Authors: Hough RF;Lingam AT;Bass BL Title: Caenorhabditis elegans mRNAs that encode a protein similar to ADARs derive from an operon containing six genes. Citation: Nucleic Acids Research 27: 3424-3432 1999 Type: ARTICLE Genes: Abstract: The Caenorhabditis elegans T20H4.4 open reading frame (GenBank accession no, U00037) predicted by Genefinder encodes a 367 amino acid protein that is 32-35% identical to the C-terminal domain of adenosine deaminases that act on RNA, We show that T20H4.4 cDNAs (GenBank accession no. AF051275) encode a larger 495 amino acid protein that is extended at its N-terminus to include a single double-stranded RNA-binding motif, and that T20H4.4 occupies the second position in a six-gene operon (5'-T20H4.5, T20H4.4, R151.8A, R151.8B, R151.7, R151.6-3'), Ten different spliced-leader (SL) sequences were found attached to T20H4.4 mRNAs, including SL1, SL2 and eight SL2-like leaders that include two new variants. Characterization of cDNAs derived from all six genes confirmed the essential features of C. elegans operons: intercistronic distances in the range of 104-257 nt between the upstream polyadenylation sites and the downstream trans-splice sites; SL2, or SL2-like leaders, attached to the downstream mRNAs. Polycistronic mRNA fragments revealed a 5'-untranslated region (5'-UTR) >705 nt, The 5'-UTR is removed in mature mRNAs from the first gene (T20H4.5) and replaced primarily by SL1, and to a lesser extent by SL2. Our study provides new information regarding operons and ------------------- Key: 3663 Medline: 99402999 Authors: Davies AG;Spike CA;Shaw JE;Herman RK Title: Functional overlap between the mec-8 gene and five sym genes in Caenorhabditis elegans. Citation: Genetics 153: 117-134 1999 Type: ARTICLE Genes: mec-2 mec-8 mel-11 sym-1 sym-2 sym-3 sym-4 sym-5 unc-52 mnDf1 mnDf2 mnDf11 mnDf19 mnDp1 Abstract: Earlier work showed that the Caenorhabditis elegans gene mec-8 encodes a regulator of alternative RNA splicing and that mec-8 null mutants have defects in sensory neurons and body muscle attachment but are generally viable and fertile. We have used a genetic screen to identify five mutations in four genes, sym-1-sym-4, that are synthetically lethal with mec-8 loss-of-function mutations. The phenotypes of sym single mutants are essentially wild type. mec-8; sym-1 embryos arrest during embryonic elongation and exhibit defects in the attachment of body muscle to extracellular cuticle. sym-1 can encode a protein containing a signal sequence and lj contiguous leucine-rich repeats. A fusion of sym-1 and the gene for green fluorescent protein rescued the synthetic lethality of mec-8; sym-1 mutants; the fusion protein was secreted from the apical hypodermal surface of the embryo. We propose that SYM-1 helps to attach body muscle to the extracellular cuticle and that another gene that is dependent upon mec-8 for pre-mRNA processing overlaps functionally with sym-1. RNA-mediated interference experiments indicated that a close relative of sym-1 functionally overlaps both sym-1 and mec-8 in affecting muscle attachment, sym-2, sym-3, and sym-4 appear to provide additional functions that are essential in the absence of mec-8(+). ------------------- Key: 3664 Medline: 99435030 Authors: Shabalina SA;Kondrashov AS Title: Pattern of selective constraint in C. elegans and C. briggsae. Citation: Genetical Research 74: 23-30 1999 Type: ARTICLE Genes: Abstract: Similarity between related genomes may carry information on selective constraint in each of them. We analysed patterns of similarity between several homologous regions of Caenorhabditis elegans and C. briggsae genomes. All homologous exons are quite similar. Alignments of introns and of intergenic sequences contain long gaps, segments where similarity is low and close to that between random sequences aligned using the same parameters, and segments of high similarity. Conservative estimates of the fractions of selectively constrained nucleotides are 72%, 17% and 18% for exons, introns and intergenic sequences, respectively. This implies that the total number of constrained nucleotides within non-coding sequences is comparable to that within coding sequences, so that at least one-third of nucleotides in C. elegans and C. briggsae genomes are under strong stabilizing selection. ------------------- Key: 3665 Medline: 10409513 Authors: Zallen JA;Kirch SA;Bargmann CI Title: Genes required for axon pathfinding and extension in the C. elegans nerve ring. Citation: Development 126: 3679-3692 1999 Type: ARTICLE Genes: ceh-23 daf-11 glr-1 sax-1 sax-2 sax-3 sax-5 sax-6 sax-7 sax-8 sax-9 unc-5 unc-6 unc-33 unc-40 unc-44 unc-76 vab-1 mnDp57 Abstract: Over half of the neurons in Caenorhabditis elegans send axon to the nerve ring, a large neuropil in the head of the animal. Genetic screens in animals that express the green fluorescent protein in a subset of sensory neurons identified eight new sax genes that affect the morphology of nerve ring axons. sax-3/robo mutations disrupt axon guidance in the nerve ring, while sax-5, sax-9 and unc-44 disrupt both axon guidance and axon extension. Axon extension and guidance proceed normally in sax-1, sax-2, sax-6, sax-7 and sax-8 mutants, but these animals exhibit later defects in the maintenance of nerve ring structure. The functions of existing guidance genes in nerve ring development were also examined, revealing that SAX-3/Robo acts in parallel to the VAB-1/Eph receptor and the UNC-6/netrin, UNC-40/DCC guidance systems for ventral guidance of axone in the amphid commissure, a major route of axon entry into the nerve ring. In addition, SAX-3/Robo and the VAB-1/Eph receptor both function to prevent aberrant axon crossing at the ventral midline, Together, these genes define pathways required for axon growth, guidance and maintenance during nervous system development. ------------------- Key: 3666 Medline: 99439888 Authors: Bowerman B;Severson AF Title: Cell division: Plant-like properties of animal cell cytokinesis. Citation: Current Biology 9: R658-R660 1999 Type: REVIEW Genes: rab-1 syn-4 zen-4 Abstract: Recent evidence that a syntaxin is required for cytokinesis in Caenorhabditis elegans embryos suggests that the mechanism of cell division in plant and animal cells may be more similar than previously imagined. ------------------- Key: 3667 Medline: Authors: Masler EP;Kovaleva ES;Sardanelli S Title: FMRFamide-like immunoactivity in Heterodera glycines (Nemata: Tylenchida). Citation: Journal of Nematology 31: 224-234 1999 Type: ARTICLE Genes: Abstract: Material antigenically related to the neuromodulatory peptide FMRFamide was detected and examined in preparations of the soybean cyst nematode, Heterodera glycines, and in the free-living nematodes Caenorhabditis elegans and Panagrellus redivivus. FMRFamide-related peptides were quantified by an enzyme-linked immunosorbent assay. Specific activities were remarkably similar among all of the vermiform members of the three species. FMRFamide-related peptide immunoactivity was present in both sexes and all stages of H. glycines examined. The highest specific activity was present in second-stage juveniles and in males, and the lowest in white and yellow females. Total FMRFamide-related peptide level per individual was highest in brown females, with 90% of the activity associated with the eggs. Peptide levels in these eggs and in second-stage juveniles were comparable and increased in adults, especially in females. Chromatographic analysis of FMRFamide-related peptide preparations from H. glycines juveniles, C. elegans, and P. redivivus revealed distinct qualitative differences between the infective plant parasite and the free-living nematodes. ------------------- Key: 3668 Medline: 99383984 Authors: Morita Y;Tilly JL Title: Oocyte apoptosis: Like sand through an hourglass. Citation: Developmental Biology 213: 1-17 1999 Type: ARTICLE Genes: ced-3 ced-4 ced-9 egl-1 Abstract: Although the study of germ cell death is arguably still in its infancy as a held, several recent breakthroughs have provided the fodder for a story, replete with episodes of apparent mass cellular suicide if not murder, that will undoubtedly serve as a research base for many laboratories over the next several years. Death is known to strike the male and female germlines with roughly equal intensity, but the innate feature of male germ cells being self-renewing while those of the female are not places the death of oocytes in a completely different light. Indeed, the functional life span of the female gonads is defined in most species, including humans, by the size and rate of depletion of the precious endowment of oocytes enclosed within follicles in the ovaries at birth. This continuous loss of oocytes throughout life, referred to by many as the female biological clock, appears to be driven by a genetic program of cell death that is composed of players and pathways conserved from worms to humans. It is on this genetic pathway, and the role of its constituent molecules in regulating female germ cell fate, that this review will focus. Emphasis will be placed on those studies using genetic-null or transgenic models to explore the functional requirement of proteins, such as Bcl-2 family members, Apaf-1, and caspases in vertebrates to CED-9, CED-4, and CED-3 in Caenorhabditis elegans, in oocyte survival and death. Furthermore, hypotheses regarding the potential impact of translating what is now known of the oocyte death pathway into new approaches for the clinical diagnosis and management of female infertility and the menopause will be offered as a means to stimulate further research in this new and exciting field. ------------------- Key: 3669 Medline: 20191166 Authors: Behe MJ Title: Tracts of adenosine and cytidine residues in the genomes of prokaryotes and eukaryotes. Citation: DNA Sequence 8: 375-383 1999 Type: ARTICLE Genes: Abstract: Large segments of the S. cerevisiae, C. elegans, D. melanogaster, mouse, and human genomes, as well as the genomes of four bacterial species, have been analyzed for the occurrence of tracts of separated, alternating, and mixed adenosine and cytidine residues. Several surprising features have been observed. Although both yeast and nematode DNA are rich in AT base pairs, the genomes of these organisms have widely different biases for long homonucleotide tracts. Yeast has many long tracts of oligoadenosine, while C. elegans has an extraordinary abundance of oligocytidine tracts. Tracts of alternating A-C residues are overrepresented in most eukaryotic organisms examined. Tracts of mixed adenosine and cytidine residues, however, are especially frequent in the human ------------------- Key: 3670 Medline: Authors: Fire A Title: RNA-triggered gene silencing. Citation: Trends in Genetics 15: 358-363 1999 Type: REVIEW Genes: Abstract: Double-stranded RNA (dsRNA) has recently been shown to trigger sequence-specific gene silencing in a wide variety of organisms, including nematodes, plants, trypanosomes, fruit flies and planaria; meanwhile an as yet uncharacterized RNA trigger has been shown to induce DNA methylation in several different plant systems. In addition to providing a surprisingly effective set of tools to interfere selectively with gene function, these observations are spurring new inquiries to understand RNA-triggered genetic-control mechanisms and their ------------------- Key: 3671 Medline: Authors: Lewis A;Khatchatouriants A;Treinin M;Chen Z;Peleg G;Friedman N;Bouevitch O;Rothman Z;Loew L;Sheres M Title: Second-harmonic generation of biological interfaces: probing the membrane protein bacteriorhodopsin and imaging membrane potential around GFP molecules at specific sites in neuronal cells of C. elegan Citation: Chemical Physics 245: 133-144 1999 Type: ARTICLE Genes: Abstract: econd-harmonic generation (SHG) is applied to problems of probing membrane proteins and functionally imaging around selective sites and at single molecules in biological membranes. The membrane protein bacteriorhodopsin (bR) has been shown to have large second-harmonic (SH) intensities that are modulated by protein/retinylidene chromophore interactions. The nonlinear optical properties of model compounds, which simulate these protein chromophore interactions in retinal proteins, are studied in this work by surface SHG and by hyper-Rayleigh scattering. Our results indicate that non-conjugated charges and hydrogen bonding effects have a large effect on the molecular hyperpolarizability of the retinal chromophore. However, mbR, the model system studies suggest that polarizable amino acids strongly affect the vertically excited state of the retinylidene chromophore and appear to play the major role in the observed protein enhancement (> 50%) of the retinylidene chromophore molecular hyperpolarizability and associated induced dipole. Furthermore, the data provide insights on emulating these interactions for the design of organic nonlinear optical materials. Our studies have also led to the development of dyes with large SH intensities that can be embedded in cell membranes and can functionally image membrane potential. Single molecules of such dyes in selected single molecular regions of a cell membrane have been detected. SHG from green fluorescent protein (GFP) selectively expressed in concert with a specific protein in neuronal cells in a transgenic form of the worm C. elegans is also reported. The membrane potential around the GFP molecules expressed in these cells has been imaged with SHG in live animals. ------------------- Key: 3672 Medline: Authors: Blaxter ML;De Ley P;Garey JR;Liu LX;Scheldeman P;Vierstraete A;Vanfleteren JR;Mackey LY;Dorris M;Frisse LM;Vida JT;Thomas WK Title: A molecular evolutionary framework for the phylum Nematoda. Citation: Nature 392: 71-75 1998 Type: ARTICLE Genes: Abstract: Nematodes are important: parasitic nematodes threaten the health of plants, animals and humans on a global scale; interstitial nematodes pervade sediment and soil ecosystems in overwhelming numbers; and Caenorhabditis elegans is a favourite experimental model system. A lack of clearly homologous characters and the absence of an informative fossil record have prevented us from deriving a consistent evolutionary framework for the phylum. Here we present a phylogenetic analysis, using 53 small subunit ribosomal DNA sequences from a wide range of nematodes. With this analysis, we can compare animal-parasitic, plant-parasitic and free-living taxa using a common measurement. Our results indicate that convergent morphological evolution may be extensive and that present higher-level classification of the Nematoda will need revision. We identify five major clades within the phylum, all of which include parasitic species. We suggest that animal parasitism arose independently at least four times, and plant parasitism three times. We clarify the relationship of C. elegans to major parasitic groups; this will allow more effective exploitation of our genetic and biological knowledge of this model species. ------------------- Key: 3673 Medline: Authors: Berger A Title: Gonads are the key to a long life. Citation: BMJ 318: 1506- 1999 Type: REVIEW Genes: Abstract: Biochemists have found that the lifespan of the nematode Caenorhabditis elegans is controlled by its reproductive system, meaning that successful reproduction means a shorter life. ------------------- Key: 3674 Medline: Authors: Tear G Title: Neuronal guidance: A genetic perspective. Citation: Trends in Genetics 15: 113-118 1999 Type: REVIEW Genes: sax-3 unc-5 unc-6 unc-34 unc-40 unc-73 unc-115 unc-129 Abstract: Remarkable advances have been made recently to identify the molecules required for the development of neural connections within the brain. A range of ligands and receptors have been uncovered that guide extending neurons to appropriate targets and away from inappropriate areas. These molecules point to the signalling mechanisms that guide the neurons and provide entry points for the further dissection of this process. Here I highlight the part genetic screens and analyses have played in revealing some of the key players in neuronal guidance. ------------------- Key: 3675 Medline: 99415810 Authors: Zetka MC;Kawasaki I;Strome S;Muller F Title: Synapsis and chiasma formation in Caenorhabditis elegans require HIM-3, a meiotic chromosome core component that functions in chromosome segregation. Citation: Genes & Development 13: 2258-2270 1999 Type: ARTICLE Genes: him-3 rad-4 sDp2 sDp3 Abstract: Meiotic chromosomes are organized about a proteinaceous core that forms between replicated sister chromatids. We have isolated a Caenorhabditis elegans gene, him-3, which encodes a meiosis-specific component of chromosome cores with some similarity to the yeast lateral element protein Hop1p. Antibodies raised against HIM-3 localize the protein to condensing chromosomes in early prophase I and to the cores of both synapsed and desynapsed chromosomes. In RNA interference experiments, chromosomes appear to condense normally in the absence of detectable protein but fail to synapse and form chiasmata, indicating that HIM-3 is essential for these processes. Hypomorphs of him-3, although being synapsis proficient, show severe reductions in the frequency of crossing-over, demonstrating that HIM-3 has a role in establishing normal levels of interhomolog exchange. Him-3 mutants also show defects in meiotic chromosome segregation and the persistence of the protein at the chromosome core until the metaphase I-anaphase I transition suggests that HIM-3 may play a role in sister chromatid cohesion. The analysis of him-3 provides the first functional description of a chromosome core component in a multicellular organism and suggests that a mechanistic link exists between the early meiotic events of synapsis and recombination, and later events such as segregation. ------------------- Key: 3677 Medline: 99418626 Authors: Schafer WR Title: How do antidepressants work? Prospects for genetic analysis of drug mechanisms. Citation: Cell 98: 551-554 1999 Type: REVIEW Genes: ndg-4 nrf-6 Abstract: Fluoxetine (a.k.a. Prozac) is well known for its ability to treat clinical depression, one of the most prevalent of all psychiatric disorders. Yet the mechanism by which fluoxetine actually functions to relieve depression is not well understood. Fluoxetine is the best-known member of a class of antidepressant drugs known as serotonin-selective reuptake inhibitors (SSRIs). In popular accounts, their antidepressant action is usually explained in the context of along-standing model of depression called the serotonin hypothesis. According to this model, levels of seratonergic neurotransmission in the forebrain are a key determinant of mood: high activity results in euphoria, low activity results in dysphoria. Depression is said to be caused by chronically low levels of serotonergic transmission. SSRIs interfere with the activity of the serotonin transporter (5-HTT), a reuptake molecule that removes serotonin from the synapse; thus, the putative low levels of synaptic serotonin in the depressed patient are elevated, and depression is relieved. Consistent with this model, many other antidepressants, including tricyclics (e.g., clomipramine) and monoamine oxidase inhibitors, also potentiate serotonergic transmission by interfering with serotonin reuptake or degradation. ------------------- Key: 3678 Medline: 10517634 Authors: Zhen M;Jin Y Title: The liprin protein SYD-2 regulates the differentiation of presynaptic termini in C. elegans. Citation: Nature 401: 371-375 1999 Type: ARTICLE Genes: rab-3 snb-1 snt-1 syd-2 unc-13 unc-25 Abstract: At synaptic junctions, specialized subcellular structures occur in both pre- and postsynaptic cells. Most presynaptic termini contain electron-dense membrane structures(1), often referred to as active zones, which function in vesicle docking and release(2). The components of those active zones and how they are formed are largely unknown. We report here that a mutation in the Caenorhabditis elegans syd-2 (for synapse-defective) gene causes a diffused localization of several presynaptic proteins and of a synaptic-vesicle membrane associated green fluorescent protein (GFP) marker(3,4). Ultrastructural analysis revealed that the active zones of syd-2 mutants were significantly lengthened, whereas the total number of vesicles per synapse and the number of vesicles at the prominent active zones were comparable to those in wild-type animals. Synaptic transmission is partially impaired in syn-2 mutants. syd-2 encodes a member of the liprin (for LAR-interacting protein) family of proteins which interact with LAR-type (for leukocyte common antigen related) receptor proteins with tyrosine phosphatase activity (RPTPs)(5,6). SYD-2 protein is localized at presynaptic termini independently of the presence of vesicles, and functions cell autonomously. We propose that SYD-2 regulates the differentiation of presynaptic termini in particular the formation of the active zone, by acting as an intracellular anchor for RPTP signalling at synaptic ------------------- Key: 3679 Medline: 99365277 Authors: Kim S;Ren X-C;Fox E;Wadsworth WG Title: SDQR migrations in Caenorhabditis elegans are controlled by multiple guidance cues and changing responses to netrin UNC-6. Citation: Development 126: 3881-3890 1999 Type: ARTICLE Genes: mec-3 mec-4 mec-7 unc-5 unc-6 unc-40 unc-119 Abstract: The netrin guidance cue, UNC-6, and the netrin receptors, UNC-5 and UNC-40, guide SDQR cell and axon migrations in C. elegans. In wild-type larvae, SDQR migrations are away from ventral UNC-6-expressing cells, suggesting that UNC-6 repels SDQR. In unc-6 null larvae, SDQR migrations are towards the ventral midline, indicating a response to other guidance cues that directs the migrations ventrally. Although ectopic UNC-6 expression dorsal to the SDQR cell body would be predicted to cause ventral SDQR migrations in unc-6 null larvae, in fact, more migrations are directed dorsally, suggesting that SDQR is not always repelled from the dorsal source of UNC-6. UNC-5 is required for dorsal SDQR migrations, but not for the ventral migrations in unc-6 null larvae. UNC-40 appears to moderate both the response to UNC-6 and to the other cues. Our results show that SDQR responds to multiple guidance cues and they suggest that, besides UNC-6, other factors influence whether an UNC-6 responsive cell migrates toward or away from an UNC-6 source in vivo. We propose that multiple signals elicited by the guidance cues are integrated and interpreted by SDQR and that the response to UNC-6 can change depending on the combination of cues encountered during migration. These responses determine the final dorsoventral position of the SDQR cell and axon. ------------------- Key: 3680 Medline: 99445226 Authors: Barr MM;Sternberg PW Title: A polycystic kidney-disease gene homologue required for male mating behavior in C. elegans. Citation: Nature 401: 386-389 1999 Type: ARTICLE Genes: che-3 daf-10 osm-1 osm-5 osm-6 lov-1 pkd-2 mnDf21 Abstract: The stereotyped mating behaviour of the Caenorhabditis elegans male is made up of several substeps: response, backing, turning, vulva location, spicule insertion and sperm transfer. The complexity of this behaviour is reflected in the sexually dimorphic anatomy and nervous system(1). Behavioural functions have been assigned to most of the male-specific sensory neurons by means of cell ablations; for example, the hook sensory neurons HOA and HOB are specifically required for vulva location(2). We have investigated how sensory perception of the hermaphrodite by the C. elegans male controls mating behaviours. Here we identify a gene, lov-1 (for location of vulva), that is required for two male sensory behaviours: response and vulva location. lov-1 encodes a putative membrane protein with a mucin-like, serine-threonine-rich amino terminus' followed by two blocks of homology to human polycystins, products of the autosomal dominant polycystic kidney-disease loci PKD1 and PKD2 (ref 4). LOV-1 is the closest C. elegans homologue of PKD1. lov-1 is expressed in adult males in sensory neurons of the rays, hook and head, which mediate response, vulva location, and potentially chemotaxis to hermaphrodites, respectively(2,5). PKD-2, the C. elegans homologue of PKD2, is localized to the same neurons as LOV-1, suggesting that they function in the same ------------------- Key: 3681 Medline: 99445215 Authors: Emmons SW;Somlo S Title: Mating, channels and kidney cysts. Citation: Nature 401: 339-340 1999 Type: REVIEW Genes: lov-1 pkd-2 Abstract: Advances in human genetics have meant that the genes mutated in human diseases can be identified exclusively by their location in the genome. But how do we work out the cellular functions of the associated protein products? Reports on pages 383 and 386 of this issue begin to address this problem for two proteins - polycystin-1 (PKD1) and polycystin-2 (PKD2) - that are defective in human kidney disease. From their studies of the nematode worm Caenorhabditis elegans, Barr and Sternberg present evidence that homologues of the polycystins act together in a signal-transduction pathway in sensory neurons. Chen et al., by contrast, have used an oocyte-expression system in the from Xenopus laevis to show that a homologue of PKD2 is associated with the activity of a cation channel. These results support the hypothesis that polycystin-related proteins belong to a hitherto unknown class of signal-transduction molecules. ------------------- Key: 3682 Medline: 99429980 Authors: Stein LD Title: Internet access to the C. elegans genome. Citation: Trends in Genetics 15: 425-427 1999 Type: ARTICLE Genes: Abstract: In December 1998, the genome of the small soil-dwelling nematode Caenorhabditis elegans became the most recent model to fall to the collective efforts of the Genome Project, its complete 97 Mbp genome taking its place alongside those of Saccharomyces cerevisiae, Escherichia coli and numerous other microorganisms. The availability of the C. elegans sequence means that, for the first time, the complete genome of a fully functional multicellular animal is available to the scientific community, along with a rich infrastructure of genetic, behavioral, physiological and developmental data about the organism. ------------------- Key: 3683 Medline: Authors: Dreyfus DH;Gelfand EW Title: Comparative analysis of invertebrate Tc6 sequences that resemble the vertebrate V(D)J recombination signal sequences (RSS). Citation: Molecular Immunology 36: 481-488 1999 Type: ARTICLE Genes: Abstract: Invertebrate cells lack the p53 recombination checkpoint but contain mobile DNA sequences that transpose by a mechanism in part shared with excision of the V(D)J recombination signal sequences (RSS). In this work, inversion, deletion, and duplication of sequences associated with an invertebrate C. elegans Tc6 element is described. The structure of this C. elegans sequence and other dispersed Tc6 elements suggests that covalently closed 'hairpin' structures are not unique to excision of the V(D)J RSS by the RAG proteins, but rather can be generated by transposases at transposon termini leading to characteristic inversion and duplication events. Comparative analysis of recombination events at invertebrate sequences resembling the vertebrate V(D)J RSS may be useful in understanding V(D)J recombination-mediated recombination events in malignant vertebrate cells or genetic diseases such as ataxia telangectasia, in which the ------------------- Key: 3684 Medline: Authors: Goto S;Nakamura A;Radak Z;Nakamoto H;Takahashi R;Yasuda K;Sakurai Y;Ishii N Title: Carbonylated proteins in aging and exercise: immunoblot approaches. Citation: Mechanisms of Ageing & Development 107: 245-253 1999 Type: ARTICLE Genes: mev-1 Abstract: Protein carbonyls were studied in aging and exercise by immunoblot followed by one- or two-dimensional polyacrylamide gel electrophoresis using antibodies against 2,4-dinitrophenylhydrazones. Proteins of rat kidneys exhibited significant age-related increase in the amount of carbonyl while those of the brain and liver did not. Major carbonylated proteins in the kidney included serum albumin. In nematodes in which protein carbonyls increased with age, one of the carbonylated proteins was identified as vitellogenin, an egg-yolk protein. A possible biological significance of this protein present in abundance even after egg-laying stages is discussed in terms of protection against oxidative stress. Exhaustive exercise induced significant increase in the carbonylation of selected but unidentified proteins in the lung. This oxidative stress might be caused by xanthine oxidase in this tissue and hypoxanthine derived from ATP-depleted muscles. Exercise at high altitude caused higher carbonylation of the skeletal muscle proteins, most notably a protein likely to be actin, than that at sea level but no significant difference was observed in lipid peroxidation. These studies emphasize the value of immunoblot analysis of tissue protein carbonyls in a variety of situations where oxidative stress is likely involved. ------------------- Key: 3685 Medline: Authors: Deutsch M;Long M Title: Intron-exon structures of eukaryotic model organisms. Citation: Nucleic Acids Research 27: 3219-3228 1999 Type: ARTICLE Genes: Abstract: To investigate the distribution of intron-exon structures of eukaryotic genes, we have constructed a general exon database comprising all available intron-containing genes and exon databases from 10 eukaryotic model organisms: Homo sapiens, Mus musculus, Gallus gallus, Rattus norvegicus, Arabidopsis thaliana, Zea mays, Schirosaccharomyces pombe, Aspergillus, Caenorhabditis elegans and Drosophila. We purged redundant genes to avoid the possible bias brought about by redundancy in the databases. After discarding those questionable introns that do not contain correct splice sites, the final database contained 17 102 introns, 21 019 exons and 2903 independent or quasi-independent genes, On average, a eukaryotic gene contains 3.7 introns per kb protein coding region. The exon distribution peaks around 30-40 residues and most introns are 40-125 nt long. The variable intron-exon structures of the 10 model organisms reveal two interesting statistical phenomena, which cast light on some previous speculations. (i) Genome size seems to be correlated with total intron length per gene. For example, invertebrate introns are smaller than those of human genes, while yeast introns are shorter than invertebrate introns, However, this correlation is weak, suggesting that other factors besides genome size may also affect intron size. (ii) Introns smaller than 50 nt are significantly less frequent than longer introns, possibly resulting from a minimum intron size requirement for intron splicing. ------------------- Key: 3686 Medline: 99410454 Authors: Fitzgerald DJ;Anderson JN Title: Selective nucleosome disruption by drugs that bind in the minor groove of DNA. Citation: Journal of Biological Chemistry 274: 27128-27138 1999 Type: ARTICLE Genes: Abstract: Previous studies have shown that drugs which bind in the DNA minor groove reduce the curvature of bent DNA. In this article, we examined the effects of these drugs on the nucleosome assembly of DNA molecules that display different degrees of intrinsic curvature, DAPI (4,6-diamidino-2-phenylindole) inhibited the assembly of a histone octamer onto a 192-base pair circular DNA fragment from Caenorhabditis elegans and destabilized a nucleosome that was previously assembled on this segment. The inhibitory effect was highly selective since it was not seen with nonbent molecules, bent molecules with noncircular shapes, or total genomic DNA. This marked template specificity was attributed to the binding of the ligand to multiple oligo A-tracts distributed over the length of the fragment, A likely mechanism for the effect is that the bound ligand prevents the further compression of the DNA into the minor groove which is required for assembly of DNA into nucleosomes. To further characterize the effects of the drug on chromatin formation, a nucleosome was assembled onto a 322-base pair DNA fragment that contained the circular element and a flanking nonbent segment of DNA. The position of the nucleosome along the fragment was then determined using a variety of nuclease probes including exonuclease III, micrococcal nuclease, DNase I, and restriction enzymes. The results of these studies revealed that the nucleosome was preferentially positioned along the circular element in the absence of DAPI but assembled onto the nonbent flanking sequence in the presence of the drug. DAPI also induced the directional movement of the nucleosome from the circular element onto the nonbent flanking sequence when a nucleosome preassembled onto this template was exposed to the drug ------------------- Key: 3687 Medline: Authors: Ailion M;Inoue T;Weaver CI;Holdcraft RW;Thomas JH Title: Neurosecretory control of aging in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 96: 10944- 1999 Type: CORRECT Genes: daf-2 daf-16 unc-31 unc-64 Abstract: ------------------- Key: 3689 Medline: 99431668 Authors: Vajo Z;King LM;Jonassen T;Wilkin DJ;Ho N;Munnich A;Clarke CF;Francomano CA Title: Conservation of the Caenorhabditis elegans timing gene clk-1 from yeast to human: a gene required for ubiquinone biosynthesis with potential implications for aging. Citation: Mammalian Genome 10: 1000-1004 1999 Type: ARTICLE Genes: clk-1 Abstract: Mutations in the Caenorhabditis elegans gene clk-1 have a major effect on slowing development and increasing life span. The Saccharomyces cerevisiae homolog COQ7 encodes a mitochondrial protein involved in ubiquinone biosynthesis and, hence, is required for respiration and gluconeogenesis. In this study, RT-PCR and 5' RACE were used to isolate both human and mouse clk-1/COQ7 homologs. Human CLK-1 was mapped to Chr 16(p12-13.1) by Radiation Hybrid (RH) and fluorescence in situ hybridization (FISH) methods. The number and location of human CLK1 introns were determined, and the location of introns TI and TV are the same as in C. elegans. Northern blot analysis showed that three different isoforms of CLK-1 mRNA are present in several tissues and that the isoforms differ in the amount of expression. The functional equivalence of human CLK-1 to the yeast COQ7 homolog was tested by introducing either a single or multicopy plasmid containing human CLK-1 cDNA into yeast coq7 deletion strains and assaying for growth on a nonfermentable carbon source. The human CLK-1 gene was able to functionally complement yeast coq7 deletion mutants. The protein similarities and the conservation of function of the CLK-1/clk-I/COQ7 gene products suggest a potential link between the production of ubiquinone and ------------------- Key: 3690 Medline: 99421694 Authors: Geier G;Banaj HJ;Heid H;Bini L;Pallini V;Zwilling R Title: Aspartyl proteases in Caenorhabditis elegans-Isolation, identification and characterization by a combined use of affinity chromatography, two-dimensional gel electrophoresis, microsequencing and dat.. Citation: European Journal of Biochemistry 264: 872-879 1999 Type: ARTICLE Genes: Abstract: Crude homogenates of the nematode Caenorhabditis elegans exhibit maximal proteolytic activity under acidic pH conditions. About 90% of this activity is inhibited by the oligopeptide pepstatin, which specifically inhibits the activity of aspartyl proteases such as pepsin, cathepsins D and E or renin. We have purified enzymes responsible for this proteolytic activity by a single-step affinity chromatography on pepstatin-agarose. Analysis of the purified fraction by 1D SDS gel electrophoresis revealed six bands ranging from 35 to 52 kDa. After electrotransfer to poly(vinylidene difluoride) membranes, all bands were successfully subjected to N-terminal microsequencing. On 2D gels, the purified protein bands split into 19 spots which, after renewed microsequencing, were identified as isoelectric variants of the six proteins already described. The N-termini obtained for these proteins could be correlated to genomic DNA sequences determined in the course of the C. elegans genome sequencing project. All these sequences were predicted to code for expressed proteins as collected in the WORMPEP database. Five of the six coding sequences identified in this study were found to contain the typical active-site consensus sequence of aspartyl proteases and displayed an overall amino acid identity between 25 and 66% as compared to aspartyl proteases from other organisms. In addition to the five aspartyl proteases detected at the protein level, we have identified the coding sequences for seven other enzymes of this protease family by a similarity search in the genomic DNA of C. elegans which has recently been completely ------------------- Key: 3691 Medline: 99439915 Authors: Moerman DG Title: Organ morphogenesis: A metalloprotease prepares the way. Citation: Current Biology 9: R701-R703 1999 Type: REVIEW Genes: gon-1 Abstract: In the nematode Caenorhabditis elegans gonad shape and size is determined by the migration of a leader cell, which is at the tip of the growing gonad arm. A metalloprotease secreted by the leader cell has recently been found to play an essential role in this process, preparing the way ahead for the cell's migration. ------------------- Key: 3692 Medline: 99439892 Authors: Kraemer B;Crittenden S;Gallegos M;Moulder G;Barstead R;Kimble J;Wickens M Title: NANOS-3 and FBF proteins physically interact to control the sperm-oocyte switch in Caenorhabditis elegans. Citation: Current Biology 9: 1009-1018 1999 Type: ARTICLE Genes: ced-3 cpb-1 fbf-1 fbf-2 fem-3 nos-1 nos-2 nos-3 Abstract: Background: The Caenorhabditis elegans FBF protein and its Drosophila relative, Pumilio, define a large family of eukaryotic RNA-binding proteins. By binding regulatory elements in the 3' untranslated regions (UTRs) of their cognate RNAs, FBF and Pumilio have key post-transcriptional roles in early developmental decisions. In C. elegans, FBF is required for repression of fem-3 mRNA to achieve the hermaphrodite switch from spermatogenesis to oogenesis. Results: We report here that FBF and NANOS-3 (NOS-3), one of three C. elegans Nanos homologs, interact with each other in both yeast two-hybrid and in vitro assays. We have delineated the portions of each protein required for this interaction. Worms lacking nanos function were derived either by RNA-mediated interference (nos-1 and nos-2) or by use of a deletion mutant (nos-3). The roles of the three nos genes overlap during germ-line development. In certain nos-deficient animals, the hermaphrodite sperm-oocyte switch was defective, leading to the production of excess sperm and no oocytes. In other nos-deficient animals, the entire germ line died during larval development. This germ-line death did not require CED-3, a protease required for apoptosis. Conclusions: The data suggest that NOS-3 participates in the sperm-oocyte switch through its physical interaction with FBF, forming a regulatory complex that controls fem-3 mRNA. NOS-1 and NOS-2 also function in the switch, but do not interact directly with FBF. The three C. elegans nanos genes, like Drosophila nanos, are also critical for germ-line survival. We propose that this may have been the primitive function of nanos genes. ------------------- Key: 3693 Medline: 99428139 Authors: Dal Santo P;Logan MA;Chisholm AD;Jorgensen EM Title: The inositol triphosphate receptor regulates a 50-second behavioral rhythm in C. elegans. Citation: Cell 98: 757-767 1999 Type: ARTICLE Genes: dec-4 itr-1 lfe-1 stDf7 Abstract: The C. elegans defecation cycle is characterized by the contraction of three distinct sets of muscles every 50 s. Our data indicate that this cycle is regulated by periodic calcium release mediated by the inositol trisphosphate receptor (IP3 receptor). Mutations in the IF, receptor slow down or eliminate the cycle, while overexpression speeds up the cycle. The IP3 receptor controls these periodic muscle contractions nonautonomously from the intestine. In the intestinal cells, calcium levels oscillate with the same period as the defecation cycle and peak calcium levels immediately precede the first muscle contraction. Mutations in the IF, receptor slow or eliminate these calcium oscillations. Thus, the IP3 receptor is an essential component of the timekeeper for this cycle and represents a novel mechanism for the control of behavioral rhythms. ------------------- Key: 3694 Medline: 10546898 Authors: Labbe JC;Hekimi S;Rokeach LA Title: Assessing the function of the Ro ribonucleoprotein complex using Caenorhabditis elegans as a biological tool. Citation: Biochemistry & Cell Biology 77: 349-354 1999 Type: ARTICLE Genes: rop-1 yrn-1 Abstract: The Ro ribonucleoprotein complex (Ro RNP) was initially described as an autoimmune target in human diseases such as systemic lupus erythematosus and Sjogren's syndrome. In Xenopus and human cells, its general structure is composed of one major protein of 60 kDa, Ro60, that binds to one of four small RNA molecules, designated Y RNAs. Although no function has been assigned to the Ro RNP, Ro60 has been shown to bind mutant 5S ribosomal RNA (rRNA) molecules in Xenopus oocytes, suggesting a role for Ro60 in 5S rRNA biogenesis. Ro60 has also been shown to participate in the regulation of the translational fate of the L4 ribosomal protein mRNA by interacting with the 5' untranslated region, again suggesting its possible implication in ribosome biogenesis. To identify the function of Ro RNP we have taken a genetic approach in the nematode Caenorhabditis elegans. As such, we characterized the gene encoding the protein ROP-1, the homologue of the human Ro60 protein. Here, we review the phenotypic analysis of C. elegans rop-1(-) mutants and integrate these results into a model for the function of the Ro RNP particle. ------------------- Key: 3696 Medline: 10587376 Authors: Nowell MA;de Pomerai DI;Pritchard DI Title: Caenorhabditis elegans as a biomonitor for immunological stress in nematodes. Citation: Parasite Immunology 21: 495-505 1999 Type: ARTICLE Genes: Abstract: An experimental system has been developed using Caenorhabditis elegans (Secernentea: Rhabditida), to monitor immunological stress in nematodes. The transgenic C. elegans strain PC72 carries a lacZ reporter gene fused to a C. elegans hsp16-1 gene, which is inducible for beta-galactosidase activity at the heat stress temperature of 26 degrees C. The investigate the possibility of using PC72 to monitor immunological stress, its surface coat was targeted, to mimic immune attack, by raising immune sera against surface coat components selectively removed by the cationic detergent cetyltrimethylammoniunm bromide. initially, a highly significant induction of beta-galaclosidase activity was seen in PC72 incubated in either surface-reactive or naive rabbit serum. Complement (C3) was detected over the entire surface of adult PC72 and was thought to be responsible for stress-induction with naive sera. When the immunoglobulin (Ig)G fraction of naive sera was used in isolation, no stress-induction was seen. In contrast a two-fold increase in beta-galactosidase activity was seen in the presence of surface-reactive IgG (SR-IgG) which recognised surface components of between 6 and 40 kDa in western blot. The belief that surface reactive IgG could induce a stress response was reinforced by analysis of hsp-16 protein expression. Cationised ferritin was then used to assess whether stress-induction was truly a surface reactive event; binding of cationised ferritin to the nematode surface also resulted in two-fold induction of beta-galactosidase activity. To investigate the downstream biological effects of stress induction, worm growth and fecundity were measured in the presence of IgG preparations. A significant reduction, was seen in both worm length and fecundity only when larvae were incubated in surface-reactive IgG, compared to both naive IgG and K-medium controls. In conclusion, it would appear that C. elegans is a suitable model to monitor the induction of immunological stress at the level of the nematode surface coat. Given the ability of nematode surface antigens to protect the vaccinated host in animal model systems, and the close phylogenetic relationships which exist between C. elegans and nematodes of medical and veterinary importance, it is conceivable that the immunological targets in or on the surface of C. elegans warrant rapid identification. ------------------- Key: 3697 Medline: 20140210 Authors: Nurrish S;Segalat L;Kaplan JM Title: Serotonin inhibition of synaptic transmission: G alpha(o) decreases the abundance of UNC-13 at release sites. Citation: Neuron 24: 231-242 1999 Type: ARTICLE Genes: cat-1 dgk-1 egl-10 goa-1 npr-1 unc-13 Abstract: We show that serotonin inhibits synaptic transmission at C. elegans neuromuscular junctions, and we describe a signaling pathway that mediates this effect. Release of acetylcholine from motor neurons was assayed by measuring the sensitivity of intact animals to the acetylcholinesterase inhibitor aldicarb. Fly this assay, exogenous serotonin inhibited acetylcholine release, whereas serotonin antagonists stimulated release. The effects of serotonin on synaptic transmission were mediated by GOA-1 (a G alpha(o) subunit) and DGK-1 (a diacylglycerol [DAG] kinase), both of which act in the ventral cord motor neurons. Mutants lacking goa-1 Got, accumulated abnormally high levels of the DAG-binding protein UNC-13 at motor neuron nerve terminals, suggesting that serotonin inhibits synaptic transmission by decreasing the abundance of UNC-13 ------------------- Key: 3698 Medline: 10518212 Authors: Metzstein MM;Horvitz HR Title: The C. elegans cell death specification gene ces-1 encodes a snail family zinc finger protein. Citation: Molecular Cell 4: 309-319 1999 Type: ARTICLE Genes: ced-3 ced-4 ced-9 ces-1 ces-2 cpn-1 Abstract: The ces-1 and ces-2 genes of C. elegans control the programmed deaths of specific neurons. Genetic evidence suggests that ces-2 functions to kill these neurons by negatively regulating the protective activity of ces-l. ces-2 encodes a protein closely related to the vertebrate PAR family of bZIP transcription factors, and a ces-2/ces-1-like pathway may play a role in regulating programmed cell death in mammalian lymphocytes. Here we show that ces-1 encodes a Snail family zinc finger protein, most similar in sequence to the Drosophila neuronal differentiation protein Scratch. We define an element important for ces-1 regulation and provide evidence that CES-2 can bind to a site within this element and thus may directly repress ces-1 transcription. Our results suggest that a transcriptional cascade controls the deaths of specific cells in C. elegans. ------------------- Key: 3699 Medline: 99444910 Authors: Fischer SEJ;van Luenen HGAM;Plasterk RHA Title: Cis requirements for trasposition of Tc1-like transposons in C. elegans. Citation: Molecular & General Genetics 262: 268-274 1999 Type: ARTICLE Genes: Abstract: The Caenorhabditis elegans transposons Tc1 and Tc3 are able to transpose in heterologous systems such as human cell lines and zebrafish. Because these transposons might be useful vectors for transgenesis and mutagenesis of diverse species, we determined the minimal cis requirements for transposition. Deletion mapping of the transposon ends shows that fewer than 100 bp are sufficient for transposition of Tc3. Unlike Tc1, Tc3 has a second, internal transposase binding site at each transposon end. We found that these binding sites play no major role in the transposition reaction, since they can be deleted without reduction of the transposition frequency. Site-directed mutagenesis was performed on the conserved terminal base pairs at the Tc3 ends. The four terminal base pairs at the ends of the Tc3 inverted repeats were shown to be required for efficient transposition. Finally, increasing the length of the transposon from 1.9 kb to 12.5 kb reduced the transposition frequency by 20-fold, both in vivo and in ------------------- Key: 3700 Medline: 99445509 Authors: Moilanen LH;Fukushige T;Freedman JH Title: Regulation of metallothionein gene transcription-Identification of upstream regulatory elements and transcription factors responsible for cell-specific expression of the metallothionein genes from Citation: Journal of Biological Chemistry 274: 29655-29665 1999 Type: ARTICLE Genes: end-1 elt-1 elt-2 mtl-1 mtl-2 Abstract: Metallothioneins are small, cysteine-rich proteins that function in metal detoxification and homeostasis. Metallothionein transcription is controlled by cell-specific factors, as well as developmentally modulated and metal-responsive pathways. By using the nematode Caenorhabditis elegans as a model system, the mechanism that controls cell-specific metallothionein transcription in vivo was investigated. The inducible expression of the C. elegans metallothionein genes, mtl-1 and mtl-2, occurs exclusively in intestinal cells. Sequence comparisons of these genes with other C. elegans intestinal cell-specific genes identified multiple repeats of GATA transcription factor-binding sites (i.e. GATA elements). In vivo deletion and site-directed mutation analyses confirm that one GATA element in mtl-1 and two in mtl-2 are required for transcription. Electrophoretic mobility shift assays show that the C. elegans GATA transcription factor ELT-2 specifically binds to these elements. Ectopic expression of ELT-2 in non-intestinal cells of C. elegans activates mtl-2 transcription in these cells. Likewise, mtl-2 is not expressed in nematodes in which elt-2 has been disrupted. These results indicate that cell-specific transcription of the C. elegans metallothionein genes is regulated by the binding of ELT-2 to GATA elements in these promoters. Furthermore, a model is proposed where ELT-2 constitutively activates metallothionein expression; however, a second metal-responsive factor prevents transcription in the absence of metals. ------------------- Key: 3701 Medline: 99432244 Authors: Van Voorhies WA;Ward S Title: Genetic and environmental conditions that increase longevity in Caenorhabditis elegans decrease metabolic Citation: Proceedings of the National Academy of Sciences USA 96: 11399-11403 1999 Type: ARTICLE Genes: age-1 clk-1 daf-2 daf-16 fer-15 Abstract: Mutations that increase the longevity of the soil nematode Caenorhabditis elegans could define genes involved in a process specific for aging. Alternatively, these mutations could reduce animal metabolic rate and increase longevity as a consequence. In ectotherms, longevity is often negatively correlated with metabolic rate. Consistent with these observations, environmental conditions that reduce the metabolic rate of C. elegans also extend longevity. We found that the metabolic rate of long-lived C. elegans mutants is reduced compared with that of wild-type worms and that a genetic suppressor that restored normal longevity to long-lived mutants restored normal metabolic rate. Thus, the increased longevity of some long-lived C. elegans mutants may be a consequence of a reduction in their metabolic rate, rather than an alteration of a genetic pathway that leads to enhanced longevity while maintaining normal physiology. The actual mechanism responsible for the inverse correlation between metabolic ------------------- Key: 3702 Medline: 99452252 Authors: Buchwitz BJ;Ahmad K;Moore LL;Roth MB;Henikoff S Title: Cell division - A histone-H3-like protein in C. elegans. Citation: Nature 401: 547-548 1999 Type: ARTICLE Genes: hcp-3 Abstract: The segregation of a chromosome during mitosis is mediated by a region of the chromosome known as the centromere, which organizes the kinetochore, to which the spindle microtubules attach. Many organisms have monocentric chromosomes, in which the centromeres amp to single loci, whereas others, including the nematode Caenorhabditis elegans, have holocentric chromosomes, in which non-localized kinetochores extend along the length of each chromosome. The centromeres of monocentric chromosomes use specialized nucleosomes containing histone-H3-like proteins (known as CENP-A in mammals and Cse4 in the yeast Saccharomyces cerevisiae). Here we show that a C. elegans histone-H3-like protein is necessary for the proper segregation of chromosomes during mitosis and identifies the centromeres of these holocentric chromosomes, indicating the both holocentric and monocentric chromosomes ------------------- Key: 3703 Medline: 20035771 Authors: Wheelan SJ;Boguski MS;Duret L;Makalowski W Title: Human and nematode orthologs - lessons from the analysis of 1800 human genes and the proteome of Caenorhabditis Citation: Gene 238: 163-170 1999 Type: ARTICLE Genes: Abstract: Recently, we have defined and analyzed over 1800 orthologous human and rodent genes. Here we extend this work to compare human and Caenorhabditis elegans coding sequences. 1880 human proteins were compared with about 20000 predicted nematode proteins presumably comprising nearly the complete proteome of C. elegans, We found that 44% of human/rodent orthologs have convincing nematode counterparts. On average, the amino acid similarity and identity between aligned human and C. elegans orthologous gene products are 69.3% and 49.1% respectively, and the nucleotide identity is 49.8%. Detailed investigation of our results suggests that some nematode gene predictions are incorrect, leading to erroneous pairing with human genes (e.g. calcineurin and polymerase II elongation factor III). Furthermore, other proteins (i.e. homologs of human ribosomal proteins S20 and L41, thymosin) are missing entirely from the nematode proteome, suggesting that it may not be complete. These results underscore the fact that metazoan gene prediction is a very challenging task and that most computer-predicted nematode genes require supporting evidence of their existence from comparative ------------------- Key: 3704 Medline: 99439763 Authors: Gonczy P;Pichler S;Kirkham M;Hyman AA Title: Cytoplasmic dynein is required for distinct aspects of MTOC positioning, including centrosome separation, in the one cell stage Caenorhabditis elegans embryo. Citation: Journal of Cell Biology 147: 135-150 1999 Type: ARTICLE Genes: dhc-1 Abstract: We have investigated the role of cytoplasmic dynein in microtubule organizing center (MTOC) positioning using RNA-mediated interference (RNAi) in Caenorhabditis elegans to deplete the product of the dynein heavy chain gene dhc-1. Analysis with time-lapse differential interference contrast microscopy and indirect immunofluorescence revealed that pronuclear migration and centrosome separation failed in one cell stage dhc-1 (RNAi) embryos. These phenotypes were also observed when the dynactin components p50/dynamitin or p150(Glued) were depleted with RNAi. Moreover, in 15% of dhc-1 (RNAi) embryos, centrosomes failed to remain in proximity of the male pronucleus. When dynein heavy chain function was diminished only partially with RNAi, centrosome separation took place, but orientation of the mitotic spindle was defective. Therefore, cytoplasmic dynein is required for multiple aspects of MTOC positioning in the one cell stage C. elegans embryo. In conjunction with our observation of cytoplasmic dynein distribution at the periphery of nuclei, these results lead us to propose a mechanism in which cytoplasmic dynein anchored on the nucleus drives ------------------- Key: 3705 Medline: 99439940 Authors: Liu LX;Spoerke JM;Mulligan EL;Chen J;Reardon B;Westlund B;Sun L;Abel K;Armstrong B;Hardiman G;King J;McCague L;Basson M;Clover R;Johnson CD L Title: High-throughput isolation of Caenorhabditis elegans deletion mutants. Citation: Genome Research 9: 859-867 1999 Type: ARTICLE Genes: akt-1 cdc-25 csp-1 cul-2 daf-18 daf-21 hop-1 lim-6 mod-1 npc-1 npc-2 osm-10 sel-12 tip-1 xfl-1 Abstract: The nematode Caenorhabditis elegans is the First animal whose genome is completely sequenced, providing a rich source of gene information relevant to metazoan biology and human disease. This abundant sequence information permits a broad-based gene inactivation approach in C. elegans, in which chemically mutagenized nematode populations are screened by PCR for deletion mutations in a specific targeted gene. By handling mutagenized worm growth, genomic DNA templates, PCR screens, and mutant recovery ail in 96-well microtiter plates, we have scaled up this approach to isolate deletion mutations in >100 genes to date. Four chemical mutagens, including ethyl methane sulfonate, ethlynitrosourea, diepoxyoctane, and ultraviolet-activated trimethylpsoralen, induced detectable deletions at comparable Frequencies. The deletions averaged similar to 1400 bp in size when using a -3 kb screening window. The vast majority of detected deletions removed portions of one or more exons, likely resulting in loss of gene function. This approach requires only the knowledge of a target gene sequence and a suitable mutagen, and thus provides a scalable systematic approach to gene inactivation for any organism that can be handled in high density arrays. ------------------- Key: 3706 Medline: 10508660 Authors: Blelloch R;Newman C;Kimble J Title: Control of cell migration during Caenorhabditis elegans development. Citation: Current Opinion in Cell Biology 11: 608-613 1999 Type: REVIEW Genes: bar-1 ced-5 egl-15 egl-17 egl-20 gon-1 lin-17 lin-39 mab-5 mig-2 mig-13 unc-5 unc-6 unc-40 unc-73 unc-129 vab-8 Abstract: In Caenorhabditis elegans, cell migration is guided by localized cues, including molecules such as EGL-17/FGF and UNC-6/netrin, These external cues are linked to an intracellular response to migrate, at least in part, by CED-5, a homolog of DOCK180/MBC, and MIG-2, a Rac-like GTPase, In addition, metalloproteases are required for a cell migration that controls organ shape. ------------------- Key: 3707 Medline: Authors: Slack FJ;Ruvkun G Title: A novel repeat domain that is often associated with RING finger and B-box motifs. Citation: Trends in Biochemical Sciences 23: 474-475 1999 Type: ARTICLE Genes: lin-41 ncl-1 Abstract: The RING-B-Box-Coiled-coil (RBCC) family consists of proteins that have a RING finger, and one or two B-Box motifs followed by a coiled-coil domain. The Cys/His-rich RING finger and B-box domains each chelate zinc and might be involved in protein-protein and/or protein-nucleic-acid interactions. Members of the RBCC family have variable subcellular localizations and have been implicated in a variety of processes. ------------------- Key: 3708 Medline: Authors: Sommer RJ Title: Convergence and the interplay of evolution and development. Citation: Evolution & Development 1: 8-10 1999 Type: REVIEW Genes: Abstract: Developmental constraints have been defined as "biases on the production of variant phenotypes or limitations on phenotypic variability caused by the structure, character, composition, or dynamics of developmental systems". The term has widely been discussed, but is far from being generally accepted. One reason might be that is has so far not been possible to test experimentally the concept of restraint. Experimental tests are difficult because the hypothesis is supported only by the failure or the limitation of seeing phenotypic variation, which can always hypothetically be explained by stabilizing selection. This article suggests an approach to study the potential molecular basis for developmental constraints. ------------------- Key: 3709 Medline: Authors: Power RS;de Pomerai DI Title: Effect of single and paired metal inputs in soil on a stress-inducible transgenic nematode. Citation: Archives of Environmental Contamination and Toxicology 37: 503-511 1999 Type: ARTICLE Genes: Abstract: A toxicity test using a transgenic strain of the free-living soil nematode Caenorhabditis elegans carrying a stress-inducible P-galactosidase reporter has been adapted for use in soil biomonitoring. High concentrations (250 mu g . g(-1)) of cadmium are required to induce the stress response in worms exposed to Lufa 2.2 soil. Even at relatively high concentrations, the response to copper and zinc additions alone is minimal, yet combinations of cadmium and copper in the test soil induce a larger response than with cadmium alone at the same concentration. In contrast, the addition of both zinc and cadmium induces a lower response than cadmium additions alone. Analysis of the interstitial water suggests that there is preferential occupation by copper of sorption sites in the soil, allowing more cadmium to remain in solution. Conversely, cadmium and zinc would appear to interact similarly with the soil constituents, resulting in an increase of both metals in solution with increased additions to the soil. Aquatic tests mimic the results of the soil test, so it is not increased cadmium availability alone that causes an increased stress response when both cadmium and copper are present. The presence of other metals could reduce the amount of cadmium available, which may be one factor in the zinc moderation of the stress response to cadmium. Intracellular mechanisms may also contribute to the copper enhancement of the stress response to cadmium. ------------------- Key: 3710 Medline: 99439600 Authors: Tepass U Title: Genetic analysis of cadherin function in animal morphogenesis. Citation: Current Opinion in Cell Biology 11: 540-548 1999 Type: REVIEW Genes: cdh-3 hmp-1 hmp-2 hmr-1 jam-1 Abstract: Cadherins are a superfamily of Ca2+-dependent adhesion molecules found in metazoans. Several classes of cadherins have been defined from which two - classic cadherins and Fat-like cadherins - have been studied by genetic approaches. Recent in vivo studies in Caenorhabditis elegans and Drosophila show that cadherins play an active role in a number of distinct morphogenetic processes, Classic cadherins function in epithelial polarization, epithelial sheet or tube fusion, cell migration, cell sorting, and axonal patterning. Fat-like cadherins are required for epithelial morphogenesis, proliferation control, and epithelial planar polarization. ------------------- Key: 3711 Medline: 10535731 Authors: Tabara H;Sarkissian M;Kelly WG;Fleenor J;Grishok A;Timmons L;Fire A;Mello CC Title: The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Citation: Cell 99: 123-132 1999 Type: ARTICLE Genes: mes-2 mes-3 mes-4 mes-6 mut-2 mut-6 mut-7 rde-1 rde-2 rde-3 rde-4 sqt-3 unc-22 eDf1 mDf3 nDf31 sDf29 sDf35 Abstract: Double-stranded (ds) RNA can induce sequence-specific inhibition of gene function in several organisms. However, both the mechanism and the physiological role of the interference process remain mysterious. In order to study the interference process, we have selected C. elegans mutants resistant to dsRNA-mediated interference (RNAi). Two loci, rde-1 and rde-4, are defined by mutants strongly resistant to RNAi but with no obvious defects in growth or development. We show that rde-1 is a member of the piwi/sting/argonaute/zwille/elF2C gene family conserved from plants to vertebrates. Interestingly, several, but not all, RNAi-deficient strains exhibit mobilization of the endogenous transposons. We discuss implications for the mechanism of RNAi and the possibility that one natural function of RNAi is transposon silencing. ------------------- Key: 3712 Medline: Authors: Sugimoto A;Miura M Title: Death signalling in C. elegans and activation mechanisms of caspases. Citation: "Apoptosis Genes". JW Wilson, C Booth CS Potten (eds). : 167-203 1998 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-9 ced-10 ced-11 ces-1 ces-2 dad-1 deg-1 egl-1 lin-24 lin-33 mec-4 mec-10 nuc-1 Abstract: Cell proliferation and cell death are two opposing sides of the same coin. The development and homeostasis of multicellular organisms requires the accurate control of both processes. The death that occurs normally as a process of development is called 'programmed cell death' or 'apoptosis'. The phenomenon of developmentally programmed cell death has been known for more than 100 years, but it is only in the last decade that its molecular mechanisms have begun to be uncovered. The nematode Caenorhabditis elegans is one of the few experimental systems in which a genetic approach is available to dissect the processes of programmed cell death, and in fact, findings from studies using C. elegans have already played a very important role in elucidating these mechanisms. Here, we summarise the progress to date in understanding how cell death is controlled in C. elegans, and review the main machinery of programmed cell death/apoptosis with respect to its evolutionary conservation between C. elegans and other species. ------------------- Key: 3713 Medline: Authors: Anton AH;Berk AI Title: Utilization of ethanol by Caenorhabditis elegans. Citation: Research Communications in Alcohol & Substances of Abuse 19: 29-36 1998 Type: ARTICLE Genes: Abstract: In an attempt to develop a worm model for studying alcoholism in man, the non-parasitic roundworm Caenorhabditis elegans (C.e.), was exposed daily to a non-lethal amount of ethanol for over a year. Rather than being harmful, the worms thrived on this regimen. Apparently, the absence of ethanol-sensitive, mammalian organs and a different intermediary metabolism of ethanol, allow the worms to utilize the alcohol for useful energy and biosynthetic mechanisms. Thus, C.e. probably would not be the appropriate animal model in which to study the basis of alcoholism in man. ------------------- Key: 3715 Medline: 99443780 Authors: Mullen GP;Rogalski TM;Bush JA;Gorji PR;Moerman DG Title: Complex patterns of alternative splicing mediate the spatial and temporal distribution of perlecan/UNC-52 in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 10: 3205-3221 1999 Type: ARTICLE Genes: mec-8 unc-52 mnDp34 Abstract: The unc-52 gene encodes the nematode homologue of mammalian perlecan, the major heparan sulfate proteoglycan of the extracellular matrix. This is a large complex protein with regions similar to low-density lipoprotein receptors, laminin, and neural cell adhesion molecules (NCAMs). In this study, we extend our earlier work and demonstrate that a number of complex isoforms of this protein are expressed through alternative splicing. We identified three major classes of perlecan isoforms: a short form lacking the NCAM region and the C-terminal agrin-like region; a medium form containing the NCAM region, but still lacking the agrin-like region; and a newly identified long form that contains all five domains present in mammalian perlecan. Using region-specific antibodies and unc-52 mutants, we reveal a complex spatial and temporal expression pattern for these UNC-52 isoforms. As well, using a series of mutations affecting different regions and thus different isoforms of UNC-52, we demonstrate that the medium NCAM-containing isoforms are sufficient for myofilament lattice assembly in developing nematode body-wall muscle. Neither short isoforms nor isoforms containing the C-terminal agrin-like region are essential for sarcomere assembly or muscle cell attachment, and their role in ------------------- Key: 3716 Medline: 99454945 Authors: George RL;Wu X;Huang W;Fei YJ;Leibach FH;Ganapathy V Title: Molecular cloning and functional characterization of a polyspecific organic anion transporter from Caenorhabditis elegans. Citation: Journal of Pharmacology and Experimental Therapeutics 291: 596-603 1999 Type: ARTICLE Genes: Abstract: We have cloned a polyspecific organic anion transporter from Caenorhabditis elegans and elucidated its functional characteristics. The C. elegans anion transporter (CeOAT1) codes for a protein of 526 amino acids containing 12 putative transmembrane domains. It exhibits significant homology at the level of amino acid sequence to the C. elegans organic cation transporter and to the mammalian organic cation and anion transporters. The function of CeOAT1 was investigated by expressing the transporter heterologously in mammalian cells. CeOAT1 transports p-aminohippurate (PAH) in a Na+-independent manner. The transport mechanism appears to involve anion exchange because CeOAT1-mediated PAH transport is stimulated by a cell-to-medium concentration gradient of alpha-ketoglutarate or fumarate generated by coexpression in the cells of a mammalian Na+-coupled dicarboxylate transporter. CeOAT1 exhibits broad specificity, accepting anions such as folate, indomethacin, furosemide, probenecid, and benzylpenicillin as substrates. The Michaelis-Menten constant for the prototypical organic anion PAH is 0.43 +/- 0.07 mM. This constitutes the first report of the molecular and functional identification of a polyspecific organic anion transporter in C. elegans. ------------------- Key: 3717 Medline: 99455093 Authors: Aspock G;Kagoshima H;Niklaus G;Burglin TR Title: Caenorhabditis elegans has scores of hedgehog-related genes: Sequence and expression analysis. Citation: Genome Research 9: 909-923 1999 Type: ARTICLE Genes: grd-1 grd-2 grd-3 grd-4 grd-5 grd-6 grd-7 grd-8 grd-9 grd-10 grd-11 grd-13 grd-14 wrt-1 wrt-2 wrt-3 wrt-4 wrt-5 wrt-5 wrt-7 wrt-8 wrt-9 wrt-10 Abstract: Previously, we have described novel families of genes, warthog (wrt) and groundhog (grd), in Caenorhabditis elegans. They are related to Hedgehog (Hh) through the carboxy-terminal autoprocessing domain [called Hog or Hint). A comprehensive survey revealed 10 genes with Hog/Hint modules in C. elegans. Five of these are associated with a Wart domain in wrt genes, and three with multiple copies of the Ground domain in grd genes. Both the Wart domain and the Ground domain occur also in genes encoding no Hog domain. Further, we define a new group of genes related to the grd genes, called ground-like (grl). Overall, C. elegans has more than 50 genes belonging to these gene families. Phylogenetic and sequence analysis shows that the wrt,grd,and grl genes are derived from each other. Further examination reveals a sequence motif with similarity to the core of the amino-terminal-signaling domain of Hh proteins. Our data suggest that the wrt,grd,grl,and hh genes are derived from a single ancestral gene. wrt, grd, and grl genes are also present in other nematodes, but so far not in any other phyla. Conversely, hh is not found presently in C. elegans nor other nematodes. Thus, the nematode genes could be the homologs of Hh molecules in other phyla. The membrane molecule Patched has been shown previously to be a receptor of Hh. Many Patched-related proteins are present ire C. elegans, which may be targets of the hh-related genes. No Hedgehog-interacting protein (Hip) was found. We analyzed the expression patterns of eight wrt and eight grd genes. The results show that some closely related genes are expressed in the same tissues, but, overall, the expression patterns are diverse, comprising hypodermis, seam cells, the excretory cell, sheath and socket cells, and different ------------------- Key: 3718 Medline: 99455094 Authors: Bowen NJ;McDonald JF Title: Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements. Citation: Genome Research 9: 924-935 1999 Type: ARTICLE Genes: Abstract: Retrotransposons are the most abundant and widespread class of eukaryotic transposable elements. The recent genome sequencing of Caenorhabditis elegans has provided an unprecedented opportunity to analyze the evolutionary relationships among the entire complement of retrotransposons within a multicellular eukaryotic organism. In this article we report the results of an analysis of retroviral-like long terminal repeat retrotransposons in C. elegans that indicate that this class of elements may be even more abundant and divergent than previously expected. The unexpected presence, in C. elegans, of an element displaying a number of characteristics previously thought to be unique to vertebrate retroviruses suggests an ancient lineage for ------------------- Key: 3719 Medline: 99442379 Authors: Chamberlin HM;Brown KB;Sternberg PW;Thomas JB Title: Characterization of seven genes affecting Caenorhabditis elegans hindgut development. Citation: Genetics 153: 731-742 1999 Type: ARTICLE Genes: cdh-3 egl-5 egl-38 lin-48 lin-49 lin-58 mab-9 sem-4 eDf18 eDf19 mDf7 qDf3 sDf121 sDf130 yDf10 Abstract: We have identified and characterized 12 mutations in seven genes that affect the development of the Caenorhabditis elegans hindgut. We find that the mutations can disrupt the postembryonic development of the male-specific blast cells within the hindgut, the hindgut morphology in both males and hermaphrodites, and in some cases, the expression of a hindgut marker in hermaphrodite animals. Mutations in several of the genes also affect viability. On the basis of their mutant phenotypes, we propose that the genes fall into four distinct classes: (1) egl-5 is required for regional identity of the tail; (2) sem-4 is required for a variety of ectodermal and mesodermal cell types, including cells in the hindgut; (3) two genes, lin-49 and lin-59, affect development of many cells, including hindgut; and (4) three genes, mab-9, egl-38, and lin-48, are required for patterning fates within the hindgut, making certain hindgut cells different from others. We also describe a new allele of the Pax gene egl-38 that is temperature sensitive and affects the conserved beta-hairpin of the EGL-38 paired domain. Our results suggest that a combination of different factors contribute to normal C. elegans hindgut ------------------- Key: 3720 Medline: 99442380 Authors: Jakubowski J;Kornfeld K Title: A local, high-density, single-nucleotide polymorphism map used to clone Caenorhabditis elegans cdf-1. Citation: Genetics 153: 743-752 1999 Type: ARTICLE Genes: cdf-1 let-60 lon-2 mup-2 unc-6 uDf1 Abstract: Ras-mediated signaling is required for induction of vulval cell fates during Caenorhabditis elegans development. By screening for suppressors of the multivulva phenotype caused by constitutively active let-60 ras, we identified the mutation n2527. To clone the gene affected by n2527, we developed a method for high-resolution mapping. We took advantage of the genomic DNA sequence of the N2 strain by using DNA sequencing to scan for single-nucleotide polymorphisms (SNPs) at defined genomic positions of the RC301 strain. An average of one polymorphism per 1.4 kb was detected in predicted intergenic regions. Because of this high frequency, DNA sequencing is an efficient method to scan for SNPs. By alternating between identifying SNPs and mapping n2527 using selected recombinants, we generated an SNP map of progressively higher density. An intensive search for SNPs resulted in a local map with an average marker spacing of similar to 4 kb. This was used to map n2527 to a 9.6-kb interval. The small size of this interval made it feasible to use DNA sequencing to identify the molecular lesion. In principle, this approach can be used for high-resolution mapping of any C. elegans mutation. Furthermore, this approach can be applied to other species as the genomic sequence becomes available. The n2527 mutation affects a previously uncharacterized gene that we named cdf-1, as it encodes a predicted protein with significant similarity to members of the cation diffusion facilitator family. ------------------- Key: 3721 Medline: 99423662 Authors: Buechner M;Hall DH;Bhatt H;Hedgecock EM Title: Cystic canal mutants in Caenorhabditis elegans are defective in the apical membrane domain of the renal Citation: Developmental Biology 214: 227-241 1999 Type: ARTICLE Genes: exc-1 exc-2 exc-3 exc-4 exc-5 exc-6 exc-7 exc-8 exc-9 let-4 let-653 sma-1 eDf6 eDf7 eDf9 eDf12 eDf16 eDf18 eDf19 mDf7 mnDf1 mnDf2 mnDf4 mnDf5 mnDf7 mnDf8 mnDf9 mnDf10 mnDf11 mnDf13 mnDf15 mnDf16 mnDf17 mnDf18 mnDf19 mnDf20 mnDf21 mnDf27 mnDf41 mnDf42 mnDf43 mnDf58 mnDf59 mnDf66 mnDf68 mnDf71 mnDf83 mnDf89 nDf19 sDf2 sDf22 yDf10 mnDp1 mnDp31 sDp3 Abstract: The excretory cell extends a tubular process, or canal, along the basolateral surface of the epidermis to form the nematode renal epithelium. This cell can undergo normal tubulogenesis in isolated cell culture. Mutations in 12 genes cause excretory canal cysts in Caenorhabditis elegans. Genetic interactions, and their similar phenotypes, suggest these genes may encode functionally related proteins. Depending upon genotype and individual canal, defects range from focal cysts, flanked by normal width segments, to regional cysts involving the entire tubule. Oftentimes the enlarged regions are convoluted or partially septated. In mutants with very large cysts, renal function is measurably impaired. Based on histology and ultrastructure, canal cysts likely result from defects of the apical membrane domain. These mutants provide a model of tubulocystic disease without hyperplasia or basement membrane abnormalities. Similar apical mechanisms could regulate tubular morphology of vertebrate nephrons. ------------------- Key: 3722 Medline: 20004390 Authors: Ketting RF;Haverkamp THA;van Luenen HGAM;Plasterk RKH Title: mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Citation: Cell 99: 133-141 1999 Type: ARTICLE Genes: mut-2 mut-4 mut-5 mut-6 mut-7 rde-1 Abstract: While all known natural isolates of C. elegans contain multiple copies of the Tc1 transposon, which are active in the soma, Tc1 transposition is fully silenced in the germline of many strains. We mutagenized one such silenced strain and isolated mutants in which Tct had been activated in the germline ("mutators"). Interestingly, many other transposons of unrelated sequence had also become active. Most of these mutants are resistant to RNA interference (RNAi). We found one of the mutated genes, mut-7, to encode a protein with homology to RNaseD. This provides support for the notion that RNAi works by dsRNA-directed, enzymatic RNA degradation. We propose a model in which MUT-7, guided by transposon-derived dsRNA, represses transposition by degrading transposon-specific messengers, thus preventing transposase production and transposition. ------------------- Key: 3723 Medline: Authors: Hirabayashi J Title: Mutations in possible glycosylation genes, sqv-3, 7 and 8, of C. elegans cause abnormal vulval formation. Citation: Trends in Glycoscience and Glycotechnology 11: 211-212 1999 Type: ARTICLE Genes: sqv-3 sqv-7 sqv-8 Abstract: Apoptosis and gastrulation are critical biological events required for normal development of multicellular animals. As a glycobiologist, you may easily imagine that both of these phenomena involve specific carbohydrate recognition, but actually it is rather difficult to prove. The nematode C. elegans seems to be an ideal model animal for such a proof, because its complete cell lineages have already been established, and more recently, the genome project for this organism has been accomplished. In addition, vulval formation which consists of invagination of epitherial cells underlying the cuticular layer into the inner tissues has been well studied. Essentially, this process is analogous to gastrulation. Recently, 8 genes names sqv-1-8 have been identified as those involved in normal vulval formation by a representative C. elegans genetic group [Herman, T., Hartwieg, E., and Horvitz, R. (1999) Proc. Natl. Acad. Sci. USA, 96, 968-973]. To our surprise, it turned out that three of the (sqv-3,7,8) were quite similar to the known mammalian genes encoding glucuronyltransferase, galactose transferase, and sugar nucleotide transporter [Herman, T., and Horvitz, R. (1999) Proc. Natl. Acad. Sci. US 96, 974-979]. ------------------- Key: 3724 Medline: Authors: Freeman MN;Peredney CL;Williams PL Title: A soil bioassay using the nematode Caenorhabditis elegans. Citation: "Environmental Toxicology and Risk Assessment: Standardization of Biomarkers for Endocrine Disruption and Environmental Assessment: ASTM STP 1364." DS Henshel, MC Black and MC Harrass (eds). West Conshohocken, PA. 8: 305-318 1999 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans is a free-living soil nematode that is commonly used as a biological model. Recently, much work has been done using the nematode as a toxicological model as well. Much of the work involving C. elegans has been performed in aquatic media, since it lives in the interstitial water of soil. However, testing in soil would be expected to more accurately reproduce the organism's normal environment and may take into consideration other factors not available in an aquatic test, i.e., toxicant availability effects due to sorption, various chemical interactions, etc. This study used a modification of a previous experimental protocol to determine 24h LC50 values for Cu in a Cecil series soil mixture, and examined the use of CuCl2 as a reference toxicant for soil toxicity testing with C. elegans. Three different methods of determining percent lethality were used, each dependent on how the number of worms missing after the recovery process was used in the lethality calculations. Only tests having >/= 80% worm recovery and >/= 90% control survival were used in determining the LC50S, by Probit analysis. The replicate LC50 values generated a control chart for each method of calculating percent lethality. The coefficient of variation (CV) for each of the three methods was 0). Further analysis revealed that the average direction of movement after a pirouette was up the gradient. These observations suggest that chemotaxis is produced by a series of pirouettes that reorient the animal to the gradient. We tested this idea by imposing the correlation between pirouettes and dC/dt on a stochastic point model of worm motion. The model exhibited chemotaxis behavior in a radial gradient and also in a novel planar gradient. Thus, the pirouette model of C. elegans chemotaxis is sufficient and general. ------------------- Key: 3741 Medline: 20001961 Authors: Nakamura A;Yasuda K;Adachi H;Sakurai Y;Ishii N;Goto S Title: Vitellogenin-6 is a major carbonylated protein in aged nematode, Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 264: 580-583 1999 Type: ARTICLE Genes: Abstract: Recently we found that protein carbonyl content increases with age in wild-type as well as long- and short-lived Caenorhabditis elegans nematodes in inverse correlation with life span (Adachi et-al., J. Gerontol. 53A B240-B244, 1998; Yasuda et al., J. Gerontol. 54A, B47-B51, 1999). In the present study, we investigated carbonyl modification of individual proteins in young and old wild-type nematodes by two-dimensional immunoblot using antibodies against 2,4-dinitrophenylhydrazones. A protein with apparent molecular weight of 110 kDa was found to be a major carbonylated protein in aged animals. Amino acid sequence of peptide fragments of the protein was identical to that of vitellogenin-6, a yolk protein synthesized in and secreted from the intestine during egg-laying stage. Although the function(s) of the protein in aged nematodes is unclear, we suggest that the protein may have a role to protect other cellular components from oxidation because of its metal binding capacity. ------------------- Key: 3742 Medline: 20036006 Authors: Lackner MR;Nurrish SJ;Kaplan JM Title: Facilitation of synaptic transmission by EGL-30 G(q)alpha and EGL-8 PLC beta: DAG binding to UNC-13 is required to stimulate acetylcholine release. Citation: Neuron 24: 335-346 1999 Type: ARTICLE Genes: acr-2 dgk-1 egl-8 egl-30 goa-1 rab-3 snt-1 unc-13 unc-29 Abstract: We show that neurotransmitter release at Caenorhabditis elegans neuromuscular junctions is facilitated by a presynaptic pathway composed of a G(q)alpha (EGL-30), EGL-8 phospholipase C beta (PLC beta), and the diacylglycerol- (DAG-) binding protein UNC-13. Activation of this pathway increased release of acetylcholine at neuromuscular junctions, whereas inactivation decreased release. Phorbol esters stimulated acetylcholine release, and this effect was blocked by a mutation that eliminates phorbol ester binding to UNC-13. Expression of a constitutively membrane-bound form of UNC-13 restored acetylcholine release to mutants lacking the egl-8 PLC beta. Activation of this pathway with muscarinic agonists caused UNC-13 to accumulate in punctate structures in the ventral nerve cord. These results suggest that presynaptic DAG facilitates synaptic transmission and that part of this ------------------- Key: 3743 Medline: 20036007 Authors: Zheng Y;Brockie PJ;Mellem JE;Madsen DM;Maricq AV Title: Neuronal control of locomotion in C. elegans is modified by a dominant mutation in the GLR-1 ionotropic glutamate receptor. Citation: Neuron 24: 347-361 1999 Type: ARTICLE Genes: ced-1 eat-4 glr-1 mec-3 mec-4 nmr-1 sra-6 unc-86 Abstract: How simple neuronal circuits control behavior is not well understood at the molecular or genetic level. In Caenorhabditis elegans, foraging behavior consists of long, forward movements interrupted by brief reversals. To determine how this pattern is generated and regulated, we have developed novel perturbation techniques that allow us to depolarize selected neurons in vivo using the dominant glutamate receptor mutation identified in the Lurcher mouse. Transgenic worms that expressed a mutated C. elegans glutamate receptor in interneurons that control locomotion displayed a remarkable and unexpected change in their behavior-they rapidly alternated between forward and backward coordinated movement. Our findings suggest that the gating of movement reversals is controlled in a partially distributed fashion by a small subset of interneurons and that this gating is modified by sensory ------------------- Key: 3744 Medline: 20062179 Authors: Shim YH Title: elt-1, a gene encoding a Caenorhabditis elegans GATA transcription factor, is highly expressed in the germ lines with msp genes as the potential targets. Citation: Molecules & Cells 9: 535-541 1999 Type: ARTICLE Genes: elt-1 fem-2 fem-3 glp-4 him-8 Abstract: The Caenorhabditis elegans ELT-1 protein, a homolog of the vertebrate GATA transcription factor family, is a transcription activator that can recognize the GATA motif, We previously showed that the elt-1 mRNA was primarily expressed in C. elegans embryos. To examine whether the elt-1 mRNA in embryos is maternal, paternal or zygotic, Northern blot analysis was performed with RNA isolated from the C. elegans germ-line mutant strains, fem-2 (b245)lf, fem-3 (q20)gf, him-3 (e1489), and glp-4 (bn2). This analysis revealed that the high level of elt-1 mRNA in the C. elegans embryos resulted from either the maternal or the paternal transcription, rather than from the zygotic expression. These results further demonstrated that elt-1 was highly expressed in the germ-line of both sexes. To investigate the possible target genes for the ELT-1 protein in the germ line, the ELT-1 protein was expressed and tested for its binding specificity to the GATA motif that is present in the promoter region of the C. elegans major sperm protein genes. It was found that two conserved cis-elements, AGATCT and AGATAA, in the proximal promoter region of the msp-113 gene provided the best recognition site for ELT-I. Mutational analysis showed that the GATC core sequence was necessary for strong transactivation of the reporter gene, and that the combination of GATC and GATA motif resulted in a stronger transactivation by ELT-1 than either the duplicated GATC or GATA motif. These results suggest that the potential target for the ELT-1 protein in the germ-line may be one of the major sperm ------------------- Key: 3745 Medline: Authors: Bird DM;Opperman CH;Jones SJM;Baillie DL Title: The Caenorhabditis elegans genome: A guide in the post genomics age. Citation: Annual Review of Phytopathology 37: 247-265 1999 Type: REVIEW Genes: Abstract: The completion of the entire genome sequence of the free-living nematode, Caenorhabditis elegans is a tremendous milestone in modern biology. Not only will scientists be poring over data mined from this resource, but techniques and methodologies developed along the way have changed the way we can approach biological questions. The completion of the C. elegans genomic sequence will be of particular importance to scientists working on parasitic nematodes. In many cases, these nematode species present intractable challenges to those interested in their biology and genetics. The data already compared from parasites to the C. elegans database reveals a wealth of opportunities for parasite biologists. It is likely that many of the same genes will be present in parasites and that these genes will have similar functions. Additional information regarding differences between free-living and parasitic species will provide insight into the evolution and nature of parasitism. Finally, genetic and genomic approaches to the study of parasitic nematodes now have a clearly marked path to follow. ------------------- Key: 3746 Medline: 99391992 Authors: Richmond JE;Jorgensen EM Title: One GABA and two acetylcholine receptors function at the C. elegans neuromuscular junction. Citation: Nature Neuroscience 2: 791-797 1999 Type: ARTICLE Genes: unc-29 unc-38 unc-49 Abstract: We describe an electrophysiological preparation of the neuromuscular junction of the nematode C. elegans, which adds to its considerable genetic and genomic resources. Mutant analysis, pharmacology and patch-clamp recording showed that the body wall muscles of wild-type animals expressed a GABA receptor and two acetylcholine receptors. The muscle GABA response was abolished in animals lacking the GABA receptor gene unc-49. One acetylcholine receptor was activated by the nematocide levamisole. This response was eliminated in mutants lacking either the unc-38 or unc-29 genes, which encode alpha and non-alpha acetylcholine receptor subunits, respectively. The second, previously undescribed, acetylcholine receptor was activated by nicotine, desensitized rapidly and was selectively blocked by dihydro-beta-erythroidine, thus explaining the residual motility of unc-38 and unc-29 mutants. By recording spontaneous endogenous currents and selectively eliminating each of these receptors, we demonstrated that all three receptor types function at ------------------- Key: 3747 Medline: 20028439 Authors: Milne CA;Hodgkin J Title: ETR-1, a homologue of a protein linked to myotonic dystrophy, is essential for muscle development in Caenorhabditis elegans. Citation: Current Biology 9: 1243-1246 1999 Type: ARTICLE Genes: etr-1 let-502 mup-2 Abstract: Post-transcriptional gene processing by RNA-binding proteins (RBPs) has crucial roles during development [1,2]. Here, we report the identification of ETR-1 (ELAV-type RNA-binding protein), a muscle-specific REP in the nematode Caenorhabditis elegans, ETR-1 is related to the family of RBPs defined by the protein ELAV, which is essential for neurogenesis in the fruit fly Drosophila; members of the family possess two consecutive RNA recognition motifs (RRMs) separated from a third, carboxy-terminal RRM by a tether region of variable length [3-6], Its closest homologue, CUG-binding protein (CUG-bp), is a human REP that has been implicated in the disease myotonic dystrophy and binds CUG repeats in the 3' untranslated region (UTR) of the mRNA for myotonic dystrophy protein kinase (DMPK) [7,8]. Inactivation of etr-1 by RNA-mediated interference resulted in embryonic lethality. Embryos failed to elongate and became paralysed, a phenotype characteristic of C. elegans Pat mutants, which are defective in muscle formation and function [9]. The data indicate that etr-1 is essential for muscle development in C. elegans, perhaps by playing a role in post-transcriptional processing of some muscle component, and thus suggesting a possible conservation of gene function with human CUG-bp. ------------------- Key: 3748 Medline: 20017520 Authors: Jagannathan S;Laughton DL;Critten CL;Skinner TM;Horoszok L;Wolstenholme AJ Title: Ligand-gated chloride channel subunits encoded by the Haemonchus contortus and Ascaris suum orthologues of the Caenorhabditis elegans gbr-2 (avr-14) gene. Citation: Molecular & Biochemical Parasitology 103: 129-140 1999 Type: ARTICLE Genes: avr-14 gbr-2 gbr-5 Abstract: The alternatively-spliced Caenorhabditis elegans gbr-2/avr-14 gene encodes two subunits of the nematode ligand-gated chloride channel family which forms an important molecular target for the avermectin and related anthelminthics. We used reverse transcriptase-polymerase chain reaction (RT-PCR) techniques to isolate cDNAs encoding the products of the gbr-2/avr-14 orthologues from the parasitic nematodes Haemonchus contortus and Ascaris suum. The predicted polypeptides possess all the characteristics of subunits of the ligand-gated chloride channels, sharing greater than 80% amino-acid identity with their counterparts in C. elegans and with partial sequences from the filarial species Onchocerca volvulus and Dirofilaria immitis. The pattern of alternative splicing of the gbr-2/avr-14 gene observed in C. elegans is conserved in H. contortus but may not be in A. suum. Affinity-purified anti-GBR-2 antibodies were used to study the expression of these subunits in adult worms and they reacted specifically with the nerve ring, the ventral and dorsal nerve cords, the anterior portion of the dorsal sub-lateral cord and motor-neuron commissures in H. contortus. Specific immunofluorescence of the nerve cords was confirmed in A. suum; isolated muscle cells did not ------------------- Key: 3749 Medline: 10531027 Authors: Raich WB;Agbunag C;Hardin J Title: Rapid epithelial-sheet sealing in the Caenorhabditis elegans embryo requires cadherin-dependent filopodial Citation: Current Biology 9: 1139-1146 1999 Type: ARTICLE Genes: bar-1 hmp-1 hmp-2 hmr-1 jam-1 wrm-1 Abstract: Background: During embryonic development, epithelia with free edges must join together to create continuous tissues that seal the interior of the organism from the outside environment; failure of epithelial sealing underlies several common human birth defects. Sealing of epithelial sheets in embryos can be extremely rapid, dramatically exceeding the rate of adherens junction formation by epithelial cells in culture or during healing of epithelial wounds. Little is known about the dynamic redistribution of cellular junctional components during such events in living embryos. Results: We have used time-lapse, multiphoton laser-scanning microscopy and green fluorescent protein fusion proteins to analyze the sealing of the Caenorhabditis elegans epidermis in living embryos. Rapid recruitment of alpha-catenin to sites of filopodial contact between contralateral migrating epithelial cells, concomitant with clearing of cytoplasmic alpha-catenin, resulted in formation of nascent junctions; this pre ceded the formation of mature junctions. Surprisingly, upon inactivation of the entire cadherin-catenin complex, only adhesive strengthening between filopodia was reproducibly affected. Other ventral epidermal cells, which did not extend filopodia and appeared to seal along the ventral midline by coordinated changes in cell shape, successfully adhered in the absence of these proteins. Conclusions: We propose that 'filopodial priming' - prealignment of bundled actin in filopodia combined with the rapid recruitment of alpha-catenin from cytoplasmic reserves at sites of filopodial contact - accounts for the rapid rate of sealing of the embryonic epidermis of C. elegans. Filopodial priming may provide a general mechanism for rapid creation of adherens junctions during epithelial-sheet sealing in ------------------- Key: 3750 Medline: Authors: Murakami S;Johnson TE Title: Life extension and stress resistance in Caenorhabditis elegans modulated by the tkr-1 gene. Citation: Current Biology 9: R791- 1999 Type: CORRECT Genes: old-1 tkr-1 Abstract: In this Brief Communication, which appeared in the 14 September 1998 issue of Current Biology, the UV dose was reported erroneously. The dose reported was 20 J/m2 but the actual dose used was 0.4 J/cm2. Also, the gene formally referred to as tkr-1 has since been renamed old-1 (overexpression longevity determination). ------------------- Key: 3751 Medline: 20014992 Authors: Signor D;Wedaman KP;Orozco JT;Dwyer ND;Bargmann CI;Rose LS;Scholey JM Title: Role of a class DHC1b dynein in retrograde transport of IFT motors and IFT raft particles along cilia, but not dendrites, in chemosensory neurons of living Caenorhabditis elegans. Citation: Journal of Cell Biology 147: 519-530 1999 Type: ARTICLE Genes: che-3 osm-1 osm-3 osm-6 Abstract: The heterotrimeric motor protein, kinesin-II, and its presumptive cargo. can be observed moving anterogradely at 0.7 mu m/s by intraflagellar transport (IF-T) within sensory cilia of chemosensory neurons of living Caenorhabditis elegans! using a fluorescence microscope-based transport assay (Orozco, J.T., K.P. Wedaman, D. Signor, H. Brown, L. Rose, and J.M. Scholey. 1999. Nature. 398:674). Here, we report that kinesin-II, and two of its presumptive cargo molecules, OSM-1 and OSM-6, all move at similar to 1.1 mu m/s in the retrograde direction along cilia and dendrites, which is consistent with the hypothesis that these proteins are retrieved from the distal endings of the cilia by a retrograde transport pathway that moves them along cilia and then dendrites, back to the neuronal cell body. To test the hypothesis that the minus end-directed microtubule motor protein, cytoplasmic dynein, drives this retrograde transport pathway, we visualized movement of kinesin-II and its cargo along dendrites and cilia in a che-3 cytoplasmic dynein mutant background, and observed an inhibition of retrograde transport in cilia but not in dendrites. In contrast, anterograde IFT proceeds normally in che-3 mutants. Thus, we propose that the class DHC1b cytoplasmic dynein, CHE-3, is specifically responsible for the retrograde transport of the anterograde motor, kinesin-II, and its cargo within sensory cilia, but not within dendrites. ------------------- Key: 3752 Medline: 10518501 Authors: Park M;Krause MW Title: Regulation of postembryonic G1 cell cycle progression in Caenorhabditis elegans by a cyclin D/CDK-like complex. Citation: Development 126: 4849-4860 1999 Type: ARTICLE Genes: cdk-4 cul-1 cyd-1 Abstract: In many organisms, initiation and progression through the G(1) phase of the cell cycle requires the activity of G(1)-specific cyclins (cyclin D and cyclin E) and their associated cyclin-dependent kinases (CDK2, CDK4, CDK6). We show here that the Caenorhabditis elegans genes cyd-1 and cdk-4, encoding proteins similar to cyclin D and its cognate cyclin-dependent kinases, respectively, are necessary for proper division of postembryonic blast cells. Animals deficient for cyd-1 and/or cdk-4 activity have behavioral and developmental defects that result from the inability of the postembryonic blast cells to escape G(1) cell cycle arrest. Moreover, ectopic expression of cyd-1 and cdk-4 in transgenic animals is sufficient to activate a S-phase reporter gene. We observe no embryonic defects associated with depletion of either of these two gene products, suggesting that their essential functions are restricted to postembryonic development. We propose that the cyd-1 and cdk-4 gene products are an integral part of the developmental control of larval cell proliferation through the regulation of G(1) progression. ------------------- Key: 3753 Medline: 20014851 Authors: Basham SE;Rose LS Title: Mutations in ooc-5 and ooc-3 disrupt oocyte formation and the reestablishment of asymmetric PAR protein localization in two-cell Caenorhabditis elegans embryos. Citation: Developmental Biology 215: 253-263 1999 Type: ARTICLE Genes: ooc-3 ooc-5 par-1 par-2 par-3 mnDf67 mnDf90 Abstract: The early development of Caenorhabditis elegans embryos is characterized by a series of asymmetric divisions in which the mitotic spindle is repeatedly oriented on the same axis due to a rotation of the nuclear-centrosome complex. To identify genes involved in the control of spindle orientation, we have screened maternal-effect lethal mutants for alterations in cleavage pattern. Here we describe mutations in ooc-5 and ooc-3, which were isolated on the basis of a nuclear rotation defect in the P-1 cell of two-cell embryos. These mutations are novel in that they affect the asymmetric localization of PAR proteins at the two-cell stage, but not at the one-cell stage. In wild-type two-cell embryos, PAR-3 protein is present around the entire periphery of the AB cell and prevents nuclear rotation in this cell. In contrast, PAR-2 functions to allow nuclear rotation in the P-1 cell by restricting PAR-3 localization to the anterior periphery of P-1. In ooc-5 and ooc-3 mutant embryos, PAR-3 was mislocalized around the periphery of P-1, while PAR-2 was reduced or absent. The germ-line-specific P granules were also mislocalized at the two-cell stage. Mutations in ooc-5 and ooc-3 also result in reduced-size oocytes and embryos. However, par-3 ooc double-mutant embryos can exhibit nuclear rotation, indicating that small size per se does not prevent rotation and that PAR-3 mislocalization contributes to the failure of rotation in ooc mutants. We therefore postulate that wild-type ooc-5 and ooc-3 function in oogenesis and in the reestablishment of asymmetric domains of PAR proteins at ------------------- Key: 3754 Medline: 20014856 Authors: Miyabayashi T;Palfreyman MT;Sluder AE;Slack F;Sengupta P Title: Expression and function of members of a divergent nuclear receptor family in Caenorhabditis elegans. Citation: Developmental Biology 215: 314-331 1999 Type: ARTICLE Genes: odr-7 nhr-1 nhr-16 nhr-20 nhr-22 nhr-28 nhr-38 nhr-44 nhr-50 nhr-54 nhr-55 nhr-57 nhr-66 nhr-68 nhr-72 nhr-73 nhr-74 nhr-75 nhr-76 nhr-77 nhr-78 nhr-79 nhr-80 nhr-81 nhr-82 nhr-83 nhr-84 nhr-89 Abstract: Nuclear receptors (NRs) are a large class of ligand-regulated transcriptional modulators that have been shown to play roles in many developmental processes. The Caenorhabditis elegans genome is predicted to encode a large and divergent family of NR proteins. The functions of most of these genes are unknown. As a first step toward defining their roles, we have initiated an expression and functional survey of a subset of these genes. In this study, we demonstrate expression of 21 of 28 NR genes examined, indicating that a large fraction of the predicted genes likely encode functional gene products. We show that five genes are expressed predominantly in neuronal cells, while others are expressed in multiple cell types. Interestingly, we find that eight genes are expressed exclusively in the lateral hypodermal (seam) cells. These eight genes share a high degree of overall homology and cluster in a neighbor-joining tree derived from sequence analysis of the NRs, suggesting that they arose by gene duplication from a common ancestor. We show that overexpression of each of three members of this subfamily results in similar developmental defects, consistent with a redundant role for these genes in the function of the ------------------- Key: 3755 Medline: 10498684 Authors: Knobel KM;Jorgensen EM;Bastiani MJ Title: Growth cones stall and collapse during axon outgrowth in Caenorhabditis elegans. Citation: Development 126: 4489-4498 1999 Type: ARTICLE Genes: ceh-23 unc-47 Abstract: During nervous system development, neurons form synaptic contacts with distant target cells. These connections are formed by the extension of axonal processes along predetermined pathways. Axon outgrowth is directed by growth cones located at the tips of these neuronal processes. Although the behavior of growth tones has been well-characterized in vitro, it is difficult to observe growth cones in vivo. We have observed motor neuron growth cones migrating in living Caenorhabditis elegans larvae using time-lapse confocal microscopy. Specifically, we observed the VD motor neurons extend axons from the ventral to dorsal nerve cord during the L2 stage. The growth cones of these neurons are round and migrate rapidly across the epidermis if they are unobstructed. When they contact axons of the lateral nerve fascicles, growth cones stall and spread out along the fascicle to form anvil-shaped structures. After pausing for a few minutes, they extend lamellipodia beyond the fascicle and resume migration toward the dorsal nerve cord. Growth cones stall again when they contact the body wall muscles. These muscles are tightly attached to the epidermis by narrowly spaced circumferential attachment structures. Stalled growth cones extend fingers dorsally between these hypodermal attachment structures. When a single finger has projected through the body wall muscle quadrant, the growth cone located on the ventral side of the muscle collapses and a new growth cone forms at the dorsal tip of the predominating finger. Thus, we observe that complete growth cone collapse occurs in vivo and not just in culture assays. In contrast to studies indicating that collapse occurs upon contact with repulsive substrata, collapse of the VD growth cones may result from an intrinsic signal that serves to maintain growth cone primacy and conserve cellular material. ------------------- Key: 3756 Medline: 99456784 Authors: Wiegner O;Schierenberg E Title: Regulative development in a nematode embryo: A hierarchy of cell fate transformations. Citation: Developmental Biology 215: 1-12 1999 Type: ARTICLE Genes: Abstract: Cell specification during embryogenesis of the model system Caenorhabditis elegans involves a combination of inductive and autonomous mechanisms. We have begun to study the development of other nematodes to investigate how well cell-specification mechanisms are preserved among closely related species. Here we report that the embryo of the soil nematode Acrobeloides nanus expresses a so far undescribed regulative potential. When, for instance, the first somatic founder cell AB is eliminated it is replaced by its posterior neighbor EMS, which in turn is replaced by the C cell. This allows-different from C. elegans-the development of partial embryos up to hatching and sometimes to fertile adults. Thus, early somatic blastomeres in A. nanus are multipotent, each being capable of giving rise to more than one somatic founder cell. Lost germ-line cells, however, are not replaced. A model is presented, according to which in A. nanus cellular identities are assigned by specific reciprocal inhibitory cell-cell interactions absent in C. elegans. Differences and similarities in cell specification between the two species are discussed and related to different developmental strategies. ------------------- Key: 3757 Medline: 20026158 Authors: Winnier AR;Meir JYJ;Ross JM;Tavernarakis N;Driscoll M;Ishihara T;Katsura I;Miller DM Title: UNC-4/UNC-37-dependent repression of motor neuron-specific genes controls synaptic choice in Caenorhabditis elegans. Citation: Genes & Development 13: 2774-2786 1999 Type: ARTICLE Genes: acr-5 del-1 unc-4 unc-37 Abstract: The UNC-4 homeoprotein and the Groucho-like corepressor UNC-37 specify synaptic choice in the Caenorhabditis elegans motor neuron circuit. In unc-4 mutants, VA motor neurons are miswired with inputs from interneurons normally reserved for their lineal sisters, the VB motor neurons. Here we show that UNC-4 and UNC-37 function together in VA motor neurons to repress VB-specific genes and that this activity depends on physical contact between UNC-37 and a conserved Engrailed-like repressor domain (ehl) in UNC-4. Missense mutations in the UNC-4 ehl domain disrupt interactions between UNC-4 and UNC-37 and result in the loss of UNC-4-dependent repressor activity in vivo. A compensatory amino acid substitution in UNC-37 suppresses specific unc-4 alleles by restoring physical interactions with UNC-4 as well as UNC-4-dependent repression of VB-specific genes. We propose that repression of VB-specific genes by UNC-4 and UNC-37 is necessary for the creation of wild-type inputs to VA motor neurons. The existence of mammalian homologs of UNC-4 and UNC-37 indicates that a similar mechanism could regulate synaptic ------------------- Key: 3758 Medline: 20026163 Authors: Rappleye CA;Paredez AR;Smith CW;McDonald KL;Aroian RV Title: The coronin-like protein POD-1 is required for anterior-posterior axis formation and cellular architecture in the nematode Caenorhabditis elegans. Citation: Genes & Development 13: 2838-2851 1999 Type: ARTICLE Genes: nmy-2 par-1 par-2 par-3 par-4 par-5 par-6 pod-1 eDf2 tDf8 Abstract: Establishment of anterior-posterior (a-p) polarity in the Caenorhabditis elegans embryo depends on filamentous (F-) actin. Previously, we isolated an E-actin-binding protein that was enriched in the anterior cortex of the one-cell embryo and was hypothesized to link developmental polarity to the actin cytoskeleton. Here, we identify this protein, POD-I, as a new member of the coronin family of actin-binding proteins. We have generated a deletion within the pod-1 gene. Elimination of POD-1 from early embryos results in a loss of physical and molecular asymmetries along the a-p axis. For example, PAR-1 and PAR-3, which themselves are polarized and required for a-p polarity, are delocalized in pod-1 mutant embryos. However, unlike loss of PAR proteins, loss of POD-I gives rise to the formation of abnormal cellular structures, namely large vesicles of endocytic origin, membrane protrusions, unstable cell divisions, a defective eggshell, and deposition of extracellular material. We conclude that, analogous to coronin, POD-I plays an important role in intracellular trafficking and organizing specific aspects of the actin cytoskeleton. We propose models to explain how the role of POD-1 in basic cellular processes could be linked to the generation of polarity along the embryonic a-p axis. ------------------- Key: 3759 Medline: 20035956 Authors: Shirasu K;Lahaye T;Tan M-W;Zhou F;Azevedo C;Schulze-Lefert Title: A novel class of eukaryotic zinc-binding proteins is required for disease resistance signaling in barley and development in C. elegans. Citation: Cell 99: 355-366 1999 Type: ARTICLE Genes: apx-1 chp-1 Abstract: Barley Rar1 is a convergence point in the signaling of resistance to powdery mildew, triggered by multiple race-specific resistance (R) genes. Rar1 is shown to function upstream of H2O2 accumulation in attacked host cells, which precedes localized host cell death. We isolated Rar1 by map-based cloning. The sequence of the deduced 25.5 kDa protein reveals two copies of a 60-amino acid domain, CHORD, conserved in tandem organization in protozoa, plants, and metazoa. CHORD defines a novel eukaryotic Zn2+-binding domain. Silencing of the C. elegans CHORD-containing gene, chp, results in semisterility and embryo lethality, suggesting an essential function of the wild-type gene in nematode development. Our findings indicate that plant R genes have recruited a fundamental cellular control element for signaling of disease ------------------- Key: 3760 Medline: 20035959 Authors: Troemel ER;Sagasti A;Bargmann CI Title: Lateral signaling mediated by axon contact and calcium entry regulates asymmetric odorant receptor expression in C. elegans. Citation: Cell 99: 387-398 1999 Type: ARTICLE Genes: daf-11 egl-2 gcy-5 glp-1 lin-12 nsy-1 nsy-2 nsy-3 odr-1 odr-2 odr-10 sax-3 sax-5 snt-1 str-2 tax-2 tax-4 unc-2 unc-7 unc-13 unc-33 unc-36 unc-43 unc-44 unc-76 unc-104 Abstract: C. elegans detects several odorants with the bilaterally symmetric pair of AWC olfactory neurons. A stochastic, coordinated decision ensures that the candidate odorant receptor gene str-2 is expressed in only one AWC neuron in each animal-either the left or the right neuron, but never both. An interaction between the two AWC neurons generates asymmetric str-2 expression in a process that requires normal axon guidance and probably AWC axon contact. This interaction induces str-a expression by reducing calcium signaling through a voltage-dependent Ca2+ channel and the CaM kinase II UNC-43. CaMKII activity acts as a switch in the initial decision to express str-2; thus, calcium signals can define distinct cell types during neuronal development. A cGMP signaling pathway that is used in olfaction maintains str-2 expression after the initial ------------------- Key: 3761 Medline: 99449579 Authors: Fujiwara M;Ishihara T;Katsura I Title: A novel WD40 protein, CHE-2, acts cell-autonomously in the formation of C. elegans sensory cilia. Citation: Development 126: 4839-4848 1999 Type: ARTICLE Genes: che-2 meDf6 Abstract: To elucidate the mechanism of sensory cilium formation, we analyzed mutants in the Caenorhabditis elegans che-2 gene. These mutants have extremely short cilia with rm abnormal posterior projection, and show defects :in behaviors that are mediated by ciliated sensory neurons. The che-2 gene encodes a new member of the WD40 protein family, suggesting that it acts in protein-protein interaction. Analysis of mutation sites showed that both the aminoterminal WD40 repeats and the carboxyl-terminal non-WD40 domain are necessary for the CHE-2 function. CHE-2-tagged green fluorescent protein is localized at the cilia of almost all the ciliated sensory neurons. Expression of che-2 in a subset of sensory neurons of a che-2 mutant by using a heterologous promoter resulted in restoration of the functions and cilium morphology of only the che-2-expressing neurons. Thus, che-2 acts cell-autonomously. This technique can be used in the future for determining the function of each type of che-2-expressing sensory neuron. Using green fluorescent protein, we found that the extension of cilia in wild-type animals took place at the late embryonic stage, whereas the cilia of che-2 mutant animals remained always short during development. Hence, the abnormal posterior projection is due to the inability of cilia to extend, rather than degeneration of cilia once correctly formed. Expression of che-2 in a che-2 mutant under a heat shock promoter showed that the extension of cilia, surprisingly, can occur even at the adult stage, and that such cilia can function ------------------- Key: 3762 Medline: 99449581 Authors: Subramaniam K;Seydoux G Title: nos-1 and nos-2, two genes related to Drosophila nanos, regulate primordial germ cell development and survival in Caenorhabditis elegans. Citation: Development 126: 4861-4871 1999 Type: ARTICLE Genes: ced-4 cki-1 fbf-1 fbf-2 glp-1 glp-4 lin-26 nos-1 nos-2 nos-3 puf-6 puf-7 puf-8 tra-2 Abstract: In Drosophila, the posterior determinant nanos is required for embryonic patterning and for primordial germ cell (PGC) development. We have identified three genes in Caenorhabditis elegans that contain a putative zinc-binding domain similar to the one found in nanos, and show that two of these genes function during PGC development. Like Drosophila nanos, C. elegans nos-1 and nos-2 are not generally required for PGC fate specification, but instead regulate specific aspects of PGC development. nos-2 is expressed in PGCs around the time of gastrulation from a maternal RNA associated with P granules, and is required for the efficient incorporation of PGCs into the somatic gonad. nos-1 is expressed in PGCs after gastrulation, and is required redundantly with nos-2 to prevent PGCs from dividing in starved animals and to maintain germ cell viability during larval development. In the absence of nos-1 and nos-2, germ cells cease proliferation at the end of the second larval stage, and die in a manner that is partially dependent on the apoptosis gene ced-4. Our results also indicate that putative RNA-binding proteins related to Drosophila Pumilio are required for the same PGC processes as nos-1 and nos-2. These studies demonstrate that evolutionarily distant organisms utilize conserved factors to regulate early germ cell development and survival, and that these factors include members of the nanos and pumilio gene families. ------------------- Key: 3763 Medline: 20110919 Authors: Lin R;Avery L Title: Policing rogue genes. Citation: Nature 402: 128-129 1999 Type: REVIEW Genes: mut-7 pos-1 rde-1 rde-2 rde-3 rde-4 Abstract: Life is based on social contract, genes work for the good of the organism, and they are reproduced. But certain rogue genes, called transposons, wantonly reproduce at the expense of the organism, inserting new copies of themselves all over the genome. Reporting in Cell, Tabara et al., and Ketting et al. now show that organisms have systems to hold transposons in check. They suggest that one of the clues that organisms use to detect illicit activity is double-stranded RNA, and their results could explain the reason for the mysterious phenomenon of RNA interference. ------------------- Key: 3764 Medline: 20110933 Authors: Rongo C;Kaplan JM Title: CaMKII regulates the density of central glutamatergic synapses in vivo. Citation: Nature 402: 195-199 1999 Type: ARTICLE Genes: egl-19 glr-1 snt-1 unc-2 unc-13 unc-18 unc-36 unc-43 unc-64 unc-104 Abstract: Synaptic connections undergo a dynamic process of stabilization or elimination during development, and this process is thought to be critical in memory and learning and in establishing the specificity of synaptic connections(1). The type II calcium- and calmodulin-dependent protein kinase (CaMKII) has been proposed to be pivotal in regulating synaptic strength(2-4) and in maturation of synapses during developments. Here we describe how CaMKII regulates the formation of central glutamatergic synapses in Caenorhabditis elegans, During larval development, the density of ventral nerve cord synapses containing the GLR-1 glutamate receptor is held constant despite marked changes in neurite length. The coupling of synapse number to neurite length requires both CaMKII and voltage-gated calcium channels. CaMKII regulates GLR-1 by at least two distinct mechanisms: regulating transport of GLR-1 from cell bodies to neurites; and regulating the addition or maintenance of GLR-1 to ------------------- Key: 3765 Medline: 10647014 Authors: Reiner DJ; Newton EM;Tian H;Thomas JH Title: Diverse behavioural defects caused by mutations in Caenorhabditis elegans unc-43 CaM Kinase II. Citation: Nature 402: 199-203 1999 Type: ARTICLE Genes: dec-4 egl-2 egl-19 egl-36 itr-1 lef-1 tax-4 unc-43 unc-103 Abstract: Calcium/calmodulin-dependent serine/threonine kinase type II (CaMKII) is one of the most abundant proteins in the mammalian brain, where it is thought to regulate synaptic plasticity and other processes(1-3). Activation of the multisubunit kinase(4) by calcium is effectively cooperative and can persist long after transient calcium rises(1,5,6). Despite extensive biochemical characterization of CaMKII and identification of numerous in vitro kinase targets(1), little is known about its function in vivo. Here we report that unc-43 encodes the only Caenorhabditis elegans CaMKII. A gain-of-function unc-43 mutation reduces locomotory activity, alters excitation of three muscle types and lengthens the period of the motor output of a behavioural clock. Null unc-43 mutations cause phenotypes generally opposite to those of the gain-of-function mutation. Mutations in the unc-103 potassium channel gene suppress a gain-of-function phenotype of unc-43 in one tissue without affecting other tissues; thus, UNC-103 may be a tissue-specific target of ------------------- Key: 3766 Medline: 20046439 Authors: Cunha A;Azevedo RBR;Emmons SW;Leroi AM Title: Variable cell number in nematodes. Citation: Nature 402: 253- 1999 Type: REVIEW Genes: Abstract: Studies of the nematode worm Caenorhabditis elegans have led to the widely held belief that individuals of a given nematode species are characterized by a property known as eutely, in which all individuals have the same total number of cells. This property, which is peculiar to nematodes and a few other phyla, has raised the question of whether the developmental mechanisms of nematodes differ from those of larger metazoans. Here we show that many, perhaps most, nematode species are not eutelic in at least one organ, the epidermis, and that in this respect they resemble other model organisms such as fruitflies and mice. ------------------- Key: 3767 Medline: Authors: Davidson EH;Ruvkun G Title: Themes from a NASA workshop on gene regulatory processes in development and evolution. Citation: Journal of Experimental Zoology 285: 104-115 1999 Type: REVIEW Genes: mes-2 mes-6 ttx-3 Abstract: A memorable workshop, focused on causal mechanisms in metazoan evolution and sponsored by NASA, was held in early June 1998, at MBL. The workshop was organized by Mike Levine and Eric H. Davidson, and it included the PI and associates from 12 different laboratories, a total of about 30 people. Each laboratory had about two and one half hours in which to represent its recent research and cast up its current ideas for an often intense discussion. In the following we have tried to enunciate some of the major themes that emerged, and to reflect on their implications. The opinions voiced are our own. We would like to tender apologies over those contributions we have not been able to include, but this is not, strictly speaking, a meeting review. Rather we have focused on those topics that bear more directly on evolutionary mechanisms, and have therefore slighted some presentations (including some of our own), that were oriented mainly toward developmental ------------------- Key: 3768 Medline: 10517632 Authors: Peters JM;McKay RM;McKay JP;Graff JM Title: Casein kinase I transduces Wnt signals. Citation: Nature 401: 345-350 1999 Type: ARTICLE Genes: apr-1 kin-19 mom-2 Abstract: The Wnt signalling cascade is essential for the development of both invertebrates and vertebrates, and is altered during tumorigenesis. Although a general framework for Wnt signalling has been elucidated, not all of the components have been identified. Here we describe a serine kinase, casein kinase I (CKI), which was isolated by expression cloning in Xenopus embryos. CKI reproduces several properties of Wnt signals, including generation of complete dorsal axes, stabilization of beta-catenin and induction of genes that are direct targets of Wnt signals. Dominant-negative forms of CKI and a pharmacological blocker of CKI inhibited Wnt signals in Xenopus. Inhibiting CKI in Caenorhabditis elegans generated worms with a mom phenotype, indicative of a loss of Wnt signals. In addition, CKI bound to and increased the phosphorylation of dishevelled, a known component of the Wnt pathway. These data indicate that CKI may be a conserved component of the ------------------- Key: 3769 Medline: 20020327 Authors: Caffrey DR;O'Neill LAJ;Shields DC Title: The evolution of the MAP kinase pathways: Coduplication of interacting proteins leads to new signaling cascades. Citation: Journal of Molecular Evolution 49: 567-582 1999 Type: REVIEW Genes: Abstract: The MAP-kinase pathways are intracellular signaling modules that are likely to exist in all eukaryotes. We provide an evolutionary model for these signaling pathways by focusing on the gene duplications that have occurred since the divergence of animals from yeast. Construction of evolutionary trees with confidence assessed by bootstrap clearly shows that the mammalian JNK and p38 pathways arose from an ancestral hyperosmolarity pathway after the split from yeast and before the split from C. elegans. These coduplications of interacting proteins at the MAPK and MEK levels have since evolved toward substrate specificity, thus giving distinct pathways. Mammalian duplications since the split from C. elegans are often associated with divergent tissue distribution but do not appear to confer detectable substrate specificity. The yeast kinase cascades have undergone similar fundamental functional changes since the split from mammals, with duplications giving rise to central signaling components of the filamentous and hypoosmolarity pathways. Experimentally defined cross-talk between yeast pheromone and hyperosmolarity pathways is mirrored with corresponding cross-talk in mammalian pathways, suggesting the existence of ancient orthologous cross-talk; our analysis of gene duplications at all levels of the cascade is consistent with this model but does not always provide significant bootstrap support. Our data also provide insights at different levels of the cascade where conflicting experimental evidence exists. ------------------- Key: 3770 Medline: 20020670 Authors: Burglin TR;Aspock G Title: Exon duplication from a fork head to a homeodomain protein. Citation: Development Genes & Evolution 209: 629-633 1999 Type: ARTICLE Genes: ceh-43 fkh-1 pha-4 Abstract: The evolution of complex organisms such as animals requires a large expansion of the number of genes controlling developmental events. In addition, it is thought that domains are shuffled between genes to further increase the complexity and generate new types of genes and functions. Working with the Caenorhabditis elegans homeobox gene ceh-43, the orthologue of fly Distal-less (Dll), we observed sequence similarity to the C. elegans gene fkh-1. Now, with the complete genomic sequence available, we examined this similarity in detail. The region of similarity is confined essentially to one exon in the carboxy terminus of the two genes. Based on the gene structure, we think that an exon of fkh-1 was duplicated to the carboxy terminus of ceh-43, where it was incorporated as the last exon. This duplication event seems to have happened recently since the similarity on the nucleotide level is higher than the sequence similarity between fkh-1 of C. elegans and C. briggsae. Potentially the duplication event was mediated via a short region of sequence similarity between the two open reading frames of the genes. This duplication event clear shows that a part of a gene can successfully be juxtaposed to another gene. These ------------------- Key: 3771 Medline: 20027121 Authors: Weinshenker D;Wei A;Salkoff L;Thomas JH Title: Block of an ether-a-go-go-like K+ channel by imipramine rescues egl-2 excitation defects in Caenorhabditis elegans. Citation: Journal of Neuroscience 19: 9831-9840 1999 Type: ARTICLE Genes: egl-2 sDf34 Abstract: K+ channels are key regulators of cellular excitability. Mutations that activate K+ channels can lower cellular excitability, whereas those that inhibit K+ channels may increase excitability. We show that the Caenorhabditis elegans egl-2 gene encodes an eag K+ channel and that a gain-of-function mutation in egl-2 blocks excitation in neurons and muscles by causing the channel to open at inappropriately negative voltages. Tricyclic antidepressants reverse egl-2(gf) mutant phenotypes, suggesting that EGL-2 is a tricyclic target. We verified this by showing that EGL-2 currents are inhibited by imipramine. Similar inhibition is observed with the mouse homolog MEAG, suggesting that inhibition of EAG-like channels may mediate some clinical side effects of this ------------------- Key: 3772 Medline: 20014988 Authors: Moore LL;Morrison M;Roth MB Title: HCP-1, a protein involved in chromosome segregation, is localized to the centromere of mitotic chromosomes in Caenorhabditis elegans. Citation: Journal of Cell Biology 147: 471-479 1999 Type: ARTICLE Genes: hcp-1 hcp-2 Abstract: To learn more about holocentric chromosome structure and function; we generated a monoclonal antibody (mAb), 6C4, that recognizes the poleward face of mitotic chromosomes in Caenorhabditis elegans. Early in mitosis, mAb 6C4 stains dots through out the nucleoplasm. Later in prophase, mAb 6C4 stains structures on opposing faces of chromosomes which orient towards the centrosomes at metaphase. Colocalization with an antibody against a centromeric histone H3-like protein and the MPM-2 antibody, which identifies a kinetochore-associated phospho-epitope present in a variety of organisms, shows that the mAb 6C4 staining is present adjacent to the centromere. Expression screening using mAb 6C4 identified a protein in C. elegans that we named HCP-1 (for holocentric protein 1). We also identified a second protein from the C. elegans genome sequence database, HCP-2, that is 54% similar to HCP-1,When expression of HCP-1 is reduced by RNA interference (RNAi), staining with mAb 6C4 is eliminated, indicating that hcp-l encodes the major mAb 6C4 antigen. RNAi with hcp-l and hcp-2 together results in aberrant anaphases and embryonic arrest at similar to 100 cells with different amounts of DNA in individual nuclei. These results suggest that HCP-1 is a: centromere-associated protein that is involved in the fidelity of chromosome segregation. ------------------- Key: 3773 Medline: 20097422 Authors: Foll RL;Pleyers A;Lewandovski GJ;Wermter C;Hegemann V;Paul RJ Title: Anaerobiosis in the nematode Caenorhabditis elegans. Citation: Comparative Biochemistry & Physiology B-Biochemistry & Molecular Biology 124: 269-280 1999 Type: ARTICLE Genes: Abstract: In Caenorhabditis elegans, mortality rates and changes in concentrations of carbohydrate stores and anaerobic end products were determined in anoxic (test) and normoxic (control) animals at two different temperatures (10 and 20 degrees C). The anoxic tolerance of the free-living nematode proved to be well-developed: at 10 degrees C, about 50% of animals had survived a period of 50 h of anoxia. The carbohydrate stores (approximately 30 mmol glycosyl units kg(-1) freshweight (FW)) were reduced by two-thirds within 24 h of anoxia at both temperatures. L-lactate, acetate, succinate, and propionate were identified as the main anaerobic end products. The amounts and proportions of the end products were dependent on temperature. They did not accumulate very much in the tissues, but were mainly excreted. During anoxia, the metabolism of C. elegans was depressed to 3-4% of the aerobic value. The food-source Escherichia coli was found to be at least partly alive in the gut of the animals. To separate between anaerobiosis in animals and bacteria, cleaning procedures were applied, and additional control measurements were made: anaerobic end products produced either by E. coli alone or by bacteria-free (axenic) bred nematodes were quantified at identical incubation ------------------- Key: 3774 Medline: 20020241 Authors: Yang J;Kramer JM Title: Proteolytic processing of Caenorhabditis elegans SQT-1 cuticle collagen is inhibited in right roller mutants whereas cross-linking is inhibited in left roller mutants. Citation: Journal of Biological Chemistry 274: 32744-32749 1999 Type: ARTICLE Genes: rol-6 sqt-1 Abstract: The sqt-1 gene encodes a C. elegans cuticle collagen that when defective can cause dramatic alterations of organismal morphology. Specific antisera were used to examine the assembly of wild-type and mutant SQT-1 in the cuticle. Wild-type SQT-1 chains associate into dimer, tetramer, and higher oligomers that are cross-linked by non-reducible, presumably tyrosine-derived, covalent bonds. The SQT-1 pattern differs from the bulk of cuticle collagens which are found in trimer and larger forms. sqt-1 mutations that cause left-handed helical twisting of animals remove a conserved carboxyl-domain cysteine and inhibit formation of these non-reducible bonds. SQT-1 monomers accumulate and novel trimer-sized products form. A conserved tyrosine immediately adjacent to the affected cysteine suggests that disulfide bond formation is required for this tyrosine to form a cross-link. sqt-1 mutations that cause right-handed helical twisting affect conserved arginines in a predicted cleavage site for a subtilisin-like protease. These mutant SQT-1 molecules retain residues an the amino side of the predicted cleavage site and are larger than wild-type by the amount expected if cleavage failed to occur. The conservation of this site in all nematode cuticle collagens indicates that they are all synthesized as procollagens that are processed by subtilisin-like proteases. ------------------- Key: 3775 Medline: 20014703 Authors: Miguel-Aliaga I;Culetto E;Walker DS;Baylis HA;Sattelle DB;Davies KE Title: The Caenorhabditis elegans orthologue of the human gene responsible for spinal muscular atrophy is a maternal product critical for germline maturation and embryonic viability. Citation: Human Molecular Genetics 8: 2133-2143 1999 Type: ARTICLE Genes: egl-32 Abstract: Spinal muscular atrophy (SMA) is a common disorder characterized by loss of lower motor neurones of the spinal cord. The disease is caused by mutations in the survival motor neurone (SMN) gene, SMN is ubiquitously expressed and evolutionarily conserved, and its role in RNA processing has been well established. However, these properties do not explain the observed specificity of motor neurone death. To gain further insight into the function of SMN, we have isolated and characterized the Caenorhabditis elegans orthologue of the SMN gene (CeSMN). Here we show that CeSMN is transmitted maternally as a predominantly nuclear factor, which remains present in all the blastomeres throughout embryonic development and onwards into adulthood. In adult nematodes, a CeSMN-green fluorescent protein fusion protein is expressed in a number of cell types including the germline. Both disruption of the endogenous CeSMN function and overexpression of the gene result in a severe decrease in the number of progeny and in locomotive defects. In addition, its transient knockdown leads to sterility caused by a defect in germ cell maturation. The expression pattern and functional properties so far observed for CeSMN, together with its unusual behaviour in the germline, indicate that SMN may be involved in specific gene expression events at these very early developmental stages. We have also identified a deletion in the CeSMN promoter region in egl-32. This mutant may become a useful genetic tool with which to explore regulation of CeSMN and hence provide possible clues for novel therapeutic strategies for SMA. ------------------- Key: 3776 Medline: 20014917 Authors: Shook DR;Johnson TE Title: Quantitative trait loci affecting survival and fertility-related traits in Caenorhabditis elegans show genotype-environment interactions, pleiotropy and Citation: Genetics 153: 1233-1243 1999 Type: ARTICLE Genes: Abstract: We have identified, using composite interval mapping, quantitative trait loci (QTL) affecting a variety of life history traits (LHTs) in the nematode Caenorhabditis elegans. Using recombinant inbred strains assayed on the surface of agar plates, we found QTL for survival, early fertility, age of onset of sexual maturity, and population growth rate. There was no overall correlation between survival on solid media and previous measures of survival in liquid media. Of thr four survival QTL found in these two environments, two have genotype-environment interactions (GEIs). Epistatic inter-actions between markers were detected for four traits. A multiple regression approach was used to deter-mine which single markers and epistatic interactions best explained the phenotypic variance for each trait. The amount of phenotypic variance accounted for by genetic effects ranged from 13% (for internal hatching) to 46% (for population growth). Epistatic effects accounted for 9-11% of the phenotypic variance for three traits. Two regions containing QTL that affected more than one fertility-related trait were found. This study serves as an example of the power of QTL mapping for dissecting the genetic architecture of a suite of LHTs and indicates the potential importance of environment and GEIs in the ------------------- Key: 3777 Medline: 20014918 Authors: Bosher JM;Dufourcq P;Sookhareea S;Labouesse M Title: RNA interference can target pre-mRNA: Consequences for gene expression in a Caenorhabditis elegans operon. Citation: Genetics 153: 1245-1256 1999 Type: ARTICLE Genes: lin-15 lin-26 lir-1 lir-2 ppp-1 tra-2 mcDf1 mcDf3 mnDf88 mnDf106 Abstract: In nematodes, flies, trypanosomes, and planarians, introduction of double-stranded RNA results in sequence-specific inactivation of gene function, a process termed RNA interference (RNAi). We demonstrate that RNAi against the Caenorhabditis elegans gene lir-1, which is part of the lir-1/lin-26 operon, induced phenotypes very different from a newly isolated lir-1 null mutation. Specifically, lir-1(RNAi) induced embryonic lethality reminiscent of moderately strong lin-26 alleles, whereas the lir-1 null mutant was viable. We show that the lir-1 (RNAi) phenotypes resulted from a severe loss of lin-26 gene expression. In addition, we found that RNAi directed against lir-1 or lin-26 introns induced similar phenotypes, so we conclude that lir-1(RNAi) targets the lir-1/lin-26 pre-mRNA. This provides direct evidence that RNA interference can prevent gene expression by targeting nuclear transcripts. Our results highlight that caution may be necessary when interpreting RNA interference without the benefit of mutant alleles. ------------------- Key: 3778 Medline: 20014919 Authors: Liu J;Tzou P;Hill RJ;Sternberg PW Title: Structural requirements for the tissue-specific and tissue-general functions of the Caenorhabditis elegans epidermal growth factor LIN-3. Citation: Genetics 153: 1257-1269 1999 Type: ARTICLE Genes: let-23 let-60 lin-1 lin-3 Abstract: Caenorhabditis elegans lin-3 encodes a homolog of the epidermal growth factor (EGF) family of growth factors. LIN-S is the inductive signal for hermaphrodite vulval differentiation, and it is required for animal viability, hermaphrodite fertility, and the specification of anterior cell fates in the male B cell lineage. We describe the cloning of a lin-3 homolog from C. briggsae, sequence comparison of C. elegans lin-3 with C. briggsae lin-3, and the determination of molecular lesions in alleles of C. elegans lin-3, including three new alleles. We also analyzed the severity of phenotypes caused by the new and existing alleles of lin-3. Correlation of mutant phenotypes and their molecular lesions, as well as sequence comparison between two species, reveal that the EGF motif and the N-terminal portion of the cytoplasmic domain are important for the functions of LIN-S in all tissues, while the C-terminal portion of the cytoplasmic domain is involved in the tissue-specific functions of lin-3. We discuss how the structure of lin-3 contributes to its functions in multiple developmental processes. ------------------- Key: 3779 Medline: 20014920 Authors: Zalevsky J;MacQueen AJ;Duffy JB;Kemphues KJ;Villeneuve AM Title: Crossing over during Caenorhabditis elegans meiosis requires a conserved MutS-based pathway that is partially dispensable in budding yeast. Citation: Genetics 153: 1271-1283 1999 Type: ARTICLE Genes: him-14 xol-1 mnDf30 mnDf88 mnDf105 Abstract: Formation of crossovers between homologous chromosomes during Caenorhabditis elegans meiosis requires the him-14 gene. Loss of him-14 function severely reduces crossing over, resulting in lack of chiasmata between homologs and consequent missegregation. Cytological analysis showing that homologs are paired and aligned in him-14 pachytene nuclei, together with temperature-shift experiments showing that him-14 functions during the pachytene stage, indicate that him-14 is not needed to establish pairing or synapsis and likely has a more direct role in crossover formation. him-14 encodes a germline-specific member of the MutS family of DNA mismatch repair (MMR) proteins, him-14 has no apparent role in MMR, but like its Saccharomyces cerevisiae ortholog MSH4, has a specialized rule in promoting crossing over during meiosis. Despite this conservation, worms and yeast differ significantly in their reliance on this pathway: whereas worms use this pathway to generate most, if not all, crossovers, yeast still form 30-50% of their normal number of crossovers when this pathway is absent. This differential reliance may reflect differential stability of crossover-competent recombination intermediates, or alternatively, the presence of two different pathways for crossover formation in yeast, only one of which predominates during nematode meiosis. We discuss a model in which HIM-14 promotes crossing over by interfering with Holliday junction branch migration. ------------------- Key: 3780 Medline: 20011119 Authors: Chow KL;Chan KW Title: Stress-induced phenocopy of C. elegans defines functional steps of sensory organ differentiation. Citation: Development Growth & Differentiation 41: 629-637 1999 Type: ARTICLE Genes: dpy-18 egl-5 lep-1 lin-32 mab-1 mab-5 mab-7 mab-18 mab-20 mab-21 mab-22 mab-26 ram-1 ram-2 ram-3 ram-4 ram-5 sma-2 sma-3 sma-4 sqt-1 Abstract: The differentiation of male specific sensory rays in the nematode Caenorhabditis elegans is a complex process regulated by multiple genetic components. A novel approach with heat shock treatment was employed to show that multistep regulation is involved in this process. Intervention in this stepwise regulation resulted in phenocopy of specific gene mutations. The results suggest that differential gene function acting at a precise time frame is necessary to guide the normal differentiation of sensory rays. ------------------- Key: 3781 Medline: 99457343 Authors: Richmond JE;Davis WS;Jorgensen EM Title: UNC-13 is required for synaptic vesicle fusion in C. elegans. Citation: Nature Neuroscience 2: 959-964 1999 Type: ARTICLE Genes: unc-13 unc-25 unc-49 Abstract: We analyzed the synaptic physiology of unc-13 mutants in the nematode C, elegans. Mutants of unc-13 had normal nervous system architecture, and the densities of synapses and postsynaptic receptors were normal at the neuromuscular junction. However, the number of synaptic vesicles at neuromuscular junctions was two- to threefold greater in unc-13 mutants than in wild-type animals. Most importantly, evoked release at both GABAergic and cholinergic synapses was almost absent in unc-13 null alleles, as determined by whole-cell, voltage-clamp techniques. Although mutant synapses had morphologically docked vesicles, these vesicles were not competent for release as assayed by spontaneous release in calcium-free solution or by the application of hyperosmotic saline. These experiments support models in which UNC-13 mediates either fusion of vesicles during exocytosis or priming of vesicles for ------------------- Key: 3782 Medline: Authors: Aamodt S Title: Synaptic physiology in C. elegans. Citation: Nature Neuroscience 2: 782- 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3783 Medline: 20383351 Authors: Loer CM;Davidson B;McKerrow J Title: A phenylalanine hydroxylase gene from the nematode C. elegans is expressed in the hypodermis. Citation: Journal of Neurogenetics 13: 157-180 1999 Type: ARTICLE Genes: bas-2 rol-6 unc-119 Abstract: We have identified an aromatic amino acid hydroxylase gene from the nematode C. elegans that likely encodes the worm phenylalanine hydroxylase (PheH). The predicted amino acid sequence is most similar to that of other PheH and TrpA proteins. Reporter gene fusions and staining with an antibody to mammalian PheH indicate the gene is expressed in hypodermal cells. A fusion protein expressed in bacteria can convert phenylalanine to tyrosine, and, to a lesser extent, tryptophan to 5-hydroxytryptophan. We hypothesize that the protein is necessary to produce additional tyrosine for protein crosslinking in the nematode cuticle. ------------------- Key: 3784 Medline: 20036932 Authors: Popovici C;Roubin R;Coulier F;Pontarotti P;Birnbaum D Title: The family of Caenorhabditis elegans tyrosine kinase receptors: Similarities and differences with mammalian receptors. Citation: Genome Research 9: 1026-1039 1999 Type: REVIEW Genes: cam-1 daf-2 egl-15 kin-8 kin-15 kin-16 let-23 vab-1 Abstract: Transmembrane receptors with tyrosine kinase activity (RTK) constitute a superfamily of proteins present in all metazoans that is associated with the control and regulation of cellular processes. They have been the focus of numerous studies and are a good subject for comparative analyses of multigene families in different species aimed at understanding metazoan evolution. The sequence of the genome of the nematode worm Caenorhabditis elegans is available. This offers a good opportunity to study the superfamily of nematode RTKs in its entirety and to compare it with its mammalian counterpart. We show that the C. elegans RTKs constitute various groups with different phylogenetic relationships with mammalian RTKs. A group of four RTKs show structural similarity with the three mammalian receptors For the vascular endothelial growth Factors. Another group comprises RTKs with a short extracellular region, a feature not known in mammals; the genes encoding these RTKs are clustered on chromosome II with other gene families, including genes encoding chitinase-like proteins. Most of the C. elegans RTKs have no direct orthologous relationship with any mammalian RTK, providing an illustration of the importance of the separate ------------------- Key: 3785 Medline: 20029743 Authors: Gieseler K;Abdel-Dayem M;Segalat L Title: In vitro interactions of Caenorhabditis elegans dystrophin with dystrobrevin and syntrophin. Citation: FEBS Letters 461: 59-62 1999 Type: ARTICLE Genes: dyb-1 dys-1 Abstract: Dystrophin, the product of the gene mutated in Duchenne muscular dystrophy (DMD) is bound by its C-terminus to a protein complex including the related protein dystrobrevin. Both proteins contain a putative coiled-coil domain consisting of two cr-helices. It has been reported that the two proteins bind to each other by the first one of the two alpha -helices. We have revisited this question using the Caenorhabdiutis elegans homologs of dystrophin and dystrobrevin. In vitro interaction occurs through the more conserved second helix. We propose a new model of dystrophin interactions with associated proteins. ------------------- Key: 3786 Medline: 20045036 Authors: Liu QA;Hengartner MO Title: Human CED-6 encodes a functional homologue of the Caenorhabditis elegans engulfment protein CED-6. Citation: Current Biology 9: 1347-1350 1999 Type: ARTICLE Genes: ced-6 Abstract: The rapid engulfment of apoptotic cells is a specialized innate immune response used by organisms to remove apoptotic cells. In mammals, several receptors that recognize apoptotic cells have been identified; molecules that transduce signals from these receptors to downstream cytoskeleton molecules have not been found, however [1-3]. Our previous analysis of the engulfment gene ced-6 in Caenorhabditis elegans has suggested that CED-6 is an adaptor protein that participates in a signal transduction pathway that mediates the specific recognition and engulfment of apoptotic cells [1]. Here, we describe our isolation and characterization of a human cDNA encoding a protein, hCED-6, with strong sequence similarity to C. elegans CED-6. As is the case with the worm protein, hCED-6 contains a phosphotyrosine-binding (PTB) domain and potential Src-homology domain 3 (SH3) binding sites. Both CED-6 and hCED-6 contain a predicted coiled-coil domain in the middle region. The hCED-6 protein lacks the extended carboxyl terminus found in worm CED-6; this carboxy-terminal extension appears not to be essential for CED-6 function in C. elegans, however. Overexpression of hCED-6 rescues the engulfment defect of ced-6 mutants in C. elegans significantly, suggesting that hCED-6 is a functional homologue of C. elegans CED-6 Human ced-6 is expressed widely in most human tissues. Thus, CED-6, and the CED-6 signal transduction pathway, might be conserved from C. elegans to humans and are present in most, if not all, human tissues. ------------------- Key: 3787 Medline: 10590837 Authors: Link CD;Cypser JR;Johnson CJ;Johnson TE Title: Direct observation of stress response in Caenorhabditis elegans using a reporter transgene. Citation: Cell Stress & Chaperones 4: 235-242 1999 Type: ARTICLE Genes: unc-54 Abstract: Transgenic Caenorhabditis elegans expressing jellyfish Green Fluorescent Protein under the control of the promoter for the inducible small heat shock protein gene hsp-16-2 have been constructed. Transgene expression parallels that of the endogenous hsp-16 gene, and, therefore, allows direct visualization, localization, and quantitation of hsp-16 expression in living animals. In addition to the expected upregulation by heat shock, we show that a variety of stresses, including exposure to superoxide-generating redox-cycling quinones and the expression of the human beta amyloid peptide, specifically induce the reporter transgene. The quinone induction is suppressed by coincubation with L-ascorbate. The ability to directly observe the stress response in living animals significantly simplifies the identification of both exogenous treatments and genetic alterations that modulate stress response, and possibly life span, in C. elegans. ------------------- Key: 3788 Medline: 20014526 Authors: Takamiya S;Matsui T;Taka H;Murayama K;Matsuda M;Aoki T Title: Free-living nematodes Caenorhabditis elegans possess in their mitochondria an additional rhodoquinone, an essential component of the eukaryotic fumarate reductase system. Citation: Archives of Biochemistry & Biophysics 371: 284-289 1999 Type: ARTICLE Genes: Abstract: The respiratory chain of Caenorhabditis elegans was characterized in mitochondria isolated from aerobically grown nematodes. Nematode mitochondria contain ubiquinone-9 as a major component and rhodoquinone-9 as a minor component. The ratio of ubiquinone-9/rhodoquinone-9 is higher in C. elegans mitochondria than in mitochondria from second-stage larvae of Ascaris suum, the free-living stage of porcine gut-dwelling nematode. The individual oxidoreductase activities comprising succinate oxidase and the amount of substrate-reducible cytochromes are comparable to those of mitochondria from second-stage larvae of A. suum, The specific activity of fumarate reductase is lower in C. elegans mitochondria than in mitochondria from second-stage larvae of A. suum, but still higher than in mammalian mitochondria. These results indicate that the free-living nematode C. elegans is capable of synthesizing rhodoquinone, as distinguished from aerobic mammalian species, although its mitochondria appear more aerobic than A. suam larval mitochondria. ------------------- Key: 3789 Medline: 9925641 Authors: Jacobs D;Glossip D;Xing H;Muslin A;Kornfeld K Title: Multiple docking sites on substrate proteins form a modular system that mediates recognition by ERK MAP kinase. Citation: Genes & Development 13: 163-175 1999 Type: ARTICLE Genes: ksr-1 lin-1 mek-2 Abstract: MAP kinases phosphorylate specific groups of substrate proteins. Here we show that the amino acid sequence FXFP is an evolutionarily conserved docking site that mediates ERK MAP kinase binding to substrates in multiple protein families. FXFP and the D box, a different docking site, forma a modular recognition system, as they can function independently or in combination. FXFP is specific for ERK, whereas the D box mediates binding to ERK and JNK MAP kinase, suggesting that the partially overlapping substrate specificities to ERK and JNK result from recognition of shared and unique docking sites. These findings enabled us to predicts new EFK substrates and design peptide inhibitors of EFK that functioned in vitro and in vivo. ------------------- Key: 3790 Medline: 20085748 Authors: Labrousse AM;Zappaterra MD;Rube DA;van der Bliek AM Title: C. elegans dynamin-related protein DRP-1 controls severing of the mitochondrial outer membrane. Citation: Molecular Cell 4: 815-826 1999 Type: ARTICLE Genes: drp-1 dyn-1 hlh-8 myo-3 Abstract: Little is known about the mechanism of mitochondrial division. We show here that mitochondria are disrupted by mutations in a C. elegans dynamin-related protein (DRP-1). Mutant DRP-1 causes the mitochondrial matrix to retract into large blebs that are both surrounded and connected by tubules of outer membrane. This indicates that scission of the mitochondrial outer membrane is inhibited, while scission of the inner membrane still occurs. Overexpressed wild-type DRP-1 causes mitochondria to become excessively fragmented, consistent with an active role in mitochondrial scission. DRP-1 fused to GFP is observed in spots on mitochondria where scission eventually occurs. These data indicate that wild-type DRP-1 contributes to the final stages of mitochondrial division by controlling scission of the mitochondrial outer membrane. ------------------- Key: 3791 Medline: 20081939 Authors: Dhawan R;Dusenbery DB;Williams PL Title: Comparison of lethality, reproduction, and behavior as toxicological endpoints in the nematode Caenorhabditis elegans. Citation: Journal of Toxicology and Environmental Health Part A 58: 451-462 1999 Type: ARTICLE Genes: Abstract: This study describes a new approach for assessing behavioral changes following toxicant exposure and compares the method to other common endpoints used in environmental toxicology. The nematode Caenorhabditis elegans was exposed to a range of ethanol concentrations to determine its effect on survival, reproduction and behavior. Each endpoint was evaluated for its sensitivity by comparing LC50, RC50 (concentration at which there is a 50% reduction in number of offspring as compared to controls), and BC50 (concentration at which there is a 50% reduction in movement as compared to controls) values for ethanol exposure. Worms showed 24-h lethality at concentrations of ethanol in the range of 83 g/L to 99 g/L. Reproduction in C elegans was estimated by counting the number of off-spring after 3 d of exposure, which decreased with the increase in ethanol concentration from 8 g/L to 71 g/L. Behavior was quantified by using a new computer tracking method which can simultaneously assess hundreds of nematodes and provides several behavioral parameters in real time. Worms showed some hyperactivity increased movement) at very low ethanol concentrations (0.8 g/L and 2.4 g/Li and a decrease in movement at higher ethanol concentrations 14 g/L to 40 g/Li. A comparison for sensitivity between the three endpoints was performed. Behavior and reproduction responses were found to be similar and, as expected, both are much more sensitive indicators of toxicity than lethality. The advantages and disadvantages of the computer ------------------- Key: 3792 Medline: 20251944 Authors: Yochem J;Sundaram M;Bucher EA Title: Mosaic analysis in Caenorhabditis elegans. Citation: "Methods in Molecular Biology, Vol. 135: Developmental Biology Protocols", RS Tuan and CW Lo (eds). Humana Press, Inc. Totowa, NJ. 1: 447-462 1999 Type: REVIEW Genes: ace-1 ced-3 ced-4 daf-6 dpy-4 dpy-17 dpy-18 emo-1 glp-1 let-23 let-60 lin-31 mab-5 mab-21 mpk-1 ncl-1 osm-1 pag-3 sup-10 sur-5 unc-3 unc-7 unc-26 unc-29 unc-30 unc-36 Abstract: The complete description of its nearly invariant cell lineage and the growing availability of cloned genes and markers for the cell lineage make Caenorhabditis elegans particularly favorable for mosaic analysis, and the literature is rich in examples that prove the usefulness of this approach. Because genetic mosaic analysis in C. elegans has recently been reviewed by Herman who developed many of the techniques, this review will be more concerned with the recent technical advances rather than with an extensive background of the approach. First we shall present a brief summary of the principles of mosaic analysis as it is typically performed in C. elegans. This will be followed by a description of markers that indicate mosaicism and by a discussion of a hypothetical analysis of an essential gene. ------------------- Key: 3793 Medline: 99322306 Authors: Braeckman BP;Vanfleteren JR Title: Stress-inducible mechanisms of life-span extension in yeast, eubacteria and metazoans. Citation: Trends in Microbiology 7: 270-271 1999 Type: REVIEW Genes: age-1 clk-1 daf-2 spe-26 tkr-1 Abstract: As outlined by Michal Jazwinski in his recent review, multiple pathways appear to play a role in determining yeast longevity. One mechanism involves the illegitimate replication of extrachromosomal rDNA circles to toxic levels. A similar sequence of events involving excision, circularization and unfettered replication of mitochondrial (mt) DNA (called senDNA) induces senescence in the fungus Podospora anserina. ------------------- Key: 3794 Medline: 20053801 Authors: Yatin SM;Varadarajan S;Link CD;Butterfield DA Title: In vitro and in vivo oxidative stress associated with Alzheimer's amyloid beta-peptide (1-42). Citation: Neurobiology of Aging 20: 325-330 1999 Type: ARTICLE Genes: unc-54 Abstract: The amyloid beta-peptide (A beta)-associated free radical oxidative stress model for neuronal death in Alzheimer's disease (AD) brain predicts that neuronal protein oxidation is a consequence of A beta-associated free radicals [8]. In this study we have used both in vitro and in vivo models of beta-amyloid (A beta) toxicity to detect free radical induced oxidative stress by the measure of protein carbonyl levels. These model systems employed cultured hippocampal neurons exposed to exogenous synthetic A beta(1-42) and transgenic Caenorhabditis elegans (C. elegans) animals expressing A beta(1-42). We also investigated the importance of the A beta(1-42) Met(35) residue for free radical formation in peptide solution and for peptide-induced protein oxidation and neuronal toxicity in these model systems. A beta(1-42) in solution yielded an EPR spectrum, suggesting that free radicals are associated with this peptide; however, neither the reverse [A beta(42-1)] nor methionine-substituted peptide [A beta(1-42)Met(35)Nle] gave significant EPR spectra, suggesting the importance of the methionine residue in free radical formation. A beta(1-42) addition to cultured hippocampal neurons led to both neurotoxicity (30.1% cell death, p < 0.001) and increased protein oxidation (158% of controls, p < 0.001), and both of those effects were not observed with reverse or Met(35)Nle substituted peptides. C. elegans transgenic animals expressing human A beta(1-42) also had significantly increased in vivo protein carbonyls (176% of control animals, p < 0.001), consistent with our model. In contrast, transgenic animals with a Met(35)cys substitution in A beta(1-42) showed no increased protein carbonyls in vivo, in support of the hypothesis that methionine is important in A beta-associated free radical oxidative stress. These results are discussed with reference to the A beta-associated free radical oxidative ------------------- Key: 3795 Medline: 10564810 Authors: Lim HH;Park BJ;Choi HS;Park CS;Eom SH;Ahnn J Title: Identification and characterization of a putative C. elegans potassium channel gene (Ce-slo-2) distantly related to Ca2+-activated K+ channels. Citation: Gene 240: 35-43 1999 Type: ARTICLE Genes: Abstract: Two putative homologues of large conductance Ca2+-activated KI channel alpha-subunit gene (slowpoke or slo) were revealed by C. elegans genome sequencing. One of the two genes, F08B12.3 (Ce-slo-2), shows a relatively low amino acid sequence similarity to other Slo sequences and lacks key functional motifs, which are important for calcium and voltage sensing. However, its overall structure and regions of homology, which are conserved in all Slo proteins, suggest that Ce-SLO-2 should belong to the Slo channel family. We have cloned a full-length cDNA of the Ce-slo-2, which encodes a protein containing six putative transmembrane segments with a K+-selective pore and a large C-terminal cytosolic domain. Green fluorescent protein (GFP) and whole-mount immunostaining analyses revealed that Ce-slo-2 is specifically expressed in neuronal cells at the nerve ring, at the ventral nerve cord of the mid-body, and at the tail region. We have also identified a putative human counterpart of Ce-slo-2 from a human brain EST database, which shows a stretch of highly conserved amino acid residues. Northern blot and mRNA dot blot analyses revealed a strong and specific expression in brain and skeletal muscle. Taken together, our data suggest that Ce-slo-2 may constitute an evolutionarily conserved gene encoding a potassium channel that has specific functions in neuronal cells. ------------------- Key: 3796 Medline: 20065150 Authors: Roubin R;Naert K;Popovici C;Vatcher G;Coulier F;Thierry-Mieg J;Pontarotti P;Birnbaum D;Baillie Title: let-756, A C. elegans fgf essential for worm development. Citation: Oncogene 18: 6741-6747 1999 Type: ARTICLE Genes: egl-17 let-713 let-721 let-725 let-756 mel-32 nDf16 nDf17 nDf20 sDf125 sDf127 sDp3 Abstract: In vertebrates, Fibroblast Growth Factors (FGFs) and their receptors are involved in various developmental and pathological processes, including neoplasia. The number of FGFs and their large range of activities have made the understanding of their precise functions difficult. Investigating their biology in other species might be enlightening. A sequence encoding a putative protein presenting 30-40% identity with the conserved core of vertebrate FGFs has been identified by the C. elegans sequencing consortium. We show here that this gene is transcribed and encodes a putative protein of 425 amino acids (aa). The gene is expressed at all stages of development beyond late embryogenesis, peaking at the larval stages. Loss-of-function mutants of the let-756 gene are rescued by the wild type fgf gene in germline transformation experiments. Two partial loss-of-function alleles, s2613 and s2809, have a mutation that replaces aa 317 by a stop. The truncated protein retains the FGF core but lacks a C-terminus portion. These worms are small and develop slowly into clear and scrawny, yet viable and fertile adults. A third allele, s2887, is inactivated by an inversion that disrupts the first exon. It causes a developmental arrest early in the larval stages. Thus, in contrast to the other nematode fgf gene egl-17, let-756/fgf is essential for worm development. ------------------- Key: 3797 Medline: 10567397 Authors: Schriever AM;Friedrich T;Pusch M;Jentsch TJ Title: CLC chloride channels in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 274: 34238-34244 1999 Type: ARTICLE Genes: pha-1 Abstract: The genome of the nematode Caenorhabditis elegans encodes six putative chloride channels (CeCLC-1 through CeCLC-6) that represent all three known branches of the mammalian CLC gene family. Using promoter fragments to drive the expression of the green fluorescent protein, CeCLC-2, -3, and -4 expression was studied in transgenic C. elegans. CeCLC-4 was specifically expressed in the large H-shaped excretory cell, where it was co-expressed with CeCLC-3, which is also expressed in other cells, including neurons, muscles, and epithelial cells. Also, CeCLC-2 was expressed in several cells of the nervous system, intestinal cells, and vulval muscle cells. Similar to mammalian CLC proteins, only two nematode CLC channels elicited detectable plasma membrane currents in Xenopus oocytes, CeCLC-3 currents were inwardly rectifying and were activated by positive prepulses. Its complex gating behavior can be explained by two gates, at least one of which depends on extracellular anions. In this respect it resembles some mammalian chloride channels with which it also shares a preference of chloride over iodide. C. elegans thus provides new opportunities to understand common mechanisms underlying structure and function in CLC channels and will allow for a genetic dissection of chloride channels in this simple model organism. ------------------- Key: 3798 Medline: 20040597 Authors: Plowman GD;Sudarsanam S;Bingham J;Whyte D;Hunter T Title: The protein kinases of Caenorhabditis elegans: A model for signal transduction in multicellular organisms. Citation: Proceedings of the National Academy of Sciences USA 96: 13603-13610 1999 Type: REVIEW Genes: Abstract: Caenorhabditis elegans should soon be the first multicellular organism whose complete genomic sequence has been determined. This achievement provides a unique opportunity for a comprehensive assessment of the signal transduction molecules required for the existence of a multicellular animal. Although the worm C. elegans may not much resemble humans, the molecules that regulate signal transduction in these two organisms prove to be quite similar. We focus here on the content and diversity of protein kinases present in worms, together with an assessment of other classes of proteins that regulate protein phosphorylation. By systematic analysis of the 19,099 predicted C. elegans proteins, and thorough analysis of the finished and unfinished genomic sequences, we have identified 411 full length protein kinases and 21 partial kinase fragments. We also describe 82 additional proteins that are predicted to be structurally similar to conventional protein kinases even though they share minimal primary sequence identity. Finally, the richness of phosphorylation-dependent signaling pathways in worms is further supported with the identification of 185 protein phosphatases and 128 phosphoprotein-binding domains (SH2, PTB, STYX, SBF, 14-3-3, FHA, and WW) in the worm genome. ------------------- Key: 3799 Medline: Authors: Hoss S;Haitzer M;Transpunger W;Steinberg CEW Title: Growth and fertility of Caenorhabditis elegans (Nematoda) in unpolluted freshwater sediments: Response to particle size distribution and organic content. Citation: Environmental Toxicology and Chemistry 18: 2921-2925 1999 Type: REVIEW Genes: Abstract: The nematode Caenorhabditis elegans (Maupas) was exposed in a sediment bioassay to 26 different unpolluted freshwater sediments varying in particle size distribution (2.5-18% clay, 25.7-68.2% silt, 18.7-70.9% sand) and organic content (2.5-77.1%). We examined the variation of the test endpoints body length, eggs per worm, and percentage of gravid worms. Caenorhabditis elegans tolerated all investigated sediments, with at least 80% (total mean 96.6%) of the worms reaching the stage of reproductive adults. Variation in body length was small (total mean 1,235 +/- 97.8 mu m), but significant differences among the various sediments were found. We found a weak correlation of body length with particle size distribution, indicating that the nematodes grew better in coarser sediments. The number of eggs per worm showed relatively high variation among treatments (total mean 12.4 +/- 4.8) and also within treatments (mean +/- 5-95%). C. elegans is a suitable test organism for freshwater sediment bioassays, using body length and percentage of gravid worms as test endpoints. ------------------- Key: 3800 Medline: Authors: Ohmachi M;Sugimoto A;Iino Y;Yamamoto M Title: kel-1, a novel kelch-related gene in Caenorhabditis elegans is expressed in pharyngeal gland cells and is required for the feeding process. Citation: Genes to Cells 4: 487- 1999 Type: CORRECT Genes: Abstract: Due to an unfortunate error in the printing of Figures 1B and 1C, the lettering was not very clear in the final version. They are reproduced here and should be pasted over those that appeared in issues 6 to the journal. ------------------- Key: 3801 Medline: Authors: Kao HT;Porton B;Hilfiker S;Stefani G;Pieribone VA;DeSalle R;Greengard P Title: Molecular evolution of the synapsin gene family. Citation: Journal of Experimental Zoology 285: 360-377 1999 Type: ARTICLE Genes: Abstract: Synapsins, a family of synaptic vesicle proteins, play a crucial role in the regulation of neurotransmission and synaptogenesis. They have been identified in a variety of invertebrate and vertebrate species, including human, rat (Rattus norvegicus), cow (Bos taurus), longfin squid (Loligo pealei), and fruit fly (Drosophila melanogaster). Here, synapsins were cloned from three additional species: frog (Xenopus laevis), lamprey (Lampetra fluviatilis), and nematode (Caenorhabditis elegans). Synapsin protein sequences from all these species were then used to explore the molecular phylogeny of these important neuronal, phosphoproteins. The ancestral condition of a single synapsin gene probably gave rise to the vertebrate synapsin gene family comprised of at least three synapsin genes (I, II, and III) in higher vertebrates. Synapsins possess multiple domains, which have evolved at different rates throughout evolution. In invertebrate synapsins, the most conserved domains are C and E. During the evolution of vertebrates, at least two gene duplication events are hypothesized to have given rise to the synapsin gene family. This was accompanied by the emergence of an additional conserved domain, termed A. ------------------- Key: 3802 Medline: Authors: Haitzer M;Abbt-Braun G;Traunspurger W;Steinberg CEW Title: Effects of humic substances on the bioconcentration of polycyclic aromatic hydrocarbons: Correlations with spectroscopic and chemical properties of humic substances. Citation: Environmental Toxicology and Chemistry 18: 2782-2788 1999 Type: ARTICLE Genes: Abstract: The presence of dissolved humic substances (HS, fulvic and humic acids) generally reduces the uptake of hydrophobic organic compounds into aquatic organisms. The extent of this effect depends both on the concentration and on the origin of the HS. The aim of this study was to investigate the role of qualitative differences between HS from different origins. The effects of seven different HS on the bioconcentration of pyrene and benzo[a]pyrene (BaP) in the nematode Caenorhabditis elegans were related to the spectroscopic and chemical properties of the HS. The effect of each humic material on the bioconcentration of pyrene or BaP was quantified as a "biologically determined" partition coefficient K-DOC. We observed significant linear relationships between K-DOC and the atomic H/C ratio, the specific absorptivity at 254 nm, the content of aromatic carbons (as determined by C-13 nuclear magnetic resonance spectroscopy, the copper-complexing capacity, the content of phenolic OH groups, and the molecular weight of the HS. There was no discernible relationship of K-DOC with the atomic (N + O)/C ratio, an indicator of the polarity of HS. Taken together, our results show that the variability in the effects of HS from different origins could be related to variations in bulk properties of the HS. Parameters describing the aromaticity of the humic materials seemed to be most useful for estimating effects of HS on the bioconcentration of pyrene and BaP. ------------------- Key: 3803 Medline: Authors: Hope IA Title: Background on Caenorhabditis elegans. Citation: "C. elegans. A Practical Approach." IA Hope (ed). Oxford University Press, NY. : 1-15 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3804 Medline: Authors: Blaxter M Title: The genome project and sequence homology to other species. Citation: "C. elegans. A Practical Approach." IA Hope (ed). Oxford University Press, NY. : 17-37 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3805 Medline: Authors: Thierry-Mieg J;Thierry-Mieg D;Potdevin M;Stein L Title: C. elegans and the web. Citation: "C. elegans. A Practical Approach." IA Hope (ed). Oxford University Press, NY. : 39-50 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3806 Medline: Authors: Stiernagle T Title: Maintenance of C. elegans. Citation: "C. elegans. A Practical Approach." IA Hope (ed). Oxford University Press, NY. : 51-67 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3807 Medline: Authors: Jin Y Title: Transformation. Citation: "C. elegans. A Practical Approach." IA Hope (ed). Oxford University Press, NY. : 69-96 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3808 Medline: Authors: Barstead RJ Title: Reverse genetics. Citation: "C. elegans. A Practical Approach." IA Hope (ed). Oxford University Press, NY. : 97-118 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3809 Medline: Authors: Schnabel R Title: Microscopy. Citation: "C. elegans. A Practical Approach." IA Hope (ed). Oxford University Press, NY. : 119-141 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3810 Medline: Authors: Thomas JH;Lockery S Title: Neurobiology. Citation: "C. elegans. A Practical Approach." IA Hope (ed). Oxford University Press, NY. : 143-179 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3811 Medline: Authors: Mounsey A;Molin L;Hope IA Title: Gene expression patterns. Citation: "C. elegans. A Practical Approach." IA Hope (ed). Oxford University Press, NY. : 181-199 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3812 Medline: Authors: Johnstone IL Title: Molecular biology. Citation: "C. elegans. A Practical Approach." IA Hope (ed). Oxford University Press, NY. : 201-225 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3813 Medline: Authors: Mains PE;McGhee JD Title: Biochemistry of C. elegans. Citation: "C. elegans. A Practical Approach." IA Hope (ed). Oxford University Press, NY. : 227-244 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3814 Medline: Authors: Hodgkin J Title: Conventional genetics. Citation: "C. elegans. A Practical Approach." IA Hope (ed). Oxford University Press, NY. : 245-270 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 3815 Medline: 10581274 Authors: Shaham S;Reddien PW;Davies B;Horvitz HR Title: Mutational analysis of the Caenorhabditis elegans cell-death gene ced-3. Citation: Genetics 153: 1655-1671 1999 Type: ARTICLE Genes: ced-1 ced-3 ced-4 ced-8 ced-9 sDf21 Abstract: Mutations in the gene ced-3, which encodes a protease similar to interleukin-lp converting enzyme and related proteins termed caspases, prevent programmed cell death in the nematode Caenorhabditis elegans. We used site-directed mutagenesis to demonstrate that both the presumptive active-site cysteine of the CED-3 protease and the aspartate residues at sites of processing of the CED-3 proprotein are required for programmed cell death in vivo. We characterized die phenotypes caused by and the molecular lesions of 52 ced-3 alleles. These alleles can be ordered in a graded phenotypic series. Of the 30 amino acid sites altered by ced-3 missense mutations, 29 are conserved with at least one other caspase, suggesting that these residues define sites important for the functions of all caspases. Animals homozygous for the ced-3(n2452) allele, which is deleted for the region of the ced-3 gene that encodes the protease domain, seemed to be incompletely blocked in programmed cell death, suggesting that some programmed cell death can occur independently of CED-3 protease activity. ------------------- Key: 3816 Medline: 20079501 Authors: Petalcorin MIR;Oka T;Koga M;Ogura K;Wada Y;Ohshima Y;Futai Title: Disruption of clh-1, a chloride channel gene, results in a wider body of Caenorhabditis elegans. Citation: Journal of Molecular Biology 294: 347-355 1999 Type: ARTICLE Genes: clh-1 Abstract: We cloned the clh-1 gene coding for a putative ClC chloride channel in Caenorhabditis elegans. The gene product exhibited a high degree of homology with human ClC-1 and ClC-2. The clh-1 gene was predominantly expressed in the hypodermis, including seam cells. Null mutations of clh-1 caused a significantly wider body and an abnormal alae structure. High osmolarity in the culture medium restored the normal body width of the clh-1 mutants. These results suggest that the clh-1 gene contributes to maintenance of the body width through regulation of osmolarity. ------------------- Key: 3817 Medline: 10606272 Authors: Mazroui R;Pouti A;Kramer A Title: Splicing factor SF1 from Drosophila and Caenorhabditis: Presence of an N-terminal RS domain and requirement for viability. Citation: RNA 5: 1615-1631 1999 Type: ARTICLE Genes: cyp-13 uaf-2 Abstract: Splicing factor SF1 contributes to the recognition of the 3' splice site by interacting with U2AF(65) and binding to the intron branch site during the formation of the early splicing complex E. These interactions and the essential functional domains of SF1 are highly conserved in Saccharomyces cerevisiae. We have isolated cDNAs encoding SF1 from Drosophila (Dm) and Caenorhabditis (Ce). The encoded proteins share the U2AF(65) interaction domain, a hnRNP K homology domain, and one or two zinc knuckles required for RNA binding as well as Pro-rich C-terminal sequences with their yeast and mammalian counterparts. In contrast to SF1 in other species, DmSF1 and CeSF1 are characterized by an N-terminal region enriched in Ser, Arg, Lys, and Asp residues with homology to the RS domains of several splicing proteins. These domains mediate protein-protein or protein-RNA interactions, suggesting an additional role for DmSF1 and CeSF1 in pre-mRNA splicing. Human (Hs), fly, and worm SF1 interact equally well with HsU2AF(65) or the Drosophila homolog DmU2AF(50). Moreover, DmSF1 lacking its N terminus is functional in prespliceosome formation in a HeLa splicing system, emphasizing the conserved nature of interactions at an early step in spliceosome assembly. The Ce-SF1 gene is located in a polycistronic transcription unit downstream of the genes encoding U2AF(35) (uaf-2) and a cyclophilin (cyp-13), implying the coordinate transcriptional regulation of these genes. Injection of double-stranded RNA into C. elegans results in embryonic lethality; thus, the SF1 gene is essential not only in yeast but also in at least one metazoan. ------------------- Key: 3818 Medline: 10619031 Authors: Whangbo J;Kenyon C Title: A Wnt signaling system that specifies two patterns of cell migration in C. elegans. Citation: Molecular Cell 4: 851-858 1999 Type: ARTICLE Genes: bar-1 egl-20 lin-17 mab-5 Abstract: In C. elegans, a bilateral pair of neuroblasts, QL and QR, give rise to cells that migrate in opposite directions along the anteroposterior (A/P) body axis. QL and its descendants migrate posteriorly whereas QR and its descendants migrate anteriorly. We find that a Wnt family member, EGL-20, acts in a dose-dependent manner to specify these opposite migratory behaviors. High levels of EGL-20 promote posterior migration by activating a canonical Wnt signal transduction pathway, whereas tow levels promote anterior migration by activating a separate, undefined pathway. We find that the two Q cells respond differently to EGL-20 because they have different response thresholds. Thus, in this system two distinct dose-dependent responses are specified not by graded levels of the Wnt signal, but instead by left-right asymmetrical differences in the cellular responsiveness to Wnt signaling. ------------------- Key: 3819 Medline: 20079510 Authors: Baylis HA;Furuichi T;Yoshikawa F;Mikoshiba K;Sattelle DB Title: Inositol 1,4,5-trisphosphate receptors are strongly expressed in the nervous system, pharynx, intestine, gonad and excretory cell of Caenorhabditis elegans and are encoded by a single gene (itr-1). Citation: Journal of Molecular Biology 294: 467-476 1999 Type: ARTICLE Genes: itr-1 let-23 lfe-1 Abstract: Inositol 1,4,5-trisphosphate (InsP(3)) activates receptors (InsP(3)Rs) that mediate intracellular Ca2+ release, thereby modulating intracellular calcium signals and regulating important aspects of cellular physiology and gene expression. To further our understanding of InsP(3)Rs we have characterised InsP(3)Rs and the InsP(3)R gene, itr-1, from the model organism Caenorhabditis elegans. cDNAs encoding InsP(3)Rs were cloned enabling us to: (a) identify three putative transcription start sites that result in alternative mRNA 5' ends: (b) detect alternative splicing at three sites and: (c) determine the full genomic organisation of the itr-1 gene. The InsP(3)R protein (ITR-1) is similar to 42% identical with known InsP(3)Rs and possesses conserved structural features. When the putative InsP(3) binding domain was expressed in Escherichia coli, specific binding of InsP(3) was detected. Using antibodies against ITR-1 we detected a protein of 220 kDa in C. elegans membranes. These antibodies and itr-1::GFP (green fluorescent protein) reporter constructs were used to determine the expression pattern of itr-1 in C. elegans. Strong expression was observed in the intestine, pharynx, nerve ring, excretory cell and gonad. These results demonstrate the high degree of structural and functional conservation of InsP(3)Rs from nematodes to mammals and the utility of C. elegans as a system for studies on InsP(3)R mediated signalling. ------------------- Key: 3820 Medline: 20044744 Authors: Dornan J;Page AP;Taylor P;Wu SY;Winter AD;Husi H;Walkinshaw MD Title: Biochemical and structural characterization of a divergent loop cyclophilin from Caenorhabditis elegans. Citation: Journal of Biological Chemistry 274: 34877-34883 1999 Type: ARTICLE Genes: cyp-3 Abstract: Cyclophilin 3 (CYP-3) is one of the most abundantly expressed cyclophilin isoforms in the free living nematode Caenorhabditis elegans, The detailed post-embryonic expression pattern of the cyp-3 transcript is unusual, peaking during early larval development. The spatial expression pattern was examined via reporter gene analysis demonstrating that the cyp-3 transcript is exclusively expressed in the single anterior excretory cell. Recombinant cyclophilin 3 has been purified, crystallized and solved to a resolution of 1.8 Angstrom. The peptidyl-prolyl isomerase activity of CYP-3 has been characterized against the substrate N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide, and gives a k(cat)/K-m value of 2.4 x 10(6) M-1 s(-1). The immunosuppressive drug cyclosporin A binds and inhibits CYP-3 with an IC50 value of 16 nM, comparable with the range of values found for human cyclophilin A The x-ray structure shows that the overall fold and active site geometry is similar to other cyclophilin structures. There are however a number of distinctive features, and we use this structure and amino acid sequence alignment analysis to identify a subgroup of "divergent-loop cyclophilins". This subgroup has a number of uniquely conserved features: an additional loop between residues 48 and 54 (KSGKPLH); two cysteine residues (Cys(40) and Cys(168)) that are in close proximity but remain in the unoxidized form, and two Other conserved residues, His(54) and Glu(83). We suggest that these features are functionally important for the role played by this class of cyclophilins during cellular responses to stress caused by changes in the redox environment or by upregulation of cellular activity. This study represents a detailed biological, biochemical, and structural characterization of a single cyclophilin isoform ------------------- Key: 3821 Medline: 20029649 Authors: Drickamer K;Dodd RB Title: C-type lectin-like domains in Caenorhabditis elegans: predictions from the complete genome sequence. Citation: Glycobiology 9: 1357-1369 1999 Type: ARTICLE Genes: Abstract: Protein modules related to the C-type carbohydrate-recognition domains of animal lectins are found in at least 125 proteins encoded in the Caenorhabditis elegans genome. Within these proteins, 183 C-type lectin-like domains (CTLDs) have been identified. The proteins have been classified based on the overall arrangement of modules within the polypeptides and based on sequence similarity between the CTLDs. The C. elegans proteins generally have different domain organization from known mammalian proteins containing CTLDs. Most of the CTLDs are divergent in sequence from those in mammalian proteins, However, 19 show conservation of most of the amino acid residues that ligate Ca2+ to form a carbohydrate-binding site in vertebrate C-type carbohydrate-recognition domains. Seven of these domains are particularly similar in sequence to mannose- and N-acetylglucosamine-binding domains in the vicinity of this ------------------- Key: 3822 Medline: 20047897 Authors: Hsieh J;Liu J;Kostas SA;Chang C;Sternberg PW;Fire A Title: The RING finger/B-box factor TAM-1 and a retinoblastoma-like protein LIN-35 modulate context-dependent gene silencing in Caenorhabditis elegans. Citation: Genes & Development 13: 2958-2970 1999 Type: ARTICLE Genes: egl-15 glr-1 hda-1 hlh-1 let-2 let-23 let-60 let-858 lin-2 lin-3 lin-8 lin-9 lin-11 lin-15 lin-35 lin-36 lin-38 lin-51 lin-52 lin-53 mab-5 myo-3 rps-5 tam-1 unc-22 unc-54 unc-119 nDf32 Abstract: Context-dependent gene silencing is used by many organisms to stably modulate gene activity for large chromosomal regions. We have used tandem array transgenes as a model substrate in a screen for Caenorhabditis elegans mutants that affect context-dependent gene silencing in somatic tissues. This screen yielded multiple alleles of a previously uncharacterized gene, designated tam-1 (for tandem-array-modifier). Loss-of-function mutations in tam-1 led to a dramatic reduction in the activity of numerous highly repeated transgenes. These effects were apparently context dependent, as nonrepetitive transgenes retained activity in a tam-1 mutant background. In addition to the dramatic alterations in transgene activity, tam-1 mutants showed modest alterations in expression of a subset of endogenous cellular genes. These effects include genetic interactions that place tam-1 into a group called the class B synMuv genes (for a Synthetic Multivulva phenotype); this family plays a negative role in the regulation of RAS pathway activity in C. elegans. Loss-of-function mutants in other members of the class-B synMuv family, including lin-35, which encodes a protein similar to the tumor suppressor Rb, exhibit a hypersilencing in somatic transgenes similar to that of tam-1 mutants. Molecular analysis reveals that tam-1 encodes a broadly expressed nuclear protein with RING finger and B-box motifs. ------------------- Key: 3823 Medline: 20070548 Authors: Suprenant KA;Tuxhorn JA;Daggett MAF;Ahrens DP;Hostetler A;Palange JM;VanWinkle CE;Livingston BT Title: Conservation of the WD-repeat, microtubule-binding protein, EMAP, in sea urchins, humans, and the nematode C. elegans. Citation: Development Genes & Evolution 210: 2-10 2000 Type: ARTICLE Genes: Abstract: The echinoderm microtubule-associated protein (EMAP) is the most abundant microtubule-binding protein in the first cleavage mitotic apparatus in sea urchin embryos. The first goal of this study was to determine whether there is sufficient EMAP in the egg and embryo to modify microtubule dynamics during the early cleavages divisions and whether EMAP functions at a specific time or place in the embryo. To accomplish this goal, we examined the relative abundance, tissue distribution, and temporal pattern of EMAP expression during embryonic development. The second goal of this study was to identify important functional domains within the EMAP coding sequence. A conserved sequence might reveal a potential microtubule-binding domain. We cloned, sequenced and compared overlapping EMAP cDNAs from two different sea urchin species that diverged approximately 80 million years ago, and compared these with cDNA sequences from a vertebrate and nematode species. From quantitative immunoblots, we determined the EMAP concentration in eggs to be 4 mu M. The steady-state levels of EMAP mRNA and protein accumulated during development, and all three germ layers expressed EMAP. During the early stages of development, EMAP and tubulin were both abundant in the ectoderm, mesoderm and endoderm. However, during late gastrulation and the formation of the early pluteus larvae, EMAP was enriched in the mesoderm, while tubulin staining was most abundant in the archenteron. These results indicate that EMAP may have tissue-specific functions in the late stage embryo. To identify conserved functional domains, we compared the predicted amino acid sequence encoded by Strongylocentrotus purpuratus and Lytechinus variegatus EMAP cDNAs, and determined that these two sea urchin EMAPs were 95% conserved and shared an identical domain organization. A parsimonious analysis of these sea urchin protein sequences, as well as human and C. elegans EMAP sequences was used to construct a gene tree. Together these results suggest that EMAP is an important microtubule protein required at all developmental stages of sea urchins, and whose cellular function may be conserved ------------------- Key: 3824 Medline: 20047718 Authors: Troemel ER Title: Chemosensory signaling in C. elegans. Citation: BioEssays 21: 1011-1020 1999 Type: REVIEW Genes: adp-1 gpa-2 gpa-3 gpa-5 odr-3 odr-4 odr-8 odr-10 osm-9 tax-2 tax-4 Abstract: The nematode Caenorhabditis elegans can sense and respond to hundreds of different chemicals with a simple nervous system, making it an excellent model for studies of chemosensation. The chemosensory neurons that mediate responses to different chemicals have been identified through laser ablation studies, providing a cellular context for chemosensory signaling. Genetic and molecular analyses indicate that chemosensation in nematodes involves G protein signaling pathways, as it does in vertebrates, but the receptors and G proteins involved belong to nematode-specific gene families. It is likely that about 500 different chemosensory receptors are used to detect the large spectrum of chemicals to which C. elegans responds, and one of these receptors has been matched with its odorant ligand. C. elegans olfactory responses are also subject to regulation based on experience, allowing the nematode to respond to a complex and changing chemical ------------------- Key: 3825 Medline: 20031448 Authors: You C;Mackay EA;Gehrig PM;Hunziker PE;Kagi JHR Title: Purification and characterization of recombinant Caenorhabditis elegans metallothionein. Citation: Archives of Biochemistry & Biophysics 372: 44-52 1999 Type: ARTICLE Genes: Abstract: The roundworm Caenorhabditis elegans adapted for survival at high concentrations of Cd(II) expresses two isoforms of metallothionein, CeMT-I and CeMT-II, To characterize one of these proteins CeMT-II was prepared as its Cd containing form by expressing its cDNA heterologously in Escherichia coli, The purified 63-amino-acid protein was identified as the desired product by ion-spray mass spectrometry and was found to resemble in most of its chemical and spectroscopic features the metallothioneins of other animal phyla. The recombinant protein contains a total of 18 cysteine residues and, as documented by electrophoresis and mass spectrometry, binds firmly six Cd ions through the cysteine's side chains. The Cd-113 NMR spectrum features six Cd-113 resonances. Their chemical shift positions between 615 and 675 ppm denote the existence of clusters of tetrahedrally coordinated cadmium thiolate complexes. The metal thiolate coordination dominates also the electronic far-UV absorption spectrum. It is characterized by a massive absorption profile with Cd thiolate shoulders at 255 and 235 nm, Upon replacement of Cd by Zn the profile was blue-shifted by 30 nm. ------------------- Key: 3826 Medline: Authors: Louvet-Vallee S;Felix MA Title: Regulatory cross-talk between gonad and aging in C. Citation: M S-Medecine Sciences 15: 1293-1294 1999 Type: ARTICLE Genes: daf-2 daf-16 Abstract: In French. ------------------- Key: 3827 Medline: 20050663 Authors: Fares H;Greenwald I Title: SEL-5, a serine-threonine kinase that facilitates lin-12 activity in Caenorhabditis elegans. Citation: Genetics 153: 1641-1654 1999 Type: ARTICLE Genes: abl-1 lag-2 lin-12 lin-35 sel-5 sDf121 sDp3 Abstract: Ligands present on neighboring cells activate receptors of the LIN-12/Notch family by inducing a proteolytic cleavage event that releases the intracellular domain. Mutations that appear to eliminate sel-5 activity are able to suppress constitutive activity of lin-12(d) mutations that are point mutations in the extracellular domain of LIN-12, but cannot suppress lin-12(intra), the untethered intracellular domain. These results suggest that sel-5 acts prior to or during ligand-dependent release of the intracellular domain. In addition, sel-5 suppression of lin-12(d) mutations is tissue specific: loss of sel-5 activity can suppress defects in the anchor cell/ventral uterine precursor cell fate decision and a sex myoblast/coelomocyte decision, but cannot suppress defects in two different ventral hypodermal cell fate decisions in hermaphrodites and males. sel-5 encodes at least two proteins, from alternatively spliced mRNAs, that share an amino-terminal region and differ in the carboxy-terminal region. The amino-terminal region contains the hallmarks of a serine/threonine kinase domain, which is most similar to ------------------- Key: 3828 Medline: 20050665 Authors: Rajaram S;Spangler TL;Sedensky MM;Morgan PG Title: A stomatin and a degenerin interact to control anesthetic activity in Caenorhabditis elegans. Citation: Genetics 153: 1673-1682 1999 Type: ARTICLE Genes: mec-2 unc-1 unc-7 unc-8 unc-9 unc-79 unc-80 Abstract: The mechanism of action of volatile anesthetics is unknown. In Caenorhabditis elegans, mutations in the gene unc-1 alter anesthetic sensitivity. The protein UNCI is a close homologue of the mammalian protein stomatin. Mammalian stomatin is thought to interact with an as-yet-unknown ion channel to control sodium flux. Using both reporter constructs and translational fusion constructs for UNC-1 and green fluorescent protein (GFP), we have shown that UNC-1 is expressed primarily within the nervous system. The expression pattern of UNCI is similar to that of UNC-8, a sodium channel homologue. We examined the interaction of multiple alleles of unc-1 and unc-8 with each other and with other genes affecting anesthetic sensitivity. The data indicate that the protein products of these genes interact, and that an UNC-1/UNC-8 complex is a possible anesthetic target. We propose that membrane-associated protein complexes may represent a general target for volatile anesthetics. ------------------- Key: 3829 Medline: 20056449 Authors: Feng H;Zhong W;Punkosdy G;Gu S;Zhou L;Seabolt EK;Kipreos ET Title: CUL-2 is required for the G1-to-S-phase transition and mitotic chromosome condensation in Caenorhabditis elegans. Citation: Nature Cell Biology 1: 486-492 1999 Type: ARTICLE Genes: cki-1 cki-2 cul-1 cul-2 mei-1 Abstract: The human cullin protein CUL-2 functions in a ubiquitin-ligase complex with the von Hippel-Lindau (VHL) tumour suppressor protein. Here we show that, in Caenorhabditis elegans, cul-2 is expressed in proliferating cells and is required at two distinct points in the cell cycle, the G1-to-S-phase transition and mitosis. cul-2 mutant germ cells undergo a G1-phase arrest that correlates with accumulation of CKI-1, a member of the CIP/KIP family of cyclin-dependent-kinase inhibitors. In cul-2 mutant embryos, mitotic chromosomes are unable to condense, leading to unequal DNA segregation, chromosome bridging and the formation of multiple nuclei. ------------------- Key: 3830 Medline: 20056453 Authors: Kitagawa R;Rose AM Title: Components of the spindle-assembly checkpoint are essential in Caenorhabditis elegans. Citation: Nature Cell Biology 1: 514-521 1999 Type: ARTICLE Genes: glp-1 lin-12 mdf-1 mdf-2 Abstract: The spindle-assembly checkpoint ensures that, during mitosis and meiosis, chromosomes do not segregate until they are properly attached to the microtubules of the spindle. Here we show that mdf-l and mdf-2 are components of the spindle-assembly checkpoint in Caenorhabditis elegans, and are essential for the long-term survival and fertility of this organism. Loss of function of either of these genes leads to the accumulation of a variety of defects, including chromosome abnormalities, X-chromosome non-disjunction or loss, problems in gonad development, and embryonic lethality. Antibodies that recognize the MDF-2 protein localize to nuclei of the cleaving embryo in a cell-cycle-dependent manner. mdf-l, a gene encoding a product that interacts with MDF-2, is required for cell-cycle arrest and proper chromosome segregation in premeiotic germ cells treated with nocodoazole, a microtubule-depolymerizing agent. In the absence of mdf gene products, errors in chromosome segregation arise and accumulate, ultimately leading to genetic lethality. ------------------- Key: 3831 Medline: 10588660 Authors: Grant B;Hirsh D Title: Receptor-mediated endocytosis in the Caenorhabditis elegans oocyte. Citation: Molecular Biology of the Cell 10: 4311-4326 1999 Type: ARTICLE Genes: dyn-1 emo-1 lrp-1 rme-2 Abstract: The Caenorhabditis elegans oocyte is a highly amenable system for forward and reverse genetic analysis of receptor-mediated endocytosis. We describe the use of transgenic strains expressing a vitellogenin::green fluorescent protein (YP170::GFP) fusion to monitor yolk endocytosis by the C. elegans oocyte in vivo. This YP170::GFP reporter was used to assay the functions of C, elegans predicted proteins homologous to vertebrate endocytosis factors using RNA-mediated interference. We show that the basic components and pathways of endocytic trafficking are conserved between C. elegans and vertebrates, and that this system can be, used to test the endocytic functions of any new gene. We also used the YP170::GFP assay to identify rme (receptor-mediated endocytosis) mutants. We describe a new member of the low-density lipoprotein receptor superfamily, RME-2, identified in our screens for endocytosis defective mutants. We show that RME-2 is the C. elegans yolk ------------------- Key: 3832 Medline: Authors: Cole DG Title: Kinesin-II, coming and going. Citation: Journal of Cell Biology 147: 463-465 1999 Type: REVIEW Genes: che-3 Abstract: Eukaryotic cells are constantly challenged with a variety of transport problems. These are encountered during membrane trafficking, distribution of mitochondria and other membrane-bounded organelles, mRNA localization, and during special events such as mitosis and meiosis. Much of this transport is mediated by the concerted efforts of kinesins, dyneins, and myosins, the molecular motors that operate along the cytoskeletal network of microtubules and actin filaments. Differentiated cells generate special transport needs, such as the long distance axonal transport of materials in neuronal cells, the bidirectional intraflagellar transport of proteinaceous rafts in ciliated cells, and the dispersion and aggregation of pigment granules in melanophores. One motor protein that has been adapted to operate in these three specialized movements is kinesin-II, also known as the heterotrimeric kinesin, KIF3A/3B, and KRP(85/95). This paper briefly summarizes two independent studies that (a) identify a normally soluble enzyme as a cargo of kinesin-II during anterograde axonal transport, and (b) indicate that kinesin-II is carried as a cargo during retrograde intraflagellar transport within neuronal sensory cilia. ------------------- Key: 3833 Medline: Authors: Thieringer H;Sahota S;Mano I;Driscoll M Title: C. elegans members of the DEG/ENaC channel superfamily: form and function. Citation: "Current Topics in Membranes. Amiloride-sensitive sodium channels, physiology and functional diversity." D. Benos (ed). Academic Press. 47: 297-314 1999 Type: REVIEW Genes: deg-1 del-1 flr-1 let-2 mec-2 mec-4 mec-5 mec-10 mec-12 sup-40 sup-41 sup-42 sup-43 unc-8 unc-105 Abstract: ------------------- Key: 3834 Medline: 20083484 Authors: Thomas JH Title: Lifespan: The effects of sensory deprivation. Citation: Nature 402: 740-741 1999 Type: REVIEW Genes: daf-2 daf-7 daf-16 Abstract: Once, lifespan genetics was largely the domain of theorists, who tried to explain why an organism's genes so cavalierly allow individual somas to die. But a flood of papers on the nematode worm Caenorhabditis elegans has brought the subject into the realm of serious experimental analysis. The latest studies (1,2), including a report by Apfeld and Kenyon (1) on page 804 of this issue, indicate that the nervous system has a key function in regulating lifespan. Perhaps we are, indeed, only as old as we think ------------------- Key: 3835 Medline: 20083490 Authors: Apfeld J;Kenyon C Title: Regulation of lifespan by sensory perception in Caenorhabditis elegans. Citation: Nature 402: 804-809 1999 Type: ARTICLE Genes: che-2 che-3 che-11 che-13 daf-2 daf-6 daf-10 daf-16 daf-19 mec-1 mec-8 osm-1 osm-3 osm-5 osm-6 tax-2 tax-4 ttx-1 Abstract: Caenorhabditis elegans senses environmental signals through ciliated sensory neurons located primarily in sensory organs in the head and tail. Cilia function as sensory receptors, and mutants with defective sensory cilia have impaired sensory perception(1,2) Cilia are membrane-bound microtubule-based structures and in C. elegans are only found at the dendritic endings of sensory neurons(3). Here we show that mutations that cause defects in sensory cilia or their support cells, or in sensory signal transduction, extend lifespan. Our findings imply that sensory perception regulates the lifespan of this animal, and suggest that in nature, its Lifespan may be regulated by environmental ------------------- Key: 3836 Medline: 10617207 Authors: Zorio DAR;Blumenthal T Title: Both subunits of U2AF recognize the 3' splice site in Caenorhabditis elegans. Citation: Nature 402: 835-838 1999 Type: ARTICLE Genes: uaf-1 uaf-2 Abstract: Introns are defined by sequences that bind components of the splicing machinery. The branchpoint consensus, polypyrimidine (poly(Y)) tract, and AG at the splice boundary comprise the mammalian 3' splice site(1), Although the AG is crucial for the recognition of introns with relatively short poly(Y) tracts, which are termed 'AG-dependent introns'(2), the molecule responsible for AG recognition has never been identified. A key player in 3' splice site definition is the essential heterodimeric splicing factor U2AF, which facilitates the interaction of the U2 small nuclear ribonucleoprotein particle with the branch point. The U2AF subunit with a relative molecular mass (M-r 65K) of 65,000 (U2AF(65)) binds to the poly(Y) tract(3-7), whereas the role of the 35K subunit (U2AF(35))(8) has not been clearly defined. It is not required for splicing in vitro(4) but it plays a critical role in vivo(9,10) Caenorhabiditis elegans introns have a highly conserved U(4)CAG/R at their 3' splice sites instead of branch-point and poly(Y) consensus sequences(11). Nevertheless, C. elegans has U2AF (refs 10, 12). Here we show that both U2AF subunits crosslink to the 3' splice site. Our results suggest that the U2AF(65)-U2AF(35) complex identifies the U(4)CAG/R, with U2AF35 being responsible for recognition of the canonical AG. ------------------- Key: 3837 Medline: 20109311 Authors: Kim SK Title: Reading the worm genome. Citation: Science 287: 52-53 2000 Type: REVIEW Genes: lin-15 lin-36 lin-37 Abstract: A powerful, top-down, holistic approach in biological research is to identify all of the components of a particular cellular process, so that one can define the global picture first and then use it as a framework to understand how the individual components of the process fit together. On page 116 of this issue, Wahout et al. report that they have started to compile a global map of interactions between all of the proteins in the worm Caenorhabditis elegans (1). These investigators commandeered a small number of well-studied proteins to establish the technical and conceptual framework for this mammoth protein-binding project. Their ultimate goal is to illuminate all of the protein-protein interactions in this animal, and to combine this information with that from other functional genomics approaches to work out what each worm gene does. ------------------- Key: 3838 Medline: 20107413 Authors: Olsen PH;Ambros V Title: The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initation of translation. Citation: Developmental Biology 216: 671-680 1999 Type: ARTICLE Genes: lin-4 lin-14 Abstract: lin-4 encodes a small RNA that is complementary to sequences in the 3' untranslated region (UTR) of lin-14 mRNA and that acts to developmentally repress the accumulation of LIN-14 protein. This repression is essential for the proper timing of numerous events of Caenorhabditis elegans larval development. We have investigated the mechanism of lin-4 RNA action by examining the fate of lin-14 mRNA in vivo during the time that lin-4 RNA is expressed. Our results indicate that the rate of synthesis of lin-14 mRNA, its state of polyadenylation, its abundance in the cytoplasmic fraction, and its polysomal sedimentation profile do not change in response to the accumulation of lin-4 RNA. Our results indicate that association of lin-4 RNA with the 3' UTR of lin-14 mRNA permits normal biogenesis of lin-14 mRNA, and normal translational initiation, but inhibits step(s) thereafter, such as translational elongation and/or the release of ------------------- Key: 3839 Medline: 20082953 Authors: Walhout AJM;Sordella R;Lu X;Hartley JL;Temple GF;Brasch MA;Thierry-Mieg N;Vidal M Title: Protein interaction mapping in C. elegans using proteins involved in vulval development. Citation: Science 287: 116-122 2000 Type: ARTICLE Genes: bar-1 egr-1 emb-5 gap-1 hda-1 ksr-1 lag-1 lag-2 let-23 let-60 lin-1 lin-2 lin-3 lin-7 lin-9 lin-10 lin-12 lin-15 lin-25 lin-31 lin-36 lin-37 lin-39 lin-45 lin-53 mek-2 mpk-1 ptp-2 sel-1 sel-10 sel-12 sem-5 sli-1 sup-17 sur-8 Abstract: Protein interaction mapping using large-scale two-hybrid analysis has been proposed as a way to functionally annotate large numbers of uncharacterized proteins predicted by complete genome sequences. This approach was examined in Caenorhabditis elegans, starting with 27 proteins involved in vulval development. The resulting map reveals both known and new potential interactions and provides a functional annotation for approximately 100 uncharacterized gene products. A protein interaction mapping project is now feasible for C. elegans on a genome-wide scale and should contribute to the understanding of molecular mechanisms in this organism and ------------------- Key: 3840 Medline: 20085453 Authors: Davis MW;Fleischhauer R;Dent JA;Joho RH;Avery L Title: A mutation in the C. elegans EXP-2 potassium channel that alters feeding behavior. Citation: Science 286: 2501-2504 1999 Type: ARTICLE Genes: exp-2 mnDp26 sDf30 sDf44 Abstract: The nematode pharynx has a potassium channel with unusual properties, which allows the muscles to repolarize quickly and with the proper delay. Here, the Caenorhabditis elegans exp-2 gene is shown to encode this channel. EXP-2 is a Kv-type (voltage-activated) potassium channel that has inward-rectifying properties resembling those of the structurally dissimilar human ether-a-go-go-related gene (HERG) channel. Null and gain-of-function mutations affect pharyngeal muscle excitability in ways that are consistent with the electrophysiological behavior of the channel, and thereby demonstrate a direct Link between the kinetics of this unusual channel and behavior. ------------------- Key: 3841 Medline: 10588887 Authors: Blelloch R;Santa Anna-Arriola S;Gao D;Li Y;Hodgkin J;Kimble J Title: The gon-1 gene is required for gonadal morphogenesis in Caenorhabditis elegans. Citation: Developmental Biology 216: 382-393 1999 Type: ARTICLE Genes: gon-1 lag-2 lim-7 unc-5 eDf19 mDf7 Abstract: In wild-type Caenorhabditis elegans, the gonad is a complex epithelial tube that consists of long arms composed predominantly of germline tissue as well as somatic structures specialized for particular reproductive functions. In gon-1 mutants, the adult gonad is severely disorganized with essentially no arm extension and no recognizable somatic structure. The developmental defects in gon-1 mutants are limited to the gonad; other cells, tissues, and organs appear to develop normally. Previous work defined the regulatory "leader" cells as crucial for extension of the gonadal arms (J. E. Kimble and J G White, 1981, Dev. Biol. 81, 208-219). In gon-1 mutants, the leader cells are specified correctly, but they fail to migrate and gonadal arms are not generated. In addition, gon-1 is required for morphogenesis of the gonadal somatic structures. This second role appears to be independent of that required for leader migration. Parallel studies have shown that gon-1 encodes a secreted metalloprotease (R. Blelloch and J. Kimble, 1999, Nature 399, 586-590). We discuss how a metalloprotease may control two aspects of gonadal morphogenesis. ------------------- Key: 3842 Medline: 20057760 Authors: Leung B;Hermann GJ;Priess JR Title: Organogenesis of the Caenorhabditis elegans intestine. Citation: Developmental Biology 216: 114-134 1999 Type: ARTICLE Genes: jam-1 Abstract: The intestine of Caenorhabditis elegans is an epithelial tube consisting of only 20 cells and is derived clonally from a single embryonic blastomere called E. We describe the cellular events that shape the intestine. These events include cytoplasmic polarization of cells in the intestinal primordium, the intercalation of specific sets of cells, the generation of an extracellular cavity within the primordium, and adherens junction formation. The polarization of the intestinal primordium is associated with the generation of an asymmetric microtubule cytoskeleton, and microtubule function plays a role in subsequent cell polarity. We show that an isolated E blastomere is capable of generating polarized intestinal cells, indicating that some of the major events in intestinal organogenesis do not depend upon interactions with surrounding tissues. We compare and contrast intestinal organogenesis with some of the basic steps in development of a second epithelial organ, the pharynx, and suggest how these differences lead to organs with distinct ------------------- Key: 3843 Medline: 20084449 Authors: Chin-Sang ID;George SE;Ding M;Moseley SL;Lynch AS;Chisholm AD Title: The ephrin VAB-2/EFN-1 functions in neuronal signaling to regulate epidermal morphogenesis in C. elegans. Citation: Cell 99: 781-790 1999 Type: ARTICLE Genes: efn-1 jam-1 pax-3 unc-119 vab-1 vab-2 Abstract: The Eph receptor VAB-1 is required in neurons for epidermal morphogenesis during C. elegans embryogenesis. Two models were proposed for the nonautonomous role of VAB-1: neuronal VAB-1 might signal directly to epidermis, or VAB-1 signaling between neurons might be required for epidermal development. We show that the ephrin VAB-2 (also known as EFN-1) is a ligand for VAB-1 and can function in neurons to regulate epidermal morphogenesis. In the absence of VAB-1 signaling, ephrin-expressing neurons are disorganized. vab-2/efn-1 mutations synergize with vab-1 kinase alleles, suggesting that VAB-2/EFN-1 may partly function in a kinase-independent VAB-1 pathway. Our data indicate that ephrin signaling between neurons is required nonautonomously for epidermal morphogenesis in C. elegans. ------------------- Key: 3844 Medline: 20042301 Authors: Lints R;Emmons SW Title: Patterning of dopaminergic neurotransmitter identity among Caenorhabditis elegans ray sensory neurons by a TGFB family signaling pathway and a Hox gene. Citation: Development 126: 5819-5831 1999 Type: ARTICLE Genes: cat-2 daf-1 daf-3 daf-4 daf-8 dbl-1 egl-5 jam-1 osm-6 sma-2 sma-3 sma-4 sma-6 unc-129 Abstract: We have investigated the mechanism that patterns dopamine expression among Caenorhabditis elegans male ray sensory neurons. Dopamine is expressed by the A-type sensory neurons in three out of the nine pairs of rays. We used expression of a tyrosine hydroxylase reporter transgene as well as direct assays for dopamine to study the genetic requirements for adoption of the dopaminergic cell fate. In loss-of-function mutants affecting a TGF beta family signaling pathway, the DBL-1 pathway, dopaminergic identity is adopted irregularly by a wider subset of the rays. Ectopic expression of the pathway ligand, DBL-1, from a heat-shock-driven transgene results in adoption of dopaminergic identity by rays 3-9; rays 1 and 2 are refractory. The rays are therefore prepatterned with respect to their competence to be induced by a DBL-1 pathway signal. Temperature-shift experiments with a temperature-sensitive type II receptor mutant, as well as heat-shock induction experiments, show that the DBL-1 pathway acts during an interval that extends from two to one cell generation before ray neurons are born and begin to differentiate. In a mutant of the AbdominalB class Hox gene egl-5, rays that normally express EGL-5 do not adopt dopaminergic fate and cannot be induced to express DA when DBL-1 is provided by a heat-shock-driven dbl-1 transgene. Therefore, egl-5 is required for making a subset of rays capable of adopting dopaminergic identity, while the function of the DBL-1 pathway signal is to pattern the realization of this capability. ------------------- Key: 3845 Medline: 99445235 Authors: Chitwood DJ Title: Biochemistry and function of nematode steroids. Citation: Critical Reviews in Biochemistry and Molecular Biology 34: 273-284 1999 Type: REVIEW Genes: Abstract: Although largely hidden from public view, nematodes are among the most numerous and ecologically diverse multicellular organisms inhabiting the planet. Although most species are microbivorous, numerous species are economically or medically important parasites of plants and animals. As Cobb wrote 80 years ago, "If all the matter in the universe except the nematodes were swept away, our world would still be dimly recognizable, and if, as disembodied spirits, we could then investigate it, we should find its mountains, hills, vales, rivers, lakes and oceans represented by a film of nematodes. The locations of towns would be decipherable, since for every massing of human beings there would be a corresponding massing of certain nematodes. The location of the various plants and animals would still be decipherable, and has we sufficient knowledge, in many cases their species could be determined by an examination of their erstwhile nematode parasites". ------------------- Key: 3846 Medline: Authors: Hu K;Li J;Webster JM Title: Nematicidal metabolites produced by Photorhabdus luminescens (Enterobacteriaceae), bacterial symbiont of entomopathogenic nematodes. Citation: Nematology 1: 457-469 1999 Type: ARTICLE Genes: Abstract: The secondary metabolites, 3,5-dihydroxy-4-isopropylstilbene (ST) and indole, from the culture filtrate of Photorhabdus luminescens MD, were shown to have nematicidal properties. ST caused nearly 100% mortality of 54 and adults of Aphelenchoides rhytium, Bursaphelenchus spp. and Caenorhabditis elegans at 100 mu g/ml, but had no effect on J2 of Meloidogyne incognita or infective juveniles (IJ) of Heterorhabditis megidis at 200 mu g/ml. Indole was lethal to several nematode species at 300 mu g/ml, and caused a high percentage of Bursaphelenchus spp. (54 and adults), M, incognita (J2) and Heterorhabditis spp. (IJ) to be paralysed at 300, 100 and 400 mu g/ml, respectively. Both ST and indole inhibited egg hatch of M, incognita. ST repelled IJ of some Steinernema spp. but not IJ of Heterorhabditis spp., and indole repelled IJ of some species of both Steinernema and Heterorhabditis. ST, but not indole, was produced in nematode-infected larval Galleria mellonella. after 24 h ------------------- Key: 3847 Medline: Authors: Baird SE Title: Natural and experimental associations of Caenorhabditis remanei with Trachelipus rathkii and other terrestrial isopods. Citation: Nematology 1: 471-475 1999 Type: ARTICLE Genes: Abstract: Caenorhabditis remanei was found in association with the terrestrial isopod Trachelipus rathkii at several wooded locations in southwestern Ohio. These associations were as developmentally arrested dauer larvae. The sites of association were the inner surfaces of the dorsal plates and ventral appendages. C. remanei associations also were observed with Armadillidium nasatum, Cylisticus convexus, and Porcellio scaber. They were not observed with Porcellio spinicornis even though Fl spinicornis populations were intermingled with infested populations of T. rathkii. Consistent with the observed natural associations, C. remanei dauers were experimentally able to infest T. rathkii and P. scaber. Dauer larvae responded to confinement with isopods by nictating and by climbing upon these potential hosts. Experimental infestations were able to persist for at least five days. Long-term infestations ------------------- Key: 3848 Medline: Authors: Tavernarakis N;Driscoll M;Kyrpides NC Title: The SPFH domain: implicated in regulating targeted protein turnover in stomatins and other membrane-associated proteins. Citation: Trends in Biochemical Sciences 24: 425-427 1999 Type: REVIEW Genes: mec-2 unc-1 unc-24 Abstract: Stromatin, also known as band 7.2b protein, is one of the major integral membrane proteins of human erythrocytes. This protein is apparently absent in the red cell membranes of patients suffering form overhydrated hereditary stomatocytosis, a form of autosomal dominant hemolytic anemia. Although he protein is missing, no mutations have been found within the stomatin gene in patients with this condition. However, an aberrant splice mutation associated with multi-system pathology early in life suggests that the protein is crucial for development (A. Argent, J. Delaunay and G. Stewart, pers. commun.). the genome of the nematode Caenorhabditis elegans encodes nine stomatin-related genes, three of which have been genetically characterized. MEC-2 is a protein expressed predominantly in six touch-receptor neurons and plays an essential role in mechanotransduction, whereas UNC-24 is required for normal locomotion. UNC-1 also affects locomotion and is required for normal responsiveness to volatile anesthetics. ------------------- Key: 3850 Medline: 20025931 Authors: Newman AP;Acton GZ;Hartwieg E;Horvitz HR;Sternberg PW Title: The lin-11 LIM domain transcription factor is necessary for morphogenesis of C. elegans uterine cells. Citation: Development 126: 5319-5326 1999 Type: ARTICLE Genes: lin-11 lin-12 Abstract: The Caenorhabditis elegans hermaphrodite egg-laying system comprises several tissues, including the uterus and vulva. lin-11 encodes a LIM domain transcription factor needed for certain vulval precursor cells to divide asymmetrically. Based on lin-11 expression studies and the lin-11 mutant phenotype, we find that lin-11 is also required for C. elegans uterine morphogenesis, Specifically, lin-11 is expressed in the ventral uterine intermediate precursor pi cells and their progeny (the utse and uv1 cells), which connect the uterus to the vulva. Like pi cell induction, the uterine lin-11 expression responds to the uterine anchor cell and the lin-12-encoded receptor. In wild type animals, the utse, which forms the planar process at the uterine-vulval interface, fuses with the anchor cell. We found that, in lin-11 mutants, utse differentiation was abnormal, the utse failed to fuse with the anchor cell and a functional uterine-vulval connection was not made. These findings indicate that lin-11 is essential for uterine-vulval morphogenesis. ------------------- Key: 3851 Medline: 10556063 Authors: Koga M;Take-uchi M;Tameishi T;Ohshima Y Title: Control of DAF-7 TGF-B expression and neuronal process development by a receptor tyrosine kinase KIN-8 in Caenorhabditis elegans. Citation: Development 126: 5387-5398 1999 Type: ARTICLE Genes: daf-1 daf-3 daf-6 daf-7 kin-8 mgDf90 mnDf68 Abstract: KIN-8 in C. elegans is highly homologous to human ROR1 and 2 receptor tyrosine kinases of unknown functions. These kinases belong to a new subfamily related to the Trk subfamily. A kin-8 promoter::gfp fusion gene was expressed in ASI and many other neurons as well as in pharyngeal and head muscles. A kin-8 deletion mutant was isolated and shelved constitutive dauer larva formation (Daf-c) phenotype: about half of the F-1 progeny became dauer larvae when they were cultivated on an old lawn of E. coli as food. Among the cells expressing kin-8::gfp, only ASI sensory neurons are known to express DAF-7 TGF-beta, a key molecule preventing dauer larva formation. In the kin-8 deletion mutant, expression of daf-7::gfp in ASI was greatly reduced, dye-filling in ASI was specifically lost and ASI sensory processes did not completely extend into the amphid pore. The Daf-c phenotype was suppressed by daf-7 cDNA expression or a daf-3 null mutation. ASI-directed expression of kin-8 cDNA under the daf-7 promoter or expression by a heat shock promoter rescued the dye-filling defect, but not the Daf-c phenotype, of the kin-8 mutant. These results show that the kin-8 mutation causes the Daf-c phenotype through reduction of the daf-7 gene expression and that KIN-8 function is cell-autonomous for the dye-filling in ASI, KIN-8 is required for the process development of ASI, and also involved in promotion of daf-7 expression through a physiological or ------------------- Key: 3852 Medline: 20087234 Authors: Surzycki SA;Belknap WR Title: Repetitive-DNA elements are similarly distributed on Caenorhabditis elegans autosomes. Citation: Proceedings of the National Academy of Sciences USA 97: 245-249 2000 Type: ARTICLE Genes: Abstract: The positions of approximate to 4,800 individual miniature inverted-repeat transposable element (MITE)-like repeats from four families were mapped on the Caenorhabditis elegans chromosomes. These families represent 1-2% of the total sequence of the organism. The four MITE families (Cele1, Cele2, Cele14, and Cele42) displayed distinct chromosomal distribution profiles. For example, the Cele14 MITEs were observed clustering near the ends of the autosomes. In contrast, the Cele2 MITEs displayed an even distribution through the central autosome domains, with no evidence for clustering at the ends, Both the number of elements and the distribution patterns of each family were conserved on all five C. elegans autosomes, The distribution profiles indicate chromosomal polarity and suggest that the current genetic and physical maps of chromosomes II, III, and X are inverted with respect to the other chromosomes. The degree of conservation of both the number and distribution of these elements on the five autosomes suggests a role in defining specific chromosomal ------------------- Key: 3853 Medline: 20113600 Authors: Johnstone IL Title: Cuticle collagen genes: expression in C. elegans. Citation: Trends in Genetics 16: 21-27 2000 Type: REVIEW Genes: bli-1 bli-2 col-12 cyp-9 dpy-2 dpy-7 dpy-10 dpy-13 lrp-1 nhr-23 pdi-1 pdi-2 rol-6 sqt-1 sqt-3 Abstract: Collagen is a structural protein used in the generation of a wide variety of animal extracellular matrices. The exoskeleton of the free-living nematode, Caenorhabditis elegans, is a complex collagen matrix that is tractable to genetic research. Mutations in individual cuticle collagen genes can cause exoskeletal defects that alter the shape of the animal. The complete sequence of the C. elegans genome indicates upwards of 150 distinct collagen genes that probably contribute to this structure. During the synthesis of this matrix, individual collagen genes are expressed in distinct temporal periods, which might facilitate the formation of specific interactions between distinct collagens. ------------------- Key: 3854 Medline: 20113601 Authors: Patterson GI;Padgett RW Title: TGFB-related pathways: roles in Caenorhabditis elegans development. Citation: Trends in Genetics 16: 27-33 2000 Type: REVIEW Genes: akt-1 akt-2 cet-1 daf-1 daf-3 daf-4 daf-5 daf-7 daf-8 daf-12 daf-14 daf-16 dbl-1 lin-31 myo-2 sma-2 sma-3 sma-4 sma-6 tig-2 unc-129 Abstract: Genetic and molecular analysis in Caenorhabditis elegans has produced new insights into how TGF beta-related pathways transduce signals and the developmental processes in which they function. These pathways are essential regulators of dauer formation, body-size determination, male copulatory structures and axonal guidance. Here, we review the insights that have come from standard molecular genetic experiments and discuss how the recently completed genome sequence has contributed to our understanding of ------------------- Key: 3855 Medline: 20076852 Authors: Aravind L;Subramanian G Title: Origin of multicellular eukaryotes - insights from proteome comparisons. Citation: Current Opinion in Genetics & Development 9: 688-694 1999 Type: REVIEW Genes: unc-73 Abstract: The complete genomes of the yeast Saccharomyces cerevisiae and the nematode worm Caenorhabditis elegans have recently become available allowing the comparison of the complete protein sets of a unicellular and multicellular eukaryote for the first time. These comparisons reveal some striking trends in terms of expansions or extensive shuffling of specific domains that are involved in regulatory functions and signaling. Similar comparisons with the available sequence data from the plant Arabidopsis thaliana produce consistent results. These observations have provided useful insights regarding the origin of multicellular organisms. ------------------- Key: 3856 Medline: Authors: Karandikar M;Cobb MH Title: Scaffolding and protein interactions in MAP kinase modules. Citation: Cell Calcium 26: 219-226 1999 Type: REVIEW Genes: Abstract: MAP kinases are a family of protein kinases that are ubiquitously expressed and play roles in most signal transduction pathways. They are activated within protein kinase cascades consisting of at least three kinases acting in series. In many, if not all cases, the three-kinase cascade, conveniently referred to as a MAP kinase module, is organized on scaffolds with a variety of forms and functions. This review discusses similarities and differences in scaffolding proteins and mechanisms in yeast, flies, worms and mammals. ------------------- Key: 3857 Medline: Authors: Labbe JC;Hekimi S;Rokeach LA Title: A possible link between posttranslational processing of ROP-1 and cleavage of the RoRNP-associated Y RNA during Caenorhabditis elegans larval development. Citation: Biochemistry & Cell Biology 77: 400-401 1999 Type: ARTICLE Genes: Abstract: The Ro ribonucleoprotein complex (RoRNP) has been initially described as an autoimmune target in human diseases such as systemic lupus erythematosus and Sjogren's syndrome. In most human cells, its general structure in composed of one major protein of 60 kDa, Ro60, that binds to one of four small RNA molecules, designated Y RNAs. Although no function has been assigned to the RoRNP, Ro60 has been shown to bind to mutant 5S rRNA molecules in Xenopus oocytes, suggesting a role for Ro60 in 5S rRNA biogenesis. Ro60 has also been shown to participate in the regulation of the translational fate of the L4 ribosomal protein mRNA by interacting with the 5' untranslated region, again suggesting its possible implication in ribosome biogenesis. To identify the function of RoRNP, we have taken a genetic approach in the nematode Caenorhabditis elegans. ------------------- Key: 3858 Medline: 20079594 Authors: Kwon JY;Park JM;Gim BS;Han SJ;Lee J;Kim YJ Title: Caenorhabditis elegans Mediator complexes are required for developmental-specific transcriptional activation. Citation: Proceedings of the National Academy of Sciences USA 96: 14990-14995 1999 Type: ARTICLE Genes: ceh-13 nhr-2 rps-5 sur-5 Abstract: Mediator proteins are required for transcriptional regulation of most genes in yeast. Mammalian Mediator homologs also function as transcriptional coactivators in vitro; however, their physiological role in gene-specific transcription is not yet known. To determine the role of Mediator proteins in the development of complex organisms, we purified putative Mediator complexes from Caenorhabditis elegans and analyzed their phenotypes in vivo. C. elegans Mediator homologs were assembled into two multiprotein complexes. RNA interference assays showed that the CeMed6, CeMed7, and CeMed10/CeNut2 gene products are required for the expression of developmentally regulated genes, but are dispensable for expression of the ubiquitously expressed genes tested in this study. Therefore, the gene-specific function of Mediator as an integrator of transcriptional regulatory signals is evolutionarily conserved and is essential for C. elegans development. ------------------- Key: 3859 Medline: 20079600 Authors: Mochii M;Yoshida S;Morita K;Kohara Y;Ueno N Title: Identification of transforming growth factor-beta-regulated genes in Caenorhabditis elegans by differential hybridization of arrayed cDNAs. Citation: Proceedings of the National Academy of Sciences USA 96: 15020-15025 1999 Type: ARTICLE Genes: dbl-1 lon-2 sma-2 Abstract: Members of the transforming growth factor-beta family play critical roles in body patterning, in both vertebrates and invertebrates. One transforming growth factor-beta-related gene, dbl-1, has been shown to regulate body length and male ray patterning in Caenorhabditis elegans. We screened arrayed cDNAs to identify downstream target genes for the DBL-1 signaling by using differential hybridization. C. elegans cDNAs representing 7,584 independent genes were arrayed on a nylon membrane at high density and hybridized with P-33-labeled DNA probes synthesized from the mRNAs of wild-type, dbl-1, sma-2 and Ion-2 worms, Signals for all the spots representing hybridized DNA were quantified and compared among strains. The screening identified 22 and 2 clones, which were positively and negatively regulated, respectively, by the DBL-1 signal. Northern hybridization confirmed the expression profiles of most of the clones, indicating good reliability of the differential hybridization using arrayed cDNAs. In situ hybridization analysis revealed the spatial and temporal expression patterns of each clone and showed that at least four genes, including the gene for the type I receptor for DBL1, sma-6 were transcriptionally regulated by the DBL-1 signal. ------------------- Key: 3860 Medline: 20079631 Authors: Darby C;Cosma CL;Thomas JH;Manoil C Title: Lethal paralysis of Caenorhabditis elegans by Pseudomonas aeruginosa. Citation: Proceedings of the National Academy of Sciences USA 96: 15202-15207 1999 Type: ARTICLE Genes: egl-9 Abstract: Identification of host factors that interact with pathogens is crucial to an understanding of infectious disease, but direct screening for host mutations to aid in this task is not feasible in mammals. The nematode Caenorhabditis elegans is a genetically tractable alternative for investigating the pathogenic bacterium Pseudomonas aeruginosa. A P. aeruginosa toxin, produced at high cell density under control of the quorum-sensing regulators LasR and RhlR, rapidly and lethally paralyzes C. elegans. Loss-of-function mutations in C. elegans egl-9, a gene required for normal egg laying, confer strong resistance to the paralysis. Thus, activation of EGL-9 or of a pathway that includes it may lead to the paralysis. The molecular identity of egl-9 was determined by transformation rescue and DNA sequencing. A mammalian homologue of EGL-9 is expressed in tissues in which exposure to P. aeroginosa ------------------- Key: 3861 Medline: 20191328 Authors: Chang C;Sternberg PW Title: C. elegans vulval development as a model system to study the cancer biology of EGFR signaling. Citation: Cancer and Metastasis Reviews 18: 203-213 1999 Type: REVIEW Genes: gap-1 itr-1 ksr-1 let-23 let-60 lfe-1 lfe-2 lin-1 lin-3 lin-8 lin-9 lin-15 lin-35 lin-36 lin-37 lin-38 lin-45 lin-51 lin-52 lin-53 lin-54 lin-55 lin-56 mek-2 mpk-1 ptp-2 rok-1 sem-5 sli-1 soc-2 sos-1 sur-1 sur-5 sur-8 unc-101 Abstract: Molecular genetic studies of C. elegans vulval development have helped to define an evolutionarily conserved signaling pathway from an EGF-like ligand through EGF-receptor, Ras and MAP kinase to the nucleus. Further studies have identified novel positive regulators such as KSR-1 and SUR-8/SOC-2 and negative regulators such as cbl/SLI-1. The many negative regulatory proteins might serve to prevent inappropriate signaling, and thus are analogous to tumor suppressor genes. ------------------- Key: 3862 Medline: 20191333 Authors: Fraser AG Title: Programmed cell death in C. elegans. Citation: Cancer & Metastasis Reviews 18: 285-294 1999 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ces-1 ces-2 egl-1 nuc-1 Abstract: Genetic screens in the hermaphrodite nematode worm Caenorhabditis elegans resulted in the identification of the basal conserved machinery of apoptosis, arguably the single most important finding for our understanding of cell death. The last two years have seen enormous progress in the elucidation of the molecular interactions that lie at the heart of this conserved machinery, along with major insights both into how cell death is activated in the worm and into the mechanism of recognition and engulfment of the cell corpses. In this review, I set out the current models of cell death regulation and execution in C. elegans, focussing in particular on the similarities between cell death in C. elegans and vertebrates. Finally, I attempt to highlight key areas for future progress in cell death research in C. elegans and explore additional ways in which the worm can be used to understand the regulation of cell ------------------- Key: 3863 Medline: 20119898 Authors: Ochoa C;Rodriguez M;Dominguez L;Saldana J;Di Maio R;Alonso-Villalobos P;Grueiro MMM Title: Nematocide activity of 6,7-diarylpteridines in three experimental models. Citation: Journal of Helminthology 73: 333-336 1999 Type: ARTICLE Genes: Abstract: The in vitro nematocide activity of seventeen 6,7-diarylpteridines has been tested using three different experimental models, Caenorhabditis elegans, Nippostrongylus brasiliensis and Heligmosomoides polygyrus. The method of evaluation of inhibition in the secretion of acetylcholinesterase by H. polygyrus seems to be the most indicated to avoid false positives. The in vivo activities, against Trichinella spiralis, of the most in vitro active pteridines have been assayed. All pteridine derivatives bearing 6,7-di-p-bromophenyl substituents have shown in vitro nematocide activites in the three experimental models used. Amongst all the pteridines tested in vivo, only 2,4-pteridinedithione derivatives exhibited moderate activity. ------------------- Key: 3864 Medline: 20100976 Authors: Hwang JM;Chang DJ;Kim US;Lee YS;Park YS;Kaang BK;Cho NJ Title: Cloning and functional characterization of a Caenorhabditis elegans muscarinic acetylcholine receptor. Citation: Receptors & Channels 6: 415-424 1999 Type: ARTICLE Genes: gar-3 Abstract: A cDNA clone encoding a muscarinic acetylcholine receptor (mAChR) has been isolated from the nematode Caenorhabditis elegans. The nematode mAChR, consisted of 585 amino acids, displays a high degree of amino acid sequence homology to other invertebrate and vertebrate mAChRs. Excluding a highly variable middle portion of the third intracellular loop, the C. elegans mAChR shares about 51% amino acid sequence identity with a Drosophila mAChR and 42-44% identity with human m1-m5 mAChR subtypes. Comparison of the cDNA sequence with the corresponding genomic sequence reveals that the C. elegans mAChR gene contains ten introns, eight of them in the coding region. Pharmacological profiles of the C. elegans mAChR expressed in Chinese hamster ovary (CHO) cells were shown to be similar to those of mammalian counterparts, indicating that ligand binding domains of the receptor have been conserved during evolution. When this cloned receptor was expressed in Xenopus oocytes, acetylcholine evoked a transient Cl- current. Furthermore, activation of the receptor with oxotremorine, acetylcholine or carbachol resulted in the stimulation of phosphatidylinositol metabolism in CHO cells, suggesting that the receptor is coupled to ------------------- Key: 3865 Medline: 20101233 Authors: Wang X;Roy PJ;Holland SJ;Zhang LW;Culotti JG;Pawson T Title: Multiple ephrins control cell organization in C. elegans using kinase-dependent and -independent functions of the VAB-1 Eph receptor. Citation: Molecular Cell 4: 903-913 1999 Type: ARTICLE Genes: efn-1 efn-2 efn-3 efn-4 vab-1 vab-2 Abstract: Eph receptor (EphR) tyrosine kinases and their ephrin ligands mediate direct cell-to-cell signaling. The C. elegans genome encodes four potential GPI-modified ephrins (EFN-1 to -4) and one EphR (VAB-1). Single and multiple ephrin mutants reveal functions for EFN-1, EFN-2, and EFN-3 in epidermal cell organization that, in aggregate, mirror those of VAB-1. Ephrin mutants have defects in head morphology and enclosure of the embryo by the epidermis and identify ephrin-EphR signaling functions involved in aligning and fusing tail and head epidermal cells, respectively. Biochemical analyses indicate that EFN-1, EFN-2, and EFN-3 jointly activate the VAB-1 tyrosine kinase in vivo. Mutant phenotypes and expression pattern analysis suggest that multiple ephrins are involved in distinct aspects of kinase-dependent and kinase-independent VAB-1 signaling required for proper cell organization during development in C. elegans. ------------------- Key: 3866 Medline: 20142321 Authors: Blomberg N;Sattler M;Nilges M Title: Letter to the editor: 1H, 15N, and 13C resonance assignment of the PH domain from C. elegans UNC-89. Citation: Journal of Biomolecular NMR 15: 269-270 1999 Type: LETTER Genes: unc-89 Abstract: Pleckstrin Homology (PH) domains form one of the largest families of signaling domains. Originally identified as an internal repeat in pleckstrin, PH domains have now been found in proteins with widespread functions such as phospholipases, GTPase regulating proteins, protein kinases, and cytoskeletal proteins. ------------------- Key: 3867 Medline: 20074913 Authors: Giugia JB;Gieseler K;Arpagaus M;Segalat L Title: Mutations in the dystrophin-like dys-1 gene of Caenorhabditis elegans result in reduced acetylcholinesterase activity. Citation: FEBS Letters 461: 270-272 1999 Type: ARTICLE Genes: ace-1 ace-2 ace-3 dys-1 Abstract: Mutations of the Caenorhabditis elegans dystrophin/utrophin-like dys-1 gene lead to hyperactivity and hypercontraction of the animals. In addition dys-1 mutants are hypersensitive to acetylcholine and acetylcholinesterase inhibitors. We investigated this phenotype further by assaying acetylcholinesterase activity. Total extracts from three different dys-1 alleles showed significantly less acetylcholinesterase-specific activity than wild-type controls. In addition. double mutants carrying a mutation in the dys-1 gene plus a mutation in either of the two major acetylcholinesterase genes (ace-1 and ace-2) display locomotor defects consistent with a strong reduction of acetylcholinesterases, whereas none of the single mutants does. Therefore, in C. elegans, disruption of the dystrophin/utrophin-like dys-1 gene affects ------------------- Key: 3868 Medline: 20050608 Authors: Gerdt S;Dennis RD;Borgonie G;Schnabel R;Geyer R Title: Isolation, characterization and immunolocalization of phosphorylcholine-substituted glycolipids in developmental stages of Caenorhabditis elegans. Citation: European Journal of Biochemistry 266: 952-963 1999 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans displays three neutral glycosphingolipids with structural homology to glycosphingolipids from the porcine nematode parasite, Ascaris suum. The present findings extend the degree of structural conservation between the two nematode species to glycosphingolipids with a phosphodiester substitution. Using a combination of hydrofluoric acid pretreatment, immunochemical characterization and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, three zwitterionic, phosphorylcholine-substituted glycosphingolipids could be identified in the neutral glycolipid fraction of C. elegans. The components were isolated as their zwitterionic, phosphorylcholine-substituted, pyridylaminated oligosaccharides by HPLC. Structural analysis was performed using hydrofluoric acid treatment, partial acid hydrolysis, methylation analysis, gas chromatography-mass spectrometry, cleavage with exoglycosidases and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Their chemical structures are proposed as: component Nz1, GalNAc(beta 1-4)[phosphorylcholine]GlcNAc(beta 1-3)Man(beta 1-4)Glc-ceramide; component Nz2, Gal(alpha 1-3)Gal- NAc(beta 1-4)[phosphorylcholine]-GlcNAc(beta 1-3)Man(beta 1-4)Glc-ceramide; and component Nz3, Gal(beta 1-3)-Gal(alpha 1-3)GalNAc(beta 1-4)[phosphorylcholine]GlcNAc(beta 1-3)Man(beta 1-4)Glc-ceramide. The oligosaccharide core is characteristic of the biosynthetic arthro-carbohydrate series of protostomial glycosphingolipids. The ceramide moiety was specified by a d17: 1 sphingoid-base with iso-branching and anteiso-branching, and 2-hydroxy, saturated fatty acids as represented by docosanoic and tetracosanoic acids. Analysis of the spatial and temporal expression of the phosphorylcholine epitope, during embryonic and postembryonic development, showed it to be localized predominantly in seam cells and basement membranes, respectively. In early embryonic ontogenesis the phosphorylcholine epitope was only lipid bound, while in late embryonic and postembryonic development this epitope ------------------- Key: 3869 Medline: 20050624 Authors: Yap SF;Chen W;Lim L Title: Molecular characterization of the Caenorhabditis elegans Rho GDP-dissociation inhibitor. Citation: European Journal of Biochemistry 266: 1090-1100 1999 Type: ARTICLE Genes: Abstract: GDP-dissociation inhibitors (GDIs) form one of the classes of regulatory proteins that modulate the cycling of the Ras superfamily of GTPases between active GTP-bound and inactive GDP-bound states. We report here the characterization of the Caenorhabditis elegans RhoGDI (CeRhoGDI) as part of our investigations into Rho-GTPase signalling pathways that are involved in nematode development. CeRhoGDI is a 23-kDa protein that is localized predominantly in the cytosol. CeRhoGDI interacts only with the lipid-modified forms of C. elegans Rho-GTPases, CeRhoA, CeRac1 and Cdc42Ce, in vitro and is able to solubilize the membrane-bound forms of these GTPases. CeRhoGDI recognizes the GTPases in both GTP- and GDP-bound forms; hence it inhibits both the guanine-nucleotide dissociation and GTP-hydrolysis activities. The inhibitory activity towards the GTP-bound GTPases is weak compared with that towards GDP-bound GTPases. CeRhoGDI is expressed throughout development and is highly expressed in marginal and vulval epithelial cells, in sperm cells and spicules. Taken together, our results suggest that CeRhoGDI may be involved in specific morphogenetic events mediated by the C. elegans ------------------- Key: 3870 Medline: 20087271 Authors: Tissenbaum HA;Hawdon J;Perregaux M;Hotez P;Guarente L;Ruvkun G Title: A common muscarinic pathway for diapause recovery in the distantly related nematode species Caenorhabditis elegans and Ancylostoma caninum. Citation: Proceedings of the National Academy of Sciences USA 97: 460-465 2000 Type: ARTICLE Genes: age-1 daf-2 daf-4 daf-7 daf-8 daf-14 daf-22 Abstract: Converging TGF-beta and insulin-like neuroendocrine signaling pathways regulate whether Caenorhabditis elegans develops reproductively or arrests at the dauer larval stage. We examined whether neurotransmitters act in the dauer entry or recovery pathways. Muscarinic: agonists promote recovery from dauer arrest induced by pheromone as well as by mutations in the TGF-beta pathway. Dauer recovery in these animals is inhibited by the muscarinic antagonist atropine. Muscarinic agonists do not induce dauer recovery of either daf-a or age-1 mutant animals, which have defects in the insulin-like signaling pathway. These data suggest that a metabotropic acetylcholine signaling pathway activates an insulin-like signal during C. elegans dauer recovery. Analogous and perhaps homologous cholinergic regulation of mammalian insulin release by the autonomic nervous system has been noted. In the parasitic nematode Ancylostoma caninum, the dauer larval stage is the infective stage, and recovery to the reproductive stage normally is induced by host factors. Muscarinic agonists also induce and atropine potently inhibits in vitro recovery of A. caninum dauer arrest. We suggest that host or parasite insulin-like signals may regulate recovery of A. caninum and could be potential targets for ------------------- Key: 3871 Medline: 20088283 Authors: Kay AR;Alfonso A;Alford S;Cline HT;Holgado AM;Sakmann B;Snitsarev VA;Stricker TP;Takahashi M;Wu LG Title: Imaging synaptic activity in intact brain and slices with FM1-43 in C. elegans, lamprey, and rat. Citation: Neuron 24: 809-817 1999 Type: ARTICLE Genes: Abstract: The fluorescent probe FM1-43 has been used extensively for imaging vesicle recycling; however, high nonspecific adsorption resulting in elevated background levels has precluded its use in certain tissues, notably brain slices. We have found that a sulfobutylated derivative of beta-cyclodextrin (ADVASEP-7) has a higher affinity for FM1-43 than the plasma membrane. ADVASEP-7 was used as a carrier to remove FM1-43 nonspecifically bound to the outer leaf let of the plasma membrane or extracellular molecules, significantly reducing background staining. This has enabled us to visualize synaptic vesicle recycling in the nematode C. elegans, intact lamprey spinal cord, and rat brain slices. ------------------- Key: 3872 Medline: 20102060 Authors: Vanfleteren JR;Braeckman BP Title: Mechanisms of life span determination in Caenorhabditis elegans. Citation: Neurobiology of Aging 20: 487-502 1999 Type: REVIEW Genes: age-1 akt-1 akt-2 clk-1 clk-2 clk-3 ctl-1 daf-2 daf-12 daf-16 daf-18 eat-2 fer-15 gro-1 mev-1 rad-8 sod-1 sod-2 sod-3 sod-4 spe-9 spe-26 Abstract: Molecular analysis of several gerontogenes of Caenorhabditis elegans has led to the discovery of at least two life span-controlling pathways. An insulin-like signaling cascade consisting of proteins encoded by the genes daf-2, age-1, akt-1, akt-2, daf-16 and daf-18 regulates dauer diapause, reproduction, and longevity. This pathway regulates all three processes systemically. daf-12 interacts with it, affecting dauer diapause and longevity. Life span extension mediated by this pathway probably results from the activation of an enhanced life-maintenance program, which is normally operative during dauer diapause. A different mechanism is specified by the clock genes clk-1, clk-2, clk-3 and gro-1, which regulate metabolic activity and the pace of many temporal processes including longevity. There is some controversy as to whether the life span extension observed in these mutants requires the activity of daf-16. All known gerontogenes appear to confer resistance to environmental stress, usually multiple stress factors, including oxidative stress, high temperature, and exposure to ultraviolet radiation. Caloric restriction extends longevity substantially, and may act by activating the enhanced life-maintenance program. ------------------- Key: 3873 Medline: 20102061 Authors: Cypser JR;Johnson TE Title: The spe-10 mutant has longer life and increased stress resistance. Citation: Neurobiology of Aging 20: 503-512 1999 Type: ARTICLE Genes: age-1 age-2 clk-1 daf-2 daf-4 daf-7 daf-16 eat-2 old-1 spe-10 spe-26 Abstract: We investigated the life span of spe-10 mutant nematodes. We also tested resistance of spe-10 mutants to ultraviolet (UV) light, heat, and paraquat and examined the relationship between resistance to UV light and the fertility defect of these animals. The spe-10 mutation significantly increased mean life span. Additionally, the mutation significantly increased resistance to both UV light and to heat. Resistance to paraquat was not significantly different from that of wild-type, nor were any dauers formed at 27 degrees C. No significant correlation was found between the UV resistance and the fertility defect, nor was the UV resistance attributable to a hermetic effect. These results reinforce the importance of stress resistance in specifying increased life span and indirectly suggest that this fertility defect is not a direct cause of life span extension. ------------------- Key: 3874 Medline: 20102062 Authors: Babar P;Adamson C;Walker GA;Walker DW;Lithgow GJ Title: P13-kinase inhibition induces dauer formation, thermotolerance and longevity in C. elegans. Citation: Neurobiology of Aging 20: 513-519 1999 Type: ARTICLE Genes: age-1 Abstract: The effects of 2-(4-Morpholinyl)- 8-phenyl-4H-1-benzopyran-4-one (LY294002), an inhibitor of mammalian phosphatidylinositol 3-OH kinase, was tested on an insulin signaling like pathway in the nematode Caenorhabditis elegans. Populations of C. elegans were treated with LY294002 at different stases of the life cycle, and its effects on development, thermotolerance and longevity were assessed. At concentrations of 160 mu M and above, LY294002 significantly induced both dauer formation and thermotolerance. Treatment of adult worms also resulted in a small, but significant, increase in life span. The results presented are consistent with the view that a neuroendocrine signaling pathway functions in adult worms to determine stress resistance and longevity. ------------------- Key: 3875 Medline: 20076450 Authors: Liao Y;Kariya K;Hu CD;Shibatohge M;Goshima M;Okada T;Watari Y;Gao X;Jin TG;Yamawaki-Kataoka Y;Kataoka T Title: RA-GEF, a novel Rap1A guanine nucleotide exchange factor containing a Ras/Rap1A-associating domain, is conserved between nematode and humans. Citation: Journal of Biological Chemistry 274: 37815-37820 1999 Type: ARTICLE Genes: let-60 Abstract: A yeast two-hybrid screening for Ras-binding proteins in nematode Caenorhabditis elegans has identified a guanine nucleotide exchange factor (GEF) containing a Ras/Rap1A-associating (RA) domain, termed Ce-RA-GEF. Both Ce-RA-GEF and its human counterpart Hs-RA-GEF possessed a PSD-95/DlgA/ZO-1 (PDZ) domain and a Ras exchanger motif (REM) domain in addition to the RA and GEF domains. They also contained a region homologous to a cyclic nucleotide monophosphate-binding domain, which turned out to be incapable of binding cAMP or cGMP. Although the REM and GEF domains are conserved with other GEFs acting on Ras family small GTP-binding proteins, the RA and PDZ domains are unseen in any of them. Hs-RA-GEF exhibited not only a GTP-dependent binding activity to Rap1A at its RA domain but also an activity to stimulate GDP/GTP exchange of Rap1A both in vitro and in, vivo at the segment containing its REM and GEF domains. However, it did not exhibit any binding or GEF activity toward Ras. On the other hand, Ce-RA-GEF associated with and stimulated GDP/GTP exchange of both Ras and Rap1A These results indicate that Ce-RA-GEF and Hs-RA-G;EF define a novel class of Rap1A GEF molecules, which are conserved through evolution. ------------------- Key: 3876 Medline: 20115123 Authors: Branicky R;Benard C;Hekimi S Title: clk-1, mitochondria,and physiological rates. Citation: BioEssays 22: 48-56 2000 Type: REVIEW Genes: clk-1 clk-2 clk-3 gro-1 Abstract: Mutations in the C. elegans maternal-effect gene clk-1 are highly pleiotropic, affecting the duration of diverse developmental and behavioral processes. They result in an average slowing of embryonic and post-embryonic development, adult rhythmic behaviors, reproduction, and aging.((1)) CLK-1 is a highly conserved mitochondrial protein,((2,3)) but even severe clk-1 mutations affect mitochondrial respiration only slightly.((3)) Here, we review the evidence supporting the regulatory role of clk-1 in physiological timing. We also discuss possible models for the action of CLK-1, in particular, one proposing that CLK-1 is involved in the coordination of mitochondrial and ------------------- Key: 3877 Medline: 20094762 Authors: Malik HS;Eickbush TH Title: NeSL-1, an ancient lineage of site-specific non-LTR retrotransposons from Caenorhabditis elegans. Citation: Genetics 154: 193-203 2000 Type: ARTICLE Genes: Abstract: Phylogenetic analyses of non-LTR retrotransposons suggest that all elements can be divided into 11 lineages. The 3 oldest Lineages show target site specificity for unique locations in the genome and encode an endonuclease with an active site similar to certain restriction enzymes. The more "modern" non-LTR lineages possess an apurinic endonuclease-like domain and generally lack site specificity. The genome sequence of Caenorhabditis elegans reveals the presence of a non-LTR retrotransposon that resembles the older elements, in that it contains a single open reading frame with a carboxyl-terminal restriction-like endonuclease domain. Located near the N-terminal end of the ORF is a cysteine protease domain not round ill any other non-LTR element. The N2 strain of C. elegans appears to contain only one full-length and several 5' truncated copies of this element. The elements specifically insert in die Spliced leader-1 genes; hence the element has been named NeSL-1 (Nematode Spliced Leader-1). Phylogenetic analysis confirms that NeSL-1 branches very early in the non-LTR lineage and that it represents a 12th lineage of non-LTR elements. The target specificity of NeSL-1 for the spliced leader exons and the similarity of its structure to that of R2 elements leads to a simple model for its expression and retrotransposition. ------------------- Key: 3878 Medline: Authors: Delattre M;Felix MA Title: Connection of vulval and uterine epithelia in Caenorhabditis elegans. Citation: Biology of the Cell 91: 573-583 1999 Type: REVIEW Genes: cog-1 cog-2 lag-2 let-23 lin-2 lin-3 lin-7 lin-10 lin-12 Abstract: In the Caenorhabditis elegans hermaphrodite, the establishment of the egg-laying system requires the connection of two epithelial tubes: the uterus of the gonad and the vulva in the underlying ectoderm. A specialized uterine cell, the anchor cell (AC), plays a central role in specifying the fates of the uterine and vulval precursor cells via the EGF-Ras-MAP kinase and the Notch/Delta signaling pathways. This central and common inducing source ensures that the two sets of cells are in register and it specifies the cell types that build the T-shaped connection between uterus and vulva. On either side, progeny of the induced cells form lumen structures and undergo stereotyped cell-to-cell fusion, thereby building epithelial tubes. Finally, the anchor cell fuses with a uterine syncytium and thus leaves only a thin cellular process between the lumen of the uterus and the vulva. In the adult, the fertilized eggs exit the lumen of the uterus through the vulva. This relatively simple developmental process serves as a model to study the biology of cells during organogenesis, such as intercellular signaling, cell polarity, invasion of basal laminae and epithelia, cell recognition and cell fusion. The anchor cell is a particularly interesting cell as it coordinates the development of its neighboring cells by using different signaling pathways at different times. ------------------- Key: 3879 Medline: Authors: Zhang YC;Baldwin JG Title: Ultrastructure of the esophagus of Diplenteron sp. (Diplogasterida) to test hypotheses of homology with Rhabditida and Tylenchida. Citation: Journal of Nematology 31: 1-19 1999 Type: ARTICLE Genes: Abstract: The ultrastructure of the isthmus and basal bulb (postcorpus) of Diplenteron sp. (Diplogasterida) was revealed through transmission electron micrographs of serial sections. The postcorpus is glandular and muscular. There are 26 cells in the postcorpus, including 6 marginal (two sets of three), 6 muscle (two sets of three), 3 gland, and 11 nerve cells. Most of the cell bodies, including the nuclei, are in the basal bulb. Unlike Caenorhabditis elegans, Diplenteron sp. has three gland cells. The glands are embedded in a muscular framework in both taxa, but each gland cell is much bigger in Diplenteron sp. than in C. elegans. Each of the anterior set of three marginal cells is located at the apex of the esophageal lumen and overlaps slightly with one of the posterior sets of three marginal cells. All six marginal cells in Diplenteron sp. have homologs in C. elegans. The anterior set of radial muscle cells is V-shaped and is homologous to m5 muscle cells in C. elegans. The posterior set of muscle cells appears to be homologous to m6 muscle cells in C. elegans. Diplenteron sp. does not have muscle cells corresponding to the m7 cells associated with the "grinder" in C. elegans, which is absent in diplogasterids. The single saucer-shaped muscle cell, m8, covering the posterior wall of the basal bulb in C. elegans was not observed in Diplenteron sp. The structure of the esophageal-intestinal junction in Diplenteron sp. is similar to that of C. elegans in being composed of five epithelial cells. Neurons appear to be more abundant in Diplenteron sp. than in C. elegans. Ultrastructure of the esophagus in diplogasterids, rhabditids, cephalobids, and tylenchids will be useful in testing classical and recent competing hypotheses of ------------------- Key: 3880 Medline: Authors: Mendel J Title: G(o) Directly (or indirectly) to G(q). Citation: Neuron 24: 287-288 1999 Type: REVIEW Genes: dgk-1 eat-16 egl-8 egl-30 goa-1 unc-13 Abstract: A fundamental mechanism for regulating synaptic transmission is the control of neurotransmitter secretion by presynaptic neurons. Recent papers, including two in this issue of Neuron, indicate that a hierarchical network of G proteins controls, among other things, release of the neurotransmitter acetylcholine (ACh) at the neuromuscular junction in C. elegans. ------------------- Key: 3881 Medline: 20110504 Authors: Lundblad V Title: A tale of ends. Citation: Nature 401: 149-150 2000 Type: REVIEW Genes: mrt-2 Abstract: During the past few years in the field of chromosome biology, much attention has focused on the very tip of the chromosome - the telomere. This is because functional telomeres are essential for continuous cellular proliferation, an observation that has profound implications for our understanding of ageing and cancer. Studies of telomere biology have been aided by the discovery of numerous genes required for telomere replication in ciliates, yeast, mice and humans. But missing from this genetic pantheon has been the nematode worm Caenorhabditis elegans, one of the premier organisms for gene identification and analysis. Now, however, on page 159 of this issue, Ahmed and Hodgkin describe an elegant screen for C. elegans mutants with mortal germ lines. The first gene to be characterized from this work, mortal germline-2 (mrt-2), plays double duty in the nucleus - it is required not only for telomere replication, but also for monitoring damaged DNA. ------------------- Key: 3882 Medline: 20092735 Authors: Chen PJ;Singal A;Kimble J;Ellis RE Title: A novel member of the Tob family of proteins contros sexual fate in Caenorhabditis elegans germ cells. Citation: Developmental Biology 217: 77-90 2000 Type: ARTICLE Genes: fog-3 spf-1 mnDf111 nDf23 nDf24 nDf25 qDf5 qDf8 qDf9 qDf10 qDf11 qDf12 qDf13 qDf14 qDf15 Abstract: Although many cell fates differ between males and females, probably the most ancient type of sexual dimorphism is the decision of germ cells to develop as sperm or as oocytes. Genetic analyses of Caenorhabditis elegans suggest that fog-3 might directly control this decision. We used transformation rescue to clone the fog-3 gene and show that it produces a single major transcript of approximately 1150 nucleotides. This transcript is predicted to encode a protein of 263 amino acids. One mutation causes a frame shift at the sixth codon and is thus likely to define the null phenotype of fog-3. Although the carboxyl-terminus of FOG-3 is novel, the amino-terminal domain is similar to that of the Tob, BTG1, and BTG2 proteins from vertebrates, which might suppress proliferation or promote differentiation. This domain is essential for FOG-3 activity, since six of eight missense mutations map to this region. Furthermore, this domain of BTG1 and BTG2 interacts with a transcriptional regulatory complex that has been conserved in all eukaryotes. Thus, one possibility is that FOG-3 controls transcription of genes required for germ cells to initiate spermatogenesis rather than oogenesis. This model implies that FOG-3 is required throughout an animal's life for germ cells to initiate spermatogenesis. We used RNA-mediated interference to demonstrate that fog-3 is indeed required continuously, which is consistent with this model. ------------------- Key: 3883 Medline: 10625546 Authors: Inoue T;Thomas JH Title: Targets of TGF-B signaling in Caenorhabditis elegans dauer formation. Citation: Developmental Biology 217: 192-204 2000 Type: ARTICLE Genes: aex-3 daf-1 daf-2 daf-3 daf-4 daf-7 daf-8 daf-11 daf-14 elt-2 myo-2 rol-6 unc-54 eDf18 eDf19 mDf7 sDp3 Abstract: Caenorhabditis elegans dauer formation is controlled by multiple environmental factors. The chemosensory neuron ASI regulates dauer formation by secretion of DAF-7/TGF-beta, but the molecular targets of the DAF-7 ligand are incompletely defined and the cellular targets are unknown. We genetically characterized and cloned a putative transducer of DAF-7 signaling called daf-14 and found that it encodes a Smad protein. DAF-14 Smad has a highly unusual structure completely lacking the N-terminal domain found in all other Smad proteins known to date, daf-14 genetically interacts with daf-8, which encodes another Smad, and the interaction suggests partial functional redundancy between these two Smad proteins. We also studied the cellular targets of DAF-7 signaling by studying the sites of action of daf-14 and daf-4, the putative receptor for DAF-7. daf-14::gfp is expressed in multiple tissues that are remodeled during dauer formation. However, analysis of mosaics generated by free duplication loss and tissue-specific expression constructs indicate cell-nonautonomous function of daf-e arguing against direct DAF-7 signaling to tissues throughout the animal. Instead, these experiments suggest the nervous system as a target of DAF-7 signaling and that the nervous system in turn regulates dauer formation by other tissues. ------------------- Key: 3884 Medline: 20063219 Authors: Costanzo MC;Hogan JD;Cusick ME;Davis BP;Fancher AM;Hodges PE;Kondu P;Lengieza C;Lew-Smith JE;Lingner C;Roberg-Perez KJ;Tillberg M;Brooks JE;Garrels JI Title: The Yeast Proteome Database (YPD) and Caenorhabditis elegans Proteome Database (WormPD): comprehensive resources for the organization and comparison of model organism protein information. Citation: Nucleic Acids Research 28: 73-76 2000 Type: ARTICLE Genes: Abstract: The Yeast Proteome Database (YPD(TM)) has been for several years a resource for organized and accessible information about the proteins of Saccharomyces cerevisiae. We have now extended the YPD format to create a database containing complete proteome information about the model organism Caenorhabditis elegans (WormPD(TM)). YPD and WormPD are designed for use not on ly by their respective research communities but also by the broader scientific community. In both databases, information gleaned from the literature is presented in a consistent, user-friendly Protein Report format: a single Web page presenting all available-knowledge about a particular protein. Each Protein Report begins with a Title Line, a concise description of the function of that protein that is continually updated as curators review new literature, Properties and functions of the protein are presented in tabular form in the upper part of the Report, and free-text annotations organized by topic are presented in the lower part. Each Protein Report ends with a comprehensive reference list whose entries are linked to their MEDLINE abstracts. YPD and WormPD are seamlessly integrated, with extensive links between the species. They are freely accessible to academic users on the WWW at http://www.proteome.com/databases/index.html, and are ------------------- Key: 3885 Medline: 20063224 Authors: Kent WJ;Zahler AM Title: The Intronerator: exploring introns and alternative splicing in Caenorhabditis elegans. Citation: Nucleic Acids Research 28: 91-93 2000 Type: ARTICLE Genes: Abstract: The Intronerator (http://www.cse.ucsc.edu/similar to kent/intronerator/) is a set of web-based tools for exploring RNA splicing and gene structure in Caenorhabditis elegans. It includes a display of cDNA alignments with the genomic sequence, a catalog of alternatively spliced genes and a database of introns, The cDNA alignments include >100 000 ESTs and almost 1000 full-length cDNAs. ESTs from embryos and mixed stage animals as well as full-length cDNAs can be compared in the alignment display with each other and with predicted genes. The alt-splicing catalog includes 844 open reading frames for which there is evidence of alternative splicing of pre-mRNA, The intron database includes 28 478 introns, and can be searched for patterns near the splice junctions. ------------------- Key: 3886 Medline: 20110513 Authors: Ahmed S;Hodgkin J Title: MRT-2 checkpoint protein is required for germline immortality and telomere replication in C. elegans. Citation: Nature 403: 159-164 2000 Type: ARTICLE Genes: hpr-1 mrt-2 mut-2 eT4 eT5 eT6 Abstract: The germ line is an immortal cell lineage that is passed indefinitely from one generation to the next. To identify the genes that are required for germline immortality, we isolated Caenorhabditis elegans mutants with mortal germ lines-worms that can reproduce for several healthy generations but eventually become sterile. One of these mortal germline (mrt) mutants, mrt-2, exhibits progressive telomere shortening and accumulates end-to-end chromosome fusions in later generations, indicating that the MRT-2 protein is required for telomere replication. In addition, the germ line of mrt-2 is hypersensitive to X-rays and to transposon activity. Therefore, mrt-2 has defects in responding both to damaged DNA and to normal double-strand breaks present at telomeres. mrt-2 encodes a homologue of a checkpoint gene that is required to sense DMA damage in yeast. These results indicate that telomeres may be identified as a type of DNA damage and then repaired by the telomere-replication enzyme telomerase. ------------------- Key: 3887 Medline: 10620784 Authors: Hutter H Title: New ways to look at axons in Caenorhabditis elegans. Citation: Microscopy Research & Technique 48: 47-54 2000 Type: ARTICLE Genes: Abstract: In the nematode Caenorhabditis elegans, a well-established model organism for the analysis of nervous system development and function, nerve processes can be labelled in the intact animal with markers based on the "Green Fluorescent Protein" (GFP). The generation of GFP variants with improved brightness and modified emission spectra potentiated the use of this marker for in vivo labelling of subcellular structures. This made it possible to label different groups of neurons and their axons in the same animal with GFP variants of different spectral characteristics. Here I show with double labelling experiments that spatial relationships of axons in small axon bundles can now be resolved at the light microscopic level. In the future this will largely circumvent the need for time-consuming electron microscopic reconstructions to detect local defects in axon outgrowth. Furthermore, I demonstrate that neuronal processes can now be traced even in the head ganglia, an area of the nervous system that was previously-almost inaccessible for analysis due to the compact arrangement of cell bodies and axons. ------------------- Key: 3888 Medline: 20096716 Authors: Lorson MA;Horvitz HR;van den Heuvel S Title: LIN-5 is a novel component of the spindle apparatus required for chromosome segregation and cleavage plane specification in Caenorhabditis elegans. Citation: Journal of Cell Biology 148: 73-86 2000 Type: ARTICLE Genes: lin-5 mnDf100 Abstract: Successful divisions of eukaryotic cells require accurate and coordinated cycles of DNA replication, spindle formation, chromosome segregation, and cytoplasmic cleavage. The Caenorhabditis elegans gene lin-5 is essential for multiple aspects of cell division. Cells in lin-5 null mutants enter mitosis at the normal time and form bipolar spindles, but fail chromosome alignment at the metaphase plate, sister chromatid separation, and cytokinesis. Despite these defects, cells exit from mitosis without delay and progress through subsequent rounds of DNA replication, centrosome duplication, and abortive mitoses. In addition, early embryos that lack lin-5 function show defects in spindle positioning and cleavage plane specification. The lin-5 gene en-codes a novel protein with a central coiled-coil domain. This protein localizes to the spindle apparatus in a cell cycle- and microtubule-dependent manner. The LIN-5 protein is located at the centrosomes throughout mitosis, at the kinetochore microtubules in metaphase cells, and at the spindle during meiosis. Our results show that LIN-5 is a novel component of the spindle apparatus required for chromosome and spindle movements, cytoplasmic cleavage, and correct alternation of the S and RI phases of the cell cycle. ------------------- Key: 3889 Medline: 20080740 Authors: Li C;Kim K;Nelson LS Title: FMRFamide-related neuropeptide gene family in Caenorhabditis elegans. Citation: Brain Research 848: 26-34 1999 Type: ARTICLE Genes: flp-1 flp-2 flp-3 flp-4 flp-5 flp-6 flp-7 flp-8 flp-9 flp-10 flp-11 flp-12 flp-13 flp-14 flp-15 flp-16 flp-17 flp-18 flp-19 flp-20 flp-21 flp-22 goa-1 mof-1 mof-2 mof-3 Abstract: Neuropeptides are used as signaling molecules in the nervous system of most organisms, including mammals. The family of FMRFamide (Phe-Met-Arg-Phe-NH2)-like neuropeptides (FaRPs) all share an RFamide sequence at their C-termini and have been shown to have diverse functions in the central and peripheral nervous systems. In the nematode Caenorhabditis elegans, FMRFamide-like peptides (FaRPs) are expressed in at least 10% of the neurons, including motor, sensory, and interneurons that art: involved in movement, feeding, defecation, and reproduction. Twenty-two genes, designated flp-l through flp-22, encode FaRPs in C. elegans, although there are likely to be additional flp genes to be identified. Each flp gene encodes a different set of FaRPs, yielding a predicted total of 59 distinct FaRPs; a few of the genes may also encode non-FaRPs. Inactivation of some of the flp genes indicates that at least one flp gene has unique functions, while at least two flp genes appear to have overlapping functions with other flp genes. These results suggest that a complex family of FaRPs have varied roles through all stages of development and in adulthood in C. ------------------- Key: 3890 Medline: 10632580 Authors: Fleischhauer R;Davis MW;Dzhura I;Neely A;Avery L;Joho RH Title: Ultrafast inactivation causes inward rectification in a voltage-gated K+ channel from Caenorhabditis elegans. Citation: Journal of Neuroscience 20: 511-520 2000 Type: ARTICLE Genes: exp-2 Abstract: The exp-2 gene in the nematode Caenorhabditis elegans influences the shape and duration of the action potential of pharyngeal muscle cells. Several loss-of-function mutations in exp-2 lead to broadening of the action potential and to a concomitant slowing of the pumping action of the pharynx. In contrast, a gain-of-function mutation leads to narrow action potentials and shallow pumping. We cloned and functionally characterized the exp-2 gene. The exp-2 gene is homologous to genes of the family of voltage-gated K+ channels (Kv type). The Xenopus oocyte-expressed EXP-2 channel, although structurally closely related to Kv-type channels, is functionally distinct and very similar to the human ether-a-gogo-related gene (HERG) K+ channel. In response to depolarization, EXP-2 activates slowly and inactivates very rapidly. On repolarization, recovery from inactivation is also rapid and strongly voltage-dependent. These kinetic properties make the Kv-type EXP-2 channel an inward rectifier that resembles the structurally unrelated HERG channel. Apart from many similarities to HERG, however, the molecular mechanism of fast inactivation appears to be different. Moreover, the single-channel conductance is 5- to 10-fold larger than that of HERG and most Kv-type K+ channels. It appears that the inward rectification mechanism by rapid inactivation has evolved independently in two distinct classes of structurally unrelated, voltage-gated K+ ------------------- Key: 3891 Medline: 10648570 Authors: Ao W;Pilgrim D Title: Caenorhabditis elegans UNC-45 is a component of muscle thick filaments and colocalizes with myosin heavy chain B, but not myosin heavy chain A. Citation: Journal of Cell Biology 148: 375-384 2000 Type: ARTICLE Genes: myo-3 sup-3 unc-45 unc-54 Abstract: In the nematode Caenorhabditis elegans, animals mutant in the gene encoding the protein product of the unc-45 gene (UNC-45) have disorganized muscle thick filaments in body wall muscles. Although UNC-45 contains tetratricopeptide repeats (TPR) as well as limited similarity to fungal proteins: no biochemical role has yet been found. UNC-45 reporters are expressed exclusively in muscle cells, and a functional reporter fusion is localized in the body wall muscles in a pattern identical to thick filament A-bands. UNC-45 colocalizes with myosin heavy chain (MHC) B in wild-type worms as well as in temperature-sensitive (ts) unc-45 mutants, but not in a mutant in which MHC B is absent. Surprisingly, UNC-45 localization is also not seen in MHC B mutants, in which the level of MHC A is increased, resulting in near-normal muscle thick filament structure. Thus, filament assembly can be independent of UNC-45, UNC-45 shows a localization pattern identical to and dependent on MHC B and a function that appears to be MHC B-dependent. We propose that UNC-45 is a peripheral component of muscle thick filaments due to its localization with MHC B. The role of UNC-45 in thick filament assembly seems restricted to a cofactor for assembly or ------------------- Key: 3892 Medline: 20137502 Authors: Bae SC;Lee J Title: cDNA cloning of run, a Caenorhabditis elegans Runt domain encoding gene. Citation: Gene 24: 255-258 2000 Type: ARTICLE Genes: Abstract: PEBP2/CBF is a heterodimeric transcription factor composed of alpha and beta subunits. The essential roles of mammalian PEBP2 alpha genes, PEBP2aA/CBFA1 and PEBP2 alpha B/CBFA2 in osteogenesis and hematopoiesis have been well documented. The PEBP2 alpha proteins contain a 128 amino acid (aa) region which is highly homologous to Drosophila melanogaster runt and lozenge. The evolutionarily conserved region has been named the Runt domain. In this study, we isolated a cDNA encoding the Caenorhabditis elegans homolog of mammalian PEBP2 alpha. The cDNA encodes a 301-aa protein with a highly conserved Runt domain. In addition, a IWRPF five aa motif is present at the C-terminal end. ------------------- Key: 3893 Medline: 20133239 Authors: Ali MY;Siddiqui SS Title: cDNA cloning and expression of a C-terminus motor kinesin-like protein KLP-17, involved in chromosomal movement in Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 267: 643-650 2000 Type: ARTICLE Genes: klp-3 klp-15 klp-16 klp-17 let-21 let-853 let-857 let-858 Abstract: Members of the kinesin protein family transport intracellular cargo to their correct cellular destination. Previously we have characterized the klp-3 gene from Caenorhabditis elegans, which encodes an ortholog of the retrograde C-terminus kinesin motors, such as Drosophila NCD, and yeast KAR3, involved in the chromosomal movement. Here we report the cloning of a full-length klp-17 cDNA in C. elegans, encoding a C-terminus kinesin of 605 amino residues. KLP-17 sequence defines a novel phylogenetic group, distinct from the NCD/KAR3 family. Interestingly, the klp-17 gene transcript is restricted to the nuclear compartment, as deduced by the RNA in situ hybridization in embryos. The klp-17::gfp-expressing transgenic animals do not display any GFP fluorescence signal, but expression of the extra chromosomal arrays cause production of abnormal males, and embryos with morphological defects and lethality in the progeny. Similarly, the klp-17 RNA interference assay results in embryonic death, arrested embryos, and polyploid cells. Thus, KLP-17 represents a new motor protein that mediates chromosome movement, essential for cell divisions during metazoan development. ------------------- Key: 3894 Medline: 20155003 Authors: Mori I Title: Genetics of chemotaxis and thermotaxis in the nematode Caenorhabditis elegans. Citation: Annual Review of Genetics 33: 399-422 1999 Type: REVIEW Genes: adp-1 gpa-2 lin-11 lrn-1 lrn-2 odr-3 odr-4 odr-7 odr-8 odr-10 osm-9 tax-2 tax-4 tax-6 ttx-3 unc-86 Abstract: Molecular genetic analysis of chemotaxis and thermotaxis in Caenorhabditis elegans has revealed the molecular bases of olfaction, taste, and thermosensation, which, in turn, has demonstrated that sensory signaling in C. elegans is very similar to that in vertebrates. A cyclic nucleotide-gated channel (TAX-2/'TAX-4) that is highly homologous to the olfactory and photoreceptor channels in vertebrates is required for taste and thermosensation, in addition to olfaction. A cation channel (OSM-9) that is closely related to a capsaicin receptor channel is required for olfactory adaptation in one olfactory neuron and olfactory sensation in the other ol-factory neuron. A novel Ga protein (ODR-3) is essential for olfactory responses in all olfactory neurons and aversive responses in a polymodal sensory neuron. A G protein-coupled seven-transmembrane receptor (ODR-10) is the first olfactory receptor whose ligand was elucidated. Using chemotaxis and thermotaxis as behavioral paradigms, neural plasticity including learning and memory can be studied genetically in C. elegans. ------------------- Key: 3895 Medline: Authors: Kondo K Title: How to search for a C. elegans homolog of your gene. Citation: Trends in Glycoscience and Glycotechnology 11: 287-295 1999 Type: ARTICLE Genes: Abstract: A nematode Caenorhabditis elegans has been used as a model organism for the study of animal development and neurons. Recently, essentially complete DNA sequence of the genome was determined and published [Science (1998), 282, 2011-2045]. C. elegans has become of interest in studying the genes whose biological functions are unknown to biologists who are not studying C. elegans, because not only classic genetics but also reverse genetics such as gene knockout can be used in C. elegans. In this manuscript I will briefly explain the methods of searching for the C. elegans homologue of your interested genes using the Internet. How to use DDBJ has already been described [TIGG (1999), 11, 119-127]. Here I write about the homepages of Washington University Genome Sequencing Center, The Sanger Center and ACeDB. ------------------- Key: 3896 Medline: Authors: Scharfe C;Zaccaria P;Hoertnagle K;Jaksch M;Klopstock T;Dembowski M;Lill R;Prokisch H;Gerbitz KD;Neupert W;Mewes HW;Meitinger T Title: MITOP, the mitochondrial proteome database: 2000 update. Citation: Nucleic Acids Research 28: 155-158 2000 Type: ARTICLE Genes: Abstract: MITOP (http://www.mips.biochem.mpg.de/proj/medgen/mitop/) is a comprehensive database for genetic and functional information on both nuclear- and mitochondrial-encoded proteins and their genes. The five species files-Saccharomyces cerevisiae, Mus musdulus, Caenorhabditis elegans, Neurospora crassa and Homo sapiens-include annotated data derived from a variety of online resources and the literature. A wide spectrum of search facilities is given in the overlapping sections 'Gene catalogues', 'Protein catalogues', 'Homologies', 'Pathways and metabolism' and 'Human disease catalogue' including extensive references and hyperlinks to other:databases. Central features are the results of various homology searches, which should facilitate the investigations into interspecies relationships. Precomputed PASTA searches using all the MITOP yeast protein entries and a list of the best human EST hits with graphical cluster alignments related to the yeast reference sequence are presented. The orthologue tables with:cross-listings to all the protein entries for each species in MITOP have been expanded by adding the genomes of Rickettsia prowazeckii and Escherichia coli. To find new mitochondrial proteins the complete yeast genome has been analyzed using the MITOPROT program which identifies mitochondrial targeting sequences. The 'Human disease catalogue' contains tables with a total of 110 human diseases related to mitochondrial protein abnormalities, sorted by clinical criteria and age of onset, MITOP should contribute to the systematic genetic characterization of the mitochondrial proteome in relation ------------------- Key: 3897 Medline: Authors: Sanchez R;Pieper U;Mirkovic N;de Bakker PIW;Wittenstein E;Sali A Title: ModBase, a database of annotated comparative protein structure models. Citation: Nucleic Acids Research 28: 250-253 2000 Type: ARTICLE Genes: Abstract: MODBASE is a queryable database of annotated comparative protein structure models. The models are derived by MODPIPE, an automated modeling pipeline relying on the programs PSI-BLAST and MODELLER. The database currently contains 3D models for substantial portions of approximately 17 000 proteins from 10 complete genomes, including those of Caenorhabditis elegans, Saccharomyces cerevisiae and Escherichia coli, as well as all the available sequences from Arabidopsis thaliana and Homo sapiens. The database also includes fold assignments and alignments on which the models were based. In addition, special care is taken to assess the quality of the models. ModBase is accessible through a web interface at http://guitar.rockefeller.edu/modbase/. ------------------- Key: 3898 Medline: 20173822 Authors: Kurz CL;Ewbank JJ Title: Caenorhabditis elegans for the study of host-pathogen interactions. Citation: Trends in Microbiology 8: 142-144 2000 Type: ARTICLE Genes: Abstract: The nematode worm Caenorhabditis elegans, for which the complete genome sequence is available, has several other advantages as an experimental system, and has already been widely used as a model for the study of vertebrate biology. Recent investigations have revealed that C. elegans could also be an extremely useful model system in the study of bacterial pathogenesis and have reinforced the notion that common virulence and host defence mechanisms exist. ------------------- Key: 3899 Medline: 10935465 Authors: Chinnaiyan AM Title: The apoptosome: heart and soul of the cell death machine. Citation: Neoplasia 1: 5-15 1999 Type: REVIEW Genes: ced-3 ced-4 ced-9 egl-1 Abstract: Apoptosis is a fundamental biologic process by which metazoan cells orchestrate their own self-demise. Genetic analyses of the nematode C elegans identified three core components of the suicide apparatus which include CED-3, CED-4, and CED-9. An analogous set of core constituents exists in mammalian cells and includes caspase-9, Apaf-1, and bcl-2/xL, respectively. CED-3 and CED-4, along with their mammalian counterparts, function to kill cells, whereas CED-9 and its mammalian equivalents protect cells from death. These central components biochemically intermingle in a ternary complex recently dubbed the "apoptosome." The C elegans protein EGL-1 and its mammalian counterparts, pro-apoptotic members of the bcl-2 family, induce cell death by disrupting apoptosome interactions. Thus, EGL-1 may represent a primordial signal integrator for the apoptosome. Various biochemical processes including oligomerization, adenosine triphosphate ATP/dATP binding, and cytochrome c interaction play a role in regulating the ternary death complex. Recent studies suggest that cell death receptors, such as CD95, may amplify their suicide signal by activating the apoptosome. These mutual associations by core components of the suicide apparatus provide a molecular framework in which diverse death signals likely interface. Understanding the apoptosome and its cellular connections will facilitate the design of novel therapeutic strategies for cancer and other disease states in which apoptosis plays a pivotal role. ------------------- Key: 3900 Medline: Authors: Hengartner MO Title: Programmed cell death in the nematode C. elegans. Citation: Recent Progress in Hormone Research 54: 213-222 1999 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-9 ced-10 ced-12 ces-1 ces-2 egl-1 nuc-1 Abstract: Programmed cell death is a common feature during animal development. In the nematode C. elegans, more than 12 genes have been identified that function in the apoptotic killing and elimination of 131 of the 1090 cells that are generated during hermaphrodite development. These genes divide the process of programmed cell death into three distinct steps: execution of the death sentence; engulfment of dying cells; and degradation of dead, engulfed cells. Biochemical characterization of the genes in this pathway has led to the identification of an apoptotic machinery that mediates apoptotic death in this species. The proximal cause of apoptosis in C. elegans is the activation of the caspase homolog CED-3 from the inactive zymogen (proCED-3) into the mature protease. This activation is mediated by the Apaf-1 homolog CED-4. In cells that should survive, CED-3 and CED-4 pro-apoptotic activity is antagonized by the Bcl-2 family member CED-9. CED-9 has been proposed to prevent death by sequestering CED-4 and proCED-3 in an inactive ternary complex, the apoptosome. In cells fated to die, CED-9 is, in turn, inactivated by the pro-apoptotic BH3 domain-containing protein EGL-1, likely through a direct protein-protein interaction. The structural and functional conservation of cell death genes between nematodes and mammals strongly suggests that the apoptotic program is ancient in origin and that all metazoans share a common mechanism of apoptotic cell killing. ------------------- Key: 3901 Medline: Authors: Steele RE;Stover NA;Sakaguchi M Title: Appearance and disappearance of Syk family protein-tyrosine kinase genes during metazoan evolution. Citation: Gene 239: 91-97 1999 Type: ARTICLE Genes: Abstract: Syk family protein-tyrosine kinases are essential components of immunoreceptor signaling in mammalian lymphocytes. The absence of Syk genes from the Caenorhabiditis elegans genome suggests that this kinase family is of recent evolutionary origin. Surprisingly, we have found that Hydra vulgaris, a member of the early diverging animal phylum Cnidaria, contains a gene encoding a Syk kinase. Phylogenetic analysis indicates that a single Syk family gene was present in animals prior to the gene duplication that gave rise to Syk and ZAP-70, the two mammalian Syk family genes. C. elegans also lacks a Shark protein-tyrosine kinase gene, which we show is a member of a sister group to the Syk family. We conclude that both Syk and Shark genes were lost from the genome of an ancestor of C. elegans. This natural gene knockout result indicates that neither Syk nor Shark kinases are essential for processes held in common between the nematode and other metazoans. The Hydra Syk gene is expressed in epithelial cells, a site consistent with a role for Hydra Syk in ------------------- Key: 3902 Medline: 10655066 Authors: Tavernarakis N;Wang SL;Dorovkov M;Ryazanov A;Driscoll M Title: Heritable and inducible genetic interference by double-stranded DNA encoded by transgenes. Citation: Nature Genetics 24: 180-183 2000 Type: ARTICLE Genes: efk-1 mec-4 myo-2 unc-8 unc-119 Abstract: Double-stranded RNA interference (RNAi) is an effective method for disrupting expression of specific genes in Caenorhabditis elegans and other organisms(1-5). Applications of this reverse-genetics tool, however, am somewhat restricted in nematodes because introduced dsRNA is not stably inherited(5). Another difficulty is that RNAi disruption of late-acting genes has been generally less consistent than that of embryonically expressed genes, perhaps because the concentration of dsRNA becomes lower as cellular division proceeds or as developmental time advances(1). In particular, some neuronally expressed genes appear refractory to dsRNA-mediated interference. We sought to extend the applicability of RNAi by in vivo expression of heritable inverted-repeat (IR) genes. We assayed the efficacy of in vivo-driven RNAi in three situations for which heritable, inducible RNAi would be advantageous: (i) production of large numbers of animals deficient for gene activities required for viability or reproduction; (ii) generation of large populations of phenocopy mutants for biochemical analysis; and (iii) effective gene inactivation in the nervous system. We report that heritable IR genes confer potent and specific gene inactivation for each of these applications. We suggest that a similar strategy might be used to test for dsRNA interference effects in higher organisms in which it is feasible to construct transgenic animals, but impossible to directly or transiently introduce high concentrations of dsRNA. ------------------- Key: 3903 Medline: 20140136 Authors: Sze JY;Victor M;Loer C;Shi Y;Ruvkun G Title: Food and metabolic signalling defects in a Caenorhabditis elegans serotonin-synthesis mutant. Citation: Nature 403: 560-564 2000 Type: ARTICLE Genes: daf-3 daf-7 daf-16 egl-1 tph-1 mgDf50 mgDf90 Abstract: The functions of serotonin have been assigned through serotonin-receptor-specific drugs and mutants(1,2); however because a constellation of receptors remains when a single receptor subtype is inhibited, the coordinate responses to modulation of serotonin levels may be missed. Here we report the analysis of behavioural and neuroendocrine defects caused by a complete lack of serotonin signalling. Analysis of the C. elegans genome sequence showed that there is a single tryptophan hydroxylase gene (tph-1)-the key enzyme for serotonin biosynthesis. Animals bearing a tph-1 deletion mutation do not synthesize serotonin but are fully viable. The tph-1 mutant shows abnormalities in behaviour and metabolism that are normally coupled with the sensation and ingestion of food: rates of feeding and egg laying are decreased; large amounts of fat are stored; reproductive lifespan is increased; and some animals arrest at the metabolically inactive dauer stage. This metabolic dysregulation is, in part, due to downregulation of tranforming growth factor-beta and insulin-like neuroendocrine signals. The action of the C. elegans serotonergic system in metabolic control is similar to mammalian serotonergic input to metabolism and obesity. ------------------- Key: 3904 Medline: 20136864 Authors: Kudo M;Chen T;Nakabayashi K;Hsu SY;Hsueh AJW Title: The nematode leucine-rich repeat-containing, G protein-coupled receptor (LGR) protein homologous to vertebrate gonadotropin and thyrotropin receptors is constitutively activated in mammalian cells. Citation: Molecular Endocrinology 14: 272-284 2000 Type: ARTICLE Genes: Abstract: The receptors for LH, FSH, and TSH belong to the large G protein-coupled, seven-transmembrane (TM) protein family and are unique in having a large N-terminal extracellular (ecto-) domain containing leucine-rich repeats important for interactions with the large glycoprotein hormone ligands. Recent studies indicated the evolution of an expanding family of homologous leucine-rich repeat-containing, G protein-coupled receptors (LGRs), including the three known glycoprotein hormone receptors; mammalian LGR4 and LGR5; and LGRs in sea anemone, fly, and snail. We isolated nematode LGR cDNA and characterized its gene from the Caenorhabditis elegans genome. This receptor cDNA encodes 929 amino acids consisting of a signal peptide for membrane insertion, an ectodomain with nine leucine-rich repeats, a seven-TM region, and a long C-terminal tail. The nematode LGR has five potential N-linked glycosylation sites in its ectodomain and multiple consensus phosphorylation sites for protein kinase A and C in the cytoplasmic loop and C tail. The nematode receptor gene has 13 exons; its TM region and C tail, unlike mammalian glycoprotein hormone receptors, are encoded by multiple exons. Sequence alignments showed that the TM region of the nematode receptor has 30% identity and 50% similarity to the same region in mammalian glycoprotein hormone receptors. Although human 293T cells expressing the nematode LGR protein do not respond to human glycoprotein hormones, these cells exhibited major increases in basal cAMP production in the absence of ligand stimulation, reaching levels com-parable to those in cells expressing a constitutively activated mutant human LH receptor found in patients with familial male-limited precocious puberty. Analysis of cAMP production mediated by chimeric receptors further indicated that the ectodomain and TM region of the nematode LGR and human LH receptor are interchangeable and the TM region of the nematode LGR is responsible for constitutive receptor activation. Thus, the identification and characterization of the nematode receptor provides the basis for understanding the evolutionary relationship of diverse LGRs and for future analysis of mechanisms underlying the activation of glycoprotein hormone receptors ------------------- Key: 3905 Medline: 20127700 Authors: Otto E;Kispert A;Schatzle S;Lescher B;Rensing C;Hildebrandt F Title: Nephrocystin: gene expression and sequence conservation between human, mouse, and Caenorhabditis elegans. Citation: Journal of the American Society of Nephrology 11: 270-282 2000 Type: ARTICLE Genes: Abstract: Juvenile nephronophthisis, an autosomal recessive cystic kidney disease, is the primary genetic cause for chronic renal failure in children. The gene (NPHP1) for nephronophthisis type 1 has recently been identified. Its gene product, nephrocystin, is a novel protein of unknown function, which contains a src-homology 3 domain. To study tissue expression and analyze amino acid sequence conservation of nephrocystin, the full-length murine Nphp1 cDNA sequence was obtained and Northern and in situ hybridization analyses were performed for extensive expression studies. The results demonstrate widespread but relatively weak NPHP1 expression in the human adult. In the adult mouse there is strong expression in testis. This expression occurs specifically in cell stages of the first meiotic division and thereafter. bl situ hybridization to whole mouse embryos demonstrated widespread and uniform expression at all developmental stages. Amino acid sequence conservation studies in human, mouse, and Caenorhabditis elegans show that in nephrocystin the src-homology 3 domain is embedded in a novel context of other putative domains of protein-protein interaction, such as coiled-coil and E-rich domains. It is concluded that for multiple putative protein-protein interaction domains of nephrocystin, sequence conservation dates back at least to Caenorhabditis elegans. The previously described discrepancy between widespread tissue expression and the restriction of symptoms to the kidney has now been confirmed by an in-depth expression study. ------------------- Key: 3906 Medline: 20112779 Authors: Toyoda H;Kinoshita-Toyoda A;Selleck SB Title: Structural analysis of glycosaminoglycans in Drosophila and Caenorhabditis elegans and demonstration that tout-velu, a Drosophila gene related to EXT tumor suppressors, affect heparan sulfate in vivo. Citation: Journal of Biological Chemistry 275: 2269-2275 2000 Type: ARTICLE Genes: Abstract: We have devised a sensitive method for the isolation and structural analysis of glycosaminoglycans from two genetically tractable model organisms, the fruit fly, Drosophila melanogaster, and the nematode, Caenorhabditis elegans. We detected chondroitin/chondroitin sulfate- and heparan sulfate-derived disaccharides in both organisms. Chondroitinase digestion of glycosaminoglycans from adult Drosophila produced both nonsulfated and 4-O-sulfated unsaturated disaccharides, whereas only unsulfated forms were detected in C. elegans. Heparin lyases released disaccharides bearing N-, 2-O-, and 6-O-sulfated species, including mono-, di-, and trisulfated forms, We observed tissue- and stage-specific differences in both chondroitin sulfate and heparan sulfate composition in Drosophila. We have also applied these methods toward the analysis of tout-velu, an EXT-related gene in Drosophila that controls the tissue distribution of the growth factor Hedgehog. The proteins encoded by the vertebrate tumor suppressor genes EXT1 and 2, show heparan sulfate co-polymerase activity, and it has been proposed that tout-velu affects Hedgehog activity via its role in heparan sulfate biosynthesis. Analysis of total glycosaminoglycans from tout-velu mutant larvae show marked reductions in heparan sulfate but not chondroitin sulfate, consistent with its proposed function as a heparan sulfate co-polymerase. ------------------- Key: 3907 Medline: 20157043 Authors: Shibata Y;Fujii T;Dent JA;Fujisawa H;Takagi S Title: EAT-20, a novel transmembrane protein with EGF motifs, is required for efficient feeding in Caenorhabditis elegans. Citation: Genetics 154: 635-646 2000 Type: ARTICLE Genes: eat-4 eat-6 eat-8 eat-10 eat-11 eat-13 eat-17 eat-20 let-15 let-18 let-38 let-40 mnDf13 mnDf43 mnDp1 Abstract: The pharynx of Caenorhabditis elegans is a neuromuscular organ responsible for feeding, concentrating food by its pumping movement. A class of mutants, the eat mutants, are defective in this behavior. We have identified a novel eat gene, eat-20, encoding a unique transmembrane protein with three EGF motifs. Staining with a specific polyclonal antibody reveals that EAT-20 is expressed predominantly in the pharyngeal muscles and a subset of neurons. Some hypodermal cells also express EAT-20, eat-20 mutant animals are starved, have smaller brood sizes, and have prolonged egg-laying periods. The starvation apparently results from pharyngeal pumping defects, including a reduced pumping rate and "slippery pumping," in which the contents of the pharynx sometimes move rostrally. However, electrical activity of eat-20 mutants appears normal by ------------------- Key: 3908 Medline: 10653620 Authors: Junkersdorf B;Bauer H;Gutzeit HO Title: Electromagnetic fields enhance the stress response at elevated temperatures in the nematode Caenorhabditis elegans. Citation: Bioelectromagnetics 21: 100-106 2000 Type: ARTICLE Genes: Abstract: We have studied the effect of extremely law frequency electromagnetic fields (ELF/EMF) in the presence of a second stressor (mild heat shock) on the expression of a lacZ reporter gene under the control of hsp16 or hsp70 promoters in two transgenic strains of C. elegans. The expression of the reporter gene was studied by scoring animals with induced beta-galactosidase activity after staining in toto or by biochemical quantitation of the enzyme activity, respectively. In our experimental setup we were able to expose the animals to 50 Hz magnetic flux density of 0-150 mu T and at the same time control temperature with high precision (+/-0.1 degrees C). Experimental conditions were defined for which EMF strongly enhances the expression of the reporter gene. ------------------- Key: 3909 Medline: 20144366 Authors: Gogonea CB;Gogonea V;Ali YM;Merz KM;Siddiqui SS Title: Computational prediction of the three-dimensional structures for the Caenorhabditis elegans tubulin family. Citation: Journal of Molecular Graphics 17: 90-100 1999 Type: ARTICLE Genes: ben-1 tba-1 tba-2 tba-3 tba-4 tba-5 tba-6 tba-7 tba-8 tba-9 tbb-1 tbb-2 tbb-3 tbb-4 tbb-5 tbb-6 tbg-1 Abstract: In this article we characterize, from a structural point of view, all 16 members of the tubulin gene family of Caenorhabditis elegans (9 alpha-tubulins, 6 beta-tubulins, and 1 gamma-tubulin). We obtained their tertiary structures by computationally modifying the X-ray crystal structure of the pig brain alpha/beta-tubulin dimer published by Nogales et al. [Nature (London) 1998;391:199-203]. Our computational protocol involves changing the amino acids (with MIDAS; Jarvis et al., UCSF MIDAS. University of California, San Francisco, 1986) in the 3D structure of pig brain alpha/beta-tubulin dimer followed by geometry optimization with the AMBER force field (Perlman et al., AMBER 4. University of California, San Francisco, 1990). We subsequently analyze and compare the resulting structures in terms of the differences in their secondary and tertiary structures. In addition, we compare the pattern of hydrogen bonds and hydrophobic contacts in the guanosine triphosphate (GTP)-binding site for all members of the tubulin family. Our computational results show that, except for gamma-tubulin, all members of the C. elegans tubulin family have similar secondary and 3D structures and that the change in the pattern of hydrogen bonds in the GTP-binding site may be used to assess the relative stability of different alpha/beta-tubulin dimers formed by monomers of the tubulin family. ------------------- Key: 3910 Medline: 20134712 Authors: Hutter H;Vogel BE;Plenefisch JD;Norris CR;Proenca RB;Spieth J;Guo C;Mastwal S;Zhu X;Scheel J;Hedgecock EM Title: Conservation and novelty in the evolution of cell adhesion and extracellular matrix. Citation: Science 287: 989-994 2000 Type: REVIEW Genes: emb-9 epi-1 him-5 ina-1 inb-1 lam-1 let-2 lov-1 mec-5 mec-9 nid-1 pat-2 pat-3 ost-1 unc-52 Abstract: New proteins and modules have been invented throughout evolution. Gene "birth dates" in Caenorhabditis elegans range from the origins of cellular life through adaptation to a soil habitat. Possibly half are "metazoan" genes, having arisen sometime between the yeast-metazoan and nematode-chordate separations. These include basement membrane and cel adhesion molecules implicated in tissue organization. by contrast epithelial surfaces facing the environment have specialized components invented within the nematode lineage. Moreover, interstitial matrices were likely elaborated within the vertebrate lineage. A strategy for concerted evolution of new gene families, as well as conservation of adaptive genes, may underlie the differences between heterochromatin and euchromatin. ------------------- Key: 3911 Medline: 10693745 Authors: Plenefisch J;Xiao H;Mei B;Geng J;Komuniecki PR;Komuniecki R Title: Secretion of a novel class of iFABPs in nematodes: coordinate use of the Ascaris/Caenorhabditis model systems. Citation: Molecular & Biochemical Parasitology 105: 223-236 2000 Type: ARTICLE Genes: lbp-1 lbp-2 lbp-3 lbp-4 lbp-5 lbp-6 lbp-7 lbp-8 Abstract: A novel fatty acid binding protein, As-p18 is secreted into both the perivitelline and perienteric fluids of the parasitic nematode, Ascaris suum, and at least eight potential homologues of As-p18 have been identified in the Caenorhabditis elegans genome. The products of the three most closely related homologues are fatty acid binding proteins (LBP-1, LBP-2 and LBP-3) which contain putative secretory signals. Phylogenetic analysis revealed that these secreted fatty acid binding proteins comprise a distinct gene class within the fatty acid binding protein family and are possibly unique to nematodes. To examine the potential sites of As-p18 secretion, the expression of the putative promoters of the C. elegans homologues was examined with GFP reporter constructs. The developmental expression of lbp-1 was identical to that of As-p18 and consistent with the secretion of LBP-1 from the hypodermis to the perivitelline fluid. The expression patterns of lbp-2 and lbp-3 were consistent with the secretion of LBP-2 and LBP-3 from muscle into the perienteric fluid later in development. These studies demonstrate that at least some perivitelline fluid proteins appear to be secreted from the hypodermis prior to the formation of the cuticle and, perhaps more importantly, that this coordinate C. elegans/A. storm approach may be potentially useful for examining a number of key physiological processes in ------------------- Key: 3912 Medline: 20170552 Authors: Yang Y;Wilson DL Title: Isolating aging mutants: a novel method yields three strains of the nematode Caenorhabditis elegans with extended life spans. Citation: Mechanisms of Ageing & Development 113: 101-116 2000 Type: ARTICLE Genes: Abstract: We designed a novel procedure for the isolation of mutant strains with significantly increased life spans in the nematode Caenorhabditis elegans. This procedure involves using heat-shock to screen a large number of animals and isolate a few which are more resistant to heat-shock stress. From the heat-shock-resistant animals, three mutant strains, HG25, HG96, and HG246, all exhibiting increased life span, were isolated. One mutant strain (HG246) develops more slowly than the wild-type strain, N2. Two mutant strains, HG96 and HG246, exhibit lower fertility than the wild-type. Each of the three mutant strains has a normal appearance. Their locomotive behavior also appears normal; only HG246 shows slightly slower movement. Their feedings behavior appears normal, and the males of HG25 and HG96 show normal mating behavior. However, the males of HG246, either are defective in their mating ability or their sperm are defective. The results indicate that heat-shock can be used as a means to facilitate the isolation of mutants which have longer life expectancy. ------------------- Key: 3913 Medline: 20127925 Authors: Angelo RG;Rubin CS Title: Characterization of structural features that mediate the tethering of Caenorhabditis elegans protein kinase A to a novel A kinase anchor protein - Insights into the anchoring of PKAI isoforms. Citation: Journal of Biological Chemistry 275: 4351-4362 2000 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans protein kinase A (PKAI(CE)) is tethered to organelles in vivo. A unique A kinase anchor protein (AKAP(CE)) avidly binds the RI-like regulatory subunits (R-CE) of PKAI(CE) and stringently discriminates against RII alpha and RII beta subunits, the preferred ligands for classical AKAPs, We elucidated structural features that stabilize AKAP(CE).R-CE complexes and confer atypical R isoform specificity on the anchor protein. Three large aliphatic amino acids (Leu(236), Ile(248), and Leu(252)) in the tethering domain of AKAP(CE) (residues 236-255) are crucial for ligation of R-CE. Their side chains apparently generate a precisely configured hydrophobic binding pocket that accommodates an apolar surface on RCE dimers, Basic residues (His(254)-Arg(255)-Lys(256)) at the C terminus of the tethering site set an upper limit on affinity for R-CE. A central dipeptide (phe(243)-Ser(244)) contributes critical and distinctive properties of the tethering site. Ser(244) is essential for selective binding of R-CE and exclusion of RII isoforms, The aromatic hydrophobic character of phe(243) ensures maximal R-CE binding activity, thereby supporting a "gatekeeper" function of Ser(244). Substitution of phe(243)-Ser(244) With Leu-Val generated an RII-specific AKAP. R-CE and RII subunits contain similar dimerization domains. AKAP-binding domains of R-CE (residues 23-47) and RII differ markedly in size, amino acid sequence, and docking specificity. Four hydrophobic residues (Cys(23), Val(27), Ile(32), and Cys(44)) in R-CE are crucial for avid binding with AKAP(CE), whereas side chains from Leu(20), Leu(35), Val(36), Ile(40), and Ile(41) have little impact on complex formation. Tyr(26) is embedded in the docking domain, but its aromatic ring is required for R-CE-R-CE dimerization. Residues 236-255 in AKAP(CE) also constitute a binding site for mammalian RI alpha. RI alpha (PKAI alpha) is tightly sequestered by AKAP(CE) in vitro (K-D = similar to 10 10 nM) and in the environment of intact cells. The tethering domain of AKAP(CE) provides a molecular module for manipulating intracellular localization of RI and elucidating functions ------------------- Key: 3914 Medline: 20133646 Authors: Liu QA;Hengartner MO Title: The molecular mechanism of programmed cell death in C. elegans. Citation: Annals of the New York Academy of Sciences 887: 92-104 1999 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-9 ced-10 ced-12 ces-1 ces-2 egl-1 Abstract: Programmed cell death or apoptosis plays a fundamental role during animal development, metamorphosis, and tissue homeostasis. It is a genetically controlled physiological process that comprises two distinct and sequential processes: the death of cells, and their subsequent removal by engulfing cells. In the nematode C. elegans, genetic studies led to the discovery of 15 genes that function in programmed cell death (FIG. 1). These 15 genes have been divided into four groups based on the order of their activity during the process of programmed cell death: (1) those involved in the decision making (ces-1 and ces-2); (2) in the process of execution (ced-3, ced-4, ced-9 and egl-1); (3) in the engulfment of dying cells by engulfing cells (ced-1, ced-2, ced-5, ced-6, ced-7, ced-10, ced-12); and (4) those in the degradation of cell corpses within engulfing cells (nuc-1). In the last five years, several genes in the genetic pathway of programmed cell death have been shown to be conserved across a wide range of species; all genes involved in the step of execution in C. elegans have their corresponding mammalian homologs (FIG. 2). Furthermore, emerging evidence from molecular studies of engulfment genes in several species suggests that the signaling process from apoptotic cells to engulfing cells and the subsequent engulfment process might be also conserved across species (TABLE 1). ------------------- Key: 3915 Medline: 20140861 Authors: Li C;Nelson LS;Kim K;Nathoo A;Hart AC Title: Neuropeptide gene families in the nematode Caenorhabditis elegans. Citation: Annals of the New York Academy of Sciences 897: 239-252 Type: REVIEW Genes: bor-1 flp-1 flp-2 flp-3 flp-4 flp-5 flp-6 flp-7 flp-8 flp-9 flp-10 flp-11 flp-12 flp-13 flp-14 flp-15 flp-16 flp-17 flp-18 flp-19 flp-20 nlp-1 nlp-2 nlp-3 nlp-4 nlp-5 nlp-6 nlp-7 nlp-8 nlp-9 nlp-10 nlp-11 nlp-12 nlp-13 nlp-14 nlp-15 nlp-16 nlp-17 nlp-18 nlp-19 nlp-20 nlp-21 Abstract: Neuropeptides have diverse roles in the function and development of the nervous system. With the completion of the sequencing of the C. elegans genome, rapid identification of nematode neuropeptide genes is possible. To date, 41 C. elegans neuropeptide genes have been identified. Of these genes, 20 genes, named flp (FMRFamide-like peptide) genes, encode FMRFamide-related proteis (FaRPs). Deletion of one of the flp genes, flp-1, results in several behavioral defects, suggesting that at least one flp gene is not functionally redundant with other flp genes. Twenty-one genes, named neuropeptide-like protein (nlp) genes, encode peptides distinct from the FaRP family. The predicted nlp-1 and nlp-2 neuropeptides have modest similarity to buccalin and myomodulin, respectively. Cellular expression patterns and genetic analysis of flp and nlp genes suggest that neuropeptides in nematodes also have widespread and varied roles in nervous system ------------------- Key: 3916 Medline: 21150903 Authors: Baird SE;Yen WC Title: Reproductive isolation in Caenorhabditis elegans: terminal phenotypes of hybrid embryos. Citation: Evolution & Development 2: 9-15 2000 Type: ARTICLE Genes: emb-5 emb-13 emb-16 emb-23 emb-31 fog-2 gad-1 Abstract: Several interspecific combinations of the "elegans" group of Caenorhabditis species are cross-fertile. Most F1 hybrids from these crosses arrest during embryogenesis. Developmental defects observed in hybrid embryos include defects in gastrulation initiation, defects in embryonic compaction, and defects in embryonic elongation. These reproductive barriers have arisen multiple times in the evolution of Caenorhabditis. ------------------- Key: 3917 Medline: 20119491 Authors: Hobert O;Westphal H Title: Functions of LIM-homeobox genes. Citation: Trends in Genetics 16: 75-83 2000 Type: REVIEW Genes: ceh-14 lim-4 lim-6 lim-7 lin-11 mec-3 mec-4 mec-7 ttx-3 unc-86 Abstract: Homeobox genes play fundamental roles in development. They can be subdivided into several subfamilies, one of which is the LIM-homeobox subfamily. The primary structure of LIM-homeobox genes has been remarkably conserved through evolution. Have their functions similarly been conserved? A host of new data has been derived from mutational analysis in diverse organisms, such as nematodes, flies and vertebrates. These studies have revealed a prominent involvement of LIM-homeodomain proteins in tissue patterning and differentiation, and their function in neural patterning is evident in all organisms studied to date. Here, we summarize the recent findings on LIM-homeobox gene function, compare the function of these genes from different organisms and describe specific ------------------- Key: 3918 Medline: 20122687 Authors: Bosher JM;Labouesse M Title: RNA interference: genetic wand and genetic watchdog. Citation: Nature Cell Biology 2: E31-E36 2000 Type: REVIEW Genes: mes-2 mes-6 mut-2 mut-6 mut-7 qde-1 rde-1 rde-2 rde-3 rde-4 Abstract: In many species, introduction of double-stranded RNA (dsRNA) induces potent and specific gene silencing, a phenomenon called RNA interference or RNAi. The apparently widespread nature of RNAi in eukaryotes, ranging from trypanosome to mouse, has sparked great interest from both applied and fundamental standpoints. Here we review the technical improvements being made to increase the experimental potential of this technique. We also discuss recent advances in uncovering the proteins that act during the RNAi process, discoveries that have revealed enticing links between transposition, transgene silencing and RNAi. ------------------- Key: 3919 Medline: Authors: Teichmann SA;Chothia C;Gerstein M Title: Advances in structural genomics. Citation: Current Opinion in Structural Biology 9: 390-399 1999 Type: REVIEW Genes: Abstract: New computational techniques have allowed protein folds to be assigned to all or parts of between a quarter (Caenorhabditis elegans) and a half (Mycoplasma genitalium) of the individual protein sequences in different genomes. These assignments give a new perspective on domain structures, gene duplications, protein families and protein folds in genome sequences. ------------------- Key: 3920 Medline: Authors: Copley RR;Schultz J;Ponting CP;Bork P Title: Protein families in multicellular organisms. Citation: Current Opinion in Structural Biology 9: 408-415 1999 Type: REVIEW Genes: Abstract: The complete sequence of the nematode worm Caenorhabditis elegans contains the genetic machinery that is required to undertake the core biological processes of single cells. However, the genome also encodes proteins that are associated with multicellularity, as well as others that are lineage-specific expansions of phylogenetically widespread families and yet more that are absent in non-nematodes. Ongoing analysis is beginning to illuminate the similarities and differences among human proteins and proteins that are encoded by the genomes of the multicellular worm and the unicellular yeast, and will be essential in determining the reliability of transferring experimental data among phylogenetically distant species. ------------------- Key: 3921 Medline: 20138498 Authors: Robertson HM Title: The large srh family of chemoreceptor genes in Caenorhabditis nematodes reveals processes of genome evolution involving large duplications and deletions and intron gains and losses. Citation: Genome Research 10: 192-203 2000 Type: ARTICLE Genes: srh-1 srh-9 srh-16 srh-39 srh-45 srh-51 srh-75 srh-129 srh-130 srh-163 srh-184 srh-268 srh-275 Abstract: The srh family of chemoreceptors in the nematode Caenorhabditis elegans is very large, containing 214 genes and 90 pseudogenes. It is related to the str, stl, and srd families of seven-transmembrane or serpentine receptors. Like these three families, most srh genes are concentrated on chromosome V, and mapping of their chromosomal locations on a phylogenetic tl-ee reveals 27 different movements of genes to other chromosomes. Mapping of intron gains and losses onto the phylogenetic tree reveals that the last common ancestral gene of the family had five introns, which are inferred to have been lost 70 times independently during evolution of the Family. In addition, seven intron gains are revealed, three of which are Fairly recent. Comparisons with 20 family members in the C. briggsae genome confirms these patterns, including two intron losses in C, briggsae since the species split. There are 14 clear C. elegans orthologs for these 20 genes, whose average amino acid divergence of 68% allows estimation of 85 gene duplications in the C. elegans lineage since the species split. The absence of six orthologs in C. elegans also indicates that gene loss occurs; consideration of all deletions and terminal truncations of srh pseudogenes reveals that large deletions are common. Together these observations provide insight into the evolutionary dynamics ------------------- Key: 3922 Medline: 20156370 Authors: Aamodt E;Shen L;Marra M;Schein J;Rose B;McDermott JB Title: Conservation of sequence and function of the pag-3 genes from C. elegans and C. briggsae. Citation: Gene 243: 67-74 2000 Type: ARTICLE Genes: pag-3 Abstract: The Caenorhabditis briggsae homologue of the Caenorhabditis elegans pag-3 gene was cloned and sequenced. When transformed into a C. elegans pag-3 mutant, the C. briggsae pag-3 gene rescued the pag-3 reverse kinker and lethargic phenotypes. The C. elegans pag-3 gene fused to lacZ was expressed in the same pattern in C. elegans and C. briggsae. Unlike many gene homologues compared between C. elegans and C. briggsae, extensive sequence conservation was found in the non-coding regions upstream of the pag-3 exons, in several of the introns and in the downstream non-coding region. Furthermore, the splice acceptor and splice donor sites were conserved, and the size of the introns and exons was surprisingly similar. The predicted protein sequence of C. briggsae PAG-3 was 85% identical to the protein sequence of C. elegans PAG-3. Because so much of the non-coding region of pag-3 was conserved, the control of pag-3 may be quite complex, involving the binding of many trans-acting factors. These results suggest the evolutionary conservation of the pag-3 gene sequence, ------------------- Key: 3923 Medline: 20072620 Authors: Sadler PL;Shakes, DC Title: Anucleate Caenorhabditis elegans sperm can crawl, fertilize oocytes and direct anterior-posterior polarization of the 1-cell embryo. Citation: Development 127: 355-366 2000 Type: ARTICLE Genes: emb-27 emb-30 fem-1 him-5 Abstract: It has long been appreciated that spermiogenesis, the cellular transformation of sessile spermatids into motile spermatozoa, occurs in the absence of new DNA transcription. However, few studies have addressed whether the physical presence of a sperm nucleus is required either during spermiogenesis or for subsequent sperm functions during egg activation and early zygotic development. To determine the role of the sperm nucleus in these processes, we analyzed two C. elegans mutants whose spermatids lack DNA. Here we show that these anucleate sperm not only differentiate into mature functional spermatozoa, but they also crawl toward and fertilize oocytes. Furthermore, we show that these anucleate sperm induce both normal egg activation and anterior-posterior polarity in the 1-cell C. elegans embryo. The latter finding demonstrates for the first time that although the anterior-posterior embryonic axis in C. elegans is specified by sperm, the sperm pronucleus itself is not required. Also unaffected is the completion of oocyte meiosis, formation of an impermeable eggshell, migration of the oocyte pronucleus, and the separation and expansion of the sperm-contributed centrosomes. Our investigation of these mutants confirms that, in C. elegans, neither the sperm chromatin mass nor a sperm pronucleus is required for spermiogenesis, proper egg activation, or the induction of anterior-posterior ------------------- Key: 3924 Medline: 20098497 Authors: Su MW;Merz DC;Killeen MT;Zhou YW;Zheng H;Kramer JM;Hedgecock EM;Culotti JG Title: Regulation of the UNC-5 netrin receptor initiates the first reorientation of migrating distal tip cells in Caenorhabditis elegans. Citation: Development 127: 585-594 2000 Type: ARTICLE Genes: daf-12 dig-1 emb-9 him-5 mig-4 mig-6 mig-8 unc-5 unc-6 unc-40 Abstract: Cell migrations play a critical role in animal development and organogenesis. Here, we describe a mechanism by which the migration behaviour of a particular cell type is regulated temporally and coordinated with over-all development of the organism. The hermaphrodite distal tip cells (DTCs) of Caenorhabditis elegans migrate along the body wall in three sequential phases distinguished by the orientation of their movements, which alternate between the anteroposterior and dorsoventral axes. The ventral-to-dorsal second migration phase requires the UNC-6 netrin guidance cue and its receptors UNC-5 and UNC-40, as well as additional, UNC-6-independent guidance systems. We provide evidence that the transcriptional upregulation of unc-5 in the DTCs is coincident with the initiation of the second migration phase, and that premature UNC-5 expression in these cells induces precocious turning in an UNC-6-dependent manner. The DAF-12 steroid hormone receptor, which regulates developmental stage transitions in C. elegans, is required for initiating the first DTC turn and for coincident unc-5 upregulation. We also present evidence for the existence of a mechanism that opposes or inhibits UNC-5 function during the longitudinal first migration phase and for a mechanism that facilitates UNC-5 function during turning. The facilitating mechanism presumably does not involve transcriptional regulation of unc-5 but may represent an inhibition of the phase 1 mechanism that opposes or inhibits UNC-5. These results, therefore, reveal the existence of two mechanisms that regulate the UNC-5 receptor that are critical for responsiveness to the UNC-6 netrin guidance cue and for linking the directional guidance of migrating distal tip ------------------- Key: 3925 Medline: 20146206 Authors: Tan MW;Ausubel FM Title: Caenorhabditis elegans: a model genetic host to study Pseudomonas aeruginosa pathogenesis. Citation: Current Opinion in Microbiology 3: 29-34 2000 Type: REVIEW Genes: abf-1 abf-2 egl-9 mev-1 pgp-1 pgp-3 rad-8 Abstract: In the past year, a Caenorhabditis elegans-Pseudomonas aeruginosa pathogenesis model has been developed to facilitate the systematic dissection of both host and pathogen genes involved in pathogenic interactions. Analysis of the P. aeruginosa-C. elegans interaction should shed light on the larger question of how organisms interact at the molecular level in antagonistic relationships. ------------------- Key: 3926 Medline: 20316624 Authors: Maduro MF;Gordon M;Jacobs R;Pilgrim DB Title: The UNC-119 family of neural proteins is functionally conserved between humans, Drosophila and C. elegans. Citation: Journal of Neurogenetics 13: 191-212 2000 Type: ARTICLE Genes: unc-119 Abstract: C. elegans animals mutant for the unc-119 gene exhibit movement, sensory and behavioral abnormalities. Consistent with a nervous system role, unc-119 reporter genes are expressed throughout the C. elegans nervous system. The UNC-119 protein has strong sequence similarity to the predicted protein from a human gene, HRG4/HsUNC-119, whose transcript is abundant in the retina. Using these similarities, we have identified a Drosphila homolog. DmUNC-119, which is expressed in the Drosophila nervous system. The pre-dieted C. elegans, human and Drosophila gene products are conserved across two domains. Expression of portions of HRG4/HsUNC-119 or DmUNC-119, directed by the unc-119 promoter, can fully rescue the C. elegans unc-119 mutant phenotype. We rested the ability of portions of HRG4/HsUNC-119 to rescue, and found that its function in C. elegans requires the conserved carboxyl terminus, while the dissimilar amino terminus is dispensable. UNC-119, HRG4 and DmUNC-119 constitute members of a new class of neural genes whose common function has been maintained through metazoan evolution. ------------------- Key: 3927 Medline: 20289891 Authors: Ko FCF;Chow KL Title: Mutations with sensory ray defect unmask cuticular glycoprotein antigens in Caenorhabditis elegans male tail. Citation: Development Growth & Differentiation 42: 69-77 2000 Type: ARTICLE Genes: dpy-18 him-5 mab-7 ram-1 ram-2 ram-3 ram-4 ram-5 Abstract: Caenorhabditis elegans male tail has nine pairs of bilaterally symmetric ray processes extended into a cuticular fan. The formation of these structures involves both cell lineage differentiation and cellular morphogenesis. Nine mutations were examined, all of which presented an amorphous ray phenotype. Glycoconjugates carrying an N-acetylglucosamine (GlcNAc) epitope were detected at a high level in their male bursa. It was shown that these antigens are not responsible for the morphological defects. It was further demonstrated that these ram and mab gene products represent critical components for male tail cuticle organization. Mutations of them abolish the integrity of the male bursal cuticle and unmask the underlying GlcNAc epitope. ------------------- Key: 3928 Medline: 10688797 Authors: Chen F;Hersh BM;Conradt B;Zhou Z;Riemer D;Gruenbaum Y;Horvitz HR Title: Translocation of C. elegans CED-4 to nuclear membranes during programmed cell death. Citation: Science 287: 1485-1489 2000 Type: ARTICLE Genes: ced-3 ced-4 ced-9 egl-1 Abstract: The Caenorhabditis elegans Bcl-2-like protein CED-9 prevents programmed cell death by antagonizing the Apaf-1-like cell-death activator CED-4. Endogenous CED-9 and CED-4 proteins localized to mitochondria in wild-type embryos, in which most cells survive. By contrast, in embryos in which cells had been induced to die, CED-4 assumed a perinuclear localization. CED-4 translocation induced by the cell-death activator EGL-1 was blocked by a gain-of-function mutation in ced-9 but was not dependent on ced-3 function, suggesting that CED-4 translocation precedes caspase activation and the execution phase of programmed cell death. Thus, a change in the subcellular localization of CED-4 may drive programmed cell death. ------------------- Key: 3929 Medline: 20168806 Authors: Reinhart BJ;Slack FJ;Basson M;Pasquinelli AE;Bettinger JC;Rougvie AE;Horvitz HR;Ruvkun G Title: The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Citation: Nature 403: 901-906 2000 Type: ARTICLE Genes: let-7 lin-4 lin-14 lin-28 lin-29 lin-41 lin-42 Abstract: The C. elegans heterochronic gene pathway consists of a cascade of regulatory genes that are temporally controlled to specify the timing of developmental events(1). Mutations in heterochronic genes cause temporal transformations in cell fates in which stage-specific events are omitted or reiterated(2). Here we show that let-7 is a heterochronic switch gene. Loss of let-7 gene activity causes reiteration of larval cell fates during the adult stage, whereas increased let-7 gene dosage causes precocious expression of adult fates during larval stages. let-7 encodes a temporally regulated 21-nucleotide RNA that is complementary to elements in the 3' untranslated regions of the heterochronic genes lin-14, lin-28, lin-41, lin-42 and daf-12, indicating that expression of these genes may be directly controlled by let-7. A reporter gene bearing the lin-41 3' untranslated region is temporally regulated in a let-7-dependent manner. A second regulatory RNA, lin-4, negatively regulates lin-14 and lin-28 through RNA-RNA interactions with their 3' untranslated regions(3,4). We propose that the sequential stage-specific expression of the lin-4 and let-7 regulatory RNAs triggers transitions in the complement of heterochronic regulatory proteins to ------------------- Key: 3930 Medline: 20153773 Authors: Thompson SR;Goodwin EB;Wickens M Title: Rapid deadenylation and poly(A)-dependent translational repression mediated by the Caenorhabditis elegans tra-2 3' untranslated region in Xenopus embryos. Citation: Molecular and Cellular Biology 20: 2129-2137 2000 Type: ARTICLE Genes: tra-2 Abstract: The 3' untranslated region (3'UTR) of many eukaryotic mRNAs is essential for their control during early development. Negative translational control elements in 3'UTRs regulate pattern formation, cell fate, and sex determination in a variety of organisms. tra-2 mRNA in Caenorhabditis elegans is required for female development but must be repressed to permit spermatogenesis in hermaphrodites. Translational repression of tra-2 mRNA in C. elegans is mediated by tandemly repeated elements in its 3'UTR; these elements are called TGEs (for tra-2 and GLI element). To examine the mechanism of TGE-mediated repression, we first demonstrate that TGE-mediated translational repression occurs in Xenopus embryos and that Xenopus egg extracts contain a TGE-specific binding factor. Translational repression by the TGEs requires that the mRNA possess a poly(A) tail. We show that in C. elegans, the poly(A) tail of wild-type tra-2 mRNA is shorter than that of a mutant mRNA lacking the TGEs. To determine whether TGEs regulate poly(A) length directly, synthetic tra-2 3'UTRs with and without the TGEs were injected into Xenopus embryos. We find that TGEs accelerate the rate of deadenylation and permit the last 15 adenosines to be removed from the RNA, resulting in the accumulation of fully deadenylated molecules. We conclude that TGE-mediated translational repression involves either interference with poly(A)'s function in translation and/or regulated deadenylation. ------------------- Key: 3931 Medline: 20153788 Authors: Hong Y;Lee RC;Ambros V Title: Structure and function analysis of LIN-14, a temporal regulator of postembryonic developmental events in Caenorhabditis elegans. Citation: Molecular and Cellular Biology 20: 2285-2295 2000 Type: ARTICLE Genes: lin-4 lin-14 Abstract: During postembryonic development of Caenorhabditis elegans, the heterochronic gene lin-14 controls the timing of developmental events in diverse cell types. Three alternative lin-II transcripts are predicted to encode isoforms of a novel nuclear protein that differ in their amino-terminal domains. In this paper, we report that the alternative amino-terminal domains of LIN-14 are dispensable and that a carboxy-terminal region within exons 9 to 13 is necessary and sufficient for in vivo LIN-14 function. A transgene capable of expressing only one of the three alternative lin-14 gene products rescues a lin-14 null mutation and is developmentally regulated by lin-4. This shows that the deployment of alternative lin-II gene products is not critical for the ability of LIN-14 to regulate downstream genes in diverse cell types or for the in vivo regulation of LIN-14 level by lin-4. The carboxy-terminal region of LIN-14 contains an unusual expanded nuclear localization domain which is essential for LIN-14 function. These results support the view that LIN-14 controls developmental timing in C. elegans by regulating gene expression in the nucleus. ------------------- Key: 3932 Medline: 20316627 Authors: Tavernarakis N;Driscoll M Title: Caenorhabditis elegans degenerins and vertebrate ENaC ion channels contain an extracellular domain related to venom neurotoxins. Citation: Journal of Neurogenetics 13: 257-264 2000 Type: ARTICLE Genes: deg-1 del-1 mec-4 mec-10 unc-8 Abstract: The DEG/ENaC (DEGenerin/Epithelial Na+ Channel) superfamily includes closely related ion channel subunits from divergent species ranging from the simple nematode Caenorhabditis elegans to humans. Members of this protein group play roles in several important processes including transduction of mechanical stimuli, sodium re-absorption and blood pressure regulation. Structure/function relationships in members of this superfamily are just beginning to be elaborated. Using a bioinformatics approach: we identified a novel structural element in the extracellular region of DEG/ENaC proteins that exhibits significant similarity to venom neurotoxins. Since venom neurotoxins bind to sodium channels at high affinity, we suggest that the related domain embedded in DEG/ENaC channels may interact with other regions of the channel or ------------------- Key: 3933 Medline: 20123837 Authors: Li W;Boswell R;Wood WB Title: mag-1, a homolog of Drosophila mago nashi, regulates hermaphrodite germ-line sex determination in Caenorhabditis elegans. Citation: Developmental Biology 218: 172-182 2000 Type: ARTICLE Genes: fbf-1 fbf-2 fem-1 fem-2 fem-3 fog-1 fog-2 gld-1 her-1 mag-1 mog-1 mog-2 mog-3 mog-4 mog-5 mog-6 tra-2 Abstract: The Caenorhabditis elegans gene mag-1 can substitute functionally for its homolog mago nashi in Drosophila and is predicted to encode a protein that exhibits 80% identity and 88% similarity to Mago nashi (P. A. Newmark et al., 1997, Development 120, 3197-3207). We have used RNA-mediated interference (RNAi) to analyze the phenotypic consequences of impairing mag-1 function in C. elegans. We show here that mag-1(RNAi) causes masculinization of the germ line (Mog phenotype) in RNA-injected hermaphrodites, suggesting that mag-1 is involved in hermaphrodite germ-line sex determination. Epistasis analysis shows that ectopic sperm production caused by mag-1(RNAi) is prevented by loss-of-function (lf) mutations in fog-2, gld-1, fem-1, fem-2 fem-3, and fog-1, all of which cause germ-line feminization in XX hermaphrodites, but not by a her-1(lf) mutation which causes germ-line feminization only in XO males. These results suggest that mag-1 interacts with the fog, fem, and gld genes and acts independently of her-1. We propose that mag-1 normally allows oogenesis by inhibiting function of one or more of these masculinizing genes, which act during the fourth larval stage to promote transient sperm production in the hermaphrodite germ line. When the Mog phenotype is suppressed by a fog-2(if) mutation, mag-1(RNAi) also causes lethality in the progeny embryos of RNA-injected, mated hermaphrodites, suggesting an essential role for mag-1 during embryogenesis. The defective embryos arrest during morphogenesis with an apparent elongation defect. The distribution pattern of a JAM-1::GFP reporter, which is localized to boundaries of hypodermal cells, shows that hypodermis is disorganized in these embryos. The temporal expression pattern of the mag-1 gene prior to and during morphogenesis appears to be consistent with an essential role of mag-1 in embryonic hypodermal organization and elongation. ------------------- Key: 3934 Medline: 20145436 Authors: Park YS;Lee YS;Cho NJ;Kaang BK Title: Alternative splicing of gar-1, a Caenorhabditis elegans G-protein-linked acetylcholine receptor gene. Citation: Biochemical and Biophysical Research Communications 268: 354-358 2000 Type: ARTICLE Genes: gar-1 Abstract: We have recently identified a gene, designated gar-1, coding for a novel form of G-protein-linked acetylcholine (ACh) receptor in Caenorhabditis elegans. Although this receptor is most closely related to muscarinic ACh receptors (mAChRs), electrophysiological analyses have shown that ligand binding specificity of the receptor is distinct from that of mAChRs. Here we report that three receptor isoforms are generated by alternative splicing of the gar-1 transcript. These receptor isoforms differ only in the third intracellular loop that is considered to be important for G protein coupling. The three splice variants, when expressed in Xenopus oocyte, displayed similar pharmacological profiles and signaling activities. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis showed that the three gar-1 mRNAs are present at all developmental stages examined. The results in this study provide evidence that alternative splicing is involved in promoting molecular diversity of G-protein-linked ACh receptors. ------------------- Key: 3935 Medline: 20174716 Authors: Aboobaker AA;Blaxter ML Title: Medical significance of Caenorhabditis elegans. Citation: Annals of Medicine 32: 23-30 2000 Type: REVIEW Genes: abl-1 ced-3 cyk-1 egl-15 fer-1 npc-1 pkd-2 sel-12 sma-4 vab-3 Abstract: Caenorhabditis elegans is now the model organism of choice for a growing number of researchers. A combination of its apparent simplicity, exquisite genetics, the existence of a full molecular toolkit and a complete genome sequence makes it ideal for rapid and effective study of gene function. A survey of the C. elegans genome indicates that this 'simple' worm contains many genes with a high degree of similarity to human disease genes. For many human disease genes it has proven, and will continue to prove, difficult to elucidate their function by direct study. In such cases simpler model organisms may prove to be a more productive starting point. The basic function of a human disease gene may be studied in the background of C. elegans, in which the most important interactions are likely to be conserved, providing an insight into disease process in humans. Here we consider the significance of this modality for human disease processes and discuss how C. elegans may, in some cases, be ideal in the study of the function of human disease genes and act as a model for groups of parasitic nematodes that have a severe impact on world health. ------------------- Key: 3936 Medline: Authors: Feng L;Liao XH Title: A summary of the study on developmental molecular biology of C. elegans as a model system. Citation: Progress in Biochemistry and Biophysics 27: 13-16 2000 Type: REVIEW Genes: Abstract: ------------------- Key: 3937 Medline: 20148537 Authors: Zhao H;Nonet ML Title: A retrograde signal is involved in activity-dependent remodeling at a C. elegans neuromuscular junction. Citation: Development 127: 1253-1266 2000 Type: ARTICLE Genes: cat-1 cha-1 eat-4 egl-36 lin-14 myo-3 rab-3 snb-1 snt-1 unc-4 unc-11 unc-13 unc-17 unc-18 unc-25 unc-29 unc-54 Abstract: We have characterized how perturbations of normal synaptic activity influence the morphology of cholinergic SAB motor neurons that innervate head muscle in C. elegans. Mutations disrupting components of the presynaptic release apparatus, acetylcholine (ACh) synthesis or ACh loading into synaptic vesicles each induced sprouting of SAB axonal processes. These sprouts usually arose in the middle of the normal innervation zone and terminated with a single presynaptic varicosity. Sprouting SAB neurons with a similar morphology were also observed upon reducing activity in muscle, either by using mutants lacking a functional nicotinic ACh receptor subunit or through muscle-specific expression of a gain-of function potassium channel. Analysis of temperature-sensitive mutants in the choline acetyltransferase gene revealed that the sprouting response to inactivity was developmentally regulated; reduction of synaptic activity in early larval stages, but not in late larval stages, induced both sprouting and addition of varicosities. Our results indicate that activity levels regulate the structure of certain synaptic connections between nerve and muscle in C. elegans. One component of this regulatory machinery is a retrograde signal from the postsynaptic cell that mediates the formation of synaptic connections. ------------------- Key: 3938 Medline: 20115425 Authors: Chamberlin HM; Thomas JH Title: The bromodomain protein LIN-49 and trithorax-related protein LIN-59 affect development and gene expression in Caenorhabditis elegans. Citation: Development 127: 713-723 2000 Type: ARTICLE Genes: egl-5 lin-22 lin-49 lin-59 mab-5 mes-2 mes-6 sDf18 Abstract: We have molecularly characterized the lin-49 and lin-59 genes in C. elegans, and found their products are related to Drosophila trithorax group (trx-G) proteins and other proteins implicated in chromatin remodelling. LIN-49 is structurally most similar to the human bromodomain protein BR140, and LIN-59 is most similar to the Drosophila trx-G protein ASH1. In C. elegans, lin-49 and lin-59 are required for the normal development of the mating structures of the adult male tail, for the normal morphology and function of hindgut (rectum) cells in both males and hermaphrodites and for the maintenance of structural integrity in the hindgut and egg-laying system in adults. Expression of the Hox genes egl-5 and mab-5 is reduced in lin-49 and lin-59 mutants, suggesting lin-49 and lin-59 regulate HOM-C gene expression in C. elegans as the trx-G genes do in Drosophila. lin-49 and lin-59 transgenes are expressed widely throughout C. elegans animals. Thus, in contrast to the C. elegans Polycomb group (Pc-G)-related genes mes-2 and mes-6 that function primarily in the germline, we propose lin-49 and lin-59 function in somatic development similar to the Drosophila trx-G genes. ------------------- Key: 3939 Medline: 20115429 Authors: Roy PJ;Zheng H;Warren CE;Culotti JG Title: mab-20 encodes Semaphorin-2a and is required to prevent ectopic cell contacts during epidermal morphogenesis in Caenorhabditis elegans. Citation: Development 127: 755-767 2000 Type: ARTICLE Genes: mab-20 vab-1 Abstract: The Semaphorins are a family of transmembrane proteins known to elicit growth cone repulsion and collapse. We made and characterized a putative null mutant of the C. elegans gene semaphorin-2a (Ce-sema-2a). This mutant failed to complement mutants of mab-20 (Baird, S. E,, Fitch, D. H., Kassem, I. A, A. and Emmons, S. W. (1991) Development 113, 515-526). In addition to low-frequency axon guidance errors, mab-20 mutants have unexpected defects in epidermal morphogenesis. Errant epidermal cell migrations affect secreted and epidermal enclosure of the embryo, body shape and sensory rays of the male tail. These phenotypic traits are explained by the formation of inappropriate contacts between cells of similar type and suggest that Ce-Sema-2a may normally prevent formation or stabilization of ectopic adhesive contacts between these cells. ------------------- Key: 3940 Medline: 20135979 Authors: Kolmerer B;Clayton J;Benes V;Allen T;Ferguson C;Leonard K;Weber U;Knekt M;Ansorge W;Labeit S;Bullard B Title: Sequence and expression of the kettin gene in Drosophila melanogaster and Caenorhabditis elegans. Citation: Journal of Molecular Biology 296: 435-448 2000 Type: ARTICLE Genes: let-336 let-447 let-448 let-458 Abstract: Kettin is a large modular protein associated with thin filaments in the Z-disc region of insect muscles. The sequence of a 21.3 kb contig of the Drosophila gene has been determined. The corresponding protein sequence has 35 immunoglobulin-like (Ig) domains which are separated by shorter linker sequences, except near the N and C termini of the molecule where linker sequences are short or missing. This confirms a model in which each Ig domain binds to an actin protomer. The Drosophila kettin gene is at 62C 1-3 on the third chromosome. Two P-element insertions, l(3)j1D7 and l(3)rL182 are in the kettin gene, and complementation tests showed that existing l(3)dre8 mutations are in the same gene. The RNA was detected in wild-type Drosophila embryos at stage 11, first in the gut invagination region of the mesoderm, and by stage 13 in both visceral and somatic mesoderm. Somatic mesoderm expression became segmental at stage 13. RNA expression was greatly reduced in embryos of P-element homozygotes but normal in heterozygotes. The structure of the flight muscle in all the heterozygous mutants was normal, including the myofibril-cuticle connections, and they were able to fly. Kettin sequence homologous to the Drosophila protein, was identified in the Caenorhabditis elegans genome database. The RNA was detected in pharyngeal, body wall and anal depressor muscles of larvae and adult worms, as well as in the male gonad. Antibody to insect kettin labelled the pharyngeal, body wall, anal depressor and proximal gonadal muscles in adult worms. Body wall muscles were labelled in an obliquely striated pattern consistent with the Z-disc localisation in insect muscle. The relationship of kettin to D-titin, which has been assigned to the same chromosomal locus in Drosophila, is discussed. ------------------- Key: 3941 Medline: 20115424 Authors: Much JW;Slade DJ;Klampert K;Garriga G;Wightman B Title: The fax-1 nuclear hormone receptor regulates axon pathfinding and neurotransmission. Citation: Development 127: 703-712 2000 Type: ARTICLE Genes: fax-1 flp-1 unc-42 unc-115 mnDp33 yDp14 Abstract: Specification of neuron identity requires the activation of a number of discrete developmental programs. Among these is pathway selection by growth cones: in order for a neuron's growth cone to respond appropriately to guidance cues presented by other cells or the extracellular matrix, the neuron must express genes to mediate the response. The fax-1 gene of C. elegans is required for pathfinding of axons that extend along the ventral nerve cord. We show that fax-1 is also required for pathfinding of axons in the nerve ring, the largest nerve bundle in the nematode, and for normal expression of FMRFamide-like neurotransmitters in the AVK interneurons. The fax-1 gene encodes a member of the superfamily of nuclear hormone receptors and has a DNA- binding domain related to the human PNR and Drosophila Tailless proteins. We observe fax-1 expression in embryonic neurons, including the AVK interneurons, just prior to axon extension, but after neurogenesis. These data suggest that fax-1 coordinately regulates the transcription of genes that function in the selection of axon pathways, neurotransmitter expression and, perhaps, other aspects of the specification of neuron identity. ------------------- Key: 3942 Medline: 20129930 Authors: Karashima T;Sugimoto A;Yamamoto M Title: Caenorhabditis elegans homologue of the human azoospermia factor DAZ is required for oogenesis but not for spermatogenesis. Citation: Development 127: 1069-1079 2000 Type: ARTICLE Genes: daz-1 fem-3 fog-3 gld-1 glp-4 ccDf5 mIn1 Abstract: DAZ (Deleted in Azoospermia), the putative azoospermia factor gene in human, encodes a ribonucleoprotein-type RNA-binding protein required for spermatogenesis. A Drosophila homologue of DAZ, called bottle, is also essential for spermatogenesis. A mouse homologue, Dazla, is implicated in both spermatogenesis and oogenesis. Here, we report the identification and characterization of daz-1, the single DAZ homologue in the nematode Caenorhabditis elegans. Loss of daz-1 function caused sterility in hermaphrodites, by blocking oogenesis at the pachytene stage of meiosis I. Epistasis analysis suggested that this gene executes its function succeeding gld-1, which governs the early pachytene stage in the oogenic pathway. Spermatogenesis did not appear to be affected in daz-1 hermaphrodites. Males defective in daz-1 produced sperm fully competent in fertilization. Analysis employing sex-determination mutants indicated that the daz-1 function was required for meiosis of female germline regardless of the sea of the soma. Transcription of daz-1 was restricted to the germline, starting prior to the onset of meiosis and was most conspicuous in cells undergoing oogenesis. Thus, daz-1 in C. elegans is an essential factor for female meiosis but, unlike other DAZ family members so far reported, it is dispensable for male meiosis. ------------------- Key: 3943 Medline: 10683173 Authors: Plenefisch JD;Zhu X;Hedgecock EM Title: Fragile skeletal muscle attachments in dystrophic mutants of Caenorhabditis elegans: isolation and characterization of the mua genes. Citation: Development 127: 1197-1207 2000 Type: ARTICLE Genes: mua-1 mua-2 mua-3 mua-4 mua-5 mua-6 mua-7 mua-8 mua-9 mua-10 smg-1 unc-23 unc-54 vab-10 ctDf2 ctDf3 eDf2 mDf7 maDf4 mnDf1 mnDf4 mnDf8 mnDf30 mnDf31 mnDf39 mnDf41 mnDf52 mnDf96 nDf16 nDf19 nDf40 sDf60 tDf7 tDf8 yDf10 mnDp1 sDp3 Abstract: Over 30 Caenorhabditis elegans mutants were identified with normal muscle differentiation and initial locomotion followed by catastrophic detachment of skeletal muscles from the body wall. Reducing the strength of muscle contraction in these mutants with a myosin gene mutation suppresses muscle detachment. These dystrophic mutants identify a novel class of genes required for growth and maintenance of functional muscle attachments, not exceptional alleles of genes required for muscle differentiation and contractility. Nine new genes, named mua, and two previously published loci, unc-23 and vab-10, cause fragile muscle attachments. The primary sites of muscle detachment, including the plane of tissue separation, are characteristic for each gene. We suggest these genes identify feedback mechanisms whereby local strain regulates the extent of myofibril contraction and the placement of new muscle attachments in functioning muscles. Finally, we draw some comparisons to vertebrate ------------------- Key: 3944 Medline: 20171270 Authors: Watts JL;Morton DG;Bestman J;Kemphues KJ Title: The C. elegans par-4 gene encodes a putative serine-threonine kinase required for establishing embryonic asymmetry. Citation: Development 127: 1467-1475 2000 Type: ARTICLE Genes: par-1 par-2 par-3 par-4 par-5 par-6 Abstract: During the first cell cycle of Caenorhabditis elegans embryogenesis, asymmetries are established that are essential for determining the subsequent developmental fates of the daughter cells. The maternally expressed par genes are required for establishing this polarity. The products of several of the par genes have been found to be themselves asymmetrically distributed in the first cell cycle. We have identified the par-4 gene of C. elegans, and find that it encodes a putative serine-threonine kinase with similarity to a human kinase associated with Peutz-Jeghers Syndrome, LKB1 (STK11), and a Xenopus egg and embryo kinase, XEEK1, Several strong par-4 mutant alleles are missense mutations that alter conserved residues within the kinase domain, suggesting that kinase activity is essential for PAR-4 function. We find that the PAR-4 protein is present in the gonads, oocytes and early embryos of C. elegans, and is both cytoplasmically and cortically distributed. The cortical distribution begins at the late 1-cell stage, is more pronounced at the 2- and 4-cell stages and is reduced at late stages of embryonic development. We find no asymmetry in the distribution of PAR-4 protein in C. elegans embryos. The distribution of PAR-4 protein in early embryos is unaffected by mutations ------------------- Key: 3945 Medline: 10603471 Authors: Thorpe CJ;Schlesinger A;Bowerman B Title: Wnt signalling in Caenorhabditis elegans: regulating repressors and polarizing the cytoskeleton. Citation: Trends in Cell Biology 10: 10-17 2000 Type: REVIEW Genes: ama-1 apr-1 bar-1 hmp-1 hmp-2 lit-1 mom-1 mom-2 mom-3 mom-4 mom-5 pes-10 pop-1 sgg-1 wrm-1 Abstract: Wnt proteins are secreted, cysteine-rich glycoprotein ligands with numerous roles during animal development. Recent studies of endoderm induction during embryogenesis ill the nematode Caenorhabditis elegans challenge the prevailing view that Wnt signalling specifies cell fate by converting transcriptional repressors into activators. Instead, a mitogen-activated protein kinase (MAPK)-related pathway converges with Wnt signalling in C. elegans to relieve transcriptional repression. Futhermore, Wnt signalling induces endoderm in part by aligning the mitotic spindle in a responding cell along the anterior-posterior bony axis. To orient mitotic spindles, Wnt signalling might directly target the cytoskeleton, prior to any regulation of gene transcription in responding cells. ------------------- Key: 3946 Medline: 20156789 Authors: Enmark E;Gustafsson JA Title: Nematode genome sequence dramatically extends the nuclear receptor superfamily. Citation: Trends in Pharmacological Sciences 21: 85-87 2000 Type: ARTICLE Genes: nhr-2 odr-7 Abstract: Nuclear receptors represent a large class of ligand-activated transcriptional regulators; about 70 members of-this protein family have been cloned from mammalian or insect species. Thus, it came as a great surprise when the recent completion of the Caenorhabditis elegans genome revealed at least 228 genes for nuclear receptors. Clearly, some of these receptors are homologues of known receptors, but most lack homologues in other species. Whether these receptors possess homologues in mammalian species is of great interest; if these do exist the size of the nuclear receptor superfamily could also expand dramatically in humans. ------------------- Key: 3947 Medline: 20116099 Authors: Okuda T;Haga T;Kanai Y;Endou H;Ishihara T;Katsura I Title: Identification and characterization of the high-affinity choline transporter. Citation: Nature Neuroscience 3: 120-125 2000 Type: ARTICLE Genes: cho-1 Abstract: In cholinergic neurons, high-affinity choline uptake in presynaptic terminals is the rate-limiting step in acetylcholine synthesis. Using information provided by the Caenorhabditis elegans Genome Project, we cloned a cDNA encoding the high-affinity choline transporter from C. elegans (cho-1). We subsequently used this clone to isolate the corresponding cDNA from rat (CHT1). CHT1 is not homologous to neurotransmitter transporters, but is homologous to members of the Na+-dependent glucose transporter family. Expression of CHT1 mRNA is restricted to cholinergic neurons. The characteristics of CHT1-mediated choline uptake essentially match those of high-affinity choline uptake in rat brain synaptosomes. ------------------- Key: 3948 Medline: 20173871 Authors: Reddien PW;Horvitz HR Title: CED-2/CrkII and CED-10/Rac control phagocytosis and cell migration in Caenorhabditis elegans. Citation: Nature Cell Biology 2: 131-136 2000 Type: ARTICLE Genes: ced-2 ced-5 ced-10 rac-1 Abstract: Engulfment of apoptotic cells in Caenorhabditis elegans is controlled by two partially redundant pathways. Mutations in genes in one of these pathways, defined by the genes ced-2, ced-5 and ced-10, result in defects both in the engulfment of dying cells and in the migrations of the two distal tip cells of the developing gonad. Here we find that ced-2 and ced-10 encode proteins similar to the human adaptor protein Crkll and the human GTPase Rac, respectively. Together with the previous observation that ced-5 encodes a protein similar to human DOCK180, our findings define a signalling pathway that controls phagocytosis and cell migration. We provide evidence that CED-2 and CED-10 function in engulfing rather than dying cells to control the phagocytosis of cell corpses, that CED-2 and CED-5 physically interact, and that ced-10 probably functions downstream of ced-2 and ced-5. We propose that CED-2/Crkll and CED-5/DOCK180 function to activate CED-10/Rac in a GTPase signalling pathway that ------------------- Key: 3949 Medline: 20198305 Authors: Teichmann SA;Chothia C Title: Immunoglobulin superfamily proteins in Caenorhabditis elegans. Citation: Journal of Molecular Biology 296: 1367-1383 2000 Type: ARTICLE Genes: cam-1 clr-1 dig-1 dim-1 egl-15 kin-8 sax-3 unc-5 unc-6 unc-22 unc-40 unc-52 unc-73 unc-89 zig-1 zig-2 zig-3 zig-4 zig-5 zig-6 zig-7 zig-8 Abstract: The predicted proteins of the genome of Caenorhabditis elegans were analysed by various sequence comparison methods to identify the repertoire of proteins that are members of the immunoglobulin superfamily (IgSF). The IgSF is one of the largest families of protein domain in this genome and likely to be one of the major families in other multicellular eukaryotes too. This is because members of the superfamily are involved in a variety of functions including cell-cell recognition, cell-surface receptors, muscle structure and, in higher organisms, the immune system. Sixty-four proteins with 488 I set IgSF domains were identified largely by using Hidden Markov models. The domain architectures of the protein products of these 64 genes are described. Twenty-one of these had been characterised previously. We show that another 25 are related to proteins of known function. The C. elegans IgSF proteins can be classified into five broad categories: muscle proteins, protein kinases and phosphatases, three categories of proteins involved in the development of the nervous system, leucine-rich repeat containing proteins and proteins without homologues of known function, of which there are 18. The 19 proteins involved in nervous system development that are not kinases or phosphatases are homologues of neuroglian, axonin, NCAM, wrapper, klingon, ICCR and nephrin or belong to the recently identified zig gene family. Out of the set of 64 genes, 22 are on the X chromosome. This study should be seen as an initial description of the IgSF repertoire in C. elegans, because the current gene definitions may contain a number of errors, especially in the case of long sequences, and there may be IgSF genes that have not yet been detected. However, the proteins described here do provide an overview of the bulk of the repertoire of immunoglobulin superfamily members in C. elegans, a framework for refinement and extension of the repertoire as gene and protein definitions improve, and the basis for investigations of their function and for comparisons with the repertoires of other ------------------- Key: 3950 Medline: 10757761 Authors: Roller AB;Hoffman DC;Zahler AM Title: The allele-specific suppressor sup-39 alters use of cryptic splice sites in Caenorhabditis elegans. Citation: Genetics 154: 1169-1179 2000 Type: ARTICLE Genes: smg-3 sup-39 unc-73 Abstract: Mutations in the Caenorhabditis elegans sup-39 gene cause allele-specific suppression of the uncoordination defect of unc-73(e936). e936 is a point mutation that changes the canonical G at the 5' end of intron 16 to a U. This mutation activates three splice donors, two of which define introns beginning with the canonical GU. Use of these two cryptic splice sites causes loss of reading frame; interestingly these messages are not substrates for nonsense-mediated decay. The third splice donor, used in 10% of steady-state e936 messages, is the mutated splice donor at the wild-type position, which defines an intron beginning with UU. In the presence of a sup-39 mutation, these same three splice donors are used, but the ratio of messages produced by splicing at these sites changes, The percentage of unc-73(e936) messages containing the wild-type splice junction is increased to 33% with a corresponding increase in the level of UNC-73 protein. This sup-39-induced change was also observed when the e936 mutant intron region was inserted into a heterologous splicing reporter construct transfected into worms. Experiments with splicing reporter constructs showed that the degree of 5' splice site match to the splicing consensus sequence can strongly influence cryptic splice site choice. We propose that mutant SUP-39 is a new type of informational suppressor that alters the use of weak splice ------------------- Key: 3951 Medline: 20221725 Authors: Waggoner LE;Hardaker LA;Golik S;Schafer WR Title: Effect of a neuropeptide gene on behavioral states in Caenorhabditis elegans egg-laying. Citation: Genetics 154: 1181-1192 2000 Type: ARTICLE Genes: cat-4 egl-1 flp-1 goa-1 Abstract: Egg-laying behavior in the nematode Caenorhabditis elegans involves fluctuation between alternative behavioral states: an inactive state, during which eggs are retained in the uterus, and an active state, during which eggs are laid in bursts. We have found that the flp-1 gene, which encodes a group of structurally related neuropeptides, functions specifically to promote the switch from the inactive to the active egg-laying state. Recessive mutations in flp-1 caused a significant increase in the duration of the inactive phase, Vet egg-laying within the active phase was normal. This pattern resembled that previously observed in mutants defective in the biosynthesis of serotonin, a neuromodulator implicated in induction of the active phase. Although flp-1 mutants were sensitive to stimulation of egg-laying by serotonin, the magnitude of their serotonin response was abnormally low. Thus, the flp-1-encoded peptides and serotonin function most likely function in concert to facilitate the onset of the active egg-laying phase. Interestingly, we observed that flp-1 is necessary for animals to down-regulate their rate of egg-laying in the absence of food. Because flp-1 is known to be expressed in interneurons that are postsynaptic to a variety of chemosensory cells, the FLP-1 peptides may function to regulate the activity of the egg-laying circuitry in response to sensory cues. ------------------- Key: 3952 Medline: 20221726 Authors: Keightly PD;Bataillon TM Title: Multigeneration maximum-likelihood analysis applied to mutation-accumulation experiments in Caenorhabditis Citation: Genetics 154: 1193-1201 2000 Type: ARTICLE Genes: Abstract: We develop a maximum-likelihood (ML) approach to estimate genomic mutation rates (U) and average homozygous mutation effects: (s) from mutation-accumulation (MX) experiments in which phenotypic assays are carried out in several generations. We use simulations to compare the procedure's performance with the method of moments traditionally used to analyze MA data. Similar precision is obtained if mutation effects are small relative to the environmental standard deviation, bur. ML can give estimates of mutation parameters that have lower sampling variances than those obtained by the method of moments if mutations with large effects have accumulated. The inclusion of data from intermediate generations may improve the precision. We analyze life-history trait data from two Caenorhabditis elegans MA experiments. Under a model with equal mutation effects, thr two experiments provide similar estimates for U of similar to 0.005 per haploid, averaged over traits. Estimates of s ar-e more divergent and average at -0.51 and -0.13 in the two studies. Detailed analysis shows that changes of mean and variance of genetic values of MA lines in both C. elegans experiments are dominated by mutations with large effects, but the analysis does not rule out the presence of a large class of deleterious mutations with very small effects. ------------------- Key: 3953 Medline: 10551368 Authors: Jackstadt P;Wilm TP;Zahner H;Hobom G Title: Transformation of nematodes via ballistic DNA transfer. Citation: Molecular & Biochemical Parasitology 103: 261-266 1999 Type: ARTICLE Genes: Abstract: Ballistic DNA transfer with tungsten or gold particles was originally used in plant cell transformation, but has been applied more recently in other organisms including mice and rabbits, and was also used for human DNA vaccination purposes. ------------------- Key: 3954 Medline: 20183947 Authors: Dent JA;Smith MM;Vassilatis DK;Avery L Title: The genetics of ivermectin resistance in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 97: 2674-2679 2000 Type: ARTICLE Genes: avr-14 avr-15 che-3 dyf-11 gbr-1 gbr-2 glc-1 osm-1 osm-5 unc-7 unc-9 Abstract: The ability of organisms to evolve resistance threatens the effectiveness of every antibiotic drug. We show that in the nematode Caenorhabditis elegans, simultaneous mutation of three genes, avr-14, avr-15, and glc-1, encoding glutamate-gated chloride channel (GIuCl) alpha-type subunits confers high-level resistance to the antiparasitic drug ivermectin, In contrast, mutating any two channel genes confers modest or no resistance. We propose a model in which ivermectin sensitivity in C. elegans is mediated by genes affecting parallel genetic pathways defined by the family of GluCl genes. The sensitivity of these pathways is further modulated by unc-7, unc-9, and the Dyf (dye filling defective) genes, which alter the structure of the nervous system. Our results suggest that the evolution of drug resistance can be slowed by targeting antibiotic drugs to several members of a multigene family. ------------------- Key: 3955 Medline: 20210770 Authors: Hirotsu T;Saeki S;Yamamoto M;Iino Y Title: The Ras-MAPK pathway is important for olfaction in Caenorhabditis elegans. Citation: Nature 404: 289-293 2000 Type: ARTICLE Genes: gcy-10 ksr-1 let-60 lin-1 lin-45 mek-2 mpk-1 odr-3 sem-5 tax-2 tax-4 unc-2 Abstract: The Ras-MAPK (mitogen-activated protein kinase) signal transduction pathway is well known to control cellular proliferation and differentiation in response to extracellular signals, but its other functions are less understood. In Caenorhabditis elegans this pathway regulates several developmental events, such as vulval induction and progression of meiosis(1), but its function in the nervous system is unknown. Here we report that the Ras-MAPK pathway is involved in olfaction in this organism. Mutational inactivation and hyperactivation of this pathway impairs efficiency of chemotaxis to a set of odorants. Experiments in which let-60 ras was expressed using a heat-shock promoter and a cell-specific promoter show that a normal activity of LET-60 Ras is required in mature olfactory neurons. Application of the odorant isoamylalcohol to wild-type animals leads to the activation of MAP kinase in olfactory neurons within 10 seconds. This induction is dependent on the function of the nucleotide-gated channel TAX-2/TAX-4 and the voltage-activated calcium channel subunit UNC-2. These results suggest a dynamic regulatory role for the Ras-MAPK pathway in perception and transmission of sensory signals ------------------- Key: 3956 Medline: 20210772 Authors: Ketting RF;Plasterk RHA Title: A genetic link between co-suppression and RNA interference in C. elegans. Citation: Nature 404: 296-298 2000 Type: ARTICLE Genes: fem-1 gld-1 mrt-2 mut-2 mut-6 mut-7 mut-8 mut-9 rde-1 Abstract: Originally discovered in plants(1,2), the phenomenon of co-suppression by transgenic DNA has since been observed in many organisms from fungi(3) to animals(4-7): introduction of transgenic copies of a gene results in reduced expression of the transgene as well as the endogenous gene. The effect depends on sequence identity between transgene and endogenous gene. Some cases of cosuppression resemble RNA interference (the experimental silencing of genes by the introduction of double-stranded RNA)(8), as RNA seems to be both an important initiator and a target in these processes(9-13). Here we show that co-suppression in Caenorhabditis elegans is also probably mediated by RNA molecules. Both RNA interference(14,15) and co-suppression(16) have been implicated in the silencing of transposons. We now report that mutants of C. elegans that are defective in transposon silencing and RNA interference (mut-2, mut-7, mut-8 and mut-9) are in addition resistant to co-suppression. This indicates that RNA interference and co-suppression in C. elegans may be mediated at least in part by the same molecular machinery, possibly through RNA-guided degradation of messenger RNA molecules. ------------------- Key: 3957 Medline: 20183676 Authors: Wu YC;Stanfield GM;Horvitz HR Title: NUC-1, a Caenorhabditis elegans DNase II homolog, functions in an intermediate step of DNA degradation during Citation: Genes & Development 14: 536-548 2000 Type: ARTICLE Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 Abstract: One hallmark of apoptosis is the degradation of chromosomal. DNA. We cloned the Caenorhabditis elegans gene nuc-1, which is involved in the degradation of the DNA of apoptotic cells, and found that nuc-1 encodes a homolog of mammalian DNase II. We used the TUNEL technique, to assay DNA degradation in nuc-1 and other mutants defective in programmed cell death and discovered that TUNEL labels apoptotic cells only during a transient intermediate stage. Mutations in nuc-1 allowed the generation of TUNEL-reactive DNA but blocked the conversion of TUNEL-reactive DNA to a subsequent TUNEL-unreactive state. Completion of DNA degradation did not occur in the absence of cell-corpse engulfment. Our data suggest that the process of degradation of the DNA of a cell corpse occurs in at least three distinct steps and requires activities provided by both the dying and the engulfing cell. ------------------- Key: 3958 Medline: 20183681 Authors: Woollard A;Hodgkin J Title: The Caenorhabditis elegans fate-determining gene mab-9 encodes a T-box protein required to pattern the posterior hindgut. Citation: Genes & Development 14: 596-603 2000 Type: ARTICLE Genes: egl-5 lag-1 mab-9 sup-5 Abstract: Caenorhabditis elegans mab-9 mutants are defective in hindgut and male tail development because of cell fate transformations in two posterior blast cells, B and F. We have cloned mab-9 and show that it encodes a member of the T-box family of transcriptional regulators. MAB-9 localizes to the nucleus of B and F and their descendents during development, suggesting that it acts cell autonomously in the posterior hindgut to direct cell fate. T-box genes related to brachyury have also been implicated in hindgut patterning, and our results support models for an evolutionarily ancient role for these genes in hindgut formation. ------------------- Key: 3959 Medline: 20160687 Authors: Pitt JN;Schisa JA;Priess JR Title: P granules in the germ cells of Caenorhabditis elegans adults are associated with clusters of nuclear pores and contain RNA. Citation: Developmental Biology 219: 315-333 2000 Type: ARTICLE Genes: fem-1 Abstract: The germ cells, and germ cell precursors, in the nematode Caenorhabditis elegans contain distinctive granules called P granules. During early embryogenesis, P granules are segregated asymmetrically into those blastomeres that eventually produce the germ line. Because of the correlation between P granule distribution and the development of the germ line, P granules are widely thought to function in some aspect of germ line specification or differentiation. Most of the analysis of P granule structure and localization has focused on the early embryo, when P granules are located in the cytoplasm. However, during most of development P granules are associated with germ cell nuclei. We report here an ultrastructural analysis of the nuclear-associated P granules in the germ cells of the adult hermaphrodite gonad. We show that P granules are tightly associated with nuclear pores and that the positions of certain structures within the P granules correspond to the positions of pores on the nuclear envelope. We present immunocytochemical and ultrastructural data suggesting that P granules can associate, or remain associated, with pore-like structures even after they detach from the nuclear envelope during oogenesis. Finally, we show that nuclear-associated P granules in the gonad contain RNA, complementing previous studies showing that cytoplasmic P granules in embryos contain RNA. ------------------- Key: 3960 Medline: 20160451 Authors: Gengyo-Ando K;Mitani S Title: Characterization of mutations induced by ethyl methanesulfonate, UV, and trimethylpsoralen in the nematode Caenorhabditis elegans. Citation: Biochemical and Biophyscial Research Communications 269: 64-69 2000 Type: ARTICLE Genes: ben-1 unc-22 Abstract: The genome project of the nematode Caenorhabditis elegans is completed. It is important and useful to disrupt nematode genes to know their function. We treated wild-type animals with potential candidates for mutagens for reverse genetics, EMS (ethyl methanesulfonate), short-wavelength UV, and long-wavelength UV in the presence of TMP (trimethylpsoralen). We estimated forward mutation rates by counting the occurrence of a marker unc-22 mutation. me found that the forward mutation rate by TMP/UV could be comparable with EMS by improving the frequency one order higher than before. We next isolated mutants of another marker gene ben-1 and examined the probability for the deletion mutations by PCR and sequencing. Deletion mutations were found only by TMP/UV method, which suggested TMP/UV is the choice for deletion mutagenesis among these methods. As a pilot experiment, we could isolate actual deletion mutations at a much higher frequency than ------------------- Key: 3961 Medline: Authors: Szerencsei RT;Tucker JE;Cooper CB;Winkfein RJ;Farrell PJ;Iatrou K;Schnetkamp PPM Title: Minimal domain requirement for cation transport by the potassium-dependent Na/Ca-K exchanger: Comparison with an NCKX paralog from Caenorhabditis elegans. Citation: Journal of Biological Chemistry 275: 669-676 2000 Type: ARTICLE Genes: Abstract: The retinal rod Na/Ca-K exchanger (NCKX) is a unique calcium extrusion protein utilizing both inward sodium gradient and outward potassium gradient. Three mammalian rod NCKX cDNAs have been cloned to date, but quantitative analysis of NCKX function in heterologous systems has proven difficult. Here, we describe a simple system for quantitative analysis of NCKX function; stable transformation of cultured insect cells with the novel pEA1/153A vector containing NCKX cDNAs was combined with measurements of potassium-dependent Ca-45 uptake in sodium-loaded cells. We carried out structure-function studies on NCKX with the following results: 1) two-thirds of the full-length sequence of bovine NCKX could be deleted without affecting potassium-dependent calcium transport and without affecting key properties of the potassium binding site; 2) the affinity of NCKX for potassium was about 10-fold greater in choline medium when compared with lithium medium; this shift was observed in rod outer segments or in cells expressing fall-length rod NCKX, the above deletion mutant, or a distantly related NCKX paralog cloned from Caenorhabditis elegans. We conclude that the potassium binding site is highly conserved among members of the NCKX family and is formed by residues located within the two sets of transmembrane spanning segments in the NCKX ------------------- Key: 3962 Medline: 20196008 Authors: Rubin GM;Yandell MD;Wortman JR;Miklos GLG;Nelson CR;Hariharan IK;Fortini ME;Li PW;Apweiler R;Fleischmann W;Cherry JM;Henikoff S;Skupski MP;Misra S;Ashburner M;Birney E;Boguski MS;Brody T;Brokstein P;C Title: Comparative genomics of the eukaryotes. Citation: Science 287: 2204-2215 2000 Type: ARTICLE Genes: Abstract: A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae-and the proteins they are predicted to encode-was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease. ------------------- Key: 3963 Medline: 20222265 Authors: Sharp PA;Zamore PD Title: RNA interference. Citation: Science 287: 2431-2433 2000 Type: REVIEW Genes: ego-1 mut-7 rde-1 rde-2 rde-4 Abstract: The mechanical sounds of robots and the electronic hum of computers are features of 21st-century life. Despite the joys of increasing automation, simple experiments still produce wonderful new discoveries in molecular biology. The realization several years ago that double-stranded RNA (dsRNA) is a key player in one form of posttranscriptional gene silencing indicated that a new field of great importance was about to be created (1). The study of how RNA regulates gene expression called RNA interference (RNAi)- has an exciting future, and the report by Grishok et al. on page 2494 of this issue (2) provides further support for such optimism. ------------------- Key: 3964 Medline: 20207007 Authors: Grishok A;Tabara H;Mello CC Title: Genetic requirements for inheritance of RNAi in C. elegans. Citation: Science 287: 2494-2497 2000 Type: ARTICLE Genes: mut-7 rde-1 rde-2 rde-4 Abstract: In Caenorhabditis elegans, the introduction of double-stranded RNA Triggers sequence-specific generic interference (RNAi) that is transmitted to offspring. The inheritance properties associated with this phenomenon were examined. Transmission of the interference effect occurred through a dominant extragenic agent. The wild-type activities of the RNAi pathway genes rde-1 and rde-4 were required for the formation of this interfering agent but were not needed for interference thereafter. In contrast, the rde-2 and mut-7 genes were required downstream for interference. These findings provide evidence for germ line transmission of an extragenic sequence-specific silencing factor and implicate rde-1 and rde-4 in the formation of the inherited agent. ------------------- Key: 3965 Medline: 20189836 Authors: Ali MY;Siddiqui ZK;Malik AB;Siddiqui SS Title: A novel C-terminal kinesin subfamily may be involved in chromosomal movement in Caenorhabditis elegans. Citation: FEBS Letters 470: 70-76 2000 Type: ARTICLE Genes: klp-3 klp-15 klp-16 klp-17 Abstract: C-terminal kinesin motor proteins, such as the Drosophila NCD and yeast KAR3, are involved in chromosomal segregation. Previously we have described two orthologs of NCD in Caenorhabditis elegans, KLP-3 and KLP-17, which also participate in chromosome movement. Here we report cDNA cloning of klp-15 and klp-16, and the expression pattern of the genes encoding C-terminal motor kinesins including klp-15 and klp-16, Interestingly KLP-15 and KLP-16 form a unique class of C-terminal kinesins, distinct from the previously known C-terminal motors in other organisms. Using in situ hybridization and RNA interference assay, we show that although all of these motors mediate chromosome segregation, they do so in a combination of unique and overlapping manners, suggesting a complex hierarchy of kinesin motor function in metazoans. ------------------- Key: 3966 Medline: Authors: Saran S Title: Programmed cell death. Citation: Current Science 78: 575-586 2000 Type: REVIEW Genes: Abstract: Programmed cell death (PCD) occurs during development in all the animals studied so far, but the molecular basis has been recently discovered. Apoptosis is a highly organized and genetically controlled mechanism which helps in maintaining the homeostasis in multicellular organisms. This paper reviews the recent developments in the field of PCD. Emphasis has been laid on the recent developments in the Caenorhabditis elegans cell death programme. This process is well characterized by some biochemical and cytological events. Three key genes in the PCD of C. elegans have been characterized. The ced-3 and ced-4 genes function in the killing of cells while the ced-9 gene prevents this phenomenon. The ced-9 (cell death suppressor) and ced-3 (cell death inducer) genes encode proteins which share a functional and structural homology with the mammalian proto-oncogene bcl-2 and interleukin-1 beta converting enzyme, respectively. These findings reveal key molecules that control life and death decisions in vertebrates. Characterization of these genes has revealed that the process of PCD is evolutionarily conserved and has shed light on the molecular nature of the apoptotic ------------------- Key: 3967 Medline: 20143423 Authors: Sood R;Porter AC;Ma K;Quilliam LA;Wek RC Title: Pancreatic eukaryotic initiation factor-2 alpha kinase (PEK) homologues in humans, Drosophila melanogaster and Caenorhabditis elegans that mediate translational control in response to endoplasmic .... Citation: Biochemical Journal 346: 281-293 2000 Type: ARTICLE Genes: Abstract: In response to different cellular stresses, a family of protein kinases regulates translation by phosphorylation of the a:subunit of eukaryotic initiation factor-2 (eIF-2 alpha). Recently, we identified a new family member, pancreatic eIF-2 alpha kinase (PEK) from rat pancreas. PEK, also referred to as RNA-dependent protein kinase (PKR)-like endoplasmic reticulum (ER) kinase (PERK) is a transmembrane protein implicated in translational control in response to stresses that impair protein folding in the ER. In this study, we identified and characterized PEK homologues from humans, Drosophila melanogaster and Caenorhabditis elegans. Expression of human PEK mRNA was found in over 50 different tissues examined, with highest levels in secretory tissues. In mammalian cells subjected to ER stress, we found that elevated eIF-2 alpha phosphorylation was coincident with increased PEK autophosphorylation and eIF-2 alpha kinase activity. Activation of PEK was abolished by deletion of PEK N-terminal sequences located in the ER lumen. To address the role of C. elegans PEK in translational control, we expressed this kinase in yeast and found that it inhibits growth by hyperphosphorylation of eIF-2 alpha and inhibition of eIF-2B. Furthermore, we found that vaccinia virus K3L protein, an inhibitor of the eIF-2 alpha kinase PKR involved in an anti-viral defence pathway, also reduced PEK activity. These results suggest that decreased translation initiation by PEK during ER stress may provide the cell with an opportunity to remedy the folding problem prior to introducing newly synthesized proteins into the secretory pathway. ------------------- Key: 3968 Medline: 20202625 Authors: Puoti A;Kimble J Title: The hermaphrodite sperm/oocyte switch requires the Caenorhabditis elegans homologs of PRP2 and PRP22. Citation: Proceedings of the National Academy of Sciences USA 97: 3276-3281 2000 Type: ARTICLE Genes: fem-3 mog-1 mog-4 mog-5 mnDf30 mnDf96 Abstract: Sex determination in the hermaphrodite germ line of Caenorhabditis elegans is controlled posttranscriptionally. The switch from spermatogenesis to oogenesis relies an regulation of the fem-3 sex-determining gene via a regulatory element in the fem-3 3' untranslated region. Previous work showed that at least six mag genes are required for repression by the fem3 3' untranslated region, and that one of those genes, mog-1, encodes a DEAH-box protein. In this paper, we report the cloning of mog-4 and mog-5 and the finding that mog-4 and mog-5 also encode DEAH-box proteins. Our molecular identification of mog-4 and mog-5 relied on genetic mapping and transformation rescue and was confirmed by a missense mutation in each gene. A phylogenetic: analysis revealed that the C. elegans MOG-1, MOG-4, and MOG-5 proteins are closely related to the yeast proteins PRP16, PRP2, and PRP22, respectively. In view of their effect on fem3 regulation and their homology to PRP16 PRP2, and PRP22, we propose that MOG-1, MOG-4, and MOG-5 are required for posttranscriptional regulation, perhaps by modifying the conformation of ribonucleoprotein ------------------- Key: 3969 Medline: 10729338 Authors: Hong K;Mano I;Driscoll M Title: In vivo structure-function analyses of Caenorhabditis elegans MEC-4, a candidate mechanosensory ion channel subunit. Citation: Journal of Neuroscience 20: 2575-2588 2000 Type: ARTICLE Genes: mec-4 Abstract: Mechanosensory signaling mediated by mechanically gated ion channels constitutes the basis for the senses of touch and hearing and contributes fundamentally to the development and homeostasis of all organisms. Despite this profound importance in biology, little is known of the molecular identities or functional requirements of mechanically gated ion channels. We report a genetically based structure-function analysis of the candidate mechanotransducing channel subunit MEC-4, a core component of a touch-sensing complex in Caenorhabditis elegans and a member of the DEG/ENaC superfamily. We identify molecular lesions in 40 EMS-induced mec-4 alleles and further probe residue and domain function using site-directed approaches. Our analysis highlights residues and subdomains critical for MEC-4 activity and suggests possible roles of these in channel assembly and/or function. We describe a class of substitutions that disrupt normal channel activity in touch transduction but remain permissive for neurotoxic channel hyperactivation, and we show that expression of an N-terminal MEC-4 fragment interferes with in vivo channel function. These data advance working models for the MEC-4 mechanotransducing channel and identify residues, unique to MEC-4 or the MEC-4 degenerin subfamily, that might be specifically required for mechanotransducing function. Because many other substitutions identified by our study affect residues conserved within the DEG/ENaC channel superfamily, this work also provides a broad view of structure-function relations in the superfamily as a whole. Because the C. elegans genome encodes representatives of a large number of eukaryotic channel classes, we suggest that similar genetic-based structure-activity studies might be generally applied to generate insight into the in vivo function of diverse channel types. ------------------- Key: 3970 Medline: 10734099 Authors: Ding L;Candido EPM Title: HSP25, a small heat shock protein associated with dense bodies and M-lines of body wall muscle in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 275: 9510-9517 2000 Type: ARTICLE Genes: Abstract: HSP25, a previously uncharacterized member of the alpha-crystallin family of small heat shock proteins in Caenorhabditis elegans, has been examined using biochemical and immunological techniques. HSP25 is the second largest of 16 identifiable small heat shock proteins in the nematode and is expressed at all developmental stages under normal growth conditions. Recombinant HSP25 produced in Escherichia coil exists predominantly as small oligomers (dimers to tetramers) and possesses chaperone activity against citrate synthase in vitro. In C. elegans, HSP25 is localized to dense bodies and M-lines in body wall muscle, to the lining of the pharynx, and to the junctions between cells of the spermathecal wall. Affinity chromatography of nematode extracts on a column of immobilized HSP25 resulted in specific binding of vinculin and alpha-actinin but not actin, as revealed by Western blotting. These results suggest a role for HSP25 in the organization or maintenance of the myofilament lattice and adherens junctions in C. elegans. ------------------- Key: 3971 Medline: 20200452 Authors: Fei YJ;Romero MF;Krause M;Liu JC;Huang W;Ganapathy V;Leibach FH Title: A novel H+-coupled oligopeptide transporter (OPT3) from Caenorhabditis elegans with a predominant function as a H+ channel and an exclusive expression in neurons. Citation: Journal of Biological Chemistry 275: 9563-9571 2000 Type: ARTICLE Genes: Abstract: We have cloned and functionally characterized a novel, neuron-specific, H+-coupled oligopeptide transporter (OPT3) from Caenorhabditis elegans that functions predominantly as a H+ channel. The opt3 gene is similar to 4.4 kilobases long and consists of 13 exons. The cDNA codes for a protein of 701 amino acids with 11 putative transmembrane domains. When expressed in mammalian cells and in Xenopus laevis oocytes, OPT3 cDNA induces H+-coupled transport of the dipeptide glycylsarcosine, Electrophysiological studies of the transport function of OPT3 in Xenopus oocytes show that this transporter, although capable of mediating H+-coupled peptide transport, functions predominantly as a H+ channel. The H+ channel activity of OPT3 is similar to 3-4-fold greater than the H+/peptide cotransport activity as determined by measurements of H+ gradient-induced inward currents in the absence and presence of the dipeptide using the two-microelectrode voltage clamp technique, A downhill influx of H+ was accompanied by a large intracellular acidification as evidenced from the changes in intracellular pH using an ion-selective microelectrode. The H+ channel activity exhibits a K-0.5(H) of 1.0 mu M at a membrane potential of -50 mV. At the level of primary structure, OPT3 has moderate homology with OPT1 and OPT2, two other Hf-coupled oligopeptide transporters previously cloned from C. elegans, Expression studies using the opt3::gfp fusion constructs in transgenic C. elegans demonstrate that opt3 gene is exclusively expressed in neurons. OPT3 may play an important physiological role as a pH balancer in the maintenance of H+ homeostasis in C. ------------------- Key: 3972 Medline: 20200449 Authors: Su HP;Brugnera E;Van Criekinge W;Smits E;Hengartner M;Bogaert T;Ravichandran KS Title: Identification and characterization of a dimerization domain in CED-6, an adapter protein involved in engulfment of apoptotic cells. Citation: Journal of Biological Chemistry 275: 9542-9549 2000 Type: ARTICLE Genes: ced-6 Abstract: Phagocytosis of apoptotic cells is a key step in the completion of programmed cell death that occurs throughout life in multicellular organisms. The molecular events involved in clearance of apoptotic cells are just beginning to be elucidated. Recently, CED-6, an adapter protein involved in engulfment has been cloned in Caenorhabditis elegans and in humans. CED-6 is composed of a phosphotyrosine-binding (PTB) domain and a proline-rich C-terminal domain with no apparent catalytic domain. Since PTB domains, originally identified in Shc, mediate intracellular signaling downstream of cell surface receptors, CED-6 has also been proposed to mediate intracellular signals leading to engulfment. In this report, we demonstrate that CED-6 dimerizes through a leucine zipper domain that is immediately adjacent to the PTB domain, Several lines of evidence based on co-immunoprecipitation studies, yeast two-hybrid assays, and gel filtration studies suggest that CED-B exists as a dimer in vivo. Through mutational analyses, we show that the leucine zipper is necessary and sufficient for CED-6 dimerization and that this dimerization is conserved among C. elegans, rodent, and human CED-6 proteins. We propose that dimerization may have unique implications for ligand binding via CED-6 and its function during the phagocytosis ------------------- Key: 3973 Medline: 20156233 Authors: Togo SH;Maebuchi M;Yokota S;Bun-ya M;Kawahara A;Kamiryo T Title: Immunological detection of alkaline-diaminobenzidine-negative peroxisomes of the nematode Caenorhabditis elegans: Purification and unique pH optima of peroxisomal catalase. Citation: European Journal of Biochemistry 267: 1307-1312 2000 Type: ARTICLE Genes: Abstract: We purified catalase-2 of the nematode Caenorhabditis elegans and identified peroxisomes in this organism. The peroxisomes of C. elegans were not detectable by cytochemical staining using 3,3'-diaminobenzidine, a commonly used method depending on the peroxidase activity of peroxisomal catalase at pH 9 in which genuine peroxidases are inactive. The cDNA sequences of C. elegans predict two catalases very similar to each other throughout the molecule, except for the short C-terminal sequence; catalase-2 (500 residues long) carries a peroxisomal targeting signal 1-like sequence (Ser-His-Ile), whereas catalase-1 does not. The catalase purified to near homogeneity from the homogenate of C. elegans cells consisted of a subunit of 57 kDa and was specifically recognized by anti-(catalase-2) serum but not by anti-(catalase-1) serum. Subcellular fractionation and indirect immunoelectron microscopy of the nematode detected catalase-2 inside vesicles judged to be peroxisomes using morphological criteria. The purified enzyme (220 kDa) was tetrameric, similar to many catalases from various sources, but exhibited unique pH optima for catalase (pH 6) and peroxidase (pH 4) activities; the latter value is unusually low and explains why the peroxidase activity was undetectable using the standard alkaline diaminobenzidine-staining method. These results indicate that catalase-2 is peroxisomal and verify that it can be used as a marker enzyme for C. elegans peroxisomes. ------------------- Key: 3974 Medline: Authors: Brimecombe MJ;De Leij FAAM;Lynch JM Title: Effect of introduced Pseudomonas fluorescens strains on soil nematode and protozoan populations in the rhizosphere of wheat and pea. Citation: Microbial Ecology 38: 387-397 2000 Type: ARTICLE Genes: Abstract: Previous studies have shown that inoculation of pea seeds with Pseudomonas fluorescens strains F113lacZY or F113G22 increased mineralization of organic nitrogen in the rhizosphere. In contrast, inoculation of the same strains onto wheat seeds reduced mineralization of N from organic residues incorporated into soil. In the present study, we report on a likely explanation of this phenomenon, which appears to be governed by the effect of plant-microbe interactions on bacterial-feeding nematodes and protozoa. In soil microcosm tests, inoculation of pea seeds with Pseudomonas fluorescens strains F113lacZY or F113G22 resulted in an increase in the number of nematodes and protozoa in the rhizosphere as compared to noninoculated controls. This trend was repeated using a model sand system into which the bacteriophagous nematode Caenorhabditis elegans was introduced. It was subsequently found that non-inoculated germinating pea seeds exerted a nematicidal effect on C. elegans, which was remedied by inoculation with either strain F113lacZY or F113G22. This suggests that nematicidal compounds released by the germinating pea seeds were metabolized by the microbial inoculants before they affected nematode populations in the spermosphere or rhizosphere of pea. In contrast, inoculation of wheat plants resulted in significantly lower nematode populations in the rhizosphere, whereas protozoan numbers were unaffected. No nematicidal effects of inoculated or noninoculated wheat seeds could be found, suggesting that microfaunal populations were affected at a later stage during plant growth. Because of their key roles in accelerating the turnover of microbially immobilized N and organic matter, plants that support a larger microfaunal population are likely to benefit from a higher availability of inorganic nitrogen. Therefore, an understanding of plant-microbe interactions and their effects on soil microfaunal populations is essential in order to assess the effects of microbial inocula on plant mineral nutrition. ------------------- Key: 3975 Medline: Authors: Ali MY;Khan MLA;Shakir MA;Kobayashi KF;Nishiwaki K;Siddiqui SS Title: Expression and cDNA cloning of klp-12 gene encoding an ortholog of the chicken chromokinesin, mediating chromosome segregation in Caenorhabditis elegans. Citation: Journal of Biochemistry and Molecular Biology 33: 138-147 2000 Type: ARTICLE Genes: klp-1 klp-12 klp-15 klp-16 klp-17 Abstract: In eukaryotes, chromosomes undergo a series of complex and coordinated movements during cell division. The kinesin motor proteins, such as the chicken Chromokinesin, are known to bind DNA and transport chromosomes on spindle microtubles. We previously cloned a family of retrograde C-terminus kinesins in Caenorhabditis elegans that mediate chromosomal movement during embryonic development. Here we report the cloning of a C. elegans klp-12 cDNA, encoding an ortholog of chicken Chromokinesin and mouse KIF4. The KLP-12 protein contains 1609 amino acid and harbors two leucine zipper motifs. The in situ RNA hybridization in embryonic stages shows that the klp-12 gene is expressed during the entire embryonic development. The RNA interference assay reveals that, similar to the role of Chromokinesin, klp-12 functions in chromosome segregation. These results support the notion that during mitosis both types, the anterograde N-terminus kinesins such as KLP-12 and the retrograde C- terminus kinesins, such as KLP-3, KLP-15, KLP-16, and KLP-17, may coordinate chromosome assembly at the metaphase plate and chromosomal segregation towards the spindle poles in C. elegans. ------------------- Key: 3976 Medline: 20226625 Authors: Li ZH;Liu DP;Wang J;Guo ZC;Yin WX;Liang CC Title: Inversion and transposition of Tc1 transposon of C. elegans in mammalian cells. Citation: Somatic Cell and Molecular Genetics 24: 363-369 1998 Type: ARTICLE Genes: Abstract: Tc1/mariner transposons are widespread in the eukaryotes. In vitro transposition test indicated that the transposase is the only protein that is needed in transpositions. It was shown later that the reconstructed Tc1-like transposon, "sleeping beauty" in fish, and the Tc1 transposon in C. elegans jumps in human cells. This discovery indicates that the Tc1/mariner transposon may be engineered as a somatic gene therapy vector if coupled with an efficient gene delivery system. We introduced the Tc1 transposon from C. elegans into different mammalian cell lines and detected the transposition events, indicating that Tc1 transposon functions in different mammalian cells. Interestingly, a high inversion frequency of the transposon was also detected, suggesting that this type of transposon may add variations to host genome when it is horizontally transferred into a new species. ------------------- Key: 3977 Medline: 20337975 Authors: Swoboda P;Adler HT;Thomas JH Title: The RFX-type transcription factor DAF-19 regulates sensory neuron cilium formation in C. elegans. Citation: Molecular Cell 5: 411-421 2000 Type: ARTICLE Genes: ceh-23 che-2 che-3 che-11 daf-10 daf-11 daf-19 daf-21 egl-2 egl-28 gcy-5 gcy-8 gcy-32 nrf-6 odr-3 odr-4 odr-7 odr-10 osm-1 osm-3 osm-6 osm-9 srb-6 str-1 tub-1 unc-54 Abstract: Many types of sensory neurons contain modified cilia where sensory signal transduction occurs. We report that the C. elegans gene daf-le encodes an RFX-type transcription factor that is expressed specifically in all ciliated sensory neurons. Loss of daf-19 function causes the absence of cilia, resulting in severe sensory defects. Several genes that function in all ciliated sensory neurons have an RFX target site in their promoters and require daf-le function. Several other genes that function in subsets of ciliated sensory neurons do not have an RFX target site and are not daf-19 dependent. These results suggest that expression of the shared components of sensory cilia is activated by daf-19, whereas cell-type-specific expression occurs independently of daf-19. ------------------- Key: 3979 Medline: 20217227 Authors: Kim S;Wadsworth WG Title: Positioning of longitudinal nerves in C. elegans by Citation: Science 288: 150-154 2000 Type: ARTICLE Genes: nid-1 unc-5 unc-6 unc-40 Abstract: Basement membranes can help determine pathways of migrating axons. Although members of the nidogen (entactin) protein family are structural components of basement membranes, we find that nidogen is not required for basement membrane assembly in the nematode Caenorhabditis elegans. Nidogen is Localized to body wall basement membranes and is required to direct longitudinal nerves dorsoventrally and to direct axons at the midlines. By examining migration of a single axon in vivo, we show that nidogen is required for the axon to switch from circumferential to Longitudinal migration. Specialized basement membranes may thus regulate nerve position. ------------------- Key: 3980 Medline: 20234759 Authors: L'Etoile ND;Bargmann CI Title: Olfaction and odor discrimination are mediated by the C. elegans guanylyl cyclase ODR-1. Citation: Neuron 25: 575-586 2000 Type: ARTICLE Genes: daf-11 gpa-2 odr-1 odr-3 osm-9 tax-2 tax-4 Abstract: Animals in complex environments must discriminate between salient and uninformative sensory cues. Caenorhabditis elegans uses one pair of olfactory neurons called AWC to sense many different odorants, yet the animal can distinguish each odorant from the others in discrimination assays. We demonstrate that the transmembrane guanylyl cyclase ODR-1 is essential for responses to all AWC-sensed odorants. ODR-1 appears to be a shared signaling component downstream of odorant receptors. Overexpression of ODR-1 protein indicates that ODR-1 can influence odor discrimination and adaptation as well as olfaction. Adaptation to one odorant, butanone, is disrupted by ODR-1 overexpression. Olfactory discrimination is also disrupted by ODR-1 overexpression, probably by overproduction of the shared second messenger cGMP. We propose that AWC odorant signaling pathways are insulated to permit odor discrimination. ------------------- Key: 3981 Medline: 20234760 Authors: Cassata G;Kagoshima H;Andachi Y;Kohara Y;Durrenberger MB;Hall DH;Burglin TR Title: The LIM homeobox gene ceh-14 confers thermosensory function to the AFD neurons in Caenorhabditis elegans. Citation: Neuron 25: 587-597 2000 Type: ARTICLE Genes: ceh-14 gcy-8 lin-11 tax-4 ttx-1 ttx-3 uDf1 Abstract: In Caenorhabditis elegans three pairs of neurons, AFD, AIY, and AIZ, play a key role in thermosensation. The LIM homeobox gene ceh-14 is expressed in the AFD thermosensory neurons. ceh-14 mutant animals display athermotactic behaviors, although the neurons are still present and differentiated. Two other LIM homeobox genes, ttx-3 and lin-11, function in the two interneurons AIY and AIZ, respectively. Thus, the three key thermosensory neurons are specified by three different LIM homeobox genes. ceh-14 ttx-3 lin-11 triple mutant animals have a basic cryophilic thermotaxis behavior indicative of a second thermotaxis pathway. Misexpression of ceh-14 in chemosensory neurons can restore thermotactic behavior without impairing the chemosensory function. Thus, ceh-14 confers thermosensory function to neurons. ------------------- Key: 3982 Medline: Authors: Das P;Maduzia LL;Padgett RW Title: Genetic approaches to TGF Beta signaling pathways. Citation: Cytokine & Growth Factor Reviews 10: 179-186 1999 Type: REVIEW Genes: daf-1 daf-4 Abstract: In this review, we provide a summary of the genetic analysis of TGFBeta signal transduction, as well as its role in various human diseases and mouse models. We also use discoveries in the TGFBeta pathway as an example to highlight some of the techniques used in the invertebrate world of C. elegans and Drosophila to further our understanding of this, and other, signaling systems. The roles of such techniques in elucidating diverse pathways, as well as pathways of human disease genes, will become more important as the information from the genome projects increases and as the development of genetics tools to analyze them becomes more powerful. Given the conservation of signaling mechanisms, there will be increasing synergy between studies in invertebrates and vertebrates in future years for solving different cellular pathways. ------------------- Key: 3983 Medline: 10882128 Authors: Stanfield GM;Horvitz HR Title: The ced-8 gene controls the timing of programmed cell deaths in C. elegans. Citation: Molecular Cell 5: 423-433 2000 Type: ARTICLE Genes: ced-3 ced-4 ced-5 ced-7 ced-8 ced-9 nuc-1 yDf2 Abstract: Loss-of-function mutations in the gene ced-8 lead to the late appearance of cell corpses during embryonic development in C. elegans. ced-8 functions downstream of or in parallel to the regulatory cell death gene ced-9 and may function as a cell death effector downstream of the caspase encoded by the programmed cell death killer gene ced-3. In ced-8 mutants, embryonic programmed cell death probably initiates normally but proceeds slowly, ced-8 encodes a transmembrane protein that appears to be localized to the plasma membrane. The CED-8 protein is similar to human XK, a putative membrane transport protein implicated in McLeod Syndrome, a form of hereditary neuroacanthocytosis. ------------------- Key: 3984 Medline: 20337977 Authors: Gartner A;Milstein S;Ahmed S;Hodgkin J;Hengartner MO Title: A conserved checkpoint pathway mediates DNA damage-induced apoptosis and cell cycle arrest in C. elegans. Citation: Molecular Cell 5: 435-443 2000 Type: ARTICLE Genes: ced-3 ced-4 ced-9 egl-1 him-7 mrt-2 rad-5 rad-51 spo-11 Abstract: To maintain genomic stability following DNA damage, multicellular organisms activate checkpoints that induce cell cycle arrest or apoptosis. Here we show that genotoxic stress blocks cell proliferation and induces apoptosis of germ cells in the nematode C. elegans. Accumulation of recombination intermediates similarly leads to the demise of affected cells. Checkpoint-induced apoptosis is mediated by the core apoptotic machinery (CED-S/CED-4/CED-3) but is genetically distinct from somatic cell death and physiological germ cell death. Mutations in three genes-mrt-2, which encodes the C. elegans homolog of the S. pombe rad1 checkpoint gene, rad-5, and him-7-block both DNA damage-induced apoptosis and cell proliferation arrest. Our results implicate rad1 homologs in DNA damage-induced apoptosis in animals. ------------------- Key: 3985 Medline: 20239013 Authors: Johnsen RC;Jones SJM;Rose AM Title: Mutational accessibility of essential genes on chromosome I (left) in Caenorhabditis elegans. Citation: Molecular & General Genetics 263: 239-252 2000 Type: ARTICLE Genes: let-121 let-122 let-123 let-124 let-126 let-128 let-129 let-546 let-547 let-572 let-130 let-131 let-132 let-133 let-134 let-362 let-548 let-571 let-135 let-136 let-137 let-138 let-139 let-140 let-141 let-142 let-143 let-144 let-549 let-573 lin-6 let-145 let-146 let-147 let-148 let-149 let-150 let-151 let-152 let-153 let-154 let-155 let-156 let-157 let-158 let-159 let-160 let-161 let-162 let-537 let-360 let-365 let-163 let-164 let-357 let-368 let-372 let-586 let-597 let-615 let-518 let-585 let-369 let-515 let-517 let-550 let-574 let-575 let-576 let-577 let-578 let-579 let-580 let-581 let-582 let-583 let-584 let-587 let-356 let-366 let-373 let-501 let-509 let-510 let-511 let-516 let-589 let-593 let-600 let-353 let-503 let-504 let-505 let-506 let-507 let-354 let-374 let-502 let-588 let-590 let-508 let-351 let-375 let-114 let-626 let-627 let-609 let-619 let-624 let-625 let-628 let-629 let-630 let-631 let-632 let-633 let-634 let-636 let-637 let-641 let-359 let-364 let-635 let-638 let-639 let-640 let-125 let-526 let-642 let-643 let-644 let-361 let-371 let-595 let-645 let-646 let-647 let-648 let-363 let-519 let-613 let-649 let-650 let-101 let-102 let-103 let-104 let-105 let-106 let-107 let-108 let-109 let-110 let-352 let-596 let-590 let-612 let-618 let-111 let-594 let-598 let-112 let-113 let-370 let-355 let-622 let-623 let-127 let-367 let-592 let-614 let-620 let-621 let-531 let-532 let-530 let-395 let-376 let-117 let-378 let-393 let-513 let-379 let-377 let-388 let-514 let-603 let-116 let-119 let-384 let-391 let-512 let-602 let-115 let-396 let-611 let-381 let-601 let-380 let-387 let-606 let-608 let-610 let-386 let-604 let-382 let-390 let-607 let-118 let-392 let-383 let-120 let-385 let-394 let-399 let-521 let-543 let-389 let-400 let-520 let-397 let-398 let-528 let-529 let-534 let-544 let-545 let-605 let-522 let-523 let-525 let-524 let-527 bli-4 lin-6 him-1 unc-37 sem-4 hDp3 hDp12 hDp13 hDp15 hDp16 hDp17 hDp18 hDp19 hDp21 hDp22 hDp24 hDp25 hDp29 hDp30 hDp31 hDp33 hDp35 hDp37 hDp41 hDp48 hDp54 hDp58 hDp62 hDp72 hDp76 hDp78 sDp2 hDf6 hDf7 hDf8 hDf10 qDf3 sDf4 tDf3 hDf24 hDf25 hDf26 hDf27 hDf28 hDf29 Abstract: We have analyzed a region of approximately 5.4 million base pairs for mutations, which under standard laboratory conditions result in developmental arrest, sterility, or maternal-effect lethality in Caenorhabditis elegans. Lethal mutations were isolated, maintained, and genetically manipulated as homozygotes using sDp2 - a duplication of the left half of chromosome I. All of the lethals and rearrangements used in this analysis were balanced by sDp2. Relatively low doses of mutagen, (approximately 15 mM ethylmethane sulfate; EMS), were used so as to limit the occurrence of second-site mutations, thus increasing the probability of recovering single nucleotide substitutions. Treatment of over 32,400 marked chromosomes resulted in 486 analyzed mutations. In this paper, we add 133 previously unidentified let genes, isolated in the EMS screens, and one let gene identified by a gamma-ray induced mutation, to our collection of 103 essential genes. We also recovered lethal alleles of genes for which visible mutants already existed. In total, eight deficiencies and alleles of 237 essential genes were identified. Eighty-nine of the previously unidentified let genes are represented by more than one lethal allele. Statistical analysis indicates a minimum estimate of 400 essential genes in the region of chromosome I balanced by sDp2. This region occupies approximately half of chromosome I, and contains over 1135 protein-coding genes predicted from the genomic sequence data. Thus, approximately one-third of the predicted genes are estimated to be essential. Of these approximately 60% are represented by lethal alleles. Less than 2% of the lethal-bearing strains recovered in our analysis, including the eight genetically definable deficiencies, carried more than one lethal, mutation. Several screens were used to recover mutations for this analysis. Because all the mutations were isolated using the same balancer, under similar screening conditions, it was possible to compare intervals within the sDp2 region with each other. The fraction of essential genes that present relatively large targets for EMS was highest within the central cluster ------------------- Key: 3986 Medline: 20241456 Authors: Peixoto CA;Alves LC;de Melo JV;de Souza W Title: Ultrastructural analyses of the Caenorhabditis elegans sqt-1(sc13) left roller mutant. Citation: Journal of Parasitology 86: 269-274 2000 Type: ARTICLE Genes: rol-6 sqt-1 Abstract: The sqt-1 gene is 1 of the several loci in Caenorhabditis elegans that primarily affects organismal morphology. Certain mutations in the sqt-1 gene can produce left roller animals, i.e., they rotate around their long axis and move in circular paths. We describe the morphological alterations seen in the cuticle of the left roller sqt-1(sc13). Deep-etched replica analyses showed that the fibrous layer is composed of a unique strand of parallel fibers, instead of the 2 meeting at an angle of 60 degrees as observed in the wild-type strain. In addition, honeycomb elements, fibers organized in a pentagonal fashion above the fibrous layer; completely fill the intermediate layer that is empty spaces in the wild type. These morphological alterations are likely to be involved in generating the helical twist of the sqt-1(sc13) left roller mutant. ------------------- Key: 3987 Medline: 20209441 Authors: Keiper BD;Lamphear BJ;Deshpande AM;Jankowska-Anyszka M;Aamodt EJ;Blumenthal T;Rhoads RE Title: Functional characterization of five eIF4E isoforms in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 275: 10590-10596 2000 Type: ARTICLE Genes: ife-1 ife-2 ife-3 ife-4 ife-5 Abstract: Recognition of the 5'-cap structure of mRNA by eIF4E is a critical step in the recruitment of most mRNAs to the ribosome. In Caenorhabditis elegans, similar to 70% of mRNAs contain an unusual 2,2,7-trimethylguanosine cap structure as a result of trans-splicing onto the 5' end of the pre-mRNA, The characterization of three eIF4E isoforms in C. elegans (IFE-1, IFE-2, and IFE-3) was reported previously. The present study describes two more eIF4E isoforms expressed in C. elegans, IFE-4 and IFE-5. We analyzed the requirement of each isoform for viability by RNA interference. IFE-3, the most closely related to mammalian eIF4E-1, binds only 7-methylguanosine caps and is essential for viability. In contrast, three closely related isoforms (IFE-1, IFE-2, and IFE-8) bind 2,2,7-trimethylguanosine caps and are partially redundant, but at least one functional isoform is required for viability. IFE-4, which binds only 7-methylguanosine caps, is most closely related to an unusual eIF4E isoform found in plants (nCBP) and mammals (4E-HP) and is not essential for viability in any combination of IFE knockout. ife-2 ife-3 ife-4, and ife-5 mRNAs are themselves trans-spliced to SL1 spliced leaders. ife-1 mRNA is trans-spliced to an SL2 leader, indicating that its gene resides in a ------------------- Key: 3988 Medline: 20211404 Authors: Longman D;Johnstone IL;Caceres JF Title: Functional characterization of SR and SR-related genes in Caenorhabditis elegans. Citation: EMBO Journal 19: 1625-1637 2000 Type: REVIEW Genes: ama-1 cpr-5 hlh-1 hrp-1 mog-5 ptb-1 srr-1 rsk-1 rsp-1 rsp-2 rsp-3 rsp-4 rsp-5 rsp-6 rsp-7 rsp-8 rsr-1 tsr-1 uaf-1 uaf-2 unc-52 Abstract: The SR proteins constitute a family of nuclear phosphoproteins, which are required for constitutive splicing and also influence alternative splicing regulation. Initially, it was suggested that SR proteins were functionally redundant in constitutive splicing. However, differences have been observed in alternative splicing regulation, suggesting unique functions for individual SR proteins. Homology searches of the Caenorhabditis elegans genome identified seven genes encoding putative orthologues of the human factors SF2/ASF, SRp20, SC35, SRp40, SRp75 and p54, and also several SR-related genes, To address the issue of functional redundancy, we used dsRNA interference (RNAi) to inhibit specific SR protein function during C. elegans development. RNAi with CeSF2/ASF caused late embryonic lethality, suggesting that this gene has an essential function during C. elegans development, RNAi with other SR genes resulted in no obvious phenotype, which is indicative of gene redundancy. Simultaneous interference of two or more SR proteins in certain combinations caused lethality or other developmental defects. RNAi with CeSRPK, an SR protein kinase, resulted in early embryonic lethality, suggesting an essential role for SR protein phosphorylation during ------------------- Key: 3989 Medline: 20214829 Authors: Furuta T;Tuck S;Kirchner J;Koch B;Auty R;Kitagawa R;Rose AM;Greenstein D Title: EMB-30: An APC4 homologue required for metaphase-to-anaphase transitions during meiosis and mitosis in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 11: 1401-1419 2000 Type: ARTICLE Genes: emb-30 fog-2 fog-3 let-23 mdf-1 tnDf2 Abstract: Here we show that emb-30 is required for metaphase-to-anaphase transitions during meiosis and mitosis in Caenorhabditis elegans. Germline-specific emb-30 mutant alleles block the meiotic divisions. Mutant oocytes, fertilized by wild-type sperm, set up a meiotic spindle but do not progress to anaphase I. As a result, polar bodies are not produced, pronuclei fail to form, and cytokinesis does not occur. Severe-reduction-of-function emb-30 alleles (class I alleles) result in zygotic sterility and lead to germline and somatic defects that are consistent with an essential role in promoting the metaphase-to-anaphase transition during mitosis. Analysis of the vulval cell lineages in these emb-30(class I) mutant animals suggests that mitosis is lengthened and eventually arrested when maternally contributed emb-30 becomes limiting. By further reducing maternal emb-30 function contributed to class I mutant animals, we show that emb-30 is required for the metaphase-to-anaphase transition in many, if not all, cells. Metaphase arrest in emb-30 mutants is not due to activation of the spindle assembly checkpoint but rather reflects an essential emb-30 requirement for M-phase progression. A reduction in emb-30 activity can suppress the lethality and sterility caused by a null mutation in mdf-l, a component of the spindle assembly checkpoint machinery. This result suggests that delaying anaphase onset can bypass the spindle checkpoint requirement for normal development. Positional cloning established that emb-30 encodes the likely C. elegans orthologue of APC4/Lid1, a component of the anaphase-promoting complex/cyclosome, required for the metaphase-to-anaphase transition. Thus, the anaphase-promoting complex/cyclosome is likely to be required for all metaphase-to-anaphase transitions in a multicellular organism. ------------------- Key: 3990 Medline: 20284888 Authors: Hubbard EJA;Greenstein D Title: The Caenorhabditis elegans gonad: A test tube for cell and developmental biology. Citation: Developmental Dynamics 218: 2-22 2000 Type: REVIEW Genes: cdh-1 ced-2 ced-3 ced-4 ced-5 ced-9 ceh-1 cog-2 daf-12 egl-1 egl-38 ego-1 emb-30 emo-1 fbf-1 fbf-2 fem-3 gld-1 gld-2 glh-1 glh-2 glp-1 glp-3 glp-4 gon-1 gon-2 ina-1 itr-1 lag-1 lag-2 let-23 let-60 lfe-1 lfe-2 lim-7 lin-3 lin-11 lin-12 lin-36 mek-2 mel-11 mes-2 mes-3 mes-4 mes-6 mex-1 mig-8 mpk-1 mup-2 ncc-1 nos-1 nos-2 pgl-1 pie-1 pos-1 rme-1 sel-1 sel-5 sel-9 sel-10 sup-17 sur-1 unc-5 unc-6 unc-40 unc-73 vab-3 Abstract: Sexual reproduction of multicellular organisms depends critically on the coordinate development of the germ line and somatic gonad, a process known as gonadogenesis. Together these tissues ensure the formation of functional gametes and, in the female of many species, create a context for production and further development of the zygote. Since the future of the species hangs in the balance, it is not surprising that gonadogenesis is a complex process involving conserved and multi-faceted developmental mechanisms. Genetic, anatomical, cell biological, and molecular experiments have established the nematode Caenorhabditis elegans as a paradigm for studying gonadogenesis. Furthermore, these studies demonstrate the utility of C. elegans gonadogenesis for exploring broad issues in cell and developmental biology, such as cell fate specification, morphogenesis, cell signaling, cell cycle control, and programmed cell death. The synergy of molecular genetics and cell biology conducted at single-cell resolution in real time permits an extraordinary depth of analysis in this organism. In this review, we first describe the embryonic and post-embryonic development and morphology of the C. elegans gonad. Next we recount seminal experiments that established the field, highlight recent results that provide insight into conserved developmental mechanisms, and present future ------------------- Key: 3991 Medline: 20229698 Authors: Hoier EF;Mohler WA;Kim SK;Hajnal A Title: The Caenorhabditis elegans APC-related gene apr-1 is required for epithelial cell migration and Hox gene expression. Citation: Genes & Development 14: 874-886 2000 Type: ARTICLE Genes: apr-1 bar-1 ceh-13 hmp-1 hmp-2 hmr-1 lin-39 wrm-1 Abstract: Inactivation of the Caenorhabditis elegans APC-related gene (apr-1) has pointed at two separate functions of apr-1. First, apr-1 is required for the migration of epithelial cells during morphogenesis of the embryo. In this process, APR-1 may act in a Cadherin/alpha-Catenin/beta-Catenin complex as a component of adherens junctions. Second, apr-1 is required for Hox gene expression, most likely by positively regulating the activity of the Wingless signaling pathway. During embryogenesis, apr-1 is required for the expression of ceh-13 labial in anterior seam and muscle cells and during larval development, apr-1 is necessary for the expression of lin-39 deformed in the vulval precursor cells. Thus, APR-1 may positively regulate the activity of the beta-Catenin/Armadillo-related proteins HMP-2 in migrating epithelial cells and BAR-1 in the vulval precursor cells. ------------------- Key: 3992 Medline: 20253095 Authors: Birnby DA;Link EL;Vowels JJ;Tian H;Colacurcio PL;Thomas JH Title: A transmembrane guanylyl cyclase (DAF-11) and Hsp90 (DAF-21) regulate a common set of chemosensory behaviors in Caenorhabditis elegans. Citation: Genetics 155: 85-104 2000 Type: ARTICLE Genes: daf-1 daf-2 daf-4 daf-7 daf-8 daf-11 daf-12 daf-14 daf-21 daf-28 gcy-1 gcy-2 gcy-3 gcy-4 gcy-5 gcy-6 gcy-7 gcy-9 gcy-10 gcy-11 gcy-12 gcy-13 gcy-14 tax-4 itDf2 nDf42 ctDp11 Abstract: Caenorhabditis elegans daf-11 and daf-21 mutants share defects in specific chemosensory responses mediated by several classes of sensory neurons, indicating that these two genes have closely related functions in an assortment of chemosensory pathways. We report that daf-11 encodes one of a large family of C. elegans transmembrane guanylyl cyclases (TM-GCs). The cyclic GMP analogue 8-bromo-cCMP rescues a sensory defect in both daf-11 and daf-21 mutants, supporting a role for DAF-11 guanylyl cyclase activity in this process and further suggesting that daf-21 acts at a similar step, daf-11:gfp fusions are expressed in five identified pairs of chemosensory neurons in a pattern consistent with most daf-11 mutant phenotypes. We also show that daf-21 encodes the heat-shock protein 90 (Hsp90), a chaperone with numerous specific protein targets. We show that the viable chemosensory-deficient daf-21 mutation is an unusual allele resulting from a single amino acid substitution and that the daf-21 null phenotype is early larval lethality. These results demonstrate that cGMP is a prominent second messenger in C. elegans chemosensory transduction and suggest a previously unknown role for Hsp90 in regulating cGMP levels. ------------------- Key: 3993 Medline: 20253096 Authors: Haag ES;Kimble J Title: Regulatory elements required for development of Caenorhabditis elegans hermaphrodites are conserved in the tra-2 homologue of C. remanie, a male/female sister Citation: Genetics 155: 105-116 2000 Type: ARTICLE Genes: ppp-1 tra-2 Abstract: The Caenorhabditis elegans hermaphrodite is essentially a female that produces sperm. In C. elegans, tra-2 promotes female fates and must be repressed to achieve hermaphrodite spermatogenesis. In an effort to learn how mating systems evolve, we have cloned tra-2 from C. remanei, the closest gonochoristic relative of C. elegans. We found its structure to be similar to that of Ce-tra-2 but its sequence to be divergent. RNA interference demonstrates that Cr-tra-2 promotes female fates. Two sites of tra-2 regulation are required for the onset of hermaphrodite spermatogenesis in C. elegans. One, the MX legion of TRA-2, is as well conserved in C. remanei as it is in C. briggsae (another male/hermaphrodite species), suggesting that this control is not unique to hermaphrodites. Another, the DRE/TGE element of the tra-2 3' UTR, was not detected by sequence analysis. However, gel-shift assays demonstrate that a factor in C. remanei can bind specifically to the: Cr-tra-2 3' UTR, suggesting that this translational control is also conserved. We propose that, both controls are general and do not constitute a novel "switch" that enables sexual mosaicism in hermaphrodites. However, subtle quantitative or qualitative differences in their employment may underlie differences in mating system seen in ------------------- Key: 3994 Medline: 20266296 Authors: Winter AD;Page AP Title: Prolyl 4-hydroxylase is an essential procollagen-modifying enzyme required for exoskeleton formation and the maintenance of body shape in the nematode Caenorhabditis elegans. Citation: Molecular and Cellular Biology 20: 4084-4093 2000 Type: ARTICLE Genes: dpy-7 dpy-10 dpy-18 phy-1 phy-2 pdi-2 Abstract: The multienzyme complex prolyl 4-hydroxylase catalyzes the hydroxylation of proline residues and acts as a chaperone during collagen synthesis in multicellular organisms. The beta subunit of this complex is identical to protein disulfide isomerase (PDI). The free-living nematode Caenorhabditis elegans is encased in a collagenous exoskeleton and represents an excellent model for the study of collagen biosynthesis and extracellular matrix formation. In this study, we examined prolyl 4-hydroxylase alpha-subunit (PHY; EC 1.14.11.2)- and beta-subunit (PDI; EC 5.3.4.1)-encoding genes with respect to their role in collagen modification and formation of the C. elegans exoskeleton. We identified genes encoding two PHYs and a single associated PDI and showed that all three are expressed in collagen-synthesizing ectodermal cells at times of maximal collagen synthesis. Disruption of the pdi gene via RNA interference resulted in embryonic lethality, Similarly, the combined phy genes are required for embryonic development. Interference with phy-1 resulted in a morphologically dumpy phenotype, which we determined to be identical to the uncharacterized dpy-18 locus. Two dpy-18 mutant strains were shown to have null alleles for phy-1 and to have a reduced hydroxyproline content in their exoskeleton collagens. This study demonstrates in vivo that this enzyme complex plays a central role in extracellular matrix formation and is essential for normal metazoan development. ------------------- Key: 3995 Medline: 20304676 Authors: Gomes AV;Wahlestedt C Title: Altered behavior following RNA interference knockdown of a C. elegans G-protein coupled receptor by ingested double stranded RNA. Citation: European Journal of Pharmacology 397: R3-R5 2000 Type: ARTICLE Genes: npr-1 unc-22 Abstract: Using a systematic and continuous delivery method based on feeding on a particular strain of transformed Escherichia coli to induce double stranded RNA-mediated interference, we targeted the product of the npr-1 gene, a putative Caenorhabditis elegans homologue of a neuropeptide Y receptor, a G-protein coupled receptor. We were able to reproduce the social behavior observed for the naturally occurring nrp-1 mutant when wild type N2 Bristol eggs developed in a lawn of bacteria producing double stranded RNA for npr-1. This facile approach may also be useful when studying the function of other worm G-protein coupled receptors. ------------------- Key: 3996 Medline: 20226060 Authors: Shoichet SA;Malik TH;Rothman JH;Shivdasani RA Title: Action of the Caenorhabditis elegans GATA factor END-1 in Xenopus suggests that similar mechanisms initiate endoderm development in ecdysozoa and vertebrates. Citation: Proceedings of the National Academy of Sciences USA 97: 4076-4081 2000 Type: ARTICLE Genes: end-1 Abstract: In ecdysozoan protostomes, including arthropods and nematodes, transcription factors of the GATA family specify the endoderm: Drosophila dGATAb (ABF/Serpent) and Caenorhabditis elegans END-1 play important roles in generating this primary germ layer. end-1 is the earliest expressed endoderm-specific gene known in C. elegans and appears to initiate the program of gene expression required for endoderm differentiation, including a cascade of GATA factors required for development and maintenance of the intestine. Among vertebrate GATA proteins, the GATA-4/5/6 subfamily regulates aspects of late endoderm development, but a role for GATA factors in establishing the endoderm is unknown. We show here that END-1 binds to the canonical target DNA sequence WGATAR with specificity similar to that of vertebrate GATA-1 and GATA-4, and that it functions as a transcriptional activator. We exploited this activity of END-1 to demonstrate that establishment of the vertebrate endoderm, like that of invertebrate species, also appears to involve GATA transcriptional activity. Like the known vertebrate endoderm regulators Mixer and Sox17, END-1 is a potent activator of endoderm differentiation in isolated Xenopus ectoderm. Moreover, a dominant inhibitory GATA-binding fusion protein abrogates endoderm differentiation in intact embryos. By examining these effects in conjunction with those of Mixer- and Sox17 beta-activating and dominant inhibitory constructs, we further establish the likely relationships between GATA activity and these regulators in early development of the vertebrate endoderm. These results suggest that GATA factors may function sequentially to regulate endoderm differentiation in both protostomes and deuterostomes. ------------------- Key: 3997 Medline: 10850666 Authors: Kim S;Lee J;Ahnn J Title: Analysis of the flt-1 gene encoding a ECM protein, flectin, in Caenorhabditis elegans. Citation: Molecules & Cells 10: 226-231 2000 Type: ARTICLE Genes: flt-1 Abstract: Flectin is a new type of extracellular matrix protein and its function was suggested to provide a microenvironment of great elasticity. The C. elegans genome database revealed the presence of a flectin homologue, flt-1, which shows approximately 40% similarity (20% identity) to chick flectin, Here me propose a new gene structure for the flt-1 based on our experiments and the partial cDNA clones obtained from Y. Kohara and further suggest that the previous gene prediction is incorrect. FLT-1 is shown to be expressed in various neurons, hypodermal cells, distal tip cells and vulva epithelial cells, Immunostaining results with anti-FLT-1 antibody, further confirm the FLT-1 expression in vulva epithelial cells. The lipophilic dye, DiI, was used to identify the head neurons expressing GFP and results indicated that none of the head neurons expressing GFP are the 6 chemosensory neurons. In order to determine the function of flt-1 gene, RNA-mediated interference (RNAi) experiments were conducted. ------------------- Key: 3998 Medline: 20211483 Authors: Gems D;Riddle DL Title: Genetic, behavioral and environmental determinants of male longevity in Caenorhabditis elegans. Citation: Genetics 154: 1597-1610 2000 Type: ARTICLE Genes: daf-2 daf-16 fer-15 fog-2 lon-2 unc-4 unc-6 unc-10 unc-13 unc-24 unc-29 unc-32 unc-35 unc-64 unc-76 Abstract: Males of the nematode Caenorhabditis elegans are shorter lived than hermaphrodites when maintained in single-sex groups. We observed that groups of young males form clumps and that solitary males live longer, indicating that male-male interactions reduce life span. By contrast, grouped or isolated hermaphrodites exhibited the same longevity. In one wild isolate of C. elegans, AB2, there was evidence of copulation between males. Nine uncoordinated (unc) mutations were used to block clumping behavior. These mutations had little effect on hermaphrodite life span in most cases, yet many increased male longevity even beyond that of solitary wild-type males. In one case, the neuronal function mutant unc64(e246), hermaphrodite life span was also increased by up to 60%. The longevity of unc-4(e120), unc-13(e51), and unc-32(e189) males exceeded that of hermaphrodites by 70-120%. This difference appears to reflect a difference in sex-specific life span potential revealed in the absence of male behavior that is detrimental to survival. The greater longevity of males appears not to be affected by daf-2, but is influenced by daf-16. In the absence of male-male interactions, median (but not maximum) male life span was variable. This variability was reduced when dead bacteria were used as food. Maintenance on dead bacteria extended ------------------- Key: 3999 Medline: 20239641 Authors: Peyou-Ndi MM;Watts JL;Browse J Title: Identification and characterization of an animal Delta(12) fatty acid desaturase gene by heterologous expression in Saccharomyces cerevisiae. Citation: Archives of Biochemistry & Biophysics 376: 399-408 2000 Type: ARTICLE Genes: fat-1 fat-2 fat-3 fat-4 Abstract: We have cloned a Caenorhabditis elegans cDNA encoding a Delta 12 fatty acid desaturase and demonstrated its activity by heterologous expression in Saccharomyces cerevisiae. The predicted protein is highly homologous both to the cloned plant genes with similar function and to the published sequence of the C. elegans omega-3 fatty acid desaturase. In addition, it conforms to the structural constraints expected of a membrane-bound fatty acid desaturase including the canonical histidine-rich regions. This is the first report of a cloned animal Delta(12) desaturase gene. Expression of this cDNA in yeast resulted in the accumulation of 16:2 and 18:2 (linoleic) acids. The increase of membrane fluidity brought about by this change in unsaturation was measured. The production of polyunsaturated fatty acids in yeast cells and the concomitant increase in membrane fluidity was correlated with a modest increase in growth rate at low temperature and with increased resistance to ethanol and oxidative ------------------- Key: 4052 Medline: Authors: Wood WB and the Community of C. elegans Researchers (eds) Title: The Nematode Caenorhabditis elegans. Citation: Cold Spring Harbor Laboratory Press. : 1-667 1988 Type: BOOK Genes: Abstract: ------------------- Key: 4055 Medline: Authors: Zuckerman BM (ed) Title: "Nematodes as biological models, Volume 1: Behavioral and Developmental Models." Citation: Academic Press, NY 1: 1-312 1980 Type: BOOK Genes: Abstract: ------------------- Key: 4056 Medline: Authors: Zuckerman BM (ed) Title: "Nematodes as biological models, Volume 2: Aging and other model systems." Citation: Academic Press, NY 2: 1-306 1980 Type: BOOK Genes: Abstract: ------------------- Key: 4068 Medline: Authors: Wilkins AS Title: Genetic Analysis of Animal Development, 2nd edition. Citation: Wiley-Liss, Inc., NY : 1-546 1992 Type: BOOK Genes: Abstract: ------------------- Key: 4069 Medline: Authors: Epstein HF;Shakes DC (eds) Title: Caenorhabditis elegans: Modern Biological Analysis of an Organism. Citation: Methods in Cell Biology. Academic Press, Inc. San Diego 48: 1-654 1995 Type: BOOK Genes: Abstract: ------------------- Key: 4070 Medline: Authors: Achacoso TB;Yamamoto WS Title: AY's Neuroanatomy of C. elegans for Computation. Citation: CRC Press, Boca Raton, FL. : 1-281 1992 Type: BOOK Genes: Abstract: ------------------- Key: 4071 Medline: Authors: Riddle DL;Blumenthal T;Meyer BJ;Priess JR (eds) Title: C. elegans II. Citation: Cold Spring Harbor Laboratory Press. II: 1-1222 1997 Type: BOOK Genes: Abstract: This book is part of an on-going series presenting collections of original research papers and literature reviews on diverse topics in molecular and cellular biology. This volume houses 34 literature reviews and research summaries on various aspects of the biology of Caenorhabditis elegans, a nematode of extraordinary usefulness as a research model. Topics include: the genome, mutation, transcription and its regulation, sex determination, male development, nervous system patterning, feeding and defecation, neural plasticity, and evolution. Appendices house a list of characterized genes, on-line resources, and other information. The text is illustrated, indexed, and includes a common bibliography of over 2000 literature citations. ------------------- Key: 4072 Medline: Authors: Hope IA (ed) Title: C. elegans. A Practical Approach. Citation: Oxford University Press, NY. : 1-281 1999 Type: BOOK Genes: Abstract: ------------------- Key: 4073 Medline: Authors: Felix MA;Labouesse M;Segalat L Title: Caenorhabditis elegans. Un organisme modele en biologie. Citation: Hermann, Editeurs des Sciences et des Arts. Paris, France. 58: 1-192 2002 Type: BOOK Genes: Abstract: L'espèce Caenorhabditis elegans fut décrite en 1900 à Alger par E. Maupas, qui s'intéressait à son mode de reproduction hermaphrodite. Plus tard, vers le milieu du vingtième siècle, V. Nigon et ses collaboratuers à Lyon étudièrent les reorganizations cellulaires accompagnant la fecundation et les premiers clivages. J. Brun isola les preiers mutants morpholgiques. ------------------- Key: 4074 Medline: Authors: Brown A Title: In the Beginning Was the Worm. Finding the Secrets of Life in a Tiny Hermaphrodite. Citation: Columbia University Press, New York. : 1-252 2003 Type: BOOK Genes: Abstract: ------------------- Key: 4100 Medline: 10376213 Authors: Ouyang B;Wang Y;Wei D Title: Caenorhabditis elegans contains structural homologs of human prk and plk. Citation: DNA Sequence 10: 109-113 1999 Type: ARTICLE Genes: Abstract: We and others have recently reported cloning and characterization of human prk and plk, members of the polo family of protein serine/threonine kinases that includes the budding yeast cdc5 and Drosophila melanoganster polo. The cdc5 gene is essential for cell cycle progression through mitosis and controls adaptation to the yeast DNA damage checkpoint. Here we report the identification of two new cdc5 homologs from Ceanorhabditis elegans, named plc1 and plc2. The deduced amino acid sequences of Plc1 and Plc2 share strong homology with both human Prk and Plk. plc1 and plc2 genes are closely linked on chromosome III and share 40% residue identity, suggesting that gene duplication followed by independent evolution gives rise to multiple polo homologous genes within a species. Similar to polo family members in other species, two distinct domains are present in Plc1 and Plc2 with the N-terminal half being the putative kinase domain. Interestingly, Plc2, unlike Plc1, contains a less conserved polo box within the C-terminal half of the protein, suggesting a functional division between these two kinases. ------------------- Key: 4101 Medline: 20140862 Authors: Masler EP;Kovaleva ES;Sardanelli S Title: Comparison of FaRP immunoreactivity in free-living nematodes and in the plant-parasitic nematode Heterodera Citation: Annals of the New York Academy of Sciences 897: 253-263 Type: ARTICLE Genes: Abstract: The family of FMRFamide-related peptides (FaRPs) is widely distributed among invertebrates, where the peptides serve as neuromodulators. Published reports indicate that numerous FaRP sequences exist in free-living and animal parasitic nematodes. Using a FMRFamide ELISA, FaRP immunoreactivity was detected in extracts of the soybean cyst nematode, Heterodera glycines, in both sexes and at all developmental stages. HPLC-ELISA results revealed a number of immunoreactive components in H. glycines preparations, and a comparison with extracts of the free-living nematodes Caenorhabditis elegans and Panagrellus redivivus showed significant qualitative differences in FaRP immunoreactivity between the plant parasite and the two free-living nematodes. Total and specific immunoreactivities varied during H. glycines development, with the highest specific activity in juveniles and males, and the highest total activity in mature females. Total female immunoreactivity was located primarily within the mature eggs. A significant portion, however, was associated with the female body, perhaps with ------------------- Key: 4102 Medline: 21146606 Authors: Haitzer M;Lohmannsroben HG;Steinberg CEW;Zimmermann U Title: In vivo laser-induced fluorescence detection of pyrene in nematodes and determination of pyrene binding constants for humic substances by fluorescence quenching and bioconcentration experiments. Citation: Journal of Experimental Monitoring 2: 145-149 2000 Type: ARTICLE Genes: Abstract: The bioconcentration of pyrene by bacterivorous thread worms (nematodes) of the species Caenorhabditis elegans was studied with laser-induced fluorescence (LIF) spectroscopy, fluorescence imaging and a radiotracer method. The vibronic band intensities of the LIF spectra indicated that the microenvironment of pyrene in the nematodes was similar to a low-polarity solvent, and thus provided direct evidence that pyrene was accumulated in lipid-rich areas inside the nematodes. The concentration of pyrene in the nematodes was estimated from the monomer/excimer fluorescence intensity ratio. Results from this method were in fair agreement with results using C-14 labeled pyrene for measuring pyrene bioconcentration. Preliminary results indicated that LIF measurements of pyrene may be possible even in single nematodes. Fluorescence microscopic observations revealed that pyrene was not adsorbed on the outside of the organisms, but was strongly concentrated in restricted areas inside the worms. In the second part of the study, the effects of six different humic substances (HS) on the bioconcentration of pyrene were investigated and sorption coefficients (K-DOC) calculated from reductions in bioconcentration (K-DOC(biol)) were compared with sorption coefficients measured with a fluorescence quenching technique (K-DOC(flu)). The results of these two different experimental methods agreed well (with K-DOC(BIOL) being slightly lower than K-DOC(flu)), indicating that the fraction of pyrene that was determined as freely dissolved by the fluorescence quenching method was comparable to the bioavailable fraction. ------------------- Key: 4103 Medline: 20231512 Authors: Culetto E;Sattelle DB Title: A role for Caenorhabditis elegans in understanding the function and interactions of human disease genes. Citation: Human Molecular Genetics 9: 869-877 2000 Type: ARTICLE Genes: daf-3 daf-5 daf-12 dys-1 egl-32 lov-1 Abstract: A growing number of medical research teams have begun to explore the experimental advantages of using a genetic animal model, the nematode worm Caenorhabditis elegans, with a view to enhancing our understanding of genes underlying human congenital disorders. In this study, we have compared sequences of positionally cloned human disease genes with the C. elegans database of predicted genes. Drawing on examples from spinal muscular atrophy, polycystic kidney disease, muscular dystrophy and Alzheimer's disease, we illustrate how data from C. elegans can yield new insights into the function and interactions ------------------- Key: 4104 Medline: 20244748 Authors: Masselon C;Anderson GA;Harkewicz R;Bruce JE;Pasa-Tolic L;Smith RD Title: Accurate mass multiplexed tandem mass spectrometry for high-throughput polypeptide identification from mixtures. Citation: Analytical Chemistry 72: 1918-1924 2000 Type: ARTICLE Genes: Abstract: We report a new tandem mass spectrometric approach for the improved identification of polypeptides from mixtures (e.g., using genomic databases). The approach involves the dissociation of several species simultaneously in a single experiment and provides both increased speed and sensitivity, The data analysis makes use of the known fragmentation pathways for polypeptides and highly accurate mass measurements for both the set of parent polypeptides and their fragments. The accurate mass information makes it possible to attribute most fragments to a specific parent species. We provide an initial demonstration of this multiplexed tandem MS approach using an FTICR mass spectrometer with a mixture of seven polypeptides dissociated using infrared irradiation from a CO2 laser. The peptides were added to, and then successfully identified from, the largest genomic database yet available (C. elegans), which is equivalent in complexity to that for a specific differentiated mammalian cell type. Additionally, since only a few enzymatic fragments are necessary to unambiguously identify a protein from an appropriate database, it is anticipated that the multiplexed MS/MS method will allow the more rapid identification of complex protein mixtures with on-line separation of their enzymatically produced polypeptides. ------------------- Key: 4105 Medline: 20140859 Authors: Geary TG;Marks NJ;Maule AG;Bowman JW;Alexander-Bowman SJ;Day TA;Larsen MJ;Kubiak TM;Davis JP;Thompson DP Title: Pharmacology of FMRFamide-related peptides in helminths. Citation: Annals of the New York Academy of Sciences 897: 212-227 Type: REVIEW Genes: afp-1 flp-1 flp-4 flp-5 flp-8 flp-12 flp-13 flp-15 flp-18 npr-1 Abstract: Nervous systems of helminths are highly peptidergic. Species in the phylum Nematoda (roundworms) possess at least 50 FMRFamide-related peptides (FaRPs), with more yet to be identified. To date, few non-FaRP neuropeptides have been identified in these organisms, though evidence suggests that other families are present. FaRPergic systems have important functions in nematode neuromuscular control. In contrast, species in the phylum Platyhelminthes (flatworms) apparently utilize fewer FaRPs than do nematodes; those species examined possess one or two FaRPs. Other neuropeptides, such as neuropeptide F (NPF), play key roles in flatworm physiology. Although progress has been made in the characterization of FaRP pharmacology in helminths, much remains to be learned. Most studies on nematodes have been done with Ascaris suum because of its large size. However, thanks to the Caenorhabditis elegans genome project, we know most about the FaRP complement of this free-living animal. That essentially all C. elegans FaRPs are active on at least one A. suum neuromuscular system argues for conservation of ligand-receptor recognition features among the Nematoda. Structure-activity studies on nematode FaRPs have revealed that structure-activity relationship (SAR) "rules" differ considerably among the FaRPs. Second messenger studies, along with experiments on ionic dependence and anatomical requirements for activity, reveal that FaRPs act through many different mechanisms. Platyhelminth FaRPs are myoexcitatory, and no evidence exists of multiple FaRP receptors in flatworms. Interestingly, there are examples of cross-phylum activity, with some nematode FaRPs being active on flatworm muscle. The extent to which other invertebrate FaRPs show cross-phylum activity remains to be determined. How FaRPergic nerves contribute to the control of behavior in helminths, and are integrated with ------------------- Key: 4106 Medline: 20096718 Authors: Hakeda S;Endo S;Saigo K Title: Requirements of Kettin, a giant muscle protein highly conserved in overall structure in evolution, for normal muscle function, viability, and flight activity of Drosophila. Citation: Journal of Cell Biology 148: 101-114 2000 Type: ARTICLE Genes: Abstract: Kettin is a giant muscle protein originally identified in insect flight muscle Z-discs. Here, we determined the entire nucleotide sequence of Drosophila melanogaster kettin, deduced the amino acid sequence of its protein product (540 kD) along with that of the Caenorhabditis elegans counterpart, and found that the overall primary structure of Kettin has been highly conserved in evolution. The main body of Drosophila Kettin consists of 35 immunoglobulin C2 domains separated by spacers. The central two thirds of spacers are constant in length and share in common two conserved motifs, putative actin binding sites. Neither fibronectin type III nor kinase domains were found. Kettin is present at the Z-disc in several muscle types. Genetic analysis showed that kettin is essential for the formation and maintenance of normal sarcomere structure of muscles and muscle tendons. Accordingly, embryos lacking kettin activity cannot hatch nor can adult flies heterozygous for the kettin mutation fly. ------------------- Key: 4107 Medline: 20117008 Authors: Baumeister R Title: The physiological role of presenilins in cellular differentiation: lessons from model organisms. Citation: European Archives of Psychiatry & Clinical Neuroscience 249: 280-287 1999 Type: REVIEW Genes: hop-1 lin-12 sel-12 spe-4 Abstract: Mutations in the human presenilin genes cause the most frequent and aggressive forms of Alzheimer's Disease. They results in an increase of the 42 amino acid variant of amyloid beta peptide that rapidly aggregates into neurotoxic plaques. In addition, lack of presenilin activity prevents the proteolytic cleavage of the Notch receptor of intercellular signaling. The biological role of presenilins is evolutionary conserved in animals. This review summarizes recent results obtained from animal models to understand presenilin activity and malfunction. ------------------- Key: 4108 Medline: Authors: Kappen C Title: Analysis of a complete homeobox gene repertoire: Implications for the evolution of diversity. Citation: Proceedings of the National Academy of Sciences USA 97: 4481-4486 2000 Type: ARTICLE Genes: Abstract: The completion of sequencing projects for various organisms has already advanced our insight into the evolution of entire genomes and the role of gene duplications. One multigene family that has served as a paradigm for the study of gene duplications and molecular evolution is the family of homeodomain-encoding genes. I present here an analysis of the homeodomain repertoire of an entire genome, that of the nematode Caenorhabditis elegans, in relation to our current knowledge of these genes in plants, arthropods, and mammals. A methodological framework is developed that proposes approaches for the analysis of homeodomain repertoires and multigene families in general. ------------------- Key: 4109 Medline: 20243724 Authors: Van Auken K;Weaver DC;Edgar LG;Wood WB Title: Caenorhabditis elegans embryonic axial patterning requires two recently discovered posterior-group Hox genes. Citation: Proceedings of the National Academy of Sciences USA 97: 4499-4503 2000 Type: ARTICLE Genes: ceh-13 egl-5 mab-5 nob-1 pal-1 php-3 eDp6 Abstract: Hox genes encode highly conserved transcription factors that control regional identities of cells and tissues along the developing anterior-posterior axis, probably in all bilaterian metazoans. However, in invertebrate embryos other than Drosophila, Hox gene functions remain largely unknown except by inference from sequence similarities and expression patterns. Recent genomic sequencing has shown that Caenorhabditis elegans has three Hox genes of the posterior paralog group [Ruvkun, G. & Hobert, O. (1998) Science 282, 2033-2041]. However, only one has been previously identified genetically, and it is not required for embryonic development [Chisholm, A. (1991) Development (Cambridge, U.K.) 111, 921-932]. Herein, we report identification of the remaining two posterior paralogs as the nob-1 gene and the neighboring php-3 gene. Elimination of nob-1 and php-3 functions causes gross embryonic defects in both posterior patterning and morphogenetic movements of the posterior hypodermis, as well as posterior-to-anterior cell fate transformations and lethality. The only other Hox gene essential for embryogenesis is the labial/Hox1 homolog ceh-13 required for more anterior patterning [Brunschwig, K., Wittmann, C., Schnabel, R., Burglin, T. R., Tobler, H. & Muller, F. (1999) Development (Cambridge, U.K.) 126, 1537-1546]. Therefore, essential embryonic patterning in C. elegans requires only Hox genes of the anterior and posterior paralog groups, raising interesting questions about evolution of the medial-group genes. ------------------- Key: 4110 Medline: 20243765 Authors: Friedman L;Higgin JJ;Moulder G;Barstead R;Raines RT;Kimble Title: Prolyl 4-hydroxylase is required for viability and morphogenesis in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 97: 4736-4741 2000 Type: ARTICLE Genes: dpy-18 phy-2 Abstract: The genome of Caenorhabditis elegans possesses two genes, dpy-18 and phy-2 that encode alpha subunits of the enzyme prolyl 4-hydroxylase. We have generated deletions within each gene to eliminate prolyl 4-hydroxylase activity from the animal. The dpy-18 mutant has an aberrant body morphology, consistent with a role of prolyl 4-hydroxylase in formation of the body cuticle. The phy-2 mutant is phenotypically wild type. However, the dpy-18; phy-2 double mutant is not viable, suggesting an essential role for prolyl 4-hydroxylase that is normally accomplished by either dpy-18 or phy-2. The effects of the double mutation were mimicked by small-molecule inhibitors of prolyl 4-hydroxylase, validating the genetic results and suggesting that C. elegans can serve as a model system for the discovery of new inhibitors. ------------------- Key: 4111 Medline: 20337950 Authors: Slack FJ;Basson M;Liu Z;Ambros V;Horvitz HR;Ruvkun G Title: The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Citation: Molecular Cell 5: 659-669 2000 Type: ARTICLE Genes: let-7 lin-29 lin-41 ncl-1 mnDf111 nDf23 nDf24 nDf30 Abstract: Null mutations in the C. elegans heterochronic gene lin-41 cause precocious expression of adult fates at larval stages. Increased lin-41 activity causes the opposite phenotype, reiteration of larval fates. let-7 mutations cause similar reiterated heterochronic phenotypes that are suppressed by lin-41 mutations, showing that lin-41 is negatively regulated by let-7. lin-41 negatively regulates the timing of LIN-29 adult specification transcription factor expression. lin-41 encodes an RBCC protein, and two elements in the lin-41 3'UTR are complementary to the 21 nucleotide let-7 regulatory RNA. A lin-41::GFP fusion gene is downregulated in the tissues affected by lin-41 at the time that the let-7 regulatory RNA is upregulated. We suggest that late larval activation of let-7 RNA expression downregulates LIN-41 to relieve inhibition of lin-29. ------------------- Key: 4112 Medline: 20337951 Authors: Schubert CM;Lin R;de Vries CJ;Plasterk RHA;Priess JR Title: MEX-5 and MEX-6 function to establish soma/germline asymmetry in early C. elegans embryos. Citation: Molecular Cell 5: 671-682 2000 Type: ARTICLE Genes: glp-1 let-324 mex-1 mex-3 mex-5 mex-6 pal-1 par-1 par-2 par-3 pie-1 pkc-3 pos-1 skn-1 nDf27 sDf66 Abstract: An asymmetrical network of cortically localized PAR proteins forms shortly after fertilization of the C. elegans egg. This network is required for subsequent asymmetries in the expression patterns of several proteins that are encoded by nonlocalized, maternally expressed mRNAs. We provide evidence that two nearly identical genes, mex-5 and mex-6, link PAR asymmetry to those subsequent protein asymmetries. MEX-5 is a novel, cytoplasmic protein that is localized through PAR activities to the anterior pole of the 1-cell stage embryo. MEX-5 localization is reciprocal to that of a group of posterior-localized proteins called germline proteins. Ectopic expression of MEX-5 is sufficient to inhibit the expression of germline proteins, suggesting that MEX-5 functions to inhibit anterior expression of the germline proteins. ------------------- Key: 4113 Medline: 20245489 Authors: Sokol SB;Kuwabara PE Title: Proteolysis in Caenorhabditis elegans sex determination: cleavage of TRA-2A by TRA-3. Citation: Genes & Development 14: 901-906 2000 Type: ARTICLE Genes: fem-1 fem-2 fem-3 her-1 laf-1 tra-1 tra-2 tra-3 vit-2 Abstract: The Caenorhabditis elegans tra-3 gene promotes female development in XX hermaphrodites and encodes an atypical calpain regulatory protease lacking calcium-binding EP hands. We report that despite the absence of EF hands, TRA-3 has calcium-dependent proteolytic activity and its proteolytic domain is essential for in vivo function. We show that the membrane protein TRA-2A, which promotes XX female development by repressing the masculinizing protein FEM-3, is a TRA-3 substrate. Cleavage of TRA-PA by TRA-3 generates a peptide predicted to have feminizing activity. These results indicate that proteolysis regulated by calcium may control some aspects of sexual cell fate in C. ------------------- Key: 4114 Medline: 20259870 Authors: Rankin CH;Gannon T;Wicks SR Title: Developmental analysis of habituation in the nematode C. elegans. Citation: Developmental Psychobiology 36: 261-270 2000 Type: ARTICLE Genes: Abstract: Habituation and spontaneous recovery from habituation to tap were studied across development in C. elegans. Unlike adult worms, larval worms do not consistently swim backwards to tap, but reverse half of the time and accelerate forward half of the time. In adult worms, the tap response is produced by the integration of two competing circuits: The head touch circuit, mediated by ALM and AVM sensory neurons, produces backward movement (reversals); the tail touch circuit, mediated by PLM neurons, produces forward movement (accelerations). Because the response type changes over development, habituation of each of the subcircuits was studied separately. Habituation of the head touch circuit was studied by laser ablating PLM, and habituation of the tail circuit was studied by ablating ALM. Worms were tested at six stages of development at either 10- or 60-s interstimulus intervals. All stages of development showed normal habituation and spontaneous recovery at both interstimulus intervals. ------------------- Key: 4115 Medline: 10822257 Authors: Goldstein B Title: When cells tell their neighbors which direction to divide. Citation: Developmental Dynamics 218: 23-29 2000 Type: REVIEW Genes: apr-1 cwn-1 cwn-2 dhc-1 dnc-1 dnc-2 egl-20 gpb-1 gsk-3 let-99 lin-5 lin-45 mes-1 nmy-2 ooc-3 ooc-5 par-1 par-2 par-3 par-4 par-5 par-6 pie-1 pkc-3 pod-1 pop-1 rot-1 rot-2 rot-3 stu-10 stu-11 wrm-1 Abstract: Many cells must divide in specific orientations, yet for only a handful of cases do we have some understanding of how cells choose division orientations. We know of only a few cases where division orientations are controlled by specific cell-cell interactions. These cases are of interest, because they tell us something new and seemingly fundamental about how cells can function during development. Here, the evidence that interactions control division orientation in some cells of the early C. elegans embryo is presented, and what is known about how contact can regulate division orientation is discussed. Whether contact-mediated division orientation is a peculiarity of C. elegans or whether it may be more widespread is ------------------- Key: 4116 Medline: 20284890 Authors: Shemer G;Podbilewicz B Title: Fusomorphogenesis: Cell fusion in organ formation. Citation: Developmental Dynamics 218: 30-51 2000 Type: REVIEW Genes: adm-1 adm-2 ceh-13 duf-1 egl-27 elf-1 lep-1 let-60 lin-25 lin-29 lin-39 mab-5 ref-1 Abstract: Cell fusion is a universal process that occurs during fertilization and in the formation of organs such as muscles, placenta, and bones. Very little is known about the molecular and cellular mechanisms of cell fusion during pattern formation. Here we review the dynamic anatomy of all cell fusions during embryonic and postembryonic development in an organism. Nearly all the cell fates and cell lineages are invariant in the nematode C. elegans and one third of the cells that are born fuse to form 44 syncytia in a reproducible and stereotyped way. To explain the function of cell fusion in organ formation we propose the fusomorphogenetic model as a simple cellular mechanism to efficiently redistribute membranes using a combination of cell fusion and polarized membrane recycling during morphogenesis. Thus, regulated intercellular and intracellular membrane fusion processes may drive elongation of the embryo as well as postembryonic organ formation in C. elegans. Finally, we use the fusomorphogenetic hypothesis to explain the role of cell fusion in the formation of organs like muscles, bones, and placenta in mammals and other species and to speculate on how the intracellular machinery that drive ------------------- Key: 4117 Medline: 20267882 Authors: Szewczyk NJ;Hartman JJ;Barmada SJ;Jacobson LA Title: Genetic defects in acetylcholine signalling promote protein degradation in muscle cells of Caenorhabditis elegans. Citation: Journal of Cell Science 113: 2003-2010 2000 Type: ARTICLE Genes: cha-1 lev-1 sup-7 unc-13 unc-17 unc-25 unc-29 unc-38 unc-47 unc-54 Abstract: A myosin-lacZ fusion, expressed in 103 muscle cells of Caenorhabditis elegans, reports on how proteolysis in muscle is controlled by neural and intramuscular signals. Upon acute starvation, the fusion protein is degraded in the posterior 63 cells of the body-wall muscle, but remains stable in 32 anterior body-wall muscles and 8 vulval muscle cells. This distinction correlates with differences in the innervation of these cells. Reporter protein in the head and vulval muscles becomes labile upon genetic 'denervation' in mutants that have blocks in pre-synaptic synthesis or release of acetylcholine (ACh) or post-synaptic reception at nicotinic ACh receptors (nAChR), whereas protein in all 103 muscles is stabilized by the nicotinic agonist levamisole in the absence of ACh production. Levamisole does nor stabilize muscle protein in nAChR mutants that are behaviorally resistant to levamisole, Neural inputs thus exert negative control over the proteolytic process in muscle by stimulating muscle ------------------- Key: 4118 Medline: 20221600 Authors: Kim YC;Lee J;Koo HS Title: Functional characterization of Caenorhabditis elegans DNA topoisomerase III alpha. Citation: Nucleic Acids Research 28: 2012-2017 2000 Type: ARTICLE Genes: Abstract: To investigate the function of a DNA topoisomerase III enzyme in Caenorhabditis elegans, the full-length cDNA of C. elegans DNA topoisomerase III alpha was cloned. The deduced amino acid sequence exhibited identities of 48 and 39% with those of human DNA topoisomerase III alpha and Saccharomyces cerevisiae DNA topoisomerase III, respectively. The overexpressed polypeptide showed an optimal activity for removing negative DNA supercoils at a relatively high temperature of 52-57 degrees C, which is similar to the optimum temperatures of other eukaryotic DNA topoisomerase III enzymes. When topoisomerase III alpha expression was interfered with by a cognate double-stranded RNA injection, pleiotropic phenotypes with abnormalities in germ cell proliferation, oogenesis and embryogenesis appeared. These phenotypes were well correlated with mRNA expression localized in the meiotic cells of gonad and early embryonic cells. ------------------- Key: 4119 Medline: 20289794 Authors: Walker DW;McColl G;Jenkins NL;Harris J;Lithgow GJ Title: Evolution of lifespan in C. elegans. Citation: Nature 405: 296-297 2000 Type: REVIEW Genes: age-1 Abstract: It was proposed almost 50 years ago that ageing is non-adaptive and is the consequence of a decline in the force of natural selection with age. This lead to the theory that ageing results from detrimental effects late in life of genes that act beneficially in early life, so any genetic alteration that increases life span might be expected to reduce fitness, for example. We show here that a mutation that greatly increases the lifespan of the nematode Caenorhabditis elegans does indeed exhibit a fitness cost, as demonstrated during starvation cycles that may mimic field conditions, thereby validating the pleiotrophy theory of aging. ------------------- Key: 4120 Medline: 10830967 Authors: Petcherski AG;Kimble J Title: LAG-3 is a putative transcriptional activator in the C. elegans Notch pathway. Citation: Nature 405: 364-368 2000 Type: ARTICLE Genes: apx-1 glp-1 lag-1 lag-2 lag-3 lin-12 Abstract: Notch signalling controls growth, differentiation and patterning during normal animal development(1,2); in humans, aberrant Notch signalling has been implicated in cancer and stroke(3,4). The mechanism of Notch signalling is thought to require cleavage of the receptor in response to ligand binding(5), movement of the receptor's intracellular domain to the nucleus(6,7), and binding of that intracellular domain to a CSL (for CBF1, Suppressor of Hairless, LAG-1)(8,9) protein. Here we identify LAG-3, a glutamine-rich protein that forms a ternary complex together with the LAG-1 DNA-binding protein(10) and the receptor's intracellular domain. Receptors with mutant ankyrin repeats that abrogate signal transduction are incapable of complex formation both in yeast and in vitro. Using RNA interference, we find that LAG-3 activity is crucial in Caenorhabditis elegans for both GLP-1 and LIN-12 signalling. LAG-3 is a potent transcriptional activator in yeast, and a Myc-tagged LAG-3 is predominantly nuclear in C. elegans. We propose that GLP-1 and LIN-12 promote signalling by recruiting LAG-3 to target promoters, where it functions as a transcriptional activator. ------------------- Key: 4121 Medline: 20243640 Authors: Rikke BA;Murakami S;Johnson TE Title: Parology and orthology of tyrosine kinases that can extend the life span of Caenorhabditis elegans. Citation: Molecular Biology and Evolution 17: 671-683 2000 Type: ARTICLE Genes: daf-2 egl-15 kin-15 kin-16 let-23 old-1 old-2 tkr-1 tkr-2 Abstract: Modification of any one of three transmembrane protein tyrosine kinase (PTK) genes, old-1, old-2 (formerly tkr-1 and tkr-2, respectively), and daf-2 can extend the mean and maximum life span of the nematode Caenorhabditis elegans. To identify paralogs and orthologs, we delineated relationships between these three PTKs and all known transmembrane PTKs and all known mammalian nontransmembrane PTKs using molecular phylogenetics. The tree includes a number of invertebrate receptor PTKs and a novel mammalian receptor PTK (inferred from the expressed-sequence tag database) that have not previously been analyzed. old-1 and old-2 were found to be members of a surprisingly large C. elegans PTK family having 16 members. Interestingly, only four members of this transmembrane family appeared to have receptor domains (immunoglobulin-like in each case). The C-terminal domain of this family was found to have a unique sequence motif that could be important for downstream signaling. Among mammalian PTKs, the old-1/old-2 family appeared to be most closely related to the Pdgfr, Fgfr, Ret, and Tie/Tek families. However, these families appeared to have split too early from the old-1/old-2 family to be orthologs, suggesting that a mammalian ortholog could yet be discovered. An extensive search of the expressed-sequence tag database suggested no additional candidate orthologs. In contrast to old-1 and old-2, daf-2 had no C. elegans paralogs. Although daf-2 was most closely related to the mammalian insulin receptor family, a hydra insulin receptor-like sequence suggested that daf-2 might not be an ortholog of the insulin receptor family. Among PTKs, the old-1/old-2 family and daf-2 were not particularly closely related, raising the possibility that other PTK families might extend life: span. On a more general note, our survey of the expressed-sequence tag database suggested that few, if any, additional mammalian PTK families are likely to be discovered. The one novel family that was discovered could represent a novel oncogene family, given the prevalence of oncogenes among PTKs. Finally, the PTK tree was consistent with nematodes and fruit flies being as divergent as nematodes and mammals, suggesting that life extension mechanisms shared by nematodes and fruit flies would be reasonable candidates ------------------- Key: 4122 Medline: 20275594 Authors: Vancoppenolle B;Claeys M;Borgonie G;Tytgat T;Coomans A Title: Evaluation of fixation methods for ultrastructural study of Caenorhabditis elegans embyros. Citation: Microscopy Research and Technique 49: 212-216 2000 Type: ARTICLE Genes: Abstract: Various fixation methods for transmission electron microscopy (TEM) were tested on Caenorhabditis elegans embryos. By combining various techniques, using 3.4% chitinase in combination with 1% alpha-chymotripsin, we were able to establish a new fixation procedure that for the first time preserves both membranes and internal cellular ultrastructure of C. elegans embryos in different stages of development. This unique procedure will enable a hitherto unattainable standard for TEM research of C. elegans embryos. Sectioning of specific developmental stages fixed with this method allows a detailed study of ultrastructural aspects of embryogenesis. ------------------- Key: 4123 Medline: 20237590 Authors: Shemer G;Kishore R;Podbilewicz B Title: Ring formation drives invagination of the vulva in Caenorhabditis elegans: Ras, cell fusion, and cell migration determine structural fates. Citation: Developmental Biology 221: 233-248 2000 Type: ARTICLE Genes: lin-12 lin-15 lin-39 let-60 Abstract: Directed cell rearrangements occur during gastrulation, neurulation, and organ formation. Despite the identification of developmental processes in which invagination is a critical component of pattern formation, little is known regarding the underlying cellular and molecular details. Caenorhabditis elegans vulval epithelial cells undergo morphological changes that generate an invagination through the formation of seven stacked rings. Here, we study the dynamics of ring formation during multivulva morphogenesis of a let-60/ras gain-of-function mutant as a model system to explore the cellular mechanisms that drive invagination. The behavior of individual cells was analyzed in a let-60/ras mutant by three-dimensional confocal microscopy. We showed that stereotyped cell fusion events occur within the rings that form functional and nonfunctional vulvae in a let-60/ras mutant. Expression of let-60/ras gain-of-function results in abnormal cell migration, ectopic cell fusion, and structural fate transformation. Within each developing vulva the anterior and posterior halves develop autonomously. Contrary to prevailing hypotheses which proposed three cell fates (1 degrees, 2 degrees, and 3 degrees), we found that each of the seven rings is a product of a discrete structural pathway that is derived from arrays of seven distinct cell fates (A, B, C, D, E, P, and H). We have also shown how autonomous ring formation is the morphogenetic force that ------------------- Key: 4124 Medline: 10772806 Authors: Gissendanner CR;Sluder AE Title: nrh-25, the Caenorhabditis elegans ortholog of ftz-f1, is required for epidermal and somatic gonad development. Citation: Developmental Biology 221: 259-272 2000 Type: ARTICLE Genes: him-8 jam-1 nhr-25 Abstract: We have analyzed the expression and function of the Caenorhabditis elegans gene nhr-25, a member of the widely conserved FTZ-F1 family of nuclear receptors. The gene encodes two protein isoforms, only one of which has a DNA binding domain. nhr-25 is transcribed during embryonic and larval development. A nhr-25::GFP fusion gene is expressed in the epidermis, the developing somatic gonad, and a subset of other epithelial cells. RNA-mediated interference indicates a requirement for nhr-25 function during development: disruption of nhr-25 function leads to embryonic arrest due to failure of the epidermally mediated process of embryo elongation. Animals that survive to hatching arrest as misshapen larvae that occasionally exhibit defects in shedding molted cuticle. In addition, somatic gonad development is defective in these larvae. These results further establish the importance of FTZ-F1 nuclear receptors in molting and developmental control across evolutionarily distant phyla. ------------------- Key: 4125 Medline: 20252714 Authors: Peredney CL;Williams PL Title: Utility of Caenorhabditis elegans for assessing heavy metal contamination in artificial soil. Citation: Archives of Environmental Contamination & Toxicology 39: 113-118 2000 Type: ARTICLE Genes: Abstract: There is an increasing need for the development of soil bioassay protocols. Currently the only internationally standardized soil test organism is the lumbricid earthworm Eisenia fetida. Many alternate soil test organisms have been proposed. This work compares Caenorhabditis elegans to several other test organisms, including E. fetida, for heavy metals in soil. In this evaluation, such factors as ease of testing and culturing, duration of testing, soil volume needed, and the sensitivity of the organism were considered. Results show that C. elegans is more sensitive than most other organisms evaluated and is similar in response to E. fetida. The second issue compares C. elegans LC50 values to heavy metals criteria specified in the US EPA regulations for land application of sewage sludge. Currently, the regulations are set on total metals in the soil and do not consider bioavailability of the metals. Regulations do not consider soil physiochemical properties, such as organic matter content, clay content, and cation exchange capacity, which have been shown to affect the availability of metals to soil organisms. While the C. elegans LC50 values are above standard values in artificial soil, work in our lab indicates that the LC(50)s are below regulation values for other soil types. Due to the ease of culturing and testing, good sensitivity, along with the wealth of biological information and ecological relevance, C. elegans is a good organism for use in soil bioassays. ------------------- Key: 4126 Medline: 20266357 Authors: Flemming AJ;Shen ZZ;Cunha A;Emmons SW;Leroi AM Title: Somatic polyploidization and cellular proliferation drive body size evolution in nematodes. Citation: Proceedings of the National Academy of Sciences USA 97: 5285-5290 2000 Type: ARTICLE Genes: daf-4 dpy-2 sma-2 Abstract: Most of the hypodermis of a rhabditid nematode such as Caenorhabditis elegans is a single syncytium. The size of this syncytium (as measured by body size) has evolved repeatedly in the rhabditid nematodes. Two cellular mechanisms are important in the evolution of body size: changes in the numbers of cells that fuse with the syncytium, and the extent of its acellular growth. Thus nematodes differ from mammals and other invertebrates in which body size evolution is caused by changes in cell number alone. The evolution of acellular syncytial growth in nematodes is also associated with changes in the ploidy of hypodermal nuclei. These nuclei are polyploid as a consequence of iterative rounds of endoreduplication, and this endocycle has evolved repeatedly. The association between acellular growth and endoreduplication is also seen in C. elegans mutations that interrupt transforming growth factor-beta signaling and that result in dwarfism and deficiencies in hypodermal ploidy. The transforming growth factor-beta pathway is a candidate for being involved in nematode body size evolution. ------------------- Key: 4127 Medline: 10811831 Authors: Moorthy S;Chen L;Bennett V Title: Caenorhabditis elegans beta-G spectrin is dispensable for establishment of epithelial polarity, but essential for muscular and neuronal function. Citation: Journal of Cell Biology 149: 915-930 2000 Type: ARTICLE Genes: bgs-1 sma-1 spc-1 unc-70 Abstract: The Caenorhabditis elegans genome encodes one alpha spectrin subunit, a beta spectrin subunit (beta-G), and a beta-H spectrin subunit. Our experiments show that the phenotype resulting from the loss of the C. elegans alpha spectrin is reproduced by tandem depletion of both beta-G and beta-H spectrins. We propose that alpha spectrin combines with the beta-G and beta-H subunits to form alpha/beta-G and alpha/beta-H heteromers that perform the entire repertoire of spectrin function in the nematode. The expression patterns of nematode beta-G spectrin and vertebrate beta spectrins exhibit three striking parallels including: (1) beta spectrins are associated with the sites of cell-cell contact in epithelial tissues; (2) the highest levels of beta-G spectrin occur in the nervous system; and (3) beta spectrin-G in striated muscle is associated with points of attachment of the myofilament apparatus to adjacent cells. Nematode beta-G spectrin associates with plasma membranes at sites of cell-cell contact, beginning at the two-cell stage, and with a dramatic increase in intensity after gastrulation when most cell proliferation has been completed. Strikingly, depletion of nematode beta-G spectrin by RNA-mediated interference to undetectable levels does not affect the establishment of structural and functional polarity in epidermis and intestine. Contrary to recent speculation, beta-G spectrin is not associated with internal membranes and depletion of beta-G spectrin was not associated with any detectable defects in secretion. Instead beta-G spectrin-deficient nematodes arrest as early larvae with progressive defects in the musculature and nervous system. Therefore, C. elegans beta-G spectrin is required for normal muscle and neuron function, but is dispensable for embryonic elongation and establishment of early epithelial polarity. We hypothesize that heteromeric spectrin evolved in metazoans in response to the needs of cells in the context of mechanically integrated tissues that can withstand the ------------------- Key: 4128 Medline: 10811832 Authors: Hammarlund M;Davis WS;Jorgensen EM Title: Mutations in beta-spectrin disrupt axon outgrowth and sarcomere structure. Citation: Journal of Cell Biology 149: 931-942 2000 Type: ARTICLE Genes: unc-54 unc-70 Abstract: beta-Spectrin is a major component of the membrane skeleton, a structure found at the plasma membrane of most animal cells. beta-Spectrin and the membrane skeleton have been proposed to stabilize cell membranes, generate cell polarity, or localize specific membrane proteins. We demonstrate that the Caenorhabditis elegans homologue of beta-spectrin is encoded by the unc-70 gene. unc-70 null mutants develop slowly, and the adults are paralyzed and dumpy. However, the membrane integrity is not impaired in unc-70 animals, nor is cell polarity affected. Thus, beta-spectrin is not essential for general membrane integrity or for cell polarity. However, beta-spectrin is required for a subset of processes at cell membranes. In neurons, the loss of beta-spectrin leads to abnormal axon outgrowth. In muscles, a loss of beta-spectrin leads to disorganization of the myofilament lattice, discontinuities in the dense bodies, and a reduction or loss of the sarcoplasmic reticulum. These defects are consistent with beta-spectrin function in anchoring proteins at cell membranes. ------------------- Key: 4129 Medline: 20270024 Authors: Srayko M;Buster DW;Bazirgan OA;McNally FJ;Mains PE Title: MEI-1/MEI-2 katanin-like microtubule severing activity is required for Caenorhabditis elegans meiosis. Citation: Genes & Development 14: 1072-1084 2000 Type: ARTICLE Genes: fem-1 fem-3 glp-1 mei-1 mei-2 mel-26 zyg-9 hDp19 hDp39 hDp54 sDp2 Abstract: The Caenorhabditis elegans meiotic spindle is morphologically distinct from the first mitotic spindle, yet both structures form in the same cytoplasm similar to 20 minutes apart. The mei-1 and mei-2 genes of C. elegans are required for the establishment of the oocyte meiotic spindle but are not required for mitotic spindle function. mei-1 encodes an AAA ATPase family member with similarity to the p60 catalytic subunit of the heterodimeric sea urchin microtubule-severing protein, katanin. We report that mei-2 encodes a 280-amino acid protein containing a region similar to the p80-targeting subunit of katanin. MEI-1 and MEI-2 antibodies decorate the polar ends of meiotic spindle microtubules and meiotic chromatin. We find that the subcellular location of MEI-2 depends on wild-type mei-1 activity and vice versa. These experiments, combined with MEI-1 and MEI-2's similarity to p60 and p80 katanin, suggest that the C. elegans proteins function as a complex. In support of this idea, MEI-1 and MEI-2 physically associate in HeLa cells. Furthermore, co-expression of MEI-1 and MEI-2 in HeLa cells results in the disassembly of microtubules. These data lead us to conclude that MEI-1/MEI-2 microtubule-severing activity is required for meiotic spindle organization in C. elegans. ------------------- Key: 4130 Medline: Authors: Meller VH Title: Dosage compensation: making 1X equal 2X. Citation: Trends in Cell Biology 10: 54-59 2000 Type: REVIEW Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 mix-1 sdc-1 sdc-2 sdc-3 sex-1 xol-1 Abstract: Animals that have XX females and XY or XO males have differing noses of X-linked genes in each sex. Overcoming this is the most immediate and vital aspect of sexual differentiation. A number of systems that accurately compensate for sex-chromosome dosage have evolved independently: silencing a single X chromosome ill female mammals, downregulating both X chromosomes in hermaphrodite Caenorhabditis elegans and upregulating the X chromosome in male Drosophila all equalize X-linked gene expression. Each organism uses a largely non-overlapping set of molecules to achieve the same outcome: 1X = 2X. ------------------- Key: 4131 Medline: 20296338 Authors: de Pomerai D;Daniells C;David H;Allan J;Duce I;Mutwakil M;Thomas D;Sewell P;Tattersall J;Jones D;Candido P Title: Non-thermal heat-shock response to microwaves. Citation: Nature 405: 417-418 2000 Type: REVIEW Genes: Abstract: Exposure limits set for microwave radiation assume that any biological effects result from tissue heating: non-thermal effects have been reported but remain controversial. We show here that prolonged exposure to low-intensity microwave fields can induce heat-shock responses in the soil nematode Caenorhabditis elegans. This effect appears to be non-thermal, suggesting that current exposure limits set for microwave equipment may need to be reconsidered. ------------------- Key: 4132 Medline: 20237731 Authors: Andrade MA;Ponting CP;Gibson TJ;Bork P Title: Homology-based method for identification of proteins using statistical significance estimates. Citation: Journal of Molecular Biology 298: 521-537 2000 Type: ARTICLE Genes: Abstract: Short protein repeats, frequently with a length between 20 and 40 residues, represent a significant fraction of known proteins. Many repeats appear to possess high amino acid substitution rates and thus recognition of repeat homologues is highly problematic. Even if the presence of a certain repeat family is known, the exact locations and the number of repetitive units often cannot be determined using current methods. We have devised an iterative algorithm based on optimal and sub-optimal score distributions from profile analysis that estimates the significance of all repeats that are detected in a single sequence. This procedure allows the identification of homologues at alignment scores lower than the highest optimal alignment score for non-homologous sequences. The method has been used to investigate the occurrence of eleven families of repeats in Saccharomyces cerevisiae, Caenorhabditis elegans and Homo sapiens accounting for 1055, 2205 and 2320 repeats, respectively. For these examples, the method is both more sensitive and more selective than conventional homology search procedures. The method allowed the detection in the SwissProt database of more than 2000 previously unrecognised repeats belonging to the 11 families. In addition, the method was used to merge several repeat families that previously were supposed to be distinct, indicating common phylogenetic origins for these ------------------- Key: 4133 Medline: 20272150 Authors: Lai CH;Chou CY;Ch'ang LY;Liu CS;Lin WC Title: Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative Citation: Genome Research 10: 703-713 2000 Type: ARTICLE Genes: Abstract: Modern biomedical research greatly benefits from large-scale genome-sequencing projects ranging from studies of viruses, bacteria, and yeast to multicellular organisms, like Caenorhabditis elegans. Comparative genomic studies offer a vast array of prospects for identification and functional annotation of human ortholog genes. We presented a novel comparative proteomic approach for assembling human gene contigs and assisting gene discovery. The C. elegans proteome was used as an alignment template to assist in novel human gene identification from human EST nucleotide databases. Among the available 18,452 C. elegans protein sequences, our results indicate that at least 83% (15,344 sequences) of C. elegans proteome has human homologous genes, with 7,954 records of C. elegans proteins matching known human gene transcripts. Only 11% or less of C. elegans proteome contains nematode-specific genes. We found that the remaining 7,390 sequences might lead to discoveries of novel human genes, and over 150 putative full-length human gene transcripts were assembled upon ------------------- Key: 4134 Medline: 10830161 Authors: Kemphues K Title: PARsing embryonic polarity. Citation: Cell 101: 345-348 2000 Type: REVIEW Genes: glp-1 mex-1 mex-3 mex-5 mex-6 pal-1 par-1 par-2 par-3 par-4 par-6 pie-1 pkc-3 pos-1 skn-1 Abstract: Current understanding of the way in which embryonic polarity is established relies heavily on studies of maternal effect lethal mutants in D. melanogaster and C. elegans. Although the analysis in worms began in earnest about a decade after the explosion of information from flies, we now know enough about both systems to make comparisons meaningful, and to ask whether there are conserved mechanisms used for establishing embryonic polarity. Thus far, the single common feature is translational repression, which has been shown to localize important fate regulators in both systems. Now, however, in this issue of Cell, Shulman and colleagues report an analysis in D. melanogaster of the first molecule to play an important and perhaps conserved role in both animals, ------------------- Key: 4135 Medline: 20237578 Authors: Felix MA;De Ley P;Sommer RJ;Frisse L;Nadler SA;Thomas WK;Vanfleteren J;Sternberg PW Title: Evolution of vulva development in the Cephalobina (Nematode). Citation: Developmental Biology 221: 68-86 2000 Type: ARTICLE Genes: Abstract: Ventral cord and vulva development are analyzed in a large sample of nematode species of the suborder Cephalobina. We find a specific range of evolutionary variations at distinct developmental steps. (1) Unlike Caenorhabditis elegans and relatives, the vulva is formed from the four precursor cells P(5-8).p or, exceptionally, from P(6, 7).p only. (2) The vulval competence group is restricted to these four cells or is larger. (3) The fates of more anterior and posterior Pn.p cells vary between closely related species (mostly cell death versus epidermal fate). (4) The mechanism of vulval cell fate patterning varies within a single genus, even between strains of the same species. (5) We describe the first example of a vulval cell lineage that is asymmetric between the anterior and the posterior sides of the vulva. For a selection of the investigated taxa, phylogenetic trees were constructed in order to map vulval characters and infer evolutionary polarities. We can conclude that in this group, death of the Pn.p cells probably constitutes a derived character state compared to a syncytial fate. Rhabditophanes sp. and Strongyloides ratti are placed as sister taxa, probably sharing an exclusive common ancestor in which the number of precursor cells forming the vulva was reduced from four to ------------------- Key: 4136 Medline: 10790327 Authors: Wicks SR;de Vries CJ;van Luenen HGAM;Plasterk RHA Title: CHE-3, a cytosolic dynein heavy chain, is required for sensory cilia structure and function in Caenorhabditis elegans. Citation: Developmental Biology 221: 295-307 2000 Type: ARTICLE Genes: che-3 Abstract: Forward genetic screens using novel assays of nematode chemotaxis to soluble compounds identified three independent transposon-insertion mutations in the gene encoding the Caenorhabditis elegans dynein heavy chain (DHC) 1b isoform. These disruptions were mapped and cloned using a newly developed PCR-based transposon display. The mutations were demonstrated to be allelic to the che-3 genetic locus. This isoform of dynein shows temporally and spatially restricted expression in ciliated sensory neurons, and mutants show progressive developmental defects of the chemosensory cilia. These results are consistent with a role for this motor protein in the process of intraflagellar transport; DHC 1b acts in concert with a number of other proteins to establish and maintain the structural integrity of the ciliated sensory endings in C. ------------------- Key: 4137 Medline: 20172040 Authors: Smardon A;Spoerke JM;Stacey SC;Klein ME;Mackin N;Maine EM Title: EGO-1 is related to RNA-directed RNA polymerase and functions in germ-line development and RNA interference in C. elegans. Citation: Current Biology 10: 169-178 2000 Type: ARTICLE Genes: ego-1 fog-3 gld-1 lag-1 mog-1 mpk-1 ncc-1 rrf-1 rrf-2 rrf-3 unc-22 unc-29 unc-32 vit-2 gaDp1 ozDf5 Abstract: Background: Cell-fate determination requires that cells choose between alternative developmental pathways. For example, germ cells in the nematode worm Caenorhabditis elegans choose between mitotic and meiotic division, and between oogenesis and spermatogenesis. Germ-line mitosis depends on a somatic signal that is mediated by a Notch-type signaling pathway. The ego-1 gene was originally identified on the basis of genetic interactions with the receptor in this pathway and was also shown to be required for oogenesis. Here, we provide more insight into the role of ego-1 in germ-line development. Results: We have determined the ego-1 gene structure and the molecular basis of ego-1 alleles. Putative ego-1 null mutants had multiple, previously unreported defects in germ-line development. The ego-1 transcript was found predominantly in the germ line. The predicted EGO-1 protein was found to be related to the tomato RNA-directed RNA polymerase (RdRP) and to Neurospora crassa QDE-1, two proteins implicated in post-transcriptional gene silencing (PTGS). For a number of germ-line-expressed genes, ego-1 mutants were resistant to a form of PTGS called RNA interference. Conclusions: The ego-1 gene is the first example of a gene encoding an RdRP-related protein with an essential developmental function. The ego-1 gene is also required for a robust response to RNA interference by certain genes. Hence, a protein required for germ-line development in C. elegans may be a component of the RNA ------------------- Key: 4138 Medline: 20312180 Authors: Walker MY;Hawley RS Title: Hanging on to your homolog: the roles of pairing, synapsis and recombination in the maintenance of homolog adhesion. Citation: Chromosoma 109: 3-9 2000 Type: REVIEW Genes: him-3 Abstract: Homologous chromosomes initially undergo weak alignments that bring homologous sequences into register during meiosis. These alignments can be facilitated by two types of mechanisms: interstitial homology searches and telomere-telomere alignments. As prophase (and chromatin compaction) proceeds, these initial pairings or alignments need to be stabilized. In at least some organisms, such as Saccharomyces cerevisiae and S. pombe, these pairings can apparently be maintained by the creation of recombination intermediates. In contrast, synapsis during zygotene may be able to facilitate and/or maintain chromosome pairing even in the absence of exchange in several higher organisms. It thus seems possible that the synaptonemal complex plays a role both in maintaining homolog adhesion during meiotic prophase and, more speculatively, in facilitating meiotic exchange. ------------------- Key: 4139 Medline: Authors: Birchler JA;Pal Bhadra M;Bhadra U Title: Making noise about silence: repression of repeated genes in animals. Citation: Current Opinion in Genetics & Development 10: 211-216 2000 Type: REVIEW Genes: mut-7 Abstract: Repeated copies of genes, whether in tandem or dispersed, are often recognized by the cell and silenced. Tandem repeat silencing is associated with a heterochromatin-like complex. Dispersed gene silencing can be mediated by the repressive Polycomb Group complex or involve post-transcriptional silencing presumably involving double-stranded RNA. The I retrotransposable element in Drosophila appears to be susceptible to dispersed gene silencing, potentially by both posttranscriptional and transcriptional processes. Some mutations that eliminate RNA interference in Caenorhabditis elegans result in the mobilization of many transposons and two of these mutations desilence tandem repeats in the germline. One challenge for the future is to determine the nature of any relationship between post-transcriptionally and transcriptionally based mechanisms. The silencing mechanisms potentially act as a protection against high expression of transposons and viruses. ------------------- Key: 4140 Medline: Authors: Blaxter M;Aslett M;Guiliano D;Daub J;The Filarial Genome Project Title: Parasitic helminth genomics. Citation: Parasitology 118: S39-S51 1999 Type: REVIEW Genes: Abstract: The initiation of genome projects on helminths of medical importance promises to yield new drug targets and vaccine candidates in unprecedented numbers. In order to exploit this emerging data it is essential that the user community is aware of the scope and quality of data available, and that the genome projects provide analyses of the raw data to highlight potential genes of interest. Core bioinformatics support for the parasite genome projects has promoted these approaches. In the Brugia genome project, a combination of expressed sequence tag sequencing from multiple DNA libraries representing the complete filarial nematode lifecycle, and comparative analysis of the sequence dataset, particularly using the complete genome sequence of the model nematode C. elegans, has proved very effective in gene discovery. ------------------- Key: 4141 Medline: 20277458 Authors: Gems D;Riddle DL Title: Defining wild-type life span in Caenorhabditis elegans. Citation: Journal of Gerontology 55: B215-B219 2000 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans reproduces predominantly as a self-fertilizing hermaphrodite, and this drives laboratory populations to be homozygous at all genetic loci. Passaging of stocks can lead to fixation of spontaneous mutations, especially when the latter do not result in a selective disadvantage under laboratory conditions. Life span may be with a trait, since a comparison of six wild-type N2 Lines derived from a common ancestor (but maintained separately in several laboratories) revealed four variants with median adult life spans ranging from 12.0 +/- 0.8 to 17.0 +/- 0.6 days at 20 degrees C. Fertility was also reduced in the tao shortest-lived strains. We determined which life span most closely corresponds to that of the authentic wild type by two means. Firstly, N2 hermaphrodites were compared with seven C. elegans wild isolates. The latter were found to resemble only the longest-lived N2 strain. Comparison of male life spans of sis lines also revealed additional strain variation. Secondly, life spans of F1 progeny issuing from crosses between N2 variants showed that short life spans were recessive, indicating that they result from loss-of-function mutations. We infer that the longest-lived N2 variant best resembles the original N2 isolate. This is the N2 male stock currently distributed by the ------------------- Key: 4142 Medline: 20302490 Authors: Thacker C;Rose AM Title: A look at the Caenorhabditis elegans Kex2/Subtilisin-like proprotein convertase family. Citation: BioEssays 22: 545-553 2000 Type: REVIEW Genes: aex-5 bli-4 egl-3 kpc-1 kpc-2 kpc-3 kpc-4 Abstract: Significant advances have recently been made in our understanding of the mechanisms of activation of proteins that require processing. Often this involves endoproteolytic cleavage of precursor forms at basic residues, and is carried out by a group of serine endoproteinases, termed the proprotein convertases. In mammals, seven different convertases have been identified to date. These act in both the regulated secretory pathway for the processing of prohormones and proneuropeptides and in the constitutive secretory pathway, in which a variety of proproteins are activated endoproteolytically. The recently completed sequence of the nematode Caenorhabditis elegans genome affords a unique opportunity to examine the entire proprotein convertase family in a multicellular organism. Here we review the nature of the family, emphasising the structural features, characteristic of the four nematode genes, that supply all of the necessary functions unique to this group of serine endoproteinases. Studies of the C. elegans genes not only provide important information about the evaluation of this gene family but should help to illuminate the roles of these proteins in ------------------- Key: 4143 Medline: Authors: Schierenberg E Title: Early development of nematode embryos: differences and similarities. Citation: Nematology 2: 57-64 2000 Type: ARTICLE Genes: Abstract: To determine whether embryogenesis of Caenorhabditis elegans is typical for nematodes in general, we started to analyse in comparison several aspects of development in various nematode species. The differences we observed can be subdivided into two classes, those visible in the intact embryo and those requiring experimental interference. Particularly obvious differences of both types were revealed between C. elegans (Rhabditidae) and Acrobeloides nanus (Cephalobidae). Not only does the spatial and temporal pattern of early events differ but also that of intercellular communication and cell specification. Our data suggest that some developmental variations are characteristic for certain nematode groups and therefore may be useful as phylogenetic markers. In contrast, we detected little evidence so far for environmental influence on early developmental processes. ------------------- Key: 4144 Medline: Authors: Podbilewicz B Title: Membrane fusion as a morphogenetic force in nematode development. Citation: Nematology 2: 99-111 2000 Type: REVIEW Genes: lep-1 let-60 lin-15 Abstract: In Caenorhabditis elegans almost all the epithelial cells fuse to form permanent syncytia. Cells in the vulva and hypodermis fuse autonomously to produce ring shaped cells with defined structures and functions. Analysis of temporal and spatial sequence of events together with ultrastructural characterisation of cell fusion intermediates show that fusion pores in specific domains of the membranes dilate and subsequently vesicles are formed. The fusomorphogenetic hypothesis states that these vesicles are targeted to different domains of the plasma membrane where they fuse, thereby causing changes in cell shape. It is proposed that cell fusion and polarised membrane recycling are involved in the formation of ring cells. Fusomorphogenesis is a working model to investigate the forces that drive pattern formation and generate diversity of developmental mechanisms in nematodes. ------------------- Key: 4145 Medline: 10811890 Authors: Satyal SH;Schmidt E;Kitagawa K;Sondheimer N;Lindquist S;Kramer JM;Morimoto RI Title: Polyglutamine aggregates alter protein folding homeostasis in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 97: 5750-5755 2000 Type: ARTICLE Genes: myo-2 unc-54 Abstract: Expansion of polyglutamine repeats in several unrelated proteins causes neurodegenerative diseases with distinct but related pathologies, To provide a model system for investigating common pathogenic features, we have examined the behavior of polyglutamine expansions expressed in Caenorhabditis elegans. The expression of polyglutamine repeats as green fluorescent protein (CFP)-fusion proteins in body wall muscle cells causes discrete cytoplasmic aggregates that appear early in embryogenesis and correlates with a delay in larval to adult development. The heat shock response is activated idiosyncratically in individual cells in a polyglutamine length-dependent fashion. The toxic effect of polyglutamine expression and the formation of aggregates can be reversed by coexpression of the yeast chaperone Hsp104. The altered homeostasis associated with polyglutamine aggregates causes both the sequestration of an otherwise soluble protein with shorter arrays of glutamine repeats and the relocalization of a nuclear glutamine-rich protein. These observations of induced aggregation and relocalization have implications for disorders involving protein aggregation. ------------------- Key: 4146 Medline: 10839353 Authors: Zhen M;Huang X;Bamber B;Jin Y Title: Regulation of presynaptic terminal organization by C. elegans RMP-1, a putative guanine nucleotide exchanger with a RING-H2 finger domain. Citation: Neuron 26: 331-343 2000 Type: ARTICLE Genes: rpm-1 snb-1 snt-1 syd-2 syd-3 unc-5 unc-49 eDf1 mDf1 nDf31 stDf47 stDf29 Abstract: Presynaptic terminals contain highly organized subcellular structures to facilitate neurotransmitter release. In C. elegans, the typical presynaptic terminal has an electron-dense active zone surrounded by synaptic vesicles. Loss-of-function mutations in the rpm-1 gene result in abnormally structured presynaptic terminals in GABAergic neuromuscular junctions (NMJs), most often manifested as a single presynaptic terminal containing multiple active zones. The RPM-1 protein has an RCC1-like guanine nucleotide exchange factor (GEF) domain and a RING-HP finger. RPM-1 is most similar to the Drosophila presynaptic protein Highwire (HIW) and the mammalian Myc binding protein Pam. RPM-1 is localized to the presynaptic region independent of synaptic vesicles and functions cell autonomously. The temperature-sensitive period of rpm-1 coincides with the time of synaptogenesis. rpm-1 may regulate the spatial arrangement, or restrict the formation, of presynaptic structures. ------------------- Key: 4147 Medline: 20296164 Authors: Schaefer AM;Hadwiger GD;Nonet ML Title: rpm-1, a conserved neuronal gene that regulates targeting and synaptogenesis in C. elegans. Citation: Neuron 26: 345-356 2000 Type: ARTICLE Genes: mec-7 mec-18 rpm-1 mDf1 sDf29 sDf47 Abstract: Little is known of mechanisms regulating presynaptic differentiation. We identified rpm-1 in a screen for mutants with defects in patterning of a presynaptic marker at certain interneuronal synapses. The predicted RPM-1 protein contains zinc binding, RCC1, and other conserved motifs. In rpm-1 mutants, mechanosensory neurons fail to accumulate tagged vesicles, retract synaptic branches, and ectopically extend axons. Some motor neurons branch and overgrow; others show altered synaptic organization. Expression of RPM-1 in the presynaptic mechanosensory neurons is sufficient to rescue phenotypes in these cells. Certain rpm-1 phenotypes are temperature sensitive, revealing that RPM-1 function can be bypassed by maintaining mutants at the permissive temperature at stages commensurate with synapse formation in wild-type animals. These results indicate that RPM-1 functions cell autonomously during synaptogenesis to regulate neuronal ------------------- Key: 4148 Medline: 20280018 Authors: Rankin CH;Wicks SR Title: Mutations of the Caenorhabditis elegans brain-specific inorganic phosphate transporter eat-4 affect habituation of the tap-withdrawal response without affecting the response itself. Citation: Journal of Neuroscience 20: 4337-4344 2000 Type: ARTICLE Genes: eat-4 Abstract: The studies reported here were designed to investigate the role of the mutation eat-4 in the response to tap and in habituation in the nematode Caenorhabditis elegans. In C. elegans eat-4 has been found to affect a number of glutamatergic pathways. It has been hypothesized to positively regulate glutaminase activity and therefore glutamatergic neurotransmission. In the eat-4(ky5) loss-of-function worms, there is presumably insufficient glutamate available for sustained transmission. In the experiments reported here eat-4 worms showed no differences from wild-type in the magnitude of response to a single tap, indicating that the neural circuit underlying the response was intact and functional in the mutant worms. However, when eat-4 worms were given repeated taps the resulting habituation was different from that seen in wild-type worms: eat-4 worms habituate more rapidly and recover more slowly than wild-type worms at all interstimulus intervals tested. In addition, eat-4 worms do not show dishabituation. The same transgene rescues pharyngeal activity defects and both the habituation and dishabituation deficits seen in the eat-4 worms. Our results suggest that neurotransmitter regulation plays a role in habituation and may play a role in dishabituation. ------------------- Key: 4149 Medline: 20329238 Authors: Watts JL;Browse J Title: A palmitoyl-CoA-specific Delta 9 fatty acid desaturase from Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 272: 263-269 2000 Type: ARTICLE Genes: fat-5 fat-6 fat-7 Abstract: Biosynthesis of polyunsaturated fatty acids in C. elegans is initiated by the introduction of a double bond at the Delta 9 position of a saturated fatty acid. We identified three C. elegans fatty acid desaturase genes related to the yeast Delta 9 desaturase OLE1 and the rat stearoyl-CoA desaturase SCD1. Heterologous expression of all three genes rescues the fatty acid auxotrophy of the yeast Delta 9 desaturase mutant ole1. Examination of the fatty acid composition of the transgenic yeast reveals striking differences in the substrate specificities of these desaturases. Two desaturases, FAT-6 and FAT-7, readily desaturate stearic acid (18:0) and show less activity on palmitic acid (16:0). In contrast, the other desaturase, FAT-B, readily desaturates palmitic acid (16:0), but shows nearly undetectable activity on the common Delta 9 substrate stearic acid. This is the first report of a palmitoyl-CoA-specific membrane fatty acid desaturase. ------------------- Key: 4150 Medline: Authors: Felix MA;Delattre M;Dichtel ML Title: Comparative developmental studies using Oscheius/Dolichorhabditis sp. CEW1 (Rhabditidae). Citation: Nematology 2: 89-98 2000 Type: ARTICLE Genes: let-60 unc-22 Abstract: In order to study the evolution of nematode vulva development, we focus on Oscheius/Dolichorhabditis sp. CEW1 (Rhabditidae) in comparison with Caenorhabditis elegans. In this species, the fates of the vulval precursor cells are determined by two successive nested inductions by the uterine anchor cell (instead of a single one in C. elegans). This hermaphroditic species can be cultured and handled like C. elegans. We review vulva development in this species. We present some molecular tools and the sequence of the Ras gene. This species is amenable to genetic analysis and we discuss the isolation of ------------------- Key: 4151 Medline: 20333432 Authors: Morris J;Lehmann R;Navarro C Title: PARallels in axis formation. Citation: Science 288: 1759-1760 2000 Type: REVIEW Genes: mex-5 mex-6 nmy-2 par-1 par-2 par-3 pie-1 Abstract: The anterior-to-posterior axis of a frutfly or worm embryo is determined even before the first division of the fertilized egg. As the embryo undergoes successive cell divisions, cells at one end are destined to produce anterior structures (such as the fly head or worm pharyngeal muscle cells), whereas cells at the other end are destined to produce posterior structures (such as the germ cells that give rise to egg and sperm). ------------------- Key: 4152 Medline: Authors: Carta LK;Carta DG Title: Nematode specific gravity profiles and applications to flotation extraction and taxonomy. Citation: Nematology 2: 201-210 2000 Type: ARTICLE Genes: Abstract: A technique is described that refines the standard sugar flotation procedure used to isolate nematodes from their surroundings. By centrifuging nematodes in a number of increasing specific gravity solutions and plotting the fraction floating, the cumulative probability distribution of the population's specific gravity is generated. By assuming normality, the population mean, mu, and standard deviation, sigma, are found by a nonlinear least squares procedure. These density parameters along with their error covariance matrix may be used as a taxonomic physical character. A chi-squared test is derived for comparing populations. Mean and standard deviation pairs (mu, sigma) were found for the specific gravities of the adult stage of the plant parasites Pratylenchus agilis (1.068, 0.017), P. scribneri (1.073, 0.028), P. penetrans (1.058, 0.008) and the bacterial-feeder Caenorhabditis elegans (1.091, ------------------- Key: 4153 Medline: 20302485 Authors: Chen Z;Han M Title: Building a protein interaction map: research in the post-genome era. Citation: BioEssays 22: 503-506 2000 Type: REVIEW Genes: Abstract: With the extensive amount of information generated by genome-wide sequencing, the entire set of gene products in an organism can now be predicted. The challenge of understanding the function of each gene in the genome has led to the development of many large-scale and high-throughput experimental techniques. Recently, two papers, Walhout et al.((1)) and Uetz et al.,((2)) have described studies that add a new functional dimension to research conducted on a genome-wide scale. These two groups have utilized the yeast two-hybrid system to identify interactions among the entire complement of proteins encoded by the Caenorhabditis elegans and the Saccharomyces cerevisiae genomes, respectively. Using a set of 29 genes that have been previously characterized, Walhout et al. demonstrated the feasibility and efficiency of this technique by building an interaction matrix among a large number of proteins. On an even larger scale, Uetz et al. conducted two-hybrid analyses using proteins that represent over 87% of the total gene products in yeast and identified interactions for about 15% of the total yeast proteins. ------------------- Key: 4154 Medline: 20233826 Authors: Corsi AK;Kostas SA;Fire A;Krause M Title: Caenorhabditis elegans Twist plays an essential role in non-striated muscle development. Citation: Development 127: 2041-2051 2000 Type: ARTICLE Genes: aex-1 ceh-24 egl-15 hlh-1 hlh-8 lin-12 mab-5 myo-3 pal-1 Abstract: The basic helix-loop-helix (bHLH) transcription factor Twist plays a role in mesodermal development in both invertebrates and vertebrates. In an effort to understand the role of the unique Caenorhabditis elegans Twist homolog, hlh-8, we analyzed mesodermal development in animals with a deletion in the hlh-8 locus. This deletion was predicted to represent a null allele because the HLH domain is missing and the reading frame for the protein is disrupted. Animals lacking CeTwist function were constipated and egg-laying defective. Both of these defects were rescued in transgenic mutant animals expressing wild-type hlh-8. Observing a series of mesoderm-specific markers allowed us to characterize the loss of hlh-8 function more thoroughly. Our results demonstrate that CeTwist performs an essential role in the proper development of a subset of mesodermal tissues in C. elegans. We found that CeTwist was required for the formation of three out of the four non-striated enteric muscles born in the embryo. In contrast, CeTwist was not required for the formation of the embryonically derived striated muscles. Most of the post-embryonic mesoderm develops from a single lineage. CeTwist was necessary for appropriate patterning in this lineage and was required for expression of two downstream target genes, but was not required for the expression of myosin, a marker of differentiation. Our results suggest that mesodermal ------------------- Key: 4156 Medline: 20259785 Authors: Coulson A;Kuwabara P Title: Interview: Nematode functional genomics. Citation: Yeast 17: 43-47 2000 Type: REVIEW Genes: Abstract: ------------------- Key: 4157 Medline: 20326777 Authors: Kaji H;Tsuji T;Mawuenyega KG;Wakamiya A;Taoka M;Isobe T Title: Profiling of Caenorhabditis elegans proteins using two-dimensional gel electrophoresis and matrix assisted laser desorption/ionization-time of flight-mass spectrometry. Citation: Electrophoresis 21: 1755-1765 2000 Type: ARTICLE Genes: mlc-3 sod-2 unc-60 Abstract: The nematode Caenorhabditis elegans (C. elegans) is the first animal whose whole 97 Mb genome sequence, encoding ca. 19 000 open reading frames (ORF's), has been essentially determined. We tried to establish a 2-DE map of the nematode proteome by means of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). A soluble protein fraction of mixed stages of the worm, wild-type strain N2, was applied to 2-D PAGE. After Coomassie Brilliant Blue (CBB) staining, 1200 spots were detected and 140 major spots were excised from the gel and subjected to in-gel digestion with Achromobacter protease I (lysyl endopeptidase). Resulting peptides were analyzed by matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) followed by peptide mass fingerprinting for protein identification. With this approach we have obtained a two-dimensional electrophoresis (2-DE) protein map in which 69 spots were localized as landmarks for comparison of expression profiles to elucidate the basis of various biological events. ------------------- Key: 4158 Medline: 20287747 Authors: Meyer BJ Title: Sex in the worm - counting and compensating X-chromosome dose. Citation: Trends in Genetics 16: 247-253 2000 Type: REVIEW Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 fox-1 her-1 mix-1 sdc-2 sdc-3 sex-1 xol-1 Abstract: The nematode Caenorhabditis elegans counts its X chromosomes to determine sex and to activate the process of dosage compensation, which ensures that males (XO) and hermaphrodites (XX) express equal levels of most X-chromosome products. The number of X chromosomes is communicated by a set of X-rinked genes called X-signal elements, which repress the master sex-determination switch gene xol-1 via two distinct, dose-dependent molecular mechanisms in XX embryos. X-chromosome gene dosage is compensated by a specialized protein complex that includes evolutionarily conserved components of mitotic and meiotic machinery. This complex assembles on both X chromosomes of hermaphrodites to repress transcription by half. The recruitment of chromosome segregation proteins to the new task of regulating X-chromosome-wide gene expression points to the evolutionary origin of nematode dosage compensation. ------------------- Key: 4159 Medline: 20184001 Authors: Harteneck C;Plant TD;Schultz G Title: From worm to man: three subfamilies of TRP channels. Citation: Trends in Neurosciences 23: 159-166 2000 Type: REVIEW Genes: ced-11 gon-2 osm-9 Abstract: A steadily increasing number of cDNAs for proteins that are structurally related to the TRP ion channels have been cloned in recent years. All these proteins display a topology of six transmembrane segments that is shared with some voltage-gated channels and the cyclic-nucleotide-gated channels. The TRP channels can be divided, on the basis of their homology, into three TRP channel (TRPC) subfamilies: short (S), long (L) and osm (O). From the evidence available to date, this subdivision can also be made according to channel function. Thus, the STRPC family, which includes Drosophila TRP and TRPL and the mammalian homologues, TRPC1-7, is a family of Ca2+-permeable cation channels that are activated subsequent to receptor-mediated stimulation of different isoforms of phospholipase C. Members of the OTRPC family are Ca2+-permeable channels involved in pain transduction (vanilloid and vanilloid-like receptors), epithelial Ca2+ transport and, at least in Caenorhabditis elegans, in chemo-, mechano- and osmoregulation. The LTRPC family is less well ------------------- Key: 4160 Medline: Authors: Zimmerman CM;Padgett RW Title: Transforming growth factor beta signaling mediators and modulators. Citation: Gene 249: 17-30 2000 Type: REVIEW Genes: daf-1 daf-3 daf-4 daf-7 daf-8 daf-14 dbl-1 sma-2 sma-3 sma-4 sma-6 Abstract: Transforming growth factor beta is a multi-functional growth and differentiation factor responsible for regulating many diverse biological processes in both vertebrate and invertebrate species. Among the most dramatic of TGF beta's effects are those associated with specification of cell fates during development and inhibition of cell cycle progression. The core TGF beta signaling pathway has now been described using a synergistic combination of genetic and biochemical approaches. Transmembrane receptors with intrinsic protein serine kinase activity bind ligand in the extracellular milieu and then phosphorylate intracellular proteins known as Smads. Phosphorylated Smads form heterooligomers and translocate into the nucleus where they can modulate transcriptional responses. More recent studies indicate that many other proteins serve as modulators of Smad activity, and ultimately define specific cellular responses to TGF beta. Here we describe both the simplistic core TGF beta signaling pathway and the growing number of proteins that impinge on this pathway at the level of Smad function ------------------- Key: 4161 Medline: 20264077 Authors: Sym M;Basson M;Johnson C Title: A model for Niemann-Pick type C disease in the nematode Caenorhabditis elegans. Citation: Current Biology 10: 527-530 2000 Type: ARTICLE Genes: npc-1 npc-2 Abstract: Niemann-Pick type C (NP-C) disease is a progressive neurodegenerative disorder characterized by the inappropriate accumulation of unesterified cholesterol in lysosomes [1]. NP C patients show various defects including hepatosplenomegaly, ataxia, dystonia and dementia, Most cases of NP C are associated with inactivating mutations of the NPC1 gene [2], which encodes a protein implicated in the retrograde transport of sterols and other cargo from lysosomes [3]. Furthermore, localization of the NPC1 protein to lysosomal/endosomal compartments is essential for proper transport [4], To create a model of NP C disease in a simple, genetically tractable organism, we generated deletion mutations in two Caenorhabditis elegans homologs of the human NPC1 gene, designated npc-l and npc-a. Animals mutant for npc-l developed slowly, laid eggs prematurely, and were hypersensitive to cholesterol deprivation. Furthermore, npc-l; npc-a double-mutant animals inappropriately formed dauer larvae under favorable growth conditions. These phenotypes in C. elegans provide a model system for both genetic and chemical suppressor screening that could identify promising drug targets and leads for NP-C disease. ------------------- Key: 4162 Medline: 20300916 Authors: Beaudoin F;Michaelson LV;Hey SJ;Lewis MJ;Shewry PR;Sayanova O;Napier JA Title: Heterologous reconstitution in yeast of the polyunsaturated fatty acid biosynthetic pathway. Citation: Proceedings of the National Academy of Sciences USA 97: 6421-6426 2000 Type: ARTICLE Genes: Abstract: A Caenorhabditis elegans ORF encoding the presumptive condensing enzyme activity of a fatty acid elongase has been characterized functionally by heterologous expression in yeast. This ORF (F56H 11.4) shows low similarity to Saccharomyces cerevisiae genes involved in fatty acid elongation. The substrate specificity of the C. elegans enzyme indicated a preference for Delta(6)-desaturated C18 polyunsaturated fatty acids. Coexpression of this activity with fatty acid desaturases required for the synthesis of C20 polyunsaturated fatty acids resulted in the accumulation of arachidonic acid from linoleic acid and eicosapentaenoic acid from alpha-linolenic acid. These results demonstrate the reconstitution of the n-3 and n-6 polyunsaturated fatty acid biosynthetic pathways. The C. elegans ORF is likely to interact with endogenous components of a yeast elongation system, with the heterologous nematode condensing enzyme F56H11.4 causing a redirection of enzymatic activity toward polyunsaturated ------------------- Key: 4163 Medline: 10848606 Authors: Rockelein I;Rohrig S;Donhauser R;Eimer S;Baumeister R Title: Identification of amino acid residues in the Caenorhabditis elegans POU protein UNC-86 that mediate UNC-86-MEC-3-DNA ternary complex formation. Citation: Molecular and Cellular Biology 20: 4806-4813 2000 Type: ARTICLE Genes: mec-3 unc-86 Abstract: The POU homeodomain protein UNC-86 and the LIM homeodomain protein MEC-3 are essential for the differentiation of the six mechanoreceptor neurons in the nematode Caenorhabditis elegans. Previous studies have indicated that UNC-86 and MEC-3 bind cooperatively to at least three sites in the mec-3 promoter and synergistically activate transcription. However, the molecular details of the interactions of UNC-86 with MEC-3 and DNA have not been investigated so far. Here we used a yeast system to identify the functional domains in UNC-86 required for transcriptional activation and to characterize the interaction of UNC-86 with MEC-3 in vivo. Our results suggest that transcriptional activation is mediated by the amino terminus of UNC-86, whereas amino acids in the POU domain mediate DNA binding and interaction with MEC-3. By random mutagenesis, we identified mutations that only affect the DNA binding properties of UNC-86, as well as mutations that prevent coactivation by MEC-3. We demonstrated that both the POU-specific domain and the homeodomain of UNC-86, as well as DNA bases adjacent to the proposed UNC-86 binding site, are involved in the formation of a transcriptionally active complex with MEC-3. These data suggest that some residues involved in the contact of UNC-86 with MEC-3 also contribute to the interaction of the functionally nonrelated POU protein Oct-1 with Oca-B, whereas other positions have different roles. ------------------- Key: 4164 Medline: 20320265 Authors: Fasiuddin A;Campbell WC Title: Haemonchus contortus (Nematoda: Trichostrongylidae) is much more sensitive than Caenorhabditis elegans (Nematoda: Rhabditidae) to the ovicidal action of thiabendazole. Citation: Journal of Parasitology 86: 629-630 2000 Type: ARTICLE Genes: Abstract: When eggs of the trichostrongylid nematode Haemonchus contortus were exposed to thiabendazole, the concentration required to prevent hatching in 90% of the eggs (MIC90) was found to be 0.1 mu g/ ml (using 1% dimethylsulfoxide [DMSO] as solvent). In contrast, eggs of the free-living rhabditid nematode Caenorhabditis elegans hatched at normal rates at a concentration 200 times higher, i.e., 20 mu g/ml, and showed only a partial inhibitory effect at a concentration 1,200 times higher, i.e., 120 mu g/ml (in 3% DMSO). Because solubility limitations precluded the testing of higher concentrations of thiabendazole, a more soluble derivative, 5-([1-methylethoxyl carbonylamino)-2-(4-thiazloyl)-1H-benzimidazolyliminoacetic acid N,N-diethylethanamine salt, was rested against C. elegans eggs. The MIC90 was found to be 400 mu g/ml, and although the derivative was not tested against H. contortus eggs, this finding further suggests that C. elegans eggs have an exceptionally low degree of benzimidazole sensitivity. ------------------- Key: 4165 Medline: Authors: Rich T;Allen R;Trowsdale J Title: How low can Toll go? Citation: Trends in Genetics 16: 292-294 2000 Type: ARTICLE Genes: Abstract: How far down the phylogenic tree should we look for the origins of innate immunity? We know that mammalian cells respond to microbes using Toll-like signalling systems that are remarkably similar in arthropods. Prototypes of these pathways might have arisen in more primitive phyla (initially, perhaps, to regulate development) and their identification would help us to reconstruct the evolution of this facet of immunity. Elements of Toll pathways exist in plants. Does this mean that the last common ancestor of plants, chordates and arthropods, which was a unicellular eukaryote, expressed a Toll-like pathway, or is a similar developmental logic at work in all multicellular life-forms? To address some of these issues we decided to seek a 'worm' Toll pathway, concentrating on the simple and versatile metazoan, Caenorhabditis elegans. ------------------- Key: 4166 Medline: 20317264 Authors: Duret L Title: tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Citation: Trends in Genetics 16: 287-289 2000 Type: ARTICLE Genes: Abstract: Although they encode the same amino acids, synonymous codons are not all used at the same frequency. Such codon usage biases occur in most species and could be the result of mutational biases, natural selection acting on silent changes in DNA, or both. Selection on synonymous codon positions is thought to lead to a co-adaptation of codon usage and tRNA content to optimize the efficiency of translation. Such a selective pressure to reduce the cost of translation is expected to be stronger for genes that are expressed at high levels. In agreement with that model, in some unicellular organisms such as Escherichia coli or Saccharomyces cerevisiae, codons that are used preferentially correspond to the most abundant tRNA species, and there is a positive correlation between codon usage bias and the level of gene expression. ------------------- Key: 4167 Medline: 20325485 Authors: Nishiwaki K;Hisamoto N;Matsumoto K Title: A metalloprotease disintegrin that controls cell migration in Caenorhabditis elegans. Citation: Science 288: 2205-2208 2000 Type: ARTICLE Genes: mig-17 unc-5 unc-6 unc-40 Abstract: In Caenorhabditis elegans, the gonad acquires two U-shaped arms by the directed migration of its distal tip cells (DTCs) along the body wall basement membranes. Correct migration of DTCs requires the mig-17 gene, which encodes a member of the metalloprotease-disintegrin protein family. The MIG-17 protein is secreted from muscle cells of the body wall and Localizes in the basement membranes of gonad. This localization is dependent on the disintegrin-like domain of MIG-17 and its catalytic activity. These results suggest that the MIG-17 metalloprotease directs migration of DTCs by remodeling the basement membrane. ------------------- Key: 4168 Medline: 20352658 Authors: Hardin J Title: A degrading way to make an organ. Citation: Science 288: 2142-2143 2000 Type: REVIEW Genes: gon-1 mig-17 unc-5 unc-6 unc-40 unc-129 Abstract: Building an organ is a precise business. Organ rudiments must often navigate through a complex, three-dimensional terrain as their shape is transformed, and they must do so in a way that is carefully orchestrated with other concurrent developmental events. Many organ rudiments develop as tubular structures that are elaborated as the rudiment grows... ------------------- Key: 4169 Medline: Authors: Peredney CL;Williams PL Title: Comparison of the toxicological effects of nitrate versus chloride metallic salts on Caenorhabditis elegans in soil. Citation: "Environmental Toxicology and Risk Assessment: Recent Achievements in Environmental Fate and Transport". FT Price, KV Brix and NK Lane (eds), ASTM, West Conshohocken, PA. 9: 256-268 2000 Type: ARTICLE Genes: Abstract: There is growing interest in the use of bioindicators to assess metal toxicity in soil. The current ASTM Standard Guide for Conducting Laboratory Soil Toxicity Test with the lumbricid earthworm Eisenia fetida (E 1676-97) uses a common earthworm. The nematode Caenorhabditis elegans is a natural soil inhabitant with many characteristics that make an ideal alternate test organism. It has been used to assess metal toxicity in aquatic media, agar plates and in soil. Work is currently underway on the design of a C. elegans procedure for metals in soil. The objective of this study was to determine differences in LC50S between the chloride salt and the nitrate salt forms of cadmium, copper, lead, nickel, and zinc, in three types of soil: Cecil, Tifton, and ASTM artificial soil. Results indicated that the toxicological effect of the metallic salt varies and is dependent on the particular metal. For Cd and Pb the nitrate form is more toxic while Cu and Ni are more toxic in the chloride form. The composition of the soil also effected toxicity, with the metal being the least toxic in ASTM soil and more toxic in the Tifton soil. This strongly correlated with organic matter and clay content of the soil. It is important to determine the effects of carrier salt form and soil composition on metal toxicity, not only in order to standardize the protocol for C. elegans soil toxicity testing, but also in establishing acceptable exposure concentrations in the soil. ------------------- Key: 4170 Medline: Authors: Boyd WA;Anderson GL;Dusenbery DB;Williams PL Title: Computer tracking method for assessing behavioral changes in the nematode Caenorhabditis elegans. Citation: "Environmental Toxicology and Risk Assessment: Recent Achievements in Environmental Fate and Transport". FT Price, KV Brix and NK Lane (eds), ASTM, West Conshohocken, PA. 9: 225-238 2000 Type: ARTICLE Genes: Abstract: Computer tracking of Caenorhabditis elegans, a free-living soil nematode, is a promising tool to assess behavioral changes upon exposure to contaminants. A short life cycle, a known genetic make-up, thoroughly studied behavior, and a completely mapped nervous system make C. elegans an attractive soil test organism with many advantages over the commonly used earthworm. Although many toxicity tests have been performed with C. elegans, the majority focused on mortality, a much less sensitive endpoint than behavior. A computer tracking system has been developed to monitor behavioral changes using C. elegans. Because conditions unrelated to specific toxicant exposures, such as changes in temperature, developmental stage, and presence of adequate food sources, can affect behavior, there is a need to standardize tracking procedures. To this end, we have developed reference charts for control movement comparing the movement of four and five day-old adult nematodes. The use of K-medium versus deionized (DI) H2O for pre-tracking rinses was also investigated. A final reference chart compared the behavioral responses of nematodes at various food densities (i.e. bacterial concentrations). ------------------- Key: 4171 Medline: 20172048 Authors: Solari F;Ahringer J Title: NURD-complex genes antagonise Ras-induced vulval development in Caenorhabditis elegans. Citation: Current Biology 10: 223-226 2000 Type: ARTICLE Genes: chd-3 chd-4 egl-27 egr-1 hda-1 let-60 lin-1 lin-8 lin-9 lin-15 lin-31 lin-35 lin-36 lin-37 lin-38 lin-40 lin-51 lin-52 lin-53 lin-54 lin-55 lin-56 rba-1 Abstract: Chromatin-modifying complexes are important for transcriptional control, but their roles in the regulation of development are poorly understood. Here, we show that components of the nucleosome remodelling and histone deacetylase (NURD) complex [1-5] antagonise vulval development, which is induced by the pas signal transduction pathway. In three of the six equivalent vulval precursor cells, the pas pathway is active, leading to the production of vulval fates [6]; in the remaining three, the pas pathway is inhibited and vulval fates repressed. Inhibition of pas signaling occurs in part through the action of the synthetic multivulval (synMuv) genes, which comprise two functionally redundant pathways (synMuvA and synMuvB) [7]. We found that five Caenorhabditis elegans members of the NURD chromatin remodelling complex inhibit vulval development through both the synMuvA and synMuvB pathways (hda-1, rba-1, lin-53, chd-3 and chd-4); a further two members, the MTA1-related genes egr-1 and egl-27, act only in the synMuvA pathway. We propose that the synMuvA and synMuvB pathways function redundantly to recruit or activate a core NURD complex, which then represses vulval developmental target genes by local histone deacetylation. These results emphasise the importance of chromatin regulation in developmental decisions. Furthermore, inhibition of Ras signaling suggests a possible link ------------------- Key: 4172 Medline: 20172061 Authors: Chess A Title: Odorant receptors: axon contact-mediated diversity. Citation: Current Biology 10: R152-R154 2000 Type: REVIEW Genes: str-2 Abstract: To make the most of a small number of neurons, the nematode olfactory system includes neurons that are bilaterally symmetrical in morphology, but differ in the sets of genes they express. An intriguing recent example is the axon contact-mediated asymmetry in expression of the str-2 odorant receptor gene. ------------------- Key: 4173 Medline: 20172057 Authors: Hunter CP Title: Gene silencing: Shrinking the black box of RNAi. Citation: Current Biology 10: R137-R140 2000 Type: REVIEW Genes: ego-1 mut-7 pos-1 rde-1 rde-2 rde-3 rde-4 rrf-1 rrf-2 rrf-3 unc-22 Abstract: The mysterious mechanism whereby the mere presence of double-stranded RNA can Inactivate specific genes is yielding its secrets. Recent results identifying cellular components required for RNAi in Caenorhabditis elegans Indicate that the mechanism is conserved, ancient and may provide a defense against selfish DNA. ------------------- Key: 4174 Medline: 20189612 Authors: Zhu X;Joh K;Hedgecock EM;Hori K Title: Identification of epi-1 locus as a laminin alpha chain gene in the nematode Caenorhabditis elegans and characterization of epi-1 mutant alleles. Citation: DNA Sequence 10: 207-217 1999 Type: ARTICLE Genes: epi-1 Abstract: A new genetic locus, epi-1, has been identified and mapped, which affects epithelialization of various tissues in the nematode, Caenorhabditis elegans. Seven independent epi-1 mutant alleles have been obtained. These mutants have a wide spectrum of abnormalities, all seem to be caused by a primary defect of basement membrane. We have identified the epi-1 gene as a structural gene of laminin alpha chain. The sequence analyses of the gene and cDNAs revealed that the gene consists of 15 exons and encodes a protein of 3704 amino acids in an open reading frame of 11115 base pairs. The nematode alpha chain is similar to its vertebrate and fly orthologs in the domain structure. The mRNA is trans-spliced to SL1 leader RNA as many of the nematode mRNAs. Mutation sites have been identified in four alleles. Two alleles have nonsense mutations and produce truncated proteins lacking the domain necessary for the formation of a heterotrimeric laminin molecule. The other two alleles have missense mutations in domains VI and IIIb, ------------------- Key: 4175 Medline: 20222520 Authors: Butler D Title: The worm's turn to claim Internet fame. Citation: Nature 404: 425- 2000 Type: REVIEW Genes: Abstract: Caenorhabditis elegans, the favourite worm of developmental biology, now has its own Internet portal site. Wormbase, which can be found at http://www.wormbase.org, aims to bring together all available information on the millimetre-long soil nematode's genetics and biology. ------------------- Key: 4176 Medline: 20122553 Authors: Johnson CD;Liu LX Title: Novel antimicrobial targets from combined pathogen and host genetics. Citation: Proceedings of the National Academy of Sciences USA 97: 958-959 2000 Type: REVIEW Genes: egl-9 Abstract: The identification of drug targets for a given human disease, whether it is mainly environmental or genetic in origin, rests on an understanding of the molecular chain of events that unfold in the disease process. Anatomic pathology, biochemistry, cellular physiology, and pharmacology consitute the main traditional approaches towards identifying potential therapeutic targets... ------------------- Key: 4177 Medline: 20210757 Authors: Catalanotto C;Azzalin G;Macino G;Cogoni C Title: Gene silencing in worms and fungi. Citation: Nature 404: 245- 2000 Type: REVIEW Genes: rde-1 Abstract: The introduction into cells of foreign nucleic acid molecules can induce sequence-specific gene silencing in some organisms. Here we show that two distantly related organisms, the nematode Caenorhabditis elegans and the fungus Neurospora crassa, which have quite different mechanisms of gene silencing, both use a similar protein to control the process. This suggests that they may share an ancestral mechanim that evolved to protect the genome against invasion by foreign DNA. ------------------- Key: 4178 Medline: 20277478 Authors: Khan MLA;Ali MY;Siddiqui ZK;Shakir MA;Ohnishi H;Nishikawa K;Siddiqui SS Title: C. elegans KLP-11/OSM-3/KAP-1: Orthologs of the sea urchin kinesin-II, and mouse KIF3A/KIFB/KAP3 kinesin complexes. Citation: DNA Research 7: 121-125 2000 Type: ARTICLE Genes: kap-1 klp-11 osm-3 Abstract: Kinesins are intracellular multimeric transport motor proteins that move cellular cargo on microtubule tracks. It has been shown that the sea urchin KRP85/95 holoenzyme associates with a KAP115 non-motor protein, forming a heterotrimeric complex in vitro, called the Kinesin-II. Here we describe isolation of a cDNA clone corresponding to the klp-11 kinesin in C. elegans. Our sequence analysis of the encoded KLP-11 shows that it shares high homology with the OSM-3 kinesin. We also describe a nematode cDNA encoding KAP-1 that shares extensive homology with the sea urchin KAP115 kinesin associated protein. Sequence-based structural analysis of the OSM-3, KLP-11, and KAP-1, presented here suggests that these may form a heterotrimeric complex. We also describe the presence of a Drosophila armadillo consensus motif in CeKAP-1, first found in spKAP115, that suggests a possible role for the KAP-1 in signal transduction. ------------------- Key: 4179 Medline: 20312879 Authors: Min DS;Cho NJ;Yoon SH;Lee YH;Hahn SJ;Lee KH;Kim MS;Jo YH Title: Phospholipase C, protein kinase C, Ca2+/calmodulin-dependent protein kinase II, and tyrosine phosphorylation are involved in carbachol-induced phospholipase D activation in Chinese hamster ovary ce... Citation: Journal of Neurochemistry 75: 274-281 2000 Type: ARTICLE Genes: gar-1 gar-3 Abstract: Recently, we have isolated a cDNA encoding a muscarinic acetylcholine receptor (mAChR) from Caenorhabditis elegans. To investigate the regulation of phospholipase D (PLD) signaling via a muscarinic receptor, we generated stable transfected Chinese hamster ovary (CHO) cells that overexpress the mAChR of C. elegans (CHO-GAR-3). Carbachol (CCh) induced inositol phosphate formation and a significantly higher Ca2+ elevation and stimulated PLD activity through the mAChR; this was insensitive to pertussis toxin, but its activity was abolished by the phospholipase C (PLC) inhibitor U73122. Western blot analysis revealed several apparent tyrosine-phosphorylated protein bands after CCh treatment. The CCh-induced PLD activation and tyrosine phosphorylation were significantly reduced by the protein kinase C (PKC) inhibitor calphostin C and down-regulation of PKC and the tyrosine kinase inhibitor genistein. Moreover, the Ca2+/calmodulin-dependent protein kinase If (CaM kinase II) inhibitor KN62, in addition to chelation of extracellular or intracellular Ca2+ by EGTA and BAPTA/AM, abolished CCh-induced PLD activation and protein tyrosine phosphorylation. Taken together, these results suggest that the PLC/PKC-PLD pathway and the CaM kinase Il/tyrosine kinase-PLD pathway are involved in the activation of PLD ------------------- Key: 4180 Medline: 10764728 Authors: Chan SL;Yee KSY;Tan KML;Yu VC Title: The Caenorhabditis elegans sex determination protein FEM-1 is a CED-3 substrate that associates with CED-4 and mediates apoptosis in mammalian cells. Citation: Journal of Biological Chemistry 275: 17925-17928 2000 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: Sex-specific elimination of cells by apoptosis plays a role in sex determination in Caenorhabditis elegans. Recently, a mammalian pro-apoptotic protein named F1A alpha has been identified. F1A alpha shares extensive homology throughout the entire protein with the C. elegans protein, FEM-1, which is essential for achieving all aspects of the male phenotype in the nematode. In this report, the role of FEM-1 in apoptosis was investigated. Overexpression of FEM-1 induces caspase-dependent apoptosis in mammalian cells. FEM-1 is cleaved in vitro by the C. elegans caspase, CED-3, generating an N-terminal cleavage product that corresponds to the minimal effector domain for apoptosis. Furthermore, CED-4 associates with FEM-1 in vitro and in vivo in mammalian cells and potentiates FEM-1-mediated apoptosis. Similarly, Apaf-1, the mammalian homologue of CED-4 was found to associate with F1A alpha. These data suggest that FEM-1 and F1A alpha may mediate apoptosis by communicating directly with the core machinery of ------------------- Key: 4181 Medline: 20317034 Authors: Antebi A;Yeh WH;Tait D;Hedgecock EM;Riddle DL Title: daf-12 encodes a nuclear receptor that regulates the dauer diapause and developmental age in C. elegans. Citation: Genes & Development 14: 1512-1527 2000 Type: ARTICLE Genes: daf-2 daf-4 daf-12 nhr-8 nhr-48 Abstract: The daf-12 gene acts at the convergence of pathways regulating larval diapause, developmental age, and adult longevity in Caenorhabditis elegans. It encodes a nuclear receptor most closely related to two C. elegans receptors, NHR-8 and NHR-48, Drosophila DHR96, and vertebrate vitamin D and pregnane-X receptors. daf-12 has three predicted protein isoforms, two of which contain DNA- and ligand-binding domains, and one of which contains the ligand-binding domain only. Mutations cluster in DNA- and ligand-binding domains, but correspond to distinct phenotypic classes. DAF-12 is expressed widely in target tissues from embryo to adult, but is upregulated during midlarval stages. In the adult, expression persists in nervous system and somatic gonad, two tissues that regulate adult longevity. We propose that DAF-12 integrates hormonal signals in cellular targets to coordinate major life ------------------- Key: 4182 Medline: Authors: Phelan P Title: Gap junction communication in invertebrates: The innexin gene family. Citation: Current Trends in Membranes 49: 389-422 2000 Type: REVIEW Genes: eat-5 unc-7 unc-9 Abstract: Given the extent of genetic conservation through evolution, it is paradoxical that the structural components of gap junctions do not appear to be conserved throughout the animal kingdom. Electrical synapses in the escape systems of the crayfish ventral nerve cord and the goldfish spinal cord subserve the same basic function and, apart from subtle differences, are ultrastructurally alike. Therefore, one reasonably might expect them to be formed from homologous proteins. Yet despite much effort, connexins, the molecules that form gap junctions in vertebrates, have not been identified unequivocally in any invertebrate. In the wake of the sequencing of the Caenorhabditis (C.) elegans genome, I review the evidence that intercellular channels in the nematode and the other model genetic invertebrate, Drosophila melanogaster, are formed from an apparently separate family of proteins, ------------------- Key: 4183 Medline: 10769231 Authors: Pichler S;Gonczy P;Schnabel H;Pozniakowski A;Ashford A;Schnabel R;Hyman AA Title: OOC-3, a novel putative transmembrane protein required for establishment of cortical domains and spindle orientation in the P1 blastomere of C. elegans embryos. Citation: Development 127: 2063-2073 2000 Type: ARTICLE Genes: mel-19 ooc-3 par-2 par-3 mnDf87 mnDf88 mnDf89 mnDf90 Abstract: Asymmetric cell divisions require the establishment of an axis of polarity, which is subsequently communicated to downstream events. During the asymmetric cell division of the P-1 blastomere in C. elegans, establishment of polarity depends on the establishment of anterior and posterior cortical domains, defined by the localization of the PAR proteins, followed by the orientation of the mitotic spindle along the previously established axis of polarity. To identify genes required for these events, we have screened a collection of maternal-effect lethal mutations on chromosome II of C. elegans. We have identified a mutation in one gene, ooc-3, with mis-oriented division axes at the two-cell stage. Here we describe the phenotypic and molecular characterization of ooc-3, ooc-3 is required for the correct localization of PAR-2 and PAR-3 cortical domains after the first cell division. OOC-3 is a novel putative transmembrane protein, which localizes to a reticular membrane compartment, probably the endoplasmic reticulum, that spans the whole cytoplasm and is enriched on the nuclear envelope and cell-cell boundaries. Our results show that ooc-3 is required to form the cortical domains essential for polarity after cell division. ------------------- Key: 4184 Medline: 20338859 Authors: Rankin CH Title: Context conditioning in habituation in the nematode Caenorhabditis elegans. Citation: Behavioral Neuroscience 114: 496-505 2000 Type: ARTICLE Genes: Abstract: Habituation has traditionally been considered a nonassociative form of learning. However, recent research suggests that retention of this nonassociative form of learning may be aided by associations formed during training. An example of this is context conditioning, in which animals that are trained and tested in the presence of a contextual cue show greater retention than animals trained and tested in different environments. This article reports context conditioning in habituation in the nematode Caenorhabditis elegans. The results showed that retention of habituation to tap at both 10- and 60-s interstimulus intervals was significantly greater if training and testing occurred in the presence of the same chemosensory cue (NaCH3COO). This context conditioning showed both extinction and latent inhibition, demonstrating that these simple worms with only 302 neurons are capable of associative context conditioning. ------------------- Key: 4186 Medline: 10902689 Authors: Zhang YC;Baldwin JG Title: Ultrastructure of the post-corpus of Zeldia punctata (Cephalobina) for analysis of the evolutionary framework of nematodes related to Caenorhabditis elegans (Rhabditina). Citation: Proceedings of the Royal Society of London B 267: 1229-1238 2000 Type: ARTICLE Genes: Abstract: The ultrastructure of the post-corpus of Zeldia punctata (Cephalobina) was compared with previous observations of Caenorhabditis elegans (Rhabditina) and Diplenteron sp. (Diplogastrina) with the goal of interpreting the morphological evolution of the feeding structures in the Secernentea. The post-corpus of Z punctata consists of six marginal, 13 muscle, five gland and seven nerve cells. The most anterior of four layers of muscle cells consists of six mononucleate cells in Z. punctata. The homologous layer in C. elegans and Diplenteron consists of three binucleate cells, suggesting a unique derived character (synapomorphy) shared between the Rhabditina and Diplogastrina. Contrary to Diplenteron sp. where we observed three oesophageal glands, Z. punctata and C. elegans have five oesophageal glands. We question this shared character as reflecting a common evolution between the Cephalobina and Rhabditina, because there are strong arguments for functional (adaptive) convergence of the five glands in these bacterial feeders. Convergence is further suggested by the mosaic distribution of three versus five glands throughout the Nemata; this distribution creates difficulties in establishing character polarity. Although morphological data are often laborious to recover and interpret, we nevertheless view 'reciprocal illumination' between molecular and morphological characters as the most promising and robust process for reconstructing the ------------------- Key: 4187 Medline: 20356330 Authors: Shim J;Lee J Title: Molecular genetic analysis of apm-2 and aps-2, genes encoding the medium and small chains of the AP-2 clathrin-associated protein complex in the nematode Caenorhabditis elegans. Citation: Molecules & Cells 10: 309-316 2000 Type: ARTICLE Genes: apm-2 aps-2 Abstract: In this report, we analyzed the apm-2 and aps-2 genes, which encode the nematode homologues of the medium chain acid the small chain of the plasma membrane-associated clathrin-associated protein complex AP-2, respectively. We determined the genomic structure of the two genes. We show that apm-2 and aps-2 genes are expressed in most, if not all, cells during embryogenesis, and that the two genes are expressed primarily in neurons and some hypodermal cells following hatching through adulthood. RNA interference experiments showed that the reduction of either apm-2 or aps-2 gene function causes embryonic lethality, larval lethality at various stages of development, and other morphological defects in the larval stages. These results indicate that apm-2 and aps-2 gene functions are required during both embryogenesis and larval stages, and that their functions may be required in proper neuronal functions. ------------------- Key: 4188 Medline: 20265922 Authors: Goutte C;Hepler W;Mickey KM;Priess JR Title: aph-2 encodes a novel extracellular protein required for GLP-1-mediated signaling. Citation: Development 127: 2481-2492 2000 Type: ARTICLE Genes: aph-1 aph-2 apx-1 glp-1 hDf9 qDf5 qDf6 Abstract: In animal development, numerous cell-cell interactions are mediated by the GLP-1/LIN-12/NOTCH family of transmembrane receptors. These proteins function in a signaling pathway that appears to be conserved from nematodes to humans. We show here that the aph3 gene is a new component of the GLP-1 signaling pathway in the early Caenorhabditis elegans embryo, and that proteins with sequence similarity to the APH-2 protein are found in Drosophila and vertebrates. During the GLP-1-mediated cell interactions in the C. elegans embryo, APH-2 is associated with the cell surfaces of both the signaling, and the responding, blastomeres. Analysis of chimeric embryos that are composed of aph-2(+) and aph-2(-) blastomeres suggests that aph-2(+) function may be provided by either the signaling or responding blastomere. ------------------- Key: 4189 Medline: 20328026 Authors: Gotoh O Title: Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps. Citation: Bioinformatics 16: 190-202 2000 Type: ARTICLE Genes: Abstract: Motivation: Locating protein-coding exons (CDSs) on a eukaryotic genomic DNA sequence is the initial and an essential step in predicting the functions of the genes embedded in that part of the genome. Accurate prediction of CDSs may be achieved by directly matching the DNA sequence with a known protein sequence or profile of ct homologous family member(s). Results: A new convention for encoding a DNA sequence into a series of 23 possible letters (translated codon or tron code) was devised to improve this type of analysis. Using this convention, a dynamic programming algorithm was developed to align a DNA sequence and a protein sequence or profile so that the spliced and translated sequence optimally matches the reference the same as the standard protein sequence alignment allowing for long gaps. The objective function also takes account of frameshift errors, coding potentials, and translational initiation, termination and splicing signals. This method was tested on Caenorhabditis elegans genes of known structures. The accuracy of prediction measured in terms of a correlation coefficient (CC) was about 95% at the nucleotide level for the 288 genes tested and 97.0% for the 170 genes whose product and closest homologue share more than 30% identical amino acids. We also propose a strategy to improve the accuracy of prediction for a set of paralogous genes by means of iterative gene prediction and reconstruction of the reference profile derived from the predicted sequences. ------------------- Key: 4190 Medline: Authors: Dokholyan NV;Buldyrev SV;Havlin S;Stanley HE Title: Distributions of dimeric tandem repeats in non-coding and coding DNA sequences. Citation: Journal of Theoretical Biology 202: 273-282 2000 Type: ARTICLE Genes: Abstract: We study the length distribution functions for the 16 possible distinct dimeric tandem repeats in DNA sequences of diverse taxonomic partitions of GenBank (known human and mouse genomes, and complete genomes of Caenorhabditis elegans and yeast). For coding DNA, we find that all 16 distribution functions are exponential. For non-coding DNA, the distribution functions for most of the dimeric repeats have surprisingly long tails, that fit a power-law function. We hypothesize that: (i) the exponential distributions of dimeric repeats in protein coding sequences indicate strong evolutionary pressure against tandem repeat expansion in coding DNA sequences; and (ii) long tails in the distributions of dimers in non-coding DNA may be a result of various mutational mechanisms. These long, non-exponential tails in the distribution of dimeric repeats in non-coding DNA are hypothesized to be due to the higher tolerance of non-coding DNA to mutations. By comparing genomes of various phylogenetic types of organisms, we find that the shapes of the distributions are not universal, but rather depend on the specific class of ------------------- Key: 4191 Medline: 20211427 Authors: Berthonneau E;Mirande M Title: A gene fusion event in the evolution of aminoacy-tRNA synthetases. Citation: FEBS Letters 470: 300-304 2000 Type: ARTICLE Genes: Abstract: The genes of glutamyl- and prolyl-tRNA synthetases (GluRS and ProRS) are organized differently in the three kingdoms of the tree of life. In bacteria and archaea, distinct genes encode the two proteins. In several organisms from the eukaryotic phylum of coelomate metazoans, the two polypeptides are carried by a single polypeptide chain to form a bifunctional protein. The linker region is made of imperfectly repeated units also recovered as singular or plural elements connected as N-terminal or C-terminal polypeptide extensions in various eukaryotic aminoacyl-tRNA synthetases. Phylogenetic analysis points to the monophyletic origin of this polypeptide motif appended to six different members of the synthetase family, belonging to either of the two classes of aminoacyl-tRNA synthetases. In particular, the monospecific GluRS and ProRS from Caenorhabditis elegans, an acoelomate metazoan, exhibit this recurrent motif as a C-terminal or N-terminal appendage, respectively. Our analysis of the extant motifs suggests a possible series of events responsible for a gene fusion that gave rise to the bifunctional glutamyl-prolyl-tRNA synthetase through recombination between genomic sequences encoding the repeated units. ------------------- Key: 4192 Medline: Authors: Liu J;Kipreos ET Title: Evolution of cyclin-dependent kinases (CDKs) and CDK-activating kinases (CAKs): Differential conservation of CAKs in yeast and metazoa. Citation: Molecular Biology and Evolution 17: 1061-1074 2000 Type: ARTICLE Genes: cdk-1 cdk-4 cdk-5 cdk-7 cdk-8 cdk-9 ncc-1 ptc-1 Abstract: Cyclin-dependent kinases (CDKs) function as central regulators of both the cell cycle and transcription. CDK activation depends on phosphorylation by a CDK-activating kinase (CAK). Different CAKs have been identified in budding yeast, fission yeast, and metazoans. All known CAKs belong to the extended CDK family. The sole budding yeast CAK, CAK1, and one of the two CAKs in fission yeast, csk1, have diverged considerably from other CDKs. Cell cycle regulatory components have been largely conserved in eukaryotes; however, orthologs of neither CAK1 nor csk1 have been identified in other species to date. To determine the evolutionary relationships of yeast and metazoan CAKs, we performed a phylogenetic analysis of the extended CDK family in budding yeast, fission yeast, humans, the fruit fly Drosophila melanogaster, and the nematode Caenorhabditis elegans. We observed that there were 10 clades for CDK-related genes, of which seven appeared ancestral, containing both yeast and metazoan genes. The four clades that contain CDKs that regulate transcription by phosphorylating the carboxyl-terminal domain (CTD) of RNA Polymerase II generally have only a single orthologous gene in each species of yeast and metazoans. In contrast, the ancestral cell cycle CDK (analogous to budding yeast CDC28) gave rise to a number of genes in metazoans, as did the ancestor of budding yeast PHO85. One ancestral clade is unique in that there are fission yeast and metazoan members, but there is no budding yeast ortholog, suggesting that it was lost subsequent to evolutionary divergence. Interestingly, CAK1 and csk1 branch together with high bootstrap support values. We used both the relative apparent synapomorphy analysis (RASA) method in combination with the S-F method of sampling reduced character sets and gamma-corrected distance methods to confirm that the CAK1/csk1 association was not an artifact of long-branch attraction. This result suggests that CAK1 and csk1 are orthologs and that a central aspect of CAK regulation has been conserved in budding and fission yeast. Although there are metazoan CDK-family members for which we could not define ancestral lineage, our analysis failed to identify metazoan CAK1/csk1 orthologs, suggesting that if the CAK1/csk1 gene existed in the metazoan ancestor, it has not been conserved. ------------------- Key: 4193 Medline: 20350263 Authors: Meredith D;Boyd CAR Title: Structure and function of eukaryotic peptide transporters. Citation: Cellular & Molecular Life Sciences 57: 754-778 2000 Type: REVIEW Genes: Abstract: The cotransport of protons and peptides is now recognised as a major route by which dietary nitrogen is absorbed from the intestine, and filtered protein reabsorbed in the kidney. Recently, molecular biology has had a very substantial impact on the study of peptide transport, and here we review the molecular and functional information available within the framework of physiology. To this end we consider not only the mammalian peptide transporters and their tissue distribution and regulation but also those from other species (including Caenorhabditis elegans) which make up the proton-dependent oligopeptide transport superfamily. In addition, understanding the binding requirements for transported substrates may allow future design and targeted tissue delivery of peptide and peptidomimetic drugs. Finally, we aim to highlight some of the less well understood areas of peptide transport, in the hope that it will stimulate further research into this challenging yet exciting topic. ------------------- Key: 4194 Medline: 20353051 Authors: Kerr R;Lev-Ram V;Baird G;Vincent P;Tsien RY;Schafer WR Title: Optical imaging of calcium transients in neurons and pharyngeal muscle of C. elegans. Citation: Neuron 26: 583-594 2000 Type: ARTICLE Genes: egl-19 unc-36 Abstract: Electrophysiology and optical indicators have been used in vertebrate systems to investigate excitable cell firing and calcium transients, but both techniques have been difficult to apply in organisms with powerful reverse genetics. To overcome this limitation, we expressed cameleon proteins, genetically encoded calcium indicators, in the pharyngeal muscle of the nematode worm Caenorhabditis elegans. In intact transgenic animals expressing cameleons, fluorescence ratio changes accompanied muscular contraction, verifying detection of calcium transients. By comparing the magnitude and duration of calcium influx in wild-type and mutant animals, we were able to determine the effects of calcium channel proteins on pharyngeal calcium transients. We also successfully used cameleons to detect electrically evoked calcium transients in individual C. elegans neurons. This technique therefore should have broad applications in analyzing the regulation of excitable cell activity in genetically tractable organisms. ------------------- Key: 4195 Medline: 10896158 Authors: Sawin ER;Ranganathan R;Horvitz HR Title: C. elegans locomotory rate is modulated by the environment through a dopaminergic pathway and by experience through a serotonergic pathway. Citation: Neuron 26: 619-631 2000 Type: ARTICLE Genes: bas-1 cat-2 cat-4 dgk-1 goa-1 mod-1 mod-6 Abstract: Caenorhabditis elegans modulates its locomotory rate in response to its food, bacteria, in two ways. First, well-fed wild-type animals move more slowly in the presence of bacteria than in the absence of bacteria. This basal slowing response is mediated by a dopamine-containing neural circuit that senses a mechanical attribute of bacteria and may be an adaptive mechanism that increases the amount of time animals spend in the presence of food. Second, food-deprived wild-type animals, when transferred to bacteria, display a dramatically enhanced slowing response that ensures that the animals do not leave their newly encountered source of food. This experience-dependent response is mediated by serotonergic neurotransmission and is potentiated by fluoxetine (Prozac). The basal and enhanced slowing responses are distinct and separable neuromodulatory components of a genetically tractable paradigm of behavioral plasticity. ------------------- Key: 4196 Medline: 20330160 Authors: Jantsch-Plunger V;Gonczy P;Romano A;Schnabel H;Hamill D;Schnabel R;Hyman AA;Glotzer M Title: CYK-4: A Rho family GTPase activiting protein (GAP) required for central spindle formation and cytokinesis. Citation: Journal of Cell Biology 149: 1391-1404 2000 Type: ARTICLE Genes: cyk-4 lit-1 zen-4 ctDf2 ctDf3 tDf6 tDf10 Abstract: During cytokinesis of animal cells, the mitotic spindle plays at least two roles. Initially, the spindle positions the contractile ring. Subsequently, the central spindle, which is composed of microtubule bundles that form during anaphase, promotes a late step in cytokinesis. How the central spindle assembles and functions in cytokinesis is poorly understood. The cyk-4 gene has been identified by genetic analysis in Caenorhabditis elegans. Embryos from cyk-4(t1689ts) mutant hermaphrodites initiate, but fail to complete, cytokinesis. These embryos also fail to assemble the central spindle. We show that the cyk-4 gene encodes a GTPase activating protein (GAP) for Rho family GTPases. CYK-4 activates GTP hydrolysis by RhoA, Rac1, and Cdc42 in vitro. RNA-mediated interference of RhoA, Rad, and Cdc42 indicates that only RhoA is essential for cytokinesis and, thus, RhoA is the likely target of CYK-4 GAP activity for cytokinesis. CYK-4 and a CYK-4:GFP fusion protein localize to the central spindle and persist at cell division remnants. CYK-4 localization is dependent on the kinesin-like protein ZEN-4/CeMKLP1 and vice versa. These data suggest that CYK-4 and ZEN-4/CeMKLP1 cooperate in central spindle assembly. Central spindle localization of CYK-4 could accelerate GTP hydrolysis by RhoA, thereby allowing contractile ring disassembly and completion of cytokinesis. ------------------- Key: 4197 Medline: 10899109 Authors: Yu RYL;Nguyen CQ;Hall DH;Chow KL Title: Expression of ram-5 in the structural cell is required for sensory ray morphogenesis in Caenorhabditis elegans male tail. Citation: EMBO Journal 19: 3542-3555 2000 Type: ARTICLE Genes: mab-7 ram-1 ram-2 ram-3 ram-4 ram-5 Abstract: Tissue morphogenesis requires complex cellular interaction and communication. The sensory ray in the Caenorhabditis elegans male tail has a simple cellular make-up and a non-essential function, thus providing an ideal model for studying the mechanisms guiding morphogenesis. We present here the analysis of a novel gene, ram-5, mutations of which are characterized by abnormal lumpy rays in the male tail. Microscopic analysis and behavioral studies revealed that lumpy rays contain operational sensory neurons. However, abnormalities were observed in the hypodermis and structural cells as well as in appositions between these two cell types. Molecular cloning and expression studies revealed that the ram-5 gene encodes a transmembrane protein localized in sensory ray support cells, the structural cells. Expression of ram-5 in these cells is required for normal ray morphogenesis, ram-5-dependent cell-cell communication is implicated in organizing the structural cell and the hypodermis, potentially through adhesion at the structural cell-hypodermal cell border. ------------------- Key: 4198 Medline: 20347034 Authors: Dernburg AF;Zalevsky J;Colaiacovo MP;Villeneuve AM Title: Transgene-mediated cosuppression in the C. elegans Citation: Genes & Development 14: 1578-1583 2000 Type: ARTICLE Genes: dpy-30 him-1 him-14 msh-5 mut-2 rde-1 rde-2 spo-11 Abstract: Functional silencing of chromosomal loci can be induced by transgenes (cosuppression) or by introduction of double-stranded RNA (RNAi). Here, we demonstrate the generality of and define rules for a transgene-mediated cosuppression phenomenon in the Caenorhabditis elegans germ line. Functional repression is not a consequence of persistent physical association between transgenes and endogenous genes or of mutations in affected genes. The cosuppression mechanism likely involves an RNA mediator that defines its target specificity, reminiscent of RNAi. Cosuppression is strongly abrogated in rde-2 and mut-7 mutants, but is not blocked in an rde-1 mutant, indicating that cosuppression and RNAi have overlapping but distinct genetic requirements. ------------------- Key: 4199 Medline: 20323149 Authors: Savage-Dunn C;Tokarz F;Wang H;Cohen S;Giannikas C;Padgett Title: SMA-3 Smad has specific and critical functions in DBL-1/SMA-6 TGFB-related signaling. Citation: Developmental Biology 223: 70-76 2000 Type: ARTICLE Genes: dbl-1 sma-1 sma-2 sma-3 sma-4 sma-6 nDf16 Abstract: A TGF beta signal transduction cascade controls body size and male tail morphogenesis in the nematode Caenorhabditis elegans. We have analyzed the function of the sma-3 Smad gene, one of three Smad genes that function in this pathway. Null mutations in sma-3 are at least as severe as null mutations in the ligand and type I receptor genes, dbl-1 and sma-6, indicating that the other Smads do not function in the absence of SMA-3. Furthermore, null mutations in sma-3 do not cause defects in egg laying or in regulation of the developmentally arrested dauer larva stage, indicating no overlapping function with another C. elegans TGF beta signaling pathway. The sma-3 gene is widely expressed at all developmental stages in hermaphrodites and males. The molecular lesions associated with eight sma-3 alleles of varying severity have been determined. The missense mutations cluster in two previously identified regions important for Smad function. ------------------- Key: 4200 Medline: 20340272 Authors: O'Connell KF;Maxwell KN;White JG Title: The spd-2 gene is required for polarization of the anteroposterior axis and formation of the sperm asters in the Caenorhabditis elegans zygote. Citation: Developmental Biology 222: 55-70 2000 Type: ARTICLE Genes: par-2 par-3 spd-2 Abstract: In the Caenorhabditis elegans zygote, polarization of the anteroposterior (AP) axis occurs during a brief period of reorganization that follows fertilization and results in the establishment of discrete cytoplasmic and cortical domains. In the cytoplasm, germ-line or P granules are circulated by an actomyosin-driven fountain now of cytoplasm and localize to the posterior, while in the cortex, two proteins required for AP polarity, PAR-2 and PAR-3, localize to the posterior and the anterior, respectively. The identity of the positional cue that determines AP axis orientation is not known, although it has been postulated to be a component of the sperm pronucleus/centrosome complex (SPCC) as the position of the SPCC correlates with the orientation of the AP axis and the direction of the fountain flows. Here, we show that mutations in the spd-e gene disrupt polarization of the AP axis. In mutant zygotes, the fountain now of cytoplasm and associated asymmetric cortical contractions are absent, P granules do not localize, and cortical PAR-3 does not become asymmetrically distributed. Interestingly, cortical PAR-2 localizes randomly to either or both poles. The random positioning of PAR-2 requires PAR-3 and indicates that a spd-g-dependent mechanism normally modulates PAR-2/PAR-3 interactions to correctly position PAR-P at the posterior. sgd-2 mutations also disrupt formation of the SPCC by delaying and attenuating the formation of sperm asters until after the period of reorganization, suggesting that spd-e mutations disrupt formation of the positional cue. Our results also indicate that sperm asters are not essential for pronuclear migration but are required for rapid female pronuclear movement and premitotic positioning ------------------- Key: 4201 Medline: 20372200 Authors: Wittenburg N;Eimer S;Lakowski B;Rohrig S;Rudolph C;Baumeister R Title: Presenilin is required for proper morphology and function of neurons in C. elegans. Citation: Nature 406: 306-309 2000 Type: ARTICLE Genes: egl-19 glp-1 hop-1 lin-12 sel-12 ttx-3 Abstract: Mutations in the human presenilin genes cause the most frequent and aggressive forms of familial Alzheimer's disease (FAD)(1). Here we show that in addition to its role in cell fate decisions in nonneuronal tissues(2-4), presenilin activity is required in terminally differentiated neurons in vivo. Mutations in the Caenorhabditis elegans presenilin genes sel-12 and hop-1 result in a defect in the temperature memory of the animals. This defect is caused by the loss of presenilin function in two cholinergic interneurons that display neurite morphology defects in presenilin mutants. The morphology and function of the affected neurons in sel-12 mutant animals can be restored by expressing sel-12 only in these cells. The wild-type human presenilin PS1, but not the FAD mutant PS1 A246E, can also rescue these morphological defects. As lin-12 mutant animals display similar morphological and functional defects to presenilin mutants, we suggest that presenilins mediate their activity in postmitotic neurons by facilitating Notch signalling. These data indicate cell-autonomous and evolutionarily conserved control of neural morphology and function by ------------------- Key: 4202 Medline: 10880475 Authors: Melendez A;Greenwald I Title: Caenorhabditis elegans lin-13, a member of the LIN-35 Rb class of genes involved in vulval development, encodes a protein with zinc fingers and an LXCXE motif. Citation: Genetics 155: 1127-1137 2000 Type: ARTICLE Genes: lin-8 lin-13 lin-15 lin-35 lin-38 smg-1 unc-36 unc-54 unc-93 nDf16 Abstract: The SynMuv genes appear to be involved in providing a signal that inhibits vulval precursor cells from adopting vulval fates in Caenorhabditis elegans. One group of SynMuv genes, termed class B, includes genes encoding proteins related to the tumor suppressor Rb and RbAp48, a protein that binds Rb. Here, we provide genetic evidence that lin-13 behaves as a class B SynMuv gene. We show that null alleles of lin-13 are temperature sensitive and maternally rescued, resulting in phenotypes ranging in severity from L2 arrest (when both maternal and zygotic activities are removed at 25 degrees), to sterile Multivulva (when only zygotic activity is removed at 25 degrees), to sterile non-Multivulva (when both maternal and zygotic activities are removed at 15 degrees), to wild-type/class B SynMuv (when only zygotic activity is removed at 15 degrees). We also show that LIN-13 is a nuclear protein that contains multiple zinc fingers and a motif, LXCXE, that has been implicated in Rb binding. These results together suggest a role for LIN-13 in Rb-mediated repression of vulval fates. ------------------- Key: 4203 Medline: 10880476 Authors: Hill KL;Harfe BD;Dobbins CA;L'Hernault SW Title: dpy-18 encodes an alpha subunit of prolyl-4-hydroxylase in Caenorhabditis elegans. Citation: Genetics 155: 1139-1148 2000 Type: ARTICLE Genes: dpy-18 tDf7 Abstract: Collagen is an extracellular matrix (ECM) component encoded by a large multigene family in multicellular animals. Procollagen is post-translationally modified by prolyl-4-hydroxylase (EC 1.14.11.2) before secretion and participation in ECM formation. Therefore, collagen processing and regulation can be studied by examining this required interaction of prolyl-4-hydroxylase with procollagen. High-resolution polymorphism mapping was used to place the Caenorhabditis elegans dpy-18 gene on the physical map, and we show that it encodes a prolyl-4-hydroxylase alpha catalytic subunit. The Dpy phenotype of dpy-18(e364) amber mutants is more severe when this mutation is in trans to the noncomplementing deficiency tDf7, while the dpy-18(e499) deletion mutant exhibits the same phenotype as dpy-18(e499)/tDf7 Furthermore, dpy-18 RNA. interference (RNAi) in wild-type worms results in Dpy progeny, while dpy-18 (RNAi) in dpy-18(e499) mutants does not alter the Dpy phenotype of their progeny. These observations suggest that the dpg-18 null phenotype is Dpy. A dpy-18::gfp promoter fusion construct is expressed throughout the hypodermis within the cells that abundantly produce the cuticle collagens, as well as in certain head and posterior neurons. While prolyl-4-hydroxylase has been studied extensively by biochemical techniques, this is the first report of a mutationally defined prolyl-4-hydroxylase in any animal. ------------------- Key: 4204 Medline: Authors: Haag ES;Kimble J Title: Regulatory elements required for development of Caenorhabditis elegans hermaphrodites are conserved in the TRA-2 homolog of Caenorhabditis remanei, a male/female sister species. Citation: Genetics 155: 1485- 2000 Type: CORRECT Genes: Abstract: ------------------- Key: 4205 Medline: 20300330 Authors: Adachi H;Ishii N Title: Effects of tocotrienols on life span and protein carbonylation in Caenorhabditis elegans. Citation: Journal of Gerontology A 55: B280-B285 2000 Type: ARTICLE Genes: Abstract: To assess the efficiency of tocotrienols against oxidative damage, we have demonstrated in a model-system nematode, Caenorhahditis elegans, that tocotrienol administration reduced the accumulation of protein carbonyl (a good indicator of oxidative damage during aging) and consequently extended the mean life span (LS), but nut the maximum LS. Conversely, or-tocopherol acetate did not affect these parameters, ris a way to evaluate the protective ability of tocotrienols against oxidative stress, the life spans of animals administrated tocotrienols before or after exposure to ultraviolet B-induced oxidative stress were measured. Ultraviolet B irradiation shortened the mean LS of animals, whereas preadministration of tocotrienols recovered the mean LS to that of unirradiated animals. Interestingly, postadministration also extended the mean LS mure than that of unirradiated animals, and administration through the LS conferred greater protection. Thus, the administration of tocotrienols to animals results in a reduction of oxidative stress risks. These data indicated that tocotrienols merit further investigation as possible agents for antiaging and oxidative stress prevention. In addition, they suggest that C. elegans will continue to provide provocative clues into ------------------- Key: 4206 Medline: 20336634 Authors: Malik HS;Burke WD;Eickbush TH Title: Putative telomerase catalytic subunits from Giardia lamblia and Caenorhabditis elegans. Citation: Gene 251: 101-108 2000 Type: ARTICLE Genes: Abstract: Eukaryotic chromosomes end in short nucleotide repeats that are added by the enzyme telomerase. The catalytic subunit of telomerase has been shown to be most closely related in sequence to reverse transcriptases encoded by eukaryotic retrotransposable elements. This raises the question as to whether the telomerase subunit was present in the first eukaryotes or was derived during early eukaryote evolution from the replication machinery of a retrotransposable element. We present the sequence of a putative telomerase catalytic subunit from the diplomonad parasite, Giardia lamblia. The G. lamblia subunit appears to have most of the characteristics of other sequenced telomerases, except that it lacks the conserved telomerase-specific 'T' motif previously identified in other eukaryotic genes. Searching genomic databases with the G. lamblia sequence, we also identified a potential telomerase catalytic subunit from Caenorhabditis elegans. The C. elegans subunit is uncharacteristically short, and lacks several motifs found in all other telomerases. The identification of a G. lambia telomerase similar to that of most other eukaryotes suggests that telomerase dates back to the earliest extant marker of eukaryotic evolution. The atypical C. elegans telomerase, on the other hand, raises intriguing biochemical questions concerning sub-domains of the telomerase catalytic subunit previously considered indispensable. The enzymatic machinery for telomere formation in C. elegans is likely to differ substantially ------------------- Key: 4207 Medline: 10884418 Authors: Doyle TG;Wen C;Greenwald I Title: SEL-8, a nuclear protein required for LIN-12 and GLP-1 signaling in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 97: 7877-7881 2000 Type: ARTICLE Genes: glp-1 lag-1 lin-12 sel-8 Abstract: LIN-12 and GLP-1 are members of the LIN-12/Notch family of receptors that mediate cell-cell interactions during development. The sel-8 gene had been identified previously in a screen for suppressors of a mutation that constitutively activates LIN-12. Here, we report that sel-8 is essential for lin-12- and glp-1-mediated signaling, and that SEL-8 is a glutamine-rich nuclear protein. We postulate that SEL-8 serves as a transcriptional coactivator or as an assembly factor for transcription complexes that contain the LIN-12 or GLP-1 intracellular ------------------- Key: 4208 Medline: 20332258 Authors: Eisenhaber B;Bork P;Yuan Y;Loffler G;Eisenhaber F Title: Automated annotation of GPI anchor sites: case study C. elegans. Citation: Trends in Biochemical Sciences 25: 340-341 2000 Type: ARTICLE Genes: Abstract: Background: Sec1-like molecules have been implicated in a Variety of eukaryotic vesicle transport processes including neurotransmitter release by exocytosis. They regulate vesicle transport by binding to a t-SNARE from the syntaxin family. This process is thought to prevent SNARE complex formation, a protein complex required for membrane fusion. Whereas Sec1 molecules are essential for neurotransmitter release and other secretory events, their interaction with syntaxin molecules seems to represent a negative regulatory step in secretion. Results: Here we report the X-ray crystal structure of a neuronal Sec1 homologue from squid, s-Sec1, at 2.4 Angstrom resolution. Neuronal s-Sec1 is a modular protein that folds into a V-shaped three-domain assembly. Peptide and mutagenesis studies are discussed with respect to the mechanism of Sec1 regulation, Comparison of the structure of squid s-Sec1 with the previously determined structure of rat neuronal Sec1 (n-Sec1) bound to syntaxin-1a indicates conformational rearrangements in domain III induced by syntaxin binding. Conclusions: The crystal structure of s-Sec1 provides the molecular scaffold for a number of molecular interactions that have been reported to affect Sec1 function. The structural differences observed between s-Sec1 and the structure of a rat n-Sec1-syntaxin-1a complex suggest that local conformational changes are sufficient to release syntaxin-1a from neuronal Sec1, an active process that is thought to involve additional effector molecule(s). ------------------- Key: 4209 Medline: 20334288 Authors: Kawano T;Ito Y;Ishiguro M;Takuwa K;Nakajima T;Kimura Y Title: Molecular cloning and characterization of a new insulin/IGF-like peptide of the nematode Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 273: 431-436 2000 Type: ARTICLE Genes: ins-18 Abstract: Diapause, aging, and fat accumulation in Caenorhabditis elegans are regulated by DAF-2, a homolog of mammalian insulin/insulin-like growth factor-I (IGF-I) receptors. We have cloned and characterized a C. elegans gene encoding a new insulin/IGF-like peptide. The gene containing three exons encodes a precursor protein 95 residue long. Although the putative precursor contains a signal peptide, B chain, C peptide, and A chain like the preproinsulin, the mature peptide consists of one polypeptide-like IGF. The predicted tertiary structure seems similar to crystal structure of insulin. Therefore, the peptide may be a hybrid molecule of insulin and IGF. The peptide expression was detected at the embryonic and several larval stages. Disruption of the peptide production led to an extended life span like the daf-2 mutation, suggesting that the peptide should be one of the ligands of the DAF-2. This is the first description of the peptide that mediates animal longevity. ------------------- Key: 4210 Medline: 20334341 Authors: Xu WL;Dunn CA;Bessman MJ Title: Cloning and characterization of the NADH pyrophosphatases from Caenorhabditis elegans and Saccharomyces cerevisae, members of a Nudix hydrolase subfamily. Citation: Biochemical and Biophysical Research Communications 273: 753-758 2000 Type: ARTICLE Genes: Abstract: Two genes from Caenorhabditis elegans and Saccharomyces cerevisiae, coding for enzymes homologous to the Nudix hydrolase family of nucleotide pyrophosphatases, have been cloned and expressed in Escherichia coli. The purified enzymes are homodimers of 39.1 and 43.5 kDa, respectively, are activated by Mg2+ and Mn2+, and are 30 to 50 times more active on NADH than on NAD(+). They both have a conserved array of amino acids downstream of the Nudix box first seen in the orthologous enzyme from E. coli which designates them as members of an NADH pyrophosphatase subfamily of the Nudix hydrolases. ------------------- Key: 4211 Medline: 20334382 Authors: Koushika SP;Nonet ML Title: Sorting and transport in C. elegans: a model system with a sequenced genome. Citation: Current Opinion in Cell Biology 12: 517-523 2000 Type: REVIEW Genes: arf-1 che-3 dhc-1 dnc-1 dnc-2 dpy-23 drp-1 dyn-1 klp-3 lin-12 osm-1 osm-3 osm-6 rab-3 ric-4 rme-2 snb-1 unc-11 unc-64 unc-101 unc-104 unc-116 vab-8 zen-4 Abstract: In the past few years, yeast and cultured cells have been the model systems of choice for the study of protein sorting and transport. Recently, there has been a surge in research in these areas in Caenorhabditis elegans, with advances in experimental techniques and genomics, New in vivo assays that monitor endocytosis and neuronal transport have been used to delineate roles for several genes in these processes. ------------------- Key: 4212 Medline: 10893272 Authors: Rogalski TM;Mullen GP;Gilbert MM;Williams BD;Moerman DG Title: The unc-112 gene in Caenorhabditis elegans encodes a novel component of cell-matrix adhesion structures required for integrin localization in the muscle cell membrane. Citation: Journal of Cell Biology 150: 253-264 2000 Type: ARTICLE Genes: deb-1 pat-2 pat-3 pat-4 unc-52 unc-112 yDf9 yDf11 Abstract: Embryos homozygous for mutations in the unc-52, pat-2, pat-3, and unc-112 genes of C. elegans exhibit a similar Pat phenotype, Myosin and actin are not organized into sarcomeres in the body wall muscle cells of these mutants, and dense body and M-line components fail to assemble. The unc-52 (perlecan), pat-2 (alpha-integrin), and pat-3 (P-integrin) genes encode ECM or transmembrane proteins found at the cell-matrix adhesion sites of both dense bodies and M-lines. This study describes the identification of the unc-112 gene product, a novel, membrane-associated, intracellular protein that colocalizes with integrin at cell-matrix adhesion complexes. The 720-amino acid UNC-112 protein is homologous to Mig-2, a human protein of unknown function. These two proteins share a region of homology with talin and members of the FERM super-family of proteins. We have determined that a functional UNC-112:: GFP fusion protein colocalizes with PAT-3/beta-integrin in both adult and embryonic body wall muscle. We also have determined that UNC-112 is required to organize PAT-3/beta-integrin after it is integrated into the basal cell membrane, but is not required to organize UNC-52/perlecan in the basement membrane, nor for DEB-1/vinculin to localize with PAT-3/beta-integrin, Furthermore, UNC-112 requires the presence of UNC-52/perlecan and PAT-YP-integrin, but not DEB-1/vinculin to become localized to the muscle cell membrane. ------------------- Key: 4213 Medline: 20341084 Authors: Chang C;Hopper NA;Sternberg PW Title: Caenorhabditis elegans SOS-1 is necessary for multiple Ras-mediated developmental signals. Citation: EMBO Journal 19: 3283-3294 2000 Type: ARTICLE Genes: clr-1 egl-15 gap-1 him-5 let-23 let-60 let-341 lin-3 lin-15 ptp-2 sem-5 sli-1 sos-1 Abstract: Vulval induction in Caenorhabditis elegans has helped define an evolutionarily conserved signal transduction pathway from receptor tyrosine kinases (RTKs) through the adaptor protein SEM-5 to RAS, One component present in other organisms, a guanine nucleotide exchange factor for Ras, has been missing in C.elegans. To understand the regulation of this pathway it is crucial to have all positive-acting components in hand. Here we describe the identification, cloning and genetic characterization of C.elegans SOS-1, a putative guanine nucleotide exchanger for LET-60 RAS, RNA interference experiments suggest that SOS-1 participates in RAS-dependent signaling events downstream of LET-23 EGFR, EGL-15 FGFR and an unknown RTK, We demonstrate that the previously identified let-341 gene encodes SOS-1. Analyzing vulval development in a let-341 null mutant, we find an SOS-1-independent pathway involved in the activation of RAS signaling. This SOS-1-independent signaling is not inhibited by SLI-1/Cbl and is not mediated by PTP-2/SHP, raising the possibility that there could be ------------------- Key: 4214 Medline: 20342795 Authors: Legouis R;Gansmuller A;Sookhareea S;Bosher JM;Baillie DL;Labouesse M Title: LET-413 is a basolateral protein required for the assembly of adherens junctions in Caenorhabditis elegans. Citation: Nature Cell Biology 2: 415-422 2000 Type: ARTICLE Genes: hmp-1 hmp-2 hmr-1 let-413 sur-8 sDf35 Abstract: Epithelial cells are polarized, with apical and basal compartments demarcated by tight and adherens junctions. Proper establishment of these subapical junctions is critical for normal development and histogenesis, We report the characterization of the gene let-413 which has a critical role in assembling adherens junctions in Caenorhabditis elegans, In let-413 mutants, adherens junctions are abnormal and mislocalized to more basolateral positions, epithelial cell polarity is affected and the actin cytoskeleton is disorganized. The LET-413 protein contains one PDZ domain and 16 leucine-rich repeats with high homology to proteins known to interact with small GTPases, Strikingly, LET-413 localizes to the basolateral membrane. We suggest that LET-413 acts as an adaptor protein involved in polarizing protein trafficking in epithelial cells. ------------------- Key: 4215 Medline: 10660671 Authors: Chase D;Serafinas C;Ashcroft N;Kosinski M;Longo D;Ferris DK;Golden A Title: The Polo-like kinase PLK-1 is required for nuclear envelope breakdown and the completion of meiosis in Caenorhabditis elegans. Citation: Genesis 26: 26-41 2000 Type: ARTICLE Genes: air-1 cdc-25 egl-19 ncc-1 plk-1 Abstract: The Polo-like kinases are key regulatory molecules required during the cell cycle for the successful completion of mitosis. We have cloned a C. elegans homolog of the Drosophila melanogaster polo gene (designated plk-1 for C. elegans polo-like kinase-l) and present the subcellular localization of the PLK-1 protein during the meiotic and mitotic cell cycles in C. elegans oocytes and embryos, respectively. Disruption of PLK-1 expression by RNA-mediated interference (RNAi) disrupts normal oocyte and embryonic development. Inspection of oocytes revealed a defect in nuclear envelope breakdown (NEBD) before ovulation. This defect in NEED was also observed in oocytes that were depleted of the cyclin-dependent kinase NCC-1 (C. elegans homolog of Cdc2), The plk-1 RNAI oocytes were fertilized; however the resulting embryos were unable to separate their meiotic chromosomes or form and extrude polar bodies. These defects led to embryonic arrest as ------------------- Key: 4216 Medline: 20351438 Authors: Schaller MD Title: UNC112: A new regulator of cell-extracellular matrix adhesions? Citation: Journal of Cell Biology 150: F9-F12 2000 Type: REVIEW Genes: deb-1 mig-2 pat-2 pat-3 pat-10 unc-52 unc-112 Abstract: Genetic analyses of Drosophila and Caenorhabditis elegans have yielded invaluable insights into many basic biological processes, perhaps most notably in the fields of receptor tyrosine kinase signaling and apoptosis. In this issue of The Journal of Cell Biology, the identification of UNC-112 as a new cytoskeletal component that may function in the assembly of cell-extracellular matrix adhesions in the muscle of C. elegans is described (Rogalski et al., 2000). Since the components of dense bodies of the C. elegans muscle are similar to the components of focal adhesions in non-muscle cells, this finding may have broader implications for the assembly of cell-extracellular matrix ------------------- Key: 4217 Medline: 20297188 Authors: Hekimi S Title: Crossroads of aging in the nematode Caenorhabditis elegans. Citation: "Results and Problems in Cell Differentiation. Molecular Biology of Aging." S. Hekimi (ed). Springer-Verlag, Berlin Heidelberg. 29: 81-112 2000 Type: REVIEW Genes: age-1 clk-1 clk-2 clk-3 ctl-1 daf-2 daf-16 eat-1 eat-2 eat-3 eat-5 eat-6 eat-7 eat-10 eat-13 eat-18 gro-1 mal-2 unc-1 unc-4 unc-6 unc-7 unc-9 unc-24 unc-25 unc-26 unc-30 unc-46 unc-47 unc-49 unc-79 unc-80 Abstract: Aging can be defined in three ways: (1) as a progressive increase in the probability of dying of nonaccidental causes, (2) as a progressive increase in the probability of being afflicted with a number of specific diseases, such as cancer, cardiovascular diseases, and neurodegenerative diseases, and (3) as a progressive increase in the prevalence of features that are not in themselves pathological, but which are linked to chronological age, like wrinkled skin or white hair. In recent years, several investigators have used definition (1) and the measure of life span in the nematode Caenorhabditis elegans to study genetic, cellular, and molecular mechanisms that might be responsible for the aging process in all organisms. ------------------- Key: 4218 Medline: 20297189 Authors: Herndon LA;Driscoll M Title: Contributions of cell death to aging in C. elegans. Citation: "Results and Problems in Cell Differentiation. Molecular Biology of Aging." S. Hekimi (ed). Springer-Verlag, Berlin Heidelberg. 29: 113-129 2000 Type: REVIEW Genes: age-1 ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ced-12 clk-1 ctl-1 daf-2 daf-12 daf-16 daf-18 daf-23 daf-28 deg-1 deg-3 mec-4 mec-10 spe-26 tkr-1 Abstract: There is little question that cell death contributes in a significant way to development, homeostasis, and disease. The roles of cell death and cell-death genes in the process of aging, however, have not been clearly elaborated. The nematode C. elegans has proven to be a powerful genetic model system for studying both cell death and aging. Mutations affecting either cellular death or animal life span have been identified, providing the tools to evaluate genetic contributions of cell death to aging. Here, we briefly review the genetics of life span and the genetics of cell death in C. elegans. We discuss what is known of the contributions of apoptotic and necrotic cell death genes to aging and highlight pressing questions for more detailed evaluation of the role of cell death in aging. ------------------- Key: 4219 Medline: 20297190 Authors: Lithgow GJ Title: Stress response and aging in Caenorhabditis elegans. Citation: "Results and Problems in Cell Differentiation. Molecular Biology of Aging." S. Hekimi (ed). Springer-Verlag, Berlin Heidelberg. 29: 131-148 2000 Type: REVIEW Genes: Abstract: ------------------- Key: 4220 Medline: 20297191 Authors: Ishii N;Hartman PS Title: Oxidative stress and aging in Caenorhabditis elegans. Citation: "Results and Problems in Cell Differentiation. Molecular Biology of Aging." S. Hekimi (ed). Springer-Verlag, Berlin Heidelberg. 29: 149-164 2000 Type: REVIEW Genes: cyt-1 ced-9 fem-3 mev-1 mev-2 mev-3 rad-8 Abstract: Aging is controlled by a complex interplay of both genetic and environmental factors. Because of this, many theories have been advanced that seek to explain the etiology of both cellular and organismal aging. In some cases, these theories are not mutually exclusive... ------------------- Key: 4221 Medline: Authors: Shearwin-Whyatt LM;Kumar S Title: Caspases in developmental cell death. Citation: IUBMB Life 48: 143-150 1999 Type: REVIEW Genes: ced-3 ced-4 ced-9 egl-1 Abstract: Caspases are a family of evolutionarily conserved cysteine proteases that constitute the effector arm of the apoptotic machinery. Studies in Caenorhabditis elegans, Drosophila melanogaster, and mouse point to evolutionarily conserved caspase function in developmentally programmed cell death in metazoans. Whereas in the nematode all developmental cell death is mediated by a single caspase, in Drosophila and the mouse some caspases appear to regulate cell death in a spatio-temporally restricted manner. This article reviews what we currently know about the roles of various caspases in the execution of developmentally programmed cell death and what may be expected from future research in ------------------- Key: 4222 Medline: Authors: Filippov V;Solovyev V;Filippova M;Gill SS Title: A novel type of RNase III family proteins in eukaryotes. Citation: Gene 245: 213-221 2000 Type: ARTICLE Genes: Abstract: The RNase III family of double-stranded RNA-specific endonucleases is characterized by the presence of a highly conserved 9 amino acid stretch in their catalytic center known as the RNase III signature motif. We isolated the drosha gene, a new member of this family in Drosophila melanogaster. Characterization of this gene revealed the presence of two RNase III signature motifs in its sequence that may indicate that it is capable of forming an active catalytic center as a monomer. The drosha protein also contains an 825 amino acid N-terminus with an unknown function. A search for the known homologues of the drosha protein revealed that it has a similarity to two adjacent annotated genes identified during C. elegans genome sequencing. Analysis of the genomic region of these genes by the Fgenesh program and sequencing of the EST cDNA clone derived from it revealed that this region encodes only one gene. This newly identified gene in nematode genome shares a high similarity to Drosophila drosha throughout its entire protein sequence. A potential drosha homologue is also found among the deposited human cDNA sequences. A comparison of these drosha proteins to other members of the RNase III family indicates that they form a new group of proteins within this family. ------------------- Key: 4223 Medline: 20503488 Authors: Jazwinski SM Title: Aging and longevity genes. Citation: Acta Biochimica Polonica 47: 269-279 2000 Type: REVIEW Genes: age-1 akt-1 akt-2 clk-1 ctl-1 daf-2 daf-12 daf-16 daf-18 daf-23 mev-1 old-1 spe-26 Abstract: The genetics of aging has made substantial strides in the past decade. This progress has been confined primarily to model organisms, such as filamentous fungi, yeast, nematodes, fruit flies, and mice, in which some thirty-five genes that determine life span have been cloned. These genes encode a wide array of cellular functions, indicating that there must be multiple mechanisms of aging. Nevertheless, some generalizations are already beginning to emerge. Pt is now clear that there are at least four broad physiological processes that play a role in aging: metabolic control, resistance to stress, gene dysregulation, and genetic stability. The first two of these at least are common themes that connect aging in yeast, nematodes, and fruit flies, and this convergence extends to caloric restriction, which postpones senescence and increases life span in rodents. Many of the human homologs of the longevity genes found in model organisms have been identified. This will lead to their use as candidate human longevity genes in population genetic studies. The urgency for such studies is great: The population is graying, and this research holds the promise ------------------- Key: 4224 Medline: 20213673 Authors: Fay DS;Han M Title: The synthetic multivulval genes of C. elegans: functional redundancy, Ras-antagonism, and cell fate determination. Citation: Genesis 26: 279-284 2000 Type: REVIEW Genes: hda-1 let-60 lin-3 lin-8 lin-9 lin-13 lin-15 lin-35 lin-36 lin-37 lin-38 lin-51 lin-52 lin-53 lin-54 lin-55 lin-56 tam-1 Abstract: Development of the C. elegans vulva requires coordination between a strikingly complex set of molecular regulators and pathways. In particular, the correct specification of vulval cell-fates requires both the activation of RTK/Ras/Map kinase members as well as negative regulation by a set of genes known as the SynMuvs. SynMuvs comprise two functionally redundant sets of genes that appear to antagonize Ras pathway signaling. In this way, SynMuv genes act to limit the number of cells adopting vulval fates. Recently, a number of SynMuv genes have been shown to encode worm homologs of the Rb transcriptional-regulatory complex. These and other results are discussed and we present several models for understanding the role of SynMuv genes in vulval development. ------------------- Key: 4225 Medline: 20213666 Authors: Rajaram S;Sedensky MM;Morgan PG Title: The sequence and associated null phenotype of a C. elegans neurocalcin-like gene. Citation: Genesis: The Journal of Genetics & Development 26: 234-239 2000 Type: ARTICLE Genes: gas-1 ncs-1 ncs-2 ncs-3 unc-1 unc-79 Abstract: The neuronal calcium sensor (NCS) proteins belong to a subfamily of the EF-hand calcium binding proteins. These proteins are primarily expressed in the nervous system and currently include more than 20 members across species [Nakayama et al,, J Mol Evol 34:416-448, 1992]. Two homologues of the ncs genes, Ce-ncs-1 and Ce-ncs-2, have recently been identified in the nematode C. elegans. Here we report the cDNA sequence of a third C. elegans ncs homologue, Ce-ncs-3. We demonstrate that a null mutation in this gene caused by a large deletion in the locus does not confer a visible phenotype in C. elegans. This, in addition to the strong homology between Ce-NCS-3 and the other C. elegans NCS proteins, may indicate functional redundancy between the three genes. ------------------- Key: 4226 Medline: 20251933 Authors: Heid PJ;Hardin J Title: Cell lineage analysis. Videomicroscopy techniques. Citation: Methods in Molecular Biology 135: 323-330 2000 Type: ARTICLE Genes: itDf2 Abstract: Complete or partial embryonic cell lineages are available for several animal model systems. In the case of the nematode Caenorhabditis elegans, the entire embryonic cell lineage has been determined and is largely invariant. This makes cell lineage analysis a potentially useful tool for assessing mutant phenotypes in C. elegans. Indeed, lineage analysis of some mutants has shown that one cell can be transformed into a different cell resulting in duplication or absence of certain tissues... ------------------- Key: 4227 Medline: 20378188 Authors: Sambongi Y;Takeda K;Wakabayashi T;Ueda I;Wada Y;Futai M Title: Caenorhabditis elegans senses protons through amphid chemosensory neurons: proton signals elicit avoidance behavior. Citation: Neuroreport 11: 2229-2232 2000 Type: ARTICLE Genes: che-2 osm-9 tax-2 tax-4 ttx-1 Abstract: Acidic pH is known to cause pain sensation through nociceptive neurons as well as taste transduction in mammals. Caenorhabditis elegans avoids an acidic environment (pH lower than similar to 4.0) formed by organic or inorganic acids. This avoidance behavior was dependent on multiple amphid chemosensory neurons, and inhibited by a mutation of capsaicin receptor homologue, and by the addition of amiloride and ruthenium red (inhibitors of proton-gated Na+ channels and capsaicin receptors, respectively). These results indicate that C. elegans recognizes protons as a nociceptive stimulus, through multiple neurons, which elicits avoidance behavior. It is of special interest that a system similar to that of mammalian signal transduction is responsible for this nematode's acid avoidance. ------------------- Key: 4228 Medline: 20344909 Authors: Cherkasova V;Ayyadevara S;Egilmez N;Reis RS Title: Diverse Caenorhabditis elegans genes that are upregulated in dauer larvae also show elevated transcript levels in long-lived, aged, or starved adults. Citation: Journal of Molecular Biology 300: 433-448 2000 Type: ARTICLE Genes: daf-2 daf-7 daf-12 daf-16 emb-27 spe-9 Abstract: Under adverse conditions, the nematode Caenorhabditis elegans undergoes reversible developmental arrest as dauer larvae, an alternative third larval stage adapted for dispersal and long-term survival. Following such arrest, which may exceed three times their usual Life-span, worms resume development to form reproductive adults of normal subsequent longevity. Mutations of genes in the dauer-formation (daf) pathway can extend life-span two- to fourfold, even in adults that mature without diapause. To identify transcript-level changes that might contribute to extended survival, we prepared a subtractive cDNA library of messages more abundant in dauer than in non-dauer (L3) larvae. Six genes were confirmed as three- to ninefold upregulated in dauer larvae, after correction for mRNA load: genes encoding poly(A)-binding protein (PABP), heat-shock proteins hsp70 and hsp90, and three novel genes of uncertain function. The novel genes encode a partial homologue of human activating signal cointegrator 1 (ASC-1), a GTP-binding homologue of a ribosomal protein, and an SH3-domain protein. Transcript levels for all except hsp70 increased during aging in two C. elegans strains, whereas the three novel genes (and possibly PABP) were also induced to varying degrees by starvation of adults. All six genes are expressed at higher levels in young adults of long-lived daf mutant strains than in normal-longevity controls, suggesting that increased expression of these genes may play a protective function, thus favoring survival in diverse contexts. ------------------- Key: 4229 Medline: 20311358 Authors: Kuznicki KA;Smith PA;Leung-Chiu WMA;Estevez AO;Scott HC;Bennett KL Title: Combinatorial RNA interference indicates GLH-4 can compensate for GLH-1; these two P granule components are critical for fertility in C. elegans. Citation: Development 127: 2907-2916 2000 Type: ARTICLE Genes: fem-1 fem-3 fog-2 gld-1 glh-1 glh-2 glh-3 glh-4 glp-1 glp-4 him-8 pgl-1 Abstract: We report that four putative germline RNA helicases, GLHs, are components of the germline-specific P granules in Caenorhabditis elegans. GLH-3 and GLH-4, newly discovered, belong to a multi-gene glh family. Although GLHs are homologous to Drosophila VASA, a polar granule component necessary for oogenesis and embryonic pattern formation, the GLHs are distinguished by containing multiple? CCHC zinc fingers. RNA-mediated interference (RNAi) reveals the GLHs are critical for oogenesis, By RNAi at 20 degrees C, when either loss of GLH-1 or GLH-4 alone has no effect, loss of both GLH-1 and GLH-4 results in 97% sterility in the glh-1/4(RNAi) offspring of injected hermaphrodites. glh-1/4(RNAi) germlines are under-proliferated and are without oocytes, glh-1/4(RNAi) animals produce sperm; however, spermatogenesis is delayed and the sperm are defective. P granules are still present in glh-1/4(RNAi) sterile worms as revealed with antibodies against the remaining GLH-2 and GLH-3 proteins, indicating the GLHs function independently in P granule assembly. These studies reveal that C. elegans can use GLH-1 or GLH-4 to promote germline development. ------------------- Key: 4230 Medline: 20349381 Authors: Golden A Title: Cytoplasmic flow and the establishment of polarity in C. elegans 1-cell embryos. Citation: Current Opinion in Genetics & Development 10: 414-420 2000 Type: REVIEW Genes: emb-27 emb-30 fem-1 mlc-4 nmy-2 nop-1 par-1 par-2 par-3 par-4 pie-1 pod-1 spd-2 spe-11 Abstract: Early Caenorhabditis elegans embryos provide an excellent model for the study of developmental processes. Development can be studied by direct observation under the light microscope and can be perturbed using laser manipulations, drug inhibitor treatments, and genetic mutants. The first division of the C. elegans embryo is asymmetric, generating two daughter cells unequal in size and developmental fate. These distinct fates are generated by the partitioning of cytoplasmic determinants during the first mitotic cell cycle. Partitioning of these determinants is thought to be driven by cytoplasmic flow. Recent studies in C, elegans in the past year have identified a number of components necessary for this flow, giving us a clearer picture of the molecular mechanisms underlying developmental asymmetry. ------------------- Key: 4231 Medline: 20349383 Authors: Ambros V Title: Control of developmental timing in Caenorhabditis elegans. Citation: Current Opinion in Genetics & Development 10: 428-433 2000 Type: REVIEW Genes: daf-12 let-7 lin-4 lin-14 lin-28 lin-29 lin-41 lin-42 Abstract: Studies of the nematode Caenorhabditis elegans have identified genetic and molecular mechanisms controlling temporal patterns of developmental events. Mutations in genes of the C. elegans heterochronic pathway cause altered temporal patterns of larval development, in which cells at certain larval stages execute cell division patterns or differentiation programs normally specific for other stages. The products of the heterochronic genes include transcriptional and translational regulators and two different cases of novel small translational regulatory RNAs. Other genes of the pathway encode evolutionarily conserved proteins, including a homolog of the Drosophila Period circadian timing regulator, and a member of the nuclear receptor family of proteins. These regulators interact with each other to elaborate stage-specific regulatory switches and act through downstream effecters to control the timing of cell-type-specific developmental events. ------------------- Key: 4232 Medline: Authors: Tsai R;Yu Q Title: Nematicidal activity of monoterpenoid compounds against economically important nematodes in agriculture. Citation: Journal of Essential Oil Research 12: 350-354 2000 Type: ARTICLE Genes: Abstract: The phase-out of increasing numbers of synthetic nematicides has prompted an urgent need for environmentally benign and effective products to protect crops from nematode damage. We tested a group of selected plant-origin monoterpenoid compounds for their nematicidal activities, and found some of them could be potent nematicides. Most of the monoterpenoids were more toxic than the commercial nematicide oxamyl (13.4% mortality at 250 mu g/mL) against the soil saprophytic nematode Caenorhabditis elegans, among which carvacrol and thymol were the most potent (100% mortality at 250 mu g/mL). (-)-Perillaldehyde, eugenol, geraniol and menthol were of moderate nematicidal activity at the same concentration, with mortality at 97%, 91%, 90% and 84%, respectively, against C. elegans. Nematicidal activity against the root lesion nematodes Pratylenchus penetrans was generally less potent, but citronellol, carvacrol and (-)-perillaldehyde were more toxic (mortality at 250 mu g/mL were 87%, 78% and 56%, respectively) than oxamyl (50%). Thymol showed similar (50%) mortality to that of oxamyl. ------------------- Key: 4233 Medline: 20359840 Authors: Toth G;Gaspari Z;Jurka J Title: Microsatellites in different eukaryotic genomes: survey and analysis. Citation: Genome Research 10: 967-981 2000 Type: ARTICLE Genes: Abstract: We examined the abundance of microsatellites with repeated unit lengths of 1-6 base pairs in several eukaryotic taxonomic groups: primates, rodents, other mammals, nonmammalian vertebrates, arthropods, Caenorhabditis elegans, plants, yeast, and other fungi. Distribution of simple sequence repeats was compared between exons, introns, and intergenic regions. Tri- and hexanucleotide repeats prevail in protein-coding exons of all taxa, whereas the dependence of repeat abundance on the length of the repeated unit shows a very different pattenl as well as taxon-specific variation in intergenic regions and introns. Although it is known that coding and noncoding regions differ significantly in their microsatellite distribution, in addition we could demonstrate characteristic differences between intergenic regions and introns. We observed striking relative abundance of (CCG)(n) . (CGG)(n) trinucleotide repeats in intergenic regions of all vertebrates, in contrast to the almost complete lack of this motif from introns. Taxon-specific variation could also be detected in the frequency distributions of simple sequence motifs. Our results suggest that strand-slippage theories alone are insufficient to explain microsatellite distribution in the genome as a whole. Other possible factors contributing to the observed divergence are ------------------- Key: 4234 Medline: 21228822 Authors: Bun-ya M;Maebuchi M;Togo SH;Kurosawa T;Hashimoto T;Kamiryo Title: Metabolic significance and expression of Caenorhabditis elegans type II 3-oxoacyl-CoA thiolase. Citation: Cell Biochemistry and Biophysics 32: 291-293 2000 Type: ARTICLE Genes: Abstract: The authors cloned the cDNA of the nematode Caenorhabditis elegans encoding a 44-kDa protein (P-44), which is similar to sterol carrier protein x (SCPx). Genomic DNA data and Northern blot analysis excluded the possibility of P-44 forming SCPx-like fusion protein. P-44 is required in the formation of bile acid in vitro from CoA esters of their enoyl-form intermediate in the presence of D-3-hydroxyacyl-CoA dehydratase/D-3-dehydrogenase bifunctional protein. Also, rat SCPx converts 24-hydroxy-form intermediate to bile acid under similar conditions. From this and other evidence, P-44 and SCPx were catagorized as type II thiolase. The mRNA encoding P-44 was detected in every developmental stage of C. elegans: egg, larval stages, and adult. P-44, therefore, seems essentail for the normal functioning of this ------------------- Key: 4235 Medline: Authors: Sommer RJ Title: Evolution of nematode development. Citation: Current Opinion in Genetics & Development 10: 443-448 2000 Type: REVIEW Genes: ced-3 lin-3 lin-39 mab-5 pop-1 Abstract: Multiple evolutionary variations occur in the cellular and genetic programming of nematode development. Many changes involve alterations of inductive interactions. Surprisingly, inductive processes vary during evolution, irrespective of changes in the final cell lineages and morphological structures. Genetic studies in some nematodes also shed light on the underlying mechanisms of ------------------- Key: 4236 Medline: 20202559 Authors: Jaroszewski L;Rychlewski L;Reed JC;Godzik A Title: ATP-activated oligomerization as a mechanism for apoptosis regulation: fold and mechanisms prediction for CED-4. Citation: Proteins 39: 197-203 2000 Type: ARTICLE Genes: ced-4 Abstract: Fold recognition algorithm FFAS (Rychlewski et al., Protein Sci, 2000;9:232-241) was used to match the nucleotide-binding adaptor shared by APAF-1, certain R gene products and CED-4 (NB-ARC domain) to the structure of the D2 domain of N-ethylemaleimide-Sensitive Fusion Protein and the delta; subunit of clamp loader of DNA polymerase III. The predicted structure consists of the p-loop ATP-binding domain, followed by two alpha-helical domains that regulate the oligomerization process. This prediction suggests a detailed molecular mechanism for the "induced proximity" hypothesis (Salvesen and Dixit, Proc Natl Acad Sci USA 1999;96:10964-10967) for CED3/caspase-9 activation by CED4/APAF-1 complex. According to this model, the ATP binding acts as a trigger in CED-4 oligomerization and the helical domain immediately following the ATP-binding domain provides additional mechanisms for regulation of the oligomerization process. This model explains most of known experimental data about CED-4-mediated caspase activation and, at the same time, suggest experiments that could test this hypothesis. ------------------- Key: 4237 Medline: 10952315 Authors: Korswagen HC;Herman MA;Clevers HC Title: Distinct beta-catenins mediate adhesion and signalling functions in C. elegans. Citation: Nature 406: 527-532 2000 Type: ARTICLE Genes: bar-1 egl-20 hmp-1 hmp-1 hmr-1 lin-17 lit-1 mab-5 mom-4 pop-1 wrm-1 Abstract: In flies and vertebrates, Armadillo/beta-catenin forms a complex with Tcf/Lef-1 transcription factors, serving as an essential coactivator to mediate Wnt signalling. It also associates with cadherins to mediate adhesion. In Caenorhabditis elegans, three putative beta-catenin homologues have been identified: WRM-1, BAR-1 and HMP-2. WRM-1 and the Tcf homologue POP-1 mediate Wnt signalling by a mechanism that has challenged current views of the Wnt pathway(1-3). Here we show that BAR-1 is the only beta-catenin homologue that interacts directly with POP-1. BAR-1 mediates Wnt signalling by forming a BAR-1/POP-1 bipartite transcription factor that activates expression of Wnt target genes such as the Hox gene mab-5. HMP-2 is the only beta-catenin homologue that interacts with the single cadherin of C. elegans, HMR-1. We conclude that a canonical Wnt pathway exists in C. elegans. Furthermore, our analysis shows that the functions of C. elegans beta-catenins in adhesion and in signalling are performed by separate proteins. ------------------- Key: 4238 Medline: 20357338 Authors: Walker AK;See R;Batchelder C;Kophengnavong T;Gronniger JT;Shi Y;Blackwell TK Title: A conserved transcription motif suggesting functional parallels between Caenorhabditis elegans SKN-1 and Cap'n'Collar-related basic leucine zipper proteins. Citation: Journal of Biological Chemistry 275: 22166-22171 2000 Type: ARTICLE Genes: cbp-1 skn-1 srg-1 Abstract: In Caenorhabditis elegans, the predicted transcription factor SKN-1 is required for embryonic endodermal and mesodermal specification and for maintaining differentiated intestinal cells post-embryonically. The SKN-1 DNA-binding region is related to the Cap'n'Collar (CNC) family of basic leucine zipper proteins, but uniquely, SKN-1 binds DNA as a monomer. CNC proteins are absent in C. elegans, however; and their involvement in the endoderm and mesoderm suggests some functional parallels to SKN-1. Using a cell culture assay, we show that SKN-1 induces transcription and contains three potent activation domains. The functional core of one domain is a short motif, the DIDLID element, which is highly conserved in a subgroup of vertebrate CNC proteins. The DIDLID element is important for SKN-1-driven transcription, suggesting a likely significance in other CNC proteins. SKN-1 binds to and activates transcription through the p300/cAMP-rrespossvv element-binding protein-binding protein (CBP) coactivator, supporting the genetic prediction that SKN-1 recruits the C. elegans p300/CBP ortholog, CBP-1. The DIDLID element appears to act independently of p300/CBP, however, suggesting a distinct conserved target. The evolutionarily preservation of the DIDLID transcriptional element supports the model that SKN-1 and some CNC proteins interact with analogous cofactors and may have preserved some similar functions despite having divergent DNA-binding domains. ------------------- Key: 4239 Medline: 20363723 Authors: Thacker C;Srayko M;Rose AM Title: Mutational analysis of bli-4/kpc-4 reveals critical residues required for proprotein convertase function in C. Citation: Gene 252: 15-25 2000 Type: ARTICLE Genes: bli-4 kpc-4 sDp2 Abstract: Kex2/subtilisin-like proteinase activity is required for the production of the adult cuticle in the nematode Caenorhabditis elegans. Deletion of the carboxy termini of four of the bli-4/kpc-4 convertase isoforms results in blistering of the adult cuticle. The blisters vary in severity (expressivity) and are not evident in all individuals (reduced penetrance). We have isolated 13 bli-4/kpc-4 mutants that arrest development in late embryogenesis. Using a PCR-based heteroduplex technique, we have identified nucleotide changes responsible for eight of these lethal mutations. The lesions reside within the first 12 exons that are shared by all of the bli-4/kpc-4 gene products, with the majority of mutations clustered within the protease domain. This finding suggests that the protease domain represents a large mutable target. Among these mutations, allele h384 represents a molecular null mutant in which the catalytically essential serine residue (Ser415) is replaced by phenylalanine. Novel missense mutations that change the identity of amino acids evolutionary conserved in all kex2/subtilisin-convertases highlight critical residues essential for activity. We examined the functional activity of BLI-4/KPC-4 products expressed from several lethal mutants by testing their effect on the variable penetrance of blistering exhibited by the e937 allele. We found that the combination of a bli-4/kpc-4 lethal mutation in tuans to the bli-4 (e937) mutation was sufficient to cause severe blistering in heteroallelic progeny, even in the presence of a known ------------------- Key: 4240 Medline: 20363734 Authors: Huang K;Johnson KD;Petcherski AG;Vandergon T;Mosser EA;Copeland NG;Jenkins NA;Kimble J;Bresnick EH Title: A HECT domain ubiquitin ligase closely related to the mammalian protein WWP1 is essential for Caenorhabditis elegans embryogenesis. Citation: Gene 252: 137-145 2000 Type: ARTICLE Genes: Abstract: The highly conserved ubiquitin/proteasome pathway controls the degradation of many critical regulatory proteins. Proteins are posttranslationally conjugated to ubiquitin through a concerted set of reactions involving activating (E1), conjugating (E2), and ligase (E3) enzymes. Ubiquitination targets proteins for proteolysis via the proteasome and may regulate protein function independent of proteolysis. We describe the cloning and functional analysis of new members of the HECT domain family of E3 ubiquitin ligases. Murine Wwp1 encoded a broadly expressed protein containing a C2 domain, four WW domains, and a catalytic HECT domain. A Caenorhabditis elegans gene was cloned encoding a HECT domain protein (CeWWP1), which was highly homologous to murine and human WWP1. Disruption of CeWwp1 via RNA interference yielded an embryonic lethal phenotype, despite the presence of at least six additional C. elegans genes encoding HECT domain proteins. The embryonic lethality was characterized by grossly abnormal morphogenesis during late embryogenesis, despite normal proliferation early in embryogenesis. CeWWP1 must therefore have unique and nonredundant functions critical for ------------------- Key: 4241 Medline: 20363735 Authors: Lyon CJ;Evans CJ;Bill BR;Otsuka AJ;Aguilera RJ Title: The C. elegans apoptotic nuclease NUC-1 is related in sequence and activity to mammalian DNase II. Citation: Gene 252: 147-154 2000 Type: ARTICLE Genes: nuc-1 Abstract: The Caenorhabditis elegans nuc-1 gene has previously been implicated in programmed cell death due to the presence of persistent undegraded apoptotic DNA in nuc-1 mutant animals. In this report, we describe the cloning and characterization of nuc-1, which encodes an acidic nuclease with significant sequence similarity to mammalian DNase II. Database searches performed with human DNase II protein sequence revealed a significant similarity with the predicted C. elegans C07B5.5 ORF. Subsequent analysis of crude C. elegans protein extracts revealed that wild-type animals contained a potent endonuclease activity with a cleavage preference similar to DNase II, while nuc-1 mutant worms demonstrated a marked reduction in this nuclease activity. Sequence analysis of C07B5.5 DNA and mRNA also revealed that nuc-1(e1392), but not wild-type animals contained a nonsense mutation within the C07B5.5 coding region. Furthermore, nuc-1 transgenic lines carrying the wild-type C07B5.5 locus demonstrated a complete complementation of the nuc-1 mutant phenotype. Our results therefore provide compelling evidence that the C07B5.5 gene encodes the NUC-1 apoptotic nuclease and that this nuclease is related in sequence and activity to DNase II. ------------------- Key: 4242 Medline: 20363736 Authors: Krieser RJ;Eastman A Title: Deoxyribonuclease II: structure and chromosomal localization of the murine gene, and comparison with the genomic structure of the human and three C. elegans Citation: Gene 252: 155-162 2000 Type: ARTICLE Genes: Abstract: Deoxyribonuclease II (DNase II) has been implicated in diverse functions including degradation of foreign DNA, genomic instability, and in mediating the DNA digestion associated with apoptosis. The production of a mouse deleted for DNase II would clearly help to discriminate these functions. We have cloned and sequenced the mouse gene encoding DNase II. It was found to have a similar intron/exon structure to the human gene, although introns 3 and 5 are considerably shorter. The gene is located on mouse chromosome 8. The order of genes at this locus is mGCDH, mEKLF, mDNase II, mSAST, which is the same order that these genes are found on human chromosome 19. The GenBank database contains incorrect expressed sequence tags (ESTs) for the 3' end of the mouse mRNA. Furthermore, the gene structure of two of the three homologs in C. elegans is also incorrectly predicted in the database. We have established the correct intron/exon structure for these genes and show the conserved sequence and structure of the C. elegans, murine and human genes. ------------------- Key: 4243 Medline: 10899123 Authors: Rohrig S;Rockelein I;Donhauser P;Baumeister R Title: Protein interaction surface of the POU transcription factor UNC-86 selectively used in touch neurons. Citation: EMBO Journal 19: 3694-3703 2000 Type: ARTICLE Genes: gcy-32 mec-2 mec-3 mec-7 tph-1 unc-86 Abstract: The Caenorhabditis elegans POU protein UNC-86 specifies the HSN motor neurons, which are required for egg-laying, and six mechanosensory neurons. To investigate how UNC-86 controls neuronal specification, we characterized two UNC-86 mutants that do not respond to touch but show wild-type egg-laying behavior. Residues P145 and L195, which are altered by these mutations, are located in the POU-specific domain and abolish the physical interaction of UNC-86 with the LIM homeodomain protein, MEC-3. This results in a failure to maintain mec-3 expression and in loss of expression of the mechanosensory neuron-specific gene, mec-2, unc-86-dependent expression of genes in other neurons is not impaired. We conclude that distinct residues in the POU domain of UNC-86 are involved in modulating UNC-86 activity during its specification of different neurons. A structural model of the UNC-86 POU domain, including base pairs and amino acid residues required for MEC-3 interaction, revealed that P145 and L195 are part of a hydrophobic pocket which is similar to the OCA-B-binding domain of the mammalian POU protein, Oct-1. ------------------- Key: 4244 Medline: 20341065 Authors: Dichoso D;Brodigan T;Chwoe KY;Lee JS;Llacer R;Park M;Corsi AK;Kostas SA;Fire A;Ahnn J;Krause M Title: The MADS-box factor CeMEF2 is not essential for Caenorhabditis elegans myogenesis and development. Citation: Developmental Biology 223: 431-440 2000 Type: ARTICLE Genes: hlh-1 hlh-8 mef-2 pha-1 Abstract: MEF2 is an evolutionarily conserved MADS (MCM1, Agamous, Deficiens, and serum response factor) box-type transcription factor that plays a critical role in vertebrate and Drosophila melanogaster myogenesis. We have addressed the developmental role of the single MEF2-like factor, CeMEF2, in Caenorhabditis elegans. Using expression assays and two mef-2 deletion alleles, we show that CeMEF2 is not required for proper myogenesis or development. Moreover, a putative null mef-2 allele fails to enhance or suppress the phenotypes of mutants in CeMyoD or CeTwist. Our results suggest that despite its evolutionary conservation of sequence and DNA binding properties, CeMEF2 has adopted a divergent role in development in the nematode compared with Drosophila and vertebrates. ------------------- Key: 4245 Medline: 21060777 Authors: Ding L;Candido EPM Title: HSP43, a small heat-shock protein localized to specific cells of the vulva and spermatheca in the nematode Caenorhabditis elegans. Citation: Biochemical Journal 349: 409-412 2000 Type: ARTICLE Genes: Abstract: Heat-shock protein 43 (HSP43) of Caenorhabditis elegans is prominently expressed in the utse cell, which attaches the uterus to the hypodermis, the uvl cells joining the vulva and the uterus, the spermathecal valve and junctions between cells of the spermathecal cage. In body-wall muscle, HSP43 forms a punctate pattern of circumferential lines, probably corresponding to regions where the hypodermis contacts the muscle cells. ------------------- Key: 4246 Medline: 20336833 Authors: Francoijs CJJ;Klomp JPG;Knegtel RMA Title: Sequence annotation of nuclear receptor ligand-binding domains by automated homology modeling. Citation: Protein Engineering 13: 391-394 2000 Type: ARTICLE Genes: Abstract: The quality of three-dimensional homology models derived from protein sequences pro,ides an independent measure of the suitability of a protein sequence for a certain fold. We have used automated homology modeling and model assessment tools to identify putative nuclear hormone receptor ligand-binding domains in the genome of Caenorhabditis elegans. Our results indicate that the availability of multiple crystal structures is crucial to obtaining useful models in this receptor family. The majority of annotated mammalian nuclear hormone receptors could be assigned to a ligand-binding domain fold by using the best model derived from any of four template structures. This strategy also assigned the ligand-binding domain fold to a number of C. elegans sequences without prior annotation. Interestingly, the retinoic acid receptor crystal structure contributed most to the number of sequences that could be assigned to a ligand-binding domain fold. Several causes for this can be suggested, including the high quality of this protein structure in terms of our assessment tools, similarity between the biological function or ligand of this receptor and the modeled genes ------------------- Key: 4247 Medline: 20362016 Authors: Walhout AJM;Boulton SJ;Vidal M Title: Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Citation: Yeast 17: 88-94 2000 Type: REVIEW Genes: Abstract: The availability of complete genome sequences necessitates the development of standardized functional assays to analyse the tens of thousands of predicted gene products in high-throughput experimental settings, Such approaches are collectively referred to as 'functional genomics', One approach to investigate the properties of a proteome of interest is by systematic analysis of protein-protein interactions. So far, the yeast two-hybrid system is the most commonly used method for large-scale, high-throughput identification of potential protein-protein interactions. Here, we discuss several technical features of variants of the two-hybrid systems in light of data recently obtained from different protein interaction mapping projects for the budding yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. ------------------- Key: 4248 Medline: Authors: Conrads TP;Anderson GA;Veenstra TD;Pasa-Tolic L;Smith RD Title: Utility of accurate mass tags for proteome-wide protein identification. Citation: Analytical Chemistry 72: 3349-3354 2000 Type: ARTICLE Genes: Abstract: An enabling capability for proteomics would be the ability to study protein expression on a global scale. While several different: separation and analysis options are being investigated to advance the practice of proteomics, mass spectrometry (MS) is rapidly becoming the core instrumental technology used to characterize the large number of proteins that constitute a proteome. To be most effective, proteomic measurements must be high-throughput, ideally allowing thousands of proteins to be identified on a time scale of hours. Most strategies of identification by MS rely on the analysis of enzymatically produced peptides originating from an isolated protein followed by either peptide mapping or tandem MS (MS/MS) to obtain sequence information for a single peptide. In the case of peptide mapping, several peptide masses are needed to unambiguously identify a protein with the typically achieved mass measurement accuracies (MMA). The ability to identify proteins based on the mass of a single peptide (i,e., an accurate mass tag; AMT) is proposed and is largely dependent on the MMA that can be achieved. To determine the MMA necessary to enable the use of AMTs for proteome-wide protein identification, we analyzed the predicted proteins and their tryptic fragments from Saccharomyces cerevisiae and Caenorhabditis elegans. The results show that low ppm (i,e,, similar to 1 ppm) level measurements have practical utility for analysis of small proteomes. Additionally, up to 85% of the peptides predicted from these organisms can function as AMTs at sub-ppm MMA levels attainable using Fourier transform ion cyclotron resonance MS. Additional information, such as sequence constraints, should enable even more complex proteomes to be studied at more modest mass measurement accuracies. Once AMTs are established, subsequent high-throughput measurements of proteomes (e,g,, after perturbations) will be greatly facilitated. ------------------- Key: 4249 Medline: 21060752 Authors: Furuyama T;Nakazawa T;Nakano I;Mori N Title: Identification of the differential distribution patterns of mRNAs and consensus binding sequences for mouse DAF-16 homologues. Citation: Biochemical Journal 349: 629-634 2000 Type: ARTICLE Genes: daf-16 sod-3 Abstract: daf-16 is a forkhead-type transcription factor, functioning downstream of insulin-like signals, and is known to be critical to the regulation of life span in Caenorhabditis elegans. Mammalian DAF-16 homologues include AFX, FKHR and FKHRL1, which contain a conserved forkhead domain and three putative phosphorylation sites for the Ser/Thr kinase Akt/protein kinase B (PKB), as well as for DAF-16. To assess the function of the homologues, we examined tissue distribution patterns of mRNAs for DAF-16 homologues in mice. In the embryos, expressions of AFX, FKHR and FKHRL1 mRNAs were complementary to each other and were highest in muscle, adipose tissue and embryonic liver. The characteristic expression pattern remained in the adult, except that signals of FKHRL1 became evident in more tissues, including the brain. In order to clarify whether each DAF-16 homologue had different target genes, we determined the consensus sequences for the binding of DAF-16 and the mouse homologues. The binding sequences for all four proteins shared a core sequence, TTGTTTAC, daf-16 family protein-binding element (DBE) binding protein. However, electrophoretic mobility shift assay showed that: the binding affinity of DAF-16 homologues to the core sequence was stronger than that to the insulin-responsive element in the insulin-like growth factor binding protein-1 promoter region, which has been identified as a binding sequence for them. We identified one copy of the DBE upstream of the first exon of sod-3 by searching the genomic database of C. elegans. Taken together, DAF-IB homologues can fundamentally regulate the common target genes in insulin-responsive tissues and the specificity to target genes of each protein is partially determined by the differences in their expression patterns. ------------------- Key: 4250 Medline: Authors: Dierick H;Bejsovec A Title: Cellular mechanisms of Wingless/Wnt signal transduction. Citation: Current Topics in Developmental Biology 43: 153-190 1999 Type: REVIEW Genes: apr-1 lin-17 lin-44 mom-1 mom-2 mom-5 pop-1 wrm-1 Abstract: Wg/Wnt signaling regulates cell proliferation and differentiation in species as divergent as nematodes, flies, frogs, and humans. Many components of this highly conserved process have been characterized and work from a number of laboratories is beginning to elucidate the mechanism by which this class of secreted growth factor triggers cellular decisions. ------------------- Key: 4251 Medline: 20351461 Authors: Combes D;Fedon Y;Grauso M;Toutant JP;Arpagaus M Title: Four genes encode acetylcholinesterases in the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. cDNA sequences, genomic structures, mutations and in vivo expression. Citation: Journal of Molecular Biology 300: 727-742 2000 Type: ARTICLE Genes: ace-1 ace-2 ace-3 ace-4 Abstract: We report the full coding sequences and the genomic organization of the four genes encoding acetylcholinesterase (AChE) in Caenorhabditis elegans and Caenorhabditis briggsae, in relation to the properties of the encoded enzymes. ace-1 and ace-2, located on chromosome X and I, respectively, encode two AChEs (ACE-1 and ACE-2) that present 35% identity. The C-terminal end of ACE-1 is homologous to the C terminus of T subunits of vertebrate AChEs. ACE-1 oligomerizes into amphiphilic tetramers. ACE-2 has a hydrophobic C terminus of H type. It associates into glycolipid-anchored dimers. In C. elegans and C. briggsae, ace-3 and ace-4 are organized in tandem on chromosome II, with only 356 nt and 369 nt, respectively, between the stop codon of ace-4 (upstream gene) and the ATG of ace-3. ace-3 produces only 5 % of the total AChE activity. It encodes an H subunit that associates into dimers of glycolipid-anchored catalytic subunits, which are highly resistant to the usual AChE inhibitors, and which hydrolyze butyrylthiocholine faster than acetylthiocholine. ACE-4 is closer to ACE-3 (54 % identity) than to ACE-1 or ACE-2. The usual sequence FGESAG surrounding the active serine residue in cholinesterases is changed to FGQSAG in ace-4. ACE-4 was not detected by our current biochemical methods, although the gene is transcribed in vivo. However the level of ace-4 mRNAs is far lower than those of ace-1, ace-2 and ace-3. The ace-2, ace-3 and ace-4 transcripts were found to be trans-spliced by both SL1 and SL2, although these genes are not included in typical operons. The molecular bases of null mutations g72 (ace-2), p1304 and dc2 (ace-3) have been identified. ------------------- Key: 4252 Medline: Authors: Johnson TE;Shook D;Murakami S;Cypser J Title: Increased resistance to stress is a marker for gerontogenes leading to increased health and longevity in nematodes. Citation: "Molecular Biology of Aging, Alfred Benzon Symposium 44", VA Borh, BFC Clark, T Stevnsner (eds). Munksgaard, Copenhagen. 44: 25-34 1999 Type: REVIEW Genes: age-1 clk-1 clk-2 clk-3 daf-2 daf-4 daf-7 daf-16 daf-23 gro-1 rad-8 spe-26 tkr-1 Abstract: "Gerontogenes" (genes that affect the rate of aging) can be defined operationally to refer to genes that can be altered such that a longer than normal maximum lifespan is the result. The last two decades of research in aging have demonstrated overwhelmingly that gerontogenes exist and modulate the rate of aging. The first direct demonstration that genes play a role in the aging process was carried out in the nematode Caenorhabditis elegans. Despite original prejudices that the aging process is "ineluctable" or that genes controlling longevity cannot be selected for, these results and others have shown that the process of aging, just as other biological processes, is specified by the gene. This is not to say that aging is programmed. Statements by noted developmental biologists that aging must be programmed to prevent competition with offspring are untenable for the nematode C. elegans, which has billions of descendents by the time its hypothetical "death program" kicks in to kill it. In the text below I will provide an overview, first of work primarily from my laboratory having to do with the detection and study of gerontogene variants using multigenic approaches. Subsequent work on mutants, initially from my lab but more recently from a variety of other labs as well, showing the molecular nature of these gerontogenes will be subsequently reviewed. Finally, we will close with a discussion of the role of resistance to stress in determining life-extension: a hypothesis that is gaining increasing support from a wide variety of observations in both invertebrate and vertebrate ------------------- Key: 4253 Medline: Authors: Ahringer J Title: NuRD and SIN3 - histone deacetylase complexes in development. Citation: Trends in Genetics 16: 351-356 2000 Type: REVIEW Genes: cbp-1 chd-3 chd-4 egl-27 egr-1 hda-1 lin-53 rba-1 rba-2 Abstract: Transcription repression mediated through histone deacetylase (HDAC) complexes is widespread, and mechanisms by which HDAC complexes act have been revealed by extensive studies in vitro and in cell culture. However, until recently, little has been known about the developmental roles of histone deacetylation. Mutants now exist for a number of members of the two major HDAC complexes (NuRD and SIN3) and some associated proteins. The emerging picture is that these complexes have specific functions in development, rather than being required for most cellular ------------------- Key: 4254 Medline: 10862717 Authors: Kostich M;Fire A;Fambrough DM Title: Identification and molecular-genetic characterization of a LAMP/CD68-like protein from Caenorhabditis elegans. Citation: Journal of Cell Science 113: 2595-2606 2000 Type: ARTICLE Genes: lmp-1 Abstract: Lysosome constitute (LAMPs) constitute a family of vertebrate proteins located predominantly in lysosomes, with lesser amounts present in endosomes and at the cell surface. Macrosialin/CD68s are similar to LAMPs in their subcellular distribution and amino acid sequence and presumed structure across the carboxyl terminal two thirds of their length. The functions of LAMPs and CD68s are not known. In the present study, a bioinformatics approach was used to identify a Caenorhabditis elegans protein (LMP-1) with sequence and presumed structural similarity to LAMPs and CD68s. LMP-I appears to be the only membrane protein in C. elegans that carries a GYXX Phi vertebrate lysosomal targeting sequence at its C terminus (where Phi is a large, hydrophobic residue). LMP-1 was found to be present from early embryonic stages through adulthood and to be predominantly localized at the periphery of a population of large, membrane-bound organelles, called granules, that are seen throughout the early embryo but in later stages are restricted to the cells of the intestine. Analysis of an LMP-1 deficient C. elegans mutant revealed that LMP-1 is not required for viability under laboratory conditions, but the absence of LMP-1 leads to an alteration in intestinal granule populations, with apparent loss of one type of ------------------- Key: 4255 Medline: Authors: Cioci LK;Qiu L;Freedman JH Title: Transgenic strains of the nematode Caenorhabditis elegans as biomonitors of metal contamination. Citation: Environmental Toxicology & Chemistry 19: 2122-2129 2000 Type: ARTICLE Genes: mtl-2 Abstract: Transition metal contamination poses a serious environmental and human health threat. The bioavailability of transition metals in environmental samples can best be assessed with living organisms. A transgenic strain of the free-living soil nematode Caenorhabditis elegans has been engineered for monitoring the bioavailability of metals. A reporter transgene consisting of a fragment of the promoter from the C. elegans metallothionein-2 gene (mtl-2) that controls the transcription of a beta-galactosidase reporter (lacZ) has been integrated into the genome of this organism. By using these transgenic C. elegans, the toxicological response to metals in samples can be quickly measured with a simple histochemical staining assay. The C. elegans that contain the mtl-2:lacZ transgene provide a more sensitive assay of exposure to cadmium, mercury, zinc, and nickel than 24-h LC50 assays or those using nematodes with heat-shock protein-based reporter transgenes. This study demonstrates that C. elegans that contain mtl-2:lacZ transgenes can function as sensitive toxicological ------------------- Key: 4256 Medline: 20323174 Authors: Chen PJ;Ellis RE Title: TRA-1A regulates transcription of fog-3, which controls germ cell fate in C. elegans. Citation: Development 127: 3119-3129 2000 Type: ARTICLE Genes: fbf-1 fbf-2 fem-1 fem-2 fem-3 fog-1 fog-2 fog-3 fox-1 gld-1 her-1 laf-1 mog-1 mog-2 mog-3 mog-4 mog-5 mog-6 nos-3 sdc-1 sdc-2 sdc-3 sex-1 spf-1 tra-1 tra-2 tra-3 xol-1 Abstract: In C. elegans, the zinc-finger protein TRA-1A is thought to be the final arbiter of somatic sexual identity. We show that fog-3, which is required for germ cells to become sperm rather than oocytes, is a target of TRA-1A. First, northern analyses and RT-PCR experiments indicate that expression of fog-3 is controlled by tra-1. Second, studies of double mutants show that this control could be direct. Third, the fog-3 promoter contains multiple sites that bind TRA-1A in gel shift assays, and mutations in these sites alter activity of fog-3 in vivo. These results establish fog-3 as one of the first known targets of transcriptional regulation by TRA-1A. Furthermore, they show that tra-1 controls a terminal regulator of sexual fate in germ cells, just as it is thought to do in the soma. ------------------- Key: 4257 Medline: Authors: Brownlee D;Holden-Dye L;Walker R Title: The range and biological activity of FMRFamide-related peptides and classical neurotransmitters in nematodes. Citation: Advances in Parasitology 45: 110-180 2000 Type: REVIEW Genes: ace-1 ace-2 ace-3 acr-2 acr-3 afp-1 avr-15 bas-1 cat-1 cat-2 cat-3 cat-4 cat-5 che-3 daf-10 deg-3 egl-2 flp-1 flp-2 flp-3 flp-4 flp-5 flp-6 flp-7 flp-8 flp-9 flp-10 flp-11 flp-12 flp-13 flp-14 flp-15 flp-16 flp-17 flp-18 goa-1 lev-1 osm-3 unc-17 unc-25 unc-29 unc-30 unc-38 unc-46 unc-47 unc-49 unc-50 Abstract: Nematodes include both major parasites of humans, livestock and plants in addition to free-living species such as Caenorhabditis elegans. The nematode nervous system (especially in C. elegans) is exceptionally well defined in terms of the number, location and projections of the small number of neurons in the nervous system and their integration into circuits involved in regulatory behaviours vital to their survival. This review will summarize what is known about the biological activity of neurotransmitters in nematodes: the biosynthetic pathways and genes involved, their receptors, inactivation mechanisms and secondary messenger signalling systems. It will cover the "classical" transmitters such as acetylcholine (ACh), GABA, glutamate, serotonin, dopamine, octopamine, noradrenaline and nitric oxide. The localization of peptides throughout the nematode nervous system is summarized, in addition to the isolation of nematode neuropeptides by both traditional biochemical techniques and more modern genetic means. The major contribution of the completion of the C. elegans genome-sequencing program is highlighted throughout. Efforts to unravel neurotransmitter action in various physiological actions such as locomotion, feeding and reproduction are detailed as well as the various inactivation mechanisms for the current complement of nematode transmitters. ------------------- Key: 4258 Medline: 20362084 Authors: Kuwabara PE;Coulson A Title: RNAi - Prospects for a general technique for determining gene function. Citation: Parasitology Today 16: 347-349 2000 Type: REVIEW Genes: Abstract: Gene discovery programs centred around expressed sequence tag (EST) and genome sequencing projects have predictably led to an exponential surge in the number of parasite gene sequences deposited in public databases. To take advantage of this wealth of sequence information, it is essential to develop rapid methods for elucidating the biological function or mode of action of individual genes. Here, Patricia Kuwabara and Alan Coulson discuss the virtues of a powerful epigenetic gene disruption technique, RNA-mediated interference (RNAi), which was originally developed for the nematode Caenorhabditis elegans. It is anticipated that this technique will not only provide insights into genefunction, but also help investigators to mine the genome for candidate drug intervention or vaccine development targets, some of which may not be readily apparent on the basis of sequence information alone. ------------------- Key: 4259 Medline: 20388557 Authors: Pickeral OK;Li JZ;Barrow I;Boguski MS;Makalowski W;Zhang J Title: Classical oncogenes and tumor suppressor genes: A comparative genomics perspective. Citation: Neoplasia 2: 280-286 2000 Type: ARTICLE Genes: Abstract: We have curated a reference set of cancer-related genes and reanalyzed their sequences in the light of molecular information and resources that have become available since they were first cloned. Homology studies were carried out for human oncogenes and tumor suppressors, compared with the complete proteome of the nematode, Caenorhabditis elegans, and partial proteomes of mouse and rat and the fruit fly, Drosophila melanogaster. Our results demonstrate that simple, semi-automated bioinformatics approaches to identifying putative functionally equivalent gene products in different organisms may often be misleading. An electronic supplement to this article provides an integrated view of our comparative genomics analysis as well as mapping data, physical cDNA resources and links to published literature and reviews, thus creating a "window" into the genomes of humans and other organisms for cancer ------------------- Key: 4260 Medline: Authors: Palmieri L;Runswick MJ;Fiermonte G;Walker JE;Palmieri F Title: Yeast mitochondrial carriers: Bacterial expression, biochemical identification and metabolic significance. Citation: Journal of Bioenergetics & Biomembranes 32: 67-77 2000 Type: ARTICLE Genes: Abstract: The genome of Saccharomyces cerevisiae encodes 35 members of a family proteins that transport metabolites and substrates across the inner membranes of mitochondria. They include three isoforms of the ADP/ATP translocase and the phosphate and citrate carriers. At the start of our work, the functions of the remaining 30 members of the family were unknown. We are attempting to identify these 30 proteins by overexpression of the proteins in specially selected host strains of Escherichia coli that allow the carriers to accumulate at high levels in the form of inclusion bodies. The purified proteins are then reconstituted into proteoliposomes where their transport properties are studied. Thus far, we have identified the dicarboxylate, succinate-fumarate and ornithine carriers. Bacterial overexpression and functional identification, together with characterization of yeast knockout strains, has brought insight into the physiological significance of these transporters. The yeast dicarboxylate carrier sequence has been used to identify the orthologous protein in Caenorhabditis elegans and, in turn, this latter sequence has been used to establish the sequence of the human ortholog. ------------------- Key: 4261 Medline: 20368157 Authors: Kawano T;Fujita M;Sakamoto H Title: Unique and redundant functions of SR proteins, a conserved family of splicing factors, in Caenorhabditis elegans development. Citation: Mechanisms of Development 95: 67-76 2000 Type: ARTICLE Genes: mom-2 srp-1 srp-2 srp-3 srp-4 srp-5 Abstract: Serine/arginine-rich proteins (SR proteins) constitute a family of RNA-binding proteins conserved throughout metazoans. The SR proteins are essential for constitutive pre-mRNA splicing and also affect regulated pre-mRNA splicing. We identified five putative genes encoding SR proteins (referred to as srp genes) in Caenorhabditis elegans, examined their expression using the gfp gene as a reporter, and suppressed their functions by double-stranded RNA-mediated interference (RNAi). The srp::gfp fusion genes were expressed in the nuclei of most somatic cells and showed no obvious tissue- or stage-specific expression. Simultaneous RNAi of the five srp genes resulted in embryonic lethality, whereas RNAi of individual srp genes caused no obvious morphological abnormality in the F1 progeny, indicating functional redundancy of the SR proteins. However, RNAi of several combinations of srp genes caused various developmental abnormalities, such as abnormal somatic gonad structures, delayed shift of the germ cell sexual differentiation, and abnormal spermatogenesis. Our results suggest that individual SR proteins have unique but somewhat redundant functions in C. ------------------- Key: 4262 Medline: 20400802 Authors: Bernhard N;van der Kooy D Title: A behavioral and genetic dissection of two forms of olfactory plasticity in Caenorhabditis elegans: adaptation and habituation. Citation: Learning & Memory 7: 199-212 2000 Type: ARTICLE Genes: odr-1 odr-10 Abstract: Continuous presentation of an olfactory stimulus causes a decrement of the chemotaxis response in the nematode Caenorhabditis elegans. However, the differences between the learning process of habituation (a readily reversible decrease in behavioral response) and other types of olfactory plasticity such as adaptation (a decrement in response due to sensory fatigue, which cannot be dishabituated) have not been addressed. The volatile odorant diacetyl (DA) was used within a single paradigm to assess the distinct processes of olfactory adaptation and habituation. Preexposing and testing worms to 100% DA vapors caused a chemotaxis decrement that was not reversible despite the presentation of potentially dishabituating stimuli. This DA adaptation was abolished in worms with an odr-10 mutation (encoding a high-affinity DA receptor on the AWA neuron), even though naive chemotaxis remained unaffected. Conversely, DA adaptation remained intact in odr-1 mutants (defective in AWC neuron-mediated olfactory behavior), even though naive chemotaxis to DA decreased. Surprisingly, exposure to vapors of intermediate concentrations of DA (0.01% and 25%) did not cause worms to exhibit any response decrement. In contrast to preexposure to high DA concentrations, preexposure to low DA concentrations (0.001%) produced habituation of the chemotaxis response (a dishabituating stimulus could reverse the response decrement back to baseline levels). The distinct behavioral effects produced by DA preexposure highlight a concentration-dependent dissociation between two decremental olfactory processes: adaptation at high DA concentrations versus habituation at low DA concentrations. ------------------- Key: 4263 Medline: 10934329 Authors: Merz DC;Culotti JG Title: Genetic analysis of growth cone migrations in Caenorhabditis elegans. Citation: Journal of Neurobiology 44: 281-288 2000 Type: REVIEW Genes: mab-20 mig-2 seu-1 seu-2 seu-3 unc-5 unc-6 unc-34 unc-40 unc-44 unc-73 unc-129 Abstract: Model organisms like Caenorhabditis elegans allow the study of growth cone motility and guidance in vivo. We are using circumferential axon guidance in C. elegans to study both the mechanisms of guidance and the interactions between different guidance systems in vivo. A genetic screen has identified suppressors of the specific axon guidance defects caused by ectopic expression of UNC-5, the repulsive receptor for the UNC-6/netrin guidance cue. These mutations identify eight genes whose products are required for the function of UNC-5 in these cells. In principle, the functions of some of these genes may involve unc-73, which encodes a multidomain, cytoplasmic protein that is an activator of the rac and rho GTPases. Loss of UNC-73 causes errors in axon guidance, and it is hypothesized that UNC-73 acts in multiple signaling pathways used by guidance receptors on the grow th cone surface to regulate the underlying cytoskeleton. Here we summarize and discuss these recent developments that are advancing our understanding of growth cone signal transduction in vivo. ------------------- Key: 4264 Medline: 20384581 Authors: Marroquin LD;Elyassnia D;Griffitts JS;Feitelson JS;Aroian Title: Bacillus thuringiensis (Bt) toxin susceptibility and isolation of resistance mutants in the nematode Caenorhabditis elegans. Citation: Genetics 155: 1693-1699 2000 Type: ARTICLE Genes: bre-1 bre-2 bre-3 bre-4 bre-5 Abstract: The protein toxins produced by Bacillus thuringiensis (Bt) are the most widely used natural insecticides in agriculture. Despite successful and extensive use of these toxins in transgenic crops, little is known about toxicity and resistance pathways in target insects since these organisms are not ideal for molecular genetic studies. To address this limitation and to investigate the potential use of these toxins to control parasitic nematodes, we are studying Bt toxin action and resistance in Caenorhabditis elegans. We demonstrate for the first time that a single Bt toxin can target a nematode. When fed Bt toxin, C. elegans hermaphrodites undergo extensive damage to the gut, a decrease in fertility, and death, consistent with toxin effects: in insects. We have screened for and isolated 10 recessive mutants that resist the toxin's effects on the intestine, on fertility, and on viability. These mutants define five genes, indicating that more components are required for Bt toxicity than previously known. We find that a second, unrelated nematicidal Bt toxin mat utilize a different toxicity pathway. Our data indicate that C. elegans can be used to undertake detailed molecular genetic analysis of Bt toxin pathways and that Bt toxins hold promise as nematicides. ------------------- Key: 4265 Medline: 20381004 Authors: Kuwabara PE;Lee MH;Schedl T;Jefferis GSXE Title: A C. elegans patched gene, ptc-1, functions in germ-line cytokinesis. Citation: Genes & Development 14: 1933-1944 2000 Type: ARTICLE Genes: npc-1 npc-2 ptc-1 ptc-2 ptc-3 ptd-1 ptd-2 ptr-1 ptr-2 ptr-3 ptr-4 ptr-5 ptr-6 ptr-7 ptr-8 ptr-9 ptr-10 ptr-11 ptr-12 ptr-13 ptr-14 ptr-15 ptr-16 ptr-17 ptr-18 ptr-19 ptr-20 ptr-21 ptr-22 ptr-23 scp-1 tra-2 Abstract: Patched (Ptc), initially identified in Drosophila, defines a class of multipass membrane proteins that control cell fate and cell proliferation. Biochemical studies in vertebrates indicate that the membrane proteins Ptc and Smoothened (Smo) form a receptor complex that binds Hedgehog (Hh) morphogens, Smo transduces the Hh signal to downstream effecters. The Caenorhabditis elegans genome encodes two Ptc homologs and one related pseudogene but does not encode obvious Hh or Smo homologs. We have analyzed ptc-l by RNAi and mutational deletion and find that it is an essential gene, although the absence of ptc-l has no detectable effect on body patterning or proliferation. Therefore, the C. elegans ptc-l gene is functional despite the lack of Hh and Smo homologs. We find that the activity and expression of ptc-l is essentially confined to the germ line and its progenitors, ptc-l null mutants are sterile with multinucleate germ cells arising from a probable cytokinesis defect. We have also identified a surprisingly large family of PTC-related proteins containing sterol-sensing domains, including homologs of Drosophila dispatched, in C. elegans and other phyla. These results suggest that the PTC superfamily has multiple ------------------- Key: 4266 Medline: 20369599 Authors: Murakami S;Tedesco PM;Cypser JR;Johnson TE Title: Molecular genetic mechanisms of life span manipulation in Caenorhabditis elegans. Citation: Annals of the New York Academy of Sciences 908: 40-49 2000 Type: ARTICLE Genes: age-1 age-2 akt-1 akt-2 clk-1 clk-2 clk-3 ctl-1 daf-2 daf-4 daf-7 daf-16 daf-18 daf-23 daf-28 eat-2 eat-6 eat-13 eat-18 gro-1 old-1 spe-10 spe-26 tkr-1 unc-26 unc-31 unc-64 Abstract: Aging and a limited life span are fundamental biological realities. Recent studies have demonstrated that longevity can be manipulated and have revealed molecular mechanisms underlying longevity control in the soil nematode Caenorhabditis elegans. Signals from both neurons and the gonad appear to negatively regulate longevity. One tissue-specific signal involves an insulin-like phosphatidylinositol 3-OH kinse pathway, dependent upon the DAF-16 forkhead transcription factor. These signals regulate mechanisms determining longevity that include the OLD-1 (formerly referred to as TKR-1) receptor tyrosine kinse. Interestingly, increased resistance to environmental stress shows a strong correlation with life ------------------- Key: 4267 Medline: 20369630 Authors: Sampayo JN;Jenkins NL;Lithgow GJ Title: Using stress resistance to isolate novel longevity mutations in Caenorhabditis elegans. Citation: Annals of the New York Academy of Sciences 908: 324-326 Type: ARTICLE Genes: age-1 Abstract: Up to 30 single gene mutations have been identified in the free-living nematode worm Caenorhabditis elegans that extend both mean and maximum life span (Age mutations). All Age mutations tested also confer increased thermotolerance (Itt). The Itt phenotype allows for the rapid and economic isolation of mutant lines with extended ------------------- Key: 4268 Medline: 20427259 Authors: Hsu JY;Sun ZW;Li X;Reuben M;Tatchell K;Bishop DK;Grushcow JM;Brame CJ;Caldwell JA;Hunt DF;Lin R;Smith MM;Allis CD Title: Mitotic phosphorylation of histone H3 is governed by IpI1/aurora kinse and Glc7/PP1 phosphatase in budding yeast and nematodes. Citation: Cell 102: 279-291 2000 Type: ARTICLE Genes: air-1 air-2 Abstract: Phosphorylation of histone H3 at serine 10 occurs during mitosis and meiosis in a wide range of eukaryotes and has been shown to be required for proper chromosome transmission in Tetrahymena. Here we report that Ipl1/aurora kinase and its genetically interacting phosphatase, Glc7/PP1, are responsible for the balance of H3 phosphorylation during mitosis in Saccharomyces cerevisiae and Caenorhabditis elegans. In these models, both enzymes are required for H3 phosphorylation and chromosome segregation, although a causal link between the two processes has not been demonstrated. Deregulation of human aurora kinases has been implicated in oncogenesis as a consequence of chromosome missegregation. Our findings reveal an enzyme system that regulates chromosome dynamics and controls histone phosphorylation that is conserved ------------------- Key: 4269 Medline: 20381325 Authors: Zheng R;Ghirlando R;Lee MS;Mizuuchi K;Krause M;Graigie R Title: Barrier-to-autointegration factor (BAF) bridges DNA in a discrete, higher-order nucleoprotein complex. Citation: Proceedings of the National Academy of Sciences USA 97: 8997-9002 2000 Type: ARTICLE Genes: Abstract: Barrier-to-autointegration factor (BAF) is a highly conserved cellular protein that was identified by its activity in protecting retroviral DNA against autointegration. We show that BAF has the property of bridging double-stranded DNA in a highly ordered nucleoprotein complex. Whereas BAF protein alone is a dimer in solution, upon binding DNA, BAF forms a dodecamer with DNA bound at multiple discrete sites in the complex. The interactions between BAF and DNA are entirely nonspecific with respect to DNA sequence. The dual interaction of BAF with DNA and LAP2, a protein associated with the nuclear lamina, suggests a role for LAP2 in chromosome organization. Consistent with this idea, RNA interference experiments with Caenorhabditis elegans reveal a defect in ------------------- Key: 4270 Medline: Authors: Kim SK Title: Cell polarity: new PARtners for Cdc42 and Rac. Citation: Nature Cell Biology 2: E143-E145 2000 Type: REVIEW Genes: pal-1 par-3 par-6 skn-1 Abstract: Three recent papers have reported the surprising finding that Cdc42 and Rad, both of which are known to be involved in maintaining apico-basolateral polarity of epithelial cells, can each bind to a protein complex containing Par6, Par3 and PKC zeta. These latter three proteins have known functions in the polarization of mother cells before asymmetric cell division in Caenorhabditis elegans. These latest results indicate a possible link between the mechanisms used to maintain cell polarity and to set up asymmetric cell divisions. ------------------- Key: 4271 Medline: Authors: Fricke B;Lints R;Stewart G;Drummond H;Dodt G;Driscoll M;von During M Title: Epithelial Na+ channels and stomatin are expressed in rat trigeminal mechanosensory neurons. Citation: Cell Tissue Research 299: 327-334 2000 Type: ARTICLE Genes: mec-2 mec-4 mec-10 Abstract: Caenorhabditis elegans MEC-4 and MEC-10 are subunits of the degenerin/epithelial Na+ channel (DEG/ENaC) ion channel superfamily thought to be associated with MEC-2 (a stomatin-like protein) in a mechanotransducing molecular complex in specialized touch sensory neurons. A key question is whether analogous molecular complexes in higher organisms transduce mechanical signals. To address this question, we selected mechanoreceptors of the rat vibrissal follicle-sinus complex in the mystacial pad and the trigeminal ganglia for an immunocytochemical and molecular biological study. RT-PCR of poly(A+) mRNA of rat trigeminal ganglia indicated that a-, B- and y-ENaC and stomatin mRNA are expressed in rat trigeminal ganglia. Using immunocytochemistry, we found that a-, B- and y-ENaC subunits and stomatin are localized in the perikarya of the trigeminal neurons and in a minor fraction of their termination site in the vibrissal follicle-sinus complex, where longitudinal lanceolate endings are immunopositive. We conclude that a-, B-, and y-ENaC subunits as well as the candidate interacting protein stomatin are coexpressed in a mammalian mechanoreceptor, a location consistent with a possible role in mechanotransduction. ------------------- Key: 4272 Medline: 20222482 Authors: White J Title: Worm tales. Citation: International Journal of Developmental Biology 44: 39-42 2000 Type: REVIEW Genes: Abstract: 1969 was a landmark year. But for me it was not Neil Armstrong's giant leap or Woodstock heralding the beginning of the end of the sixties that sticks in my mind. It was a visit I made to Cambridge to meet a "bloke who is starting a new project to study some sort of worm", as my head of department at the Medical Research Council's National Institute of Medical Research informed me... ------------------- Key: 4273 Medline: 20403304 Authors: Hopper NA;Lee J;Sternberg PW Title: ARK-1 inhibits EGFR signaling in C. elegans. Citation: Molecular Cell 6: 65-75 2000 Type: ARTICLE Genes: ark-1 gap-1 let-23 let-60 let-341 lin-3 lin-15 sem-5 sli-1 unc-101 sDf22 Abstract: A screen for synthetic enhancers of sli-1 identified ark-1 (for Ack-related tyrosine kinase), a novel inhibitor of let-23 EGFR signaling in C. elegans. An ark-l mutation synergizes with mutations in other negative regulators of let-23, resulting in increased RAS signaling. Genetic analysis suggests that ARK-1 acts upstream of RAS and is dependent upon SEM-5. ARK-1 inhibits LET-23-mediated ovulation, a RAS-independent function. ARK-1 physically interacts with SEM-5 in the yeast two-hybrid assay. We find that sem-5 also has a negative function in let-23-mediated ovulation and suggest that this negative function is mediated by the recruitment of inhibitors such as ARK-1. ------------------- Key: 4274 Medline: Authors: Hirabayashi J;Arata Y;Kasai K Title: Reinforcement of frontal affinity chromatography for effective analysis of lectin-oligosaccharide interactions. Citation: Journal of Chromatography 890: 261-271 2000 Type: ARTICLE Genes: Abstract: Frontal affinity chromatography is a method for quantitative analysis of biomolecular interactions. We reinforced it by incorporating various merits of a contemporary liquid chromatography system. As a model study, the interaction between an immobilized Caenorhabditis elegans galectin (LEC-6) and fluorescently labeled oligosaccharides (pyridylaminated sugars) was analyzed. LEC-6 was coupled to N-hydroxysuccinimide-activated Sepharose 4 Fast Flow (100 mu m diameter), and packed into a miniature column (e.g., 10 X 4.0 mm, 0.126 ml). Twelve pyridylaminated oligosaccharides were applied to the column through a 2-ml sample loop, and their elution patterns were monitored by fluorescence. The volume of the elution front (V) determined graphically for each sample was compared with that obtained in the presence of an excess amount of hapten saccharide, lactose (V-0); and the dissociation constant, K-d, was calculated according to the literature [K. Kasai, Y. Oda, M. Nishibawa, S. Ishii, J. Chromatogr. 376 (1986) 33]. This system also proved to be useful for an inverse confirmation; that is, application of galectins to an immobilized glycan column tin the present case, asialofetuin was immobilized on Sepharose 4 Fast Flow), and the elution profiles were monitored by fluorescence based on tryptophan. The relative affinity of various galectins for asialofetuin could be easily compared in terms of the extent of retardation. The newly constructed system proved to be extremely versatile. It enabled rapid (analysis time 12 min/cycle) and sensitive (20 nM for pyridylaminated derivatives, and 1 mu g/ml for protein) analyses of lectin-carbohydrate interactions. It should become a powerful tool for elucidation of biomolecular interactions, in particular for functional analysis of a large number of ------------------- Key: 4275 Medline: 20391980 Authors: Harris TW;Hartwieg E;Horvitz HR;Jorgensen EM Title: Mutations in synaptojanin disrupt synaptic vesicle recycling. Citation: Journal of Cell Biology 150: 589-599 2000 Type: ARTICLE Genes: unc-26 Abstract: Synaptojanin is a polyphosphoinositide phosphatase that is found at synapses and binds to proteins implicated in endocytosis. For these reasons, it has been proposed that synaptojanin is involved in the recycling of synaptic vesicles. Here, we demonstrate that the unc-26 gene encodes the Caenorhabditis elegans ortholog of synaptojanin. unc-26 mutants exhibit defects in vesicle trafficking in several tissues, but most defects are found at synaptic termini. Specifically, we observed defects in the budding of synaptic vesicles from the plasma membrane, in the uncoating of vesicles after fission, in the recovery of vesicles from endosomes, and in the tethering of vesicles to the cytoskele- ton. Thus, these results confirm studies of the mouse synaptojanin 1 mutants, which exhibit defects in the uncoating of synaptic vesicles (Cremona, O., G, Di Paolo, M.R, Wenk, A. Luthi, W.T. Kim, K. Takei, L. Daniell, Y. Nemoto, S,B, Shears, R.A. Flavell, D.A, McCormick, and P.De Camilli. 1999. Cell. 99:179-188), and further demonstrate that synaptojanin facilitates multiple steps of synaptic vesicle recycling. ------------------- Key: 4276 Medline: 20400336 Authors: Walchli S;Colinge J;van Huijsduijnen RH Title: MetaBlasts: tracing protein tyrosine phosphate gene family roots from man to Drosophila melanogaster and Caenorhabditis elegans genomes. Citation: Gene 253: 137-143 2000 Type: ARTICLE Genes: Abstract: At increasing speed, sequencing data are being made public from both complex and simple life forms. Although biomedical interests tend to focus on mammalian genes, only simple organisms allow rapid genetic manipulation and functional analysis. A prerequisite for the meaningful extrapolation of gene functional studies from invertebrates to man is that the orthologs under study are unambiguously linked. However, identifying orthologs is not trivial, especially where large gene families are involved. We present here an automated sequence analysis procedure that allows a rapid visualization of most likely ortholog pairs. We illustrate the utility of this approach for the human gene family of protein tyrosine phosphatases (PTPs) as compared with the full set of Caenorhabditis elegans and Drosophila melanogaster conceptual ORFs. The approach is based on a reciprocal series of BLAST searches, which are automatically stored and represented in an HTML-formatted table. We have used this 'MetaBlast' approach to compile lists of human PTPs and their worm and fly orthologs. Many of these PTP orthologs had not been previously identified ------------------- Key: 4277 Medline: 20372572 Authors: Garcia-Saez I;Plasterk RHA Title: Purification of the Caenorhabditis elegans transposase Tc1A refolded during gel filtration chromatography. Citation: Protein Expression & Purification 19: 355-361 2000 Type: ARTICLE Genes: Abstract: Full-length recombinant transposase Tc1A from Caenorhabditis elegans (343 amino acids) expressed in Escherichia coli BL21 in inclusion bodies has been purified in a high yield in a soluble form. The procedure includes denaturation of the inclusion bodies followed by refolding of the Tc1A protein by gel filtration. This last step is absolutely crucial to give a high yield of soluble and active protein since it allows the physical separation of the aggregates from intermediates that give rise to correctly refolded protein, This step is very sensitive to the concentration of protein. Good yields of refolded protein are obtained by refolding 2 to 12 mg of denatured protein. The other purification steps involve the initial use of gel filtration under denaturing conditions and a final step of ion-exchange chromatography. Biological activity of the purified protein was confirmed in an ilE vitro transposon excision assay and its DNA-binding capacity by UV crosslinking. This new Tc1A purification procedure gives a yield of 12-16 mg/liter E, coli culture, ------------------- Key: 4278 Medline: 20389388 Authors: Shim J;Sternberg PW;Lee J Title: Distinct and redundant functions of u1 medium chains of the AP-1 clathrin-associated protein complex in the nematode Caenorhabditis elegans. Citation: Molecular Biology of the Cell 11: 2743-2756 2000 Type: ARTICLE Genes: apm-1 apm-2 let-23 sli-1 unc-101 Abstract: In the nematode Caenorhabditis elegans, there exist two mu 1 medium chains of the AP-1 clathrin-associated protein complex. Mutations of unc-101, the gene that encodes one of the mu 1 chains, cause pleiotropic effects (Lee et nl., 1994). In this report, we identified and analyzed the second mu 1 chain gene, apm-1. Unlike the mammalian homologs, the two medium chains are expressed ubiquitously throughout development. RNA interference (RNAi) experiments with apm-1 showed that apm-1 and unc-101 were redundant in embryogenesis and in vulval development. Consistent with this, a hybrid protein containing APM-1, when overexpressed, rescued the phenotype of an unc-101 mutant. However, single disruptions of apm-1 or unc-101 have distinct phenotypes, indicating that the two medium chains may have distinct functions. RNAi of any one of the small or large chains of AP-1 complex (sigma 1, beta 1, or gamma) showed a phenotype identical to that caused by the simultaneous disruption of unc-101 and apm-1, but not that by single disruption of either gene. This suggests that the two medium chains may share large and small chains in the AP-1 complexes. Thus, apm-1 and unc-101 encode two highly related mu 1 chains that share redundant and distinct functions within AP-1 clathrin-associated protein complexes ------------------- Key: 4279 Medline: 20396592 Authors: Brown NH Title: Cell-cell adhesion via the ECM: integrin genetics in fly and worm. Citation: Matrix Biology 19: 191-201 2000 Type: REVIEW Genes: ina-1 pat-2 pat-3 Abstract: Integrins are essential for the development of the two genetically tractable invertebrate model organisms, the nematode worm Caenorhabditis elegans and the fruit fly Drosophila melanogaster. Just two integrins are present in C. elegans: one putative RGD binding integrin alpha pat-2 beta pat-3, corresponding to Drosophila alpha PS2 beta PS and vertebrate alpha 5 beta 1, alpha V beta 1 and alpha 8 beta 1, and one putative laminin binding integrin alpha rina-1 beta pat-3, corresponding to Drosophila alpha PS1 beta PS and vertebrate alpha 3 beta 1, alpha 6 beta 1 and alpha 7 beta 1. in this review, the function of this minimal set of integrins during the development of these two invertebrates is compared. Despite the differences in bodyplan and developmental strategy, integrin adhesion to the extracellular matrix is required for similar processes: the formation of the link that translates muscle contraction into movement of the exoskeleton, cell migration, and morphogenetic interactions between epithelia. Other integrin functions, such as regulation of gene expression, have not yet been experimentally demonstrated in both organisms. Additional proteins have been characterised in each organism that are essential for integrin function, including extracellular matrix ligands and intracellular interacting proteins, but so far different proteins have been found in the two organisms. This in part represents the fact that the characterisation of the full set of interacting proteins is not complete in either system. However, in other cases different proteins appear to be used for similar functions in the two animals. The continued use of genetic approaches to identify proteins required for integrin function in these two model organisms should lead to the identification of the minimal set of conserved components that form integrin adhesive ------------------- Key: 4280 Medline: 20414750 Authors: Kent WJ;Zahler AM Title: Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Citation: Genome Research 10: 1115-1125 2000 Type: ARTICLE Genes: ace-1 ace-3 ace-4 act-4 add-2 avr-15 bli-4 cbp-1 ceh-6 cha-1 cmk-1 col-2 col-8 cpr-5 csr-1 daf-18 deg-3 del-1 des-2 dhc-1 dom-3 drp-1 eat-6 eft-2 egl-2 exp-2 fat-3 fem-1 fem-2 flp-13 gas-1 gcy-13 gcy-33 gcy-6 glc-3 glp-1 goa-1 gpb-1 gpd-1 gpd-2 gpd-3 gpd-4 her-1 his-10 his-11 his-12 his-29 his-31 his-32 his-33 his-34 his-35 his-38 his-5 his-6 his-7 his-8 his-9 hsb-1 hum-3 ife-4 ima-3 itr-1 jnk-1 kin-13 kin-15 kin-16 klc-1 kup-1 lec-2 lec-3 let-2 let-70 let-721 let-805 let-858 let-99 lev-1 lgx-1 lin-12 lin-2 lin-25 lin-3 lin-46 lrp-1 lrx-1 mab-3 mai-1 mec-10 mec-12 mec-9 mel-32 mix-1 mom-5 msp-113 msp-142 msp-19 msp-31 msp-32 msp-33 msp-38 msp-51 msp-53 mua-3 mxl-1 myo-1 myo-2 myo-3 ncc-1 nhr-14 nhr-21 nhr-8 nid-1 par-3 pgp-2 pgp-3 pgp-4 rab-3 rrp-1 sel-12 sex-1 skn-1 sma-3 sma-6 spe-9 sqt-1 sqv-3 syd-2 tax-2 tba-1 tba-2 tnc-1 twk-11 twk-17 unc-115 unc-17 unc-22 unc-24 unc-30 unc-33 unc-43 unc-45 unc-47 unc-5 uvt-1 vab-8 vha-1 vha-2 vit-1 vit-2 vit-5 Abstract: A new algorithm, WABA, was developed for doing large-scale alignments between genomic DNA of different species. WABA was used to align 8 million bases of Caenorhabditis briggsae genomic DNA against the entire 97-million-base Caenorhabditis elegans genome. The alignment, including C. briggsae homologs of 154 genetically characterized C. elegans genes and many times this number of largely uncharacterized ORFs, can be browsed and searched on the Web (http://www.cse.ucsc.edu/similar to kent/intronerator). The alignment confirms that patterns of conservation can be useful in identifying regulatory regions and rarely expressed coding regions. Conserved regulatory elements can be identified inside coding exons by examining the level of divergence at the wobble position of codons. The alignment reveals a bimodal size distribution of syntenic regions. Over 250 introns are present in one species but not the other. The 3' and 5' intron splice sites have more similarity to each other in introns unique to one species than in C. elegans introns as a whole, suggesting a possible mechanism for intron removal. ------------------- Key: 4281 Medline: 20407250 Authors: Dong MQ;Chase D;Patikoglou GA;Koelle MR Title: Multiple RGS proteins alter neural G protein signaling to allow C. elegans to rapidly change behavior when fed. Citation: Genes & Development 14: 2003-2014 2000 Type: ARTICLE Genes: eat-16 egl-10 egl-30 goa-1 rgs-1 rgs-2 rgs-3 rgs-4 rgs-5 rgs-6 rgs-7 rgs-8 rgs-9 rgs-10 rgs-11 Abstract: Regulators of G protein signaling (RGS proteins) inhibit heterotrimeric G protein signaling by activating G protein GTPase activity. Many mammalian RGS proteins are expressed in the brain and can act in vitro on the neural G protein G, but the biological purpose of this multiplicity of regulators is not clear. We have analyzed all 13 RGS genes in Caenorhabditis elegans and found that three of them influence the aspect of egg-laying behavior controlled by G signaling. A previously studied RGS protein, EGL-10, affects egg laying under all conditions tested. The other two RGS proteins, RGS-1 and RGS-2, act as G(o) GTPase activators in vitro but, unlike EGL-10, they do not strongly affect egg laying when worms are allowed to feed constantly. However, rgs-1; rgs-2 double mutants fail to rapidly induce egg-laying behavior when refed after starvation. Thus EGL-10 sets baseline levels of signaling, while RGS-1 and RGS-2 appear to redundantly alter signaling to cause appropriate behavioral responses to food. ------------------- Key: 4282 Medline: 20347027 Authors: Gunther CV;Georgi LL;Riddle DL Title: A Caenorhabditis elegans type I TGFbeta receptor can function in the absence of type II kinase to promote larval development. Citation: Development 127: 3337-3347 2000 Type: ARTICLE Genes: daf-1 daf-4 daf-7 Abstract: The daf-4 gene encodes a type II bone morphogenetic protein receptor in Caenorhabditis elegans that regulates dauer larva formation, body size and male tail patterning. The putative type I receptor partner for DAF-4 in regulating dauer larva formation is DAF-1, Genetic tests of the mechanism of activation of these receptors show that DAF-1 can signal in the absence of DAF-4 kinase activity. A daf-1 mutation enhances dauer formation in a daf-4 null background, whereas overexpression of daf-1 partially rescues a daf-4 mutant. DAF-1 alone cannot fully compensate for the loss of DAF-4 activity, indicating that nondauer development normally results from the activities of both receptors. DAF-1 signaling in the absence of a type II kinase is unique in the type I receptor family. The activity may be an evolutionary remnant, owing to daf-1's origin near the type I/type II divergence, or it may be an innovation that evolved in nematodes, daf-1 and daf-4 promoters both mediated expression of green fluorescent protein in the nervous system, indicating that a DAF-1/DAF-4 receptor complex may activate a neuronal signaling pathway. Signaling from a strong DAF-1/DAF-4 receptor complex or a weaker DAF-1 receptor alone may provide larvae with more precise control of the dauer/nondauer decision in a range of environmental ------------------- Key: 4283 Medline: 20347029 Authors: Pujol N;Torregrossa P;Ewbank JJ;Brunet JF Title: The homeodomain protein CePHOX2/CEH-17 controls antero-posterior axonal growth in C. elegans. Citation: Development 127: 3361-3371 2000 Type: ARTICLE Genes: ceh-8 ceh-10 ceh-17 glr-1 unc-4 unc-42 vab-8 Abstract: An essential aspect of a neuron's identity is the pattern of its axonal projections. In C. elegans, axons extend either longitudinally or circumferentially in response to distinct molecular cues, some of which have been identified. It is currently unclear, however, how the differential capacity to respond to these cues is transcriptionally implemented in distinct neuronal subtypes. Here, we characterise a C. elegans paired-like homeobox gene, CePhox2/ceh-17, expressed in five head neurons, ALA and the 4 SIAs, all of which project axons towards the tail along the lateral and sublateral cords. Abrogation of ceh-17 function, while leaving intact many phenotypic traits of these neurons, disrupts their antero-posterior axonal elongation beyond the mid-body region. Conversely, ectopic expression of ceh-17 in the mechanoreceptors, several of which are known to pioneer their tract, leads to exaggerated longitudinal axonal outgrowth. Thus, ceh-17 is a novel gene involved in ------------------- Key: 4284 Medline: 20393806 Authors: Ayyadevara S;Thaden JJ;Reis RJS Title: Anchor polymerase chain reaction display: A high-throughput method to resolve, score, and isolate dimorphic genetic markers based on interspersed repetitive DNA elements. Citation: Analytical Biochemistry 284: 19-28 2000 Type: ARTICLE Genes: Abstract: enes which confer a disease when mutated, or for which population variability contributes to a quantitative trait such as longevity or disease susceptibility, can be localized in the genetic map by use of an appropriately dense set of polymorphic DNA markers. Here we describe an anchor PCR method for high-throughput genotyping, which can be used to amplify the DNA segments flanking an interspersed repetitive sequence such as a transposon, and to limit the number of product bands per reaction to facilitate marker resolution. We used this method to amplify and display DNA fragments flanking the Tc1 transposable elements from different strains of the nematode Caenorhabditis elegans, varying widely in insert number, and to analyze marker segregation in recombinant inbred lines generated from an interstrain cross. Since essentially all eukaryotic genomes contain abundant interspersed repeat families, many of which are dimorphic (for presence or absence of specific elements) among populations, this method can be used for rapid genotyping and fine-scale chromosomal mapping in many species, including those for which extensive mapping and sequencing ------------------- Key: 4285 Medline: 20389515 Authors: Galat A Title: Sequence diversification of the FK506-binding proteins in several different genomes. Citation: European Journal of Biochemistry 267: 4945-4959 2000 Type: ARTICLE Genes: Abstract: Sequences of FK506-binding proteins (FKBPs) from four genomes of the following organisms were compared: the prokaryote Escherichia coli, the lower eukaryote Saccharomyces cerevisiae, the plant Arabidopsis thaliana, the nematode Caenorhabditis elegans and a composite of 14 unique FKBPs from two mammalian organisms Homo sapiens (man) and Mus musculus (domestic mouse). A singular FK506-like binding domain (FKBD) has about 12 kDa and occurs in the form of archetypal FKBP-12 and as a part of different proteins ranging in size from 13 to 135 kDa. Some organisms may contain a variable number of proteins which consist from two to four consecutively fused FKBDs. In the 12-kDa subgroup of archetypal FKBPs sequence identity (ID) varies from 100 to 83% (mammalian FKBPs-12), 75-50% in mammalian vs. invertebrate FKBPs-12, and fall to about 30% for pairwise sequence comparisons of mammalian and bacterial FKBPs-12 which suggests that their sequences are divergent. Multiple sequence alignment of FKBPs from the four genomes and a set of unique mammalian FKBPs does not contain any explicit consensus sequence but certain sequence positions have conserved physico-chemical characteristics. Variations of hydrophobicity and bulkiness in the multiple sequence alignment are nonsymmetrical because the physico-chemical properties of the aligned sequences changed during evolution. These variations at the sequence positions which are crucial for binding the immunosuppressive macrolide FK506 and peptidyl-prolyl cis/trans isomerase (PPIase) activity are small. ------------------- Key: 4286 Medline: 20347023 Authors: Jungblut B;Sommer RJ Title: Novel cell-cell interactions during vulva development in Pristionchus pacificus. Citation: Development 127: 3295-3303 2000 Type: ARTICLE Genes: mab-5 Abstract: Vulva development differs between Caenorhabditis elegans and Pristionchus pacificus in several ways. Seven of 12 ventral epidermal cells in P. pacificus die of apoptosis, whereas homologous cells in C. elegans fuse with the hypodermal syncytium. Vulva induction is a one-step process in C. elegans, but requires a continuous interaction between the gonad and the epidermis in P. pacificus. Here we describe several novel cell-cell interactions in P. pacificus, focusing on the vulva precursor cell P8.p and the mesoblast M. P8.p in P. pacificus, unlike its homologous cell in C. elegans, is incompetent to respond to gonadal signaling in the absence of other vulva precursor cells, but can respond to lateral signaling from a neighboring vulval precursor. P8.p provides an inhibitory signal that determines the developmental competence of P(5,7).p. This lateral inhibition acts via the mesoblast M and is regulated by the homeotic gene Ppa-mab-5. In Ppa-mab-5 mutants, M is misspecified and provides inductive signaling to the vulval precursor cells, including P8.p. Taken together, vulva development in P. pacificus displays novel cell-cell interactions involving the mesoblast M and P8.p. In particular, P8.p represents a new ventral epidermal cell type, which is characterized by novel interactions and a specific response to gonadal signaling. ------------------- Key: 4287 Medline: 20414744 Authors: Baillie DL;Rose AR Title: WABA Success: A tool for sequence comparison between large genomes. Citation: Genome Research 10: 1071-1073 2000 Type: REVIEW Genes: bli-4 Abstract: Whole-genome sequence comparisons between bacterial sequences are one thing, but try comparing two eukaryotic genomes, each containing tens or hundreds of millions of nucleotides. And try to do it on your desktop machine in your office or at home. That is what Kent and Zahler have tried, and the results are presented in this issue of Genome Research. The use of evolutionary conservation to unveil functional information contained within genomes is not new. In the case of the nematode, comparisons of Caenorhabditis elegans to its close relative Caenorhabditis briggsae go back as far as Emmons et al. ------------------- Key: 4288 Medline: Authors: Chauvet S;Ewbank JJ Title: Caenorhabditis elegans: un model d'etude des interactions hote-organisme pathogene. Citation: M S-Medecine Sciences 16: 912-916 2000 Type: REVIEW Genes: age-1 egl-9 mev-1 pgp-1 pgp-3 rad-8 Abstract: In French. ------------------- Key: 4289 Medline: 20335002 Authors: Moss EG Title: Non-coding RNAs: Lightning strikes twice. Citation: Current Biology 10: R436-R439 2000 Type: REVIEW Genes: daf-12 let-7 lin-4 lin-14 lin-28 lin-29 lin-41 lin-42 Abstract: A second case has been found of a nematode gene involved in developmental timing that encodes a short, non-coding RNA. Both RNAs are expressed at specific times and appear to repress target genes by interacting with their 3' untranslated regions. A coincidence? Or does this pathway attract small RNA regulators? ------------------- Key: 4290 Medline: Authors: Sugimoto A;Karashima T;Yamamoto M Title: Regulation of gametogenesis and meiosis in the nematode C. elegans. Citation: Journal of Reproduction and Development 46S: 25-26 2000 Type: ARTICLE Genes: daz-1 Abstract: Gametogenesis in multicellular organisms is a complex process in which specialized cellular differentiation and the meiotic cell cycle are coordinated to produce oocytes and sperm. The DAZ (Deleted in Axoospermia) gene family provides one of the few lines of evidence that argue for evolutionary conservation of gametogenesis at the molecular level. ------------------- Key: 4291 Medline: Authors: Strippoli P;Lenzi L;Petrini M;Carinci P;Zannotti M Title: A new gene family including DSCR1 (Down Syndrome Candidate Region 1) and ZAKI-4: Characterization from yeast to human and identification of DSCR1-like 2, a novel human member (DSCR1L2). Citation: Genomics 64: 252-263 2000 Type: ARTICLE Genes: Abstract: A new gene family has been identified on the basis of in-depth bioinformatics analysis of the Down syndrome candidate region 1 (DSCR1) gene, located on 21q22.1. We have determined the complete coding sequences of similar genes in Saccharomyces cerevisiae and Caenorhabditis elegans, as well as that of a novel human gene, named DSCR1L2 (DSCR1-lik 2). Peripheral blood leukocyte cDNA sequencing predicts as its product a 241-amino-acid protein highly similar to products of the human genes DSCR1 and ZAKI-4 (HGMW-approved symbol DSCR1L1). The highest level of expression of DSCR1L2 mRNA was found by Northern blot analysis in heart and skeletal muscles, liver, kidney and peripheral blood leukocytes (three transcripts of 3.2, 5.2, and 7.5 kb). The gene consists of four exons and spans about 22 kb on chromosome 1 (1p33-p35.3) (Human Chromosome 1, Sanger Center). Exon/intron organization is highly conserved between DSCR1 and DSCR1L2. Two alternative DSCR1L2 mRNA splicing forms have been recognized, with one lacking 10 amino acids in the middle of the protein. Analysis of expressed sequence tags. (ESTs) showed SCR1L2 expression in fetal tissues (hear, liver, and spleen) and in adenocarcinomas. ESTs related to the murine DSCR1L2 orthologue are found in the 2-cell stage mouse embryo, in developing brain stem and spinal cord, and in thymus and T cells. The most prominent feature identified in the protein family is a central short, unique serine-proline motif (including an ISPPXSPP box), which is strongly conserved from yeast to human but is absent in bacteria. Moreover, homology with the RNA-binding domain was weakly but consistently detected in a stretch of 80 amino acids at the amino-terminus by fine sequences analysis based on tools utilizing both hidden Markov models and BLAST. The identification of this new gene gamily should allow a better understanding of the functions of the genes ------------------- Key: 4292 Medline: Authors: Azevedo RBR;Cunha A;Emmons SW;Leroi AM Title: The demise of the Platonic worm. Citation: Nematology 2: 71-79 2000 Type: ARTICLE Genes: Abstract: Nematodes are generally considered to have an adult cell number that does not vary among wildtype individuals as a consequence of invariant cell lineages (eutely). However, there is extensive evidence that at least some cell lineages can be variable in nematodes. In a comparative study of 13 free-living nematode species, we have shown that the adult epidermis of most species contalned variable numbers of nuclei and that this variance was positively correlated with mean epidermal nuclear number. Here we present simulations of the lateral seam cell lineages of four species and show that variance in cell number is influenced by lineage topology, as well as by the frequency of lineage variants. We show that the epidermal variability of Panagrellus redivivus cannot be accounted for by the complexity of its lineage, but requires higher levels of lineage variability than are found in Caenorhabditis elegans, Oscheius myriophila and Rhabditella ctopleura. Our findings suggest that many nematodes may have tissues composed of indeterminate numbers of cells formed from variable lineages and, as such, resemble other metazoans. ------------------- Key: 4293 Medline: Authors: Lacenere CJ;Sternberg PW Title: Regulation of EGF receptor signaling in the fruitfly D. melanogaster and the nematode C. elegans. Citation: Breast Disease 11: 19-30 2000 Type: REVIEW Genes: gap-1 let-23 let-60 lfe-1 lfe-2 lin-2 lin-3 lin-7 lin-10 sem-5 sli-1 unc-101 Abstract: Mammals contain four members (HER1/EGFR, HER2/Neu, HER3, and HER4) of the epidermal growth factor (EGFR) family, which transduce extracellular signals by EGF family peptide growth factors. Upon binding of ligand with receptor, dimerization and auto-phosphorylation of the receptor results in a cascade of events which transmit signal from the cell surface to the nucleus. Amplification and/or uncontrolled signaling of these receptors is associated with many cancers. 10 to 34% of human breast cancers are associated with amplification or overexpression of the HER2/neu oncogene, an EGFR homolog. Signaling from the EGFR plays a critical role in the development of many organisms including the nematode Caenorhabditis elegans and the fruitfly Drosophila melanogaster, each of which contain a single EGFR homolog. The powerful genetic techniques offered by these organisms has allowed new components of the EGFR signal transduction pathway to be identified as well as lending insight into the basis of tissue ------------------- Key: 4294 Medline: 20425276 Authors: Melov S;Ravenscroft J;Malik S;Gill MS;Walker DW;Clayton PE;Wallace DC;Malfroy B;Doctrow SR;Lithgow GJ Title: Extension of life-span with superoxide dismutase/catalase mimetics. Citation: Science 289: 1567-1569 2000 Type: ARTICLE Genes: age-1 mev-1 Abstract: We tested the theory that reactive oxygen species cause aging. We augmented the natural antioxidant systems of Caenorhabditis elegans with small synthetic superoxide dismutase/catalase mimetics. Treatment of wild-type worms increased their mean Life-span by a mean of 44 percent, and treatment of prematurely aging worms resulted in normalization of their life-span (a 67 percent increase). It appears that oxidative stress is a major determinant of Life-span and that it can be counteracted by pharmacological intervention. ------------------- Key: 4295 Medline: 10997580 Authors: Shingai R Title: Durations and frequencies of free locomotion in wild type and GABAergic mutants of Caenorhabditis elegans. Citation: Neuroscience Research 38: 71-83 2000 Type: ARTICLE Genes: unc-25 unc-47 Abstract: We investigated how much time wild-type Caenorhabditis elegans (Bristol N2) nematodes and the GABA-deficient unc25 mutant and the vesicular GABA transporter-deficient unc47 mutant spent moving. The worms were allowed to move freely on the surface of agarose plates either with or without the food bacterium OP50. We identified forward movement, backward movement, resting and turns by watching images on video and computer displays. Forward movement lasted longer and rests were briefer without, than with, bacteria. Frequency distributions except for backward movement fitted a sum of two exponential functions. The duration of backward movement was not strongly influenced by exposure to bacteria, whereas the frequency of backward movements increased in their presence. The duration of forward movement of unc25 nematodes had no long component, thus differing from that of N2 and unc47 strain nematodes in treatments with and without bacteria. The durations of resting in these mutants were much longer than in the N2 strain, especially in the absence of bacteria. The turn frequency of unc47 nematodes had a higher short component than that of the wild type N2 and unc25 nematodes, in the absence of bacteria. A neural network model is discussed in conjunction with the features of mutants and current knowledge of GABAergic neural transmission. ------------------- Key: 4296 Medline: 20439482 Authors: Miller KG;Emerson MD;McManus JR;Rand JB Title: RIC-8(synembryn): A novel conserved protein that is required for G(q)alpha signaling in the C. elegans nervous Citation: Neuron 27: 289-299 2000 Type: ARTICLE Genes: dgk-1 egl-30 goa-1 ric-8 Abstract: Recent studies describe a network of signaling proteins centered around G(o)alpha and G(q)alpha that regulates neurotransmitter secretion in C. elegans by controlling the production and consumption of diacylglycerol (DAG). We sought other components of the G(o)alpha-G(o)alpha signaling network by screening for aldicarb-resistant mutants with phenotypes similar to egl-30 (G(o)alpha) mutants. In so doing, we identified ric-8, which encodes a novel protein named RIC-8 (synembryn). Through cDNA analysis, we show that RIC-8 is conserved in vertebrates. Through immunostaining, we show that RIC-8 is concentrated in the cytoplasm of neurons. Exogenous application of phorbol esters or loss of DGK-1 (diacylglycerol kinase) rescues ric-8 mutant phenotypes. A genetic analysis suggests that RIC-8 functions upstream of, or in ------------------- Key: 4297 Medline: 20414676 Authors: Evans D;Blumenthal T Title: Trans splicing of polycistronic Caenorhabditis elegans pre-mRNAs: Analysis of the SL2 RNA. Citation: Molecular and Cellular Biology 20: 6659-6667 2000 Type: ARTICLE Genes: gpd-2 gpd-3 Abstract: Genes in Caenorhabditis elegans operons are transcribed as polycistronic pre-mRNAs in which downstream gene products are trans spliced to a specialized spliced leader, SL2. SL2 is donated by a 110-nucleotide RNA, SL2 RNA, present in the cell as an Sm-bound snRNP. SL2 RNA can be conceptually folded into a phylogenetically conserved three-stem-loop secondary structure. Here we report an in vivo mutational analysis of the SL2 RNA. Some sequences can be changed without consequence, while other changes result in a substantial loss of trans splicing. Interestingly, the spliced leader itself can be dramatically altered, such that the first stem-loop cannot form, with only a relatively small loss in trans-splicing efficiency. However, the primary sequence of stem II is crucial for SL2 trans splicing. Similarly, the conserved primary sequence of the third stem-loop plays a key role in trans splicing. While mutations in stem-loop III allow snRNP formation, a single nucleotide substitution in the loop prevents trans splicing. In contrast, the analogous region of SL1 RNA is not highly conserved, and its mutation does not abrogate function. Thus, stem-loop III appears to confer a specific function to SL2 RNA. Finally, an upstream sequence, previously predicted to be a proximal sequence element, is shown to be required for SL2 RNA expression. ------------------- Key: 4298 Medline: Authors: Wergin WP;Yaklich RW;Carta LK;Erbe EF;Murphy CA Title: Effect of an ice-nucleating activity agent on subzero survival of nematode juveniles. Citation: Journal of Nematology 32: 198-204 2000 Type: ARTICLE Genes: Abstract: Juveniles of five species of nematodes, Caenorhabditis elegans, Panagrellus redivivus, Pratylenchus agilis, Pristionchus pacificus, and Distolabrellus veechi, were added to solutions with (treatment) and without (control) a commercial ice-nucleating activity (INA) agent. Ten-microliter droplets of the solutions containing the juveniles were placed on glass microscope slides and transferred to a temperature-controlled freeze plate where the temperature was reduced to -6 to -8 degrees C. At this temperature, the droplets containing the INA agent froze while those without the agent remained liquid. After 2 minutes, the temperature of the plate was raised to 24 degrees C, and the slides were examined with a light microscope to determine the viability of the juveniles. The results showed that usually most juveniles (43% to 88%, depending on species) in solutions that did not contain the INA agent (controls) were active, indicating that the juveniles were capable of supercooling and were thereby protected from the subzero temperatures. Alternatively, less than 10% of the juveniles that had frozen for 2 minutes in solutions containing the INA agent remained viable, indicating that inoculative freezing of the solution was lethal to the supercooled juveniles. Our results suggest that, in geographical areas where winter temperatures may not be sufficiently low or sustained to freeze soil, the addition of an INA agent may help induce ice nucleation and thereby reduce the populations of nematode species that are unable to survive when the soil ------------------- Key: 4299 Medline: 20408986 Authors: Tcherepanova I;Bhattacharyya L;Rubin CS;Freedman JH Title: Aspartic proteases from the nematode Caenorhabditis elegans - Structural organization and development and cell-specific expression of asp-1. Citation: Journal of Biological Chemistry 275: 26359-26369 2000 Type: ARTICLE Genes: asp-1 cad-1 Abstract: A Caenorhabditis elegans gene (asp-1) and cDNA that encode a homologue of cathepsin D aspartic protease were cloned and characterized. The asp-1 mRNA is transcribed from a single exon, and it begins with the SL1 trans-splice leader sequence. The protein (ASP-1) is expressed as a 396-amino acid, 42.7-kDa pre-pro-peptide that is post-translationally processed into a similar to 40-kDa lysosomal protein. ASP-1 shares similar to 60% sequence identity with the aspartic protease precursor from the nematode Strongyloides stercoralis. The amino acid sequences adjacent to the two active site aspartic acid residues in ASP-1 are 100% identical to those in other eukaryotic aspartic proteases. In addition, ASP-1 contains conserved, potential disulfide bond-forming cysteine residues and N-glycosylation sites. The asp-1 gene is exclusively transcribed in the intestinal cells, with the highest levels of expression observed at late embryonic and early larval stages of development. asp-1 transcription is not observed in adult nematodes or mature larvae. Furthermore, transcription predominantly occurs in eight anterior cells of the intestine (int6-int8). Analyses of ASP-1 nucleotide and amino acid sequences revealed the presence of five additional C. ------------------- Key: 4300 Medline: 20387158 Authors: Grant K;Hanna-Rose W;Han M Title: sem-4 promotes vulval cell fate determination in Caenorhabditis elegans through regulation of lin-39 hox. Citation: Developmental Biology 224: 496-506 2000 Type: ARTICLE Genes: let-60 lin-12 lin-39 lin-45 mab-5 sem-4 Abstract: Vulval cell-fate determination in Caenorhabditis elegans requires the action of numerous gene products, including components of the Ras/Raf/MAPK signaling cascade and the hox gene lin-39. sem-4 encodes a zinc finger protein with previously characterized roles in fate specification of sex myoblasts, coelomocytes, and multiple neuronal lineages in C. elegans (M. Basson and R. Horvitz, 1996, Genes Dev. 10, 1953-1965). By characterizing three new alleles of sem-4 that we identified in a screen for vulval-defective mutants, we determined that loss of sem-4 activity results in abnormal specification of the secondary vulval cell lineages. We analyzed sem-4 interactions with other genes involved in vulval differentiation and determined that sem-4 does not function directly in the Ras-mediated signal transduction pathway but acts in close association with and upstream of lin-39 to promote vulval cell fate. We demonstrate that sem-4 regulates lin-39 expression and propose that sem-4 is a regulator of lin-39 in the vulval cell-fate determination pathway that may act to link lin-39 to incoming signals. ------------------- Key: 4301 Medline: Authors: Smardon A;Spoerke JM;Stacey SC;Klein ME;Mackin N;Maine EM Title: EGO-1 is related to RNA-directed RNA polymerase and functions in germline development and RNA interference in C. elegans. Citation: Current Biology 10: R393-R394 2000 Type: REVIEW Genes: Abstract: In this Research Paper, which appeared in the 24 February 2000 issue of Current Biology, part of the sequences in Figure 5,S1 was cut off. ------------------- Key: 4302 Medline: 20419844 Authors: Coates D;Siviter R;Isaac RE Title: Exploring the Caenorhabditis elegans and Drosophila melanogaster genomes to understand neuropeptide and peptidase function. Citation: Biochemical Society Transactions 28: 464-469 2000 Type: REVIEW Genes: Abstract: Comparison of peptidase gene families in the newly released Drosophila melanogaster and Caenorhabditis elegans genomes highlights important differences in peptidase distributions with relevance to the evolution of both form and function in these two organisms and can help to identify the most appropriate model when using comparative studies relevant to the human condition. ------------------- Key: 4303 Medline: 10983970 Authors: Speliotes EK;Uren A;Vaux D;Horvitz HR Title: The survivin-like C. elegans BIR-1 protein acts with the aurora-like kinase AIR-2 to affect chromosomes and the spindle midzone. Citation: Molecular Cell 6: 211-223 2000 Type: ARTICLE Genes: air-2 bir-1 ced-3 ced-4 cyk-1 zen-4 Abstract: Baculoviral IAP repeat proteins (BIRPs) may affect cell death, cell division, and tumorigenesis. The C. elegans BIRP BIR-l was localized to chromosomes and to the spindle midzone. Embryos and fertilized oocytes lacking BIR-1 had defects in chromosome behavior, spindle midzone formation, and cytokinesis. We observed indistinguishable defects in fertilized oocytes and embryos lacking the Aurora-like kinase AIR-2. AIR-2 was not present on chromosomes in the absence of BIR-I. Histone H3 phosphorylation and HCP-1 staining, which marks kinetochores, were reduced in the absence of either BIR-1 or AIR-2. We propose that BIR-l localizes AIR-2 to chromosomes and perhaps to the spindle midzone, where AIR-2 phosphorylates proteins that affect chromosome behavior and spindle midzone organization. The human BIRP survivin, which is upregulated in tumors, could partially substitute for BIR-1 in C. elegans. Deregulation of bir-l promotes changes in ploidy, suggesting that similar deregulation of mammalian BIRPs may contribute to tumorigenesis. ------------------- Key: 4304 Medline: 10983990 Authors: Reese KJ;Dunn MA;Waddle JA;Seydoux G Title: Asymmetric segregation of PIE-1 in C. elegans is mediated by two complementary mechanisms that act through separate PIE-1 protein domains. Citation: Molecular Cell 6: 445-455 2000 Type: ARTICLE Genes: let-858 mex-1 par-1 pie-1 pos-1 smg-1 Abstract: The CCCH finger protein PIE-I is a regulator of germ cell fate that segregates with the germ lineage in early embryos. At each asymmetric division, PIE-1 is inherited preferentially by the germline daughter and is excluded from the somatic daughter. We show that this asymmetry is regulated at the protein level by two complementary mechanisms. The first acts before cell division to enrich PIE-1 in the cytoplasm destined for the germline daughter. The second acts after cell division to eliminate any PIE-1 left in the somatic daughter. The latter mechanism depends on PIE-1's first CCCH finger (ZF1), which targets PIE-1 for degradation in somatic blastomeres. ZF1s in two other germline proteins, POS-1 and MEX-1,are also degraded in somatic blastomeres, suggesting that localized degradation also acts on these proteins to exclude them from somatic lineages. ------------------- Key: 4306 Medline: Authors: Lane MA Title: Metabolic mechanisms of longevity: Caloric restriction in mammals and longevity mutations in Caenorhabditis elegans: A common pathway? Citation: Age 23: 1-7 2000 Type: REVIEW Genes: Abstract: Several recent studies in Caenorhabditis elegans have reported significant extension of the lifespan by probable loss of function mutations in various genes. When sequenced, many of these genes exhibited significant homology to genes in the mammalian insulin signaling cascade. For example, the daf-2 gene that has been shown to regulate lifespan in C elegans shares significant sequence homology with the insulin and IGF-1 receptor genes in mammals. Another longevity gene in the nematode, age- 1, is homologous with the p110 subunit of phosphatidylinositol 3-kinase in mammals. This enzyme functions early in the mammalian insulin response cascade to influence many important cellular growth and metabolic processes. These findings and others have led to the suggestion that lifespan regulation in nematodes is controlled by a mechanism similar to that involved in lifespan extension by caloric restriction in mammals. Many intriguing similarities exist between these two model systems providing some support for this idea. However, at present there is insufficient data to conclude that similar genes or mechanisms regulate lifespan determination in nematodes ------------------- Key: 4307 Medline: 10971802 Authors: Rabin Y;Podbilewicz B Title: Temperature-controlled microscopy for imaging living cells: apparatus, thermal analysis and temperature dependency of embryonic elongation in Caenorhabditis elegans. Citation: Journal of Microscopy 199: 214-223 2000 Type: ARTICLE Genes: Abstract: A new experimental apparatus for temperature-controlled microscopy has been developed for the study of the temperature dependency of developmental processes in the nematode Caenorhabditis elegans. However, the application of this apparatus is rather general and can be used for a wide range of temperatures between - 10 and 90 degrees C. The new apparatus is easy to use, inexpensive, simple to construct, and is designed for precise temperature control of oil-immersion microscopy using epifluorescence. Thermal analysis of the experimental apparatus shows the effects of each of its components, as well as the effects of uncertainty in temperature measurements. Finally, results of this study indicate that: (i) embryos incubated and imaged at temperatures of 8 degrees C and below do not elongate; (ii) the initial elongation rate is strongly temperature-dependent between 9 and 25 degrees C. ------------------- Key: 4308 Medline: 20418097 Authors: del Peso L;Gonzalez VM;Inohara N;Ellis RE;Nunez G Title: Disruption of the CED-9*CED-4 complex by EGL-1 is a critical step for programmed cell death in Caenorhabditis Citation: Journal of Biological Chemistry 275: 27205-27211 2000 Type: ARTICLE Genes: ced-3 ced-4 ced-9 egl-1 Abstract: In the nematode Caenorhabditis elegans, the apoptotic machinery is composed of four basic elements: the caspase CED-3, the Apaf-1 homologue CED-4, and the Bcl-2 family members CED-9 and EGL-1. The ced-9(n1950) gain-of-function mutation prevents most, if not all, somatic cell deaths in C. elegans. It encodes a CED-9 protein with a glycine-to-glutamate substitution at position 169, which is located within the highly conserved Bcl-2 homology 1 domain, We performed biochemical analyses with the CED-9G169E protein to gain insight into the mechanism of programmed cell death, We find that CED-9G169E retains the ability to bind both EGL-1 and CED-4, although its affinity for EGL-1 is reduced. In contrast to the behavior of wild-type CED-9, the interaction between CED-9G169E and CED-4 is not disrupted by expression of EGL-1. Furthermore, CED-4 and CED-9G169E co-localizes with EGL-1 to the mitochondria in mammalian cells, and expression of EGL-1 does not induce translocation of CED-4 to the cytosol, Finally, the ability of EGL-1 to promote apoptosis is impaired by the replacement of wild-type CED-9 with CED-9G169E, and this effect is correlated with the inability of EGL-1 to induce the displacement of CED-4 from the CED-9 CED-4 complex. These studies suggest that the release of CED-4 from the CED-9.CED-4 complex is a necessary step for induction of programmed cell death in C. ------------------- Key: 4309 Medline: 20536488 Authors: Satoh A;Hazuki M;Kojima K;Hirabayashi J;Matsumoto I Title: Ligand-binding properties of annexin from Caenorhabditis elegans (annexin XVI, Nex-1). Citation: Journal of Biochemistry 128: 377-381 2000 Type: ARTICLE Genes: nex-1 Abstract: Annexins are structurally related proteins that bind phospholipids in a calcium-dependent manner. Recently, we showed that annexins IV V, and VI also bind glycosaminoglycans in a calcium-dependent manner. Annexins are widely distributed from lower to higher eukaryotes, and the nematode Caenorhabditis elegans has been found to contain Nex-1, an annexin homologue. Here, we characterize the ligand-binding properties of Nex-1 using recombinant Nex-1. Nex-1 binds to liposomes containing phosphatidylserine. The apparent K-d was calculated by Biacore to be 4.4 nM. Compared to mammalian annexins, the Nex-1 phospholipid-binding specificities were similar whereas the K-d values were one order of magnitude larger. The Nex-1 glycosaminoglycan-binding specificities were investigated by affinity chromatography and solid-phase assays. Nex-1 binds to heparin, heparan sulfate, and chondroitin sulfate but not to chondroitin and chemically N- or O-desulfated heparin. Besides phospholipids, heparan sulfate and/or chondroitin (sulfate), probably on perlecan, could be endogenous ligands of Nex-1. ------------------- Key: 4310 Medline: 20435731 Authors: Daniels SA;Ailion M;Thomas JH;Sengupta P Title: egl-4 acts through a transforming growth factor-beta/SMAD pathway in Caenorhabditis elegans to regulate multiple neuronal circuits in response to sensory cues. Citation: Genetics 156: 123-141 2000 Type: ARTICLE Genes: daf-2 daf-3 daf-4 daf-5 daf-7 daf-11 daf-12 daf-14 daf-16 egl-4 egl-32 flp-1 odr-9 odr-10 osm-3 osm-6 tax-4 tph-1 unc-3 unc-31 unc-64 Abstract: Sensory cues regulate several aspects of behavior and development in Caenorhabditis elegans, including entry into and exit from an alternative developmental stage called the dauer larva. Three parallel pathways, including a TGF-P-like pathway, regulate dauer formation. The mechanisms by which the activities of these pathways are regulated by sensory signals are largely unknown. The gene egl-4 was initially identified based on its egg-laying defects. We show here that egl-4 has many pleiotropies, including defects in chemosensory behavior, body size, synaptic transmission, and dauer formation. Our results are consistent with a role for egl-4 in relaying sensory cues to multiple behavioral and developmental circuits in C. elegans. By epistasis analysis, we also place egl-4 in the TGF-P-like branch and show that a SMAD gene functions downstream of egl-4 in multiple egl-4-regulated pathways, ------------------- Key: 4311 Medline: 20435732 Authors: Keightley PD;Davies EK;Peters AD;Shaw RG Title: Properties of ethylmethane sulfonate-induced mutations affecting life-history traits in Caenorhabditis elegans and inferences about bivariate distributions of mutation effects. Citation: Genetics 156: 143-154 2000 Type: ARTICLE Genes: Abstract: The homozygous effects of ethylmethane sulfonate (EMS)-induced mutations in Caenorhabditis elegans are compared across life-history traits. Mutagenesis has a greater effect on early than late reproductive output, since EMS-induced mutations tend to cause delayed reproduction. Mutagenesis changes the mean and variance of longevity much less than reproductive output traits. Mutations that increase total or early productivity are not detected, but the net effect of mutations is to increase and decrease late productivity to approximately equal extents. Although most mutations decrease longevity, a mutant line with increased longevity was found. A flattening of mortality curves with age is noted, particularly in EMS lines. We infer that less than one-tenth of mutations that have fitness effects in natural conditions are detected in the laboratory, and such mutations have moderately large effects (similar to 20% of the mean). Mutational correlations for life-history traits are strong and positive. Correlations between early or late productivity and longevity are of similar magnitude. We develop a maximum-likelihood procedure to infer bivariate distributions of mutation effects. We show that strong mutation-induced genetic correlations do not necessarily imply strong directional correlations between mutational effects, since correlation is also generated by lines ------------------- Key: 4312 Medline: 10970880 Authors: Zhang H;Emmons SW Title: A C. elegans mediator protein confers regulatory selectivity on lineage-specific expression of a transcription factor gene. Citation: Genes & Development 14: 2161-2172 2000 Type: ARTICLE Genes: bar-1 egl-5 egl-20 lin-15 lin-17 lin-44 mab-5 pal-1 pop-1 pry-1 sop-1 sDp3 Abstract: The Caenorhabditis elegans caudal homolog, pal-1, is required for neurogenesis in the male tail. We show that expression of pal-1 in the postembryonic neuroblast cell V6 can be initiated by two alternate pathways. One pathway, acting in wild type, requires a regulatory element in the fifth pal-1 intron. The other pathway, independent of this element, is normally repressed by the newly identified gene sop-1, which encodes a homolog of the mammalian Mediator complex protein TRAP230. In sop-1 mutants, pal-1 is activated by a pathway that is stimulated by bar-1/beta-catenin, a component of the Wnt signal transduction pathway. The results support a physiological role of the Mediator complex in conveying regulatory signals to the transcriptional apparatus. ------------------- Key: 4313 Medline: 20428552 Authors: Mitrovich QM;Anderson P Title: Unproductively spliced ribosomal protein mRNAs are natural targets of mRNA surveillance in C. elegans. Citation: Genes & Development 14: 2173-2184 2000 Type: ARTICLE Genes: eft-3 rpl-1 rpl-2 rpl-3 rpl-5 rpl-7 rpl-10 rpl-12 rpl-13 rpl-15 rpl-16 rpl-24 rpl-32 smg-1 smg-2 Abstract: Messenger RNA surveillance, the selective and rapid degradation of mRNAs containing premature stop codons, occurs in all eukaryotes tested. The biological role of this decay pathway, however, is not well understood. To identify natural substrates of mRNA surveillance, we used a cDNA-based representational difference analysis to identify mRNAs whose abundance increases in Caenorhabditis elegans smg(-) mutants, which are deficient for mRNA surveillance. Alternatively spliced mRNAs of genes encoding ribosomal proteins L3, L7a, L10a, and L12 are abundant natural targets of mRNA surveillance. Each of these genes expresses two distinct mRNAs. A productively spliced mRNA, whose abundance does not change in smg(-) mutants, encodes a normal, full-length, ribosomal protein. An unproductively spliced mRNA, whose abundance increases dramatically in smg(-) mutants, contains premature stop codons because of incomplete removal of an alternatively spliced intron. In transgenic animals expressing elevated quantities of RPL-12, a greater proportion of endogenous rpl-12 transcript is spliced unproductively. Thus, RPL-12 appears to autoregulate its own splicing, with unproductively spliced mRNAs being degraded by mRNA surveillance. We demonstrate further that alternative splicing of rpl introns is conserved among widely diverged nematodes. Our results suggest that one important role of mRNA surveillance is to eliminate unproductive by-products of ------------------- Key: 4314 Medline: 20432108 Authors: Beitel GJ;Lambie EJ;Horvitz HR Title: The C. elegans gene lin-9, which acts in an Rb-related pathway, is required for gonadal sheath cell development and encodes a novel protein. Citation: Gene 254: 253-263 2000 Type: ARTICLE Genes: lin-9 Abstract: The Caenorhabditis elegans gene lin-9 functions in an Rb-related pathway chat acts antagonistically to a receptor tyrosine kinase/Ras signal transduction pathway controlling vulval induction. We show that lin-9 is also required for the development of the sheath cells in the hermaphrodite gonad and for the development of the male spicule, rays and gonad. lin-9 is transcribed as two alternatively spliced 2.4 kb messages, which use two distinct polyadenylation sites and are SL1 trans-spliced. The conceptual translation of lin-9 cDNA sequences predicts proteins of 642 and 644 amino acids with a significant similarity to predicted Drosophila and vertebrate proteins. We suggest that lin-9 is the founding member of a new protein family that functions in Rb-related pathways in many species. ------------------- Key: 4315 Medline: 10903169 Authors: Hermann GJ;Leung B;Priess JR Title: Left-right asymmetry in C. elegans intestine organogenesis involves a LIN-12/Notch signaling pathway. Citation: Development 127: 3429-3440 2000 Type: ARTICLE Genes: apx-1 ceh-13 elt-1 glp-1 lag-1 lag-2 lin-12 lin-39 lit-1 mab-5 spn-1 unc-5 unc-6 unc-40 Abstract: The C. elegans intestine is a simple tube consisting of a monolayer of epithelial cells. During embryogenesis, cells in the anterior of the intestinal primordium undergo reproducible movements that lead to an invariant, asymmetrical 'twist' in the intestine. We have analyzed the development of twist to determine how left-right and anterior-posterior asymmetries are generated within the intestinal primordium. The twist requires the LIN-12/Notch-like signaling pathway of C. elegans. All cells within the intestinal primordium initially express LIN-12, a receptor related to Notch; however, only cells in the left half of the primordium contact external, nonintestinal cells that express LAG-2, a ligand related to Delta. LIN-12 and LAG-2 mediated interactions result in the left primordial cells expressing lower levels of LIN-12 than the right primordial cells. We propose that this asymmetrical pattern of LIN-12 expression is the basis for asymmetry in later cell-cell interactions within the primordium that lead directly to intestinal twist. Like the interactions that initially establish LIN-12 asymmetry, the later interactions are mediated by LIN-12. The later interactions, however, involve a different ligand related to Delta, called APX-1. We show that the anterior-posterior asymmetry in intestinal twist involves the kinase LIT-1, which is part of a signaling pathway in early embryogenesis that generates anterior-posterior differences between ------------------- Key: 4316 Medline: 10980430 Authors: Hanna-Rose W;Han M Title: Getting signals crossed in C. elegans. Citation: Current Opinion in Genetics & Development 10: 523-528 2000 Type: REVIEW Genes: age-1 akt-1 akt-2 apr-1 bar-1 daf-1 daf-2 daf-3 daf-4 daf-7 daf-8 daf-14 daf-16 daf-18 egl-5 let-23 let-60 lin-3 lin-12 lin-15 lin-17 lin-35 lin-36 lin-37 lin-39 lin-44 lit-1 mom-2 mom-4 mom-5 pop-1 sem-4 wrm-1 Abstract: The induction of an appropriate cellular response to a stimulus often depends on the intricate interplay between multiple signaling pathways. Recent work utilizing Caenorhabditis elegans has enabled the identification of points of convergence between signaling pathways and permitted the elucidation of how multiple signals work in concert to ensure a proper response. ------------------- Key: 4317 Medline: 10914006 Authors: Ledwich D;Wu YC;Driscoll M;Xue D Title: Analysis of programmed cell death in the nematode Caenorhabditis elegans. Citation: Apoptosis 322: 76-88 2000 Type: REVIEW Genes: Abstract: The nematode Caenorhabditis elegans has been shown to be an excellent model organism with which to study the mechanisms of programmed cell death because of its powerful genetics and the ability to study cell death with single-cell resolution. In this chapter, we describe methods that are commonly used to examine various aspects of programmed cell death in C. elegans. These methods, in combination with genetic analyses, have helped identify and characterize many components of the C. elegans cell death pathway, illuminating the mechanisms by which these components affect programmed cell death. ------------------- Key: 4318 Medline: 10993067 Authors: Yu G;Nishimura M;Arawaka S;Levitan D;Zhang LL;Tandon A;Song YQ;Rogaeva E;Chen FS;Kawaral T;Supala A;Levesque L;Yu H;Yang DS;Holmes E;Millman P;Liang Y;Zhang DM;Xu DH;Sato C;Rogaev E;Smith M;Janus C... Title: Nicastrin modulates presenilin-mediated notch/glp-1 signal transduction and beta APP processing. Citation: Nature 407: 48-54 2000 Type: ARTICLE Genes: aph-1 aph-2 glp-1 hop-1 sel-12 Abstract: Nicastrin, a transmembrane glycoprotein, forms high molecular weight complexes with presenilin 1 and presenilin 2. Suppression of nicastrin expression in Caenorhabditis elegans embryos induces a subset of notch/glp-1 phenotypes similar to those induced by simultaneous null mutations in both presenilin homologues of C. elegans(sel-12 and hop-1). Nicastrin also binds carboxy-terminal derivatives of beta-amyloid precursor protein (beta APP), and modulates the production of the amyloid beta-peptide (A beta) from these derivatives. Missense mutations in a conserved hydrophilic domain of nicastrin increase A beta(42) and A beta(40) peptide secretion. Deletions in this domain inhibit A beta production. Nicastrin and presenilins are therefore likely to be functional components of a multimeric complex necessary for the intramembranous proteolysis of proteins such as Notch/GLP-1 and beta APP. ------------------- Key: 4319 Medline: 20408884 Authors: Guipponi M;Brunschwig K;Chamoun Z;Scott HS;Shibuya K;Kudoh J;Delezoide AL;El Samadi S;Chettouh Z;Rossier C;Shimizu N;Mueller F;Delabar JM;Antonarakis SE Title: C21orf5, a novel human chromosome 21 gene, has a Caenorhabditis elegans ortholog (pad-1) required for embryonic patterning. Citation: Genomics 68: 30-40 2000 Type: ARTICLE Genes: pad-1 Abstract: To contribute to the development of the transcription map of human chromosome 21 (HC21), we isolated a new transcript, C21orf5 (chromosome 21 open reading frame 5), encoding a predicted 2298-amino-acid protein. Analysis of the genomic DNA sequence revealed that C21orf5 consists of 37 exons that extend over 130 kb and maps between the CBR3 (carbonyl reductase 3) and the KIAA0136 genes. Northern blot analyses showed a ubiquitously expressed RNA species of 8.5 kb. RNA in situ hybridization on brain sections of normal human embryos revealed a strong labeling in restricted areas of the cerebral cortex. In silico analysis of the deduced C21orf5 protein revealed several highly probable transmembrane segments but no known protein domains or homology with known proteins. However, there were significant homologies to several hypothetical Caenorhabditis elegans proteins and Drosophila melanogaster genomic sequences. To investigate the function of C21orf5, we isolated the cDNA of the C. elegans ortholog and performed double-stranded RNA-mediated genetic interference experiments. The major phenotype observed in the progeny of injected animals was embryonic lethality. Most of the tissues of the embryo failed to undergo proper patterning during gastrulation, and morphogenesis did not occur; thus we termed the ortholog pad-1, for patterning defective 1. These results indicated that pad-1 is essential for the development and the survival of C. elegans. This study provides the first example of the use of C. elegans as a model to study the function of genes on human chromosome 21 that might be involved in Down syndrome. ------------------- Key: 4320 Medline: 20414396 Authors: Pace HC;Hodawadekar SC;Draganescu A;Huang J;Bieganowski P;Pekarsky Y;Croce CM;Brenner C Title: Crystal structure of the worm NitFhit Rosetta Stone protein reveals a Nit tetramer binding two Fhit dimers. Citation: Current Biology 10: 907-917 2000 Type: ARTICLE Genes: Abstract: Background: The nucleotide-binding protein Fhit, among the earliest and most frequently inactivated proteins in lung cancer, suppresses tumor formation by inducing apoptosis. In invertebrates, Fhit is encoded as a fusion protein with Nit, a member of the nitrilase superfamily. In mice, the Nit1 and Fhit genes have nearly identical expression profiles. According to the Rosetta Stone hypothesis, if the separate Nit and Fhit genes could be shown to occur in the same subset of genomes (that is, to share a phylogenetic profile), then the existence of a fusion protein in invertebrates and the coordinated expression of separate mRNAs in mouse suggest that Nit and Fhit function in the same pathway and that the structure of invertebrate NitFhit may reflect the nature of Nit-Fhit interactions. Results: To satisfy the phylogenetic profile criterion for functional significance of protein fusion events, we cloned additional Nit homologs from organisms with Fhit homologs, We used fluorescent nucleotide analogs of ApppA to follow the purification and to characterize the nucleotide specificity of NitFhit from Caenorhabditis elegans, crystallized the 200 kDa tetrameric complex, and solved the structure of NitFhit from a single mercury derivative phased by two-wavelength anomalous diffraction. Conclusions: Nit monomers possess a new a-P-P-a sandwich fold with a presumptive Cys-Glu-Lys catalytic triad. Nit assembles into a tetrameric, 52-stranded beta box that binds Fhit dimers at opposite poles and displays Nit active sites around the middle of the complex. The most carboxy-terminal beta strand of each Nit monomer exits the core of the Nit tetramer and interacts with Fhit, Residence in the NitFhit complex does not alter the nucleotide specificity of Fhit dimers, which are oriented with ------------------- Key: 4321 Medline: 20403905 Authors: McGhee JD Title: Homologous tails? Or tales of homology? Citation: BioEssays 22: 781-785 2000 Type: REVIEW Genes: mab-9 Abstract: Classical mutations at the mouse Brachyury (T) locus were discovered because they lead to shortened tails in heterozygous newborns, no tail (ntl) mutants in the zebrafish, as their name suggests, show a similar phenotype. In Drosophila, mutants in the brachyenteron (byn) gene disrupt hindgut formation. These genes all encode T-box proteins, a class of sequence-specific DNA binding proteins and transcription factors. Mutations in the C. elegans mab-9 gene cause massive defects in the male tail because of failed fate decisions in two tail progenitor cells. In a recent paper, Woollard and Hodgkin((1)) have cloned the mab-9 gene and found that it too encodes a T-box protein, similar to Brachyury in vertebrates and brachyenteron in Drosophila. The authors suggest that their results support models for an evolutionarily ancient role for these genes in hindgut formation. We will discuss this proposal and try to decide whether the gene sequences, gene interactions and gene expression patterns allow any conclusions to be made about ------------------- Key: 4322 Medline: Authors: Plasterk RHA;Ketting RF Title: The silence of the genes. Citation: Current Opinion in Genetics & Development 10: 562-567 2000 Type: REVIEW Genes: mut-7 mut-8 mut-9 rde-1 rde-2 rde-3 Abstract: About two years ago, it was recognized that introduction of double-stranded RNA (dsRNA) had a potent effect on gene expression, in particular on mRNA stability. Since then, this process has been found to occur in many different organisms, and to bear a strong resemblance to a previously recognized process in plants, called cosuppression. Both genetic and biochemical studies have started to unravel the mysteries of RNA interference: genes involved in this process are being identified and in vitro studies are giving the first hints of what is happening to both the dsRNA and the affected mRNA molecules after the introduction of the dsRNA. ------------------- Key: 4323 Medline: 20461149 Authors: Berkowitz LA;Strome S Title: MES-1, a protein required for unequal divisions of the germline in early C. elegans embryos, resembles receptor tyrosine kinases and is localized to the boundary between the germline and gut cells. Citation: Development 127: 4419-4431 2000 Type: ARTICLE Genes: glp-4 let-99 mes-1 mex-1 mom-2 mom-4 par-1 par-2 par-3 par-4 par-6 pie-1 pop-1 pos-1 Abstract: During Caenorhabditis elegans embryogenesis the primordial germ cell, P-4, is generated via a series of unequal divisions, These divisions produce germline blastomeres (P-1, P-2, P-3, P4) that differ from their somatic sisters in their size, fate and cytoplasmic content (e.g. germ granules), mes-1 mutant embryos display the striking phenotype of transformation of P-4 into a muscle precursor, like its somatic sister. A loss of polarity in P-2 and P-3 cell-specific events underlies the Mes-1 phenotype, In mes-1 embryos, P-2 and P-3 undergo symmetric divisions and partition germ granules to both daughters. This paper shows that mes-1 encodes a receptor tyrosine kinase-like protein, though it lacks several residues conserved in all kinases and therefore is predicted not to have kinase activity. Immunolocalization analysis shows that MES-1 is present in four- to 24-cell embryos, where it is localized in a crescent at the junction between the germline cell and its neighboring gut cell. This is the region of P-2 and P-3 to which the spindle and P granules must move to ensure normal division asymmetry and cytoplasmic partitioning. Indeed, during early stages of mitosis in P-2 and P-3, one centrosome is positioned adjacent to the MES-1 crescent. Staining of isolated blastomeres demonstrated that MES-1 was present in the membrane of the germline blastomeres, consistent with a cell-autonomous function. Analysis of MES-1 distribution in various cell-fate and patterning mutants suggests that its localization is not dependent on the correct fate of either the germline or the gut blastomere but is dependent upon correct spatial organization of the embryo. Our results suggest that MES-1 directly positions the developing mitotic spindle and its associated P granules within P-2 and P-3, or provides an orientation signal for P-2- and P-3-specific events. ------------------- Key: 4324 Medline: 20461153 Authors: Yi W;Ross JM;Zarkower D Title: mab-3 is a direct tra-1 target gene regulating diverse aspects of C. elegans male sexual development and behavior. Citation: Development 127: 4469-4480 2000 Type: ARTICLE Genes: hlh-1 lin-22 lin-32 lov-1 mab-3 mab-5 pdk-2 srd-1 tra-1 Abstract: Sex determination is controlled by global regulatory genes, such as tra-l in Caenorhabditis elegans, Sex lethal in Drosophila, or Sry in mammals, How these genes coordinate sexual differentiation throughout the body is a key unanswered question, tra-1 encodes a zinc finger transcription factor, TRA-1A, that regulates, directly or indirectly, all genes required for sexual development, mab-3 (male abnormal 3), acts downstream of tra-l and is known to be required for sexual differentiation of at least two tissues, mab-3 directly regulates yolk protein transcription in the intestine and specifies male sense organ differentiation in the nervous system. It encodes a transcription factor related to the products of the Drosophila sexual regulator doublesex (dsx), which also regulates yolk protein transcription and male sense-organ differentiation. The similarities between mab-3 and dsx led us to suggest that some aspects of sex determination may be evolutionarily conserved. Here we find that mab-3 is also required for expression of male-specific genes in sensory neurons of the head and tail and for male interaction with hermaphrodites. These roles in male development and behavior suggest further functional similarity to dsx, In male sensory ray differentiation we find that MAB-3 acts synergistically with LIN-32, a neurogenic bHLH transcription factor. Expression of LIN-32 is spatially restricted by the combined action of the Hox gene mab-5 and the hairy homolog lin-22, while MAB-3 is expressed throughout the lateral hypodermis, Finally, we find that mab-3 transcription is directly regulated in the intestine by TRA-1A, providing a molecular link between the global regulatory pathway and terminal sexual differentiation. ------------------- Key: 4325 Medline: 20446268 Authors: Domeier ME;Morse DP;Knight SW;Portereiko M;Bass BL;Mango SE Title: A link between RNA interference and nonsense-mediated decay in Caenorhabditis elegans. Citation: Science 289: 1928-1930 2000 Type: ARTICLE Genes: ego-1 mex-3 mut-2 mut-7 pha-4 rde-1 rde-2 rde-3 rde-4 smg-1 smg-2 smg-3 smg-4 smg-5 unc-22 unc-54 Abstract: Double-stranded RNA (dsRNA) inhibits expression of homologous genes by a process' involving messenger RNA degradation. To gain insight into the mechanism of degradation, we examined how RNA interference is affected by mutations in the smg genes, which are required for nonsense-mediated decay. For three of six smg genes tested, mutations resulted in animals that were initially silenced by dsRNA but then recovered; wild-type animals remained silenced. The Levels of target messenger RNAs were restored during recovery, and RNA editing and degradation of the dsRNA were identical to those of the wild type. We suggest that persistence of RNA interference relies on a subset of smg genes. ------------------- Key: 4326 Medline: 20469056 Authors: Aoki H;Sato S;Takanami T;Ishihara T;Katsura I;Takahashi H;Higashitani A Title: Characterization of Ce-atl-1, an ATM-like gene from Caenorhabditis elegans. Citation: Molecular & General Genetics 264: 119-126 2000 Type: ARTICLE Genes: act-1 atl-1 gld-1 glp-1 Abstract: An ATM-like gene was identified in the genome of Caenorhabditis elegans. The putative product of the gene, termed Ce-atl-1 (C. elegans ATM-like 1) consists of 2514 amino acid residues. The C-terminal sequence, which contains a PI-3 kinase-like domain, showed good homology with the products of the gene MEC1/ESR1 from budding yeast, the rad3(+) gene of fission yeast and mammalian A TR (ataxia-telangiectasia and rad3(+) related) genes. The results of RNA-mediated interference indicated that the major phenotype associated with repression of Ce-atl-1 was lethality (approximately 50-80%) during early embryogenesis. Among the surviving progeny, males (XO animals) arose at a high frequency (2-30%). In addition, 5% of oocyte chromosomes demonstrated aneuploidy due to a defect in pre-meiotic chromosomal segregation. Gene expression analyses indicated that Ce-atl-1 mRNA was expressed in all larval stages and that its level increased about fivefold in the adult stage. The adult expression level was de creased in the glp-4 mutant, which is defective in germ line proliferation. Ce-atl-1 was strongly expressed in both the mitotic and meiotic cells of adult gonads. In summary, Ce-atl-1 appears to be important for early embryogenesis, and loss of its function results in a defect in chromosome segregation, similar to what has been observed for AT-related proteins. ------------------- Key: 4327 Medline: 20425188 Authors: McGaw LJ;Jager AK;van Staden J Title: Antibacterial, anthelmintic and anti-amoebic activity in South African medicinal plants. Citation: Journal of Ethnopharmacology 72: 247-263 2000 Type: ARTICLE Genes: Abstract: Hexane, ethanol and water extracts of plants used by South African traditional healers for treating stomach ailments were screened for antibacterial anthelmintic and anti-amoebic activities. To evaluate antibacterial activity, the disc-diffusion assay was used against several Gram-positive and Gram-negative species. Minimal inhibitory concentration values were determined with a microdilution assay. Ethanolic extracts showed the greatest activity, and Gram-positive bacteria were the most susceptible microorganisms. The free-living nematode Caenorhabditis elegans was used in two different assays to evaluate anthelmintic activity. A microdilution technique was employed to investigate anti-amoebic activity against the enteropathogenic Entamoeba histolytica. These assays were suitable for the screening of a large number of extracts at one time. Several plants exhibited significant activity against these test organisms. ------------------- Key: 4328 Medline: Authors: Quimby BB;Lamitina T;L'Hernault SW;Corbett AH Title: The mechanism of Ran import into the nucleus by nuclear transport factor 2. Citation: Journal of Biological Chemistry 275: 28575-28582 2000 Type: ARTICLE Genes: spe-9 Abstract: The small GTPase Ran is essential for virtually all nucleocytoplasmic transport events. It is hypothesized that Ran drives vectorial transport of macromolecules into and out of the nucleus via the establishment of a Ran gradient between the cytoplasm and nucleoplasm. Although Ran shuttles between the nucleus and cytoplasm, it is concentrated in the nucleus at steady state. We show that nuclear transport factor 2 (NTF2) is required to concentrate Ran in the nucleus in the budding yeast, Saccharomyces cerevisiae. To analyze the mechanism of Ran import into the nucleus by NTF2, we use mutants in a variety of nuclear transport factors along with biochemical analyses of NTF2 complexes. We find that Ran remains concentrated in the nucleus when importin-mediated protein import is disrupted and demonstrate that NTF2 does not form a stable complex with the transport receptor, importin-beta. Consistent with a critical role for NTF2 in establishing and maintaining the Ran gradient, we show that NTP2 is required for early embryogenesis in Caenorhabditis elegans. Our data distinguish between two possible mechanisms for Ran import by NTF2 and demonstrate that Ran import is independent from importin-beta-mediated protein ------------------- Key: 4329 Medline: 20429642 Authors: Asahina M;Ishihara T;Jindra M;Kohara Y;Katsura I;Hirose S Title: The conserved nuclear receptor Ftz-F1 is required for embryogenesis, moulting and reproduction in Caenorhabditis elegans. Citation: Genes to Cells 5: 711-723 2000 Type: ARTICLE Genes: nhr-23 nhr-25 nDf19 Abstract: Background: Nuclear receptors are essential players in the development of all metazoans. The nematode Caenorhabditis elegans possesses more than 200 putative nuclear receptor genes, several times more than the number known in any other organism. Very few of these transcription factors are conserved with components of the steroid response pathways in vertebrates and arthropods. Ftz-F1, one of the evolutionarily oldest nuclear receptor types, is required for steroidogenesis and sexual differentiation in mice and for segmentation and metamorphosis in Drosophila. Results: We employed two complementary approaches, direct mutagenesis and RNA interference, to explore the role of nhr-25, a C. elegans ortholog of Ftz-F1. Deletion mutants show that nhr-25 is essential for embryogenesis. RNA interference reveals additional requirements throughout the postembryonic life, namely in moulting and differentiation of the gonad and vulva. All these defects are consistent with the nhr-25 expression pattern, determined by in situ hybridization and GFP reporter activity. Conclusions: Our data link the C. elegans Ftz-F1 ortholog with a number of developmental processes. Significantly, its role in the periodical replacement of cuticle (moulting) appears to be evolutionarily shared with insects and thus supports the monophyletic origin of moulting. ------------------- Key: 4330 Medline: 20458301 Authors: Vassilieva LL;Hook AM;Lynch M Title: The fitness effects of spontaneous mutations in Caenorhabditis elegans. Citation: Evolution 54: 1234-1246 2000 Type: ARTICLE Genes: Abstract: Spontaneous mutation to mildly deleterious alleles has emerged as a potentially unifying component of a variety of observations in evolutionary genetics and molecular evolution. However, the biological significance of hypotheses based on mildly deleterious mutation depends critically on the rate at which new mutations arise on their average effects. A long-term mutation-accumulation experiment with replicate lines of the nematode Caenorhabditis elegans maintained by single-progeny descent indicates that recurrent spontaneous mutation causes approximately 0.1% decline in fitness per generation, which is about an order of magnitude less than that suggested by previous studies with Drosophila. Two rather different approaches, Bateman-Mukai and maximum likelihood, suggest that this observation, along with the observed rate of increase in the variance of fitness among lines, is consistent with a genomic deleterious mutation rate for fitness approximately 0.03 per generation and with an average homozygous effect of approximately 12%. The distribution of mutational effects for fitness appears to have a relatively low coefficient of variation, being no more extreme than expected for a negative exponential, and for one composite fitness measure (total progeny production) approaches constancy of effects. These results are derived from assays in a benign environment. At stressful temperature, estimates of the genomic deleterious mutation rate (for genes expressed at such temperatures) is sixfold lower, whereas those for the average homozygous effect is approximately eightfold higher. Our results are reasonably compatible with existing estimates for flies, when one considers the differences between these species in the number of germ-line cell divisions per generation and the magnitude of transposable element activity. ------------------- Key: 4331 Medline: Authors: Iwasaki K;Toyonaga R Title: The Rab3 GDP/GTP exchange factor homolog AEX-3 has a duel function in synaptic transmission. Citation: EMBO Journal 19: 4806-4816 2000 Type: ARTICLE Genes: aex-3 cab-1 jkk-1 mek-2 mpk-1 rab-3 Abstract: Guanine nucleotide exchange is essential for Rab GTPase activities in regulating intracellular vesicle trafficking. This exchange process is facilitated by guanine nucleotide exchange factor (GEF), Previously, we identified Caenorhabditis elegans AEX-3 as a GEF for Rab3 GTPase. Here we demonstrate that AEX-3 regulates neural activities through a second, previously unrecognized pathway via interactions with the novel protein CAB-I. CAB-I is 425 amino acids long and has an 80 amino acid motif in common with the mouse neural protein NPDC-1. cab-1 and rab-3 mutants have different behavioral defects, and RAB-3 localization and function are apparently normal in cab-1 mutants, indicating that the CAB-1 pathway is distinct from the RAB-3 pathway. The aex-3 mutant phenotype resembles the sum of the rab-3 and cab-1 mutant phenotypes, indicating that AEX-3 regulates two different pathways for neural activities. We propose that connection of multiple pathways may be an important feature of Rab GEFs to coordinate various cellular events. ------------------- Key: 4332 Medline: 20453779 Authors: Chamberlin HM Title: Nematode development: An evolutionary fugue. Citation: Current Biology 10: R631-R633 2000 Type: REVIEW Genes: Abstract: Recent studies of vulva development in the nematode Pristionchus pacificus have identified cell interactions that do not appear to occur in Caenorhabditis elegans, The new results underscore the diversity of patterning mechanisms that can produce structures with similar cellular morphology. ------------------- Key: 4333 Medline: 20453781 Authors: Bowerman B Title: Embryonic polarity: Protein stability in asymmetric cell division. Citation: Current Biology 10: R637-R641 2000 Type: ARTICLE Genes: glp-1 mex-1 mex-3 mex-5 mex-6 pal-1 par-1 par-2 par-3 par-4 par-5 par-6 pie-1 pkc-1 pod-1 pos-1 skn-1 Abstract: Recent work on pattern formation in Caenorhabditis elegans has uncovered a new mechanism of asymmetric cell division: the cytoplasm is polarized by cortical proteins, and this polarization then influences the stability of other maternally expressed proteins that in turn determine early embryonic cell fates. ------------------- Key: 4334 Medline: 10973497 Authors: Nasrin N;Ogg S;Cahill CM;Biggs W;Nui S;Dore J;Calvo D;Shi Y;Ruvkun G;Alexander-Bridges MC Title: DAF-16 recruits the CREB-binding protein coactivator complex to the insulin-like growth factor binding protein 1 promoter in HEPG2 cells. Citation: Proceedings of the National Academy of Sciences USA 97: 10412-10417 2000 Type: ARTICLE Genes: daf-16 Abstract: Insulin negatively regulates expression of the insulin-like growth factor binding protein 1 (IGFBP-1) gene by means of an insulin-responsive element (IRE) that also contributes to glucocorticoid stimulation of this gene. We find that the Caenorhabditis elegans protein DAF-16 binds the IGFBP-1 IRE with specificity similar to that of the forkhead (FKH) factor(s) that act both to enhance glucocorticoid responsiveness and to mediate the negative effect of insulin at this site. In HepG2 cells, DAF-16 and its mammalian homologs, FKHR, FKHRL1. and AFX, activate transcription through the IGFBP-1.IRE; this effect is inhibited by the viral oncoprotein E1A, but not by mutants of E1A that fail to interact with the coactivator p300/CREB-binding protein (CBP). We show that DAF-16 and FKHR can interact with both the KIX and E1A/SRC interaction domains of p300/CBP, as well as the steroid receptor coactivator (SRC). A C-terminal deletion mutant of DAF-16 that is nonfunctional in C. elegans fails to bind the KIX domain of CBP, fails to activate transcription through the IGFBP-1-IRE, and inhibits activation of the IGFBP-1 promoter by glucocorticoids. Thus, the interaction of DAF-16 homologs with the KIX domain of CBP is essential to basal and glucocorticoid-stimulated transactivation. Although AFX interacts with the KIX domain of CBP, it does not interact with SRC and does not respond to glucocorticoids or insulin. Thus, we conclude that DAF-16 and FKHR act as accessory factors to the glucocorticoid response, by recruiting the p300/CBP/SRC coactivator complex to an FKH factor site in the IGFBP-1 promoter, which allows the cell to integrate the effects of ------------------- Key: 4335 Medline: 20372677 Authors: Quarmby L Title: Cellular Samurai: katanin and the severing of microtubules. Citation: Journal of Cell Science 113: 2821-2827 2000 Type: REVIEW Genes: mei-1 mei-2 Abstract: Recent biochemical studies of the AAA ATPase, katanin, provide a foundation for understanding how microtubules might be severed along their length. These in vitro studies are complemented by a series of recent reports of direct in vivo observation of microtubule breakage, which indicate that the in vitro phenomenon of catalysed microtubule severing is likely to be physiological. There is also new evidence that microtubule severing by katanin is important for the production of non-centrosomal microtubules in cells such as neurons and epithelial cells. Although it has been difficult to establish the role of katanin in mitosis, new genetic evidence indicates that a katanin-like protein, MEI-1, plays an essential role in meiosis in C. elegans. Finally, new proteins involved in the severing of axonemal microtubules have been discovered in the deflagellation system of Chlamydomonas. ------------------- Key: 4336 Medline: 10508607 Authors: Raff JW Title: Nuclear migration: the missing (L)UNC? Citation: Current Biology 9: R708-R710 1999 Type: REVIEW Genes: unc-84 Abstract: In many cells, centrosomes are required to position nuclei at specific locations in the cytoplasm. The nature of the link between centrosomes and nuclei is mysterious, but the recently characterised UNC84 protein appears to be ------------------- Key: 4337 Medline: 10508601 Authors: Bejsovec A Title: Signal transduction: Wnt signalling shows its versatility. Citation: Current Biology 9: R684-R687 1999 Type: REVIEW Genes: lit-1 mom-2 mom-4 mom-5 pop-1 wrm-1 Abstract: Wnt signalling controls many different cell fate choices in a wide variety of animal species. Recent studies have revealed that regulatory interactions at several steps in the pathway can modify its outcome, helping to explain how the same pathway can, in different contexts, have very different characteristics and consequences. ------------------- Key: 4339 Medline: 10982402 Authors: Lee KK;Gruenbaum Y;Spann P;Liu J;Wilson KL Title: C. elegans nuclear envelope proteins emerin, MAN1, lamin, and nucleoporins reveal unique timing of nuclear envelope breakdown during mitosis. Citation: Molecular Biology of the Cell 11: 3089-3099 2000 Type: ARTICLE Genes: emr-1 lem-2 lem-3 Abstract: Emerin, MAN1, and LAP2 are integral membrane proteins of the vertebrate nuclear envelope. They share a 43-residue N-terminal motif termed the LEM domain. We found three putative LEM domain genes in Caenorhabditis elegans, designated emr-1, lem-2, and lem-3. We analyzed emr-1, which encodes Ce-emerin, and lem-2, which encodes Ce-MAN1. Ce-emerin and Ce-MAN1 migrate on SDS-PAGE as 17- and 52-kDa proteins, respectively. Based on their biochemical extraction properties and immunolocalization, both Ce-emerin and Ce-MAN1 are integral membrane proteins localized at the nuclear envelope. We used antibodies against Ce-MAN1, Ce-emerin, nucleoporins, and Ce-lamin to determine the timing of nuclear envelope breakdown during mitosis in C. elegans. The C. elegans nuclear envelope disassembles very late compared with vertebrates and Drosophila. The nuclear membranes remained intact everywhere except near spindle poles during metaphase and early anaphase, fully disassembling only during mid-late anaphase. Disassembly of pore complexes, and to a lesser extent the lamina, depended on embryo age: pore complexes were absent during metaphase in >30-cell embryos but existed until anaphase in 2- to 24-cell embryos. Intranuclear mRNA splicing factors disassembled after prophase. The timing of nuclear disassembly in C. elegans is novel and may reflect its evolutionary position between unicellular and more complex eukaryotes. ------------------- Key: 4340 Medline: 10982409 Authors: Zallen JA;Peckol EL;Tobin DM;Bargmann CI Title: Neuronal cell shape and neurite initiation are regulated by the Ndr kinase SAX-1, a member of the Orb6/COT-1/Warts serine/threonine kinase family. Citation: Molecular Biology of the Cell 11: 3177-3190 2000 Type: ARTICLE Genes: sax-1 sax-2 tax-4 unc-43 Abstract: The Caenorhabditis elegans sax-1 gene regulates several aspects of neuronal cell shape. sax-1 mutants have expanded cell bodies and Ectopic neurites in many classes of neurons, suggesting that SAX-1 functions to restrict cell and neurite growth. The ectopic neurites in sensory neurons of sax-1 mutants resemble the defects caused by decreased sensory activity. However, the activity-dependent pathway, mediated in part by the UNC-43 calcium/calmodulin-dependent kinase II, functions in parallel with SAX-1 to suppress neurite initiation, sax-1 encodes a serine/threonine kinase in the Ndr family that is related to the Orb6 (Schizosaccharomyces pombe), Warts/Lats (Drosophila), and COT-1 (Neurospora) kinases that function in cell shape regulation. These kinases have similarity to Rho kinases but lack consensus Rho-binding domains. Dominant negative mutations in the C. elegans RhoA GTPase cause neuronal cell shape defects similar to those of sax-1 mutants, and genetic interactions between rhoA and sax-1 suggest shared functions. These results suggest that SAX-1/Ndr kinases are endogenous inhibitors of neurite initiation and cell ------------------- Key: 4341 Medline: 20449033 Authors: Oka T;Futai M Title: Requirement of V-ATPase for ovulation and embryogenesis in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 275: 29556-29561 2000 Type: ARTICLE Genes: vha-1 vha-2 vha-3 vha-4 vha-11 Abstract: Immunofluorescence analysis indicated that VHA-11, the C subunit of Caenorhabditis elegans V-ATPase, was localized in dot-like structures around the nuclei of early embryonic cells and was also detected in embryonic intestinal cells after comma stage. Vital staining with acridine orange showed that the intestinal cells had acidic compartments generated by V-ATPase, consistent with the intracellular localization of VHA-11. RNA interference could efficiently silence vha-ll gene expression: introduction of vha-ll double strand RNA led to embryonic lethality. Worms injected with the vha-11 double strand RNA produced embryos that became lethal. The development of embryos was arrested at various stages. However, their numbers gradually decreased, and the worms eventually became sterile due to the failure of ovulation. Similar results were obtained for RNA interference of the V-ATPase proteolipid genes. These results suggest that V-ATPases, and thus inside-acidic organelles, are required for ovulation and embryogenesis. ------------------- Key: 4342 Medline: 20442532 Authors: LeBlanc MD;Aspeslagh G;Buggia NP;Dyer BD Title: An annotated catalog of inverted repeats of Caenorhabditis elegans chromosomes III and X, with observations concerning odd/even biases and conserved motifs. Citation: Genome Research 10: 1381-1392 2000 Type: ARTICLE Genes: Abstract: We have taken a computational approach to the problem of discovering and deciphering the grammar and syntax of gene regulation in eukaryotes. A logical first step is to produce an annotated catalog of all regulatory sites in a given genome. Likely candidates for such sites are direct and indirect repeats, including three subcategories of indirect repeats: inverted (palindromic), everted, and mirror-image repeats. To that end we have produced a searchable database of inverted repeats of chromosomes III and X of Caenorhabditis elegans the first completely sequenced multicellular eukaryote. Initial results from the use of this catalog are observations concerning odd/even biases in perfect IRs. The potential usefulness of the catalog as a discovery tool for promoters was shown for some of the genes involved with G-protein functions and for heat shock protein 104 (hsp104). ------------------- Key: 4343 Medline: Authors: Malik HS;Henikoff S;Eickbush TH Title: Poised for contagion: Evolutionary origins of the infectious abilities of invertebrate retroviruses. Citation: Genome Research 10: 1307-1318 2000 Type: ARTICLE Genes: Abstract: Phylogenetic analyses suggest that long-terminal repeat (LTR) bearing retrotransposable elements can acquire additional open-reading frames that can enable them to mediate infection. Whereas this process is best documented in the origin of the vertebrate retroviruses and their acquisition of an envelope (env) gene, similar independent events may have occurred in insects, nematodes, and plants. The origins of env-like genes are unclear, and are often masked by the antiquity of the original acquisitions and by their rapid rate of evolution. In this report, we present evidence that in three other possible transitions of LTR retrotransposons to retroviruses, an envelope-like gene was acquired from a viral source. First, the gypsy and related LTR retrotransposable elements (the insect errantiviruses) have acquired their envelope-like gene from a class of insect baculoviruses (double-stranded DNA viruses with no RNA stage). Second, the Cer retroviruses in the Caenorhabditis elegans genome acquired their envelope gene from a Phleboviral (single ambisense-stranded RNA viruses) source. Third, the Tas retroviral envelope (Ascaris lumricoides) may have been obtained from Herpesviridae (double-stranded DNA viruses, no RNA stage). These represent the only cases in which the env gene of a retrovirus has been traced back to its original source. This has implications for the evolutionary history of retroviruses as well as for the potential ability of all LTR-retrotransposable elements to become infectious agents. ------------------- Key: 4344 Medline: 10903569 Authors: Yuan A;Dourado M;Butler A;Walton N;Wei A;Salkoff L Title: SLO-2, a K+ channel with an unusual Cl- dependence. Citation: Nature Neuroscience 3: 771-779 2000 Type: ARTICLE Genes: slo-1 slo-2 Abstract: The gating of different potassium channels depends on many diverse factors. We now report a unique example of a K+ channel with a Cl- dependence. The slo-2 gene was cloned from Caenorhabditis elegans and is widely expressed in both neurons and muscles; it was highly abundant, as suggested by its high representation in the C. elegans EST database. SLO-2, like its paralogue, SLO-1, was also dependent on Ca2+. We show by site-directed mutagenesis that its requirements for both Cl- and Ca2+ are synergistic and associated with the same functional domain. SLO-2's dependence on Cl- implies that intracellular Cl- homeostasis may be important in regulating cellular excitability through this unusual K+ channel. ------------------- Key: 4345 Medline: 20259784 Authors: Wixon J;Blaxter M;Hope I;Barstead R;Kim S Title: Caenorhabditis elegans. Citation: Yeast 17: 37-42 2000 Type: REVIEW Genes: Abstract: Transparent, free-living nematode worm. Unsegmented body plan with full set of differentiated tissues (neural, endoderm, ectoderm and muscle). Genome size approximately 97 Mb, as five autosomes and one X sex chromosome. Fully sequenced genome, which comprises approximately 20 000 predicted genes. Defined cell lineage. Has made major contribution to studies of development, cell-to-cell signalling, cell ageing and cell death processes. Large-scale gene deletion, microarray analysis of gene expression and two-hybrid protein interaction analysis projects under way. Comparative studies mainly with C. briggsae, but also with other free-living and parasitic nematodes. ------------------- Key: 4346 Medline: 20372184 Authors: Pinder JC;Baines AJ Title: A protein accumulator. Citation: Nature 406: 253-254 2000 Type: REVIEW Genes: dys-1 unc-54 unc-70 Abstract: We thought we knew what spectrin does. Is it not the elastic, membrane-bound protein that prevents red blood cells from rupturing as they circulate in the bloodstream? And does it not have the same supporting function in other cells? The second assumption has seldom been questioned over the past two decades, but has just been overturned by the power of experimental genetics, as described in three reports in the Journal of Cell Biology. The results may bear on human diseases such as muscular dystrophy. ------------------- Key: 4347 Medline: 20465303 Authors: Denver DR;Morris K;Lynch M;Vassilieva LL;Thomas WK Title: High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans. Citation: Science 289: 2342-2344 2000 Type: ARTICLE Genes: Abstract: Mutations in the mitochondrial genome have been implicated in numerous human geneticdisorders and offer important data for phylogenetic, forensic. and population genetic studies.Using a long-term series of Caenorhabditis elegans mutation accumulation lines, we performed awide-scale screen for mutations in the mitochondrial genome that revealed a mutation rate that istwo orders of magnitude higher than previous indirect estimates, a highly biased mutationalspectrum, multiple mutations affecting coding function, as welt as mutational hotspots athomopolymeric nucleotide stretches. ------------------- Key: 4348 Medline: 11005858 Authors: Bulik DA;Wei G;Toyoda H;Kinoshita-Toyoda A;Waldrip WR;Esko JD;Robbins PW;Selleck SB Title: sqv-3, -7, and -8, a set of genes affecting morphogenesis in Caenorhabditis elegans, encode enzymes required for glycosaminoglycan biosynthesis. Citation: Proceedings of the National Academy of Sciences USA 97: 10838-10843 2000 Type: ARTICLE Genes: sqv-3 sqv-7 sqv-8 Abstract: sqv (squashed vulva) genes comprise a set of eight independent loci in Caenorhabditis elegans required zygotically for the invagination of vulval epithelial cells and maternally for normal oocyte formation and embryogenesis. Sequencing of sqv-3, sqv-7, and sqv-8 suggested a role for the encoded proteins in glycolipid or glycoprotein biosynthesis. Using a combination of in vitro analysis of SQV enzymatic activities, sqv(+)-mediated rescue of vertebrate cell lines, and biochemical characterization of sqv mutants, we show that sqv-3, -7, and -8 all affect the biosynthesis of glycosaminoglycans and therefore compromise the function of one specific class of glycoconjugates, proteoglycans. These findings establish the importance of proteoglycans and their associated glycosaminoglycans in epithelial morphogenesis and patterning during C. elegans development. ------------------- Key: 4349 Medline: 11030340 Authors: Reinke V;Smith HE;Nance J;Wang J;Van Doren C;Begley R;Jones SJM;Davis EB;Scherer S;Ward S;Kim SK Title: A global profile of germline expression in C. elegans. Citation: Molecular Cell 6: 605-616 2000 Type: ARTICLE Genes: air-2 cyb-1 cyb-3 emb-5 fbf-2 fem-1 fem-3 fer-1 fog-3 gld-1 glp-1 glp-4 him-3 him-6 lag-1 lin-12 mei-1 mes-2 mex-1 mig-5 mom-2 mre-11 msh-5 msp-31 ncc-1 pgl-1 plk-1 prg-1 prg-2 rad-50 rme-2 spe-11 spe-17 spe-26 spo-11 ssp-10 Abstract: We used DNA microarrays to profile gene expression patterns in the C. elegans germline and identified 1416 germline-enriched transcripts that define three groups. The sperm-enriched group contains an unusually large number of protein kinases and phosphatases. The oocyte-enriched group includes potentially new components of embryonic signaling pathways. The germline-intrinsic group, defined as genes expressed similarly in germlines making only sperm or only oocytes, contains a family of piwi-related genes that may be important for stem cell proliferation. Finally, examination of the chromosomal location of germline transcripts revealed that sperm-enriched and germline-intrinsic genes are nearly absent from the X chromosome, but oocyte-enriched genes are not. ------------------- Key: 4350 Medline: 11030341 Authors: Sawa H;Kouike H;Okano H Title: Components of the SWI/SNF complex are required for asymmetric cell division in C. elegans. Citation: Molecular Cell 6: 617-624 2000 Type: ARTICLE Genes: egl-27 lin-17 lin-44 lit-1 psa-1 psa-4 rde-1 unc-29 Abstract: Asymmetric cell division is a fundamental process that produces cellular diversity during development. We have identified two mutants in C. elegans (psa-1 and psa-4) in which the asymmetry of T cell division is disrupted. psa-1 and psa-4 encode homologs of yeast SWI3 and SWI2/SNF2, respectively, which are components of the SWI/SNF complex. We show by RNA interference assay that homologs of other components of SWI/SNF are also involved in T cell division. psa-1 and psa-4 are likely to be required in the T cell during mitosis to cause asymmetric cell division. Because the SWI/SNF complex is required for asymmetric division in S. cerevisiae, these results demonstrate that at least some aspects of the mechanism of asymmetric cell division are conserved between yeast and a multicellular organism. ------------------- Key: 4351 Medline: 20483266 Authors: Kaltenbach L;Horner MA;Rothman JH;Mango SE Title: The TBP-like factor CeTLF is required to activate RNA polymerase II transcription during C. elegans Citation: Molecular Cell 6: 705-713 2000 Type: ARTICLE Genes: end-1 his-24 nhr-2 pes-10 tlf-1 unc-47 Abstract: Metazoans possess two TATA-binding protein homologs, the general transcription factor TBP and a related factor called TLF. Four models have been proposed for the role of TLF in RNA polymerase II (Pol Il) transcription: (1) TLF and TBP function redundantly, (2) TLF antagonizes TBP, (3) TLF is a tissue-specific TBP, or (4) TLF and TBP have distinct activities. Here we report that CeTLF is required to express a subset of Pol II genes and associates with at least one of these genes in vivo. CeTLF is also necessary to establish bulk transcription during early embryogenesis. Since CeTLF and CeTBP are expressed at comparable levels in the same cells, these findings suggest CeTLF performs a unique function in activating Pol II transcription distinct from that of CeTBP. ------------------- Key: 4352 Medline: 20483267 Authors: Dantonel JC;Quintin S;Lakatos L;Labouesse M;Tora L Title: TBP-like factor is required for embryonic RNA polymerase II transcription in C. elegans. Citation: Molecular Cell 6: 715-722 2000 Type: ARTICLE Genes: hlh-1 hlh-2 lin-26 pha-1 tlf-1 Abstract: Recently, a novel family of TATA binding protein (TBP)like factors (TLFs) have been described in metazoan organisms; however, their function has not yet been elucidated. Using Caenorhabditis elegans (Ce) as a model, we demonstrate that CeTLF is required in vivo for zygotic transcription during embryogenesis. Elimination of CeTLF expression by RNA interference caused embryonic lethality either due to the lack of expression of early patterning genes or to their ectopic expression. Moreover, the absence of CeTLF in vivo prevented the correct soma-specific phosphorylation of RNA polymerase II (Pol II). Thus, CeTLF may positively or negatively regulate Pol II transcription, depending on the developmental stage of the embryo. ------------------- Key: 4353 Medline: 10903161 Authors: Van Voorhies WA;Ward S Title: Broad oxygen tolerance in the nematode Caenorhabditis elegans. Citation: Journal of Experimental Biology 203: 2467-2478 2000 Type: ARTICLE Genes: Abstract: This study examined the effects of oxygen tensions ranging from 0 to 90 kPa on the metabolic rate (rate of carbon dioxide production), movement and survivorship of the free-living soil nematode Caenorhabditis elegans, C. elegans requires oxygen to develop and survive. However, it can maintain a normal metabolic rate at oxygen levels of 3.6 kPa and has near-normal metabolic rates at oxygen levels as low as 2 kPa. The ability to withstand low ambient oxygen levels appears to be a consequence of the small body size of C. elegans, which allows diffusion to supply oxygen readily to the cells without requiring any specialized respiratory or metabolic adaptations. Thus, the small size of this organism pre-adapts C. elegans to living in soil environments that commonly become hypoxic. Movement in C. elegans appears to have a relatively minor metabolic cost. Several developmental stages of C. elegans were able to withstand up to 24 h of anoxia without major mortality. Longer periods of anoxia significantly increased mortality, particularly for eggs. Remarkably, long-term exposure to 100% oxygen had no effect on the metabolic rate of C. elegans, and populations were abl ------------------- Key: 4354 Medline: 20460864 Authors: Morgan PG;Radke GW;Sedensky MM Title: Effects of nonimmobilizers and halothane on Caenorhabditis elegans. Citation: Anesthesia & Analgesia 91: 1007-1012 2000 Type: ARTICLE Genes: gas-1 unc-1 unc-79 Abstract: We studied the effects of two nonimmobilizers, a transitional compound, and halothane on the nematode, Caenorhabditis elegans, by using reversible immobility as an end point. By themselves, the nonimmobilizers did not immobilize any of the four strains of animals tested. Toluene appears to be a transitional compound for all strains tested. The additive effects of the nonimmobilizers with halothane were also studied. Similar to results seen in studies of mice, the nonimmobilizers were antagonistic to halothane in the wild type nematode. However, the nonimmobilizers did not affect the 50% effective concentrations of halothane for two other mutant strains. For halothane, the slopes of the dose response curves were smaller in more sensitive strains compared with the wild type. As in mammals, nonimmobilizers antagonize the effects of halothane on the nematode, C. elegans. The variation in slopes in the response to halothane in different strains is consistent with multiple sites of action. These results support the use of C. elegans as a model for the study of anesthetics. ------------------- Key: 4355 Medline: 20486976 Authors: Walker RJ;Franks CJ;Pemberton D;Rogers C;Holden-Dye L Title: Physiological and pharmacological studies on nematodes. Citation: Acta Biologica Hungarica 51: 379-394 2000 Type: ARTICLE Genes: Abstract: Classical transmitters and neuroactive peptides act as transmitters or modulators within the central and peripheral nervous systems of nematodes, for example Ascaris suum and Caenorhabditis elegans. Acetylcholine (ACh) and gamma-aminobutyric acid (GABA) are respectively the excitatory and inhibitory transmitters onto somatic body wall muscle while 5-hydroxytrypamine (5-HT) is the excitatory transmitter onto pharyngeal muscle. 5-HT also reduces ACh-induced contractions of somatic muscle and this action of 5-HT is mediated through activation of adenylate cyclase while that on pharyngeal muscle is mediated through inositol phosphate activation. Glutamate, dopamine and octopamine also have transmitter roles in nematodes. Neuroactive peptides of the RFamide family can excite somatic muscle, for example, AF-1 (KNEFIRFamide), AF-2 (KHEYLRFamide), AF-3 (AVPGVLRFamide) and AF-4 (GDVPGVLRFamide) or inhibit and relax this muscle, for example, PF-I (SDPNFLRFamide), PF2 (SADPNFLRFamide) and PF-4 (KPNIRFamide). In addition PF-3 (AF-8) (KSAYMRFamide) has a biphasic action on pharyngeal muscle, excitation followed by inhibition while AF-I only inhibits this muscle. The peptide effects can be either pre- or postsynaptic or both and are likely to be mediated through second messenger systems. In addition these peptides modulate the action of classical transmitters, particularly ------------------- Key: 4356 Medline: 20476769 Authors: Wolkow CA;Kimura KD;Lee MS;Ruvkun G Title: Regulation of C. elegans life-span by insulinlike signaling in the nervous system. Citation: Science 290: 147-150 2000 Type: ARTICLE Genes: age-1 daf-2 dpy-30 ges-1 mec-7 unc-14 unc-54 unc-119 Abstract: An insulinlike signaling pathway controls Caenorhabditis elegans aging. metabolism, and development. Mutations in the daf-2 insulin receptor-like gene or the downstream age-1 phosphoinositide 3-kinase gene extend adult life-span by two- to threefold. To identify tissues where this pathway regulates aging and metabolism, we restored daf-2 pathway signaling to only neurons, muscle, or intestine. Insulinlike signaling in neurons alone was sufficient to specify wild-type life-span, but muscle or intestinal signaling was not. However, restoring daf-2 pathway signaling to muscle rescued metabolic defects, thus decoupling regulation of life-span and metabolism. These findings point to the nervous system as a central regulator ------------------- Key: 4357 Medline: 20500226 Authors: Meier P;Finch A;Evan G Title: Apoptosis in development. Citation: Nature 407: 796-801 2000 Type: REVIEW Genes: ced-3 ced-4 ced-9 ces-1 ces-2 egl-1 tra-1 Abstract: Essential to the construction, maintenance and repair of tissues is the ability to induce suicide of supernumerary, misplaced or damaged cells with high specificity and efficiency. Study of three principal organisms - the nematode, fruitfly and mouse - indicate that cell suicide is implemented through the activation of an evolutionarily conserved molecular programme intrinsic to all metazoan cells. Dysfunctions in the regulation or execution of cell suicide are implicated in a wide range of developmental abnormalities and diseases. ------------------- Key: 4358 Medline: 20449394 Authors: Cassata G;Kuhn F;Witmer A;Kirchhofer R;Burglin TR Title: A steep thermal gradient thermotaxis assay for the nematode Caenorhabditis elegans. Citation: Genesis 27: 141-144 2000 Type: ARTICLE Genes: ceh-14 ttx-3 Abstract: The nematode Caenorhabditis elegans with its well-described nervous system is one of the multicellular organisms of choice to study thermotaxis. The neuronal circuitry for thermosensation has been analyzed at the level of individual cells. Two methods have previously been described to study the behavior of C. elegans with respect to temperature: 1) isothermal tracking assays and 2) linear thermal gradients (Hedgecock and Russell, 1975). Here we present a short linear thermal gradient assay which is faster and which allows statistical evaluation of different populations using a thermotaxis index. Thin agar plates are used on which a temperature gradient from about 10 degrees to 30 degrees is induced over the distance of about 5 cm. The short linear thermal gradient uses inexpensive materials so that multiple tests can be performed in parallel in a short period of time. ------------------- Key: 4359 Medline: 20450864 Authors: Hood TE;Calabrese EJ;Zuckerman BM Title: Detection of an estrogen receptor in two nematode species and inhibition of binding and development by environmental chemicals. Citation: Ecotoxicology & Environmental Safety 47: 74-81 2000 Type: ARTICLE Genes: Abstract: The presence of estrogen receptors or binding proteins was demonstrated in the free-living nematode species Panagrellus redivivus and Caenorhabditis elegans by radioimmunoassay. Twenty-five nanomolar concentrations of toxaphene, dieldrin, and dieldrin plus nonylphenol significantly inhibited estrogen binding to the receptor in P. redivivus. Binding was inhibited but not significantly by 25 nM nonylphenol, toxaphene plus dieldrin, or toxaphene plus nonylphenol. The current research supports the hypothesis that dieldrin, nonylphenol, and toxaphene may mimic estrogen, altering the normal pathways of estrogen metabolism Based on observations of secondary sex structures, estrogenic chemicals had no effect on sex ratios or growth in Panagrellus redivivus, but caused a ------------------- Key: 4360 Medline: 10993673 Authors: Cassata G;Rohrig S;Kuhn F;Hauri HP;Baumeister R;Burglin TR Title: The Caenorhabditis elegans Ldb/NLI/Clim orthologue ldb-1 is required for neuronal function. Citation: Developmental Biology 226: 45-56 2000 Type: ARTICLE Genes: ceh-14 ldb-1 lim-6 lin-11 mec-2 mec-3 ttx-3 Abstract: LIM homeodomain (LIM-HD) and nuclear LIM-only proteins play important roles in a variety of developmental processes in animals. In some cases their activities are modulated by a nuclear LIM binding protein family called Ldb/NLI/Clim. Here we characterize the Ldb/NLI/Clim orthologue ldb-1 of the nematode Caenorhabditis elegans. Two alternatively spliced variants exist, which differ in their amino-termini. The ldb-1 orthologue of Caenorhabditis briggsae has the same structure as that of C. elegans and is highly conserved throughout the open reading frame, while conservation to ny and vertebrate proteins is restricted to specific domains: the dimerization domain, the nuclear localization sequence, and the LIM interaction domain. C. elegans ldb-1 is expressed in neurogenic tissues in embryos, in all neurons in larval and adult stages, and in vulval cells, gonadal sheath cells, and some body muscle cells. C. elegans LDB-1 is able to specifically bind LIM domains in yeast two-hybrid assays. RNA inactivation studies suggest that C. elegans ldb-1 is not required for the differentiation of neurons that express the respective LIM-HD genes or for LIM-HD gene autoregulation. In contrast, ldb-1 is necessary for several neuronal functions mediated by LIM-HD proteins, including the transcriptional activation of mec-2 the mechanosensory neuron-specific ------------------- Key: 4361 Medline: 20450853 Authors: Tam T;Mathews E;Snutch TP;Schafer WR Title: Voltage-gated calcium channels direct neuronal migration in Caenorhabditis elegans. Citation: Developmental Biology 226: 104-117 2000 Type: ARTICLE Genes: egl-19 snt-1 unc-2 unc-43 Abstract: Calcium signaling is known to be important for regulating the guidance of migrating neurons, yet the molecular mechanisms underlying this process are not well understood. We have found that two different voltage-gated calcium channels are important for the accurate guidance of postembryonic neuronal migrations in the nematode Caenorhabditis elegans. In mutants carrying loss of function alleles of the calcium channel gene unc-2, the touch receptor neuron AVM and the interneuron SDQR often migrated inappropriately, leading to misplacement of their cell bodies. However, the AVM neurons in unc-2 mutant animals extended axons in a wild-type pattern, suggesting that the UNC-2 calcium channel specifically directs migration of the neuronal cell body and is not required for axonal pathfinding. In contrast, mutations in egl-19, which affect a different voltage-gated calcium channel, affected the migration of the AVM and SDQR bodies, as well as the guidance of the AVM axon. Thus, cell migration and axonal pathfinding in the AVM neurons appear to involve distinct calcium channel subtypes. Mutants defective in the unc-43/CaM kinase gene showed a defect in SDQR and AVM positioning that resembled that of unc-2 mutants; thus, CaM kinase may function as an effector of the UNC-2-mediated calcium influx in guiding cell migration. ------------------- Key: 4362 Medline: 20450855 Authors: Branda CS;Stern MJ Title: Mechanisms controlling sex myoblast migration in Caenorhabditis elegans hermaphrodites. Citation: Developmental Biology 226: 137-151 2000 Type: ARTICLE Genes: egl-17 let-23 lin-3 mab-20 mab-26 sax-3 unc-3 unc-5 unc-6 unc-14 unc-30 unc-33 unc-34 unc-40 unc-44 unc-51 unc-53 unc-62 unc-76 vab-1 Abstract: Sex myoblast migration in C. elegans hermaphrodites is controlled by multiple guidance mechanisms. A gonad-dependent attraction functions to guide the sex myoblasts to their precise final positions flanking the gonad. In the absence of this attraction, a gonad-dependent repulsion is revealed. In addition to gonad-dependent influences, a gonad-independent mechanism propels the sex myoblasts anteriorly to a broad range of positions near the center of the animal. Here we describe a temporal analysis of sex myoblast migration that reveals when the gonad-dependent attraction and the gonad-independent mechanisms normally function. We provide evidence that EGL-17, a fibroblast growth factor-like protein, is expressed in the gonadal cells required to attract the sex myoblasts to their precise final positions, further supporting our model that EGL-17 defines the gonad-dependent attractant. Furthermore, cell ablation experiments reveal that EGL-17 and the gonad-dependent repellent likely emanate from the same cellular sources. Analyses of candidate mutations for their effects on the gonad-dependent repulsion reveal that a set of genes known to affect multiple aspects of axonogenesis, unc-14, unc-33, unc-44, and unc-51, is essential for this repulsive mechanism. In addition, we have discovered that a SAX-3/Roundabout-dependent mechanism is used to maintain the sex myoblasts along the ventral muscle quadrants. ------------------- Key: 4363 Medline: 20450856 Authors: Jones D;Candido EPM Title: The NED-8 conjugating system in Caenorhabditis elegans is required for embryogenesis and terminal differentiation of the hypodermis. Citation: Developmental Biology 226: 152-165 2000 Type: ARTICLE Genes: ned-8 uba-3 ubc-12 ubq-1 ula-1 Abstract: This work has identified the enzymes involved in the activation and conjugation of the ubiquitin-like protein NED-8 in Caenorhabditis elegans. A C. elegans conjugating enzyme, UBC-12, is highly specific in its ability to utilize NED-8 as a substrate. Immunostaining shows that NED-8 is conjugated in vivo to a major target protein with a conjugate size of 90 kDa. While the amount of this conjugate is developmentally regulated with reduced levels in the larval stages, the mRNA encoding C. elegans UBC-12 is constitutively produced throughout development, as is NED-8 itself. The importance of the NED-8 conjugating system in C. elegans was determined by RNA interference (RNAi) assays using double-stranded RNA encoding NED-8, UBC-12 or the NED-8 activating enzyme component ULA-1. The progeny of both ned-8 and ubc-12 RNAi-treated hermaphrodites either arrested during embryonic development or underwent abnormal postembryonic development. The effect on postembryonic development was pleiotropic, the most frequent gross abnormality being vulval eversion during the L4 stage. Individuals with an everted vulva either burst at the L4 to adult molt or gave rise to adults incapable of egg laying. Additionally, both ned-8 and ubc-12 RNAi induced a striking abnormality in the alae, structures produced by the lateral hypodermal seam cells in the adult nematode. Affected alae were patchy and frequently diverged around a central space. Vulval defects were also produced by RNAi directed at C. elegans ula-1. This is the first demonstration of a requirement for NED-8 conjugation in ------------------- Key: 4364 Medline: 20464946 Authors: Meesapyodsuk D;Reed DW;Savile CK;Buist PH;Ambrose SJ;Covello PS Title: Characterization of the regiochemistry and cryptoregiochemistry of a Caenorhabditis elegans fatty acid desaturase (FAT-1) expressed in Saccharomyces cerevisiae. Citation: Biochemistry 39: 11948-11954 2000 Type: ARTICLE Genes: fat-1 Abstract: To characterize the fatty acid desaturase produced by the fat-1 gene from the nematode Caenorhabditis elegans, the functional expression of this enzyme was effected in the yeast Saccharomyces cerevisiae. The CC-MS analysis of desaturated products derived from various fatty acids, including deuterium-labeled thia fatty acids supplied to growing cultures of transformed yeast, has defined the substrate requirements, regiochemistry, and cryptoregiochemistry of the enzyme. The desaturase acts on substrates of 16-20 carbons with a preference for omega-6 fatty acids, and its regioselectivity was confirmed to be that of an omega-3 desaturase. (omega-x refers to a double bond or desaturation between carbons x and x+1, counting from the methyl end of a fatty acid.) The primary deuterium kinetic isotope effects (KIEs) at C-15 and C-16 of a C18 fatty acid analogue were measured via competitive incubation experiments: While k(H)/k(D) at the omega-3 position was shown to be large (7.8 +/- 0.4), essentially no KIE at the omega-2 position was observed (k(H)/k(D) = 0.99 +/- 0.04). This result indicates that omega-3 desaturation is initiated by an energetically difficult C-H bond cleavage at the carbon closer to the carboxyl terminus. The results are discussed in the context of a general model relating the structure and function of membrane-bound fatty acid desaturases featuring differing ------------------- Key: 4365 Medline: 20399000 Authors: Conradt B Title: Programmed cell death and its regulation and initiation in C. elegans. Citation: Ernst Schering Research Foundation Workshop 29: 35-55 2000 Type: REVIEW Genes: ced-3 ced-4 ced-9 ces-1 ces-2 egl-1 Abstract: The proliferation of cells is an integral part of development and tissue homeostatsis in multicellular animals(reviewed by Raff 1996; Folletee and O'farrel 1997). Two opposing processes, the division of cells on one hand and the programmed death of cells on the other hand, determine the overall rate of cell proliferation, The proper regulation of these two physiological processes is therefore a crucial aspect of development and of tissue homeostatsis(reviewed by Edgar and Lehner 1996; Shrr 1997;Jacobson et al. 1997). While the importance of the process of cell division has long been recognized, the role and extent of programmed cell death, or apoptosis, has only been realized within the last decades (Glucksmann 1950; Kerr et al. 19972). Massive programmed cell death occurs, for instance, during the development of the nervous system and in the immune system: more than 50% on all neurons and oligodendrocytes formed in the periperal and central vertebrate nervous system undergo programmed cell death neurogenesis... ------------------- Key: 4366 Medline: 20398999 Authors: Jansen G;Thijssen KL;Werner P;van der Horst M;Hazendonk E;Plasterk RH Title: The heterotrimeric G protein genes of Caenorhabditis elegans. Citation: Ernst Schering Research Foundation Workshop 29: 13-34 2000 Type: REVIEW Genes: egl-30 goa-1 gpa-1 gpa-2 gpa-3 gpa-4 gpa-5 gpa-6 gpa-7 gpa-8 gpa-9 gpa-10 gpa-11 gpa-12 gpa-13 gpa-14 gpa-15 gpa-16 gpb-1 gpb-2 gpc-1 gpc-2 gsa-1 odr-3 Abstract: Caenorhabditis elegans is the first animal, and the first multicellular organism, for which the complete genomic sequence has been determined. One of the new possibilities in post-sequence genetics is the immediate analysis of complete gene families. A first approximation analysis of gene function involves the determination of expression patterns, and the description of loss-of-function as well as gain-of-function phenotypes. We performed such studies for the complete family of G protein alpha subunits. ------------------- Key: 4367 Medline: 20360611 Authors: Gerstein M;Lin J;Hegyi H Title: Protein folds in the worm genome. Citation: Pacific Symposium on Biocomputing : 30-41 2000 Type: ARTICLE Genes: Abstract: We survey the protein folds in the worm genome, using pairwise and multiple-sequence comparison methods (i.e. FASTA and PSI-blast). Overall, we find that approximately 250 folds match approximately 8000 domains in approximately 4500 ORFs, about 32 matches per fold involving a quarter of the total worm ORFs. We compare the folds in the worm genome to those in other model organisms, in particular yeast and E. coli, and find that the worm shares more folds with the phylogenetically closer yeast than with E. coli. There appear to be 36 folds unique to the worm compared to these two model organisms, and many of these are obviously implicated in aspects of multicellularity. The most common fold in the worm genome is the immunoglobulin fold, and many of the common folds are repeated in various combinations and permutations in multidomain proteins. In addition, an approach is presented for the identification of "sure" and "marginal" membrane proteins. When applied to the worm genome, this reveals a much greater relative prevalence of proteins with seven transmembrane helices in comparison to the other completely sequenced genomes, which are not of metazoans. Combining these analyses with some other simple filters allows one to identify ORFs that potentially code for soluble proteins of unknown fold, which may be promising targets for experimental investigation in structural genomics. A regularly updated worm fold analysis will be available from ------------------- Key: 4368 Medline: Authors: Doerks T;Bork P;Kamberov E;Makarova O;Muecke S;Margolis B Title: L27, a novel heterodimerization domain in receptor targeting proteins Lin-2 and Lin-7. Citation: Trends in Biochemical Sciences 25: 317-318 2000 Type: ARTICLE Genes: let-23 lin-2 lin-7 lin-10 Abstract: Membrane-associated guanylate kinases (MAGUKs) are emerging as pivotal for the organization of cell-surface proteins and their interaction with the cytoskeleton. They are involved in cell junction organization and tumour suppression. Recent work has indicated that the Caenorhabditis elegans MAGUK protein Lin-2 is crucial for the proper targeting of the worm growth factor receptor Let-23 to the basolateral surface of epithelial cells. Lin-7 and Lin-10 are also required for the basolateral targeting of this receptor in worm and form a complex with ------------------- Key: 4369 Medline: 20435420 Authors: Brown NH Title: An integrin chicken and egg problem: which comes first, the extracellular matrix or the cytoskeleton? Citation: Current Opinion in Cell Biology 12: 629-633 2000 Type: REVIEW Genes: pat-2 pat-3 unc-97 unc-112 Abstract: Integrins have the ability to organise macromolecular structures both inside and outside the cell. Analysis of integrin function in the developing embryos of worms and flies suggests that, although the extracellular matrix directs integrins to organise intracellular proteins, the cytoskeleton may have the first word. ------------------- Key: 4370 Medline: 11043553 Authors: Zhang DM;Levitan D;Yu G;Nishimura M;Chen F;Tandon A;Kawarai T;Arawaka S;Supala A;Song YQ;Rogaeva E;Liang Y;Holmes E;Milman P;Sato C;Zhang L;St. George-Hyslop P Title: Mutation of the conserved N-terminal cysteine (Cys92) of human presenilin 1 causes increased A beta(42) secretion in mammalian cells but impaired Notch/lin-12 signalling in C. elegans. Citation: Neuroreport 11: 3227-3230 2000 Type: ARTICLE Genes: lin-12 sel-12 Abstract: The presenilin proteins are involved in the proteolytic processing of transmembrane proteins such as Notch/lin-12 and the beta-amyloid precursor protein (beta APP). Mutation of a conserved cysteine (Cys60Ser) in the C. elegans presenilin sel-12 has a loss-of-function effect on Notch/lin-12 processing similar to that of null mutations in sel-12. In contrast, in mammalian cells, most missense mutations increase gamma-secretase cleavage of beta APP. We report here that mutation of this conserved cysteine (Cys92Ser) in human presenilin I confers a loss-of-function effect in C. elegans, but causes increased A beta(42) secretion in mammalian cells. These data suggest that the role of presenilins in Notch/lin-12 signalling and beta APP processing are either separately regulated activities or independent activities of the presenilins. ------------------- Key: 4371 Medline: 11029035 Authors: Pilon M;Peng XR;Spence AM;Plasterk RHA;Dosch HM Title: The diabetes autoantigen ICA69 and its Caenorhabditis elegans homologue, ric-19, are conserved regulators of neuroendocrine secretion. Citation: Molecular Biology of the Cell 11: 3277-3288 2000 Type: ARTICLE Genes: ric-19 Abstract: ICA69 is a diabetes autoantigen with no homologue of known function. Given that most diabetes autoantigens are associated with neuroendocrine secretory vesicles, we sought to determine if this is also the case for ICA69 and whether this protein participates in the process of neuroendocrine secretion. Western blot analysis of ICA69 tissue distribution in the mouse revealed a correlation between expression levels and secretory activity, with the highest expression levels in brain, pancreas, and stomach mucosa. Subcellular fractionation of mouse brain revealed that although most of the ICA69 pool is cytosolic and soluble, a subpopulation is membrane-bound and coenriched with synaptic vesicles. We used immunostaining in the HIT insulin-secreting beta-cell Line to show that ICA69 localizes in a punctate manner distinct from the insulin granules, suggesting an association with the synaptic-like microvesicles found in these cells. To pursue functional studies on ICA69, we chose to use the model organism Caenorhabditis elegans, for which a homologue of ICA69 exists. We show that the promoter of the C. elegans ICA69 homologue is specifically expressed in all neurons and specialized secretory cells. A deletion mutant was isolated and found to exhibit resistance to the drug aldicarb (an inhibitor of acetylcholinesterase), suggesting defective neurotransmitter secretion in the mutant. On the basis of the aldicarbresistance phenotype, we named the gene ric-19 (resistance to inhibitors of cholinesterase-19). The resistance to aldicarb was rescued by introducing a ric-19 transgene into the ric-19 mutant background. This is the first study aimed at dissecting ICA69 function, and our results are consistent with the interpretation that ICA69/RIC-19 is an evolutionarily conserved cytosolic protein participating in the process of neuroendocrine secretion via association with certain secretory vesicles. ------------------- Key: 4372 Medline: 20483775 Authors: Kohn RE;Duerr JS:McManus JR;Duke A;Rakow TL;Maruyama H;Moulder G;Maruyama IN;Barstead RJ;Rand JB Title: Expression of multiple UNC-13 proteins in the Caenorhabditis elegans nervous system. Citation: Molecular Biology of the Cell 11: 3441-3452 2000 Type: ARTICLE Genes: unc-13 Abstract: The Caenorhabditis elegans UNC-13 protein and its mammalian homologues are important for normal neurotransmitter release, We have identified a set of transcripts from the unc-13 locus in C. elegans resulting from alternative splicing and apparent alternative promoters. These transcripts encode proteins that are identical in their C-terminal regions but that vary in their N-terminal regions. The most abundant protein form is localized to most or all synapses. We have analyzed the sequence alterations, immunostaining patterns, and behavioral phenotypes of 31 independent unc-13 alleles. Many of these mutations are transcript-specific; their phenotypes suggest that the different UNC-13 forms have different cellular functions. We have also isolated a deletion allele that is predicted to disrupt all UNC-13 protein products; animals homozygous for this null allele are able to complete embryogenesis and hatch, but they die as paralyzed first-stage larvae. Transgenic expression of the entire gene rescues the behavior of mutants fully; transgenic overexpression of one of the transcripts can partially compensate for the genetic loss of another. This finding suggests some degree of functional overlap of the different ------------------- Key: 4373 Medline: Authors: Schierenberg E Title: New approaches to a better understanding of nematode phylogeny: molecular and developmental studies. Citation: Journal of Zoological Systematics & Evolutionary Research 38: 129-132 2000 Type: ARTICLE Genes: Abstract: Recent studies making use of ribosomal DNA sequences have led to a wealth of new information that can be used to construct phylogenetic trees and compare them with those derived from more traditional approaches. Here, some examples are presented where the molecular data have stimulated alternative views. To determine whether differences in developmental processes can be used as markers for intraphyletic relationships, comparative studies of nematode embryogenesis have been performed. These results indicate that considerable deviations from the standard pattern found in the model system Caenorhabditis elegans exist which appear to be characteristic for certain subgroups within the taxon ------------------- Key: 4374 Medline: Authors: Braeckman BP;Houthoofd K;Vanfleteren JR Title: Patterns of metabolic activity during aging of the wild type and longevity mutants of Caenorhabditis elegans. Citation: Age 23: 55-73 2000 Type: ARTICLE Genes: age-1 akt-1 akt-2 clk-1 clk-2 clk-3 ctl-1 daf-2 daf-12 daf-16 daf-18 daf-23 eat-2 fer-15 gro-1 mev-1 pdk-1 rad-8 sod-1 sod-2 sod-3 sod-4 tkr-1 unc-31 unc-64 Abstract: At least three mechanisms determine life span in Caenorhabditis elegans. An insulin-like signaling pathway regulates dauer diapause, reproduction and longevity. Reduction- or loss-of-function mutations in this pathway can extend longevity substantially, suggesting that the wild-type alleles shorten life span. The mutations extend life span by activating components of a dauer longevity assurance program in adult life, resulting in altered metabolism and enhanced stress resistance. The Clock (Clk) genes regulate many temporal processes, including life span. Mutation in the Clk genes clk-1 and gro-1 mildly affect energy production, but repress energy consumption dramatically, thereby reducing the rate of anabolic metabolism and lengthening life span. Dietary restriction, either imposed by mutation or by the culture medium increases longevity and uncovers a third mechanism of life span determination. Dietary restriction likely elicits the longevity assurance program. There is still uncertainty as to whether these pathways converge on daf-16 to activate downstream longevity effector genes such as ctl-l and sod-3. There is overwhelming evidence that the interplay between reactive oxygen species (ROS) and the capacity to resist oxidative stress controls the aging process and longevity. It is as yet not clear whether metabolic homeostasis collapses with age as a direct result of ROS-derived damage or is selectively repressed by longevity-determining genes. The dramatic decline of protein turnover during senescence results in the accumulation of altered enzymes and in a gradual decline of metabolic performance eventually followed by fatal failure ------------------- Key: 4375 Medline: Authors: Thaden JJ;Reis RJS Title: Ammonia, respiration, and longevity in nematodes: Insights on metabolic regulation of life span from temporal rescaling. Citation: Age 23: 75-84 2000 Type: ARTICLE Genes: age-1 clk-1 clk-2 clk-3 daf-2 daf-12 daf-16 gro-1 Abstract: To better understand metabolic correlates of longevity, we used a graphical technique to compare the adult temporal patterns of several markers of metabolic activity - ammonia elimination, oxygen consumption rate, ATP levels, and (in freeze-permeabilized worms) the rate of NADPH-activated, lucigenin-mediated superoxide formation - as observed by us and others in normal and long-lived mutant Caenorhabditis elegans strains. All of these traits declined with time, and when their logarithms were plotted against time, appeared reasonably linear for most of the duration of the experiments. The profiles for ammonia output conformed well to parallel regression lines; those for the other metabolic parameters varied widely in slope as originally plotted by the authors, but much less so when replotted as logarithms against adjusted time, scaled by the reciprocal of strain longevity. This is consistent with coregulation of life span, respiration rate, ATP levels, lucigenin reactivity, but not ammonia excretion, by a physiological clock distinguishable from chronologic time. Plots, scaled appropriately for equalized slopes, highlighted y-axis intercept differences among strains. On rescaled plots, these constitute deviations from the expectation based on 'strain-specific clock' differences alone. With one exception, y-intercept effects were observed only for mutants in an insulin-like signaling pathway. ------------------- Key: 4376 Medline: 11027209 Authors: Kunkel MT;Johnstone DB;Thomas JH;Salkoff L Title: Mutants of a temperature-sensitive two-P domain potassium channel. Citation: Journal of Neuroscience 20: 7517-7524 2000 Type: ARTICLE Genes: mah-2 twk-18 unc-110 Abstract: Within the Caenorhabditis elegans genome there exist at least 42 genes encoding TWK (two-P domain K+) channels, potassium channel subunits that contain two pore regions and four transmembrane domains. We now report the first functional characterization of a TWK channel from C. elegans. Although potassium channels have been reported to be activated by a variety of factors, TWK-18 currents increase dramatically with increases in temperature. Two mutant alleles of the twk-18 gene confer uncoordinated movement and paralysis in C. elegans. Expression of wild-type and mutant TWK-18 channels in Xenopus oocytes showed that mutant channels express much larger potassium currents than wild-type channels. Promoter-green fluorescent protein fusion experiments indicate that TWK-18 is expressed in body wall muscle. Our genetic and physiological data suggest that the movement defects observed in mutant twk-18 animals may be explained by an increased activity of the mutant TWK-18 channels. ------------------- Key: 4377 Medline: 20469350 Authors: Kelly KO;Dernburg AF;Stanfield GM;Villeneuve AM Title: Caenorhabditis elegans msh-5 is required for both normal and radiation-induced meiotic crossing-over but not for completion of meiosis. Citation: Genetics 156: 617-630 2000 Type: ARTICLE Genes: mre-11 msh-5 spo-11 Abstract: Crossing over and chiasma formation during Caenorhabditis elegans meiosis require msh-5 which encodes a conserved germline-specific MutS family member, msh-5 mutant oocytes lack chiasmata between homologous chromosomes, and crossover frequencies are severely reduced in both oocyte and spermatocyte meiosis. Artificially induced DNA breaks do not bypass the requirement for msh-5, suggesting that msh-5 functions after the initiation step of meiotic recombination. msh-5 mutants are apparently competent to repair breaks induced during meiosis, but accomplish repair in a way that does not lead to crossovers between homologs. These results combine with data from budding yeast to establish a conserved role for Msh5 proteins in promoting the crossover outcome of meiotic recombination events. Apart from the crossover deficit, progression through meiotic prophase is largely unperturbed in msh-5 mutants. Homologous chromosomes are fully aligned at the pachytene stage, and germ cells survive to complete meiosis and gametogenesis with high efficiency. Our demonstration that artificially induced breaks generate crossovers and chiasmata using the normal meiotic recombination machinery suggests (1) that association of breaks with a preinitiation complex is not a prerequisite for entering the meiotic recombination path way and (2) that the decision for a subset of recombination events to become crossovers is made after the initiation step. ------------------- Key: 4378 Medline: 20469351 Authors: Hoppe PE;Waterston RH Title: A region of the myosin rod important for interaction with paramyosin in Caenorhabditis elegans striated muscle. Citation: Genetics 156: 631-643 2000 Type: ARTICLE Genes: myo-3 sup-3 unc-15 unc-54 Abstract: The precise arrangement of molecules within the thick filament, as well as the mechanisms by which this arrangement is specified, remains unclear. In this article, we have exploited a unique genetic interaction between one isoform of myosin heavy chain (MHC) and paramyosin in Caenorhabditis elegans to probe the molecular interaction between MHC and paramyosin in vivo. Using chimeric myosin constructs, we have defined a 322-residue region of the MHC A rod critical for suppression of the structural and motility defects associated with the unc-15(e73) allele. Chimeric constructs lacking this region of MHC A either fail to suppress, or act as dominant enhancers of, the e73 phenotype. Although the 322-residue region is required for suppression activity, our data suggest that sequences along the length of the rod also play a role in the isoform-specific interaction between MHC A and paramyosin. Our genetic and cell biological analyses of construct behavior suggest that the 322-residue region of MHC A is important for thick filament stability. We present a model in which this region mediates an arid interaction between MHC A and paramyosin in parallel arrangement in formation of the filament arms. ------------------- Key: 4379 Medline: 20472595 Authors: Sarafi-Reinach TR;Sengupta P Title: The forkhead domain gene unc-130 generates chemosensory neuron diversity in C. elegans. Citation: Genes & Development 14: 2472-2485 2000 Type: ARTICLE Genes: ced-3 egl-2 gcy-8 gpa-5 lin-26 odr-7 ops-1 osm-6 sra-6 str-1 str-2 str-3 tax-2 ttx-3 unc-30 unc-130 Abstract: Coenorhabditis elegans responds to its complex chemical environment using a small number of chemosensory neurons. Each of these neurons exhibits a unique sensory response repertoire. The developmental mechanisms that generate this diversity of function are largely unknown. Many C. elegans chemosensory neurons, including the AWA and ASG neurons, arise as lineal sisters of an asymmetric division. Here we describe the gene unc-130, which plays a role in the generation of the AWA and ASG neurons. In unc-130 mutants, the ASG neurons adopt the fate of the AWA neurons, unc-130 encodes a member of the forkhead domain family of transcription factors, and is expressed in the precursors to AWA and ASG neurons. Misexpression of unc-130 in the AWA neurons is partly sufficient to repress the AWA fate, but not to promote ASG fate, unc-130 also plays a role in the development of additional chemosensory neurons. Our experiments show that the ASG neurons share a developmental default state in common with three types of olfactory neurons. We propose that distinct cell fates and hence diversity of function in the chemosensory neurons of C. elegans are generated in a hierarchical manner, utilizing both lineage-dependent and independent mechanisms. ------------------- Key: 4380 Medline: 20472596 Authors: Nash B;Colavita A;Zheng H;Roy PJ;Culotti JG Title: The Forkhead transcription factor UNC-130 is required for the graded spatial expression of the UNC-129 TGF-beta guidance factor in C. elegans. Citation: Genes & Development 14: 2486-2500 2000 Type: ARTICLE Genes: daf-4 dbl-1 unc-5 unc-6 unc-40 unc-129 unc-130 mnDf77 Abstract: Secreted proteins required for cellular movements along the circumference of the body wall in Caenorhabditis elegans include UNC-6/netrin and the novel TGF-beta UNC-129. Expression of these proteins is graded along the dorsoventral (D/V) axis, providing polarity information to guide migrations. Here we show that the graded expression of UNC-129 in dorsal but not ventral body muscles depends on unc-130, which encodes a Forkhead transcription factor. The phenotype of unc-130 mutants closely mimics the reported effects of ectopically expressing unc-129 in both dorsal and ventral body muscles (Colavita et al. 1998). This fits our present finding that unc-130 cell autonomously represses unc-129 expression in the ventral body muscles. Thus the cell-specific effects of unc-130 on ventral, but not dorsal, body muscle expression of unc-229 accounts for the D/V polarity information required for UNC-129-mediated guidance. Genetic interactions between unc-130 and other guidance genes show that several molecular pathways function in parallel to guide the ventral to dorsal migration of distal tip cells (DTCs) and axonal growth cones in C. elegans. Genetic interactions confirm that UNC-129 does not require the only known type II TGF-beta receptor in C. elegans (DAF-4) for its guidance functions. Also, unc-130 is partially required for male tail morphogenesis and for embryogenesis. ------------------- Key: 4381 Medline: 20515633 Authors: Koga M;Zwaal R;Guan KL;Avery L;Ohshima Y Title: A Caenorhabditis elegans MAP kinase kinase, MEK-1, is involved in stress responses. Citation: EMBO Journal 19: 5148-5156 2000 Type: ARTICLE Genes: eat-5 eat-11 eat-18 lin-17 mek-1 Abstract: The c-Jun N-terminal kinase (JNK), a member of the mitogen-activated protein kinase (MAPK) family, was shown to be involved in the response to various stresses in cultured cells. However, there is little in vivo evidence indicating a role for a JNK pathway in the stress response of an organism. We identified the Caenorhabditis elegans mek-1 gene, which encodes a 347 amino acid protein highly homologous to mammalian MKK7, an activator of JNK, Mek-1 reporter fusion proteins are expressed in pharyngeal muscle, uterus, a portion of intestine, and neurons. A mek-1 deletion mutant is hypersensitive to copper and cadmium ions and to starvation. A wild-type mek-1 transgene rescued the hypersensitivity to the metal ions. Double mutants of mek-1 with an eat-5, eat-II or eat-18 mutation, which are characterized by a limited feeding defect, showed distinct growth defects under normal conditions. Expression of an activated form of MEK-1 in the whole animal or specifically in the pharynx inhibited pharyngeal pumping. These results suggest a role for mek-1 in stress responses, with a focus in the pharynx and/or intestine. ------------------- Key: 4382 Medline: 20411180 Authors: Fay DS;Han M Title: Mutations in cye-1, a Caenorhabditis elegans cyclin E homolog, reveal coordination between cell-cycle control and vulval development. Citation: Development 127: 4049-4060 2000 Type: ARTICLE Genes: cye-1 cul-1 evl-10 let-60 lin-15 lin-36 Abstract: We have identified strong loss-of-function mutations in the C. elegans cyclin E gene, cye-1. Mutations in cye-1 lead to the underproliferation of many postembryonic blast lineages as well as defects in fertility and gut-cell endoreduplication, In addition, cye-1 is required maternally, but not zygotically for embryonic development. Our analysis of vulval development in cye-1 mutants suggests that a timing mechanism may control the onset of vulval cell terminal differentiation: once induced, these cells appear to differentiate after a set amount of time, rather than a specific number of division cycles. cye-1 mutants also show an increase in the percentage of vulval precursor cells (VPCs) that adopt vulval cell fates, indicating that cell-cycle length can play a role in the proper patterning of vulval cells. By analyzing cul-1 mutants, we further demonstrate that vulval cell terminal differentiation can be uncoupled from associated changes in vulval cell division planes. ------------------- Key: 4383 Medline: 20453785 Authors: Gieseler K;Grisoni K;Segalat L Title: Genetic suppression of phenotypes arising from mutations in dystrophin-related genes in Caenorhabditis elegans. Citation: Current Biology 10: 1092-1097 2000 Type: ARTICLE Genes: dyc-1 dys-1 hlh-1 Abstract: Background: Dystrophin is the product of the gene that is mutated in Duchenne muscular dystrophy (DMD), a progressive neuromuscular disease for which no treatment is available. Mice carrying a mutation in the gene for dystrophin (mdx mice) display only a mild phenotype, but it is aggravated when combined with a mutation in the MyoD gene. The nematode worm Caenorhabditis elegans has a dystrophin homologue (dys-1), but null mutations in dys-1 do not result in muscle degeneration. Results: We generated worms carrying both the dys-1 null mutation cx18, and a weak mutation, cc561ts, of the C. elegans MyoD homologue hlh-1. The double mutants displayed a time-dependent impairment of locomotion and egg laying, a phenotype not seen in the single mutants, and extensive muscle degeneration. This result allowed us to look for genes that, when misexpressed, could suppress the dys-1; hlh-1 phenotype. When overexpressed, the dyc-1 gene - whose loss-of-function phenotype resembles that of dys-1 - partially suppressed the dys-1; hlh-1 phenotype. The dyc-1 gene encodes a novel protein sharing similarities with the mammalian neural nitric oxide synthase (nNOS)-binding protein CAPON, and is expressed in the muscles of the worm. Conclusions: As a C. elegans model for dystrophin-dependent myopathy, the dys-1; hlh-1 worms should permit the identification of genes, and ultimately drugs, that would reverse the muscle ------------------- Key: 4384 Medline: 20453786 Authors: Michaux G;Gansmuller A;Hindelang C;Labouesse M Title: CHE-14, a protein with a sterol-sensing domain, is required for apical sorting in C. elegans ectodermal epithelial cells. Citation: Current Biology 10: 1098-1107 2000 Type: ARTICLE Genes: cav-1 cav-2 che-14 lin-26 lrp-1 Abstract: Background: Polarised trafficking of proteins is critical for normal expression of the epithelial phenotype, but its genetic control is not understood. The regulatory gene lin-26 is essential for normal epithelial differentiation in the nematode Caenorhabditis elegans. To identify potential effecters of lin-26, we characterised mutations that result in lin-26-like phenotypes. Here, we report the phenotypic and molecular analysis of one such mutant line, che-14. Results: Mutations in che-14 resulted in several partially penetrant phenotypes affecting the function of most epithelial or epithelial-like cells of the ectoderm, including the hypodermis, excretory canal, vulva, rectum and several support cells. The defects were generally linked to the accumulation of vesicles or amorphous material near the apical surface, suggesting that secretion was defective. The CHE-14 protein showed similarity to proteins containing sterol-sensing domains, including Dispatched, Patched and NPC1. A fusion protein between full-length CHE-14 and the green fluorescent protein became localised to the apical surface of epithelial cells that require che-14 function. Deletions that removed the predicted transmembrane domains or extracellular loops of CHE-14 abolished apical localisation and function of the protein. Conclusions: We propose that CHE-14 is involved in a novel secretory pathway dedicated to the exocytosis of lipid-modified proteins at the apical surface of certain epithelial cells. Our data raise the possibility that the primordial function of proteins containing a sterol-sensing domain is to control vesicle trafficking: CHE-14 and Dispatched in exocytosis, Patched and NPC1 in endocytosis. ------------------- Key: 4385 Medline: Authors: Mohler WA;Squirrell JM Title: Multiphoton imaging of embryonic development. Citation: "Imaging Neurons: A Laboratory Manual." R Yuste, F Lanni, A Konnerth (eds); Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. : 21.1-21.11 2000 Type: ARTICLE Genes: Abstract: Embryos are unique in their combination of pluripotency, three-dimensionality, and the swiftness of subcellular and developmental rearrangements. In some species, it is possible to observe the entire organism taking form within a microscope field. Capturing the spatial and temporal dynamic complexity of embryogenesis tests the limits of both culture and microscopy techniques. Observing specific fluorescently labeled components during embryonic development promises to reveal the roles of organelles and molecules in a native and reproducible context. However, to gain a thorough understanding of such dynamic biological systems, one must record events of interest as they occur, while limiting the perturbations caused by the observation techniques. In this chapter, we discuss our experiences using the relatively new technology of multiphoton laser scanning microscopy to examine the development of mammalian and nematode embryos in four dimensions. ------------------- Key: 4386 Medline: 20508107 Authors: Hill AA;Hunter CP;Tsung BT;Tucker-Kellogg G;Brown EL Title: Genomic analysis of gene expression in C. elegans. Citation: Science 290: 809-812 2000 Type: ARTICLE Genes: Abstract: Until now, genome-wide transcriptional profiling has been Limited to single-cell organisms. The nematode Caenorhabditis elegans is a well-characterized metazoan in which the expression of all genes can be monitored by oligonucleotide arrays. We used such arrays to quantitate the expression of C. elegans genes throughout the development of this organism. The results provide an estimate of the number of expressed genes in the nematode, reveal relations between gene function and gene expression that can guide analysis of uncharacterized worm genes, and demonstrate a shift in expression from evolutionarily conserved genes to worm-specific genes over the course of development. ------------------- Key: 4387 Medline: 21061411 Authors: Ding L;Candido EPM Title: Association of several small heat-shock proteins with reproductive tissues in the nematode Caenorhabditis Citation: Biochemical Journal 351: 13-17 2000 Type: ARTICLE Genes: Abstract: Immunohistochemical data on 10 of the 14 small heat-shock (smHSPs) proteins in fourth larval stage and adult Caenorhabditis elegans show that the tissues expressing the greatest number of smHSPs are vulva (HSP12s, HSP43 and, under stress, HSP16s) and spermatheca (HSP12s, HSP25, HSP43 and, under stress, HSP16s). HSP43 is also expressed in male tail structures, and following heat-shock HSP16s are expressed in spermatids and spermatozoa. ------------------- Key: 4388 Medline: 11032868 Authors: Lee YS;Park YS;Nam S;Suh SJ;Lee J;Kaang BK;Cho NJ Title: Characterization of GAR-2, a novel G protein-linked acetylcholine receptor from Caenorhabditis elegans. Citation: Journal of Neurochemistry 75: 1800-1809 2000 Type: ARTICLE Genes: gar-1 gar-2 gar-3 Abstract: We have previously identified two G protein-linked acetylcholine receptors (GARs), GAR-1 and GAR-3, in the nematode Caenorhabditis elegans. Whereas GAR-3 is a homologue of muscarinic acetylcholine receptors (mAChRs), GAR-1 is similar to but pharmacologically distinct from mAChRs. In the current work we isolated a new type of GAR using C. elegans genome sequence information. This receptor, named GAR-2, consists of 614 amino acid residues and has seven putative transmembrane domains. Database searches indicate that GAR-2 is most similar to GAR-1 and closely related to GAR-3/mAChRs. The overall amino acid sequence identities to GAR-1 and GAR-3 are similar to 32 and similar to 23%, respectively. When GAR-2 was coexpressed with the G protein-activated inwardly rectifying K+ (GIRK1) channel in Xenopus oocytes, acetylcholine was able to evoke the GIRK current in a dose-dependent fashion. Oxotremorine, a classical muscarinic agonist, had little effect on the receptor, indicating that GAR-2 is pharmacologically different from mAChRs but rather similar to GAR-1. GAR-2 differs from GAR-1, however, in that it showed virtually no response to muscarinic antagonists such as atropine, scopolamine, and pirenzepine. Expression studies using green fluorescent protein reporter gene fusion revealed that GAR-2 is expressed in a subset of C. elegans neurons, distinct from those expressing GAR-1. Together with our previous reports, this study demonstrates that diverse types of GARs are ------------------- Key: 4389 Medline: 11050385 Authors: Kaitna S;Mendoza M;Jantsch-Plunger V;Glotzer M Title: Incenp and an Aurora-like kinase form a complex essential for chromosome segregation and efficient completion of cytokinesis. Citation: Current Biology 10: 1172-1181 2000 Type: ARTICLE Genes: air-1 air-2 lep-1 lep-2 Abstract: Background: In animal cells, cytokinesis begins shortly after the sister chromatids move to the spindle poles. The inner centromere protein (Incenp) has been implicated in both chromosome segregation and cytokinesis, but it is not known exactly how it mediates these two distinct processes. Results: We identified two Caenorhabditis elegans proteins, ICP-1 and ICP-2, with significant homology in their carboxyl termini to the corresponding region of vertebrate Incenp. Embryos depleted of ICP-1 by RNA-mediated interference had defects in both chromosome segregation and cytokinesis. Depletion of the Aurora-like kinase AIR-2 resulted in a similar phenotype. The carboxy-terminal region of Incenp is also homologous to that in Sli15p, a budding yeast protein that functions with the yeast Aurora kinase IpI1p. ICP-I bound C. elegans AIR-2 in vitro, and the corresponding mammalian orthologs Incenp and AIRK2 could be co-immunoprecipitated from cell extracts. A significant fraction of embryos depleted of ICP-1 and AIR-2 completed one cell division over the course of several cell cycles. ICP-1 promoted the stable localization of ZEN-4 (also known as CeMKLP1), a kinesin-like protein required for central spindle assembly. Conclusions: ICP-I and AIR-2 are part of a complex that is essential for chromosome segregation and for efficient completion of cytokinesis. We propose that this complex acts by promoting dissolution of sister chromatid cohesion and the assembly of the central ------------------- Key: 4390 Medline: 20467461 Authors: Burglin TR Title: A two channel four-dimensional image recording and viewing system with automatic drift correction. Citation: Journal of Microscopy 200: 75-80 2000 Type: ARTICLE Genes: Abstract: Four-dimensional image acquisition systems have been described to analyse various developmental processes, for example, the Caenorhabditis elegans cell lineage. A practical problem that is often encountered during recordings is mechanical slippage of the microscope stage, causing the sample to drift out of focus. Furthermore, with the advent of green fluorescent protein (GFP) as an in vivo marker, affordable two-channel imaging systems are needed to correlate gene expression with changes through development. To overcome the mechanical drift a device-independent, software-only solution for the MacOS was devised that can compensate for Z-axis drifts in sample position. The software also allows recording of 4D stacks in two channels. To correct for drift, a small reference object beside the main object to be recorded is kept in focus using a simple autofocus principle, and this automatic drift correction allows for effective 4D recordings. In addition to the Z-axis drives and the shutters of the microscope, a video camera can be computer controlled to switch between two light levels. Second channel live GFP recordings are presently limited by the fact that the high intensity of the blue light heats and kills C. elegans embyros quickly. To view and annotate the stacks a MacOS viewing application was developed. ------------------- Key: 4391 Medline: 20422671 Authors: Nakamura Y;Miura K;Fujino Y;Iwao H;Ogita S;Yamanaka S Title: Evolution, structure, and expression of GNPI/Oscillin orthologous genes. Citation: Genomics 68: 179-186 2000 Type: ARTICLE Genes: Abstract: Oscillin was identified from hamster sperm as a factor responsible for oocyte calcium oscillations. However, its high level of homology with the bacterial glucosamine-6-phosphate isomerase suggests that it may play more fundamental roles. In the current study, we identified Oscillin orthologs from Caenorhabditis elegans, Drosophila melanogaster, mouse, and human. Their amino acid identities with hamster oscillin were 67.0, 72.3, 97.6, and 95.5%, respectively. No Oscillin orthologs were found in Saccharomyces cerevisiae. The human Oscillin gene (HGMW-approved symbol GNPI) spans 12.4 kb and consists of eight exons. The position of the fourth intron was conserved in other species. The human Oscillin promoter has features characteristic of housekeeping genes, including a GC-rich content, multiple SP1 binding sites, and the absence of a TATA motif. Human and mouse Oscillin genes were ubiquitously expressed in all tissues examined. These data showed that Oscillin is a housekeeping gene conserved throughout evolution and do not support the notion that Oscillin is the sperm-specific factor responsible for ------------------- Key: 4392 Medline: Authors: Gruenbaum Y Title: The nuclear lamina: new insights from worms and flies. Citation: Cellular & Molecular Biology Letters 5: 244- 2000 Type: REVIEW Genes: Abstract: ------------------- Key: 4393 Medline: 20530158 Authors: Feany MB Title: Studying human neurodegenerative diseases in flies and worms. Citation: Journal of Neuropathology & Experimental Neurology 59: 847-856 2000 Type: ARTICLE Genes: ced-3 deg-1 lin-12 mec-4 mec-10 sel-12 unc-105 Abstract: Invertebrate models of several human neurodegenerative diseases have recently been described. These models faithfully replicate key neuropathological features of the human disorders. Because the basic cell biology of the nervous system is very similar in vertebrates and invertebrates, the sophisticated and rapid genetic analysis feasible in Drosophila and C. elegans promises significant insight into human neurodegenerative syndromes. In addition, the short lifespan, small size, and ease of culturing make worms and flies ideal for drug testing. ------------------- Key: 4394 Medline: Authors: Liu CY;Schroder M;Kaufman RJ Title: Ligand-independent dimerization activates the stress response kinases IRE1 and PERK in the lumen of the endoplasmic reticulum. Citation: Journal of Biological Chemistry 275: 24881-24885 2000 Type: ARTICLE Genes: Abstract: IRE1 and PERK are type I transmembrane serine/threonine protein kinases that are activated by unfolded proteins in the endoplasmic reticulum (ER) to signal adaptive responses. IRE1 is present in all eukaryotic cells and signals the unfolded protein response through its kinase and endoribonuclease activities. PERK signals phosphorylation of a translation initiation factor to inhibit protein synthesis in higher eukaryotic cells but is absent in the Saccharomyces cerevisiae genome. The amino acid sequences of the amino-terminal ER luminal domains (NLDs) from IRE1 and PERK display limited homology and have diverged among species. In this study, we have demonstrated that the NLD of yeast Ire1p is required for signaling. However, the NLDs from human IRE1alpha and murine IRE1beta and the Caenorhabditis elegans IRE1 and PERK function as replacements for the S. cerevisiae Ire1p-NLD to signal the unfolded protein response. Replacement of the Ire1p-NLD with a functional leucine zipper dimerization motif yielded a constitutively active kinase that surprisingly was further activated by ER stress. These results demonstrate that ER stress-induced dimerization of the NLD is sufficient for IRE1 and PERK activation and is conserved through evolution. We propose that ligand-independent activation of IRE1 and PERK permits homodimerization upon accumulation of unfolded proteins in the lumen of the ER. ------------------- Key: 4395 Medline: 20482047 Authors: Gurvitz A;Langer S;Piskacek M;Hamilton B;Ruis H;Hartig A Title: Predicting the function and subcellular location of Caenorhabditis elegans proteins similar to Saccharomyces cerevisiae beta-oxidation enzymes. Citation: Yeast 17: 188-200 2000 Type: ARTICLE Genes: fat-2 fat-3 pex-5 Abstract: The role of peroxisomal processes in the maintenance of neurons has not been thoroughly investigated. We propose using Caenorhabditis elegans as a model organism for studying the molecular basis underlying neurodegeneration in certain human peroxisomal disorders, e.g. Zellweger syndrome, since the nematode neural network is well characterized and relatively simple in function. Here we have identified C. elegans PEX-5 (C34C6.6) representing the receptor for peroxisomal targeting signal type I (PTSI), defective in patients with such disorders. PEX-5 interacted strongly in a two-hybrid assay with Gal4p-SKL, and a screen using PEX-5 identified interaction partners that were predominantly terminated with PTS1 or its variants. A list of C. elegans proteins with similarities to well-characterized yeast P-oxidation enzymes was compiled by homology probing. The possible subcellular localization of these orthologues was predicted using an algorithm based on trafficking signals. Examining the C termini of selected nematode proteins for PTS1 function substantiated predictions made regarding the proteins' peroxisomal location. It is concluded that the eukaryotic PEX5-dependent route for importing PTS1-containing proteins into peroxisomes is conserved in nematodes, C. elegans might emerge as an attractive model system for studying the importance of peroxisomes and affiliated processes in neurodegeneration, and also for studying a P-oxidation process that is potentially compartmentalized in both mitochondria and peroxisomes. ------------------- Key: 4396 Medline: 11040214 Authors: Luitjens C;Gallegos M;Kraemer B;Kimble J;Wickens M Title: CPEB proteins control two key steps in spermatogenesis in C. elegans. Citation: Genes & Development 14: 2596-2609 2000 Type: ARTICLE Genes: cbp-1 cbp-2 cbp-3 cbp-4 fem-1 fem-3 fog-1 fog-2 glp-1 glp-4 him-5 Abstract: Cytoplasmic polyadenylation element binding (CPEB) proteins bind to and regulate the translation of specific mRNAs. CPEBs from Xenopus, Drosophila, and Spisula participate in oogenesis. In this report, we examine the biological roles of all identifiable CPEB homologs in a single organism, Caenorhabditis elegans. We find four homologs in the C. elegans genome: cbp-1, cpb-2, cpb-3, and fog-1. Surprisingly, two homologs, CPB-1 and FOG-1, have key functions in spermatogenesis and are dispensable for oogenesis. CPB-2 and CPB-3 also appear not to be required for oogenesis. CPB-1 is essential for progression through meiosis: cpb-1(RNAi) spermatocytes fail to undergo the meiotic cell divisions. CPB-1 protein is present in the germ line just prior to overt spermatogenesis; once sperm differentiation begins, CPB-1 disappears. CPB-1 physically interacts with EBF, another RNA-binding protein and 3' UTR regulator. In addition to its role in controlling the sperm/oocyte switch, we find that EBF also appears to be required for spermatogenesis, consistent with its interaction with CPEB. A second CPEB homolog, FOG-1, is required for specification of the sperm fate. The fog-1 gene produces fog-1(L) and fog-1(S) transcripts. The fog-1(L) RNA is enriched in animals making sperm and is predicted to encode a larger protein; fog-1(S) RNA is enriched in animals making oocytes and is predicted to encode a smaller protein. The relative abundance of the two mRNAs is controlled temporally during germ-line development and by the sex determination pathway in a fashion that suggests that the fog-1(L) species encodes the active form. In sum, our results demonstrate that, in C. elegans, two CPEB proteins have distinct functions in the germ line, both in spermatogenesis: FOG-1 specifies the sperm cell fate and CPB-1 executes that decision. ------------------- Key: 4397 Medline: 20504438 Authors: Parrish J;Metters H;Chen L;Xue D Title: Demonstration of the in vivo interaction of key cell death regulators by structure-based design of second-site suppressors. Citation: Proceedings of the National Academy of Sciences USA 97: 11916-11921 2000 Type: ARTICLE Genes: ced-1 ced-4 ced-9 egl-1 Abstract: Demonstrating in vivo interaction of two important biomolecules and the relevance of the interaction to a biological process have been difficult issues in biomedical research. Here, we report the use of a homology modeling approach to establish the significance of protein interactions in governing the activation of programmed cell death in Caenorhabditis elegans. A protein interaction cascade has been postulated to mediate activation of cell death in nematodes, in which the BH3-domain-containing (Bcl-2 homology region 3) protein EGL-1 binds the cell-death inhibitor CED-9 and induces release of the death-activating protein CED-4 from inhibitory CED-4/CED-9 complexes. We show here that an unusual gain-of-function:mutation in ced-9 (substitution of glycine 169 to glutamate) that results in potent inhibition of most nematode cell deaths impairs the binding of EGL-1 to CED-9 and ECL-1-induced release of CED-4 from CED-4/CED-9 complexes. Based on a modeled EGL-1/CED-9 complex structure, we generated second-site compensatory mutations in EGL-1 that partially restore the binding of EGL-1 to CED-9(G169E) and EGL-1-induced release of CED-4 from CED-4/CED-9(G169E) complexes. Importantly, these mutations also significantly suppress the death-protective activity of CED-9(G169E) in vivo. These results establish that direct physical interaction between EGL-1 and CED-9 is essential for the release of CED-4 and the activation of cell death. The structure-based design of second-site suppressors via homology modeling should be widely applicable for probing important molecular interactions ------------------- Key: 4398 Medline: 20507597 Authors: Johnson TE;Cypser J;de Castro E;de Castro S;Henderson S;Murakami S;Rikke B;Tedesco P;Link C Title: Gerontogenes mediate health and longevity in nematodes through increasing resistance to environmental toxins and stressors. Citation: Experimental Gerontology 35: 687-694 2000 Type: ARTICLE Genes: age-1 clk-1 daf-2 daf-4 daf-7 daf-16 daf-23 old-1 spe-26 Abstract: More than 40 mutants in Caenorhabditis elegans have been demonstrated to lead to increased life span (a rigorous, operational test for being a gerontogene) of 20% or more ("Age" mutants). Age mutants alter rate-limiting determinants of longevity; moreover, important genes are identified independent of prior hypotheses as to actual mode of gene action in extending longevity and/or "slowing" aging. Age mutants define as many as nine (possibly) distinct pathways and/or modes of action, as defined by primary phenotype. Three well-studied mutants (age-1, clk-1, and spe-26) alter age-specific mortality rates in characteristic fashions; in age-1 mutants, especially, the changes in mortality rates are quite dramatic. All Age mutants (so far without exception) increase response to several (but not all) stresses, including heat, UV, and reactive oxidants. We have used directed strategies, as well as random mutagenesis, to identify novel genes increasing the worm's ability to resist stress. Two genes (daf-16 and old-1) yield over-expression strains that are stress resistant and long-lived. A variety of approaches to assess transcriptional alterations associated with increased longevity are underway. We suggest that the role of the Age genes in both longevity and stress resistance indicates that a major evolutionary determinant of longevity is the ability to respond to stress. ------------------- Key: 4399 Medline: 20531762 Authors: Pasquinelli AE;Reinhart BJ;Slack F;Martindale MQ;Kuroda MI;Maller B;Hayward DC;Ball EE;Degnan B;Muller P;Spring J;Srinivasan A;Fishman M;Finnerty J;Corbo J;Levine M;Leahy P;Davidson E;Ruvkun G Title: Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Citation: Nature 408: 86-89 2000 Type: ARTICLE Genes: let-7 lin-4 lin-14 lin-41 Abstract: Two small RNAs regulate the timing of Caenorhabditis elegans development(1,2). Transition from the first to the second larval stage fates requires the 22-nucleotide lin-4 RNA(1,3,4), and transition from late larval to adult cell fates requires the 21-nucleotide let-7 RNA 2. The lin-4 and let-7 RNA genes are not homologous to each other, but are each complementary to sequences in the 3' untranslated regions of a set of protein-coding target genes that are normally negatively regulated by the RNAs1,2,5,6. Here we have detected let-7 RNAs of similar to 21 nucleotides in samples from a wide range of animal species, including vertebrate, ascidian, hemichordate, mollusc, annelid and arthropod, but not in RNAs from several cnidarian and poriferan species, Saccharomyces cerevisiae, Escherichia coli or Arabidopsis. We did not detect lin-4 RNA in these species. We found that let-7 temporal regulation is also conserved: let-7 RNA expression is first detected at late larval stages in C. elegans and Drosophila, at 48 hours after fertilization in zebrafish, and in adult stages of annelids and molluscs. The let-7 regulatory RNA may control late temporal transitions during development across animal phylogeny. ------------------- Key: 4400 Medline: 20531763 Authors: Wallenfang MR;Seydoux G Title: Polarization of the anterior-posterior axis of C. elegans is a microtubule-directed process. Citation: Nature 408: 89-92 2000 Type: ARTICLE Genes: air-1 emb-27 emb-30 mat-1 mat-2 mat-3 ncc-1 par-1 par-2 par-3 pie-1 spd-2 Abstract: In Caenorhabditis elegans, polarity along the anterior-posterior (A/P) axis is established shortly after fertilization and is determined by the sperm, whose position specifies the posterior end of the embryo(1). Although many factors required for the establishment of A/P polarity have been described(2,3), the nature of the spatial cue provided by the sperm remains unknown. Here we show that a microtubule-organizing centre is necessary and sufficient to establish several aspects of A/P polarity. In wildtype embryos, appearance of the first molecular asymmetries along the A/P axis correlates with and requires nucleation of microtubules by the sperm-derived centrosomes (sperm asters). In mutant embryos arrested in meiosis, sperm asters fail to form, and posterior is defined by the position of the persistent meiotic spindle rather than by the position of the sperm. Together, our data indicate that the primary spatial cue for A/P polarity in C. elegans derives from microtubules emanating from the sperm asters. Our findings support a parallel(4-7) between C. elegans zygotes and other cells, such as Drosophila oocytes, which rely on microtubules to regulate polarity. ------------------- Key: 4401 Medline: 11053114 Authors: Khatchatouriants A;Lewis A;Rothman Z;Loew L;Treinin M Title: GFP is a selective non-linear optical sensor of electrophysiological processes in Caenorhabditis elegans. Citation: Biophysical Journal 79: 2345-2352 2000 Type: ARTICLE Genes: deg-3 des-2 mec-2 Abstract: Electrophysiology of the nematode Caenorhabditis elegans has the potential to bridge the wealth of information on the molecular biology and anatomy of this organism with the responses of selected cells and cellular neural networks associated with a behavioral response. In this paper we report that the nonlinear optical phenomenon of second harmonic generation (SHG) can be detected using green fluorescent protein (GFP) chimeras expressed in selected cells of living animals. Alterations in the SHG signal as a result of receptor ligand interactions and mechanical stimulation of the mechanosensory cells indicate that this signal is very sensitive to membrane potential. The results suggest that this approach to membrane potential measurements in C. elegans and in other biological systems could effectively couple data on selective locations within specific cells with functional responses that are associated with behavioral and sensory processes. ------------------- Key: 4402 Medline: 20548709 Authors: Fraser AG;Kamath RS;Zipperlen P;Martinez-Campos M;Sohrmann M;Ahringer J Title: Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Citation: Nature 408: 325-330 2000 Type: ARTICLE Genes: apr-1 ceh-6 cye-1 dhc-1 goa-1 gsk-3 hlh-2 hmp-2 hmr-1 kin-10 lam-1 let-502 lin-11 lin-41 mei-1 mei-2 mel-26 mom-5 nhr-2 nhr-23 nmy-2 par-6 pfn-1 pop-1 tba-2 unc-11 unc-15 unc-37 unc-73 unc-89 Abstract: Complete genomic sequence is known for two multicellular eukaryotes, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, and it will soon be known for humans. However, biological function has been assigned to only a small proportion of the predicted genes in any animal. Here we have used RNA-mediated interference (RNAi) to target nearly 90% of predicted genes on C. elegans chromosome I by feeding worms with bacteria that express double-stranded RNA. We have assigned function to 13.9% of the genes analysed, increasing the number of sequenced genes with known phenotypes on chromosome I from 70 to 378. Although most genes with sterile or embryonic lethal RNAi phenotypes are involved in basal cell metabolism, many genes giving post-embryonic phenotypes have conserved sequences but unknown function. In addition, conserved genes are significantly more likely to have an RNAi phenotype than are genes with no conservation. We have constructed a reusable library of bacterial clones that will permit unlimited RNAi screens in the future; this should help develop a more complete view of the relationships between the genome, gene function and the ------------------- Key: 4403 Medline: 20548710 Authors: Gonczy P;Echeverri C;Oegema K;Coulson A;Jones SJM;Copley RR;Duperon J;Oegema J;Brehm M;Cassin E;Hannak E;Kirkham M;Pichler S;Flohrs K;Goessen A;Leidel S;Alleaume AM;Martin C;Ozlu N;Bork P;Hymann AA Title: Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Citation: Nature 408: 331-336 2000 Type: ARTICLE Genes: act-5 arf-1 cct-5 cct-6 cul-2 cyk-1 cyk-4 dnc-2 egl-45 emb-30 mlc-4 ncc-1 par-2 par-3 plk-1 pod-1 ubq-1 ubq-2 unc-32 Abstract: Genome sequencing projects generate a wealth of information; however, the ultimate goal of such projects is to accelerate the identification of the biological function of genes. This creates a need for comprehensive studies to fill the gap between sequence and function. Here we report the results of a functional genomic screen to identify genes required for cell division in Caenorhabditis elegans. We inhibited the expression of similar to 96% of the similar to2,300 predicted open reading frames on chromosome III using RNA-mediated interference (RNAi). By using an in vivo time-lapse differential interference contrast microscopy assay, we identified 133 genes (similar to6%) necessary for distinct cellular processes in early embryos. Our results indicate that these genes represent most of the genes on chromosome III that are required for proper cell division in C. elegans embryos. The complete data set, including sample time-lapse recordings, has been deposited in an open access database. We found that similar to 47% of the genes associated with a differential interference contrast phenotype have clear orthologues in other eukaryotes, indicating that this screen provides putative gene functions for other species as well. ------------------- Key: 4404 Medline: 20519442 Authors: Inoue T;Thomas JH Title: Suppressors of transforming growth factor beta pathway mutants in the Caenorhabditis elegans dauer formation pathway. Citation: Genetics 156: 1035-1046 2000 Type: ARTICLE Genes: age-1 akt-1 daf-1 daf-2 daf-3 daf-4 daf-5 daf-7 daf-8 daf-11 daf-12 daf-14 daf-16 daf-18 dpy-20 pdk-1 scd-1 scd-2 Abstract: The dauer is a developmentally arrested alternative third larval stage of Caenorhabditis elegans. Entry into this state is regulated by environmental cues, including temperature, food, and the concentration of constitutively secreted dauer pheromone. Genetically, three parallel pathways have been found that regulate this process. Of these, the group 2 pathway, which includes die genes daf-1, daf-3, daf-4, daf-5, daf-7: daf-8, and dnf-14, mediates the transduction of environmental signals through the ASI chemosensory neuron and encodes a TGF-P-related signaling pathway. To identify additional genes that function in this pathway, we carried out a screen for suppressors of mutations in daf-l, daf-8, and daf-14. From die total of 36 mutations, seven complementation groups were identified. Three complementation groups correspond to the previously described genes daf-3, daf-5, and daf-12. Three correspond to novel genes scd-l, scd-2 and scd-3. Genetic analysis of these scd genes is presented here. A fourth complementation group was represented by a single mutation sa315, which affects the daf-2/age-1 insulin-related signaling pathway. ------------------- Key: 4405 Medline: 20519443 Authors: Ailion M;Thomas JH Title: Dauer formation induced by high temperatures in Caenorhabditis elegans. Citation: Genetics 156: 1047-1067 2000 Type: ARTICLE Genes: age-1 akt-1 akt-2 che-2 che-3 che-10 che-11 che-13 daf-1 daf-2 daf-3 daf-4 daf-5 daf-7 daf-8 daf-10 daf-11 daf-12 daf-14 daf-16 daf-21 daf-22 dyf-1 dyf-4 dyf-6 dyf-9 dyf-11 dyf-12 mec-1 mec-8 osm-1 osm-3 osm-5 osm-6 pdk-1 tax-2 tax-4 tra-2 ttx-1 unc-3 unc-31 unc-64 Abstract: Dauer formation in Caenorhabditis elegans is regulated by several environmental stimuli, including a pheromone and temperature. Dauer formation is moderately induced as the growth temperature increases from 15 degrees to 25 degrees. Here we show that dauer formation is very strongly induced at a temperature of 27 degrees in both wild-type animals and mutants such as unc-64, unc-31, and unc-3, which do not form dauers at 25 degrees. A 27 degrees temperature stimulus is sufficient to induce dauer formation in wild-type animals independent of pheromone. Analysis of previously described dauer mutants at 27 degrees reveals a number of surprising results. Several classes of mutants (dyf, daf-3 tax-4, and tax-2) that are defective in dauer formation at lower temperatures reverse their phenotypes at 27 degrees and form dauers constitutively. Epistasis experiments place unc-64 and unc-31 at a different position in the dauer pathway from unc-3 We also uncover new branches of the dauer pathway at 27 degrees that are not detected at 25 degrees. We show that epistatic gene inter actions can show both quantitative and qualitative differences depending on environmental conditions. Finally, we discuss some of the possible ecological implications of dauer induction by high temperatures. ------------------- Key: 4406 Medline: 11063685 Authors: Robatzek M;Thomas JH Title: Calcium/calmodulin-dependent protein kinase II regulates Caenorhabditis elegans locomotion in concert with G(o)/G(q) signaling network. Citation: Genetics 156: 1069-1082 2000 Type: ARTICLE Genes: dgk-1 eat-11 eat-16 egl-10 egl-30 goa-1 sag-1 unc-43 unc-93 unc-103 unc-110 Abstract: Caenorhabditis elegans locomotion is a complex behavior generated by a defined set of motor neurons and interneurons. Genetic analysis shows that UNC-43, the C. elegans Ca2+/calmodulin protein kinase II (CaMKII), controls locomotion rate. Elevated UNC-43 activity, from a gain-of-function mutation, causes severely lethargic locomotion, presumably by inappropriate phosphorylation of targets. In a genetic screen for suppressors of this phenotype, we identified multiple alleles of four genes in a G(o)/G(q) G-protein signaling network, which has been shown to regulate synaptic activity via diacylglycerol. Mutations in goa-1, dgk-1, eat-16, or eat-II strongly or completely suppressed unc-43(gf) lethargy, but affected other mutants with reduced locomotion only weakly. We conclude that CaMKII and G(o)/G(q) pathway's act in concert to regulate synaptic activity, perhaps through a direct interaction between CaMKII and G(o). ------------------- Key: 4407 Medline: 20519445 Authors: Nilsson L;Tiensuu T;Tuck S Title: Caenorhabditis elegans lin-25: A study of its role in multiple cell fate specification events involving ras and the identification and characterization of evolutionarily conserved domains. Citation: Genetics 156: 1083-1096 2000 Type: ARTICLE Genes: clr-1 egl-15 let-23 let-60 lin-15 lin-25 lin-39 sur-2 Abstract: Caenorhabditis elegans lin-25 functions downstream of let-60 ms in the genetic pathway for the induction of the 1 degrees cell fate during vulval development and encodes a novel 130-kD protein. The biochemical activity of LIN-25 is presently unknown, but the protein appears to function together with SUR-2, whose human homologue binds to Mediator, a protein complex required for transcriptional regulation. We describe here experiments that indicate that, besides its role in vulval development, lin-25 also participates in the fate specification of a number of other cells in the worm that are known to require Ras-mediated signaling. We also describe the cloning of a lin-25 orthologue from C. briggsae. Sequence comparisons suggest that the gene is evolving relatively rapidly. By characterizing the molecular lesions associated with 10 lin-25 mutant alleles and by assaying in vivo die activity of mutants lin-25 generated in vitro, we have identified three domains within LIN-25 that are required for activity or stability. We have also identified a sequence that is required for efficient nuclear translocation. We discuss how lin-25 might act in cell fate specification in C. elegans within the context of models for lin-25 function in cell identity and cell signaling. ------------------- Key: 4408 Medline: 11063687 Authors: Eisenmann DM;Kim SK Title: Protruding vulva mutants identify novel loci and Wnt signaling factors that function during Caenorhabditis elegans vulva development. Citation: Genetics 156: 1097-1116 2000 Type: ARTICLE Genes: bar-1 dig-1 egl-18 let-60 lin-1 lin-2 lin-14 lin-17 lin-18 lin-25 lin-26 lin-28 lin-29 lin-31 mig-14 mom-3 pvl-2 pvl-3 pvl-4 pvl-5 pvl-6 sem-4 unc-59 unc-83 unc-84 mnDf30 mnDf39 mnDf63 mnDf66 mnDf87 mnDf89 mnDf90 mnDf99 mnDf106 mnDf108 mnDf109 nDf19 nDf24 sDf4 sDf20 uDf1 Abstract: The Caenorhabditis elegans vulva develops from the progeny of three vulval precursor cells ((VPCs) induced to divide and differentiate by a signal from the somatic gonad. Evolutionarily conserved Ras and Notch extracellular signaling pathways are known to function during this process. To identify novel loci acting in vulval development, we carried out a genetic screen for mutants having a protruding-vulva (Pvl) mutant phenotype. Here we report the initial genetic characterization of several novel loci: bar-1, pvl-4, pvl-5, and pvl-6. In addition, on the basis of their Pvl phenotypes, we show that the previously identified genes lin-26, mom-3/mig-14, egl-18, and sem-4 also function during vulval development. Our characterization indicates that (1) pvl-4 and pvl-5 are required for generation/survival of the VPCs; (2) bar-1, nom-3/mig-14, egl-18, and sem-4 play a role in WC fate specification; (3) lin-26 is required for proper VPC fate execution; and (4) pvl-6 acts during vulval morphogenesis. In addition, two of these genes, bar-1 and mom-3/mig-14, are known to function in processes regulated by Wnt signaling, suggesting that a Wnt signaling pathway is acting during vulval development. ------------------- Key: 4409 Medline: 20433243 Authors: Hallam S;Singer E;Waring D;Jin YS Title: The C. elegans NeuroD homolog cnd-1 functions in multiple aspects of motor neuron fate specification. Citation: Development 127: 4239-4252 2000 Type: ARTICLE Genes: acr-2 ced-3 cnd-1 lin-26 unc-3 unc-4 unc-25 unc-30 sDf121 Abstract: The basic helix-loop-helix transcription factor NeuroD (Neurod1) has been implicated in neuronal fate determination, differentiation and survival. Here we report the expression and functional analysis of end-1, a C. elegans NeuroD homolog. cnd-1 expression was first detected in neuroblasts of the AB lineage in 14 cell embryos and maintained in many neuronal descendants of the AB lineage during embryogenesis, diminishing in most terminally differentiated neurons prior to hatching. Specifically, cnd-1 reporter genes were expressed in the precursors of the embryonic ventral cord motor neurons and their progeny. A loss-of-function mutant, cnd-1(ju29), exhibited multiple defects in the ventral cord motor neurons. First, the number of motor neurons was reduced, possibly caused by the premature withdrawal of the precursors from mitotic cycles. Second, the strict correlation between the fate of a motor neuron with respect to its lineage and position in the ventral cord was disrupted, as manifested by the variable expression pattern of motor neuron fate specific markers. Third, motor neurons also exhibited defects in terminal differentiation characteristics including axonal morphology and synaptic connectivity. Finally, the expression patterns of three neuronal type-specific transcription factors, unc-3, unc-4 and unc-30, were altered. Our data suggest that cnd-1 may specify the identity of ventral cord motor neurons both by maintaining the mitotic competence of their precursors and by modulating the expression of neuronal type-specific determination factors. cnd-1 appears to have combined the functions of several vertebrate neurogenic bHLH proteins and may represent an ancestral form of this protein family. ------------------- Key: 4410 Medline: 20538939 Authors: Chamberlain JS;Benian GM Title: Muscular dystrophy: the worm turns to genetic disease. Citation: Current Biology 10: R795-R797 2000 Type: REVIEW Genes: dyb-1 dyc-1 dys-1 hlh-1 Abstract: A new animal model for studying muscular dystrophy, a mutant form of the nematode Caenorhabditis elegans, brings the power of worm genetics to bear on the search for a cure for this disease; work on this worm has already led to the identification of a novel component that can suppress the mutant phenotype. ------------------- Key: 4411 Medline: Authors: Ankeny RA Title: Fashioning descriptive models in biology: Of worms and wiring diagrams. Citation: Philosophy of Science 67: S260-S272 2000 Type: REVIEW Genes: Abstract: The biological sciences have become increasingly reliant on so-called 'model organisms'. I argue that in this domain, the concept of a descriptive model is essential for understanding scientific practice. Using a case study, I show how such a model was formulated in a preexplanatory context for subsequent use as a prototype from which explanations ultimately may be generated both within the immediate domain of the original model and in additional, related domains. To develop this concept of a descriptive model, I focus on use of the nematode worm Caenorhabditis elegans and the wiring diagrams that were developed as models of its neural structure. In addition, implications of the concept of a descriptive model, particularly its relevance for the data-phenomena distinction as well as its relation to long-standing debates on realism, are briefly examined. ------------------- Key: 4412 Medline: Authors: Schaffner KF Title: Behavior at the organismal and molecular levels: The case of C. elegans. Citation: Philosophy of Science 67: S273-S288 2000 Type: REVIEW Genes: Abstract: Caenorhabditis elegans (C. elegans) is a tiny worm that has become the focus of a large number of worldwide research projects examining its genetics, development, neuroscience, and behavior. Recently several groups of investigators have begun to tie together the behavior of the organism and the underlying genes, neural circuits, and molecular processes implemented in those circuits. Behavior is quintessentially organismal-it is the organism as a whole that moves and mates-but the explanations are devised at the molecular and neurocircuit levels, and tested in populations using protocols that span many levels of aggregation. Following a brief review of the main relevant features of C. elegans, I describe some of these circuits, and then discuss two contrasting approaches in behavioral genetics and neural network analysis of the worm. Finally, outline the rudiments of a "field and focus" explanation model using the two contrasting approaches. ------------------- Key: 4413 Medline: 11058122 Authors: Takanami T;Mori A;Takahashi H;Higashitani A Title: Hyper-resistance of meiotic cells to radiation due to a strong expression of a single recA-like gene in Caenorhabditis elegans. Citation: Nucleic Acids Research 28: 4232-4236 2000 Type: ARTICLE Genes: glp-4 Abstract: Sensitivity of meiotic cells to DNA damaging agents is little understood. We have demonstrated that the meiotic-pachytene nuclei in the Caenorhabditis elegans gonad are hyper-resistant to X-ray irradiation, but not to UV irradiation, whereas the early embryonic cells after fertilization and the full grown oocytes are not. The Ce-rdh-1 gene [RAD51, DMC1 (LIM15), homolog 1 or Ce-rad-51], which is essential for the meiotic recombination, is the only bacterial recA-like gene in the nematode genome, and is strongly expressed in the meiotic cells. Following silencing of the Ce-rdh-1 gene by RNA interference, the meiotic cells become more sensitive to X-ray irradiation than the early embryonic cells. This is the first report that meiotic cells are hyper-resistant to DNA strand breaks due to the high level of expression of the enzyme(s) involved in meiotic homologous recombination. ------------------- Key: 4414 Medline: 20525509 Authors: Kang SH;Kramer JM Title: Nidogen is nonessential and not required for normal type IV collagen localization in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 11: 3911-3923 2000 Type: ARTICLE Genes: nid-1 Abstract: Nidogen (entactin) can form a ternary complex with type IV collagen and laminin and is thought to play a critical role in basement membrane assembly. We show that the Caenorhabditis elegans nidogen homologue nid-1 generates three isoforms that differ in numbers of rod domain endothelial growth factor repeats and are differentially expressed during development. NID-1 appears at the start of embryonic morphogenesis associated with muscle cells and subsequently accumulates on pharyngeal, intestinal, and gonad primordia. In larvae and adults NID-1 is detected in most basement membranes but accumulates most strongly around the nerve ring and developing gonad. NID-1 is concentrated under dense bodies, at the edges of muscle quadrants, and on the sublateral nerves that run under muscles. Two deletions in nid-1 were isolated: cg119 is a molecular null, whereas cg118 produces truncated NID-1 missing the G2 collagen TV binding domain. Neither deletion causes overt abnormal phenotypes, except for mildly reduced fecundity. Truncated cg118 NID-1 shows wild-type localization, demonstrating that the G2 domain is not necessary for nidogen assembly. Both nid-1 mutants assemble type IV collagen in a completely wild-type pattern, demonstrating that nidogen is not essential for type IV collagen assembly into basement membranes. ------------------- Key: 4415 Medline: 20550429 Authors: Ranganathan R;Cannon SC;Horvitz HR Title: MOD-1 is a serotonin-gated chloride channel that modulates locomotory behaviour in C. elegans. Citation: Nature 408: 470-475 2000 Type: ARTICLE Genes: mod-1 Abstract: The neurotransmitter and neuromodulator serotonin (5-HT) functions by binding either to metabotropic G-protein-coupled receptors (for example, 5-HT1, 5-HT2, 5-HT4 to 5-HT7), which mediate 'slow' modulatory responses through numerous second messenger pathways(1), or to the ionotropic 5-HT3 receptor, a non-selective cation channel that mediates 'fast' membrane depolarizations(2). Here we report that the gene mod-1 (for modulation of locomotion defective) from the nematode Caenorhabditis elegans encodes a new type of ionotropic 5-HT receptor, a 5-HT-gated chloride channel. The predicted MOD-1 protein is similar to members of the nicotinic acetylcholine receptor family of ligand-gated ion channels, in particular to GABA (gamma -aminobutyric acid)- and glycine-gated chloride channels. The MOD-1 channel has distinctive ion selectivity and pharmacological properties. The reversal potential of the MOD-1 channel is dependent on the concentration of chloride ions but not of cations. The MOD-1 channel is not blocked by calcium ions or 5-HT3a-specific antagonists but is inhibited by the metabotropic 5-HT receptor antagonists mianserin and methiothepin. mod-1 mutant animals are defective in a 5-HT-mediated experience-dependent behaviour(3) and are resistant to exogenous 5-HT, confirming that MOD-1 functions as a 5-HT receptor in vivo. ------------------- Key: 4416 Medline: 11071918 Authors: Liu J;Ben-Shahar TR;Riemer D;Treinin M;Spann P;Weber K;Fire A;Gruenbaum Y Title: Essential roles for Caenorhabditis elegans lamin gene in nuclear organization, cell cycle progression, and spatial organization of nuclear pore complexes. Citation: Molecular Biology of the Cell 11: 3937-3947 2000 Type: ARTICLE Genes: lmn-1 Abstract: Caenorhabditis elegans has a single lamin gene, designated lmn-1 (previously termed CeLam-1). Antibodies raised against the lmn-1 product (Ce-lamin) detected a 64-kDa nuclear envelope protein. Ce-lamin was detected in the nuclear periphery of all cells except sperm and was found in the nuclear interior in embryonic cells and in a fraction of adult cells. Reductions in the amount of Ce-lamin protein produce embryonic lethality. Although the majority of affected embryos survive to produce several hundred nuclei, defects can be detected as early as the first nuclear divisions. Abnormalities include rapid changes in nuclear morphology during interphase, loss of chromosomes, unequal separation of chromosomes into daughter nuclei, abnormal condensation of chromatin, an increase in DNA content, and abnormal distribution of nuclear pore complexes (NPCs). Under conditions of incomplete RNA interference, a fraction of embryos escaped embryonic arrest and continue to develop through larval life. These animals exhibit additional phenotypes including sterility and defective segregation of chromosomes in germ cells. Our observations show that: lmn-1 is an essential gene in C. elegans, and that the nuclear lamins are involved in chromatin organization, cell cycle progression, chromosome segregation, and correct spacing of NPCs. ------------------- Key: 4417 Medline: 20525517 Authors: Yoon CH;Chang C;Hopper NA;Lesa GM;Sternberg PW Title: Requirements of multiple domains of SLI-1, a Caenorhabditis elegans homologue of c-Cbl, and an inhibitory tyrosine in LET-23 in regulating vulval differentiation. Citation: Molecular Biology of the Cell 11: 4019-4031 2000 Type: ARTICLE Genes: ark-1 gap-1 let-23 let-60 sem-5 sli-1 sDf8 Abstract: SLI-1, a Caenorhabditis elegans homologue of the proto-oncogene product c-Cbl, is a negative regulator of LET-23-mediated vulval differentiation. Lack of SLI-1 activity can compensate for decreased function of the LET-23 epidermal growth factor receptor, the SEM-5 adaptor, but not the LET-60 MS, suggesting that SLI-1 acts before RAS activation. SLI-1 and c-Cbl comprise an N-terminal region (termed SLI-1:N/Cbl-N, containing a four-helix bundle, an EF hand calcium binding domain, and a divergent SH2 domain) followed by a RING finger domain and a proline-rich C-terminus. In a transgenic functional assay, the proline-rich C-terminal domain is not essential for sli-1(+) function. A protein lacking the SH2 and RING finger domains has no activity, but a chimeric protein with the SH2 and RING finger domains of SLI-1 replaced by the equivalent domains of c-Cbl has activity. The ICING finger domain of c-Cbl has been shown recently to enhance ubiquitination of active RTKs by acting as an E3 ubiquitin-protein ligase. We find that the RING finger domain of SLI-1 is partially dispensable. Further, we identify an inhibitory tyrosine of LET-23 requiring sli-1(+) for its effects: removal of this tyrosine closely mimics the loss of sli-1 but not of another negative regulator, ark-1. Thus, we suggest that this inhibitory tyrosine mediates its effects through SLI-1, which in turn inhibits signaling upstream of LET-60 RAS in a manner not ------------------- Key: 4418 Medline: 20530905 Authors: Remm M;Sonnhammer E Title: Classification of transmembrane protein families in the Caenorhabditis elegans genome and identification of human orthologs. Citation: Genome Research 10: 1679-1689 2000 Type: ARTICLE Genes: Abstract: The complete genome sequence of the nematode Caenorhabditis elegans provides an excellent basis for studying the distribution and evolution of protein families in higher eukaryotes. Three Fundamental questions are as follows: How many paralog clusters exist in one species, how many of these are shared with other species, and how many proteins can be assigned a functional counterpart in other species? We have addressed these questions in a detailed study of predicted membrane proteins in C. elegans and their mammalian homologs. All worm proteins predicted to contain at least two transmembrane segments were clustered on the basis of sequence similarity. This resulted in 189 groups with two or more sequences, containing, in total, 2647 worm proteins. Hidden Markov models (HMMs) were created for each family, and were used to retrieve mammalian homologs from the SWISSPROT, TREMBL, and VTS databases. About one-half of these clusters had mammalian homologs. Putative worm-mammalian orthologs were extracted by use of nine different phylogenetic methods and BLAST. Eight clusters initially thought to be worm-specific were assigned mammalian homologs after searching EST and genomic sequences. A compilation of 174 orthology assignments made with high confidence is presented. [Tables describing transmembrane protein families and orthology assignments are available from ftp.cgr.ki.se/pub/data/worm.] ------------------- Key: 4419 Medline: 20530906 Authors: Koch R;van Luenen HGAM;van der Horst M;Thijssen KL;Plasterk RHA Title: Single nucleotide polymorphisms in wild isolates of Caenorhabditis elegans. Citation: Genome Research 10: 1690-1696 2000 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans (isolate N2 from Bristol, UK) is the first animal of which the complete genome sequence was available. We sampled genomic DNA of natural isolates of C. elegans From four different locations (Australia, Germany, California, and Wisconsin) and found single nucleotide polymorphisms (SNPs) by comparing with the Bristol strain. SNPs are under-represented in coding regions, and many were found to be third base silent codon mutations. We tested 19 additional natural isolates for the presence and distribution of SNPs originally found in one of the four strains. Most SNPs are present in isolates from around the globe and thus are older than the latest contact between these strains. An exception is formed by an isolate from an island (Hawaii) that contains many unique SNPs, absent in the tested isolates from the rest of the world, it has been noticed previously that conserved genes (as defined by homology to genes in Saccharomyces cerevisiae) cluster in the chromosome centers. We round that the SNP frequency outside these regions is 4.5 times higher, supporting the notion of a higher rate of evolution of genes on the chromosome arms. ------------------- Key: 4420 Medline: 11092748 Authors: Chase D;Golden A;Heidecker G;Ferris DK Title: Caenorhabditis elegans contains a third Polo-like kinase gene. Citation: DNA Sequence 11: 327-334 2000 Type: ARTICLE Genes: Abstract: The Polo family of serine/ threonine kinases have been implicated in cell cycle control in a number of diverse organisms. Their localization and biochemical activity suggest that they play an important role in centrosome maturation, G2-to-M phase progression, the promotion of anaphase, and cytokinesis. The Polo family of kinases is distinct from other serine/threonine kinases in that they all contain a polo-box sequence motif in their non-catalytic C-terminal domain. Recently, it was reported that two Polo-related kinases, Plc1 and Plc2, are present in C. elegans. Plc2 has diverged from Plc1 with poor homology within the polo-box sequence and only had 40% amino acid identity with Plc1. We report here the full-length cDNA sequence of another Polo-related kinase from C. elegans. The predicted protein product has greater than 70% amino acid identity with PLK-1/Plc1, and has a highly conserved polo-box domain. ------------------- Key: 4421 Medline: 20525610 Authors: Norman KR;Moerman DG Title: The let-268 locus of Caenorhabditis elegans encodes a procollagen lysyl hydroxylase that is essential for type IV collagen secretion. Citation: Developmental Biology 227: 690-705 2000 Type: ARTICLE Genes: emb-9 let-2 let-242 let-244 let-245 let-268 eDf21 mnC1 mnDf12 mnDf28 mnDf30 mnDf57 mnDf60 mnDf62 mnDf68 mnDf71 mnDf83 mnDf105 Abstract: Basement membranes are thin sheets of specialized extracellular matrix molecules that are important for supplying mechanical support and for providing an interactive surface for cell morphology. Prior to secretion and assembly, basement membrane molecules undergo intracellular processing, which is essential for their function. We have identified several mutations in a procollagen processing enzyme, lysyl hydroxylase (let-268). The Caenorhabditis elegans lysyl hydroxylase is highly similar to the vertebrate lysyl hydroxylase, containing all essential motifs required for enzymatic activity, and is the only lysyl hydroxylase found in the C. elegans sequenced genome. In the absence of C. elegans lysyl hydroxylase, type IV collagen is expressed; however, it is retained within the type IV collagen-producing cells. This observation indicates that in let-268 mutants the processing and secretion of type IV collagen is disrupted. Our examination of the body wall muscle in these mutant animals reveals normal myofilament assembly prior to contraction. However, once body wall muscle contraction commences the muscle cells separate from the underlying epidermal layer (the hypodermis) and the myofilaments become disorganized. These observations indicate that type IV collagen is required in the basement membrane for mechanical support and not for organogenesis of the body ------------------- Key: 4422 Medline: 11072073 Authors: Snow MI;Larsen PL Title: Structure and expression of daf-12: a nuclear hormone receptor with three isoforms that are involved in development and aging in Caenorhabditis elegans. Citation: Biochimica et Biophysica Acta - Gene Structure & Expression 1494: 104-116 2000 Type: ARTICLE Genes: daf-3 daf-7 daf-12 daf-16 Abstract: During Caenorhabditis elegans early larval development environmental conditions promote a cascade of signaling molecules to direct growth to the reproductive adult or to arrest development as a dauer larva. Two parallel chemosensory signal transduction pathways, one of which is transforming growth factor (TGF)-beta -like, converge on the daf-12 gene to regulate dauer formation. A third insulin-like signaling pathway interacts with the daf-12 pathway to regulate both dauer formation and adult longevity. To further understand the role of daf-12 in these processes, we have molecularly characterized this gene. We establish rescue of the mutant dauer defective phenotype with a genomic clone. We show that three transcripts of different lengths, due to differential splicing, are made from the daf-12 gene. The deduced protein isoforms are similar to both DNA- and ligand-binding domains of nuclear hormone receptors. The three daf-12 transcripts are produced throughout development and expression increases during the preparation for and execution of dauer formation. Analysis of various daf mutant strains suggests that the isoform ratios of daf-12 steady-state mRNA are not changed by reduction of function in the TGF-P and insulin signaling components of the dauer pathway. The daf-12 promoter directs expression of GFP in the pharynx. daf-12 is a C. elegans nuclear hormone receptor with multiple isoforms, is expressed throughout development in distinct cells, and functions ------------------- Key: 4423 Medline: 11078724 Authors: Nehrke K;Begenisich T;Pilato J;Melvin JE Title: Model organisms: New insights into ion channel and transporter function. Caenorhabditis elegans ClC-type chloride channels: novel variants and functional Citation: Americal Journal of Physiology - Cell Physiology 279: C2052-C2066 2000 Type: ARTICLE Genes: clh-1 clh-2 clh-3 clh-4 clh-5 clh-6 Abstract: Six ClC-type chloride channel genes have been identified in Caenorhabditis elegans, termed clh-1 through clh-6. cDNA sequences from these genes suggest that clh-2, clh-3, and clh-4 may code for multiple channel variants, bringing the total to at least nine channel types in this nematode. Promoter-driven green fluorescent protein (GFP) expression in transgenic animals indicates that the protein CLH-5 is expressed ubiquitously. CLH-6 is expressed mainly in nonneuronal cells, and the remaining isoforms vary from those restricted to a single cell to those expressed in over a dozen cells of the nematode. In an Sf9 cell expression system, recombinant CLH-2b, CLH-4b, and CLH-5 did not form functional plasma membrane channels. In contrast, both CLH-1 and CLH-3b produced strong, inward-rectifying chloride currents similar to those arising from mammalian ClC2, but which operate over different voltage ranges. Our demonstration of multiple CLH protein variants and comparison of expression patterns among the clh gene family provides a framework, in combination with the electrical properties of the recombinant channels, to further examine the physiology and cell-specific role each isoform plays in this simple model ------------------- Key: 4424 Medline: 20504472 Authors: Marcotte EM;Xenarios I;van der Bliek AM;Eisenberg D Title: Localizing proteins in the cell from their phylogenetic profiles. Citation: Proceedings of the National Academy of Sciences USA 97: 12115-12120 2000 Type: ARTICLE Genes: Abstract: We introduce a computational method for identifying subcellular locations of proteins from the phylogenetic distribution of the homologs of organellar proteins. This method is based on the observation that proteins localized to a given organelle by experiments tend to share a characteristic phylogenetic distribution of their homologs-a phylogenetic profile. Therefore any other protein can be localized by its phylogenetic profile. Application of this method to mitochondrial proteins reveals that nucleus-encoded proteins previously known to be destined for mitochondria fall into three groups: prokaryote-derived, eukaryote-derived, and organism-specific (i,e,, found only in the organism under study). Prokaryote-derived mitochondrial proteins can be identified effectively by their phylogenetic profiles. In the yeast Saccharomyces cerevisiae, 361 nucleus-encoded mitochondrial proteins can be identified at 50% accuracy with 58% coverage. From these values and the proportion of conserved mitochondrial genes, it can be inferred that approximate to 630 genes, or 10% of the nuclear genome, is devoted to mitochondrial function. In the worm Caenorhabditis elegans, we estimate that there are approximate to 660 nucleus-encoded mitochondrial genes, or 4% of its genome, with approximate to 400 of these genes contributed from the prokaryotic mitochondrial ancestor. The large fraction of organism-specific and eukaryote-derived genes suggests that mitochondria perform specialized roles absent from prokaryotic mitochondrial ancestors. We observe measurably distinct phylogenetic profiles among proteins from different subcellular compartments, allowing the general use of prokaryotic ------------------- Key: 4425 Medline: 20539715 Authors: Guarente L;Kenyon C Title: Genetic pathways that regulate ageing in model organisms. Citation: Nature 408: 255-262 2000 Type: REVIEW Genes: age-1 akt-1 akt-2 clk-1 ctl-1 daf-2 daf-16 daf-18 mev-1 pdk-1 sod-3 tkr-1 Abstract: Searches for genes involved in the ageing process have been made in genetically tractable model organisms such as yeast, the nematode Caenorhabditis elegans, Drosophila melanogaster fruitflies and mice. These genetic studies have established that ageing is indeed regulated by specific genes, and have allowed an analysis of the pathways involved, linking physiology, signal transduction and gene regulation. Intriguing similarities in the phenotypes of many of these mutants indicate that the mutations may also perturb regulatory systems that control ------------------- Key: 4426 Medline: 20545828 Authors: Terskikh A;Fradkov A;Ermakova G;Zaraisky A;Tan P;Kajava AV;Zhao X;Lukyanov S;Matz M;Kim S;Weissman I;Siebert P Title: "Fluorescent timer": Protein that changes color with time. Citation: Science 290: 1585-1588 2000 Type: ARTICLE Genes: Abstract: We generated a mutant of the red fluorescent protein drFP583. The mutant (E5) changes its fluorescence from green to red over time. The rate of color conversion is independent of protein concentration and therefore can be used to trace time-dependent expression. We used in vivo labeling with E5 to measure expression from the heat shock-dependent promoter in Caenorhabditis elegans and from the Otx-2 promoter in developing Xenopus embryos. Thus, E5 is a "fluorescent timer" that can be used to monitor both activation and downregulation of target promoters on the whole-organism scale. ------------------- Key: 4427 Medline: Authors: McGuire AM;Church GM Title: Predicting regulons and their cis-regulatory motifs by comparative genomics. Citation: Nucleic Acids Research 28: 4523-4530 2000 Type: ARTICLE Genes: Abstract: We have combined and compared three techniques for predicting functional interactions based on comparative genomics (methods based on conserved operons, protein fusions and correlated evolution) and optimized these methods to predict coregulated seas of genes in 24 complete genomes, including Saccharomyces cerevisiae, Caenorhabditis elegans and 22 prokaryotes. The method based on conserved operons was the most useful for this purpose. Upstream regions of the genes comprising these predicted regulons were then used to search for regulatory motifs in 22 prokaryotic genomes using the motif-discovery program AlignACE, Many significant upstream motifs, including five known Escherichia coli regulatory motifs, were identified in this manner. The presence of a significant regulatory motif was used to refine the members of the predicted regulons to generate a final set of predicted regulons that share significant regulatory elements. ------------------- Key: 4428 Medline: 11105754 Authors: Michel F;Schumperli D;Muller B Title: Specificities of Caenorhabditis elegans and human hairpin binding proteins for the first nucleotide in the histone mRNA hairpin loop. Citation: RNA 6: 1539-1550 2000 Type: ARTICLE Genes: Abstract: The 3' ends of animal replication-dependent histone mRNAs are formed by endonucleolytic cleavage of the primary transcripts downstream of a highly conserved RNA hairpin. The hairpin-binding protein (HBP) binds to this RNA element and is involved in histone RNA 3' processing. A minimal RNA-binding domain (RBD) of similar to 73 amino acids that has no similarity with other known RNA-binding motifs was identified in human HBP [Wang Z-F et al., Genes & Dev, 1996, 10:3028-3040]. The primary sequence identity between human and Caenorhabditis elegans RBDs is 55% compared to 38% for the full-length proteins, We analyzed whether differences between C. elegans and human HBP and hairpins are reflected in the specificity of RNA binding. The C. elegans HBP and its RBB recognize only their cognate RNA hairpins, whereas the human HBP or RED can bind both the mammalian and the C. elegans hairpins. This selectivity of C. elegans HBP is mostly mediated by the first nucleotide in the loop, which is C in C. elegans and U in all other metazoans. By converting amino acids in the human RED to the corresponding C. elegans residues at places where the latter deviates from the consensus, we could identify two amino acid segments that contribute to selectivity for the first nucleotide of the hairpin loop. ------------------- Key: 4429 Medline: 20542109 Authors: Labbe JC;Burgess J;Rokeach LA;Hekimi S Title: ROP-1, an RNA quality-control pathway component, affects Caenorhabditis elegans dauer formation. Citation: Proceedings of the National Academy of Sciences USA 97: 13233-13238 2000 Type: ARTICLE Genes: age-1 daf-2 daf-7 daf-11 daf-12 daf-16 rop-1 Abstract: Caenorhabditis elegans dauer formation is an alternative larval developmental pathway that the worm can take when environmental conditions become detrimental. Animals can survive several months in this stress-resistant stage and can resume normal development when growth conditions improve. Although the worms integrate a variety of sensory information to commit to dauer formation, it is currently unknown whether they also monitor internal cellular damage. The Ro ribonucleoprotein complex, which was initially described as a human autoantigen, is composed of one major 60-kDa protein, Ro60, that binds to one of four small RNA molecules, designated Y RNAs. Ro60 has been shown to bind mutant 5S rRNA molecules in Xenopus oocytes, suggesting a role for Ro60 in 5S rRNA biogenesis. Analysis of ribosomes from a C. elegans rop-1(-) strain, which is null for the expression of Ro60, demonstrated that they contain a high percentage of mutant 5S rRNA molecules, thereby strengthening the notion of a link between the rop-l gene product and 5S rRNA quality control. The Ro particle was recently shown to be involved in the resistance of Deinococcus radiodurans to UV irradiation, suggesting a role for the Ro complex in stress resistance. We have studied the role of rop-1 in dauer formation. We present genetic and biochemical evidence that rop-1 interacts with dauer-formation genes and is involved in the regulation of the worms' entry into the dauer stage. Furthermore, we find that the rop-1 gene product undergoes a proteolytic processing step that is regulated hy the dauer formation pathway via an aspartic proteinase. These results suggest that the Ro particle may function in an RNA quality-control checkpoint for dauer formation. ------------------- Key: 4430 Medline: 11114722 Authors: Cizeau J;Ray J;Chen G;Gietz RD;Greenberg AH Title: The C. elegans orthologue ceBNIP3 interacts with CED-9 and CED-3 but kills through a BH3- and caspase-independent mechanism. Citation: Oncogene 19: 5453-5463 2000 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: We have studied ceBNIP3, the orthologue of BNIP3 in C. elegans. Sequence analysis reveals that the different domains of BNIP3 have been conserved throughout evolution. ceBNIP3 contains a C-terminal transmembrane (TM) domain, a conserved domain (CD) of 19 amino acids, a BCL-2 homology-3 (BH3)-like domain and a PEST sequence. ceBNIP3 is expressed primarily as a 25 kDa monomer and a 50 kDa homodimer. After transfection, ceBNIP3 protein is rapidly degraded through a ubiquitin-dependent pathway by the proteasome. Like BNIP3, the TM domain of ceBNIP3 mediates the localization of the protein to mitochondria and is also necessary for homodimerization and cell death in mammalian cells. Neither the putative BH3 domain nor conserved domain is necessary for killing. ceBNIP3 protein interacts with CED-9 and BCL-X-L, but unlike other pro-apoptotic BCL-2 family members, the BH3-like domain does not participate in dimerization, The ceBNIP3 TM domain mediates interaction with both CED-9 and BCL-XL. ceBNIP3 interacts with CED-3 but co-expression of CED-3 and ceBNIP3 does not significantly enhance induction of cell death in the presence or absence of CED-4, ceBNIP3 kills mammalian cells by a caspase-independent mechanism. In conclusion, we find that although ceBNIP3 interacts with CED-9 and CED-3 it kills by a BH3- and caspase-independent mechanism. ------------------- Key: 4431 Medline: 11106747 Authors: Parrish S;Fleenor J;Xu SQ;Mello C;Fire A Title: Functional anatomy of a dsRNA trigger: Differential requirement for the two trigger strands in RNA Citation: Molecular Cell 6: 1077-1087 2000 Type: ARTICLE Genes: unc-22 unc-54 Abstract: In RNA-mediated interference (RNAi), externally provided mixtures of sense and antisense RNA trigger concerted degradation of homologous cellular RNAs. We show that RNAi requires duplex formation between the two trigger strands, that the duplex must include a region of identity between trigger and target RNAs, and that duplexes as short as 26 bp can trigger RNAi. Consistent with in vitro observations, a fraction of input dsRNA is converted in vivo to short segments of similar to 25 nt. Interference assays with modified dsRNAs indicate precise chemical requirements for both bases and backbone of the RNA trigger. Strikingly, certain modifications are well tolerated on the sense, but not the antisense, strand, indicating that the two trigger strands have distinct roles in the interference process. ------------------- Key: 4432 Medline: 21018745 Authors: Williams PL;Anderson GL;Johnstone JL;Nunn AD;Tweedle MF;Wedeking P Title: Caenorhabditis elegans as an alternative animal species. Citation: Journal of Toxicology and Environmental Health Part A 61: 641-647 2000 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans has proven useful in toxicity testing of known toxicants, but its potential for assessing the toxicity of new pharmaceuticals is relatively unexplored. In this study the procedures used in aquatic testing of toxicants were modified to permit testing of small amounts (<40 mg) of gadolinium-based magnetic resonance imaging ( MRI) compounds. Five blinded compounds were tested. The toxicity of these compounds determined using C. elegans was compared to existing mammalian test system data ( minimum lethal dose [MLD] values for mice). Four of five compounds tested had the same relative sensitivity with C. elegans as with the mouse test system. Testing with C. elegans is efficient and could markedly reduce the cost of screening potentially useful compounds. ------------------- Key: 4433 Medline: 11086294 Authors: Zahn TR;MacMorris MA;Dong W;Day R;Hutton JC Title: IDA-1, a Caenorhabditis elegans homolog of the diabetic autoantigens IA-2 and phogrin, is expressed in peptidergic neurons in the worm. Citation: Journal of Comparative Neurology 429: 127-143 2000 Type: ARTICLE Genes: ced-3 egl-1 ida-1 kpc-2 Abstract: The closely related mammalian proteins IA-2 and phogrin are protein tyrosine phosphatase-like receptor proteins spanning the membrane of dense core vesicles of neuroendocrine tissues. They are of interest as molecular components of the secretory machinery and as major targets of autoimmunity in type I diabetes mellitus. The Caenorhabdltis elegans genome has a single copy of an IA-2/phogrin homolog ida-l III (islet cell diabetic autoantigen), which encodes the ida-1 (B0244.2) gene product as a series of 12 exons over a 10-kb region of chromosome III. The full-length sequence of the ida-1 cDNA encoded a 767-amino acid type 1 transmembrane protein of 87 kDa. The PTP catalytic site consensus sequence of IDA-1, like IA-2 and phogrin, diverged and would not be active. Expression of green fluorescent protein (GFP) under the ida-1 gene promoter showed activity in a subset of around 30 neurons with sensory functions and the uv1 cells of the vulva in hermaphrodites. Males showed additional expression in male-specific neurons. In situ experiments in rat brain showing the distribution of IA-2 and phogrin suggested a complimentary and overlapping pattern compared with the proprotein convertases PC1 and PC2. In C. elegans, IDA-1-expressing cells comprised a subset of those expressing the PC2 homolog KPC-2 (C51E3.7), consistent with IDA-1 being a component of neuropeptide-containing dense core vesicles. The results support the hypothesis that C. elegans IDA-1 is the functional homolog of IA-2 and phogrin in mammals. Analysis of the function of IDA-1 should contribute to our understanding of the function of these proteins in signal transduction, vesicle locomotion, and ------------------- Key: 4434 Medline: Authors: de Pomerai D;Daniells C;David H;Allan J;Duce I;Mutwakil M;Thomas D;Sewell P;Tattersall J;Jones D;Candido P Title: Microwave radiation induces a heat-shock response and enhances growth in the nematode Caenorhabditis elegans. Citation: IEEE Transactions on Microwave Theory & Techniques 48: 2076-2081 2000 Type: ARTICLE Genes: Abstract: This paper shows that prolonged (overnight) exposure to continuous microwave fields (750 MHz, 0.5 W) can induce both a heat-shuck response and enhanced growth in the nematode worm Caenorhabditis elegans. Exposures were conducted in a TEM cell with matched load, producing an E-field of approximately 45 V m(-1) at the center (where test worms are placed). Biomonitoring of heat-shock responses has been simplified by using two transgenic strains (PC72 and PC161), which both carry stress-inducible reporter constructs, respectively, placing lacZ (beta -galactosidase) and lacZ plus green fluorescent protein expression under the control of C. elegans hsp16-1 promoters. In situ localization of reporter expression reveals a minority of test worms, which respond strongly to microwave exposure. Enzyme activity measurements average these reporter responses across many thousands of individual worms, giving a reliable indication of the overall stress imposed on a population. The temperature profile of reporter responses induced by microwave exposure parallels that induced in controls by heat alone, but is displaced down the temperature scale by some 3 degrees C. Length measurements were conducted at intervals in synchronized C. elegans cultures seeded with L1 larvae. Using pooled data from nine separate runs, growth was stimulated by 8.5% after overnight microwave exposure (relative to controls), and this disparity increased to 11% after 24 h of further growth without irradiation. Both heat-shock responses and increased growth would be consistent with a modest increase in temperature, raising the possibility that microwave exposure might cause limited heating in this system. However, there is no detectable rise in the temperature of either medium or worms during overnight exposure under these conditions, discounting both generalized and localized (worm-specific) heating effects. We conclude that both growth and heat-shock responses are induced by microwave exposure through one or more ------------------- Key: 4435 Medline: 21110553 Authors: Kagoshima H;Sommer R;Reinhart BJ;Cassata G;Ruvkun G;Burglin TR Title: Graded expression of ceh-14 reporters in the hypodermis is induced by a gonadal signal. Citation: Development Genes & Evolution 210: 564-569 2000 Type: ARTICLE Genes: ceh-14 egl-17 him-5 lin-3 lin-12 Abstract: Caenorhabditis elegans, is the orthologue of the vertebrate Lhx3/Lhx4 genes. ceh-14 reporter constructs are expressed in several different cell types: head and tail neurons, spermatheca and hypodermis. An intriguing aspect of the hypodermal expression pattern is that it takes the form of a gradient which is strongest in the central body region in L4 to young adult hermaphrodites. Promoter deletion analyses revealed that important regulatory elements for hypodermal expression are located within the transcribed region of ceh-14. Since a large part of the hypodermis is a syncytium, we hypothesized that this expression is triggered in a non-cell-autonomous fashion, a possible source being the underlying gonad. In males, which have a different gonadal organisation, the ceh-14 reporter constructs are expressed in a gradient that is strongest in the tail. By laser ablation of the gonadal precursor cells we found that ceh-14 reporter construct expression is eliminated in the hermaphrodite hypodermis, suggesting that the gonad plays a role in the generation of the gradient. Several signaling pathways are known in the gonad and the vulva, thus we crossed the mutations lin-3, egl-17 and lin-12 with the ceh-14 reporter lines. However, the expression of the reporter constructs is not affected in these mutant backgrounds. This suggests that another, presently unknown, signal triggers the graded hypodermal ------------------- Key: 4436 Medline: 11023862 Authors: Whangbo J;Harris J;Kenyon C Title: Multiple levels of regulation specify the polarity of an asymmetric cell division in C. elegans. Citation: Development 127: 4587-4598 2000 Type: ARTICLE Genes: bar-1 egl-20 lin-17 lin-18 lin-44 mig-1 mig-14 pry-1 Abstract: Wnt signaling systems play important roles in the generation of cell and tissue polarity during development. We describe a Wnt signaling system that acts in a new way to orient the polarity of an epidermal cell division in C. elegans. In this system, the EGL-20/Wnt signal acts in a permissive fashion to polarize the asymmetric division of a cell called V5. EGL-20 regulates this polarization by counteracting lateral signals from neighboring cells that would otherwise reverse the polarity of the V5 cell division. Our findings indicate that this lateral signaling pathway also involves Wnt pathway components. Overexpression of EGL-20 disrupts both the asymmetry and polarity of lateral epidermal cell divisions all along the anteroposterior (A/P) body axis. Together our findings suggest that multiple, inter-related Wnt signaling systems may act together to polarize asymmetric cell divisions in ------------------- Key: 4437 Medline: 11023868 Authors: Honigberg L;Kenyon C Title: Establishment of left/right asymmetry in neuroblast migration by UNC-40/DCC, UNC-73/Trio and DPY-19 proteins in C. elegans. Citation: Development 127: 4655-4668 2000 Type: ARTICLE Genes: dpy-19 egl-20 mab-5 unc-5 unc-6 unc-40 unc-73 Abstract: The bilateral C. elegans neuroblasts QL and QR are born in the same anterior/posterior (A/P) position, but polarize and migrate left/right asymmetrically: QL migrates toward the posterior and QR migrates toward the anterior. After their migrations, QL but not QR switches on the Hox gene mab-5. We find that the UNC-40/netrin receptor and a novel transmembrane protein DPY-19 are required to orient these cells correctly. In unc-40 or dpy-19 mutants, the Q cells polarize randomly; in fact, an individual Q cell polarizes in multiple directions over time. In addition, either cell can express MAB-5, Both UNC-40 and DPY-19, as well as the Trio/GTPase exchange factor homolog UNC-73, are required for full polarization and migration. Thus, these proteins appear to participate in a signaling system that orients and polarizes these migrating cells in a left/right asymmetrical fashion during development. The C. elegans netrin UNC-6, which guides many cells and axons along the dorsoventral axis, is not involved in Q cell polarization, suggesting that a different netrin-like ligand serves to polarize these cells along the anteroposterior axis. ------------------- Key: 4438 Medline: 20556452 Authors: Chin-Sang ID;Chisholm AD Title: Form of the worm: genetics of epidermal morphogenesis in C. elegans. Citation: Trends in Genetics 16: 544-551 2000 Type: REVIEW Genes: deb-1 efn-1 egl-19 emb-9 hmp-1 hmp-2 hmr-1 let-2 let-413 let-502 let-805 mab-20 mel-11 mlc-4 mup-4 myo-3 nhr-25 pat-2 pat-3 sma-1 spc-1 sqt-3 vab-1 vab-2 vab-3 vab-7 Abstract: The development of the epidermis of the nematode worm Caenorhabditis elegans illustrates many common processes of epithelial morphogenesis. In the worm, these morphogenetic movements have been described with single-cell resolution, and the roles of individual cells have been probed in laser killing experiments. Genetic dissection is yielding insights into the molecular mechanisms of these complex morphogenetic processes. ------------------- Key: 4439 Medline: 20515608 Authors: Kipreos ET;Gohel SP;Hedgecock EM Title: The C. elegans F-box/WD-repeat protein LIN-23 functions to limit cell division during development. Citation: Development 127: 5071-5082 2000 Type: ARTICLE Genes: let-858 lin-23 ncl-1 sel-10 mnDf30 Abstract: In multicellular eukaryotes, a complex program of developmental signals regulates cell growth and division by controlling the synthesis, activation and degradation of G(1) cell cycle regulators. Here we describe the lin-23 gene of Caenorhabditis elegans, which is required to restrain cell proliferation in response to developmental cues. In lin-23 null mutants, all postembryonic blast cells undergo extra divisions, creating supernumerary cells that can differentiate and function normally. In contrast to the inability to regulate the extent of blast cell division in lin-23 mutants, the timing of initial cell cycle entry of blast cells is not affected, lin-23 encodes an F-box/WD-repeat protein that is orthologous to the Saccharomyces cerevisiae gene MET30, the Drosophila melanogaster gene slmb and the human gene beta TRCP, all of which function as components of SCF ubiquitin-ligase complexes. Lass of function of the Drosophila slmb gene causes the growth of ectopic appendages in a non-cell autonomous manner, In contrast, lin-23 functions cell autonomously to negatively regulate cell cycle progression, thereby allowing cell cycle exit in response to developmental signals. ------------------- Key: 4440 Medline: 20531741 Authors: Adoutte A Title: Small but mighty timekeepers. Citation: Nature 408: 37-38 2000 Type: REVIEW Genes: let-7 lin-4 lin-21 Abstract: A tiny RNA molecule ensures that the larvae of a roundworm develop into adults. The discovery of this RNA in many other animal groups implies that this way of keeping developmental time may be universal. ------------------- Key: 4441 Medline: Authors: Dhawan R;Dusenbery DB;Williams PL Title: A comparison of metal-induced lethality and behavioral responses in the nematode Caenorhabditis elegans. Citation: Environmental Toxicology and Chemistry 19: 3061-3067 2000 Type: ARTICLE Genes: Abstract: Behavioral changes are believed to be a sensitive indicator of toxicant exposure but can be very difficult to quantify. Using the free-living soil nematode Caenorhabditis elegans, a computer tracking system was used that measures several behavioral parameters for approximately 100 subjects on a real-time basis. Toxicant exposures can be performed in soil, on agar plates, or in aquatic media. Following the exposure period, the worms are transferred to a thin-layered agar slab for viewing in dark-held illumination by a video camera interfaced directly to a computer. Information can be obtained on a number of behavioral parameters including number of subjects moving, their individual rates of locomotion, and the frequency of change in direction. Exposure to five metals (Pb, Cu, Cd, Al, and Zn) were tested in this study to evaluate behavioral changes in the worm. The nematodes were exposed for 24 h to concentrations of an individual metal in aquatic medium representing the interstitial pore water within the soil. Under identical conditions, concurrent LC50 and BC50 (concentration at which movement is reduced by 50% compared with controls) values were determined for each metal tested. The results from computer tracking revealed significant changes in rare of locomotion at concentrations of less than 10% of the respective LC50 ------------------- Key: 4442 Medline: 20556132 Authors: Miller LM;Hess HA;Doroquez DB;Andrews NM Title: Null mutations in the lin-31 gene indicate two functions during Caenorhabditis elegans vulval development. Citation: Genetics 156: 1595-1602 2000 Type: ARTICLE Genes: lin-31 Abstract: The lin-31 gene is required for the proper specification of vulval cell fates in the nematode Caenorhabditis elegans and encodes a member of the winged-helix family of transcription factors. Members of this important family have been identified in many organisms and are known to bind specific DNA targets involved in a variety of developmental processes. DNA sequencing of 13 lin-31 alleles revealed six nonsense mutations and two missense mutations within the DNA-binding domain, plus three deletions, one transposon insertion, and one frameshift mutation that all cause large-scale disruptions in the gene. The missense mutations are amino acid substitutions in the DNA-binding domain and probably disrupt interactions of the LIN-31 transcription factor with its DNA target. In addition, detailed phenotypic analysis of all 19 alleles showed similar penetrances for several characteristics examined. From our analysis we conclude: (1) the null phenotype of lin-31 is the phenotype displayed by almost all of the existing alleles, (2) the DNA-binding domain plays a critical role in LIN-31 function, and (3) direct screens for multivulva and vulvaless mutants will probably ------------------- Key: 4443 Medline: 20556133 Authors: Lieb JD;Ortiz de Solorzano C;Garcia Rodriguez E;Jones A;Angelo M;Lockett S;Meyer BJ Title: The Caenorhabditis elegans dosage compensation machinery is recruited to X chromosome DNA attached to an autosome. Citation: Genetics 156: 1603-1621 2000 Type: ARTICLE Genes: dpy-26 dpy-27 mnDp10 mnDp27 stDp2 yDp14 Abstract: The dosage compensation machinery of Caenorhabditis elegans is targeted specifically to the X chromosomes of hermaphrodites (XX) to reduce gene expression by half. Many of the trans-acting factors that direct the dosage compensation machinery to X have been identified, but none of the proposed cis-acting X chromosome-recognition elements needed to recruit dosage compensation components have been found. To study X chromosome recognition, we explored whether portions of an X chromosome attached to an autosome are competent to bind the C. elegans dosage compensation complex (DCC). To do so, we devised a three-dimensional in situ approach that allowed us to compare the volume, position, and number of chromosomal and subchromosomal bodies bound by the dosage compensation machinery in wild-type XX nuclei and XX nuclei carrying an X duplication. The dosage compensation complex was found to associate with a duplication of the right 30% of X, but the complex did not spread onto adjacent autosomal sequences. This result indicates that all the information required to specify X chromosome identity resides on the duplication and that the dosage compensation machinery can localize to a site distinct from the full-length hermaphrodite X chromosome. In contrast, smaller duplications of other regions of X appeared to not support localization of the DCC. In a separate effort to identify cis-acting X recognition elements, we used a computational approach to analyze genomic DNA sequences for the presence of short motifs that were abundant and overrepresented on X relative to autosomes. Fourteen families of X-enriched motifs were discovered and mapped onto the X chromosome. ------------------- Key: 4444 Medline: 20556134 Authors: Nance J;Davis EB;Ward S Title: spe-29 encodes a small predicted protein required for the initiation of sperm activation in Caenorhabditis elegans. Citation: Genetics 156: 1623-1633 2000 Type: ARTICLE Genes: fer-1 spe-8 spe-12 spe-27 spe-29 eDf19 mDf7 Abstract: Caenorhabditis elegans spermatidis complete a dramatic morphogensis to crawling spermatozoa in the absence of an actin- or tubulin-based cytoskeleton and without synthesizing new gene products. Mutations in three genes (spe-8, spe-12, and spe-27) prevent the initiation of this morphogensis, termed activation. Males with mutations in any of these genes are fertile. By contrast, mutant hermaphrodites are self-sterile when unmated due to a failure in spermatid activation. Intriguingly, mutant hermaphrodites are self-functional spermatozoa and become self-fertile upon mating, suggesting that spermatids can be activated by male seminal fluid. Here we describe a mutation in a fourth gene, spe-29, which mimics the phenotype of spe-8, spe-12, adn spe-27 mutants. spe-29 sperm are defective in the initiation of hermaphrodite sperm activation, yet they maintain the ability to complete the morphogenetic rearrangements that follow. Mutant alleles of spe-12, spe-27, and spe-29 exhibit genetic interactions that suggest that the wild-type products of spe-29 gene, which is expressed specifically in the sperm-producing germ line and is predicted to encode a ------------------- Key: 4445 Medline: 20556135 Authors: Peters AD;Keightley PD Title: A test for epistasis among induced mutations in Caenorhabditis elegans. Citation: Genetics 156: 1635-1647 2000 Type: ARTICLE Genes: Abstract: Synergistic epistasis, in which deleterious mutations tend to magnify each other's effects, is a necessary component of the mutational deterministic hypothesis for the maintenance of sexual production. We tested for epistasis for life-history traits in the soil nematode Caenorhabditis elegans by inducing mutations in two genetic backgrounds: a wild-type strain and a set of genetically loaded lines that contain large numbers of independent mildly detrimental mutations. There was no significant difference between the effect of now mutations on the wild-type background and the genetically loaded background for four out of five fitness correlates. In these four cases, the maximum level of epistasis compatible with the data was very low. The fifth trait, late productivity, is not likely to be an important component of fitness. This suggests either that specific environmental conditions are required to cause epistasis or that synergistic epistasis is not a general phenomenon. We also suggest a new mechanism by which deleterious mutations may provide air advantage to sexual reproduction under low selection coefficients. ------------------- Key: 4446 Medline: 20556136 Authors: Miller KG;Rand JB Title: A role for RIC-8 (synembryn) and GOA-1(Goa) in regulating a subset of centrosome movements during early embryogenesis in Caenorhabditis elegans. Citation: Genetics 156: 1649-1660 2000 Type: ARTICLE Genes: dgk-1 goa-1 ric-8 Abstract: RIC-8 (synembryn) and GOA-1 (G(o)alpha) are key components of a signaling network that regulates neuro-transmitter secretion in Caenorhabditis elegans. Here we show that ric-8 and goa-1 reduction of function mutants exhibit partial embryonic lethality. Through Nomarski analysis we show that goa-l and ric-8 mutant embryos exhibit defects in multiple events that involve centrosomes, including one-cell posterior centrosome rocking, P-1 centrosome flattening, mitotic spindle alignment, and nuclear migration. In ric-8 reduction of function backgrounds, the embryonic lethality, spindle misalignments and delayed nuclear migration are strongly enhanced by a 50% reduction in maternal goa-l gene dosage. Several other microfilament- and microtubule-mediated events, as well as overall embryonic polarity, appear unperturbed in the mutants. In addition, our results suggest that RIG-8 and GOA-1 do not have roles in centrosome replication, ill the diametric movements of daughter centrosomes along the nuclear membrane, or in the extension of microtubules from centrosomes. Through immunostaining we show that GOA-1 (G(o)alpha) localizes to cell cortices as well as near centrosomes. Our results demonstrate that two components of a neuronal signal transduction pathway also play a role in centrosome movements during early embryogenesis. ------------------- Key: 4447 Medline: 20556137 Authors: Duret L;Marais G;Biemont C Title: Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans. Citation: Genetics 156: 1661-1669 2000 Type: ARTICLE Genes: Abstract: We analyzed the distribution of transposable elements (TEs: transposons, LTR retrotransposons, and non-LTR retrotransposons) in the chromosomes of the nematode Caenorhabditis elegans. The density of transposons (DNA-based elements) along the chromosomes was found to be positively correlated with recombination rate, but this relationship was not observed for LTR or non-LTR retrotransposons (RNA-based elements). Gene (coding region) density is higher in regions of low recombination rate. However, the lower TE density ill these regions is not due to the counterselection of TE insertions within exons since the same positive correlation between TE density and recombination rate was found in noncoding regions (both in introns and intergenic DNA). These data are not compatible with a global model of selection acting against TE insertions, for which an accumulation of elements in regions of reduced recombination is expected. We also found no evidence for a stronger selection against TE insertions on the X chromosome compared to the autosomes. The difference in distribution of the DNA and RNA-based elements along the chromosomes in relation to recombination rate can be explained by differences in the transposition ------------------- Key: 4448 Medline: 20556138 Authors: Piekny AJ;Wissmann A;Mains PE Title: Embryonic morphogenesis in Caenorhabditis elegans integrates the activity of LET-502 Rho-binding kinase, MEL-11 myosin phosphatase, DAF-2 insulin receptor and FEM-2 PP2c phosphatase. Citation: Genetics 156: 1671-1689 2000 Type: ARTICLE Genes: age-1 daf-2 daf-16 fem-1 fem-2 fem-3 let-502 mel-11 mig-2 mlc-4 tra-1 tra-3 unc-73 hDf6 Abstract: Let-502 rho-binding kinase and mel-11 myosin phosphatase regulate Caenorhabditis elegans embryonic morphogenesis. Genetic analysis presented here establishes the following modes of let-502 action: (i) loss of only maternal let-502 results in abnormal early cleavages, (ii) loss of both zygotic and maternal let-502 causes elongation defects, and (iii) loss of only zygotic let-502 results in sterility. The morphogenetic function of let-502 and mel-II is apparently redundant with another pathway since elimination of these two genes resulted in progeny that underwent near-normal elongation. Triple mutant analysis indicated that unc-73 (Rho/Rac guanine exchange factor) and mlc-4 (myosin light chain) act in parallel to or downstream of let-502/mel-11. In contrast mig-2 (Rho/Rac), daf-2 (insulin receptor), and age-1 (PI3 kinase) act within the let-502/mel-11 pathway. Mutations in the sex-determination gene fem-2 which encodes a PP2c phosphatase (unrelated to the MEL-11 phosphatase), enhanced mutations of let-502 and suppressed those of mel-11. fem-2's elongation function appears to be independent of its role in sexual identity since the sex-determination genes fem-1, fem-3, tra-1, and tra-3 had no effect on mel-11 or let-502. By itself, fem-2 affects morphogensis with low penetrance. fem-2 blocked the near-normal elongation of let-502; mel-11 indicating that fem-2 acts in a parallel elongation pathway. The action of two redundant pathways likely ensures accurate elongation of the C. elegans embryo. ------------------- Key: 4449 Medline: 20564077 Authors: Encalada SE;Martin PR;Phillips JB;Lyczak R;Hamill DR;Swan KA;Bowerman B Title: DNA replication defects delay cell division and disrupt cell polarity in early Caenorhabditis elegans embryos. Citation: Developmental Biology 228: 225-238 2000 Type: ARTICLE Genes: div-1 div-2 emb-13 emb-34 lin-2 pie-1 skn-1 zyg-7 Abstract: In early Caenorhabditis elegans embryos, asymmetric cell divisions produce descendants with asynchronous cell cycle times. To investigate the relationship between cell cycle regulation and pattern formation, we have identified a collection of embryonic-lethal mutants in which cell divisions are delayed and cell fate patterns are abnormal. In div (for division delayed) mutant embryos, embryonic cell divisions are delayed but remain asynchronous. Some div mutants produce well-differentiated cell types, but they frequently lack the endodermal and mesodermal cell fates normally specified by a transcriptional activator called SKN-1. We show that mislocalization of PIE-1, a negative regulator of SKN-1, prevents the specification of endoderm and mesoderm in div-1 mutant embryos. In addition to defects in the normally asymmetric distribution of PIE-1, div mutants also exhibit other losses of asymmetry during early embryonic cleavages. The daughters of normally asymmetric divisions are nearly equal in size, and cytoplasmic P-granules are not properly localized to germline precursors in div mutant embryos. Thus the proper timing of cell division appears to be important for multiple aspects of asymmetric cell division. One div gene, div-1, encodes the B subunit of the DNA polymerase alpha -primase complex. Reducing the function of other DNA replication genes also results in a delayed division phenotype and embryonic lethality. Thus the other div genes we have identified are likely to encode additional components of the DNA replication machinery in C. elegans. ------------------- Key: 4450 Medline: 11112335 Authors: Friedman L;Santa Anna-Arriola S;Hodgkin J;Kimble J Title: gon-4, a cell lineage regulator required for gonadogenesis in Caenorhabditis elegans. Citation: Developmental Biology 228: 350-362 2000 Type: ARTICLE Genes: elt-1 glp-1 gon-1 gon-4 lag-2 lim-7 pes-1 eDf19 mDf7 Abstract: The gon-4 gene is required for gonadogenesis in the nematode Caenorhabditis elegans. Normally, two precursor cells, Z1 and Z4, follow a reproducible pattern of cell divisions to generate the mature somatic gonadal structures (e.g., uterus in hermaphrodites, vas deferens in males). In contrast, in gon-4 mutants, the Z1/Z4 cell lineages are variably aborted in both hermaphrodites and males: Z1 and Z4 divide much later than normal and subsequent divisions are either absent or severely delayed. In gon-4 adults, normal somatic gonadal structures are never observed, and germ-line and vulval tissues, which depend on somatic gonadal cues for their development, are also aberrant. In contrast, nongonadal tissues and the timing of other developmental events (e.g., molts) appear to be normal in gon-4 mutants. The gon-4 alleles are predicted to be strong loss-of-function or null alleles by both genetic and molecular criteria. We have cloned gon-4 in an attempt to learn how it regulates gonadogenesis. The gon-4 gene encodes a novel, acidic protein. A GON-4::GFP fusion protein, which rescues a gon-4 mutant to fertility, is expressed in somatic gonadal cells during early gonadal development. Furthermore, this fusion protein is nuclear. We conclude that gon-4 is a regulator of the early lineage of Z1 and Z4 and suggest that it is a part of a genetic program common to the regulation of both hermaphrodite and ------------------- Key: 4451 Medline: 20556641 Authors: Waggoner LE;Dickinson KA;Poole DS;Tabuse Y;Miwa J;Schafer Title: Long-term nicotine adaptation in Caenorhabditis elegans involves PKC-dependent changes in nicotinic receptor abundance. Citation: Journal of Neuroscience 20: 8802-8811 2000 Type: ARTICLE Genes: lev-1 lev-8 lev-9 myo-3 tpa-1 unc-4 unc-29 Abstract: Chronic exposure to nicotine leads to long-term changes in both the abundance and activity of nicotinic acetylcholine receptors, processes thought to contribute to nicotine addiction. We have found that in Caenorhabditis elegans, prolonged nicotine treatment results in a long-lasting decrease in the abundance of nicotinic receptors that control egg-laying. In naive animals, acute exposure to cholinergic agonists led to the efficient stimulation of egg-laying, a response mediated by a nicotinic receptor functionally expressed in the vulval muscle cells. Overnight exposure to nicotine led to a specific and long-lasting change in egg-laying behavior, which rendered the nicotine-adapted animals insensitive to simulation of egg-laying by the nicotinic agonist and was accompanied by a promoter-independent reduction in receptor protein levels. Mutants defective in the gene tpa-1, which encodes a homolog of protein kinase C (PKC), failed to undergo adaptation to nicotine; after chronic nicotine exposure they remained sensitive to cholinergic agonists and retained high levels of receptor protein in the vulval muscles. These results suggest that PKC-dependent signaling pathways may promote nicotine adaptation via regulation of nicotinic receptor synthesis or degradation. ------------------- Key: 4452 Medline: 20490776 Authors: Bobinnec Y;Fukuda M;Nishida E Title: Identification and characterization of Caenorhabditis elegans gamma-tubulin in dividing cells and differentiated tissues. Citation: Journal of Cell Science 113: 3747-3459 2000 Type: ARTICLE Genes: tbg-1 Abstract: gamma -Tubulin is an essential component of the microtubule-nucleation machinery and therefore plays a crucial role during mitosis. To gain further insights into the function of this protein in the events that take place during embryogenesis and differentiation, we carried out detailed studies on gamma -tubulin during all the developmental stages of Caenorhabditis elegans. We identified the gamma -tubulin gene from this organism and analyzed the localization of the protein by both immunofluorescence and GFP reporter construct. We show that gamma -tubulin association with the centrosome is highly dynamic in mitotic cells, being massively recruited at prophase and released at anatelophase. This accumulation in mitotic centrosomes is dramatic during the first embryonic divisions. We provide the first description of the morphological changes at the centrosome level during the orientation of the mitotic spindle and the flattening of the posterior aster. Loss of function of the gamma -tubulin gene by RNAi induces a strong polyploidization of mitotic germ cells and embryos, but does not affect meiosis and pronuclear migration. In addition, we demonstrate the prominent redistribution of gamma -tubulin in adults at basal bodies of amphid and phasmid neurons, and at the apical membrane of polarized intestinal cells. ------------------- Key: 4453 Medline: 20490783 Authors: Nguyen TQ;Sawa H;Okano H;White JG Title: The C. elegans septin genes, unc-59 and unc-61, are required for normal postembryonic cytokineses and morphogenesis but have no essential function in Citation: Journal of Cell Science 113: 3825-3837 2000 Type: ARTICLE Genes: unc-59 unc-61 Abstract: Septins have been shown to play important roles in cytokinesis in diverse organisms ranging from yeast to mammals. In this study, we show that both the unc-59 and unc-61 loci encode Caenouhabditis elegans septins. Genomic database searches indicate that unc-59 and unc-61 are probably the only septin genes in the C. elegans genome. UNC-59 and UNC-61 localize to the leading edge of cleavage furrows and eventually reside at the midbody, Analysis of unc-59 and unc-61 mutants revealed that each septin requires the presence of the other for localization to the cytokinetic furrow. Surprisingly, unc-59 and unc-61 mutants generally have normal embryonic development; however, defects were observed in post-embryonic development affecting the morphogenesis of the vulva, male tail, gonad, and sensory neurons. These defects can be at least partially attributed to failures in post-embryonic cytokineses although our data also suggest other possible roles for septins, unc-59 and unc-61 double mutants show similar defects to each of the single mutants. ------------------- Key: 4454 Medline: 20539921 Authors: Higashitani A;Aoki H;Mori A;Sasagawa Y;Takanami T;Takahashi H Title: Caenorhabditis elegans Chk2-like gene is essential for meiosis but dispensable for DNA repair. Citation: FEBS Letters 485: 35-39 2000 Type: ARTICLE Genes: glp-4 him-3 spo-11 Abstract: A Chk2-like gene was identified in the genome of Caenorhabditis elegans. The putative gene product, termed Ce-chk-2 consists of 450 amino acid residues, and shows good homology with the Chk2/Cds1 gene family. The results of RNA-mediated interference (RNAi) indicated that the F1 generation from dsRNA injected animals grew to adulthood, but approximately 95% of their eggs (F2) died during early embryogenesis, Among the few surviving progeny, males (XO animals) arose at an abnormally high frequency (30%). In addition, 12 univalents were observed in full grown oocytes of the F1, while six bivalents were normally observed in mild-type oocytes, Ce-chk-2 gene expression increased in the adult stage, and their expression level decreased in the glp-4 mutant, which is defective in germ line proliferation. The radiation sensitivity of F1 embryos carrying Ce-chk-2 RNAi was not significantly affected. ------------------- Key: 4455 Medline: 20459810 Authors: O'Connell KF Title: The centrosome of the early C. elegans embryo: Inheritance, assembly, replication, and developmental roles. Citation: Current Topics in Developmental Biology 49: 365-384 2000 Type: REVIEW Genes: air-1 air-2 emb-27 emb-30 mlc-4 nmy-2 par-2 par-3 pie-1 plk-1 spd-2 tbg-1 zyg-1 zyg-9 Abstract: The main advantage of C. elegans as an experimental model lies in its simplicity. The full-grown adult is about 1 mm in length and composed of fewer than 1000 somatic nuclei. It has a short reproductive cycle of approximately 3 days and simple nutritional requirements, feeding primarily on bacteria.... ------------------- Key: 4456 Medline: 11132151 Authors: Rich T;Allen RL;Lucas AM;Stewart A;Trowsdale J Title: Pellino-related sequences from Caenorhabditis elegans and Homo sapiens. Citation: Immunogenetics 52: 145-149 2000 Type: ARTICLE Genes: Abstract: Toll receptor systems play an important role in our innate immune response to microbial infection (Rock et al. 1998). Studies of related pathways in arthropods (Hoffmann et all. 1999; Imler and Hofmann 2000) have led to key advances in our understanding of these processes. Until recently, however, the possibility that Toll signals may activate both immune and/or developmental pathways in Caenorhabditis elegans has been largely ignored. Early failures to identify Toll receptors or NFB-like transcription factors in the C. elegans genome (Ruvkun and Hobert 1998) let to the assumption that its Toll pathway was inoperable. Therefore, given the paucity of knowledge on innate immune responses for these animals, there was no impetus to develop C. elegans pathogenicity models. Recent database searches, however, have identified components of the elusive C. elegans Toll receptor pathway (Rich et al. 2000; Tan et al. 1999). The existence of a rudimentary immune response is further supported by evidence that antimicrobial peptides are encoded within the C. elegans genome (Tan and Ausubel 2000). In fact, C. elegans is susceptible to infection from several different pathogens, making this genetically tractable invertebrate an attractive model to study host-pathogen interactions. These developments are particularly important for the study of pathogens such as Pseudomonas aeruginosa whose natural hosts include humans. A suitable C. elegans model could, for example, provided a rapid system to screen candidate antibacterial drugs. Consequently, it has now become important to identify and isolate cDNAs for each component of the C. elegans Toll pathway. ------------------- Key: 4457 Medline: 20542041 Authors: Reinitz CA;Herfel HG;Messinger LA;Stretton AOW Title: Changes in locomotory behavior and cAMP produced in Ascaris suum by neuropeptides from Ascaris suum or Caenorhabditis elegans. Citation: Molecular & Biochemical Parasitology 111: 185-197 2000 Type: ARTICLE Genes: afp-1 flp-3 flp-4 flp-7 flp-8 flp-9 flp-12 flp-13 flp-15 Abstract: Injection of Ascaris FMRFamide-like (AF) peptides and peptides encoded by genes in Caenorhabditis elegans were analyzed for effects on locomotion, body waveforms, and cAMP concentrations in adult female Ascaris suum. Injection of AF1 (KNEFIRFamide) or AF2 (KHEYLRFamide) inhibited the propagation of locomotory waves and reduced the number of waveforms, decreased the body length, and caused a large, long-lasting increase in cAMP. Muscle tissue was identified as a major source of the cAMP response induced by AF1. The AF1 analog AF1R6A did not affect cAMP levels by itself, but inhibited the cAMP response produced by AF1. AF8 (KSAYMRFamide) produced ventral coiling in the behavioral assay, and AF10 (GFGDEMSMPGVLRFamide) decreased the body length and increased the number of body waveforms. In dorsal muscle strips, AF10 produced a long-lasting contraction. Neither AF8 nor AF10 changed cAMP concentrations. AF17 (FDRDFMHFamide) increased body length and decreased cAMP. The neuropeptides encoded by C. elegans genes flp-4, flp-7, flp-9, and flp-13 produced paralysis and loss of waveforms, increased body length and, like AF17, decreased cAMP. Three new predicted peptides from C. elegans genome sequences were synthesized and tested. One produced ventral coiling but no change in cAMP; the other two gave no detectable responses. The fact that C. elegans neuropeptides produce behavioral and physiological effects in A. suum suggests that structurally related peptides may exist in A. suum. The profound changes in cAMP produced by some neuropeptides has important implications for understanding cAMP signaling and shows that neuropeptide-mediated signal transduction pathways are potential targets for anthelmintic drug development. ------------------- Key: 4458 Medline: 20553263 Authors: Rand JB;Duerr JS;Frisby DL Title: Neurogenetics of vesicular transporters in C. elegans. Citation: FASEB Journal 14: 2414-2422 2000 Type: REVIEW Genes: avr-14 avr-15 bas-2 cat-1 cha-1 eat-4 glc-1 glr-1 glt-1 tph-1 unc-17 unc-25 unc-30 unc-47 unc-104 Abstract: The nematode Caenorhabditis elegans has a number of advantages for the analysis of synaptic molecules. These include a simple nervous system in which all cells are identified and synaptic connectivity is known and reproducible, a large collection of mutants and powerful methods of genetic analysis, simple methods for the generation and analysis of transgenic animals, and a number of relatively simple quantifiable behaviors. Studies in C. elegans have made major contributions to our understanding of vesicular transmitter transporters. Two of the four classes of vesicular transporters so far identified (VAChT and VGAT) were first described and cloned in C. elegans; in both cases, the genes were first identified and cloned by means of mutations causing a suggestive phenotype (1, 2). The phenotypes of eat-4 mutants and the cell biology of the EAT-4 protein were critical in the identification of this protein as the vesicular glutamate transporter (3, 4). In addition, the unusual gem structure associated with the cholinergic locus was first described in C. elegans (5). The biochemical properties of the nematode transporters are surprisingly similar to their vertebrate counterparts, and they can be assayed under similar conditions using the same types of mammalian cells (6, 7). In addition, mild and severe mutants (including knockouts) are available for each of the four C. elegans vesicular transporters, which has permitted a careful evaluation of the role(s) of vesicular transport in transmitter-specific behaviors. Accordingly, it seems appropriate at this time to present the current status of the field. In this review, we will first discuss the properties of C. elegans vesicular transporters and transporter mutants, and then explore some of the lessons and insights C. elegans research has provided to the field of vesicular transport. ------------------- Key: 4459 Medline: 20565869 Authors: Raymond V;Mongan NP;Sattelle DB Title: Anthelmintic actions of homomer-forming nicotinic acetylcholine receptor subunits: chicken alpha-7 and ACR-16 from the nematode Caenorhabditis elegans. Citation: Neuroscience 101: 785-791 2000 Type: ARTICLE Genes: Abstract: Two homomer-forming nicotinic acetylcholine receptor subunits with 47% identity in their amino acid sequences were employed to compare the actions of cholinergic anthelmintics and ivermectin on expressed vertebrate and nematode nicotinic receptors of known molecular composition. Voltage-clamp electrophysiology was used to study recombinant nicotinic receptors expressed in Xenopus laevis oocytes following nuclear injection of cDNA encoding either chicken alpha7 or Caenorhabditis elegans ACR-16 (Ce21) subunits, Butamisole, morantel and metyridine were without agonist actions on either alpha7 or ACR-16 nicotinic receptors in the range 10 nM-1 mM. However, butamisole (pIC(50) = 4.9 for both alpha7 and ACR-16) and morantel (PIC50 = 5.6 for alpha7 and 5.7 for ACR-16) antagonized responses of both alpha7 and ACR-16 receptors to acetylcholine. Metyridine (1 mM) did not affect responses to acetylcholine of either receptor. Oxantel was without agonist actions on ACR-16, but was an acetylcholine antagonist (pIC(50) = 5.4). In contrast, it was found to have low efficacy agonist action (pEC(50) = 4.4) on alpha7 at concentrations in the range 10-300 muM. In agreement with a previous study, ivermectin (30 muM), an agonist of L-glutamate-gated chloride channels, enhanced the amplitude of responses to acetylcholine of alpha7 nicotinic receptors. However, this same concentration of ivermectin (30 muM) did not potentiate the acetylcholine-induced responses of ACR-16, but rather resulted in a slight attenuation. We conclude that oxantel and ivermectin have identified new pharmacological differences between the chicken alpha7 nicotinic receptor and its C. elegans ------------------- Key: 4460 Medline: Authors: Motley AM;Hettema EH;Ketting R;Plasterk R;Tabak HF Title: Caenorhabditis elegans has a single pathway to target matrix proteins to peroxisomes. Citation: EMBO Reports 1: 40-46 2000 Type: ARTICLE Genes: Abstract: All eukaryotes so far studied, including animals, plants, yeasts and trypanosomes, have two pathways to target proteins to peroxisomes. These two pathways are specific for the two types of peroxisome targeting signal (PTS) present on peroxisomal matrix proteins. Remarkably, the complete genome sequence of Caenorhabditis elegans lacks the genes encoding proteins specific for the PTS2 targeting pathway. Here we show, by expression of green fluorescent protein (GFP) reporters for both pathways, that the PTS2 pathway is indeed absent in C. elegans. Lack of this pathway in man causes severe disease due to mislocalization of PTS2-containing proteins. This raises the question as to how C. elegans has accommodated the absence of the PTS2 pathway. We found by in silico analysis that C. elegans orthologues of PTS2-containing proteins have acquired a PTS1. We propose that switching of targeting signals has allowed the PTS2 pathway to be lost in the phylogenetic lineage leading to C. elegans. ------------------- Key: 4461 Medline: 11044397 Authors: Molin L;Mounsey A;Aslam S;Bauer P;Young J;James M;Sharma-Oates A;Hope IA Title: Evolutionary conservation of redundancy between a diverged pair of forkhead transcription factor homologues. Citation: Development 127: 4825-4835 2000 Type: ARTICLE Genes: daf-16 fkh-2 lin-31 pes-1 pha-4 unc-130 leDf1 Abstract: The Caenorhabditis elegans gene pes-1 encodes a transcription factor of the forkhead family and is expressed in specific cells of the early embryo. Despite these observations suggesting pes-1 to have an important regulatory role in embryogenesis, inactivation of pes-1 caused no apparent phenotype. This lack of phenotype is a consequence of genetic redundancy. Whereas a weak, transitory effect was observed upon disruption of just T14G12.4 (renamed fkh-2) gene function, simultaneous disruption of the activity of both fkh-2 and pes-1 resulted in a penetrant lethal phenotype. Sequence comparison suggests these two forkhead genes are not closely related and the functional association of fkh-2 and pes-1 was only explored because of the similarity of their expression patterns. Conservation of the fkh-2/pes-1 genetic redundancy between C. elegans and the related species C. briggsae was demonstrated. Interestingly the redundancy in C. briggsae is not as complete as in C. elegans and this could be explained by alterations of pes-1 specific to the C. briggsae ancestry. With overlapping function retained on an evolutionary time-scale, genetic redundancy may be extensive and expression pattern data could, as here, have a crucial role in characterization of developmental ------------------- Key: 4462 Medline: 20582453 Authors: Chung S;Gumienny TL;Hengartner MO;Driscoll M Title: A common set of engulfment genes mediates removal of both apoptotic and necrotic cell corpses in C. elegans. Citation: Nature Cell Biology 2: 931-937 2000 Type: ARTICLE Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ced-12 deg-1 deg-3 egl-1 mec-4 Abstract: Similar to mammalian excitotoxic cell death, necrotic-like cell death (NCD) in Caenorhabditis elegans can be initiated by hyperactive ion channels. Here we investigate the requirements for genes that execute and regulate programmed cell death (PCD) in necrotic-like neuronal death caused by a toxic MEG-4 channel. Neither the kinetics of necrosis onset nor the total number of necrotic corpses generated is altered by any C. elegans mutation known to block PCD, which provides genetic evidence that, the activating mechanisms for NCD and apoptotic cell death are distinct. In contrast, all previously reported ced genes required for phagocytotic removal of apoptotic corpses, as well as ced-12, a new engulfment gene we have identified, are required for efficient elimination of corpses generated by distinct necrosis-inducing stimuli. Our results show that a common set of genes acts to eliminate cell corpses irrespective of the mode of cell death, and provide the first identification of the C. elegans genes that are required for orderly removal of necrotic cells. As phagocytotic mechanisms seem to be conserved from nematodes to humans, our findings indicate that injured necrotic cells in higher organisms might also be eliminated before lysis through a controlled process of corpse removal, a hypothesis that has significant therapeutic implications. ------------------- Key: 4463 Medline: 20566918 Authors: Newman AP;Inoue T;Wang M;Sternberg PW Title: The Caenorhabditis elegans heterochronic gene lin-29 coordinates the vulval-uterine-epidermal connections. Citation: Current Biology 10: 1479-1488 2000 Type: ARTICLE Genes: egl-17 egl-29 lag-2 lin-1 lin-3 lin-4 lin-11 lin-12 lin-14 lin-28 lin-29 zmp-1 mnDf77 mnDf78 mnDf90 Abstract: Background: The development of a connection between the uterus and the vulva in the nematode Caenorhabditis elegans requires specification of a uterine cell called the utse, and its attachment to the vulva and the epidermal seam cells. The uterine pi cells generate the utse and uv1 cells, which also connect the uterus to the vulva. The uterine anchor cell (AC) induces the vulva through LIN-3/epidermal growth factor (EGF) signaling, and the pi cells through LIN-12/Notch signaling. Here, we report that a gene required for seam cell maturation is also required for specification of the utse and for vulval differentiation, and thus helps to coordinate development of the vulval-uterine-seam cell connection. Results: We cloned the egl-29 gene, which is necessary for induction of uterine pi cells, and found it to be allelic to lin-29, which encodes a zinc finger transcription factor that is necessary for the terminal differentiation of epidermal seam cells. In the uterus, lin-29 functioned upstream of lin-12 in the induction of pi cells and was necessary to maintain expression in the AC of lag-2, which encodes a ligand for LIN-12. Conclusions: The lin-29 gene controls gene expression in the epidermal seam cells, uterus and vulva, and may help to coordinate the terminal development of these three tissues by regulating the timing of late ------------------- Key: 4464 Medline: 20566919 Authors: Kelleher JF;Mandell MA:Moulder G;Hill KL;L'Hernault SW;Barstead R;Titus MA Title: Myosin VI is required for asymmetric segregation of cellular components during C. elegans spermatogenesis. Citation: Current Biology 10: 1489-1496 2000 Type: ARTICLE Genes: hum-3 spe-8 spe-13 spe-15 hDf7 Abstract: Background: The asymmetric division of cells and unequal allocation of cell contents is essential for correct development. This process of active segregation is poorly understood but in many instances has been shown to depend on the cytoskeleton. Motor proteins moving along actin filaments and microtubules are logical candidates to provide the motive force for asymmetric sorting of cell contents. The role of myosins in such processes has been suggested, but few examples of their involvement are known. Results: Analysis of a Caenorhabditis elegans class VI myosin deletion mutant reveals a role for this motor protein in the segregation of cell components during spermatogenesis. Mutant spermatocytes cannot efficiently deliver mitochondria and endoplasmic reticulum/Golgi-derived fibrous-body membranous organelle complexes to budding spermatids, and fail to remove actin filaments and microtubules from the spermatids. The segregation defects are not due to a global sorting failure as nuclear inheritance is unaffected. Conclusions: C. elegans myosin VI has an important role in the unequal partitioning of both organelles and cytoskeletal ------------------- Key: 4465 Medline: 11114525 Authors: Aballay A;Yorgey P;Ausubel FM Title: Salmonella typhimurium proliferates and establishes a persistent infection in the intestine of Caenorhabditis elegans. Citation: Current Biology 10: 1539-1542 2000 Type: ARTICLE Genes: fer-1 Abstract: Genetic analysis of host-pathogen interactions has been hampered by the lack of genetically tractable models of such interactions. We showed previously that the human opportunistic pathogen Pseudomonas aeruginosa kills Caenorhabditis elegans, that P. aeruginosa and C. elegans genes can be identified that affect this killing, and that most of these P. aeruginosa genes are also important for mammalian pathogenesis. Here, we show that Salmonella typhimurium as well as other Salmonella enterica serovars including S. enteritidis and S. dublin can also kill C. elegans. When C. elegans is placed on a lawn of S. typhimurium, the bacteria accumulate in the lumen of the worm intestine and the nematodes die over the course of several days. This killing requires contact with live bacterial cells. The worms die with similar kinetics when placed on a lawn of S. typhimurium for a relatively short time (3-5 hours) before transfer to a lawn of E. coil. After the transfer to E. coil, a high titer of S. typhimurium persists in the C. elegans intestinal lumen for the rest of the worms' life. Furthermore, feeding for 5 hours on a 1:1000 mixture of S. typhimurium and E. coli followed by transfer to 100% E. coil, also led to death after several days. This killing correlated with an increase in the titer of S. typhimurium in the C. elegans lumen, which reached 10,000 bacteria per worm. These data indicate that, in contrast to P. aeruginosa, a small inoculum of S. typhimurium can proliferate in the C. elegans intestine and establish a persistent infection. S. typhimurium mutated in the PhoP/PhoQ signal transduction system caused significantly less killing of C. elegans. ------------------- Key: 4466 Medline: 20566930 Authors: Labrousse A;Chauvet S;Couillault C;Kurz CL;Ewbank JJ Title: Caenorhabditis elegans is a model host for Salmonella typhimurium. Citation: Current Biology 10: 1543-1545 2000 Type: ARTICLE Genes: fur-1 phm-2 Abstract: The idea of using simple, genetically tractable host organisms to study the virulence mechanisms of pathogens dates back at least to the work of Darmon and Depraitere [1]. They proposed using the predatory amoeba Dictyostelium discoideum as a model host, an approach that has proved to be valid in the case of the intracellular pathogen Legionella pneumophila [2]. Research from the Ausubel laboratory has clearly established the nematode Caenorhabditis elegans as an attractive model host for the study of Pseudomonas aeruginosa pathogenesis [3]. P. aeruginosa is a bacterium that is capable of infecting plants, insects and mammals. Other pathogens with a similarly broad host range have also been shown to infect C. elegans [3,4]. Nevertheless, the need to determine the universality of C. elegans as a model host, especially with regards pathogens that have a naturally restricted host specificity, has rightly been expressed [5]. We report here that the enterobacterium Salmonella typhimurium, generally considered to be a highly adapted pathogen with a narrow range of target hosts [6], is capable of infecting and killing C. elegans. Furthermore, mutant strains that exhibit a reduced virulence in mammals were also attenuated for their virulence in C. elegans, showing that the nematode may constitute a useful model system for the study of this important human pathogen. ------------------- Key: 4467 Medline: 20538190 Authors: Marin I;Siegal ML;Baker BS Title: The evolution of dosage-compensaton mechanisms. Citation: BioEssays 22: 1106-1114 2000 Type: REVIEW Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 her-1 mix-1 sdc-2 sdc-3 xol-1 Abstract: Dosage compensation is the process by which the expression levels of sex-linked genes are altered in one sex to offset a difference in sex-chromosome number between females and males of a heterogametic species. Degeneration of a sex-limited chromosome to produce heterogamety is a common, perhaps unavoidable, feature of sex-chromosome evolution. Selective pressure to equalize sex-linked gene expression in the two sexes accompanies degeneration, thereby driving the evolution of dosage-compensation mechanisms. Studies of model species indicate that what appear to be very different mechanisms have evolved in different lineages: the male X chromosome is hypertranscribed in drosophilid flies, both hermaphrodite X chromosomes are downregulated in the nematode Caenorhabditis elegans, and one X is inactivated in mammalian females. Moreover, comparative genomic studies demonstrate that the trans-acting factors (proteins and non-coding RNAs) that have been shown to mediate dosage compensation are unrelated among the three lineages. Some tantalizing similarities in the fly and mammalian mechanisms, however, remain to be explained ------------------- Key: 4468 Medline: 20512078 Authors: Cho JH;Oh YS;Park KW;Yu JR;Choi KY;Shin JY;Kim DH;Park WJ;Hamada T;Kagawa H;Maryon EB;Bandyopadhyay J;Ahnn J Title: Calsequestrin, a calcium sequestering protein localized at the sarcoplasmic reticulum, is not essential for body-wall muscle function in Caenorhabditis elegans. Citation: Journal of Cell Science 113: 3947-3958 2000 Type: ARTICLE Genes: csq-1 unc-6 unc-29 unc-68 mnDf4 mnDf10 Abstract: Calsequestrin is the major calcium-binding protein of cardiac and skeletal muscles whose function is to sequester Ca2+ in the lumen of the sarcoplasmic reticulum (SR). Here we describe the identification and functional characterization of a C. elegans calsequestrin gene (csq-1). CSQ-1 shows moderate similarity (50% similarity, 30% identity) to rabbit skeletal calsequestrin. Unlike mammals, which have two different genes encoding cardiac and fast-twitch skeletal muscle isoforms, csq-1 is the only calsequestrin gene in the C. elegans genome. We show that csq-1 is highly expressed in the body-wall muscles, beginning in mid-embryogenesis and maintained through the adult stage. In body-wall muscle cells, CSQ-1 is localized to sarcoplasmic membranes surrounding sarcomeric structures, in the regions where ryanodine receptors (UNC-68) are located. Mutation in UNC-68 affects CSQ-1 localization, suggesting that the two possibly interact in vivo. Genetic analyses of chromosomal deficiency mutants deleting csq-1 show that CSQ-1 is not essential for initiation of embryonic muscle formation and. contraction. Furthermore, double-stranded RNA injection resulted in animals completely lacking CSQ-1 in body-wall muscles with no observable defects in locomotion. These findings suggest that although CSQ-1 is one of the major calcium-binding proteins in the body-wall muscles of C. elegans, it is not essential for body-wall muscle formation and contraction ------------------- Key: 4469 Medline: 20512083 Authors: Liu F;Ortiz I;Hutagalung A;Bauer CC;Cook RG;Epstein HF Title: Differential assembly of alpha- and gamma-filagenins into thick filaments in Caenorhabditis elegans. Citation: Journal of Cell Science 113: 4001-4012 2000 Type: ARTICLE Genes: Abstract: Muscle thick filaments are highly organized supramolecular assemblies of myosin and associated proteins with lengths, diameters and flexural rigidities characteristic of their source. The cores of body wall muscle thick filaments of the nematode Caenorhabditis elegans are tubular structures of paramyosin sub-filaments coupled by filagenins and have been proposed to serve as templates for the assembly of native thick filaments. We have characterized alpha- and gamma -filagenins, two novel proteins of the cores with calculated molecular masses of 30,043 and 19,601 and isoelectric points of 10.52 and 11.49, respectively. Western blot and immunoelectron microscopy using affinity-purified antibodies confirmed that the two proteins are core components. Immunoelectron microscopy of the cores revealed that they assemble with different periodicities. Immunofluorescence microscopy showed that alpha -filagenin is localized in the medial regions of the A-bands of body wall muscle cells whereas gamma -filagenin is localized in the flanking regions, and that alpha -filagenin is expressed in 1.5-twofold embryos while gamma -filagenin becomes detectable only in later ermiform embryos. The expression of both proteins continues throughout later stages of development. C. elegans body wall muscle thick filaments of these developmental stages have distinct lengths. Our results suggest that the differential assembly of alpha- and gamma -filagenins into thick filaments of distinct lengths may be developmentally ------------------- Key: 4470 Medline: 20565532 Authors: Herrgard S;Jambeck P;Taylor SS;Subramaniam S Title: Domain architecture of a Caenorhabditis elegans AKAP suggests a novel AKAP function. Citation: FEBS Letters 486: 107-111 2000 Type: ARTICLE Genes: Abstract: A-kinase anchoring proteins (AKAPs) are adapter proteins that are involved in directing cAMP-dependent protein kinase and some other signaling enzymes to certain intracellular locations. In this study, we investigate the domain architecture of an AKAP from Caenorhabditis elegans (AKAP(CE)). We show that AKAP(CE) shares two domains with the Smad anchor for receptor activation, a FYVE-finger and a transforming growth factor beta (TGF beta) receptor binding domain, suggesting that AKAP(CE) may interact with a receptor belonging to the TGF beta receptor family. This predicted novel AKAP function supports the recent view of AKAPs as adapter proteins that can be involved in various signaling pathways. ------------------- Key: 4471 Medline: 20566942 Authors: Sommer RJ Title: Comparative genetics: A third model nematode species. Citation: Current Biology 10: R879-R881 2000 Type: ARTICLE Genes: Abstract: Recent studies have introduced Oscheius sp. CEW1 as a third nematode species accessible to genetic analysis, joining the better known Caenorhabditis elegans and Pristionchus pacificus. A group of vulva-defective mutants in Oscheius has been identified, with defects not seen in C. elegans. ------------------- Key: 4472 Medline: 20565735 Authors: Yamamoto S;Watanabe Y;van der Spek PJ;Watanabe T;Fujimoto H;Hanaoka F;Ohkuma Y Title: Studies of nematode TFIIE function reveal a link between Ser-5 phosphorylation of RNA polymerase II and the transition from transcription initiation to elongation. Citation: Molecular and Cellular Biology 21: 1-15 2001 Type: ARTICLE Genes: Abstract: The general transcription factor TFIIE plays important roles in transcription initiation and in the transition to elongation. However, little is known about its function during these steps. Here we demonstrate for the first time that TFIIH-mediated phosphorylation of RNA polymerase II (Pol II) is essential for the transition to elongation. This phosphorylation occurs at serine position 5 (Ser-5) of the carboxy-terminal domain (CTD) heptapeptide sequence of the largest subunit of Pol II. In a human in vitro transcription system with a supercoiled template, this process was studied using a human TFIIE (hTFIIE) homolog from Caenorhabditis elegans (ceTFIIE alpha and ceTFIIE beta), ceTFIIE beta could partially replace hTFIIE beta, whereas ceTFIIE alpha could not replace hTFIIE alpha, We present the studies of TFIIE binding to general transcription factors and the effects of subunit substitution on CTD phosphorylation. As a result, ceTFIIE alpha did not bind tightly to hTFIIE beta, and ceTFIIE beta showed a similar profile for binding to its human counterpart and supported an intermediate level of CTD phosphorylation. Using antibodies against phosphorylated serine at either Ser-2 or Ser-5 of the CTD, we found that ceTFIIE beta induced Ser-5 phosphorylation very little but induced Ser-2 phosphorylation normally, in contrast to wild-type hTFIIE, which induced phosphorylation at both Ser-2 and Ser-5. In transcription transition assays using a linear template, ceTFIIE beta was markedly defective in its ability to support the transition to elongation. These observations provide evidence of TFIIE involvement in the transition and suggest that Ser-5 phosphorylation is essential for Pol II to be in the processive elongation ------------------- Key: 4473 Medline: 21021984 Authors: Tan W;Zolotukhin AS;Bear J;Patenaude DJ;Felber BK Title: The mRNA export in Caenorhabditis elegans is mediated by Ce-NXF-1, an ortholog of human TAP/NXF and Saccharomyces cerevisiae Mex67p. Citation: RNA 6: 1762-1772 2000 Type: ARTICLE Genes: Abstract: Human TAP and Saccharomyces cerevisiae Mex67p belong to a family of proteins that mediate mRNA export. Computer searches identified previously two Caenorhabditis elegans genes, C15H11.3 and C15H11.6, that encode putative homologs of hTAP and Mex67p (Segref et al., EMBO J, 1997, 16:3256-3271). Using RNA interference experiments in C. elegans, we found that functional knockout of C15H11.3 resulted in nuclear accumulation of poly(A)-containing RNAs and was lethal for both embryos and adult nematodes. No embryonic or progeny abnormality was observed in functional knockout of C15H11.6. Taken together, these data established that the C15H11.3 gene product is an ortholog of hTAP and Mex67p; thus, it was named Ce-NXF-1. Ce-NXF-1 binds RNA directly and is a nucleocytoplasmic shuttle protein accumulating in the nucleoplasm and at the nuclear rim. The rim association is mediated via unique signals present in the C-terminal portion of all TAP/NXF and Mex67p proteins. This region was shown to interact with the PC-repeat domains of nucleoporins Nup98, Nup153, and Nup214, indicating that the rim association occurs through components of the nuclear pore complex. In summary, Ce-NXF-1 belongs together with hTAP and Mex67p to a family of proteins that participate in mRNA export and can provide a direct molecular link between mRNAs and components of the nuclear pore complex. Therefore, despite differences in mRNA metabolism between these species, they utilize a ------------------- Key: 4474 Medline: 11114162 Authors: Wen C;Levitan D;Li X;Greenwald I Title: spr-2, a suppressor of the egg-laying defect caused by loss of sel-12 presenilin in Caenorhabditis elegans, is a member of the SET protein subfamily. Citation: Proceedings of the National Academy of Sciences USA 97: 14524-14529 2000 Type: ARTICLE Genes: hop-1 sel-12 spr-1 spr-2 spr-3 Abstract: Presenilin plays critical roles in the genesis of Alzheimer's disease and in UN-12/Notch signaling during development. Here, we describe a screen far genes that influence presenilin level or activity in Caenorhabditis elegans. We identified four spr (suppressor of presenilin) genes by reverting the egg-laying defective phenotype caused by a null allele of the sel-12 presenilin gene. We analyzed the spr-2 gene in some detail. We show that loss of spr-2 activity suppresses the egg-laying defective phenotype of different sel-12 alleles and re quires activity of the hop-1 presenilin gene, suggesting that suppression is accomplished by elevating presenilin activity rather than by bypassing the need for presenilin activity. We also show that SPR-2 is a nuclear protein and is a member of a protein subfamily that includes human SET, which has been identified in numerous different biochemical assays and at translocation breakpoints associated with a subtype of acute myeloid leukemia. ------------------- Key: 4475 Medline: Authors: Perelman D;Lu NC Title: Requirements for branched chain amino acids and their interactions in the nematode Caenorhabditis elegans. Citation: Nematology 2: 501-506 2000 Type: ARTICLE Genes: Abstract: Branched chain amino acid (BCAA) requirements and their interactions were studied in the nematode Caenorhabditis elegans. Optimal, deficiency and toxic levels affecting nematode population growth were determined for each of the three BCAAs. The optimal range for leucine was 0.72-2.8; for isoleucine, 0.86-1.7; and for valine, 0.51-4.1 mg ml(-1). Leucine at high concentrations was toxic. When isoleucine and valine were both added at high concentrations, they also exerted a marked toxic effect. The interactions of the branched chain amino acids found among vertebrate animals were not observed in C. elegans. ------------------- Key: 4476 Medline: 20544953 Authors: Kuroyanagi H;Kimura T;Wada K;Hisamoto N;Matsumoto K;Hagiwara M Title: SPK-1, a C. elegans SR protein kinse homologue, is essential for embryogenesis and required for germline Citation: Mechanisms of Development 99: 51-64 2000 Type: ARTICLE Genes: ama-1 glp-1 him-5 rde-1 rde-2 rde-3 spk-1 Abstract: SR-protein kinases (SRPKs) and their substrates, serine/arginine-rich pre-mRNA splicing factors, are key components of splicing machinery and are well conserved across phyla. Despite extensive biochemical investigation, the physiological functions of SRPKs remain unclear. In the present study, cDNAs for SPK-1, a C. elegans SRPK homologue, and CeSF2, an SPK-1 substrate, were cloned. SPK-1 binds directly to and phosphorylates the RS domain of CeSF2 in vitro. Both spk-1 and CeSF2 are predominantly expressed in germlines. RNA interference (RNAi) experiments revealed that spk-1 and CeSF2 play an essential role at the embryonic stage of C. elegans. Furthermore, RNAi studies demonstrated that spk-1 is required for germline development in C. elegans. We provide evidence that RNAi, achieved by the soaking of L1 larvae, is beneficial in the study of gene function in post-embryonic germline ------------------- Key: 4477 Medline: Authors: Mori T;Mohamed ASA;Sato M;Yamasaki T Title: Ellagitannin toxicity in the free-living soil inhabiting nematode, Caenorhabditis elegans. Citation: Journal of Pesticide Science 25: 405-409 2000 Type: ARTICLE Genes: Abstract: Great losses to crop productivity are annually induced by plant-parasitic nematodes. However, nematicides available for the last few decades have been imperfect with respect to environmental safety or healthy life. The need to develop new generation nematicides, less hazardous for Mammalia, is urgent. The free-living soil-inhabiting nematode, Caenorhabditis elegans, is an excellent laboratory animal in terms of being easily cultured, its short life cycle and normally hermaphroditic mode of reproduction. Therefore, it has been long popular as a useful screen for nematicides, anthelmintics, neurotoxins and environmental pollutants. Using C. elegans as a test animal, thus far screening of nematicidal compounds from methanol extracts of 230 wild plant species covering 190 genera among 77 families in Kagawa, Japan, has been performed in our laboratory for two years. The ellagitannin-rich fruit of Cornaceae Cornus officinalis has been used as one of the ingredients in the Kanpo medicine, Hachimi-gan. A macrocyclic ellagitannin dimer isolated from Woodfordia fruticosa exhibits antitumor activity. This paper deals with ellagitannin toxicity in the ------------------- Key: 4478 Medline: Authors: Mohamed ASA;Mori T;Islam SQ;Sato M;Yamasaki T Title: Lethal activity of galo- and condensed tannins against the free-living soil-inhabiting nematode, Caenorhabditis elegans. Citation: Journal of Pesticide Science 25: 410-415 2000 Type: ARTICLE Genes: Abstract: Great amounts of structurally diverse tannins are annually produced. Tannins have been well known as food phytochemicals (e.g. 3T-O-a-L-arabinopyranosyl-ent-epicatechin-(2a->O-7,4a->8)-e picatechin in cacao mass), medicinal properties (e.g. geraniin in Geranium thunbergii as tonic or antidiarrhoic) or tanning materials for leather manufacture (e.g. wattle tannins in Acacia mollissima). Recently, condensed tannin dimers (procyanidins B-1 and B-3) and its polymers were isolated from Pinus densiflora and characterized as members of the oviposition-stimulating multicomponent system in pine for the cerambycid beetle, Monochamus alternatus. Condensed tannins have also been regarded as antifeedants for phytophagous insects. A marine phlorotannin preparation, polymer of phloroglucinol, obtained from the brown alga Sargassum furvellum inhibits growth of the green algae Dunaliella and Enteromorpha spp. This paper describes isolation and identification of gallo- and condensed tannins and their nematicidal acitivity against the soil-inhabiting nematode, Caenorhabditis elegans. ------------------- Key: 4479 Medline: 20528370 Authors: Bingham J;Plowman GD;Sudarsanam S Title: Informatics issues in large-scale sequence analysis: Elucidating the protein kinases of C. elegans. Citation: Journal of Cellular Biochemistry 80: 181-186 2000 Type: ARTICLE Genes: Abstract: With the availability of the nearly complete genomic sequence of C. elegans, the first multicellular organism to be sequenced, molecular biology has definitely entered the postgenomic era. Annotation of the genomic sequence, which refers to identifying the genes and other biologically relevant sections of the genome, is an important and nontrivial next step. A first-pass annotation will be necessarily incomplete but will drive further biological experiments, which in turn will help to annotate the genome better. Given the scale of the genome sequence analysis, it is clear that the annotation should be automated as much as possible without sacrificing the quality of analysis. In this work, we outline our approach to identifying the protein kinases of C. elegans from the genomic sequence. We describe new tools we have developed for analysis, management and visualization of genomic data. By developing modular and scalable solutions, this study has provided a framework for future analysis of the Drosophila and human genomes. ------------------- Key: 4480 Medline: 20573926 Authors: Lum DH;Kuwabara PE;Zarkower D;Spence AM Title: Direct protein-protein interaction between the intracellular domain of TRA-2 and the transcription factor TRA-1A modulates feminizing activity in C. elegans. Citation: Genes & Development 14: 3153-3165 2000 Type: ARTICLE Genes: fem-3 tra-1 tra-2 Abstract: In the nematode Caenorhabditis elegans, the zinc finger transcriptional regulator TRA-1A directs XX somatic cells to adopt female fates. The membrane protein TRA-2A indirectly activates TRA-1A by binding and inhibiting a masculinizing protein, FEM-3. Here rye report that a part of the intracellular domain of TRA-2A, distinct from the FEM-3 binding region, directly binds TRA-1A. Overproduction of this TRA-1A-binding region has tra-1-dependent feminizing activity in somatic tissues, indicating that the interaction enhances TRA-1A activity. Consistent with this hypothesis, we show that tra-2(mx) mutations, which weakly masculinize somatic tissues, disrupt the TRA-2/TRA-1A interaction. Paradoxically, tra-2(mx) mutations feminize the XX germ line, as do tra-1 mutations mapping to the TRA-2 binding domain. We propose that these mutations render tra-2 insensitive to a negative regulator in the XX germ line, and we speculate that this regulator targets the TRA-2/TRA-1 complex. The intracellular domain of TRA-2A is likely to be produced as a soluble protein in vivo through proteolytic cleavage of TRA-2A or through translation of an XX germ line-specific mRNA. We further show that tagged derivatives of the intracellular domain of TRA-2 localize to the nucleus, supporting the hypothesis that this domain is capable of modulating TRA-1A activity in a manner reminiscent of Notch and Su(H). ------------------- Key: 4481 Medline: 20515606 Authors: Wang M;Sternberg PW Title: Patterning of the C. elegans primary vulval lineage by RAS and Wnt pathways. Citation: Development 127: 5047-5058 2000 Type: ARTICLE Genes: dig-1 let-23 lin-1 lin-12 lin-17 lin-18 lin-31 unc-6 zmp-1 Abstract: In C. elegans, the descendants of the 1 degrees vulval precursor cell (VPC) establish, a fixed spatial pattern of two different cell fates: E-F-F-E. The two inner granddaughters attach to the somatic gonadal anchor cell (AC) and generate four vulF cells, while the two outer granddaughters produce four vulE progeny. zmp-1::GFP, a molecular marker that distinguishes these two fates, is expressed in vulE cells, but not vulF cells. We demonstrate that a short-range AC signal is required to ensure that the pattern of vulE and vulF fates is properly established. In addition, signaling between the inner and outer 1 degrees VPC descendants, as well as intrinsic polarity of the 1 degrees VPC daughters, is involved in the asymmetric divisions of the 1 degrees VPC daughters and the proper orientation of the outcome. Finally, we provide evidence that RAS signaling is used during this new AC signaling event, while the Wnt receptor LIN-17 appears to mediate signaling between the inner and outer 1 degrees VPC descendants. ------------------- Key: 4482 Medline: 11060243 Authors: Liu J;Fire A Title: Overlapping roles of two Hox genes and the exd ortholog ceh-20 in diversification of the C. elegans postembryonic mesoderm. Citation: Development 127: 5179-5190 2000 Type: ARTICLE Genes: ceh-13 ceh-20 egl-5 egl-15 hlh-2 hlh-8 lin-39 mab-5 myo-3 Abstract: Members of the Box family of homeoproteins and their cofactors play a central role in pattern formation of all germ layers. During postembryonic development of C. elegans, non-gonadal mesoderm arises from a single mesoblast cell M. Starting in the first larval stage, M divides to produce 14 striated muscles, 16 non-striated muscles, and two non-muscle cells (coelomocytes). We investigated the role of the C. elegans Hox cluster and of the exd ortholog ceh-20 in patterning of the postembryonic mesoderm. By examining the M lineage and its differentiation products in different Hox mutant combinations, we found an essential but overlapping role for two of the Hox cluster genes, lin-39 and mab-5, in diversification of the postembryonic mesoderm. This role of the two Hox gene products required the CEH-20 cofactor. One target of these two Hox genes is the C. elegans twist ortholog hlh-8. Using both in vitro and in vivo assays, we demonstrated that twist is a direct target of Hox activation. We present evidence from mutant phenotypes that twist is not the only target for Hox genes in the M lineage: in particular we show that lin-39 mab-5 double mutants exhibit a more severe M lineage defect than the ------------------- Key: 4483 Medline: 21176844 Authors: Paul RJ;Gohla J;Foll R;Schneckenburger H Title: Metabolic adaptations to environmental changes in Caenorhabditis elegans. Citation: Comparative Biochemistry & Physiology B-Biochemistry & Molecular Biology 127: 469-479 2000 Type: ARTICLE Genes: Abstract: Metabolic adaptations to environmental changes were studied in Caenorhabditis elegans. To assess adjustments in enzyme function, maximum activities of key enzymes of main metabolic pathways were determined. After a 12 h incubation at varying temperatures (10, 20 degreesC) and oxygen supplies (normoxia or anoxia), the activities of the following enzymes were determined at two measuring temperatures in tissue extracts: lactate dehydrogenase (LDH; anaerobic glycolysis), 3-hydroxyacyl-CoA-dehydrogenase (HCDH; fatty acid oxidation), isocitrate dehydrogenases (NAD-IDH, NADP-IDH; tricarboxylic acid cycle) and isocitrate lyase (ICL; glyoxylate cycle). Incubation at 20 degreesC induced a strong increase in maximum LDH activity. Anoxic incubation caused maximum HCDH and NADP-IDH activities and, at 10 degreesC incubation, LDH activity to increase. Maximum NAD-IDH and ICL activities were not influenced by any type of incubation. In order to study the time course of metabolic adaptations to varying oxygen supplies, relative quantities of free and protein-bound NADH were determined in living C. elegans using time-resolved fluorescence spectroscopy. During several hours of anoxia, free and protein-bound NADH showed different time courses. One main result was that just at the moment when the protein-bound NADH had reached a constant level, and the free NADH started to increase rapidly, the worms fell into a rigor state. The data on enzyme activity and NADH fluorescence can be interpreted on the basis of a two-stage model of ------------------- Key: 4484 Medline: 11134076 Authors: Golden A;Sadler PL;Wallenfang MR;Schumacher JM;Hamill DR;Bates G;Bowerman B;Seydoux G;Shakes DC Title: Metaphase to anaphase (mat) transition-defective mutants in Caenorhabditis elegans. Citation: Journal of Cell Biology 151: 1469-1482 2000 Type: ARTICLE Genes: emb-1 emb-27 emb-30 mat-1 mat-2 mat-3 hDf6 mnDf77 mnDf86 mnDf90 sDf4 tDf9 hDp31 mnDp37 Abstract: The metaphase to anaphase transition is a critical stage of the eukaryotic cell cycle, and, thus, it is highly regulated. Errors during this transition can lead to chromosome segregation defects and death of the organism. In genetic screens for temperature-sensitive maternal effect embryonic lethal (Me1) mutants, we have identified 32 mutants in the nematode Caenorhabditis elegans in which fertilized embryos arrest as one-cell embryos. In these mutant embryos, the oocyte chromosomes arrest in metaphase of meiosis I without transitioning to anaphase or producing polar bodies. An additional block in M phase exit is evidenced by the failure to form pronuclei and the persistence of phosphohistone H3 and MPM-2 antibody staining. Spermatocyte meiosis is also perturbed; primary spermatocytes arrest in metaphase of meiosis I and fail to produce secondary spermatocytes. Analogous mitotic defects cause M phase delays in mitotic germline proliferation. We have named this class of mutants "mat" for metaphase to anaphase transition defective. These mutants, representing six different complementation groups, all map near genes that encode subunits of the anaphase promoting complex or cyclosome, and, here, we show that one of the genes, emb-27, encodes the C. elegans CDC16 ortholog. ------------------- Key: 4485 Medline: 21066156 Authors: Dichtel ML;Louvet-Vallee S;Viney ME;Felix MA;Sternberg PW Title: Control of vulval cell division number in the nematode Oscheius/Dolichorhabditis sp. CEW1. Citation: Genetics 157: 183-197 2001 Type: ARTICLE Genes: Abstract: Spatial patterning of vulval precursor cell fates is achieved through a different two-stage induction mechanism in the nematode Oscheius/Dolichorhabditis sp. CEW1 compared with Caenorhabditis elegans. We therefore performed a genetic screen for vulva mutants in Oscheius sp. CEW1. Most mutants display phenotypes unknown in C. elegans. Here we present the largest mutant category, which affects division number of the vulva precursors P(4-8).p without changing their fate. Among these mutations, some reduce the number of divisions of P4.p and P8.p specifically. Two mutants omit the second cell cycle of all vulval lineages. A large subset of mutants under-go additional rounds of vulval divisions. 5 also found precocious and retarded heterochronic mutants. Whereas the C. elegans vulval lineage mutants carl be interpreted as overall (homeotic) changes in precursor cell fates with concomitant cell cycle changes, the mutants described in Oscheius sp. CEW1 do not affect overall precursor fate and thereby dissociate the genetic mechanisms controlling vulval cell cycle and fate. Laser ablation experiments in these mutants reveal that the two first vulval divisions in Oscheius sp. CEW1 appear to be redundantly controlled by a gonad-independent mechanism and by a gonadal signal that operates partially independently of vulval rate induction. ------------------- Key: 4486 Medline: 20560879 Authors: Kitamura K;Amano S;Hosono R Title: Contribution of neurons to habituation to mechanical stimulation in Caenorhabditis elegans. Citation: Journal of Neurobiology 46: 29-40 2001 Type: ARTICLE Genes: Abstract: In Caenorhabditis elegans, a light touch induces a locomotor response. Repeated touches, however, result in an attenuation of response, that is, habituation. Withdrawal responses elicited by anterior touch are controlled by anterior mechanosensory neurons (AVM and ALMs), and by four pairs of interneurons (AVA, AVB, AVD, and PVC) (Chalfie et al., 1985; White et al., 1986). To identify the neurons that participate in habituation, we ablated these neurons with laser microbeam and investigated the resulting habituation of the operated animals. The animals lacking both left and right homologues AVDLR were habituated more rapidly than intact animals. We propose that chemical synapses at AVD play a critical role in the habituation of ------------------- Key: 4487 Medline: 11013240 Authors: Okochi M;Eimer S;Bottcher A;Baumeister R;Romig H;Walter J;Capell A;Steiner H;Haass C Title: A loss of function mutant of the presenilin homologue SEL-12 undergoes aberrant endoproteolysis in Caenorhabditis elegans and increases Abeta42 generation in human cells. Citation: Journal of Biological Chemistry 275: 40925-40932 2001 Type: ARTICLE Genes: sel-12 Abstract: The familial Alzheimer's disease-associated presenilins (PSs) occur as a dimeric complex of proteolytically generated fragments, which functionally supports endoproteolysis of Notch and the beta -amyloid precursor protein (beta APP). A homologous gene, sel-12, has been identified in Caenorhabditis elegans. We now demonstrate that wild-type (wt) SEL-12 undergoes endoproteolytic cleavage in C. elegans similar to the PSs in human tissue. In contrast, SEL-12 C60S protein expressed from the sel-12(ar131) allele is miscleaved in C. elegans, resulting in a larger mutant N-terminal fragment. Neither SEL-12 wt nor C60S undergo endoproteolytic processing upon expression in human cells, suggesting that SEL-12 is cleaved by a C. elegans-specific endoproteolytic activity. The loss of function of sel-12 in C. elegans is not associated with a dominant negative activity in human cells, because SEL-12 C60S and the corresponding PS1 C92S mutation do not interfere with Notch1 cleavage. Moreover, both mutant variants increase the aberrant production of the highly amyloidogenic 42-amino acid version of amyloid beta-peptide similar to familial Alzheimer's disease-associated human PS mutants. Our data therefore demonstrate that the C60S mutation in SEL-12 is associated with aberrant endoproteolysis and a loss of function in C. elegans, whereas a gain of misfunction is observed upon expression in human cells. ------------------- Key: 4488 Medline: 20568772 Authors: Kuwahara M;Asai T;Sato K;Shinbo I;Terada Y;Marumo F;Sasaki Title: Functional characterization of a water channel of the nematode Caenorhabditis elegans. Citation: Biochimica et Biophysica Acta-Gene Structure & Expression 1517: 107-112 2000 Type: ARTICLE Genes: Abstract: A genome project for the species Caenorhabditis elegans has demonstrated the presence of eight cDNAs belonging to the major intrinsic protein (MIP) family. We previously characterized one of these cDNAs known as C01G6.1. C01G6.1 was confirmed to be a water channel and newly designated as AQP-CE1 [Am. J. Physiol. 275 (1998) C1459-C1464]. In this paper, we examined the function of another MIP protein encoded by F40F9.9. This cDNA encodes a 274-amino acid protein showing a high sequence identity with mammalian aquaporin-8 (AQP8) water channel (35%) and d-TIP (34%), an AQP of Arabidopsis. The expression of F40F9.9 in Xenopus oocytes increased the osmotic water permeability (P-f) 10.4-fold, and the activation energy for P-f from Arrhenius plot was 4.7 kcal/mol, suggesting that F40F9.9 is a water channel (AQP-CE2). AQP-CE2 was not permeable to glycerol or urea. Oocyte P-f was reversibly inhibited by 58% after an incubation with 0.3 mM HgCl2. To identify the mercury-sensitive site, four individual cysteine residues in AQP-CE2 (at positions 47, 132, 149, 259) were altered to serine by site-directed mutagenesis. Of these mutants, only C132S had a P-f similar to that of the wild-type together with an acquired mercury resistance, suggesting that Cys-132 is the mercury-sensitive site. Similar results were obtained by the mutation of Cys-132 to alanine (C132A). Replacement of Cys-132 with tryptophan decreased P-f by 64%, but P-f was still 2.5 times higher than that of the control. Cys-132 is located in the transmembrane helix 3, close to the transition to the extracellular loop C. These results suggest that the transmembrane helix 3, including Cys-132, might participate in the aqueous pore formation, or, alternatively, that Cys-132 might contribute to the construction of the AQP protein. ------------------- Key: 4489 Medline: 11134517 Authors: Jiang M;Ryu J;Kiraly M;Duke K;Reinke V;Kim SK Title: Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 98: 218-223 2001 Type: ARTICLE Genes: apr-1 bar-1 egl-20 ham-2 hda-1 her-1 him-5 him-8 lin-9 lin-15 lin-35 lin-36 lin-44 lin-53 lov-1 mab-3 mab-9 mab-31 mom-2 mom-5 pkd-2 pop-1 rba-1 rba-2 sex-1 sra-1 sra-6 srd-1 vab-3 wrm-1 Abstract: We have constructed DNA microarrays containing 17.871 genes, representing about 94% of the 18,967 genes currently annotated in the Caenorhabditis elegans genome. These DNA microarrays can be used as a tool to define a nearly complete molecular profile of gene expression levels associated with different developmental stages, growth conditions, or worm strains. Here, we used these full-genome DNA microarrays to show the relative levels of gene expression for nearly every gene during development, from eggs through adulthood. These expression data can help reveal when a gene may act during development. We also compared gene expression in males to that of hermaphrodites and found a total of 2,171 sex-regulated genes (P < 0.05). The sex-regulated genes provide a global view of the differences between the sexes at a molecular level and identify many genes likely to be involved in sex-specific differentiation and behavior. ------------------- Key: 4490 Medline: 11076749 Authors: Clifford R;Lee MH;Nayak S;Ohmachi M;Giorgini F;Schedl T Title: FOG-2, a novel F-box containing protein, associates with the GLD-1 RNA binding protein and directs male sex determination in the C. elegans hermaphrodite germline. Citation: Development 127: 5265-5276 2000 Type: ARTICLE Genes: fog-2 ftr-1 gld-1 tra-2 ozDf1 ozDf2 Abstract: Male sex determination in the Caenorhabditis elegans hermaphrodite germline requires translational repression of tra-2 mRNA by the GLD-1 RNA binding protein. We cloned fog-2 by finding that its gene product physically interacts with GLD-1, forming a FOG-2/GLD-1/tra-2 3'untranslated region ternary complex. FOG-2 has an N-terminal F-box and a novel C-terminal domain called FTH, Canonical F-box proteins act as bridging components of the SCF ubiquitin ligase complex; the N-terminal F-box binds a Skp1 homolog, recruiting ubiquination machinery, while a C-terminal protein-protein interaction domain binds a specific substrate for degradation. However, since both fog-2 and gld-1 are necessary for spermatogenesis, FOG-2 cannot target GLD-1 for ubiquitin-mediated degradation. We propose that FOG-2 also acts as a bridge, bringing GLD-1 bound to tra-2 mRNA into a multiprotein translational repression complex, thus representing a novel function for an F-box protein. fog-2 is a member of a large, apparently rapidly evolving, C. elegans gene family that has expanded, in part, by local duplications; fog-2 related genes have not been found outside nematodes. Fog-2 may have arisen during evolution of self-fertile hermaphroditism from an ancestral female/male species. ------------------- Key: 4491 Medline: 11076750 Authors: von Zelewsky T;Palladino F;Brunschwig K;Tobler H;Hajnal A;Muller F Title: The C. elegans Mi-2 chromatin-remodelling proteins function in vulval cell fate determination. Citation: Development 127: 5277-5284 2000 Type: ARTICLE Genes: Abstract: The Mi-2 protein is the central component of the recently isolated NuRD nucleosome remodelling and histone deacetylase complex. Although the NuRD complex has been the subject of extensive biochemical analyses, little is known about its biological function. Here we show that the two C. elegans Mi-2 homologues, LET-418 and CHD-3, play essential roles during development. The two proteins possess both shared and unique functions during vulval cell fate determination, including antagonism of the Ras signalling pathway required for vulval cell fate induction and the proper execution of the 2 degrees cell fate of vulval precursor cells, a process under the control of LIN-12 ------------------- Key: 4492 Medline: 20530494 Authors: Portman DS;Emmons SW Title: The basic helix-loop-helix transcription factors LIN-32 and HLH-2 function together in multiple steps of a C. elegans neuronal sublineage. Citation: Development 127: 5415-5426 2000 Type: ARTICLE Genes: cat-2 hlh-2 lin-32 mab-5 pkd-2 Abstract: bHLH transcription factors function in neuronal development in organisms as diverse as worms and vertebrates. In the C. elegans male tail, a neuronal sublineage clonally gives rise to the three cell types (two neurons and a structural cell) of each sensory ray. We show here that the bHLH genes lin-32 and hlh-2 are necessary for the specification of multiple cell fates within this sublineage, and for the proper elaboration of differentiated cell characteristics. Mutations in lin-32, a member of the atonal family, can cause failures at each of these steps, resulting in the formation of rays that lack fully-differentiated neurons, neurons that lack cognate rays, and ray cells defective in the number and morphology of their processes. Mutations in hlh-2, the gene encoding the C. elegans E/daughterless ortholog, enhance the ray defects caused by lin-32 mutations. In vitro, LIN-32 can heterodimerize with HLH-2 and bind to an E-box-containing probe. Mutations in these genes interfere with this activity in a manner consistent with the degree of ray defects observed in vivo. We propose that LIN-32 and HLH-2 function as a heterodimer to activate different sets of targets, at multiple steps in the ray sublineage. During ray development, lin-32 performs roles of proneural, neuronal precursor, and differentiation genes of other systems. ------------------- Key: 4493 Medline: 11135305 Authors: Simske JS;Hardin J Title: Getting into shape: epidermal morphogenesis in Caenorhabditis elegans embyros. Citation: BioEssays 23: 12-23 2001 Type: REVIEW Genes: apr-1 die-1 efn-1 efn-2 efn-3 hmp-1 hmp-2 hmr-1 jam-1 let-413 let-502 mab-20 mel-11 mig-2 mlc-4 sma-1 spc-1 unc-73 vab-1 vab-2 wrm-1 zen-4 Abstract: The change in shape of the C. elegans embryo from an ovoid bail of cells into a worm-shaped larva is driven by three events within the cells of the hypodermis (epidermis): (1) intercalation of two rows of dorsal cells, (2) enclosure of the ventral surface by hypodermis, and (3) elongation of the embryo. White the behavior of the hypodermal cells involved in each of these processes differs dramatically, it is clear that F-actin and microtubules have essential functions in each of these processes, whereas contraction of actomyosin structures appears to be involved specifically in elongation. Molecular analysis of these processes is revealing components specific to C. elegans as well as components found in other systems. Since C. elegans hypodermal eel Is demonstrate dramatically different behaviors during intercalation, enclosure and elongation, the study of cytoskeletal dynamics in these processes may reveal both unique and conserved activities during distinct epithelial morphogenetic movements. ------------------- Key: 4494 Medline: Authors: Stein L;Sternberg P;Durbin R;Thierry-Mieg J;Spieth J Title: WormBase: network access to the genome and biology of Caenorhabditis elegans. Citation: Nucleic Acids Research 29: 82-86 2001 Type: ARTICLE Genes: Abstract: WormBase (hffp://www.wormbase.org) is a web-based resource for the Caenorhabdifis elegans genome and its biology. it builds upon the existing ACeDB database of the C.elegans genome by providing data curation services, a significantly expanded range of subject areas and a user-friendly front end. ------------------- Key: 4495 Medline: 20577425 Authors: Signor D;Rose LS;Scholey JM Title: Analysis of the roles of kinesin and dynein motors in microtubule-based transport in the Caenorhabditis elegans nervous system. Citation: Methods 22: 317-325 2000 Type: ARTICLE Genes: Abstract: The heteromeric kinesins constitute a subfamily of kinesin-related motor complexes that function in several distinct intracellular transport events. The founding member of this sub-family, heterotrimeric kinesin II, has been purified and characterized from early sea urchin embryos, where it was shown using antibody perturbation to be required for the synthesis of motile cilia, presumably by driving the anterograde transport of raft complexes. To further characterize heteromeric kinesin transport pathways, and to attempt to identify cargo molecules, we are using the model organism Caenorhabditis elegans to exploit its well-characterized nervous system and simple genetics. Here we describe methods for large-scale nematode growth and partial purification of kinesin-related holoenzymes from C. elegans, and an in vivo transport assay that allows the direct labeling and visualization of motor complexes and putative cargo molecules moving in living C. elegans neurons. This transport assay is being used to characterize the in vivo transport properties of motor enzymes in living cells, and to exploit a number of existing mutations in C. elegans that may represent constituents of heteromeric kinesin-driven transport pathways, for example, the retrograde intraflagellar transport motor CHE-3 dynein, as well as cargo molecules ------------------- Key: 4496 Medline: 21075943 Authors: Arata Y;Hirabayashi J;Kasai KI Title: Application of reinforced frontal affinity chromatography and advanced processing procedure to the study of the binding property of a Caenorhabditis elegans galectin. Citation: Journal of Chromatography 905: 337-343 2001 Type: ARTICLE Genes: Abstract: Frontal affinity chromatography is a very useful and simple method to analyze molecular interactions between an analyte and an immobilized ligand by calculating the extent of "retardation" of the elution front. We developed a very simple and efficient data-processing procedure that enables the measurement of very small differences in retardation with precision. This procedure was successfully applied to comparison of the binding properties of recombinant C. elegans galectins for their ligand. ------------------- Key: 4497 Medline: 21066155 Authors: Reinhart BJ;Ruvkun G Title: Isoform-specific mutations in the Caenorhabditis elegans heterochronic gene lin-14 affect stage-specific patterning. Citation: Genetics 157: 199-209 2001 Type: ARTICLE Genes: lin-4 lin-14 Abstract: The Caenorhabditis elegans heterochronic gene lin-14 specifies the temporal sequence of postembryonic developmental events. lin-14, which encodes differentially spliced LIN-14A and LIN-14B1/B2 protein isoforms, acts at distinct times during the first larval stage to specify first and second larval stage-specific cell lineages. Proposed models for the molecular basis of these two lin-14 gene activities have included the production of functionally distinct isoforms and the generation of a temporal gradient of LIN-14 protein. We report here that loss of the LIN-14B1/B2 isoforms alone affects one of the two lin-14 temporal patterning functions, the specification of second lan al stage lineages. A temporal expression difference between LIN-14A and LIN-14B1/B2 is not responsible for the stage-specific phenotype: protein levels of all LIN-14 isoforms are high in early first larval stage animals and decrease during the first larval stage. However, LIN-14A can partially substitute for LIN-14B1/B2 when expressed at a higher-than-normal level in the late L1 stage. These data indicate that LIN-14B1/B2 isoforms do not provide a distinct function of the lin-14 locus in developmental timing but rather mall contribute to an overall level of LIN-14 protein that is the critical ------------------- Key: 4498 Medline: 21066154 Authors: Chou JH;Bargmann CI;Sengupta P Title: The Caenorhabditis elegans odr-2 gene encodes a novel Ly-6-related protein required for olfaction. Citation: Genetics 157: 211-224 2001 Type: ARTICLE Genes: hot-1 hot-2 hot-3 hot-4 hot-5 hot-6 odr-1 odr-2 odr-7 nDf32 sDf30 Abstract: Caenorhabditis elegans odr-2 mutants are defective in the ability to chemotax to odorants that are recognized by the two AWC olfactory neurons. Like mall) other olfactory mutants, they retain responses to high concentrations of AWC-sensed odors; we show here that these residual responses are caused by the ability of other olfactory neurons (the AWA neurons) to be recruited at high odor concentrations. odr-2 encodes a membrane-associated protein related. to the LV-G superfamily of GPI-linked signaling proteins and is the founding member of a C. elegans gene family with at least seven other members. Alternative splicing of odr-2 yields three predicted proteins that differ only at the extreme amino terminus. The three isoforms have different promoters, and one isoform mar; have a unique role in olfaction. An epitope-tagged ODR-2 protein is expressed at high levels in sensor) neurons, motor neurons, and interneurons and is enriched in axons. The AWC neurons are superficially normal ill their development and structure in odr-2 mutants, but their function is impaired. Our results suggest that ODR-2 may regulate AWC signaling within the neuronal network required ------------------- Key: 4499 Medline: 20575906 Authors: Edgar LG;Carr S;Wang H;Wood WB Title: Zygotic expression of the caudal homolog pal-1 is required for posterior patterning in Caenorhabditis elegans embryogenesis. Citation: Developmental Biology 229: 71-88 2001 Type: ARTICLE Genes: pal-1 rhDf1 sDf130 Abstract: Previous work has shown that the Caenorhabditis elegans gene pal-1, a homolog of Drosophila caudal, is required maternally for blastomere specification in the early embryo and postembryonically for tail development in males. We show here that embryonic (zygotic) transcription of pal-1 is also required for posterior patterning during later embryogenesis. Embryos homozygous for strong loss-of-function mutations arrest as nonviable L1 larvae with gross posterior defects. PAL-1 protein produced from zygotic transcripts is expressed dynamically during gastrulation and morphogenesis in specific cells of all major lineages except the germ line. Most expressing cells are undergoing cell movements or forming midline structures or both. Mutant embryos exhibit defects involving most of the expressing cells. Aberrant early cell positions are observed in posterior hypodermis, both in the C-lineage cells that express pal-1 and in the neighboring hypodermal seam cell precursors, which do not, as well as in posterior muscle derived from the C and D lineages. Defects in late gastrulation, ventral hypodermal enclosure, and formation of the rectum result from failures of cell movements of ABp and MS descendants. Limited mosaic analysis supports the view that most of the required pal-1 functions are cell autonomous. ------------------- Key: 4500 Medline: 21042006 Authors: Arata Y;Sekiguchi M;Hirabayashi J;Kasai K Title: Effects of the substitution of conserved amino acid residues on the sugar-binding property of the tandem-repeat 32-kDa galectin of the nematode Caenorhabditis elegans. Citation: Biological & Pharmaceutical Bulletin 24: 14-18 2001 Type: ARTICLE Genes: Abstract: The 32-kDa galectin (LEC-I) of the nematode Caenorhabditis elegans (C. elegans) is composed of tno tandemly repeated homologous sequences, each containing a carbohydrate-recognition domain (CRD). Using the polymerase chain reaction (PCR) with LEC-1 cDNA as a template and "megaprimers", we performed site-directed mutagenesis to substitute conserved amino acid residues in these domains. The resultant mutated LEC-1s were produced in E. coli, and their binding abilities were estimated by affinity chromatography. When one of the conserved amino acid residues in the first lectin domain was substituted, the binding ability of the mutant protein to asialofetuin-agarose was reduced but still remained. The binding ability of such mutants was similar to that of the recombinant half molecule containing the second lectin domain (Ch). However, when mutations n cre introduced into the second lectin domain, the binding ability of these mutant lectins to asialofetuin-agarose n as significantly reduced just like the half recombinant molecule containing the first lectin domain (Nh). The different effects of the substitution of amino acid residues on the two lectin domains suggest that the binding properties of the two sites are different and that LEG-I acts as a "heterobifunctionaI crosslinker." ------------------- Key: 4501 Medline: Authors: Gamulin V;Muller IM;Muller WEG Title: Sponge proteins are more similar to those of Homo sapiens than to Caenorhabditis elegans. Citation: Biological Journal of the Linnean Society 71: 821-828 2001 Type: ARTICLE Genes: Abstract: We compared 42 phylogenetically conserved proteins from four marine sponges [Porifera] with almost the complete set of Caenorhabditis elegans proteins and all known proteins from humans. The majority of the sponge proteins are significantly more similar to human than to C. elegans orthologues/homologues. This finding reflects the accelerated evolutionary rate in the C. elegans lineage, since sponges split off first from the common ancestor of all multicellular animals. Furthermore, three sponge/human proteins were not found in C. elegans: (2-5)A synthetase, DNA repair helicase and lens py-crystallin. Sponges are the source of the most ancient proteins already present in the common ancestor of all multicellular organisms. Some of these proteins were lost later during the evolution of individual animal lineages. These 'found/lost' proteins may serve as molecular markers for an improved systematics of Metazoa. In addition, phylogenetically conserved sponge proteins can be very helpful for the evaluation of differences in evolutionary rates in different animal lineages. We therefore propose sponges as the reference animals in molecular evolutionary studies of Metazoa. ------------------- Key: 4502 Medline: 20566934 Authors: Wilkie TM Title: G-protein signaling: Satisfying the basic necessities of life. Citation: Current Biology 10: R853-R856 2000 Type: REVIEW Genes: dgk-1 eat-16 egl-10 gpb-2 rgs-1 rgs-2 unc-13 unc-29 Abstract: Recent studies have shed light on the role of G-protein signaling, and in particular the regulatory RGS proteins, in behavioral adaptations of the round worm Caenorhabditis elegans; similar signaling pathways underlie analogous physiology and behaviors in mammals. ------------------- Key: 4503 Medline: 11163239 Authors: Zhou Z;Hartwieg E;Horvitz HR Title: CED-1 is a transmembrane receptor that mediates cell corpse engulfment in C. elegans. Citation: Cell 104: 43-56 2001 Type: ARTICLE Genes: ced-1 ced-2 ced-5 ced-6 ced-7 ced-10 Abstract: We cloned the C. elegans gene ced-1, which is required for the engulfment of cells undergoing programmed cell death, ced-1 encodes a transmembrane protein similar to human SREC (Scavenger Receptor from Endothelial Cells). We showed that ced-1 is expressed in and functions in engulfing cells. The CED-1 protein localizes to cell membranes and clusters around neighboring cell corpses. CED-1 failed to cluster around cell corpses in mutants defective in the engulfment gene ced-7. Motifs in the intracellular domain of CED-1 known to interact with PTB and SH2 domains were necessary for engulfment but not for clustering. Our results indicate that CED-1 is a cell surface phagocytic receptor that recognizes cell corpses. We suggest that the ABC transporter CED-7 promotes cell corpse recognition by CED-1, possibly by exposing a phospholipid ligand on the surfaces of cell corpses. ------------------- Key: 4504 Medline: 20530499 Authors: Kramerova IA;Kawaguchi N;Fessler LI;Nelson RE;Chen Y;Kramerov AA;Kusche-Gullberg M;Kramer JM;Ackley BD;Sieron AL;Prockop DJ;Fessler JH Title: Papilin in development; a pericellular protein with a homology to the ADAMTS metalloproteinases. Citation: Development 127: 5475-5485 2000 Type: ARTICLE Genes: gon-1 Abstract: Papilin is an extracellular matrix glycoprotein that we have found to be involved in, (1) thin matrix layers during gastrulation, (2) matrix associated with wandering, phagocytic hemocytes, (3) basement membranes and (4) space-filling matrix during Drosophila development. Determination of its cDNA sequence led to the identification of Caenorhabditis and mammalian papilins. A distinctly conserved 'papilin cassette' of domains at the amino-end of papilins is also the carboxyl-end of the ADAMTS subgroup of secreted, matrix-associated metalloproteinases; this cassette contains one thrombospondin type 1 (TSR) domain, a specific cysteine-rich domain and several partial TSR domains. In vitro, papilin non-competitively inhibits procollagen N-proteinase, an ADAMTS metalloproteinase. Inhibiting papilin synthesis in Drosophila or Caenorhabditis causes defective cell arrangements and embryonic death. Ectopic expression of papilin in Drosophila causes lethal abnormalities in muscle, Malpighian tubule and trachea formation. We suggest that papilin influences cell rearrangements and may modulate metalloproteinases during ------------------- Key: 4505 Medline: 20574742 Authors: Tatusov RL;Natale DA;Garkavtsev IV;Tatusova TA;Shankavaram UT;Rao BS;Kiryutin B;Galperin MY;Fedorova ND;Koonin EV Title: The COG database: new developments in phylogenetic classification of proteins from complete genomes. Citation: Nucleic Acids Research 29: 22-28 2001 Type: ARTICLE Genes: Abstract: The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of bacteria, archaea and the yeast Saccharomyces cerevisiae (http://www.ncbi.nlm.nih,gov/COG). In addition, a supplement to the COGs is available, in which proteins encoded in the genomes of two multicellular eukaryotes, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, and shared with bacteria and/or archaea were included. The new features added to the COG database include information pages with structural and functional details on each COG and literature references, improvements of the COGNITOR program that is used to fit new proteins into the COGs, and classification of genomes and COGs constructed by using principal component analysis. ------------------- Key: 4506 Medline: 20574756 Authors: Costanzo MC;Crawford ME;Hirschman JE;Kranz JE;Olsen P;Robertson LS;Skrzypek MS;Braun BR;Hopkins KL;Kondu P;Lengieza C;Lew-Smith JE;Tillberg M;Garrels JI Title: YPD, PombePD and WormPD: model organism volumes of the BioKnowledge Library, an integrated resource for protein information. Citation: Nucleic Acids Research 29: 75-79 2001 Type: ARTICLE Genes: Abstract: The BioKnowledge Library is a relational database and web site (http:www.proteome.com) composed of protein-specific information collected from the scientific literature. Each Protein Report on the web site summarizes and displays published information about a single protein, including its biochemical function, role in the cell and in the whole organism, localization, mutant phenotype and genetic interactions, regulation, domains and motifs, interactions with other proteins and other relevant data. This report describes four species-specific volumes of the BioKnowledge Library, concerned with the model organisms Saccharomyces cerevisiae (YPD), Schizosaccharomyces pombe (PombePD) and Caenorhabditis elegans (WormPD), and with the fungal pathogen Candida albicans (CalPD(TM)). Protein Reports of each species are unified in format, easily searchable and extensively cross-referenced between species. The relevance of these comprehensively curated resources to analysis of proteins in other species is discussed, and is illustrated by a survey of model organism proteins that have similarity to human proteins involved in disease. ------------------- Key: 4507 Medline: Authors: Hsieh J;Fire A Title: Recognition and silencing of repeated DNA. Citation: Annual Review of Genetics 34: 187-204 2000 Type: REVIEW Genes: mes-2 mes-3 mes-4 mes-6 mut-7 rde-2 rde-3 tam-1 Abstract: Mechanisms for repetition of DNA pose both opportunities and challenges to a functional genome: opportunities for increasing gene expression by amplification of useful sequences, and challenges of controlling amplification by unwanted sequences such as transposons and viruses. Experiments in numerous organisms have suggested the likely existence of a general mechanism for recognition of repeated character in DNA. This review focuses (a) on the nature of these recognition mechanisms, and (b) on types of chromatin modification and gene silencing that are used to control repeated DNA. ------------------- Key: 4508 Medline: 21103687 Authors: Hill E;Broadbent ID;Chothia C;Pettitt J Title: Cadherin superfamily proteins in Caenorhabditis elegans and Drosophila melanogaster. Citation: Journal of Molecular Biology 305: 1011-1024 2001 Type: ARTICLE Genes: cdh-1 cdh-3 cdh-4 cdh-5 cdh-6 cdh-7 cdh-8 cdh-9 cdh-10 cdh-11 cdh-12 hmr-1 Abstract: The ability to form selective cell-cell adhesions is an essential property of metazoan cells. Members of the cadherin superfamily are important regulators of this process in both vertebrates and invertebrates. With the advent of genome sequencing projects, determination of the full repertoire of cadherins available to an organism is possible and here we present the identification and analysis of the cadherin repertoires in the genomes of Caenorhabditis elegans and Drosophila melanogaster. Hidden Markov models of cadherin domains were matched to the protein sequences obtained from the translation of the predicted gene sequences. Matches were made to 21 C. elegans and 18 D. melanogaster sequences. Experimental and theoretical work on C. elegans sequences, and data from ESTs, show that three pairs of genes, and two triplets, should be merged to form five single genes. It also produced sequence changes at one or both of the 5' and 3' termini of half the sequences. Ln D. melanogaster it is probable that two of the cadherin genes should also be merged together and that three cadherin genes should be merged with other neighbouring genes. Of the 15 cadherin proteins found in C. elegans, 13 have the features of cell surface proteins, signal sequences and transmembrane helices; the other two have only signal sequences. Of the 17 in D. melanogaster, 11 at present have both features and another five have transmembrane helices. The evidence currently available suggests about one-third of the cadherins in the two organisms can be grouped into subfamilies in which all, or parts of, the molecules are conserved. Each organism also has a similar to 980 residue protein (CDH-11 and CG11059) with two cadherin domains and whose sequences match well over their entire length two proteins from human brain. Two proteins in C. elegans, HMR-1A and HMR-1B, and three in D. melanogaster, CadN, Shg and CG7527, have cytoplasmic domains homologous to those of the classical cadherin genes of chordates but their extracellular regions have different domain structures. Other common subclasses include the seven-helix membrane cadherins, Fat-like protocadherins and the Ret-like cadherins. At present, the remaining cadherins have no obvious similarities in their extracellular domain architecture or homologies to their cytoplasmic domains and may, therefore, represent species-specific or ------------------- Key: 4509 Medline: 11178279 Authors: Kamath RS;Martinez-Campos M;Zipperlen P;Fraser AG;Ahringer Title: Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans. Citation: Genome Biology 2: 1-10 2000 Type: ARTICLE Genes: apr-1 bir-1 ceh-6 cyk-1 dhc-1 dif-1 dnc-1 egl-27 gpb-1 hlh-2 mei-1 mex-3 pal-1 par-1 par-2 par-3 par-6 plk-1 rba-2 skn-1 unc-22 unc-37 Abstract: BACKGROUND: In Caenorhabditis elegans, injection of double-stranded RNA (dsRNA) results in the specific inactivation of genes containing homologous sequences, a technique termed RNA-mediated interference (RNAi). It has previously been shown that RNAi can also be achieved by feeding worms Escherichia coli expressing dsRNA corresponding to a specific gene; this mode of dsRNA introduction is conventionally considered to be less efficient than direct injection, however, and has therefore seen limited use, even though it is considerably less labor-intensive. RESULTS: Here we present an optimized feeding method that results in phenotypes at least as strong as those produced by direct injection of dsRNA for embryonic lethal genes, and stronger for genes with post-embryonic phenotypes. In addition, the interference effect generated by feeding can be titrated to uncover a series of hypomorphic phenotypes informative about the functions of a given gene. Using this method, we screened 86 random genes on consecutive cosmids and identified functions for 13 new genes. These included two genes producing an uncoordinated phenotype (a previously uncharacterized POU homeodomain gene, ceh-6, and a gene encoding a MADS-box protein) and one gene encoding a novel protein that results in a high-incidence-of-males phenotype. CONCLUSIONS: RNAi by feeding can provide significant information about the functions of an individual gene beyond that provided by injection. Moreover, it can be used for special applications for which injection or the use of mutants is sometimes impracticable (for example, titration, biochemistry and large-scale screening). Thus, RNAi by feeding should make possible new experimental approaches for the use of genomic sequence ------------------- Key: 4510 Medline: 21098744 Authors: Bossinger O;Klebes A;Segbert C;Theres C;Knust E Title: Zonula adherens formation in Caenorhabditis elegans requires dlg-1, the homologue of the Drosophila gene discs Citation: Developmental Biology 230: 29-42 2001 Type: ARTICLE Genes: crb-1 crl-1 dlg-1 hmp-1 hmp-2 hmr-1 let-413 mnDf41 Abstract: The correct assembly of junction components, such as E-cadherin and beta -catenin, into the zonula adherens is fundamental for the function of epithelia, both in flies and in vertebrates. In C. elegans, however, the cadherin-catenin system is not essential for general adhesion, raising the question as to the genetic basis controlling junction morphogenesis in nematodes. Here we show that dlg-1, the C. elegans homologue of the Drosophila tumour-suppressor gene discs-large, plays a crucial role in epithelial development. DLG-1 is restricted to adherens junctions of all embryonic epithelia, which contrasts with the localisation of the Drosophila and vertebrate homologues in septate and tight junctions, respectively. Proper localisation of DLG-1 requires the basolateral LET-413 protein, but is independent of the cadherin-catenin system. Embryos in which dlg-1 activity was eliminated by RNA-mediated interference fail to form a continuous belt of junction-associated antigens and arrest development. Loss of dlg-1 activity differentially affects localisation of proteins normally enriched apically to the zonula adherens. While the distribution of an atypical protein kinase C (PKC-3) and other cytoplasmic proteins (PAR-3, PAR-6) is not affected in dlg-1 (RNAi) embryos, the transmembrane protein encoded by crb-1, the C. elegans homologue of Drosophila crumbs, is no longer concentrated in this domain. In contrast to Drosophila, however, crb-1 and a second crb-like gene are not essential for epithelial development in C. elegans. Together the data indicate that several aspects of the spatial organisation of epithelial cells and its genetic control differ between flies, worms, and vertebrates, while others are conserved. The molecular nature of DLG-1 makes it a likely candidate to participate in the organisation of a protein scaffold that controls the assembly of junction components into the zonula adherens. ------------------- Key: 4511 Medline: 11136229 Authors: Jonassen T;Larsen PL;Clarke CF Title: A dietary source of coenzyme Q is essential for growth of long-lived Caenorhabditis elegans clk-1 mutants. Citation: Proceedings of the National Academy of Sciences USA 98: 421-426 2001 Type: ARTICLE Genes: clk-1 daf-2 Abstract: Mutations in the clk-1 gene of the nematode Caenorhabditis elegans result in slowed development, sluggish adult behaviors, and an increased lifespan. CLK-1 is a mitochondrial polypeptide with sequence and functional conservation from human to yeast. Coq7p, the Saccharomyces cerevisiae homologue, is essential for ubiquinone (coenzyme Q or Q) synthesis and therefore respiration. However, based on assays of respiratory function, it has been reported that the primary defect in the C. elegans clk-1 mutants is not in Q biosynthesis. How do the clk-1 mutant worms have essentially normal rates of respiration, when biochemical studies in yeast suggest a Q deficiency? Nematodes are routinely fed Escherichia coli strains containing a rich supply of Q. To study the Q synthesized by C. elegans, we cultured worms on an E. coli mutant that lacks Q and found that clk-1 mutants display early developmental arrest from eggs, or sterility emerging from dauer stage. Provision of Q-replete E. coli rescues these defects. Lipid analysis showed that clk-1 worms lack the nematode Qs isoform and instead contain a large amount of a metabolite that is slightly more polar than Qs. The clk-1 mutants also have increased levels of Qs, the E, coli isoform, and rhodoquinone-9. These results show that the clk-1 mutations result in Q auxotrophy evident only when Q is removed from the diet, and that the aging and developmental phenotypes previously described are consistent with altered Q levels and distribution. ------------------- Key: 4512 Medline: 11175356 Authors: Hart AH;Reventar R;Bernstein A Title: Genetic analysis of ETS genes in C. elegans. Citation: Oncogene 19: 6400-6408 2000 Type: ARTICLE Genes: let-23 let-60 mek-2 mpk-1 sem-5 unc-130 Abstract: The recent completion of the Caenorhabditis elegans genome has revealed that this nematode worm has 10 members of the ETS gene family. Isolation and analysis of C. elegans mutants and subsequent screens to identify interacting genes can proceed very quickly in this model organism. Molecular genetic analysis of the receptor tyrosine kinase-Ras-MAP kinase signaling pathway in C. elegans identified the ETS family transcription factor Lin-1 as a nuclear effector of this evolutionarily conserved signal transduction pathway. Here we review classical genetic approaches used to discover the role of Lin-1 in the Ras-MAP kinase signaling pathway and describe new technologies that can be applied to the analyses of signaling pathways and transcription factor regulatory ------------------- Key: 4513 Medline: 21082086 Authors: Grill SW;Gonczy P;Stelzer EHK;Hyman AA Title: Polarity controls forces governing asymmetric spindle positioning in the Caenorhabditis elegans embryo. Citation: Nature 409: 630-633 2001 Type: ARTICLE Genes: par-2 par-3 Abstract: Cell divisions that create daughter cells of different sizes are crucial for the generation of cell diversity during animal development(1). In such asymmetric divisions, the mitotic spindle must be asymmetrically positioned at the end of anaphase(2,3). The mechanisms by which cell polarity translates to asymmetric spindle positioning remain unclear. Here we examine the nature of the forces governing asymmetric spindle positioning in the single-cell-stage Caenorhabditis elegans embryo. To reveal the forces that act on each spindle pole, we removed the central spindle in living embryos either physically with an ultraviolet laser microbeam, or genetically by RNA-mediated interference of a kinesin(4). We show that pulling forces external to the spindle act on the two spindle poles. A stronger net force acts on the posterior pole, thereby explaining the overall posterior displacement seen in wild-type embryos. We also show that the net force acting on each spindle pole is under control of the par genes that are required for cell polarity along the anterior-posterior embryonic axis. Finally, we discuss simple mathematical models that describe the main features of spindle pole behaviour. Our work suggests a mechanism for generating asymmetry in spindle positioning by varying the net pulling force that acts on each spindle pole, thus allowing for the generation of daughter cells with different sizes. ------------------- Key: 4514 Medline: 21106309 Authors: Xiao GQ;Wang J;Tangen T;Giacomini KM Title: A novel proton-dependent nucleoside transporter, CeCNT3, from Caenorhabditis elegans. Citation: Molecular Pharmacology 59: 339-348 2001 Type: ARTICLE Genes: Abstract: In this study, we describe the cloning and characterization of a proton-dependent, broadly selective nucleoside transporter from Caenorhabditis elegans. Recently, we constructed a broadly selective nucleoside transporter which accepts both purine and pyrimidine nucleosides. Based on these studies, we hypothesized that CNTs with novel substrate selectivities exist in nature and that a CNT homolog in the C. elegans genomic database may function as a broadly selective nucleoside transporter. We cloned the cDNA for this transporter, termed CeCNT3 because of its broad selectivity, using polymerase chain reaction-based methods. CeCNT3 is predicted to have 575 amino acid residues (63.4 kDa) with 11 to 14 putative transmembrane domains and exhibits similar to 30% identity to members of the mammalian CNT family. This transporter exhibits a novel substrate selectivity, transporting a wide range of purine and pyrimidine nucleosides (inosine, guanosine, adenosine, uridine, and thymidine) but not cytidine. The apparent K-m values for inosine and thymidine are 15.2 +/- 5.3 muM and 11.0 +/- 2.4 muM, respectively. Kinetic studies demonstrate that purine and pyrimidine nucleosides share a common recognition site in the transporter. In contrast to all known members of the mammalian CNT family, CeCNT3-mediated transport of nucleosides is proton-, but not sodium-, dependent. Mutation of tyrosine 332 in CeCNT3 decreased both the maximum uptake rate and apparent K-m of thymidine, suggesting that this residue is in the domain of nucleoside recognition and translocation. The broad nucleoside specificity of CeCNT3 may be explained by this and other residues that restrict purine and pyrimidine nucleoside uptake and that discriminate among pyrimidine nucleosides. ------------------- Key: 4515 Medline: Authors: Fitch DHA Title: Evolution of "Rhabditidae" and the male tail. Citation: Journal of Nematology 32: 235-244 2000 Type: ARTICLE Genes: Abstract: Evolution of diverse male tail epidermal features of representative species in the family Rhabditidae (Nematoda:Rhabditida) was mapped by parsimony on a molecular phylogeny inferred with nearly complete DNA sequences of small subunit ribosomal RNA genes. Although the molecular phylogeny is consistent with some previously proposed relationships, there are also some major differences, suggesting a revision of rhabditid taxonomy is required. To reconstruct male tail evolution, character states and homologies were determined with the aid of developmental profiling at the level of single cells. Because the model genetic system Caenorhabditis elegans is a member of Rhabditidae and allows the genetic and developmental mechanisms of morphogenesis to be elucidated, candidate genes and pathways can be proposed for several of the reconstructed evolutionary changes in male tail ------------------- Key: 4516 Medline: 21038585 Authors: Gems D Title: An integrated theory of ageing in the nematode Caenorhabditis elegans. Citation: Journal of Anatomy 197: 521-528 2000 Type: ARTICLE Genes: age-1 clk-1 ctl-1 daf-2 eat-2 mev-1 Abstract: Numerous theories of ageing have been proposed, and many have been tested experimentally, particularly using nematode models such as Caenorhabditis elegans. By combining those theories of ageing that remain plausible with recent findings from studies of C. elegans life span mutants, an integrated theory of ageing has been devised. This is formed from 3 interconnected elements: the evolutionary theory of ageing, the oxidative damage theory of ageing, and a nonadaptive programmed ageing theory. This tripartite theory of ageing gives rise to a number of predictions that may be tested experimentally. ------------------- Key: 4517 Medline: 11122376 Authors: Yoda A;Sawa H;Okano H Title: MSI-1, a neural RNA-binding protein, is involved in male mating behaviour in Caenorhabditis elegans. Citation: Genes to Cells 5: 885-895 2000 Type: ARTICLE Genes: cat-4 him-5 msi-1 Abstract: Background: Neural RNA-binding proteins are thought to play important roles in neural development and the functional regulation of postmitotic neurones by mediating post-transcriptional gene regulation. RNA-binding proteins belonging to the Musashi family are highly expressed in the nervous system; however, their roles are poorly understood. Results: We identified a Caenorhabditis elegans Musashi homologue, MSI-1, whose RNA-recognition motifs show extensive similarity to those of Drosphila and vertebrate Musashi proteins. We isolated a msi-1 mutant and found males with this mutation to have a mating defect. C. elegans male mating behaviour includes a distinct series of steps: response to contact, backing, turning, vulva location, spicule insertion, and sperm transfer. msi-l is required for the turning and vulva location steps. Like other Musashi family members, MSI-1 is expressed specifically in neural cells, including male-specific neurones required for turning and vulva location. However, msi-1 was not expressed in proliferating neural progenitors in C. elegans, unlike the Musashi family genes in other systems. Conclusions: Our results suggest that msi-l is expressed specifically in postmitotic neurones in C. elegans. msi-1 is required for full development of male mating behaviour, possibly through regulation of msi-1 ------------------- Key: 4518 Medline: 11206415 Authors: Cai T;Krause MW;Odenwald WF;Toyama R;Notkins AL Title: The IA-2 gene family: homologs in Caenorhabditis elegans, Drosophila and zebrafish. Citation: Diabetologia 44: 81-88 2001 Type: ARTICLE Genes: ida-1 Abstract: Aims/hypothesis. IA-2 and IA-2 beta are major autoantigens in Type I (insulin-dependent) diabetes mellitus and are expressed in neuroendocrine tissues including the brain and pancreatic islets of Langerhans. Based on sequence analysis, IA-2 and IA-2 beta are transmembrane protein tyrosine phosphatases but lack phosphatase activity because of critical amino acid substitutions in the catalytic domain. We studied the evolutionary conservation of IA-2 and IA-2 beta genes and searched for homologs in non-mammalian vertebrates and invertebrates. Methods. IA-2 from various species was identified from EST sequences or cloned from cDNA libraries or both. Expression in tissues was determined by transfection and in situ hybridization. Results. We identified homologs of IA-2 in C, elegans, Drosophila, and zebrafish which showed 46, 58 and 82% identity and 60, 65 and 87 % similarity, respectively, to the amino acids of the intracellular domain of human IA-2. Further studies showed that IA-2 was expressed in the neural tissues of the three species. Comparison of the genomic structure of the intracellular domain of human IA-2 with that of human IA-2 beta showed that they were nearly identical and comparison of the intron-exon boundaries of Drosophila IA-2 with human IA-2 and IA-2 beta showed a high degree of relatedness. Conclusion/Interpretation. Based on these findings and sequence analysis of IA-2 homologs in mammals, we conclude that there is an IA-2 gene family which is a part of the larger protein tyrosine phosphatase superfamily. The IA-2 and IA-2 beta genes represent two distinct subgroups within the IA-2 family which originated over 500 million years ago, long before the development of the pancreatic islets of Langerhans. ------------------- Key: 4519 Medline: 21094570 Authors: Doe CQ;Bowerman B Title: Asymmetric cell division: fly neuroblast meets worm zygote. Citation: Current Opinion in Cell Biology 13: 68-75 2001 Type: REVIEW Genes: mex-5 mex-6 mlc-4 nmy-2 par-1 par-2 par-3 par-4 par-6 pie-1 pkc-3 pod-1 Abstract: Both Drosophila neuroblasts and Caenorhabditis elegans zygotes use a conserved protein complex to establish cell polarity and regulate spindle orientation. Mammalian epithelia also use this complex to regulate apical/basal polarity. Recent results have allowed us to compare the mechanisms regulating asymmetric cell division in Drosophila neuroblasts and the C. elegans zygote. ------------------- Key: 4520 Medline: 21100341 Authors: Rudel D;Kimble J Title: Conservation of glp-1 regulation and function in nematodes. Citation: Genetics 157: 639-654 2001 Type: ARTICLE Genes: glp-1 lin-12 Abstract: The Caenorhabditis elegans (Ce) glp-1 gene encodes a Notch-like receptor. We have cloned glp-1 from C. briggsae (Cb) and C. remanei (Cr), two Caenorhabditis species that have diverged from C. elegans by roughly 20-40 million years. By sequence analysis, we find that the Cb-GLP-1 and Cr-GLP-1 proteins have retained the same motif architecture as Ce-GLP-1, including number of domains. In addition, two regions (CC-linker and regions flanking the ANK repeats) are as highly conserved as regions previously recognized as essential for signaling (e.g., ANK repeats). Phylogenetic analysis of glp-1 sequences suggests a C. briggsae/C. remanei clade with C. elegans as a sister taxon. Using RNAi to test biological functions, we find that Ce-glp-1, Cb-glp-1, and Cr-glp-1 are all required for proliferation of germline stem cells and for specifying blastomere fates in the embryo. In addition, certain biological roles of Cb-glp-1, e.g., in the vulva, have diverged from those of Ce-glp-1 and Cr-glp-1, suggesting a change in either regulation or function of the Cb-glp-1 gene during evolution. Finally, the regulation of glp-1 mRNA, previously analyzed for Ce-glp-1, is conserved in Cb-glp-1, and we identify conserved 3' UTR sequences that may serve as regulatory elements. ------------------- Key: 4521 Medline: 21098746 Authors: Miskowski J;Li Y;Kimble J Title: The sys-1 gene and sexual dimorphism during gonadogenesis in Caenorhabditis elegans. Citation: Developmental Biology 230: 61-73 2001 Type: ARTICLE Genes: lag-2 sys-1 qDf5 qDf14 Abstract: In wild-type Caenorhabditis elegans, the hermaphrodite gonad is a symmetrical structure, whereas the male gonad is asymmetric. Two cellular processes are critical for the generation of these sexually dimorphic gonadal shapes during early larval development. First, regulatory "leader" cells that control tube extension and gonadal shape are generated. Second, the somatic gonadal precursor cells migrate and become rearranged to establish the adult pattern. In this paper, we introduce sys-1, a gene required for early organization of the hermaphrodite, but not the male, gonad. The sys-1(q544) allele behaves genetically as a strong loss-of-function mutant and putative null. All hermaphrodites that are homozygous for sys-1(q544) possess a grossly malformed gonad and are sterile; in contrast, sys-1(q544) males exhibit much later and only partially penetrant gonadal defects. The sys-1(q544) hermaphrodites exhibit two striking early gonadal defects. First, the cell lineages of Z1 and Z4, the somatic gonadal progenitor cells, produce extra cells during L2, but the regulatory cells that control gonadal shape are not generated. Second, somatic gonadal precursor cells do not cluster centrally during late L2, and the somatic gonadal primordium typical of hermaphrodites is not established. In contrast, the early male gonadal lineage is asymmetric as normal, the somatic gonadal primordium typical of males is established correctly, and the male adult gonadal structures can be normal. We conclude that the primary role of sys-1 is to establish the shape and polarity of the hermaphrodite ------------------- Key: 4522 Medline: Authors: Siklos S;Jasper JA;Wicks SR;Rankin CH Title: Interactions between an endogenous oscillator and response to tap in C. elegans. Citation: Psychobiology 28: 571-580 2000 Type: ARTICLE Genes: Abstract: In this study, we investigated the interaction between the endogenous oscillator governing defecation in Caenorhabditis elegans and the worm's response to a mechanical stimulus, a tap. The results showed that the defecation cycle became progressively longer over the life span of the worm. Taps changed the phase of the defecation cycle, and taps delivered at different phases of the defecation cycle had significantly different effects on the phase change observed. In contrast, the phase of the defecation cycle in which the tap was delivered had very Little effect on either the frequency or the magnitude of the response to the tap. The phase change by the taps habituated slowly over multiple taps. There was no effect of tap delivery at a consistent phase of the defecation cycle; therefore, interaction between tap and defecation cannot account for much of the variance seen in a normal ------------------- Key: 4523 Medline: 21094513 Authors: Crump JG;Zhen M;Jin Y;Bargmann CI Title: The SAD-1 kinase regulates presynaptic vesicle clustering and axon termination. Citation: Neuron 29: 115-129 2001 Type: ARTICLE Genes: daf-7 par-1 rpm-1 sad-1 sad-2 sad-3 smg-3 snb-1 snt-1 syd-2 unc-11 unc-31 unc-33 unc-43 unc-51 unc-104 unc-115 Abstract: During synapse formation, presynaptic axon outgrowth is terminated, presynaptic clusters of vesicles are associated with active zone proteins, and active zones are aligned with postsynaptic neurotransmitter receptors. We report here the identification of a novel serine/threonine kinase, SAD-1,that regulates several aspects of presynaptic differentiation in C. elegans. In sad-1 mutant animals presynaptic vesicle clusters in sensory neurons and motor neurons are diffuse and disorganized. Sensory axons fail to terminate in sad-1 mutants, whereas overexpression of SAD-1 causes sensory axons to terminate prematurely. SAD-1 protein is expressed in the nervous system and localizes to synapse-rich regions of the axons. SAD-1 is related to PAR-1, a kinase that regulates cell polarity during asymmetric cell division. Overexpression of SAD-1 causes mislocalization of vesicle proteins to dendrites, suggesting that sad-1 affects axonal-dendritic polarity as well as synaptic development. ------------------- Key: 4524 Medline: 21106358 Authors: Huang T;Kuersten S;Deshpande AM;Spieth J;MacMorris M;Blumenthal T Title: Intercistronic region required for polycistronic pre-mRNA processing in Caenorhabditis elegans. Citation: Molecular and Cellular Biology 21: 1111-1120 2001 Type: ARTICLE Genes: cyp-9 gpd-2 gpd-3 lin-26 lir-1 lir-2 mai-1 pdi-1 ppp-1 rpl-29 rpp-1 tra-2 Abstract: In Caenorhabditis elegans, polycistronic pre-mRNAs are processed by cleavage and polyadenylation at the 3' ends of the upstream genes and trans splicing, generally to the specialized spliced leader SL2, at the 5' ends of the downstream genes. Previous studies have indicated a relationship between these two events in the processing of a heat. shock-induced gpd-2-gpd-3 polycistronic pre-mRNA, Here, we report mutational analysis of the intercistronic region of this operon by linker scan analysis, Surprisingly, no sequences downstream of the 3' end were important for 3'-end formation. In contrast, a U-rich (Ur) element located 29 bp downstream of the site of 3'-end formation was shown to be important for downstream mRNA biosynthesis. This similar to 20-bp element is sufficient for SL2 trans splicing and mRNA accumulation when transplanted to a heterologous context. Furthermore, when the downstream gene was replaced by a gene from another organism, no loss of trans-splicing specificity was observed, suggesting that the Ur element may be the primary signal required for downstream mRNA processing. ------------------- Key: 4525 Medline: 21106378 Authors: Oishi I;Iwai K;Kagohashi Y;Fujimoto H;Kariya K;Kataoka T;Sawa H;Okano H;Otani H;Yamamura H;Minami Y Title: Critical role of Caenorhabditis elegans homologs of Cds1 (Chk2)-related kinases in meiotic recombination. Citation: Molecular and Cellular Biology 21: 1329-1335 2001 Type: ARTICLE Genes: dpy-6 dpy-18 glp-1 unc-3 unc-25 unc-54 Abstract: Although chromosomal segregation at meiosis I is the critical process for genetic reassortment and inheritance, little is known about molecules involved in this process in metazoa. Here we show by utilizing double-stranded RNA (dsRNA)-mediated genetic interference that novel protein kinases (Ce-CDS-1 and Ce-CDS-2) related to Cds1 (Chk2) play an essential role in meiotic recombination in Caenorhabditis elegans. Injection of dsRNA into adult animals resulted in the inhibition of meiotic crossing over and induced the loss of chiasmata at diakinesis in oocytes of F-1 animals. However, electron microscopic analysis revealed that synaptonemal complex formation in pachytene nuclei of the same progeny of injected animals appeared to be normal. Thus, Ce-CDS-1 and Ce-CDS-2 are the first example of Cds1-related kinases that are required for meiotic recombination in multicellular organisms. ------------------- Key: 4526 Medline: 21077042 Authors: Thatcher JD;Fernandez AP;Beaster-Jones L;Haun C;Okkema PG Title: The Caenorhabditis elegans peb-1 gene encodes a novel DNA-binding protein involved in morphogenesis of the pharynx, vulva, and hindgut. Citation: Developmental Biology 229: 480-493 2001 Type: ARTICLE Genes: peb-1 pha-4 Abstract: Gene expression in the Caenorhabditis elegans pharynx is regulated in part by organ-specific signals, which in the myo-2 gene target a regulatory sequence called the C subelement. C subelement activity requires the organ specification factor PHA-4 a winged-helix transcription factor expressed in all pharyngeal cells. To identify additional factors involved in pharyngeal organogenesis, we performed a yeast one-hybrid screen for C subelement binding proteins. Here we describe the novel factor FEB-I, which is coexpressed with PHA-4 in many pharyngeal cell types, including muscles, epithelial cells, marginal cells, and glands, but is undetectable in the pharyngeal nervous system. PEB-1 is also detected outside the pharynx in cells surrounding the rectum and vulva, as well as in the germ line. Reduction of peb-1 function using RNAi results in morphological defects in the somatic tissues in which peb-1 is expressed. We have mapped the FEB-I DNA-binding domain to a 158-residue region, which is unrelated to known DNA-binding proteins but shares some sequence similarity to the Drosophila Mod(mdg4) proteins. FEB-I specifically recognizes a site in the C subelement that partially overlaps the PHA-4 binding site. Both the PEB-1 and the PHA-4 binding sites are necessary for strong C subelement enhancer activity in some cells iu which these factors are coexpressed. In contrast the FEB-I site is dispensable for C subelement activity in pharyngeal neurons. We propose that PEB-1 functions with PHA-4 to activate target gene expression in cells in which they are coexpressed. ------------------- Key: 4527 Medline: 21067400 Authors: Jin SW;Kimble J;Ellis RE Title: Regulation of cell fate in Caenorhabditis elegans by a novel cytoplasmic polyadenylation element binding protein. Citation: Developmental Biology 229: 537-553 2001 Type: ARTICLE Genes: fem-3 fog-1 glp-4 qDf3 qDf4 Abstract: The fog-1 gene of Caenorhabditis elegans specifies that germ cells differentiate as sperm rather than as oocytes. We cloned fog-1 through a combination of transformation rescue experiments, RNA-mediated inactivation, and mutant analyses. Our results show that fog-1 produces two transcripts, both of which are found in germ cells but not in the soma. Furthermore, two deletion mutants alter these transcripts and are likely to eliminate fog-1 activity. The larger transcript is expressed under the control of sex-determination genes, is necessary for fog-1 activity, and is sufficient to rescue a fog-1 mutant. This transcript encodes a novel member of the CPEB family of RNA-binding proteins. Because CPEB proteins in Xenopus and Drosophila regulate gene expression at the level of translation, we propose that FOG-1 controls germ cell fates by regulating the translation of specific messenger RNAs. ------------------- Key: 4528 Medline: 11708211 Authors: Gems D Title: Longevity and ageing in parasitic and free-living Citation: Biogerontology 1: 289-307 2001 Type: REVIEW Genes: Abstract: In the developing field of biological gerontology, rapid advances have recently been made in the genetics of ageing in the nematode Caenorhabditis elegans. The aim of this work is to develop an understanding of the general mechanisms determining the ageing process. Within the last decade the prospect of actually achieving this somewhat hubristic aim has begun to look startlingly real. In this context, knowledge of every aspect of the biology of ageing in nematodes is of added interest. Here the patterns of ageing observed among parasitic and free-living nematodes are surveyed and compared. Like insects, nematode species exhibit enormous differences in the rate of ageing, with maximum life spans varying over more than a 1000-fold range, from three days in free-living Rhabdias bufonis adults, to at least 15 years in the filarial parasite Loa loa. The possible evolutionary and mechanistic causes of such differences in ageing are discussed. ------------------- Key: 4529 Medline: 21108871 Authors: Sprengel R;Aronoff R;Volkner M;Schmitt B;Mosbach R;Kuner T Title: Glutamate receptor channel signatures. Citation: Trends in Pharmacological Sciences 22: 7-10 2001 Type: REVIEW Genes: glr-1 glr-2 glr-3 glr-4 glr-5 glr-6 nmr-1 nmr-2 Abstract: Genes encoding glutamate receptor channel subunits were identified in genomes from Drosophila melanogaster and Caenorhabditis elegans by homology search with amino acid sequences that participate in the conserved channel pore. The predicted sequences of the putative glutamate receptor subunits revealed a distinct channel pore signature for each receptor subtype and for most of them, related members were found in C. elegans and Drosophila. ------------------- Key: 4530 Medline: Authors: Yu L;Gaitatzes C;Neer E;Smith TF Title: Thirty-plus functional families from a single motif. Citation: Protein Science 9: 2470-2476 2001 Type: ARTICLE Genes: Abstract: It is now possible to identify over 30 functional subfamilies among the WD-repeat-containing proteins found in the completed genomes. The majority of these subfamilies have at least one member for which experimental data allow assignment to a cellular pathway or process. Half of the 63 WD-repeat-containing proteins in Saccharomyces cerevisiae, half of the 70 in Caenorhabditis elegans, and a third of the 100 plus predicted in Drosophila can be assigned to 23 of these functional subfamilies. Perhaps indicative of the future, 33 WD-repeat-containing proteins from the partial genome of Arabidopsis thaliana can now be assigned to 18 of these subfamilies. These assignments have been made possible by combining traditional sequence similarity with an implied common beta propeller structural context to obtain measures of protein-protein surface similarity. The beta propeller structural context is represented in the form of a Hidden Markov Model. The procedure is completely ------------------- Key: 4531 Medline: 21199842 Authors: Momin RA;Nair MG Title: Mosquitocidal, nematicidal, and antifungal compounds from Apium graveolens L. seeds. Citation: Journal of Agricultural & Food Science 49: 142-145 2001 Type: ARTICLE Genes: Abstract: The methanolic extract of Apium graveolens seeds was investigated for bioactive compounds and resulted in the isolation and characterization of mosquitocidal, nematicidal, and antifungal compounds sedanolide (1), senkyunolide-N (2), and senkyunolide-J (3). Their structures were determined by IH and C-13 NMR spectral methods. Compounds 1-3 gave 100% mortality at 25, 100, and 100 mug mL(-1), respectively, on the nematode, Panagrellus redivivus. Compound 1 showed 100% mortality at 50 mug mL(-1) on nematode, Caenorhabditis elegans, and fourth-instar mosquito larvae, Aedes aegyptii. Also, it inhibited the growth of Candida albicans and Candida. parapsilasis at 100 mug mL(-1). Compounds 2 and 3 were isolated for the first time from A. graveolens. This is the first report of the mosquitocidal, nematicidal, and antifungal activities of compounds 1-3. ------------------- Key: 4532 Medline: Authors: Thomas GH Title: Spectrin: the ghost in the machine. Citation: BioEssays 23: 152-160 2001 Type: REVIEW Genes: sma-1 spc-1 unc-70 Abstract: It has long been speculated that spectrin, the actin crosslinking and molecular scaffold protein, is involved in the development of apicobasal polarity in epithelia. While spectrins can undoubtedly influence the protein content of specific membrane domains, recent genetic evidence indicates that this activity is not necessary for the establishment or maintenance of this axis. Instead, these studies point to critical roles in tissue stability and morphogenesis. A possible role in cellular contractility is highlighted in this review. ------------------- Key: 4533 Medline: Authors: Hoss S;Bergtold M;Haitzer M;Traunspurger W;Steinberg CE Title: Refractory dissolved organic matter can influence the reproduction of Caenorhabditis elegans (Nematoda). Citation: Freshwater Biology 46: 1-10 2001 Type: ARTICLE Genes: Abstract: 1. We investigated the effect of refractory dissolved organic matter (refractory DOM: fulvic acids (FAs) and ultrafiltrates (UFs)), isolated from five different sources, on the reproduction of the bacterivorous nematode Caenorhabditis elegans. Nematodes were exposed to DOM (0.5-64 mg L-1 dissolved organic carbon) during a whole life cycle (72 h). At the end of the test, the number of offspring per worm was determined. 2. We also studied the effect of refractory DOM on abundance, cell size, and activity of the bacteria (Escherichia coli) that were used as a food source for the nematodes, to assess possible indirect effects of DOM via the food organisms. 3. The effects of DOM on the reproduction of C. elegans varied, depending on the origin and concentration of DOM. FAs isolated from a soil leachate and from the effluent of a waste water plant, as well as UFs from a humic lake and from a marsh, stimulated the reproduction of C. elegans. FAs from ground water had no effect, while FAs from a humic lake inhibited the reproduction of the nematodes. All effects occurred at ecologically relevant DOM concentrations and showed clear dose-response relationships. 4. Neither bacterial abundance nor cell size were influenced by refractory DOM. Bacterial activity was unaffected by four types of DOM. Only FAs from the humic lake caused a significant decrease in bacterial activity over 72 h. 5. The negative effect of FAs from the humic lake on nematode reproduction may be a consequence of a lower bacterial activity in this treatment. The positive effects of refractory DOM, however, could not be related to bacterial parameters. Therefore, we assume that the DOM directly influenced the reproduction of C. elegans. We speculate that refractory DOM can potentially be an additional carbon source or a source of trace nutrients influencing the reproduction of C. elegans. Adsorption of refractory DOM on bacterial cells, serving as food for the nematodes, may have been an important factor for the availability of DOM for C. elegans. ------------------- Key: 4534 Medline: 21064445 Authors: Jungblut B;Sommer RJ Title: The nematode even-skipped homolog vab-7 regulates gonad and vulva position in Pristionchus pacificus. Citation: Development 128: 253-261 2001 Type: ARTICLE Genes: vab-7 Abstract: In free-living nematodes, developmental processes like the formation of the vulva, can be studied at a cellular level. Cell lineage and ablation studies have been carried out in various nematode species and multiple changes in vulval patterning have been identified. In Pristionchus pacificus, vulva formation differs from Caenorhabditis elegans with respect to several autonomous and conditional aspects of cell fate specification. To understand the molecular basis of these evolutionary changes, we have performed a genetic analysis of vulva formation in I! pacificus. Here, we describe two mutants where the vulva is shifted posteriorly, affecting which precursor cells will form vulval tissue in P! pacificus. Mutant animals show a concomitant posterior displacement of the gonadal anchor cell, indicating that the gonad and the vulva are affected in a similar way. We show that mutations in the even-skipped homolog of nematodes, vab-7, cause these posterior displacements. In addition, cell ablation studies in the vab-7 mutant indicate that the altered position of the gonad not only changes the cell fate pattern but also the developmental competence of vulval precursor cells. Investigation of Cel-vab-7 mutant animals showed a similar but weaker vulva defective phenotype to the one described ------------------- Key: 4535 Medline: Authors: Jung S-K;Ahnn JH Title: Genetic analysis of jh2 mutation near the unc-29 locus of chromosome I in Caenorhabditis elegans. Citation: Korean Journal of Genetics 22: 331-340 2000 Type: ARTICLE Genes: dpy-5 fog-3 lin-11 unc-13 unc-29 nDf29 Abstract: Six lethal mutations near the unc-29 locus on chromosome I of Caenorhabditis elegans have been isolated previously. Among these mutants, one particular mutant (jh2) showed interesting terminal defect, which suggest that embryos of this mutant suffer specific defects in posterior body parts during early development. As the first step to further characterize the mutation, we have performed genetic outcrossing using three genetic markers of dpy-5(e61), dpy-5(e61 unc-13(e1091), unc-13(e1091) lin-11(n566) in the gene cluster region near the unc-29 locus. Following outcrosses, three-factor crosses were conducted to place the jh2 mutation on a precise genetic map near the unc-29 locus on chromosome I. The results of three-factor crosses have placed the jh2 mutation to the region between 4.41 and 4.54 map unit right from the center of chromosome I, which corresponds to approximately a 200 kb region in the physical map. ------------------- Key: 4536 Medline: 21113170 Authors: Harrison PM;Echols N;Gerstein MB Title: Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome. Citation: Nucleic Acids Research 29: 818-830 2001 Type: ARTICLE Genes: Abstract: Pseudogenes are non-functioning copies of genes in genomic DNA, which may either result from reverse transcription from an mRNA transcript (processed pseudogenes) or from gene duplication and subsequent disablement (non-processed pseudogenes). As pseudogenes are apparently 'dead', they usually have a variety of obvious disablements (e.g., insertions, deletions, frameshifts and truncations) relative to their functioning homologs. We have derived an initial estimate of the size, distribution and characteristics of the pseudogene population in the Caenorhabditis elegans genome, performing a survey in 'molecular archaeology'. Corresponding to the 18 576 annotated proteins in the worm (i.e., in Wormpep18), we have found an estimated total of 2168 pseudogenes, about one for every eight genes. Few of these appear to be processed. Details of our pseudogene assignments are available from http://bioinfo. mbb.yale.edu/genome/worm/pseudogene. The population of pseudogenes differs significantly from that of genes in a number of respects: (i) pseudogenes are distributed unevenly across the genome relative to genes, with a disproportionate number on chromosome IV; (ii) the density of pseudogenes is higher on the arms of the chromosomes; (iii) the amino acid composition of pseudogenes is midway between that of genes and (translations of) random intergenic DNA, with enrichment of Phe, lie, Leu and Lys, and depletion of Asp, Ale, Glu and Gly relative to the worm proteome; and (iv) the most common protein folds and families differ somewhat between genes and pseudogenes-whereas the most common fold found in the worm proteome is the immunoglobulin fold and the most common 'pseudofold' is the C-type lectin. In addition, the size of a gene family bears little overall relationship to the size of its corresponding pseudogene complement, indicating a highly dynamic genome. There are in fact a number of families associated with large populations of pseudogenes. For example, one family of seven-transmembrane receptors (represented by gene B0334.7) has one pseudogene for every four genes, and another uncharacterized family (represented by gene B0403.1) is approximately two-thirds pseudogenic. ------------------- Key: 4537 Medline: 11058602 Authors: Arata Y;Hirabayashi J;Kasai K Title: Sugar-binding properties of the two lectin domains of the tandem repeat-type galectin LEC-1 (N32) of Caenorhabditis elegans. Citation: Journal of Biological Chemistry 276: 3068-3077 2001 Type: ARTICLE Genes: Abstract: The 32-kDa galectin (LEC-1 or N32) of the nematode Caenorhabditis elegans is the first example of a tandem repeat-type galectin and is composed of two domains, each of which is homologous to typical vertebrate 14kDa-type galectins. To elucidate the biological meaning of this unique structure containing two probable sugar binding sites in one molecule, we analyzed in detail the sugar binding properties of the two domains by using a newly improved frontal affinity chromatography system. The whole molecule (LEC-1), the N-terminal lectin domain (Nh), and the C-terminal lectin domain (Ch) were expressed in Escherichia coli, purified, and immobilized on HiTrap gel agarose columns, and the extent of retardation of various sugars by the columns was measured. To raise the sensitivity of the system, we used 35 different fluorescence-labeled oligosaccharides (pyridylaminated (PA) sugars). All immobilized proteins showed affinity for N-acetyllactosamine-containing N-linked complex-type sugar chains, and the binding was stronger for more branched sugars. Ch showed 2-5-fold stronger binding toward all complex-type sugars compared with Nh. Both Nh and Oh preferred Gal beta1-3GlcNAc to Gal beta1-4GlcNAc. Because the Fuc alphal-2Gal beta1-3GlcNAc (H antigen) structure was found to interact with all immobilized protein columns significantly, the K-d value of pentasaccharide Fuc alpha1-2Gal beta1-3GlcNAc beta1-3Gal beta1-4Glc-PA for each column was determined by analyzing the concentration dependence. Obtained values for immobilized LEC-1, Nh, and Ch were 6.0 x 10(-5), 1.3 x 10(-4), and 6.5 x 10(-5) M, respectively. The most significant difference between Nh and Oh was in their affinity for GalNAc alpha1-3 (Fuc alpha1-2) Gal beta1-3GlcNAc beta1-3Gal beta1-4Glc-PA, which contains the blood group A antigen; the K-d value for immobilized Nh was 4.8 x 10(-5) M, and that for Ch was 8.1 x 10(-4) M. The present results clearly indicate that the two sugar binding sites of LEC-1 have different sugar ------------------- Key: 4538 Medline: 11175756 Authors: Greener T;Grant B;Zhang Y;Wu X;Greene LE;Hirsh D;Eisenberg Title: Caenorhabditis elegans auxilin: a J-domain protein essential for clathrin-mediated endocytosis in vivo. Citation: Nature Cell Biology 3: 215-219 2001 Type: ARTICLE Genes: Abstract: The budding of clathrin-coated vesicles is essential for protein transport. After budding, clathrin must be uncoated before the Vesicles can fuse with other membranous structures. In vitro, the molecular chaperone Hsc70 uncoats clathrin-coated vesicles in an ATP-dependent process that requires a specific J-domain protein such as auxilin. However, there is little evidence that either Hsc70 or auxilin is essential in vivo. Here we show that C. elegans has a single auxilin homologue that is identical to mammalian auxilin in its in vitro activity. When RNA-mediated interference (RNAi) is used to inhibit auxilin expression in C. elegans, oocytes show markedly reduced receptor-mediated endocytosis of yolk protein tagged with green fluorescent protein (GFP). In addition, most of these worms arrest during larval development, exhibit defective distribution of GFP-clathrin in many cell types, and show a marked change in clathrin dynamics, as determined by fluorescence recovery after photobleaching (FRAP). We conclude that auxilin is required for in vivo clathrin-mediated endocytosis and development in C. ------------------- Key: 4539 Medline: 21065925 Authors: Hodgkin J;Kuwabara PE;Corneliussen B Title: A novel bacterial pathogen, Microbacterium nematophilum, induces mrophological change in the nematode Caenorhabditis elegans. Citation: Current Biology 10: 1615-1618 2001 Type: ARTICLE Genes: air-2 srf-1 srf-2 srf-3 srf-4 srf-5 srf-6 srf-8 srf-9 stu-7 Abstract: The Dar (deformed anal region) phenotype, characterized by a distinctive swollen tail, was first detected in a variant strain of Caenorhabditis elegans which appeared spontaneously in 1986 during routine genetic crosses [1,2], Dar isolates were initially analysed as morphological mutants, but we report here that two independent isolates carry an unusual bacterial infection different from those previously described [3], which is the cause of the oar phenotype. The infectious agent is a new species of coryneform bacterium, named Microbacterium nematophilum n. sp., which fortuitously contaminated cultures of C. elegans. The bacteria adhere to the rectal and post anal cuticle of susceptible nematodes, and induce substantial local swelling of the underlying hypodermal tissue. The swelling leads to constipation and slowed growth in the infected worms, but the infection is otherwise non lethal. Certain mutants of C. elegans with altered surface antigenicity are resistant to infection. The induced deformation appears to be part of a survival strategy for the bacteria, as C. elegans are potentially their ------------------- Key: 4540 Medline: 21065924 Authors: Piano F;Schetter AJ;Mangone M;Stein L;Kemphues KJ Title: RNAi analysis of genes expressed in the ovary of Caenorhabditis elegans. Citation: Current Biology 10: 1619-1622 2001 Type: ARTICLE Genes: act-2 daf-21 dhc-1 emb-5 klp-15 mei-1 mex-3 mex-5 mex-6 sur-6 Abstract: As a step towards comprehensive functional analysis of genomes, systematic gene knockout projects have been initiated in several organisms [1]. In metazoans like C. elegans, however, maternal contribution can mask the effects of gene knockouts on embryogenesis. RNA interference (RNAi) provides an alternative rapid approach to obtain loss-of-function information that can also reveal embryonic roles for the genes targeted [2,3]. We have used RNAi to analyze a random set of ovarian transcripts and have identified 81 genes with essential roles in embryogenesis, Surprisingly, none of them maps on the X chromosome. Of these 81 genes, 68 showed defects before the eight-cell stage and could be grouped into ten phenotypic classes. To archive and distribute these data we have developed a database system directly linked to the C. elegans database (Wormbase). We conclude that screening cDNA libraries by RNAi is an efficient way of obtaining in vivo function for a large group of genes. Furthermore, this approach is directly applicable to other organisms sensitive to RNAi and whose genomes have not yet been ------------------- Key: 4541 Medline: 21100342 Authors: Ayyadevara S;Ayyadevara R;Hou S;Thaden JJ;Reis RJS Title: Genetic mapping of quantitative trait loci governing longevity of Caenorhabditis elegans in recombinant-inbred progeny of a Bergerac BO X RC301 interstrain cross. Citation: Genetics 157: 655-666 2001 Type: ARTICLE Genes: age-1 clk-1 clk-2 clk-3 ctl-1 daf-2 daf-12 daf-16 daf-18 gro-1 mev-1 rad-8 sod-1 sod-2 spe-10 spe-26 Abstract: Recombinant-inbred populations, generated from a cross between Caenorhabditis elegans strains Bergerac-BO and RC301, were used to identify quantitative trait loci (QTL) affecting nematode longevity. Genotypes of young controls and longevity-selected worms (the last-surviving 1% from a synchronously aged population) were assessed at dimorphic transposon-specific markers by multiplex polymerase chain reaction. The power of genetic mapping was enhanced, in a novel experimental design, through map expansion by accrual of recombinations over several generations, internally controlled longevity selection from a genetically heterogeneous, homozygous population, and selective genotyping of extremely long-lived worms. Analysis of individual markers indicated seven life-span QTL, situated near markers on chromosomes I (tcbn2), III (stP127), IV (stP13), V (stP6, stP23, and stP128), and X (stP41). These loci were corroborated, and mapped with increased precision, by nonparametric interval mapping-which supported all loci implicated by single-marker analysis. In addition, a life-span QTL on chromosome II (stP100-stP196), was significant only by interval mapping. Congenic lines were constructed for the longevity QTL on chromosomes III and X, by backcrossing the Bergerac-BO QTL allele into an RC301 background with selection for flanking markers. Survival data for these lines demonstrated consistent and significant effects of each QTL on life span. ------------------- Key: 4542 Medline: 11161219 Authors: Berset T;Hoier EF;Battu G;Canevascini S;Hajnal A Title: Notch inhibition of Ras signaling through MAP kinase phosphatase LIP-1 during C. elegans vulval development. Citation: Science 291: 1055-1058 2001 Type: ARTICLE Genes: lag-1 let-23 let-60 lin-1 lin-7 lin-15 lin-25 lin-31 lip-1 mpk-1 sem-5 Abstract: During Caenorhabditis elegans vulval development, a signal from the anchor cell stimulates the RTK/RAS/MAPK (receptor tyrosine kinase/RAS/mitogen-activated protein kinase) signaling pathway in the closest vulval precursor cell P6.p to induce the primary fate. A Lateral signal from P6.p then activates the Notch signaling pathway in the neighboring tells P5.p and P7.p to prevent them from adopting the primary fate and to specify the secondary fate. The MAP kinase phosphatase LIP-1 mediates this lateral inhibition of the primary fate. LIN-12/NOTCH up-regulates lip-1 transcription in P5.p and P7.p where LIP-1 inactivates the MAP kinase to inhibit primary fate specification. LIP-1 thus Links the two signaling pathways to generate a ------------------- Key: 4543 Medline: Authors: Momin RA;Ramsewak RS;Nair MG Title: Bioactive compounds and 1,3-Di[(cis)-9-octadecenoyl]-2-[(cis,cis)-9,12-octadecadien oyl]glycerol from Apium Graveolens L. seeds. Citation: Journal of Agricultural and Food Chemistry 48: 3785-3788 2000 Type: ARTICLE Genes: Abstract: Bioassay-directed isolation and purification of the hexane extract of Apium graveolens L. seeds led to the characterization of three compounds: beta-selinene (1), 3-n-butyl-4,5-dihydrophthalide (2) and 5-allyl-2-methoxyphenol (3). The structures of these compounds were established by using 1H and 13C NMR spectral methods. Compounds, 1-3 demonstrated 100% mortality on fourth-instar Aedes aegyptii larvae at 50, 25, and 200 mug mL-1, respectively, in 24 h. Also, 2 inhibited the growth of Candida albicans and Candida kruseii at 100 mug mL-1. It inhibited both topoisomerase-I and -II enzyme activities at 100 mug mL-1. Compound 2 displayed 100% mortality at 12.5 and 50 mug mL-1, respectively, when tested on nematodes, Panagrellus redivivus and Caenorhabditis elegans. The triglyceride, 1,3-di((cis)-9-octadecenoyl)-2-((cis,cis)-9,12-octadecadien oyl)glycerol (4) and 3 were isolated for the first time from A. graveolens seeds, although 4 was not biologically ------------------- Key: 4544 Medline: 20504805 Authors: Severson AF;Hamill DR;Carter JC;Schumacher J;Bowerman B Title: The Aurora-related kinase AIR-2 recruits ZEN-4/CeMKLP1 to the mitotic spindle at metaphase and is required for cytokinesis. Citation: Current Biology 10: 1162-1171 2000 Type: ARTICLE Genes: air-2 cyk-1 hcp-1 hcp-2 hcp-3 icp-1 let-603 zen-4 Abstract: Background: The Aurora/IpI1p-related kinase AIR-2 is required for mitotic chromosome segregation and cytokinesis in early Caenorhabditis elegans embryos. Previous studies have relied on non-conditional mutations or RNA-mediated interference (RNAi) to inactivate AIR-2. It has therefore not been possible to determine whether AIR-2 functions directly in cytokinesis or if the cleavage defect results indirectly from the failure to segregate DNA. One intriguing hypothesis is that AIR-2 acts to localize the mitotic kinesin-like protein ZEN-4 (also known as CeMKLP1), which later functions in cytokinesis. Results: Using conditional alleles, we established that AIR-2 is required at metaphase or early anaphase for normal segregation of chromosomes, localization of ZEN-4, and cytokinesis. ZEN-4 is first required late in cytokinesis, and also functions to maintain cell separation through much of the subsequent interphase. DNA segregation defects alone were not sufficient to disrupt cytokinesis in other mutants, suggesting that AIR-2 acts specifically during cytokinesis through ZEN-4. AIR-2 and ZEN-4 shared similar genetic interactions with the formin homology (FH) protein CYK-1, suggesting that AIR-2 and ZEN-4 function in a single pathway, in parallel to a contractile ring pathway that includes CYK-1. Using in vitro co-immunoprecipitation experiments, we found that AIR-2 and ZEN-4 interact directly. Conclusions: AIR-2 has two functions during mitosis: one in chromosome segregation, and a second, independent function in cytokinesis through ZEN-4. AIR-2 and ZEN-4 may act in parallel to a second pathway that ------------------- Key: 4545 Medline: 11238406 Authors: Praitis V;Casey E;Collar D;Austin J Title: Creation of low-copy integrated transgenic lines in Caenorhabditis elegans. Citation: Genetics 157: 1217-1226 2001 Type: ARTICLE Genes: dpy-1 dpy-4 dpy-5 dpy-6 dpy-10 dpy-11 dpy-13 dpy-14 dpy-17 dpy-18 dpy-20 myo-2 pic-1 sma-1 sup-7 unc-119 Abstract: In Caenorhabditis elegans, transgenic lines are typically created by injecting DNA into the hermaphrodite germline to form multicopy extrachromosomal DNA arrays. This technique is a reliable means of expressing transgenes in C. elegans, but its use has limitations. Because extrachromosomal arrays are semistable, only a fraction of the animals in a transgenic extrachromosomal array line are transformed. In addition, because extrachromosomal arrays can contain hundreds of copies of the transforming DNA, transgenes may be overexpressed, misexpressed, or silenced. We have developed an alternative method for C. elegans transformation, using microparticle bombardment, that produces single- and low-copy chromosomal insertions. Using this method, we find that it is possible to create integrated transgenic lines that reproducibly express GFP reporter constructs without the variations in expression level and pattern frequently exhibited by extrachromosomal array lines. In addition, we find that low-copy integrated lines can also be used to express transgenes in the C. elegans germline, where conventional extrachromosomal arrays typically fail to express due to germline silencing. ------------------- Key: 4546 Medline: 21128812 Authors: Liu Y;Huang T;MacMorris M;Blumenthal T Title: Interplay between AAUAAA and the trans-splice site in processing of a Caenorhabditis elegans operon pre-mRNA. Citation: RNA 7: 176-181 2001 Type: ARTICLE Genes: gpd-2 gpd-3 mai-1 Abstract: About half of Caenorhabditis elegans genes have a 1-2 bp mismatch to the canonical AAUAAA hexamer that signals 3' end formation. One rare variant, AGUAAA, is found at the 3' end of the mai-l gene, the first gene in an operon also containing gpd-2 and gpd-3. When we expressed this operon under heat shock control, 3' end formation dependent on the AGUAAA was very inefficient, but could be rescued by a single bp change to create a perfect AAUAAA. When AGUAAA was present, most 3' ends formed at a different site, 100 bp farther downstream, right at the gpd-2 trans-splice site. Surprisingly, 3' end formation at this site did not require any observable match to the AAUAAA consensus. It is possible that 3' end formation at this site occurs by a novel mechanism-trans-splicing-dependent cleavage-as deletion of the trans-splice site prevented 3' end formation here. Changing the AGUAAA to AAUAAA also influenced the trans-splicing process: with AGUAAA, most of the gpd-2 product was trans-spliced to SL1, rather than SL2, which is normally used at downstream operon trans-splice sites. However, with AAUAAA, SL2 trans-splicing of gpd-2 was increased. Our results imply that (1) the AAUAAA consensus controls 3' end formation frequency in C. elegans; (2) the AAUAAA is important in determining SL2 trans-splicing events more than 100 bp downstream; end (3) in some circumstances, 3' end formation may occur by a trans-splicing-dependent mechanism. ------------------- Key: 4547 Medline: 11165764 Authors: Bianchi L;Miller DM;George AL Title: Expression of a CIC chloride channel in Caenorhabditis elegans gamma-aminobutyric acid-ergic neurons. Citation: Neuroscience Letters 299: 177-180 2001 Type: ARTICLE Genes: clh-1 clh-2 clh-3 clh-4 clh-5 clh-6 Abstract: In this study, we report the complete cDNA sequence, genomic organization and expression pattern of the Caenorhabditis elegans CIC chloride channel gene, clh-6. Two different types of reporter gene fusions suggest that clh-6 expression is restricted to two gamma-aminobutyric acid-ergic RME neurons. These results are in striking contrast with the wide tissue distribution of messenger RNA for the related mammalian isoforms, CIC-6 a nd CIC-7. The restricted expression pattern of clh-6 provides a unique opportunity to study the biological function of a neuronal CIC chloride channel. ------------------- Key: 4548 Medline: 21103689 Authors: Muller SA;Haner M;Ortiz I;Aebi U;Epstein HF Title: STEM analysis of Caenorhabditis elegans muscle thick filaments: Evidence for microdifferentiated substructures. Citation: Journal of Molecular Biology 305: 1035-1044 2001 Type: ARTICLE Genes: Abstract: In the thick filaments of body muscle in Caenorhabditis elegans, myosin A and myosin B isoforms and a subpopulation of paramyosin, a homologue of myosin heavy chain rods, are organized about a tubular core. As determined by scanning transmission electron microscopy, the thick filaments show a continuous decrease in mass-per-length (MPL) from their central zones to their polar regions. This is consistent with previously reported morphological studies and suggests that both their content and structural organization are microdifferentiated as a function of position. The cores are composed of a second distinct subpopulation of paramyosin in association with the alpha beta, and gamma -filagenins. MPL measurements suggest that cores are formed from seven subfilaments containing four strands of paramyosin molecules, rather than the two originally proposed. The periodic locations of the filegenins within different regions and the presence of a central zone where myosin A is located, implies that the cores are also microdifferentiated with respect to molecular content and structure. This differentiation may result from a novel "induced strain" assembly mechanism based upon the interaction of the filagenins, paramyosin and myosin A. The cores may then serve as "differentiated templates" for the assembly of myosin B and paramyosin in the tapering, microdifferentiated polar regions of the thick filaments. ------------------- Key: 4549 Medline: 21015573 Authors: Seydoux G;Schedl T Title: The germline in C. elegans: Origins, proliferation, and silencing. Citation: International Review of Cytology - A Survey of Cell Biology 203: 139-185 2001 Type: REVIEW Genes: apx-1 cey-2 ego-1 ego-2 ego-3 ego-4 ego-5 fbf-1 fbf-2 fem-3 gld-1 gld-2 glh-1 glh-2 glh-3 glh-4 glp-1 glp-4 lag-1 lag-2 let-858 lin-12 mes-1 mes-2 mes-3 mes-4 mes-6 mex-1 mex-3 mlc-4 mut-2 mut-7 nmy-2 nos-1 nos-2 nos-3 pal-1 par-1 par-2 pgl-1 pgl-2 pgl-3 pie-1 pos-1 rde-1 rde-2 rde-3 rde-4 Abstract: Germ cells are essential for reproduction, yet the molecular mechanisms that underlie their unique development are only beginning to be understood. Here we review important events that lead to the establishment of the germline and the initiation of meiotic development in C. elegans. Formation of the germline begins in the pregastrulation embryo, where it depends on polarization along the anterior/posterior axis and on the asymmetric segregation of P granules and associated factors. During postembryonic development, the germline expands using the GLP-1/Notch signaling pathway to promote proliferation and regulate entry into meiosis. Throughout their development, germ cells also employ unique "silencing" mechanisms to regulate their genome and protect themselves against unwanted expression from repetitive sequences including transposable elements. Together these mechanisms preserve the health and reproductive potential of the germline. ------------------- Key: 4550 Medline: 21015579 Authors: Clements D;Rex M;Woodland HR Title: Initiation and early patterning of the endoderm. Citation: International Review of Cytology - A Survey of Cell Biology 203: 383-446 2001 Type: REVIEW Genes: apr-1 cpr-1 elt-1 end-1 end-2 end-3 ges-1 gsk-3 lit-1 mom-1 mom-2 mom-3 mom-4 mom-5 pha-4 pie-1 pop-1 skn-1 wrm-1 Abstract: We review the early stages of endoderm formation in the major animal models. In Amphibia maternal molecules are important in initiating endoderm formation. This is followed by successive signaling events that establish and then pattern the endoderm. In other organisms there are differences in endodermal development, particularly in the initial, prephylotypic stages. Later many of the same key families of transcription factors and signaling cassettes are used in all animals, but more work will be needed to establish exact evolutionary homologies. ------------------- Key: 4551 Medline: 11167007 Authors: Cho JH;Bandyopadhyay J;Lee J;Park CS;Ahnn J Title: Two isoforms of sarco/endoplasmic reticulum calcium ATPase (SERCA) are essential in Caenorhabditis elegans. Citation: Gene 261: 211-219 2000 Type: ARTICLE Genes: ser-1 Abstract: SERCA (Sarco/Endoplasmic Reticulum Calcium ATPase), a membrane bound Ca2+-/Mg2+- dependent ATPase that sequesters Ca2+ into the SR/ER lumen, is one of the essential components for the maintenance of intracellular Ca2+ homeostasis. Here we describe the identification and functional characterization of a C. elegans SERCA gene (ser-1). ser-l is a single gene alternatively spliced at its carboxyl terminus to form two isoforms (SER-1A and SER-1B) and displays a high homology (70% identity, 80% similarity) with mammalian SERCAs. Green fluorescent protein (GFP) and whole-mount immunostaining analyses reveal that SER-1 expresses in neuronal cells, body wall muscles, pharyngeal and vulval muscles, excretory cells, and vulva epithelial cells. Furthermore, SER-1::GFP expresses during embryonic stages and the expression is maintained through the adult stages. Double-stranded RNA injection (also known as RNAi) targeted to each SER-I isoform results in severe phenotypic defects: ser-IA(RNAi) animals show embryonic lethality, whereas ser-IB(RNAi) results in L1 larval arrest phenotype. These findings suggest that both isoforms of C. elegans SERCA, like in mammals, are essential for embryonic development and ------------------- Key: 4552 Medline: 11167013 Authors: Takemoto T;Sasaki Y;Hamajima N;Goshima Y;Nonaka M;Kimura H Title: Cloning and characterization of the Caenorhabditis elegans CeCRMP/DHP-1 and -2; common ancestors of CRMP and dihydropyrimidinase? Citation: Gene 261: 259-267 2000 Type: ARTICLE Genes: unc-33 Abstract: The vertebrate CRMP (collapsin-response-mediator protein) gene family comprises at least four members. These CRMPs exhibit about 60% amino acid identity with vertebrate dihydropyrimidinase (DHP), an amidohydrolase involved in the pyrimidine degradation pathway. CRMP is also referred to as DRP (DHP-related protein), TOAD-64 (turned on after division, 64 kDa) and Ulip (Unc-33-like phosphoprotein). These vertebrate CRMPs are expressed mainly in early neuronal differentiation, which suggests that they play a role in neuronal development. In this study we isolated two cDNA clones from nematode C. elegans based on their sequence homology to vertebrate CRMPs and DHP. These two molecules, termed CeCRMP/DHP-1 and -2, turned out to be Ulip-B and -A. respectively, which were previously identified in the C, elegans genomic database by Byk et al. (1998). These newly isolated molecules were believed to represent a common ancestral state before the gene duplication between CRMPs and DHP. CeCRMP/DHP-1 and -2 protein retained all putative zinc-binding residues thought to be essential for the amidohydrolase activity of DHP and exhibited a weak amidohydrolase activity when 5-bromo-dihydrouracil was used as a substrate. Whole-mount in situ hybridization and expression analysis using GFP fusions revealed that CeCRMP/DHP-1 was transiently expressed in the hypodermis of C. elegans during the early larva stage. CeCRMP/DHP-1 was also expressed in a single nerve cell between the pharynx and ring neuropil. On the other hand, expression of CeCRMP/DHP-2 was observed in the body wall muscle throughout the lifespan of C. elegans. These results indicate that a major site of CeCRMP/DHP-1 and -2 expression is non-neuronal. Targeted gene disruption of CeCRMP/DHP-2 caused no particular difference in appearance or movement phenotype. ------------------- Key: 4553 Medline: Authors: Beaudoin F;Michaelson LV;Lewis MJ;Shewry PR;Sayanova O;Napier JA Title: Production of C-20 polyunsaturated fatty acids (PUFAs) by pathway engineering: identification of a PUFA elongase component from Caenorhabditis elegans. Citation: Biochemical Society Transactions 28: 661-663 2000 Type: ARTICLE Genes: Abstract: Using a combination of database-mining and functional characterization, we have identified a component of the polyunsaturated fatty acid (PUFA) elongase. Go-expression of this elongating activitiy with fatty acid desaturases has allowed us to heterologously reconstitute the PUFA biosynthetic pathway. Both these enzymes (desaturases and elongase components) have undergone gene-duplication events which provide a paradigm for the diverged nature of PUFA biosynthetic activities. ------------------- Key: 4554 Medline: Authors: Bouvier-Nave P;Benveniste P;Noiriel A;Schaller H Title: Expression in yeast of an acyl-CoA:diacylglycerol acyltransferase cDNA from Caenorhabditis elegans. Citation: Biochemical Society Transactions 28: 692-695 2000 Type: ARTICLE Genes: Abstract: We have identified a cDNA from the nematode worm Caenorhabditis elegans that encodes an acyl-CoA:diacylglycerol acyltransferase (DGAT). Its expression in Saccharomyces cerevisiae resulted in an increase both in triacylglycerol content and in microsomal oleyl-CoA: diacylglycerol acyltransferase activity. Such effects were similar to those of characterized plant DGAT genes. This is the first DGAT gene isolated from an invertebrate. The phylogenetic relationships between DGATs and animal and yeast acyl-CoA:sterol acyltransferases are illustrated. ------------------- Key: 4555 Medline: Authors: Meesapyodsuk D;Reed DW;Savile CK;Buist PH;Schafer UA;Ambrose SJ;Covello PS Title: Substrate specificity, regioselectivity and cryptoregiochemistry of plant and animal omega-3 fatty acid desaturases. Citation: Biochemical Society Transactions 28: 632-635 2000 Type: ARTICLE Genes: fat-1 fat-2 Abstract: In order to define the substrate requirements, regiochemistry and cryptoregiochemistry of the omega -3 fatty acid desaturases involved in polyunsaturated fatty acid formation, the genes Fad3 and fat-1 from Brassica napus and the nematode Caenorhabditis elegans respectively were expressed in baker's yeast (Saccharomyces cerevisiae). Various fatty acids, including deuterium-labelled thia-fatty acids, were supplied to growing cultures of transformed yeast. The results from GC-MS analysis of the desaturated products indicate that both the plant and animal desaturases act on unsaturated substrates of 16-20 carbons with a preference for omega -6-unsaturated fatty acids. The regioselectivities of both enzymes were confirmed to be that of omega -3 desaturases. The primary deuterium kinetic isotope effects at C-15 and C-16 of a C-18 fatty acid analogue were measured via competitive incubation experiments. Whereas k(H)/k(D) at the omega -3 position was shown to be large, essentially no kinetic isotope effect at the omega -2 position was observed for the plant or the nematode enzymes. These results indicate that omega -3 desaturation is initiated by an energetically difficult C-H bond cleavage at the carbon closer to the carboxyl terminus. These results will be discussed in the context of a general model relating the structure and function of membrane-bound fatty acid desaturases featuring different regioselectivities. ------------------- Key: 4556 Medline: Authors: Das T;Thurmond JM;Bobik E;Leonard AE;Parker-Barnes JM;Huang YS;Mukerji P Title: Polyunsaturated fatty acid-specific elongation enzymes. Citation: Biochemical Society Transactions 28: 658-660 2000 Type: ARTICLE Genes: Abstract: We have isolated a novel gene (GLELO) from Mortierella alpina and its homologue (CEELO1) from Caenorhabditis elegans and demonstrate the involvement of their encoded proteins in the elongation of C-18 polyunsaturated fatty acids. ------------------- Key: 4557 Medline: 21100425 Authors: Xie T;Ding D Title: Investigating 42 candidate orthologous protein groups by molecular evolutionary analysis on genome scale. Citation: Gene 261: 305-310 2000 Type: ARTICLE Genes: Abstract: It is one of key problems for comparative genomics to accurately identify orthologous genes/proteins. Here 42 quartettes of human, yeast Saccharomyces cerevisiae, nematode Caenorhabditis elegans, and fruit fly Drosophila melanogaster candidate orthologs, defined by using similarity-based highest hit criteria (Mushegian et al., 1998 Genome Res. 8. 590-598), were reconsidered according to molecular evolutionary analysis. We found that only 14 of the 42 candidate orthologous groups can be identified to have truly one-to-one orthologous relationships, whereas other groups were characterized by one (many)-to-many orthologous relationships or even more complex scenarios involving gene duplications and/or gene losses. The result could imply that the classical one-to-one orthology might be not as common as typically accepted and automated similarity-based methods should be used with caution when accurate orthology/paralogy discrimination is required. ------------------- Key: 4558 Medline: 20541602 Authors: Luzi L;Confalonieri S;Di Fiore PP;Pelicci PG Title: Evolution of Shc functions from nematode to human. Citation: Current Opinion in Genetics & Development 10: 668-674 2000 Type: ARTICLE Genes: Abstract: The Shc protein family is characterized by the (CH2)-PTB-CH1-SH1 modularity. Its complexity increased during evolution from one locus in Drosophila (dShc), to at least three loci in mammals (shc, rai and sli). The three mammalian loci encode, because of alternative initiation codon usage and splicing patterns, at least six Shc-like proteins. Genetic and biological evidence indicates that the mmmalian Shc isoforms regulate functions as diverse as growth (p52/p46Shc), apoptosis (p66Shc) and life-span (p66Shc). Available structure-function data and analysis of sequence similarities of Shc-like genes and proteins suggest complex diversification of Shc functions during evolution. Notably, Ras activation, the best-characterized Shc activity, appears to be a recent evolutionary ------------------- Key: 4559 Medline: 20533203 Authors: Strange K Title: Model organisms: comparative physiology or just physiology? Citation: American Journal of Physiology-Cell Physiology 279: C2050-C2051 2000 Type: REVIEW Genes: Abstract: A new field referred to as "functional genomics" (or, from a physiologist's perspective, "physiological genomics") has emerged in the wake of genome sequencing. Functional genomics is defined as the assignment of function to identified genes and, importantly, the elucidation of the organization, integration, and control of networks of proteins that give rise to specific biological processes. It is widely recognized that the significant challenges posed by attempts to define the genetic basis of physiology necessitate the study of experimentally more manipulable "model organisms". ------------------- Key: 4560 Medline: 20574758 Authors: Stein L;Mangone M;Schwarz E;Durbin R;Thierry-Mieg J;Spieth J;Sternberg P Title: WormBase: network access to the genome and biology of Caenorhabditis elegans. Citation: Nucleic Acids Research 29: 1012- 2001 Type: ARTICLE Genes: Abstract: ------------------- Key: 4561 Medline: 21106482 Authors: Redmond DL;Clucas C;Johnstone IL;Knox DP Title: Expression of Haemonchus contortus pepsinogen in Caenorhabditis elegans. Citation: Molecular & Biochemical Parasitology 112: 125-131 2001 Type: ARTICLE Genes: cpr-5 unc-76 Abstract: A genomic copy of a gut-expressed Haemonchus contortus candidate Vaccine antigen, pepsinogen, was isolated using the polymerase chain reaction (PCR). The isolated sequence was 4 kb in length and contained eight introns ranging in size from 54 to 1475 base pairs. This sequence, together with its 3' non-coding DNA region containing a polyadenylation signal sequence, was cloned into the Bluescript SK+ vector immediately downstream of the Caenorhabditis elegans cpr-5 gene promoter. This promoter has been shown previously to direct protein expression to the gut of C. elegans. The construct was micro-injected into DR96 unc-76(e911) mutant C. elegans together with a rescue plasmid and transgenic worms identified by reversion back to wild-type phenotype. Two transgenic lines of C. elegans were established. The presence of the injected construct and of the Haemonchus pepsinogen transcript in transgenic worms was confirmed by PCR analysis. Correct splicing of intronic sequences was observed. Immunohistochemistry showed expression of the Haemonchus pepsinogen protein in the gut of transgenic C. elegans, with reactivity evident in the larval and adult stages. Expression of the Haemonchus pepsinogen in C. elegans affirms the role of C. elegans as a model for parasitic nematodes and demonstrates its potential as a vector for expression of candidate Vaccine antigens from parasitic ------------------- Key: 4562 Medline: 11181837 Authors: Stansberry J;Baude EJ;Taylor MK;Chen PJ;Jin SW;Ellis RE;Uhler MD Title: A cGMP-dependent protein kinase is implicated in wild-type motility in C. elegans. Citation: Journal of Neurochemistry 76: 1177-1187 2001 Type: ARTICLE Genes: cgk-1 Abstract: In mammals, cyclic GMP and cGMP-dependent protein kinases (cGKs) have been implicated in the regulation of many neuronal functions including long-term potentiation and long-term depression of synaptic efficacy. To develop Caenorhabditis elegans as a model system for studying the neuronal function of the cGKs, we cloned and characterized the cgk-1 gene. A combination of approaches showed that cgk-1 produces three transcripts, which differ in their first exon but are similar in length. Northern analysis of C. elegans RNA, performed with a probe designed to hybridize to all three transcripts, confirmed that a major 3.0 kb cgk-1 transcript is present at all stages of development. To determine if the CGK-1C protein was a cGMP-dependent protein kinase, CGK-1C was expressed in S/9 cells and purified. CGK-1C shows a K-a of 190 +/- 14 nM for cGMP and 18.4 +/- 2 muM for cAMP. Furthermore, CGK-1C undergoes autophosphorylation in a cGMP-dependent manner and is inhibited by the commonly used cGK inhibitor, KT5823. To determine which cells expressed CGK-1C, a 2.4-kb DNA fragment from the promoter of CGK-1C was used to drive GFP expression. The CGK-1C reporter construct is strongly expressed in the ventral nerve cord and in several other neurons as well as the marginal cells of the pharynx and intestine. Finally, RNA-mediated interference of CGK-1 resulted in movement defects in nematode larvae. These results provide the first demonstration that cGMP-dependent protein kinase is present in neurons of C.elegans and show that this kinase is required for normal motility. ------------------- Key: 4563 Medline: Authors: Barstead R Title: Genome-wide RNAi. Citation: Current Opinion in Chemical Biology 5: 63-66 2001 Type: REVIEW Genes: ego-1 lin-26 lir-1 mut-7 par-1 rde-1 Abstract: In many species, double-stranded RNA can specifically and effectively silence genes. This newly discovered biological phenomenon, called RNA interference (RNAi), has practical implications for functional genomics. As shown by two recent reports, RNAi provides a rapid method to test the function of genes in the nematode Caenorhabditis elegans; most of the genes on C. elegans chromosome I and III have now been tested for RNAi phenotypes. The results validate RNAi as a powerful functional genomics tool for C. elegans, and point the way for similar large-scale studies in other ------------------- Key: 4564 Medline: 21135254 Authors: Hengartner MO Title: Apoptosis: Corralling the corpses. Citation: Cell 104: 325-328 2001 Type: REVIEW Genes: ced-1 ced-2 ced-5 ced-6 ced-7 ced-10 ced-12 Abstract: One of the most impressive features of apoptosis is how quickly it all happens. One minute the cell is happily sitting there on its plastic lawn; the next-boom!-it is in convulsions, writhing in its death throes. Many a QuickTime movie has been produced to illustrate this point. Unfortunately, most of these movies stop shortly after the cell falls apart. While less photogenic, what happens to the remains of the cell after the camera stops rolling is no less impressive-at least in vivo. ------------------- Key: 4565 Medline: Authors: Link CD;Johnson CJ;Fonte V;Paupard MC;Hall DH;Styren S;Mathis CA;Klunk WE Title: Visualization of fibrillar amyloid deposits in living, transgenic Caenorhabditis elegans animals using the sensitive amyloid dye, X-34. Citation: Neurobiology of Aging 22: 217-226 2001 Type: ARTICLE Genes: Abstract: Transgenic Caenorhabditis elegans animals can be engineered to express high levels of the human beta amyloid peptide (Abeta). Histochemistry of fixed tissue from these animals reveals deposits reactive with the amyloid-specific dyes Congo Red and thioflavin S (Fay et al., J. Neurochem 71:1616, 1998). Here we show by immune-electron microscopy that these animals contain intracellular immunoreactive deposits with classic amyloid fibrillar ultrastructure. These deposits can be visualized in living animals using the newly developed, intensively fluorescent, amyloid-specific dye X-34. This in vivo staining allows monitoring of amyloid deposition in individual animals over time. The specificity of this staining is demonstrated by examining transgenic animals expressing high levels of a non-fibrillar beta peptide variant, the beta single-chain dimer. These animals have deposits immunoreactive with anti-beta antibodies, but do not have X-34 deposits or deposits with a fibrillar ultrastructure. X-34 can also be used in vivo to visualize putative amyloid deposits resulting from accumulation of human transthyretin, another amyloidic protein. In vivo amyloid staining with X-34 may be a useful tool for monitoring anti-amyloidic treatments in real time or screening for genetic alterations that affect amyloid formation. ------------------- Key: 4566 Medline: 21137347 Authors: Tissenbaum HA;Guarente L Title: Increased dosage of a sir-2 gene extends lifespan in Caenorhabditis elegans. Citation: Nature 410: 227-230 2001 Type: ARTICLE Genes: age-1 daf-1 daf-2 daf-4 daf-16 sir-2 unc-31 unc-64 hDp3 mDp1 mDp4 mnDp1 mgDf50 Abstract: In Caenorhabditis elegans, mutations that reduce the activity of an insulin-like receptor (daf-2)(1) or a phosphatidylinositol-3-OH kinase (age-1)(2) favour entry into the dauer state during larval development(3) and extend lifespan in adults(3-6). Downregulation of this pathway activates a forkhead transcription factor (daf-16)(7,8), which may regulate targets that promote dauer formation in larvae and stress resistance and longevity in adults(9). In yeast, the SIR2 gene determines the lifespan of mother cells, and adding an extra copy of SIR2 extends lifespan(10). Sir2 mediates chromatin silencing through a histone deacetylase activity that depends on NAD (nicotinamide adenine dinucleotide) as a cofactor(11-13). We have surveyed the lifespan of C. elegans strains containing duplications of chromosomal regions. Here we report that a duplication containing sir-2.1-the C. elegans gene most homologous to yeast SIR2-confers a lifespan that is extended by up to 50%. Genetic analysis indicates that the sir-2.1 transgene functions upstream of daf-16 in the insulin-like signalling pathway. Our findings suggest that Sir2 proteins may couple longevity to nutrient availability in many eukaryotic ------------------- Key: 4567 Medline: 11222641 Authors: Brockie PJ;Madsen DM;Zheng Y;Mellem J;Maricq AV Title: Differential expression of glutamate receptor subunits in the nervous system of Caenorhabditis elegans and their regulation by the homeodomain protein UNC-42. Citation: Journal of Neuroscience 21: 1510-1522 2001 Type: ARTICLE Genes: glr-1 glr-2 glr-3 glr-4 glr-5 glr-6 gr-7 glr-8 nmr-1 nmr-2 unc-42 Abstract: In almost all nervous systems, rapid excitatory synaptic communication is mediated by a diversity of ionotropic glutamate receptors. In Caenorhabditis elegans, 10 putative ionotropic glutamate receptor subunits have been identified, a surprising number for an organism with only 302 neurons. Sequence analysis of the predicted proteins identified two NMDA and eight non-NMDA receptor subunits. Here we describe the complete distribution of these subunits in the nervous system of C. elegans. Receptor subunits were found almost exclusively in interneurons and motor neurons, but no expression was detected in muscle cells. Interestingly, some neurons expressed only a single subunit, suggesting that these may form functional homomeric channels. Conversely, interneurons of the locomotory control circuit (AVA, AVB, AVD, AVE, and PVC) coexpressed up to six subunits, suggesting that these subunits interact to generate a diversity of heteromeric glutamate receptor channels that regulate various aspects of worm movement. We also show that expression of these subunits in this circuit is differentially regulated by the homeodomain protein UNC-42 and that UNC-42 is also required for axonal pathfinding of neurons in the circuit. In wild-type worms, the axons of AVA, AVD, and AVE lie in the ventral cord, whereas in unc-42 mutants, the axons are anteriorly, laterally, or dorsally displaced, and the mutant worms have sensory and locomotory defects. ------------------- Key: 4568 Medline: 21136503 Authors: Gower NJD;Temple GR;Schein JE;Marra M;Walker DS;Baylis HA Title: Dissection of the promoter region of the inositol 1,4,5-triphospate receptor gene, itr-1, in C. elegans: A molecular basis for cell-specific expression of IP3R isoforms. Citation: Journal of Molecular Biology 306: 145-157 2001 Type: ARTICLE Genes: ceh-22 ceh-24 elt-1 elt-2 elt-3 end-1 ges-1 itr-1 myo-2 pha-4 skn-1 Abstract: Inositol 1,4,5-trisphosphate receptors in Caenorhabditis elegans are encoded by a single gene, itr-1. This provides a powerful system in which to dissect the mechanisms that control the tissue-specific expression of molecules that determine the specificity of calcium signalling We first identified the Caenorhabditis briggsae orthologue of itr-1, Cbitr-1. Comparison of the two itr-1 genes revealed that the chromosomal organisation, gene structure and predicted cDNA and protein sequences were all conserved. The conserved gene structure supports the hypothesis that the itr-1 gene has three promoters, each of which gives rise to an alternative mRNA and hence unique protein. To test this and to identify the roles of the three putative promoters (pA, pB and pC) in regulating itr-2 expression we fused each promoter to the green fluorescent protein gene and identified their expression patterns, introduction of these transgenes into C. elegans identified unique and defined patterns of green fluorescent protein expression directed by each promoter: pA directs expression in the pharyngeal terminal bulb, the rectal epithelial cells and vulva; pB directs expression in the motor neurone PDA, the amphid socket cells and the spermatheca; pC directs expression in the spermathecal valve, uterine sheath cells, pharyngeal isthmus and intestine. Thus tissue-specific expression of itr-1 variants is directed by three promoters and this results in adjacent cells in the same tissue containing different inositol trisphosphate receptor isoforms. Within pA, four short regions (pA-A to pA-D) of sequence conservation between C. elegans and C. briggsae were identified. Deletion analysis demonstrated that the region containing pA-C is required for expression in the terminal bulb and rectal epithelial cells and the region containing pA-D is required for expression in the vulva. pA-C includes sequences similar to the binding sites for transcription factors that have been demonstrated to be important in pharyngeal development and gene expression. ------------------- Key: 4569 Medline: Authors: Ono S;McGough A;Pope BJ;Tolbert VT;Bui A;Pohl J;Benian GM;Gernert KM;Weeds AG Title: The C-terminal tail of UNC-60B (actin depolymerizing factor/cofilin) is critical for maintaining its stable association with F-actin and is implicated in the second actin-binding site. Citation: Journal of Biological Chemistry 276: 5952-5958 2001 Type: ARTICLE Genes: unc-60 Abstract: Actin depolymerizing factor (ADF)/cofilin changes the twist of actin filaments by binding two longitudinally associated actin subunits, In the absence of an atomic model of the ADF/cofilin-F-actin complex, we have identified residues in ADF/cofilin that are essential for filament binding. Here, we have characterized the C-terminal tail of UNC-60B (a nematode ADF/cofilin isoform) as a novel determinant for its association with F-actin, Removal of the C-terminal isoleucine (Ile(152)) by carboxypeptidase A or truncation by mutagenesis eliminated F-actin binding activity but strongly enhanced actin depolymerizing activity, Replacement of Ile(152) by Ala had a similar but less marked effect; F-actin binding was weakened and depolymerizing activity slightly enhanced. Truncation of both Arg(151) and Ile(152) or replacement of Arg(151) with Ala also abolished F-actin binding and enhanced depolymerizing activity. Loss of F-actin binding in these mutants was accompanied by loss or greatly decreased severing activity. All of the variants of UNC-60B interacted with G-actin in an indistinguishable manner from wild type. Cryoelectron microscopy showed that UNC-60B changed the twist of F-actin to a similar extent to vertebrate ADF/cofilins. Helical reconstruction and structural modeling of UNC-60B-F-actin complex reveal how the C terminus of UNC-60B might be involved in one of the ------------------- Key: 4570 Medline: Authors: Ishii N Title: Oxidative stress and aging in Caenorhabditis elegans. Citation: Free Radical Research 33: 857-864 2000 Type: ARTICLE Genes: cyt-1 mev-1 Abstract: Much attention has been focused on the hypothesis that oxidative damage plays in cellular and organismal aging. A mev-1 (kn1) mutant of Caenorhabditis elegans, isolated on the basis of its methyl viologen (paraquat) hypersensitivity, is also hypersensitive to elevated oxygen levels. Unlike the wild type, its life span decreases dramatically as oxygen concentrations are increased from 1% to 60%. Strains, which bear this mutation, accumulate fluorescent materials and protein carbonyl groups, markers of aging, at faster rates than the wild type. We have cloned mev-1. gene by transformation rescue and found that it is, in fact, the previously sequenced gene (cyt-1) that encodes succinate dehydrogenase cytochrome b. A missense mutation abolishes complex II activity in the mitochondrial membrane but not succinate dehydrogenase enzyme activity per se. These data suggest that CYT-1 directly participates in electron transport from FADH(2) to coenzyme Q. Moreover, mutational inactivation of this process renders animals susceptible to oxidative stress and, as a result, leads to premature aging. ------------------- Key: 4571 Medline: 21098749 Authors: Singson A Title: Every sperm is sacred: Fertilization in Caenorhabditis elegans. Citation: Developmental Biology 230: 101-109 2001 Type: REVIEW Genes: fer-14 fer-15 spe-8 spe-9 spe-11 spe-12 spe-13 spe-19 spe-27 spe-29 spe-36 spe-38 Abstract: The nematode Caenorhabditis elegans is an attractive model system for the study of fertilization. C. elegans exists as a self-fertilizing hermaphrodite or as a male. This unusual situation provides an excellent opportunity to identify and maintain sterile mutants that affect sperm and no other cells. Analysis of these mutants can identify genes that encode proteins required for gamete recognition, adhesion, signaling, fusion, and/or activation at fertilization. These genes can also provide a starting point for the identification of additional molecules required for fertility. This review describes progress in the genetic and molecular dissection of fertilization in C. elegans and related studies on sperm competition. ------------------- Key: 4572 Medline: 21137983 Authors: Robertson HM Title: Updating the str and srj (stl) families of chemoreceptors in Caenorhabditis nematodes reveals frequent gene movement within and between chromosomes. Citation: Chemical Senses 26: 151-159 2001 Type: ARTICLE Genes: odr-10 srj-19 srj-20 str-1 str-2 str-3 str-11 str-12 str-13 str-44 str-48 str-49 str-50 str-51 str-94 str-112 str-115 str-116 str-117 str-249 Abstract: The seven transmembrane receptor (str) and srj (renamed from stl) families of chemoreceptors have been updated and the genes formally named following completion di the Caenorhabditis elegans genome sequencing project. Analysis bf gene locations revealed that 84% of the 320 genes and pseudogenes in these two families reside on the large chromosome V. Movements to other chromosomes, especially chromosome IV, have nevertheless been relatively common, but only one has led to further gene family diversification. Comparisons with homologs in C. briggsae indicated that 22.5% of these genes have been newly formed by gene duplication since the species split, while also showing that four have been lost by large deletions These patterns of gene evolution are similar to those revealed by analysis of the equally large srh family of chemoreceptors, and are likely to reflect general features of nematode genome dynamics: THUS large random deletions presumably balance the rapid proliferation of genes and their degeneration into pseudogenes, while gene movement within and between chromosomes keeps these nematode genomes in ------------------- Key: 4573 Medline: 11178968 Authors: Azim MK;Grossmann JG;Zaidi ZH Title: Homology modeling of nematode Caenorhabditis elegans CED3 protein-inhibitor complex. Citation: Biochemical and Biophysical Research Communications 281: 115-121 2001 Type: ARTICLE Genes: Abstract: CED3 protein, the product of a gene necessary for programmed cell death in the nematode Caenorhabditis elegans, is related to a highly specific cysteine protease family i.e., caspases. A tertiary-structural model has keen constructed of a complex of the CED3 protein with tetrapeptide-aldehyde inhibitor, Ac-DEVD-CHO. The conformation of CED3 protein active site and the general binding features of inhibitor residues are similar to those observed in other caspases. The loop segment (Phe380-Pro387) binds with the P4 Asp in a different fashion compared to caspase-3. The comparative modeling of active sites from caspase-3 and CED3 protein indicated that although these enzymes require Asp at the position P4, variation could occur in the binding of this residue at the S4 subsite. This model allowed the definition of substrate specificity of CED3 protein from the structural standpoint and provided insight in designing of mutants for structure-function studies of this classical caspase ------------------- Key: 4574 Medline: 11226309 Authors: Aballay A;Ausubel FM Title: Programmed cell death mediated by ced-3 and ced-4 protects Caenorhabditis elegans from Salmonella typhimurium-mediated killing. Citation: Proceedings of the National Academy of Sciences USA 98: 2735-2739 2001 Type: ARTICLE Genes: ced-3 ced-4 ced-9 ces-1 ces-2 egl-1 Abstract: Programmed cell death (PCD) in mammals has been implicated in several disease states including cancer, autoimmune disease, and neurodegenerative disease. In Caenorhabditis elegans, PCD is a normal component of development. We find that Salmonella typhimurium colonization of the C. elegans intestine leads to an increased level of cell death in the worm gonad. S. typhimurium-mediated germ-line cell death is not observed in C. elegans ced-3 and ced-4 mutants in which developmentally regulated cell death is blocked, and ced-3 and ced-4: mutants are hypersensitive to S. typhimurium-mediated killing. These results suggest that PCD may be involved in the C. elegans defense response to pathogen attack. ------------------- Key: 4575 Medline: 21135099 Authors: Reboul J;Vaglio P;Tzellas N;Thierry-Mieg N;Moore T;Jackson C;Shin-i T;Kohara Y;Thierry-Mieg D;Thierry-Mieg J;Lee H;Hitti J;Doucette-Stamm L;Hartley JL;Temple GF;Brasch MA;Vandenhaute J;Lamesch PE;Hill Title: Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans. Citation: Nature Genetics 27: 332-336 2001 Type: ARTICLE Genes: Abstract: The genome sequences of Caenorhabditis elegans. Drosophila melanogaster and Arabidopsis thaliana have been predicted to contain 19,000, 13,600 and 25,500 genes, respectively(1-3). Before this information can be fully used for evolutionary and functional studies, several issues need to be addressed. First, the gene number estimates obtained in silico and not yet supported by any experimental data need to be verified. For example, it seems biologically paradoxical that C.elegans would have 50% more genes than Drosophilia. Second, intron/exon predictions need to be tested experimentally. Third, complete sets of open reading frames (ORFs). or "ORFeomes."(4) need to be cloned into various expression vectors. To address these issues simultaneously, we have designed and applied to C. elegans the following strategy. Predicted ORFs are amplified by PCR from a highly representative cDNA library(4) using ORF-specific primers, cloned by Gateway recombination cloning(4-6) and then sequenced to generate ORF sequence tags (OSTs) as a way to verify identity and splicing. In a sample (n=1,222) of the nearly 10,000 genes predicted ab initio (that is, for which no expressed sequence tag (EST) is available so far), at least 70% were verified by OSTs. We also observed that 27% of these experimentally confirmed genes have a structure different from that predicted by GeneFinder. We now have experimental evidence that supports the existence of at least 17,300 genes in C. elegans. Hence we suggest that gene counts based primarily on ESTs may underestimate the ------------------- Key: 4576 Medline: 21155307 Authors: Gotta M;Ahringer J Title: Distinct roles for G alpha and G beta gamma in regulating spindle position and orientation in Caenorhabditis elegans embryos. Citation: Nature Cell Biology 3: 297-300 2001 Type: ARTICLE Genes: egl-30 gpa-7 gpa-12 gpa-16 gpb-1 gpc-1 gpc-2 goa-1 gsa-1 zyg-9 Abstract: Correct placement and orientation of the mitotic spindle is essential for segregation of localized components and positioning of daughter cells. Although these processes are important in many cells, few factors that regulate spindle placement are known. Previous work has shown that GPB-1, the G beta subunit of a heterotrimeric G protein, is required for orientation of early cell division axes in C. elegans embryos. Here we show that GOA-1 (a G alpha (0)) and the related GPA-16 are the functionally redundant Get subunits and that GPC-2 is the relevant G gamma subunit that is required for spindle orientation in the early embryo. We show that G alpha and G beta gamma are involved in controlling distinct microtubule-dependent processes. G beta gamma is important in regulating migration of the centrosome around the nucleus and hence in orientating the mitotic spindle. G alpha is required for asymmetric spindle positioning in the one-celled embryo. ------------------- Key: 4577 Medline: 21169934 Authors: Hu S;Lee R;Zhang Z;Krylov SN;Dovichi NJ Title: Protein analysis of an individual Caenorhabditis elegans single-cell embryo by capillary electrophoresis. Citation: Journal of Chromatography B 752: 307-310 2001 Type: ARTICLE Genes: Abstract: We present a simple one-dimensional electrophoretic map of the expressed proteins in a Caenorhabditis elegans embryo. The embryo was taken from an adult nematode, injected into a 50-mum I.D. capillary, and lysed. The proteins were fluorescently labeled and then separated by capillary electrophoresis and detected by laser-induced fluorescence. Over 20 components were resolved in the 22-min separation. The dynamic range was outstanding for this separation, noise in the baseline was less than 0.01%; the amplitude of the largest component. ------------------- Key: 4578 Medline: Authors: Kranewitter WJ;Ylanne J;Gimona M Title: UNC-87 is an actin-bundling protein. Citation: Journal of Biological Chemistry 276: 6306-6312 2001 Type: ARTICLE Genes: unc-87 Abstract: The Caenorhabditis elegans unc-87 gene product is essential for the maintenance of the nematode body wall muscle where it is found colocalized with actin in the I band. The molecular domain structure of the protein reveals similarity to the C-terminal repeat region of the smooth muscle actin-binding protein calponin. In this study we investigated the in vitro function of UNC-87 using both the full-length recombinant molecule and several truncated mutants. According to analytical ultracentrifugation UNC-87 occurs as a monomer in solution. UNC-87 cosedimented with both smooth and skeletal muscle F-actin, but not with monomeric G-actin, and exhibited potent actin filament bundling activity. Actin binding was independent of the presence of tropomyosin and the actin cross-linking proteins filamin and cu-actinin. Consistent with its actin bundling activity in vitro, UNC-87 tagged with green fluorescent protein associated with and promoted the formation of actin stress fiber bundles in living cells. These data identify UNC-87 as an actin-bundling protein and highlight the calponin-like repeats as a novel ------------------- Key: 4579 Medline: 11171341 Authors: Herman MA Title: C. elegans POP-1/TCF functions in a canonical Wnt pathway that controls cell migration and in a noncanonical Wnt pathway that controls cell polarity. Citation: Development 128: 581-590 2001 Type: ARTICLE Genes: apr-1 bar-1 egl-20 hmp-2 lin-17 lin-44 lit-1 mab-5 mig-5 mom-1 mom-2 mom-4 mom-5 pop-1 rde-1 sgg-1 wrm-1 Abstract: In Caenorhabditis elegans, Wnt signaling pathways are important in controlling cell polarity and cell migrations. In the embryo, a novel Wnt pathway functions through a beta -catenin homolog, WRM-1, to downregulate the levels of POP-1/Tcf in the posterior daughter of the EMS blastomere. The level of POP-1 is also lower in the posterior daughters of many anteroposterior asymmetric cell divisions during development. I have found that this is the case for of a pair of postembryonic blast cells in the tail. In wild-type animals, the level of POP-1 is lower in the posterior daughters of the two T cells, TL and TR. Furthermore, in lin-44/Wnt mutants, in which the polarities of the T cell divisions are frequently reversed, the level of POP-1 is frequently lower in the anterior daughters of the T cells. I have used a novel RNA-mediated interference technique to interfere specifically with pop-1 zygotic function and have determined that pop-1 is required for wild-type T cell polarity. Surprisingly, none of the three C. elegans beta-catenin homologs appeared to function with POP-1 to control T cell polarity. Wnt signaling by EGL-20/Wnt controls the migration of the descendants of the QL neuroblast by regulating the expression the Hox gene mab-5. Interfering with pop-1 zygotic function caused defects in the migration of the QL descendants that mimicked the defects in egl-20/Wnt mutants and blocked the expression of mab-5. This suggests that POP-1 functions in the canonical Wnt pathway to control QL descendant migration and in novel Wnt pathways to control EMS and T cell polarities. ------------------- Key: 4580 Medline: 11708615 Authors: Michalski AI;Johnson ME;Cypser JR;Yashin AI Title: Heating stress patterns in Caenorhabditis elegans longevity and survivorship. Citation: Biogerontology 2: 35-44 2001 Type: ARTICLE Genes: Abstract: Survival data from Caenorhabditis elegans strain TJ1060 (spe-9; fer-15) following brief exposure to 35 degrees C have been investigated. Three experiments with 3-day-old worms were conducted with heat duration ranging between 0 and 12 hours. A statistically significant increase in life expectancy was observed in the groups heated for less than 2 hours, as compared to the unheated control groups. In different experiments P-values for the observed life spans under the hypothesis that heating has no influence on longevity were P < 0.004 after 0.5 hour heat, P < 0.012 after 1 hour heat and P < 0.055 after 2 hours of heating. A biphasic survival model with Gamma distributed frailty has been constructed to describe the survival of worms after heating. The increase in the remaining life expectancy is determined by more effective protection by heat-induced substances in the ages younger than 27 days. The unheated control group demonstrated acquired heterogeneity of frailty with chronological age while the heat-induced substances defend the worms in a universal way and protect against the development of frailty. ------------------- Key: 4581 Medline: 21154912 Authors: Friedman R;Hughes AL Title: Gene duplication and the structure of eukaryotic genomes. Citation: Genome Research 11: 373-381 2001 Type: ARTICLE Genes: Abstract: A simple method for understanding how gene duplication has contributed to genomic structure was applied to the complete genomes of Caenorhabditis elegans, Drosophila melanogaster, and yeast Saccharomyces cerevisiae. By this method, the genes belonging to gene families (the paranome) were identified, and the extent of sharing of two or more families between genomic windows was compared with that expected under a null model. The results showed significant evidence of duplication of genomic blocks in both C. elegans and yeast. In C. elegans, the five block duplications identified all occurred intra-chromosomally, and all but one occurred quite recently. In yeast, by contrast, 39 duplicated blocks were identified, and all but one of these was inter-chromosomal. Of these 39 blocks, 28 showed evidence of ancient duplication, possibly as a result of an ancient polyploidization event. By contrast, three blocks showed evidence of very recent duplication, while seven others showed a mixture of ancient and recent duplication events. Thus, duplication of genomic blocks has been an ongoing feature of yeast evolution over the past 200-300 million years. ------------------- Key: 4582 Medline: Authors: Boulton SJ;Vincent S;Vidal M Title: Use of protein-interaction maps to formulate biological questions. Citation: Current Opinion in Chemical Biology 5: 57-62 2001 Type: REVIEW Genes: glp-1 lag-1 lag-3 Abstract: Protein-interaction mapping approaches generate functional information for large numbers of genes that are predicted from complete genome sequences. This information, released as databases available on the Internet, is likely to transform the way biologists formulate and then address their questions of interest. ------------------- Key: 4583 Medline: Authors: Ball CA;Cherry JM Title: Genome comparisons highlight similarity and diversity within the eukaryotic kingdoms. Citation: Current Opinion in Chemical Biology 5: 86-89 2001 Type: REVIEW Genes: Abstract: In 2000, the number of completely sequenced eukaryotic genomes increased to four. The addition of Drosophila and Arabidopsis into this cohort permits additional insights into the processes that have shaped evolution. Analysis and comparisons of both completed genomes and partially sequenced genomes have already shed light on mechanisms such as gene duplication and gene loss that have long been hypothesized to be major forces in speciation. Indeed, duplicate gene pairs in Saccharomyces, Arabidopsis, Caenorhabditis and Drosophila are high: 30%, 60%, 48% and 40%, respectively. Evidence of horizontal gene-transfer, thought to be a major evolutionary force in bacteria, has been found in Arabidopsis. The release of the 'first draft' of the human genome sequence in 2000 heralds a new stage of biological study. Understanding the as-yet-unannotated human genome will be largely based on conclusions, techniques and tools developed during the analysis and comparison of the genome of these four model organisms. ------------------- Key: 4584 Medline: Authors: Turner AJ;Isaac RE;Coates D Title: The neprilysin (NEP) family of zinc metalloendopeptidases: genomics and function. Citation: BioEssays 23: 261-269 2001 Type: REVIEW Genes: Abstract: Neprilysin (NEP), a thermolysin-like zinc metalloendopeptidase, plays an important role in turning off peptide signalling events at the cell surface. It is involved in the metabolism of a number of regulatory peptides of the mammalian nervous, cardiovascular, inflammatory and immune systems. Examples include enkephalins, tachykinins, natriuretic and chemotactic peptides. NEP is an integral plasma membrane ectopeptidase of the M13 family of zinc peptidases. Other related mammalian NEP-like enzymes include the endothelin-converting enzymes (ECE-1 and ECE-2), KELL and PEX. A number of novel mammalian homologues of NEP have also recently been described. NEP family members are potential therapeutic targets, for example in cardiovascular and inflammatory disorders, and potent and selective inhibitors such as phosphoramidon have contributed to understanding enzyme function. Inhibitor design should be facilitated by the recent three-dimensional structural solution of the MEP-phosphoramidon complex. For several of the family members, however, a well-defined physiological function or substrate is lacking. Knowledge of the complete genomes of Caenorhabditis elegans and Drosophila melanogaster allows the full complement of NEP-like activities to be analysed in a single organism. These model organisms also provide convenient systems for examining cell-specific expression, developmental and functional roles of this peptidase ------------------- Key: 4585 Medline: 21241715 Authors: Anderson GL;Boyd WA;Williams PL Title: Assessment of sublethal endpoints for toxicity testing with the nematode Caenorhabditis elegans. Citation: Environmental Toxicology and Chemistry 20: 833-838 2001 Type: ARTICLE Genes: Abstract: Toxicity tests in invertebrates often use sublethal endpoints, which may exhibit different sensitivity for various toxicants. Our objective was to characterize the sensitivity of movement, feeding, growth, and reproduction as endpoints for heavy metal toxicity testing with Caenorhabditis elegans. Growth and feeding were assessed in the same nematode samples used to assess movement and reproduction. Median effective concentrations (EC50s) for 24-h exposures to Pb, Cu, and Cd were determined for movement, feeding, and growth and a 72-h EC50 was derived for reproduction. The order of toxicity was Cu > Pb > Cd for each endpoint, including lethality and movement. There were no differences in sensitivity among endpoints for any metal. When exposed for 4 h at (sublethal) concentrations that were 14 times the 24-h EC50 value, Pb and Cu reduced feeding to the same extent while movement was reduced significantly more by Pb than by Cu. Thus, a difference in sensitivity of endpoints was apparent at 4 h, which was not evident at 24 h. These observations suggest potentially different mechanisms of toxicity for 24- and 4-h tests. ------------------- Key: 4586 Medline: Authors: Zarkower D Title: Establishing sexual dimorphism: Conservation amidst diversity? Citation: Nature Reviews Genetics 2: 175-185 2001 Type: REVIEW Genes: egl-1 fem-1 fem-2 fem-3 egl-1 lin-22 lin-28 lin-32 mab-3 mab-5 sdc-1 sdc-2 sdc-3 tra-1 tra-2 tra-3 xol-1 Abstract: The molecular mechanisms that control sexual dimorphism are very different in distantly related animals. Did sex determination arise several times with different regulatory mechanisms, or is it an ancient process with little surviving evidence of ancestral genes? The recent identification of related sexual regulators in different phyla indicates that some aspects of sexual regulation might be ancient. Studies of sex-determining mechanisms are beginning to reveal how sexual dimorphism arises and evolves. ------------------- Key: 4587 Medline: 21143060 Authors: Sanjuan R;Marin I Title: Tracing the origin of the compensasome: Evolutionary history of DEAH helicase and MYST acetyltransferase gene Citation: Molecular Biology and Evolution 18: 330-343 2001 Type: ARTICLE Genes: mog-1 mog-4 mog-5 Abstract: Dosage compensation in Drosophila is mediated by a complex of proteins and RNAs called the "compensasome." Two of the genes that encode proteins of the complex, maleless (mle) and males-absent-on-the-first (mof), respectively, belong to the DEAH helicase and MYST acetyltransferase gene families. We performed comprehensive phylogenetic and structural analyses to determine the evolutionary histories of these two gene families and thus to better understand the origin of the compensasome. All of the members of the DEAH and MYST families of the completely sequenced Saccharomyces cerevisiae and Caenorhabditis elegans genomes, as well as those so far (June 2000) found in Drosophila melanogaster (for which the euchromatic part of the genome has also been fully sequenced) and Homo sapiens, were analyzed. We describe a total of 39 DEAH helicases in these four species. Almost all of them can be grouped in just three main branches. The first branch includes the yeast PRP2, PRP16, PRP22, and PRP43 splicing factors and their orthologs in animal species. Each PRP gene has a single ortholog in metazoans. The second branch includes just four genes, found in yeast (Ecm16) and Drosophila (kurz) and their orthologs in humans and Caenorhabditis. The third branch includes (1) a single yeast gene (YLR419w); (2) six Drosophila genes, including maleless and spindle-E/homeless; (3) four human genes, among them the ortholog of maleless, which encodes RNA helicase A; and (4) three C. elegans genes, including orthologs of maleless and spindle-E. Thus, this branch has largely expanded in metazoans. We also show that, for the whole DEAH family, only MLE and its metazoan orthologs have acquired new protein domains since the fungi/animals split. We found a total of 17 MYST family proteins in the four analyzed species. We determined putative orthologs of mof in both C. elegans and H. sapiens, and we show that the most likely ortholog in yeast is the Sas2 gene. Moreover, a paralog of mof exists in Drosophila. All of these results, together with those found for a third member of the compensasome, msl-3, suggest that this complex emerged after the fungi/animals split and that it may be present in mammalian species. Both gene duplication and the acquisition of new protein modules may have played important roles in the ------------------- Key: 4588 Medline: 21189990 Authors: Trachtulec Z;Forejt J Title: Synteny of orthologous genes conserved in mammals, snake, fly, nematode, and fission yeast. Citation: Mammalian Genome 12: 227-231 2001 Type: ARTICLE Genes: ceh-20 glp-1 lin-12 prk-1 prk-2 unc-93 Abstract: Four mouse genes. programmed cell death 2 (Pdcd2 or Rp8), brain protein 44-like (Brp44l), bystin-like (Bysl), and uncoordinated-93-like (Unc93l) genes were mapped to Chromosome (Chr) 17. The orthologs of these and other mouse Chr 17 genes are localized on Chr III of Caenorhabditis elegans, thus defining a syntenic group conserved between vertebrates and nonvertebrates. In human, mouse, and snake, the PDCD2-, and TATA-binding protein (TBP)-encoding genes are adjacent tail-to-tail. The TBP-and PDCD2-encoding genes are linked also in Drosophila, and, together with proteasomal subunit C5 gene, they are syntenic in human, mouse, C. elegans, and Schizosaccharomyces pombe. The orthologs of tightly linked C. elegans genes, coding for BRP44L and PDCD2, map to about 2-Mb interval on human region 6q27 and on mouse Chr 17. Hitherto, 13 members of synteny conserved between C. elegans and vertebrates have been detected, of which six are located on Drosophila Chr X. Such a distribution of transcription units is nonrandom and could indicate a long-range cis-acting relationship among the genes within the conserved syntenic group. ------------------- Key: 4589 Medline: 21108348 Authors: Aravind L;Dixit VM;Koonin EV Title: Apoptotic molecular machinery: Vastly increased complexity in vertebrates revealed by genome comparisons. Citation: Science 291: 1279-1284 2001 Type: ARTICLE Genes: Abstract: A comparison of the proteins encoded in the recently (nearly) completed human genome to those from the fly and nematode genomes reveals a major increase in the complexity of the apoptotic molecular machinery in vertebrates, in terms of both the number of proteins involved and their domain architecture. Several components of the apoptotic system are shared by humans and flies, to the exclusion of nematodes, which seems to support the existence of a coelomate clade in animal evolution. A considerable repertoire of apoptotic protein domains was detected in Actinomycetes and Cyanobacteria, which suggests a major contribution of horizontal gene transfer to the early evolution of apoptosis. ------------------- Key: 4590 Medline: Authors: Dolinski C;Baldwin JG;Thomas WK Title: Comparative survey of early embryogenesis of Secernentea (Nematoda), with phylogenetic implications. Citation: Canadian Journal of Zoology 79: 82-94 2001 Type: ARTICLE Genes: Abstract: Insight into the evolution of class Secernentea (Nematoda) for the purpose of providing a phylogenetic context for the model Caenorhabditis elegans is being gained from the use of molecular character sets. Such phylogenies provide a framework for mapping the evolution of diversity in some early-development characters for 70 species and 19 families of Secernentea. These characters include (i) whether AB and P1 blastomeres initially develop at the same (synchronous) or different (asynchronous) rates, (ii) whether AB and P1 are initially aligned along the linear axis of the embryo (tandem pattern) or obliquely (rhomboidal pattern), and (iii) whether the founder germ cell, P4, is established early, i.e., by the sixth cleavage, or later. Evolutionary polarity of characters was evaluated through outgroup comparisons. From our data the following inferences are made. The derived character, late establishment of P4, evolved primarily in the ancestor of the monophyletic groups Diplogastrina, Rhabditina, and Panagrolaimidae. Asynchronous development is convergent, defining one clade of Tylenchina as well as Cephalobina, and also arising independently in Aphelenchina. The rhomboidal embryo is ancestral to the tandem-pattern embryo that defines a second clade of Tylenchina. Early-embryo characters are congruent with the polyphyly of Cephalobina and Aphelenchina, as has been demonstrated by molecular phylogenies. Many aspects of early embryogenesis, rather than being highly conserved, evolve at a rate appropriate ------------------- Key: 4591 Medline: 21150570 Authors: Miller MA;Nguyen VQ;Lee MH;Kosinski M;Schedl T;Caprioli RM;Greenstein D Title: A sperm cytoskeletal protein that signals oocyte meiotic maturation and ovulation. Citation: Science 291: 2144-2147 2001 Type: ARTICLE Genes: fog-2 mpk-1 Abstract: Caenorhabditis elegans oocytes, like those of most animals, arrest during meiotic prophase. Sperm promote the resumption of meiosis (maturation) and contraction of smooth muscle-like gonadal sheath cells, which are required for ovulation. We show that the major sperm cytoskeletal protein (MSP) is a bipartite signal for oocyte maturation and sheath contraction. MSP also functions in sperm locomotion, playing a role analogous to actin. Thus, during evolution, MSP has acquired extracellular signaling and intracellular cytoskeletal functions for reproduction. Proteins with MSP-like domains are found in plants, fungi, and other animals, suggesting that related signaling functions may exist in other phyla. ------------------- Key: 4592 Medline: 21137246 Authors: Hartman PS;Hlavacek A;Wilde H;Lewicki D;Schubert W;Kern RG;Kazarians GA;Benton EV;Benton ER;Nelson GA Title: A comparison of mutations induced by accelerated iron particles versus those induced by low earth orbit space radiation in the FEM-3 gene of Caenorhabditis elegans. Citation: Mutation Research 474: 47-55 2001 Type: ARTICLE Genes: fem-3 Abstract: The fem-3 gene of Caenorhabditis elegans was employed to determine the mutation frequency as well as the nature of mutations induced by low earth orbit space radiation ambient to Space Shuttle flight STS-76. Recovered mutations were compared to those induced by accelerated iron ions generated by the AGS synchrotron accelerator at Brookhaven National Laboratory. For logistical reasons, dauer larvae were prepared at TCU, transported to either Kennedy Space Center or Brookhaven National Laboratory, flown in space or irradiated, returned to TCU and screened for mutants. A total of 25 fem-3 mutants were recovered after the shuttle flight and yielded a mutation frequency of 2.1 x 10(-5). roughly 3.3-fold higher than the spontaneous rate of 6.3 x 10(-6). Four of the mutations were homozygous inviable, suggesting that they were large deletions encompassing fem-3 as well as neighboring, essential genes. Southern blot analyses revealed that one of the 25 contained a polymorphism in fem-3, further evidence that space radiation can induce deletions. While no polymorphisms were detected among the iron ion-induced mutations, three of the 15 mutants were homozygous inviable. which is in keeping with previous observations that high LET iron particles generate deficiencies. These data provide evidence, albeit indirect, that an important mutagenic component of ambient space radiation is high LET charged particles such as iron ------------------- Key: 4593 Medline: 21160284 Authors: Gilleard JS;McGhee JD Title: Activation of hypodermal differentiation in the Caenorhabditis elegans embryo by GATA transcription factors ELT-1 and ELT-3. Citation: Molecular and Cellular Biology 21: 2533-2544 2001 Type: ARTICLE Genes: dpy-7 elt-1 elt-2 elt-3 elt-5 elt-6 end-1 lin-26 Abstract: The Caenorhabditis elegans GATA transcription factor genes elt-1 and elt-3 are expressed in the embryonic hypodermis (also called the epidermis). elt-l is expressed in precursor cells and is essential for the production of most hypodermal cells (22). elt-3 is expressed in all of the major hypodermal cells except the lateral seam cells, and expression is initiated immediately after the terminal division of precursor lineages (13). Although this expression pattern suggests a role for ELT-3 in hypodermal development, no functional studies have yet been performed. In the present paper, we show that either elt-3 or elt-1 is sufficient, when force expressed in early embryonic blastomeres, to activate a program of hypodermal differentiation even in blastomeres that are not hypodermal precursors in wild-type embryos. We have deleted the elt-3 gene and shown that ELT-3 is not essential for either hypodermal cell differentiation or the viability of the organism. We showed that ELT-3 can activate hypodermal gene expression in the absence of ELT-1 and that, conversely, ELT-1 can activate hypodermal gene expression in the absence of ELT-3. Overall, the combined results of the mutant phenotypes, initial expression times, and our forced-expression experiments suggest that ELT-3 acts downstream of ELT-1 in a redundant pathway controlling hypodermal cell differentiation. ------------------- Key: 4594 Medline: 21143910 Authors: Lickteig KM;Duerr JS;Frisby DL;Hall DH;Rand JB;Miller DM Title: Regulation of neurotransmitter vesicles by the homeodomain protein UNC-4 and its transcriptional corepressor UNC-37/Groucho in Caenorhabditis elegans cholinergic motor neurons. Citation: Journal of Neuroscience 21: 2001-2014 2001 Type: ARTICLE Genes: rab-3 unc-4 unc-11 unc-17 unc-18 unc-37 Abstract: Motor neuron function depends on neurotransmitter release from synaptic vesicles (SVs). Here we show that the UNC-4 homeoprotein and its transcriptional corepressor protein UNC-37 regulate SV protein levels in specific Caenorhabditis elegans motor neurons. UNC-4 is expressed in four classes (DA, VA, VC, and SAB) of cholinergic motor neurons. Antibody staining reveals that five different vesicular proteins (UNC-17, choline acetyltransferase, Synaptotagmin, Synaptobrevin, and RAB-3) are substantially reduced in unc-4 and unc-37 mutants in these cells; nonvesicular neuronal proteins (Syntaxin, UNC-18, and UNC-11) are not affected, however. Ultrastructural analysis of VA motor neurons in the mutant unc-4( e120) confirms that SV number in the presynaptic zone is reduced (similar to 40%) whereas axonal diameter and synaptic morphology are not visibly altered. Because the UNC-4-UNC-37 complex has been shown to mediate transcriptional repression, we propose that these effects are performed via an intermediate gene. Our results are consistent with a model in which this unc-4 target gene ("gene-x") functions at a post-transcriptional level as a negative regulator of SV biogenesis or stability. Experiments with a temperature-sensitive unc-4 mutant show that the adult level of SV proteins strictly depends on unc-4 function during a critical period of motor neuron differentiation. unc-4 activity during this sensitive larval stage is also required for the creation of proper synaptic inputs to VA motor neurons. The temporal correlation of these events may mean that a common unc-4-dependent mechanism controls both the specificity of synaptic inputs as well as the strength of synaptic outputs for these motor neurons. ------------------- Key: 4595 Medline: 11244089 Authors: Miyadera H;Amino H;Hiraishi A;Taka H;Murayama K;Miyoshi H;Sakamoto K;Ishii N;Hekimi S;Kita K Title: Altered quinone biosynthesis in the long-lived clk-1 mutants of Caenorhabditis elegans. Citation: Journal of Biological Chemistry 276: 7713-7716 2001 Type: ARTICLE Genes: clk-1 Abstract: Mutations in the clk-1 gene of Caenorhabditis elegans result in an extended life span and an average slowing down of developmental and behavioral rates. However, it has not been possible to identify biochemical changes that might underlie the extension of life span observed in clk-1 mutants, and therefore the function of CLK-1 in C. elegans remains unknown. In this report, we analyzed the effect of clk-1 mutation on ubiquinone (UQ(9)) biosynthesis and show that clk-1 mutants mitochondria do not contain detectable levels of UQ(9). Instead, the UQ(9) biosynthesis intermediate, demethoxyubiquinone (DMQ(9)), is present at high levels. This result demonstrates that CLK-1 is absolutely required for the biosynthesis of UQ(9) in C. elegans. Interestingly, the activity levels of NADH-cytochrome c reductase and succinate-cytochrome c reductase in mutant mitochondria are very similar to those in the wild-type, suggesting that DMQ(9) can function as an electron carrier in the respiratory chain. To test this possibility, the short side chain derivative DMQ(2) was chemically synthesized. We find that DMQ(2) can act as an electron acceptor for both complex I and complex II in clk-1 mutant mitochondria, while another ubiquinone biosynthesis precursor, 3-hydroxy-UQ(2), cannot. The accumulation of DMQ(9) and its use in mutant mitochondria indicate, for the first time in any organism, a link between the alteration in the quinone species used in ------------------- Key: 4596 Medline: 21135651 Authors: Chin GM;Villeneuve AM Title: C. elegans mre-11 is required for meiotic recombination and DNA repair but is dispensable for the meiotic G(2) DNA damage checkpoint. Citation: Genes & Development 15: 522-534 2001 Type: ARTICLE Genes: mre-11 msh-5 Abstract: We investigated the roles of Caenorhabditis elegans MRE-11 in multiple cellular processes required to maintain genome integrity. Although yeast Mre11 is known to promote genome stability through several diverse pathways, inviability of vertebrate cells that lack Mre11 has hindered elucidation of the in vivo roles of this conserved protein in metazoan biology. Worms homozygous for an mre-11 null mutation are viable, allowing us to demonstrate in vivo requirements for MRE-11 in meiotic recombination and DNA repair. In mre-11 mutants, meiotic crossovers are not detected, and oocyte chromosomes lack chiasmata but appear otherwise intact, gamma -irradiation of mre-11 mutant germ cells during meiotic prophase eliminates progeny survivorship and induces chromosome fragmentation and other cytologically visible abnormalities, indicating a defect in repair of radiation-induced chromosome damage. Whereas mre-11 mutant germ cells are repair-deficient, they retain function of the meiotic G(2) DNA damage checkpoint that triggers germ cell apoptosis in response to ionizing radiation. Although mre-11/mre-11 animals derived from heterozygous parents are viable and produce many embryos, there is a marked drop both in the number and survivorship of embryos produced by succeeding generations. This progressive loss of fecundity and viability indicates that MRE-11 performs a function essential for maintaining reproductive capacity in the species. ------------------- Key: 4597 Medline: 11223248 Authors: Timmons L;Court DL;Fire A Title: Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans. Citation: Gene 263: 103-112 2001 Type: ARTICLE Genes: fem-1 hlh-1 let-858 myo-3 unc-22 unc-54 unc-119 Abstract: Genetic interference mediated by double-stranded RNA (RNAi) has been a valuable tool in the analysis of gene function in Caenorhabditis elegans. Here we report an efficient induction of RNAi using bacteria to deliver double-stranded RNA. This method makes use of bacteria that are deficient in RNaseIII, an enzyme that normally degrades a majority of dsRNAs in the bacterial cell. Bacteria deficient for RNaseIII were engineered to produce high quantities of specific dsRNA segments. When fed to C. elegans, such engineered bacteria were found to produce populations of RNAi-affected animals with phenotypes that were comparable in expressivity to the corresponding loss-of-function mutants. We found the method to be most effective in inducing RNAi for non-neuronal tissue of late larval and adult hermaphrodites, with decreased effectiveness in the nervous system, in early larval stages, and in males. Bacteria-induced RNAi phenotypes could be maintained over the course of several generations with continuous feeding, allowing for convenient assessments of the biological consequences of specific genetic interference and of continuous exposure to dsRNAs. ------------------- Key: 4598 Medline: 21125234 Authors: Frame IG;Cutfield JF;Poulter RTM Title: New BEL-like LTR-retrotransposons in Fugu rubripes, Caenorhabditis elegans, and Drosophila melanogaster. Citation: Gene 263: 219-230 2001 Type: ARTICLE Genes: Abstract: The EEL group of retroelements is present in greater numbers, variety and taxonomic range than may have been thought previously. In addition to the insects, nematodes and schistosomes, EEL-like elements are present in echinoderms, urochordates, and at least two highly diverged species of fish. We describe one new full-length EEL-Like element in Fugu that we call Suzu, another in Drosophila that we call Tinker, and seven new families in C. elegans. Many of the C. elegans elements have an unusual insertion at the 5' end. The previously known Roo, TRAM and Telemac are also EEL-like retrotransposons. Some EEL-like elements have captured an envelope gene, probably from other retroelements in some cases but from a phlebovirus in one ------------------- Key: 4599 Medline: 21159829 Authors: Barsyte D;Lovejoy DA;Lithgow GJ Title: Longevity and heavy metal resistance in daf-2 and age-1 long-lived mutants of Caenorhabditis elegans. Citation: FASEB Journal 15: 627-634 2001 Type: ARTICLE Genes: age-1 daf-2 daf-7 daf-16 Abstract: In the nematode Caenorhabditis elegans, dauer formation, stress resistance, and longevity are determined in part by DAF-2 (insulin receptor-like protein), AGE-1 (phosphatidylinositol-3-OH kinase catalytic subunit), and DAF-16 (forkhead transcription factor). Mutations in daf-2 and age-1 result in increased resistance to heat, oxidants, and UV. We have discovered that daf-2 and age-1 mutations result in increased Cd and Cu ion resistance in a 24 h toxicity assay. Lethal concentration (LC50) values for Cd and Cu ions in daf-2 and age-1 mutants were significantly (P<0.001) higher than in wild-type nematodes. However, LC50 values in daf-16;age-1 mutants were not significantly different, implying that metal resistance is influenced by a DAF-16-related function. As metallothionein (MT) proteins play a major role in metal detoxification, we examined the expression of MT genes both under noninducing conditions and after exposure to sublethal and acute heavy metal stress. MT1 mRNA levels were significantly (P<0.05) higher in daf-2 mutants compared to age-1 mutants and wild-type C. elegans under basal conditions. After 10 mM Cd treatment, induction of MT1 and MT2 mRNA was three- and twofold higher, respectively, in daf-2 mutant worms than in wild-type. However, a sublethal concentration of Cd (0.1 mM) resulted in even higher (three- to sevenfold) levels of both MT mRNAs in all strains, Cu did not induce MTI or MT2 mRNAs. These results are consistent with a model in which the insulin-signaling pathway determines life span through regulation of stress protein genes.-Barsyte, D., Lovejoy, D. A., Lithgow, G. J. Longevity and heavy metal resistance in daf-2 and age-1 long-lived mutants of Caenorhabditis elegans. ------------------- Key: 4600 Medline: 21150861 Authors: Villeneuve AM Title: Development - How to stimulate your partner. Citation: Science 291: 2009- 2001 Type: REVIEW Genes: Abstract: Animals have evolved a plethora of elaborate mechanisms to ensure successful sexual reproduction. These run the gamut from intricate mating rituals and release of pheromones, which aid in the identification of appropriate partners, to cell-cell signaling events that coordinate the timing of meiosis (cell division of egg and sperm precursors), gamete formation, and fertilization. The nematode Caenorhabditis elegans, an unrepentant minimalist of the animal kingdom, maximizes the efficiency of its reproductive resources several ways. ------------------- Key: 4601 Medline: 11110798 Authors: Pujol N;Bonnerot C;Ewbank JJ;Kohara Y;Thierry-Mieg D Title: The Caenorhabditis elegans unc-32 gene encodes alternative forms of a vacuolar ATPase alpha subunit. Citation: Journal of Biological Chemistry 276: 11913-11921 2001 Type: ARTICLE Genes: sup-7 unc-32 vha-5 vha-6 vha-7 nDf17 Abstract: Eukaryotes possess multiple isoforms of the a subunit of the V-0 complex of vacuolar-type Ht-ATPases (V-ATPases). Mutations in the V-ATPase a3 isoform have recently been shown to result in osteopetrosis, a fatal disease in humans, but no function has yet been ascribed to other isoforms. In Caenorhabditis elegans, the unc-32 mutant was originally isolated on the basis of its movement defect. We have isolated four new mutant alleles, the strongest of which is embryonic lethal. We show here that unc-32 corresponds to one of the four genes encoding a V-ATPase a subunit in the nematode, and we present their expression patterns and a molecular analysis of the gene family, unc-32 gives rise via alternative splicing to at least six transcripts. In the uncoordinated alleles, the transcript unc-32 B is affected, suggesting that it encodes an isoform that is targeted to synaptic vesicles of cholinergic neurons, where it would control neurotransmitter uptake or release. Other isoforms expressed widely during embryogenesis are mutated in the lethal alleles and would be involved in other acidic organelles. Our results indicate that V-ATPase a subunit genes are highly regulated and have tissue-specific function. ------------------- Key: 4602 Medline: 21150111 Authors: Wang S;Kimble J Title: The TRA-1 transcription factor binds TRA-2 to regulate sexual fates in Caenorhabditis elegans. Citation: EMBO Journal 20: 1363-1372 2001 Type: ARTICLE Genes: fem-3 tra-1 tra-2 Abstract: The tra-1 and tra-2 sex-determining genes promote female fates in Caenorhabditis elegans. Classical genetic studies placed tra-1 as the terminal regulator of the pathway with tra-2 acting upstream as a regulator of regulators of tra-1. Here we report the surprising result that the TRA-1 transcription factor binds the intracellular domain of the TRA-2 membrane protein. This binding is dependent on the MX regulatory domain, a region of the TRA-2 intracellular domain shown previously to be critical for the onset of hermaphrodite spermatogenesis. The functional importance of the TRA-1-TRA-2 physical interaction is supported by genetic interactions between tra-1(0) and tra-2(mx) mutations: a reduction of tra-1 gene dose from two copies to one copy enhances the tra-2(mx) feminization phenotype, but has no apparent somatic effect. In Caenorhabditis briggsae, we also find an MX-dependent interaction between Cb-TRA-1 and Cb-TRA-2, hut intriguingly, no cross-species interactions are seen. The conservation of the TRA-1-TRA-2 interaction underscores its importance in sex ------------------- Key: 4603 Medline: 11290289 Authors: Haycraft CJ;Swoboda P;Taulman PD;Thomas JH;Yoder BK Title: The C. elegans homolog of the murine cystic kidney disease gene Tg737 functions in a ciliogenic pathway and is disrupted in osm-5 mutant worms. Citation: Development 128: 1493-1505 2001 Type: ARTICLE Genes: che-2 che-3 daf-19 osm-1 osm-5 osm-6 Abstract: Cilia and flagella are important organelles involved in diverse functions such as fluid and cell movement, sensory perception and embryonic patterning. They are devoid of protein synthesis, thus their formation and maintenance requires the movement of protein complexes from the cytoplasm into the cilium and flagellum axoneme by intraflagellar transport (IFT), a conserved process common to all ciliated or flagellated eukaryotic cells. We report that mutations in the Caenorhabditis elegans gene Y41g9a.1 are responsible for the ciliary defects in osm-5 mutant worms. This was confirmed by transgenic rescue of osm-5(p813) mutants using the wild-type Y41g9a.1 gene. osm-5 encodes a tetratricopeptide repeat (TPR)-containing protein that is the homolog of murine polaris (Tg737), a protein associated with cystic kidney disease and left-right axis patterning defects in the mouse. osm-5 is expressed in ciliated sensory neurons in C. elegans and its expression is regulated by DAF-19, an RFX-type transcription factor that governs the expression of other genes involved in cilia formation in the worm. Similar to murine polaris, the OSM-5 protein was found to concentrate at the cilium base and within the cilium axoneme as shown by an OSM-5::GFP translational fusion and immunofluorescence. Furthermore, time-lapse imaging of OSM-5::GFP fusion protein shows fluorescent particle migration within the cilia. Overall, the data support a crucial role for osm-5 in a conserved ciliogenic pathway, most likely as a component of the IFT process. ------------------- Key: 4604 Medline: Authors: Schaefer AM;Nonet ML Title: Cellular and molecular insights into presynaptic assembly. Citation: Current Opinion in Neurobiology 11: 127-134 2001 Type: REVIEW Genes: rpm-1 sad-1 syd-2 unc-13 unc-104 Abstract: Little is known about the development of presynaptic specializations. Recent studies that visualize tagged synaptic components in cultured cells and in vivo have identified molecular participants and reveal common features in cellular processs of presynaptic assembly. ------------------- Key: 4605 Medline: Authors: Sharp PA Title: RNA interference - 2001. Citation: Genes & Development 15: 485-490 2001 Type: REVIEW Genes: mut-7 rde-1 rde-2 rde-3 smg-2 smg-5 smg-6 Abstract: In the few years since the discovery of RNA interference, it has become clear that this process is ancient. RNAi, the oldest and most ubiquitous antiviral system, appeared before the divergence of plants and animals. Because aspects of RNAi, known as cosuppression, also control the expression of transposable elements and repetitive sequences, the interplay of RNAi and transposon activities have almost certainly shaped the structure of the genome of most organisms. Surprisingly, we are only now beginning to explore the molecular processes responsible for RNAi and to appreciate the breadth of its function in biology. Practical applications of this knowledge have allowed rapid surveys of gene functions (see Fraser et al. 2000 and Gonczey et al. 2000 for RNAi analysis of genes on chromosome I and III of Caenorhabditis elegans) and will possibly result in new therapeutic interventions. ------------------- Key: 4606 Medline: 21147911 Authors: Chen J;Carey JR;Ferris H Title: Comparative demography of isogenic populations of Caenorhabditis elegans. Citation: Experimental Gerontology 36: 431-440 2001 Type: ARTICLE Genes: age-1 clk-1 Abstract: Demographic characteristics of the bacterial-feeding nematode Caenorhabditis elegans were determined in two long-lived mutant strains, TJ1052 (age-1), CB4876 (clk-1), and a wild-type strain, N2. Within each strain, there was little correlation between longevity and reproduction for individuals that lived longer than 10 days. Long-lived mutant strains produced fewer eggs than the wild type. Mean total life spans were 13.2 days for the wild type, 21.9 days for age-1, and 15.8 days for clk-1; maximum life spans were 24 days for the wild type, 47 days for age-1, and 32 days for clk-1. Differences in total life span resulted primarily from longer post-reproductive survival. The mean post-reproductive life spans were longer than the wild type by 183% in age-1 and 60% in clk-1. We conclude that (i) post-reproductive survival is not correlated with egg production within isogenic populations of C. elegans, and (ii) the relationship between reproduction and longevity differs among isogenic populations with specific longevity genes. ------------------- Key: 4607 Medline: 21149781 Authors: Horoszok L;Raymond V;Sattelle DB;Wolstenholme AJ Title: GLC-3: a novel fipronil and BIDN-sensitive, but picrotoxinin-insensitive, L-glutamate-gated chloride channel subunit from Caenorhabditis elegans. Citation: British Journal of Pharmacology 132: 1247-1254 2001 Type: ARTICLE Genes: glc-3 Abstract: We report the cloning and expression of a novel Caenorhabditis elegans polypeptide, GLC-3, with high sequence identity to previously cloned L-glutamate-gated chloride channel subunits from nematodes and insects. Expression of glc-3 cRNA in Xenopus oocytes resulted in the formation of homo-oligomeric L-glutamate-gated chloride channels with robust and rapidly desensitizing currents, an EC50 of 1.9 +/- 0.03 mM and a Hill coefficient of 1.5 +/- 0.1. GABA, glycine, histamine and NMDA all failed to activate the GLC-3 homo-oligomer at concentrations of 1 mM. The anthelminthic, ivermectin, directly and irreversibly activated the L-glutamate-gated channel with an EC50 of 0.4 +/- 0.02 muM. The GLC-3 channels were selective for chloride ions, as shown by the shift in the reversal potential for L-glutamate-gated currents after the reduction of external Cl- from 107.6 to 62.5 mM. Picrotoxinin failed to inhibit L-glutamate agonist responses at concentrations up to 1 mM. The polycyclic dinitrile, 3,3-bis-trifluoromethyl-bicyclo[2,2,1]heptane-2,2-dicarboni trile (BIDN), completely blocked L-glutamate-induced chloride currents recorded from oocytes expressing GLC-3 with an IC50 of 0.2 +/- 0.07 muM. The phenylpyrazole insecticide, fipronil, reversibly inhibited L-glutamate-gated currents recorded from the GLC-3 receptor with an IC50 of 11.5 +/- 0.11 muM. 5 In this study, we detail the unusual antagonist pharmacology of a new GluCl subunit from C. elegans. Unlike all other native and recombinant nematode GluCl reported to date, the GLC-3 receptor is insensitive to picrotoxinin, but is sensitive to two other channel blockers, BIDN and fipronil. Further study of this receptor may provide insights into the ------------------- Key: 4608 Medline: 21157410 Authors: Ono S Title: The Caenorhabditis elegans unc-78 gene encodes a homologue of actin-interacting protein 1 required for organized assembly of muscle actin filaments. Citation: Journal of Cell Biology 152: 1313-1319 2001 Type: ARTICLE Genes: unc-60 unc-78 Abstract: Assembly and maintenance of myofibrils require dynamic regulation of the actin cytoskeleton. In Caenorhabditis elegans. UNC-60B, a muscle-specific actin depolymerizing factor (ADF)/cofilin isoform, is required for proper actin filament assembly in body wall muscle (Ono, S., D.L. Baillie, and G.M. Benian. 1999. J. Cell Biol. 145:491-502). Here, I show that UNC-78 is a homologue of actin-interacting protein 1 (AIP1) and functions as a novel regulator of actin organization in myofibrils. In unc-78 mutants, the striated organization of actin filaments is disrupted, and large actin aggregates are formed in the body wall muscle cells, resulting in defects in their motility. Point mutations in unc-78 alleles change conserved residues within different WD repeats of the UNC-78 protein and cause less severe phenotypes than a deletion allele, suggesting that these mutations partially impair the function of UNC-78. UNC-60B is normally localized in the diffuse cytoplasm and to the myofibrils in wild type but mislocalized to the actin aggregates in unc-78 mutants. Similar Unc-78 phenotypes are observed in both embryonic and adult muscles. Thus, AIP1 is an important regulator of actin filament organization and localization of ADF/cofilin during development of ------------------- Key: 4609 Medline: Authors: Pierce-Shimomura JT;Faumont S;Gaston MR;Pearson BJ;Lockery SR Title: The homeobox gene lim-6 is required for dinstinct chemosensory representations in C. elegans. Citation: Nature 410: 694-698 2001 Type: ARTICLE Genes: gcy-5 gcy-6 gcy-7 lim-6 Abstract: The ability to discriminate between different chemical stimuli is crucial for food detection, spatial orientation and other adaptive behaviours in animals. In the nematode Caenorhabditis elegans, spatial orientation in gradients of soluble chemoattractants (chemotaxis) is controlled mainly by a single pair of chemosensory neurons(1). These two neurons, ASEL and ASER, are left-right homologues in terms of the disposition of their somata and processes, morphology of specialized sensory endings, synaptic partners and expression profile of many genes(2,3). However, recent gene-expression studies have revealed unexpected asymmetries between ASEL and ASER. ASEL expresses the putative receptor guanylyl cyclase genes gcy-6 and gcy-7, whereas ASER expresses gcy-5 (ref. 4). In addition, only ASEL expresses the homeobox gene lim-6, an orthologue of the human LMX1 subfamily of homeobox genes(5). Here we show, using laser ablation of neurons and whole-cell patch-clamp electrophysiology, that the asymmetries between ASEL and ASER extend to the functional level. ASEL is primarily sensitive to sodium, whereas ASER is primarily sensitive to chloride and potassium. Furthermore, we rnd that lim-6 is required for this functional asymmetry and for the ability to distinguish sodium from chloride. Thus, a homeobox gene increases the representational capacity of the nervous system by establishing asymmetric functions in a bilaterally ------------------- Key: 4610 Medline: Authors: Wes PD;Bargmann CI Title: C. elegans odour discrimination requires asymmetric diversity in olfactory neurons. Citation: Nature 410: 698-701 2001 Type: ARTICLE Genes: egl-2 nsy-1 nsy-2 nsy-3 odr-7 odr-10 str-2 unc-4 Abstract: Caenorhabditis elegans senses at least five attractive odours with a single pair of olfactory neurons, AWC, but can distinguish among these odours in behavioural assays(1). The two AWC neurons are structurally and functionally similar, but the G-protein-coupled receptor STR-2 is randomly expressed in either the left or the right AWC neuron, never in both(2). Here we describe the isolation of a mutant, ky542, with specific defects in odour discrimination and odour chemotaxis. ky542 is an allele of nsy-1, a neuronal symmetry, or Nsy, mutant in which STR-2 is expressed in both AWC neurons(2). Other Nsy mutants exhibit discrimination and olfactory defects like those of nsy-1 mutants. Laser ablation of the AWC neuron that does not express STR-2 (AWC(OFF)) recapitulates the behavioural phenotype of Nsy mutants, whereas laser ablation of the STR-2-expressing AWC neuron (AWC(ON)) causes different chemotaxis defects. We propose that odour discrimination can be achieved by segregating the detection of different odours into distinct olfactory neurons or into unique combinations of olfactory neurons. ------------------- Key: 4611 Medline: Authors: Pujol N;Ewbank JJ Title: C. elegans: from sequencing to systematic functional genomic. Citation: M S-Medecine Sciences 17: 355-357 2001 Type: REVIEW Genes: Abstract: In French. ------------------- Key: 4612 Medline: 21198767 Authors: Kiehl TR;Shibata H;Pulst SM Title: The ortholog of human ataxin-2 is essential for early embryonic patterning in C. elegans. Citation: Journal of Molecular Neuroscience 15: 231-241 2000 Type: ARTICLE Genes: atx-2 fox-1 Abstract: Ataxin-2, the gene product of the human spinocerebellar ataxia type 2 (SCA2) gene, is a protein of unknown function. Ataxin-2 interacts with ataxin-2-binding-protein 1 (A2BP1), a member of a novel family of putative RNA-binding proteins. Because the sequences of ataxin-2 and A2BP1 are evolutionarily conserved, we investigated functional aspects and expression pattern in the nematode Caenorhabditis elegans. Human ataxin-2 has 20.1% amino acid identity and 43.9% similarity to its C. elegans ortholog, designated ATX-2, that encodes a predicted 1026 aa protein. One of the worm orthologs of human A2BP1 is the numerator element FOX-1, with an overall 29.8% aa identity. We studied the expression pattern of atx-2 using the endogenous promotor coupled with a GFP expression vector. Atx-2 was widely expressed in the adult worm with strong expression in muscle and nervous tissue. It was also heavily expressed in the embryo. In order to elucidate the function of atx-2 and fox-2, we conducted RNA interference (RNAi) studies. The interfering dsRNA was introduced into larval L4 stage worms of the N2 strain by microinjection or soaking. DsRNA-representing the full-length atx-2 gene resulted in arrested embryonic development in the offspring of all 58 microinjected worms. Nomarski imaging showed embryos in different stages of developmental arrest, indicating an essential role of atx-2 for early embryonic development. When fox-2 was targeted by RNAi, there was a marked reduction in the number of eggs per worm. The results presented here underline previous findings about the interaction of human ataxin-2 and A2BP1. ------------------- Key: 4613 Medline: 21321260 Authors: Marais G;Duret L Title: Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans. Citation: Journal of Molecular Evolution 52: 275-280 2001 Type: ARTICLE Genes: Abstract: In many unicellular organisms, invertebrates, and plants, synonymous codon usage biases result from a coadaptation between codon usage and tRNAs abundance to optimize the efficiency of protein synthesis. However, it remains unclear whether natural selection acts at the level of the speed or the accuracy of mRNAs translation. Here we show that codon usage can improve the fidelity of protein synthesis in multicellular species. As predicted by the model of selection for translational accuracy, we find that the frequency of codons optimal for translation is significantly higher at codons encoding for conserved amino acids than at codons encoding for nonconserved amino acids in 548 genes compared between Caenorhabditis elegans and Homo sapiens. Although this model predicts that codon bias correlates positively with gene length, a negative correlation between codon bias and gene length has been observed in eukaryotes. This suggests that selection for fidelity of protein synthesis is not the main factor responsible for codon biases. The relationship between codon bias and gene length remains unexplained. Exploring the differences in gene expression process in eukaryotes and prokaryotes should provide new insights to understand this key question of codon usage. ------------------- Key: 4614 Medline: 21140165 Authors: Gieseler K;Mariol MC;Bessou C;Migaud M;Franks CJ;Holden-Dye L;Segalat L Title: Molecular, genetic and physiological characterisation of dystrobrevin-like (dyb-1) mutants of Caenorhabditis Citation: Journal of Molecular Biology 307: 107-117 2001 Type: ARTICLE Genes: ace-1 ace-2 dyb-1 dys-1 hlh-1 Abstract: Dystrobrevins are protein components of the dystrophin complex, whose disruption leads to Duchenne muscular dystrophy and related diseases. The Caenorhabditis elegans dystrobrevin gene (dtb-1) encodes a protein 38 % identical with its mammalian counterparts. The C. elegans dystrobrevin is expressed in muscles and neurons. We characterised C. elegans dyb-1 mutants and showed that: (1) their behavioural phenotype resembles that of dystrophin (dys-1) mutants; (2) the phenotype of dyb-1 dys-1 double mutants is not different from the single ones; (3) dyb-1 mutants are more sensitive than wild-type animals to reductions of acetylcholinesterase levels and have an increased response to acetylcholine; (4) dyb-1 mutations alone do not lead to muscle degeneration, but synergistically produce a progressive myopathy when combined with a mild MyoD/hlh-1 mutation. All together, these findings further substantiate the role of dystrobrevins in cholinergic transmission and as functional ------------------- Key: 4615 Medline: 21157401 Authors: Ackley BD;Crew JR;Elamaa H;Pihlajaniemi T;Kuo CJ;Kramer JM Title: The NC1/endostatin domain of Caenorhabditis elegans type XVIII collagen affects cell migration and axon guidance. Citation: Journal of Cell Biology 152: 1219-1232 2001 Type: ARTICLE Genes: cle-1 mec-7 unc-40 unc-129 nDf23 Abstract: Type XVIII collagen is a homotrimeric basement membrane molecule of unknown function, whose COOH-terminal NC1 domain contains endostatin (ES), a potent antiangiogenic agent. The Caenorhabditis elegans collagen XVIII homologue, cle-1, encodes three developmentally regulated protein isoforms expressed predominantly in neurons. The CLE-1 protein is found in low amounts in all basement membranes but accumulates at high levels in the nervous system. Deletion of the cle-1 NC1 domain results in viable fertile animals that display multiple cell migration and axon guidance defects. Particular defects can be rescued by ectopic expression of the NC1 domain, which is shown to be capable of forming trimers. In contrast, expression of monomeric ES does not rescue but dominantly causes cell and axon migration defects that phenocopy the NC1 deletion, suggesting that ES inhibits the promigratory activity of the NC1 domain. These results indicate that the cle-1 NC1/ES domain regulates cell and axon migrations in C. ------------------- Key: 4616 Medline: 11171401 Authors: Zhang H;Emmons SW Title: The novel C. elegans gene sop-3 modulates Wnt signaling to regulate Hox gene expression. Citation: Development 128: 767-777 2001 Type: ARTICLE Genes: bar-1 egl-5 egl-20 mab-5 pal-1 sop-1 sop-3 sDp3 Abstract: We describe the properties of a new gene, sop-3, that is required for the regulated expression of a C. elegans Hox gene, egl-5, in a postembryonic neuroectodermal cell lineage. Regulated expression of egl-5 in this cell lineage is necessary for development of the sensory rays of the male tail, sop-3 encodes a predicted novel protein of 1475 amino acids without clear homologs in other organisms. However, the sequence contains motifs consisting of homopolymeric runs of amino acids found in several other transcriptional regulators, some of which also act in Hox gene regulatory pathways. The genetic properties of sop-3 are very similar to those of sop-1, which encodes a component of the transcriptional Mediator complex, and mutations in the two genes are synthetic lethal. This suggests that SOP-3 may act at the level of the Mediator complex in regulating transcription initiation, In a sop-3 loss-of-function background, egl-5 is expressed ectopically in lineage branches that normally do not express this gene. Such expression is dependent on the Hox gene mab-5, as it is in branches where egl-5 is normally expressed, Ectopic egl-5 expression is also dependent on the Wnt pathway. Thus, sop-3 contributes to the combinatorial control of egl-5 by blocking egl-5 activation by MAB-5 and the Wnt pathway in inappropriate lineage branches. ------------------- Key: 4617 Medline: 21098964 Authors: Burglin TR;Ruvkun G Title: Regulation of ectodermal and excretory function by the C. elegans POU homeobox gene ceh-6. Citation: Development 128: 779-790 2001 Type: ARTICLE Genes: ceh-6 ceh-18 egl-5 unc-86 vha-1 Abstract: Caenorhabditis elegans has three POU homeobox genes, unc-86, ceh-6 and ceh-18.ceh-6 is the ortholog of vertebrate Brn1, Brn2, SCIP/Oct6 and Brn4 and by Cf1a/drifter/ventral veinless, Comparison of C. elegans and C. briggsae CEH-B shows that it is highly conserved. C. elegans has only three POU homeobox genes, while Drosophila has five that fall into four families. Immunofluorescent detection of the CEH-6 protein reveals that it is expressed in particular head and ventral cord neurons, as well as in rectal epithelial cells, and in the excretory cell, which is required for osmoregulation. A deletion of the ceh-6 locus causes 80% embryonic lethality. During morphogenesis, embryos extrude cells in the rectal region of the tail or rupture, indicative of a defect in the rectal epithelial cells that express ceh-6. Those embryos that hatch are sick and develop vacuoles, a phenotype similar to that caused by laser ablation of the excretory cell. A GFP reporter construct expressed in the excretory cell reveals inappropriate canal structures in the ceh-6 null mutant. Members of the POU-III family are expressed in tissues involved in osmoregulation and secretion in a number of species. We propose that one evolutionary conserved function of the POU-III transcription factor class could be the regulation of genes that mediate ------------------- Key: 4618 Medline: 21145241 Authors: Carthew RW Title: Gene silencing by double-stranded RNA. Citation: Current Opinion in Cell Biology 13: 244-248 2001 Type: ARTICLE Genes: ego-1 mut-7 rde-1 rde-2 smg-2 smg-5 smg-6 Abstract: Eukaryotes silence gene expression in the presence of double-stranded RNA homologous to the silenced gene. Silencing occurs by the targeted degradation of mRNA. Biochemical reactions that recapitulate this phenomenon generate RNA fragments of 21-23 nucleotides from the double-stranded RNA. These stably associate with an RNA endonuclease and probably serve as a discriminator to select mRNAs. Once selected, mRNAs are cleaved at sites 21-23 nucleotides apart. This mechanism, termed RNAi, has functional links to viral defense and silencing phenomena, such as cosuppression. It also functions to repress the hopping of transposable elements. ------------------- Key: 4619 Medline: 11259660 Authors: Berninsone P;Hwang HY;Zemtseva I;Horvitz HR;Hirschberg CB Title: SQV-7, a protein involved in Caenorhabditis elegans epithelial invagination and early embryogenesis, transports UDP-glucuronic acid, UDP-N-acetylgalactosamine, and UDP-galactose. Citation: Proceedings of the National Academy of Sciences USA 98: 3738-3743 2001 Type: ARTICLE Genes: sqv-7 Abstract: Caenorhabditis elegans sqv mutants are defective in vulval epithelial invagination and have a severe reduction in hermaphrodite fertility. The gene sqv-7 encodes a multitransmembrane hydrophobic protein resembling nucleotide sugar transporters of the Golgi membrane. A Golgi vesicle enriched fraction of Saccharomyces cerevisiae expressing SQV-7 transported UDP-glucuronic acid, UDP-N-acetylgalactosamine, and UDP-galactose (Gal) in a temperature-dependent and saturable manner. These nucleotide sugars are competitive, alternate, noncooperative substrates. The two mutant sqv-7 missense alleles resulted in a severe reduction of these three transport activities. SQV-7 did not transport CMP-sialic acid, GDP-fucose, UDP-N-acetylglucosamine, UDP-glucose, or GDP-mannose. SQV-7 is able to transport UDP-Gal in vivo, as shown by its ability to complement the phenotype of Madin-Darby canine kidney ricin resistant cells, a mammalian cell line deficient in UDP-Gal transport into the Golgi. These results demonstrate that unlike most nucleotide sugar transporters, SQV-7 can transport multiple distinct nucleotide sugars. We propose that SQV-7 translocates multiple nucleotide sugars into the Golgi lumen for the biosynthesis of glycoconjugates that play a ------------------- Key: 4620 Medline: 11259654 Authors: Kang ZB;Ge Y;Chen Z;Cluette-Brown J;Laposata M;Leaf A;Kang JX Title: Adenoviral gene transfer of Caenorhabditis elegans n-3 fatty acid desaturase optimizes fatty acid composition in mammalian cells. Citation: Proceedings of the National Academy of Sciences USA 98: 4050-4054 2001 Type: ARTICLE Genes: fat-1 Abstract: Omega-3 polyunsaturated fatty acids (PUFAs) are essential components required for normal cellular function and have been shown to exert many preventive and therapeutic actions. The amount of n-3 PUFAs is insufficient in most Western people, whereas the level of n-6 PUFAs is relatively too high, with an n-6/n-3 ratio of >18. These two classes of PUFAs are metabolically and functionally distinct and often have important opposing physiological functions; their balance is important for homeostasis and normal development. Elevating tissue concentrations of n-3 PUFAs in mammals relies on chronic dietary intake of fat rich in n-3 PUFAs, because mammalian cells lack enzymatic activities necessary either to synthesize the precursor of n-3 PUFAs or to convert n-6 to n-3 PUFAs. Here we report that adenovirus-mediated introduction of the Caenorhabditis elegans fat-1 gene encoding an n-3 fatty acid desaturase into mammalian cells can quickly and effectively elevate the cellular n - 3 PUFA contents and dramatically balance the ratio of n-6/n-3 PUFAs, Heterologous expression of the fat-1 gene in rat cardiac myocytes rendered cells capable of converting various n-6 PUFAs to the corresponding n-3 PUFAs, and changed the n-6/n-3 ratio from about 15:1 to 1:1. In addition, an eicosanoid derived from n-6 PUFA (i.e., arachidonic acid) was reduced significantly in the transgenic cells. This study demonstrates an effective approach to modifying fatty acid composition of mammalian cells and also provides a basis for potential applications of this gene transfer in experimental and clinical ------------------- Key: 4621 Medline: 21173895 Authors: Yassin L;Gillo B;Kahan T;Halevi S;Eshel M;Treinin M Title: Characterization of the DEG-3/DES-2 receptor: A nicotinic acetylcholine receptor that mutates to cause neuronal degeneration. Citation: Molecular & Cellular Neuroscience 17: 589-599 2001 Type: ARTICLE Genes: deg-3 des-2 Abstract: The nicotinic acetylcholine receptor family (nAChR) is a large family of acetylcholine-gated cation channels. Here we characterize the Caenorhabditis elegans DEG-3/DES-2 nAChR, a receptor identified due to its involvement in neuronal degeneration. Pharmacological analysis of a DEG-3/DES-2 receptor expressed in Xenopus oocytes shows that this receptor is preferentially activated by choline. This choline sensitivity of the DEG-3/DES-2 channel can explain its role in neuronal degeneration, as shown by the toxic effects of choline on oocytes expressing the mutant DEG-3/DES-2 channel. We also show that in C. elegans the DEG-3/DES-2 receptor is localized to nonsynaptic regions, including the sensory endings of chemosensory neurons. This localization is in agreement with a role for this receptor in chemosensation of choline, as inferred from a defect in chemotaxis for choline seen in deg-3 mutants. Thus, this work also provides evidence for the diversity of nonsynaptic activities associated with nAChRs. ------------------- Key: 4622 Medline: 21174021 Authors: Rose JK;Rankin CH Title: Analysis of habituation in Caenorhabditis elegans. Citation: Learning & Memory 8: 63-69 2001 Type: REVIEW Genes: avr-14 avr-15 eat-4 glr-1 nmr-1 Abstract: Although the nonassociative form of learning, habituation, is often described as the simplest form of learning, remarkably little is known about the cellular processes underlying its behavioral expression. Here, we review research on habituation in the nematode Caenorhabditis elegans that addresses habituation at behavioral, neural circuit, and genetic levels. This work highlights the need to understand the dynamics of a behavior before attempting to determine its underlying mechanism. In many cases knowing the characteristics of a behavior can direct or guide a search for underlying cellular mechanisms. We have highlighted the importance of interstimulus interval (ISI) in both short- and long-term habituation and suggested that different cellular mechanisms might underlie habituation at different ISIs. Like other organisms, C. elegans shows both accumulation of habituation with repeated training blocks and long-term retention of spaced or distributed training, but not for massed training. Exposure to heat shock during the interblock intervals eliminates the long-term memory for habituation but not the accumulation of short-term habituation over blocks of training. Analyses using laser ablation of identified neurons, and of identified mutants have shown that there are multiple sites of plasticity for the response and that glutamate plays a role in long-term retention habituation training. ------------------- Key: 4623 Medline: Authors: Pierce SB;Costa M;Wisotzkey R;Devadhar S;Homburger SA;Buchman AR;Ferguson KC;Heller J;Platt DM;Pasquinelli AA;Liu LX;Doberstein SK;Ruvkun G Title: Regulation of DAF-2 receptor signaling by human insulin and ins-1, a member of the unusually large and diverse C. elegans insulin gene family. Citation: Genes & Development 15: 672-686 2001 Type: ARTICLE Genes: daf-2 daf-3 daf-7 daf-16 ins-1 ins-2 ins-3 ins-4 ins-5 ins-6 ins-7 ins-8 ins-9 ins-10 ins-11 ins-12 ins-13 ins-14 ins-15 ins-16 ins-17 ins-18 ins-19 ins-20 ins-21 ins-22 ins-23 ins-24 ins-25 ins-26 ins-27 ins-28 ins-29 ins-30 ins-31 ins-32 ins-33 ins-34 ins-35 ins-36 Abstract: The activity of the DAF-2 insulin-like receptor is required for Caenorhabditis elegans reproductive growth and normal adult life span. Informatic analysis identified 37 C. elegans genes predicted to encode insulin-like peptides. Many of these genes are divergent insulin superfamily members, and many are clustered, indicating recent diversification of the family. The ins genes are primarily expressed in neurons, including sensory neurons, a subset of which are required for reproductive development. Structural predictions and likely C-peptide cleavage sites typical of mammalian insulins suggest that ins-1 is most closely related to insulin. Overexpression of ins-1, or expression of human insulin under the control of ins-1 regulatory sequences, causes partially penetrant arrest at the dauer stage and enhances dauer arrest in weak daf-2 mutants, suggesting that INS-1 and human insulin antagonize DAF-2 insulin-like signaling. A deletion of the ins-1 coding region does not enhance or suppress dauer arrest, indicating a functional redundancy among the 37 ins genes. Of five other ins genes tested, the only other one bearing a predicted C peptide also antagonizes daf-e signaling, whereas four ins genes without a C peptide do not, indicating functional diversity within the ins family. ------------------- Key: 4624 Medline: 11274062 Authors: Wu J;Duggan A;Chalfie M Title: Inhibition of touch cell fate by egl-44 and egl-46 in C. elegans. Citation: Genes & Development 15: 789-802 2001 Type: ARTICLE Genes: egl-1 egl-44 egl-46 mec-3 mec-4 mec-7 mec-18 unc-86 Abstract: In wild-type Caenorhabditis elegans, six cells develop as receptors for gentle touch. In eg1-44 and eg1-46 mutants, two other neurons, the FLP cells, express touch receptor-like features. eg1-44 and eg1-46 also affect the differentiation of other neurons including the HSN neurons, two cells needed for egg laying, eg1-44 encodes a member of the transcription enhancer factor family. The product of the eg1-46 gene, two Drosophila proteins, and two proteins in human and mice define a new family of zinc finger proteins. Both eg1-44 and eg1-46 are expressed in FLP and HSN neurons (and other cells); expression of eg1-46 is dependent on eg1-44 in the FLP cells but not in the HSN cells. Wild-type touch cells express egl-46 but not eg1-44. Moreover, ectopic expression of eg1-44 in the touch cells prevents touch cell differentiation in an egl-46-dependent manner. The sequences of these genes and their nuclear location as seen with FLP fusions indicate that they repress transcription of touch cell characteristics in the ------------------- Key: 4625 Medline: 21175846 Authors: Lagido C;Pettitt J;Porter AJR;Paton GI;Glover LA Title: Development and application of bioluminescent Caenorhabditis elegans as multicellular eukaryotic Citation: FEBS Letters 493: 36-39 2001 Type: ARTICLE Genes: Abstract: We describe a novel approach to assess toxicity to the free-living nematode Caenorhabditis elegans that relies on the ability of firefly luciferase to report on endogenous ATP levels. We have constructed bioluminescent C. elegans with the luc gene under control of a constitutive promoter. Light reduction was observed in response to increasing temperature, concentrations of copper, lead and 3,5-dichlorophenol. This was due to increased mortality coupled with decreased metabolic activity in the surviving animals. The light emitted by the transgenic nematodes gave a rapid, real-time indication of metabolic status. This forms the basis of rapid and biologically relevant toxicity tests. ------------------- Key: 4626 Medline: 21153169 Authors: Hill KL;L'Hernault SW Title: Analyses of reproductive interactions that occur after heterospecific matings within the genus Caenorhabditis. Citation: Developmental Biology 232: 105-114 2001 Type: ARTICLE Genes: cby-3 daf-4 dpy-5 fem-1 fog-1 him-5 let-88 spe-4 spe-8 unc-13 sDp2 Abstract: Formation of zygotes in internally fertilizing organisms requires a number of successful interactions between oocytes and sperm within a receptive female reproductive tract. These interactions are usually assumed to be species-specific. For most species, it is either not possible to inseminate females with sperm from a different species or not possible to observe the consequences of such an insemination because the female is opaque. Nematodes of the genus Caenorhabditis are optically transparent and prior work indicates copulation between individuals of two different species is possible. We have used a series of vital stains and other cytological methods to analyze sperm after cross-species mating. We present here a series of analyses of the postcopulatory, prefertilization interactions among three Caenorhabditis species and find that reproductive biology is conserved, to varying degrees, among all three species. This approach allows investigation into which in vivo interactions between sperm and both oocytes and the somatic gonad have been maintained during the reproductive isolation that accompanies speciation. ------------------- Key: 4627 Medline: 11222143 Authors: Vogel BE;Hedgecock EM Title: Hemicentin, a conserved extracellular member of the immunoglobulin superfamily, organizes epithelial and other cell attachments into oriented line-shaped junctions. Citation: Development 128: 883-894 2001 Type: ARTICLE Genes: him-4 him-5 mec-1 mec-5 mec-9 unc-30 unc-55 Abstract: him-4 mutations cause a novel syndrome of tissue fragility, defective cell migration and chromosome instability in Caenorhabditis elegans. Null mutants have abnormal escape reflex, mispositioning of the vas deferens and uterus, and mitotic chromosome loss and multinucleate cells in the germline. The him-4 gene product, hemicentin, is a conserved extracellular matrix protein with 48 tandem immunoglobulin repeats flanked by novel terminal domains. Secreted from skeletal muscle and gonadal leader cells, hemicentin assembles into fine tracks at specific sites, where it contracts broad regions of cell contact into oriented linear junctions. Some tracks organize hemidesmosomes in the overlying epidermis. Hemicentin tracks facilitate mechanosensory neuron anchorage to the epidermis, gliding of the developing gonad along epithelial basement membranes and germline cellularization. ------------------- Key: 4628 Medline: Authors: Blomberg N;Baraldi E;Sattler M;Saraste M;Nilges M Title: Structure of a PH domain from the C. elegans muscle protein UNC-89 suggests a novel function. Citation: Structure 8: 1079-1087 2000 Type: ARTICLE Genes: unc-89 Abstract: BACKGROUND: Pleckstrin homology (PH) domains constitute a structurally conserved family present in many signaling and regulatory proteins. PH domains have been shown to bind to phospholipids, and many function in membrane targeting. They generally have a strong electrostatic polarization and interact with negatively charged phospholipids via the positive pole. On the basis of electrostatic modeling, however, we have previously identified a class of PH domains with a predominantly negative charge and predicted that these domains recognize other targets. Here, we report the first experimental structure of such a PH domain. RESULTS: The structure of the PH domain from Caenorhabditis elegans muscle protein UNC-89 has been determined by heteronuclear NMR. The domain adopts the classic PH fold, but has an unusual closed conformation of the "inositol binding loops. This creates a small opening to a deep hydrophobic pocket lined with negative charges on one side, and provides a molecular explanation for the lack of association with inositol-1,4,5-triphosphate. As predicted, the PH domain of UNC-89 has a strongly negative overall electrostatic potential, modeling the Dbl homology (DH)-linked PH domains from the C. elegans genome shows that a large proportion of these modules are negatively charged. CONCLUSIONS: We present the first structure of a PH domain with a strong negative overall electrostatic potential. The presence of a deep pocket lined with negative charges suggests that the domain binds to ligands other than acidic phospholipids. The abundance of this class of PH domain in the C. elegans genome suggests a prominent role in mediating protein-protein interactions. ------------------- Key: 4629 Medline: 21127212 Authors: Cowen T Title: A heady message for lifespan regulation. Citation: Trends in Genetics 17: 109-113 2001 Type: REVIEW Genes: age-1 daf-2 daf-16 unc-14 unc-119 Abstract: Mutant Caenorhabditis elegans in which the age-1 and daf-2 genes (involved in insulin-receptor-like signalling) are expressed at low levels exhibit extended lifespan. Wolkow and colleagues recently showed that restricted re-expression of age-1 and daf-2 genes in neurons of these mutants rescues wild-type lifespan as effectively as ubiquitous re-expression. Low levels of insulin-like signalling in neurons might control longevity by enhancing protection against free radical damage. However, in mammalian cells (including neurons) reduced insulin-like signalling is generally thought to be deleterious to antioxidant defence and to neuron survival. Here we discuss the new work and several hypotheses to explain this ------------------- Key: 4630 Medline: 21142273 Authors: Jedrusik MA;Schulze E Title: A single histone H1 isoform (H1.1) is essential for chromatin silencing and germline development in Caenorhabditis elegans. Citation: Development 128: 1069-1080 2001 Type: ARTICLE Genes: him-8 let-858 mes-2 mes-3 mes-4 pha-1 Abstract: In remarkable contrast to somatic cells, the germline of the nematode Caenorhabditis elegans efficiently silences transgenic DNA. The molecular mechanisms responsible for this have been shown to implicate chromatin proteins encoded by the mes genes (Kelly, W. G. and Fire, A. (1998) Development 125, 2451-2456), of which two are the C. elegans homologs of Polycomb Group gene transcriptional repressors. We have analyzed the contribution of the histone H1 gene family to this specific aspect of germ cells in C. elegans. We show with isotype-specific double stranded RNA-mediated interference (RNAi) that a single member of this gene family (H1.1) is essential for the repression of a silenced reporter-transgene in the germline of hermaphrodites and males, whereas no change is found in the somatic expression of this reporter. Additionally, RNA-mediated interference with H1.1 gene expression can cause a phenotype with severe affection of germline proliferation and differentiation in the hermaphrodite, and even sterility (5%-11% penetrance). These and further features observed in histone H1.1 RNAi experiments are also characteristic of the mes phenotype (Garvin, C., Holdeman, R. and Strome, S. (1998) Genetics 148, 167-185), which is believed to result from the desilencing of genes required for somatic differentiation in the germline. Our observations therefore support this interpretation of the mes phenotype and they identify a single histone H1 isoform (H1.1) as a new component specifically involved in chromatin silencing in the germline of C. elegans. ------------------- Key: 4631 Medline: 21216586 Authors: Tenenhaus C;Subramaniam K;Dunn MA;Seydoux G Title: PIE-1 is a bifunctional protein that regulates maternal and zygotic gene expression in the embryonic germ line of Caenorhabditis elegans. Citation: Genes & Development 15: 1031-1040 2001 Type: ARTICLE Genes: ama-1 cey-2 nos-2 pie-1 smg-1 eDp6 Abstract: The CCCH zinc finger protein PIE-1 is an essential regulator of germ cell fate that segregates with the germ lineage during the first cleavages of the Caenorhabditis elegans embryo. We have shown previously that one function of PIE-1 is to inhibit mRNA transcription. Here we show that PIE-1 has a second function in germ cells; it is required for efficient expression of the maternally encoded Nanos homolog NOS-2. This second function is genetically separable from PIE-1's inhibitory effect on transcription. A mutation in PIE-1's second CCCH finger reduces NOS-2 expression without affecting transcriptional repression and causes primordial germ cells to stray away from the somatic gonad, occasionally exiting the embryo entirely. Our results indicate that PIE-1 promotes germ cell fate by two independent mechanisms as follows: (1) inhibition of transcription, which blocks zygotic programs that drive somatic development, and (2) activation of protein expression from nos-2 and possibly other maternal RNAs, which promotes primordial germ cell development. ------------------- Key: 4632 Medline: 11801179 Authors: Rivas E;Eddy SR Title: Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Citation: Bioinformatics 16: 583-605 2000 Type: ARTICLE Genes: Abstract: MOTIVATION: Several results in the literature suggest that biologically interesting RNAs have secondary structures that are more stable than expected by chance. Based on these observations, we developed a scanning algorithm for detecting noncoding RNA genes in genome sequences, using a fully probabilistic version of the Zuker minimum-energy folding algorithm. RESULTS: Preliminary results were encouraging, but certain anomalies led us to do a carefully controlled investigation of this class of methods. Ultimately, our results argue that for the probabilistic model there is indeed a statistical effect, but it comes mostly from local base-composition bias and not from RNA secondary structure. For the thermodynamic implementation (which evaluates statistical significance by doing Monte Carlo shuffling in fixed-length sequence windows, thus eliminating the base-composition effect) the signals for noncoding RNAs are still usually indistinguishable from noise, especially when certain statistical artifacts resulting from local base-composition inhomogeneity are taken into account. We conclude that although a distinct, stable secondary structure is undoubtedly important in most noncoding RNAs, the stability of most noncoding RNA secondary structures is not sufficiently different from the predicted stability of a random sequence to be useful as a general genefinding approach. ------------------- Key: 4633 Medline: Authors: Bargmann C Title: Simple organisms. Citation: Neurobiology of Disease 7: 520-522 2000 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: How are researchers now able to study the complex human genome with such insight and accuracy? The answer lies in nearly a century of research with very simple organisms: the fruit fly, Drosophila melanogaster, which is about 1/8 in. in size, and the roundworm, Caenorhabditis elegans, about the size of a comma on this page. ------------------- Key: 4634 Medline: 11463371 Authors: Page BD;Guedes S;Waring D;Priess JR Title: The C. elegans E2F- and DP-related proteins are required for embyronic asymmetry and negatively regulate Ras/MAPK signaling. Citation: Molecular Cell 7: 451-460 2001 Type: ARTICLE Genes: dpl-1 efl-1 fem-1 glp-1 let-23 let-60 lin-2 lin-45 mex-1 mex-5 mex-6 mpk-1 pie-1 sem-5 skn-1 Abstract: Early C. elegans embryos exhibit protein asymmetries that allow rapid diversification of cells. Establishing these asymmetries requires the novel protein MEX-5. We show that mutations in the efl-1 and dpl-1 genes cause defects in protein localization resembling defects caused by mutations in mex-5. efl-1 and dpl-1 encode homologs of vertebrate E2F and DP proteins that regulate transcription as a heterodimer. efl-l and dpl-1 mutants have elevated levels of activated Map kinase in oocytes. Their mutant phenotype and that of mex-5 mutants can be suppressed by reducing Ras/Map kinase signaling. We propose this signaling pathway has a role in embryonic asymmetry and that EFL-1/DPL-1 control the level of Map kinase activation. ------------------- Key: 4635 Medline: 11463372 Authors: Ceol CJ;Horvitz HR Title: dpl-1 DP and efl-1 E2F act with lin-35 Rb to antagonize Ras signaling in C. elegans vulval development. Citation: Molecular Cell 7: 461-473 2001 Type: ARTICLE Genes: dpl-1 efl-1 efl-2 let-23 let-60 lin-3 lin-15 lin-35 lin-38 lin-45 mpk-1 sem-5 mnDf67 Abstract: The synthetic multivulva (synMuv) genes define two functionally redundant pathways that antagonize RTK/Ras signaling during Caenorhabditis elegans vulval induction. The synMuv gene lin-35 encodes a protein similar to the mammalian tumor suppressor pRB and has been proposed to act as a transcriptional repressor. Studies using mammalian cells have shown that pRB can prevent cell cycle progression by inhibiting DP/E2F-mediated transcriptional activation. We identified C. elegans genes that encode proteins similar to DP or E2F. Loss-of-function mutations in two of these genes, dpl-1 DP and efl-1 E2F, caused the same vulval abnormalities as do lin-35 Rb loss-of-function mutations. We propose that rather than being inhibited by lin-35 Rb, dpl-1 DP and efl-l E2F act with lin-35 Rb in transcriptional repression to antagonize RTK/Ras signaling ------------------- Key: 4636 Medline: 11463373 Authors: Maduro MF;Meneghini MD;Bowerman B;Broitman-Maduro G;Rothman JH Title: Restriction of mesendoderm to a single blastomere by the combined action of SKN-1 and a GSK-3 beta homolog is mediated by MED-1 and -2 in C. elegans. Citation: Molecular Cell 7: 475-485 2001 Type: ARTICLE Genes: end-1 end-3 glp-1 lag-2 lit-1 med-1 med-2 mex-1 pal-1 pop-1 pop-2 pos-1 sgg-1 wrm-1 Abstract: The endoderm and much of the mesoderm arise from the EMS cell in the four-cell C. elegans embryo. We report that the MED-1 and -2 GATA factors specify the entire fate of EMS, which otherwise produces two C-like mesectodermal progenitors. The meds are direct-targets of the maternal SKN-1 transcription factor; however, their forced expression can direct SKN-1-independent reprogramming of non-EMS cells into mesendodermal progenitors. We find that SGG-1/GSK-3 beta kinase acts both as a Wnt-dependent activator of endoderm in EMS and an apparently Wnt-independent repressor of the meds in the C lineage, indicating a dual role for this kinase in mesendoderm development. Our results suggest that a broad tissue territory, mesendoderm, in vertebrates has been confined to a single cell in nematodes through a common gene regulatory ------------------- Key: 4637 Medline: 11405335 Authors: Kuwabara PE;O'Neil N Title: The use of functional genomics in C. elegans for studying human development and disease. Citation: Journal of Inherited Metabolic Disease 24: 127-138 2001 Type: REVIEW Genes: Abstract: The 100 Mb Caenorhabditis elegans genome sequence is the first animal genome to be sequenced in its entirety. Many reverse-genetics tools have been developed to mine the genome sequence and to facilitate the jump between the identification of a gene sequence and the understanding of its function. Here we discuss how C. elegans can contribute to understanding of the function of genes involved in human development and disease. ------------------- Key: 4638 Medline: 11134024 Authors: Zhang L;Wu SL;Rubin CS Title: A novel adapter protein employs a phosphotyrosine binding domain and exceptionally basic N-terminal domains to capture and localize an atypicl protein kinase C. Citation: Journal of Biological Chemistry 276: 10463-10475 2001 Type: ARTICLE Genes: Abstract: Atypical protein kinase C isoforms (aPKCs) transmit regulatory signals to effector proteins located in the cytoplasm, nucleus, cytoskeleton, and membranes. Mechanisms by which aPKCs encounter and control effector proteins in various microenvironments are poorly understood. By using a protein interaction screen, we discovered two novel proteins that adapt a Caenorhabditis elegans aPKC (PKC3) for specialized (localized) functions; protein kinase C adapter 1 (CKA1, 593 amino acids) and CKA1S (549 amino acids) are derived from a unique mRNA by alternative utilization of two translation initiation codons. CKA1S and CKA1 are routed to the cell periphery by exceptionally basic N-terminal regions that include classical phosphorylation site domains (PSDs). Tethering of PKC3 is mediated by a segment of CKA1 that constitutes a phosphotyrosine binding (PTB) domain. Two aromatic amino acids (Phe(175) and Phe(221)) are indispensable for creation of a PKC3-binding surface and/or stabilization of CKA1 aPKC complexes. Patterns of CKA1 gene promoter activity and CKA1/CKA1S protein localization in vivo overlap with patterns established for PKC3 expression and distribution. Transfection experiments demonstrated that CKA1/CKA1S sequesters PKC3 in intact cells. Structural information in CKA1/CKA1S enables delivery of adapters to the lateral plasma membrane surface (near tight junctions) in polarized epithelial cells. Thus, a PTB domain and PSDs collaborate in a novel fashion in CKA1/CKA1S to enable tethering and targeting of PKC3. Avid ligation of a PKC isoform is a previously unappreciated function for a PTB ------------------- Key: 4639 Medline: 11134025 Authors: Zhang L;Wu SL;Rubin CS Title: Structural properties and mechanisms that govern association of C kinase adapter 1 with protein kinase C3 and the cell periphery. Citation: Journal of Biological Chemistry 276: 10476-10484 2001 Type: ARTICLE Genes: Abstract: Association of an atypical protein kinase C (aPKC) with an adapter protein can affect the location, activity, substrate specificity, and physiological role of the phosphotransferase, Knowledge of mechanisms that govern formation and intracellular targeting of aPKC adapter protein complexes is limited. Caenorhabditis elegans protein kinase C adapter proteins (CKA1 and CKA1S) bind and target aPKCs and provide prototypes for mechanistic analysis. CKA1 binds an aPKC (PKC3) via a phosphotyrosine binding (PTB) domain. A distinct, Arg/Lys-rich N-terminal region targets CKA1 to the cell periphery. We discovered that a short segment ((212)GGIDNGAFHEHEI(224)) of the V-2 (linker) region of PKC3 creates a binding surface that interacts with the PTB domain of CKA1/CKA1S. The docking domain of PKC3 differs from classical PTB ligands by the absence of Tyr and Pro. Substitution of Ile(214), Asn(216), or Phe(219) with Ala abrogates binding of PKC3 with CKA1; these residues cooperatively configure a docking site that complements an apolar surface of the CKA1 PTB domain. Phosphorylation site domains (PSD1, residues 11-25; PSD2, residues 61-77) in CKA1 route the adapter land tethered PKC3) to the cell periphery, Phosphorylation of Ser(17) and Ser(65) in PSDs 1 and 2 elicits translocation of CKA1 from the cell surface to cytoplasm, Activities of DAG-stimulated PKCs and opposing protein Ser/Thr phosphatases can dynamically regulate the distribution of adapter protein between the cell periphery and cytoplasm. ------------------- Key: 4640 Medline: 21132635 Authors: Wang MQ;Sternberg PW Title: Pattern formation during C. elegans vulval induction. Citation: Current Topics in Developmental Biology 51: 189-220 2001 Type: REVIEW Genes: ark-1 bar-1 ceh-13 chd-3 chd-4 cki-1 egl-27 egr-1 gap-1 hda-1 ksr-1 let-23 let-60 let-341 lin-1 lin-2 lin-3 lin-4 lin-7 lin-8 lin=9 lin-10 lin-12 lin-14 lin-15 lin-25 lin-28 lin-31 lin-35 lin-36 lin-37 lin-38 lin-39 lin-45 lin-51 lin-52 lin-53 lin-54 lin-55 lin-56 mab-5 mek-2 mpk-1 ptp-2 rba-1 sel-1 sel-10 sel-12 sem-5 sli-1 soc-2 sur-2 sur-5 sur-6 sup-17 sur-8 tam-1 unc-101 Abstract: Studies of C. elegans vulval development provide insights into the process of pattern formation during animal development. The invariant pattern of vulval precursor cell fates is specified by the integration of at least two signaling systems. Recent findings suggest that multiple, partially redundant mechanisms are involved in patterning the vulval precursor cells. The inductive signal activates the LET-60/RAS signaling pathway and induces the 1 degree fate, whereas the lateral signal mediated by LIN-12/Notch is required for specification of the 2 degrees fate. Several regulatory pathways antagonize the RAS signaling pathway and specify the non-vulval 3 degrees fate in the absence of induction. The temporal and spatial regulation of VPC competence and production of the inductive and the lateral signal are precisely coordinated to ensure the wild-type vulval pattern. ------------------- Key: 4641 Medline: 11525245 Authors: Sok J;Calfon M;Lu J;Lichtlen P;Clark SG;Ron D Title: Arsenite-inducible RNA-associated protein (AIRAP) protects cells from arsenite toxicity. Citation: Cell Stress & Chaperones 6: 6-15 2001 Type: ARTICLE Genes: aip-1 ire-1 Abstract: Exposure of cells to arsenicals activates multiple stress pathways resulting in the induction of specific genes whose identity and role in the adaptation to arsenical-induced cellular stress are poorly understood. We report here the identification of a novel gene encoding an arsenite-inducible, cysteine- and histidine-rich RNA-associated protein, AIRAP, that is conserved among mammals, Drosophila and C. elegans. Immunochemistry and cell fractionation experiments indicate that, when induced, AIRAP is present in both the nucleus and the cytoplasm, and cross-linking experiments indicate that it associates with RNA in vivo. The expression of a C. elegans homologue of AIRAP, aip-l, is also induced by exposure to arsenite, and expression of an aip-1::gfp transgene is most pronounced in hypodermal cells. RNA-mediated interference (RNAi) of aip-1 lowers the resistance of nematodes to arsenite yet does not appear to affect viability under standard growth conditions. These experiments suggest a role for AIRAP/AIP-1 in protecting cells from the toxic effects of ------------------- Key: 4642 Medline: Authors: Gottlieb RA Title: Mitochondria: execution central. Citation: FEBS Letters 482: 6-12 2000 Type: REVIEW Genes: ced-3 ced-4 ced-9 Abstract: Mitochondria play an essential function in eukaryotic life and death. They also play a central role in apoptosis regulation, reflected by the convergence of Bcl-2 family members on the mitochondrial outer membrane, and the presence of 'death factors' in the intermembrane space. Mitochondrial structure and function must be taken into consideration when evaluating mechanisms for cytochrome c release. The core machinery for caspase activation is conserved from Caenorhabditis elegans to man, and we consider parallels in the role of mitochondria in this process. ------------------- Key: 4643 Medline: 21189517 Authors: Selleck SB Title: Genetic dissection of proteoglycan function in Drosophila and C. elegans. Citation: Seminars in Cell & Developmental Biology 12: 127-134 2001 Type: REVIEW Genes: sqv-1 sqv-2 sqv-3 sqv-4 sqv-5 sqv-6 sqv-7 sqv-8 unc-52 Abstract: Genetic analysis of the signaling pathways that govern patterning during development in the fruitfly Drosophila melanogaster and in the nematode C. elegans have provided insight into the in vivo functions of proteoglycans and their associated glycosaminoglycans. These studies have shown that patterning events dictated by Fibroblast Growth Factor Receptors, Wnt, Transforming Growth Factor-beta (TGF-beta), and Hedgehog families of growth factors are regulated by proteoglycans. Recent biochemical and structural analyses have shown that the molecular machinery of glycosaminoglycan biosynthesis is highly conserved between these invertebrate organisms and mammals. Drosophila and C. elegans therefore provide powerful model systems for exploring the varied functions proteoglycans and their glycosaminoglycan modifications. ------------------- Key: 4644 Medline: 21198111 Authors: Salkoff L;Butler A;Fawcett G;Kunkel M;McArdle C;Paz-y-Mino G;Nonet M;Walton N;Wang ZW;Yuan A;Wei A Title: Evolution tunes the excitability of individual neurons. Citation: Neuroscience 103: 853-859 2001 Type: ARTICLE Genes: twk-4 twk-23 twk-24 Abstract: The relationship between the genome and the evolution of the nervous system may differ between an animal like C. elegans with 302 neurons, and mammals with tens of billions of neurons. Here we report that a class of nonconserved potassium channels highly expanded in C. elegans may play a special role in the evolution of its nervous system. The C. elegans genome contains an extended gene family of potassium channels whose members fall into two evolutionary divergent classes. One class constitutes an ancient conserved "set" of K+ channels with orthologues in both humans and Drosophila(1,24) and a second larger class made up of rapidly evolving genes unique to C. elegans.(24) Chief among this second class are novel potassium channels having four transmembrane domains per subunit(6,8,14,20) that function as regulated leak conductances to modulate cell electrical excitability. This inventory of novel potassium channels is far larger in C. elegans than in humans or Drosophila, We found that, unlike conserved channel genes, the majority of these genes are expressed in very few cells. We also identified DNA enhancer elements associated with these genes that direct gene expression to individual neurons. We conclude that C. elegans may maintain an exceptionally large inventory of these channels (as well as ligand-gated channels') as an adaptive mechanism to "fine tune" individual neurons, making the most of its limited circuitry. ------------------- Key: 4645 Medline: 21203796 Authors: Pemberton DJ;Franks CJ;Walker RJ;Holden-Dye L Title: Characterization of glutamate-gated chloride channels in the pharynx of wild-type and mutant Caenorhabditis elegans delineates the role of the subunit GluCl-a2 in the function of the native receptor. Citation: Molecular Pharmacology 59: 1037-1043 2001 Type: ARTICLE Genes: avr-15 Abstract: Glutamate-gated chloride (GluCl) channels are the site of action of the anthelmintic ivermectin. Previously, the Xenopus laevis oocyte expression system has been used to characterize GluCl channels cloned from Caenorhabditis elegans. However, information on the native, pharmacologically relevant receptors is lacking. Here, we have used a quantitative pharmacological approach and intracellular recording techniques of C. elegans pharynx to characterize them. The glutamate response was a rapidly desensitizing, reversible, chloride-dependent depolarization (EC50 = 166 muM), only weakly antagonized by picrotoxin. The order of potency of agonists was ibotenate > L-glutamate > kainate = quisqualate. Ivermectin potently and irreversibly depolarized the muscle (EC50 = 2.7 nM). No further depolarization was seen with coapplication of maximal glutamate during the maximal ivermectin response, indicating that ivermectin depolarizes the muscle by the same ionic mechanism as glutamate (i.e., chloride). The potency of ivermectin on the pharynx was greater than at any of the GluCl subunits expressed in X. laevis oocytes. This effect of ivermectin was abolished in the mutant avr-15, which lacks a functional GluCl-alpha (2) subunit. However, a chloride-dependent, nondesensitizing response to glutamate persisted. Therefore, the GluCl-alpha (2) subunit confers ivermectin sensitivity and a high-affinity desensitizing glutamate response on the native pharyngeal ------------------- Key: 4646 Medline: 21215641 Authors: O'Lone RB;Campbell WC Title: Effect of refrigeration on the antinematodal efficacy of ivermectin. Citation: Journal of Parasitology 87: 452-454 2001 Type: ARTICLE Genes: avr-15 Abstract: Several observations have suggested that the anthelmintic ivermectin can affect nematodes by non-oral entry into the nematode body. To investigate this possibility further, we refrigerated Caenorhabditis elegans at 5 C to prevent its locomotion and to block the pharyngeal pumping that is so prominent a feature of its feeding. Worms were exposed to ivermectin (1-25 mug/ml) at that temperature for 1 hr,after which the medium was replaced by unmedicated medium at room temperature. After 1 hr at room temperature the worms were examined and counted to determine the degree to which irreversible immobilization had occurred. The drug was significantly less effective at 5 C than at room temperature. This reduction in potency could be attributed to a general cold-induced decline in the rate of the biochemical processes involved in drug action. Alternatively, the reduction could be attributed to the cold-induced blockade of pharyngeal pumping, which would suggest that the efficacy of ivermectin is partially the result of oral intake of drug. The fact that antinematodal efficacy was not entirely abrogated and reached a significant level despite blockade of pharyngeal pumping supports the former interpretation and is in accord with earlier indications that ivermectin can enter by non-oral routes. This conclusion is further supported by the observation that ivermectin is active against the nonfeeding third-stage larva of Haemonchus contortus. ------------------- Key: 4647 Medline: 21186071 Authors: West RJ;Sun AY;Church DL;Lambie EJ Title: The C. elegans gon-2 gene encodes a putative TRP cation channel protein required for mitotic cell cycle Citation: Gene 266: 103-110 2001 Type: ARTICLE Genes: gon-2 Abstract: The C. elegans gon-2 gene is required for the post-embryonic mitotic cell divisions of the gonadal precursor cells. A single major transcript of approximately 6.7 kb is derived from the gon-2 locus. This mRNA encodes a protein related to the TRP family of cation channels and has a high degree of similarity to several vertebrate genes, including melastatin. Mutant alleles of gon-2 affect evolutionarily conserved amino acid residues. Northern analyses suggest that gon-2 expression is not limited to ------------------- Key: 4648 Medline: 11290452 Authors: Campbell AM;Teesdale-Spittle PH;Barrett J;Liebau E;Jefferies JR;Brophy PM Title: A common class of nematode glutathione S-transferase (GST) revealed by the theoretical proteome of the model organism Caenorhabditis elegans. Citation: Comparative Biochemistry & Physiology B-Biochemistry & Molecular Biology 128: 701-708 2001 Type: ARTICLE Genes: Abstract: The genome verified C. elegans free-living nematode model is a new tool for investigating gene expression in human and animal nematode parasites. There is limited information on designating glutathione S-transferase (GST) to specific classes in lower invertebrates such as nematodes. Following cloning, amino acid sequence alignment, recombinant expression and Western blotting we provide evidence of a new GST class in nematodes or lower invertebrates. ------------------- Key: 4649 Medline: 11287347 Authors: Sedensky MM;Siefker JM;Morgan PG Title: Model organisms: New insights into ion channel and transporter function. Stomatin homologues interact in Caenorhabditis elegans. Citation: American Journal of Physiology - Cell Physiology 280: C1340-C1348 2001 Type: ARTICLE Genes: unc-1 unc-24 eDf28 Abstract: In C. elegans the protein UNC-1 is a major determinant of anesthetic sensitivity and is a close homologue of the mammalian protein stomatin. In humans stomatin is missing from erythrocyte membranes in the hemolytic disease overhydrated hereditary stomatocytosis, despite an apparently normal stomatin gene. Overhydrated hereditary stomatocytosis is characterized by alteration of the normal transmembrane gradients of sodium and potassium. Stomatin has been shown to interact genetically with sodium channels. It is also postulated that stomatin is important in the organization of lipid rafts. We demonstrate here that antibodies against UNC-1 stain the major nerve tracts of Caenorhabditis elegans, with very intense staining of the nerve ring. We also found that a gene encoding a stomatin-like protein, UNC-24, affects anesthetic sensitivity and is genetically epistatic to unc-1. In the absence of UNC-24, the staining of the nerve ring by anti-UNC-1 is abolished, despite normal transcriptional levels of the unc-1 mRNA. Western blots indicate that UNC-24 probably affects the stability of the UNC-1 protein. UNC-24 may therefore be necessary for the correct placement of UNC-1 in the cell membrane and organization of lipid ------------------- Key: 4650 Medline: 21154835 Authors: Rutledge E;Bianchi L;Christensen M;Boehmer C;Morrison R;Broslat A;Beld AM;Geroge AL;Greenstein D;Strange K Title: CLH-3, a ClC-2 anion channel ortholog activated during meiotic maturation in C. elegans oocytes. Citation: Current Biology 11: 161-170 2001 Type: ARTICLE Genes: clh-1 clh-2 clh-3 clh-4 clh-5 clh-6 fog-2 Abstract: Background: CIC anion channels are ubiquitous and have been identified in organisms as diverse as bacteria and humans. Despite their widespread expression and likely physiological importance, the function and regulation of most ClCs are obscure. The nematode Caenorhabditis elegans offers significant experimental advantages for defining ClC biology. These advantages include a fully sequenced genome, cellular and molecular manipulability, and genetic tractability. Results: We show by patch clamp electrophysiology that C. elegans oocytes express a hyperpolarization- and swelling-activated Cl- current with biophysical characteristics strongly resembling those of mammalian ClC-2. Double-stranded RNA-mediated gene interference (RNAi) and single-oocyte RT-PCR demonstrated that the channel is encoded by clh-3, one of six C. elegans CIC genes. CLH-3 is inactive in immature oocytes but can be triggered by cell swelling. However, CLH-3 plays no apparent role in oocyte volume homeostasis. The physiological signal for channel activation is the induction of oocyte meiotic maturation. During meiotic maturation, the contractile activity of gonadal sheath cells, which surround oocytes and are coupled to them via gap junctions, increases dramatically. These ovulatory sheath cell contractions are initiated prematurely in animals in which CLH-3 expression is disrupted by RNAi. Conclusions: The inwardly rectifying Cl- current in C. elegans oocytes is due to the activity of a CIC channel encoded by clh-3. Functional and structural similarities suggest that CLH-3 and mammalian ClC-2 are orthologs. CLH-3 is activated during oocyte meiotic maturation and functions in part to modulate ovulatory contractions of gap ------------------- Key: 4651 Medline: 21154836 Authors: Maeda I;Kohara Y;Yamamoto M;Sugimoto A Title: Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi. Citation: Current Biology 11: 171-176 2001 Type: ARTICLE Genes: ama-1 daz-1 dpy-13 emb-5 fem-1 gld-1 glp-1 lin-1 mei-1 mes-1 mes-3 pat-3 unc-22 Abstract: Genome-wide analysis of gene function is essential for the post-genome era, and development of efficient and economical technology suitable for it has been in demand. Here we report a large-scale inactivation of the expressed genes in the nematode Caenorhabditis elegans, For this purpose, we have established a high-throughput "RNAi-by-soaking" methodology by modifying the conventional RNAi method [1, 2], A set of tag-sequenced, nonredundant cDNAs corresponding to approximately 10,000 genes [3] (representing half of the predicted genes [4]) was used for the systematic RNAi analysis. We have processed approximately 2500 genes to date. In development, 27% of them showed detectable phenotypes, such as embryonic lethality, postembryonic lethality, sterility, and morphological abnormality. Of these, we analyzed the phenotypes of Fl sterility in detail, and we have identified 24 genes that might play important roles in germline development. Combined with the ongoing analysis of expression patterns of these cDNAs [3, 5], the functional information obtained in this work will provide a starting point for the further analysis of each gene. Another finding from this screening is that the incidence of essential genes is significantly lower in the X chromosome ------------------- Key: 4652 Medline: 21154849 Authors: Kim SK Title: Functional genomics: The worm scores a knockout. Citation: Current Biology 11: R85-R87 2001 Type: REVIEW Genes: Abstract: Following the completion of the genome sequence of Caenorhabditis elegans, four independent studies have now assessed the functions of more than a third of the worm's genes by analysing the phenotypes caused when each of a large set of genes is inactivated by RNA interference. ------------------- Key: 4653 Medline: Authors: Nass R;Miller DM;Blakely RD Title: C. elegans: a novel pharmacogenetic model to study Parkinson's disease. Citation: Parkinsonism & Related Disorders 7: 185-191 2001 Type: ARTICLE Genes: bas-1 cat-1 cat-2 cat-4 dat-1 Abstract: Parkinson's disease (PD) is characterized by the degeneration of dopaminergic neurons in the substantia nigra pars compacta. Although the use of vertebrate and tissue culture systems continue to provide valuable insight into the pathology of the neurodegeneration, the molecular determinants involved in the etiology of the disease remain elusive. Because of the high conservation of genes and metabolic pathways between invertebrates and humans, as well as the availability of genetic strategies to identify novel proteins, protein interactions and drug targets, genetic analysis using invertebrate model systems has enormous potential in deducing the factors involved in neuronal disease. In this article, we discuss the opportunities for the use of the nematode Caenorhabditis elegans (C. elegans) for gaining insight into the molecular mechanisms and pathways involved in PD. ------------------- Key: 4654 Medline: 21305902 Authors: Kay AJ;Hunter CP Title: CDC-42 regulates PAR protein localization and function to control cellular and embyronic polarity in C. elegans. Citation: Current Biology 11: 474-481 2001 Type: ARTICLE Genes: cdc-42 par-2 par-3 Abstract: Background: The polarization of the anterior-posterior axis (A-P) of the Caenorhabditis elegans zygote depends on the activity of the par genes and the presence of intact microfilaments, Functional links between the PAR proteins and the cytoskeleton, however, have not been fully explored. It has recently been shown that in mammalian cells, some PAR homologs form a complex with activated Cdc42, a Rho GTPase that is implicated in the control of actin organization and cellular polarity. A role for Cdc42 in the establishment of embryonic polarity in C. elegans has not been described. Results: To investigate the function of Cdc42 in the control of cellular and embryonic polarity in C. elegans, we used RNA-mediated interference (RNAi) to inhibit cdc-42 activity in the early embryo. Here, we demonstrate that RNAi of cdc-42 disrupts manifestations of polarity in the early embryo, that these phenotypes depend on par-2 and par-3 gene function, and that cdc-42 is required for the localization of the PAR proteins. Conclusions: Our genetic analysis of the regulatory relationships between cdc-42 and the par genes demonstrates that Cdc42 organizes embryonic polarity by controlling the localization and activity of the PAR proteins. Combined with the recent biochemical analysis of their mammalian homologs, these results simultaneously identify both a regulator of the PAR proteins, activated ------------------- Key: 4655 Medline: Authors: Fares H;Greenwald I Title: Regulation of endocytosis by CUP-5, the Caenorhabditis elegans mucolipin-1 homolog. Citation: Nature Genetics 28: 64-68 2001 Type: ARTICLE Genes: cup-5 Abstract: Loss of the human 1mucolipin-l gene underlies mucolipidosis type IV (MLIV), a lysosomal storage disease that results in severe developmental neuropathology(1-3). Unlike other lysosomal storage diseases, MLIV is not associated with a lack of lysosomal hydrolases(4); instead, MLIV cells display abnormal endocytosis of lipids and accumulate large vesicles, indicating that a defect in endocytosis may underlie the disease(4-6). Here we report the identification of a loss-of-function mutation in the Caenorhabditis elegans mucolipin-1 homolog, cup-5, and show that this mutation results in an enhanced rate of uptake of fluid-phase markers, decreased degradation of endocytosed protein and accumulation of large vacuoles. Overexpression of cup-5(+) causes the opposite phenotype, indicating that cup-5 activity controls aspects of endocytosis. Studies in model organisms such as C. elegans have helped illuminate fundamental mechanisms involved in normal cellular function and human disease; thus the C. elegans cup-5 mutant may be a useful model for studying conserved aspects of mucolipin-1 structure and function and for assessing the effects of potential therapeutic compounds. ------------------- Key: 4656 Medline: 11124266 Authors: Cahill CM;Tzivion G;Nasrin N;Ogg S;Dore J;Ruvkun G;Alexander-Bridges M Title: Phosphatidylinositol 3-kinase signaling inhibits DAF-16 DNA binding and function via 14-3-3-dependent and 14-3-3-independent pathways. Citation: Journal of Biological Chemistry 276: 13402-13410 2001 Type: ARTICLE Genes: daf-16 Abstract: In Caenorhabditis elegans, an insulin-like signaling pathway to phosphatidylinositol S-kinase (PI 3-kinase) and AKT negatively regulates the activity of DAF-16, a Forkhead transcription factor. We show that in mammalian cells, C, elegans DAF-16 is a direct target of AKT and that AKT phosphorylation generates 14-3-3 binding sites and regulates the nuclear/cytoplasmic distribution of DAF-16 as previously shown for its mammalian homologs FKHR and FKHRL1. In vitro, interaction of AKT-phosphorylated DAF-16 with 14-3-3 prevents DAF-16 binding to its target site in the insulin-like growth factor binding protein-1 gene, the insulin response element. In HepG2 cells, insulin signaling to PI 3-kinase/AKT inhibits the ability of a GAL4 DNA binding domain/DAF-16 fusion protein to activate transcription via the insulinlike growth factor binding protein-1-insulin response element, but not the GAL4 DNA binding site, which suggests that insulin inhibits the interaction of DAF-16 with its cognate DNA site. Elimination of the DAF-16/1433 association by mutation of the AKT/14-3-3 sites in DAF-16, prevents 14-3-3 inhibition of DAF-16 DNA binding and insulin inhibition of DAF-16 function. Similarly, inhibition of the DAF-16/14-3-3 association by exposure of cells to the PI 3-kinase inhibitor LY294002, enhances DAF-16 DNA binding and transcription activity. Surprisingly constitutively nuclear DAF-16 mutants that lack AKT/14-3-3 binding sites also show enhanced DNA binding and transcription activity in response to LY294002, pointing to a 14-3-3-independent mode of regulation. Thus, our results demonstrate at least two mechanisms, one 14-3-3-dependent and the other 14-3-3-independent, whereby PI S-kinase signaling regulates DAF-16 DNA binding and transcription function. ------------------- Key: 4657 Medline: 21221078 Authors: Xu L;Fong Y;Strome S Title: The Caenorhabditis elegans maternal-effect sterile proteins, MES-2, MES-3, and MES-6, are associated in a complex in embryos. Citation: Proceedings of the National Academy of Sciences USA 98: 5061-5066 2001 Type: ARTICLE Genes: mes-2 mes-3 mes-4 mes-6 Abstract: The Caenorhabditis elegans maternal-effect sterile genes, mes-1, mes-3, mes-4 and mes-6, encode nuclear proteins that are essential for germ-line development. They are thought to be involved in a common process because their mutant phenotypes are similar. MES-2 and MES-6 are homologs of Enhancer of zeste and extra sex combs, both members of the Polycomb group of chromatin regulators in insects and vertebrates. MES-3 is a novel protein, and MES-Q is a SET-domain protein. To investigate whether the MES proteins interact and likely function as a complex, we performed biochemical analyses on C. elegans embryo extracts. Results of immunoprecipitation experiments indicate that MES-2, MES-3. and MES-B are associated in a complex and that MES-4 is not associated with this complex. Based on in vitro binding assays, MES-2 and MES-C interact directly, via the amino terminal portion of MES-2. Sucrose density gradient fractionation and gel filtration chromatography were performed to determine the Stokes radius and sedimentation coefficient of the MES-2 / MES-3 / MES-6 complex. Based on those two values, we estimate that the molecular mass of the complex is approximate to 1255 kDa, close to the sum of the three known components. Our results suggest that the two C. elegans Polycomb group homologs (MES-2 and MES-C) associate with a novel partner (MES-3) to regulate germ-line development in C. elegans. ------------------- Key: 4658 Medline: 21192555 Authors: Joshua GWP Title: Functional analysis of leucine aminopeptidase in Caenorhabditis elegans. Citation: Molecular & Biochemical Parasitology 113: 223-232 2001 Type: ARTICLE Genes: lap-1 lap-2 Abstract: To investigate the function of the enzyme leucine aminopeptidase in nematodes, a Caenorhabditis elegans leucine aminopeptidase gene identified in the genome sequence was functionally analysed by transfection of a leucine aminopeptidase beta -galactosidase reporter construct and characterisation of a null mutant. The leucine aminopeptidase transgene is expressed along the length of the gut, and immunolocalisation shows thr enzyme in the buccal cavity. pharynx, anterior gut and rectum. It is constitutively expressed as seen by analysis of cDNAs constructed from mRNAs of nematodes taken at 2 h intervals through the life-cycle. and by western blot analysis of protein from the same set of nematodes. Leucine aminopeptidase null mutants had a slower growth rate and delayed onset of egg-laying. We suggest that in C. elegans, leucine aminopeptidase is a digestive enzyme. ------------------- Key: 4659 Medline: 11134055 Authors: Van Baelen K;Vanoevelen J;Missiaen L;Raeymaekers L;Wuytack Title: The golgi PMR1 P-type ATPase of Caenorhabditis elegans - Identification of the gene and demonstration of calcium and manganse transport. Citation: Journal of Biological Chemistry 276: 10683-10691 2001 Type: ARTICLE Genes: Abstract: In recent years, it has been well established that the Ca2+ concentration in the lumen of intracellular organelles is a key determinant of cell function. Despite the fact that essential functions of the Golgi apparatus depend on the Ca2+ and Mn2+ concentration in its lumen, little is known on the transport system responsible for ion accumulation. The Gels ion pump PMR1 has been functionally studied only in yeast, In humans, mutations in the orthologous gene ATP2C1 cause Hailey-Hailey disease. We report here the identification of the PMR1 homologue in the model organism Caenorhabditis elegans and after ectopic expression the direct study of its ion transport in permeabilized COS-1 cells. The C. elegans genome is predicted to contain a single PMR1 orthologue on chromosome I. We found evidence for alternative splicing in the 5'-untranslated region, but no indication for the generation of different protein isoforms. C. elegans PMR1 overexpressed in COS-1 cells transports Ca2+ and Mn2+ with high affinity into the Golgi apparatus in a thapsigargin-insensitive manner. Part of the accumulated Ca2+ can be released by inositol 1,4,5-trisphosphate, in agreement with the idea that the Gels apparatus is an inositol 1,4,5-trisphosphate-sensitive Ca2+ store. ------------------- Key: 4660 Medline: 21186043 Authors: Kim J;Poole DS;Waggoner LE;Kempf A;Ramirez DS;Treschow PA;Schafer WR Title: Genes affecting the activity of nicotinic receptors involved in Caenorhabditis elegans egg-laying behavior. Citation: Genetics 157: 1599-1610 2001 Type: ARTICLE Genes: egl-1 lev-1 lev-8 lev-9 lev-10 unc-29 unc-38 unc-63 unc-74 Abstract: Egg-laying behavior in Caenorhabditis elegans is regulated by multiple neurotransmitters, including acetylcholine and serotonin. Agonists of nicotinic acetylcholine receptors such as nicotine and levamisole stimulate egg laying; however, the generic and molecular basis for cholinergic neurotransmission in the egg-laying circuitry is not well understood. Here we describe the egg-laying phenotypes of eight levamisole resistance genes, which affect the activity of levamisole-sensitive nicotinic receptors in nematodes. Seven of these gents, including the nicotinic receptor subunit genes unc-29, unc-38, and lev-1, were essential for the stimulation of egg laying by levamisole, though they had only subtle effects on egg-laying behavior in the absence of drug. Thus, these genes appear to encode components of a nicotinic receptor that can promote egg laying but is not necessary for egg-laying muscle contraction. Since the levamisole-receptor mutants responded to other cholinergic drugs, other acetylcholine receptors are likely to function in parallel with the levamisole-sensitive receptors to mediate cholinergic neurotransmission in the egg-laying circuitry. In addition, since expression of functional unc-29 in muscle cells restored levamisole sensitivity under some but not all conditions, both neuronal and muscle cell UNC-29 receptors are likely to contribute to the regulation of egg-laying behavior. Mutations in one levamisole receptor gene, unc-38, also conferred both hypersensitivity and reduced peak response to serotonin: thus nicotinic receptors may play a role in regulating serotonin response pathways in ------------------- Key: 4661 Medline: 21186044 Authors: Shioi G;Shoji M;Nakamura M;Ishihara T;Katsura I;Fujisawa H;Takagi S Title: Mutations affecting nerve attachment of Caenorhabditis elegans. Citation: Genetics 157: 1611-1622 2001 Type: ARTICLE Genes: mua-1 mua-5 mua-6 mup-4 ven-1 ven-2 ven-3 arDf1 mnDf57 mnDf66 mnDf84 mnDf86 mnDf87 mnDf88 mnDf90 mnDf97 nDf42 wDf1 yDf8 yDf9 yDf11 yDf12 Abstract: Using a pan-neuronal GFP marker, a morphological screen was performed to detect Caenorhabditis elegans larval lethal mutants with severely disorganized major nerve cords. We recovered and characterized 21 mutants that displayed displacement or detachment of the ventral nerve cord from the body wall (Ven: ventral cord abnormal). Six mutations defined three novel genetic loci: ven-1, ven-2, and ven-3. Fifteen mutations proved to be alleles of previously identified muscle attachment/positioning genes, mup-4, mua-1, mua-5, and mua-6. All the mutants also displayed muscle attachment/positioning defects characteristic of mua/mup mutants. The pan-neuronal GFP marker also revealed that mutants of other mua/mup loci, such as mup-1, mup-2 and mua-2, exhibited the Ven defect. The hypodermis, the excretory canal, and the gonad were morphologically abnormal in some of the mutants. The pleiotropic nature of the defects indicates that ven and mua/mup genes are required generally for the maintenance of attachment of tissues to the body wall in C. elegans. ------------------- Key: 4662 Medline: 21294970 Authors: Delattre M;Felix MA Title: Development and evolution of a variable left-right asymmetry in nematodes: The handedness of P11/P12 Citation: Developmental Biology 232: 362-371 2001 Type: ARTICLE Genes: bar-1 egl-5 lag-2 lin-3 lin-12 lin-17 lin-44 Abstract: In Caenorhabditis elegans, two lateral blast cells called P(11/12)L and P(11/12)R are symmetric left-right homologs at hatching, migrate subsequently in opposite anteroposterior directions during the first larval stage, and adopt two different fates, thus breaking the symmetry between them. Our results show that, unlike most other cell fate decisions in C. elegans, the orientation of P(11/12)L/R migration is highly biased, but not fixed. The handedness of their migration is linked to whole body handedness and is randomized in lin-12/Notch mutants and by ablation of the Y cell. Migration handedness is independent of P11 and P12 fate determination, previously shown to require the LIN-44/Wnt and the LIN-3/EGF pathways (L. I. Jiang and P. W. Sternberg, 1998, Development 125, 2337-2347). We further show that several changes in P(11/12)L/R asymmetry have occurred during nematode evolution: loss of asymmetry or reversals in orientation of migration. Strikingly, for most species studied, handedness of migration is highly biased but not fixed. Thus, whereas the final cell fate pattern of P11/12 is invariant, the developmental route leading to it is subject both to developmental indeterminacy and to evolutionary variations. ------------------- Key: 4663 Medline: Authors: Engle MR;Singh SP;Nanduri B;Ji X;Zimniak P Title: Invertebrate glutathione transferases conjugating 4-hydroxynonenal: CeGST 5.4 from Caenorhabditis elegans. Citation: Chemico-Biological Interactions 133: 244-248 2001 Type: ARTICLE Genes: Abstract: Formation of 4-hydroxyalkenals appears to be an obligatory consequence of aerobic metabolism, especially respiration. Mammals have evolved a special group of alpha -class GSTs with high catalytic activity towards 4-hydroxyalkenals, We now identified an invertebrate (Caenorhabditis elegans) GST with the same activity, named CeGST 5.4. The enzyme is closely related to the pi class of GSTs. This finding demonstrates that conjugation of 4-hydroxyalkenals is phylogenetically widespread and thus probably physiologically essential, at least in aerobes. ------------------- Key: 4664 Medline: Authors: van Rossum AJ;Jefferies J;Young CJ;Barrett J;Tait A;Brophy PM Title: Glutathione S-transferase (GST) functional genomics: role of Caenorhabditis elegans in investigating GST expression in parasitic nematodes. Citation: Chemico-Biological Interactions 133: 274-277 2001 Type: ARTICLE Genes: Abstract: The Caenorhabditis elegans proteome outlines the first complete profile of the GST system in a metazoan animal. We have exploited this free-living nematode functional genomic model to dissect GST expression in parasitic nematodes. GST is an adult intestinal nematode's 'Achilles Heel', since the apparent down-regulation of other parasite detoxification enzymes means that the GST system is central to protection against external assault (chemotherapeutics, intestinal toxins, immune effector system) and internally derived cytotoxins (lipid peroxidation products). We report the relationship between GSTs from the economically important sheep nematode, Haemonchus contortus and C elegans model. Sequence alignment and 2D-electrophoresis support validation of C elegans as a model for studying GSTs in parasitic nematodes. ------------------- Key: 4665 Medline: Authors: Thomas JH Title: Nematodes are smarter then you think. Citation: Neuron 30: 7-8 2001 Type: REVIEW Genes: ncs-1 Abstract: Weighing in at about 5 ug, with 302 neurons and 5000 synapses, C. elegans is unlikely to prove theorems, write poetry, or challenge Mike Tyson. Still, remarkable behavioral complexity is packed into this tiny worm. ------------------- Key: 4666 Medline: Authors: Gomez M;de Castro E;Guarin E;Sasakura H;Kuhara A;Mori I;Bartfai T;Bargmann CI;Nef P Title: Ca2+ signaling via the neuronal calcium sensor-1 regulates associative learning and memory in C. elegans. Citation: Neuron 30: 241-248 2001 Type: ARTICLE Genes: gyc-8 ncs-1 ttx-3 Abstract: On a radial temperature gradient, C. elegans worms migrate, after conditioning with food, toward their cultivation temperature and move along this isotherm. This experience-dependent behavior is called isothermal tracking (IT). Here we show that the neuron-specific calcium sensor-1 (NCS-1) is essential for optimal IT. ncs-1 knockout animals show major defects in IT behavior, although their chemotactic, locomotor, and thermal avoidance behaviors are normal. The knockout phenotype can be rescued by reintroducing wildtype NCS-1 into the AIY interneuron, a key component of the thermotaxis network. A loss-of-function form of NCS-1 incapable of binding calcium does not restore IT, whereas NCS-1 overexpression enhances IT performance levels, accelerates learning (faster acquisition), and produces a memory with slower extinction. Thus, proper calcium signaling via NCS-1 defines a novel pathway essential for associative learning and memory. ------------------- Key: 4667 Medline: 11121397 Authors: Kitagawa H;Egusa N;Tamura J;Kusche-Gullberg M;Lindahl U;Sugahara K Title: rib-2, a Caenorhabditis elegans homolog of the human tumor suppressor EXT genes encodes a novel alpha 1,4-N-acetylglucosaminyltransferase involved in the biosynthetic initiation and elogation of hepar Citation: Journal of Biological Chemistry 276: 4834-4838 2001 Type: ARTICLE Genes: rib-1 rib-2 Abstract: The proteins encoded by the EXT1, EXT2, and EXTL2 genes, members of the hereditary multiple exostoses gene family of tumor suppressors, are glycosyltransferases required for the heparan sulfate biosynthesis. Only two homologous genes, rib-1 and rib-2, of the mammalian EXT genes were identified in the Caenorhabditis elegans genome. Although heparan sulfate is found in C. elegans, the involvement of the rib-1 and rib-2 proteins in heparan sulfate biosynthesis remains unclear. In the present study, the substrate specificity of a soluble recombinant form of the rib-a protein was determined and compared with those of the recombinant forms of the mammalian EXT1, EXT2, and EXTL2 proteins. The present findings revealed that the rib-2 protein was a unique alpha1,4-N-acetylglucosaminyltransferase involved in the biosynthetic initiation and elongation of heparan sulfate. In contrast, the findings confirmed the previous observations that both the EXT1 and EXT2 proteins were heparan sulfate copolymerases with both alpha1,4-N-acetylglucosaminyltransferase and beta1,4-glucuronyl-transferase activities, which are involved only in the elongation step of the heparan sulfate chain, and that the EXTL2 protein was an alpha1,4-N-acetylglucosaminyltransferase involved only in the initiation of heparan sulfate synthesis. These findings suggest that the biosynthetic mechanism of heparan sulfate in C. elegans is distinct from that reported for the ------------------- Key: 4668 Medline: Authors: Sternberg PW Title: Working in the post-genomic C. elegans world. Citation: Cell 105: 173-176 2001 Type: REVIEW Genes: Abstract: In 1998, The C. elegans Sequencing Consortium (1998) announced the essentially complete Caenorhabditis elegans genomic sequence, setting a high standard for sequencing multicellular genomes. As of April 2001, the C. elegans genome, including repetitive regions, is >99.6% complete with sequence equivalent to what many genome projects call phase III. How has this changed the lives of C. elegans researchers, and our view of the worm? ------------------- Key: 4669 Medline: Authors: Sagasti A;Hisamoto N;Hyodo J;Tanaka-Hino M;Matsumoto K;Bargmann CI Title: The CaMKII UNC-43 activates the MAPKKK NSY-1 to execute a lateral signaling decision required for asymmetric olfactory neuron fates. Citation: Cell 105: 221-232 2001 Type: ARTICLE Genes: nsy-1 nsy-2 nsy-3 odr-1 odr-3 str-2 unc-2 unc-36 unc-43 unc-76 Abstract: A stochastic cell fate decision mediated by axon contact and calcium signaling causes one of the two bilaterally symmetric AWC neurons, either AWCL or AWCR, to express the candidate olfactory receptor str-2 nsy-1 mutants express str-2 in both neurons, disrupting AWC asymmetry, nsy-1 encodes a homolog of the human MAP kinase kinase kinase (MAPKKK) ASK1, an activator of JNK and p38 kinases. Based on genetic epistasis analysis, nsy-1 appears to act downstream of the CaMKII unc-43, and NSY-1 associates with UNC-43, suggesting that UNC-43/CaMKII activates the NSY-1 MAP kinase cassette. Mosaic analysis demonstrates that UNC-43 and NSY-1 act primarily in a cell-autonomous execution step that represses str-2 expression in one AWC cell, downstream of the initial lateral signaling pathway that coordinates the fates of the two cells. ------------------- Key: 4670 Medline: 21237973 Authors: Phelan P;Starich TA Title: Innexins get into the gap. Citation: BioEssays 23: 388-396 2001 Type: REVIEW Genes: eat-5 inx-1 inx-2 inx-3 inx-4 inx-5 inx-6 inx-7 inx-8 inx-9 inx-10 inx-11 inx-12 inx-13 inx-14 inx-15 inx-16 inx-17 inx-18 inx-19 inx-20 inx-21 inx-22 unc-7 unc-9 unc-104 Abstract: Connexins were first identified in the 1970s as the molecular components of vertebrate gap junctions. Since then a large literature has accumulated on the cell and molecular biology of this multi-gene family culminating recently in the findings that connexin mutations are implicated in a variety of human diseases. Over two decades, the terms "connexin" and "gap junction" had become almost synonymous. In the last few years a second family of gap-junction genes, the innexins, has emerged. These have been shown to form intercellular channels in genetically tractable invertebrate organisms such as Drosophila melanogaster and Caenorhabditis elegans. The completed genomic sequences for the fly and worm allow identification of the full complement of innexin genes in these two organisms and provide valuable resources for genetic ------------------- Key: 4671 Medline: 11358149 Authors: Schrimpf SP;Langen H;Gomes AV;Wahlestedt C Title: A two-dimensional protein map of Caenorhabditis elegans. Citation: Electrophoresis 22: 1224-1232 2001 Type: ARTICLE Genes: Abstract: A protein map of Caenorhabditis elegans was constructed by using two-dimensional gel electrophoresis followed by peptide mass fingerprinting. A whole worm extract of a mixed population was separated on immobilized pH gradient strips 4-7 L, 3-10 NL, 6-11 L and 12% sodium dodecyl sulfate-polyacrylamide gel eletrophoresis (SDS-PAGE) gels. Gels were stained with colloidal Coomassie blue and 286 spots representing 152 proteins were subsequently identified by matrix-assisted laser desorption/ionization-mass spectrometry after in-gel digestion with trypsin. Most of the identified proteins with known cellular function were enzymes related to carbohydrate and lipid metabolism, or structural proteins with subcellular locations in the cytoplasm, mitochondria ------------------- Key: 4672 Medline: 11262230 Authors: Schisa JA;Pitt JN;Priess JR Title: Analysis of RNA associated with P granules in germ cells of C. elegans adults. Citation: Development 128: 1287-1298 2001 Type: ARTICLE Genes: fem-1 gld-1 glh-1 glh-2 glh-3 glh-4 mex-1 nos-2 par-3 pgl-1 pos-1 skn-1 Abstract: P granules are cytoplasmic structures of unknown function that are associated with germ nuclei in the C. elegans gonad, and are localized exclusively to germ cells, or germ cell precursors, throughout the life cycle. All the known protein components of P granules contain putative RNA-binding motifs, suggesting that RNA is involved in either the structure or function of the granules. However, no specific mRNAs have been identified within P granules in the gonad. We show here that P granules normally contain a low level of RNA, and describe conditions that increase this level. We present evidence that several, diverse mRNAs, including pos-1, mex-1, par-3, skn-1, nos-2 and gld-1 mRNA, are present at least transiently within P granules. In contrast, actin and tubulin mRNA and rRNA are either not present in P granules, or are present at relatively low levels. We show that pgl-1 and the glh (Vasa-related) gene family, which encode protein components of P granules, do not appear essential for RNA to concentrate in P granules; these proteins may instead function in events that are a prerequisite for RNAs to be transported efficiently from the nuclear surface. ------------------- Key: 4673 Medline: Authors: Leroi AM Title: Molecular signals versus the Loi de Balancement. Citation: Trends in Ecology & Evolution 16: 24-29 2001 Type: REVIEW Genes: age-1 daf-2 daf-16 daf-23 fer-15 fog-2 Abstract: Life history tradeoffs are often thought to be caused by the allocation of limited resources among competing traits such as reproduction, somatic growth and maintenance. One line of evidence supporting this comes from eliminating reproduction, for example, by surgically removing gonads, However, recent evidence from the nematode Caenorhabditis elegans suggests that the apparent tradeoffs it shows might not be due to resource allocation at all but rather to the effects of a molecular signal originating in the germ line that represses longevity. These results should cause us to rethink the interpretation of many classic experiments in life history evolution. ------------------- Key: 4674 Medline: Authors: Luhn K;Wild MK;Eckhardt M;Gerardy-Schahn R;Vestweber D Title: The gene defective in leukocyte adhesion deficiency II encodes a putative GDP-fucose transporter. Citation: Nature Genetics 28: 69-72 2001 Type: ARTICLE Genes: sqv-7 Abstract: Leukocyte adhesion deficiency II(LAD II) is characterized by the lack of fucosylated glycoconjugates, including selectin ligands, causing immunodeficiency and severe mental and growth retardation(1-3) No deficiency in fucosyltransferase activities(2,4) or in the activities of enzymes involved in GDP-fucose biosynthesis(5) has been found. Instead, the transport of GDP-fucose into isolated Golgi vesicles of LAD II cells appeared to be reduced(6). To identify the gene mutated in LAD II, we cloned 12 cDNAs from Caenorhabditis elegans, encoding multi-spanning transmembrane proteins with homology to known nucleotide sugar transporters, and transfected them into fibroblasts from an LAD II patient. One of these clones re-established expression of fucosylated glycoconjugates with high efficiency and allowed us to identify a human homolog with 55% identity, which also directed re-expression of fucosylated glycoconjugates, Both proteins were localized to the Golgi, The corresponding endogenous protein in LAD II cells had an R147C amino acid change in the conserved fourth transmembrane region. Overexpression of this mutant protein in cells from a patient with LAD did not rescue fucosylation, demonstrating that the point mutation affected the activity of the protein. Thus, we have identified the first putative CDP fucose transporter, which has been highly conserved throughout evolution. A point mutation in its gene is responsible for the disease in this ------------------- Key: 4675 Medline: 21350286 Authors: Wang W;Lim WA;Jakalian A;Wang J;Wang J;Luo R;Bayly CI;Kollman PA Title: An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis. Citation: Journal of the American Chemical Society 123: 3986-3994 Type: ARTICLE Genes: sem-5 Abstract: The Src-homology-3 (SH3) domain of the Caenorhabditis elegans protein Sem-5 binds proline-rich sequences. It is reported that the SH3 domains broadly accept amide: N-substituted residues instead of only recognizing prolines on the basis of side chain shape or rigidity. We have studied the interactions between Sem-5 and its ligands using molecular dynamics (MD), free energy calculations, and sequence analysis. Relative binding free energies, estimated by a method called MM/PBSA, between different substitutions at sites - 1, 0, and +2 of the peptide are consistent with the experimental data. A new method to calculate atomic partial charges. AM1-BCC method, is also used in the binding foe energy calculations for different N-substitutions at site -1. The results are very similar to those obtained from widely used RESP charges in the AMBER force field. AM1-BCC charges can be calculated more rapidly for any organic molecule than can the RESP charges. Therefore, their use can enable a broader and more efficient application of the MM/PBSA method in drug design. Examination of each component of the free energy leads to the construction of van der Weals interaction energy profiles for each ligand as well as for wild-type and mutant Sem-5 proteins. The profiles and free energy calculations indicate that the van der Waals interactions between the ligands and the receptor determine whether an N- or a C alpha -substituted residue is favored at each site. A VC value (defined as a product of the conservation percentage of each residue and its van der WaaIs interaction energy with the ligand) is used to identify several residues on the receptor that are critical for specificity and binding affinity. This VC value may have a potential use in identifying crucial residues for any Ligand-protein or protein-protein system. h Mutations at two of those crucial residues, N190 and N206, are examined. One mutation, N190I, is predicted to reduce the selectivity of the N-substituted residue at site -1 of the ligand and is shown to bind similarly with N- and C alpha -substituted ------------------- Key: 4676 Medline: Authors: McCarter JP;Bird DM;Clifton SW;Waterston RH Title: Nematode gene sequences, December 2000 update. Citation: Journal of Nematology 32: 331-333 2000 Type: REVIEW Genes: Abstract: High-throughput sequencing is revolutionizing molecular nematology by providing the sequences of thousands of genes never before characterized. The most rapid and cost-effective route to gene discovery for nematode genomes is the generation of expressed sequence tags (ESTs), single-pass reads from random cDNA library clones that provide 300-600 nucleotides of sequence from a gene. ------------------- Key: 4677 Medline: 21235187 Authors: Ledent V;Vervoort M Title: The basic helix-loop-helix protein family: Comparative genomics and phylogenetic analysis. Citation: Genome Research 11: 754-770 2001 Type: ARTICLE Genes: aha-1 cnd-1 hlh-1 hlh-2 hlh-3 hlh-8 lin-22 lin-32 unc-3 Abstract: The basic Helix-Loop-Helix (bHLH) proteins are transcription factors that play important roles during the development of various metazoans including fly, nematode, and vertebrates. They are also involved in human diseases, particularly in cancerogenesis. We made an extensive search for bHLH sequences in the completely sequenced genomes of Caenorhabditis elegans and of Drosophila melanogaster. We found 35 and 56 different genes, respectively, which may represent the complete set of bHLH of these organisms. A phylogenetic analysis of these genes, together with a large number (>350) of bHLH from other sources, led trs to define 44 orthologous families among which 36 include bHLH from animals only, and two have representatives in both yeasts and animals. In addition, we identified two bHLH motifs present only in yeast, and four chat are present only in plants; however, the latter number is certainly an underestimate. Most animal families (35/38) comprise fly, nematode, and vertebrate genes, suggesting that their common ancestor, which lived in pre-Cambrian times (600 million years ago) already owned as many as 35 different ------------------- Key: 4678 Medline: 21261870 Authors: Delattre M;Felix MA Title: Polymorphism and evoluton of vulval precursor cell lineages within two nematode genera, Caenorhabditis and Oscheius. Citation: Current Biology 11: 631-643 2001 Type: ARTICLE Genes: Abstract: Background: The cell lineage of nematodes is mostly invariant for a given species, but varies between species. One can thus wonder how a cell lineage varies during evolution. We have started a microevolutionary approach within two genera by observing lineage variations of vulval precursor cells in different natural nematode populations of the same and closely related species. Results: In Caenorhabditis elegans, the P3.p cell lineage is variable within a genetically homogeneous population and polymorphic between wild strains. Irrespective of its division pattern, P3.p is competent to form vulval tissue in different C. elegans strains, whereas it is not competent in C. briggsae. In Oscheius sp. 1, P4.p and P8.p lineages are strongly polymorphic. Within each genus, these intraspecies polymorphisms in cell lineages are amplified between closely related species. In Oscheius sp. 1, the large polymorphisms in P4.p and P8.p lineages allowed us to undertake a genetic analysis of the variation between two pairs of strains. Multiple loci are involved in cell lineage differences, and variation at one locus appears to have a relatively strong effect. In addition to these large lineage variations in cells that do not normally contribute to the vulva, we find minor variations (errors) in vulval lineages, which represent the precision level of the vulval-patterning process and point to a selection pressure for maintenance of a large vulval equivalence group. Conclusions: Polymorphisms in vulval cell lineage are found within a given nematode species, and could be instrumental in explaining evolutionary variations between closely ------------------- Key: 4679 Medline: 11295562 Authors: Habeos I;Papavassiliou AG Title: Type 2 diabetes mellitus and worm longevity: a transcriptional link to cure? Citation: Trends in Endocrinology & Metabolism 12: 139-140 2001 Type: ARTICLE Genes: age-1 daf-2 daf-16 pdk-1 Abstract: In Caenorhabditis elegans, an insulin-like signalling pathway culminates in a transcription factor (TF) that is homologous to a subfamily of Tps responsible for the regulation of a subset of insulin-responsive genes in humans. Under harsh conditions, C. elegans reduces signalling through this pathway and arrests developmentally in a manner that is similar to the metabolic syndrome of humans. We propose that an understanding of this pathway could lead to drugs with optimal potency and selectivity in the treatment of type 2 diabetes mellitus. ------------------- Key: 4680 Medline: Authors: Mikola J;Sulkava P Title: Responses of microbial-feeding nematodes to organic matter distribution and predation in experimental soil habitat. Citation: Soil Biology & Biochemistry 33: 811-817 2001 Type: ARTICLE Genes: Abstract: Soils are spatially heterogeneous environments, a condition which is likely to affect the structure and function of soil food webs. To study the influence of soil organic matter distribution on decomposer food webs, we established microcosms that contained either: (1) large patches of initially sterile humus-litter mixture placed within sterile sand matrix (creating a large-patch habitat; LPH); or (2) blend of sand and humus-litter mixture (creating a small-patch habitat; SPH). Ten species of bacteria and ten species of fungi, and two bacterial-feeding (Acrobeloides tricornis, Caenorhabditis elegans) and two fungal-feeding (Aphelenchus avenae, Aphelenchoides sp.) nematodes were added to both habitats to form the two lowest trophic levels of the food web. Microbivore predation was manipulated by adding a predatory nematode (Prionchulus punctatus) to half of the replicates of both habitats. The microcosms were destructively sampled three times during the 15-week experiment to estimate nematode biomass. The biomasses of A. tricornis and C. elegans were on average 35% and 21% lower, respectively, in LPH than in SPH, whereas the biomass of the two fungivores was not affected by organic matter distribution. Top predator biomass was higher in LPH than in SPH at the first and second samplings. The top predator had both negative and positive effects on its prey species, and the effects varied with sampling. The biomass ratio between fungivores and bacterivores was marginally higher (P = 0.080) in LPH (average 1:14) than in SPH (1:20), and significantly higher in the presence (1:13) than in the absence (1:25) of the top predator. In LPH, 69% of A. tricornis and 84% of top predator biomass was found in sand, while the majority (83%) of C. elegans lived in patches. At the end of the experiment a higher proportion of A. tricornis and A. avenae lived in parches in the presence than in the absence of the top predator. The results infer that organic matter distribution may affect the biomass of microbial-feeding and predatory nematodes in soil and produce a shift between the bacterial and fungal energy channels. Mechanisms mediating the effects of organic matter distribution on microbivores and on the top predator seem to differ, however, and therefore a change in organic matter distribution may increase biomass at one trophic level ------------------- Key: 4681 Medline: 11320215 Authors: Marais G;Mouchiroud D;Duret L Title: Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Citation: Proceedings of the National Academy of Sciences USA 98: 5688-5692 2001 Type: REVIEW Genes: Abstract: Understanding the factors responsible for variations in mutation patterns and selection efficacy along chromosomes is a prerequisite for deciphering genome sequences. Population genetics models predict a positive correlation between the efficacy of selection at a given locus and the local rate of recombination because of Hill-Robertson effects. Codon usage is considered one of the most striking examples that support this prediction at the molecular level. In a wide range of species including Caenorhabditis elegans and Drosophila melanogaster, codon usage is essentially shaped by selection acting for translational efficiency. Codon usage bias correlates positively with recombination rate in Drosophila, apparently supporting the hypothesis that selection on codon usage is improved by recombination. Here we present an exhaustive analysis of codon usage in C. elegans and D. melanogaster complete genomes. We show that in both genomes there is a positive correlation between recombination rate and the frequency of optimal codons. However, we demonstrate that in both species, this effect is due to a mutational bias toward G and C bases in regions of high recombination rate, possibly as a direct consequence of the recombination process. The correlation between codon usage bias and recombination rate in these species appears to be essentially determined by recombination-dependent mutational patterns, rather than selective effects. This result highlights that it is necessary to take into account the mutagenic effect of recombination to understand the evolutionary role and impact of recombination. ------------------- Key: 4682 Medline: 21223176 Authors: Hekimi S;Benard C;Branicky R;Burgess J;Hihi AK;Rea S Title: Why only time will tell. Citation: Mechanisms of Ageing & Development 122: 571-594 2001 Type: REVIEW Genes: age-1 akt-1 akt-2 clk-1 clk-2 clk-3 ctl-1 daf-2 daf-16 eat-2 eat-6 gro-1 mev-1 sod-3 tkr-1 unc-31 unc-64 Abstract: The nematode Caenorhabditis elegans has become a model system for the study of the genetic basis of aging. In particular, many mutations that extend life span have been identified in this organism. When loss-of-function mutations in a gene lead to life span extension, it is a necessary conclusion that the gene normally limits life span in the wild type. The effect of a given mutation depends on a number of environmental and genetic conditions. For example, the combination of two mutations can result in additive, synergistic, subtractive, or epistatic effects on life span. Valuable insight into the processes that determine life span can be obtained from such genetic analyses, especially when interpreted with caution, and when molecular information about the interacting genes is available. Thus, genetic and molecular analyses have implicated several genes classes (dnf, clk and eat) in life span determination and ha iie indicated that aging is affected by alteration of several biological processes, namely dormancy, physiological rates, food ------------------- Key: 4683 Medline: 21223180 Authors: Braeckman BP;Houthoofd K;Vanfleteren JR Title: Insulin-like signaling, metabolism, stress resistance and aging in Caenorhabditis elegans. Citation: Mechanisms of Ageing & Development 122: 673-693 2001 Type: ARTICLE Genes: age-1 akt-1 akt-2 clk-1 clk-2 clk-3 ctl-1 daf-2 daf-10 daf-12 daf-16 daf-18 daf-23 daf-28 eat-2 gro-1 mev-1 olk-1 osm-3 pdk-1 sod-1 sod-2 sod-3 tkr-1 unc-31 unc-64 Abstract: The nervous system acts as a major regulator of the life span of Caenorhabditis elegans. Temperature and chemical stimuli from the environment are integrated with internal signals from the reproductive system to specify adult longevity. An insulin-like signaling cascade acts in neurons and coordinates control of senescence of the entire organism by regulating metabolism and a stress response mechanism. Caloric restriction extends life span, possibly by activation of the stress response program. ------------------- Key: 4684 Medline: Authors: Funabashi Y;Kawamura K;Oshio K;Morita S;Osana Y;Akiyama E;Oka K Title: Native response of C. elegans encoded in its neuron Citation: Journal of the Physical Society of Japan 70: 1154-1161 2001 Type: ARTICLE Genes: Abstract: For the physical study of the native responses of Caenorhabditis elegans (C. elegans), probability distribution of random walkers on the neuron graph is studied. Here, the neuron graph is a graph which represents the synaptic connection of neurons of the worm. Connection of a sensory neuron to various motor neurons are represented by an index named accessibility. Accessibilities from 39 sensory neurons to all of motor neurons are computed and tile formers are classified into three groups. It is found that this classification coincides with the grouping by native responses caused by those sensory neurons. This coincidence implies the usefulness of the random walker model for the analysis of the neural network. The connectivity represented by the major paths of random walkers is a significant factor to interpret relation between external disturbance and resultant movement in the native response of the worm. This native response of the worm is encoded by the connectivity of vertices in the neuron graph. ------------------- Key: 4685 Medline: 21231610 Authors: Du H;Chalfie M Title: Genes regulating touch cell development in Caenorhabditis elegans. Citation: Genetics 158: 197-207 2001 Type: ARTICLE Genes: egl-17 lin-32 mec-2 mec-3 mec-7 mig-1 mig-21 unc-40 unc-51 unc-73 unc-86 vab-15 Abstract: To identify genes regulating the development of the six touch receptor neurons, we screened the F-2 progeny of mutated animals expressing an integrated mec-2::gfp transgene that is expressed mainly in these touch cells. From 2638 mutated haploid genomes, we obtained 11 mutations representing 11 genes that affected the production, migration, or outgrowth of the touch cells. Eight of these mutations were in known genes, and 2 defined new genes (mig-21 and vab-15). The mig-21 mutation is tile first known to affect the asymmetry of the migrations of Q neuroblasts, the cells that give rise to two of the six touch cells. vab-15 is a msh-like homeobox gene that appears to be needed for the proper production of touch cell precursors, since vab-15 animals lacked the four more posterior touch cells. The remaining touch cells (the ALM cells) were present but mispositioned. A similar touch cell phenotype is produced by mutations in lin-32. A more severe phenotype; i.e., animals often lacked ALM cells, was seen in lin-32 vab-15 double mutants, suggesting that these genes acted redundantly in ALM differentiation. In addition to the touch cell abnormalities, vab-15 animals variably exhibit embryonic or larval lethality, cell degenerations, malformation of the posterior body, uncoordinated movement, and defective egg laying. ------------------- Key: 4686 Medline: 21231611 Authors: Yook KJ;Proulx SR;Jorgensen EM Title: Rules of nonallelic noncomplementation at the synapse in Caenorhabditis elegans. Citation: Genetics 158: 209-220 2001 Type: ARTICLE Genes: cha-1 dpy-23 snb-1 syd-2 unc-13 unc-17 unc-18 unc-29 unc-64 unc-104 Abstract: Nonallelic noncomplementation occurs when recessive mutations in two different loci fail to complement one another, in other words, the double heterozygote exhibits a phenotype. We observed tl-lat mutations in the genes encoding the physically interacting synaptic proteins UNC-13 and syntaxin/UNC-64 failed to complement one another in the nematode Caenorhabditis elegans. Noncomplementation was not observed between null alleles of these genes and thus this genetic interaction does not occur with a simple decrease in dosage at the two loci. However, noncomplementation was observed if at least one gene encoded a partially functional gene product. Thus, this genetic interaction requires a poisonous gene product to sensitize the genetic background. Nonallelic noncomplementation was not limited to intel acting proteins: Although the strongest effects were observed between loci encoding gene products that bind to one another, interactions were also observed between proteins that do not directly interact but are members of the same complex. We also observed noncomplementation between genes that function at distant points in the same pathway, implying that physical interactions are not required for nonallelic noncomplementation. Finally, we observed tt-lat mutations in genes that Function in different processes such as neurotransmitter synthesis or synaptic development complement one another. Thus, this genetic interaction is specific fur genes acting in the same pathway. that is, for genes acting in synaptic reside trafficking. ------------------- Key: 4687 Medline: 21231612 Authors: van der Linden AM;Simmer F;Cuppen E;Plasterk RHA Title: The G-protein B-subunit GPB-2 in Caenorhabditis elegans regulates the G(o)alpha-G(q)alpha signaling network through interactions with the regulator of G-protein signaling proteins EGL-10 and EAT-16. Citation: Genetics 158: 221-235 2001 Type: ARTICLE Genes: dgk-1 eat-16 egl-8 egl-10 egl-30 goa-1 gpb-1 gpb-2 Abstract: The genome of Caenorhabditis elegans harbors two genes for G-protein beta -subunits. Here, we describe tile characterization of the second G-protein beta -subunit gene gpb-2. In contrast to gpb-1, gpb-2 is not an essential gene even though, like gpb-1, gpb-2 is expressed during development, in the nervous system, and in muscle cells. A loss-of-function mutation in gpb-2 produces a variety of behavioral defects, including delayed egg laying and reduced pharyngeal pumping. Genetic analysis shows that GPB-2 interacts with the GOA-1 (homologue of mammalian G(o)alpha) and EGL-30 (homologue of mammalian G(q)alpha) signaling pathways. GPB-2 is most similar to the divergent mammalian G beta5 subunit, which has been shown to mediate a specific interaction with a G gamma -subunit-like (GGL) domain of RGS proteins. We show here that GPB-2 physically acid genetically interacts with tile GGL-containing RGS proteins EGL-10 and EAT-16. Taken together, our results suggest that GPB-2 works in concert with tile RGS proteins EGL-10 and EAT-16 to regulate GOA-1 (G(o)alpha) and EGL-30 (G(q)alpha) signaling. ------------------- Key: 4688 Medline: 21231613 Authors: Sugimoto A;Kusano A;Hozak RR;Derry WB;Zhu J;Rothman JH Title: Many genomic regions are required for normal embryonic programmed cell death in Caenorhabditis elegans. Citation: Genetics 158: 237-252 2001 Type: ARTICLE Genes: unc-45 hDf10 tDf3 qDf3 hDf6 qDf16 ozDf5 nDf24 nDf30 hDf9 eDf3 eDf9 nDf3 ccDf5 maDf4 mnDf30 mnDf88 mnDf63 mnDf89 jDf2 sDf124 nDf11 rhDf1 sDf130 sDf121 nDf40 eDf2 mDf5 nDf41 stDf7 eDf19 mDf7 nDf27 sDf21 sDf23 sDf74 sDf28 sDf42 sDf45 sDf33 sDf26 sDf50 sDf30 sDf35 ctDf1 arDf1 nDf42 tDf2 yDf8 yDf4 yDf6 oxDf2 syDf1 uDf1 stDf5 nDf19 mnDf1 Abstract: To identify genes involved in programmed cell death (PCD) in Caenorhabditis elegans, we screened a comprehensive set of chromosomal deficiencies for alterations in the pattern of PCD throughout embryonic development. From a set of 58 deficiencies, which collectively remove similar to 74% of the genome, four distinct classes were identified. In class I (20 deficiencies), no significant deviation from wild type in the temporal pattern of cell corpses was observed, indicating that much of the genome does not contain zygotic genes that perform conspicuous roles in embryonic PCD. The class II deficiencies (16 deficiencies defining at least 11 distinct genomic regions) led to no or fewer-than-normal cell corpses. Some of these cause premature cell division arrest, probably explaining the diminution in cell corpse number; however, others have little effect on cell proliferation, indicating that tile reduced cell corpse number is not a direct result of premature embryonic arrest. In class III (18 deficiencies defining at least 16 unique regions), an excess of cell corpses was observed. The developmental stage at which the extra corpses were observed varied among the class III deficiencies, suggesting the existence of genes that perform temporal-specific functions in PCD. The four deficiencies in class TV (defining at least three unique regions), showed unusually large corpses that were, ill some cases, attributable to extremely premature arrest in cell division without a concomitant block in PCD. Deficiencies in this last class suggest that the cell death program does not require normal embryonic cell proliferation to be activated and suggest that while some genes required for cell division might also be required for cell death, others are not. Most of the regions identified by these deficiencies do not contain previously identified zygotic cell death genes. There are, therefore, a substantial number of as yet unidentified genes required for normal PCD in C. elegans. ------------------- Key: 4689 Medline: 21219334 Authors: Lee MH;Park H;Shim G;Lee J;Koo HS Title: Regulation of gene expression, cellular localization, and in vivo function of Caenorhabditis elegans DNA Citation: Genes to Cells 6: 303-312 2001 Type: ARTICLE Genes: Abstract: Background: DNA topoisomerase I is dispensable in yeast, but is essential during the embryogenesis of Drosophila and mouse. In order to determine functions of the enzyme in the development of Caenorhabditis elegans, phenotypes resulting from the deficiency were observed and correlated with the expression of the gene. Results: The transcriptional regulation of the C. elegans DNA topoisomerase I gene was investigated by mRNA localization and reporter gene expression in C. elegans. The mRNA was expressed in the gonad and in the early embryos, followed by a rapid decrease in its level during the late embryonic stage. A reporter gene expression induced by the 5'-upstream DNA sequence appeared at the comma stage of embryos, continued through the L1 larval stage, and began to decrease gradually afterwards. The DNA topoisomerase I protein was immuno-localized in the nuclei of meiotic gonad cells and interphase embryonic cells, and unexpectedly in centrosomes of mitotic embryonic cells. Double-stranded RNA interference of DNA topoisomerase I gene expression resulted in pleiotropic phenotypes showing abnormal gonadogenesis, oocyte development and embryogenesis. Conclusion: These phenotypes, along with expressional regulations, demonstrate that DNA topoisomerase I plays important roles in rapidly growing germ cells and embryonic ------------------- Key: 4690 Medline: 21240127 Authors: Wysocka J;Liu Y;Kobayashi R;Herr W Title: Developmental and cell-cycle regulation of Caenorhabditis elegans HCF phosphorylation. Citation: Biochemistry 40: 5786-5794 2001 Type: ARTICLE Genes: Abstract: HCF-1 is a mammalian protein required for cell proliferation. It is also involved in transcriptional activation of herpes-simplex-virus immediate-early gene transcription in association with the viral transactivator VP16. HCF-1 and a related protein called HCF-2 possess a homologue in Caenorhabditis elegans that can associate with and activate VP16. Here, we demonstrate developmental regulation of C. elegans HCF (CeHCF) phosphorylation: a hyperphosphorylated form of CeHCF is present in embryos, whereas a hypophosphorylated form is present in L1 larvae. The phosphorylation patterns of endogenous CeHCF in worms and ectopically synthesized CeHCF in mammalian cells are remarkably similar, suggesting that the way CeHCF can be recognized by kinases is conserved in animals. Phosphorylation-site mapping of endogenous CeHCF, however, revealed that phosphorylation occurs at four clustered sites in the region of the protein that is not highly conserved among HCF proteins and is not required for VP16-induced complex formation. Indeed, phosphorylation of either CeHCF or human HCF-1 appears to be dispensable for association with VP16. All four CeHCF phosphorylation sites match the consensus recognition site for the cell-cycle kinases CDC2 and CDK2. Consistent with this similarity and with the developmental phosphorylation of CeHCF in C. elegans embryos, CeHCF phosphorylation is cell-cycle-regulated in mammalian cells. ------------------- Key: 4691 Medline: 11350757 Authors: Duerr JS;Gaskin J;Rand JB Title: Identified neurons in C. elegans coexpress vesicular transporters for acetylcholine and monoamines. Citation: American Journal of Physiology - Cell Physiology 280: C1616-C1622 2001 Type: ARTICLE Genes: bas-1 cat-1 cha-1 egl-1 lin-39 tph-1 unc-17 unc-104 Abstract: We have identified four neurons (VC4, VC5, HSNL, HSNR) in Caenorhabditis elegans adult hermaphrodites that express both the vesicular acetylcholine transporter and the vesicular monoamine transporter. All four of these cells are motor neurons that innervate the egg-laying muscles of the vulva. In addition, they all express choline acetyltransferase, the synthetic enzyme for acetylcholine. The distributions of the vesicular acetylcholine transporter and the vesicular monoamine transporter are not identical within the individual cells. In mutants deficient for either of these transporters, there is no apparent compensatory change in the expression of the remaining transporter. This is the first report of neurons that express two different vesicular neurotransmitter ------------------- Key: 4692 Medline: 11516642 Authors: Pujol N;Link EM;Liu LX;Kurz CL;Alloing G;Tan MW;Ray KP;Solari R;Johnson CD;Ewbank JJ Title: A reverse genetic analysis of components of the Toll signaling pathway in Caenorhabditis elegans. Citation: Current Biology 11: 809-821 2001 Type: ARTICLE Genes: che-2 ikb-1 pik-1 tol-1 trf-1 Abstract: Background: Both animals and plants respond rapidly to pathogens by inducing the expression of defense-related genes. Whether such an inducible system of innate immunity is present in the model nematode Caenorhabditis elegans is currently an open question. Among conserved signaling pathways important for innate immunity, the Toll pathway is the best characterized. In Drosophila, this pathway also has an essential developmental role. C. elegans possesses structural homologs of components of this pathway, and this observation raises the possibility that a Toll pathway might also function in nematodes to trigger defense mechanisms or to control development. Results: We have generated and characterized deletion mutants for four genes supposed to function in a nematode Toll signaling pathway. These genes are tol-1, trf-1, pik-1, and ikb-1 and are homologous to the Drosophila melanogaster Toll, dTraf pelle, and cactus genes, respectively. Of these four genes, only tol-l is required for nematode development. None of them are important for the resistance of C. elegans to a number of pathogens. On the other hand, C. elegans is capable of distinguishing different bacterial species and has a tendency to avoid certain pathogens, including Serratia marcescens. The tol-1 mutants are defective in their avoidance of pathogenic S. marcescens, although other chemosensory behaviors are wild type. Conclusions: In C. elegans, tol-1 is important for development and pathogen recognition, as is Toll in Drosophila, but remarkably for the latter role, it functions in the context of a behavioral mechanism that keeps worms away from potential ------------------- Key: 4693 Medline: Authors: Sommer RJ;Witte H;Schlak I Title: Towards a microevolutionary approach in evolutionary developmental biology: Biogeography of the nematode genus Pristionchus (Diplogastridae). Citation: Zoology-Analysis of Complex Systems 103: 91-98 2001 Type: ARTICLE Genes: ced-3 lin-12 lin-39 Abstract: The free-living nematode Pristionchus pacificus has been described as a satellite organism for functional comparative studies in developmental biology. Like the model organism Caenorhabditis elegans, P. pacificus is easily culturable in the laboratory. P. pacificus, is a hermaphroditic species, with a 4-day life cycle, but unlike most nematodes which pass through 4 juvenile stages during their development, P. pacific:us has only three juvenile stages. The combination of cellular, genetic and molecular studies has made P. pacificus a perfect model system for studying evolutionary developmental biology. One process that has been studied in detail is the development of the vulva. Genetic and molecular studies have revealed that the function of several genes involved in vulva development differs between P. pacificus and C. elegans. Here, we review our macroevolutionary comparison between P. pacificus and C. elegans and provide data on the biogeography of the genus Pristionchus. The genus has a world-wide distribution with strains from Northern America, Europe, Madagascar and New Zealand. Sequence analyses of the rDNA internal transcribed spacer (ITS) region and mating experiments revealed that the 12 hermaphroditic strains studied, belong to three different species. Strains isolated from Northern America belong predominantly to Pristionchus pacificus, whereas the european strains are members of Pristionchus maupasi and a new species yet to be ------------------- Key: 4694 Medline: 21173878 Authors: Sluder AE;Maina CV Title: Nuclear receptors in nematodes: themes and variations. Citation: Trends in Genetics 17: 206-213 2001 Type: ARTICLE Genes: daf-12 fax-1 nhr-2 nhr-6 nhr-8 nhr-23 nhr-25 nhr-41 nhr-48 nhr-64 nhr-67 nhr-69 nhr-85 nhr-91 odr-7 sex-1 unc-55 xol-1 Abstract: Large-scale sequencing efforts are providing new perspectives on similarities and differences among species. Sequences encoding nuclear receptor (NR) transcription factors furnish one striking example of this. The three complete or nearly complete metazoan genome sequences - those of the nematode Caenorhabditis elegans, the fruit fly (Drosophila melanogaster) and the human - reveal dramatically different numbers of predicted NR genes: 270 for the nematode, 21 for the fruit fly and similar to 50 for the human. Although some classes of NRs present in insects and mammals are also represented among the nematode genes, most of the C. elegans NR sequences are distinct from those known in other phyla. Questions regarding the evolution and function of NR genes in nematodes, framed by the abundance and diversity of these genes in the C. elegans genome, are the focus of this article. ------------------- Key: 4695 Medline: Authors: Ono S Title: The Caenorhabditis elegans unc-78 gene encodes a homologue of actin-interacting protein 1 required for organised assembly of muscle actin filaments. Citation: Journal of Cell Biology 153: 889- 2001 Type: CORRECT Genes: Abstract: ------------------- Key: 4696 Medline: Authors: Tajima T;Watanabe N;Kogawa Y;Takiguchi N;Kato J;Ikeda T;Kuroda A;Ohtake H Title: Chemotaxis of the nematode Caenorhabditis elegans toward cycloheximide and quinine hydrochloride. Citation: Journal of Bioscience & Bioengineering 91: 322-324 2001 Type: ARTICLE Genes: Abstract: We investigated the chemotaxis of the nematode Caenorhabditis elegans toward cycloheximide, denatonium benzoate, 6-n-propyl-2-thiouracil, and quinine hydrochloride. Interestingly, C. elegans was strongly attracted to cycloheximide, while avoiding quinine hydrochloride. This is the first report thus far to describe the chemotactic responses of C. elegans toward bitter tastants for humans. ------------------- Key: 4697 Medline: 21272200 Authors: Skop AR;Bergmann D;Mohler WA;White JG Title: Completion of cytokinesis in C. elegans requires a brefeldin A-sensitive membrane accumulation at the cleavage furrow apex. Citation: Current Biology 11: 735-746 2001 Type: ARTICLE Genes: rab-8 rab-11 Abstract: Background: The terminal phase of cytokinesis in eukaryotic cells involves breakage of the intercellular canal containing the spindle midzone and resealing of the daughter cells. Recent observations suggest that the spindle midzone is required for this process. In this study, we investigated the possibility that targeted secretion in the vicinity of the spindle midzone is required for the execution of the terminal phase of cytokinesis. Results: We inhibited secretion in early C. elegans embryos by treatment with brefeldin A (BFA), Using 4D recordings of dividing cells, we showed that BFA induced stereotyped failures in the terminal phase of cytokinesis; although the furrow ingressed normally, after a few minutes the furrow completely regressed, even though spindle midzone and midbody microtubules appeared normal. In addition, using an FM1-43 membrane probe, we found that membrane accumulated locally at the apices of the late cleavage furrows that form the persisting intercellular canals between daughter cells. However, in BFA-treated embryos this membrane accumulation did not occur, which possibly accounts for the observed cleavage failures. Conclusions: We have shown that BFA disrupts the terminal phase of cytokinesis in the embryonic blastomeres of C. elegans. We observed that membrane accumulates at the apices of the late cleavage furrow by means of a BFA-sensitive mechanism. We suggest that this local membrane accumulation is necessary for the completion of cytokinesis and speculate that the spindle midzone region of animal cells is functionally equivalent to the phragmoplast of plants and acts to target secretion to the ------------------- Key: 4698 Medline: 21233103 Authors: Kwon S;Song WK;Park CS;Ahnn J Title: Characterization of a novel gene expressed in neuromuscular tissues and centrosomes in Caenorhabditis elegans. Citation: Cell Biochemistry & Function 19: 79-88 2001 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans has many advantages for studying gene function at the organism level. In particular, completion of the genome sequencing has made it feasible to study gene structure and function of both known and novel proteins. As a result of a database search for muscle-specific genes, a gene F43D9.1 was found which showed muscle-specific expression as revealed by the in situ hybridization pattern from the Expressed Sequence Tag (EST) database. A homology search of F43D9.1 protein sequences showed no significant homology with other known proteins, except that it showed very weak sequence similarity with the band 4.1 protein superfamily. Northern blot analysis reveals a single transcript 3.7 kb in size which is consistent with the predicted gene structure. The expression pattern of F43D9.1 was investigated using the gfp reporter gene, acid it has shown to be expressed in neuronal cells including sensory neurons and interneurons in the head region. To further characterize F43D9.1, whole-mount immunostaining was performed with anti-F43D9.1 antibody, which showed specific signals in head neurons, body-wall muscle cells, some other unidentified neuronal cells, and centrosomes of the dividing cells during embryogenesis. Taken together with its predicted membrane topology, we speculate that the F43D9.1 gene, which encodes a novel transmembrane protein and contains a band 4.1-like domain, may function in neuromuscular cells, and may play an important role during cell division in C. elegans. ------------------- Key: 4699 Medline: 21264242 Authors: O'Connell KF;Caron C;Kopish KR;Hurd DD;Kemphues KJ;Li Y;White JG Title: The C. elegans zyg-1 gene encodes a regulator of centrosome duplication with distinct maternal and paternal roles in the embryo. Citation: Cell 105: 547-558 2001 Type: ARTICLE Genes: zyg-1 ccDf5 Abstract: Centrosome duplication is a critical step in assembly of the bipolar mitotic spindle, but the molecular mechanisms regulating this process during the cell cycle and during animal development are poorly understood. Here, we report that the zyg-1 gene of Caenorhabditis elegans is an essential regulator of centrosome duplication. ZYG-1 is a protein kinase specifically required for daughter centriole formation that localizes transiently to centrosomes and acts at least one cell cycle prior to each spindle assembly event. In the embryo, ZYG-1 participates in a unique regulatory scheme whereby paternal ZYG-1 regulates duplication and bipolar spindle assembly during the first cell cycle, and maternal ZYG-1 regulates these processes thereafter. ZYG-1 is therefore a key molecular component of the centrosome/centriole duplication process. ------------------- Key: 4700 Medline: Authors: Wintle RF;Van Tol HHM Title: Dopamine signaling in Caenorhabditis elegans - potential for parkinsonism research. Citation: Parkinsonism & Related Disorders 7: 177-183 2001 Type: REVIEW Genes: bas-1 cat-1 cat-2 cat-3 cat-4 cat-5 cat-6 egl-2 tyr-1 tyr-2 tyr-3 unc-2 Abstract: The nematode Caenorhabditis elegans is an attractive model system for the study of many biological processes. It possesses a simple nervous system with known anatomy and connectivity, is conveniently and cheaply cultured in the laboratory, and is amenable to many genetic manipulations that are impossible in mammalian systems. The recent completion of the C. elegans genome sequence provides a rich resource of genomic and bioinformatic data to researchers in diverse fields. This organism, however, has been underexploited in the studies of many basic processes related to nervous system function, neuropsychiatric disorders and neuromuscular function. Anatomical, biochemical, behavioral, pharmacological and genetic evidence accumulated to date strongly suggests that dopamine is used as a neurotransmitter by C. elegans, and that its effects are mediated through pathway(s) that share many features with those of mammals. DNA sequence analysis reveals genes highly homologous to those encoding mammalian dopamine receptors. Probably, C. elegans has dopamine receptors that transduce environmental cues into behaviors, and these receptors pharmacologically most closely resemble the D2 family. Here we present a review of the current state of research into the dopamine system of the worm, focussing on its potential for use in the study of biological processes related to parkinsonism. ------------------- Key: 4701 Medline: 21275952 Authors: Larsen PL Title: Asking the age-old question. Citation: Nature Genetics 28: 102-104 2001 Type: REVIEW Genes: age-1 akt-1 akt-2 daf-2 daf-16 daf-18 pdk-1 Abstract: Control of lifespan in Caenorhabditis elegans by the DAF-2 insulin-like signaling pathway requires daf-16. which encodes a member of the forkhead family of transcription factors. A new study provides evidence that DAF-2 negatively regulates DAF-16 activity by promoting its retention in the cytoplasm. But, constitutive targeting of DAF-16 to the nucleus is not sufficient to extend lifespan, revealing a new layer of complexity in the genetic control of aging in the nematode. ------------------- Key: 4702 Medline: 11381260 Authors: Lin K;Hsin H;Libina N;Kenyon C Title: Regulation of the Caenorhabditis elegans longevity protein DAF-16 by insulin/IGF-1 and germline signaling. Citation: Nature Genetics 28: 139-145 2001 Type: ARTICLE Genes: age-1 akt-1 akt-2 daf-2 daf-16 daf-18 Abstract: The lifespan of Caenorhabditis elegans is regulated by the insulin/insulin-like growth factor (IGF)-1 receptor homolog DAF-2, which signals through a conserved phosphatidylinositol 3-kinase (PI 3-kinase)/Akt pathway(1-7) Mutants in this pathway remain youthful and active much longer than normal animals and can live more than twice as long, This lifespan extension requires DAF-16, a forkhead/winged-helix transcription factor(8,9). DAF-16 is thought to be the main target of the DAF-2 pathway. Insulin/IGF-1 signaling is thought to lead to phosphorylation of DAF-16 by AKT activity, which in turn shortens lifespan. Here, we show that the DAF-2 pathway prevents DAF-16 accumulation in nuclei. Disrupting Akt-consensus phosphorylation sites in DAF-16 causes nuclear accumulation in wild-type animals, but, surprisingly, has little effect on lifespan. Thus the DAF-2 pathway must have additional outputs. Lifespan in C. elegans can be extended by perturbing sensory neurons or germ cells(10,11). In both cases, lifespan extension requires DAF-16. We find that both sensory neurons and germline activity regulate DAF-16 accumulation in nuclei, but the nuclear localization patterns are different. Together these findings reveal unexpected complexity in the DAF-16-dependent pathways that regulate aging. ------------------- Key: 4703 Medline: 21275970 Authors: Wicks SR;Yeh RT;Gish WR;Waterston RH;Plasterk RHA Title: Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Citation: Nature Genetics 28: 160-164 2001 Type: ARTICLE Genes: dyf-5 Abstract: Single nucleotide polymorphisms (SNPs) are valuable genetic markers of human disease(1-3). They also comprise the highest potential density marker set available for mapping experimentally derived mutations in model organisms such as Caenorhabditis elegans. To facilitate the positional cloning of mutations we have identified polymorphisms in CB4856, an isolate from a Hawaiian island that shows a uniformly high density of polymorphisms compared with the reference Bristol N2 strain. Based on 5.4 Mbp of aligned sequences, we predicted 6.222 polymorphisms. Furthermore, 3,457 of these markers modify restriction enzyme recognition sites ('snip-SNPs') and are therefore easily detected as RFLPs. Of these, 493 were experimentally confirmed by restriction digest to produce a snip-SNP map of the worm genome. A mapping strategy using snip-SNPs and bulked segregant analysis(4) (BSA) is outlined. CB4856 is crossed into a mutant strain, and exclusion of CB4856 alleles of a subset of snip-SNPs in mutant progeny is assesed with BSA. The proximity of a linked marker to the mutation is estimated by the relative proportion of each form of the biallelic marker in populations of wildtype and mutant genomes. The usefulness of this approach is illustrated by the rapid mapping of the dyf-5 gene. ------------------- Key: 4704 Medline: 11356862 Authors: Zhou HM;Brust-Mascher I;Scholey JM Title: Direct visualization of the movement of the monomeric axonal transport motor UNC-104 along neuronal processes in living Caenorhabditis elegans. Citation: Journal of Neuroscience 21: 3749-3755 2001 Type: ARTICLE Genes: unc-104 Abstract: The formation and function of axons depends on the microtubule-based transport of cellular components from their sites of synthesis in the neuronal cell body to their sites of utilization at the axon terminus. To directly visualize this axonal transport in a living organism, we constructed transgenic lines of Caenorhabditis elegans that express green fluorescent protein fused to the monomeric synaptic vesicle transport motor, UNC-104. This UNC-104::GFP construct rescued the Unc-104 mutant phenotype and was expressed throughout the nervous system. Using time-lapse confocal fluorescence microscopy, we were able to visualize fluorescent motor proteins moving in both directions along neuronal processes, some of which were identified definitely as axons and others as dendrites. Using kymograph analysis, we followed the movement of >900 particles. Most of them moved in one direction, but not necessarily at the same velocity. Ten percent of the observed particles reversed direction of movement during the period of observation, and 10% exhibited periods of movement interspersed with pauses. During episodes of persistent movement, particles moved at an average velocity of 1.02 mum/sec, which is close to the in vitro velocity of microtubule gliding driven by purified monomeric kinesin at high motor density. To our knowledge, this is the first direct visualization and analysis of the movement of specifically labeled microtubule motor proteins along axons ------------------- Key: 4705 Medline: 11368911 Authors: Aronoff R;Baran R;Hodgkin J Title: Molecular identification of smg-4, required for mRNA surveillance in C. elegans. Citation: Gene 268: 153-164 2001 Type: ARTICLE Genes: smg-4 unc-54 sDf29 Abstract: Premature termination codons trigger a process in eukaryotes known as nonsense mediated decay or mRNA surveillance, resulting in the rapid decay of the aberrant transcript. Studies in C. elegans have shown this system is mediated by seven smg genes and can prevent the accumulation of toxic, truncated peptides. Here we report the cloning of smg-4 by physical mapping and functional rescue assays. The minimal rescuing activity is found within a genomic operon, encoding a novel protein. The final exon of the gene is alternatively spliced for expression of two different isoforms. Although no known genes were found to exhibit significant homology to smg-4, a novel conserved domain has been identified by alignment with sequences defined by expressed sequence tags (ESTs) from a variety of organisms. Furthermore, we describe a homolog from C. briggsae, which will rescue C. elegans smg-4 mutants. The C. elegans gene has been fused to green fluorescent protein (GFP). This SMG4:GFP fusion exhibits nuclear accumulation and diffuse cytoplasmic staining, and further localizes to what appear to be perinuclear and ------------------- Key: 4706 Medline: 21235055 Authors: Tagawa A;Rappleye CA;Aroian RV Title: pod-2, along with pod-1, defines a new class of genes required for polarity in the early Caenorhabditis elegans embryo. Citation: Developmental Biology 233: 412-424 2001 Type: ARTICLE Genes: emb-20 par-1 par-2 par-3 par-4 pie-1 pod-1 pod-2 ccDf11 Abstract: The asymmetric division of the one-cell Caenorhabditis elegans zygote gives rise to two cells of different size and fate, thereby establishing the animal's anterior-posterior (a-p) axis. Through genetics, a number of genes required for this polarity have been characterized, but many components remain unidentified. Recently, our laboratory discovered a mutation in the pod-1 gene (for polarity and osmotic defective) that uniquely perturbed polarity and osmotic protection. Here, we describe a new C. elegans polarity gene identified during screens for conditional embryonic lethals. Embryos in which this gene has been mutated show a loss of physical and developmental asymmetries in the one-cell embryo, including the mislocalization of PAR and POD-1 proteins required for early polarity. Furthermore, mutant embryos are osmotically sensitive, allowing us to designate this gene pod-2. Thus, pod-2, along with pod-1, defines a nc rv class of C. elegans polarity genes. Genetic analyses indicate that pod-2 functions in the same pathway as pod-1. Temperature-shift studies indicate that pod-2 is required during oogenesis, indicating that aspects of embryonic polarization may precede fertilization. pod-2 mutant embryos also exhibit a unique germline inheritance defect in which germline identity localizes to the wrong spot in the one-cell embryo and is therefore inherited by the wrong cell at the four-cell stage. Our data suggest that pod-2 ------------------- Key: 4707 Medline: 11336509 Authors: Portereiko MF;Mango SE Title: Early morphogenesis of the Caenorhabditis elegans pharynx. Citation: Developmental Biology 233: 482-494 2001 Type: ARTICLE Genes: jam-1 let-2 mig-2 pha-4 pop-1 Abstract: We investigated the cellular behaviors that accompany the early stages of pharyngeal morphogenesis in Caenorhabditis elegans. The embryonic pharynx develops from a ball of cells into a linear tube connected anteriorly to the buccal cavity and posteriorly to the midgut. By using GFP reporters localized to discrete subcellular regions, we show that pharyngeal morphogenesis can be divided into three stages: (1) lengthening of the nascent pharyngeal lumen by reorientation of apicobasal polarity of anterior pharyngeal cells ("Reorientation"), (2) formation of an epithelium by the buccal cavity cells, which mechanically couples the buccal cavity to the pharynx and anterior epidermis ("Epithelialization"), and (3) a concomitant movement of the pharynx anteriorly and the epidermis of the mouth posteriorly to bring the pharynx, buccal cavity, and mouth into close apposition ("Contraction"). Several models can account for these cellular behaviors, and we distinguish between them by physically or genetically ablating cells within the digestive tract. These studies provide the first description of how the pharynx primordium develops into an epithelial tube, and reveal that pharyngeal morphogenesis resembles aspects of mammalian ------------------- Key: 4708 Medline: 21248411 Authors: Madi A;Kele Z;Janaky T;Punyiczki M;Fesus L Title: Identification of protein substrates for transglutaminase in Caenorhabdits elegans. Citation: Biochemical and Biophysical Research Communications 283: 964-968 2001 Type: ARTICLE Genes: Abstract: Transglutaminase-dependent cross-linking of proteins leads to protein polymerisation that confers stability as well as resistance to mechanical disruption and chemical attack. Various transglutaminases have been implicated in a wide range of biological phenomena occurring in both extracellular and intracellular compartments, but further clarification of the physiological role of these enzymes requires identification of possible substrate molecules. Here we report the detection, purification, and identification of two proteins, enolase and ATP synthase cu subunit as glutamine donor protein substrates for the transglutaminase of the nematode Caenorhabditis elegans. ------------------- Key: 4709 Medline: 21216776 Authors: Saeki S;Yamamoto M;Iino Y Title: Plasticity of chemotaxis revealed by paired presentation of a chemoattractant and starvation in the nematode Caenorhabditis elegans. Citation: Journal of Experimental Biology 204: 1757-1764 2001 Type: ARTICLE Genes: Abstract: While the basic functioning of the nervous system of Caenorhabditis elegans has been extensively studied, its behavioural plasticities have not been fully explored because of the limited availability of assay systems. We report here a simple form of chemotaxis plasticity in this organism: when worms are starved on plates that contain NaCl, their chemotaxis towards NaCl falls dramatically. This conditioning requires both the presence of NaCl and the absence of a bacterial food source, indicating that it is not merely adaptation or habituation, but that it is likely to be a form of associative learning. While chemotaxis towards volatile chemoattractants does not change significantly after conditioning with NaCl, chemotaxis towards other water-soluble attractants does decrease. This suggests that an altered response of a cell or a group of cells specifically involved in chemotaxis towards water-soluble chemoattractants is responsible for the behavioural alteration. The decrease in chemotaxis occurred slowly over 3-4 h of conditioning and returned quickly to the original level when either of the conditioning stimuli, NaCl or starvation, was removed. The application of serotonin partially blocked this reduction in chemotaxis, consistent with the proposed function of this neurotransmitter in food signalling. Using this assay, we have isolated three mutants with reduced plasticity, This assay system expands the opportunities for studying the molecular and cellular mechanisms of behavioural plasticity in C. elegans. ------------------- Key: 4710 Medline: 21211295 Authors: Alper S;Kenyon C Title: REF-1, a protein with two bHLH domains, alters the pattern of cell fusion in C. elegans by regulating Hox protein activity. Citation: Development 128: 1793-1804 2001 Type: ARTICLE Genes: egl-5 lin-12 lin-22 lin-39 mab-5 ref-1 unc-37 mnDf29 mnDf57 mnDf59 mnDf63 mnDf66 mnDf83 Abstract: Hox genes control the choice of cell fates along the anteroposterior (AP) body axis of many organisms. In C. elegans, two Hox genes, lin-39 and mab-5, control the cell fusion decision of the 12 ventrally located Pn.p cells. Specific Pn,p cells fuse with an epidermal syncytium, hyp7, in a sexually dimorphic pattern. In hermaphrodites, Pn.p cells in the mid-body region remain unfused whereas in males, Pn,p cells adopt an alternating pattern of syncytial and unfused fates. The complexity of these fusion patterns arises because the activities of these two Hox proteins are regulated in a sex-specific manner. MAB-5 activity is inhibited in hermaphrodite Pn.p cells and thus MAB-5 normally only affects the male Pn,p fusion pattern. Here we identify a gene, ref-1, that regulates the hermaphrodite Pn,p cell fusion pattern largely by regulating MAB-5 activity in these cells. Mutation of ref-l also affects the fate of other epidermal cells in distinct AP body regions. ref-l encodes a protein with two basic helix-loop-helix domains distantly related to those of the hairy/Enhancer of split family. ref-l, and another hairy homolog, lin-22, regulate similar cell fate decisions in different body regions along the C. elegans AP body axis. ------------------- Key: 4711 Medline: 21211297 Authors: Geles KG;Adam SA Title: Germline and developmental roles of the nuclear transport factor importin alpha 3 in C. elegans. Citation: Development 128: 1817-1829 2001 Type: ARTICLE Genes: fem-3 gld-1 glp-1 him-1 ima-1 ima-2 ima-3 Abstract: The importin alpha family of transport factors mediates the nuclear import of classical nuclear localization signal-containing proteins. In order to understand how multiple importin alpha proteins are regulated both in individual cells and in a whole organism, the three importin alpha (ima) genes of Caenorhabditis elegans have been identified and studied. All three IMAs are expressed in the germline; however, only IMA-3 is expressed in the soma. RNA interference (RNAi) experiments demonstrate that IMA-3 is required for the progression of meiotic prophase I during oocyte development. Loss of IMA-3 expression leads also to a disruption of the nuclear pore complex accompanied by the mis-localization of P granules. A range of defects occurring in ima3(RNAi) F-1 progeny further supports a role for IMA-3 during embryonic and larval development. The functional association of IMA-3,vith distinct cellular events, its expression pattern and intracellular localization indicate that regulation of the nuclear transport machinery is involved in the control of ------------------- Key: 4712 Medline: 21272236 Authors: Gems D;Partridge L Title: Insulin/IGF signalling and ageing: seeing the bigger picture. Citation: Current Opinion in Genetics & Development 11: 287-292 2001 Type: REVIEW Genes: age-1 daf-2 daf-12 daf-16 tph-1 Abstract: Although the underlying mechanisms of ageing are not understood, it is known that the longevity of the nematode Caenorhabditis elegans is modulated by an insulin/IGF-signalling pathway. The focus now is on how this pathway is regulated, how it controls nematode ageing, and how this relates to the ageing process in higher ------------------- Key: 4713 Medline: 21148080 Authors: Chase DL;Patikoglou GA;Koelle MR Title: Two RGS proteins that inhibit G alpha(o) and G alpha(q) signaling in C. elegans neurons require a G beta(5)-like subunit for function. Citation: Current Biology 11: 222-231 2001 Type: ARTICLE Genes: eat-16 egl-10 egl-30 goa-1 gpb-1 gpb-2 Abstract: Background: Gp proteins have traditionally been thought to complex with Gy proteins to function as subunits of G protein heterotrimers. The divergent G beta (5) protein, however, can bind either Gy proteins or regulator of G protein signaling (RGS) proteins that contain a G gamma-like (GGL) domain. RGS proteins inhibit G protein signaling by acting as Ga GTPase activators. While GP, appears to bind RGS proteins in vivo, its association with Gy proteins in vivo has not been clearly demonstrated. It is unclear how Gp, might influence RGS activity, In C. elegans there are exactly two GGL-containing RGS proteins, EGL-10 and EAT-16, and they inhibit G alpha (o) and G alpha (q) signaling, respectively. Results: We knocked out the gene encoding the C. elegans G beta (5) ortholog, GPB-2, to determine its physiological roles in G protein signaling. The gpb-2 mutation reduces the functions of EGL-10 and EAT-16 to levels comparable to those found in egl-10 and eat-16 null mutants. gpb-2 knockout animals are viable, and exhibit no obvious defects beyond those that can be attributed to a reduction of EGL-10 or EAT-16 function. GPB-2 protein is nearly absent in eat-16, egl-10 double mutants, and EGL-10 protein is severely diminished in gpb-2 mutants. Conclusions: G beta (5) functions in vivo complexed with GGL-containing RGS proteins. In the absence of G beta (5), these RGS proteins have little or no function. The formation of RGS-G beta (5) complexes is required for the expression or stability of both the RGS and G beta (5) proteins. Appropriate RGS-G beta (5) complexes regulate both G alpha (o) and G alpha (q) ------------------- Key: 4714 Medline: 11250160 Authors: Robatzek M;Niacaris T;Steger K;Avery L;Thomas JH Title: eat-11 encodes GPB-2, a G beta(5) ortholog that interacts with G(o)alpha and G(q)alpha to regulate C. elegans behavior. Citation: Current Biology 11: 288-293 2001 Type: ARTICLE Genes: dgk-1 eat-11 eat-16 egl-8 egl-10 egl-30 goa-1 gpb-2 unc-43 Abstract: In C. elegans, a G(o)/G(q) signaling network regulates locomotion and egg laying [1-8]. Genetic analysis shows that activated Ca2+/calmodulin-dependent protein kinase II (CaMKII) is suppressed by perturbations of this network, which include loss of the GOA-1 G(o)alpha, DGK-1 diacylglycerol kinase. EAT-16 16 protein gamma subunit-like (GGL)-containing RGS protein, or an unidentified protein encoded by the gene eat-11 [9]. We cloned eat-11 and report that it encodes the G beta (5) ortholog GPB-2, Gp, binds specifically to GGL-containing RGS proteins, and the G beta (5)/RGS complex can promote the GTP-hydrolyzing activity of G alpha subunits [10, 11]. However, little is known about how this interaction affects G protein signaling in vivo. In addition to EAT-16, the GGL-containing RGS protein EGL-10 participates in G(o)/G(q) signaling; EGL-10 appears to act as an RGS for the GOA-1 G,cw, while EAT-16 appears to act as an RGS for the EGL-30 G(q)alpha [4, 5]. We have combined behavioral, electrophysiological, and pharmacological approaches to show that GPB-2 is a central member of the G(o)/G(q) network and that GPB-2 may interact with both the EGL-10 and EAT-16 RGS proteins to mediate the opposing activities of G,cw and G,a. These interactions provide a mechanism for the modulation of behavior by antagonistic G protein networks. ------------------- Key: 4715 Medline: 11301258 Authors: Qin H;Rosenbaum JL;Barr MM Title: An autosomal recessive polycystic kidney disease gene homolog is involved in intraflagellar transport in C. elegans ciliated sensory neurons. Citation: Current Biology 11: 457-461 2001 Type: ARTICLE Genes: che-2 che-11 daf-10 osm-1 osm-5 osm-6 Abstract: In this report, we show that the Caenorhabditis elegans gene osm-5 is homologous to the Chlamydomonas gene IFT88 and the mouse autosomal recessive polycystic kidney disease (ARPKD) gene, Tg737. The function of this ARPKD gene may be evolutionarily conserved: mutations result in defective ciliogenesis in worms [1], algae [2], and mice [2, 3]. Intraflagellar transport (IFT) is essential for the development and maintenance of motile and sensory cilia [4]. The biochemically isolated IFT particle from Chlamydomonas flagella is composed of 16 polypeptides in one of two Complexes (A and B) [5, 6] whose movement is powered by kinesin II (anterograde) and cytoplasmic dynein (retrograde) [7-9]. We demonstrate that OSM-5 (a Complex B polypeptide), DAF-10 and CHE-11 (two Complex A polypeptides), and CHE-2 [10], a previously uncategorized IFT polypeptide, all move at the same rate in C. elegans sensory cilia. In the absence of osm-5, the C. elegans autosomal dominant PKD (ADPKD) gene products [11] accumulate in stunted cilia, suggesting that abnormal or lack of cilia or defects in IFT may result in diseases such ------------------- Key: 4716 Medline: 21426582 Authors: Gumienny TL;Hengartner MO Title: How the worm removes corpses: the nematode C. elegans as a model system to study engulfment. Citation: Cell Death and Differentiation 8: 564-568 2001 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-5 ced-6 ced-7 ced-10 ced-12 Abstract: Apoptotic with the removal of the dying cells from the organism. This removal is brought forth through a rapid and specific engulfment of the doomed cell by one of its neighbors. Over half a dozen genes have been identified that function in this process in the worm. Many of these engulfment genes have functional homologs in Drosophila and higher vertebrates. Indeed, there is growing evidence supporting the hypothesis that the pathways that mediate the removal of apoptotic cells might be, at least in part, conserved through evolution. ------------------- Key: 4717 Medline: 2128325b Authors: Ankeny RA Title: The natural history of Caenorhabditis elegans research. Citation: Nature Reviews Genetics 2: 474-479 2001 Type: REVIEW Genes: Abstract: The nematode Caenorhabditis elegans is well known to practising biologists as a model organism. Early work with C. elegans is best understood as part of a descriptive tradition in biological practice. Although the resources that have been generated by the C. elegans community have been revolutionary, they were produced by traditional methods and approaches. Here, I review the choice and use of the worm as an experimental organism for genetics and neurobiology that began in the 1960s. ------------------- Key: 4718 Medline: 11389442 Authors: Grant B;Zhang Y;Paupard MC:Lin SX;Hall DH;Hirsh D Title: Evidence that RME-1, a conserved C. elegans EH-domain protein, functions in endocytic recycling. Citation: Nature Cell Biology 3: 573-579 2001 Type: ARTICLE Genes: dyn-1 rme-1 sDf26 sDf30 sDp30 Abstract: In genetic screens for new endocytosis genes in Caenorhabditis elegans we identified RME-1, a member of a conserved class of Epsl5-homology (EH)-domain proteins. Here we show that RME-1 is associated with the periphery of endocytic organelles, which is consistent with a direct role in endocytic transport. Endocytic defects in rme-l mutants indicate that the protein is likely to have a function in endocytic recycling. Evidence from studies of mammalian RME-1 also points to a function for RME-1 in recycling, specifically in the exit of membrane proteins from recycling endosomes. These studies show a conserved function in endocytic recycling for the RME-1 family of EH ------------------- Key: 4719 Medline: 11278828 Authors: Kayser EB;Morgan PG;Hoppel CL;Sedensky MM Title: Mitochondrial expression and function of GAS-1 in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 276: 20551-20558 2001 Type: ARTICLE Genes: gas-1 unc-7 mnDp1 Abstract: A mutation in the gene gas-1 alters sensitivity to volatile anesthetics, fecundity, and life span in the nematode Caenorhabditis elegans. gas-1 encodes a close homologue of the 49-kDa iron protein subunit of Complex I of the mitochondrial electron transport chain from bovine heart. gas-1 is widely expressed in the nematode neuromuscular system and in a subcellular pattern consistent with that of a mitochondrial protein. Pharmacological studies indicate that gas-1 functions partially via presynaptic effects. In addition, a mutation in the gas-1 gene profoundly decreases Complex I-dependent metabolism in mitochondria as measured by rates of both oxidative phosphorylation and electron transport. An increase in Complex II-dependent metabolism also is seen in mitochondria from gas-1 animals. There is no apparent alteration in physical structure in mitochondria from gas-1 nematodes compared with those from wild type. These data indicate that gas-1 is the major 49-kDa protein of complex I and that the GAS-1 protein is critical to mitochondrial function in C. elegans. They also reveal the importance of mitochondrial function in determining not only aging and life span, but also anesthetic sensitivity, in this model organism. ------------------- Key: 4720 Medline: 11274160 Authors: Li Y;Dowbenko D;Lasky LA Title: Caenorhabditis elegans PIAK, a phospholipid-independent kinase that activates the AKT/PKB survival kinase. Citation: Journal of Biological Chemistry 276: 20323-20329 2001 Type: ARTICLE Genes: Abstract: Phospholipid-dependent kinase 1 (PDK 1) is a 3'-phospholipid-responsive serine/threonine kinase that plays a critical role in cell survival by phosphorylating and activating the anti-apoptotic AKT/PKB kinase, While PDK 1 is clearly an important component of the cell survival machinery, the potential for phospholipid-independent activation of the AKT/PKB survival pathway has not been extensively examined at the molecular level. We have identified a second form of PDK 1 in the nematode Caenorhabditis elegans that we have termed PIAK. (phospholipid-independent AKT/PKB kinase). PIAK is highly homologous to C. elegans and mammalian PDK 1 with the exception that the novel kinase lacks a phospholipid binding pleckstrin homology domain. The domain structure of PIAK suggests that it might be a phospholipid-independent kinase, and PIAK phosphorylates mammalian AKT/PKB at the activating Thr(308) residue in the presence of the phosphatidylinositol (PI) 3-kinase inhibitors as well as in the absence of growth factors. In addition, PIAK is capable of inducing the phospholipid-independent, AKT/PKB-induced phosphorylation of the AFX-type forkhead transcription factor, resulting in its cytoplasmic localization. Because the nuclear localization of this transcription factor induces an apoptotic state, this PIAK-mediated cytoplasmic sequestration allows for cell survival. Finally, PIAK activity appears to be induced by various inhibitors of cell cycle G(1) progression. These data suggest an alternate, phosphatidylinositol 3-kinase-independent mechanism for the activation of the AKT/PKB survival pathway that may be utilized during periods of cellular ------------------- Key: 4721 Medline: 21297224 Authors: van Swinderen B;Metz LB;Shebester LD;Mendel JE;Sternberg PW;Crowder CM Title: G(o) alpha regulates volatile anesthetic action in Caenorhabditis elegans. Citation: Genetics 158: 643-655 2001 Type: ARTICLE Genes: dgk-1 eat-16 egl-10 goa-1 sag-1 unc-64 Abstract: To identify genes controlling volatile anesthetic (VA) action, we have screened through existing Caenorhabditis elegans mutants and found that strains with a reduction in Go signaling are VA resistant. Loss-of-function mutants of the gene goa-l, which codes for the alpha -subunit of Go, have EC(50)s for the VA isoflurane of 1.7- to 2.4-fold that of wild type. Strains overexpressing egl-10, which codes for an RGS protein negatively regulating goa-l, are also isoflurane resistant. However, sensitivity to halothane, a structurally distinct VA, is differentially affected by Go pathway mutants. The RGS overexpressing strains, a goa-l missense mutant found to carry a novel mutation near the GTP-binding domain, and eat-16(rf) mutants, which suppress goa-1(gf) mutations, are all halothane resistant; gon-1(null) mutants have wild-type sensitivities. Double mutant strains carrying mutations in both goa-l and unc-64, which codes for a neuronal syntaxin previously found to regulate VA sensitivity, show that the syntaxin mutant phenotypes depend in part on goa-l expression. Pharmacological assays using the cholinesterase inhibitor aldicarb suggest that VAs and GOA-1 similarly downregulate cholinergic neurotransmitter release in C. elegans. Thus, the mechanism of action of VAs in C. elegans is regulated by Goa, and presynaptic Go alpha -effectors are candidate VA molecular targets. ------------------- Key: 4722 Medline: 11390355 Authors: Pasierbek P;Jantsch M;Melcher M;Schleiffer A;Schweizer D;Loidl J Title: A Caenorhabditis elegans cohesion protein with functions in meiotic chromosome pairing and disjunction. Citation: Genes & Development 15: 1349-1360 2001 Type: ARTICLE Genes: coh-1 coh-2 coh-3 him-8 rec-8 spo-11 Abstract: We have studied four Caenorhabditis elegans homologs of the Rad21/Scc1/Rec8 sister-chromatid cohesion protein family. Based on the RNAi phenotype and protein localization, it is concluded that one of them, W02A2.6p, is the likely worm ortholog of yeast Rec8p. The depletion of C. elegans W02A2.6p (called REC-8) by RNAi, induced univalent formation and splitting of chromosomes into sister chromatids at diakinesis. Chromosome synapsis at pachytene was defective, but primary homology recognition seemed unaffected, as a closer-than-random association of homologous fluorescence in situ hybridization (FISH) signals at leptotene/zygotene was observed. Depletion of REC-8 also induced chromosome fragmentation at diakinesis. We interpret these fragments as products of unrepaired meiotic double-stranded DNA breaks (DSBs), because fragmentation was suppressed in a spo-11 background. Thus, REC-8 seems to be required for successful repair of DSBs. The occurrence of DSBs in REC-8-depleted meiocytes suggests that DSB formation does not depend on homologous synapsis. Anti-REC-8 immunostaining decorated synaptonemal complexes (SCs) at pachytene and chromosomal axes in bivalents and univalents at diakinesis. Between metaphase I and metaphase II, REC-8 is partially lost from the chromosomes. The partial loss of REC-8 from chromosomes between metaphase I and metaphase II suggests that worm REC-8 might function similarly to yeast Rec8p. The loss of yeast Rec8p from chromosome arms at meiosis I and centromeres at meiosis II coordinates the disjunction of homologs and sister ------------------- Key: 4723 Medline: 11516648 Authors: Lindblom TH;Pierce GJ;Sluder AE Title: A C. elegans orphan nuclear receptor contributes to xenobiotic resistance. Citation: Current Biology 11: 864-868 2001 Type: ARTICLE Genes: daf-12 nhr-8 pgp-1 pgp-3 Abstract: Lipophilic endocrine signals in metazoans, including the steroid, thyroid, and retinoid hormones, alter gene expression in target cells by binding to and modulating the activity of nuclear receptor (MR) transcription factors [1]. In vertebrates, xenobiotic and pharmacologic compounds can regulate the expression of protective metabolic enzymes via specific "xenobiotic sensing" NRs [2-4]. Here, we report evidence suggesting that this activity is an ancient conserved function for the NR class containing these receptors. Specifically, we show that a Caenorhabditis elegans member of this NR class, nhr-8, is required for wild-type levels of resistance to the toxins colchicine and chloroquine. The nhr-8 promoter is active in the nematode gut, a tissue that also expresses the ABC transporter, PGP-3, which contributes to defense against these toxins [5]. In contrast to pgp-3 mutants, nhr-8 mutants are not more sensitive than wild-type to pyocyanin-dependent killing by the pathogenic bacterium Pseudomonas aeruginosa. We conclude that NHR-8 functions in the nematode xenobiotic defense system and that NHR-8 and PGP-9 have overlapping, but distinct, spectra of toxin specificity. ------------------- Key: 4724 Medline: 21315354 Authors: O'Quinn AL;Wiegand EM;Jeddeloh JA Title: Burkholderia pseudomallei kills the nematode Caenorhabditis elegans using an endotoxin-mediated paralysis. Citation: Cellular Microbiology 3: 381-393 2001 Type: ARTICLE Genes: avr-14 avr-15 egl-9 egl-19 unc-2 unc-22 unc-36 unc-43 Abstract: We investigated a non-mammalian host model system for fitness in genetic screening for virulence-attenuating mutations in the potential biowarfare agents Burkholderia pseudomallei and Burkholderia mallei. We determined that B. pseudomallei is able to cause 'disease-like' symptoms and kill the nematode Caenorhabditis elegans. Analysis of killing in the surrogate disease model with B. pseudomallei mutants indicated that killing did not require lipopolysaccharide (LPS) O-antigen, aminoglycoside/macrolide efflux pumping, type II pathway-secreted exoenzymes or motility. Burkholderia thailandensis and some strains of Burkholderia cepacia also killed nematodes. Manipulation of the nematode host genotype suggests that the neuromuscular intoxication caused by both B. pseudomallei and B. thailandensis acts in part through a disruption of normal Ca2+ signal transduction. Both species produce a UV-sensitive, gamma-irradiation-resistant, limited diffusion, paralytic agent as part of their nematode pathogenic mechanism. The results of this investigation suggest that killing by B. pseudomallei is an active process in C. elegans, and that the C. elegans model might be useful for the identification of vertebrate animal virulence factors in B. pseudomallei. ------------------- Key: 4725 Medline: 21305903 Authors: Gotta M;Abraham MC;Ahringer J Title: CDC-42 controls early cell polarity and spindle orientation in C. elegans. Citation: Current Biology 11: 482-488 2001 Type: ARTICLE Genes: cdc-42 par-1 par-2 par-3 par-6 pkc-3 Abstract: Background: Generation of asymmetry in the one-cell embryo of C. elegans establishes the anterior-posterior axis (A-P), and is necessary far the proper identity of early blastomeres. Conserved PAR proteins are asymmetrically distributed and are required for the generation of this early asymmetry. The small G protein Cdc42 is a key regulator of polarity in other systems, and recently it has been shown to interact with the mammalian homolog of PAR-6. The function of Cdc42 in C elegans had not yet been investigated, however. Results: Here, we show that C. elegans cdc-42 plays an essential role in the polarity of the one-cell embryo and the proper localization of PAR proteins. Inhibition of cdc-42 using RNA interference results in embryos with a phenotype that is nearly identical to par-3, par-6, and pkc-3 mutants, and asymmetric localization of these and other PAR proteins is lost. We further show that C. elegans CDC-42 physically interacts with PAR-6 in a yeast two-hybrid system, consistent with data on the interaction of human homologs. Conclusions: Our results show that CDC-42 acts in concert with the PAR proteins to control the polarity of the C. elegans embryo, and provide evidence that the interaction of CDC-42 and the PAR-3/PAR-6/PKC-3 complex has been evolutionarily conserved as a functional unit. ------------------- Key: 4726 Medline: Authors: Link EM;Hardiman G;Sluder AE;Johnson CD;Liu LX Title: Therapeutic target discovery using Caenorhabditis elegans. Citation: Pharmacogenetics 1: 203-217 2000 Type: REVIEW Genes: age-1 akt-1 akt-2 ced-9 daf-2 daf-16 daf-18 egl-10 hop-1 lov-1 odr-7 pdk-1 sel-12 spe-4 unc-29 Abstract: Use of the human genome sequence in disease therapy will require efficient identification of disease-causing and disease-associated genes with functions that are amenable to pharmacological manipulation. The validation and development of such genes as therapeutic targets requires information about both the genes' functions and the biochemical pathways in which they participate. One powerful means of obtaining such information is the study of homologous genes in model organisms amenable to laboratory manipulation. Among model organisms the nematode Caenorhabditis elegans offers several advantages, including well-established techniques for genetic and experimental manipulation and the first completed genome sequence for a multicellular organism. Molecular genetic experiments using C. elegans can contribute at several levels to drug discovery programs, from elucidation of genetic functions and pathways to the validation of candidate targets. Additionally, the ease of culture allows adaptation of the nematode for use in high-throughput chemical screens for the identification of ------------------- Key: 4727 Medline: 11493519 Authors: Altun-Gultekin Z;Andachi Y;Tsalik E L;Pilgrim D;Kohara Y;Hobert O Title: A regulatory cascade of three homeobox genes, ceh-10, ttx-3 and ceh-23, controls cell fate specification of a defined interneuron class in C. elegans. Citation: Development 128: 1951-1969 2001 Type: ARTICLE Genes: aex-3 ceh-10 ceh-23 che-3 che-11 daf-6 daf-7 eat-6 flp-1 gcy-5 gcy-8 ina-1 kal-1 lin-11 lin-12 odr-10 osm-6 osm-10 rab-3 sax-2 sax-3 ser-2 snb-1 sra-11 srb-6 srd-1 sre-1 str-2 tax-2 tax-4 ttx-3 unc-5 unc-6 unc-7 unc-13 unc-17 unc-18 unc-25 unc-31 unc-33 unc-40 unc-43 unc-44 unc-53 unc-54 unc-64 unc-73 unc-76 unc-104 unc-115 unc-119 unc-122 zig-2 zig-3 Abstract: The development of the nervous system requires the coordinated activity of a variety of regulatory factors that define the individual properties of specific neuronal subtypes. We report a regulatory cascade composed of three homeodomain proteins that act to define the properties of a specific interneuron class in the nematode C. elegans. We describe a set of differentiation markers characteristic for the AIY interneuron class and show that the ceh-10 paired-type and ttx-3 LIM-type homeobox genes function to regulate all known subtype-specific features of the AIY interneurons. In contrast, the acquisition of several pan-neuronal features is unaffected in ceh-10 and ttx-3 mutants, suggesting that the activity of these homeobox genes separates pan-neuronal from subtype-specific differentiation programs. The LIM homeobox gene ttx-3 appears to play a central role in regulation of AIY differentiation. Not only are all AIY subtype characteristics lost in ttx-3 mutants, but ectopic misexpression of ttx-3 is also sufficient to induce AIY-like features in a restricted set of neurons. One of the targets of ceh-10 and ttx-3 is a novel type of homeobox gene, ceh-23. We show that ceh-23 is not required for the initial adoption of AIY differentiation characteristics, but instead is required to maintain the expression of one defined AIY differentiation feature. Finally, we demonstrate that the regulatory relationship between ceh-10, ttx-3 and ceh-23 is only partially conserved in other neurons in the nervous system. Our findings illustrate the complexity of transcriptional regulation in the nervous system and provide an example for the intricate interdependence of transcription factor action. ------------------- Key: 4728 Medline: Authors: Jornvall H;Shafqat J;Persson B Title: Variations and constant patterns in eukaryotic MDR enzymes. Conclusions from novel structures and characterized Citation: Chemico-Biological Interactions 130: 491-498 2001 Type: ARTICLE Genes: Abstract: Medium-chain dehydrogenases/reductases (MDR) alcohol dehydrogenases exhibit multiple forms through a number of gene duplications. A crucial duplication was the one leading from the glutathione-dependent formaldehyde dehydrogenase line to the liver alcohol dehydrogenase (ADH) lines of vertebrates, the first duplication of which can now be further positioned at early vertebrate times. Similarly, screening of MDR forms in recently completed eukaryotic genomes of Caenorhabditis elegans and Drosophila melanogaster suggest that the MDR family may constitute a moderately sized protein family centered around a limited number of enzyme activities of five different structural types. ------------------- Key: 4729 Medline: Authors: Gibson G Title: Developmental evolution: The unbearable likeness of beings. Citation: Current Biology 11: R345-R348 2001 Type: REVIEW Genes: Abstract: Comparative studies have revealed a remarkable range of genetic changes in the mechanisms that pattern the nematode vulva. Two new studies identify genetic variation within nematode species that affects cell division and competence in vulval precursors. ------------------- Key: 4730 Medline: Authors: Tavernarakis N;Everett JK;Kyrpides NC;Driscoll M Title: Structural and functional features of the intracellular amino terminus of DEG/ENaC ion channels. Citation: Current Biology 11: R205-R208 2001 Type: REVIEW Genes: deg-1 del-1 flr-1 mec-4 mec-10 unc-8 unc-105 Abstract: The degenerin/epithelial sodium channel (DEG/ ENaC) protein family includes related ion channel subunits from organisms ranging from the simple nematode Caenorhabditis elegans to humans. Members of this protein family have been implicated in functions as diverse as touch transduction and proprioception [1-4], pain sensation and maintenance of sodium balance [5]. ------------------- Key: 4731 Medline: 21078638 Authors: Easton A;Guven K;de Pomerai DI Title: Toxicity of the dithiocarbamate fungicide Mancozeb to the nontarget soil nematode, Caenorhabditis elegans. Citation: Journal of Molecular Toxicology 15: 15-25 2001 Type: ARTICLE Genes: Abstract: We have previously shown that the dithiocarbamate fungicide, Mancozeb, strongly induces lacZ reporter expression from an endogenous heat-shock promoter (hsp16) in the PC72 transgenic strain of the nematode Caenorhabditis elegans. Such evidence of organismal stress, in a nontarget species at subapplication concentrations, was much less apparent for the related fungicide, Maneb, which only weakly induced reporter expression. We now show that reporter induction by Mancozeb is marginal (<60%) after a few hours' exposure, but increases substantially (to almost 10-fold) after overnight exposure. In conjunction with our previous results using intermediate exposure periods, this suggests that the factor limiting reporter responses is likely to be a slow rate of uptake and/or metabolism of the fungicide. We confirm that a potentially toxic metabolite of dithiocarbamate fungicides, namely ethylenethiourea (ETU), has minimal toxicity toward C. elegans, even after prolonged exposure at high concentrations. We demonstrate that exposure to Mancozeb (but not ETU) significantly inhibits larval growth in C. elegans, although this parameter is not markedly more sensitive than reporter induction as a toxicological endpoint. Finally, we have used two-dimensional electrophoresis to show that high concentrations of both Maneb and Mancozeb drastically simplify the protein spot profile compared with controls. However, only in the latter case is there evidence of novel proteins being induced. Both fungicides appear toxic to C. elegans, but only ------------------- Key: 4732 Medline: 21281226 Authors: Mohsen AWA;Navarette B;Vockley J Title: Identification of Caenorhabditis elegans isovaleryl-CoA dehydrogenase and structural comparison with other acyl-CoA dehydrogenases. Citation: Molecular Genetics & Metabolism 73: 126-137 2001 Type: ARTICLE Genes: Abstract: Isovaleryl-CoA dehydrogenase (IVD) is a flavoenzyme, which catalyzes the conversion of isovaleryl-CoA to 3-methylcrotonyl-CoA in the leucine catabolism pathway and transfers electrons to the electron-transferring flavoprotein (ETF). IVDs from human and rat have been identified and characterized previously. In this study, the gene coding for Caenorhabditis elegans IVD has been identified from a published cDNA sequence and molecular modeling has been performed using the human IVD atomic coordinates. The coding sequence for the mature form of the enzyme was expressed in Escherichia coli, and the recombinant nematode IVD enzyme was purified to essential homogeneity. Its spectrum is typical of recombinant FAD-containing acyl-CoA dehydrogenases and shows a minor broad absorption band at 650-700 nm characteristic of an IVD:CoA persulfide charge-transfer complex. Following treatment of the enzyme with sodium dithionite to remove the bound CoA persulfide, the K-m values for isovaleryl-, butyryl-, valeryl-, and hexanoyl-CoA were estimated to be 2.5, 36.2, 10.5, and 33.8 muM, respectively, using the ETF fluorescence reduction assay. The catalytic efficiency (k(cat)/K-m) for these substrates was 56.9, 1.3, 13.7, and 3.2 muM(-1). min(-1) per mole of FAD, respectively. The apparent binding constant (K-D (app)) of the recombinant IVD determined spectrally for isovaleryl-CoA was 0.34 muM. These kinetic parameters confirm that isovaleryl-CoA is the preferred substrate for the purified enzyme. The variability in the protein structure among known and putative IVDs from various species is discussed in the context of possible mechanisms for modulating enzyme ------------------- Key: 4733 Medline: 21247000 Authors: Boulianne GL Title: Neuronal regulation of lifespan: clues from flies and Citation: Mechanisms of Ageing & Development 122: 883-894 2001 Type: ARTICLE Genes: age-1 daf-2 daf-16 unc-31 unc-64 Abstract: Aging is a universal but poorly understood biological process that involves a complex interplay between environmental and genetic factors. Model organisms such as C. elegans and Drosophila have provided an opportunity to starch for and identify specific genes that affect life span. Interestingly, increasing evidence suggests that many of these gents affect lifespan by exerting their effects in a limited number of cell types and. in particular, neurons. indicating that the nervous system may be a central regulator of organismal lifespan. ------------------- Key: 4734 Medline: 21295189 Authors: Dernburg AF Title: Here, there, and everywhere: Kinetochore function on holocentric chromosomes. Citation: Journal of Cell Biology 153: F33-F38 2001 Type: REVIEW Genes: hcp-1 hcp-2 hcp-3 hcp-4 him-10 icp-1 Abstract: Cytologists have long observed that individual eukaryotic species segregate their chromosomes in one of two apparently different ways. Monocentric chromosomes attach to microtubules at a particular region (the centromere) and move toward the pole during anaphase with the centromere leading. In contrast, holocentric chromosomes bind to microtubules along their entire length and move broadside to the pole from the metaphase plate. Holocentric chromosomes are scattered throughout the plant and animal kingdoms, and may be products of convergent evolution. Alternatively, the ancestral eukaryotic chromosome may have been holocentric, in which case the restriction of kinetic activity to a specialized region must have been an evolutionary event that occurred again and again. ------------------- Key: 4735 Medline: 21295177 Authors: Moore LL;Roth MB Title: HCP-4, a CENP-C-like protein in Caenorhabditis elegans, is required for resolution of sister centromeres. Citation: Journal of Cell Biology 153: 1199-1207 2001 Type: ARTICLE Genes: hcp-1 hcp-3 hcp-4 Abstract: The centromere plays a critical role in the segregation of chromosomes during mitosis. In mammals, sister centromeres are resolved from one another in the G2 phase of the cell cycle. During prophase, chromosomes condense with sister centromeres oriented in a back to back configuration enabling only one chromatid to be captured by each half spindle. To study this process, we identified a centromere protein (CENP)-C-like protein, holocentric protein (HCP)-4, in Caenorhabditis elegans based on sequence identity, loss of function phenotype, and centromeric localization. HCP-4 is found in the cytoplasm during interphase, but is nuclear localized in mitosis, where it localizes specifically to the centromere. The localization of HCP-4 to the centromere is dependent on the centromeric histone HCP-3; in addition, HCP-3 and HCP-4 are both required for localization of a CENP-F-like protein, HCP-1, indicating an ordered assembly pathway. Loss of HCP-I expression by RNA-mediated interference resulted in a failure to generate resolution of sister centromeres on chromosomes, suggesting that HCP-4 is required for sister centromere resolution. These chromosomes also failed to form a functional kinetochore. Thus, the CENP-C-like protein HCP-4 is essential for both resolution sister centromeres and attachment to the mitotic ------------------- Key: 4736 Medline: 21295178 Authors: Oegema K;Desai A;Rybina S;Kirkham M;Hyman AA Title: Functional analysis of kinetochore assembly in Caenorhabditis elegans. Citation: Journal of Cell Biology 153: 1209-1225 2001 Type: ARTICLE Genes: air-2 bir-1 hcp-1 hcp-2 hcp-3 his-11 tbg-1 Abstract: In all eukaryotes, segregation of mitotic chromosomes requires their interaction with spindle microtubules. To dissect this interaction, we use live and fixed assays in the one-cell stage Caenorhabditis elegans embryo. We compare the consequences of depleting homologues of the centromeric histone CENP-A, the kinetochore structural component CENP-C, and the chromosomal passenger protein INCENP. Depletion of either CeCENP-A or CeCENP-C results in an identical "kinetochore null" phenotype, characterized by complete failure of mitotic chromosome segregation as well as failure to recruit other kinetochore components and to assemble a mechanically stable spindle. The similarity of their depletion phenotypes, combined with a requirement for CeCENP-A. to localize CeCENP-C but not vice versa, suggest that a key step in kinetochore assembly is the recruitment of CENP-C by CENP-A-containing chromatin. Parallel analysis of CeINCENP-depleted embryos revealed mitotic chromosome segregation defects different from those observed in the absence of CeCENP-A/C. Defects are observed before and during anaphase, but the chromatin separates into two equivalently sized masses. Mechanically stable spindles assemble that show defects later in anaphase and telophase. Furthermore, kinetochore assembly and the recruitment of CeINCENP to chromosomes are independent. These results suggest distinct roles for the kinetochore and the chromosomal passengers in mitotic chromosome segregation. ------------------- Key: 4737 Medline: 21295179 Authors: Howe M;McDonald KL;Albertson DG;Meyer BJ Title: HIM-10 is required for kinetochore structure and function on Caenorhabditis elegans holocentric chromosomes. Citation: Journal of Cell Biology 153: 1227-1238 2001 Type: ARTICLE Genes: him-10 hcp-3 sDf121 sDf127 Abstract: Macromolecular structures called kinetochores attach and move chromosomes within the spindle during chromosome segregation. Using electron microscopy, we identified a structure on the holocentric mitotic and meiotic chromosomes of Caenorhabditis elegans that resembles the mammalian kinetochore. This structure faces the poles on mitotic chromosomes but encircles meiotic chromosomes. Worm kinetochores require the evolutionarily conserved HIM-10 protein for their structure and function. HIM-10 localizes to the kinetochores and mediates attachment of chromosomes to the spindle. Depletion of HIM-10 disrupts kinetochore structure, causes a failure of bipolar spindle attachment, and results in chromosome nondisjunction. HIM-10 is related to the Nuf2 kinetochore proteins conserved from yeast to humans. Thus, the extended kinetochores characteristic of C. elegans holocentric chromosomes provide a guide to the structure, molecular architecture, and function of conventional kinetochores. ------------------- Key: 4738 Medline: 11313333 Authors: Vatamaniuk OK;Bucher EA;Ward JT;Rea PA Title: A new pathway for heavy metal detoxification in animals: Phytochelatin synthase is required for cadmium tolerance in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 276: 20817-20820 2001 Type: ARTICLE Genes: Abstract: Increasing emissions of heavy metals such as cadmium, mercury, and arsenic into the environment pose an acute problem for all organisms. Considerations of the biochemical basis of heavy metal detoxification in animals have focused exclusively on two classes of peptides, the thiol tripeptide, glutathione (GSH, gamma -Glu Cys-Gly), and a diverse family of cysteine-rich low molecular weight proteins, the metallothioneins. Plants and some fungi, however, not only deploy GSH and metallothioneins for metal detoxification but also synthesize another class of heavy metal binding peptides termed phytochelatins (PCs) from GSH. Here we show that PC-mediated heavy metal detoxification is not restricted to plants and some fungi but extends to animals by demonstrating that the ce-pcs-l gene of the nematode worm Caenorhabditis elegans encodes a functional PC synthase whose activity is critical for heavy metal tolerance in the intact organism. ------------------- Key: 4739 Medline: 11262399 Authors: Ohtsuki T;Watanabe Y;Takemoto C;Kawai G;Ueda T;Kita K;Kojima S;Kaziro Y;Nyborg J;Watanabe K Title: An "elongated" translation elongation factor Tu for truncated tRNAs in nematode mitochondria. Citation: Journal of Biological Chemistry 276: 21571-21577 2001 Type: ARTICLE Genes: Abstract: We have found the gene for a translation elongation factor Tu (EF-Tu) homologue in the genome of the nematode Caenorhabditis elegans. Because the corresponding protein was detected immunologically in a nematode mitochondrial (mt) extract, it could be regarded as a nematode mt EF-Tu. The protein possesses an extension of about 57 amino acids (we call this domain 3') at the C terminus, which is not found in any other known EF-Tu. Because most nematode mt tRNAs lack a T stem, domain 3' may be related to this feature. The nematode EF-Tu bound to nematode T stem-lacking tRNA, but bacterial EF-Tu was unable to do so. A series of domain exchange experiments strongly suggested that domains 3 and 3' are essential for binding to T stem-lacking tRNAs, This finding may constitute a novel example of the co-evolution of a structurally simplified RNA and the cognate RNA-binding protein, the latter having apparently acquired an additional domain to compensate for the lack of a binding site(s) on the RNA. ------------------- Key: 4740 Medline: Authors: Zang X;Maizels RM Title: Serine proteinase inhibitors from nematodes and the arms race between host and pathogen. Citation: Trends in Biochemical Sciences 26: 191-197 2001 Type: REVIEW Genes: Abstract: Serine proteinase inhibitors are encoded by a large gene family of long evolutionary standing. Recent discoveries of parasite proteins that inhibit human serine proteinases, together with the complete genomic sequence from Caenorhabditis elegans, have provided a set of new serine proteinase inhibitors from more primitive metazoan animals such as nematodes. The structural features (e.g. reactive centre residues), gene organization (including intron arrangements) and inhibitory function and targets (e.g. inflammatory and coagulation pathway proteinase) all contribute important new insights into proteinase inhibitor evolution. Some parasite products have evolved that block enzymes in the mammalian host, but the human host responds with a significant immune response to the parasite inhibitors. Thus, infection produces a finely balanced conflict between host and pathogen at the molecular level, and this might have accelerated the evolution of these proteins in parasitic species as well as their hosts. ------------------- Key: 4741 Medline: 21273135 Authors: Cheeseman CL;Delany NS;Woods DJ;Wolstenholme AJ Title: High-affinity ivermectin binding to recombinant subunits of the Haemonchus contortus glutamate-gated chloride channel. Citation: Molecular & Biochemical Parasitology 114: 161-168 2001 Type: ARTICLE Genes: avr-14 avr-15 gbr-2 glc-1 glc-2 glc-3 Abstract: Glutamate-gated chloride channels (GluCls) are targets for the avermectin anthelmintics. A family of five GluCl subunit genes encoding seven subunits has been identified in Caenorhabditis elegans. We have previously shown that two orthologous genes in the parasite, Haemonchus contortus, encode three GluCl subunits (HcGluCl beta, Hcgbr-2A and Hcgbr-2B) with high aminoacid identity (>80%) to their C. elegans counterparts. We amplified and cloned a further subunit cDNA, HcGluCl alpha, from H. contortus eggs. Sequence comparisons suggested that this subunit was closely related to, but not orthologous with, the C. elegans GluCl alpha1, alpha2 or alpha3/GBR-2 subunits (similar to 55% amino-acid identity). The HcGluCl alpha cDNA from an ivermectin-resistant isolate contained no coding changes from the wild-type. All of the known H. contortus GluCl cDNA clones were subcloned into the expression vector pcDNA3.1 and transiently expressed in COS-7 cells. As predicted by functional data from the C. elegans orthologues, the Hcgbr-2A and HcGluCl beta subunits failed to bind [H-3]ivermectin. The Hcgbr-2B and HcGluCl alpha subunits bound [H-3]ivermectin with high affinity; the K-d values were 70 +/- 16 and 26 +/- 12 pM, respectively. This binding was inhibited by a variety of avermectins, though cold ivermectin was the most potent inhibitor of [H-3] ivermectin binding. Picrotoxin, fipronil, glutamate and GABA all failed to compete for ivermectin binding to either subunit. The affinity of [H-3]ivermectin binding to H. contortus L3 P2 larval membrane preparations was re-examined and found to be 70 +/- 7 pM. The properties of orthologous GluCl subunits are likely to be conserved across species, but the repertoire and relative importance of those subunits may vary. ------------------- Key: 4742 Medline: 21309999 Authors: Kostrouchova M;Krause M;Kostrouch Z;Rall JE Title: Nuclear hormone receptor CHR3 is a critical regulator of all four larval molts of the nematode Caenorhabditis Citation: Proceedings of the National Academy of Sciences USA 98: 7360-7365 2001 Type: ARTICLE Genes: Abstract: CHR3 (nhr-23, NF1F4), the homologue of Drosophila DHR3 and mammalian ROR/RZR/RevErbA nuclear hormone receptors. is important for proper epidermal development and molting in the nematode Caenorhabditis elegans. Disruption of CHR3 (nhr-23) function leads to developmental changes, including incomplete molting and a short, fat (dumpy) phenotype. Here, we studied the role of CHR3 during larval development by using expression assays and RNA-mediated interference. We show that the levels of expression of CHR3 (nhr-23) cycle during larval development and reduction of CHR3 function during each intermolt period result in defects at all subsequent molts. Assaying candidate gene expression in populations of animals treated with CHR3 (nhr-23) RNA-mediated interference has identified dpy-7 as a potential gene acting downstream of CHR3. These results define CHR3 as a critical regulator of all C. elegans molts and begin to define the molecular pathway for its function. ------------------- Key: 4743 Medline: 11452313 Authors: Parrish J;Li L;Klotz K;Ledwich D;Wang X;Xue D Title: Mitochondrial endonuclease G is important for apoptosis in C. elegans. Citation: Nature 412: 90-94 2001 Type: ARTICLE Genes: ced-3 ced-4 ced-8 ced-9 cps-6 nuc-1 Abstract: Programmed cell death (apoptosis) is a tightly regulated process of cell disassembly in which dying cells and their nuclei shrink and fragment and the chromosomal DNA is degraded into internucleosomal repeats(1-3). Here we report the characterization of the cps-6 gene, which appears to function downstream of, or in parallel to, the cell-death protease CED-3 of Caenorhabditis elegans in the DNA degradation process during apoptosis. cps-6 encodes a homologue of human mitochondrial endonuclease G(4,5), and its protein product similarly localizes to mitochondria in C. elegans. Reduction of cps-6 activity caused by a genetic mutation or RNA-mediated interference (RNAi) affects normal DNA degradation, as revealed by increased staining in a TUNEL assay, and results in delayed appearance of cell corpses during development in C. elegans. This observation provides in vivo evidence that the DNA degradation process is important for proper progression of apoptosis. CPS-6 is the first mitochondrial protein identified to be involved in programmed cell death in C. elegans, underscoring the conserved and important role of mitochondria in the execution of apoptosis. ------------------- Key: 4744 Medline: 21286825 Authors: Hartman PS;Ishii N;Kayser EB;Morgan PG;Sedensky MM Title: Mitochondrial mutations differentially affect aging, mutabiligy and anesthetic sensitivity in Caenorhabditis elegans. Citation: Mechanisms of Ageing & Development 122: 1187-1201 2001 Type: ARTICLE Genes: Abstract: In the nematode Caenorhabditis elegans, mutations have been previously isolated that affect the activities of Complex I (gas-1) and Complex II (mev-1), two of the five membrane-bound complexes that control electron flow in mitochondrial respiration. We compared the effects of gas-1 and mev-1 mutations on different traits influenced by mitochondrial function. Mutations in Complex I and II both increased sensitivity to free radicals as measured during development and in aging animals. However, gas-1 and mev-1 mutations differentially affected mutability and anesthetic sensitivity. Specifically, gas-1 was anesthetic hypersensitive but not hypermutable while mev-1 was hypermutable but displayed normal responses to anesthetics. These results indicate that Complexes I and II may differ in their effects on behavior and development, and are consistent with the wide variation in phenotypes that result from mitochondrial changes in other organisms. ------------------- Key: 4745 Medline: 21311605 Authors: Lee JS;Min DS;Park C;Park CS;Cho NJ Title: Phytosphingosine and C2-phytoceramide induce cell death and inhibit carbachol-stimulated phospholipase D activation in Chinese hamster ovary cells expressing the Caenorhabditis elegans muscarinic acet Citation: FEBS Letters 499: 82-86 2001 Type: ARTICLE Genes: Abstract: Sphingolipid metabolites, such as sphingosine and ceramide, are known to play important roles in cell proliferation, differentiation and apoptosis, but the physiological roles of phytosphingosine (PHS) and phytoceramide (PHC) are poorly understood. In this study we investigated the effects of PI-IS, C2-PHC ((N-acetylPHS) and C6-PHC (N-hexanoylPHS) on cell growth and intracellular signalling enzymes. Treatment of Chinese hamster ovary (CHO) cells with PI-IS, C2-PHC or C6-PHC resulted in cell death in a time- and dose-dependent manner. C2-PHC induced internucleosomal DNA fragmentation, whereas PHS or C6-PHC had little if any effect on DNA fragmentation under the same experimental conditions. Both PI-IS and C2-PHC inhibited carbachol-induced activation of phospholipase D (PLD), but not of phospholipase C (PLC), in CHO cells expressing the Caenorhabditis elegans muscarinic acetylcholine receptor (mAChR), On the other hand, no significant effect of C6-PHC on PLD or PLC was observed, Our results show that PI-IS and C2-PHC exert strong cytotoxic effects on CHO cells and modulate the ------------------- Key: 4746 Medline: 21308934 Authors: Suzuki N;Buechner M;Nishiwaki K;Hall DH;Nakanishi H;Takai Y;Hisamoto N;Matsumoto K Title: A putative GDP-GTP exchange factor is required for development of the excretory cell in Caenorhabditis Citation: EMBO Reports 2: 530-535 2001 Type: ARTICLE Genes: Abstract: The Caenorhabditis elegans excretory cell extends tubular processes, called canals, along the basolateral surface of the epidermis. Mutations in the exc-5 gene cause tubulocystic defects in this canal. Ultrastructural analysis suggests that exc-5 is required for the proper placement of cytoskeletal elements at the apical epithelial surface. exc-5 encodes a protein homologous to guanine nucleotide exchange factors and contains motif architecture similar to that of FGD1, which is responsible for faciogenital dysplasia. exc-5 interacts genetically with mig-2 which encodes Rho GTPase. These results suggest that EXC-5 controls the structural organization of the excretory canal by regulating Rho family GTPase activities. ------------------- Key: 4747 Medline: 21255318 Authors: Rogalski TM;Mullen GP;Bush JA;Gilchrist EJ;Moerman DG Title: UNC-52/perlecan isoform diversity and function in Caenorhabditis elegans. Citation: Biochemical Society Transactions 29: 171-176 2001 Type: ARTICLE Genes: act-123 deb-1 lev-11 mec-8 pat-2 pat-3 pat-4 pat-10 unc-52 unc-97 unc-112 Abstract: The unc-52 gene encodes the nematode homologue of mammalian perlecan, the major heparan sulphate proteoglycan of the extracellular matrix. This is a large complex protein with regions similar to low-density lipoprotein receptors, laminin and neural cell-adhesion molecules. Three major classes of UNC-52/perlecan isoforms are produced through alternative splicing, and these distinct proteins exhibit complex spatial and temporal expression patterns throughout development. The unc-52 gene plays an essential role in myofilament assembly in body-wall muscle during embryonic development. ------------------- Key: 4748 Medline: 11323434 Authors: Ono K;Ohtomo T;Sato S;Sugamata Y;Suzuki M;Hisamoto N;Ninomiya-Tsuji J;Tsuchiya M;Matsumoto K Title: An evolutionarily conserved motif in the TAB1 C-terminal region is necessary for interaction with and activation of TAK1 MAPKKK. Citation: Journal of Biological Chemistry 276: 24396-24400 2001 Type: ARTICLE Genes: mom-4 tap-1 Abstract: TAK1, a member of the MAPKKK family, is involved in the intracellular signaling pathways mediated by transforming growth factor beta, interleukin 1, and Wnt,.TAK1 kinase activity is specifically activated by the TAK1-binding protein TAB1. The C-terminal 68-amino acid sequence of TAB1 (TAB1-C68) is sufficient for TAX1 interaction and activation. Analysis of various truncated versions of TAB1-C68 defined a C-terminal 30-amino acid sequence (TAB1-C30) necessary for TAK1 binding and activation. NMR studies revealed that the TAB1-C30 region has a unique cu-helical structure. We identified a conserved sequence motif, PYVDXA/TXF, in the C-terminal domain of mammalian TAB1, Xenopus TAB1, and its Caenorhabditis elegans homolog TAP-I, suggesting that this motif constitutes a specific TAK1 docking site. Alanine substitution mutagenesis showed that, TAB1 Phe484, located in the conserved motif, is crucial for TAK1 binding and activation. The C. elegans homolog of TAB1, TAP-1, was able to interact with and activate the C. elegans homolog of TAK1, MOM-4. However, the site in TAP-1 corresponding to Phe-484 of TAB1 is an alanine residue (Ala-364), and changing this residue to Phe abrogates the ability of TAP-1 to interact with and activate MOM-4. These results suggest that the Phe or Ala residue within the conserved motif of the TAB1-related proteins is important for interaction with and activation of specific TAK1 MAPKKK family members in vivo. ------------------- Key: 4749 Medline: Authors: Dodd RB;Drickamer K Title: Lectin-like proteins in model organisms: implications for evolution of carbohydrate-binding activity. Citation: Glycobiology 11: 71R-79R 2001 Type: ARTICLE Genes: Abstract: Classes of intracellular lectins that recognize core-type structures and mediate intracellular glycoprotein trafficking are present in vertebrates, model invertebrates such as Caenorhabditis elegans and Drosophila melanogaster, plants, and yeasts. Lectins that recognize more complex structures at the cell surface, such as C-type lectins and galectins, are also found in invertebrate organisms as well as vertebrates, but the functions of these proteins have evolved differently in different animal lineages. ------------------- Key: 4750 Medline: 21273296 Authors: Maruyama H;Rakow TL;Maruyama IN Title: Synaptic exocytosis and nervous system development impaired in Caenorhabditis elegans unc-13 mutants. Citation: Neuroscience 104: 287-297 2001 Type: ARTICLE Genes: ace-1 ace-2 ace-3 rab-3 snt-1 unc-13 unc-17 sDf5 sDf6 Abstract: C. elegans mutants defective in unc-13 exhibited severe behavioral abnormalities including paralyzed locomotion and slow pharyngeal pumping and irregular defecation cycle. Consistent with the phenotypes, the mutants accumulated abnormally high levels of the neurotransmitter acetylcholine and were resistant to acetylcholinesterase inhibitors. The unc-13 gene was expressed in most, if not all, neurons when analyzed by using chimeric constructs consisting of the unc-13 promoter and green fluorescence protein or beta -galactosidase reporter gene. While Ca2+-regulated acetylcholine release is lacking, the mutants were still able to release acetylcholine in vivo and in vitro at similar levels to that mediated by the regulated mechanism. Double mutants defective in both unc-13 and other genes involved in synaptic transmission showed the Unc-13 phenotype. rather than other mutant phenotypes, in terms of locomotion as well as of acetylcholine accumulation. Furthermore, electron microscopic reconstruction of the mutant nervous system uncovered that a majority of neurons developed and connected as those in the wild type except for subtle abnormalities including inappropriate connections through gap junctions and morphological alterations of neurons. These results demonstrate that the unc-13 gene product plays an essential role at a late stage in Ca2+-regulated synaptic exocytosis. Neurotransmitters released through the Ca2+-regulated mechanism are required for, but do not play major roles in the nervous system development. The large amount of Ca2+-independent neurotransmitter release observed in the unc-13 mutants suggests that there may be a distinct mechanism from evoked or spontaneous release in ------------------- Key: 4751 Medline: 11449278 Authors: Reddien PW;Cameron S;Horvitz HR Title: Phagocytosis promotes programmed cell death in C. elegans. Citation: Nature 412: 198-202 2001 Type: ARTICLE Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-9 ced-10 ced-12 egl-1 Abstract: In the nematode Caenorhabditis elegans programmed cell death requires the killer genes egl-1, ced-4 and ced-3 (refs 1 and 2), and the engulfment of dying cells requires the genes ced-1, ced-2, ced-5, ced-6, ced-7, ced-10 and ced-12 (refs 3-5). Here we show that engulfment promotes programmed cell death. Mutations that cause partial loss of function of killer genes allow the survival of some cells that are programmed to die, and mutations in engulfment genes enhance the frequency of this cell survival. Furthermore, mutations in engulfment genes alone allow the survival and differentiation of some cells that would normally die. Engulfment genes probably act in engulfing cells to promote death, as the expression in engulfing cells of ced-1, which encodes a receptor that recognizes cell corpses(6), rescues the cell-killing defects of ced-1 mutants. We propose that engulfing cells act to ensure that cells triggered to undergo programmed cell death by the CED-3 caspase(7) die rather than recover after the initial ------------------- Key: 4752 Medline: 11449279 Authors: Hoeppner DJ;Hengartner MO;Schnabel R Title: Engulfment genes cooperate with ced-3 to promote cell death in Caenorhabditis elegans. Citation: Nature 412: 202-206 2001 Type: ARTICLE Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-9 ced-10 ced-12 egl-1 Abstract: Genetic studies have identified over a dozen genes that function in programmed cell death (apoptosis) in the nematode Caenorhabditis elegans(1-3). Although the ultimate effects on cell survival or engulfment of mutations in each cell death gene have been extensively described, much less is known about how these mutations affect the kinetics of death and engulfment, or the interactions between these two processes. We have used four-dimensional-Nomarski time-lapse video microscopy to follow in detail how cell death genes regulate the extent and kinetics of apoptotic cell death and removal in the early C. elegans embryo. Here we show that blocking engulfment enhances cell survival when cells are subjected to weak pro-apoptotic signals. Thus, genes that mediate corpse removal can also function to actively kill cells. ------------------- Key: 4753 Medline: 21286780 Authors: Nuttley WM;Harbinder S;van der Kooy D Title: Regulation of distinct attractive and aversive mechanisms mediating benzaldehyde chemotaxis in Caenorhabditis Citation: Learning & Memory 8: 170-181 2001 Type: ARTICLE Genes: adp-1 eat-4 odr-3 odr-10 osm-9 Abstract: Olfactory-mediated chemotaxis in nematodes provides a relatively simple system to study biological mechanisms of information processing. Analysis of the kinetics of chemotaxis in response to 100% benzaldehyde revealed an initial attractive response that is followed by a strong aversion to the odorant. We show that this behavior is mediated by two genetically separable attraction and aversion-mediating response pathways. The attraction initially dominates behavior but with prolonged exposure habituation leads to a behavioral change, such that the odorant becomes repulsive. This olfactory habituation is susceptible to dishabituation, thereby re-establishing the attractive response to the odorant. Re-examination of the putative olfactory adaptation mutant adp-1(ky20) revealed that the phenotype observed in this line is due to a supersensitivity to a dishabituating stimulus, rather than a defect in the adaptation to odorants per se. A modified benzaldehyde chemotaxis assay was developed and used for the isolation of a mutant with a specific defect in habituation kinetics, expressed as a persistence of the attractive response. ------------------- Key: 4754 Medline: 11445592 Authors: Walker GA;White TM;McColl G;Jenkins NL;Babich S;Candido EPM;Johnson TE;Lithgow GJ Title: Heat shock protein accumulation is upregulated in a long-lived mutant of Caenorhabditis elegans. Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 56: B281-B287 2001 Type: ARTICLE Genes: age-1 daf-2 daf-16 daf-18 Abstract: We present evidence for elevated levels of heat shock protein 16 (HSP16) in an intrinsically thermotolerant, long-lived strain of Caenorhabditis elegans during and after heat stress. Mutation of the age-1 gene, encoding a phosphatidylinositol 3-kinase catalytic subunit, results in both extended life span (Age) and increased intrinsic thermotolerance (Itt) in adult hermaphrodites. We subjected age-synchronous cohorts of worms to lethal and nonlethal thermal stress and observed the accumulation of a small (16-18 kd) heat-shock-specific polypeptide detected by an antibody raised against C. elegans HSP16. Strains carrying the mutation hx546 consistently accumulated HSP16 to higher levels than a wild-type strain. Significantly, overaccumulation of HSP16 in the age-1(hx546) strain following heat was observed throughout the adult life span. A chimeric transgene containing the Escherichia coli beta -galactosidase gene fused to a C. elegans HSP16-41 transcriptional promoter was introduced into wild-type and age-1(hx546) backgrounds. Heat-inducible expression of the transgene was elevated in the age-1(hx546) strain compared with the wild-type strain under a wide variety of heat shock and recovery conditions. These observations are consistent with a model in which Age mutations exhibit thermotolerance and extended life span as a result of elevated levels of molecular chaperones. ------------------- Key: 4755 Medline: 21354267 Authors: Kuwabara PE;Perry MD Title: It ain't over till it's ova: germline sex determination in C. elegans. Citation: BioEssays 23: 596-604 2001 Type: REVIEW Genes: cpb-1 fbf-1 fbf-2 fem-1 fem-2 fem-3 fog-1 fog-2 fog-3 fox-1 gld-1 her-1 laf-1 mag-1 mog-1 mog-2 mog-3 mog-4 mog-5 mog-6 nos-1 nos-2 sdc-1 sdc-2 sdc-3 sex-1 tra-1 tra-2 tra-3 xol-1 Abstract: Sex determination in most organisms involves a simple binary fate choice between male or female development; the outcome of this decision has profound effects on organismal biology, biochemistry and behaviour. In the nematode C. elegans, there is also a binary choice, either male or hermaphrodite. In C. elegans, distinct genetic pathways control somatic and germline sexual cell tate. Both pathways share a common set of globally acting regulatory genes; however, germline-specific regulatory genes also participate in the decision to make male or female gametes. The determination of sexual fate in the germline of the facultative hermaphrodite poses a special problem, because first sperm then oocytes are produced. It has emerged that additional layers of post-transcriptional regulation have been imposed to modulate the activities of the global sex-determining genes, tra-2 and fem-3; the balance between these activities is crucial in controlling sexual cell fate in the hermaphrodite germline. ------------------- Key: 4756 Medline: 11424156 Authors: Miyakawa T;Yamada S;Harada S;Ishimori T;Yamamoto H;Hosono R Title: Exposure of Caenorhabditis elegans to extremely low frequency high magnetic fields induces stress responses. Citation: Bioelectromagnetics 22: 333-339 2001 Type: ARTICLE Genes: unc-18 Abstract: Responses of the small hear shock protein gene, hsp-16, were examined in transgenic Caenorhabditis elegans exposed to electromagnetic fields. Expression of the hsp-16-lacZ gene was enhanced when transgenic animals were exposed to magnetic fields up to 0.5 T at 60 Hz. The hsp-16 promoter was more efficiently expressed at the embryonic than at the post-embryonic stage irrespective of exposure. Promoter activity was more sensitive to the stimulus in the intestine at the post-embryonic stage. Evidence is presented that the induction occurs at the transcriptional ------------------- Key: 4757 Medline: 12760063 Authors: Hofmann ER;Milstein S;Hengartner MO Title: DNA-damage-induced checkpoint pathways in the nematode Caenorhabditis elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 65: 467-473 2000 Type: REVIEW Genes: ced-3 ced-4 ced-9 cep-1 dam-1 egl-1 hpr-1 mrt-1 mut-7 ncc-1 rad-5 rad-51 spo-11 xnp-1 Abstract: Genomic instability is believed to be an enabling characteristic of cancer (Hanahan and Weinberg 2000). Therefore, it is not surprising that sophisticated mechanisms exist to maintain the integrity of the genome. Damage to DNA triggers checkpoint controls that result in cell cycle arrest and repair of the lesion (Nurse, 1997, 2000; Weinert 1998). In multicellular organisms, when DNA damage is extensive, these potentially harmful cells are eliminated by apoptosis (Enoch and Norbury 1995; Evan and Littlewood 1998)... ------------------- Key: 4758 Medline: Authors: Grant WN;Viney ME Title: Post-genomic nematode parasitology. Citation: International Journal for Parasitology 31: 879-888 2001 Type: REVIEW Genes: Abstract: The future direction of post-genomic nematode parasitology should focus on the function of the genes that are defined by large-scale expressed sequence tag sequencing and on broader questions about the genetic basis of parasitism. Functional characterisation will require the application of high throughput technologies that have been developed in other fields, including genome mapping strategies and DNA microarray analysis. These will be greatly aided by the development and application of appropriate model organisms. It is: crucial that the field make the transition from a narrow focus on one or a few genes at a time to a focus on whole genomes in order to fully realise the potential of the expressed sequence tag and other genomic projects currently under way. ------------------- Key: 4759 Medline: 11680876 Authors: Hirabayashi J;Arata Y;Kasai K Title: Glycome project: Concept, strategy and preliminary application to Caenorhabditis elegans. Citation: Proteomics 1: 295-303 2001 Type: ARTICLE Genes: Abstract: Glycans play a central role as potential mediators between complex cell societies, because all living organisms consist of cells covered with diverse carbohydrate chains reflecting various cell types and states. However, we have no idea how diverse these carbohydrate chains actually are. The main purpose of this article is to persuade life scientists to realize the fundamental importance of taking some action by becoming involved in "glycomics". "Glycome" is a term meaning the whole set of glycans produced by individual organisms, as the third bioinformative macromolecules to be elucidated next to the genome and proteome. Here a basic strategy is presented. The essence of the project includes the following. (af glycopeptides, but not glycans released from their core proteins, are targeted for linkage to genome databases; Ib) Caenorhabditis elegans is used as the first model organism for this project, since its genome project has already been completed; (c) four essential attributes are adopted to characterize each glycopeptide: (i) cosmid identification number (ID), (ii) molecular weight (M-r), (iii) retention (Rs) of pyridylaminated (PA) oligosacharides in 2-D mapping, and (iv) dissociation constants (K-d's) of PA-oligosaccharides for a set of lectins. Thus, the obtained ID, M-r, R and K-d's construct the glycome database, which will be open as the previous genome and proteome databases. For the project to proceed the "glyco-catch" method is proposed, where a group of target glycopeptides are captured by means of lectin-affinity chromatography after protease digestion. Already glycopeptides from asialofetuin and ovalbumin were successfully captured by galectin-agarose and Con A-agarose, respectively. Further, to examine the practical validity of the method, we extracted membrane proteins from C. elegans with 1% Triton X-100, and isolated specific glycopeptides by use of the same galectin column. One of the glycopeptides was successfully identified in the C. elegans genome database. Finally, for determination of K-d between glycopeptides and lectins, a recently reinforced frontal affinity chromatography (FAC) is proposed as an ------------------- Key: 4760 Medline: 21332313 Authors: Goldman RD Title: Worms reveal essential functions for intermediate Citation: Proceedings of the National Academy of Sciences USA 98: 7659-7661 2001 Type: REVIEW Genes: Intermediate filaments (IF) represent one of the three major cytoskeletal systems found in animal cells. Their somewhat uninspired name was originally derived from their 10-nm diameter, which lies between that of smaller actin-containing microfilaments and larger microtubules. This name, however, belies their importance as critical players in the organization of cells and tissues of vertebrate systems. Abstract: ------------------- Key: 4761 Medline: 11427699 Authors: Karabinos A;Schmidt H;Harborth J;Schnabel R;Weber K Title: Essential roles for four cytoplasmic intermediate filament proteins in Caenorhabditis elegans development. Citation: Proceedings of the National Academy of Sciences USA 98: 7863-7868 2001 Type: ARTICLE Genes: Abstract: The structural proteins of the cytoplasmic intermediate filaments (IFs) arise in the nematode Caenorhabditis elegans from eight reported genes and an additional three genes now identified in the complete genome. With the use of double-stranded RNA interference (RNAi) for all 11 C. elegans genes encoding cytoplasmic IF proteins, we observe phenotypes for the five genes A1, A2, A3, B1, and CZ. These range from embryonic lethality (B1) and embryonic/larval lethality (A3) to larval lethality (Al and AZ) and a mild dumpy phenotype of adults (C2). Phenotypes A2 and A3 involve displaced body muscles and paralysis. They probably arise by reduction of hypodermal IFs that participate in the transmission of force from the muscle cells to the cuticle. The B1 phenotype has multiple morphogenetic defects, and the Al phenotype is arrested at the L1 stage. Thus, at least four IF genes are essential for C. elegans development. Their RNAi phenotypes are lethal defects due to silencing of single IF genes. In contrast to C. elegans, no IF genes have been identified in the complete Drosophila genome, posing the question of how Drosophila can compensate for the lack of these proteins, which are essential in mammals and C. elegans. We speculate that the lack of IF proteins in Drosophila can be viewed as cytoskeletal alteration in which, for instance, stable microtubules, often arranged as bundles, substitute for ------------------- Key: 4762 Medline: 11427734 Authors: Jiang H;Guo R;Powell-Coffman JA Title: The Caenorhabditis elegans hif-1 gene encodes a bHLH-PAS protein that is required for adaptation to hypoxia. Citation: Proceedings of the National Academy of Sciences USA 98: 7916-7921 2001 Type: ARTICLE Genes: aha-1 ahr-1 hif-1 Abstract: Hypoxia-inducible factor, a heterodimeric transcription complex, regulates cellular and systemic responses to low oxygen levels (hypoxia) during normal mammalian development or tumor progression. Here, we present evidence that a similar complex mediates response to hypoxia in Caenorhabditis elegans. This complex consists of HIF-1 and AHA-1, which are encoded by C. elegans homologs of the hypoxia-inducible factor (HIF) alpha and beta subunits, respectively. hif-1 mutants exhibit no severe defects under standard laboratory conditions, but they are unable to adapt to hypoxia. Although wild-type animals can survive and reproduce in 1% oxygen, the majority of hif-1-defective animals die in these conditions. We show that the expression of an HIF-1:green fluorescent protein fusion protein is induced by hypoxia and is subsequently reduced upon reoxygenation. Both hif-1 and aha-1 are expressed in most cell types, and the gene products can be coimmunoprecipitated. We conclude that the mechanisms of hypoxia signaling are likely conserved among metazoans. Additionally, we find that nuclear localization of AHA-1 is disrupted in an hif-1 mutant. This finding suggests that heterodimerization may be a prerequisite for efficient nuclear translocation of AHA-1. ------------------- Key: 4763 Medline: 21354097 Authors: Richmond JE;Weimer RM;Jorgensen EM Title: An open forum of syntaxin bypasses the requirement for UNC-13 in vesicle priming. Citation: Nature 412: 338-341 2001 Type: ARTICLE Genes: unc-2 unc-13 unc-64 Abstract: The priming step of synaptic vesicle exocytosis is thought to require the formation of the SNARE complex, which comprises the proteins synaptobrevin, SNAP-25 and syntaxin(1-3). In solution syntaxin adopts a default, closed configuration that is incompatible with formation of the SNARE complex(4). Specifically, the amino terminus of syntaxin binds the SNARE motif and occludes interactions with the other SNARE proteins. The N terminus of syntaxin also binds the presynaptic protein UNC-13 (ref. 5). Studies in mouse, Drosophila and Caenorhabditis elegans suggest that UNC-13 functions at a post-docking step of exocytosis, most likely during synaptic vesicle priming(6-8). Therefore, UNC-13 binding to the N terminus of syntaxin may promote the open configuration of syntaxin(9). To test this model, we engineered mutations into C. elegans syntaxin that cause the protein to adopt the open configuration constitutively(4). Here we demonstrate that the open form of syntaxin can bypass the requirement for UNC-13 in synaptic vesicle priming. Thus, it is likely that UNC-13 primes synaptic vesicles for fusion by promoting the open configuration of syntaxin. ------------------- Key: 4764 Medline: 21332105 Authors: Spike CA;Shaw JE;Herman RK Title: Analysis of smu-1, a gene that regulates the alternative splicing of unc-52 pre-mRNA in Caenorhabditis elegans. Citation: Molecular and Cellular Biology 21: 4985-4995 2001 Type: ARTICLE Genes: mec-8 mut-6 smu-1 smu-2 unc-52 hDf15 hDf16 Abstract: Mutations in the smu-1 gene of Caenorhabditis elegans were previously shown to suppress mutations in the genes mec-8 and unc-52. mec-8 encodes a putative RNA binding protein that affects the accumulation of specific alternatively spliced mRNA isoforms produced by unc-52 and other genes. unc-52 encodes a set of basement membrane proteins, homologs of mammalian perlecan, that are important for body wall muscle assembly and attachment to basement membrane, hypodermis, and cuticle. We show that a presumptive null mutation in smu-1 suppresses nonsense mutations in exon 17 but not exon 18 of unc-52 and enhances the phenotype conferred by an unc-52 splice site mutation in intron 16. We have used reverse transcription-PCR and RNase protection to show that loss-of-function smu-1 mutations enhance accumulation in larvae of an alternatively spliced isoform that skips exon 17 but not exon 18 of unc-52. We have identified smu-1 molecularly; it encodes a nuclearly localized protein that contains five WD motifs and is ubiquitously expressed. The SMU-1 amino acid sequence is more than 60% identical to a predicted human protein of unknown function. We propose that smu-1 encodes a trans-acting factor that regulates the alternative splicing of the pre-mRNA of unc-52 and other genes. ------------------- Key: 4765 Medline: 21385302 Authors: McMahon L;Legouis R;Vonesch JL;Labouesse M Title: Assembly of C. elegans apical junctions involves positioning and compaction by LET-413 and protein aggregation by the MAGUK protein DLG-1. Citation: Journal of Cell Science 114: 2265-2277 2001 Type: ARTICLE Genes: che-14 dlg-1 hmp-1 jam-1 let-413 par-3 par-6 Abstract: Specialised subapical junctions play a critical role in maintaining epithelial cell polarity and tissue integrity, and provide a platform for intracellular signalling. Here we analyse the roles of C. elegans genes let-413 and dlg-1, a homologue of Drosophila lethal discs large, in the assembly of the C. elegans apical junction (CeAJ), and provide the first characterisation of this structure, We have identified dlg-1 as an essential gene in an RNA interference screen against C. elegans homologues of genes encoding proteins involved in tight or septate junction formation. We show that DLG-1 colocalises with the junctional protein JAM-1 at CeAJs in a unit distinct from HMP-1/alpha -catenin, and apical to the laterally localised LET-413, Loss of dlg-1 activity leads to JAM-1 mislocalisation and the disappearance of the electron-dense component of the CeAJs, but only mild adhesion and polarity defects. In contrast, loss of let-413 activity leads to the formation of basally extended discontinuous CeAJs and strong adhesion and polarity defects. Interestingly, in LET-413-deficient embryos, CeAJ markers are localised along the lateral membrane in a manner resembling that observed in wildtype embryos at the onset of epithelial differentiation. We conclude that the primary function of LET-413 is to correctly position CeAJ components at a discrete subapical position. Furthermore, we propose that DLG-1 is required to aggregate JAM-1 and other proteins forming the electron-dense CeAJ structure. Our data suggest that epithelial adhesion is maintained by several redundant systems in C. elegans. ------------------- Key: 4766 Medline: 11312268 Authors: Ramulu P;Nathans J Title: Cellular and subcellular localization, N-terminal acylation, and calcium binding of Caenorhabditis elegans protein phosphatase with EF-hands. Citation: Journal of Biological Chemistry 276: 25127-25135 2001 Type: ARTICLE Genes: Abstract: The RdgC/PPEF family of serine/threonine protein phosphatases is distinguished by the presence of C-terminal EF-hands and neuron-specific expression, including frequent expression in primary sensory neurons. Here we report that the sole Caenorhabditis elegans PPEF (CePPEF) homolog is also highly expressed in primary sensory neurons and is not found outside the nervous system. Neurons expressing CePPEF include the ciliary chemosensory neurons AWE and AWC; and within these neurons, CePPEF is highly enriched in the sensory cilia. In transgenic C. elegans and in transfected 293 cells, CePPEF is membrane-associated, and the N terminus of CePPEF is necessary and sufficient for this membrane association. [H-3]Myristate and [H-3]palmitate labeling studies in 293 cells demonstrated that this association was mediated by myristoylation at Gly(2) and palmitoylation at Cys(3). Introducing the G2A or C3S mutation into CePPEF greatly reduced membrane association in 293 cells and in transgenic nematodes. A recombinant C-terminal fragment of CePPEF containing two putative EF-hands bound between one and two Ca2+ ions/protein, and mutation of residues presumed to ligand calcium in the two putative EF-hands led to diminished calcium binding. These results establish the first direct evidence for fatty acylation and calcium binding of a PPEF family member and demonstrate a remarkable conservation of sensory neuron expression among the members of this distinctive family of ------------------- Key: 4767 Medline: 11445542 Authors: MacQueen AJ;Villeneuve AM Title: Nuclear reorganization and homologous chromosome pairing during meiotic prophase require C. elegans chk-2. Citation: Genes & Development 15: 1674-1687 2001 Type: ARTICLE Genes: chk-2 rad-51 spo-11 ozDf1 ozDf2 Abstract: Analysis of mutants defective in meiotic chromosome pairing has uncovered a role for Caenorhabditis: elegans chk-2 in initial establishment of pairing between homologous chromosomes during early meiotic prophase. chk-e is also required for the major spatial reorganization of nuclei that normally accompanies the onset of pairing, suggesting a mechanistic coupling of these two events. Despite failures in pairing, nuclear reorganization, and crossover recombination, chk-e mutants undergo many other aspects of meiotic chromosome morphogenesis and complete gametogenesis. Although chk-2 encodes a C. elegans ortholog of the Cds1/Chk2 checkpoint protein kinases, germ-line nuclei in chk-2 mutants are competent to arrest proliferation in response to replication inhibition and to trigger DNA damage checkpoint responses to ionizing radiation. However, chk-2 mutants are defective in triggering the pachytene DNA damage checkpoint in response to an intermediate block in the meiotic recombination pathway, suggesting that chk-2 is required either for initiation of meiotic recombination or for monitoring a specific subset of DNA damage lesions. Wt propose that chk-2 functions during premeiotic S phase to enable chromosomes to become competent for subsequent meiotic prophase events and/or to coordinate replication with entry ------------------- Key: 4768 Medline: 21308465 Authors: Guerardel Y;Balanzino L;Maes E;Leroy Y;Coddeville B;Oriol R;Strecker G Title: The nematode Caenorhabditis elegans synthesizes unusual O-linked glycans: identification of glucose-substituted mucin-type O-glycans and short chondroitin-like oligosaccharides. Citation: Biochemical Journal 357: 167-182 2001 Type: ARTICLE Genes: sqv-3 sqv-8 Abstract: The free-living nematode Caenorhabditis elegans is a relevant model for studies on the role of glycoconjugates during development of multicellular organisms. Several genes coding for glycosyltransferases involved in the synthesis of N- and O-linked glycans have already been isolated, but, apart from repetitive dimers of glycosaminoglycans, no detailed structure of either type of component has been published so far. This study aimed to establish the structures of the major O-glycans synthesized by C. Elegans to give an insight into the endogenous glycosyltransferase activities expressed in this organism. By the use of NMR and MS, we have resolved the sequence of seven of these components that present very unusual features, Most of them were characterized by the type-1 core substituted on Gal and/or GalNAc by (beta1-4)Glc and (beta1-6)Glc residues. Another compound exhibited the GalNAc(beta1-4)N-acetylglucosaminitol sequence in the terminal position, to which was attached a tetramer of beta -Gal substituted by both Fuc and 2-O-methyl-fucose residues. Our experimental procedure led also to the isolation of glycosaminoglycan-like components acid oligomannosyl-type N-glycans. In particular, the data confirmed that C. elegans synthesizes the ubiquitous linker sequence GlcA(beta1-3)Gal(beta1-3)Gal(beta1-4)Xyl. ------------------- Key: 4769 Medline: 11447255 Authors: Hanazawa M;Mochii M;Ueno N;Kohara Y;Iino Y Title: Use of cDNA subtraction and RNA interference screens in combination reveals genes required for germ-line development in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 98: 8686-8691 2001 Type: ARTICLE Genes: glh-1 glp-1 glp-4 lag-2 let-60 lim-7 mex-1 pos-1 tra-2 Abstract: Caenorhabditis elegans is an ideal organism for the study of the molecular basis of fundamental biological processes such as germline development, especially because of availability of the whole genome sequence and applicability of the RNA interference (RNAi) technique. To identify genes involved in germ-line development, we produced subtracted cDNA pools either enriched for or deprived of the cDNAs from germ-line tissues. We then performed differential hybridization on the high-density cDNA grid, on which about 7,600 nonoverlapping expressed sequence tag (EST) clones were spotted, to identify a set of genes specifically expressed in the germ line. One hundred and sixty-eight clones were then tested with the RNAi technique. Of these, 15 clones showed sterility with a variety of defects in germ-line development. Seven of them led to the production of unfertilized eggs, because of defects in spermatogenesis (4 clones), or defects in the oocytes (3 clones). The other 8 clones led to failure of oogenesis. These failures were caused by germ-line proliferation defect (Glp phenotype), meiotic arrest, and defects in sperm-oocyte switch (Mog phenotype) among others. These results demonstrate the efficacy of the screening strategy using the EST library combined with the RNAi technique in C. elegans. ------------------- Key: 4770 Medline: 21347559 Authors: Merz DC;Zheng H;Killeen MT;Krizus A;Culotti JG Title: Multiple signaling mechanisms of the UNC-6/netrin receptors UNC-5 and UNC-40/DCC in vivo. Citation: Genetics 158: 1071-1080 2001 Type: ARTICLE Genes: gon-1 unc-5 unc-6 unc-40 Abstract: Cell and growth cone migrations along the dorsoventral axis of Caenorhabditis elegans are mediated by the UNC-5 and UNC-40 receptor subtypes for the secreted UNC-6 guidance cue. To characterize UNC-6 receptor function in vivo we have examined genetic interactions between unc-5 and unc-40 in the migrations of the hermaphrodite distal tip cells. We report that cell migration defects as severe as those associated with a null mutation in unc-6 are produced only by null mutations in both unc-5 and unc-40, indicating that either receptor retains some partial function in the absence of the other. We show that hypomorphic unc-5 alleles exhibit two distinct types of interallelic genetic interactions. In an unc-40 wild-type genetic background, some pairs of hypomorphic unc-5 alleles exhibit a partial allelic complementation. In an unc-40 null background, however, we observed that unc-5 hypomorphs exhibit dominant negative effects. We propose that the UNC-5 and UNC-40 netrin receptors can function to mediate chemorepulsion in DTC migrations either independently or together, and the observed genetic interactions suggest that this flexibility in modes of signaling results from the formation of a variety of oligomeric receptor complexes. ------------------- Key: 4771 Medline: 21347560 Authors: Le QH;Turcotte K;Bureau T Title: Tc8, a Tourist-like transposon in Caenorhabditis elegans. Citation: Genetics 158: 1081-1088 2001 Type: ARTICLE Genes: Abstract: Members of the Tourist family of miniature inverted-repeat transposable elements (MITEs) are very abundant among a nide variety of plants, are frequently found associated with normal plant genes, and thus are thought to be important players in the organization and evolution of plant genomes. In Arabidopsis, the recent discovery of a Tourist member harboring a putative transposase has shed new light on the mobility and evolution of MITEs. Here, we analyze a family of Tourist transposons endogenous to the genome of the nematode Caenorhabditis elegans (Bristol N2). One member of this large family is 7568 bp in length, harbors an ORF similar to the putative Tourist transposase from Arabidopsis, and is related to the IS5 family of bacterial insertion sequences (IS). Using database searches, we found expressed sequence tags (ESTs) similar to the putative Tourist transposases in plants, insects, and vertebrates. Taken together, our data suggest that Tourist-like and IS5-like transposons form a superfamily of potentially active elements ubiquitous to prokaryotic and eukaryotic genomes. ------------------- Key: 4772 Medline: 21354308 Authors: Grishok A;Pasquinelli AE;Conte D;Li N;Parrish S;Ha I;Baillie DL;Fire A;Ruvkun G;Mello CC Title: Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Citation: Cell 106: 23-34 2001 Type: ARTICLE Genes: alg-1 alg-2 dcr-1 let07 let-740 lin-4 lin-14 lin-41 rde-1 sqt-3 unc-22 Abstract: RNAi is a gene-silencing phenomenon triggered by double-stranded (ds) RNA and involves the generation of 21 to 26 nt RNA segments that guide mRNA destruction. In Caenorhabditis elegans, lin-4 and let-7 encode small temporal RNAs (stRNAs) of 22 nt that regulate stage-specific development. Here we show that inactivation of genes related to RNAi pathway genes, a homolog of Drosophila Dicer (dcr-1), and two homologs of rde-1 (alg-1 and alg-2), cause heterochronic phenotypes similar to lin-4 and let-7 mutations. Further we show that dcr-1, alg-1, and alg-2 are necessary for the maturation and activity of the lin-4 and let-7 stRNAs. Our findings suggest that a common processing machinery generates guide RNAs that mediate both RNAi and endogenous gene regulation. ------------------- Key: 4773 Medline: Authors: Fallon PG;Allen RL;Rich T Title: Primitive Toll signalling: bugs, flies, worms and man. Citation: Trends in Immunology 22: 63-66 2001 Type: REVIEW Genes: Abstract: A current area of interplay between immunologists, geneticists and developmental biologists concerns how Toll receptors assumed their dual roles in pathogen recognition end insect embryo patterning. The development of mechanisms that recognize and control infectious pathogens has been essential for the survival of metazoan organisms. Here, Padraic Fallen and colleagues consider the insights that might be gained from using nematodes to study immune signalling pathways. ------------------- Key: 4774 Medline: 21378706 Authors: Ambros V Title: Dicing up RNAs. Citation: Science 293: 811-813 2001 Type: REVIEW Genes: alg-1 alg-2 dcr-1 let-7 lin-4 lin-14 lin-28 rde-1 rde-2 Abstract: RNA molecules are a constant source of joy to molecular biologists: They come in all shapes and sizes, and perform diverse informational, structural, and catalytic tricks in living cells. Perhaps less appreciated is their facility for regulating gene expression. Small regulatory RNAs figure prominently in two fascinating phenomena: gene inactivation by RNA interference (RNAi), and the control of gene expression during development. ------------------- Key: 4775 Medline: Authors: Hutvagner G;McLachlan J;Pasquinelli AE;Balint E;Tuschl T;Zamore PD Title: A cellular function for the RNA-interference enzyme dicer in the maturation of the let-7 small temporal RNA. Citation: Science 293: 834-838 2001 Type: ARTICLE Genes: let-7 lin-4 Abstract: The 21-nucleotide small temporal RNA (stRNA) let-7 regulates developmental timing in Caenorhabditis elegans and probably in other bilateral animals. We present in vivo and in vitro evidence that in Drosophila melanogaster a developmentally regulated precursor RNA is cleaved by an RNA interference-like mechanism to produce mature let-7 stRNA. Targeted destruction in cultured human cells of the messenger RNA encoding the enzyme Dicer, which acts in the RNA interference pathway, leads to accumulation of the let-7 precursor. Thus, the RNA interference and stRNA pathways intersect. Both pathways require the RNA-processing enzyme Dicer to produce the active small-RNA component that represses gene expression. ------------------- Key: 4776 Medline: 21378718 Authors: Griffitts JS;Whitacre JL;Stevens DE;Aroian RV Title: Bt toxin resistance from loss of a putative carbohydrate-modifying enzyme. Citation: Science 293: 860-864 2001 Type: ARTICLE Genes: bre-5 Abstract: The development of resistance is the main threat to the long-term use of toxins from Bacillus thuringiensis (Bt) in transgenic plants. Here we report the cloning of a Bt toxin resistance gene, Caenorhabditis elegans bre-5, which encodes a putative beta -1,3-galactosyltransferase. Lack of bre-5 in the intestine led to resistance to the Bt toxin Cry5B. Wild-type but not bre-5 mutant animals were found to uptake toxin into their gut cells, consistent with bre-5 mutants lacking toxin-binding sites on their apical gut. bre-5 mutants displayed resistance to Cry14A, a Bt toxin lethal to both nematodes and insects; this indicates that resistance by loss of carbohydrate modification is relevant to multiple Bt toxins. ------------------- Key: 4777 Medline: Authors: Pierce-Shimomura JT;Faumont S;Gaston MR;Pearson BJ;Lockery SR Title: The homeobox gene lim-6 is required for distinct chemosensory representations in C. elegans. Citation: Nature 412: 566- 2001 Type: CORRECT Genes: Abstract: The ability to discriminate between different chemical stimuli is crucial for food detection, spatial orientation and other adaptive behaviours in animals. In the nematode Caenorhabditis elegans, spatial orientation in gradients of soluble chemoattractants (chemotaxis) is controlled mainly by a single pair of chemosensory neurons(1). These two neurons, ASEL and ASER, are left-right homologues in terms of the disposition of their somata and processes, morphology of specialized sensory endings, synaptic partners and expression profile of many genes(2,3). However, recent gene-expression studies have revealed unexpected asymmetries between ASEL and ASER. ASEL expresses the putative receptor guanylyl cyclase genes gcy-6 and gcy-7, whereas ASER expresses gcy-5 (ref. 4). In addition, only ASEL expresses the homeobox gene lim-6, an orthologue of the human LMX1 subfamily of homeobox genes(5). Here we show, using laser ablation of neurons and whole-cell patch-clamp electrophysiology, that the asymmetries between ASEL and ASER extend to the functional level. ASEL is primarily sensitive to sodium, whereas ASER is primarily sensitive to chloride and potassium. Furthermore, we find that lim-6 is required for this functional asymmetry and for the ability to distinguish sodium from chloride. Thus, a homeobox gene increases the representational capacity of the nervous system by establishing asymmetric functions in a bilaterally ------------------- Key: 4778 Medline: 11457923 Authors: Paupard MC;Miller A;Grant B;Hirsh D;Hall DH Title: Immuno-EM localization of GFP-tagged yolk proteins in C. elegan using microwave fixation. Citation: Journal of Histochemistry & Cytochemistry 49: 949-956 2001 Type: ARTICLE Genes: rme-2 Abstract: Because of the presence of a low-permeability cuticle covering the animal, fixation of C. elegans tissue for immunoelectron microscopy has proved very difficult. Here we applied a microwave fixation protocol to improve penetration of fixatives before postembedding immunogold labeling. Using this technique, we were able to successfully localize several components of yolk (YP170) trafficking in both wild-type and transgenic strains expressing a vitellogenin::green fluorescent protein fusion (YP170::GFP). Green fluorescent protein (GFP) and its variants are commonly used as markers to localize proteins in transgenic C. elegans using fluorescence microscopy. We have developed a robust method to localize GFP at the EM level. This procedure is applicable to the characterization of transgenic strains in which GFP is used to mark particular proteins or cell types and will undoubtedly be very useful for high-resolution analysis of marked ------------------- Key: 4779 Medline: 21325938 Authors: Clemens S;Schroeder JI;Degenkolb T Title: Caenorhabditis elegans expresses a functional phytochelatin synthase. Citation: European Journal of Biochemistry 268: 3640-3643 2001 Type: ARTICLE Genes: Abstract: The formation of phytochelatins, small metal-binding glutathione-derived peptides, is one of the well-studied responses of plants to toxic metal exposure. Phytochelatins have also been detected in some fungi and some marine diatoms. Genes encoding phytochelatin synthases (PCS) have recently been cloned from Arabidopsis, wheat and Schizosaccharomyces pombe. Surprisingly, database searches revealed the presence of a homologous gene in the Caenorhabditis elegans genome, DDBJ/EMBL/GenBank accession no. 266513. Here we show that C. elegans indeed expresses a gene coding for a functional phytochelatin synthase. CePCS complements the Cd2+ sensitivity of a Schizosaccharomyces pombe PCS knock-out strain and confers phytochelatin synthase activity to these cells. Thus, phytochelatins may play a role for metal homeostasis also in certain animals. ------------------- Key: 4780 Medline: 11437447 Authors: Quintin S;Michaux G;McMahon L;Gansmuller A;Labouesse M Title: The Caenorhabditis elegans gene lin-26 can trigger epithelial differentiation without conferring tissue specificity. Citation: Developmental Biology 235: 410-421 2001 Type: ARTICLE Genes: che-14 dlg-1 dpy-7 dpy-20 elt-1 elt-3 end-1 jam-1 let-502 lin-26 lir-1 mec-3 pha-4 Abstract: How epithelial cell fates become specified is poorly understood. We have previously shown that the putative C2H2 zinc-finger transcription factor LIN-26 is required for the differentiation of ectodermal and mesodermal epithelial cells in Caenorhabditis elegans. Here, we report that ectopic LIN-26 expression during early gastrulation transforms most blastomeres into epithelial-like cells. Specifically, LIN-26 induced the expression of three epithelial markers: the adherens junction protein JAM-1; DLG-1, which is essential for the assembly of JAM-1 at junctions; and CHE-14, which is involved in apical trafficking. Furthermore, ultrastructural studies revealed that ectopic LIN-26 expression induced the formation of adherens-like junctions. However, ectopic lin-26 expression did not confer any tissue-specific cell fate, such as the epidermal cell fate, as evidenced from the observation that several epidermal-specific genes were not induced. Conversely, we show that epidermal cells displayed some polarity defects in lin-26 mutants. We conclude that lin-26 can induce epithelial differentiation and that epitheliogenesis is not a default pathway in C. elegans. ------------------- Key: 4781 Medline: 11456452 Authors: Heid PJ;Raich WB;Smith R;Mohler WA;Simokat K;Gendreau SB;Rothman JH;Hardin J Title: The zinc finger protein DIE-1 is required for late events during epithelial cell rearrangement in C. elegans. Citation: Developmental Biology 236: 165-180 2001 Type: ARTICLE Genes: die-1 eff-1 lbp-1 let-23 let-31 let-242 let-243 let-244 let-268 mnDf12 mnDf14 mnDf28 mnDf61 mnDf62 mnDf63 mnDf66 mnDf 68 mnDf71 mnDf83 mnDf89 wDf5 Abstract: The mechanism by which epithelial cells undergo directed rearrangement is central to morphogenesis, yet the regulation of these movements remains poorly understood. We have investigated epithelial cell rearrangement (intercalation) in the dorsal hypodermis, or embryonic epidermis, of the C. elegans embryo by analyzing the die-1(w34) mutant, which fails to undergo normal intercalation. Dorsal hypodermal cells of die-1(w34) homozygous embryos initiate but fail to complete the process of intercalation. Multiphoton microscopy reveals that intercalating cells extend monopolar, basolateral protrusions in their direction of migration; posterior dorsal hypodermal cells in die-1(w34) mutants appear to extend protrusions normally, but fail to translocate their cell bodies to complete rearrangement. Despite abnormal intercalation, the subsequent morphogenetic movements that enclose the embryo with epithelial cells and the process of dorsal cell fusion still occur. However, elongation of the embryo into a wormlike shape is disrupted in die-1(w34) embryos, suggesting that intercalation may be necessary for subsequent elongation of the embryo. Actin filaments are not properly organized within the dorsal hypodermis of die-1(w34) embryos, consistent with intercalation's being a necessary prerequisite for elongation. The die-1 gene encodes a C2H2 zinc finger protein containing four fingers, which likely acts as a transcriptional regulator. DIE-1 is present in the nuclei of hypodermal, muscle, gut, and pharyngeal cells, its distribution suggests that DIE-1 acts in each of these tissues to regulate morphogenetic movements. die-l(w34) mutants display morphogenetic defects in the pharynx, gut, and muscle quadrants, in addition to the defects in the dorsal hypodermis, consistent with the DIE-1 expression pattern. Mosaic analysis indicates that DIE-1 is autonomously required in the posterior dorsal hypodermis for intercalation. Our analysis documents for the first time the dynamics of protrusive activity during epithelial cell rearrangement. Moreover, our analysis of die-1 shows that the events of epithelial cell rearrangement are under transcriptional control, and that early and later phases of epithelial cell rearrangement are genetically distinguishable. ------------------- Key: 4782 Medline: Authors: Gotta M;Ahringer J Title: Axis determination in C. elegans: initating and transducing polarity. Citation: Current Opinion in Genetics & Development 11: 367-373 2001 Type: REVIEW Genes: ags-3 goa-1 let-99 mex-1 mex-5 mex-6 mlc-4 nmy-2 ooc-3 ooc-5 par-1 par-2 par-3 par-6 pie-1 pkc-1 pod-1 pod-2 pos-1 ric-8 spd-2 spn-1 Abstract: The anterior-posterior axis in Caenorhabditis elegans is determined by the sperm and leads to the asymmetric localisation of PAR (partitioning-defective) proteins, which are critical for polarity. New findings demonstrate that sperm asters play a critical role and suggest models for how PAR asymmetry is established. In addition, studies of blastomere fate determination and heterotrimeric G proteins have started to uncover how initial polarity may be translated into the asymmetric distribution of maternal proteins and the control of spindle position. ------------------- Key: 4783 Medline: 21273559 Authors: Hope IA Title: Broadcast interference - functional genomics. Citation: Trends in Genetics 17: 297-299 2001 Type: REVIEW Genes: Abstract: Four recent papers mark a major shift in functional genomic analysis for multicellular organisms. RNA-mediated interference was applied to inactivate individual genes systematically on a genomic scale. These studies subjected a third of the genes in the genome of Caenorhabditis elegans to reverse genetic analysis. ------------------- Key: 4784 Medline: 11353865 Authors: Morita K;Shimizu M;Shibuya H;Ueno N Title: A DAF-1-binding protein BRA-1 is a negative regulator of DAF-7 TGF-B signaling. Citation: Proceedings of the National Academy of Sciences USA 98: 6284-6288 2001 Type: ARTICLE Genes: bra-1 bra-2 daf-1 daf-2 daf-7 daf-11 daf-14 mut-2 Abstract: We have identified homologs of a human BMP receptor-associated molecule BRAM1 in Caenorhabditis elegans. One of them, BRA-1, has been found to bind DAF-1, the type I receptor in the DAF-7 transforming growth factor-beta pathway through the conserved C-terminal region. As analyzed using a BRA-1::GFP (green fluorescent protein) fusion gene product, the bra-1 gene is expressed in amphid neurons such as ASK, ASI, and ASG, where daf-1 is also expressed. A loss-of-function mutation in bra-1 exhibits robust suppression of the Daf-c phenotype caused by the DAF-7 pathway mutations. We propose that BRA-1 represents a novel class of receptor-associated molecules that negatively regulate transforming growth factor-beta ------------------- Key: 4785 Medline: 11408582 Authors: Strome S;Powers J;Dunn M;Reese K;Malone CJ;White J;Seydoux G;Saxton W Title: Spindle dynamics and the role of gamma-tubulin in early Caenorhabditis elegans embryos. Citation: Molecular Biology of the Cell 12: 1751-1764 2001 Type: ARTICLE Genes: pie-1 tnDf2 Abstract: gamma -Tubulin is a ubiquitous and highly conserved component of centrosomes in eukaryotic cells. Genetic and biochemical studies have demonstrated that gamma -tubulin functions as part of a complex to nucleate microtubule polymerization from centrosomes. We show that, as in other organisms, Caenorhabditis elegans gamma -tubulin is concentrated in centrosomes. To study centrosome dynamics in embryos, we generated transgenic worms that express GFP::gamma -tubulin or GFP::beta -tubulin in the maternal germ line and early embryos. Multiphoton microscopy of embryos produced by these worms revealed the time course of daughter centrosome appearance and growth and the differential behavior of centrosomes destined for germ line and somatic blastomeres. To study the role of gamma -tubulin in nucleation and organization of spindle microtubules, we used RNA interference (RNAi) to deplete C. elegans embryos of gamma -tubulin. gamma -Tubulin (RNAi) embryos failed in chromosome segregation, but surprisingly, they contained extensive microtubule arrays. Moderately affected embryos contained bipolar spindles with dense and long astral microtubule arrays but with poorly organized kinetochore and interpolar microtubules. Severely affected embryos contained collapsed spindles with numerous long astral microtubules. Our results suggest that,gamma -tubulin is not absolutely required for microtubule nucleation in C. elegans but is required for the normal organization and function of kinetochore and interpolar ------------------- Key: 4786 Medline: 21301812 Authors: Matyash V;Geier C;Henske A;Mukherjee S;Hirsh D;Thiele C;Grant B;Maxfield FR;Kurzchalia TV Title: Distribution and transport of cholesterol in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 12: 1725-1736 2001 Type: ARTICLE Genes: fer-1 him-8 rme-2 Abstract: Cholesterol transport is an essential process in all multicellular organisms. In this study we applied two recently developed approaches to investigate the distribution and molecular mechanisms of cholesterol transport in Caenorhabditis elegans. The distribution of cholesterol in living worms was studied by imaging its fluorescent analog, dehydroergosterol, which we applied to the animals by feeding. Dehydroergosterol accumulates primarily in the pharynx, nerve ring, excretory gland cell, and gut of L1-L3 larvae. Later, the bulk of dehydroergosterol accumulates in oocytes and spermatozoa. Males display exceptionally strong labeling of spermatids, which suggests a possible role for cholesterol in sperm development. In a complementary approach, we used a photoactivatable cholesterol analog to identify cholesterol-binding proteins in C. elegans. Three major and several minor proteins were found specifically cross-linked to photocholesterol after UV irradiation. The major proteins were identified as vitellogenins. rme-2 mutants, which lack the vitellogenin receptor, fail to accumulate dehydroergosterol in oocytes and embryos and instead accumulate dehydroergosterol in the body cavity along with vitellogenin. Thus, uptake of cholesterol by C. elegans oocytes occurs via an endocytotic pathway involving yolk proteins. The pathway is a likely evolutionary ancestor of mammalian cholesterol transport. ------------------- Key: 4787 Medline: 21341785 Authors: Lehmann R Title: Cell migration in invertebrates: clues from border and distal tip cells. Citation: Current Opinion in Genetics & Development 11: 457-463 2001 Type: REVIEW Genes: ced-2 ced-5 ced-10 daf-4 daf-12 dbl-1 gon-1 mig-8 mig-17 unc-5 unc-6 unc-40 unc-129 unc-130 Abstract: Recent studies in two invertebrate systems, border cells in Drosophila melanogaster and distal tip cells in Caenorhabditis elegans, have provided important insight into the mechanisms of directed cell migration. These migrating cells are guided by extracellular signals, such as EGF, TGF-P and netrin. In addition, metalloproteases alter the extracellular matrix of the tissue through which these cells migrate. Along the migratory path, migrating cells respond to changes in guidance signals by altering the expression of receptor signaling pathways. Finally, Dock180, CrklI and the GTPase Rac link the extracellular signals to the cellular machinery that controls cell ------------------- Key: 4788 Medline: Authors: Strauss E Title: Longevity: Growing old together. Citation: Science 292: 41-43 2001 Type: REVIEW Genes: daf-2 Abstract: Simple evolutionary arguments don't demand that organisms share mechanisms of aging. But new work is strengthening the case that common processes control the life-spans of biology's favorite model systems. ------------------- Key: 4789 Medline: 21242529 Authors: Macdonald P Title: Diversity in translational regulation. Citation: Current Opinion in Cell Biology 13: 326-331 2001 Type: REVIEW Genes: fem-3 let-7 lin-4 lin-14 Abstract: Translational control of individual mRNAs relies on cis-regulatory elements, which are often found in the 3' untranslated region. The best characterized of these regulate cytoplasmic polyadenylation, and much of this process can now be defined in terms of molecular interactions, protein modifications and their consequences. Biochemical and genetic approaches have advanced the understanding of the many instances of translational regulation that are crucial for body patterning in Drosophila. For example, in vitro translation systems have been used to study the regulatory mechanisms, and genetic interactions have been instrumental in establishing a link between a regulatory factor and a component of the translational apparatus. Although most examples of control are thought to affect the initiation of translation, two classes of regulatory factors, one a protein and one a short non-coding RNA now appear to inhibit protein synthesis during elongation. Diversity seems to be a central feature of translational control, both in mechanisms themselves and in the situations where this form ------------------- Key: 4790 Medline: Authors: Park BJ;Lee JI;Lee J;Kim S;Choi KY;Park CS;Ahnn J Title: Isolation of deletion mutants by reverse genetics in Caenorhabditis elegans. Citation: Korean Journal of Biological Sciences 5: 65-69 2001 Type: ARTICLE Genes: Abstract: Obtaining mutant animals is important for studying the function of a particular gene. A chemical mutagenesis was first carried out to generate mutations in C. elegans. In this study, we used ultraviolet-activated 4,5',8-trimethylpsoralen to induce small deletion mutations. A library of mutagenized worms was prepared for recovery of candidate animals and stored at 15 degree C during screening instead of being made into a frozen stock library. In order to isolate deletion mutations in target genes, a polymerase chain reaction (PCR)-based screening method was used. As a result, two independent mutants with deletions of approximately 1.0 kb and 1.3 kb were isolated. This modified and improved reverse genetic approach was proven to be effective and practical for isolating mutant animals to study gene function at the organismal level. ------------------- Key: 4791 Medline: 11447285 Authors: Kapitonov VV;Jurka J Title: Rolling-circle transposons in eukaryotes. Citation: Proceedings of the National Academy of Sciences 98: 8714-8719 2001 Type: ARTICLE Genes: Abstract: All eukaryotic DNA transposons reported so far belong to a single category of elements transposed by the so-called "cut-and-paste" mechanism. Here, we report a previously unknown category of eukaryotic DNA transposons. Helitron, which transpose by rolling-circle replication. Autonomous Helitrons encode a 5 ' -to-3 ' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons. Helitron-like transposons have conservative 5 ' -TC and CTRR-3 ' termini and do not have terminal inverted repeats. They contain 16- to 20-bp hairpins separated by 10-12 nucleotides from the 3 ' -end and transpose precisely between the 5 ' -A and T-3 ', with no modifications of the AT target sites. Together with their multiple diverged nonautonomous descendants, Helitrons constitute approximate to2% of both the Arabidopsis thaliana and Caenorhabditis elegans genomes and also colonize the Oriza sativa genome. Sequence conservation suggests that Helitrons continue to be ------------------- Key: 4792 Medline: 21349919 Authors: Nagendra HG;Harrington AE;Harmer NJ;Pellegrini L;Blundell TL;Burke DF Title: Sequence analysis and comparative modeling of fly and worm fibroblast growth factor receptors indicate that the determinants for FGF and heparin binding are retained in evolution. Citation: FEBS Letters 501: 51-58 2001 Type: ARTICLE Genes: Abstract: The presence of a large number of fibroblast growth factors (FGFs) and multiple splice forms of their receptors (FGFRs) in higher vertebrates makes the three-dimensional (3D) analysis of FGF interactions with their receptors a formidable task. The situation differs in Caenorhabditis elegans (worm) and Drosophila melanogaster (fruit fly), where only one or two FGF and FCFR sequences have been identified. Structural studies of the FGF-FGFR complexes in such primitive organisms should reveal the basic features of the ligand-receptor interactions as they first emerged through evolution. We have analysed the sequences of worm and fly FGFs and FGFRs and used the recently determined crystal structure of the human FGF1-FGFR2-heparin ternary complex [Pellegrini, L., Burke, D.F., von Delft, F., Mulloy, B, and Blundell, T.L. (2000) Nature 407, 1029-34] to construct 3D models of the homologous complexes. In spite of a low sequence similarity with their human counter; parts, key structural features required for ligand-receptor and protein-heparin binding in humans are conserved in the fly and worm FGF-FGFR-heparin complexes. Analyses of the models show tha ------------------- Key: 4793 Medline: Authors: Gutzeit HO Title: Biological effects of ELF-EMF enhanced stress response: New insights and new questions. Citation: Electro- and Magnetobiology 20: 15-26 2001 Type: ARTICLE Genes: Abstract: The effect of extremely low frequency electromagnetic fields (ELF-EMF) on gene expression and early development has been investigated in two different transgenic animals, the nematode Caenorhabditis elegans and Drosophila melanogaster, respectively. ELF-EMF enhanced biological reactions considerably in the presence of a second stressor (mild heat shock). In C. elegans, this effect could be demonstrated at the level of heat shock protein (hsp) gene expression by means of a lacZ reporter gene controlled by an hsp 16 or hsp 70 promoter. In Drosophila, the same experimental strategy led to ELF-EMF induced developmental defects, as well as to a considerable retardation of development. The findings are discussed with respect to possible molecular mechanisms that might explain the observed synergistic ELF-EMF induced enhancement of the stress response. An experimental approach is suggested which may help to unravel the involved signal transduction ------------------- Key: 4794 Medline: 21349355 Authors: Gamenara D;Pandolfi E;Saldana J;Dominguez L;Martinez MM;Seoane G Title: Nematocidal activity of natural polyphenols from Bryophytes and their derivatives. Citation: Arzneimittel-Forschung 51: 506-510 2001 Type: ARTICLE Genes: Abstract: The nematocidal in vivo activity of three natural perrottetins (phenolic bisbibenzylethers) and eleven diphenyl ethers used as synthetic precursors has been assayed using two different experimental models, Caenorhabditis elegans and Nippostrongylus brasiliensis. Nine compounds showed some activity against C. elegans and nine against N. brasiliensis. For the former model, three compounds displayed an activity similar to that of the standards, whereas for N. brasiliensis none of the tested compounds was as active as the standards. From the in vitro results, five compounds (3, 4, 8, 9, 13) could be selected as lead compounds to continue the search far improved activity. ------------------- Key: 4795 Medline: 21313692 Authors: Katti MV;Ranjekar PK;Gupta VS Title: Differential distribution of simple sequence repeats in eukaryotic genome sequences. Citation: Molecular Biology and Evolution 18: 1161-1167 2001 Type: ARTICLE Genes: Abstract: Complete chromosome/genome sequences available from humans, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, and Saccharomyces cerevisiae were analyzed for the occurrence of mono-, di-, tri-, and tetranucleotide repeats. In all of the genomes studied, dinucleotide repeat stretches tended to be longer than other repeats. Additionally, tetranucleotide repeats in humans and trinucleotide repeats in Drosophila also seemed to be longer. Although the trends for different repeats are similar between different chromosomes within a genome, the density of repeats may vary between different chromosomes of the same species. The abundance or rarity of various di- and trinucleotide repeats in different genomes cannot be explained by nucleotide composition of a sequence or potential of repeated motifs to form alternative DNA structures. This suggests that in addition to nucleotide composition of repeat motifs, characteristic DNA replication/repair/recombination machinery might play an important role in the genesis of repeats. Moreover, analysis of complete genome coding DNA sequences of Drosophila, C. elegans, and yeast indicated that expansions of codon repeats corresponding to small hydrophilic amino acids are tolerated more, while strong selection pressures probably eliminate codon repeats encoding hydrophobic and basic amino acids. The locations and sequences of all of the repeat loci detected in genome sequences and coding DNA sequences are available at http://www.ncl-india.org/ssr and could be useful for further studies. ------------------- Key: 4796 Medline: 21345286 Authors: Sanford C;Perry MD Title: Asymmetrically distributed oligonucleotide repeats in the Caenorhabditis elegans genome sequence that map to regions important for meiotic chromosome segregation. Citation: Nucleic Acids Research 29: 2920-2926 2001 Type: ARTICLE Genes: Abstract: The roundworm Caenorhabditis elegans has a haploid karyotype containing six linear chromosomes. The termini of worm chromosomes have been proposed to play an important role in meiotic prophase, either when homologs are participating in a genome-wide search for their proper partners or in the initiation of synapsis. For each chromosome one end appears to stimulate crossing-over with the correct homolog; the other end lacks this property. We have used a bioinformatics approach to identify six repetitive sequence elements in the sequenced C. elegans genome whose distribution closely parallels these putative meiotic pairing centers (MPC) or homolog recognition regions (HRR). We propose that these six DNA sequence elements, which are largely chromosome specific, may correspond to the genetically defined HRR/MPC elements. ------------------- Key: 4797 Medline: 21342289 Authors: De Stasio EA;Dorman S Title: Optimization of ENU mutagenesis of Caenorhabditis elegans. Citation: Mutation Research-Genetic Toxicology & Environmental Mutagenesis 495: 81-88 2001 Type: ARTICLE Genes: egl-30 spe-10 spe-37 unc-93 Abstract: Chemical mutagenesis of Caenorhabditis elegans has relied primarily on EMS to produce missense mutations. The drawback of EMS mutagenesis is that the molecular lesions are primarily G/C --> A/T transitions. ENU has been shown to produce a different spectrum of mutations, but its greater toxicity to C. elegans makes it a difficult mutagen to use. We describe here methods for minimizing ENU toxicity in C. elegans. Methods include preparing ENU stocks in absolute ethanol and storing stock solutions for not more than 2 weeks at -20 degreesC. To maintain reasonable brood sizes of mutagenized animals, mutagenic solutions should not exceed 1.0 mM ENU. We provide data which suggest ENU is degraded or altered to more toxic products in aqueous solution, but less so in solvents such ------------------- Key: 4798 Medline: 11470827 Authors: Hong L;Elbl T;Ward J;Franzini-Armstrong C;Rybicka KK;Gatewood BK;Baillie DL;Bucher EA Title: MUP-4 is a novel transmembrane protein with functions in epithelial cell adhesion in Caenorhabditis elegans. Citation: Journal of Cell Biology 154: 403-414 2001 Type: ARTICLE Genes: mua-3 mup-2 mup-4 Abstract: Tissue functions and mechanical coupling of cells must be integrated throughout development. A striking example of this coupling is the interactions of body wall muscle and hypodermal cells in Caenorhabditis elegans. These tissues are intimately associated in development and their interactions generate structures that provide a continuous mechanical link to transmit muscle forces across the hypodermis to the cuticle. Previously, we established that mup-4 is essential in embryonic epithelial (hypodermal) morphogenesis and maintenance of muscle position. Here, we report that mup-4 encodes a novel transmembrane protein that is required for attachments between the apical epithelial surface and the cuticular matrix. Its extracellular domain includes epidermal growth factor-like repeats, a von Willebrand factor A domain, and two sea urchin enterokinase modules. Its intracellular domain is homologous to filaggrin, an intermediate filament (IF)-associated protein that regulates IF compaction and that has not previously been reported as part of a junctional complex. MUP-4 colocalizes with epithelial hemidesmosomes overlying body wall muscles, beginning at the time of embryonic cuticle maturation, as well as with other sites of mechanical coupling. These findings support that MUP-4 is a junctional protein that functions in IF tethering, cell-matrix adherence, and mechanical coupling ------------------- Key: 4799 Medline: 21363576 Authors: Bercher M;Wahl J;Vogel BE;Lu C;Hedgecock ME;Hall DH;Plenefisch JD Title: mua-3, a gene required for mechanical tissue integrity in Caenorhabditis elegans, encodes a novel transmembrane protein of epithelial attachment complexes. Citation: Journal of Cell Biology 154: 415-426 2001 Type: ARTICLE Genes: mua-3 mup-4 unc-52 Abstract: Normal locomotion of the nematode Caenorhabditis elegans requires transmission of contractile force through a series of mechanical linkages from the myofibrillar lattice of the body wall muscles, across an intervening extracellular matrix and epithelium (the hypodermis) to the cuticle. Mutations in mua-3 cause a separation of the hypodermis from the cuticle, suggesting this gene is required for maintaining hypodermal-cuticle attachment as the animal grows in size postembryonically. mua-3 encodes a predicted 3,767 amino acid protein with a large extracellular domain, a single transmembrane helix, and a smaller cytoplasmic domain. The extracellular domain contains four distinct protein modules: 5 low density lipoprotein type A, 52 epidermal growth factor, I von Willebrand factor A, and 2 sea urchin-enterokinase-agrin modules. MUA-3 localizes to the hypodermal hemidesmosomes and to other sites of mechanically robust transepithelial attachments, including the rectum, vulva, mechanosensory neurons, and excretory duct/pore. In addition, it is shown that MUA-3 colocalizes with cytoplasmic intermediate filaments (IFs) at these sites. Thus, MUA-3 appears to be a protein that links the IF cytoskeleton of nematode epithelia to the cuticle at sites of mechanical stress. ------------------- Key: 4800 Medline: 11506282 Authors: Cypser J;Johnson TE Title: Hormesis extends the correlation between stress resistance and life span in long-lived mutants of Caenorhabditis elegans. Citation: Human & Experimental Toxicology 20: 295-296 2001 Type: ARTICLE Genes: Abstract: In general we agree with Dr. Rattan's thesis. Mutations that increase both life span and resistance to environmental stress have been documented in model systems as diverse as Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus. The correlation between life extension (Age) and increased stress resistance is well established in C. elegans carrying single-gene ------------------- Key: 4801 Medline: 11500979 Authors: Ho SH;So GMK;Chow KL Title: Postembryonic expression of Caenorhabditis elegans mab-21 and its requirement in sensory ray differentiation. Citation: Developmental Dynamics 221: 422-430 2001 Type: ARTICLE Genes: mab-21 Abstract: The male tail sensory rays in Caenorhabditis elegans are complex copulatory structures, the normal patterning of which requires a number of regulatory genes. Among them, mab-21 specifies the identity of sensory ray 6. By using green fluorescent protein reporters, we identify multiple cis-acting elements that control the developmental expression of mab-21. Traced with a functional mab-21::gfp gene driven by authentic regulatory sequences, mab-21 expression could be detected in hypodermal, neuronal, muscle, and ray cells. We showed here that the expression of mab-21 in the hypoderm-is and neuronal cells was dispensable for its function mi ray 6. In contrast, its expression in the ray 6 structural cell and neurons as conferred by its 3' enhancer was crucial for determining the correct ray 6 identity. ------------------- Key: 4802 Medline: Authors: Goldstein B Title: Embryonic polarity: a role for microtubules. Citation: Current Biology 10: R820-R822 2000 Type: REVIEW Genes: air-1 mat-1 ncc-1 par-1 par-2 par-3 pie-1 spd-2 Abstract: Researchers have suspected that initial polarization of the Caenorhabditis elegans embryo might be directed by microtubules, but demonstrating this has faced obstacles. A new study has cleverly bypassed these obstacles. ------------------- Key: 4803 Medline: Authors: Polinko ES;Strome S Title: Depletion of a Cks homolog in C. elegans embryos uncovers a post-metaphase role in both meiosis and mitosis. Citation: Current Biology 10: 1471-1474 2000 Type: ARTICLE Genes: cks-1 cks-2 mei-1 Abstract: In eukaryotic cells, the key regulators of cell-cycle transitions are the cyclin-dependent kinases (CDKs). The best studied CDK is a component of the M-phase promoting factor (MPF), which promotes entry into and progression through meiosis and mitosis. One of the enduring mysteries of the MPF complex has been the role of Cks/Suc1, a highly conserved member of the cell-cycle machinery in eukaryotes [1,2]. Cks has been proposed to be involved in activation of MPF [3], general interactions of MPF with its mitotic substrates [4] and/or inactivation of MPF [5,6]. We identified two Cks homologs in the genome of Caenorhabditis elegans and used RNA-mediated interference (RNAi) to investigate their roles in development. Whereas cks-2(RNAi) embryos display no apparent defects, cks-1(RNAi) embryos display defects in both meiosis and mitosis. Specifically, cks-1(RNAi) embryos fail to exit M phase properly. We propose that CKS-1 has an essential role in the inactivation of MPF during early C. elegans embryogenesis. ------------------- Key: 4804 Medline: 21380238 Authors: Johnson TE;Wu D;Tedesco P;Dames S;Vaupel JW Title: Age-specific demographic profiles of longevity mutants in Caenorhabditis elegans show segmental effects. Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 56: B331-B339 2001 Type: ARTICLE Genes: age-1 clk-1 clk-2 clk-3 daf-2 daf-16 eat-1 eat-2 eat-3 eat-6 eat-13 eat-18 fer-15 gro-1 pdk-1 spe-9 spe-10 spe-26 Abstract: Demographic profiles of several single-gene longevity mutants of the nematode Caenorhabditis elegans reveal segmental (age-specific) effects on mortality. The mortality profiles of wild-type worms were examined across multiple replicate cultures containing 100,000 or more nematodes and found to be quite replicable, although clear environmental effects are routinely found. The combined profile of wild type was compared with those of three long-lived mutants to determine how age-specific mortality is altered by mutations in age-1, clk-1, or spe-26. In all four genotypes, death rates fit a two-stage Gompertz model better than a one-stage Gompertz; that is, mortality levels off at later ages. The largest genetic effect on mortality was that of an age-1 mutation, which lowered mortality more than fivefold at most later ages. In contrast, a spe-26 mutant had a tenfold lower mortality until approximately 2 weeks of age but ultimately achieved a higher mortality, whereas clk-1 mutants show slightly higher mortality than wild type during the fertile period, early in life, but ultimately level off at lower mortality. Each mutant thus has a distinctive profile of age-specific mortalities that could suggest the time of action of each gene. ------------------- Key: 4805 Medline: 21376140 Authors: Jones SJM;Riddle DL;Pouzyrev AT;Velculescu VE;Hillier L;Eddy SR;Stricklin SL;Baillie DL;Waterston R;Marra MA Title: Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans. Citation: Genome Research 11: 1346-1352 2001 Type: ARTICLE Genes: age-1 akt-1 clk-1 ctl-1 daf-1 daf-2 daf-3 daf-4 daf-7 daf-11 daf-16 daf-18 daf-19 daf-23 gro-1 ins-1 pdk-1 sir-2 sod-1 sod-3 sod-4 spe-26 tts-1 Abstract: Gene expression in a developmentally arrested, long-lived dauer Population of Caenorhabditis elegans was compared with a nondauer (mixed-stage) population by using serial analysis of gene expression (SAGE). Dauer (152,314) and nondauer (148,324) SAGE tags identified If,130 of the predicted 19,100 C elegans genes. Genes implicated previously in longevity were expressed abundantly in the dauer library, and new genes potentially important in dauer biology were discovered. Two thousand six hundred eighteen genes were detected only in the nondauer population, whereas 2016 genes were detected only in the dauer, showing that dauer larvae show a surprisingly complex gene expression profile. Evidence for differentially expressed gene transcript isoforms was obtained for 162 genes. HI histones. were differentially expressed, raising the possibility of alternative chromatin packaging. The most abundant tag from dauer larvae (20-fold more abundant than in the nondauer profile) corresponds to a new, unpredicted gene we have named tts-1 (transcribed telomere-like sequence), which may interact with telomeres or telomere-associated proteins. Abundant antisense mitochondrial transcripts (2% of all tags), suggest the existence of an antisense-mediated: regulatory mechanism in C. elegans mitochondria. In addition to providing a robust tool for gene expression studies, the SAGE approach already has provided the advantage of new gene/transcript discovery ------------------- Key: 4806 Medline: 11502258 Authors: Dwyer ND;Adler CE;Crump JG;L'Etiole ND;Bargmann CI Title: Polarized dendritic transport and the AP-1 mu-1 clathrin adapter UNC-101 localize odorant receptors to olfactory cilia. Citation: Neuron 31: 277-287 2001 Type: ARTICLE Genes: daf-19 dpy-23 dyn-1 glr-1 odr-4 odr-10 osm-9 snb-2 str-1 str-2 str-3 unc-11 unc-101 Abstract: Odorant receptors and signaling proteins are localized to sensory cilia on olfactory dendrites. Using a GFP-tagged odorant receptor protein, Caenorhabditis elegans ODR-10, we characterized protein sorting and transport in olfactory neurons in vivo. ODR-10 is transported in rapidly moving dendritic vesicles that shuttle between the cell body and the cilia. Anterograde and retrograde vesicles move at different speeds, suggesting that dendrites have polarized transport mechanisms. Residues immediately after the seventh membrane-spanning domain of ODR-10 are required for localization; these residues are conserved in many G protein-coupled receptors. UNC-101 encodes a mu1 subunit of the AP-1 clathrin adaptor complex. In unc-101 mutants, dendritic vesicles are absent, ODR-10 receptor is evenly distributed over the plasma membrane, and other cilia membrane proteins are also mislocalized, implicating AP-1 in protein sorting to olfactory cilia. ------------------- Key: 4807 Medline: Authors: Gratzer H;Ahlf W Title: Adjustment of a formulated sediment for sediment testing with Caenorhabditis elegans (Nematoda). Citation: Acta Hydrochimica et Hydrobiologica 29: 41-46 2001 Type: ARTICLE Genes: Abstract: The OECD soil, which is standardised for use in the sediment toxicity with the midge Chironomus riparius revealed inhibition of the nematode Caenorhabditis elegans in body growth length and egg production of 41.0 % and 84 %, respectively. 18 formulated sediments were tested to optimise the sediment composition for growth and reproduction of C. elegans. Their components were chosen to simulate native sediments, whereby different quantities and different clay minerals were tested. The mixture that we found to be optimal in our experiments consisted of 5 % sphagnum peat, 70 % calcitic sand, 0.5 % dolomite limestone, 4.5 % iron(Ill) oxide, and a clay combination of 1.5 % chlorite and 18.5 % aluminium(III) oxide. When applying this mixture to C. riparius, the new formulated sediment improved also growth in comparison to the OECD ------------------- Key: 4808 Medline: 21311641 Authors: Yonemura I;Mabuchi I Title: Heterogeneity of mRNA coding for Caenorhabditis elegans coronin-like protein. Citation: Gene 271: 255-259 2001 Type: ARTICLE Genes: Abstract: We analyzed transcripts coding for the nematode Caenorhabditis elegans coronin, which had been identified by the genome project of C. elegans. We found that the gene coding for the C. elegans coronin has an alternatively spliced exon containing an alternative 5' splice site in the 3'-region. Moreover, two exons are internally cleaved by a mechanism different from the conventional splicing rules. In consequence, the gene produces five kinds of ------------------- Key: 4809 Medline: 21380261 Authors: Ranganathan R;Sawin ER;Trent C;Horvitz HR Title: Mutations in the Caenorhabditis elegans serotonin reuptake transporter MOD-5 reveal serotonin-dependent and -independent activities of fluoxetine. Citation: Journal of Neuroscience 21: 5871-5884 2001 Type: ARTICLE Genes: bas-1 cat-4 egl-1 goa-1 mod-1 mod-5 tph-1 Abstract: We isolated two mutants defective in the uptake of exogenous serotonin (5-HT) into the neurosecretory motor neurons of Caenorhabditis elegans. These mutants were hypersensitive to exogenous 5-HT and hyper-responsive in the experience-dependent enhanced slowing response to food modulated by 5-HT. The two allelic mutations defined the gene mod-5 (modulation of locomotion defective), which encodes the only serotonin reuptake transporter (SERT) in C. elegans. The selective serotonin reuptake inhibitor fluoxetine (Prozac) potentiated the enhanced slowing response, and this potentiation required mod-5 function, establishing a 5-HT- and SERT-dependent behavioral effect of fluoxetine in C. elegans. By contrast, other responses of C. elegans to fluoxetine were independent of MOD-5 SERT and 5-HT. Further analysis of the MOD-5-independent behavioral effects of fluoxetine could lead to the identification of novel targets of fluoxetine and could facilitate the development of more specific human ------------------- Key: 4810 Medline: 11451999 Authors: Zhang Y;Grant B;Hirsh D Title: RME-8, a conserved J-domain protein, is required for endocytosis in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 12: 2011-2021 2001 Type: ARTICLE Genes: rme-8 hDf9 mnDf111 nDf24 nDf25 ozDf5 qDf16 sDf6 Abstract: By genetic analysis of Caenorhabditis elegans mutants defective in yolk uptake, we have identified new molecules functioning in the endocytosis pathway. Here we describe a novel J-domain-containing protein, RME-8, identified by such genetic analysis. RME-8 is required for receptor-mediated endocytosis and fluid-phase endocytosis in various cell types and is essential for C. elegans development and viability. In the macrophage-like coelomocytes, RME-8 localizes to the limiting membrane of large endosomes. Endocytosis markers taken up by the coelomocytes rapidly accumulate in these large RME-8-positive endosomes, concentrate in internal sub-endosomal structures, and later appear in RME-8-negative lysosomes. rme-8 mutant coelomocytes fail to accumulate visible quantities of endocytosis markers. These observations show that RME-8 functions in endosomal trafficking before the lysosome. RME-8 homologues are found in multicellular organisms from plants to humans but not in the yeast Saccharomyces cerevisiae. These sequence homologies suggest that RME-8 fulfills a conserved function ------------------- Key: 4811 Medline: 21376046 Authors: Zipperlen P;Fraser AG;Kamath RS;Martinez-Campos M;Ahringer Title: Roles for 147 embryonic lethal genes on C. elegans chromosome I identified by RNA interference and video microscopy. Citation: EMBO Journal 20: 3984-3992 2001 Type: ARTICLE Genes: apr-1 chp-1 dad-1 dhc-1 ego-1 goa-1 gsk-3 hlh-2 hmp-2 hmr-1 icp-1 klp-15 klp-16 kup-2 let-502 mei-1 mei-2 mel-26 mex-3 mom-4 mom-5 nhr-2 nmy-2 par-6 pfn-1 pop-1 rab-5 rba-1 rba-2 sup-17 sur-6 tba-1 tba-2 unc-37 unc-73 Abstract: Early embryonic development involves complex events such as the regulation of cell division and the establishment of embryonic polarity. To identify genes involved in these events, we collected four-dimensional time-lapse video recordings of the first three cell divisions and analysed terminal phenotypes after RNA interference of 147 embryonic lethal genes previously identified in a systematic screen of Caenorhabditis elegans chromosome I. Over half gave defects in early processes such as meiosis, the assembly or position of the first mitotic spindle, cytokinesis, and proper nuclear positioning. For some phenotypic classes, the majority of genes are involved in a shared biochemical process. In addition, we identified loss-of-function phenotypes for genes of unknown function, but for which homologues exist in other organisms, shedding light on the function of these uncharacterized genes. When applied to the whole genome, this approach should identify the vast majority of genes required for early cell processes, paving the way for a greatly improved understanding of these processes and their regulation at the molecular level. ------------------- Key: 4812 Medline: 21376507 Authors: Salcini AE;Hilliard MA;Croce A;Arbucci S;Luzzi P;Tacchetti C;Daniell L;De Camilli P;Pelicci PG;Di Fiore PP;Bazzicalupo P Title: The Eps15 C. elegans homolog EHS-1 is implicated in synaptic vesicle recycling. Citation: Nature Cell Biology 3: 755-760 2001 Type: ARTICLE Genes: dyn-1 ehs-1 Abstract: Eps15 represents the prototype of a family of evolutionarily conserved proteins that are characterized by the presence of the EH domain, a protein-protein interaction module(1,2), and that are involved in many aspects of intracellular vesicular sorting(3). Although biochemical and functional studies have implicated Eps15 in endocytosis(4,5), its function in the endocytic machinery remains unclear. Here we show that the Caenorhabditis elegans gene, zk1248.3 (ehs-1), is the orthologue of Eps15 in nematodes, and that its product, EHS-1, localizes to synaptic-rich regions. ehs-l-impaired worms showed temperature-dependent depletion of synaptic vesicles and uncoordinated movement. These phenotypes could be correlated with a presynaptic defect in neurotransmission. Impairment of EHS-1 function in dyn-1(ky51) worms, which express a mutant form of dynamin and display a temperature-sensitive locomotion defects, resulted in a worsening of the dyn-1 phenotype and uncoordination at the permissive temperature. Thus, ehs-1 and dyn-1 interact genetically. Moreover, mammalian Eps15 and dynamin protein were shown to interact in vivo. Taken together, our results indicate that EHS-1 acts in synaptic vesicle recycling and that its function might be linked to that of dynamin. ------------------- Key: 4813 Medline: 21402918 Authors: Tsang WY;Sayles LC;Grad LI;Pilgrim DB;Lemire BD Title: Mitochondrial respiratory chain deficiency in Caenorhabditis elegans results in developmental arrest and increased life span. Citation: Journal of Biological Chemistry 276: 32240-32246 2001 Type: ARTICLE Genes: atp-2 daf-2 daf-7 nuo-1 mIn1 sDp3 qC1 Abstract: The growth and development of Caenorhabditis elegans are energy-dependent and rely on the mitochondrial respiratory chain (MRC) as the major source of ATP. The MRC is composed of similar to 70 nuclear, and 12 mitochondrial gene products. Complexes I and V are multisubunit proteins of the MRC. The nuo-1 gene encodes the NADH- and FAIN-binding subunit of complex I, the NADH-ubiquinone oxidoreductase. The atp-2 gene en. codes the active-site subunit of complex V, the ATP synthase. The nuo-1 (ua1) and atp-2(ua2) mutations are both lethal. They result in developmental arrest at the third larval stage (L3), arrest of gonad development at the second larval stage (L2), and impaired mobility, pharyngeal pumping, and defecation. Surprisingly, the nuo-1 and atp-2 mutations significantly lengthen the life spans of the arrested animals. When MRC biogenesis is blocked by chloramphenicol or doxycycline (inhibitors of mitochondrial translation), a quantitative and homogeneous developmental arrest as L3 larvae also results. The common phenotype induced by the mutations and drugs suggests that the L3-to-L4 transition may involve an energy-sensing developmental checkpoint. Since similar to 200 gene products are needed for MRC assembly and mtDNA replication, transcription, and translation, we predict that L3 arrest will be characteristic of mutations in these genes. ------------------- Key: 4814 Medline: 21340264 Authors: Chong H;Lee J;Guan KL Title: Positive and negative regulation of Raf kinase activity and function by phosphorylation. Citation: EMBO Journal 20: 3716-3727 2001 Type: ARTICLE Genes: lin-45 Abstract: Activating and inhibitory phosphorylation mechanisms play an essential role in regulating Raf kinase activity. Here we demonstrate that phosphorylation of C-Raf in the kinase activation loop (residues T491 and S494) is necessary, but not sufficient, for activation. C-Raf has additional activating phosphorylation sites at S338 and Y341. Mutating all four of these residues to acidic residues, S338D/Y341D/T491E/S494D (DDED), in C-Raf results in constitutive activity. However, acidic residue substitutions at the corresponding activation loop sites in B-Raf are sufficient to confer constitutive activity. B-Raf and C-Raf also utilize similar inhibitory phosphorylation mechanisms to regulate kinase activity. B-Raf has multiple inhibitory phosphorylation sites necessary for full kinase inhibition where C-Raf requires only one. We examined the functional significance of these inhibitory and activating phosphorylations in Caenorhabditis elegans lin-45 Raf. Eliminating the inhibitory phosphorylation or mimicking activating phosphorylation sites is sufficient to confer constitutive activity upon lin-45 Raf and induce multi-vulva phenotypes in C.elegans. Our results demonstrate that different members of the Raf family kinases have both common and distinct phosphorylation mechanisms to regulate kinase activity and biological ------------------- Key: 4815 Medline: Authors: Wagner A Title: Birth and death of duplicated genes in completely sequenced eukaryotes. Citation: Trends in Genetics 17: 237-239 2001 Type: REVIEW Genes: Abstract: Gene and genome duplications are commonly regarded as being of major evolutionary significance. But how often does gene duplication occur? And, once duplicated, what are the fates of duplicated genes? How do they contribute to evolution? In a recent article, Lynch and Conery analyze divergence between duplicate genes from six eukaryotic genomes. They estimate the rate of gene duplication, the rate of gene loss after duplication and the strength of selection experienced by duplicate genes. They conclude that although the rate of gene duplications is high, so is the rate of gene loss, and they argue that gene duplications could be a major factor in speciation. ------------------- Key: 4816 Medline: Authors: Rodaway A;Patient R Title: Mesendoderm: An ancient germ layer? Citation: Cell 105: 169-172 2001 Type: REVIEW Genes: ceh-22 med-1 med-2 pha-4 pie-1 pop-1 skn-1 Abstract: Formation of the three primary germ layers, ectoderm, mesoderm, and endoderm, is an early distinction between groups of cells in developing embryos. Our understanding of their generation in vertebrates has benefitted from the classical experiments of Nieuwkoop and his colleagues (referenced in Nieuwkoop, 1997), in which explants of tissue from the animal hemisphere of amphibian embryos (fated to form ectoderm) apposed to explants of vegetal tissue (fated to form endoderm) were induced to form mesoderm. These results have been widely interpreted as indicating that mesoderm forms at the interface between presumptive endoderm and presumptive ectoderm as a consequence of inductive signals from the former to the latter. However, recent data from nematodes and zebrafish suggest that endoderm and some portion of the mesoderm may derive from a bipotential layer of cells, called the mesendoderm. In addition, the genes involved in this ------------------- Key: 4817 Medline: Authors: Kenyon C Title: A conserved regulatory system for aging. Citation: Cell 105: 165-168 2001 Type: REVIEW Genes: akt-1 akt-2 daf-2 daf-12 daf-16 igf-1 pdk-1 sir-2 Abstract: While many processes in biology, such as cell differentiation and development, increase complexity, the aging process increases entropy and culminates in the death of the animal. Thus, the discovery that single gene mutations in many organisms can extend lifespan dramatically was surprising. These mutations indicated that the aging process is subject to regulation; it is not as random and haphazard as it seems. Even more surprising are some recent findings suggesting that a conserved system regulating lifespan may have arisen early in evolution. ------------------- Key: 4818 Medline: Authors: Stearns T Title: Centrosome duplication: a centriolar pas de deux. Citation: Cell 105: 417-420 2001 Type: REVIEW Genes: zyg-1 Abstract: The microtubule organizing center, or centrosome, is an unusual organelle. Unlike most organelles, it is not bounded by a membrane, yet it is distinct from the surrounding cytoplasm. It is at the center of important processes in animal and fungal cells, yet many plant cells completely lack it. And perhaps most perplexingly, the centrosome duplicates precisely once per cell cycle, yet the molecular mechanism of duplication remains obscure. ------------------- Key: 4819 Medline: 20525849 Authors: Lynch M;Conery JS Title: The evolutionary fate and consequences of duplicate genes. Citation: Science 290: 1151-1155 2001 Type: ARTICLE Genes: Abstract: Gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, but it is unclear how often gene duplicates arise and how frequently they evolve new functions. Observations from the genomic databases for several eukaryotic species suggest that duplicate genes arise at a very high rate, on average 0.01 per gene per million years. Most duplicated genes experience a brief period of relaxed selection early in their history, with a moderate fraction of them evolving in an effectively neutral manner during this period. However, the vast majority of gene duplicates are silenced within a few million years, with the few survivors subsequently experiencing strong purifying selection. Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new ------------------- Key: 4820 Medline: Authors: Espinosa F;Fleischhauer R;McMahon A;Joho RH Title: Dynamic interaction of S5 and S6 during voltage-controlled gating in a potassium channel. Citation: Journal of General Physiology 118: 157-169 2001 Type: ARTICLE Genes: exp-2 Abstract: A gain-of-function mutation in the Caenorhabditis elegans exp-2 K+-channel gene is caused by a cysteine-to-tyrosine change (C480Y) in the sixth transmembrane segment of the channel (Davis, M.W, R. Fleisch-hauer, J.A. Dent, R.H.Joho, and L. Avery. 1999. Science. 286:2501-2504). In contrast to wild-type EXP-2 channels, homotetrameric C480Y mutant channels are open even at - 160 mV, explaining the lethality of the homozygous mutant. We modeled the structure of EXP-2 on the 3-D scaffold of the K+ channel KcsA. In the C480Y mutant, tyrosine 480 protrudes from S6 to near S5, suggesting that the bulky side chain may provide steric hindrance to the rotation of S6 that has been proposed to accompany the open-closed state transitions (Perozo, E., D.M. Cortes, and L.G. Cuello. 1999. Science. 285:73-78). We tested the hypothesis that only small side chains at position 480 allow the channel to close, but that bulky side chains trap the channel in the open state. Mutants with small side chain substitutions (Gly and Ser) behave like wild type; in contrast, bulky side chain substitutions (Trp, Phe, Leu, Ile, Val, and His) generate channels that conduct K+ ions at potentials as negative as - 120 mV. The side chain at position 480 in S6 in the pore model is close to and may interact With a conserved glycine (G421) in S5. Replacement of G421 with bulky side chains also leads to channels that are trapped in an active state, suggesting that S5 and S6 interact with each other during voltage-dependent open-closed state transitions, and that bulky side chains prevent the dynamic changes necessary for permanent channel closing. Single-channel recordings show that mutant channels open frequently at negative membrane potentials indicating that they fail to reach long-lasting, i.e., stable, closed states. Our data support a "two-gate model" with a pore gate responsible for the brief, voltage-independent openings and a separately located, voltage-activated gate (Liu, Y, and R.H.Joho. 1998. Pflugers Arch. 435: 654-661). ------------------- Key: 4821 Medline: 11685900 Authors: Hashmi S;Tawe W;Lustigman S Title: Caenorhabditis elegans and the study of gene function in parasites. Citation: Trends in Parasitology 17: 387-393 2001 Type: REVIEW Genes: col-12 cpl-1 cpr-1 cpr-3 cpr-4 cpr-5 cpr-6 cpz-1 gcp-1 gpd-1 mif-1 mif-2 mif-3 pcp-1 pep-1 rol-6 Abstract: The free-living nematode Caenorhabditis elegans is a tractable experimental model system for the study of both vertebrate and invertebrate biology. Its most significant advantages are its simplicity, both in anatomy and in genomic organization, and the elaborate methods that have been developed to attribute function to previously uncharacterized genes. Importantly, > 40% of parasitic nematode genes exhibit high levels of homology to genes within the C. elegans genome. Studying such genes using the C. elegans model should yield new insights into key molecules and their possible implications in parasite survival, leading to the discovery of new drug targets and vaccine candidates. ------------------- Key: 4822 Medline: 21363829 Authors: Yashin AI;Cypser JR;Johnson TE;Michalski AI;Boyko SI;Novoseltsev VN Title: Ageing and survival after different doses of heat shock: the results of analysis of data from stress experiments with the nematode worm Caenorhabditis elegans. Citation: Mechanisms of Ageing & Development 122: 1477-1495 2001 Type: ARTICLE Genes: fer-15 spe-9 Abstract: Stress experiments performed on a population of sterilised nematode worms (Caenorhabditis elegans) show a clear hormesis effect after short exposure and clear debilitation effects after long exposure to heat shock. An intermediate duration of exposure results in a mixture of these two effects. In this latter case the survival curves for populations in the stress and control groups intersect. In this paper we develop an adaptation model of stress and apply it to the analysis of survival data from three such stress experiments. We show that the model can be used to explain empirical age-patterns of mortality and survival observed in these experiments. We discuss possible biological mechanisms involved in stress response and directions for further research. ------------------- Key: 4823 Medline: 21367732 Authors: Sugawara K;Morita K;Ueno N;Shibuya H Title: BIP, a BRAM-interacting protein involved in TGF-B signalling, regulates body length in Caenorhabditis Citation: Genes to Cells 6: 599-606 2001 Type: ARTICLE Genes: dbl-1 lon-1 Abstract: Background: The TGF-P superfamily has diverse biological activities and is involved in the early development of animals. We previously identified a novel family member, BMP receptor associated molecule (BRAM), which binds to the intracellular domain of BMP type IA receptor and is involved in the BMP signalling pathway. Results: To identify novel molecules involved in TGF-beta signalling pathways, we performed yeast two-hybrid screening using BRAM as bait. From a Xenopus cDNA library, we cloned a cDNA encoding 693 amino acids and containing the motif for an oxysterol binding protein (OSBP), which we designated BRAM interacting protein (BIP). We then isolated a BIP homologue from the Caenorhabditis elegans that encodes 733 amino acids and also contains the OSBP-like motif. Immunoprecipitation and Western blotting studies revealed that C. elegans BIP could interact with the C. elegans BRAM homologues BRA-1 and BRA-2. C. elegans BIP was expressed in pharyngeal muscle, hypodermis and several neuronal cells, an expression pattern overlaps with those of BRA-1 and BRA-2. Finally, we found that inhibition of BIP expression in C. elegans by double stranded RNA interference produces a Sma phenotype. Conclusions: BIP was isolated using the yeast two-hybrid systems. BIP may function in the TGF-beta pathway and regulate body length in C. elegans. ------------------- Key: 4824 Medline: Authors: Grandien K;Sommer RJ Title: Functional comparison of the nematode Hox gene lin-39 in C. elegans and P. pacificus reveals evolutionary conservation of protein function despite divergence of primary Citation: Genes & Development 15: 2161-2172 2001 Type: ARTICLE Genes: ced-3 lin-39 Abstract: Hox transcription factors have been implicated in playing a central role in the evolution of animal morphology. Many studies indicate the evolutionary importance of regulatory changes in Hox genes, but little is known about the role of functional changes in Hox proteins. In the nematodes Pristionchus pacificus and Caenorhabditis elegans, developmental processes can be compared at the cellular, genetic, and molecular levels and differences in gene function can be identified. The Hox gene Rn-39 is involved in the regulation of nematode vulva development. Comparison of known lin-39 mutations in P. pacificus and C. elegans revealed both conservation and changes of gene function. Here, we study evolutionary changes of Rn-39 function using hybrid transgenes and site-directed mutagenesis in an in vivo assay using C. elegans lin-39 mutants. Our data show that despite the functional differences of LIN-39 between the two species, Ppa-LIN-39, when driven by Cel-lin-39 regulatory elements, can functionally replace Cel-lin-39. Furthermore, we show that the MAPK docking and phosphorylation motifs unique for Cel-LIN-39 are dispensable for Cel-lin-39 functions therefore, the evolution of lin-39 function is driven by changes in regulatory elements rather than changes in the protein ------------------- Key: 4825 Medline: 21369529 Authors: Dozier C;Kagoshima H;Niklaus G;Cassata G;Burglin TR Title: The Caenorhabditis elegans Six/sine oculis class homeobox gene ceh-32 is required for head morphogenesis. Citation: Developmental Biology 236: 289-303 2001 Type: ARTICLE Genes: ceh-32 ceh-33 ceh-34 ceh-35 vab-3 Abstract: Caenorhabditis elegans has four members of the Six/sine oculis class of homeobox genes, ceh-32, ceh-33, ceh-34, and ceh-35. Proteins encoded by this gene family are transcription factors sharing two conserved domains, the homeodomain and the Six/sine oculis domain, both involved in DNA binding. ceh-32 expression was detected during embryogenesis in hypodermal and neuronal precursor cells and later in descendants of these cells as well as in gonadal sheath cells. RNAi inactivation studies suggest that ceh-32 plays a role in head morphogenesis, like vab-3, the C. elegans Pax-6 orthologue. ceh-32 and vab-3 are coexpressed in head hypodermal cells and ceh-32 mRNA levels are reduced in vab-3 mutants. Moreover, ectopic expression of VAB-3 in transgenic worms is able to induce ceh-32 ectopically. In addition, we demonstrate that VAB-3 is able to bind directly to the ceh-32 upstream regulatory region in vitro and to activate reporter gene transcription in a yeast one-hybrid system. Out results suggest that VAB-3 acts upstream of ceh-32 during head morphogenesis and directly induces ceh-32. Thus, ceh-32 appears to be the first target gene of VAB-3 identified so far. ------------------- Key: 4826 Medline: 21423415 Authors: Johnson AD;Fitzsimmons D;Hagman J;Chamberlin HM Title: EGL-38 Pax regulates the ovo-related gene lin-48 during Caenorhabditis elegans organ development. Citation: Development 128: 2857-2865 2001 Type: ARTICLE Genes: egl-38 lin-48 Abstract: The Pax gene egl-38 plays an important role in the development of several organs in C. elegans. To understand how a Pax transcription factor influences distinct developmental choices in different cells and tissue types, we have characterized a second gene, lin-48. lin-48 functions with egl-38 in the development of one structure, the hindgut, but not in other tissues such as the egg-laying system. We show that lin-48 encodes a C2H2 zinc-finger protein that is similar to the product of the Drosophila gene ovo and is expressed in the hindgut cells that develop abnormally in lin-48 mutants. We present evidence that lin-48 is a target for EGL-38 in hindgut cells. We show that lin-48 requires egl-38 for its expression in the hindgut. Using deletion analysis, we have identified two elements in the lin-48 promoter that are necessary for lin-48 expression. We demonstrate that EGL-38 binds with high affinity to one of these elements. In addition, we have observed genetic interactions between mutations in the lin-48 promoter and specific alleles of egl-38. These experiments demonstrate a functional link between Pax and Ovo transcription factors, and provide a model for how Pax transcription factors can regulate different target genes in different cells. ------------------- Key: 4827 Medline: Authors: Goodwin EB Title: Translational repression: Not just a Puf of smoke. Citation: Current Biology 11: R607-R609 2001 Type: REVIEW Genes: cpb-1 fbf-1 fbf-2 fem-3 nos-3 Abstract: Proteins containing Puf domains interact with cofactors to form complexes that bind RNAs and control diverse developmental events. Recent studies have shed light on how the Puf family of proteins regulates mRNA activity. ------------------- Key: 4828 Medline: Authors: Wendland B Title: Round-trip ticket: recycling to the plasma membrane requires RME-1. Citation: Nature Cell Biology 3: E133-E135 2001 Type: REVIEW Genes: rme-1 Abstract: The endosomal system includes distinct endocytic compartments where decisions are made that determine the destinations of extracellular and plasma membrane materials that have been internalized. A new family of proteins has been found that governs the exit of material from one of these endocytic organelles, the endosomal recycling compartment (ERC). ------------------- Key: 4829 Medline: Authors: George AL;Bianchi L;Link EM;Vanoye CG Title: From stones to bones: the biology of ClC channels. Citation: Current Biology 11: R620-R628 2001 Type: REVIEW Genes: clh-1 clh-2 clh-3 clh-4 clh-5 clh-6 Abstract: Chloride (Cl-) is the most abundant extracellular anion in multicellular organisms. Passive movement of Cl- through membrane ion channels enables several cellular and physiological processes including transepithelial salt transport, electrical excitability, cell volume regulation and acidification of internal and external compartments. One family of proteins mediating Cl- permeability, the CIC channels, has emerged as important for all of these biological processes. The importance of CIC channels has in part been realized through studies of inherited human diseases and genetically engineered mice that display a wide range of phenotypes from kidney stones to petrified bones. These recent findings have demonstrated many eclectic functions of CIC channels and have placed Cl- channels in the physiological limelight. ------------------- Key: 4830 Medline: 11389441 Authors: Lin SX;Grant B;Hirsh D;Maxfield FR Title: Rme-1 regulates the distribution and function of the endocytic recycling compartment in mammalian cells. Citation: Nature Cell Biology 3: 567-572 2001 Type: ARTICLE Genes: rme-1 Abstract: RME-1 is an Eps15-homology (EH)-domain protein that was identified in a genetic screen for endocytosis gene in Caenorhabditis elegans. When expressed in a CHO cell line, the worm RME-1 protein and a mouse homologue are both associated with the endocytic recycling compartment. Here we show that expression of a dominant-negative construct with a point mutation near the EH domain results in redistribution of the endocytic recycling compartment and slowing down of transferrin receptor recycling. The delivery of a TGN38 chimaeric protein to the trans-Golgi network is also slowed down. The function of Rme-1 in endocytic recycling is evolutionarily conserved in metazoans as shown by the protein's properties in C. ------------------- Key: 4831 Medline: 11481446 Authors: Caplen NJ;Parrish S;Imani F;Fire A;Morgan RA Title: Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate Citation: Proceedings of the National Academy of Sciences USA 98: 9742-9747 2001 Type: ARTICLE Genes: unc-22 Abstract: Short interfering RNAs (siRNAs) are double-stranded RNAs of approximate to 21-25 nucleotides that have been shown to function as key intermediaries in triggering sequence-specific RNA degradation during posttranscriptional gene silencing in plants and RNA interference in invertebrates. siRNAs have a characteristic structure, with 5'-phosphate/3'-hydroxyl ends and a 2-base 3' overhang on each strand of the duplex. In this study, we present data that synthetic siRNAs can induce gene-specific inhibition of expression in Caenorhabditis elegans and in cell lines from humans and mice. In each case, the interference by siRNAs was superior to the inhibition of gene expression mediated by single-stranded antisense oligonucleotides. The siRNAs seem to avoid the well documented nonspecific effects triggered by longer double-stranded RNAs in mammalian cells. These observations may open a path toward the use of siRNAs as a reverse genetic and therapeutic tool in mammalian cells. ------------------- Key: 4832 Medline: 11514443 Authors: Chen PJ;Cho S;Jin SW;Ellis RE Title: Specification of germ cell fates by FOG-3 has been conserved during nematode evolution. Citation: Genetics 158: 1513-1525 2001 Type: ARTICLE Genes: fog-3 Abstract: Rapid changes in sexual traits are ubiquitous in evolution. To analyze this phenomenon, we are studying species of the genus Caenorhabditis. These animals use one of two different mating systems-male/ hermaphroditic, like the model organism Caenorhabditis elegans, or male/female, like C. remanei. Since hermaphrodites are essentially females that produce sperm for self-fertilization, elucidating the control of cell fate in the germ line in each species could provide the key to understanding how these mating systems evolved. In C. clegans, FOG-3 is required to specify that germ cells become sperm. Thus, we cloned its homologs from both C. remanei and C. briggsae. Each species produces a single homolog of FOG-3, and RNA-mediated interference indicates that FOG-3 functions in each species to specify that germ cells develop as sperm rather than as oocytes. What factors account for the different mating systems? Northern analyses and RT-PCR data reveal that the expression of fog-3 is always correlated with spermatogenesis. Since the promoters for all three fog-3 genes contain binding sites for the transcription factor TRA-1A and are capable of driving expression of fog-3 in C elegans hermaphrodites, we propose that alterations in the upstream sex-determination pathway, perhaps acting through TRA-1A, allow spermatogenesis in C. elegans and C. briggsae ------------------- Key: 4833 Medline: 21423416 Authors: Koh K;Rothman JH Title: ELT-5 and ELT-6 are required continuously to regulate epidermal seam cell differentiation and cell fusion in C. elegans. Citation: Development 128: 2867-2880 2001 Type: ARTICLE Genes: elt-1 elt-3 elt-5 elt-6 nhr-72 nhr-73 nhr-74 nhr-75 nhr-77 nhr-81 nhr-82 nhr-89 unc-119 Abstract: The C. elegans epidermis is a simple epithelium comprised of three major cell types, the seam, syncytial and P cells. While specification of all major epidermal cells is known to require the ELT-1 GATA transcription factor, little is known about how the individual epidermal cell types are specified. We report that elt-5 and -6, adjacent genes encoding GATA factors, are essential for the development of the lateral epidermal cells, the seam cells. Inhibition of elt-5 and -6 function by RNA-mediated interference results in penetrant late embryonic and early larval lethality. Seam cells in affected animals do not differentiate properly: the alae, seam-specific cuticular structures, are generally absent and expression of several seam-specific markers is blocked. In addition, elt-3, which encodes another GATA factor normally expressed in non-seam epidermis, is often ectopically expressed in the seam cells of affected animals, demonstrating that ELT-5 and -6 repress elt-3 expression in wild-type seam cells. Seam cells in affected animals often undergo inappropriate fusion with the epidermal syncytia. interference of elt-5 and -6 function during larval development can cause fusion of all seam cells with the surrounding syncytia and pronounced defects in molting. elt-5 and -6 are both expressed in seam cells and many other cells, and are apparently functionally interchangeable. Their expression is controlled by separable tissue-specific regulatory elements and the apportionment of monocistronic versus dicistronic transcription of both genes appears to be subject to cell-type-specific regulation. Collectively, these findings indicate that elt-5 and -6 function continuously throughout C. elegans development to regulate ------------------- Key: 4834 Medline: 21405065 Authors: Ueda T;Katsuzaki H;Terami H;Ohtsuka H;Kagawa H;Murase T;Kajiwara Y;Yoshioka O;Iio T Title: Calcium-bindings of wild type and mutant troponin Cs of Caenorhabditis elegans. Citation: Biochemica et Biophysica Acta-Protein Structure & Molecular Enzymology 1548: 220-228 2001 Type: ARTICLE Genes: Abstract: Apparent Ca2+-binding constant (K-app) of Caenorhabditis elegans troponin C (CeTnC) was determined by a fluorescence titration method. The K-app of the N-domain Ca2+-binding site of CeTnC was 7.9 +/- 1.6 x 10(5) M-1 and that of the C-domain site was 1.2 +/- 0.6 x 10(6) M-1, respectively. Mg2+-dependence of the K-app showed that both Ca2+-binding sites did not bind competitively Mg2+. The Ca2+ dissociation rate constant (k(off)) of CeTnC was determined by the fluorescence stopped-flow method. The k(off) of the N-domain Ca2+-binding site of CeTnC was 703 +/- 208 s(-1) and that of the C-domain site was 286 +/- 33 s(-1), respectively. From these values we could calculate the Ca2+-binding rate constant (k(on)) as to be 5.6 +/- 2.8 x 10(8) M-1 s(-1) for the N-domain site and 3.4 +/- 2.1 x 10(8) M (1) s(-1) for the C-domain site, respectively. These results mean that all Ca2+-binding sites of CeTnC are low affinity, fast dissociating and Ca2+-specific sites. Evolutional function of TnC between vertebrate and invertebrate and biological functions of wild type and ------------------- Key: 4835 Medline: Authors: Ghenea S;Takeuchi M;Motoyama J;Sasamoto K;Kunau W-H;Kamiryo T;Bun-ya M Title: The cDNA sequence and expression of the AAA-family peroxin genes pex-1 and pex-6 from the nematode Caenorhabditis elegans. Citation: Zoological Science 18: 675-681 2001 Type: ARTICLE Genes: pex-1 pex-6 Abstract: We cloned cDNAs encoding two peroxins, PEX-1 and PEX-6, of the nematode Caenorhabditis elegans. Peroxins are proteins that play essential roles in peroxisome biogenesis and are encoded by pex genes. Among the peroxins, PEX-1 and PEX-6 constitute the subfamily 2 of AAA (ATPases associated with diverse cellular activities) proteins. Each cDNA agreed well with the respective mRNA in size (3.4 kb for pex-1 and 2.3 kb for pex-6) and did not carry any spliced leader sequence. The pex-1 cDNA was composed of 24 exons, which were encoded by a genomic region containing three open reading frames (ORFs), c11h1.4, c11h1.5, and c11h1.6; the predicted ORF c11h1.5 was encompassed in the 15th intron. Although many exon-intron borders in pex-1 were inconsistent with those predicted for c11h1.4 and c11h1.6, those in pex-6 coincided with those for the ORF f39g3.7. The pex-1 and pex-6 genes encoded proteins with 996 and 720 amino acid residues, respectively. Both pex-1 mRNA and pex-6 mRNA were detectable mainly in intestinal cells throughout the life cycle of C. elegans. ------------------- Key: 4836 Medline: 21432025 Authors: Brockie PJ;Mellem JE;Hills T;Madsen DM;Maricq AV Title: The C. elegans glutamate receptor subunit NMR-1 is required for slow NMDA-activated currents that regulate reversal frequency during locomotion. Citation: Neuron 31: 617-630 2001 Type: ARTICLE Genes: glr-1 nmr-1 Abstract: The N-methyl-D-aspartate (NMDA) subtype of glutamate receptor is important for synaptic plasticity and nervous system development and function. We have used genetic and electrophysiological methods to demonstrate that NMR-1, a Caenorhabditis elegans NMDA-type ionotropic glutamate receptor subunit, plays a role in the control of movement and foraging behavior. nmr-1 mutants show a lower probability of switching from forward to backward movement and a reduced ability to navigate a complex environment. Electrical recordings from the interneuron AVA show that NMDA-dependent currents are selectively disrupted in nmr-1 mutants. We also show that a slowly desensitizing variant of a non-NMDA receptor can rescue the nmr-1 mutant phenotype. We propose that NMDA receptors in C. elegans provide long-lived currents that modulate the frequency of movement reversals during foraging behavior. ------------------- Key: 4837 Medline: 21429431 Authors: Bessereau J-L;Wright A;Williams DC;Schuske K;Davis MW;Jorgensen EM Title: Mobilization of a Drosophila transposon in the Caenorhabditis elegans germ line. Citation: Nature 413: 70-74 2001 Type: ARTICLE Genes: glh-2 gpa-2 myo-2 rol-6 unc-49 unc-122 Abstract: Transposons have been enormously useful for genetic analysis in both Drosophila and bacteria. Mutagenic insertions constitute molecular tags that are used to rapidly clone the mutated gene. Such techniques would be especially advantageous in the nematode Caenorhabditis elegans, as the entire sequence of the genome has been determined. Several different types of endogenous transposons are present in C. elegans, and these can be mobilized in mutator strains (reviewed in ref. 1). Unfortunately, use of these native transposons for regulated transposition in C. elegans is limited. First, all strains contain multiple copies of these transposons and thus new insertions do not provide unique tags. Second, mutator strains tend to activate the transposition of several classes of transposons, so that the type of transposon associated with a particular mutation is not known. Here we demonstrate that the Drosophila mariner element Mos1 can be mobilized in C. elegans. First, efficient mobilization of Mos1 is possible in somatic cells. Second, heritable insertions of the transposon can be generated in the germ line. Third, genes that have been mutated by insertion can be rapidly identified using inverse polymerase chain reaction. Fourth, these insertions can subsequently be remobilized to generate deletion and ------------------- Key: 4838 Medline: 11514616 Authors: Zhao H;Nonet ML Title: A conserved mechanism of synaptogyrin localization. Citation: Molecular Biology of the Cell 12: 2275-2289 2001 Type: ARTICLE Genes: aex-3 dpy-23 rab-3 rbf-1 snb-1 sng-1 unc-11 unc-26 unc-104 Abstract: We have studied the localization of synaptogyrin family members in vivo. Both native and green fluorescent protein (GFP)-tagged Caenorhabditis elegans synaptogyrin (SNG-1) are expressed in neurons and synaptically localized. Deletion and mutational analysis with the use of GFP-tagged SNG-1 has defined a 38 amino acid sequence within the C terminus of SNG-1 and a single arginine in the cytoplasmic loop between transmembrane domain 2 and 3 that are required for SNG-1 localization. These domains may represent components of signals that target synaptogyrin for endocytosis from the plasma membrane and direct synaptogyrin to synaptic vesicles, respectively. In chimeric studies, these regions were sufficient to relocalize cellugyrin, a nonneuronal form of synaptogyrin, from nonsynaptic regions such as the sensory dendrites and the cell body to synaptic vesicles. Furthermore, GFP-tagged rat synaptogyrin is synaptically localized in neurons of C. elegans and in cultured hippocampal neurons. Similarly, the C-terminal domain of rat synaptogyrin is necessary for localization in hippocampal neurons. Our study suggests that the mechanisms for synaptogyrin localization are likely to be conserved from C. elegans to vertebrates. ------------------- Key: 4839 Medline: 21408176 Authors: Westmoreland JJ:McEwen J;Moore BA;Jin Y;Condie BG Title: Conserved function of Caenorhabditis elegans UNC-30 and mouse Pitx2 in controllig GABAergic neuron differentiation. Citation: Journal of Neuroscience 21: 6810-6819 2001 Type: ARTICLE Genes: unc-25 unc-30 Abstract: We are taking a cross-species approach to identify genes that are required for mammalian GABAergic neuron differentiation. On the basis of homeodomain similarity, the vertebrate Pitx genes appear to be orthologs of unc-30, a Caenorhabditis elegans gene necessary for differentiation of the GABAergic phenotype of type D neurons. One of the Pitx genes, Pitx2, is expressed in regions of GABAergic neurogenesis in the mammalian brain. These observations led us to test the functional conservation of the mouse Pitx2 and worm unc-30 genes using a rescue assay. Pitx2 rescues the GABAergic differentiation defect and partially rescues the axon guidance and behavioral phenotypes of unc-30 mutants, indicating a high degree of functional conservation between these evolutionarily related genes. Previous studies show that UNC-30 directly regulates the unc-25/glutamate decarboxylase gene that encodes the enzyme for GABA synthesis. We find that the promoter regions of the mouse and human genes coding for the 67 kDa glutamate decarboxylase (Gad1) also contain binding sites matching the UNC-30/Pitx2 consensus binding site sequence. We show that these sites specifically bind to Pitx2 protein in vitro and that in transfected neuroblastoma cells, the Pitx2 binding sites contribute to the basal activity of the Gad1 promoter. Furthermore, in cotransfection experiments, we find that Pitx2 strongly activates the Gad1 promoter. These results indicate that Pitx2 may regulate Gad1 expression in mammals, suggesting a new role for this key developmental transcription factor as a regulator of GABAergic differentiation during mammalian neural development. Our results suggest that some of the mechanisms regulating GABAergic differentiation are ------------------- Key: 4840 Medline: 11502758 Authors: Chen L;Ong B;Bennett V Title: LAD-1, the Caenorhabditis elegans L1CAM homologue, participates in embryonic and gonadal morphogenesis and is a substrate for fibroblast growth factor receptor pathway-dependent phosphotyrosine-based Citation: Journal of Cell Biology 154: 841-855 2001 Type: ARTICLE Genes: egl-15 lad-1 kin-8 let-23 unc-44 vab-1 eDf18 eDf19 nDf41 stDf7 stDf8 Abstract: This study shows that L1-like adhesion (LAD-1), the sole Caenorhabditis elegans homologue of the L1 family of neuronal adhesion molecules, is required for proper development of the germline and the early embryo and embryonic and gonadal morphogenesis. In addition, the ubiquitously expressed LAD-1, which binds to ankyrin-G, colocalizes with the C. elegans ankyrin, UNC-44, in multiple tissues at sites of cell-cell contact. Finally, we show that LAD-1 is phosphorylated in a fibroblast growth factor receptor (FGFR) pathway-dependent manner on a tyrosine residue in the highly conserved ankyrin-binding motif, FIGQY, which was shown previously to abolish the L1 family of cell adhesion molecule (L1 CAM) binding to ankyrin in cultured cells. Immunofluorescence studies revealed that FIGQY-tyrosine-phosphorylated LAD-1 does not colocalize with nonphosphorylated LAD-1 or UNC-44 ankyrin but instead is localized to sites that undergo mechanical stress in polarized epithelia and axon-body wall muscle junctions. These findings suggest a novel ankyrin-independent role for LAD-1 related to FGFR signaling. Taken together, these results indicate that L1CAMs constitute a family of ubiquitous adhesion molecules, which participate in tissue morphogenesis and ------------------- Key: 4841 Medline: 11514595 Authors: Edens WA;Sharling L;Cheng G;Shapira R;Kinkade JM;Lee T;Edens HA;Tang X;Sullards C;Flaherty DB;Benian GM;Lambeth Title: Tyrosine cross-linking of extracellular matrix is catalyzed by Duox, a multidomain oxidase/peroxidase with homology to the phagocyte oxidase subunit gp91 phox. Citation: Journal of Cell Biology 154: 879-891 2001 Type: ARTICLE Genes: bli-1 bli-2 col-2 col-6 col-14 col-17 col-35 col-36 col-37 col-41 dpy-2 dpy-7 dpy-10 dpy-13 rol-6 rol-8 sqt-1 sqt-3 Abstract: High molecular weight homologues of gp91 phox, the superoxide-generating subunit of phagocyte nicotinamide adenine dinucleotide phosphate (NADPH)-oxidase, have been identified in human (h) and Caenorhahditis elegans (Ce), and are termed Duox for "dual oxidase" because they have both a peroxidase homology domain and a gp91 phox domain. A topology model predicts that the enzyme will utilize cytosolic NADPH to generate reactive oxygen, but the function of the ecto peroxidase domain was unknown. Ce-Duox1 is expressed in hypodermal cells underlying the cuticle of larval animals. To investigate function, RNA interference (RNAi) was carried out in C. elegans. RNAi animals showed complex phenotypes similar to those described previously in mutations in collagen biosynthesis that are known to affect the cuticle, an extracellular matrix. Electron micrographs showed gross abnormalities in the cuticle of RNAi animals. In cuticle, collagen and other proteins are cross-linked via di- and trityrosine linkages, and these linkages were absent in RNAi animals. The expressed peroxidase domains of both Ce-Duox1 and h-Duox showed peroxidase activity and catalyzed crosslinking of free tyrosine ethyl ester. Thus, Ce-Duox catalyzes the cross-linking of tyrosine residues involved in the ------------------- Key: 4842 Medline: 11441002 Authors: Oka T;Toyomura T;Honjo K;Wada Y;Futai M Title: Four subunit alpha isoforms of Caenorhabditis elegans vacuolar H+-ATPase - Cell-specific expression during development. Citation: Journal of Biological Chemistry 276: 33079-33085 2001 Type: ARTICLE Genes: unc-32 vha-1 vha-2 vha-3 vha-4 vha-5 vha-6 vha-7 vha-8 vha-11 Abstract: We have identified four genes (vha-5, vha-6, vha-7, and unc-32) coding for vacuolar-type proton-translocating ATPase (V-ATPase) subunit a in Caenorhabditis elegans, the first example of four distinct isoforms in eukaryotes. Their products had nine putative transmembrane regions, exhibited 43-60% identity and 62-84% similarity with the bovine subunit al isoform, and retained 11 amino acid residues essential for yeast V-ATPase activity (Leng, X. H., Manolson, M. F., and Forgac, M. (1998) J. Biol. Chem. 273, 6717-6723). The similarities, together with the results of immunoprecipitation, suggest that these isoforms are components of V-ATPase. Transgenic and immunofluorescence analyses revealed that these genes were strongly expressed in distinct cells; vha-5 was strongly expressed in an H-shaped excretory cell, vha-6 was strongly expressed in intestine, vha-7 was strongly expressed in hypodermis, and unc-32 was strongly expressed in nerve cells. Furthermore, the vha-7 and unc-32 genes were also expressed in the uteri of hermaphrodites. RNA interference analysis showed that the double-stranded RNA for unc-32 caused embryonic lethality similar to that seen with other subunit genes (vha-1, vha-4, and vha-11) (Oka, T., and Futai, M. (2000) J. Biol. Chem. 275, 29556-29561). The progenies of worms injected with the vha-5 or vha-6 double-stranded RNA became died at a specific larval stage, whereas the vha-7 double-stranded RNA showed no effect on development. These results suggest that V-ATPases with these isoforms generate acidic compartments essential for ------------------- Key: 4843 Medline: Authors: Kawamura K;Funabashi Y;Morita S;Omata K;Oshio K;Osana Y;Oka K Title: Does a randomly organized electrical circuit function as a neuronal system? Citation: Japanese Journal of Applied Physics Part 1 40: 2095-2099 2001 Type: ARTICLE Genes: Abstract: It is argued that a randomly fabricated electric circuit functions as an information processor. Indeed, the neuronal system of Caenorhabditis elegans (C. elegans) is a random network which processes various information for the survival of the worm. After properties of the connectivity of the neuronal system of the worm are reviewed to emphasize its randomness, it is confirmed that a network of resistors, which is topologically homologous to the neuronal network of C. elegans, can encode a decision table which is similar to the decision table of the native responses of the worm. Some structural properties, which are advantageous for the functioning of a random resistor network for an information processor, are discussed. In addition, it is suggested that a network of resistors with these propeties is a bundle of intertwisted wires connected ------------------- Key: 4844 Medline: 21426454 Authors: Delattre M;Felix MA Title: Microevolutionary studies in nematodes: a beginning. Citation: BioEssays 23: 807-819 2001 Type: REVIEW Genes: Abstract: Comparisons between related species often allow the detailed genetic analysis of evolutionary processes. Here we advocate the use of the nematode Caenorhabditis elegans (and several other rhabditid species) as model systems for microevolutionary studies. Compared to Drosophila species, which have been a mainstay of such studies, C. elegans has a self-fertilising mode of reproduction, a shorter life cycle and a convenient cell-level analysis of phenotypic variation. Data concerning its population genetics and ecology are still scarce, however. We review molecular, behavioral and developmental intraspecific polymorphisms for populations of C. elegans, Oscheius sp. 1 and Pristionchus pacificus. Focusing on vulval development, which has been well characterized in several species, we discuss relationships between patterns of variations: (1) for a given genotype (developmental variants), (2) after mutagenesis (mutability), (3) in different populations of the same species (polymorphisms) and (4) between closely related species. These studies have revealed that evolutionary variations between sister species affect those characters that show phenotypic developmental variants, that are mutable and that are polymorphic within species. ------------------- Key: 4845 Medline: 21402350 Authors: Takahashi M;Asaumi S;Honda S;Suzuki Y;Nakai D;Kuroyanagi H;Shimizu T;Honda Y;Shirasawa T Title: Mouse coq7/clk-1 orthologue rescued slowed rhythmic behavior and extended life span of clk-1 longevity mutant in Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 286: 534-540 2001 Type: ARTICLE Genes: clk-1 rol-6 Abstract: The coq7/clk-1 gene was isolated from the long-lived mutant of Caenorhabditis elegans and was suggested to play a regulatory role in biological rhythm and longevity. The mouse COQ7 is homologous to Saccharomyces cerevisiae COQ7/CAT5 that is required for the biosynthesis of coenzyme Q (ubiquinone), an essential messenger in mitochondrial respiration. In the present study, we characterized the expression and processing of mouse COQ7. We found that COQ7 is highly expressed in tissues with high energy demand such as heart, muscle, liver, and kidney in mice. Biochemical analysis revealed that COQ7 is targeted to mitochondria where it is processed to mature form. Transgenic expression of mouse coq7 completely rescued the slowed rhythmic behaviors of clk-1 such as defecation. In life-span analysis, transgenic expression reverted the extended life span of clk-1 to the comparable level with wild-type control. These data strongly suggested that coq7 plays a pivotal role in the regulation of biological rhythms and the determination of life span in mammalian species. ------------------- Key: 4846 Medline: 11444042 Authors: Gonczy P;Grill S;Stelzer EHK;Kirkham M;Hyman AA Title: Spindle positioning during the asymmetric first cell division of Caenorhabditis elegans embryos. Citation: Novart Foundation 237: 164-181 2001 Type: ARTICLE Genes: par-1 par-2 par-3 par-6 zyg-8 Abstract: Cell division during development in many cases generates daughter cells that differ not only in fate, but also in size. We investigate the mechanisms that ensure proper spindle positioning during such asymetric divisions using the one-cell stage Caenorhabitis elegans embryo model system. We utilized a UV laser microbeam as an in vivo microtubule-serving device to probe the forces driving spindle postioning. Our results indicate that extra-spindle pulling forces acting on the posterior spindle pole appear more extensive than those acting on the anterior one, thus explaining the overall posterior spindle displacement that leads to the asymmetric division of the wild-type one-cell embryo. In seperate work, we analysed a locus called zyg-8, which plays a key role in ensuring proper spindle postioning. Our data show thatt zyg-8 locus in the course of a large scale RNAi-based functional genomics screeen. ZYG-8 harbours two notable protein domains: Ca2+/calmoduling-dependent kinase domain, and a domain related to doublecorting, a human microtubule-associated protein involved in neuronal migration. ------------------- Key: 4847 Medline: 11444045 Authors: Ambros V Title: The temporal control of cell cycle and cell fate in Caenorhabditis elegans. Citation: Novart Foundation 237: 203-220 2001 Type: REVIEW Genes: cdk-1 cki-1 cki-2 cul-1 cul-2 cyd-1 daf-12 let-23 lin-3 lin-12 lin-14 lin-28 lin-29 lin-35 ncc-1 Abstract: The nematode Caenorhabditis elegans develops through two major phases: the first phase, embyrogenesis, consists of a rapid series of cleavage cell divisions leading to morphogenesis of a first stage larva. The second phase is postembryonic development, which consists of developmentally regulated cell cycles that occur during the four larval stages leading to the adult. Precursor cells set aside during embryogenesis divide through stereotypical cell lineage patterns during the four larval stages to generate larval and adult structures. The precise timing of the postembryonic cell divisions is under strict control, in most cases with a developmentally regulated G1. In certain postembryonic cell lineages, various aspects of the cell division cycle, including cell cycle exit, or G1/S progression, are controlled by temporal regulatory genes of the heterochronic gene pathway. Heterochronic genes also control the timing of numerous other developmental events, indicating that this pathway functions to coordinate the schedule of cell division and cellular differentiation throughout the animal. Some choices of cell fate that occur in response to inductive or lateral signals are linked to cell cycle progression, suggesting that cell cycle phase can confer a critical period for developmental potential in certain cells. ------------------- Key: 4848 Medline: 11555413 Authors: Harris TW;Schuske K;Jorgensen EM Title: Studies of synaptic vesicle endocytosis in the nematode C. elegans. Citation: Traffic 2: 597-605 2001 Type: ARTICLE Genes: dpy-23 dyn-1 ehs-1 snt-1 unc-11 unc-26 unc-41 Abstract: After synaptic vesicle exocytosis, synaptic vesicle proteins must be retrieved from the plasma membrane, sorted away from other membrane proteins, and reconstituted into a functional synaptic vesicle. The nematode Caenorhabditis elegans is an organism well suited for a genetic analysis of this process. In particular, three types of genetic studies have contributed to our understanding of synaptic vesicle endocytosis. First, screens for mutants defective in synaptic vesicle recycling have identified new proteins that function specifically in neurons. Second, RNA interference has been used to quickly confirm the roles of known proteins in endocytosis. Third, gene targeting techniques have elucidated the roles of genes thought to play modulatory or subtle roles in synaptic vesicle recycling. We describe a molecular model for synaptic vesicle recycling and discuss how protein disruption experiments in C. elegans have contributed to this model. ------------------- Key: 4849 Medline: 21424801 Authors: Kim SK Title: HTTP://C. elegans: Mining the functional genomic landscape. Citation: Nature Reviews Genetics 2: 681-689 2001 Type: REVIEW Genes: Abstract: Caenorhabditis elegans is a powerful animal model for the study of functional genomics. The completed and well-annotated DNA sequence is available and a systematic study of gene function by RNA-interference-mediated knockdown of every gene is in progress. Full-genome DNA microarrays and DNA chips can be used to determine expression changes at different stages of development and in different mutant backgrounds, and a protein-interaction map based on the yeast two-hybrid approach is in progress. These high-capacity approaches to studying gene function will provide new insights into invertebrate and vertebrate biology. ------------------- Key: 4850 Medline: 21424802 Authors: Rougvie AE Title: Control of developmental timing in animals. Citation: Nature Reviews Genetics 2: 690-701 2001 Type: REVIEW Genes: alg-1 alg-2 col-17 col-19 daf-12 dcr-1 let-7 lin-4 lin-14 lin-28 lin-29 lin-41 lin-42 lin-46 lin-58 Abstract: The molecular mechanisms that time development are now being deciphered in various organisms, particularly in Caenorhabditis elegans. Key recent findings indicate that certain C. elegans timekeeping genes are conserved across phyla, and their developmental expression patterns indicate that a timing function might also be conserved. Small regulatory RNAs have crucial roles in the timing mechanism, and the cellular machinery required for production of these RNAs intersects with that used to process double-stranded RNAs during RNA interference. ------------------- Key: 4851 Medline: 21435989 Authors: Masler EP;Kovaleva ES;Sardanelli S Title: Aminopeptidase-like activities in Caenorhabditis elegans and the soybean cyst nematode, Heterodera glycines. Citation: Journal of Helminthology 75: 267-272 2001 Type: ARTICLE Genes: Abstract: Aminopeptidase-like activities in crude whole body extracts of the free-living nematode Caenorhabditis elegans and the plant parasitic soybean cyst nematode Heterodera glycines were examined. General characteristics including pH optima, heat lability, and inactivation of enzyme by organic solvent were the same for the two species. All developmental stages of H. glycines exhibited activity. In older females, activity was present primarily in the eggs. Affinity for the substrate L-alanine-4-nitroanilide was the same regardless of the stage examined, and was similar for the two species (K-m = 2.3 +/- 0.3 mm for C. elegans and 2.9 +/- 0.2 mM for H. glycines). Nearly all (> 95%) of C. elegans aminopeptidase-like activity was present in the soluble fraction of the extract, while H. glycines activity was distributed between the soluble and membrane fractions. Specific activities of the soluble enzymes were highest in C. elegans and H. glycines juveniles. The C. elegans enzyme was susceptible to a number of aminopeptidase inhibitors, particularly to amastatin and leuhistin, each of which inhibited aminopeptidase-like activity more than 90% at 90 mum. In H. glycines, aminopeptidase-like activity was inhibited 39% by amastatin at 900 muM. The apparent molecular weight of the soluble C. elegans enzyme is 70-80 kDa. Some activity in H. glycines is present in the 70-80 kDa range, but most activity (80-90%) is associated with a very high molecular weight (> 240 kDa) component. ------------------- Key: 4852 Medline: 11898851 Authors: Tavernarakis N;Driscoll M Title: Mechanotransduction in Caenorhabditis elegans - The role of DEG/ENaC ion channels. Citation: Cell Biochemistry and Biophysics 35: 1-18 2001 Type: REVIEW Genes: deg-1 del-1 flr-1 mec-4 mec-10 unc-8 unc-105 Abstract: One of the looming mysteries in signal transduction today is the question of how mechanical signals, such as pressure or mechanical force delivered to a cell, are interpreted to direct biological responses. All living organisms, and probably all cells, have the ability to sense and respond to mechanical stimuli. At the single-cell level, mechanical signaling underlies cell-volume control and specialized responses such as the prevention of poly-spermy in fertilization. At the level of the whole organism, mechanotransduction underlies processes as diverse as stretch-activated reflexes in vascular epithelium and smooth muscles; gravitaxis and turgor control in plants; tissue development and morphogenesis; and the senses of touch, hearing, and balance. Intense genetic, molecular, and electrophysiological studies in organisms ranging from nematodes to mammals have highlighted members of the recently discovered DEG/ENaC family of ion channels as strong candidates for the elusive metazoan mechanotransducer. Here, we discuss the evidence that links DEG/ENaC ion channels to mechanotransduction and review the function of Caenorhabditis elegans members of this family called degenerins and their role in mediating mechanosensitive behaviors in the worm. ------------------- Key: 4853 Medline: 11688559 Authors: Kwon JY;Lee J Title: Biological significance of a universally conserved transcription mediator in metazoan developmental signaling pathways. Citation: Development 128: 3095-3104 2001 Type: ARTICLE Genes: let-23 let-60 let-332 let-339 let-343 let-346 let-404 let-425 let-438 let-442 let-468 lin-3 med-6 pal-1 rde-1 sop-1 nDf32 sDf20 sDf30 Abstract: Transcription mediators are known to be required for regulated transcription in yeast and higher eukaryotes. However, little is known about the specific roles of mediators in vivo during development. In this report, we have characterized the biological functions of the C elegans gene med-6, which is the homolog of the yeast mediator med-6. We first identified a genetic mutation in the med-6 gene by comparing genetic and physical maps and determining the molecular lesion. Next, we demonstrated that med-6 plays an important role in metazoan development by regulating the transcription of genes in evolutionarily conserved signaling pathways. We showed that med-6 is involved in the transcription of genes of the Ras pathway by showing that med-6 RNAi suppressed phenotypes associated with gain-of-function alleles of let-23 and let-60, and enhanced those associated with a reduction-of-function allele of lin-3. We also found that med-6 is involved in male ray development, which is partly mediated by the Wnt pathway. As MED-6 is universally conserved, including in yeast, and the mediator-related proteins that function in vulval and male ray development are metazoan specific, our results suggest the role of med-6 as a point of convergence where signals transmitted through metazoan-specific mediator-related proteins meet. In addition, RNAi experiments in rde-1 background showed that maternal and zygotic med-6 activities have distinct roles in ------------------- Key: 4854 Medline: 11553327 Authors: Barr MM;DeModena J;Braun D;Nguyen CQ;Hall DH;Sternberg PW Title: The Caenorhabditis elegans autosomal dominant polycystic kidney disease gene homologs lov-1 and pkd-2 act in the same pathway. Citation: Current Biology 11: 1341-1346 2001 Type: ARTICLE Genes: lov-1 pkd-2 Abstract: Autosomal dominant polycystic kidney disease (ADPKD) strikes 1 in 1000 individuals and often results in end-stage renal failure. Mutations in either PKD1 or PKD2 account for 95% of all cases [1 -3]. It has recently been demonstrated that polycystin-1 and polycystin-2 (encoded by PKD1 and PKD2, respectively) assemble to form a cation channel in vitro [4]. Here we determine that the Caenorhabditis elegans PKD1 and PKD2 homologs, lov-1 [5] and pkd-2, act in the same pathway in vivo. Mutations in either lov-1 or pkd-2 result in identical male sensory behavioral defects. Also, pkd-2;lov-1 double mutants are no more severe than either of the single mutants, indicating that lov-1 and pkd-2 act together. LOV-1::GFP and PKD-2::GFP are expressed in the same male-specific sensory neurons and are concentrated in cilia and cell bodies. Cytoplasmic, nonnuclear staining in cell bodies is punctate, suggesting that one pool of PKD-2 is localized to intracellular membranes while another is found in sensory cilia. In contrast to defects in the C. elegans autosomal recessive PKD gene osm-5 [6-8], the cilia of lov-1 and pkd-2 single mutants and of lov-1;pkd-2 double mutants are normal as judged by electron microscopy, demonstrating that lov-1 and pkd-2 are not required for ultrastructural ------------------- Key: 4855 Medline: 11530201 Authors: Altmann F;Fabini G;Ahorn H;Wilson IBH Title: Genetic model organisms in the study of N-glycans. Citation: Biochimie 83: 703-712 2001 Type: REVIEW Genes: Abstract: Recently the genomic sequences of three multicellular eukaryotes, Caenorhabditis elegans, Drosophila Melanogaster and Arabidopsis thaliana, have been elucidated. A number of cDNAs encoding glycosyltransferases demonstrated to have a role in N-linked glycosylation have already been cloned from these organisms, e.g., GlcNAc transferases and alphal,3-fucosyltransferases. However, many more homologues of glycosyltransferases and other glycan modifying enzymes have been predicted by analysis of the genome sequences, but the predictions of full length open reading frames appear to be particularly poor in Caenorhabditis. The use of these organisms as models in glycobiology may be hampered since they all have N-linked glycosylation repertoires unlike those of mammals. Arabidopsis and Drosophila have glycosylation similar to that of other plants or insects, while our new data from MALDI-TOF analysis of PNGase A-released neutral N-glycans of Caenorhabditis indicate that there exists a range of pauci- and oligomannosidic structures, with up to four fucose residues and up to two O-methyl groups. With all these three 'genetic model organisms', however, much more work is required for a full understanding of their glycobiology. ------------------- Key: 4856 Medline: 21442073 Authors: Kim SK;Lund J;Kiraly M;Duke K;Jiang M;Stuart JM;Eizinger A;Wylie BN;Davidson GS Title: A gene expression map for Caenorhabditis elegans. Citation: Science 293: 2087-2092 2001 Type: ARTICLE Genes: egl-19 egl-30 ges-1 unc-52 Abstract: We have assembled data from Caenorhabditis elegans DNA microarray experiments involving many growth conditions, developmental stages, and varieties of mutants. Co-regulated genes were grouped together and visualized in a three-dimensional expression map that displays correlations of gene expression profiles as distances in two dimensions and gene density in the third dimension. The gene expression map can be used as a gene discovery toot to identify genes that are co-regulated with known sets of genes (such as heat shock, growth control genes, germ line genes, and so forth) or to uncover previously unknown genetic functions (such as genomic instability in mates and sperm caused by specific transposons). ------------------- Key: 4857 Medline: 11535834 Authors: Garsin DA;Sifri CD;Mylonakis E;Qin X;Singh KV;Murray BE;Calderwood SB;Ausubel FM Title: A simple model host for identifying Gram-positive virulence factors. Citation: Proceedings of the National Academy of Sciences USA 98: 10892-10897 2001 Type: ARTICLE Genes: Abstract: We demonstrate the use of the nematode Caenorhabditis elegans as a facile and inexpensive model host for several Gram-positive human bacterial pathogens. Enterococcus faecalis, Streptococcus pneumoniae, and Staphylococcus aureus, but not Bacillus subtilis, Enterococcus faecium, or Streptococcus pyogenes, kill adult C elegans. Focusing our studies on the enterococcal species, we found that both E. faecalis and E. faecium kill C elegans eggs and hatchlings, although only E. faecalis kills the adults. In the case of adults, a low inoculum of E, faecalis grows to a high titer in the C elegans intestine, resulting in a persistent infection that cannot be eradicated by prolonged feeding on E. faecium. Interestingly, a high titer of E. faecium also accumulates in the nematode gut, but does not affect the longevity of the worms. Two E. faecalis virulence-related factors that play an important role in mammalian models of infection, tsr, a putative quorum-sensing system, and cytolysin, are also important for nematode killing. We exploit the apparent parallels between Gram-positive infection in simple and more complex organisms by using the nematode to identify an E. faecalis virulence factor, ScrB, which is relevant to mammalian pathogenesis. ------------------- Key: 4858 Medline: 11553721 Authors: Park BJ;Lee DG;Yu JR;Jung SK;Choi K;Lee J;Kim YS;Lee JI;Kwon JY;Singson A;Song WK;Eom SH;Park CS;Kim DH;Bandyopadhyay J;Ahnn J Title: Calreticulin, a calcium-binding molecular chaperone, is required for stress response and fertility in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 12: 2835-2845 2001 Type: ARTICLE Genes: crt-1 itr-1 lfe-1 vit-2 Abstract: Calreticulin (CRT), a Ca2+-binding protein known to have many cellular functions, including regulation of Ca2+ homoeostasis and chaperone activity, is essential for heart and brain development during embryogenesis in mice. Here, we report the functional characterization of Caenorhabditis elegans calreticulin (crt-1). A crt-1 null mutant does not result in embryonic lethality but shows temperature-dependent reproduction defects. In C. elegans CRT-1 is expressed in the intestine, pharynx, body-wall muscles, head neurons, coelomocytes, and in sperm. crt-1 males exhibit reduced mating efficiency and defects late in sperm development in addition to defects in oocyte development and/or somatic gonad function in hermaphrodites. Furthermore, crt-1 and itr-1 (inositol triphosphate receptor) together are required for normal behavioral rhythms. crt-1 transcript level is elevated under stress conditions, suggesting that CRT-1 may be important for stress-induced chaperoning function in C. ------------------- Key: 4859 Medline: 21409869 Authors: Cinar HN;Sweet KL;Hosemann KE;Earley K;Newman AP Title: The SEL-12 presenilin mediates induction of the Caenorhabditis elegans uterine pi cell fate. Citation: Developmental Biology 237: 173-182 2001 Type: ARTICLE Genes: cog-2 egl-13 hop-1 lin-12 sel-12 meDf6 yDp13 Abstract: During Caenorhabditis elegans hermaphrodite development, the anchor cell induces the vulva and the uterine a cells whose daughters connect to the vulva, thereby organizing the uterine-vulval connection. Both the initial selection of a single anchor cell during the anchor cell vs. ventral uterine precursor cell decision and the subsequent induction of the a cell fate by the anchor cell are mediated by the lin-12 gene. Members of the presenilin gene family can cause early onset Alzheimer's disease when mutated and are also required for LIN-12/Notch signaling during development. We have shown that, in C. elegans, mutation of the sel-12-encoded presenilin results in pi cell induction defects. By contrast, other lin-12-mediated cell fate decisions occur normally in sel-12 mutants due to the redundant function of a second C. elegans presenilin called HOP-1. We found that the sel-12 egg-laying defect was partially rescued by expression of the sel-12 gene in the pi cells. sel-12-mediated pi cell fate specification provides a useful system for the analysis of presenilin function at single cell resolution. ------------------- Key: 4860 Medline: 21418823 Authors: Marks NJ;Shaw C;Halton DW;Thompson DP;Geary TG;Li C;Maule Title: Isolation and preliminary biological assessment of AADGAPLIRFamide and SVPGVLRFamide from Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 286: 1170-1176 2001 Type: ARTICLE Genes: flp-13 Abstract: To date, 9 FMRFamide-related peptides (FaRPs) have been structurally characterised from Caenorhabditis elegans. Radioimmunometrical screening of an ethanolic extract of C. elegans revealed the presence of two additional FaRPs that were purified by reverse-phase HPLC and subjected to Edman degradation analysis and gas-phase sequencing. Unequivocal primary structures for the two FaRPs were determined as Ala-Ala-Asp-Gly-Ala-Pro-Leu-Ile-Arg-Phe-NH2 and Ser-Val-Pro-Gly-Val-Leu-Arg-Phe-NH2. Using MALDI-TOF mass. spectrometry, the molecular masses of the peptides were found to be 1032 Da (MH) and 875 Da (MH)(+), respectively. Two copies of AADGAPLIRFamide are predicted to be encoded on the precursor gene termed flp-13, while one copy of SVPGVLRFamide is located on flp-18. Synthetic replicates of the peptides were tested on Ascaris suum somatic muscle to assess bioactivity. ADDGAPLIRFamide had inhibitory effects on A. suum muscle strips, which occurred over a range of concentrations from a threshold for activity of 10 nM to 10 muM. SVPGVLRFamide was excitatory on A. suum somatic musculature from a threshold concentration for activity of 1 nM to 10 muM. The inhibitory and excitatory effects of AADGAPLIRFamide and SVPGVLRFamide, respectively, were the same for dorsal and ventral muscle strips as well as innervated and denervated preparations, suggesting that these physiological effects are not nerve cord dependent. Addition of ADDGAPLIRFamide (10 muM) to muscle strips preincubated in high-K+ and -Ca2+-free medium resulted in a normal inhibitory response. Peptide addition to muscle strips preincubated in Cl--free medium showed no inhibitory response, suggesting that the inhibitory response of the peptide may be chloride mediated. A normal excitatory response was noted following the addition of 10 muM SVPGVLRFamide to muscle strips preincubated in high-K+, Ca2+- and Cl--free media. ------------------- Key: 4861 Medline: 11439453 Authors: Morrison GE;van der Kooy D Title: A mutation in the AMPA-type glutamate receptor, glr-1, blocks olfactory associative and nonassociative learning in Caenorhabditis elegans. Citation: Behavioral Neuroscience 115: 640-649 2001 Type: ARTICLE Genes: glr-1 lrn-1 lrn-2 osm-9 Abstract: The alpha -amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA)-type ionotropic glutamate receptor mediates fast excitatory neurotransmission in the vertebrate brain and is important for synaptic plasticity and the initial induction of long-term potentiation (LTP). This study found that the putative Caenorhabditis elegans AMPA receptor gene. glr-1. plays a significant role in experience-dependent behavior in C. elegans. glr-1 mutants are deficient in an olfactory associative learning task, in which diacetyl (DA) is paired with acetic acid solution. glr-1 mutant nematodes are also impaired in nonassociative learning (habituation) with the same DA stimulus. The C elegans learning mutants, lrn-1 and lrn-2. are impaired in chemosensory associative learning yet have no deficits in habituation. The results suggest that although associative and nonassociative learning can be genetically dissociated (lrn-1 and lrn-2), they also share some common molecular processes, including glr-1-mediated neurotransmission. ------------------- Key: 4862 Medline: 21437633 Authors: Darby C;Falkow S Title: Mimicry of a G protein mutation by pertussis toxin expression in transgenic Caenorhabditis elegans. Citation: Infection and Immunity 69: 6271-6275 2001 Type: ARTICLE Genes: goa-1 Abstract: Pathogens produce virulence factors that interact directly with host molecules, but in many cases the host targets are unknown. The genetic and molecular identification of these orphan targets is often not feasible with mammalian experimental models. However, a substantial number of known targets are molecules and pathways that are conserved among eukaryotes, and therefore the use of nonmammalian model hosts to identify orphan targets may prove useful. To demonstrate the feasibility of this approach, we transformed the nematode Caenorhabditis elegans with a gene encoding the catalytic subunit of pertussis toxin (PTX), which in mammals inactivates G(o/i)alpha proteins. Expression of PTX in C. elegans produced phenotypes almost identical to those of a null mutation in the nematode gene encoding G(o/i)alpha. Furthermore, PTX suppressed the phenotype of a constitutively active form of nematode G(o/i)alpha protein. These results indicate that PTX is functional in nematodes and acts specifically on the C. elegans homologue of the mammalian target. ------------------- Key: 4863 Medline: 21403250 Authors: Link CD Title: Transgenic invertebrate models of age-associated neurodegenerative diseases. Citation: Mechanisms of Ageing & Development 122: 1639-1649 2001 Type: REVIEW Genes: Abstract: Transgenic Drosophila melanogaster and Caenorhabditis elegans strains have been engineered to express human proteins associated with neurodegenerative diseases. These model systems include transgenic animals expressing beta-amyloid peptide (Alzheimer's disease), polyglutamine repeat proteins (Huntington's disease, Spinocerebellar ataxia), and alpha-synuclein (Parkinson's disease). In most of these invertebrate models, some aspects of the human diseases are reproduced, Although expression of all these proteins in transgenic mice has been instructive, the invertebrate models offer experimental advantages (e.g. forward genetic screens) that can potentially address some of the outstanding questions regarding the cellular processes underlying these diseases. This review considers what has been learned from these invertebrate models, and speculates what further insight may be gained from them. ------------------- Key: 4864 Medline: 11544035 Authors: Ohno S Title: Intercellular junctions and cellular polarity: the PAR-aPKC complex, a conserved core cassette playing fundamental roles in cell polarity. Citation: Current Opinion in Cell Biology 13: 641-648 2001 Type: REVIEW Genes: goa-1 gpa-16 gpc-2 mex-5 mex-6 par-1 par-3 par-6 pkc-3 Abstract: Two PDZ-domain-containing adapter-like proteins, PAR-3 and PAR-6, and a protein kinase, atypical protein kinase C (PKC), cooperate together to establish cell polarity in a variety of biological contexts. These include asymmetric cell division in early Caenorhabditis elegans embryo and Drosophila neuroblasts, as well as the establishment and maintenance of apical-basal polarity in Drosophila and mammalian epithelial cells. Recent studies on the role of this PAR-aPKC complex in epithelia[ cell polarization provide new insights into the molecular basis of epithelial junctional formation and cell polarity. ------------------- Key: 4865 Medline: Authors: Schierenberg E Title: Three sons of fortune: early embryogenesis, evolution and ecology of nematodes. Citation: BioEssays 23: 841-847 2001 Type: REVIEW Genes: Abstract: Comparative analysis of nematode development has revealed considerable variations in how the fates of embryonic cells are specified. Such early variations seem enigmatic as they do not influence the resultant structure or performance of the emerging animal. Three different nematode species are used to consider why alternative ways to reach the same goal may have been established during evolution and why early steps of embryogenesis are particularly variable. A scenario is sketched with a shift from late to early cell specification, along with an increase in maternal contribution and developmental tempo and a decrease in regulative potential expressing different developmental strategies. Future studies of larger numbers of species are needed to assess the extent of such variations and to understand more fully the underlying mechanisms, rules and driving forces. ------------------- Key: 4866 Medline: 21357549 Authors: Kelley S Title: Getting started with Acedb. Citation: Briefings in Bioinformatics 1: 131-137 2001 Type: REVIEW Genes: Abstract: Acedb is one of the more venerable pieces of Genomics software. Acedb was originally created in 1992 by Richard Durbin and Jean Thierry-Mieg to manage the data from the Caenorhabditis elegans mapping project and subsequently the C. elegans sequencing project. From beginnings as a C. elegans-specific tool, it has been continuously developed into a flexible suite of data management, display and scripting tools providing facilities for managing and annotation mapping information and DNA and peptide sequences.This paper gives a basic overview of the Acedb suite, and step-by-step guidance on how to download and install Acedb. It is intended to take an Acedb novice to stage where they can begin to experiment and explore the facilities that are available. ------------------- Key: 4867 Medline: 21352309 Authors: Tavernarakis N;Driscoll M Title: Degenerins. At the core of the metazoan mechanotransducer? Citation: Annals of the New York Academy of Sciences 940: 28-41 2001 Type: REVIEW Genes: deg-1 del-1 flr-1 mec-4 mec-10 unc-8 unc-105 Abstract: Mechanosensory signaling, believed to be mediated by mechanically gated ion channels, constitutes the basis for the senses of touch and hearing, and contributes fundamentally to the development and homeostasis of all organisms. Despite this profound importance in biology, little is known of the molecular identities or functional requirements of mechanically gated ion channels. Genetic analyses of touch sensation and locomotion in Caenorhabditis elegans have implicated a new class of ion channels, the degenerins (DEG) in nematode mechanotransduction. Related fly and vertebrate proteins, the epithelial sodium channel (ENaC) family, have been implicated in several important processes, including transduction of mechanical stimuli, pain sensation, gametogenesis, sodium reabsorption, and blood pressure regulation. Still-to-be-discovered DEG/ENaC proteins may compose the core of the elusive human mechanotransducer. ------------------- Key: 4868 Medline: 21339781 Authors: Meyer BJ Title: Sex and death of a worm: assessing and repressing X chromosomes. Citation: Harvey Lectures 95: 85-105 2000 Type: REVIEW Genes: dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 fox-1 her-1 mix-1 sdc-1 sdc-2 sdc-3 sex-1 xol-1 Abstract: A fundamental problem in biology is to determine how small quantitative differences in molecular signals are translated into alternative developmental fates and how developmental decisions are controlled by genetic regulatory hierarchies. A separate problem is to understand how gene expression is regulated at the level of whole chromosomes. Establishing the mechanistic link between higher-order chromatin structure and the regulation of gene expression is central to understanding this problem. These biological topics are addressed in this review through experiments that reveal the mechanisms by which the model organism Caenorhabditis elegans specifies its choice of sexual fate and regulates X chromosome-wide gene expression through the process of dosage compensation. ------------------- Key: 4869 Medline: 21312160 Authors: Guarente L Title: SIR2 and aging - the exception that proves the rule. Citation: Trends in Genetics 17: 391-392 2001 Type: REVIEW Genes: age-1 akt-1 akt-2 daf-2 daf-16 sir-2.1 Abstract: One of the holy grails of medicine is the possibility of an increase in lifespan without a decrease in vitality. However, the causes and processes of human aging are still unclear. One evolutionary theory is that in the post-reproductive stage of life, selective forces decline allowing many vital systems to deteriorate. This suggests that intervention will be difficult, if not impossible. However, molecular geneticists propose an aging process that is programmed (like other developmental processes) and regulated by single genes, meaning that intervention could be possible. Here, I discuss a way of reconciling these two views that could have major implications for healthcare. ------------------- Key: 4870 Medline: 11486053 Authors: Knight SW;Bass BL Title: A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Citation: Science 293: 2269-2271 2001 Type: ARTICLE Genes: dcr-1 ego-1 gld-1 let-7 mpk-1 rde-1 rde-2 rde-3 sur-5 unc-22 unc-54 Abstract: An early event in RNA interference (RNAi) is the cleavage of the initiating double-stranded RNA (dsRNA) to short pieces, 21 to 23 nucleotides in length. Here we describe a null mutation in dicer-1 (dcr-1), a gene proposed to encode the enzyme that generates these short RNAs. We find that dcr-1(-/-) animals have defects in RNAi under some, but not all, conditions. Mutant animals have germ line defects that lead to sterility, suggesting that cleavage of dsRNA to short pieces is a requisite event in normal development. ------------------- Key: 4871 Medline: 11567102 Authors: Ozhogina OA;Trexler M;Banyai L;Llinas M;Patthy L Title: Origin of fibronextin type II (FN2) modules: Structural analyses of distantly-related members of the kringle family identify the kringle domain of neurotrypsin as a potential link between FN2 domains Citation: Protein Science 10: 2114-2122 2001 Type: ARTICLE Genes: Abstract: Analysis of complete genome sequences has made it clear that fibronectin type II (FN2) modules are present only in the vertebrate lineage, raising intriguing questions about the origin of this module type. Kringle domains display many similarities to FN2 domains; therefore it was suggested previously that they are highly divergent descendants of the same ancestral protein-fold. Since kringles are present in arthropodes, nematodes, and invertebrate chordates as well as in vertebrates, it is suggested that the FN2 domain arose in the vertebrate lineage through major structural modification of the more ancestral kringle fold. To explore this structural transition, in the present work we compare key structural features of two highly divergent kringle domains (the kringle of Caenorhabditis elegans Ror receptor tyrosine kinase and the kringle of rat neurotrypsin) with those of plasminogen kringles and FN2 domains. Our NMR conformation fingerprinting analysis indicates that characteristic H-1-NMR markers of kringle or FN2 native folding, such as the dispersion of Trp aromatic connectivities and shifts of the Leu(46)/Thr(16) methyl signals, both decrease in the order kringles > neurotrypsin kringle > FN2 domains. These results suggest that the neurotrypsin kringle may represent an intermediate form between typical kringles and FN2 ------------------- Key: 4872 Medline: Authors: Morita S;Oshio K;Osana Y;Funabashi Y;Oka K;Kawamura K Title: Geometrical structure of the neuronal network of Caenorhabditis elegans. Citation: Physica A 298: 553-561 2001 Type: ARTICLE Genes: Abstract: The neuronal network of the soil nematode Caenorhabditis elegans (C. elegans), which is a good prototype for biological studies, is investigated. Here, the neuronal network is simplified as a graph. We use three indicators to characterize the graph; vertex degree, generalized eccentricity (GE), and complete subgraphs. The graph has the central part and the strong clustering structure. We present a simple model, which shows that the neuronal network has a high-dimensional geometrical structure. ------------------- Key: 4873 Medline: 11522349 Authors: Jasmer DP;Roth J;Myler PJ Title: Cathespin B-like cystein proteases and Caenorhabditis elegans homologues dominate gene products expressed in adult Haemonchus contortus intestine. Citation: Molecular & Biochemical Parasitology 116: 159-169 2001 Type: ARTICLE Genes: Abstract: Proteins expressed by nematode intestinal cells are potential targets for parasite control by immune or chemical based strategies. To expand our knowledge on nematode intestinal proteins, expressed sequence tags were generated for 131 cDNA clones from the intestine of adult female Haemonchus contortus. An estimated 55 distinct protein genes or gene families were identified. Predicted proteins represented diverse functions. Several predicted polypeptides were related to H. contortus proteins implicated in inducing protective immunity against challenge infections of this parasite. The dominant intestinal transcripts were represented by cathepsin B-like cysteine protease genes (cbl) (17% of protein coding expressed sequence tags (ESTs) analyzed). An estimated 11 previously undescribed 61 genes were identified, doubting the recognized members of this gene family. Multiple C-type lectin sequences were identified. Other notable sequences included a predicted Y-box binding protein, serine/threonine kinases and a cyclin E-like sequence. Predicted protein homologues were found in Caenorhabditis elegans for all but one H. contortus sequence (99%), while fewer homologues from other parasitic nematodes were found. Many of the proteases, lipase and C-type lectin homologues in C. elegans had apparent signal peptides, suggesting that they are secreted. Several gene products had no obvious similarity outside the phylum Nematoda. The ESTs identified intestinal genes with potential application to immune control, understanding of basic intestinal regulatory processes and refinement of nematode genomic resources. ------------------- Key: 4874 Medline: 21424424 Authors: Majewska A;Yuste R Title: Topology of gap junction networks in C. elegans. Citation: Journal of Theoretical Biology 212: 155-167 2001 Type: ARTICLE Genes: Abstract: Gap junctions are prevalent in every nervous system, but their role in information processing remains largely unknown. In C. elegans, the role of gap junctional communication in touch sensitivity has been demonstrated. In this animal, the entire complement of gap junctions in the nervous system is documented. therefore providing a good model for the computational investigation of circuit functions of gap junctions. We explored several hypotheses about the role of gap junctions in the nervous system of C. elegans by systematically analysing an anatomical database with recursive algorithms. We find that gap junctions connect different sets of neurons from those connected by chemical synapses. In addition, when analysing the topology of the gap-junction networks, we find that, surprisingly, most (92%) neurons in the worm are linked in a single gap-junction network. The worm nervous system can only be divided into smaller networks by assuming that two or more gap junctions are necessary for functional coupling or that neural activity has limited propagation. However, these groups, and others identified using algorithms with subsets or combinations of restrictive criteria, do not correspond to any known circuits identified in genetic and behavioral studies. Finally, we notice that the function of some gap junctions appears linked to their precise location on the neuronal processes. We propose that the location of the gap junctions within the neuron determines their functional role. ------------------- Key: 4875 Medline: 21431812 Authors: Kurokawa H;Osawa M;Kurihara H;Katayama N;Tokumitsu H;Swindells MB;Kainosho M;Ikura M Title: Target-induced conformational adaptation of calmodulin revealed by the crystal structure of a complex with nematode Ca2+/calmodulin-dependent kinase kinase peptide. Citation: Journal of Molecular Biology 312: 59-68 2001 Type: ARTICLE Genes: Abstract: Calmodulin (CaM) is a ubiquitous calcium (Ca2+) sensor which binds and regulates protein serine/threonine kinases along with many other proteins in a Ca2+-dependent manner. For thus multi-functionality, conformational plasticity is essential; however, the nature and magnitude of CaM's plasticity still remains largely undetermined. Here, we present the 1.8 Angstrom resolution crystal structure of Ca2+/CaM, complexed with the 27-residue synthetic peptide corresponding to the CaM-binding domain of the nematode Caenorhabditis elegans Ca2+/CaM-dependent kinase kinase (CaMKK). The peptide bound in this crystal structure is a homologue of the previously NMR-derived complex with rat CaMKK, but benefits from improved structural resolution. Careful comparison of the present structure to previous crystal structures of CaM complexed with unrelated peptides derived from myosin light chain kinase and CaM kinase II, allow a quantitative analysis of the differences in the relative orientation of the N and C-terminal domains of CaM, defined as a screw axis rotation angle ranging from 156 degrees to 196 degrees. The principal differences in CaM interaction with various peptides are associated with the N-terminal domain of CaM. Unlike the C-terminal domain, which remains unchanged internally, the N-terminal domain of CaM displays significant differences in the EF-hand helix orientation between this and other CaM structures. Three hydrogen bonds between CaM and the peptide (E87-R336, E87-T339 and K75-T339) along with two salt bridges (E11-R349 and E114-K334) are the most probable determinants for the binding direction of the CaMKK peptide to CaM. ------------------- Key: 4876 Medline: 11569921 Authors: Ishiguro H;Yasuda K;Ishii N;Ihara K;Ohkubo T;Hiyoshi M;Ono K;Senoo-Matsuda N;Shinohara O;Yosshii F;Murakami M;Hartman PS;Tsuda M Title: Enhancement of oxidative damage to cultured cells and Caenorhabditis elegans by mitochondrial electron transport inhibitors. Citation: Iubmb Life 51: 263-268 2001 Type: ARTICLE Genes: mev-1 Abstract: The mechanisms that lead to mitochondrial damage under oxidative stress conditions were examined in primary and cultured cells as well as in the nematode Caenorhabditis elegans (C elegans) treated simultaneously with electron transport inhibitors and oxygen gas. Oxygen loading enhanced the damage of PC 12 cells by thenoyltrifluoroacetone (TTFA, a complex II inhibitor), but did not by rotenone (a complex I inhibitor), antimycin (a complex III inhibitor), and sodium azide (a complex IV inhibitor). In primary hepatocytes, the enhancement was observed with the addition of sodium azide and rotenone, but not by TTFA or antimycin. In the nematode, only rotenone and TTFA enhanced the sensitivity under hyperoxia. These results demonstrate that highly specific inhibitors of electron transport can induce oxygen hypersensitivity in cell levels such as PC 12 cells and primary hepatocytes, and animal level of C. elegans. In addition the cell damage is different dependent on cell type and organism. ------------------- Key: 4877 Medline: 21450307 Authors: Friesen JA;Liu MF;Kent C Title: Cloning and characterization of a lipid-activated CTP: phosphocholin cytidylyltransferase from Caenorhabditis elegans: identification of a 21-residue segment critical for lipid activation. Citation: Biochimica et Biophysica Acta-Molecular & Cell Biology of Lipids 1533: 86-98 2001 Type: ARTICLE Genes: Abstract: The genome of the nematode Caenorhabditis elegans contains several genes that appear to encode proteins similar to CTP:phosphocholine cytidylyltransferase (CCT). We have isolated a 1044-nucleotide cDNA clone from a C. elegans cDNA library that encodes the 347-amino acid version of CCT that is most similar to previously-identified CCTs. Native and His-tagged forms were expressed and purified using a baculovirus expression system. The enzyme was maximally activated by 5 muM phosphatidylcholine:oleate (50:50) vesicles with a k(cat) value in the presence of lipid 37-fold greater than the k(cat) value in the absence of lipid. To localize the region of C. elegans CCT critical for lipid activation, a series of C-terminal truncation mutants was analyzed. CCT truncated after amino acids 225 or 245 was quite active in the absence of lipids and not further activated in the presence of lipids, supporting the concept that the lipid-activation segment is inhibitory to catalysis in the absence of lipids. CCT truncated after amino acids 266, 281, or 319 was activated by lipid similar to wild-type enzyme. Kinetic analysis in the absence of lipid revealed the lipid-independent CCT truncated after amino acid 245 to have a k(cat) value 15-fold greater than either full-length CCT or CCT truncated after amino acid 266. We conclude that elements critical for activation of C. elegans CCT by lipids are contained within amino acids 246-266, that this region is inhibitory in the absence of lipids, and that the inhibition is relieved by the association of the enzyme with lipid. ------------------- Key: 4878 Medline: 11572964 Authors: Peckol EL;Troemel ER;Bargmann CI Title: Sensory experience and sensory activity regulate chemosensory receptor gene expression in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 98: 11032-11038 2001 Type: ARTICLE Genes: che-3 daf-7 daf-22 egl-19 odr-10 osm-6 sra-6 srd-1 str-2 str-3 tax-2 tax-4 unc-2 unc-36 Abstract: Changes in the environment cause both short-term and long-term changes in an animal's behavior. Here we show that specific sensory experiences cause changes in chemosensory receptor gene expression that may alter sensory perception in the nematode Caenorhabditis elegans. Three predicted chemosensory receptor genes expressed in the ASI chemosensory neurons, srd-1, str-2, and str-3, are repressed by exposure to the dauer pheromone, a signal of crowding. Repression occurs at pheromone concentrations below those that induce formation of the alternative dauer larva stage, suggesting that exposure to pheromones can alter the chemosensory behaviors of non-dauer animals. In addition, ASI expression of srd-1, but not str-2 and str-3, is induced by sensory activity of the ASI neurons. Expression of two receptor genes is regulated by developmental entry into the dauer larva stage. srd-1 expression in ASI neurons is repressed in dauer larvae. str-2 expression in dauer animals is induced in the ASI neurons, but repressed in the AWC neurons. The ASI and AWC neurons remodel in the dauer stage, and these results suggest that their sensory specificity changes as well. We suggest that experience-dependent changes in chemosensory receptor gene expression may modify olfactory behaviors. ------------------- Key: 4879 Medline: 11580895 Authors: Satterlee JS;Sasakura H;Kuhara A;Berkeley M;Mori I;Sengupta P Title: Specification of the thermosensory neuron fate in C. elegans requires ttx-1, a homolog of otd/Otx. Citation: Neuron 31: 943-956 2001 Type: ARTICLE Genes: ceh-14 daf-2 daf-7 gcy-8 lin-11 nhr-38 odr-3 odr-10 osm-6 osm-10 rol-9 str-1 str-2 tax-2 tax-4 ttx-1 ttx-3 Abstract: Temperature is a critical modulator of animal metabolism and behavior, yet the mechanisms underlying the development and function of thermosensory neurons are poorly understood. C. elegans senses temperature using the AFD thermosensory neurons. Mutations in the gene ttx-1 affect AFD neuron function. Here, we show that ttx-1 regulates all differentiated characteristics of the AFD neurons. ttx-1 mutants are defective in a thermotactic behavior and exhibit deregulated thermosensory inputs into a neuroendocrine signaling pathway. ttx-1 encodes a member of the conserved OTD/ OTX homeodomain protein family and is expressed in the AFD neurons. Misexpression of ttx-1 converts other sensory neurons to an AFD-like fate. Our results extend a previously noted conservation of developmental mechanisms between the thermosensory circuit in C. elegans and the vertebrate photosensory circuit, suggesting an evolutionary link between thermosensation and ------------------- Key: 4880 Medline: 11580896 Authors: Xu K;Tavernarakis N;Driscoll M Title: Necrotic cell death in C. elegans requires the function of calreticulin and regulators of Ca2+ release from the endoplasmic reticulum. Citation: Neuron 31: 957-971 2001 Type: ARTICLE Genes: cnx-1 crt-1 deg-1 deg-3 itr-1 mec-4 unc-8 unc-68 unc-105 nDf18 adDf1059 Abstract: In C. elegans, a hyperactivated MEC-4(d) ion channel induces necrotic-like neuronal death that is distinct from apoptosis. We report that null mutations in calreticulin suppress both mec-4(d)-induced cell death and the necrotic cell death induced by expression of a constitutively activated Gas subunit. RNAi-mediated knockdown of calnexin, mutations in the ER Ca2+ release channels unc-68 (ryanodine receptor) or itr-1 (inositol 1,4,5 triphosphate receptor), and pharmacological manipulations that block ER Call release also suppress death. Conversely, thapsigargin-induced ER Ca2+ release can restore mec-4(d)-induced cell death when calreticulin is absent. We conclude that high [Ca2+](i) is a requirement for necrosis in C. elegans and suggest that an essential step in the death mechanism is release of ER-based Ca2+ stores. ER-driven Ca2+ release has previously been implicated in mammalian necrosis, suggesting necrotic death mechanisms ------------------- Key: 4881 Medline: 21473256 Authors: Veronico P;Gray LJ;Jones JT;Bazzicalupo P;Arbucci S;Cortese MR;Di Vito M;De Giorgi C Title: Nematode chitin synthases: gene structure, expression and function in Caenorhabditis elegans and the plant parasitic nematode Meloidogyne artiellia. Citation: Molecular Genetics and Genomics 266: 28-34 2001 Type: ARTICLE Genes: Abstract: Although the presence of chitin in nematodes is well documented little is known about its synthesis in this phyletic group. The recently completed genome sequence of Caenorhabditis elegans predicts two sequences with homology to chitin synthases (chitin-UDP acetylglucosaminyl transferase; EC 2.4.1.16). We show that these genes are differentially expressed in a pattern that may reflect different functional roles. One gene is expressed predominantly in the adult hermaphrodite (the main egg-producing stage in the nematode) and later larval stages, which is consistent with a role in production of chitin for the eggshell. The other gene, however, is expressed in the cells that form the pharynx, and only in the period directly preceding a moult. These data suggest that the product of this gene is involved in synthesis of the feeding apparatus, which is replaced during each moult. We have also isolated a full-length genomic sequence of a chitin synthase orthologue from the plant parasitic nematode Meloidogyne artiellia. The single gene present in M. artiellia shows an expression pattern that is consistent with a role for the protein in production of the eggshell. ------------------- Key: 4882 Medline: 11473126 Authors: Lee M;Cram EJ;Shen B;Schwarzbauer JE Title: Roles for beta pat-3 integrins in development and function of Caenorhabditis elegans muscles and gonads. Citation: Journal of Biological Chemistry 276: 36404-36410 2001 Type: ARTICLE Genes: ced-10 ina-1 lag-2 pat-3 Abstract: Heterodimeric integrin receptors for extracellular matrix (ECM) play vital roles in bidirectional signaling during tissue development, organization, remodeling, and repair. The beta integrin subunit cytoplasmic domain is essential for transmission of many of these signals and overexpression of an impaired beta tail in cultured cells inhibits endogenous integrins. Unlike vertebrates, which have at least nine beta subunit genes, the nematode Caenorhabditis elegans expresses only one beta subunit (beta pat-3), and a null mutation in this gene causes embryonic lethality. To determine the functions of integrins during larval development and in adult tissues, we have taken a dominant negative approach by expression of an HA-beta tail transgene composed of a hemagglutinin (RA) epitope tag extracellular domain connected to the beta pat-3 transmembrane and cytoplasmic domains. Expression of this transgene in muscle and gonad, major sites of integrin expression, caused a variety of phenotypes dependent on the level of transgene expression. Abnormalities in body wall and sex muscles led to uncoordinated movement and egg-laying defects. Significant anomalies in migration and pathfinding were caused by tissue-specific expression of HA-beta tail in the distal tip cells (DTC), the cells that direct gonad morphogenesis. A pat-3 gene with Tyr to Phe mutations in the cytoplasmic domain was able to rescue pat-3 null animals but also showed DTC migration defects. These results show that beta pat-3 plays important roles in post-embryonic organogenesis and tissue function. ------------------- Key: 4883 Medline: 11560892 Authors: Fares H;Greenwald I Title: Genetic analysis of endocytosis in Caenorhabditis elegans: coelomocyte uptake defective mutants. Citation: Genetics 159: 133-145 2001 Type: ARTICLE Genes: bli-5 ced-2 ced-5 ced-9 cha-1 cup-1 cup-2 cup-3 cup-4 cup-5 cup-6 cup-7 cup-8 cup-9 cup-10 cup-11 cyk-1 dpy-5 dpy-7 dpy-9 dpy-11 dpy-13 dpy-14 dpy-17 dpy-18 dpy-24 dyf-2 dyf-3 dyf-4 dyf-5 dyf-13 dyn-1 eat-1 eat-7 eat-10 eat-20 emb-29 glp-4 him-5 lag-2 lin-1 lin-10 mab-18 mig-2 nrf-4 nrf-5 nrf-6 pod-1 rme-1 rme-6 rme-8 rol-6 sec-5 sec-8 sma-1 sma-3 snt-1 sqt-3 unc-4 unc-6 unc-11 unc-13 unc-17 unc-18 unc-25 unc-26 unc-29 unc-30 unc-31 unc-32 unc-33 unc-34 unc-36 unc-39 unc-42 unc-54 unc-60 unc-64 unc-69 unc-73 unc-76 unc-78 unc-97 unc-101 unc-104 unc-115 sDf26 sDf28 sDf31 sDf32 sDf42 sDf45 sDf46 sDf60 Abstract: The coelomocytes of Caenorhabditis elegans are scavenger cells that continuously and nonspecifically endocytose fluid front the pseudococlom (body cavity). Green fluorescent protein (GFP) secreted into the pseudocoelom from body wall muscle cells is endocytosed and degraded by coelomocytes. We show that toxin-mediated ablation of coelomocytes results in viable animals that fail to endocytose pseudocoelomic GFP, indicating that endocytosis by coelomocytes is not essential for growth or survival of C. elegans tinder normal laboratory, conditions. We examined known viable endocytosis mutants, and performed RNAi for other known endocytosis genes, for coelomocyte uptake defective (Cup) phenotyes. We also screened fur riew genes involved in endocytosis by isolating viable mutants with Cup defects; this screen identified 14 different genes, many with multiple alleles. A variety of Cup terminal phenotypes were observed, consistent with defects at various steps in the endocytic pathway. Available molecular information indicates that the Cup mutant screen has identified novel components of the endocytosis machinery that are conserved in mammals but not in Saccharomyces cerevisiae, the only other organism for which largescale genetic screens for endocytosis mutants have ------------------- Key: 4884 Medline: 11560893 Authors: Lemieux J;Lakowski B;Webb A;Meng Y;Ubach A;Bussiere F;Barnes T;Hekimi S Title: Regulation of physiological rates in Caenorhabditis elegans by a tRNA-modifying enzyme in the mitochondria. Citation: Genetics 159: 147-157 2001 Type: ARTICLE Genes: gop-1 gop-2 gop-3 gro-1 hap-1 sDf121 Abstract: We show that the phenotype associated with gro-1(e2400) comprises the whole suite of features that characterize the phenotype of the dl mutants in Caenorhabditis elegans, including deregulated developmental, behavioral, and reproductive rates, as well as increased life span and a maternal effect. We cloned gro-1 and found that it encodes a highly conserved cellular enzyme, isopentenylpyroptiosphate:tRNA transferase (IPT), which modifies a subset of tRNTAs. In yeast, two forms of the enzyme are produced by alternative translation initiation, oric of which is mitochondrial. In the gro-1 transcript there are also two possible initiator ATGs, between which there is a sequence predicted to encode a mitochondrial localization signal. A functional GRO-1::GFP fusion protein is localized diffusely throughout the cytoplasm and nucleus. A GRO-1:GFP initiated from the first methionine is localized exclusively to the mitochondria and rescues the mutant phenotype. In contrast, a protein initiated from the second methionine is localized diffusely throughout the cell and does not rescue the mutant phenotype. As oxygen consumption and ATP concentration have been reported to be unaffected in gro-1 mutants, our observations suggest that GRO-1 acts in mitochondria and regulates global physiology by unknown mechanisms. ------------------- Key: 4885 Medline: 11560894 Authors: Natarajan L;Witwer NE;Eisenmann DM Title: The divergent Caenorhabditis elegans beta-catenin proteins BAR-1, WRM-1 and HMP-2 make distinct protein interactions but retain functional redundancy in vivo. Citation: Genetics 159: 159-172 2001 Type: ARTICLE Genes: bar-1 egl-27 hmp-2 wrm-1 Abstract: beta -Catenins function both in cell adhesion as part of the cadherin/catenin complex and in Writ signal transduction as transcription factors. Vertebrates express two related proteins, beta -catenin and plakoglobin, while Drosophila has a single family member, Armadillo. Caenorhabditis elegans expresses three beta -catenin-related proteins, BAR-1, HMP-2, and WRM-1, which are quite diverged sequence from each other and other beta -catenins. While BAR-1 and WRM-1 are known to act in Wnt-mediated processes, and HMP-2 acts in a complex with cadherin/alpha -catenin homologs, it is unclear whether all three proteins retain the other functions of beta -catenin. Here we show that BAR-1, like vertebrate beta -catenin, has redundant transcription activation domains in its amino- and carboxyl-terminal regions but that HMP-2 and WRM-1 also possess the ability to activate transcription. We show via yeast two-hybrid analysis that these three proteins display distinct patterns of protein interactions. Surprisingly, we find that both WRM-1 and HMP-2 can substitute for BAR-1 in C. elegans when expressed from the bar-1 promoter. Therefore, although their mutant phenotypes and protein interaction patterns strongly suggest that the functions of beta -catenin in other species have been segregated among three diverged proteins in C. elegans, these proteins still retain sufficient similarity to display functional ------------------- Key: 4886 Medline: 21446504 Authors: Lee MH;Schedl T Title: Identification of in vivo mRNA targets of GLD-1, a maxi-KH motif containing protein required for C. elegans germ cell development. Citation: Genes & Development 15: 2408-2420 2001 Type: ARTICLE Genes: cej-1 fbf-1 fbf-2 fog-3 gld-1 lin-45 mpk-1 ncc-1 puf-5 puf-6 puf-7 puf-10 rme-2 tra-2 Abstract: Caenorhabditis elegans GLD-1, a KH motif containing RNA-binding protein of the GSG/STAR subfamily, controls diverse aspects of germ line development, suggesting that it may have multiple mRNA targets. We used an immunoprecipitation/subtractive hybridization/cloning strategy to identify 15 mRNAs that are putative targets of GLD-1 binding and regulation. For one target, the rme-2 yolk receptor mRNA, GLD-1 acts as a translational repressor to spatially restrict RME-2 accumulation, and thus yolk uptake, to late-stage oocytes. We found that GLD-1 binds sequences in both 5 ' coding and the 3 ' untranslated region of rme-2 mRNA. Initial characterization of the other 14 targets shows that (1) they are coexpressed with GLD-1; (2) they can have mutant/RNA-mediated interference depletion phenotypes indicating functions in germ line development or as maternal products necessary for early embryogenesis; and (3) GLD-1 may coregulate mRNAs corresponding to functionally redundant subsets of genes within two gene families. Thus, a diverse set of genes have come under GLD-1-mediated regulation to achieve normal germ line development. Previous work identified tra-2 as a GLD-1 target for germ line sex determination. Comparisons of GLD-1-mediated translational control of rme-2 and tra-2 suggests that the mechanisms may differ for distinct target ------------------- Key: 4887 Medline: 21450669 Authors: Yi SY;Joeng KS;Kweon JU;Cho JW;Chung IK;Lee J Title: A single-stranded telomere binding protein in the nematode Caenorhabditis elegans. Citation: FEBS Letters 505: 301-306 2001 Type: ARTICLE Genes: Abstract: We identified and characterized a protein (STB-1) from the nuclear extract of Caenorhabditis elegans that specifically binds single-stranded telomere DNA sequences, but not the corresponding RNA sequences. STB-1 binding activity is specific to the nematode telomere, but not to the human or plant telomere. STB-1 requires the core nucleotides of GCTTAGG and three spacer nucleotides in front of them for binding. While any single nucleotide change in the core sequence abolishes binding, the spacer nucleotides tolerate substitution. STB-1 was determined to be a basic protein of 45 kDa by Southwestern analyses. STB-1 forms a stable complex with DNA once bound to the telomere. ------------------- Key: 4888 Medline: 11559592 Authors: Davy A;Bello P;Thierry-Mieg N;Vaglio P;Hitti J;Doucette-Stamm L;Thierry-Mieg D;Reboul J;Boulton S;Walhout AJM;Coux O;Vidal M Title: A protein-protein interaction map of the Caenorhabditis elegans 26S proteasome. Citation: EMBO Reports 2: 821-828 2001 Type: ARTICLE Genes: Abstract: The ubiquitin-proteasome proteolytic pathway is pivotal in most biological processes. Despite a great level of information available for the eukaryotic 26S proteasome-the protease responsible for the degradation of ubiquitylated proteins-several structural and functional questions remain unanswered. To gain more insight into the assembly and function of the metazoan 26S proteasome, a two-hybrid-based protein interaction map was generated using 30 Caenorhabditis elegans proteasome subunits. The results recapitulate interactions reported for other organisms and reveal new potential interactions both within the 19S regulatory complex and between the 19S and 20S subcomplexes. Moreover, novel potential proteasome interactors were identified, including an E3 ubiquitin ligase, transcription factors, chaperone proteins and other proteins not yet functionally annotated. By providing a wealth of novel biological hypotheses, this interaction map constitutes a framework for further analysis of the ubiquitin-proteasome pathway in a multicellular organism amenable to both classical genetics and functional ------------------- Key: 4889 Medline: Authors: Villanueva A;Lozano J;Morales A;Lin X;Deng X;Hengartner MO;Kolesnick RN Title: jkk-1 and mek-1 regulate body movement coordination and response to heavy metals through jnk-1 in Caenorhabditis elegans. Citation: EMBO Journal 20: 5114-5128 2001 Type: ARTICLE Genes: jkk-1 jnk-1 mek-1 mkk-4 unc-25 unc-30 unc-47 Abstract: Although in vitro evidence suggests two c-Jun N-terminal kinase (JNK) kinases, MKK4 and MKK7, transactivate JNK, in vivo confirmation is incomplete. In fact, JNK deficiency may differ from the composite deficiency of MKK4 and MKK7 in Drosophila and mice. Recently, the Caenorhabditis elegans homolog of human JNK, jnk-1, and two MKK-7s, mek-1 and jkk-1, were cloned. Here we characterize jnk-1, which encodes two isoforms JNK-1 alpha and JNK-1 beta. A null allele,jnk-1(gk7), yielded worms with defective body movement coordination and modest mechanosensory deficits. Similarly to jkk-1 mutants, elimination of GABAergic signals suppressed the jnk-1(gk7) locomotion defect. Like mek-1 nulls, jnk-1(gk7) showed copper and cadmium hypersensitivity. Conditional expression of JNK-1 isoforms rescued these defects, suggesting that they are not due to developmental errors. While jkk-1 or mek-1 inactivation mimicked jnk-1(gk7) locomotion and heavy metal stress defects, respectively, mkk-4 inactivation did not, but rather yielded defective egg laying. Our results delineate at least two different JNK pathways through jkk-1 and mek-1 in C. elegans, and define interaction between MKK7, but not MKK4, and JNK. ------------------- Key: 4890 Medline: 21450603 Authors: Walker AK;Rothman JH;Shi Y;Blackwell TK Title: Distinct requirements for C. elegans TAF(II)s in early embryonic transcription. Citation: EMBO Journal 20: 5269-5279 2001 Type: ARTICLE Genes: ama-1 cki-1 elt-5 end-1 let-858 med-1 med-2 pes-10 pha-4 rps-5 sur-5 taf-1 taf-2 taf-3.1 taf-3.2 taf-4 taf-5 taf-6 taf-7.1 taf-7.2 taf-7.3 taf-8.1 taf-8.2 taf-9 taf-10 taf-11 ttb-1 Abstract: TAF(II)s are conserved components of the TFIID, TFTC and SAGA-related mRNA transcription complexes. In yeast (y), yTAF(II)17 is required broadly for transcription, but various other TAF(II)s appear to have more specialized functions. It is important to determine how TAF(II)s contribute to transcription in metazoans, which have larger and more diverse genomes. We have examined TAF(II) functions in early Caenorhabditis elegans embryos, which can survive without transcription for several cell generations. We show that taf-10 (yTAF(II)7) and taf-11 (yTAF(II)25) are required for a significant fraction of transcription, but apparently are not needed for expression of multiple developmental and other metazoan-specific genes. In contrast, taf-5 (yTAF(II)48; human TAF(II)130) seems to be required for essentially all early embryonic mRNA transcription. We conclude that TAF-10 and TAF-11 have modular functions in metazoans, and can be bypassed at many metazoan-specific genes. The broad involvement of TAF-5 in mRNA transcription in vivo suggests a requirement for either TFIID or a TFTC-like complex. ------------------- Key: 4891 Medline: 21458927 Authors: Koushika SP;Richmond JE;Hadwiger G;Weimer RM;Jorgensen EM;Nonet ML Title: A post-docking role for active zone protein Rim. Citation: Nature Neuroscience 4: 997-1005 2001 Type: ARTICLE Genes: aex-3 rab-3 rbf-1 unc-10 unc-13 unc-104 Abstract: Rim1 was previously identified as a Rab3 effector localized to the presynaptic active zone in vertebrates. Here we demonstrate that C. elegans unc-10 mutants lacking Rim are viable, but exhibit behavioral and physiological defects that are more severe than those of Rab3 mutants. Rim is localized to synaptic sites in C. elegans, but the ultrastructure of the presynaptic densities is normal in Rim mutants. Moreover, normal levels of docked synaptic vesicles were observed in mutants, suggesting that Rim is not involved in the docking process. The level of fusion competent vesicles at release sites was reduced fivefold in Rim mutants, but calcium sensitivity of release events was unchanged. Furthermore, expression of a constitutively open form of syntaxin suppressed the physiological defects of Rim mutants, suggesting Rim normally acts to regulate conformational changes in syntaxin. These data suggest Rim acts after vesicle docking likely via regulating priming. ------------------- Key: 4892 Medline: 11586287 Authors: Chamberlin HM Title: The adaptable lin-39. Citation: Nature Genetics 29: 106-107 2001 Type: REVIEW Genes: lin-3 lin-39 Abstract: Comparative studies of nematode development provide a powerful framework for investigating the evolution of developmental mechanisms. A recent report also demonstrates how comparative work can inform our understanding of basic developmental signaling pathways. In particular, investigation of the differences in vulva development between Caenorhabditis elegans and Pristionchus pacificus has clarified the molecular relationship between an epidermal growth factor-Ras-MAP kinase signaling pathway and downstream Hox transcription factor activity. ------------------- Key: 4893 Medline: 11574826 Authors: Lloyd TE;Bellen HJ Title: pRIMing synaptic vesicles for fusion. Citation: Nature Neuroscience 4: 965-966 2001 Type: REVIEW Genes: unc-13 Abstract: A characterization of C. elegans lacking the gene for Rim suggests that this protein may be involved in pruning synaptic vesicles for fusion, not in docking or organizing active zones. ------------------- Key: 4894 Medline: 11592725 Authors: Napier JA;Michaelson LV Title: Genomic and functional characterization of polyunsaturated fatty acid biosynthesis in Caenorhabditis elegans. Citation: Lipids 36: 761-766 2001 Type: REVIEW Genes: fat-1 fat-2 fat-3 fat-4 fat-5 fat-6 fat-7 pea-1 Abstract: The biosynthetic pathway for polyunsaturated fatty acids in the model animal Caenorhabditis elegans was examined in the context of the completed genome sequence. The genomic organization and location of seven desaturase genes and one elongase activity, all previously identified by functional characterization, were elucidated. A pathway for the biosynthesis of polyunsaturated fatty acids in C. elegans was proposed based on these genes. The role of gene duplication in enzyme evolution and proliferation is discussed. ------------------- Key: 4895 Medline: 11685578 Authors: Dawe AL;Caldwell KA;Harris PM;Morris NR;Caldwell GA Title: Evolutionarily conserved nuclear migration genes required for early embryonic development in Caenorhabditis elegans. Citation: Development Genes & Evolution 211: 434-441 2001 Type: ARTICLE Genes: lis-1 nud-1 Abstract: The nudF and nudC genes of the fungus Aspergillus nidulans encode proteins that are members of two evolutionarily conserved families. In A. nidulans these proteins mediate nuclear migration along the hyphae. The human ortholog of nudF is Lis1, a gene essential for neuronal migration in the developing cerebral cortex. The mammalian ortholog of nudC encodes a protein that interacts with Lis1. We have identified orthologs of nudC and Lis1 from the nematode Caenorhabditis elegans. Heterologous expression of the C. elegans nudC ortholog, nud-1, complements the A. nidulans nudC3 mutant, demonstrating evolutionary conservation of function. A C. elegans nud-1::GFP fusion produces sustained fluorescence in sensory neurons and embryos, and transient fluorescence in the gonad, gut, vulva, ventral cord, and hypodermal seam cells. Fusion of GFP to C. elegans lis-1 revealed expression in all major neuronal processes of the animal as well as the multinucleate spermathecal valves and adult seam cells. Phenotypic analysis of either nud-1 and lis-1 by RNA interference yielded similar phenotypes, including embryonic lethality, sterility, altered vulval morphology, and uncoordinated movement. Digital time-lapse video microscopy was used to determine that RNAi-treated embryos exhibited nuclear positioning defects in early embryonic cell division similar to those reported for dynein/dynactin depletion. These results demonstrate that the LIS-1/NUDC-like proteins of C. elegans represent a link between nuclear positioning, cell division, and neuronal function. ------------------- Key: 4896 Medline: 11591319 Authors: Murakami S;Johnson TE Title: The OLD-1 positive regulator of longevity and stress resistance is under DAF-16 regulation in Caenorhabditis elegans. Citation: Current Biology 11: 1517-1523 2001 Type: ARTICLE Genes: age-1 akt-1 akt-2 clk-1 daf-2 daf-16 old-1 tkr-1 unc-31 unc-64 Abstract: Aging and limited life span are fundamentalbiological phenomena observed in a variety of species [1]. Approximately 55 genes have been identified that can extend longevity when altered in Caenorhabditis elegans [2-5]. These genes include an insulin-like receptor (daf-2) and a phosphatidylinositol 3-OH kinase (age-1) regulating a forkhead transcription factor (daf-16) [6, 7], as well as genes mediating metabolic throughput [8], sensory perception [9], and reproduction [10]. Moreover, these mutant alleles both extend life span and increase resistance to ultraviolet (UV) radiation [11], heat [12], and oxidative stress [13-15], though the stress resistance of clk-1 is controversial. With the exception of old-1 and perhaps some other genes [16-19], all of the life-extension alleles are hypomorphic or nullomorphic. Here, we show that the OLD-1 transmembrane tyrosine kinase (formerly TKR-1; [16, 20]) is expressed in a variety of tissues, is stress inducible, and is a positive regulator of longevity and stress resistance. The transcription of old-1 is upregulated in long-lived age-1 and daf-2 mutants and is upregulated in response to heat, UV light, and starvation. Both RT-PCR and analysis of an OLD1::GFP tag suggest that old-1 expression is dependent on daf-16. Importantly, old-1 is required for the life extension of age-1 and daf-2 mutants. This study reveals a new system for specifying longevity and stress resistance and suggests possible mechanisms for mediating life extension by dietary ------------------- Key: 4897 Medline: 11595183 Authors: Gumienny TL;Brugnera E;Tosello-Trampont AC;Kinchen JM;Haney LB;Nishiwaki K;Walk SF;Nemergut ME;Macara IG;Francis R;Schedl T;Qin Y;Van Aelst L;Hengartner MO;Ravichandran KS Title: CED-12/ELMO, a novel member of the CrkII/DOCK180/Rac pathway, is required for phagocytosis and cell migration. Citation: Cell 107: 27-41 2001 Type: ARTICLE Genes: ced-1 ced-2 ced-3 ced-5 ced-6 ced-7 ced-10 ced-12 Abstract: The C. elegans genes ced-2, ced-5, and ced-10, and their mammalian homologs crkII, dock180, and rac1, mediate cytoskeletal rearrangements during phagocytosis of apoptotic cells and cell motility. Here, we describe an additional member of this signaling pathway, ced-12, and its mammalian homologs, elmo1 and elmo2. In C. elegans, CED-12 is required for engulfment of dying cells and for cell migrations. In mammalian cells, ELMO1 functionally cooperates with CrkII and Dock180 to promote phagocytosis and cell shape changes. CED-12/ELMO-1 binds directly to CED-5/ Dock180; this evolutionarily conserved complex stimulates a Rac-GEF, leading to Rac1 activation and cytoskeletal rearrangements. These studies identify CED-12/ELMO as an upstream regulator of Rac1 that affects engulfment and cell migration from C. elegans to mammals. ------------------- Key: 4898 Medline: 11595184 Authors: Epstein ACR;Gleadle JM;McNeill LA;Hewitson KS;O'Rourke J;Mole DR;Mukherji M;Metzen E;Wilson MI;Dhanda A;Tian Y-M;Masson N;Hamilton DL;Jaakkola P;Barstead R;Hodgkin J;Maxwell PH;Pugh CW;Schofield CJ;Ra Title: C. elegans EGL-9 and mammalian homologs define a family of dioxygenases that regulate HIF by prolyl hydroxylation. Citation: Cell 107: 43-54 2001 Type: ARTICLE Genes: age-1 clk-1 ctl-1 daf-2 daf-18 egl-9 gas-1 mev-1 mev-2 mev-3 phy-1 phy-2 vhl-1 Abstract: HIF is a transcriptional complex that plays a central role in mammalian oxygen homeostasis. Recent studies have defined posttranslational modification by prolyl hydroxylation as a key regulatory event that targets HIF-alpha. subunits for proteasomal destruction via the von Hippel-Lindau ubiquitylation complex. Here, we define a conserved HIF-VHL-prolyl hydroxylase pathway in C. elegans, and use a genetic approach to identify EGL-9 as a dioxygenase that regulates HIF by prolyl hydroxylation. In mammalian cells, we show that the HIF-prolyl hydroxylases are represented by a series of isoforms bearing a conserved 2-histidine-1-carboxylate iron coordination motif at the catalytic site. Direct modulation of recombinant enzyme activity by graded hypoxia, iron chelation, and cobaltous ions mirrors the characteristics of HIF induction in vivo, fulfilling requirements for these enzymes being oxygen sensors that regulate HIF. ------------------- Key: 4899 Medline: 11703940 Authors: Wu YC;Tsai M-C;Cheng L-C;Chou C-J;Weng N-Y Title: C. elegans CED-12 acts in the conserved CrkII/DOCK180/Rac pathway to control cell migration and cell corpse engulfment. Citation: Developmental Cell 1: 491-502 2001 Type: ARTICLE Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-10 ced-12 mnDf111 qDf5 qDf8 qDf9 qDf10 qDf15 Abstract: We have identified and characterized a novel C. elegans gene, ced-12, that functions in the conserved GTPase signaling pathway mediated by CED-2/Crkll, CED-5/DOCK180, and CED-10/Rac to control cell migration and phagocytosis of apoptotic cells. We provide evidence that ced-12 likely acts upstream of ced-10 during cell migration and phagocytosis and that CED-12 physically interacts with CED-5 and forms a ternary complex with CED-2 in vitro. We propose that the formation and localization of a CED-2-CED-5-CED-12 ternary complex to the plasma membrane activates CED-10, leading to the cytoskeletal reorganization that occurs in the polarized extension of cell surfaces in engulfing cells and migrating cells. We suggest that CED-12 counterparts in higher organisms regulate cytoskeleton dynamics, as CED-12 does in C. ------------------- Key: 4900 Medline: 11604136 Authors: Hao JC;Wu TW;Fujisawa K;Culotti JG;Gengyo-Ando K;Mitani S;Moulder G;Barstead R;Tessier-Lavigne M;Bargmann CI Title: C. elegans Slit acts in midline, dorsal-ventral, and anterior-posterior guidance via the SAX-3/Robo receptor. Citation: Neuron 32: 25-38 2001 Type: ARTICLE Genes: rab-3 sax-3 slt-1 unc-6 unc-40 Abstract: Robo receptors interact with ligands of the Slit family. The nematode C. elegans has one Robo receptor (SAX-3) and one Slit protein (SLT-1), which direct ventral axon guidance and guidance at the midline. In larvae, slt-1 expression in dorsal muscles repels axons to promote ventral guidance. SLT-1 acts through the SAX-3 receptor, in parallel with the ventral attractant UNC-6 (Netrin). Removing both UNC-6 and SLT-1 eliminates all ventral guidance information for some axons, revealing an underlying longitudinal guidance pathway. In the embryo, slt-1 is expressed at high levels in anterior epidermis. Embryonic expression of SLT-1 provides anterior-posterior guidance information to migrating CAN neurons. Surprisingly, slt-1 mutants do not exhibit the nerve ring and epithelial defects of sax-3 mutants, suggesting that SAX-3 has both Slit-dependent and Slit-independent ------------------- Key: 4901 Medline: 11598181 Authors: Yoder JH;Han M Title: Cytoplasmic dynein light intermediate chain is required for discrete aspects of mitosis in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 12: 2921-2933 2001 Type: ARTICLE Genes: dhc-1 dli-1 sDf22 Abstract: We describe phenotypic characterization of dli-1, the Caenorhabditis elegans homolog of cytoplasmic dynein light intermediate chain (LIC), a subunit of the cytoplasmic dynein motor complex. Animals homozygous for loss-of-function mutations in dli-1 exhibit stochastic failed divisions in late larval cell lineages, resulting in zygotic sterility. dli-1 is required for dynein function during mitosis. Depletion of the dli-1 gene product through RNA-mediated gene interference (RNAi) reveals an early embryonic requirement. One-cell dli-1 (RNAi) embryos exhibit failed cell division attempts, resulting from a variety of mitotic defects. Specifically, pronuclear migration, centrosome separation, and centrosome association with the male pronuclear envelope are defective in dli-1(RNAi) embryos. Meiotic spindle formation, however, is not affected in these embryos. DLI-1, like its vertebrate homologs, contains a putative nucleotide-binding domain similar to those found in the ATP-binding cassette transporter family of ATPases as well as other nucleotide-binding and -hydrolyzing proteins. Amino acid substitutions in a conserved lysine residue, known to be required for nucleotide binding, confers complete rescue in a dli-1 mutant background, indicating this is not an essential domain for DLI-1 function. ------------------- Key: 4902 Medline: 11591663 Authors: Gallagher LA;Manoil C Title: Pseudomonas aeruginosa PAO1 kills Caenorhabditis elegans by cyanide poisoning. Citation: Journal of Bacteriology 183: 6207-6214 2001 Type: ARTICLE Genes: Abstract: In this report we describe experiments to investigate a simple virulence model in which Pseudomonas aeruginosa PAO1 rapidly paralyzes and kills the nematode Caenorhabditis elegans. Our results imply that hydrogen cyanide is the sole or primary toxic factor produced by P. aeruginosa that is responsible for killing of the nematode. Four lines of evidence support this conclusion. First, a transposon insertion mutation in a gene encoding a subunit of hydrogen cyanide synthase (hcnC) eliminated nematode killing. Second, the 17 avirulent mutants examined all exhibited reduced cyanide synthesis, and the residual production levels correlated with killing efficiency. Third, exposure to exogenous cyanide alone at levels comparable to the level produced by PAO1 killed nematodes with kinetics similar to those observed with bacteria. The killing was not enhanced if hcnC mutant bacteria were present during cyanide exposure. And fourth, a nematode mutant (egl-9) resistant to P. aeruginosa was also resistant to killing by exogenous cyanide in the absence of bacteria. A model for nematode killing based on inhibition of mitochondrial cytochrome oxidase is presented. The action of cyanide helps account for the unusually broad host range of virulence of P. aeruginosa and may contribute to the pathogenesis in opportunistic human infections due to the ------------------- Key: 4903 Medline: 11581161 Authors: Evans D;Perez I;MacMorris M;Leake D;Wilusz CJ;Blumenthal T Title: A complex containing CstF-64 and the SL2 snRNP connects mRNA 3' end formation and trans-splicing in C. elegans Citation: Genes & Development 15: 2562-2571 2001 Type: ARTICLE Genes: gpd-2 gpd-3 mai-1 rrs-1 Abstract: Polycistronic pre-mRNAs from Caenorhabditis elegans are processed by 3' end formation of the upstream mRNA and SL2-specffic trans-splicing of the downstream mRNA. These processes usually occur within an -100-nucleotide region and are mechanistically coupled. In this paper, we report a complex in C. elegans extracts containing the 3' end formation protein CstF-64 and the SL2 snRNP. This complex, immunoprecipitated,with alpha CstF-64 antibody, contains SL2 RNA, but not SL1 RNA or other U snRNAs. Using mutational analysis we have been able to uncouple SL2 snRNP function and identity. SL2 RNA with a mutation in stem/loop III is functional in vivo as a trans-splice donor, but fails to splice to SL2-accepting trans-splice sites, suggesting that it has lost its identity as an SL2 snRNP. Importantly, stem/loop III mutations prevent association of SL2 RNA with CstF-64. In contrast, a mutation in stem II that inactivates the SL2 snRNP still permits complex formation with CstF-64. Therefore, SL2 RNA stem/loop III is required for both SL2 identity and formation of a complex containing CstF-64, but not for trans-splicing. These results provide a molecular framework for the coupling of 3' end formation and trans-splicing in the processing of polycistronic pre-mRNAs from C. elegans operons. ------------------- Key: 4904 Medline: 11591388 Authors: Hollis RP;Lagido C;Pettitt J;Porter AJR;Killham K;Paton GI;Glover LA Title: Toxicity of the bacterial luciferase substrate, n-decyl aldehyde, to Saccharomyces cerevisiae and Caenorhabditis elegans. Citation: FEBS Letters 506: 140-142 2001 Type: ARTICLE Genes: Abstract: This study determined that the bacterial luciferase fusion gene (luxAB) was not a suitable in vivo gene reporter in the model eukaryotic organisms Saccharomyces cerevisiae and Caenorhabditis elegans. LuxAB expressing S. cerevisiae strains displayed distinctive rapid decays in luminescence upon addition of the bacterial luciferase substrate, n-decyl aldehyde, suggesting a toxic response. Growth studies and toxicity bioassays have subsequently confirmed, that the aldehyde substrate was toxic to both organisms at concentrations well tolerated by Escherichia coh. As the addition of aldehyde is an integral part of the bacterial luciferase activity assay, our results do not support the use of lux reporter genes for in vivo analyses in these model eukaryotic organisms. ------------------- Key: 4905 Medline: 11546739 Authors: Navarro RE;Shim EY;Kohara Y;Singson A;Blackwell TK Title: cgh-1, a conserved predicted RNA helicase required for gametogenesis and protection from physiological germline apoptosis in C. elegans. Citation: Development 128: 3221-3232 2001 Type: ARTICLE Genes: ced-1 ced-3 ced-4 ced-9 cgh-1 fem-1 fem-3 fog-2 glp-4 him-8 mpk-1 rde-1 spo-11 Abstract: A high frequency of apoptosis is a conserved hallmark of oocyte development. In C. elegans, about half of all developing oocytes are normally killed by a physiological germline-specific apoptosis pathway, apparently so that they donate cytoplasm to the survivors. We have investigated the functions of CGH-1, the C. elegans ortholog of the predicted RNA helicase ste13/ME31B/RCK/p54, which is germline-associated in metazoans and required for sexual reproduction in yeast. We show that CGH-1 is expressed specifically in the germline and early embryo, and is localized to P granules and other possible mRNA-protein particles. cgh-1 is required for oocyte and sperm function. It is also needed to prevent the physiological germline apoptosis mechanism killing essentially all developing oocytes, making lack of cgh-1 function the first stimulus identified that can trigger this mechanism. We conclude that cgh-1 and its orthologs may perform conserved functions during gametogenesis, that in C. elegans certain aspects of oocyte development are monitored by the physiological germline apoptosis pathway, and that similar surveillance mechanisms may contribute to germline apoptosis in other species. ------------------- Key: 4906 Medline: 11546744 Authors: Sarafi-Reinach TR;Melkman T;Hobert O;Sengupta P Title: The lin-11 LIM homeobox gene specifies olfactory and chemosensory neuron fates in C. elegans. Citation: Development 128: 3269-3281 2001 Type: ARTICLE Genes: ceh-14 ceh-23 gcy-5 gcy-8 gcy-10 glr-1 gpa-5 lim-4 lim-6 lin-11 mec-3 odr-1 odr-7 odr-10 ops-1 osm-6 snt-1 sra-6 srb-6 sre-1 str-1 str-2 str-3 ttx-3 unc-13 unc-42 unc-86 unc-130 Abstract: Chemosensory neuron diversity in C. elegans arises from the action of transcription factors that specify different aspects of sensory neuron fate. In the AWB and AWA olfactory neurons, the LIM homeobox gene lim-4 and the nuclear hormone receptor gene odr-7 are required to confer AWB and AWA-specific characteristics respectively, and to repress an AWC olfactory neuron-like default fate. Here, we show that AWA neuron fate is also regulated by a member of the LIM homeobox gene family, lin-11. lin-11 regulates AWA olfactory neuron differentiation by initiating expression of odr-7, which then autoregulates to maintain expression. lin-11 also regulates the fate of the ASG chemosensory neurons, which are the lineal sisters of the AWA neurons. We show that lin-11 is expressed dynamically in the AWA and ASG neurons, and that misexpression of lin-11 is sufficient to promote an ASG, but not an AWA fate, in a subset of neuron types. Our results suggest that differential temporal regulation of lin-11, presumably together with its interaction with asymmetrically segregated factors, results in the generation of the distinct AWA and ASG sensory neuron types. We propose that a LIM code may be an important contributor to the generation of functional diversity in a subset of olfactory and chemosensory neurons ------------------- Key: 4907 Medline: 11598180 Authors: Boehm M;Bonifacino JS Title: Adaptins: the final recount. Citation: Molecular Biology of the Cell 12: 2907-2920 2001 Type: ARTICLE Genes: Abstract: Adaptins are subunits of adaptor protein (AP) complexes involved in the formation of intracellular transport vesicles and in the selection of cargo for incorporation into the vesicles. In this article, we report the results of a survey for adaptins from sequenced genomes including those of man, mouse, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, the plant Arabidopsis thaliana, and the yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe. We find that humans, mice, and Arabidopsis thaliana have four AP complexes (AP-1, AP-2, AP-3, and AP-4), whereas D. melanogaster, C. elegans, S. cerevisiae, and S. pombe have only three (AP-1, AP-2, and AP-3). Additional diversification of AP complexes arises from the existence of adaptin isoforms encoded by distinct genes or resulting from alternative splicing of mRNAs. We complete the assignment of adaptins to AP complexes and provide information on the chromosomal localization, exon-intron structure, and pseudogenes for the different adaptins. In addition, we discuss the structural and evolutionary relationships of the adaptins and the genetic analyses of their function. Finally, we extend our survey to adaptin-related proteins such as the GGAs and stonins, which contain domains homologous to the adaptins. ------------------- Key: 4908 Medline: 11566846 Authors: Jungblut B;Pires-daSilva A;Sommer RJ Title: Formation of the egg-laying system in Pristionchus pacificus requires complex interactions between gonadal, mesodermal and epidermal tissues and does not rely on single cell inductions. Citation: Development 128: 3395-3404 2001 Type: ARTICLE Genes: egl-17 lin-39 mab-5 vab-7 Abstract: The invariant cell lineage of nematodes allows the formation of organ systems, like the egg-laying system, to be studied at a single cell level. The Caenorhabditis elegans egg-laying system is made up of the vulva, the mesodermal gonad and muscles and several neurons. The gonad plays a central role in patterning the underlying ectoderm to form the vulva and guiding the migration of the sex myoblasts to their final position. In Pristionchus pacificus, the egg-laying system is homologous to C elegans, but comparative studies revealed several differences at the cellular and molecular levels during vulval formation. For example, the mesoblast M participates in lateral inhibition, a process that influences the fate of two vulval precursor cells. Here, we describe the M lineage in Pristionchus and show that both the dorsal and ventral M sublineages are involved in lateral inhibition. Mutations in the homeotic gene Ppa-mab-5 cause severe misspecification of the M lineage, resembling more the C elegans Twist than the mab-5 phenotype. Ectopic differentiation of P8.p in Ppa-mab-5 results from at least two separate interactions between M and P8.p. Thus, interactions among the Pristionchus egg-laying system are complex, involving multiple cells of different tissues ------------------- Key: 4909 Medline: 11555287 Authors: Yorgey P;Rahme LG;Tan M-W;Ausubel FM Title: The roles of mucD and alginate in the virulence of Pseudomonas aeruginose in plants, nematodes and mice. Citation: Molecular Microbiology 41: 1063-1076 2001 Type: ARTICLE Genes: pgp-1 pgp-3 Abstract: We are exploiting the broad host range of the human opportunistic pathogen Pseudomonas aeruginosa strain PA14 to elucidate the molecular basis of bacterial virulence in plants, nematodes, insects and mice. In this report, we characterize the role that two PA14 gene products, MucD and AlgD, play in virulence. MucD is orthologous to the Escherichia coli periplasmic protease and chaperone DegP. DegP homologues are known virulence factors that play a protective role in stress responses in various species. AlgD is an enzyme involved in the biosynthesis of the exopolysaccharide alginate, which is hyperinduced in mucD mutants. A PA14 mucD mutant was significantly impaired in its ability to cause disease in Arabidopsis thaliana and mice and to kill the nematode Caenorhabditis elegans. Moreover, MucD was found to be required for the production of an extracellular toxin involved in C. elegans killing. In contrast, a PA14 algD mutant was not impaired in virulence in plants, nematodes or mice. A mucDalgD double mutant had the same phenotype as the mucD single mutant in the plant and nematode pathogenesis models. However, the mucDalgD double mutant was synergistically reduced in virulence in mice, suggesting that alginate can partially compensate for the loss of MucD function in mouse ------------------- Key: 4910 Medline: Authors: Moss EG Title: RNA interference: It's a small RNA world. Citation: Current Biology 11: R772-R775 2001 Type: REVIEW Genes: alg-1 alg-2 dcr-1 let-7 lin-4 lin-14 lin-28 lin-41 prg-1 prg-2 rde-1 Abstract: Short RNAs regulate gene expression in many species. Some are generated from any double-stranded RNA and degrade complementary RNAs; others are encoded by genes and repress specific mRNAs. Both, it turns out, are processed and handled by similar proteins. These pathways offer a glimpse into a world of small RNAs. ------------------- Key: 4911 Medline: 11591341 Authors: Henson PM;Bratton DL;Fadok VA Title: Apoptotic cell removal. Citation: Current Biology 11: R795-R805 2001 Type: REVIEW Genes: ced-1 ced-2 ced-5 ced-6 ced-7 ced-10 ced-12 nuc-1 Abstract: Ingestion by professional or amateur phagocytes is the fate of most cells that undergo apoptosis. Studies in both Caenorhabditis elegans and mammals are now converging to reveal some of the key mechanisms and consequences of this removal process. At least seven corpse removal genes in nematodes have mammalian equivalents, and represent elements of signaling pathways involved in uptake. In mammals, a wide variety of apoptotic cell recognition receptors has been implicated and appears to be divided into two categories, involved in tethering the apoptotic cell or triggering an uptake mechanism related to macropinocytosis. Apoptotic cell removal is normally efficient and non-inflammatory. By contrast, the process may become subverted by parasites to yield a more favorable growth environment, or in other cases lead to fibrosis. Removal may also clinch the apoptotic process itself in cells not yet completely committed to death. ------------------- Key: 4912 Medline: 11675589 Authors: Kanaya S;Yamada Y;Kinouchi M;Kudo Y;Ikemura T Title: Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by miltivariate analysis. Citation: Journal of Molecular Evolution 53: 290-298 2001 Type: ARTICLE Genes: Abstract: The species-specific diversity of codon usage in five eukaryotes (Schizosaccharomyces pombe, Caenorhabditis elegans, Drosophila melanogaster, Xenopus laevis, and Homo sapiens) was investigated with principal component analysis. Optimal codons for translation were predicted on the basis of tRNA-gene copy numbers. Highly expressed genes, such as those encoding ribosomal proteins and histones in S. pombe, C. elegans, and D. melanogaster have biased patterns of codon usage which have been observed in a wide range of unicellular organisms. In S. pombe and C elegans, codons contributing positively to the principal component with the largest variance (Z(1)-parameter) corresponded to the optimal codons which were predicted on the basis of tRNA gene numbers. In D. melanogaster, this correlation was less evident, and the codons contributing positively to the Z(1)-parameter corresponded primarily to codons with a C or G in the codon third position. In X. laevis and H. sapiens, codon usage in the genes encoding ribosomal proteins and histones was not significantly biased, suggesting that the primary factor influencing codon-usage diversity in these species is not translation efficiency. Codon-usage diversity in these species is known to reflect primarily isochore structures. In the present study, the second additional factor was explained by the level of use of codons containing CG-dinucleotides, and this is discussed with respect to transcription regulation via methylation of CG-dinucleotides, which is observed in ------------------- Key: 4913 Medline: 11701657 Authors: Finch CE;Ruvkun G Title: The genetics of aging. Citation: Annual Review of Genomics & Human Genetics 2: 435-462 2001 Type: REVIEW Genes: age-1 akt-1 akt-2 clk-1 ctl-1 daf-1 daf-2 daf-3 daf-4 daf-5 daf-7 daf-8 daf-11 daf-12 daf-14 daf-16 daf-18 daf-21 pdk-1 sod-3 tph-1 Abstract: The genetic analysis of life span has only begun in mammals, invertebrates, such as Caenorhabditis elegans and Drosophila, and yeast. Even at this primitive stage of the genetic analysis of aging, the physiological observations that rate of metabolism is intimately tied to life span is supported. In many examples from mice to worms to flies to yeast, genetic variants that affect life span also modify metabolism. Insulin signaling regulates life span coordinately with reproduction, metabolism, and free radical protective gene regulation in C. elegans. This may be related to the findings that caloric restriction also regulates mammalian aging, perhaps via the modulation of insulin-like signaling pathways. The nervous system has been implicated as a key tissue where insulin-like signaling and free radical protective pathways regulate life span in C. elegans and Drosophila. Genes that determine the life span could act in neuroendocrine cells in diverse animals. The involvement of insulin-like hormones suggests that the plasticity in life spans evident in animal phylogeny may be due to variation in the timing of release of hormones that control vitality and mortality as well as variation in the response to those hormones. Pedigree analysis of human aging may reveal variations in the orthologs of the insulin pathway genes and coupled pathways that regulate invertebrate aging. Thus, genetic approaches may identify a set of circuits that was established in ancestral metazoans to regulate their ------------------- Key: 4914 Medline: Authors: Mukherjee S;Bal S;Saha P Title: Protein interaction maps using yeast two-hybrid assay. Citation: Current Science 81: 458-464 2001 Type: REVIEW Genes: Abstract: With the availability of several completed genome sequences, the analyses of large-scale interactions among the proteins encoded by them become important to decipher the complexities of biological systems involving intricate networks of macromolecular interactions. Various approaches have been developed to generate systematic genome-wide protein interaction maps (PIMs), which provide functional information of many unknown proteins. Among many methods, the yeast two-hybrid (Y2H) system is popular because it is an in vivo and inexpensive technique and easily amenable for genome-wide application. Analyses of proteomes of E. coli virus T7, vaccinia virus, yeast Saccharomyces cerevisiae, human pathogen Helicobactor pylori and nematode Caenorhabditis elegans have been carried out using Y2H. The resulting PIMs have identified functions of many proteins and generated several new hypotheses for further experimentation. ------------------- Key: 4915 Medline: 11543631 Authors: Craxton M Title: Genomic analysis of synaptotagmin genes. Citation: Genomics 77: 43-49 2001 Type: ARTICLE Genes: Abstract: I used TBLASTn to probe DNA sequence databases with a consensus peptide sequence corresponding to the most highly conserved region of the rodent synaptotagmin (Syt) gene family, which is within the C2B domain. I found human homologues for all known rodent genes, and found six further human genomic loci which encode potential family members. I found eight potential family members in Caenorhabditis elegans, six in Drosophila melanogaster, and four in Arabidopsis thaliana. The C. elegans Syt1 homologue uniquely encodes two alternative C2B exons, one or the other of which is expressed at a time. Comparison of the genomic structures of the Syt genes makes clear the different phylogenies of the different subgroups. Knowledge of the genomic structures will aid the systematic investigation of alternative splicing in Syt genes. ------------------- Key: 4916 Medline: Authors: Wei J-Z;Hale K;Carta LK;Aroian RV Title: Are Bt toxins nematicides? Citation: Phytopathology 91: S145- 2001 Type: ARTICLE Genes: Abstract: Bacillus thuringiensis (Bt) delta-endotoxins, a family of crystal (Cry) proteins, are widely used as insecticides in agriculture. Recently, we described that Bt toxins may be also effective nematicides. To more fully address the potential of Cry toxins as nematicides to control plant-parasitic-nematodes: (PPNs), we analyzed the toxicities of eight Cry proteins (Cry 5A, 5B, 6A, 6B, 12A, 13A, 14A, and 21A) on five free-living nematodes (C. elegans, Pristionchus pacificus, Panagrellus redivivus, Acrobeloides, and Distolabrellus veechi). The results of general toxicity assays, morphology, and brood size indicated that indeed some of these Cry proteins are potent nematicidal toxins. However, some had little effect on nematodes. One nematode species was resistant to all toxins. We found that one Bt toxin could be trimmed to a small 42 kD active core that was toxic to almost all these diverse nematodes. We believe that Bt toxins show good potential to control PPNs. ------------------- Key: 4918 Medline: Authors: Boyd WA;Stringer VA;Williams PL Title: Metal LC50s of a soil nematode compared to published earthworm data. Citation: "Environmental Toxicology and Risk Assessment: Implications for Environmental Decisions." BM Greenberg, RN Hull, MH Roberts Jr., RW Gensemer, Eds., American Society for Testing and Materials, Standard Technical Publication 1403. 10: 223-235 2001 Type: ARTICLE Genes: Abstract: A comparison of the acute LC50s for five metals between the standard test organism Eisenia fetida and the soil nematode Caenorhabditis elegans was made. Although the test with C. elegans is shorter (24 h vs. 2 weeks) and uses less soil or testing medium (2.33 g vs. 200 g dry weight) than that for E. fetida, LC50s were comparable for the earthworm and the nematode. The current study further investigated similarities by extending the exposure time to 48 h. Comparisions were made to 24-h C. elegans data, published E. fetida data, and U.S. Environmental Protection Agency (EPA) allowable concentrations. The nitrate salts of Pb, Ni, Cd, Zn, and Cu were used to generate LC50s. Two naturally occurring soils in Georgia were chosen to compare different soil properties on the metals' toxicity. Tifton soil was sampled from the southern region of Georgia and is characterized by relatively high sand and low clay and soil organic matter (SOM) contents. Cecil soil, in contrast, is found in the Piedmont region of Georgia and is characterized by relatively high amounts of clay and SOM. As anticipated, extending the exposure time to 48 h significantly increased the toxicity (i.e. decreased the LC50s) of the metals compared to published 24-h C. elegans data. Physical-chemical properties of soils are known to affect the binding of polyvalent metals and thus the bioavailability and toxicity of these metals. Increasing clay and SOM contents allow for an increased capacity to bind metals. For this reason, LC50s were higher in Cecil than in Tifton soil. Because tests using C. elegans are rapid, reliable, and generate data comparable to that of the earthworm, we suggest further studies that may lead to the standardization of the nematode for use as a soil toxicity-testing organism. ------------------- Key: 4919 Medline: 11557844 Authors: Derry WB;Putzke AP;Rothman JH Title: Caenorhabditis elegans p53: Role in apoptosis, meiosis, and stress resistance. Citation: Science 294: 591-595 2001 Type: ARTICLE Genes: ced-3 ced-4 cep-1 mrt-2 rad-5 unc-22 Abstract: We have identified a homolog of the mammalian p53 tumor suppressor protein in the nematode Caenorhabditis elegans that is expressed ubiquitously in embryos. The gene encoding this protein, cep-1, promotes DNA damage-induced apoptosis and is required for normal meiotic chromosome segregation in the germ line. Moreover, although somatic apoptosis is unaffected, cep-1 mutants show hypersensitivity to hypoxia-induced lethality and decreased longevity in response to starvation-induced stress. Overexpression of cep-1 promotes widespread caspase-independent cell death, demonstrating the critical importance of regulating p53 function at appropriate levels. These findings show that C. elegans p53 mediates multiple stress responses in the soma, and mediates apoptosis and meiotic chromosome segregation in the germ ------------------- Key: 4920 Medline: 11680844 Authors: Parrish S;Fire A Title: Distinct roles for RDE-1 and RDE-4 during RNA interference in Caenorhabditis elegans. Citation: RNA 7: 1397-1402 2001 Type: ARTICLE Genes: rde-1 rde-4 unc-22 Abstract: RNA interference (RNAi) is a cellular defense mechanism that uses double-stranded RNA (dsRNA) as a sequence-specific trigger to guide the degradation of homologous single-stranded RNAs. RNAi is a multistep process involving several proteins and at least one type of RNA intermediate, a population of small 21-25 nt RNAs (called siRNAs) that are initially derived from cleavage of the dsRNA trigger. Genetic screens in Caenorhabditis elegans have identified numerous mutations that cause partial or complete loss of RNAi. In this work, we analyzed cleavage of injected dsRNA to produce the initial siRNA population in animals mutant for rde-1 and rde-4, two genes that are essential for RNAi but that are not required for organismal viability or fertility. Our results suggest distinct roles for RDE-1 and RDE-4 in the interference process. Although null mutants lacking rde-1 show no phenotypic response to dsRNA, the amount of siRNAs generated from an injected dsRNA trigger was comparable to that of wild-type. By contrast, mutations in rde-4 substantially reduced the population of siRNAs derived from an injected dsRNA trigger. Injection of chemically synthesized 24- or 25-nt siRNAs could circumvent RNAi resistance in rde-4 mutants, whereas no bypass was observed in rde-1 mutants. These results support a model in which RDE-4 is involved before or during production of siRNAs, whereas RDE-1 acts after the siRNAs have been formed. ------------------- Key: 4921 Medline: 11514551 Authors: Missiaen L;Van Acker K;Parys JB;De Smedt H;Van Baelen K;Weidema AF;Vanoevelen J;Raeymaekers L;Renders J;Callewaert G;Rizzuto R;Wuytack F Title: Baseline cytosolic Ca2+ oscillations derived from a non-endoplasmic reticulum Ca2+ store. Citation: Journal of Biological Chemistry 276: 39161-39170 2001 Type: ARTICLE Genes: Abstract: Cytosolic Ca2+ oscillations can be due to cycles of release and re-uptake of internally stored Ca2+. To investigate the nature of these Ca2+ stores, we expressed the Pmr1 Ca2+ pump of Caenorhabditis elegans in COS-1 cells and pretreated the cells with thapsigargin to prevent Ca2+ uptake by the sarco(endo)plasmic reticulum Ca2+-ATPase. Pmr1 co-localized with the Golgi-specific 58K protein and was targeted to a Ca2+ store that was less leaky for Ca2+ than the endoplasmic reticulum and whose inositol trisphosphate receptors were less sensitive to inositol trisphosphate and ATP than those in the endoplasmic reticulum. ATP-stimulated Pmr1-overexpressing cells responded after a latency to extracellular Ca2+ with a regenerative Ca2+ signal, which could be prevented by caffeine. They also produced very stable ilimaquinone-sensitive baseline Ca2+ spikes, even in the presence of thapsigargin. Such responses never occurred in non-transfected cells or in cells that overexpressed the type-1 sarco(endo)plasmic reticulum Ca(2+-)ATPase. Abortive Ca2+ spikes also occurred in histamine-stimulated untransfected HeLa cells pretreated with thapsigargin, and they too were inhibited by ilimaquinone. We conclude that the Pmr1-induced Ca2+ store, which probably corresponds to the Golgi compartment, can play a crucial role in setting ------------------- Key: 4922 Medline: 11590119 Authors: Oeda T;Shimohama S;Kitagawa N;Kohno R;Imura T;Shibasaki H;Ishii N Title: Oxidative stress causes abnormal accumulation of familial amyotrophic lateral sclerosis-related mutant SOD1 in transgenic Caenorhabditis elegans. Citation: Human Molecular Genetics 10: 2013-2023 2001 Type: ARTICLE Genes: sod-1 sod-2 sod-3 Abstract: Mutations in the Cu/Zn superoxide dismutase (SOD1) genes are present in similar to 20% of families suffering from familial amyotrophic lateral sclerosis (FALS). Results from several transgenic studies in which FALS-related SOD1 mutations have been expressed have suggested that mutant SOD1 proteins induce cytotoxicity through a toxic gain of function, although the specific mechanism of this has not been fully clarified. To investigate the mechanism of toxicity induced by the mutant SOD1 associated with FALS, we generated transgenic Caenorhabditis elegans strains that contain wild-type and mutant human A4V, G37R and G93A SOD1 recombinant plasmids. The transgenic strains expressing mutant human SOD1 showed greater vulnerability to oxidative stress induced by 0.2 mM paraquat than a control that contained the wild-type human SOD1. In the absence of oxidative stress, mutant human SOD1 proteins were degraded more rapidly than the wild-type human SOD1 protein in C.elegans. In the presence of oxidative stress, however, this rapid degradation was inhibited, and the transgenic C.elegans co-expressing mutant human SOD1 and green fluorescent proteins (GFPs) in muscle tissues demonstrated discrete aggregates in the adult stage. These results suggest that oxidative damage inhibits the degradation of FALS-related mutant human SOD1 proteins, resulting in an aberrant accumulation of mutant proteins that might contribute to the cytotoxicity. ------------------- Key: 4923 Medline: 11641272 Authors: Ketting RF;Fischer SEJ;Bernstein E;Sijen T;Hannon GJ;Plasterk RHA Title: Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Citation: Genes & Development 15: 2654-2659 2001 Type: ARTICLE Genes: dcr-1 let-7 lin-4 lin-41 mut-15 Abstract: Double-stranded RNAs can suppress expression of homologous genes through an evolutionarily conserved process named RNA interference (RNAi) or post-transcriptional gene silencing (PTGS). One mechanism underlying silencing is degradation of target mRNAs by an RNP complex, which contains similar to 22 nt of siRNAs as guides to substrate selection. A bidentate nuclease called Dicer has been implicated as the protein responsible for siRNA production. Here we characterize the Caenorhabditis elegans ortholog of Dicer (K12H4.8; dcr-1) in vivo and in vitro. dcr-1 mutants show a defect in RNAi. Furthermore, a combination of phenotypic abnormalities and RNA analysis suggests a role for dcr-1 in a regulatory pathway comprised of small temporal RNA (let-7) and its target (e.g., lin-41). ------------------- Key: 4924 Medline: 11606206 Authors: Laurent V;Brooks DR;Coates D;Isaac RE Title: Functional expression and characterization of the cytoplasmic aminopeptidase P of Caenorhabditis elegans. Citation: European Journal of Biochemistry 268: 5430-5438 2001 Type: ARTICLE Genes: Abstract: Aminopeptidase P (AP-P; X-Pro aminopeptidase; EC 3.4.11.9) cleaves the N-terminal X-Pro bond of peptides and occurs in mammals as both cytosolic and plasma membrane forms, encoded by separate genes. In mammals, the plasma membrane AP-P can function as a kininase, but little is known about the physiological role of the cytosolic enzyme. The C. elegans genome contains a single gene encoding AP-P (W03G9.4), analysis of which predicts regions displaying high levels of amino-acid sequence homology between the predicted gene product and mammalian cytoplasmic AP-P, with the absolute conservation of key catalytic residues. The sequence of an EST (yk9lg4), comprising the open reading frame of W03G9.4, confirmed the predicted genomic structure of the gene and the prediction that W03G9.4 codes for a nonsecreted protein with a molecular mass of 68 kDa. Nematodes transformed with a promoter reporter construct, W03G9.4::GFP, showed high levels of fluorescence in the intestine of larvae and adult hermaphrodites, indicating that the intestine is a major site of W03G9.4 expression. yk9lg4 tagged with a hexahistidine and DLYDDDDK peptide epitope was expressed in Escherichia coli to yield, after affinity purification, a recombinant protein with a molecular mass of 71 kDa. The recombinant W03G9.4 removed the N-terminal amino acid from bradykinin (RPPGFSPFR), a Caenorhabditis elegans neuropeptide (KPSFVRFamide) and Lem Trp 1 (APSGFLGVRamide), but did not display activity towards angiotensin I (NRVYIHPFHL), des-Arg bradykinin and AF1 (KNEFIRFamide). The activity towards bradykinin was inhibited by EDTA and 1, 10 phenanthroline, as expected for a metalloenzyme, and also by apstatin (IC50, 1 muM), a selective inhibitor of mammalian AP-P. A K-m of 45 muM and an optimum pH of 7-8 was observed with bradykinin as the substrate. The activity of the nematode AP-P, like its mammalian counterparts, was strongly influenced by metal ions, with Co2+ Mn2+ and Zn2+ all inhibiting the hydrolysis of bradykinin. We conclude that W03G9.4 codes for a cytoplasmic AP-P with very similar enzymatic properties to those of mammalian AP-P, and we suggest that the enzyme has a physiological role in the intracellular hydrolysis of proline-containing peptides absorbed from the lumen of the ------------------- Key: 4925 Medline: 11544101 Authors: Savage-Dunn C Title: Targets of TGF Beta-related signaling in Caenorhabditis elegans. Citation: Cytokine and Growth Factor Reviews 12: 305-312 2001 Type: REVIEW Genes: bra-1 cat-2 daf-1 daf-3 daf-4 daf-5 daf-7 daf-8 daf-12 daf-14 dbl-1 egl-4 egl-32 lin-31 lon-1 myo-2 scd-1 scd-2 scd-3 sma-2 sma-3 sma-4 sma-6 tig-1 unc-129 Abstract: With the characterization of the Smads 5 years ago, it became possible to trace the TGFB signal transduction pathway from the plasma membrane to the nucleus. Since that time, many Smad interaction partners, cofactors and target genes have been identified using a variety of experimental approaches and model systems. Understanding how these generate tissue specificity and crosstalk between pathways is an ongoing puruit for the field of TGFB signal transduction. The nematode Caenorhabditis elegans provides a simple, genetically tractable model organism in which to address this goal. This review will examine progress towards the identification of cellular and molecular targets of TGFB-related signaling in C. elegans. ------------------- Key: 4926 Medline: 11672865 Authors: Mango SE Title: Stop making nonSense: the C. elegans smg genes. Citation: Trends in Genetics 17: 646-653 2001 Type: REVIEW Genes: avr-14 dpy-5 emb-30 fem-1 glp-1 lin-29 smg-1 smg-2 smg-3 smg-4 smg-5 smg-6 smg-7 uag-1 unc-49 unc-54 unc-73 unc-76 Abstract: Cells monitor the quality of their mRNAs and degrade any transcripts that are poorly or incompletely translated. In the nematode, Caenorhabditis elegans, degradation by the mRNA surveillance pathway depends on seven smg genes. Three of these genes also have a role in a second mRNA degradation pathway called RNA interference (RNAi), which is triggered by double-stranded RNA (dsRNA). Here I describe what is known about the smg genes and their potential functions in these two mRNA degradation pathways. ------------------- Key: 4927 Medline: 11679671 Authors: Lau Nelson C;Lim LP;Weinstein EG;Bartel DP Title: An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Citation: Science 294: 858-862 2001 Type: ARTICLE Genes: glp-4 let-7 lin-4 mir-1 mir-2 mir-34 mir-35 mir-36 mir-37 mir-38 mir-39 mir-40 mir-41 mir-42 mir-43 mir-44 mir-45 mir-46 mir-47 mir-48 mir-49 mir-50 mir-51 mir-52 mir-53 mir-54 mir-55 mir-56 mir-57 mir-58 mir-59 mir-60 mir-61 mir-62 mir-63 mir-64 mir-65 mir-66 mir-67 mir-68 mir-69 mir-70 mir-71 mir-72 mir-73 mir-74 mir-75 mir-76 mir-77 mir-78 mir-79 mir-80 mir-81 mir-82 mir-83 mir-84 mir-85 mir-86 Abstract: Two small temporal RNAs (stRNAs), lin-4 and let-7, control developmental timing in Caenorhabditis elegans. We find that these two regulatory RNAs are members of a large class of 21- to 24-nucleotide noncoding RNAs, called microRNAs (miRNAs). We report on 55 previously unknown miRNAs in C. elegans. The miRNAs have diverse expression patterns during development: a let-7 paralog is temporally coexpressed with let-7; miRNAs encoded in a single genomic cluster are coexpressed during embryogenesis; and still other miRNAs are expressed constitutively throughout development. Potential orthologs of several of these miRNA genes were identified in Drosophila and human genomes. The abundance of these tiny RNAs, their expression patterns, and their evolutionary conservation imply that, as a class, miRNAs have broad regulatory functions in animals. ------------------- Key: 4928 Medline: 11679672 Authors: Lee RC;Ambros V Title: An extensive class of small RNAs in Caenorhabditis elegans. Citation: Science 294: 862-864 2001 Type: ARTICLE Genes: dcr-1 let-7 lin-4 mir-1 mir-2 mir-42 mir-43 mir-52 mir-58 mir-60 mir-62 mir-72 mir-80 mir-81 mir-87 mir-88 mir-89 mir-90 Abstract: The lin-4 and let-7 antisense RNAs are temporal regulators that control the timing of developmental events in Caenorhabditis elegans by inhibiting translation of target mRNAs. let-7 RNA is conserved among bilaterian animals, suggesting that this class of small RNAs [microRNAs (miRNAs)] is evolutionarily ancient. Using bioinformatics and cDNA cloning, we found 15 new miRNA genes in C. elegans. Several of these genes express small transcripts that vary In abundance during C. elegans larval development, and three of them have apparent homologs in mammals and/or insects. Small noncoding RNAs of the miRNA class appear to be numerous and diverse. ------------------- Key: 4929 Medline: Authors: Park JO;Hargreaves JR;Cole ALJ;Ghisalberti EL;Gams W;Sivasithamparam K Title: Cuticular disruption and mortality of Caenorhabditis elegans exposed to culture filtrate of Byssochlamys nivea Citation: Nematology 3: 355-363 2001 Type: ARTICLE Genes: Abstract: A strain of a Byssochlamys nivea, isolated from saline mud in Western Australia as a part of statewide survey of soil fungi for nematophagous activity, was evaluated for its effect on nematodes. Culture filtrate of the fungus grown on potato dextrose broth for 7 days caused structural changes in the cuticle, aggregation of individuals, and mortality of Caenorhabditis elegans. In addition, the culture filtrate completely inhibited hatching of C. elegans eggs. Exudates from agar colonies also caused cuticular disruption and mortality of C. elegans. The cuticular disruption observed, not reported in nematodes before, was initiated in the labial region and spread towards the posterior region of the nematode within 10 min of application. This reaction occurred only in live nematodes. Cuticular disruption and mortality caused by the culture filtrate varied according to growth conditions. The active compound(s) in the culture filtrate were thermostable (100 degreesC for 1 h); however freezing the culture filtrate (-20 degreesC for 2 days) eliminated the activities, as did dialysis (< 14 000 molecular weight). Cuticular disruption and mortality were also observed when the nematode was exposed to culture filtrates of two other strains of B. nivea supplied by CBS, The Netherlands. The culture filtrate also inhibited in vitro growth of the plant-pathogenic fungi Fusarium oxysporum, Gaeumannomyces graminis var. tritici, Phytophthora cinnamomi, Pythium irregulare and Rhizoctonia solani. ------------------- Key: 4930 Medline: Authors: Baird SE Title: Strain-specific variation in the pattern of caudal papillae in Caenorhabditis briggsae (Nematoda: Rhabditidae); implications for species identification. Citation: Nematology 3: 373-376 2001 Type: ARTICLE Genes: egl-5 mab-5 Abstract: Caenorhabditis briggsae is a member of the 'elegans group', a monophyletic clade of seven species within Caenorhabditis. Species identifications within this group are difficult. C. briggsae and C. elegans can be distinguished in that they are hermaphroditic whereas the other members of the elegans group are gonochoristic. C. briggsae and C. clavopapillata can be distinguished from other elegans group members based on their patterns of ------------------- Key: 4931 Medline: 11745661 Authors: Rogers CM;Franks CJ;Walker RJ;Burke JF;Holden-Dye L Title: Regulation of the pharynx of Caenorhabditis elegans by 5-HT, octopamine, and FMRFamide-like neuropeptides. Citation: Journal of Neurobiology 49: 235-244 2001 Type: ARTICLE Genes: cat-1 cat-4 flp-1 flp-3 flp-5 flp-6 flp-8 flp-9 flp-13 flp-14 flp-16 goa-1 snb-1 tph-1 Abstract: More than fifty FMRFamide-like neuropeptides have been identified in nematodes. We addressed the role of a subset of these in the control of nematode feeding by electrophysiological recording of the activity of C. elegans pharynx. AF1 (KNEFIRFamide), AF2 (KHEYLPFamide), AF8 (KSAYMRFamide), and GAKFIRFamide (encoded by the C elegans genes flp-8, flp-14, flp-6, and flp-5, respectively) increased pharyngeal action potential frequency, in a manner similar to 5-HT. In contrast, SDPNFLRFamide, SADPNFLRFamide, SAEPFGTMRFamide, KPSVRFamide, APEASPFIRFamide, and AQTVRFamide (encoded by the C elegans genes flp-1; flp-1; flp-3; flp-9; flp-13, and flp-16, respectively) inhibited the pharynx in a manner similar to octopamine. Only three of the neuropeptides had potent effects at low nanomolar concentrations, consistent with a physiological role in pharyngeal regulation. Therefore, we assessed whether these three peptides mediated their actions either directly on the pharynx or indirectly via the neural circuit controlling its activity by comparing actions between wild-type and mutants with deficits in synaptic signaling. Our data support the conclusion that AF1 and SAEPFGTMRFamide regulate the activity of the pharynx indirectly, whereas APEASPFIRFamide exerts its action directly. These results are in agreement with the expression pattern for the genes encoding the neuropeptides (Mm and Li, 1999) as both flp-8 and flp-3 are expressed in extrapharyngeal neurons, whereas flp-13 is expressed in 15, a neuron with synaptic output to the pharyngeal muscle. These results provide the first, direct, functional information on the action of neuropeptides in C elegans. Furthermore, we provide evidence for a putative inhibitory peptidergic synapse, which is likely to have a ------------------- Key: 4932 Medline: 11580201 Authors: Combes D;Fedon Y;Toutant JP;Arpagaus M Title: Acetylcholinesterase genes in the nematode Caenorhabditis elegans. Citation: International Review of Cytology - A Survey of Cell Biology 209: 207-239 2001 Type: REVIEW Genes: ace-1 ace-2 ace-3 ace-4 Abstract: Acetylcholinesterase (ACheE, EC 3.1.1.7) is responsible for the termination of cholinergic nerve transmission. It is the target of organophosphates and carbamates, two types of chemical pesticides being used extensively in agriculture and veterinary medicine against insects and nematodes. Whereas there is usually one single gene encoding AChE in insects, nematodes are one of the rare phyla where multiple ace genes have been unambiguously identified. We have taken advantage of the nematode Caenorhabditis elegans model to identify the four genes encoding AChE in this species. Two genes, ace-1 and ace-2, encode two major AChEs with different pharmacological properties and tissue repartition: ace-1 is expressed in muscle cells and a few neurons, whereas ace-2 is mainly expressed in motoneurons. ace-3 represents a minor proportion of the total AChE activity and is expressed in only a few cells, but it is able to sustain double null mutants ace-1; ace-2. It is resistant to usual cholinesterase inhibitors. ace-4 was transcribed but the corresponding enzyme was not detected ------------------- Key: 4933 Medline: 11683918 Authors: Lee J;Jee C;Lee JI;Lee MH;Lee MH;Koo HS;Chung CH;Ahnn J Title: A deubiquitinating enzyme, UCH/CeUBP130, has an essential role in the formation of a functional microtubule-organizing centre (MTOC) during early cleavage Citation: Genes to Cells 6: 899-911 2001 Type: ARTICLE Genes: uch-1 Abstract: Background: Denbiquitinating enzymes generate monomeric ubiquitin in protein degradation pathways and are known to be important for the early development in many organisms. Results: RNA interference experiments targeted for a UBP homologue, UCH/CeUBP130, in C. elegans resulted in cell division defective embryos. Immunostaining localized UCH/CeUBP130 in the sperm and at the microtubule-organizing centre (MTOC) during early cleavage. Furthermore, the embryonic lethal phenotype was rescued by mating with wild-type males. Conclusions: Since it is known that the MTOC in the fertilized embryo is contributed by sperm asters in C. elegans, we suggest that UCH/CeUBP130 and ubiquitin protein degradation pathways may be involved in microtubule-based sperm aster formation. Therefore UCH/CeUBP130 is necessary for the formation of a functional MTOC in the fertilized embryo of C. elegans. ------------------- Key: 4934 Medline: 11681734 Authors: Knight CG;Azevedo RBR;Leroi AM Title: Testing life-history pleiotropy in Caenorhabditis elegans. Citation: Evolution 55: 1795-1804 2001 Type: ARTICLE Genes: Abstract: Much life-history theory assumes that alleles segregating in natural populations pleiotropically affect life-history traits. This assumption, while plausible, has rarely been tested directly. Here we investigate the genetic relationship between two traits often suggested to be connected by pleiotropy: maternal body size and fertility. We carry out a quantitative trait locus (QTL) analysis on two isolates of the free-living nematode Caenorhabditis elegans, and identify two body size and three fertility QTLs. We find that one of the fertility QTLs colocalizes with the two body size QTLs on Chromosome IV. Further analysis, however, shows that these QTLs are genetically separable. Thus, none of the five body size or fertility QTLs identified here shows detectable pleiotropy for the assayed traits. The evolutionary origin of these QTLs, possible candidate loci, and the significance for life-history evolution are discussed. ------------------- Key: 4935 Medline: 11600454 Authors: Puoti A;Pugnale P;Belfiore M;Schlappi AC;Saudan Z Title: RNA and sex determination in Caenorhabditis elegans: Post-transcriptional regulation of the sex-determining gene tra-2 and fem-3 mRNAs in the Caenorhabditis elegans hermaphrodite. Citation: EMBO Reports 2: 899-904 2001 Type: REVIEW Genes: fbf-1 fbf-2 fem-3 fog-2 gld-1 laf-1 lin-29 lin-41 mog-1 mog-4 mog-5 nos-1 nos-2 nos-3 tra-2 Abstract: The Caenorhabditis elegans hermaphrodite sequentially produces sperm and oocytes from a single pool of precursors. Therefore, the hermaphrodite's germ line is the site of two major cell fate decisions: a germ cell precursor first undergoes a mitosis/meiosis decision and then a sperm/oocyte decision. While the mitosis/meiosis decision is governed by Notch/GLP-1 signalling, the sperm/oocyte decision relies on post-transcriptional regulation, of two key mRNAs, tra-2 and fem-3. This review focuses on factors that are required for the silencing of these mRNAs, which results in the sequential production of sperm and oocytes. Most factors that regulate the expression of tra-2 and fem-3 are homologous to proteins involved in RNA regulation in yeast, mammals or Drosophila, suggesting that at least some of the molecular mechanisms regulating the two worm mRNAs have been conserved ------------------- Key: 4936 Medline: 11604120 Authors: Goldstein B Title: On the evolution of early development in the Nematoda. Citation: Philosophical Transactions of the Royal Society of London - Series B: Biological Sciences 356: 1521-1531 2001 Type: REVIEW Genes: Abstract: The phylum Nematoda serves as an excellent model system for exploring how development evolves, using a comparative approach to developmental genetics. More than 100 laboratories are studying developmental mechanisms in the nematode Caenorhabditis elegans, and many of the methods that have been developed for C. elegans can be applied to other nematodes. This review summarizes what is known so far about steps in early development that have evolved in the nematodes, and proposes potential experiments that could make use of these data to further our understanding of how development evolves. The promise of such a comparative approach to developmental genetics is to fill a wide gap in our understanding of evolution-a gap spanning from mutations in developmental genes through to their phenotypic results, on which natural selection may act. ------------------- Key: 4937 Medline: 11691930 Authors: Nguyen L;Round J;O'Connell R:Geurts P;Funes-Duran M;Wong J;Jongeward G;Vierra CA Title: Isolation and characterization of the activated B-cell factor 1 homolog in Caenorhabditis elegans. Citation: Nucleic Acids Research 29: 4423-4432 2001 Type: ARTICLE Genes: egl-15 Abstract: Members of the basic helix-loop-helix (bHLH) family of transcription factors regulate a wide array of developmental processes in many cell types, including cell fate specification, differentiation and morphogenesis. Our studies describe the cloning of a gene from the nematode Caenorhabditis elegans that is closely related to the vertebrate-activated B-cell factor (ABF) gene. The nematode gene product CeABF-1 was detected by northern blot analysis from RNA isolated from pooled nematodes representing different developmental stages. The developmental expression profile of CeABF-1 was shown by RT-PCR analysis to be predominantly expressed in the larval stages L3 and L4, with lower levels observed in the L2 larval stage and adult. We also show that CeABF-1 is capable of forming heterodimers with E2A proteins and binding E-box target sites. Mammalian cells transfected with CeABF-1 expression plasmids were capable of blocking E2A-mediated gene transcription, but full repression activity required the presence of two conserved amino acid residues found within the first helix of the CeABF-1 bHLH domain. These results suggest a conserved mechanism of gene repression between certain class II bHLH and class I bHLH proteins found in vertebrates and invertebrates. ------------------- Key: 4938 Medline: 11533026 Authors: Tong J;Killeen M;Steven R;Binns KL;Culotti J;Pawson T Title: Netrin stimulates tyrosine phosphorylation of the UNC-5 family of netrin receptors and induces Shp2 binding to the RCM cytodomain. Citation: Journal of Biological Chemistry 276: 40917-40925 2001 Type: ARTICLE Genes: unc-5 unc-6 unc-40 Abstract: Caenorhabditis elegans UNC-5 and its mammalian homologues such as RCM are receptors for the secreted axon guidance cue UNC-6/netrin and are required to mediate the repulsive effects of UNC-6/netrin on growth cones. We find that C. elegans UNC-5 and mouse RCM are phosphorylated on tyrosine in vivo. C. elegans UNC-5 tyrosine phosphorylation is reduced in unc-6 null mutants, and RCM tyrosine phosphorylation is induced by netrin-1 in transfected HEK-293 cells, demonstrating that phosphorylation of UNC-5 proteins is enhanced by UNC-6/netrin stimulation in both worms and mammalian cells. An activated Src tyrosine kinase induces phosphorylation of RCM at multiple cytoplasmic tyrosine residues creating potential binding sites for cytoplasmic signaling proteins. Indeed, the NH2-terminal SH2 domain of the Shp2 tyrosine phosphatase bound specifically to a Tyr(568) RCM phosphopeptide. Furthermore, Shp2 associated with RCM in a netrin-dependent manner in transfected cells, and co-immunoprecipitated with RCM from an embryonic mouse brain lysate. A Y568F mutant RCM receptor failed to bind Shp2 and was more highly phosphorylated on tyrosine than the wild type receptor. These results suggest that netrin-stimulated phosphorylation of RCM Tyr(568) recruits Shp2 to the cell membrane where it can potentially modify RCM ------------------- Key: 4939 Medline: 11672983 Authors: Johnson TE;de Castro E;de Castro SH;Cypser J;Henderson S;Tedesco P Title: Relationship between increased longevity and stress resistance as assessed through gerontogene mutations in Caenorhabditis elegans. Citation: Experimental Gerontology 36: 1609-1617 2001 Type: ARTICLE Genes: age-1 daf-2 daf-4 daf-7 daf-16 daf-23 daf-28 mev-1 old-1 spe-26 Abstract: We review the status of the hypothesis that interventions that increase the resistance to stress offer the potential for effective life prolongation and increased health. The work focuses on research in the nematode worm Caenorhabditis elegans and describes both published and unpublished results consistent with this hypothesis. Correlations between stress resistance and longevity among many gerontogene mutants is provided. ------------------- Key: 4940 Medline: 11641215 Authors: Amiri A;Keiper BD;Kawasaki I;Fan Y;Kohara Y;Rhoads RE;Strome S Title: An isoform of eIF4E is a component of germ granules and is required for spermatogenesis in C. elegans. Citation: Development 128: 3899-3912 2001 Type: ARTICLE Genes: fem-2 fem-3 glp-4 ife-1 ife-2 ife-3 ife-4 ife-5 pgl-1 rde-1 rpp-1 Abstract: Control of gene expression at the translational level is crucial for many developmental processes. The mRNA cap-binding protein, eIF4E, is a key player in regulation of translation initiation; appropriate levels of eIF4E are essential for normal cell-cycle regulation and tissue differentiation. The observation that eIF4E levels are elevated during gametogenesis in several organisms suggests that eIF4E might have a specific role in gamete formation as well. We show that one of the five isoforms of C. elegans eIF4E, IFE-1, is enriched in the germline and is a component of germ granules (P granules). The association of IFE-1 with P granules requires the P-granule protein PGL-1. In vitro PGL-1 interacts directly with IFE-1, but not with the other four isoforms of eIF4E. Analysis of animals depleted of IFE-1 by RNAi shows that IFE-1 is required for spermatogenesis, specifically for efficient progression through the meiotic divisions and for the production of functional sperm, in both hermaphrodites and males. The requirement for IFE-1 is highly sensitive to temperature. IFE-1 is not required for oogenesis, as ife-1(RNAi) hermaphrodites produce viable progeny when normal sperm are supplied. Consistent with a primary role in spermatogenesis, ife-1 m-RNA levels are highest in regions of the gonad undergoing spermatogenesis. Our results suggest that C. elegans spermatogenesis requires either this specific isoform. of eIF4E or an elevated level of ------------------- Key: 4941 Medline: 11641227 Authors: Benard C;McCright B;Zhang Y;Felkai S;Lakowski B;Hekimi S Title: The C. elegans maternal effect gene clk-2 is essential for embryonic development, encodes a protein homologous to yeast Tel2p and affects telomere length. Citation: Development 128: 4045-4055 2001 Type: ARTICLE Genes: clk-2 cux-7 fem-3 glp-4 lin-39 Abstract: The Caenorhabditis elegans maternal-effect clk genes are involved in the temporal control of development and behavior. We report the genetic and molecular characterization of clk-2. A temperature-sensitive mutation in the gene clk-2 affects embryonic and post-embryonic development, reproduction, and rhythmic behaviors. Yet, virtually all phenotypes are fully maternally rescued. Embryonic development strictly requires the activity of maternal clk-2 during a narrow time window between oocyte maturation and the two- to four-cell embryonic stage. Positional cloning of clk-2 reveals that it encodes a protein homologous to S. cerevisiae Tel2p. In yeast, the gene TEL2 regulates telomere length and participates in gene silencing at subtelomeric regions. In C elegans, elk-2 mutants have elongated telomeres, and clk-2 overexpression can lead to telomere shortening. Tel2p. has been reported to bind to telomeric DNA repeats in vitro. However, we find that a functional CLK-2::GFP fusion protein is cytoplasmic in worms. We discuss how the phenotype of clk-2 mutants could be the result of altered patterns of gene expression. ------------------- Key: 4942 Medline: 11641230 Authors: Knobel KM;Davis WS;Jorgensen EM;Bastiani MJ Title: UNC-119 suppresses axon branching in C. elegans. Citation: Development 128: 4079-4092 2001 Type: ARTICLE Genes: acr-5 unc-119 Abstract: The architecture of the differentiated nervous system is stable but the molecular mechanisms that are required for stabilization are unknown. We characterized the gene unc-119 in the nematode Caenorhabditis elegans and demonstrate that it is required to stabilize the differentiated structure of the nervous system. In unc-119 mutants, motor neuron commissures are excessively branched in adults. However, live imaging demonstrated that growth cone behavior during extension was fairly normal with the exception that the overall rate of migration was reduced. Later, after development was complete, secondary growth cones sprouted from existing motor neuron axons and cell bodies. These new growth cones extended supernumerary branches to the dorsal nerve cord at the same time the previously formed axons retracted. These defects could be suppressed by expressing the UNC-119 protein after embryonic development; thus demonstrating that UNC-119 is required for the maintenance of the nervous system architecture. Finally, UNC-119 is located in neuron cell bodies and axons and acts cell-autonomously to inhibit axon ------------------- Key: 4943 Medline: 11689700 Authors: Schutzman J;Borland CZ;Newman JC;Robinson MK;Kokel M;Stern MJ Title: The Caenorhabditis elegans EGL-15 signaling pathway implicates a DOS-like multisubstrate adaptor protein in fibroblast growth factor signal transduction. Citation: Molecular and Cellular Biology 21: 8104-8116 2001 Type: ARTICLE Genes: clr-1 egl-15 let-60 let-341 mek-2 mpk-1 ptp-2 sem-5 soc-2 Abstract: EGL-15 is a fibroblast growth factor receptor in the nematode Caenorhabditis elegans. Components that mediate EGL-15 signaling have been identified via mutations that confer a Clear (CIr) phenotype, indicative of hyperactivity of this pathway, or a suppressor-of-Clr (Soc) phenotype, indicative of reduced pathway activity. We have isolated a gain-of-function allele of let-60 ras that confers a Cir phenotype and implicated both let-60 ras and components of a mitogen-activated protein kinase cascade in EGL-15 signaling by their Soc phenotype. Epistasis analysis indicates that the gene soc-1 functions in EGL-15 signaling by acting either upstream of or independently of LET-60 RAS. soc-1 encodes a multisubstrate adaptor protein with an amino-terminal pleckstrin homology domain that is structurally similar to the DOS protein in Drosophila and mammalian GAB1. DOS is known to act with the cytoplasmic tyrosine phosphatase Corkscrew (CSW) in signaling pathways in Drosophila. Similarly, the C. elegans CSW ortholog PTP-2 was found to be involved in EGL-15 signaling. Structure-function analysis of SOC-1 and phenotypic analysis of single and double mutants are consistent with a model in which SOC-1 and PTP-2 act together in a pathway downstream of EGL-15 and the Src homology domain 2 (SH2)/SH3-adaptor protein SEM-5/GRB2 contributes to SOC-1-independent activities of EGL-15. ------------------- Key: 4944 Medline: 11676537 Authors: Anyanful A;Sakube Y;Takuwa K;Kagawa H Title: The third and fourth tropomyosin isoforms of Caenorhabditis elegans are expressed in the pharynx and intestines and are essential for development and morphology. Citation: Journal of Molecular Biology 313: 525-537 2001 Type: ARTICLE Genes: ceh-22 ges-1 lev-11 myo-2 tmy-1 Abstract: The tropomyosin gene tmy-1/lev-11 of Caenorhabditis elegans spans 14.5 kb Science and Technology and encodes three isoforms by alternative splicing. To identify, characterize and compare the genome and tissue expression of a fourth isoform, the technique of rapid amplification of cDNA ends and microinjection with lacZ and gfp fusion plasmids were employed. We elucidated CeT-MIV, a fourth isoform of tmy-1, which encoded a 256 residue polypep tide. CeTMIV isoform had a similar promoter region to CeTMIII isoform, but was alternatively spliced to generate a cDNA that differed in two, exons. The tmy-1::lacZ and tiny-1::gfp fusion genes, with 3.2 kb promoter sequence and 1.1 kb of CeTMIV isoform specific exons, were expressed in the pharyngeal and intestinal cells. Further unidirectional deletion of the sequence located the primary promoter region 853 by upstream from the initial codon. We show within the upstream region, the presence of B and C subelement-like sequences of myo-2, which may be used to stimulate pharyngeal expression. Despite the presence of a ges-1 like sequence, we were unable to locate the two GATA sites required for intestinal expression. Reassessing tissue expression for CeTMIII isoform with newly constructed fusion plasmids, we showed further expression in germ-line tissue and intestinal cells in addition to pharyngeal expression. Finally, to demonstrate that tropomyosin is essential for development, we inactivated the body wall and pharynx-specific isoforms by RNA-mediated interference. In addition to 50-75 % embryonic lethality in both cases, the worms that survived body wall interference had abnormal body morphology and uncoordinated movements, and those that survived pharynx interference had deformed pharynges and gut regions. These results show the function of tropomyosin in normal muscle filament assembly and embryonic development, and illustrate the different expression patterns characteristic of tropomyosin isoforms in C. ------------------- Key: 4945 Medline: 11687251 Authors: Morino K;Katsumi H;Akahori Y;Iba Y;Shinohara M;Ukai Y;Kohara Y;Kurosawa Y Title: Antibody fusions with fluorescent proteins: a versatile reagent for profiling protein expression. Citation: Journal of Immunological Methods 257: 175-184 2001 Type: ARTICLE Genes: Abstract: We developed a system by which antibodies, fused to fluorescent proteins with different wavelengths, can be prepared within a month against various antigens. An antibody library composed of a large number of single-chain Fv-CL fragment was constructed by means of a phage-display system. The constructs were designed to facilitate changing of the protein forms by simple enzyme manipulation. In the present study, we adopted a molecular form of antibody in which a single-chain Fv-CL fragment is fused with a green fluorescent protein (GFP) or red fluorescent protein (RFP). In addition, a His-tag was inserted between CL and GFP (or RFP). We describe the utility of this system using Caenorhabditis elegans embryo as a model. ------------------- Key: 4946 Medline: 11746760 Authors: Kanugula S;Pegg AE Title: Novel DNA repair alkyltransferase from Caenorhabditis elegans. Citation: Environmental & Molecular Mutagenesis 38: 235-243 2001 Type: ARTICLE Genes: agt-1 agt-2 Abstract: O-6-Alkylguanine DNA-alkyltransferase (AGT) is a widely distributed DNA repair protein that protects living organisms from endogenous and exogenous alkylation damage to DNA at the O-6-position of guanine. The search of the C. elegans genome database for an AGT protein revealed the presence of a protein (cAGT-2) with some similarity to known AGTs in addition to the easily recognized cAGT-1 protein. The predicted protein sequence of cAGT-2 contains the amino acid sequence -ProCys-HisPro- at the presumed active site of the protein, whereas all other known AGTs have -ProCys-HisArg-. A truncated version of the cAGT-2 protein was expressed in E. coli. This purified recombinant protein was able to repair O-6-methyl-guanine and O-4-methylthymine adducts in DNA in vitro and also reacted with the bulky benzyl adduct in O-6-benzylguanine. This fragment of cAGT-2 (104 amino acids) is the smallest protein possessing AGT activity yet described. The full-length cAGT-2 protein (274 amino acids) totally lacks the N-terminal domain present in all other known AGTs but has a long C-terminal extension that has significant homology to histone 1C. Expression of cAGT-2 in an E. coli strain lacking endogenous AGT activity provided modest but statistically significant resistance to the toxicity of N-methyl-N'-nitro-N-nitrosoguanidine, confirming that ------------------- Key: 4947 Medline: 11747075 Authors: Aspock G;Burglin TR Title: The Caenorhabditis elegans Distal-less ortholog ceh-43 is required for development of the anterior hypodermis. Citation: Developmental Dynamics 222: 403-409 2001 Type: ARTICLE Genes: ceh-43 jam-1 Abstract: Homeobox genes of the Distal-less (Dll) class are expressed in developing appendages as well as in the central nervous system in invertebrates and vertebrates. Mutant analyses in mice and Drosophila have implicated these genes in outgrowth of structures, cell adhesion, cell migration, and cell fate decisions. We have investigated the expression and function of ceh-43, the Dll ortholog from the nematode Caenorhabditis elegans, by using gfp reporter constructs and double-stranded RNA-mediated interference (RNAi). Our results show that, as in the fly, the C. elegans Dll ortholog seems to play a role in cell adhesion. An antibody against the butterfly Distal-less homeodomain stains the nervous system of C. elegans embryos (Panganiban et al. [1997] Proc Natl Acad Sci USA. 94:5162-5166). GFP expression under the control of the ceh-43 promoter looks similar, although strong expression is primarily confined to the head hypodermis and to neuronal support cells. ceh43(RNAi) results in 100% lethality at embryonic or early larval stages. At the beginning of morphogenesis, ceh-43(RNAi) embryos start to lose cells through a hole in the head hypodermis. They either rupture interiorly as elongation proceeds, or they elongate normally to threefold egg length with the pharynx not connected to the mouth. Elongated ceh-43(RNAi) animals die before or soon after hatching with a fluid-filled pseudocoel and large vacuoles. These phenotypes suggest a role for ceh-43 in development of adhesive properties in the head hypodermis that connects the epithelia of the skin and the digestive tract. Furthermore, possible defects in the excretory system may result at least in part from a requirement for ceh-43 in the CAN neurons where ceh-43::gfp is also expressed. ------------------- Key: 4948 Medline: 11696341 Authors: Hahn BS;Labouesse M Title: Tissue integrity: Hemidesmosomes and resistance to stress. Citation: Current Biology 11: R858-R861 2001 Type: REVIEW Genes: mua-3 mup-4 Abstract: How do animal tissues resist the shearing forces to which they are exposed during locomotion or harsh encounters with the environment? Genetic analysis in Caenorhabditis elegans is furthering our understanding of the nature and function of the attachments that preserve tissue integrity. ------------------- Key: 4949 Medline: 11696343 Authors: Meier B;Ahmed S Title: Checkpoints: chromosome pairing takes an unexpected twist. Citation: Current Biology 11: R865-R868 2001 Type: REVIEW Genes: chk-2 rad-5 Abstract: When meiotic cells complete S phase, homologous chromosomes pair, synapse and undergo recombination. A checkpoint protein is somehow required for meiotic chromosome pairing in C. elegans, thus providing a direct link between S phase and the rest of the meiotic program. ------------------- Key: 4950 Medline: 11696327 Authors: Mariol MC;Segalat L Title: Muscular degeneration in the absence of dystrophin is a calcium-dependent process. Citation: Current Biology 11: 1691-1694 2001 Type: ARTICLE Genes: dys-1 egl-19 hlh-1 Abstract: Duchenne muscular dystrophy (DMD) is a progressive degenerative muscular disease that is due to mutations in the dystrophin gene [1]. Neither the function of dystrophin nor the physiopathology of the disease have been clearly established yet. Several groups have reported elevated calcium concentrations in the mdx mouse model of DMD, but the effect of calcium levels on the progression of the disease continues to be a matter of debate [2-4]. Here, we show that, in Caenorhabditis elegans, a gain-of-function mutation in the egl-19 calcium channel gene dramatically increases muscle degeneration in dystrophin mutants. Conversely, RNAi-mediated inhibition of egl-19 function reduces muscle degeneration by half. Therefore, our results demonstrate that calcium channel activity is a critical factor in the progression of dystrophin-dependent muscle degeneration. ------------------- Key: 4951 Medline: 11696330 Authors: Lim CS;Mian IS;Dernburg AF;Campisi J Title: C. elegans clk-2, a gene that limits life span, encodes a telomere length regulator similar to yeast telomere binding protein Tel2p. Citation: Current Biology 11: 1706-1710 2001 Type: ARTICLE Genes: clk-2 Abstract: An important quest in modern biology is to identify genes involved in aging. Model organisms such as the nematode Caenorhabditis elegans are particularly useful in this regard. The C. elegans genome has been sequenced [1], and single gene mutations that extend adult life span have been identified [2]. Among these longevity-controlling loci are four apparently unrelated genes that belong to the clk family [3-5]. In mammals, telomere length and structure can influence cellular, and possibly organismal, aging [6]. Here, we show that clk-2 encodes a regulator of telomere length in C. elegans. ------------------- Key: 4952 Medline: 11696333 Authors: Schumacher B;Hofmann K;Boulton S;Gartner A Title: The C. elegans homolog of the p53 tumor suppressor is required for DNA damage-induced apoptosis. Citation: Current Biology 11: 1722-1727 2001 Type: ARTICLE Genes: ced-3 ced-4 cep-1 mrt-2 rad-5 Abstract: In mammals, one of the key regulators necessary for responding to genotoxic stress is the p53 transcription factor. p53 is the single most commonly mutated tumor suppressor gene in human cancers [1]. Here we report the identification of a C. elegans homolog of mammalian p53. Using RNAi and DNA cosuppression technology, we show that C. elegans p53 (cep-1) is required for DNA damage-induced apoptosis in the C. elegans germline. However, cep-1 RNAi does not affect programmed cell death occurring during worm development and physiological (radiation-independent) germ cell death. The DNA binding domain of CEP-1 is related to vertebrate p53 members and possesses the conserved residues most frequently mutated in human tumors. Consistent with this, CEP-1 acts as a transcription factor and is able to activate a transcriptional reporter containing consensus human p53 binding sites. Our data support the notion that p53-mediated transcriptional regulation is part of an ancestral pathway mediating DNA damage-induced apoptosis and reveals C. elegans as a genetically tractable model organism for studying the p53 apoptotic pathway. ------------------- Key: 4953 Medline: 11679654 Authors: Ruvkun G Title: Glimpses of a tiny RNA world. Citation: Science 294: 797-799 2001 Type: REVIEW Genes: let-7 lin-4 Abstract: Over the years, a steady stream of structural and regulatory RNAs have been identified. Three papers published in this issue on pages 853, 858, and 862 from the Tuschl, Bartel, and Ambros labs continue the tradition, but now prospecting for tiny RNAs of 22 nucleotides (nt). The chain of reasoning that simultaneously attracted these groups to 22 nt is convoluted but interesting. ------------------- Key: 4954 Medline: 11600704 Authors: Fitzsimmons D;Lutz R;Wheat W;Chamberlin HM;Hagman J Title: Highly conserved amino acids in Pax and Ets proteins are required for DNA binding and ternary complex assembly. Citation: Nucleic Acids Research 29: 4154-4165 2001 Type: ARTICLE Genes: egl-38 lin-1 Abstract: Combinatorial association of DNA-binding proteins on composite binding sites enhances their nucleotide sequence specificity and functional synergy. As a paradigm for these interactions, Pax-5 (BSAP) assembles ternary complexes with Ets proteins on the B cell-specific mb-1 promoter through interactions between their respective DNA-binding domains. Pax-5 recruits Ets-1 to bind the promoter, but not the closely related Ets protein SAP1a. Here we show that, while several different mutations increase binding of SAP1a to an optimized Ets binding site, only conversion of Val68 to an acidic amino acid facilitates ternary complex assembly with Pax-5 on the mb-1 promoter. This suggests that enhanced DNA binding by SAP1 a is not sufficient for recruitment by Pax-5, but instead involves protein-protein interactions mediated by the acidic side chain. Recruitment of Ets proteins by Pax-5 requires GIn22 within the N-terminal beta -hairpin motif of its paired domain. The beta -hairpin also participates in recognition of a subset of Pax-5-binding sites. Thus, Pax-5 incorporates protein-protein interaction and DNA recognition functions in a single motif. The Caenorhabditis elegans Pax protein EGL-38 also binds specifically to the mb-1 promoter and recruits murine Ets-1 or the C.elegans Ets protein T08H4.3, but not the related LIN-1 protein. Together, our results define specific amino acid requirements for Pax-Ets ternary complex assembly and show that the mechanism is conserved between evolutionarily related proteins of diverse animal species. Moreover, the data suggest that interactions between Pax and Ets proteins are an important mechanism that regulates fundamental biological processes in worms and humans. ------------------- Key: 4955 Medline: Authors: Carta LK Title: Bacterial-feeding nematode growth and preference for biocontrol isolates of the bacterium Burkholderia cepacia. Citation: Journal of Nematology 32: 362-369 2000 Type: ARTICLE Genes: Abstract: The potential of different bacterial-feeding Rhabditida to consume isolates of Burkhoderia cepacis with known agricultural biocontrol ability was examined. Caenorhabditis elegans, Diploscapter sp., Oscheius myriophila, Pelodera strongyloides, Pristionchus pacifus, Zeldia punctata, Panagrellus redivivus, and Distolabrellus veechi were tested for growth on and preference for Escherichia coli OP50 or B. cepacia maize soil isolates and J82, BcF, M36, Bc2, and PHQM100. Considerable growth and preference variations occurred between nematode taza on individual bacterial isolates, and between different bacterial isolates on a given nematode. Populations of Diploscapter sp. and P. redivivus were most strongly supressed. Only Z. puncatata and P. pacifus grew will on all isolates, though Z. Punctata preferentially accumulated on growth-supportive Bc2 and M36, and avoided less supportive J82 and PHQM100. Isolates with plant-parasitic nmaticidal properties and poor fungicidal properties supported the best growth of three members of the Rhabditidae, C. elegans, O. myriophilaand P. strongyloides. Distoabrellus veechi avoided commercial nemaicde M36 more ------------------- Key: 4956 Medline: Authors: Black MC;Williams PL Title: Preliminary assessment of metal toxicity in the middle Tisza River (Hungary) flood plain. Citation: Journal of Soils & Sediments 1: 213-216 2001 Type: ARTICLE Genes: Abstract: Cyanide and heavy metals were accidentally released from a mine waste lagoon in Romania into tributaries ultimately draining in to the Tisza River. Within two months of the cyanide accident two subsequent heavy metal waste spills further contaminated the Tisza River, followed by severe spring flooding, which potentially spread the contamination to soils adjacent to the river. Flood plain soils and shoreline sediments were sampled from two locations on the middle Tisza River and a reference site to conduct a preliminary assessment of metal content and toxicity. Ten-day sediment toxicity tests were conducted with the amphipod, Hyalella azteca and 24h soil toxicity tests were conducted with the nematode (Caenorhabditis elegans). High concentrations of cadmium, copper, zinc, lead and arsenic were detected in soil and sediment samples. However, no mortality was observed in Hyalella exposed to Tisza River sidements and only up to 27% mortality of C. elegans was observed in flood plain soils. Low mortalities are attributed to reduced metal bioavailability caused by high soil cation exchange capacities and possible interactions with sediment organic matter or sulfides. Future studies should focus on factors that alter metal bioavailability and their relationships to potential toxicity of organisms exposed to Tisza River sediments and flood plain soils. ------------------- Key: 4957 Medline: Authors: Johnson TE Title: SAGE thoughts on aging. Citation: Genome Research 11: 1323-1324 2001 Type: REVIEW Genes: age-1 akt-1 clk-1 daf-2 daf-6 daf-18 gro-1 ins-1 old-1 pdk-1 sir-2 sod-1 sod-2 sod-3 sod-4 spe-26 Abstract: The scientific method, and genetic analysis in particular, is based upon identifying variations between individuals of the same species. The study of Jones et al. in this issue reveals variation in transcript abundance between two developmental stages of the nematode Caenorhabditis elegns. In this case, the variation is not genetically specified ut is induced bt the environment as part of a shift to an alternate developmental form, the daur larva. In this type of whole-genome analyses, it is assumed that such studies would reveal differences in transcript abundance that would be casusall associated with distinct molecular and morphological transformations driving development. Much of this paper is conjecture about how the observed differences in transcriipt abundance specify observed differences in longevity(or, more precisely, in mortality rate). ------------------- Key: 4958 Medline: 11703934 Authors: Conradt B Title: Cell engulfment, no sooner ced than done. Citation: Developmental Cell 1: 445-447 2001 Type: REVIEW Genes: ced-1 ced-2 ced-5 ced-6 ced-7 ced-10 ced-12 Abstract: Three genes, ced-2, ced-5, and ced-10 are required for both cell corpse engulfment and distal tip cell migration in C. elegans. Recently, a fourth gene, ced-12, has been identified that is required for these two processes. ced-12 encodes a novel, conserved adaptor molecule involved in the activation of Rho/Rac/CDC42-like GTPases. ------------------- Key: 4959 Medline: 11687661 Authors: Spencer AG;Orita S;Malone CJ;Han M Title: A RHO GTPase-mediated pathway is required during P cell migration in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 98: 13132-13137 2001 Type: ARTICLE Genes: ced-10 col-10 let-502 mig-2 rac-1 rho-1 unc-47 unc-73 Abstract: The Rho family of guanine triphosphate hydrolases controls various cellular processes, including cell migration. We describe here the demonstration of a role for a RhoA GTPase homologue during cell migration in Caenorhabditis elegans. We show that eliminating or reducing rho-1 gene function by using a dominant-negative transgene or dsRNA interference results in a severe defect in migration of hypodermal P cells to a ventral position. Biochemical and genetic data also suggest that unc-73, which encodes a Trio-like guanine nucleotide exchange factor, may act as an activator of rho-1 in the migration process. Mutations in let-502 ROCK, a homologue of a RhoA effector in mammals, also cause defects in P cell migration, suggesting that it may be one of several effectors acting downstream of rho-1 during P cell migration. Finally, we provide evidence to support the idea that other small Rac subfamily small GTPases act redundantly and in parallel to RHO-1 in this specific cell migration event. ------------------- Key: 4960 Medline: 11687635 Authors: Parker JA;Connolly JB;Wellington C;Hayden M;Dausset J;Neri Title: Expanded polyglutamines in Caenorhabditis elegans cause axonal abnormalities and severe dysfunction of PLM mechanosensory neurons without cell death. Citation: Proceedings of the National Academy of Sciences USA 98: 13318-13323 2001 Type: ARTICLE Genes: Abstract: Huntington's disease (HD) is a dominant neurodegenerative disease caused by polyglutamine (polyQ) expansion in the protein huntingtin (htt). HD pathogenesis appears to involve the production of mutated N-terminal htt, cytoplasmic and nuclear aggregation of htt, and abnormal activity of htt interactor proteins essential to neuronal survival. Before cell death, neuronal dysfunction may be an important step of HD pathogenesis. To explore polyQ-mediated neuronal toxicity, we expressed the first 57 amino acids of human htt containing normal [19 Gin residues (Gins)] and expanded (88 or 128 Gins) polyQ fused to fluorescent marker proteins in the six touch receptor neurons of Caenorhabditis elegans. Expanded polyQ produced touch insensitivity in young adults. Noticeably, only 28 +/- 6% of animals with 128 Gins were touch sensitive in the tail, as mediated by the PLM neurons. Similar perinuclear deposits and faint nuclear accumulation of fusion proteins with 19, 88, and 128 Gins were observed. In contrast, significant deposits and morphological abnormalities in PLM cell axons were observed with expanded polyQ (128 Gins) and partially correlated with touch insensitivity. PLM cell death was not detected in young or old adults. These animals indicate that significant neuronal dysfunction without cell death may be induced by expanded polyQ and may correlate with axonal insults, and not cell body aggregates. These animals also provide a suitable model to perform in vivo suppression of polyQ-mediated neuronal ------------------- Key: 4961 Medline: 11715019 Authors: Koppen M;Simske JS;Sims PA;Firestein BL;Hall DH;Radice AD;Rongo C;Hardin JD Title: Cooperative regulation of AJM-1 controls junctional integrity in Caenorhabditis elegans epithelia. Citation: Nature Cell Biology 3: 983-991 2001 Type: ARTICLE Genes: ajm-1 dlg-1 let-413 sDf35 Abstract: The function of epithelial cell sheets depends on the integrity of specialized cell-cell junctions that connect neighbouring cells. We have characterized the novel coiled-coil protein AJM-1, which localizes to an apical junctional domain of Caenorhabditis elegans epithelia basal to the HMR-HMP (cadherin-catenin) complex. In the absence of AJM-1, the integrity of this domain is compromised. Proper AJM-1 localization requires LET-413 and DLG-1, homologues of the Drosophila tumour suppressors Scribble and Discs large, respectively. DLG-1 physically interacts with AJM-1 and is required for its normal apical distribution, and LET-413 mediates the rapid accumulation of both DLG-1 and AJM-1 in the apical domain. In the absence of both dlg-1 and let-413 function AJM-1 is almost completely lost from apical junctions in embryos, whereas HMP-1 (alpha -catenin) localization is only mildly affected. We conclude that LET-413 and DLG-1 cooperatively control AJM-1 localization and that AJM-1 controls the integrity of a distinct apical junctional domain in C. ------------------- Key: 4962 Medline: 11606224 Authors: Krause S;Sommer A;Fischer P;Brophy PM;Walter RD;Liebau E Title: Gene structure of the extracellular glutathione S-transferase from Onchocerca volvulus and its overexpression and promoter analysis in transgenic Caenorhabditis elegans. Citation: Molecular & Biochemical Parasitology 117: 145-154 2001 Type: ARTICLE Genes: Abstract: Two highly similar genes encoding unique extracellular, glycosylated glutathione S-transferases (GSTs) of the human-pathogenic nematode, Onchocerca volvulus (Ov-GST1a and Ov-GST1b), have been isolated and characterised, The genes are approximate to 3 kb in length and consist of seven exons interrupted by introns of approximate to 100 bp in length, with the exception of intron II, which is approximate to 1.6 kb in length. Interestingly, exon I and II encode a signal peptide and an N-terminal extension before sequence homology to other GSTs begins. The 5' flanking region was sequenced and analysed for transcription factor binding sites. Consistent with the lack of a TATA box. analysis of the mRNAs by primer extension showed multiple transcription start sites spread over a 60 bp region. To examine the activity and specificity of the Ov-GST1a gene promoter, we have exploited Caenorhabditis elegans as a heterologous transformation system. To analyse whether transgenic C. elegans are able to carry out processing and post-transcriptional modifications of the Ov-GST1a correctly. the protein was ectopically overexpressed in C. elegans. The parasite-derived Ov-GST1a gene product was correctly processed in transgenic C. elegans and posttranslational modifications., such as signal peptide cleavage and N-glycosylation, were performed successfully. This further demonstrates the potential of C. elegans as a host for expression of candidate vaccine antigens from O. volvulus and affirms the role of C. elegans as a model for ------------------- Key: 4963 Medline: 11677050 Authors: Murakami M;Koga M;Ohshima Y Title: DAF-7/TGF-B expression required for the normal larval development in C. elegans is controlled by a presumed guanylyl cyclase DAF-11. Citation: Mechanisms of Development 109: 27-35 2001 Type: ARTICLE Genes: che-2 che-3 daf-1 daf-2 daf-3 daf-4 daf-5 daf-6 daf-7 daf-8 daf-10 daf-11 daf-12 daf-14 daf-16 daf-21 daf-22 gpa-4 gpa-9 gpa-10 gpa-14 lin-44 Abstract: In C. elegans development, unfavorable growth conditions lead a larva to an arrested and enduring form called a dauer. To elucidate components upstream of DAF-7/TGF-beta in this control pathway, we isolated a mutant that was defective in daf-7 promoter::gfp reporter expression and showed an arrested (dauer-constitutive) phenotype. It has a new mutation in the daf-11 gene encoding a transmembrane guanylyl cyclase. We show that daf-11 gene and a related gene daf-21 act upstream of daf-7, and cilium-related genes che-2 and che-3 are placed between daf-11 and daf-7, in the genetic pathway controlling dauer formation. Expression of daf-11 cDNA by cell specific promoters suggests that daf-11 acts cell autonomously in ASI chemosensory neurons for daf-7 expression. ------------------- Key: 4964 Medline: 11602346 Authors: Michaux G;Legouis R;Labouesse M Title: Epithelial biology: lessons from Caenorhabditis elegans. Citation: Gene 277: 83-100 2001 Type: REVIEW Genes: ajm-1 apr-1 bar-1 che-14 cog-2 dlg-1 elt-1 elt-2 elt-5 elt-6 end-1 end-3 ges-1 glp-1 hmp-1 hpm-2 hmr-1 lag-1 lag-2 let-23 let-413 let-502 let-805 lin-2 lin-7 lin-10 lin-11 lin-12 lin-26 lin-29 lit-1 lrp-1 med-1 med-2 mom-1 mua-3 mup-4 nhr-23 nhr-25 nhr-75 nhr-81 nhr-82 pha-1 pha-4 pop-1 skn-1 sqv-1 sqv-7 sqv-8 Abstract: Epithelial cells are essential and abundant in all multicellular animals where their dynamic cell shape changes orchestrate morphogenesis of the embryo and individual organs. Genetic analysis in the simple nematode Caenorhabditis elegans provides some clues to the mechanisms isms that are involved in specifying epithelial cell fates and in controlling specific epithelial processes such as junction assembly, trafficking or cell fusion and cell adhesion. Here we review recent findings concerning C elegans epithelial cells, focusing in particular on epithelial polarity, and transcriptional control. ------------------- Key: 4965 Medline: 11698187 Authors: Sommer RJ Title: As good as they get: cells in nematode vulva development and evolution. Citation: Current Opinion in Cell Biology 13: 715-720 2001 Type: REVIEW Genes: cul-1 cye-1 lin-12 mab-5 Abstract: Cells are important modules of biological systems, and many evolutionary alterations involve changes in cell determination and cell proliferation. Genetic and molecular comparisons of nematode vulva development between Caenorhabditis, Pristionchus and Oscheius indicate that although the vulva is a stable organ, cell determination and proliferation change dramatically during nematode ------------------- Key: 4966 Medline: 11697852 Authors: Menzel R;Bogaert T;Achazi R Title: A systematic gene expression screen of Caenorhabditis elegans cytochrome P450 genes reveals CYP35 as strongly xenobiotic inducible. Citation: Archives of Biochemistry & Biophysics 395: 158-168 2001 Type: ARTICLE Genes: Abstract: The soil nematode Caenorhabditis elegans is one of the simplest animals having the status of a laboratory model. Its genome contains 80 cytochrome P450 genes (CYP). In order to study CYP gene expression in C. elegans mixed stages and synchronized hermaphrodites were exposed to IS known xenobiotic cytochrome P450 inducers. Messenger RNA expression was detected by DNA arrays and semiquantitative RTPCR. Using subfamily-specific primers, a pooled set of exon-rich CYP fragments could be amplified. In this way it was possible to systematically check the influence of different inducers on CYP expression at the same time. The well-known CYP1A inducers beta -naphthoflavone, PCB52, and lansoprazol were the most active and in particular they strongly induced almost all CYP35 isoforms. A few number of further CYP forms were found to be inducible by other xenobiotics like phenobarbital, atrazine, and clofibrate. In addition, a transgenic C. elegans line expressing CYP under control of the CYP35A2 promoter showed a strong induction of the fusion by beta -naphthoflavone in the ------------------- Key: 4967 Medline: 11676486 Authors: Dotan I;Ziv E;Dafni N;Beckman JS;McCann RO;Glover CVC;Canaani D Title: Functional conservation between the human, nematode, and yeast CK2 cell cycle genes. Citation: Biochemical and Biophysical Research Communications 288: 603-609 2001 Type: ARTICLE Genes: Abstract: Protein kinase CK2 (formerly casein kinase II) is a highly conserved serine/threonine protein kinase ubiquitous in eukaryotic organisms. Previously, we have shown that CK2 is required for cell cycle progression and essential for the viability of the yeast Saccharomyces cerevisiae. We now report that either the human or the nematode Caenorhabditis elegans CK2 alpha catalytic subunit can substitute for the yeast catalytic subunits. Additionally, expression of the human CK2 regulatory subunit (CK2 beta) can suppress the temperature sensitivity of either of the two yeast CK2 mutant catalytic subunits. Taken together, these observations reinforce the view that the CK2 cell cycle progression genes have been highly conserved during evolution from yeast to humans, not only in structure but also in function. ------------------- Key: 4968 Medline: Authors: Pereira-Leal JB;Seabra MC Title: Evolution of the Rab family of small GTP-binding proteins. Citation: Journal of Molecular Biology 313: 889-901 2001 Type: ARTICLE Genes: Abstract: Rab proteins are small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as membrane-associated molecular switches. Here, we have identified the complete Rab families in the Caenorhabditis elegans (29 members), Drosophila melanogaster (29), Homo sapiens (60) and Arabidopsis thaliana (57), and we defined criteria for annotation of this protein family in each organism. We studied sequence conservation patterns and observed that the RabF motifs and the RabSF regions previously described in mammalian Rabs are conserved across species. This is consistent with conserved recognition mechanisms by general regulators and specific effectors. We used phylogenetic analysis and other approaches to reconstruct the multiplication of the Rab family and observed that this family shows a strict phylogeny of function as opposed to a phylogeny of species. Furthermore, we observed that Rabs co-segregating in phylogenetic trees show a pattern of similar cellular localisation and/or function. Therefore, animal and fungi Rab proteins can be grouped in "Rab functional groups" according to their segregating patterns in phylogenetic trees. These functional groups reflect similarity of sequence, localisation. and/or function, and may also represent shared ancestry. Rab functional groups can help the understanding of the functional evolution of the Rab family in particular and vesicular transport in general, and may be used to predict general functions for novel Rab ------------------- Key: 4969 Medline: 11691848 Authors: Friedman R;Hughes AL Title: Pattern and timing of gene duplication in animal genomes. Citation: Genome Research 11: 1842-1847 2001 Type: ARTICLE Genes: Abstract: Duplication of genes, giving rise to multigene families, has been a characteristic feature of the evolution of eukaryotic genomes. In the case of vertebrates, it has been proposed that an increase in gene number resulted from two rounds of duplication of the entire genome by polyploidization (the 2R hypothesis). In the most extensive test to date of this hypothesis, we compared gene numbers in homologous families and conducted phylogenetic analyses of gene families with two to eight members in the complete genomes of Caenorhabditis elegans and Drosophila melanogaster and the available portion of the human genome. Although the human genome showed a higher proportion of recent gene duplications than the other animal genomes, the proportion of duplications after the deuterostome-protostome split was constant across families, with no peak of such duplications in four-member families, contrary to the expectation of the 2R hypothesis. A substantial majority (70.9%) of human four-member families and four-member clusters in larger families showed topologies inconsistent with two rounds of polyploidization ------------------- Key: 4970 Medline: 21383056 Authors: Andersen SSL Title: Zyg-1: elegans personified. Citation: Trends in Cell Biology 11: 321-322 2001 Type: REVIEW Genes: zyg-1 Abstract: In vertebrates and higher eukaryotes such as Caenorhabditis elegans and Drosophila melanogaster, microtubules are in each cell primarily nucleated and organized by the centrosome, which has as its center a pair of centrioles. In recent years, it has become clear that bipolar spindle assembly is possible without centrosomes, and it appears that the centrosome might be required for proper spindle positioning rather than for spindle assembly. ------------------- Key: 4971 Medline: 21426997 Authors: Nicodeme P Title: Fast approximate motif statistics. Citation: Journal of Computational Biology 8: 235-248 2001 Type: ARTICLE Genes: Abstract: We present in this article a fast approximate method for computing the statistics of a number of non-self-overlapping matches of motifs in a random text in the nonuniform Bernoulli model. This method is well suited for protein motifs where the probability of self-overlap of motifs is small. For 96% of the PROSITE motifs, the expectations of occurrences of the motifs in a 7-million-amino-acids random database are computed by the approximate method with less than 1% error when compared with the exact method. Processing of the whole PROSITE takes about 30 seconds with the approximate method. We apply this new method to a comparison of the C. elegans and ------------------- Key: 4972 Medline: 21473523 Authors: Mitchell WA;Porter M;Kuwabara P;Mole SE Title: Genomic structure of three CLN3-like genes in Caenorhabditis elegans. Citation: European Journal of Paediatric Neurology 5SA: 121-125 2001 Type: ARTICLE Genes: Abstract: The genome of Caenorhabditis elegans is predicted to carry three genes similar to CLN3, the gene underlying juvenile neuronal ceroid lipofuscinosis. All three genes are transcribed and the genomic structure has been determined. The number and position of exons for two of the genes differ from that predicted from the genomic sequence, but no discrepancies with the genomic nucleotide sequence were found. Gene F07B10.1 (cln-3.1) is predicted to have 7 exons and to encode a protein of 424 amino acids. Gene C01G8.2 (cln-3.2) has 9 exons and encodes a protein of 435 amino acids. Gene ZC190.1 (cln-3.3) is predicted to have 9 exons and to encode a protein of 416 amino acids. ------------------- Key: 4973 Medline: 21473522 Authors: De Voer G;Jansen G;van Ommen GJ;Peters DJ;Taschner PE Title: Caenorhabditis elegans homologues of the CLN3 gene, mutated in juvenile neuronal ceroid lipofuscinosis. Citation: European Journal of Paediatric Neurology 5SA: 115-120 2001 Type: ARTICLE Genes: Abstract: Neuronal ceroid lipofuscinoses (NCLs) are the most common hereditary neurodegenerative disorders of childhood. The first symptom of this heterogeneous group of devastating lysosomal storage diseases is progressive visual failure. The different forms of NCL can be distinguished by age of onset, clinical features and the characteristics of the accumulated materials. The juvenile form, Batten-Spielmeyer-Vogt disease which is caused by mutations in the CLN3 gene, is the most frequent form of the disease in which loss of vision becomes apparent around the age of 5-8 years. The gene was found to encode a novel integral membrane protein localizing to the lysosomes, confirming that the primary defect in NCL is in lysosomal function. The CLN3 protein function is still unknown, and is examined in several model organisms. We are studying the nematode Caenorhabditis elegans, and have identified three CLN3 homologues. In order to investigate the role of the CLN3 protein in C. elegans, Cecln-3 deletion mutants are being isolated from an ethyl methanesulphonate (EMS)-induced deletion mutant library. Examination of these mutants may provide us with information that will help in dissecting the processes in which the CLN3 protein is involved. In this library two mutated C. elegans Cln-3 loci have been identified, of which one mutant, NL748, was isolated. This mutant contains a deletion of the whole gene. The deletion mutant was characterized with regard to life expectancy, and showed no significant differences when compared with wild-type. ------------------- Key: 4974 Medline: 11707307 Authors: Geary TG;Thompson DP Title: Caenorhabditis elegans: how good a model for veterinary parasites? Citation: Veterinary Parasitology 101: 371-386 2001 Type: ARTICLE Genes: Abstract: The organism about which most is known on a molecular level is a nematode, the free-living organism Caenorhabditis elegans. This organism has served as a reasonable model for the discovery of anthelmintic drugs and for research on the mechanism of action of anthelmintics. Useful information on mechanisms of anthelmintic resistance has also been obtained from studies on C elegans. Unfortunately, there has not been a large-scale extension of genetic techniques developed in C elegans to research on parasitic species of veterinary (or human) parasites. Much can be learned about the essentials of nematode biology by studying C. elegans, but discovering the basic biology of nematode parasitism can only be gained through comparative studies on multiple ------------------- Key: 4975 Medline: 11717458 Authors: Nathoo AN;Moeller RA;Westlund BA;Hart AC Title: Identification of neuropeptide-like protein gene families in Caenorhabditis elegans and other species. Citation: Proceedings of the National Academy of Sciences USA 98: 14000-14005 2001 Type: ARTICLE Genes: nlp-1 nlp-2 nlp-3 nlp-4 nlp-5 nlp-6 nlp-7 nlp-8 nlp-9 nlp-10 nlp-11 nlp-12 nlp-13 nlp-14 nlp-15 nlp-16 nlp-17 nlp-18 nlp-19 nlp-20 nlp-21 nlp-22 nlp-23 nlp-24 nlp-25 nlp-26 nlp-27 nlp-28 nlp-29 nlp-30 nlp-31 nlp-32 Abstract: Neuropeptides play critical roles in synaptic signaling in all nervous systems. Unlike classical neurotransmitters, peptidergic neurotransmitters are encoded as preproproteins that are posttranslationally processed to yield bioactive neuropeptides. To identify novel peptidergic neurotransmitters, the Caenorhabditis elegans genome was searched for predicted proteins with the structural hallmarks of neuropeptide preproproteins. Thirty-two C elegans neuropeptide-like protein (nlp) genes were identified. The nlp genes define at least 11 families of putative neuropeptides with unique motifs; similar expressed sequence tags were identified in other invertebrate species for all 11 families. Six of these families are defined by putative bioactive motifs (FAFA, GGxYamide, MRxamide, LQFamide, LxDxamide, and GGARAF); the remaining five families are related to allatostatin, myomodulin, buccalin/drosulfakinin, orcokinin, and APGWamide neuropeptides (MGL/Famide, FRPamide, MSFamide, GFxGF, and YGGWamide families, respectively). Most C elegans nlp gene expression is in neurons. The C elegans nlp genes and similar genes encoding putative neuropeptides in other species are likely to play diverse roles in nervous system function. ------------------- Key: 4976 Medline: 11717359 Authors: Staunton J;Ganetzky B;Nonet ML Title: Rabphilin potentiates soluble N-ethylmaleimide sensitive factor attachment protein receptor function independently of rab-3. Citation: Journal of Neuroscience 21: 9255-9264 2001 Type: ARTICLE Genes: aex-3 rab-3 rbf-1 ric-4 snb-1 snt-1 unc-10 unc-64 unc-104 Abstract: Rabphilin, a putative rab effector, interacts specifically with the GTP-bound form of the synaptic vesicle-associated protein rab3a. In this study, we define in vivo functions for rabphilin through the characterization of mutants that disrupt the Caenorhabditis elegans rabphilin homolog. The mutants do not display the general synaptic defects associated with rab3 lesions, as assayed at the pharmacological, physiological, and ultrastructural level. However, rabphilin mutants exhibit severe lethargy in the absence of mechanical stimulation. Furthermore, rabphilin mutations display strong synergistic interactions with hypomorphic lesions in the syntaxin, synaptosomal-associated protein of 25 kDa, and synaptobrevin soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) genes; double mutants were nonresponsive to mechanical stimulation. These synergistic interactions were independent of rab3 function and were not observed in rab3-SNARE double mutants. Our data reveal rab3-independent functions for rabphilin in the potentiation of SNARE function. ------------------- Key: 4977 Medline: 11717360 Authors: Kass J;Jacob TC;Kim P;Kaplan JM Title: The EGL-3 proprotein convertase regulates mechanosensory responses of Caenorhabditis elegans. Citation: Journal of Neuroscience 21: 9265-9272 2001 Type: ARTICLE Genes: eat-4 egl-3 glr-1 Abstract: Neuroactive peptides are packaged as proproteins into dense core vesicles or secretory granules, where they are cleaved at dibasic residues by copackaged proprotein convertases. We show here that the Caenorhabditis elegans egl-3 gene encodes a protein that is 57% identical to mouse proprotein convertase type 2 (PC2), and we provide evidence that this convertase regulates mechanosensory responses. Nose touch sensitivity (mediated by ASH sensory neurons) is defective in mutants lacking GLR-1 glutamate receptors (GluRs); however, mutations eliminating the egl-3 PC2 restored nose touch sensitivity to glr-1 GluR mutants. By contrast, body touch sensitivity (mediated by the touch cells) is greatly diminished in egl-3 PC2 mutants. Taken together, these results suggest that egl-3 PC2-processed peptides normally regulate the responsiveness of C. elegans to mechanical stimuli. ------------------- Key: 4978 Medline: 11745666 Authors: Hardaker LA;Singer E;Kerr R;Zhou G;Schafer WR Title: Serotonin modulates locomotory behavior and coordinates egg-laying and movement in Caenorhabditis elegans. Citation: Journal of Neurobiology 49: 303-313 2001 Type: ARTICLE Genes: bas-1 cat-4 egl-1 glr-1 nmr-1 tph-1 Abstract: Biogenic amines have been implicated in the modulation of neural circuits involved in diverse behaviors in a wide variety of organisms. In the nematode C elegans, serotonin has been shown to modulate the temporal pattern of egg-laying behavior. Here we show that serotonergic neurotransmission is also required for modulation of the timing of behavioral events associated with locomotion and for coordinating locomotive behavior with egg-laying. Using an automated tracking system to record locomotory behavior over long time periods, we determined that both the direction and velocity of movement fluctuate in a stochastic pattern in wild-type worms. During periods of active egg-laying, the patterns of reversals and velocity were altered: velocity increased transiently before egg-laying events, while reversals increased in frequency following egg-laying events. The temporal coordination between egg-laying and locomotion was dependent on the serotonergic HSN egg-laying motorneurons as well as the decision-making AVF interneurons, which receive synaptic input from the HSNs. Serotonin-deficient mutants also failed to coordinate egg-laying and locomotion and exhibited an abnormally low overall reversal frequency. Thus, serotonin appears to function specifically to facilitate increased locomotion during periods of active egglaying, and to function generally to modulate decisionmaking neurons that promote forward movement. ------------------- Key: 4979 Medline: 11559701 Authors: Zwaal RR;Van Baelen K;Groenen JTM;Van Geel A;Rottiers V;Kaletta T;Dode L;Raeymaekers L;Wuytack F;Bogaert T Title: The sarco-endoplasmic reticulum Ca2+ ATPase is required for development and muscle function in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 276: 43557-43563 2001 Type: ARTICLE Genes: sca-1 Abstract: The sarco-endoplasmic reticulum Ca2+-transport ATPase (SERCA) loads intracellular releasable Ca2+ stores by transporting cytosolic Ca2+ into the endoplasmic (ER) or sarcoplasmic reticulum (SR). We characterized the only SERCA homologue of the nematode Caenorhabditis elegans, which is encoded by the sca-1 gene. The sca-1 transcript is alternatively spliced in a similar mode as the vertebrate SERCA2 transcript, giving rise to two protein variants: CeSERCAa and CeSERCAb. These proteins showed structural and functional conservation to the vertebrate SERCA2a/b proteins. The CeSERCAs were primarily expressed in contractile tissues. Loss of CeSERCA through gene ablation or RNA interference resulted in contractile dysfunctioning and in early larval or embryonic lethality, respectively.Similar defects could be induced pharmacologically using the SERCA-specific inhibitor thapsigargin, which bound CeSERCA at a conserved site. The conservation of SERCA2 homologues in C. elegans will allow genetic and chemical suppressor analyses to identify promising drug targets and lead molecules for treatment of SERCA-related diseases such as heart disease. ------------------- Key: 4980 Medline: 11722567 Authors: Thompson FJ;Cockroft AC;Wheatley I;Britton C;Devaney E Title: Heat shock and developmental expression of hsp83 in the filarial nematode Brugia pahangi. Citation: European Journal of Biochemistry 268: 5808-5815 2001 Type: ARTICLE Genes: Abstract: hsp83 was cloned from the filarial nematode Brugia pahangi. The mRNA was constitutively expressed at 37 degreesC in life cycle stages that live in the mammalian host (microfilariae and adult worms). Heat shock resulted in only a minimal increase in levels of transcription. A genomic copy of hsp83 was isolated and was shown to contain 11 introns while sequencing of the 5' upstream region revealed several heat shock elements. Using a chloramphenicol acetyltransferase (CAT) reporter gene construct the expression of hsp83 from B. pahangi (Bp-hsp83) was studied by transfection of COS-7 cells. Similar to the expression pattern in the parasite, CAT activity was detected at 37 degreesC and was not influenced by heat shock. When the free-living nematode Caenorhabditis elegans was transfected with the same construct, CAT activity was not observed at normal growth temperatures (21 degreesC) or under moderate heat shock conditions (28 degreesC). However exposure to more severe heat shock (35 degreesC) resulted in an increase in CAT activity. These results suggest that Bp-hsp83 has a temperature threshold greater than or equal to 35 degreesC for expression. ------------------- Key: 4981 Medline: 11719187 Authors: Sijen T;Fleenor J;Simmer F;Thijssen KL;Parrish S;Timmons L;Plasterk RHA;Fire A Title: On the role of RNA amplification in dsRNA-triggered gene silencing. Citation: Cell 107: 465-476 2001 Type: ARTICLE Genes: ego-1 mut-7 par-1 pop-1 pos-1 rde-1 rde-4 rrf-1 rrf-2 rrf-3 unc-15 unc-22 unc-52 Abstract: We have investigated the role of trigger RNA amplification during RNA interference (RNAi) in Caenorhabditis elegans. Analysis of small interfering RNAs (siRNAs) produced during RNAi in C. elegans revealed a substantial fraction that cannot derive directly from input dsRNA. Instead, a population of siRNAs (termed secondary siRNAs) appeared to derive from the action of a cellular RNA-directed RNA polymerase (RdRP) on mRNAs. that are being targeted by the RNAi mechanism. The distribution of secondary siRNAs exhibited a distinct polarity (5'-->3' on the antisense strand), suggesting a cyclic amplification process in which RdRP is primed by existing siRNAs. This amplification mechanism substantially augments the potency of RNAi-based surveillance, while ensuring that the RNAi machinery will focus on expressed mRNAs. ------------------- Key: 4982 Medline: 11713668 Authors: Edgley ML;Riddle DL Title: LG II balancer chromosomes in Caenorhabditis elegans: mT1(II;III) and the mIn1 set of dominantly and recessively marked inversions. Citation: Molecular Genetics & Genomics 266: 385-395 2001 Type: ARTICLE Genes: dpy-10 unc-4 mC4 mC5 mC6 mC7 mIn1 mT1 mnC1 Abstract: Two new genetic balancers for chromosome II of Caenorhabditis elegans were isolated and characterized. mIn1 was shown to be an inversion of a large central portion of the chromosome, extending from lin-31 to rol-1, that includes most of the genes on the chromosome. It balances a region to the left of the gene cluster that was previously not covered by any of the available balancers. mIn1 recombines efficiently with the normal chromosome II in regions outside the rearrangement at both ends, and appears to enhance recombination frequency adjacent to the inversion breakpoints. Eight variant strains of mIn1 were isolated, including forms that carry recessive morphological or lethal markers, an unmarked form, and one that carries an integrated transgene that confers a semi-dominant green fluorescent protein (GFP) phenotype. This set of variants makes mIn1 useful for a wide variety of applications. The second balancer, mT1, was shown to be a II; III translocation that suppresses recombination on the right arms of chromosomes II and III. It balances chromosome II from the region between bli-2 and dpy-10 to the right end of the chromosome, and chromosome III from the region between daf-2 and unc-93 to the right end. These rearrangements provide the means to stabilize efficiently most of the genes on chromosome Il and may be useful for studies of chromosome pairing and recombination. ------------------- Key: 4983 Medline: 11694581 Authors: Firestein BL;Rongo C Title: DLG-1 is a MAGUK similar to SAP97 and is required for adherens junction formation. Citation: Molecular Biology of the Cell 12: 3465.-3475 2001 Type: ARTICLE Genes: cpi-1 dlg-1 hmp-1 hmp-2 hmr-1 let-413 Abstract: Cellular junctions are critical for intercellular communication and for the assembly of cells into tissues. Cell junctions often consist of tight junctions, which form a permeability barrier and prevent the diffusion of lipids and proteins between cell compartments, and adherens junctions, which control the adhesion of cells and link cortical actin filaments to attachment sites on the plasma membrane. Proper tight junction formation and cell polarity require the function of membrane-associated guanylate kinases (MAGUKs) that contain the PDZ protein-protein interaction domain. In contrast, less is known about how adherens junctions are assembled. Here we describe how the PDZ-containing protein DLG-1 is required for the proper formation and function of adherens junctions in Caenorhabditis elegans. DLG-1 is a MAGUK protein that is most similar in sequence to mammalian SAP97, which is found at both synapses of the CNS, as well as at cell junctions of epithelia. DLG-1 is localized to adherens junctions, and DLG-1 localization is mediated by an amino-terminal domain shared with SAP97 but not found in other MAGUK family members. DLG-1 recruits other proteins and signaling molecules to adherens junctions, while embryos that lack DLG-1 fail to recruit the proteins AJM-1 and CPI-1 to adherens junctions. DLG-1 is required for the proper organization of the actin cytoskeleton. and for the morphological elongation of embryos. In contrast to other proteins that have been observed to affect adherens junction assembly and function, DLG-1 is not required to maintain cell polarity. Our results suggest a new function for MAGUK proteins distinct from their role in cell ------------------- Key: 4984 Medline: 11527963 Authors: Senoo-Matsuda N;Yasuda K;Tsuda M;Ohkubo T;Yoshimura S;Nakazawa H;Hartman PS;Ishii N Title: A defect in the cytochrome b large subunit in complex II causes both superoxide anion overproduction and abnormal energy metabolism in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 276: 41553-41558 2001 Type: ARTICLE Genes: mev-1 Abstract: A mev-1(kn1) mutant of the nematode Caenorhabditis elegans is defective in the cytochrome b large subunit (Cyt-1/ceSDHC) in complex II of the mitochondrial electron transport chain. We have previously shown that a mutation in mev-1 causes shortened life span and rapid accumulation of aging markers such as fluorescent materials and protein carbonyls in an oxygen-dependent fashion. However, it remains unclear as to whether this hypersensitivity is caused by direct toxicity of the exogenous oxygen or by the damage of endogenous reactive oxygen species derived from mitochondria. Here we report important biochemical changes in mev-1 animals that serve to explain their abnormalities under normoxic conditions: (i) an overproduction of superoxide anion from mitochondria; and (ii) a reciprocal reduction in glutathione content even under atmospheric oxygen. In addition, unlike wild type, the levels of superoxide anion production from mev-1 mitochondria were significantly elevated under hyperoxia. Under normal circumstances, it is well known that superoxide anion is produced at complexes I and III in the electron transport system. Our data suggest that the mev-1(kn1) mutation increases superoxide anion production at complex II itself rather than at complexes I and III. The mev-1 mutant also had a lactate level 2-fold higher than wild type, indicative of lactic acidosis, a hallmark of human mitochondrial diseases. These data indicate that Cyt-1/ceSDHC plays an important role not only in energy metabolism but also in superoxide anion production that is critically involved in sensitivity to atmospheric oxygen. ------------------- Key: 4985 Medline: 11551909 Authors: Zhu H;Duerr JS;Varoqui H;McManus JR;Rand JB;Erickson JD Title: Analysis of point mutations in the Caenorhabditis elegans vesicular acetylcholine transporter reveals domains involved in substrate translocation. Citation: Journal of Biological Chemistry 276: 41580-41587 2001 Type: ARTICLE Genes: unc-17 Abstract: Cholinergic neurotransmission depends upon the regulated release of acetylcholine. This requires the loading of acetylcholine into synaptic vesicles by the vesicular acetylcholine transporter (VAChT). Here, we identify point mutants in Caenorhabditis elegans that map to highly conserved regions of the VAChT gene of Caenorhabditis elegans (CeVAChT) (unc-17) and exhibit behavioral phenotypes consistent with a reduction in vesicular transport activity and neurosecretion. Several of these mutants express normal amounts of VAChT protein and exhibit appropriate targeting of VAChT to synaptic vesicles. By site-directed mutagenesis, we have replaced the conserved amino acid residues found in human VAChT with the mutated residue in CeVAChT and stably expressed these cDNAs in PC-12 cells. These mutants display selective defects in initial acetylcholine ;transport velocity (K-m), with values ranging from 2- to 8-fold lower than that of the wild-type. One of these mutants has lost its specific interaction with vesamicol, a selective inhibitor of VAChT, and displays vesamicol-insensitive uptake of acetylcholine. The relative order of behavioral severity of the CeVAChT point mutants is identical to the order of reduced affinity of VAChT for acetylcholine in vitro. This indicates that specific structural changes in VAChT translate into specific alterations in the intrinsic parameters of transport and in the storage and synaptic release of ------------------- Key: 4986 Medline: 11598105 Authors: Crowder CM;Westover EJ;Kumar AS;Ostlund RE;Covey DF Title: Enantiospecificity of cholesterol function in vivo. Citation: Journal of Biological Chemistry 276: 44369-44372 2001 Type: ARTICLE Genes: Abstract: The importance of the absolute configuration of cholesterol for its function in vivo is unknown. To directly test this question in viva, we synthesized the enantiomer of cholesterol (ent-cholesterol) and tested its ability to substitute for natural cholesterol (not-cholesterol) in the growth, viability, and behavior of Caenorhabditis elegans, a cholesterol auxotroph. First-generation animals grown on ent-cholesterol were viable with only mild behavioral defects. However, ent-cholesterol produced 100% lethality/arrest of their second generation progeny. Isotopically labeled ent-cholesterol incorporated into animals, indicating that its lethality was not secondary to cholesterol starvation. When mixed with not-cholesterol, ent-cholesterol was not inert; rather, it antagonized the activity of not-cholesterol. These results demonstrate for the first tine that the absolute configuration of cholesterol, not just its physical properties, is essential for its functions in viva. ------------------- Key: 4987 Medline: 11568185 Authors: Christensen M;Strange M Title: Developmental regulation of a novel outwardly rectifying mechanosensitive anion channel in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 276: 45024-45030 2001 Type: ARTICLE Genes: gcy-5 mec-4 mec-7 Abstract: The nematode Caenorhabditis elegans offers unique experimental advantages for defining the molecular basis of anion channel function and regulation. However, the relative inaccessibility of somatic cells in adult animals greatly limits direct electrophysiologcal studies of channel activity. We developed methods to routinely isolate and patch clamp C. elegans embryo cells and oocytes and to culture and patch clamp neurons and muscle cells. Dissociated embryonic cells express a robust outwardly rectifying anion current that is activated by membrane stretch and depolarization. This current, termed I-Cl,I-mec, is inhibited by anion and mechanosensitive channel inhibitors. I-Cl,I-mec has broad anion selectivity and the channel has a unitary conductance of 5-7 picosiemens. I-Cl,I-mec is not detectable in whole-cell or isolated patch recordings from oocytes, cultured muscle cells, and cultured neurons but is expressed in single cell and later embryos. Channel density is high, and the current is observed in >80% of membrane patches. Macroscopic currents of 40-120 pA at +100 mV are typically observed in inside-out membrane patches formed using low resistance patch pipettes. Isolated membrane patches of early embryonic cells therefore contain 60-200 I-Cl,I-mec channels. The apparent activation of I-Cl,I-mec shortly after fertilization and its down-regulation in terminally differentiated cells suggests that the channel may play important roles in embryogenesis and/or cytokinesis. ------------------- Key: 4988 Medline: 11731497 Authors: Ganko EW;Fielman KT;McDonald JF Title: Evolutionary history of Cer elements and their impact on the C. elegans genome. Citation: Genome Research 11: 2066-2074 2001 Type: ARTICLE Genes: Abstract: We report the results of sequence analysis and chromosomal distribution of all distinguishable long terminal repeat (LTR) retrotransposons (Cer elements) in the Caenorhabditis elegans genome. Included in this analysis are all readily recognizable full-length and fragmented elements, as well as solo LTRs. Our results indicate that there are 19 families of Cer elements, some of which display significant subfamily structure. Cer elements call be clustered based on their tRNA primer binding sites (PBSs). These clusters are in concordance with our reverse transcriptase- and LTR-based phylogenies. Although we find that most Cer elements are located in the gene depauperate chromosome ends, some elements are located in or near putative genes and may contribute to gene structure and function. The results of RT-PCR analyses are consistent with this ------------------- Key: 4989 Medline: 11731501 Authors: Boudet N;Aubourg S;Toffano-Nioche C;Kreis M;Lecharny A Title: Evolution of intron/exon structure of DEAD helicase family genes in Arabidopsis, Caenorhabditis, and Drosophila. Citation: Genome Research 11: 2101-2114 2001 Type: ARTICLE Genes: glh-1 glh-2 glh-3 glh-4 Abstract: The DEAD box RNA helicase (RH) proteins are homologs involved in diverse cellular functions in all of the organisms from prokaryotes to eukaryotes. Nevertheless, there is a lack of conservation in the splicing pattern in the 53 Arabidopsis thaliana (AtRHs), the 32 Caenorhabditis elegans (CeRHs) and the 29 Drosophila melanogaster (DmRHs) genes. Of the 153 different observed intron positions, 4 are conserved between AtRHs, CeRHs, and DmRHs, and one position is also found in RHs from yeast and human. Of the 27 different AtRH structures with introns, 20 have at least one predicted ancient intron in the regions coding for the catalytic domain. In all of the organisms examined, we found at least one gene with most of its intron predicted to be ancient. In A, thaliana, the large diversity in RH structures suggests that duplications of the ancestral RH were followed by a high number of intron deletions and additions. The very high bias toward phase 0 introns is in favor of intron addition, preferentially in phase 0. Results from this comparative study of the same gene family in a plant and in two animals are discussed in terms of the general mechanisms of gene family evolution. ------------------- Key: 4990 Medline: 11728440 Authors: Kwon JY;Kim-Ha J;Lee BJ;Lee J Title: The MED-7 transcriptional mediator encoded by let-49 is required for gonad and germ cell development in Caenorhabditis elegans. Citation: FEBS Letters 508: 305-308 2001 Type: ARTICLE Genes: let-49 let-524 lev-11 mad-1 med-6 med-7 med-10 Abstract: Transcription mediators are evolutionarily conserved from yeast to human. We previously reported the specific in vivo roles of mediators during development. Transcriptional mediators including med-6, med-7, and med-10 were shown to be involved in the regulated transcription of specific genes., but not in the transcription of ubiquitous genes. In this report we have identified and characterized the Caenorhabditis elegans med-7 gene. A genetic mutation in the med-7 gene was identified by comparing genetic and physical maps and determining the molecular lesion. let-49 was found to have a nonsense mutation in the coding region of the med-17 gene. The identification of let-49 as the med-7 gene was confirmed by rescue experiments. The phenotype of the let-49 mutation indicated that the med-7 gene is required for normal postembryonic development. RNAi experiments showed that med-7 is also involved in embryogenesis and the gonad and germ cell development. ------------------- Key: 4991 Medline: 11764163 Authors: Hoss S;Henschel T;Haitzer M;Traunspurger W;Steinberg CEW Title: Toxicity of cadmium to Caenorhabditis elegans (Nematoda) in whole sediment and pore water - The ambiguous role of organic matter. Citation: Environmental Toxicology & Chemistry 20: 2794-2801 2001 Type: ARTICLE Genes: Abstract: A bioassay using the nematode Caenorhabditis elegans was performed with natural sediment that had been spiked with organic matter (36-117 g total organic carbon/kg dry wt) and cadmium (Cd: 10-1,200 mg/kg wet wt). Whole sediment and pore water were tested to study the influence of particulate organic matter (POM) and dissolved organic matter (DOM) on Cd toxicity and to compare the toxicity of the two sediment phases. Toxicity was measured with nematode growth as test parameter. No toxicity was observed if sediment concentrations of Cd were below concentrations of acid-volatile sulfides (AVS). At higher Cd concentrations. toxicity in whole sediment and pore water increased with increasing organic content. This phenomenon was explained by an increase of DOM concentrations in organically enriched treatments and a resulting solubilization of Cd due to Cd complexation by DOM. Because DOM did not alter the bioavailability of Cd for the nematodes, bacteria, serving as food, might have functioned as vectors for Cd-DOM complexes, so that Cd could have become available in the gut of the nematodes. A higher toxicity in whole sediment compared to in pore water in the organically enriched treatments indicated that POM-bound Cd may have contributed to the toxicity of Cd to C. elegans. ------------------- Key: 4992 Medline: 11761713 Authors: Liao VHC;Freedman JH Title: Characterization of a cadmium-inducible isoform of pyruvate carboxylase from Caenorhabditis elegans. Citation: DNA Sequence 12: 137-145 2001 Type: ARTICLE Genes: Abstract: A homologue of pyruvate carboxylase was isolated as an expressed sequence tag during the identification of cadmium-responsive genes in Caenorhabditis elegans. The C. elegans protein, designated PYC-1, is predicted to contain 1,175 amino acids with a molecular mass of 129,284. Amino acid sequence analysis indicates that PYC-1 will be translocated into mitochondria, FYC-1 has high levels of amino acid sequence identity with other pyruvate carboxylases. The highest levels of identity are in the putative transcarboxylation, biotin carboxylation and biotin carboxyl carrier domains. ------------------- Key: 4993 Medline: 11784027 Authors: Maine EM Title: RNAi as a tool for understanding germline development in Caenorhabditis elegans: Uses and cautions. Citation: Developmental Biology 239: 177-189 2001 Type: ARTICLE Genes: air-1 air-2 bir-1cdc-1 cdc-2 cdc-3 cdc-4 cdc-25 cdk-4 cds-1 cds-2 cks-1 cyd-1 cye-1 cyk-1 czw-1 dhc-1 dnc-1 dnc-2 ego-1 fbf-1 fbf-2 fog-2 glc -1 gld-1 her-1 him-3 lag-3 lin-5 lmn-1 mag-1 mdf-1 mdf-2 mei-1 mei-2 mex-5 mex-6 mlc-4 mut-6 mut-7 ncc-1 nmy-2 nos-1 nos-2 par-1 par-3 pie-1 pkc-3 plk-1 prg-1 prg-2 ptc-1 puf-7 puf-7 puf-8 rde-1 rdh-1 sel-8 spk-1 syn-4 tra-2 zen-4 Abstract: RNA-mediated genetic interference (RNAi) has become a very useful tool for analyzing gene function in development and other processes. RNAi can be used as a complement to traditional genetic studies or as a primary means of determining biological function. However, the efficacy of RNAi depends on a variety of factors that the researcher must take into consideration. This review focuses on germline development in the nematode, Caenorhabditis elegans, and discusses the uses and limitations of RNAi in providing new information about gene function as well as the possible endogenous role RNAi plays in germline ------------------- Key: 4994 Medline: 11784040 Authors: Marshall SDG;McGhee JD Title: Coordination of ges-1 expression between the Caenorhabditis pharynx and intestine. Citation: Developmental Biology 239: 350-363 2001 Type: ARTICLE Genes: elt-2 ges-1 pha-4 Abstract: We have previously shown that the Caenorhabditis elegans gut-specific esterase gene (Ce-ges-1) has the unusual ability to be expressed in different modules of the embryonic digestive tract (anterior pharynx, posterior pharynx, and rectum) depending on sequence elements within the Ce-ges-1 promoter. In the present paper, we analyze the expression of the ges-1 homolog (Cb-ges-1) from the related nematode Caenorhabditis briggsae and show that Cb-ges-1 also has the ability to switch expression between gut and pharynx + rectum. The control of this expression switch centres on a tandem pair of WGATAR sites in the Cb-ges-1 5'-flanking region, just as it does in Ce-ges-1. We use sequence alignments and subsequent deletions to identify a region at the 3'-end of both Ce-ges-1 and Ce-ges-1 that acts as the ges-1 cryptic pharynx enhancer whose activity is revealed by removal of the 5' WGATAR sites. This region contains a conserved binding site for PHA-4 (the C. elegans ortholog of forkhead/HNF3 alpha, (beta,gamma factors), which is expressed in all cells of the developing pharynx and a subset of cells of the developing rectum. We propose a model in which the normal expression of ges-1 is controlled by the gut-specific GATA factor ELT-2. We propose that, in the pharynx (and rectum), PHA-4 is normally bound to the ges-1 3'-enhancer sequence but that the activation function of PHA-4 is kept repressed by a (presently unknown) factor binding in the vicinity of the 5' WGATAR sites. We suggest that this control circuitry is maintained in Caenorhabditis because pharyngeal expression of ges-1 is advantageous only under certain developmental ------------------- Key: 4995 Medline: 11684665 Authors: Gomes JE;Encalada SE;Swan KA;Shelton CA;Carter JC;Bowerman Title: The maternal gene spn-4 encodes a predicted RRM protein required for mitotic spindle orientation and cell fate patterning in early C. elegans embryos. Citation: Development 128: 4301-4314 2001 Type: ARTICLE Genes: elt-2 end-1 med-1 mex-5 mex-6 mom-2 pal-1 par-2 par-3 pie-1 skn-1 spn-4 vab-7 Abstract: C. elegans embryogenesis begins with a stereotyped sequence of asymmetric cell divisions that are largely responsible for establishing the nematode body plan. These early asymmetries are specified after fertilization by the widely conserved, cortically enriched PAR and PKC-3 proteins, which include three kinases and two PDZ domain proteins. During asymmetric cell divisions in the early embryo, centrosome pairs initially are positioned on transverse axes but then rotate to align with the anteroposterior embryonic axis. We show that rotation of the centrosomal/nuclear complex in an embryonic cell called P-1 requires a maternally expressed gene we name spn-4. The predicted SPN-4 protein contains a single RNA recognition motif (RRM), and belongs to a small subfamily of RRM proteins that includes one Drosophila and two human family members. Remarkably, in mutant embryos lacking spn-4 function the transversely oriented 'P-1' mitotic spindle appears to re-specify the axis of cell polarity, and the division remains asymmetric. spn-4 also is required for other developmental processes, including the specification of mesendoderm, the restriction of mesectoderm fate to P-1 descendants, and germline quiescence during embryogenesis. We suggest that SPN-4 post-transcriptionally regulates the expression of multiple developmental regulators. Such SPN-4 targets might then act more specifically to generate a subset of the anterior-posterior asymmetries initially specified after fertilization by the more generally ------------------- Key: 4996 Medline: 11684669 Authors: Boxem M;van den Heuvel S Title: lin-35 Rb and cki-1 Cip/Kip cooperate in developmental regulation of G1 progression in C. elegans. Citation: Development 128: 4349-4359 2001 Type: ARTICLE Genes: cdk-4 cki-1 cki-2 cyd-1 lin-35 heDf1 Abstract: We have investigated the regulation of cell-cycle entry in C. elegans, taking advantage of its largely invariant and completely described pattern of somatic cell divisions. In a genetic screen, we identified mutations in cyd-1 cyclin D and cdk-4 Cdk4/6. Recent results indicated that during Drosophila development, cyclin D-dependent kinases regulate cell growth rather than cell division. However, our data indicate that C. elegans cyd-1 primarily controls G1 progression. To investigate whether cyd-1 and cdk-4 solely act to overcome GI inhibition by retinoblastoma family members, we constructed double mutants that completely eliminate the function of the retinoblastoma family and cyclin D-Cdk4/6 kinases. Inactivation of lin-35 Rb, the single Rb-related gene in C elegans, substantially reduced the DNA replication and cell-division defects in cyd-1 and cdk-4 mutant animals. These results demonstrate that lin-35 Rb is an important negative regulator of G1/S progression and probably a downstream target for cyd-1 and cdk-4. However, as the suppression by lin-35 Rb is not complete, cyd-1 and cdk-4 probably have additional targets. An additional level of control over G1 progression is provided by Cip/Kip kinase inhibitors. We demonstrate that lin-35 Rb and cki-1 Cip/Kip contribute nonoverlapping levels of G1/S inhibition in C. elegans. Surprisingly, loss of cki-1, but not lin-35, results in precocious entry into S phase. We suggest that a rate limiting role for cki-1 Cip/Kip rather than lin-35 Rb explains the lack or cell-cycle phenotype of lin-35 mutant animals. ------------------- Key: 4997 Medline: 11728305 Authors: Siomos MF;Badrinath A;Pasierbek P;Livingstone D;White J;Glotzer M;Nasmyth K Title: Separase is required for chromosome segregation during meiosis I in Caenorhabditis elegans. Citation: Current Biology 11: 1825-1835 2001 Type: ARTICLE Genes: sep-1 spo-11 qDf3 qDf4 Abstract: Background: Chromosome segregation during mitosis and meiosis is triggered by dissolution of sister chromatid cohesion, which is mediated by the cohesin complex. Mitotic sister chromatid disjunction requires that cohesion be lost along the entire length of chromosomes, whereas homolog segregation at meiosis I only requires loss of cohesion along chromosome arms. During animal cell mitosis, cohesin is lost in two steps. A nonproteolytic mechanism removes cohesin along chromosome arms during prophase, while the proteolytic cleavage of cohesin's Scc1 subunit by separase removes centromeric cohesin at anaphase. In Saccharomyces cerevisiae and Caenorhabditis elegans, meiotic sister chromatid cohesion is mediated by Rec8, a meiosis-specific variant of cohesin's Scc1 subunit. Homolog segregation in S. cerevisiae is triggered by separase-mediated cleavage of Rec8 along chromosome arms. In principle, chiasmata could be resolved proteolytically by separase or nonproteolytically using a mechanism similar to the mitotic "prophase pathway." Results: Inactivation of separase in C. elegans has little or no effect on homolog alignment on the meiosis I spindle but prevents their timely disjunction. It also interferes with chromatid separation during subsequent embryonic mitotic divisions but does not directly affect cytokinesis. Surprisingly, separase inactivation also causes osmosensitive embryos, possibly due to a defect in the extraembryonic structures, referred to as the "eggshell." Conclusions: Separase is essential for homologous chromosome disjunction during meiosis I. Proteolytic cleavage, presumably of Rec8, might be a common trigger for the first meiotic division in eukaryotic cells. Cleavage of proteins other than REC-8 might be necessary to render the eggshell impermeable to solutes. ------------------- Key: 4998 Medline: 11728311 Authors: Chen Z;Han M Title: C. elegans Rb, NuRD, and Ras regulate lin-39-mediated cell fusion during vulval fate specification. Citation: Current Biology 11: 1874-1879 2001 Type: ARTICLE Genes: dpl-1 efl-1 hda-1 let-23 let-60 let-341 lin-1 lin-3 lin-8 lin-15 lin-35 lin-37 lin-38 lin-39 lin-53 mab-5 mpk-1 Abstract: The tumor suppressor Rb and the NuRD (nucleosome remodeling and histone deacetylation) complex have been implicated in transcriptional repression during cell cycle progression and cell fate specification [1, 2]. The Rb/E2F complex physically interacts with and thus recruits the NuRD complex to actively repress transcription [3-7]. Caenorhabditis elegans counterparts of Rb, E2F/DP, and some NuRD complex components appear to function in a common class B synthetic Multivulva (synMuv) pathway to antagonize RTK/Ras signaling during vulval fate specification [8-11]. Therefore, it has been suggested that they function together in a single complex to repress vulva-specific gene transcription [8, 9, 11]. However, little is known about the in vivo interactions between these class B synMuv genes and their relationships with other pathways in specific cellular processes during vulval development. We show that C. elegans Rb/E2F and NuRD complexes antagonize Ras activity by controlling a lin-39 Hox-mediated cell fusion event that regulates the competence of vulval cells. Interestingly, Rb/E2F and NuRD complexes exhibit very different genetic properties. While the NuRD complex negatively regulates lin-39 Hox activity, likely by downregulating its expression, RB/E2F appears to play dual roles in regulating lin-39: a negative role in controlling its activity and a previously uncharacterized positive role ------------------- Key: 4999 Medline: 11795473 Authors: Kokke BPA;Boelens WC;de Jong WW Title: The lack of chaperonelike activity of Caenorhabditis elegans Hsp12.2 cannot be restored by domain swapping with human alpha B-crystallin. Citation: Cell Stress & Chaperones 6: 360-367 2001 Type: ARTICLE Genes: Abstract: The small heat shock proteins Hsp 12.2 and (alphaB-crystallin differ in that the former occurs as tetramers, without chaperonelike activity, whereas the latter forms multimers and is a good chaperone. To investigate whether the lack of chaperone activity of Hspl 2.2 is primarily due to its tetrameric structure or rather to intrinsic sequence features, we engineered chimeric proteins by swapping the N-terminal, C-terminal, and tail regions of Hsp12.2 and alphaB-crystallin, designated as n-c-t and N-C-T, respectively. Three of the chimeric sHsps, namely N-c-T, n-c-T, and N-C-t, showed nativelike secondary and quaternary structures as measured by circular dichroism and gel permeation chromatography. Combining the conserved a-crystallin domain of Hsp12.2 with the N-terminal and tail regions of (YB-crystallin (N-c-T) resulted in multimeric complexes, but did not restore chaperonelike activity. Replacing the tail region of Hsp12.2 with that of alphaB-crystallin (n-c-T) did not alter the tetrameric structure and lack of chaperone activity. Similarly, providing (alphaB-crystallin with the tail of Hsp12.2 (N-C-t) did not substantially influence the multimeric complex size, but it reduced the chaperoning ability, especially for small substrates. These results suggest that the conserved alpha -crystallin domain of Hsp12.2 is intrinsically unsuitable to confer chaperonelike activity and confirms that the tail region in alphaB-crystallin modulates chaperonelike capacity in a substrate-dependent manner. ------------------- Key: 5000 Medline: 11700045 Authors: Suh S;Park YS;Lee YS;Cho TJ;Kaang BK;Cho NJ Title: Three functional isoforms of GAR-2, a Caenorhabditis elegans G-protein-linked acetylcholine receptor, are produced by alternative splicing. Citation: Biochemical and Biophysical Research Communications 288: 1238-1243 2001 Type: ARTICLE Genes: gar-2 Abstract: We have previously isolated a cDNA clone from Caenorhabditis elegans that encodes a novel form of G-protein-linked acetylcholine receptor, termed GAR-2. GAR-2 is similar to but pharmacologically distinct from muscarinic acetylcholine receptors. Here we report the identification of two gar-2 cDNA clones that are different from the previous one. These newly identified cDNAs encode polypeptides of 664 and 627 amino acids, whereas the previous one encodes a polypeptide of 614 amino acids. The three GAR-2 isoforms, which differ only in the third intracellular loop, arise from alternative splicing. Electrophysiological analyses using the Xenopus oocyte system showed that all three GAR-2 isoforms couple to the activation of G-protein-gated inwardly rectifying K+ (GIRK1) channel with similar drug specificity. Our results indicate that alternative splicing plays an important role in promoting molecular diversity of G-protein-linked ------------------- Key: 5001 Medline: 11708805 Authors: Yoshida M;Sugimoto A;Ohshima Y;Takeshima H Title: Important role of junctophilin in nematode motor function. Citation: Biochemical and Biophysical Research Communications 289: 234-239 2001 Type: ARTICLE Genes: myo-3 Abstract: Junctional complexes between the plasma membrane and endoplasmic/sareoplasmic reticulum are shared by excitable cells and seem to be the structural ground for cross-talk between cell-surface and intracellular ionic channels. Our current studies have identified junctophilins (JPs) as members of a novel transmembrane protein family in the junctional membrane complex. Biochemical and gene-knockout studies have suggested that JPs contribute to the formation of the junctional membrane complex by spanning the intracellular store membrane and interacting with the plasma membrane. We report here invertebrate JPs in fruit fly and nematode. Three distinct JP subtype genes are found in the mammalian genome, while a single JP gene exists in either invertebrate genome. Mammalian and invertebrate JPs share characteristic structural features, although some intervening sequences are found in invertebrate JPs. A reporter assay indicated that the JP gene is predominantly activated in muscle cells in nematode. Nematodes, in which expression of JP was inhibited by RNA-mediated interference (RNAi), showed hypolocomotion. Taking account of the cell-type-specific expression and data from previous reports, the hypolocomotion is likely to be due to the deficiency of junctional membrane structures and the resulting reduction of Ca2+ signaling during excitation-contraction coupling in muscle cells. ------------------- Key: 5002 Medline: 11559703 Authors: Tan KML;Chan SL;Tan KO;Yu VC Title: The Caenorhabditis elegans sex-determining protein FEM-2 and its human homologue, hFEM-2, are Ca2+/calmodulin-dependent protein kinase phosphatases that Citation: Journal of Biological Chemistry 276: 44193-44202 2001 Type: ARTICLE Genes: fem-1 fem-2 fem-3 Abstract: In Caenorhabditis elegans, fem-1, fem-2, and fem-3 play pivotal roles in sex determination. Recently, a mammalian homologue of the C. elegans sex-determining protein FEM-1, F1A alpha, has been described. Although there is little evidence to link F1A alpha to sex determination, F1A alpha and FEM-1 both promote apoptosis in mammalian cells. Here we report the identification and characterization of a human homologue of the C. elegans sex-determining protein FEM-2, hFEM-2. Similar to FEM-2, hFEM-2 exhibited PP2C phosphatase activity and associated with FEM-3. hFEM-2 shows striking similarity (79% amino acid identity) to rat Ca2+/calmodulin (CaM)-dependent protein kinase phosphatase (rCaMKPase). hFEM-2 and FEM-2, but not PP2C alpha, were demonstrated to dephosphorylate CaM kinase H efficiently in vitro, suggesting that hFEM-2 and FEM-2 are specific phosphatases for CaM kinase. Furthermore, hFEM-2 and FEM-2 associated with F1A alpha and FEM-1 respectively. Overexpression of hFEM-2, FEM-2, or rCaMKPase all mediated apoptosis in mammalian cells. The catalytically active, but not the inactive, forms of hFEM-2 induced caspase-dependent apoptosis, which was blocked by Bcl-XL or a dominant negative mutant of caspase-9. Taken together, our data suggest that hFEM-2 and rCaMKPase are mammalian homologues of FEM-2 and they are evolutionarily conserved CaM kinase phosphatases that may have a role in apoptosis signaling. ------------------- Key: 5003 Medline: 11707322 Authors: Marson AL;Tarr DEK;Scott AL Title: Macrophage migration inhibitory factor (MIF) transcription is significantly elevated in Caenorhabditis elegans dauer larvae. Citation: Gene 278: 53-62 2001 Type: ARTICLE Genes: col-1 mif-1 mif-2 mif-3 mif-4 Abstract: Macrophage migration inhibitory factor (MIF) from vertebrate species is a molecule that exerts a wide-range of effects in inflammatory responses, cell activation and cell differentiation. Several species of parasitic nematodes have been shown to express genes encoding orthologues of the mammalian MIF that appear to play a key role in immune evasion by modifying the activity of host cells. In addition, MIF accumulates in nematode somatic cells where its role has not yet been defined. In order to identify the role that MIF plays in the cell biology of nematodes, we have characterized the members of the mif gene family in the free-living species Caenorhabditis elegans. Unlike the single mif gene found in humans and mice, C. elegans expresses four distinct mif genes: Ce-mif-1, Ce-mif-2, Ce-mif-3 and Ce-mif-4. The Ce-MIF proteins are between 15-30% identical to each other, 34-38% identical to the MIFs from the parasitic nematode Brugia malayi, and 22-35% identical to mammalian MIFs. The transcription of Ce-mif-2 and Ce-mif-3, but not Ce-mif-1, was upregulated >100-fold compared to L2 levels when the worms entered the dauer stage. The transcription levels of Ce-mif-2 and Ce-mif-3 fell to near baseline a few hours after exit from dauer. Ce-MIF/GFP transgenic animals and immunostaining were used to demonstrate that the main sites of MIF production are in the hypodermis, body wall muscles and in the nuclei of developing embryos. The results suggest a role for C. elegans MIF in cellular maintenance during periods of adverse conditions that lead to ------------------- Key: 5004 Medline: 11714673 Authors: Lundquist EA;Reddien PW;Hartwieg E;Horvitz HR;Bargmann CI Title: Three C. elegans RAC proteins and several alternative RAC regulators control axon guidance, cell migration and apoptotic cell phagocytosis. Citation: Development 128: 4475-4488 2001 Type: ARTICLE Genes: ced-2 ced-5 ced-10 mig-2 rac-2 rac-3 unc-73 Abstract: The Caenorhabditis elegans genome contains three rac-like genes, ced-10, mig-2, and rac-2. We report that ced-10, mig-2 and rac-2 act redundantly in axon pathfinding: inactivating one gene had little effect, but inactivating two or more genes perturbed both axon outgrowth and guidance. mig-2 and ced-10 also have redundant functions in some cell migrations. By contrast, ced-10 is uniquely required for cell-corpse phagocytosis, and mig-2 and rac-2 have only subtle roles in this process. Rac activators are also used differentially. The UNC-73 Trio Rac GTP exchange factor affected all Rac pathways in axon pathfinding and cell migration but did not affect cell-corpse phagocytosis. CED-5 DOCK180, which acts with CED-10 Rac in cell-corpse phagocytosis, acted with MIG-2 but not CED-10 in axon pathfinding. Thus, distinct regulatory proteins modulate Rac activation and function in different developmental processes. ------------------- Key: 5005 Medline: 11714689 Authors: Basham SE;Rose LS Title: The Caenorhabditis elegans polarity gene ooc-5 encodes a Torsin-related protein of the AAA ATPase superfamily. Citation: Development 128: 4645-4656 2001 Type: ARTICLE Genes: ooc-3 ooc-5 mnDf61 mnDf67 mnDf85 Abstract: The PAR proteins are required for polarity and asymmetric localization of cell fate determinants in C. elegans embryos. In addition, several of the PAR proteins are conserved and localized asymmetrically in polarized cells in Drosophila, Xenopus and mammals. We have previously shown that ooc-5 and ooc-3 mutations result in defects in spindle orientation and polarity in early C elegans embryos. In particular, mutations in these genes affect the reestablishment of PAR protein asymmetry in the Pi cell of two-cell embryos. We now report that ooc-5 encodes a putative ATPase of the Clp/Hsp100 and AAA superfamilies of proteins, with highest sequence similarity to Torsin proteins; the gene for human Torsin A is mutated in individuals with early-onset torsion dystonia, a neuromuscular disease. Although Clp/Hsp100 and AAA family proteins have roles in diverse cellular activities, many are involved in the assembly or disassembly of proteins or protein complexes; thus, OOC-5 may function as a chaperone. OOC-5 protein co-localizes with a marker of the endoplasmic reticulum in all blastomeres of the early C. elegans embryo, in a pattern indistinguishable from that of OOC-3 protein. Furthermore, OOC-5 localization depends on the normal function of the ooc-3 gene. These results suggest that OOC-3 and OOC-5 function in the secretion of proteins required for the localization of PAR proteins in the P-1 cell, and may have implications for the study of torsion ------------------- Key: 5006 Medline: 11746231 Authors: Borland CZ;Schutzman JL;Stern MJ Title: Fibroblast growth factor signaling in Caenorhabditis elegans. Citation: BioEssays 23: 1120-1130 2001 Type: REVIEW Genes: clr-1 egl-15 egl-17 gap-1 gap-2 let-60 let-341 let-756 lin-45 mek-2 mpk-1 ptp-2 sem-5 soc-1 soc-2 sur-8 Abstract: Growth factor receptor tyrosine kinases (RTKs), such as the fibroblast growth factor receptor (FGFR), play a major role in how cells communicate with their environment. FGFR signaling is crucial for normal development, and its misregulation in humans has been linked to developmental abnormalities and cancer. The precise molecular mechanisms by which FGFRs transduce extracellular signals to eff ect specific biologic responses is an area of intense research. Genetic analyses in model organisms have played a central role in our evolving understanding of these signal transduction cascades. Genetic studies in the nematode C. elegans have contributed to our knowledge of FGFR signaling by identifying genes involved in FGFR signal transduction and linking their gene products together into signaling modules. This review will describe FGFR-mediated signal transduction in C. elegans and focus on how these studies have contributed to our understanding of how FGFRs orchestrate the assembly of intracellular signaling pathways. ------------------- Key: 5007 Medline: 11718925 Authors: Hekimi S;Burgess J;Bussiere F;Meng Y;Benard C Title: Genetics of lifespan in C. elegans - molecular diversity, physiological complexity, mechanistic simplicity. Citation: Trends in Genetics 17: 712-718 2001 Type: REVIEW Genes: age-1 akt-1 akt-2 clk-1 clk-2 daf-2 daf-16 gro-1 sir-2 Abstract: The nematode Caenorhabditis elegans is used as a model system for the study of aging. Several mutant strains that have an increased lifespan have been isolated and characterized genetically and molecularly. Molecular analysis reveals that diverse types of gene products can affect worm lifespan, including proteins active in signal transduction, transcription and silencing factors, mitochondrial enzymes, and at least one protein that affects telomere length. Genetic analysis, however, suggests that these activities all converge on a few key mechanisms that impinge on lifespan, namely the production, repair and prevention of molecular damage. ------------------- Key: 5008 Medline: Authors: Bignone FA Title: Structural complexity of early embryos - A study on the nematode Caenorhabditis elegans. Citation: Journal of Biological Physics 27: 257-283 2001 Type: ARTICLE Genes: Abstract: ------------------- Key: 5009 Medline: Authors: Srinivasan J;Pires-daSilva A;Gutierrez A;Zheng M;Jungblut B;Witte H;Schlak I;Sommer RJ Title: Microevolutionary analysis of the nematode genus Pristionchus suggests a recent evolution of redundant developmental mechanisms during vulval formation. Citation: Evolution & Development 3: 229-240 2001 Type: ARTICLE Genes: Abstract: ------------------- Key: 5010 Medline: 11730970 Authors: Enmark E;Gustafsson JA Title: Comparing nuclear receptors in worms, flies and humans. Citation: Trends in Pharmacological Sciences 22: 611-615 2001 Type: REVIEW Genes: Abstract: Complete nucleotide sequences are now available for different species of the animal kingdom: Caenorhabditis elegans - a nematode, Drosophila - an insect, and humans - a mammal. Such information makes it possible to compare the set of nuclear receptors found in these organisms, and to discuss the possible reasons for the differences observed. The human genome sequencing identified few new receptors, which implies that most nuclear receptors have now been found. However, information about polymorphisms and regulating sequences, obtained through genomic sequencing, will be important for understanding receptor function and disease mechanisms. The surprisingly large number of nuclear receptors in C. elegans might have implications for the development of pharmaceuticals and the understanding of the function of these animals. By contrast, Drosophila has few nuclear receptors; however, examination of the unique nuclear receptors provides information about the function of these receptors. ------------------- Key: 5011 Medline: 11726271 Authors: Natsuka S;Takubo R;Seki R;Ikura K Title: Molecular cloning and expression of Caenorhabditis elegans ERp57-homologue with transglutaminase activity. Citation: Journal of Biochemistry 130: 731-735 2001 Type: ARTICLE Genes: Abstract: Formation of cross-linking between proteins via a gamma -glutamyl-epsilon -lysine residue is an important process in many biological phenomena including apoptosis. Formation of this linkage is catalyzed by the enzyme transglutaminase, which is widely distributed from bacteria to the animal kingdom. The simple multi-cellular organism Caenorhabditis elegans also possesses transglutaminase activity associated with apoptosis [Madi, A. et al. (1998) Eur. J. Biochem. 253, 583-590], but no gene with significant homology to vertebrate or bacterial transglutaminases has been found in the C. elegans genome sequence database. On the other hand, protein disulfide isomerases were recently recognized as a new family of transglutaminases [Chandrashekar, R. et aL (1998) Proc. Natl. Acad Sci. USA 95, 531-536]. To identify the molecule with transglutaminase activity in C. elegans, we isolated from C. elegans a gene homologous to ERp57, which encodes a protein disulfide isomerase, expressed it in recombinant form, and characterized the transglutaminase and protein disulfide isomerase activities of the resultant protein. The C. elegans ERp57 protein had both enzyme activities, and the transglutaminase activity had similar characteristics to the activity in lysate of the whole worm. These results suggested that the ERp57 homologue was ------------------- Key: 5012 Medline: Authors: Gerhard GS Title: Caloric restriction in nonmammalian models. Citation: Journal of Anti-Aging Medicine 4: 205-213 2001 Type: REVIEW Genes: Abstract: The well-known effects of caloric restriction (CR) upon life span have been studied in a number of nonmammalian species, from yeast to fish. Early work focused on determining whether CR could prolong life span, which it does in most organisms thus far examined. More recently, studies done with invertebrates models, including yeast, Caenorhabditis elegans, and Drosophila, have suggested potential mechanistic commonalities with CR. In this review, a survey of data collected from the application of CR to a number of nonmammalian models is presented, as well as the potential molecular overlap arising from work done ------------------- Key: 5013 Medline: Authors: van Rossum AJ;Brophy PM;Tait A;Barrett J;Jefferies JR Title: Proteomic identification of glutathione S-transferases from the model nematode Caenorhabditis elegans. Citation: Proteomics 1: 1463-1468 2001 Type: ARTICLE Genes: Abstract: Glutathione affinity chromatography and two-dimensional electrophoresis (2-DE) were used to purify glutathione binding proteins from Caenorhabditis elegans. All proteins identified after peptide mass fingerprinting using matrix-assisted laser desorption/ionization-time of flight were found to belong to the glutathione S-transferase (GST) superfamily. From the 26 individual spots identified, 12 different GSTs were isolated. Of these, five were found on the gel only once, whilst the remaining seven were represented by 21 separate spots. Most of the GSTs identified were of the nematode specific class, however, three Alpha class GSTs, a Pi and a Sigma class GST were also isolated. ------------------- Key: 5014 Medline: 11738026 Authors: Byrd DT;Kawasaki M;Walcoff M;Hisamoto N;Matsumoto K;Jin Y Title: UNC-16, a JNK-signaling scaffold protein, regulates vesicle transport in C. elegans. Citation: Neuron 32: 787-800 2001 Type: ARTICLE Genes: jkk-1 jnk-1 klc-1 klc-2 sek-1 unc-16 unc-104 unc-116 nDf40 qDf2 sDf110 sDf127 Abstract: Transport of synaptic components is a regulated process. Loss-of-function mutations in the C. elegans unc-16 gene result in the mislocalization of synaptic vesicle and glutamate receptor markers. unc-16 encodes a homolog of mouse JSAP1/JIP3 and Drosophila Sunday Driver. Like JSAP1/JIP3, UNC-16 physically interacts with JNK. and JNK kinases. Deletion mutations in Caenorhabditis elegans JNK and JNK kinases result in similar mislocalization of synaptic vesicle markers and enhance weak unc-16 mutant phenotypes. unc-116 kinesin heavy chain mutants also mislocalize synaptic vesicle markers, as well as a functional UNC16::GFP. Intriguingly, unc-16 mutations partially suppress the vesicle retention defect in unc-104 KIF1A kinesin mutants. Cur results suggest that UNC-16 may regulate the localization of vesicular cargo by integrating JNK signaling and kinesin-1 transport. ------------------- Key: 5015 Medline: 11738032 Authors: Wang ZW;Saifee O;Nonet ML;Salkoff L Title: SLO-1 potassium channels control quantal content of neurotransmitter release at the C. elegans neuromuscular junction. Citation: Neuron 32: 867-881 2001 Type: ARTICLE Genes: slo-1 unc-64 Abstract: Six mutants of SLO-1, a large-conductance, Ca2+-activated K+ channel of C. elegans, were obtained in a genetic screen for regulators of neurotransmitter release. Mutants were isolated by their ability to suppress lethargy of an unc-64 syntaxin mutant that restricts neurotransmitter release. We measured evoked postsynaptic currents at the neuromuscular junction in both wild-type and mutants and observed that the removal of SLO-1 greatly increased quanta[ content primarily by increasing duration of release. The selective isolation of slo-1 as the only ion channel mutant derived from a whole genomic screen to detect regulators of neurotransmitter release suggests that SLO-1 plays an important, if not unique, role in regulating ------------------- Key: 5017 Medline: 11719577 Authors: Achaz G;Netter P;Coissac E Title: Study of intrachromosomal duplications among the eukaryotic genomes. Citation: Molecular Biology and Evolution 18: 2280-2288 2001 Type: ARTICLE Genes: Abstract: Complete eukaryote chromosomes were investigated for intrachromosomal duplications of nucleotide sequences. The analysis was performed by looking for nonexact repeats on two complete genomes, Saccharomyces cerevisiae and Caenorhabditis elegans, and four partial ones, Drosphila melanogaster, Plasmodium falciparum, Arabidopsis thaliana, and Homo sapiens. Through this analysis, we show that all eukaryote chromosomes exhibit similar characteristics for their intrachromosomal repeats, suggesting similar dynamics: many direct repeats have their two copies physically close together, and these close direct repeats are more similar and shorter than the other repeats. On the contrary, there are almost no close inverted repeats. These results support a model for the dynamics of duplication. This model is based on a continuous genesis of tandem repeats and implies that most of the distant and inverted repeats originate from these tandem repeats by further chromosomal rearrangements (insertions, inversions, and deletions). Remnants of these predicted rearrangements have been brought out through fine analysis of the chromosome sequence. Despite these dynamics, shared by all eukaryotes, each genome exhibits its own style of intrachromosomal duplication: the density of repeated elements is similar in all chromosomes issued from the same genome, but is different between species. This density was further related to the relative rates of duplication, deletion, and mutation proper to each species. One should notice that the density of repeats in the X chromosome of C. elegans is much lower than in the autosomes of that organism, suggesting that the exchange between homologous chromosomes ------------------- Key: 5018 Medline: 11729148 Authors: Branicky R;Shibata Y;Feng J;Hekimi S Title: Phenotypic and suppressor analysis of defecation in clk-1 mutants reveals that reaction to changes in temperature is an active process in Caenorhabditis elegans. Citation: Genetics 159: 997-1006 2001 Type: ARTICLE Genes: clk-1 dec-7 dsc-1 dsc-2 dsc-3 dsc-4 dsc-5 flr-3 flr-4 Abstract: Mutations in the Caenohabditis elegans maternal-effect gene clk-1 affect cellular, developmental, and behavioral timing. They result in a slowing of the cell cycle, embryonic and postembryonic development, reproduction, and aging, as well as of the defecation, swimming, and pharyngeal pumping cycles. Here, we analyze the defecation behavior in clk-1 mutants, phenotypically and genetically. When wild-type worms are grown at 20 degrees and shifted to a new temperature, the defecation cycle length is significantly affected by that new temperature. In contrast. we find that when clk-1 mutants are shifted, the defecation cycle length is unaffected by that new temperature. We carried out a screen for mutations that Suppress the slow defecation phenotype at 20 degrees and identified two distinct classes of genes, which we call dsc for defecation suppressor of elk-1. Mutations in one class also restore the ability to react normally to changes in temperature, while mutations in the other class do not. Together. these results suggest that dk-1 is necessary for readjusting the defecation cycle length in response to changes in temperature. On the other hand, in the absence of clk-1 activity, we observe temperature compensation, a mechanism that maintains a constant defecation period iii the face of changes in temperature. ------------------- Key: 5019 Medline: 11729149 Authors: Xu L;Paulsen J;Yoo Y;Goodwin EB;Strome S Title: Caenorhabditis elegans MES-3 is a target of GLD-1 and functions epigenetically in germline development. Citation: Genetics 159: 1007-1017 2001 Type: ARTICLE Genes: gld-1 glp-1 mes-2 mes-3 mes-4 mes-6 hDp20 Abstract: The maternal-effect sterile (MES) proteins are maternally supplied regulators of germline development in Caenorhabditis elegans. In the hermaphrodite progeny from mes mutant mothers, the germline dies during larval development. On the basis of the similarities of MES-2 and MES-6 to known transcriptional regulators and on the basis of the effects of mes mutations on transgene expression in the germline, the MES proteins are predicted to be transcriptional repressors. One of the MES proteins, MES-3, is a novel protein with no recognizable motifs. In this article we show that MES-3 is localized in the nuclei of embryos and germ cells, consistent with its predicted role in transcriptional regulation. Its distribution in the germline and in early embryos does not depend on the wild-type functions of the other MES proteins. However, its nuclear localization in midstage embryos and its persistence in the primordial germ cells depend on wildtype MES-2 and MES-6. These results are consistent with biochemical data showing that MES-2, MES-3, and MES-6 associate in a complex in embryos. The distribution of MES-3 in the adult germline is regulated by the translational repressor GLD-l: MES-3 is absent from the region of the germline where GLD-1 is known to be present, MES-3 is overexpressed in the germline of gld-l mutants, and GLD-1 specifically binds the mes-3 3' untranslated region (3' UTR). Analysis of temperature-shifted mes-3(bn21ts) worms and embryos indicates that MES-3 function is required in the mother's germline and during embryogenesis to ensure subsequent normal germline development. We propose that MES-3 acts epigenetically to induce a germline state that is inherited through both meiosis and mitosis and that is essential for survival of ------------------- Key: 5020 Medline: 11729150 Authors: Xu L;Strome S Title: Depletion of a novel SET-domain protein enhances the sterility of mes-3 and mes-4 mutants of Caenorhabditis elegans. Citation: Genetics 159: 1019-1029 2001 Type: ARTICLE Genes: fem-2 glp-4 mes-2 mes-3 mes-4 mes-6 set-2 hDp20 Abstract: Four maternal-effect sterile genes, mes-2, mes-3, mes-4, and mes-6, are essential for germline development in Caenorhabditis elegans. Homozygous mes progeny from heterozygous mothers are themselves fertile but produce sterile progeny with underproliferated and degenerated germlines. All four mes genes encode chromatin-associated proteins, two of which resemble known regulators of gene expression. To identify additional components in the MES pathway, we used RNA-mediated interference (RNAi) to test candidate genes for enhancement of the Mes mutant phenotype. Enhancement in this assay was induction of sterility a generation earlier, in the otherwise fertile homozygous progeny of heterozygous mothers, which previous results had suggested represent a sensitized genetic background. We tested seven genes predicted to encode regulators of chromatin organization for RNAi-induced enhancement of mes-3 sterility and identified one enhancer, called set-2 after the SET domain encoded by the gene. Depletion of SET-2 also enhances the sterile phenotype of mes-4 but not of mes-2 or mes-6 set-2 encodes two alternatively spliced transcripts, set-2(L) and set-2(L), both of which are enriched in the germline of adults. In the adult germline, SET-2(L). protein is localized in mitotic and mid-late-stage meiotic nuclei but is undetectable in early pachytene nuclei. SET-2(L) protein is localized in all nuclei of embryos. The localization of SET-2(L) does not depend on any of the four MES proteins, and none of the MES proteins depend on SET-2 for their normal localization. Our results Suggest that SET-2 participates along with the MES proteins in promoting ------------------- Key: 5021 Medline: 11784045 Authors: Yoshida S;Morita K;Mochii M;Ueno N Title: Hypodermal expression of Caenorhabditis elegans TGF-B type I receptor SMA-6 is essential for the growth and maintenance of body length. Citation: Developmental Biology 240: 32-45 2001 Type: ARTICLE Genes: daf-4 dbl-1 dpy-7 mtl-2 myo-2 rol-6 sma-2 sma-3 sma-4 sma-6 Abstract: There are several transforming growth factor-beta (TGF-beta) pathways in the nematode Caenorhabditis elegans. One of these pathways regulates body length and is composed of the ligand DBL-1, serine/threonine protein kinase receptors SMA-6 and DAF-4, and cytoplasmic signaling components SMA-2, SMA-3, and SMA-4. To further examine the molecular mechanisms of body-length regulation in the nematode by the TGF-beta pathway, we examined the regional requirement for the type-I receptor SMA-6. Using a SMA-6::GFP (green fluorescent protein) reporter gene, sma-6 was highly expressed in the hypodermis, unlike the type-II receptor DAF-4, which is reported to be ubiquitously expressed. We then examined the ability of SMA-6 expression in different regions of the C. elegans body to rescue the sma-6 phenotype (small) and found that hypodermal expression of SMA-6 is necessary and sufficient for the growth and maintenance of body length. We also demonstrate that GATA sequences in the sma-6 promoter contribute to the hypodermal expression of sma-6. ------------------- Key: 5022 Medline: 11731470 Authors: Chen Z;Han M Title: Role of C. elegans lin-40 MTA in vulval fate specification and morphogenesis. Citation: Development 128: 4911-4921 2001 Type: ARTICLE Genes: egl-27 egr-1 let-60 lin-8 lin-9 lin-15 lin-35 lin-36 lin-37 lin-38 lin-40 Abstract: Vulval differentiation in Caenorhabditis elegans involves several fundamental cellular events, including cell fusion, division and migration. We have characterized the role of the lin-40 (also known as egr-1) gene in these cellular processes. LIN-40 is homologous to the metastasis-associated factor 1 (MTA1) in mammals, which has been identified as a component of the nucleosome remodeling and histone deacetylation (NuRD) complex that functions as a transcriptional co-repressor. We show here that lin-40 negatively regulates vulval fate specification at least partly by promoting cell fusion between the vulval precursor cells and the hypodermal syncytium at an early larval stage. This inhibitory function of lin-40 might be carried out by downregulating lin-39 Hox expression. We also show that lin-40 is specifically required for cell divisions along the transverse orientation during vulval ------------------- Key: 5023 Medline: 11747818 Authors: Longman D;McGarvey T;McCracken S;Johnstone IL;Blencowe BJ;Caceres JF Title: Multiple interactions between SRm160 and SR family proteins in enhancer-dependent splicing and development of C. elegans. Citation: Current Biology 11: 1923-1933 2001 Type: ARTICLE Genes: rsp-3 rsr-2 Abstract: Background: SR family and SR-related proteins assemble on exonic splicing enhancer (ESE) sequences to promote both constitutive and regulated splicing. The SRm160 splicing coactivator, an SR-related nuclear matrix protein of 160 kDa, is important for the splicing of specific constitutive and ESE-dependent pre-mRNAs. Results: In the present study, we show that SRm 160 is required to promote pre-mRNA splicing mediated by a large population of functional ESE sequences within a randomized 18 nucleoticle sequence. This suggests that it functions as a general coactivator by interacting with different SIR family/SR-related proteins bound to different ESE sequences. Consistent with this, several SR family and SR-related proteins coimmunoprecipitated specifically with SRm160 in the presence of low salt. We used RNA interference (RNAi) in Caenorhabditis elegans to determine whether interactions between CeSRm 160 and different CeSR family proteins are important in a whole-organism context. Previously we showed that RNAi of CeSRm 160 and individual CeSR family genes other than CeSF2/ASF results in no obvious phenotype, which is indicative of gene redundancy, In the present study, we demonstrate that RNAi of CeSRm 160 in combination with any CeSR family gene results in the production of unfertilized oocytes by the injected mother. Conclusions: The observation that simultaneous suppression of CeSRm 160 and individual CeSR family proteins results in a distinct phenotype is indicative of critical functional interactions between these factors. Our results provide biochemical and genetic evidence indicating that interactions between SRm 160 and multiple SR family proteins are important for both optimal splicing activity and for proper development. ------------------- Key: 5024 Medline: 11747819 Authors: Ahmed S;Alpi A;Hengartner MO;Gartner A Title: C. elegans RAD-5/CLK-2 defines a new DNA damage checkpoint protein. Citation: Current Biology 11: 1934-1944 2001 Type: ARTICLE Genes: clk-1 clk-2 clk-3 gro-1 mrt-2 rad-5 Abstract: Background: In response to genotoxic stress, cells activate checkpoint pathways that lead to a transient cell cycle arrest that allows for DNA repair or to apoptosis, which triggers the demise of genetically damaged cells. Results: During positional cloning of the C. elegans rad-5 DNA damage checkpoint gene, we found, surprisingly, that rad-5(mn159) is allelic with clk-2(qm37), a mutant previously implicated in regulation of biological rhythms and life span. However, clk-2(qm37) is the only C. elegans clock mutant that is defective for the DNA damage checkpoint. We show that rad-5/clk-2 acts in a pathway that partially overlaps with the conserved C. elegans mrt-2/S. cerevisiae RAD17/S. pombe rad1 (+) checkpoint pathway. In addition, rad-5/clk-2 also regulates the S phase replication checkpoint in C. elegans. Positional cloning reveals that the RAD-5/CLK-2 DNA damage checkpoint protein is homologous to S, cerevisiae Tel2p, an essential DNA binding protein that regulates telomere length in, yeast. However, the partial loss-of-function C. elegans rad-5(mn 159) and clk-2(qm37) checkpoint mutations have little effect on telomere length, and analysis of the partial loss-of-function of S. cerevisiae tel2-1 mutant failed to reveal typical DNA damage checkpoint defects. Conclusions: Using C. elegans genetics we define the novel DNA damage checkpoint protein RAD-5/CLK-2, which may play a role in oncogenesis. Given that Tel2p has been shown to bind to a variety of nucleic, acid structures in vitro, we speculate that the RAD-5/CLK-2 checkpoint protein may act at sites of DNA damage, either as a sensor of DNA damage or to aid in ------------------- Key: 5025 Medline: 11747821 Authors: Lee RYN;Hench J;Ruvkun G Title: Regulation of C. elegans DAF-16 and its human ortholog FKHRL1 by the daf-2 insulin-like signaling pathway. Citation: Current Biology 11: 1950-1957 2001 Type: ARTICLE Genes: akt-1 akt-2 daf-2 daf-7 daf-16 mgDf47 Abstract: C. elegans insulin-like signaling regulates metabolism, development, and life span. This signaling pathway negatively regulates the activity of the forkhead transcription factor DAF-16. daf-16 encodes multiple isoforms that are expressed in distinct tissue types and are probable orthologs of human FKHRL1, FKHR, and AFX. We show that human FKHRL1 can partially replace DAF-16, proving the orthology. In mammalian cells, insulin and insulin-like growth factor signaling activate AKT/PKB kinase to negatively regulate the nuclear localization of DAF-16 homologs (reviewed in [1]). We show that the absence of AKT consensus sites on DAF-16 is sufficient to cause dauer arrest in daf-2(+) animals, proving that daf-16 is the major output of insulin signaling in C. elegans. FKHR, FKRHL1, and AFX may similarly be the major outputs of mammalian insulin signaling. daf-2 insulin signaling, via AKT kinases, negatively regulates DAF-16 by controlling its nuclear localization. Surprisingly, we find that daf-7 TGF-beta signaling also regulates DAF-16 nuclear localization specifically at the time when the animal makes the commitment between diapause and reproductive development. daf-16 function is supported by the combined action of two distinct promoter/enhancer elements, whereas the coding sequences of two major DAF-16 isoforms are interchangeable. Together, these observations suggest that the combined effects of transcriptional and posttranslational regulation of daf-16 transduce insulin-like signals in C. elegans and perhaps more ------------------- Key: 5026 Medline: 11747825 Authors: Henderson ST;Johnson TE Title: daf-16 integrates developmental and environmental inputs to mediate aging in the nematode Caenorhabditis elegans. Citation: Current Biology 11: 1975-1980 2001 Type: ARTICLE Genes: age-1 akt-1 akt-2 clk-1 daf-2 daf-16 eat-2 Abstract: Evolutionary models of aging propose that a tradeoff exists between the resources an organism devotes to reproduction and growth and those devoted to cellular maintenance and repair, such that an optimal life history always entails an imperfect ability to resist stress. Yet, since environmental stressors, such as caloric restriction [1] or exposure to mild stress [2, 3], can increase stress resistance and life span, it is possible that a common genetic mechanism could regulate the allocation of resources in response to a changing environment (for overview, see [4-7]). Consistent with predictions of evolutionary trade-off models, we show that nematodes carrying an integrated DAF-16::GFP transgene grow and reproduce more slowly yet are more stress resistant and longer lived than controls carrying the integration marker alone. We also show that the nuclear localization of the DAF-16::GFP fusion protein responds to environmental inputs as well as genetic. Environmental stresses, such as starvation, heat, and oxidative stress, cause rapid nuclear localization of DAF-16. In conditions rich in food, we find that DAF-16::GFP is inhibited from entry into the nucleus by daf-2 and akt-1/akt-2, both components of insulin-like signaling in nematodes. We suggest that changes in the subcellular localization of DAF-16 by environmental cues allows for rapid reallocation of resources in response to a ------------------- Key: 5027 Medline: 11747813 Authors: Garcia LR;Mehta P;Sternberg PW Title: Regulation of distinct muscle behaviors controls the C. elegans male's copulatory spicules during mating. Citation: Cell 107: 777-788 2001 Type: ARTICLE Genes: cha-1 egl-19 egl-30 unc-17 unc-29 unc-31 unc-38 unc-64 unc-68 Abstract: We demonstrate through cell ablation, molecular genetic, and pharmacological approaches that during C. elegans male mating behavior, the male inserts his copulatory spicules into the hermaphrodite by regulating periodic and prolonged spicule muscle contractions. Distinct cholinergic neurons use different ACh receptors and calcium channels in the spicule muscles to mediate these contractile behaviors. The PCB and PCC sensory neurons facilitate periodic contraction through muscle-encoded UNC-68 ryanodine receptor calcium channels. The SPC motor neurons trigger prolonged contraction through EGL-19 L-type voltage-gated calcium channels. The male gonad then lengthens the duration of EGL-19-mediated prolonged muscle contraction. This regulation of muscle contraction provides a paradigm to explain how animals initiate, monitor, and maintain a behavioral motor program. ------------------- Key: 5028 Medline: 11738085 Authors: Abdelghany HM;Gasmi L;Cartwright JL;Bailey S;Rafferty JB;McLennan AG Title: Cloning, characterisation and crystallisation of a diadenosine 5',5'''-P-1,P-4-tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans. Citation: Biochemica et Biophysica Acta - Protein Structure & Molecular Enzymology 1550: 27-36 2001 Type: ARTICLE Genes: Abstract: Asymmetrically cleaving diadenosine 5',5(m)-P-1,P-4-tetraphosphate (AP(4)A) hydrolase activity has been detected in extracts of adult Caenorhabditis elegans and the corresponding cDNA amplified and expressed in Escherichia coh. As expected, sequence analysis shows the enzyme to be a member of the Nudix hydrolase family. The purified recombinant enzyme behaves as a typical animal Ap(4)A hydrolase. It hydrolyses AP(4)A with a K-m of 7 muM and k(cat) of 27 s(-1) producing AMP and ATP as products. It is also active towards other adenosine and diadenosine polyphosphates with four or more phosphate groups, but not diadenosine triphosphate, always generating ATP as one of the products, It is inhibited non-competitively by fluoride (K-i = 25 muM) and competitively by adenosine 5'-tetraphosphate with AP(4)A as substrate (K-i = 10 nM). Crystals of diffraction quality with the morphology of rectangular plates were readily obtained and preliminary data collected. These crystals diffract to a minimum d-spacing of 2 Angstrom and belong to either space group C222 or C222(1). Phylogenetic analysis of known and putative AP(4)A hydrolases of the Nudix family suggests that they fall into two groups comprising plant and Proteobacterial enzymes on the one hand and animal and archaeal enzymes on the other. Complete structural determination of the C. elegans AP(4)A hydrolase will help determine the basis of this grouping. ------------------- Key: 5029 Medline: 11728866 Authors: Nickerson CA Title: Putting C. elegans to Gram-positive use. Citation: Trends in Microbiology 9: 581- 2001 Type: REVIEW Genes: Abstract: Investigations into host-pathogen interactions have revealed several microbial virulence mechanisms are shared between pathogens that infect mammalian, plant and invertebrate hosts. Likewise, recent evidence suggests that there are similarities in the host defense responses following microbial infection. ------------------- Key: 5030 Medline: 11744632 Authors: Warren CE;Krizus A;Dennis JW Title: Complementary expression patterns of six nonessential Caenorhabditis elegans core2/I N-acetylglucosaminyltransferase homologues. Citation: Glycobiology 11: 979-988 2001 Type: ARTICLE Genes: gly-1 gly-15 gly-16 gly-17 gly-18 gly-19 sra-12 Abstract: The Caenorhabditis elegans genome contains 18 sequences related to mammalian core 2/I N-acetylglucosaminyltransferases. The six most closely related genes (gly-1 and gly-15 to gly-19) likely encode active enzymes, because are all transcribed and do not appear to be pseudogenes. Polypeptide divergence and the gene structures are both concordant with a common ancestor at the time of radiation from mammals that underwent three rounds of duplication and, most recently, a tandem duplication. Polypeptide alignments with mammalian homologues do not indicate whether the enzyme specificities are core 2, 4, or I-like or novel, but do clearly demonstrate the secondary structure characteristics of glycosyltransferases. The six homologues have essentially nonoverlapping expression patterns, unrelated by tissue type or cell lineage. The extent varies widely; gly-15 is expressed only in two gland cells, whereas gly-18 is broadly expressed in diverse cell types. gly-1, -15, -18 and -19 are expressed during adulthood; gly-16 and gly-17 appear to be restricted to embryonic or early larval stages. The parsimonious interpretation of the expression pattern and sequence data is that the catalytic activities are similar but with diverged promoters. Null alleles of three of the genes were generated without causing gross abnormality in homozygous animals. RNA-mediated interference experiments also failed to induce defects in the four genes tested. Nevertheless, the nematode has evolved six diverged core 2 GlcNAc-T-like genes, and we postulate that these arose in response to selection pressures to which C. elegans is not ordinarily subjected ------------------- Key: 5031 Medline: 11790304 Authors: Broadbent ID;Pettitt J Title: The C. elegans hmr-1 gene can encode a neuronal classic cadherin involved in the regulation of axon fasciculation. Citation: Current Biology 12: 59-63 2002 Type: ARTICLE Genes: hrm-1 Abstract: Nervous system morphogenesis is characterized by extensive interactions between individual axon growth cones and their cellular environments. Selective cell adhesion is one mechanism by which the growth of an axon can be modulated, and members of the classic cadherin group of cell adhesion molecules have been shown to play a role in this process in both vertebrates and Drosophila [1-4]. In Drosophila, there are two classic cadherins: one involved primarily in regulating the morphogenesis of epithelia [5, 6], and the other, DN-cadherin [3], required almost exclusively in neuronal development. In contrast, C. elegans has a single classic cadherin gene, hmr-1, whose function is required for epithelial morphogenesis [7]. We show here that hmr-1 also encodes a second classic cadherin via a novel mechanism involving an alternative, neuron-specific promoter, coupled with alternative splicing. This novel HMR-1 isoform is very similar to DN-cadherin, and a mutant strain that specifically lacks the function of this isoform displays defects in the fasciculation and outgrowth of a subset of motor neuron processes; a phenotype that resembles loss of DN-cadherin function in Drosophila. These results indicate that Drosophila and C. elegans share a conserved, cadherin-dependent mechanism involved in regulating axonal patterning and fasciculation. ------------------- Key: 5032 Medline: 11751687 Authors: Gao J;Estrada L;Cho S;Ellis RE;Gorski JL Title: The Caenorhabditis elegans homolog of FGD1, the human Cdc42 gene responsible for faciogenital dysplasia, is critical for excretory cell morphogenesis. Citation: Human Molecular Genetics 26: 3049-3062 2001 Type: ARTICLE Genes: fgd-1 exc-5 Abstract: FGD1 mutations result in faciogenital dysplasia, an X-linked human disease that affects skeletogenesis. FGD1 encodes a guanine nucleotide exchange factor (GEF) that specifically activates the Rho GTPase Cdc42. To gain insight into the function of FGD1, we have isolated and characterized fgd-1, the Caenorhabditis elegans homolog of the human FGD1 gene. Comparative sequence analyses show that fgd-1 and FGD1 share a similar structural organization and a high degree of sequence identity throughout shared signaling domains. In nematodes, interference with fgd-1 expression results in excretory cell abnormalities and cystic dilation of the excretory cell canals. Molecular lesions associated with two exc-5 alleles affect the fgd-1 gene, and fgd-1 transgenic expression rescues the Exc-5 phenotype. Together, these data confirm that the fgd-1 transcript corresponds to the exc-5 gene. Transgenic expression studies show that fgd-1 has a limited pattern of expression that is confined to the excretory cell during development, a finding that suggests that the C.elegans FGD-1 protein might function in a cell autonomous manner. Serial observations indicate that fgd-1 mutations lead to developmental excretory cell abnormalities that cause cystic dilation and interfere with canal process extension. Based on these data, we conclude that fgd-1 is the C.elegans homolog of the human FGD1 gene, a new member of the FGD1-related family of RhoGEF genes, and that fgd-1 plays a critical role in excretory cell morphogenesis and ------------------- Key: 5033 Medline: 11733138 Authors: Berman KS;Hutchison M;Avery L;Cobb MH Title: kin-18, a C. elegans protein kinase involved in feeding. Citation: Gene 279: 137-147 2001 Type: ARTICLE Genes: kin-18 mek-1 myo-2 Abstract: TAO1 and TAO2 are recently described protein kinases whose initial characterization has placed them at the mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) kinase kinase (MEKK) level of stress-responsive MAPK pathways. Because their physiological roles have not been identified, we sought to study their C elegans homolog to learn more about their functions. kin-18 encodes a previously uncharacterized protein in C. elegans whose catalytic domain shares over 60% identity with TAO1 and TAO2. We demonstrate that KIN-18 is a protein of 120 kDa whose promoter is active in the pharynx and intestine of C. elegans. To learn more about TAO/KIN-18 function, we studied how expression of constitutively active forms of TAO1 or KIN-18 would affect the physiology of intact worms. Strains Of C elegans expressing active forms of TAO1 or KIN-18 exhibit altered pharyngeal electrophysiology as measured by electropharyngeogram. These worms grow more slowly and lay fewer eggs, phenotypes that could result from reduced feeding. We have also identified a C elegans gene that encodes a protein kinase similar to mammalian MAPK/ERK Kinase (MEK) 4 whose promoter is active in the pharynx. It is phosphorylated by TAO1 in vitro and physically interacts ------------------- Key: 5034 Medline: 11749961 Authors: Rea S Title: CLK-1/Coq7p is a DMQ mono-oxygenase and a new family member of the di-iron carboxylate protein family. Citation: FEBS Letters 509: 389-394 2001 Type: ARTICLE Genes: clk-1 Abstract: Strains of Caenorhabditis elegans mutant for clk-1 exhibit a 20-40% increase in mean lifespan. clk-1 encodes a mitochondrial protein thought to be either an enzyme or regulatory molecule acting within the ubiquinone biosynthesis pathway. Here CLK-1 is shown to be related to the ubiquinol oxidase, alternative oxidase, and belong to the functionally diverse di-iron-carboxylate protein family which includes bacterioferritin and methane mono-oxygenase. Construction and analysis of a homology model indicates CLK-1 is a 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone mono-oxygenase as originally predicted. Analysis of known CLK-1/Coq7p mutations also supports this notion. These findings raise the possibility of developing CLK-1-specific inhibitors to test for lifespan extension in higher organisms. ------------------- Key: 5035 Medline: 11738147 Authors: Butov A;Johnson T;Cypser J;Sannikov I;Volkov M;Sehl M;Yashin A Title: Hormesis and debilitation effects in stress experiments using the nematode worm Caenorhabditis elegans: the model of balance between cell damage and HSP levels. Citation: Experimental Gerontology 37: 57-66 2001 Type: ARTICLE Genes: Abstract: In this article, we discuss mechanisms responsible for the effects of heat treatment on increasing subsequent survival in the nematode worm Caenorhabditis elegans. We assume that the balance between damage associated with exposure to thermal stress and the level of heat shock proteins produced plays a key role in forming the age-pattern of mortality and survival in stress experiments. We propose a stochastic model of stress, which describes the accumulation of damage in the cells of the worm as the worm ages. The model replicates the age trajectories of experimental survival curves in three experiments in which worms were heat-treated for 0, 1, 2, 4, 6, or 8 h. We also discuss analytical results and directions of further research. The proposed method of stochastic modelling of survival data provides a new approach that can be used to model, analyse and extrapolate experimental results. ------------------- Key: 5036 Medline: 11780124 Authors: Calfon M;Zeng H;Urano F;Till JH;Hubbard SR;Harding HP;Clark SG;Ron D Title: IRE1 couples endoplasmic reticulum load to secretory capacity by processing the XBP-1 mRNA. Citation: Nature 415: 92-96 2002 Type: ARTICLE Genes: ire-1 ise-1 upr-1 xbp-1 Abstract: The unfolded protein response (UPR), caused by stress, matches the folding capacity of endoplasmic reticulum (ER) to the load of client proteins in the organelle(1,2). In yeast, processing of HAC1 mRNA by activated Ire1 leads to synthesis of the transcription factor Hac1 and activation of the UPR3. The responses to activated IRE1 in metazoans are less well understood. Here we demonstrate that mutations in either ire-1 or the transcription-factor-encoding xbp-1 gene abolished the UPR in Caenorhabditis elegans. Mammalian XBP-1 is essential for immunoglobulin secretion and development of plasma cells(4), and high levels of XBP-1 messenger RNA are found in specialized secretory cells(5). Activation of the UPR causes IRE1-dependent splicing of a small intron from the XBP-1 mRNA both in C. elegans and mice. The protein encoded by the processed murine XBP-1 mRNA accumulated during the UPR, whereas the protein encoded by unprocessed mRNA did not. Purified mouse IRE1 accurately cleaved XBP-1 mRNA in vitro, indicating that XBP-1 mRNA is a direct target of IRE1 endonucleolytic activity. Our findings suggest that physiological ER load regulates a developmental decision in ------------------- Key: 5037 Medline: 11778030 Authors: Tatar M;Rand DM Title: Dietary advice on Q. Citation: Science 295: 54-55 2001 Type: REVIEW Genes: clk-1 daf-2 daf-12 Abstract: How much you eat, not what you eat, seems to make a difference in the aging process. It is well established that reduced calorie consumption robustly extends adult life expectancy in a variety of animal models. Now, on page 120 of this issue, Larsen and Clarke show that diet quality also affects aging. In the worm Caenorhabditis elegans, reduced consumption of coenzyme Q (Q) dramatically extends longevity. ------------------- Key: 5038 Medline: 11778046 Authors: Larsen PL;Clarke CF Title: Extension of life-span in Caenorhabditis elegans by a diet lacking coenzyme Q. Citation: Science 295: 120-123 2002 Type: ARTICLE Genes: clk-1 daf-2 daf-12 daf-16 fer-15 Abstract: The isoprenylated benzoquinone coenzyme Q is a redox-active lipid es sential for electron transport in aerobic respiration. Here, we show that withdrawal of coenzyme Q (Q) from the diet of wild-type nematodes extends adult life-span by similar to 60%. The longevity of clk-1, daf-2, daf-12, and daf-16 mutants is also extended by a Q-less diet. These results establish the importance of Q in life-span determination. The findings suggest that Q and the daf-2 pathway intersect at the mitochondria and imply that a concerted production coupled with enhanced scavenging of reactive oxygen species contributes to the substantial life-span extension. ------------------- Key: 5039 Medline: 11778048 Authors: Boulton SJ;Gartner A;Reboul J;Vaglio P;Dyson N;Hill DE;Vidal M Title: Combined functional genomic maps of the C. elegans DNA damage response. Citation: Science 295: 127-131 2002 Type: ARTICLE Genes: atl-1 atm-1 blm-1 coh-2 daf-21 exo-3 hda-3 hku-70 hku-80 hpr-9 hpr-17 hsr-9 hus-1 kin-20 mms-2 mre-11 mrt-2 pcn-1 pdi-1 pdi-2 prp-1 rad-50 rad-51 rad-54 rfc-1 rfc-3 rfc-4 rfs-1 ubc-9 ubc-13 Abstract: Many human cancers originate from defects in the DNA damage response (DDR). Although much is known about this process, it is likely that additional DDR genes remain to be discovered. To identify such genes, we used a strategy that combines protein-protein interaction mapping and large-scale phenotypic analysis in Caenorhabditis elegans. Together, these approaches identified 12 worm DDR orthologs and 11 novel DDR genes. One of these is the putative ortholog of hBCL3, a gene frequently altered in chronic lymphocytic leukemia. Thus, the combination of functional genomic mapping approaches in model organisms may facilitate the identification and characterization of genes involved in cancer and, perhaps, other human diseases. ------------------- Key: 5040 Medline: 11756550 Authors: Nam S;Jin YH;Li QL;Lee KY;Jeong GB;Ito Y;Lee J;Bae SC Title: Expression pattern, regulation, and biological role of Runt domain transcription factor, run, in Caenorhabditis Citation: Molecular and Cellular Biology 22: 547-554 2002 Type: ARTICLE Genes: elt-1 elt-2 end-1 Abstract: The Caenorhabditis elegans run gene encodes a Runt domain factor. Runx1, Runx2, and Runx3 are the three known mammalian homologs of run. Runx1, which plays an essential role in hematopoiesis, has been identified at the breakpoint of chromosome translocations that are responsible for human leukemia. Runx2 plays an essential role in osteogenesis, and inactivation of one allele of Runx2 is responsible for the human disease cleidocranial dysplasia. To understand the role of run in C. elegans, we used transgenic ran::GFP reporter constructs and a double-stranded RNA-mediated interference method. The expression of run was detected as early as the bean stage exclusively in the nuclei of seam hypodermal cells and lasted until the L3 stage. At the larval stage, expression of run was additionally detected in intestinal cells. The regulatory elements responsible for the postembryonic hypodermal seam cells and intestinal cells were separately located within a 7.2-kb-long intron region. This is the first report demonstrating that an intron region is essential for stage-specific and cell type-specific expression of a C elegans gene. RNA interference analysis targeting the run gene resulted in an early larva-lethal phenotype, with apparent malformation of the hypodermis and intestine. These results suggest that run is involved in the development of a functional hypodermis and gut in C elegans. The highly conserved role of the Runt domain transcription factor in gut development during evolution ------------------- Key: 5041 Medline: 11748251 Authors: Hannak E;Kirkham M;Hyman AA;Oegema K Title: Aurora-A kinase is required for centrosome maturation in Caenorhabditis elegans. Citation: Journal of Cell Biology 155: 1109-1115 2001 Type: ARTICLE Genes: air-1 zyg-9 Abstract: Centrosomes mature as cells enter mitosis, accumulating gamma -tubulin and other pericentriolar material (PCM) components. This occurs concomitant with an increase in the number of centrosomally organized microtubules (MTs). Here, we use RNA-mediated interference (RNAi) to examine the role of the aurora-A kinase, AlR-1, during centrosome maturation in Caenorhabditis elegans. In air-1(RNAi) embryos, centrosomes separate normally, an event that occurs before maturation in C. elegans. After nuclear envelope breakdown, the separated centrosomes collapse together, and spindle assembly fails. In mitotic air-1(RNAi) embryos, centrosomal alpha -tubulin fluorescence intensity accumulates to only 40% of wild-type levels, suggesting a defect in the maturation process. Consistent with this hypothesis, we find that AIR-1 is required for the increase in centrosomal gamma -tubulin and two other PCM components, ZYG-9 and CeGrip, as embryos enter mitosis. Furthermore, the AIR-1-dependent increase in centrosomal gamma -tubulin does not require MTs. These results suggest that aurora-A kinases are required to execute a MT-independent pathway for the recruitment of PCNA during centrosome maturation. ------------------- Key: 5042 Medline: 11742996 Authors: Calvo D;Victor M;Gay F;Sui G;Luke MPS;Dufourcq P;Wen G;Maduro M;Rothman J;Shi Y Title: A POP-1 repressor complex restricts inappropriate cell type-specific gene transcription during Caenorhabditis elegans embryogenesis. Citation: EMBO Journal 20: 7197-7208 2001 Type: ARTICLE Genes: cbp-1 end-1 hda-1 hda-3 pop-1 unc-37 Abstract: In Caenorhabditis elegans, histone acetyltransferase CBP-1 counteracts the repressive activity of the histone deacetylase HDA-1 to allow endoderm differentiation, which is specified by the E cell. In the sister MS cell, the endoderm fate is prevented by the action of an HMG box-containing protein, POP-1, through an unknown mechanism. In this study, we show that CBP-1, HDA-1 and POP-1 converge on end-1, an initial endoderm-determining gene. In the E lineage, an essential function of CBP-1 appears to be the activation of end-1 transcription. We further identify a molecular mechanism for the endoderm-suppressive effect of POP-1 in the MS lineage by demonstrating that POP-1 functions as a transcriptional repressor that inhibits inappropriate end-1 transcription. We provide evidence that POP-1 represses transcription via the recruitment of HDA-1 and UNC-37, the C.elegans homolog of the co-repressor Groucho. These findings demonstrate the importance of the interplay between acetyltransferases and deacetylases in the regulation of a critical cell fate-determining gene during development. Furthermore, they identify a strategy by which concerted actions of historic deacetylases and other co-repressors ensure maximal repression of inappropriate cell type-specific gene ------------------- Key: 5043 Medline: 11779458 Authors: Ambros V Title: microRNAs: tiny regulators with great potential. Citation: Cell 107: 823-826 2001 Type: REVIEW Genes: let-7 lin-4 lin-14 lin-28 Abstract: Animal genomes contain an abundance of small genes that produce regulatory RNAs of about 22 nucleotides in length. These microRNAs are diverse in sequence and expression patterns, and are evolutionarily widespread, suggesting that they may participate in a wide range of genetic regulatory pathways. ------------------- Key: 5044 Medline: 11779465 Authors: Shen X;Ellis RE;Lee K;Liu CY;Yang K;Solomon A;Yoshida H;Morimoto R;Kurnit DM;Mori K;Kaufman RJ Title: Complementary signaling pathways regulate the unfolded protein response and are required for C. elegans development. Citation: Cell 107: 893-903 2001 Type: ARTICLE Genes: ire-1 pek-1 xbp-1 Abstract: The unfolded protein response (UPR) is a transcriptional and translational intracellular signaling pathway activated by the accumulation of unfolded proteins in the lumen of the endoplasmic reticulum (ER). We have used C. elegans as a genetic model system to dissect UPR signaling in a multicellular organism. C. elegans requires ire-l-mediated splicing of xbp-1 mRNA for UPR gene transcription and survival upon ER stress. In addition, ire-1/xbp-1 acts with pek-1, a protein kinase that mediates translation attenuation, in complementary pathways that are essential for worm development and survival. We propose that UPR transcriptional activation by ire-1 as well as translational attenuation by pek-1 maintain ER homeostasis. The results demonstrate that the UPR and ER homeostasis are essential for metazoan development. ------------------- Key: 5045 Medline: 11779801 Authors: Jin SW;Arno N;Cohen A;Shah A;Xu QJ;Chen N;Ellis RE Title: In Caenorhabditis elegans, the RNA-binding domains of the cytoplasmic polyadenylation element binding protein FOG-1 are needed to regulate germ cell fates. Citation: Genetics 159: 1617-1630 2001 Type: ARTICLE Genes: fog-1 qDf4 Abstract: FOG-1 controls germ cell fates in the nematode Caenorhabditis elegans. Sequence analyses revealed that FOG-1 is a cytoplasmic polyadenylation element binding (CPEB) protein; similar proteins from other species have been shown to bind messenger RNAs and regulate their translation. Our analyses of fog-1 mutations indicate that each of the three RNA-binding domains of FOG-1 is essential for activity. In addition, biochemical tests show that FOG-1 is capable of binding RNA sequences in the 3'-untranslated region of its mm message. Finally, genetic assays reveal that fog-1 functions zygotically, that the small fog-1 transcript has no detectable function, and that missense mutations in fog-1 cause a dominant negative phenotype. This last observation suggests that FOG-1 acts in a complex, or as a multimer, to regulate translation. On the basis of these data, we propose that FOG-1 binds RNA to regulate germ cell fates and that it does so by controlling the translation of its targets. One of these targets might be the fog-1 transcript itself. ------------------- Key: 5046 Medline: Authors: Lambie EJ Title: Cell proliferation and growth in C. elegans. Citation: BioEssays 24: 38-53 2002 Type: REVIEW Genes: akt-1 akt-2 bar-1 cdk-4 cet-1 chr-3 cki-1 cul-2 cyd-1 cye-1 daf-2 daf-12 daf-16 dbl-1 dpl-1 egl-17 efl-1 emb-27 gld-1 gld-2 glp-1 glp-3 glp-4 gon-2 gon-4 hda-4 lag-1 let-23 let-60 lin-1 lin-3 lin-4 lin-12 lin-14 lin-23 lin-25 lin-28 lin-31 lin-35 lin-39 mab-5 ncc-1 ncl-1 nhr-25 nos-1 nos-2 sma-2 sma-3 sma-4 sma-6 sur-2 Abstract: The cell division and differentiation events that occur during the development of the nematode Caenorhabditis elegans are nearly identical between different individuals, a feature that distinguishes this organism from larger and more complex metazoans, such as humans and Drosophila. In view of this discrepancy, it might be expected that the regulation of cell growth, division and differentiation in C. elegans would involve mechanisms separate from those utilized in larger animals. However, the results of recent genetic, molecular and cellular studies indicate that C. elegans employs an arsenal of developmental regulatory mechanisms quite similar to those wielded by its arthropod and vertebrate relatives. Thus, the nematode system is providing both novel and complementary insights into the general problem of how growth and patterning events are integrated in development. This review offers a general perspective on the regulation of cell division and growth in C. elegans, emphasizing recent studies of these crucial aspects of development. ------------------- Key: 5047 Medline: 11544104 Authors: Rongo C Title: Disparate cell types use a shared complex of PDZ proteins for polarized protein localization. Citation: Cytokine & Growth Factor Reviews 12: 349-359 2001 Type: REVIEW Genes: glr-1 let-23 let-60 lin-2 lin-3 lin-7 lin-10 Abstract: Based on their morphology and function, epithelial cells and neurons appear to have very little in common; however, growing evidence suggests that these two disparate cell types share an underlying polarization pathway responsible for sorting proteins to specific subcellular sites. An evolutionarily conserved complex of PDZ domain-containing proteins thought to be responsible for polarized protein localization has been identified from both brain and epithelial tissue, both from mammals and from the nematode C. elegans. Some of th most recent data on PDZ proteins and the proteins with which they interact are summarized. In particular, some of the more recently proposed models for their function in cells, and the in vivo and in vitro data that support these models are focused upon. ------------------- Key: 5048 Medline: Authors: Hagen F;Layden M;Nehrke K;Gentile K;Berbach K;Tsao CC;Forsythe M Title: Mucin-type O-glycosylation in C. elegans is initiated by a family of glycosyltransferases. Citation: Trends in Glycoscience and Glycotechnology 13: 463-479 2001 Type: ARTICLE Genes: Abstract: ------------------- Key: 5049 Medline: Authors: Hirabayashi J;Arata Y;Hayama K;Kasai K Title: Galectins from the nematode Caenorhabditis elegans and the glycome project. Citation: Trends in Glycoscience and Glycotechnology 13: 533-549 2001 Type: REVIEW Genes: Abstract: ------------------- Key: 5050 Medline: Authors: Hirabayashi J Title: Loss-of-function of a glycosyltransferase results in resistance to Bacillus toxins in C. elegans. Citation: Trends in Glycoscience and Glycotechnology 13: 555-556 2001 Type: ARTICLE Genes: Abstract: ------------------- Key: 5051 Medline: 11410594 Authors: Tsang WY;Lemire BD Title: Mitochondrial genome content is regulated during nematode development. Citation: Biochemical and Biophysical Research Communications 291: 8-16 2002 Type: ARTICLE Genes: fem-1 fem-3 glp-1 glp-4 him-8 Abstract: Growth and development rely on the mitochondrial respiratory chain (MRC) as the major source of ATP. We measured the mitochondrial DNA (mtDNA) copy number of each of the Caenorhabditis elegans developmental stages. Embryos, L1, L2, and L3 larvae all have similar to25,000 copies of maternally derived mtDNA. The copy number increases fivefold in L4 larvae and a further sixfold in adult hermaphrodites, but only twofold in adult males. The majority of mtDNA in adult worms is germline associated, and germline-deficient mutants show markedly reduced mtDNA contents With sperm-deficient or oocyte-deficient mutants, we confirm that mtDNA amplification is primarily associated with oocyte production. When mtDNA replication is inhibited, a quantitative and homogeneous arrest as L3 larvae occurs. Thus, mtDNA amplification is a necessary component of normal development and its regulation may involve an energy-sensing decision or checkpoint that can be invoked when mitochondrial energy generation is ------------------- Key: 5052 Medline: Authors: L'Hernault SW;Singson AW Title: Developmental genetics of spermatogenesis in the nematode Caenorhabditis elegans. Citation: "The Testis: From Stell Cell to Sperm Function". E Goldberg (ed). Springer-Verlag, New York. : 109-119 2000 Type: REVIEW Genes: spe-4 spe-5 spe-9 Abstract: In both mammals and C. elegans, spermatogenesis is the process where a spermatogonial cell undergoes a series of divisions to produce a highly differentiated cell, the spermatozoon. Spermatogonial cellular divisions are incomplete in mammals so that all subsequent stages occur in a syncitium. The situation is similar in C. elegans, where spermatogonial nuclei initially share a common cytoplasm. Spermatogonial divisions in both mammals and C. elegans are regulated by signaling from gonadal accessory ------------------- Key: 5053 Medline: 11748140 Authors: Starr DA;Hermann GJ;Malone CJ;Fixsen W;Priess JR;Horvitz HR;Han M Title: unc-83 encodes a novel component of the nuclear envelope and is essential for proper nuclear migration. Citation: Development 128: 5039-5050 2001 Type: ARTICLE Genes: exp-2 let-502 unc-73 unc-83 unc-84 mnDp26 sDf30 Abstract: Nuclear migration plays an essential role in the growth and development of a wide variety of eukaryotes. Mutations in unc-84, which encodes a conserved component of the nuclear envelope, have been shown to disrupt nuclear migration in two C. elegans tissues. We show that mutations in unc-83 disrupt nuclear migration in a similar manner in migrating P cells, hyp7 precursors and the intestinal primordium, but have no obvious defects in the association of centrosomes with nuclei or the structure of the nuclear lamina of migrating nuclei. We also show that unc-83 encodes a novel transmembrane protein. We identified three unc-83 transcripts that are expressed in a tissue-specific manner. Antibodies against UNC-83 co-localized to the nuclear envelope with lamin and UNC-84. Unlike UNC84, UNC-83 localized to only specific nuclei, many of which were migratory. UNC-83 failed to localize to the nuclear envelope in unc-84 mutants with lesions in the conserved SUN domain of UNC-84, and UNC-83 interacted with the SUN domain of UNC-84 in vitro, suggesting that these two proteins function together during nuclear migration. We favor a model in which UNC-84 directly recruits UNC-83 to the nuclear envelope where they help transfer force between the cytoskeleton and the nucleus. ------------------- Key: 5054 Medline: 11740945 Authors: Gerisch B;Weitzel C;Kober-Eisermann C;Rottiers V;Antebi A Title: A hormonal signaling pathway influencing C. elegans metabolism, reproductive development, and life span. Citation: Developmental Cell 1: 841-851 2001 Type: ARTICLE Genes: daf-3 daf-9 daf-12 daf-16 mig-8 mcDf2 mgDf50 stDf1 Abstract: During C. elegans development, animals must choose between reproductive growth or dauer diapause in response to sensory cues. Insulin/IGF-I and TGF-B signaling converge on the orphan nuclear receptor daf-12 to mediate this choice. Here we show that daf-9 acts downstream of these inputs but upstream of daf-12. daf-9 and daf-12 mutants have similar larval defects and modulate insulin/IGF-I and gonadal signals that regulate adult life span. daf-9 encodes a cytochrome P450 related to vertebrate steroidogenic hydroxylases, suggesting that it could metabolize a DAF-12 ligand. Sterols may be the daf-9 substrate and daf-12 ligand because cholesterol deprivation phenocopies mutant defects. Sensory neurons, hypodermis, and somatic gonadal cells expressing daf-9 identify potential endocrine tissues. Evidently, lipophilic hormones influence nematode metabolism, diapause, and life ------------------- Key: 5055 Medline: 11703944 Authors: Segal SP;Graves LE;Verheyden J;Goodwin EB Title: RNA-regulated TRA-1 nuclear export controls sexual fate. Citation: Developmental Cell 1: 539-551 2001 Type: ARTICLE Genes: fem-1 glp-1 ima-3 tra-1 tra-2 vit-2 Abstract: TRA-1, a member of the GLI family of transcription factors, is required for C. elegans female development. We find that TRA-1 has a sex-specific distribution consistent with its role in female development: nuclear TRA-1 is higher in hermaphrodite intestines and in specific germline regions than in males. TRA-1 patterns rely on nuclear export since treatment with leptomycin B, a CRM1-dependent export inhibitor, increases nuclear TRA-1 in males. TRA-1 export requires TRA-1 binding to the tra-2 3' untranslated region (3' UTR), as disruption of binding increases nuclear TRA-1 and female development. Our data are consistent with coexport of a TRA-1/tra2 mRNA complex reducing TRA-1 nuclear activity, and identify an interesting RNA-based mechanism for controlling transcriptional activity and cell fate determination. ------------------- Key: 5056 Medline: 11823633 Authors: Gaudet J;Mango SE Title: Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4. Citation: Science 295: 821-825 2002 Type: ARTICLE Genes: ceh-22 myo-2 par-1 pha-4 skn-1 tph-1 Abstract: The pha-4 locus encodes a forkhead box A (FoxA/HNF3) transcription factor homolog that specifies organ identity for Caenorhabditis elegans pharyngeal cells. We used microarrays to identify pharyngeal genes and analyzed those genes to determine which were direct PHA-4 targets. Our data suggest that PHA-4 directly activates most or all pharyngeal genes. Furthermore, the relative affinity of PHA-4 for different TRTTKRY (R=A/G, K=T/G, Y=T/C) elements modulates the onset of gene expression, providing a mechanism to activate pharyngeal genes at different developmental stages. We suggest that direct transcriptional regulation of entire gene networks may be a common feature of organ identity genes. ------------------- Key: 5057 Medline: Authors: Gillespie PG;Walker RG Title: Molecular basis of mechanosensory transduction. Citation: Nature 413: 194-202 2001 Type: REVIEW Genes: deg-1 mec-2 mec-4 mec-5 mec-6 mec-7 mec-9 mec-10 mec-12 unc-8 unc-105 Abstract: Mechanotransduction - a cell's conversion of a mechanical stimulus into an electrical signal - reveals vital features of an organism's environment. From hair cells and skin mechanoreceptors in vertebrates, to bristle receptors in flies and touch receptors in worms, mechanically sensitive cells are essential in the life of an organism. The scarcity of these cells and the uniqueness of their transduction mechanisms have conspired to slow molecular characterization of the ensembles that carry out mechanotransduction. But recent progress in both invertebrates and vertebrates is beginning to reveal the identities of proteins essential for transduction. ------------------- Key: 5058 Medline: Authors: Brose N;Rosenmund C;Rettig J Title: Regulation of transmitter release by Unc-13 and its homologues. Citation: Current Opinion in Neurobiology 10: 303-311 2000 Type: REVIEW Genes: unc-13 Abstract: Neurotransmitters are released by Ca2+-triggered exocytotic fusion of synaptic vesicles. Before fusion, vesicles dock at a specialised presynaptic plasma membrane region, the active zone, where they are primed to a fusion competent state. The nature of this priming reaction has long been enigmatic. Recent evidence demonstrates that priming is an essential and rate-limiting step in secretion from neurons and neuroendocrine cells. Members of the UNc-13 protein family, which are highly conserved during evolution and act as novel targets of the diacylglycerol second-messenger pathway, have been identified to play an essential role in this process. ------------------- Key: 5059 Medline: Authors: Walhout AJM;Vidal M Title: Protein interaction maps for model organisms. Citation: Nature Reviews Molecular Cell Biology 2: 55-62 2001 Type: REVIEW Genes: ced-3 ced-4 ced-9 egr-1 hda-1 lag-2 let-23 let-60 lin-7 lin-9 lin-12 lin-15 lin-35 lin-36 lin-37 lin-53 Abstract: Until recently, classical genetics and biochemistry were the main techniques used to investigate how organisms develop, reproduce, behave and age. But with the availability of complete genome sequences new approaches are emerging. Complete sets of proteins - "proteomes" - can be predicted from genome sequences and used to characterize protein functions globally. For example, through the large-scale identification of physical protein-protein interactions, comprehensive protein interaction maps are being generated. And these maps might help us to understand the processes that control the ------------------- Key: 5060 Medline: Authors: Zamore PD Title: RNA interference: listening to the sound of silence. Citation: Nature Structural Biology 8: 746-750 2001 Type: REVIEW Genes: let-7 lin-4 mut-2 mut-7 mut-8 mut-9 rde-1 Abstract: The term RNA interference (RNAi) describes the use of double-stranded RNA to target specific mRNAs for degredation, thereby silencing their expression. RNAi is one manifestation of a broad class of RNA silencing phenomena that are found in plants, animals and fungi. The discovery of RNAi has changed our understanding of how cells guard their genomes, led to the development of new strategies for blocking gene function, and may yet yield RNA-based drugs to treat human disease. ------------------- Key: 5061 Medline: Authors: Yu TW;Bargmann CI Title: Dynamic regulation of axon guidance. Citation: Nature Neuroscience 4: 1169-1176 2001 Type: REVIEW Genes: efn-1 efn-2 efn-3 efn-4 mab-20 plx-1 plx-2 sax-3 slt-1 smp-1 unc-5 unc-6 unc-40 unc-129 unc-130 vab-1 vab-2 Abstract: To reach their proper targets, axons rely upon the actions of highly conserved families of attractive and repulsive guidance molecules, including the netrins, Slits, semaphorins and ephrins. These guidance systems are used to generate an astonishingly varied set of neuronal circuits. Here we consider the mechanisms by which a few guidance systems can be used to generate diverse outcomes. Recent studies have revealed extensive transcriptional and post-transcriptional regulation of guidance cues and their regulators, as well as combinatorial mechanisms that integrate information from different families of guidance cues. ------------------- Key: 5062 Medline: Authors: Eddy SR Title: Non-coding RNA genes and the modern RNA world. Citation: Nature Reviews Genetics 2: 919-929 2001 Type: REVIEW Genes: alg-1 alg-2 let-7 lin-4 lin-14 lin-28 lin-41 lin-42 rde-1 Abstract: Non-coding RNA (ncRNA) genes produce functional RNA molecules rather than encoding proteins. However, almost all means of gene identification assume that genes encode proteins, so even in the era of complete genome sequences, ncRNA genes have been effectively invisible. Recently, several different systematic screens have identified a surprisingly large number of new ncRNA genes. Non-coding RNAs seem to be particularly abundant in roles that require highly specific nucleic acid recognition without complex catalysis, such as in directing post-transcriptional regulation of gene expression or in guiding RNA modifications. ------------------- Key: 5063 Medline: Authors: Wendland B Title: Round-trip ticket: recycling to the plasma membrane requires RME-1. Citation: Nature Cell Biology 3: E133-E135 2001 Type: REVIEW Genes: rme-1 Abstract: The endosomal system includes distinct endocytic compartments where decisions are made that determine the destinations of extracellular and plasma membrane materials that have been internalized. A new family of proteins has been found that governs the exit of material from one of these endocytic organelles, the endosomal recycling compartment (ERC). ------------------- Key: 5064 Medline: 11809975 Authors: Aurelio O;Hall DH;Hobert O Title: Immunoglobulin-domain proteins required for maintenance of ventral nerve cord organization. Citation: Science 295: 686-690 2002 Type: ARTICLE Genes: del-1 flp-1 kal-1 sra-6 unc-6 unc-47 unc-97 unc-129 zig-1 zig-2 zig-3 zig-4 zig-5 zig-8 Abstract: During development, neurons extend axons along defined routes to specific target cells. We show that additional mechanisms ensure that axons maintain their correct positioning in defined axonal tracts. After termination of axonal outgrowth and target recognition, axons in the ventral nerve cord (VNC) of Caenorhabditis elegans require the presence of a specific VNC neuron, PVT, to maintain their correct positioning in the left and right fascicles of the VNC, PVT may exert its stabilizing function by the temporarily tightly controlled secretion of 2-immunogobulin (Ig)- domain proteins encoded by the zig genes. Dedicated axon maintenance mechanisms may be widely used to ensure the preservation of functional coronal circuitries. ------------------- Key: 5065 Medline: 11799246 Authors: Arantes-Oliveira N;Apfeld J;Dillin A;Kenyon C Title: Regulation of life-span by germ-line stem cells in Caenorhabditis elegans. Citation: Science 295: 502-505 2002 Type: ARTICLE Genes: daf-9 daf-12 daf-16 daz-1 fem-3 fog-1 fog-2 fog-3 gld-1 glp-1 him-5 mes-1 unc-50 Abstract: The germ line of the nematode Caenorhabditis elegans influences life-span; when the germ-line precursor cells are removed, life-span is increased dramatically. We find that neither sperm, nor oocytes, nor meiotic precursor cells are responsible for this effect. Rather life-span is influenced by the proliferating germ-line stem cells. These cells, as well as a downstream transcriptional regulator, act in the adult to influence aging, indicating that the aging process remains plastic during adulthood. We propose that the germ-line stem cells affect life-span by influencing the production of, or the response to, a steroid hormone that promotes longevity. ------------------- Key: 5066 Medline: 11784090 Authors: Levitan D;Yu G;Hyslop PSG;Goutte C Title: APH-2/nicastrin functions in LIN-12/Notch signaling in the Caenorhabditis elegans somatic gonad. Citation: Developmental Biology 240: 654-661 2001 Type: ARTICLE Genes: aph-2 glp-1 lin-12 sel-12 Abstract: Nicastrin is a recently identified member of high-molecular weight complexes containing presenilin. The Caenorhabditis elegans homolog of nicastrin, aph-2, was shown to be required for GLP-1/Notch signaling in the early embryo. In addition to the maternal-effect embryonic lethal phenotype, aph-2 mutant animals also display an egg-laying defect. We show that this latter defect is related to the SEL-12/presenilin egg-laying defect. We also show that aph-2 and sel-12 genetically interact and cooperate to regulate LIN-12/Notch signaling in the development of the somatic gonad. In addition, aph-2 and lin-12/Notch genetically interact. We illustrate a new role for aph-2 in facilitating lin-12 signaling in the somatic gonad, thus providing evidence that APH-2 is involved in both GLP-1/Notch- and LIN-12/Notch-mediated signaling events. Finally, we demonstrate that nicastrin can partially substitute for aph-2, suggesting a conservation of function between these proteins. ------------------- Key: 5067 Medline: 11781331 Authors: Grosshans H;Slack FJ Title: Micro-RNAs: small is plentiful. Citation: Journal of Cell Biology 156: 17-21 2002 Type: REVIEW Genes: dcr-1 alg-1 alg-2 let-7 lin-4 lin-14 lin-28 lin-41 Abstract: Two small temporally regulated RNAs (stRNAs)* of similar to22 nucleotides regulate timing of gene expression during development of the nematode C elegans. This regulation occurs at a posttranscriptional, presumably translational, level and is distinct from RNA interference (RNAi). One of the two stRNAs, let-7, as well as its target gene, lin-41, are highly conserved even in humans, suggesting a wide employment of stRNA-mediated gene regulation. Recent reports indicate that these two stRNAs are indeed likely to represent only the tip of an iceberg with hundreds or more of additional micro-RNAs (miRNAs) existing in metazoans. miRNAs might thus be previously underestimated key participants in the field of gene regulation. ------------------- Key: 5068 Medline: 11782551 Authors: Karlin S;Brocchieri L;Bergman A;Mrazek J;Gentles AJ Title: Amino acid runs in eukaryotic proteomes and disease associations. Citation: Proceedings of the National Academy of Sciences USA 99: 333-338 2002 Type: ARTICLE Genes: Abstract: We present a comparative proteome analysis of the five complete eukaryoticgenomes (human, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Arabidopsis thaliana), focusing on individual and multiple amino acid runs, charge and hydrophobic runs. We found that human proteins with multiple long runs are often associated with diseases, these include long glutamine runs that induce neurological disorders, various cancers, categories of leukemias (mostly involving chromosomal translocations), and an abundance of Ca2+ and K+ channel proteins. Many human proteins with multiple runs function in development and/or transcription regulation and are Drosophila homeotic homologs. A large number of these proteins are expressed in the nervous system. More than 80% of Drosophila proteins with multiple runs seem to function in transcription regulation. The most frequent amino acid runs in Drosophila sequences occur for glutamine, alanine, and serine, whereas human sequences highlight glutamate, proline, and leucine. The most frequent runs in yeast are of serine, glutamine, and acidic residues. Compared with the other eukaryotic proteomes, amino acid runs are significantly more abundant in the fly. This finding might be interpreted in terms of innate differences in DNA-replication processes, repair mechanisms, DNA-modification systems, and mutational biases. There are striking differences in amino acid runs for glutamine, asparagine, and leucine among the five ------------------- Key: 5069 Medline: 1149252 Authors: Green DR;Beere HM Title: Apoptosis: Mostly dead. Citation: Nature 412: 133-135 2001 Type: REVIEW Genes: ced-3 ced-4 ced-9 egl-1 Abstract: In all animals, the process of programmed cell suicide (apoptosis) is coordinated by enzymes known as caspases, which cut up key substrates in the cell. The dying cell is then neatly packaged, engulfed by neighbouring "phagocytic" cells, and cleared from the body without fanfare, leaving no evidence of the catastrophic events that preceded. It has always been assumed that there is a "point of no return" in this death cascade - at or shortly before the time at which caspases are activated - beyond which the process of cell execution proceeds inexorably. This view is challenged by Reddien et al. and Hoeppner et al. on pages 198 and 202 of this issue. It seems that cells in which caspases have been activated can in fact progress through a state of being "mostly dead", a stage that physically resembles the early phase of apoptosis but from ------------------- Key: 5070 Medline: 11809943 Authors: Vogel G Title: Genes keep neurons' house in order. Citation: Science 295: 599-601 2002 Type: REVIEW Genes: zig-4 Abstract: As any homeowner knows, timely maintenance is vital for keeping a building functioning properly after construction is finished. The same is evidently true for the complex architecture of the nervous system - at least in the roundworm. On page 686, neuroscientists Oliver Hobert, Oscar Aurelio, and David Hall describe a new family of proteins that help keep the wiring of the worm's nervous system tangle free. ------------------- Key: 5071 Medline: Authors: Hengartner MO Title: Apoptosis: DNA destroyers. Citation: Nature 412: 27-29 2001 Type: REVIEW Genes: ced-3 cps-6 Abstract: The degredation of DNA is one of the hallmarks of programmed cell death (apoptosis). When forced to commit suicide, apoptotic cells - like good secret agents - grimly destroy their "instruction book," chewing up their genomic DNA into tiny morsels. Until now, only two DNA-destroying enzymes (nucleases) with a clear role in cell death were known, one in mammals and one in the nematode worm Caenorhabditis elegans. But, on pages 90-99 of this issue, Li and colleagues and Parrish and co-workers show that another nuclease, endonuclease G (endoG), also contributes to the carnage, and might even influence the likelihood that a cell will live or die. ------------------- Key: 5072 Medline: Authors: de Pomerai DI;Dawe A;Djerbib L;Allan J;Brunt G;Daniells C Title: Growth and maturation of the nematode Caenorhabditis elegans following exposure to weak microwave fields. Citation: Enzyme and Microbial Technology 30: 73-79 2002 Type: ARTICLE Genes: Abstract: Prolonged exposure to weak microwave fields (750-1000 MHz, 0.5 W) at 25degreesC induces a heat-shock response in transgenic C. elegans strains carrying hsp16 reporter genes [1]. A comparable response to heat alone requires a substantially higher temperature of 28degreesC, suggesting that microwave heating of worms or of the system as a whole might provide a sufficient explanation, although this can be ruled out by indirect arguments [1]. Here we investigate two further biological consequences of prolonged microwave exposure at 25degreesC in synchronised cultures of wild-type worm larvae, namely alterations in (i) growth rate (GR) and (ii) the proportion of worms later maturing into egg-bearing adults (MP). Both of these parameters are significantly increased following microwave exposure (GR by 8-11%, and MP by 28-40%), whereas both are significantly decreased (GR by 10% and MP almost abolished) after mild heat treatment at 28degreesC for the same period. It follows that the biological consequences of microwave exposure are opposite to, and therefore incompatible with, those attributable to mild heating. This evidence does not in itself necessitate a non-thermal mechanism, but does eliminate explanations that invoke the bulk heating of tissues by microwaves. This latter, however, remains the sole basis for current regulations governing microwave ------------------- Key: 5073 Medline: 11743719 Authors: Yu H;Larsen PL Title: DAF-16-dependent and independent expression targets of DAF-2 insulin receptor-like pathway in Caenorhabditis elegans include FKBPs. Citation: Journal of Molecular Biology 314: 1017-1028 2001 Type: ARTICLE Genes: col-2 daf-2 daf-16 dao-1 dao-2 dao-3 dao-4 dao-5 dao-6 dao-7 dao-8 dao-9 sod-1 Abstract: The daf-2 insulin-like receptor pathway regulates development and lifespan in Caenorhabditis elegans. Reduced DAF-2 signaling leads to changes in downstream targets via the daf-16 gene, a fork-head transcription factor which is regulated by DAF-2, and results in extended life-span. Here, we describe the first identification of genes whose expression is controlled by the DAF-2 signaling cascade. dao-1, dao-2, dao-3, dao-4, dao-8 and dao-9 are down-regulated daf-2 mutant adults compared to wild-type adults, zwhereas dao-5, dao-6 and dao-7 are up-regulated. The latter genes are negatively regulated by DAF-2 signaling and positively regulated by DAF-16. Positive regulation by DAF-2 on dao-1, dao-4 and dao-8 was mediated by DAF-16, whereas daf-16 mediates only part of DAF-2 signaling for dao-2 and dao-9. Regulation by DAF-2 is most likely DAF-16 independent for dao-3 and hsp-90. RNA levels of dao-5 and dao-6 showed elevated expression in daf-2 adults, as well as being strongly expressed in dauer larvae. In contrast, hsp-90 transcript levels are low in daf-2 mutant adults though they are enriched in dauer larvae, indicating overlapping but not identical mechanisms of efficient life maintenance in stress-resistant dauer larvae and long-lived daf-2 mutant adults. dao-1, dao-8 and dao-9 are homologs of the FK506 binding proteins that interact with the mammalian insulin pathway. dao-3 encodes a putative methylenetetrahydrofolate dehydrogenase. DAO-5 shows 33% identity with human nucleolar phosphoprotein P130. dao-7 is similar to the mammalian ZFP36 protein. Distinct regulatory patterns of dao genes implicate their diverse positions within the signaling network of DAF-2 pathway, and suggest they have unique contributions to development, metabolism and longevity. ------------------- Key: 5074 Medline: Authors: Nurrish SJ Title: An overview of C. elegans trafficking mutants. Citation: Traffic 3: 2-10 2002 Type: REVIEW Genes: aex-3 apm-1 che-14 dgk-1 drp-1 dyb-1 dyn-1 dys-1 eat-16 egl-8 egl-10 egl-30 fer-1 fer-6 goa-1 gpb-2 lin-2 lin-7 lin-10 npc-1 npc-2 odr-4 odr-8 odr-10 pod-1 rab-3 ric-8 ric-19 rpm-1 sad-1 sel-9 snb-1 snt-1 spe-4 spe-5 spe-6 spe-10 spe-15 spe-17 syd-2 syn-3 syn-4 unc-10 unc-11 unc-13 unc-18 unc-26 unc-31 unc-43 unc-64 unc-101 unc-104 Abstract: t is almost 40 years since Sydney Brenner introduced Caenorhabditis elegans as a model genetic system. During that time mutants with defects in intracellular trafficking have been identified in a diverse range of screens for abnormalities. This should, of course, come as no surprise as it is hard to imagine any biological process in which the regulated movement of vesicles within the cells is not critical at some step. Almost all of these genes have mammalian homologs, and yet the role of many of these homologs has not been investigated. Perhaps the protein that regulates your favorite trafficking step has already been identified in C elegans? Here I provide a brief overview of those trafficking mutants identified in C elegans and where you can read more about them. ------------------- Key: 5075 Medline: Authors: Fares H;Grant B Title: Deciphering endocytosis in Caenorhabditis elegans. Citation: Traffic 3: 11-19 2002 Type: REVIEW Genes: ced-1 ced-2 ced-5 ced-6 ced-7 ced-10 ced-12 cup-1 cup-4 cup-5 ndg-4 nrf-4 nrf-5 nrf-6 pod-1 rme-1 rme-2 rme-6 rme-8 snt-1 unc-11 unc-26 Abstract: We discuss in this review recent studies using the worm Caenorhabditis elegans to decipher endocytic trafficking in a multicellular organism. Recent advances, including in vivo assay systems, new genetic screens, comparative functional analysis of conserved proteins, and RNA-mediated interference (RNAi) in C. elegans, are being used to study the functions of known membrane trafficking factors and to identify new ones. The ability to monitor endocytosis in vivo in worms allows one to test current endocytosis models and to demonstrate the physiological significance of factors identified by genetic and biochemical methods. The available human genome sequence facilitates comparative studies where human homologs of new factors identified in C. elegans can be quickly assayed for similar function using traditional cell biological methods in mammalian cell systems. New studies in C. elegans have used a combination of these techniques to reveal novel metazoan-specific trafficking factors required for endocytosis. Many more metazoan-specific trafficking factors and insights into the mechanisms of endocytosis are likely to be uncovered by analysis in C. elegans. ------------------- Key: 5076 Medline: Authors: Siddiqui SS Title: Metazoan motor models: kinesin superfamily in C. elegans. Citation: Traffic 3: 20-28 2002 Type: REVIEW Genes: kap-1 khc-1 klc-1 klc-2 klp-1 klp-2 klp-3 klp-4 klp-5 klp-6 klp-7 klp-8 klp-9 klp-10 klp-11 klp-12 klp-13 klp-14 klp-15 klp-16 klp-17 klp-18 klp-19 klp-20 lin-10 osm-3 unc-104 unc-116 vab-8 zen-4 Abstract: In eukaryotic cells members of the kinesin family mediate intracellular transport by carrying cellular cargo on microtubule tracks. The nematode Caenorhabditis elegans genome encodes 21 members of the kinesin family, which show significant homology to their mammalian orthologs. Based on motor domain sequence homology and placement of the motor domain in the protein, the C. elegans kinesins have been placed in eight distinct groups; members of which participate in embryonic development, protein transport, synaptic membrane vesicles movement and in the axonal growth. Among 21 kinesins, at least 11 play a central role in spindle movement and chromosomal segregation. Understanding the function of C. elegans kinesins and related proteins may help navigate through the intricacies of intracellular traffic in a simple animal. ------------------- Key: 5077 Medline: 11809977 Authors: Tijsterman M;Ketting RF;Okihara KL;Sijen T;Plasterk RHA Title: RNA helicase MUT-14-dependent gene silencing triggered in C. elegans by short antisense RNAs. Citation: Science 295: 694-697 2002 Type: ARTICLE Genes: dcr-1 mut-7 mut-14 pos-1 rde-1 rde-4 unc-22 Abstract: Posttranscriptional gene silencing in Caenorhabditis elegans results from exposure to double-stranded RNA (dsRNA), a phenomenon designated as RNA interference (RNAi), or from co-suppression, in which transgenic DNA leads to silencing of both the transgene and the endogenous gene. Here we show that single-stranded RNA oligomers of antisense polarity can also be potent inducers of gene silencing. As is the case for co-suppression, antisense RNAs act independently of the RNAi genes rde-1 and rde-4 but require the mutator/RNAi gene mut-7 and a putative DEAD box RNA helicase, mut-14. Our data favor the hypothesis that gene silencing is accomplished by RNA primer extension using the mRNA as template, leading to dsRNA that is ------------------- Key: 5078 Medline: 11706003 Authors: Hihi AK;Gao Y;Hekimi S Title: Ubiquinone is necessary for Caenorhabditis elegans development at mitochondrial and non-mitochondrial sites. Citation: Journal of Biological Chemistry 277: 2202-2206 2002 Type: ARTICLE Genes: clk-1 coq-2 daf-2 dpy-4 dpy-9 eat-2 mau-2 Abstract: Ubiquinone (UQ) is a lipid co-factor that is involved in numerous enzymatic processes and is present in most cellular membranes. In particular, UQ is a crucial electron carrier in the mitochondrial respiratory chain. Recently, it was shown that clk-1 mutants of the nematode worm Caenorhabditis elegans do not synthesize UQ(9) but instead accumulate demethoxyubiquinone (DMQ(9)), a biosynthetic precursor of UQ(9) (the subscript refers to the length of the isoprenoid side chain). DMQ(9) is capable of carrying out the function of UQ(9) in the respiratory chain, as demonstrated by the functional competence of mitochondria isolated from clk-1 mutants, and the ability of DMQ(9) to act as a co-factor for respiratory enzymes in vitro. However, despite the presence of functional mitochondria, clk-1 mutant worms fail to complete development when feeding on bacteria that do not produce UQ(8). Here we show that clk-1 mutants cannot grow on bacteria producing only DMQ(8) and that worm coq-3 mutants, which produce neither UQ(9) nor DMQ(9), arrest development even on bacteria producing UQ(8). These results indicate that UQ is required for nematode development at mitochondrial and non-mitochondrial sites and that DMQ cannot functionally replace UQ at those non-mitochondrial sites. ------------------- Key: 5079 Medline: 11784094 Authors: Morton DG;Shakes DC;Nugent S;Dichoso D;Wang W;Golden A;Kemphues KJ Title: The Caenorhabditis elegans par-5 gene encodes a 14-3-3 protein required for cellular asymmetry in the early Citation: Developmental Biology 241: 47-58 2002 Type: ARTICLE Genes: dpy-20 ftt-1 ftt-2 par-1 par-2 par-3 par-5 par-6 pkc-3 unc-22 sDf8 Abstract: The establishment of anterior-posterior polarity in the Caenorhabditis elegans embryo requires the activity of the maternally expressed par genes. We report the identification and analysis of a new par gene, par-5. We show that par-5 is required for asynchrony and asymmetry in the first embryonic cell divisions, normal pseudocleavage, normal cleavage spindle orientation at the two-cell stage, and localization of P granules and MEX-5 during the first and subsequent cell cycles. Furthermore, par-5 activity is required in the first cell cycle for the asymmetric cortical localization of PAR-1 and PAR-2 to the posterior, and PAR-3, PAR-6, and PKC-3 to the anterior. When PAR-5 is reduced by mutation or by RNA interference, these proteins spread around the cortex of the one-cell embryo and partially overlap. We have shown by sequence analysis of par-5 mutants and by RNA interference that the par-5 gene is the same as the ftt-1 gene, and encodes a 14-3-3 protein. The PAR-5 14-3-3 protein is present in,gonads, oocytes, and early embryos, but is not asymmetrically distributed. Our analysis indicates that the par-5 14-3-3 gene plays a crucial role in the early events leading to ------------------- Key: 5080 Medline: 11799068 Authors: Kostas SA;Fire A Title: The T-box factor MLS-1 acts as a molecular switch during specification of nonstriated muscle in C. elegans. Citation: Genes & Development 16: 257-269 2002 Type: ARTICLE Genes: ceh-24 egl-15 hlh-8 mls-1 myo-3 rgs-2 Abstract: We have isolated mutations in a gene mls-1 that is required for proper specification of nonstriated muscle fates in Caenorhabditis elegans. Loss of MLS-1 activity causes uterine muscle precursors to forego their normal fates, instead differentiating as vulval muscles. We have cloned mls-1 and shown that the product is a member of the T-box family of transcriptional regulators. MLS-1 acts as a cell fate determinant in that ectopic expression can transform other cell types to uterine muscle precursors. Uterine muscle patterning is executed by regulation of MLS-1 at several different levels. The mls-1 promoter is activated by the C. elegans orthologs of Twist and Daughterless, but is only active in a subset of the lineage where these two transcription factors are present. mls-1 activity also appears to be regulated by posttranscriptional processes, as expression occurs in both uterine and vulval muscle precursors. ------------------- Key: 5081 Medline: 11805331 Authors: Patel MN;Knight CG;Karageorgi C;Leroi AM Title: Evolution of germ-line signals that regulate growth and aging in nematodes. Citation: Proceedings of the National Academy of Sciences USA 99: 769-774 2002 Type: ARTICLE Genes: daf-16 dbl-1 fer-6 Abstract: We show that a signal from the germ line represses growth in the nematode Caenorhabditis elegans. Laser-microbeam ablation of cells that give rise to the germ line causes adults to become giant. Ablation of these cells in self-sterile mutant worms also causes gigantism, suggesting that the germ line represses growth because it is the source of a growth-antagonizing signal rather than because of a sink of resources required for reproduction. The C. elegans germ line also emits a signal that represses longevity. This longevity-repressing signal requires the activity of DAF-16, a fork-head/winged-helix transcription factor, but we find that that the growth-repressing signal does not. The growth-repressing signal also does not require the activity of DBL-1, a transforming growth factor P-related protein that promotes growth in worms. By ablating the germ-line precursors of other species of free-living nematodes, we also found that both the growth-repressing and longevity-repressing signals are evolutionarily variable. Some species have both signals; others have just one or the other. We suggest that variation in germ-line signaling contributes to body size and life-history diversity in the nematodes. ------------------- Key: 5082 Medline: 11792846 Authors: Goutte C;Tsunozaki M;Hale VA;Priess JR Title: APH-1 is a multipass membrane protein essential for the Notch signaling pathway in Caenorhabditis elegans embryos. Citation: Proceedings of the National Academy of Sciences USA 99: 775-779 2002 Type: ARTICLE Genes: aph-1 aph-2 glp-1 nDf25 Abstract: Early embryonic cells in Caenorhabditis elegans embryos interact through a signaling pathway closely related to the Notch signaling pathway in Drosophila and vertebrates. Components of this pathway include a ligand, receptor, the presenilin proteins, and a novel protein, APH-2, that is related to the Nicastrin protein in humans. Here we identify the aph-1 gene as a new component of the Notch pathway in Caenorhabditis elegans. aph-1 is predicted to encode a novel, highly conserved multipass membrane protein. We show that aph-1 and the presenilin genes share a similar function in that they are both required for proper cell-surface localization of APH-2/Nicastrin. ------------------- Key: 5083 Medline: 11835581 Authors: Shim YH;Chun JH;Lee EY;Paik YK Title: Role of cholesterol in germ-line development of Caenorhabditis elegans. Citation: Molecular Reproduction and Development 61: 358-366 2002 Type: ARTICLE Genes: fem-2 Abstract: We investigated the effects of cholesterol starvation on Caenorhabditis elegans development at both embryonic and post-embryonic stages by examining brood size, embryonic lethality, growth rate, and worm size. The brood sizes of worms grown without cholesterol were substantially reduced in subsequent generations as compared to the control group with cholesterol: 13, 33, and 39% at the first, the second, and the third generation, respectively. The growth rate was also reduced by 20%-26%. Worms became adults after 120-130 hr incubation at 20degreesC. Embryonic lethality was detected in the range of 1.6%-2.9% as compared to 0.8% of the control group. The percent development from an embryo to an adult was lowered by an average of 10%. Further analyses of germ line development to understand the reduction of brood size revealed that both germ line proliferation and differentiation were affected, and the most striking effect was seen in oogenesis. Defective oogenesis resulted in endomitotic oocytes (Emo, 22% at F1, 26% at F2, and 30% at F3). Thus, cholesterol appears to be required for all developmental stages of C. elegans. ------------------- Key: 5084 Medline: Authors: Stothard P;Hansen D;Pilgrim D Title: Evolution of the PP2C family in Caenorhabditis: rapid divergence of the sex-determining protein FEM-2. Citation: Journal of Molecular Evolution 54: 267-282 2002 Type: ARTICLE Genes: fem-2 Abstract: To investigate the causes and functional significance of rapid sex-determining protein evolution we compared three Caenorhabditis elegans genes encoding members of the protein phosphatase 2C (PP2C) family with their orthologs from another Caenorhabditis species (strain CB5161). One of the genes encodes FEM-2, a sex-determining protein, while the others have no known sex-determining role. FEM-2's PP2C domain was found to be more diverged than the other PP2C domains, supporting the notion that sex-determining proteins are subjected to selective pressures that allow for or cause rapid divergence. Comparison of the positions of amino acid substitutions in FEM-2 with a solved three-dimensional structure suggests that the catalytic face of the protein is highly conserved among C. elegans, CB5161, and another closely related species C. briggsae. However, the non-conserved regions of FEM-2 cannot be said to lack functional importance, since fem-2 transgenes from the other species were unable to rescue the germ-line defect caused by a C. elegans fem-2 mutation. To test whether fem-2 functions as a sex-determining gene in the other Caenorhabditis species we used RNA-mediated interference (RNAi). fem-2 (RNAi) in C elegans and C. briggsae caused germ-line feminization, but had no noticeable effect in CB5161. Thus the function of fem-2 in ------------------- Key: 5085 Medline: 11782412 Authors: Kodama Y;Rothman JR;Sugimoto A;Yamamoto M Title: The stem-loop binding protein CDL-1 is required for chromosome condensation, progression of cell death and morphogenesis in Caenorhabditis elegans. Citation: Development 129: 187-196 2002 Type: ARTICLE Genes: cdl-1 ced-1 ced-3 ced-4 ced-5 ced-9 mnDf83 mnDf87 mnDf89 mnDf90 Abstract: Histones play important roles not only in the structural changes of chromatin but also in regulating gene expression. Expression of histones is partly regulated post-transcriptionally by the stem-loop binding protein (SLBP)/hairpin binding protein (HBP). We report the developmental function of CDL-1, the C elegans homologue of SLBP/HBP. In the C. elegans cdl-1 mutants, cell corpses resulting from programmed cell death appear later and persist much longer than those in the wild type. They also exhibit distinct morphological defects in body elongation and movement of the pharyngeal cells toward the buccal opening. The CDL-1 protein binds to the stem-loop structures in the 3'-UTR of C. elegans core histone mRNAs, and the mutant forms of this protein show reduced binding activities. A decrease in the amount of core histone proteins phenocopied the cdl-1 mutant embryos, suggesting that CDL-1 contributes to the proper expression of core histone proteins. We propose that loss-of-function of cdl-1 causes aberrant chromatin structure, which affects the cell cycle and cell death, as well as transcription of genes essential for morphogenesis. ------------------- Key: 5086 Medline: 11782415 Authors: Jia K;Albert PS;Riddle DL Title: DAF-9, a cytochrome P450 regulating C. elegans larval development and adult longevity. Citation: Development 129: 221-231 2002 Type: ARTICLE Genes: age-1 daf-2 daf-3 daf-7 daf-9 daf-12 daf-16 Abstract: The daf-9 gene functions to integrate transforming growth factor-beta and insulin-like signaling pathways to regulate Caenorhabditis elegans larval development. Mutations in daf-9 result in transient dauer-like larval arrest, abnormal reproductive development, molting defects and increased adult longevity. The phenotype is sterol-dependent, and dependent on the activity of DAF-12, a nuclear hormone receptor. Genetic tests show that daf-9 is upstream of daf-12 in the genetic pathways for larval development and adult longevity. daf-9 encodes a cytochrome P450 related to those involved in biosynthesis of steroid hormones in mammals. We propose that it specifies a step in the biosynthetic pathway for a DAF-12 ligand, which might be a steroid. The surprising cellular specificity of daf-9 expression (predominantly in two sensory neurons) supports a previously unrecognized role for these cells in neuroendocrine control of larval development, reproduction and life span. ------------------- Key: 5087 Medline: 11818075 Authors: Saigusa T;Ishizaki S;Watabiki S;Ishii N;Tanakadate A;Tamai Y;Hasegawa K Title: Circadian behavioural rhythm in Caenorhabditis elegans. Citation: Current Biology 12: R46-R47 2002 Type: ARTICLE Genes: lin-42 Abstract: Transcriptional/translational feedback loops between clock genes such as per and tim - first cloned in Drosophila - and their protein products are thought to constitute the core of the circadian clock. A representative of the early metazoan body plan, the nematode (roundworm) Caenorhabditis elegans has had its complete cell lineage traced and it is known that it has many molecular components in common with those of the vertebrates. Recent studies have shown that C. elegans carries a per hmologue, lin-42, and that its mRNA levels oscillate synchronously with approximately 6 hr molting cycles at the postembyronic developmental stage. ------------------- Key: 5088 Medline: 11818076 Authors: Kippert F;Saunders DS;Blaxter ML Title: Caenorhabditis elegans has a circadian clock. Citation: Current Biology 12: R47-R49 2002 Type: REVIEW Genes: Circadian clocks, biological timing mechanisms that serve to synchronize organismal behavior and physiology with the day/night cycle, have been found in most eukaryotic organisms where they have been sought. Loci which when mutated disrupt clock function have been identified and the molecular dissection of circadian clocks has provided valuable insights into the underlying mechanisms of this universal biological phenomenon. Abstract: ------------------- Key: 5089 Medline: 11779177 Authors: Seiffert SM;Vier J;Hacker G Title: Subcellular localization, oligomerization, and ATP-binding of Caenorhabditis elegans CED-4. Citation: Biochemical and Biophysical Research Communications 290: 359-365 2002 Type: ARTICLE Genes: ced-3 ced-4 Abstract: Caspase family cell death proteases are activated during apoptosis through the oligomerization of caspase-binding "adapter" proteins. In the nematode Caenorhabditis elegans one adapter protein, CED-4, exists. Here we report an analysis of CED-4 protein expressed in insect Sf9 cells by infection with recombinant baculovirus. During expression, CED-4 assumed a perinuclear spherical or reticular localization where it was partly resistant to extraction with nonionic detergents. Both purified FLAG-CED-4 and GST-FLAG-CED-4 proteins were present in solution as large complexes. FLAG-CED-4 complexes were estimated by gel filtration to have a molecular weight of approximately 500 kDa to > 1.2 MDa, while GST-FLAG-CED-4 complexes appeared somewhat smaller. Unlike its mammalian homologue Apaf-1, CED-4 exhibited a marked preference for ATP over dATP in filter binding studies and in competition experiments. ATP hydrolysis was required neither for complex stability nor for binding of CED-3. These features are likely to be relevant for CED-4's function as a caspase adapter. ------------------- Key: 5090 Medline: 11809970 Authors: Barral JM;Hutagalung AH;Brinker A;Hartl FU;Epstein HF Title: Role of the myosin assembly protein UNC-45 as a molecular chaperone for myosin. Citation: Science 295: 669-671 2002 Type: ARTICLE Genes: unc-45 Abstract: The organization of myosin into motile cellular structures requires precise temporal and spatial regulation. Proteins containing a UCS (UNC-45/CRO1/She4p) domain are necessary for the incorporation of myosin into the contractite ring during cytokinesis and into thick filaments during muscle development. We report that the carboxyl-terminal regions of UNC-45 bound and exerted chaperone activity on the myosin head. The amino-terminal tetratricopeptide repeat domain of UNC-45 bound the molecular chaperone Hsp90. Thus, UNC-45 functions both as a molecular chaperone and as an Hsp90 co-chaperone for myosin, which can explain previous findings of altered assembly and decreased accumulation of myosin in UNC-45 mutants of Caenorhabditis elegans. ------------------- Key: 5091 Medline: 11804562 Authors: Nonet ML Title: AEXpulsing a retrograde signal. Citation: Neuron 33: 155-156 2002 Type: REVIEW Genes: aex-1 eax-5 unc-13 Abstract: A variety of secreted components have been identified as retrograde signals mediating diverse aspects of synaptic development, maintenance, and plasticity; however, little is known about the mechanisms mediating the release of secreted retrograde signals. Doi and Iwasaki (this issue of Neuron) implicate AEX-1, a protein distantly related to the UNC-13/Munc13 family, as an attractive candidate regulator of the retrograde release machinery in muscle. ------------------- Key: 5092 Medline: 11804572 Authors: Doi M;Iwasaki K Title: Regulation of retrograde signaling at neuromuscular junctions by the novel C2 domain protein AEX-1. Citation: Neuron 33: 249-259 2002 Type: ARTICLE Genes: aex-1 aex-5 dgk-1 egl-8 egl-30 gld-1 goa-1 lev-1 lin-15 lrp-1 snb-1 unc-13 unc-29 unc-49 tgDf1 Abstract: Retrograde signaling from postsynaptic cells to presynaptic neurons Is essential for regulation of synaptic development, maintenance, and plasticity. Here we report that the novel protein AEX-1 controls retrograde signaling at neuromuscular junctions in C. elegans. aex-1 mutants show neural defects including reduced presynaptic activity and abnormal localization of the synaptic vesicle fusion protein UNC-13. Muscle-specific AEX-1 expression rescues these defects but neuron-specific expression does not. AEX-1 has an UNC-13 homologous domain and appears to regulate exocytosis in muscles. This retrograde signaling requires prohormone-convertase function in muscles, suggesting that a peptide is the retrograde signal. This signal regulates synaptic vesicle release via the EGL-30 Gqalpha protein at presynaptic terminals. ------------------- Key: 5093 Medline: Authors: McPartland JM;Glass M Title: Nematicidal effects of hemp (Cannabis sativa) may not be mediated by cannabinoid receptors. Citation: New Zealand Journal of Crop & Horticultural Science 29: 301-307 2001 Type: ARTICLE Genes: Abstract: Few nematodes infest the roots of hemp (Cannabis sativa L.) plants, and hemp plant extracts have been utilised as botanical nematicides. The responsible constituent may be Delta(9)-tetrahydrocannabinol (Delta(9)-THC). In humans, Delta(9)-THC exerts its effects via a family of G protein-coupled receptors, known as cannabinoid (CB) receptors. CB receptors are phylogenetically ancient, and occur in many vertebrates and invertebrates. We therefore searched for evidence of CB receptors in nematodes. All nematode cDNA sequences at GenBank, including the entire genome of Caenorhabditis elegans, were screened for homologs of human CB receptors using BLAST 2.0 as a sequence alignment search engine. We also searched for homologs of fatty acid amide hydrolase (FAAH), the enzyme in vertebrates that metabolises the endogenous ligands of CB receptors. Several C. elegans gene products with low homology to CB receptors and FAAH were identified. Close examination of these sequences revealed crippling substitutions at critical amino acid residues. These results suggest the genes for CB receptors are absent in C. elegans, and the nematicidal activities of Delta(9)-THC and Cannabis are not mediated through CB receptors. ------------------- Key: 5094 Medline: 11820809 Authors: Streit A;Kohler R;Marty T;Belfiore M;Takacs-Vellai K;Vigano MA;Schnabel R;Affolter M;Mueller F Title: Conserved regulation of the Caenorhabditis elegans labial/Hox1 gene ceh-13. Citation: Developmental Biology 242: 96-108 2002 Type: ARTICLE Genes: ceh-13 ceh-20 pop-1 Abstract: Caenorhabditis elegans contains a set of six cluster-type homeobox (Hox) genes that are required during larval development. Some of them, but unlike in flies not all of them, are also required during embryogenesis. It has been suggested that the control of the embryonic expression of the worm Hox genes might differ from that of other species by being regulated in a lineal rather than a regional mode. Here, we present a trans-species analysis of the cis-regulatory region of ceh-13, the worm ortholog of the Drosophila labial and the vertebrate Hox1 genes, and find that the molecular mechanisms that regulate its expression may be similar to what has been found in species that follow a regulative, non-cell-autonomous mode of development. We have identified two enhancer fragments that are involved in different aspects of the embryonic ceh-13 expression pattern. We show that important features of comma-stage expression depend on an autoregulatory input that requires ceh-13 and ceh-20 functions. Our data show that the molecular nature of Hox1 class gene autoregulation has been conserved between worms, flies, and vertebrates. The second regulatory sequence is sufficient to drive correct early embryonic expression of ceh-13. Interestingly, this enhancer fragment acts as a response element of the Wnt/WG signaling pathway in Drosophila ------------------- Key: 5095 Medline: 11832245 Authors: Rappleye CA;Tagawa A;Lyczak R;Bowerman B;Aroian RV Title: The anaphase-promoting complex and separin are required for embryonic anterior-posterior axis formation. Citation: Developmental Cell 2: 195-206 2002 Type: ARTICLE Genes: emb-27 emb-30 mat-1 mat-2 mat-3 par-2 par-3 pie-1 pod-3 pod-4 pod-5 pod-6 ubq-2 mnDf69 Abstract: Polarization of the one-cell C. elegans embryo establishes the animal's anterior-posterior (a-p) axis. We have identified reduction-of-function anaphase-promoting complex (APC) mutations that eliminate a-p polarity. We also demonstrate that the APC activator cdc20 is required for polarity. The APC excludes PAR-3 from the posterior cortex, allowing PAR-2 to accumulate there. The APC is also required for tight cortical association and posterior movement of the paternal pronucleus and its associated centrosome. Depletion of the protease separin, a downstream target of the APC, causes similar pronuclear and a-p polarity defects. We propose that the APC/separin pathway promotes close association of the centrosome with the cortex, which in turn excludes PAR-3 from the posterior pole early in a-p axis formation. ------------------- Key: 5096 Medline: Authors: Davis ES;Wille L;Chestnut BA;Sadler PL;Shakes DC;Golden A Title: Multiple subunits of the Caenorhabditis elegans anaphase-promoting complex are required for chromosome segregation during meiosis I. Citation: Genetics 160: 805-813 2002 Type: ARTICLE Genes: apc-1 apc-2 apc-4 apc-5 apc-10 apc-11 cdc-16 cdc-23 cdc-27 emb-27 emb-30 evl-22 mat-1 mat-2 mat-3 rec-8 Abstract: Two genes, originally identified in genetic screens for Caenorhabditis elegans mutants that arrest in metaphase of meiosis 1, prove to encode subunits of the anaphase-promoting complex or cyclosome (APC/C). RNA interference studies reveal that these and other APC/C subunits are essential for the segregation of chromosomal homologs during meiosis I. Further, chromosome segregation during meiosis I requires APC/C functions in addition to the release of sister chromatid cohesion. ------------------- Key: 5097 Medline: 11814642 Authors: Suo S;Sasagawa N;Ishiura S Title: Identification of a dopamine receptor from Caenorhabditis elegans. Citation: Neuroscience Letters 319: 13-16 2002 Type: ARTICLE Genes: Abstract: The neurotransmitter dopamine regulates locomotion and egg laying in the nematode Caenorhabditis elegans. We have cloned a cDNA encoding the C. elegans G protein-coupled receptor (CeDOP1). The deduced amino acid sequence of the cloned cDNA shows high sequence similarities with D1-like dopamine receptors from other species. Three splice variants that differ in the length of the predicted third intracellular loop and C-terminal tail were identified. COS-7 cells transiently transfected with CeDOP1 showed high affinity binding to [1251] iodo-lysergic acid diethylamide (K-D = 3.43 +/- 0.83 nM). Dopamine showed the highest affinity (K-i = 0.186 muM) for this receptor among several vertebrate and invertebrate amine neurotransmitters tested, suggesting that the natural ligand for this receptor is dopamine. ------------------- Key: 5098 Medline: 11832225 Authors: Lanjuin A;Sengupta P Title: Regulation of chemosensory receptor expression and sensory signaling by the KIN-29 Ser/Thr kinase. Citation: Neuron 33: 369-381 2002 Type: ARTICLE Genes: daf-5 daf-16 egl-4 kin-29 lim-4 odr-1 odr-4 odr-10 osm-6 sma-11 sns-8 sra-6 sra-9 sre-1 srg-8 srg-13 sro-1 str-1 str-2 str-3 str-219 str-220 tax-4 tph-1 unc-3 unc-14 unc-31 mgDf50 Abstract: Sensory signals regulate multiple developmental and behavioral circuits in C. elegans, providing a genetically tractable system in which to investigate the mechanisms underlying the acquisition and integration of sensory information. kin-29 mutants are defective in the expression of a set of chemoreceptor genes, and exhibit characteristics associated with altered sensory signaling, including increased lifespan, decreased body size, and deregulated entry into the dauer developmental stage. kin-29 encodes a Ser/Thr kinase with similarity to the MARK and AMPK/SNF1 family of kinases. We show that KIN-29 acts cell-autonomously and non-cell-autonomously in sensory neurons to regulate chemoreceptor expression, body size, and the dauer decision, suggesting that kin-29 function is essential for the correct acquisition and transduction of sensory information. ------------------- Key: 5099 Medline: 11707440 Authors: Hashmi S;Britton C;Liu J;Guiliano DB;Oksov Y;Lustigman S Title: Cathepsin L is essential for embryogenesis and development of Caenorhabditis elegans. Citation: Journal of Biological Chemistry 277: 3477-3486 2002 Type: ARTICLE Genes: cpl-1 Abstract: Cysteine proteases play critical biological roles in both intracellular and extracellular processes. We characterized Ce-cpl-1, a Caenorhabditis elegans cathepsin L-like cysteine protease. RNA interference with Ce-cpl-1 activity resulted in embryonic lethality and a transient delayed growth of larvae to egg producing adults, suggesting an essential role for cpl-1 during embryogenesis, and most likely during post-embryonic development. Cpl-1 gene (Ce-cpl-1:lacZ) is widely expressed in the intestine and hypodermal cells of transgenic worms, while the fusion protein (Ce-CPL-1::GFP) was expressed in the hypodermis, pharynx, and gonad. The CPL-1 native protein accumulates in early to late stage embryos and becomes highly concentrated in gut cells during late embryonic development. CPL-1 is also present near the periphery of the eggshell as well as in the cuticle of larval stages suggesting that it may function not only in embryogenesis but also in further development of the worm. Although the precise role of Ce-CPL-1 during embryogenesis is not yet clear it could be involved in the processing of nutrients responsible for synthesis and/or in the degradation of eggshell. Moreover, an increase in the cpl-1 mRNA is seen in the intermolt period approximately 4 h prior to each molt. During this process Ce-CPL-1 may act as a proteolytic enzyme in the processing/degradation of cuticular or other proteins. Similar localization of a related cathepsin L in the filarial nematode Onchocerca volvulus, eggshell and cuticle, suggests that some of the Ce-CPL-1 function during development may be conserved in other parasitic nematodes. ------------------- Key: 5100 Medline: 11856370 Authors: Kim YC;Lee MH;Ryu SS;Kim JH;Koo HS Title: Coaction of DNA topoisomerase III alpha and a RecQ homologue during the germ-line mitosis in Caenorhabditis Citation: Genes to Cells 7: 19-27 2002 Type: ARTICLE Genes: ced-3 him-6 Abstract: Background: Among the four RecQ homologues predicted from the Caenorhabditis elegans genomic DNA sequence, T04A11.6 is most similar to Bloom syndrome's protein in humans. To investigate a possible interaction of the protein with topoisomerase IIIalpha (TOP3alpha), as observed between TOP3 and RecQ homologues in yeast and human, the top3alpha gene expression was suppressed by RNA interference (RNAi) in the him-6(e1104) C. elegans strain which is mutated in T04A11.6 (F Mueller & C. Wicky, personal communication). Results: Germ cells in the gonads of the progeny him-6(e1104);top3alpha(RNAi) showed severe chromosomal abnormalities and were arrested during mitosis with a subsequent failure in meiotic entry. Most of the aberrant chromosomes were stained by the TUNEL assay but not by the SYTO12 dye, suggesting extensive DNA breaks not associated with apoptosis. The phenotypes in the germ cells of him-6(e1104);top3alpha(RNAi) were also observed in the progeny produced by double RNA interference of the top3alpha and him-6 gene expression, though at a reduced level. The over-expressed TOP3alpha and Him-6 proteins showed specific physical interaction in vitro, in agreement with the genetic interaction in C. elegans. Conclusion: In C. elegans, TOP3alpha and the RecQ homologue (T04A11.6) contribute to genome stability during germ-line mitosis, probably by acting in a complex. ------------------- Key: 5101 Medline: 11751575 Authors: Victor M;Bei Y;Gay F;Calvo D;Mello C;Shi Y Title: HAT activity is essential for CBP-1-dependent transcription and differentiation in Caenorhabditis elegans. Citation: EMBO Reports 3: 50-55 2002 Type: ARTICLE Genes: cbp-1 elt-2 hlh-1 hlh-2 Abstract: The p300/CBP family of transcriptional coactivators possesses multiple functional domains, including a histone acetyltransferase (HAT) and several activation domains. A number of models have been proposed to account for their roles in transcriptional activation, including interactions with basal transcription machinery and chromatin remodeling. However, individual contributions of these domains to transcriptional activation and their significance in living organisms remain unclear. We addressed the importance of the HAT activity of CPB-1, the worm ortholog of p300/CBP, in Caenorhabditis elegans with three different and complementary approaches. These include allele-specific RNA-mediated interference (RNAi), genetic rescue and the use of a specific chemical inhibitor of the p300/CBP HAT. Our findings demonstrate that HAT activity is of primary importance for CBP-1 to regulate transcription and to promote differentiation during C. elegans ------------------- Key: 5102 Medline: 11751572 Authors: Tanaka-Hino M;Sagasti A;Hisamoto N;Kawasaki M;Nakano S;Ninomiya-Tsuji J;Bargmann CI;Matsumoto K Title: SEK-1 MAPKK mediates Ca2+ signaling to determine neuronal asymmetric development in Caenorhabditis elegans. Citation: EMBO Reports 3: 56-62 2002 Type: ARTICLE Genes: nsy-1 odr-3 sek-1 str-2 unc-2 unc-36 unc-43 Abstract: The mitogen-activated protein kinase (MAPK) pathway is a highly conserved signaling cascade that converts extracellular signals into various outputs. In Caenorhabditis elegans, asymmetric expression of the candidate odorant receptor STR-2 in either the left or the right of two bilaterally symmetrical olfactory AWC neurons is regulated by axon contact and Ca2+ signaling. We show that the MAPK kinase (MAPKK) SEK-1 is required for asymmetric expression in AWC neurons. Genetic and biochemical analyses reveal that SEK-1 functions in a pathway downstream of UNC-43 and NSY-1, Ca2+/calmodulin-dependent protein kinase II (CaMKII) and MAPK kinase kinase (MAPKKK), respectively. Thus, the NSY-1-SEK-1-MAPK cascade is activated by Ca2+ signaling through CaMKII and establishes asymmetric cell fate decision during neuronal development. ------------------- Key: 5103 Medline: 11784109 Authors: Hanna-Rose W;Han M Title: The Caenorhabditis elegans EGL-26 protein mediates vulval cell morphogenesis. Citation: Developmental Biology 241: 247-258 2002 Type: ARTICLE Genes: egl-26 jam-1 nDf3 Abstract: In screens for Caenorhabditis elegans mutants defective in vulval morphogenesis, we isolated multiple mutants in which the uterus and the vulva fail to make a functional connection, resulting in an egg-laying defective phenotype. Two of these connection of gonad defective (Cog) mutants carry alleles of the egl-26 gene. We demonstrate that vulval lineages in egl-26 mutant animals are normal, but one vulval cell, vu1F, adopts an abnormal morphology. This results in formation of an abnormally thick layer of vulval tissue at the apex of the vulva and a physical blockage of the exit to the vulva from the uterus. egl-26 was cloned and is predicted to encode a novel protein. Mosaic analysis indicates that egl-26 activity is required in the primary vulval lineage for vu1F morphogenesis. Expression of a functional translational fusion of EGL-26 to GFP was observed within the primary vulval lineage only in vulE, which neighbors vu1F. EGL-26 is localized at the apical edge of the vu1E cell. It is thus possible that vu1E acts to instruct morphological changes in the neighboring cell, vu1F, in an interaction mediated by EGL-26. ------------------- Key: 5104 Medline: 11784116 Authors: Kishore RS;Sundaram MV Title: ced-10 Rac and mig-2 function redundantly and act with unc-73 Trio to control the orientation of vulval cell divisions and migrations in Caenorhabditis elegans. Citation: Developmental Biology 241: 339-348 2002 Type: ARTICLE Genes: ced-10 lin-31 mig-2 unc-73 Abstract: Vulval development in the nematode Caenorhabiditis elegans can be divided into a fate specification phase controlled in part by let-60 Ras, and a fate execution phase involving stereotypical patterns of cell division and migration controlled in part by lin-17 Frizzled. Since the small GTPase Rac has been implicated as a downstream target of both Ras and Frizzled and influences cytoskeletal dynamics, we investigated the role of Rac signaling during each phase of vulval development. We show that the Rac gene ced-10 and the Rac-related gene mig-2 are redundantly required for the proper orientation of certain vulval cell divisions, suggesting a role in spindle positioning. red-10 Rae and mig-2 are also redundantly required for vulval cell migrations and play a minor role in vulval fate specification. Constitutively active and dominant-negative mutant forms of mig-2 cause vulval defects that are very similar to those seen in red-10;mig-2 double loss-of-function mutants, indicating that they interfere with the functions of both red-10 Rae and mig-2. Mutations in unc-73 (a Trio-like guanine nucleotide exchange factor) cause similar vulval defects, suggesting that UNC-73 is an exchange factor for both CED-10 and MIG-2. We discuss the similarities and differences between the cellular defects seen in Rae mutants and let-60 Ras or lin-17 Frizzled mutants. ------------------- Key: 5105 Medline: Authors: Banerjee D;Slack F Title: Control of developmental timing by small temporal RNAs: a paradigm for RNA-mediated regulation of gene expression. Citation: BioEssays 24: 119-129 2002 Type: REVIEW Genes: alg-1 alg-2 daf-12 dcr-1 let-7 lin-4 lin-14 lin-28 lin-29 lin-41 lin-42 Abstract: Heterochronic genes control the timing of developmental programs. In C. elegans, two key genes in the heterochronic pathway, lin-4 and let-7, encode small temporally expressed RNAs (stRNAs) that are not translated into protein. These stRNAs exert negative post-transcriptional regulation by binding to complementary sequences in the 3' untranslated regions of their target genes. stRNAs are transcribed as longer precursor RNAs that are processed by the RNase Dicer/DCR-1 and members of the RDE-1/AGO1 family of proteins, which are better known for their roles in RNA interference (RNAi). However, stRNA function appears unrelated to RNAi. Both sequence and temporal regulation of let-7 stRNA is conserved in other animal species suggesting that this is an evolutionarily ancient gene. Indeed, C. elegans, Drosophila and humans encode at least 86 other RNAs with similar structural features to lin-4 and let-7 We postulate that other small non-coding RNAs may function as stRNAs to control temporal identity during development in C. elegans and other organisms. ------------------- Key: 5106 Medline: Authors: Kohra S;Kuwahara K;Takao Y;Ishibashi Y;Lee HC;Arizono K;Tominaga N Title: Effect of bisphenol-A on the feeding behavior of Caenorhabditis elegans. Citation: Journal of Health Science 48: 93-95 2002 Type: ARTICLE Genes: Abstract: ------------------- Key: 5107 Medline: 11830642 Authors: Degtyareva NP;Greenwell P;Hofmann ER;Hengartner MO;Zhang L;Culotti JG;Petes TD Title: Caenorhabditis elegans DNA mismatch repair gene msh-2 is required for microsatellite stability and maintenance of genome integrity. Citation: Proceedings of the National Academy of Sciences USA 99: 2158-2163 2002 Type: ARTICLE Genes: msh-2 unc-58 Abstract: Mismatch repair genes are important in maintaining the fidelity of DNA replication. To determine the function of the Caenorhabditis elegans homologue of the MSH2 mismatch repair gene (msh-2), we isolated a strain of C elegans with an insertion of the transposable element Tc1 within msh-2. Early-passage msh-2 mutants were similar to wild-type worms with regard to lifespan and meiotic chromosome segregation but had slightly reduced fertility. The mutant worms had reduced DNA damage-induced germ-line apoptosis after genotoxic stress. The msh-2 mutants also had elevated levels of microsatellite instability and increased rates of reversion of the dominant unc-58(e665) mutation. In addition, serially passaged cultures of msh-2 worms died out much more quickly than those of wild-type worms. These results demonstrate that msh-2 function in C elegans is important in regulating both short- and long-term genomic stability. ------------------- Key: 5108 Medline: 11847342 Authors: Kurz T;Pintard L;Willis JH;Hamill DR;Gonczy P;Peter M;Bowerman B Title: Cytoskeletal regulation by the Nedd8 ubiquitin-like protein modification pathway. Citation: Science 295: 1294-1298 2002 Type: ARTICLE Genes: air-2 cyk-1 cul-2 cul-3 mei-1 mei-2 mlc-4 ned-8 rfl-1 ubc-12 ula-1 zen-4 Abstract: The Nedd8 ubiquitin-like protein modification pathway regulates cell-cycle progression. Our analysis of Nedd8 requirements during Caenorhabditis elegans embryogenesis indicates that the cytoskeleton is another target. Nedd8 conjugation negatively regulated contractility of the microfilament-rich cell cortex during pronuclear migration and again during cytokinesis. The Nedd8 pathway also was required after meiosis to negatively regulate katanin, a microtubule-severing complex, permitting the assembly of a large mitotic spindle. We propose that Nedd8-modified cullin, as part of an E3 ubiquitin ligase complex, targets katanin for degradation during the transition from meiosis to mitosis. ------------------- Key: 5109 Medline: 11818544 Authors: Simon JM;Sternberg PW Title: Evidence of a mate-finding cue in the hermaphrodite nematode Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 99: 1598-1603 2002 Type: ARTICLE Genes: him-5 him-8 lov-1 osm-5 osm-6 pkd-2 Abstract: When males of the roundworm Caenorhabditis elegans come into association with their hermaphroditic counterparts they cease foraging behavior and begin to mate. Here we detail several assays used to demonstrate that a diffusible cue is correlated with this process. This cue is sexually dimorphic, given off only by the hermaphrodite and eliciting a response only in the male. Males are attracted to, reverse direction of movement frequently, and remain in regions of agar conditioned with hermaphrodites. From our studies we suggest a form of kinesis that works by attracting males to their mating partners from a distance and functions, once males arrive, in holding attracted males in close proximity. The hermaphrodite vulva is not required for the cue. Males from general sensory mutants osm-5 and osm-6 fail to respond to the cue, whereas male-specific mutants lov-1 and pkd-2 respond. Finally, that males from multiple isolates of C elegans also respond similarly to this cue indicates that this cue is robust and has been maintained during recent evolution. ------------------- Key: 5110 Medline: 11821530 Authors: Strange K Title: Of mice and worms: novel insights into ClC-2 anion channel physiology. Citation: News in Physiological Sciences 17: 11-16 2002 Type: REVIEW Genes: clh-1 clh-2 clh-3 clh-4 clh-5 clh-6 Abstract: CIC anion channels are found in all major groups of organisms. Recent studies in nematodes and mice suggest that the function and regulation of CIC-2 have been conserved over vast evolutionary time spans. These studies illustrate the experimental advantages of using genomically defined non-mammalian model organisms for characterizing CIC channel functional genomics. ------------------- Key: 5111 Medline: 11835058 Authors: Wodarz A Title: Establishing cell polarity in development. Citation: Nature Cell Biology 4: E39-E44 2002 Type: REVIEW Genes: jam-1 mlc-4 ncc-1 nmy-2 ooc-3 ooc-5 par-1 par-2 par-3 par-6 pie-1 pkc-3 pod-1 pod-2 spd-2 Abstract: Polarity is a common feature of many different cell types, including the Caenorhabditis elegans zygote, the Drosophila oocyte and mammalian epithelial cells. The initial establishment of cell polarity: depends on asymmetric cues that lead to reorganization of the cytoskeleton and polarized localization of several cortical proteins that act downstream of the polarization cues. The past year revealed that homologs of the C. elegans par (partitioning defective) genes are also essential for establishing polarity in Drosophila and vertebrate cells. There is growing evidence that the proteins encoded by these genes interact with key regulators of both the actin and the microtubule cytoskeletons. ------------------- Key: 5112 Medline: Authors: Kurz CL;Pujol N Title: C. elegans: huge mountains of data. Citation: M S-Medecine Sciences 18: 97-99 2002 Type: REVIEW Genes: Abstract: ------------------- Key: 5113 Medline: 11706026 Authors: Furst J;Ritter M;Rudzki J;Danzl J;Gschwentner M;Scandella E;Jakab M;Konig M;Oehl B;Lang F;Deetjen P;Paulmichl M Title: ICln ion channel splice variants in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 277: 4435-4445 2002 Type: ARTICLE Genes: Abstract: ICln is an ion channel identified by expression cloning using a cDNA library from Madin-Darby canine kidney cells. In all organisms tested so far, only one transcript for the ICln protein could be identified. Here we show that two splice variants of the ICln ion channel can be found in Caenorhabditis elegans. Moreover,, we show that these two splice variants of the ICln channel protein, which we termed IClnN1 and IClnN2, can be functionally reconstituted and tested in an artificial lipid bilayer. In these experiments, the IClnN1-induced currents showed no voltage-dependent inactivation, whereas the IClnN2-induced currents fully inactivated at positive potentials. The molecular entity responsible for the voltage-dependent inactivation of IClnN2 is a cluster of positively charged amino acids encoded by exon 2a, which is absent in IClnN1. Our experiments suggest a mechanism of channel inactivation that is similar to the "ball and chain" model proposed for the Shaker potassium channel, i.e. a cluster of positively charged amino acids hinders ion permeation through the channel by a molecular and voltage-dependent interaction at the inner vestibulum of the pore. This hypothesis is supported by the finding that synthetic peptides with the same amino acid sequence as the positive cluster can transform the IClnN1-induced current to the current observed after reconstitution of IClnN2. Furthermore, we show that the nematode ICln gene is embedded in an operon harboring two additional genes, which we termed Nx and Ny. Co-reconstitution of Nx and IClnN2 and functional analysis of the related currents revealed a functional interaction between the two proteins, as evidenced by the fact that the IClnN2-induced current in the presence of Nx was no longer voltage-sensitive. The experiments described indicate that the genome organization in nematodes allows an effective approach for the identification of functional partner ------------------- Key: 5114 Medline: 11814685 Authors: Tu Z;Shao H Title: Intra- and inter-specific diversity of Tc3-like transposons in nematodes and insects and implications for their evolution and transposition. Citation: Gene 282: 133-142 2002 Type: ARTICLE Genes: Abstract: Tc3 of Caenorhabditis elegans is one of the founding members of the Tc1 family which includes DNA transposons in vertebrates, insects, nematodes and fungi. It is one of the best characterized eukaryotic transposons in terms of structure and transposition mechanism. A Tc3-like transposon MsqTc3 has been recently described in a mosquito. Here we present the characterization of a number of Tc3-like transposons in C. elegans, Caenorhabditis briggsae, and Drosophila melanogaster, which has revealed high levels of inter- and intra-specific diversity and further suggests a broad distribution of the Tc3-like transposons. These newly defined transposons and the previously described Tc3 and MsqTc3 form a highly divergent yet distinct clade in the Tc1 family. The above phylogenetic analysis of the Tc3-like transposons and their high levels of intra-specific diversity underscore interesting questions of their evolutionary dynamics in their respective hosts. The majority of the Tc3-like transposons contain two putative binding sites for their transposases. The first is near the terminus and the second is approximately 164-184 bp from the first site. Comparative analysis suggests that the second binding site may have been maintained for an important function in vivo. There is a large amount of variation in the length (27-566 bp) and structure of the terminal inverted repeats (TIRs) of Tc3-like transposons. Long (318-566 bp) TIRs that extend significantly beyond the second binding site are only found in the first described Tc3 and its close relatives, whose transposases form a recently derived clade among the Tc3-like transposons. Thus, these unique TIRs may have evolved recently together with their corresponding ------------------- Key: 5115 Medline: 11807031 Authors: Nance J;Priess JR Title: Cell polarity and gastrulation in C. elegans. Citation: Development 129: 387-397 2002 Type: ARTICLE Genes: ama-1 end-1 hmr-1 lit-1 mex-1 nmy-2 par-2 par-3 par-6 pha-4 pie-1 pgl-1 zuDf2 Abstract: Gastrulation in C. elegans embryos involves formation of a blastocoel and the ingression of surface cells into the blastocoel. Mutations in the par-3 gene cause abnormal separations between embryonic cells, suggesting that the PAR-3 protein has a role in blastocoel formation. In normal development, PAR proteins localize to either the apical or basal surfaces of cells prior to blastocoel formation; we demonstrate that this localization is determined by cell contacts. Cells that ingress into the blastocoel undergo an 387 apical flattening associated with an apical concentration of non-muscle myosin. We provide evidence that ingression times are determined by genes that control cell fate, though interactions with neighboring cells can prevent ingression. ------------------- Key: 5116 Medline: 11807036 Authors: Siegfried KR;Kimble J Title: POP-1 controls axis formation during early gonadogenesis in C. elegans. Citation: Development 129: 443-453 2002 Type: ARTICLE Genes: bar-1 cfz-1 cwn-1 cwn-2 egl2- fog-1 lin-12 lin-17 lin-44 lit-1 mek-2 mom-1 mom-2 mom-4 mom-5 pop-1 rde-1 sys-2 wrm-1 tDf3 tDf4 Abstract: The shape and polarity of the C elegans gonad is defined during early gonadogenesis by two somatic gonadal precursor cells, Z1 and Z4, and their descendants. Z1 and Z4 divide asymmetrically to establish the proximal-distal axes of the gonad and to generate regulatory leader cells that control organ shape. In this paper, we report that pop-1, the C elegans TCF/LEF-1 transcription factor, controls the first Z1/Z4 asymmetric division and hence controls proximal-distal axis formation. We have identified two pop-1(Sys) alleles (for symmetrical misters) that render the Z1/Z4 divisions symmetrical. The pop-1(q645) allele is fully penetrant for the Sys gonadogenesis defect in hermaphrodites, but affects male gonads weakly; pop-l(q645) alters a conserved amino acid in the beta-catenin binding domain. The pop-1(q624) allele is weakly penetrant for multiple defects and appears to be a partial loss-of-function mutation; pop-1(q624) alters a conserved amino acid in the HMG-box DNA binding domain. Zygotic pop-1(RNAi) confirms the role of pop-1 in Z1/Z4 asymmetry and reveals additional roles of pop-1, including one in leader cell migration. Two other Wnt pathway regulators, wrm-1 and lit-1, have the same effect as pop-1 on Z1/Z4 asymmetry. Therefore, wrm-1 and lit-1 are required for pop-1 function, rather than opposing it as observed in the early embryo. We conclude that POP-1 controls the Z1/Z4 asymmetric division and thereby establishes the proximaldistal axes of the gonad. This control over proximal-distal polarity extends our view of Wnt signaling in C. elegans, which had previously been known to control ------------------- Key: 5117 Medline: 11807039 Authors: Kelly WG;Schaner CE;Dernburg AF;Lee MH;Kim SK;Villeneuve AM;Reinke V Title: X-chromosome silencing in the germline of C. elegans. Citation: Development 129: 479-492 2002 Type: ARTICLE Genes: let-809 let-858 pha-1 mnT10 sDp1 sDp3 Abstract: Germline maintenance in the nematode C elegans requires global repressive mechanisms that involve chromatin organization. During meiosis, the X chromosome in both sexes exhibits a striking reduction of histone modifications that correlate with transcriptional activation when compared with the genome as a whole. The histone modification spectrum on the X chromosome corresponds with a lack of transcriptional competence, as measured by reporter transgene arrays. The X chromosome in XO males is structurally analogous to the sex body in mammals, contains a histone modification associated with 479 heterochromatin in other species and is inactivated throughout meiosis. The synapsed X chromosomes in hermaphrodites also appear to be silenced in early meiosis, but genes on the X chromosome are detectably expressed at later stages of oocyte meiosis. Silencing of the sex chromosome during early meiosis is a conserved feature throughout the nematode phylum, and is not limited to ------------------- Key: 5118 Medline: 11861167 Authors: Jin YS Title: Synaptogenesis: insights from worm and fly. Citation: Current Opinion in Neurobiology 12: 71-79 2002 Type: REVIEW Genes: ina-1 pat-3 ptp-3 rpm-1 sad-1 spc-1 syd-2 unc-10 unc-26 unc-70 Abstract: Synapse formation is the ultimate step in wiring a nervous system. Synapses are remarkably diverse in size and shape, and are regulated dynamically. Recently, live observations combined with ultrastructural analysis have revealed many details of the cellular interactions that precede synapse formation. Genetic screens in Caenorhabditis elegans and Drosophila have implicated signaling pathways that may involve small G-proteins, ubiquitin-mediated protein degradation and selective cell adhesion in target recognition, synaptic assembly and growth. ------------------- Key: 5119 Medline: 11834377 Authors: Aballay A;Ausubel FM Title: Caenorhabditis elegans as a host for the study of host-pathogen interactions. Citation: Current Opinion in Microbiology 5: 97-101 2002 Type: REVIEW Genes: age-1 ced-3 ced-4 ced-9 egl-9 egl-19 mev-1 rad-8 srf-2 srf-3 srf-5 unc-43 Abstract: Recently, pathogenicity models that involve the killing of the genetically tractable nematode Caenorhabditis elegans by human pathogens have been developed. From the perspective of the pathogen, the advantage of these models is that thousands of mutagenized bacteria clones can be individually screened for avirulent mutants on separate petri plates seeded with C. elegans. The advantages of using C. elegans to study host responses to pathogen attack are the extensive genetic and genomic resources available and the relative ease of identifying C. elegans mutants that exhibit altered susceptibility to pathogen attack. The use of Caenorhabditis elegans as the host for a variety of human pathogens is discussed. ------------------- Key: 5120 Medline: 11839294 Authors: Goodwin EB;Ellis RE Title: Turning clustering loops: sex determination in Caenorhabditis elegans. Citation: Current Biology 12: R111-R120 2002 Type: REVIEW Genes: egl-1 fbf-1 fbf-2 fem-1 fem-2 fem-3 fog-1 fog-2 fog-3 fox-1 gld-1 her-1 laf-1 mab-3 mog-1 mog-2 mog-3 mog-4 mog-5 mog-6 sdc-1 sdc-2 sdc-3 sex-1 tra-1 tra-2 xol-1 Abstract: The nematode Caenorhabditis elegans has two sexes: males and hermaphrodites. Hermaphrodites are essentially female animals that produce sperm and oocytes. In the past few years tremendous progress has been made towards understanding how sexual identity is controlled in the worm. These analyses have revealed that the regulatory pathway controlling sexual development is far from linear and that it contains a number of loops and branches that play crucial roles in regulating sexual development. This review summarizes our current understanding of the mechanisms that regulate sexual cell fate in C. elegans. ------------------- Key: 5121 Medline: Authors: Cotter PJ;Caffrey DR;Shields DC Title: Improved database searches for orthologous sequences by conditioning on outgroup sequences. Citation: Bioinformatics 18: 83-91 2002 Type: ARTICLE Genes: Abstract: Motivation: Searches of biological sequence databases are usually focussed on distinguishing significant from random matches. However, the increasing abundance of related sequences on databases present a second challenge: to distinguish the evolutionarily most closely related sequences (often orthologues) from more distantly related homologues. This is particularly important when searching a database of partial sequences, where short orthologous sequences from a non-conserved region will score much more poorly than non-orthologous (outgroup) sequences from a conserved region. Results: Such inferences are shown to be improved by conditioning the search results on the scores of an outgroup sequence. The log-odds score for each target sequence identified on the database has the log-odds score of the outgroup sequence subtracted from it. A test group of Caenorhabditis elegans kinase sequences and their identified C.elegans outgroups were searched against a test database of human Expressed Sequence Tag (EST) sequences, where the sets of true target sequences were known in advance. The outgroup conditioned method was shown to identify 58% more true positives ahead of the first false positive, compared to the straightforward search without an outgroup. A test dataset of 151 proteins drawn from the C.elegans genome, where the putative 'outgroup' was assigned automatically, similarly found 50% more true positives using outgroup conditioning. Thus, outgroup conditioning provides a means to improve the results of database searching with little increase in the search ------------------- Key: 5122 Medline: 11879640 Authors: Mohler WA;Shemer G;del Campo JJ;Valansi C;Opoku-Serebuoh E;Scranton V;Assaf N;White JG;Podbilewicz B Title: The type I membrane protein EFF-1 is essential for developmental cell fusion. Citation: Developmental Cell 2: 355-362 2002 Type: ARTICLE Genes: eff-1 lbp-1 mnDf105 Abstract: Multinucleate cells are widespread in nature, yet the mechanism by which cells fuse their plasma membranes is poorly understood. To identify animal fusogens, we performed new screens for mutations that abolish cell fusion within tissues of C. elegans throughout development. We identified the gene eff-1, which is expressed as cells acquire fusion competence and encodes a novel integral membrane protein. EFF-1 sequence motifs suggest physicochemical actions that could cause adjacent bilayers to fuse. Mutations in the extracellular domain of EFF-1 completely block epithelia[ cell membrane fusion without affecting other prefusion events such as cell generation, patterning, differentiation, and adhesion. Thus, EFF-1 is a key component in the mechanism of cell fusion, a process essential to normal animal development. ------------------- Key: 5123 Medline: 11877381 Authors: Soto MC;Qadota H;Kasuya K;Inoue M;Tsuboi D;Mello CC;Kaibuchi K Title: The GEX-2 and GEX-3 proteins are required for tissue morphogenesis and cell migrations in C. elegans. Citation: Genes & Development 16: 620-632 2002 Type: ARTICLE Genes: ajm-1 apx-1 ced-10 gex-2 gex-3 jam-1 let-99 lin-24 mig-2 rac-1 rac-2 sDf2 sDf21 sDf22 sDf66 Abstract: During body morphogenesis precisely coordinated cell movements and cell shape changes organize the newly differentiated cells of an embryo into functional tissues. Here we describe two genes, gex-2 and gex-3, whose activities are necessary for initial steps of body morphogenesis in Caenorhabditis elegans. In the absence of gex-2 and gex-3 activities, cells differentiate properly but fail to become organized. The external hypodermal cells fail to spread over and enclose the embryo and instead cluster on the dorsal side. Postembryonically gex-3 activity is required for egg laying and for proper morphogenesis of the gonad. GEX-2 and GEX-3 proteins colocalize to cell boundaries and appear to directly interact. GEX-2 and GEX-3 are highly conserved, with vertebrate homologs implicated in binding the small GTPase Rac and a GEX-3 Drosophila homolog, HEM2/NAP1/KETTE, that interacts genetically with Rac pathway mutants. Our findings suggest that GEX-2 and GEX-3 may function at cell boundaries to regulate cell migrations and cell shape changes required for proper morphogenesis and development. ------------------- Key: 5124 Medline: 11795393 Authors: Custodia N;Won SJ;Novillo A;Weiland M;Li C;Callard IP Title: Caenorhabditis elegans as an environmental monitor using DNA microarray analysis. Citation: Annals of the New York Academy of Sciences 948: 32-42 2001 Type: ARTICLE Genes: hsp-1 hsp-2 mab-3 mtl-1 vit-1 vit-2 vit-5 vit-6 Abstract: In order to assist in the identification of possible endocrine disrupting chemicals (EDC) in groundwater, we are developing Caenorhabditis elegans as a high throughput bioassay system in which responses to EDC may be detected by gene expression using DNA microarray analysis. As a first step we examined gene expression patterns and vitellogenin responses of this organism to vertebrate steroid, in liquid culture. Western blotting showed the expected number and size of vitellogenin translation products after estrogen exposure. At 10(-9) M, vitellogenin decreased, but at 10(-7) and 10(-5), vitellogenin was increased. Testosterone (10(-5) M) increased the synthesis of vitellogenin, but progesterone-treated cultures (10(-5) M) had less vitellogenin. Using DNA microarray analysis, we examined the pattern of gene expression after progesterone (10(-5), 10(-7), and 10(-9) M), estrogen (10(-5) M) and testosterone (10(-9) M) exposure, with special attention to the traditional biomarker genes used in environmental studies [vitellogenin, cytochrome P450 (CYP), glutathione s-transferase (GST), metallothionein (MT), and heat shock proteins (HSP).] GST and P450 genes were affected by estrogen (10(-5) M) and progesterone (10(-5) and 10(-7) M) treatments. For vitellogenin genes, estrogen treatment (10(-5) M) caused overexpression of the vit-2 and vit-6 genes (2.68 and 3.25 times, respectively). After progesterone treatment (10(-7) M), the vit-5 and vit-6 were down-regulated and vit-1 up-regulated (3.59-fold). Concentrations of testosterone and progesterone at 10(-9) M did not influence the expression of the vit, CYP, or GST genes. Although the analysis is incomplete, and low doses and combinations of EDC need to be tested, these preliminary results indicate C. elegans may be a useful ------------------- Key: 5125 Medline: Authors: Steinberg CEW;Hoss S;Bruggemann R Title: Further evidence that humic substances have the potential to modulate the reproduction of the nematode Caenorhabditis elegans. Citation: International Review of Hydrobiology 87: 121-133 2002 Type: ARTICLE Genes: Abstract: Humic isolates have previously been shown to modulate the reproduction of the nematode, Caenorhabditis elegans MAUPAS. The aim of this study was to find out if a hormone-like effect is an intrinsic feature of humic substances. Therefore, the same nematode bioassay was used with ten humic substances (XAD and/or reverse osmosis isolates). The results confirmed the hormone-like effect of humic substances. nine isolates significantly increased the numbers of offspring per worm, one isolate did not modulate the reproduction of C. elegans. This effect occurred with XAD isolates and with reverse osmosis isolates as well. Thus, this effect is an intrinsic feature of humic substances. This reproduction modulating potential of humic substances may be due to alkylaromatics that are major structural and photo stable structural components, rather than to sterols that are only minor structural components. This is a new view about the direct interactions of humic with aquatic organisms. The effects haven been mathematically modeled by a simple approach, considering a hormone-like effect (beta) and a non-hormone like effect, such as nutrient effect (alpha) on growth. The different effects observed can be interpreted in terms of trade-offs between these two competing mode of actions. ------------------- Key: 5126 Medline: 11856526 Authors: Christensen M;Estevez A;Yin X;Fox R;Morrison R;McDonnell M;Gleason C;Miller DM;Strange K Title: A primary culture system for functional analysis of C. elegans neurons and muscle cells. Citation: Neuron 33: 503-514 2002 Type: ARTICLE Genes: acr-5 del-1 gyc-5 mec-7 myo-3 opt-3 unc-4 unc-13 unc-54 unc-119 Abstract: C. elegans has provided important insights into neuromuscular system function and development. However, the animal's small size limits access to individual neurons and muscle cells for physiological, biochemical, and molecular study. We describe here primary culture methods that allow C. elegans embryonic cells to differentiate into neurons and muscle cells in vitro. Morphological, electrophysiological, and GFP reporter studies demonstrate that the differentiation and functional properties of cultured cells are similar to those observed in vivo. Enriched populations of cells expressing specific GFP reporters can be generated by fluorescence-activated cell sorting. Addition of double-stranded RNA to the culture medium induces dramatic knockdown of targeted gene expression. Primary nematode cell culture provides a new foundation for a wide variety of experimental opportunities heretofore unavailable in the field. ------------------- Key: 5127 Medline: 11875573 Authors: Goodman MB;Ernstrom GG;Chelur DS;O'Hagan R;Yao CA;Chalfie M Title: MEC-2 regulates C. elegans DEG/ENaC channels needed for mechanosensation. Citation: Nature 415: 1039-1042 2002 Type: ARTICLE Genes: mec-2 mec-4 mec-10 Abstract: Touch sensitivity in animals relies on nerve endings in the skin that convert mechanical force into electrical signals. In the nematode Caenorhabditis elegans, gentle touch to the body wall is sensed by six mechanosensory neurons(1) that express two amiloride-sensitive Na+ channel proteins (DEG/ENaC). These proteins, MEC-4 and MEC-10, are required for touch sensation and can mutate to cause neuronal degeneration(2,3). Here we show that these mutant or 'd' forms of MEC-4 and MEC-10 produce a constitutively active, amiloride-sensitive ionic current when co-expressed in Xenopus oocytes, but not on their own. MEC-2, a stomatin-related protein needed for touch sensitivity(4), increased the activity of mutant channels about 40-fold and allowed currents to be detected with wild-type MEC-4 and MEC-10. Whereas neither the central, stomatin-like domain of MEC-2 nor human stomatin retained the activity of full-length MEC-2, both produced amiloride-sensitive currents with MEC-4d. Our findings indicate that MEC-2 regulates MEC-4/MEC-10 ion channels and raise the possibility that similar ion channels may be formed by stomatin-like proteins and DEG/ENaC proteins that are co-expressed in both vertebrates and invertebrates(5-8). Some of these channels may mediate mechanosensory ------------------- Key: 5128 Medline: Authors: Yamanaka A;Yada M;Imaki H;Koga M;Ohshima Y;Nakayama KI Title: Multiple Skp1-related proteins in Caenorhabditis elegans: diverse patterns of interaction with Cullins and F-box proteins. Citation: Current Biology 12: 267-275 2002 Type: ARTICLE Genes: skr-1 skr-2 skr-3 skr-4 skr-5 skr-6 skr-7 skr-8 skr-9 skr-10 skr-11 skr-12 skr-13 skr-14 skr-15 skr-16 skr-17 skr-18 skr-19 skr-20 skr-21 Abstract: Background: The ubiquitin-proteasome pathway of proteolysis controls the abundance of specific regulatory proteins. The SCF complex is a type of ubiquitin-protein ligase (E3) that contributes to this pathway in many biological systems. In yeast and mammals, the SCF complex consists of common components, including Skp1, Cdc53/Cul1, and Rbx1, as well as variable components known as F-box proteins. Whereas only one functional Skp1 gene is present in the human genome, the genome of Caenorhabditis elegans has now been shown to contain at least 21 Skp1-related (skr) genes. The biochemical properties, expression, and function of the C. elegans SKR proteins were examined. Results: Of the 17 SKR proteins examined, eight (SKR-1, -2, -3, -4, -7, -8, -9, and -10) were shown to interact with C. elegans CUL1 by yeast two-hybrid analysis or a coimmunoprecipitation assay in mammalian cells. Furthermore, SKR proteins exhibited diverse binding specificities for C. elegans F-box proteins. The tissue specificity of expression of the CUL1-interacting SKR proteins was also varied. Suppression of skr-1 or skr-2 genes by double-stranded RNA interference resulted in embryonic death, whereas that of skr-7, -8, -9, or -10 was associated with slow growth and morphological abnormalities. Conclusions: The multiple C. elegans SKR proteins exhibit marked differences in their association with Cullins and F-box proteins, in tissue specificity of expression, and in phenotypes associated with functional suppression by RNAi At least eight of the SKR proteins may, like F-box proteins, act as variable components of the SCF ------------------- Key: 5129 Medline: Authors: Nayak S;Santiago FE;Jin H;Lin D;Schedl T;Kipreos ET Title: The Caenorhabditis elegans Skp1-related gene family: diverse functions in cell proliferation, morphogenesis, and Citation: Current Biology 12: 277-287 2002 Type: ARTICLE Genes: cul-1 cul-2 cul-3 cul-4 cul-5 cul-6 him-3 skr-1 skr-2 skr-3 skr-4 skr-5 skr-6 skr-7 skr-8 skr-9 skr-10 skr-11 skr-12 skr-13 skr-14 skr-15 skr-16 skr-17 skr-18 skr-19 skr-20 skr-21 Abstract: Background: The SCF ubiquitin-ligase complex targets the ubiquitin-mediated degradation of proteins in multiple dynamic cellular processes. A key SCF component is the Skp1 protein that functions within the complex to link the substrate-recognition subunit to a cullin that in turn binds the ubiquitin-conjugating enzyme. In contrast to yeast and humans, Caenorhabditis elegans contains multiple expressed Skp1-related (skr) genes. Results: The 21 Skp1-related (skr) genes in C. elegans form one phylogenetic clade, suggesting that a single ancestral Skp1 gene underwent independent expansion in C. elegans. The cellular and developmental functions of the 21 C. elegans skr genes were probed by dsRNA-mediated gene inactivation (RNAi). The RNAi phenotypes of the skr genes fall into two classes. First, the highly similar skr-7, -8, -9, and -10 genes are required for posterior body morphogenesis, embryonic and larval development, and cell proliferation. Second, the related skr-1 and -2 genes are required for the restraint of cell proliferation, progression through the pachytene stage of meiosis, and the formation of bivalent chromosomes at diakinesis. CUL-1 was found to interact with SKR-1, -2, -3, -7, -8, and -10 in the yeast two-hybrid system. Interestingly, SKR-3 could interact with both CUL-1 and its close paralog CUL-6. Conclusions: Members of the expanded skr gene family in C. elegans perform critical functions in regulating cell proliferation, meiosis, and morphogenesis. The finding that multiple SKRs are able to bind cullins suggests an extensive set of combinatorial SCF ------------------- Key: 5130 Medline: 11772394 Authors: Kato Y;Aizawa T;Hoshino H;Kawano K;Nitta K;Zhang H Title: abf-1 and abf-2, ASABF-type antimicrobial peptide genes in Caenorhabditis elegans. Citation: Biochemical Journal 361: 221-230 2002 Type: ARTICLE Genes: abf-1 abf-2 glp-4 Abstract: Two genes encoding the ASABF (Ascaris suum antibacterial factor)-type antimicrobial peptide, abf-1 and abf-2, were identified in Caenorhabditis elegans. Recombinant ABF-2 exhibited potent microbicidal activity against Gram-positive and Grain-negative bacteria, and yeasts. The tissue-specific distribution estimated by immunofluorescence staining and transgenic analysis of a gfp fusion gene (where GFP corresponds to green fluorescent protein) suggested that ABF-2 contributes to surface defence in the pharynx. abf-1 contains a single intron at a conserved position, suggesting that asabf and abf originated from a common ancestor. Both transcripts for abf-1 and abf-2 were detected as two distinct forms, i.e. spliced leader (SL)1-trans-spliced with a long 5'-untranslated region (UTR) and SL-less with a short 5'-UTR. A polycistronic precursor RNA encoding ABF-1 and ABF-2 was detected, suggesting that these genes form an operon. An 'opportunistic operon' model for regulation of abf genes, including the generation of short SL-less transcripts, is proposed. In conclusion, C. elegans should have an immune defence system due to the antimicrobial peptides. C. elegans can be a novel model for innate immunity. Furthermore, the combination of biochemical identification in Ascaris suum and homologue hunting in C. elegans should be a powerful method of finding rapidly evolved proteins, such as some immune-related molecules in ------------------- Key: 5131 Medline: 11847114 Authors: Clucas C;Cabello J;Bussing I;Schnabel R;Johnstone IL Title: Oncogenic potential of a C. elegans cdc25 gene is demonstrated by a gain-of-function allele. Citation: EMBO Journal 21: 665-674 2002 Type: ARTICLE Genes: cdc-25.1 cdc-25.2 cdc-25.3 cdc-25.4 cpr-5 elt-2 let-602 let-604 let-607 hDf8 Abstract: In multicellular organisms, developmental programmes must integrate with central cell cycle regulation to co-ordinate developmental decisions with cell proliferation. Hyperplasia caused by deregulated proliferation without significant change to other aspects of developmental behaviour is a probable step towards full oncogenesis in many malignancies. CDC25 phosphatase promotes progression through the eukaryotic cell cycle by dephosphorylation of cyclin-dependent kinase and, in humans, different cdc25 family members have been implicated as potential oncogenes. Demonstrating the direct oncogenic potential of a cdc25 gene, we identify a gain-of-function mutant allele of the Caenorhabditis elegans gene cdc-25.1 that causes a deregulated proliferation of intestinal cells resulting in hyperplasia, while other aspects of intestinal cell function are retained. Using RNA-mediated interference, we demonstrate modulation of the oncogenic behaviour of this mutant, and show that a reduction of the wild-type cdc-25.1 activity can cause a failure of proliferation of intestinal and other cell types. That gain and loss of CDC-25.1 activity has opposite effects on cellular proliferation indicates its critical role in controlling C.elegans cell number. ------------------- Key: 5132 Medline: Authors: Moss EG Title: MicroRNAs: Hidden in the genome. Citation: Current Biology 12: R138-R140 2002 Type: REVIEW Genes: let-7 lin-4 Abstract: Genes for tiny RNAs have been found to be plentiful in the genomes of worms, flies, humans and probably all animals. Some of these microRNAs have been conserved through evolution, and many are expressed only at specific times or places. How they act is just beginning to be understood, but their importance to biology is likely to be great. ------------------- Key: 5133 Medline: 11852047 Authors: Miyadera H;Kano K;Miyoshi H;Ishii N;Hekimi S;Kita K Title: Quinones in long-lived clk-1 mutants of Caenorhabditis elegans. Citation: FEBS Letters 512: 33-37 2002 Type: ARTICLE Genes: clk-1 daf-2 eat-2 Abstract: Ubiquinone (UQ) (coenzyme Q) is a lipophilic redoxactive molecule that functions as an electron carrier in the mitochondrial electron transport chain. Electron transfer via UQ involves the formation of semiubiquinone radicals, which causes the generation of superoxide radicals upon reaction with oxygen. In the reduced form, UQ functions as a lipid-soluble antioxidant, and protects cells from lipid peroxidation. Thus, UQ is also important as a lipophilic regulator of oxidative stress. Recently, a study on long-lived clk-1 mutants of Caenorhabditis elegans demonstrated that biosynthesis of UQ is dramatically altered in mutant mitochondria. Demethoxy ubiquinone (DMQ), that accumulates in clk-4 mutants in place of UQ, may contribute to the extension of life span. Here we elucidate the possible mechanisms of life span extension in clk-1 mutants, with particular emphasis on the electrochemical property of DMQ. Recent findings on the biochemical function of CLK-1 are also discussed. ------------------- Key: 5134 Medline: 11861554 Authors: Rinaldo C;Bazzicalupo P;Ederle S;Hilliard M;La Volpe A Title: Roles for Caenorhabditis elegans rad-51 in meiosis and in resistance to ionizing radiation during development. Citation: Genetics 160: 471-479 2002 Type: ARTICLE Genes: ced-3 him-3 mre-11 msh-5 mut-7 nuc-1 rad-51 spo-11 Abstract: We have investigated the role of Caenorhabditis elegans RAD-51 during meiotic prophase and embryogenesis, making use of the silencing effect of RNA interference (RNAi). rad-51 RNAi leads to severe defects in chromosome morphology in diakinesis oocytes. We have explored the effect of rad-51 RNAi in mutants lacking fundamental Components Of the recombination machinery. If double-strand breaks are prevented by spo-11 mutation, rad-51 RNAi does not affect chromosome appearance. This is consistent with a role for RAD-51 downstream of the initiation of recombination. In the absence of MRE-11, as in the absence of SPO-11, RAD-51 depletion has no effect on the chromosomes, which appear intact, thus indicating a role for MRE-11 in DSB induction. Intriguingly , rad-51 silencing in oocytes that lack MSH-5 leads to chromosome fragmentation, a novel trait that is distinct from that seen in msh-5 mutants and in rad-51 RNAi oocytes, suggesting new potential roles for the msh-5 gene. Silencing of the rad-51 gene also causes a reduction in fecundity, which is suppressed by mutation in the DNA damage checkpoint gene rad-5, but not in the cell death effector gene ced-3. Finally, RAD-51 depletion is also seen to affect the soma, resulting in hypersensitivity to ------------------- Key: 5135 Medline: Authors: Hsu V;Zobel CL;Lambie EJ;Schedl T;Kornfeld K Title: Caenorhabditis elegans lin-45 raf is essential for larval viability, fertility and the induction of vulval cell Citation: Genetics 160: 481-492 2002 Type: ARTICLE Genes: gon-2 let-60 lin-1 lin-12 lin-15 lin-31 lin-45 mek-2 mpk-1 sup-11 nDf41 Abstract: The protein kinase Raf is an important signaling protein. Raf activation is initiated by an interaction with GTP-bound Ras, and Raf functions in signal transmission by phosphorylating and activating a mitogen-activated protein (MAP) kinase kinase named MEK We identified 13 mutations in the Caenorhabditis elegans lin-45 raf gene by screening for hermaphrodites with abnormal vulval formation or germline function. Weak, intermediate, and strong loss-of-function or null mutations were isolated. The phenotype caused by the most severe mutations demonstrates that lin-45 is essential for larval viability, fertility and the induction of vulval cell fates. The lin-45(null) phenotype is similar to the mek-2(null) and mpk-l(null) phenotypes, indicating that LIN-45, MEK-2, and MPK-1 ERR MAP kinase function in a predominantly linear signaling pathway. The lin-45 alleles include three missense mutations that affect the Ras-binding domain, three missense mutations that affect the protein kinase domain, two missense mutations that affect the C-terminal binding domain, three nonsense mutations, and one small deletion. The analysis of the missense mutations indicates that ras binding, 14-3-3-binding, and protein kinase activity are necessary for full Raf function and suggests that a 14-3-3 protein positively regulates Raf-mediated signaling during C. ------------------- Key: 5136 Medline: Authors: Zhang H;Emmons SW Title: Caenorhabditis elegans unc-37/groucho interacts genetically with components of the transcriptional mediator complex. Citation: Genetics 160: 799-803 2002 Type: ARTICLE Genes: bar-1 egl-5 lin-22 lin-32 mab-5 pal-1 sop-1 sop-3 sur-2 unc-37 Abstract: Groucho functions as a general corepressor by modulating chromatin structure and has a widespread role in many developmental processes. Here we show that Groucho may also interact with the basal transcriptional machinery. Mutations in Caenorhabditis elegans groucho interact with mutations in components of the transcriptional Mediator complex, resulting in synthetic lethality and loss of male sensory neurons. ------------------- Key: 5137 Medline: 11850412 Authors: Fay DS;Keenan S;Han M Title: fzr-1 and lin-35/Rb function redundantly to control cell proliferation in C. elegans as revealed by a nonbiased synthetic screen. Citation: Genes & Development 16: 503-517 2002 Type: ARTICLE Genes: chd-4 efl-1 fzr-1 hda-1 lin-3 lin-8 lin-15 lin-23 lin-35 lin-36 lin-53 slr-1 Abstract: We report here a synthetic-lethal screen in Caenorhabditis elegans that overcomes a number of obstacles associated with the analysis of functionally redundant genes. Using this approach, we have identified mutations that synthetically interact with lin-35/Rb, a SynMuv gene and the sole member of the Rb/pocket protein family in C. elegans. Unlike the original SynMuv screens, our approach is completely nonbiased and can theoretically be applied to any situation in which a mutation fails to produce a detectable phenotype. From this screen we have identified fzr-1, a gene that synthetically interacts with lin-35 to produce global defects in cell proliferation control. fzr-1 encodes the C. elegans homolog of Cdh1/Hct1/FZR, a gene product shown in other systems to regulate the APC cyclosome. We have also uncovered genetic interactions between fzr-1 and a subset of class B SynMuv genes, and between lin-35 and the putative SCF regulator lin-23. We propose that lin-35, fzr-1, and lin-23 function redundantly to control cell cycle progression through the regulation of ------------------- Key: 5138 Medline: 11874923 Authors: Rugarli EI;Di Schiavi E;Hilliard MA;Arbucci S;Ghezzi C;Facciolli A;Coppola G;Ballabio A;Bazzicalupo P Title: The Kallmann syndrome gene homolog in C. elegans is involved in epidermal morphogenesis and neurite branching. Citation: Development 129: 1283-1294 2002 Type: ARTICLE Genes: him-5 him-8 kal-1 lin-15 eDf3 eDf24 Abstract: Kallmann syndrome is an inherited disorder defined by the association of anosmia and hypogonadism, owing to impaired targeting and migration of olfactory axons and gonadotropin-releasing hormone secreting neurons. The gene responsible for the X-linked form of Kallmann syndrome, KAL-1, encodes a secreted protein of still elusive function. It has been proposed that KAL-1 might be involved in some aspects of olfactory axon guidance. However, the unavailability of a mouse model, and the difficulties in studying cellular and axonal migration in vertebrates have hampered an understanding of its function. We have identified the C elegans homolog, kal-1, and document its function in vivo. We show that kal-1 is part of a mechanism by which neurons influence migration and adhesion of epidermal cells undergoing morphogenesis during ventral enclosure and male tail formation. We also show that kal-1 affects neurite outgrowth in vivo by modulating branching. Finally, we find that human KAL-1 cDNA can compensate for the loss of worm kal-1 and that overexpression of worm or human KAL-1 cDNAs in the nematode results in the same phenotypes. These data indicate functional conservation between the human and nematode proteins and establish C elegans as a powerful animal in which to investigate KAL function in vivo. Our findings add a new player to the set of molecules, which appear to underlie both morphogenesis and axonal/neuronal navigation in vertebrates and invertebrates. ------------------- Key: 5139 Medline: 11861916 Authors: Webb CT;Shabalina SA;Ogurtsov AY;Kondrashov AS Title: Analysis of similarity within 142 pairs of orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae. Citation: Nucleic Acids Research 30: 1233-1239 2002 Type: ARTICLE Genes: Abstract: Patterns of similarity between genomes of related species reflect the distribution of selective constraint within DNA. We analyzed alignments of 142 orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae and found a mosaic pattern with regions of high similarity (phylogenetic footprints) interspersed with non-alignable sequences. Footprints cover similar to20% of intergenic regions, often occur in clumps and are rare within 5' UTRs but common within 3' UTRs. The footprints have a higher ratio of transitions to transversions than expected at random and a higher GC content than the rest of the intergenic region. The number of footprints and the GC content of footprints within an intergenic region are higher when genes are oriented so that their 5' ends form the boundaries of the intergenic region. Overall, the patterns and characteristics identified here, along with other comparative and experimental studies, suggest that many footprints have a regulatory function, although other types of function are also possible. These conclusions may be quite general across eukaryotes, and the characteristics of conserved regulatory elements determined from genomic comparisons can be useful in prediction of regulation sites within individual DNA sequences. ------------------- Key: 5140 Medline: 11891667 Authors: Otsuka AJ;Boontrakulpoontawee P;Rebeiz N;Domanus M;Otsuka D;Velamparampil N;Chan S;Wyngaerde MV;Campagna S;Cox A Title: Novel UNC-44 AO13 ankyrin is required for axonal guidance in C. elegans, contains six highly repetitive STEP blocks separated by seven potential transmembrane domains, and is localized to neuronal pro Citation: Journal of Neurobiology 50: 333-349 2002 Type: ARTICLE Genes: unc-5 unc-6 unc-33 unc-40 unc-44 unc-51 unc-76 Abstract: Conventional ankyrins are cortical cytoskeletal proteins that form an ankyrin-spectrin meshwork underlying the plasma membrane. We report here the unusual structure of a novel ankyrin (AO13 ankyrin, 775,369 Da, 6994 aa,, pI = 4.45) that is required for proper axonal guidance in Caenorhabditis elegans. AO13 ankyrin contains the ANK repeat and spectrin-binding domains found in other ankyrins, but differs from all others in that the acidic carboxyl region contains six blocks of serine/threonine/glutamic acid/proline rich (STEP) repeats separated by seven hydrophobic domains. The STEP repeat blocks are composed primarily of sequences related to ETTTTTTVTREHFEPED(E/D)X(n)VVESEEYSASGSPVPSE (E/K)DVE(H/R)VI, and the hydrophobic domains contain sequences related to PESGEESDGEGFGSKVLGFAKK[AGMVAGGVVAAPVALAAVGA]KAAYDALKKDDDEE, which includes a potential transmembrane domain (in brackets). Recombinant protein fragments of AO13 ankyrin were used to prepare polyclonal antisera against the spectrin-binding domain (AO271 Ab), the conventional ankyrin regulatory domain (AO280 Ab), the AO13 ankyrin STEP domain (AO346 Ab), the AO13 ankyrin STEP + hydrophobic domain (AO289 Ab), and against two carboxyl terminal domain fragments (AO263 Ab and AO327 Ab). Western blot analysis with these Ab probes demonstrated multiple protein isoforms. By immunofluorescence microscopy, the antispectrin-binding and regulatory domain (AO271 and AO280) antibodies recognized many cell types, including neurons., and stained the junctions between cells. The AO13 ankyrin-specific (AO289 and AO346) antibodies showed a neurally restricted pattern, staining nerve processes and the periphery of neural cell bodies. These results are ------------------- Key: 5141 Medline: Authors: Masler EP Title: Aminopeptidases in Caenorhabditis elegans and Panagrellus redivivus: detection using peptide and non-peptide substrates. Citation: Journal of Helminthology 76: 45-52 2002 Type: ARTICLE Genes: Abstract: Aminopeptidase activities were detected in extracts of the free-living nematodes Caenorhabditis elegans and Panagrellus redivivus using the aminoacyl substrate L-alanine-4-nitroanilide. The activities exhibited similarities in Km (C. elegans = 2.22 mM; P. redivivus = 2.09 mM) and specific activity (C. elegans = 1.38+/-0.43 mAU min(-1) mug(-1); P. redivivus, 1.23+/-0.18 mAU min(-1) mug(-1)). Each is inhibited competitively by amastatin (C. elegans IC50 = 0.46 muM; P. redivivus IC50 = 15.90 muM) and non-competitively by leuhistin (C. elegans IC50 = 3.00 muM; P. redivivus IC50 = 37.35 muM). The bioactive peptides adipokinetic hormone and substance P decrease the apparent aminopeptidase activities of each extract suggesting that the peptides compete with the Ala-pNA as substrates. With each extract, adipokinetic hormone appeared to be the more effective substrate. Digestion of adipokinetic hormone by C. elegans and P. redivivus extracts in the presence and absence of 1 mM amastatin produced distinct chromatographic profiles that suggest different digestion patterns for the two species. However, amastatin had clear effects on chromatographic profiles from each species indicating that an aminopeptidase is involved in the digestion of the peptide substrates. The data presented indicate that extracts of free-living nematodes are capable of metabolizing peptide hormones, and that this metabolism involves substrate-selective aminopeptidases. ------------------- Key: 5142 Medline: 11865041 Authors: Pettitt J;Crombie C;Schumperli D;Muller B Title: The Caenorhabditis elegans histone hairpin-binding protein is required for core histone gene expression and is essential for embryonic and postembryonic cell division. Citation: Journal of Cell Science 115: 857-866 2002 Type: ARTICLE Genes: hcp-3 his-1 his-2 his-3 his-4 his-5 his-6 his-7 his-8 his-9 his-10 his-11 his-12 his-13 his-14 his-15 his-16 his-17 his-18 his-19 his-20 his-21 his-22 his-27 his-28 his-30 his-31 his-32 his-33 his-34 his-35 his-37 his-38 his-39 Abstract: As in all metazoans, the replication-dependent histone genes of Caenorhabditis elegans lack introns and contain a short hairpin structure in the 3' untranslated region. This hairpin structure is a key element for post-transcriptional regulation of histone gene expression and determines mRNA 3' end formation, nuclear export, translation and mRNA decay. All these steps contribute to the S-phase-specific expression of the replication-dependent histone genes. The hairpin structure is the binding site for histone hairpin-binding protein that is required for hairpin-dependent regulation. Here, we demonstrate that the C elegans histone hairpin-binding protein gene is transcribed in dividing cells during embryogenesis and postembryonic development. Depletion of histone hairpin-binding protein (HBP) function in early embryos using RNA-mediated interference leads to an embryonic-lethal phenotype brought about by defects in chromosome condensation. A similar phenotype was obtained by depleting histones H3 and H4 in early embryos, indicating that the defects in hairpin-binding protein-depleted embryos are caused by reduced histone biosynthesis. We have confirmed this by showing that HBP depletion reduces histone gene expression. Depletion of HBP during postembryonic development also results in defects in cell division during late larval development. In addition, we have observed defects in the specification of vulval cell fate in animals depleted for histone H3 and H4, which indicates that histone proteins are required for cell fate regulation during vulval development. ------------------- Key: 5143 Medline: Authors: Bailey S;Sedelnikova SE;Blackburn GM;Abdelghany HM;McLennan AG;Rafferty JB Title: Crystallization of a complex of Caenorhabditis elegans diadenosine tetraphosphate hydrolase and non-hydrolysable substrate analogue, AppCH(2)ppA. Citation: Acta Crystallographica Section D-Biological Crystallography 58: 526-528 2002 Type: ARTICLE Genes: Abstract: The molecule diadenosine tetraphosphate (Ap(4)A) has been suggested to be a component of the cellular response to metabolic stress and/or, via the intracellular Ap(3)A/Ap(4)A ratio, to be involved in differentiation and apoptosis. Thus, the enzyme Ap(4)A hydrolase has a key metabolic role through regulation of the intracellular Ap(4)A levels. Crystals of this enzyme from the nematode Caenorhabditis elegans have been obtained in the presence of a non-hydrolysable substrate analogue, AppCH(2)ppA. The crystals belong to space group P2(1), unit-cell parameters a = 57.6, b = 36.8, c = 68.9 Angstrom, beta = 114.2degrees, and diffract to approximately 2.0 Angstrom. Determination of the structure of this complex will provide insights into the substrate specificity and catalytic activity of this class of enzymes. ------------------- Key: 5144 Medline: 11867644 Authors: Yashin AI;Cypser JW;Johnson TE;Michalski AI;Boyko SI;Novoseltsev VN Title: Heat shock changes the heterogeneity distribution in populations of Caenorhabditis elegans: Does it tell us anything about the biological mechanism of stress response? Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 57: B83-B92 2002 Type: ARTICLE Genes: fer-15 spe-9 Abstract: In this paper we analyze Survival data of populations of sterilized nematodes. Caenorhabditis elegans. exposed to heat shocks of different duration at the beginning of their adult lives. There are clear hormesis effects after short exposure to heat and clear debilitation effects after long exposure. Intermediate durations result in a mixture of these two effects. In this latter case. the survival curves for the control and experimental populations intersect. We show that observed effects may be explained by using a model of discrete heterogeneity. According to this model. each Population of worms in the experiment is a mixture of subcohorts of frail, normal. and robust individuals: exposure to heat changes the initial proportion of worms in the subcohorts (heterogeneity distribution): and these changes depend on the duration Of exposure. In other words, exposure to heat does not influence mortality rates (survival functions) in the subcohorts but does cause individuals to move from one subcohort to another. In a biological interpretation of this finding we hypothesize that. when coping with stress. the organisms of storms use several lines of defense. Switching these lines of ana off in response to stress in individual organisms Generates the spectrum of observed survival effects at the population level. We discuss possible molecular biological mechanisms of stress response and directions for further research. ------------------- Key: 5145 Medline: 11867647 Authors: Cypser JR;Johnson TE Title: Multiple stressors in Caenorhabditis elegans induce stress hormesis and extended longevity. Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 57: B109-B114 2002 Type: ARTICLE Genes: fer-15 spe-9 Abstract: We demonstrate here that the nematode Caenorhabditis elegans displays broad hormetic abilities. Hormesis is the induction of beneficial effects by exposure to lock doses of otherwise harmful chemical or physical agents. Heat as well as pretreatment with hyperbaric oxygen or juglone (a chemical that generates reactive oxygen species) significantly increased resistance to the same challenge. Cross-tolerance between juglone and oxygen was also observed. The same heat or oxygen pretreatment regimens that induced subsequent stress resistance also increased life expectancy and maximum life span of populations undergoing normal aging. Pretreatment with ultraviolet or ionizing radiation did not promote subsequent resistance or increased longevity. In dose-response studies. induced thermotolerance paralleled the induced increase in life expectancy, which is consistent with a common origin. ------------------- Key: 5146 Medline: 11861885 Authors: Gu Z;Cavalcanti A;Chen FC;Bouman P;Li WH Title: Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Citation: Molecular Biology and Evolution 19: 256-262 2002 Type: ARTICLE Genes: Abstract: We conducted a detailed analysis of duplicate genes in three complete genoms: yeast, Drosophila, and Caenorhabditis elegans. For two proteins belonging to the same family we used the criteria ( 1 ) their similarity is greater than or equal to1 ( 1 = 30% if L greater than or equal to 150 a.a. and I = 0.01n + 4.8L(-0.321) (exp) if L < 150 a.a.. where n = 6 and L is the length of the alignable region), and (2) the length of the alignable region between the two sequences is greater than or equal to80% of the longer protein. We found it very important to delete isoforms (caused by alternative splicing). same genes with different names. and proteins derived from repetitive elements. We estimated that there Acre 530, 674, and 1,219 protein families in yeast. Drosophila. and C. elegans, respectively. So, as expected, cast has the smallest number of duplicate genes. However, for the duplicate pairs with the number of substitutions per synonymous site (K-s) < 0.01. Drosophila has only seven pairs. whereas yeast has 58 pairs and nematode has 153 pairs. After considering the possible effects of codon usage bias and gene coil version. these numbers became 6, 55, and 147, respectively. Thus. Drosophila appears to have much fewer young duplicate genes than do yeast and nematode. The larger numbers of duplicate pairs with K-s < 0.01 in yeast and C. elegans were probably largely caused by block duplications. At any rate, it is clear that the genome of Drosophila melanogaster has undergone few gene duplications in the recent past and has much fewer gene families than C. elegans. ------------------- Key: 5147 Medline: 11867711 Authors: Nass R;Hall DH;Miller DM;Blakely RD Title: Neurotoxin-induced degeneration of dopamine neurons in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 99: 3264-3269 2002 Type: ARTICLE Genes: ced-1 ced-3 ced-4 dat-1 Abstract: Parkinson's disease is a complex neurodegenerative disorder characterized by the death of brain dopamine neurons. In mammals, dopamine neuronal degeneration can be triggered through exposure to neurotoxins accumulated by the presynaptic dopamine transporter (DAT), including 6-hydroxydopamine (6-OHDA) and 1-methyl-4-phenylpyridinium. We have established a system for the pharmacological and genetic evaluation of neurotoxin-induced dopamine neuronal death in Caenorhabditis elegans. Brief (11 h) exposure of green fluorescent protein-tagged, living worms to 6-OHDA causes selective degeneration of dopamine neurons. We demonstrate that agents that interfere with DAT function protect against 6-OHDA toxicity. 6-OHDA-triggered neural degeneration does not require the CED-3/CED-4 cell death pathway, but is abolished by the genetic disruption of the C. elegans DAT. ------------------- Key: 5148 Medline: 11879652 Authors: Kuhara A;Inada H;Katsura I;Mori I Title: Negative regulation and gain control of sensory neurons by the C. elegans calcineurin TAX-6. Citation: Neuron 33: 751-763 2002 Type: ARTICLE Genes: gcy-8 ges-1 myo-3 odr-3 osm-9 tax-2 tax-4 tax-6 ttx-3 unc-3 unc-14 Abstract: Animals sense and adapt to variable environments by regulating appropriate sensory signal transduction pathways. Here, we show that calcineurin plays a key role in regulating the gain of sensory neuron responsiveness across multiple modalities. C. elegans animals bearing a loss-of-function mutation in TAX-6, a calcineurin A subunit, exhibit pleiotropic abnormalities, including many aberrant sensory behaviors. The tax-6 mutant defect in thermosensation is consistent with hyperactivation of the AFD thermosensory neurons. Conversely, constitutive activation of TAX-6 causes a behavioral phenotype consistent with inactivation of AFD neurons. In olfactory neurons, the impaired olfactory response of tax-6 mutants to an AWC-sensed odorant is caused by hyperadaptation, which is suppressible by a mutation causing defective olfactory adaptation. Taken together, our results suggest that stimulus-evoked calcium entry activates calcineurin, which in turn negatively regulates multiple aspects of sensory signaling. ------------------- Key: 5150 Medline: 11867526 Authors: Jansen G;Weinkove D;Plasterk RHA Title: The G protein gamma subunit gpc-1 of the nematode C. elegans is involved in taste adaptation. Citation: EMBO Journal 21: 986-994 2002 Type: ARTICLE Genes: adp-1gpc-1 gpc-2 osm-9 Abstract: Caenorhabditis elegans has two heterotrimeric G-protein gamma subunits, gpc-1 and gpc-2. Although GPC-1 is specifically expressed in sensory neurons, it is not essential for the detection of odorants or salts. To test whether GPC-1 is involved in sensory plasticity, we developed a water soluble compound adaptation assay. The behaviour of wild-type animals in this assay confirms that prolonged exposure to salts can abolish chemo-attraction to these compounds. This process is time and concentration dependent, partly salt specific and reversible. In contrast, gpc-1 mutant animals show clear deficits in their ability to adapt to NaAc, NaCl and NH4Cl, but normal wild-type adaptation to odorants. Two other loci previously implicated in odorant adaptation, adp-1 and osm-9, are also involved in adaptation to salts. Our finding that G proteins, OSM-9 and ADP-1 are involved in taste adaptation offer the first molecular insight into this process. ------------------- Key: 5151 Medline: 11867529 Authors: Halevi S;McKay J;Palfreyman M;Yassin L;Eshel M;Jorgensen E;Treinin M Title: The C. elegans ric-3 gene is required for maturation of nicotinic acetylcholine receptors. Citation: EMBO Journal 21: 1012-1020 2002 Type: ARTICLE Genes: deg-3 des-2 des-5 myo-3 ric-3 Abstract: Mutations in ric-3 (resistant to inhibitors of c holinesterase) suppress the neuronal degenerations caused by a gain of function mutation in the Caenorhabditis elegans DEG-3 acetylcholine receptor. RIC-3 is a novel protein with two transmembrane domains and extensive coiled-coil domains. It is expressed in both muscles and neurons, and the protein is concentrated within the cell bodies. We demonstrate that RIC-3 is required for the function of at least four nicotinic acetylcholine receptors. However, GABA and glutamate receptors expressed in the same cells are unaffected. In ric-3 mutants, the DEG-3 receptor accumulates in the cell body instead of in the cell processes. Moreover, co-expression of ric-3 in Xenopus laevis oocytes enhances the activity of the C.elegans DEG-3/DES-2 and of the rat alpha-7 acetylcholine receptors. Together, these data suggest that RIC-3 is specifically required for the maturation of acetylcholine ------------------- Key: 5152 Medline: 11867534 Authors: Morita K;Flemming AJ;Sugihara Y;Mochii M;Suzuki Y;Yoshida S;Wood WB;Kohara Y;Leroi AM;Ueno N Title: A Caenorhabditis elegans TGF-B, DBL-1, controls the expression of LON-1, a PR-related protein, that regulates polyploidization and body length. Citation: EMBO Journal 21: 1063-1073 2002 Type: ARTICLE Genes: dbl-1 lon-1 sma-2 sma-3 sma-4 Abstract: Using cDNA-based array analysis combined with double-stranded RNA interference (dsRNAi), we have identified yk298h6 as a target gene of Caenorhabditis elegans TGF-beta signaling. Worms overexpressing dbl-1, a TGF-beta ligand, are 16% longer than wild type. Array analysis shows yk298h6 to be one of several genes suppressed in such worms. Disruption of yk298h6 function by dsRNAi also resulted in long worms, suggesting that it is a negative regulator of body length. yk298h6 was then mapped to, and shown to be identical to, lon-1, a known gene that affects body length. lon-1 encodes a 312 amino acid protein with a motif sequence that is conserved from plants to humans. Expression studies confirm that LON-1 is repressed by DBL-1, suggesting that LON-1 is a novel downstream component of the C. elegans TGF-beta growth regulation pathway. Consistent with this, LON-1 is expressed mainly in the larval and adult hypodermis and has dose-dependent effects on body length associated with changes in hypodermal ploidy, but not hypodermal cell proliferation. ------------------- Key: 5153 Medline: 11861469 Authors: Esmaeili B;Ross JM;Neades C;Miller DM;Ahringer J Title: The C. elegans even-skipped homologue, vab-7, specifies DB motoneurone identity and axon trajectory. Citation: Development 129: 853-862 2002 Type: ARTICLE Genes: acr-5 cha-1 unc-3 unc-4 unc-17 unc-25 unc-37 unc-29 vab-7 Abstract: Locomotory activity is defined by the specification of motoneurone subtypes. In the nematode, C elegans, DA and DB motoneurones innervate dorsal muscles and function to induce movement in the backwards or forwards direction, respectively. These two neurone classes express separate sets of genes and extend axons with oppositely directed trajectories; anterior (DA) versus posterior (1311). The DA-specific homeoprotein UNC-4 interacts with UNC-37/Groucho to repress the DB gene, acr-5 (nicotinic acetylcholine receptor subunit). We show that the C. elegans even-skipped-like homoedomain protein, VAB-7, coordinately regulates different aspects of the DB motoneurone fate, in part by repressing unc-4. Wild-type DB motoneurones express VAB-7, have posteriorly directed axons, express ACR-5 and lack expression of the homeodomain protein UNC-4. In a vab-7 mutant, ectopic UNC-4 represses acr-5 and induces an anteriorly directed DB axon trajectory. Thus, vab-7 indirectly promotes DB-specific gene expression and posteriorly directed axon outgrowth by preventing UNC-4 repression of 11313 differentiation. Ectopic expression of VAB-7 also induces D-B traits in an unc-4-independent manner, suggesting that VAB-7 can act through a parallel pathway. This work supports a model in which a complementary pair of homeodomain transcription factors (VAB-7 and UNC-4) specifies differences between DA and DB neurones through inhibition of the alternative fates. The recent findings that Even-skipped transcriptional repressor activity specifies neurone identity and axon guidance in the mouse and Drosophila motoneurone circuit points to an ancient origin for homeoprotein-dependent mechanisms of neuronal ------------------- Key: 5154 Medline: Authors: Dlakic M Title: A new family of putative insulin receptor-like proteins in C. elegans. Citation: Current Biology 12: R155-R157 2002 Type: REVIEW Genes: daf-2 Abstract: Delayed senescence in C. elegans is controlled by an insulin receptor-like gene which regulates both reproductive development and metabolism in a manner similar to the corresponding mammalian pathway. However, despite the large number of insulin-like ligands in C. elegans, only one protein has been identified. ------------------- Key: 5155 Medline: Authors: Ohmachi M;Rocheleau CE;Church D;Lambie E;Schedl T;Sundaram MV Title: C. elegans ksr-1 and ksr-2 have both unique and redundant functions and are required for MPK-1 ERK phosphorylation. Citation: Current Biology 12: 427-433 2002 Type: ARTICLE Genes: ksr-1 ksr-2 let-60 lin-1 lin-45 mek-2 mpk-1 sur-8 Abstract: Kinase Suppressor of Ras (KSR) is a conserved protein that positively regulates Ras signaling and may function as a scaffold for Raf, MEK, and ERK [1]. However, the precise role of KSR is not well understood, and some observations have suggested that KSR might act in a parallel pathway. In C. elegans, ksr-1 is only required for a specific Ras-mediated process (sex myoblast migration) and is a nonessential positive regulator of other Ras-mediated developmental events [2, 3]. We report the existence of a second C. elegans ksr gene, ksr-2, which is required for Ras-mediated signaling during germline meiotic progression and functions redundantly with ksr-1 during development of the excretory system, hermaphrodite vulva, and male spicules. Thus, while the ksr-1 and ksr-2 genes are individually required only for specific Ras-dependent processes, together these two genes appear necessary for most aspects of Ras-mediated signaling in C. elegans. The finding that ksr-2; ksr-1 double mutants have strong ras-like phenotypes and severely reduced or absent levels of diphosphorylated MPK-1 ERK strongly supports models where KSR acts to promote the activation or maintenance of the Raf/MEK/ERK kinase cascade. ------------------- Key: 5156 Medline: Authors: Ewbank JJ Title: Tackling both sides of the host-pathogen equation with Caenorhabditis elegans. Citation: Microbes and Infection 4: 247-256 2002 Type: REVIEW Genes: Abstract: If one is interested in dissecting the complex interactions that exist between host and pathogen, the nematode worm Caenorhabditis elegans is perhaps not the first model host that comes to mind. In this review I will introduce 'the worm' and try to show how it is, in fact, well suited to the identification of universal virulence factors and holds great promise for the study of conserved mechanisms of innate immunity. ------------------- Key: 5157 Medline: 11896167 Authors: Wang Q;Wadsworth WG Title: The C domain of netrin UNC-6 silences calcium/calmodulin-dependent protein kinase- and diacylglycerol-dependent axon branching in Caenorhabditis elegans. Citation: Journal of Neuroscience 22: 2274-2282 2002 Type: ARTICLE Genes: dgk-1 egl-8 egl-30 npr-1 unc-2 unc-5 unc-6 unc-36 unc-40 unc-43 Abstract: Second messenger systems mediate neuronal responses to extracellular factors that elicit axon branching, turning, and guidance. We found that mutations in Caenorhabditis elegans that affect components of second messenger systems, a G-protein subunit, phospholipase Cbeta, diacylglycerol (DAG) kinase, and calcium/calmodulin-dependent protein kinase (CaMKII), have no obvious effect on axon responses to UNC-6 except in animals in which the N-terminal fragment, UNC-6DeltaC, is expressed. In these animals, the mutations enhance or suppress ectopic branching of certain axons. Netrin UNC-6 is an extracellular protein that guides circumferential migrations, and UNC-6DeltaC has UNC-6 guidance activity. We propose that the guidance response elicited by the UNC-6 N-terminal domains involves mechanisms that can induce branching that is sensitive to CaMKII- and DAG-dependent signaling, and that the UNC-6 C domain is required in cis to the N-terminal domains to silence the branching and to maintain proper axon ------------------- Key: 5158 Medline: 11870211 Authors: Gruenbaum Y;Lee KK;Liu J;Cohen M;Wilson KL Title: The expression, lamin-dependent localization and RNAi depletion phenotype for emerin in C. elegans. Citation: Journal of Cell Science 115: 923-929 2002 Type: ARTICLE Genes: emr-1 lem-2 lem-3 lmn-1 unc-84 Abstract: Emerin belongs to the LEM-domain family of nuclear membrane proteins, which are conserved in metazoans from C elegans to humans. Loss of emerin in humans causes the X-linked form of Emery-Dreifuss muscular dystrophy (EDMD), but the disease mechanism is not understood. We have begun to address the function of emerin in C elegans, a genetically tractable nematode. The emerin gene (emr-1) is conserved in C elegans. We detect Ce-emerin protein in the nuclear envelopes of all cell types except sperm, and find that Ce-emerin coimmunoprecipitates with Ce-lamin from embryo lysates. We show for the first time in any organism that nuclear lamins are essential for the nuclear envelope localization of emerin during early development. We further show that four other types of nuclear envelope proteins, including fellow LEM-domain protein Ce-MAN1, as well as Ce-lamin, UNC-84 and nucleoporins do not depend on Ce-emerin for their localization. This result suggests that emerin is not essential to organize or localize the only lamin (B-type) expressed in C. elegans. We also analyzed the RNAi phenotype resulting from the loss of emerin function in C. elegans under laboratory growth conditions, and found no detectable phenotype throughout development. We propose that C. elegans is an appropriate system in which to study the molecular mechanisms of emerin function ------------------- Key: 5159 Medline: 11884032 Authors: Seggerson K;Tang L;Moss EG Title: Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation. Citation: Developmental Biology 243: 215-225 2002 Type: ARTICLE Genes: daf-12 lin-4 lin-14 lin-28 lin-46 Abstract: The heterochronic gene lin-28 of the nematode Caenorhabditis elegans controls the relative timing of diverse developmental events during the animal's larval stages. lin-28 is stage-specifically regulated by two genetic circuits: negatively by the 22-nt RNA lin-4 and positively by the heterochronic gene lin-14. Here, we show that lin-28 is repressed during normal development by a mechanism that acts on its mRNA after translation initiation. We provide evidence that lin-14 inhibits a negative regulation that is independent of the lin-4 RNA and involves the gene daf-12, which encodes a nuclear hormone receptor. The lin-4-independent repression does not affect the initiation of translation on the lin-28 mRNA, and like the lin-4-mediated repression, acts through the gene's 3'-untranlsated region. in addition, we find that lin-4 is not sufficient to cause repression of lin-28 if the lin-4-independent circuit is inhibited. Therefore, the lin-4-independent circuit likely contributes substantially to the down-regulation of lin-28 that occurs during normal development. The role of lin-4 may be to initiate or potentiate the lin-4-independent circuit. We speculate that a parallel lin-4-independent regulatory mechanism regulates the expression of lin-14. ------------------- Key: 5160 Medline: 11830574 Authors: Huang NN;Mootz DE;Walhout AJM;Vidal M;Hunter CP Title: MEX-3 interacting proteins link cell polarity to asymmetric gene expression in Caenorhabditis elegans. Citation: Development 129: 747-759 2002 Type: ARTICLE Genes: mex-3 mex-5 mex-6 pal-1 par-1 par-3 par-4 pos-1 skn-1 spn-4 Abstract: The KH domain protein MEX-3 is central to the temporal and spatial control of PAL-1 expression in the C. elegans early embryo. PAL-1 is a Caudal-like homeodomain protein that is required to specify the fate of posterior blastomeres. While pal-1 mRNA is present throughout the oocyte and early, embryo, PAL-1 protein is expressed only in posterior blastomeres, starting at the four-cell stage. To better understand how PAL-1 expression is regulated temporally and spatially, we have identified MEX-3 interacting proteins (MIPs) and characterized in detail two that are required for the patterning of PAL-1 expression. RNA interference of MEX-6, a CCCH zinc-finger protein, or SPN-4, an RNA recognition motif protein, causes PAL-1 to be expressed in all four blastomeres starting at the four-cell stage. Genetic analysis of the interactions between these mip genes and the par genes, which provide polarity information in the early embryo, defines convergent genetic pathways that regulate MEX-3 stability and activity to control the spatial pattern of PAL-1 expression. These experiments suggest that par-1 and par-4 affect distinct processes. par-1 is required for many aspects of embryonic polarity, including the restriction of MEX-3 and MEX-6 activity to the anterior blastomeres. We find that PAL-1 is not expressed in par-1 mutants, because MEX-3 and MEX6 remain active in the posterior blastomeres. The role of par-4 is less well understood. Our analysis suggests that par-4 is required to inactivate MEX-3 at the four-cell stage. Thus, PAL-1 is not expressed in par-4 mutants because MEX-3 remains active in all blastomeres. We propose that MEX-6 and SPN-4 act with MEX-3 to translate the temporal and spatial information provided by the early acting par genes into the asymmetric expression of the cell fate determinant ------------------- Key: 5161 Medline: Authors: Fedorov A;Saxonov S;Gilbert W Title: Regularities of context-dependent codon bias in eukaryotic genes. Citation: Nucleic Acids Research 30: 1192-1197 2002 Type: ARTICLE Genes: Abstract: Nucleotides surrounding a codon influence the choice of this particular codon from among the group of possible synonymous codons. The strongest influence on codon usage arises from the nucleotide immediately following the codon and is known as the N-1 context. We studied the relative abundance of codons with N-1 contexts in genes from four eukaryotes for which the entire genomes have been sequenced: Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana. For all the studied organisms it was found that 90% of the codons have a statistically significant N-1 context-dependent codon bias. The relative abundance of each codon with an N-1 context was compared with the relative abundance of the same 4mer oligonucleotide in the whole genome. This comparison showed that in about half of. all cases the context-dependent codon bias could not be explained by the sequence composition of the genome. Ranking statistics were applied to compare context-dependent codon biases for codons from different synonymous groups. We found regularities in N-1 context-dependent codon bias with respect to the codon nucleotide composition. Codons with the same nucleotides in the second and third positions and the same N-1 context have a statistically significant ------------------- Key: 5162 Medline: 11972154 Authors: Partridge L;Gems D Title: Mechanisms of ageing: public or private? Citation: Nature Reviews Genetics 3: 165-175 2002 Type: REVIEW Genes: age-1 daf-2 daf-12 daf-16 ins-1 Abstract: Ageing - the decline in survival and fecundity with advancing age - is caused by damage to macromolecules and tissues. Ageing is not a programmed process, in the sense that no genes are known to have evolved specifically to cause damage and ageing. Mechanisms of ageing might therefore not be expected to be as highly conserved between distantly related organisms as are mechanisms of development and metabolism. However, evidence is mounting that modulators of the rate of ageing are conserved over large evolutionary distances. As we discuss in this review, this conservation might stem from mechanisms that match reproductive rate to nutrient supply. ------------------- Key: 5163 Medline: Authors: Tan MW;Ausubel FM Title: Alternative models in microbial pathogens. Citation: Methods in Microbiology 31: 461-475 2002 Type: ARTICLE Genes: aex-2 eat-13 fer-1 glp-4 phm-2 unc-25 Abstract: The struggle for survival is one of the most potent forces that drives evolution. To survive, an organism needs to overcome a variety of biotic and abiotic insults. The most common biotic insult comes in the form of antagonistic interactions between organisms, such as interactions between bacterial pathogens and their hosts. ------------------- Key: 5164 Medline: 11991046 Authors: Burglin TR;Cassata G Title: Loss and gain of domains during evolution of cut superclass homeobox genes. Citation: International Journal of Developmental Biology 46: 115-123 2002 Type: ARTICLE Genes: ceh-21 ceh-38 ceh-39 ceh-41 ceh-44 Abstract: The cut superclass of homeobox genes has been divided into three classes: CUX, ONECUT and SATB. Given the various completed genomes, we have now made a comprehensive survey. We find that there are only two cut domain containing genes in Drosophila, one CUX and one ONECUT type. Caenorhabditis elegans has undergone an expansion of the ONECUT subclass genes and has a gene cluster with three ONECUT class genes, one of which has lost the cut domain. Two of these genes contain a conserved sequence motif, termed OCAM, which also occurs in another gene in C. elegans, this motif seems to be nematode specific. A recently uncovered C. elegans CUX gene has sequence conservation in its amino-terminus with vertebrate CUX proteins. Further, the 5' end of this gene containing the conserved region can undergo alternative splicing to give rise to a protein with a different carboxy-terminus lacking the cut- and homeodomain. This protein is conserved in its entirety with vertebrate genes termed CASP - which are also alternative splice products of the CUX genes - and with plant and fungal genes. The highly divergent SATB genes share a conserved amino terminal domain, COMPASS, with the Drosophila defective proventriculus gene and a C. elegans ORF. These two "COMPASS" family genes encode two highly divergent homeodomains, may be homologues of the SATB genes and thus probably belong to the cut superclass, too. ------------------- Key: 5165 Medline: 11901546 Authors: Saito RM;van den Heuvel S Title: Malignant worms: What cancer research can learn from C. elegans. Citation: Cancer Investigation 20: 264-275 2002 Type: REVIEW Genes: air-1 air-2 akt-1 akt-2 apc-1 bar-1 cdk-4 ced-3 ced-4 ced-9 ces-1 ces-2 cki-1 cyd-1 cye-1 daf-4 daf-7 daf-18 egl-1 hmp-2 let-23 let-60 lin-12 lin-35 lin-45 mdf-1 mdf-2 pop-1 sli-1 sma-4 wrm-1 Abstract: An important goal in cancer research is to identify and understand the molecular changes that transform normal cells into tumor cells. Ultimately, these insights should translate into opportunities for improved diagnosis and treatment. Over the past two decades, cancer researchers have identified an extensive series of genes that contribute to neoplastic transformation when genetically altered. A detailed understanding of how the normal and mutated gene products function in biological processes should expand the possibilities for therapeutic intervention. Revealing how a given gene acts amidst the tens of thousands of other genes in the cell remains a challenging task which usually requires a combination of genetic, molecular, biochemical, and cell biological approaches in a number of model systems. Over the past 25 years, genetic studies in the nematode Caenorhabditis elegans have made important contributions to our ------------------- Key: 5166 Medline: 11535590 Authors: Wu Y;Egerton G;Underwood AP;Sakuda S;Bianco AE Title: Expression and secretion of a larval-specific chitinase (family 18 glycosyl hydrolase) by the infective stages of the parasitic nematode, Onchocerca volvulus. Citation: Journal of Biological Chemistry 276: 42557-42564 2001 Type: ARTICLE Genes: Abstract: A recently reported chitinase gene, expressed in the infective, third-stage (L3) larvae of the human filarial parasite Onchocerca volvulus, belongs to the family 18 glycosyl hydrolases and has been designated Ov-chi-1. The gene product of Ov-chi-1 is chitinolytic. Allosamidin ablates activity of the native enzyme in a dose-dependent manner but did not significantly inhibit the moulting of L3 larvae. Mono-specific antibodies were used to characterize Ov-CHI-1 as a 60-kDa protein expressed almost exclusively in L3 stages. Immunoelectron microscopy showed that Ov-CHI-1 expression is initiated in late L2 larvae and increases markedly in infective, L3 larvae. It is synthesized exclusively in the glandular esophagus and stored within discrete secretory granules. Secretion occurs through de-granulation during post-infective development, and the primary route of transport appears to be via the pseudo-coelom. An orthologue of Ov-chi-1 was detected in Caenorhabditis elegans by BLAST analysis. It is constitutively expressed at a low level and is overexpressed in dauer larvae and embryonated eggs. It is chitinolytic. We conclude that Ov-CHI-1 is a highly stage-specific enzyme that may have a role in infectivity of the parasite, aiding escape from the vector or participating in early post-infective migration and/or development. The identification of an orthologue in C. elegans opens the way for further studies into the biological function(s) of this intriguing parasite product. ------------------- Key: 5167 Medline: 11783006 Authors: Kuchenthal CA;Chen W;Okkema PG Title: Multiple enhancers contribute to expression of the NK-2 homeobox gene ceh-22 in C. elegans pharyngeal muscle. Citation: Genesis 31: 156-166 2001 Type: ARTICLE Genes: ceh-22 Abstract: Gene expression in the pharyngeal muscles of C. elegans is regulated in part by the NK-2 family homeodomain factor CEH-22, which is structurally and functionally related to Drosophila Tinman and the vertebrate Nkx2-5 factors. ceh-22 is expressed exclusively in the pharyngeal muscles and is the earliest gene known to be expressed in this tissue. Here we characterize the ceh-22 promoter region in transgenic C. elegans. A 1.9-kb fragment upstream of ceh-22 is sufficient to regulate reporter gene expression in a pattern identical to the endogenous gene. Within this promoter we identified two transcriptional enhancers and characterized their cell type and temporal specificity. The distal enhancer becomes active in the pharynx near the time that ceh-22 expression initiates; however, it becomes active more broadly later in development. The proximal enhancer becomes active after the onset of ceh-22 expression, but it is active specifically in the ceh-22-expressing pharyngeal muscles. We suggest these enhancers respond to distinct signals that initiate and maintain ceh-22 gene expression. Proximal enhancer activity requires a short segment containing a CEH-22 responsive element, suggesting that CEH-22 autoregulates its own ------------------- Key: 5168 Medline: 11901171 Authors: Ono S;Ono K Title: Tropomyosin inhibits ADF/cofilin-dependent actin filament dynamics. Citation: Journal of Cell Biology 156: 1065-1076 2002 Type: ARTICLE Genes: unc-60 Abstract: Tropomyosin binds to actin filaments and is implicated in stabilization of actin cytoskeleton. We examined biochemical and cell biological properties of Caenorhabditis elegans tropomyosin (CeTM) and obtained evidence that CeTM is antagonistic to ADF/cofilin-dependent actin filament dynamics. We purified CeTM, actin, and UNC-60B (a muscle-specific ADF/cofilin isoform), all of which are derived from C elegans, and showed that CeTM and UNC-60B bound to F-actin in a mutually exclusive manner. CeTM inhibited UNC-60B-induced actin depolymerization and enhancement of actin polymerization. Within isolated native thin filaments, actin and CeTM were detected as major components, whereas UNC-60B was present at a trace amount. Purified UNC-60B was unable to interact with the native thin filaments unless CeTM and other associated proteins were removed by high-salt extraction. Purified CeTM was sufficient to restore the resistance of the salt-extracted filaments from UNC-60B. In muscle cells, CeTM and UNC-60B were localized in different patterns. Suppression of CeTM by RNA interference resulted in disorganized actin filaments and paralyzed worms in wild-type background. However, in an ADF/cofilin mutant background, suppression of CeTM did not worsen actin organization and worm motility. These results suggest that tropomyosin is a physiological inhibitor of ADF/cofilin-dependent actin ------------------- Key: 5169 Medline: 11896189 Authors: Zambrano N;Bimonte M;Arbucci S;Gianni D;Russo T;Bazzicalupo P Title: feh-1 and apl-1, the Caenorhabditis elegans orthologues of mammalian Fe65 and beta-amyloid precursor protein genes, are involved in the same pathway that controls nematode pharyngeal pumping. Citation: Journal of Cell Science 115: 1411-1422 2002 Type: ARTICLE Genes: apl-1 feh-1 Abstract: The multigenic family of mammalian Fe65s encodes three highly similar proteins with the same modular organisation: a WW domain and two phosphotyrosine-binding domains. The PTB2 domain of these proteins binds to the cytosolic domains of the Alzheimer's P-amyloid precursor protein APP and related proteins APLP1 and APLP2, generating a highly redundant system that is hard to dissect by reverse genetics. By searching potential Fe65-like genes in the nematode Caenorhabditis elegans, we identified a single gene, feh-1 ((Fe) under bar 65 (h) under bar omolog-1), encoding a protein with a high sequence similarity to mammalian Fe65s. FEH-1 is also functionally related to mammalian orthologues; in fact its PTB2 domain binds to APL-1, the product of the C. elegans orthologue of APP. Staining with specific antibodies show that the neuromuscular structures of the pharynx are the sites in which FEH-1 is present at highest levels. Expression studies with reporters indicate that the feh-1 gene is also expressed by a subset of the worm neurons. We generated and isolated a deletion allele of feh-1, and the corresponding homozygous mutants arrest as late embryos or as L1 larvae, demonstrating for the first time an essential role for a Fe65-like gene in vivo. The pharynx of homozygous larvae does not contract and the worms cannot feed. Analysis of pharyngeal pumping in heterozygous worms and in feh-1 RNA-interfered worms indicates that dosage of feh-1 function affects the rate of pharyngeal contraction in C. elegans. Interference with apl-1 double-stranded RNA showed a similar effect on pharyngeal pumping, suggesting that FEH-1 and APL-1 are involved in the same pathway. The non-redundant system of the nematode will prove useful for studying the basic biology of the Fe65-APP interaction and the molecular events regulated by this evolutionarily conserved system of interacting proteins. ------------------- Key: 5170 Medline: Authors: Wolkow CA Title: Life span: getting the signal from the nervous system. Citation: Trends in Neurosciences 25: 212-216 2002 Type: REVIEW Genes: age-1 ctl-1 daf-2 daf-16 sod-3 unc-2 unc-16 Abstract: Life span is determined by both environmental and genetic influences. The importance of genes is illustrated by the fact that single gene mutations extend life span in nematodes, fruit flies and mice. Recent reports reveal that the life span of Caenorhabditis elegans is controlled by insulin-like signals from the nervous system. Hormones that control life span have recently been identified in fruit flies and mice. These findings suggest that neuroendocrine pathways could constitute an important determinant of life span across phylogeny. This review examines the evidence for nervous system control of longevity and discusses the implications for popular models for aging. ------------------- Key: 5171 Medline: 11834782 Authors: Winston WM;Molodowitch C;Hunter CP Title: Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1. Citation: Science 295: 2456-2459 2002 Type: ARTICLE Genes: mex-3 mex-6 myo-2 myo-3 rde-1 rde-4 sid-1 sid-2 sid-3 unc-22 unc-54 Abstract: Double-stranded RNA-mediated gene interference (RNAi) in Caenorhabditis elegans systemically inhibits gene expression throughout the organism. To investigate how gene-specific silencing information is transmitted between cells, we constructed a strain that permits visualization of systemic RNAi. We used this strain to identify systemic RNA interference-deficient (sid) loci required to spread gene-silencing information between tissues but not to initiate or maintain an RNAi response. One of these loci, sid-1, encodes a conserved protein with predicted transmembrane domains. SID-1 is expressed in cells sensitive to RNAi, is localized to the cell periphery, and is required cell-autonomously for systemic RNAi. ------------------- Key: 5172 Medline: 11907270 Authors: Lee KK;Starr D;Cohen M;Liu J;Han M;Wilson KL;Gruenbaum Y Title: Lamin-dependent localization of UNC-84, a protein required for nuclear migration in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 13: 892-901 2002 Type: ARTICLE Genes: anc-1 unc-83 unc-84 Abstract: Mutations in the Caenorhabditis elegans unc-84 gene cause defects in nuclear migration and anchoring. We show that endogenous UNC-84 protein colocalizes with Ce-lamin at the nuclear envelope and that the envelope localization of UNC-84 requires Ce-lamin. We also show that during mitosis, UNC-84 remains at the nuclear periphery until late anaphase, similar to known inner nuclear membrane proteins. UNC-84 protein is first detected at the 26-cell stage and thereafter is present in most cells during development and in adults. UNC-84 is properly expressed in unc-83 and anc-1 lines, which have phenotypes similar to unc-84, suggesting that neither the expression nor nuclear envelope localization of UNC-84 depends on UNC-83 or ANC-1 proteins. The envelope localization of Ce-lamin, Ce-emerin, Ce-MAN1, and nucleoporins are unaffected by the loss of UNC-84. UNC-84 is not required for centrosome attachment to the nucleus because centrosomes are localized normally in unc-84 hyp7 cells despite a nuclear migration defect. Models for UNC-84 localization are discussed. ------------------- Key: 5173 Medline: 11914278 Authors: Hagstrom KA;Holmes VF;Cozzarelli NR;Meyer BJ Title: C. elegans condensin promotes mitotic chromosome architecture, centromere organization, and sister chromatid segregation during mitosis and meiosis. Citation: Genes & Development 16: 729-742 2002 Type: ARTICLE Genes: air-2 dpy-27 hcp-3 him-10 mix-1 smc-2 smc-4 Abstract: Chromosome segregation and X-chromosome gene regulation in Caenorhabditis elegans share the component MIX-1, a mitotic protein that also represses X-linked genes during dosage compensation. MIX-1 achieves its dual roles through interactions with different protein partners. To repress gene expression, MIX-1 acts in an X-chromosome complex that resembles the mitotic condensin complex yet lacks chromosome segregation function. Here we show that MIX-1 interacts with a mitotic condensin subunit, SMC-4, to achieve chromosome segregation. The SMC-4/MIX-1 complex positively supercoils DNA in vitro and is required for mitotic chromosome structure and segregation in vivo. Thus, C. elegans has two condensin complexes, one conserved for mitosis and another specialized for gene regulation. SMC-4 and MIX-1 colocalize with centromere proteins on condensed mitotic chromosomes and are required for the restricted orientation of centromeres toward spindle poles. This cell cycle-dependent localization requires AIR-2/AuroraB kinase. Depletion of SMC-4/MIX-1 causes aberrant mitotic chromosome structure and segregation, but not dramatic decondensation at metaphase. Moreover, SMC-4/MIX-1 depletion disrupts sister chromatid segregation during meiosis II but not homologous chromosome segregation during meiosis 1, although both processes require chromosome condensation. These results imply that condensin is not simply required for compaction, but plays a more complex role in chromosome architecture that is essential for mitotic and meiotic sister chromatid segregation. ------------------- Key: 5174 Medline: 11871396 Authors: Knight CG;Patel MN;Azevedo RBR;Leroi AM Title: A novel mode of ecdysozoan growth in Caenorhabditis Citation: Evolution & Development 4: 16-27 2002 Type: ARTICLE Genes: Abstract: Whereas growth in many ecdysozoa is associated with only molting, larval growth in nematodes, specifically Caenorhabditis elegans, is thought to be continuous and exponential. However, this has never been closely investigated. Here we report several detailed studies of growth in wildtype and dwarf C. elegans strains. We find that apparent exponential growth between hatching and adulthood comprises a series of linear phases, one per larval stage, with the linear growth rate increasing at successive molts. Although most structures grow continuously, the buccal cavity does not; instead, it grows saltationally at molts, like arthropod structures. We speculate that these saltational changes in mouth size permit changes in growth rate and that molting exists in nematodes to facilitate rapid growth. We study the cellular basis of this growth in the hypodermis. At each larval stage, lateral seam cells produce daughters that fuse with hyp7, a syncytium covering most of the worm. We find that seam cells and fusing daughter cells obtain larger sizes in successive molts. The total seam cell volume remains constant relative to the size of the worm. However, fusing daughter cells contributes only a very small amount directly to hypodermal growth, suggesting that most hyp7 growth must be intrinsic. Thus, dwarfism mutations studied principally act via adult syncytial growth, with cell size being near normal in both dbl-1 and dpy-2 mutant worms. We speculate that the main function of seam cell proliferation may be to supply the hypodermis with additional genomes for the purpose of growth. ------------------- Key: 5175 Medline: 11895430 Authors: Grisoni K;Gieseler K;Segalat L Title: Dystrobrevin requires a dystrophin-binding domain to function in Caenorhabditis elegans. Citation: European Journal of Biochemistry 269: 1607-1612 2002 Type: ARTICLE Genes: dyb-1 dys-1 Abstract: Dystrobrevin is one of the intracellular components of the transmembrane dystrophin-glycoprotein complex (DGC). The functional role of this complex in normal and pathological situations has not yet been clearly established. Dystrobrevin disappears from the muscle membrane in Duchenne muscular dystrophy (DMD), which results from dystrophin mutations, as well as in limb girdle muscular dystrophies (LGMD), which results from mutations affecting other members of the DGC complex. These findings therefore suggest that dystrobrevin may play a pivotal role in the progression of these clinically related diseases. In this study, we used the Caenorhabditis elegans model to address the question of the relationship between dystrobrevin binding to dystrophin and dystrobrevin function. Deletions of the dystrobrevin protein were performed and the ability of the mutated forms to bind to dystrophin was tested both in vitro and in a two-hybrid assay, as well as their ability to rescue dystrobrevin (dyb-1) mutations in C. elegans. The deletions affecting the second helix of the Dyb-1 coiled-coil domain abolished the binding of dystrobrevin to dystrophin both in vitro and in the two-hybrid assay. These deletions also abolished the rescuing activity of a functional transgene in vivo. These results are consistent with a model according to which dystrobrevin must bind to dystrophin to be able to function ------------------- Key: 5176 Medline: 11850401 Authors: Couteau F;Guerry F;Muller F;Palladino F Title: A heterochromatin protein 1 homologue in Caenorhabditis elegans acts in germline and vulval development. Citation: EMBO Reports 3: 235-241 2002 Type: ARTICLE Genes: hpl-1 hpl-2 let-23 lin-8 lin-9 lin-15 lin-35 lin-36 lin-37 lin-38 lin-53 Abstract: Proteins of the highly conserved heterochromatin protein 1 (HP1) family have been found to function in the dynamic organization of nuclear architecture and in gene regulation throughout the eukaryotic kingdom. In addition to being key players in heterochromatin-mediated gene silencing, HP1 proteins may also contribute to the transcriptional repression of euchromatic genes via the recruitment to specific promoters. To investigate the role played by these different activities in specific developmental pathways, we identified HP1 homologues in the genome of Caenorhabditis elegans and used RNA-mediated interference to study their function. We show that one of the homologues, HPL-2, is required for the formation of a functional germline and for the development of the vulva by acting in an Rb-related pathway. We suggest that, by acting as repressors of gene expression, HP1 proteins may fulfil specific functions in both somatic and germline differentiation processes throughout development. ------------------- Key: 5177 Medline: 11874914 Authors: Ko FCF;Chow KL Title: A novel thioredoxin-like protein encoded by the C. elegans dpy-11 gene is required for body and sensory organ morphogenesis. Citation: Development 129: 1185-1194 2002 Type: ARTICLE Genes: dpy-11 Abstract: Sensory ray morphogenesis in C. elegans requires active cellular interaction regulated by multiple genetic activities. We report here the cloning of one of these genes, dpy-11, which encodes a membrane-associated thioredoxin-like protein. The DPY-11 protein is made exclusively in the hypodermis and resides in the cytoplasmic compartment. Whereas the TRX domain of DPY-11 displays a catalytic activity in vitro, mapping of lesions in different mutant alleles and functional analysis of deletion transgenes reveal that both this enzymatic activity and transmembrane topology are essential for determining body shape and ray morphology. Based on the abnormal features in both the expressing and non-expressing ray cells, we propose that the DPY-11 is required in the hypodermis for modification of its substrates. In turn, ray cell interaction and the whole morphogenetic process can be modulated by these substrate molecules. ------------------- Key: 5178 Medline: 11909538 Authors: Bamba C;Bobinnec Y;Fukuda M;Nishida E Title: The GTPase Ran regulates chromosome positioning and nuclear envelope assembly in vivo. Citation: Current Biology 12: 503-507 2002 Type: ARTICLE Genes: Abstract: The GTPase Ran is known to regulate transport of proteins across the nuclear envelope [1, 2]. Recently, Ran has been shown to promote microtubule polymerization and spindle assembly around chromatin in Xenopus mitotic extracts [3-7] and to stimulate nuclear envelope assembly in Xenopus [8, 9] or HeLa cell extracts [10]. However, these in vitro findings have not been tested in living cells and do not necessarily describe the generalized model of Ran functions [11-13]. Here we present several lines of evidence that Ran is indispensable for correct chromosome positioning and nuclear envelope assembly in C. elegans. Embryos deprived of Ran by RNAi showed metaphase chromosome misalignment and aberrant chromosome segregation, while astral microtubules seemed unaffected. Depletion of RCC1 or RanGAP by RNAi resulted in essentially the same defects. The immunofluorescent staining showed that Ran localizes to kinetochore regions of metaphase and anaphase chromosomes, suggesting the role of Ran in linking chromosomes to kinetochore microtubules. Ran was shown to localize to the nuclear envelope at telophase and during interphase in early embryos, and the depletion of Ran resulted in failure of nuclear envelope assembly. Thus, Ran is crucially involved in chromosome positioning and nuclear envelope ------------------- Key: 5179 Medline: 11906745 Authors: Baumeister R;Ge LM Title: The worm in us - Caenorhabditis elegans as a model of human disease. Citation: Trends in Biotechnology 20: 147-148 2002 Type: REVIEW Genes: sel-12 Abstract: In the post-genomic era, the identification and validation of potential human disease-causing or disease-associated genes are of major importance. Model organisms have an essential role in this process and might help to make these genes and their products amenable to pharmacological intervention. ------------------- Key: 5181 Medline: 11826060 Authors: Franks CJ;Pemberton D;Vinogradova I;Cook A;Walker RJ;Holden-Dye L Title: Ionic basis of the resting membrane potential and action potential in the pharyngeal muscle of Caenorhabditis elegans. Citation: Journal of Neurophysiology 87: 954-961 2002 Type: ARTICLE Genes: Abstract: The pharynx of C. elegans is a rhythmically active muscle that pumps bacteria into the gut of the nematode. This activity is maintained by action potentials, which qualitatively bear a resemblance to vertebrate cardiac action potentials. Here, the ionic basis of the resting membrane potential and pharyngeal action potential has been characterized using intracellular recording techniques. The resting membrane potential is largely determined by a K+ permeability, and a ouabain-sensitive, electrogenic pump. As previously suggested, the action potential is at least partly dependent on voltage-gated Ca2+ channels, as the amplitude was increased as extracellular Ca2+ was increased, and decreased by L-type Ca2+ channel blockers verapamil and nifedipine. Barium caused a marked prolongation of action potential duration, suggesting that a calcium-activated K+ current may contribute to repolarization. Most notably, however, we found that action potentials were abolished in the absence of external Na+. This may be due, at least in part, to a Na+-dependent pacemaker potential. In addition, the persistence of action potentials in nominally free Ca2+, the inhibition by Na+ channel blockers procaine and quinidine, and the increase in action potential frequency caused by veratridine, a toxin that alters activation of voltage-gated Na+ channels, point to the involvement of a voltage-gated Na+ current. Voltage-clamp analysis is required for detailed characterization of this current, and this is in progress. Nonetheless, these observations are quite surprising in view of the lack of any obvious candidate genes for voltage-gated Na+ channels in the C. elegans genome. It would therefore be informative to re-evaluate the data from these homology searches, with the aim of identifying the gene(s) conferring this Na+, quinidine, and veratridine ------------------- Key: 5182 Medline: Authors: Holt SJ;Cress WA;Van Staden J Title: Evidence for dynamic alteration in histone gene clusters of Caenorhabditis elegans: a topoisomerase II connection. Citation: Genetical Research 79: 11-22 2002 Type: ARTICLE Genes: his-9 his-10 his-11 his-12 his-13 his-14 his-15 his-16 his-17 his-18 his-19 his-20 his-21 his-22 his-27 his-28 his-29 his-30 his-31 his-32 his-33 his-34 Abstract: Chromatin integrity is maintained throughout the cell cycle through repair mechanisms and intrinsically by the ordered packaging of DNA in association with histone proteins; however, aberrant rearrangements within and between chromosomes do occur. The role of the nuclear matrix protein topoisomerase II (TopoII) in generating chromosome breakpoints has been a focus of recent investigations. TopoII preferentially binds in vitro to scaffold-associated regions (SARs) and is involved in many DNA processing activities that require chromosome untangling. SARs, biochemically defined DNA elements rich in A + T, have been proposed to serve as structural boundaries for chromatin loops and to delineate functional domains. In our investigation of gene compartmentalization in a eukaryotic genome, SAR-associated nucleotide motifs from Drosophila were mapped in the regions of three histone gene clusters in an in silico analysis of the genome of Caenorhabditis elegans. Sites with similarity to the 15 bp consensus for TopoII cleavage were found predominantly in A + T enriched intergenic regions. Reiteration of sites matching the TopoII core consensus led to the identification of a novel core histone gene on chromosome IV and provided evidence for duplication and inversion in each of the three histone gene clusters. Breakpoint analysis of DNA flanking reiterated regions revealed potential sites for TopoII cleavage and a base composition phenomenon suggestive of a trigger for inversion events. ------------------- Key: 5183 Medline: 11942615 Authors: Bowerman B Title: Cytokinesis in the C. elegans embryo: Regulating contractile forces and a late role for the central spindle. Citation: Cell Structure & Function 26: 603-607 2001 Type: REVIEW Genes: cyk-1 cyk-4 mlc-4 nmy-2 par-1 pfn-1 zen-4 Abstract: Genetic and molecular studies in the nematode Caenorhabditis elegans have identified multiple essential pathways that regulate and execute cytokinesis in early embryonic cells. These pathways influence both the microfilament cytoskeleton and the microtubule cytoskeleton. Microfilaments are enriched throughout the Cell cortex at all times during the cell cycle in embryonic cells. Cortical microfilaments are required for multiple processes in embryonic cells, including polar body extrusion during meiosis, anterior-posterior axis specification by the sperm-donated microtubule-organizing center, and cytokinesis during mitosis. In addition to contractile apparatus proteins that are required positively for cleavage furrow ingression, the Nedd8 ubiquitin-like protein modification pathway negatively regulates contractile forces outside the cleavage furrow during cytokinesis. Another pathway that acts positively during cytokinesis involves the mitotic spindle. The central spindle, where anti-parallel non-kinetochore microtubules overlap and are cross-linked, is required for a late step in cytokinesis, and other pathway(s) involved in membrane addition during cytokinesis may also require the central spindle. The amenability of C. elegans to classical genetics, the case of reducing gene function with RNA interference, the completion of the genome sequence, and the availability of transgenic GFP fusion proteins that render the cytoskeleton fluorescent, all serve to make the early worm embryo an especially promising system for further advances in the identification of cytokinesis ------------------- Key: 5184 Medline: 11890665 Authors: Uchida Y;Ogata M;Mori Y;Oh-hora M;Hatano N;Hamaoka T Title: Localization of PTP-FERM in Nerve Processes through its FERM domain. Citation: Biochemical and Biophysical Research Communications 292: 13-19 2002 Type: ARTICLE Genes: Abstract: PTP-FERM is a protein tyrosine phosphatase (PTP) of Caenorhabditis elegans containing a FERM domain and a PDZ domain. Here we report the characterization of PTP-FERM and the essential role of its FERM domain in the localization of PTP-FERM in the worm. There are at least three alternatively spliced PTP-FERM isoforms, all of which contain a band 4.1/FERM domain, a PDZ domain, and a catalytic domain. PTP-FERM possessed phosphatase activity. PTP-FERM was expressed predominantly in neurons in the nerve ring and the ventral nerve cord. PTP-FERM was found in the nerve processes and to be enriched in the perimembrane region. Studies using various deletion mutants revealed that the FERM domain was essential and sufficient for the subcellular localization. These results suggest the essential role of the FERM domain in the function of PTP-FERM in the neurons of C. elegans. ------------------- Key: 5185 Medline: Authors: Warren CE;Krizus A;Partridge EA;Dennis JW Title: Caenorhabditis elegans gly-1, a core 2/I N-acetylglucosaminyltransferase homologue, is a glucosyltransferase. Citation: Glycobiology 12: 8G-9G 2002 Type: ADDEND Genes: gly-1 gly-18 Abstract: We recently reported the initial characterisation of a family of 6 C. elegans genes that were homologous to mammalian core 2 N-acetylglucosaminyltransferases (Warren et al, 2001). ------------------- Key: 5186 Medline: 11901115 Authors: Stewart AD;Phillips PC Title: Selection and maintenance of androdioecy in Caenorhabditis elegans. Citation: Genetics 160: 975-982 2002 Type: ARTICLE Genes: fog-2 Abstract: Caenorhabditis elegans is an androdioecious nematode composed of selfing hermaphrodites and rare males. A model of male maintenance demonstrates that selfing rates in hermaphrodites cannot be too high or else the frequency of males will be driven down to the rate of spontaneous nondisjunction of the X chromosome. After their outcrossing ability is assessed, males are found to skirt the frequency range in which they would be maintained. When male maintenance is directly assessed by elevating male frequency and observing the frequency change through time, males are gradually eliminated from the population. Males, therefore, appear to reproduce at a rate just below that necessary for them to be maintained. Populations polymorphic for a mutation (fog-2) that effectively changes hermaphrodites into females demonstrate that there is strong selection against dioecy. Factors such as variation in male mating ability and inbreeding depression could potentially lead to the long-term maintenance of males. ------------------- Key: 5187 Medline: 11901116 Authors: Chasnov JR;Chow KL Title: Why are there males in the hermaphroditic species Caenorhabditis elegans? Citation: Genetics 160: 983-994 2002 Type: ARTICLE Genes: him-8 Abstract: The free-living nematode worm Caenorhabditis elegans reproduces primarily as a self-fertilizing hermaphrodite, yet. males are maintained in wild-type populations at low frequency. To determine the role of males in C. elegans, we develop a mathematical model for the genetic system of hermaphrodites that can either self-fertilize or be fertilized by males and we perform laboratory observations and experiments on both C. elegans and a related dioecious species C. remanei. We show that the mating efficiency of C. elegans is poor compared to a dioecious species and that C. elegans males are more attracted to C. remanei females than the), arc to their conspecific hermaphrodites. We postulate that a genetic mutation occurred during the evolution of C. elegans hermaphrodites, resulting in the loss of an attracting sex pheromone present in the ancestor of both C. elegans and C. remanei. Our findings suggest that males are maintained in C. elegans because of the particular genetic system inherited from its dioecious ancestor and because of nonadaptive spontaneous nondisjunction of sex chromosomes, which occurs during meiosis in the hermaphrodite. A theoretical argument shows that the low frequency of male mating observed in C. elegans can support male-specific genes against mutational degeneration. This results in the continuing presence of functional males in a 99.9% hermaphroditic species in which outcrossing is disadvantageous to hermaphrodites. ------------------- Key: 5188 Medline: 11880358 Authors: Zhao X;Yang Y;Fitch DA;Herman MA Title: TLP-1 is an asymmetric cell fate determinant that responds to Wnt signals and controls male tail tip morphogenesis in C. elegans. Citation: Development 129: 1497-1508 2002 Type: ARTICLE Genes: lin-17 lin-44 tlp-1 nDf27 sDf21 sDf23 Abstract: We have isolated mutations defining a new gene, tlp-1, that affect asymmetric cell fates and morphogenesis during the development of the C. elegans tail. tlp-1 mutations cause defects in the specification of asymmetric cell fates in the descendants of the T blast cell, whose polarity is controlled by Wnt signaling and cause abnormal male tail development leading to the formation of a posterior protrusion reminiscent of `leptoderan', or pointy tailed, nematode species. In wild-type C. elegans males, which have a 'peloderan' or rounded tail, retraction oaf the tail tip hypodermis involves a temporally ordered set of cell fusions and changes in cell shape that appear to be heterochronically delayed in tlp-1 males, suggesting that subtle changes in these events can bring about evolutionary changes in morphology. tlp-1 encodes a C2H2 zinc-finger protein that is a member of the Sp family of transcription factors. A TLP-1::GFP fusion protein is expressed in the nuclei of many cells during early embryogenesis and then becomes restricted primarily to posterior cells. At hatching, it is expressed in several head neurons, the posterior intestine cells, tail hypodermal cells, the T cells and specific T-cell descendents in a pattern that suggests TLP-1 may be asymmetrically expressed during the divisions of the T cell lineage. Furthermore, the asymmetry of TLP-1 expression and function appears to be controlled by Wnt signals that control T cell polarity. These results suggest that tlp-1 encodes a transcription factor required for cellular asymmetry that functions downstream of Wnt signals that control cell polarity, as well as in cell fusion and patterning in the C. elegans tail. ------------------- Key: 5189 Medline: 11796737 Authors: Kuno K;Baba C;Asaka A;Matsushima C;Matsushima K;Hosono R Title: The Caenorhabditis elegans ADAMTS family gene adt-1 is necessary for morphogenesis of the male copulatory organs. Citation: Journal of Biological Chemistry 277: 12228-12236 2002 Type: ARTICLE Genes: adt-1 gon-1 Abstract: Remodeling of the extracellular matrix (EM is pivotal for various biological processes, including organ morphology and development. The Caenorhabditis elegans male tail has male-specific copulatory organs, the rays and the fan. Ray morphogenesis, which involves a rapid remodeling of the ECM, is an important model of morphogenesis, although its mechanism is poorly understood. ADAMTS (a disintegrin-like and metalloproteinase with thrombospondin type I motifs) is a novel metalloproteinase family that is thought to be an important regulator for ECM remodeling during development and pathological states. We report here that a new C. elegans ADAMTS family gene, adt-1, plays an important regulatory role in ray morphogenesis. Inactivation of the adt-1 gene resulted in morphological changes in the rays as well as the appearance of abnormal protuberances around the rays. In addition, mating ability was remarkably impaired in adt-1 deletion mutant males. Furthermore, we found that the green fluorescent protein reporter driven by the adt-1 promoter was specifically expressed throughout the rays in the male tail. We hypothesize that ADT-1 controls the ray extension process via remodeling of the ECM in the cuticle. ------------------- Key: 5190 Medline: 11904372 Authors: Hersh BM;Hartwieg E;Horvitz HR Title: The Caenorhabditis elegans mucolipin-like gene cup-5 is essential for viability and regulates lysosomes in multiple cell types. Citation: Proceedings of the National Academy of Sciences USA 99: 4355-4360 2002 Type: ARTICLE Genes: ced-1 ced-3 ced-4 ced-9 cup-5 sem-4 nDf16 Abstract: The misregulation of programmed cell death, or apoptosis, contributes to the pathogenesis of many diseases. We used Nomarski microscopy to screen for mutants containing refractile cell corpses in a C: elegans strain in which all programmed cell death is blocked and such corpses are absent. We isolated a mutant strain that accumulates refractile bodies resembling irregular cell corpses. We rescued this mutant phenotype with the C. elegans mucolipidosis type IV (ML-IV) homolog, the recently identified cup-5 (coelomocyte-uptake defective) gene. ML-IV is a human autosomal recessive lysosomal storage disease characterized by psychomotor retardation and ophthalmological abnormalities. Our null mutations in cup-5 cause maternal-effect lethality. In addition, cup-5 mutants contain excess lysosomes in many and possibly all cell types and contain lamellar structures similar to those observed in ML-IV cell lines. The human ML-IV gene is capable of rescuing both the maternal-effect lethality and the lysosome-accumulation abnormality of cup-5 mutants. cup-5 mutants seem to contain excess apoptotic cells as detected by staining with terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling. We suggest that the increased apoptosis seen in cup-5 mutants is a secondary consequence of the lysosomal defect, and that abnormalities in apoptosis may be associated with human lysosomal storage disorders. ------------------- Key: 5191 Medline: 11962590 Authors: Hobert O Title: PCR fusion-based approach to create reporter gene constructs for expression analysis in transgenic C. Citation: Biotechniques 32: 728-730 2002 Type: ARTICLE Genes: Abstract: In the nematode Caenorhabditis elegans, gene expression patterns are most often determined by generating a fusion of the promoter gene under study to a reporter gene such as lacZ or gfp. ------------------- Key: 5192 Medline: 11932009 Authors: Pasquinelli AE Title: MicroRNAs: deviants no longer. Citation: Trends in Genetics 18: 171-173 2002 Type: REVIEW Genes: alg-1 alg-2 let-7 lin-4 lin-14 lin-41 rde-1 Abstract: Almost ten years ago, the Ambros laboratory made the extraordinary discovery that a gene essential for development in Caenorhabditis elegans encoded a 22-nucleotide, untranslated RNA. Further genetic studies in this nematode revealed the existence of a second tiny RNA gene that turned out to be conserved in animals as diverse as flies and humans. Now, the Ambros, Bartel and Tuschl laboratories have proven that those odd RNAs were just the first examples of a large family of RNAs, termed microRNAs (miRNAs). Although untranslated RNA genes, such as transfer RNAs and ribosomal RNAs, perform essential housekeeping roles in all living organisms, growing numbers of other RNAs, some widely conserved across phyla and others limited to certain species, are being uncovered and shown to fulfill specific duties. The discovery of miRNAs establishes a new class of regulatory RNAs and highlights the existence of unexpected RNA genes that, although ancient, are not extinct. ------------------- Key: 5193 Medline: 11904378 Authors: Dudley NR;Labbe JC;Goldstein B Title: Using RNA interference to identify genes required for RNA interference. Citation: Proceedings of the National Academy of Sciences USA 99: 4191-4196 2002 Type: ARTICLE Genes: dcr-1 gfl-1 glp-1 hmp-2 mes-2 mes-3 mes-4 mes-6 mom-2 mut-7 par-2 pos-1 unc-22 unc-54 zfp-1 Abstract: RNA interference (RNAi) is a phenomenon in which doublestranded RNA (dsRNA) silences endogenous gene expression. By injecting pools of dsRNAs into Caenorhabditis elegans, we identified a dsRNA that acts as a potent suppressor of the RNAi mechanism. We have used coinjection of dsRNAs to identify four additional candidates for genes involved in the RNAi mechanism in C. elegans. Three of the genes are C. elegans mes genes, some of which encode homologs of the Drosophila chromatin-binding Polycomb-group proteins. We have used loss-of-function mutants to confirm a role for mes-3, -4, and -6 in RNAL Interestingly, introducing very low levels of dsRNA can bypass a requirement for these genes in RNAL The finding that genes predicted to encode proteins that associate with chromatin are involved in RNAi in C. elegans raises the possibility that chromatin may play a role in RNAi in animals, as it does in plants. ------------------- Key: 5194 Medline: 11922622 Authors: Tsuboi D;Qadota H;Kasuya K;Amano M;Kaibuchi K Title: Isolation of the interacting molecules with GEX-3 by a novel functional screening. Citation: Biochemical and Biophysical Research Communications 292: 697-701 2002 Type: ARTICLE Genes: dyn-1 emb-9 gei-1 gei-2 gei-3 gei-4 gei-5 gei-6 gei-7 gei-8 gei-9 gei-10 gei-11 gei-12 gei-13 gei-14 gei-15 gei-16 gei-17 gei-18 gei-19 gei-20 gei-21 gei-22 gex-2 gex-3 lin-13 lin-26 puf-6 zpf-1 Abstract: To screen for important molecules that interact with a gene of interest in Caenorhabditis elegans (C. elegans), we established a novel functional screening system using the yeast two-hybrid system with the RNA interference technique. Our screening system makes it possible to identify the molecular machinery involved in the function of a gene of interest starting with the cDNA of this gene. As a model case, we examined the molecular machinery involved in the function of GEX-3, an essential factor of tissue morphogenesis. We identified many interacting molecules by yeast two-hybrid screening and could detect some functional interactions using this novel functional ------------------- Key: 5195 Medline: Authors: Kuwabara PE;Labouesse M Title: The sterol-sensing domain: multiple families, a unique Citation: Trends in Genetics 18: 193-201 2002 Type: REVIEW Genes: che-14 lrp-1 npc-1 npc-2 ptc-1 Abstract: The 'sterol-sensing domain' (SSD) is conserved across phyla and is present in several membrane proteins, such as Patched (a Hedgehog receptor) and NPC-1 (the protein defective in Niemann-Pick type C1 disease). The role of the SSD is perhaps best understood from the standpoint of its involvement in cholesterol homeostasis. This article discusses how the SSD appears to function as a regulatory domain involved in linking vesicle trafficking and protein localization with such varied processes as cholesterol homeostasis, cell signalling and cytokinesis. ------------------- Key: 5196 Medline: Authors: Su HP;Nakada-Tsukui K;Tosello-Trampont AC;Li Y;Bu G;Henson PM;Ravichandran KS Title: Interaction of CED-6/GULP, an adapter protein involved in engulfment of apoptotic cells with CED-1 and CD91/low density kipoprotein receptor-related protein (LRP). Citation: Journal of Biological Chemistry 277: 11772-11779 2002 Type: ARTICLE Genes: ced-1 ced-2 ced-5 ced-6 ced-7 ced-10 ced-12 Abstract: The prompt clearance of cells undergoing apoptosis is critical during embryonic development, normal tissue turnover, as well as inflammation and autoimmunity. The molecular details of the engulfment of apoptotic cells are not fully understood. ced-6 and its human homologue gulp, encode an adapter protein, whose function in engulfment is highly evolutionarily conserved; however, the upstream and downstream components of CED-6 mediated signaling are not known. Recently, ced-1 has been shown to encode a transmembrane protein on phagocytic cells, with two functional sequence motifs in its cytoplasmic tail that are important for engulfment. In this study, using a combination of biochemical approaches and yeast two-hybrid analysis, we present evidence for a physical interaction between GULP/CED-6 and one of the two motifs (NPXY motif) in the cytoplasmic tail of CED-1. The phosphotyrosine binding domain of GULP was necessary and sufficient for this interaction. Since the precise mammalian homologue of CED-1 is not known, we undertook a database search for human proteins that contain the motifs shown to be important for CED-6 function and identified CD91/LRP (low density lipoprotein receptor-related protein) as one candidate. Interestingly, recent studies have also identified CD91/LRP as a receptor involved in the phagocytosis of apoptotic cells in mammals. The GULP phosphotyrosine binding domain was able to specifically interact with one specific NPXY motif in the CD91 cytoplasmic tail. During these studies we have also identified the mouse GULP sequence. These studies suggest a physical link between CED-1 or CD91/LRP and the adapter protein CED-6/GULP during engulfment of apoptotic cells and further elucidate the pathway suggested by the genetic ------------------- Key: 5197 Medline: 11849636 Authors: Beall MJ;Pearce EJ Title: Transforming growth factor-beta and insulin-like signalling pathways in parasitic helminths. Citation: International Journal for Parasitology 32: 399-404 2002 Type: REVIEW Genes: age-1 akt-1 akt-2 daf-1 daf-2 daf-3 daf-4 daf-7 daf-8 daf-14 daf-16 dbl-1 pdk-1 sma-2 sma-3 sma-4 sma-6 Abstract: The signal transduction pathways involved in regulating developmental arrest in the free-living nematode, Caenorhabditis elegans, are fairly well characterised. However, much less is known about how these processes may influence the developmental timing and maturation in helminth parasites. Here, we provide an overview of two signalling pathways implicated in the regulation of dauer larva formation in C. elegans, the insulin-like signalling pathway and the transforming growth factor-beta pathway, and explore what is known about these signalling pathways in a variety of parasitic helminths. Understanding the differences about how these pathways are affected by environmental cues in free-living versus parasitic species of helminths may provide insights into novel mechanisms for the control or prevention of helminth-induced disease. ------------------- Key: 5198 Medline: 11702779 Authors: Detwiler MR;Reuben M;Li X;Rogers E;Lin R Title: Two zinc finger proteins, OMA-1 and OMA-2, are redundantly required for oocyte maturation in C. elegans. Citation: Developmental Cell 1: 187-199 2001 Type: ARTICLE Genes: air-2 gem-3 glp-4 lin-3 mex-1 mex-5 mex-6 oma-1 oma-2 pie-1 pos-1 wee-1.3 Abstract: Oocytes are released from meiotic prophase I arrest through a process termed oocyte maturation. We present here a genetic characterization of oocyte maturation, using C. elegans as a model system. We show that two TIS11 zinc finger-containing proteins, OMA-1 and OMA-2, express specifically in maturing oocytes and function redundantly in oocyte maturation. Oocytes in oma-1;oma-2 mutants initiate but do not complete maturation and arrest at a defined point in prophase I. Two maturation signal-induced molecular events, including the maintenance of activated MAP kinase, do not occur in Oma oocytes. The Oma prophase arrest is released by inactivation of a MYT-1-like kinase, suggesting that OMA-1 and OMA-2 function upstream of MYT-1 as positive regulators of prophase progression during meiotic maturation. ------------------- Key: 5199 Medline: 11702948 Authors: Gonczy P;Bellanger JM;Kirkham M;Pozniakowski A;Baumer K;Phillips JB;Hyman AA Title: zyg-8, a gene required for spindle positioning in C. elegans, encodes a Doublecortin-related kinase that promotes microtubule assembly. Citation: Developmental Cell 1: 363-375 2001 Type: ARTICLE Genes: apo-1 par-1 par-2 par-3 pgl-1 zyg-8 zyg-9 tDf5 Abstract: Proper spindle positioning is essential for spatial control of cell division. Here, we show that zyg-8 plays a key role in spindle positioning during asymmetric division of one-cell stage C. elegans embryos by promoting microtubule assembly during anaphase. ZYG-8 harbors a kinase domain and a domain related to Doublecortin, a microtubule-associated protein (MAP) affected in patients with neuronal migration disorders. Sequencing of zyg-8 mutant alleles demonstrates that both domains are essential for function. ZYG-8 binds to microtubules in vitro, colocalizes with microtubules in vivo, and promotes stabilization of microtubules to drug or cold depolymerization in COS-7 cells. Our findings demonstrate that ZYG-8 is a MAP crucial for proper spindle positioning in C. elegans, and indicate that the function of the Doublecortin domain in modulating microtubule dynamics is conserved across metazoan evolution. ------------------- Key: 5200 Medline: 11703939 Authors: Zhou Z;Caron E;Hartwieg E;Hall A;Horvitz HR Title: The C. elegans PH domain protein CED-12 regulates cytoskeletal reorganization via a Rho/Rac GTPase signaling pathway. Citation: Developmental Cell 1: 477-489 2001 Type: ARTICLE Genes: ced-1 ced-2 ced-5 ced-6 ced-7 ced-10 ced-12 qDf5 qDf7 qDf8 qDf9 Abstract: The C. elegans gene ced-12 functions in the engulfment of apoptotic cells and in cell migration, acting in a signaling pathway with ced-2 Crkll, ced-5 DOCK180, and ced-10 Rac GTPase and acting upstream of ced-10 Rac. ced-12 encodes a protein with a pleckstrin homology (PH) domain and an SH3 binding motif, both of which are important for ced-12 function. CED-12 acts in engulfing cells for cell corpse engulfment and interacts physically with CED-5, which contains an SH3 domain. CED-12 has Drosophila and human counterparts. Expression of CED-12 and its counterparts in murine Swiss 3T3 fibroblasts induced Rho GTPase-dependent formation of actin filament bundles. We propose that through interactions with membranes and with a CED-2/CED-5 protein complex, CED-12 regulates Rho/Rac GTPase signaling and leads to cytoskeletal reorganization by an evolutionarily conserved mechanism. ------------------- Key: 5201 Medline: 11703937 Authors: Thummel CS Title: Molecular mechanisms of developmental timing in C. elegans and Drosophila. Citation: Developmental Cell 1: 453-465 2001 Type: REVIEW Genes: col-19 daf-9 daf-12 let-7 lin-4 lin-14 lin-28 lin-29 lin-41 lin-42 lrp-1 nhr-23 nhr-25 Abstract: Characterization of the heterochronic genes has provided a strong foundation for understanding the molecular mechanisms of developmental timing in C. elegans. In apparent contrast, studies of developmental timing in Drosophila have demonstrated a central role for gene cascades triggered by the steroid hormone ecdysone. In this review, I survey the molecular mechanisms of developmental timing in C. elegans and Drosophila and outline how common regulatory pathways are beginning to emerge. ------------------- Key: 5202 Medline: 11703935 Authors: Bonini NM Title: Stores to die for. Citation: Developmental Cell 1: 447-448 2001 Type: REVIEW Genes: ced-3 mec-4 Abstract: Genes that regulate apoptosis are well defined. In contrast, it has not been clear what genes are central to necrotic cell loss. In the September 27th issue of Neuron, Xu et al. (2001) report a critical role for genes that regulate storage and release of Ca2+ from the endoplasmic reticulum as important to necrotic-like cellular degeneration in Caenorhabditis elegans. ------------------- Key: 5203 Medline: 11703092 Authors: Berman K;McKay J;Avery L;Cobb M Title: Isolation and characterization of pmk-(1-3): Three p38 homologs in Caenorhabditis elegans. Citation: Molecular Cell Biology Research Communications 4: 337-344 2001 Type: ARTICLE Genes: pmk-1 pmk-2 pmk-3 Abstract: p38, a member of the mitogen-activated protein kinase (MAPK) superfamily, is activated in response to a variety of cellular stresses and ligands. Since the genome of the nematode C. elegans has been sequenced, we sought to identify and characterize the nematode homolog of mammalian p38. By sequence analysis and RT-PCR, we isolated cDNAs encoding three kinases, PMK-1, PMK-2, and PMK-3, which we call p38 map kinases due to their high sequence identity with p38. The three genes are contiguous on chromosome IV and comprise an operon. By use of a GFP reporter, we found that the promoter of the pmks is active throughout the intestine. An active form of MAPK/ERK kinase 6 (MEK6) phosphorylated and activated recombinant PMK-1 and PMK-2 in vitro. PMK-1 and PMK-2 phosphorylated activating transcription factor-2 (ATF-2), indicating an activity similar to mammalian p38. When transfected into mammalian cells, these kinases, like p38, are stimulated by osmotic stresses. ------------------- Key: 5204 Medline: 11709184 Authors: Feng J;Bussiere F;Hekimi S Title: Mitochondrial electron transport is a key determinant of life span in Caenorhabditis elegans. Citation: Developmental Cell 1: 633-644 2001 Type: ARTICLE Genes: ctb-1 daf-2 daf-16 isp-1 sod-3 Abstract: Increased protection from reactive oxygen species (ROS) is believed to increase life span. However, it has not been clearly demonstrated that endogenous ROS production actually limits normal life span. We have identified a mutation in the Caenorhabditis elegans iron sulfur protein (isp-1) of mitochondrial complex III, which results in low oxygen consumption, decreased sensitivity to ROS, and increased life span. Furthermore, combining isp-1(qm150) with a mutation (daf-2) that increases resistance to ROS does not result in any significant further increase in adult life span. These findings indicate that both isp-1 and daf-2 mutations increase life span by lowering oxidative stress and result in the maximum life span increase that can be produced in this way. ------------------- Key: 5205 Medline: 11718814 Authors: Tavernarakis T;Driscoll M Title: Caloric restriction and lifespan: a role for protein turnover? Citation: Mechanisms of Ageing & Development 123: 215-229 2002 Type: ARTICLE Genes: age-1 clk-1 daf-16 Abstract: Oxidative damage to cellular macromolecules has been postulated to be a major contributor to the ageing of diverse organisms. Oxidative damage can be limited by maintaining high anti-oxidant defenses and by clearing/repairing damage efficiently. Protein turnover is one of the main routes by which functional proteins are maintained and damaged proteins are removed. Protein turnover rates decline with age, which might contribute to the accumulation of damaged proteins in ageing cells. Interestingly, protein turnover rates are maintained at high levels in caloric restricted animals. Whether changes in protein turnover are a cause or a consequence of ageing is not clear, and this question has not been a focal point of modern ageing research. Here we survey work on protein turnover and ageing and suggest that powerful genetic models such as the nematode Caenorhabditis elegans are well suited for a thorough investigation of this long-standing ------------------- Key: 5206 Medline: 11718805 Authors: Braeckman BP;Houthoofd K;De Vreese A;Vanfleteren JR Title: Assaying metabolic activity in ageing Caenorhabditis elegans. Citation: Mechanisms of Ageing & Development 123: 105-119 2002 Type: ARTICLE Genes: clk-1 gro-1 mev-1 rad-8 Abstract: Accurate measures of physiological and metabolic condition could provide more insight into how longevity genes and signalling pathways affect global metabolic activity and life span. The present study is essentially a methodological treatise in which we describe and evaluate a number of methods to assess changes of metabolic activity in ageing Caenorhabditis elegans. Oxygen consumption and CO(2) production rate assays, and measurement of the heat output by microcalorimetry are performed using live worms. For other assays, frozen (-75 degrees C) samples can be used. A lucigenin-mediated light production assay provides information on the metabolic capacity (scope for metabolic activity) of the worms just before freezing. Assaying ATP and ADP levels provides a measure of the instantly available energy. The XTT assay measures the activity of enzymes that can reduce XTT. Blue fluorescence emitted at 420-470 nm is a potentially useful biomarker of the rate of ageing. A protein quantification protocol for normalising all data for quantitative comparisons is presented. We illustrate how these methods can validate or disprove models of gene action inferred from molecular ------------------- Key: 5207 Medline: 11782310 Authors: Tissenbaum HA;Guarente L Title: Model organisms as a guide to mammalian aging. Citation: Developmental Cell 2: 9-19 2002 Type: REVIEW Genes: age-1 akt-1 akt-2 clk-1 clk-2 clk-3 ctl-1 daf-2 daf-9 daf-12 daf-16 eat-2 gro-1 ins-1 ins-18 isp-1 mev-1 old-1 pdk-1 sod-1 sod-2 sod-3 unc-31 unc-64 Abstract: Recent studies on aging in model systems such as yeast and roundworms have revealed conserved regulation of the process in response to nutrient availability and specific genes that appear to mediate this regulation. Here we review these findings with a focus on the nematode Caenorhabditis elegans and the budding yeast Saccharomyces cerevisiae and highlight general features of the regulation of aging that may have implications for mammals. ------------------- Key: 5208 Medline: 11782313 Authors: Mishima M;Kaitna S;Glotzer M Title: Central spindle assembly and cytokinesis require a kinesin-like protein/RhoGAP complex with microtubule bundling activity. Citation: Developmental Cell 2: 41-54 2002 Type: ARTICLE Genes: cyk-4 zen-4 Abstract: A late step in cytokinesis requires the central spindle, which forms during anaphase by the bundling of antiparallel nonkinetochore microtubules. Microtubule bundling and completion of cytokinesis require ZEN-4/CeMKLP-1, a kinesin-like protein, and CYK-4, which contains a RhoGAP domain. We show that CYK-4 and ZEN-4 exist in a complex in vivo that can be reconstituted in vitro. The N terminus of CYK-4 binds the central region of ZEN-4, including the neck linker. Genetic suppression data prove the functional significance of this interaction. An analogous complex, containing equimolar amounts of a CYK-4 ortholog and MKLP-1, was purified from mammalian cells. Biochemical studies indicate that this complex, named centralspindlin, is a heterotetramer. Centralspindlin, but not its individual components, strongly promotes microtubule ------------------- Key: 5209 Medline: Authors: Severson AF;Bowerman B Title: Cytokinesis: Closing in on the central spindle. Citation: Developmental Cell 2: 4-6 2002 Type: REVIEW Genes: cyk-4 zen-4 Abstract: The central spindle is important for the completion of cytokinesis. Genetic and biochemical approaches have identified a tetrameric complex, made up of a mitotic kinesin-like protein and a Rho-GTPase activating protein, that mediates central spindle assembly. ------------------- Key: 5210 Medline: 11737938 Authors: Hodgkin J Title: What does a worm want with 20,000 genes? Citation: Genome Biology 2: 2008.-2008. 2001 Type: REVIEW Genes: egl-1 glp-1 let-7 lin-4 lin-12 Abstract: The number of genes predicted for the Caenorhabditis elegans genome is remarkably high: appoximately 20,000, if both protein-coding and RNA-coding genes are counted. This article discusses possible explanations for such a high value. ------------------- Key: 5211 Medline: 11744039 Authors: Gershon H;Gershon D Title: Caenorhabditis elegans - a paradigm for aging research: advantages and limitations. Citation: Mechanisms of Ageing & Development 123: 261-274 2002 Type: REVIEW Genes: age-1 clk-1 clk-2 clk-3 daf-2 daf-12 daf-16 daf-18 eat-2 eat-3 eat-6 eat-7 eat-18 gro-1 Abstract: In 1967, as we became interested in the biology of aging, we were faced with the following basic biological paradox: organisms are endowed with the capacity to detect and repair damage encountered at the molecular and cellular levels and yet functional capacity declines with time. In accordance with Strehler's suggestion (Time, Cells, and Aging, 2nd ed., Academic Press, New York, 1962), we adopted the basic premise that the underlying mechanisms of aging are common to all multi-cellular organisms. A search for a suitable experimental organism that fulfills the basic criteria for an appropriate model for aging research (Exp. Gerontol. 5 (1970) 7; Mech. Ageing Dev. 117 (2000) 21) led us to the selection of nematodes as a model for our initial series of experiments. Nematodes have thus been used in aging research for three decades. This review critically examines the major merits and shortcomings of this model organism for aging research and argues for greater appreciation of the need to understand the biology of the nematode life cycle not only as it is maintained in the laboratory, but also as it evolved and lives in nature. ------------------- Key: 5212 Medline: 11937063 Authors: Bailey S;Sedelnikova SE;Blackburn GM;Abdelghany HM;Baker PJ;McLennan AG;Rafferty JB Title: The crystal structure of diadenosine tetraphosphate hydrolase from Caenorhabditis elegans in free and binary complex forms. Citation: Structure 10: 589-600 2002 Type: ARTICLE Genes: Abstract: The crystal structure of C. elegans Ap(4)A hydrolase has been determined for the free enzyme and a binary complex at 2.0 Angstrom. and 1.8 Angstrom, respectively. Ap(4)A hydrolase has a key role in regulating the intracellular Ap(4)A levels and hence potentially the cellular response to metabolic stress and/or differentiation and apoptosis via the Ap(3)A/Ap(4)A ratio. The structures reveal that the enzyme has the mixed alpha/beta fold of the Nudix family and also show how the enzyme binds and locates its substrate with respect to the catalytic machinery of the Nudix motif. These results suggest how the enzyme can catalyze the hydrolysis of a range of related dinucleoside tetraphosphate, but not triphosphate, compounds through precise orientation of key elements of the substrate. ------------------- Key: 5213 Medline: Authors: Hodgkin J Title: The worm - Caenorhabditis elegans. Citation: Scientist 16: 20-21 2002 Type: REVIEW Genes: Abstract: In the dozen years from 1965 onward, Sydner Brenner laid the groundwork for making Caenorhabditis elegans a major system for genetics, neurobiology, and developmental biology research. ------------------- Key: 5214 Medline: 11940660 Authors: Dufourcq P;Victor M;Gay F;Calvo D;Hodgkin J;Shi Y Title: Functional requirement for histone deacetylase 1 in Caenorhabditis elegans gonadogenesis. Citation: Molecular and Cellular Biology 22: 3024-3034 2002 Type: ARTICLE Genes: cdh-1 egl-26 gon-10 hda-1 lag-2 lim-7 lin-15 Abstract: Historic acetylation and deacetylation have been implicated in the regulation of gene expression. Molecular studies have shown that histone deacetylases (HDACs) function as transcriptional repressors. However, very little is known about their roles during development in multicellular organisms. We previously demonstrated that inhibition of maternal and zygotic expression of histone deacetylase 1 (HDA-1) causes embryonic lethality in Caenorhabditis elegans. Here, we report the identification of an hda-1 genetic mutant which has also been called a gon-10 mutant (for gonadogenesis defective 10) and show that loss of HDA-1 zygotic expression results in specific postembryonic defects in gonadogenesis and vulval development. We provide evidence that the lag-2 gene, which plays a role in gonadogenesis and vulval development and encodes a Notch ligand, is derepressed in gon-10 animals, suggesting that lag-2 may be a target of HDA-1. Our findings reveal a novel and specific function for the ubiquitously expressed HDA-1 in C. elegans gonadogenesis and place hda-1 in the Notch signaling pathway. ------------------- Key: 5215 Medline: 11937488 Authors: Chu DS;Dawes HE;Lieb JD;Chan RC;Kuo AF;Meyer BJ Title: A molecular link between gene-specific and chromosome-wide transcriptional repression. Citation: Genes & Development 16: 796-805 2002 Type: ARTICLE Genes: dpy-26 dpy-27 her-1 mix-1 sdc-1 sdc-2 sdc-3 Abstract: Gene-specific and chromosome-wide mechanisms of transcriptional regulation control development in multicellular organisms. SDC-2, the determinant of hermaphrodite fate in Caenorhabditis elegans, is a paradigm for both modes of regulation. SDC-2 represses transcription of X chromosomes to achieve dosage compensation, and it also represses the male sex-determination gene her-1 to elicit hermaphrodite differentiation. We show here that SDC-2 recruits the entire dosage compensation complex to her-1, directing this X-chromosome repression machinery to silence an individual, autosomal gene. Functional dissection of her-1 in vivo revealed DNA recognition elements required for SDC-2 binding, recruitment of the dosage compensation complex, and transcriptional repression. Elements within her-1 differed in location, sequence, and strength of repression, implying that the dosage compensation complex may regulate transcription along the X chromosome using diverse recognition elements that play distinct roles in repression. ------------------- Key: 5216 Medline: Authors: Roggo L;Bernard V;Kovacs AL;Rose AM;Savoy F;Zetka M;Wymann MP;Mueller F Title: Membrane transport in Caenorhabditis elegans: an essential role for VPS34 at the nuclear membrane. Citation: EMBO Journal 21: 1673-1683 2002 Type: ARTICLE Genes: let-512 lrp-1 Abstract: Here we present a detailed genetic analysis of let-512/vps34 that encodes the Caenorhabditis elegans homologue of the yeast phosphatidylinositol 3-kinase Vps34p. LET-512/VPS34 has essential functions and is ubiquitously expressed in all tissues and developmental stages. It accumulates at a perinuclear region, and mutations in let-512/vps34 result in an expansion of the outer nuclear membrane as well as in a mislocalization and subsequent complete lack of expression of LRP-1, a C.elegans LDL receptor normally associated with the apical surface of hypodermal cells. Using a GFP::2xFYVE fusion protein we found that the phosphatidylinositol 3-phosphate (PtdIns 3-P) product of LET-512/VPS34 is associated with a multitude of intracellular membranes and vesicles located at the periphery, including endocytic vesicles. We propose that LET-512/VPS34 is required for membrane transport from the outer nuclear membrane towards the cell periphery. Thus, LET-512/VPS34 may regulate the secretory pathway in a much broader range of compartments than was previously ------------------- Key: 5217 Medline: 11937038 Authors: Rothman JH Title: Aging: from radiant youth to an abrupt end. Citation: Current Biology 12: R239-R241 2002 Type: REVIEW Genes: clk-1 clk-2 clk-3 mrt-2 rad-5 Abstract: A gene that controls growth rate, radiation resistance and lifespan in the nematode Caenorhabditis elegans has been found to encode a homologue of a yeast telomere maintenance factor, raising the possibility that checkpoint control, telomere maintenance and aging may be linked in unanticipated ways. ------------------- Key: 5218 Medline: 11967148 Authors: Poinat P;De Arcangelis A;Sookhareea S;Zhu X;Hedgecock EM;Labouesse ML;Georges-Labouesse E Title: A conserved interaction between B1 integrin/PAT-3 and Nck-interacting kinase/MIG-15 that mediates commissural axon navigation in C. elegans. Citation: Current Biology 12: 622-631 2002 Type: ARTICLE Genes: ced-10 ina-1 lin-26 mig-2 mig-15 pat-2 pat-3 rac-1 rac-2 unc-25 unc-47 unc-54 Abstract: Background: Integrins are heterodimeric (alphabeta) transmembrane receptors for extracellular matrix (ECM) ligands. Through interactions with molecular partners at cell junctions, they provide a connection between the ECM and the cytoskeleton and regulate many aspects of cell behavior. A number of integrin-associated molecules have been identified; however, in many cases, their function and role in the animal remain to be clarified. Results: We have identified the Nck-interacting kinase (NIK), a member of the STE20/germinal center kinase (GCK) family, as a partner for the beta1A integrin cytoplasmic domain. We find that NIK is expressed in the nervous system and other tissues in mouse embryos and colocalizes with actin and beta1 integrin in cellular protrusions in transfected cells. To demonstrate the functional significance of this interaction, we used Caenorhabditis elegans, since it has only one beta (PAT-3) integrin chain, two alpha (INA-1 and PAT-2) integrin chains, and a well-conserved NIK ortholog (MIG-15). Using three methods, we show that reducing mig-15 activity results in premature branching of commissures. A significant aggravation of this defect is observed when mig-15 activity is compromised in a weak ina-1 background. Neuronal-specific RNA interference against mig-15 or pat-3 leads to similar axonal defects, thus showing that both mig-15 and pat-3 act cell autonomously in neurons. Finally, we show a genetic interaction between mig-15, ina-1, and genes that encode Rac GTPases. Conclusions. Using several models, we provide the first evidence that the kinase NIK and integrins interact in vitro and in vivo. This interaction is required for proper axonal navigation in C. ------------------- Key: 5219 Medline: 11916877 Authors: Leitz G;Fallman E;Tuck S;Axner O Title: Stress response in Caenorhabditis elegans caused by optical tweezers: wavelengths, power, and time dependence. Citation: Biophysical Journal 82: 2224-2231 2002 Type: ARTICLE Genes: Abstract: Optical tweezers have emerged as a powerful technique for micromanipulation of living cells. Although the technique often has been claimed to be nonintrusive, evidence has appeared that this is not always the case. This work presents evidence that near-infrared continuous-wave laser light from optical tweezers can produce stress in Caenorhabditis elegans. A transgenic strain of C. elegans, carrying an integrated heat-shock-responsive reporter gene, has been exposed to laser light under a variety of illumination conditions. It was found that gene expression was most often induced by light of 760 nm, and least by 810 nm. The stress response increased with laser power and irradiation time. At 810 nm, significant gene expression could be observed at 360 mW of illumination, which is more than one order of magnitude above that normally used in optical tweezers. In the 700-760-nm range, the results show that the stress response is caused by photochemical processes, whereas at 810 nm, it mainly has a photothermal origin. These results give further evidence that the 700-760-nm wavelength region is unsuitable for optical tweezers and suggest that work at 810 nm at normal laser powers does not cause stress at the cellular level. ------------------- Key: 5220 Medline: 11965435 Authors: Lerat E;Capy P;Biemont C Title: Codon usage by transposable elements and their host genes in five species. Citation: Journal of Molecular Evolution 54: 625-637 2002 Type: ARTICLE Genes: Abstract: We compared the codon usage of sequences of transposable elements (TEs) with that of host genes from the species Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Saccharomyces cerevisiae, and Homo sapiens. Factorial correspondence analysis showed that, regardless of the base composition of the genome, the TEs differed from the genes of their host species by their AT-richness. In all species, the percentage of A + T on the third codon position of the TEs was higher than that on the first codon position and lower than that in the noncoding DNA of the genomes. This indicates that the codon choice is not simply the outcome of mutational bias but is also subject to selection constraints. A tendency toward higher A + T on the third position than on the first position was also found in the host genes of A. thaliana, C. elegans, and S. cerevisiae but not in those of D. melanogaster and H. sapiens. This strongly suggests that the AT choice is a host-independent characteristic common to all TEs. The codon usage of TEs generally appeared to be different from the mean of the host acnes. In the AT-rich genomes of Arabidopsis thaliana, Caenorhabditis elegans, and Saccharomyces cerevisiae, the codon usage bias of TEs was similar to that of weakly expressed genes. In the GC-rich genome of D. melanogaster, however, the bias in codon usage of the TEs clearly differed from that of weakly expressed genes. These findings suggest that selection acts on TEs and that TEs may display specific behavior within the host genomes. ------------------- Key: 5221 Medline: 11937484 Authors: Blackwell TK;Walker AK Title: Getting the right dose of repression. Citation: Genes & Development 16: 769-772 2002 Type: REVIEW Genes: dpy-26 dpy-27 dpy-30 her-1 mix-1 sdc-1 sdc-2 sdc-3 Abstract: In recent years, it has become apparent that eukaryotic transcriptional repression mechanisms are remarkably varied in their modes of action and effects. Repression can be established by proteins that act over a short range, or at a long distance. Some mechanisms of repression are readily reversible, but others establish a heritable state of long-term silencing... ------------------- Key: 5222 Medline: Authors: Liu Y;Rohrschneider LR Title: The gift of Gab. Citation: FEBS Letters 515: 1-7 2002 Type: REVIEW Genes: egl-15 let-60 Abstract: Gab proteins, including mammalian Gab1, Gab2, Gab3, Drosophila DOS and Caenorhabditis elegans Soc1, comprise a growing family of scaffolding/docking molecules involved in multiple signaling pathways mediated by receptor tyrosine kinases (RTKs) and non-RTK receptors. This paper reviews the structure/function relationships of Gab proteins and their biological roles during normal growth, differentiation and development programs. ------------------- Key: 5223 Medline: Authors: Mongan NP;Jones AK;Smith GR;Sansom MSP;Sattelle DB Title: Novel alpha 7-like nicotinic acetylcholine receptor subunits in the nematode Caenorhabditis elegans. Citation: Protein Science 11: 1162-1171 2002 Type: ARTICLE Genes: acr-2 acr-3 acr-4 acr-5 acr-6 acr-7 acr-8 acr-9 acr-10 acr-11 acr-12 acr-13 acr-14 acr-15 acr-16 acr-17 acr-18 acr-19 acr-20 acr-21 acr-22 acr-23 deg-3 des-2 lev-1 unc-29 unc-38 unc-63 Abstract: We have used reverse-transcription-polymerase chain reaction (RT-PCR) and DNA sequencing techniques to confirm the transcription of seven (six alpha and one non-alpha) novel candidate nicotinic acetylcholine receptor (nAChR) subunit-encoding genes identified in the genome sequence of the nematode Caenorhabditis elegans. Compared to vertebrate nAChR subunits. they most closely resemble the homomer-forming. neuronal alpha7 subunit. Comparison of the predicted amino acid sequences of the new nAChR subunits with those described previously in C. elegans reveals five subunits (four a and one non-alpha) which resemble the DEG-3-like group of subunits. To date. this highly divergent nAChR subunit group is unique to C. elegans. ACR-22 is the first non-a member of the DEG-3-like group of subunits to be identified. Two new members of the related ACR-16-like nAChR group of subunits have also been shown to be transcribed, making the ACR-16-like Subunit group the largest in C. elegans. Residues in the a subunit second transmembrane region (M2) which contribute to the channel lining show variations with implications for channel function. For example, in ACR-22, the highly conserved 0' lysine of M2 is replaced by histidine. Restrained molecular dynamics simulations have been used to generate molecular models of homo-pentameric M2 helix bundles for the novel subunits. enabling identification and display of pore-lining and protein inter-face residues. The number and diversity of genes encoding C. elegans nAChR subunits with similarities to the homomer-forming vertebrate alpha7 subunits and the identification of related non-a subunits. only found in C. elegans to date, suggest that at least some of these subunits may contribute to heteromers in ------------------- Key: 5224 Medline: 11960010 Authors: Wallenfang MR;Seydoux G Title: cdk-7 is required for mRNA transcription and cell cycle progression in Caenorhabditis elegans embryos. Citation: Proceedings of the National Academy of Sciences USA 99: 5527-5532 2002 Type: ARTICLE Genes: cdk-7 cey-2 end-1 pes-10 tDf3 Abstract: CDK7 is a cyclin-dependent kinase proposed to function in two essential cellular processes: transcription and cell cycle regulation. CDK7 is the kinase subunit of the general transcription factor TFIIH that phosphorylates the C-terminal domain (CTD) of RNA polymerase 11, and has been shown to be broadly required for transcription in Saccharomyces cerevisiae. CDK7 can also phosphorylate CDKs that promote cell cycle progression, and has been shown to function as a CDK-activating kinase (CAK) in Schizosaccharomyces pombe and Drosophila melanogaster. That CDK7 performs both functions in metazoans has been difficult to prove because transcription is essential for cell cycle progression in most cells. We have isolated a temperature-sensitive mutation in Caenorhabditis elegans cdk-7 and have used it to analyze the role of cdk-7 in embryonic blastomeres, where cell cycle progression is independent of transcription. Partial loss of cdk-7 activity leads to a general decrease in CTD phosphorylation and embryonic transcription, and severe loss of cdk-7 activity blocks all cell divisions. Our results support a dual role for metazoan CDK7 as a broadly required CTD kinase, and as a CAK essential for cell cycle progression. ------------------- Key: 5225 Medline: 11896188 Authors: Sumiyoshi E;Sugimoto A;Yamamoto M Title: Protein phosphatase 4 is required for centrosome maturation in mitosis and sperm meiosis in C. elegans. Citation: Journal of Cell Science 115: 1403-1410 2002 Type: ARTICLE Genes: fem-1 fem-2 pph-4.1 pph-4.2 rde-1 Abstract: The centrosome consists of two centrioles surrounded by the pericentriolar material (PCM). In late G2 phase, centrosomes enlarge by recruiting extra PCM, and concomitantly its microtubule nucleation activity increases dramatically. The regulatory mechanisms of this dynamic change of centrosomes are not well understood. Protein phosphatase 4 (PP4) is known to localize to mitotic centrosomes in mammals and Drosophila. An involvement of PP4 in the mitotic spindle assembly has been implicated in Drosophila, but in vivo functions of PP4 in other organisms are largely unknown. Here we characterize two Caenorhabditis elegans PP4 genes, named pph-4.1 and pph-4.2. Inhibition of the function of each gene by RNA-mediated interference (RNAi) revealed that PPH-4.1 was essential for embryogenesis but PPH-4.2 was not. More specifically, PPH-4.1 was required for the formation of spindles in mitosis and sperm meiosis. However, this phosphatase was apparently dispensable for female meiotic divisions, which do not depend on centrosomes. In the cell depleted of pph-4.1 activity, localization of gamma-tubulin and a Polo-like kinase homologue to the centrosome was severely disturbed. Immunofluorescence staining revealed that PPH-4.1 was present at centrosomes from prophase to telophase, but not during interphase. These results indicate that PPH-4.1 is a centrosomal protein involved in the recruitment of PCM components to the centrosome, and is essential for the activation of microtubule nucleation potential of the centrosome. Furthermore, chiasmata between homologous chromosomes were often absent in oocytes that lacked pph-4.1 activity. Thus, besides promoting spindle formation, PPH-4.1 appears to play a role in either the establishment or the maintenance of chiasmata during ------------------- Key: 5226 Medline: 11959845 Authors: Shaham S;Bargmann CI Title: Control of neuronal subtype identity by the C. elegans ARID protein CFI-1. Citation: Genes & Development 16: 972-983 2002 Type: ARTICLE Genes: ced-3 cfi-1 glr-1 glr-4 lin-31 lov-1 mec-4 nmr-1 odr-2 pkd-2 unc-86 qDf5 Abstract: The Caenorhabditis elegans hermaphrodite nervous system is composed of 302 neurons that fall into at least 118 diverse classes. Here we describe cfi-1, a gene that contributes to the development of neutonal diversity. cfi-1 promotes appropriate differentiation of the URA sensory neurons and inhibits URA from expressing the male-specific CEM neuronal fate. The UNC-86 POU homeodomain protein is present in CEM and URA neurons, and can promote expression of CEM-specific genes in both CEM and URA, but CFI-1 inhibits expression of these genes in the URA cells. cfi-1 also promotes appropriate differentiation and glutamate receptor expression in the AVD and PVC interneurons. cfi-1 encodes a conserved neuron- and muscle-restricted DNA-binding protein containing an A/T rich interaction domain (ARID). ARID proteins regulate early patterning and muscle fate in Drosophila, but they have not previously been implicated in the control of neuronal subtype identity. ------------------- Key: 5227 Medline: Authors: Yokoyama K;Fukumoto K;Murakami T;Harada S;Hosono R;Wadhwa R;Mitsui Y;Ohkuma S Title: Extended longevity of Caenorhabditis elegans by knocking in extra copies of hsp70F, a homolog of mot-2 (mortalin)/mthsp70/Grp75. Citation: FEBS Letters 516: 53-57 2002 Type: ARTICLE Genes: mot-2 Abstract: The Caenorhabditis elegans homolog of mortalin/mthsp70/Grp75; (called mot-2 hereafter) was isolated by screening of a nematode cDNA library with mouse mot-2 cDNA. The isolated clone matched to hsp70F of C elegans. Analysis with two of the antibodies raised against hsp70F revealed that unlike mammalian mot-2, it is heat inducible. Transient induction of hsp70F by heat shock led to a slight (< 13%) extension in the C elegans life span. The transgenic worms that constitutively over-expressed hsp70F predominantly in muscle showed life span extension (similar to 43% for mean and similar to 45% for maximum life span) as compared to the wild-type and green fluorescent protein-transgenic worms. Life span extension of human cells was obtained by over-expression of mot-2 [Kaul et al. (2000) FEBS Lett. 474, 159-164]. Our results show, for the first time, that this member of the hsp70 family governs the longevity of worms and thus there are common pathways that determine mammalian and worm ------------------- Key: 5228 Medline: Authors: Gorbunova V;Seluanov A Title: CLK-1 protein has DNA binding activity specific to O-L region of mitochondrial DNA. Citation: FEBS Letters 516: 279-284 2002 Type: ARTICLE Genes: clk-1 Abstract: Mutations in the clk-1 gene of Caerzorhahditis elegans extend worm life span and slow down a variety of physiological processes. Here we report that C. elegans CLK-1 as well as its mouse homologue have DNA binding activity that is specific to the O-L region of mitochondrial DNA. DNA binding activity of CLK-1 is inhibited by ADP, and is altered by mutations that extend nematode life span. Our results suggest that, in addition to its enzymatic function in ubiquinone biosynthesis, CLK-1 is involved in the regulation of mtDNA replication or ------------------- Key: 5229 Medline: Authors: Cameron S;Clark SG;McDermott JB;Aamodt E;Horvitz HR Title: PAG-3, a Zn-finger transcription factor, determines neuroblast fate in C. elegans. Citation: Development 129: 1763-1774 2002 Type: ARTICLE Genes: ced-1 ced-3 egl-5 lin-15 lin-39 mab-5 pag-3 mnDf19 mnDp1 Abstract: During Caenorhabditis elegans development, the patterns of cell divisions, cell fates and programmed cell deaths are reproducible from animal to animal. In a search for mutants with abnormal patterns of programmed cell deaths in the ventral nerve cord, we identified mutations in the gene pag-3, which encodes a zinc-finger transcription factor similar to the mammalian Gfi-1 and Drosophila Senseless proteins. In pag-3 mutants, specific neuroblasts express the pattern of divisions normally associated with their mother cells, producing with each reiteration an abnormal anterior daughter neuroblast and an extra posterior daughter cell that either terminally differentiates or undergoes programmed cell death, which accounts for the extra cell corpses seen in pag-3 mutants. In addition, some neurons do not adopt their normal fates in pag-3 mutants. The phenotype of pag-3 mutants and the expression pattern of the PAG-3 protein suggest that in some lineages pag-3 couples the determination of neuroblast cell fate to subsequent neuronal differentiation. We propose that pag-3 counterparts in other organisms determine blast cell identity and for this reason may lead to cell lineage defects and cell proliferation when mutated. ------------------- Key: 5230 Medline: Authors: Agostoni E;Gobessi S;Petrini E;Monte M;Schneider C Title: Cloning and characterization of the C. elegans gas1 homolog: phas-1. Citation: Biochemica et Biophysica Acta - Gene Structure & Expression 1574: 1-9 2002 Type: ARTICLE Genes: ced-1 phas-1 Abstract: Among the set of genes expressed during the quiescent G0 phase of the cell cycle (gas genes), gas1 encodes for a GPI anchor protein associated to the plasma membrane, which is able to induce growth arrest when overexpressed in proliferating fibroblasts. In this report we describe the isolation and characterization of a gas1 Cetenorhabditis elegans homolog, phas-1, that seems to be transcribed as an operon together with a gene encoding for a protein similar to human acid ceramidases. Phas-1 structure is very similar to its mammalian homolog conserving almost all cysteine residues and it is expressed in the pharynx from its early formation, in the two-fold embryo, until the adult stage. Surprisingly, while phas-1 is expressed in all developmental stages, with the exception of the clatter larva, the ceramidase-like encoding gene, co-expressed in the same operon together with phas-1, is absent in embryos and is very abundantly expressed in the dauer larva. Overexpression of phas-1 in growing NIH3T3 fibroblasts is able to inhibit the S-phase entry in a similar manner as its murine homolog. On the other hand, when phas-1 is overexpressed or ablated in C elegans, no specific phenotype due to its transcription alteration can be observed, despite its localized expression suggesting a ------------------- Key: 5231 Medline: 11998879 Authors: Tosi S;Annovazzi L;Tosi I;Iadarola P;Caretta G Title: Collagenase production in an Antarctic strain of Arthrobotrys tortor Jarowaja. Citation: Mycopathologia 153: 157-162 2001 Type: ARTICLE Genes: Abstract: This paper describes the results of a comparative screening between the nematophagous Antractic fungus Arthrobotrys tortor and other species of that genus for the production of extracellular collagenases. The nematode species used in this study was Caenorhabditis elegans, feeding on Escherichia coli cultures. Determination of collagenase activity was made by using insoluble collagen from bovine Achilles tendon and determining the amount of solubilized hydroxyproline produced. The results show that the total amount of collagenase produced by the Antarctic strain of A. tortor was about threefold higher than that observed for the other species. In the Antarctic strain, collagenase was shown to be a constitutive enzyme. ------------------- Key: 5232 Medline: 11847225 Authors: Ma D;Nelson LS;LeCoz K;Poole C;Carlow CKS Title: A novel cyclophilin from parasitic and free-living nematodes with a unique substrate- and drug-binding domain. Citation: Journal of Biological Chemistry 277: 14925-14932 2002 Type: ARTICLE Genes: Abstract: A highly diversified member of the cyclophilin family of peptidyl-prolyl cis-trans isomerases has been isolated from the human parasite Onchocerca volvulus (OvCYP-16). This 25-kDa cyclophilin shares 43-46% similarity to other filarial cyclophilins but does not belong to any of the groups previously defined in invertebrates or vertebrates. A homolog was also isolated from Caenorhabditis elegans (CeCYP-16). Both recombinant O. volvulus and C. elegans cyclophilins were found to possess an enzyme activity with similar substrate preference and insensitivity to cyclosporin A. They represent novel cyclophilins with important differences in the composition of the drug-binding site in particular, namely, a Glu(124) (C. elegans) or Asp(123) (O. volvulus) residue present in a critical position. Site-directed mutagenesis studies and kinetic characterization demonstrated that the single residue dictates the degree of binding to substrate and cyclosporin A. CeCYP-16::GFP-expressing lines were generated with expression in the anterior and posterior distal portions of the intestine, in all larval stages and adults. An exception was found in the dauer stage, where fluorescence was observed in both the cell bodies and processes of the ventral chord motor neurons but was absent from the intestine. These studies highlight the extensive diversification of cyclophilins in an important human parasite and a closely related model organism. ------------------- Key: 5233 Medline: 11972048 Authors: Watts JL;Browse J Title: Genetic dissection of polyunsaturated fatty acid synthesis in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 99: 5854-5859 2002 Type: ARTICLE Genes: fat-1 fat-2 fat-3 fat-4 elo-1 elo-2 Abstract: Polyunsaturated fatty acids (PUFAs) are important membrane components and precursors of signaling molecules. To investigate the roles of these fatty acids in growth, development, and neurological function in an animal system, we isolated Caenorhabditis elegans mutants deficient in PUFA synthesis by direct analysis of fatty acid composition. C elegans possesses all the desaturase and elongase activities to synthesize arachidonic acid and eicosapentaenoic acid from saturated fatty acid precursors. In our screen we identified mutants with defects in each fatty acid desaturation and elongation step of the PUFA biosynthetic pathway. The fatty acid compositions of the mutants reveal the substrate preferences of the desaturase and elongase enzymes and clearly demarcate the steps of this pathway. The mutants show that C elegans does not require n3 or Delta5-unsaturated PUFAs for normal development under laboratory conditions. However, mutants with more severe PUFA deficiencies display growth and neurological defects. The mutants provide tools for investigating the roles of PUFAs in membrane biology and cell function in this animal model. ------------------- Key: 5234 Medline: 11988165 Authors: Bianchi L;Driscoll M Title: Protons at the gate: DEG/ENaC ion channels help us feel and remember. Citation: Neuron 34: 337-340 2002 Type: REVIEW Genes: deg-1 del-1 flr-1 mec-2 mec-4 mec-5 mec-7 mec-9 mec-10 mec-12 unc-8 unc-105 Abstract: The DEG/ENaC ion channel family contributes to channels of striking functional diversity. Neuronally expressed family members include the C. elegans degenerins that mediate touch and are thought to be mechanically gated, and the mammalian ASICs, which are gated by protons. ASICs affect a range of sensory functions that includes perception of gentle touch, harsh touch, heat, sour taste, and pain. Family member ASIC1 is now implicated in long-term potentiation, suggesting that minute fluxes in synaptic pH may activate ASICs to enhance learning. ------------------- Key: 5235 Medline: 11950942 Authors: Walker DS;Gower NJD;Ly S;Bradley GL;Baylis HA Title: Regulated disruption of inositol 1,4,5-trisphosphate signaling in Caenorhabditis elegans reveals new functions in feeding and embryogenesis. Citation: Molecular Biology of the Cell 13: 1329-1337 2002 Type: ARTICLE Genes: dec-4 elt-2 itr-1 Abstract: Inositol 1,4,5-trisphosphate (IP3) is an important second messenger in animal cells and is central to a wide range of cellular responses. The major intracellular activity of IP3 is to regulate release of Ca2+ from intracellular stores through IP3 receptors (IP(3)Rs). We describe a system for the transient disruption of IP3 signaling in the model organism Caenorhabditis elegans. The IP3 binding domain of the C. elegans IP3R, ITR-1, was expressed from heat shock-induced promoters in live animals. This results in a dominant-negative effect caused by the overexpressed IP3 binding domain acting as an IP3 "sponge." Disruption of IP3 signaling resulted in disrupted defecation, a phenotype predicted by previous genetic studies. This approach also identified two new IP3-mediated processes. First, the up-regulation of pharyngeal pumping in response to food is dependent on IP3 signaling. RNA-mediated interference studies and analysis of itr-1 mutants show that this process is also IP3R dependent. Second, the tissue-specific expression of the dominant-negative construct enabled us to circumvent the sterility associated with loss Of IP3 signaling through the IP3R and thus determine that IP3-mediated signaling is required for multiple steps in embryogenesis, including cytokinesis and gastrulation. ------------------- Key: 5236 Medline: Authors: Bulow HE;Berry KL;Topper LH;Peles E;Hobert O Title: Heparan sulfate proteoglycan-dependent induction of axon branching and axon misrouting by the Kallmann syndrome gene kal-1. Citation: Proceedings of the National Academy of Science USA 99: 6346-6351 2002 Type: ARTICLE Genes: egl-15 gcy-8 him-4 ina-1 kal-1 lin-17 mab-20 mig-17 sax-3 slt-1 sma-1 ttx-3 unc-5 unc-6 unc-13 unc-33 unc-34 unc-40 unc-44 unc-51 unc-52 unc-53 unc-69 unc-70 unc-71 unc-73 unc-76 unc-104 unc-116 unc-119 vab-1 Abstract: Kallmann syndrome is a neurological disorder characterized by various behavioral and neuroanatomical defects. The X-linked form of this disease is caused by mutations in the KAL-1 gene, which codes for a secreted molecule that is expressed in restricted regions of the brain. Its molecular mechanism of action has thus far remained largely elusive. We show here that expression of the Caenorhabditis elegans homolog of KAL-1 in selected sensory and interneuron classes causes a highly penetrant, dosage-dependent, and cell autonomous axon-branching phenotype. in a different cellular context, heterologous C elegans kal-1 expression causes a highly penetrant axon-misrouting phenotype. The axon-branching and -misrouting activities require different domains of the KAL-1 protein. In a genetic modifier screen we isolated several loci that either suppress or enhance the kal-1-induced axonal defects, one of which codes for an enzyme that modifies specific residues in heparan sulfate proteoglycans, namely heparan-60-sulfotransferase. We hypothesize that KAL-1 binds by means of a heparan sulfate proteoglycan to its cognate receptor or other extracellular cues to induce axonal branching and axon misrouting. ------------------- Key: 5237 Medline: Authors: Jorgensen EM;Mango SE Title: The art and design of genetic screens: Caenorhabditis elegans. Citation: Nature Reviews Genetics 3: 356-369 2002 Type: REVIEW Genes: dif-1 dpy-21 dpy-26 dpy-27 dpy-28 dpy-30 end-1 end-3 exp-2 fem-1 fem-2 fem-3 glp-1 her-1 him-5 lag-1 lag-2 let-23 let-60 let-340 lin-1 lin-3 lin-8 lin-12 lin-15 lin-38 lin-45 mec-8 mek-2 mpk-1 mrt-2 npr-1 rpm-1 sad-1 sax-3 sdc-1 sdc-2 sdc-3 sem-5 skn-1 sos-1 tam-1 tra-1 tra-2 tra-3 ttx-1 unc-4 unc-6 unc-24 unc-30 unc-32 unc-36 unc-37 unc-52 vab-1 vab-2 xol-1 Abstract: The nematode Caenorhabditis elegans was chosen as a model genetic organism because its attributes, chiefly its hermaphroditic lifestyle and rapid generation time, make it suitable for the isolation and characterization of genetic mutants. The most important challenge for the geneticist is to design a genetic screen that will identify mutations that specifically disrupt the biological process of interest. Since 1974, when Sydney Brenner published his pioneering genetic screen, researchers have developed increasingly powerful methods for identifying genes and genetic pathways in C. elegans. ------------------- Key: 5238 Medline: Authors: Darby C;Hsu JW;Ghori N;Falkow S Title: Caenorhabditis elegans - Plague bacteria biofilm blocks food intake. Citation: Nature 417: 243-244 2002 Type: ARTICLE Genes: phm-2 Abstract: Bubonic plague is transmitted to mammals, including humans, by the bites of fleas whose digestive tracts are blocked by a mass of the bacterium Yersinia pestis. In these fleas, the plague-causing bacteria are surrounded by an extracellular matrix of unknown composition, and the blockage depends on a group of bacterial genes known as the hmsHFRS operon. Here we show that Y. pestis creates an hmsHFRS-dependent extracellular biofilm to inhibit feeding by the nematode Caenorhabditis elegans. ------------------- Key: 5239 Medline: Authors: Franc NC Title: Phagocytosis of apoptotic cells in mammals, Caenorhabditis elegans and Drosophila melanogaster: molecular mechanisms and physiological consequences. Citation: Frontiers in Bioscience 7: D1298-D1313 2002 Type: REVIEW Genes: ced-1 ced-2 ced-5 ced-6 ced-7 ced-10 ced-12 Abstract: Phagocytosis is the necessary corollary of apoptosis. It leads to the clearance of apoptotic cells by phagocytes, which can be professional or amateur. I review the know molecular aspects of phagocytosis of apoptotic corpses in mammals, Caenorhabditis elegans and Drosophila melanogaster from the point of view of the phagocyte and the apoptotic corpse. I highlight recent advances made in the field and discuss the physiological outcomes and consequences of this process. Indeed, phagocytosis of apoptotic cells is important in shaping or remodeling tissues to maintain their integrity and specialized functions during development and wound healing. It also contributes to the development of inflammation and/or its resolution after a injury or infection. This perhaps explains why the molecular mechanisms of phagocytosis of apoptotic cells are redundant and complex in mammals and suggests why they appear to have been mostly conserved through evolution. Caenorhabditis elegans has already proven to be useful in genetically dissecting the molecular mechanisms underlying phagocytosis of apoptotic corpses by amateur neighboring cells. Drosophila melanogaster will become the model of choice in genetically dissecting the molecular mechanisms underlying phagocytosis of apoptotic cells by professional phagocytes such as macrophages. ------------------- Key: 5241 Medline: Authors: Reuben M;Lin R Title: Germline X chromosomes exhibit contrasting patterns of histone H3 methylation in Caenorhabditis elegans. Citation: Developmental Biology 245: 71-82 2002 Type: ARTICLE Genes: her-1 let-858 tra-2 Abstract: In mammals, one of the two somatic X chromosomes in the female is inactivated, thereby equalizing X chromosome-derived transcription in the two sexes, a process known as dosage compensation. In the germline, however, the situation is quite different. Both X chromosomes are transcriptionally active during female oogenesis, whereas the X and Y chromosomes are transcriptionally silent during male spermatogenesis. Previous studies suggest that Caenorhabditis elegans germline X chromosomes might have different transcriptional activity in the two sexes in a manner similar to that in mammals. Using antibodies specific to H3 methylated at either lysine 4 or lysine 9, we show that the pattern of site-specific H3 methylation is different between X chromosomes and autosomes as well as between germline X chromosomes from the two sexes in C. elegans. We show that the pachytene germline X chromosomes in both sexes lack Me(K4)H3 when compared with autosomes, consistent with their being transcriptionally inactive. This transcriptional inactivity of germline X chromosomes is apparently transient in hermaphrodites because both X chromosomes stain brightly for Me(K4)H3 after germ nuclei exit pachytene. The male single X chromosome, on the other hand, remains devoid of Me(K4)H3 staining throughout the germline. Instead, the male germline X chromosome exhibits a high level of Me(K9)H3 that is not detected on any other chromosomes in either sex, consistent with stable silencing of this chromosome. Using mutants defective in the sex determination pathway, we show that X-chromosomal Me(K9)H3 staining is determined by the sexual phenotype, and not karyotype, of the animal. We detect a similar high level of Me(K9)H3 in male mouse XY bodies, suggesting an evolutionarily conserved mechanism for silencing the X ------------------- Key: 5242 Medline: 12007416 Authors: Hilliard M;Bargmann CI;Bazzicalupo P Title: C. elegans responds to chemical repellents by integrating sensory inputs from the head and the tail. Citation: Current Biology 12: 730-734 2002 Type: ARTICLE Genes: che-3 daf-10 mec-4 mec-10 osm-1 osm-3 osm-5 osm-6 osm-9 osm-10 tax-4 Abstract: The phasmids are bilateral sensory organs located in the tail of Caenorhabditis elegans and other nematodes. The similar structures of the phasmids and the amphid chemosensory organs in the head have long suggested a chemosensory function for the phasmids [1]. However, the PHA and PHB phasmid neurons are not required for chemotaxis [2, 3] or for dauer formation [4], and no direct proof of a chemosensory function of the phasmids has been obtained. C. elegans avoids toxic chemicals by reversing its movement, and this behavior is mediated by sensory neurons of the amphid, particularly, the ASH neurons [5, 6]. Here we show that the PHA and PHB phasmid neurons function as chemosensory cells that negatively modulate reversals to repellents. The antagonistic activity of head and tail sensory neurons is integrated to generate appropriate escape behaviors: detection of a repellent by head neurons mediates reversals, which are suppressed by antagonistic inputs from tail neurons. Our results suggest that C. elegans senses repellents by defining a head-to-tail spatial map of the chemical environment. ------------------- Key: 5243 Medline: 11969199 Authors: Ogurusu T;Shingai R Title: Enhancement of in situ hybridization signals in Caenorhabditis elegans by tyramide signal amplification. Citation: Analytical Biochemistry 304: 133-135 2002 Type: ARTICLE Genes: unc-25 unc-29 Abstract: The nematode C. elegans is widely used by researchers in biological experiments because of its proven excellence. In many cases, patterns of gene expression are informative. A number of reported methods for studying patterns of gene expression in C. elegans include the use of reporter fusions, immunocytochemistry, and in situ hybridization. ------------------- Key: 5244 Medline: 11977078 Authors: Sloboda RD Title: A healthy understanding of intraflagellar transport. Citation: Cell Motility and the Cytoskeleton 52: 1-8 2002 Type: REVIEW Genes: che-2 che-3 che-11 daf-10 lov-1 pkd-1 pkd-2 osm-1 osm-3 osm-5 osm-6 Abstract: A microtubule-dependent motility process called intraflagellar transport (IFT) occurs beneath the plasma membrane of cilia and flagella. IFT was first observed in Chlamydomonas, and orthologs of some of the polypeptides involved in IFT have recently been identified in other organisms, including C. elegans and the mouse. In addition to a role in the assembly and maintenance of cilia and flagella, evidence is reviewed here that indicates defects in the process of IFT may be related to problems with human health. Moreover, recent data suggest the possibility of two new roles for IFT in cell function. The first is in transcriptional control of the genes encoding ciliary and flagellar proteins. IFT could provide a mechanism whereby the cell senses the presence or absence of its cilia or flagella and responds by turning on gene transcription resulting in replacement of the missing organelle. The second role is in signal transduction, whereby cilia act as sensors of the external cellular environment and transduce information about the surroundings into intracellular signals that are sent via IFT to the cell body, thus inducing an appropriate cellular response to the environment. ------------------- Key: 5245 Medline: 12024031 Authors: Szewczyk NJ;Peterson BK;Jacobson LA Title: Activation of Ras and the mitogen-activated protein kinase pathway promotes protein degradation in muscle cells of Caenorhabditis elegans. Citation: Molecular and Cellular Biology 22: 4181-4188 2002 Type: ARTICLE Genes: gap-1 gap-2 let-23 let-60 lin-45 mek-2 mpk-1 unc-54 Abstract: To discover and study intracellular signals that regulate proteolysis in muscle, we have employed transgenic strains of Caenorhabditis elegans that produce a soluble LacZ reporter protein limited to body-wall and vulval muscles. This reporter protein is stable in well-fed wild-type animals, but its degradation is triggered upon a shift to 25degreesC in a strain carrying a temperature-sensitive activating mutation in the Ras oncogene homologue let-60. These mutants are not physiologically starved, inasmuch as growth rates are normal at 25degreesC. Ras-induced degradation is not prevented by the presence of cycloheximide added at or before the temperature shift and thus uses preexisting proteolytic systems and signaling components. Furthermore, degradation is triggered when adult animals are shifted to conditions of 25degreesC, confirming that Ras acutely promotes protein degradation in muscles whose developmental history is normal. Reduction-of-function mutations in the downstream protein kinase Raf (lin-45), MEK (mek-2), or mitogen-activated protein kinase (MAPK) (mpk-1) prevent Ras-induced protein degradation, whereas activated MPK-1 is sufficient to trigger degradation, indicating that this kinase cascade is the principal route by which Ras signaling triggers protein degradation in muscle. This pathway is activated in hypodermal cells by the LET-23 epidermal growth factor receptor homologue, but an activating mutation in let-23 does not promote proteolysis in muscle. Starvation-induced LacZ reporter degradation is unaffected by reduction-of-function mutations in Ras, Raf, MEK, or MAPK, implying that Ras activation and starvation trigger proteolysis by mechanisms that are at least partially independent. This is the first evidence that Ras-Raf-MEK-MAPK signaling activates protein degradation in ------------------- Key: 5246 Medline: 12061955 Authors: LaMunyon CW;Ward S Title: Evolution of larger sperm in response to experimentally increased sperm competition in Caenorhabditis elegans. Citation: Proceedings of the Royal Society of London B 269: 1125-1128 2002 Type: ARTICLE Genes: spe-8 Abstract: Sperm morphology evolves rapidly, resulting in an exceptional diversity of sperm size and shape across animal phyla. This swift evolution has been thought to prevent fertilizations between closely related species. Alternatively, recent correlative analyses suggest that competition among sperm from more than one male may cause sperm diversity, but these hypotheses have not been tested. Here, we test experimentally the effect of sperm competition on sperm-size evolution using the nematode Caenorhabditis elegans. This worm has a three day generation time, which allowed the study to cover many generations. Sperm volume increased nearly 20% over 60 generations in lines genetically induced to have high levels of sperm competition compared with those of control lines. These results show that sperm competition can and does cause morphological evolution of sperm and, therefore, can explain much of the diversity in sperm morphology. ------------------- Key: 5247 Medline: Authors: Roy F;Therrien M Title: MAP kinase module: the Ksr connection. Citation: Current Biology 12: R325-R327 2002 Type: REVIEW Genes: ksr-1 ksr-2 let-60 Abstract: Ksr has been genetically defined as a component of the Ras/MAP kinase pathway, but its role has been unclear. New studies now provide evidence that Ksr is important for signal transmission within the MAP kinase module, where it apparently acts as a location-regulated scaffold connecting MEK to Raf. ------------------- Key: 5248 Medline: 11973609 Authors: Puthalakath H;Strasser A Title: Keeping killers on a tight leash: transcriptional and posttranscriptional control of the pro-apoptotic activity of BH3-only proteins. Citation: Cell Death and Differentiation 9: 505-512 2002 Type: REVIEW Genes: ced-3 ced-4 ced-9 ces-1 ces-2 egl-1 tra-1 Abstract: BH3-only proteins are structurally distant members of the Bcl-2 protein family that trigger apoptosis. Genetic experiments have shown that these proteins are essential initiators of programmed cell death in species as distantly related as mice and C. elegans. BH3-only proteins share with each other and with the remainder of the Bcl-2 family only a nine amino acid BH3 (Bcl-2 Homology) region, Mutational analyses have demonstrated that this domain is required for their ability to bind to Bcl-2-like pro-survival proteins and to initiate apoptosis. So far only one BH3-only protein, EGL-1, has been identified in C. elegans and it is required for all developmentally programmed death of somatic cells in this species, In contrast, mammals have at least 10 BH3-only proteins that differ in their expression pattern and mode of activation. Studies in gene targeted mice have indicated that different BH3-only proteins are required for the initiation of distinct apoptotic stimuli. The pro-apoptotic activities of BH3-only proteins are stringently controlled by a variety mechanisms. C. elegans egl-1 as well as mammalian hrk/dp5, noxa, puma/ bbc3 and bim/bod are regulated by a diverse range of transcription factors. Certain BH3-only proteins, including Bad, Bik/Nbk, Bid, Bim/Bod and Bmf, are restrained by posttranslational modifications that cause their sequestration from pro-survival Bcl-2 family members. In this review we describe current knowledge of the functions and transcriptional as well as post-translational control mechanisms of BH3-only proteins. ------------------- Key: 5249 Medline: Authors: Ge Y;Chen Z;Kang ZB;Cluette-Brown J;Laposata M;Kang JX Title: Effects of adenoviral gene transfer of C. elegans n-3 fatty acid desaturase on the lipid profile and growth of human breast cancer cells. Citation: Anticancer Research 22: 537-543 2002 Type: ARTICLE Genes: fat-1 Abstract: Background: Current evidence from both experimental and human studies indicates that omega-6 polyunsaturated fatty acids (n-6 PUFAs) promote breast tumor development, whereas long-chain n-3 polyunsaturated fatty acids (n-3 PUFAs) exert suppressive effects. The ratio of n-6 to n-3 fatty acids appears to be an important factor in controlling tumor development. Human cells usually have a very high n-6/n-3 fatty acid ratio because they cannot convert n-6 PUFAs to n-3 PUFAs due to lack of an n-3 desaturase found in C. elegans. Materials and Methods: Adenoviral strategies were used to introduce the C. elegans fat-1 gene encoding an n-3 fatty acid desaturase into human breast cancer cells followed by examination of the n-6/n-3 fatty acid ratio and growth of the cells. Results: Infection of MCF-7 cells with an adenovirus carrying the fat-1 gene resulted in a high expression of the n-3 fatty acid desaturase. Lipid analysis indicated a remarkable increase in the levels of n-3 PUFAs accompanied with a large decrease in the contents of n-6 PUFAs, leading to a change of the n-6/n-3 ratio from 12.0 to 0.8. Accordingly, production of the eicosanoids derived from n-6 PUFA was reduced significantly in cells expressing the fat-1 gene. Importantly, the gene transfer induced mass cell death and inhibited cell proliferation. Conclusion: The gene transfer of the n-3 fatty acid desaturase, as a novel approach, can effectively modify the n-6/n-3 fatty acid ratio of human tumor cells and provide an anticancer effect, without the need of exogenous n-3 PUFA supplementation. These data also increase the understanding of the effects of n-3 fatty acids and the n-6/n-3 ratio on cancer prevention and treatment. ------------------- Key: 5250 Medline: 12019228 Authors: Rocheleau CE;Howard RM;Goldman AP;Volk ML;Girard LJ;Sundaram MV Title: A lin-45 raf enhancer screen identifies eor-1, eor-2 and unusual alleles of Ras pathway genes in Caenorhabditis elegans. Citation: Genetics 161: 121-131 2002 Type: ARTICLE Genes: eor-1 eor-2 gap-1 ksr-1 let-4 let-23 let-60 let-277 let-278 let-279 let-280 let-281 let-282 let-284 let-341 lin-1 lin-3 lin-25 lin-45 mek-2 mpk-1 sem-5 sur-2 sur-6 mDf7 mDf8 Abstract: In Caenorhabditis elegans, the Ras/Raf/MEK/ERK signal transduction pathway controls multiple processes including excretory system development, P12 fate specification, and vulval cell fate specification. To identify positive regulators of Ras signaling, we conducted a genetic screen for mutations that enhance the excretory system and egg laying defects of hypomorphic lin-45 raf mutants. This screen identified unusual alleles of several known Ras pathway genes, including a mutation removing the second SH3 domain of the sem-5/Grb2 adaptor, a temperature-sensitive mutation in the helical hairpin of let-341/Sos, a gain-of-function mutation affecting a potential phosphorylation site of the lin-1 Ets domain transcription factor, a dominant-negative allele of ksr-1, and hypomorphic alleles of sur-6/PP2A-B, sur-2/Mediator, and lin-25. In addition, this screen identified multiple alleles of two newly identified genes, eor-1 and eor-2, that play a relatively weak role in vulval fate specification but positively regulate Ras signaling during excretory system development and P12 fate specification. The spectrum of identified mutations argues strongly for the specificity of the enhancer screen and for a close involvement of eor-1 and eor-2 in Ras signaling. ------------------- Key: 5251 Medline: Authors: Huang X;Cheng HJ;Tessier-Lavigne M;Jin Y Title: MAX-1, a novel PH/MyTH4/FERM domain cytoplasmic protein implicated in netrin-mediated axon repulsion. Citation: Neuron 34: 563-576 2002 Type: ARTICLE Genes: mab-9 max-1 max-2 max-3 max-4 max-5 max-6 sax-3 unc-3 unc-5 unc-6 unc-34 unc-40 unc-71 unc-73 unc-119 unc-129 arDf1 nDf42 yDf8 yDf12 Abstract: The netrin UNC-6 repels motor axons by activating the UNC-5 receptor alone or in combination with the UNC-40/DCC receptor. In a genetic screen for C. elegans mutants exhibiting partial defects in motor axon projections, we isolated the max-1 gene (required for motor neuron axon guidance). max-1 loss-of-function mutations cause fully penetrant but variable axon guidance defects. Mutations in unc-5 and unc-6, but not in unc-40 dominantly enhance the mutant phenotypes of max-1, whereas overexpression of unc-5 or unc-6, but not of unc-40, bypasses the requirement for max-1. MAX-1 proteins contain PH, MyTH4, and FERM domains and appear to be localized to neuronal processes. Human MAX-1 and UNC5H2 colocalize in discrete subcellular regions of transfected cells. Our results suggest a possible role for MAX-1 in netrin-induced axon repulsion by modulating the UNC-5 receptor signaling pathway. ------------------- Key: 5252 Medline: Authors: Castillo-Davis CI;Hartl DL Title: Genome evolution and developmental constraint in Caenorhabditis elegans. Citation: Molecular Biology and Evolution 19: 728-735 2002 Type: ARTICLE Genes: Abstract: It has been hypothesized that evolutionary changes will be more frequent in later ontogeny than early ontogeny because of developmental constraint. To test this hypothesis, a genomewide examination of molecular evolution through ontogeny was carried out using comparative genomic data in Caenorhabditis elegans and Caenorhabditis briggsae. We found that the mean rate of amino acid replacement is not significantly different between genes expressed during and after embryogenesis. However, synonymous substitution rates differed significantly between these two classes. A genomewide survey of correlation between codon bias and expression level found codon bias to be significantly correlated with mRNA expression (r(s) = -0.30 and P < 10-(131)) but does not alone explain difference, in dS between classes. Surprisingly. it was found that genes expressed after embryogenesis have a significantly greater number of duplicates in both the C. elegans and C briggsae genomes (P < 10(-20) and P < 10(-13)) when compared with early-expressed and nonmodulated genes. A similarity in the distribution of duplicates of nonmodulated and early-expressed genes, as well as a disproportionately higher number of early pseudogenes, lend support to the hypothesis that this difference in duplicate number is caused by selection against gene duplicates of early-expressed genes. reflecting developmental constraint. Developmental constraint at the level of gene duplication may have important implications for macroevolutionary change. ------------------- Key: 5253 Medline: 11891226 Authors: Riihimaa P;Nissi R;Page AP;Winter AD;Keskiaho K;Kivirikko KI;Myllyharju J Title: Egg shell collagen formation in Caenorhabditis elegans involves a novel prolyl 4-hydroxylase expressed in spermatheca and embryos and possessing many unique properties. Citation: Journal of Biological Chemistry 277: 18238-18243 2002 Type: ARTICLE Genes: phy-1 phy-2 phy-3 Abstract: The collagen prolyl 4-hydroxylases (EC 1.14.11.2) play a critical role in the synthesis of all collagens. The enzymes from all vertebrate species studied are alpha(2)beta(2) tetramers, in which the beta subunit is identical to protein disulfide isomerase (PDI). Two isoforms of the catalytic a subunit, PHY-1 and PHY-2, have previously been characterized from Caenorhabditis elegans. We report here on the cloning and characterization of a third C. elegans a subunit isoform, PHY-3. It is much shorter than the previously characterized vertebrate and C. elegans a subunits and shows 23-30% amino acid sequence identity to PHY-1 and PHY-2 within the catalytic C-terminal region. Recombinant PHY-3 coexpressed in insect cells with a C. elegans PDI isoform that does not associate with PHY-1 was found to be an active prolyl 4-hydroxylase. The phy-3 gene consists of five exons, and its expression pattern differs distinctly from the hypodermally expressed phy-1 and phy-2 in that it is expressed in embryos, late larval stages, and adult nematodes, expression in the latter being restricted to the spermatheca. Nematodes homozygous for a phy-3 deletion are phenotypically of the wild type and fertile, but the 4-hydroxyproline content of phy-3(-/-) early embryos was reduced by about 90%. PHY-3 is thus likely to be involved in the synthesis of collagens in early embryos, probably of those in the egg shell. ------------------- Key: 5254 Medline: Authors: Scholey JM Title: Rafting along the axon on Unc104 motors. Citation: Developmental Cell 2: 515-516 2002 Type: REVIEW Genes: unc-104 Abstract: Neurotransmission depends upon the fast axonal transport of synaptic vesicle precursors by the monomeric kinesin Unc104, a motor whose mechanism of action is a topic of debate. New work suggests that the formation of lipid raft domains triggers the assembly of vesicle-bound Unc104 dimers and the concomitant activation of processive movement, facilitating efficient long-range vesicle ------------------- Key: 5255 Medline: Authors: Bruinsma JJ;Jirakulaporn T;Muslin AJ;Kornfeld K Title: Zinc ions and cation diffusion facilitator proteins regulate Ras-mediated signaling. Citation: Developmental Cell 2: 567-578 2002 Type: ARTICLE Genes: cdf-1 let-23 let-60 lin-1 lin-12 lin-15 Abstract: C. elegans cdf-1 was identified in a genetic screen for regulators of Ras-mediated signaling. CDF-1 is a cation diffusion facilitator protein that is structurally and functionally similar to vertebrate ZnT-1. These proteins have an evolutionarily conserved function as positive regulators of the Ras pathway, and the Ras pathway has an evolutionarily conserved ability to respond to CDF proteins. CDF proteins regulate Ras-mediated signaling by promoting Zn2+ efflux and reducing the concentration of cytosolic Zn2+, and cytosolic Zn2+ negatively regulates Ras-mediated signaling. Physiological concentrations of Zn2+ cause a significant inhibition of Ras-mediated signaling. These findings suggest that Zn2+ negatively regulates a conserved element of the signaling pathway and that Zn2+ regulation is important for maintaining the inactive state of the Ras pathway. ------------------- Key: 5256 Medline: Authors: Antoshechkin I;Han M Title: The C. elegans evl-20 gene is a homolog of the small GTPase ARL2 and regulates cytoskeleton dynamics during cytokinesis and morphogenesis. Citation: Developmental Cell 2: 579-591 2002 Type: ARTICLE Genes: ajm-1 egl-17 evl-20 hmp-1 hmp-2 hmr-1 Abstract: The in vivo functions of ARF-like members of the Ras superfamily of GTPases are relatively unexplored. Here we describe the analysis of C. elegans evl-20 gene that encodes a functional homolog of human ARL2. Elimination of evl-20 function results in abnormal vulval, gonad, and male tail development and disrupts embryonic proliferation, hypodermal enclosure, and elongation. Loss of evl-20 function causes specific defects in the microtubule cytoskeleton, which is the likely molecular basis for the observed defects. EVL-20 is closely associated with both the cell cortex and astral microtubules, suggesting that it may directly interact with microtubule structures at those locations. Our data indicate that EVL-20 functions in the cytoplasm and at the plasma membrane to regulate cytoskeletal dynamics during cytokinesis and morphogenesis. ------------------- Key: 5257 Medline: 11959816 Authors: Fujii T;Nakao F;Shibata Y;Shioi G;Kodama E;Fujisawa H;Takagi S Title: Caenorhabditis elegans plexinA, PLX-1, interacts with transmembrane semaphorins and regulates epidermal morphogenesis. Citation: Development 129: 2053-2063 2002 Type: ARTICLE Genes: mab-20 plx-1 plx-2 Abstract: The plexin family transmembrane proteins are putative receptors for semaphorins, which are implicated in the morphogenesis of animal embryos, including axonal guidance. We have generated and characterized putative null mutants of the C. elegans plexinA gene, plx-1. plx-1 mutants exhibited morphological defects: displacement of ray 1 and discontinuous alae. The epidermal precursors for the affected organs were aberrantly arranged in the mutants, and a plx-1::gfp transgene was expressed in these epidermal precursor cells as they underwent dynamic morphological changes. Suppression of C. elegans transmembrane semaphorins, Ce-Sema-1a and Ce-Sema-1b, by RNA interference caused a displacement of ray 1 similar to that of plx-1 mutants, whereas mutants for the Ce-Sema-2a/mab-20 gene, which encodes a secreted-type semaphorin, exhibited phenotypes distinct from those of plx-1 mutants. A heterologous expression system showed that Ce-Sema-1a, but not Ce-Sema-2a, physically bound to PLX-1. Our results indicate that PLX-1 functions as a receptor for transmembrane-type semaphorins, and, though Ce-Sema-2a and PLX-1 both play roles in the regulation of cellular morphology during epidermal morphogenesis, they function rather independently. ------------------- Key: 5258 Medline: Authors: Ginzburg VE;Roy PJ;Culotti JG Title: Semaphorin 1a and semaphorin 1b are required for correct epidermal cell positioning and adhesion during morphogenesis in C. elegans. Citation: Development 129: 2065-2078 2002 Type: ARTICLE Genes: smp-1 smp-2 eDf14 sDf4 Abstract: The semaphorin family comprises secreted and transmembrane proteins involved in axon guidance and cell migration. We have isolated and characterized deletion mutants of C. elegans semaphorin 1a (Ce-sema-1a or smp-1) and semaphorin 1b (Ce-sema-1b or smp-2) genes. Both mutants exhibit defects in epidermal functions. For example, the R1.a-derived ray precursor cells frequently fail to change anterior/posterior positions completely relative to their sister tail lateral epidermal precursor cell R1.p, causing ray 1 to be formed anterior to its normal position next to ray 2. The ray cells, which normally separate from the lateral tail seam cell (SET) at the end of L4 stage, remains connected to the SET cell even in adult mutant males. The ray 1 defects are partially penetrant in each single Ce-sema-1 mutant at 20degreesC, but are greatly enhanced in Ce-sema-1 double mutants, suggesting that Ce-Sema-1a and Ce-Sema-1b function in parallel to regulate ray 1 position. Both mutants also have defects in other aspects of epidermal functions, including head and tail epidermal morphogenesis and touch cell axon migration, whereas, smp-1 mutants alone have defects in defecation and brood size. A feature of smp-1 mutants that is shared with mutants of mab-20 (which encodes Sema-2a) is the abnormal perdurance of contacts between epidermal cells. ------------------- Key: 5259 Medline: Authors: Harrington RJ;Gutch MJ;Hengartner MO;Tonks NK;Chisholm AD Title: The C. elegans LAR-like receptor tyrosine phosphatase PTP-3 and the VAB-1 Eph receptor tyrosine kinase have partly redundant functions in morphogenesis. Citation: Development 129: 2141-2153 2002 Type: ARTICLE Genes: clr-1 efn-1 efn-2 efn-3 ina-1 ptp-3 vab-1 mnDf57 mnDf83 mnDf89 mnDf90 Abstract: Receptor-like protein-tyrosine phosphatases (RPTPs) form a diverse family of cell surface molecules whose functions remain poorly understood. The LAR subfamily of RPTPs has been implicated in axon guidance and neural development. Here we report the molecular and genetic analysis of the C. elegans LAR subfamily member PTP-3. PTP-3 isoforms are expressed in many tissues in early embryogenesis, and later become localized to neuronal processes and to epithelial adherens junctions. Loss of function in ptp-3 causes low-penetrance defects in gastrulation and epidermal development similar to those of VAB-1 Eph receptor tyrosine kinase mutants. Loss of function in ptp-3 synergistically enhances phenotypes of mutations in the C. elegans Eph receptor VAB-1 and a subset of its ephrin ligands, but does not show specific interactions with several other RTKs or morphogenetic mutants. The genetic interaction of vab-1 and ptp-3 suggests that LAR-like RPTPs and Eph receptors have related and partly redundant functions in C. elegans morphogenesis. ------------------- Key: 5260 Medline: Authors: Kostic I;Roy R Title: Organ-specific cell division abnormalities caused by mutation in a general cell cycle regulator in C. elegans. Citation: Development 129: 2155-2165 2002 Type: ARTICLE Genes: cdc-25.1 cki-1 cyd-1 cye-1 elt-2 mom-2 pop-1 hDf8 qDf16 Abstract: The precise control of cell division during development is pivotal for morphogenesis and the correct formation of tissues and organs. One important gene family involved in such control is the p21/p27/p57 class of negative cell cycle regulators. Loss of function of the C. elegans p27 homolog, cki-1, causes extra cell divisions in numerous tissues including the hypodermis, the vulva, and the intestine. We have sought to better understand how cell divisions are controlled upstream or in parallel to cki-1 in specific organs during C. elegans development. By taking advantage of the invariant cell lineage of C. elegans, we used an intestinal-specific GFP reporter in a screen to identify mutants that undergo cell division abnormalities in the intestinal lineage. We have isolated a mutant with twice the wild-type complement of intestinal cells, all of which arise during mid-embryogenesis. This mutant, called rr31, is a fully dominant, maternal-effect, gain-of-function mutation in the cdc-25.1 cell cycle phosphatase that sensitizes the intestinal lineage to an extra cell division. We showed that cdc-25.1 acts at the G1/S transition, as ectopic expression of CDC-25.1 caused entry into S phase in intestinal cells. In addition, we showed that the cdc-25.1(gf) requires cyclin E. The extra cell division defect was shown to be restricted to the E lineage and the E fate is necessary and sufficient to ------------------- Key: 5261 Medline: 12015115 Authors: Mackinnon AC;Qadota H;Norman KR;Moerman DG;Williams DB Title: C. elegans PAT-4/ILK functions as an adaptor protein within integrin adhesion complexes. Citation: Current Biology 12: 787-797 2002 Type: ARTICLE Genes: deb-1 pat-2 pat-3 pat-4 unc-52 unc-89 unc-97 unc-112 Abstract: Background: Mammalian integrin-linked kinase (ILK) was identified in a yeast two-hybrid screen for proteins binding the integrin beta(1) subunit cytoplasmic domain. ILK has been implicated in integrin-mediated signaling and is also an adaptor within integrin-associated cytoskeletal complexes. Results: We identified the C. elegans pat-4 gene in previous genetic screens for mutants unable to assemble integrin-mediated muscle cell attachments. Here, we report that pat-4 encodes the sole C. elegans homolog of ILK. In pat-4 null mutants, embryonic muscle cells form integrin foci, but the subsequent recruitment of vinculin and UNC-89 as well as actin and myosin filaments to these in vivo focal adhesion analogs is blocked. Conversely, PAT-4/ILK requires the ECM component UNC-52/perlecan, the transmembrane protein integrin, and the novel cytoplasmic attachment protein UNC-112 to be properly recruited to nascent attachments. Transgenically expressed "kinase-dead" ILK fully rescues pat-4 loss-of-function mutants. We also identify UNC-112 as a new binding partner for ILK. Conclusions: Our data strengthens the emerging view that ILK functions primarily as an adaptor protein within integrin adhesion complexes and identifies UNC-112 as a new ------------------- Key: 5262 Medline: 12015132 Authors: Glotzer M;Dechant R Title: Cytokinesis: regulated by destruction. Citation: Current Biology 12: R344-R346 2002 Type: REVIEW Genes: cul-3 mei-1 mel-26 rfl-1 Abstract: Important transitions in the cell cycle are regulated by ubiquitin-dependent degradation of specific proteins. Recent data indicate that cytokinesis is also regulated by proteolysis. ------------------- Key: 5263 Medline: 12015134 Authors: Zervas CG;Brown NH Title: Integrin adhesion: when is a kinase a kinase? Citation: Current Biology 12: R350-R351 2002 Type: REVIEW Genes: pat-2 pat-3 pat-4 unc-52 unc-97 unc-112 Abstract: Recent genetic studies in the worm Caenorhabditis elegans and fruitfly Drosophila have revealed the essential role integrin-linked kinase plays in integrin adhesion - but it apparently acts in this role as an adaptor rather than a kinase. ------------------- Key: 5264 Medline: 12015116 Authors: Kaitna S;Pasierbek P;Jantsch M;Loidl J;Glotzer M Title: The aurora B kinase AIR-2 regulates kinetochores during mitosis and is required for separation of homologous chromosomes during meiosis. Citation: Current Biology 12: 798-812 2002 Type: ARTICLE Genes: air-2 mix-1 rec-8 sep-1 smc-4 spo-11 Abstract: Background: Mitotic chromosome segregation depends on bi-orientation and capture of sister kinetochores by microtubules emanating from opposite spindle poles and the near synchronous loss of sister chromatid cohesion. During meiosis I, in contrast, sister kinetochores orient to the same pole, and homologous kinetochores are captured by microtubules emanating from opposite spindle poles. Additionally, mechanisms exist that prevent complete loss of cohesion during meiosis I. These features ensure that homologs separate during meiosis I and sister chromatids remain together until meiosis II. The mechanisms responsible for orienting kinetochores in mitosis and for causing asynchronous loss of cohesion during meiosis are not well understood. Results: During mitosis in C. elegans, aurora B kinase, AIR-2, is not required for sister chromatid separation, but it is required for chromosome segregation. Condensin recruitment during metaphase requires AIR-2; however, condensin functions during prometaphase, independent of AIR-2. During metaphase, AIR-2 promotes chromosome congression to the metaphase plate, perhaps by inhibiting attachment of chromatids to both spindle poles. During meiosis in AIR-2-depleted oocytes, congression of bivalents appears normal, but segregation fails. Localization of AIR-2 on meiotic bivalents suggests this kinase promotes separation of homologs by promoting the loss of cohesion distal to the single chiasma. Inactivation of the phosphatase that antagonizes AIR-2 causes premature separation of chromatids during meiosis 1, in a separase-dependent reaction. Conclusions: Aurora B functions to resolve chiasmata during meiosis I and to regulate kinetochore function during mitosis. Condensin mediates chromosome condensation during prophase, and condensin-independent pathways contribute to chromosome condensation during metaphase. ------------------- Key: 5265 Medline: Authors: Crittenden SL;Bernstein DS;Bachorik JL;Thompson BE;Gallegos M;Petcherski AG;Moulder G;Barstead R;Wickens M;Kimble J Title: A conserved RNA-binding protein controls germline stem cells in Caenorhabditis elegans. Citation: Nature 417: 660-663 2002 Type: ARTICLE Genes: fbf-1 fbf-2 fem-3 gld-1 tra-2 Abstract: Germline stem cells are defined by their unique ability to generate more of themselves as well as differentiated gametes(1). The molecular mechanisms controlling the decision between self-renewal and differentiation are central unsolved problems in developmental biology with potentially broad medical implications. In Caenorhabditis elegans, germline stem cells are controlled by the somatic distal tip cell(2,3). FBF-1 and FBF-2, two nearly identical proteins, which together are called FBF ('fem-3 mRNA binding factor'), were originally discovered as regulators of germline sex determination(4). Here we report that FBF also controls germline stem cells: in an fbf-1 fbf-2 double mutant, germline proliferation is initially normal, but stem cells are not maintained. We suggest that FBF controls germline stem cells, at least in part, by repressing gld-1, which itself promotes commitment to the meiotic cell cycle(5,6). FBF belongs to the PUF family ('Pumilio and FBF') of RNA-binding proteins(7). Pumilio controls germline stem cells in Drosophila females(8,9),and, in lower eukaryotes, PUF proteins promote continued mitoses(10,11). We suggest that regulation by PUF proteins may be an ancient and widespread mechanism for control of stem cells. ------------------- Key: 5266 Medline: 12068805 Authors: Gan YH;Chua KL;Chua HH;Liu B;Hii CS;Chong HL;Tan P Title: Characterization of Burkholderia pseudomallei infection and identification of novel virulence factors using a Caenorhabditis elegans host system. Citation: Molecular Microbiology 44: 1185-1197 2002 Type: ARTICLE Genes: age-1 egl-9 Abstract: The environmental saphrophyte Burkholderia pseudomallei is the causative agent of melioidosis, a systemic, potentially life-threatening condition endemic to many parts of south-east Asia and northern Australia. We have used the soil nematode Caenorhabditis elegans as a model host to characterize the mechanisms by which this bacterium mounts a successful infection. We find that C. elegans is susceptible to a broad range of Burkholderia species, and that the virulence mechanisms used by this pathogen to kill nematodes may be similar to those used to infect mammals. We also find that the specific dynamics of the C. elegans-B. pseudomallei host-pathogen interaction can be highly influenced by environmental factors, and that nematode killing results at least in part from the presence of a diffusible toxin. Finally, by screening for bacterial mutants attenuated in their ability to kill C. elegans , we genetically identify several new potential virulence factors in B. pseudomallei . The use of C. elegans as a model host should greatly facilitate future investigations into how B. pseudomallei can interact with host organisms. ------------------- Key: 5267 Medline: 12006646 Authors: Padilla PA;Nystul TG;Zager RA;Johnson ACM;Roth MB Title: Dephosphorylation of cell cycle-regulated proteins correlates with anoxia-induced suspended animation in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 13: 1473-1483 2002 Type: ARTICLE Genes: hif-1 Abstract: Some metazoans have evolved the capacity to survive severe oxygen deprivation. The nematode, Caenorliabditis elegans, exposed to anoxia (0 kPa, 0% 02) enters into a recoverable state of suspended animation during all stages of the life cycle. That is, all microscopically observable movement ceases including cell division, developmental progression, feeding, and motility. To understand suspended animation, we compared oxygen-deprived embryos to nontreated embryos in both wild-type and hif-1 mutants. We found that hif-1 mutants survive anoxia, suggesting that the mechanism's for anoxia survival are different from those required for hypoxia. Examination of wild-type embryos exposed to anoxia show that blastomeres arrest in interphase, prophase, metaphase, and telophase but not anaphase. Analysis of the energetic state of anoxic embryos indicated a reversible depression in the ATP to ADP ratio. Given that a decrease in ATP concentrations likely affects a variety of cellular processes, including signal transduction, we compared the phosphorylation state of several proteins in anoxic embryos and normoxic embryos. We found that the phosphorylation state of histone H3 and cell cycle-regulated proteins recognized by the MPM-2 antibody were not detectable in anoxic embryos. Thus, dephosphorylation of specific proteins correlate with the establishment and/or maintenance of a state of anoxia-induced suspended ------------------- Key: 5268 Medline: 12006659 Authors: Bui YK;Sternberg PW Title: Caenorhabditis elegans inositol 5-phosphatase homolog negatively regulates inositol 1,4,5-triphosphate signaling in ovulation. Citation: Molecular Biology of the Cell 13: 1641-1651 2002 Type: ARTICLE Genes: ipp-2 ipp-5 itr-1 let-23 lfe-1 lfe-2 lin-3 nlp-8 Abstract: Ovulation in Caenorizabditis elegans requires inositol 1,4,5-triphosphate (IP3) signaling activated by the epidermal growth factor (EGF)-receptor homolog LET-23. We generated a deletion mutant of a type I 5-phosphatase, ipp-5, and found a novel ovulation phenotype whereby the spermatheca hyperextends to engulf two oocytes per ovulation cycle. The temporal and spatial expression of IPP-5 is consistent with its proposed inhibition of IP3 signaling in the adult spermatheca. ipp-5 acts downstream of let-23, and interacts with let-23-mediated IP3 signaling pathway genes. We infer that IPP-5 negatively regulates IP3 signaling to ensure proper spermathecal contraction. ------------------- Key: 5269 Medline: 12006669 Authors: Rolls MM;Hall DH;Victor M;Stelzer EHK;Rapoport TA Title: Targeting of rough endoplasmic reticulum membrane proteins and ribosomes in invertebrate neurons. Citation: Molecular Biology of the Cell 13: 1778-1791 2002 Type: ARTICLE Genes: glr-1 Abstract: The endoplasmic reticulum (ER) is divided into rough and smooth domains (RER and SER). The two domains share most proteins, but RER is enriched in some membrane proteins by an unknown mechanism. We studied RER protein targeting by expressing fluorescent protein fusions to ER membrane proteins in Caenorhabditis elegans. In several cell types RER and general ER proteins colocalized, but in neurons RER proteins were concentrated in the cell body, whereas general ER proteins were also found in neurites. Surprisingly RER membrane proteins diffused rapidly within the cell body, indicating they are not localized by immobilization. Ribosomes were also concentrated in the cell body, suggesting they may be in part responsible for targeting RER membrane proteins. ------------------- Key: 5270 Medline: Authors: Honda Y;Honda S Title: Oxidative stress and life span determination in the nematode Caenorhabditis elegans. Citation: Annals of the New York Academy of Sciences 959: 466-474 Type: REVIEW Genes: age-1 akt-1 akt-2 clk-1 clk-2 clk-3 ctl-1 daf-1 daf-2 daf-7 daf-11 daf-16 daf-18 gro-1 pdk-1 sod-1 sod-2 sod-3 sod-4 Abstract: The free radical theory of aging proposes that oxidative stress is one of the determinants of an organism?s life span. In Caenorhabditis elegans, genetic or environmental changes have been shown to modulate life span. Here we discuss whether changes in the generation and destruction of free radicals are implicated in these life span modulations. Changes in culture oxygen concentrations that are considered to reflect free radical generation perturb the life span. The life spans under high and low oxygen concentrations were shorter and longer, respectively, than those under normoxic conditions. Short-term exposure to high oxygen concentration lengthens the life span. This is considered to be the result of an increase in antioxidant defense induced by short-term oxidative stress. Mutations in genes such as age-1 and daf-2 that compose the insulin-like signaling network conferred oxidative stress resistance and an increase in Mn-SOD gene expression as well as life span extension. ------------------- Key: 5271 Medline: 12137228 Authors: Johnson TE;Henderson S;Murakami S;de Castro E;de Castro SH;Cypser J;Rikke B;Tedesco P;Link C Title: Longevity genes in the nematode Caenorhabditis elegans also mediate increased resistance to stress and prevent disease. Citation: Journal of Inherited Metabolic Disease 25: 197-206 2002 Type: REVIEW Genes: age-1 clk-1 daf-2 daf-4 daf-7 daf-16 daf-23 old-1 spe-2 spe-6 spe-26 tkr-1 Abstract: More than 40 single-gene mutants in Caenorhabditis elegans have been demonstrated to lead to increased lifespan (a rigorous, operational test for being a gerontogene) of 20% or more; these are referred to collectively as 'Age' mutants. Age mutants must change key functions that are rate-limiting determinants of longevity; moreover, important genes can be identified independently of prior hypotheses as to actual mode of gene action in extending longevity and/or 'slowing' of ageing. These Age mutants define as many as nine (possibly) distinct pathways and/or modes of action, as defined by primary phenotype. Each of three well-studied mutants (age-1, clk-1, and spe-26) alters age-specific mortality rates in a fashion unique to itself. In age-1 mutants, the decreases in mortality rates are quite dramatic, with an almost tenfold drop in mortality throughout most of life. All Age mutants (so far without exception) increase the ability of the worm to respond to several (but not all) stresses, including heat, UV, and reactive oxidants. We have used directed strategies as well as random mutagenesis to identify novel genes that increase the worm's ability to resist stress. Two genes (daf-16 and old-1) are epistatic to the long-life phenotype of most mutants and also yield over-expression strains that are stress-resistant and long-lived. We have also used a variety of approaches to determine what transcriptional alterations are associated with increased longevity (and with ageing itself), including whole-genome expression studies using microarrays and GFP reporter constructs. We suggest that the role of the Age genes in both longevity and stress resistance indicates that a major evolutionary determinant of longevity is the ability to respond to stress. In mammals, both dietary restriction and hormesis are phenomena in which the endogenous level of resistance to stress has been upregulated; both of these interventions extend longevity, suggesting possible evolutionary ------------------- Key: 5272 Medline: 12019225 Authors: Nystrom J;Shen ZZ;Aili M;Flemming AJ;Leroi A;Tuck S Title: Increased or decreased levels of Caenorhabditis elegans lon-3, a gene encoding a collagen, cause reciprocal changes in body length. Citation: Genetics 161: 83-97 2002 Type: ARTICLE Genes: apm-2 col-6 daf-4 daf-7 dbl-1dpy-2 dpy-5 dpy-6 dpy-7 dpy-8 dpy-9 dpy-10 dpy-11 dpy-13 dpy-14 dpy-17 dpy-18 dpy-19 dpy-20 dpy-21 dpy-26 dpy-27 dpy-28 dpy-29 dpy-30 him-8 lon-1 lon-3 rol-6 sdc-3 sma-2 sqt-1 sqt-3 arDf1 Abstract: Body length in C. elegans is regulated by a member of the TGFbeta family, DBL-1. Loss-of-function mutations in dbl-1, or in genes encoding components of the signaling pathway it activates, cause worms to be shorter than wild type and slightly thinner (Sma). Overexpression of dbl-1 confers the Lon phenotype characterized by an increase in body length. We show here that loss-of-function mutations in dbl-1 and lon-1, respectively, cause a decrease or increase in the ploidy of nuclei in tile hypodermal syncytial cell, hyp7. To learn snore about the regulation of body length in C. elegans we carried out a genetic screen for new mutations causing a Lon phenotype. We report here the cloning and characterization of lon-3. lon-3 is shown to encode a putative cuticle collagen that is expressed in hypodermal cells. We show that, whereas putative null mutations in lon-3 (or reduction of lon-3 activity by RNAi) causes a Lon phenotype, increasing lon-3 gene copy number causes a marked reduction in body length. Morphometric analyses indicate that the lon-3 loss-of-function phenotype resembles that caused by overexpression of dbl-1. Furthermore, phenotypes caused by defects in dbl-1 or lon-3 expression are in both cases suppressed by a null mutation in sqt-1, a second cuticle collagen gene. However, whereas loss of dbl-1 activity causes a reduction in hypodermal endoreduplication, the reduction in body length associated with overexpression of lon-3 occurs in the absence of defects in hypodermal ploidy. ------------------- Key: 5273 Medline: 12019226 Authors: Graustein A;Gaspar JM;Walters JR;Palopoli MF Title: Levels of DNA polymorphism vary with mating system in the nematode genus Caenorhabditis. Citation: Genetics 161: 99-107 2002 Type: ARTICLE Genes: glp-1 spe-9 tra-2 Abstract: Self-fertilizing species often harbor less genetic variation than cross-fertilizing species, and at least four different models have been proposed to explain this trend. To investigate further the relationship between mating system and genetic variation, levels of DNA sequence polymorphism were compared among three closely related species in the genus Caenorhabditis: two self-fertilizing species, Caenorhabditis elegans and C. briggsae, and one cross-fertilizing species, C. remanei. As expected, estimates of silent site nucleotide diversity were lower in the two self-fertilizing species. For the mitochondrial genome, diversity in the selling species averaged 42% of diversity in C. remanei. Interestingly, the reduction in genetic variation was much greater for the nuclear than for the mitochondrial genome. For two nuclear genes, diversity in the selfing species averaged 6 and 13% of diversity in C. remanei. We argue that either population bottlenecks or the repeated action of natural selection, coupled with high levels of selfing, are likely to explain the observed reductions in species-wide genetic diversity. ------------------- Key: 5274 Medline: 12019227 Authors: van Swinderen B;Metz LB;Shebester LD;Crowder CM Title: A Caenorhabditis elegans pheromone antagonizes volatile anesthetic action through a Go-coupled pathway. Citation: Genetics 161: 109-119 2002 Type: ARTICLE Genes: bas-1 cat-2 cat-4 che-2 che-3 che-11 che-13 daf-1 daf-3 daf-4 daf-5 daf-7 daf-8 daf-10 daf-11 daf-12 daf-21 daf-22 eat-16 egl-10 egl-30 glr-1 goa-1 gpb-2 osm-1 osm-3 osm-5 osm-6 ric-4 sag-1 snb-1 unc-25 unc-49 unc-64 Abstract: Volatile anesthetics (VAs) disrupt nervous system function by an ill-defined mechanism with no known specific antagonists. During the course of characterizing the response of the nematode C. elegans to VAs, we discovered that a C. elegans pheromone antagonizes the VA halothane. Acute exposure to pheromone rendered wild-type C. elegans resistant to clinical concentrations of halothane, increasing the EC50 from 0,43 +/- 0.03 to 0.90 +/- 0.02. C. elegans mutants that disrupt the function of sensory neurons required for the action of the previously characterized dauer pheromone blocked pheromone induced resistance (Pir) to halothane. Pheromone preparations from loss-of-function mutants of daf-22, a gene required for dauer pheromone production, lacked the halothane-resistance activity, suggesting that dauer and Pir pheromone are identical. However, the pathways for pheromone's effects on dauer formation and VA action were not identical. Not all mutations that alter dauer formation affected the Pir phenotype. Further, mutations in genes not known to be involved in dauer formation completely blocked Pir, including those altering signaling through the G proteins Goalpha and Gqalpha. A model in which sensory neurons transduce the pheromone activity through antagonistic Go and Gq pathways, modulating VA action against neurotransmitter release machinery, is proposed. ------------------- Key: 5275 Medline: 12019229 Authors: Moorman C;Plasterk RHA Title: Functional characterization of the adenylyl cyclase gene sgs-1 by analysis of a mutational spectrum in Caenorhabditis elegans. Citation: Genetics 161: 133-142 2002 Type: ARTICLE Genes: sgs-1 Abstract: The sgs-1 (suppressor of activated Galpha) gene encodes one of the four adenylyl cyclases in the nematode C. elegans and is most similar to mammalian adenylyl cyclase type IX. We isolated a complete loss-of-function mutation in sgs-1 and found it to result in animals with retarded development that arrest in variable larval stages. sgs-1 mutant animals exhibit lethargic movement and pharyngeal pumping and (while not reaching adulthood) have a mean life span that is >50% extended compared to wild type. An extensive set of reduction-of-function mutations in sgs-1 was isolated in a screen for suppressors of a neuronal degeneration phenotype induced by the expression of a constitutively active version of the heterotrimeric Galpha(s) subunit of C. elegans. Although most of these mutations change conserved residues within the catalytic domains of sgs-1, mutations in the less-conserved transmembrane domains are also found. The sgs-1 reduction-of function mutants are viable and have reduced locomotion rates, but do not show defects in pharyngeal pumping or life span. ------------------- Key: 5276 Medline: 12019230 Authors: Muhlrad PJ;Ward S Title: Spermiogenesis initiation in Caenorhabditis elegans involves a casein kinase 1 encoded by the spe-6 gene. Citation: Genetics 161: 143-155 2002 Type: ARTICLE Genes: fer-1 spe-6 spe-8 spe-12 spe-27 spe-29 ctDf2 ctDf3 tDf2 Abstract: Immature spermatids from Caenorhabditis elegans are stimulated by an external activation signal to reorganize their membranes and cytoskeleton to form crawling spermatozoa. This rapid maturation, termed spermiogenesis, occurs without any new gene expression. To better understand this signal transduction pathway, we isolated suppressors of a mutation in the spe-27 gene, which is part of the pathway. The suppressors bypass the requirement for spe-27, as well as three other genes that act in this pathway, spe-8, spe-12, and spe-29. Eighteen of the suppressor mutations are new alleles of spe-6, a previously identified gene required for an early stage of spermatogenesis. The original spe-6 mutations are loss-of-function alleles that prevent major sperm protein (MSP) assembly in the fibrous bodies of spermatocytes and arrest development in meiosis. We have isolated the spe-6 gene and find that it encodes a predicted protein-serine/threonine kinase in the casein kinase 1 family. The suppressor mutations appear to be reduction-of-function alleles. We propose a model whereby SPE-6, in addition to its early role in spermatocyte development, inhibits spermiogenesis until the activation signal is received. The activation signal is transduced through SPE-8, SPE-12, SPE-27, and SPE-29 to relieve SPE-6 repression, thus triggering the formation of crawling ------------------- Key: 5277 Medline: 12023306 Authors: Gleason JE;Korswagen HC;Eisenmann DM Title: Activatin of Wnt signaling bypasses the requirement for RTK/Ras signaling during C. elegans vulval induction. Citation: Genes & Development 16: 1281-1290 2002 Type: ARTICLE Genes: apr-1 bar-1 let-23 let-60 lin-31 lin-39 lin-45 mig-14 pop-1 pry-1 Abstract: During Caenorhabditis elegans vulval development, activation of receptor tyrosine kinase/Ras and Notch signaling pathways causes three vulval precursor cells (VPCs) to adopt induced cell fates. A Wnt signaling pathway also acts in cell fate specification by the VPCs, via regulation of the Hox gene lin-39. We show here that either mutation of pry-1 or expression of an activated BAR-1 beta-catenin protein causes an Overinduced phenotype, in which greater than three VPCs adopt induced cell fates. This indicates that pry-1, which encodes a C. elegans axin homolog, acts as a negative regulator of Wnt signaling in the VPCs. Loss of activity of the APC homolog apr-1 increases the penetrance of this Overinduced phenotype, suggesting that APR-1 may play a negative role in Wnt signaling in this process in C. elegans similar to APC proteins in other systems. The Overinduced phenotype is suppressed by reduction of function of the genes pop-1 TCF and lin-39 Hox. Surprisingly, the Overinduced phenotype caused by hyperactivated Wnt signaling is not dependent on signaling through the Ras pathway. These data suggest that hyperactivation of Wnt signaling is sufficient to cause VPCs to adopt induced fates and that a canonical Wnt pathway may play an important role during C. elegans vulval ------------------- Key: 5278 Medline: 12023307 Authors: Korswagen HC;Coudreuse DYM;Betist MC;van de Water S;Zivkovic D;Clevers HC Title: The axin-like protein PRY-1 is a negative regulator of a canonical Wnt pathway in C. elegans. Citation: Genes & Development 16: 1291-1302 2002 Type: ARTICLE Genes: apr-1 bar-1 dsh-1 dsh-2 egl-10 egl-20 hmp-2 mab-5 mig-5 pop-1 pry-1 sgg-1 Abstract: Axin, APC, and the kinase GSK3beta are part of a destruction complex that regulates the stability of the Wnt pathway effector beta-catenin. In C. elegans, several Wnt-controlled developmental processes have been described, but an Axin ortholog has not been found in the genome sequence and SGG-1/GSK3beta, and the APC-related protein APR-1 have been shown to act in a positive, rather than negative fashion in Writ signaling. We have shown previously that the EGL-20/Wnt-dependent expression of the homeobox gene mab-5 in the Q neuroblast lineage requires BAR-1/beta-catenin and POP-1/Tef. Here, we have investigated how BAR-1 is regulated by the EGL-20 pathway. First, we have characterized a negative regulator of the EGL-20 pathway, pry-1. We show that pry-1 encodes an RGS and DIX domain-containing protein that is distantly related to Axin/Conductin. Our results demonstrate that despite its sequence divergence, PRY-1 is a functional Axin homolog. We show that PRY-I interacts with BAR-1, SGG-1, and APR-1 and that overexpression of PRY-1 inhibits mab-5 expression. Furthermore, pry-1 rescues the zebrafish axin1 mutation masterblind, showing that it can functionally interact with vertebrate destruction complex components. Finally, we show that SGG-1, in addition to its positive regulatory role in early embryonic Wnt signaling, may function as a negative regulator of the EGL-20 pathway. We conclude that a highly divergent destruction complex consisting of PRY-1, SGG-1, and APR-1 regulates BAR-1/beta-catenin signaling in C. ------------------- Key: 5279 Medline: 12015284 Authors: Humphrey JA;Sedensky MM;Morgan PG Title: Understanding anesthesia: making genetic sense of the absence of senses. Citation: Human Molecular Genetics 11: 1241-1249 2002 Type: REVIEW Genes: gas-1 unc-1 unc-24 unc-79 Abstract: The discovery of the phenomenon of anesthesia over 150 years ago was a watershed event that revolutionized the practice of medicine. Despite their annual use in millions of patients, the mechanism by which volatile anesthetics produce reversible loss of consciousness remains a mystery. The inherent problems in studying loss of consciousness in humans are legion. However, multiple model organisms are currently being exploited to apply the powerful tools of modern molecular genetics to this question. Mutants in yeast, nematodes, fruit flies and mice have been produced that display abnormalities in their response to volatile anesthetics. Each organism possesses unique advantages and difficulties as a model system, and each reveals different molecules that control its response to anesthetics. Nonetheless, the accumulating body of genetic evidence points to multiple targets for volatile anesthetics. Not only will understanding how volatile anesthetics work yield better and safer anesthetics, but, in addition, these remarkable compounds may ultimately serve as probes to understand the nature of consciousness itself. ------------------- Key: 5280 Medline: 11997337 Authors: GuhaThakurta D;Palomar L;Stormo GD;Tedesco P;Johnson TE;Walker DW;Lithgow G;Kim S;Link CD Title: Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. Citation: Genome Research 12: 701-712 2002 Type: ARTICLE Genes: age-1 ces-2 hsp-16-2 hsp-16-41 skn-1 Abstract: We report here the identification of a previously unknown transcription regulatory element for heat shock (HS) genes in Caenorhabditis elegans. We monitored the expression pattern of 11,917 genes from C elegans to determine the genes that were up-regulated on HS. Twenty eight genes were observed to be consistently up-regulated in several different repetitions of the experiments. We analyzed the upstream regions of these genes using computational DNA pattern recognition methods. Two potential cis-regulatory motifs were identified in this way. One of these motifs (TTCTAGAA) was the DNA binding motif for the heat shock factor (HSF), whereas the other (GGGTGTC) was previously unreported in the literature. We determined the significance of these motifs for the HS genes using different statistical tests and parameters. Comparative sequence analysis of orthologous HS genes from C elegans and Caenorhabditis briggsae indicated that the identified DNA regulatory motifs are conserved across related species. The role of the identified DNA sites in regulation of HS genes was tested by in vitro mutagenesis of a green fluorescent protein (GFP) reporter transgene driven by the C elegans hsp-16-2 promoter. DNA sites corresponding to both motifs are shown to play a significant role in up-regulation of the hsp-16-2 gene oil HS. This is one of the rare instances in which a novel regulatory element, identified using computational methods, is shown to be biologically active. The contributions of individual sites toward induction of transcription on HS are nonadditive, which indicates interaction and cross-talk between the sites, possibly through the transcription factors (TFs) binding to these sites. ------------------- Key: 5281 Medline: Authors: Mounsey A;Bauer P;Hope IA Title: Evidence suggesting that a fifth of annotated Caenorhabditis elegans genes may be pseudogenes. Citation: Genome Research 12: 770-775 2002 Type: ARTICLE Genes: Abstract: Only a minority of the genes, identified in the Caenorhabditis elegans genome sequence data by computer analysis, have been characterized experimentally. We attempted to determine the expression patterns for a random sample of the annotated genes using reporter gene fusions. A low success rate was obtained for evolutionarily recently duplicated genes. Analysis of the data suggests that this is not due to conditional or low-level expression. The remaining explanation is that most of the annotated genes in the recently duplicated category are pseudogenes, a proportion corresponding to 20% of all of the annotated C elegans genes. Further Support for this Surprisingly high figure was sought by comparing sequences for families of recently duplicated C elegans genes. Although only a preliminary analysis, clear evidence for a gene having been recently inactivated by genetic drift was found for many genes in the recently duplicated category. At least 4% of the annotated C elegans genes call be recognized as pseudogenes simply from closer inspection of the sequence data. Lessons learned in identifying pseudogenes in C elegans could be of value in the annotation of the genomes of other species where, although there may be fewer pseudogenes, they may be harder to detect. ------------------- Key: 5282 Medline: Authors: Iwahashi J;Kawasaki I;Kohara Y;Gengyo-Ando K;Mitani S;Ohshima Y;Hamada N;Hara K;Kashiwagi T;Toyoda T Title: Caenorhabditis elegans reticulon interacts with RME-1 during embryogenesis. Citation: Biochemical and Biophysical Research Communications 293: 698-704 2002 Type: ARTICLE Genes: ced-9 rme-1 Abstract: Reticulon (RTN) family proteins are localized in the endoplasmic reticulum (ER). At least four different RTN genes have been identified in mammals. but in most cases. the functions of the encoded proteins except mammalian RTN4-A and RTN4-B are unknown. Each RTN gene produces 1-3 proteins by different promoters and alternative splicing. In Caenorhabditis elegans, there is a single gene (rtn gene) encoding three reticulon proteins, nRTN-A, B, and C. mRNA of nRTN-C is expressed in germ cells and embryos. However. nRTN-C protein is only expressed during embryogenesis and rapidly disappears after hatch. By yeast two-hybrid screening. two clones encoding the same C-terminal region of RME-1, a protein functioning in the endocytic recycling, were isolated. These findings suggest that nRTN-C functions in the endocytic pathway during ------------------- Key: 5283 Medline: Authors: Plasterk RHA Title: RNA silencing: the genome's immune system. Citation: Science 296: 1263-1265 2002 Type: REVIEW Genes: Abstract: Genomes are databases sensitive to invasion by viruses. In recent years, a defense mechanism has been discovered, which turns out to be conserved among eukaryotes. The system can be compared to the immune system in several ways: It has specificity against foreign elements and the ability to amplify and raise a massive response against an invading nucleic acid. The latter property is beginning to be understood at the molecular level. ------------------- Key: 5284 Medline: Authors: Zamore PD Title: Ancient pathways programmed by small RNAs. Citation: Science 296: 1265-1269 2002 Type: REVIEW Genes: mut-7 rde-1 rde-2 rde-4 Abstract: Double-stranded RNA can now be used in a wide variety of eukaryotes to suppress the expression of virtually any gene, allowing the rapid analysis of that gene's function, a technique known as RNA interference. But how cells use the information in double-stranded RNA to suppress gene expression and why they contain the machinery to do so remain the subjects of intense scrutiny. Current evidence suggests that RNA interference and other "RNA silencing" phenomena reflect an elaborate cellular apparatus that eliminates abundant but defective messenger RNAs and defends against molecular parasites such as transposons and ------------------- Key: 5285 Medline: Authors: Ghenea S;Takeuchi M;Motoyama J;Sasamoto K;Kunau W-H;Kamiryo T;Bun-ya M Title: The cDNA sequence and expression of the AAA-family peroxin genes pex-1 and pex-6 from the nematode Caenorhabditis elegans. Citation: Zoological Science 19: 249- 2002 Type: CORRECT Genes: pex-1 pex-6 prx-1 prx-6 Abstract: The authors would like to correct errors in the gene names of C. elegans, pex-1 and pex-6 to prx-1 and prx-6 respectively. ------------------- Key: 5286 Medline: 12064609 Authors: Starich T;Sheehan M;Jadrich J;Shaw J Title: Innexins in C. elegans. Citation: Cell Communication & Adhesion 8: 311-314 2001 Type: REVIEW Genes: Abstract: Innexins are functionally analogous to the vertebrate connexins, and the innexin family of gap junction proteins has been identified in many invertebrates, including Drosophila and C. elegans. The genome sequencing project has identified 25 innexins in C. elegans. We are particularly interested in the roles that gap junctions may play in embryonic development and in wiring of the nervous system. To identify the particular C. elegans innexins that are involved in these processes, we are examining their expression patterns using specific antibodies and translational GFP fusions. In addition we are investigating mutant, RNAi and overexpression phenotypes for many of these genes. To date, we have generated specific antibodies to the non-conserved carboxyl termini of 5 innexins. We have constructed GFP translational fusions for 17 innexins and observed expression patterns for 13 of these genes. In total we have characterized expression patterns representing 14 innexins. Mutations have been identified in 5 of these genes, and at least 3 others have RNAi mutant phenotypes. Generalities emerging from our studies include: 1) most tissues and many individual cells express more than one innexin, 2) some innexins are expressed widely, while others are expressed in only a few cells, and 3) there is a potential for functional pairing of innexins. ------------------- Key: 5287 Medline: Authors: Choi KY;Ji YJ;Jee C;Kim DH;Ahnn J Title: Characterization of CeHDA-7, a class II histone deacetylase interacting with MEF-2 in Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 293: 1295-1300 2002 Type: ARTICLE Genes: hda-7 mef-2 Abstract: As a result of screen searching for proteins interacting with MEF-2 transcription factor, we have identified the hda-7 gene in Caenorhabditis elegans. The hda-7 locus encodes a class II histone deacetylase containing a highly conserved catalytic domain. C elegans HDA-7 protein translated in vitro demonstrated a direct interaction with CeMEF-2, as shown in other organisms. CeHDA-7 is abundantly expressed in body-wall muscle cells, neurons, and hypodermal seam cells, similar to CeMEF-2 expression patterns. Consistent with previously known phenotypes observed in mef-2 deletion mutants [Dev. Biol. 223 (2000) 431], RNA interference targeted for hda-7 did not result in muscle function or developmental defects. ------------------- Key: 5288 Medline: Authors: Kohra S;Tominaga N;Takao Y;Nagae M;Ishibashi Y;Ueda K;Arizono K Title: A rapid respiratory toxicity test using Caenorhabditis elegans with an oxygen electrode system. Citation: Journal of Health Science 48: 269-272 2002 Type: ARTICLE Genes: Abstract: We describe a novel approach to evaluating the respiratory toxicity of chemicals in the free-living nematode Caenorhabditis elegans. Using DOX-96KT, a general purpose, multi-channel dissolved oxygen (DO) measuring system, we measured the DO concentration in culture media containing C. elegans exposed to chemicals to assay for respiratory toxicity. The current value, which is an index of the dissolved oxygen concentration in culture media, was measured every 10 sec for 30 min at 24degreeC. We focused on the respiration levels of the exposed worms between 500 and 1800 sec. This method produces results that are similar to the computer tracking system measuring behavioral toxicity. Since it can do multiple dilution series tests at a given time, it is useful for concentration-activity correlation studies. This novel technique is not only an alternative to the computer tracking system for measuring behavioral toxicity but also a rapid sublethal toxicity test for chemical hazard assessment. ------------------- Key: 5289 Medline: Authors: MacColl G;Bouloux P;Quinton R Title: Kallmann syndrome: adhesion, afferents, and anosmia. Citation: Neuron 34: 675-678 2002 Type: REVIEW Genes: kal-1 ttx-3 unc-119 Abstract: Three new studies into the function of human anosmin-1 and related proteins in C. elegans and rodents show that these influence axon branching and axon targeting. The rodent anosmin appears to work at two stages of development, initially promoting axon outgrowth from the olfactory bulb and then stimulating branching from axons into the olfactory cortex. CeKal-1 further influences morphogenesis, and, as the human and nematode anosmins are functionally conserved, these studies provide insights into the pathogenesis of Kallmann syndrome (KS). ------------------- Key: 5290 Medline: Authors: Gieseler K;Grisoni K;Mariol MC;Segalat L Title: Overexpression of dystrobrevin delays locomotion defects and muscle degeneration in a dystrophin-deficient Caenorhabditis elegans. Citation: Neuromuscular Disorders 12: 371-377 2002 Type: ARTICLE Genes: dyb-1 dys-1 hlh-1 Abstract: Duchenne muscular dystrophy is one of the most common neuromuscular diseases. It is caused by mutations in the dystrophin gene. Dystrobrevins are dystrophin-associated proteins potentially involved in signal transduction. The nematode Caenorhabditis elegans possesses one dystrophin-like and one dystrobrevin-like (dyb-1) gene. Mutations of dyb-1 and dys-1 lead to similar phenotypes, comprising hyperactivity and a tendency to hypercontract, which suggest that these proteins may participate in a common function. We show here that overexpression of the Dyb-1 protein delays the onset of the myopathy observed in the C. elegans double Mutant (dys-1; hlh-1 mutations). This finding indicates that, in C. elegans, ( 1) the absence of dystrophin can be partly compensated for by extra doses of dystrobrevin, and (2) dystrobrevin is partly functional in absence of dystrophin. ------------------- Key: 5291 Medline: Authors: Conradt B Title: With a little help from your friends: cells don't die Citation: Nature Cell Biology 4: E139-E143 2002 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ced-12 cps-6 egl-1 nuc-1 Abstract: Phagocytes have long been known to engulf and degrade apoptotic cells. Recent studies in mammals and the nematode Caenorhabditis elegans have shed some light on the conserved molecular mechanisms involved in this process. A series of results now challenge the traditional view of phagocytes as simply scavengers, 'cleaning up' after apoptosis to prevent inflammatory responses, and hence tissue damage. Instead, they suggest that phagocytes are active in the induction and/or execution of apoptosis in ------------------- Key: 5292 Medline: 12175490 Authors: Fujita M;Takasaki T;Nakajima N;Kawano T;Shimura Y;Sakamoto Title: MRG-1, a mortality factor-related chromodomain protein, is required maternally for primordial germ cells to initiate mitotic proliferation in C. elegans. Citation: Mechanisms of Development 114: 61-69 2002 Type: ARTICLE Genes: fem-3 glp-4 lag-2 mrg-1 pgl-1 rde-1 Abstract: We identified MRG-1, a Caenorhabditis elegans chromodomain-containing protein that is similar to the human mortality factor-related gene 15 product (MRG15). RNA-mediated interference (RNAi) of mrg-1 resulted in complete absence of the germline in both hermaphrodite and male adults. Examination of the expression of PGL-1, a component of P granules, revealed that two primordial germ cells (PGCs) are produced during embryogenesis in mrg-1(RNAi) animals, but these PGCs cannot undergo mitotic proliferation, and they ultimately degenerate during post-embryonic development. Zygotic RNAi experiments using RNAi-deficient hermaphrodites and wild-type males demonstrated that MRG-1 functions maternally. Moreover, immunoblot analysis using mutant animals with germline deficiencies indicated that MRG-1 is synthesized predominantly in oocytes. These results suggest that MRG-1 is required maternally to form normal PGCs with the potential to start mitotic proliferation during post-embryonic development. ------------------- Key: 5293 Medline: Authors: Tabuchi K;Sudhof TC Title: Structure and evolution of neurexin genes: insight into the mechanisms of alternative splicing. Citation: Genomics 79: 849-859 2002 Type: ARTICLE Genes: Abstract: Neurexins are neuron-specific vertebrate proteins with hundreds of differentially spliced isoforms that may function in synapse organization. We now show that Drosophila melanogaster and Caenorhabditis elegans express a single gene encoding only an alpha-neurexin, whereas humans and mice express three genes, each of which encodes alpha- and beta-neurexins transcribed from separate promoters. The neurexin genes are very large (up to 1.62 Mb), with the neurexin-3 gene occupying almost 2% of human chromosome 14. Although invertebrate and vertebrate neurexins exhibit a high degree of evolutionary conservation, only vertebrate neurexins are subject to extensive alternative splicing that uses mechanisms ranging from strings of mini-exons to multiple alternative splice donor and acceptor sites. Consistent with their proposed role in synapse specification, neurexins thus have evolved from relatively simple genes in invertebrates to diversified genes in vertebrates with multiple promoters and extensive alternative splicing. ------------------- Key: 5294 Medline: Authors: Ashcroft N;Golden A Title: CDC-25.1 regulates germline proliferation in Caenorhabditis elegans. Citation: Genesis 33: 1-7 2002 Type: ARTICLE Genes: cdc-25.1 cdc-25.2 cdc-25.3 cdc-25.4 Abstract: The cell cycles in C. elegans are tightly controlled but appear to use the same regulators found in other organisms. Four homologues of the dual-specificity phosphatase Cdc25 are present in the C. elegans genome. In our study, we have characterized a deletion mutant for one of these orthologues. We show that embryonic defects are absent in cdc-25.1 homozygous mutants, presumably because of maternally contributed CDC-25.1 product. These embryos hatch and develop into sterile adults. The adults do not appear to have any somatic defects. The sterility results from inadequate germline proliferation. Germline precursors divide slowly and produce abnormally sized daughter cells. Only three to four rounds of germ-cell division occur before they die during the L3 and L4 larval stages. ------------------- Key: 5295 Medline: 12027435 Authors: Maduro MF;Rothman JH Title: Making worm guts: the gene regulatory network of the Caenorhabditis elegans endoderm. Citation: Developmental Biology 246: 68-85 2002 Type: REVIEW Genes: asp-1 cpr-1elt-1 elt-4 elt-7 emb-5 end-1 end-3 gad-1 ges-1 glp-1 lag-1 lag-2 lin-12 lit-1 med-1 med-2 mom-1 mtl-1 mtl-2 pal-1 pie-1 pop-1 pos-1 sgg-1 skn-1 spn-4 srg-12 vha-6 vit-2 wrm-1 Abstract: The nematode Caenorhabditis elegans is a triploblastic ecdysozoan, which, although it contains too few cells during embryogenesis to create discernible germ "layers," deploys similar programs for germ layer differentiation used in animals with many more cells. The endoderm arises from a single progenitor, the E cell, and is selected from among three possible fates by a three-state combinatorial regulatory system involving intersecting cell-intrinsic and intercellular signals. The core gene regulatory cascade that drives endoderm development, extending from early maternal regulators to terminal differentiation genes, is characterized by activation of successive tiers of transcription factors, including a sequential cascade of redundant GATA transcription factors. Each tier is punctuated by a cell division, raising the possibility that intercession of one cell cycle round, or DNA replication, is required for activation of the next tier. The existence of each tier in the regulatory hierarchy is justified by the assignment of a unique task and each invariably performs at least two functions: to activate the regulators in the next tier and to perform one other activity distinct from that of the next tier. While the regulatory inputs that initiate endoderm development are highly divergent, they mobilize a gene regulatory network for endoderm development that appears to be common to all triploblastic metazoans. Genome-wide functional genomic approaches, including identification of >800 transcripts that exhibit the same regulatory patterns as a number of endoderm-specific genes, are contributing to elucidation of the complete endoderm gene regulatory network in C. elegans. Dissection of the architecture of the C. elegans endoderm network may provide insights into the evolutionary plasticity and origins of this germ layer. ------------------- Key: 5296 Medline: 12062070 Authors: Sengupta P Title: Chemosensation: tasting with the tail. Citation: Current Biology 12: R386-R388 2002 Type: REVIEW Genes: Abstract: Animals employ multiple mechanisms to detect the presence and location of environmental stimuli. Recent work suggests that Caenorhabditis elegans uses chemosensory information provided by spatially distinct sensilla to generate a sensory map of its environment and to avoid noxious compounds. ------------------- Key: 5297 Medline: 12062074 Authors: Labbe JC;Goldstein B Title: Embryonic development: a new SPN on cell fate Citation: Current Biology 12: R396-R398 2002 Type: REVIEW Genes: glp-1 mex-1 mex-3 mex-5 mex-6 pal-1 par-1 par-2 par-3 par-6 pie-1 pkc-3 pos-1 skn-1 spn-4 Abstract: The recent identification and characterization of the Caenorhabditis elegans gene spn-4 has shed new light on the mechanisms that link embryonic polarity to the specification of cell fates. ------------------- Key: 5298 Medline: 12062054 Authors: Boxem M;van den Heuvel S Title: C. elegans class B synthetic multivulva genes act in G1 regulation. Citation: Current Biology 12: 906-911 2002 Type: ARTICLE Genes: cdk-4 chd-3 cki-1 cki-2 cyd-1 dpl-1 efl-1 efl-2 egl-27 egr-1 hda-1 let-418 lin-8 lin-9 lin -15 lin-35 lin-36 lin-37 lin-38 lin-53 tam-1 Abstract: The single C. elegans member of the retinoblastoma gene family, lin-35 Rb, was originally identified as a synthetic Multivulva (synMuv) gene [1]. These genes form two redundant classes, A and B, that repress ectopic vulval cell fate induction [2, 3]. Recently, we demonstrated that lin-35 Rb also acts as a negative regulator of G(1) progression and likely is the major target of cyd-1 Cyclin D and cdk-4 CDK4/6 [4]. Here,we describe G(1) control functions for several other class B synMuv genes. We found that efl-1 E2F negatively regulates cell cycle entry, while dpl-1 DP appeared to act both as a positive and negative regulator. In addition, we identified a negative G(1) regulatory function for lin-9 ALY, as well as lin-15B and lin-36, which encode novel proteins. Inactivation of lin-35 Rb, efl-1, or lin-36 allowed S phase entry in the absence of cyd-1/cdk-4 and increased ectopic cell division when combined with cki-1 Cip/Kip RNAi. These data are consistent with lin-35 Rb, efl-1, and lin-36 acting in a common pathway or complex that negatively regulates G(1) progression. In contrast, lin-15B appeared to act in parallel to lin-35. Our results demonstrate the potential for genetic identification of novel G(1) regulators in C. ------------------- Key: 5299 Medline: 12062062 Authors: Walker DS;Ly S;Lockwood KC;Baylis HA Title: A direct interaction between IP3 receptors and myosin II regulates IP3 signaling in C. elegans. Citation: Current Biology 12: 951-956 2002 Type: ARTICLE Genes: itr-1 myo-1 myo-3 nmy-2 unc-54 Abstract: Molecular and physiological studies of cells implicate interactions between the cytoskeleton and the intracellular calcium signalling machinery as an important mechanism for the regulation of calcium signalling [1-11]. However, little is known about the functions of such mechanisms in animals. A key component of the calcium signalling network is the intracellular release of calcium in response to the production of the second messenger inositol 1,4,5-trisphosphate (IP3), mediated by the IP3 receptor (IP3R) [12-14]. We show that C. elegans IP(3)Rs, encoded by the gene itr-1, interact directly with myosin II. The interactions between two myosin proteins, UNC-54 and MYO-1, and ITR-1 were identified in a yeast two-hybrid screen and subsequently confirmed in vivo and in vitro. We defined the interaction sites on both the IP3R and MYO-1. To test the effect of disrupting the interaction in vivo we over-expressed interacting fragments of both proteins in C. elegans. This decreased the animal's ability to upregulate pharyngeal pumping in response to food. This is a known IP3-mediated process [15]. Other IP3-mediated processes, e.g., defecation [16], were unaffected. Thus it appears that interactions between IP(3)Rs and myosin are required for maintaining the specificity of IP3 signalling in C. elegans and probably more generally. ------------------- Key: 5300 Medline: Authors: Ishihara T;Iino Y;Mohri A;Mori I;Gengyo-Ando K;Mitani S;Katsura I Title: HEN-1, a secretory protein with an LDL receptor motif, regulates sensory integration and learning in Caenorhabditis elegans. Citation: Cell 109: 639-649 2002 Type: ARTICLE Genes: hen-1 ttx-3 unc-104 Abstract: Animals sense many environmental stimuli simultaneously and integrate various sensory signals within the nervous system both to generate proper behavioral responses and also to form relevant memories. HEN-1, a secretory protein with an LDL receptor motif, regulates such processes in Caenorhabditis elegans. The hen-1 mutants show defects in the integration of two sensory signals and in behavioral plasticity by paired stimuli, although their sensation capability seems to be identical to that of the wild-type. The HEN-1 protein is expressed in two pairs of neurons, but expression in other neurons is sufficient for wild-type behavior. In addition, expression of HEN-1 at the adult stage is sufficient. Thus, HEN-1 regulates sensory processing non-cell-autonomously in the mature neuronal circuit. ------------------- Key: 5301 Medline: 12077420 Authors: Fong Y;Bender L;Wang W;Strome S Title: Regulation of the different chromatin states of autosomes and X chromosomes in the germ line of C. elegans. Citation: Science 296: 2235-2238 2002 Type: ARTICLE Genes: mes-2 mes-3 mes-4 mes-6 Abstract: The Maternal-Effect Sterile (MES) proteins are essential for germline viability in Caenorhabditis elegans. Here, we report that MES-4, a SET-domain protein, binds to the autosomes but not to the X chromosomes. MES-2, MES-3, and MES-6 are required to exclude MES-4 and markers of active chromatin from the X chromosomes. These findings strengthen the emerging view that in the C. elegans germ line, the X chromosomes differ in chromatin state from the autosomes and are generally silenced. We propose that all four MES proteins participate in X-chromosome silencing, and that the role of MES-4 is to exclude repressors from the autosomes, thus enabling efficient repression of the Xs. ------------------- Key: 5302 Medline: 12048240 Authors: Morse DP;Aruscavage PJ;Bass BL Title: RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by adenosine deaminases that act on RNA. Citation: Proceedings of the National Academy of Sciences USA 99: 7906-7911 2002 Type: ARTICLE Genes: pop-1 Abstract: Adenosine deaminases that act on RNA (ADARs) constitute a family of RNA-editing enzymes that convert adenosine to inosine within double-stranded regions of RNA. We previously developed a method to identify inosine-containing RNAs and used it to identify five ADAR substrates in Calenorhabditis elegans. Here we use the same method to identify five additional C elegans substrates, including three mRNAs that encode proteins known to affect neuronal functions. All 10 of the C elegans substrates are edited in long stem-loop structures located in noncoding regions, and thus contrast with previously identified substrates of other organisms, in which ADARs target codons. To determine whether editing in noncoding regions was a conserved ADAR function, we applied our method to poly(A)(+) RNA of human brain and identified 19 previously unknown ADAIR substrates. The substrates were strikingly similar to those observed in C elegans, since editing was confined to 3' untranslated regions, introns, and a noncoding RNA. Also similar to what was found in C elegans, 15 of the 19 substrates were edited in repetitive elements. The identities of the newly identified ADAR substrates suggest that RNA editing may influence many biologically important processes, and that for many metazoa, A-to-I conversion in coding regions may be the exception rather ------------------- Key: 5303 Medline: Authors: Blumenthal T;Evans D;Link CL;Guffanti A;Lawson D;Thierry-Mieg J;Thierry-Mieg D;Chiu WL;Duke K;Kiraly M;Kim SK Title: A global analysis of Caenorhabditis elegans operons. Citation: Nature 417: 851-854 2002 Type: ARTICLE Genes: Abstract: The nematode worm Caenorhabditis elegans and its relatives are unique among animals in having operons(1). Operons are regulated multigene transcription units, in which polycistronic premessenger RNA (pre-mRNA coding for multiple peptides) is processed to monocistronic mRNAs. This occurs by 3' end formation and trans-splicing using the specialized SL2 small nuclear ribonucleoprotein particle(2) for downstream mRNAs(1). Previously, the correlation between downstream location in an operon and SL2 trans-splicing has been strong, but anecdotal(3). Although only 28 operons have been reported, the complete sequence of the C. elegans genome reveals numerous gene clusters(4). To determine how many of these clusters represent operons, we probed full-genome microarrays for SL2-containing mRNAs. We found significant enrichment for about 1,200 genes, including most of a group of several hundred genes represented by complementary DNAs that contain SL2 sequence. Analysis of their genomic arrangements indicates that >90% are downstream genes, falling in 790 distinct operons. Our evidence indicates that the genome contains at least 1,000 operons, 2-8 genes long, that contain about 15% of all C. elegans genes. Numerous examples of co-transcription of genes encoding functionally related proteins are evident. Inspection of the operon list should reveal previously unknown functional ------------------- Key: 5304 Medline: Authors: Goodman MB;Ernstrom GG;Chelur DS;O'Hagan R;Yao CA;Chalfie M Title: MEC-2 regulates C. elegans DEG/ENaC channels needed for mechanosensation. Citation: Nature 417: 880- 2002 Type: ADDEND Genes: mec-2 mec-4 mec-10 Abstract: ------------------- Key: 5305 Medline: Authors: Baker AME;Roberts TM;Stewart M Title: 2.6A resolution crystal structure of helices of the motile major sperm protein (MSP) of Caenorhabditis elegans. Citation: Journal of Molecular Biology 319: 491-499 2002 Type: ARTICLE Genes: Abstract: The amoeboid locomotion of nematode sperm is mediated by the assembly dynamics of the major sperm protein (MSP). MSP forms fibrous networks based on a hierarchy of macromolecular assemblies: helical subfilaments are built from MSP dimers; filaments are formed from two subfilaments coiling round one another; and filaments themselves super-coil to produce bundles. To provide a structural context for understanding the role of these macromolecular assemblies in cell locomotion, we have determined the 2.6 Angstrom resolution structure of crystals of Caenorhabditis elegans MSP that are constructed from helices of MSP chains that are analogous to the subfilaments from which filaments are constructed. Comparison with the crystal structures of dimers and helical assemblies of Ascaris suum MSP has identified five conserved interaction interfaces that suggest how subfilaments interact in filaments and how filaments can form bundles. The interfaces frequently involve the loop containing residues 78-85, which is divergent between MSP homologues, and the loop containing residues 98-103, which is highly conserved. ------------------- Key: 5306 Medline: 12054666 Authors: Beeber C;Kieras FJ Title: Characterization of the chondroitin sulfates in wild type Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 293: 1374-1376 2002 Type: ARTICLE Genes: Abstract: The purpose of this study was to isolate and characterize the GAGs from the wild type nematode Caenorhabditis elegans in preparation for the characterization of the transgenic form constructed by Link [Proc. Natl. Acad. Sci. USA 92 (1995) 9368] which expresses various forms of P-peptide (or A4 peptide). This peptide forms deposits very similar to the ones found in the neuritic plaques and neurofibrillary tangles in Alzheimer disease (AD). Characterization has been accomplished by degradation with specific enzymes and analysis of the products by TLC and HPLC. The results were compared with earlier works and shown to differ in disaccharide content. ------------------- Key: 5307 Medline: Authors: Heid PJ;Voos E;Soll DR Title: 3D-DIASemb: a computer-assisted system for reconstructing and motion analyzing in 4D every cell and nucleus in a developing embryo. Citation: Developmental Biology 245: 329-347 2002 Type: ARTICLE Genes: Abstract: A computer-assisted three-dimensional (3D) system, 3D-DIASemb, has been developed that allows reconstruction and motion analysis of cells and nuclei in a developing embryo. In the system, 75 optical sections through a live embryo are collected in the z axis by using differential interference contrast microscopy. Optical sections for one reconstruction are collected in a 2.5-s period, and this process is repeated every 5 s. The outer perimeter and nuclear perimeter of each cell in the embryo are outlined in each optical section converted into ß-spline models, and used to construct 3D faceted images of the surface and nucleus of every cell in the developing embryo. Because all individual components of the embryo (i.e., each cell surface and each nuclear surface) are individually reconstructed, 3D-DIASemb allows isolation and analysis of (1) all or select nuclei in the absence of cell surfaces, (2) any single cell lineage, and (3) any single nuclear lineage through embryogenesis. Because all reconstructions represent mathematical models, 3D-DIASemb compute over 100 motility and dynamic morphology parameters for every cell, nucleus, or group of cells in the developing embryo at time intervals as short as 5 s. Finally, 3D-DIASemb reconstructs and motion analyzes cytoplasmic flow through the generation and analysis of "vector flow plots." To demonstrate the unique capabilities of this new technology, a Caenorhabditis elegans embryo is reconstructed and motion analyzed through the 28-cell stage. Although 3D-DIASemb was developed by using the C. elegans embryo as the experimental model, it can be applied to other embryonic systems. 3D-DIASemb therefore provides a new method for reconstructing and motion analyzing in 4D every cell and nucleus in a live, developing embryo, and should provide a powerful tool for assessing the effects of drugs, environmental perturbations, and mutations on the cellular and nuclear dynamics accompanying embryogenesis. ------------------- Key: 5308 Medline: 12101400 Authors: Cheung I;Schertzer M;Rose A;Lansdorp PM Title: Disruption of dog-1 in Caenorhabditis elegans triggers deletions upstream of guanine-rich DNA. Citation: Nature Genetics 31: 405-409 2002 Type: ARTICLE Genes: dog-1 msh-2 vab-1 Abstract: Genetic integrity is crucial to normal cell function, and mutations in genes required for DNA replication and repair underlie various forms of genetic instability and disease, including cancer. One structural feature of intact genomes is runs of homopolymeric dC/dG. Here we describe an unusual mutator phenotype in Caenorhabditis elegans characterized by deletions that start around the 3' end of polyguanine tracts and terminate at variable positions 5' from such tracts. We observed deletions throughout genomic DNA in about half of polyguanine tracts examined, especially those containing 22 or more consecutive guanine nucleotides. The mutator phenotype results from disruption of the predicted gene F33H2.1, which encodes a protein with characteristics of a DEAH helicase and which we have named dog-1 (for deletions of guanine-rich DNA). Nematodes mutated in dog-1 showed germline as well as somatic deletions in genes containing polyguanine tracts, such as vab-1. We propose that DOG-1 is required to resolve the secondary structures of guanine-rich DNA that occasionally form during lagging-strand DNA synthesis. ------------------- Key: 5309 Medline: Authors: Jinks-Robertson S Title: The genome's best friend. Citation: Nature Genetics 31: 331-332 2002 Type: REVIEW Genes: dog-1 Abstract: DNA replication through mononucleotide runs is frequently associated with slippage of DNA polymerase, leading to the insertion or deletion of a small number of base pairs. A new study shows that, in the absence of DOG-1, a putative helicase, long pol(dG/C) runs are associated with deletions that extend into flanking DNA sequences. This mutational signature may be related to the ability of poly(dG) to form secondary structures such as G-quadruplex DNA, and may contribute to the genomic instability of tumor cells. ------------------- Key: 5310 Medline: 1206745 Authors: Scott BA;Avidan MS;Crowder CM Title: Regulation of hypoxic death in C. elegans by the insulin/IGF receptor homolog DAF-2. Citation: Science 296: 2388-2391 2002 Type: ARTICLE Genes: age-1 akt-1 daf-2 daf-16 daf-18 old-1 pdk-1 Abstract: To identify genetic determinants of hypoxic cell death, we screened for hypoxia-resistant (Hyp) mutants in Caenorhabditis elegans and found that specific reduction-of-function (rf) mutants of daf-2, an insulin/insulinlike growth factor (IGF) receptor (INR) homolog gene, were profoundly Hyp. The hypoxia resistance was acutely inducible just before hypoxic exposure and was mediated through an AKT-1/PDK-1/forkhead transcription factor pathway overlapping with but distinct from signaling pathways regulating life-span and stress resistance. Selective neuronal and muscle expression of daf-2(+) restored hypoxic death, and daf-2(rf) prevented hypoxia-induced muscle and neuronal cell death, which demonstrates a potential for INR modulation in prophylaxis against hypoxic injury of neurons and myocytes. ------------------- Key: 5311 Medline: 11940606 Authors: Rogers E;Bishop JD;Waddle JA;Schumacher JM;Lin R Title: The aurora kinase AIR-2 functions in the release of chromosome cohesion in Caenorhabditis elegans meiosis. Citation: Journal of Cell Biology 157: 219-229 2002 Type: ARTICLE Genes: air-2 rec-8 Abstract: Accurate chromosome segregation during cell division requires not only the establishment, but also the precise, regulated release of chromosome cohesion. Chromosome dynamics during meiosis are more complicated, because homologues separate at anaphase I whereas sister chromatids remain attached until anaphase II. How the selective release of chromosome cohesion is regulated during meiosis remains unclear. We show that the aurora-B kinase AIR-2 regulates the selective release of chromosome cohesion during Caenorhabditis elegans meiosis. AIR-2 localizes to subchromosomal regions corresponding to last points of contact between homologues in metaphase I and between sister chromatids in metaphase II. Depletion of AIR-2 by RNA interference (RNAi) prevents chromosome separation at both anaphases, with concomitant prevention of meiotic cohesin REC-8 release from meiotic chromosomes. We show that AIR-2 phosphorylates REC-8 at a major amino acid in vitro. Interestingly, depletion of two PP1 phosphatases, CeGLC-7alpha and CeGLC-7beta, abolishes the restricted localization pattern of AIR-2. In Ceglc-7alpha/beta(RNAi) embryos, AIR-2 is detected on the entire bivalent. Concurrently, chromosomal REC-8 is dramatically reduced and sister chromatids are separated precociously at anaphase I in Ceglc-7alpha/beta(RNAi) embryos. We propose that AIR-2 promotes the release of chromosome cohesion via phosphorylation of REC-8 at specific chromosomal locations and that CeGLC-7alpha/beta, directly or indirectly, antagonize AIR-2 activity. ------------------- Key: 5312 Medline: 11869734 Authors: Lithgow GJ;Walker GA Title: Stress resistance as a determinate of C. elegans lifespan. Citation: Mechanisms of Ageing & Development 123: 765-771 2002 Type: REVIEW Genes: age-1 akt-1 akt-2 daf-2 daf-16 daf-18 mtl-1 mtl-2 old-1 pdk-1 pdk-2 Abstract: It is difficult to exaggerate the progress that has been made in biogerontology over the last 15 years. As with all scientific revolutions, a few experiments in a small number of laboratories have changed the way in which we think about and design experiments. As a result of these experiments, there is much evidence to suggest that a rudimentary understanding of some of the processes that cause aging will be available in the next decade. One particular area of progress is the molecular genetics of lifespan. Although one may draw some distinctions between chronological lifespan and normal aging, extended lifespan remains one of the best indicators that an intervention in an aging process has been made. The isolation of a long-lived variant of a laboratory invertebrate is now essentially a trivial project but the information obtained from this approach is proving invaluable. As with most other biological problems, the most important experimental developments are coming from studying simple organisms in a ------------------- Key: 5313 Medline: 11814595 Authors: Vatamaniuk OK;Bucher EA;Ward JT;Rea PA Title: Worms take the "phyto" out of "phytochelatins". Citation: Trends in Biotechnology 20: 61-64 2002 Type: REVIEW Genes: pcs-1 Abstract: Phytochelatin synthase is the enzyme responsible for the synthesis of heavy-metal-binding peptides (phytochelatins) from glutathione and related thiols. It has recently been determined that it is not only restricted to plants and some fungi, as was once thought, but also has an essential role in heavy-metal detoxification in the model nematode Caenorhabditis elegans. These findings and others that demonstrate phytochelatin synthase-coding sequences in the genomes of several other invertebrates, including pathogenic nematodes, schistosomes and roundworms, herald a new era in phytochelatin research, in which these novel post-translationally synthesized peptides will not only be investigated in the context of phytoremediation but also from a clinical parasitological standpoint. ------------------- Key: 5314 Medline: Authors: Edgley M;D'Souza A;Moulder G;McKay S;Shen B;Gilchrist E;Moerman D;Barstead R Title: Improved detection of small deletions in complex polls of DNA. Citation: Nucleic Acids Research 30: e52-e55 2002 Type: ARTICLE Genes: dim-1 Abstract: About 40% of the genes in the nematode Caenorhabditis elegans have homologs in humans. Based on the history of this model system, it is clear that the application of genetic methods to the study of this set of genes would provide important clues to their function in humans. To facilitate such genetic studies, we are engaged in a project to derive deletion alleles in every gene in this set. Our standard methods make use of nested PCR to hunt for animals in mutagenized populations that carry deletions at a given locus. The deletion bearing animals exist initially in mixed populations where the majority of the animals are wild type at the target. Therefore, the production of the PCR fragment representing the deletion allele competes with the production of the wild type fragment. The size of the deletion fragment relative to wild type determines whether it can compete to a level where it can be detected above the background. Using our standard conditions, we have found that when the deletion is <600 bp, the deletion fragment does not compete effectively with the production of the wild type fragment in PCR. Therefore, although our standard methods work well to detect mutants with deletions >600 bp, they do not work well to detect mutants with smaller deletions. Here we report a new strategy to detect small deletion alleles in complex DNA pools. Our new strategy is a modification of our standard PCR based screens. In the first round of the nested PCR, we include a third PCR primer between the two external primers. The presence of this third primer leads to the production of three fragments from wild type DNA. We configure the system so that two of these three fragments cannot serve as a template in the second round of the nested PCR. The addition of this third primer, therefore, handicaps the amplification from wild type template. On the other hand, the amplification of mutant fragments where the binding site for the third primer is deleted is unabated. Overall, we see at least a 500-fold increase in the sensitivity for small deletion fragments using our new method. Using this new method, we report the recovery of ------------------- Key: 5315 Medline: 12073031 Authors: Boontrakulpoontawee P;Otsuka AJ Title: Mutational analysis of the Caenorhabditis elegans ankyrin gene unc-44 demonstrates that the large spliceoform is critical for neural development. Citation: Molecular Genetics & Genomics 267: 291-302 2002 Type: ARTICLE Genes: unc-44 Abstract: In Coenorhabditis elegans, unc-44 mutations affect axonal outgrowth and guidance, leading to locomotory defects. The wild-type unc-44 gene encodes a family of ankyrin proteins, which, in addition to the conventional ankyrins, includes a novel ankyrin isoform with an extended C-terminal domain, referred to AO13 ankyrin. Six spontaneous unc-44 mutations and their reversions were analyzed in order to localize regions critical for gene function. The q331::Tc1 and rh1013::Tc1 mutations were mapped to the portion of the gene encoding the conventional ankyrins, mn339 had an uncharacterized 2-kb insertion in the serine/threonine/glutamic cid/proline-rich (STEP) repeat block 5, st200::Tc5(variant) and rh1042::Tc1 were localized near the C-terminus, and mn259 resulted from two Tc1 insertions, one in STEP block 6 and the other near the C-terminus. Tc1 excisions in several revertants resulted either in the restoration of the wild-type sequence, or were associated with small in-frame deletions or insertions. Reversion of mn339 resulted in the net excision of 2463 bp of genomic DNA, including the region encoding parts of STEP blocks 5 and 6 and the intervening hydrophobic region. Interestingly, additional Tc1 insertions at a 5' exon/intron boundary were found in revertants of st200 and rh1042. Reversion of the st200::Tc5 mutation resulted in excision of the Tc5 element, and the insertion of two copies of Tc1 at different sites. The wild-type unc-44 gene produces multiple transcripts - shorter RNAs determined to be approximately 1, 3.2, 5, 6, and 7 kb long, and two large transcripts estimated to be 22 and 26 kb in length. The largest transcripts were affected by all unc-44 mutations and are proposed to be essential ------------------- Key: 5316 Medline: 12064941 Authors: Tzur YB;Hersh BM;Horvitz HR;Gruenbaum Y Title: Fate of the nuclear lamina during Caenorhabditis elegans apoptosis. Citation: Journal of Structural Biology 137: 146-153 2002 Type: ARTICLE Genes: ced-3 ced-4 egl-1 unc-1 Abstract: In vertebrates and in Drosophila, lamins and lamin-associated proteins are primary targets for cleavage by caspases. Eliminating mammalian lamins causes apoptosis, whereas expressing mutant lamins that cannot be cleaved by caspase-6 delay apoptosis. Caenorhabditis elegans has a single lamin protein, Ce-lamin, and a caspase, CED-3, that is responsible for most if not all somatic apoptosis. In this study we show that in C. elegans embryos induced to undergo apoptosis Ce-lamin is degraded surprisingly late. In such embryos CED-4 translocated to the nuclear envelope but the cytological localization of Ce-lamin remained similar to that in wild-type embryos. TUNEL labeling indicated that Ce-lamin was degraded only after DNA is fragmented. Ce-lamin, Ce-emerin, or Ce-MAN1 were not cleaved by recombinant CED-3, showing that these lamina proteins are not substrates for CED-3 cleavage. These results suggest that lamin cleavage probably is not essential for apoptosis in C. elegans. ------------------- Key: 5317 Medline: Authors: Kaltschmidt JA;Brand AH Title: Asymmetric cell division: microtubule dynamics and spindle asymmetry. Citation: Journal of Cell Science 115: 2257-2264 2002 Type: REVIEW Genes: ags-3.2 ags-3.3 par-1 par-2 par-3 Abstract: Asymmetric cell division can produce daughter cells with different developmental fates and is often accompanied by a difference in cell size. A number of recent genetic and in vivo imaging studies in Drosophila and Caenorhabditis elegans have begun to elucidate the mechanisms underlying the rearrangements of the cytoskeleton that result in eccentrically positioned cleavage planes. As a result, we are starting to gain an insight into the complex nature of the signals controlling cytoskeletal dynamics in the dividing cell. In this commentary we discuss recent findings on how the mitotic spindle is positioned and on cleavage site induction and place them in the context of cell size asymmetry in different model organisms. ------------------- Key: 5318 Medline: 12006612 Authors: Piekny AJ;Mains PE Title: Rho-binding kinase (LET-502) and myosin phosphate (MEL-11) regulate cytokinesis in the early Caenorhabditis elegans embryo. Citation: Journal of Cell Science 115: 2271-2282 2002 Type: ARTICLE Genes: cyk-1 cyk-4 let-502 mel-11 mlc-4 nmy-2 Abstract: Rho-binding kinase and myosin phosphatase regulate the contraction of actomyosin filaments in non-muscle and smooth muscle cells. Previously, we described the role of C. elegans genes encoding Rho-binding kinase (let-502) and myosin phosphatase targeting subunit (mel-11) in epidermal cell-shape changes that drive morphogenesis and in spermathecal contraction. Here we analyze their roles in a third contractile event, cytokinesis within early embryos. We demonstrate that these genes function together to regulate the rate of cleavage furrow contraction, with Rho-binding kinase/LET-502 mediating contraction, whereas myosin phosphatase/MEL-11 acts as a brake to contraction: early embryonic cleavage often fails or is slowed when let-502 is mutated, whereas mel-11 mutations result in ectopic furrowing and faster furrow ingression. These phenotypes correspond to changes in the levels of phosphorylated regulatory non-muscle myosin light chain (rMLC). The gene products of let-502 and mel-11 colocalize at cleavage furrows, and their mutations alleviate one another's defects. rMLC is phosphorylated in let-502; mel-11 double mutants, indicating that a kinase is able to phosphorylate rMLC in the absence of both LET-502 and MEL-11. Genetic and molecular epistasis experiments place LET-502 and MEL-11 in a cytokinetic pathway. LET-502 and MEL-11 regulate the activity of non-muscle myosin after actin, non-muscle myosin heavy chain/NMY-2, regulatory non-muscle myosin light chain/MLC-4 and early formin/CYK-1 have formed a contractile ring. Proteins including Rho GTPase activating protein/CYK-4 and late CYK-1, which are required for late stages of cytokinesis, function downstream of LET-502 and MEL-11. ------------------- Key: 5319 Medline: 12006614 Authors: Kaitna S;Schnabel H;Schnabel R;Hyman AA;Glotzer M Title: A ubiquitin C-terminal hydrolase is required to maintain osmotic balance and execute actin-dependent processes in the early C. elegans embryo. Citation: Journal of Cell Science 115: 2293-2302 2002 Type: ARTICLE Genes: cyk-3 Abstract: In the early Caenorhabditis elegans embryo, establishment of cell polarity and cytokinesis are both dependent upon reorganization of the actin cytoskeleton. Mutations in the cyk-3 gene cause maternal effect embryonic lethality. Embryos produced by homozygous cyk-3 mutant animals become multinucleate. We have further analyzed the cyk-3 mutant phenotype and have found that cyk-3 mutant embryos fail to properly polarize the actin cytoskeleton and fail to segregate germline determinants. In addition, they fail to assemble an intact cleavage furrow. However, we have found that cyk-3 mutant embryos are intrinsically defective in osmotic regulation and that the cytokinesis defects can be partially rescued by providing osmotic support. The cyk-3 gene has been identified and found to encode a ubiquitin C-terminal hydrolase that is active against model substrates. These data indicate that the deubiquitination of certain substrates by CYK-3 is crucial for cellular osmoregulation. Defects in osmoregulation appear to indirectly affect actin-dependent processes. ------------------- Key: 5320 Medline: 12011109 Authors: Hannak E;Oegema K;Kirkham M;Gonczy P;Habermann B;Hyman AA Title: The kinetically dominant assembly pathway for centrosomal asters in Caenorhabditis elegans is gamma-tubulin Citation: Journal of Cell Biology 157: 591-602 2002 Type: ARTICLE Genes: dhc-1 gip-1 sas-3 tbg-1 zyg-9 Abstract: gamma-Tubulin-containing complexes are thought to nucleate and anchor centrosomal microtubules (MTs). Surprisingly, a recent study (Strome, S., J. Powers, M. Dunn, K. Reese, C.J. Malone, J. White, G. Seydoux, and W. Saxton. Mol. Biol. Cell. 12:1751-1764) showed that centrosomal asters form in Caenorhabditis elegans embryos depleted of gamma-tubulin by RNA-mediated interference (RNAi). Here, we investigate the nucleation and organization of centrosomal MT asters in C. elegans embryos severely compromised for gamma-tubulin function. We characterize embryos depleted of similar to98% centrosomal gamma-tubulin by RNAi, embryos expressing a mutant form of gamma-tubulin, and embryos depleted of a gamma-tubulin-associated protein, CeGrip-1. In all cases, centrosomal asters fail to form during interphase but assemble as embryos enter mitosis. The formation of these mitotic asters does not require ZYG-9, a centrosomal MT-associated protein, or cytoplasmic dynein, a minus end-directed motor that contributes to self-organization of mitotic asters in other organisms. By kinetically monitoring MT regrowth from cold-treated mitotis centrosomes in vivo, we show that centrosomal nucleating activity is severely compromised by gamma-tubulin depletion. Thus, although unknown mechanisms can support partial assembly of mitotic centrosomal asters, gamma-tubulin is the kinetically dominant centrosomal MT ------------------- Key: 5321 Medline: 11994313 Authors: Norman KR;Moerman DG Title: Alpha spectrin is essential for morphogenesis and body wall muscle formation in Caenorhabditis elegans. Citation: Journal of Cell Biology 157: 665-677 2002 Type: ARTICLE Genes: egl-19 let-502 mlc-4 sma-1 spc-1 unc-70 syDf1 Abstract: A common feature of multicellular animals is the ubiquitous presence of the spectrin cytoskeleton. Although discovered over 30 yr ago, the function of spectrin in nonerythrocytes has remained elusive. We have found that the spc-1 gene encodes the only alpha spectrin gene in the Caenorhabditis elegans genome. During embryogenesis, a spectrin localizes to the cell membrane in most if not all cells, starting at the first cell stage. Interestingly, this localization is dependent on beta spectrin but not beta(Heavy) spectrin. Furthermore, analysis of spc-1 mutants indicates that beta spectrin requires a spectrin to be stably recruited to the cell membrane. Animals lacking functional a spectrin fail to complete embryonic elongation and die just after hatching. These mutant animals have defects in the organization of the hypodermal apical actin cytoskeleton that is required for elongation. in addition, we find that the process of elongation is required for the proper differentiation of the body wall muscle. Specifically, when compared with myofilaments in wild-type animals the myofilaments of the body wall muscle in mutant animals are abnormally oriented relative to the longitudinal axis of the embryo, and the body wall muscle cells do not undergo normal cell shape changes. ------------------- Key: 5322 Medline: 12080088 Authors: Stear JH;Roth MB Title: Characterization of HCP-6, a C. elegans protein required to prevent chromosome twisting and merotelic attachment. Citation: Genes & Development 16: 1498-1508 2002 Type: ARTICLE Genes: hcp-6 Abstract: Previous studies of mitosis show that capture of single kinetochores by microtubules from both centrosomes (merotelic orientation) is a major cause of aneuploidy. We have characterized hcp-6, a temperature-sensitive chromosome segregation mutant in C. elegans that exhibits chromosomes attached to both poles via a single sister kinetochore. We demonstrate that the primary defect in this mutant is a failure to fully condense chromosomes during prophase. Although centromere formation and sister centromere resolution remain unaffected in hcp-6, the chromosomes lack the rigidity of wild-type chromosomes and twist around the long axis of the chromosome. As such, they are unable to establish a proper orientation at prometaphase, allowing individual kinetochores to be captured by microtubules from both poles. We therefore propose that chromosome rigidity plays an essential role in maintaining chromosome orientation to prevent merotelic ------------------- Key: 5323 Medline: 12044672 Authors: Smith MP;Laws TR;Atkins TP;Oyston PCF;de Pomerai DI;Titball RW Title: A liquid-based method for the assessment of bacterial pathogenicity using the nematode Caenorhabditis elegans. Citation: FEMS Microbiology Letters 210: 181-185 2002 Type: ARTICLE Genes: phm-2 Abstract: Caenorhabditis elegans has previously been used as an alternative to mammalian models of infection with bacterial pathogens. We have developed a liquid-based assay to measure the effect of bacteria on the feeding ability of C elegans. Using this assay we have shown that Pseudomonas aeruginosa strain PA14, Burkholderia pseudomallei and Yersinia pestis were able to inhibit feeding of C elegans strain N2. An increase in sensitivity of the assay was achieved by using C elegans mutant phm-2, in place of the wild-type strain. Using this assay, P. aeruginosa PA01 inhibited the feeding of C elegans mutant phm-2. Such liquid-based feeding assays are ideally suited to the high-throughput screening of mutants of bacterial ------------------- Key: 5324 Medline: 12015302 Authors: Corsi AK;Brodigan TM;Jorgensen EM;Krause M Title: Characterization of a dominant negative C. elegans Twist mutant protein with implications for human Saethre-Chotzen syndrome. Citation: Development 129: 2761-2772 2002 Type: ARTICLE Genes: ceh-24 hlh-8 Abstract: Twist is a transcription factor that is required for mesodermal cell fates in all animals studied to date. Mutations of this locus in humans have been identified as the cause of the craniofacial disorder Saethre-Chotzen syndrome. The Caenorhabditis elegans Twist homolog is required for the development of a subset of the mesoderm. A semidominant allele of the gene that codes for CeTwist, hlh-8, has defects that occur earlier in the mesodermal lineage than a previously studied null allele of the gene. The semidominant allele has a charge change (E29K) in the basic DNA-binding domain of CeTwist. Surprisingly, the mutant protein retains DNA-binding activity as both a homodimer and a heterodimer with its partner E/Daughterless (CeE/DA). However, the mutant protein blocks the activation of the promoter of a target gene. Therefore, the mutant CeTwist may cause cellular defects as a dominant negative protein by binding to target promoters as a homo- or heterodimer and then blocking transcription. Similar phenotypes as those caused by the E29K mutation were observed when amino acid substitutions in the DNA-binding domain that are associated with the human Saethre-Chotzen syndrome were engineered into the C. elegans protein. These data suggest that Saethre-Chotzen syndrome may be caused, in some cases, by dominant negative proteins, rather than by haploinsufficiency of the locus. ------------------- Key: 5325 Medline: 12051826 Authors: Maduzia LL;Gumienny TL;Zimmerman CM;Wang H;Shetgiri P;Krishna S;Roberts AF;Padgett RW Title: lon-1 regulates Caenorhabditis elegans body size downstream of the dbl-1 TGFB signaling pathway. Citation: Developmental Biology 246: 418-428 2002 Type: ARTICLE Genes: dbl-1 lon-1 sma-2 sma-3 sma-4 sma-5 Abstract: In Caenorhabditis elegans, two well-characterized TGF beta signaling cascades have been identified: the Small/Male tail abnormal (Sma/Mab) and Dauer formation (Daf) pathways. The Sma/Mab pathway regulates body size morphogenesis and male tail development. The ligand of the pathway, dbl-1, transmits its signal through two receptor serine threonine kinases, daf-4 and sma-6, which in turn regulate the activity of the Smads, sma-2, sma-3, and sma-4. In general, Smads have been shown to both positively and negatively regulate the transcriptional activity of downstream target genes in various organisms. In C. elegans, however, target genes have remained elusive. We have cloned and characterized lon-1, a gene with homology to the cysteine-rich secretory protein (CRISP) family of proteins. lon-1 regulates body size morphogenesis, but does not affect male tail development. lon-1 is expressed in hypodermal tissues, which is the focus of body size determination, similar to sma-2, sma-4, and sma-6. Using genetic methods, we show that lon-1 lies downstream of the Sma/Mab signaling cascade and demonstrate that lon-1 mRNA levels are up-regulated in sma-6-null mutant animals. This provides evidence that lon-1 is negatively regulated by Sma/Mab pathway signaling. Taken together, these data identify lon-1 as a novel downstream target gene of the dbl-1 TGF beta-like signaling pathway. ------------------- Key: 5326 Medline: 11917031 Authors: Boutla A;Kalantidis K;Tavernarakis N;Tsagris M;Tabler M Title: Induction of RNA interference in Caenorhabditis elegans by RNAs derived from plants exhibiting post-transcriptional gene silencing. Citation: Nucleic Acids Research 30: 1688-1694 2002 Type: ARTICLE Genes: Abstract: The term 'gene silencing' refers to transcriptional and post-transcriptional control of gene expression. Related processes are found across kingdoms in plants and animals. We intended to test whether particular RNA constituents of a silenced plant can induce silencing in an animal. We generated Nicotiana benthamiana lines that expressed green fluorescent protein (GFP) from a transgene. Plants in which GFP expression was spontaneously silenced showed siRNAs characteristic of post-transcriptional gene silencing (PTGS). RNA extracts prepared from silenced plants were injected into a GFP-expressing strain of Caenorhabditis elegans, where they induced RNA interference (RNAi). Extracts from non-silenced plants were inactive. This directly demonstrates a relationship and a mechanistic link between PTGS and RNAi. Controls confirmed that the silencing agent was an RNA. Size fractionation on denaturing gels revealed that an RNA of apprx85 nt was most active in inducing silencing in the worm. Northern blot analysis of the region in question did not detect a prominent GFP-specific RNA of sense or antisense polarity, indicating that the RNA species which induced silencing was present only in low concentration or did not hybridize due to formation of an intra-molecular double strand. In view of its high activity, it is possible that this agent is responsible for the systemic spread of silencing in plants and it might represent the aberrant RNA, a previously postulated inducer of silencing. ------------------- Key: 5327 Medline: Authors: Schwarz EM;Stein LD;Sternberg PW Title: Caenorhabditis elegans databases. Citation: Current Genomics 3: 111-119 2002 Type: REVIEW Genes: Abstract: ------------------- Key: 5328 Medline: Authors: Reinke V Title: Defining development through gene expression profiling. Citation: Current Genomics 3: 95-109 2002 Type: REVIEW Genes: Abstract: ------------------- Key: 5329 Medline: Authors: Rual JF;Lamesch P;van den Haute J;Vidal M Title: The Caenorhabditis elegans interactome mapping project. Citation: Current Genomics 3: 83-93 2002 Type: REVIEW Genes: Abstract: ------------------- Key: 5330 Medline: Authors: Piano F;Gunsalus K Title: RNAi-based functional genomics in Caenorhabditis elegans. Citation: Current Genomics 3: 69-81 2002 Type: REVIEW Genes: Abstract: ------------------- Key: 5331 Medline: Authors: Jansen G Title: Gene inactivation in Caenorhabditis elegans. Citation: Current Genomics 3: 59-67 2002 Type: ARTICLE Genes: Abstract: ------------------- Key: 5332 Medline: Authors: Neri C Title: Preface: Caenorhabditis elegans postgenomic era and the biological practice. Citation: Current Genomics 3: 55-57 2002 Type: REVIEW Genes: Abstract: ------------------- Key: 5333 Medline: Authors: Ishii N;Kita K;Hartman PS Title: Mitochondrial contributions to aging in the nematode Caenorhabditis elegans. Citation: Current Genomics 2: 349-355 2001 Type: REVIEW Genes: clk-1 gas-1 mev-1 Abstract: Free radicals and their sequelae figure prominently in cellular and organismal aging. Generated primarily in mitochondria as unwanted products of oxidative phosphorylation, free radicals induce a wide variety of damage that compromises molecular, cellular and organismal integrity. The free-living nematode Caenorhabditis elegans has been employed widely to explore life span. Conversely, genetic analyses of mutants that shorten life span have also provided insights into aging as it occurs in wild type. In this review we focus on three such "aging" mutants of C. elegans (mev-1, gas-1, and clk-1). Although isolated in different laboratories and using different selection criteria, all three affect aging by perturbing mitochondrial structure and/or function. gas-1 encodes a subunit of complex I, one of the five membrane-bound mitochondrial complexes that comprise the electron transport system. Originally isolated because they are hypersensitive to volatile anesthetics, gas-1 mutants were subsequently found to be hypersensitive to oxidative stress, presented in the form of either hyperoxia or methyl viologen. mev-1 encodes a subunit of complex II and was initially studied on the basis of its aging, hypermutability, abnormal mitochondrial structure, compromised DNA repair capacity and increased endogenous levels of free radicals. clk-1 encodes a protein homologous to the yeast coq7/cat5 gene product. clk-1 mutations result in reduced rates of certain developmental and behavioral phenomena as well as in an extended life span. In yeast, coq7/cat5 mutants were reported to be defective in respiration due to a deficiency in the biosynthesis of ubiquinone. It has been hypothesized that the involvement of clk-1/coq7/cat5 in ubiquinone biosynthesis is regulatory because clk-1 mutants show normal rates of mitochondrial respiration. The phenotypes of each of these three mutants will be presented, with ------------------- Key: 5334 Medline: Authors: Segalat L Title: Genetic analysis of behavior in the nematode Caenorhabditis elegans. Citation: CRC Methods in Cellular and Molecular Neuropathology Series. Neurobehavioral genetics: Methods and applications. BC Jones, P Mormede (eds). : 373-381 1999 Type: REVIEW Genes: Abstract: ------------------- Key: 5335 Medline: Authors: Candido EPM Title: The small heat shock proteins of the nematode Caenorhabditis elegans: structure, regulation and biology. Citation: Progress in Molecular & Subcellular Biology. Small Stress Proteins. AP Arrigo, WEG Muller (eds). : 61-78 2002 Type: REVIEW Genes: Abstract: ------------------- Key: 5336 Medline: 12078522 Authors: Link CD;Johnson CJ Title: Reporter transgenes for the study of oxidant stress in Caenorhabditis elegans. Citation: Methods in Enzymology 353: 497-505 2002 Type: REVIEW Genes: Abstract: ------------------- Key: 5337 Medline: 11806825 Authors: Jones D;Crowe E;Stevens TA;Candido EP Title: Functional and phylogenetic analysis of the ubiquitylation system in Caenorhabditis elegans: ubiquitin-conjugating enzymes, ubiquitin-activating enzymes, and ubiquitin-like proteins. Citation: Genome Biology 3(1): 2.1-2.15 2002 Type: REVIEW Genes: aos-1 let-70 ned-8 uba-1 uba-2 uba-3 ubc-1 ubc-2 ubc-3 ubc-6 ubc-7 ubc-8 ubc-12 ubc-13 ubc-14 ubc-15 ubc-16 ubc-17 ubc-18 ubc-19 ubc-21 ubc-22 ubc-23 ubc-24 uev-1 uev-2 uev-3 ula-1 Abstract: BACKGROUND: The eukaryotic ubiquitin-conjugation system sets the turnover rate of many proteins and includes activating enzymes (E1s), conjugating enzymes (UBCs/E2s), and ubiquitin-protein ligases (E3s), which are responsible for activation, covalent attachment and substrate recognition, respectively. There are also ubiquitin-like proteins with distinct functions, which require their own E1s and E2s for attachment. We describe the results of RNA interference (RNAi) experiments on the E1s, UBC/E2s and ubiquitin-like proteins in Caenorhabditis elegans. We also present a phylogenetic analysis of UBCs. RESULTS: The C. elegans genome encodes 20 UBCs and three ubiquitin E2 variant proteins. RNAi shows that only four UBCs are essential for embryogenesis: LET-70 (UBC-2), a functional homolog of yeast Ubc4/5p, UBC-9, an ortholog of yeast Ubc9p, which transfers the ubiquitin-like modifier SUMO, UBC-12, an ortholog of yeast Ubc12p, which transfers the ubiquitin-like modifier Rub1/Nedd8, and UBC-14, an ortholog of Drosophila Courtless. RNAi of ubc-20, an ortholog of yeast UBC1, results in a low frequency of arrested larval development. Phylogenetic analysis of C. elegans, Drosophila and human UBCs shows that this protein family can be divided into 18 groups, 13 of which include members from all three species. The activating enzymes and the ubiquitin-like proteins NED-8 and SUMO are required for embryogenesis. CONCLUSIONS: The number of UBC genes appears to increase with developmental complexity, and our results suggest functional overlap in many of these enzymes. The ubiquitin-like proteins NED-8 and SUMO and their corresponding activating enzymes are required for ------------------- Key: 5338 Medline: Authors: Belfiore M;Mathies LD;Pugnale P;Moulder G;Barstead R;Kimble J;Puoti A Title: The MEP-1 zinc-finger protein acts with MOG DEAH box proteins to control gene expression via the fem-3 3'-untranslated region in Caenorhabditis elegans. Citation: RNA 8: 725-739 2002 Type: ARTICLE Genes: fbf-1 fbf-2 fem-3 glp-1 mep-1 mog-1 mog-4 mog-5 nos-3 Abstract: Cell fates in the Caenorhabditis elegans germline are regulated, at least 1. in part, at the posttranscriptional level. For example, the switch from spermatogenesis to oogenesis in the hermaphrodite relies on posttranscriptional repression of the fem-3 mRNA via its 3' untranslated region (UTR). Previous studies identified three DEAH box proteins, MOG-1, MOG-4, and MOG-5, that are critical for the fem-3 3' UTR control. Here we describe MEP-1, a zinc-finger protein that binds specifically to each of these three MOG proteins and that is required for repression by the fem-3 3' UTR in vivo. To investigate its in vivo function, we generated a mep-1 deletion mutant. The mep-1 null phenotype suggests a broad role for MEP-1 in C. elegans development, as it is associated with early larval arrest. In addition, mep-1 mutants can be defective in gonadogenesis and oocyte production when derived from a heterozygous mother. We suggest that MEP-1 acts together with the MOG proteins to repress fem-3 mRNA and that it also functions in other pathways to control development ------------------- Key: 5339 Medline: 12038976 Authors: Natsuka S;Adachi J;Kawaguchi M;Nakakita S;Hase S;Ichikawa A;Ikura K Title: Structural analysis of N-linked glycans in Caenorhabditis elegans. Citation: Journal of Biochemistry 131: 807-813 2002 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans is an excellent model for morphogenetic research. However, little information is available on the structure of cell-surface glycans in C. elegans, although several lines of evidence have suggested a role for these glycans in cell-cell interactions during development. In this study, we analyzed N-glycan structures. Oligosaccharides liberated by hydrazinolysis from a total membrane fraction were labeled by pyridylamination, and around 90% of the N-glycans were detected as neutral oligosaccharides. The most dominant structure was Man(alpha)1-6(Man(alpha)1-3)Man(beta)1-4GlcNAc(beta)1-4GlcN Ac, which is commonly found in insects. Branching structures of major oligomannose-type glycans were the same as those found in mammals. Structures that had a core fucose or non-reducing end N-acetylglucosamine were also identified, but ordinary complex-type glycans with ------------------- Key: 5340 Medline: 12072462 Authors: Tijsterman M;Pothof J;Plasterk RHA Title: Frequent germline mutations and somatic repeat instability in DNA mismatch-repair-deficient Caenorhabditis elegans. Citation: Genetics 161: 651-660 2002 Type: ARTICLE Genes: mlh-1 msh-2 msh-3 msh-6 pms-2 unc-93 Abstract: Mismatch-repair-deficient mutants were initially recognized as mutation-prone derivatives of bacteria, and later mismatch repair deficiency was found to predispose humans to colon cancers (HNPCC). We generated mismatch-repair-deficient Caenorhabditis elegans by deleting the msh-6 gene and analyzed the fidelity of transmission of genetic information to subsequent generations. msh-6-defective animals show an elevated level of spontaneous mutants in both the male and female germline; also repeated DNA tracts are unstable. To monitor DNA repeat instability in somatic tissue, we developed a sensitive system, making use of heat-shock promoter-driven lacZ transgenes, but with a repeat that puts this reporter gene out of frame. In genetic msh-6-deficient animals lacZ+ patches are observed as a result of somatic repeat instability. RNA interference by feeding wild-type animals dsRNA homologous to msh-2 or msh-6 also resulted in somatic DNA instability, as well as in germline mutagenesis, indicating that one can use C. elegans as a model system to discover genes involved in maintaining DNA stability by large-scale RNAi screens. ------------------- Key: 5341 Medline: 12142026 Authors: Maduro MF;Lin R;Rothman JH Title: Dynamics of a developmental switch: recursive intracellular and intranuclear redistribution of Caenorhabditis elegans POP-1 parallels Wnt-inhibited transcriptional repression. Citation: Developmental Biology 248: 128-142 2002 Type: ARTICLE Genes: apr-1 bar-1 cbp-1 end-1 end-3 hda-1 lit-1 med-1 med-2 mom-2 mom-5 pop-1 sgg-1 wrm-1 Abstract: POP-1, a Tcf/Lef factor, functions throughout Caenorhabditis elegans development as a Wnt-dependent reiterative switch to generate nonequivalent sister cells that are born by anterior-posterior cell divisions. We have observed the interaction between POP-1 and a target gene that it represses as it responds to Wnt signaling. Dynamic observations in living embryos reveal that POP-1 undergoes Wnt-dependent nucleocytoplasmic redistribution immediately following cytokinesis, explaining the differential nuclear POP-1 levels in nonequivalent sister cells. In unsignaled (anterior) but not Wnt-signaled (posterior) sister cells, POP-1 progressively coalesces into subnuclear domains during interphase, coincident with its action as a repressor. While the asymmetric distribution of POP-1 in nonequivalent sisters apparently requires a 124-amino-acid internal domain, neither the HMG box nor beta-catenin interaction domains are required. We find that a transcriptional activator, MED-1, associates in vivo with the end-1 and end-3 target genes in the mesoderm (anterior sister) and in the endoderm (posterior sister) following the asymmetric cell division that subdivides the mesendoderm. However, in the anterior sister, binding of POP-1 to the end-1 and end-3 genes blocks their expression. In vivo, binding of POP-1 to the end-1 and end-3 targets (in the posterior sister) is blocked by Wnt/MAPK signaling. Thus, a Tcf/Lef factor represses transactivation of genes in an unsignaled daughter cell by abrogating the function ------------------- Key: 5342 Medline: 12136014 Authors: Garigan D;Hsu AL;Fraser AG;Kamath RS;Ahringer J;Kenyon C Title: Genetic analysis of tissue aging in Caenorhabditis elegans: a role for heat-shock factor and bacterial proliferation. Citation: Genetics 161: 1101-1112 2002 Type: ARTICLE Genes: ced-3 daf-2 daf-16 fem-1 fer-15 hsf-1 Abstract: The genetic analysis of life span has revealed many interesting genes and pathways; however, our understanding of aging has been limited by the lack of a way to assay the aging process itself. Here we show that the tissues of aging worms have a characteristic appearance that is easy to recognize and quantify using Nomarski optics. We have used this assay to determine whether life-span mutations affect the rate of aging, to identify animals that age more rapidly than normal, and to infer the cause of death in C. elegans. Mutations that reduce insulin/IGF-1 signaling double the life span of C. elegans, and we find that tissue decline is slowed in these mutants. Thus this endocrine system appears to influence the rate at which tissues age. This effect extends even to the germline, which is the only mitotically active tissue in the adult. We find that Nomarski microscopy also allows a ready distinction between short.-lived mutants that age more rapidly than normal and those that are simply sick, and we have identified an RNAi clone that confers a dramatic rapid-aging phenotype. This clone encodes the C. elegans heat-shock factor (HSF), a transcription factor that regulates the response to heat and oxidative stress. This suggests that heat-shock proteins, many of which act as chaperones, may function in normal animals to slow the rate of aging. Finally, we have identified a cause of death of C. elegans: namely, proliferating bacteria. This suggests that increased susceptibility to bacterial infections contributes to ------------------- Key: 5343 Medline: 12140320 Authors: Farrer T;Roller AB;Kent WJ;Zahler AM Title: Analysis of the role of Caenorhabditis elegans GC-AG introns in regulated splicing. Citation: Nucleic Acids Research 30: 3360-3367 2002 Type: ARTICLE Genes: eat-6 eat-16 itr-1 let-2 lin-2 lin-46 mec-9 mec-10 pag-3 sma-1 tlf-1 Abstract: GC-AG introns represent 0.7% of total human pre-mRNA introns. To study the function of GC-AG introns in splicing regulation, 196 cDNA-confirmed GC-AG introns were identified in Caenorhabditis elegans. These represent 0.6% of the cDNA- confirmed intron data set for this organism. Eleven of these GC-AG introns are involved in alternative splicing. In a comparison of the genomic sequences of homologous genes between C.elegans and Caenorhabditis briggsae for 26 GC-AG introns, the C at the +2 position is conserved in only five of these introns. A system to experimentally test the function of GC-AG introns in alternative splicing was developed. Results from these experiments indicate that the conserved C at the +2 position of the tenth intron of the let-2 gene is essential for developmentally regulated alternative splicing. This C allows the splice donor to function as a very weak splice site that works in balance with an alternative GT splice donor. A weak GT splice donor can functionally replace the GC splice donor and allow for splicing regulation. These results indicate that while the majority of GC-AG introns appear to be constitutively spliced and have no evolutionary constraints to prevent them from being GT-AG introns, a subset of GC-AG introns is involved in alternative splicing and the C at the +2 position of these introns can have an important role in splicing regulation. ------------------- Key: 5344 Medline: 12130541 Authors: Howard RM;Sundaram MV Title: C. elegans EOR-1/PLZF and EOR-2 positively regulate Ras and Wnt signaling and function redundantly with LIN-25 and the SUR-2 Mediator component. Citation: Genes & Developement 16: 1815-1827 2002 Type: ARTICLE Genes: bar-1 egl-5 eor-1 eor-2 let-23 let-60 lin-1 lin-15 lin-25 lin-31 lin-36 lin-39 mpk-1 pry-1 sur-2 sur-8 Abstract: In Caenorhabditis elegans, Ras/ERK and Wnt/beta-catenin signaling pathways cooperate to induce P12 and vulval cell fates in a Hox-dependent manner. Here we describe eor-1 and eor-2, two new positively acting nuclear components of the Ras and Wnt pathways. eor-1 and eor-2 act downstream or in parallel to ERK and function redundantly with the Mediator complex gene sur-2 and the functionally related gene lin-25, such that removal of both eor-1/eor-2 and sur-2/lin-25 mimics the removal of a main Ras pathway component. Furthermore, the eor-1 and eor-2 mutant backgrounds reveal an essential role for the Elk1-related gene lin-1. eor-1 and eor-2 also act downstream or in parallel to pry-1 Axin and therefore act at the convergence of the Ras and Wnt pathways. eor-1 encodes the ortholog of human PLZF, a BTB/zinc-finger transcription factor that is fused to RARalpha in acute promyelocytic leukemia. eor-2 encodes a novel protein. EOR-1/PLZF and EOR-2 appear to function closely together and cooperate with Hox genes to promote the expression of Ras- and Wnt-responsive genes. Further studies of eor-1 and eor-2 may provide insight into the roles of PLZF in normal development and leukemogenesis. ------------------- Key: 5345 Medline: 12084813 Authors: Kostrouchova M;Housa D;Kostrouch Z;Saudek V;Rall JE Title: SKIP is an indispensable factor for Caenorhabditis elegans development. Citation: Proceedings of the National Academy of Sciences USA 99: 9254-9259 2002 Type: ARTICLE Genes: ama-1 bir-1 skp-1 Abstract: SKI-binding protein (SKIP) is a transcription cofactor present in all eukaryotes. Here we show that SKIP is a unique protein that is required for Caenorhabditis elegans viability and development. Expression of CeSKIP (skp-1) assayed by RT-PCR and by GFP fluorescence in transgenic lines starts in embryos and continues to adulthood. Loss of CeSKIP activity by RNA-mediated inhibition results in early embryonic arrest similar to that seen following inhibition of RNA polymerase II. RNA polymerase II phosphorylation appears normal early in CeSKIP RNA-mediated inhibition treated embryos although the expression of several embryonic GFP reporter genes is severely restricted or absent. Our data suggest that CeSKIP is an essential component of many RNA polymerase II transcription complexes and is indispensable for C. elegans development. ------------------- Key: 5346 Medline: 12095617 Authors: Lee MH;Ahn B;Choi IS;Koo HS Title: The gene expression and deficiency phenotypes of Cockayne syndrome B protein in Caenorhabditis elegans. Citation: FEBS Letters 522: 47-51 2002 Type: ARTICLE Genes: Abstract: The Caenorhabditis elegans Cockayne syndrome B protein homologue is encoded by 10 exons of the predicted open reading frame F53H4.1. The gene is expressed in germ cells and all somatic cells of the embryonic to adult stage. Although the gene expression was ubiquitous, its expression level was relatively higher in dividing cells and cells that play fundamental roles in essential physiological functions such as feeding, sensation, and reproduction. RNA interference of the gene hypersensitized C. elegans to UV radiation, as observed in enhanced germ cell proliferation arrest and apoptosis, and increased embryonic lethality, suggesting its role in nucleotide excision repair. ------------------- Key: 5347 Medline: 12121631 Authors: Gomes JE;Bowerman B Title: Caenorhabditis elegans par genes. Citation: Current Biology 12: R444- 2002 Type: REVIEW Genes: let-99 mex-1 mex-3 mex-5 mex-6 par-1 par-2 par-3 par-6 pie-1 pkc-3 pos-1 spn-4 Abstract: Six par genes (par-1 through par-6) have been identified in Caenorhabditis elegans. Loss-of-function mutations in any par locus results in loss of anterior-posterior (AP) asymmetries during the first two embryonic cell divisions. This results in a failure to restrict developmental regulators to specific embryonic cells, mitotic spindle orientation defects and abnormal cell fate pattering. In sum, the par genes appear responsible for establishing asymmetries that define the AP body axis in C. elegans. ------------------- Key: 5348 Medline: 12121640 Authors: Witze E;Rothman JE Title: Cell fusion: an EFFicient sculptor. Citation: Current Biology 12: R467-R469 2002 Type: REVIEW Genes: eff-1 lin-39 mab-5 Abstract: Mutations in the eff-1 gene of Caenorhabditis elegans, which prevent all cell-cell fusions in the nematode's epidermis, have revealed developmental roles for cell fusion. An extracellular fusogen-like domain in EFF-1 suggests it might direct the fusion of lipid bilayers. ------------------- Key: 5349 Medline: 12123612 Authors: Burbea M;Dreier L;Dittman JS;Grunwald ME;Kaplan JM Title: Ubiquitin and AP180 regulate the abundance of GLR-1 glutamate receptors at postsynaptic elements in C. elegans. Citation: Neuron 35: 107-120 2002 Type: ARTICLE Genes: eat-4 glr-1 unc-11 Abstract: Regulated delivery and removal of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) glutamate receptors (GluRs) from postsynaptic elements has been proposed as a mechanism for regulating synaptic strength. Here we test the role of ubiquitin in regulating synapses that contain a C. elegans GluR, GLR-1. GLR-1 receptors were ubiquitinated in vivo. Mutations that decreased ubiquitination of GLR-1 increased the abundance of GLR-1 at synapses and altered locomotion behavior in a manner that is consistent with increased synaptic strength. By contrast, overexpression of ubiquitin decreased the abundance of GLR-1 at synapses and decreased the density of GLR-1-containing synapses, and these effects were prevented by mutations in the unc-11 gene, which encodes a clathrin adaptin protein (AP180). These results suggest that ubiquitination of GLR-1 receptors regulates synaptic strength and the formation or stability of GLR-1-containing synapses. ------------------- Key: 5350 Medline: 12160748 Authors: Tobin DM;Madsen DM;Kahn-Kirby A;Peckol EL;Moulder G;Barstead R;Maricq AV;Bargmann CI Title: Combinatorial expression of TRPV channel proteins defines their sensory functions and subcellular localization in C. elegans neurons. Citation: Neuron 35: 307-318 2002 Type: ARTICLE Genes: eat-4 glr-1 ocr-1 ocr-2 ocr-3 ocr-4 odr-3 osm-9 osm-10 tax-2 tax-4 Abstract: C. elegans OSM-9 is a TRPV channel protein involved in sensory transduction and adaptation. Here, we show that distinct sensory functions arise from different combinations of OSM-9 and related OCR TRPV proteins. Both OSM-9 and OCR-2 are essential for several forms of sensory transduction, including olfaction, osmosensation, mechanosensation, and chemosensation. In neurons that express both OSM-9 and OCR-2, tagged OCR-2 and OSM-9 proteins reside in sensory cilia and promote each other's localization to cilia. In neurons that express only OSM-9, tagged OSM-9 protein resides in the cell body and acts in sensory adaptation rather than sensory transduction. Thus, alternative combinations of TRPV proteins may direct different functions in distinct subcellular locations. Animals expressing the mammalian TRPV1 (VR1) channel in ASH nociceptor neurons avoid the TRPV1 ligand capsaicin, allowing selective, drug-inducible activation of a specific ------------------- Key: 5351 Medline: Authors: Kruger O;Ladewig J;Koster K;Ragg H Title: Widespread occurrence of serpin genes with multiple reactive centre-containing exon cassettes in insects and Citation: Gene 293: 97-105 2002 Type: ARTICLE Genes: spn-1 spn-7 Abstract: By applying homology-search and text-mining programs we have found that the Drosophila serine protease inhibitor (serpin) gene sp4 harbours four reactive centre-coding exons. The mutually exclusive use of these cassettes in combination with alternatively selectable exons at the 5'-end or in the 3'-untranslated region of the gene allows generation of more than ten different transcripts, all of which are expressed in dependent on the splice pattern - either may be secreted, reside in the endoplasmic reticulum, or may be located in the cytoplasm. An examination revealed the presence of two serpin genes, each coding for two or three likely alternative reactive centre exon cassettes, respectively, also in the Caenorhabditis elegans genome. The occurrence of such serpin genes in some groups of metazoan reflects a parsimonious way to enlarge the adaptive ability of these organisms to cope with a plethora of different serine and cysteine proteases. ------------------- Key: 5352 Medline: 12119097 Authors: Terranova R;Pujol N;Fasano L;Djabali M Title: Characterisation of set-1, a conserved PR/SET domain gene in Caenorhabditis elegans. Citation: Gene 292: 33-41 2002 Type: ARTICLE Genes: lin-59 mes-2 mes-4 set-1 set-2 Abstract: The SET domain is a highly conserved domain shared between proteins of the antagonistic trithorax and Polycomb groups. It has been shown to play an important role in the assembly of either transcriptional activating or repressing protein complexes, and possesses a histone methyl-transferase activity. We report here the characterisation of the Caenorhabditis elegans gene, set-1, encoding a conserved SET-domain protein. We have analysed the developmental expression pattern of set-1 and show that maximal expression is observed early in development when set-1 is ubiquitously expressed. Its expression is more and more restricted as development progress. Gene inactivation by RNA interference shows that set-1 is an essential gene. Functional analysis of set-1 may contribute to the understanding of the molecular role of the SET domain. ------------------- Key: 5353 Medline: Authors: Stringham E;Pujol N;Vandekerckhove J;Bogaert T Title: unc-53 controls longitudinal migration in C. elegans. Citation: Development 129: 3367-3379 2002 Type: ARTICLE Genes: unc-53 mnDf77 mnDf87 mnDf90 Abstract: Cell migration and outgrowth are thought to be based on analogous mechanisms that require repeated cycles of process extension, reading and integration of multiple directional signals, followed by stabilization in a preferred direction, and renewed extension. We have characterized a C. elegans gene, unc-53, that appears to act cell autonomously in the migration and outgrowth of muscles, axons and excretory canals. Abrogation of unc-53 function disrupts anteroposterior outgrowth in those cells that normally express the gene. Conversely, overexpression of unc-53 in bodywall muscles leads to exaggerated outgrowth. UNC-53 is a novel protein conserved in vertebrates that contains putative SH3- and actin-binding sites. unc-53 interacts genetically with sem-5 and we demonstrated a direct interaction in vitro between UNC-53 and the SH2-SH# adaptor protein SEM-5/GRB2. Thus, unc-53 is involved in longitudinal navigation and might act by linking extracellular guidance cues to the intracellular cytoskeleton. ------------------- Key: 5354 Medline: 12135927 Authors: Sze JY;Zhang S;Li J;Ruvkun G Title: The C. elegans POU-domain transcription factor UNC-86 regulates the tph-1 tryptophan hydroxylase gene and neurite outgrowth in specific serotonergic neurons. Citation: Development 129: 3901-3911 2002 Type: ARTICLE Genes: cat-1 nss-1 tph-1 unc-86 Abstract: A fundamental question in developmental neurobiology is how a common neurotransmitter is specified in different neuronal types. We describe cell-specific regulation of the serotonergic phenotype by the C. elegans POU-transcription factor UNC-86. We show that unc-86 regulates particular aspects of the terminal neuronal identity in four classes of serotonergic neurons, but that the development of the ADF serotonergic neurons is regulated by an UNC-86-independent program. In the NSM neurons, the role of unc-86 is confined in late differentiation; the neurons are generated but do not express genes necessary for serotonergic neurotransmission. unc-86-null mutations affect the expression in NSM of tph-1, which encodes the serotonin synthetic enzyme tryptophan hydroxylase, and cat-1, which encodes a vesicular transporter that loads serotonin into synaptic vesicles, suggesting that unc-86 coordinately regulates serotonin synthesis and packaging. However, unc-86-null mutations do not impair the ability of NSM to reuptake serotonin released from the ADF serotonergic chemosensory neurons and this serotonin reuptake is sensitive to the serotonin reuptake block drugs imipramine and fluoxetine, demonstrating that serotonin synthesis and reuptake is regulated by distinct factors. The NSM neurons in unc-86-null mutants also display abnormal neurite outgrowth, suggesting a role of unc-86 in regulating this process as well. ------------------- Key: 5355 Medline: Authors: Alper S;Kenyon C Title: The zinc finger protein REF-2 functions with the HOX genes to inhibit cell fusion in the ventral epidermis of C. elegans. Citation: Development 129: 3335-3348 2002 Type: ARTICLE Genes: egl-5 egl-27 lin-39 mab-5 rde-2 ref-1 ref-2 Abstract: During larval development in C. elegans, some of the cells of the ventral epidermis, the Pn.p cells, fuse with the growing epidermal syncytium hyp7. The pattern of these cell fusions is regulated in a complex, sexually dimorphic manner. It is exxentail that some Pn.p cells remain unfused in order for some sex-specific mating structures to be generated. The pattern of Pn.p cell fusion is regulated combinatorially by two genes of the C. elegans Hox gene cluster:lin-39 and mab-5. Some of the complexity in the Pn.p cell fusion pattern arises because these two Hox proteins can regulate each other's activities. We describe a zinc-finger transcription factor, REF-2, that is required for the Pn.p cells to be generated and to remain unfused. REF-2 functions with the Hox proteins to prevents Pn.p cell fusion. ref-2 may also be a transcriptional target of the Hox proteins. ------------------- Key: 5356 Medline: 12124626 Authors: Zhang Y;Ma C;Delohery T;Nasipak B;Foat BC;Bounoutas A;Bussemaker HJ;Kim SK;Chalfie M Title: Identification of genes expressed in C. elegans touch receptor neurons. Citation: Nature 418: 331-335 2002 Type: ARTICLE Genes: acr-13 arf-3 bag-1 cap-1 cct-1 cct-2 cct-4 cyp-5 far-3 hsp-16.41 mec-1 mec-3 mec-4 mec-7 mec-9 mec-10 mec-12 mec-14 mec-18 rpl-18 rpl-20 rps-14 rps-18 sra-6 srp-1 Abstract: The extent of gene regulation in cell differentiation is poorly understood. We previously used saturation mutagenesis to identify 18 genes that are needed for the development and function of a single type of sensory neuron--the touch receptor neuron for gentle touch in Caenorhabditis elegans. One of these genes, mec-3, encodes a transcription factor that controls touch receptor differentiation. By culturing and isolating wild-type and mec-3 mutant cells from embryos and applying their amplified RNA to DNA microarrays, here we have identified genes that are known to be expressed in touch receptors, a previously uncloned gene (mec-17) that is needed for maintaining touch receptor differentiation, and more than 50 previously unknown mec-3-dependent genes. These genes are randomly distributed in the genome and under-represented both for genes that are co-expressed in operons and for multiple members of gene families. Using regions 5' of the start codon of the first 20 genes, we have also identified an over-represented heptanucleotide, AATGCAT, that is needed for the expression of touch ------------------- Key: 5357 Medline: 12074555 Authors: Gupta BP;Sternberg PW Title: Tissue-specific regulation of the LIM homeobox gene lin-11 during develoment of the Caenorhabditis elegans egg-laying system. Citation: Developmental Biology 247: 102-115 2002 Type: ARTICLE Genes: lag-1 lin-11 lin-17 Abstract: The egg-laying system of Caenorhabditis elegans hermaphrodites requires development of the vulva and its precise connection with the uterus. This process is regulated by LET-23-mediated epidermal growth factor signaling and LIN-12-mediated lateral signaling pathways. Among the nuclear factors that act downstream of these pathways, the LIM homeobox gene lin-11 plays a major role. lin-11 mutant animals are egg-laying defective because of the abnormalities in vulval lineage and uterine seam-cell formation. However, the mechanisms providing specificity to lin-11 function are not understood. Here, we examine the regulation of lin-11 during development of the egg-laying system. Our results demonstrate that the tissue-specific expression of lin-11 is controlled by two distinct regulatory elements that function as independent modules and together specify a wild-type egg-laying system. A uterine pi lineage module depends on the LIN-12/Notch signaling, while a vulval module depends on the LIN-17-mediated Wnt signaling. These results provide a unique example of the tissue-specific regulation of a LIM homeobox gene by two evolutionarily conserved signaling pathways. Finally, we provide evidence that the regulation of lin-11 by LIN-12/Notch signaling is directly mediated by the Su(H)/CBF1 family member LAG-1. ------------------- Key: 5358 Medline: 12420788 Authors: Xu X;Sassa T;Kunoh K;Hosono R Title: A mutant exhibiting abnormal habituation behavior in Caenorhabditis elegans. Citation: Journal of Neurogenetics 16: 29-44 2002 Type: ARTICLE Genes: hab-1 eDf3 eDf12 Abstract: The acquisition and retention of information by the nervous system are major processes of learning. Habituation is a simple learning process that occurs during repeated exposure to harmless stimuli. C. elegans is habituated when repeatedly given mechanical stimuli and recover from the habituation when the stimuli are stopped. A habituation abnormal mutant was isolated and assigned to a new gene hab-1 whose mutation causes slow habituation. The hab-1 mutant phenotype is remarkable at short time interval stimuli. However, hab-1 mutant worms show normal dishabituation. Ablations of neurons constituting the neural circuit for mechanical reflexes did not abolish abnormalities caused by the hab-1 mutation. ------------------- Key: 5359 Medline: 11182881 Authors: Toms N;Cooper J;Patchen B;Aamodt E Title: High copy arrays containing a sequence upstream of mec-3 alter cell migration and axonal morphology in C. elegans. Citation: BMC Developmental Biology 1:2: - 2001 Type: ARTICLE Genes: mec-3 pag-3 Abstract: Background: The Caenorhabditis elegans gene mec-3 encodes a LIM-homeodomain protein that is a master regulator of touch receptor neuron genes. Two of the touch neurons, the ALM neurons, are generated in the anterior of the animal and then migrate to near the middle of the animal. In animals transformed with a sequence upstream of mec-3, the ALM touch receptor neurons failed to migrate to their normal positions and sometimes migrated in the wrong direction, and the PLM touch receptor neurons showed axonal defects. Here we characterize this effect and identify the sequence causing the cell migration and axonal defects. Results: The ALM migration defect did not result from RNA interference (RNAi), nonspecific effects of carrying a transgenic array, expression of GFP, or the marker gene used to make the transformants. Instead, the ALM migration defect resulted from transgenic arrays containing many copies of a specific 104 bp DNA sequence. Transgenic arrays containing this sequence did not affect all cell migrations. Conclusions: The mec-3 upstream sequence appeared to be sequestering (titrating out) a specific DNA-binding factor that is required for the ALMs to migrate correctly. Because titration of this factor could reverse the direction of ALM migrations, it may be part of a program that specifies both the direction and extent of ALM migrations. mec-3 is a master regulator of touch receptor neuron genes, so the factor or factors that bind this sequence may also be involved in specifying the fate of touch receptor neurons. ------------------- Key: 5360 Medline: 11346453 Authors: Samuel ADT;Murthy VN;Hengartner MO Title: Calcium dynamics during fertilization in C. elegans. Citation: BMC Developmental Biology 1:8: - 2001 Type: ARTICLE Genes: Abstract: Background: Of the animals typically used to study fertilization-induced calcium dynamics, noneis as accessible to genetics and molecular biology as the model organism Caenorhabditis elegans. Motivated by the experimental possibilities inherent in using such a well-established model organism, we have characterized fertilization-induced calcium dynamics in C. elegans. Results: Owing to the transparency of the nematode, we have been able to study the calcium signal in C. elegans fertilization in vivo by monitoring the fluorescence of calcium indicator dyes that we introduce into the cytosol of oocytes. In C. elegans, fertilization induces a single calcium transient that is initiated soon after oocyte entry into the spermatheca, the compartment that contains sperm. Therefore, it is likely that the calcium transient is initiated by contact with sperm. This calcium elevation spreads throughout the oocyte, and decays monotonically after which the cytosolic calcium concentration returns to that preceding fertilization. Only this single calcium transient is observed. Conclusion: Development of a technique to study fertilization induced calcium transients opens several experimental possibilities, e.g., identification of the signaling events intervening sperm binding and calcium elevation, identifying the possible roles of the calcium elevation such as the completion of meiosis, the formation of the eggshell, and the ------------------- Key: 5361 Medline: 11387037 Authors: Knight RD;Shimeld SM Title: Identification of conserved C2H2 zinc-finger gene families in the Bilateria. Citation: Genome Biology 2(5): - 2001 Type: ARTICLE Genes: lin-29 mua-1 sem-4 Abstract: BACKGROUND: Identification of orthologous relationships between genes from widely divergent taxa allows partial reconstruction of the gene complement of ancestral genomes. C2H2 zinc-finger genes are one of the largest and most complex gene superfamilies in metazoan genomes, with hundreds of members in the human genome. Here we analyze C2H2 zinc-finger genes from three taxa - Drosophila, Caenorhabditis elegans and human - from which near-complete genome sequence data are available. RESULTS: Our analyses conclusively identify 39 families of genes, of which 38 can be defined as orthology groups in that they are descended from single ancestral genes in the common ancestor of Drosophila, C. elegans and humans. CONCLUSIONS: On the basis of current metazoan phylogeny, these 39 groups represent the minimum complement of C2H2 zinc-finger genes present in the genome of the bilaterian common ancestor. ------------------- Key: 5362 Medline: 11532213 Authors: Maglich JM;Sluder A;Guan X;Shi Y;McKee DD;Carrick K;Kamdar K;Willson TM;Moore JT Title: Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes. Citation: Genome Biology 2(8): 29.1-29.7 2001 Type: ARTICLE Genes: Abstract: Background: The availability of complete genome sequences enables all the member of a gene family to be identified without limitations imposed by temporal, spatial or quantitative aspects of mRNA expression. Using the nearly completed human genome sequence, we combined in silico and experimental approaches to define the complete human nuclear receptor (NR) set. This information was used to carry out a comparative genomic study of the NR superfamily. Results: Our analysis of the human genome identified two novel NR sequences. Both these contained stop codons within the coding regions, indicating that both are pseudogenes. One (HNF4-relatedP contained no introns and expressed no detectable mRNA, whereas the other (FXR-related) produced mRNA at relatively high levels in testis. If translated, the latter is predicted to encode a short, non-functional protein. Our analysis indicates that there are fewer than 50 functional human NRs, dramatically fewer than in Caenorhabditis elegans and about twice as many as in Drosophila. Searches for the >200 NRs unique to C. elegans revealed no human homologs. The comparative analysis also revealed a Drosophila member of NR subfamily NR3, confirming an ancient metazoan origin for this subfamily. Conclusion: The work provides the basis for new insights in to the evolution and functional relationships of NR superfamily members. ------------------- Key: 5363 Medline: 11182891 Authors: Bargmann CI Title: High throughput reverse genetics: RNAi screens in Caenorhabditis elegans. Citation: Genome Biology 2(2): 5.1-5.3 2001 Type: REVIEW Genes: Abstract: Two recent chromosome-wide screens for phenotypes caused by RNA-mediated interference (RNAi) in Caenorhabditis elegans have increased our understanding of essential genes in nematodes. These papers represent a major advance in functional genomics. ------------------- Key: 5364 Medline: 11831879 Authors: Donohue BA;Michelotti EL;Reader JC;Reader V;Stirling M;Tice CM Title: Design, synthesis, and biological evaluation of a library of Citation: Journal of Combinatorial Chemistry 4: 23-32 2002 Type: ARTICLE Genes: Abstract: A library of 422 1-(2-thiazolyl)-5-(trifluoromethyl)pyrazole-4-carboxamides was prepared in five steps using solution-phase chemistry. The first step in the synthesis was the reaction of ethyl 2-ethoxymethylene-3-oxo-4,4,4-trifluorobutanoate with thiosemicarbazide, which is reported in the literature to afford a 1:1 mixture of ethyl 1-thiocarbamoyl-5-(trifluoromethyl)pyrazole-4-carboxylate and ethyl 1-thiocarbamoyl-3-(trifluoromethyl)pyrazole-4-carboxylate. We reassigned the structure of the product to be a single compound, ethyl 5-hydroxy-1-thiocarbamoyl-5-(trifluoromethyl)-4,5-dihydro-1 H-pyrazole-4-ca rboxylate. This common intermediate was diversified by reaction with 17 alpha-bromoketones affording, in two steps, 17 1-(2-thiazolyl)-5-(trifluoromethyl)pyrazole-4-carboxylic acids. Scavenger resins were used to facilitate formation and purification of up to 27 amides from each of these acids in the last step. In addition, the Curtius reaction was applied to 12 of the acids followed by quenching with alcohols to afford a 108-member carbamate library. Certain compounds in the two libraries were toxic to C. elegans. ------------------- Key: 5365 Medline: Authors: Ostashevsky J Title: A polymer model for large-scale chromatin organization in lower eukaryotes. Citation: Molecular Biology of the Cell 13: 2157-2169 2002 Type: ARTICLE Genes: Abstract: A quantitative model of large-scale chromatin organization was applied to nuclei of fission yeast Schizosaccharomyces pombe (meiotic prophase and G2 phase), budding yeast Saccharomyces cerevisiae (young and senescent cells), Drosophila (embryonic cycles 10 and 14, and polytene tissues) and Caenorhabditis elegans (G1 phase). The model is based on the coil-like behavior of chromosomal fibers and the tight packing of discrete chromatin domains in a nucleus. Intrachromosomal domains are formed by chromatin anchoring to nuclear structures (e.g., the nuclear envelope). The observed sizes for confinement of chromatin diffusional motion are similar to the estimated sizes of corresponding domains. The model correctly predicts chromosome configurations (linear, Rabl, loop) and chromosome associations (homologous pairing, centromere and telomere clusters) on the basis of the geometrical constraints imposed by nuclear size and shape. Agreement between the model predictions and literature observations supports the notion that the average linear density of the 30-nm chromatin fiber is similar to4 nucleosomes per 10 nm contour length. ------------------- Key: 5366 Medline: 12082149 Authors: Jedrusik MA;Vogt S;Claus P;Schulze E Title: A novel linker histone-like protein is associated with cytoplasmic filaments in Caenorhabditis elegans. Citation: Journal of Cell Science 115: 2881-2891 2002 Type: ARTICLE Genes: unc-65 Abstract: The histone H1 complement of Caenorhabditis elegans contains a single unusual protein, H1.X. Although H1.X possesses the globular domain and the canonical three-domain structure of linker histones, the amino acid composition of H1.X is distinctly different from conventional linker histones in both terminal domains. We have characterized H1.X in C. elegans by antibody labeling, green fluorescent protein fusion protein expression and RNA interference. Unlike normal linker histones, H1.X is a cytoplasmic as well as a nuclear protein and is not associated with chromosomes. H1.X is most prominently expressed in the marginal cells of the pharynx and is associated with a peculiar cytoplasmic cytoskeletal structure therein, the tonofilaments. Additionally H1.X::GFP is expressed in the cytoplasm of body and vulva muscle cells, neurons, excretory cells and in the nucleoli of embryonic blastomeres and adult gut cells. RNA interference with H1.X results in uncoordinated and egg laying defective animals, as well as in a longitudinally enlarged pharynx. These phenotypes indicate a cytoplasmic ------------------- Key: 5367 Medline: Authors: Ryu WS;Samuel ADT Title: Thermotaxis in Caenorhabditis elegans analyzed by measuring responses to defined thermal stimuli. Citation: Journal of Neuroscience 22: 5727-5733 2002 Type: ARTICLE Genes: ttx-1 ttx-3 Abstract: In a spatial thermal gradient, Caenorhabditis elegans migrates toward and then isothermally tracks near its cultivation temperature. A current model for thermotactic behavior involves a thermophilic drive (involving the neurons AFD and AIY) and cryophilic drive (involving the neuron AIZ) that balance at the cultivation temperature. Here, we analyze the movements of individual worms responding to defined thermal gradients. We found evidence for a mechanism for migration down thermal gradients that is active at temperatures above the cultivation temperature, and a mechanism for isothermal tracking that is active near the cultivation temperature. However, we found no evidence for a mechanism for migration up thermal gradients at temperatures below the cultivation temperature that might have supported the model of opposing drives. The mechanisms for migration down gradients and isothermal tracking control the worm's movements in different manners. Migration down gradients works by shortening (lengthening) the duration of forward movement in response to positive (negative) temperature changes. Isothermal tracking works by orienting persistent forward movement to offset temperature changes. We believe preference for the cultivation temperature is not at the balance between two drives. Instead, the worm activates the mechanism for isothermal tracking near the cultivation temperature and inactivates the mechanism for migration down gradients near or below the cultivation temperature. Inactivation of the mechanism for migration down gradients near or below the cultivation temperature requires the neurons AFD and AIY. ------------------- Key: 5368 Medline: 12110183 Authors: Tabara H;Yigit E;Siomi H;Mello C Title: The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DExX-box helicase to direct RNAi in C. Citation: Cell 109: 861-871 2002 Type: ARTICLE Genes: dcr-1 drh-1 drh-2 mut-7 pos-1 rde-1 rde-2 rde-3 rde-4 Abstract: Double-stranded (ds) RNA induces potent gene silencing, termed RNA interference (RNAi). At an early step in RNAi, an RNaseIII-related enzyme, Dicer (DCR-1), processes long-trigger dsRNA into small interfering RNAs (siRNAs). DCR-1 is also required for processing endogenous regulatory RNAs called miRNAs, but how DCR-1 recognizes its endogenous and foreign substrates is not yet understood. Here we show that the C. elegans RNAi pathway gene, rde-4, encodes a dsRNA binding protein that interacts during RNAi with RNA identical to the trigger dsRNA. RDE-4 protein also interacts in vivo with DCR-1, RDE-1, and a conserved DExH-box helicase. Our findings suggest a model in which RDE-4 and RDE-1 function together to detect and retain foreign dsRNA and to present this dsRNA to DCR-1 for ------------------- Key: 5369 Medline: 12097347 Authors: Swan KA;Curtis DE;McKusick KB;Voinov AV;Mapa FA;Cancilla MR Title: High-throughput gene mapping in Caenorhabditis elegans. Citation: Genome Research 12: 1100-1105 2002 Type: ARTICLE Genes: dpy-18 Abstract: Positional cloning of mutations in model genetic systems is a powerful method for the identification of targets of medical and agricultural importance. To facilitate the high-throughput mapping of mutations in Caenorhabditis elegans, we have identified a further 9602 putative new single nucleotide polymorphisms (SNPs) between two C. elegans strains, Bristol N2 and the Hawaiian mapping strain CB4856, by sequencing inserts from a CB4856 genomic DNA library and using an informatics pipeline to compare sequences with the canonical N2 genomic sequence. When combined with data from other laboratories, our marker set of 17,189 SNPs provides even coverage of the complete worm genome. To date, we have confirmed >1099 evenly spaced SNPs (one every 91+-56 kb) across the six chromosomes and validated the utility of our SNP marker set and new fluorescence polarization-based genotyping methods for systematic and high-throughput identification of genes in C. elegans by cloning several proprietary genes. We illustrate our approach by recombination mapping and confirmation of the mutation in the cloned gene, dpy-18. ------------------- Key: 5370 Medline: 12142542 Authors: Kim DH;Feinbaum R;Alloing G;Emerson FE;Garsin DA;Inoue H;Tanaka-Hino M;Hisamoto N;Matsumoto K;Tan MW;Ausubel FM Title: A conserved p38 MAP kinase pathway in Caenorhabditis elegans innate immunity. Citation: Science 297: 623-626 2002 Type: ARTICLE Genes: esp-2 esp-8 glp-4 nsy-1 pmk-1 pmk-2 sek-1 unc-43 Abstract: A genetic screen for Caenorhabditis elegans mutants with enhanced susceptibility to killing by Pseudomonas aeruginosa led to the identification of two genes required for pathogen resistance: sek-1, which encodes a mitogen-activated protein (MAP) kinase kinase, and nsy-1, which encodes a MAP kinase kinase kinase. RNA interference assays and biochemical analysis established that a p38 ortholog, pmk-1, functions as the downstream MAP kinase required for pathogen defense. These data suggest that this MAP kinase signaling cassette represents an ancient feature of innate immune responses in evolutionarily diverse ------------------- Key: 5371 Medline: 12089340 Authors: Fonte V;Kapulkin V;Taft A;Fluet A;Friedman D;Link CD Title: Interaction of intracellular beta amyloid peptide with chaperone proteins. Citation: Proceedings of the National Academy of Sciences USA 99: 9439-9444 2002 Type: ARTICLE Genes: Abstract: Expression of the human beta amyloid peptide (Abeta) in transgenic Caenorhabditis elegans animals can lead to the formation of intracellular immunoreactive deposits as well as the formation of intracellular amyloid. We have used this model to identify proteins that interact with intracellular Abeta in vivo. Mass spectrometry analysis of proteins that specifically coinimunoprecipitate with Abeta has identified six likely chaperone proteins: two members of the HSP70 family, three alphaB-crystallin-related small heat shock proteins (HSP-16s), and a putative ortholog of a mammalian small glutamine-rich tetratricopeptide repeat-containing protein proposed to regulate HSP70 function. Quantitative reverse transcription-PCR analysis shows that the small heat shock proteins are also transcriptionally induced by Abeta expression. Immunohistochemistry demonstrates that HSP-16 protein closely colocalizes with intracellular Abeta in this model. Transgenic animals expressing a nonaggregating Abeta variant, a single-chain Abeta dimer, show an altered pattern of coimmunoprecipitating proteins and an altered cellular distribution of HSP-16. Double-stranded RNA inhibition of R05F9.10, the putative C elegans ortholog of the human small glutamine-rich tetratricopeptide-repeat-containing protein (SGT), results in suppression of toxicity associated with Abeta expression. These results suggest that chaperone function ------------------- Key: 5372 Medline: 12126229 Authors: Knust E Title: Regulation of epithelial cell shape and polarity by cell-cell adhesion. Citation: Molecular Membrane Biology 19: 113-120 2002 Type: REVIEW Genes: ajm-1 dlg-1 hmp-1 hmp-2 hmr-1 let-413 par-3 par-6 Abstract: Among all cell types that exhibit a polarized phenotype, epithelial cells are unique in that their polarity depends on the integration of the cell into a tissue, the epithelium. In recent years, the analysis of epithelial cell polarity in different epithelia and organisms has contributed to an understanding of the components involved and has further demonstrated that cell polarity and cell adhesion are intimately related to each other. Therefore, processes that mediate and modulate cell adhesion and coordinate adhesion and cell shape are fundamental for the function of epithelia. Recent results obtained in Drosophila melanogaster and Caenorhabditis elegans have provided further insight into the complex circuits regulating these processes, and have laid the direction for ------------------- Key: 5373 Medline: 12110162 Authors: Goutte C Title: Genetics leads the way to the accomplices of presenilins. Citation: Developmental Cell 3: 6-7 2002 Type: REVIEW Genes: aph-1 aph-2 hop-1lin-12 pen-2 sel-12 Abstract: Presenilins mediate they-secretase cleavage of Notch transmembrane receptors as well as the transmembrane P-amyloid precursor protein (PAPP), but they are not thought to accomplish this alone. Recent genetic screens in C. elegans, presented in this issue of Developmental Cell, identify two genes that are essential to gamma-secretase activity and may interact with presenilins. ------------------- Key: 5374 Medline: 12110170 Authors: Francis R;McGrath G;Zhang J;Ruddy DA;Sym M;Apfeld J;Nicoll M;Maxwell M;Hai B;Ellis MC;Parks AL;Xu W;Li J;Gurney M;Myers RL;Himes CS;Hiebsch R;Ruble C;Nye JS;Curtis D Title: aph-1 and pen-2 are required for Notch pathway signaling, gamma-secretase cleavage of BAPP, and presenilin protein accumulation. Citation: Developmental Cell 3: 85-97 2002 Type: ARTICLE Genes: aph-1 aph-2 glp-1 hop-1 lag-1 lag-2 lin-12 pen-2 sel-12 Abstract: Presenilins are components of the gamma-secretase protein complex that mediates intramembranous cleavage of PAPP and Notch proteins. A C. elegans genetic screen revealed two genes, aph-1 and pen-2, encoding multipass transmembrane proteins, that interact strongly with sel-12/presenilin and aph-2/nicastrin. Human aph-1 and pen-2 partially rescue the C. elegans mutant phenotypes, demonstrating conserved functions. The human genes must be provided together to rescue the mutant phenotypes, and the inclusion of presenilin-1 improves rescue, suggesting that they interact closely with each other and with presenilin. RNAi-mediated inactivation of aph-1, pen-2, or nicastrin in cultured Drosophila cells reduces gamma-secretase cleavage of PAPP and Notch substrates and reduces the levels of processed presenilin. aph-1 and pen-2, like nicastrin, are required for the activity and accumulation of gamma-secretase. ------------------- Key: 5375 Medline: 12110172 Authors: Bei Y;Hogan J;Berkowitz LA;Soto M;Rocheleau CE;Pang KM;Collins J;Mello CC Title: SRC-1 and Wnt signaling act together to specify endoderm and to control cleavage orientation in early C. elegans Citation: Developmental Cell 3: 113-125 2002 Type: ARTICLE Genes: apr-1 dsh-2 gsk-3 lit-1 mes-1 mig-5 mom-1 mom-2 mom-3 mom-4 mom-5 pop-1 src-1 wrm-1 Abstract: In early C. elegans embryos, signaling between a posterior blastomere, P2, and a ventral blastomere, EMS, specifies endoderm and orients the division axis of the EMS cell. Although Wnt signaling contributes to this polarizing interaction, no mutants identified to date abolish P2/EMS signaling. Here, we show that two tyrosine kinase-related genes, src-1 and mes-1, are required for the accumulation of phosphotyrosine between P2 and EMS. Moreover, src-1 and mes-1 mutants strongly enhance endoderm and EMS spindle rotation defects associated with Wnt pathway mutants. SRC-1 and MES-1 signal bidirectionally to control cell fate and division orientation in both EMS and P2. Our findings suggest that Wnt and Src signaling function in parallel to control developmental outcomes within a single responding cell. ------------------- Key: 5376 Medline: 12074557 Authors: Romagnolo B;Jiang M;Kiraly M;Breton C;Begley R;Wang J;Lund J;Kim SK Title: Downstream targets of let-60 Ras in Caenorhabditis elegans. Citation: Developmental Biology 247: 127-136 2002 Type: ARTICLE Genes: cat-2 ces-1 ces-2 let-23 let-60 sos-1 Abstract: In Caenorhabditis elegans, let-60 Ras controls many cellular processes, such as differentiation of vulval epithelial cells, function of chemosensory neurons, and meiotic progression in the germ line. Although much is known about the let-60 Ras signaling pathway, relatively little is understood about the target genes induced by let-60 Ras signaling that carry out terminal effector functions leading to morphological change. We have used DNA microarrays to identify 708 genes that change expression in response to activated let-60 Ras. ------------------- Key: 5377 Medline: 11937505 Authors: Warren CE;Krizus A;Roy PJ;Culotti JG;Dennis JW Title: The Caenorhabditis elegans gene, gly-2, can rescue the N-acetylglucosaminyltransferase V mutation of Lec4 cells. Citation: Journal of Biological Chemistry 277: 22829-22838 2002 Type: ARTICLE Genes: gly-2 Abstract: UDP-N-acetylglucosamine:alpha-6-d-mannoside beta-1,6-N-acetylglucosaminyltransferase V (GlcNAc-TV) is a regulator of polylactosamine-containing N-glycans and is causally involved in T cell regulation and tumor metastasis. The Caenorhabditis elegans genome contains a single orthologous gene, gly-2, that is transcribed and encodes a 669-residue type II membrane protein that is 36.7% identical to mammalian GlcNAc-TV (Mgat-5). Recombinant GLY-2 possessed GlcNAc-TV activity when assayed in vitro, and protein truncations demonstrated that the N-terminal boundary of the catalytic domain is Ile-138. gly-2 complemented the Phaseolus vulgaris leucoagglutinin binding defect of Chinese hamster ovary Lec4 cells, whereas GLY-2(L116R), an equivalent mutation to that which causes the Lec4A phenotype, could not. We conclude that the worm gene is functionally interchangeable with the mammalian form. GlcNAc-TV activity was detected in wild-type animals but not those homozygous for a deletion allele of gly-2. Activity was restored in mutant animals by an extrachromosomal array that encompassed the gly-2 gene. Green fluorescent protein reporter transgenes driven by the gly-2 promoter were expressed by developing embryos from the late comma stage onward, present in a complex subset of neurons in larvae and, in addition, the spermathecal and pharyngeal-intestinal valves and certain vulval cells of adults. However, no overt phenotypes were observed in animals homozygous for deletion alleles of gly-2. ------------------- Key: 5378 Medline: 11985779 Authors: Blair JE;Ikeo K;Gojobori T;Hedges SB Title: The evolutionary position of nematodes. Citation: BMC Evolutionary Biology 2: 7- 2002 Type: ARTICLE Genes: Abstract: Background: The complete genomes of three animals have been sequenced by global research efforts: a nematode worm (Caenorhabditis elegans), an insect (Drosophila melanogaster), and a vertebrate (Homo sapiens). Remarkably, their relationships have yet to be clarified. The confusion concerns the enigmatic position of nematodes. Traditionally, nematodes have occupied a basal position, in part because they lack a true body cavity. However, the leading hypothesis now joins nematodes with arthropods in a molting clade, Ecdysozoa, based on data from several genes. Results: We tested the Ecdysozoa hypothesis with analyses of more than 100 nuclear protein alignments, under conditions that would expose biases, and found that it was not supported. Instead, we found significant support for the traditional hypothesis, Coelomata. Our result is robust to different rates of sequence change among genes and lineages, different numbers of taxa, and different species of nematodes. Conclusion: We conclude that insects (arthropods) are genetically and evolutionarily closer to humans than to nematode worms. ------------------- Key: 5379 Medline: Authors: Tatar M Title: Germ-line stem cells call the shots. Citation: Trends in Ecology & Evolution 17: 297-298 2002 Type: REVIEW Genes: daf-2 daf-12 daf-16 daz-1 fem-3 fez-1 fog-1 fog-2 fog-3 gld-1 glp-1 mes-1 Abstract: In the nematode Caenorhabditis elegans, developmental biologists find that tissues derived from embryonic germ-line progenitor cells regulate reproductive costs. New work from the laboratory of Cynthia Kenyon demonstrates that signals that reduce adult survival are mediated by a small set of progenitor descendants, the germ-line stem cells, and by their interaction with components of the endocrine system. Caenorhabditis elegans is now providing a new way of understanding the mechanisms of tradeoffs between reproduction and ageing. ------------------- Key: 5380 Medline: 12077342 Authors: Dellaire G;Makarov EM;Cowger JJM;Longman D;Sutherland HGE;Luhrmann R;Torchia J;Bickmore WA Title: Mammalian PRP4 kinase copurifies and interacts with components of both the U5 snRNP and the N-CoR deacetylase complexes. Citation: Molecular and Cellular Biology 22: 5141-5156 2002 Type: ARTICLE Genes: Abstract: A growing body of evidence supports the coordination of pre-mRNA processing and transcriptional regulation. We demonstrate here that mammalian PRP4 kinase (PRP4K) is associated with complexes involved in both of these processes. PRP4K is implicated in pre-mRNA splicing as the homologue of the Schizosaccharomyces pombe pre-mRNA splicing kinase Prp4p, and it is enriched in SC35-containing nuclear splicing speckles. RNA interference of Caenorhabditis elegans PRP4K indicates that it is essential in metazoans. In support of a role for PRP4K in pre-mRNA splicing, we identified PRP6, SWAP, and pinin as interacting proteins and demonstrated that PRP4K is a U5 snRNP-associated kinase. In addition, BRG1 and N-CoR, components of nuclear hormone coactivator and corepressor complexes, also interact with PRP4K. PRP4K coimmunoprecipitates with N-CoR, BRG1, pinin, and PRP6, and we present data suggesting that PRP6 and BRG1 are substrates of this kinase. Lastly, PRP4K, BRG1, and PRP6 can be purified as components of the N-CoR-2 complex, and affinity-purified PRP4K/N-CoR complexes exhibit deacetylase activity. We suggest that PRP4K is an essential kinase that, in association with the both U5 snRNP and N-CoR deacetylase complexes, demonstrates a possible coordination of pre-mRNA splicing with chromatin remodeling events ------------------- Key: 5381 Medline: 12117988 Authors: Couillault C;Ewbank JJ Title: Diverse bacteria are pathogens of Caenorhabditis elegans. Citation: Infection and Immunity 70: 4705-4707 2002 Type: ARTICLE Genes: Abstract: Practically and ethically attractive as model systems, invertebrate organisms are increasingly recognized as relevant for the study of bacterial pathogenesis. We show here that the nematode Caenorhabditis elegans is susceptible to a surprisingly broad range of bacteria and may constitute a useful model for the study of both pathogens and symbionts. ------------------- Key: 5382 Medline: 12176330 Authors: Mallo GV;Kurz CL;Couillault C;Pujol N;Granjeaud S;Kohara Y;Ewbank JJ Title: Inducible antibacterial defense system in C. elegans. Citation: Current Biology 12: 1209-1214 2002 Type: ARTICLE Genes: dbl-1 grd-3 lys-1 lys-2 lys-3 lys-4 lys-5 lys-6 lys-7 lys-8 lys-9 lys-10 Abstract: The term innate immunity refers to a number of evolutionary ancient mechanisms that serve to defend animals and plants against infection. Genetically tractable model organisms, especially Drosophila, have contributed greatly to advances in our understanding of mammalian innate immunity [1, 2]. Essentially, nothing is known about immune responses in the nematode Caenorhabditis elegans [3,4]. Using high-density cDNA microarrays, we show here that infection of C. elegans by the Gram-negative bacterium Serratia marcescens provokes a marked upregulation of the expression of many genes. Among the most robustly induced are genes encoding lectins and lysozymes, known to be involved in immune responses in other organisms. Certain infection-inducible genes are under the control of the DBL-1/TGFbeta pathway [5]. We found that dbl-1 mutants exhibit increased susceptibility to infection. Conversely, overexpression of the lysozyme gene lys-1 augments the resistance of C. elegrans to S. marcescens. These results constitute the first demonstration of inducible antibacterial defenses in C. elegans and open new avenues for the investigation of evolutionary conserved mechanisms of innate immunity. ------------------- Key: 5383 Medline: 12150902 Authors: Taylor S;Bagrodia S Title: Src and Wnt converge to seal cell's fate. Citation: Molecular Cell 10: 10-11 2002 Type: REVIEW Genes: par-1 par-2 par-3 par-6 pkc-3 pop-1 mes-1 src-1 Abstract: Src family kinases (SFKs) play many roles in the development and growth of flies and mice. In the July, 2002 issue of Developmental Cell, Bei et al. show that a C. elegans SFK collaborates with the Wnt pathway to specify cell fate in early development. ------------------- Key: 5384 Medline: 12097166 Authors: Hirabayashi J;Hayama K;Kaji H;Isobe T;Kasai K Title: Affinity capturing and gene assignment of soluble glycoproteins produced by the nematode Caenorhabditis elegans. Citation: Journal of Biochemistry 132: 103-114 2002 Type: ARTICLE Genes: Abstract: Protein glycosylation is a central issue for post-genomic (proteomic) sciences. We have taken a systematic approach for analyzing soluble glycoproteins produced in the nematode Caenorhabditis elegans. The approach aims at assigning (i) genes that encode glycoproteins, (ii) sites where glycosylation occurs, and (iii) types of attached glycan structures. A soluble extract of C. elegans, as a starting material, was applied first to a concanavalin A (ConA) column (specific for high-mannose type N-glycans), and then the flow-through fraction was applied to a galectin LEC-6 (GaL6) column (specific for complex-type N-glycans). The adsorbed glycoproteins were digested with lysylendopeptidase, and the resultant glycopeptides were selectively recaptured with the same lectin columns. The glycopeptides were separated by reversed-phase chromatography and then subjected to sequence determination. As a result, 44 and 23 glycopeptides captured by the ConA and GaL6 columns, respectively, were successfully analyzed and assigned to 32 and 16 corresponding genes, respectively. For these glycopeptides, 49 N-glycosylation sites were experimentally confirmed, whereas 21 sites remained as potential sites. Of the identified genes, about 80% had apparent homologues in other species, as represented by typical secreted proteins. However, the two sets of genes assigned for the ConA and GaL6-recognized glycopeptides showed only 1 overlap with each other. Proof of the practical applicability of the glyco-catch method to a model organism, C. elegans, directs us to explore more complex multicellular organisms. ------------------- Key: 5385 Medline: Authors: Thompson FJ;Britton C;Wheatley I;Maitland K;Walker G;Anant S;Davidson NO;Devaney E Title: Biochemical and molecular characterization of two cytidine deaminases in the nematode Caenorhabditis elegans. Citation: Biochemical Journal 365: 99-107 2002 Type: ARTICLE Genes: cdd-1 cdd-2 Abstract: Two cytidine deaminases (CDDs) from the free-living nematode Caenorhabditis elegans have been cloned and characterized. Both Ce-CDD-1 and Ce-CDD-2 are authentic deaminases and both exhibit RNA-binding activity towards AU-rich templates. In order to study their temporal and spatial expression patterns in the worm, reporter gene constructs were made using approx. 2 kb of upstream sequence. Transfection of C. elegans revealed that both genes localized to the cells of the intestine, although their temporal expression patterns were different. Expression of Ce-cdd-1 peaked in the early larval stages, whereas Ce-cdd-2 was expressed in all life cycle stages examined. RNA-interference RNAi) assays were performed for both genes, either alone or in combination, but only cdd-2 RNAi produced a consistent visible phenotype. A proportion of eggs laid from these worms were swollen and distorted in ------------------- Key: 5386 Medline: 12127760 Authors: Wadsworth WG Title: Moving around in a worm: netrin UNC-6 and circumferential axon guidance in C. elegans. Citation: Trends in Neurosciences 25: 423-429 2002 Type: REVIEW Genes: unc-5 unc-6 unc-40 Abstract: How does an extracellular guidance molecule direct multiple growth cones to different positions? The answer is important for understanding the development of complex neural connections. UNC-6 is a member of the netrin family of guidance proteins. It has phylogenetically conserved domains that mediate its different guidance and branching activities. In the Caenorhabditis elegans embryo, UNC-6 is secreted ventrally and a pattern of circumferential axon tracts develops as pioneer growth cones bearing UNC-5 and UNC-40 receptors are directed towards, or away from,the ventral sources. Following the first migrations, UNC-6 from additional sources allows more complex migration patterns to emerge. In addition, at specific dorsoventral positions, locally restricted extracellular molecules alter growth cone responses to UNC-6, causing circumferentially migrating growth cones to turn and longitudinal nerves to develop. These observations show that extracellular guidance molecules can direct complex arrangements of migrating growth cones in vivo by eliciting different types of responses, by spatially and temporally regulating their expression and by working in concert with other extracellular molecules. ------------------- Key: 5387 Medline: Authors: Constans A Title: Small worms, small RNAs, big questions - Exploring small-RNA function and biology in Caenorhabditis elegans. Citation: Scientist 16: 32-34 2002 Type: REVIEW Genes: Abstract: ------------------- Key: 5388 Medline: 12134150 Authors: Castillo-Davis CI;Mekhedov SL;Hartl DL;Koonin EV;Kondrashov FA Title: Selection for short introns in highly expressed genes. Citation: Nature Genetics 31: 415-418 2002 Type: ARTICLE Genes: Abstract: Transcription is a slow and expensive process: in eukaryotes, approximately 20 nucleotides can be transcribed per second(1,2) at the expense of at least two ATP molecules per nucleotide(3). Thus, at least for highly expressed genes, transcription of long introns, which are particularly common in mammals, is costly. Using data on the expression of genes that encode proteins in Caenorhabditis elegans and Homo sapiens, we show that introns in highly expressed genes are substantially shorter than those in genes that are expressed at low levels. This difference is greater in humans, such that introns are, on average, 14 times shorter in highly expressed genes than in genes with low expression, whereas in C. elegans the difference in intron length is only twofold. In contrast, the density of introns in a gene does not strongly depend on the level of gene expression. Thus, natural selection appears to favor short introns in highly expressed genes to minimize the cost of transcription and other molecular ------------------- Key: 5389 Medline: Authors: Zhang Y;Herman B Title: Ageing and apoptosis. Citation: Mechanisms of Ageing & Development 123: 245-260 2002 Type: REVIEW Genes: age-1 akt-1 akt-2 clk-1 clk-2 clk-3 daf-2 daf-16 daf-18 gro-1 mev-1 pdk-1 sod-2 Abstract: Ageing is accompanied by a general decline of physiological function, especially at later stages, and significant increases in the incidence of cancer and other degenerative diseases. It has recently been hypothesized that alterations in apoptosis may contribute to these age-associated changes. However. whether there is a role for apoptosis in the ageing process and how ageing may modify the regulatory machinery of apoptosis remains obscure. Although the literature addressing these issues is scarce, research in this area is gaining momentum. Molecules involved in apoptosis signaling in mammals have been found to regulate ageing in organisms such as Caenorhabditis elegans and Drosophila melanogaster. Caloric restriction studies in a wide variety of organisms, ranging from yeast to mammals, suggest the conserved nature of the ageing regulatory systems. It seems very likely that signals that regulate ageing will impact apoptosis and the extent of apoptosis may then impact ageing. However, to date, there has been no direct evidence supporting the existence of such cross-communication between ageing and apoptosis in mammalian system. Here we review progress in ------------------- Key: 5390 Medline: 12048181 Authors: Bishop JD;Schumacher JM Title: Phosphorylation of the carboxyl terminus of inner centromere protein (INCENP) by the Aurora B kinase stimulates Aurora B kinase activity. Citation: Journal of Biological Chemistry 277: 27577-27580 2002 Type: ARTICLE Genes: Abstract: How the events of mitosis are coordinated is not well understood. Intriguing mitotic regulators include the chromosomal passenger proteins. Loss of either of the passengers inner centromere protein (INCENP) or the Aurora B kinase results in chromosome segregation defects and failures in cytokinesis. Furthermore, INCENP and Aurora B have identical localization patterns during mitosis and directly bind each other in vitro. These results led to the hypothesis that INCENP is a direct substrate of Aurora B. Here we show that the Caenorhabditis elegans Aurora B kinase AIR-2 specifically phosphorylated the C. elegans INCENP ICP-1 at two adjacent serines within the carboxyl terminus. Furthermore, the full length and a carboxyl-terminal fragment of ICP-1 stimulated AIR-2 kinase activity. This increase in AIR-2 activity required that AIR-2 phosphorylate ICP-1 because mutation of both serines in the AIR-2 phosphorylation site of ICP-1 abolished the potentiation of AIR-2 kinase activity by ICP-1. Thus, ICP-1 is directly phosphorylated by AIR,2 and functions in a positive feedback loop that regulates AIR-2 kinase activity. Since the Aurora B phosphorylation site within INCENP and the functions of INCENP and Aurora B have been conserved among eukaryotes, the feedback loop we have identified is also likely to be evolutionarily conserved. ------------------- Key: 5391 Medline: 12101090 Authors: Syntichaki P;Tavernarakis N Title: Death by necrosis - Uncontrollable catastrophe, or is there order behind the chaos? Citation: EMBO Reports 3: 604-609 2002 Type: REVIEW Genes: acy-1 deg-1 deg-3 des-2 mec-4 mec-6 mec-10 sgs-1 unc-8 unc-105 Abstract: Cells suffer necrotic death when exposed to extreme environmental conditions, adverse and excessive stimuli, or when deleterious mutations are encoded in their genetic material. Unlike apoptosis, which involves a highly regulated and elaborate network of biochemical events and cascades, necrosis has been considered generally to be a chaotic decadence process that effects the inexorable demise of cells otherwise not destined to die. This grim prospect is now slowly being overturned, mostly by exciting new findings in two simple model organisms, Caenorhabditis elegans and Drosophila melanogaster. Despite the wide spectrum of necrosis-initiating conditions, evidence is accumulating that execution of necrotic or neurodegenerative cell death may be carried out by a finite common set of mechanisms. ------------------- Key: 5392 Medline: 12111210 Authors: Irle T;Schierenberg E Title: Developmental potential of fused Caenorhabditis elegans oocytes: generation of giant and twin embryos. Citation: Development Genes & Evolution 212: 257-266 2002 Type: ARTICLE Genes: Abstract: With their first cleavage blastomeres in Caenorhabditis elegans are fixed to very different developmental programs going along with differential segregation of maternal gene products. To investigate whether indications for a prelocalization of cytoplasmic components can already be found in unfertilized egg cells, we fused mature C. elegans oocytes with the help of a laser microbeam. Fertilization of two fused oocytes resulting in triploid zygotes showed an essentially normal early cleavage pattern with the establishment of five somatic cell lineages and a germline and also a normal spatial arrangement of blastomeres. A considerable fraction of such embryos hatched and developed into fertile giant nematodes. The numbers of cell nuclei in freshly hatched and adult giant animals were found to be essentially the same as in untreated controls. When three fused oocytes were fertilized, two alternative patterns of early embryogenesis were observed. Half of the embryos followed the normal cleavage mode. The other half, however, developed in a twin-like fashion with all cells present in two copies, apparently due to fertilization by two sperm. In such embryos, two areas of gastrulation were established, resulting in the generation of two separate gut primordia. In summary, our results suggest that (1) in contrast to the uncleaved zygote in the mature oocyte of C. elegans no cytoplasmic regionalization exists, (2) the invariable cell numbers typical for the C. elegans embryo are not controlled via cell size, and (3) the entry of a second sperm can induce a cascade of events in the egg leading to the formation of two complete embryo anlagen. ------------------- Key: 5393 Medline: 11966472 Authors: Shatilla A;Ramotar D Title: Embryonic extracts derived from the nematode Caenorhabditis elegans remove uracil from DNA by the sequential action of uracil-DNA glycosylase and AP (apurinic/apyrimidinic) endonuclease. Citation: Biochemical Journal 365: 547-553 2002 Type: ARTICLE Genes: Abstract: DNA bases continuously undergo modifications in response to endogenous reactions such as oxidation, alkylation or deamination. The modified bases are primarily removed by DNA glycosylases, which cleave the N-glycosylic bond linking the base to the sugar, to generate an apurinic/apyrimidinic (AP) site, and this latter lesion is highly mutagenic. Previously, no study has demonstrated the processing of these lesions in the nematode Caenorhabditis elegans. Herein, we report the existence of uracil-DNA glycosylase and AP endonuclease activities in extracts derived from embryos of C. elegans. These enzyme activities were monitored using a defined 5'-end P-32-labelled 42-bp synthetic oligonucleotide substrate bearing a single uracil residue opposite guanine at position 21. The embryonic extract rapidly cleaved the substrate in a time-dependent manner to produce a 20-mer product. The extract did not excise adenine or thymine opposite guanine, although uracil opposite either adenine or thymine was processed. Addition of the highly specific inhibitor of uracil-DNA glycosylase produced by Bacillus subtilis to the extract prevented the formation of the 20-mer product, indicating that removal of uracil is catalysed by uracil-DNA glycosylase. The data suggest that the 20-mer product was generated by a sequential reaction, i.e., removal of the uracil base followed by 5'-cleavage of the AP site. Further analysis revealed that product formation was dependent upon the presence of Mg2+, suggesting that cleavage of the AP site, following uracil excision, is carried out by a Mg2+-dependent AP endonuclease. It would appear that these activities correspond to the first two steps of a putative base-excision-repair pathway in C. elegans. ------------------- Key: 5394 Medline: Authors: Benard C;Hekimi S Title: Long-lived mutants, the rate of aging, telomeres and the germline in Caenorhabditis elegans. Citation: Mechanisms of Ageing & Development 123: 869-880 2002 Type: REVIEW Genes: clk-1 clk-2 daf-2 daf-9 daf-12 daf-16 gro-1 isp-1 mrt-2 rad-5 Abstract: Studying the phenomenon of aging is interesting for many reasons including because one would like to be able to extend the life span of people. However, we believe that the aging process instill so poorly understood that it remains unclear what exactly we will have to learn about it in order to understand it. Strehler, and others, have tried to ask questions about aging at several different levels at which biological systems can be studied (Strehler, 1985, 1995). Here, we will first discuss a number of nested viewpoints on aging, and then focus on some recent studies, particularly in Caenorhabditis elegans, in which several lines of investigation intersect: the study of long-lived mutants, the properties of the germline, and the biology of telomeres. ------------------- Key: 5395 Medline: 12095247 Authors: Kalb JM;Beaster-Jones L;Fernandez AP;Okkema PG;Goszczynski B;McGhee JD Title: Interference between the PHA-4 and PEB-1 transcription factors in formation of the Caenorhabditis elegans pharynx. Citation: Journal of Molecular Biology 320: 697-704 2002 Type: ARTICLE Genes: ceh-22 elt-1 myo-2 peb-1 pha-4 zip-1 Abstract: PHA-4 is a forkhead/winged helix transcription factor that acts as an organ identity factor in the development of the Caenorhabditis elegans pharynx. PEB-1 is a novel DNA-binding protein also involved in pharyngeal morphogenesis. PHA-4 and PEB-1 bind at overlapping sites on the C183 sequence element that controls pharynx-specific expression of the C. elegans myo-2 gene. It has been suggested that PHA-4 and PEB-1 act cooperatively on the C183 sequence. In this study, we test this model and assess the C183-dependent transcriptional activity of PHA-4 and PEB-1, both individually and in combination. We show that PHA-4 and PEB-1 are both modest transcriptional activators in yeast but that co-expression of the two factors does not result in significantly increased expression of a C183-regulated reporter gene. Electrophoretic mobility-shift assays provide no evidence for the formation of a PHA-4/PEB-1 complex in vitro but rather show that PHA-4 and PEB-1 cannot bind C183 simultaneously. As we have reported previously, ectopic expression of PHA-4 in C. elegans causes ectopic expression of a C183-regulated reporter gene. We show that ectopic expression of PEB-1 cannot cause ectopic expression of the same reporter but rather ectopic PEB-1 inhibits reporter gene activation by PHA-4. Overall, our results do not support a model in which PHA-4 and PEB-1 synergize in vivo but rather support a model in which PEB-1 may negatively modulate PHA-4's ability to activate, transcription through C183 during ------------------- Key: 5396 Medline: 12136036 Authors: Baird SE Title: Haldane's rule by sexual transformation in Caenorhabditis. Citation: Genetics 161: 1349-1353 2002 Type: ARTICLE Genes: Abstract: Haldane's rule in C. briggsae X C. remanei broods was caused by sexual transformation; XX and XO hybrids were female. C. briggsae and C. remanei variants that partially suppress hybrid sexual transformation were identified. Effects of variant strains were cumulative. Hence, aberrant sex determination is a reproductive isolation mechanism in Caenorhabditis. ------------------- Key: 5397 Medline: Authors: Coghlan A;Wolfe K Title: Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Citation: Genome Research 12: 857-867 2002 Type: ARTICLE Genes: sex-1 Abstract: We compared the genome of the nematode Caenorhabditis elegans to 13% of that of Caenorhabditis briggsae, identifying 252 conserved segments along their chromosomes. We detected 517 chromosomal rearrangements, with the ratio of translocations to inversions to transpositions being apprx1:1:2. We estimate that the species diverged 50-120 million years ago, and that since then there have been 4030 rearrangements between their whole genomes. Our estimate of the rearrangement rate, 0.4-1.0 chromosomal breakages/Mb per Myr, is at least four times that of Drosophila, which was previously reported to be the fastest rate among eukaryotes. The breakpoints of translocations are strongly associated with dispersed repeats and gene family members in the C. elegans genome. ------------------- Key: 5398 Medline: 12163466 Authors: Rutledge E;Denton J;Strange K Title: Cell cycle- and swelling-induced activation of a Caenorhabditis elegans CIC channel is mediated by CeGLC-7alpha/beta phosphatases. Citation: Journal of Cell Biology 158: 435-444 2002 Type: ARTICLE Genes: clh-3 clh-5 glc-7 Abstract: CIC voltage-gated anion channels have been identified in bacteria, yeast, plants, and animals. The biophysical and structural properties of CICs have been studied extensively, but relatively little is known about their precise physiological functions. Furthermore, virtually nothing is known about the signaling pathways and molecular mechanisms that regulate channel activity. The nematode Caenorhabditis elegans provides significant experimental advantages for characterizing ion channel function and regulation. We have shown previously that the CIC Cl- channel homologue CLH-3 is expressed in C. elegans oocytes, and that it is activated during meiotic maturation and by cell swelling. We demonstrate here that depletion of intracellular ATP or removal of Mg2+, experimental maneuvers that inhibit kinase function, constitutively activate CLH-3. Maturation- and swelling-induced channel activation are inhibited by type 1 serine/threonine phosphatase inhibitors. RNA interference studies demonstrated that the type 1 protein phosphatases CeGLC-7alpha and beta, both of which play essential regulatory roles in mitotic and meiotic cell cycle events, mediate CLH-3 activation. We have suggested previously that CLH-3 and mammalian CIC-2 are orthologues that play important roles in heterologous cell-cell interactions, intercellular communication, and regulation of cell cycle-dependent physiological processes. Consistent with this hypothesis, we show that heterologously expressed rat CIC-2 is also activated by serine/threonine dephosphorylation, suggesting that the two channels have ------------------- Key: 5399 Medline: 11931230 Authors: Grishok A;Mello CC Title: RNAi (Nematodes: Caenorhabditis elegans). Citation: Advances in Genetics 46: 339-360 2002 Type: REVIEW Genes: ego-1 let-7 lin-4 mut-7 rde-1 rde-2 rde-4 Abstract: RNA interference in Caenorhabditis elegans is a type of homology dependent posttranscriptional gene silencing induced by dsRNA. In this chapter we describe the history of the discovery of RNAi, its systemic nature, inheritance, and connection to other homology-dependent silencing phenomena like co-suppression and transcriptional gene silencing. We discuss RNAi-deficient mutants in C. elegans as well as characterized components of the RNAi, pathway, the molecular mechanism of RNAi, and its possible role in development and immunity. ------------------- Key: 5400 Medline: 12093377 Authors: Ledent V;Paquet O;Vervoort M Title: Phylogenetic analysis of the human basic helix-loop-helix proteins. Citation: Genome Biology 3(6): 30.1-30.18 2002 Type: ARTICLE Genes: Abstract: BACKGROUND: The basic helix-loop-helix (bHLH) proteins are a large and complex multigene family of transcription factors with important roles in animal development, including that of fruitflies, nematodes and vertebrates. The identification of orthologous relationships among the bHLH genes from these widely divergent taxa allows reconstruction of the putative complement of bHLH genes present in the genome of their last common ancestor. RESULTS: We identified 39 different bHLH genes in the worm Caenorhabditis elegans, 58 in the fly Drosophila melanogaster and 125 in human (Homo sapiens). We defined 44 orthologous families that include most of these bHLH genes. Of these, 43 include both human and fly and/or worm genes, indicating that genes from these families were already present in the last common ancestor of worm, fly and human. Only two families contain both yeast and animal genes, and no family contains both plant and animal bHLH genes. We suggest that the diversification of bHLH genes is directly linked to the acquisition of multicellularity, and that important diversification of the bHLH repertoire occurred independently in animals and plants. CONCLUSIONS: As the last common ancestor of worm, fly and human is also that of all bilaterian animals, our analysis indicates that this ancient ancestor must have possessed at least 43 different types of bHLH, highlighting its genomic complexity. ------------------- Key: 5401 Medline: 11943069 Authors: AbdelRaheim SR;McLennan AG Title: The Caenorhabditis elegans Y87G2A.14 Nudix hydrolase is a peroxisomal coenzyme A diphosphatase. Citation: BMC Biochemistry 3: - 2002 Type: ARTICLE Genes: Abstract: Background: The number of Nudix hydrolase family members varies widely among different organisms. In order to understand the reasons for the particular spectrum possessed by a given organism, the substrate specificity and function of different family members must be established. Results: The Y87G2A.14 Nudix hydrolase gene product of Caenorhabditis elegans has been expressed as a thioredoxin fusion protein in Escherichia coli and shown to be a CoA diphosphatase with catalytic activity towards CoA and its derivatives. The products of CoA hydrolysis were 3',5'-ADP and 4'-phosphopantetheine with Km and kcat values of 220 muM and 13.8 s-1 respectively. CoAesters yielded 3',5'-ADP and the corresponding acyl-phosphopantetheine. Activity was optimal at pH 9.5 with 5 mM Mg2+ and fluoride was inhibitory with a Ki of 3 muM. The Y87G2A.14 gene product has a potential C-terminal tripeptide PTS1 peroxisomal targeting signal SKI. By fusing a Y87G2A.14cDNA to the C-terminus of yeast-enhanced green fluorescent protein, the enzyme appeared to be targeted to peroxisomes by the SKI signal when transfected into yeast cells. Deletion of SKI abolished specific targeting. Conclusions: The presence of related sequences with potential PTS1 or PTS2 peroxisomal targeting signals in other organisms suggests a conserved peroxisomal function for the CoA diphosphatase members of this group of Nudix hydrolases. ------------------- Key: 5402 Medline: Authors: Hammond SM;Caudy AA;Hannon GJ Title: Post-transcriptional gene silencing by double-stranded RNA. Citation: Nature Reviews Genetics 2: 110-119 2002 Type: REVIEW Genes: ego-1 mut-2 mut-7 rde-1 rde-2 rde-3 rde-4 Abstract: Imagine being able to knock out your favourite gene with only a day's work. Not just in one model system, but in virtually any organism: plants, flies, mice or cultured cells. This sort of experimental dream might one day become reality as we learn to harness the power of RNA interference, the process by which double-stranded RNA induces the silencing of homologous endogenous genes. How this phenomenon works is slowly becoming clear, and might help us to develop an effortless tool to probe gene function in cells and animals. ------------------- Key: 5403 Medline: Authors: Steinberg CEW;Bruggemann R Title: Ambiguous ecological control by dissolved humic matter (DHM) and natural organic matter (NOM): trade-offs between specific and non-specific effects. Citation: Acta Hydrochimica et Hydrobiologica 29: 399-411 2002 Type: ARTICLE Genes: Abstract: Several papers report on obviously contradictory biological and ecological effects of humic substances (and NOM). For instances, growth promotion as well as growth inhibition of algae and macrophytes, promotion as well as inhibition of net-heterotrophy in non-eutrophic lakes, promotion as well as inhibition of reproduction of the nematode, Caenorhabditis elegans, are reported. If one takes direct effects of humic substances (and NOM) on aquatic organisms into account that are supported by increasing empirical evidence, these obvious contradictions can be solved as trade-offs between specific and non-specific effects. For instance, net-heterotrophy in non-eutrophic lakes can be considered as (weak) inhibition of photosynthesis of algae and macrophytes (specific effect) and simultaneous promotion of heterotrophic growth (non-specific effect). If net-autotrophy predominates, a positive feed-back effect of bacteria on algae, based on growth promoting substances can be observed. These assumptions are based on recent experimental laboratory findings that include even quantitative structure activity relationships. Two more contradictory effects of humic substances (and NOM) from reports are discussed with respect to trade-offs between specific and non-specific effects: reduction/increase of adverse mineral acid effects on invertebrates as well as effects of lipophilic chemicals upon invertebrates and fishes. We present a simple concept model that is based on specific and non-specific effects of humic substances and NOM towards aquatic organisms. Applying this model to hormone-like effects of humic substances and NOM upon the nematode C. elegans, we show that both effects inhibitory and promoting can qualitatively be predicted. ------------------- Key: 5404 Medline: 12075001 Authors: Rose JK;Kaun KR;Rankin CH Title: A new group-training procedure for habituation demonstrates that presynaptic glutamate release contributes to long-term memory in Caenorhabditis elegans. Citation: Learning & Memory 9: 130-137 2002 Type: ARTICLE Genes: avr-14 avr-15 eat-4 glr-1 Abstract: In the experiments reported here we have developed a new group-training protocol for assessing long-term memory for habituation in Caenorhabditis elegans. We have replicated all of the major findings of the original single-worm protocol using the new protocol: (1) distributed training produced long-term retention of training, massed training did not; (2) distributed training at long interstimulus intervals (ISIs) produced long-term retention, short ISIs did not; and (3) long-term memory for distributed training is protein synthesis-dependent as it could be blocked by heat shock during the inter-block interval. In addition, we have shown that long-term memory for habituation is graded, depending on the number of blocks of stimuli in training. The inter-block interval must be >40 min for long-term retention of training to occur. Finally, we have tested long-term memory for habituation training in a strain of worms with a mutation in a vesicular glutamate transporter in the sensory neurons that transduce tap (eat-4). The results from these eat-4 worms indicate that glutamate release from the sensory neurons has an important role in the formation of long-term memory ror habituation. ------------------- Key: 5405 Medline: 12185850 Authors: Gonczy P Title: Mechanisms of spindle positioning: focus on flies and Citation: Trends in Cell Biology 12: 332-339 2002 Type: REVIEW Genes: ags-3.2 ags-3.3 goa-1 gpa-16 let-99 par-1 par-2 par-3 spn-4 Abstract: Accurate spindle positioning is crucial for spatial control of cell division. During metazoan development, coordination between polarity cues and spindle position also ensures correct segregation of cell fate determinants. Converging evidence indicates that spindle positioning is achieved through interactions between cortical anchors and the plus ends of microtubules, generating pulling forces acting on spindle poles. This article discusses recent findings that indicate how this mechanism might be used for spindle positioning during Drosophila and Caenorhabditis elegans development. ------------------- Key: 5406 Medline: 11896059 Authors: Wang C;Risteli M;Heikkinen J;Hussa AK;Uitto L;Myllyla R Title: Identification of amino acids important for the catalytic activity of the collagen glucosyltransferase associated with the multifunctional lysyl hydroxylase 3 (LH3). Citation: Journal of Biological Chemistry 277: 18568-18573 2002 Type: ARTICLE Genes: Abstract: Collagen glucosyltransferase (GGT) activity has recently been shown to be associated with human lysyl hydroxylase (LH) isoform 3 (LH3) (Heikkinen, J., Risteli, M., Wang, C., Latvala, J., Rossi, M., Valtavaara, M., Myllyla, R. (2000) J. Biol. Chem. 275, 36158-36163). The LH and GGT activities of the multifunctional LH3 protein modify lysyl residues in collagens posttranslationally to form hydroxylysyl and glucosylgalactosyl hydroxylysyl residues respectively. We now report that in the nematode, Caenorhabditis elegans, where only one ortholog is found for lysyl hydroxylase, the LH and GGT activities are also associated with the same gene product. The aim of the present studies is the identification of amino acids important for the catalytic activity of GGT. Our data indicate that the GGT active site is separate from the carboxyl-terminal LH active site of human LH3, the amino acids important for the GGT activity being located at the amino-terminal part of the molecule. Site-directed mutagenesis of a conserved cysteine at position 144 to isoleucine and a leucine at position 208 to isoleucine caused a marked reduction in GGT activity. These amino acids were conserved in C. elegans LH and mammalian LH3, but not in LH1 or LH2, which lack GGT activity. The data also reveal a DXD-like motif in LH3 characteristic of many glycosyltransferases and the mutagenesis of aspartates of this motif eliminated the GGT activity. Reduction in GGT activity was not accompanied by a change in the LH activity of the molecule. Thus GGT activity can be manipulated independently of LH activity in LH3. These data provide the information needed to design knock-out studies for investigation of the function of glucosylgalactosyl hydroxylysyl residues of collagens in vivo. ------------------- Key: 5407 Medline: Authors: Onami S;Hamahashi S;Nagasaki M;Miyano S;Kitano H Title: Automatic aquisition of cell lineage through 4D microscopy and analysis of early C. elegans embryogenesis. Citation: Foundations in Systems Biology. Kitano, H (ed). 1: 39-55 2001 Type: ARTICLE Genes: Abstract: ------------------- Key: 5408 Medline: 11925450 Authors: Schwientek T;Bennett EP;Flores C;Thacker J;Hollmann M;Reis CA;Behrens J;Mandel U;Keck B;Schafer MA;Haselmann K;Zubarev R;Roepstorff P;Burchell JM;Taylor-Papadimitriou J;Hollingsworth MA;Clausen H Title: Functional conservation of subfamilies of putative UDP-N-acetylgalactosamine: polypeptide N-acetylgalactosaminyltransferases in Drosophila, Caenorhabditis elegans, and mammals. Citation: Journal of Biological Chemistry 277: 22623-22638 2002 Type: ARTICLE Genes: gly-3 gly-4 gly-5 gly-6 gly-7 gly-8 gly-9 gly-10 gly-11 Abstract: The completed fruit fly genome was found to contain up to 15 putative UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (GalNAc-transferase) genes. Phylogenetic analysis of the putative catalytic domains of the large GalNAc-transferase enzyme families of Drosophila melanogaster (13 available), Caenorhabditis elegans (9 genes), and mammals (12 genes) indicated that distinct subfamilies of orthologous genes are conserved in each species. In support of this hypothesis, we provide evidence that distinctive functional properties of Drosophila and human GalNAc-transferase isoforms were exhibited by evolutionarily conserved members of two subfamilies (dGalNAc-T1 (l(2)35Aa) and GalNAc-T11; dGalNAc-T2 (CG6394) and GalNAc-T7). dGalNAc-T1 and novel human GalNAc-T11 were shown to encode functional GalNAc-transferases with the same polypeptide acceptor substrate specificity, and dGalNAc-T2 was shown to encode a GalNAc-transferase with similar GalNAc glycopeptide substrate specificity as GalNAc-T7. Previous data suggested that the putative GalNAc-transferase encoded by l(2)35Aa has a lethal phenotype (Flores, C., and Engels, W. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 2964-2969), and this was substantiated by sequencing of three lethal alleles l(2)35AaHG8, l(2)35AaSF12, and l(2)35AaSF32. The finding that subfamilies of GalNAc-transferases with distinct catalytic functions are evolutionarily conserved stresses that GalNAc-transferase isoforms may serve unique biological functions rather than providing functional redundancy, and this is further supported by the lethal phenotype of l(2)35Aa. ------------------- Key: 5409 Medline: 12045209 Authors: Letunic I;Copley RR;Bork P Title: Common exon duplication in animals and its role in alternative splicing. Citation: Human Molecular Genetics 11: 1561-1567 2002 Type: ARTICLE Genes: Abstract: When searching the genomes of human, fly and worm for cases of exon duplication, we found that about 10% of all genes contain tandemly duplicated exons. In the course of the analyses, 2438 unannotated exons were identified that are not currently included in genome databases and that are likely to be functional. The vast majority of them are likely to be involved in mutually exclusive alternative splicing events. The common nature of recent exon duplication indicates that it might have a significant role in the fast evolution of eukaryotic genes. It also provides a general mechanism for the regulation of protein function. ------------------- Key: 5410 Medline: 12182536 Authors: Yamasaki T;Sato M;Mori T;Mohamed ASA;Fujii K;Tsukioka J Title: Toxicity of tannins towards the free-living nematode Caenorhabditis elegans and the brine shrimp Artemia salina. Citation: Journal of Natural Toxins 11: 165-171 2002 Type: ARTICLE Genes: Abstract: Toxicities of gallo- and condensed tannins towards the free-living nematode Caenorhabditis elegans is dependent on the tannins' molecular sizes. In the present paper we investigate the toxicity of ellagitannins to C. elegans and the toxicity of ellagi-, gallo-, and condensed tannins to the brine shrimpArtemia salina. Ellagitannins 1 and 2 were isolated from Euphorbia supina and identified as tellimagrandin I and rugosin A methyl ester, respectively. An ellagitannin preparation from Cornus officinalis was chromatographically fractionated into ellagitannins A through H, having different molecular weights and specific rotations. Three of the ten ellagitannins, 2, G, and H produced significant toxicity towards C. elegans, showing the presence of an activity-structure relationship, as opposed to the results from tests of gallo- and condensed tannins. Ellagi-, gallo-, and condensed tannins also produced toxicity in A. salina. ------------------- Key: 5411 Medline: 12183367 Authors: Shim EY;Walker AK;Shi Y;Blackwell TK Title: CDK-9/cyclin T (P-TEFb) is required in two postinitiation pathways for transcription in the C. elegans embryo. Citation: Genes & Development 16: 2135-2146 2002 Type: ARTICLE Genes: ama-1 cdk-9 cit-1.1 cit-1.2 cki-2 elt-5 end-1 let-858 pha-4 rps-5 spt-4 spt-5 sur-5 Abstract: The metazoan transcription elongation factor P-TEFb (CDK-9/cyclin T) is essential for HIV transcription, and is recruited by some cellular activators. P-TEFb promotes elongation in vitro by overcoming pausing that requires the SPT-4/SPT-5 complex, but considerable evidence indicates that SPT-4/SPT-5 facilitates elongation in vivo. Here we used RNA interference to investigate P-TEFb functions in vivo, in the Caenorhabditis elegans embryo. We found that P-TEFb is broadly essential for expression of early embryonic genes. P-TEFb is required for phosphorylation of Ser 2 of the RNA Polymerase II C-terminal domain (CTD) repeat, but not for most CTD Ser 5 phosphorylation, supporting the model that P-TEFb phosphorylates CTD Ser 2 during elongation. Remarkably, although heat shock genes are cdk-9-dependent, they can be activated when spt-4 and spt-5 expression is inhibited along with cdk-9. This observation suggests that SPT-4/SPT-5 has an inhibitory function in vivo, and that mutually opposing influences of P-TEFb and SPT-4/SPT-5 may combine to facilitate elongation, or insure fidelity of mRNA production. Other genes are not expressed when cdk-9, spt-4, and spt-5 are inhibited simultaneously, suggesting that these genes require P-TEFb in an additional mechanism, and that they and heat shock genes are regulated through different ------------------- Key: 5412 Medline: Authors: Howard RM;Sundaram MV Title: C. elegans EOR-1/PLZF and EOR-2 positively regulate Ras and Wnt signaling and function redundantly with LIN-25 and the SUR-2 Mediator component. Citation: Genes & Development 16: 2169- 2002 Type: CORRECT Genes: eor-1 eor-2 Abstract: ------------------- Key: 5413 Medline: 12231624 Authors: Wang X;Chamberlin HM Title: Multiple regulatory changes contribute to the evolution of the Caenorhabditis lin-48 ovo gene. Citation: Genes & Development 16: 2345-2349 2002 Type: ARTICLE Genes: ces-2 lin-48 Abstract: Recent work points to the importance of changes in gene expression patterns in species-specific differences. Here, we investigate the evolution of the nematode lin-48 ovo gene. lin-48 is expressed in several cells in both Caenorhabditis elegans and Caenorhabditis briggsae, but acts in the excretory duct cell only in C. elegans. We find the differences result both from alterations in the cis-regulatory sequences and in proteins that mediate lin-48 expression. One factor that contributes to the species differences is the bZip protein CES-2. Our results indicate the accumulation of several regulatory changes affecting one gene can contribute to evolutionary change. ------------------- Key: 5414 Medline: Authors: Watts DJ;Strogatz SH Title: Collective dynamics of 'small-world' networks. Citation: Nature 393: 440-442 2002 Type: ARTICLE Genes: Abstract: Networks of coupled dynamical systems have been used to model biological oscillators, Josephson junction arrays, excitable media, neural networks, spatial games, genetic control networks and many other self-organizing systems. Ordinarily, the connection topology is assumed to be either completely regular or completely random. But many biological, technological and social networks lie somewhere between these two extremes. Here we explore simple models of networks that can be tuned through this middle ground: regular networks 'rewired' to introduce increasing amounts of disorder. We find that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs. We call the 'small-world' networks, by analogy with the small-world phenomenon (popularly known as six degrees of separation). The neural network of the worm Caenorhabditis elegans, the power grid of the western United States, and the collaboration graph of film actors are shown to be small-world networks. Models of dynamical systems with small-world coupling display enhanced signal-propagation speed, computational powers and synchronizability. In particular, infectious diseases spread more easily in small-world networks than in regular lattices. ------------------- Key: 5415 Medline: 12145186 Authors: Ahmed H;Bianchet MA;Amzel LM;Hirabayashi J;Kasai K;Giga-Hama Y;Tohda H;Vasta GR Title: Novel carbohydrate specificity of the 16-kDa galectin from Caenorhabditis elegans: binding to blood group precursor oligosaccharides (type1, type 2, Ta, and TB) and gangliosides. Citation: Glycobiology 12: 451-461 2002 Type: ARTICLE Genes: Abstract: Galectins, a family of soluble beta-galactosyl-binding lectins, are believed to mediate cell-cell and cell-extracellular matrix interactions during development, inflammation, apoptosis, and tumor metastasis. However, neither the detailed mechanisms of their function(s) nor the identities of their natural ligands have been unequivocally elucidated. Of the several galectins present in the nematode Caenorhabditis elegans, the 16-kDa "proto" type and the 32-kDa "tandem-repeat" type are the best characterized so far, but their carbohydrate specificities have not been examined in detail. Here, we report the carbohydrate-binding specificity of the recombinant C elegans 16-kDa galectin and the structural analysis of its binding site by homology modeling. Our results indicate that unlike the galectins characterized so far, the C. elegans 16-kDa galectin interacts with most blood group precursor oligosaccharides (type 1, Galbeta1,3GIcNAc, and type 2, Galbeta1,4GIcNAc; Talpha, Galbeta1,3GalNAcalpha; Tbeta, Galbeta1,3GalNAcbeta) and gangliosides containing the Tbeta structure. Homology modeling of the C elegans 16-kDa galectin CRD revealed that a shorter loop containing residues 66-69, which enables interactions of Glu(67) with both axial and equatorial -OH at C-3 of GlcNAc (in Galbeta1,4GIcNAc) or at C-4 of GaINAc (in Galbeta1,3GalNAc), provides the structural basis for this ------------------- Key: 5416 Medline: 12183571 Authors: Jansen WTM;Bolm M;Balling R;Chhatwal GS;Schnabel R Title: Hydrogen peroxide-mediated killing of Caenorhabditis elegans by Streptococcus pyogenes. Citation: Infection and Immunity 70: 5202-5207 2002 Type: ARTICLE Genes: glp-1 Abstract: Caenorhabditis elegans is currently introduced as a new, facile, and cheap model organism to study the pathogenesis of gram-negative bacteria such as Pseudomonas aeruginosa and Salmonella enterica serovar Typhimurium. The mechanisms of killing involve either diffusible exotoxins or infection-like processes. Recently, it was shown that also some gram-positive bacteria kill C. elegans, although the precise mechanisms of killing remained open. We examined C. elegans as a pathogenesis model for the gram-positive bacterium Streptococcus pyogenes, a major human pathogen capable of causing a wide spectrum of diseases. We demonstrate that S. pyogenes kills C. elegans, both on solid and in liquid medium. Unlike P. aeruginosa and S. enterica serovar Typhimurium, the killing by S. pyogenes is solely mediated by hydrogen peroxide. Killing required live streptococci; the killing capacity depends on the amount of hydrogen peroxide produced, and killing can be inhibited by catalase. Major exotoxins of S. pyogenes are not involved in the killing process as confirmed by using specific toxin inhibitors and knockout mutants. Moreover, no accumulation of S. pyogenes in C. elegans is observed, which excludes the involvement of infection-like processes. Preliminary results show that S. pneumoniae can also kill C. elegans by hydrogen peroxide production. Hydrogen peroxide-mediated killing might represent a common mechanism by which gram-positive, catalase-negative pathogens kill C. elegans. ------------------- Key: 5417 Medline: 12177204 Authors: Lim YS;Wadsworth WG Title: Identification of domains of netrin UNC-6 that mediate attractive and repulsive guidance and responses from cells and growth cones. Citation: Journal of Neuroscience 22: 7080-7087 2002 Type: ARTICLE Genes: unc-5 unc-6 unc-40 Abstract: Netrin UNC-6 is a protein secreted from ventral cells that guides cell and growth cone migrations in Caenorhabditis elegans. Previously it was shown that UNC-6 domain V-2 regulates dorsal guidance activity and domain C regulates an activity that prevents the branching of axons when they respond to the N-terminal domains. Because these results indicate that the biological activities of UNC-6 are mediated through specific domains, we systematically examined each UNC-6 domain for guidance activities. Transgenic animals expressing UNC-6 derivatives with domain deletions and mutants with selective unc-6 loss-of-function mutations were analyzed. The results indicate that the VI, V-2, and V-3 domains are primarily required for dorsal migrations and the VI and V-3 domains are required for ventral migrations. These domains are likely important for responses mediated by the UNC-5 and UNC-40 receptors, respectively. Deletion of V-3 and a V-3 point mutation selectively affect either cell or growth cone migrations, indicating that each migration requires unique interactions with UNC-6. Deletion of domain VI or of a conserved eight amino acid motif within VI causes loss of all UNC-6 guidance activities, and mutations within domain VI selectively affect different guidance activities, suggesting that domain VI regulates each response to UNC-6. We propose that individual UNC-6 domains mediate different signals, which act in parallel to regulate the morphological changes necessary for guidance. ------------------- Key: 5418 Medline: 12181365 Authors: Petriv OI;Pilgrim DB;Rachubinski RA;Titorenko VI Title: RNA interference of peroxisome-related genes in C. elegans: a new model for human peroxisomal disorders. Citation: Physiological Genomics 10: 79-91 2002 Type: ARTICLE Genes: Abstract: RNA-mediated interference (RNAi) for the posttranscriptional silencing of genes was used to evaluate the importance of various peroxisomal enzymes and peroxins for the development of Caenorhabditis elegans and to compare the roles of these proteins in the nematode to their roles in yeasts and humans. The nematode counterparts of the human ATP-binding cassette half-transporters, the enzymes alkyldihydroxyacetonephosphate synthase and Delta(3,5-)Delta(2,4) di-enoyl- CoA isomerase, the receptors for peroxisomal membrane and matrix proteins (Pex19p and Pex5p), and components of the docking and translocation machineries for matrix proteins (Pex13p and Pex12p) are essential for the development of C. elegans. Unexpectedly, RNAi silencing of the acyl-CoA synthetase-mediated activation of fatty acids, the alpha- and beta-oxidation of fatty acids, the intraperoxisomal decomposition of hydrogen peroxide, and the peroxins Pex1p, Pex2p, and Pex6p had no apparent effect on C. elegans development. The described analysis of functional gene knockouts through RNAi provides a basis for the use of C. elegans as a valuable model system with which to study the molecular and physiological defects underlying the human ------------------- Key: 5419 Medline: 12154364 Authors: Hobert O;Johnston RJ;Chang S Title: Left-right asymmetry in the nervous system: the Caenorhabditis elegans model. Citation: Nature Reviews Neuroscience 3: 629-640 2002 Type: REVIEW Genes: dpy-19 egl-20 gcy-5 gcy-6 gcy-7 lim-6 lin-12 mab-5 nid-1 str-2 unc-6 unc-40 Abstract: Although the overall architecture of the nervous system of most animals shows a large degree of bilateral symmetry, there are striking patterns of left-right (L-R) asymmetry in the brains of some species. Some structures show L-R-specific differences in size, whereas others show asymmetrical patterns of gene expression and have diversified at the functional level. The nematode Caenorhabditis elegans offers a unique opportunity to address how symmetrical neuronal assemblies deviate to create functional lateralizations. Here, we provide a detailed cellular and molecular perspective on L-R asymmetry in the nervous system of C. elegans. We also give an overview of symmetry and asymmetry in the nervous systems of other organisms. We will relate these observations to general concepts of the mechanistic and phylogenetic origin of laterality. ------------------- Key: 5420 Medline: 12194847 Authors: Lyczak R;Gomes JE;Bowerman B Title: Heads or tails - cell polarity and axis formation in the early Caenorhabditis elegans embryo. Citation: Developmental Cell 3: 157-166 2002 Type: REVIEW Genes: egl-10 glp-1 goa-1 gpa-16 let-99 lin-5 mex-1 mex-3 mex-5 mex-6 mlc-4 nmy-2 ooc-3 ooc-5 pal-1 par-1 par-2 par-3 par-4 par-5 par-6 pie-1 ric-8 skn-1 spe-11 spn-4 Abstract: In C. elegans, the first embryonic axis is established shortly after fertilization and requires both the microtubule and microfilament cytoskeleton. Cues from sperm-donated centrosomes result in a cascade of events that polarize the distribution of widely conserved PAR proteins at the cell cortex. The PAR proteins in turn polarize the cytoplasm and position mitotic spindles. Lessons learned from C. elegans should improve our understanding of how cells become polarized and divide asymmetrically during development. ------------------- Key: 5421 Medline: 12021279 Authors: Nehrke K;Melvin JE Title: The NHX family of Na+ - H+ exchangers in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 277: 29036-29044 2002 Type: ARTICLE Genes: nhx-1 nxh-2 nxh-3 nxh-4 nxh-5 nxh-6 nxh-7 nxh-8 nxh-9 Abstract: Na+-H+ exchangers prevent cellular acidification by catalyzing the electroneutral exchange of extracellular sodium for an intracellular proton. To date, seven Na+-H+ exchangers have been identified in mammals, and although several members of this family have been extensively studied and characterized, it is clear that there are major gaps in our understanding with respect to the remaining family members. To initiate the study of Na+-H+ exchangers in a genomically defined and genetically tractable model system, we have cloned the complete cDNAs and analyzed splice site variation for nine putative homologs from the nematode Caenorhabditis elegans, which we have called NHX-1 through -9. The expression patterns and cellular distributions of the NHX proteins were determined using transcriptional and translational promoter-transgene fusion constructs to green fluorescent protein. Four of the putative exchangers were expressed at the cell surface, whereas five of the exchangers were associated with the membranes of intracellular organelles. Individual isoforms were expressed exclusively in the intestine, seam cells, hypodermal cells of the main body syncytium, and the excretory cell, all of which are polarized epithelial cells, suggesting a role for these proteins in epithelial membrane transport processes in the nematode. Other isoforms were found to express either ubiquitously or in a pan-neural pattern, suggesting a more conserved role in cell pH regulation or neuronal function. Finally, we show that recombinant NHX-4, the ubiquitous nematode Na+-H+ exchanger, mediates Na+-dependent pH recovery after intracellular acidification. NHX-4 has a K(a) for Na+ of approximately 32 mm, is not Cl- -dependent, and is ------------------- Key: 5422 Medline: 12136960 Authors: Myllyharju J;Kukkola L;Winter AD;Page AP Title: The exoskeleton collagens in Caenorhabditis elegans are modified by prolyl 4-hydroxylases with unique combinations of subunits. Citation: Journal of Biological Chemistry 277: 29187-29196 2002 Type: ARTICLE Genes: dpy-18 pdi-1 pdi-2 phy-1 phy-2 phy-3 Abstract: The collagen prolyl 4-hydroxylases (P4Hs, EC ) play a critical role in the synthesis of the extracellular matrix. The enzymes characterized from vertebrates and Drosophila are alpha(2)beta(2) tetramers, in which protein disulfide isomerase (PDI) serves as the beta subunit. Two conserved alpha subunit isoforms, PHY-1 and PHY-2, have been identified in Caenorhabditis elegans. We report here that three unique P4H forms are assembled from these polypeptides and the single beta subunit PDI-2, both in a recombinant expression system and in vivo, namely a PHY-1/PHY-2/(PDI-2)(2) mixed tetramer and PHY-1/PDI-2 and PHY-2/PDI-2 dimers. The mixed tetramer is the main P4H form in wild-type C. elegans but phy-2-/- and phy-1-/- (dpy-18) mutant nematodes can compensate for its absence by increasing the assembly of the PHY-1/PDI-2 and PHY-2/PDI-2 dimers, respectively. All three of the mixed tetramer-forming polypeptides PHY-1, PHY-2, and PDI-2 are coexpressed in the cuticle collagen-synthesizing hypodermal cells. The catalytic properties of the mixed tetramer are similar to those of other P4Hs, and analogues of 2-oxoglutarate were bound to produce severe temperature-dependent effects on P4H mutant strains. Formation of the novel mixed tetramer was species-specific, and studies with hybrid recombinant PHY polypeptides showed that residues Gln(121)-Ala(271) and Asp(1)-Leu(122) in PHY-1 and PHY-2, respectively, are critical for its ------------------- Key: 5423 Medline: 12176360 Authors: Simmer F;Tijsterman M;Parrish S;Koushika SP;Nonet ML;Fire A;Ahringer J;Plasterk RHA Title: Loss of the putative RNA-directed RNA polymerase RRF-3 makes C. elegans hypersensitive to RNAi. Citation: Current Biology 12: 1317-1319 2002 Type: ARTICLE Genes: apr-1 cel-1 clr-1 cye-1 daf-2 dpy-14 dpy-18 eft-3 egl-30 efr-1 gon-4 gpc-2 gsa-1 him-3 hlh-1 hmr-1 lag-2 let-502 lin-1 lin-31 lin-49 mom-5 mut-7 mut-16 par-1 pha-1 pop-1 pos-1 ptr-2 rde-4 rec-8 ric-19 rrf-3 spo-11 unc-3 unc-4 unc-5 und-6 unc-11 unc-12 unc-13 unc-14 unc-15 unc-17 unc-22 unc-29 unc-30 unc-33 unc-36 unc-37 unc-38 unc-40 unc-47 unc-73 unc-76 unc-86 unc-87 unc-89 unc-93 unc-101 unc-104 unc-130 zyg-1 Abstract: RNA interference (RNAi) is a broadly used reverse genetics method in C. elegans [1]. Unfortunately, RNAi does not inhibit all genes [2,3]. We show that loss of function of a putative RNA-directed RNA polymerase (RdRP) of C. elegans, RRF-3, results in a substantial enhancement of sensitivity to RNAi in diverse tissues. This is particularly striking in the nervous system; neurons that are generally refractory to RNAi in a wild-type genetic background can respond effectively to interference in an rrf-3 mutant background. These data provide the first indication of physiological negative modulation of the RNAi response and implicate an RdRP-related factor in this effect. Therrf-3 strain can be useful to study genes that, in wild-type, do not show a phenotype after RNAi, and it is probably the strain of choice for genome-wide RNAi screens. ------------------- Key: 5424 Medline: 12122205 Authors: Morley JF;Brignull HR;Weyers JJ;Morimoto RI Title: The threshold for polyglutamine expansion protein aggregation and cellular toxicity is dynamic and influenced by aging in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 99: 10417-10422 2002 Type: ARTICLE Genes: age-1 daf-16 Abstract: Studies of the mutant gene in Huntington's disease, and for eight related neurodegenerative disorders, have identified polyglutamine (polyQ) expansions as a basis for cellular toxicity. This finding has led to a disease hypothesis that protein aggregation and cellular dysfunction can occur at a threshold of approximately 40 glutamine residues. Here, we test this hypothesis by expression of fluorescently tagged polyQ proteins (Q29, Q33, Q35, Q40, and Q44) in the body wall muscle cells of Caenorhabditis elegans and show that young adults exhibit a sharp boundary at 35-40 glutamines associated with the appearance of protein aggregates and loss of motility. Surprisingly, genetically identical animals expressing near-threshold polyQ repeats exhibited a high degree of variation in the appearance of protein aggregates and cellular toxicity that was dependent on repeat length and exacerbated during aging. The role of genetically determined aging pathways in the progression of age-dependent polyQ-mediated aggregation and cellular toxicity was tested by expressing Q82 in the background of age-1 mutant animals that exhibit an extended lifespan. We observed a dramatic delay of polyQ toxicity and appearance of protein aggregates. These data provide experimental support for the threshold hypothesis of polyQ-mediated toxicity in an experimental organism and emphasize the importance of the threshold as a point at which genetic modifiers and aging influence biochemical environment and protein homeostasis in the cell. ------------------- Key: 5425 Medline: 12169634 Authors: Hajnal A;Berset T Title: The Caenorhabditis elegans MAPK phosphatase LIP-1 is required for the G(2)/M meiotic arrest of developing oocytes. Citation: EMBO Journal 21: 4317-4326 2002 Type: ARTICLE Genes: fem-2 fog-1 let-60 lip-1 mpk-1 Abstract: In the Caenorhabditis elegans hermaphrodite germline, spatially restricted mitogen-activated protein kinase (MAPK) signalling controls the meiotic cell cycle. First, the MAPK signal is necessary for the germ cells to progress through pachytene of meiotic prophase I. As the germ cells exit pachytene and enter diplotene/diakinesis, MAPK is inactivated and the developing oocytes arrest in diakinesis (G2/M arrest). During oocyte maturation, a signal from the sperm reactivates MAPK to promote M phase entry. Here, we show that the MAPK phosphatase LIP-1 dephosphorylates MAPK as germ cells exit pachytene in order to maintain MAPK in an inactive state during oocyte development. Germ cells lacking LIP-1 fail to arrest the cell cycle at the G2/M boundary, and they enter a mitotic cell cycle without fertilization. LIP-1 thus coordinates oocyte cell cycle progression and maturation with ovulation and ------------------- Key: 5426 Medline: 12154385 Authors: Rankin CH Title: From gene to identified neuron to behavior in Caenorhabditis elegans. Citation: Nature Reviews Genetics 3: 622-630 2002 Type: REVIEW Genes: avr-15 daf-11 daf-21 eat-4 eat-6 egl-19 gcy-5 glr-1 gpa-9 npr-1 odr-10 osm-9 tax-2 tax-4 tpa-1 tph-1 unc-6 unc-36 unc-47 Abstract: Understanding the role of genes in behaviour is greatly enhanced by understanding how they affect the function of the neurons that underlie behaviour. The study of behavioural genetics in Caenorhabditis elegans, an organism with a nervous system small enough to allow the role of every neuron in a given behaviour to be known, has given researchers unique insights into how genes contribute to behaviour in general. Many have taken advantage of the unique feature of this worm to analyse genes from their sequence to their role in neuronal function and, ultimately, in behaviour. ------------------- Key: 5427 Medline: 12027012 Authors: Sattelle DB;Culetto E;Grauso M;Raymond V;Franks CJ;Towers P Title: Functional genomics of ionotropic acetylcholine receptors in Caenorhabditis elegans and Drosophila melanogaster. Citation: Novartis Foundation Symposium 245: 240-257 2002 Type: REVIEW Genes: acr-2 acr-3 acr-4 acr-5 acr-6 acr-7 acr-8 acr-9 acr-10 acr-11 acr-12 acr-13 acr-15 acr-16 deg-3 des-2 eat-2 eat-18 jtf-38 lev-1 lev-8 lev-9 lev-10 lev-11 ric-3 unc-22 unc-29 unc-38 unc-49 unc-50 unc-63 unc-68 unc-74 Abstract: Genetics, genomics and electrophysiology are transforming our understanding of the nicotinic acetylcholine receptors (nAChRs). Caenorhabditis elegans contains the largest known family of nAChR subunit genes (27 members), while Drosophila melanogaster contains an exclusively neuronal nAChR gene family (10 members). In C. elegans, several genetic screens have enabled the identification of nAChR subunits, along with novel proteins that act upstream and downstream of functional nAChRs. The C. elegans genome project has identified many new candidate nAChR subunits and the calculated electrostatic potential energy profiles for the M2 channel-lining regions predict considerable functional diversity. The respective roles of subunits are under investigation using forward and reverse genetics. Electrophysiological and reporter genes studies have demonstrated roles for particular subunits in levamisole-sensitive muscle nAChRs and a role for nAChRs in pharyngeal pumping. Recombinant homomeric and heteromeric C. elegans nAChRs have been expressed in Xenopus laevis oocytes. In D. melanogaster, three new nAChR alpha subunits have been cloned, one of which shows multiple variant transcripts arising from alternative splicing and A-to-I pre-mRNA editing. Thus, studies on the genetic model organisms C. elegans and D. melanogaster have revealed different routes to generating molecular and functional diversity in the nAChR gene family and are providing new insights into the in vivo functions of individual family members. ------------------- Key: 5428 Medline: 12214599 Authors: Roy PJ;Stuart JM;Lund J;Kim SK Title: Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Citation: Nature 418: 975-979 2002 Type: ARTICLE Genes: etr-1 gld-1 hlh-1 pab-1 unc-54 Abstract: Chromosomes are divided into domains of open chromatin, where genes have the potential to be expressed, and domains of closed chromatin, where genes are not expressed. Classic examples of open chromatin domains include 'puffs' on polytene chromosomes in Drosophila and extended loops from lampbrush chromosomes. If multiple genes were typically expressed together from a single open chromatin domain, the position of co-expressed genes along the chromosomes would appear clustered. To investigate whether co-expressed genes are clustered, we examined the chromosomal positions of the genes expressed in the muscle of Caenorhabditis elegans at the first larval stage. Here we show that co-expressed genes in C. elegans are clustered in groups of 2-5 along the chromosomes, suggesting that expression from a chromatin domain can extend over several genes. These observations reveal a higher-order organization of the structure of the genome, in which the order of the genes along the chromosome id correlated with their expression in ------------------- Key: 5429 Medline: Authors: GuhaThakurta D;Palomar L;Stormo GD;Tedesco P;Johnson TE;Walker DW;Lithgow G;Link CD Title: Identification of a novel cis-regulatory element involved in the heat-shock response in Caenorhabditis elegans using microarray gene-expression and computational methods. Citation: Genome Research 12: 1301- 2002 Type: CORRECT Genes: Abstract: ------------------- Key: 5430 Medline: 12161275 Authors: Popovici C;Isnardon D;Birnbaum D;Roubin R Title: Caenorhabditis elegans receptors related to mammalian vascular endothelial growth factor receptors are expressed in neural cells. Citation: Neuroscience Letters 329: 116-120 2002 Type: ARTICLE Genes: ver-1 ver-2 ver-3 ver-4 Abstract: Through a genomic survey of the Caenorhabditis elegans genome for genes encoding tyrosine kinase receptors (RTK) we identified a family of four RTKs which are structurally related to vascular enclothelial growth factor receptors (VEGFRs). We named this family the ver gene family (for Vascular Endothelial growth factor receptor Related). It was intriguing to find this type of RTK in an animal devoid of a vascular system. The common sites of expression of the ver genes are specialized cells of neural origin: ver-1 (T17A3.1) is expressed in the support (glial) cells of amphid and phasmid neurons, ver-2 (T17A3.8) in ADL, a pair of chemosensorial neurons, and ver-3 (F59F3.1) in the ALA neuron. In mammals, the VEGFRs are associated with angiogenesis and neurogenesis. We provide here the first observation that these molecules may be primarily and solely involved in neurogenesis in a living organism. ------------------- Key: 5431 Medline: Authors: Ohtsuki T;Sato A;Watanabe Y;Watanabe K Title: A unique serine-specific elongation factor Tu found in nematode mitochondria. Citation: Nature Structural Biology 9: 669-673 2002 Type: ARTICLE Genes: Abstract: The translation elongation factor Tu (EF-Tu) delivers aminoacyl-tRNAs to ribosomes by recognizing the tRNA acceptor and T stems. However, the unusual truncation observed in some animal mitochondrial tRNAs seems to prevent recognition by a canonical EF-Tu. For instance, nematode mitochondria contain tRNAs lacking a T or D arm. We recently found an atypical EF-Tu (EF-Tu1) specific for nematode mitochondrial tRNAs that lack the T arm. We have now discovered a second factor, EF-Tu2, which binds only to tRNAs that lack a D arm. EF-Tu2 seems unique in its amino acid specificity because it recognizes the aminoacyl moiety of seryl-tRNAs and the tRNA structure itself. Such EF-Tu evolution might explain tRNA structural divergence in animal mitochondria. ------------------- Key: 5432 Medline: 12186849 Authors: Urano F;Calfon M;Yoneda T;Yun C;Kiraly M;Clark SG;Ron D Title: A survival pathway for Caenorhabditis elegans with a blocked unfolded protein response. Citation: Journal of Cell Biology 158: 639-646 2002 Type: ARTICLE Genes: abu-1 ire-1 sel-1 xbp-1 Abstract: The unfolded protein response (UPR) counteracts stress caused by unprocessed ER client proteins. A genome-wide survey showed impaired induction of many UPR target genes in xbp-1 mutant Caenorhabditis elegans that are unable to signal in the highly conserved IRE1-dependent UPR pathway. However a family of genes, abu (activated in blocked UPR), was induced to higher levels in ER-stressed xbp-1 mutant animals than in ER-stressed wild-type animals. RNA-mediated interference (RNAi) inactivation of a representative abu family member, abu-1 (AC3.3), activated the ER stress marker hsp-4:.gfp in otherwise normal animals and killed 50% of ER-stressed ire-1 and xbp-1 mutant animals. Abu-1(RNAi) also enhanced the effect of inactivation of sel-1, an ER-associated protein degradation gene. The nine abu genes encode highly related type I transmembrane proteins whose lumenal domains have sequence similarity to a mammalian cell surface scavenger receptor of endothelial cells that binds chemically modified extracellular proteins and directs their lysosomal degradation. Our findings that ABU-1 is an intracellular protein located within the endomembrane system that is induced by ER stress in xbp-1 mutant animals suggest that ABU proteins may interact with abnormal ER client proteins and this function may be particularly important in animals with an impaired UPR. ------------------- Key: 5433 Medline: 12089139 Authors: Shim EY;Walker AK;Blackwell TK Title: Broad requirement for the Mediator subunit RGR-1 for transcription in the Caenorhabditis elegans embryo. Citation: Journal of Biological Chemistry 277: 30413-30416 2002 Type: ARTICLE Genes: elt-5 let-858 med-1 pha-4 pes-10 rgr-1 ttb-1 Abstract: The Mediator-related transcription co-factors integrate positive and negative inputs and recruit and activate the RNA polymerase II complex. To understand the role of Mediator during transcription, it is important to identify Mediator subunits that are essential for its functions. In the yeast Mediator, the conserved component Rgr1 is associated with multiple subunits that are required for specific activation or repression events. Yeast rgr1 is essential for viability, for certain repression mechanisms, and for activation of heat shock genes, but it is not known whether rgr1 is generally important for transcription. Here we have performed the first analysis of rgr-1 function in a metazoan. We found that in the developing Caenorhabditis elegans embryo rgr-1 is broadly required for transcription and for phosphorylation of both Ser-2 and Ser-5 of the RNA polymerase II C-terminal domain repeat. We conclude that RGR-1 fulfills a critical Mediator function that is broadly essential for metazoan mRNA transcription and that RGR-1 may be required at an early recruitment or initiation step. ------------------- Key: 5434 Medline: Authors: Britton C;Murray L Title: A cathespin L protease essential for Caenorhabditis elegans embryogenesis is functionally conserved in parasitic nematodes. Citation: Molecular & Biochemical Parasitology 122: 21-33 2002 Type: ARTICLE Genes: cpl-1 Abstract: Proteolytic enzymes are involved in processes important to development and survival of many organisms. Parasite proteases are considered potential targets of parasite control yet, for most, their precise physiological functions are unknown. Validation of potential targets requires analysis of function. We have recently identified a cathepsin L (CPL) cysteine protease, Ce-CPL-1, which is essential for embryonic development of the free-living nematode Caenorhabditis elegans. We now show that CPL genes closely related to Ce-cpl-1 are expressed in the animal parasitic nematodes Haemonchus contortus, Dictyocaulus viviparus, Teladorsagia circumcincta, Ancylostoma caninum and Ascaris suum, as well as in plant parasitic nematodes. The similarities in gene structure and encoded amino acid sequence indicate that the parasite and C. elegans CPLs are homologous enzymes. We demonstrate functional compensation of the loss of C. elegans cpl-1 by transgenic expression of the H. contortus cpl-1 gene, rescuing the embryonic lethality. These genes may therefore be orthologues, sharing the same function in both species. Targeting of this enzyme has potential in inhibiting development and transmission of parasitic nematodes. In addition, the role of CPL is important to our understanding of nematode ------------------- Key: 5435 Medline: 12211038 Authors: Cort JR;Chiang Y;Zheng D;Montelione G;Kennedy MA Title: NMR structure of conserved eukaryotic protein ZK652.3 from C. elegans: a ubiquitin-like fold. Citation: Proteins: Structure, Function, and Genetics 48: 733-736 Type: ARTICLE Genes: Abstract: Structural proteomics aims to provide one or more representative three-dimensional (3D) structures for every structural domain family in nature. As part of an international effort in structural proteomics, the Northeast Structural Genomics Consortium has targeted clusters of strongly conserved eukaryotic protein families for structural and functional analysis. On this basis, protein ZK652.3 (nes WR41/WP:CE00949/YOY3_CAEEL/ Swiss-Prot P34661/gi17557033) from Caenorhabditis elegans was selected for structure determination. Sequencing of cDNA libraries shows that homologues of ZK6582.3 occur widely in vertebrates and plants (Fig.1). However, ZK652.3 homologues are conspicuously absent from the yeast and Drosophila genomes. Expression of the ZK652.3 gene has been observed in a transcriptional profile of C. elegans, where it was one of a cluster of 89 genes whose expression levels covaried during development. The biochemical function of this protein is presently unknown. Here we describe the 3D structure of ZK652.3 determined by nuclear magnetic resonance (NMR) spectroscopy and discuss structural similarities with other proteins that provide clues to potential biochemical functions. ------------------- Key: 5436 Medline: 12243352 Authors: Park HK;Yook JS;Koo HS;Choi IS;Ahn B Title: The Caenorhabditis elegans XPA homolog of human XPA. Citation: Molecules & Cells 14: 50-55 2002 Type: ARTICLE Genes: Abstract: The Xeroderma pigmentosum complementation group A (XPA) protein that is indispensable for nucleotide excision repair of DNA damage in eukaryotes participates in photoproduct recognition. A search of the current Caenorhabditis elegans database allowed us to identify a good candidate for the XPA protein homolog. We cloned a complete cDNA of C elegans XPA (Ce-XPA) by using RT-PCR. Northern blot analysis showed that the Ce-xpa gene is expressed in all of the stages, including embryos. Ce-XPA encodes a 241-amino acid protein that is homologous to all known eukaryotic XPA. Ce-XPA RNAi caused embryonic lethality and survival lethality to UV radiation. This result suggests that Ce-XPA is involved in the repair of ------------------- Key: 5437 Medline: 12239571 Authors: Wang L;Eckmann CR;Kadyk LC;Wickens M;Kimble J Title: A regulatory cytoplasmic poly(A) polymerase in Caenorhabditis elegans. Citation: Nature 419: 312-316 2002 Type: ARTICLE Genes: gld-2 gld-3 Abstract: Messenger RNA regulation is a critical mode of controlling gene expression. Regulation of mRNA stability and translation is linked to controls of poly(A) tail length(1,2). Poly(A) lengthening can stabilize and translationally activate mRNAs, whereas poly(A) removal can trigger degradation and translational repression. Germline granules (for example, polar granules in flies, P granules in worms) are ribonucleoprotein particles implicated in translational control(3). Here we report that the Caenorhabditis elegans gene gld-2, a regulator of mitosis/meiosis decision and other germline events(4), encodes the catalytic moiety of a cytoplasmic poly(A) polymerase (PAP) that is associated with P granules in early embryos. Importantly, the GLD-2 protein sequence has diverged substantially from that of conventional eukaryotic PAPs, and lacks a recognizable RRM (RNA recognition motif)-like domain. GLD-2 has little PAP activity on its own, but is stimulated in vitro by GLD-3. GLD-3 is also a developmental regulator, and belongs to the Bicaudal-C family of RNA binding proteins(5). We suggest that GLD-2 is the prototype for a class of regulatory cytoplasmic PAPs that are recruited to specific mRNAs by a binding partner, thereby targeting those mRNAs for polyadenylation and increased expression. ------------------- Key: 5438 Medline: 12191753 Authors: Baek JH;Cosman P;Feng Z;Silver J;Schafer WR Title: Using machine vision to analyze and classify Caenorhabditis elegans behavioral phenotypes quantitatively. Citation: Journal of Neuroscience Methods 118: 9-21 2002 Type: ARTICLE Genes: egl-19 goa-1 nic-1 unc-36 unc-38 Abstract: Mutants with abnormal patterns of locomotion, also known as uncoordinated (Unc) mutants, have facilitated the genetic dissection of many important aspects of nervous system function and development in the nematode Caenorhabditis elegans. Although a large number of distinct classes of Unc mutants can be distinguished by an experienced observer, precise quantitative definitions of these classes have not been available. Here we describe a new approach for using automatically-acquired image data to quantify the locomotion patterns of wild-type and mutant worms. We designed an automated tracking and imaging system capable of following an individual animal for long time periods and saving a time-coded series of digital images representing its motion and body posture over the course of the recording. We have also devised methods for measuring specific features from these image data that can be used by the classification and regression tree classification algorithm to reliably identify the behavioral patterns of specific mutant types. Ultimately, these tools should make it possible to evaluate with quantitative precision the behavioral phenotypes of novel mutants, gene knockout lines, or pharmacological treatments. ------------------- Key: 5439 Medline: 12354282 Authors: Rex E;Komuniecki RW Title: Characterization of a tyramine receptor from Caenorhabditis elegans. Citation: Journal of Neurochemistry 82: 1352-1359 2002 Type: ARTICLE Genes: ser-2 Abstract: Octopamine (OA) plays an important role in the regulation of a number of key processes in nematodes, including pharyngeal pumping, locomotion and egg-laying. However, while putative OA receptors can be tentatively identified in the Caenorhabditis elegans database, no OA receptors have been functionally characterized from any nematode. We have isolated two cDNAs, ser-2 and ser-2a, encoding putative C.elegans serotonin/OA receptors (C02D4.2, ser-2). The sequences of these cDNAs differ from that predicted by GeneFinder and lack 42 bp of exon 2. In addition, ser-2a appears to be alternatively spliced and lacks a predicted 23 amino acids in the third intracellular loop. COS-7 cells expressing SER-2 bind [H-3]LSD in the low nM range and exhibit K(i)s for tyramine, octopamine and serotonin of 0.07, 2, and 13.7 mum, respectively. Significantly, tyramine reduces forskolin-stimulated cAMP levels in HEK293 cells stably expressing SER-2 with an IC50 of about 360 nm, suggesting that SER-2 is a tyramine receptor. ------------------- Key: 5440 Medline: 12354283 Authors: Ge Y;Wang X;Chen Z;Landman N;Lo EH;Kang JX Title: Gene transfer of the Caenorhabditis elegans n-3 fatty acid desaturase inhibits neuronal apoptosis. Citation: Journal of Neurochemistry 82: 1360-1366 2002 Type: ARTICLE Genes: fat-1 Abstract: Previous studies have shown that n-3 polyunsaturated fatty acids (PUFAs) can exert an antiapoptotic effect on neurons. The present study was designed to investigate whether the Caenorhabditis elegans fat-1 gene encoding an n-3 fatty acid desaturase (an enzyme that converts n-6 PUFAs to corresponding n-3 PUFAs) can be expressed functionally in rat cortical neurons and whether its expression can change the ratio of n-6 : n-3 fatty acids in the cell membrane and exert an effect on neuronal apoptosis. Infection of primary rat cortical cultures with Ad-fat-1 resulted in high expression of the fat-1 gene. Lipid analysis indicated a decrease in the ratio of n-6 : n-3 PUFAs from 5.9 : 1 in control cells, to 1.45 : 1 in cells expressing the n-3 fatty acid desaturase. Accordingly, the levels of prostaglandin E-2, an eicosanoid derived from n-6 PUFA, were significantly lower in cells infected with Ad-fat-1 when compared with control cells. Finally, there was a significant inhibition of growth factor withdrawal-induced apoptotic cell death in neurons expressing the fat-1 gene. These results demonstrate that expression of the fat-1 gene can inhibit apoptotic cell death in neurons and suggest that the change in the n-6 : n-3 fatty acid ratio may play a key role in this protective effect. ------------------- Key: 5441 Medline: 12058048 Authors: Yamada S;Okada Y;Ueno M;Iwata S;Deepa SS;Nishimura S;Fujita M;Van Die I;Hirabayashi Y;Sugahara K Title: Determination of the glycosaminoglycan-protein linkage region oligosaccharide structures of proteoglycans from Drosophila melanogaster and Caenorhabditis elegans. Citation: Journal of Biological Chemistry 35: 31877-31886 2002 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans and Drosophila melanogaster are relevant models for studying the roles of glycosaminoglycans (GAG) during the development of multicellular organisms. The genome projects of these organisms have revealed the existence of multiple genes related to GAG-synthesizing enzymes. Although the putative genes encoding the enzymes that synthesize the GAG-protein linkage region have also been identified, there is no direct evidence that the GAG chains bind covalently to core proteins. This study aimed to clarify whether GAG chains in these organisms are linked to core proteins through the conventional linkage region tetrasaccharide sequence found in vertebrates and whether modifications by phosphorylation and sulfation reported for vertebrates are present also in invertebrates. The linkage region oligosaccharides were isolated from C. elegans chondroitin in addition to D. melanogaster heparan and chondroitin sulfate after digestion with the respective bacterial eliminases and were then derivatized with a fluorophore 2-aminobenzamide. Their structures were characterized by gel filtration and anion-exchange high performance liquid chromatography in conjunction with enzymatic digestion and matrix-assisted laser desorption ionization time-of-flight spectrometry, which demonstrated a uniform linkage tetrasaccharide structure of -GlcUA-Gal-Gal-Xyl- or -GlcUA-Gal-Gal-Xyl(2-O-phosphate)- for C. elegans chondroitin and D. melanogaster CS, respectively. In contrast, the unmodified and phosphorylated counterparts were demonstrated in heparan sulfate of adult flies at a molar ratio of 73:27, and in that of the immortalized D. melanogaster S2 cell line at a molar ratio of 7:93, which suggests that the linkage region in the fruit fly first becomes phosphorylated uniformly on the Xyl residue and then dephosphorylated. It has been established here that GAG chains in both C. elegans and D. melanogaster are synthesized on the core protein through the ubiquitous linkage region tetrasaccharide sequence, suggesting that indispensable functions of the linkage region in the GAG ------------------- Key: 5442 Medline: 12208344 Authors: Van Voorhies WA Title: Metabolism and aging in the nematode Caenorhabditis Citation: Free Radical Biology & Medicine 33: 587-596 2002 Type: REVIEW Genes: clk-1 Abstract: Research into the causes of aging has greatly increased in recent years. Much of this interest is due to the discovery of genes in a variety of model organisms that appear to modulate aging. Studies of long-lived mutants can potentially provide valuable insights into the fundamental mechanisms of aging. While there are many advantages to the use of model organisms to study aging it is also important to consider the limitations of these systems, particularly because ectothermic (poikilothermic) organisms can survive a far greater metabolic depression than humans. As such, the consideration of only chronological longevity when assaying for long-lived mutants provides a limited perspective on the mechanisms by which longevity is increased. Additional physiological processes, such as metabolic rate, must also be assayed to provide true insight into the aging process. This is especially true in the nematode Caenorhabditis elegans, which has the natural ability to enter into a metabolically reduced state in which it can survive many times longer than its normal lifetime. The extended longevity of at least some long-lived C. elegans mutants may be due to a reduction in metabolic rate, rather than an alteration of a metabolically independent genetic mechanism specific for ------------------- Key: 5443 Medline: 12356262 Authors: Rudel D;Kimble J Title: Evolution of discrete Notch-like receptors from a distant gene duplication in Caenorhabditis. Citation: Evolution & Development 4: 319-333 2002 Type: ARTICLE Genes: glp-1 lin-12 Abstract: Caenorhabditis elegans possesses two Notch-like receptors, LIN-12 and GLP-1, which have both overlapping and individual biological functions. We examined the lin-12 and glp-1 genes in closely related nematodes to learn about their evolution. Here we report molecular and functional analyses of lin-12 orthologs from two related nematodes, C. briggsae (Cb) and C. remanei (Cr). In addition, we compare these lin-12 findings with similar studies of Cb-glp-1 and Cr-glp-1 orthologs. Cb-LIN-12 and Cr-LIN-12 retain the same number and order of motifs as Ce-LIN-12. Intriguingly, we find that LIN-12 conservation differs from that of GLP-1 in two respects. First, individual motifs are conserved to a different degree for the two receptors. For example, the transmembrane domain is 16-32% identical among LIN-12 orthologs but 65-70% identical among GLP-1 orthologs. Second, certain amino acids are conserved in a receptor-specific manner, a phenomenon most prevalent in the CC-linker. We suggest that LIN-12 and GLP-1 have been molded by selective constraints that are receptor specific and that the two proteins may not be entirely interchangeable. To analyze the functions of the lin-12 orthologs, we used RNA-mediated interference (RNAi). Cb-lin-12(RNAi) or Cr-lin-12(RNAi) progeny are nearly 100% Lag, a larval lethality typical of C. elegans lin-12 glp-1 double mutants, but not the primary defect observed in Ce-lin-12 null mutants or Ce-lin-12(RNAi). Therefore, LIN-12 functions are similar, but not identical, among the Caenorhabditis species. We suggest that ancestral functions may have been divided between LIN-12 and GLP-1 receptors in a process contributing to the retention of both genes after gene duplication (i.e., subfunctionalization). ------------------- Key: 5444 Medline: 12198170 Authors: Miyoshi H;Dwyer DS;Keiper BD;Jankowska-Anyszka M;Darzynkiewicz E;Rhoads RE Title: Discrimination between mono- and trimethylated cap structures by two isoforms of Caenorhabditis elegans. Citation: EMBO Journal 21: 4680-4690 2002 Type: ARTICLE Genes: Abstract: Primitive eukaryotes like Caenorhabditis elegans produce mRNAs capped with either m(7)GTP or m(3)(2,2,7)GTP. Caenorhabditis elegans also expresses five isoforms of the cap-binding protein eIF4E. Some isoforms (e.g. IFE-3) bind to m(7)GTP-Sepharose exclusively, whereas others (e.g. IFE-5) bind to both m(7)GTP- and m(3)(2,2,7)GTP-Sepharose. To examine specificity differences, we devised molecular models of the tertiary structures of IFE-3 and IFE-5, based on the known structure of mouse eIF4E-1. We then substituted amino acid sequences of IFE-5 with homologous sequences from IFE-3. As few as two changes (N64Y/V65L) converted the cap specificity of IFE-5 to essentially that of IFE-3. Molecular dynamics simulations suggested that the width and depth of the cap-binding cavity were larger in IFE-5 than in IFE-3 or the N64Y/V65L variant, supporting a model in which IFE-3 discriminates against m(3)(2,2,7)GTP by steric hindrance. Furthermore, the affinity of IFE-5 (but not IFE-3) for m(3)(2,2,7)GTP was reversibly increased when thiol reagents were removed. This was correlated with the formation of a disulfide bond between Cys-122 and Cys-126. Thus, translation of m(3)(2,2,7)GTP-capped mRNAs may be regulated by intracellular redox state. ------------------- Key: 5445 Medline: 12210516 Authors: Korswagen HC Title: Canonical and non-canonical Wnt signaling pathways in Caenorhabditis elegans: variations on a common signaling theme. Citation: BioEssays 24: 801-810 2002 Type: REVIEW Genes: apr-1 bar-1 cfz-2 cwn-1 cwn-2 dsh-1 dsh-2 egl-20 end-1hmp-2 kin-19 lin-3 lin-17 lin-23 lin-39 lin-44 lit-1 lrp-1 mab-5 mig-1 mig-5 mig-14 mom-1 mom-2 mom-3 mom-5 pal-1 par-1 pop-1 pry-1 sgg-1 sop-1 sop-3 tap-1 unc-37 wrm-1 Abstract: Wnt glycoproteins are signaling molecules that control a wide range of developmental processes in organisms ranging from the simple metazoan Hydra to vertebrates. Wnt signaling also plays a key role in the development of the nematode C. elegans, and is involved in cell fate specification and determination of cell polarity and cell migration. Surprisingly, the first genetic studies of Wnt signaling in C. elegans revealed major differences with the established (canonical) Wnt signaling pathways of Drosophila and vertebrates. Thus, the Wnt-dependent induction of endoderm in the early embryo and the specification of several asymmetric cell divisions during larval development are mediated by as yet novel Wnt signaling pathways that repress, rather than activate the TCF/LEF-1 transcription factor POP-1. Recently, however, it has been shown that, in addition to these divergent Wnt pathways, C. elegans also has a canonical Wnt pathway that converts POP-1 into an activator and controls the expression of several homeobox genes. Interestingly, these different Wnt pathways use distinct beta-catenins to control POP-1 function: the endoderm induction pathway requires the beta-catenin WRM-1 and parallel input from a mitogen-activated kinase (MAPK) pathway to downregulate POP-1, whereas the canonical Wnt pathway employs the beta-catenin BAR-1 to activate Wnt target gene expression. ------------------- Key: 5446 Medline: Authors: Slimko EM;McKinney S;Anderson DJ;Davidson N;Lester HA Title: Selective electrical silencing of mammalian neurons in vitro by the use of invertebrate ligand-gated chloride Citation: Journal of Neuroscience 22: 7373-7379 2002 Type: ARTICLE Genes: Abstract: Selectively reducing the excitability of specific neurons will (1) allow for the creation of animal models of human neurological disorders and (2) provide insight into the global function of specific sets of neurons. We focus on a combined genetic and pharmacological approach to silence neurons electrically. We express invertebrate ivermectin (IVM)-sensitive chloride channels (Caenorhabditis elegans GluCl alpha and beta) with a Sindbis virus and then activate these channels with IVM to produce inhibition via a CL conductance. We constructed a three-ciston Sindbis virus that expresses the alpha and beta subunits of a glutamate-gated chloride channel (GluCl) along with the green fluorescent protein (EGFP) marker. Expression of the C. elegans channel does not affect the normal spike activity of GABA/glutamate postsynaptic currents of cultured embryonic day 18 hippocampal neurons. At concentrations as low as 5 nm, IVM activates a Cl current large enough to silence infected neurons effectively. This conductance reverses in 8hr. These low concentrations of EVM do not potentiate GABA responses. Comparable results are observed with plasmid transfection of yellow fluorescent protein-tagged (EYFP) GluCl alpha and cyan fluorescent protein-tagged (ECFP) GluCl beta. The present study provides an in vitro model mimicking conditions that can be obtained in transgenic mice and in viral-mediated gene therapy. These experiments demonstrate the feasibility of using invertebrate ligand-activated Cl channels as an approach to modulate excitability. ------------------- Key: 5447 Medline: Authors: Mears JA;Cannone JJ;Stag SM;Gutell RR;Agrawal RK;Harvey SC Title: Modeling a minimal ribosome based on comparative sequence analysis. Citation: Journal of Molecular Biology 321: 215-234 2002 Type: ARTICLE Genes: Abstract: We have determined the three-dimensional organization of ribosomal RNAs and proteins essential for minimal ribosome function. Comparative sequence analysis identifies regions of the ribosome that have been evolutionarily conserved, and the spatial organization of conserved domains is determined by mapping these onto structures of the 30 S and 50 S subunits determined by X-ray crystallography. Several functional domains of the ribosome are conserved in their three-dimensional organization in the Archaea, Bacteria, Eucaryotic nuclear, mitochondria and chloroplast ribosomes. In contrast, other regions from both subunits have shifted their position in three-dimensional space during evolution, including the L11 binding domain and the alpha-sarcin-ricin loop (SRL). We examined conserved bridge interactions between the two ribosomal subunits, giving an indication of which contacts are more significant. The tRNA contacts that are conserved were also determined, highlighting functional interactions as the tRNA moves through the ribosome during protein synthesis. To augment these studies of a large collection of comparative structural models samples from all major branches on the phylogenetic tree, Caenorhabditis elegans mitochondrial rRNA is considered individually because it is among the smallest rRNA sequences known. The C. elegans model supports the large collection of comparative structure models while providing insight into the evolution of mitochondrial ribosomes. ------------------- Key: 5448 Medline: 12097341 Authors: Lespinet O;Wolf YI;Koonin EV;Aravind L Title: The role of lineage-specific gene family expansion in the evolution of eukaryotes. Citation: Genome Research 12: 1048-1059 2002 Type: ARTICLE Genes: Abstract: A computational procedure was developed for systematic detection of lineage-specific expansions (LSEs) of protein families in sequenced genomes and applied to obtain a census of LSEs in five eukaryotic species, the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the green plant Arabidopsis thaliana. A significant fraction of the proteins encoded in each of these genomes, up to 80% in A. thaliana, belong to LSEs. Many paralogous gene families in each of the analyzed species are almost entirely comprised of LSEs, indicating that their diversification occurred after the divergence of the major lineages of the eukaryotic crown group. The LSEs show readily discernible patterns of protein functions. The functional categories most prone to LSE are structural proteins, enzymes involved in an organism's response to pathogens and environmental stress, and various components of signaling pathways responsible for specificity, including ubiquitin ligase E3 subunits and transcription factors. The functions of several previously uncharacterized, vastly expanded protein families were predicted through in-depth protein sequence analysis, for example, small-molecule kinases and methylases that are expanded independently in the fly and in the nematode. The functions of several other major ILSEs remain mysterious; these protein families are attractive targets for experimental discovery of novel, lineage-specific functions in eukaryotes. LSEs seem to be one of the principal means of adaptation and one of the most important sources of organizational and regulatory diversity in crown-group ------------------- Key: 5449 Medline: Authors: Honda Y;Honda S Title: Life span extensions associated with upregulation of gene expression of antioxidant enzymes in Caenorhabditis elegans: studies of mutation in the age-1, PI3 kinase homologue and short-term exposure to Citation: Journal of the American Aging Association 24: 179-186 2001 Type: ARTICLE Genes: age-1 ctl-1 daf-2 daf-16 daf-18 fer-15 sod-1 sod-2 sod-3 Abstract: To explain trends emerging from the study of longevity mutants, a modification of the reactive oxygen species (ROS) model of aging is suggested. ROS do not appear to be produced in greater quantities during cellular activity unless specific factors are also present. These include raised cytosolic calcium and sodium ions, nitric oxide (NO) or dopamine. Metabolically active cells that are repeatedly exposed to these factors, especially in combination, show the most ROS damage and may contribute most to aging. This explains the importance of neurons, which is highlighted by genetic studies, and points to which cells are the most aging-sensitive. Control pathways disrupted in long-lived mutants are those which control one or more of these ROS promoting factors. The daf-2/daf-16 pathway may interact with these factors in several ways. Changes in control networks may be propagated from a relatively small number of cells/junctions by neural connectivity and hormonal ------------------- Key: 5450 Medline: Authors: Driver C Title: An hypothesis concerning control networks and aging in Drosophila melanogaster and Caenorhabditis elegans. Citation: Journal of the American Aging Association 24: 173-178 2001 Type: ARTICLE Genes: Abstract: To explain trends emerging from the study of longevity mutants, a modification of the reactive oxygen species (ROS) model of aging is suggested. ROS do not appear to be produced in greater quantities during cellular activity unless specific factors are also present. These include raised cytosolic calcium and sodium ions, nitric oxide (NO) or dopamine. Metabolically active cells that are repeatedly exposed to these factors, especially in combination, show the most ROS damage and may contribute most to aging. This explains the importance of neurons, which is highlighted by genetic studies, and points to which cells are the most aging-sensitive. Control pathways disrupted in long-lived mutants are those which control one or more of these ROS promoting factors. The daf-2/daf-16 pathway may interact with these factors in several ways. Changes in control networks may be propagated from a relatively small number of cells/junctions by neural connectivity and hormonal ------------------- Key: 5451 Medline: 12137732 Authors: Herman MA Title: Control of cell polarity by noncanonical Wnt signaling in C. elegans. Citation: Seminars in Cell & Developmental Biology 13: 233-241 2002 Type: REVIEW Genes: apr-1 bar-1 dsh-2 egl-5 egl-20 end-1 hmp-2 lin-17 lin-39 lin-44 lit-1 mab-5 mig-1 mig-5 mig-14 mom-1 mom-2 mom-3 mom-4 mom-5 pop-1 pry-1 sgg-1 wrm-1 Abstract: The three Caenorhabditis elegans beta-catenin each function in distinct processes: BAR-1 in canonical Wnt signaling that controls cell fates and cell migrations, HMP-2 in cell adhesion and WRM-1 in Wnt signaling pathways that function in conjunction with a mitogen-activated kinase (MAPK) pathway to control the orientations, or cell Polarities, of cells that undergo asymmetric cell divisions. In addition, WRM-1 does not interact with the canonical beta-catenin binding site in POP-1/Tcf. Thus, Wnt signaling through WRM-1 is noncanonical and, except for one division that might not include any of the three C. elegans beta-calenin, controls cell polarity in C. elegans. ------------------- Key: 5452 Medline: Authors: O'Connell KF Title: The ZYG-1 kinase, a mitotic and meiotic regulator of centriole replication. Citation: Oncogene 21: 6201-6208 2002 Type: REVIEW Genes: zyg-1 Abstract: As the primary microtubule-organizing center (MTOC) of the cell, the centrosome is a major structural determinant of the mitotic spindle. Like each chromosome, the centrosome must replicate once and only once per cell cycle in order to maintain the fidelity of nuclear division and the integrity of the genome. While the mechanisms that govern this process are not well understood and are sure to be complex, centrosome duplication can be described as involving three general steps. First, the centrosome splits to form two centrosomes, each with half the reproductive capacity of the original. Second, a replication step restores each new centrosome to full reproductive capacity. Third, the replicated centrosomes sever any remaining connections and move apart. In the past few years, several factors have been identified that regulate each of these steps. Among these factors is the ZYG-1 kinase of C. elegans, which functions during both mitotic and meiotic divisions (O?Connell et al., 2001). ------------------- Key: 5453 Medline: 12213836 Authors: Gruneberg U;Glotzer M;Gartner A;Nigg EA Title: The CeCDC-14 phosphatase is required for cytokinesis in the Caenorhabditis elegans embryo. Citation: Journal of Cell Biology 158: 901-914 2002 Type: ARTICLE Genes: air-2 cdc-14 cyk-4 zen-4 Abstract: As the primary microtubule-organizing center (MTOC) of the cell, the centrosome is a major structural determinant of the mitotic spindle. Like each chromosome, the centrosome must replicate once and only once per cell cycle in order to maintain the fidelity of nuclear division and the integrity of the genome. While the mechanisms that govern this process are not well understood and are sure to be complex, centrosome duplication can be described as involving three general steps. First, the centrosome splits to form two centrosomes, each with half the reproductive capacity of the original. Second, a replication step restores each new centrosome to full reproductive capacity. Third, the replicated centrosomes sever an remaining connections and move apart. In the past few years, several factors have been identified that regulate each of these steps. Among these factors is the ZYG-1 kinase of C. elegans, which functions during both mitotic and meiotic divisions (O'Connell et al., 2001). ------------------- Key: 5454 Medline: 12296824 Authors: Shimada M;Kawahara H;Doi H Title: Novel family of CCCH-type zinc-finger proteins, MOE-1, -2, and -3, participates in C. elegans oocyte maturation. Citation: Genes to Cells 7: 933-947 2002 Type: ARTICLE Genes: moe-1 moe-2 moe-3 oma-1 oma-2 Abstract: Background: Oocyte maturation is an important prerequisite for the production of progeny. Although several germ-line mutations have been reported, the precise mechanism by which the last step of oocyte maturation is controlled remains unclear. In Caenorhabditis elegans , CCCH-type zinc-finger proteins have been shown to be involved in germ cell formation, although their involvement in oocyte maturation has not been fully investigated. Results: Using a multiple RNAi technique, we have identified three novel redundant CCCH-type zinc-finger genes, named by us moe-1 , -2 (oma-1 , -2 ) and moe-3 , as a group related by functions and nucleotide sequence. Although a single RNAi of each moe gene was not effective, double or triple RNAi induced defects in oocyte maturation. We found that each moe transcript was expressed from the distal to proximal region of the gonad, while their corresponding proteins are accumulated exclusively in proximal oocytes, with a close association to germ granules. Although MOE-2 protein is rapidly removed from germ granules after fertilization, we found that MOE-2 associates with the centrosome-peripheral structure in dividing blastomeres. Conclusions: Our results suggest that moe gene products are unique multifunctional proteins in terms of their redundancy and characteristic behaviour during the course of oocyte maturation. These gene products participate in processes in the final step of the meiotic cell cycle control, a novel function for CCCH-type zinc-finger family proteins thus far discovered. ------------------- Key: 5455 Medline: 12200161 Authors: Thor S;Thomas JB Title: Motor neuron specification in worms, flies and mice: conserved and "lost" mechanisms. Citation: Current Opinion in Genetics & Development 12: 558-564 2002 Type: REVIEW Genes: cnd-1 lin-11 pag-3 unc-3 unc-4 unc-30 unc-55 vab-7 Abstract: Motor neuron differentiation has been studied intensively in both invertebrates and vertebrates in recent years. These studies have led to the identification of several key regulatory genes acting to generate motor neurons and to specify their subclass identities. By comparing findings from Caenorhabditis elegans, Drosophila and vertebrate model systems, it is apparent that both evolutionarily conserved and non-conserved mechanisms are used. ------------------- Key: 5456 Medline: 12225660 Authors: Long X;Spycher C;Han ZS;Rose AM;Muller F;Avruch J Title: TOR deficiency in C. elegans causes developmental arrest and intestinal atrophy by inhibition of mRNA translation. Citation: Current Biology 12: 1448-1461 2002 Type: ARTICLE Genes: let-363 sDf4 Abstract: Background: TOR is a phosphatidylinositol kinase (PIK)-related kinase that controls cell growth and proliferation in response to nutritional cues. We describe a C. elegans TOR homolog (CeTOR) and phenotypes associated with CeTOR deficiency. These phenotypes are compared with the response to starvation and the inactivation of a variety of putative TOR targets. Results: Whether caused by mutation or RNA interference, TOR deficiency results in developmental arrest at mid-to-late L3, which is accompanied by marked gonadal degeneration and a pronounced intestinal cell phenotype. A population of refractile, autofluorescent intestinal vesicles, which take up the lysosomal dye Neutral Red, increases dramatically in size, while the number of normal intestinal vesicles and the intestinal cytoplasmic volume decrease progressively. This is accompanied by an increase in the gut lumen size and a compromise in the intestine's ability to digest and absorb nutrients. CeTOR-deficient larvae exhibit no significant dauer characteristics, but share some features with starved L3 larvae. Notably, however, starved larvae do not have severe intestinal atrophy. Inactivation of C. elegans p70S6K or TAP42 homologs does not reproduce CeTOR deficiency phenotypes, nor does inactivation of C. elegans TIP41, a putative negative regulator of CeTOR function, rescue CeTOR deficiency. In contrast, inactivating the C. elegans eIF-4G homolog and eIF-2 subunits results in developmental arrest accompanied by the appearance of large, refractile intestinal vesicles and severe intestinal atrophy resembling that of CeTOR deficiency. Conclusions: The developmental arrest and intestinal phenotypes of CeTOR deficiency are due to an inhibition of global mRNA translation. Thus, TOR is a major up-stream regulator of overall mRNA translation in C. elegans, as in yeast. ------------------- Key: 5457 Medline: 12225665 Authors: Barbee SA;Lublin AL;Evans TC Title: A novel function for the Sm proteins in germ granule localization during C. elegans embryogenesis. Citation: Current Biology 12: 1502-1506 2002 Type: ARTICLE Genes: pgl-1 Abstract: General mRNA processing factors are traditionally thought to function only in the control of global gene expression. Here we show that the Sm proteins, core components of the splicesome, also regulate germ granules during early C. elegans development. Germ granules are large cytoplasmic particles that localize to germ cells and their precursors during embryogenesis of diverse organisms [1]. In C. elegrans, germ granules, called P granules, are segregated to the germline precursor cells during embryogenesis by asymmetric cell division, and they remain in germ cells at all stages of development [2]. We found that at least some Sm proteins are components of P granules. Moreover, disruption of Sm activity caused defects in P granule localization to the germ cell precursors during early embryogenesis. In contrast, loss of other splicing factor activities had no effect on germ granule control in the embryo. These observations suggest that the Sm proteins control germ granule integrity and localization in the early C. elegans embryo and that this role is independent of pre-mRNA splicing. Thus, a highly conserved splicing factor may have been adapted to control both snRNP biogenesis and the localization of components important for germ cell function. ------------------- Key: 5458 Medline: 12225671 Authors: Tijsterman M;Okihara KL;Thijssen K;Plasterk RHA Title: PPW-1, a PAZ/PIWI protein required for efficient germline RNAi, is defective in a natural isolate of C. elegans. Citation: Current Biology 12: 1535-1540 2002 Type: ARTICLE Genes: alg-1 alg-2 let-7 lin-4 par-1 par-6 pos-1 ppw-1 rab-5 rde-1 unc-15 unc-22 hDf7 Abstract: One of the remarkable aspects about RNA interference (RNAi) in Caenorhabditis elegans is that the trigger molecules, dsRNA, can be administered via the animal's food. We assayed whether this feature is a universal property of the species by testing numerous strains that have been isolated from different parts of the globe. We found that one isolate from Hawaii had a defect in RNA! that was specific to the germline and was a result of multiple mutations in a PAZ/PIWI domain-containing protein, which we named PPW-1. Deleting ppw-1 in the canonical C. elegans strain Bristol N2 makes it resistant to feeding of dsRNA directed against germline-expressed genes. PPW-1 belongs to the Argonaute family of proteins, which act in post-transcriptional gene silencing and development, and is homologous to the RNAi gene rde-1. Our data indicate that at least two members of this family are required for complete and effective RNAi in C. elegans. ------------------- Key: 5459 Medline: 12200468 Authors: Marais G;Piganeau G Title: Hill-Robertson interference is a minor determinant of variations in codon bias across Drosophila melanogaster and Caenorhabditis elegans genomes. Citation: Molecular Biology and Evolution 19: 1399-1406 2002 Type: ARTICLE Genes: Abstract: According to population genetics models, genomic regions with lower crossing-over rates are expected to experience less effective selection because of Hill-Robertson interference (HRi). The effect of genetic linkage is thought to be particularly important for a selection of weak intensity such as selection affecting codon usage. Consistent with this model, codon bias correlates positively with recombination rate in Drosophila melanogaster and Caenorhabditis elegans. However, in these species, the G+C content of both noncoding DNA and synonymous sites correlates positively with recombination, which suggests that mutation patterns and recombination are associated. To remove this effect of mutation patterns on codon bias, we used the synonymous sites of lowly expressed genes that are expected to be effectively neutral sites. We measured the differences between codon biases of highly expressed genes and their lowly expressed neighbors. In D. melanogaster we find that HRi weakly reduces selection on codon usage of genes located in regions of very low recombination; but these genes only comprise 4% of the total. In C. elegans we do not find any evidence for the effect of recombination on selection for codon bias. Computer simulations indicate that HRi poorly enhances codon bias if the local recombination rate is greater than the mutation rate. This prediction of the model is consistent with our data and with the current estimate of the mutation rate in D. melanogaster. The case of C. elegans, which is highly self-fertilizing, is discussed. Our results suggest that HRi is a minor determinant of ------------------- Key: 5461 Medline: 12220896 Authors: Teichmann SA;Babu MM Title: Conservation of gene co-regulation in prokaryotes and eukaryotes. Citation: Trends in Biotechnology 20: 407-410 2002 Type: REVIEW Genes: Abstract: Genes that are part of the same operon in prokaryotes, or have the same expression pattern in eukaryotes, are transcriptionally co-regulated. If genes are consistently co-regulated across distantly related organisms, the genes have closely associated functions. It has been shown previously that such genes have a strong tendency to belong to the same protein complex in prokaryotes, and we show by an analysis of the sequences and their expression in the yeast Saccharomyces cerevisiae and the worm Caenorhabditis elegans that this is also true for eukaryotes. Our analysis reveals that the number of conserved co-regulated genes is small in eukaryotes, as has been shown previously in prokaryotes, indicating that there are extensive variations in the gene regulatory network across organisms. ------------------- Key: 5462 Medline: 12231631 Authors: MacQueen AJ;Colaiacovo MP;McDonald K;Villeneuve AM Title: Synapsis-dependent and -independent mechanisms stabilize homolog pairing during meiotic prophase in C. elegans. Citation: Genes & Development 16: 2428-2442 2002 Type: ARTICLE Genes: syp-1 Abstract: Analysis of Caenorhabditis elegans syp-1 mutants reveals that both synapsis-dependent and -independent mechanisms contribute to stable, productive alignment of homologous chromosomes during meiotic prophase. Early prophase nuclei undergo normal reorganization in syp-1 mutants, and chromosomes initially pair. However, the polarized nuclear organization characteristic of early prophase persists for a prolonged period, and homologs dissociate prematurely; furthermore, the synaptonemal complex (SC) is absent. The predicted structure of SYP-1, its localization at the interface between intimately paired, lengthwise-aligned pachytene homologs, and its kinetics of localization with chromosomes indicate that SYP-1 is an SC structural component. A severe reduction in crossing over together with evidence for accumulated recombination intermediates in syp-1 mutants indicate that initial pairing is not sufficient for completion of exchange and implicates the SC in promoting crossover recombination. Persistence of polarized nuclear organization in syp-1 mutants suggests that SC polymerization may provide a motive force or signal that drives redispersal of chromosomes. Whereas our analysis suggests that the SC is required to stabilize pairing along the entire lengths of chromosomes, striking differences in peak pairing levels for opposite ends of chromosomes in syp-1 mutants reveal the existence of an additional mechanism that can promote local stabilization of pairing, independent of synapsis. ------------------- Key: 5463 Medline: 12231628 Authors: Lints R;Emmons SW Title: Regulation of sex-specific differentiation and mating behavior in C. elegans by a new member of the DM domain transcription factor family. Citation: Genes & Development 16: 2390-2402 2002 Type: ARTICLE Genes: cat-2 egl-5 egl-38 lin-48 mab-3 mab-23 pha-1 sma-1 sma-2 sma-3 sma-4 sma-6 tra-1 Abstract: Mutations in Caenorhabditis elegans gene mab-23 cause abnormal male tail morphology and abolish male fecundity but have no obvious effect in the hermaphrodite. Here we show that mab-23 encodes a DM (Doublesex/MAB-3) domain transcription factor necessary for specific aspects of differentiation in sex-specific tissues of the male. mab-23 is required for the patterning of posterior sensory neurons in the male nervous system, sex muscle differentiation, and morphogenesis of the posterior hypodermis, spicules, and proctodeum. Failure of mab-23 mutant males to sire progeny is due primarily to defective sex muscle-mediated turning during copulatory behavior and likely compounded by impairment of sperm passage through the proctodeum. In the male nervous system, mab-23 refines ray neuron subtype distribution by restricting expression of dopaminergic neurotransmitter identity through interactions with the Hox gene egl-5 and a TGF-beta-related signaling pathway. mab-23 has distinct roles and functions independent of mab-3, indicating different aspects of C. elegans male sexual differentiation are coordinated among DM domain family members. Our results support the hypothesis that DM domain genes derive from an ancestral male sexual regulator and suggest how regulation of sexual development has evolved in distinct ways in different phyla. ------------------- Key: 5464 Medline: 12231620 Authors: Hodgkin J Title: The remarkable ubiquity of DM domain factors as regulators of sexual phenotype: ancestry or aptitude? Citation: Genes & Development 16: 2322-2326 2002 Type: REVIEW Genes: mab-3 mab-23 tra-1 Abstract: The CM domain is a cysteine-rich DNA-binding motif first recognized in proteins encoded by the Drosophila set determination gene doublesex (Erdman and Burtis 1993; Zhu et al. 2000). As the name doublesex (dsx) suggests, this gene has functions in both sexes: Its transcripts undergo sex-specific alternative splicing, so that it can encode either a male-specific isoform, DSX(M), or a female-specific isoform, DSX(F) (Baker and Wolfner 1988; Burtis and Baker 1989). These proteins have the same N-terminal DNA-binding domain, but different C termini that confer different regulatory properties on the two forms. The expression of DSX(M) directs male development, and the expression of DSX(F) directs female development, throughout most of the somatic tissues of the fruit fly. ------------------- Key: 5465 Medline: 12168615 Authors: Fitch DHA;Sudhaus W Title: One small step for worms, one giant leap for "Bauplan?" Citation: Evolution & Development 4: 243-246 2002 Type: REVIEW Genes: Abstract: A popular hypothesis about animal diversification is that unique changes occurred in the Precambrian or Cambrian (ca. 700-500 million of years [Myr] ago) to produce the distinctive features of all animal "Baupläne" ("body plans") and that such changes have not occurred since (Gould 1989:47). In contrast, we suggest that changes similar to the key innovations initiating the appearance of these distinctive features occur repeatedly during evolution. A major example is the "inversion" of the dorsoventral axis in the evolution of chordates (Arendt and Nübler-Jung 1994), initiated by a switch in mouth position from the neural to the abneural side. Here we note that similar changes in mouth position evolved < 50 Myr ago at least twice in a group of nematodes related to Caenorhabditis elegans. Because this means that such changes were not unique to the Cambrian, they can be studied by experimental approaches in closely related extant organisms. A direct consequence of this focus on studying elemental key changes is that "Bauplan" becomes a less useful concept for understanding how animal diversity ------------------- Key: 5466 Medline: 12359262 Authors: Trappe R;Schulze E;Rzymski T;Frode S;Engel W Title: The Caenorhabditis elegans ortholog of human PHF5a shows a muscle-specific expression domain and is essential for C. elegans morphogenetic development. Citation: Biochemical and Biophysical Research Communications 297: 1049-1057 2002 Type: ARTICLE Genes: phf-5 Abstract: We have recently described a novel human and murine multigene-family that is highly conserved during evolution and shows a PHD-finger-like domain present in the deduced protein sequences. Here, we describe the cloning and characterization of the Caenorhabditis elegans ortholog of human PHF5a. Transgenic phf-5::yfp-reporter techniques in C elegans identified temporal C elegans phf-5 expression being restricted to late C elegans development. The phf-5::yfp expression starts within the morphogenetic phase of embryonic development and lasts to the stage of adult worms. Spatial phf-5 expression is muscle-specific with an expression in the developing pharynx, in body wall muscular structures, and in the anal muscles. By phf-5 RNAi we further demonstrated that PHF-5 is essential in the morphogenetic phase of C elegans embryonic development as well as in young larvae. In contrast, phf-5 RNAi does not show an evident phenotype to adult worms. Taken together, this is the first report providing evidence for a tissue and stage-specific expression of a PHF5a ortholog, named phf-5, in C elegans while our data further suggest an essential role of the encoded PHF-5 protein in morphogenetic development and muscle function. ------------------- Key: 5467 Medline: Authors: Sudhaus W;Fitch D Title: Comparative studies on the phylogeny and systematics of the Rhabditidae (Nematoda). Citation: Journal of Nematology 33: 1-70 2002 Type: ARTICLE Genes: Abstract: Because the primary goal of this work was to provide a translation of the primary (mostly morphological) data and conclusions regarding the phylogenetic relationships of taxa within Rhabditinae, only the Introduction and chapter I (Phylogenetic System of Rhabditinae, sunsu lato) of the Main Part of the original monograph have been translated in full. In addition, only those portions of other chapters that are specifically cross-referenced in Chapter I have been translated: Section 3 (Metastomal structures), Section 7 (Bursa formation and its transformations), and Section 8 (Number and arrangement of the bursal papillae) of Chapter II (Character evolution in Rhabditinae), and Section 9 (Copulatory behavior of Chapter VI (Comparative ecology and biology of Rhabiditinae). ------------------- Key: 5468 Medline: 12169658 Authors: Starr DA;Han M Title: Role of ANC-1 in tethering nuclei to the actin Citation: Science 298: 406-409 2002 Type: ARTICLE Genes: anc-1 unc-84 Abstract: Mutations in anc-1 (nuclear anchorage defective) disrupt the positioning of nuclei and mitochondria in Caenorhabditis elegans. ANC-1 is shown to consist of mostly coiled regions with a nuclear envelope localization domain (called the KASH domain) and an actin-binding domain; this structure was conserved with the Drosophila protein Msp-300 and the mammalian Syne proteins. Antibodies against ANC-1 localized cytoplasmically and were enriched at the nuclear periphery in an UNC-84 dependent manner. Overexpression of the KASH domain or the actin-binding domain caused a dominant negative anchorage defect. Thus, ANC-1 may connect nuclei to the cytoskeleton by interacting with UNC-84 at the nuclear envelope and with actin in the cytoplasm. ------------------- Key: 5469 Medline: 12202746 Authors: Nuttley WM;Atkinson-Leadbeater KP;van der Kooy D Title: Serotonin mediates food-odor associative learning in the nematode Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences 99: 12449-12454 2002 Type: ARTICLE Genes: cat-4 odr-1 tph-1 Abstract: We demonstrate that Caenorhabditis elegans is able to form an association between the presence of the odorant benzaldehyde and the food content of its environment. When exposed to 100% benzaldehyde for 1 h in the absence of food the naive attractive response is reduced, and we have found that this olfactory adaptation is attenuated by the presence of food. Contrary to nonassociative (single stimulus) learning theory, this response is not a function of the total time of exposure to benzaldehyde but rather an associative function of the ability of benzaldehyde to predict a nutrient-deficient environment. Genetic and pharmacological evidence revealed that the effects of food in this learning paradigm are mediated by serotonergic signaling. ------------------- Key: 5470 Medline: 12202952 Authors: Nickell WT;Pun RYK;Bargmann CI;Kleene SJ Title: Single ionic channels of two Caenorhabditis elegans chemosensory neurons in native membrane. Citation: Journal of Membrane Biology 189: 55-66 2002 Type: ARTICLE Genes: Abstract: The genome of Caenorhabditis elegrans contains representatives of the channel families found in both vertebrate and invertebrate nervous systems. However, it lacks the ubiquitous Hodgkin-Huxley Na+ channel that is integral to long-distance signaling in other animals. Nematode neurons are presumed to communicate by electrotonic conduction and graded depolarizations. This fundamental difference in operating principle may require different channel populations to regulate transmission and transmitter release. We have sampled ionic channels from the somata of two chemosensory neurons (AWA and AWC) of C. elegans. A Ca2+-activated, outwardly rectifying channel has a conductance of 67 pS and a reversal potential indicating selectivity for K+. An inwardly rectifying channel is active at potentials more negative than -50 mV. The inward channel is notably flickery even in the absence of divalent cations; this prevented determination of its conductance and reversal potential. Both of these channels were inactive over a range of membrane potentials near the likely cell resting potential; this would account for the region of very high membrane resistance observed in whole-cell recordings. A very-large-conductance (>100 pS), inwardly rectifying channel may account for channel-like fluctuations seen in whole-cell recordings. ------------------- Key: 5471 Medline: 12167666 Authors: Kawar ZS;Van Die I;Cummings RD Title: Molecular cloning and enzymatic characterization of a UDP-GalNAc:GlcNAcB-R B1,4-N-acetylgalactosaminyltransferase from Caenorhabditis elegans. Citation: Journal of Biological Chemistry 277: 34924-34932 2002 Type: ARTICLE Genes: sqv-3 Abstract: A common terminal structure in glycans from animal glycoproteins and glycolipids is the lactosamine sequence Galbeta4GlcNAc-R (LacNAc or LN). An alternative sequence that occurs in vertebrate as well as in invertebrate glycoconjugates is GalNAcbeta4GlcNAc-R (LacdiNAc or LDN). Whereas genes encoding beta4GalTs responsible for LN synthesis have been reported, the beta4GalNAcT(s) responsible for LDN synthesis has not been identified. Here we report the identification of a gene from Caenorhabditis elegans encoding a UDP-GalNAc:GlcNAcbeta-R beta1,4-N-acetylgalactosaminyltransferase (Cebeta4GalNAcT) that synthesizes the LDN structure. Cebeta4GalNAcT is a member of the beta4GalT family, and its cDNA is predicted to encode a 383-amino acid type 2 membrane glycoprotein. A soluble, epitope-tagged recombinant form of Cebeta4GalNAcT expressed in CHO-Lec8 cells was active using UDP-GalNAc, but not UDPGal, as a donor toward a variety of acceptor substrates containing terminal beta-linked GlcNAc in both N- and O-glycan type structures. The LDN structure of the product was verified by co-chromatography with authentic standards and H-1 NMR spectroscopy. Moreover, Chinese hamster ovary CHO-Lec8 and CHO-Lec2 cells expressing Cebeta4GalNAcT acquired LDN determinants on endogenous glycoprotein N-glycans, demonstrating that the enzyme is active in mammalian cells as an authentic beta4GalNAcT. The identification and availability of this novel enzyme should enhance our understanding of the structure and function of LDN-containing glycoconjugates. ------------------- Key: 5472 Medline: 12110687 Authors: Harris BZ;Venkatasubrahmanyan S;Lim WA Title: Coordinated folding and association of the LIN-2, -7 (L27) domain. Citation: Journal of Biological Chemistry 277: 34902-34908 2002 Type: ARTICLE Genes: glr-1 let-23 lin-2 lin-7 lin-10 Abstract: (L) under bar IN-(2) under bar, -(7) under bar (L27) homology domains are putative protein-protein interaction modules found in several scaffold proteins involved in the assembly of polarized cell-signaling structures. These specific interaction pairs are well conserved across metazoan species, from worms to man. We have expressed and purified L27 domains from multiple species and find that certain domains from proteins such as Caenorhabditis elegans LIN-2 and LIN-7 can specifically heterodimerize. Biophysical analysis of interacting L27 domains demonstrates that the domains interact with a 1:1 stoichiometry. Circular dichroism studies reveal that the domains appear to function as an obligate heterodimer; individually the domains are largely unfolded, but when associated they show a significant increase in helicity, as well as a cooperative unfolding transition. These novel obligate interacting pairs are likely to play a key role in regulating the organization of signaling proteins at ------------------- Key: 5473 Medline: 12228293 Authors: Sifri CD;Mylonakis E;Singh KV;Qin X;Garsin DA;Murray BE;Ausubel FM;Calderwood SB Title: Virulence effect of Enterococcus faecalis protease genes and the quorum-sensing locus fsr in Caenorhabditis elegans. Citation: Infection and Immunity 70: 5647-5650 2002 Type: ARTICLE Genes: Abstract: The expression of two Enterococcus faecalis extracellular virulence-related proteins, gelatinase (GelE) and serine protease (SprE), has been shown to be positively regulated by the fsr quorum-sensing system. We recently developed a novel system for studying E. faecalis pathogenicity that involves killing of the nematode worm Caenorhabditis elegans and showed that an E. faecalis fsrB mutant (strain TX5266) exhibited attenuated killing. We explore here the role of the fsr/gelE-sprE locus in pathogenicity by comparing results obtained in the nematode system with a mouse peritonitis model of E. faecalis infection. Insertion mutants of fsrA (TX5240) and fsrC (TX5242), like fsrB (TX5266), were attenuated in their ability to kill C. elegans. A deletion mutant of gelE (TX5264) and an insertion mutant of sprE (TX5243) were also attenuated in C. elegans killing, although to a lesser extent than the fsr mutants. Complementation of fsrB (TX5266) with a 6-kb fragment containing the entire fsr locus restored virulence in both the nematode and the mouse peritonitis models. The fsr mutants were not impaired in their ability to colonize the nematode intestine. These data show that extracellular proteases and the quorum-sensing fsr system are important for E. faecalis virulence in two highly divergent hosts: nematodes and mice. ------------------- Key: 5474 Medline: 12213552 Authors: Houthoofd K;Braeckman BP;Lenaerts I;Brys K;DeVreese A;Van Eygen S;Vanfleteren JR Title: Ageing is reversed, and metabolism is reset to young levels in recovering dauer larvae of C. elegans. Citation: Experimental Gerontology 37: 1015-1021 2002 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans responds to unfavourable environmental conditions by arresting development and entering diapause as a dauer larva. Dauers can survive several times the normal life span and the duration of the dauer state has no effect on postdauer life span. This led to the suggestion that dauers are non-ageing, and that dauers eventually perish as the consequence of depletion of stored nutrients. We have investigated physiological changes associated with long-term diapause survival, and found that dauer larvae slowly develop senescence-like symptoms, including decrease of metabolic capacity, aconitase enzyme activity, and ATP stores, and increase of lipofuscin- and oxidised flavin-specific fluorescence. However, these changes are reversed when the dauers recover. Thus senescence can occur before attainment of reproductive maturity, and furthermore, is reversible. Other life processes, including respiration rate and heat output, remain unaltered over four weeks of diapause at 24 degreesC. Possible determinants of the enhanced life maintenance include increased resistance to oxidative stress provided by enhanced superoxide dismutase and catalase activities, and ------------------- Key: 5475 Medline: 12372248 Authors: Lund J;Tedesco P;Duke K;Wang J;Kim SK;Johnson TE Title: Transcriptional profile of aging in C. elegans. Citation: Current Biology 12: 1566-1573 2002 Type: ARTICLE Genes: act-4 age-1 daf-2 emb-27 fer-15 hsp-1 hsp-2 hsp-3 hsp-4 hsp-16 ins-2 ins-3 ins-4 ins-5 ins-6 ins-7 ins-11 ins-17 ins-18 ins-21 ins-22 ins-23 mup-2 sip-1 sir-2.1 spe-9 Abstract: Background: Numerous gerontogene mutants leading to dramatic life extensions have been identified in the nematode Caenorhabditis elegans over the last 20 years. Analysis of these mutants has provided a basis for understanding the mechanisms driving the aging process(es). Several distinct mechanisms including an altered rate of aging, increased resistance to stress, decreased metabolic rate, or alterations in a program causing organismic aging and death have been proposed to underlie these mutants. Results: Whole-genome analysis of gene expression during chronological aging of the worm provides a rich database of age-specific changes in gene expression and represents one way to distinguish among these models. Using a rigorous statistical model with multiple replicates, we find that a relatively small number of genes (only 164) show statistically significant changes in transcript levels as aging occurs (<1 % of the genome). Expression of heat shock proteins decreases, while expression of certain transposases increases in older worms, and these findings are consistent with a higher mortality risk due to a failure in homeostenosis and destabilization of the genome in older animals. Finally, a specific subset of genes is coordinately altered both during chronological aging and in the transition from the reproductive form to the dauer, demonstrating a mechanistic overlap in aging between these two processes. Conclusions: We have performed a whole-genome analysis of changes in gene expression during aging in C. elegans that provides a molecular description of C. elegans senescence. ------------------- Key: 5476 Medline: 12361595 Authors: Bokel C;Brown NH Title: Integrins in development: moving on, responding to, and sticking to the extracellular matrix. Citation: Developmental Cell 3: 311-321 2002 Type: REVIEW Genes: ina-1 pat-3 Abstract: Integrins are cell surface receptors of the extracellular matrix present in all animals. Genetic analysis in worms, flies, and vertebrates has revealed integrin involvement in key developmental processes, and we focus here on examples of integrin functions that are comparable across these model organisms. Integrins contribute to cell movement by providing traction to migrating cells, through assembly of extracellular matrices that can serve as tracks for migration, and by transmitting guidance signals that direct cells or cell processes to their targets. Integrins also participate in signaling events that govern tissue differentiation and organogenesis. Finally, adhesion by integrin-mediated junctions allows tissues to withstand mechanical load and is essential for tissue integrity. ------------------- Key: 5477 Medline: 12363029 Authors: Liao VH-C;Freedman JH Title: Differential display analysis of gene expression in invertebrates. Citation: Cellular and Molecular Life Sciences 59: 1256-1263 2002 Type: REVIEW Genes: Abstract: Screening for differentially expressed genes is a straightforward approach to study the molecular basis for changes in gene expression. Differential display analysis has been used by investigators in diverse fields of research since it was developed. Differential display has also been the approach of choice to investigate changes in gene expression in response to various biological challenges in invertebrates. We review the application of differential display analysis of gene expression in invertebrates, and provide a specific example using this technique for novel gene discovery in the nematode ------------------- Key: 5478 Medline: Authors: Adam M;Levraud JP;Golstein P Title: Genetic approaches to programmed cell death: achievements and questions. Citation: M S-Medecine Sciences 18: 831-840 2002 Type: REVIEW Genes: Abstract: A useful approach to study molecular mechanisms of cell death is, classically, mutagenesis followed with identification of the altered gene. For caspase-dependent cell death, this has provided spectacular results in the nematode C. elegans more than in other organisms. Often different molecules have been identified as a function of the investigated organism. These differences reflect, sometimes the existence of pathways seemingly unique to certain species, sometimes selection biases linked to peculiarities of the organisms under investigation. ------------------- Key: 5479 Medline: 12173487 Authors: de Chadarevian S Title: Mapping development or how molecular is molecular biology? Citation: Pubblicazioni della Stazione Zoologica de Napoli:Secion Ii:History & Philosophy of the Life Sciences 22: 381-396 2002 Type: REVIEW Genes: Abstract: The transformation of embryology to developmental biology has been linked to the introduction of experimental approaches from molecular genetics to the study of development. This paper pursues this theme by analyzing the tools molecular biologists, moving from phage and bacterial genetics to the study of development in higher organisms, brought to their new field of investigations. The paper focuses on Sydney Brenner's move from molecular genetics to developmental biology. His attempt to turn the nematode worm Caenorhabditis elegans into a new tool for the study of development included a vast and ever expanding mapping program. Worm workers themselves did not distinguish sharply between mapping on the cellular, chromosomal or molecular level. Mapping, the paper argues, or more generally 'analytical/comparative' next to 'experimentalist' approaches (Pickstone) were not only part and parcel of Brenner's strategy to 'molecularize' the study of development, but also played a crucial role in 'classical' molecular biology. ------------------- Key: 5480 Medline: 11928496 Authors: GuhaThakurta D;Schriefer LA;Hresko MC;Waterston RH;Stormo Title: Identifying muscle regulatory elements and genes in the nematode Caenorhabditis elegans. Citation: Pacific Symposium on Biocomputing : 425-436 2002 Type: ARTICLE Genes: Abstract: We report the identification of several putative muscle-specific regulatory elements, and genes which are expressed preferentially in the muscle of the nematode Caenorhabditis elegans. We used computational pattern finding methods to identify cis-regulatory motifs from promoter regions of a set of genes known to express preferentially in muscle; each motif describes the potential binding sites for an unknown regulatory factor. The significance and specificity of the identified motifs were evaluated using several different control sequence sets. Using the motifs, we searched the entire C. elegans genome for genes whose promoter regions have a high probability of being bound by the putative regulatory factors. Genes that met this criterion and were not included in our initial set were predicted to be good candidates for muscle expression. Some of these candidates are additional, known muscle expressed genes and several others are shown here to be preferentially expressed in muscle cells by using GFP (green fluorescent protein) constructs. The methods described here can be used to predict the spatial expression pattern of many ------------------- Key: 5481 Medline: 12220486 Authors: Kjeldgaard M Title: Another worm in translation. Citation: Structure 10: 1154-1155 2002 Type: REVIEW Genes: Abstract: Elongation factor EF-Tu is a key component in the translation step of protein synthesis, where it forms a complex with amino-acyl tRNA and delivers it to the ribosome. Until now, none of the known EF-Tu molecules have discriminated between the different species of tRNA, but now a new discovery sheds light on a curious EF-Tu homolog that binds just a single tRNA species. ------------------- Key: 5482 Medline: 12215411 Authors: Picken NC;Eschenlauer S;Taylor P;Page AP;Walkinshaw MD Title: Structural and biological characterisation of the gut-associated cyclophilin B isoforms from Caenorhabditis elegans. Citation: Journal of Molecular Biology 322: 15-25 2002 Type: ARTICLE Genes: cyp-1 cyp-5 cyp-6 Abstract: The free-living nematode Caenorhabditis elegans expresses 18 cyclophilin isoforms, eight of which are conserved single domain forms, comprising two closely related secreted or type B forms (CYP-5 and CYP-6). Recombinant CYP-5 has been purified, crystallised and the X-ray structure solved to a resolution of 1.75 ANG. The detailed molecular architecture most strongly resembles the structure of human cyclophilin B with conserved changes in loop structure and N and C-terminal extensions. Interestingly, the active site pocket is occupied by a molecule of dithiothreitol though this has little effect on the geometry of the active site which is similar to other cyclophilin structures. The peptidyl-prolyl isomerase activity of CYP-5 has been characterised against the substrate N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide, and gives a kcat/Km value of 3.6X106 M-1 s-1 that compares with a value of 6.3X106 M-1 s-1 for human cyclophilin B. The immunosuppressive drug cyclosporin A binds and inhibits CYP-5 with an IC50 value of 50 nM, which is comparable to the value of 84 nM found for human cyclophilin B. CYP-6 has 67% sequence identity with CYP-5 and a molecular model was built based on the CYP-5 crystal structure. The model shows that CYP-5 and CYP-6 are likely to have very similar structures, but with a markedly increased number of negative charges distributed around the surface of CYP-6. The spatial expression patterns of the cyclophilin B isoforms were examined using transgenic animals carrying a LacZ reporter fusion to these genes, and both cyp-5 and cyp-6 are found to be expressed in an overlapping fashion in the nematode gut. The temporal expression pattern of cyp-5 was further determined and revealed a constitutive ------------------- Key: 5483 Medline: 12221132 Authors: Bandyopadhyay J;Lee J;Lee J;Lee JI;Yu JR;Jee C;Cho JH;Jung S;Lee MH;Zannoni S;Singson A;Kim DH;Koo HS;Ahnn J Title: Calcineurin, a calcium/calmodulin-dependent protein phosphatase, is involved in movement, fertility, egg laying, and growth in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 13: 3281-3293 2002 Type: ARTICLE Genes: cna-1 cnb-1 goa-1 sma-6 tax-6 unc-43 Abstract: Calcineurin is a Ca2+-calmodulin-dependent serine/threonine protein phosphatase that has been implicated in various signaling pathways. Here we report the identification and characterization of calcineurin genes in Caenorhabditis elegans (cna-1 and cnb-1), which share high homology with Drosophila and mammalian calcineurin genes. C. elegans calcineurin binds calcium and functions as a heterodimeric protein phosphatase establishing its biochemical conservation in the nematode. Calcineurin is expressed in hypodermal seam cells, body-wall muscle, vulva muscle, neuronal cells, and in sperm and the spermatheca. cnb-1 mutants showed pleiotropic defects including lethargic movement and delayed egg-laying. Interestingly, these characteristic defects resembled phenotypes observed in gain-of-function mutants of unc-43/Ca2+-calmodulin-dependent protein kinase II (CaMKII) and goa-1/Go-protein alpha-subunit. Double mutants of cnb-1 and unc-43(gf) displayed an apparent synergistic severity of movement and egg-laying defects, suggesting that calcineurin may have an antagonistic role in CaMKII-regulated phosphorylation signaling pathways in C. ------------------- Key: 5484 Medline: 12215411 Authors: Geles KG;Johnson JJ;Jong S;Adam SA Title: A role for Caenorhabditis elegans importin IMA-2 in germ line and embryonic mitosis. Citation: Molecular Biology of the Cell 13: 3138-3147 2002 Type: ARTICLE Genes: glp-1 ima-1 ima-2 ima-3 Abstract: The importin alpha family of nuclear-cytoplasmic transport factors mediates the nuclear localization of proteins containing classical nuclear localization signals. Metazoan animals express multiple importin alpha proteins, suggesting their possible roles in cell differentiation and development. Adult Caenorhabditis elegans hermaphrodites express three importin alpha proteins, IMA-1, IMA-2, and IMA-3, each with a distinct expression and localization pattern. IMA-2 was expressed exclusively in germ line cells from the early embryonic through adult stages. The protein has a dynamic pattern of localization dependent on the stage of the cell cycle. In interphase germ cells and embryonic cells, IMA-2 is cytoplasmic and nuclear envelope associated, whereas in developing oocytes, the protein is cytoplasmic and intranuclear. During mitosis in germ line cells and embryos, IMA-2 surrounded the condensed chromosomes but was not directly associated with the mitotic spindle. The timing of IMA-2 nuclear localization suggested that the protein surrounded the chromosomes after fenestration of the nuclear envelope in prometaphase. Depletion of IMA-2 by RNA-mediated gene interference (RNAi) resulted in embryonic lethality and a terminal aneuploid phenotype, ima-2(RNAi) embryos have severe defects in nuclear envelope formation, accumulating nucleoporins and lamin in the cytoplasm. We conclude that IMA-2 is required for proper chromosome dynamics in germ line and early embryonic mitosis and is involved in nuclear envelope ------------------- Key: 5485 Medline: 12441252 Authors: Buechner M Title: Tubes and the single C. elegans excretory cell. Citation: Trends in Cell Biology 12: 479-484 2002 Type: REVIEW Genes: cdc-42 exc-1 exc-2 exc-3 exc-4 exc-5 exc-7 let-4 let-653 sma-1 vha-1 Abstract: The formation and regulation of tubule shape and size is fundamental to the development and function of many tissues and organs in metazoan organisms. The excretory canals of the nematode Caenorhabditis elegans are a fascinating example of cell morphogenesis, as the tiny worm manages to create a complicated set of tubular epithelia within a single cell. In addition to the inherent attraction of studying this cytoengineering feat, the excretory cell provides a simple genetically tractable model for studying tubule formation and regulation of tubule diameter. Mutations in the exc genes alter the diameter of the lumenal surface of these tubules. Cloning of these genes reveals a set of proteins that both control tubule diameter and regulate the comparative growth of the apical and basal tubular surfaces. ------------------- Key: 5486 Medline: Authors: Colaiacovo MP;Stanfield GM;Reddy KC;Reinke V;Kim SK;Villeneuve AM Title: A targeted RNAi screen for genes involved in chromosome morphogenesis and nuclear organization in the Caenorhabditis elegans germline. Citation: Genetics 162: 113-128 2002 Type: ARTICLE Genes: adm-1 apn-1 asb-1 coh-3 cyk-4 dnj-22 exo-3 gfi-4 gld-1 gld-4 glp-1 gon-1 gon-4 hcp-1 hcp-2 him-6 him-10 him-17 hmg-3 hmg-12 klp-10 klp-14 klp-16 kup-2 msh-5 npp-1 npp-12 pms-2 pri-2 rad-50 rfc-1 rha-1set-2 skr-2 spd-5 spo-11 syp-1 syp-2 syp-3 tbg-1 Abstract: We have implemented a functional genomics strategy to identify genes involved in chromosome morphogenesis and nuclear organization during meiotic prophase in the Caenorhabditis elegans germline. This approach took advantage of a gene-expression survey that used DNA microarray technology to identify genes preferentially expressed in the germline. We defined a subset of 192 germline-enriched genes whose expression profiles were similar to those of previously identified meiosis genes and designed a screen to identify genes for which inhibition by RNA interference (RNAi) elicited defects in function or development of the germline. We obtained strong germline phenotypes for 27% of the genes tested, indicating that this targeted approach greatly enriched for genes that function in the germline. In addition to genes involved in key meiotic prophase events, we identified genes involved in meiotic progression, germline proliferation, and chromosome organization and/or segregation during mitotic ------------------- Key: 5487 Medline: 12242258 Authors: Martin E;Laloux H;Couette G;Alvarez T;Bessou C;Hauser O;Sokhareea S;Labouesse M;Segalat L Title: Identification of 1088 new transposon insertions of Caenorhabditis elegans: a pilot study toward large-scale screens. Citation: Genetics 162: 521-524 2002 Type: ARTICLE Genes: Abstract: We explored the feasibility of a strategy based on transposons to generate identified mutants of most Caenorhabditis elegans genes. A total of 1088 random new insertions of C. elegans transposons Tc1, Tc3, and Tc5 were identified by anchored PCR, some of which result in a mutant phenotype. ------------------- Key: 5488 Medline: 12399591 Authors: Dillin A;Crawford DK;Kenyon C Title: Timing requirements for insulin/IGF-1 signaling in C. elegans. Citation: Science 298: 830-834 2002 Type: ARTICLE Genes: daf-2 daf-16 dcr-1 Abstract: The insulin/IGF-1 (where IGF-1 is insulin-like growth factor 1) signaling pathway influences longevity, reproduction, and diapause in many organisms. Because of the fundamental importance of this system in animal physiology, we asked when during the animal's life it is required to regulate these different processes. We find that in Caenorhabditis elegans, the pathway acts during adulthood, to relatively advanced ages, to influence aging. In contrast, it regulates diapause during development. In addition, the pathway controls longevity and reproduction independently of one another. Together our findings show that life-span regulation can be dissociated temporally from phenotypes that might seem to decrease the quality of ------------------- Key: 5489 Medline: 12397339 Authors: Title: The old worm turns more slowly. Citation: Nature 419: 794-795 2002 Type: REVIEW Genes: age-1 Abstract: Detailed studies of cellular changes in ageing nematode worms show that they, like humans, suffer progressive muscle deterioration. Randomness of cell damage is another shared hallmark of the ageing process. ------------------- Key: 5490 Medline: 12397350 Authors: Herndon LA;Schmeissner PJ;Dudaronek JM;Brown PA;Listner KM;Sakano Y;Paupard MC;Hall DH;Driscoll M Title: Stochastic and genetic factors influence tissue-specific decline in ageing C. elegans. Citation: Nature 419: 808-814 2002 Type: ARTICLE Genes: age-1 Abstract: The nematode Caenorhabditis elegans is an important model for studying the genetics of ageing, with over 50 life-extension mutations known so far. However, little is known about the pathobiology of ageing in this species, limiting attempts to connect genotype with senescent phenotype. Using ultrastructural analysis and visualization of specific cell types with green fluorescent protein, we examined cell integrity in different tissues as the animal ages. We report remarkable preservation of the nervous system, even in advanced old age, in contrast to a gradual, progressive deterioration of muscle, resembling human sarcopenia. The age-1 (hx546) mutation, which extends lifespan by 60-100%, delayed some, but not all, cellular biomarkers of ageing. Strikingly, we found strong evidence that stochastic as well as genetic factors are significant in C. elegans ageing, with extensive variability both among same-age animals and between cells of the same type within individuals. ------------------- Key: 5491 Medline: 12204272 Authors: Vargas JD;Culetto E;Ponting CP;Miguel-Aliaga I;Davies KE;Sattelle DB Title: Cloning and developmental expression analysis of ltd-1, the Caenorhabditis elegans homologue of the mouse kyphoscoliosis (ky) gene. Citation: Mechanisms of Development 117: 289-292 2002 Type: ARTICLE Genes: ltd-1 Abstract: We have characterized the developmental expression pattern of the Caenorhabditis elegans homologue of the mouse ky gene. The Ky protein has a putative key function in muscle development and has homologues in invertebrates, fungi and a cyanobacterium. The C elegans Ky homologue gene has been named ltd-1 for LIM and transglutaminase domains gene. The LTD-1::GFP construct is expressed in developing hypodermal cells from the twofold stage embryo through adulthood. These data define the ltd-1 gene as a novel marker for C. elegans epithelial cell development. ------------------- Key: 5492 Medline: 12204276 Authors: Karabinos A;Schulze E;Klisch T;Wang J;Weber K Title: Expression profiles of the essential intermediate filament (IF) protein A2 and the IF protein C2 in the nematode Caenorhabditis elegans. Citation: Mechanisms of Development 117: 311-314 2002 Type: ARTICLE Genes: Abstract: The multigene family of intermediate filament (IF) proteins in Caenorhabditis elegans covers 11 members of which four (A1-3, B1) are essential for development. Suppression of a fifth gene (C2) results in a dumpy phenotype. Expression patterns of three essential genes (A1, A3, B1) were already reported. To begin to analyze the two remaining RNAi phenotypes we followed the expression of the A2 and C2 proteins. Expression of A2 mRNA starts in larval stage L1 and continues in the adult. Transgenic A2 promoter/gfp larvae strongly display GFP in the main body hypodermis but not in seam cells. This pattern and the muscle displacement/paralysis induced by RNAi silencing are consistent with the role of this protein in keeping the correct hypodermis/muscle relationship during development. IF protein C2 occurs in the cytoplasm and desmosomes of intestinal cells and in pharynx desmosomes. Expression of C2 starts in the late embryo and persists in all further stages. ------------------- Key: 5493 Medline: 12359064 Authors: Tabuse Y Title: Protein kinase C isotypes in C. elegans. Citation: Journal of Biochemistry 132: 519-522 2002 Type: REVIEW Genes: cdc-42 kup-1 par-2 par-3 par-6 pkc-1 pkc-2 pkc-3 tpa-1 unc-29 Abstract: The protein kinase C (PKC) family, consisting of multiple isotypes, plays a major role in cellular signaling. In the nematode Caenorhabditis elegans, four pkc genes, tpa-1, pkc-1, pkc-2 and pkc-3, have been identified and investigated. Molecular analysis of tpa-1, pkc-1, and pkc-2 has shown that each gene encodes multiple PKC isoforms with different expression patterns. One of the tpa-1 isoforms, which is expressed in vulval cells, is found to play a role in nicotine-induced adaptation. The expression of pkc-1 seems to be specific to neurons, while that of pkc-2 is detected in several types of cells including neurons and muscle cells. An aPKC member encoded by pkc-3 has been shown to play an essential role in establishing the polarity of the zygote. Recent studies have revealed that the mechanism of polarity establishment mediated by aPKC is evolutionarily conserved in diverse organisms from nematodes to mammals. C. elegans provides an excellent model system for molecular dissection of the cellular ------------------- Key: 5494 Medline: 12297283 Authors: Li P;Slimko EM;Lester HA Title: Selective elimination of glutamate activation and introduction of fluorescent proteins into a Caenorhabditis elegans chloride channel. Citation: FEBS Letters 528: 77-82 2002 Type: ARTICLE Genes: Abstract: Glutamate-gated chloride (GluCI) channels from invertebrates can be activated by ivermectin (IVM) to produce electrical silencing in mammalian neurons. To improve this GluCl/IVM strategy, we sought to mutate the Caenorhabditis eleganN GluCl channels so that they become insensitive to glutamate but retain their sensitivity to IVM. Based on structure-function studies of nicotinic acetylcholine receptor superfamily members, we tested in oocytes 19 point mutants at 16 residues in the beta-subunit likely to be involved in the response to glutamate. Y182F reduces the glutamate response by greater than six-fold, with little change to IVM responses, when coexpressed with wild-type (WT) GluCl alpha. For GluCl alphabeta(Y18217), the EC50 and Hill coefficient for glutamate are similar to those of WT, indicating that the mutant decreases the efficacy of glutamate, but not the potency. Also, fluorescent proteins (enhanced green fluorescent protein, enhanced yellow fluorescent protein, enhanced cyan fluorescent protein; XFP) were inserted into the M3-M4 loop of the GluG alpha, beta and beta(Y182F). We found no significant functional difference between these XFP-tagged receptors and WT receptors. The modified GluCl channel, without glutamate sensitivity but with a fluorescent tag, may be more useful in GluCl silencing strategies. ------------------- Key: 5495 Medline: 12297102 Authors: Wu YC;Cheng TW;Lee MC;Weng NY Title: Distinct Rac activation pathways control Caenorhabditis elegans cell migration and axon outgrowth. Citation: Developmental Biology 250: 145-155 2002 Type: ARTICLE Genes: ced-2 ced-5 ced-10 ced-12 mig-2 unc-73 Abstract: Rac GTPases act as molecular switch in various morphogenic events. However, the regulation of their activities during the development of multicellular organisms is not well understood. Caenorhabditis elegans rac genes ced-10 and mig-2 have been shown to act redundantly to control P cell migration and the axon outgrowth of D type motoneurons. We showed that ced-10 and mig-2 also control amphid axon outgrowth and amphid dendrite fasciculation in a redundant fashion. Our biochemical and genetic data indicate that unc-73, which encodes a protein related to Trio-like guanine nucleotide exchange factor, acts as a direct activator of ced-10 and mig-2 during P cell migration and axon outgrowth of D type motoneurons and amphid sensory neurons. Furthermore, rac regulators ced-2/crkII and ced-5/dock180 function genetically upstream of ced-10 and mig-2 during axon outgrowth of D type motoneurons and act upstream of mig-2 but not ced-10 during P cell migration. However, neither ced-2/crkII nor ced-5/dock180 is involved in amphid axon outgrowth. Therefore, distinct rac regulators control ced-10 and mig-2 differentially in various cellular processes. ------------------- Key: 5496 Medline: 12297370 Authors: Chu KW;Chow KL Title: Synergistic toxicity of multiple heavy metals is revealed by a biological assay using a nematode and its transgenic derivative. Citation: Aquatic Toxicology 61: 53-64 2002 Type: ARTICLE Genes: rol-6 Abstract: Caenorhabditis elegans, a free-living nematode species, was adopted for a toxicity bioassay of 10 heavy metals. The lethal concentration (LC) of these metals was determined. Based on these data, we conducted pairwise and triple metal combination testing and demonstrated that these heavy metals displayed synergistic killing effects on C. elegans larvae. Drastic increases in mortality rate up to 100% could be observed at low metal concentrations. The results illustrate the complexity of toxicity tests in biological systems and show that physical-chemical monitoring of toxicants may underestimate biohazards in environmental samples. We also demonstrate that a transgenic derivative nematode strain, KC136, carrying a heat shock promoter driven gfp reporter gene could be used to reduce the duration of an assay so that the synergistic effects among toxicants could be revealed. This derivative strain allows rapid and frequent monitoring of environmental hazards, which usually requires the handling of a large number ------------------- Key: 5497 Medline: 12422237 Authors: Stachelska A;Wieczorek Z;Ruszczynska K;Stolarski R;Pietrzak M;Lamphear BJ;Rhoads RE;Darzynkiewicz E;Jankowska-Anyszka M Title: Interaction of three Caenorhabditis elegan isoforms of translation initiation factor eIF4E with mono- and trimethylated mRNA 5' cap analogues. Citation: Acta Biochimica Polonica 49: 671-682 2002 Type: ARTICLE Genes: Abstract: Translation initiation factor eIF4E binds the m(7)G cap of eukaryotic mRNAs and mediates recruitment of mRNA to the ribosome during cap-dependent translation initiation. This event is the rate-limiting step of translation and a major target for translational control. In the nematode Caenorhabditis elegans, about 70% of genes express mRNAs with an unusual cap structure containing m(3)(2'2'7)G, which is poorly recognized by mammalian eIF4E. C. elegans expresses five isoforms of eIF4E (IFE-1, IFE-2, etc.). Three of these (IFE-3, IFE-4 and IFE-5) were investigated by means of spectroscopy and structural modelling based on mouse eIF4E bound to m(7) GDP. Intrinsic fluorescence quenching of Trp residues in the IFEs by iodide ions indicated structural differences between the apo and m(7)G cap bound proteins. Fluorescence quenching by selected cap analogues showed that only IFE-5 forms specific complexes with both m(7)G and m(3)(2,2,7)G-containing caps (K(as)2X10(6) M-1 to 7X10(6) M-1) wheras IFE-3 and IFE-4 discriminated strongly in favor of m(7)G-containing caps. These spectroscopic results quantitatively confirm earlier qualitative data derived from affinity chromatography. The dependence of K-as on pH indicated optimal cap binding of IFE-3, IFE-4 and IFE-5 at pH 7.2, lower by 0.4 pH units than that of eIF4E from human erythrocytes. These results provide insight into the molecular mechanism of recognition of structurally different caps by the highly homologous ------------------- Key: 5498 Medline: 12297039 Authors: Pirrotta V Title: Silence in the germ. Citation: Cell 110: 661-664 2002 Type: REVIEW Genes: mes-2 mes-3 mes-4 mes-6 pie-1 Abstract: Gene expression in C. elegans germline cells is subject to strict controls. A set of MES proteins, including SET domain proteins and two homologs of Polycomb group proteins, establish an epigenetically transmitted silenced state that affects X chromosome gene expression. ------------------- Key: 5499 Medline: Authors: Lagos-Quintana M;Rauhut R;Lendeckel W;Tuschl T Title: Identification of novel genes coding for small expressed RNAs. Citation: Science 294: 853-858 2002 Type: ARTICLE Genes: let-7 lin-4 Abstract: In Caenorhabditis elegans, lin-4 and let-7 encode 22- and 21-nucleotide (nt) RNAs, respectively, which function as key regulators of developmental timing. Because the appearance of these short RNAs is regulated during development, they are also referred to as small temporal RNAs (stRNAs). We show that many 21- and 22-nt expressed RNAs, termed microRNAs, exist in invertebrates and vertebrates and that some of these novel RNAs, similar to let-7 stRNA, are highly conserved. This suggests that sequence-specific, posttranscriptional regulatory mechanisms mediated by small RNAs are more general than ------------------- Key: 5500 Medline: Authors: Check E Title: Worm cast in starring role for Nobel prize. Citation: Nature 419: 548-549 2002 Type: REVIEW Genes: Abstract: A humble nematode has wormed its way into the affection of the scientific community and helped to secure this year's Nobel Prize in Physiology or Medicine. The award goes to three biologists whose work on the model organism Caenorhabditis elegans has yielded insights and spin-offs in such diverse fields as cancer research and modern ------------------- Key: 5501 Medline: Authors: Hatten ME Title: New directions in neuronal migration. Citation: Science 297: 1660-1663 2002 Type: REVIEW Genes: mig-13 unc-5 unc-6 unc-40 vab-8 Abstract: Over the past decade, genetic analyses have yielded a more molecular view of neuronal migration and its role in central nervous system development. We now realize that many of the molecular mechanisms that guide migrations in invertebrates are recapitulated in the vertebrate nervous system. These mechanisms guide dorso-ventral and anterior-posterior migrations and merge with radial migratory pathways that are prominent in the development of the mammalian cortex. This review discusses the choreography of these different migratory mechanisms within the context of the genetic approaches that have defined ------------------- Key: 5502 Medline: 12386313 Authors: Marx J Title: Nobels run the gamut from cells to the cosmos. Citation: Science 298: 526- 2002 Type: REVIEW Genes: Abstract: The nematode worm known as Caenorhabditis elegans is not much to look at. Just a millimeter long and transparent to boot, it is almost invisible to the naked eye. But in biological research the tiny worm looms large, providing a model system for studying everything from embryonic development to aging. Now, three researchers who pioneered the use of C. elegans as a model organism have won the Nobel Prize in Physiology or Medicine. ------------------- Key: 5503 Medline: Authors: von Mering C;Bork P Title: Teamed up for transcription. Citation: Nature 417: 797-798 2002 Type: REVIEW Genes: Abstract: The genomes of animals, plants and fungi seem to be relatively disorganized. Genes appear to be randomly distributed, with only a few exceptions: repeats of similar sequences caused by gene duplications, for example, and a limited number of ancient gene clusters containing functionally related genes (such as the Hox genes that are involved in control of animal development). Apart from these, the average gene is generally assumed to be independent of its neighbours, and genomes are constantly rearranged and shuffled. However, in one group of animals the nematodes (small, unsegmented worms) neighboring genes are occasionally assembled into regulatory units called operons. On page 851 of this issue, Blumenthal et al. now report the first whole-genome characterization of such operons in a mulicellular organism, an raise intriguing questions as to how (and why) they have evolved. ------------------- Key: 5504 Medline: 12397109 Authors: Lamitina ST;L'Hernault SW Title: Dominant mutations in the Caenorhabditis elegans Myt1 ortholog wee-1.3 reveal a novel domain that controls M-phase entry during spermatogenesis. Citation: Development 129: 5009-5018 2002 Type: ARTICLE Genes: let-241 smg-6 spe-37 wee-1.3 eDf21 mnDf12 mnDf28 mnDf29 mnDf30 mnDf57 mnDf58 mnDf60 mnDf63 mnDf71 mnDf88 Abstract: Regulatory phosphorylation of the Cdc2p kinase by Wee1p-type kinases prevents eukaryotic cells from entering mitosis or meiosis at an inappropriate time. The canonical Wee1p kinase is a soluble protein that functions in the eukaryotic nucleus. All metazoa also have a membrane-associated Wee1p-like kinase named Myt1, and we describe the first genetic characterization of this less well-studied kinase. The Caenorhabditis elegans Myt1 ortholog is encoded by the wee-1.3 gene, and six dominant missense mutants prevent primary spermatocytes from entering M phase but do not affect either oocyte meiosis or any mitotic division. These six dominant wee-1.3(gf) mutations are located in a four amino acid region near the C terminus and they cause self-sterility of hermaphrodites. Second-site intragenic suppressor mutations in wee-1.3(gf) restore self-fertility to these dominant sterile hermaphrodites, permitting genetic dissection of this kinase. Ten intragenic wee-1.3 suppressor mutations were recovered and they form an allelic series that includes semi-dominant, hypomorphic and null mutations. These mutants reveal that WEE-1.3 protein is required for embryonic development, germline proliferation and initiation of meiosis during spermatogenesis. This suggests that a novel, sperm-specific pathway negatively regulates WEE-1.3 to allow the G2/M transition of male meiosis I, and ------------------- Key: 5505 Medline: 12440704 Authors: Tsang WY;Lemire BD Title: Stable heteroplasmy but differential inheritance of large mitochondrial DNA deletion in nematodes. Citation: Canadian Journal of Biochemistry & Cell Biology 80: 645-654 2002 Type: ARTICLE Genes: him-8 uaDf5 Abstract: Many human mitochondrial diseases are associated with defects in the mitochondrial DNA (mtDNA). Mutated and wild-type forms of mtDNA often coexist in the same cell in a state called heteroplasmy. Here, we report the isolation of a Caenorhabditis elegans strain bearing the 3.1-kb uaDf5 deletion that removes 11 genes from the mtDNA. The uaDf5 deletion in maternally transmitted and has been maintained for at least 100 generations in a stable heteroplasmic state in which it accounts for 60% of the mtDNA content of each developmental stage. Heteroplasmy levels vary between individual animals (from 20 to 80%), but no observable phenotype is detected. The total mt DNA copy number is the uaDf5 mutant is approximately twice that of the wild type. The maternal transmission of the uaDf5 mtDNA is controlled by at least two competing processes: one process promotes the increase in the average proportion of uaDf5 mtDNA in the offspring, while the second promotes a decrease. These two forces prevent the segregation of the mtDNAs to ------------------- Key: 5506 Medline: 12141438 Authors: Caruana G Title: Genetic studies define MAGUK proteins as regulators of epithelial cell polarity. Citation: International Journal of Developmental Biology 46: 511-518 2002 Type: REVIEW Genes: let-23 lin-2 lin-3 lin-7 lin-10 Abstract: Polarized epithelial cells play critical roles during early embryonic development and organogenesis. Multi-domain scaffolding proteins belonging to the membrane associated guanylate kinase (MAGUK) family are commonly found at the plasma membrane of polarized epithelial cells. Genetic studies in Drosophila melanogaster and Caenorhabditis elegans have revealed that MAGUK proteins regulate various aspects of the polarized epithelial phenotype, including cell junction assembly, targeting of proteins to the plasma membrane and the organisation of polarized signalling complexes. This review will focus on the genetic studies that have contributed to our understanding of the MAGUK family members, Dlg and Lin-2/CASK, in controlling these processes. In addition, our recent genetic analysis of mouse Dlg, in combination with genetic and biochemical studies of Lin-2/CASK by others suggests a model placing Dlg and Lin-2/CASK within the same developmental pathway. ------------------- Key: 5507 Medline: Authors: Driscoll M;Tavernarakis N Title: Closing in on a mammalian touch receptor. Citation: Nature Neuroscience 3: 1232-1234 2002 Type: REVIEW Genes: mec-4 mec-10 unc-8 Abstract: A recent Nature paper on mice lacking the Na+ channel BNC1 shows that this channel is essential for neuronal touch receptor function and may be part of a mechanosensory complex. ------------------- Key: 5508 Medline: Authors: Dedhar S;Williams B;Hannigan G Title: Integrin-linked kinase (ILK): a regulator of integrin and growth-factor signalling. Citation: Trends in Cell Biology 9: 319-323 2002 Type: REVIEW Genes: unc-97 Abstract: Interaction of cells with the extracellular matrix (ECM) results in the regulation of cell growth, differentiation and migration by coordinated signal transduction through integrins and growth-factor receptors. Integrins achieve signaling by interaction with intracellular effectors that couple integrins and growth-factor receptors to downstream components. One well-studied effector is focal-adhesion kinase (FAK), but recently another protein kinase, integrin-linked kinase (ILK), has been identified as a receptor-proximal effector of integrin and growth-factor signaling. ILK appears to interact with and be influenced by a number of different signaling pathways, and this provides new routes for integrin-mediatied signaling. This article discusses ILK structure and function and recent genetic and biochemical evidence about the role of ILK in signal transduction. ------------------- Key: 5509 Medline: Authors: Altman LK Title: 3 win Nobel for work on suicidal cells. Citation: New York Times, October 8 : - 2002 Type: REVIEW Genes: Abstract: ------------------- Key: 5510 Medline: Authors: Manning G;Plowman GD;Hunter T;Sudarsanam S Title: Evolution of protein kinase signaling from yeast to man. Citation: Trends in Biochemical Sciences 27: 514-520 2002 Type: REVIEW Genes: Abstract: Protein phosphorylation controls many cellular processes, especially those involved in intercellular communication and coordination of complex functions. To explore the evolution of protein phosphorylation, we compared the protein kinase complements ('kinomes') of budding yeast, worm and fly, with known human kinases. We classify kinases into putative orthologous groups with conserved functions and discuss kinase families and pathways that are unique, expanded or lost in each lineage. Fly and human share several kinase families involved in immunity, neurobiology, cell cycle and morphogenesis that are absent from worm, suggesting that these functions might have evolved after the divergence of nematodes from the main metazoan lineage. ------------------- Key: 5511 Medline: 12410303 Authors: de Bono M;Tobin DM;Davis MW;Avery L;Bargmann CI Title: Social feeding in Caenorhabditis elegans is induced by neurons that detect aversive stimuli. Citation: Nature 419: 899-903 2002 Type: ARTICLE Genes: cat-4 che-13 daf-1 daf-2 daf-3 daf-5 daf-7 daf-8 daf-14 daf-16 daf-22 mec-3 mec-4 npr-1 ocr-2 odr-1 odr-2 odr-3 odr-4 odr-7 odr-8 osm-1 osm-3 osm-9 unc-25 unc-30 unc-36 Abstract: Natural Caenorhabditis elegans isolates exhibit either social or solitary feeding on bacteria. We show here that social feeding is induced by nociceptive neurons that detect adverse or stressful conditions. Ablation of the nociceptive neurons ASH and ADL transforms social animals into solitary feeders. Social feeding is probably due to the sensation of noxious chemicals by ASH and ADL neurons; it requires the genes ocr-2 and osm-9, which encode TRP-related transduction channels, and odr-4 and odr-8, which are required to localize sensory chemoreceptors to cilia. Other sensory neurons may suppress social feeding, as social feeding in ocr-2 and odr-4 mutants is restored by mutations in osm-3, a gene required for the development of 26 ciliated sensory neurons. Our data suggest a model for regulation of social feeding by opposing sensory inputs: aversive inputs to nociceptive neurons promote social feeding, whereas antagonistic inputs from neurons that express osm-3 inhibit aggregation. ------------------- Key: 5512 Medline: 12410311 Authors: Coates JC;de Bono M Title: Antagonistic pathways in neurons exposed to body fluid regulate social feeding in Caenorhabditis elegans. Citation: Nature 419: 925-929 2002 Type: REVIEW Genes: egl-2 gcy-32 npr-1 tax-2 tax-4 Abstract: Wild isolates of Caenorhabditis elegans can feed either alone or in groups(1,2). This natural variation in behaviour is associated with a single residue difference in NPR-1, a predicted G-protein-coupled neuropeptide receptor related to Neuropeptide Y receptors(2). Here we show that the NPR-1 isoform associated with solitary feeding acts in neurons exposed to the body fluid to inhibit social feeding. Furthermore, suppressing the activity of these neurons, called AQR, PQR and URX, using an activated K+ channel, inhibits social feeding. NPR-1 activity in AQR, PQR and URX neurons seems to suppress social feeding by antagonizing signalling through a cyclic GMP-gated ion channel encoded by tax-2 and tax-4. We show that mutations in tax-2 or tax-4 disrupt social feeding, and that tax-4 is required in several neurons for social feeding, including one or more of AQR, PQR and URX. The AQR, PQR and URX neurons are unusual in C. elegans because they are directly exposed to the pseudocoelomic body fluid(3). Our data suggest a model in which these neurons integrate antagonistic signals to control the choice between social and solitary feeding behaviour. ------------------- Key: 5513 Medline: 12410314 Authors: Syntichaki P;Xu K;Driscoll M;Tavernarakis N Title: Specific aspartyl and calpain proteases are required for neurodegeneration in C. elegans. Citation: Nature 419: 939-944 2002 Type: ARTICLE Genes: asp-1 asp-2 asp-3 asp-4 asp-5 asp-6 cad-1 clp-1 clp-2 clp-3 clp-4 clp-5 clp-6 clp-7 crt-1 daf-4 deg-1 deg-3 gsa-1 mec-4 tra-3 unc-52 Abstract: Necrotic cell death underlies the pathology of numerous human neurodegenerative conditions(1). In the nematode Caenorhabditis elegans, gain-of-function mutations in specific ion channel genes such as the degenerin genes deg-1 and mec-4, the acetylcholine receptor channel subunit gene deg-3 and the G(s) protein alpha-subunit gene gsa-1 evoke an analogous pattern of degenerative (necrotic-like) cell death in neurons that express the mutant proteins(2-6). An increase in concentrations of cytoplasmic calcium in dying cells, elicited either by extracellular calcium influx or by release of endoplasmic reticulum stores, is thought to comprise a major death-signalling event(7,8). But the biochemical mechanisms by which calcium triggers cellular demise remain largely unknown. Here we report that neuronal degeneration inflicted by various genetic lesions in C. elegans requires the activity of the calcium-regulated CLP-1 and TRA-3 calpain proteases and aspartyl proteases ASP-3 and ASP-4. Our findings show that two distinct classes of proteases are involved in necrotic cell death and suggest that perturbation of intracellular concentrations of calcium may initiate neuronal degeneration by deregulating proteolysis. Similar proteases may mediate necrotic cell death in humans. ------------------- Key: 5514 Medline: 12395827 Authors: Hoss S;Juttner I;Traunspurger W;Pfister G;Schramm KW;Steinberg CEW Title: Enhanced growth and reproduction of Caenorhabditis elegans (Nematoda) in the presence of 4-nonylphenol. Citation: Environmental Pollution 120: 169-172 2002 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans was exposed over a whole life-cycle (72 h) to several concentrations of 4-nonylphenol (NP; nominal concentrations: 0-350 mug/l). Growth and reproduction of C. elegans were enhanced at NP concentrations of 66 and 40 mug/l, respectively, with effects showing dose-response relationships. These stimulatory effects might be of ecological relevance in benthic habitats, where organisms can be exposed to high concentrations of NP. ------------------- Key: 5515 Medline: 12223405 Authors: Tsou MFB;Hayashi A;DeBella LR;McGrath G;Rose LS Title: LET-99 determines spindle position and is asymmetrically enriched in response to PAR polarity cues in C. elegans embryos. Citation: Development 129: 4469-4481 2002 Type: ARTICLE Genes: let-99 lrg-1 par-2 par-3 sDf22 Abstract: Asymmetric cell division depends on coordinating the position of the mitotic spindle with the axis of cellular polarity. We provide evidence that LET-99 is a link between polarity cues and the downstream machinery that determines spindle positioning in C. elegans embryos. In let-99 one-cell embryos, the nuclear-centrosome complex exhibits a hyperactive oscillation that is dynein dependent, instead of the normal anteriorly directed migration and rotation of the nuclear-centrosome complex. Furthermore, at anaphase in let-99 embryos the spindle poles do not show the characteristic asymmetric movements typical of wild type animals. LET-99 is a DEP domain protein that is asymmetrically enriched in a band that encircles P lineage cells. The LET-99 localization pattern is dependent on PAR polarity cues and correlates with nuclear rotation and anaphase spindle pole movements in wild-type embryos, as well as with changes in these movements in par mutant embryos. In particular, LET-99 is uniformly localized in one-cell par-3 embryos at the time of nuclear rotation. Rotation fails in spherical par-3 embryos in which the eggshell has been removed, but rotation occurs normally in spherical wild-type embryos. The latter results indicate that nuclear rotation in intact par-3 embryos is dictated by the geometry of the oblong egg and are consistent with the model that the LET-99 band is important for rotation in wild-type embryos. Together, the data indicate that LET-99 acts downstream of PAR-3 and PAR-2 to determine spindle positioning, potentially through the asymmetric regulation of forces on the spindle. ------------------- Key: 5516 Medline: 12396085 Authors: Wu ZX;Smith JV;Paramasivam V;Butko P;Khan I;Cypser JR;Luo Y Title: Gingko biloba extract EGb 761 increases stress resistance and extends life span of Caenorhabditis elegans. Citation: Cellular & Molecular Biology 48: 725-731 2002 Type: ARTICLE Genes: mev-1 Abstract: EGb 761, a standardized extract of Ginkgo biloba leaves, has been used in clinical trials for its beneficial effects on brain functions. In mammals, EGb 761 has been shown to enhance cognition, stress resistance, and longevity, but its molecular and cellular mechanisms are not known. In the present investigation, we used the model organism Caenorhabditis elegans to evaluate pharmacological effects of EGb 761 on aging. We tested the theory that EGb 761 augments the natural antioxidant system of C. elegans, and thus increases stress resistance and longevity. We found that treatment of the wild-type worms with EGb 761 extended their median life span by 8%. Amongst several purified components of EGb 76 1, the flavonoid tamarixetin showed the most dramatic effect: it extended the median life span by 25%. Furthermore, EGb 761 increased the wild type's resistance to acute oxidative and thermal stress by 33% and 25%, respectively. Treatment of the prematurely aging mutant worms mev-1 with EGb 761 increased their resistance to acute oxidative and thermal stress by 33% and 11%, respectively. It appears that oxidative stress, a major determinant of life span, as well as other types of stress, can be successfully counteracted by the Ginkgo biloba extract EGb 761. ------------------- Key: 5517 Medline: 12384612 Authors: Wei A;Yuan A;Fawcett G;Butler A;Davis T;Xu SY;Salkoff L Title: Efficient isolation of targeted Caenorhabditis elegans deletion strains using highly thermostable restriction endonucleases and PCR. Citation: Nucleic Acids Research 30: e110- 2002 Type: ARTICLE Genes: kqt-1 kqt-2 kqt-3 shk-1 shl-1 shw-1 shw-3 slo-2 Abstract: Reverse genetic approaches to understanding gene function would be greatly facilitated by increasing the efficiency of methods for isolating mutants without the reliance on a predicted phenotype. Established PCR-based methods of isolating deletion mutants are widely used for this purpose in Caenorhabditis elegans. However, these methods are inefficient at isolating small deletions. We report here a novel modification of PCR-based methods, employing thermostable restriction enzymes to block the synthesis of wild-type PCR product, so that only the deletion PCR product is amplified. This modification greatly increases the efficiency of isolating small targeted deletions in C.elegans. Using this method six new deletion strains were isolated from a small screen of approximately 400 000 haploid genomes, most with deletions <1.0 kb. Greater PCR detection sensitivity by this modification permitted similar to10-fold greater pooling of DNA samples, reducing the effort and reagents required for screens. In addition, effective suppression of non-specific amplification allowed multiplexing with several independent primer pairs. The increased efficiency of this technique makes it more practical for small laboratories to undertake gene knock-out screens. ------------------- Key: 5518 Medline: 12419225 Authors: Knight SW;Bass BL Title: The role of RNA editing by ADARs in RNAi. Citation: Molecular Cell 10: 809-817 2002 Type: ARTICLE Genes: adr-1 adr-2 Abstract: Adenosine deaminases that act on RNA (ADARs) are RNA-editing enzymes that deaminate adenosines to create inosines in double-stranded RNA (dsRNA). Here we demonstrate that ADARs are not required for RNA interference (RNAi) and that they do not antagonize the pathway to a detectable level when RNAi is initiated by injecting dsRNA. We find, however, that transgenes expressed in the somatic tissues of wild-type animals are silenced in strains with deletions in the two genes encoding ADARs, adr-1 and adr-2. Transgene-induced gene silencing in adr-1;adr-2 mutants depends on genes required for RNAi, suggesting that a dsRNA intermediate is involved. In wild-type animals we detect edited dsRNA corresponding to transgenes, and we propose that editing of this dsRNA prevents somatic transgenes from initiating RNAi in ------------------- Key: 5519 Medline: 12234669 Authors: Grisoni K;Martin E;Gieseler K;Mariol MC;Segalat L Title: Genetic evidence for a dystrophin-glycoprotein complex (DGC) in Caenorhabditis elegans. Citation: Gene 294: 77-86 2002 Type: ARTICLE Genes: dys-1 hlh-1 Abstract: Dystrophin is the product of the gene mutated in Duchenne muscular dystrophy (DMD). Neither the function of dystrophin nor the physiopathology of the disease have been clearly established so far. In mammals, the dystrophin-glycoprotein complex (DGC) includes dystrophin, as well as transmembrane and cytoplasmic proteins. Since Caenorhabditis elegans possesses a dystrophin-like gene (dys-1), we investigated whether homologues of the DGC members could also be found in the C. elegans genome. Conserved homologues were found for dystroglycan, delta/gamma-sarcoglyean and syntrophim. Divergent but related proteins were found for alpha- and beta-sarcoglycans. No sarcospan counterpart was found. The expression of the conserved homologues was inactivated using the RNA interference technique. Phenotypes similar to that of dys-1 were obtained, both in the wild-type background and in combination with other mutations. These results strongly suggest that a protein complex comprising ------------------- Key: 5520 Medline: 12386927 Authors: Nimmo R;Woollard A Title: Widespread organisation of C. elegans genes into operons: fact or function? Citation: BioEssays 24: 983-987 2002 Type: REVIEW Genes: apt-7 arr-1 cln-3.2 erm-1 Abstract: A recent report by Blumenthal et al.((1)) provides convincing evidence that at least 15% of Caenorhabditis elegans genes are co-transcribed within over a thousand operons. Polycistronic transcription of gene clusters is very rare in eukaryotes. The widespread occurrence of operons in C. elegans thus raises some interesting questions about the origin and function of these multigenic transcriptional-units. ------------------- Key: 5521 Medline: 12206804 Authors: Segalat L Title: Dystrophin and functionally related proteins in the nematode Caenorhabditis elegans. Citation: Neuromuscular Disorders 12: S105-S109 2002 Type: REVIEW Genes: dyb-1 dyc-1 dys-1 dys-2 dys-3 dys-4 dys-5 hlh-1 Abstract: We investigated the function of dystrophin in the nematode Caenorhabditis elegans. Although nematodes and mammals diverged early in evolution, their muscles share many structural and molecular features, thus rendering C. elegans relevant as a model to study muscle function. Dystrophin, dystrobrevin, dystroglycans and several sarcoglycans have conserved homologues in the genome of C. elegans. The major strength of the model comes from its genetic tractability, which allows the quick and easy manipulation of gene expression, either to inactivate genes, or to create transgenic animals. Over the last 2 years, work on C. elegans dystrophin has led to the identification of a putative new member of the dystrophin-glycoprotein complex, and has brought additional data suggesting that dystrophin mutations affect ion ------------------- Key: 5522 Medline: 12390481 Authors: Park JO;El Tarabily KA;Ghisalberti EL;Sivasithamparam K Title: Pathogenesis of Streptoverticillium albireticuli on Caenorhabditis elegans and its antagonism to soil-borne fungal pathogens. Citation: Letters in Applied Microbiology 35: 361-365 2002 Type: ARTICLE Genes: Abstract: Aims: To examine the biological activity of Streptoverticillium albireticuli. Methods: Isolation of S. albireticuli was carried out using the dry-heat technique. Nematicidal and pathogenic activity on Caenorhabditis elegans was measured by mortality in metabolites and colonization rate on fishmeal extract agar. Antifungal and enzymatic activities of S. albireticuli were measured by the agar plate method and the semidefined solid media method, respectively. Results: S. albireticuli showed strong nematicidal activity against C. elegans. Pathogenic activity was also evident with the colonized nematode by the isolate on fishmeal extract agar. It also showed antifungal activity against certain fungal pathogens such as Rhizoctonia solani, Phytophthora cinnamomi and Fusarium oxysporum. Significance and Impact of the Study: The discovery of an actinomycete showing pathogenic activity against the nematode may indicate the potential for it to be used as a biocontrol agent of parasitic nematodes, in addition to its ability to suppress fungal pathogens. ------------------- Key: 5523 Medline: 12163507 Authors: Zheng Q;Van Die I;Cummings RD Title: Molecular cloning and characterization of a novel alpha1,2-fucosyltransferase (CE2FT-1) from Caenorhabditis elegans. Citation: Journal of Biological Chemistry 277: 39823-39832 2002 Type: ARTICLE Genes: Abstract: Here we report the discovery of a unique fucosyltransferase (FT) in Caenorhabditis elegans. In studying the activities of FTs in extracts of adult C. elegans, we detected activity toward the unusual disaccharide acceptors Galbeta1-4Xyl-R and Galbeta1-6GlcNAc-R to generate products with the general structure Fucalpha1-2Galbeta1-R. We identified a gene encoding a unique alpha1,2FT (designated CE2FT-1), which contains an open reading frame encoding a predicted protein of 355 amino acids with the type 2 topology and domain structure typical of other glycosyltransferases. The predicted cDNA for CE2FT-1 has very low identity (5-10%) at the amino acid level to alpha1,2FT sequences in humans, rabbits, and mice. Recombinant CE2FT-1 expressed in human 293T cells has high alpha1,2FT activity toward the simple acceptor Galbeta-O-phenyl acceptor to generate Fucalpha1-2Galbeta-R, which in this respect resembles mammalian alpha1,2FTs. However, CE2FT-1 is otherwise completely different from known alpha1,2FTs in its acceptor specificity, since it is unable to fucosylate either Galbeta1-4GIcbeta-R or free lactose and prefers the unusual acceptors Galbetal-4XyIbeta-R and Galbeta1-6GlcNAc-R. Promoter analysis of the CE2FT-1 gene using green fluorescent protein reporter constructs demonstrates that CE2FT-1 is expressed in single cells of early stage embryos and exclusively in the 20 intestinal cells of L1-L-4 and adult worms. These and other results suggest that multiple fucosyltransferase genes in C. elegans may encode enzymes ------------------- Key: 5524 Medline: 12390250 Authors: Nagai-Tamai Y;Mizuno K;Hirose T;Suzuki A;Ohno S Title: Regulated protein-protein interaction between aPKC and PAR-3 plays an essential role in the polarization of epithelial cells. Citation: Genes to Cells 7: 1161-1171 2002 Type: ARTICLE Genes: par-3 Abstract: Background: Recent studies have revealed that aPKC (atypical protein kinase C), PAR-3 and PAR-6 play indispensable roles in the regulation of various cell polarization events, from worms to mammals, suggesting that they comprise an evolutionarily conserved protein machinery which is essential for cell polarization. The three proteins interact with each other to form a ternary complex and thus mutually regulate their functionality and localization. Here, we investigated the biochemical nature of the aPKC-PAR-3 interaction in detail to clarify its functional importance in cell polarity. Results: The highly conserved 26 amino acid sequence 816-841, in PAR-3 was found to be necessary and sufficient for the tight association with aPKC. Among several conserved serine/threonine residues within the region, aPKC preferentially phosphorylates serine-827 in vitro , and this phosphorylation reduces the stability of the PAR-3-aPKC interaction. Several analyses using a phospho-serine 827 specific antibody have established that this phosphorylation by aPKC occurs in vivo . Over-expression of a point mutant of PAR-3 (S827A), which is predicted to form a stable complex with aPKC, causes defects in the cell-cell contact-induced cell polarization of epithelial MDCK cells, similarly to a dominant negative mutant of aPKC. Conclusion: These results imply that serine 827 in the aPKC binding site of PAR-3 is a target of aPKC and that the regulated interaction between a protein kinase, aPKC, and its substrate, PAR-3, plays an essential ------------------- Key: 5525 Medline: 12381669 Authors: Jarriault S;Greenwald I Title: Suppressors of the egg-laying defective phenotype of sel-12 presenilin mutants implicate the CoREST corepressor complex in LIN-12/Notch signaling in C. elegans. Citation: Genes & Development 16: 2713-2728 2002 Type: ARTICLE Genes: glp-1 hda-1 hda-2 hda-3 hop-1 lin-12 spr-1 spr-5 Abstract: Presenilin is an essential component of the LIN-12/Notch signaling pathway and also plays a critical role in the genesis of Alzheimer's disease. Previously, a screen for suppressors of the egg-laying defective phenotype caused by partial loss of presenilin activity in Caenorhabditis elegans identified a number of new spr genes that are potentially involved in the regulation of LIN-12/Notch signaling or presenilin activity. Here we report the molecular identity of two spr genes, spr-1 and spr-5. Our genetic analysis indicates that loss of spr-1 elevates lin-12/Notch gene activity in many different cell fate decisions, suggesting that spr-1 is a negative regulator of LIN-12/Notch signaling. Sequence analysis revealed that spr-1 is an ortholog of human CoREST, a known corepressor. SPR-1 is localized to the nucleus and acts in a cell-autonomous manner; furthermore, human CoREST can substitute for SPR-1 in C. elegans. We also show that spr-5 encodes a homolog of p110b, another known member of the CoREST corepressor complex. Our results suggest that the CoREST corepressor complex might be functionally conserved in worms, and we discuss the potential role of SPR-1 and SPR-5 in the repression of transcription of genes involved in, or downstream of, LIN-12/Notch signal transduction. ------------------- Key: 5526 Medline: 12374613 Authors: Ishii N;Goto S;Hartman PS Title: Protein oxidation during aging of the nematode Caenorhabditis elegans. Citation: Free Radial Biology & Medicine 33: 1021-1025 2002 Type: REVIEW Genes: age-1 daf-2 daf-16 mev-1 old-1 old-2 sod-3 Abstract: The nematode Caenorhabditis elegans has proven a robust genetic model for studies of aging, including the roles of oxidative stress and protein damage. In this review, we focus on the genetics of select long-lived (e.g., age-1, daf-2, daf-16) and short-lived (e.g., mev-1) mutants that have proven useful in revealing the relationships that exist among oxidative stress, life span, and protein oxidation. The former are known to control an insulin/IGF-1-like pathway in C. elegans, while the latter affect mitochondrial function. ------------------- Key: 5527 Medline: 12367627 Authors: Broadie KS;Richmond JE Title: Establishing and sculpting the synapse in Drosophila and C. elegans. Citation: Current Opinion in Neurobiology 12: 491-498 2002 Type: REVIEW Genes: ptp-3 sad-1 spc-1 syd-2 unc-16 unc-25 unc-70 Abstract: Genetic approaches in flies and worms continue to dissect the intricate molecular machinery of chemical synapses. Investigations carried out in the last year provide important new insights into the development and modulation of the presynaptic active zones and postsynaptic receptor fields mediating synaptic function. Mutant screens have identified overlapping gene classes mediating synaptogenesis. The leucocyte common antigen-related receptor tyrosine phosphatase interacts with liprin in the formation of the active zone. Spectrins are essential for the spatial restriction of synaptic proteins to define active zones. Glutamate acts as a negative regulator of its cognate postsynaptic receptor to sculpt receptor field size. Finally, protein translation and degradation regulation emerge as possible key regulators of synaptic ------------------- Key: 5528 Medline: 12367628 Authors: Richmond JE;Broadie KS Title: The synaptic vesicle cycle: exocytosis and endocytosis in Drosophila and C. elegans. Citation: Current Opinion in Neurobiology 12: 499-507 2002 Type: REVIEW Genes: ehs-1 ric-4 slo-1 snt-1 unc-10 unc-13 unc-31 unc-41 unc-64 Abstract: Advances in the study of Drosophila melanogaster and Caenorhabditis elegans have provided key insights into the processes of neurotransmission and neuromodulation. Work in the past year has revealed that Unc-13 and Rab3a-interacting molecule regulate the conformational state of syntaxin to prime synaptic vesicle fusion. Analyses of synaptotagmin support its role as a putative calcium sensor triggering vesicular fusion and highlight the possible role of SNARE complex oligomerization in the fusion mechanism. Characterization of endophilin mutants demonstrates that kiss-and-run endocytosis is a major component of synaptic vesicle recycling. In neuromodulation, dcaps mutants provide the first genetic insight into possible roles of the CAPS protein in mediating dense core vesicle fusion and modulating synaptic ------------------- Key: 5529 Medline: 12372436 Authors: Higa S;Maeda N;Kenmochi N;Tanaka T Title: Location of 2'-O-methyl nucleotides in 26S rRNA and methylation guide snoRNAs in Caenorhabditis elegans. Citation: Bichemical and Biophysical Research Communications 297: 1344-1349 2002 Type: ARTICLE Genes: Abstract: Many nucleotides in rRNAs are modified. We devised a method to locate 2'-O-methyl nucleotide residues using a conventional DNA sequencer. We found 38 2'-O-methyl nucleotides in the 26S rRNA of Caenorhabditis elegans using this method. Fourteen of the 38 residues are conserved in both human and yeast rRNAs and 14 residues are conserved in either human or yeast rRNA. The remaining 10 nucleotides are uniquely methylated in C elegans 26S rRNA. We searched the C elegans genomic sequence for small nucleolar RNAs (snoRNAs), which guide the methylation of ribose residues, and predicted 18 snoRNA sequences that are expected to guide the methylation of some of these nucleotide residues. ------------------- Key: 5530 Medline: Authors: McCarter JP;Clifton SW;Bird DM;Waterston RH Title: Nematode gene sequences, update for June 2002. Citation: Journal of Nematology 34: 71-74 2002 Type: ARTICLE Genes: Abstract: High-throughput sequencing is revolutionizing molecular nematology by providing the sequences of thousands of genes never before characterized. The most rapid and cost-effective route to gene discovery for nematode genomes is the generation of expressed sequence tags (ESTs), single pass reads from random cDNA library clones that provide 300 to 600 nucleotides of sequence form a gene. Projects are currently under way at Washington University's Genome Sequencing Center that will generate 235,000 5'ESTs from approximately 25 nematode species by 2003 (119,448 to date). Additionally, the Sanger Institute and Edinburgh University are producing 80,000 ESTs from seven species (10,772 to date). New sequences are immediately submitted to the dbEST (database of expressed sequence tags) division of GenBank and are also available from a number of parasite-specialized Web sites (Table 1). Strategies for using ESTs, as well as discussions of the strengths and weaknesses of EST data, are available from reviews (Blaxter et al., 1999; Marra et al., 1998; McCarter et al., 200a); ------------------- Key: 5531 Medline: 12244070 Authors: Kato T;Fujita K;Takeuchi M;Kobayashi K;Natsuka S;Ikura K;Kumagai H;Yamamoto K Title: Identification of an endo-B-N-acetylglucosaminidase gene in Caenorhabditis elegans and its expression in Escherichia coli. Citation: Glycobiology 12: 581-587 2002 Type: ARTICLE Genes: Abstract: We report the identification, molecular cloning, and characterization of an endo-beta-N-acetylglucosaminidase from the nematode Caenorhabditis elegans. A search of the C. elegans genome database revealed the existence of a gene exhibiting 34% identity to Mucor hiemalis (a fungus) endo-beta-N-acetylglucosaminidase (Endo-M). Actually, the C. elegans extract contained endo-beta-N-acetylglucosaminidase activity. The putative cDNA for the C. elegans endo-beta-N-acetylglucosaminidase (Endo-CE) was amplified by polymerase chain reaction from the Uni-ZAP XR library, cloned, and sequenced. The recombinant Endo-CE expressed in Escherichia coli exhibited substrate specificity mainly for high-mannose type oligosaccharides. Man8GlcNAc2 was the best substrate for Endo-CE, and Man3GlcNAc2 was also hydrolyzed. Biantennary complex type oligosaccharides were poor substrates, and triantennary complex substrates were not hydrolyzed. Its substrate specificity was similar to those of Endo-M and endo-beta-N-acetylglucosaminidase from hen oviduct. Endo-CE was confirmed to exhibit transglycosylation activity, as seen for some microbial endo-beta-N-acetylglucosaminidases. This is the first report of the molecular cloning of an endo-beta-N-acetylglucosaminidase gene from a multicellular organism, which shows the possibility of using this well-characterized nematode as a model system for elucidating the role of this enzyme. ------------------- Key: 5532 Medline: 12388766 Authors: Bjork P;Bauren G;Jin S;Tong YG;Burglin TR;Hellman U;Wieslander L Title: A novel conserved RNA-binding domain protein, RBD-1, is essential for ribosome biogenesis. Citation: Molecular Biology of the Cell 13: 3683-3695 2002 Type: ARTICLE Genes: rbd-1 Abstract: Synthesis of the ribosomal subunits from pre-rRNA requires a large number of trans-acting proteins and small nucleolar ribonucleoprotein particles to execute base modifications, RNA cleavages, and structural rearrangements. We have characterized a novel protein, RNA-binding domain-1 (RBD-1), that is involved in ribosome biogenesis. This protein contains six consensus RNA-binding domains and is conserved as to sequence, domain organization, and cellular location from yeast to human. RBD-1 is essential in Caenorhabditis elegans. In the dipteran Chironomus tentans, RBD-1 (Ct-RBD-1) binds pre-rRNA in vitro and anti-Ct-RBD-1 antibodies repress pre-rRNA processing in vivo. Ct-RBD-1 is mainly located in the nucleolus in an RNA polymerase I transcription-dependent manner, but it is also present in discrete foci in the interchromatin and in the cytoplasm. In cytoplasmic extracts, 20-30% of Ct-RBD-1 is associated with ribosomes and, preferentially, with the 40S ribosomal subunit. Our data suggest that RBD-1 plays a role in structurally coordinating pre-rRNA during ribosome biogenesis and that this function is conserved in all eukaryotes. ------------------- Key: 5533 Medline: Authors: Yassin L;Samson AO;Halevi S;Eshel M;Treinin M Title: Mutations in the extracellular domain and in the membrane-spanning domains interfere with nicotinic acetylcholine receptor maturation. Citation: Biochemistry 41: 12329-12335 2002 Type: ARTICLE Genes: deg-3 des-2 Abstract: The deg-3 (u662) mutation is a degeneration-causing mutation in a Caenorhabditis elegans nicotinic acetylcholine receptor. In a large screen for mutations that suppress the deleterious effects this mutation we identified 32 mutations in the deg-3 gene. Among these, 11 are missense mutations, affecting seven residues within the extracellular domain or the membrane-spanning domains. All of these mutations greatly reduce the degeneration-causing activity of deg-3 (u662). All but one of these mutations cause defective localization of the DEG-3 protein, as seen in immunohistochemical analysis. Thus our screen identifies multiple residues within the nicotinic acetylcholine receptor needed for normal folding, assembly, or trafficking of this receptor. Interestingly, these mutations lead to distinct localization defects suggesting differences in their effect on DEG-3's maturation process. Specifically, mutation sin the extracellular domain lead to a phenotype more severe than mutations in the membrane-spanning domains. Differences in the effects of the mutations are also predicted by homology-based modeling, showing that some mutations in the extracellular domain are likely to disrupt the native fold of the protein, while other are likely to disrupt trafficking. ------------------- Key: 5534 Medline: 12324451 Authors: Jonassen T;Marbois BN;Faull KF;Clarke CF;Larsen PL Title: Development and fertility in Caenorhabditis elegans clk-1 mutants depend upon transport of dietary coenzyme Q8 to mitochondria. Citation: Journal of Biological Chemistry 277: 45020-45027 2002 Type: ARTICLE Genes: clk-1 Abstract: The Caenorhabditis elegans clk-1 mutants lack coenzyme Q, and instead accumulate the biosynthetic intermediate demethoxy-Q(9) (DMQ(9)). clk-1 animals grow to reproductive adults, albeit slowly, if supplied with Q(8)-containing Escherichia coli. However, if Q is withdrawn from the diet, clk-1 animals either arrest development as young larvae or become sterile adults depending upon the stage at the time of the withdrawal. To understand this stage-dependent response to a Q-less diet, the quinone content was determined during development of wild-type animals. The quinone content varies in the different developmental stages in wild-type fed Q(8)-replete E. coli. The amounts peak at the second larval stage, which coincides with the stage of arrest of clk-1 larvae fed a Q-less diet from hatching. Levels of the endogenously synthesized DMQ(9) are high in the clk1(qmM30)-arrested larvae and sterile adults fed Q-less food. Comparison of quinones from animals fed a Q-replete or a Q-less diet establishes that the Q(8) present is assimilated from the E. coli. Furthermore, this E. colispecific Q(8) is present in mitochondria isolated from fertile clk-1(qm30) adults fed a Q-replete diet. These results suggest that the uptake and transport of dietary Q(8) to mitochondria prevent the arrest and sterility phenotypes of clk-1 mutants and that DMQ is not functionally equivalent to Q. ------------------- Key: 5535 Medline: 12410296 Authors: Sokolowski MB Title: Social eating for stress. Citation: Nature 419: 893-894 2002 Type: REVIEW Genes: npr-1 ocr-2 osm-9 tax-2 tax-4 Abstract: Behavioral ecologists have shown that many animals form social groups in conditions. Neurobiological evidence for this behaviour has now been discovered in the nematode worm, Caenorhabditis elegans. On pages 899 and 925 of this issue, de Bono et al. and Coates and de Bono present striking results on the genetic, molecular and neural mechanisms underlying nematode social feeding. These discoveries provide tantalizing insights into the effects of stress in social groupings. ------------------- Key: 5536 Medline: Authors: Semenza GL Title: HIF-1, O(2), and the 3 PHDs: how animal cells signal hypoxia to the nucleus. Citation: Cell 107: 1-3 2002 Type: REVIEW Genes: egl-9 vhl-1 Abstract: Hypoxia-inducible factor 1 (HIF-1) is a global regulator of cellular and systemic O2 homeostasis in animals. A molecular basis for O2 regulated expression of the HIF-1 alpha subunit has now been determined, providing a mechanism for changes in gene expression in response to changes in cellular oxygenation. ------------------- Key: 5537 Medline: 12387956 Authors: Barbour V Title: Celebrating death - the 2002 Nobel prize in physiology or medicine. Citation: The Lancet 360: 1117- 2002 Type: REVIEW Genes: Abstract: The overwhelming complexity of higher organisms can make it hard to know where to begin to understand them. The three scientists who share this year's Nobel prize for physiology or medicine, Sydney Brenner (Salk Institute, La Jolla, CA, USA), John Sulston (Wellcome Trust Sanger Institute, Hinxton, UK), and Robert Horvitz (Massachusetts Institute of Technology, Boston, MA, USA), all chose to study a far simpler organisms - the nematode worm Caenorhabditis elegans. Although multicellular, this organism reproduces rapidly and is transparent, so that each developmental stage can be seen clearly without the need for dissection. ------------------- Key: 5538 Medline: 12360194 Authors: Baehrecke EH Title: How death shapes life during development. Citation: Nature Reviews Molecular Cell Biology 3: 779-787 2002 Type: REVIEW Genes: bir-1 bir-2 ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ced-12 csp-1 csp-2 egl-1 tra-1 Abstract: The formation of an adult animal from a fertilized embryo involves the production and death of cells. Surprisingly, many cells are produced during development with an ultimate fate of death, and defects in programmed cell death can result in developmental abnormalities. Recent studies indicate that cells can die by many different mechanisms, and these differences have implications for proper animal development and disorders such as cancer and autoimmunity. ------------------- Key: 5539 Medline: Authors: Wallis JG;Watts JL;Browse J Title: Polyunsaturated fatty acid synthesis: what will they think of next? Citation: Trends in Biochemical Sciences 27: 467-473 2002 Type: REVIEW Genes: elo-1 Abstract: Polyunsaturated fatty acids have crucial roles in membrane biology and signaling processes in most living organisms. However, it is only recently that molecular genetic approaches have allowed detailed studies of the enzymes involved in their synthesis. New evidence has revealed a range of pathways in different organisms. These include a complex sequence for synthesis of docosahexaenoic acid (22:6) in mammals and a polyketide synthase pathway in marine microbes. ------------------- Key: 5540 Medline: 12391314 Authors: Hwang HY;Horvitz HR Title: The SQV-1 UDP-glucuronic acid decarboxylase and the SQV-7 nucleotide-sugar transporter may act in the Golgi apparatus to affect Caenorhabditis elegans vulval morphogenesis and embryonic development. Citation: Proceedings of the National Academy of Sciences 99: 14218-14223 2002 Type: ARTICLE Genes: sqv-1 sqv-7 eDf18 eDf19 Abstract: Recent findings indicate that glycosaminoglycans can play important roles in animal development. The genes sqv-3,-7, and -8, which are necessary for vulval morphogenesis in Caenorhabditis elegans, affect the biosynthesis of chondroitin and heparan sulfate glycosaminoglycans. We cloned sqv-1 and showed that the SQV-1 protein is a type II transmembrane protein that functions as a UDP-glucuronic acid decarboxylase. SQV-1 localizes to punctate cytoplasmic compartments and colocalizes with the SQV-7 nucleoticle-sugar transporter, which probably acts in the Golgi apparatus. SQV-1 and SQV-7 are both expressed in the vulva and in oocytes, where they likely act in vulval morphogenesis and embryonic development, respectively. Progeny of sqv-7 and sqv-1 null mutants fail to initiate cytokinesis, possibly because they are unable to separate the plasma membrane from the eggshell, a defect analogous to that of incomplete vulval invagination. ------------------- Key: 5541 Medline: 12391315 Authors: Hwang HY;Horvitz HR Title: The Caenorhabditis elegans vulval morphogenesis gene sqv-4 encodes a UDP-glucose dehydrogenase that is temporally and spatially regulated. Citation: Proceedings of the National Academy of Sciences 99: 14224-14229 2002 Type: ARTICLE Genes: emo-1 lin-11 lin-12 sqv-1 sqv-3 sqv-4 sqv-7 sqv-8 sDf35 Abstract: The development of the Caenorhabditis elegans vulva requires the involution of epithelial cells and provides a model for organ morphogenesis. Mutations in C elegans sqv (squashed vulva) genes affect both vulval morphogenesis and embryonic development. We found that sqv-4 encodes a protein similar to UDPglucose dehydrogenases and showed that the SQV-4 protein specifically catalyzes the conversion of UDP-glucose to UDP-glucuronic acid, which is essential for the biosynthesis of chondroitin and heparan sulfate proteoglycans. SQV-4 is expressed in the vulva and in oocytes, among many other cells, and SQV-4 levels are dramatically increased in a specific subset of vulval cells during vulval morphogenesis. We propose that the regulation of UDP-glucuronic acid production in a specific subset of vulval cells helps determine the shape of the vulva. ------------------- Key: 5542 Medline: Authors: Whited JL;Garrity PA Title: Specifying axon identity with syd-1. Citation: Nature Neuroscience 5: 1107-1108 2002 Type: REVIEW Genes: syd-1 Abstract: A molecule that may be important for sorting presynaptic components into the developing axon is now revealed by a study using the genetic tools available in C. elegans. ------------------- Key: 5543 Medline: 12379863 Authors: Hallam SJ;Goncharov A;McEwen J;Baran R;Jin Y Title: SYD-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains, specifies axon identity in C. elegans. Citation: Nature Neuroscience 5: 1137-1146 2002 Type: ARTICLE Genes: lin-6 lin-7 snb-1 syd-1 syd-2 unc-10 unc-14 unc-25 unc-30 unc-49 unc-104 Abstract: Axons are defined by the presence of presynaptic specializations at specific locations. We show here that loss-of-function mutations in the C. elegans gene syd-1 cause presynaptic specializations to form in the dendritic processes of GABA-expressing motor neurons during initial differentiation. At a later developmental stage, however, syd-1 is not required for the polarity respecification of a subset of these neurons. The SYD-1 protein contains PDZ, C2 and rho-GTPase activating protein (GAP)-like domains, and is localized to presynaptic terminals in mature neurons. A truncated SYD-1 that lacks the rhoGAP domain interferes with neurite outgrowth and guidance. Our data indicate that syd-1 may be involved in specifying axon identity during initial polarity acquisition. ------------------- Key: 5544 Medline: 12379860 Authors: Yu TW;Hao JC;Lim W;Tessier-Lavigne M;Bargmann CI Title: Shared receptors in axon guidance: SAX-3/Robo signals via UNC-34/Enabled and a Netrin-independent UNC-40/DCC Citation: Nature Neuroscience 5: 1147-1154 2002 Type: ARTICLE Genes: sax-3 slt-1 unc-6 unc-34 unc-40 Abstract: The C. elegans SAX-3/Robo receptor acts in anterior-posterior, dorsal-ventral and midline guidance decisions. Here we show that SAX-3 signaling involves the C. elegans Enabled protein UNC-34 and an unexpected Netrin-independent function of the Netrin receptor UNC-40/DCC. Genetic interactions with gain- and loss-of-function mutations suggest that unc-34 and unc-40 act together with sax-3 in several guidance decisions, but the C. elegans Netrin gene unc-6 does not act in the same genetic pathways. Within the migrating axon, sax-3, unc-34 and unc-40 all act cell-autonomously. Our results support a role for UNC-34/Enabled proteins in SAX-3-mediated repulsion, and show that UNC-40/DCC can potentiate SAX-3/Robo signaling via a mechanism that may involve direct binding of the two guidance receptors. A combinatorial logic dictates alternative functions for UNC-40/DCC, which can act in attraction to UNC-6/Netrin, repulsion from Netrin (with UNC-5), or repulsion from Slit ------------------- Key: 5545 Medline: 12381812 Authors: Jospin M;Mariol MC;Segelat L;Allard B Title: Characterization of K+ currents using an in situ patch clamp technique in body wall muscle cells from Caenorhabditis elegans. Citation: Journal of Physiology 544: 373-384 2002 Type: ARTICLE Genes: slo-1 slo-2 twk-18 Abstract: The properties of K+ channels in body wall muscle cells acutely dissected from the nematode Caenorhabditis elegans were investigated at the macroscopic and unitary level using an in situ patch clamp technique. In the whole-cell configuration, depolarizations to potentials positive to -40 mV gave rise to outward currents resulting from the activation of two kinetically distinct voltage-dependent K+ currents: a fast activating and inactivating 4-aminopyridine-sensitive component and a slowly activating and maintained tetraethylammonium-sensitive component. In cell-attached patches, voltage-dependent K+ channels, with unitary conductances of 34 and 80 pS in the presence of 5 and 140 mm external K+, respectively, activated at membrane potentials positive to -40 mV. Excision revealed that these channels corresponded to Ca2+-activated K+ channels exhibiting an unusual sensitivity to internal Cl- and whose activity progressively decreased in inside-out conditions. After complete run-down of these channels, one third of inside-out patches displayed activity of another Ca2+-activated K+ channel of smaller unitary conductance (6 pS at 0 mV in the presence of 5 mm external K+). In providing a detailed description of native K+ currents in body wall muscle cells of C. elegans, this work lays the basis for further comparisons with mutants to assess the function of K+ channels in this model organism that is highly amenable to molecular and classical genetics. ------------------- Key: 5546 Medline: 12381307 Authors: Flaherty DB;Gernert KM;Shmeleva N;Tang X;Mercer KB;Borodovsky M;Benian GM Title: Titins in C. elegans with unusual features: coiled-coil domains, novel regulation of kinase activity and two new possible elastic regions. Citation: Journal of Molecular Biology 323: 533-549 2002 Type: ARTICLE Genes: atn-1 exp-2 unc-22 unc-89 Abstract: We report that there are previously unrecognized proteins in Caenorhabditis elegans that are similar to the giant muscle proteins called titins, and these are encoded by a single similar to90 kb gene. The gene structure was predicted by GeneMark.hmm and then experimentally verified. The Ce titin gene encodes polypeptides of 2.2 MDa, 1.2 MDa and 301 kDa. The 2.2 MDa isoform resembles twitchin and UNC-89 in that it contains multiple Ig (56) and FnIII (11) domains, and a single protein kinase domain. In addition, however, the 2.2 MDa isoform contains four classes of short, 14-51 residue, repeat motifs arranged mostly in many tandem copies. One of these tandem repeat regions is similar to the PEVK regions of vertebrate and fly titins. As the PEVK region is one of the main elastic elements of the titins and is also composed of short tandem repeats, this suggests that the repeat motifs in the Ce titins may have a similar elastic function. An interesting aspect of the two largest Ce titin isoforms, is that in contrast to other members of the twitchin/titin family, there are multiple regions which are likely to form coiled-coil structure. In transgenic animals, the first similar to 100 residues of the largest isoforms targets to dense bodies, the worm analogs of Z-discs. Anti-Ce titin antibodies show localization to muscle I-bands beginning at the L2-L3 larval stages and this pattern continues into adult muscle. Ce titins may not have a role in early myofibril assembly: (1) Ce titins are too short to span half a sarcomere, and the onset of their expression is well after the initial assembly of thick filaments. (2) Ce titins are not localized to I-bands in embryonic or L1 larval muscle. The Ce titin protein kinase domain is most similar to the kinase domains of the twitchins and projectin. The Ce titin kinase has protein kinase activity in vitro, and this ------------------- Key: 5547 Medline: 12391025 Authors: Jospin M;Jacquemond V;Mariol MC;Segalat L;Allard B Title: The L-type voltage-dependent Ca2+ channel EGL-19 controls body wall muscle function in Caenorhabditis elegans. Citation: Journal of Cell Biology 159: 337-347 2002 Type: ARTICLE Genes: egl-19 Abstract: Caenorhabditis elegans is a powerful model system widely used to investigate the relationships between genes and complex behaviors like locomotion. However, physiological studies at the cellular level have been restricted by the difficulty to dissect this microscopic animal. Thus, little is known about the properties of body wall muscle cells used for locomotion. Using in situ patch clamp technique, we show that body wall muscle cells generate spontaneous spike potentials and develop graded action potentials in response to injection of positive current of increasing amplitude. in the presence of K+ channel blockers, membrane depolarization elicited Ca2+ currents inhibited by nifedipine and exhibiting Ca2+-dependent inactivation. Our results give evidence that the Ca2+ channel involved belongs to the L-type class and corresponds to EGL-19, a putative Ca2+ channel originally thought to be a member of this class on the basis of genomic data. Using Ca2+ fluorescence imaging on patch-clamped muscle cells, we demonstrate that the Ca2+ transients elicited by membrane depolarization are under the control of Ca2+ entry through L-type Ca2+ channels in reduction of function egl-19 mutant muscle cells, Ca2+ currents displayed slower activation kinetics and provided a significantly smaller Ca2+ entry, whereas the threshold for Ca2+ transients was shifted toward positive membrane potentials. ------------------- Key: 5548 Medline: 12399386 Authors: Azevedo RBR;Keightley PD;Lauren-Maatta C;Vassilieva LL;Lynch M;Leroi AM Title: Spontaneous mutational variation for body size in Caenorhabditis elegans. Citation: Genetics 165: 755-765 2002 Type: ARTICLE Genes: Abstract: We measured the impact of new mutations on genetic variation for body size in two independent sets of C. elegans spontaneous mutation-accumulation (MA) lines, derived from the N2 strain, that had been maintained by selfing for 60 or 152 generations. The two sets of lines gave broadly consistent results. The change of among-line genetic variation between cryopreserved controls and the MA lines implied that broad sense heritability increased by 0.4% per generation. Overall, MA reduced mean body size by similar to0.1% per generation. The genome-wide rate for mutations with detectable effects on size was estimated to be similar to0.0025 per haploid genome per generation, and their mean effects were similar to20%. The proportion of mutations that increase body size was estimated by maximum likelihood to be no more than 20%, suggesting that the amount of mutational variation available for selection for increased size could be quite small. This hypothesis was supported by an artificial selection experiment on adult body size, started from a single highly inbred N2 individual. We observed a strongly asymmetrical response to selection of a magnitude consistent with the input of mutational variance observed in the MA experiment. ------------------- Key: 5549 Medline: 12399387 Authors: Hodgkin J Title: Exploring the envelope: systematic alteration in the sex-determination system of the nematode Caenorhabditis elegans. Citation: Genetics 162: 767-780 2002 Type: ARTICLE Genes: dpy-26 dpy-27 fem-1 fem-2 fem-3 fog-1 fog-2 her-1 sdc-1 sdc-2 sdc-3 sup-34 tra-1 tra-2 tra-3 xol-1 eDp25 eT1 eT5 mnT12 Abstract: The natural sexes of the nematode Caenorhabditis elegans are the self-fertilizing hermaphrodite (XX) and the male (XO). The underlying genetic pathway controlling sexual phenotype has been extensively investigated. Mutations in key regulatory genes have been used to create a series of stable populations in which sex is determined not by X chromosome dosage, but in a variety of other ways, many of which mimic the diverse sex-determination systems found in different animal species. Most of these artificial strains have male and female sexes. Each of seven autosomal genes can be made to adopt a role as the primary determinant of sex, and each of the five autosomes can carry the primary determinant, thereby becoming a sex chromosome. Strains with sex determination by fragment chromosomes, episomes, compound chromosomes, or environmental factors have also been constructed. The creation of these strains demonstrates the ease with which one sex-determination system can be transformed into another. ------------------- Key: 5550 Medline: 12442775 Authors: Gerhardt A;Schmidt S;Hoss S Title: Measurement of movement patterns of Caenorhabditis elegans (Nematoda) with the Multispecies Freshwater Biomonitor (MFB) - a potential new method to study a behavioral toxicity parameter of nematodes i Citation: Environmental Pollution 120: 513-516 2002 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans receives increasing attention in sediment ecotoxicology and new toxicity tests with sensitive test parameters are under development. In this study, the motility of C. elegans could be measured for the first time online in sediment, using the Multispecies Freshwater Biomonitor. Whereas single nematodes could not be recorded, groups of 10 nematodes gave typical locomotive signals in different media (water, agar, sediment) with comparable precision and accuracy. The results of this study encourage to develop a new rapid online whole-sediment toxicity test with behaviour as ------------------- Key: 5551 Medline: 12401168 Authors: Kindt KS;Tam T;Whiteman S;Schafer WR Title: Serotonin promotes G(o)-dependent neuronal migration in Caenorhabditis elegans. Citation: Current Biology 12: 1738-1747 2002 Type: ARTICLE Genes: bas-1 cat-1 cat-2 cat-4 dgk-1 egl-8 egl-30 goa-1 tph-1 Abstract: Background: The directed migration of neurons during development requires attractive and repulsive cues that control the direction of migration as well as permissive cues that potentiate cell motility and responsiveness to guidance molecules. Results: Here, we show that the neurotransmitter serotonin functions as a permissive signal for embryonic and postembryonic neuronal migration in the nematode C. elegans. In serotonin-deficient mutants, the migrations of the ALM, BDU, SDOR, and AVM neurons were often foreshortened or misdirected, indicating a serotonin requirement for normal migration. Moreover, exogenous serotonin could restore motility to AVM neurons in serotonin-deficient mutants as well as induce AVM-like migrations in the normally nonmotile neuron PVM; this indicates that serotonin was functioning as a permissive cue to enable neuronal motility. The migration defects of serotonin-deficient mutants were mimicked by ablations of serotonergic neuroendocrine cells, implicating humoral release of serotonin in these processes. Mutants defective in G. and G. signaling, or in N-type voltage-gated calcium channels, showed migration phenotypes similar to serotonin-deficient mutants, and these molecules appeared to genetically function downstream of serotonin in the control of neuronal migration. Conclusions: Thus, serotonin is important for promoting directed neuronal migration in the developing C. elegans nervous system. We hypothesize that serotonin may promote cell motility through G protein-dependent modulation of voltage-gated calcium channels in the migrating cell. ------------------- Key: 5552 Medline: 12223207 Authors: Arkblad EL;Egorov M;Shakhparonov M;Romanova L;Polzikov M;Rydstrom J Title: Expression of proton-pumping nicotinamide nucleotide transhydrogenase in mouse, human brain and C. elegans. Citation: Comparative Biochemistry & Physiology B 133: 13-21 2002 Type: ARTICLE Genes: nnt-1 Abstract: Proton-translocating nicotinamide nucleotide transhydrogenase is located in the mitochondrial inner membrane and catalyzes the reduction of NADP(+) by NADH to NADPH and NAD(+). The present investigation describes the expression of the transhydrogenase gene in various mouse organs, subsections of the human brain and Caenorhabditis elegans. In the mouse, the expression was highest in heart tissue (100%) followed by kidney (64%), testis (52%), adrenal gland (41%), liver (35%), pancreas (34%), bladder (26%), lung (25%), ovary (21%) and brain (14%). The expression in brain tissue was further investigated in the human brain which showed a distribution that apparently varied as a function of neuronal density, a result that was supported by estimations of expression in C elegans using Green Fluorescent Protein (GFP) controlled by the transhydrogenase promoter. GFP-expressing C elegans lines showed a clear concentration of fluorescence to the gut, the pharyngeal-intestinal valve and certain neurons. It is concluded that the transhydrogenase gene is expressed to various extents in all cell types in mouse, human and C elegans. ------------------- Key: 5553 Medline: 12437115 Authors: Takahashi M;Iwasaki H;Inoue H;Takahashi K Title: Reverse genetic analysis of the Caenorhabditis elegans 26S proteasome subunits by RNA interference. Citation: Biological Chemistry 383: 1263-1266 2002 Type: ARTICLE Genes: Abstract: Reverse genetic analysis was performed on the Caenorhabditis elegans 26S proteasome subunit genes by doublestranded RNAmediated interference (RNAi). Embryonic and postembryonic lethality was caused by interference of all of the eight tested 20S core subunits and all of the 19S regulatory particle subunits except for CeRpn9, CeRpn10, and Ce Rpn12, where RNAi caused no abnormality. However, synthetic suppression of CeRpn10 and CeRpn12 was lethal, whereas neither the combination of Ce Rpn9 with CeRpn10 nor with CeRpn12 resulted in abnormalities in RNAi. These results indicate that the 26S proteasome is indispensable for embryogenesis and postembryonic development, although Ce Rpn9, CeRpn10, and CeRpn12 are not essential, at least under the conditions used. CeRpn10 and Ce Rpn12 are considered to compensate for the suppression ------------------- Key: 5554 Medline: Authors: Adams JM;Cory S Title: Apoptosomes: engines for caspase activation. Citation: Current Opinion in Cell Biology 14: 715-720 2002 Type: REVIEW Genes: ced-3 ced-4 ced-9 egl-1 Abstract: Activation of the caspases that initiate apoptosis typically requires cognate scaffold proteins, including CED-4 in Caenorhabditis elegans, Apaf-1 in mammals and Dark in Drosophila. Each scaffold protein oligomerizes procaspases into a complex called the apoptosome, but the regulation and biological roles of the scaffolds differ. Whereas CED-4 is restrained by the Bcl-2 homologue CED-9, Apaf-1 is inhibited by its WD40 repeat region, until it is activated by cytochrome c, derived from damaged mitochondria. Although Dark also has a WD40 region, its activation does not seem to involve cytochrome c. CED-4 is essential for apoptosis in the worm and Dark for many apoptotic responses in the fly, but the Apaf-1/caspase-9 system probably amplifies rather than initiates the ------------------- Key: 5555 Medline: Authors: Krieser RJ;White K Title: Engulfment mechanism of apoptotic cells. Citation: Current Opinion in Cell Biology 14: 734-738 2002 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-5 ced-6 ced-7 ced-10 ced-12 nuc-1 Abstract: Apoptotic cells are engulfed and removed by phagocytes. This ensures proper development of the organism and can modulate immune responses. Recent studies have examined molecules on apoptotic cells, such as phosphatidylserine, which may signal for engulfment through multiple receptors. Apoptotic recognition mechanisms may vary with the apoptotic and engulfing cell type, and even with the age of ------------------- Key: 5556 Medline: Authors: Xue D;Wu YC;Shah MS Title: Programmed cell death in C. elegans: the genetic framework. Citation: Frontiers in Molecular Biology. Apoptosis. MD Jacobson and N McCarthy (eds). 40: 23-55 2002 Type: REVIEW Genes: Abstract: ------------------- Key: 5557 Medline: 12413907 Authors: Eimer S;Donhauser R;Baumeister R Title: The Caenorhabditis elegans presenilin sel-12 is required for mesodermal patterning and muscle function. Citation: Developmental Biology 251: 178-192 2002 Type: ARTICLE Genes: cog-2 egl-15 hlh-8 hop-1 lin-12 myo-3 sel-12 ttx-3 unc-54 Abstract: Mutations in presenilin genes impair Notch signalling and, in humans, have been implicated in the development of familial Alzheimer's disease. We show here that a reduction of the activity of the Caenorhabditis elegans presenilin sel-12 results in a late defect during sex muscle development. The morphological abnormalities and functional deficits in the sex muscles contribute to the egg-laying defects seen in sel-12 hermaphrodites and to the severely reduced mating efficiency of sel-12 males. Both defects can be rescued by expressing sel-12 from the h1h-8 promoter that is active during the development of the sex muscle-specific M lineage, but not by expressing sel-12 from late muscle-specific promoters. Both weak and strong sel-12 mutations cause defects in the sex muscles that resemble the defects we found in lin-12 hypomorphic alleles, suggesting a previously uncharacterised LIN-12 signalling event late in postembryonic mesoderm development. Together with a previous study indicating a role of lin-12 and sel-12 during the specification of the pi cell lineage required for proper vulva-uterine connection, our data suggest that the failure of sel-12 animals to lay eggs properly is caused by defects in at least two independent signalling events in different ------------------- Key: 5558 Medline: 12446902 Authors: Wang X;Yang C;Chai J;Shi Y;Xue D Title: Mechanisms of AIF-mediated apoptotic DNA degradation in Caenorhabditis elegans. Citation: Science 298: 1587-1592 2002 Type: ARTICLE Genes: ced-3 ced-4 ced-8 ced-9 cps-6 egl-1 nuc-1 wah-1 Abstract: Apoptosis-inducing factor (AIF), a mitochondrial oxidoreductase, is released into the cytoplasm to induce cell death in response to apoptotic signals. However, the mechanisms underlying this process have not been resolved. We report that inactivation of the Caenorhabditis elegans AIF homolog wah-1 by RNA interference delayed the normal progression of apoptosis and caused a defect in apoptotic DNA degradation. WAH-1 localized in C. elegans mitochondria and was released into the cytosol and nucleus by the BH3-domain protein EGL-1 in a caspase (CED-3)-dependent manner. In addition, WAH-1 associated and cooperated with the mitochondrial endonuclease CPS-6/endonuclease G (EndoG) to promote DNA degradation and apoptosis. Thus, AIF and EndoG de. ne a single, mitochondria-initiated apoptotic DNA degradation pathway that is conserved between C. elegans and mammals. ------------------- Key: 5559 Medline: 12385749 Authors: Zhang Y;Chalfie M Title: MTD-1, a touch-cell-specific membrane protein with a subtle effect on touch sensitivity. Citation: Mechanisms of Development 119: 3-7 2002 Type: ARTICLE Genes: cyp-7 inf-1 mec-3 mec-4 mec-5 mec-6 mec-7 mec-18 mtd-1 rpl-18 Abstract: We have used representational difference analysis (RDA) applied to cDNA to isolate transcripts regulated by MEC-3, a transcription factor needed for the differentiation of the six touch receptor neurons in Caenorhabditis elegans. Six percent of 595 cDNAs isolated by cDNA RDA were mec-3-dependent. These cDNAs represented mRNA from two previously known genes, mec-18 and mec-7, and one new gene, mtd-1 (mec-three-dependent). mtd-1 encodes a novel transmembrane protein that is exclusively expressed in the six touch cells throughout development. mtd-1 loss results in a subtle defect in the touch receptor neurons. Neither mtd-1 RNAi nor a. putative mtd-1 loss-of-function mutation resulted in touch insensitivity, but both enhanced the touch insensitivity of mec-6(u247), a temperature sensitive allele, at the permissive temperature. ------------------- Key: 5560 Medline: 12189149 Authors: Liao VHC;Dong J;Freedman JH Title: Molecular characterization of a novel, cadmium-inducible gene from the nematode Caenorhabditis elegans. Citation: Journal of Biological Chemistry 277: 42049-42059 2002 Type: ARTICLE Genes: cdr-1 Abstract: Cadmium is an environmental contaminant that is both a human toxicant and carcinogen. To inhibit cadmium-induced damage, cells respond by increasing the expression of genes that encode stress-response proteins. We previously reported the identification of 48 cadmium-inducible mRNAs in the nematode Caenorhabditis elegans. Here we describe a new cadmium-responsive gene, designated cdr-1, whose rate and level of inducible expression parallel those of the C. elegans metallothioneins. The CDR-1 mRNA contains an open reading frame of 831 bp and encodes a predicted 32-kDa, integral membrane protein. Following cadmium exposure, cdr-1 is transcribed exclusively in intestinal cells of post-embryonic C. elegans. In vivo, the CDR-1 protein is targeted specifically to the intestinal cell lysosomes. cdr-1 transcription is significantly induced by cadmium but not by other tested stressors. These results indicate that cdr-1 expression is regulated by cadmium and in a cell-specific fashion. Inhibition of CDR-1 expression renders C. elegans susceptible to cadmium toxicity. In conclusion, cdr-1 defines a new class of cadmium-inducible genes and encodes an integral membrane, lysosomal protein. This protein functions to protect against cadmium toxicity. ------------------- Key: 5561 Medline: Authors: Sanchez P;Linares JF;Ruiz-Diez B;Campanario E;Navas A;Baquero F;Martinez JL Title: Fitness of in vitro selected Pseudomonas aeruginose nalB and nfxB multdrug resistant mutants. Citation: Journal of Antimicrobial Chemotherapy 50: 657-664 2002 Type: ARTICLE Genes: Abstract: Overproduction of multidrug resistance (MDR) efflux pumps is involved in the resistance to a wide range of compounds in bacteria. These determinants extrude antibiotics, but also bacterial metabolites like quorum-sensing signals. Non-regulated extrusion of bacterial metabolites might produce a metabolic burden, so that MDR-overproducing mutants could have a reduced fitness when compared with their parental strains. To test such a possibility, we have compared the behaviour of two MDR Pseudomonas aeruginosa in vitro selected mutants (nalB and nfxB) with their isogenic parental strain with respect to some properties with potential relevance for the survival in the environment and the virulence of this bacterial species. Overproduction of the MDR determinants MexABOprM (nalB mutant) and MexCDOprJ (nfxB mutant) decreased the survival in water, the production of phenazines and proteases, and the virulence (using a Caenorhabditis elegans model system) of the P. aeruginosa mutants. In contrast, the capability of forming biofilms was not impaired. The simple models tested in the present work can enable the analysis of the fitness of large numbers of antibiotic-resistant bacteria by using more realistic approaches than the in vitro competition assays currently used. ------------------- Key: 5562 Medline: 12376829 Authors: Yokota S;Togo SH;Maebuchi M;Bun-ya M;Haraguchi CM;Kamiryo T Title: Peroxisomes of the nematode Caenorhabditis elegans: distribution and morphological characteristics. Citation: Histochemistry & Cell Biology 118: 329-336 2002 Type: ARTICLE Genes: Abstract: We analyzed the distribution and morphological characteristics of peroxisomes in the nematode Caenorhabditis elegans by routine electron microscopy, immunoelectron microscopy, and morphometry. Peroxisomes were mainly contained in the epithelial cells of the digestive tract and pharyngeal gland, but some were observed in other cells. Their shape varied from round to twisted. The matrix of most peroxisomes was coarse and uneven, and contained electron-dense nucleoids and frequently tubular substructures. The diameter of peroxisomes in the gut (0.185 mum) was smaller than that in pharyngeal gland (0.262 mum). The volume density of peroxisomes per 100 mum(2) of cytoplasm was 1.86 in the gut and 1.75 in the pharyngeal gland. After treatment with clofibrate, the diameter of peroxisomes increased approximately 1.11-fold in the gut and 1.2-fold in the pharyngeal gland. The volume density of peroxisomes also increased by 2.2-fold in the gut and 2.6-fold in the pharyngeal gland. The labeling density for catalase-2 was almost identical between gut and pharyngeal gland peroxisomes. The results show that in C elegans peroxisomes mainly distribute in the epithelial cells of the gut and pharyngeal gland. Peroxisomes of the pharyngeal gland are larger than those of the gut, but peroxisomes of both ------------------- Key: 5563 Medline: 12231504 Authors: Kimura Y;Corcoran EE;Eto K;Gengyo-Ando K;Muramatsu M;Kobayashi R;Freedman JH;Mitani S;Hagiwara M;Means AR;Tokumitsu H Title: A CaMK cascade activates CRE-mediated transcription in neurons of Caenorhabditis elegans. Citation: EMBO Reports 3: 962-966 2002 Type: ARTICLE Genes: ckk-1 cmk-1 crh-1 Abstract: Calcium (Ca2+) signals regulate a diverse set of cellular responses, from proliferation to muscular contraction and neuro-endocrine secretion. The ubiquitous Ca2+ sensor, calmodulin (CaM), translates changes in local intracellular Ca2+ concentrations into changes in enzyme activities. Among its targets, the Ca2+/CaM-dependent protein kinases I and IV (CaMKs) are capable of transducing intraneuronal signals, and these kinases are implicated in neuronal gene regulation that mediates synaptic plasticity in mammals. Recently, the cyclic AMP response element binding protein (CREB) has been proposed as a target for a CaMK cascade involving not only CaMKI or CaMKIV, but also an upstream kinase kinase that is also CaM regulated (CaMKK). Here, we report that all components of this pathway are coexpressed in head neurons of Caenorhabditis elegans. Utilizing a transgenic approach to visualize CREB-dependent transcription in vivo, we show that this CaMK cascade regulates CRE-mediated transcription in a subset of head ------------------- Key: 5564 Medline: 12411496 Authors: Eimer S;Lakowski B;Donhauser R;Baumeister R Title: Loss of spr-5 bypasses the requirement for the C. elegans presenilin sel-12 by derepressing hop-1. Citation: EMBO Journal 21: 5787-5796 2002 Type: ARTICLE Genes: gon-10 hda-1 hda-1 hda-3 hop-1 lin-12 sel-12 spr-1 spr-5 Abstract: Presenilins are part of a protease complex that is responsible for the intramembraneous cleavage of the amyloid precursor protein involved in Alzheimer's disease and of Notch receptors. In Caenorhabditis elegans, mutations in the presenilin sel-12 result in a highly penetrant egg-laying defect. spr-5 was identified as an extragenic suppressor of the sel-12 mutant phenotype. The SPR-5 protein has similarity to the human polyamine oxidase-like protein encoded by KIAA0601 that is part of the HDAC-CoREST co-repressor complex. Suppression of sel-12 by spr-5 requires the activity of HOP-1, the second somatic presenilin in C.elegans. spr-5 mutants derepress hop-1 expression 20- to 30-fold in the early larval stages when hop-1 normally is almost undetectable. SPR-1, a C.elegans homologue of CoREST, physically interacts with SPR-5. Moreover, down-regulation of SPR-1 by mutation or RNA interference also bypasses the need for sel-12. These data strongly suggest that SPR-5 and SPR-1 are part of a CoREST-like co-repressor complex in C.elegans. This complex might be recruited to the hop-1 locus controlling its expression during development. ------------------- Key: 5565 Medline: 12431374 Authors: Hamill DR;Severson AF;Carter JC;Bowerman B Title: Centrosome maturation and mitotic spindle assembly in C. elegans require SPD-5, a protein with multiple coiled-coil domains. Citation: Developmental Cell 3: 673-684 2002 Type: ARTICLE Genes: air-1 dhc-1 let-354 let-361 let-363 let-364 let-371 spd-2 spd-5 zyg-1 zyg-8 zyg-9 hDf28 Abstract: The maternally expressed C. elegans gene spd-5 encodes a centrosomal protein with multiple coiled-coil domains. During mitosis in mutants with reduced levels of SPD-5, microtubules assemble but radiate from condensed chromosomes without forming a spindle, and mitosis fails. SPD-5 is required for the centrosomal localization of gamma-tubulin, XMAP-215, and Aurora A kinase family members, but SPD-5 accumulates at centrosomes in mutants lacking these proteins. Furthermore, SPD-5 interacts genetically with a dynein heavy chain. We propose that SPD-5, along with dynein, is required for centrosome maturation and mitotic spindle assembly. ------------------- Key: 5566 Medline: 12431376 Authors: Eckmann CR;Kraemer B;Wickens M;Kimble J Title: GLD-3, a Bicaudal-C homolog that inhibits FBF to control germline sex determination in C. elegans. Citation: Developmental Cell 3: 697-710 2002 Type: ARTICLE Genes: bcc-1 fbf-1 fbf-2 fem-3 fog-1 gld-3 glp-4 rde-1 smg-4 mnDf30 mnDf108 Abstract: The FBF RNA binding proteins control multiple aspects of C. elegans germline development, including sex determination. FBF promotes the oocyte fate at the expense of spermatogenesis by binding a regulatory element in the fem-3 3'UTR and repressing this sex-determining gene. Here we report the discovery of GLD-3, a Bicaudal-C homolog and cytoplasmic protein that physically interacts with FBF. Using RNAi and a gld-3 deletion mutant, we show that GLD-3 promotes the sperm fate, a sex determination effect opposite to that of FBF. By epistasis analysis, GLD-3 acts upstream of FBF, and, in a yeast three-hybrid assay, GLD-3 interferes specifically with FBF binding to the fem-3 3'UTR. We propose that GLD-3 binds FBF and thereby inhibits its repression of target mRNAs. ------------------- Key: 5567 Medline: 12397107 Authors: Wang J;Tokarz R;Savage-Dunn C Title: The expression of TGF Beta signal transducers in the hypodermis regulates body size in C. elegans. Citation: Development 129: 4989-4998 2002 Type: ARTICLE Genes: daf-4 dbl-1 dpy-7 elt-2 elt-3 him-5 myo-2 sma-1 sma-2 sma-3 sma-4 sma-6 tmy-1 vha-6 vha-7 Abstract: In C. elegans, a TGFbeta-related signaling pathway regulates body size. Loss of function of the signaling ligand (dbl-1), receptors (daf-4 and sma-6) or Smads (sma-2, sma-3 and sma-4) results in viable, but smaller animals because of a reduction in postembryonic growth. We have investigated the tissue specificity of this pathway in body size regulation. We show that different tissues are reduced in size by different proportions, with hypodermal blast cell size most closely proportional to body size. We show that SMA-3 Smad is expressed in pharynx, intestine and hypodermis, as has been previously reported for the type I receptor SMA-6. Furthermore, we find that SMA-3::GFP is nuclear localized in all of these tissues, and that nuclear localization is enhanced by SMA-6 activity. Interestingly, SMA-3 protein accumulation was found to be negatively regulated by the level of Sma/Mab pathway activity. Using genetic mosaic analysis and directed expression of SMA-3, we find that SMA-3 activity in the hypodermis is necessary and sufficient for normal body size. As dbl-1 is expressed primarily in the nervous system, these results suggest a model in which postembryonic growth of hypodermal cells is regulated by TGFbeta-related signaling from the nervous system to the hypodermis. ------------------- Key: 5568 Medline: 12397108 Authors: Spike CA;Davies AG;Shaw JE;Herman RK Title: MEC-8 regulates alternative splicing of unc-52 transcripts in C. elegans hypodermal cells. Citation: Development 129: 4999-5008 2002 Type: ARTICLE Genes: mec-8 unc-52 Abstract: Previous work has shown that C elegans MEC-8 is a putative RNA-binding protein that promotes specific alternative splices of unc-52 transcripts. unc-52 encodes homologs of mammalian perlecan that are located extracellularly between muscle and hypodermis and are essential for muscle development in both embryos and larvae. We show that MEC-8 is a nuclear protein found in hypodermis at most stages of development and not in most late embryonic or larval body-wall muscle. We have also found that overexpression of MEC-8 in hypodermis but not muscle can suppress certain unc-52 mutant phenotypes. These are unexpected results because it has been proposed that UNC-52 is produced exclusively by muscle. We have constructed various tissue-specific unc-52 minigenes fused to a gene for green fluorescent protein that have allowed us to monitor tissue-specific mec-8-dependent alternative splicing; we show that mec-8 must be expressed in the same cell type as the unc-52 minigene in order to regulate its expression, supporting the view that MEC-8 acts directly on unc-52 transcripts and that UNC-52 must be synthesized primarily by the hypodermis. Indeed, our analysis of unc-52 genetic mosaics has shown that the focus of unc-52 action is not in body-wall muscle but most likely is in hypodermis. ------------------- Key: 5569 Medline: 12419202 Authors: Nicholas HR;Hodgkin J Title: Innate immunity: the worm fights back. Citation: Current Biology 12: R731-R732 2002 Type: REVIEW Genes: dbl-1 esp-8 lys-1 lys-7 lys-8 nsy-1 pmk-1 sek-1 Abstract: Innate immunity is an evolutionarily ancient defense system that enables animals and plants to resist invading microorganisms. Recent studies have demonstrated the existence of innate immune responses in Caenorhabditis elegans. ------------------- Key: 5570 Medline: 12419203 Authors: Trautmann S;McCollum D Title: Cell cycle: new functions for Cdc14 family phosphatases. Citation: Current Biology 12: R733-R735 2002 Type: REVIEW Genes: Abstract: The Cdc14 phosphatase was identified by its requirement for mitotic exit in budding yeast. Cdc14 homologs exist throughout the eukaryotic kingdom, but it was unclear whether their function would also be conserved. Recent analyses in fission yeast, humans and now C. elegans suggest numerous other functions for this family of ------------------- Key: 5571 Medline: 12417407 Authors: Bulik DA;Robbins PW Title: The Caenorhabditis elegans sqv genes and functions of proteoglycans in development. Citation: Biochimica et Biophysica Acta 1573: 247-257 2002 Type: REVIEW Genes: dig-2 lag-2 let-23 let-60 lin-2 lin-3 lin-7 lin-12 lin-15 lin-39 pat-2 pat-3 rib-2 sem-5 sqv-3 sqv-7 sqv-8 unc-52 Abstract: In the nematode Caenorhabditis elegans, the vulva is a simple tubular structure linking the gonads with the external cuticle. In this review we summarize knowledge of inter- and intracellular signaling during vulval development and of the genes required for vulval invagination. Mutants of one set of these genes, the sqv genes, have a normal number of vulval precursor cells (VPCs) with an unperturbed cell lineage but the invagination space, normally a tube, is either collapsed or absent. We review evidence that the sqv genes are involved in glycosaminoglycan synthesis and speculate on ways in which defective glycosaminoglycan formation might lead to ------------------- Key: 5572 Medline: 12417407 Authors: Chen S;Tan J;Reinhold VN;Spence AM:Schachter H Title: UDP-N-acetylglucosamine: alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I and UDP-N-acetylglucosamine: alpha-6-D-mannoside beta-1,2-N-acetylglucosaminyltransferase II in Caenorhabditis e Citation: Biochimica et Biophysica Acta 1573: 271-279 2002 Type: ARTICLE Genes: gly-12 gly-13 gly-14 Abstract: UDP-N-acetylglucosamine:alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I (GnT I) and UDP-N-acetylglucosamine:alpha-6-D-mannoside beta-1,2-N-acetylglucosaminyltransferase II (GnT 11) are key enzymes in the synthesis of Asn-linked hybrid and complex glycans. We have cloned cDNAs from Caenorhabditis elegans for three genes homologous to mammalian GnT I (designated gly-12, gly-13 and gly-14) and one gene homologous to mammalian GnT II. All four cDNAs encode proteins which have the domain structure typical of previously cloned Golgi-type glycosyltransferases and show enzymatic activity (GnT I and GnT 11, respectively) on expression in transgenic worms. We have isolated worm mutants lacking the three GnT I genes by the method of ultraviolet irradiation in the presence of trimethylpsoralen (TMP); null mutants for GnT 11 have not yet been obtained. The gly-12 and gly-14 mutants as well as the gly-14;gly-12 double mutant displayed wild-type phenotypes indicating that neither gly-12 nor gly-14 is necessary for worm development under standard laboratory conditions. This finding and other data indicate that the GLY-13 protein is the major functional GnT I in C elegans. The mutation lacking the gly-13 gene is partially lethal and the few survivors display severe morphological and behavioral defects. We have shown that the observed phenotype co-segregates with the gly-13 deletion in genetic mapping experiments although a second mutation near the gly-13 gene cannot as yet be ruled out. Our data indicate that complex and hybrid N-glycans may play critical roles in the morphogenesis of C elegans, as they have been shown ------------------- Key: 5573 Medline: 12433066 Authors: Van Gilst M;Gissendanner CR;Sluder AE Title: Diversity and function of orphan nuclear receptors in nematodes. Citation: Critical Reviews in Eukaryotic Gene Expression 12: 65-88 2002 Type: REVIEW Genes: daf-8 daf-12 fax-1 nhr-1 nhr-2 nhr-6 nhr-8 nhr-10 nhr-11 nhr-18 nhr-23 nhr-25 nhr-28 nhr-34 nhr-41 nhr-44 nhr-48 nhr-55 nhr--64 nhr-67 nhr-69 nhr-85 nhr-91 odr-7 sex-1 unc-55 Abstract: Nuclear receptors (NRs) have key regulatory functions in a wide range of biological processes and are one of the most abundant classes of transcriptional regulators in metazoans. NRs are particularly numerous in nematodes, in which the NR gene family has undergone extensive expansion and diversification, providing an evolutionary structure function experiment that is yielding new perspectives on the mechanisms of NR function and on nematode biology. The genome sequence of the free-living nematode Caenorhabditis elegans reveals 270 predicted NR genes, more than fivefold more than observed for any other species to date, though existing data suggest that NR genes are similarly abundant in other nematodes. Most of the currently available information regarding the functions of nematode NRs comes from ongoing studies with C. elegans, and we review here what has been learned thus far in three key areas: the relationships of C. elegans NRs to those in other species; the biochemical consequences of nematode NR sequence diversity. ------------------- Key: 5574 Medline: 12421359 Authors: Feng XP;Hayashi J;Beech RN;Prichard RK Title: Study of the nematode putative GABA type-A receptor subunits: evidence for modulation by ivermectin. Citation: Journal of Neurochemistry 83: 870-878 2002 Type: ARTICLE Genes: gab-1 Abstract: Two alleles of the HG1 gene, which encodes a putative GABA receptor alpha/gamma subunit, were isolated from Haemonchus contortus. These two alleles were shown previously to be associated with ivermectin susceptibility (HG1A) and resistance (HG1E), respectively. Sequence analysis indicates that they differ in four amino acids. To explore the functional properties of the two alleles, a full-length cDNA encoding the beta subunit, a key functional component of the GABA receptor, was isolated from Caenorhabditis elegans (gab-1, corresponding to the GenBank locus ZC482.1) and coexpressed in Xenopus oocytes with the HG1 alleles. When gab-1 was coexpressed with either the HG1A allele or the HG1E allele in Xenopus oocytes, gamma-aminobutyric acid (GABA)-responsive channels with different sensitivity to the agonist were formed. The effects of ivermectin on the hetero-oligomeric receptors were determined. Application of ivermectin alone had no effect on the receptors. However, when coapplied with 10 micro m GABA, ivermectin potentiated the GABA-evoked current of the GAB-1/HG1A receptor, but attenuated the GABA response of the GAB-1/HG1E receptor. We demonstrated that the coexpressed HG1 and GAB-1 receptors are GABA-responsive, and provide evidence for the possible involvement of GABA receptors in the mechanism of ivermectin resistance. ------------------- Key: 5575 Medline: 12471246 Authors: Pellettieri J;Seydoux G Title: Anterior-posterior polarity in C. elegans and Drosophila - PARallels and differences. Citation: Science 298: 1946-1950 2002 Type: REVIEW Genes: mex-5 mex-6 par-1 par-2 par-3 par-4 par-5 par-6 pie-1 pkc-3 Abstract: The eggs of Caenorhabditis elegans and Drosophila bear little similarity to each other, yet both depend on the par genes for control of anterior-posterior polarity. Here we explore possible common roles for the par genes (pars) in converting transient asymmetries into stably polarized axes. Although clear mechanistic parallels remain to be established, par-dependent regulation of microtubule dynamics and protein stability emerge as common themes. ------------------- Key: 5576 Medline: 12471248 Authors: Knust E;Bossinger O Title: Composition and formation of intercellular junctions in epithelial cells. Citation: Science 298: 1955-1959 2002 Type: REVIEW Genes: ajm-1 cdc-42 crb-1 dlg-1 erm-1 hmp-1 hmp-2 hmr-1 lad-1 let-413 par-3 par-6 pkc-3 sma-1 Abstract: The polarized nature of epithelial cells is manifested by the nonrandom partitioning of organelles within the cells, the concentration of intercellular junctions at one pole, and the asymmetric distribution of proteins and lipids within the plasma membrane. These features allow epithelia to fulfill their specific tasks, such as targeted uptake and secretion of molecules and the segregation of different tissue compartments. The accessibility of Drosophila melanogaster and Caenorhabditis elegans to genetic and cell biological analyses, combined with the study of mammalian cells in culture, provides an ideal basis for understanding the mechanisms that control the establishment and maintenance of epithelial cell polarity and tissue integrity. Here, we focus on some of the best-studied junctions and membrane-associated protein complexes and their relation to cell polarity. Comparisons between fly, worm, and vertebrate epithelia reveal marked similarities with respect to the molecules used, and pronounced differences in the organization of the junctions ------------------- Key: 5577 Medline: 12411600 Authors: Arudchandran A;Cerritelli SM;Bowen NJ;Chen X;Krause MW;Crouch RJ Title: Multiple ribonuclease H-encoding genes in the Caenorhabditis elegans genome contrasts with the two typical ribonuclease H-encoding genes in the human genome. Citation: Molecular Biology and Evolution 19: 1910-1919 2002 Type: ARTICLE Genes: Abstract: Database searches of the Caenorhabditis elegans and human genomic DNA sequences revealed genes encoding ribonuclease HI (RNase HI) and RNase H2 in each genome. The human genome contains a single copy of each gene, whereas C. elegans has four genes encoding RNase HI-related proteins and one gene for RNase H2. By analyzing the mRNAs produced from the C. elegans genes, examining the amino acid sequence of the predicted protein, and expressing the proteins in Esherichia coli we have identified two active RNase H1-like proteins. One is similar to other eukaryotic RNases H1, whereas the second RNase H (rnh-1.1) is unique. The rnh-1.0 gene is transcribed as a dicistronic message with three dsRNA-binding domains; the mature mRNA is transspliced with SL2 splice leader and contains only one dsRNA-binding domain. Formation of RNase HI is further regulated by differential cis-splicing events. A single rnh-2 gene, encoding a protein similar to several other eukaryotic RNase H2L's, also has been examined. The diversity and enzymatic properties of RNase H homologues are other examples of expansion of protein families in C. elegans. The presence of two RNases HI in C. elegans suggests that two enzymes are required in this rather simple organism to perform the functions that are accomplished by a single enzyme in more complex organisms. Phylogenetic analysis indicates that the active C. elegans RNases HI are distantly related to one another and that the C. elegans RNase HI is more closely related to the human RNase HI. The database searches also suggest that RNase H domains of LTR-retrotransposons in C. elegans are quite unrelated to cellular RNases HI, but numerous RNase H domains of human endogenous retroviruses are more closely related to ------------------- Key: 5578 Medline: 12395383 Authors: Manser J;Wood WB;Perry MD Title: Extragenic suppressors of a dominant masculinizing her-1 mutation in C. elegans identify two new genes that affect sex determination in different ways. Citation: Genesis 34: 184-195 2002 Type: ARTICLE Genes: her-1 let-2 lin-15 sdc-1 sdc-3 sup-26 sup-27 tra-1 tra-2 xol-1 mnDp37 Abstract: The her-1 regulatory switch gene in C. elegans sex determination is normally active in XO animals, resulting in male development, and inactive in XX animals, allowing hermaphrodite development. The her1(n695gf) mutation results in the incomplete transformation of XX animals into phenotypic males. We describe four extragenic mutations that suppress the masculinized phenotype of her-1(n695gf) XX. They define two previously undescribed genes, sup-26 and sup-27. All four mutations exhibit semidominance of suppression and by themselves have no visible effects on sex determination in otherwise genotypically wild-type XX or XO animals. Analysis of interactions with mutations in the major sex-determining genes show that sup-26 and sup-27 influence sex determination in fundamentally different ways. sup-26 appears to act independently of her-1 to negatively modulate synthesis or function of tra-2 in both XX and XO animals. sup-27 may play a role in X-chromosome dosage compensation and influence sex determination ------------------- Key: 5579 Medline: 12424127 Authors: McKay SJ;Jones SJM Title: AcePrimer: automation of PCR primer design based on gene structure. Citation: Bioinformatics 18: 1538-1539 2002 Type: ARTICLE Genes: Abstract: AcePrimer is an internet-accessed application based on CGI/Perl programming that designs PCR primers to search for deletion alleles in Caenorhabditis elegans gene knockout experiments and uses electronic PCR to search the entire genomic DNA sequence for potential false priming or multiple PCR amplification targets. Features such as the ability to target specific exons with the 'poison primer' approach and evaluation of primers with electronic PCR provide a flexible, web-based approach to design effective primers whilst minimizing the need for empirical optimization of PCR experiments. ------------------- Key: 5580 Medline: Authors: Title: Nematode net Nobel. Citation: Nature Cell Biology 4: E243- 2002 Type: REVIEW Genes: Abstract: ------------------- Key: 5581 Medline: 12356904 Authors: Hutagalung AH;Landsverk ML;Price MG;Epstein HF Title: The UCS family of myosin chaperones. Citation: Journal of Cell Science 115: 3983-3990 2002 Type: REVIEW Genes: nmy-2 unc-45 Abstract: The canonical UCS (UNC-45/Crol/She4p) protein, Caenorhabditis elegans UNC-45, was one of the earliest molecules to be shown genetically to be necessary for sarcomere assembly. Genetic analyses of homologues in several fungal species indicate that the conserved UCS domain functionally interacts with conventional type II and unconventional type V myosins. In C. elegans and other invertebrate species, UNC-45 and its orthologues interact with both sarcomeric and non-sarcomeric myosins whereas, in vertebrates, there are two UNC-45 isoforms: a general cell (GC) and a striated muscle (SM) isoform. Although the mechanism of action of UCS proteins is unknown, recent biochemical studies suggest that they may act as molecular chaperones that facilitate the folding and/or maturation of myosin. ------------------- Key: 5582 Medline: Authors: Killeen M;Tong J;Krizus A;Steven R;Scott I;Pawson T;Culotti J Title: UNC-5 function requires phosphorylation of cytoplasmic tyrosine 482, but its UNC-40-independent functions also require a region between the ZU-5 and Death Domains. Citation: Developmental Biology 251: 348-366 2002 Type: ARTICLE Genes: unc-5 unc-6 unc-40 Abstract: Members of the UNC-5 protein family are transmembrane receptors for UNC-6/netrin guidance cues. To analyze the functional roles of different UNC-5 domains, we sequenced mutations in seven severe and three weak alleles of unc-5 in Caenorhabditis elegans. Four severe alleles contain nonsense mutations. Two weak alleles are truncations of the cytodomain, but one is a missense mutation in an extracellular immunoglobulin domain. To survey the function of different regions of UNC-5, wild-type and mutant unc-5::HA transgenes were tested for their ability to rescue the unc-5(e53) null mutant. Our data reveal partial functional requirements for the extracellular domains and identify a portion of the cytoplasmic juxtamembrane (JM) region as essential for rescue of migrations. When nine cytodomain tyrosines, including seven in the JM region, are mutated to phenylalanine, UNC-5 function and tyrosine phosphorylation are largely compromised. When F482 in the JM region of the mutant protein is reverted to tyrosine, UNC-5 tyrosine phosphorylation and in vivo function are largely recovered, suggesting that Y482 phosphorylation is critical to UNC-5 function in vivo. Our data also show that part of the ZU-5 motif is required for UNC-40-independent signaling of UNC-5. ------------------- Key: 5583 Medline: 12435362 Authors: Smith P;Leung-Chiu WM;Montgomery R;Orsborn A;Kuznicki K;Gressman-Coberly E;Mutapcic L;Bennett K Title: The GLH proteins, Caenorhabditis elegans P granule components, associate with CSN-5 and KGB-1, proteins necessary for fertility, and with ZYX-1, a predicted cytoskeletal protein. Citation: Developmental Biology 251: 333-347 2002 Type: ARTICLE Genes: csn-5 glh-1 glh-2 glh-3 glh-4 kgb-1 zyx-1 Abstract: The GLH proteins belong to a family of four germline RNA helicases in Caenorhabditis elegans. These putative ATP-dependent enzymes localize to the P granules, which are nonmembranous complexes of protein and RNA exclusively found in the cytoplasm of all C. elegans germ cells and germ cell precursors. To determine what proteins the GLHs bind, C. elegans cDNA libraries were screened by the yeast two-hybrid method, using GLHs as bait. Three interacting proteins, CSN-5, KGB-1, and ZYX-1, were identified and further characterized. GST pull-down assays independently established that these proteins bind GLHs. CSN-5 is closely related to the subunit 5 protein of COP9 signalosomes, conserved multiprotein complexes of plants and animals. RNA interference (RNAi) with csn-5 results in sterile worms with small gonads and no oocytes, a defect essentially identical to that produced by RNAi with a combination of glh-1 and glh-4. KGB-1 is a putative JNK MAP kinase that GLHs bind. A kgb-1 deletion strain has a temperature-sensitive, sterile phenotype characterized by the absence of mature oocytes and the presence of trapped, immature oocytes that have undergone endoreplication. ZYX-1 is a LIM domain protein most like vertebrate Zyxin, a cytoskeletal adaptor protein. In C. elegans, while zyx-1 appears to be a single copy gene, neither RNAi depletion nor a zyx-1 deletion strain results in an obvious phenotype. These three conserved proteins are the first members in each of their families reported to associate with germline helicases. Similar to the loss of GLH-1 and GLH-4, loss of either CSN-5 or KGB-1 causes oogenesis to cease, but does not affect the initial assembly of P ------------------- Key: 5584 Medline: Authors: Chen J;Acton TB;Basu SK;Montelione GT;Inouye M Title: Enhancement of the solubility of proteins overexpressed in Escherichia coli by heat shock. Citation: Journal of Molecular Microbiology & Biotechnology 4: 519-524 2002 Type: ARTICLE Genes: Abstract: Protein misfolding resulting in the formation of inclusion bodies is one of the major problems during protein overexpression in Escherichia coli. In this paper, we introduce a new method, which is simply to heat shock a cell culture prior to protein induction, allowing effective enhancement of the solubility and thereby the yield of overexpressed proteins in E. coli. Using this method, we show that the solubility of the E. coli protein KsgA-DELTAN is significantly increased when overexpressed from a T7 promoter. In addition, we also show that the solubility of several Caenorhabditis elegans proteins are also enhanced after heat-shock treatment when expressed in E. coli. Taken together, these results suggest that the "heat-shock protocol" is a generalizable and useful method for increasing the solubility of many proteins overexpressed in E. coli. ------------------- Key: 5585 Medline: 12486229 Authors: Faber PW;Voisine C;King DC;Bates EA;Hart AC Title: Glutamine/proline-rich PQE-1 proteins protect Caenorhabditis elegans neurons from huntingtin Citation: Proceedings of the National Academy of Sciences USA 99: 17131-17136 2002 Type: ARTICLE Genes: Abstract: Huntington's disease is a progressive neurodegenerative disease caused by a polyglutamine (polyQ) repeat expansion in the huntingtin protein [Huntington's Disease Collaborative Research Group (1993) Cell 72, 971-983]. To understand the mechanism by which polyQ repeats cause neurodegeneration and cell death, we modeled polyQ neurotoxicity in Caenorhabditis elegans. In our model, expression of N-terminal fragments of human huntingtin causes polyQ-dependent degeneration of neurons. We conducted a genetic screen to identify proteins that protect neurons from the toxic effects of expanded polyQ tracts. Loss of polyQ enhancer-1 (pqe-1) gene function strongly and specifically exacerbates neurodegeneration and cell death, whereas overexpression of a pqe-1 cDNA protects C. elegans neurons from the toxic effects of expanded huntingtin fragments. A glutamine/proline-rich domain, along with a charged domain, is critical for PQE-1 protein function. Analysis of pqe-1 suggests that proteins exist that specifically protect neurons from the toxic effects of expanded polyQ disease proteins. ------------------- Key: 5586 Medline: 12242228 Authors: Srinivasan J;Sinz W;Lanz C;Brand A;Nandakumar R;Raddatz G;Witte H;Keller H;Kipping I;Pires-daSilva A;Jesse T;Millare J;de Both M;Schuster SC;Sommer RJ Title: A bacterial artificial chromosome-based genetic linkage map of the nematode Pristionchus pacificus. Citation: Genetics 162: 129-134 2002 Type: ARTICLE Genes: Abstract: To understand the evolution of developmental processes, nonmodel organisms in the nematodes, insects, and vertebrates are compared with established model systems. Often, these comparisons suffer from the inability to apply sophisticated technologies to these nonmodel species. In the nematode Pristionchus pacifus, cellular and genetic analyses are used to compare vulva development to that of Caenorhabditis elegans. However, substantial changes in gene function between P. pacifus and C. elegans limit the use of candidate gene approaches in studying P. pacifus mutations. To facilitate map-based cloning of mutations in P. pacifus, we constructed a BAC-based genetic linkage map. A BAC library of 13,440 clones was generated and completely end sequenced. By comparing BAC end and EST sequences between the ?wild-type? strain P. pacifus var. California and the polymorphic strain P. pacifus var. Washington, 133 single-stranded conformational polymorphisms were identified. These markers were tested on a meiotic mapping panel of 46 randomly picked F2 animals after a cross of the two strains, providing the first genetic linkage map of P. pacifus. A mapping strategy using two selected markers per chromosome was devised and the efficiency of this approach was illustrated by the mapping of the Ppa-unc1/Twichin ------------------- Key: 5587 Medline: Authors: Van Voorhies WA Title: Metabolism and lifespan. Citation: Experimental Gerontology 36: 55-64 2001 Type: REVIEW Genes: Abstract: There has recently been a great deal of scientific and popular interest in identifying the causes of aging. Currently one of the most popular mechanistic explanations for the aging process links the production of free radicals and other oxidants (often termed reactive oxygen species or ROS) produced during aerobic respiration to biomolecular damage that results in aging. While there is a large amount of correlative data supporting the importance of ROS to aging it remains to be determined if ROS are a primary cause of aging. It is essential to remember that aging is a complicated process which may have different causal mechanisms between different species and multiple causal mechanisms within species. ------------------- Key: 5588 Medline: Authors: Van Voorhies WA Title: Hormesis and aging. Citation: Human & Experimental Toxicology 20: 315-317 2002 Type: REVIEW Genes: Abstract: Rattan?s article on the potential use of hormesis in aging research provides a well-reasoned and insightful overview of both the factors responsible for aging and the importance of stress responses in potentially modulating senescence. Rattan proceeds from the premise that the causal mechanisms responsible for aging are likely to vary not only between, and within species, but also even between different cell types of the same individual. As such, aging may have different causal mechanisms between different species, and multiple causal mechanisms within species. As a direct consequence of this, it is unlikely that a single cause of aging will be common to all ------------------- Key: 5589 Medline: Authors: Winter CE Title: Yolk proteins and their precursors in non-arthropod protostomes, with emphasis on nematodes. Citation: "Reproductive Biology of Invertebrates", AS Raikhel and TW Sappington (eds). Science Publishers Inc. Enfield, NH and Plymouth UK. XII: 1-27 2002 Type: REVIEW Genes: cpr-1 elt-1 elt-2 elt-3 end-1 kpc-1 mab-3 vit-1 vit-2 vit-3 vit-4 vit-5 vit-6 Abstract: ------------------- Key: 5590 Medline: 12438649 Authors: Mylonakis E;Ausubel FM;Perfect JR;Heitman J;Calderwood SB Title: Killing of Caenorhabditis elegans by Cryptococcus neoformans as a model of yeast pathogenesis. Citation: Proceedings of the National Academy of Sciences USA 99: 15675-15680 2002 Type: ARTICLE Genes: Abstract: We found that the well-studied nematode Caenorhabditis elegans can use various yeasts, including Cryptococcus laurentii and Cryptococcus kuetzingii, as a sole source of food, producing similar brood sizes compared with growth on its usual laboratory food source Escherichia coli OP50. C elegans grown on these yeasts had a life span similar to (C laurentii) or longer than (C kuetzingii) those fed on E. coli. However, the human pathogenic yeast Cryptococcus neoformans killed C elegans, and the C neoformans polysaccharide capsule as well as several C neoformans genes previously shown to be involved in mammalian virulence were also shown to play a role in C elegans killing. These included genes associated with signal transduction pathways (GPA1, PKA1, PKR1, and RAP), laccase production (LAC1), and the alpha mating type. C neoformans adenine auxotrophs, which are less virulent in mammals, were also less virulent in C elegans. These results support the model that mammalian pathogenesis of C neoformans may be a consequence of adaptations that have evolved during the interaction of C neoformans with environmental predators such as free-living nematodes and amoebae and suggest that C elegans can be used as a simple model host in which C neoformans pathogenesis can be readily studied. ------------------- Key: 5591 Medline: 12478294 Authors: Chelur DS;Ernstrom GG;Goodman MB;Yao CA;Chen L;O'Hagan R;Chalfie M Title: The mechanosensory protein MEC-6 is a subunit of the C. elegans touch-cell degenerin channel. Citation: Nature 420: 669-673 2002 Type: ARTICLE Genes: mec-2 mec-4 mec-6 mec-10 mec-18 Abstract: Mechanosensory transduction in touch receptor neurons is believed to be mediated by DEG/ENaC (degenerin/epithelial Na+ channel) proteins in nematodes and mammals(1). In the nematode Caenorhabditis elegans, gain-of-function mutations in the degenerin genes mec-4 and mec-10 (denoted mec-4(d) and mec-10(d), respectively) cause degeneration of the touch cells(2,3). This phenotype is completely suppressed by mutation in a third gene, mec-6 (refs 3, 4), that is needed for touch sensitivity. This last gene is also required for the function of other degenerins(4-8). Here we show that mec-6 encodes a single-pass membrane-spanning protein with limited similarity to paraoxonases, which are implicated in human coronary heart disease(9). This gene is expressed in muscle cells and in many neurons, including the six touch receptor neurons. MEC-6 increases amiloride-sensitive Na+ currents produced by MEC-4(d)/MEC-10(d) by similar to30-fold, and functions synergistically with MEC-2 (a stomatin-like protein(10) that regulates MEC-4(d)/MEC-10(d) channel activity(11)) to increase the currents by 200-fold. MEC-6 physically interacts with all three channel proteins. In vivo, MEC-6 colocalizes with MEC-4, and is required for punctate MEC-4 expression along touch-neuron processes. We propose that MEC-6 is a part of the degenerin channel complex that may ------------------- Key: 5592 Medline: 12478297 Authors: Shaye DD;Greenwald I Title: Endocytosis-mediated downregulation of LIN-12/Notch upon Ras activation in Caenorhabditis elegans. Citation: Nature 420: 686-690 2002 Type: ARTICLE Genes: egl-17 lin-12 sur-2 Abstract: The coordination of signals from different pathways is important for cell fate specification during animal development. Here, we define a novel mode of crosstalk between the epidermal growth factor receptor/Ras/mitogen-activated protein kinase cascade and the LIN-12/Notch pathway during Caenorhabditis elegans vulval development. Six vulval precursor cells (VPCs) are initially equivalent but adopt different fates as a result of an inductive signal mediated by the Ras pathway and a lateral signal mediated by the LIN-12/Notch pathway(1). One consequence of activating Ras is a reduction of LIN-12 protein in P6.p (ref. 2), the VPC believed to be the source of the lateral signal. Here we identify a 'downregulation targeting signal' (DTS) in the LIN-12 intracellular domain, which encompasses a di-leucine-containing endocytic sorting motif. The DTS seems to be required for internalization of LIN-12, and on Ras activation it might mediate altered endocytic routing of LIN-12, leading to downregulation. We also show that if LIN-12 is stabilized in P6.p, lateral signalling is compromised, indicating that LIN-12 downregulation is important in the appropriate specification of cell fates in vivo. ------------------- Key: 5593 Medline: 12425951 Authors: Braeckman BP;Houthoofd K;Brys K;Lenaerts I;De Vreese A;Van Eygen S;Raes H;Vanfleteren JR Title: No reduction of energy metabolism in Clk mutants. Citation: Mechanisms of Ageing & Development 123: 1447-1456 2002 Type: ARTICLE Genes: clk-1 clk-2 clk-3 gro-1 Abstract: Mutation in any of the four clock genes (clk-1, clk-2, clk-3, gro-1) causes an average slowing down of many temporal processes, and an increase of mean life span. The latter effect has been linked to the slow phenotype, and it has been the ageing process. To test this model we measured several parameters describing metabolic output in wild type worms and all four Clk mutants. We found no gross changes in metabolic output, as assessed from oxygen consumption and heat production rates, lucigenin-mediated light production capacity, ATP content, and lipofuscin autofluorescence. Catalase and superoxide dismutase (SOD) were variably altered, but not cooperatively, as would be expected to enhance reactive oxygen species (ROX) scavenging activity. Thus we conclude that the prolonged life span of Clk mutant cannot be attributed to reduced metabolic rate or an increased activity of the major antioxidant enzymes catalase and SOD. ------------------- Key: 5594 Medline: 12436418 Authors: Schafer WR Title: Genetic analysis of nicotinic signaling in worms and flies. Citation: Journal of Neurobiology 53: 535-541 2002 Type: REVIEW Genes: acr-16 deg-3 des-2 lev-1 lev-9 ric-3 tpa-1 unc-29 unc-38 unc-50 unc-63 unc-74 Abstract: The nicotinic acetylcholine receptor is among the most thoroughly characterized molecules in the nervous system, and its role in mediating fast cholinergic neurotransmission has been broadly conserved in both vertebrates and invertebrates. However, the accessory molecules that facilitate or regulate nicotinic signaling remain mostly unknown. One approach to identify such molecules is to use molecular genetics in a simple, experimentally accessible organism to identify genes required for nicotinic signaling and to determine the molecular identity of the mutant genes through molecular cloning. Because cellular signaling pathways are often highly conserved between different animal phyla, the information gained from studies of simple organisms has historically provided many critical insights into more complex organisms, including humans. Genetic screens essentially make no prior assumptions about the types of molecules involved in the process being studied; thus, they are well suited for identifying previously unknown components of cell signaling pathways. The sophisticated genetic tools available in organisms such as the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster have also proven extremely powerful in elucidating complex biologic pathways in the absence of prior biochemical information and for assessing a molecule's in vivo function of in the context of an intact nervous system. This review describes how genetic analysis has been used to investigate nicotinic signaling mechanisms in worms and flies, and the prospects for using these studies to gain insight into nicotinic receptor function ------------------- Key: 5595 Medline: 12421563 Authors: Hamada T;Sakube Y;Ahnn J;Kim DH;Kagawa H Title: Molecular dissection, tissue localization and Ca2+ binding of the ryanodine receptor of Caenorhabditis elegans. Citation: Journal of Molecular Biology 324: 123-135 2002 Type: ARTICLE Genes: ryr-1 unc-68 Abstract: The ryanodine receptor of Caenorhabditis elegans (CeRyR) which contains 5071 amino acid residues, is encoded by a single gene, ryr-1/unc-68. The unc-68(kh30) mutation, isolated in an animal showing abnormal response to the anesthetic ketamine, has the substitution Ser1444Asn in CeRyR, predicted to be a phosphorylation site. To elucidate the function of the region of CeRyR, and to determine the localization of CeRyR in this animal, ten region-peptides were produced in Escherichia coli by using expression plasmids and eight antisera were raised against these fusion peptides. One antibody against the region corresponding to the kh30 mutation site enabled detection of CeRyR from mutant animals both in Western analysis and in situ. Specificity of this antiserum was demonstrated using Western analysis, which showed the full size and the partial size bands in wildtype and in the Tc1-induced deletion mutant animals, respectively, but no corresponding bands in unc-68 null mutant animals. CeRyR was detected in I-bands of muscle sarcomeres by double immunostaining. CeRyR was found in the body wall, pharyngeal, vulval, anal and sex muscles of adult worms and also found to be present in embryonic muscle, but not in non-muscle cells. Two EF-hand motifs and the C terminus were demonstrated to be Ca2+ binding regions. On the basis of these results, we propose a model for the functional domains of CeRyR, which agrees well with the model of mammalian skeletal RyR, which is based on proteolysis and cross-linking analysis. We discuss the usefulness and limitations of the molecular dissection approach, which uses peptides and peptide-specific antibodies to determine the local structure and function of individual domains within a large ------------------- Key: 5596 Medline: 12426375 Authors: Tonkin LA;Saccomanno L;Morse DP;Brodigan T;Krause M;Bass BL Title: RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans. Citation: EMBO Journal 22: 6025-6035 2002 Type: ARTICLE Genes: adr-1 adr-2 Abstract: Here we take advantage of the well-characterized and simple nervous system of Caenorhabditis elegans to further our understanding of the functions of RNA editing. We describe the two C.elegans ADAR genes, adr-1 and adr-2, and characterize strains containing homozygous deletions in each, or both, of these genes. We find that adr-1 is expressed in most, if not all, cells of the C.elegans nervous system and also in the developing vulva. Using chemotaxis assays, we show that both ADARs are important for normal behavior. Biochemical, molecular and phenotypic analyses indicate that ADR-1 and ADR-2 have distinct roles in C.elegans, but sometimes act together. ------------------- Key: 5597 Medline: 12445383 Authors: Hofmann ER;Milstein S;Boulton SJ;Ye M;Hofmann JJ;Stergiou L;Gartner A;Vidal M;Hengartner MO Title: Caenorhabditis elegans HUS-1 is a DNA damage checkpoint protein required for genome stability and EGL-1-mediated apoptosis. Citation: Current Biology 12: 1908-1918 2002 Type: ARTICLE Genes: ced-3 cep-1 cki-1 cki-2 dam-1 egl-1 glp-4 hpr-17 hus-1 mrt-2 rad-5 unc-119 Abstract: Background: The inability to efficiently repair DNA damage or remove cells with severely damaged genomes has been linked to several human cancers. Studies in yeasts and mammals have identified several genes that are required for proper activation of cell cycle checkpoints following various types of DNA damage. However, in metazoans, DNA damage can induce apoptosis as well. How DNA damage activates the apoptotic machinery is not fully understood. Results: We demonstrate here that the Caenorhabditis elegans gene hus-1 is required for DNA damage-induced cell cycle arrest and apoptosis. Following DNA damage, HUS-1 relocalizes and forms distinct foci that overlap with chromatin. Relocalization does not require the novel checkpoint protein RAD-5; rather, relocalization appears more frequently in rad-5 mutants, suggesting that RAD-5 plays a role in repair. HUS-1 is required for genome stability, as demonstrated by increased frequency of spontaneous mutations, chromosome nondisjunction, and telomere shortening. Finally, we show that DNA damage increases expression of the proapoptotic gene egl-1, a response that requires hus-1 and the p53 homolog cep-1. Conclusions: Our findings suggest that the RAD-5 checkpoint protein is not required for HUS-1 to relocalize following DNA damage. Furthermore, our studies reveal a new function of HUS-1 in the prevention of telomere shortening and mortalization of germ cells. DNA damage-induced germ cell death is abrogated in hus-1 mutants, in part, due to the inability of these mutants to activate egl-1 transcription in a cep-1/p53dependent manner. Thus, HUS-1 is required for p53-dependent activation of a BH3 domain protein in C. elegans. ------------------- Key: 5598 Medline: 12445390 Authors: Walhout AJM;Reboul J;Shtanko O;Bertin N;Vaglio P;Ge H;Lee H;Doucette-Stamm L;Gunsalus KC;Schetter AJ;Morton DG;Kemphues KJ;Reinke V;Kim SK;Piano F;Vidal M Title: Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Citation: Current Biology 12: 1952-1958 2002 Type: ARTICLE Genes: Abstract: By integrating functional genomic and proteomic mapping approaches, biological hypotheses should be formulated with increasing levels of confidence [1-5]. For example, yeast interactome and transcriptome data can be correlated in biologically meaningful ways [69]. Here, we combine interactome mapping data generated for a multicellular organism with data from both large-scale phenotypic analysis ("phenome mapping") and transcriptome profiling. First, we generated a two-hybrid interactome map of the Caenorhabditis elegans germline by using 600 transcripts enriched in this tissue [10]. We compared this map to a phenome map of the germline obtained by RNA interference (RNAi) [34] and to a transcriptome map obtained by clustering worm genes across 553 expression profiling experiments [11]. In this dataset, we find that essential proteins have a tendency to interact with each other, that pairs of genes encoding interacting proteins tend to exhibit similar expression profiles, and that, for similar to24% of germline interactions, both partners show overlapping embryonic lethal or high incidence of males RNAi phenotypes and similar expression profiles. We propose that these interactions are most likely to be relevant to germline biology. Similar integration of interactome, phenome, and transcriptome data should be possible for other biological processes in the nematode and for other ------------------- Key: 5599 Medline: 12445391 Authors: Piano F;Schetter AJ;Morton DG;Gunsalus KC;Reinke V;Kim SK;Kemphues KJ Title: Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Citation: Current Biology 12: 1959-1964 2002 Type: ARTICLE Genes: Abstract: Recently, a set of 766 genes that are enriched in the ovary as compared to the soma was identified by microarray analysis [1]. Here, we report a functional analysis of 98% of these genes by RNA interference (RNAi). Over half the genes tested showed at least one detectable phenotype, most commonly embryonic lethality, consistent with the expectation that ovary transcripts would be enriched for genes that are essential,in basic cellular and developmental processes. We find that essential genes are more likely to be conserved and to be highly expressed in the ovary. We extend previous observations [2, 3] and find that fewer than the expected number of ovary-expressed essential genes are present on the X chromosome. We characterized early embryonic defects for 161 genes and used time-lapse microscopy to systematically describe the defects for each gene in terms of 47 RNAi-associated phenotypes. In this paper, we discuss the use of these data to group genes into "phenoclusters"; in the accompanying paper, we use these data as one component in the integration of different types of large-scale functional analyses [4]. We find that phenoclusters correlate well with sequence-based functional predictions and thus may be useful in predicting functions of uncharacterized genes. ------------------- Key: 5600 Medline: 12145714 Authors: Gagnon SN;Hengartner MO;Desnoyers S Title: The genes pme-1 and pme-2 encode two poly(ADP-ribose) polymerases in Caenorhabditis elegans. Citation: Biochemical Journal 368: 263-271 2002 Type: ARTICLE Genes: pme-1 pme-2 pme-3 pme-4 pme-5 pme-6 Abstract: Poly(ADP-ribose) polymerases (PARPs) are an expanding, well-conserved family of enzymes found in many metazoan species, including plants. The enzyme catalyses poly(ADP-ribosyl)ation, a post-translational modification that is important in DNA repair and programmed cell death. In the present study, we report the finding of an endogenous source of poly(ADP-ribosyl)ation in total extracts of the nematode Caenorhabditis elegans. Two cDNAs encoding highly similar proteins to human PARP-I (huPARP-1) and huPARP-2 are described, and we propose to name the corresponding enzymes poly(ADP-ribose) metabolism enzyme I (PME-1) and PME-2 respectively. PME-1 (108 kDa) shares 31 % identity with huPARP-1 and has an overall structure similar to other PARP-I subfamily members. It contains sequences having considerable similarity to zinc-finger motifs I and 11, as well as with the catalytic domain of huPARP-1. PME-2 (61 kDa) has structural similarities with the catalytic domain of PARPs in general and shares 24% identity with huPARP-2. Recombinant PME-1 and PME-2 display PARP activity, which may partially account for the similar activity found in the worm. A partial duplication of the pme-1 gene with pseudogene-like features was found in the nematode genome. Messenger RNA for pme-1 are 5'-tagged with splice leader 1, whereas those for pme-2 are tagged with splice leader 2, suggesting an operon-like expression for pme-2. The express ion pattern of pme-1 and pme-2 is also developmentally regulated. Together, these results show that PARP-1 and -2 are conserved in evolution and must have important functions in multicellular organisms. We propose using C. elegans as a model to understand better the ------------------- Key: 5601 Medline: 12142272 Authors: Pasquinelli AE;Ruvkun G Title: Control of developmental timing by microRNAs and their targets. Citation: Annual Review of Cell & Developmental Biology 18: 495-513 2002 Type: REVIEW Genes: alg-1 alg-2 daf-12 dcr-1 ego-1 let-7 lin-4 lin-14 lin-28 lin-29 lin-41 lin-42 mir-84 rde-1 Abstract: In Caenorhabditis elegans the timing of many developmental events is regulated by heterochronic genes. Such genes orchestrate the timing of cell divisions and fates appropriate for the developmental stage of an organism. Analyses of heterochronic mutations in the nematode C. elegans have revealed a genetic pathway that controls the timing of post-embryonic cell divisions and fates. Two of the genes in this pathway encode small regulatory RNAs. The 22 nucleotide (nt) RNAs downregulate the expression of protein-coding mRNAs of target heterochronic genes. Analogous variations in the timing of appearance of particular features have been noted among closely related species, suggesting that such explicit control of developmental timing may not be exclusive to C. elegans. In fact, some of the genes that globally pattern the temporal progression of C. elegans development, including one of the tiny RNA genes, are conserved and temporally regulated across much of animal phylogeny, suggesting that the molecular mechanisms of temporal control are ancient and universal. A very large family of tiny RNA genes called microRNAs, which are similar in structure to the heterochronic regulatory RNAs, have been detected in diverse animal species and are likely to be present in most metazoans. Functions of the newly discovered microRNAs are not yet known. Other examples of temporal programs during growth include the exquisitely choreographed temporal sequences of developmental fates in neurogenesis in Drosophila and the sequential programs of epidermal coloration in insect wing patterning. An interesting possibility is that microRNAs mediate transitions on a variety of time scales to pattern the activities of particular target protein-coding genes and in turn generate sets of cells over a period of time. Plasticity in these microRNA genes or their targets may lead to changes in relative developmental timing between related species, or heterochronic change. Instead of inventing new gene functions, even subtle changes in temporal expression of pre-existing control genes can result in speciation by altering the time at which they function. ------------------- Key: 5602 Medline: 12477393 Authors: Haag ES;Wang S;Kimble J Title: Rapid coevolution of the nematode sex-determining genes fem-3 and tra-2. Citation: Current Biology 12: 2035-2041 2002 Type: ARTICLE Genes: fem-1 fem-2 fem-3 tra-2 twk-19 Abstract: Unlike many features of metazoan development, sex determination is not widely conserved among phyla [1-3]. However, the recent demonstration [4] that one gene family controls sexual development in Drosophila, C. elegans, and vertebrates suggests that sex determination mechanisms may have evolved from a common pathway that has diverged radically since the Cambrian. Sex determination gene sequences often evolve quickly (e.g., [5, 69 7]), but it is not known how this relates to higher-order pathways or what selective or neutral forces are driving it. In such a rapidly evolving developmental pathway, the fate of functionally linked genes is of particular interest. To investigate a pair of such genes, we cloned orthologs of the key C. elegans male-promoting gene fem-3 from two sister species, C. briggsae and C. remanei. We employed RNA interference to show that in all three species, the male-promoting function of fem-3 and its epistatic relationship with its female-promoting upstream repressor, tra-2, are conserved. Consistent with this, the FEM-3 protein interacts with TRA-2 in each species, but in a strictly species-specific manner. Because FEM-3 is the most divergent protein yet described in Caenorhabditis and the FEM-3 binding domain of TRA-2 is itself hypervariable [8, 9], a key protein-protein interaction is rapidly evolving in concert. Extrapolation of this result to larger phylogenetic scales helps explain the dissimilarity of the sex determination systems across phyla. ------------------- Key: 5603 Medline: 12498681 Authors: Severson AF;Baillie DL;Bowerman B Title: A Formin Homology protein and a Profilin are required for cytokinesis and Arp2/3-independent assembly of cortical microfilaments in C. elegans. Citation: Current Biology 12: 2066-2075 2002 Type: ARTICLE Genes: act-5 arp-2 arp-3 cyk-1 mlc-4 nmy-2 pfn-1 Abstract: Background: F-actin is enriched at the cortex of embryonic cells in the nematode Caenorhabditis elegans and is required for multiple processes that include the establishment of an anterior-posterior (A-P) axis and cytokinesis. However, the mechanisms that regulate cortical microfilament (MF) assembly remain poorly understood. Results: We show here that a profilin called PFN-1 accumulates at the cortex independent of the actin cytoskeleton and is required for the assembly or maintenance of cortical MFs and myosin. Reducing PFN-1 levels by RNAi results in cytokinesis and A-P polarity defects. PFN-1 binds to the Formin Homology (FH) protein CYK-1, which also is required for cortical MFs. In contrast to PFN-1 and CYK-1, the Arp2/3 complex appears to be dispensable for the assembly of cortical MFs, for A-P polarity, and for cytokinesis. Instead, the Arp2/3 complex is required for cell migrations that occur during gastrulation and may also be involved in cellular rearrangements required for epidermal enclosure prior to elongation of ovoid embryos into vermiform larvae. Conclusions: We conclude that the FH protein CYK-1 and the profilin PFN-1 mediate the Arp2/3-independent assembly of MFs and are required for cytokinesis in the early embryo. These data suggest that CYK-1 and PFN-1 may nucleate MFs, as has recently been shown for an FH protein and a profilin ------------------- Key: 5604 Medline: 12498686 Authors: Kitagawa R;Law E;Tang L;Rose AM Title: The Cdc20 homolog, FZY-1, and its interacting protein, IFY-1, are required for proper chromosome segregation in Caenorhabditis elegans. Citation: Current Biology 12: 2118-2123 2002 Type: ARTICLE Genes: emb-30 fzy-1 ify-1 mdf-1 mdf-2 hDf35 Abstract: Accurate chromosome segregation is achieved by a series of highly regulated processes that culminate in the meta phase-to-anaphase transition of the cell cycle. In the budding yeast Saccharomyces cerevisiae, the degradation of the securin protein Pds1 [1-3] reverses the binding and inhibition of the separase protein Esp1 [4]. Esp1 cleaves Scc1. That cleavage promotes the dissociation of the cohesin complex from the chromosomes [5,6] and leads the separation of sister chromatids. Proteolysis of Pds1 is regulated by the anaphase-promoting complex (APC), a large multi-subunit E3 ubiquitin ligase [7] whose activity is regulated by Cdc20/Fizzy [8-11]. We have previously shown that the Caenorhabditis elegans genes mdf-1/MAD1 and mdf-2/MAD2 encode key members of the spindle checkpoint [12]. Loss of function of either gene leads to an accumulation of somatic and heritable defects and ultimately results in death. Here we show that a missense mutation in fzy-1/CDC20/Fizzy suppresses mdf-1 lethality. We identified a FZY-1-interacting protein, IFY-1, a novel destruction-box protein. IFY-1 accumulates in one-cell-arrested emb-30/APC4 embryos and interacts with SEP-1, a C. elegrans separase, suggesting that IFY-1 ------------------- Key: 5605 Medline: 12507426 Authors: Unhavaithaya Y;Shin TH;Miliaras N;Lee J;Oyama T;Mello CC Title: MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. Citation: Cell 111: 991-1002 2002 Type: ARTICLE Genes: glh-1 glh-2 glh-4 hda-1 let-418 lin-15 lin-36 mep-1 mes-2 mes-3 mes-4 mes-6 myo-2 pie-1 pgl-1 Abstract: A rapid cascade of regulatory events defines the developmental fates of embryonic cells. However, once established, these developmental fates and the underlying transcriptional programs can be remarkably stable. Here, we describe two proteins, MEP-1 and LET-418/Mi-2, required for maintenance of somatic differentiation in C. elegans. In animals lacking MEP-1 and LET-418, germline-specific genes become derepressed in somatic cells, and Polycomb group (PcG) and SET domain-related proteins promote this ectopic expression. MEP-1 and LET-418 interact in vivo with the germline-protein PIE-1. Our findings support a model in which PIE-1 inhibits MEP-1 and associated factors to maintain the pluripotency of germ cells, while at later times MEP-1 and LET-418 remodel chromatin to establish new stage- or cell-type-specific differentiation potential. ------------------- Key: 5606 Medline: 12526801 Authors: Bargmann C;Hodgkin J Title: Accolade for elegans. Citation: Cell 111: 759-762 2002 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-9 lin-12 nuc-1 Abstract: In 1963, Sydney Brenner, one of the founders of molecular biology, had reached an intellectual impasse. He felt that there were few advances left in that field that would have the significance of the discovery of mRNA and the elucidation of the genetic code, both of which he had participated in, and in any case with so many Americans joining in, the chemical details of replication and so forth would all be worked out soon. Brenner thought large thoughts, and the questions that were left seemed too ------------------- Key: 5607 Medline: 12506000 Authors: Struckhoff EC;Lundquist EA Title: The actin-binding protein UNC-115 is an effector of Ras signaling during axon pathfinding in C. elegans. Citation: Development 130: 693-704 2003 Type: ARTICLE Genes: ced-10 mig-2 rac-2 rac-3 rho-1 unc-73 unc-115 Abstract: Rac GTPases control cell shape by regulating downstream effectors that influence the actin cytoskeleton. UNC-115, a putative actin-binding protein similar to human abLIM/limatin, has previously been implicated in axon pathfinding. We have discovered the role of UNC-115 as a downstream cytoskeletal effector of Rac signaling in axon pathfinding. We show that unc-115 double mutants with ced-10 Rac, mig-2 Rac or unc-73 GEF but not with rac-2/3 Rac displayed synthetic axon pathfinding defects, and that loss of unc-115 function suppressed the formation of ectopic plasma membrane extensions induced by constitutively-active rac-2 in neurons. Furthermore, we show that UNC-115 can bind to actin filaments. Thus, UNC-115 is an actin-binding protein that acts downstream of Rac signaling in axon pathfinding. ------------------- Key: 5608 Medline: 12466198 Authors: Lee JY;Goldstein B Title: Mechanisms of cell positioning during C. elegans gastrulation. Citation: Development 130: 307-320 2003 Type: ARTICLE Genes: gad-1 mom-2 Abstract: Cell rearrangements are crucial during development. In this study, we use C. elegans gastrulation as a simple model to investigate the mechanisms of cell positioning. During C. elegans gastrulation, two endodermal precursor cells move from the ventral surface to the center of the embryo, leaving a gap between these ingressing cells and the eggshell. Six neighboring cells converge under the endodermal precursors, filling this gap. Using an in vitro system, we observed that these movements occurred consistently in the absence of the eggshell and the vitelline envelope. We found that movement of the neighbors towards each other is not dependent on chemotactic signaling between these cells. We further found that C. elegans gastrulation requires intact microfilaments, but not microtubules. The primary mechanism of microfilament-based motility does not appear to be through protrusive structures, such as lamellipodia or filopodia. Instead, our results suggest an alternative mechanism. We found that myosin activity is required for gastrulation, that the apical sides of the ingressing cells contract, and that the ingressing cells determine the direction of movement of their neighboring cells. Based on these results, we propose that ingression is driven by an actomyosin-based contraction of the apical side of the ingressing cells, which pulls neighboring cells underneath. We conclude that apical constriction can function to position blastomeres in early embryos, even before ------------------- Key: 5609 Medline: 12399309 Authors: Koh K;Peyrot SM;Wood CG;Wagmaister JA;Maduro MF;Eisenmann DM;Rothman JH Title: Cell fates and fusion in the C. elegans vulval primordium are regulated by the EGL-18 and ELT-6 GATA factors - apparent direct targets of the LIN-39 Hox protein. Citation: Development 129: 5171-5180 2002 Type: ARTICLE Genes: egl-18 elt-5 elt-6 lin-39 Abstract: Development of the vulva in C. elegans is mediated by the combinatorial action of several convergent regulatory inputs, three of which, the Ras, Writ and Rb-related pathways, act by regulating expression of the lin-39 Hox gene. LIN-39 specifies cell fates and regulates cell fusion in the mid-body region, leading to formation of the vulva. In the lateral seam epidermis, differentiation and cell fusion have been shown to be regulated by two GATA-type transcription factors, ELT-5 and -6. We report that ELT-5 is encoded by the egl-18 gene, which was previously shown to promote formation of a functional vulva. Furthermore, we find that EGL-18 (ELT-5), and its paralogue ELT-6, are redundantly required to regulate cell fates and fusion in the vulval primordium and are essential to form a vulva. Elimination of egl-18 and elt-6 activity results in arrest by the first larval stage; however, in animals rescued for this larval lethality by expression of ELT-6 in non-vulval cells, the post-embryonic cells (P3.p-P8.p) that normally become vulval precursor cells often fuse with the surrounding epidermal syncytium or undergo fewer than normal cell divisions, reminiscent of lin-39 mutants. Moreover, egl-18/elt-6 reporter gene expression in the developing vulva is attenuated in lin-39(rf) mutants, and overexpression of egl-18 can partially rescue the vulval defects caused by reduced lin-39 activity. LIN-39/CEH-20 heterodimers bind two consensus HOX/PBC sites in a vulval enhancer region of egl-18/elt-6, one of which is essential for vulval expression of egl-18/elt-6 reporter constructs. These findings demonstrate that the EGL-18 and ELT-6 GATA factors are essential, genetically redundant regulators of cell fates and fusion in the developing vulva and are apparent direct transcriptional targets of the LIN-39 Hox protein. ------------------- Key: 5610 Medline: 12482710 Authors: Palmer RE;Inoue T;Sherwood DR;Jiang LI;Sternberg PW Title: Caenorhabditis elegans cog-1 locus encodes GTX/Nkx6.1 homeodomain proteins and regulates multiple aspects of reproductive system development. Citation: Developmental Biology 252: 202-213 2002 Type: ARTICLE Genes: cog-1 lin-11 Abstract: The development of the reproductive system in Caenorhabditis elegans is a well-established model system for patterning and organogenesis. We report the characterization of the cog-1 gene, mutations in which cause novel phenotypes in late patterning in vulval lineages, establishment of the vulva-uterine connection, development and function of the spermathecal-uterine junction, and the development of vas deferens-proctodeal connection in the male. We positionally cloned cog-1 and found that it encodes a homeobox protein most similar to the mammalian GTX and Nkx6.1 proteins. Analysis of cog-1 transcripts revealed that cog-1 is likely a complex locus with two promoters. Two mutant alleles of cog-1 differentially affect alternative transcripts and cause different phenotypes, suggesting that the two forms of ------------------- Key: 5611 Medline: 12502736 Authors: Shemer G;Podbilewicz B Title: LIN-39/Hox triggers cell division and represses EFF-1/fusogen-dependent vulval cell fusion. Citation: Genes & Development 16: 3136-3141 2002 Type: ARTICLE Genes: ceh-20 eff-1 lin-39 Abstract: General mechanisms by which Hox genes establish cell fates are known. However, a few Hox effectors mediating cell behaviors have been identified. Here we found the first effector of LIN-39/HoxD4/Dfd in Caenorhabditis elegans. In specific vulval precursor cells (VPCs), LIN-39 represses early and late expression of EFF-1, a membrane protein essential for cell fusion. Repression of eff-1 is also achieved by the activity of CEH-20/Exd/Pbx, a known cofactor of Hox proteins. Unfused VPCs in lin-39(-),eff-1(-) double mutants fail to divide but migrate, executing vulval fates. Thus, Bn-39 is essential for inhibition of EFF-1-dependent cell fusion and stimulation of cell proliferation during vulva formation. ------------------- Key: 5612 Medline: 12464635 Authors: Nolan KM;Sarafi-Reinach TR;Horne JG;Saffer AM;Sengupta P Title: The DAF-7 TGF-beta signaling pathway regulates chemosensory receptor gene expression in C. elegans. Citation: Genes & Development 16: 3061-3073 2002 Type: ARTICLE Genes: daf-2 daf-3 daf-4 daf-7 daf-8 daf-12 daf-14 dbl-1 odr-10 sra-6 srd-1 sre-1 srg-8 srg-13 str-1 str-2 str-3 unc-129 Abstract: Regulation of chemoreceptor gene expression in response to environmental or developmental cues provides a mechanism by which animals can alter their sensory responses. Here we demonstrate a role for the daf-7 TGF-beta pathway in the regulation of expression of a subset of chemoreceptor genes in Caenorhabditis elegans. We describe a novel role of this pathway in maintaining receptor gene expression in the adult and show that the DAF-4 type II TGF-beta receptor functions cell-autonomously to modulate chemoreceptor expression. We also find that the alteration of receptor gene expression in the ASI chemosensory neurons by environmental signals, such as levels of a constitutively produced pheromone, may be mediated via a DAF-7-independent pathway. Receptor gene expression in the ASI and ASH sensory neurons appears to be regulated via distinct mechanisms. Our results suggest that the expression of individual chemoreceptor genes in C. elegans is subject to multiple modes of regulation, thereby ensuring that animals exhibit the responses most appropriate for their ------------------- Key: 5613 Medline: 12361949 Authors: Cipollo JF;Costello CE;Hirschberg CB Title: The fine structure of Caenorhabditis elegans N-glycans. Citation: Journal of Biological Chemistry 277: 49143-49157 2002 Type: ARTICLE Genes: gly-2 Abstract: We report the fine structure of a nearly contiguous series of N-glycans from the soil nematode Caenorhabditis elegans. Five major classes are revealed including high mannose, mammalian-type complex, hybrid, fuco-pausimannosidic (five mannose residues or fewer substituted with fucose), and phosphocholine oligosaccharides. The high mannose, complex, and hybrid N-glycan series show a high degree of conservation with the mammalian biosynthetic pathways. The fuco-pausimannosidic glycans contain a novel terminal fucose substitution of mannose. The phosphocholine oligosaccharides are high mannose type and are multiply substituted with phosphocholine. Although phosphocholine oligosaccharides are known immunomodulators in human nematode and trematode infections, C. elegans is unique as a non-parasitic nematode containing phosphocholine N-glycans. Therefore, studies in C. elegans should aid in the elucidation of the biosynthetic pathway(s) of this class of biomedically relevant compounds. Results presented here show that C. elegans has a functional orthologue for nearly every known enzyme found to be deficient in congenital disorders of glycosylation types I and II. This nematode is well characterized genetically and developmentally. Therefore, elucidation of its N-glycome, as shown in this report, may place it among the useful systems used to investigate human disorders of glycoconjugate synthesis such as the congenital disorders ------------------- Key: 5614 Medline: 12393910 Authors: Wolkow CA;Munoz MJ;Riddle DL;Ruvkun G Title: Insulin receptor substrate and p55 orthologous adaptor proteins function in the Caenorhabditis elegans daf-2/insulin-like signaling pathway. Citation: Journal of Biological Chemistry 277: 49591-49597 2002 Type: ARTICLE Genes: aap-1 age-1 akt-1 daf-2 ist-1 Abstract: An insulin-like signaling pathway regulates development and lifespan in Caenorhabditis elegdns. Genetic screens that identified many components of the C. elegans insulin pathway did not identify homologs of insulin receptor substrates or the phosphoinositide 3-kinase (PI3K) adaptor/regulatory subunit, which are both required for signaling by mammalian insulin/insulin-like growth factor I pathways. The C. elegans genome contains one homolog of each protein. The C. elegans versions of insulin receptor substrate (IST-1) and PI3K p50/p55 (AAP-1) share moderate sequence similarity with their vertebrate and Drosophila counterparts. Genetic experiments show that ist-1 and aap-1 potentiate C. elegans insulin-like signaling, although they are not required for signaling in the pathway under most conditions. Worms lacking AAP-1 activity because of the mutation aap-1(m889) constitutively arrest development at the dauer larval stage when raised at high temperatures. aap-1 mutants also live longer than wild-type animals, a phenotype observed in other C. elegans mutants with defects in DAF-2 signaling. Interestingly, IST-1 appears to be required for signaling through a pathway that may act in ------------------- Key: 5615 Medline: 12354761 Authors: Patikoglou GA;Koelle MR Title: An N-terminal region of Caenorhabditis elegans RGS proteins signals EGL-10 and EAT-16 directs inhibition of G-alpha(o) versus G-alpha(q) signaling. Citation: Journal of Biological Chemistry 277: 47004-47013 2002 Type: ARTICLE Genes: eat-16 egl-10 rgs-1 Abstract: Regulator of G protein signaling (RGS) proteins contain an RGS domain that inhibits Galpha signaling by activating Galpha GTPase activity. Certain RGS proteins also contain a Ggamma-like (GGL) domain and a poorly characterized but conserved N-terminal region. We assessed the functions of these subregions in the Caenorhabditis elegans RGS proteins EGL-10 and EAT-16, which selectively inhibit GOA-1 (Galpha(o)) and EGL-30 (Galpha(q)), respectively. Using transgenes in C. elegans, we expressed EGL-10, EAT-16, their subregions, or EGL-10/EAT-16 chimeras. The chimeras showed that the GGL/RGS region of either protein can act on either GOA-1 or EGL-30 and that a key factor determining Ga target selectivity is the manner in which the N-terminal and GGL/RGS regions are linked. We also found that coexpressing N-terminal and GGL/RGS fragments of EGL-10 gave full EGL-10 activity, whereas either fragment alone gave little activity. Biochemical analysis showed that coexpressing the two fragments caused both to increase in abundance and also caused the GGL/RGS fragment to move to the membrane, where the N-terminal fragment is localized. By coimmunoprecipitation, we found that the N-terminal fragment complexes with the C-terminal fragment and its associated Gbeta subunit, GPB-2. We conclude that the N-terminal region directs inhibition of Galpha signaling by forming a complex with the GGL/RGS region and affecting its stability, membrane localization, and Galpha target ------------------- Key: 5616 Medline: 12482907 Authors: Starr DA;Han M Title: ANChors away: an actin based mechanism of nuclear positioning. Citation: Journal of Cell Science 116: 211-216 2003 Type: REVIEW Genes: anc-1 unc-83 unc-84 Abstract: Mechanisms for nuclear migration and nuclear anchorage function together to control nuclear positioning. Both tubulin and actin networks play important roles in nuclear positioning. The actin cytoskeleton. has been shown to position nuclei in a variety of systems from yeast to plants and animals. It can either act as a stable skeleton to anchor nuclei or supply the active force to move nuclei. Two C elegans genes and their homologues play important roles in these processes. Syne/ANC-1 anchors nuclei by directly tethering the nuclear envelope to the actin cytoskeleton, and UNC-84/SUN functions at the nuclear envelope to recruit Syne/ANC-1. ------------------- Key: 5617 Medline: 12486700 Authors: Emmons SW;Lipton J Title: Genetic basis of male sexual behavior. Citation: Journal of Neurobiology 54: 93-110 2003 Type: REVIEW Genes: cat-2 egl-1 egl-5 egl-19 lin-32 lov-1 mab-3 mab-5 mab-9 mab-23 mod-5 pkd-2 tra-1 unc-29 unc-38 unc-68 unc-77 Abstract: Male sexual behavior is increasingly the focus of genetic study in a variety of animals. Genetic analysis in the soil roundworm Caenorhabditis elegans and the fruit fly Drosophila melanogaster has lead to identification of genes and circuits that govern behaviors ranging from motivation and mate-searching to courtship and copulation. Some worm and fly genes have counterparts with related functions in higher animals and many more such correspondences can be expected. Analysis of mutations in mammals can potentially lead to insights into such issues as monogamous versus promiscuous sexual behavior and sexual orientation. Genetic analysis of sexual behavior has implications for understanding how the nervous system generates and controls a complex behavior. It can also help us to gain an appreciation of how behavior is encoded by genes and their regulatory sequences. ------------------- Key: 5618 Medline: 12486705 Authors: Hobert O Title: Behavioral plasticity in C. elegans: paradigms, circuits, genes. Citation: Journal of Neurobiology 54: 203-223 2003 Type: REVIEW Genes: acy-1 acy-2 adp-1 bas-1 cat-2 ceh-14 dgk-1 eat-4 egl-2 egl-19 egl-30 egl-36 egl-43 exp-2 flp-1 ftt-2 glr-1 goa-1 gpc-1 hen-1 kin-1 kin-13 lim-4 lim-6 lin-11 lin-18 lrn-1 lrn-2 mab-18 mec-3 mec-4 mec-10 mod-1 mod-5 ncs-1 nmr-1 nmr-2 odr-7 odr-10 osm-9 sax-3 sgs-1 snb-1 tax-2 tax-4 tax-6 tph-1 ttx-1 ttx-3 unc-2 unc-3 unc-4 unc-6 unc-8 unc-13 unc-17 unc-18 unc-25 unc-36 unc-38 unc-40 unc-43 unc-49 unc-86 unc-130 vab-3 Abstract: Life in the soil is an intellectual and practical challenge that the nematode Caenorhabditis elegans masters by utilizing 302 neurons. The nervous system assembled by these 302 neurons is capable of executing a variety of behaviors, some of respectable complexity. The simplicity of the nervous system, its thoroughly characterized structure, several sets of well-defined behaviors, and its genetic amenability combined with its isogenic background make C. elegans an attractive model organism to study the genetics of behavior. This review describes several behavioral plasticity paradigms in C. elegans and their underlying neuronal circuits and then goes on to review the forward genetic analysis that has been undertaken to identify genes involved in the execution of these behaviors. Lastly, the review outlines how reverse genetics and genomic approaches can guide the analysis of the role of genes in behavior and why and how they will complement the forward genetic analysis of behavior. ------------------- Key: 5619 Medline: 12495614 Authors: Schafer WR Title: PKG and the neural basis for behavioral phenotypes. Citation: Neuron 36: 991-993 2002 Type: REVIEW Genes: adp-1 egl-4 osm-9 tax-2 Abstract: Cyclic GMP-dependent protein kinase (PKG) has been implicated in the regulation of diverse aspects of vertebrate and insect behavior, yet the mechanisms underlying these effects are poorly understood. In this issue of Neuron, Fujiwara et al. and L'Etoile et al. address the neural basis for PKG function in C. elegans and demonstrate the power of behavioral genetic analysis in simple systems in the elucidation of neuronal signaling mechanisms in vivo. ------------------- Key: 5620 Medline: 12495623 Authors: L'Etoile ND;Coburn CM;Eastham J;Kistler A;Gallegos G;Bargmann CI Title: The cyclic GMP-dependent protein kinase EGL-4 regulates olfactory adaptation in C. elegans. Citation: Neuron 36: 1079-1089 2002 Type: ARTICLE Genes: daf-11 egl-4 gpa-2 odr-1 odr-3 str-2 tax-2 tax-4 Abstract: Prolonged odor exposure causes a specific, reversible adaptation of olfactory responses. A genetic screen for negative regulators of olfaction uncovered mutations in the cGMP-dependent protein kinase EGL-4 that disrupt olfactory adaptation in C. elegans. G protein-coupled olfactory receptors within the AWC olfactory neuron signal through cGMP and a cGMP-gated channel. The cGMP-dependent kinase functions in AWC neurons during odor exposure to direct adaptation to AWC-sensed odors, suggesting that adaptation is a cell intrinsic process initiated by cGMP. A predicted phosphorylation site on the beta subunit of the cGMP-gated channel is required for adaptation after short odor exposure, suggesting that phosphorylation of signaling molecules generates adaptation at early time points. A predicted nuclear localization signal within EGL-4 is required for adaptation after longer odor exposure, suggesting that nuclear translocation of EGL-4 triggers late forms of adaptation. ------------------- Key: 5621 Medline: 12495624 Authors: Fujiwara M;Sengupta P;McIntire SL Title: Regulation of body size and behavioral state of C. elegans by sensory perception and the EGL-4 cGMP-dependent protein kinase. Citation: Neuron 36: 1091-1102 2002 Type: ARTICLE Genes: chb-1 chb-2 chb-3 chb-4 che-2 che-3 dbl-1 egl-4 egl-8 egl-30 gpa-3 lon-1 odr-3 osm-6 tax-2 tax-4 Abstract: The growth and behavior of higher organisms depend on the accurate perception and integration of sensory stimuli by the nervous system. We show that defects in sensory perception in C. elegans result in abnormalities in the growth of the animal and in the expression of alternative behavioral states. Our analysis suggests that sensory neurons modulate neural or neuroendocrine functions, regulating both bodily growth and behavioral state. We identify genes likely to be required for these functions downstream of sensory inputs. Here, we characterize one of these genes as egl-4, which we show encodes a cGMP-dependent protein kinase. We demonstrate that this cGMP-dependent kinase functions in neurons of C. elegans to regulate multiple developmental and behavioral processes including the orchestrated growth of the animal and the expression of particular behavioral states. ------------------- Key: 5622 Medline: 12467596 Authors: Mellem JE;Brockie PJ;Zheng Y;Madsen DM;Maricq AV Title: Decoding of polymodal sensory stimuli by postsynaptic glutamate receptors in C. elegans. Citation: Neuron 36: 933-944 2002 Type: ARTICLE Genes: eat-4 egl-3 glr-1 glr-2 nmr-1 osm-10 Abstract: The C. elegans polymodal ASH sensory neurons detect mechanical, osmotic, and chemical stimuli and release glutamate to signal avoidance responses. To investigate the mechanisms of this polymodal signaling, we have characterized the role of postsynaptic glutamate receptors in mediating the response to these distinct stimuli. By studying the behavioral and electrophysiological properties of worms defective for non-NMDA (GLR-1 and GLR-2) and NMDA (NMR-1) receptor subunits, we show that while the osmotic avoidance response requires both NMDA and non-NMDA receptors, the response to mechanical stimuli only requires non-NMDA receptors. Furthermore, analysis of the EGL-3 proprotein convertase provides additional evidence that polymodal signaling in C. elegans occurs via the differential activation of postsynaptic glutamate receptor subtypes. ------------------- Key: 5623 Medline: 12490713 Authors: Ohtsuki T;Sakurai M;Sato A;Watanabe K Title: Characterization of the interaction between the nucleotide exchange factor EF-Ts from nematode mitochondria and elongation factor Tu. Citation: Nucleic Acids Research 30: 5444-5451 2002 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans mitochondria have two elongation factor (EF)-Tu species, denoted EF-Tu1 and EF-Tu2. Recombinant nematode EF-Ts purified from Escherichia coli bound both of these molecules and also stimulated the translational activity of EF-Tu, indicating that the nematode EF-Ts homolog is a functional EF-Ts protein of mitochondria. Complexes formed by the interaction of nematode EF-Ts with EF-Tu1 and EF-Tu2 could be detected by native gel electrophoresis and purified by gel filtration. Although the nematode mitochondrial (mt) EF-Tu molecules are extremely unstable and easily form aggregates, native gel electrophoresis and gel filtration analysis revealed that EF-Tu.EF-Ts complexes are significantly more soluble. This indicates that nematode EF-Ts can be used to stabilize homologous EF-Tu molecules for experimental purposes. The EF-Ts bound to two eubacterial EF-Tu species (E.coli and Thermus thermophilus). Although the EF-Ts did not bind to bovine mt EF-Tu, it could bind to a chimeric nematode-bovine EF-Tu molecule containing domains 1 and 2 from bovine mt EF-Tu. Thus, the nematode EF-Ts appears to have a broad specificity for EF-Tu molecules from different ------------------- Key: 5624 Medline: 12471266 Authors: Dillin A;Hsu AL;Arantes-Oliveira N;Lehrer-Graiwer J;Hsin H;Fraser AG;Kamath RS;Ahringer J;Kenyon C Title: Rates of behavior and aging specified by mitochondrial function during development. Citation: Science 298: 2398-2401 2002 Type: ARTICLE Genes: atp-3 cco-1 clk-1 cyc-1 daf-2 daf-4 daf-16 dcr-1 isp-1 Abstract: To explore the role of mitochondrial activity in the aging process, we have lowered the activity of the electron transport chain and adenosine 5'-triphosphate (ATP) synthase with RNA interference (RNAi) in Caenorhabditis elegans. These perturbations reduced body size and behavioral rates and extended adult life-span. Restoring messenger RNA to near-normal levels during adulthood did not elevate ATP levels and did not correct any of these phenotypes. Conversely, inhibiting respiratory-chain components during adulthood only did not reset behavioral rates and did not affect life-span. Thus, the developing animal appears to contain a regulatory system that monitors mitochondrial activity early in life and, in response, establishes rates of respiration, behavior, and aging that persist during adulthood. ------------------- Key: 5625 Medline: 12142361 Authors: Reinke V;White KP Title: Developmental genomic approaches in model organisms. Citation: Annual Review of Genomics & Human Genetics 3: 153-178 2002 Type: REVIEW Genes: glp-4 pha-4 Abstract: Functional genomics technologies can help decipher how information encoded in the genome is translated into morphology, physiology, and behavior during the development of complex organisms. A number of researchers have begun to apply DNA microarrays and other functional genomics approaches to study development. Here we review recent studies that take the first steps toward relating genome-wide information to developmental events, we discuss recent genomics approaches taken in animal model systems used to study human disease, and we outline methods that may be useful for constructing genome-wide maps of developmental processes. ------------------- Key: 5626 Medline: Authors: Tominaga N;Tomoeda M;Kohra S;Takao Y;Nagae M;Ueda K;Ishibashi Y;Kai T;Arizono K Title: A convenient sublethal assay of alkylphenol and organotin compounds using the nematode Caenorhabditis elegans. Citation: Journal of Health Science 48: 555-559 2002 Type: ARTICLE Genes: Abstract: The free-living nematode, Caenorhabditis elegans (C. elegans) was adopted as a multicellular biosensor of biological toxicity from alkylphenols and organotin compounds. Alkylphenols were found to affect reproduction at lower doses than indicated by the acute toxicity assay. In particular, nonylphenol altered the reproduction rate of C. elegans at a dose 10- to 100-fold lower than the 50% lethal concentration (LC50). A comparison of the number of viable worms and eggs suggested that alkylphenols and organotin compounds possess hatching toxicity. A 0.1 mu M dose of organotin compounds caused a significant decrease, in the order of 20-50%, in reproduction of the worms, and an abnormal male: hermaphrodite ratio was observed. C. elegans therefore appears to represent a potent and sensitive organism with which to evaluate the biological effects of chemicals. In particular, the sensitivity of reproduction as an endpoint is highly useful for assessing the sublethal effects of chemicals. ------------------- Key: 5627 Medline: Authors: Ura K;Kai T;Sakata S;Iguchi T;Arizono K Title: Aquatic acute toxicity testing using the nematode Caenorhabditis elegans. Citation: Journal of Health Science 48: 583-586 2002 Type: ARTICLE Genes: Abstract: To evaluate the toxicity of environmental chemicals to invertebrates, a static bioassay was developed in the laboratory using the Caenorhabditis elegans (C. elegans). First, reproducibility of this aquatic acute toxicity test system was confirmed. In order to estimate chemical toxicities in C. elegans, worms were subsequently exposed to eleven different xenobiotics. Mortality after 24hr was adopted as the endpoint of toxicity. We found that benzo[a]pyrene, nonylphenol, benzophenone, bisphenol A and cadmium chloride affected viability of C. elegans. These data suggest that C. elegans is a suitable toxicity test organism for environmental xenobiotic chemicals, and that lethality can be used as a testing endpoint. ------------------- Key: 5628 Medline: Authors: Campagnola PJ;Millard AC;Terasaki M;Hoppe PE;Malone CJ;Mohler WA Title: Three-dimensional high-resolution second-harmonic generation imaging of endogenous structural proteins in biological tissues. Citation: Biophysical Journal 82: 493-508 2002 Type: ARTICLE Genes: Abstract: We find that several key endogenous protein structures give rise to intense second-harmonic generation (SHG)nonabsorptive frequency doubling of an excitation laser line. Second-harmonic imaging microscopy (SHIM) on a laser-scanning system proves, therefore, to be a powerful and unique tool for high-resolution, high-contrast, three-dimensional studies of live cell and tissue architecture. Unlike fluorescence, SHG suffers no inherent photobleaching or toxicity and does not require exogenous labels. Unlike polarization microscopy, SHIM provides intrinsic confocality and deep sectioning in complex tissues. In this study, we demonstrate the clarity of SHIM optical sectioning within unfixed, unstained thick specimens. SHIM and two-photon excited fluorescence (TPEF) were combined in a dual-mode nonlinear microscopy to elucidate the molecular sources of SHG in live cells and tissues. SHG arose not only from coiled-coil complexes within connective tissues and muscle thick filaments, but also from microtubule arrays within interphase and mitotic cells. Both polarization dependence and a local symmetry cancellation effect of SHG allowed the signal from species generating the second harmonic to be decoded, by ratiometric correlation with TPEF, to yield information on local structure below optical resolution. The physical origin of SHG within these tissues is addressed and is attributed to the laser interaction with dipolar protein structures that is enhanced by the intrinsic chirality of the protein helices. ------------------- Key: 5629 Medline: 12399316 Authors: Van Auken K;Weaver D;Robertson B;Sundaram M;Saldi T;Edgar L;Elling U;Lee M;Boese Q;Wood WB Title: Roles of the Homothorax/Meis/Prep homolog UNC-62 and the Exd/Pbx homologs CEH-20 and CEH-40 in C. elegans embryogenesis. Citation: Development 129: 5255-5238 2002 Type: ARTICLE Genes: ceh-25 ceh-26 ceh-40 nob-1 pal-1 php-3 unc-62 nDf16 sDf26 sDf27 sDf50 svDp1 Abstract: Co-factor homeodomain proteins such as Drosophila Homothorax (Hth) and Extradenticle (Exd) and their respective vertebrate homologs, the Meis/Prep and Pbx proteins, can increase the DNA-binding specificity of Hox protein transcription factors and appear to be required for many of their developmental functions. We show that the unc-62 gene encodes the C elegans ortholog of Hth, and that maternal-effect unc-62 mutations can cause severe posterior disorganization during embryogenesis (Nob phenotype), superficially similar to that seen in embryos lacking function of either the two posterior-group Hox genes nob-1 and php-3 or the caudal homolog pal-1. Other zygotically acting unc-62 alleles cause earlier embryonic arrest or incompletely penetrant larval lethality with variable morphogenetic defects among the survivors, suggesting that unc-62 functions are required at several stages of development. The differential accumulation of four unc-62 transcripts is consistent with multiple functions. The C. elegans exd homologs ceh-20 and ceh-40 interact genetically with unc-62 and may have overlapping roles in ernbryogenesis: neither CEH-20 nor CEH-40 appears to be required when the other is present, but loss of both functions causes incompletely penetrant embryonic lethality in the presence of unc-62(+) and complete embryonic lethality in the presence of an unc-62 hypomorphic allele. ------------------- Key: 5630 Medline: 12459721 Authors: Simpson P Title: Evolution of development in closely related species of flies and worms. Citation: Nature Reviews Genetics 3: 907-917 2002 Type: REVIEW Genes: lin-39 Abstract: One of the main challenges in evolutionary biology is to identify the molecular changes that underlie phenotypic differences that are of evolutionary significance. Comparative studies of early development have shown that changes in the spatio-temporal use of regulatory genes, as well as changes in the specificity of regulatory proteins, are correlated with important differences in morphology between phylogenetically distant species. However, it is not known how such changes take place in natural populations, and whether they result from a single, or many small, additive events. Extending this approach to the study of development of closely related species promises to enrich this debate. ------------------- Key: 5631 Medline: 12403719 Authors: Chin-Sang ID;Moseley SL;Ding M;Harrington RJ;George SE;Chisholm AD Title: The divergent C. elegans ephrin EFN-4 functions in embryonic morphogenesis in a pathway independent of the VAB-1 Eph receptor. Citation: Development 129: 5499-5510 2002 Type: ARTICLE Genes: efn-1 efn-2 efn-3 efn-4 mab-20 mab-26 ptp-3 vab-1 vab-2 Abstract: The C. elegans genome encodes a single Eph receptor tyrosine kinase, VAB-1, which functions in neurons to control epidermal morphogenesis. Four members of the ephrin family of ligands for Eph receptors have been identified in C. elegans. Three ephrins (EFN-1/VAB-2, EFN-2 and EFN-3) have been previously shown to function in VAB-1 signaling. We show that mutations in the gene mab-26 affect the fourth C. elegans ephrin, EFN-4. We show that efn-4 also functions in embryonic morphogenesis, and that it is expressed in the developing nervous system. Interestingly, efn-4 mutations display synergistic interactions with mutations in the VAB-1 receptor and in the EFN-1 ephrin, indicating that EFN-4 may function independently of the VAB-1 Eph receptor in morphogenesis. Mutations in the LAR-like receptor tyrosine phosphatase PTP-3 and in the Semaphorin-2A homolog MAB-20 disrupt embryonic neural morphogenesis. efn-4 mutations synergize with ptp-3 mutations, but not with mab-20 mutations, suggesting that EFN-4 and Semaphorin signaling could function in a common pathway or in opposing pathways in C. elegans ------------------- Key: 5632 Medline: 12441291 Authors: Moghal N;Sternberg PW Title: A component of the transcriptional mediator complex inhibits RAS-dependent vulval fate specification in C. Citation: Development 130: 57-69 2003 Type: ARTICLE Genes: bar-1 dpy-4 dpy-22 let-23 let-60 lin-3 pry-1 sop-1 Abstract: Negative regulation of receptor tyrosine kinase (RTK)/RAS signaling pathways is important for normal development and the prevention of disease in humans. We have used a genetic screen in C. elegans to identify genes that antagonize the activity of activated LET-23, a member of the EGFR family of RTKs. We identified two loss-of-function mutations in dpy-22, previously cloned as sop-1, that promote the ability of activated LET-23 to induce ectopic vulval fates. DPY-22 is a glutamine-rich protein that is most similar to human TRAP230, a component of a transcriptional mediator complex. DPY-22 has previously been shown to regulate WNT responses through inhibition of the beta-catenin-like protein BAR-1. We provide evidence that DPY-22 also inhibits RAS-dependent vulval fate specification independently of BAR-1, and probably regulates the activities of multiple transcription factors during development. Furthermore, we demonstrate that although inhibition of BAR-1-dependent gene expression has been shown to require the C-terminal glutamine-rich region, this region is dispensable for inhibition of RAS-dependent cell differentiation. Thus, the glutamine-rich region contributes to specificity of this class of mediator ------------------- Key: 5633 Medline: 12490565 Authors: Aurelio O;Boulin T;Hobert O Title: Identification of spatial and temporal cues that regulate postembryonic expression of axon maintenance factors in the C. elegans ventral nerve cord. Citation: Development 130: 599-610 2003 Type: ARTICLE Genes: ceh-14 flp-1 gpa-2 lim-6 lin-14 lin-28 lin-42 myo-3 pin-2 srq-1 unc-47 zig-1 zig-2 zig-3 zig-4 zig-8 Abstract: Patterns of gene expression are under precise spatial and temporal control. A particularly striking example is represented by several members of the zig gene family, which code for secreted immunoglobulin domain proteins required for maintaining ventral nerve cord organization in Caenorhabditis elegans. These genes are coordinately expressed in a single interneuron in the ventral nerve cord, known as PVT. Their expression is initiated at a precise postembryonic stage, long after PVT has been generated in mid-embryogenesis. We define spatial and temporal cues that are required for the precise regulation of zig gene expression. We find that two LIM homeobox genes, the Lhx3-class gene ceh-14 and the Lmx-class gene lim-6 are coordinately required for zig gene expression in PVT. Temporal control of zig gene expression is conferred by the heterochronic gene lin-14, a nuclear factor previously implicated in developmental timing in various contexts. Loss of the lim-6 and ceh-14 transcription factors and the developmental timer lin-14 cause not only a loss of zig gene expression but also lead to defects in the maintenance of ventral nerve cord architecture. Overriding the normal spatiotemporal control of zig gene expression through expression of one of the zig genes under control of heterologous promoters also causes axon patterning defects in the ventral nerve cord. Our findings illustrate the importance of spatial and temporal control of gene expression in the nervous system and, furthermore, implicate heterochronic genes in postmitotic neural ------------------- Key: 5634 Medline: 12468887 Authors: Klumpp S;Hermesmeier J;Selke D;Baumeister R;Kellner R;Krieglstein J Title: Protein histidine phosphatase: a novel enzyme with potency for neuronal signaling. Citation: Journal of Cerebral Blood Flow & Metabolism 22: 1420-1424 2002 Type: ARTICLE Genes: Abstract: The importance of reversible phosphorylation for neuronal signaling and cell survival is well recognized. Knowledge in vertebrates, however, is so far limited to O-phosphates from serine, threonine, and tyrosine. The authors describe an enzyme acting on N-phosphates. It is the first protein histidine phosphatase identified in vertebrates. This histidine phosphatase is ubiquitously expressed in mammalian tissues including brain. Characterization and sequencing showed a yet unknown protein with no similarity to other phosphatases. In Caenorhabditis elegans, the homolog of this histidine phosphatase was exclusively expressed in neurons, suggesting a distinct role of reversible histidine phosphorylation in neuronal functions. ------------------- Key: 5635 Medline: Authors: Fisher DI;Safrany ST;Strike P;McLennan AG;Cartwright JL Title: Nudix hydrolases that degrade dinucleoside and diphosphoinositol polyphosphates also have 5-phosphoribosyl 1-pyrophosphate (PRPP) pyrophosphatase activity that generates the glycolytic activator... Citation: Journal of Biological Chemistry 277: 47313-47317 2002 Type: ARTICLE Genes: Abstract: A total of 17 Nudix hydrolases were tested for their ability to hydrolyze 5-phosphoribosyl 1-pyrophosphate (PRPP). All 11 enzymes that were active toward dinucleoside polyphosphates with 4 or more phosphate groups as substrates were also able to hydrolyze PRPP, whereas the 6 that could not and that have coenzyme A, NDP-sugars, or pyridine nucleotides as preferred substrates did not degrade PRPP. The products of hydrolysis were ribose 1,5-bisphosphate and P-i. Active PRPP pyrophosphatases included the diphosphoinositol polyphosphate phosphohydrolase (DIPP) subfamily of Nudix hydrolases, which also degrade the non-nucleotide diphosphoinositol polyphosphates. K-m and k(cat) values for PRPP hydrolysis for the Deinococcus radiodurans DR2356 (di)nucleoside polyphosphate hydrolase, the human diadenosine tetraphosphate hydrolase, and human DIPP-1 (diadenosine hexaphosphate and diphosphoinositol polyphosphate hydrolase) were 1 nM and 1.5 s(-1), 0.13 mM and 0.057 s(-1), and 0.38 mM and 1.0 s(-1), respectively. Active site mutants of the Caenorhabditis elegans diadenosine tetraphosphate hydrolase had no activity, confirming that the same active site is responsible for nucleotide and PRPP hydrolysis. Comparison of the specificity constants for nucleotide, diphosphoinositol polyphosphate, and PRPP hydrolysis suggests that PRPP is a significant substrate for the D. radiodurans DR2356 enzyme and for the DIPP subfamily. In the latter case, generation of the glycolytic activator ribose 1,5-bisphosphate may be a new function for ------------------- Key: 5636 Medline: 12454651 Authors: Reinke V Title: Functional exploration of the C. elegans genome using DNA microarrays. Citation: Nature Genetics 32S: 541-546 2002 Type: REVIEW Genes: mec-3 mec-17 pab-1 pha-4 syp-1 unc-86 Abstract: Global changes in gene expression underlie developmental processes such as organogenesis, embryogenesis and aging in Caenorhabditis elegans. Recently developed methods allow gene expression profiles to be determined selectively for individual tissues and cell types. Results from both whole-animal and tissue-specific expression profiling have provided an unprecedented view into genome organization and gene function. Integration of these results with other types of functional genomics data gathered from RNA-mediated interference and yeast two-hybrid analyses will allow rapid identification and exploration of the complex functional gene networks that govern C. elegans ------------------- Key: 5637 Medline: 12475958 Authors: Askjaer P;Galy V;Hannak E;Mattaj IW Title: Ran GTPase cycle and importins alpha and beta are essential for spindle formation and nuclear envelope assembly in living Caenorhabditis elegans embryos. Citation: Molecular Biology of the Cell 13: 4355-4370 2002 Type: ARTICLE Genes: emr-1 ima-1 ima-2 ima-3 imb-1 npp-10 pie-1 ran-1 ran-2 ran-3 unc-119 Abstract: The small GTPase Ran has been found to play pivotal roles in several aspects of cell function. We have investigated the role of the Ran GTPase cycle in spindle formation and nuclear envelope assembly in dividing Caenorhabditis elegans embryos in real time. We found that Ran and its cofactors RanBP2, RanGAP, and RCC1 are all essential for reformation of the nuclear envelope after cell division. Reducing the expression of any of these components of the Ran GTPase cycle by RNAi leads to strong extranuclear clustering of integral nuclear envelope proteins and nucleoporins. Ran, RanBP2, and RanGAP are also required for building a mitotic spindle, whereas astral microtubules are normal in the absence of these proteins. RCC1(RNAi) embryos have similar abnormalities in the initial phase of spindle formation but eventually recover to form a bipolar spindle. Irregular chromatin structures and chromatin bridges due to spindle failure were frequently observed in embryos where the Ran cycle was perturbed. In addition, connection between the centrosomes and the male pronucleus, and thus centrosome positioning, depends upon the Ran cycle components. Finally, we have demonstrated that both IMA-2 and IMB-1, the homologues of vertebrate importin alpha and beta, are essential for both spindle assembly and nuclear formation in early embryos. ------------------- Key: 5638 Medline: 12454064 Authors: Meneely PM;Farago AF;Kauffman TM Title: Crossover distribution and high interference for both the X chromosome and an autosome during oogenesis and spermatogenesis in Caenorhabditis elegans. Citation: Genetics 162: 1169-1177 2002 Type: ARTICLE Genes: him-6 Abstract: Regulation of both the number and the location of crossovers during meiosis is important for normal chromosome segregation. We used sequence-tagged site polymorphisms to examine the distribution of all crossovers on the X chromosome during oogenesis and on one autosome during both oogenesis and spermatogenesis in Caenorhabditis elegans. The X chromosome has essentially one crossover during oogenesis, with only three possible double crossover exceptions among 220 recombinant X chromosomes. All three had one of the two crossovers in the same chromosomal interval, suggesting that crossovers in that interval do not cause interference. No other interval was associated with double crossovers. Very high interference was also found on an autosome during oogenesis, implying that each chromosome has only one crossover during oogenesis. During spermatogenesis, recombination on this autosome was reduced by similar to30% compared to oogenesis, but the relative distribution of the residual crossovers was only slightly different. In contrast to previous results with other autosomes, no double crossover chromosomes were observed. Despite an increased frequency of nonrecombinant chromosomes, segregation of a nonrecombinant autosome during spermatogenesis appears to occur normally. This indicates that an achiasmate segregation system helps to ensure faithful disjunction of autosomes during ------------------- Key: 5639 Medline: 12434334 Authors: Furuta T;Baillie DL;Schumacher JM Title: Caenorhabditis elegans Aurora A kinase AIR-1 is required for postembryonic cell divisions and germline development. Citation: Genesis 34: 244-250 2002 Type: ARTICLE Genes: air-1 air-2 dpy-11 emb-22 let-335 let-405 let-408 let-411 let-412 let-413 let-414 let-423 let-424 let-436 let-445 let-449 let-456 let-464 let-470 let-474 mig-6 mom-2 rol-3 srf-9 sDf20 sDf29 sDf35 Abstract: Many kinases are required for progression through the eukaryotic cell cycle. The Aurora kinases comprise a highly conserved family of serine/threonine kinases that have been implicated in chromosome segregation and cytokinesis in several organisms. We have isolated a sterile Caenorhabditis elegans mutant in which the majority of the locus encoding the Aurora A kinase air-1 has been deleted. Complementation tests with previously isolated sterile mutations in the air-1 genetic interval demonstrate that the air-1 and let-412 loci are identical. Previous analysis of AIR-1 function by RNA-mediated interference (RNAi) has shown that AIR-1 is required for embryonic survival. The characterization of the three sterile air-1 mutant alleles described here extends these studies by revealing an allelic series that differentially affects postembryonic cell divisions and germline development. ------------------- Key: 5640 Medline: 12468090 Authors: Sakurai A;Fujimori S;Kochiwa H;Kitamura-Abe S;Washio T;Saito R;Carninci P;Hayashizaki Y;Tomita M Title: On biased distribution of introns in various eukaryotes. Citation: Gene 300: 89-95 2002 Type: ARTICLE Genes: Abstract: We conducted comprehensive analyses on intron positions in the Mus musculus genome by comparing genomic sequences in the GenBank database and cDNA sequences in the mouse cDNA library recently developed by Riken Genomic Sciences Center. Our results confirm that introns have a tendency to be located toward the 5' end of the gene. The same type of analysis was conducted in the coding region of seven eukaryotes (Saccharomyces cerevisiae, Plasmodium falciparian, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Homo sapiens, Arabidopsis thaliana). Introns in genes with a single intron have a locational bias toward the 5' end in all species except A. thaliana, We also measured the distance front the start codon to the position of the intron, and found that single introns prefer the location immediately after the start codon in S. cerevisiae and P. falciparum. We discuss three possible explanations for these findings: (1) they are the consequence of intron loss by reverse-transcriptase: (2) they are necessary to accommodate the function; and (3) they are concerned with the mechanism of pro-mRNA splicing. ------------------- Key: 5641 Medline: 12468102 Authors: Fukushima A;Ikemura T;Kinouchi M;Oshima T;Kudo Y;Mori H;Kanaya S Title: Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis. Citation: Gene 300: 203-211 2002 Type: ARTICLE Genes: Abstract: We used a power spectrum method to identify periodic patterns in nucleotide sequence. and characterized nucleotide sequences that confer periodicities to prokaryotic and eukaryotic genomes. A 10-bp periodicity was prevalent in hyperthermophilic bacteria and archaebacteria, and an 11-bp periodicity was prevalent in cubacteria. The 10-bp periodicity was also prevalent in the eukaryotes such as the worrn Caenorhabditis elegans. Additionally, in the worm genome, a 68-bp periodicity in chromosome I, a 59-bp periodicity in chromosome II, and a 94-bp periodicity in chromosome III were found. In human chromosomes 21 and 22, approximately 167- or 84-bp periodicity was detected along the entire length of these chromosomes. Because the 167-bp is identical to the length of DNA that forms two complete helical turns in nucleosome organization, we speculated that the respective sequences may correspond to arrays of a special compact form of nucleosomes clustered in specific regions of the human chromosomes. This periodic element contained a high frequency of TGG. TGG-rich sequences are known to form a specific subset of folded DNA structures, and therefore, the sequences might have potential to form specific higher order structures related to the clustered occurrence of a specific form of the speculated ------------------- Key: 5642 Medline: 12411744 Authors: Kaletta T;Van der Craen M;Van Geel A;Dewulf N;Bogaert T;Branden M;King KV;Buechner M;Barstead R;Hyink D;Li HP;Geng L;Burrow C;Wilson P Title: Towards understanding the polycystins. Citation: Nephron Experimental Nephrology 93: e9-e17 2003 Type: ARTICLE Genes: him-5 lov-1 pkd-2 Abstract: Autosomal dominant polycystic kidney disease (ADPKD) is a very common inherited disease caused by mutation in PKD1 or PKD2 genes characterized by progressive enlargement of fluid-filled cysts and loss of renal function [1]. Previous studies proposed a role for human polycystin-1 in renal morphogenesis acting as a matrix receptor in focal adhesions and for polycystin-2 as a putative calcium channel [2,3]. The genome of Caenorhabditis elegans contains 2 new members of the polycystin family: lov-1, the homolog for PKD1; and pkd-2, the homolog for PKD2 [4; this paper]. Mutation analysis in C. elegans showed similarly compromised male mating behaviors in all single and double lov-1 and pkd-2 mutants, indicating their participation in a single genetic pathway. Expression analysis localized LOV-1 and PKD-2 to the ends of sensory neurons in the head, consistent with functions as chemo- or mechanosensors. Human and C. elegans PKD1 and PKD2 homologs, transfected into mammalian renal epithelial cells, co-localized with paxillin in focal adhesions suggesting function in a single biological pathway. Based on the role of polycystins in C. elegans sensory neuron function and conservation of PKD pathways we suggest that polycystins act as sensors of the extracellular environment, initiating, via focal adhesion assemble, intracellular transduction events in neuronal or morphogenetic processes. ------------------- Key: 5643 Medline: Authors: Pires-daSilva A;Sommer RJ Title: The evolution of signalling pathways in animal development. Citation: Nature Reviews Genetics 4: 39-49 2003 Type: REVIEW Genes: egl-1 fem-1 fem-2 fem-3 gsk-3 her-1 let-23 lin-31 mab-3 pry-1 sdc-1 sdc-2 sdc-3 tra-1 tra-2 tra-3 xol-1 Abstract: Despite the bewildering number of cell types and patterns found in the animal kingdom, only a few signalling pathways are required to generate them. Most cell-cell interactions during embryonic development involve the Hedgehog, Wnt, transforming growth factor-beta, receptor tyrosine kinase, Notch, JAK/STAT and nuclear hormone pathways. Looking at how these pathways evolved might provide insights into how a few signalling pathways can generate so much cellular and morphological diversity during the development of individual organisms and the evolution of animal body ------------------- Key: 5644 Medline: 11593035 Authors: Levitan D;Lee J;Song L;Manning R;Wong G;Parker E;Zhang L Title: PS1 N- and C-terminal fragments form a complex that functions in APP processing and Notch signaling. Citation: Proceedings of the National Academy of Sciences USA 98: 12186-12190 2001 Type: ARTICLE Genes: sel-12 Abstract: Presenilin proteins play critical roles in the proteolytic processing of both Notch and amyloid precursor protein (APP). Presenilin itself undergoes endoproteolytic processing to generate an N-terminal and C-terminal fragment. As demonstrated previously, overexpression of presenilin 1 (PS1) holoprotein does not change the levels of the N-terminal and C-terminal fragments (NTF and CTF). When we coexpress the PS1 NTF and CTF, marked increases in the cellular levels of these fragments are seen. By coexpressing the PS1 NTF and CTF, we demonstrate conclusively that a noncovalent complex of the NTF and CTF is the active species of presenilin. However, although the PS1 NTF/CTF complex is necessary for gamma-secretase activity, it is not sufficient. Independent overexpression of the PS1 NTF and CTF was also used to show that the Asp-257 and Asp-385 mutations in PS1 decrease Abeta production by a direct effect on gamma-secretase activity and not by the inhibition of PS1 endoproteolysis. ------------------- Key: 5645 Medline: Authors: Tittel JN;Steller H Title: A comparison of programmed cell death between species. Citation: Genome Biology 1(3): 3.1-3.6 2000 Type: REVIEW Genes: ced-3 ced-4 ced-9 egl-1 Abstract: Key components of the programmed cell death pathway are conserved between Caenorhabditis elegans, Drosophila melanogaster and humans. The search for additional homologs has been facilitated by the availability of the entire genomic sequence for each of these organisms. ------------------- Key: 5646 Medline: 12467974 Authors: Gomez-Escobar N;Gregory WF;Britton C;Murray L;Corton C;Hall N;Daub J;Blaxter ML;Maizels RM Title: Abundant larval transcript-1 and -2 genes from Brugia malayi: diversity of genomic environments but conservation of 5' promoter sequences functional in Caenorhabditis elegans. Citation: Molecular & Biochemical Parasitology 125: 59-71 2002 Type: ARTICLE Genes: alt-1 alt-2 Abstract: The genomic organisation of two abundant larval transcript (alt) genes from the filarial nematode Brugia malayi has been defined. The products of these genes are 78% identical in amino acid sequence, and are highly expressed in a stage-specific manner by mosquito-borne infective larvae. alt-1 is present as two near-identical copies organised in an inverted repeat of similar to7.6 kb, occupying a total of 16 kb of the genome. alt-2 is a single-copy gene at a different locus to alt-1. The two alt-1 genes (alt-1.1 and -1.2) are 99.7% identical in coding sequence and 99.5% in intronic sequences. Both alt-1 and -2 contain 3 introns, and the third intron of alt-2 exhibits a size polymorphism evident in different individual parasites from the laboratory-maintained strain. Genomic sequence up and down-stream from alt-1.1/1.2 (26 and 6 kb, respectively) and alt-2 (6 and 4 kb, respectively) show that neither gene is in a multiple array or an operon. Most notably, the neighbouring genes of alt-1 and -2 show no similarity to each other, or to the genes flanking the distant alt homologue in Caenorhabditis elegans. Despite this diversity in flanking genes, the 5' UTR tracts extending some 800 by upstream of each B. malayi alt gene show a high degree of similarity (overall 59% identity with tracts of 77-86% identity). Surmising that this region may contain conserved promoter elements, constructs containing the B. malayi alt 5' UTR with or without coding sequence were made fused to beta-galactosidase reporter protein. These constructs were injected into the syncytical gonad of C. elegans and progeny stained for beta-gal expression. Our results show relatively strong expression in the gut cells of C elegans for both alt-1 and -2 constructs, commencing in larval worms and continuing into adulthood. Moreover, expression was enhanced when constructs contained segments of alt-1 coding and intronic sequence in addition to the S' UTR. We conclude that the high level of alt transcription in filarial L3s is not due to expression from a multi-copy gene family but to a set of strong promoter elements shared between the two alt genes. ------------------- Key: 5647 Medline: 12470895 Authors: Yanase S;Yasuda K;Ishii N Title: Adaptive responses to oxidative damage in three mutants of Caenorhabditis elegans (age-1, mev-1 and daf-16) that affect life span. Citation: Mechanisms of Ageing & Development 123: 1579-1587 2002 Type: ARTICLE Genes: age-1 ctl-1 ctl-2 daf-16 mev-1 sod-1 sod-2 sod-3 sod-4 Abstract: Oxidative damage shortens the life span of the nematode Caenorhabditis elegans (C elegans), even in an age-1 mutant that is characterized by a long life and oxygen resistance. We found that daily short-term exposure (3 h) to hyperoxia further extended the life span of age-1, a phenomenon known as an adaptive response. age-1 also showed resistance to paraquat and heat. Acute hyperoxic treatment did not extend the life spans of wild type, daf-16 or mev-1. daf-16 mutant had a slightly shorter life span compared to wild type and was sensitive to heat and paraquat. The daf-16 phenotype resembles that of mev-1 showing a short life and oxygen sensitivity. We measured mRNA levels of superoxide dismutase genes (sod-1 through 4), catalase genes (clt-1 and ctl-2), known to encode anti-oxidant enzymes, and found they were elevated in age-1 young adults. On the other hand, in daf-16 and mev-1, the expression of sod-1, sod-2 and sod-3 genes was lower rather than in wild type. Conversely, ctl-1 and ctl-2 genes expression was significantly elevated in daf-16 and mev-1. This suggests that DAF-16, a forkhead/winged-helix transcription factor, whose expression is suppressed by AGE-1, phosphoinositide 3-kinase (PI3-kinase), regulates anti-oxidant genes as well as energy metabolism under atmospheric conditions. However, the level of gene expression of SOD and catalase was not elevated by short-term exposure to 90% oxygen in wild type, mev-1, daf-16 and even age-1. This suggests that SOD and catalase do not play a role in the adaptive response against oxidative stress under hyperoxia, at least under these experimental conditions. ------------------- Key: 5648 Medline: 12490171 Authors: Cohen M;Tzur YB;Neufeld E;Feinstein N;Delannoy MR;Wilson KL;Gruenbaum Y Title: Transmission electron microscope studies of the nuclear envelope in Caenorhabditis elegans. Citation: Journal of Structural Biology 140: 232-240 2002 Type: ARTICLE Genes: lmn-1 Abstract: Nuclear membranes and nuclear pore complexes (NPCs) are conserved in both animals and plants. However, the lamina composition and the dimensions of NPCs vary between plants, yeast, and vertebrates. In this study, we established a protocol that preserves the structure of Caenorhabditis elegans embryonic cells for high-resolution studies with thin-section transmission electron microscopy (TEM). We show that the NPCs are bigger in C. elegans embryos than in yeast, with dimensions similar to those in higher eukaryotes. We also localized the C elegans nuclear envelope proteins Ce-lamin and Ce-emerin by pre-embedding gold labeling immunoelectron microscopy. Both proteins are present at or near the inner nuclear membrane. A fraction of Ce-lamin, but not Ce-emerin, is present in the nuclear interior. Removing the nuclear membranes leaves both Ce-lamin and Ce-emerin associated with the chromatin. Eliminating the single lamin protein caused cell death as visualized by characteristic changes in nuclear architecture including condensation of chromatin, clustering of NPCs, membrane blebbing, and the presence of vesicles inside the nucleus. Taken together, these results show evolutionarily conserved protein localization, interactions, and functions of the C. elegans nuclear ------------------- Key: 5649 Medline: 12221106 Authors: Li S;Finley J;Liu ZJ;Qiu SH;Chen H;Luan CH;Carson M;Tsao J;Johnson D;Lin G;Zhao J;Thomas W;Nagy LA;Sha B;DeLucas LJ;Wang BC;Luo M Title: Crystal structure of the cytoskeleton-associated protein glycine-rich (CAP-Gly) domain. Citation: Journal of Biological Chemistry 277: 48596-48601 2002 Type: ARTICLE Genes: Abstract: Cytoskeleton-associated proteins (CAPs) are involved in the organization of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of the CAP-Gly domain of Caenorhabditis elegans F53F4.3 protein, solved by single wavelength sulfur-anomalous phasing, revealed a novel protein fold containing three beta-sheets. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove. Residues in the groove are highly conserved as measured from the information content of the aligned sequences. The C-terminal tail of another molecule in the crystal is bound in this groove. ------------------- Key: 5650 Medline: 12503753 Authors: David HE;Dawe AS;De Pomerai DI;Jones D;Candido EPM;Daniells C Title: Construction and evaluation of a transgenic hsp16-GFP-lacZ Caenorhabditis elegans strain for environmental monitoring. Citation: Environmental Toxicology & Chemistry 22: 111-118 2003 Type: ARTICLE Genes: Abstract: A novel integrated transgenic Caenorhabditis elegans strain (PC 161) incorporates a double reporter construct with green fluorescent protein (GFP) and lacZ genes fused in-frame into the second exon of the hsp16-1 gene. This construct also includes the Simian Virus 40 (SV40) nuclear localization signal such that the fusion protein accumulates in the nuclei of expressing cells. The PC161 strain was used to monitor the effects of several known stressors, including heat, cadmium, and microwave radiation. The time course of induction was similar for both reporters but was strongly influenced by pretreatment conditions. The PC161 worms kept at 15 C beforehand showed a steady increase in reporter expression (up to at least 16 h) when heated to 30 degreesC. However, if washed on ice prior to heat stress at 30 degreesC, PC 161 worms showed a much steeper rise in reporter expression, reaching a maximum after 2.5 h and then plateauing. Heat shock induced strong expression of both reporter genes in all tissues apart from the germ line and early embryos. A highly significant linear dose-response relationship was observed for both transgenes with increasing c/* admium concentrations (5-100 mug/ml). Prolonged exposure to microwave radiation (750 MHz and 0.5 W for 16 h) also induced expression of both transgenes at 25 and (to some extent) 27degreesC, but only beta-galactosidase activity was detectable at 23degreesC, and neither reporter was delectably expressed at 21degreesC. Throughout all exposures, the lacZ reporter product was more readily detectable than coexpressed GFP However, the GFP reporter affords opportunities to monitor the stress response in living worms. ------------------- Key: 5651 Medline: 12474376 Authors: Tan MW Title: Identification of host and pathogen factors involved in virulence using Caenorhabditis elegans. Citation: Methods in Enzymology 358: 13-28 2002 Type: REVIEW Genes: aex-2 eat-13 egl-9 mev-1 phm-2 rad-8 srf-2 srf-3 srf-5 unc-25 Abstract: Functional interactions between pathogen and host are crucial to the process of pathogenicity and by identifying and characterizing genes involved in host defense mechanisms and the pathogen response to these mechanisms, we can understand pathogenicity more fully. To identify the complex cascades of events that are triggered in the host and the pathogen during an infection, ideally both the host and the pathogen should be genetically tractable. A Caenohabditis elegans-Pseudomonas aeruginosa pathogenesis model has been developed that allows us to tap into the multifaceted power of functional genomics and genetics to systematically and comprehensively dissect both the virulence determinants of the pathogen and innate immune system of the host in a single experimental system. By studying pathogenesis in a genetically tractable host such as C. elegans, both the animal host and pathogen can be genetically altered and the effects of these alterations on pathogenesis/host immunity can be readily tested. Moreover, complete genome sequences are available for both C. elegans and P. aeruginosa, thus bringing to bear numerous genomics resources and technologies to the study of host-pathogen interactions. Comparison to the complete human genome has revealed that 43% of the C. elegans proteins have sequence similarities to predicted human proteins, suggesting that C. elegans may be a valid model for studies of numerous disease processes, including the innate immune response to infectious agents. The use of C. elegans as a model host to study host-pathogen interactions has been extended to include several other human bacterial pathogens, such as gram-negative bacteria Salmonella enterica, Serratia marcescens, Burkhoderia pseudomallei, and gram-positive bacteria Enterococcus faecalis, Streptococcus pneumoniae, and Staphylococcus aureus. ------------------- Key: 5652 Medline: Authors: Matsuno T;Ura K;Sonoda R;Kohara Y;Uesugi H;Arizono K;Iguchi T;Tominaga N Title: Sensing chemical substances using gene-expression patterns in Caenorhabditis elegans. Citation: Sens Mater 14: 395-406 2002 Type: ARTICLE Genes: Abstract: ------------------- Key: 5653 Medline: 12490197 Authors: Hurd DD;Kemphues KJ Title: PAR-1 is required for morphogenesis of the Caenorhabditis elegans vulva. Citation: Developmental Biology 253: 54-65 2003 Type: ARTICLE Genes: ajm-1 cdh-3 egl-17 hmp-1 let-413 lin-11 nmy-2 par-1 par-3 par-6 Abstract: The Caenorhabditis elegans vulva provides a simple model for the genetic analysis of pattern formation and organ morphogenesis during metazoan development. We have discovered an essential role for the polarity protein PAR-1 in the development of the vulva. Postembryonic RNA interference of PAR-1 causes a protruding vulva phenotype. We found that depleting PAR-1 during the development of the vulva has no detectable effect on fate specification or precursor proliferation, but instead seems to specifically alter morphogenesis. Using an apical junction-associated GFP marker, we discovered that PAR-1 depletion causes a failure of the two mirror-symmetric halves of the vulva to join into a single, coherent organ. The cells that normally form the ventral vulval rings fail to make contact or adhere and consequently form incomplete toroids, and dorsal rings adopt variably abnormal morphologies. We also found that PAR-1 undergoes a redistribution from apical junctions to basolateral domains during morphogenesis. Despite a known role for PAR-1 in cell polarity, we have observed no detectable differences in the distribution of various markers of epithelial cell polarity. We propose that PAR-1 activity at the cell cortex is critical for mediating cell shape changes, cell surface composition, or cell signaling during vulval morphogenesis. ------------------- Key: 5654 Medline: 12529635 Authors: Kamath RS;Fraser AG;Dong Y;Poulin G;Durbin R;Gotta M;Kanapin A;Le Bot N;Moreno S;SOhrmann M;Welchman DP;Ziperlen P;Ahringer J Title: Systemic functional analysis of the Caenorhabditis elegans genome using RNAi. Citation: Nature 421: 231-237 2003 Type: ARTICLE Genes: apr-1 cam-1 ceh-32 cyk-1 egl-15 egl-19 epi-1 ifa-2 kin-8 lig-1 lin-12 lin-39 lis-1 mgl-1 nhr-25 rba-2 sma-4 tra-1 unc-15 unc-44 vha-12 Abstract: A principal challenge currently facing biologists is how to connect the complete DNA sequence of an organism to its development and behaviour. Large-scale targeted-deletions have been successful in defining gene functions in the single-celled yeast Saccharomyces cerevisiae, but comparable analyses have yet to be performed in an animal. Here we describe the use of RNA interference to inhibit the function of similar to86% of the 19,427 predicted genes of C. elegans. We identified mutant phenotypes for 1,722 genes, about two-thirds of which were not previously associated with a phenotype. We find that genes of similar functions are clustered in distinct, multi-megabase regions of individual chromosomes; genes in these regions tend to share transcriptional profiles. Our resulting data set and reusable RNAi library of 16,757 bacterial clones will facilitate systematic analyses of the connections among gene sequence, chromosomal location and gene function in C. elegans. ------------------- Key: 5655 Medline: 12529643 Authors: Ashrafi K;Chang FY;Watts JL;Fraser AG;Kamath RS;Ahringer J;Ruvkun G Title: Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Citation: Nature 421: 268-272 2003 Type: ARTICLE Genes: daf-2 daf-3 daf-12 daf-18 tph-1 tub-1 Abstract: Regulation of body fat storage involves signalling between centres that regulate feeding in the brain and sites of fat storage and use in the body(1,2). Here we describe an assay for analysing fat storage and mobilization in living Caenorhabditis elegans. By using RNA-mediated interference (RNAi)(3,4) to disrupt the expression of each of the 16,757 worm genes, we have systematically screened the C. elegans genome for genes necessary for normal fat storage. We identify 305 gene inactivations that cause reduced body fat and 112 gene inactivations that cause increased fat storage. Analysis of the fat-reducing gene inactivations in insulin, serotonin and tubby signalling mutants of C. elegans, which have increased body fat, identifies a core set of fat regulatory genes as well as pathway-specific fat regulators. Many of the newly identified worm fat regulatory genes have mammalian homologues, some of which are known to function in fat regulation. Other C. elegans fat regulatory genes that are conserved across animal phylogeny, but have not previously been implicated in fat storage, may point to ancient and universal features of fat storage regulation, and identify targets for treating obesity and its associated diseases. ------------------- Key: 5656 Medline: 12559405 Authors: Houthoofd K;Braeckman BP;Lenaerts I;Brys K;De Vreese A;Van Eygen S;Vanfleteren JR Title: No reduction of metabolic rate in food restricted Caenorhabditis elegans. Citation: Experimental Gerontology 37: 1357-1367 2002 Type: ARTICLE Genes: eat-2 glp-4 Abstract: Dietary restriction (DR) is the most consistent means of extending life span throughout the animal kingdom. Multiple mechanisms by which DR may act have been proposed but none are clearly predominant. We asked whether metabolic rate and stress resistance is altered in Caenorhabditis elegans in response to DR. DR was imposed in two complementary ways: by growing wild-type worms in liquid medium supplemented with reduced concentrations of bacteria and by using eat-2 mutants, which have a feeding defect. Metabolic rate was not reduced when we fed wild-type worms reduced food and was up-regulated in the eat-2 mutants in liquid culture, as assessed by oxygen consumption rate and heat production. The specific activity levels of the antioxidant enzymes superoxide dismutase (SOD) and catalase showed small increases when we reduced food in wildtype worms, but restricted worms acquired no elevated protection against paraquat and hydrogen peroxide. eat-2 mutants showed elevated specific activities of SOD and catalase relative to wild type in liquid culture. These results indicate that the effects imparted by DR and the eat-2 mutation are not identical, and they contradict, at least in C. elegans, the widespread belief that CR acts by lowering the rate of metabolism. ------------------- Key: 5657 Medline: 12559406 Authors: Houthoofd K;Braeckman BP;Lenaerts I;Brys K;De Vreese A;Van Eygen S;Vanfleteren JR Title: Axenic growth up-regulates mass-specific metabolic rate, stress resistance, and extends life span in Caenorhabditis elegans. Citation: Experimental Gerontology 37: 1371-1378 2002 Type: ARTICLE Genes: eat-2 Abstract: Culture in axenic medium causes two-fold increases in the length of development and adult life span in Caenorhabditis elegans. We asked whether axenic medium imposes dietary restriction (ADR), and causes changes in metabolic activity and stress resistance. Eat mutants, which have a reduced food intake, were studied in parallel with wild-type worms to assess potential synergistic actions of axenic culture and food restriction. We found that axenic culture enhances metabolic activity as assessed by mass-specific oxygen consumption rate and heat production. Axenic culture also caused higher activities of the antioxidant enzymes superoxide dismutase and catalase. and led to increased resistance to high temperature, which was further exacerbated by mutation in eat-2. These results show that axenic medium up-regulates a variety of somatic maintenance functions including oxidative and thermal stress resistance and that food restriction due to axenic growth and to mutation in eat-2 are very similar but not identical. ------------------- Key: 5658 Medline: Authors: Mikami A;Tynan SH;Hama T;Luby-Phelps K;Saito T;Crandall JE;Besharse JC;Vallee RB Title: Molecular structure of cytoplasmic dynein 2 and its distribution in neuronal and ciliated cells. Citation: Journal of Cell Science 115: 4801-4808 2002 Type: ARTICLE Genes: che-3 Abstract: Cytoplasmic dynein is involved in a wide variety of cellular functions. In addition to the initially characterized form (MAP 1Cdynein 1), a second form of cytoplasmic dynein (dynein 2) has been identified and implicated in intraflagellar transport (IFT) in lower eukaryotes and in Golgi organization in vertebrates. In the current study, the primary structure of the full-length dynein 2 heavy chain (HC) was determined from cDNA sequence. The dynein 1 and dynein 2 sequences were similar within the motor region, and around the light intermediate chain (LIC)-binding site within the N-terminal stem region. The dynein 2 HC co-immunoprecipitated with LIC3, a homologue of dynein 1 LICs. Dynein 2 mRNA was abundant in the ependymal layer of the neural tube and in the olfactory epithelium. Antibodies to dynein 2 HC, LIC3 and a component of IFT particles strongly stained the ependymal layer lining the lateral ventricles. Both dynein 2 HC and LIC3 staining was also observed associated with connecting cilia in the retina and within primary cilia of non-neuronal cultured cells. These data support a specific role for dynein 2 in the generation and maintenance of ------------------- Key: 5659 Medline: 12447374 Authors: Lee SS;Lee RYN;Fraser AG;Kamath RS;Ahringer J;Ruvkun G Title: A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity. Citation: Nature Genetics 33: 40-48 2003 Type: ARTICLE Genes: age-1 clk-1daf-2 daf-16 lrs-2 unc-29 Abstract: We report a systematic RNA interference (RNAi) screen of 5,690 Caenorhabditis elegans genes for gene inactivations that increase lifespan. We found that genes important for mitochondrial function stand out as a principal group of genes affecting C. elegans lifespan. A classical genetic screen identified a mutation in the mitochondrial leucyl-tRNA synthetase gene (lrs-2) that impaired mitochondrial function and was associated with longer-lifespan. The long-lived worms with impaired mitochondria had lower ATP content and oxygen consumption, but differential responses to free-radical and other stresses. These data suggest that the longer lifespan of C. elegans with compromised mitochrondria cannot simply be assigned to lower free radical production and suggest a more complex coupling of metabolism and longevity. ------------------- Key: 5661 Medline: 12486699 Authors: de Bono M Title: Molecular approaches to aggregation behavior and social attachment. Citation: Journal of Neurobiology 54: 78-92 2003 Type: REVIEW Genes: daf-7 npr-1 Abstract: In many animal species individuals aggregate to live in groups. A range of experimental approaches in different animals, including studies of social feeding in nematodes, maternal behavior in rats and sheep, and pair-bonding in voles, are providing insights into the neural bases for these behaviors. These studies are delineating multiple neural circuits and gene networks in the brain that interact in ways that are as yet poorly understood to coordinate social behavior. ------------------- Key: 5662 Medline: 12569420 Authors: Cavalcanti ARO;Ferreira R;Gu Z;Li WH Title: Patterns of gene duplication in Saccharomyces cerevisiae and Caenorhabditis elegans. Citation: Journal of Molecular Evolution 56: 28-37 2003 Type: ARTICLE Genes: Abstract: In this paper we present a new method for detecting block duplications in a genome. It is more stringent than previous ones in that it requires a more rigorous definition of paralogous genes and that it requires the paralogous proteins on the two blocks to be contiguous. In addition, it provides three criterion choices: (1) the same composition (i.e., having the same paralogues in the two windows), (2) the same composition and gene order, and (3) the same composition, gene order, and gene orientation. The method is completely automated, requiring no visual inspection as in previous methods. We applied it to analyze the complete genomes of S. cerevisiae and C. elegans. In yeast we detected fewer duplicated blocks than previously reported. In C. elegans, however, we detected more block duplications than previously reported, indicating that although our method has a more stringent definition of block duplication than previous ones, it may be more sensitive in detection because it considers every possible window rather than only fixed nonoverlapping windows. Our results show that block duplication is a common phenomenon in both organisms. The patterns of block duplication in the two species are, however, markedly different. The yeast shows much more extensive block duplication than the nematode, with some chromosomes having more than 40% of the duplications derived from block duplications. Moreover, in the yeast the majority of block duplications occurred between chromosomes, while in the nematode most block duplications occurred within chromosomes. ------------------- Key: 5663 Medline: 12521609 Authors: Keaney M;Gems D Title: No increase in lifespan in Caenorhabditis elegans upon treatment with the superoxide dismutase mimetic EUK-8. Citation: Free Radical Biology & Medicine 34: 277-282 2003 Type: ARTICLE Genes: fog-2 Abstract: The superoxide dismulase mimetic EUK-8 has been reported to extend lifespan in the nematode Caenorhabditis elegans. However, in five trials administering EUK-8 in liquid culture with E. coli, and two trials using defined liquid medium, we observed no increase in C elegans lifespan. Instead we saw a dose-dependent reduction of lifespan and fertility. We conclude that extension of C. elegans lifespan by EUK-8 may only occur under very particular culture conditions. ------------------- Key: 5664 Medline: 12498685 Authors: Thompson HM;Skop AR;Euteneuer R;Meyer BJ;McNiven MA Title: The large GTPase dynamin associates with the spindle midzone and is required for cytokinesis. Citation: Current Biology 12: 2111-2117 2002 Type: ARTICLE Genes: dyn-1 Abstract: Cytokinesis involves the concerted efforts of the microtubule and actin cytoskeletons as well as vesicle trafficking and membrane remodeling to form the cleavage furrow and complete daughter cell separation (for reviews, see [1-6]). The exact mechanisms that support membrane remodeling during cytokinesis remain largely undefined. In this study, we report that the large GTPase dynamin, a protein involved in membrane tubulation and vesiculation [7, 8], is essential for successful cytokinesis. Using biochemical and morphological methods, we demonstrate that dynamin localizes to the spindle midzone and the subsequent intercellular bridge in mammalian cells and is also enriched in spindle midbody extracts. In Caenorhabditis elegans, dynamin localized to newly formed cleavage furrow membranes and accumulated at the midbody of dividing embryos in a manner similar to dynamin localization in mammalian cells. Further, dynamin function appears necessary for cytokinesis, as C. elegans embryos from a dyn-1 ts strain [9], as well as dynamin RNAi-treated embryos, showed a marked defect in the late stages of cytokinesis. These findings indicate that, during mitosis, conventional dynamin is recruited to the spindle midzone and the subsequent intercellular bridge, where it plays an essential role in the final separation of dividing cells. ------------------- Key: 5665 Medline: 12545543 Authors: Hawkins NC;Garriga G;Beh CT Title: Creating precise GFP fusions in plasmids using yeast homologous recombination. Citation: Biotechniques 34: 74+- 2003 Type: ARTICLE Genes: Abstract: Using a combination of primer amplification, homologous recombination, and yeast genetics, we established a method for creating precise promoter and protein fusions in genes originating from organisms other than yeast. One major advantage of this new method is its versatility. Fusions can be produced within a target gene without constraints regarding the site of insertion. Thus, fusions can be generated within a target sequence exactly at the site desired, and all sequences upstream and downstream of the insertion site were preserved. To illustrate the general applicability of this technique, we fused the gene encoding GFP to a Caenorhabditis elegans homologue of the dishevelled gene, dsh-2. This approach is not restricted to GFP fusions but can be utilized to create fusions between almost any two sequences regardless of the source. Therefore, this method provides a flexible alternative to other PCR-mediated techniques. ------------------- Key: 5666 Medline: Authors: Ernstrom GG;Chalfie M Title: Genetics of sensory mechanotransduction. Citation: Annual Review of Genetics 36: 411-453 2002 Type: REVIEW Genes: deg-1 eat-4 egl-3 glr-1 him-4 lin-10 mec-1 mec-2 mec-3 mec-4 mec-5 mec-6 mec-7 mec-9 mec-10 mec-12 mec-14 mec-15 mec-17 mec-18 ocr-2 odr-3 osm-9 unc-8 unc-105 Abstract: The molecular mechanisms for the transduction of light and chemical signals in animals are fairly well understood. In contrast, the processes by which the senses of touch, balance, hearing, and proprioception are transduced are still largely unknown. Biochemical approaches to identify transduction components are difficult to use with mechanosensory systems, but genetic approaches are proving more successful. Genetic research in several organisms has demonstrated the importance of cytoskeletal, extracellular, and membrane components for sensory mechanotransduction. In particular, researchers have identified channel proteins in the DEG/ENaC and TRP families that are necessary for signaling in a variety of mechanosensory cells. Proof that these proteins are components of the transduction channel, however, is incomplete. ------------------- Key: 5667 Medline: Authors: Tijsterman M;Ketting RF;Plasterk RHA Title: The genetics of RNA silencing. Citation: Annual Review of Genetics 36: 489-519 2002 Type: REVIEW Genes: dcr-1 ego-1 mut-7 mut-14 rde-1 rde-2 rde-3 rde-4 rrf-1 rrf-3 smg-2 Abstract: Although initially recognized as a handy tool to reduce gene expression, RNA silencing, triggered by double-stranded RNA molecules, is now recognized as a mechanism for cellular protection and cleansing: It defends the genome against molecular parasites such as viruses and transposons, while removing abundant but aberrant nonfunctional messenger RNAs. The underlying mechanisms in distinct gene silencing phenomena in different genetic systems, such as cosuppression in plants and RNAi in animals, are very similar. There are common RNA intermediates, and similar genes are required in RNA silencing pathways in protozoa, plants, fungi, and animals, thus indicating an ancient pathway. This chapter gives an overview of both biochemical and genetic approaches leading to the current understanding of the molecular mechanism of RNA silencing and its probable biological function. ------------------- Key: 5668 Medline: Authors: Alfred J Title: C. elegans - an innate choice? Citation: Nature Reviews Immunology 2: 632-633 2002 Type: REVIEW Genes: dbl-1 lys-1 nsy-1 pmk-1 pmk-2 sek-1 Abstract: Much of what we know about innate immunity comes from studies in Drosophila. Two papers now show that Caenorhabditis elegans, another genetically tractable organism, might be a useful additional model for studying innate immunity. The results show that C. elegans has an inducible response to pathogen infection and that this response shares many features with innate immunity in other organisms. ------------------- Key: 5669 Medline: 12533505 Authors: Kuwabara PE Title: The multifaceted C. elegans major sperm protein: an ephrin signaling antagonist in oocyte maturation. Citation: Genes & Development 17: 155-161 2003 Type: REVIEW Genes: air-2 ceh-18 efn-1 efn-2 efn-3 efn-4 let-60 mek-2 mpk-1 rrf-1 sur-1 vab-1 vab-2 Abstract: In sexually reproducing animals, the ability to coordinate oocyte maturation and sperm availability has profound effects on reproductive success. In Caenorhabditis elegans, cell-cell signaling is crucial for promoting germline development, oocyte maturation, and ovulation. In this issue of Genes & Development, Miller et al. (2003) provide new insights into the role that sperm play in oocyte maturation and ovulation. Even before sperm and oocyte have the opportunity to meet, sperm establish their presence by signaling to oocytes and the somatic gonad. In turn, oocytes respond by resuming meiotic cell cycle progression and preparing for fertilization. ------------------- Key: 5670 Medline: 12533508 Authors: Miller MA;Ruest PJ;Kosinski M;Hanks SK:Greenstein D Title: An Eph receptor sperm-sensing control mechanism for oocyte meiotic maturation in Caenorhabditis elegans. Citation: Genes & Development 17: 187-200 2003 Type: ARTICLE Genes: ceh-18 efn-2 efn-3 efn-4 em0-1 fem-3 fog-2 fog-3 mpk-1 rrf-1 vab-1 vab-2 Abstract: During sexual reproduction in most animals, oocytes arrest in meiotic prophase and resume meiosis (meiotic maturation) in response to sperm or somatic cell signals. Despite progress in delineating mitogen-activated protein kinase (MAPK) and CDK/cyclin activation pathways involved in meiotic maturation, it is less clear how these pathways are regulated at the cell surface. The Caenorhabditis elegans major sperm protein (MSP) signals oocytes, which are arrested in meiotic prophase, to resume meiosis and ovulate. We used DNA microarray data and an in situ binding assay to identify the VAB-1 Eph receptor protein-tyrosine kinase as an MSP receptor. We show that VAB-1 and a somatic gonadal sheath cell-dependent pathway, defined by the CEH-18 POU-class homeoprotein, negatively regulate meiotic maturation and MAPK activation. MSP antagonizes these inhibitory signaling circuits, in part by binding VAB-1 on oocytes and sheath cells. Our results define a sperm-sensing control mechanism that inhibits oocyte maturation, MAPK activation, and ovulation when sperm are unavailable for fertilization. MSP-domain proteins are found in diverse animal taxa, where they may regulate contact-dependent Eph receptor signaling pathways. ------------------- Key: 5671 Medline: 12518036 Authors: Merris M;Wadsworth WG;Khamrai U;Bittman R;Chitwood DJ;Lenard J Title: Sterol effects and sites of sterol accumulation in Caenorhabditis elegans: developmental requirements for 4 alpha-methyl sterols. Citation: Journal of Lipid Research 44: 172-181 2003 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans requires sterol, usually supplied as cholesterol, but this is enzymatically modified, and different sterols can substitute. Sterol deprivation decreased brood size and adult growth in the first generation, and completely, reversibly, arrested growth as larvae in the second. After one generation of sterol deprivation, 10 ng/ml cholesterol allowed delayed laying of a few eggs, but full growth required 300 ng/ml. C. elegans synthesizes two unusual 4alpha-methyl sterols (4MSs), but each 4MS supported only limited growth as the sole sterol. However, addition of only 10 ng of cholesterol to 1,000 ng of 4MS restored full growth and egg-laying, suggesting that both a 4MS and an unmethylated sterol are required for development. Filipin stained sterols in only a few specific cells: the excretory gland cell, two amphid socket cells, two phasmid socket cells and, in males, spicule socket cells. Sterols were also present in the pharynx and in the intestine of feeding animals in a proximal-to-distal gradient. This non-random sterol distribution, the low concentration requirements, and the effects of 4MSs argues that sterols are unlikely to be used for bulk structural modification of cell membranes, but may be required as hormone precursors and/or developmental effectors. ------------------- Key: 5672 Medline: 12655770 Authors: Schachter H;Chen S;Zhang W;Spence AM;Zhu S;Callahan JW;Mahuran DJ;Fan X;Bagshaw RD;She YM;Rosa JC;Reinhold VN Title: Functional posttranslational proteomics approach to study the role of N-glycans in the development of Caenorhabditis elegans. Citation: Biochemical Society Symposium 69: 1-21 2002 Type: REVIEW Genes: gly-12 gly-13 gly-14 Abstract: Glycosylation is one of the most common post-translational protein modifications. Carbohydrate-mediated interactions between cells and their environment are important in differentiation, embryogenesis, inflammation, cancer and metastasis and other processes. Humans and mice with mutations that prevent normal N-glycosylation show multi-systemic defects in embryogenesis, thereby proving that these molecules are essential for normal development; however, a large number of proteins undergo defective glycosylation in these human and mouse mutants, and it is therefore difficult to determine the precise molecular roles of specific N-glycans on individual proteins. We describe here a 'functional post-translational proteomics' approach that is designed to determine the role of N-glycans on individual glycoproteins in the development of Caenorhabditis elegans. ------------------- Key: 5673 Medline: 12655779 Authors: Haslam SM;Gems D;Morris HR;Dell A Title: The glycomes of Caenorhabditis elegans and other model organisms. Citation: Biochemical Society Symposium 69: 117-134 2002 Type: REVIEW Genes: Abstract: There is no doubt that the immense amount of information that is being generated by the initial sequencing and secondary interrogation of various genomes will change the face of glycobiological research. However, a major area of concern is that detailed structural knowledge of the ultimate products of genes that are identified as being involved in glycoconjugate biosynthesis is still limited. This is illustrated clearly by the nematode worm Caenorhabditis elegans, which was the first multicellular organism to have its entire genome sequenced. To date, only limited structural data on the glycosylated molecules of this organism have been reported. Our laboratory is addressing this problem by performing detailed MS structural characterization of the N-linked glycans of C. elegans; high-mannose structures dominate, with only minor amounts of complex-type structures. Novel, highly fucosylated truncated structures are also present which are difucosylated on the proximal N-acetylglucosamine of the chitobiose core as well as containing unusual Fuca1-2Gal1-2Man as peripheral structures. The implications of these results in terms of the identification of ligands for genomically predicted lectins and potential glycosyltransferases are discussed in this chapter. Current knowledge on the glycomes of other model organisms such as Dictyostelium discoideum, Saccaromyces cerevisiae and Drosophila melanogaster is also discussed ------------------- Key: 5674 Medline: Authors: Ichimiya H;Huet RG;Hartman P;Amino H;Kita K;Ishii N Title: Complex II inactivation is lethal in the nematode Caenorhabditis elegans. Citation: Mitochondrion 2: 191-198 2002 Type: ARTICLE Genes: gas-1 mev-1 Abstract: RNA-mediated interference (RNAi) was employed to systematically inactivate the four subunits of complex II in the mitochondrial electron transport chain. Embryonic lethality was the predominant result of inactivating three subunits (ceSDHB, ceSDHC, and ceSDHD) when using the soaking method to inactivate RNA. The feeding method was employed to deliver dsRNA from the fourth subunit (ceSDHA) to wild-type, mev-1 (mutated in ceSDHC of complex II), and gas-1 animals (mutated in a complex I gene). Survival was reduced only in the mev-1 genetic background, and in an oxygen-dependent fashion. Collectively, these data provide further evidence that compromised complex II integrity can result in sensitivity to oxidative stress. ------------------- Key: 5675 Medline: 12533596 Authors: Samuel ADT;Silva RA;Murthy VN Title: Synaptic activity of the AFD neuron in Caenorhabditis elegans correlates with thermotactic memory. Citation: Journal of Neuroscience 23: 373-376 2003 Type: ARTICLE Genes: unc-13 Abstract: Thermotactic behavior in Caenorhabditis elegans is sensitive to both a worm's ambient temperature (T-amb) and its memory of the temperature of its cultivation (T-cult). The AFD neuron is part of a neural circuit that underlies thermotactic behavior. By monitoring the fluorescence of pH-sensitive green fluorescent protein localized to synaptic vesicles, we measured the rate of the synaptic release of AFD in worms cultivated at temperatures between 15 and 25degreesC, and subjected to fixed, ambient temperatures in the same range. We found that the rate of AFD synaptic release is high if either T-amb > T-cult or T-amb > T-cult, but AFD synaptic release is low if T-amb congruent to T-cult. This suggests that AFD encodes a direct comparison between T-amb and T-cult. ------------------- Key: 5676 Medline: 12488092 Authors: Karabinos A;Schunemann J;Meyer M;Aebi U;Weber K Title: The single nuclear lamin of Caenorhabditis elegans forms in vitro stable intermediate filaments and paracrystals with a reduced axial peroidicity. Citation: Journal of Molecular Biology 325: 241-247 2003 Type: ARTICLE Genes: Abstract: The lamins of the tunicate Ciona intestinalis and the nematode Caenorhabditis elegans show unusual sequence features when compared to the more than 35 metazoan lamin sequences currently known. We therefore analyzed the in vitro assembly of these two lamins by electron microscopy using chicken lamin B2 as a control. While lamin dimers usually appear as a rod carrying two globules at one end, these globules are absent from Ciona lamin, which lacks the central 105-residue region of the tail domain. The deletion of 14 residues or two heptads from the coiled coil rod domain of the single C. elegans lamin results in a 1.5-nm shortening of the dimer rod. Similarly, the paracrystals assembled from the C. elegans lamin exhibit a 3.1-nm reduction of the true axial repeat compared to that of chicken lamin B2 paracrystals. We speculate that the banding pattern in the C. elegans lamin paracrystals arises from a relative stagger between dimers and/or a positioning of the globular tail domain relative to the central rod that is distinct from that observed in chicken lamin B2 paracrystals. Here we show that a nuclear lamin can assemble in vitro into 10-nm intermediate filaments (IFs). C. elegans lamin in low ionic strength Tris-buffers at a pH of 7.2-7.4 provides a stable population of lamin IFs. Some implications of this filament formation are discussed. ------------------- Key: 5677 Medline: 12532273 Authors: Okamura H;Yasuhara JC;Fambrough DM;Takeyasu K Title: P-type ATPases in Caenorhabditis and Drosophila: implications for evolution of the P-type ATPase subunit families with special reference to the Na,K-ATPase and H,K-ATPase subgroup. Citation: Journal of Membrane Biology 191: 13-24 2003 Type: ARTICLE Genes: cua-1 eat-6 mca-1 mca-2 mca-3 mca-4 Abstract: Here we show a complete list of the P-type ATPase genes in Caenorhabditis elegans and Drosophila melanogaster. A detailed comparison of the deduced amino-acid sequences in combination with phylogenetic and chromosomal analyses has revealed the following: (1) The diversity of this gene family has been achieved by two major evolutionary steps; the establishment of the major P-type ATPase subgroups with distinct substrate (ion) specificities in a common ancestor of vertebrate and invertebrate, followed by the evolution of multiple isoforms occurring independently in vertebrate and invertebrate phyla. (2) Pairs of genes that have intimate phylogenetic relationship are frequently found in proximity on the same chromosome. (3) Some of the Na,K- and H,K-ATPase isoforms in D. melanogaster and C. elegans lack motifs shown to be important for alpha/beta-subunit assembly, suggesting that such alpha- and beta-subunits might exist by themselves (lonely subunits). The mutation rates for these Subunits are much faster than those for the subunits with recognizable assembly domains. (4) The lonely alpha-subunits also lack the major site for ouabain binding that apparently arose before the separation or vertebrates and invertebrates and thus well before the separation of vertebrate Na,K-ATPases and H,K-ATPases. These findings support the idea that a relaxation of functional constraints would increase the rate of evolution and provide clues for identifying the origins of inhibitor sensitivity, subunit assembly, and separation of Na,K- and ------------------- Key: 5678 Medline: 12417582 Authors: Winter AD;Myllyharju J;Page AP Title: A hypodermally expressed prolyl 4-hydroxylase from the filarial nematode Brugia malayi is soluble and active in the absence of protein disulfide isomerase. Citation: Journal of Biological Chemistry 278: 2554-2562 2003 Type: ARTICLE Genes: dpy-18 pdi-1 pdi-2 phy-1 phy-2 Abstract: The collagen prolyl 4-hydroxylase (P4H) class of enzymes catalyze the hydroxylation of prolines in the XPro-Gly repeats of collagen chains. This modification is central to the synthesis of all collagens. Most P4Hs are alpha(2)beta(2) tetramers with the catalytic activity residing in the a subunits. The beta subunits are identical to the enzyme protein disuffide isomerase. The nematode cuticle is a collagenous extracellular matrix required for maintenance of the worm body shape. Examination of the model nematode Caenorhabditis elegans has demonstrated that its unique P4Hs are essential for viability and body morphology. The filarial parasite Brugia malayi is a causative agent of lymphatic filariasis in humans. We report here on the cloning and characterization of a B. malayi P4H with unusual properties. The recombinant B. malayi a subunit, PHY-1, is a soluble and active P4H by itself, and it does not become associated with protein disulfide isomerase. The active enzyme form is a homotetramer with catalytic and inhibition properties similar to those of the C. elegans P4Hs. High levels of B. malayi phy-1 transcript expression were observed in all developmental stages examined, and its expression was localized to the cuticle-synthesizing hypodermal tissue in the heterologous host C. elegans. Although active by itself, the B. malayi PRY-1 was not able to replace enzyme ------------------- Key: 5679 Medline: 12524326 Authors: Hodgkin J Title: One lucky XX male: isolation of the first Caenorhabditis elegans sex-determination mutants. Citation: Genetics 162: 1501-1504 2002 Type: REVIEW Genes: dpy-21 dpy-26 mab-3 tra-1 tra-2 tra-3 Abstract: This article marks the 25th anniversary of a paper reporting the first sex-determination mutants to be found in the nematode Caenorhabditis elegans. The isolation of these mutants initiated an extensive analysis of nematode sex determination and dosage compensation, carried out by a number of laboratories over the subsequent decades. As a result, the process of sex determination is now one of the most thoroughly understood parts of C. elegans development, in both genetic and molecular terms. It has also proved to have interesting repercussions on the study of sex determination in other organisms. ------------------- Key: 5680 Medline: 12524338 Authors: Suzuki Y;Morris GA;Han M;Wood WB Title: A cuticle collagen encoded by the lon-3 gene may be a target of TGF-beta signaling in determining Caenorhabditis elegans body shape. Citation: Genetics 162: 1631-1639 2002 Type: ARTICLE Genes: cye-1 dbl-1 dpy-2 dpy-7 dpy-9 lon-1 lon-2 lon-3 sma-4 sma-6 sqt-1 unc-13 unc-46 ctDf1 Abstract: The signaling pathway initiated by the TGF-beta family member DBL-1 in Caenorhabditis elegans controls body shape in a dose-dependent manner. Loss-of-function (lf) mutations in the dbl-1 gene cause a short, small body (Sma phenotype), whereas overexpression of dbl-1 causes a long body (Lon phenotype). To understand the cellular mechanisms underlying these phenotypes, we have isolated suppressors of the Sma phenotype resulting from a db1-(lf) mutation. Two of these suppressors are mutations in the lon-3 gene, of which four additional alleles are known. We show that lon-3 encodes a collagen that is a component of the C. elegans cuticle. Genetic and reporter-gene expression analyses suggest that lon-3 is involved in determination of body shape and is post-transcriptionally regulated by the dbl-1 pathway. These results support the possibility that TGF-beta signaling controls C. elegans body shape by regulating cuticle composition. ------------------- Key: 5681 Medline: 12527374 Authors: Hirose T;Koga M;Ohshima Y;Okada M Title: Distinct roles of the Src family kinases, SRC-1 and KIN-22, that are negatively regulated by CSK-1 in C. elegans. Citation: FEBS Letters 534: 133-138 2003 Type: ARTICLE Genes: csk-1 kin-22 src-1 Abstract: To elucidate the primitive roles of the Src family kinases (SFKs), here we characterized Caenorhabditis elegans orthologues of SFKs (src-1 and kin-22) and their regulator kinase Csk (csk-1). SRC-1 and KIN-22 possess the C-terminal regulatory tyrosines characteristic of SFKs, and their activities are negatively regulated by CSK-1 in a yeast expression system. The src-1 and csk-1 genes are co-expressed in some head neurons, the anchor cell and the tail region, while kin-22 and esk-1 genes are co-expressed in pharyngeal muscles and tail region. Expression of KIN-22 induced morphological defects in the pharynx, whereas expression of SRC-1 did not show any overt phenotype in adult. RNA interference of src-1, but not that of kin-22, caused a developmental arrest in early development. These results suggest that SRC-1 and KIN-22 play distinct roles under the control of CSK-1. ------------------- Key: 5682 Medline: 12507493 Authors: Callebaut I;Mignotte V;Souchet M;Mornon JP Title: EMI domains are widespread and reveal the probable orthologs of the Caenorhabditis elegans CED-1 protein. Citation: Biochemical and Biophysical Research Communications 300: 619-623 2003 Type: ARTICLE Genes: ced-1 Abstract: The EMI domain, first named after its presence in proteins of the EMILIN family, was identified here in several metazoan proteins with various domain architectures, among which the mammalian NEU1/NG3 proteins and Caenorhabditis elegans CED-1, identified as a transmembrane receptor that mediates cell corpse engulfment. Functional data available for EMILIN proteins suggest that the EMI domain could be a protein-protein interaction module. Sequence profiles specific of the EMI family of domains led to identify the probable orthologs of the C. elegans CED-1 protein in mammals and insects, which were yet uncovered. ------------------- Key: 5683 Medline: Authors: Ahringer J Title: Control of cell polarity and mitotic spindle positioning in animal cells. Citation: Current Opinion in Cell Biology 15: 73-81 2003 Type: REVIEW Genes: ags-3.2 ags-3.3 cdc-42 egl-10 let-99 par-1 par-2 par-3 par-4 par-5 par-6 pkc-3 spn-4 Abstract: Cell polarity is an essential feature of many animal cells. It is critical for epithelial formation and function, for correct partitioning of fate-determining molecules, and for individual cells to chemotax or grow in a defined direction. For some of these processes, the position and orientation of the mitotic spindle must be coupled to cell polarity for correct positioning of daughter cells and inheritance of localised molecules. Recent work in several different systems has led to the realisation that similar mechanisms dictate the establishment of polarity and subsequent spindle positioning in many animal cells. Microtubules and conserved PAR proteins are essential mediators of cell polarity, and mitotic spindle positioning depends on heterotrimeric G protein signalling and the ------------------- Key: 5684 Medline: Authors: Etienne-Manneville S;Hall A Title: Cell polarity: Par6, aPKC and cytoskeletal crosstalk. Citation: Current Opinion in Cell Biology 15: 67-72 2003 Type: REVIEW Genes: cdc-42 par-3 par-6 pkc-3 Abstract: Par6 and atypical protein kinase C are key players in the establishment of cell polarity. First discovered in Caenorhabditis elegans, the function of this protein complex in all multicellular organisms. Recent work is beginning to throw light on how it converts information generated by extracellular cues into intracellular ------------------- Key: 5685 Medline: 12473450 Authors: Kampkotter A;Volkmann TE;Hegi de Castro S;Leiers B;Klotz LO;Johnson TE;Link CD;Henkle-Duhrsen K Title: Functional analysis of the glutathione S-transferase 3 from Onchocerca volvulus (Ov-GST-3): a parasite GST confers increased resistance to oxidative stress in Caenorhabditis elegans. Citation: Journal of Molecular Biology 325: 25-37 2003 Type: ARTICLE Genes: Abstract: This study examined the genomic organisation of the coding region of the glutathione S-transferase 3 (Ov-GST-3) from the human parasitic nematode Onchocerca volvulus; alternative splicing leads to three different transcripts (Ov-GST-3/1; Ov-GST-3/2 and Ov-GST-3/3). Since the expression of Ov-GST-3 is inducible by oxidative stress, it is assumed that it is involved in the defense against reactive oxygen species (ROS) resulting from cellular metabolism. Furthermore, we suggest that Ov-GST-3 plays an important role in the protection of the parasite against ROS derived from the host's immune system. To experimentally investigate these speculations, we generated Caenorhabditis elegans lines transgenic for Ov-GST-3 (AK1) and examined their resistance to artificially generated ROS. The AK1 worms extrachromosomal and integrated lines) were found to be much more resistant to internal (juglone) and external (hypoxanthine/xanthine oxidase) oxidative stress than wild-type C.elegans worms. RNA interference experiments targeted to the Ov-GST-3 transcripts resulted in decreased resistance, confirming that this effect is due to the transgenic expression of Ov-GST-3. These results clearly demonstrate that the Ov-GST-3 gene confers an increased resistance to oxidative stress. This study also shows the applicability of C.elegans as a model organism for the functional characterization of genes from (parasitic) nematode species which are not accessible to genetic manipulations. ------------------- Key: 5686 Medline: 12390245 Authors: Takeda K;Ichijo H Title: Neuronal p38 MAPK signalling: an emerging regulator of cell fate and function in the nervous system. Citation: Genes to Cells 7: 1099-1111 2002 Type: REVIEW Genes: jnk-1 nsy-1 pmk-1 sek-1 str-2 unc-2 unc-36 unc-43 Abstract: p38 mitogen-activated protein kinases (MAPKs), together with extracellular signal-regulated kinases (ERKs) and c-Jun N-terminal kinases (JNKs), constitute the MAPK family. Multiple intracellular signalling pathways that converge on MAPKs exist in all eukaryotic cells and play pivotal roles in a wide variety of cellular functions. p38 MAPKs and JNKs, also termed stress-activated protein kinases (SAPKs), are preferentially activated by various cytotoxic stresses and cytokines and appear to be potent regulators of stress-induced apoptosis. Whereas JNKs have been shown to play pivotal roles in the regulation of neuronal apoptosis, the role of p38 MAPKs in the nervous system is poorly understood. However, accumulating evidence from mammalian cell culture systems and the strong genetic tool C. elegans suggests that neuronal p38 signalling has diverse functions beyond the control of cell death and survival. This review focuses on possible roles for the p38 pathway in the nervous system, with principal emphasis placed on the roles in neuronal cell fate decision ------------------- Key: 5687 Medline: 12536132 Authors: Francis MM;Mellem JE;Maricq AV Title: Bridging the gap between genes and behavior: recent advances in the electrophysiological analysis of neural function in Caenorhabditis elegans. Citation: Trends in Neurosciences 26: 90-99 2003 Type: ARTICLE Genes: eat-4 egl-3 glr-1 glr-2 nmr-1 ric-3 slo-1 unc-64 Abstract: The nematode Caenorhabditis elegans has long been popular with researchers interested in fundamental issues of neural development, sensory processing and behavior. Recently, advances in applying electrophysiological techniques to C. elegans have made this genetically tractable organism considerably more attractive to neurobiologists studying the molecular mechanisms of synaptic organization and function. The development of techniques that involve voltage-clamp of specific neurons and muscles has allowed the coupling of genetic perturbation techniques with electrophysiological analyses of nervous system function. Recent studies combining these biophysical and genetic techniques have provided novel insights into the mechanisms of presynaptic neurotransmitter release, postsynaptic responses to neurotransmitters and information processing by neural circuits. ------------------- Key: 5688 Medline: 12553575 Authors: Winter MD;McPherson MJ;Atkinson HJ Title: Neuronal uptake of pesticides disrupts chemosensory cells of nematodes. Citation: Parasitology 125: 561-565 2003 Type: ARTICLE Genes: Abstract: Low doses of the acetylcholinesterase-inhibiting carbamate nematicides disrupt chemoreception in plant-parasitic nematodes. Fluorescein isothiocyanate (FITC)/dextran conjugates up to 12 kDa are taken up from the external medium by certain chemosensory neurons in Caenorhabditis elegans. Similar chemoreceptive neurons of the non-feeding infective stage of Heterodera glycines (so bean cyst nematode) fill with FITC and the nuclei of their cell bodies selectively stain with bisbenzimide. The widely used nematicide aldicarb disrupts the chemoreceptive response of H. glycines with 50% inhibition at very low concentrations (ca 1 pM), some 10(-6)-fold lower than required to affect locomotion. Similarly, the anthelmintic levamisole had this effect at 1 nM. Peptides selected as mimetics of aldicarb and levamisole also disrupt chemoreception in H. glycines and Globodera pallida at 10(-3)-fold or lower concentration than required to inhibit locomotion. We propose an uptake pathway for aldicarb, levamisole, peptide mimetics and other soluble molecules by retrograde transport along dendrites of chemoreceptive neurons to the cell bodies and synapses where they act. This may prove to be a general mechanism for the low-dose effects of some nematicides and ------------------- Key: 5689 Medline: 12499859 Authors: Milani N;Guarin E;Renfer E;Nef P;Andres-Barquin PJ Title: Functional expression of a mammalian olfactory receptor in Caenorhabditis elegans. Citation: NeuroReport 13: 2515-2520 2002 Type: ARTICLE Genes: Abstract: The olfactory system in both vertebrates and invertebrates can recognize and distinguish thousands of chemical signals. Olfactory receptors are responsible for the early molecular events in the detection of volatile compounds and the perception of smell. Recently, candidate olfactory receptor genes have been identified in several organisms, but their characterization is far from been completed due to the difficulty to functionally express them in heterologous systems. To circumvent such difficulty, we expressed a mammalian olfactory gene, rat 17, in the nematode Caenorhabditis elegans. We generated transgenic worms expressing 17 in AWA or AWB chemosensory neurons and performed behavioural assays using different concentrations of the rat 17 receptor agonist octanal. Pure octanal was repellent for wild-type worms whereas a 1:10 dilution was attractant. Expression of 17 in AWB neurons counteracted the volatile attraction to diluted octanal observed in control wild-type worms. Furthermore, expression of 17 in AWA neurons counteracted the volatile avoidance to pure octanal observed in wild-type worms. These results indicate that it is possible to functionally express mammalian olfactory receptors in C. elegans providing a research tool to efficiently search for specific olfactory receptor ligands and to extend our understanding of the molecular basis of olfaction. ------------------- Key: 5690 Medline: 12610632 Authors: Taub J;Lau JF;Ma C;Hahn JH;Hoque R;Rothblatt J;Chalfie M Title: A cytosolic catalase is needed to extend adult lifespan in C. elegans daf-C and clk-1 mutants. Citation: Nature 421: 764- 2003 Type: CORRECT Genes: ctl-1 Abstract: We no longer have confidence in our observations associating a reduction in adult lifespan with a putative mutation in the Caenorhabditis elegans catalase gene ctl-1 and therefore retract this paper... ------------------- Key: 5691 Medline: 12543075 Authors: Mohler W;Millard AC;Campagnola PJ Title: Second harmonic generation imaging of endogenous structural proteins. Citation: Methods 29: 97-109 2003 Type: ARTICLE Genes: Abstract: We show that structural protein arrays consisting largely of collagen, myosin, and tubulin, and their associated proteins can be imaged in three dimensions with high contrast and resolution by laser-scanning second harmonic generation (SHG) microscopy. SHG is a nonlinear optical scheme and this form of microscopy shares several common advantages with multiphoton excited fluorescence, namely, intrinsic three-dimensionality and reduced out-of-plane photobleaching and phototoxicity. SHG does not arise from absorption and in-plane photodamage considerations are therefore also greatly reduced. In particular, structural protein arrays that are highly ordered and birefringent produce large SHG signals without the need for any exogenous labels. We demonstrate that thick tissues including muscle and bone can be imaged and sectioned through several hundred micrometers of depth. Combining SHG with two-photon excited green fluorescent protein (GFP) imaging allows inference of the molecular origin of the SHG contrast in Caenorhabditis elegans sarcomeres. Symmetry and organization of microtubule structures in dividing C. elegans embryos are similarly studied by comparing the endogenous tubulin contrast with that of GFP::tubulin fluorescence. It is found that SHG provides molecular level data on radial and lateral symmetries that GFP constructs cannot. The physical basis of SHG is discussed and compared with that of two-photon excitation as well as that of polarization microscopy. Due to the intrinsic sectioning, lack of photobleaching, and availability of molecular level data, SHG is a powerful tool for in vivo imaging. ------------------- Key: 5692 Medline: 12542701 Authors: Eneqvist T;Lundberg E;Nilsson L;Abagyan R;Sauer-Eriksson AE Title: The transthyretin-related protein family. Citation: European Journal of Biochemistry 270: 518-532 2003 Type: ARTICLE Genes: Abstract: A number of proteins related to the homotetrameric transport protein transthyretin (TTR) forms a highly conserved protein family, which we present in an integrated analysis of data from different sources combined with an initial biochemical characterization. Homologues of the transthyretin-related protein (TRP) can be found in a wide range of species including bacteria, plants and animals, whereas transthyretins have so far only been identified in vertebrates. A multiple sequence alignment of 49 TRP sequences from 47 species to TTR suggests that the tertiary and quaternary features of the three-dimensional structure are most likely preserved. Interestingly, while some of the TRP orthologues show as little as 30% identity, the residues at the putative ligand-binding site are almost entirely conserved. RT/PCR analysis in Caenorhabditis elegans confirms that one TRP gene is transcribed, spliced and predominantly expressed in the worm, which suggests that at least one of the two C. elegans TRP genes encodes a functional protein. We used double-stranded RNA-mediated interference techniques in order to determine the loss-of-function phenotype for the two TRP genes in C. elegans but detected no apparent phenotype. The cloning and initial characterization of purified TRP from Escherichia coli reveals that, while still forming a homotetramer, this protein does not recognize thyroid hormones that are the natural ligands of TTR. The ligand for TRP is not known; however, genomic data support a functional role involving purine catabolism especially linked to urate oxidase (uricase) activity. ------------------- Key: 5693 Medline: 12674502 Authors: Ndjonka D;Da'dara A;Walter RD;Luersen K Title: Caenorhabditis elegans S-adenosylmethionine decarboxylase is highly stimulated by putrescine but exhibits a low specificity for activator binding. Citation: Biological Chemistry 384: 83-91 2003 Type: ARTICLE Genes: pha-1 Abstract: S-Adenosylmethionine decarboxylase (AdoMetDC) is a key enzyme of the polyamine synthetic pathway providing decarboxylated S-adenosylmethionine for the formation of spermidine and spermine, respectively. The catalytic activity of the AdoMetDC from the free living nematode Caenorhabditis elegans highly depends on the presence of an activator molecule. Putrescine, a well-known stimulator of mammalian AdoMetDC activity, enhances the catalytic activity of the nematode enzyme 350-fold. Putrescine stimulation is discussed as a regulatory mechanism to relate putrescine abundance with the synthesis of spermidine and spermine. In contrast to any other known AdoMetDC, spermidine and spermine also represent significant activators of the nematode enzyme. However, the biological significance of the observed stimulation by these higher polyamines is unclear. Although C. elegans AdoMetDC exhibits a low specificity toward activator molecules, the amino acid residues that were shown to be involved in putrescine binding of the human enzyme are conserved in the nematode enzyme. Exchanging these residues by sitedirected mutagenesis indicates that at least three residues, Thr(192), Glu(194) and Glu(274), most likely contribute to activator binding in the C. elegans AdoMetDC. Interestingly, the mutant Glu(194)Gln exhibits a 100-fold enhanced basal activity in the absence of any stimulator, suggesting that this mutant protein mimics the conformational change usually induced by activator molecules. Furthermore, site directed mutagenesis revealed that at least Glu(33), Ser(83), Arg(91) and Lys(95) are involved in posttranslational processing of C. elegans ------------------- Key: 5694 Medline: 12617807 Authors: Inoue T;Sherwood DR;Aspoeck G;Butler JA;Gupta BP;Kirouac M;Wang M;Lee PY;Kramer JM;Hope I;Burglin TR;Sternberg PW Title: Gene expression markers for Caenorhabditis elegans vulval cells. Citation: Gene Expression Patterns 2: 235-241 2002 Type: ARTICLE Genes: cdh-3 ceh-2 egl-17 zmp-1 Abstract: The analysis of cell fate patterning during the vulval development of Caenorhabditis elegans has relied mostly on the direct observation of cell divisions and cell movements (cell lineage analysis). However, reconstruction of the developing vulva from EM serial sections has suggested seven different cell types (vulA, vulB1, vulB2, vulC, vulD, vulE, and vulF), many of which cannot be distinguished based on such observations. Here we report the vulval expression of seven genes, egl-17, cdh-3, ceh-2, zmp-1, B0034.1, T04B2.6 and F47B8.6 based ongfp, cfp and yfp (green fluorescent protein and color variants) reporter fusions. Each gene expresses in a specific subset of vulval cells, and is therefore useful as a marker for vulval cell fates. Together, expressions of markers distinguish six cell types, and reveal a strict temporal control of gene expression in the developing vulva. ------------------- Key: 5695 Medline: 12586701 Authors: Pepper ASR;Killian DJ;Hubbard EJA Title: Genetic analysis of Caenorhabditis elegans glp-1 mutants suggests receptor interaction or competition. Citation: Genetics 163: 115-132 2003 Type: ARTICLE Genes: ego-3 glp-1 hop-1 lag-1 lag-2 lin-12 mog-1 sel-9 sel-10 sel-12 sup-17 mnDp68 qDp3 Abstract: glp-l encodes a member of the highly conserved LIN-12/Notch family of receptors that mediates the mitosis/meiosis decision in the C. elegans germline. We have characterized three mutations that represent a new genetic and phenotypic class of glp-l mutants, glp-l(Pro). The glp-l(Pro) mutants display gainof-function germline pattern defects, most notably a proximal proliferation (Pro) phenotype. Each of three glp-l(Pro) alleles encodes a single amino acid change in the extracellular part of the receptor: two in the LIN-12/Notch repeats (LNRs) and one between the LNRs and the transmembrane domain. Unlike other previously described gain-of-function mutations that affect this region of LIN-12/Notch family receptors, the genetic behavior of glp-l(Pro) alleles is not consistent with simple hypermorphic activity. Instead, the mutant phenotype is suppressed by wild-type doses of glp-l. Moreover, a trans-heterozygous combination of two highly penetrant glp-l(Pro) mutations is mutually suppressing. These results lend support to a model for a higher-order receptor complex and/or competition among receptor proteins for limiting factors that are required for proper regulation of receptor activity. Double-mutant analysis with suppressors and enhancers of lin-12 and glp-l further suggests that the functional defect in glp-l(Pro) mutants occurs prior to or at the level of ligand interaction. ------------------- Key: 5696 Medline: 12524001 Authors: O'Kane CJ Title: Modelling human diseases in Drosophila and Caenorhabditis. Citation: Seminars in Cell & Developmental Biology 14: 3-10 2003 Type: REVIEW Genes: Abstract: Drosophila (fruitfly) and Caenorhabditis (nematode worm) are useful model organisms for understanding many molecular and cellular mechanisms of human disease. Work on them is powered by versatile gene discovery methods, output of their genome projects, and a biology that has much in common with that of humans. They contain homologues of most human disease genes. Many aspects of human disease, and of defences against disease, are also found in flies and worms. These include cancer, ageing, neurodegeneration, infectious disease, innate immunity, and dysfunction of neurotransmitter and endocrine systems. ------------------- Key: 5697 Medline: 12560808 Authors: Blumenthal T;Gleason KS Title: Caenorhabditis elegans operons: form and function. Citation: Nature Reviews Genetics 4: 110-118 2003 Type: REVIEW Genes: ced-9 coq-1 coq-3 coq-4 coq-5 cox-15 cyp-1 cyp-5 cpy-9 cpy-11 cpy-12 cpy-13 cpy-14 cpy-16 cyt-1 deg-3 des-2 dom-3 fib-1 gpd-2 gpd-3 grp-1 inf-1 leo-1 lin-15 lin-53 mai-1 mes-3 num-1 npp-4 pdi-1 rba-1 rba-2 rpa-0 rpa-1 rpa-3 rps-4 rps-16 set-2 sir-2.1 tpi-1 uaf-2 Abstract: Nematodes are unusual among animals in having a substantial proportion of their genes arranged in polycistronic clusters that are similar to bacterial operons. Recently, a nearly complete database of the Caenorhabditis elegans genes that are transcribed in operons has been produced. Analysis of this database has identified the types of genes that are contained in the operons and the extent to which operons co-regulate genes of related function. ------------------- Key: 5698 Medline: 12524540 Authors: Bergamaschi D;Samuels Y;O'Neil NJ;Trigiante G;Crook T;Hsieh JK;O'Connor DJ;Zhong S;Campargue I;Tomlinson ML;Kuwabara PE;Lu X Title: iASPP oncoprotein is a key inhibitor of p53 conserved from worm to human. Citation: Nature Genetics 33: 162-167 2003 Type: ARTICLE Genes: ape-1 cep-1 Abstract: We have previously shown that ASPP1 and ASPP2 are specific activators of p53; one mechanism by which wild-type p53 is tolerated in human breast carcinomas is through loss of ASPP activity. We have further shown that 53BP2, which corresponds to a C-terminal fragment of ASPP2, acts as a dominant negative inhibitor of p53 (ref. 1). Hence, an inhibitory form of ASPP resembling 53BP2 could allow cells to bypass the tumor-suppressor functions of p53 and the ASPP proteins. Here, we characterize such a protein, iASPP (inhibitory member of the ASPP family), encoded by PPP1R13L in humans and ape-1 in Caenorhabditis elegans. iASPP is an evolutionarily conserved inhibitor of p53; inhibition of iASPP by RNA-mediated interference or antisense RNA in C elegans or human cells, respectively, induces p53-dependent apoptosis. Moreover, iASPP is an oncoprotein that cooperates with Ras, E1A and E7, but not mutant p53, to transform cells in vitro. Increased expression of iASPP also confers resistance to ultraviolet radiation and to cisplatin-induced apoptosis. iASPP expression is upregulated in human breast carcinomas expressing wild-type p53 and normal levels of ASPP. Inhibition of iASPP could provide an important new strategy for treating tumors ------------------- Key: 5699 Medline: Authors: Penninger JM;Kroemer G Title: Mitochondria, AIF and caspases - rivaling for cell death execution. Citation: Nature Cell Biology 5: 97-99 2003 Type: REVIEW Genes: ced-3 ced-4 ced-9 egl-1 Abstract: In both the nematode Caenorhabditis elegans and mammals, two proteins released from the mitochondrion - apoptosis inducing factor (AIF) and endonuclease G - cooperate in executing programmed cell death. Although both factors can kill cells in a caspase-independent fashion, new studies indicate that their translocation from mitochondria depends, in part, on caspase activation. Together, these data raise new questions about the functional hierarchy between caspases, AIF and mitochondrial membrane ------------------- Key: 5700 Medline: 12643540 Authors: Mawuenyega KG;Kaji H;Yamauchi Y;Shinkawa T;Saito H;Taoka M;Takahashi N;Isobe T Title: Large-scale identification of Caenorhabditis elegans proteins by multidimensional liquid chromatography - tandem mass spectrometry. Citation: Journal of Proteome Research 2: 23-35 2003 Type: ARTICLE Genes: acy-1 asp-3 asp-4 cav-1 ced-7 cht-1 cnx-1 col-38 dur-1 eat-6 far-1 far-2 fkb-1 gfi-1 glt-2 him-4 hsp-3 ida-1 itx-1 jam-1 kin-11 lam-1 lbp-1 lpb-2 let-2 let-805 lrp-1 mca-1 mua-3 mup-4 ooc-3 ost-1 pat-3 pat-6 pdi-1 pdi-2 pgp-1 pgp-3 pgp-4 ptr-23 rps-21 sft-4 snb-1 sto-1 twk-2 unc-1 unc-9 unc-32 unc-43 unc-68 unc-103 vha-2 vha-5 vit-1 vit-2 vit-3 vit-4 vit-5 vit-6 Abstract: A proteome of a model organism, Caenorhabditis elegans, was analyzed by an integrated liquid chromatography (LC)-based protein identification system, which was constructed by microscale two-dimensional liquid chromatography (2DLC) coupled with electrospray ionization (ESI) tandem mass spectrometry (MS/MS) on a high-resolution hybrid mass spectrometer with an automated data analysis system. Soluble and insoluble protein fractions were prepared from a mixed growth phase culture of the worm C. elegans, digested with trypsin, and fractionated separately on the 2DLC system. The separated peptides were directly analyzed by on-line ESI-MS/MS in a data-dependent mode, and the resultant spectral data were automatically processed to search a genome sequence database, wormpep 66, for protein identification. The total number of proteins of the composite proteome identified in this method was 1616, including 110 secreted/targeted proteins and 242 transmembrane proteins. The codon adaptation indices of the identified proteins suggested that the system could identify proteins of relatively low abundance, which are difficult to identify by conventional 2D-gel electrophoresis (GE) followed by an offline mass spectrometric analysis such as peptide mass fingerprinting. Among the similar to5400 peptides assigned in this study, many peptides with post-translational modifications, such as N-terminal acetylation and phosphorylation, were detected. This expression profile of C. elegans, containing 571 hypothetical gene products, will serve as the basic data of a major proteome set expressed in the worm. ------------------- Key: 5701 Medline: Authors: Hardaker LA;Singer E;Kerr R;Zhou G;Schafer WR Title: Serotonin modulates locomotory behavior and coordinates egg-laying and movement in Caenorhabditis elegans. Citation: Journal of Neurobiology 54: 537- 2003 Type: CORRECT Genes: cat-4 egl-1 glr-1 nmr-1 tph-1 Abstract: ------------------- Key: 5702 Medline: 12477893 Authors: Niacaris T;Avery L Title: Serotonin regulates repolarization of the C. elegans pharyngeal muscle. Citation: Journal of Experimental Biology 206: 223-231 2003 Type: ARTICLE Genes: avr-15 eat-2 eat-18 tph-1 Abstract: Caenorhabditis elegans feeds by rhythmically contracting its pharynx to ingest bacteria. The rate of pharyngeal contraction is increased by serotonin and suppressed by octopamine. Using an electrophysiological assay, we show that serotonin and octopamine regulate two additional aspects of pharyngeal behavior. Serotonin decreases the duration of the pharyngeal action potential and enhances activity of the pharyngeal M3 motor neurons. Gramine, a competitive serotonin antagonist, and octopamine have effects opposite to those of serotonin: gramine and octopamine increase action potential duration and suppress M3 activity. The effects of serotonin, gramine and octopamine on action potential duration are dependent on the pharyngeal motor neurons MC and M3. When the MC and M3 motor neurons are functionally defective, serotonin and octopamine do not regulate the action potential. Our data suggest that serotonin alters pharyngeal physiology to allow for rapid contraction-relaxation cycles. Reciprocal regulation of pharyngeal behavior by serotonin and octopamine provides a mechanism for adapting to the presence and absence of food, respectively. ------------------- Key: 5703 Medline: 12438312 Authors: Gourley BL;Parker SB;Jones BJ;Zumbrennen KB;Leibold EA Title: Cytosolic aconitase and ferritin are regulated by iron in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 278: 3227-3234 2003 Type: ARTICLE Genes: aco-1 aco-2 ftn-1 ftn-2 gei-22 Abstract: Iron regulatory protein-1 (IRP-1) is a cytosolic RNA-binding protein that is a regulator of iron homeostasis in mammalian cells. IRP-1 binds to RNA structures, known as iron-responsive elements, located in the untranslated regions of specific mRNAs, and it regulates the translation or stability of these mRNAs. Iron regulates IRP-1 activity by converting it from an RNA-binding apoprotein into a [4Fe-4S] cluster protein exhibiting aconitase activity. IRP-1 is widely found in prokaryotes and eukaryotes. Here, we report the biochemical characterization and regulation of an IRP-1 homolog in Caenorhabditis elegans (GEI-22/ACO-1). GEI-22/ACO-1 is expressed in the cytosol of cells of the hypodermis and the intestine. Like mammalian IRP-1/aconitases, GEI-22/ACO-1 exhibits aconitase activity and is post-translationally regulated by iron. Although GEI-22/ACO-1 shares striking resemblance to mammalian IRP-1, it fails to bind RNA. This is consistent with the lack of iron-responsive elements in the C. elegans ferritin genes, ftn-1 and ftn-2. While mammalian ferritin H and L mRNAs are translationally regulated by iron, the amounts of C. elegans ftn-1 and ftn-2 mRNAs are increased by iron and decreased by iron chelation. Excess iron did not significantly alter worm development but did shorten their life span. These studies indicated that iron homeostasis in C. elegans shares some similarities with those of ------------------- Key: 5704 Medline: 12424233 Authors: Eschenlauer SCP;Page AP Title: The Caenorhabditis elegans ERp60 homolog protein disulfide isomerase-3 has disulfide isomerase and transglutaminase-like cross-linking activity and is involved in the maintenance of body morphology. Citation: Journal of Biological Chemistry 278: 4227-4237 2003 Type: ARTICLE Genes: dpy-3 dpy-5 dpy-7 dpy-8 dpy-10 dpy-11 dpy-13 dpy-18 pdi-3 phy-2 phy-3 sqt-1 sqt-3 unc-119 Abstract: A novel protein disulfide isomerase gene, pdi-3, was isolated from the nematode Caenorhabditis elegans. This gene encodes an enzyme related to the ERp60 class of thioredoxin proteins and was found to exhibit unusual enzymatic properties. Recombinant protein displayed both disulfide bond isomerase activity and calcium-dependent transglutaminase-like cross-linking activity. The pdi-3 transcript was developmentally constitutively expressed, and the encoded protein is present in many tissues including the gut and the hypodermis. The nematode hypodermis synthesizes the essential collagenous extracellular matrix (ECM) called the cuticle. Transcript disruption via double-stranded RNA interference resulted in dramatic and specific synthetic phenotypes in several C. elegans mutant alleles with weakened cuticles: sqt-3(e2117), dpy-18(e364, ok162, and bx26). These nematodes displayed severe dumpy phenotypes and disrupted lateral alae, a destabilized cuticle and abnormal male and hermaphrodite tail morphologies. These defects were confirmed to be consistent with hypodermal seam cell abnormalities and corresponded with the severe disruption of a cuticle collagen. Wild type nematodes did not exhibit observable morphological defects; however, cuticle collagen localization was mildly disrupted following pdi-3 RNA interference. The unusual thioredoxin enzyme, protein disulfide isomerase-3, may therefore play a role in ECM assembly. This enzyme is required for the proper maintenance of postembryonic body shape in strains with a weakened cuticle, perhaps through ECM stabilization via cross-linking activity, disulfide isomerase protein folding activity, protein disulfide isomerase-chaperone activity, ------------------- Key: 5705 Medline: 12566401 Authors: Lercher MJ;Blumenthal T;Hurst LD Title: Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. Citation: Genome Research 13: 238-243 2003 Type: ARTICLE Genes: Abstract: In many eukaryotic species, gene order is not random. In humans, flies, and yeast, there is clustering of coexpressed genes that cannot be explained as a trivial consequence of tandem duplication. In the worm genome this is taken a step further with many genes being organized into operons. Here we analyze the relationship between gene location and expression in Caenorhabditis elegans and find evidence for at least three different processes resulting in local expression similarity. Not surprisingly, the strongest effect comes from genes organized in operons. However, coexpression within operons is not perfect, and is influenced by some distance-dependent regulation. Beyond operons, there is a relationship between physical distance, expression similarity, and sequence similarity, acting over several megabases. This is consistent with a model of tandem duplicate genes diverging over time in sequence and expression pattern, while moving apart owing to chromosomal rearrangements. However, at a very local level, nonduplicate genes on opposite strands (hence not in operons) show similar expression patterns. This suggests that such genes may share regulatory elements or be regulated at the level of chromatin structure. The central importance of tandem duplicate genes in these patterns renders the worm genome different from both yeast and ------------------- Key: 5706 Medline: 12530957 Authors: Dawes-Hoang RE;Zallen JA;Wieschaus EF Title: Bringing classical embryology to C. elegans gastrulation. Citation: Developmental Cell 4: 6-8 2003 Type: REVIEW Genes: Abstract: In a recent paper, Lee and Goldstein develop an explant assay that recapitulates key aspects of gastrulation in C. elegans and permits classical embryological manipulations. The resulting detailed analysis of cell behavior will ultimately extend to broader issues, such as, whether morphogenesis can be described as the sum of single-cell events or if unique phenomena emerge at the multicellular level. ------------------- Key: 5707 Medline: 12530969 Authors: McKay RM;McKay JP;Avery L;Graff JM Title: C. elegans: a model for exploring the genetics of fat storage. Citation: Developmental Cell 4: 131-142 2003 Type: ARTICLE Genes: eat-2 mac-1 lpd-1 lpd-2 lpd-3 lpd-4 lpd-5 lpd-6 lpd-7 lpd-8 lpd-9 Abstract: To gain insights into the genetic cascades that regulate fat biology, we evaluated C. elegans as an appropriate model organism. We generated worms that lack two transcription factors, SREBP and C/EBP, crucial for formation of mammalian fat. Worms deficient in either of these genes displayed a lipid-depleted phenotype-pale, skinny, larval-arrested worms that lack fat stores. On the basis of this phenotype, we used a reverse genetic screen to identify several additional genes that play a role in worm lipid storage. Two of the genes encode components of the mitochondrial respiratory chain (MRC). When the MRC was inhibited chemically in worms or in a mammalian adipocyte model, fat accumulation was markedly reduced. A third encodes lpd-3, whose homolog is also required for fat storage in a mammalian model. These data suggest that C. elegans is a genetically tractable model to study the mechanisms that underlie the biology of fat-storing ------------------- Key: 5708 Medline: 12606285 Authors: Brodigan TM;Liu J;Park M;Kipreos ET;Krause M Title: Cyclin E expression during development in Caenorhabditis elegans. Citation: Developmental Biology 254: 102-115 2003 Type: ARTICLE Genes: cdk-4 cye-1 Abstract: Our interest in the coordination of cell cycle control and differentiation has led us to investigate the Caenorhabditis elegans cye-1 gene encoding the G(1) cell cycle regulator cyclin E. We have studied the expression and function of cye-1 by using monoclonal antibodies directed against CYE-1 protein, cye-1::GFP reporter genes, and a cye-1 chromosomal deletion mutation. We show that a ubiquitous embryonic pattern of expression becomes restricted and dynamic during postembryonic development. Promoter analysis reveals a relatively small region of cis-acting sequences that are necessary for the complex pattern of expression of this gene. Our studies demonstrate that two other G(1) cell cycle genes, encoding cyclin D and CDK4/6, have similarly compact promoter requirements. This suggests that a relatively simple mechanism of regulation may underlie the dynamic developmental patterns of expression exhibited by these three G(1) cell cycle genes. Our analysis of a new cye-1 deletion allele confirms and extends previous studies of two point mutations in the ------------------- Key: 5709 Medline: 12526744 Authors: Aballay A;Drenkard E;Hilbun LR;Ausubel FM Title: Caenorhabditis elegans innate immune response triggered by Salmonella enterica requires intact LPS and is mediated by a MAPK signaling pathway. Citation: Current Biology 13: 47-52 2003 Type: ARTICLE Genes: ced-9 nsy-1 pik-1 pmk-1 sek-1 tol-1 trf-1 Abstract: Compared to mammals, insects, and plants, relatively little is known about innate immune responses in the nematode Caenorhabditis elegans. Previous work showed that Salmonella enterica serovars cause a persistent infection in the C. elegans intestine [1, 2] that triggers gonadal programmed cell death (PCD) and that C. elegans cell death (ced) mutants are more susceptible to Salmonella-mediated killing [3]. To further dissect the role of PCD in C. elegans innate immunity, we identified both C. elegans and S. enterica factors that affect the elicitation of Salmonella-induced PCD. Salmonella-elicited PCD was shown to require the C. elegans homolog of the mammalian p38 mitogen-activated protein kinase (MAPK) encoded by the pmk-1 gene. Inactivation of pmk-1 by RNAi blocked Salmonella-elicited PCD, and epistasis analysis showed that CED-9 lies downstream of PMK-1. Wild-type Salmonella lipopolysaccharide (LPS) was also shown to be required for the elicitation of PCD, as well as for persistence of Salmonella in the C. elegans intestine. However, a presumptive C. elegans TOLL signaling pathway did not appear to be required for the PCD response to Salmonella. These results establish a PMK-1-dependant PCD pathway as a C. elegans innate immune response to Salmonella. ------------------- Key: 5710 Medline: 12546787 Authors: Subramaniam K;Seydoux G Title: Dedifferentiation of primary spermatocytes into germ cell tumors in C. elegans lacking the Pumilio-like protein Citation: Current Biology 13: 134-139 2003 Type: ARTICLE Genes: fem-1 fem-3 gld-1 mek-2 puf-8 spe-6 tra-2 Abstract: PUF proteins are a conserved family of RNA binding proteins that regulate RNA stability and translation by binding to specific sequences in 3'-untranslated regions. Drosophila PUMILIO and C. elegans FBF are essential for self-renewal of germline stem cells, suggesting that a common function of PUF proteins may be to sustain mitotic proliferation of stem cells [1]. Here, we show that PUF-8, the C. elegans PUF most related to PUMILIO, performs a different function in germ cells that have begun meiosis: in primary spermatocytes, puf-8 is required to maintain meiosis and prevent the return to mitosis. Primary spermatocytes lacking PUF-8 complete meiotic prophase but do not undergo normal meiotic divisions. Instead, they dedifferentiate back into mitotically cycling germ cells and form rapidly growing tumors. These findings reveal an unexpected ability for germ cells that have completed meiotic prophase to return to the mitotic cycle, and they support the view that PUF proteins regulate multiple transitions during germline ------------------- Key: 5711 Medline: 12526742 Authors: Aboobaker AA;Blaxter ML Title: Hox gene loss during dynamic evolution of the nematode cluster. Citation: Current Biology 13: 37-40 2003 Type: ARTICLE Genes: ceh-13 egl-5 lin-39 mab-5 nob-1 php-3 Abstract: Hox genes are important: their central role in anterior-posterior patterning provides a framework for molecular comparison of animal body plan evolution [1]. The nematode Caenorhabditis elegans stands out as having a greatly reduced Hox gene complement [2]. To address this, orthologs of C. elegans Hox genes were identified in six species from across the Nematoda, and they show that rapid homeodomain sequence evolution is a general feature of nematode Hox genes. Some nematodes express additional Hox genes belonging to orthology groups that are absent from C. elegans but present in other bilaterian animals. Analysis of the genomic environment of a newly identified Brugia malayi Hox6-8 ortholog (Bm-ant-1) revealed that it lay downstream of the Bm-egl-5 Hox gene and that their homeodomain exons are alternately cis spliced to the same 5' exon. This organization may represent an intermediate state in Hox gene loss via redundancy. The Hox clusters of nematodes are the product of a dynamic mix of gene loss and rapid sequence evolution, with the most derived state observed in the model C. elegans. ------------------- Key: 5712 Medline: Authors: Lithgow GJ;Gill MS Title: Cost-free longevity in mice? Citation: Nature 421: 125-126 2003 Type: REVIEW Genes: daf-2 Abstract: Studies of worms have revealed hundreds of proteins that, when mutated, extend lifespan. Can this work tell us anything about mammalian ageing? A look at the effects of one such protein on lab mice suggests that it can. ------------------- Key: 5713 Medline: 12586703 Authors: Sivasundar A;Hey J Title: Population genetics of Caenorhabditis elegans: the paradox of low polymorphism in a widespread species. Citation: Genetics 163: 147-157 2003 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide. ------------------- Key: 5714 Medline: 12610294 Authors: Tatar M;Bartke A;Antebi A Title: The endocrine regulation of aging by insulin-like signals. Citation: Science 299: 1346-1351 2003 Type: REVIEW Genes: age-1 daf-2 daf-9 daf-12 daf-16 Abstract: Reduced signaling of insulin-like peptides increases the life-span of nematodes, flies, and rodents. In the nematode and the fly, secondary hormones downstream of insulin-like signaling appear to regulate aging. In mammals, the order in which the hormones act is unresolved because insulin, insulin-like growth factor-1, growth hormone, and thyroid hormones are interdependent. In all species examined to date, endocrine manipulations can slow aging without concurrent costs in reproduction, but with inevitable increases in stress resistance. Despite the similarities among mammals and invertebrates in insulin-like peptides and their signal cascade, more research is needed to determine whether these signals control aging in the same way in all the species by the same mechanism. ------------------- Key: 5715 Medline: 12610295 Authors: Hekimi S;Guarente L Title: Genetics and the specificity of the aging process. Citation: Science 299: 1351-1354 2003 Type: REVIEW Genes: clk-1 ctb-1 daf-2 daf-12 isp-1 sir-2.1 Abstract: The identification and study of long-lived mutant animals has provided valuable insights into the mechanisms that limit the life-span of organisms. Findings with the gene SIR2 suggest that the rate of aging can be regulated under certain conditions. Indeed, increased expression of SIR2 lengthens life-span by acting on biological processes that promote survival under conditions of scarcity. In addition, studies of mutant strains of Caenorhabditis elegans, in particular daf-2, clk-1, and isp-1 mutants, suggest that the biology of reactive oxygen species in the mitochondria and elsewhere might be the main determinant of life-span in this organism. Thus, the aging process may be more specific than previously anticipated on evolutionary grounds. ------------------- Key: 5716 Medline: 12579260 Authors: Ichimiya H;Hino O;Kohara Y;Ishii N Title: VBP-1 is necessary for morphogenesis in Caenorhabditis elegans. Citation: Oncology Reports 10: 293-295 2003 Type: ARTICLE Genes: vbp-1 Abstract: VBP-1 has been isolated as a novel protein binding to the von Hippel-Lindau (VHL) tumor suppressor gene product. The fundamental function of the gene was examined in the nematode, Caenorhabditis elegans (C. elegans). The C. elegans VBP-1 gene was expressed in adults only in the gonads and was also expressed in early stage embryos. Double-stranded RNA interference (RNAi) against VBP-1 resulted in an arrest of embryogenesis at morula stages. This suggests that the VBP-1 product is necessary for morphogenesis. ------------------- Key: 5717 Medline: 12519966 Authors: Harris TW;Lee R;Schwarz E;Bradnam K;Lawson D;Chen W;Blasier D;Kenny E;Cunningham F;Kishore R;Chan J;Muller HM;Petcherski A;Thorisson G;Day A;Bieri T;Rogers A;Chen CK;Spieth J;Sternberg P;Durbin R;Stei Title: WormBase: a cross-species database for comparative Citation: Nucleic Acids Research 31: 133-137 2003 Type: ARTICLE Genes: Abstract: WormBase (http://www.wormbase.org/) is a web-accessible central data repository for information about Caenorhabditis elegans and related nematodes. The past two years have seen a significant expansion in the biological scope of WormBase, including the integration of large-scale, genome-wide data sets, the inclusion of genome sequence and gene predictions from related species and active literature curation. This expansion of data has also driven the development and refinement of user interfaces and operability, including a new Genome Browser, new searches and facilities for data access and the inclusion of extensive documentation. These advances have expanded WormBase beyond the obvious target audience of C. elegans researchers, to include researchers wishing to explore problems in functional and comparative genomics within the ------------------- Key: 5718 Medline: 12519990 Authors: Vaglio P;Lamesch P;Reboul J;Rual JF;Martinez M;Hill D;Vidal M Title: WorfDB: the Caenorhabditis elegans ORFeome database. Citation: Nucleic Acids Research 31: 237-240 2003 Type: ARTICLE Genes: Abstract: WorfDB (Worm ORFeome DataBase; http://worfdb.dfci.harvard.edu) was created to integrate and disseminate the data from the cloning of complete set of similar to19000 predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans ( also referred to as the 'worm ORFeome'). WorfDB serves as a central data repository enabling the scientific community to search for availability and quality of cloned ORFs. So far, ORF sequence tags (OSTs) obtained for all individual clones have allowed exon structure corrections for similar to3400 ORFs originally predicted by the C. elegans sequencing consortium. In addition, we now have OSTs for similar to4300 predicted genes for which no ESTs were available. The database contains this OST information along with data pertinent to the cloning process. WorfDB could serve as a model database for other metazoan ORFeome cloning projects. ------------------- Key: 5719 Medline: 12526772 Authors: Gitai Z;Yu TW;Lundquist EA;Tessier-Lavigne M;Bargmann CI Title: The netrin receptor UNC-40/DCC stimulates axon attraction and outgrowth through Enabled and, in parallel, Rac and UNC-115/AbLIM. Citation: Neuron 37: 53-65 2003 Type: ARTICLE Genes: ced-10 mig-2 sax-3 slt-1 unc-5 unc-6 unc-34 unc-40 unc-44 unc-51 unc-60 unc-73 unc-76 unc-115 vab-1 Abstract: Netrins promote axon outgrowth and turning through DCC/UNC-40 receptors. To characterize Netrin signaling, we generated a gain-of-function UNC-40 molecule, MYR::UNC-40. MYR::UNC-40 causes axon guidance defects, excess axon branching, and excessive axon and cell body outgrowth. These defects are suppressed by loss-of-function mutations in ced-10 (a Rac GTPase), unc-34 (an Enabled homolog), and unc-115 (a putative actin binding protein). ced-10, unc-34, and unc-115 also function in endogenous unc-40 signaling. Our results indicate that Enabled functions in axonal attraction as well as axon repulsion. UNC-40 has two conserved cytoplasmic motifs that mediate distinct downstream pathways: CED-10, UNC-115, and the UNC-40 P2 motif act in one pathway, and UNC-34 and the UNC-40 P1 motif act in the other. Thus, UNC-40 might act as a scaffold to deliver several independent signals to the actin cytoskeleton. ------------------- Key: 5720 Medline: Authors: Masler EP Title: In vitro metabolism of an insect neuropeptide by homogenates of the nematode Caenorhabditis elegans. Citation: Journal of Helminthology 77: 43-48 2003 Type: ARTICLE Genes: Abstract: The cytosolic fraction of homogenates from the free-living soil nematode Caenorhabditis elegans is capable of metabolizing the insect neuropeptide adipokinetic hormone, a decapeptide blocked at the N-terminus by a pGlu residue. Analysis of digests by RP-HPLC and LC-MS revealed that an initial endoproteolytic cleavage step produced a heptapeptide with an unblocked N-terminus that can serve as a substrate for aminopeptidases. The aminopeptidase activity is depressed in the presence of the inhibitor amastatin; the initial product of the endoproteolytic step accumulates during incubation, and expected aminopeptidase product peptides are reduced in amount, as assessed by chromatographic peak size. The absence of some expected peptide fragments in the reaction mixtures suggests that multiple proteases contribute to short peptide half-lives. Comparison of the adipokinetic hormone digestion in C. elegans to that reported previously for insects reveals the same general pattern of peptide fragment production. ------------------- Key: 5721 Medline: 12475970 Authors: Abdelghany HM;Bailey S;Blackburn GM;Rafferty JB;McLennan AG Title: Analysis of the catalytic and binding residues of the diadenosine tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans by site-directed mutagenesis. Citation: Journal of Biological Chemistry 278: 4435-4439 2003 Type: ARTICLE Genes: Abstract: The contributions to substrate binding and catalysis of 13 amino acid residues of the Caenorhabditis elegans diadenosine tetraphosphate pyrophosphohydrolase (Ap(4)A hydrolase) predicted from the crystal structure of an enzyme-inhibitor complex have been investigated by site-directed mutagenesis. Sixteen glutathione S-transferase-Ap(4)A hydrolase fusion proteins were expressed and their k(cat) and K-m values determined after removal of the glutathione S-transferase domain. As expected for a Nudix hydrolase, the wild type k(cat) of 23 s(-1) was reduced by 10(5)-, 10(3)-, and 30-fold, respectively, by replacement of the conserved P-phosphate-binding catalytic residues Glu(56), Glu(52), and Glu(103) by Gln. K-m values were not affected, indicating a lack of importance for substrate binding. In contrast, mutating His(31) to Val or Ala and Lys(83) to Met produced 10- and 16-fold increases in K. compared with the wild type value of 8.8 muM. These residues stabilize the P-1-phosphate. H31V and H31A had a normal kcat but K83M showed a 37-fold reduction in k(cat). Lys(36) also stabilizes the P-1-phosphate and a K36M mutant had a 10-fold reduced kcat but a relatively normal K-m. Thus both Lys(36) and Lys(83) may play a role in catalysis. The previously suggested roles of Tyr(27), His(38), Lys(79), and Lys(81) in stabilizing the P-2 and P-3-phosphates were not confirmed by mutagenesis, indicating the absence of phosphate-specific binding contacts in this region. Also, mutating both Tyr(76) and Tyr(121), which clamp one substrate adenosine moiety between them in the crystal structure, to Ala only increased K-m 4-fold. It is concluded that interactions with the P-1- and P-4-phosphates are minimum and sufficient requirements for substrate binding by this class of enzyme, indicating that ------------------- Key: 5722 Medline: 12554684 Authors: Caldwell GA;Cao S;Sexton EG;Gelwix CC;Bevel JP;Caldwell KA Title: Suppression of polyglutamine-induced protein aggregation in Caenorhabditis elegans by torsin proteins. Citation: Human Molecular Genetics 12: 307-319 2003 Type: ARTICLE Genes: ooc-5 tor-1 tor-2 Abstract: Torsion dystonia is an autosomal dominant movement disorder characterized by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA+ proteins. We have established the nematode, Caenorhabditis elegans, as a model system for examining torsin activity. Using an in vivo assay for polyglutamine repeat-induced protein aggregation in living animals, we have determined that ectopic overexpression of both human and C. elegans torsin proteins results in a dramatic reduction of polyglutamine-dependent protein aggregation in a manner similar to that previously reported for molecular chaperones. The suppressive effects of torsin overexpression persisted as animals aged, whereas a mutant nematode torsin protein was incapable of ameliorating aggregate formation. Antibody staining of transgenic animals indicated that both the C. elegans torsin-related protein TOR-2 and ubiquitin were localized to sites of protein aggregation. These data represent the first functional evidence of a role for torsins in effectively managing protein folding and suggest that possible breakdown in a neuroprotective mechanism that is, in part, ------------------- Key: 5723 Medline: 12554664 Authors: Anders KR;Grimson A;Anderson P Title: SMG-5, required for C. elegans nonsense-mediated mRNA decay, associates with SMG-3 and protein phosphatase 2A. Citation: EMBO Journal 22: 641-650 2003 Type: ARTICLE Genes: smg-1 smg-2 smg-3 smg-4 smg-5 smg-6 smg-7 unc-54 Abstract: mRNAs that contain premature stop codons are degraded selectively and rapidly in eukaryotes, a phenomenon termed 'nonsense-mediated mRNA decay' (NMD). We report here molecular analysis of smg-5, which encodes a novel protein required for NMD in Caenorhabditis elegans. Using a combination of immunoprecipitation and yeast two-hybrid assays, we identified a series of protein-protein interactions involving SMG-5. SMG-5 interacts with at least four proteins: (i) SMG-7, a previously identified protein required for NMD; (ii) SMG-2, a phosphorylated protein required for NMD in worms, yeasts and mammals; (iii) PR65, the structural subunit of protein phosphatase 2A (PP2A); and (iv) PP2A(C), the catalytic subunit of PP2A. Previous work demonstrated that both SMG-5 and SMG-7 are required for efficient dephosphorylation of SMG-2. Our results suggest that PP2A is the SMG-2 phosphatase, and the role of SMG-5 is to direct PP2A to its SMG-2 substrate. We discuss cycles of SMG-2 phosphorylation and their roles in NMD. ------------------- Key: 5724 Medline: 12573233 Authors: Salisbury JL Title: Centrosomes: coiled-coils organize the cell center. Citation: Current Biology 13: R88-R90 2003 Type: REVIEW Genes: dhc-1 spd-2 spd-5 Abstract: The centrosome serves as a structural context for cytoplasmic organization. Recent studies on mutants of the nematode worm Caenorhabditis elegans have provided new insight into the framework to which microtubules and key regulators of centrosome behavior are anchored. ------------------- Key: 5725 Medline: 12458202 Authors: Walker AK;Blackwell TK Title: A broad but restricted requirement for TAF-5 (human TAF(II)100) for embryonic transcription in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 278: 6181-6186 2003 Type: ARTICLE Genes: ama-1 cdk-9 cki-1 hsp-16.2 let-858 pes-10 rgr-1 rps-5 sur-5 taf-4 taf-5 taf-9 taf-10 Abstract: As conserved components of the transcription factor (TF) IID- and TFTC/SAGA-related complexes, TATA-binding protein-associated factors (TAF(II)s) are important for eukaryotic mRNA transcription. In yeast, genetic analyses suggest that, although some individual TAF(II)s are required for transcription of most genes, others have highly specialized functions. Much less is known about the functions of TAF(II)s in metazoans, which have more complex genomes that include many tissue-specific genes. TAF-5 (human (h) TAF(II)100) is of particular interest because it is predicted to have an important structural role. Here we describe the first genetics-based analysis of TAF-5 in a metazoan. By performing RNA interference in Caenorhabditis elegans embryos, which can survive for several cell generations without transcription, we found that taf-5 is important for a significant fraction of transcription. However, TAF-5 is apparently not essential for the expression of multiple developmental and other metazoan-specific genes. This phenotype remarkably resembles the previously described effects of similarly depleting two C. elegans histone fold TAF(II)s, TAF-9 (hTAF(II)31/32) and TAF-10 (hTAF(II)130), but is distinct from the widespread transcription block caused by TAF-4 (hTAF(II)130) depletion. Our findings suggest that TAF-5, TAF-9, and TAF-10 are part of a functional module of TFIID- and TFTC/SAGA-related complexes that can be bypassed in many metazoan-specific genes. ------------------- Key: 5726 Medline: 12480943 Authors: Fei YJ;Inoue K;Ganapathy V Title: Structural and functional characteristics of two sodium-coupled dicarboxylate transporters (ceNaDC1 and ceNaDC2) from Caenorhabditis elegans and their relevance to life span. Citation: Journal of Biological Chemistry 278: 6136-6144 2003 Type: ARTICLE Genes: Abstract: We have cloned and functionally characterized two Na+-coupled dicarboxylate transporters, namely ceNaDC1 and ceNaDC2, from Caenorhabditis elegans. These two transporters show significant sequence homology with the product of the Indy gene identified in Drosophila melanogaster and with the Na+-coupled dicarboxylate transporters NaDC1 and NaDC3 identified in mammals. In a mammalian cell heterologous expression system, the cloned ceNaDC1 and ceNaDC2 mediate Na+-coupled transport of various dicarboxylates. With succinate as the substrate, ceNaDC1 exhibits much lower affinity compared with ceNaDC2. Thus, ceNaDC1 and ceNaDC2 correspond at the functional level to the mammalian NaDC1 and NaDC3, respectively. The nadc1 and nadc2 genes are not expressed at the embryonic stage, but the expression is detectable all through the early larva stage to the adult stage. Tissue-specific expression pattern studies using a reporter gene fusion approach in transgenic C. elegans show that both genes are co-expressed in the intestinal tract, an organ responsible for not only the digestion and absorption of nutrients but also for the storage of energy in this organism. Independent knockdown of the function of these two transporters in C. elegans using the strategy of RNA interference suggests that NaDC1 is not associated with the regulation of average life span in this organism, whereas the knockdown of NaDC2 function leads to a significant increase in the average life span. Disruption of the function of the high affinity Na+-coupled dicarboxylate transporter NaDC2 in C. elegans may lead to decreased availability of dicarboxylates for cellular production of metabolic energy, thus creating a biological state similar to that of caloric restriction, and consequently leading to ------------------- Key: 5727 Medline: 12586702 Authors: Louvet-Vallee S;Kolotuev I;Podbilewicz B;Felix MA Title: Control of vulval competence and centering in the nematode Oscheius sp. 1 CEW1. Citation: Genetics 163: 133-146 2003 Type: ARTICLE Genes: Abstract: To compare vulva development mechanisms in the nematode Oscheius sp. 1 to those known in Caenorhabditis elegans, we performed a genetic screen for vulva mutants in Oscheius sp. 1 CEW1. Here we present one large category of mutations that we call cov, which affect the specification of the Pn.p ventral epidermal cells along the antero-posterior axis. The Pn.p cells are numbered from 1 to 12 from anterior to posterior. In wild-type Oscheius sp. 1 CEW1, the P(4-8).p cells are competent to form the vulva and the progeny of P(5-7).p actually form the vulva, with the descendants of P6.p adopting a central vulval fate. Among the 17 mutations (defining 13 genes) that we characterize here, group 1 mutations completely or partially abolish P(4-8).p competence, and this correlates with early fusion of the Pn.p cells to the epidermal syncytium. In this group, we found a putative null mutation in the lin-39 HOM-C homolog, the associated phenotype of which could be weakly mimicked by injection of a morpholino against Osp1-lin-39 in the mother's germ line. Using cell ablation in a partially penetrant competence mutant, we show that vulval competence is partially controlled by a gonadal signal. Most other mutants found in the screen display phenotypes unknown in C. elegans. Group 2 mutants show a partial penetrance of Pn.p competence loss and an abnormal centering of the vulva on P5.p, suggesting that these two processes are coregulated by the same pathway in Oscheius sp. 1. Group 3 mutants display an enlarged competence group that includes P3.p, thus demonstrating the existence of a specific mechanism inhibiting P3.p competence. Group 4 mutants display an abnormal centering of the vulval pattern on P7.p and suggest that a specific mechanism centers the vulval pattern on a single Pn.p cell. ------------------- Key: 5728 Medline: 12586704 Authors: Kniazeva M;Sieber M;McCauley S;Zhang K;Watts JL;Han M Title: Suppression of the ELO-2 FA elongation activity results in alterations of the fatty acid composition and multiple physiological defects, including abnormal ultradian rhythms, in Caenorhabditis elegans Citation: Genetics 163: 159-169 2003 Type: ARTICLE Genes: elo-1 elo-2 fat-2 fat-3 Abstract: While the general steps of fatty acid (FA) biosynthesis are well understood, the individual enzymes involved in the elongation of long chain saturated and polyunsaturated FA (PUFA) are largely unknown. Recent research indicates that these enzymes might be of considerable physiological importance for human health. We use Caenorhabditis elegans to study FA elongation activities and associated abnormal phenotypes. In this article we report that the predicted C. elegans F11E6.5/ELO-2 is a functional enzyme with the FA elongation activity. It is responsible for the elongation of palmitic acid and is involved in PUFA biosynthesis. RNAi-mediated suppression of ELO-2 causes an accumulation of palmitate and an associated decrease in the PUFA fraction in triacylglycerides and phospholipid classes. This imbalance in the FA composition results in multiple phenotypic defects such as slow growth, small body size, reproductive defects, and changes in rhythmic behavior. ELO-2 cooperates with the previously reported ELO-1 in 20-carbon PUFA production, and at least one of the enzymes must function to provide normal growth and development in C. elegans. The presented data indicate that suppression of a single enzyme of the FA elongation machinery is enough to affect various organs and systems in worms. This effect resembles syndromic disorders in humans. ------------------- Key: 5729 Medline: 12586705 Authors: Munoz MJ;Riddle DL Title: Positive selection of Caenorhabditis elegans mutants with increased stress resistance and longevity. Citation: Genetics 163: 171-180 2003 Type: ARTICLE Genes: aap-1 age-1 daf-1 daf-2 daf-7 daf-16 dyf-2 liv-2 liv-4 liv-5 unc-13 unc-18 unc-31 unc-64 Abstract: We developed selective conditions for long-lived mutants of the nematode Caenorbabditis elegans by subjecting the first larval stage (L1) to thermal stress at 30degrees for 7 days. The surviving larvae developed to fertile adults after the temperature was shifted to 15degrees. A total of one million F-2 progeny and a half million F-3 progeny of ethyl-methanesulfonate-mutagenized animals were treated in three separate experiments. Among the 81 putative mutants that recovered and matured to the reproductive adult, 63 retested as thermotolerant and 49 (80%) exhibited a >15% increase in mean life span. All the known classes of dauer formation (Daf) mutant that affect longevity were found, including six new alleles of daf-2, and a unique temperature-sensifive, dauer-constitutive allele of age 1. Alleles of dyf-2 and unc-13 were isolated, and mutants of unc-18, a gene that interacts with unc-13, were also found to be long lived. Thirteen additional mutations define at least four new genes. ------------------- Key: 5730 Medline: 12568714 Authors: Hope IA;Mounsey A;Bauer P;Aslam S Title: The forkhead gene family of Caenorhabditis elegans. Citation: Gene 304: 43-55 2003 Type: ARTICLE Genes: daf-16 fkh-2 fkh-3 fkh-4 fkh-5 fkh-6 fkh-7 fkh-8 fkh-9 fkh-10 lin-31 pes-1 pha-4 unc-130 Abstract: The forkhead genes encode a family of transcriptional regulators with important roles in the control of animal development. The genomic sequence has revealed Caenorhabditis elegans has 15 forkhead genes of which six had been experimentally characterised previously. The remaining nine have now been investigated by RNAi and reporter gene expression pattern analysis. Two (B0286.5 and F26B1.7) have key developmental roles, four (F26D12.1, K03C7.2, F40H3.4 and C25A1.2) are expressed in, and may function in, the nervous system and three (C29F7.4, C29F7.5 and F26A1.2), which are closely related to each other, do not appear to be essential. Conservation with forkhead genes in the closely related nematode Caenorhabditis briggsae does not appear to correspond completely with demonstrated functionality in C. elegans. Comparisons of expression patterns and RNAi/mutant phenotypes for all 15 C. elegans forkhead genes reveal the potential complexity of functional interactions for this gene family. ------------------- Key: 5731 Medline: Authors: Bultrini E;Pizzi E;Del Giudice P;Frontali C Title: Pentamer vocabularies characterizing introns and intron-like intergenic tracts from Caenorhabditis elegans and Drosophila melanogaster. Citation: Gene 304: 183-192 2003 Type: ARTICLE Genes: Abstract: Overall compositional properties at the level of bases, dinucleotides and longer oligos characterize genomes of different species. In Caenorhabditis elegans, using recurrence analysis, we recognized the existence of a long-range con-elation in the oligonucleotide usage of introns and intergenic regions. Through correlation analysis, this is confirmed here to be a genome-wide property of C. elegans non-coding portions. We then investigate the possibility of extracting a typical vocabulary through statistical analysis of experimentally confirmed introns of sufficient length I(> I kb), deprived of known splice signals, the focus being on distributed lexical features rather than on localized motifs. Lexical preferences typical of introns could be exposed using principal component analysis of pentanucleotide frequency distributions, both in C. elegans and in Drosophila melanogaster. In either species, the introns' pentamer preferences are largely shared by intergenic tracts. The pentamer vocabularies extracted for the two species exhibit interesting symmetry properties and overlap in part. A more extensive investigation of the interspecies relationship at the level of oligonucleotide preferences in non-coding regions, not related by sequence similarity, might form the basis of new approaches for the study of the evolutionary behaviour of these regions. ------------------- Key: 5732 Medline: 12543270 Authors: McCulloch D;Gems D Title: Body size, insulin/IGF signaling and aging in the nematode Caenorhabditis elegans. Citation: Experimental Gerontology 38: 129-136 2003 Type: ARTICLE Genes: daf-2 dpy-7 dpy-10 dpy-13 lon-1 lon-2 sma-1 sma-3 sma-4 Abstract: A number of recent studies of aging in Drosophila, mice and dogs have shown an association between reduced body size and increased lifespan. It is unclear (a) whether such an association is a general feature of animal species; and (b) whether the association reflects an effect of body size on aging, or pleiotropic effects of common determinants of growth and aging. To address these issues, we have studied the relationship between size and lifespan in the nematode Caenorhabditis elegans, and surveyed related findings in Drosophila. In C. elegans, we compared 12 wild isolates with varying body size and lifespan, but saw no correspondence between these traits. We also examined aging in giant and dwarf mutants, but observed only reduced lifespan in all cases. In a comparison of 15 long-lived daf-2 insulin/IGF receptor mutants, we saw a positive correlation between body length and lifespan, and up to a 28% increase in daf-2 mutant body volume. Thus, in C. elegans, insulin/IGF signaling may limit growth rather than promote it. Studies of Drosophila show no consistent correlation between body size and lifespan. These results indicate that the negative correlation between body size and lifespan seen in some mammals is not typical of invertebrates, but support the view that co-variation of size and longevity may occur via effects on insulin/IGF ------------------- Key: 5733 Medline: 12565862 Authors: Morio H;Honda Y;Toyoda H;Nakajima M;Kurosawa H;Shirasawa T Title: EXT gene family member rib-2 is essential for embryonic development and heparan sulfate biosynthesis in Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 301: 317-323 2003 Type: ARTICLE Genes: rib-2 nDf17 Abstract: EXT gene family members including EXT1, EXT2, and EXTL2 are glycosyltransferases required for heparan sulfate biosynthesis. To examine the biological functions of rib-2, a member of the Caenorhabditis elegans EXT gene family, we generated a mutant worm lacking the rib-2 gene using the UV-TMP method followed by sib-selection. Inactivation of rib-2 alleles induced developmental abnormalities in F2 and F3 homozygous worms, while F1 heterozygotes showed a normal morphology. The F2 homozygous progeny generated from the F1 heterozygous hermaphrodites somehow developed to adult stage but exhibited abnormal characteristics such as developmental delay and egg-laying defects. The F3 homozygous progeny from the F2 homozygous hermaphrodites showed early developmental defects and most of the F3 worms stopped developing during the gastrulation stage. Whole-mount staining analysis for heparan sulfate using Toluidine blue (pH 2.5) revealed a defect of heparan sulfate biosynthesis in the F2 homozygotes. The analysis using fluorometric post-column high-performance liquid chromatography also uncovered reduced production of heparan sulfate in the rib-2 mutant. These results indicate that rib-2 is essential for embryonic development and heparan ------------------- Key: 5734 Medline: 12415122 Authors: Nass R;Blakely RD Title: The Caenorhabditis elegans dopaminergic system: opportunities for insights into dopamine transport and neurodegeneration. Citation: Annual Review of Pharmacology and Toxicology 43: 521-544 2003 Type: REVIEW Genes: bas-1 cat-1 cat-2 cat-4 ced-3 ced-4 ced-9 csp-1 csp-2 csp-3 unc-2 unc-18 unc-64 unc-104 unc-116 Abstract: The neurotransmitter dopamine (DA) plays a central role in the coordination of movement, attention, and the recognition of reward. Loss of DA from the basal ganglia, as a consequence of degeneration of neurons in the substantia nigra, triggers postural instability and Parkinson's disease (PD). DA transporters (DATs) regulate synaptic DA availability and provide a conduit for the uptake of DA mimetic neurotoxins, which can be used to evoke neuronal death and Parkinson-like syndrome. Recently, we have explored the sensitivity of DA neurons in the nematode Caenorhabditis elegans to the Parkinsonian-inducing neurotoxin 6-hydroxydopamine (6-OHDA) and found striking similarities, including DAT dependence, to neurodegeneration observed in mammalian models. In this review, we present our findings in the context of molecular and behavioral dimensions of DA signaling in C. elegans with an eye toward opportunities for uncovering DAT mutants, DAT regulators, and components of toxin-mediated ------------------- Key: 5735 Medline: 12588843 Authors: Cuenca AA;Schetter A;Aceto D;Kemphues K;Seydoux G Title: Polarization of the C. elegans zygote proceeds via distinct establishment and maintenance phases. Citation: Development 130: 1255-1265 2003 Type: ARTICLE Genes: mex-5 mex-6 nmy-2 par-1 par-2 par-3 par-6 pie-1 pkc-3 Abstract: Polarization of the C elegans zygote along the anterior-posterior axis depends on cortically enriched (PAR) and cytoplasmic (MEX-5/6) proteins, which function together to localize determinants (e.g. PIE-1) in response to a polarizing cue associated with the sperm asters. Using time-lapse microscopy and GFP fusions, we have analyzed the localization dynamics of PAR-2, PAR-6, MEX-5, MEX-6 and PIE-1 in wild-type and mutant embryos. These studies reveal that polarization involves two genetically and temporally distinct phases. During the first phase (establishment), the sperm asters at one end of the embryo exclude the PAR-3/PAR-6/PKC3 complex from the nearby cortex, allowing the ring finger protein PAR-2 to accumulate in an expanding 'posterior' domain. Onset of the establishment phase involves the non-muscle myosin NMY-2 and the 14-3-3 protein PAR-5. The kinase PAR-1 and the CCCH finger proteins MEX-5 and MEX-6 also function during the establishment phase in a feedback loop to regulate growth of the posterior domain. The second phase begins after pronuclear meeting, when the sperm asters begin to invade the anterior. During this phase (maintenance), PAR-2 maintains anterior-posterior polarity by excluding the PAR-3/PAR-6/PKC3 complex from the posterior. These findings provide a model for how PAR and MEX proteins convert a transient asymmetry into a stably polarized axis. ------------------- Key: 5736 Medline: 12600937 Authors: Pothof J;van Haaften G;Thijssen K;Kamath RS;Fraser AG;Ahringer J;Plasterk RHA;Tijsterman M Title: Identification of genes that protect the C. elegans genome against mutations by genome-wide RNAi. Citation: Genes & Development 17: 443-448 2003 Type: ARTICLE Genes: cul-1 cul-5 cul-6 djn-15 djn-25 hda-1 hda-2 hil-1 hpr-17 mlh-1 mrt-2 msh-2 msh-6 pme-1 pme-6 pms-2 pqn-28 rfc-1 rfc-3 sir-2.2 skr-15 Abstract: An RNA interference (RNAi)-based genome-wide screen was performed to detect genes that contribute to genome stability in somatic cells of Caenorhabditis elegans. We identified 61 such genes; these also affect spontaneous mutagenesis in the germ line. Their sequence suggests a role in DNA repair and/or replication, in chromatin remodeling, or in cell cycle control; there are also many novel genes that are highly conserved from yeast to human. Because known mutator genes are causally involved in many hereditary and sporadic human cancers, it is likely that some of these new mutators are equally relevant in cancer ------------------- Key: 5737 Medline: 12486703 Authors: Wolf FW;Heberlein U Title: Invertebrate models of drug abuse. Citation: Journal of Neurobiology 54: 161-178 2003 Type: ARTICLE Genes: lev-1 unc-29 unc-38 Abstract: Susceptibility to drug addiction depends on genetic and environmental factors and their complex interactions. Studies with mammalian models have identified molecular targets, neurochemical systems, and brain regions that mediate some of the addictive properties of abused drugs. Yet, our understanding of how the primary effects of drugs lead to addiction remains incomplete. Recently, researchers have turned to the invertebrate model systems Drosophila melanogaster and Caenorhabditis elegans to dissect the mechanisms by which abused drugs modulate behavior. Due to their sophisticated genetics, relatively simple anatomy, and their remarkable molecular similarity to mammals, these invertebrate models should provide useful insights into the mechanisms of drug action. Here we review recent behavioral and genetic studies in flies and worms on the effects of ethanol, cocaine, and nicotine, three of the most widely abused drugs in the world. ------------------- Key: 5738 Medline: 12587699 Authors: Deepak M;Dipankar G;Prashanth D;Asha MK;Amit A;Venkataraman BV Title: Tribulosin and beta-sitosterol-D-glucoside, the anthelmintic principles of Tribulus terrestris. Citation: Phytomedicine 9: 753-756 2002 Type: ARTICLE Genes: Abstract: Successive extracts of Tribulus terrestris prepared using petroleum ether, chloroform, 50% methanol and water were tested for anthelmintic activity in-vitro using the nematode Caenorhabditis elegans. The activity could be detected only in 50% methanol extract which on further bioactivity guided fractionation and chromatographic separation yielded a spirostanol type saponin, tribulosin and beta-sitosterol-D-glucoside. Both the compounds exhibited anthelmintic activity with ED50 of 76.25 and 82.50 microg/ml respectively. ------------------- Key: 5739 Medline: 12600319 Authors: Kirkham M;Muller-Reichert T;Oegema K;Grill S;Hyman AA Title: SAS-4 is a C. elegans centriolar protein that controls centrosome size. Citation: Cell 112: 575-587 2003 Type: ARTICLE Genes: sas-4 zyg-1 zyg-9 Abstract: Centrosomes consist of a centriole pair surrounded by pericentriolar material (PCM). Previous work suggested that centrioles are required to organize PCM to form a structurally stable organelle. Here, we characterize SAS-4, a centriole component in Caenorhabditis elegans. Like tubulin, SAS-4 is incorporated into centrioles during their duplication and remains stably associated thereafter. In the absence of SAS-4, centriole duplication fails. Partial depletion of SAS-4 results in structurally defective centrioles that contain reduced levels of SAS-4 and organize proportionally less PCM. Thus, SAS-4 is a centriole-associated component whose amount dictates centrosome size. These results provide novel insight into the poorly understood role of centrioles as centrosomal organizers. ------------------- Key: 5740 Medline: 12606046 Authors: Shim J;Im SH;Lee J Title: Tissue-specific expression, heat inducibility, and biological roles of two hsp16 genes in Caenorhabditis elegans. Citation: FEBS Letters 537: 139-145 2003 Type: ARTICLE Genes: Abstract: In this report we have examined two new heat shock protein (HSP16) proteins in the nematode Caenorhabditis elegans encoded by the open reading frames F08H9.3 and F08H9.4. The F08H9.3 and F08H9.4 genes are oriented in the same direction next to each other on the chromosome, not sharing any promoter region, unlike other hsp16 genes that share common promoters in pairs. The F08H9.3 and F08H9.4 proteins were expressed in a tissue-specific manner, unlike the other four HSP16 proteins. F08H9.3 was expressed in the pharynx, and F08H9.4 in the excretory canal and a few neuronal cells. While F08H9.3 was weakly induced by heat shock only in the same tissue as under the normal condition, F08H9.4 was newly induced in the intestine. RNA interference experiments showed that these two proteinsare required for survival under the heat shock condition. ------------------- Key: 5742 Medline: 12610537 Authors: Nagy A;Perrimon N;Sandmeyer S;Plasterk R Title: Tailoring the genome: the power of genetic approaches. Citation: Nature Genetics 33S: 276-284 2003 Type: REVIEW Genes: Abstract: In the last century, genetics has developed into one of the most powerful tools for addressing basic questions concerning inheritance, development, individual and social operations and death. Here we summarize the current approaches to these questions in four of the most advanced models organisms: Saccharomyces cerevisiae (yeast), Caenorhabditis elegans (worm), Drosophila melanogaster (fly) and Mus musculus (mouse). The genomes of each of these four models have been sequenced, and all have well developed methods of efficient genetic manipulations. ------------------- Key: 5743 Medline: 12598644 Authors: Wei JZ;Hale K;Carta L;Platzer E;Wong C;Fang SC;Aroian RV Title: Bacillus thuringiensis crystal proteins that target nematodes. Citation: Proceedings of the National Academy of Sciences USA 100: 2760-2765 2003 Type: ARTICLE Genes: Abstract: Bacillus thuringiensis (Bt) crystal proteins are pore-forming toxins used as insecticides around the world. Previously, the extent to which these proteins might also target the invertebrate phylum Nematoda has been mostly ignored. We have expressed seven different crystal toxin proteins from two largely unstudied Bt crystal protein subfamilies. By assaying their toxicity on diverse free-living nematode species, we demonstrate that four of these crystal proteins are active against multiple nematode species and that each nematode species tested is susceptible to at least one toxin. We also demonstrate that a rat intestinal nematode is susceptible to some of the nematicidal crystal proteins, indicating these may hold promise in controlling vertebrate-parasitic nematodes. Toxicity in nematodes correlates with damage to the intestine, consistent with the mechanism of crystal toxin action in insects. Structure-function analyses indicate that one novel nematicidal crystal protein can be engineered to a small 43-kDa active core. These data demonstrate that at least two Bt crystal protein subfamilies contain nematicidal toxins. ------------------- Key: 5744 Medline: Authors: Kiontke K;Hironaka M;Sudhaus W Title: Description of Caenorhabditis japonica n. sp (Nematoda: Rhabditida) associated with the burrower bug Parastrachia japonensis (Heteropter: Cydnidae) in Japan. Citation: Nematology 4: 933-941 2002 Type: ARTICLE Genes: Abstract: Caenorhabditis japonica n. sp. is described from Parastrachia japonensis from Japan. The species is closely related to species of the Caenorhabditis elegans group and shares many characters with them. It differs from these species in having blunt spicule tips of complex shape and in lacking a terminal notch in the bursa velum. Caenorhabditis japonica n. sp. is further characterised by an anterior end with the lips fused in pairs, long and pointed stegostomal teeth, long fringes on the anterior bursa margin and the form of the genital papillae (GP4 reduced). The species is integrated into the phylogenetic tree of Caenorhabditis. Some resulting consequences for character evolution within Caenorhabditis are discussed. Caenorhabditis japonica n. sp. is associated with a burrower bug, thereby adding a new component to the diverse ------------------- Key: 5745 Medline: 12661765 Authors: Lee KH;Lee MH;Lee TH;Han JW;Park YJ;Ahnn J;Seo YS;Koo HS Title: Dna2 requirement for normal reproduction of Caenorhabditis elegans is temperature-dependent. Citation: Molecules & Cells 15: 81-86 2003 Type: ARTICLE Genes: Abstract: To determine the function of Dna2 in a multicellular organism, the Caenorhabditis elegans Dna2 expression was probed and deletion mutant phenotypes were analyzed. Dna2 was localized to the nuclei of C. elegans oocytes and early embryos by immunostaining or green fluorescent protein-tagging. A homozygous dna2 deletion mutant showed a reduced brood size and embryonic lethality, and the phenotypes greatly depended on growth temperature and aggravated in the succeeding generation. The mutant embryos also showed delayed cell divisions, which together with temperature-dependence of the mutant phenotypes supported the well-conserved role of Dna2 in DNA replication. ------------------- Key: 5746 Medline: Authors: Fujita M;Takasaki T;Nakajima N;Kawano T;Shimura Y;Sakamoto Title: Corrigendum to "MRG-1, a mortality factor-related chromodomain protein, is required maternally for primordial germ cells to initiate mitotic proliferation in C. Citation: Mechanisms of Development 120: 397- 2003 Type: CORRECT Genes: mrg-1 Abstract: ------------------- Key: 5747 Medline: 12619137 Authors: Thein MC;McCormack G;Winter AD;Johnstone IL;Shoemaker CB;Page AP Title: Caenorhabditis elegans exoskeleton collagen COL-19: an adult-specific marker for collagen modification and assembly, and the analysis of organismal morphology. Citation: Developmental Dynamics 226: 523-539 2003 Type: ARTICLE Genes: bli-1 bli-3 bli-4 bli-5 col-19 daf-2 dpy--2 dpy-3 dpy-4 dpy-5 dpy-7 dpy-8 dpy-9 dpy-10 dpy-11 dpy-13 dpy-17 dpy-18 lon-1 lon-2 lon-3 rol-6 sma-2 sqt-1 sqt-2 sqt-3 Abstract: The integral role that collagens play in the morphogenesis of the nematode exoskeleton or cuticle makes them a useful marker in the examination of the collagen synthesizing machinery. In this study, a green fluorescent protein- collagen fusion has been constructed by using the Caenorhabditis elegans adult-specific, hypodermally synthesized collagen COL-19. In wild-type nematodes, this collagen marker localized to the circumferential annular rings and the lateral trilaminar alae of the cuticle. Crosses carried out between a COL-19::GFP integrated strain and several morphologically mutant strains, including blister, dumpy, long, small, squat, and roller revealed significant COL-19 disruption that was predominantly strain-specific and provided a structural basis for the associated phenotypes. Disruption was most notable in the cuticle overlying the lateral seam cell syncytium, and confirmed the presence of two distinct forms of hypodermis, namely the circumferentially contracting lateral seam cells and the laterally contracting ventral-dorsal hypodermis. The effect of a single aberrant collagen being sufficient to mediate widespread collagen disruption was exemplified by the collagen mutant strain dpy-5 and its disrupted COL-19::GFP and DPY-7 collagen expression patterns. Through the disrupted pattern of COL-19 and DPY-7 in a thioredoxin mutant, dpy-11, and through RNA interference of a dual oxidase enzyme and a vesicular transport protein, we also show the efficacy of the COL-19::GFP strain as a marker for aberrant cuticle collagen synthesis and, thus, for the identification of factors involved in the construction of collagenous extracellular matrices. ------------------- Key: 5748 Medline: 12593984 Authors: Hobert O;Buelow H Title: Development and maintenance of neuronal architecture at the ventral midline of C. elegans. Citation: Current Opinion in Neurobiology 13: 70-78 2003 Type: REVIEW Genes: cle-1 kal-1 nid-1 sax-3 sax-5 sax-9 slt-1 unc-5 unc-6 unc-40 vab-1 zig-4 Abstract: Work in flies, nematodes and vertebrates has shown that genes involved in axon patterning at the ventral midline are functionally conserved across phylogeny. Recent studies in Caenorhabditis elegans have implicated several new extracellular molecules, such as nidogen and heparan sulfate proteoglycans, in axonal tract formation at the midline. Furthermore, a conceptually new mechanism that regulates the maintenance of axon positioning at the midline has been described in C. elegans. ------------------- Key: 5749 Medline: 12596226 Authors: Stothard P;Pilgrim D Title: Sex-determination gene and pathway evolution in nematodes. Citation: BioEssays 25: 221-231 2003 Type: REVIEW Genes: fbf-1 fbf-2 fem-1 fem-2 fem-3 fog-1 fog-2 fog-3 fox-1 gld-1 her-1 laf-1 mab-3 mog-1 mog-2 mog-3 mog-4 mog-5 mog-6 nos-1 nos-2 nos-3 sdc-1 sdc-2 sdc-3 sex-1 tra-1 tra-2 tra-3 xol-1 Abstract: The pathway that controls sexual fate in the nematode Caenorhabditis elegans has been well characterized at the molecular level. By identifying differences between the sex-determination mechanisms in C. elegans and other nematode species, it should be possible to understand how complex sex-determining pathways evolve. Towards this goal, orthologues of many of the C. elegans sex regulators have been isolated from other members of the genus Caenorhabditis. Rapid sequence evolution is observed in every case, but several of the orthologues appear to have conserved sex-determining roles. Thus extensive sequence divergence does not necessarily coincide with changes in pathway structure, although the same forces may contribute to both. This review summarizes recent findings and, with reference to results from other animals, offers explanations for why sex-determining genes and pathways appear to be evolving rapidly. Experimental strategies that hold promise for illuminating pathway differences between nematodes are also discussed. ------------------- Key: 5750 Medline: 12628167 Authors: Yuan A;Santi CM;Wei A;Wang ZW;Pollak K;Nonet M;Kaczmarek L;Crowder CM;Salkoff L Title: The sodium-activated potassium channel is encoded by a member of the Slo gene family. Citation: Neuron 37: 765-773 2003 Type: ARTICLE Genes: slo-2 Abstract: Na+-activated potassium channels (K-Na) have been identified in cardiomyocytes and neurons where they may provide protection against ischemia. We now report that K-Na is encoded by the rSlo2 gene (also called Slack), the mammalian ortholog of slo-2 in C. elegans. rSlo2, heterologously expressed, shares many properties of native K-Na including activation by intracellular Na+, high conductance, and prominent subconductance states. In addition to activation by Na+, we report that rSLO-2 channels are cooperatively activated by intracellular Cl-, similar to C. elegans SLO-2 channels. Since intracellular Na+ and Cl- both rise in oxygen-deprived cells, coactivation may more effectively trigger the activity of rSLO-2 channels in ischemia. In C. elegans, mutational and physiological analysis revealed that the SLO-2 current is a major component of the delayed rectifier. We demonstrate in C. elegans that slo-2 mutants are hypersensitive to hypoxia, suggesting a conserved role for the slo-2 gene ------------------- Key: 5751 Medline: 12600716 Authors: Link CD;Taft A;Kapulkin V;Duke K;Kim S;Fei Q;Wood DE;Sahagan BG Title: Gene expression analysis in a transgenic Caenorhabditis elegans Alzheimer's disease model. Citation: Neurobiology of Aging 24: 397-413 2003 Type: ARTICLE Genes: acr-8 act-3 csq-1 gpd-1 gcy-7 lbp-2 let-7 let-858 mlc-3 osm-6 smg-1 tnc-1 twk-5 Abstract: We have engineered transgenic Caenorhabditis elegans animals to inducibly express the human beta amyloid peptide (Abeta). Gene expression changes resulting from Abeta induction have been monitored by cDNA hybridization to glass slide microarrays containing probes for almost all known or predicted C. elegans genes. Using statistical criteria, we have identified 67 up-regulated and 240 down-regulated genes. Subsets of these regulated genes have been tested and confirmed by quantitative RT-PCR. To investigate whether genes identified in this model system also show gene expression changes in Alzheimer's disease (AD) brain, we have also used quantitative RT-PCR to examine in post-mortem AD brain tissue transcript levels of alphaB-crystallin (CRYAB) and tumor necrosis factor-induced protein 1 (TNFAIP1), human homologs of genes found to be robustly induced in the transgenic C. elegans model. Both CRYAB and TNFAIP1 show increased transcript levels in AD brains, supporting the validity of this approach. ------------------- Key: 5752 Medline: 12600717 Authors: Drake J;Link CD;Butterfield DA Title: Oxidative stress precedes fibrillar deposition of Alzheimer's disease amyloid beta-peptide (1-42) in a transgenic Caenorhabditis elegans model. Citation: Neurobiology of Aging 24: 415-420 2003 Type: ARTICLE Genes: myo-3 rol-6 smg-1 unc-54 Abstract: Alzheimer's disease is a progressive, neurodegenerative disorder characterized by senile plaques and neurofibrillary components. Abeta(1-42) is a principal component of senile plaques and is thought to be central to the pathogenesis of the disease. The Alzheimer's disease brain is under significant oxidative stress, and the Abeta(1-42) peptide is known to cause oxidative stress in vitro. One controversy in the amyloid hypothesis is whether or not Abeta plaques are required for toxicity. We have employed a temperature-inducible Abeta expression system in Caenorhabditis elegans to create a strain of worms, CL4176, in which Abeta(1-42) is expressed with a non-permissive temperature of 23 degreesC. The CL4176 strain allows examination of the temporal relationship between Abeta expression, oxidative stress, and Abeta fibril formation. CL4176 were under increased oxidative stress, evidenced by increased protein oxidation indexed by increased carbonyl levels, 24 and 32 h after temperature upshift as compared to the control strain, CL1175. The increased oxidative stress in CL4176 occurred in the absence of Abeta fibril formation, consistent with the notion that the toxic species in Abeta toxicity is pre-fibrillar Abeta and not the Abeta fibril. These results are discussed with reference to Alzheimer's disease. ------------------- Key: 5753 Medline: 12610523 Authors: Driscoll M;Gerstbrein B Title: Dying for a cause: invertebrate genetics takes on human neurodegeneration. Citation: Nature Reviews Genetics 4: 181-194 2003 Type: REVIEW Genes: acy-1 aph-1 aph-2 apl-1 asp-3 asp-4 atx-2 ced-3 clp-1 cnx-1 crt-1 cup-5 daf-2 daf-16 daf-18 deg-3 hop-1 itr-1 mec-4 pen-1 pen-2 pqe-1 sel-10 sel-12 sgs-1 tra-1 unc-2 unc-68 Abstract: If invertebrate neurons are injured by hostile environments or aberrant proteins they die much like human neurons, indicating that the powerful advantages of invertebrate molecular genetics might be successfully used for testing specific hypotheses about human neurological diseases, for drug discovery and for non-biased screens for suppressors and enhancers of neurodegeneration. Recent molecular dissection of the genetic requirements for hypoxia, excitotoxicity and death in models of Alzheimer disease, polyglutamine-expansion disorders, Parkinson disease and more, is providing mechanistic insights into neurotoxicity and suggesting new therapeutic interventions. An emerging theme is that neuronal crises of distinct origins might converge to disrupt common cellular functions, such as protein folding and turnover. ------------------- Key: 5754 Medline: 12502713 Authors: Garofalo A;Rowlinson MC;Amambua NA;Hughes JM;Kelly SM;Price NC;Cooper A;Watson DG;Kennedy MW;Bradley JE Title: The FAR protein family of the nematode Caenorhabditis elegans - differential lipid binding properties, structural characteristics, and developmental regulation. Citation: Journal of Biological Chemistry 278: 8065-8074 2003 Type: ARTICLE Genes: far-1 far-2 far-3 far-4 far-5 far-6 far-7 far-8 Abstract: Parasitic nematodes of humans and plants secrete a structurally novel type of fatty acid- and retinol-binding protein, FAR, into the tissues they occupy. These proteins may interfere with intercellular lipid signaling to manipulate the defense reactions of the host or acquire essential lipids for the parasites. The genome of the nematode Caenorhabditis elegans encodes eight FAR-like proteins (Ce-FAR-1 to -8). These fall into three discrete groups as indicated by phylogenetic sequence comparisons and intron positions, the proteins from parasitic nematodes falling into group A. Recombinant Ce-FAR-1 to -7 were produced in Escherichia coli and tested for lipid binding in fluorescence-based assays. Ce-FAR-1 to -6 bound DAUDA (11-((5-dimethylaminonaphthalene-1-sulfonyl)amino)undecanoi c acid), cis-parinaric acid, and retinol with dissociation constants in the micromolar range, whereas Ce-FAR-7 bound the latter two lipids relatively poorly. Each protein produced a characteristic shift in peak fluorescence emission of DAUDA, and one (Ce-FAR-5) produced a shift greater than has been observed previously for any lipid-binding protein. Selected Ce-FAR proteins were analyzed by circular dichroism (CD) and differential scanning calorimetry, were, found to be helix-rich, and exhibited high thermal stability (transition midpoint, 82.7 degreesC). CD and secondary structure predictions, however, both indicated that Ce-FAR-7 possesses substantially less helix than the other FAR proteins. The genes encoding the Ce-FAR proteins were found to be transcribed differentially through the life cycle of C. elegans, such that Ce-far-4 was transcribed at highest levels in the fourth larval stage, and Ce-far-3 and -7 predominated in males. ------------------- Key: 5755 Medline: 12618395 Authors: Ayyadevara S;Ayyadevara R;Vertino A;Galecki A;Thaden JJ;Reis RJS Title: Genetic loci modulating fitness and life span in Caenorhabditis elegans: categorical trait interval mapping in CL2a X Bergerac-BO recombinant inbred worms. Citation: Genetics 163: 557-570 2003 Type: ARTICLE Genes: Abstract: Quantitative trait loci (QTL) can implicate an unbiased sampling of genes underlying a complex, polygenic phenotype. QTL affecting longevity in Caenorhabditis elegans were mapped using a CL2a X Bergerac-BO recombinant-inbred population. Genotypes were compared at 30 transposon-specific markers for two paired sample sets totaling 171 young controls and 172 longevity-selected worms (the last-surviving 1%) from a synchronously aged population. A third sample set, totaling 161 worms from an independent culture, was analyzed for confirmation of loci. At least six highly significant QTL affecting life span were detected both by single-marker (chi(2)) analysis and by two interval-mapping procedures-one intended for nonparametric traits and another developed specifically for mapping of categorical traits. These life-span QTL were located on chromosomes I (near the hP4 locus), III (near stP127), IV (near stP44), V (a cluster of three peaks, near stP192, stP23, and stP6), and X (two distinct peaks, near stP129 and stP2). Epistatic effects on longevity were also analyzed by Fisher's exact test, which indicated a significant life-span interaction between markers on chromosomes V (stP128) and 111 (stP127). Several further interactions were significant in the initial unselected population; two of these, between distal loci on chromosome V, were completely eliminated in the long-lived subset. Allelic longevity effects for two QTL, on chromosomes IV and V, were confirmed in backcrossed congenic lines and were highly significant in two very different environments-growth on solid agar medium and in liquid ------------------- Key: 5756 Medline: 12618396 Authors: Raich WB;Moorman C;Lacefield CO;Lehrer J;Bartsch D;Plasterk RHA;Kandel ER;Hobert O Title: Characterization of Caenorhabditis elegans homologs of the Down syndrome candidate gene DYRK1A. Citation: Genetics 163: 571-580 2003 Type: ARTICLE Genes: hpk-1 mbk-1 mbk-2 Abstract: The pathology of trisomy 21/Down syndrome includes cognitive and memory deficits. Increased expression of the dual-specificity protein kinase DYRK1A kinase (DYRK1A) appears to play a significant role in the neuropathology of Down syndrome. To shed light on the cellular role of DYRK1A and related genes we identified three DYPLK/minibrain-like genes in the genome sequence of Caenorhabditis elegans, termed mbk-1, mbk-2, and hpk-1. We found these genes to be widely expressed and to localize to distinct subcellular compartments. We isolated deletion alleles in all three genes and show that loss of mbk-1, the gene most closely related to DYRK1A, causes no obvious defects, while another gene, mbk-2, is essential for viability. The overexpression of DYRK1A in Down syndrome led us to examine the effects of overexpression of its C. elegans ortholog mbk-1. We found that animals containing additional copies of the mbk-1 gene display behavioral defects in chemotaxis toward volatile chemoattractants and that the extent of these defects correlates,with mbk-1 gene dosage. Using tissue-specific and inducible promoters, we show that additional copies of mbk-1 can impair olfaction cell-autonomously in mature, fully differentiated neurons and that this impairment is reversible. Our results suggest that increased gene dosage of human DYRK1A in trisomy 21 may disrupt the function of fully differentiated neurons and that this disruption is reversible. ------------------- Key: 5757 Medline: 12618397 Authors: Watts JL;Phillips E;Griffing KR;Browse J Title: Deficiencies of C20 polyunsaturated fatty acids cause behavioral and developmental defects in Caenorhabditis elegans fat-3 mutants. Citation: Genetics 163: 581-589 2003 Type: ARTICLE Genes: fat-3 fat-4 unc-54 unc-105 Abstract: Arachidonic acid and other long-chain polyunsaturated fatty acids (PUFAs) are important structural components of membranes and are implicated in diverse signaling pathways. The Delta6 desaturation of linoleic and linolenic acids is the rate-limiting step in the synthesis of these molecules. C elegans fat-3 mutants lack Delta6 desaturase activity and fail to produce C20 PUFAs. We examined these mutants and found that development and behavior were affected as a consequence of C20 PUFA deficiency. While fat-3 mutants are viable, they grow slowly, display considerably less spontaneous movement, have an altered body shape, and produce fewer progeny than do wild type. In addition, the timing of an ultradian rhythm, the defecation cycle, is lengthened compared to wild type. Since all these defects can be ameliorated by supplementing the nematode diet with gamma-linolenic acid or C20 PUFAs of either the n6 or the n3 series, we can establish a causal link between fatty acid deficiency and phenotype. Similar epidermal tissue defects and slow growth arc hallmarks of human fatty acid deficiency. ------------------- Key: 5758 Medline: 12685560 Authors: Franchini A;Peruzzi E;Ottaviani E Title: Morphochemical age-related changes in the nematode Caenorhabditis elegans: immunoperoxidase localization of cytokine- and growth factor-like molecules. Citation: European Journal of Histochemistry 47: 75-80 2003 Type: ARTICLE Genes: Abstract: Morphochemical age-related features in the hermaphrodite Caenorhabditis elegans are reported. The study of worms of different ages shows a gradual decline in response to the various histochemical reactions and a disorganization of the components of the gonad during ageing. Using an immunocytochemical procedure, we show for the first time the presence of immunoreactive IL-1alpha and PDGF-AB molecules in neurons from young adult C. elegans. Moreover, TNF-alpha- and PDGF-AB-like molecules are also present in the secretory cells of the pharyngeal terminal bulb. The number of positive cells to anti-cytokine and anti-growth factor antibodies decreases in older worms, suggesting that these molecules may play an important role in worm ageing. The present investigation therefore supports the findings in the literature obtained with different approaches on the crucial role of the nervous and reproductive systems in the life span of C. elegans. ------------------- Key: 5759 Medline: 12620193 Authors: Ookuma S;Fukuda M;Nishida E Title: Identification of a DAF-16 transcriptional target gene, scl-1, that regulates longevity and stress resistance in Caenorhabditis elegans. Citation: Current Biology 13: 427-431 2003 Type: ARTICLE Genes: age-1 daf-2 daf-16 scl-1 Abstract: In Caenorhabditis elegans, an insulin-like signaling pathway, which includes the daf-2 and age-1 genes, controls longevity and stress resistance (1, 2]. Downregulation of this pathway activates the forkhead transcription factor DAF-16, whose transcriptional targets are suggested to play an essential role in controlling the phenotypes governed by this pathway [3, 4]. We have surveyed the genes that have the DAF-16 consensus binding element (DBE) [5] within putative regulatory regions. Here, we show that one such gene, termed scl-1, is a positive regulator of longevity and stress resistance. Expression of scl-1 is upregulated in long-lived daf-2 and age-1 mutants and is undetectable in a short-lived daf-16 mutant. SCL-1 is a putative secretory protein with an SCP domain and is homologous to the mammalian cysteine-rich secretory protein (CRISP) family. scl-1 is required for the extension of the life span of daf-2 and age-1 mutants, and down-regulation of scl-1 reduces both life span and stress resistance of this animal. SCL-1, whose expression is dependent on DAF-16, is the first example of a putative secretory protein that positively regulates longevity and stress resistance. ------------------- Key: 5760 Medline: 12628183 Authors: Shen K;Bargmann CI Title: The immunoglobulin superfamily protein SYG-1 determines the location of specific synapses in C. elegans. Citation: Cell 112: 619-630 2003 Type: ARTICLE Genes: egl-15 egl-17 lin-3 lin-15 lin-39 mig-1 syg-1 unc-6 unc-40 unc-86 unc-104 Abstract: During nervous system development, neurons form reproducible synapses onto specific targets. Here, we analyze the development of stereotyped synapses of the C. elegans HSNL neuron in vivo. Postsynaptic neurons and muscles were not required for accurate synaptic vesicle clustering in HSNL. Instead, vulval epithelial cells that contact HSNL act as synaptic guidepost cells that direct HSNL presynaptic vesicles to adjacent regions. The mutant syg-1(ky652) has defects in synapse formation that resemble those in animals that lack vulval epithelial cells: HSNL synaptic vesicles fail to accumulate at normal synaptic locations and form ectopic anterior clusters. syg-1 encodes an immunoglobulin superfamily protein that acts in the presynaptic HSNL axon. SYG-1 protein is localized to the site of future synapses, where it initiates synapse formation and localizes synaptic connections in response to the epithelial signal. SYG-1 is related to Drosophila IrreC and vertebrate NEPH1 proteins, which mediate cell-cell recognition in diverse developmental contexts. ------------------- Key: 5761 Medline: 12584125 Authors: Parkinson J;Blaxter M Title: SimiTri - visualizing similarity relationships for groups of sequences. Citation: Bioinformatics 19: 390-395 2003 Type: ARTICLE Genes: Abstract: Global sequence comparisons between large datasets, such as those arising from genome projects, can be problematic to display and analyze. We have developed SimiTiri, a Java/Perl-based application, which allows simultaneous display and analysis of relative similarity relationships of the dataset of interest to three different databases. We illustrate its utility in identifying Caenorhabditis elegans genes that have distinct patterns of phylogenetic affinity suggestive of horizontal gene transfer. SimiTri is freely downloadable from http://www.nematodes.org/SimiTri/ and the source code is ------------------- Key: 5762 Medline: Authors: de Melo JV;de Souza W;Peixoto CA Title: Ultrastructural analyses of the Caenorhabditis elegans DR847 bli-1(n361) mutant which produces abnormal cuticle Citation: Journal of Submicroscopic Cytology & Pathology 34: 291-297 2002 Type: ARTICLE Genes: bli-1 Abstract: The bli-1 gene of Caenorhabditis elegans has been previously described as a mutation which disrupts the structure of the adult-stage cuticle causing the formation of fluid-filled blisters. We investigated the blistering phenotype exhibiting n361 allele and observed a gradual blister formation in adult nematodes. In the course several fine changes occurred including a high electron density granulous material filling the intermediate layer, alterations on struts structure, and finally the total disappearance of the fibrous and basal layers. With the ethanolic phosphotungstic acid technique (E-PTA), which localizes basic proteins, reaction product was observed in the cortical layer of the wild strain, whereas in the mutant strain an irregular labelling pattern was observed in this region. The granulous material inside the intermediate layer of the mutant strain showed also a strong reaction. An imidazole-buffered osmium tetroxide solution was used to visualize lipids at ultrastructural level, however no dense product was detected in the cuticle of both strains of C. elegans. Based on these results we postulated that the blistering phenotype is due to an altered function of bli-1 gene, which is probably ------------------- Key: 5763 Medline: 12592563 Authors: Garofalo A;Kennedy MW;Bradley JE Title: The FAR proteins of parasitic nematodes: their possible involvement in the pathogenesis of infection and the use of Caenorhabditis elegans as a model system to evaluate their function. Citation: Medical Microbiology and Immunology 192: 47-52 2003 Type: ARTICLE Genes: far-1 far-2 far-3 far-4 far-6 far-7 Abstract: Parasitic nematodes secrete a structurally novel class of fatty acid and retinol-binding (FAR) protein into the surrounding tissues of the host. These proteins are of interest because they may play an important role in scavenging fatty acids and retinoids from the host that are essential for the survival of the parasite and also because the localised depletion of such lipids may have immunomodulatory effects that compromise the host immune response. Research into the biological function(s) of the FAR proteins has been severely hampered by the difficulties associated with the life-cycle propagation of parasitic nematodes and the current intractability of the parasites to reverse-genetic studies. The genome of the free-living nematode Caenorhabditis elegans, however, encodes eight FAR-like proteins, and in this review we compare the FAR proteins of C. elegans and parasitic nematodes, and we discuss the suitability of C. elegans as a model system to investigate the biological function(s) of the FAR proteins of parasitic nematodes. ------------------- Key: 5764 Medline: 12636915 Authors: Dechant R;Glotzer M Title: Centrosome separation and central spindle assembly act in redundant pathways that regulate microtubule density and trigger cleavage furrow formation. Citation: Developmental Cell 4: 333-344 2003 Type: ARTICLE Genes: air-2 cyk-1 let-21 par-1 par-2 par-3 zen-4 Abstract: The mitotic spindle provides the spatial cue that coordinates cytokinesis with nuclear division. However, the specific property of the mitotic spindle that mediates this spatial regulation remains obscure, in part because different aspects of the mitotic spindle appear to have furrow inducing activity in different systems. We show that in C. elegans embryos, although the central spindle is usually dispensable for furrow initiation, it becomes essential for furrow formation when the extent of centrosome separation during anaphase is reduced. Measurements of microtubule density demonstrate that furrow formation occurs in the vicinity of a local minimum of microtubule density. Reduction of the extent of spindle elongation or disruption of the central spindle causes delayed formation of the cleavage furrow. These data suggest that reduced microtubule density triggers cleavage furrow initiation and demonstrate that redundant mechanisms direct efficient formation of the cleavage furrow. ------------------- Key: 5765 Medline: 12636923 Authors: Leidel S;Gonczy P Title: SAS-4 is essential for centrosome duplication in C. elegans and is recruited to daughter centrioles once per cell Citation: Developmental Cell 4: 431-439 2003 Type: ARTICLE Genes: plk-1 sas-4 zyg-1 Abstract: The mechanisms governing centrosome duplication remain poorly understood. We identified a gene called sas-4 that is essential for this process in C. elegans. SAS-4 encodes a predicted coiled-coil protein that localizes to a tiny dot in the center of centrosomes throughout the cell cycle. FRAP experiments with GFP-SAS-4 transgenic embryos reveal that SAS-4 is recruited to the centrosome once per cell cycle, at the time of organelle duplication. Additional evidence indicates that SAS-4 is recruited to the daughter centriole or a closely associated structure. These findings identify SAS-4 recruitment as a key step in the centrosome duplication cycle. ------------------- Key: 5766 Medline: 12590349 Authors: Lahl V;Halama C;Schierenberg E Title: Comparative and experimental embryogenesis of Plectidae (Nematoda). Citation: Developmental Genes and Evolution 213: 18-27 2003 Type: ARTICLE Genes: Abstract: Comparative analysis of early embryogenesis indicates that considerable differences exist among nematode species. To better understand to what extent the well-studied development of Caenorhabditis elegans is representative for nematodes in general, we extended our earlier studies to other families of this phylum. Here we report our findings on seven species of Plectidae. We found that Plectidae embryos share a number of developmental similarities with one branch of nematodes (Secernentea), including C. elegans, but not with the other branch (Adenophorea), and thus support conclusions concerning their phylogenetic position drawn from molecular data. However, Plectidae also show developmental differences to other Secernentea, suggesting an early separation from them. Prominent characteristics of Plectidae are (1) strict left-right divisions of somatic founder cells generating a prominent early bilateral symmetry and (2) a very early start of gastrulation with immigration of a single gut precursor cell. To determine whether gastrulation with two gut precursors is crucial for C. elegans embryos, we induced it to gastrulate with a single blastomere like in Plectidae. As this alteration is compatible with an essentially normal subsequent embryogenesis, cleavage of the gut precursor before gastrulation is obviously not required. As major differences exist among nematodes concerning the potential to compensate for eliminated early blastomeres, we tested this feature in one Plectus species. We found that Plectus does not replace a lost cell but behaves like C. elegans in this respect, in contrast to our previous findings in Acrobeloides nanus, another member of the Secernentea. ------------------- Key: 5767 Medline: 12538516 Authors: Baugh LR;Hill AA;Slonim DK;Brown EL;Hunter CP Title: Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome. Citation: Development 130: 889-900 2003 Type: ARTICLE Genes: act-1 ama-1 cey-1 dpy-30 elt-1 elt-2 end-1 end-3 fkh-2 gld-1 glp-1 hlh-1 lin-26 med-1/2 mex-1 ncc-1 nos-2 par-3 pes-1 pos-1 skn-1 tba-2 tbb-2 vab-7 Abstract: Temporal profiles of transcript abundance during embryonic development were obtained by whole-genome expression analysis from precisely staged C. elegans embryos. The result is a highly resolved time course that commences with the zygote and extends into midgastrulation, spanning the transition from maternal to embryonic control of development and including the presumptive specification of most major cell fates. Transcripts for nearly half (8890) of the predicted open reading frames are detected and expression levels for the majority of them (>70%) change over time. The transcriptome is stable up to the four-cell stage where it begins rapidly changing until the rate of change plateaus before gastrulation. At gastrulation temporal patterns of maternal degradation and embryonic expression intersect indicating a mid-blastula. transition from maternal to embryonic control of development. In addition, we find that embryonic genes tend to be expressed transiently on a time scale consistent with developmental decisions being made with each cell cycle. Furthermore, overall rates of synthesis and degradation are matched such that the transcriptome maintains a steady-state frequency distribution. Finally, a versatile analytical platform based on cluster analysis and developmental classification of genes is provided. ------------------- Key: 5768 Medline: 12538523 Authors: Gutierrez A;Knoch L;Witte H;Sommer RJ Title: Functional specificity of the nematode Hox gene mab-5. Citation: Development 130: 983-993 2003 Type: ARTICLE Genes: egl-5 lin-39 mab-5 Abstract: Hox genes encode evolutionarily conserved transcription factors involved in morphological specification along the anteroposterior body axis of animals. The two most striking features of Hox genes are colinearity and the strong sequence conservation. Among all animals studied so far, the nematode Caenorhabditis elegans contains one of the most divergent Hox clusters. The core cluster contains only four members, which in part deviate from the colinearity rule. In addition, orthologous and paralogous nematode Hox sequences diverged substantially. Given these nematode-specific features, we asked how these Hox proteins evolved and how they provide functional specificity. We investigated the role of MAB-5 during ray formation and established an in vivo assay using Cel-mab5 regulatory elements to express orthologous, paralogous and chimeric cDNAs in a Cel-mab-5 mutant background. We show that the MAB-5 ortholog from Pristionchus pacificus, but not the C elegans paralogous Hox proteins can rescue Cel-mab-5. Experiments with chimeric, truncated and mutagenized Hox proteins suggest the specificity to be conferred by the N-terminal arm and helix 1, but not helix H of the ------------------- Key: 5769 Medline: 12595721 Authors: Gavira JA;Claxton DP;Wang JH;Toh D;Meehan EJ;DiGiammarino Title: Purification, cyrstallization and preliminary X-ray analysis of Caenorhabditis elegans ubiquitin-conjugation Citation: Acta Crystallographica Section D-Biological Crystallography 59: 544-546 2003 Type: ARTICLE Genes: let-70 ubc-2 Abstract: M7.1 is a class IV ubiquitin-conjugation enzyme (UBC) that belongs to the ubiquitination cascade in Caenorhabditis elegans. The clone for this UBC has been overexpressed in Escherichia coli and the 16.7 kDa protein was purified from the soluble fraction. M7.1 was crystallized by sitting-drop vapor diffusion in 10% ethanol, 1.5 M NaCl at 277.5 K. Crystals diffracted to 1.75 Angstrom and belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 44.3, b = 54.3, c = 60.2 Angstrom. The asymmetric unit contains a single monomer. A molecular-replacement model has been determined and refinement is in progress. ------------------- Key: 5770 Medline: Authors: Lee RYN;Sternberg PW Title: Building a cell and anatomy ontology of Caenorhabditis elegans. Citation: Comparative and Functional Genomics 4: 121-126 2003 Type: REVIEW Genes: Abstract: We are endowed with a rich knowledge about Caenorhabditis elegans. Its stereotyped anatomy and development has stimulated research and resulted in the accumulation of cell-based information concerning gene expression, and the role of specific cells in developmental signalling and behaviorural circuits. To make the information more accessible to sophisticated queries and automated retrieval systems, WormBase has begun to construct a C. elegans cell and anatomy ontology. Here we present our strategies and progress. ------------------- Key: 5771 Medline: 12762036 Authors: Wickens M;Bernstein D;Crittenden S;Luitjens C;Kimble J Title: PUF proteins and 3' UTR regulation in the Caenorhabditis elegans germline. Citation: Cold Spring Harbor Symposia on Quantitative Biology 66: 337-343 2001 Type: REVIEW Genes: fbf-1 fbf-2 fem-3 Abstract: In a simple and too common view, mRNAs are a dull milepost between DNA and protein in the Central Dogma. They acquire middling interest as guides for the ribosome, tRNAs, and translation factors. Yet mRNAs have lives of their own, lives that the cell cares about enormously. mRNAs are born, leave home, mate with ribosomes, produce proteins, and die, all as the cell sees fit. Powerful forces ? in the form of specific mRNA-binding proteins and their cohorts ? guide individual mRNAs into unique variations on this common path. These proteins govern mRNA stability, localization, and translation. ------------------- Key: 5772 Medline: Authors: Tominaga N;Ura K;Kawakami M;Kawaguchi T;Kohra S;Mitsui Y;Iguchi T;Arizono K Title: Caenorhabditis elegans responses to specific steroid hormones. Citation: Journal of Health Science 49: 28-33 2003 Type: ARTICLE Genes: Abstract: In this paper, Caenorhabditis elegans (C. elegans) is proposed as a model organism for studying chemical effects over multiple generations. We investigated whether C. elegans responds to vertebrate steroid hormones. We found that estrogenic steroids, especially estradiol (E2), have a cholesterol-like potency in supporting the reproduction of C. elegans. In contrast, testosterone (TS) and diethylstilbestrol (DES) did not display this potency. On the other hand, E2, TS and DES supressed the fecundity rate of C. elegans, when culture carried out with cholesterol. Moreover effect of TS accumulated over generation, in contrast to the other chemicals tested. These data suggested that with convenient biomarkers such as fecundity, C. elegans might be an effective model organism for studying chemical actions, including the disruption of ------------------- Key: 5773 Medline: 12538235 Authors: Pandey A;Peri S;Thacker C;Whipple CA;Collins JJ;Mann M Title: Computational and experimental analysis reveals a novel Src family kinase in the C. elegans genome. Citation: Bioinformatics 19: 169-172 2003 Type: ARTICLE Genes: daf-2 let-23 vab-1 Abstract: Motivation: The complete genomes of a number of organisms have already been sequenced. However, the vast majority of annotated genes are derived by gene prediction methods. It is important to not only validate the predicted coding regions but also to identify genes that may have been missed by these programs. Methods: We searched the entire C. elegans genomic sequence database maintained by the Sanger Center using human c-Src sequence in a TBLASN search. We have confirmed one of the predicted regions by isolation of a cDNA and carried out a phylogenetic analysis of Src kinase family members in the worm, fly and several vertebrate species. Results: Our analysis identified a novel tyrosine kinase in the C. elegans genome that contains functional features typical of the Src family kinases that we have designated as Src-1. The open reading frame contains a conserved N-terminal myristoylation site and a tyrosine residue within the C-terminus that is crucial for regulating the activity of Src kinases. Our phylogenetic analysis of Src family members from C. elegans, Drosophila and other higher organisms revealed a relationship among Src kinases from C. elegans and ------------------- Key: 5774 Medline: 12571101 Authors: Hirose T;Nakano Y;Nagamatsu Y;Misumi T;Ohta H;Ohshima Y Title: Cyclic GMP-dependent protein kinase EGL-4 controls body size and lifespan in C. elegans. Citation: Development 130: 1089-1099 2003 Type: ARTICLE Genes: daf-2 daf-3 daf-4 daf-16 dbl-1 egl-4 lon-1 lon-2 lon-3 sma-2 sma-3 sma-4 sma-6 Abstract: We designed an automatic system to measure body length, diameters and volume of a C elegans worm. By using this system, mutants with an increased body volume exceeding 50% were isolated. Four of them are grossly normal in morphology and development, grow longer to be almost twice as big, and have weak egg-laying defects and extended lifespan. All the four mutants have a mutation in the egl-4 gene. We show that the egl-4 gene encodes cGMP-dependent protein kinases. egl-4 promoter::gfp fusion genes are mainly expressed in head neurons, hypodermis, intestine and body wall muscles. Procedures to analyze morphology and volume of major organs were developed. The results indicate that volumes of intestine, hypodermis and muscle and cell volumes in intestine and muscle are increased in the egl-4 mutants, whereas cell numbers are not. Experiments on genetic interaction suggest that the cGMP-EGL-4 signaling pathway represses body size and lifespan through DBL-1/TGF-beta and insulin pathways, respectively. ------------------- Key: 5775 Medline: Authors: Barr MM Title: Super models Citation: Physiological Genomics 13: 15-24 2003 Type: REVIEW Genes: Abstract: Model organisms have been used over a century to understand basic, conserved biological processes. The study of these experimental systems began with genetics and development, moved into molecular and cellular biology, and most recently propelled into functional genomics and proteomics. The goal of this review is simple: to discuss the place of model organisms in "The Age of the Ome": the genome, the transcriptome, and the proteome. This review will address the following questions. What exactly is a model organism? What characteristics make an excellent model system? Using the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans as examples, this review will discuss these issues with the aim of demonstrating how model organisms remain indispensable scientific tools for understanding complex biological pathways and human ------------------- Key: 5776 Medline: 12657671 Authors: Jacob TC;Kaplan JM Title: The EGL-21 carboxypeptidase E facilitates acetylcholine release at Caenorhabditis elegans neuromuscular junctions. Citation: Journal of Neuroscience 23: 2122-2130 2003 Type: ARTICLE Genes: egl-3 egl-21 unc-104 Abstract: Proneuropeptides are packaged into dense-core vesicles in which they are processed into active peptides by copackaged enzymes. Proprotein convertases (PCs) cleave precursors after dibasic residues, and carboxypeptidases remove basic residues from the C terminals. We show here that the Caenorhabditis elegans egl-21 gene encodes a protein that is very similar to carboxypeptidase E (CPE) and is broadly expressed in the nervous system. Mutants lacking either egl-21 CPE or egl-3, which encodes the C. elegans ortholog of PC type 2 (PC2), were defective for processing endogenously expressed FMRFamide (Phe-Met-Arg-Phe-NH2)-related peptides (FaRPs). Mutants lacking the unc-104 kinesin motor protein were defective for anterograde movement of dense-core vesicle components, including egl-3 PC2, egl-21 CPE, and FaRPs. We provide evidence that egl-3 PC2 and egl-21 CPE mutants have diminished acetylcholine release at neuromuscular junctions (NMJs). Taken together, these results suggest that egl-21 CPE and egl-3 PC2 process endogenous neuropeptides that facilitate acetylcholine release at C. elegans NMJs. ------------------- Key: 5777 Medline: 12659736 Authors: Kaji H;Isobe T Title: Protein database of Caenorhabditis elegans. Citation: Journal of Chromatography B 787: 91-99 2003 Type: REVIEW Genes: Abstract: Whole genome sequencing of the free-living nematode Caenorhabditis elegans is a prominent achievement in genomics and uncovers the existence of enormous known and unknown gene products. Characterization and linking of all gene products are the next challenging theme of biology. Genome-wide researches are already progressing on C. elegans and the fruits of these efforts are accessible through the internet. To link the sequence-function relationship, proteomic research has been applied to provide comprehensive information of the worm proteins. In addition to 2-dimensional gel electrophoresis for visualization of the proteome, recent advances in liquid chromatography (LC)-based technologies have allowed the large-scale analysis of proteins and are at cutting-edge of high-throughput analysis of focused proteome. ------------------- Key: 5778 Medline: 12642612 Authors: Tsou MFB;Ku W;Hayashi A;Rose LS Title: PAR-dependent and geometry-dependent mechanisms of spindle positioning. Citation: Journal of Cell Biology 160: 845-855 2003 Type: ARTICLE Genes: let-99 par-2 par-3 Abstract: During intrinsically asymmetric division, the spindle is oriented onto a polarized axis specified by a group of conserved PAR proteins. Extrinsic geometric asymmetry generated by cell shape also affects spindle orientation in some systems, but how intrinsic and extrinsic mechanisms coexist without interfering with each other is unknown. In some asymmetrically dividing cells of the wild-type Caenorhabditis elegans embryo, nuclear rotation directed toward the anterior cortex orients the forming spindle. We find that in such cells, a PAR-dependent mechanism dominates and causes rotation onto the polarized axis regardless of cell shape. However, when geometric asymmetry is removed, free nuclear rotation in the center of the cell is observed, indicating that the anterior-directed nature of rotation in unaltered embryos is an effect of cell shape. This free rotation is inconsistent with the prevailing model for nuclear rotation, the specialized cortical site model. in contrast, in par-3 mutant embryos, a geometry-dependent mechanism becomes active and causes directed nuclear rotation. These results lead to the model that in wild-type embryos both PAR-3 and PAR-2 are essential for nuclear rotation in asymmetrically dividing cells, but that PAR-3 inhibits geometry-dependent rotation in nonpolarized cells, thus preventing cell shape from interfering with spindle orientation. ------------------- Key: 5779 Medline: 12581801 Authors: Van Voorhies W Title: The metabolic rate of Caenorhabditis elegans dauer larvae: comments on a recent paper by Houthoofd et al. Citation: Experimental Gerontology 38: 343-344 2003 Type: REVIEW Genes: Abstract: ------------------- Key: 5780 Medline: 12581802 Authors: Hertweck M;Hoppe T;Baumeister R Title: C. elegans, a model for aging with high-throughput Citation: Experimental Gerontology 38: 345-346 2003 Type: REVIEW Genes: daf-2 Abstract: The 1 mm long nematode Caenorhabditis elegans is one of the prime animal models to study the genetics of aging. Wild type animals under laboratory conditions live only for an average of 18 days, whereas mutations in about 50 genes have been identified that extend longevity up to sixfold. High-throughput analyses have been devised that allow large-scale analysis to identify additional genes, as well as compounds that affect life-span. ------------------- Key: 5781 Medline: 12646146 Authors: Putzke AP;Rothman JH Title: Gastrulation: PARtaking of the bottle. Citation: Current Biology 13: R223-R225 2003 Type: REVIEW Genes: emb-5 gad-1 par-2 par-3 par-6 Abstract: Gastrulation in C. elegans embryos involves ingression of individual cells, but is driven by apical constriction of the kind that promotes migration of epithelial cell sheets. Recent work shows that PAR proteins, known for their role in polarization and unequal cell division, are also associated with the polarization that establishes this apical constriction. ------------------- Key: 5782 Medline: 12646147 Authors: Chao MY;Hart AC Title: Sensory biology: how the nose knows. Citation: Current Biology 13: R226-R228 2003 Type: REVIEW Genes: egl-3 glr-1 glr-2 glr-4 glr-5 nmr-1 nmr-2 Abstract: Sensory information is encoded as patterns of synaptic activity. Recent evidence suggests that differential synaptic release and use of postsynaptic glutamate receptors is critical for encoding information from ------------------- Key: 5783 Medline: 12646136 Authors: van der Linden AM;Moorman C;Cuppen E;Korswagen HC;Plasterk RHA Title: Hyperactivation of the G(12)-mediated signaling pathway in Caenorhabditis elegans induces a developmental growth arrest via protein kinase C. Citation: Current Biology 13: 516-521 2003 Type: ARTICLE Genes: gpa-12 tpa-1 Abstract: The G(12) type of heterotrimeric G-proteins play an important role in development and behave as potent oncogenes in cultured cells [1-5]. However, little is known about the molecular nature of the components that act in the G(12)-signaling pathway in an organism. We characterized a C. elegans Galpha subunit gene, gpa-12, which is a homolog of mammalian G(12)/G(13)alpha, and found that animals defective in gpa-12 are viable. Expression of activated GPA-12 (G(12)QL) results in a developmental growth arrest caused by a feeding behavior defect that is due to a dramatic reduction in pharyngeal pumping. To elucidate the molecular nature of the signaling pathways in which G12 participates, we screened for suppressors of the G12QL phenotype. We isolated 50 suppressors that contain mutations in tpa-1, which encodes two protein kinase C isoforms, TPA-1A and TPA-1B, most similar to PKCtheta/delta. TPA-1 mediates the action of the tumor promoter PMA [6]. Expression of G12QL and treatment of wild-type animals with PMA induce an identical growth arrest caused by inhibition of larval feeding, which is dependent on TPA-1A and TPA-1B function. These results suggest that TPA-1 is a downstream target of both G(12) signaling and PMA in modulating feeding and growth in C. elegans. Taken together, our findings provide a potential molecular mechanism for the transforming capability of ------------------- Key: 5784 Medline: 12733639 Authors: Takanami T;Mori A;Takahashi H;Horiuchi S;Higashitani A Title: Caenorhabditis elegans Ce-rdh-1/rad-51 functions after double-strand break formation of meiotic recombination. Citation: Chromosome Research 11: 125-135 2003 Type: ARTICLE Genes: chk-2 rad-51 rdh-1 spo-11 Abstract: During meiotic prophase 1, homologous recombination is accompanied by dynamic chromosomal changes. The Ce-rdh-1/rad-51 gene is the only bacterial recA-like gene in the nematode C. elegans genome. Upon depletion of Ce-rdh-1/rad-51 using the RNA interference method, abnormal 'kinked' chromosomes can be observed in mature oocytes at diakinesis, whereas synapsis between homologous chromosomes during the pachytene stage is normal. Following fertilization, Ce-rdh-1/rad-51-depleted embryos die early in embryogenesis, and their nuclei exhibit abnormal chromosome fragments and bridges. From epistasis analyses with Ce-spo-11 defective mutant and ionizing radiation, it is indicated that Ce-rdh-1/rad-51 functions after double-strand break (DSB) formation of meiotic recombination. Under the Ce-chk-2 defective condition, whose meiotic synapsis and meiotic recombination between homologous chromosomes are completely inhibited, the Ce-rdh-1/rad51 is normally expressed in the gonadal cells. Moreover, it seems that exogenous DSBs in the Ce-chk-2 defective nuclei at the pachytene stage can be repaired between sister chromatids in a Ce-rdh-1/rad-51-dependent manner. These results indicate that Ce-rdh-1/rad51 functions after both endogenous and exogenous DSB formation during meiosis, but not as 'pairing centers' for meiotic ------------------- Key: 5785 Medline: 12642390 Authors: Bamber BA;Twyman RE;Jorgensen EM Title: Pharmacological characterization of the homomeric and heteromeric UNC-49 GABA receptors in C. elegans. Citation: British Journal of Pharmacology 138: 883-893 2003 Type: ARTICLE Genes: avr-15 unc-49 Abstract: UNC-49B and UNC-49C are T-aminobutyric acid (GABA) receptor subunits encoded by the Caenorhabditis elegans unc-49 gene. UNC-49B forms a homomeric GABA receptor, or can co-assemble with UNC-49C to form a heteromeric receptor. The pharmacological properties of UNC-49B homomers and UNC-49B/C heteromers were investigated in Xenopus oocytes. The UNC-49 subunits are most closely related to the bicuculline- and benzodiazepine-in sensitive RDL GABA receptors of insects. Consistent with this classification, bicuculline (10 mum) did not inhibit, nor did diazepam (10 mum) enhance UNC-49B homomeric or UNC-49B/C heteromeric receptors. The UNC-49C subunit strongly affects the pharmacology of UNC-49B/C heteromeric receptors. UNC-49B homomers were much more picrotoxin sensitive than UNC-49B/C heteromers (IC50=0.9+/-0.2 mum and 166+/-42 mum, respectively). Pentobarbitone enhancement was greater for UNC-49B homomers compared to UNC-49B/C heteromers. Propofol (50,um) slightly enhanced UNC-49B homomers but slightly inhibited UNC-49B/C heteromers. Penicillin G (10 mm) inhibited UNC-49B homomers less strongly than UNC-49B/C heteromers (30% compared to 53% inhibition, respectively). Several aspects of UNC-49 pharmacology were unusual. Picrotoxin sensitivity strongly correlates with dieldrin sensitivity, yet UNC-49B homomers were highly dieldrin resistant. The enhancing neurosteroid pregnanolone (5beta-pregnan-3alpha-ol-20-one; 10 mum) strongly inhibited both UNC-49 receptors. Alphaxalone (10 mum), another enhancing neurosteroid, did not affect UNC-49B homomers, but slightly inhibited UNC-49B/C heteromers. UNC-49 subunits and mammalian GABA(A) receptor alpha, beta, and gamma subunit classes all share roughly the same degree of sequence similarity. Thus, although they are most similar to other invertebrate GABA receptors, the UNC-49 receptors share significant structural and pharmacological overlap ------------------- Key: 5786 Medline: 12651157 Authors: Haycraft CJ;Schafer JC;Zhang Q;Taulman PD;Yoder BK Title: Identification of CHE-13, a novel intraflagellar transport protein required for cilia formation. Citation: Experimental Cell Research 284: 251-263 2003 Type: ARTICLE Genes: che-13 daf-19 hip-1 osm-5 osm-6 Abstract: Cilia are present on cells of many eukaryotic organisms and recent data in the mouse suggest that ciliary defects can cause severe developmental abnormalities and disease. Studies across eukaryotic systems indicate that cilia are constructed and maintained through a highly conserved process termed intraflagellar transport (IFT), for which many of the proteins involved have yet to be identified. 11717 describes the movement of large protein particles consisting of an A and a B complex along the cilia axoneme in anterograde and retrograde directions. Herein we describe a novel C. elegans gene, F59C6.7/9, that is required for cilia assembly and whose function is disrupted in che-13 ciliogenic mutants. As previously shown for all IFT complex B genes identified to date, expression of che-13 (F59C6.7/9) is regulated by the RFX-type transcription factor DAF-19, suggesting a conserved transcriptional pathway in ciliogenesis. Fluorescent-tagged CHE-13 protein concentrates at the base of cilia and moves along the axoneme as expected for an IFT protein. Furthermore, loss of che-13 differentially affects the localization of two known IFT complex B proteins, OSM-5 and OSM-6, implying that CHE-13 functions as part of this complex. Overall, our data confirm that CHE-13 is an IFT protein and further that the IFT particle assembles in an ordered process through specific protein-protein ------------------- Key: 5787 Medline: 12663863 Authors: Strange K Title: From genes to integrative physiology: ion channel and transporter biology in Caenorhabditis elegans. Citation: Physiological Reviews 83: 377-415 2003 Type: REVIEW Genes: avr-15 ced-7 ced-11 clh-1 clh-2 clh-3 clh-4 clh-5 clh-6 crt-1 dat-1 dec-4 eat-4 exp-2 fer-1 glr-1 gon-2 itr-1 lov-1 mec-1 mec-2 mec-4 mec-5 mec-6 mec-7 mec-9 mec-10 mec-12 mod-1 myo-3 nmr-1 ocr-2 osm-9 pkd-1 pkd-2 slo-1 unc-4 unc-47 unc-64 unc-119 Abstract: The stunning progress in molecular biology that has occurred over the last 50 years drove a powerful reductionist approach to the study of physiology. That same progress now forms the foundation for the next revolution in physiological research. This revolution will be focused on integrative physiology, which seeks to understand multicomponent processes and the underlying pathways of information flow from an organism's "parts" to increasingly complex levels of organization. Genetically tractable and genomically defined nonmammalian model organisms such as the nematode Caenorhabditis elegans provide powerful experimental advantages for elucidating gene function and the molecular workings of complex systems. This review has two main goals. The first goal is to describe the experimental utility of C. elegans for investigating basic physiological problems. A detailed overview of C. elegans biology and the experimental tools, resources, and strategies available for its study is provided. The second goal of this review is to describe how forward and reverse genetic approaches and direct behavioral and physiological measurements in C. elegans have generated novel insights into the integrative physiology of ion channels and transporters. Where appropriate, I describe how insights from C. elegans have provided new understanding of the physiology of membrane transport processes in mammals. ------------------- Key: 5788 Medline: 12644560 Authors: Denver DR;Morris K;Thomas WK Title: Phylogenetics in Caenorhabditis elegans: an analysis of divergence and outcrossing. Citation: Molecular Biology and Evolution 20: 393-400 2003 Type: ARTICLE Genes: Abstract: This study establishes a phylogenetic framework for the natural geographic isolates of the widely studied nematode species Caenorhabditis elegans. Virtually complete mitochondrial genomes are sequenced from 27 C. elegans natural isolates to characterize mitochondrial divergence patterns and to investigate the evolutionary history of the C. elegans hermaphrodite lineages. Phylogenetic analysis of mitochondrial sequences reveals the presence of two major C. elegans hermaphrodite clades (designated clade I and clade II). Fifty-six nuclear loci, widely distributed across the five autosomes and the X chromosome, are also analyzed in a subset of the C. elegans isolates to evaluate nuclear divergence patterns and the extent of mating between different strains. A comparison of the phylogenetic tree derived from mitochondrial data with the phylogenetic tree derived from nuclear data reveals only one inconsistency in the distribution of isolates into clades I and II, suggesting that mating between divergent C. elegans strains is an infrequent event in the wild. ------------------- Key: 5789 Medline: 12648766 Authors: Slimko EM;Lester HA Title: Codon optimization of Caenorhabditis elegans GluCl ion channel genes for mammalian cells dramatically improves expression levels. Citation: Journal of Neuroscience Methods 124: 75-81 2003 Type: ARTICLE Genes: Abstract: Organisms use synonymous codons in a highly non-random fashion. These codon usage biases sometimes frustrate attempts to express high levels of exogenous genes in hosts of widely divergent species. The Caenorhabelitis elegans GluClalpha1 and GluClbeta genes form a functional glutamate and ivermectin-gated chloride channel when expressed in Xenopus oocytes, but expression is weak in mammalian cells. We have constructed synthetic genes that retain the amino acid sequence of the wild-type GluCl channel proteins, but use codons that are optimal for mammalian cell expression. We have tagged the native and codon-optimized GluCl cDNAs with enhanced yellow fluorescent protein (EYFP, GluClalpha1 subunit) and enhanced cyan fluorescent protein (EFCP, GluClbeta subunit), expressed the channels in E18 rat hippocampal neurons and measured the relative expression levels of the two genes with fluorescence microscopy as well as with electrophysiology. Codon optimization provides. a 6- to 9-fold increase in expression, allowing the conclusions that the ivermectin-gated channel has an EC50 of 1.2 nM and a Hill. coefficient of 1.9. We also confirm that the Y182F mutation in the codon-optimized 0 subunit results in a heteromeric channel that retains the response to ivermectin while reducing the response to 100 M glutamate by 7-fold. The engineered GluCl channel is the first codon-optimized membrane protein expressed in mammalian cells and may be useful for selectively silencing specific neuronal populations in vivo. ------------------- Key: 5790 Medline: 12651889 Authors: Gay F;Calvo D;Lo MC;Ceron J;Maduro M;Lin R;Shi Y Title: Acetylation regulates subcellular localization of the Wnt signaling nuclear effector POP-1. Citation: Genes & Development 17: 717-722 2003 Type: ARTICLE Genes: med-1 pop-1 Abstract: Lymphoid enhancer factor/T-cell factor (LEF/TCF) are transcription factors that mediate the Wnt signaling pathway, and have crucial roles during embryonic development in various organisms. Here we report that acetylation enhances nuclear retention of POP-1, the Caenorhabditis elegans LEF/TCF homolog, through increasing nuclear import and blocking nuclear export. We identify three lysines that are acetylated in vivo, and demonstrate their essential requirement for proper nuclear localization and biological activity of POP-1 during C. elegans embryogenesis. The conservation of these lysines among other LEF/TCF family members suggests that acetylation may be an important, evolutionarily conserved mechanism regulating subcellular distribution of LEF/TCF factors. ------------------- Key: 5791 Medline: 12651893 Authors: Zhang F;Barboric M;Blackwell TK;Peterlin BM Title: A model of repression: CTD analogs and PIE-1 inhibit transcriptional elongation by P-TEFb. Citation: Genes & Development 17: 748-758 2003 Type: ARTICLE Genes: pie-1 Abstract: The positive transcription elongation factor b (P-TEFb) contains cyclin T1 (CycT1) and cyclin-dependent kinase 9 (Cdk9). For activating the expression of eukaryotic genes, the histidine-rich sequence in CycT1 binds the heptapeptide repeats in the C-terminal domain (CTD) of RNA polymerase II (RNAPII), whereupon Cdk9 phosphorylates the CTD. We found that alanine-substituted heptapeptide repeats that cannot be phosphorylated also bind CycT1. When placed near transcription units, these CTD analogs block effects of P-TEFb. Remarkably, the transcriptional repressor PIE-1 from Caenorhabditis elegans behaves analogously. It binds CycT1 via an alanine-containing heptapeptide repeat and inhibits transcriptional elongation. Thus, our findings reveal a new mechanism by which repressors inhibit eukaryotic transcription. ------------------- Key: 5792 Medline: 12648474 Authors: Moghal N;Sternberg PW Title: The epidermal growth factor system in Caenorhabditis elegans. Citation: Experimental Cell Research 284: 150-159 2003 Type: REVIEW Genes: apm-1 ark-1 bar-1 cdf-1 ced-10 dpl-1 dpy-22 efl-1 efl-2 egl-15 eor-1 eor-2 gap-1 ipp-5 ksr-1 ksr-2 let-23 let-60 let-341 let-419 lfe-1 lfe-2 lin-1 lin-2 lin-3 lin-7 lin-10 lin-12 lin-15 lin-25 lin-31 lin-35 lin-36 lin-39 lin-45 lin-53 mek-2 mig-2 mpk-1 pry-1 ptp-2 sem-5 sli-1 soc-2 sur-1 sur-2 sur-6 sur-8 unc-73 unc-101 zmp-1 Abstract: The single known epidermal growth factor-like growth factor and single epidermal growth factor receptor in Caenorhabditis elegans mediate two types of processes, each via a distinct signal transduction pathway. Several instances of cell fate specification during organogenesis require the RAS-MAP kinase pathway, as well as multiple nuclear factors. By contrast, appropriate myoepithelial contractions during ovulation involve IP3-mediated signal transduction. Positive modulators of the RAS pathway include KSR, SUR-8, phosphatase PP2A, and a zinc cation diffusion facilitator. Negative regulators of the RAS pathway include homologs of CBL, GAP-1, ACK, and MAP kinase phosphatase, while negative regulators of the IP3 pathway are enzymes that modify IP3. In addition to its stimulation of RAS activity, the GRB2 homolog SEM-5 acts negatively on both signaling pathways, as does the Ack-related kinase ------------------- Key: 5793 Medline: 12655636 Authors: Gumienny TL;Padgett RW Title: A small issue addressed. Citation: BioEssays 25: 305-308 2003 Type: REVIEW Genes: daf-4 daf-7 dbl-1 dpy-2 lon-1 lon-3 sma-2 sma-3 sma-4 sma-6 tig-1 unc-129 Abstract: Cell size is an important determinant of body size. While the genetic mechanisms of cell size regulation have been well studied in yeast, this process has only recently been addressed in multicellular organisms. One recent report by Wang et al. (2002) shows that in the nematode C. elegans, the TGFbeta-like pathway acts in the hypodermis to regulate cell size and consequently body size.((1)) This finding is an exciting step in discovering the molecular mechanisms that control cell and body size. ------------------- Key: 5794 Medline: 12487630 Authors: Cadinanos J;Schmidt WK;Fueyo A;Varela I;Lopez-Otin C;Freije JMP Title: Identification, functional expression and enzymic analysis of two distinct CaaX proteases from Caenorhabditis elegans. Citation: Biochemical Journal 370: 1047-1054 2003 Type: ARTICLE Genes: Abstract: Post-translational processing of proteins such as the Ras GTPases, which contain a C-terminal CaaX motif (where C stands for cysteine, a for aliphatic and X is one of several amino acids), includes prenylation, proteolytic removal of the C-terminal tripeptide and carboxy-methylation of the isoprenylcysteine residue. In the present study, we report the presence of two distinct CaaX-proteolytic activities in membrane extracts from Caenorhabditis elegans, which are sensitive to EDTA and Tos-Phe-CH2Cl (tosylphenylalanylchloromethane; 'TPCK') respectively. A protein similar to the mammalian and yeast farnesylated-proteins converting enzyme-1 (FACE-1)/Ste24p CaaX metalloprotease, encoded by a hypothetical gene (CeFACE-1/C04F12.10) found in C. elegans chromosome 1, probably accounts for the EDTA-sensitive activity. An orthologue of FACE-2/Rce1p, the enzyme responsible for the proteolytic maturation of Ras oncoproteins and other prenylated substrates, probably accounts for the Tos-Phe-CH2Cl-sensitive activity, even though the gene for FACE-2/Rcel has not been previously identified in this model organism. We have identified a previously overlooked gene in C. elegans chromosome V, which codes for a 266-amino-acid protein (CeFACE-2) with 30 % sequence identity to human FACE-2/Rce1. We show that both CeFACE-1 and CeFACE-2 have the ability to promote production of the farnesylated yeast pheromone a-factor in vivo and to cleave a farnesylated peptide in vitro. These results indicate that CeFACE-1 and CeFACE-2 are bona fide CaaX proteases and support the evolutionary conservation of this proteolytic system in eukaryotes. ------------------- Key: 5795 Medline: 12655640 Authors: Leatherman JL;Jongens TA Title: Transcriptional silencing and translational control: key features of early germline development. Citation: BioEssays 25: 326-335 2003 Type: REVIEW Genes: glh-1 glh-2 glh-3 glh-4 mes-2 mes-6 pie-1 Abstract: The germ lineage has been studied for a long time because of its crucial role in the propagation and survival of a species. While this lineage, in contrast to the soma, is clearly unique in its totipotent ability to produce a new organism, it has now been found also to have specific features at the cellular level. One feature, a period of transcriptional quiescence in the early germ cell precursors, has been observed in both Drosophila and C. elegans, where it is essential for the formation and the survival of the germline. In addition, there are numerous instances where these early germ cells are reliant on translational regulation, especially in Drosophila. The genes that are important for these two functions, the mechanisms of their action, and studies in vertebrate organisms that reveal similarities as well as some potential differences in early germ cell development are ------------------- Key: 5796 Medline: 12639709 Authors: Chong H;Vikis HG;Guan KL Title: Mechanisms of regulating the Raf kinase family. Citation: Cellular Signalling 15: 463-469 2003 Type: REVIEW Genes: lin-45 Abstract: The MAP Kinase pathway is a key signalling mechanism that regulates many cellular functions such as cell growth, transformation and apoptosis. One of the essential components of this pathway is the serine/threonine kinase, Raf. Raf (MAPKK kinase, MAPKKK) relays the extracellular signal from the receptor/Ras complex to a cascade of cytosolic kinases by phosphorylating and activating MAPK/ERK kinase (MEK; MAPK kinase, MAPKK) that phosphorylates and activates extracellular signal regulated kinase (ERK; mitogen-activated protein kinase, MAPK), which phosphorylates various cytoplasmic and nuclear proteins. Regulation of both Ras and Raf is crucial in the proper maintenance of cell growth as oncogenic mutations in these genes lead to high transforming activity. Ras is mutated in 30% of all human cancers and B-Raf is mutated in 60% of malignant melanomas. The mechanisms that regulate the small GTPase Ras as well as the downstream kinases MEK and extracellular signal regulated kinase (ERK) are well understood. However, the regulation of Raf is complex and involves the integration of other signalling pathways as well as intramolecular interactions, phosphorylation, dephosphorylation and protein-protein interactions. From studies using mammalian isoforms of Raf, as well as C elegans lin45-Raf, common patterns and unique differences of regulation have emerged. This review will summarize recent findings on the regulation of Raf kinase. ------------------- Key: 5797 Medline: 12554873 Authors: Alder MN;Dames S;Gaudet J;Mango SE Title: Gene silencing in Caenorhabditis elegans by transitive RNA interference. Citation: RNA 9: 25-32 2003 Type: ARTICLE Genes: pha-4 tlf-1 unc-22 unc-60 Abstract: When a cell is exposed to double-stranded RNA (dsRNA), mRNA from the homologous gene is selectively degraded by a process called RNA interference (RNAi). Here, we provide evidence that dsRNA is amplified in Caenorhabditis elegans to ensure a robust RNAi response. Our data suggest a model in which mRNA targeted by RNAi functions as a template for 5' to 3' synthesis of new dsRNA (termed transitive RNAi). Strikingly, the effect is nonautonomous: dsRNA targeted to a gene expressed in one cell type can lead to transitive RNAi-mediated silencing of a second gene expressed in a distinct cell type. These data suggest dsRNA synthesized in vivo can mediate systemic RNAi. ------------------- Key: 5798 Medline: 12684444 Authors: Gally C;Bessereau JL Title: GABA is dispensable for the formation of juncational GABA receptor clusters in Caenorhabditis elegans. Citation: Journal of Neuroscience 23: 2591-2599 2003 Type: ARTICLE Genes: lin-6 unc-5 unc-13 unc-18 unc-25 unc-31 unc-49 unc-104 Abstract: At GABAergic synapses, GABA receptors form high-density clusters opposite GABA release sites. Whether GABA release per se plays a role in the formation of GABA receptor clusters remains uncertain. To address this question in vivo, we characterized GABA receptor clustering in the nematode Caenorhabditis elegans. In C. elegans, body wall muscles receive excitatory inputs from cholinergic motor neurons and inhibitory inputs from GABAergic neurons. Using immunohistochemistry and green fluorescent protein-tagged proteins, we observed that the muscle GABA receptor UNC-49 is precisely clustered opposite GABA release sites. During development, these clusters appear slightly after the detection of presynaptic vesicles. If motor axons are mislocalized as in unc-5 mutants, GABA receptors cluster opposite ectopic axons at GABA release sites. Together, these data imply that a motor neuron-derived factor is instructing GABA receptor clustering. Presynaptic localization of this clustering activity requires the neuronal kinesin UNC-104, suggesting that release of GABA from synaptic vesicles may represent the clustering signal. However, unc-25 mutants do not synthesize GABA but do cluster postsynaptic GABA receptors indistinguishably from the wild type. Therefore, at GABAergic neuromuscular junctions, GABA receptor clustering requires nerve-muscle interaction but not GABA neurotransmission. ------------------- Key: 5799 Medline: 12684455 Authors: Garcia LR;Sternberg PW Title: Caenorhabditis elegans UNC-103 ERG-like potassium channel regulates contractile behaviors of sex muscles in males before and during mating. Citation: Journal of Neuroscience 23: 2696-2705 2003 Type: ARTICLE Genes: cat-1 cha-1 egl-19 unc-2 unc-13 unc-31 unc-49 unc-64 unc-68 unc-103 Abstract: During mating behavior the Caenorhabditis elegans male must regulate periodic and prolonged protractor muscle contractions to insert his copulatory spicules into his mate. The protractors undergo periodic contractions to allow the spicules to reattempt insertion if a previous thrust failed to breach the vulva. When the spicule tips penetrate the vulva, the protractors undergo prolonged contraction to keep the spicules inside the hermaphrodite until sperm transfer is complete. To understand how these contractions are regulated, we isolated EMS-induced mutations that cause males to execute prolonged contraction inappropriately. Loss-of-function mutations in the unc-103 ERG-like K+ channel gene cause the protractor muscles to contract in the absence of mating stimulation. unc-103-induced spicule protraction can be suppressed by killing the SPC motor neurons and the anal depressor muscle: cells that directly contact the protractors. Also, reduction in acetylcholine suppresses unc-103-induced protraction, suggesting that UNC-103 keeps cholinergic neurons from stimulating the protractors before mating behavior. UNC-103 also regulates the timing of spicule protraction during mating behavior. unc-103 males that do not display mating-independent spicule protraction show abnormal spicule insertion behavior during sex. In contrast to wild-type males, unc-103 mutants execute prolonged contractions spontaneously within sequences of periodic protractor contractions. The premature prolonged contractions cause the spicules to extend from the male tail before the spicule tips penetrate the vulva. These observations demonstrate that unc-103 controls various ------------------- Key: 5800 Medline: 12584198 Authors: Hwang HY;Olson SK;Brown JR;Esko JD;Horvitz HR Title: The Caenorhabditis elegans genes sqv-2 and sqv-6, which are required for vulval morphogenesis, encode glycosaminoglycan galactosyltransferase II and xylosyltransferase. Citation: Journal of Biological Chemistry 278: 11735-11738 2003 Type: ARTICLE Genes: sqv-2 sqv-6 Abstract: In mutants defective in any of eight Caenorhabditis elegans sqv (squashed vulva) genes, the vulval extracellular space fails to expand during vulval morphogenesis. Strong sqv mutations result in maternal-effect lethality, caused in part by the failure of the progeny of homozygous mutants to initiate cytokinesis and associated with the failure to form an extracellular space between the egg and the eggshell. Recent studies have implicated glycosaminoglycans in these processes. Here we report the cloning and characterization of sqv-2 and sqv-6. sqv-6 encodes a protein similar to human xylosyltransferases. Transfection of sqv-6 restored xylosyltransferase activity to and rescued the glycosaminoglycan biosynthesis defect of a xylosyltransferase mutant hamster cell line. sqv-2 encodes a protein similar to human galactosyltransferase II. A recombinant SQV-2 fusion protein had galactosyltransferase II activity with substrate specificity similar to that of human galactosyltransferase II. We conclude that C. elegans SQV-6 and SQV-2 likely act in concert with other SQV proteins to catalyze the stepwise formation of the proteoglycan core protein linkage tetrasaccharide GlcAbeta1,3Galbeta1 3Gabeta1,4Xylbeta-O-(Ser), which is common to the two major types of glycosaminoglycans in vertebrates, chondroitin and heparan sulfate. Our results strongly support a model in which C. elegans vulval morphogenesis and zygotic cytokinesis depend on the expression of glycosaminoglycans. ------------------- Key: 5801 Medline: 12533541 Authors: Bianchi L;Kwok SM;Driscoll M;Sesti F Title: A potassium channel-MiRP complex controls neurosensory function in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 278: 12415-12424 2003 Type: ARTICLE Genes: kvs-1 mps-1 Abstract: MinK-related peptides (MiRPs) are single transmembrane proteins that associate with mammalian voltage-gated K+ subunits. Here we report the cloning and functional characterization of a MiRP beta-subunit, MPS-1, and of a voltage-gated pore-forming potassium subunit, KVS-1, from the nematode Caenorhabditis elegans. mps-1 is expressed in chemosensory and mechanosensory neurons and co-localizes with kvs-1 in a subset of these. Inactivation of either mps-1 or kvs-1 by RNA interference (RNAi) causes partially overlapping neuronal defects and results in broad-spectrum neuronal dysfunction, including defective chemotaxis, disrupted mechanotransduction, and impaired locomotion. Inactivation of one subunit by RNAi dramatically suppresses the expression of the partner subunit only in cells where the two proteins co-localize. Co-expression of MPS-1 and KVS-1 in mammalian cells gives rise to a potassium current distinct from the KVS-1 current. Taken together these data indicate that potassium currents constitute a basic determinant for C. elegans neuronal function and unravel a unifying principle of evolutionary significance: that potassium channels in various organisms use MiRPs to generate uniqueness of function with rich variation in the details. ------------------- Key: 5802 Medline: 12556527 Authors: Kitagawa N;Shimohama S;Oeda T;Uemura K;Kohno R;Kuzuya A;Shibasaki H;Ishii N Title: The role of presenilin-1 homologue gene sel-12 of Caenorhabditis elegans in apoptotic activities. Citation: Journal of Biological Chemistry 278: 12130-12134 2003 Type: ARTICLE Genes: ced-3 ced-4 mev-1 sel-12 unc-1 Abstract: Many cases of autosomal dominant early onset familial Alzheimer's disease result from mutations in presenilin-l (PSI). In this study, we examined the role of the PS1 homologue gene sel-12 of Caenorhabditis elegans under oxidative stress and clarified the sel-12-induced apoptosis. A genetic null allele mutant, sel-12(ar171), showed resistance to oxidative stress and prevented mitochondrial dysfunction-induced apoptosis. On the other hand, another allele mutant, sel-12(ar131), that carries a missense mutation showed a proapoptotic activity, which may be the result of a gain of function property. Also, sel-12 (ar131)-induced apoptosis was ced-3- and ced-4-dependent. Dantrolene, which specifically inhibits Ca2+ release from endoplasmic reticulum stores, prevents sel-12(ar131)-induced apoptosis. SEL-12, which is localized in the endoplasmic reticulum, may induce apoptosis through abnormal calcium release from the endoplasmic reticulum. Together, with the previous finding that human PSI could substitute for SEL-12, these results suggest the similar involvement of PS1-inducing apoptosis under oxidative stress and mitochondrial dysfunction in the Alzheimer's ------------------- Key: 5803 Medline: 12654843 Authors: Sifri CD;Begun J;Ausubel FM;Calderwood SB Title: Caenorhabditis elegans as a model host for Staphylococcus aureus pathogenesis. Citation: Infection and Immunity 71: 2208-2217 2003 Type: ARTICLE Genes: esp-2 esp-8 nsy-1 sek-1 Abstract: Staphylococcus aureus, an important pathogen of humans and other warm-blooded animals, is also capable of killing the nematode Caenorhabditis elegans. Here, we show that C. elegans organisms that are fed S. aureus die over the course of several days in a process that is correlated with the accumulation of bacteria within the nematode digestive tract. Several S. aureus virulence determinants known or speculated to be important in rnammalian pathogenesis, including the quorum-sensing global virulence regulatory system agr and the global virulence regulator sarA, the alternative sigma factor sigma(B), alpha-hemolysin, and V8 serine protease, are required for full pathogenicity in nematodes. In addition, several defined C. elegans mutants were examined for susceptibility to S. aureus infection. Enhanced susceptibility to S. aureus killing was observed with loss-of-function mutations in the C. elegans genes esp-2/sek-1 and esp-8/nsy-1, which encode components of a conserved p38 MAP kinase signaling pathway involved in nematode defense against multiple pathogens. These results suggest that key aspects of S. aureus pathogenesis have been conserved, irrespective of the host, and that specific C. elegans host factors can alter susceptibility to this gram-positive human pathogen. ------------------- Key: 5804 Medline: 12663531 Authors: Rogalski M;Gilbert MM;Devenport D;Norman KR;Moerman DG Title: DIM-1, a novel immunoglobulin superfamily protein in Caenorhabditis elegans, is necessary for maintaining bodywall muscle integrity. Citation: Genetics 163: 905-915 2003 Type: ARTICLE Genes: dim-1 unc-112 raDf2 raDf4 raDf6 raDf7 raDf8 raDf9 raDf10 raDf11 raDf12 uDf1 Abstract: The UNC-112 protein is required during initial muscle assembly in C. elegans to form dense bodies and M-lines. Loss of this protein results in arrest at the twofold stage of embryogenesis. In contrast, a missense mutation in unc-112 results in viable animals that have disorganized bodywall muscle and are paralyzed as adults. Loss or reduction of dim-1 gene function can suppress the severe muscle disruption and paralysis exhibited by these mutant hermaphrodites. The overall muscle structure in hermaphrodites lacking a functional dim-1 gene is slightly disorganized, and the myofilament lattice is not as strongly anchored to the muscle cell membrane as it is in wild-type muscle. The dim-1 gene encodes two polypepticles that contain three Ig-like repeats. The short DIM-1 protein isoform consists entirely of three Ig repeats and is sufficient for wild-type bodywall muscle structure and stability. DIM-1 (S) localizes to the region of the muscle cell membrane around and between the dense bodies, which are the structures that anchor the actin filaments and may play a role in stabilizing the thin rather than the thick filament components of the sarcomere. ------------------- Key: 5805 Medline: 12670864 Authors: Nelson DW;Padgett RW Title: Insulin worms its way into the spotlight. Citation: Genes & Development 17: 813-818 2003 Type: REVIEW Genes: aap-1 age-1 akt-1 akt-2 daf-1 daf-2 daf-7 daf-16 daf-28 ins-1 ins-2 ins-3 ins-4 ins-5 ins-6 ins-7 ins-8 ins-9 ins-17 ins-18 ins-19 ins-21 ins-22 ins-23 ins-31 ist-1 Abstract: Obesity and the occurrence of diabetes are on the rise. Much of this is attributable to a more sedentary lifestyle and high caloric intake in industrialized countries and is a major cause of a variety of health problems. Obesity and diabetes are intimately linked to insulin, which increases glucose uptake in cells and serves as a primary regulator of blood glucose levels. Insulin has been an important target of investigation for decades, as indicated by its sequence determination by Sanger and colleagues in 1955, and is now the subject of renewed interest. ------------------- Key: 5806 Medline: 12654724 Authors: Hua QX;Nakagawa SH;Wilken J;Ramos RR;Jia W;Bass J;Weiss MA Title: A divergent INS protein in Caenorhabditis elegans structurally resembles human insulin and activates the human insulin receptor. Citation: Genes & Development 17: 826-831 2003 Type: ARTICLE Genes: ins-6 Abstract: Caenorhabditis elegans contains a family of putative insulin-like genes proposed to regulate dauer arrest and senescence. These sequences often lack characteristic sequence features of human insulin essential for its folding, structure, and function. Here, we describe the structure and receptor-binding properties of INS-6, a single-chain polypeptide expressed in specific neurons. Despite multiple nonconservative changes in sequence, INS-6 recapitulates an insulin-like fold. Although lacking classical receptor-binding determinants, INS-6 binds to and activates the human insulin receptor. Its activity is greater than that of an analogous single-chain human insulin analog. ------------------- Key: 5807 Medline: 12654727 Authors: Li W;Kennedy SG;Ruvkun G Title: daf-28 encodes a C. elegans insulin superfamily member that is regulated by environmental cues and acts in the DAF-2 signaling pathway. Citation: Genes & Development 17: 844-858 2003 Type: ARTICLE Genes: daf-1 daf-2 daf-6 daf-7 daf-11 daf-22 daf-28 ins-1 ins-2 ins-4 ins-6 ins-7 ins-9 ins-17 ins-21 ins-22 ins-23 osm-1 tax-4 Abstract: In Caenorhabditis elegans, the decision to enter a developmentally arrested dauer larval stage is triggered by a combination of signals from sensory neurons in response to environmental cues, which include a dauer pheromone. These sensory inputs are coupled to the parallel DAF-2/insulin receptor-like and DAF-7/TGFbeta-like signaling pathways. Although sensory inputs have been shown to physiologically regulate DAF-7/TGFbeta expression, no such regulation of insulin-like ligands in the DAF-2 pathway has been reported. We show here that daf-28 encodes an insulin-like protein, which when mutated causes dauer arrest and down-regulation of DAF-2/IR signaling. A daf-28:: GFP fusion gene is expressed in ASI and ASJ, two sensory neurons that regulate dauer arrest. daf-28:: GFP expression in ASI and ASJ is down-regulated under dauer-inducing conditions and in mutants of DAF-11/guanylyl cyclase, a predicted component of the dauer-pheromone-sensing pathway. Thus, daf-28 expression in sensory neurons is regulated by the environmental cues that normally trigger dauer arrest. Among the 38 C. elegans insulin genes, daf-28 is so far the only insulin mutant to affect dauer arrest. daf-28 was revealed from this functional redundancy by a dominant-negative allele that disrupts a probable proteolytic processing site required for insulin maturation. This DAF-28 mutant is likely to be ------------------- Key: 5808 Medline: 12666209 Authors: Tsang WY;Lemire BD Title: Mitochondrial ATP synthase controls larval developmental cell nonautonomously in Caenorhabditis elegans. Citation: Developmental Dynamics 226: 719-726 2003 Type: ARTICLE Genes: atp-2 svDp1 Abstract: The mitochondrial respiratory chain is composed of five protein complexes capable of generating cellular energy in the form of ATIP. Defects in mitochondrial energy production can result in a wide variety of diseases with tissue-specific effects. We previously have isolated a mutation in the atp-2 gene, which encodes the active site or beta-subunit of complex V in Caenorhabditis elegans. This atp-2(ua2) mutation is lethal, resulting in developmental arrest at the third larval stage (L3). In this report, we use mosaic analysis to identify the tissues in which atp-2 gene activity is dispensable for development past the L3 stage. The loss of atp-2 in any tissue can provoke arrest at the L3 stage. However, animals with a loss of the atp-2 gene in the ABa lineage, which gives rise to neuronal, pharyngeal, and hypodermal cells, and/or the E lineage, which gives rise to the intestinal cells, can occasionally develop past L3. Loss of atp-2 gene function in the lineages that give rise to the body muscles is invariably associated with developmental arrest. This finding suggests that the body muscles may play a key role in regulating development. We conclude that atp-2 functions cell nonautonomously in this developmental process. Our findings suggest that atp-2 is involved in the production or the regulation of a global, developmental signal ------------------- Key: 5809 Medline: 12654300 Authors: Merz DC;Alves G;Kawano T;Zheng H;Culotti JG Title: UNC-52/perlecan affects gonadal leader cell migrations in C. elegans hermaphrodites through alterations in growth factor signaling. Citation: Developmental Biology 256: 173-186 2003 Type: ARTICLE Genes: cet-1 clr-1 dbl-1 dpy-11 egl-17 egl-20 emb-9 lin-3 mec-8 unc-5 unc-6 unc-22 unc-40 unc-52 unc-54 unc-129 Abstract: The unc-52 gene of Claenorhabditis elegans encodes a homologue of the basement membrane heparan sulfate proteoglycan perlecan. Viable alleles reduce the abundance of UNC-52 in late larval stages and increase the frequency of distal tip cell (DTC) migration defects caused by mutations disrupting the UNC-6/netrin guidance system. These unc-52 alleles do not cause circumferential DTC migration defects in an otherwise wild-type genetic background. The effects of unc-52 mutations on DTC migrations are distinct from effects on myofilament organization and can be partially suppressed by mutations in several genes encoding growth factor-like molecules, including EGL-17/FGF, UNC-129/TGF-beta, DBL-1/TGF-beta, and EGL-20/WNT. We propose that UNC-52 serves dual roles in C. elegans larval development in the maintenance of muscle structure and the regulation of growth factor-like ------------------- Key: 5810 Medline: 12588839 Authors: Uchida O;Nakano H;Koga M;Ohshima Y Title: The C. elegans che-1 gene encodes a zinc finger transcription factor required for specification of the ASE chemosensory neurons. Citation: Development 130: 1215-1224 2003 Type: ARTICLE Genes: ceh-23 che-1 flr-1 gpa-10 gpa-14 gcy-5 gcy-6 gcy-7 lim-4 lim-6 lin-44 odr-3 odr-10 srg-8 tax-2 sDf4 Abstract: Chemotaxis to water-soluble chemicals such as NaCl is an important behavior of C. elegans when seeking food. ASE chemosensory neurons have a major role in this behavior. We show that che-1, defined by chemotaxis defects, encodes a zinc-finger protein similar to the GLASS transcription factor required for photoreceptor cell differentiation in Drosophila, and that che-1 is essential for specification and function of ASE neurons. Expression of a che-1::gfp fusion construct was predominant in ASE. In che-1 mutants, expression of genes characterizing ASE such as seven-transmembrane receptors, guanylate cyclases and a cyclic-nucleotide gated channel is lost. Ectopic expression of che-1 cDNA induced expression of ASE-specific marker genes, a dye-filling defect in neurons other than ASE and dauer formation. ------------------- Key: 5811 Medline: 12676107 Authors: Patterson GI Title: Aging: new targets, new functions. Citation: Current Biology 13: R279-R281 2003 Type: REVIEW Genes: daf-2 daf-16 hsf-1 lon-2 old-1 scl-1 sir-2.1 Abstract: The DAF-16 transcription factor controls aging in C. elegans as part of an insulin-like signaling pathway. Identification of a target of DAF-16 has opened a new window into the aging process. ------------------- Key: 5812 Medline: 12646499 Authors: Bennett MD;Leitch IJ;Price HJ;Johnston JS Title: Comparisons with Caenorhabditis (100 Mb) and Drosophila (175 Mb) using flow cytometry show genome size in Arabidopsis to be 157 Mb and thus 25% larger than the Arabidopsis genome initiative estimate o Citation: Annals of Botany 91: 547-557 2003 Type: ARTICLE Genes: Abstract: Recent genome sequencing papers have given genome sizes of 180 Mb for Drosophila melanogaster Iso-1 and 125 Mb for Arabidopsis thaliana Columbia. The former agrees with early cytochemical estimates, but numerous cytometric estimates of around 170 Mb imply that a genome size of 125 Mb for arabidopsis is an underestimate. In this study, nuclei of species pairs were compared directly using flow cytometry. Co-run Columbia and Iso-1 female gave a 2C peak for arabidopsis only approx. 15% below that for drosophila, and 16C endopolyploid Columbia nuclei had approx. 15% more DNA than 2C chicken nuclei (with gtoreq2280 Mb). Caenorhabditis elegans Bristol N2 (genome size approx. 100 Mb) co-run with Columbia or Iso-1 gave a 2C peak for drosophila approx. 75% above that for 2C C. elegans, and a 2C peak for arabidopsis approx. 57% above that for C. elegans. This confirms that 1C in drosophila is approx. 175 Mb and, combined with other evidence, leads us to conclude that the genome size of arabidopsis is not approx. 125 Mb, but probably approx. 157 Mb. It is likely that the discrepancy represents extra repeated sequences in unsequenced gaps in heterochromatic regions. Complete sequencing of the arabidopsis genome until no gaps remain at telomeres, nucleolar organizing regions or centromeres is still needed to provide the first precise angiosperm C-value as a benchmark calibration standard for plant genomes, and to ensure that no genes have been missed in arabidopsis, especially in centromeric regions, which are clearly larger than once imagined. ------------------- Key: 5813 Medline: 12690206 Authors: Lee SS;Kennedy S;Tolenen AC;Ruvkun G Title: DAF-16 target genes that control C. elegans life-span and metabolism. Citation: Science 300: 644-647 2003 Type: ARTICLE Genes: age-1 daf-2 daf-16 hpd-1 mrp-5 pnk-1 rbp-2 rrf-3 Abstract: Signaling from the DAF-2/insulin receptor to the DAF-16/FOXO transcription factor controls longevity, metabolism, and development in disparate phyla. To identify genes that mediate the conserved biological outputs of daf-2/insulin-like signaling, we used comparative genomics to identify 17 orthologous genes from Caenorhabditis and Drosophila, each of which bears a DAF-16 binding site in the promoter region. One-third of these DAF-16 downstream candidate genes were regulated by daf-2/insulin-like signaling in C. elegans, and RNA interference inactivation of the candidates showed that many of these genes mediate distinct aspects of daf-16 function, including longevity, metabolism, and development. ------------------- Key: 5814 Medline: 12694294 Authors: Jovelin R;Ajie BC;Phillips PC Title: Molecular evolution and quantitative variation for chemosensory behaviour in the nematode genus Citation: Molecular Ecology 12: 1325-1337 2003 Type: ARTICLE Genes: odr-3 Abstract: Caenorhabditis elegans is a model organism in biology, yet despite the tremendous information generated from genetic, genomic and functional analyses, C. elegans has rarely been used to address questions in ecological genetics. Here, we analyse genetic variation for chemosensory behaviour, an ecologically important trait that is also genetically well characterized, at both the phenotypic and molecular levels within three species of the genus Caenorhabditis. We show that the G-protein ODR-3 plays an important role in chemosensory avoidance behaviour and identify orthologues of odr-3 in C. briggsae and C. remanei. Both quantitative genetic analysis of chemosensory behaviour and molecular population genetic analysis of odr-3 show that there is little genetic variation among a worldwide collection of isolates of the primarily selfing C. elegans, whereas there is substantially more variation within a single population of the outcrossing C. remanei. Although there are a large number of substitutions at silent sites within odr-3 among the three species, molecular evolution at the protein level is extremely conserved, suggesting that odr-3 plays an important role in cell signalling during chemosensation and/or neuronal cilia development in C. remanei and in C. briggsae as it does in C. elegans. Our results suggest that C. remanei may be a more suitable subject for ecological and evolutionary genetic studies than C. elegans. ------------------- Key: 5815 Medline: 12686594 Authors: McMahon L;Muriel JM;Roberts B;Quinn M;Johnstone IL Title: Two sets of interacting collagens from functionally distinct substructures within a Caenorhabditis elegans extracellular matrix. Citation: Molecular Biology of the Cell 14: 1366-1378 2003 Type: ARTICLE Genes: dpy-2 dpy-3 dpy-5 dpy-7 dpy-8 dpy-10 dpy-13 rol-6 sqt-1 sqt-3 Abstract: A ubiquitous feature of collagens is protein interaction, the trimerization of monomers to form a triple helix followed by higher order interactions during the formation of the mature extracellular matrix. The Caenorhabditis elegans cuticle is a complex extracellular matrix consisting predominantly of cuticle collagens, which are encoded by a family of similar to154 genes. We identify two discrete interacting sets of collagens and show that they form functionally distinct matrix substructures. We show that mutation in or RNA-mediated interference of a gene encoding a collagen belonging to one interacting set affects the assembly of other members of that set, but not those belonging to the other set. During cuticle synthesis, the collagen genes are expressed in a distinct temporal series, which we hypothesize exists to facilitate partner finding and the formation of appropriate interactions between encoded collagens. Consistent with this hypothesis, we find for the two identified interacting sets that the individual members of each set are temporally coexpressed, whereas the two sets are expressed similar to2 h apart during matrix synthesis. ------------------- Key: 5816 Medline: 12686618 Authors: Hoppe PE;Andrews RC;Parikh PD Title: Differential requirement for the nonhelical tailpiece and the C terminus of the myosin rod in Caenorhabditis elegans muscle. Citation: Molecular Biology of the Cell 14: 1677-1690 2003 Type: ARTICLE Genes: myo-3 unc-54 eDf1 Abstract: Myosin heavy chain (MHC) is a large, multidomain protein important for both cellular structure and contraction. To examine the functional role of two C-terminal domains, the end of the coiled-coil rod and the nonhelical tailpiece, we have generated constructs in which residues within these domains are removed or mutated, and examined their behavior in Caenorhabditis elegans striated muscle. Genetic tests demonstrate that MHC lacking only tailpiece residues is competent to support the timely onset of embryonic contractions, and therefore viability, in animals lacking full-length MHC. Antibody staining experiments show that this truncated molecule localizes as wild type in early stages of development, but may be defective in processes important for thick filament organization later in embryogenesis. Ultrastructural analysis reveals thick filaments of normal morphology in disorganized arrangement, as well as occasional abnormal assemblages. In contrast, molecules in which the four terminal residues of the coiled coil are absent or mutated fail to rescue animals lacking endogenous MHC. Loss of these four residues is associated with delayed protein localization and delayed contractile function during early embryogenesis. Our results suggest that these two MHC domains, the rod and the tailpiece, are required for distinct steps during muscle development. ------------------- Key: 5817 Medline: 12618005 Authors: Munoz MJ Title: Longevity and heat stress regulation in Caenorhabditis elegans. Citation: Mechanisms of Ageing & Development 124: 43-48 2003 Type: REVIEW Genes: aap-1 age-1 akt-1 akt-2 clk-1 daf-2 daf-9 daf-12 daf-16 eat-2 glp-1 mes-1 old-1 pdk-1 Abstract: Aging is the most complex phenotype for a multicellular organism. This process is now being under severe investigation. Here I will review the different processes known to affect longevity in the nematode Caenorhabditis elegans and their relationship with thermotolerance. All the longevity mutants that have been tested so far show an increase in stress resistance. In particular, long-lived mutants affected in the IGF/insulin pathway and those affected in the germ-line formation are both thermotolerant and long-lived. The mechanisms that activate the stress resistance are now been understood including the DAF-16 fork head transcription factor transport to the nucleus and the activation of genes involved in the defense to stress. The high correlation between stress resistance and longevity suggests that the same molecular activities that defend the cell from stress can defend the cell from the damage caused by aging. ------------------- Key: 5818 Medline: 12679144 Authors: Roeder T Title: Metabotropic histamine receptors - nothing for invertebrates? Citation: European Journal of Pharmacology 466: 85-90 2003 Type: REVIEW Genes: gar-1 gar-2 gar-3 Abstract: Histamine, a major neurotransmitter both in vertebrates and invertebrates, transmits its actions through a set of well-known receptors. In vertebrates, these receptors belong to the family of G-protein-coupled receptors. In invertebrates, the few well-characterized actions of histamine are transmitted through ionotropic histamine receptors. To evaluate if metabotropic histamine receptors are part of the invertebrate histaminergic signaling cascade, I identified the complete set of metabotropic bioamine receptors from two invertebrates, whose entire genome has been sequenced: the fruitfly Drosophila melanogaster and the soil nematode Caenorhabditis elegans. A comparison with representatives of all groups of metabotropic bioamine receptors from vertebrates and invertebrates showed that none of these receptors clusters together with any of the four groups of vertebrate histamine receptors. This implies that no direct homologues to vertebrate metabotropic histamine receptor are present in invertebrates. Therefore, it is reasonable to account that the histaminergic neurotransmission in invertebrates is exclusively transmitted through ionotropic histamine receptors and that metabotropic histamine receptors evolved after the split between vertebrates and invertebrates. ------------------- Key: 5819 Medline: 12660152 Authors: Kurz CL;Chauvet S;Andres E;Aurouze M;Vallet I;Michel GPF;Uh M;Celli J;Filloux A;de Bentzmann S;Steinmetz I;Hoffmann JA;Finlay BB;Gorvel JP;Ferrandon D;Ewbank JJ Title: Virulence factors of the human opportunistic pathogen Serratia marcenscens identified by in vivo screening. Citation: EMBO Journal 22: 1451-1460 2003 Type: ARTICLE Genes: Abstract: The human opportunistic pathogen Serratia marcescens is a bacterium with a broad host range, and represents a growing problem for public health. Serratia marcescens kills Caenorhabditis elegans after colonizing the nematode's intestine. We used C. elegans to screen a bank of transposon-induced S. marcescens mutants and isolated 23 clones with an attenuated virulence. Nine of the selected bacterial clones also showed a reduced virulence in an insect model of infection. Of these, three exhibited a reduced cytotoxicity in vitro, and among them one was also markedly attenuated in its virulence in a murine lung infection model. For 21 of the 23 mutants, the transposon insertion site was identified. This revealed that among the genes necessary for full in vivo virulence are those that function in lipopolysaccharide (LPS) biosynthesis, iron uptake and hemolysin production. Using this system we also identified novel conserved virulence factors required for Pseudomonas aeruginosa pathogenicity. This study extends the utility of C. elegans as an in vivo model for the study of bacterial virulence and advances the molecular understanding of S. marcescens pathogenicity. ------------------- Key: 5820 Medline: 12648677 Authors: Grant BD;Wilkinson HA Title: Functional genomic maps in Caenorhabditis elegans. Citation: Current Opinion in Cell Biology 15: 206-212 2003 Type: REVIEW Genes: fem-1 fem-3 glp-4 mec-3 mec-17 mre-11 mrt-2 rad-51 rrf-3 syp-1 syp-2 syp-3 Abstract: The completion of the Caenorhabditis elegans genome sequence was the initial step toward the use of whole-genome analysis in this model organism. Advances in C. elegans genomics include transcript profiling, gene-function screens using RNA-mediated interference, and protein-interaction mapping using the yeast two-hybrid system. Recent reports have employed these methods to gain new insights into diverse biological problems such as tissue-specific gene expression, cell-fate specification, genome organization, the DNA damage response, and early embryonic development. These studies combined genomic approaches to probe complex biological pathways on an ------------------- Key: 5821 Medline: 12729220 Authors: Boyd WA;Williams PL Title: Availability of metals to the nematode Caenorhabditis elegans: toxicity based on total concentrations in soil and extracted fractions. Citation: Environmental Toxicology and Chemistry 22: 1100-1106 2003 Type: ARTICLE Genes: Abstract: Current regulation of metals in soils is based on total metal concentrations rather than on actual exposure concentrations. Considering the extreme variation in soil physicochemical properties, total concentrations are not reflective of the availability and resultant toxicity of metals in different soils. In this study, the availability of Cd, Cu, Ni, Pb, and Zn to the free-living soil nematode Caenorhabditis elegans was assessed after 24-h exposure in three soils using a sequential soil extraction procedure. Albany soil, sampled from southern Georgia, USA, is characterized by a high sand content, whereas Cecil soil from the Piedmont region of Georgia contains higher fractions of clay and organic matter. The final soil was an American Society for Testing and Materials (ASTM) artificial medium composed of peat, kaolin clay, sand, and calcium carbonate. Based on their compositions, ASTM medium would sorb metals most strongly and Albany soil the least strongly. In fact, 24-h lethal concentrations to 50% (LC50s) of nematodes for the five metals as determined by the total metal concentration followed this trend. In addition, water-extractable metals were lowest in ASTM medium and highest in Albany soil when spiked at the same concentrations. Our data show the need to consider soil type when performing toxicological tests and establishing site-specific metal concentrations in soil. ------------------- Key: 5822 Medline: 12702662 Authors: Ogura K;Kishimoto N;Mitani S;Gengyo-Ando K;Kohara Y Title: Translational control of maternal glp-1 mRNA by POS-1 and its interacting protein SPN-4 in Caenorhabditis elegans. Citation: Development 130: 2495-2503 2003 Type: ARTICLE Genes: glp-1 let-92 pos-1 spn-4 Abstract: The translation of maternal glp-1 mRNAs is regulated temporally and spatially in C elegans embryos. The 3' UTR (untranslated region) of the maternal glp-1 mRNA is important for both kinds of regulation. The spatial control region is required to suppress translation in the posterior blastomeres. The temporal one is required to suppress translation in oocytes and one-cell stage embryos. We show that a CCCH zinc-finger protein, POS-1, represses glp-1 mRNA translation by binding to the spatial control region. We identified an RNP-type RNA-binding protein, SPN-4, as a POS-1-interacting protein. SPN-4 is present developmentally from the oocyte to the early embryo and its distribution overlaps with that of POS-1 in the cytoplasm and P granules of the posterior blastomeres. SPN-4 binds to a subregion of the temporal control region in the 3' UTR and is required for the translation of glp-1 mRNA in the anterior blastomeres. We propose that the balance between POS-1 and SPN-4 controls the translation of maternal glp-1 mRNA. ------------------- Key: 5823 Medline: 12620985 Authors: Shakes DC;Sadler PL;Schumacher JM;Abdolrasulnia M;Golden A Title: Developmental defects observed in hypomorphic anaphase-promoting complex mutants are linked to cell cycle abnormalities. Citation: Development 130: 1605-1620 2003 Type: ARTICLE Genes: apc-1 apc-3 apc-4 apc-6 apc-8 cdc-16 cdc-23 cdc-27 emb-27 emb-30 mat-1 mat-2 mat-3 Abstract: sIn C elegans, mutants in the anaphase-promoting complex or cyclosome (APC/C) exhibit defects in germline proliferation, the formation of the vulva and male tail, and the metaphase to anaphase transition of meiosis I. Oocytes lacking APC/C activity can be fertilized but arrest in metaphase of meiosis I and are blocked from further development. To examine the cell cycle and developmental consequences of reducing but not fully depleting APC/C activity, we analyzed defects in embryos and larvae of mat1/cdc-27 mutants grown at semi-permissive temperatures. Hypomorphic embryos developed to the multicellular stage but were slow to complete meiosis I and displayed aberrant meiotic chromosome separation. More severely affected embryos skipped meiosis 11 altogether and exhibited striking defects in meiotic exit. These latter embryos failed to produce normal eggshells or establish normal asymmetries prior to the first mitotic division. In developing larvae, extended M-phase delays in late-dividing cell lineages were associated with defects in the morphogenesis of the male tail. This study reveals the importance of dosage-specific mutants in analyzing molecular functions of a ubiquitously functioning protein within different cell types and tissues, and striking correlations between specific abnormalities in cell cycle ------------------- Key: 5824 Medline: 12679387 Authors: Ono K;Parast M;Alberico C;Benian GM;Ono S Title: Specific requirement for two ADF/cofilin isoforms in distinct actin-dependent processes in Caenorhabditis elegans. Citation: Journal of Cell Science 116: 2073-2085 2003 Type: ARTICLE Genes: sup-12 unc-60 Abstract: Actin depolymerizing factor (ADF)/cofflin is an essential enhancer of actin turnover. Multicellular organisms express multiple ADF/cofilin isoforms in different patterns of tissue distribution. However, the functional significance of different ADF/cofilin isoforms is not understood. The Caenorhabdifis elegans unc-60 gene generates two ADF/cofilins, UNC-60A and UNC-60B, by alternative splicing. These two ADF/cofilin proteins have different effects on actin dynamics in vitro, but their functional difference in vivo remains unclear. Here, we demonstrate that the two isoforms are expressed in different tissues and are required for distinct morphogenetic processes. UNC-60A was ubiquitously expressed in most embryonic cells and enriched in adult gonads, intestine and oocytes. In contrast, UNC-60B was specifically expressed in the body wall muscle, vulva and spermatheca. RNA interference of UNC-60A caused embryonic lethality with variable defects in cytokinesis and developmental patterning. In severely affected embryos, a cleavage furrow was formed and progressed but reversed before completion of the cleavage. Also, in some affected embryos, positioning of the blastomeres became abnormal, which resulted in embryonic arrest. In contrast, an unc-60B-null mutant was homozygous viable, underwent normal early embryogenesis and caused disorganization of actin filaments specifically in body wall muscle. These results suggest that the ADF/cofilin isoforms play distinct roles in specific aspects of actin reorganization in vivo. ------------------- Key: 5825 Medline: 12672692 Authors: Lim LP;Lau NC;Weinstein EG;Abdelhakim A;Yekta S;Rhoades MW;Burge CB;Bartel DP Title: The microRNAs of Caenorhabditis elegans. Citation: Genes & Development 17: 991-1008 2003 Type: ARTICLE Genes: Abstract: MicroRNAs (miRNAs) are an abundant class of tiny RNAs thought to regulate the expression of protein-coding genes in plants and animals. In the present study, we describe a computational procedure to identify miRNA genes conserved in more than one genome. Applying this program, known as MiRscan, together with molecular identification and validation methods, we have identified most of the miRNA genes in the nematode Caenorhabditis elegans. The total number of validated miRNA genes stands at 88, with no more than 35 genes remaining to be detected or validated. These 88 miRNA genes represent 48 gene families; 46 of these families (comprising 86 of the 88 genes) are conserved in Caenorhabditis briggsae, and 22 families are conserved in humans. More than a third of the worm miRNAs, including newly identified members of the lin-4 and let-7 gene families, are differentially expressed during larval development, suggesting a role for these miRNAs in mediating larval developmental transitions. Most are present at very high steady-state levels-more than 1000 molecules per cell, with some exceeding 50,000 molecules per cell. Our census of the worm miRNAs and their expression patterns helps define this class of noncoding RNAs, lays the groundwork for functional studies, and provides the tools for more comprehensive analyses of miRNA ------------------- Key: 5826 Medline: 12672694 Authors: Luz JG;Hassig CA;Pickle C;Godzik A;Meyer BJ;Wilson IA Title: XOL-1, primary determinant of sexual fate in C. elegans, is a GHMP kinase family member and a structural prototype for a calss of developmental regulators. Citation: Genes & Development 17: 977-990 2003 Type: ARTICLE Genes: xol-1 Abstract: In Caenorhabditis elegans, an X chromosome-counting mechanism specifies sexual fate. Specific genes termed X-signal elements, which are present on the X chromosome, act in a concerted dose-dependent fashion to regulate levels of the developmental switch gene xol-1. In turn, xol-1 levels determine sexual fate and the activation state of the dosage compensation mechanism. The crystal structure of the XOL-1 protein at 1.55 Angstrom resolution unexpectedly reveals that xol-1 encodes a GHMP kinase family member, despite sequence identity of 10% or less. Because GHMP kinases, thus far, have only been characterized as small molecule kinases involved in metabolic pathways, for example, amino acid and cholesterol synthesis, XOL-1 is the first member that controls nonmetabolic processes. Biochemical investigations demonstrated that XOL-1 does not bind ATP under standard conditions, suggesting that XOL-1 acts by a mechanism distinct from that of other GHMP kinases. In addition, we have cloned a XOL-1 ortholog from Caenorhabditis briggsae, a related nematode that diverged from C. elegans similar to50-100 million years ago. These findings demonstrate an unanticipated role for GHMP kinase family members as mediators of sexual differentiation and dosage compensation and, possibly, other aspects of differentiation and ------------------- Key: 5827 Medline: 12725727 Authors: Labbe JC;Maddox PS;Salmon ED;Goldstein B Title: PAR proteins regulate microtubule dynamics at the cell cortex in C. elegans. Citation: Current Biology 13: 707-714 2003 Type: ARTICLE Genes: goa-1 gpa-16 par-1 par-2 par-3 Abstract: Background: The PAR proteins are known to be localized asymmetrically in polarized C. elegans, Drosophila and human cells and to participate in several cellula; processes, including asymmetric cell division and spindle orientation. Although astral microtubules are known to play roles in these processes, their behavior during these events remains poorly understood. Results: We have developed a method that makes it possible to examine the residence time of individual astral microtubules at the cell cortex of developing embryos. Using this method, we found that microtubules are more dynamic at the posterior cortex of the C. elegans embryo compared to the anterior cortex during spindle displacement. We further observed that this asymmetry depends on the PAR-3 protein and heterotrimeric G protein signaling, and that the PAR-2 protein affects microtubule dynamics by restricting PAR-3 activity to the anterior of the embryo. Conclusions: These results indicate that PAR proteins function to regulate microtubule dynamics at the cortex during microtubule-dependent cellular processes. ------------------- Key: 5828 Medline: 12684533 Authors: Liu J;Lee KK;Segura-Totten M;Neufeld E;Wilson KL;Gruenbaum Title: MAN1 and emerin have overlapping function(s) essential for chromosome segregation and cell division in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 100: 4598-4603 2003 Type: ARTICLE Genes: emr-1 lem-2 lmn-1 Abstract: Emerin and MAN1 are LEM domain-containing integral membrane proteins of the vertebrate nuclear envelope. The function of MAN1 is unknown, whereas emerin is known to interact with nuclear lamins, barrier-to-auto integration factor (BAF), nesprin-1alpha, and a transcription repressor. Mutations in emerin cause X-linked recessive Emery-Dreifuss muscular dystrophy. Emerin and MAN1 homologs are both conserved in Caenorhabditis elegans, but loss of Ce-emerin has no detectable phenotype. We therefore used C elegans to test the hypothesis that Ce-MAN1 overlaps functionally with Ce-emerin. Supporting this model, Ce-MAN1 interacted directly with Ce-lamin and Ce-BAF in vitro and required Ce-lamin for its nuclear envelope localization. Interestingly, RNA interference-mediated removal of approximate to90% of Ce-MAN1 was lethal to approximate to15% of embryos. However, in the absence of Ce-emerin, approximate to90% reduction of Ce-MAN1 was lethal to all embryos by the 100-cell stage, with a phenotype involving repeated cycles of anaphase chromosome bridging and cytokinesis ["cell untimely torn" (cut) phenotype]. Immunostaining showed that the anaphase-bridged chromatin specifically retained a mitosis-specific phosphohistone H3 epitope and failed to recruit detectable Ce-lamin or Ce-BAF. These findings show that LEM domain proteins are essential for cell division and that Ce-emerin and Ce-MAN1 share at least one and possibly multiple overlapping functions, which may be relevant to Emery-Dreifuss muscular ------------------- Key: 5829 Medline: 12684004 Authors: Lee JI;Dhakal BK;Lee J;Bandyopadhyay J;Jeong SY;Eom SH;Kim DH;Ahnn J Title: The Caenorhabditis elegans homologue of Down Syndrome critical region 1, RCN-1, inhibits multiple functions of the phosphatase calcineurin. Citation: Journal of Molecular Biology 328: 147-156 2003 Type: ARTICLE Genes: cna-1 cnb-1 rcn-1 tax-6 Abstract: A conserved family of calcineurin-regulating proteins whose members have been implicated in several disease models such as Down syndrome, Alzheimer's disease, and cardiac hypertrophy has been identified in several organisms including yeast, mice, and humans. We have characterized Caenorhabditis elegans rcn-1, which belongs to this family of calcineurin regulators, and shows approximately 40% identity with the human homologue DSCR-1. rcn-1 is expressed in hypodermal cells, nerve cords and various neurons, vulva epithelial and muscle cells, marginal cells of the pharynx,. and structures of the male tail. rcn-1 expression is upregulated by calcineurin activity. RCN-1 binds to calcineurin A from C. elegans lysate in a calcium-dependent manner, and inhibits bovine calcineurin phosphatase activity dose-dependently. In addition, overexpression of RCN-1 results in calcineurin-deficient phenotypes such as small body size, cuticle defects, fertility defects, slow growth, and serotonin-resistant egg-laying defects. Moreover, phenotypes observed in gain-of-function calcineurin mutant animals were restored to normal by RCN-1 overexpression. These results demostrate an effective and specific inhibition of calcineurin in vitro as well as in vivo by RCN-1. ------------------- Key: 5830 Medline: 12695495 Authors: Severson AF;Bowerman B Title: Myosin and the PAR proteins polarize microfilament-dependent forces that shape and position mitotic spindles in Caenorhabditis elegans. Citation: Journal of Cell Biology 161: 21-26 2003 Type: ARTICLE Genes: dnc-1 mlc-4 nmy-2 par-2 par-3 pfn-1 Abstract: In Caenorhabditis elegans, the partitioning proteins (PARs), microfilaments (MFs), dynein, dynactin, and a nonmuscle myosin 11 all localize to the cortex of early embryonic cells. Both the PARs and the actomyosin cytoskeleton are required to polarize the anterior-posterior (a-p) body axis in one-cell zygotes, but it remains unknown how MFs influence embryonic polarity. Here we show that MFs are required for the cortical localization of PAR-2 and PAR-3. Furthermore, we show that PAR polarity regulates MF-dependent cortical forces applied to astral microtubules (MTs). These forces, which appear to be mediated by dynein and dynactin, produce changes in the shape and orientation of mitotic spindles. Unlike MFs, dynein, and dynactin, myosin 11 is not required for the production of these forces. Instead, myosin influences embryonic polarity by limiting PAR-3 to the anterior cortex. This in turn produces asymmetry in the forces applied to MTs at each pole and allows PAR-2 to accumulate in the posterior cortex of a one-cell zygote and maintain ------------------- Key: 5831 Medline: 12670516 Authors: Boag PR;Ren P;Newton SE;Gasser RB Title: Molecular characterisation of a male-specific serine/threonine phsophatase from Oesophagostomum dentatum (Nematoda: Strongylida), and functional analysis of homologues in Caenorhabditis elegans. Citation: International Journal for Parasitology 33: 313-325 2003 Type: ARTICLE Genes: Abstract: A male-specifically expressed sequence tag was used as a probe to screen adult male Oesophagostomum dentatum (Nematoda: Strongylida) gene libraries. The cDNA clones isolated coded for a serine/threonine protein phosphatase with similar to85% identity to two Caenorhabditis elegans proteins implicated in reproduction. However. the genomic structures for the two species were distinct, in that the O. dentatum gene contained seven introns, whereas the C. elegans homologues contained three (two of which were conserved between the two nematodes). The promoters of all three nematode genes contained two putative GATA motifs separated by six to seven nucleotides and located within 100 nucleotides of the predicted transcriptional start site. RNA interference (RNAi) experiments in C. elegans. targetting the two homologues, revealed a consistent reduction in the number of progeny produced by treated worms, indicating a functional role in reproduction. Expression of green fluorescent protein, directed by the putative promoters for the C. elegans phosphatase genes, was analysed in transgenic C. elegans. The present results suggest that there is a significant degree of conservation between O. dentatum and C. elegans in the features and function of the serine/threonine protein phosphatase characterised, which should have implications for detailed investigations into molecular reproductive processes of some parasitic nematodes. ------------------- Key: 5832 Medline: 12679102 Authors: Zhao X;Sawa H;Herman MA Title: tcl-2 encodes a novel protein that acts synergistically with Wnt signaling pathways in C. elegans. Citation: Developmental Biology 256: 276-289 2003 Type: ARTICLE Genes: let-23 lin-17 lin-44 lit-1 pop-1 sys-1 tcl-2 tlp-1 Abstract: Mutations in tcl-2 cause defects in the specification of the fates of the descendants of the TL and TR blast cells, whose polarity is regulated by lin-44/Wnt and lin-17/frizzled, during Caenorhabditis elegans development. In wild-type animals, POP-1/TCF/LEF, is asymmetrically distributed to the T cell daughters, resulting in a higher level of POP-1 in the nucleus of the anterior daughter. The POP-1 asymmetric distribution is controlled by lin-44 and lin-17. However, in tcl-2 mutants, POP-1 is equally distributed to T cell daughters as is observed in lin-17 mutants, indicating that, like lin-17, tcl-2 functions upstream of pop-L In addition, tcl-2 mutations cause defects in the development of the gonad and the specification of fate of the posterior daughter of the P12 cell, both of which are controlled by the Wnt pathway. Double mutant analyses indicate that tcl-2 can act synergistically with the Wnt pathway to control gonad development as well as P12 descendant cell fate specification. tcl-2 encodes a novel protein. A functional tcl-2::gfp construct was weakly expressed in the nuclei of the T cell and its descendants. Our results suggest that tcl-2 functions with Wnt pathways to control T cell fate specification, gonad development, and P12 cell fate ------------------- Key: 5833 Medline: 12679103 Authors: Fujita M;Hawkinson D;King KV;Hall DH;Sakamoto H;Buechner M Title: The role of the ELAV homologue EXC-7 in the development of the Caenorhabditis elegans excretory canals. Citation: Developmental Biology 256: 290-301 2003 Type: ARTICLE Genes: exc-3 exc-6 exc-7 sma-1 Abstract: The exc mutations of Caenorhabditis elegans alter the position and shape of the apical cytoskeleton in polarized epithelial cells. Mutants in exc-7 form small cysts throughout the tubular excretory canals that regulate organismal osmolarity. We have cloned the exc-7 gene, the closest nematode homologue to the neural RNA-binding protein ELAV. EXC-7 is expressed in the canal for a short time midway through embryogenesis. Cysts in exc-7 mutants do not develop until several hours later, beginning at the time of hatching. We find that the first larval period is when the canal completes the majority of its outgrowth, and adds new apical cytoskeleton at a rapid rate. Ultrastructural studies show that exc-7 mutant defects resemble loss of beta(H)-spectrin (encoded by sma-1) at the distal ends of the excretory canals. In addition, exc-7 mutants exhibit synergistic excretory canal defects with mutations in sma-1, and EXC-7 binds sma-1 mRNA. These data imply that EXC-7 protein may affect expression of sma-1 and other genes to effect proper development of the excretory ------------------- Key: 5834 Medline: 12679110 Authors: Hahn AC;Emmons SW Title: The roles of an ephrin and a semaphorin in patterning cell-cell contacts in C. elegans sensory organ development. Citation: Developmental Biology 256: 379-388 2003 Type: ARTICLE Genes: egl-5 efn-4 mab-5 mab-18 mab-20 sma-6 vab-1 Abstract: Ephrins and semaphorins regulate a wide variety of developmental processes, including axon guidance and cell migration. We have studied the roles of the ephrin EFN-4 and the semaphorin MAB-20 in patterning cell-cell contacts among the cells that give rise to the ray sensory organs of Caenorhabditis elegans. In wild-type, contacts at adherens junctions form only between cells belonging to the same ray. In efn-4 and mab-20 mutants, ectopic contacts form between cells belonging to different rays. Ectopic contacts also occur in mutants in regulatory genes that specify ray morphological identity. We used efn-4 and mab-20 reporters to investigate whether these ray identity genes function through activating expression of efn-4 or mab-20 in ray cells. mab-20 reporter expression in ray cells was unaffected by mutants in the Pax6 homolog mab-18 and the Hox genes egl-5 and mab-5, suggesting that these genes do not regulate mab-20 expression. We find that mab-18 is necessary for activating efn-4 reporter expression, but this activity alone is not sufficient to account for mab-18 function in controlling cell-cell contact formation. In egl-5 mutants, efn-4 reporter expression in certain ray cells was increased, inconsistent with a simple repulsion model for efn-4 action. The evidence indicates that ray identity genes primarily regulate ray morphogenesis by pathways other than through regulation of expression of ------------------- Key: 5835 Medline: 12679112 Authors: Starich TA;Miller A;Nguyen RL;Hall DH;Shaw JE Title: The Caenorhabditis elegans innexin INX-3 is localized to gap junctions and is essential for embryonic development. Citation: Developmental Biology 256: 403-417 2003 Type: ARTICLE Genes: inx-3 lwDf11 lwDf12 stDf1 mnDp30 Abstract: Innexins are the proposed structural components of gap junctions in invertebrates. Antibodies that specifically recognize the Caenorhabditis elegans innexin protein INX-3 were generated and used to examine the patterns of inx-3 gene expression and the subcellular sites of INX-3 localization. INX-3 is first detected in two-cell embryos, concentrated at the intercellular interface, and is expressed ubiquitously throughout the cellular proliferation phase of embryogenesis. During embryonic morphogenesis, INX-3 expression becomes more restricted. Postembryonically, INX-3 is expressed transiently in several cell types, while expression in the posterior pharynx persists throughout development. Through immuno-EM techniques, INX-3 was observed at gap junctions in the adult pharynx, providing supporting evidence that innexins are components of gap junctions. An inx-3 mutant was isolated through a combined genetic and immunocytochemical screen. Homozygous inx-3 mutants exhibit defects during embryonic morphogenesis. At the comma stage of early morphogenesis, variable numbers of cells are lost from the anterior of inx-3(lw68) mutants. A range of terminal defects is seen later in embryogenesis, including localized rupture of the hypodermis, failure of the midbody to elongate properly, abnormal contacts between hypodermal cells, and failure of the pharynx to attach to the anterior ------------------- Key: 5836 Medline: 12820649 Authors: Massie MR;Lapoczka EM;Boggs KD;Stine KE;White GE Title: Exposure to the metabolic inhibitor sodium azide induces stress protein expression and thermotolerance in the nematode Caenorhabditis elegans. Citation: Cell Stress & Chaperones 8: 1-7 2003 Type: ARTICLE Genes: daf-2 daf-7 daf-14 daf-21 Abstract: Historically, sodium azide has been used to anesthetize the nematode Caenorhabditis elegans; however, the mechanism by Which it survives this exposure is not understood. In this study, we report that exposure of Wild-type C elegans to 10 mM sodium azide for up to 90 minutes confers thermotolerance (defined as significantly increased survival probability [SP] at 37degreesC) on the animal. In addition, sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed enhanced Hsp70 expression, whereas Western blot analysis revealed the induction of Hsp16. We also tested the only known C elegans Hsp mutant daf-21 (codes for H sp90), which constitutively enters the stress-resistant state known as the dauer larvae. Daf-21 mutants also acquire sodium azide-induced thermotolerance, whereas 3 non-Hsp, constitutive dauer-forming mutants exhibited a variable response to azide exposure. We conclude that the ability of C elegans to survive exposure to azide is associated with the induction of at least 2 ------------------- Key: 5837 Medline: 12820659 Authors: David CL;Smith HE;Raynes DA;Pulcini EJ;Whitesell L Title: Expression of a unique drug-resistant Hsp90 ortholog by the nematode Caenorhabditis elegans. Citation: Cell Stress & Chaperones 8: 93-104 2003 Type: ARTICLE Genes: daf-21 Abstract: In all species studied to date, the function of heat shock protein 90 (Hsp90), a ubiquitous and evolutionarily conserved molecular chaperone, is inhibited selectively by the natural product drugs geldanamycin (GA) and radicicol. Crystal structures of the N-terminal region of yeast and human Hsp90 have revealed that these compounds interact with the chaperone in a Bergerat-type adenine nucleotide-binding fold shared throughout the gyrase, Hsp90, histidine kinase mutL (GHKL) superfamily of adenosine triphosphatases. To better understand the consequences of disrupting Hsp90 function in a genetically tractable multicellular organism, we exposed the soil-dwelling nematode Caenorhabditis elegans to GA under a variety of conditions designed to optimize drug uptake. Mutations in the gene encoding C elegans Hsp90 affect larval viability, dauer development, fertility, and life span. However, exposure of worms to GA produced no discernable phenotypes, although the amino acid sequence of worm Hsp90 is 85% homologous to that of human Hsp90. Consistent with this observation, we found that solid phase-immobilized GA failed to bind worm Hsp90 from worm protein extracts or when translated in a rabbit reticulocyte lysate system. Further, affinity precipitation studies using chimeric worm-vertebrate fusion proteins or worm C-terminal truncations expressed in reticulocyte lysate revealed that the conserved nucleotide-binding fold of worm Hsp90 exhibits the novel ability to bind adenosine triphosphate but not GA. Despite its unusual GA resistance, worm Hsp90 appeared fully functional when expressed in a vertebrate background. It heterodimerized with its vertebrate counterpart and showed no-evidence of compromising its essential cellular functions. Heterologous expression of worm Hsp90 in tumor cells, however, did not render them GA resistant. These findings provide new insights into the nature of unusual N-terminal nucleotide-binding fold of Hsp90 and suggest that ------------------- Key: 5838 Medline: 12691982 Authors: Kajita A;Yamamura M;Kohara Y Title: Computer simulation of the cellular arrangement using physical model in early cleavage of the nematode Caenorhabditis elegans. Citation: Bioinformatics 19: 704-716 2003 Type: ARTICLE Genes: Abstract: Motivation: The ultimate goal of bioinformatics is to reconstruct biological systems in the computer. Since biological systems have many levels, it is important to focus on an appropriate level. In our first application of computer modeling to the early development of the nematode Caenorhabditis elegans, we focus on the cellular arrangement in early embryos. This plays a very important role in cell fate determination by cell-cell interaction, and is regarded as a system, one level higher than the system of gene regulation within cells. It is largely restricted by physical conditions that seemed feasible to model by computer. Results: We constructed a computer model of the C.elegans embryo, currently up to the 4-cell stage, using a deformable and dividable triangulated network. The model is based solely on cellular-level dynamics. We found that the optimal ranges of three parameters that affect the elongation of dividing cells led, in computer simulations, to almost the same cellular arrangements as in real embryos. The nature of the model and the relationship with real embryos are discussed. ------------------- Key: 5839 Medline: 12653634 Authors: Turnbull J;Drummond K;Huang Z;Kinnunen T;Ford-Perriss M;Murphy M;Guimond S Title: Heparan sulphate sulphotransferase expression in mice and Caenorhabditis elegans. Citation: Biochemical Society Transactions 31: 343-348 2003 Type: ARTICLE Genes: hst-1 hst-2 hst-3 hst-6 rib-2 sqv-1 sqv-3 sqv-4 sqv-7 sqv-8 Abstract: Heparan sulphate (HS) acts as a multifunctional cell regulator, with specific sulphated saccharide sequences designed for selective interactions with many proteins. Functionally, these interactions result in regulation of the protein activities, and there is growing evidence that cells can dynamically alter the structure of HS sequences that they display. HS biosynthesis involves the action of a complex set of enzymes with polymerase, epimerase and sulphotransferase (ST) activities. in higher organisms, multiple isoforms of STs decorate the nascent HS chains with specific patterns of sulphation that confer selective biological functions. The study of HSSTs in model organisms provides a valuable opportunity to examine the expression of these enzymes in relation to the structure and activities of the HS produced. Here we describe that, in mice, there are stage-specific combinations of HSST isoenzymes that underlie the synthesis of different HS species at different times in the developing brain. This differential expression of HSSTs results in the synthesis of structurally variant HS species that form functional signalling complexes with specific fibroblast growth factors and their receptors. Regulated synthesis of specific HS species could be a mechanism for the regulation of proliferation and differentiation in the developing brain. We also describe evidence that a Coenorhabditis elegans orthologue of the mammalian 20ST enzyme, called HST-2, is essential for the normal development of this nematode. Together, these studies emphasize the importance of HSSTs in the biosynthesis of functionally variant HS proteoglycans, and demonstrate the importance of these complex regulatory molecules in developmental processes. ------------------- Key: 5840 Medline: 12711920 Authors: Kayser EB;Hoppel CL;Morgan PG;Sedensky MM Title: A mutation in mitochondrial complex I increases ethanol sensitivity in Caenorhabditis elegans. Citation: Alcoholism: Clinical and Experimental Research 27: 584-592 2003 Type: ARTICLE Genes: gas-1 Abstract: Background: The gene gas-1 encodes the 49-kDa subunit of complex I of the mitochondrial electron transport chain in Caenorhabditis elegans. A mutation in gas-1 profoundly increases sensitivity to ethanol and decreases complex I-dependent metabolism in mitochondria. Methods: Mitochondria were isolated from wild-type and, gas-1 strains of C. elegans. The effects of ethanol on complex I-, ll-, and III-dependent oxidative phosphorylation were measured for mitochondria from each strain. Reversibility of the effects of ethanol was determined by measuring oxidative phosphorylation after removal of mitochondria from 1.5 M ethanol. The effects of ethanol on mitochondrial structure were visualized with electron microscopy. Results: We found that ethanol inhibited complex I-, II-, and III-dependent oxidative phosphorylation in isolated wild-type mitochondria at concentrations that immobilize intact worms. It is important to note that the inhibitory effects of ethanol on mitochondria from either C. elegans or rat skeletal muscle were reversible even at molar concentrations. Complex I activity was lower in mitochondria from gas-1 animals than in mitochondria from wild-type animals at equal ethanol concentrations. Complex II activity was higher in gas-1 than in wild-type mitochondria at all concentrations of ethanol. No difference was seen between the strains in the sensitivity of complex III to ethanol. Conclusions: The difference in ethanol sensitivities between gas-1 and wild-type nematodes results solely from altered complex I function. At the respective concentrations of ethanol that immobilize whole animals, mitochondria from each strain of worms displayed identical rates of complex I-dependent state 3 respiration. We conclude that a threshold value of complex I activity controls the transition from mobility to immobility of C. ------------------- Key: 5841 Medline: 12710960 Authors: Cui M;Han M Title: Cis regulatory requirements for vulval cell-specific expression of the Caenorhabditis elegans fibroblast growth factor gene egl-17. Citation: Developmental Biology 257: 104-116 2003 Type: ARTICLE Genes: cog-2 eff-1 egl-17 lin-1 lin-31 lin-39 pop-1 Abstract: The Caenorhabditis elegans EGL-17/FGF protein is involved in the gonadal signaling that guides the migrations of sex myoblasts (SMs). egl-17::GFP reporter constructs are expressed dynamically in vulval cell lineages. Expression in the primary vulval cells is correlated with the precise positioning of SMs. We have investigated the cis-regulatory requirements for cell- and stage-specific expression of egl-17. Three enhancer elements that specify the expression of the egl-17::GFP reporter gene in primary or secondary vulval cells at certain stages were identified. Sequence analysis has suggested a number of potential transcription factor binding sites within the enhancer elements. egl-17 is most likely a direct target of the LIN-39 Hox protein because mutations either in the lin-39/hox gene or at the consensus HOX/PBC binding site within the distal enhancer of the egl-17 gene eliminated distal enhancer-activated egl-17 expression. Since expression of egl-17::GFP driven by the distal enhancer can no longer be turned off at late stages in lin-1 and lin-31 mutants, egl-17 may also be regulated by Ras signaling through repression of LIN-1 and LIN-31 activities. Interspecies transformation experiments showed that egl-17 cis-regulatory elements are structurally and functionally conserved between C. elegans and C ------------------- Key: 5842 Medline: 12710959 Authors: Kirouac M;Sternberg PW Title: cis-regulatory control of three cell fate-specific genes in vulval organogenesis of Caenorhabditis elegans and C. briggsae. Citation: Developmental Biology 257: 85-103 2003 Type: ARTICLE Genes: cdh-3 egl-17 zmp-1 Abstract: The great-grandprogeny of the Caenorhabditis elegans vulval precursor cells (VPCs) adopt one of the final vulA, B 1, B2, C, D, E, and F cell fates in a precise spatial pattern. This pattern of vulval cell types is likely to depend on the cis-regulatory regions of the transcriptional targets of intercellular signals in vulval development. egl-17, zmp-1, and cdh-3 are expressed differentially in the developing vulva cells, providing a potential readout for different signaling pathways. To understand how such pathways interact to specify unique vulval cell types in a precise pattern, we have identified cis-regulatory regions sufficient to confer vulval cell type-specific regulation when fused in cis to the basal pes-10 promoter. We have identified the C. briggsae homologs of these three genes, with their corresponding control regions, and tested these regions in both C. elegans and C. briggsae. These regions of similarity in C. elegans and C. briggsae upstream of egl-17, zmp-1, and cdh-3 promote expression in vulval cells and the anchor cell (AC). By using the cis-regulatory analysis and phylogenetic footprinting, we have identified overrepresented sequences involved in conferring vulval and ------------------- Key: 5843 Medline: 12640035 Authors: Sawa M;Suetsugu S;Sugimoto A;Miki H;Yamamoto M;Takenawa T Title: Essential role of the C. elegans Arp2/3 complex in cell migration during ventral enclosure. Citation: Journal of Cell Science 116: 1505-1518 2003 Type: ARTICLE Genes: arx-1 arx-2 arx-4 arx-5 arx-6 arx-7 gex-2 gex-3 hmp-1 hmp-2 lin-26 wsp-1 Abstract: Migration of cells through the reorganization of the actin cytoskeleton is essential for morphogenesis of multicellular animals. In a cell culture system, the actin-related protein (Arp) 2/3 complex functions as a nucleation core for actin polymerization when activated by the members of the WASP (Wiskott-Aldrich syndrome protein) family. However, the regulation of cell motility in vivo remains poorly understood. Here we report that homologues of the mammalian Arp2/3 complex and N-WASP in Caenorhabditis elegans play an important role in hypodermal cell migration during morphogenesis, a process known as ventral enclosure. In the absence of one of any of the C. elegans Arp2/3 complex subunits (ARX-1, ARX-2, ARX-4, ARX-5, ARX-6 or ARX-7) or of N-WASP (WSP-1), hypodermal cell migration led by actin-rich filopodia formation is inhibited during ventral enclosure owing to the reduction of filamentous actin formation. However, there is no effect on differentiation of hypodermal cells and dorsal intercalation. Disruption of the function of ARX-1 and WSP-1 in hypodermal cells also resulted in hypodermal cell arrest during ventral enclosure, suggesting that their function is cell autonomous. WSP-1 protein activated Arp2/3-mediated actin polymerization in vitro. Consistent with these results, the Arp2/3 complex and WSP-1 colocalized at the leading edge of migrating hypodermal cells. The stable localization of WSP-1 was dependent on the presence of Arp2/3 complex, suggesting an interaction between the Arp2/3 complex and WSP-1 in vivo. ------------------- Key: 5844 Medline: 12576475 Authors: Srinivasan P;Piano F;Shatkin AJ Title: mRNA capping enzyme requirement for Caenorhabditis elegans viability. Citation: Journal of Biological Chemistry 278: 14168-14173 2003 Type: ARTICLE Genes: cel-1 Abstract: Capping of the initiated 5' ends of RNA polymerase II products is evolutionarily and functionally conserved from yeasts to humans. The m 7 GpppN cap promotes RNA stability, processing, transport, and translation. Deletion of capping enzymes in yeasts was shown to be lethal due to rapid exonucleolytic degradation of un-capped transcripts or failure of capped but unmethylated RNA to initiate protein synthesis. Using RNA interference and Caenorhabditis elegans we have found that RNA capping is also essential for metazoan viability. C. elegans bifunctional capping enzyme was cloned, and capping activity by the expressed protein as well as growth complementation of yeast deletion strains missing either RNA triphosphatase or guanylyltransferase required terminal sequences not present in the previously isolated cel-1 clone. By RNA interference analysis we show that cel-1 is required for embryogenesis. cel-1(RNAi) embryos formed cytoplasmic granules characteristic of a phenocluster of RNA processing genes and died early in development. ------------------- Key: 5845 Medline: 12576476 Authors: Takagi T;Walker AK;Sawa C;Diehn F;Takase Y;Blackwell TK;Buratowski S Title: The Caenorhabditis elegans mRNA 5'-capping enzyme. Citation: Journal of Biological Chemistry 278: 14174-14184 2003 Type: ARTICLE Genes: ced-1 Abstract: Eukaryotic mRNA capping enzymes are bifunctional, carrying both RNA triphosphatase (RTPase) and guanylyltransferase (GTase) activities. The Caenorhabditis elegans CEL-1 capping enzyme consists of an N-terminal region with RTPase activity and a C-terminal region that resembles known GTases, However, CEL-1 has not previously been shown to have GTase activity. Cloning of the cel-1 cDNA shows that the full-length protein has 623 amino acids, including an additional 38 residues at the C termini and 12 residues at the N termini not originally predicted from the genomic sequence. Full-length CEL-1 has RTPase and GTase activities, and the cDNA can functionally replace the capping enzyme genes in Saccharomyces cerevisiae. The CEL-1 RTPase domain is related by sequence to protein-tyrosine phosphatases; therefore, mutagenesis of residues predicted to be important for RTPase activity was carried out. CEL-1 uses a mechanism similar to protein-tyrosine phosphatases, except that there was not an absolute requirement for a conserved acidic residue that acts as a proton donor. CEL-1 shows a strong preference for RNA substrates of at least three nucleotides in length. RNA-mediated interference in C. elegans embryos shows that lack of CEL-1 causes development to arrest with a phenotype similar to that seen when RNA polymerase 11 elongation activity is disrupted. Therefore, capping is essential for gene expression in ------------------- Key: 5846 Medline: 12704112 Authors: Schierack P;Lucius R;Sonnenburg B;Schilling K;Hartmann S Title: Parasite-specific immunomodulatory functions of filarial cystatin. Citation: Infection and Immunity 71: 2422-2429 2003 Type: ARTICLE Genes: Abstract: Cystatins of parasitic nematodes are well-described pathogenicity factors which contribute to downregulation of T-cell proliferation of their hosts and induce anti-inflammatory cytokine responses. We compared the immunomodulatory effects of two cystatins of the filarial nematodes Onchocerca volvalus and Acanthocheilonema viteae with two homologous proteins of the free-living nematode Caenorhabditis elegans. Like filarial cystatins, the C. elegans cystatins (rCysele1 and rCysele2) possessed domains relevant for inhibition of papain-like proteases and were biologically active inhibitors of human cathepsins B, L, and S. However, the inhibition of cathepsin B by C. elegans cystatin was much stronger. C. elegans cystatins lacked a domain involved in inhibition of legumain-like proteases that was present in O. volvulus cystatin. Filarial cystatins suppressed the proliferation of human peripheral blood mononuclear cells (PBMC) and murine spleen cells, while the C. elegans cystatins had this effect to a much lesser extent. Whereas filarial cystatins markedly increased the production of interleukin (IL)-10, C. elegans cystatins increased the production of IL-12 and gamma interferon (IFN-gamma) by human PBMC. The cystatins of both the filariae and C. elegans induced an upregulation of inducible nitric oxide by IFN-gamma-stimulated murine macrophages. These data suggest that filarial cystatins but not the C. elegans cystatins downregulate proliferative responses of host cells due to characteristics which might reflect an adaptation of filariae to their parasitic life ------------------- Key: 5847 Medline: 12713492 Authors: Kothe M;Antl M;Huber B;Stoecker K;Ebrecht D;Steinmetz I;Eberl L Title: Killing of Caenorhabditis elegans by Burkholderia cepacia is controlled by the cep quorum-sensing system. Citation: Cellular Microbiology 5: 343-351 2003 Type: ARTICLE Genes: phm-2 Abstract: Burkholderia cepacia H111, which was isolated from a cystic fibrosis patient, effectively kills the nematode Caenorhabditis elegans . Depending on the medium used for growth of the bacterium two different killing modes were observed. On high-osmolarity medium the nematodes became paralysed and died within 24 h. Using filter assays we provide evidence that this killing mode involves the production of an extracellular toxin. On nematode growth medium killing occurs over the course of 2-3 days and involves the accumulation of bacteria in the intestinal lumen of C. elegans . We demonstrate that the cep quorum-sensing system of H111 is required for efficient killing of C. elegans under both killing conditions. Using the C. elegans phm-2 mutant that has a non-functional grinder evidence is provided that the cep system is required to enter the intestinal lumen but is dispensable for the colonization of the gut. Furthermore, we demonstrate that the type II secretion machinery is not essential for nematode killing. ------------------- Key: 5848 Medline: 12684055 Authors: Blasko B;Madi A;Fesus L Title: Thioredoxin motif of Caenorhabditis elegans PDI-3 provides Cys and His catalytic residues for transglutaminase activity. Citation: Biochemical and Biophysical Research Communications 303: 1142-1147 2003 Type: ARTICLE Genes: Abstract: Previous reports have suggested that protein disulfide isomerases (PDIs) have transglutaminase (TGase) activity [1]. The structural basis of this reaction has not been revealed. We demonstrate here that Caenorhabditis elegans PDI-3 can function as a Ca2+-dependent TGase in assays based on modification of protein- and peptide-bound glutamine residues. By site-directed mutagenesis the second cysteine residue of the -CysGlyHisCys- motif in the thioredoxin domain of the enzyme protein was found to be the active site of the transamidation reaction and chemical modification of histidine in their motif blocked TGase ------------------- Key: 5849 Medline: 12524464 Authors: Goodman MB;Schwarz EM Title: Transducing touch in Caenorhabditis elegans. Citation: Annual Review of Physiology 65: 429-452 2003 Type: REVIEW Genes: cup-5 deg-1 del-1 gon-2 let-2 lov-1 mec-1 mec-2 mec-3 mec-4 mec-5 mec-6 mec-7 mec-9 mec-10 mec-12 ocr-1 ocr-2 ocr-3 ocr-4 osm-9 pkd-2 unc-1 unc-8 unc-105 Abstract: Mechanosensation has been studied for decades, but understanding of its molecular mechanism is only now emerging from studies in Caenorhabditis elegans and Drosophila melanogaster. In both cases, the entry point proved to be genetic screens that allowed molecules needed for mechanosensation to be identified without any prior understanding of the likely components. In C. elegans, genetic screens revealed molecules needed for touch sensation along the body wall and other regions of force sensitivity. Members of two extensive membrane protein families have emerged as candidate sensory mechanotransduction channels: mec-4 and mec-10, which encode amiloride-sensitive channels (ASCs or DEG/ENaCs), and osm-9, which encodes a TRP ion channel. There are roughly 50 other members of these families whose functions in C. elegans are unknown. This article classifies these channels in C. elegans, with an emphasis on insights into their function derived from mutation. We also review the neuronal cell types in which these channels might be expressed and mediate mechanotransduction. ------------------- Key: 5850 Medline: 12700416 Authors: Cheng Q;Valmas N;Reilly PEB;Collins PJ;Kopittke R;Ebert PR Title: Caenorhabditis elegans mutants resistant to phosphine toxicity show increased longevity and cross-resistance to the synergistic action of oxygen. Citation: Toxicological Sciences 73: 60-65 2003 Type: ARTICLE Genes: pre-1 pre-7 pre-33 Abstract: Phosphine (hydrogen phosphide, PH3) is the fumigant most widely used to protect stored products from pest infestation. Despite the importance of this chemical, little is known about its mode of action. We have created three phosphine-resistant lines (pre-1, pre-7, pre-33) in the model organism C. elegans, with LC50 values 2, 5, and 9 times greater than the fully susceptible parental strain. Molecular oxygen was shown to be an extremely effective synergist with phosphine as, under hyperoxic conditions, 100% mortality was observed in wild-type nematodes exposed to 0.1 mg/l phosphine, a nonlethal concentration in air. All three mutants were resistant to the synergistic effects of oxygen in proportion to their resistance to phosphine with one mutant, pre-33, showing complete resistance to this synergism. We take the proportionality of cross-resistance between phosphine and the synergistic effect of oxygen to imply that all three mutants circumvent a mechanism of phosphine toxicity that is directly coupled to oxygen metabolism. Compared with the wild-type strain, all three mutants have an extended average life expectancy of from 12.5 to 25.3%. This is consistent with the proposed involvement of oxidative stress in both phosphine toxicity and ageing. Because the wild-type and mutant nematodes develop at the same rate, the longevity is unlikely to be caused by a clk-type reduction in oxidative metabolism, a potential alternative mechanism of phosphine resistance. ------------------- Key: 5851 Medline: 12750521 Authors: Hsu AL;Murphy CT;Kenyon C Title: Regulation of aging and age-related disease by DAF-16 and heat-shock factor. Citation: Science 300: 1142-1145 2003 Type: ARTICLE Genes: daf-2 daf-16 eat-2 hsf-1 hsp-16.1 hsp-16.49 hsp-12.6 hsp-70 hsp-90 isp-1 mtl-1 sip-1 sod-3 unc-33 Abstract: The Caenorhabditis elegans transcription factor HSF-1, which regulates the heat-shock response, also influences aging. Reducing hsf-1 activity accelerates tissue aging and shortens life-span, and we show that hsf-1 overexpression extends life-span. We find that HSF-1, like the transcription factor DAF-16, is required for daf-2-insulin/IGF-1 receptor mutations to extend life-span. Our findings suggest this is because HSF-1 and DAF-16 together activate expression of specific genes, including genes encoding small heat-shock proteins, which in turn promote longevity. The small heat-shock proteins also delay the onset of polyglutamine-expansion protein aggregation, suggesting that these proteins couple the normal aging process to this type of age-related disease. ------------------- Key: 5852 Medline: 12696058 Authors: Symersky J;Li SL;Carson M;Luo M Title: Structural genomics of Caenorhabditis elegans: Triosephosphate isomerase. Citation: Proteins: Structure, Function, and Genetics 51: 484-486 Type: ARTICLE Genes: Abstract: Triosephosphate isomerase (TIM, E.C. 5.3.1.1) catalyzes the reversible isomerization of dihydroxyacetone phosphate to D-glyceraldehyde 3-phosphate in the glycolytic pathway. It is a well-studied enzyme conserved in function across eukarya, bacteria, and archaea. ------------------- Key: 5853 Medline: 12682297 Authors: Kostrouchova M;Kostrouch Z;Saudek V;Piatigrosky J;Rall JE Title: BIR-1, a Caenorhabditis elegans homologue of Survivin, regulates transcription and development. Citation: Proceedings of the National Academy of Sciences USA 100: 5240-5245 2003 Type: ARTICLE Genes: bir-1 dpy-7 elt-2 hlh-8 Abstract: bir-1, a Caenorhabditis elegans inhibitor-of-apoptosis gene homologous to Survivin is organized in an operon with the transcription cofactor C elegans SKIP (skp-1). Because genes arranged in operons are frequently linked functionally, we have asked whether BIR-1 also functions in transcription. bir-1 inhibition resulted in multiple developmental defects that overlapped with C elegans SKIP loss-of-function phenotypes: retention of eggs, dumpy, movement defects, and lethality. bir-1 RNA-mediated interference decreased expression of several gfp transgenes and the endogenous genes dpy-7 and hlh-1. Immunoblot analysis revealed decreased phosphoacetylated histones in bir-1 RNA-mediated interference-treated worms. In a heterologous transfection system, BIR-1 augments thyroid hormone-regulated transcription and has an additive effect with SKIP. These results show that BIR-1 functions in the regulation of transcription and development. ------------------- Key: 5854 Medline: 12728280 Authors: Kurz CL;Ewbank JJ Title: Caenorhabditis elegans: an emerging genetic model for the study of innate immunity. Citation: Nature Reviews Genetics 4: 380-390 2003 Type: REVIEW Genes: cel-1 daf-1 daf-2 daf-3 daf-4 daf-7 daf-8 daf-14 daf-16 dbl-1 esp-2 esp-8 jkk-1 jnk-1 let-357 lin-45 lit-1 lon-1 lys-8 mek-1 mek-2 mom-4 mpk-2 nsy-1 pmk-1 pmk-2 pmk-3 pop-1 scl-1 sek-1 sma-2 sma-3 sma-4 sma-6 tig-2 unc-43 unc-129 Abstract: Invaluable insights into how animals, humans included, defend themselves against infection have been provided by more than a decade of genetic studies that have used fruitflies. In the past few years, attention has also turned to another simple animal model, the nematode worm Caenorhabditis elegans. What exactly have we learned from the work in Drosophila? And will research with C. elegans teach us anything new about our response to pathogen attack?. ------------------- Key: 5855 Medline: 12721544 Authors: Boone C;Andrews B Title: ORFeomics: correcting the wiggle in worm genes. Citation: Nature Genetics 34: 8-9 2003 Type: REVIEW Genes: Abstract: A new study attempts to amplify and clone all the predicted protein-encoding open reading frames (ORFs) for Caenorhabditis elegans. This analysis confirms many of the predicted genes but suggests roughly 50% of them require correction. Recombining the ORFs into a number of different expression systems can generate functional proteomics kits for characterizing protein activity and interaction networks. ------------------- Key: 5856 Medline: 12679813 Authors: Reboul J;Vaglio P;Rual JF;Lamesch P;Martinez M;Armstrong CM;Li S;Jacotot L;Bertin N;Janky R;Moore T;Hudson JR;Hartley JL;Brasch MA;Vandenhaute J;Boulton S;Endress GA;Jenna S;Chevet E;Papasotiropoulos Title: C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Citation: Nature Genetics 34: 35-41 2003 Type: REVIEW Genes: Abstract: To verify the genome annotation and to create a resource to functionally characterize the proteome, we attempted to Gateway-clone all predicted protein-encoding open reading frames (ORFs), or the 'ORFeome,' of Caenorhabditis elegans. We successfully cloned approximately 12,000 ORFs (ORFeome 1.1), of which roughly 4,000 correspond to genes that are untouched by any cDNA or expressed-sequence tag (EST). More than 50% of predicted genes needed corrections in their intron-exon structures. Notably, approximately 11,000 C. elegans proteins can now be expressed under many conditions and characterized using various high-throughput strategies, including large-scale interactome mapping. We suggest that similar ORFeome projects will be valuable for other organisms, including humans. ------------------- Key: 5857 Medline: 12718884 Authors: Parrish JZ;Xue D Title: Functional genomic analysis of apoptotic DNA degradation in C. elegans. Citation: Molecular Cell 11: 987-996 2003 Type: ARTICLE Genes: ced-3 ced-4 ced-5 ced-7 crn-1 crn-2 crn-3 crn-4 crn-5 crn-6 cps-6 cyp-13 nuc-1 wah-1 Abstract: Chromosomal DNA degradation is critical for cell death execution and is a hallmark of apoptosis, yet little is known about how this process is executed. Using an RNAi-based functional genomic approach, we have identified seven additional cell death-related nucleases (crn genes), which along with two known nucleases (CPS-6 and NUC-1) comprise at least two independent pathways that contribute to cell killing, and likely signaling for phagocytosis, by degrading chromosomal DNA. Several crn genes have human homologs that are important for RNA processing, protein folding, DNA replication, and DNA damage repair, suggesting dual roles for CRN nucleases in cell survival and cell death. It should now be possible to systematically decipher the mechanisms of apoptotic DNA degradation. ------------------- Key: 5858 Medline: 12717735 Authors: Savage-Dunn C;Maduzia LL;Zimmerman CM;Roberts AF;Cohen S;Tokarz R;Padgett RW Title: Genetic screen for small body size mutants in C. elegans reveals many TGF beta pathway components. Citation: Genesis 35: 239-247 2003 Type: ARTICLE Genes: daf-4 dbl-1 lon-1 sma-1 sma-2 sma-3 sma-4 sma-6 sma-9 sma-10 sma-11 sma-12 sma-13 sma-14 sma-16 sma-17 sma-18 sma-19 sma-20 mDf1 nDf19 sDf35 sDf47 syDf1 mnDp1 yDp5 yDp9 Abstract: In the nematode Caenorhabditis elegans, a TGFbeta-related signaling pathway regulates body size and male tail morphogenesis. We sought to identify genes encoding components or modifiers of this pathway in a large-scale genetic screen. Remarkably, this screen was able to identify essentially all core components of the TGFbeta signaling pathway. Among 34 Small mutants, many mutations disrupt genes encoding recognizable components of the TGFbeta pathway: DBL-1 ligand, DAF-4 type 11 receptor, SMA-6 type I receptor, and SMA-2, SMA-3, and SMA-4 Smads. Moreover, we find that at least 11 additional complementation groups can mutate to the Small phenotype. Four of these 11 genes, sma-9, sma-14, sma-16, and sma-20 affect male tail morphogenesis as well as body size. Two genes, sma-11 and sma-20, also influence regulation of the developmentally arrested dauer larval stage, suggesting a role in a second characterized TGFbeta pathway in C. elegans. Other genes may represent tissue-specific factors or parallel pathways for body size control. Because of the conservation of TGFbeta signaling pathways, homologs of these genes may be involved in tissue specificity and/or crosstalk of TGFbeta pathways in other animals. ------------------- Key: 5859 Medline: 12620986 Authors: Wang J;Kim SK Title: Global analysis of dauer gene expression in Caenorhabditis elegans. Citation: Development 130: 1621-1634 2003 Type: ARTICLE Genes: ctl-1 daf-9 daf-16 daf-21 hsp-20 mrp-2 nhr-45 nhr-46 nhr-63 pgp-3 pyc-1 sod-3 Abstract: The dauer is a developmental stage in C. elegans that exhibits increased longevity, stress resistance, nictation and altered metabolism compared with normal worms. We have used DNA microarrays to profile gene expression differences during the transition from the dauer state to the non-dauer state and after feeding of starved L1 animals, and have identified 1984 genes that show significant expression changes. This analysis includes genes that encode transcription factors and components of signaling pathways that could regulate the entry to and exit from the dauer state, and genes that encode components of metabolic pathways important for dauer survival and longevity. Homologs of C elegans dauer-enriched genes may be involved in the disease process in parasitic nematodes. ------------------- Key: 5860 Medline: 12750326 Authors: Fischer SEJ;Wienholds E;Plasterk RHA Title: Continuous exchange of sequence information between dispersed Tc1 transposons in the Caenorhabditis elegans genome. Citation: Genetics 164: 127-134 2003 Type: ARTICLE Genes: mut-7 Abstract: In a genome-wide analysis of the active transposons in Caenorhabditis elegans we determined the localization and sequence of all copies of each of the six active transposon families. Most copies of the most active transposons, Tc1 and Tc3, are intact but individually have a unique sequence, because of unique patterns of single-nucleotide polymorphisms. The sequence of each of the 32 Tc1 elements is invariant in the C. elegans strain N2, which has no germline transposition. However, at the same 32 Tc1 loci in strains with germline transposition, Tc1 elements can acquire the sequence of Tc1 elements elsewhere in the N2 genome or a chimeric sequence derived from two dispersed Tc1 elements. We hypothesize that (luring double-strand-break repair after Tc1 excision, the template for repair can switch from the Tc1 element on the sister chromatid or homologous chromosome to a Tc1 copy elsewhere in the genome. Thus, the population of active transposable elements in C. elegans is highly dynamic because of a continuous exchange of sequence information between individual copies, potentially allowing a higher evolution rate than that found in endogenous genes. ------------------- Key: 5861 Medline: 12750327 Authors: Thomas JH;Ceol CJ;Schwartz HT;Horvitz HR Title: New genes that interact with lin-35 Rb to negatively regulate the let-60 ras pathway in Caenorhabditis elegans. Citation: Genetics 164: 135-151 2003 Type: ARTICLE Genes: dpl-1 let-60 lin-8 lin-9 lin-13 lin-15 lin-35 lin-36 lin-37 lin-38 lin-52 lin-53 lin-54 lin-56 mnDf46 mnDf67 mnDf85 nDf40 Abstract: Previous studies have shown that a synthetic multivulva phenotype results front mutations in genes that antagonize the ras-mediated intercellular signaling system responsible for vulval induction in Caenohabditis elegans. Synthetic multivulva Imitations define two classes of genes, A and B, and a mutation in a gene of each class is required to produce the multivulva phenotype. The ectopic vulval tissue in multivulva animals is generated by vulval precursor cells that in the wild type do not generate vulval tissue. One of the class B synthetic multivulva genes, lin-35, encodes a protein sintilar to the retinoblastoma (Rb) protein. In this article, we describe the isolation and characterization of 50 synthetic multivulva mutations, the identification of new, components of both the class A and class B lin-35 Rb pathways, and the cloning of lin-52, a class B gene that may have a conserved role in Rb-mediated ------------------- Key: 5862 Medline: 12750328 Authors: Keane J;Avery L Title: Mechanosensory inputs influence Caenorhabditis elegans pharyngeal activity via ivermectin sensitivity genes. Citation: Genetics 164: 153-162 2003 Type: ARTICLE Genes: avr-14 avr-15 cat-2 cha-1 daf-7 daf-8 eat-2 eat-4 eat-18 egl-30 glc-1 glr-1 goa-1 mec-3 mec-7 osm-3 tph-1 unc-1 unc-7 unc-25 unc-29 Abstract: Mechanical stimulation induces opposite behavioral responses in the adult and daucer pharynx. Tail tap of adults inhibits pharyngeal pumping via a pahway involving the innexin gene unc-7 and components of the glutamatergic pathway encoded by the genes avr-14 and avr-15. Tail tap of dauers stimulates pumping through a mechanism involving Galphao and Galphaq. The nematocidal drug ivermectin is believed to kill worms by opening a glutamate-gated chloride channel (AVR-15) on pharyngeal muscle, causing complete pumping inhibition. However, ivermectin can also inhibit pumping in the absence of this channel. We propose that one of the ways ivermectin could prevent pumping, in the absence of the AVR-15 ivermectinhinding channel on pharynx muscle, is to target ANTR-14 and AVR-15, which are expressed in the inhibitory pathway linking ------------------- Key: 5863 Medline: 12709403 Authors: Asencio C;Rodriquez-Aguilera JC;Ruiz-Ferrer M;Vela J;Navas Title: Silencing of ubiquinone biosynthesis genes extends life span in Caenorhabditis elegans. Citation: FASEB Journal 17: U276-U295 2003 Type: ARTICLE Genes: clk-1 coq-1 coq-2 coq-3 coq-4 coq-5 coq-6 coq-7 coq-8 Abstract: Ubiquinone (coenzyme Q; Q) is a key factor in the mitochondria electron transport chain, but it also functions as an antioxidant and as a cofactor of mitochondrial uncoupling proteins. Furthermore, Q isoforms balance in Caenorhabditis elegans is determined by both dietary intake and endogenous biosynthesis. In the absence of synthesis, withdrawal of dietery Q8 in adulthood extends life span. Thus, Q plays an important role in the aging process and understanding its synthesis acquires a new impetus. We have identified by RNA interference (RNAi) eight genes, including clk-1, involved in ubiquinone biosynthesis in C. elegans feeding animals with dsRNA-containing Escherichia coli HT115 strains. Silenced C. elegans showed lower levels of both endogenous Q9 and Q8 provided by diet, produced less superoxide without a significant modification of mitochondrial electron chain, and extended life span compared with non-interfered animals. E. coli strains harboring dsRNA also interfered with their own Q8 biosynthesis. These findings suggest that more efficient electron transport between a lower amount of Q and electron transport capacity of the mitochondrial complexes leads to less production of reactive oxygen species that contributes to extension of ------------------- Key: 5865 Medline: Authors: Miyakawa T;Harada S;Ishimori T;Yamamoto H;Hosono R;Yamada S Title: Profile of development to genes under extremely low frequency magnetic fields with Caenorhabditis elegans. Citation: Int J A El 14: 323-326 2001 Type: ARTICLE Genes: Abstract: ------------------- Key: 5866 Medline: 12736304 Authors: Lee KZ;Eizinger A;Nandakumar R;Schuster SC;Sommer RJ Title: Limited microsynteny between the genomes of Pristionchus pacificus and Caenorhabditis elegans. Citation: Nucleic Acids Research 31: 2553-2560 2003 Type: ARTICLE Genes: arl-1 pal-1 ptr-1 Abstract: Nematodes are an attractive group of organisms for studying the evolution of developmental processes. Pristionchus pacificus was established as a satellite organism for comparing vulva development and other processes to Caenorhabditis elegans. The generation of a genetic linkage map of P.pacificus has provided a first insight into the structure and organization of the genome of this species. Pristionchus pacificus and C.elegans are separated from one another by >100 000 000 years such that the structure of the genomes of these two nematodes might differ substantially. To evaluate the amount of synteny between the two genomes, we have obtained 126 kb of continuous genomic sequence of P.pacificus, flanking the developmental patterning gene pal-1. Of the 20 predicted open reading frames in this interval, 11 have C.elegans orthologs. Ten of these 11 orthologs are located on C.elegans chromosome III, indicating the existence of synteny. However, most of these genes are distributed over a 12 Mb interval of the C.elegans genome and only three pairs of genes show microsynteny. Thus, intrachromosomal rearrangements occur frequently in nematodes, limiting the likelihood of identifying orthologous genes of P.pacificus and C.elegans based on positional information within the two genomes. ------------------- Key: 5867 Medline: 12761549 Authors: Hwang HY;Olson SK;Esko JD;Horvitz HR Title: Caenorhabditis elegans early embryogenesis and vulval morphogenesis require chondroitin biosynthesis. Citation: Nature 423: 439-443 2003 Type: ARTICLE Genes: sqv-5 qDf5 qDf7 qDf8 qDf9 qDf10 Abstract: Defects in glycosaminoglycan biosynthesis disrupt animal development and can cause human disease(1-4). So far much of the focus on glycosaminoglycans has been on heparan sulphate. Mutations in eight squashed vulva (sqv) genes in Caenorhabditis elegans cause defects in cytokinesis during embryogenesis and in vulval morphogenesis during postembryonic development(5,6). Seven of the eight sqv genes have been shown to control the biosynthesis of the glycosaminoglycans chondroitin and heparan sulphate(6-11). Here we present the molecular identification and characterization of the eighth gene, sqv-5. This gene encodes a bifunctional glycosyltransferase that is probably localized to the Golgi apparatus and is responsible for the biosynthesis of chondroitin but not heparan sulphate. Our findings show that chondroitin is crucial for both cytokinesis and morphogenesis during C. elegans ------------------- Key: 5868 Medline: 12761550 Authors: Mizuguchi S;Uyama T;Kitagawa H;Nomura KH;Dejima K;Gengyo-Ando K;Mitani S;Sugahara K;Nomura K Title: Chondroitin proteoglycans are involved in cell division of Caenorhabditis elegans. Citation: Nature 423: 443-448 2003 Type: ARTICLE Genes: ced-2 ced-5 ced-10 rib-1 rib-2 sqv-3 sqv-8 Abstract: Glycosaminoglycans such as heparan sulphate and chondroitin sulphate are extracellular sugar chains involved in intercellular signalling. Disruptions of genes encoding enzymes that mediate glycosaminoglycan biosynthesis have severe consequences in Drosophila and mice(1-5). Mutations in the Drosophila gene sugarless, which encodes a UDP-glucose dehydrogenase, impair developmental signalling through the Wnt family member Wingless, and signalling by the fibroblast growth factor and Hedgehog pathways. Heparan sulphate is involved in these pathways(6-8), but little is known about the involvement of chondroitin. Undersulphated and oversulphated chondroitin sulphate chains have been implicated in other biological processes, however, including adhesion of erythrocytes infected with malaria parasite to human placenta and regulation of neural development(9,10). To investigate chondroitin functions, we cloned a chondroitin synthase homologue of Caenorhabditis elegans and depleted expression of its product by RNA-mediated interference and deletion mutagenesis. Here we report that blocking chondroitin synthesis results in cytokinesis defects in early embryogenesis. Reversion of cytokinesis is often observed in chondroitin-depleted embryos, and cell division eventually stops, resulting in early embryonic death. Our findings show that chondroitin is required for embryonic cytokinesis and cell division. ------------------- Key: 5869 Medline: 12679551 Authors: Cutter AD;Payseur BA Title: Selection at linked sites in the partial selfer Caenorhabditis elegans. Citation: Molecular Biology and Evolution 20: 665-673 2003 Type: ARTICLE Genes: Abstract: Natural selection can produce a correlation between local recombination rates and levels of neutral DNA polymorphism as a consequence of genetic hitchhiking and background selection. Theory suggests that selection at linked sites should affect patterns of neutral variation in partially selling populations more dramatically than in outcrossing populations. However, empirical investigations of selection at linked sites have focused primarily on outcrossing species. To assess the potential role of selection as a determinant of neutral polymorphism in the context of partial self-fertilization, we conducted a multivariate analysis of single-nucleotide polymorphism (SNP) density throughout the genome of the nematode Caenorhabditis elegans. We based the analysis on a published SNP data set and partitioned the genome into windows to calculate SNP densities, recombination rates, and gene densities across all six chromosomes. Our analyses identify a strong, positive correlation between recombination rate and neutral polymorphism (as estimated by noncoding SNP density) across the genome of C. elegans. Furthermore, we find that levels of neutral polymorphism are lower in gene-dense regions than in gene-poor regions in some analyses. Analyses incorporating local estimates of divergence between C. elegans and C. briggsae indicate that a mutational explanation alone is unlikely to explain the observed patterns. Consequently, we interpret these findings as evidence that natural selection shapes genome-wide patterns of neutral polymorphism in C. elegans. Our study provides the first demonstration of such an effect in a partially selfing animal. Explicit models of genetic hitchhiking and background selection can each adequately describe the relationship between recombination rate and SNP density, but only when they incorporate selfing rate. Clarification of the relative roles of genetic hitchhiking and background selection in C. elegans awaits the development of specific theoretical predictions that account for partial self-fertilization and biased sex ratios. ------------------- Key: 5870 Medline: 12724425 Authors: Jedrusik MA;Schulze E Title: Telomeric position effect variegation in Saccharomyces cerevisiae by Caenorhabditis elegans linker histones suggests a mechanistic connection between germ line and telomeric silencing. Citation: Molecular and Cellular Biology 23: 3681-3691 2003 Type: ARTICLE Genes: let-858 mrt-2 pha-1 set-2 sir-2.1 Abstract: Linker histones are nonessential for the life of single-celled eukaryotes. Linker histones, however, can be important components of specific developmental programs in multicellular animals and plants. For Caenorhabditis elegans a single linker histone variant (H1.1) is essential in a chromatin silencing process which is crucial for the proliferation and differentiation of the hermaphrodite germ line. In this study we analyzed the whole linker histone complement of C. elegans by telomeric position effect variegation in budding yeast. In this assay an indicator gene (URA3) placed close to the repressive telomeric chromatin structure is subject to epigenetically inherited gene inactivation. Just one out of seven C. elegans linker histones (H1.1) was able to enhance the telomeric position effect in budding yeast. Since these results reflect the biological function of H1.1 in C. elegans, we suggest that chromatin silencing in C. elegans is governed by molecular mechanisms related to the telomere-dependent silencing in budding yeast. We confirmed this hypothesis by testing C. elegans homologs of three yeast genes which are established modifiers of the yeast telomeric chromatin structure (SIR2, SET1, and RAD17) for their influence on repeat-dependent transgene silencing for C. elegans. ------------------- Key: 5871 Medline: 12736328 Authors: Ackley BD;Kang SH;Crew JR;Suh C;Jin Y;Kramer JM Title: The basement membrane components nidogen and type XVIII collagen regulate organization of neuromuscular junctions in Caenorhabditis elegans. Citation: Journal of Neuroscience 23: 3577-3587 2003 Type: ARTICLE Genes: cle-1 nid-1 Abstract: Vertebrate neuromuscular junctions (NMJs) contain specialized basal laminas enriched for proteins not found at high concentrations extrasynaptically. Alterations in NMJ basement membrane components can result in loss of NMJ structural integrity and lead to muscular dystrophies. We demonstrate here that the conserved Caenorhabditis elegans basement membrane-associated molecules nidogen/entactin (NID-1) and type XVIII collagen (CLE-1) are associated with axons and particularly enriched near synaptic contacts. NID-1 is concentrated laterally, between the nerve cord and muscles, whereas CLE-1 is concentrated dorsal to the ventral nerve cord and ventral to the dorsal nerve cord, above the regions where synapses form. Mutations in these molecules cause specific and distinct defects in the organization of neuromuscular junctions. The mutant animals exhibit mild movement defects and altered responses to an inhibitor of acetylcholinesterase and a cholinergic agonist, indicating altered synaptic function. Our results provide the first demonstration that basement membrane molecules are important for NMJ formation and/or maintenance in C. elegans and that collagen XVIII and nidogen can have important roles in synapse organization. ------------------- Key: 5872 Medline: 12707312 Authors: Romano A;Guse A;Krascenicova I;Schnabel H;Schnabel R;Glotzer M Title: CSC-1: a subunit of the Aurora B kinase complex that binds to the Survivin-like protein BIR-1 and the Incenp-like protein ICP-1. Citation: Journal of Cell Biology 161: 229-236 2003 Type: ARTICLE Genes: air-2 bir-1 csc-1 icp-1 Abstract: The Aurora B kinase complex is a critical regulator of chromosome segregation and cytokinesis. In Caenorhabditis elegans, AIR-2 (Aurora B) function requires ICP-1 (Incenp) and BIR-1 (Survivin). In various systems, Aurora B binds to orthologues of these proteins. Through genetic analysis, we have identified a new subunit of the Aurora B kinase complex, CSC-1. C. elegans embryos depleted of CSC-1, AIR-2, ICP-1, or BIR-1 have identical phenotypes. CSC-1, BIR-1, and ICP-1 are interdependent for their localization, and all are required for AIR-2 localization. In vitro, CSC-1 binds directly to BIR-1. The CSC-1/BIR-1 complex, but not the individual subunits, associates with ICP-1. CSC-1 associates with ICP-1, BIR-1, and AIR-2 in vivo. ICP-1 dramatically stimulates AIR-2 kinase activity. This activity is not stimulated by CSC-1/BIR-1, suggesting that these two subunits function as targeting subunits for AIR-2 ------------------- Key: 5873 Medline: 12695325 Authors: Lee JM;Sonnhammer ELL Title: Genomic gene clustering analysis of pathways in eukaryotes. Citation: Genome Research 13: 875-882 2003 Type: ARTICLE Genes: Abstract: Genomic clustering of genes in a pathway is commonly found in prokaryotes due to transcriptional operons, but these are not present in most eukaryotes. Yet, there might be clustering to a lesser extent of pathway members in eukaryotic genomes, that assist coregulation of a set of functionally cooperating genes. We analyzed five sequenced eukaryotic genomes for clustering of genes assigned to the same pathway in the KEGG database. Between 98% and 30% of the analyzed pathways in a genome were found to exhibit significantly higher clustering levels than expected by chance. in descending order by the level of clustering, the genomes studied were Saccharomyces cerevisiae, Homo sapiens, Caenorhabditis elegans, Arabidopsis thaliana, and Drosophila melanogaster. Surprisingly, there is not much agreement between genomes in terms of which pathways are most clustered. Only seven of 69 pathways found in all species were significantly clustered in all five of them. This species-specific pattern of pathway clustering may reflect adaptations or evolutionary events unique to a particular lineage. We note that although operons are common in C elegans, only 58% of the pathways showed significant clustering, which is less than in human. Virtually all pathways in S. cerevisiae showed significant ------------------- Key: 5874 Medline: 12689596 Authors: Arur S;Uche UE;Rezaul K;Fong M;Scranton V;Cowan AE;Mohler W;Han DK Title: Annexin I is an endogenous ligand that mediates apoptotic cell engulfment. Citation: Developmental Cell 4: 587-598 2003 Type: ARTICLE Genes: anx-1 ced-1 ced-5 ced-7 nex-1 nex-2 rrf-3 Abstract: Engulfment of apoptotic cells requires presentation of new cell surface ligands by the dying cells. Using a differential proteomics technology, we identify that annexin I is a caspase-dependent engulfment ligand; it is recruited from the cytosol and exported to the outer plasma membrane leaflet, colocalizes with phosphatidylserine, and is required for efficient clearance of apoptotic cells. Furthermore, phosphatidylserine receptor (PSR) clustering around apoptotic cells indicates a requirement for annexin I. In the nematode Caenorhabditis elegans, downregulation of the annexin homolog prevents efficient engulfment of pharyngeal cell corpses. These results provide novel mechanistic insights into how apoptotic cells are removed and may explain a pathogenic mechanism of chronic inflammatory diseases where annexin I autoantibodies have been described. ------------------- Key: 5875 Medline: 12697306 Authors: Zhang H;Kato Y Title: Common structural properties found in the CS(alpha)(beta)-type antimicrobial peptides in nematodes and mollusks: evidence fo the same evolutionary origin? Citation: Developmental & Comparative Immunology 27: 499-503 2003 Type: ARTICLE Genes: Abstract: The structural properties of the Ascaris suum antibacterial factor (ASABF)-type antimicrobial peptides, isolated from nematodes, were compared with the CSalphabeta-type antimicrobial peptides found in other organisms. The spacing of the half-cystine residues, cysteine pairings, and organization of the precursor were different from the 'classical' CSalphabeta-type antimicrobial peptides, such as drosomycin and plant defensins, and identical only to the MGD and myticin in mollusks. In addition, ABF-5, a member of the ASABF-type antimicrobial peptides in Caenorhabditis elegans, is predicted to contain a basic mature region and an acidic pro-region, similar to MGD and myticin. These results suggest that the ASABF-type antimicrobial peptides, MGD and myticin are similar in ------------------- Key: 5876 Medline: 12802075 Authors: Schafer JC;Haycraft CJ;Thomas JH;Yoder BK;Swoboda P Title: XBX-1 encodes a dynein light intermediate chain required for retrograde intraflagellar transport and cilia assembly in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 14: 2057-2070 2003 Type: ARTICLE Genes: che-3 che-11 che-13 daf-18 dyf-4 osm-5 osm-6 xbx-1 Abstract: Intraflagellar transport (IFT) is a process required for flagella and cilia assembly that describes the dynein and kinesin mediated movement of particles along axonemes that consists of an A and a B complex, defects in which disrupt retrograde and anterograde transport, respectively. Herein, we describe a novel Caenorhabditis elegans gene, xbx-1, that is required for retrograde IFT and shares homology with a mammalian dynein light intermediate chain (D2LIC). xbx-1 expression in ciliated sensory neurons is regulated by the transcription factor DAF-19, as demonstrated previously for genes encoding IFT complex B proteins. XBX-1 localizes to the base of the cilia and undergoes anterograde and retrograde movement along the axoneme. Disruption of xbx-1 results in cilia defects and causes behavioral abnormalities observed in other cilia mutants. Analysis of cilia in xbx-1 mutants reveals that they are shortened and have a bulb like structure in which IFT proteins accumulate. The role of XBX-1 in IFT was further confirmed by analyzing the effect that other IFT mutations have on XBX-1 localization and movement. In contrast to other IFT proteins, retrograde XBX-1 movement was detected in complex A mutants. Our results suggest that the DLIC protein XBX-1 functions together with the CHE-3 dynein in retrograde IFT, downstream of the complex A proteins. ------------------- Key: 5877 Medline: 12665560 Authors: Thieringer H;Moellers B;Dodt G;Kunau WH;Driscoll M Title: Modeling human peroxisome biogenesis disorders in the nematode Caenorhabditis elegans. Citation: Journal of Cell Science 16: 1797-1804 2003 Type: ARTICLE Genes: prx-1 prx-2 prx-3 prx-5 prx-6 prx-11 prx-12 prx-13 prx-16 wrs-2 Abstract: Peroxisomes are ubiquitous eukaryotic organelles. The proteins required for peroxisome biogenesis are called peroxins, and mutations in the peroxin genes cause the devastating human developmental syndromes called the peroxisome biogenesis disorders. Our interest is in elaborating the roles that peroxisomes play in Caenorhabditis elegans development, and in establishing an invertebrate model system for the human peroxisome biogenesis disorders. The genome of C elegans encodes homologs of 11 of the 13 human peroxins. We disrupted five nematode peroxins using RNA interference (RNAi) and found that RNAi knockdown of each one causes an early larval arrest at the L1 stage. Using a green fluorescent protein reporter targeted to the peroxisome, we establish that peroxisomal import is impaired in prx-5(RNAi) nematodes. prx-5(RNAi) animals are blocked very early in the L1 stage and do not initiate normal postembryonic cell divisions, similar to starvation-arrested larvae. Cell and axonal migrations that normally occur during the L1 stage also appear blocked. We conclude that peroxisome function is required for C. elegans postembryonic development and that disruption of peroxisome assembly by prx-5(RNAi) prevents scheduled postembryonic cell divisions. Defects in the cellular localization of peroxisomal proteins and in development are shared features of human and nematode peroxisome biogenesis disorders. In setting up a C. elegans model of peroxisomal biogenesis disorders, we suggest that genetic screens for suppression of the Prx developmental block will facilitate identification of novel intervention strategies and may provide new insights into human disease pathogenesis. ------------------- Key: 5878 Medline: 12730122 Authors: Srinivasan DG;Fisk RM;Xu H;van den Heuvel S Title: A complex of LIN-5 and GPR proteins regulates G protein signaling and spindle function in C. elegans. Citation: Genes & Development 17: 1225-1239 2003 Type: ARTICLE Genes: ags-3 goa-1 gpa-16 gpb-2 gpr-1 gpr-2 lin-5 lin-15 mes-1 mom-5 par-1 par-2 par-3 par-4 par-6 src-1 Abstract: The Caenorhabditis elegans coiled-coil protein LIN-5 mediates several processes in cell division that depend on spindle forces, including alignment and segregation of chromosomes and positioning of the spindle. Here, we describe two closely related proteins, GPR-1 and GPR-2 (G protein regulator), which associate with LIN-5 in vivo and in vitro and depend on LIN-5 for localization to the spindle and cell cortex. GPR-1/GPR-2 contain a GoLoco/GPR motif that mediates interaction with GDP-bound Galpha(i/o). Inactivation of lin-5, gpr-1/gpr-2, or the Galpha(i/o) genes goa-1 and gpa-16 all cause highly similar chromosome segregation and spindle positioning defects, indicating a positive role for the LIN-5 and GPR proteins in G protein signaling. The lin-5 and gpr-1/gpr-2 genes appear to act downstream of the par polarity genes in the one- and two-cell stages and downstream of the tyrosine kinase-related genes mes-1 and src-1 at the four-cell stage. Together, these results indicate that GPR-1/GPR-2 in association with LIN-5 activate G protein signaling to affect spindle force. Polarity determinants may regulate LIN-5/GPR/Galpha locally to create the asymmetric forces that drive spindle movement. Results in C. elegans and other species are consistent with a novel model for receptor-independent activation of Galpha(i/o). signaling. ------------------- Key: 5879 Medline: 12747828 Authors: Ambros V;Lee RC;Lavanway A;Williams PT;Jewell D Title: MicroRNAs and other tiny endogenous RNAs in C. elegans. Citation: Current Biology 13: 807-818 2003 Type: ARTICLE Genes: let-7 lin-4 mir-1 mir-2 mir-4 mir-8 mir-10 mir-12 mir-13 mir-23 mir-25 mir-29 mir-30 mir-31 mir-32 mir-47 mir-48 mir-51 mir-57 mir-58 mir-67 mir-72 mir-73 mir-75 mir-80 mir-81 mir-82 mir-83 mir-84 mir-92 mir-99 mir-100 mir-102 mir-124 mir-125 mir-131 mir-137 mir-141 mir-182 mir-183 mir-200 mir-203 mir-206 mir-227 mir-228 mir-229 mir-230 mir-231 mir-232 mir-233 mir-234 mir-235 mir-236 mir-237 mir-238 mir-239 mir-256 mir-257 mir-258 mir-259 mir-260 mir-261 mir-262 Abstract: Background: MicroRNAs (miRNAs) are small noncoding RNAs that are processed from hairpin precursor transcripts by Dicer. miRNAs probably inhibit translation of mRNAs via imprecise antisense base-pairing. Small interfering RNAs (siRNAs) are similar in size to miRNAs, but they recognize targets by precise complementarity and elicit RNA-mediated interference (RNA!). We employed cDNA sequencing and comparative genomics to identify additional C. elegans small RNAs with properties similar to miRNAs and siRNAs. Results: We found three broad classes of small RNAs in C. elegans: (1) 21 new miRNA genes (we estimate that C. elegans contains approximately 100 distinct miRNA genes, about 30% of which are conserved in vertebrates; (2),33 distinct members of a class of tiny noncoding RNA (tncRNA) genes with transcripts that are similar in length to miRNAs (approximately 20-21 nt) and that are in some cases developmentally regulated but are apparently not processed from a miRNA-like hairpin precursor and are not phylogenetically conserved; (3) more than 700 distinct small antisense RNAs, about 20 nt long, that are precisely complementary to protein coding regions of more than 500 different genes and therefore seem to be endogenous siRNAs. Conclusions: The presence of diverse endogenous siRNAs in normal worms suggests ongoing, genome-wide gene silencing by RNAi. miRNAs and tncRNAs are not predicted to form complete Watson-Crick hybrids with any C. elegans RNA target, and so they are likely to regulate the activity of other genes by non-RNAi mechanisms. These results suggest that diverse modes of small RNA-mediated gene regulation ------------------- Key: 5880 Medline: 12747829 Authors: Brauchle M;Baumer K;Gonczy P Title: Differential activation of the DNA replication checkpoint contributes to asynchrony of cell division in C. elegans embryos. Citation: Current Biology 13: 819-827 2003 Type: ARTICLE Genes: atl-1 cdc-42 chk-1 chk-2 cki-1 div-1 div-2 goa-1 gpa-16 pkc-3 pri-1 rfc-4 Abstract: Background: Acquisition of lineage-specific cell cycle duration is a central feature of metazoan development. The mechanisms by which this is achieved during early embryogenesis are poorly understood. In the nematode Caenorhabditis elegans, differential cell cycle duration is apparent starting at the two-cell stage, when the larger anterior blastomere AB divides before the smaller posterior blastomere P-1. How anterior-posterior (A-P) polarity cues control this asynchrony remains to be elucidated. Results: We establish that early C. elegans embryos possess a hitherto unrecognized DNA replication checkpoint that relies on the PIl-3-like kinase atl-1 and the kinase chk-1. We demonstrate that preferential activation of this checkpoint in the P-1 blastomere contributes to asynchrony of cell division in two-cell-stage wildtype embryos. Furthermore, we show that preferential checkpoint activation is largely abrogated in embryos that undergo equal first cleavage following inactivation of Galpha signaling. Conclusion: Our findings establish that differential checkpoint activation contributes to acquisition of distinct cell cycle duration in two-cell-stage C. elegans embryos and suggest a novel mechanism coupling asymmetric division to acquisition of ------------------- Key: 5881 Medline: 12741814 Authors: Ferreon JC;Volk DE;Luxon BA;Gorenstein DG;Hilser VJ Title: Solution structure, dynamics, and thermodynamics of the native state ensemble of the Sem-5 C-terminal SH3 domain. Citation: Biochemistry 42: 5582-5591 2003 Type: ARTICLE Genes: sem-5 Abstract: Although the high-resolution structure of a protein may provide significant insight into which regions are important for function, it is well-known that proteins undergo significant conformational fluctuations, even under native conditions. This suggests that the static structure alone may not provide sufficient information for elucidation of the thermodynamic determinants of biological function and that an accurate molecular-level description of function requires knowledge of the nature and energetics of the conformational states that constitute the native state ensemble. Here the native state ensemble of the C-terminal src homology domain-3 (C-SH3) from Caenorhabditis elegans Sem-5 has been studied using a variety of high-resolution biophysical techniques. In addition to determining the first solution structure of the unliganded protein, we have performed N-15 relaxation and native state hydrogen-deuterium exchange. It is observed that the regions of greatest structural variabilility also show low protection and order parameters, suggesting a higher degree of conformational diversity. These flexible regions also coincide with those regions of Sem-5 that have been predicted by the COREX algorithm to be unfolded in many of the most probable conformational states within the native state ensemble. The implications of this agreement and the potential role of conformational heterogeneity of the observed biophysical properties are discussed. ------------------- Key: 5882 Medline: 12763049 Authors: Schulze E;Altmann ME;Adham IB;Schulze B;Frode S;Engel W Title: The maintenance of neuromuscular function requires UBC-25 in Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 305: 691-699 2003 Type: ARTICLE Genes: ubc-25 Abstract: Caenorhabditis elegans gene ubc-25 encodes a novel type of an E2 ubiquitin transferase domain (UBCc) protein, which is highly conserved in multicellular animals, but which is not present in the genomes of fungi or plants. To identify the cellular localization of UBC-25 during the development of C. elegans, we used a ubc-25::gfp reporter gene construct. These experiments showed that ubc-25 expression starts during embryogenesis and that it is restricted to neurons and muscle cells in all later stages of development as well as in adult animals. RNA interference with ubc-25 caused late-onset paralysis of most muscular functions such as locomotion, egg laying, and defecation. We therefore propose that ubc-25 in C. elegans is required for the maintenance (homeostasis) of neuromuscular functions by contributing to a tissue specific protein modification pathway, and we speculate that the adult onset phenotype results from the accumulation of target proteins which fail ------------------- Key: 5883 Medline: 12911038 Authors: Witherspoon DJ;Robertson HM Title: Neutral evolution of ten types of mariner transposons in the genomes of Caenorhabditis elegans and Caenorhabditis briggsae. Citation: Journal of Molecular Evolution 56: 751-769 2003 Type: ARTICLE Genes: Abstract: Ten types of mariner transposable elements (232 individual sequences) are present in the completed genomic DNA sequence of Caenorhabditis elegans and the partial sequence of Caenorhabditis briggsae. We analyze these replicated instances of mariner evolution and find that elements of a type have evolved within their genomes under no selection on their transposase genes. Seven of the ten reconstructed ancestral mariners carry defective transposase genes. Selection has acted during the divergence of some ancestral elements. The neutrally-evolving mariners are used to analyze the pattern of molecular evolution in Caenorhabditis. There is a significant mutational bias against transversions and significant variation in rates of change across sites. Deletions accumulate at a rate of 0.034 events/bp per substitution/site, with an average size of 166 bp (173 gaps observed). Deletions appear to obliterate preexisting deletions over time, creating larger gaps. Insertions accumulate at a rate of 0.019 events/bp per substitution/site, with an average size of 151 bp (61 events). Although the rate of deletion is lower than most estimates in other species, the large size of deletions causes rapid elimination of neutral DNA: a mariner's "half-life" (the time by which half an element's sequence should have been deleted) is -0.1 subsitutions/site. This high rate of DNA deletion may explain the compact nature of the nematode genome. ------------------- Key: 5884 Medline: Authors: Gregory WF;Parkinson J Title: Caenorhabditis elegans- applications to nematode genomics. Citation: Comparative and Functional Genomics 4: 194-202 2003 Type: REVIEW Genes: Abstract: The complete genome sequence of the free-living nematode Caenorhabditis elegans was published 4 years ago. Since then, we have seen great strides in technolgies that seek to exploit this data. Here we describe the application of some of these techniques and other advances that are helping us to understand about not only the biology of this important model organism but also the phylum Nematoda. ------------------- Key: 5885 Medline: 12732734 Authors: Vorobiev S;Strokopytov B;Drubin DG;Frieden C;Ono S;Condeelis J;Rubenstein PA;Almo SC Title: The structure of nonvertebrate actin: implications for the ATP hydrolytic mechanism. Citation: Proceedings of the National Academy of Sciences USA 100: 5760-5765 2003 Type: ARTICLE Genes: Abstract: The structures of Saccharomyces cerevisiae, Dictyostelium, and Caenorhabditis elegans actin bound to gelsolin segment-1 have been solved and refined at resolutions between 1.9 and 1.75 Angstrom. These structures reveal several features relevant to the ATP hydrolytic mechanism, including identification of the nucleophilic water and the roles of Gln-137 and His-161 in positioning and activating the catalytic water, respectively. The involvement of these residues in the catalytic mechanism is consistent with yeast genetics studies. This work highlights both structural and mechanistic similarities with the small and trimeric G proteins and restricts the types of mechanisms responsible for the considerable enhancement of ATP hydrolysis associated with actin polymerization. The conservation of functionalities involved in nucleotide binding and catalysis also provide insights into the mechanistic features of members of the family of ------------------- Key: 5886 Medline: 12714038 Authors: Myllyharju J Title: Prolyl 4-hydroxylases, the key enzymes of collagen biosynthesis. Citation: Matrix Biology 22: 15-24 2003 Type: ARTICLE Genes: phy-1 phy-2 phy-3 Abstract: The collagen prolyl 4-hydroxylases (P4Hs), enzymes residing within the endoplasmic reticulum, have a central role in the biosynthesis of collagens. In addition, cytoplasmic P4Hs play a critical role in the regulation of the hypoxia-inducible transcription factor HIFalpha. Collagen and HIF P4Hs constitute enzyme families as several isoenzymes have been identified. Two catalytic a subunit isoforms have been cloned and characterized for collagen P4Hs from vertebrates, both of them assembling into alpha(2)/beta(2) P4H tetramers in which protein disulfide isomerase (PDI) acts as the beta subunit. The catalytic properties of the two isoenzymes are very similar, but distinct differences are found in the binding properties of peptide substrates and inhibitors, and major differences are seen in the expression patterns of the isoenzymes. The nematode Caenorhabditis elegans has five P4H alpha subunit isoforms, PHY1-PHY5. The C. elegans PHY1 and PHY2, together with PDI, are expressed in the collagen synthesizing hypodermal cells and three P4H forms are assembled from them, a PHY-1/PHY-2/PDI2 mixed tetramer and PHY-1/PDI and PHY-2/PDI dimers. The mixed tetramer is the main P4H form in wild-type C elegans. PHY-3 is much shorter than PHY-1 and PHY-2, has a unique expression pattern, and is most likely involved in the synthesis of collagens in early embryos. The genome of Drosophila melanogaster contains approximately 20 P4H alpha subunit-related genes, and that of Arabidopsis thaliana six. One A. thaliana P4H has been cloned and shown to be a soluble monomer with several unexpected properties. It effectively hydroxylates poly(L-proline), (Pro-Pro-Gly)(10) and many other proline-containing peptides. ------------------- Key: 5887 Medline: 12764126 Authors: Zariwala HA;Miller AC;Faumont S;Lockery SR Title: Step response analysis of thermotaxis in Caenorhabditis elegans. Citation: Journal of Neuroscience 23: 4369-4377 2003 Type: ARTICLE Genes: ttx-1 ttx-3 unc-86 Abstract: The nematode Caenorhabditis elegans migrates toward a preferred temperature on a thermal gradient. A candidate neural network for thermotaxis in C. elegans has been identified, but the behavioral strategy implemented by this network is poorly understood. In this study, we tested whether thermal migration is achieved by modulating the probability of turning behavior, as in C. elegans chemotaxis. This was done by subjecting unrestrained wild-type, cryophilic, or thermophilic worms to rapid spatially uniform temperature steps ( 3 degreesC), up or down from the cultivation temperature. Each of the three types of worms we analyzed showed a different pair of responses to the two types of steps. Comparison of wild-type and mutant response patterns suggested a model in which thermal migration involves a unique response to the gradient depending on the orientation of the worm relative to its preferred temperature. Overall, however, turning probability was modulated in a manner consistent with a role for turning behavior in thermal migration. Our results suggest that sensory systems for thermotaxis and chemotaxis may converge on a common behavioral mechanism. ------------------- Key: 5888 Medline: 12757851 Authors: Leiers B;Kampkotter A;Grevelding CG;Link CD;Johnson TE;Henkle-Duhrsen K Title: A stress-response glutathione S-transferase confers resistance to oxidative stress in Caenorhabditis elegans. Citation: Free Radical Biology & Medicine 34: 1405-1415 2003 Type: ARTICLE Genes: Abstract: Previous studies demonstrated that the Caenorhabditis elegans GST-p24 is upregulated at the steady state mRNA level in response to oxidative stress [1]. A transcriptional upregulation was confirmed in the current study by analyzing Ce-GST-p24 promoter-reporter constructs in transgenic C elegans strains CL2166 and CL3166. The transgenic strain BL1, which overexpresses the Ce-GST-p24 enzyme (as a GFP fusion protein controlled by its own promoter), was generated to investigate the function of this enzyme in vivo. Stress experiments with BL1 demonstrated an increased resistance to intracellularly induced oxidative stress, as compared to wild type. The consequences of a decrease in the Ce-GST-p24 enzyme concentration were examined by RNAi-treatment of BL1 C. elegans to silence both the endogene and the transgene Ce-GST-p24 and by the analysis of the K08F4.7 homozygous deletion mutant. In both cases, the reduced Ce-GST-p24 enzyme level resulted in a significant decrease in the stress resistance of the nematodes. These results clearly demonstrate a direct correlation between the concentration of Ce-GST-p24 and the resistance to oxidative stress. We have demonstrated for the first time that manipulation of the expression of a single GST can modulate the organismal reponse to oxidative stress. The enzymatic activity of this detoxification enzyme was examined with various substrates, giving emphasis to lipid peroxidation products. The Ce-GST-p24 was also localized in BL1 C. elegans by confocal laser-scanning microscopy, revealing a wide-spread ------------------- Key: 5889 Medline: 12603202 Authors: Zhang W;Cao P;Chen S;Spence AM;Zhu S;Staudacher E;Schachter H Title: Synthesis of paucimannose N-glycans by Caenorhabditis elegans requires prior actions of UDP-N-acetyl-D-glucosamine:alpha-3-D-mannoside beta1,2-N-acetylglucosaminyltransferase I, alpha3,6-mannoside II Citation: Biochemical Journal 372: 53-64 2003 Type: ARTICLE Genes: gly-12 gly-13 gly-14 Abstract: We have previously reported three Caenorhabditis elegans genes (gly-12, gly-13 and gly-14) encoding UDP-N-acetyl-D-glucosamine:alpha-3-D-mannoside 1,2-N-acetylglucosaminyltrans-ferase I (GnT 1), an enzyme essential for hybrid and complex N-glycan synthesis. GLY-13 was shown to be the major GnT I in worms and to be the only GnT I cloned to date which can act on [Manalpha1,6(Manalpha1,3)Manalpha1,6](Manalpha1,3)Manbeta1, 4GlcNAcbeta1, 4GlcNAc-R, but not on Mana1,6(Manalpha1 1,3)Manbeta1-O-R substrates. We now report the kinetic constants, bivalent-metal-ion requirements, and optimal pH, temperature and Mn2+ concentration for this unusual enzyme. C. elegans glycoproteins are rich in oligomannose (Man(6-9)GlcNAc(2)) and 'paucimannose' Man(3-5)GlcNAc(2)(+/- Fuc) N-glycans, but contain only small amounts of complex and hybrid N-glycans. We show that the synthesis of paucimannose Man(3)GlcNAC(2) requires the prior actions of GnT 1, alpha3,6-mannosidase 11 and a membrane-bound beta-N-acetylglucosaminidase similar to an enzyme previously reported in insects. The beta-N-acetylglucosaminidase removes terminal N-acetyl-D-glucosamine from the GlcNAc 1, 2Manalpha1,3Manbeta- arm of Manalpha1,6(GlcNAcbeta1,2Manalpha1,3) Manbeta1,4GlcNAcbeta1,4GlcNAc-R to produce paucimannose Man(3)GlcNAc(2) N-glycan. N-acetyl-D-glucosamine removal was inhibited by two N-acetylglucosaminidase inhibitors. Terminal GlcNAc was not released from [Manalpha1,6(Manalpha1,3)Manalpha1,6](GIcNAcbeta1,2Manalpha 1,3)Man 1,4GlcNAcbeta1,4GlcNAc-R nor from the GlcNAc 1,2Manalpha1,6Manbeta- arm. These findings indicate that GLY-13 plays an important role in the synthesis of N-glycans by C. elegans and that therefore the worm should prove to be a suitable model for the study of the role of ------------------- Key: 5890 Medline: 12777783 Authors: Versees W;Van Holsbeke E;De Vox S;Decanniere K;Zegers I;Steyaert J Title: Cloning, preliminary characterization and crystallization of nucleoside hydrolases from Caenorhabditis elegans and Campylobacter jejuni. Citation: Acta Crystallographica Section D-Biological Crystallography 59: 1087-1089 2003 Type: ARTICLE Genes: Abstract: The nucleoside hydrolases (NHs) are a family of nucleoside-modifying enzymes. They play an important role in the purine-salvage pathway of many pathogenic organisms which are unable to synthesize purines de novo. Although well characterized in protozoan parasites, their precise function and mechanism remain unclear in other species. For the first time, NHs from Caenorhabditis elegans and Campylobacter jejuni, which are representatives of mesozoa and bacteria, respectively, have been cloned and purified. Steady-state kinetics indicate a different substrate-specificity profile to previously described hydrolases. Native diffraction data sets were collected from crystals of NH from each organism. The hexagonal crystals (space group P6(2)22 or P6(4)22) of NH from C. elegans diffracted to a resolution of 2.8 Angstrom, while the data set from the orthorhombic crystals (space group I222 or I2(1)2(1)2(1)) of NH from C. jejuni could be processed to 1.7 Angstrom resolution. The unit-cell parameters were a=b=102.23, c=117.27 Angstrom in the former case and a=101.13, b=100.13, c=81.37 in the latter. ------------------- Key: 5891 Medline: 12777789 Authors: Ding H;Qiu S;Bunzel RJ;Luo D;Arabashi A;Lu S;Symersky J;Nagy LA;DeLucas LJ;Li S;Luo M Title: Purification, nanocrystallization and preliminary X-ray analysis of a C-terminal part of tropomodulin protein 1, isoform A, from Caenorhabditis elegans. Citation: Acta Crystallographica Section D-Biological Crystallography 59: 1106-1108 2003 Type: ARTICLE Genes: Abstract: The C-terminal part of tropomodulin protein 1, isoform A, from Caenorhabditis elegans was expressed in Escherichia coli and purified to homogeneity. Optimized from the initial nanoscreen, crystals grew to dimensions of 0.25 x 0.15 x 0.15 mm at 277 K using 28.0%(v/v) PEG 400 as the precipitant by the hanging-drop vapor-diffusion technique. A data set of 94.9% completeness was collected to a resolution of 1.98 Angstrom at 100 K using a synchrotron X-ray source (SER-CAT). The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a=31.7, b=50.6, c=107.1 Angstrom, and contained one molecule per asymmetric unit. ------------------- Key: 5892 Medline: 12882336 Authors: Braeckman BP;Houthoofd K;Vanfleteren JR Title: Assessing metabolic activity in Caenorhabditis elegans: concepts and controversies. Citation: Aging Cell 1: 82-88 2002 Type: ARTICLE Genes: age-1 clk-1 clk-2 clk-3 daf-2 daf-16 glp-4 Abstract: It is widely believed that normal by-products of oxidative metabolism and the subsequent molecular damage inflicted by them couple the aging process to metabolic rate. Accordingly, high metabolic rates would be expected to accelerate aging, and life-extending interventions are often assumed to act by attenuating metabolic rate. Notorious examples in Caenorhabditis elegans are food restriction, mutation in the Clock genes and several genes of the insulin-like signalling pathway. Here we discuss how metabolic rate can be accurately measured and normalized, and how to deal with differences in body size. These issues are illustrated using experimental data of the long-lived mutant strains clk-1(e2519) and daf-2(e1370). Appropriate analysis shows that metabolic rates in wild-type and in the clk-1 mutant are very similar. In contrast, the metabolic rate profiles point to a metabolic shift toward enhanced efficiency of oxidative ------------------- Key: 5893 Medline: 12882337 Authors: Braeckman BP;Houthoofd K;Vanfleteren JR Title: Rebuttal to Van Voorhies: 'The influence of metabolic rate on longevity in the nematode Caenorhabditis elegans'. Citation: Aging Cell 1: 89-90 2002 Type: REVIEW Genes: age-1 fer-15 Abstract: The papers by Van Voorhies in Free Radical Biology & Medicine (33, 587-596, 2002) and in this journal claim that the major longevity-extending mutations in C. elegans essentially act by reducing metabolic rate as predicted by the rate-of-living theory, and do not alter any metabolically independent mechanism specific to aging. In contrast, we found no evidence of a reduction in metabolic rate in these mutants using different experimental approaches. Now, Van Voorhies challenges the accuracy of our experimental results. ------------------- Key: 5894 Medline: 12882338 Authors: Van Voorhies WA Title: The influence of metabolic rate on longevity in the nematode Caenorhabditis elegans. Citation: Aging Cell 1: 91-101 2002 Type: REVIEW Genes: clk-1 Abstract: Much of the recent interest in aging research is due to the discovery of genes in a variety of model organisms that appear to modulate aging. A large amount of research has focused on the use of such long-lived mutants to examine the fundamental causes of aging. While model organisms do offer many advantages for studying aging, it also critical to consider the limitations of these systems. In particular, ectothermic (poikilothermic) organisms can tolerate a much larger metabolic depression than humans. Thus, considering only chronological longevity when assaying for long-lived mutants provides a limited perspective on the mechanisms by which longevity is increased. In order to provide true insight into the aging process additional physiological processes, such as metabolic rate, must also be assayed. This is especially true in the nematode Caenorhabditis elegans, which can naturally enter into a metabolically reduced state in which it survives many times longer than its usual lifetime. Currently it is seen as controversial if long-lived C. elegans mutants retain normal metabolic function. Resolving this issue requires accurately measuring the metabolic rate of C. elegans under conditions that minimize environmental stress. Additionally, the relatively small size of C. elegans requires the use of sensitive methodologies when determining metabolic rates. Several studies indicating that long-lived C. elegans mutants have normal metabolic rates may be flawed due to the use of inappropriate measurement conditions and techniques. Comparisons of metabolic rate between long-lived and wild-type C. elegans under more optimized conditions indicate that the extended longevity of at least some long-lived C. elegans mutants may be due to a reduction in metabolic rate, rather than an alteration of a ------------------- Key: 5895 Medline: Authors: Van Voorhies WA Title: Rebuttal to Braeckman et al: 'Assessing metabolic activity in again Caenorhabditis elegans: concepts and controversies'. Citation: Aging Cell 1: 102-103 2002 Type: REVIEW Genes: clk-1 daf-2 Abstract: The reviews by Braechman et al. and Van Voorhies in this issue of Aging Cell concur on the potential importance of metabolic rate and function to longevity in C. elegans. These reviews differ though, on their assessment of whether long-lived C. elegans mutants have a reduced metabolic rate compared to wild-type worms. At the centre of this disagreement are two main issues: the importance of measurement conditions when conducting metabolic assays on C. elegans, and which techniques are appropriate for measuring the metabolic rate of an organism and subsequent analysis of such data. These issues are interconnected; if the conditions under which an organism's metabolic rate are measured have a large impact on the resulting data, conclusions drawn from data collected from animals under different conditions may be invalid irrespective of the validity of the measurement methods. Conversely, measurement techniques which produce spurious data cannot be used to draw accurate conclusions about the metabolic rate of an organism, regardless of the conditions under which the organism was maintained. ------------------- Key: 5896 Medline: 12882324 Authors: McElwee J;Bubb K;Thomas JH Title: Transcriptional outputs of the Caenorhabditis elegans forkhead protein DAF-16. Citation: Aging Cell 2: 111-121 2003 Type: ARTICLE Genes: age-1 ctl-1 daf-2 daf-16 glp-4 sod-1 Abstract: In Caenorhabditis elegans, the forkhead protein DAF-16 transduces insulin-like signals that regulate larval development and adult lifespan. To identify DAF-16-dependent transcriptional alterations that occur in a long-lived C. elegans strain, we used cDNA microarrays and genomic analysis to identify putative direct and indirect DAF-16 transcriptional target genes. Our analysis suggests that DAF-16 action regulates a wide range of physiological responses by altering the expression of genes involved in metabolism, energy generation and cellular stress responses. Furthermore, we observed a large overlap between DAF-16-dependent transcription and genes normally expressed in the long-lived dauer larval stage. Finally, we examined the in vivo role of 35 of these target genes by RNA-mediated interference and identified one gene encoding a putative protease that is necessary for the daf-2 Age ------------------- Key: 5897 Medline: 12882326 Authors: Walker GA;Lithgow GJ Title: Lifespan extension in C. elegans by a molecular chaperone dependent upon insulin-like signals. Citation: Aging Cell 1: 131-139 2003 Type: ARTICLE Genes: age-1 daf-16 hsp-16 Abstract: Insulin-like signalling is a key determinate of lifespan in diverse species including mammals but the mechanism by which this pathway influences the rate of aging is unknown. In the roundworm Caenorhabditis elegans, mutations in the insulin-like signalling pathway extend adult lifespan and are associated with up-regulation of stress response genes including those for heat shock proteins (HSPs). We tested the hypothesis that the C. elegans insulin-like signalling pathway determines longevity through modulating HSP levels. We introduced extra copies of the gene encoding HSP-16 and this conferred stress resistance and longevity both in a wildtype and a long-lived mutant strain. The DAF-16 transcription factor is essential for maximal hsp-16 expression and for lifespan extension conferred by hsp-16. This demonstrates that lifespan is determined in part by insulin-like regulation of molecular chaperones. ------------------- Key: 5898 Medline: Authors: Wu YC;Xue D Title: Programmed cell death in C. elegans. Citation: "Essentials of Apoptosis: A Guide for Basic and Clinical Research", XM Yin and Z Dong (eds). Humana Press Inc, Totowa NJ : 135-144 200 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ced-12 ces-1 ces-2 cps-6 egl-1 nuc-1 tra-1 Abstract: Studies in the nematode Caenorhabditis elegans established that programmed cell death is a normal, genetically determined part of development and is controlled by a number of specific genes. Genetic analyses have ordered these genes into a pathway. This cell death pathway is evolutionarily conserved and provides a basis for understanding programmed cell death in more compex organisms, including humans. ------------------- Key: 5899 Medline: Authors: Murakami S;Johnson TE Title: Molecular genetics of longevity and stress resistance in model organisms. Citation: Current Genomics 4: 63-74 2003 Type: REVIEW Genes: Abstract: ------------------- Key: 5900 Medline: 12754379 Authors: Dillin A Title: The specifics of small interfering RNA specificity. Citation: Proceedings of the National Academy of Sciences USA 100: 6289-6291 2003 Type: REVIEW Genes: unc-22 Abstract: The discovery of transgene silencing in plants and double-stranded RNA (dsRNA) interference in the worm Caenorhabditis elegans has led to the latest revolution in molecular biology, RNA interference (RNAi). Over 10 years ago it was noted that several transgenic plant lines each containing the same ectopic transgene not only failed to be expressed but also inhibited the expression of the endogenous gene. Similarly, a determined Craig Mello and Andy Fire, attempting to reduce gene function using using antisense RNA in the worm, discovered a minor contaminant in their antisense RNA preparation effectively and repeatedly reduced expression of the endogenous gene. In both cases, dsRNA homologous to the gene of interest was responsible for these observations. In the last 4 years, these discoveries have been extended to include protozoa, ------------------- Key: 5901 Medline: Authors: de Pomerai DI;Smith B;Dawe A;North K;Smith T;Archer DB;Duce IR;Jones D;Candido EPM Title: Microwave radiation can alter protein conformation without bulk heating. Citation: FEBS Letters 543: 93-97 2003 Type: ARTICLE Genes: Abstract: Exposure to microwave radiation enhances the aggregation of bovine serum albumin in vitro in a time- and temperature-dependent manner. Microwave radiation also promotes amyloid fibril formation by bovine insulin at 60degreesC. These alterations in protein conformation are not accompanied by measurable temperature changes, consistent with estimates from field modelling of the specific absorbed radiation (15-20 mW kg(-1)). Limited denaturation of cellular proteins could explain our previous observation that modest heat-shock responses are induced by microwave exposure in Caenorhabditis elegans. We also show that heat-shock responses both to heat and microwaves are suppressed after RNA interference ablating heat-shock factor function. ------------------- Key: 5902 Medline: 12753928 Authors: Adachi A;Shinjyo N;Fujita D;Miyoshi H;Amino H;Watanabe Y;Kita K Title: Complementation of Escherichia coli ubiF mutation by Caenorhabditis elegans CLK-1, a product of the longevity gene of the nematode worm. Citation: FEBS Letters 543: 174-178 2003 Type: ARTICLE Genes: clk-1 Abstract: Caenorhabditis elegans CLK-1 was identified from long-lived mutant worms, and is believed to be involved in ubiquinone biosynthesis. The protein belongs to the eukaryotic CLK-1/Coq7p family, which is also similar to the bacterial Coq7 family, that hydroxylates demethoxyubiquinone, resulting in the formation of hydroxyubiquinone, a precursor of ubiquinone. In Escherichia coli, the corresponding reaction is catalyzed by UbiF, a member of a distinct class of hydroxylase. Although previous studies suggested that the eukaryotic CLK-1/Coq7 family is a hydroxylase of demethoxyubiquinone, there was no direct evidence to show the enzymatic activity of the eukaryotic CLK-1/Coq7 family. Here we show that the plasmid encoding C. elegans CLK-1 supported aerobic respiration on a non-fermentable carbon source of E. coli ubiF mutant strain and rescued the ability to synthesize ubiquinone, suggesting that the eukaryotic CLK-1/Coq7p family could ------------------- Key: 5903 Medline: 12668626 Authors: Lakowski B;Eimer S;Gobel C;Bottcher A;Wagler B;Baumeister R Title: Two supperssors of sel-12 encode C2H2 zinc-finger proteins that regulate presenilin transcription in Caenorhabditis elegans. Citation: Development 130: 2117-2128 2003 Type: ARTICLE Genes: apx-1 glp-1 hop-1 lag-1 lin-12 sel-12 spe-4 spr-1 spr-3 spr-4 spr-5 sup-17 byDf1 Abstract: Mutations in presenilin genes are associated with familial Alzheimer's disease in humans and affect LIN-12/Notch signaling in all organisms tested so far. Loss of sel-12 presenilin activity in Caenorhabditis elegans results in a completely penetrant egg-laying defect. In screens for extragenic suppressors of the sel-12 egg-laying defect, we have isolated mutations in at least five genes. We report the cloning and characterization of spr-3 and spr-4, which encode large basic C2H2 zinc-finger proteins. Suppression of sel-12 by spr-3 and spr-4 requires the activity of the second presenilin gene, hop-L Mutations in both spr-3 and spr-4 de-repress hop-1 transcription in the early larval stages when hop-1 expression is normally nearly undetectable. As sel-12 and hop-1 are functionally redundant, this suggests that mutations in spr-3 and spr-4 bypass the need for one presenilin by stage-specifically derepressing the transcription of the other. Both spr-3 and spr-4 code for proteins similar to the human REST/NRSF (Re1 silencing transcription factor/neural-restrictive silencing factor) transcriptional repressors. As other Spr genes encode proteins homologous to components of the CoREST co-repressor complex that interacts with REST, and the INHAT (inhibitor of acetyltransferase) corepressor complex, our data suggest that all Spr genes may function through the same mechanism that involves transcriptional repression of the hop-1 locus. ------------------- Key: 5904 Medline: 12785095 Authors: Bullard B;Linke WA;Leonard K Title: Varieties of elastic protein in invertebrate muscles. Citation: Journal of Muscle Research and Cell Motility 23: 435-447 2002 Type: REVIEW Genes: unc-22 Abstract: Elastic proteins in the muscles of a nematode (Caenorhabditis elegans), three insects (Drosophila melanogaster, Anopheles gambiae, Bombyx mori) and a crustacean (Procambus clarkii) were compared. The sequences of thick filament proteins, twitchin in the worm and projectin in the insects, have repeating modules with fibronectin-like (Fn) and immunoglobulin-like (Ig) domains conserved between species. Projectin has additional tandem Igs and an elastic PEVK domain near the N-terminus. All the species have a second elastic protein we have called SLS protein after the Drosophila gene, sallimus. SLS protein is in the I-band. The N-terminal region has the sequence of kettin which is a spliced product of the gene composed of Ig-linker modules binding to actin. Downstream of kettin, SLS protein has two PEVK domains, unique sequence, tandem Igs, and Fn domains at the end. PEVK domains have repeating sequences: some are long and highly conserved and would have varying elasticity appropriate to different muscles. Insect indirect flight muscle (IFM) has short I-bands and electron micrographs of Lethocerus IFM show fine filaments branching from the end of thick filaments to join thin filaments before they enter the Z-disc. Projectin and kettin are in this region and the contribution of these to the high passive stiffness of Drosophila IFM myofibrils was measured from the force response to length oscillations. Kettin is attached both to actin near the Z-disc and to the end of thick filaments, and extraction of actin or digestion of kettin leads to rapid decrease in stiffness; residual tension is attributable to projectin. The wormlike chain model for polymer elasticity fitted the force-extension curve of IFM myofibrils and the number of predicted Igs in the chain is consistent with the tandem Igs in Drosophila SLS protein. We conclude that passive tension is due to kettin and projectin, either separate or ------------------- Key: 5905 Medline: 12679384 Authors: Aumais JP;Williams SN;Luo W;Nishino M;Caldwell KA;Caldwell GA;Lin SH;Yu-Lee LY Title: Role for NudC, a dynein-associated nuclear movement protein, in mitosis and cytokinesis. Citation: Journal of Cell Science 116: 1991-2003 2003 Type: ARTICLE Genes: nud-1 Abstract: NudC, a nuclear movement protein that associates with dynein, was originally cloned as a mitogen-inducible early growth response gene. NudC forms a biochemical complex with components of the dynein/dynactin complex and is suggested to play a role in translocation of nuclei in proliferating neuronal progenitors as well as in migrating neurons in culture. Here, we show that NudC plays multiple roles in mitosis and cytokinesis in cultured mammalian cells. Altering NudC levels by either small interfering RNA-mediated gene silencing or adenovirus-mediated overexpression resulted in multinucleated cells and cells with persistent intercellular connections and disorganized midzone and midbody matrix. These phenotypes suggest a failure in cytokinesis in NudC altered cells. Further, a key mitotic enzyme, polo-like kinase, is mislocalized from the centrosomes and the midbody in NudC altered cells. Gene silencing of nud-1, the Caenorhabditis elegans ortholog of NudC, led to a loss of midzone microtubules and the rapid regression of the cleavage furrow, which resulted in one-celled embryos containing two nuclei. The loss of midzone microtubule organization owing to silencing of the NudC/nud-1 gene in two systems, coupled with the loss of Plk1 from mitotic structures in mammalian cells, provide clues to the cytokinesis defect and the multinucleation phenotype. Our findings suggest that NudC functions in mitosis and cytokinesis, in part by regulating microtubule organization at the midzone and midbody. ------------------- Key: 5906 Medline: 12756326 Authors: Liu Y;Kuersten S;Huang T;Larsen A;MacMorris M;Blumenthal T Title: An uncapped RNA suggests a model for Caenorhabditis elegans polycistronic pre-mRNA processing. Citation: RNA 9: 677-687 2003 Type: ARTICLE Genes: gpd-2 gpd-3 mai-1 Abstract: Polycistronic pre-mRNAs from Caenohabditis elegans operons are processed by internal cleavage and polyadenylation to create 3' ends of mature mRNAs. This is accompanied by trans-splicing with SL2apprx100 nucleotides downstream of the 3' end formation sites to create the 5' ends of downstream mRNAs. SL2 trans-splicing depends on a U-rich element (Ur), located apprx70 nucleotides upstream of the trans-splice site in the intercistronic region (ICR), as well as a functional 3' end formation signal. Here we report the existence of a novel gene-length RNA, the Ur-RNA, starting just upstream of the Ur element. The expression of Ur-RNA is dependent on 3' end formation as well as on the presence of the Ur element, but does not require a trans-splice site. The Ur-RNA is not capped, and alteration of the location of the Ur element in either the 5' or 3' direction alters the location of the 5' end of the Ur-RNA. We propose that a 5' to 3' exonuclease degrades the precursor RNA following cleavage at the poly(A) site, stopping when it reaches the Ur element, presumably attributable to a bound protein. Part of the function of this protein can be performed by the MS2 coat protein. Recruitment of coat protein to the ICR in the absence of the Ur element results in accumulation of an RNA equivalent to Ur-RNA, and restores trans-splicing. Only SL1, however, is used. Therefore, coat protein is sufficient for blocking the exonuclease and thereby allowing formation of a substrate for trans-splicing, but it lacks the ability to recruit the SL2 snRNP. Our results also demonstrate that MS2 coat protein can be used as an in vivo block to an exonuclease, which should have utility in mRNA stability ------------------- Key: 5907 Medline: Authors: Coux O Title: An interaction map of proteasome subunits. Citation: Biochemical Society Transactions 31: 465-469 2003 Type: ARTICLE Genes: Abstract: Despite the central role of the 26 S proteasome in eukaryotic cells, many facets of its structural organization and functioning are still poorly understood. To learn more about the interactions between its different subunits, as well as its possible functional partners in cells, we performed, with Marc Vidal?s laboratory (Dana-Farber Cancer Institute, Boston, MA, USA), a systematic two-hybrid analysis using Caenorhabditis elegans 26 S proteasome subunits as baits [Davy, Bello, Theirry-Mieg, Vaglio, Hitti, Doucette-Stamm, Theirry-Mieg, Reboul, Boulton,Walhout et al. (2001) EMBO Rep. 2, 821-828]. A pair-wise matrix of all subunit combination allowed us to detect numerous possible intra-complex interactions, among which some had already been reported by others and eight were novel. Interestingly, four new interactions were detected between two ATPases of the 19 S regulatory complex and three alpha-subunits of the 20S proteolytic core. Possibly, these interactions participate in the association of these two complexes to form the 26 S proteasome. Proteasome subunit sequences were also used to screen a cDNA library to identify new interactors of the complex. Among the interactors found, most (58) have no clear connection to the proteasome, and could be either substrates or potential cofactors of this complex. Few interactors (7) could be directly or indirectly linked to proteolysis. The others (12) interacted with more than one proteasome subunit, forming ?interaction clusters? of potential biological interest. ------------------- Key: 5908 Medline: 12737799 Authors: Abrahante JE;Daul AL;Li M;Volk ML;Tennessen JM;Miller EA;Rougvie AE Title: The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs. Citation: Developmental Cell 4: 625-637 2003 Type: ARTICLE Genes: hbl-1 let-7 lin-4 lin-29 lin-41 lin-57 lwDf12 stDf1 syDf1 Abstract: Temporal control of development is an important aspect of pattern formation that awaits complete molecular analysis. We identified lin-57 as a member of the C. elegans heterochronic gene pathway, which ensures that postembryonic developmental events are appropriately timed. Loss of lin-57 function causes the hypodermis to terminally differentiate and acquire adult character prematurely. lin-57 is hbl-1, revealing a role for the worm hunchback homolog in control of developmental time. Significantly, fly hunchback (hb) temporally specifies cell fates in the nervous system. The hbl-1/lin-57 3'UTR is required for postembryonic downregulation in the hypodermis and nervous system and contains multiple putative binding sites for temporally regulated microRNAs, including let-7. Indeed, we find that hbl-1/lin-57 is regulated by let-7, at least in the nervous system. Examination of the hb 3'UTR reveals potential binding sites for known fly miRNAs. Thus, evolutionary conservation of hunchback genes may include temporal control of cell fate specification and ------------------- Key: 5909 Medline: 12737800 Authors: Lin SY;Johnson SM;Abraham M;Vella MC;Pasquinelli A;Gamberi C;Gottlieb E;Slack FJ Title: The C. elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target. Citation: Developmental Cell 4: 639-650 2003 Type: ARTICLE Genes: hbl-1 let-7 lin-4 lin-29 lin-41 mir-69 mir-84 Abstract: hunchback regulates the temporal identity of neuroblasts in Drosophila. Here we show that hbl-1, the C. elegans hunchback ortholog, also controls temporal patterning. Furthermore, hbl-1 is a probable target of microRNA regulation through its 3'UTR. hbl-1 loss-of-function causes the precocious expression of adult seam cell fates. This phenotype is similar to loss-of-function of lin-41, a known target of the let-7 microRNA. Like lin-41 mutations, hbl-1 loss-of-function partially suppresses a let-7 mutation. The hbl-1 3'UTR is both necessary and sufficient to downregulate a reporter gene during development, and the let-7 and lin-4 microRNAs are both required for HBL-1/GFP downregulation. Multiple elements in the hbl-1 3'UTR show complementarity to regulatory microRNAs, suggesting that microRNAs directly control hbl-1. MicroRNAs may likewise function to regulate Drosophila hunchback during temporal patterning of the nervous system. ------------------- Key: 5910 Medline: 12537559 Authors: Nieduszynski CA;Murray J;Carrington M Title: Whole-genome analysis of animal A- and B-type cyclins. Citation: Genome Biology 3: 70.1-70.8 2002 Type: ARTICLE Genes: Abstract: BACKGROUND: Multiple A- and B-type cyclins have been identified in animals, but their study is complicated by varying degrees of functional redundancy. A non-essential phenotype may reflect redundancy with a known or as yet unknown gene. Complete sequencing of several animal genomes has allowed us to determine the size of the mitotic cyclin gene family and therefore to start to address this issue. RESULTS: We analyzed the Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens genomes to identify known and novel A- and B-type cyclin genes and distinguish them from related pseudogenes. We find only a single functional A-type cyclin gene in invertebrates but two in vertebrates. In addition to the single functional cyclin A gene, the C. elegans genome contains numerous cyclin A pseudogenes. In contrast, the number and relationship of B-type cyclins varies considerably between organisms but all contain at least one cyclin B1-like gene and a cyclin B3 gene. CONCLUSIONS: There are three conserved families of mitotic cyclins in animals: A-, B3- and B-type. The precise number of genes within the A- and B-type families varies in different organisms, possibly as an adaptation to their distinct developmental strategies. ------------------- Key: 5911 Medline: 12812794 Authors: Stoyanov CN;Fleischmann M;Suzuki Y;Tapparel N;Gautron F;Streit A;Wood WB;Mueller F Title: Expression of the C. elegans labial orthologue ceh-13 during male tail morphogenesis. Citation: Developmental Biology 259: 137-149 2003 Type: ARTICLE Genes: ceh-13 dbl-1 sma-2 sma-3 sma-4 Abstract: Hox genes are transcriptional regulators of metazoan body regionalization along the anteroposterior axis that act by specifying positional identity in differentiating cells. ceh-13, the labial orthologue in Caenorhabditis elegans, is expressed both during embryogenesis and postembryonic development. Using GFP reporter analysis and immunocytochemistry, we discovered a spatiotemporal pattern of gene expression in the male tail during the L3 and L4 larval stages that is TGF-beta pathway-dependent. Analysis of reporter activity in transgenic animals identified a distinct promoter region driving male tail-specific ceh-13 expression. We also report the interspecies conservation of sequence motifs within this region and speculate that, in the course of evolutionary diversification, ceh-13 may have acquired new functionality while conserving its homeotic role. ------------------- Key: 5912 Medline: 12815436 Authors: Zhong WW;Feng H;Santiago FE;Kipreos ET Title: CUL-4 ubiquitin ligase maintains genome stability by restraining DNA-replication licensing Citation: Nature 423: 885-889 2003 Type: ARTICLE Genes: cdt-1 cul-4 hDf6 qDf4 Abstract: To maintain genome stability, DNA replication is strictly regulated to occur only once per cell cycle. In eukaryotes, the presence of 'licensing proteins' at replication origins during the G1 cell-cycle phase allows the formation of the pre-replicative complex(1). The removal of licensing proteins from chromatin during the S phase ensures that origins fire only once per cell cycle(1). Here we show that the CUL-4 ubiquitin ligase temporally restricts DNA-replication licensing in Caenorhabditis elegans. Inactivation of CUL-4 causes massive DNA re-replication, producing cells with up to 100C DNA content. The C. elegans orthologue of the replication-licensing factor Cdt1 (refs 2, 3) is required for DNA replication. C. elegans CDT-1 is present in G1-phase nuclei but disappears as cells enter S phase. In cells lacking CUL-4, CDT-1 levels fail to decrease during S phase and instead remain constant in the re-replicating cells. Removal of one genomic copy of cdt-1 suppresses the cul-4 re-replication phenotype. We propose that CUL-4 prevents aberrant re-initiation of DNA replication, at least in part, by facilitating the degradation of CDT-1. ------------------- Key: 5913 Medline: 12756232 Authors: Bosher JM;Hahn BS;Legouis R;Sookhareea S;Weimer RM;Gansmuller A;Chisholm AD;Rose AM;Bessereau JL;Labouesse Title: The Caenorhabditis elegans vab-10 spectraplakin isoforms protect the epidermis against internal and external forces. Citation: Journal of Cell Biology 161: 757-768 2003 Type: ARTICLE Genes: vab-10 hDf16 hDf17 Abstract: Morphogenesis of the Caenorhabditis elegans embryo is driven by actin microfilaments in the epidermis and by sarcomeres in body wall muscles. Both tissues are mechanically coupled, most likely through specialized attachment structures called fibrous organelles (FOs) that connect muscles to the cuticle across the epidermis. Here, we report the identification of new mutations in a gene known as vab-10, which lead to severe morphogenesis defects, and show that vab-10 corresponds to the C. elegans spectraplakin locus. Our analysis of vab-10 reveals novel insights into the role of this plakin subfamily. vab-10 generates isoforms related either to plectin (termed VAB-10A) or to microtubule actin cross-linking factor plakins (termed VAB-10B). Using specific antibodies and mutations, we show that VAB-10A and VAB-10B have distinct distributions and functions in the epidermis. Loss of VAB-10A impairs the integrity of FOs, leading to epidermal detachment from the cuticle and muscles, hence demonstrating that FOs are functionally and molecularly related to hemidesmosomes. We suggest that this isoform protects against forces external to the epidermis. In contrast, lack of VAB-10B leads to increased epidermal thickness during embryonic morphogenesis when epidermal cells change shape. We suggest that this isoform protects ------------------- Key: 5914 Medline: 12781129 Authors: Pintard L;Kurz T;Glaser S;Willis JH;Peter M;Bowerman B Title: Neddylation and deneddylation of CUL-3 is required to target MEI-1/Katanin for degradation at the meiosis-to-mitosis transition in C-elegans. Citation: Current Biology 13: 911-921 2003 Type: ARTICLE Genes: csn-1 csn-2 csn-3 csn-4 csn-5 csn-6 cul-3 mei-1 rfl-1 Abstract: Background: SCF (Skp1-Cullin-F-box) complexes are a major class of E3 ligases that are required to selectively target substrates for ubiquitin-dependent degradation by the 26S proteasome. Conjugation of the ubiquitin-like protein Nedd8 to the cullin subunit (neddylation) positively regulates activity of SCF complexes, most likely by increasing their affinity for the E2 conjugated to ubiquitin. The Nedd8 conjugation pathway is required in C. elegans embryos for the ubiquitin-mediated degradation of the microtubule-severing protein MEI-1/Katanin at the meiosis-to-mitosis transition. Genetic experiments suggest that this pathway controls the activity of a CUL-3-based E3 ligase. Counteracting the Nedd8 pathway, the COP9/signalosome has been shown to promote deneddylation of the cullin subunit. However, little is known about the role of neddylation and deneddylation for E3 ligase activity in vivo. Results: Here, we identified and characterized the COP9/signalosome in C. elegans and showed that it promotes deneddylation of CUL-3, a critical target of the Nedd8 conjugation pathway. As in other species, the C. elegans signalosome is a macromolecular complex containing at least six subunits that localizes in the nucleus and the cytoplasm. Reducing COP9/signalosome function by RNAi results in a failure to degrade MEI-1, leading to severe defects in microtubule-dependent processes during the first mitotic division. Intriguingly, reducing COP9/signalosome function suppresses a partial defect in the neddylation pathway; this suppression suggests that deneddylation and neddylation antagonize each other. Conclusions: We conclude that both neddylation and deneddylation of CUL-3 is required for MEI-1 degradation and propose that cycles of CUL-3 neddylation and deneddylation are necessary for its ligase activity in vivo. ------------------- Key: 5915 Medline: 12781130 Authors: Lin X;Qadota H;Moerman DG;Williams BD Title: C. elegans PAT-6/actopaxin plays a critical role in the assembly of integrin adhesion complexes in vivo. Citation: Current Biology 13: 922-932 2003 Type: ARTICLE Genes: deb-1 pat-3 pat-4 pat-6 unc-52 unc-89 unc-97 unc-112 Abstract: Background: The novel focal adhesion protein actopaxin includes tandem unconventional calponin homology (CH) domains and a less well-conserved N-terminal stretch. Dominant-negative studies have implicated actopaxin in focal adhesion formation. Results: PAT-6/actopaxin, the sole actopaxin homolog in C. elegans, is located in body wall muscle attachments that are in vivo homologs of focal adhesions. We show using pat-6 protein null alleles that PAT-6/actopaxin has critical nonredundant roles during attachment maturation. It is required to recruit UNC-89 and myofilaments; to newly forming attachments, and also to reposition the attachments so that they form the highly ordered array of dense body and M line attachments that are characteristic of mature muscle cells. PAT-6/actopaxin is not required for the deposition of UNC-52/perlecan in the basal lamina, nor for the initiation of attachment assembly, including the clustering of integrin into foci and the recruitment of attachment proteins PAT-4/ILK, UNC-112, and DEB-1/vinculin from the cytosol. PAT-6/ actopaxin, PAT-4/ILK, and UNC-112 are each required for the same steps during attachment assembly in vivo, consistent with the notion that they work together in multiprotein complex. Supporting this idea, PAT-4/ILK can simultaneously bind to PAT-6/actopaxin and UNC-112, forming a ternary complex, in yeast three-hybrid assays. Finally, we show that both calponin homology domains are required for PAT-6/actopaxin's critical functions during attachment assembly in vivo. Conclusions: We show directly by loss-of-function genetics that PAT-6/actopaxin plays essential roles during the maturation of integrin-mediated ------------------- Key: 5916 Medline: 12758145 Authors: Gee P;Kent C Title: Multiple isoforms of choline kinase from Caenorhabditis elegans: cloning, expression, purification, and characterization. Citation: Biochimica et Biophysica Acta-Proteins & Proteomics 1648: 33-42 2003 Type: ARTICLE Genes: Abstract: Choline kinase is the first enzymatic step in the CDP-choline pathway for phosphatidylcholine biosynthesis. The genome of the nematode, Caenorhabditis elegans, contains seven genes that appear likely to encode choline and/or ethanolamine kinases. We cloned five and expressed four of these genes, and purified or partially purified three of the encoded enzymes. All expressed proteins had choline kinase activity; those that most closely resemble the mammalian choline kinases were the most active. CKA-2, a very active form, was purified to near homogeneity. The K. values for CKA-2 were 1.6 and 2.4 mM for choline and ATP, respectively, and kat was 74 s(-1). CKA-2 was predominantly a homodimer as assessed by glycerol gradient sedimentation and dynamic light scattering. CKB-2, which was less similar to mammalian choline kinases, had K. values for choline and ATP of 13 and 0.7 mM, and k(cat) was 3.8 s(-1). Both of these highly purified enzymes required magnesium, had very alkaline pH optima, and were much more active with choline as substrate than with ethanolamine. These results provide a foundation for future studies on the structure and function of choline kinases, as well as studies on the genetic analysis of the function of the ------------------- Key: 5917 Medline: 12817143 Authors: Garsin DA;Villanueva JM;Begun J;Kim DH;Sifri CD;Calderwood SB;Ruvkun G;Ausubel FM Title: Long-lived C. elegans daf-2 mutants are resistant to bacterial pathogens. Citation: Science 300: 1921- 2003 Type: ARTICLE Genes: age-1 daf-2 daf-16 mgDf47 Abstract: Our laboratories have studied the mechanisms of aging and immune function in Caenorhabditis elegans. Herein we show that the mechanisms that govern these two processes may be interrelated. ------------------- Key: 5918 Medline: 12750478 Authors: Colombo K;Grill SW;Kimple RJ;Willard FS;Siderovski DP;Gonczy P Title: Translation of polarity cues into asymmetric spindle positioning in Caenorhabditis elegans embryos. Citation: Science 300: 1957-1961 2003 Type: ARTICLE Genes: goa-1 gpa-16 gpr-1 gpr-2 let-99 par-1 par-2 par-3 par-6 Abstract: Asymmetric divisions are crucial for generating cell diversity; they rely on coupling between polarity cues and spindle positioning, but how this coupling is achieved is poorly understood. In one-cell stage Caenorhabditis elegans embryos, polarity cues set by the PAR proteins mediate asymmetric spindle positioning by governing an imbalance of net pulling forces acting on spindle poles. We found that the GoLoco-containing proteins GPR-1 and GPR-2, as well as the Galpha subunits GOA-1 and GPA-16, were essential for generation of proper pulling forces. GPR-1/2 interacted with guanosine diphosphate-bound GOA-1 and were enriched on the posterior cortex in a par-3- and par-2-dependent manner. Thus, the extent of net pulling forces may depend on cortical Galpha activity, which is regulated by anterior-posterior polarity cues through GPR-1/2. ------------------- Key: 5919 Medline: 12827206 Authors: Chan RC;Chan A;Jeon M;Wu TF;Pasqualone D;Rougvie AE;Meyer Title: Chromosome cohesion is regulated by a clock gene paralogue TIM-1. Citation: Nature 423: 1002-1009 2003 Type: ARTICLE Genes: him-1 rec-8 scc-1 syp-1 tim-1 hDf6 sDf4 Abstract: Faithful transmission of the genome requires that a protein complex called cohesin establishes and maintains the regulated linkage between replicated chromosomes before their segregation(1,2). Here we report the unforeseen participation of Caenorhabditis elegans TIM-1, a paralogue of the Drosophila clock protein TIMELESS, in the regulation of chromosome cohesion. Our biochemical experiments defined the C. elegans cohesin complex and revealed its physical association with TIM-1. Functional relevance of the interaction was demonstrated by aberrant mitotic chromosome behaviour, embryonic lethality and defective meiotic chromosome cohesion caused by the disruption of either TIM-1 or cohesin. TIM-1 depletion prevented the assembly of non-SMC ( structural maintenance of chromosome) cohesin subunits onto meiotic chromosomes; however, unexpectedly, a partial cohesin complex composed of SMC components still loaded. Further disruption of cohesin activity in meiosis by the simultaneous depletion of TIM-1 and an SMC subunit decreased homologous chromosome pairing before synapsis, revealing a new role for cohesin in metazoans. On the basis of comparisons between TIMELESS homologues in worms, flies and mice, we propose that chromosome cohesion, rather than circadian clock regulation, is the ancient and conserved function for TIMELESS-like proteins. ------------------- Key: 5920 Medline: 12672828 Authors: Senoo-Matsuda N;Hartman PS;Akatsuka A;Yoshimura S;Ishii N Title: A complex II defect affects mitochondrial structure, leading to ced-3- and ced-4-dependent apoptosis and aging. Citation: Journal of Biological Chemistry 278: 22031-22036 2003 Type: ARTICLE Genes: ced-3 ced-4 ced-9 cyt-1 mev-1 Abstract: The mev-1(kn1) mutation of Caenorhabditis elegans is in Cyt-1, which encodes a subunit of succinate-coenzyme Q oxidoreductase in the mitochondrial electron transport chain. Mutants are hypersensitive to oxidative stress and age precociously in part because of increased superoxide anion production. Here, we show that mev-1 mutants are defective in succinate-coenzyme Q oxidoreductase, possess ultrastructural mitochondrial abnormalities ( especially in muscle cells), show a loss of membrane potential, have altered CED-9 and Cyt-1 protein levels under hyperoxia, and contain ced-3- and ced-4-dependent supernumerary apoptotic cells. These defects likely explain the failure of mev-1 to complete embryonic development under hyperoxia as well as its reduced life span. ------------------- Key: 5921 Medline: 12872911 Authors: Cutter AD;Aviles L;Ward S Title: The proximate determinants of sex ratio in C. elegans populations. Citation: Genetical Research 81: 91-102 2003 Type: ARTICLE Genes: him-5 Abstract: The soil nematode Caenorhabditis elegans is an example of a species in which self-fertilizing hermaphrodites predominate, but functional males continue to persist - allowing outcrossing to persevere at low levels. Hermaphrodites can produce male progeny as a consequence of sex chromosome non-disjunction or via outcrossing with males. Consequently, the genetics of sex determination coupled with the efficiency by which males find, inseminate and obtain fertilizations with hermaphrodites will influence the frequency at which males and outcrossing occurs in such populations. Behavioural and physiological traits with a heritable basis, as well as ecological characters, may influence male reproductive success and therefore sex ratio. Because sex ratio is tied to male reproductive success, sex ratio greatly affects outcrossing rates, patterns of genetic variation, and the ability of natural selection to act within populations. In this paper we explore the determinants of male frequency in C. elegans with a mathematical model and experimental data. We address the role of the genetic machinery of sex determination via sex chromosome non-disjunction on sex ratio and the influence of physiological components of C. elegans' life history that contribute to variation in sex ratio by way of male reproductive success. Finally, we discuss the short-term and long-term factors that are likely to affect sex ratio and breeding system evolution in species like C. ------------------- Key: 5922 Medline: 12791262 Authors: Pires-daSilva A;Sommer RJ Title: Finally, worm Polycomb-like genes meet Hox regulation. Citation: Developmental Cell 4: 770-772 2003 Type: REVIEW Genes: mab-3 mab-5 mes-2 mes-3 mes-6 pal-1 sop-2 Abstract: Polycomb and Trithorax group proteins have been shown to regulate Hox gene expression in files and mammals, but not in worms. Two reports in this issue of Developmental Cell establish a first link between Polycomb-like genes and Hox gene regulation in C. elegans. However, sequence comparison indicates that these genes may not be homologous to the fly Polycomb genes, suggesting that independent gene recruitment occurred during nematode evolution. ------------------- Key: 5923 Medline: 12791273 Authors: Ross JM;Zarkower D Title: Polycomb group regulation of Hox gene expression in C. elegans. Citation: Developmental Cell 4: 891-901 2003 Type: ARTICLE Genes: egl-5 lin-32 lin-39 mab-3 mab-5 mec-7 mes-2 mes-3 mes-4 mes-6 pal-1 Abstract: Polycomb group (PcG) chromatin proteins regulate homeotic genes in both animals and plants. In Drosophila and vertebrates, PcG proteins form complexes and maintain early patterns of Hox gene repression, ensuring fidelity of developmental patterning. PcG proteins in C. elegans form a complex and mediate transcriptional silencing in the germline, but no role for the C. elegans PcG homologs in somatic Hox gene regulation has been demonstrated. Surprisingly, we find that the PcG homologs MES-2. [E(Z)]- and MES-6 (ESC), along with MES-3, a protein Without known homologs, do repress Hox expression in C. elegans. mes. mutations cause anteroposterior transformations and disrupt Hox-dependent neuroblast migration. Thus, as in Drosophila, vertebrates, and plants, C. elegrans PcG proteins regulate key developmental patterning genes to establish positional identity. ------------------- Key: 5924 Medline: 12791274 Authors: Zhang H;Azevedo RBR;Lints R;Doyle C;Teng Y;Haber D;Emmons Title: Global regulation of Hox gene expression in C. elegans by a SAM domain protein. Citation: Developmental Cell 4: 903-915 2003 Type: ARTICLE Genes: bar-1 ceh-13 egl-5 elt-2 lin-39 mab-5 mec-4 pkd-2 pry-1 sop-2 tph-1 Abstract: Polycomb group (PcG)-mediated repression of C. elegrans Hox genes has not been demonstrated, and genes homologous to components of one of the PcG complexes (PRC1) have not been identified in the C. elegans genome. We find that a mechanism of general Hox gene repression exists in C. elegans, carried out in part by SOP-2, a protein related to, but not orthologous with, any PcG protein. sop-2 mutations lead to widespread ectopic expression of Hox genes and homeotic transformations. SOP-2 contains a SAM domain, a self-associating protein domain found in other repressors, including a core component of PRC1 and ETS transcription factors. Phylogenetic analysis indicates that this domain is more closely related to those of the ETS family than to those of PcG proteins. The results suggest that global repression of Hox genes has been taken over by a different branch of the SAM domain family during the evolution of nematodes. ------------------- Key: 5925 Medline: 12781683 Authors: Badrinath AS;White JG Title: Contrasting patterns of mitochondrial redistribution in the early lineages of Caenorhabditis elegans and Acrobeloides sp. PS1146. Citation: Developmental Biology 258: 70-75 2003 Type: ARTICLE Genes: nop-1 par-1 par-3 Abstract: We compared the redistribution of mitochondria in the early embryos of Caenorhabditis elegans (C. elegans) and Acrobeloides sp. PS1146 (Acrobeloides)-two nematode species where the mechanisms for embryonic axis specification are different even though subsequent development is remarkably similar (Goldstein et al., 1998). During the first cell cycle of C. elegans, mitochondria move with the bulk cytoplasmic flows that are directed toward the sperm pronucleus and aggregate at the posterior cortex during the period known as "pseudocleavage." In contrast, in Acrobeloides embryos, where prominent cytoplasmic rearrangements are absent, mitochondria that are initially distributed loosely around the pronuclei and the cytoplasm are relocated around the mitotic spindle prior to cell division. Interestingly, this rearrangement is reiterated only in the germline and not the somatic lineage. In both species, the location of the mitochondria immediately prior to cell division correlates with the known location of the germline determinants, P granules, leading us to speculate that they may be associated. ------------------- Key: 5926 Medline: 12765772 Authors: Haslam SM;Dell A Title: Hallmarks of Caenorhabditis elegans N-glycosylation: complexity and controversy. Citation: Biochimie 85: 25-32 2003 Type: REVIEW Genes: Abstract: Caenorhabditis elegans has become one of the most widely used model organisms for a range of molecular cell biological applications and is being increasingly used by glycobiologists. However, a major problem has been the lack of knowledge of the structure of the protein-linked glycans from this organism. In recent years several groups have published structural data, particularly N-glycan structural data. However, some of these data are contradictory. In this review we critically assess all the N-glycan structural data and consider how close we are in our goal of defining the glycome of C. elegans. ------------------- Key: 5927 Medline: 12770777 Authors: Chen SH;Spence AM;Schachter H Title: Isolation of null alleles of the Caenorhabditis elegans gly-12, gly-13 and gly-14 genes, all of which encode UDP-GlcNAc: alpha-3-D-mannoside beta1,2-N-acetylglucosaminyltransferase I activity. Citation: Biochimie 85: 391-401 2003 Type: ARTICLE Genes: gly-12 gly-13 gly-14 Abstract: UDP-GlcNAc: alpha-3-D-mannoside beta1,2-N-acetylglucosaminyltransferase I (GnT I) is a Golgi-resident enzyme which transfers a GlcNAc residue in beta1,2 linkage to the Manalpha1,3Manbeta-terminus of (Manalpha1,6(Manalpha1,3)Manalpha1,6)(Manalpha1,3)Manbeta1, 4GlcNAcbeta1,4G lcNAc-Asn-protein, thereby initiating the synthesis of hybrid N-glycans. Three Caenorhabditis elegans genes homologous to mammalian GnT I (designated gly-12, gly-13 and gly-14) have been cloned. All three cDNAs encode proteins with GnT I enzyme activity. We report in this paper the preparation by ultra-violet (UV) light irradiation in the presence of trimethylpsoralen, of mutants lacking either gly-12, gly-13 or gly-14. A double null mutation in the gly-12 and gly-14 genes (gly-14; gly-12) has also been prepared. These mutations are intragene deletions, removing large portions of the GnT I catalytic domain, and are therefore, all molecular nulls. The gly-12 and gly-14 mutants as well as the gly-14; gly-12 double mutant all displayed wild-type phenotypes, indicating that neither gly-12 nor gly-14 is necessary for worm development under standard laboratory conditions. In contrast, about 60% of the mutants lacking the gly-13 gene arrested as L1 larvae at 20 degreesC and the remaining 40% homozygous worms grew to adulthood but displayed severe morphological and behavioral defects despite the presence of the other two GnT I genes, gly-12 and gly-14. Attempts to rescue the gly-13 null phenotype with the wild type transgene were not successful. However, lethality co-segregated with the gly-13 deletion within 0.02 map units (mu) in genetic mapping experiments, suggesting that the gly-13 mutation is responsible for the phenotype. ------------------- Key: 5928 Medline: 12853115 Authors: Tsang WY;Lemire BD Title: The role of mitochondria in the life of the nematode Caenorhabditis elegans Citation: Biochimica et Biophysica Acta 1638: 91-105 2003 Type: REVIEW Genes: anc-1 atp-1 atp-2 atp-3 cco-1 clk-1 coq-3 ctb-1 cyc-1 daf-2 daf-12 dif-1 drp-1 fem-1 fem-3 gas-1 glp-1 isp-1 lrs-2 mev-1 nuo-1 nuo-2 uaDf5 Abstract: Mitochondria are essential organelles involved in energy metabolism via oxidative phosphorylation. They play a vital role in diverse biological processes such as aging and apoptosis. In humans, defects in the mitochondrial respiratory chain (MRC) are responsible for or associated with a bewildering variety of diseases. The nematode Caenorhabditis elegans is a simple animal and a powerful genetic and developmental model system. In this review, we discuss how the nematode model system has contributed to our understanding of mitochondrial dynamics, of the genetics and inheritance of the mitochondrial genome, and of the consequences of nuclear and mitochondrial DNA (mtDNA) mutations. Mitochondrial respiration is vital to energy metabolism but also to other aspects of multicellular life such as aging and development. We anticipate that further significant contributions to our understanding of mitochondrial function in animal biology are forthcoming with the C. elegans model system. ------------------- Key: 5929 Medline: 12597772 Authors: Patton JR;Padgett RW Title: Caenorhabditis elegans pseudouridine synthase 1 activity in vivo: tRNA is a substrate, but not U2 small nuclear RNA. Citation: Biochemical Journal 372: 595-602 2003 Type: ARTICLE Genes: Abstract: The formation of pseudouridine (Psi) from uridine is post-transcriptional and catalysed by pseudouridine synthases, several of which have been characterized from eukaryotes. Pseudouridine synthase 1 (Pus1p) has been well characterized from yeast and mice. In yeast, Pus1p has been shown to have dual substrate specificity, modifying uridines in tRNAs and at position 44 in U2 small nuclear RNA (U2 snRNA). In order to study the in vivo activity of a metazoan Pus1p, a knockout of the gene coding for the homologue of Pus1p in Caenorhabditis elegans was obtained. The deletion encompasses the first two putative exons and includes the essential aspartate that is required for activity in truA pseudouridine synthases. The locations of most modified nucleotides on small RNAs in C. elegans are not known, and the The uridine at position 27 of tRNA(Val) (AAC), a putative Pus1p-modification site, was converted into Psi in the wild-type worms, but the tRNA(Val) (AAC) from mutant worms lacked the modification. Psi formation at positions 13, 32, 38 and 39, all of which should be modified by other pseudouridine synthases, was not affected by the loss of Puslp. The absence of Puslp in C. elegans had no effect on the modification of U2 snRNA in vivo, even though worm U2 snRNA has a Psi, at position 45 (the equivalent of yeast U2 snRNA position 44) and at four other positions. This result was unexpected, given the known dual specificity of yeast Pus1p. ------------------- Key: 5930 Medline: 12781695 Authors: Lin R Title: A gain-of-function mutation in oma-1, a C. elegans gene required for oocyte maturation, results in delayed degradation of maternal proteins and embryonic lethality. Citation: Developmental Biology 258: 226-239 2003 Type: ARTICLE Genes: med-1 med-2 mex-1 mex-3 mex-5 oma-1 oma-2 pie-1 pos-1 skn-1 wrm-1 eDf18 Abstract: In vertebrates, oocytes undergo maturation, arrest in metaphase II, and can then be fertilized by sperm. Fertilization initiates molecular events that lead to the activation of early embryonic development. In Caenorhabditis elegans, where no delay between oocyte maturation and fertilization is apparent, oocyte maturation and fertilization must be tightly coordinated. It is not clear what coordinates the transition from an oocyte to an embryo in C elegans, but regulated turnover of oocyte-specific proteins contributes to the process. We describe here a gain-of-function mutation (zu405) in a gene that is essential for oocyte maturation, oma-1. In wild type animals, OMA-1 protein is expressed at a high level exclusively in oocytes and newly fertilized embryos and is degraded rapidly after the first mitotic division. The zu405 mutation results in improper degradation of the OMA-1 protein in embryos. In oma-1(zu405) embryos, the C blastomere is transformed to the EMS blastomere fate, resulting in embryonic lethality. We show that degradation of several maternally supplied cell fate determinants, including SKN-1, PIE-1, MEX-3, and MEX-5, is delayed in oma-1(zu405) mutant embryos. In wild type embryos, SKN-1 functions in EMS for EMS blastomere fate specification. A decreased level of maternal SKN-1 protein in the C blastomere relative to EMS is believed to be responsible for this cell expressing the C, instead of the EMS, fate. Delayed degradation of maternal SKN-1 protein in oma-1(zu405) embryos and resultant elevated levels in C blastomere is likely responsible for the observed C-to-EMS blastomere fate transformation. These observations suggest that oma-1, in addition to its role in oocyte maturation, contributes to early embryonic development by regulating the temporal degradation of maternal proteins in early C. elegans embryos. ------------------- Key: 5931 Medline: 12783801 Authors: Fay DS;Large E;Han M;Darland M Title: lin-35/Rb and ubc-18, an E2 ubiquitin-conjugating enzyme, function redundantly to control pharyngeal morphogenesis in C. elegans. Citation: Development 130: 3319-3330 2003 Type: ARTICLE Genes: ajm-1 chd-4 efl-1 hda-1 let-418 lin-35 lin-36 lin-37 lin-53 myo-2 pha-4 rrf-3 slr-5 ubc-18 unc-119 nDf16 Abstract: The retinoblastoma gene product has been implicated in regulation of multiple cellular and developmental processes, including a well-defined role in the control of cell cycle progression. The Caenorhabditis elegans retinoblastoma protein homolog, LIN-35, is also a key regulator of cell cycle entry and, as shown by studies of synthetic multivulval genes, plays an important role in the determination of vulval cell fates. We demonstrate an additional and unexpected function for lin-35 in organ morphogenesis. Using a genetic approach to isolate lin-35 synthetic-lethal mutations, we have identified redundant roles for lin-35 and ubc-18, a gene that encodes an E2 ubiquitin-conjugating enzyme closely related to human UBCH7. lin-35 and ubc-18 cooperate to control one or more steps during pharyngeal morphogenesis. Based on genetic and phenotypic analyses, this role for lin-35 in pharyngeal morphogenesis appears to be distinct from its cell cycle-related functions. lin-35 and ubc-18 may act in concert to regulate the levels of one ore more critical targets during C. elegans development. ------------------- Key: 5932 Medline: 12769849 Authors: Grad Y;Aach J;Hayes GD;Reinhart BJ;Church GM;Ruvkun G;Kim J Title: Computational and experimental identification of C. elegans microRNAs. Citation: Molecular Cell 11: 1253-1263 2003 Type: ARTICLE Genes: let-7 lin-4 lin-14 lin-41 mir-1 mir-2 mir-6 mir-11 mir-13 mir-27 mir-28 mir-34 mir-43 mir-47 mir-56-2 mir-72 mir-79 mir-200 mir-228 mir-236 mir-263 mir-264 mir-266 mir-269 mir-273 Abstract: MicroRNAs (miRNAs) constitute an extensive class of noncoding RNAs that are thought to regulate the expression of target genes via complementary base-pair interactions. To date, cloning has identified over 200 miRNAs from diverse eukaryotic organisms. Despite their success, such biochemical approaches are skewed toward identifying abundant miRNAs, unlike genome-wide, sequence-based computational predictions. We developed informatic methods to predict miRNAs in the C. elegans genome using sequence conservation and structural similarity to known miRNAs and generated 214 candidates. We confirmed the expression of four new miRNAs by Northern blotting and used a more sensitive PCR approach to verify the expression of ten additional candidates. Based on hypotheses underlying our computational methods, we estimate that the C. elegans genome may encode between 140 and 300 miRNAs and potentially many more. ------------------- Key: 5933 Medline: Authors: Kaji H;Saito H;Yamauchi Y;Shinkawa T;Taoka M;Hirabayashi J;Kasai K;Takahashi N;Isobe T Title: Lectin affinity capture, isotope-coded tagging and amss spectrometry to identify N-linked glycoproteins. Citation: Nature Biotechnology 21: 667-672 2003 Type: ARTICLE Genes: Abstract: We describe here a strategy for the large-scale identification of N-glycosylated proteins from a complex biological sample. The approach, termed isotope-coded glycosylation-site-specific tagging (IGOT), is based on the lectin column-mediated affinity capture of a set of glycopeptides generated by tryptic digestion of protein mixtures, followed by peptide-N-glycosidase-mediated incorporation of a stable isotope tag, O-18, specifically into the N-glycosylation site. The O-18-tagged peptides are then identified by multi-dimensional liquid chromatography-mass spectrometry (LC-MS)-based technology. The application of this method to the characterization of N-linked high-mannose and/or hybrid-type glycoproteins from an extract of Caenorhabditis elegans proteins allowed the identification of 250 glycoproteins, including 83 putative transmembrane proteins, with the simultaneous determination of 400 unique N-glycosylation sites. Because the method is applicable to the systematic identification of a wide range of glycoproteins, it should facilitate basic glycobiology research and may be useful for diagnostic applications, such as genome-wide screening for disease-related ------------------- Key: 5934 Medline: 12757752 Authors: Hu Y;Tanriverdi F;MacColl GS;Bouloux PMG Title: Kallmann's syndrome: molecular pathogenesis. Citation: International Journal of Biochemistry & Cell Biology 35: 1157-1162 2003 Type: REVIEW Genes: kal-1 Abstract: Kallmann's syndrome (KS) is a genetic condition characterised by hypogonadotrophic hypogonadism (HH) and anosmia; although these are the defining features of the condition, additional neurological and non-neurological sequel may also occur depending on the specific mode of inheritance. KS affects about 1 in 8000 males and 1 in 40,000 females, with most presentations being of the 'sporadic' type. Of the inherited forms, hitherto, only the gene responsible for the X-linked form (X-KS), namely KAL-1, has been identified and the encoded protein, anosmin-1, consists primarily of a whey acidic protein (WAP) and fibronectin-like type III (FnIII) domains which appear to mediate distinctly different protein functions. The WAP/FnIII combination is conserved in anosmins across species and recent studies in rodents and in Caenorhabditis elegans demonstrate that anosmin functions in both axonal targeting and branching. Screening for loci that modify these phenotypes in C. elegans has identified heparan-6-O-sulpbotransferase as a key interactor mediating anosmin-1 function. Furthermore, over-expression and loss of function of the C elegans Kal-1 gene disrupt epidermal morphogenesis, resulting in ventral enclosure and male tail formation defects. These findings provide novel insights into the molecular pathogenesis of X-KS. ------------------- Key: 5935 Medline: 12743019 Authors: Pleasance ED;Marra MA;Jones SJM Title: Assessment of SAGE in transcript indentification. Citation: Genome Research 13: 1203-1215 2003 Type: ARTICLE Genes: Abstract: An essential step in Serial Analysis of Gene Expression (SAGE) is tag mapping, which refers to the unambiguous determination of the gene represented by a SAGE tag. Current resources for tag mapping are incomplete, and thus do not allow assessment of the efficacy of SAGE in transcript identification. A method of tag mapping is described here and applied to the Drosophila melanogaster and Caenorhabditis elegans genomes, which permits detailed SAGE assessment and provides tag-mapping resources that were unavailable previously for these organisms. In our method, a conceptual transcriptome is constructed using genomic Sequence and annotation by extending predicted coding regions to include UTRs on the basis of EST and cDNA alignments, UTR length distributions, and polyadenylation signals. Analysis of extracted tags Suggests that, using the standard SAGE procedure, expression of 8% of D. melanogaster and 15% of C elegans genes cannot be detected unambiguously by SAGE due to shared sequence or lack of NlaIII-anchoring enzyme sites. Both increasing tag length by 2-3 bp and using Sau3A instead of NlaIII as the anchoring enzyme increases potential for transcript detection. This work identifies and quantifies genes not amenable to SAGE analysis, in addition to providing ------------------- Key: 5936 Medline: 12791258 Authors: Peisach D;Gee P;Kent C;Xu Z Title: The crystal structure of choline kinase reveals a eukaryotic protein kinase fold. Citation: Structure 11: 703-713 2003 Type: ARTICLE Genes: Abstract: Choline kinase catalyzes the ATP-dependent phosphorylation of choline, the first committed step in the CDP-choline pathway for the biosynthesis of phosphatidylcholine. The 2.0 Angstrom crystal structure of a choline kinase from C. elegans (CKA-2) reveals that the enzyme is a homodimeric protein with each monomer organized into a two-domain fold. The structure is remarkably similar to those of protein kinases and aminoglycoside phosphotransferases, despite no significant similarity in amino acid sequence. Comparisons to the structures of other kinases suggest that ATP binds to CKA-2 in a pocket formed by highly conserved and catalytically important residues. In addition, a choline binding site is proposed to be near the ATP binding pocket and formed by several structurally flexible loops. ------------------- Key: 5937 Medline: 12808038 Authors: Mito Y;Sugimoto A;Yamamoto M Title: Distinct developmenal function of two Caenorhabditis elegans homologs of the cohesin subunit Scc1/Rad21. Citation: Molecular Biology of the Cell 14: 2399-2409 2003 Type: ARTICLE Genes: coh-1 coh-2 coh-3 him-1 scc-1 scc-3 smc-1 smc-3 Abstract: Cohesin, which mediates sister chromatid cohesion, is composed of four subunits, named Scc1/Rad21, Scc3, Smc1, and Smc3 in yeast. Caenorhabditis elegans has a single homolog for each of Scc3, Smc1, and Smc3, but as many as four for Scc1/Rad21 (COH-1, SCC-1/COH-2, COH-3, and REC-8). Except for REC-8 required for meiosis, function of these C. elegans proteins remains largely unknown. Herein, we examined their possible involvement in mitosis and development. Embryos depleted of the homolog of either Scc3, or Smc1, or Smc3 by RNA interference revealed a defect in mitotic chromosome segregation but not in chromosome condensation and cytokinesis. Depletion of SCC-1/COH-2 caused similar phenotypes. SCC-1/COH-2 was present in cells destined to divide. It localized to chromosomes in a cell cycle-dependent manner. Worms depleted of COH-1 arrested at either the late embryonic or the larval stage, with no indication of mitotic dysfunction. COH-1 associated chromosomes throughout the cell cycle in all somatic cells undergoing late embryogenesis or larval development. Thus, SCC-1/COH-2 and the homologs of Scc3, Smc1, and Smc3 facilitate mitotic chromosome segregation during the development, presumably by forming a cohesin complex, whereas COH-1 seems to play a role important for development but unrelated to mitosis. ------------------- Key: 5938 Medline: 12808046 Authors: Mercer KB;Flaherty DB;Miller RK;Qadota H;Tinley TL;Moerman DG;Benian GM Title: Caenorhabditis elegans UNC-98, a C2H2 Zn finger protein, is a novel partner of UNC-97/PINCH in muscle adhesion complexes. Citation: Molecular Biology of the Cell 14: 2492-2507 2003 Type: ARTICLE Genes: unc-97 unc-98 sfDf1 stDf6 stDf6 uDf1 stDp2 Abstract: To further understand the assembly and maintenance of the muscle, contractile apparatus, we have identified a new protein, UNC-98, in the muscle of Caenorhabditis elegans. unc-98 mutants display reduced motility and a characteristic defect in muscle structure. We show that the major defect in the mutant muscle is in the M-lines and dense, bodies (Z-Iine analogs). Both functionally and compositionally, nematode M-lines and dense bodies are analogous to focal adhesions of nonmuscle cells. UNC-98 is a novel 310-residue polypeptide consisting of four C2H2 Zn fingers and several possible nuclear localization signal and nuclear export signal sequences. By use of UNC-98 antibodies and green fluorescent protein fusions (to full-length UNC-98 and UNC-98 fragments), we have shown that UNC-98 resides at M-lines, muscle cell nuclei, and possibly at dense bodies. Furthermore, we demonstrated that 1) the N-terminal 106 amino adds are both necessary and sufficient for nuclear localization, and 2) the C-terminal (fourth) Zn finger is required for localization to Wines and dense bodies. UNC-98 interacts with UNC-97, a C. elegans homolog of PINCH. We propose, that UNC-98 is both a structural component of muscle focal adhesions and a nuclear protein that influences gene expression. ------------------- Key: 5939 Medline: 12807436 Authors: Lakso M;Vartiainen S;Moilanen AM;Sirvio J;Thomas JH;Nass R;Blakely RD;Wong G Title: Dopaminergic neuronal loss and motor deficits in Caenorhabditis elegans overexpressing human Citation: Journal of Neurochemistry 86: 165-172 2003 Type: ARTICLE Genes: acr-2 aex-3 dat-1 unc-30 Abstract: Overexpression of human alpha-synuclein in model systems, including cultured neurons, drosophila and mice, leads to biochemical and pathological changes that mimic synucleopathies including Parkinson's disease. We have overexpressed both wild-type (WT) and mutant alanine53-->threonine (A53T) human alpha-synuclein by transgenic injection into Caenorhabditis elegans . Motor deficits were observed when either WT or A53T alpha-synuclein was overexpressed with a pan-neuronal or motor neuron promoter. Neuronal and dendritic loss were accelerated in all three sets of C. elegans dopaminergic neurons when human alpha-synuclein was overexpressed under the control of a dopaminergic neuron or pan-neuronal promoter, but not with a motor neuron promoter. There were no significant differences in neuronal loss between overexpressed WT and A53T forms or between worms of different ages (4 days, 10 days or 2 weeks). These results demonstrate neuronal and behavioral perturbations elicited by human alpha-synuclein in C. elegans that are dependent upon expression in specific neuron subtypes. This transgenic model in C. elegans , an invertebrate organism with excellent experimental resources for further genetic manipulation, may help facilitate dissection of pathophysiologic mechanisms of various synucleopathies. ------------------- Key: 5940 Medline: 12728011 Authors: White GE;Petry CM;Schachat F Title: The pathway of myofibrillogenesis determines the interrelationship between myosin and paramyosin synthesis in Caenorhabditis elegans. Citation: Journal of Experimental Biology 206: 1899-1906 2003 Type: ARTICLE Genes: unc-15 unc-54 Abstract: Examination of null mutants in myosin B and paramyosin yields insights into the complex mechanisms that regulate expression of the three major components of Caenorhabditis elegans body-wall muscle thick filaments myosin A, myosin B and paramyosin. In the absence of myosin B, paramyosin accumulation is reduced, although neither its synthesis nor that of myosin A is affected. This implies that the interaction of myosin B with paramyosin inhibits paramyosin degradation. By contrast, the absence of paramyosin results in reduced synthesis and accumulation of myosin B but has no effect on myosin A synthesis. The non-reciprocal effects of the null mutants on turnover and synthesis are best understood as an epigenetic phenomenon that reflects the pathway of thick filament assembly. The synthesis of myosin A and paramyosin, which are involved in the initial steps of thick filament formation, is independent of myosin B; however, a properly assembled paramyosin-containing thick filament core is essential for efficient synthesis of myosin B. ------------------- Key: 5941 Medline: 12682045 Authors: Mendel J;Heinecke K;Fyrst H;Saba JD Title: Sphingosine phosphate lyase expression is essential for normal development in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 278: 22341-22349 2003 Type: ARTICLE Genes: spl-1 Abstract: Sphingolipids are ubiquitous membrane constituents whose metabolites function as signaling molecules in eukaryotic cells. Sphingosine 1-phosphate, a key sphingolipid second messenger, regulates proliferation, motility, invasiveness, and programmed cell death. These effects of sphingosine 1-phosphate and similar phosphorylated sphingoid bases have been observed in organisms as diverse as yeast and humans. Intracellular levels of sphingosine 1-phosphate are tightly regulated by the actions of sphingosine kinase, which is responsible for its synthesis and sphingosine-1-phosphate phosphatase and sphingosine phosphate lyase, the two enzymes responsible for its catabolism. In this study, we describe the cloning of the Caenorhabditis elegans sphingosine phosphate lyase gene along with its functional expression in Saccharomyces cerevisiae. Promoter analysis indicates tissue-specific and developmental regulation of sphingosine phosphate lyase gene expression. Inhibition of C. elegans sphingosine phosphate lyase expression by RNA interference causes accumulation of phosphorylated and unphosphorylated long-chain bases and leads to poor feeding, delayed growth, reproductive abnormalities, and intestinal damage similar to the effects seen with exposure to Bacillus thuringiensis toxin. Our results show that sphingosine phosphate lyase is an essential gene in C. elegans and suggest that the sphingolipid degradative pathway plays a conserved role in regulating animal ------------------- Key: 5942 Medline: 12836820 Authors: Estes S;Lynch M Title: Rapid fitness recovery in mutationally degraded lines of Caenorhabditis elegans. Citation: Evolution 57: 1022-1030 2003 Type: ARTICLE Genes: Abstract: Deleterious mutation accumulation has been implicated in many biological phenomena and as a potentially significant threat to human health and the persistence of small populations. The vast majority of mutations with effects on fitness are known to be deleterious in a given environment, and their accumulation results in mean population fitness decline. However, whether populations are capable of recovering from negative effects of prolonged genetic bottlenecks via beneficial or compensatory mutation accumulation has not previously been tested. To address this question, long-term mutation-accumulation lines of the nematode Caenorhabditis elegans, previously propagated as single individuals each generation, were maintained in large population sizes under competitive conditions. Fitness assays of these lines and comparison to parallel mutation-accumulation lines and the ancestral control show that, while the process of fitness restoration was incomplete for some lines, full recovery of mean fitness was achieved in fewer than 80 generations. Several lines of evidence indicate that this fitness restoration was at least partially driven by compensatory mutation accumulation rather than a result of a generic form of laboratory adaptation. This surprising result has broad implications for the influence of the mutational process on many issues in evolutionary and conservation biology. ------------------- Key: 5943 Medline: Authors: Madi A;Mikkat S;Ringel B;Thiesen HJ;Glocker MO Title: Profiling stage-dependent changes of protein expression in Caenorhabditis elegans by mass spectrometric proteome analysis leads to the identification of stage-specific marker proteins. Citation: Electrophoresis 24: 1809-1817 2003 Type: ARTICLE Genes: asp-1 cct-5 dim-1 gpd-1 hsp-6 hsp-16.2 ifb-2 lec-1 lin-53 lmn-1 mdh-1 nud-1 rsp-12 sod-1 tbb-1 tbb-2 tmy-1 unc-60 vit-2 Abstract: Proteome maps obtained by synchronization of the wild-type Caenorhabditis elegans development reflected stage-dependent molecular differences and revealed dynamic cytoskeletal processes during ontogenesis. Distinct protein spots that may function as molecular markers for the corresponding developmental stages were mass spectrometrically identified. The amount of the Cu2+-Zn2+ superoxide dismutase (CE23550) and an aspartyl proteinase (CE21681) was highest in the first larval stage (L1) and decreased during the ontogenesis from the first larval stage to the adult. Tropomyosin III (CE29059) was prominently present in the first and second larval stage (L1/L2). Abundances of actin 1 or 4 (CE12358 or CE13148) and tropomyosin I (CE28782) were particularly high in multiple spots in the third larval stage (L3). Interestingly, the amount of DIM-1 protein (CE27706), reflected by two spots, was the lowest in this stage. A particular splicing factor (CE31089) was detected only in the fourth larval stage (L4), whereas a spot with high abundance representing the cuticle collagen (CE02272) was only found highly expressed in adult animals (A). In addition, a Ca2+- binding protein (CE12368) and one protein spot which has not yet been identified, both reached their maximal spot intensities in the adult stage (A). Moreover, the ASP-1, CCT-5, GPD-1, GPD-2, HSP-6, HSP-16.2, LEC-2, LEC-2, LIN-53, LMN-1, MDH-1, NUD-1, RPA-0, RSP-12, SOD-1, TBB-1, TBB-2, TMY-1, UNC-60, and VIT-2 proteins for which mutants are available and two still unidentified protein spots which were present in all developmental stages, have been reproducibly localized in proteome maps of distinct ------------------- Key: 5945 Medline: 12814548 Authors: Gotta M;Dong Y;Peterson YK;Lanier SM;Ahringer J Title: Asymmetrically distributed C. elegans homologs of AGS3/PINS control spindle position in the early embryo. Citation: Current Biology 13: 1029-1037 2003 Type: ARTICLE Genes: ags-3 gpr-1 gpr-2 lin-5 par-2 par-3 Abstract: Background: Spindle positioning during an asymmetric cell division is of fundamental importance to ensure correct size of daughter cells and segregation of determinants. In the C. elegans embryo, the first spindle is asymmetrically positioned, and this asymmetry is controlled redundantly by two heterotrimeric Galpha subunits, GOA-1 and GPA-16. The Galpha subunits act downstream of the PAR polarity proteins, which control the relative pulling forces acting on the poles. How these heterotrimeric G proteins are regulated and how they control spindle position is still unknown. Results: Here we show that the Ga subunits are regulated by a receptor-independent mechanism. RNAi depletion of gpr-1 and gpr-2, homologs of mammalian AGS3 and Drosophila PINS (receptor-independent G protein regulators), results in a phenotype identical to that of embryos depleted of both GPA-16 and GOA-1; the first cleavage is symmetric, but polarity is not affected. The loss of spindle asymmetry after RNAi of gpr-1 and gpr-2 appears to be the result of weakened pulling forces acting on the poles. The GPR protein(s) localize around the cortex of one-cell embryos and are enriched at the posterior. Thus, asymmetric G protein regulation could explain the posterior displacement of the spindle. Posterior enrichment is abolished in the absence of the PAR polarity proteins PAR-2 or PAR-3. In addition, LIN-5, a coiled-coil protein also required for spindle positioning, binds to and is required for cortical association of the GPR protein(s). Finally, we show that the GPR domain of GPR-1 and GPR-2 behaves as a GDP dissociation inhibitor for GOA-1, and its activity is thus similar to that of mammalian AGS3. Conclusions: Our results suggest that GPR-1 and/or GPR-2 control an asymmetry in forces exerted on the spindle poles by asymmetrically modulating the activity of the heterotrimeric G protein in response to a signal from the ------------------- Key: 5946 Medline: 12814550 Authors: Asano A;Asano K;Sasaki H;Furuse M;Tsukita S Title: Claudins in Caenorhabditis elegans: their distribution and barrier function in the epithelium. Citation: Current Biology 13: 1042-1046 2003 Type: ARTICLE Genes: Abstract: Claudins (similar to23 kDa) with four transmembrane domains are major cell adhesion molecules working at tight junctions in vertebrates, where the intercellular space is tightly sealed (reviewed in [1-3]). We examined here the possible occurrence of claudin-like proteins in invertebrates, which do not bear typical tight junctions. Close blast searching of the C. elegans genome database identified four claudin-related, similar to20-kDa integral membrane proteins (CLC-1 to -4), which showed sequence similarity to the vertebrate claudins. The expression and distribution of CLC-1 was then examined in detail by GFP technology as well as by immunofluorescence microscopy. CLC-1 was mainly expressed in the epithelial cells in the pharyngeal region of digestive tubes and colocalized with AJM-1 at their intercellular junctions. Then, to examine the possible involvement of CLC-1 in the barrier function, we performed RNA interference in combination with a tracer experiment: in CLC-1-deficient worms, the barrier function of the pharyngeal portion of the digestive tubes appeared to be severely affected. CLC-2 was expressed in seam cells in the hypodermis, and it also appeared to be involved in the hypodermis barrier. These findings indicated that multiple species of the claudin homologs, which are involved in the barrier function of the epithelium, exist ------------------- Key: 5947 Medline: 12809598 Authors: Ambros V Title: MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing. Citation: Cell 113: 673-676 2003 Type: REVIEW Genes: hbl-1 let-7 lin-4 lin-14 lin-28 lin-29 lin-41 Abstract: Drosophila geneticists have uncovered roles for microRNAs in the coordination of cell proliferation and cell death during development, and in stress resistance and fat metabolism. In C. elegans, a homolog of the well-known fly developmental regulator hunchbank acts downstream of the microRNAs lin-4 and let-7 in a pathway controlling ------------------- Key: 5948 Medline: 12814434 Authors: Alegado RA;Campbell MC;Chen WC;Slutz SS;Tan MW Title: Characterization of mediators of microbial virulence and innate immunity using the Caenorhabditis elegans host-pathogen model. Citation: Cellular Microbiology 5: 435-444 2003 Type: REVIEW Genes: abf-1 abf-2 ced-3 ced-4 ced-9 daf-5 daf-7 dbl-1 egl-1 ikb-1 lys-1 lys-7 lys-8 nsy-1 pik-1 pmk-1 sek-1 sma-2 sma-3 sma-4 sma-6 tol-1 trf-1 Abstract: The soil-borne nematode, Caenorhabditis elegans , is emerging as a versatile model in which to study host-pathogen interactions. The worm model has shown to be particularly effective in elucidating both microbial and animal genes involved in toxin-mediated killing. In addition, recent work on worm infection by a variety of bacterial pathogens has shown that a number of virulence regulatory genes mediate worm susceptibility. Many of these regulatory genes, including the PhoP/Q two-component regulators in Salmonella and LasR in Pseudomonas aeruginosa , have also been implicated in mammalian models suggesting that findings in the worm model will be relevant to other systems. In keeping with this concept, experiments aimed at identifying host innate immunity genes have also implicated pathways that have been suggested to play a role in plants and animals, such as the p38 MAP kinase pathway. Despite rapid forward progress using this model, much work remains to be done including the design of more sensitive methods to find effector molecules and further characterization of the exact interaction between invading pathogens and C. elegans' cellular components. ------------------- Key: 5949 Medline: 12781745 Authors: Simons G;Morton G Title: The gene-orientation structure of eukaryotes. Citation: Journal of Theoretical Biology 222: 471-475 2003 Type: ARTICLE Genes: Abstract: It is shown that the sequence of gene orientations of four eukaryotes-for those that are presently known-are well modeled by a two-state, two-parameter (first order) Markov chain. These include the six chromosomes of nematodes (C elegans), the 16 chromosomes of yeast (S. cerevisiae), the five chromosomes of Arabidopsis (A. thaliana), and the 19 scaffolds of fruit flies (D. melanogaster). Moreover, they are reasonably well modeled, more simply, by a one-parameter symmetric version of the Markov chain. Further, compelling statistical evidence is presented which suggests that the parameters particularizing the Markov chain are organism dependent rather than merely chromosome dependent. This surprising observation begs an appropriate biological explanation. Does there exist some kind of mechanism of "communication" among a eukaryote's chromosomes that serves to maintain common values for all of the chromosomal parameters? Or are the common parameter values merely a consequence of a common environment of origin for all of the chromosomes of an organism? (If so, why so?) A third possible explanation is ruled out: while there exists within the class of Markov chain models under consideration, a case that could be described as equivalent to "flipping a fair coin," a thorough-random-shuffling-of-the-genes explanation, via ------------------- Key: 5950 Medline: 12765686 Authors: Montell C Title: The venerable inveterate invertebrate TRP channels. Citation: Cell Calcium 33: 409-417 2003 Type: REVIEW Genes: gon-1 npr-1 ocr-2 osm-9 tax-2 tax-4 Abstract: The transient receptor potential (TRP) superfamily is subdivided into four main classes of cation channels, TRPC, TRPV, TRPM and TRPN, each of which includes members in worms, flies, mice and humans. While the biophysical features of many of the mammalian channels have been described, relatively little is known concerning the biological roles of these channels. Forward genetic screens in Drosophila melanogaster and Caenorhabditis elegans have led to the identification of the founding members of each of these four subfamilies. Moreover, phenotypic analyses of invertebrate mutants have contributed greatly to our understanding of the roles of TRP proteins. A recurring theme is that many of these proteins function in sensory signaling processes ranging from vision to olfaction, osmosensation, light touch, social feeding, and temperature- and mechanically-induced nociception. In addition, at least one invertebrate TRP protein is required for cell division. As many of these functions may be conserved among the mammalian TRPs, the invertebrate TRPs offer valuable genetic handles for characterizing the functions of these cation channels in vivo. ------------------- Key: 5951 Medline: Authors: Mutai H;Heller S Title: Vertebrate and invertebrate TRPV-like mechanoreceptors. Citation: Cell Calcium 33: 471-478 2003 Type: REVIEW Genes: ocr-1 ocr-2 ocr-4 osm-9 Abstract: Our senses of touch, hearing, and balance are mediated by mechanosensitive ion channels. In vertebrates, little is known about the molecular composition of these mechanoreceptors, an example of which is the transduction channel of the inner ear's receptor cells, hair cells. Members of the TRP family of ion channels are considered candidates for the vertebrate hair cell's mechanosensitive transduction channel and here we review the evidence for this candidacy. We start by examining the results of genetic screens in invertebrates that identified members of the TRP gene family as core components of mechanoreceptors. In particular, we discuss the Caenorhabditis elegans OSM-9 channel, an invertebrate TRPV channel, and the Drosophila melanogaster TRP channel NOMPC. We then evaluate basic features of TRPV4, a vertebrate member of the TRPV subfamily, which is gated by a variety of physical and chemical stimuli including temperature, osmotic pressure, and ligands. Finally, we compare the characteristics of all discussed mechanoreceptive TRP channels with the biophysical characteristics of hair cell mechanotransduction, speculating about the possible make-up of the elusive inner ear mechanoreceptor. ------------------- Key: 5952 Medline: 12815722 Authors: Shemer G;Podbilewicz B Title: The story of cell fusion: big lessons from little worms. Citation: BioEssays 25: 672-682 2003 Type: REVIEW Genes: apr-1 bar-1 ceh-13 ceh-16 ceh-20 cog-2 duf-1 eff-1 egl-13 egl-18 egl-27 elt-6 idf-1 let-60 lin-11 lin-15 lin-25 lin-29 lin-39 mab-5 ref-1 sem-4 tlp-1 Abstract: The ability of two or more cells to unite to form a new syncytial cell has been utilized in metazoans throughout evolution to form many complex organs, such as muscles, bones and placentae. This requires migration, recognition and adhesion between cells together with fusion of their plasma membranes and rearrangement of their cytoplasmic contents. Until recently, understanding of the mechanisms of cell fusion was restricted to fusion between enveloped viruses and their target cells. The identification of new factors that take part in developmental cell fusion in C. elegans opens the way to understanding how cells fuse and what the functions of this process are. In this review, we describe current knowledge on the mechanisms and putative roles of developmental cell fusion in C. elegans and how cell fusion is regulated, together with other intercellular processes, to promote organogenesis. ------------------- Key: 5953 Medline: Authors: Tomishige M;Klopfenstein DR;Vale RD Title: Conversion of Unc104/KIF1A kinesin into a processive motor after dimerization. Citation: Science 297: 2263-2267 2003 Type: ARTICLE Genes: unc-104 Abstract: Unc104/KIF1A belongs to a class of monomeric kinesin motors that have been thought ot possess an unusual motility mechanism. Unlike the unidirectional motion drive by the coordinated actions of the two heads in conventional kinesins, single-headed KIF1A was reported to undergo biased diffusional motion along microtubules. Here, we show that Unc104/KIF1A can dimerize and move unidirectionally and processively with rapid velocities characteristic of transport in living cells. These results suggest that Unc104/KIF1A operates in vivo by a mechanism similar to conventional kinesin and that regulation of motor dimerization may be used to control transport by this class of kinesins. ------------------- Key: 5954 Medline: 12736204 Authors: Gupta BP;Wang M;Sternberg PW Title: The C. elegans LIM homeobox gene lin-11 specifies multiple cell fates during vulval development. Citation: Development 130: 2589-2601 2003 Type: ARTICLE Genes: ajm-1 cdh-3 ceh-2 egl-17 jam-1 ldb-1 lin-11 myo-2 sur-5 unc-119 zmp-1 Abstract: LIM homeobox family members regulate a variety of cell fate choices during animal development. In C elegans, mutations in the LIM homeobox gene lin-11 have previously been shown to alter the cell division pattern of a subset of the 2degrees lineage vulval cells. We demonstrate multiple functions of lin-11 during vulval development. We examined the fate of vulval cells in lin-11 mutant animals using five cellular markers and found that lin-11 is necessary for the patterning of both 1degrees and 2degrees lineage cells. In the absence of lin-11 function, vulval cells fail to acquire correct identity and inappropriately fuse with each other. The expression pattern of lin-11 reveals dynamic changes during development. Using a temporally controlled overexpression system, we show that lin-11 is initially required in vulval cells for establishing the correct invagination pattern. This process involves asymmetric expression of lin-11 in the 2degrees lineage cells. Using a conditional RNAi approach, we show that lin-11 regulates vulval morphogenesis. Finally, we show that LDB-1, a NLI/Ldb1/CLIM2 family member, interacts physically with LIN-11, and is necessary for vulval morphogenesis. Together, these findings demonstrate that temporal regulation of lin-11 is crucial for the wild-type ------------------- Key: 5955 Medline: 12783787 Authors: Huang X;Huang P;Robinson MK;Stern MJ;Jin Y Title: UNC-71, a disintegrin and metalloprotease (ADAM) protein, regulates motor axon guidance and sex myoblast migration in C. elegans. Citation: Development 130: 3147-3161 2003 Type: ARTICLE Genes: acr-2 adm-1 adm-2 adm-4 glp-1 ina-1 inb-1 jam-1 max-1 mec-7 myo-3 pat-3 sem-5 str-2 sup-17 sur-5 unc-5 unc-6 unc-25 unc-33 unc-34 unc-40 unc-71 unc-115 ctDf3 eDf2 Abstract: The migration of cells and growth cones is a process that is guided by extracellular cues and requires the controlled remodeling of the extracellular matrix along the migratory path. The ADAM proteins are important regulators of cellular adhesion and recognition because they can combine regulated proteolysis with modulation of cell adhesion. WE report that the C. elegans gene unc-71 encodes a unique ADAM with an inactive metalloprotease domain. Loss-of-function mutations in unc-71 cause distinct defects in motor axon guidance and sex myoblast migration. Many unc-71 mutations affect the disintegin and the cysteine-rich domains, supporting a major function of unc-71 in cell adhesion. UNC-71 appears to be expressed in a selected set of cells Genetic mosaic analysis and tissue-specific expression studies indicate that unc-71 acts in a cell non-autonomous manner for both motor axon guidance and sex myoblast migration. Finally, double mutant analysis of unc-71 with other axon guidance signaling molecules suggest that UNC-71 probably function in a combinatorial manner with integrins and UNC-6/netrin to provide distinct axon guidance cues at specific choice ------------------- Key: 5956 Medline: Authors: Gems D;Pletcher S;Partridge L Title: Interpreting interactions between treatments that slow aging. Citation: Aging Cell 1: 1-9 2002 Type: REVIEW Genes: age-1 clk-1 clk-3 daf-2 daf-16 eat-2 sod-3 Abstract: A major challenge in current research into aging using model organisms is to establish whether different treatment resulting in slowed aging involve common or distinct mechanisms. Such treatments include gene mutation, dietary restriction (DR), and manipulation of reproduction, gonadal signals and temperature. The principal method used to determine whether these treatments act through common mechanisms is to compare the magnitude of the effect on aging of each treatment separately with that when two are applied simultaneously. In this discussion we identify five types of methodological shortcomings that have marred such studies. These are (1) submaximal lifespan-extension by individual treatments, e.g. as a result of the use of hypomorphic rather than null alleles; (2) effects of a single treatment on survival through more than one mechanism, e.g. pleiotropic effects of lifespans mutants; (3) the difficulty of interpreting the magnitude of increases in lifespan in double treatments, and failure to measure and model age-specific mortality rates; (4) the non-specific effects of life extension suppressors; and (5) the possible occurrence of artefactual mutant interactions. When considered in the light of these problems, the conclusions of a number of recent lifespan interaction studies appear questionable. We suggest six rules for avoiding the pitfalls that can beset interaction studies. ------------------- Key: 5957 Medline: 12882409 Authors: McCulloch D;Gems D Title: Evolution of male longevity bias in nematodes. Citation: Aging Cell 2: 165-173 2003 Type: ARTICLE Genes: Abstract: Many animal species exhibit sex differences in aging. In the nematode Caenorhabditis elegans, under conditions that minimize mortality, males are the longer-lived sex. In a survey of 12 independent C. elegans isolates, we find that this is a species-typical character. To test the hypothesis that the C. elegans male longevity bias evolved a s a consequence of androdioecy (having males and hermaphrodites), we compared sex-specific survival in four androdioecious and four dioecious (males and females nematode species. Contrary to expectation, in all but C. briggsae (androdioecious), males were the longer-lived sex, and this difference was greatest among dioecious species. Moreover, male lifespan was reduced in androdioecious species relative to dioecious species. The evolutionary theory of aging predicts the evolution of a sic mortality. We demonstrate that in each of eight species early adult mortality is elevated in female/hermaphrodites in the absence of food as the consequence of internal hatching of larvae (matricide). The age-independent mortality risk can favour the evolution of rapid aging in females and hermaphrodites relative to males. ------------------- Key: 5958 Medline: 12798417 Authors: Sato M;Moroi K;Nishiyama M;Zhou J;Usui H;Kasuya Y;Fukuda M;Kohara Y;Komura I;Kimura S Title: Characterization of a novel C. elegans RGS protein with a C2 domain: evidence for direct association between C2 domain and G alpha q subunit. Citation: Life Sciences 73: 917-932 2003 Type: ARTICLE Genes: Abstract: GS (regulator of G protein signaling) proteins are GTPase-activating proteins (GAPs) for heterotrimeric G protein alpha subunits and negatively regulate G protein-mediated signal transduction. In this study, we determined the cDNA sequence of a novel Caenorhabditis elegans (C. elegans) RGS protein. The predicted protein, termed C2-RGS, consists of 782 amino acids, and contain a C2 domain and an RGS domain. C2 domains are typically known to be Ca(2+) and phospholipid binding sites, found in many proteins involved in membrane traffic or signal transduction, and most of their biological roles are not identified. To study the function of C2-RGS protein, a series of six truncated versions of C2-RGS were constructed. When the full-length protein of C2-RGS was expressed transiently in AT1a-293T cells, ET-1-induced Ca(2+) responses were strongly suppressed. When each of the mutants with either RGS domain or C2 domain was expressed, the Ca(2+) responses were suppressed moderately. Furthermore, we found that C2 domain of PLC-beta1 also had a similar moderate inhibitory effect. RGS domain of C2-RGS bound to mammalian and C. elegans Galphai/o and Galphaq subunits only in the presence of GDP/AlF(4)(-), and had GAP activity to Galphai3. On the other hand, C2 domains of C2-RGS and PLC-beta1 also bound strongly to Galphaq subunit, in the presence of GDP, GDP/AlF(4)(-), and GTPgammaS, suggesting the stable persistent association between these C2 domains and Galphaq subunit at any stage during GTPase cycle. These results indicate that both the RGS domain and the C2 domain are responsible for the inhibitory effect of the full-length C2-RGS protein on Galphaq-mediated signaling, and suggest that C2 domains of C2-RGS and PLC-beta1 may act as a scaffold module to organize Galphaq and the respective whole protein molecule in a stable signaling complex, both in the absence and ------------------- Key: 5959 Medline: 12810918 Authors: MacMorris M;Brocker C;Blumenthal T Title: UAP56 levels affect viability and mRNA export in Caenorhabditis elegans. Citation: RNA 9: 847-857 2003 Type: ARTICLE Genes: aly-1 aly-2 aly-3 cpf-1 hel-1 mag-1 nxf-1 nxf-2 prp-8 rnp-2 rnp-3 rnp-7 rsp-7 sap-1 sap-49 uaf-1 uaf-2 Abstract: Expression of a gfp transgene in the intestines of living Caenorhabditis elegans has been measured following depletion by RNAi of a variety of known splicing factors and mRNA export proteins. Reduction of most splicing factors showed only a small effect on expression of the transgene in the animal injected with dsRNA, although most of these RNAi's resulted in embryonic lethality in their offspring. In contrast, RNAi of nxf-1, the worm homolog of mammalian NXF1/TAP, a key component of the mRNA export machinery, resulted in dramatic suppression of GFP expression in the injected animals. When we tested other proteins previously reported to be involved in marking mRNAs for export, we obtained widely divergent results. Whereas RNAi of the worm REF/Aly homologs had no obvious effect, either in the injected animals or their offspring, RNAi of UAP56, reported to be the partner of REF/Aly, resulted in strong suppression of GFP expression due to nuclear retention of its mRNA. Overexpression of UAP56 also resulted in rapid loss of GFP expression and lethality at all stages of development. We conclude that UAP56 plays a key role in mRNA export in C. elegans, but that REF/Aly may not. It also appears that some RNA processing factors are required for viability (e.g., U2AF, PUF60, SRp54, SAP49, PRP8, U1-70K), whereas others are not (e.g., U2A', CstF50). ------------------- Key: 5960 Medline: 12810921 Authors: Longman D;Johnstone IL;Caceres JF Title: The Ref/Aly proteins are dispensable for mRNA export and development in Caenorhabditis elegans. Citation: RNA 9: 881-891 2003 Type: ARTICLE Genes: aly-1 aly-2 aly-3 hel-1 mag-1 nxf-1 nxf-2 nxt-1 rnp-4 rnp-5 rsr-1 smg-4 Abstract: The mRNA export pathway is highly conserved throughout evolution. We have used RNA interference (RNAi) to functionally characterize bona fide RNA export factors and components of the exon-exon junction complex (EJC) in Caenorhabditis elegans. RNAi of CeNXT1/p15, the binding partner of CeNXF1/TAP, caused early embryonic lethality, demonstrating an essential function of this gene during C elegans development. Moreover, depletion of this protein resulted in nuclear accumulation of poly(A)(+) RNAs, supporting a direct role of NXT1/p15 in mRNA export in C. elegans. Previously, we have shown that RNAi of CeSRm160, a protein of the EJC complex, resulted in wild-type phenotype; in the present study, we demonstrate that RNAi of CeY14, another component of this complex, results in embryonic lethality. in contrast, depletion of the EJC component CeRNPS1 results in no discernible phenotype. Proteins of the REF/Aly family act as adaptor proteins mediating the recruitment of the mRNA export factor, NXF1/TAP, to mRNAs. The C elegans genome encodes three members of the REF/Aly family. RNAi of individual Ref genes, or codepletion of two Ref genes in different combinations, resulted in wild-type phenotype. Simultaneous suppression of all three Ref genes did not compromise viability or progression through developmental stages in the affected progeny, and only caused a minor defect in larval mobility. Furthermore, no defects in mRNA export were observed upon simultaneous depletion of all three REF proteins. These results suggest the existence of multiple adaptor proteins that mediate mRNA export in C. elegans. ------------------- Key: 5961 Medline: 12824472 Authors: Katschinski DM;Glueck SB Title: Hot worms can handle heavy metal. Focus on "HIF-1 is required for heat acclimation in the nematode Caenorhabditis elegans". Citation: Physiological Genomics 14: 1-2 2003 Type: REVIEW Genes: daf-2 egl-9 hif-1 vhl-1 Abstract: Life developed in a stressful environment. Stressors at the cellular level include heat, hypoxia, oxidative or reductive substances, mechanical or osmotic pressure, and toxic compounds like heavy metals. Various molecular pathways, more or less specific for the different stressors, developed during evolution to combat the molecular consequences of cell stress. Thermal stress induces the induction of a highly conserved protein family, the heat shock proteins (HSP). ------------------- Key: 5962 Medline: 12686697 Authors: Treinin M;Shliar J;Jiang H;Powell-Coffman JA;Bromberg Z;Horowitz M Title: HIF-1 is required for heat acclimation in the nematode Caenorhabditis elegans. Citation: Physiological Genomics 14: 17-24 2003 Type: ARTICLE Genes: daf-2 daf-16 egl-9 hif-1 vhl-1 mgDf50 Abstract: Chronic exposure to environmental heat improves tolerance via heat acclimation (AC). Our previous data on mammals indicate that reprogramming the expression of genes coding for stress proteins and energy-metabolism enzymes plays a major role. Knowledge of pathways leading to AC is limited. For their identification, we established a Caenorhabditis elegans AC model and tested mutants in which signaling pathways pertinent to acclimatory responses are mutated. AC attained by maintaining adult C. elegans at 25 degreesC for 18 h enhanced heat endurance of wild-type worms subjected to heat stress (35 degreesC) and conferred protection against hypoxia and cadmium. Survival curves demonstrated that both daf-2 (insulin receptor pathway) showing enhanced heat tolerance and daf-16 loss-of-function (a transcription factor mediating DAF-2 signaling) mutants benefit from AC, suggesting that the insulin receptor pathway does not mediate AC. In contrast, the hif-1 (hypoxia inducible factor) loss-of-function strain did not show acclimation, and non-acclimated vhl-1 and egl-9 mutants (overexpressing HIF-1) had greater heat endurance than the wild type. Like mammals, HIF-1 and HSP72 levels increased in the wild-type AC nematodes. HSP72 upregulation in AC hif-1 mutants was also observed; however, it was insufficient to improve heat/stress tolerance, suggesting that HIF-1 upregulation is essential for acclimation, whereas HSP72 upregulation in the absence of HIF-1 is inadequate. We conclude that HIF-1 upregulation is both an evolutionarily conserved and a necessary component of heat acclimation. The known targets of HIF-1 imply that metabolic adaptations are essential for AC-dependent tolerance to heat and heavy metals, in addition to their known role in hypoxic adaptation. ------------------- Key: 5963 Medline: 12809676 Authors: Suh KS;Tatunchak TT;Crutchley JM:Edwards LE;Marin KG;Yuspa SH Title: Genomic structure and promoter analysis of PKC-delta. Citation: Genomics 82: 57-67 2003 Type: ARTICLE Genes: Abstract: Protein kinase C-delta (PKC-delta) is a ubiquitously expressed kinase involved in a variety of cellular signaling pathways including cell growth, differentiation, apoptosis, tumor promotion, and carcinogenesis. While signaling pathways downstream of PKC-delta are well studied, the regulation of the gene has not been extensively analyzed. A mouse genomic DNA fragment containing the PKC-delta gene was sequenced by the primer-walking method, and the subsequent DNA sequence data were used as a query to clone Caenorhabditis elegans and human genomic homologs from the publicly available genomic databases. The genomic structures of C. elegans, mouse, rat, and human PKC-delta were analyzed, and the result revealed that PKC-delta genes comprise 12, 18, 19, and 18 exons for C. elegans, mouse, rat, and human, respectively. The translation start methionine resides in the second exon in mouse and human and in the third exon in rat. The first intron between the first exon and the exon with the translation start methionine in mammalian genes represents a very large gap, as long as 17 kb in human, indicating a complexity involved in gene splicing. Overall exon-intron genomic structure is highly conserved among mammals, while significantly diverged in C. elegans. Putative transcription factor binding sites on the 1.7-kb promoter region of the mouse gene suggest that PKC-delta might be involved in spermatogenesis, embryogenesis, development, brain generation, immune response, oxidative environment, and oncogenesis. Studies on the promoter and subsequent biological testing on mouse keratinocytes indicate that tumor necrosis factor (TNF)-alpha increases the expression of PKC-delta, and this correlates with the time of NFkappaB nuclear translocation and activation. This TNF-alpha-mediated upregulation of PKC-delta is repressed in keratinocytes that are preinfected with IkappaB superrepressor adenovirus, suggesting that NFkappaB is ------------------- Key: 5964 Medline: 12798299 Authors: Moss EG;Tang L Title: Conservation of the heterochronic regulator Lin-28, its developmental expression and microRNA complementary sites. Citation: Developmental Biology 258: 432-442 2003 Type: ARTICLE Genes: lin-28 Abstract: The heterochronic gene lin-28 is a regulator of developmental timing in the nematode Caenorhabditis elegans. It must be expressed in the first larval stage and downregulated by the second stage for normal development. This downregulation is mediated in part by lin-4, a 21-nt microRNA. If downregulation fails due to a mutation in a short sequence in the lin-28 3' UTR that is complementary to lin-4, then a variety of somatic cell lineages fail to progress normally in development. Here, we report that Lin-28 homologues exist in diverse animals, including Drosophila, Xenopus, mouse, and human. These homologues are characterized by the LIN-28 protein's unusual pairing of RNA-binding motifs: a cold shock domain (CSD) and a pair of retroviral-type CCHC zinc knuckles. Conservation of LIN-28 proteins shows them to be distinct from the other conserved family of CSD-containing proteins of animals, the Y-box proteins. Importantly, the LIN-28 proteins of Drosophila, Xenopus, and mouse each appear to be expressed and downregulated during development, consistent with a conserved role for this regulator of developmental timing. In addition, the extremely long 3' UTRs of mouse and human Lin-28 genes show extensive regions of sequence identity that contain sites complementary to the mammalian homologues of C elegans lin-4 and let-7 microRNAs, suggesting that microRNA regulation is a conserved feature of the Lin-28 gene in diverse animals. ------------------- Key: 5965 Medline: 12736202 Authors: Battu G;Hoier EF;Hajnal A Title: The C. elegans G-protein-coupled receptor SRA-13 inhibits RAS/MAPK signalling during olfaction and vulval Citation: Development 130: 2567-2577 2003 Type: ARTICLE Genes: che-3 daf-2 gpa-2 gpa-3 gpa-5 gpa-7 let-23 let-60 lin-3 lin-45 mek-2 mpk-1 osm-5 puf-8 sem-5 sra-1 sra-2 sra-3 sra-4 sra-5 sra-6 sra-7 sra-8 sra-9 sra-10 sra-11 sra-12 sra-13 srd-54 srd-55 sre-1 sre-2 sro-1 Abstract: In C. elegans, the RAS/MAPK pathway is used in different tissues to regulate various cell fate decisions. Several positive and negative regulators tightly control the activity of the RAS/MAPK pathway at different steps. We demonstrate a link between a G-protein-coupled receptor signalling pathway and the RAS/MAPK cascade. SRA-13, a member of the SRA family of chemosensory receptors, negatively regulates RAS/MAPK signalling during vulval induction and the olfaction of volatile attractants. Epistasis analysis indicates that SRA-13 inhibits the RAS/MAPK pathway at the level or upstream of MAPK. In both tissues, the vulval precursor cells and the chemosensory neurones, SRA-13 acts through the GPA-5 Galpha protein subunit, suggesting a common mechanism of crosstalk. Moreover, we find that vulval induction is repressed by food withdrawal during larval development and that SRA-13 activity is required for the suppression of vulval induction in response to food starvation. Thus, SRA-13 may serve to adapt the activity of the RAS/MAPK pathway to environmental conditions. ------------------- Key: 5966 Medline: 12736207 Authors: Marin VA;Evans TC Title: Translational repression of a C. elegans Notch mRNA by the START/KH domain protein GLD-1. Citation: Development 130: 2623-2632 2003 Type: ARTICLE Genes: gld-1 glp-1 Abstract: In C. elegans, the Notch receptor GLP-1 is localized within the germline and early embryo by translational control of glp-1 mRNA. RNA elements in the glp-1 3' untranslated region (3' UTR) are necessary for repression of glp-1 translation in germ cells, and for localization of translation to anterior cells of the early embryo. The direct regulators of glp-1 mRNA are not known. Here, we show that a 34 nucleotide region of the glp-1 3' UTR contains two regulatory elements, an element that represses translation in germ cells and posterior cells of the early embryo, and an element that inhibits repressor activity to promote translation in the embryo. Furthermore, we show that the STAR/KH domain protein GLD-1 binds directly and specifically to the repressor element. Depletion of GLD-1 activity by RNA interference causes loss of endogenous glp-1 mRNA repression in early meiotic germ cells, and in posterior cells of the early embryo. Therefore, GLD-1 is a direct repressor of glp-1 translation at two developmental stages. These results suggest a new function for GLD-1 in regulating early embryonic asymmetry. Furthermore, these observations indicate that precise control of GLD-1 activity by other regulatory factors is important to localize this Notch receptor, and contributes to the spatial organization of Notch signaling. ------------------- Key: 5967 Medline: Authors: Ono S Title: Function of ADF/cofilin in muscle cells: An important regulator of actin cytoskeletal dynamics in myofibril assembly and muscle diseases. Citation: Recent Developments in Cell Research 1: 31-44 2003 Type: REVIEW Genes: unc-60 Abstract: In muscle cells, the actin cytoskeleton is differentiated into myofibrils that are specialized contractile apparatuses. To assemble and maintain myofibrils, a specific regulatory mechanism of actin filament dynamics is required. The actin depolymerizing factor (ADF)/cofilin proteins are ubiquitous regulators of actin turnover among eukaryotes. However, muscle-specific ADF/cofilin isoforms are present in several species and play important roles in actin organization in muscle cells. This review describes the function of ADF/cofilin as an important regulator of myofibril assembly and muscle diseases. ------------------- Key: 5968 Medline: 12848268 Authors: Hoffenberg R Title: Brenner, the worm and the prize. Citation: Clinical Medicine 3: 285-286 2003 Type: REVIEW Genes: Abstract: The recent award of a Nobel Prize to Sydney Brenner crowns an astonishingly distinguished scientific career. He must have come very close to winning it several times in the past. A colleague described him as 'a visionary who sees further into the future than anyone'. This is borne out by his decision - made 40 years ago - to study a one-millimetre long worm in detail to define the, biochemical and genetic control of its development and differentiation. The impact of these studies has been so profound, with a significant bearing on human physiology and disease, that over 400 laboratories worldwide have now adopted the worm as a research tool. In this article, a brief outline is given of his work on the worm and of some of the highlights of his brilliant career. ------------------- Key: 5969 Medline: 12819787 Authors: Simske JS;Koppen M;Sims P;Hodgkin J;Yonkof A;Hardin J Title: The cell junction protein VAB-9 regulates adhesion and epidermal morphology in C. elegans. Citation: Nature Cell Biology 5: 619-625 2003 Type: ARTICLE Genes: ajm-1 dlg-1 hmp-1 hmp-2 hmr-1 vab-9 mnDf68 Abstract: Epithelial cell junctions are essential for cell polarity, adhesion and 1. morphogenesis. We have analysed VAB-9, a cell junction protein in Caenorhabditis elegans. VAB-9 is a predicted four-pass integral membrane protein that has greatest similarity to BCMP1 ( brain cell membrane protein 1, a member of the PMP22/EMP/Claudin family of cell junction proteins) and localizes to the adherens junction domain of C. elegans apical junctions(1-4). Here, we show that VAB-9 requires HMR1/ cadherin for localization to the cell membrane, and both HMP-1/alpha-catenin and HMP-2/beta-catenin for maintaining its distribution at the cell junction. In vab-9 mutants, morphological defects correlate with disorganization of F-actin at the adherens junction; however, localization of the cadherin-catenin complex and epithelial polarity is normal. These results suggest that VAB-9 regulates interactions between the cytoskeleton and the adherens junction downstream of or parallel to alpha-catenin and/or beta-catenin. Mutations in vab-9 enhance adhesion defects through functional loss of the cell junction genes apical junction molecule 1 (ajm-1) and discs large 1 (dlg-1), suggesting that VAB-9 is involved in cell adhesion. Thus, VAB-9 represents the first characterized tetraspan adherens junction protein in C. elegans and defines a new family of such proteins in higher eukaryotes. ------------------- Key: 5970 Medline: 12793758 Authors: Nelson GA;Jones TA;Chestnut A;Smith AL Title: Radiation-induced gene expression in the nematode Caenorhabditis elegans. Citation: Journal of Radiation Research 43: S199-S203 2002 Type: ARTICLE Genes: Abstract: We used the nematode C. elegans to characterize the genotoxic and cytotoxic effects of ionizing radiation in a simple animal model emphasizing the unique effects of charged particle radiation. Here we demonstrate by RT-PCR differential display and whole genome microarray hybridization experiments that gamma rays, accelerated protons and iron ions at the same physical dose lead to unique transcription pro files. 599 of 17871 genes analyzed (3.4%) showed differential expression 3 hrs after exposure to 3 Gy of radiation. 193 were up-regulated, 406 were down-regulated and 90% were affected only by a single species of radiation. A novel statistical clustering technique identified the regulatory relationships between the radiation-modulated genes and showed that genes affected by each radiation species were associated with unique regulatory clusters. This suggests that independent homeostatic mechanisms are activated in response to radiation exposure as a function of track structure or ionization density. ------------------- Key: 5971 Medline: 12871707 Authors: Johnson SM;Lin SY;Slack FJ Title: The time of appearance of the C. elegans let-7 microRNA is transcriptionally controlled utilizing a temporal regulatory element in its promoter. Citation: Developmental Biology 259: 364-379 2003 Type: ARTICLE Genes: daf-12 let-7 lin-4 lin-14 lin-28 lin-29 lin-41 mnDp1 Abstract: MicroRNAs (miRNAs) are a large family of small regulatory RNAs that are poorly understood. The let-7 miRNA regulates the timing of the developmental switch from larval to adult cell fates during Caenorhabditis elegans development. Expression of let-7 RNA is temporally regulated, with robust expression in the fourth larval and adult stages. Here, we show that, like let-7 RNA, a transcriptional fusion of the let-7 promoter to gfp is temporally regulated, indicating that let-7 is transcriptionally controlled. Temporal upregulation of let-7 transcription requires an enhancer element, the temporal regulatory element (TRE), situated about 1200 base pairs upstream of the start of the mature let-7 RNA. The TRE is both necessary and sufficient for this temporal upregulation. A TRE binding factor (TREB) is able to bind to the TRE, and a 22-base pair inverted repeat within the TRE is necessary and sufficient for this binding. We also find that the nuclear hormone receptor DAF-12 and the RNA binding protein LIN-28 are both required for the correct timing of let-7 RNA and let-7::gfp expression. We speculate that these heterochronic genes regulate let-7 expression through its ------------------- Key: 5972 Medline: 12847081 Authors: Pettitt J;Cox EA;Broadbent ID;Flett A;Hardin J Title: The Caenorhabditis elegans p120 catenin homologue, JAC-1, modulates cadherin-catenin function during epidermal morphogenesis. Citation: Journal of Cell Biology 162: 15-22 2003 Type: ARTICLE Genes: ajm-1 hmp-1 hmp-2 hmr-1 jac-1 Abstract: The cadherin-catenin complex is essential for tissue morphogenesis during animal development. In cultured mammalian cells, p120 catenin (p120ctn) is an important regulator of cadherin-catenin complex function. However, information on the role of p120ctn family members in cadherin-dependent events in vivo is limited. We have examined the role of the single Caenorhabditis elegans p120ctn homologue JAC-1 (juxtamembrane domain [JMD]-associated catenin) during epidermal morphogenesis. Similar to other p120ctn family members, JAC-1 binds the JMD of the classical cadherin HMR-1, and GFP-tagged JAC-1 localizes to adherens junctions in an HMR-1-dependent manner. Surprisingly, depleting JAC-1 expression using RNA interference (RNAi) does not result in any obvious defects in embryonic or postembryonic development. However, jac-1 (RNAi) does increase the severity and penetrance of morphogenetic defects caused by a hypomorphic mutation in the hmp-1/alpha-catenin gene. In these hmp-1 mutants, jac-1 depletion causes failure of the embryo to elongate into a worm-like shape, a process that involves contraction of the epidermis. Associated with failed elongation is the detachment of actin bundles from epidermal adherens junctions and failure to maintain cadherin in adherens junctions. These results suggest that JAC-1 acts as a positive modulator of cadherin function in C. elegans. ------------------- Key: 5973 Medline: 12810585 Authors: Aspock G;Ruvkun G;Burglin TR Title: The Caenorhabditis elegans ems class homeobox gene ceh-2 is required for M3 pharynx motoneuron function. Citation: Development 130: 3369-3378 2003 Type: ARTICLE Genes: ceh-2 ceh-40 eat-4 pha-4 tph-1 Abstract: Several homeobox genes, for example those of the ems class, play important roles in animal head development. We report on the expression pattern and function of ceh-2, the Caenorhabditis elegans ems/Emx ortholog. CEH-2 protein is restricted to the nuclei of one type of small muscle cell, one type of epithelial cell, and three types of neurons in the anterior pharynx in the head. We have generated a deletion allele of ceh-2 that removes the homeobox. Animals homozygous for this deletion are viable and fertile, but grow slightly slower and lay few eggs than wild type. We assayed the function of two types of pharynx neurons that express ceh-2, the pairs M3 and NSM. M3 activity is substantially reduced in electropharyngeograms of ceh-2 deletion mutants; this defect can account for the observed retardation in larval development, as M3 activity is known to be necessary for effective feeding. NSM function and metabolism are normal based on the assays used. All cells that express ceh-2 in wild type are present in the ceh-2 mutant and have normal morphologies. Therefore, unlike other ems/Emx genes, ceh-2 seems to be important for a late differentiation step and not for neuron specification or regional patterning. Because the CEH-2 homeodomain is well conserved, we tested whether ceh-2 can rescue ems-negative brain defects in Drosophila, despite the apparent differences in biological roles. We found that the C. elegans ems ortholog is able to substantiate for fly ems in brain development, indicating that sequence conservation rather than conservation of biological function is important. ------------------- Key: 5974 Medline: 12869753 Authors: Carrington JC;Ambros V Title: Role of microRNAs in plant and animal development. Citation: Science 301: 336-338 2003 Type: REVIEW Genes: let-7 lin-4 lin-14 lin-28 mir-80 mir-81 mir-82 Abstract: Small RNAs, including microRNAs (miRNAs) and short interfering RNAs (siRNAs), are key components of an evolutionarily conserved system of RNA-based gene regulation in eukaryotes. They are involved in many molecular interactions, including defense against viruses and regulation of gene expression during development. miRNAs interfere with expression of messenger RNAs encoding factors that control developmental timing, stem cell maintenance, and other developmental and physiological processes in plants and animals. miRNAs are negative regulators that function as specificity determinants, or guides, within complexes that inhibit protein synthesis (animals) or promote degradation (plants) of mRNA targets. ------------------- Key: 5975 Medline: Authors: Tepass U Title: Claudin complexities at the apical junctional complex. Citation: Nature Cell Biology 5: 595-597 2003 Type: REVIEW Genes: ajm-1 dlg-1 hmp-1 hmp-2 hmr-1 let-413 vab-9 Abstract: Chordate claudins are core components of tight junctions. By contrast, VAB-9, a nematode four-pass transmembrane protein related to claudins, localizes to adherens junctions and contributes to cell adhesion and actin - plasma membrane association. ------------------- Key: 5976 Medline: 12845331 Authors: Murphy CT;McCarroll SA;Bargmann CI;Fraser A;Kamath RS;Ahringer J;Li H;Kenyon C Title: Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans. Citation: Nature 424: 277-284 2003 Type: ARTICLE Genes: asp-3bir-2 ctl-1 ctl-2 daf-2 daf-16 dao-3 dod-1 dod-2 dod-3 dod-4 dod-5 dod-6 dod-7 dod-8 dod-9 dod-10 dod-11 dod-12 dod-13 dod-14 dod-15 dod-16 dod-17 dod-18 dod-19 dod-20 dod-21 dod-22 dod-23 dod-24 fat-7 gcp-1 gcy-6 gcy-18 gei-7 ges-1 gpd-2 hsp-12.6 hsp-16.1 hsp-16.2 hsp-16.11 hsp-16.49 ins-7 ins-18 lbp-7 lys-1mdl-1 mtl-1 mtl-2 nuc-1 old-1 pep-2 pes-2 sod-3 spp-1 vit-2 vit-5 Abstract: Ageing is a fundamental, unsolved mystery in biology. DAF-16, a FOXO-family transcription factor, influences the rate of ageing of Caenorhabditis elegans in response to insulin/insulin-like growth factor 1 (IGF-I) signalling. Using DNA microarray analysis, we have found that DAF-16 affects expression of a set of genes during early adulthood, the time at which this pathway is known to control ageing. Here we find that many of these genes influence the ageing process. The insulin/IGF-I pathway functions cell non-autonomously to regulate lifespan, and our findings suggest that it signals other cells, at least in part, by feedback regulation of an insulin/IGF-I homologue. Furthermore, our findings suggest that the insulin/IGF-I pathway ultimately exerts its effect on lifespan by upregulating a wide variety of genes, including cellular stress-response, antimicrobial and metabolic genes, and by downregulating specific life-shortening ------------------- Key: 5977 Medline: 12832557 Authors: Zhao B;Khare P;Feldman L;Dent JA Title: Reversal frequency in Caenorhabditis elegans represents an integrated response to the state of the animal and its environment. Citation: Journal of Neuroscience 23: 5319-5328 2003 Type: ARTICLE Genes: bas-1 che-2 egl-1 glp-1 him-8 mec-3 osm-1 Abstract: The locomotion of Caenorhabditis elegans consists of forward crawling punctuated by spontaneous reversals. To better understand the important variables that affect locomotion, we have described in detail the locomotory behavior of C elegans and identified a set of parameters that are sufficient to describe the animal's trajectory. A model of locomotion based on these parameters indicates that reversal frequency plays a central role in locomotion. We found that several variables such as humidity, gravidity, and mechanostimulation influence reversal frequency. Specifically, both gentle and harsh touch can transiently suppress reversal frequency. Thus, reversal behavior is a model for the integration of information from numerous modalities reflecting diverse aspects of the state of an organism. ------------------- Key: 5978 Medline: 12840007 Authors: Parrish JZ;Yang C;Shen B;Xue D Title: CRN-1, a Caenorhabditis elegans FEN-1 homologue, cooperates with PCS-6/EndoG to promote apoptotic DNA degradation. Citation: EMBO Journal 22: 3451-3460 2003 Type: ARTICLE Genes: ced-3 ced-4 ced-8 cps-6 crn-1 nuc-1 Abstract: Oligonucleosomal fragmentation of chromosomes in dying cells is a hallmark of apoptosis. Little is known about how it is executed or what cellular components are involved. We show that crn-1, a Caenorhabditis elegans homologue of human flap endonuclease-1 (FEN-1) that is normally involved in DNA replication and repair, is also important for apoptosis. Reduction of crn-1 activity by RNA interference resulted in cell death phenotypes similar to those displayed by a mutant lacking the mitochondrial endonuclease CPS-6/endonuclease G. CRN-1 localizes to nuclei and can associate and cooperate with CPS-6 to promote stepwise DNA fragmentation, utilizing the endonuclease activity of CPS-6 and both the 5'-3' exonuclease activity and a previously uncharacterized gap-dependent endonuclease activity of CRN-1. Our results suggest that CRN-1/FEN-1 may play a critical role in switching the state of cells from DNA replication/repair to ------------------- Key: 5979 Medline: 12698356 Authors: de Melo JV;de Souza W;Peixoto CA Title: Immunocytochemical and freeze-fracture characterization of the Caenorhabditis elegans DR847 bli-1(n361) mutant which produces abnormal cuticle blisters. Citation: Cell & Tissue Research 312: 229-235 2003 Type: ARTICLE Genes: bli-1 Abstract: The bli-1 gene of Caenorhabditis elegans has previously been described as a mutation which disrupts the structure of the adult-stage cuticle, causing the formation of fluid-filled blisters. We investigated the blistering phenotype exhibited of n361 allele through immunocytochemical and freeze-fracture techniques. In the course of the blistering process several fine changes occurred, including a high-electron-density granulous material filling the intermediate layer, alterations in strut structure, and finally the total disappearance of the fibrous and basal layers. A polyclonal antibody against a synthetic 18-amino-acid peptide of the 3A3-collagen sequence labeled all the cuticular regions of the N-2 strain of the nematode C. elegans except for the intermediate layer. Similarly, no reaction was observed in the intermediate layer of the mutant strain DR 847 bli-1 (n361), which was filled by the granulous and electron-dense material. Replicas of quick-frozen, freeze-fracture, deep-etched, and rotatory-shadowed adult forms of the mutant DR 847 bli-1 (n361) of C. elegans revealed an increased number of the filamentous structures filling the intermediate layer in older nematodes, and also a gradual destruction and disappearance of the fibrous and basal layers. Based on these results, we postulated that the blistering phenotype is due to an altered function of bli-1 gene, which is probably enzymatic. ------------------- Key: 5980 Medline: 12837290 Authors: Sassa T;Ueda-Ohba H;Kitamura K;Harada S;Hosono R Title: Role of Caenorhabditis elegans phosphatase type 1, CeGLC7beta, in metaphase to anaphase transition during embryonic development. Citation: Experimental Cell Research 287: 350-360 2003 Type: ARTICLE Genes: Abstract: In Caenorhabditis elegans embryogenesis, phosphorylation events are critical to chromosomal changes. To investigate the dephosphorylation of chromosome behavior, we cloned and characterized the cDNA that encodes C. elegans protein phosphatase type 1 (CeGLC-7beta), which is composed of 333 amino acids. CeGLC-7beta possesses a highly conserved amino acid sequence with mammalian and Drosophila protein phosphatase 1. Here, we report on the contribution of CeGLC-7beta to the dephosphorylation of histone H3 at anaphase. At the embryonic stage, CeGLC-7beta is associated with the nuclear membrane and chromosomes. The deletion of the Ceglc-7beta gene and a microinjection of double-stranded RNA produce a disorganized embryogenesis. The Ceglc-7beta gene mutation causes an abnormal accumulation of phosphorylated histone H3 and delays the mitotic process after anaphase. We propose that CeGLC-7beta is involved in chromosome dynamics including histone H3 ------------------- Key: 5981 Medline: Authors: Pasquinelli AE;McCoy A;Jimenez E;Salo E;Ruvkun G;Martindale MQ; Baguna J Title: Expression of the 22 nucleotide let-7 heterochronic RNA throughout the Metazoa: a role in life history education. Citation: Evolution & Development 5: 372-378 2003 Type: ARTICLE Genes: let-7 Abstract: The 22 nucleotide let-7 small temporal RNA has been found consistently in samples from diverse bilateria but not from sponge or cnidarians. Here we further examine the phylogenetic distribution of this regulatory RNA by sampling representatives of diverse metazoan lineages. The 22 nucleotide let-7 RNA is detectable in triclad and polyclad platyhelminths, nemertean, and chaetognath but not ctenophore or acoel metazoans. These results support recent arguments that acoels are distinct from other acoelomate platyhelminths. We argue that let-7 is not a bilaterian or triploblast synapomorphy but instead evolved later in metazoan evolution, perhaps in association with complex life history traits. ------------------- Key: 5982 Medline: 12814951 Authors: Shen C;Powell-Coffman JA Title: Genetic analysis of hypoxia signaling and response in C. elegans. Citation: Annals of the New York Academy of Sciences 995: 191-199 Type: REVIEW Genes: aha-1 egl-9 hif-1 vhl-1 Abstract: During normal development and homeostasis, animals use cellular and systemic strategies to adapt to changing oxygen levels. In mammals, hypoxic tissues secrete growth factors to induce angiogenesis, and individual cells increase anaerobic metabolism in order to sustain basic cellular functions. Many of these critical responses to decreased oxygen availability are regulated by the hypoxia-inducible factors, dimeric transcriptional complexes consisting of alpha and beta subunits. HIFalpha proteins are specialized for hypoxia response, and oxygen levels regulate their stability and activity. The C. elegans hif-1 gene is orthologous to mammalian HIFalpha genes, and C. elegans has proven to be a powerful system for the study of hypoxia-inducible factor regulation and function. Mutants lacking hif-1 function are viable in normoxic or anoxic conditions, but they cannot adapt to hypoxia. Recent genetic analyses in C. elegans led to the identification of the evolutionarily conserved enzyme that hydroxylates HIFa in an oxygen-dependent manner. Once modified, HIFalpha binds the von Hippel-Lindau tumor suppressor protein and is targeted for proteasomal degradation. Here, we briefly review the characterization of C. elegans hif-1 and interacting genes, and discuss genetic strategies for studying hypoxia signaling and ------------------- Key: 5983 Medline: Authors: Ankeny RA Title: Sequencing the genome from nematode to human: changing methods, changing science. Citation: Endeavour 27: 87-92 2003 Type: REVIEW Genes: Abstract: The history of science tends to be recounted as a story of progress from early goals and discoveries to a unified outcome, in some sense implicit from the beginning, and often due to technological advances. The sequencing of the human genome is no exception. As a crucial part of the Human Genome Project, the history of genomic sequencing is typically presented as a direct result of the discoveries of the structure of DNA and its coding function, together with practical factors such as the development of techniques which made large-scale sequencing possible. However, the history of sequencing is inevitably a more complicated story, not only about molecular biology, but also about the evolving culture of scientific practice at the end of the 20th century. ------------------- Key: 5984 Medline: 12837604 Authors: Salisbury JL Title: Centrosome size is controlled by centriolar SAS-4. Citation: Trends in Cell Biology 13: 340-343 2003 Type: REVIEW Genes: sas-4 Abstract: The centrosome consists of a pair of centrioles and a surrounding matrix of pericentriolar material that anchors microtubule nucleation sites and consequently determines the number and organization of microtubules in interphase and mitotic cells. Recent studies utilizing a functional genomics approach in the nematode worm Caenorhabditis elegans and sophisticated light and electron microscopy techniques provide new insight into how centrioles act as centrosomal organizers and use a centriolar structural element to dictate centrosome size by defining their capacity to recruit pericentriolar material. ------------------- Key: 5985 Medline: 12881570 Authors: Grill SW;Howard J;Schaffer E;Stelzer EHK;Hyman AA Title: The distribution of active force generators controls mitotic spindle position. Citation: Science 301: 518-521 2003 Type: ARTICLE Genes: gpr-1 gpr-2 Abstract: During unequal cell divisions a mitotic spindle is eccentrically positioned before cell cleavage. To determine the basis of the net force imbalance that causes spindle displacement in one-cell Caenorhabditis elegans embryos, we fragmented centrosomes with an ultraviolet laser. Analysis of the mean and variance of fragment speeds suggests that the force imbalance is due to a larger number of force generators pulling on astral microtubules of the posterior aster relative to the anterior aster. Moreover, activation of heterotrimeric guanine nucleotide-binding protein (G protein) alpha subunits is required to generate these astral forces. ------------------- Key: 5986 Medline: 12828945 Authors: Kamath RS;Ahringer J Title: Genome-wide RNAi screeing in Caenorhabditis elegans. Citation: Methods 30: 313-321 2003 Type: ARTICLE Genes: Abstract: In Caenorhabditis elegans, introduction of double-stranded RNA (dsRNA) results in the specific inactivation of an endogenous gene with corresponding sequence; this technique is known as RNA interference (RNAi). It has previously been shown that RNAi can be performed by direct microinjection of dsRNA into adult hermaphrodite worms, by soaking worms in a solution of dsRNA, or by feeding worms Escherichia coli expressing target-gene dsRNA. We have developed a simple optimized protocol exploiting this third mode of dsRNA introduction, RNAi by feeding, which allows rapid and effective analysis of gene function in C. elegans. Furthermore, we have constructed a library of bacterial strains corresponding to roughly 86% of the estimated 19,000 predicted genes in C. elegans, and we have used it to perform genome-wide analyses of gene function. This library is publicly available, reusable resource allowing for rapid large-scale RNAi experiments. We have used this library to perform genome-wide analyses of gene function in C. elegans. Here, we describe the protocols used for bacterial library construction and for high-throughput screening in C. elegans using RNAi by feeding. ------------------- Key: 5987 Medline: 12852846 Authors: Podbilewics B Title: How does a cell anchor and invade an organ? Citation: Developmental Cell 5: 5-7 2003 Type: REVIEW Genes: cog-1 cog-2 let-23 lin-3 lin-11 lin-12 lin-29 Abstract: In multicellular organisms, most cells are confined to a particular tissue. However, some cells invade organs during normal development and in diseases (e.g., angiogenesis and cancer). Recent studies reveal a fascinating step-by-step process in which specific vulval cells induce and attract a single gonadal cell to invade an epithelial tubular organ in order to connect the uterus to the vulva in C. elegans. ------------------- Key: 5988 Medline: 12852847 Authors: Golden A;Cohen-Fix O Title: Getting (chromosomes) loaded - A new role for Timeless. Citation: Developmental Cell 5: 7-9 2003 Type: REVIEW Genes: tim-1 rec-8 Abstract: A recent study in C. elegans reveals an unanticipated link between sister chromatid cohesion and the TIM-1 protein, a homolog of the Drosophila circadian rhythm protein TIMELESS. The phenotypes of tim-1 mutants suggest that cohesin subunits load onto chromosomes in a stepwise manner. Whether TIM-1 is also involved in circadian rhythms ------------------- Key: 5989 Medline: 12852849 Authors: Sherwood DR;Sternberg PW Title: Anchor cell invasion into the vulval epithelium in C. elegans. Citation: Developmental Cell 5: 21-31 2003 Type: ARTICLE Genes: cdh-3 dig-1 egl-17 lin-3 lin-10 lin-12 lin-15 lin-28 zmp-1 Abstract: An understanding of cell-invasive behavior has been limited by the lack of in vivo models where this activity can be clearly visualized and manipulated. We show that a single cell in the Caenorhabditis elegans gonad, the anchor cell (AC), initiates uterine-vulval contact through a cell invasion event. Using genetic analysis, laser ablations, and cell-specific markers, we demonstrate that AC invasion is predominantly stimulated by the 1degrees vulval lineage cells, which generate a diffusible signal that promotes AC invasive behavior toward these cells and further targets invasive processes between the two central 1degrees vulval lineage cells. We also show that AC invasion is regulated by the AC response to this cue, as well as a valval-independent mechanism that weakly drives invasion. These studies dissect the regulatory mechanisms that underlie a simple cell-invasive behavior in vivo, and introduce AC invasion as a model for understanding key checkpoints controlling cell invasion. ------------------- Key: 5990 Medline: 12842032 Authors: Labouesse M;Georges-Labouesse E Title: Cell adhesion: parallels between vertebrate and invertebrate focal adhesions. Citation: Current Biology 13: R528-R530 2003 Type: REVIEW Genes: deb-1 dim-1 mig-2 pat-4 pat-6 unc-97 unc-112 Abstract: Recent studies highlight the striking similarity between vertebrate focal adhesion plaques and Caenorhabditis elegans muscle adhesion structures and position LIM domain proteins as central players at focal adhesions. ------------------- Key: 5991 Medline: 12839787 Authors: Caldwell KN;Adler BB;Anderson GL;Williams PL;Beuchat LR Title: Ingestion of Salmonella enterica serotype Poona by a free-living nematode, Caenorhabditis elegans, and protection against inactivation by produce sanitizers. Citation: Applied and Environmental Microbiology 69: 4103-4110 2003 Type: ARTICLE Genes: Abstract: Free-living nematodes are known to ingest food-borne pathogens and may serve as vectors to contaminate preharvest fruits and vegetables. Caenorhabditis elegans was selected as a model to study the effectiveness of sanitizers in killing Salmonella enterica serotype Poona ingested by free-living nematodes. Aqueous suspensions of adult worms that had fed on S. enterica serotype Poona were treated with produce sanitizers. Treatment with 20 mug of free chlorine/ml significantly (alpha = 0.05) reduced the population of S. enterica serotype Poona compared to results for treating worms with water (control). However, there was no significant difference in the number of S. enterica serotype Poona cells surviving treatments with 20 to 500 mug of chlorine/ml, suggesting that reductions caused by treatment with 20 mug of chlorine/ml resulted from inactivation of S. enterica serotype Poona on the surface of C elegans but not cells protected by the worm cuticle after ingestion. Treatment with Sanova (850 or 1,200 mug/ml), an acidified sodium chlorite sanitizer, caused reductions of 5.74 and 6.34 log(10) CFU/worm, respectively, compared to reductions from treating worms with water. Treatment with 20 or 40 mug of Tsunami 200/ml, a peroxyacetic acid-based sanitizer, resulted in reductions of 4.83 and 5.34 log(10) CFU/ worm, respectively, compared to numbers detected on or in worms treated with water. Among the organic acids evaluated at a concentration of 2%, acetic acid was the least effective in killing S. enterica serotype Poona and lactic acid was the most effective. Treatment with up to 500 mug of chlorine/ml, 1% hydrogen peroxide, 2,550 mug of Sanova/ml, 40 tLg of Tsunami 200/ml, or 2% acetic, citric, or lactic acid had no effect on the viability or reproductive behavior of C. elegans. Treatments were also applied to cantaloupe rind and lettuce inoculated with S. enterica serotype Poona or C. elegans that had ingested S. enterica serotype Poona. Protection of ingested S. enterica serotype Poona against sanitizers applied to cantaloupe was not evident; however, ingestion afforded protection of the pathogen on lettuce. These results indicate that S. enterica serotype Poona ingested by C. elegans may be protected against treatment with chlorine and other sanitizers, although the basis for this ------------------- Key: 5992 Medline: 12871705 Authors: Pepper ASR;Lo TW;Killian DJ;Hall DH;Hubbard EJA Title: The establishment of Caenorhabditis elegans germline pattern is controlled by overlapping proximal and distal somatic gonad signals. Citation: Developmental Biology 259: 336-350 2003 Type: ARTICLE Genes: fem-1 gld-1 gld-2 glp-1 lag-2 lin-12 Abstract: We investigated the control of proliferation and differentiation in the larval Caenorhabditis elegans hermaphrodite germ line through analysis of glp-1 and lag-2 mutants, cell ablations, and ultrastructural data. After the first several rounds of germ cell division, GLP-1, a receptor of the LIN-12/Notch family, governs germline proliferation. We analyzed the proximal proliferation (Pro) phenotype in glp-1(ar202) and found that initial meiosis was delayed and spatially mispositioned. This is due, at least in part, to a heightened response of the mutant GLP-1 receptor to multiple sources of the somatic ligand LAG-2, including the proximal somatic gonad. We investigated whether proximal LAG-2 affects germline proliferation in the wild type. Our results indicate that (1) LAG-2 is necessary for GLP-1-mediated germline proliferation and prevention of early meiosis, and (2) several distinct anatomical sources of LAG-2 in the larval somatic gonad functionally overlap to promote proliferation and prevent early meiosis. Ultrastructural studies suggest that mitosis is not restricted to areas of direct DTC-germ line contact and that the germ line shares a common cytoplasm in larval stages. We propose that downregulation of the GLP-1 signaling pathway in the proximal germ line at the time of meiotic onset is under tight temporal and spatial control. ------------------- Key: 5993 Medline: 12867961 Authors: Gems D;McElwee JJ Title: Microarraying mortality. Citation: Nature 424: 259-261 2003 Type: REVIEW Genes: daf-2 daf-16 igf-1 ins-7 Abstract: Understanding how we grow old is a long-sought goal. A new large-scale study of gene expression in worms allows us to glimpse the complex biochemistry of lifespan. ------------------- Key: 5994 Medline: 12772499 Authors: Dudley NR;Goldstein B Title: RNA interference: silencing in the cytoplasm and nucleus. Citation: Current Opinion in Molecular Therapeutics 5: 113-117 2003 Type: REVIEW Genes: Abstract: Although the discovery that double-stranded RNA is able to silence gene expression was only made five years ago, methods for experimentally silencing genes have already been extended into a broad diversity of organisms, including human cells. RNA interference has also been discovered to function in physiological gene silencing. RNA interference works by causing degradation of targeted mRNAs in the cytoplasm. However, recent results suggest that RNA interference may also silence gene activity in the nucleus by remodeling chromatin and repressing the transcription of targeted genes. ------------------- Key: 5995 Medline: 12684885 Authors: von Samson-Himmelstjerna S;Harder A;Failing K;Pape M;Schnieder T Title: Analysis of codon usage in beta-tubulin sequences of helminths. Citation: Parasitology Research 90: 294-300 2003 Type: ARTICLE Genes: ben-1 mec-7 Abstract: Codon usage bias has been shown to be correlated with gene expression levels in many organisms, including the nematode Caenorhabditis elegans. Here, the codon usage (cu) characteristics for a set of currently available beta-tubulin coding sequences of helminths were assessed by calculating several indices, including the effective codon number (Nc), the intrinsic codon deviation index (ICDI), the P2 value and the mutational response index (MRI). The P2 value gives a measure of translational pressure, which has been shown to be correlated to high gene expression levels in some organisms, but it has not yet been analysed in that respect in helminths. For all but two of the C. elegans beta-tubulin coding sequences investigated, the P2 value was the only index that indicated the presence of codon usage bias. Therefore, we propose that in general the helminth beta-tubulin sequences investigated here are not expressed at high levels. Furthermore, we calculated the correlation coefficients for the cu patterns of the helminth beta-tubulin sequences compared with those of highly expressed genes in organisms such as Escherichia coli and C. elegans. It was found that beta-tubulin cu patterns for all sequences of members of the Strongylida were significantly correlated to those for highly expressed C. elegans genes. This approach provides a new measure for comparing the adaptation of cu of a particular coding sequence with that of highly expressed genes in possible expression systems. Finally, using the cu patterns of the sequences studied, a phylogenetic tree was constructed. The topology of this tree was very much in concordance with that of a phylogeny based on small subunit ribosomal DNA ------------------- Key: 5996 Medline: 12857852 Authors: Li S;Dent JA;Roy R Title: Regulation of intermuscular electrical coupling by the Caenorhabditis elegans innexin inx-6. Citation: Molecular Biology of the Cell 14: 2630-2644 2003 Type: ARTICLE Genes: avr-15 eat-2 eat-5 exp-2 inx-3 inx-6 unc-7 Abstract: The innexins represent a highly conserved protein family, the members of which make up the structural components of gap junctions in invertebrates. We have isolated and characterized a Caenorhabditis elegans gene inx-6 that encodes a new member of the innexin family required for the electrical coupling of pharyngeal muscles. inx-6(rr5) mutants complete embryogenesis without detectable abnormalities at restrictive temperature but fail to initiate postembryonic development after hatching. inx-6 is expressed in the pharynx at all larval stages, and an INX-6::GFP fusion protein showed a punctate expression pattern characteristic of gap junction proteins localized to plasma membrane plaques. Video recording and electropharyngeograms revealed that in inx6-(rr5) mutants the anterior pharyngeal (procorpus) muscles were electrically coupled to a lesser degree than the posterior metacorpus muscles, which caused a premature relaxation in the anterior pharynx and interfered with feeding. Dye-coupling experiments indicate that the gap junctions that link the procorpus to the metacorpus are functionally compromised in inx-6(rr5) mutants. We also show that another C. elegans innexin, EAT-5, can partially substitute for INX-6 function in vivo, underscoring their likely analogous function. ------------------- Key: 5997 Medline: 12857879 Authors: Timmons L;Tabara H;Mello CC;Fire AZ Title: Inducible systemic RNA silencing in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 14: 2972-2983 2003 Type: ARTICLE Genes: fed-1 let-858 myo-3 rde-4 sid-1 unc-119 vit-2 Abstract: Introduction of double-stranded RNA (dsRNA) can elicit a gene-specific RNA interference response in a variety of organisms and cell types. In many cases, this response has a systemic character in that silencing of gene expression is observed in cells distal from the site of dsRNA delivery. The molecular mechanisms underlying the mobile nature of RNA silencing are unknown. For example, although cellular entry of dsRNA is possible, cellular exit of dsRNA from normal animal cells has not been directly observed. We provide evidence that transgenic strains of Caenorhabditis elegans transcribing dsRNA from a tissue-specific promoter do not exhibit comprehensive systemic RNA interference phenotypes. In these same animals, modifications of environmental conditions can result in more robust systemic RNA silencing. Additionally, we find that genetic mutations can influence the systemic character of RNA silencing in C. elegans and can separate mechanisms underlying systemic RNA silencing into tissue-specific components. These data suggest that trafficking of RNA silencing signals in C. elegans is regulated by specific physiological and genetic ------------------- Key: 5998 Medline: 12838583 Authors: Tsalik EL;Hobert O Title: Functional mapping of neurons that control locomotory behavior in Caenorhabditis elegans. Citation: Journal of Neurobiology 56: 178-197 2003 Type: ARTICLE Genes: che-1 odr-7 odr-10 ttx-1 ttx-3 unc-86 Abstract: One approach to understanding behavior is to define the cellular components of neuronal circuits that control behavior. In the nematode Caenorhabditis elegans, neuronal circuits have been delineated based on patterns of synaptic connectivity derived from ultrastructural analysis. Individual cellular components of these anatomically defined circuits have previously been characterized on the sensory and motor neuron levels. In contrast, interneuron function has only been addressed to a limited extent. We describe here several classes of interneurons (AIY, AIZ, and RIB) that modulate locomotory behavior in C. elegans. Using mutant analysis as well as microsurgical mapping techniques, we found that the AIY neuron class serves to tonically modulate reversal frequency of animals in various sensory environments via the repression of the activity of a bistable switch composed of defined command interneurons. Furthermore, we show that the presentation of defined sensory modalities induces specific alterations in reversal behavior and that the AIY interneuron class mediates this alteration in locomotory behavior. We also found that the AIZ and RIB interneuron classes process odorsensory information in parallel to the AIY interneuron class. AIY, AIZ, and RIB are the first interneurons directly implicated in chemosensory signaling. Our neuronal mapping studies provide the framework for further genetic and functional dissections of neuronal circuits in C. elegans. ------------------- Key: 5999 Medline: 12716883 Authors: Shukla A;Raje M;Guptasarma P Title: A backbone-reversed form of an all-beta alpha-crystallin domain from a small heat-shock protein (retro-HSP12.6) folds and assembles into structured multimers. Citation: Journal of Biological Chemistry 278: 26505-26510 2003 Type: ARTICLE Genes: Abstract: The structural consequences of polypeptide backbone reversal ("retro" modification) remain largely unexplored, in particular, for the retro forms of globular all-beta-sheet proteins. To examine whether the backbone-reversed form of a model all-beta-sheet protein can fold and adopt secondary and tertiary structure, we created and examined the recombinant retro form of a 110-residue-long polypeptide, an alpha-crystallin-like small heat-shock protein, HSP12.6, from C. elegans. Following intracellular overexpression in fusion with a histidine affinity tag in Escherichia coli, purification under denaturing conditions, and removal of denaturant through dialysis, retro-HSP12.6 was found to fold to a soluble state. The folded protein was examined using fluorescence and CD spectroscopy, gel filtration chromatography, non-denaturing electrophoresis, differential scanning calorimetry, and electron microscopy and confirmed to have adopted secondary structure and assembled into a multimer. Interestingly, like its parent polypeptide, retro-HSP12.6 did not aggregate upon heating; rather, heating led to a dramatic increase in structural content and the adoption of what would appear to be a very well folded state at high temperatures. However, this was essentially reversed upon cooling with some hysteresis being observed resulting in greater structural content in the heated-cooled protein than in the unheated protein. The heated-cooled samples displayed CD spectra indicative of structural content comparable to that of any naturally occurring globular protein. Attempts are being made to ------------------- Key: 6000 Medline: 12711598 Authors: Kim SH;Hwang SB;Chung IK;Lee J Title: Sequence-specific binding to telomeric DNA by CEH-37, a homeodomain protein in the nematode Caenorhabditis elegans. Citation: Journal of Biological Chemistry 278: 28038-28044 2003 Type: ARTICLE Genes: ceh-37 mrt-2 Abstract: Caenorhabditis elegans can serve as a model system to study telomere functions due to its similarity to higher organisms in telomere structures. We report here the identification of the nematode homeodomain protein CEH-37 as a telomere-binding protein using a yeast one-hybrid screen. The predicted three-dimensional model of the homeodomain of CEH-37, which has a typical helix-loop-helix structure, was similar to that of the Myb domain of known telomere-binding proteins, which is also a helix-loop-helix protein, despite little amino acid sequence similarity. We demonstrated the specific binding of CEH-37 to the nematode telomere sequences in vitro by competition assays. We determined that CEH-37 binding required at least 1.5 repeats of TTAGGC and that the core sequence for binding was GGCTTA. We found that CEH-37 had an ability to bend telomere sequence-containing DNA, which is the case for other known telomere-binding proteins such as TRF1 and RAP1, indicating that CEH-37 may be involved in establishing or maintaining a secondary structure of the telomeres in vivo. We also demonstrated that CEH-37 was primarily co-localized to the chromosome ends in vivo, indicating that CEH-37 may play roles in telomere functions. Consistent with this, a ceh-37 mutation resulting in a truncated protein caused a weak high incidence of male phenotype, which may have been caused by chromosome instability. The identification of CEH-37 as a telomere-binding protein may represent an evolutionary conservation of telomere-binding proteins in terms of tertiary protein structure rather than primary amino acid ------------------- Key: 6001 Medline: 12814796 Authors: Van Voorhies WA Title: Is life span extension in single gene long-lived Caenorhabditis elegans mutants due to hypometabolism? Citation: Experimental Gerontology 38: 615-618 2003 Type: REVIEW Genes: atp-2 clk-1 isp-1 nuo-1 Abstract: The nematode C elegans is widely used in aging research largely because of the identification of numerous gene mutations that significantly increase worm longevity. While model organisms such as C elegans can provide important insights into aging it is also important to consider the limitations of these systems. For example, ectothermic (poikilothermic) organisms are able to tolerate a much larger metabolic depression than humans and considering only chronological longevity when assaying for long-lived mutants provides a limited perspective on the mechanisms by which longevity is increased. In order to provide true insight-into the aging process additional physiological processes, such as metabolic rate, must also be assayed. Currently it is controversial when long-lived C. elegans mutants retain normal metabolic function. Resolving this issue requires accurately measuring the metabolic rate of C elegans under conditions that minimize environmental stress. Comparisons; of metabolic rate between long-lived and wild-type C. elegans under more optimized conditions indicate that the extended longevity of at least some long-lived C. elegans mutants may be due to a reduction in metabolic rate, rather than an alteration of a metabolically-independent genetic mechanism specific to aging. Consistent with this assertion are studies showing that the disruption of mitochondrial function in C. elegans can extend worm's longevity, but typically causes worms to grow and develop more slowly than wild-type animals. ------------------- Key: 6002 Medline: 12756172 Authors: Mathies LD;Henderson ST;Kimble J Title: The C. elegans Hand gene controls embryogenesis and early gonadogenesis. Citation: Development 130: 2881-2892 2003 Type: ARTICLE Genes: ced-2 ced-3 ehn-1 ehn-3 gon-2 gon-4 hlh-1 hnd-1 lag-2 sys-1 mnDf93 nDf41 Abstract: The C elegans genome encodes a single Hand bHLH transcription factor. Either hnd-1(RNAi) or a hnd-1 deletion causes partially penetrant defects in viability and gonadogenesis. Dead embryos and young larvae are often misshapen at the posterior end. Our primary focus has been the role of hnd-1 in gonadogenesis. Wild-type C elegans has two somatic gonadal precursors and two primordial germ cells in stereotyped positions within its four-celled gonadal primordium. The hnd-1 gene affects the presence and position of both the somatic gonadal precursors and primordial germ cells within the primordium, but does not appear to have any role in later gonadogenesis. hnd-1 probably acts within the somatic gonadal precursors or their mesodermal predecessors; defects in primordial germ cells and germ line appear to be secondary. In hnd-1 mutants, somatic gonadal precursors are generated normally, but are not maintained properly and sometimes die. A similar role in controlling the maintenance of precursor fates has been described for other genes governing early organogenesis, including the zebrafish Hand gene hands off. We also report the discovery of two genes, ehn-1 and ehn-3, that have overlapping functions with hnd-1 in embryogenesis ------------------- Key: 6003 Medline: 12813206 Authors: Riddle DL Title: Neurobiology of aging: hormonal regulation of development and longevity in C. elegans. Citation: Alzheimer Disease and Associated Disorders 17: S42-S44 2003 Type: REVIEW Genes: cet-1 daf-1 daf-2 daf-3 daf-4 daf-7 daf-9 daf-12 daf-14 daf-16 sma-6 Abstract: The soil nematode Caenorhabditis elegans is a relatively simple organism for the study of animal development and behavior. The worm is conceived as a single cell and undergoes a complex process of development through four larval stages (L1-L4) before it reaches adulthood and lays eggs. It takes approximately 3 days to develop through the larval stages. After reproduction it gradually ages, loses vigor, and dies, usually within 2 to 3 weeks. ------------------- Key: 6004 Medline: 12894212 Authors: DeRenzo C;Reese KJ;Seydoux G Title: Exclusion of germ plasm proteins from somatic lineages by cullin-dependent degradation. Citation: Nature 424: 685-689 2003 Type: ARTICLE Genes: cul-2 cul-3 mex-1 mex-5 mex-6 par-1 pie-1 pos-1 zif-1 Abstract: In many animals, establishment of the germ line depends on segregation of a specialized cytoplasm, or 'germplasm', to a small number of germline precursor cells during early embryogenesis(1). Germ plasm asymmetry involves targeting of RNAs and proteins to a specific region of the oocyte and/or embryo(2). Here we demonstrate that germ plasm asymmetry also depends on degradation of germline proteins in non-germline (somatic) cells. We show that five CCCH finger proteins, components of the Caenorhabditis elegans germ plasm, are targeted for degradation by the novel CCCH-finger-binding protein ZIF-1. ZIF-1 is a SOCS-box protein that interacts with the E3 ubiquitin ligase subunit elongin C. Elongin C, the cullin CUL-2, the ring finger protein RBX-1 and the E2 ubiquitin conjugation enzyme UBC5 (also known as LET-70) are all required in vivo for CCCH finger protein degradation. Degradation is activated in somatic cells by the redundant CCCH finger proteins MEX-5 and MEX-6, which are counteracted in the germ line by the PAR-1 kinase. We propose that segregation of the germ plasm involves both stabilization of germline proteins in the germ line and cullin-dependent degradation in the soma. ------------------- Key: 6005 Medline: 12878695 Authors: Mathews EA;Garcia E;Santi CM;Mullen GP;Thacker C;Moerman DG;Snutch TP Title: Critical residues of the Caenorhabditis elegans unc-2 voltage-gated calcium channel that affect behavioral and physiological properties. Citation: Journal of Neuroscience 23: 6537-6545 2003 Type: ARTICLE Genes: unc-2 Abstract: The Caenorhabditis elegans unc-2 gene encodes a voltage-gated calcium channel alpha(1) subunit structurally related to mammalian dihydropyridine-insensitive high-threshold channels. In the present paper we describe the characterization of seven alleles of unc-2. Using an unc-2 promoter-tagged green fluorescent protein construct, we show that unc-2 is primarily expressed in motor neurons, several subsets of sensory neurons, and the HSN and VC neurons that control egg laying. Examination of behavioral phenotypes, including defecation, thrashing, and sensitivities to aldicarb and nicotine suggests that UNC-2 acts presynaptically to mediate both cholinergic and GABAergic neurotransmission. Sequence analysis of the unc-2 alleles shows that e55, ra605, ra606, ra609, and ra610 all are predicted to prematurely terminate and greatly reduce or eliminate unc-2 function. In contrast, the ra612 and ra614 alleles are missense mutations resulting in the substitution of highly conserved residues in the C terminus and the domain IVS4-IVS5 linker, respectively. Heterologous expression of a rat brain P/Q-type channel containing the ra612 mutation shows that the glycine to arginine substitution affects a variety of channel characteristics, including the voltage dependence of activation, steady-state inactivation, as well as channel kinetics. Overall, our findings suggest that UNC-2 plays a pivotal role in mediating a number of physiological processes in the nematode and also defines a number of critical residues important for calcium channel function in vivo. ------------------- Key: 6006 Medline: 12796460 Authors: Avery L;Shtonda BB Title: Food transport in the C. elegans pharynx. Citation: Journal of Experimental Biology 206: 2441-2457 2003 Type: REVIEW Genes: eat-2 eat-4 eat-5 unc-29 Abstract: Pumping of the C elegans pharynx transports food particles (bacteria) posteriorly. We examined muscle motions to determine how this posterior transport is effected. We find that the motions of the middle section of the pharynx, the anterior isthmus, are delayed relative to the anterior section, the corpus. Simulations in which particles are assumed to move at mean fluid velocity when not captured by the walls of the pharyngeal lumen show that delayed isthmus motions do indeed cause net particle transport; however, the amount is much less than in the real pharynx. We propose that the geometry of the pharyngeal lumen forces particles to the center, where they move faster than mean fluid velocity. When this acceleration is incorporated into the simulation, particles are transported efficiently. The transport mechanism we propose explains past observations that the timing of muscle relaxation is important for effective transport. Our model also makes A prediction, which we confirm, that smaller bacteria are better food sources for C elegans than large ones. ------------------- Key: 6007 Medline: 12853134 Authors: Choi KY;Ji YJ;Dhakal BK;Yu JR;Cho C;Song WK;Ahnn J Title: Vacuolar-type H+ -ATPase E subunit is required for embryogenesis and yolk transfer in Caenorhabditis elegans. Citation: Gene 311: 13-23 2003 Type: ARTICLE Genes: vha-8 Abstract: Vacuolar H+-ATPases (V-ATPases) are ATP-dependent proton pumps localized at membranes of intracellular acidic organelles and plasma membranes of various cell types. By virtue of its regulation in acidification, V-ATPase is required for many intracellular processes such as receptor-mediated endocytosis and protein sorting. Here we report the molecular characterization of the E subunit of V-ATPase in Caenorhabditis elegans. This subunit is one of the most well conserved subunits sharing approximately 57% identity with the human homologue, ATP6E. Green fluorescent protein (GFP) and whole-mount immunostaining analyses showed that V-ATPase E subunit (vha-8) is abundantly expressed in the H-shaped excretory cell, consistent with the expression patterns observed for other V-ATPase subunits. Double-stranded RNAs (or RNAi) targeted to vha-8 resulted in embryonic and larval lethality for the first filial generation, indicating that vha-8 is essential during early developmental processes. In addition, accumulation of abnormal endomitotic oocytes and defects in receptor-mediated endocytosis were observed in parental animals. These findings suggest that multiple phenotypes caused by the disruption of pH homeostasis are due to the defective V-ATPase. In summary, vha-8 encoding the E subunit of V-ATPase in C. elegans is essential for embryogenesis and receptor-mediated endocytosis. ------------------- Key: 6008 Medline: Authors: Lundquist EA Title: Rac proteins and the control of axon development. Citation: Current Opinion in Neurobiology 13: 384-390 2003 Type: REVIEW Genes: ced-5 ced-10 mig-2 rac-2 rac-3 unc-34 unc-40 unc-73 unc-115 unc-119 Abstract: Rac GTPases and their effectors control cellular morphogenesis in a wide range of developmental contexts by regulating the structure and dynamics of the actin cytoskeleton. Although much is known about the biochemistry of Racs and Rae regulators, less is known about how Racs control cellular morphogenesis, including axon development, in vivo. Recent loss-of-function genetic studies using model organisms have shown that Racs and their effectors are required for multiple aspects of axon development, including axon outgrowth, axon guidance and axon branching. Interestingly, these studies have also revealed that Rac activity is required to prune spurious axons and branches. Analyses of Racs and their upstream and downstream effectors suggest that Rae signaling is complex. Different neurons utilize distinct combinations of upstream Rae regulators during axon development, possibly reflecting responses to different axon path-finding signals, and Racs use distinct downstream effectors to mediate different aspects of axon development, possibly reflecting differential regulation of the lamellipodial and filopodial growth-cone actin-cytoskeleton domains underlying axon developmental events. ------------------- Key: 6009 Medline: 12867049 Authors: Schumacher B;Alpi A;Garter A Title: Cell cycle: check for asynchrony. Citation: Current Biology 13: R560-R562 2003 Type: REVIEW Genes: atl-1 chk-1 Abstract: During metazoan development cells destined for different fates become asymmetric, not just in morphology and developmental potential but also in cell-cycle timing. A recent study has now shown that differential cell-cycle timing in the first cell divisions of the Caenorhabditis elegans embryo is in part controlled by a DNA replication checkpoint. ------------------- Key: 6010 Medline: 12684824 Authors: Alpi A;Pasierbek P;Gartner A;Loidl J Title: Genetic and cytological characterization of the recombination protein RAD-51 in Caenorhabditis elegans. Citation: Chromosoma 112: 6-16 2003 Type: ARTICLE Genes: chk-2 him-3 let-276 mre-11 msh-5 rad-51 rec-8 spo-11 syp-1 nDf41 eT1 hT1 Abstract: We investigated the role of Caenorhabditis elegans rad-51 during meiotic prophase. We showed that rad-51 mutant worms are viable, have no defects in meiotic homology recognition and synapsis but exhibit abnormal chromosomal morphology and univalent formation at diakinesis. During meiosis RAD-51 becomes localized to distinct foci in nuclei of the transition zone of the gonad and is most abundant in nuclei at late zygotene/early pachytene. Foci then gradually disappear from chromosomes and no foci are observed in late pachytene. RAD-51 localization requires the recombination genes spo-11 and mre-11 as well as chk-2, which is necessary for homology recognition and presynaptic alignment. Mutational analysis with synapsis- and recombination-defective strains, as well as the analysis of strains bearing heterozygous translocation chromosomes, suggests that presynaptic alignment may be required for RAD-51 focus formation, whereas homologous synaptonemal complex formation is required to remove RAD-51 foci. ------------------- Key: 6011 Medline: 12865086 Authors: Moffett CL;Beckett AM;Mousley A;Geary TG;Marks NJ;Halton DW;Thompson DP;Maule AG Title: The ovijector of Ascaris suum: multiple response types revealed by Caenorhabditis elegans FMRFamide-related peptides. Citation: International Journal for Parasitology 33: 859-876 2003 Type: ARTICLE Genes: afp-1 flp-1 flp-2 flp-3 flp-4 flp-5 flp-6 flp-7 flp-8 flp-9 flp-10 flp-11 flp-12 flp-13 flp-14 flp-15 flp-16 flp-17 flp-18 flp-19 flp-20 flp-21 flp-22 Abstract: Caenorhabditis elegans possesses 22 FMRFamide-like peptide (flp) genes predicted to encode 60 different FMRFamide-related peptides with a range of C-terminal signatures. Peptides from five flp genes (1, 6, 8, 9 and 14) are known to modulate the ovijector of Ascaris suum in vitro. This study examines the physiological effects of peptides from the remaining 17 flp genes such that the variety of FNIRFamide-related peptide-induced ovijector response types can be delineated. Five categories of response were identified according to the pattern of changes in contractile behaviour and baseline tension. Peptides encoded on 16 flp genes (1, 2, 3, 4, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17 and 20) had qualitatively similar inhibitory (response type 1) actions, with the lowest activity thresholds (1 nM) recorded for peptides with FIRFamide or FLRFamide C-terminal signatures. Peptides encoded on four flp genes (2, 18, 19 and 21), and on the A. suum afp-1 gene, had excitatory actions on the ovijector (response type 2), with PGVLRFamides having the lowest activity threshold (1 nM). An flp-2 peptide (LRGEPIRFamide) induced a transient contraction of the ovijector (activity threshold, 10 nM) that was designated response type 3. Response type 4 comprised a transient contraction followed by an extended period of inactivity and was observed with peptides encoded on flp-5 (AGAKFIRFamide, APKPKFIRFarnicle), flp-8 (KNEFIRFamide) and flp-22 (SPSAKWMRFamide). SPSAKWMRFamide was the most potent peptide tested with an activity threshold of 0.1 nM. A single peptide (AMRNALVRFainide; activity threshold 0.1 muM), encoded on flp-11, induced response type 5, a shortening of the ovijector coupled with an increase in contraction frequency. Although most flp genes encode structurally related peptides that trigger one of the five ovijector response types, flp-2 and flp-11 co-encode FMRFamide-related peptides that induce distinct responses. Within the ovijector of A. suum FaRPs play a complex role involving at least five receptor subtypes or signalling ------------------- Key: 6012 Medline: 12942444 Authors: Gally C;Bessereau JL Title: C. elegans: of neurons and genes. Citation: M S-Medecine Sciences 19: 725-734 2003 Type: REVIEW Genes: ncs-1 sax-3 slt-1 snb-1 unc-4 unc-5 unc-6 unc-13 unc-40 unc-49 unc-129 Abstract: The human brain contains 100 billion neurons and probably one thousand times more synapses. Such a system can be analyzed at different complexity levels, from cognitive functions to molecular structure of ion channels. However, it remains extremely difficult to establish links between these different levels. An alternative strategy relies on the use of much simpler animals that can be easily manipulated. In 1974, S. Brenner introduced the nematode Coenorhabditis elegans as a model system. This worm has a simple nervous system that only contains 302 neurons and about 7,000 synapses. Forward genetic screens are powerful tools to identify genes required for specific neuron functions and behaviors. Moreover, studies of mutant phenotypes can identify the function of a protein in the nervous system. The data that hove been obtained in C. elegans demonstrate a fascinating conservation of the molecular and cellular biology of the neuron between worms and mammals through more than 550 million years of evolution. ------------------- Key: 6013 Medline: 12942445 Authors: Gonczy P Title: Mechanisms of cell division: lessons from a nematode. Citation: M S-Medecine Sciences 19: 735-742 2003 Type: REVIEW Genes: Abstract: The mechanisms orchestrating spatial cell division control remain poorly understood. In animal cells, the position of the mitotic spindle dictates cleavage furrow placement, and thus plays a key role in governing spatial relationships between resulting daughter cells. The one-cell stage Caenorhabditis elegans embryo is an attractive model system to investigate the mechanisms underlying spindle positioning in metozoans. In this review, the experimental advantages of this model system for an in vivo dissection of cell division processes are first discussed. Next, three lines of experiments that were conducted to dissect the mechanisms governing spindle positioning in one-cell stage C. elegans embryos are summarized. First, localized laser micro-irradiations were utilized to identify the forces acting on spindle poles during anaphase. This work revealed that there is a precise imbalance of pulling forces acting on the two spindle poles, with the forces acting on the posterior spindle pole being in slight excess, thus explaining the asymmetric spindle position achieved by the end of anaphase. Second, an RNAi-based fonctional genomic screen was carried out to identify novel components required for generating these pulling forces. This uncovered that gpr-1/gpr-2, which encode GoLoco-containing proteins, as well as the previously identified Go subunits goa-1/gpa-16, are required for generation of pulling forces on the spindle poles. Third, the zyg-8 locus was identified by mutational analysis to play a distinct role during anaphase spindle positioning. zyg-8 was found to encode a protein related to human Doublecortin, which is affected in patients with neuronal migration disorders. Moreover, ZYG-8 is a microtubule-associated protein that stabilizes microtubules against depolymerization. Together, these experimental approaches contribute to a better understanding of the mechanisms orchestrating spatial cell division control in metozoan organisms. ------------------- Key: 6014 Medline: Authors: Huang C;Hall DH;Hedgecock EM;Kao G;Karantza V;Vogel BE;Hutter H;Chisholm AD;Yurchenco PD;Wadsworth WG Title: Laminin alpha subunits and their role in C. elegans development. Citation: Development 130: 3343-3358 2003 Type: ARTICLE Genes: emb-9 epi-1 ina-1 lam-3 nid-1 pat-3 mnDf90 Abstract: Laminins are heterotrimeric (alpha/beta/gamma) glycoproteins that form a major polymer within basement membranes. Different alpha, beta and gamma subunits can assemble into various laminin isoforms that have different, but often overlapping, distributions and functions. In this study, we examine the contributions of the laminin alpha subunits to the development of C. elegans. There are two alpha, one beta and one gamma laminin subunit, suggesting two laminin isoforms that differ by their alpha subunit assemble in C. elegans. We find that near the end of gastrulation and before other basement membrane components are detected, the alpha subunits are secreted between primary tissue layers and become distributed in different patterns to the surfaces of cells. Mutations in either alpha subunit gene cause missing or disrupted extracellular matrix where the protein normally localizes. Cell-cell adhesions are abnormal: in some cases essential cell-cell adhesions are lacking, while in other cases, cells inappropriately adhere to and invade neighboring tissues. Using electron microscopy, we observe adhesion complexes at improper cell surfaces and disoriented cytoskeletal filaments. Cells throughout the animal show defective differentiation, proliferation or migration, suggesting a general disruption of cell-cell signaling. The results suggest a receptor-mediated process localizes each secreted laminin to exposed cell surfaces and that laminin is crucial for organizing extracellular matrix, receptor and intracellular proteins at those surfaces. We propose this supramolecular architecture regulates adhesions and ------------------- Key: 6015 Medline: 12783794 Authors: Ohkura K;Suzuki N;Ishihara T;Katsura I Title: SDF-9, a protein tyrosine phosphatase-like molecule, regulates the L3/dauer developmental decision through hormonal signaling in C. elegans. Citation: Development 130: 3237-3248 2003 Type: ARTICLE Genes: daf-2 daf-3 daf-5 daf-7 daf-9 daf-12 daf-16 sdf-9 unc-31 Abstract: The dauer larva of the nematode Caenorhabditis elegans is a good model system for investigating the regulation of developmental fates by environmental cues. Here we show that SDF-9, a protein tyrosine phosphatase-like molecule, is involved in the regulation of dauer larva formation. The dauer larva of sdf-9 mutants is different from a normal dauer larva but resembles the dauer-like larva of daf-9 and daf-12 dauer-constitutive mutants. Like these mutants, the dauer-constitutive phenotypes of sdf-9 mutants were greatly enhanced by cholesterol deprivation. Epistasis analyses, together with the relationship between sdf-9 mutations and daf-9 expression, suggested that SDF-9 increases the activity of DAF-9 or helps the execution of the DAF-9 function. SDF-9 was expressed in two head cells in which DAF-9 is expressed. By their position and by genetic mosaic experiments, we identified these cells as XXXL/R cells, which are known as embryonic hypodermal cells and whose function at later stages is unknown. Killing of the sdf-9-expressing cells in the wild-type first-stage larva induced formation of the dauer-like larva. Since this study on SDF-9 and former studies on DAF-9 showed that the functions of these proteins are related to those of steroids, XXXL/R cells seem to play a key role in the metabolism or function of a steroid hormone(s) that acts in dauer regulation. ------------------- Key: 6016 Medline: Authors: Ambros V;Bartel B;Bartel DP;Burge CB;Carrington JC;Chen X;Dreyfuss G;Eddy SR;Griffiths-Jones S;Marshall M;Matzke M;Ruvkun G;Tuschl T Title: A uniform system for microRNA annotation. Citation: RNA 9: 277-279 2003 Type: ARTICLE Genes: let-7 lin-4 Abstract: MicroRNAs (miRNAs) are small noncoding RNA gene products about 22 nt long that are processed by Dicer from precursors with a characteristic hairpin secondary structure. Guidelines are presented for the identification and annotation of new miRNAs from diverse organisms, particularly so that miRNAs can be reliably distinguished from other RNAs such as small interfering RNAs. We describe specific criteria for the experimental verification of miRNAs, and conventions for naming miRNAs and miRNA genes. Finally, an online clearinghouse for miRNA gene name assignments is provided by the Rfam database of RNA families. ------------------- Key: 6017 Medline: 12888489 Authors: Venkatesan K;McManus HR;Mello CC;Smith TF;Hansen U Title: Functional conservation between members of an ancient duplicated transcription factor family, LSF/Grainyhead. Citation: Nucleic Acids Research 31: 4304-4316 2003 Type: ARTICLE Genes: dbl-1 grh-1 mab-5 pcn-1 Abstract: The LSF/Grainyhead transcription factor family is involved in many important biological processes, including cell cycle, cell growth and development. In order to investigate the evolutionary conservation of these biological roles, we have characterized two new family members in Caenorhabditis elegans and Xenopus laevis. The C.elegans member, Ce-GRH-1, groups with the Grainyhead subfamily, while the X.laevis member, Xl-LSF, groups with the LSF subfamily. Ce-GRH-1 binds DNA in a sequence-specific manner identical to that of Drosophila melanogaster Grainyhead. In addition, Ce-GRH-1 binds to sequences upstream of the C.elegans gene encoding aromatic l-amino-acid decarboxylase and genes involved in post-embryonic development, mab-5 and dbl-1. All three C.elegans genes are homologs of D.melanogaster Grainyhead-regulated genes. RNA-mediated interference of Ce-grh-1 results in embryonic lethality in worms, accompanied by soft, defective cuticles. These phenotypes are strikingly similar to those observed previously in D.melanogaster grainyhead mutants, suggesting conservation of the developmental role of these family members over the course of evolution. Our phylogenetic analysis of the expanded LSF/GRH family (including other previously unrecognized proteins/ESTs) suggests that the structural and functional dichotomy of this family dates back more than 700 million years, i.e. to the time when the first multicellular organisms are thought to have arisen. ------------------- Key: 6018 Medline: Authors: Syntichaki P;Tavernarakis N Title: The biochemistry of neuronal necrosis: rogue biology? Citation: Nature Reviews Neuroscience 4: 672-684 2003 Type: REVIEW Genes: acy-1 asp-3 asp-4 clp-1 daf-2 deg-1 deg-3 des-2 gsa-1 mec-4 mec-6 sgs-1 tra-3 Abstract: When stressed beyond their tolerance, cells undergo necrosis, an acute, non-apoptotic form of cell death. Necrosis is crucial to the damage that injury and disease inflict on the nervous system. Recent discoveries have shed light onto the molecular requirements for necrosis, and provide new evidence that, as is the case for apoptosis, the mechanisms of necrotic cell death are conserved from nematodes to humans. But in contrast to apoptotic mechanisms, necrotic mechanisms did not evolve specifically to carry out necrosis. Instead, under extreme circumstances, normal cellular activities are destabilized with devastating consequences for the cell. Here, we review the mechanisms that are implicated in necrosis and discuss the events that transform them to catastrophic for cell ------------------- Key: 6019 Medline: 12897774 Authors: Kuersten S;Goodwin EB Title: The power of the 3' UTR: translational control and development. Citation: Nature Reviews Genetics 4: 626-637 2003 Type: REVIEW Genes: apx-1 fem-3 fog-1 gld-1 glp-1 hbl-1 let-7 lin-4 lin-14 lin-28 lin-41 mex-3 mex-5 mex-6 mog-1 mog-4 mog-5 pal-1 par-1 par-2 par-3 par-6 pos-1 spn-4 tra-2 Abstract: Many crucial decisions, such as the location and timing of cell division, cell-fate determination, and embryonic axes establishment, are made in the early embryo, a time in development when there is often little or no transcription. For this reason, the control of variation in gene expression in the early embryo often relies on post-transcriptional control of maternal genes. Although the early embryo is rife with translational control, controlling mRNA activity is also important in other developmental processes, such as stem-cell proliferation, sex determination, neurogenesis and erythropoiesis. ------------------- Key: 6020 Medline: 12858183 Authors: Krijgsveld J;Ketting RF;Mahmoudi T;Johansen J;Artal-Sanz M;Verrijzer CP;Plasterk RHA;Heck AJR Title: Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Citation: Nature Biotechnology 21: 927-931 2003 Type: ARTICLE Genes: glp-4 Abstract: A crucial issue in comparative proteomics is the accurate quantification of differences in protein expression levels. To achieve this, several methods have been developed in which proteins are labeled with stable isotopes either in vivo via metabolic labeling or in vitro by protein derivatization. Although metabolic labeling is the only way to obtain labeling of all proteins, it has thus far only been applied to single-celled organisms(1,2) and cells in culture(2,3). Here we describe quantitative N-15 metabolic labeling of the multicellular organisms Caenorhabditis elegans, a nematode, and Drosophila melanogaster, the common fruit fly, achieved by feeding them on N-15-labeled Escherichia coli and yeast, respectively. The relative abundance of individual proteins obtained from different samples can then be determined by mass spectrometry (MS). The applicability of the method is exemplified by the comparison of protein expression levels in two C. elegans strains, one with and one without a germ line. The methodology described provides tools for accurate quantitative proteomic studies in these model organisms. ------------------- Key: 6021 Medline: 12887685 Authors: Suo S;Sasagawa N;Ishiura S Title: Cloning and characterization of a Caenorhabditis elegans D2-like dopamine receptor. Citation: Journal of Neurochemistry 86: 869-878 2003 Type: ARTICLE Genes: cat-2 Abstract: The neurotransmitter dopamine plays an important role in the regulation of behavior in both vertebrates and invertebrates. In mammals, dopamine binds and activates two classes of dopamine receptors, D1-like and D2-like receptors. However, D2-like dopamine receptors in Caenorhabditis elegans have not yet been characterized. We have cloned a cDNA encoding a putative C. elegans D2-like dopamine receptor. The deduced amino acid sequence of the cloned cDNA shows higher sequence similarities to vertebrate D2-like dopamine receptors than to D1-like receptors. Two splice variants that differ in the length of their predicted third intracellular loops were identified. The receptor heterologously expressed in cultured cells showed high affinity binding to [(125) I]iodo-lysergic acid diethylamide. Dopamine showed the highest affinity for this receptor among several amine neurotransmitters tested. Activation of the heterologously expressed receptor led to the inhibition of cyclic AMP production, confirming that this receptor has the functional property of a D2-like receptor. We have also analyzed the expression pattern of this receptor and found that the receptor is expressed in several neurons including all the dopaminergic neurons in C. elegans. ------------------- Key: 6022 Medline: 12902378 Authors: Owen AB;Stuart J;Mach K;Villeneuve AM;Kim S Title: A gene recommender algorithm to identify coexpressed genes in C. elegans. Citation: Genome Research 13: 1828-1837 2003 Type: ARTICLE Genes: cdl-1 dpl-1 drp-1 hda-1 klp-10 lin-8 lin-9 lin-15 lin-35 lin-36 lin-38 lin-53 mcm-7 plk-1 smc-4 sup-17 wrm-1 Abstract: One of the most important uses of whole-genome expression data is for the discovery of new genes with similar function to a given list of genes (the query) already known to have closely related function. We have developed an algorithm, called the gene recommender, that ranks genes according to how strongly they correlate with a set of query genes in those experiments for which the query genes are most strongly coregulated. We used the gene recommender to find other genes coexpressed with several sets of query genes, including genes known to function in the retinoblastoma complex. Genetic experiments confirmed that one gene (JC8.6) identified by the gene recommender acts with lin-35 Rb to regulate vulval cell fates, and that another gene (wrm-l) acts antagonistically. We find that the gene recommender returns lists of genes with better precision, for fixed levels of recall, than lists generated using the C elegans expression topomap ------------------- Key: 6023 Medline: 12875742 Authors: Holt SJ;Riddle DL Title: SAGE surveys C. elegans carbohydrate metabolism: evidnce for an anaerobic shift in the long-lived dauer larva. Citation: Mechanisms of Ageing & Development 124: 779-800 2003 Type: ARTICLE Genes: Abstract: The dauer larva, a non-feeding and developmentally arrested stage of the free-living nematode Caenorhabditis elegans, is morphologically and physiologically specialized for survival and dispersal during adverse growth conditions. The ability of dauer larvae to live several times longer than the continuous developmental life span has been attributed in part to a repressed metabolism. We used serial analysis of gene expression (SAGE) profiles from dauer larvae and mixed growing stages to compare expression patterns for genes with known or predicted roles in glycolysis, gluconeogenesis, glycogen metabolism, the Krebs and glyoxylate cycles, and selected fermentation pathways. Ratios of mixed:dauer transcripts indicated non-dauer enrichment that was consistent with previously determined adult:dauer enzyme activity ratios for hexokinase (glycolysis), phosphoenolpyruvate carboxykinase and fructose 1,6-bisphosphatase (gluconeogenesis), isocitrate dehydrogenase (NADP-dependent), and isocitrate lyase-malate synthase (glyoxylate cycle). Transcripts for the majority of Krebs cycle components were not differentially represented in the two profiles. Transcript abundance for pyruvate kinase, alcohol dehydrogenase, a putative cytosolic fumarate reductase, two pyruvate dehydrogenase components, and a succinyl CoA synthetase alpha subunit implied that anaerobic pathways were upregulated in dauer larvae. Generation of nutritive fermentation byproducts and the moderation of oxidative damage are potential benefits of a hypoxic dauer interior. ------------------- Key: 6024 Medline: 12869585 Authors: An JH;Blackwell TK Title: SKN-1 links C. elegans mesendodermal specification to a conserved oxidative stress response. Citation: Genes & Development 17: 1882-1893 2003 Type: ARTICLE Genes: ctl-1 gcs-1 skn-1 sod-1 sod-2 sod-3 Abstract: During the earliest stages of Caenorhabditis elegans embryogenesis, the transcription factor SKN-1 initiates development of the digestive system and other mesendodermal tissues. Postembryonic SKN-1 functions have not been elucidated. SKN-1 binds to DNA through a unique mechanism, but is distantly related to basic leucine-zipper proteins that orchestrate the major oxidative stress response in vertebrates and yeast. Here we show that despite its distinct mode of target gene recognition, SKN-1 functions similarly to resist oxidative stress in C. elegans. During postembryonic stages, SKN-1 regulates a key Phase II detoxification gene through constitutive and stress-inducible mechanisms in the ASI chemosensory neurons and intestine, respectively. SKN-1 is present in ASI nuclei under normal conditions, and accumulates in intestinal nuclei in response to oxidative stress. skn-1 mutants are sensitive to oxidative stress and have shortened lifespans. SKN-1 represents a connection between developmental specification of the digestive system and one of its most basic functions, resistance to oxidative and xenobiotic stress. This oxidative stress response thus appears to be both widely conserved and ancient, suggesting that the mesendodermal specification role of SKN-1 was predated by its function in these detoxification mechanisms. ------------------- Key: 6025 Medline: 12885562 Authors: Morck C;Axang C;Pilon M Title: A genetic analysis of axon guidance in the C. elegans pharynx. Citation: Developmental Biology 260: 158-175 2003 Type: ARTICLE Genes: daf-9 dpy-23 efn-2 efn-3 fax-1 mab-20 mnm-1 mnm-2 mnm-3 mnm-4 mnm-5 pha-2 pha-3 phm-2 phm-3 plx-1 plx-2 sax-3 slt-1 smp-1 smp-2 unc-5 unc-6 unc-40 unc-41 unc-46 unc-51 unc-60 unc-61 unc-62 unc-69 unc-73 unc-76 unc-101 unc-104 unc-115 unc-119 unc-129 Abstract: We wish to understand how the trajectories of the twenty pharyngeal neurons of C. elegans are established. In this study we focused on the two bilateral M2 pharyngeal motorneurons, which each have their cell body located in the posterior bulb and send one axon through the isthmus and into the metacorpus. We used a GFP reporter to visualize these neurons in cell-autonomous and cell-non-autonomous axon guidance mutant backgrounds, as well as other mutant classes. Our main findings are: 1) Mutants with impaired growth cone functions, such as unc-6, unc-51, unc-73 and sax-3, often exhibit abnormal terminations and inappropriate trajectories at the distal ends of the M2 axons, i.e. within the metacorpus; and 2) Growth cone function mutants never exhibit abnormalities in the proximal part of the M2 neuron trajectories, i.e. between the cell body and the metacorpus. Our results suggest that the proximal and distal trajectories are established using distinct mechanisms, including a growth cone-independent process to establish the proximal trajectory. We isolated five novel mutants in a screen for worms exhibiting abnormal morphology of the M2 neurons. These mutants define a new gene class designated mnm (M ------------------- Key: 6026 Medline: 12885567 Authors: Yang H;McNally K;McNally FJ Title: MEI-1/katanin is required for translocation of the meiosis I spindle to the ocyte cortex in C. elegans. Citation: Developmental Biology 260: 245-259 2003 Type: ARTICLE Genes: cls-2 fer-1 fzy-1 mei-1 pfn-1 sep-1 tbb-2 zyg-9 Abstract: In most animals, successful segregation of female meiotic chromosomes involves sequential associations of the meiosis I and meiosis II spindles with the cell cortex so that extra chromosomes can be deposited in polar bodies. The resulting reduction in chromosome number is essential to prevent the generation of polyploid embryos after fertilization. Using time-lapse imaging of living Caenorhabditis elegans oocytes containing fluorescently labeled chromosomes or microtubules, we have characterized the movements of meiotic spindles relative to the cell cortex. Spindle assembly initiated several microns from the cortex. After formation of a bipolar structure, the meiosis I spindle translocated to the cortex. When microtubules were partially depleted, translocation of the bivalent chromosomes to the cortex was blocked without affecting cell cycle timing. In oocytes depleted of the microtubule-severing enzyme, MEI-1, spindles moved to the cortex, but association with the cortex was unstable. Unlike translocation of wild-type spindles, movement of MEI-1-depleted spindles was dependent on FZY-1/CDC20, a regulator of the metaphase/anaphase transition. We observed a microtubule and FZY-1/CDC20-dependent circular cytoplasmic streaming in wild-type and mei-1 mutant embryos during meiosis. We propose that, in mei-1 mutant oocytes, this cytoplasmic streaming is sufficient to drive the spindle into the cortex. Cytoplasmic streaming is not the normal spindle translocation mechanism because translocation occurred in the absence of cytoplasmic streaming in embryos depleted of either the orbit/CLASP homolog, CLS-2, or FZY-1. These results indicate a direct role of microtubule severing in translocation of the ------------------- Key: 6027 Medline: 12885569 Authors: Fukuyama M;Gendreau SB;Derry WB;Rothman JH Title: Essential embryonic roles of the CKI-1 cyclin-dependent kinase inhibitor in cell-cycle exit and morphogenesis in C. elegans. Citation: Developmental Biology 260: 273-286 2003 Type: ARTICLE Genes: ced-3 ced-4 ced-9 cki-1 cki-2 rrf-3 mnDf100 mnDf103 mcDf1 wDf5 Abstract: Following a phase of rapid proliferation, cells in developing embryos must decide when to cease division and then whether to survive and differentiate or instead undergo programmed death. In screens for genes that regulate embryonic patterning of the endoderm in Caenorhabditis elegans, we identified overlapping chromosomal deletions that define a gene required for these decisions. These deletions result in embryonic hyperplasia in multiple somatic tissues, excessive numbers of cell corpses, and profound defects in morphogenesis and differentiation. However, cell-cycle arrest of the germline is unaffected. Cell lineage analysis of these mutants revealed that cells that normally stop dividing earlier than their close relatives instead undergo an extra round of division. These deletions define a genomic region that includes cki-1 and cki-2, adjacent genes encoding members of the Cip/Kip family of cyclin-dependent kinase inhibitors. cki-1 alone can rescue the cell proliferation, programmed cell death, and differentiation and morphogenesis defects observed in these mutants. In contrast, cki-2 is not capable of significantly rescuing these phenotypes. RNA interference of cki-1 leads to embryonic lethality with phenotypes similar to, or more severe than, the deletion mutants. cki-1 and -2 gene reporters show distinct expression patterns; while both are expressed at around the time that embryonic cells exit the cell cycle, cki-2 also shows marked expression starting early in embryogenesis, when rapid cell division occurs. Our findings demonstrate that cki-1 activity plays an essential role in embryonic cell cycle arrest, differentiation and morphogenesis, and suggest that it may be required to suppress programmed cell death or engulfment ------------------- Key: 6028 Medline: 12906791 Authors: Vastenhouw NL;Fischer SEJ;Robert VJP;Thijssen KL;Fraser AG;Kamath RS;Ahringer J;Plasterk RHA Title: A genome-wide screen identifies 27 genes involved in transposon silencing in C. elegans. Citation: Current Biology 13: 1311-1316 2003 Type: ARTICLE Genes: asb-1 asg-1 mut-7 mut-8 mut-14 mut-15 mut-16 npp-4 pab-1 ppw-2 rde-6 rpl-36 rpl-38 unc-22 Abstract: Transposon jumps are a major cause of genome instability. In the C. elegans strain Bristol N2, transposons are active in somatic cells, but they are silenced in the germline [1], presumably to protect the germline from mutations. Interestingly, the transposon-silencing mechanism shares factors with the RNAi machinery [2]. To better understand the mechanism of transposon silencing, we performed a genome-wide RNAi screen for genes that, when silenced, cause transposition of TO in the C. elegans germline. We identified 27 such genes, among which are mut-16, a mutator that was previously found but not identified at the molecular level, ppw-2, a member of the argonaute family, and several factors that indicate a role for chromatin structure in the regulation of transposition. Some of the newly identified genes are also required for cosuppression and therefore represent the shared components of the two pathways. Since most of the newly identified genes have clear homologs in other species, and since transposons are found from protozoa to human, it seems likely that they also protect other genomes against transposon activity in the germline. ------------------- Key: 6029 Medline: 12906792 Authors: Loria PM;Duke A;Rand JB;Hobert O Title: Two neuronal, nuclear-localized RNA binding proteins involved in synaptic transmission. Citation: Current Biology 13: 1317-1323 2003 Type: ARTICLE Genes: exc-7 unc-13 unc-17 unc-64 unc-75 Abstract: While there is evidence that distinct protein isoforms resulting from alternative pre-mRNA splicing play critical roles in neuronal development and function, little is known about molecules regulating alternative splicing in the nervous system. Using Caenorhabditis elegans as a model for studying neuron/target communication, we report that unc-75 mutant animals display neuroanatomical and behavioral defects indicative of a role in modulating GABAergic and cholinergic neuro-transmission but not neuronal development. We show that unc-75 encodes an FIRM domain-containing RNA binding protein that is exclusively expressed in the nervous system and neurosecretory gland cells. UNC-75 protein, as well as a subset of related C. elegans FIRM proteins, localizes to dynamic nuclear speckles; this localization pattern supports a role for the protein in pre-mRNA splicing. We found that human orthologs of UNC-75, whose splicing activity has recently been documented in vitro [1, 2], are expressed nearly exclusively in brain and when expressed in C. elegans, rescue unc-75 mutant phenotypes and localize to subnuclear puncta. Furthermore, we report that the subnuclear-localized EXC-7 protein, the C. elegans ortholog of the neuron-restricted Drosophila ELAV splicing factor, acts in parallel to UNC-75 to also affect cholinergic synaptic transmission. In conclusion, we identified a new neuronal, putative pre-mRNA splicing factor, UNC-75, and show that UNC-75, as well as the C. elegans homolog of ELAV, is required for the fine tuning of synaptic transmission. These findings thus provide a novel molecular link between pre-mRNA splicing and presynaptic function. ------------------- Key: 6030 Medline: Authors: Brenner S Title: Nature's gift to science (Nobel lecture). Citation: ChemBioChem 4: 683-687 2003 Type: REVIEW Genes: Abstract: The title of my lecture is "Nature's gift to Science". It is not a lecture about one scientific journal paying respect to another, but about how the great diversity of the living world can both inspire and serve innovation in biological research. Current ideas of the uses of model organisms spring from the exemplars of the past and choosing the right organism for one's research is as important as finding the right problems to work on. In all of my research these two decisions have been closely intertwined. Without doubt, the fourth winner of the Nobel prize this year is Caenorhabditis elegans; it deserves all of the honour but, of course, it will not be able to share ------------------- Key: 6031 Medline: 12898618 Authors: Sulston JE Title: Caenorhabditis elegans: the cell lineage and beyond (Nobel lecture). Citation: ChemBioChem 4: 688-696 2003 Type: REVIEW Genes: Abstract: Thank you so very much for inviting me to be here. It gives me a mingled sense of humility at how much I owe to others, and of joy that the collective work on the worm has been recognised in this way. ------------------- Key: 6032 Medline: 12898619 Authors: Horvitz HR Title: Worms, life, and death (Nobel lecture). Citation: ChemBioChem 4: 697-711 2003 Type: REVIEW Genes: Abstract: I never expected to spend most of my life studying worms. However, when the time came for me to choose an area for my postdoctoral research, I was intrigued both with the problems of neurobiology and with the approaches of genetics. Having heard that a new "genetic organism" with a remarkably simple nervous system was being explored by Sydney Brenner - the microscopic soil nematode Caenorhabditis elegans - I decided to join Sydney in his efforts. ------------------- Key: 6033 Medline: Authors: Eliceiri KW;Fan CH;Lyons GE;White JG Title: Analysis of histology specimens using lifetime multiphoton microscopy. Citation: Journal of Biomedical Optics 8: 376-380 2003 Type: ARTICLE Genes: Abstract: Observations of cells or tissues with fluorescence microscopy can provide unique insights into cellular physiology and structure. Such information may reveal the pathological state of a tissue to the physician or information on cytoskeletal dynamics to the research scientist. However, problems of overlapping spectra, low signal, and light scatter impose serious limitations on what can be achieved in practice with fluorescence microscopy. These problems can be addressed in part by the development of new imaging modalities that make maximum use of the information present in the fluorescence signal. We describe the application of a new technology to the study of standard histological pathology specimens: a multiphoton excitation fluorescence microscope that incorporates a novel, photon-counting detector that measures the excited-state lifetimes of fluorescent probes. In initial investigations, we have applied this system to the observation of C. elegans embryos and primate histology specimens, with the objective of identifying potentially diagnostic signatures, . Our findings demonstrate that lifetime multiphoton microscopy has considerable potential as a diagnostic tool for pathological investigations. ------------------- Key: 6034 Medline: 12883006 Authors: Sze JY;Ruvkun G Title: Activity of the Caenorhabditis elegans UNC-86 POU transcription factor modulates olfactory sensitivity. Citation: Proceedings of the National Academy of Sciences USA 100: 9560-9565 2003 Type: ARTICLE Genes: lin-11 mec-7 odr-1 odr-7 unc-86 Abstract: The activity of transcription factors modulates several neural pathways that mediate complex behaviors. We describe here the role of the POU transcription factor UNC-86 in the olfactory behavior of Caenorhabditis elegans. unc-86-null mutants are defective in response to odor attractants but avoid odor repellents normally. Continuous UNC-86 activity is necessary for maintenance of odortaxis behavior; hyperactivation of UNC-86 by fusion to a VP16 activation domain dramatically enhances sensitivity to odor attractants and promotes odor-attractant adaptation. UNC-86 is not expressed in olfactory sensory neurons but is expressed throughout the life of the animal in the AIZ interneurons of the odorsensory pathway. We suggest that UNC-86 transcriptional activity regulates the expression of genes that mediate synaptic properties of AIZ and that hyperactive UNC-86::VP16 may enhance the expression of synaptic components to affect the capacity to analyze and process sensory information. ------------------- Key: 6035 Medline: 12934107 Authors: Moghal N;Sternberg PW Title: Extracellular domain determinants of LET-23 (EGF) receptor tyrosine kinase activity in Caenorhabditis elegans. Citation: Oncogene 22: 5471-5480 2003 Type: ARTICLE Genes: let-23 let-341 lin-3 mpk-1 mnDf63 Abstract: Negative regulation of ErbB/EGFR signalling pathways is important for normal development and the prevention of cancer. In a genetic screen to uncover mechanisms that negatively regulate ErbB signalling in Caenorhabditis elegans, we isolated a second-site mutation (sy621) that promotes the activity of a gain-of-function allele (sa62gf) of the let-23 (EGF) receptor tyrosine kinase. We show that activation by the sa62 mutation (C359Y) likely results from a break in the conserved disulphide-bonded eighth module at the junction of CR1 and L2. The sy621 mutation causes a G270E change in the third disulphide-bonded module of CR1, and causes no phenotype on its own, but cooperates with the sa62 mutation to. promote receptor activity. Although both sa62 single- and double-mutant receptors can function in the absence of ligand, they can be further activated by ligand. Our results support the current model for ligand-induced dimerization based on the recent crystal structures of HER3 and the EGFR, and provide more evidence for the generation of distinctly activated ErbB family members through mutation. ------------------- Key: 6036 Medline: 12894170 Authors: Kurzchalia TV;Ward S Title: Why do worms need cholesterol? Citation: Nature Cell Biology 5: 684-688 2003 Type: REVIEW Genes: daf-2 daf-12 lrp-1 nhr-23 Abstract: Cholesterol is a structural component of animal membranes that influences fluidity, permeability and formation of lipid microdomains. It is also a precursor to signalling molecules, including mammalian steroid hormones and insect ecdysones. The nematode Caenorhabditis elegans requires too little cholesterol for it to have a major role in membrane structure. Instead, its most probable signalling functions are to control molting and induce a specialized non-feeding larval stage, although no cholesterol-derived signalling molecule has yet been identified for these or any other functions. ------------------- Key: 6037 Medline: 12944970 Authors: Bloss TA;Witze ES;Rothman JH Title: Suppression of CED-3-independent apoptosis by mitochondrial beta NAC in Caenorhabditis elegans. Citation: Nature 424: 1066-1071 2003 Type: ARTICLE Genes: ced-3 ced-4 ced-9 icd-1 Abstract: To ensure cell survival, it is essential that the ubiquitous proapoptotic machinery is kept quiescent. As death is irreversible, cells must continually integrate developmental information with regulatory inputs to control the switch between repressing and activating apoptosis. Inappropriate activation or suppression of apoptosis can lead to degenerative pathologies(1) or tumorigenesis(2), respectively. Here we report that Caenorhabditis elegans inhibitor of cell death-1 (ICD-1) is necessary and sufficient to prevent apoptosis. Loss of ICD-1 leads to inappropriate apoptosis in developing and differentiated cells in various tissues. Although this apoptosis requires CED-4, it occurs independently of CED-3-the caspase essential for developmental apoptosis(3) showing that these core pro-apoptotic proteins have separable roles. Overexpressing ICD-1 inhibits the apoptosis of cells that are normally programmed to die. ICD-1 is the beta-subunit of the nascent polypeptide-associated complex (bNAC) and contains a putative caspase-cleavage site and caspase recruitment domain. It localizes primarily to mitochondria, underscoring the role of mitochondria in coordinating apoptosis(4). Human bNAC is a caspase substrate that is rapidly eliminated in dying cells(5,6), suggesting that ICD-1 apoptosis-suppressing activity may be inactivated by caspases. ------------------- Key: 6038 Medline: 12860924 Authors: Estevez AY;Roberts RK;Strange K Title: Identification of store-independent and store-operated Ca2+ conductances in Caenorhabditis elegans intestinal epithelial cells. Citation: Journal of General Physiology 122: 207-223 2003 Type: ARTICLE Genes: elt-2 Abstract: The nematode Caenorhabditis elegans offers significant experimental advantages for defining the generic basis of diverse biological processes. Genetic and physiological analyses have demonstrated that inositol-1,4,5-trisphosphate (IP3)-dependent Ca2+ oscillations in intestinal epithelial cells play a central role in regulating the nematode defecation cycle, an ultradian rhythm with a periodicity of 45-50 s. Patch clamp studies combined with behavioral assays and forward and reverse genetic screening would provide a powerful approach for defining the molecular details of oscillatory Ca2+ signaling. However, electrophysiological characterization of the intestinal epithelium has not been possible because of its relative inaccessibility. We developed primary intestinal epithelial cell cultures that circumvent this problem. Intestinal cells express two highly Ca2+-selective, voltage-independent conductances. One conductance, I-ORCa, is constitutively active, exhibits strong outward rectification, is 60-70-fold more selective for Ca2+ than Na+, is inhibited by intracellular Mg2+ with a K-1/2 of 692 muM, and is insensitive to Ca2+ store depletion. Inhibition of I(ORC)a with high intracellular Mg2+ concentrations revealed the presence of a small amplitude conductance that was activated by passive depletion of intracellular Ca2+ stores. Active depletion of Ca2+ stores with IP3 or ionomycin increased the rate of current activation similar to8- and similar to22-fold compared with passive store depletion. The store-operated conductance, I-SOC, exhibits strong inward rectification, and the channel is highly selective for Ca2+ over monovalent cations with a divalent cation selectivity sequence of Ca2+ > Ba2+ approximate to Sr2+. Reversal potentials for I-SOC could not be detected accurately between 0 and +80 mV, suggesting that P-Ca/P-Na of the channel may exceed 1,000:1. Lanthanum, SKF 96365, and 2-APB inhibit both I-ORCa and I-SOC reversibly. Our studies provide the first detailed electrophysiological characterization of voltage-independent Ca2+ conductances in C. elegans and form the foundation for ongoing genetic and molecular studies aimed at identifying the genes that encode the intestinal cell channels, for defining ------------------- Key: 6039 Medline: 12794069 Authors: Sanz MA;Tsang WY;Willems EM;Grivell LA;Lemire BD;van der Spek H;Nijtmans LGJ Title: The mitochondrial prohibitin complex is essential for embryonic viability and germline function in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 278: 32091-32099 2003 Type: ARTICLE Genes: glo-1 phb-1 phb-2 Abstract: Prohibitins in eukaryotes consist of two subunits (PHB1 and PHB2) that together form a high molecular weight complex in the mitochondrial inner membrane. The evolutionary conservation and the ubiquitous expression in mammalian tissues of the prohibitin complex suggest an important function among eukaryotes. The PHB complex has been shown to play a role in the stabilization of newly synthesized subunits of mitochondrial respiratory enzymes in the yeast Saccharomyces cerevisiae. We have used Caenorhabditis elegans as model system to study the role of the PHB complex during development of a multicellular organism. We demonstrate that prohibitins in C. elegans form a high molecular weight complex in the mitochondrial inner membrane similar to that of yeast and humans. By using RNA-mediated gene inactivation, we show that PHB proteins are essential during embryonic development and are required for somatic and germline differentiation in the larval gonad. We further demonstrate that a deficiency in PHB proteins results in altered mitochondrial biogenesis in body wall muscle cells. This paper reports a strong loss of function phenotype for prohibitin gene inactivation in a multicellular organism and shows for the first time that prohibitins serve an essential role in mitochondrial function during organismal development. ------------------- Key: 6040 Medline: 12911746 Authors: Combes D;Fedon Y;Toutant JP;Arpagaus M Title: Multiple ace genes encoding acetylcholinesterases of Caenorhabditis elegans have distinct tissue expression. Citation: European Journal of Neuroscience 18: 497-512 2003 Type: ARTICLE Genes: ace-1 ace-2 ace-3 ace-4 Abstract: ace-1 and ace-2 genes encoding acetylcholinesterase in the nematode Caenorhabditis elegans present 35% identity in coding sequences but no homology in noncoding regions (introns, 5'- and 3'-untranslated regions). A 5'-region of ace-2 was defined by rescue of ace-1 ;ace-2 mutants. When green fluorescent protein (GFP) expression was driven by this regulatory region, the resulting pattern was distinct from that of ace-1 . This latter gene is expressed in all body-wall and vulval muscle cells (Culetto et al ., 1999), whereas ace-2 is expressed almost exclusively in neurons. ace-3 and ace-4 genes are located in close proximity on chromosome II (Combes et al ., 2000). These two genes were first transcribed in vivo as a bicistronic messenger and thus constitute an ace-3 ;ace-4 operon. However, there was a very low level of monocistronic mRNA of ace-4 (the upstream gene) in vivo , and no ACE-4 enzymatic activity was ever detected. GFP expression driven by a 5' upstream region of the ace-3 ;ace-4 operon was detected in several muscle cells of the pharynx (pm3, pm4, pm5 and pm7) and in the two canal associated neurons (CAN cells). A dorsal row of body-wall muscle cells was intensively labelled in larval stages but no longer detected in adults. The distinct tissue-specific expression of ace-1 , ace-2 and ace-3 (coexpressed only in pm5 cells) indicates that ace ------------------- Key: 6041 Medline: 12914694 Authors: Xu XZS;Sternberg PW Title: A C. elegans sperm TRP protein required for sperm-egg interactions during fertilization. Citation: Cell 114: 285-297 2003 Type: ARTICLE Genes: fer-1 fer-15 fem-1 trp-3 Abstract: Fertilization, a critical step in animal reproduction, is triggered by a series of specialized sperm-egg interactions. However, the molecular mechanisms underlying fertilization are not well understood. Here, we identify a sperm-enriched C. elegans TRPC homolog, TRP-3. Mutations in trp-3 lead to sterility in both hermaphrodites and males due to a defect in their sperm. trp-3 mutant sperm are motile, but fail to fertilize oocytes after gamete contact. TRP-3 is initially localized in intracellular vesicles, and then translocates to the plasma membrane during sperm activation. This translocation coincides with a marked increase in store-operated calcium entry, providing an in vivo mechanism for the regulation of TRP-3 activity. As C. elegans oocytes lack egg coats, our data suggest that some TRPC family channels might function to mediate calcium influx during sperm-egg plasma membrane interactions leading to fertilization. ------------------- Key: 6042 Medline: 14501184 Authors: Cypser JR;Johnson TE Title: Hormesis in Caenorhabditis elegans dauer-defective mutants. Citation: Biogerontology 4: 203-214 2003 Type: ARTICLE Genes: daf-3 daf-5 daf-12 daf-16 daf-18 Abstract: We have shown that increased longevity and stress resistance can be induced by sub-lethal exposure to stressors(hormesis). Here we ask whether genes of the dauer formation pathway that are known to modulate life span in Caenorhabditis elegans are required for this hormesis. We find that loss-of-function mutations in any of three genes (daf-16, daf-18, or daf-12) not only reduce or abolish the ability to form dauers but also block the hormetic response increasing life span following sub-lethal heat stress. Indeed, the life expectancy of these dauer-defective mutants is decreased by the same pretreatments that increase the life expectancy of wild-type animals. Additionally, we find that daf-16 and daf-12 are not required for the induction of thermotolerance, but daf-18 is required for its full induction. Our results underscore the importance of the dauer-formation pathway in specifying life span by demonstrating a similar, but not identical, role in life extension attributed to hormesis. ------------------- Key: 6043 Medline: 12878200 Authors: Huang RY;Boulton SJ;Vidal M;Almo SC;Bresnick AR;Chance MR Title: High-throughput expression, purification, and characterization of recombinant Caenorhabditis elegans proteins. Citation: Biochemical and Biophysical Research Communications 307: 928-934 2003 Type: ARTICLE Genes: Abstract: Modern proteomics approaches include techniques to examine the expression, localization, modifications, and complex formation of proteins in cells. In order to address issues of protein function in vitro using classical biochemical and biophysical approaches, high-throughput methods of cloning the appropriate reading frames, and expressing and purifying proteins efficiently are an important goal of modern proteomics approaches. This process becomes more difficult as functional protcomics efforts focus on the proteins from higher organisms, since issues of correctly identifying intron-exon boundaries and efficiently expressing and solubilizing the (often) multi-domain proteins from higher eukaryotes are challenging. Recently, 12,000 open-reading-frame (ORF) sequences from Caenorhabditis elegans have become available for functional proteomics studies [Nat. Gen. 34 (2003) 35]. We have implemented a high-throughput screening procedure to express, purify, and analyze by mass spectrometry hexa-histidine-tagged C elegans ORFs in Escherichia coli using metal affinity ZipTips. We find that over 65% of the expressed proteins are of the correct mass as analyzed by matrix-assisted laser desorption MS. Many of the remaining proteins indicated to be "incorrect" can be explained by high-throughput cloning or genome database annotation errors. This provides a general understanding of the expected error rates in such high-throughput cloning projects. The ZipTip purified proteins can be further analyzed under both native and denaturing conditions for ------------------- Key: 6044 Medline: 12810601 Authors: Park FD;Priess JR Title: Establishment of POP-1 asymmetry in C. elegans embryos. Citation: Development 130: 3547-3556 2003 Type: ARTICLE Genes: glp1- goa-1 gpa-16 mom-1 mom-2 mom-4 mom-5 pop-1 Abstract: In Caenhorabtidis elegans embryos, the nuclei of sister cells that are born from anterior/posterior divisions show an invariant high/low asymmetry, respectively, in their level of the transcription factor POP-1. Previous studies have shown that POP-1 asymmetry between the daughters of an embryonic cell called EMS results in part from a Wnt-like signal provided by a neighboring cell, called P(2). We identify here additional signaling cells that play a role in POP-1 asymmetry for other early embryonic cells. Some of these cells have signaling properties similar to P(2), whereas other cells use apparently distinct signaling pathways. Although cell signaling plays a critical role in POP-1 asymmetry during the first few cell divisions, later embryonic cells have an ability to generate POP-1 asymmetry that appears to be independent of prior Wnt signaling. ------------------- Key: 6045 Medline: 12819265 Authors: Yamada Y;Ohshima Y Title: Distribution and movement of Caenorhabditis elegans on a thermal gradient. Citation: Journal of Experimental Biology 206: 2581-2593 2003 Type: ARTICLE Genes: bas-1 eat-4 egl-4 gcy-8 gpa-3 lin-11 nhr-38 tax-2 tax-4 tax-6 ttx-3 Abstract: To analyze thermal responses of Caenorhabditis elegans in detail, distribution of a worm population and movement of individual worms were examined on a linear, reproducible and broad temperature gradient. Assay methods were improved compared with those reported previously to ensure good motility and dispersion of worms. Well-fed, wild-type worms distributed over a wide temperature range of up to 10degreesC, and, within this range, worms migrated in both directions of the gradient at similar frequencies without any specific response to the growth temperature in most cases. By contrast, worms migrated down the gradient if put in a region warmer than the warm boundary of distribution. The distribution range changed depending on the growth temperature and starvation, but active avoidance of a starvation temperature was not detected. These findings contradict previous hypotheses of taxis or migration to, the growth temperature in association with food and instead indicate avoidance of a warm temperature. Our results favor a model for thermal response of C. elegans that postulates a single drive based on warm sensation rather than downward and upward drives in the physiological temperature range. Mutants in ttx-3, tax-2, tax-4 or egl-4 genes showed abnormal thermal responses, suggesting that these genes are involved in warm avoidance. Laser ablation and gene expression studies suggest that AFD neurons are not important, and tax-4 expression in neurons other than AFD is required, for warm avoidance. ------------------- Key: 6046 Medline: 12970568 Authors: Feinberg EH;Hunter CP Title: Transport of dsRNA into cells by the transmembrane protein SID-1. Citation: Science 301: 1545-1547 2003 Type: ARTICLE Genes: sid-1 Abstract: RNA interference (RNAi) spreads systemically in plants and nematodes to silence gene expression distant from the site of initiation. We previously identified a gene, sid-1, essential for systemic but not cell-autonomous RNAi in Caenorhabditis elegans. Here, we demonstrate that SID-1 is a multispan transmembrane protein that sensitizes Drosophila cells to soaking RNAi with a potency that is dependent on double-stranded RNA ( dsRNA) length. Further analyses revealed that SID-1 enables passive cellular uptake of dsRNA. These data indicate that systemic RNAi in C. elegans involves SID-1-mediated intercellular transport ------------------- Key: 6047 Medline: 12923778 Authors: Madi A;Mikkat S;Ringel B;Ulbrich M;Thiesen JH;Glocker MO Title: Mass spectrometric proteome analysis for profiling temperature-dependent changes of protein expression in wild-type Caenorhabditis elegans. Citation: Proteomics 3: 1526-1534 2003 Type: ARTICLE Genes: asp-1 gpd-2 gpd-3 gst-5 gst-7 hsp-1 hsp-16.1 iff-1 isp-1 lap-1 lbp-2 lbp-4 mlc-1 mlc-2 pas-7 pyc-1 tpi-1 unc-60 vha-8 vit-6 Abstract: We investigated the effect of cultivation temperatures on the protein expression levels in the fourth larval stage of the postembryonic development of wild-type Caenorhabditis elegans by mass spectrometric proteome analysis. From the 64 protein spots that were investigated, 5 spots were found reproducibly differently expressed when proteome maps derived from animals kept at 15degreesC and at 25degreesC, respectively, were compared. Spots of heat shock proteins HSP 70 (CE18679 or CE09682) and HSP 16 (CE1 4249) were present only in gels from protein extracts when worms were grown at 15degreesC. Spots of two metabolic enzymes, the isocitrate dehydrogenase (CE1 0345) and the aspartic proteinase (CE21681) were detected only in cultures grown at the lower temperature as well. A protein with still unknown function (CE05036) was present only in gels from worm samples grown at 25degreesC. We show for the first time by proteome analyses that cultivation of worms at the lowest temperature of the known physiological range (15degreesC) already triggers a (weak) stress response in wild-type animals. This work led to the identification of "internal control proteins" in the wild-type strain for further characterization of temperature-sensitive strains using a proteomics approach. ------------------- Key: 6048 Medline: 12739132 Authors: Gabriel EM;Campbell WC Title: Effect of ambient salinity on immobilization of Caenorhabditis elegans by nematocidal agents. Citation: Parasitology Research 90: 390-392 2003 Type: ARTICLE Genes: Abstract: The ability of three antinematodal agents to induce paralysis of Caenorhabditis elegans was examined in an aqueous medium with and without the addition of salts. The basic medium was deionized water supplemented, for control purposes, with the phosphate mixture used as a buffering agent in M9 solution. This medium was further supplemented with magnesium sulfate or sodium chloride, or both salts, at the concentrations used in M9. We report that the paralyzing property of ivermectin was enhanced by the presence of salt, while the efficacy of levamisole and chlorpromazine was reduced. ------------------- Key: 6049 Medline: 12954868 Authors: Bany IA;Dong MQ;Koelle MR Title: Genetic and cellular basis for acetylcholine inhibition of Caenorhabditis elegans egg-laying behavior. Citation: Journal of Neuroscience 23: 8060-8069 2003 Type: ARTICLE Genes: ace-1 ace-2 cha-1 egl-1 gar-2 unc-2 unc-4 unc-5 unc-8 unc-10 unc-17 unc-20 unc-29 unc-32 unc-34 unc-35 unc-37 unc-38 unc-42 unc-73 unc-75 unc-78 unc-115 Abstract: Egg-laying behavior in Caenorhabditis elegans is activated by signaling through the G-protein Galpha(q) and inhibited by signaling through a second G-protein, Galpha(o). Activation of egg laying depends on the serotonergic hermaphrodite-specific neurons (HSNs), but the neurotransmitter(s) and cell(s) that signal to inhibit egg laying are not known. Mutants for G-protein signaling genes have well characterized defects in egg laying. Here we present an analysis of mutants for other genes reported to lack inhibition of egg laying. Of the nine strongest, six have morphological defects in the ventral-type C (VC) neurons, which synapse onto both the HSNs and the egg-laying muscles and are thus the third cell type comprising the egg-laying system. Laser-ablating VC neurons could also disrupt the inhibition of egg laying. The remaining three mutants (unc-4, cha-1, and unc-17) are defective for synthesis or packaging of acetylcholine in the VCs. The egg-laying defects of unc-4, cha-1, and unc-17 were rescued by VC-specific expression of the corresponding cDNAs. In addition, increasing synaptic acetylcholine by reducing acetylcholinesterase activity, with either mutations or the inhibitor aldicarb, decreased egg laying. Finally, we found that a knock-out for the HSN-expressed receptor G-protein- coupled acetylcholine receptor 2 (GAR-2) shows a partial defect in the inhibition of egg laying and fails to respond to aldicarb. Our results show that acetylcholine released from the VC neurons inhibits egg-laying behavior. This inhibition may be caused, in part, by acetylcholine signaling onto the HSN presynaptic terminals, via GAR-2, to inhibit neurotransmitter release. ------------------- Key: 6050 Medline: 12821653 Authors: Kubiak TM;Larsen MJ;Nulf SC;Zantello MR;Burton KJ:Boman JW;Modric T;Lowery DE Title: Differential activation of "social" and "solitary" variants of the Caenorhabditis elegans G protein-coupled receptor NPR-1 by its cognate ligand AF9. Citation: Journal of Biological Chemistry 278: 33724-33729 2003 Type: ARTICLE Genes: npr-1 Abstract: Natural variations of wild Caenorhabditis elegans isolates having either Phe-215 or Val-215 in NPR-1, a putative orphan neuropeptide Y-like G protein-coupled receptor, result in either "social" or "solitary" feeding behaviors ( de Bono, M., and Bargmann, C. I. ( 1998) Cell 94, 679 - 689). We identified a nematode peptide, GLGPR-PLRF-NH2 (AF9), as a ligand activating the cloned NPR-1 receptor heterologously expressed in mammalian cells. Shifting cell culture temperatures from 37 to 28 degreesC, implemented 24 h after transfections, was essential for detectable functional expression of NPR-1. AF9 treatments linked both cloned receptor variants to activation of Gi/Go proteins and cAMP inhibition, thus allowing for classification of NPR-1 as an inhibitory G protein-coupled receptor. The Val-215 receptor isoform displayed higher binding and functional activity than its Phe-215 counterpart. This finding parallels the in vivo observation of a more potent repression of social feeding by the npr-1 gene encoding the Val-215 form of the receptor, resulting in dispersing ( solitary) animals. Since neuropeptide Y shows no sequence homology to AF9 and was functionally inactive at the cloned NPR-1, we propose to rename NPR-1 and refer to it as an AF9 ------------------- Key: 6051 Medline: 12788949 Authors: Xue Y;Fares H;Grant B;Li Z;Rose AM;Clark SG;Skolnik EY Title: Genetic analysis of the myotubularin family of phosphatases in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 278: 34380-34386 2003 Type: ARTICLE Genes: age-1 cup-10 let-512 mtm-1 mtm-3 mtm-5 mtm-6 Abstract: Myotubularins (MTMs) constitute a large family of lipid phosphatases that specifically dephosphorylate phosphatidylinositol (3) P. MTM1 and MTM2 are mutated in X-linked myotubular myopathy and Charcot-Marie-Tooth disease ( type 4B), respectively, although the mechanisms whereby MTM dysfunction leads to these diseases is unknown. To gain insight into MTM function, we undertook the study of MTMs in the nematode Caenorhabditis elegans, which possesses representative homologues of the four major subgroups of MTMs identified in mammals. As in mammals, we found that C. elegans MTMs mediate distinct functions. let-512 (vps34) encodes the C. elegans homologue of the yeast and mammalian homologue of the phosphatidylinositol 3-kinase Vps34. We found that reduction of mtm-6 (F53A2.8) function by RNA inhibition rescued the larval lethality of let-512 ( vps34) mutants and that the reduction of mtm-1 (Y110A7A. 5) activity by RNA inhibition rescued the endocytosis defect of let-512 animals. Together, these observations provide genetic evidence that MTMs negatively regulate phosphatidylinositol ( 3) P levels. Analysis of MTM expression patterns using transcriptional green fluorescence protein reporters demonstrated that these two MTMs exhibit mostly nonoverlapping expression patterns and that MTM-green fluorescence protein fusion proteins are localized to different subcellular locations. These observations suggest that some of the different functions of MTMs might, in part, be a consequence of unique expression and localization patterns. However, our finding that at least three C. elegans MTMs play essential roles in coelomocyte endocytosis, a process that also requires VPS34, indicates that MTMs do not simply turn off VPS34 but unexpectedly also function as positive regulators of ------------------- Key: 6052 Medline: 12952888 Authors: Chang S;Johnston RJ;Hobert O Title: A transcriptional regulatory cascade that controls left/right asymmetry in chemosensory neurons of C. elegans. Citation: Genes & Development 17: 2123-2137 2003 Type: ARTICLE Genes: ceh-36 che-1 cog-1 daf-44 egl-2 flp-6 gcy-5 gcy-7 lim-6 lin-49 nsy-1 nsy-2 nsy-3 odr-1 odr-3 sax-3 str-2 tax-2 tax-4 unc-2 unc-33 unc-36 unc-37 unc-43 unc-44 unc-76 vab-3 Abstract: The molecular mechanisms of differential pattern formation along the left/right (L/R) axis in the nervous system are poorly understood. The nervous system of the nematode Caenorhabditis elegans displays several examples of L/R asymmetry, including the directional asymmetry displayed by the two ASE taste receptor neurons, ASE left (ASEL) and ASE right (ASER). Although bilaterally symmetric in regard to all known morphological criteria, these two neurons display distinct chemosensory capacities that correlate with the L/R asymmetric expression of three putative sensory receptor genes, gcy-5, expressed only in ASER, and gcy-6 and gcy-7, expressed only in ASEL. In order to understand the genetic basis of L/R asymmetry establishment, we screened for mutants in which patterns of asymmetric gcy gene expression are disrupted, and we identified a cascade of several symmetrically and asymmetrically expressed transcription factors that are sequentially required to restrict gcy gene expression to either the left or right ASE cell. These factors include the zinc finger transcription factor che-1; the homeobox genes cog-1, ceh-36, and lim-6; and the transcriptional cofactors unc-37/Groucho and lin-49. Specific features of this regulatory hierarchy are sequentially acting repressive interactions and the finely balanced activity of antagonizing positive and negative regulatory factors. A key trigger for asymmetry is the L/R differential expression of the Nkx6-type COG-1 homeodomain protein. Our studies have thus identified transcriptional mediators of a putative L/R-asymmetric signaling event and suggest that vertebrate homologs of these proteins may have similar functions in regulating vertebrate brain asymmetries. ------------------- Key: 6053 Medline: Authors: Guiliano DB;Hall N;Jones SJM;Clark LN;Corton CH;Barrell BG;Blaxter ML Title: Conservation of long-range synteny and microsynteny between the genomes of tow distantly related nematodes. Citation: Genome Biology 3: 57.1-57.14 2002 Type: ARTICLE Genes: Abstract: Background: Comparisons between the genomes of the closely related nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal high rates of rearrangement, with a bias towards within-chromosome events. To assess whether this pattern is true of nematodes in general, we have used genome sequence to compare two nematode species that last shared a common ancestor approximately 300 million years ago: the model C. elegans and the filarial parasite Brugia malayi. Results: An 83 kb region flanking the gene from Bm-mif-1 (macrophage migration inhibition factor, a B. malayi homolog of a human cytokine) was sequenced. When compared to the complete genome of C. elegans, evidence for conservation of long-range synteny and microsynteny was found. Potential C. elegans orthologs for 11 of the 12 protein-coding genes predicted in the B. malayi sequence were identified. Ten of these orthologs were located on chromosome I, with eight clustered in a 2.3 Mb region. While several, relatively local, intrachromosomal rearrangements have occurred, the order, composition, and configuration of two gene clusters, each containing three genes, was conserved. Comparison of B. malayi BAC-end genome survey sequence to C. elegans also revealed a bias towards intrachromosome rearrangements. Conclusions: We suggest that intrachromosomal rearrangement is a major force driving chromosomal organization in nematodes, but is constrained by the interdigitation of functional elements ------------------- Key: 6054 Medline: 13679921 Authors: Pintard L;Willis JH;Willems A;Johnson JLF;Srayko M;Kurz T;Glaser S;Mains PE;Tyers M;Bowerman B;Peter M Title: The BTB protein MEL-26 is a substrate-specific adaptor of the CUL-3 ubiquitin-ligase. Citation: Nature 425: 311-316 2003 Type: ARTICLE Genes: cul-1 cul-2 cul-3 cul-4 cul-5 mei-1 mel-26 rfl-1 Abstract: Many biological processes, such as development and cell cycle progression are tightly controlled by selective ubiquitin-dependent degradation of key substrates. In this pathway, the E3-ligase recognizes the substrate and targets it for degradation by the 26S proteasome. The SCF (Skp1-Cul1-F-box) and ECS (Elongin C-Cul2-SOCS box) complexes are two well-defined cullin-based E3-ligases(1-3). The cullin subunits serve a scaffolding function and interact through their C terminus with the RING-finger-containing protein Hrt1/Roc1/Rbx1, and through their N terminus with Skp1 or Elongin C, respectively. In Caenorhabditis elegans, the ubiquitin-ligase activity of the CUL-3 complex is required for degradation of the microtubule-severing protein MEI-1/katanin at the meiosis-to-mitosis transition(4). However, the molecular composition of this cullin-based E3-ligase is not known. Here we identified the BTB-containing protein MEL-26 as a component required for degradation of MEI-1 in vivo. Importantly, MEL-26 specifically interacts with CUL-3 and MEI-1 in vivo and in vitro, and displays properties of a substrate-specific adaptor. Our results suggest that BTB-containing proteins may generally function as substrate-specific adaptors in Cul3-based E3-ubiquitin ligases. ------------------- Key: 6055 Medline: 13679922 Authors: Xu L;Wei Y;Reboul J;Vaglio P;Shin TH;Vidal M;Elledge SJ;Harper JW Title: BTB proteins are substrate-specific adaptors in an SCF-like modular ubiquitin ligase containing CUL-3. Citation: Nature 425: 316-321 2003 Type: ARTICLE Genes: cul-3 cul-4 mei-1 mel-26 Abstract: Programmed destruction of regulatory proteins through the ubiquitin-proteasome system is a widely used mechanism for controlling signalling pathways(1,2). Cullins(3) are proteins that function as scaffolds for modular ubiquitin ligases typified by the SCF (Skp1-Cul1-F-box) complex(4-6). The substrate selectivity of these E3 ligases is dictated by a specificity module that binds cullins. In the SCF complex, this module is composed of Skp1, which binds directly to Cul1, and a member of the F-box family of proteins(4-7). F-box proteins bind Skp1 through the F-box motif(7), and substrates by means of carboxy-terminal protein interaction domains(1,2,5). Similarly, Cul2 and Cul5 interact with BC-box-containing specificity factors through the Skp1-like protein elongin C-2. Cul3 is required for embryonic development in mammals and Caenorhabditis elegans(8-10) but its specificity module is unknown. Here we report the identification of a large family of BTB-domain proteins as substrate-specific adaptors for C. elegans CUL-3. Biochemical studies using the BTB protein MEL-26 and its genetic target MEI-1 (refs 12, 13) indicate that BTB proteins merge the functional properties of Skp1 and F-box proteins into a single polypeptide. ------------------- Key: 6056 Medline: 12957648 Authors: Gill MS;Olsen A;Sampayo JN;Lithgow GJ Title: An automated high-throughput assay for survival of the nematode Caenorhabditis elegans. Citation: Free Radical Biology & Medicine 35: 558-565 2003 Type: ARTICLE Genes: age-1 fer-15 spe-9 Abstract: Many genetic or environmental manipulations that extend life span in the nematode Caenorhabditis elegans (C elegans) also enhance survival following acute stresses such as oxidative damage and thermal stress. This coupling of stress response and aging mechanisms has proved a useful tool in identifying new genes that affect the aging process without the need for performing lengthy life span analyses. Therefore, it is likely that this approach may also be applied to the identification of pharmacological agents that extend life span through enhanced resistance to oxygen radicals or other stressors. To facilitate high-throughput drug screens in the nematode, we have developed a microtitre plate survival assay that uses uptake of the fluorescent dye SYTOX green as a marker of nematode death. An increase in throughput compared with the conventional survival assay was achieved by combining automated worm-handling technology with automated real-time fluorescence detection. We have validated this assay by examining survival during acute heat stress and protection against oxidative stress with the superoxide dismutase/catalase mimetic Euk-134. We propose that this novel method of survival analysis will accelerate the discovery of new pharmacological interventions in aging and ------------------- Key: 6057 Medline: 12950278 Authors: Inoue T;Takamura K;Yamae H;Ise N;Kawakami M;Tabuse Y;Miwa J;Yamaguchi Y Title: Caenorhabditis elegans DAF-21 (HSP90) is characteristically and predominantly expressed in germline cells: spatial and temporal analysis. Citation: Development Growth & Differentiation 45: 369-376 2003 Type: ARTICLE Genes: daf-21 Abstract: Three monoclonal antibodies against antigens that exist in the Caenorhabditis elegans germ line have previously been described. In the present study, a full-length mRNA for one of these antigens was isolated, and by sequencing its corresponding cDNA, it was predicted that the protein would show a high homology with the 90 kDa heat shock protein (HSP90) in other species, and with the protein of daf-21, a previously identified hsp90 homologue. The spatial and temporal distribution of the antigen (DAF-21) was analyzed in C. elegans, and the localization of daf-21 mRNA, as detected by in situ hybridization, agreed with that detected by the monoclonal antibody. Under normal conditions, daf-21 mRNA is characteristically distributed in postembryonic germ cells derived from Z2 and Z3 cells in both hermaphrodites and males. Under heat stress conditions, however, daf-21 mRNA was not only detected in germ cells, but also apparently expressed all over the body. In addition, the DAF-21 protein seemed to be localized in the perinuclear region of somatic cells. ------------------- Key: 6058 Medline: 12950280 Authors: Viney ME;Gardner MP;Jackson JA Title: Variation in Caenorhabditis elegans dauer formation. Citation: Development Growth & Differentiation 45: 389-396 2003 Type: ARTICLE Genes: Abstract: Dauer larvae of Caenorhabditis elegans are formed when young larvae experience conditions of low food availability and high conspecific population density; non-dauer, third stage larvae are formed in conditions of plenty. This developmental response to environmental conditions is an example of phenotypic plasticity; that is, an environmentally induced change in phenotype and, as such, a manifestation of a genotype-environment interaction. Extensive variation was found in reaction norms of phenotypic plasticity of dauer formation among wild lines of C. elegans. Recombinant-inbred lines were constructed from parental lines with very different reaction norms of dauer formation. These recombinant-inbred lines had a wide range of reaction norms, of a range greater than that set by the parental lines. The natural variation in reaction norms of dauer formation in C. elegans is, presumably, an adaptation to enhance fitness under the lines' different natural prevailing conditions. The genetic basis of this variation, as well as its phenotypic consequences, are now ripe for further investigation. ------------------- Key: 6059 Medline: 12956950 Authors: Bellanger JM;Gonczy P Title: TAC-1 and ZYG-9 form a complex that promotes microtubule assembly in C. elegans embryos. Citation: Current Biology 13: 1488-1498 2003 Type: ARTICLE Genes: air-1 dhc-1 spd-5 tac-1 tba-2 tbg-1 zyg-9 Abstract: Background: Modulation of microtubule dynamics is crucial for proper cell division. While a large body of work has made important contributions to our understanding of the mechanisms governing microtubule dynamics in vitro, much remains to be learned about how these mechanisms operate in vivo. Results: We identified TAC-1 as the sole TACC (Transforming Acidic Coiled Coil) protein in C. elegans. TAC-1 consists essentially of a TACC domain, in contrast to the much larger members of this protein family in other species. We find that tac-1 is essential for pronuclear migration and spindle elongation in one-cell-stage C. elegans embryos. Using an in vivo FRAP-based assay, we establish that inactivation of tac-1 results in defective microtubule assembly. TAC-1 is present in the cytoplasm and is enriched at centrosomes in a cell cycle-dependent manner. Centrosomal localization is independent of microtubules but requires the activity of gamma-tubulin and the Aurora-A kinase AIR-1. By conducting FRAP analysis in embryos expressing GFP-TAC-1, we find that centrosomal TAC-1 exchanges rapidly with the cytoplasmic pool. Importantly, we establist that TAC-1 physically interacts with ZYG-9, a microtubule-associated protein (MAP) of the XMAP215 family, both in vitro and in vivo. Furthermore, we also uncover that TAC-1 and ZYG-9 stabilize each other in C. elegans embryos. Conclusions: Our findings identify TAC-1 as a core structural and functional member of the evolutionarily conserved TACC family of proteins and suggest that mutual stabilization between TACC and XMAP215 proteins is a key feature ensuring microtubule assembly in ------------------- Key: 6060 Medline: 12956951 Authors: Le Bot N;Tsai MC;Andrews RK;Ahringer J Title: TAC-1, a regulator of microtubule length in the C. elegans embryo. Citation: Current Biology 13: 1499-1505 2003 Type: ARTICLE Genes: air-1 cap-2 dhc-1 tac-1 tbg-1 zyg-9 Abstract: Regulation of microtubule growth is critical for many cellular processes, including meiosis, mitosis, and nuclear migration. We carried out a genome-wide RNA! screen in Caenorhabditis elegans to identify genes required for pronuclear migration, one of the first events in embryogenesis requiring microtubules. Among these, we identified and characterized tac-1 a new member of the TACC (Transforming Acidic Coiled-Coil) family [1]. tac-1(RNAi) embryos exhibit very short microtubules nucleated from the centrosomes as well as short spindles. TAC-1 is initially enriched at the meiotic spindle poles and is later recruited to the sperm centrosome. TAC-1 localization at the centrosomes is regulated during the cell cycle with high levels during mitosis and a reduction during interphase, and is dependent on aurora kinase 1 (AIR-1), a protein involved in centrosome maturation [2]. tac-1(RNAi) embryos resemble mutants of zyg-9 [3], which encodes a previously characterized centrosomal protein of the XMAP215 family and was also found in our screen. We show that TAC-1 and ZYG-9 are dependent on one another for their localization at the centrosome, and this dependence suggests that they may function together as a complex. We conclude that TAC-1 is a major regulator of microtubule length in the C. elegans embryo. ------------------- Key: 6061 Medline: 12956952 Authors: Srayko M;Quintin S;Schwager A;Hyman AA Title: Caenorhabditis elegans TAC-1 and ZYG-9 form a complex that is essential for long astral and spindle microtubules. Citation: Current Biology 13: 1506-1511 2003 Type: ARTICLE Genes: mei-1 tac-1 zyg-9 Abstract: TACC (transforming acidic coiled-coil) proteins were first identified by their ability to transform cell lines [1], and links between human cancer and the overexpression of TACC proteins highlight the importance of understanding the biological function of this family of proteins [2]. Herein, we describe the characterization of a new member of the TACC family of proteins in Caenorhabditis elegans, TAC-1. In other systems, TACC proteins associate with the XMAP215 family of microtubule-stabilizing proteins; however, it is unclear whether TACC proteins have microtubule-based functions distinct from XMAP215. We depleted both the XMAP215 ortholog ZYG-9 and TAC-1 via dsRNA-mediated interference (RNAi). We found that tac-1(RNAi) resulted in microtubule-based defects that were very similar to zyg-9(RNAi). Furthermore, TAC-1 and ZYG-9 are required for long astral microtubules in general and long spindle microtubules during spindle assembly. Loss of either protein did not affect the alpha-tubulin immunofluorescence intensity near centrosomes; this finding suggests that microtubule nucleation was not compromised. Both proteins localize to centrosomes and the kinetochore/microtubule region of chromosomes in metaphase and early anaphase. Furthermore, we found that ZYG-9 and TAC-1 physically interact in vivo, and this interaction is important for the efficient localization of the ZYG-9/TAC-1 complex to centrosomes. ------------------- Key: 6062 Medline: 12927813 Authors: Park YS;Kim S;Shin Y;Choi B;Cho NJ Title: Alternative splicing of the muscarinic acetylcholine receptor GAR-3 in Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 308: 961-965 2003 Type: ARTICLE Genes: gar-3 Abstract: Among the three G-protein-linked acetylcholine (ACh) receptors (GAR-1, -2, and -3) in Caenorhahditis elegans (C elegans), GAR-3 appears most similar to mammalian muscarinic ACh receptors (mAChRs). The gar-3 gene, unlike mammalian mAChR genes, contains introns within the coding region. in this study, we identified an alternatively spliced isoform of GAR-3 (GAR-3a), which differs only in the third intracellular (0) loop from the previously described one (GAR-3b). GAR-3a has a 26 amino acid insert in the D loop compared with GAR-3b. Reverse transcriptase-polymerase chain reaction (RT-PCR) on stage-specific RNAs indicated that both isoforms are expressed at all developmental stages examined, with gar-3b being more abundantly expressed than gar-3a. When these two GAR-3 isoforms were expressed in Chinese hamster ovary (CHO) cells, they exhibited similar ligand binding characteristics. In response to carbachol treatment, the two isoforms stimulated phosphatidylinositol hydrolysis with similar efficacy. Together with our earlier observations that GAR-1 and GAR-2 undergo alternative splicing, this study shows that alternative splicing plays an important role in promoting molecular diversity of ------------------- Key: 6063 Medline: 12943683 Authors: Ko FCF;Chow KL Title: A mutation at the start codon defines the differential requirement of dpy-11 in Caenorhabditis elegans body hypodermis and male tail. Citation: Biochemical and Biophysical Research Communications 309: 201-208 2003 Type: ARTICLE Genes: dpy-11 Abstract: dpy-11 encodes a thioredoxin-like molecule that is important for both body and male sensory ray morphogenesis in Caenorhabditis elegans. A mutant allele, s287, has a point mutation with its start codon, AUG, converted into AUA, presumably leading to null function. Since only a weak loss-of-function phenotype was observed, we tested whether an alternative start codon or the converted AUA could be used for translation initiation with reduced efficiency. Based on a functional assay of mutant phenotype complementation and biochemical analysis examining the in vivo synthesis of wild-type and mutant proteins, we conclude that AUA can be used as a less-efficient start codon for initiating translation of DPY-11. Our results also provide direct evidence that the body hypodermis and male tail of C elegans have differential requirements of dpy-11 activity for their respective normal morphogenesis. ------------------- Key: 6064 Medline: 14570376 Authors: Sulston JE Title: C. elegans: the cell lineage and beyond Citation: Bioscience Reports 23: 49-66 2003 Type: REVIEW Genes: Abstract: Thank you so very much for inviting me to be here. It gives me a mingled sense of humility at how much I owe to others, and of joy that the collective work on the worm has been recognized in this way. ------------------- Key: 6065 Medline: 14503703 Authors: Anderson GL;Caldwell KN;Beuchat LR;Williams PL Title: Interaction of a free-living soil nematode, Caenorhabditis elegans, with surrogates of foodborne pathogenic bacteria. Citation: Journal of Food Protection 66: 1543-1549 2003 Type: ARTICLE Genes: Abstract: Free-living nematodes may harbor, protect, and disperse bacteria, including those ingested and passed in viable form in feces. These nematodes are potential vectors for human pathogens and may play a role in foodborne diseases associated with fruits and vegetables eaten raw. In this study, we evaluated the associations between a free-living soil nematode, Caenorhabditis elegans, and Escherichia coli, an avirulent strain of Salmonella Typhimurium, Listeria weshimeri, and Bacillus cereus. On agar medium, young adult worms quickly moved toward colonies of all four bacteria; over 90% of 3-day-old adult worms entered colonies within 16 min after inoculation. After 48 h, worms moved in and out of colonies of L. weshimeri and B. cereus but remained associated with E. coli and Salmonella Typhimurium colonies for at least 96 h. Young adult worms fed on cells of the four bacteria suspended in K medium. Worms survived and reproduced with the use of nutrients derived from all test bacteria, as determined for eggs laid by second-generation worms after culturing for 96 h. Development was slightly slower for worms fed gram-positive bacteria than for worms fed gram-negative bacteria. Worms that fed for 24 h on bacterial lawns formed on tryptic soy agar dispersed bacteria over a 3-h period when they were transferred to a bacteria-free agar surface. The results of the study suggest that C. elegans and perhaps other free-living nematodes are potential vectors for both gram-positive and gram-negative bacteria, including foodborne pathogens in soil. ------------------- Key: 6066 Medline: Authors: Santander J;Espinoza JC;Campano MS;Robeson J Title: Infection of Caenorhabditis elegans by Salmonella typhi Citation: Electronic Journal of Biotechnology 6: 148-152 2003 Type: ARTICLE Genes: Abstract: Several serovars of Salmonella infect and kill the nematode C. elegans. However, here we report that Salmonella typhi Ty2, a representative strain of this human pathogen, readily infects the intestinal lining of C. elegans without significantly affecting its viability. Our observation suggests that extending the use of the C. elegans model system for the study of host parasite relationships, to address the problems concerning the biology of S. typhi. ------------------- Key: 6067 Medline: Authors: Nah W;Hong SB;Baek JH Title: Feature extraction for classification of Caenorhabditis elegans behavioral phenotypes. Citation: Lect N A I 2718: 287-295 2003 Type: ARTICLE Genes: Abstract: ------------------- Key: 6068 Medline: 12919672 Authors: Rea S;Johnson TE Title: A metabolic model for life span determination in Caenorhabditis elegans. Citation: Developmental Cell 5: 197-203 2003 Type: REVIEW Genes: age-1 clk-1 daf-2 daf-12 daf-16 daf-18 isp-1 Abstract: Several studies with the nematode Caenorhabditis elegans have made the unexpected discovery that certain hypomorphic mutations in the genes encoding mitochondrial proteins result in life span extension. These mutations appear to act independently of the other known pathway that regulated life span extension, the dauer-specifying insulin/IGF-1-like pathway. Here we present a hypothesis that unifies the effects of theses two classes of genes on longevity. The central concept is that energy generation in C. elegans occurs by differential flux through two coexisting mitochondrial metabolic pathways - aerobic respiration and fermentative malate dismutation. In the latter process, fumarate is terminally reduced at complex II to succinate. We suggest that most, if not all, long-lived mutants in C. elegans utilized malate dismutation, a byproduct of which is the generation of ------------------- Key: 6069 Medline: 12904685 Authors: Brockie PJ;Maricq AV Title: Ionotropic glutamate receptors in Caenorhabditis elegans. Citation: Neurosignals 12: 108-125 2003 Type: REVIEW Genes: egl-3 glr-1 glr-2 glr-3 glr-4 glr-5 glr-6 glr-7 lin-10 nmr-1 nmr-2 unc-11 unc-43 Abstract: Ionotropic glutamate receptors (iGluRs) are an important class of heteromeric ligand-gated receptor complexes that mediate a large portion of the excitatory neurotransmission in the vertebrate CNS. Since the cloning of the first iGluR subunit in 1989, the study of this receptor family has rapidly developed in mammals and expanded to include the study of conserved glutamate receptors in simpler invertebrate systems, including the fruit fly Drosophila melanogaster and the soil nematode Caenorhabditis elegans. These model organisms have enabled the genetic analysis of glutamate receptors in the context of a simpler nervous system and provided new insights into receptor function and regulation. In this review we will focus on recent studies that have used genetic, behavioral, and electrophysiological techniques to study the function of ------------------- Key: 6070 Medline: 12958363 Authors: Melendez A;Talloczy Z;Seaman M;Eskelinen EL;Hall DH;Levine Title: Autophagy genes are essential for dauer development and life-span extension in C. elegans. Citation: Science 301: 1387-1391 2003 Type: ARTICLE Genes: bec-1 daf-2 lgg-1 lgg-2 unc-51 Abstract: Both dauer formation (a stage of developmental arrest) and adult life-span in Caenorhabditis elegans are negatively regulated by insulin-like signaling, but little is known about cellular pathways that mediate these processes. Autophagy, through the sequestration and delivery of cargo to the lysosomes, is the major route for degrading long-lived proteins and cytoplasmic organelles in eukaryotic cells. Using nematodes with a loss-of-function mutation in the insulin-like signaling pathway, we show that bec-1 the C. elegans ortholog of the yeast and mammalian autophagy gene APG6/VPS30/beclin1 is essential for normal dauer morphogenesis and life-span extension. Dauer formation is associated with increased autophagy and also requires C. elegans orthologs of the yeast autophagy genes APG1, APG7, APG8, and AUT10. Thus, autophagy is a cellular pathway essential for dauer development and life-span extension in C. elegans. ------------------- Key: 6071 Medline: 12872001 Authors: Kraemer BC;Zhang B;Leverenz JB;Thomas JH;Trojanowski JQ;Schellenberg GD Title: Neurodegeneration and defective neurotransmission in a Caenorhabditis elegans model of tauopathy. Citation: Proceedings of the National Academy of Sciences USA 100: 9980-9985 2003 Type: ARTICLE Genes: aex-3 unc-25 unc-29 unc-31 unc-64 Abstract: Frontotemporal dementia with parkinsonism chromosome 17 type (FTDP-17) is caused by mutations in MAPT, the gene encoding tau. FTDP-17 begins with executive function deficits and other abnormal behaviors, which progress to dementia. Neurodegenerative changes include accumulation of aggregated tau as neuronal and glial fibrillary tangles. Aggregated tau is seen in numerous other neurodegenerative diseases, including Alzheimer's disease (AD). We expressed normal and FTDP-17 mutant human tau (mutations p301L and V337M) in Caenorhabditis elegans to model taupathy disorders. Tau pan-neuronal expression caused progressive uncoordinated locomotion (Unc), characteristic of nervous system defects in worms. Subsequently, insoluble tau accumulates and both hyperphosphorylated in FTDP-17, AD, and other taupathies. Substantial neurodegeneration, seen as bulges and gaps in nerve cords followed by loss of neurons, occurs after insoluble tau begins to accumulate. Axons show vacuoles, membranous infoldings, and whorls with associated amorphous tau accumulations and abnormal tau-positive aggregates. FTDP-17 mutation lines had a more severe Unc phenotype, accumulated more insoluble tau at a younger age, were more resistant to cholinergic inhibitors, and had more severe axonal degeneration when compared with lines of expressing normal tau. The Unc phenotype is caused by a presynaptic defect. Postsynaptic transmission is intact. This transgenic model will enable mechanistic dissection of genes and compounds that inhibit pathological ------------------- Key: 6072 Medline: 12921736 Authors: Muriel JM;Brannan M;Taylor K;Johnstone IL;Lithgow GJ;Tuckwell D Title: M142.2 (cut-6), a novel Caenorhabditis elegans matrix gene important for dauer body shape. Citation: Developmental Biology 260: 339-351 2003 Type: ARTICLE Genes: ajm-1 cut-6 daf-1 daf-2 daf-8 daf-14 unc-76 Abstract: The cuticle of the nematode Caenorhabditis elegans is a collagenous extracellular matrix which forms the exoskeleton and defines the shape of the worm. We have characterized the C. elegans gene M142.2, and we show that this is a developmentally regulated gene important for cuticle structure. Transgenic worms expressing M142.2 promoter fused to green fluorescent protein showed that M142.2 is expressed in late embryos and L2d predauers, in the hypodermal cells which synthesize the cuticle. The same temporal pattern was seen by RT-PCR using RNA purified from specific developmental stages. A recombinant fragment of M142.2 was expressed in Escherichia coli and used to raise an antiserum. Immunohistochemistry using the antiserum localized M142.2 to the periphery of the alae of L1 and dauers, forming two longitudinal ribbons over the hypodermal cells. Loss-of-function of M142.2 by RNAi resulted in a novel phenotype: dumpy dauers which lacked alae. M142.2 therefore plays a major role in the assembly of the alae and the morphology of the dauer cuticle; because of its similarity to the other cut genes of the cuticle, we have named the gene cut-6. ------------------- Key: 6073 Medline: 14511482 Authors: Crittenden SL;Eckmann CR;Wang L;Bernstein DS;Wickens M;Kimble J Title: Regulation of the mitosis/meiosis decision in the Caenorhabditis elegans germline. Citation: Philosophical Transactions of the Royal Society of London 358B: 1359-1362 2003 Type: REVIEW Genes: fbf-1 fbf-2 gld-1 gld-2 gld-3 glp-1 lag-1 lag-2 lag-3 lin-12 nos-3 Abstract: During the development of multicellular organisms, the processes of growth and differentiation are kept in balance to generate and maintain tissues and organs of the correct size, shape and cellular composition. We have investigated the molecular controls of growth and differentiation in the Caenorhabditis elegans germline. A single somatic cell, called the distal tip cell, promotes mitotic proliferation in the adjacent germline by GLP-1/Notch signaling. Within the germline, the decisions between mitosis and meiosis and between spermatogenesis and oogenesis are controlled by a group of conserved RNA regulators. FBF, a member of the PUF (for Pumilio and FBF) family of RNA-binding proteins, promotes mitosis by repressing gld-1 mRNA activity; the GLD-1, GLD-2, GLD-3, and NOS-3 proteins promote entry into meiosis by regulating mRNAs that remain unknown. The regulatory balance between opposing FBF and GLD activities is crucial for controlling the extent of germline proliferation. PUF proteins regulate germline stem cells in both Drosophila and C. elegans and are localized to germline stem cells of the mammalian testis. Therefore, this post-transcriptional regulatory switch may be an ancient mechanism for controlling maintenance of stem cells versus differentiation. ------------------- Key: 6074 Medline: Authors: Han M Title: Caenorhabditis elegans genetics. Citation: Genetics (online text: http://www.ergito.com/main.jsp?bcs=GNTC), Cambridge, MA. : 9.1-9.31 2003 Type: REVIEW Genes: Abstract: Since the publication of the first genetic research paper on Caenorhabditis elegans (C. elegans for short) in 1974, this microscopic, free-living nematode has become a popular model organism to study development, neurobiology, and other biological problems. The ability to do powerful genetics has been the most critical reason why studies using this organism have made enormous contributions to basic biology and medical science. Therefore, C. elegans genetics should be part of any modern genetic education. In this chapter, we describe some of the unique properties of C. elegans that makes it an exceptional organism for genetic and molecular biological research. Some important genetic tools and methodologies developed by C. elegans researchers will also be introduced. We aim to connect the fundamental principles of genetics as described in early chapters with practical applications of these principles in actual research. We have chosen a few genetic pathways and biological problems as examples for illustrating the logic behind the genetic analyses and for introducing some commonly practiced strategies and methods. We do not hesitate to introduce some of the most advanced and up-to-date methods and approaches, including those developed since the genome sequence was determined in 1998. We believe today's students can go right into the heart of present research after learning the basic principle of Genetics (see the early chapters of this book) and molecular biology. In fact, in many C. elegans laboratories, undergraduate students are doing a wide variety of experiments using the genetic techniques ------------------- Key: 6075 Medline: 12947400 Authors: Fraser A Title: Worms in L.A. Citation: Nature Genetics 35: 3-5 2003 Type: REVIEW Genes: alg-1 alg-2 ces-2 fog-2 hbl-1 let-7 lin-41 lin-48 lin-58 mir-48 mir-241 rde-4 sid-1 sid-2 tra-1 unc-43 Abstract: In the year that the Nobel Prize was awarded to Sydney Brenner, Bob Horvitz and Sir John Sulston, the 14th International C. elegans meeting was bound to be a celebration as well as a scientific meeting and social get-together. The celebratory mood reached its high point during the keynote address by Sydney Brenner, the 'Father of the Worm'. The address was classic Brenner, at once provocative and Delphic, with incisive analogies, witty anecdotes and sweeping dismissals (systems biology did not fare well), all delivered with his usual flair. ------------------- Key: 6076 Medline: 12971899 Authors: Suzuki H;Kerr R;Bianchi L;Frokjaer-Jensen C;Slone D;Xue J;Gerstbrein B;Driscoll M;Schafer WR Title: In vivo imaging of C. elegans mechanosensory neurons demonstrates a specific role for the MEC-4 channel in the process of gentle touch sensation. Citation: Neuron 39: 1005-1017 2003 Type: ARTICLE Genes: cca-1 crt-1 egl-19 itr-1 mec-2 mec-4 mec-6 unc-2 unc-68 Abstract: In the nematode C. elegans, genes encoding components of a putative mechanotransducing channel complex have been identified in screens for light-touch-insensitive mutants. A long-standing question, however, is whether identified MEC proteins act directly in touch transduction or contribute indirectly by maintaining basic mechanoreceptor neuron physiology. In this study, we used the genetically encoded calcium indicator cameleon to record cellular responses of mechanosensory neurons to touch stimuli in intact, behaving nematodes. We defined a gentle touch sensory modality that adapts with a time course of approximately 500 ms and primarily senses motion rather than pressure. The DEG/ENaC channel subunit MEC-4 and channel-associated stomatin MEC-2 are specifically required for neural responses to gentle mechanical stimulation, but do not affect the basic physiology of touch neurons or their in vivo responses to harsh mechanical stimulation. These results distinguish a specific role for the MEC channel proteins in the process of gentle touch ------------------- Key: 6077 Medline: 14508492 Authors: Caudy AA;Ketting RF;Hammond SM;Denli AM;Bathoorn AMP;Tops BBJ;Silva JM;Myers MM;Hannon GJ;Plasterk RHA Title: A micrococcal nuclease homologue in RNAi effector Citation: Nature 425: 411-414 2003 Type: ARTICLE Genes: alg-1 dcr-1 let-7 lin-4 mir-52 tsn-1 vig-1 Abstract: RNA interference (RNAi) regulates gene expression by the cleavage of messenger RNA, by mRNA degradation and by preventing protein synthesis. These effects are mediated by a ribonucleoprotein complex known as RISC (RNA-induced silencing complex)(1). We have previously identified four Drosophila components (short interfering RNAs1, Argonaute 2 (ref. 2), VIG and FXR3) of a RISC enzyme that degrades specific mRNAs in response to a double-stranded-RNA trigger. Here we show that Tudor-SN (tudor staphylococcal nuclease)-a protein containing five staphylococcal/micrococcal nuclease domains and a tudor domain-is a component of the RISC enzyme in Caenorhabditis elegans, Drosophila and mammals. Although Tudor-SN contains non-canonical active-site sequences, we show that purified Tudor-SN exhibits nuclease activity similar to that of other staphylococcal nucleases. Notably, both purified Tudor-SN and RISC are inhibited by a specific competitive inhibitor of micrococcal nuclease. Tudor-SN is the first RISC subunit to be identified that contains a recognizable nuclease domain, and could therefore contribute to the RNA ------------------- Key: 6078 Medline: 14550897 Authors: Shompole S;Jasmer DP Title: Haemonchus contortus UNC-18 binds to Caenorhabditis elegans neuronal syntaxin. Citation: Molecular & Biochemical Parasitology 130: 55-59 2003 Type: ARTICLE Genes: unc-18 Abstract: Inhibition of secretion by intestinal cells of the parasitic nematode Haemonchus contortus has been implicated in causing irreversible damage to this parasite. Hence, proteins that regulate intestinal secretion may represent valuable targets for parasite control. Such proteins have been well studied in multiple eukaryotes and those involved in neurosecretion provide insight on both the protein components and mechanisms involved. Additionally, orthologous or paralogous proteins apparently regulate secretion by non-neuronal cells. ------------------- Key: 6079 Medline: 12951420 Authors: Hoshi H;Kamata Y;Uemura T Title: Effects of 17 beta-estradiol, bisphenol A and tributyltin chloride on germ cells of Caenorhabditis elegans. Citation: Journal of Veterinary Medical Science 65: 881-885 2003 Type: ARTICLE Genes: Abstract: Effects of a one-generation exposure to a natural estrogen, 17beta-estradiol (E2), and environmental pollutants such as bisphenol A (BPA) and tributyltin chloride (TBTCL) on the number of germ cells were investigated in the hermaphrodite Caenorhabditis elegans. The eggs of gravid adult worms isolated by alkaline hypochlorite treatment were seeded on a test chemical-containing NGM (nematode growth medium) agar plate without cholesterol. After incubation for 6 days at 16degreesC, the germ cells of adult worms were stained with 4',6-diamino-2-phenylindole dihydrochloricle (DAPI). The staining procedure was completed within one hour and the stained germ cells were counted under a fluorescence microscope without dissection. The number of germ cells in the worms treated with E2 (10(-10)-10(-6) M) and BPA (10(-9)-10(-5) M) was significantly increased. Maximal increases were observed at 10(-8) M E2 (156 +/- 15.3% of control) and 10(-5) M BPA (168 +/- 20.0% of control). TBTCL (10(-9)-10(-6) M) significantly decreased the number of germ cells. The minimal decrease was observed at 10(-6) M TBTCL (30.2 +/- 3.51% of control). These results indicate that changes in the number of germ cells are a sensitive indicator of the effects of chemicals on the reproductive system. Since the method described in this paper is a novel, simple, time- and money-saving bioassay, C. elegans is an excellent model with which to determine the reproductive toxicity of chemicals including environmental ------------------- Key: 6080 Medline: 12969249 Authors: Hobson RJ;Geng J;Gray AD;Komuniecki RW Title: SER-7b, a constitutively active G-alpha(s) coupled 5-HT(7)-like receptor expressed in the Caenorhabditis elegans M4 pharyngeal motorneuron. Citation: Journal of Neurochemistry 87: 22-29 2003 Type: ARTICLE Genes: ser-7 Abstract: Serotonin plays a key role in the regulation of pharyngeal pumping in nematodes. We have isolated a Caenorhabditis elegans cDNA (C09B7.1b, ser-7b) with greatest identity to the 5-HT7 receptor family. Membranes from COS-7 cells expressing SER-7b exhibit saturable [H-3]-LSD binding (K-d = 45 nM) that is inhibited by serotonin (5-HT) and tryptamine, but not by other physiological biogenic amines. Expression of SER-7b in COS-7 cells results in dramatic increase in basal cAMP levels over untransfected cells that is dependent on expression level. 5-HT further elevates cAMP levels in a dose-dependent manner (pEC(50) = 7.5 +/- 0.5). Mammalian 5-HT7 receptor inverse agonists reduce constitutive activity, with methiothepin the most potent (pIC50 = 7.8 +/- 0.1). Ser-7::GFP transcriptional fusions reveal that SER-7b appears to be expressed solely in the M4 pharyngeal motorneuron after hatching. This is the first report of a Galpha(s) coupled biogenic amine receptor in nematodes and the localization of SER-7b in the M4 pharyngeal motorneuron suggests that SER-7b may play a role in the regulation of pharyngeal pumping. ------------------- Key: 6081 Medline: 14635896 Authors: Cutter AD;Payseur BA Title: Rates of deleterious mutation and the evolution of sex in Caenorhabditis. Citation: Journal of Evolutionary Biology 16: 812-822 2003 Type: ARTICLE Genes: cal-1 ceh-13 fem-2 fog-3 glp-1 lin-14 mec-3 rpl-3 tra-2 Abstract: A variety of models propose that the accumulation of deleterious mutations plays an important role in the evolution of breeding systems. These models make predictions regarding the relative rates of protein evolution and deleterious mutation in taxa with contrasting modes of reproduction. Here we compare available coding sequences from one obligately outcrossing and two primarily selfing species of Caenorhabditis to explore the potential for mutational models to explain the evolution of breeding system in this clade. If deleterious mutations interact synergistically, the mutational deterministic hypothesis predicts that a high genomic deleterious mutation rate (U) will offset the reproductive disadvantage of outcrossing relative to asexual or selling reproduction. Therefore, C elegans and C. briggsae (both largely selling) should both exhibit lower rates of deleterious mutation than the obligately outcrossing relative C. remanei. Using a comparative approach, we estimate U to be equivalent (and <1) among all three related species. Stochastic mutational models, Muller's ratchet and Hill-Robertson interference, are expected to cause reductions in the effective population size in species that rarely outcross, thereby allowing deleterious mutations to accumulate at an elevated rate. We find only limited support for more rapid molecular evolution in selling lineages. Overall, our analyses indicate that the evolution of breeding system in this group is unlikely to be explained solely by available ------------------- Key: 6082 Medline: 12951246 Authors: Knox OGG;Killham K;Mullins CE;Wilson MJ Title: Nematode-enhanced microbial colonization of the wheat rhizosphere. Citation: FEMS Microbiology Letters 225: 227-233 2003 Type: ARTICLE Genes: Abstract: The mechanisms by which seed-applied bacteria colonize the rhizosphere in the absence of percolating water are poorly understood. Without mass flow, transport of bacteria by growing roots or soil animals, particularly nematodes may be important. We used a sand-based microcosm system to investigate the ability of three species of nematodes (Caenorhabditis elegans, Acrobeloides thornei and a Cruznema sp.) to promote rhizosphere colonization by four strains of beneficial rhizobacteria. In nearly all cases, rhizosphere colonization was substantially increased by the presence of nematodes, irrespective of bacterial or nematode species. Our results suggest that nematodes are important vectors for bacteria rhizosphere colonization in the absence of percolating water. ------------------- Key: 6083 Medline: Authors: Friedenberg NA Title: Experimental evolution of disperal in spatiotemporally variable microcosms. Citation: Ecology Letters 6: 953-959 2003 Type: ARTICLE Genes: rol-1 Abstract: The world is an uncertain place. Individuals' fates vary from place to place and from time to time. Natural selection in unpredictable environments should favour individuals that hedge their bets by dispersing offspring. I confirm this basic prediction using Caenorhabditis elegans in experimental microcosms. My results agree with evolutionary models and correlations found previously between habitat stability and individual dispersal propensity in nature. However, I also find that environmental variation that triggers conditional dispersal behaviour may not impose selection on baseline dispersal rates. These findings imply that an increased rate of disturbance in natural systems has the potential to cause an evolutionary response in the life history of impacted ------------------- Key: 6084 Medline: 12967556 Authors: Riddle DL;Gorski SM Title: Shaping and stretching life by autophagy. Citation: Developmental Cell 5: 364-365 2003 Type: REVIEW Genes: bec-1 daf-2 Abstract: In a recent study published in Science, Melendez et al. (2003) demonstrate that genes required for autophagy act downstream of insulin-like signaling, and are involved in the expression of major life history traits, including dauer larva development and adult life span. ------------------- Key: 6085 Medline: 12967564 Authors: Pellettieri J;Reinke V;Kim SK;Seydoux G Title: Coordinate activation of maternal protein degradation during the egg-to-embryo transition in C. elegans. Citation: Developmental Cell 5: 451-462 2003 Type: ARTICLE Genes: mat-1 mbk-1 mbk-2 mei-1 mei-2 mel-26 mex-5 oma-1 par-1 par-2 pie-1 pgl-1 pos-1 Abstract: The transition from egg to embryo occurs in the absence of transcription yet requires significant changes in gene activity. Here, we show that the C. elegans DYRK family kinase MBK-2 coordinates the degradation of several maternal proteins, and is essential for zygotes to complete cytokinesis and pattern the first embryonic axis. In mbk-2 mutants, the meiosis-specific katanin subunits MEI-1 and MEI-2 persist during mitosis and the first mitotic division fails. mbk-2 is also required for posterior enrichment of the germ plasm before the first cleavage, and degradation of germ plasm components in anterior cells after cleavage. MBK-2 distribution changes dramatically after fertilization during the meiotic divisions, and this change correlates with activation of mbk-2-dependent processes. We propose that MBK-2 functions as a temporal regulator of protein stability, and that coordinate activation of maternal protein degradation is one of the mechanisms that drives the transition from symmetric egg to patterned embryo. ------------------- Key: 6086 Medline: 12967565 Authors: Colaiacovo MP;MacQueen AJ;Martinez-Perez E;McDonald K;Adamo A;La Volpe A;Villeneuve AM Title: Synaptonemal complex assembly in C. elegans is dispensable for loading strand-exchange proteins but critical for proper completion of recombination. Citation: Developmental Cell 5: 463-474 2003 Type: ARTICLE Genes: him-3 him-14 msh-4 msh-5 rec-8 spo-11 syp-1 syp-2 Abstract: Here we probe the relationships between assembly of the synaptonemal complex (SC) and progression of recombination between homologous chromosomes during Caenorhabditis elegans meiosis. We identify SYP-2 as a structural component of the SC central region and show that central region assembly depends on proper morphogenesis of chromosome axes. We find that the SC central region is dispensable for initiation of recombination and for loading of DNA strand-exchange protein RAD-51, despite the fact that extensive RAD-51 loading normally occurs in the context of assembled SC. Further, persistence of RAD-51 foci and absence of crossover products in meiotic mutants suggests that SC central region components and recombination proteins MSH-4 and MSH-5 are required to promote conversion of resected double-strand breaks into stable post-strand exchange intermediates. Our data also suggest that early prophase barriers to utilization of sister chromatids as repair templates do not depend on ------------------- Key: 6087 Medline: 12941631 Authors: Finger FP;Kopish KR;White JG Title: A role for septins in cellular and axonal migration in C. elegans. Citation: Developmental Biology 261: 220-234 2003 Type: ARTICLE Genes: unc-59 unc-61 Abstract: Caenorhabditis elegans has two genes, unc-59 and unc-61, encoding septin-family GTPases. Mutations in the septin genes cause defects in locomotory behavior that have been previously attributed to cytokinesis failures in postembryonic neuroblasts. We find that mutations in either septin gene frequently cause uncoordination in newly hatched larvae in the absence of cytokinesis failures. The septins exhibit developmentally regulated expression, including expression in various neurons at times when processes are extending and synapses are forming. Motor neurons in the mutant larvae display defects in multiple aspects of axonal migration and guidance that are likely to be responsible for the locomotory behavior defects. The septins are also expressed in migrating distal. tip cells, which are leaders for gonad arm extension. Septin mutants affect morphology of the distal tip cells, as well as their migration and guidance during gonadogenesis, These results suggest that septins may be generally required for developmental migrations and pathfinding. ------------------- Key: 6088 Medline: Authors: McClintock TS;Sammeta N Title: Trafficking prerogatives of olfactory receptors. Citation: NeuroReport 14: 1547-1552 2003 Type: REVIEW Genes: odr-4 odr-10 unc-101 Abstract: Olfactory receptors lead lives of exclusivity and privilege, the monarchs of fiefdoms organized solely to carry out their instructions. Each olfactory sensory neuron expresses one allele of one of similar to1000 olfactory receptor genes. It is thought that olfactory receptor diversity is critical for the ability of animals to detect many thousands of odorants, but supporting functional evidence has been difficult to obtain because olfactory receptors expressed in heterologous cells are typically retained in the endoplasmic reticulum. The membrane trafficking entitlements enjoyed by olfactory receptors appear to be available only in mature olfactory sensory neurons. Evidence is accumulating that cell-type-specific accessory proteins regulate first the exit of olfactory receptors from the endoplasmic reticulum, and then the trafficking of olfactory receptors from post-Golgi compartments to the plasma membrane of the olfactory cilia where the receptors gain access to odorants. Critical olfactory receptor accessory proteins are known only in the nematode Caenorhabditis elegans, where the absence of a novel protein called ODR-4 or a clathrin adaptor, UNC-101, interferes with proper trafficking. Similar functional specificity also occurs in a parallel chemosensory system, the mammalian vomeronasal organ. Trafficking of the V2R type of vomeronasal receptors is mediated by a vomeronasal-specific family of major histocompatibility complex proteins. Removal of olfactory receptors from the plasma membrane may be regulated in a more conventional fashion because odor stimulation has been linked to receptor phosphorylation, to the function of G-protein coupled receptor kinase 3, and to an increase in vesicles ------------------- Key: 6089 Medline: Authors: Holbert S;Denghien I;Kiechle T;Rosenblatt A;Wellington C;Hayden MR;Margolis RL;Ross CA;Dausset J;Ferrante RJ;Neri Title: The Gln-Ala repeat transcriptional activator CA150 interacts with huntingtin: neuropathologic and genetic evidence for a role in Huntington's disease pathogenesis. Citation: Proceedings of the National Academy of Sciences USA 98: 1811-1816 2001 Type: ARTICLE Genes: Abstract: Huntington's disease (HD) is a neurodegenerative disease caused by polyglutamine expansion on the protein huntingtin (htt). Pathogenesis in HD appears to involve the formation of ubiquitinated neuronal intranuclear inclusions containing N-terminal mutated htt, abnormal protein interactions, and the aggregate sequestration of a variety of proteins (noticeably, transcription factors). To identify novel htt-interacting proteins in a simple model system, we used a yeast two-hybrid screen with a Caenorhabditis elegans activation domain library. We found a predicted WW domain protein (ZK1127.9) that interacts with N-terminal fragment of htt in two-hybrid tests. A human homologue of ZK1127.9 is CA150, a transcriptional coactivator with a N-terminal insertion that contains an imperfect (Gln-Ala) tract encoded by a polymorphic repeat DNA. CA150 interacted in vitro with full-length htt from lymphoblastoid cells. The expression of CA150, measured immunohistochemically, was markedly increased in human HD brain tissue compared with normal age-matched human brain tissue, and CA150 showed aggregate formation with partial colocalization to ubiquitin-positive aggregates. In 432 HD patients, the CA150 repeat length explains a small, but statistically significant, amount of the variability in the onset age. Our data suggest that abnormal expression of CA150, mediated by interaction with polyglutamine-expanded htt, may alter transcription and have a role in HD ------------------- Key: 6090 Medline: Authors: Holbert S;Dedeoglu A;Humbert S;Saudou F;Ferrante RJ;Neri C Title: Cdc42-interacting protein 4 binds to huntingtin: neuropathologic and biological evidence for a role in Huntington's disease. Citation: Proceedings of the National Academy of Sciences USA 100: 2712-2717 2003 Type: ARTICLE Genes: Abstract: Huntington's disease (HD) is a neurodegenerative disease caused by polyglutamine (polyQ) expansion in the protein huntingtin (htt). Pathogenesis in HD seems to involve the formation of transcription and signal transduction. To identify previously uncharacterized htt-interacting proteins in a simple model system, we used a yeast two-hybrid screen with a Caenorhabditis elegans activation domain library. We found a predicted SH3 domain protein (K08E3.3b) that interacts with N-terminal htt in two-hybrid tests. A human homolog of K08E3.3b is the Cdc42-interacting protein 4 (CIP4), a protein involved in Cdc42 and Wiskott-Aldrich syndrome protein-dependent signal transduction. CIP4 interacted in vitro with full-length htt from lymphoblastoid cells. Neuronal CIP4 immunoreactivity increased with neuropathological severity in the neostriatum of HD patients and partially colocalized to ubiquitin-positive aggregates. Marked CIP4 overexpression also was observed in Western blot from human HD brain striatum. The overexpression of CIP4 induced the death of striatal neurons. Our data suggest that CIP4 accumulation and cellular toxicity may have a role in HD ------------------- Key: 6091 Medline: Authors: Kimble J Title: Germ cell development in Caenorhabditis elegans: a brief review. Citation: "Current Problems in Germ Cell Differentiation." A McLaren and CC Wylie (eds). British Society for Developmental Biology 7: 241-255 1983 Type: REVIEW Genes: fem-2 her-1 Abstract: Most multicellular eukaryotes posses a distinct group of germ-line cells that produces oocytes in one sex and sperm in the other. The production of adult germ cells appears to involve several developmental steps. First, during early embryogenesis, one or a few cells are committd to become germ precursor cells. Secondly, after a period of proliferation, some or all germ line descendants of the germ precursor cell leave the mitotic cell cycle and enter meiotic prophase. Thirdly, the meiotic germ cell matures as either a sperm or an oocyte. In this paper, I will review our knowledge of how each of these steps might be controlled in the small non-parasitic soil nematode, Caenorhabditis elegans. ------------------- Key: 6092 Medline: Authors: Kimble J Title: Genetic control of sex determination in the germ line of C. elegans. Citation: "Results and Problems in Cell Differentiation." W Hennig (ed). Springer-Verlag, Berlin. : 117-128 1987 Type: REVIEW Genes: fem-1 fem-2 fem-3 fog-1 fog-2 her-1 mog-1 mog-2 tra-1 tra-2 tra-3 Abstract: How is a germ cell instructed to differentiate as a sperm or oocyte? This is essentially a question of sex determination asked at the cellular level. Sex determination in the germ line has been elusive to experimentation in both Drosophila and in mice. However, in the nematode, Caenorhabditis elegans, control over the choice between spermatogenesis and oogenesis has proven to be particularly accessible to genetic analysis. In this chapter, we review our current knowledge of the mechanisms in C. elegans that influence this decision. ------------------- Key: 6093 Medline: Authors: Rosenquist T;Ahringer J;Barton MK;Graham P;Okkema P;Kimble Title: Genetic control of sex determination in the hermaphrodite germ line of Caenorhabditis elegans. Citation: "Genetic of Pattern Formation and Growth Control." AP Mahowald (ed). 48th Annual Symposium of the Society for Developmental Biology. Wiley-Liss, New York. : 91-102 Type: REVIEW Genes: fem-1 fem-2 fem-3 fog-1 fog-2 her-1 mog-1 tra-1 tra-2 tra-3 Abstract: Sex determination in the C. elegans germ line addresses two major problems of biological control. First, any regulation that directs male or female development in all tissues must rely on tissue-specific controls to specify a particular pathway of differentiation (e.g., sperm or oocyte) in a single tissue. The C. elegans germ line provides several technical advantages for analyzing sex determination in a single tissue, including powerful genetic selections (Kimble, 1988) and ease of micro-injection (Kimble et al., 1982). Second, the self-fertility of the C. elegans hermaphrodite depends upon its transient production of sperm in an otherwise female animal. Analysis of sex determination in the hermaphrodite germ line should therefore shed light on the evolution of hermaphrodites from females. Here, we review our efforts towards identifying the regulatory elements that control the C. elegans hermaphrodite germ line to produce sperm and ------------------- Key: 6094 Medline: Authors: Evans TC;Goodwin EB;Kimble J Title: Translational regulation of development and maternal RNAs in Caenorhabditis elegans. Citation: Seminars in Developmental Biology 3: 381-389 1992 Type: REVIEW Genes: dpy-26 dpy-27 dpy-28 dpy-29 fem-1 fem-2 fem-3 fog-2 glp-1 her-1 lin-14 mei-1 mes-1 mes-2 mes-3 mes-4 mog-1 par-1 par-2 par-3 par-4 sdc-1 skn-1 tra-2 tra-3 Abstract: Post-transcriptional controls of mRNA activity are crucial for development of the nematode Caenorhabditis elegans. The onset of spermatogenesis in hermaphrodites is achieved by translational repression of the sex-determining gene tra-2; this repression depends on a direct repeat element (DRE) located in the 3' untranslated region (3'UTR) of the tra-2 mRNA. In addition, the switch from spermatogenesis to oogenesis in hermaphrodites depends on a negative regulatory element in the 3'UTR of the transcript of a second sex-determining gene, fem-3. Thus, post-transcriptional controls of tra-2 and fem-3 are essential for development of an XX animal as a hermaphrodite instead of a female. Post-transcriptional regulation by regulatory elements localized in the 3'UTR also influences somatic development. Thus, the tra-2 DRE also regulates tra-2 somatic expression and the 3'UTR of lin-14 is involved in the post-transcriptional regulation of larval-specific somatic cell lineages. The relevance of these controls to the regulation of maternal RNA is ------------------- Key: 6095 Medline: Authors: Wickens M;Kimble J;Strickland S Title: Translational contrl of developmental decisions. Citation: "Translational Control." JWB Hershey, MB Mathews and N Sonenberg (eds). CSHLP Monograph 30. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. : 411-450 1996 Type: REVIEW Genes: fem-3 glp-1 lin-4 lin-14 mog-1 tra-2 Abstract: At fertilization, the calm of oogenesis is broken, and the egg abruptly begins a flurry of activity. Many crucial steps - decisions concerning when and where to divide, specification of cell fates, and establishment of body axes - rely on materials the egg contains at that moment. In many animals, the first few hours of life proceed with little or no transcription. As a result, developmental regulation at these early stages is dependent on maternal cytoplasm, rather than the zygotic nucleus. The regulatory molecules accumulated during oogenesis might, in principle, be of any type, including RNA and protein. It is now clear that messenger RNAs present in the egg before fertilization (so-called maternal mRNAs) have a prominent role in early decisions. Viewed from this perspective, it is not surprising that oocytes and early embryos display an impressive array of posttrancriptional regulatory mechanisms, controlling mRNA stability, localization, and translation. ------------------- Key: 6096 Medline: Authors: Kimble J;Smith J Title: Pattern formation and developmental mechanisms. Citation: Current Opinion in Genetics & Development 6: 391-394 1996 Type: REVIEW Genes: Abstract: This issue of Current Opinion in Genetics and Development examines mechanisms by which pattern is established during the development of a broad range of organisms and in a wide variety of tissues. Perhaps the most important message to emerge is that, on the whole, developmental mechanisms have been extraordinarily well conserved during evolution. Each embryo appears to have at its disposal a fundamental 'toolkit' of regulators and regulatory pathways with which to construct an organism. Most chapters in this issue discuss the tools; the last chapter, by contrast, addresses the evolutionary question of how different embryos give rise to distinct organisms with essentially the same 'tool-kit' of molecules during development. ------------------- Key: 6097 Medline: Authors: Panganiban G;Irvine SM;Lowe C;Roehl H;Corley LS;Sherbon B;Grenier JK;Fallon JF;Kimble J;Walker M;Wray GA;Swalla BJ;Martindale MQ;Carroll SB Title: The origin and evolution of animal appendages. Citation: Proceedings of the National Academy of Sciences USA 94: 5162-5166 1997 Type: ARTICLE Genes: Abstract: Animals have evolved diverse appendages adapted for locomotion, feeding and other functions. The genetics underlying appendage formation are best understood in insects and vertebrates. The expression of the Distal-less (Dll) homeoprotein during arthropod limb outgrowth and of Dll orthologs (Dlx) in fish fin and tetrapod limb buds led us to examine whether expression of this regulatory gene may be a general feature of appendage formation in protostomes and deuterostomes. We find that Dll is expressed along the proximodistal axis of developing polychaete annelid parapodia, onychophoran lobopodia, ascidian ampullae, and even echinoderm tube feet. Dll/Dlx expression in such diverse appendages in these six coelomate phyla could be convergent, but this would have required the independent co-option of Dll/Dlx several times in evolution. It appears more likely that ectodermal Dll/Dlx expression along proximodistal axes originated once in a common ancestor and has been used subsequently to pattern body wall outgrowths in a variety of organisms. We suggest that this pre-Cambrian ancestor of most protostomes and the deuterostomes possessed elements of the genetic machinery for and may have even borne appendages. ------------------- Key: 6098 Medline: Authors: Crittenden SL;Kimble J Title: Immunofluorescence methods for C. elegans. Citation: "Cells: A Laboratory Manual." DL Spector, RD Goldman and LA Leinwand (eds). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. : 108.1-108.9 1998 Type: REVIEW Genes: Abstract: The use of antibodies to visualize the distribution and subcellular localization of gene products powerfully complements genetic and molecular analysis of gene function in C. elegans. The challenge to immunolabeling C. elegans is finding the fixation and permeabilization methods that effectively make antigens accessible without destroying the tissue morphology or the antigen. Embryos are surrounded by a chitinous eggshell and larvae and adults are surrounded by a collagenous cuticle, each of which must be permeabilized to allow penetration of antibodies. In addition, antigens and antibodies are sensitive to different fixing and permeabilizing conditions. For example, some antibodies do not work well on paraformaldehyde-fixed samples, and others are sensitive to incubation in acetone. There are many protocols used in the C. elegans field; additional protocols are summarized in Miller and Shakes (1994) and on the C. elegans World ------------------- Key: 6099 Medline: Authors: Petcherski AG;Kimble J Title: Mastermind is a putative activator for Notch. Citation: Current Biology 10: R471-R473 2000 Type: REVIEW Genes: glp-1 lag-3 Abstract: During signaling by the Notch receptor, Notch's intracellular domain is cleaved, moves to the nucleus and associates with a DNA-binding protein of the CSL class (CSL for CBF1, Suppressor of Hairless (Su(H)), LAG-1); as a result, target genes are transcriptionally activated (reviewed in [1,2]). In Caenorhabditis elegans, a glutamine-rich protein called LAG-3 forms a ternary complex with the Notch intracellular domain and LAG-1 and appears to serve as a transcriptional activator that is critical for signaling [3]. Although database searches failed to identify a LAG-3-related protein, we surmised that Notch signaling in other organisms might involve an analogous activity. ------------------- Key: 6100 Medline: Authors: Wickens M;Goodwin EB;Kimble J;Strickland S;Hentze MW Title: Translational control of developmental decisions. Citation: "Translational Control of Gene Expression." Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. : 295-370 2000 Type: REVIEW Genes: apx-1 fbf-1 fbf-2 fem-3 gld-1 glh-1 glh-2 glp-1 laf-1 let-7 lin-4 lin-14 lin-41 mex-1 mex-3 mog-1 mog-4 mog-5 nos-1 nos-2 nos-3 pal-1 pos-1 tra-1 tra-2 Abstract: At fertilization, the calm of oogenesis ends and the egg abruptly begins a flurry of activity. Many crucial steps - decisions concerning when and where to divide, specification of cell fates, and establishment of body axes - rely on materials the egg contains at that moment. In many animals, the first few hours of life proceed with little or no transcription. As a result, developmental regulation at these early stages is dependent on maternal cytoplasm rather than the zygotic nucleus. The regulatory molecules accumulated during oogenesis might, in principle, be of any type, including RNA and protein. It is clear that mRNAs present in the egg before fertilization - so-called maternal mRNAs - play a particularly prominent role in early decisions. Viewed from this perspective, it is not surprising that oocytes and early embryos display an impressive array of posttranscriptional regulatory mechanisms, controlling mRNA stability, localization, and translation. ------------------- Key: 6101 Medline: Authors: Wickens M;Bernstein DS;Kimble J;Parker R Title: A PUF family portrait: 3' UTR regulation as a way of life. Citation: Trends in Genetics 18: 150-157 2002 Type: REVIEW Genes: fbf-1 fbf-2 fem-3 lin-41 ncl-1 nos-1 nos-2 nos-3 puf-3 puf-4 puf-5 puf-6 puf-7 puf-8 puf-9 puf-10 puf-11 Abstract: In eukaryotic cells, mRNAs are exquisitely controlled, often through regulatory elements in their 3' untranslated regions (3'UTrs). Proteins that bind to those sites are key players in controlling mRNA stability, translation and localization. One family of regulatory proteins - the PUF proteins - are not only structurally related, but also bind to 3'UTRs and modulate mRNA expression in a wide variety of eukaryotic species. They do so either by enhancing turnover or repressing translation, and act combinatorially with other regulatory proteins. Here, we discuss the evolution, biological function and mechanisms of action of the PUF protein family, and suggest that a primordial function of PUF proteins is to sustain mitotic proliferation of stem cells. ------------------- Key: 6102 Medline: Authors: Barnes TM Title: Echolocation: a PCR-based strategy for reliably and rapidly mapping transposon insertion sites. Citation: Nucleic Acids Research 18: 6741-6742 1990 Type: ARTICLE Genes: lev-1 Abstract: The technique of isolating and defining genes by transposon tagging has been widely exploited in classical genetic organisms (1-3). However, it is also useful to know the location of insertion sites relative to the established structure of the gene. For example, insertions in exons indicate probable null alleles, while insertions upstream or downstream of the transcript can identify potential cis-acting regulatory sequences. Traditional methods to determine insertion sites rely on molecular cloning of the transposon-induced allele or extensive analysis of the genomic DNA by Southern blotting, both to which are laborious. Here I describe a novel strategy ('echolocation') to obtain quite precise (+/- 10 bp) estimates of the site of insertion by polymerase chain reaction (PCR; ref. 4). ------------------- Key: 6103 Medline: 14504222 Authors: Ailion M;Thomas JH Title: Isolation and characterization of high-temperature-induced dauer formation mutants in Caenorhabditis elegans. Citation: Genetics 165: 127-144 2003 Type: ARTICLE Genes: aex-1 aex-2 aex-3 aex-4 aex-5 aex-6 age-1 akt-1 bli-1 cam-1 cat-4 cha-1 che-3 che-14 clk-1 daf-1 daf-2 daf-5 daf-7 daf-8 daf-10 daf-11 daf-14 daf-16 deg-3 dpy-3 dpy-4 dpy-5 dpy-6 dpy-9 dpy-10 dpy-11 dpy-17 dpy-18 dpy-20 eat-1 eat-4 eat-6 egl-2 egl-3 egl-4 egl-9 egl-10 egl-17 egl-19 egl-21 egl-32 egl-36 egl-40 egl-46 exp-1 exp-4 flp-1 flr-4 goa-1 gpa-1 gpa-2 gpa-3 gpa-4 gpa-5 gpa-6 gpa-7 gpa-8 gpa-9 gpa-10 gpa-11 gpa-13 gpa-14 gpa-15 lin-2 lin-10 lin-11 lin-32 lin-45 lon-2 npr-1 odr-1 odr-2 odr-3 odr-4 odr-5 odr-6 osm-6 osm-9 osm-10 pbo-1 pdk-1 rol-1 rol-3 rol-6 scd-1 scd-3 sma-1 sma-2 sma-3 sma-4 snb-1 snt-1 spe-26 srd-1 tax-2 tax-4 tph-1 ttx-1 unc-1 unc-2 unc-3 unc-4 unc-5 unc-7 unc-9 unc-11unc-13 unc-16 unc-17 unc-18 unc-24 unc-25 unc-29 unc-31 unc-32 unc-33 unc-36 unc-38 unc-41 unc-42 unc-43 unc-44 unc-46 unc-47 unc-49 unc-58 unc-63 unc-64 unc-65 unc-70 unc-75 unc-76 unc-86 unc-95 unc-100 unc-101 unc-103 unc-104 unc-119 vab-8 yDf17 Abstract: Dauer formation in Caenorhabditis elegans is regulated by at least three signaling pathways, including an insulin receptor-signaling pathway. These pathways were defined by mutants that form dauers constitutively (Daf-c) at 25degrees. Screens for Daf-c mutants at 25degrees have probably been saturated, but failed to identify all the components involved in regulating dauer formation. Here we screen for Daf-c mutants at 27, a more strongly dauer-inducing condition. Mutations identified include novel classes of alleles for three known genes and alleles defining at least seven new genes, hid-1-hid-7. Many of the genes appear to act in the insulin branch of the dauer pathway, including pdk-1, akt-1, aex-6, and hid-1. We also molecularly identify hid-1 and show that it encodes a novel highly conserved putative transmembrane protein expressed in neurons. ------------------- Key: 6104 Medline: 12835395 Authors: Wacker I;Schwarz V;Hedgecock EM;Hutter H Title: zag-1, a Zn-finger homeodomain transcription factor controlling neuronal differentiation and axon outgrowth in C. elegans. Citation: Development 130: 3795-3805 2003 Type: ARTICLE Genes: del-1 epi-1 glr-1 him-4 myo-3 opt-3 sra-6 unc-3 unc-4 unc-47 unc-53 unc-129 zag-1 mDf8 mDf9 Abstract: The nervous system consists of diverse subtypes of neurons, whose identities must be specified during development. One important aspect of the differentiation program of neurons is the expression of the appropriate set of genes controlling axon pathway selection. We have identified a novel Znfinger/homeodomain containing transcription factor, zag-1, required for particular aspects of axonal pathfinding. In zag-1 mutants, motorneuron commissures either branch prematurely or fail to branch at the correct point. Ventral cord interneurons show defects in the guidance towards the ventral cord and also in the ventral cord. Several neurons misexpress differentiation markers, including glutamate receptor subunits and chemosensory receptors. zag-1 is expressed transiently in embryonic and postembryonic neurons during differentiation as well as in some mesodermal tissues. Null mutants of zag-1 are unable to swallow food and die as L1 larvae with a starved appearance, indicating that zag-1 has an additional role in pharynx development. The vertebrate homolog, deltaEF1, is highly conserved and known to act as transcriptional repressor in various tissues. Our data indicate that zag-1 also acts as transcriptional repressor controlling important aspects of terminal differentiation of neurons. ------------------- Key: 6105 Medline: 12835398 Authors: Toker AS;Teng Y;Ferreira HB;Emmons SW;Chalfie M Title: The Caenorhabditis elegans spalt-like gene sem-4 restricts touch cell fate by repressing the selector Hox gene egl-5 and the effector gene mec-3. Citation: Development 130: 3831-3840 2003 Type: ARTICLE Genes: egl-5 lin-39 mab-5 mec-3 sem-4 unc-86 Abstract: Members of the spalt (sal) gene family encode zinc-finger proteins that are putative tumor suppressors and regulate anteroposterior (AP) patterning, cellular identity, and, possibly, cell cycle progression. The mechanism through which sal genes carry out these functions is unclear. The Caenorhabditis elegans sal gene sem-4 controls the fate of several different cell types, including neurons, muscle and hypodermis. Mutation of sem-4 transforms particular tail neurons into touch-neuron-like cells. In wild-type C. elegans, six touch receptor neurons mediate the response of the worm to gentle touch. All six touch neurons normally express the LIM homeobox gene mec-3. A subset, the two PLM cells, also express the Hox gene egl-5, an Abdominal-B homolog, which we find is required for correct mec-3 expression in these cells. The abnormal touch-neuron-like-cells in sem-4 animals express mec-3; we show that a subset also express egl-5. We report: (1) that ectopic expression of sem-4 in normal touch cells represses mec-3 expression and reduces touch cell function; (2) that egl-5 expression is required for both the fate of normal PLM touch neurons in wild-type animals and the fate of a subset of abnormal touch neurons in sem-4 animals, and (3) that SEM-4 specifically binds a shared motif in the mec-3 and egl-5 promoters that mediates repression of these genes in cells in the tail. We conclude that sem-4 represses egl-5 and mec-3 through direct interaction with regulatory sequences in the promoters of these genes, that sem-4 indirectly modulates mec-3 expression through its repression of egl-5 and that this negative regulation is required for proper determination of neuronal fates. We suggest that the mechanism and targets of regulation by sem-4 are conserved throughout the sal gene family: other sal genes might regulate patterning and cellular identity through direct repression of Hox selector genes and ------------------- Key: 6106 Medline: 12835394 Authors: Clark SG;Chiu C Title: C. elegans ZAG-1, a Zn-finger-homeodomain protein, regulates axonal development and neuronal differentiation. Citation: Development 130: 3781-3794 2003 Type: ARTICLE Genes: dat-1 glr-1 lim-4 lin-11 mec-3 mec-4 odr-2 pag-3 sra-6 tph-1 unc-25 unc-86 unc-129 zag-1 Abstract: Neurons acquire distinct cell identities and implement differential gene programs to generate their appropriate neuronal attributes. On the basis of position, axonal structure and synaptic connectivity, the 302 neurons of the nematode Ceanorhabditis elegans are divided into 118 classes. The development and differentiation of many neurons require the gene zag-1, which encodes a deltaEF1/ZFH-1 Zn-finger-homeodomain protein. zag-1 mutations cause misexpression of neuron-specific genes, block formation of stereotypic axon branches, perturb neuronal migrations, and induce various axon-guidance, fasciculation and branching errors. A zag-1-GFP translational reporter is expressed transiently in most or all neurons during embryogenesis and in select neurons during the first larval stage. Analysis of the zag-1 promoter reveals that zag-1 is expressed in neurons and specific muscles, and that ZAG-1 directly represses its own expression. zag-1 activity also downregulates expression of genes involved in either the synthesis or reuptake of serotonin, dopamine and GABA. We propose that ZAG-1 acts as a transcriptional repressor to regulate multiple, discrete, neuron-specific aspects of terminal differentiation, including cell migration, axonal development and gene ------------------- Key: 6107 Medline: 12835392 Authors: Goodman SJ;Branda CS;Robinson MK;Burdine RD;Stern MJ Title: Alternative splicing affecting a novel domain in the C. elegans EGL-15 FGF receptor confers functional specificity. Citation: Development 130: 3757-3766 2003 Type: ARTICLE Genes: egl-15 egl-17 let-756 nDf19 Abstract: Fibroblast growth factor (FGF) receptors trigger a wide variety of cellular responses as diverse as cell migration, cell proliferation and cell differentiation. However, the molecular basis of the specificity of these responses is not well understood. The C. elegans FGF receptor EGL-15 similarly mediates a number of different responses, including transducing a chemoattractive signal and mediating an essential function. Analysis of the migration-specific alleles of egl-15 has identified a novel EGL-15 isoform that provides a molecular explanation for the different phenotypic effects of lesions at this locus. Alternative splicing yields two EGL-15 proteins containing different forms of a domain located within the extracellular region of the receptors immediately after the first IG domain. Neither of these two domain forms is found in any other FGF receptor. We have tested the roles of these EGL-15 receptor isoforms and their two FGF ligands for their signaling specificity. Our analyses demonstrate different physiological functions for the two receptor variants. EGL-15(5A) is required for the response to the FGF chemoattractant that guides the migrating sex myoblasts to their final positions. By contrast, EGL-15(5B) is both necessary and sufficient to elicit the essential function mediated by this receptor. ------------------- Key: 6108 Medline: 12953066 Authors: Mohri K;Ono S Title: Actin filament disassembling activity of Caenorhabditis elegans actin-interacting protein 1 (UNC-78) is dependent on filament binding by a specific ADF/cofilin isoform. Citation: Journal of Cell Science 116: 4107-4118 2003 Type: ARTICLE Genes: unc-60 unc-78 Abstract: Actin-interacting protein 1 (AIP1) is a conserved WD-repeat protein that enhances actin filament disassembly only in the presence of actin depolymerizing factor (ADF)/cofilin. In the nematode Caenorhabditis elegans, an AIP1 ortholog is encoded by the unc-78 gene that is required for organized assembly of muscle actin filaments. We produced bacterially expressed UNC-78 protein and found that it enhances actin filament disassembly preferentially in the presence of a specific ADF/cofilin isoform. Extensive and rapid filament disassembly by UNC-78 was observed in the presence of UNC-60B, a muscle-specific C. elegans ADF/cofilin isoform. UNC-78 also reduced the rate of spontaneous polymerization and enhanced subunit dissociation from filaments in the presence of UNC-60B. However, in the presence of UNC-60A, a non-muscle C. elegans ADF/cofilin isoform, UNC-78 only slightly enhanced filament disassembly. Interestingly, UNC-78 failed to enhance disassembly by mouse muscle-type cofilin. Using mutant forms of UNC6-B, we demonstrated that the F-actin-specific binding site of UNC-60B at the C terminus is required for filament disassembly by UNC-78. UNC-78 was expressed in body wall muscle and co-localized with actin where UNC-60B was also present. Surprisingly, UNC-78 was co-localized with actin in unc-60B null mutants, suggesting that the AIP1-actin interaction is not dependent on ADF/cofilin in muscle. These results suggest that UNC-78 closely collaborates with UNC-60B to regulate actin ------------------- Key: 6109 Medline: 12972602 Authors: Kubiseski TJ;Culotti J;Pawson T Title: Functional analysis of the Caenorhabditis elegans UNC-73B PH domain demonstrates a role in activation of the Rac GTPase in vitro and axon guidance in vivo. Citation: Molecular and Cellular Biology 23: 6823-6835 2003 Type: ARTICLE Genes: ced-10 mig-2 unc-73 unc-129 Abstract: The Caenorhabditis elegans UNC-73B protein regulates axon guidance through its ability to act as a guanine nucleotide exchange factor (GEF) for the CeRAC/MIG-2 GTPases. Like other GEFs for Rho family GTPases, UNC-73B has a Dbl homology (DH) catalytic domain, followed by a C-terminal pleckstrin homology (PH) domain. We have explored whether the PH domain cooperates with the adjacent DH domain to promote UNC-73B GEF activity and axonal pathfinding. We show that the UNC-73B PH domain binds preferentially to monophosphorylated phosphatidylinositides in vitro. Replacement of residues Lys1420 and Arg1422 with Gin residues within the PH domain impaired this phospholipid binding but did not affect the in vitro catalytic activity of the DH domain. In contrast, a mutant UNC-73B protein with a Trp1502-to-Ala substitution in the PH domain still interacted with phosphorylated phosphatidylinositides but had lost its GEF activity. UNC-73B minigenes containing these mutations were microinjected into C. elegans and transferred to unc-73(e936) mutant worms. Unlike the wild-type protein, neither PH domain mutant was able to rescue the unc-73 axon guidance defect. These results suggest that the UNC-73B PH domain plays distinct roles in targeting and promoting GEF activity towards the Rac GTPase, both of which are important for the directed movements of motorneurons in vivo. ------------------- Key: 6110 Medline: 12930745 Authors: Ch'ng Q;Williams L;Lie YS;Sym M;Whangbo J;Kenyon C Title: Identification of genes that regulate a left-right asymmetric neuronal migration in Caenorhabditis elegans. Citation: Genetics 164: 1355-1367 2003 Type: ARTICLE Genes: bar-1 bli-5 egl-20 him-5 lin-17 mab-5 mec-7 mig-1 mig-13 mig-14 qid-5 qid-6 qig-7 qid-8 Abstract: In C. elegans cells of the QL and QR neuroblast lineages migrate with left-right asymmetry; QL and its descendants inigrate posteriorly odiereas QR and its descendants inigrate anteriorly. One kcy step in generating this asymmetry is the expression of the Hox gene mab-5 in the QL descendants but not in the QR descendants. This asymmetry appears to be coupled to the asymmetric polarizations and movements of QL and QR as they migrate and relies on an asymmetric response to an EGL-20/Wnt signal. To identify genes involved in these complex layers of regulation and to isolate targets of mab-5 that direct posterior migrations, we screened visually for mutants with cell migration defects in the QL and QR lineages. Here, we describe a set of new mutants (qid-5, qid-6, qid-7, and qid-8) that primarily disrupt the migrations of the QL descendants. Most of these mutants were defective in mab-5 expression in the QL lineage and might identify genes that interact directly or indirectly with the EGL-20/Wnt signaling ------------------- Key: 6111 Medline: 12897069 Authors: Walker GA;Thompson FJ;Brawley A;Scanlon T;Devaney E Title: Heat shock factor functions at the convergence of the stress response and developmental pathways in Caenorhabditis elegans. Citation: FASEB Journal 17: 508-526 2003 Type: ARTICLE Genes: age-1 daf-2 daf-4 daf-7 daf-14 fer-15 kin-8 spe-9 Abstract: Heat shock factor (HSF) is best characterized as the transcriptional regulator of heat shock protein genes, required by all cells to survive periods of stress. Recent evidence suggests that HSF also functions to regulate the expression of genes involved in growth and development under normal physiological conditions. In this study, we used RNA interference (RNAi) assays to investigate the role of HSF in Caenorhabditis elegans. Exposure of wild-type worms to hsf dsRNAi constructs caused a temperature-sensitive developmental arrest at the L2/L3 stage. At normal growth temperatures, hsf(RNAi) worms that developed to adults were small and scrawny, largely infertile, and showed a significant reduction in life span. These results demonstrate that HSF is required for normal postembryonic development under physiological conditions. Following heat shock, hsf(RNAi) worms were thermosensitive and displayed a significant reduction of hsp16 expression. When hsf(RNAi) was carried out in various dauer-constitutive mutant backgrounds, a dramatic reversal of dauer formation was observed, indicating that HSF is also required in the dauer pathway. In its natural habitat of the soil, where C. elegans is exposed to a constantly fluctuating environment; the ability to integrate the stress response with development may be an essential ------------------- Key: 6112 Medline: 14499625 Authors: Pasierbek P;Fodermayr M;Jantsch V;Jantsch M;Schweizer D;Loidl J Title: The Caenorhabditis elegans SCC-3 homologue is required for meiotic synapsis and for proper chromsosme disjunction in mitosis and meiosis. Citation: Experimental Cell Research 289: 245-255 2003 Type: ARTICLE Genes: air-2 hcp-6 him-3 rec-8 scc-3 spo-11 Abstract: The product of the Caenorhabditis elegans ORF F18E2.3 is homologous to the cohesin component Scc3p. By antibody staining the product of F18E2.3 is found in interphase and early meiotic nuclei. At pachytene it localizes to the axes of meiotic chromosomes but is no longer detectable on chromatin later in meiosis or in mitoses. Depletion of the gene product by RNAi results in aberrant mitoses and meioses. In meiosis, homologous pairing is defective during early meiotic prophase and at diakinesis there occur univalents consisting of loosely connected sister chromatids or completely separated sisters. The recombination protein RAD-51 accumulates in nuclear foci at higher numbers during meiotic prophase and disappears later than in wild-type worms, suggesting a defect in the repair of meiotic double-stranded DNA breaks. Embryos showing nuclei of variable size and anaphase bridges, indicative of mitotic segregation defects, are frequently observed. In the most severely affected gonads, nuclear morphology cannot be related to any specific stage. The cytological localization and the consequences of the lack of the protein indicate that C elegans SCC-3 is essential for sister chromatid cohesion both in mitosis and in meiosis. ------------------- Key: 6113 Medline: 12692694 Authors: Solovyova AS;Meenan N;McDermott L;Garofalo A;Bradley JE;Kennedy MW;Byron O Title: The polyprotein and FAR lipid binding proteins of nematodes: shape and monomer/dimer states in ligand-free and bound forms. Citation: European Biophysics Journal 32: 465-476 2003 Type: ARTICLE Genes: Abstract: Nematodes produce two classes of small, helix-rich fatty acid- and retinol-binding proteins whose structures and in vivo functions remain to be elucidated. These are the polyprotein allergens (NPA) and the FAR proteins. The solution properties of recombinant forms of these proteins from parasitic [Ascaris suum (As) and Onchocerca volvulus (Ov)] and free-living [Caenorhabditis elegans (Ce)] nematodes have been examined. Analytical ultracentrifugation (AUC) showed that, contrary to previous findings, the rAs-NPA-1A polyprotein unit (similar to15 kDa) is a monomer, and this stoichiometry is unaltered by ligand (oleic acid) binding. The rOv-FAR-1 and rCe-FAR-5 proteins differ in that the former forms a tight dimer and the latter a monomer, and these oligomeric states are also unaffected by ligand binding or protein concentration. Sedimentation equilibrium experiments showed that the partial specific volume v of the unliganded proteins agree well with the value calculated from amino acid composition extrapolated to experimental temperature, and was unaffected upon ligand binding. Data from small-angle X-ray scattering (SAXS) indicated that both of the monomeric proteins rAs-NPA-1A and rCe-FAR-5 are globular, although slightly elongated and flattened. These data are in good agreement with shapes predicted from sedimentation velocity experiments and hydrodynamic bead modelling. On the basis of functional and secondary structural homology with the ligand-binding domain of the retinoic acid receptor RXRalpha, de novo atomic resolution structures for rAs-NPA-1A and rCe-FAR-5 have been constructed which are consistent with the SAXS and hydrodynamic data. ------------------- Key: 6114 Medline: 13678612 Authors: White J;Bednarek S Title: Cytokinesis: GAGs form the walls that separate our parts. Citation: Current Biology 13: R717-R718 2003 Type: REVIEW Genes: sqv-1 sqv-5 sqv-7 Abstract: Cytokinesis, the final step of cell division, involves the formation of membranous barriers that partition cytosol and organelles between the resultant daughter cells. Recent studies reveal a crucial role for the extracellular glycosaminoglycan chondroitin in the completion of the cleavage furrow in dividing Caenorhabditis elegans embryos. ------------------- Key: 6115 Medline: 13678597 Authors: Hillers KJ;Villeneuve AM Title: Chromosome-wide control of meiotic crossing over in C. elegans. Citation: Current Biology 13: 1641-1647 2003 Type: ARTICLE Genes: eT6 meT7 mnT12 Abstract: A central event in sexual reproduction is the reduction in chromosome number that occurs at the meiosis I division. Most eukaryotes rely on crossing over between homologs, and the resulting chiasmata, to direct meiosis I chromosome segregation, yet make very few crossovers per chromosome pair [1, 2]. This indicates that meiotic recombination must be tightly regulated to ensure that each chromosome pair enjoys the crossover necessary to ensure correct segregation. Here, we investigate control of meiotic crossing over in Caenorhabditis elegans, which averages only one crossover per chromosome pair per meiosis [3, 4], by constructing genetic maps of end-to-end fusions of whole chromosomes. Fusion of chromosomes removes the requirement for a crossover in each component chromosome segment and thereby reveals a propensity to restrict the number of crossovers such that pairs of fusion chromosomes composed of two or even three whole chromosomes enjoy but a single crossover in the majority of meioses. This regulation can operate over physical distances encompassing half the genome. The meiotic behavior of heterozygous fusion chromosomes further suggests that continuous meiotic chromosome axes, or structures that depend on properly assembled axes, may be important for crossover regulation. ------------------- Key: 6116 Medline: 12965916 Authors: Oshitani N;Hato F;Kitagawa S;Watanabe K;Fujiwara Y;Higuchi K;Matsumoto T;Arakawa T Title: Distinct elevation of levels of anti-Caenorhabditis elegans antibody in sera of patients with inflammatory bowel disease. Citation: Clinical and Diagnostic Laboratory Immunology 10: 856-861 2003 Type: ARTICLE Genes: Abstract: Dysregulation of immune responses to intestinal exogenous antigens contributes to the pathogenesis of inflammatory bowel disease, but the specific antigen responsible for the pathogenesis of inflammatory bowel disease is unknown. We measured serum antibody titers against Caenorhabditis elegans antigens. Immunoglobulin G (IgG) and IgG subclass anti-C elegans antibodies in serum samples from 29 patients with ulcerative colitis, 30 patients with Crohn's disease, 7 patients with intestinal Behcet's disease, and 11 healthy controls were measured by enzyme-linked inummosorbent assay. Serum IgG and IgG2 antibody titers against C. elegans were significantly higher in patients with inflammatory bowel disease than in controls. Antibody levels were not affected by age, gender, disease activity, extent of disease, or small bowel involvement. The anti-C. elegans antibody titer was significantly lower in patients with Crohn's disease taking mesalazine or sulfasalazine than in patients not taking these drugs. The increased immune responses to C. elegans found in patients with inflammatory bowel disease reflect dysregulated immune responses to enteric antigens, which might play a role in the pathogenesis of inflammatory bowel disease. ------------------- Key: 6117 Medline: 14512020 Authors: Sewell ST;Zhang G;Uttam A;Chamberlin HM Title: Developmental patterning in the Caenorhabditis elegans hindgut. Citation: Developmental Biology 262: 88-93 2003 Type: ARTICLE Genes: cdh-3 ceh-6 egl-5 egl-38 lin-48 mab-9 mab-23 Abstract: Developmental pattern formation allows cells within a tissue or organ to coordinate their development and establish cell types in relationship to one another. To better characterize the developmental patterning events within one organ, the C elegans hindgut, we have analyzed the expression pattern of several genes using green fluorescent protein-based reporter transgenes. In wild-type animals, these genes are expressed in subsets of hindgut cells rather than in individual cell types. In mutant animals, we find that some, but not all, genes expressed in cells with altered development exhibit a corresponding alteration of gene expression. The results are consistent with a model where a combination of factors contribute to each cell's fate, and address how developmental information ------------------- Key: 6118 Medline: 14505566 Authors: Shaham S Title: Apoptosis: a process with a (beta)NAC for complexity. Citation: Cell 114: 660-661 2003 Type: REVIEW Genes: ced-3 ced-4 ced-9 icd-1 Abstract: Most programmed cell deaths in the nematode C. elegans require ced-3 caspase activity. In a recent paper, Bloss et al. (2003) reveal a new C. elegans death inhibitor, icd-1, whose loss can promote apoptosis independently of ------------------- Key: 6119 Medline: 14517244 Authors: Szewczyk NJ;Jacobson LA Title: Activated EGL-15 FGF receptor promotes protein degradation in muscles of Caenorhabditis elegans. Citation: EMBO Journal 22: 5058-5067 2003 Type: ARTICLE Genes: clr-1 egl-15 egl-17 let-23 let-60 let-341 let-756 lin-45 mek-2 mpk-1 sem-5 soc-2 unc-54 Abstract: Signaling by fibroblast growth factors (FGFs) and their receptors has been previously implicated in control of cell proliferation, differentiation and migration. Here we report a novel role for signaling by the EGL-15 FGFR of Caenorhabditis elegans in controlling protein degradation in differentiated muscle. Activation of EGL-15, by means of a reduction of function mutation (clr-1) affecting an inhibitory phosphatase, triggers protein degradation in adult muscle cells using a pre-existing proteolytic system. This activation is not suppressed by mutation in either of the known genes encoding FGF ligands (egl-17 or let-756) but is well suppressed when both are mutated, indicating that either ligand is sufficient and at least one is necessary for FGFR activation. Activity of the Ras pathway through mitogen-activated protein kinase (MAPK) is required to trigger protein degradation. This is the first report that degradation of intracellular protein can be triggered by a growth factor receptor using an identified signal transduction pathway. The data raise the possibility that FGF-triggered proteolysis may be relevant to muscle remodeling or dedifferentiation. ------------------- Key: 6120 Medline: Authors: Thellman M;Hatzold J;Conradt B Title: The Snail-like CES-1 protein of C. elegans can block the expression of the BH3-only cell-death activator gene egl-1 by antagonizing the functions of bHLH proteins. Citation: Development 130: 4057-4071 2003 Type: ARTICLE Genes: ced-2 ces-1 ces-2 cnd-1 egl-1 hlh-2 hlh-3 hlh-4 hlh-6 hlh-12 hlh-14 tph-1 Abstract: The NSM cells of the nematode Caenorhabditis elegans differentiate into serotonergic neurons, while their sisters, the NSM sister cells, undergo programmed cell death during embryogenesis. The programmed death of the NSM sister cells is dependent on the cell-death activator EGL-1, a BH3-only protein required for programmed cell death in C. elegans, and can be prevented by a gain-of-function (gf) mutation in the cell-death specification gene ces-1, which encodes a Snail-like DNA-binding protein. Here, we show that the genes hlh-2 and hlh-3, which encode a Daughterless-like and an Achaete-scute-like bHLH protein, respectively, are required to kill the NSM sister cells. A heterodimer composed of HLH-2 and HLH-3, HLH-2/HLH-3, binds to Snail-binding sites/E-boxes in a cis-regulatory region of the egl-1 locus in vitro that is required for the death of the NSM sister cells in vivo. Hence, we propose that HLH-2/HLH-3 is a direct, cell-type specific activator of egl-1 transcription. Furthermore, the Snail-like CES-1 protein can block the death of the NSM sister cells by acting through the same Snail-binding sites/E-boxes in the egl-1 locus. In ces-1(gf) animals, CES-1 might therefore prevent the death of the NSM sister cells by successfully competing ------------------- Key: 6121 Medline: Authors: Manning DR Title: Evidence mounts for receptor-independent activation of heterotrimeric G proteins normally in vivo: positioning of the mitotic spindle in C. elegans. Citation: Science's Stke: Signal Transduction Knowledge Environment 196: PE35- 2003 Type: REVIEW Genes: goa-1 goa-16 gpr-1 gpr-2 lin-5 ric-8 Abstract: Examples of the activation of heterotrimeric G proteins in vivo by any means other than through activated cell surface receptors have been limited to pathophysiological phenomena. With the discovery of proteins apart from receptors that facilitate guanine nucleotide exchange and affect G protein subunit dissociation directly, however, the notion of receptor-independent modes of activation in normal circumstances has become a subject of great interest. Three recent publications, each focusing on G protein regulators (GPRs) in asymmetric positioning of the mitotic spindle in the early Caenorhabditis elegans embryo, provide substantial support for the likelihood of such a form of activation. The C. elegans proteins GPR-1 and GPR-2 each contain a G protein regulatory motif, which supports interaction with Galpha(i)-like subunits. Inactivation of the genes encoding GPR-1 and GPR-2 prevents the correct positioning of the mitotic spindle in the one- and two-cell embryo. This phenotype is identical to that achieved by inactivation of genes encoding the Galpha subunits GOA-1 and GPA-16. Because signaling in the one- and two-cell embryos is "intrinsic," the data suggest a GPR-dependent, receptor-independent mode of G protein activation. The GPRs interact preferentially with the guanosine diphosphate (GDP)-bound form of alpha subunits, and the GPR motif per se exhibits GDP dissociation inhibitor activity. The actions of the GPRs imply that GDP.Galpha.GPR is a key intermediate or effector in force generation relevant to ------------------- Key: 6122 Medline: 12934013 Authors: Stuart JM;Segal E;Koller D;Kim SK Title: A gene-coexpression network for global discovery of conserved genetic modules. Citation: Science 302: 249-255 2003 Type: ARTICLE Genes: Abstract: To elucidate gene function on a global scale, we identified pairs of genes that are coexpressed over 3182 DNA microarrays from humans,flies, worms, and yeast. We found 22,163 such coexpression relationships, each of which has been conserved across evolution. This conservation implies that the coexpression of these gene pairs confers a selective advantage and therefore that these genes are functionally related. Many of these relationships provide strong evidence for the involvement of new genes in core biological functions such as the cell cycle, secretion, and protein expression. We experimentally confirmed the predictions implied by some of these links and identified cell proliferation functions for several genes. By assembling these links into a gene-coexpression network, we found several components that were animal-specific as well as interrelationships between newly evolved and ancient modules. ------------------- Key: 6123 Medline: 14551437 Authors: Colavita A;Tessier-Lavigne M Title: A neurexin-related protein, BAM-2, terminates axonal branches in C. elegans. Citation: Science 302: 293-296 2003 Type: ARTICLE Genes: bam-2 cat-1 col-10 sax-1 slt-1 unc-6 unc-34 unc-40 Abstract: Neuronal axons connect to multiple target cells through the formation of collateral branches, but the mechanisms that regulate this process are largely unknown. We show that BAM-2, a neurexin-related transmembrane protein, is required for development of VC motoneuron branches in the worm Caenorhabditis elegans. Expression analysis and ectopic expression experiments suggest that BAM-2 functions as a branch termination cue and reveal a mechanism for selective control of branches that sprout off a primary ------------------- Key: 6124 Medline: 12973353 Authors: Weimer RM;Richmond JE;Davis WS;Hadwiger G;Nonet ML;Jorgensen EM Title: Defects in synaptic vesicle docking in unc-18 mutants. Citation: Nature Neuroscience 6: 1023-1030 2003 Type: ARTICLE Genes: ric-4 snb-1 snt-1 unc-13 unc-18 unc-64 Abstract: Sec1-related proteins function in most, if not all, membrane trafficking pathways in eukaryotic cells. The Sec1-related protein required in neurons for synaptic vesicle exocytosis is UNC-18. Several models for UNC-18 function during vesicle exocytosis are under consideration. We have tested these models by characterizing unc-18 mutants of the nematode Caenorhabditis elegans. In the absence of UNC-18, the size of the readily releasable pool is severely reduced. Our results show that the near absence of fusion-competent vesicles is not caused by a reduction in syntaxin levels, by a mislocalization of syntaxin, by a defect in fusion or by a failure to open syntaxin during priming. Rather, we found a reduction of docked vesicles at the active zone in unc-18 mutants, suggesting that UNC-18 functions, directly or indirectly, as a facilitator of ------------------- Key: 6125 Medline: 12898220 Authors: Adachi R;Kagawa H Title: Genetic analysis of ryanodine receptor function in Caenorhabditis elegans based on unc-68 revertants. Citation: Molecular Genetics & Genomics 269: 797-806 2003 Type: ARTICLE Genes: unc-68 mnDf6 mnDf8 Abstract: The Caenorhabditis elegans ryanodine receptor is encoded by the unc-68 gene, and functions as a Ca2+-induced Ca2+ release channel during muscle contraction. To investigate the factors that suppress calcium release and identify molecules that interact with the ryanodine receptor, we isolated revertants from two unc-68 mutants. Three of the revertants obtained from the null allele unc-68(e540), which displayed normal motility, had intragenic mutations that resulted in failure to splice out intron 21. The other two, kh53 and kh55, had amino acid insertions in the third of the four RyR domains. The brood size and the egg laying rate remain abnormal in these revertants. This suggests the third RyR domain may be required for egg laying and embryogenesis, although we can not determine a molecular mechanism. Five ketamine sensitive revertants recovered from the missense mutant unc-68(kh30) showed altered responses to caffeine, ryanodine, levamisole and ouabain relative to those of the unc-68(kh30) animals. These may carry second-site suppressor mutations, which may define genes for proteins that regulate the Ca2+ concentration in body-wall muscle. One of these mutants, kh52, shows lower motility and higher sensitivity to drugs, and this mutation was mapped to chromosome X. These observations provide a basis for the study of ryanodine receptor functions in embryogenesis and in calcium-mediated regulation of muscle contraction in C. elegans. This is the first study to show that the conserved RyR domain of the receptor acts in egg laying and embryogenesis. ------------------- Key: 6126 Medline: 14517331 Authors: Cohen M;Feinstein N;Wilson KL;Gruenbaum Y Title: Nuclear pore protein gp210 is essential for viability in HeLa cells and Caenorhabditis elegans. Citation: Molecular Biology of the Cell 14: 4230-4237 2003 Type: ARTICLE Genes: npp-12 Abstract: Gp210 is an evolutionarily conserved membrane protein of the nuclear pore complex (NPC). We studied the phenotypes produced by RNAi-induced downregulation of gp210 in both human (HeLa) cells and Caenorhabditis elegans embryos. HeLa cell viability requires Gp210 activity. The dying cells accumulated clustered NPCs and aberrant membrane structures at the nuclear envelope, suggesting that gp210 is required directly or indirectly for nuclear pore formation and dilation as well as the anchoring or structural integrity of mature NPCs. Essential roles for gp210 were confirmed in C. elegans, where RNAi-induced reduction of gp210 caused embryonic lethality. The nuclear envelopes of embryos with reduced gp210 also had aberrant nuclear membrane structures and clustered NPCs, confirming that gp210 plays critical roles at the nuclear membrane through mechanisms that are conserved from nematodes to humans. ------------------- Key: 6127 Medline: 14499607 Authors: Grisoni K;Gieseler K;Mariol MC;Martin E;Carre-Pierrat M;Moulder G;Barstead R;Segalat L Title: The stn-1 syntrophin gene of C. elegans is functionally related to dystrophin and dystrobrevin. Citation: Journal of Molecular Biology 332: 1037-1046 2003 Type: ARTICLE Genes: dyb-1 dys-1 egl-19 hlh-1 myo-3 stn-1 Abstract: Syntrophins are a family of PDZ domain-containing adaptor proteins required for receptor localization. Syntrophins are also associated with the dystrophin complex in muscles. We report here the molecular and functional characterization of the Caenorhabditis elegans gene stn-1 (F30A10.8), which encodes a syntrophin with homology to vertebrate alpha and beta-syntrophins. stn-1 is expressed in neurons and in muscles of C. elegans. stn-1 mutants resemble dystrophin (dys-1) and dystrobrevin (dyb-1) mutants: they are hyperactive, bend their heads when they move forward, tend to hypercontract, and are hypersensitive to the acetylcholinesterase inhibitor aldicarb. These phenotypes are suppressed when stn-1 is expressed under the control of a muscular promoter, indicating that they are caused by the absence of stn-1 in muscles. These results suggest that the role of syntrophin is linked to dystrophin function in C. elegans. ------------------- Key: 6128 Medline: 12871939 Authors: Kwasnicka DA;Krakowiak A;Thacker C;Brenner C;Vincent SR Title: Coordinate expression of NADPH-dependent flavin reductase, fre-1, and Hint-related 7meGMP-directed hydrolase, DCS-1. Citation: Journal of Biological Chemistry 278: 39051-39058 2003 Type: ARTICLE Genes: dcs-1 fre-1 Abstract: A novel human cytosolic flavin reductase, Nr1, was recently described that contains FMN, FAD, and NADPH cofactors. Though the targets of the related NADPH-dependent flavoprotein reductases, cytochrome P450 reductase, methionine synthase reductase, and nitric oxide synthase, are known, the cellular function of Nr1 is not clear. To explore expression and regulation of Nr1, we cloned fre-1, the Caenorhabditis elegans ortholog of Nr1, and discovered that it is transcribed as a bicistronic pre-mRNA together with dcs-1, the ortholog of the recently described scavenger mRNA decapping enzyme. We used the novel substrate, 7meGpppBODIPY, to demonstrate that DCS-1 has low micromolar specificity for guanine ribonucleotides with the 7me modification, whereas trimethylated G substrates are poor competitors. Contrary to earlier classification, DCS-1 is not a pyrophosphatase but a distant member of the Hint branch of the histidine triad superfamily of nucleotide hydrolases and transferases. These observations are consistent with the hypothesis that DCS-1 homologs may function in the metabolism of capped oligonucleotides generated following exosome-dependent degradation of short-lived mRNA transcripts. We find that fre-1 and dcs-1 are coordinately expressed through worm development, are induced by heat shock, and have a nearly identical expression profile in human tissues. Furthermore, immunocytochemical analysis of the endogenous proteins in COS cells indicates that both are present in the nucleus and concentrated in a distinct perinuclear structure. Though no connection between these enzymes had been anticipated, our data and data from global expression and protein association studies suggest that the two enzymes jointly participate in responses to DNA damage, heat shock, ------------------- Key: 6129 Medline: 12975612 Authors: Berninsone PM:Hirschberg CB Title: The nematode Caenorhabditis elegans as a model to study the roles of proteoglycans. Citation: Glycoconjugate Journal 19: 325-330 2003 Type: REVIEW Genes: hse-5 hst-1 hst-2 hst-3 hst-6 rib-1 rib-2 sqv-2 sqv-3 sqv-6 sqv-7 sqv-8 Abstract: The nematode Caenorhabditis elegans is a powerful animal model for exploring the genetic basis of metazoan development. Recent genetic and biochemical studies have revealed that the molecular machinery of glycosaminoglycan (GAG) biosynthesis and modification is highly conserved between C. elegans and mammals. In addition, genetic studies have implicated GAGs in vulval morphogenesis and zygotic cytokinesis. The extensive knowledge of C. elegans biology, including its elucidated cell lineage, together with the completed and well annotated DNA sequence and availability of reverse genetic tools, provide a platform for studying the functions of proteoglycans and their GAG ------------------- Key: 6130 Medline: 14504223 Authors: Zhu G;L'Hernault SW Title: The Caenorhabditis elegans spe-39 gene is required for intracellular membrane reorganization during spermatogenesis. Citation: Genetics 165: 145-157 2003 Type: ARTICLE Genes: dpy-11 spe-39 nDf18 nDf32 sDf20 sDf35 Abstract: Caenorhabditis elegans spermatid formation involves asymmetric partitioning of cytoplasm during the second meiotic division. This process is mediated by specialized ER/Golgi-derived fibrous body-membra-nous organelles (FB-MOs), which have a fibrous body (FB) composed of bundled major sperm protein filaments and a vesicular membranous organelle (MO). spe-39 mutant spermatocytes complete meiosis but do not usually form spermatids. Ultrastructural examination of spe-39 spermatocytes reveals that MOs are absent, while FBs are disorganized and not surrounded by the membrane envelope usually observed in wild type. Instead, spe-39 spermatocytes contain many small vesicles with internal membranes, suggesting they are related to MOs. The spe-39 gene was identified and it encodes a novel hydrophilic protein. Immunofluorescence with a specific SPE-39 antiserum reveals that it is distributed through much of the cytoplasm and not specifically associated with FB-MOs in spermatocytes and spermatids. The spe-39 gene has orthologs in Drosophila melanogaster and humans but no homolog was identified in the yeast genome. This suggests that the specialized membrane biogenesis steps that occur during C. elegans spermatogenesis are part of a conserved process that requires SPE-39 homologs in other metazoan cell types. ------------------- Key: 6131 Medline: 12954481 Authors: Houthoofd K;Braeckman BP;Johnson TE;Vanfleteren JR Title: Life extension via dietary restriction is independent of the Ins/IGF-1 signalling pathway in Caenorhabditis elegans. Citation: Experimental Gerontology 38: 947-954 2003 Type: ARTICLE Genes: daf-2 daf-12 daf-16 eat-2 Abstract: Dietary restriction (DR) increases life span in a wide variety of animals. In Caenorhabditis elegans both reduced bacterial concentration (BDR) and culture on non-bacterial, semi-defined, axenic food sources (ADR) increased longevity. An Ins/IGF-1-like (IIF) signalling pathway has been shown to specify life span in C. elegans and it has been suggested that this IIF signalling pathway mediates life extension via DR. We show that both ADR and BDR act independently with mutations in the IIF pathway to increase longevity, stress resistance, and specific activities of superoxide dismutase and catalase. Moreover, these effects are not dependent on daf-16, which is known to suppress other mutations that act through the IIF pathway. We conclude that DR extends life span by mechanisms distinct from those specified by the IIF pathway. ------------------- Key: 6132 Medline: 14521838 Authors: Keating CD;Kriek N;Daniels M;Ashcroft NR;Hopper NA;Siney EJ;Holden-Dye L;Burke JF Title: Whole-genome analysis of 60 G protein-coupled receptors in Caenorhabditis elegans by gene knockout with RNAi. Citation: Current Biology 13: 1715-1720 2003 Type: ARTICLE Genes: rrf-3 Abstract: G protein-coupled receptors (GPCRs) are the largest family of genes in animal genomes and represent more than 2% of genes in humans and C. elegans. These evolutionarily conserved seven-transmembrane proteins transduce a diverse range of signals. In view of their pivotal role in cell signaling, it is perhaps surprising that decades of genetic analysis in C. elegans, and recent genome-wide RNAi screens, have identified very few GPCR mutants [1, 2]. Therefore, we screened all GPCRs predicted to bind either small-molecule neurotransmitters or neuropeptides by using RNAi and quantitative behavioral assays. This shows that C16D6.2, C25G6.5, C26F1.6, F35G8.1, F41E7.3, and F59C12.2 are likely to be involved in reproduction, whereas C15B12.5, C10C6.2, C24A8.4, F15A8.5, F59D12.1, T02E9.1, and T05A1.1 have a role in locomotion. Gene deletions for F35G8.1 and T05A1.1 resulted in the same phenotype as that seen with RNAi. As some GPCRs may be resistant to RNAi, or may result in abnormalities not screened for here, the actual proportion of nonredundant receptors with an assayable function is probably greater. Strikingly, most phenotypes were observed for NPY-like receptors that may bind neuropeptides. This is consistent with the known actions of neuropeptides on the body wall muscle and ------------------- Key: 6133 Medline: 14516364 Authors: Muller-Reichert T;Hohenberg H;O'Toole ET;McDonald K Title: Cryoimmobilization and three-dimensional visualization of C. elegans ultrastructure. Citation: Journal of Microscopy 212: 71-80 2003 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans is one of the most important genetic systems used in current biological research. Increasingly, these genetics-based research projects are including ultrastructural analyses in their attempts to understand the molecular basis for cell function. Here, we present and review state-of-the-art methods for both ultrastructural analysis and immunogold localization in C. elegans. For the initial cryofixation, high-pressure freezing is the method of choice, and in this article we describe two different strategies to prepare these nematode worms for rapid freezing. The first method takes advantage of transparent, porous cellulose capillary tubes to contain the worms, and the second packs the worms in E. coli and/or yeast paste prior to freezing. The latter method facilitates embedding of C. elegans in a thin layer of resin so individual worms can be staged, selected and precisely orientated for serial sectioning followed by immunolabelling or electron tomography. ------------------- Key: 6134 Medline: 14516929 Authors: Kirkwood TBL Title: Genes that shape the course of ageing. Citation: Trends in Endocrinology and Metabolism 14: 345-347 2003 Type: REVIEW Genes: daf-2 daf-16 Abstract: Recent discoveries have placed the insulin signalling pathways at the heart of the genetic control of longevity. An elegant new study of genes acting downstream of these signals in the nematode worm Caenorhabditis elegans reveals a plethora of information about the complex network of mechanisms that modulate the ageing process. ------------------- Key: 6135 Medline: 14534247 Authors: de la Cruz IP;Levin JZ;Cummins C;Anderson P;Horvitz HR Title: sup-9, sup-10, and unc-93 may encode components of a two-pore K+ channel that coordinates muscle contraction in Caenorhabditis elegans. Citation: Journal of Neuroscience 23: 9133-9145 2003 Type: ARTICLE Genes: sup-5 sup-9 sup-10 sup-18 unc-93 Abstract: Genetic studies of sup-9, unc-93, and sup-10 strongly suggest that these genes encode components of a multi-subunit protein complex that coordinates muscle contraction in Caenorhabditis elegans. We cloned sup-9 and sup-10 and found that they encode a two-pore K+ channel and a novel transmembrane protein, respectively. We also found that UNC-93 and SUP-10 colocalize with SUP-9 within muscle cells, and that UNC-93 is a member of a novel multigene family that is conserved among C. elegans, Drosophila, and humans. Our results indicate that SUP-9 and perhaps other two-pore K+ channels function as multiprotein complexes, and that UNC-93 and SUP-10 likely define new classes of ion channel regulatory proteins. ------------------- Key: 6136 Medline: 14529613 Authors: Hwang SB;Lee J Title: Neuron cell type-specific SNAP-25 expression driven by multiple regulatory elements in the nematode Caenorhabditis elegans. Citation: Journal of Molecular Biology 333: 237-247 2003 Type: ARTICLE Genes: mec-3 unc-86 unc-104 Abstract: In order to characterize the mechanisms regulating neuronal expression of the nematode SNAP-25 gene, we identified the SNAP-25 genes of Caenorhabditis elegans and Caenorhabditis briggsae. Comparative sequence analysis and reporter assays revealed two putative 5' regulatory elements, P1 and P2, and four elements, I1h, I1m, I2h, and I2m, in the first intron. Nuclear extracts contained activities that bound the P2 and I1h elements. Different elements were required for SNAP-25 expression in different neuronal subsets; P1 was required in DA and DD motor neurons, and I1m and I2m were required in DB and DA neurons, respectively. P2 was active in amphid and phasmid neurons, I1h in pharyngeal neurons, and I2h in touch receptor neurons. The I2h element contained a putative binding site for transcription factor UNC-86. Both UNC-86 and MEC-3 were required for I2h activity in the mechanosensory neurons: in these neurons, GFP expression driven by I2h was abolished in animals bearing either an unc-86 null or a mec-3 null mutation, or an unc-86 mutation that leads to defective interaction with MEC-3. Deletion of the MEC-3 binding site also abolished the GFP expression. Gel mobility-shift assay results suggest that transcriptional regulation of SNAP-25 may involve multiple transcription factors. ------------------- Key: 6137 Medline: 14529618 Authors: Karabinos A;Schulze E;Schunemann J;Parry DAD;Weber K Title: In vivo and in vitro evidence that the four essential intermediate filament (IF) proteins A1, A2, A3 and B1 of the nematode Caenorhabditis elegans form an obligate heteropolymeric IF system. Citation: Journal of Molecular Biology 333: 307-319 2003 Type: ARTICLE Genes: Abstract: The in vitro polymerization and tissue-specific expression patterns of the four essential intermediate filament (IF) proteins (A1, A2, A3, B1) and the non-essential IF protein A4 were analyzed. Recombinant B1, used as a probe in blot overlay assays of the 11 Caenorhabditis elegans IF proteins, reacted strongly with proteins A1 to A4, indicating a heterotypic interaction. Obligate heteropolymeric filament assembly in vitro was confirmed by electron microscopy. Protein B1 formed long IF when mixed with an equimolar amount of A1, A2 or A3. Developmentally regulated coexpression of 131 and one or more members of the A family was found with GFP-promoter reporters. This coexpression pattern argues for a heteropolymer system in vivo. One or both splice variants of the B1 gene are always coexpressed in a tissue-specific manner with at least one member of the A family in hypodermis, pharynx, pharyngeal-intestinal valve, excretory cells, uterus, vulva and rectum. Interestingly, while the intestine normally lacks a B1/A pair, the dauer larva shows intestinal B1 and A4. These results are in line with similar postembryonic phenotypes of the hypodermis induced by RNA interference (RNAi) of genes B1, A2 and A3. Similarly, defects of the pharynx and its A1-GFP containing tonofilaments observed in the postembryonic B1 RNAi phenotype are consistent with the coexpression of B1 and A1 in the marginal cells. Thus RNAi analyses provide independent evidence for the existence of the B1/A obligate heteropolymer system in vivo. Proteins A1 and B1 have a similar and rather slow turnover rate in photobleaching experiments of the pharynx tonofilaments. ------------------- Key: 6138 Medline: Authors: Artal-Sanz M;Tsang WY;Willems EM;Grivell LA;Lemire BD;van der Spek H;Nijtmans LGJ Title: The mitochondrial prohibitin complex is essential for embryonic viability and germline function in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 278: 40416- 2003 Type: CORRECT Genes: Abstract: Dr. Artal-Sanz's name was incorrectly listed. The corrected version is shown above. ------------------- Key: 6139 Medline: 13678634 Authors: Yates DM;Portillo V;Wolstenholme AJ Title: The avermectin receptors of Haemonchus contortus and Caenorhabditis elegans. Citation: International Journal for Parasitology 33: 1183-1193 2003 Type: ARTICLE Genes: avr-14 avr-15 gbr-2 glc-1 glc-2 glc-3 glc-4 Abstract: Most of the recent evidence suggests that the avermectin/milbemycin family of anthelmintics act via specific interactions with glutamate-gated chloride channels. These channels are encoded by a small family of genes in nematodes, though the composition of the gene family and the function of the individual members of the family may vary between species. We review our current knowledge concerning the properties of the glutamate-gated chloride channels from Caenorhabditis elegans and the related parasite, Haemonchus contortus. We conclude that the biological effects of the avermectins/milbemycins can be largely explained by the known pharmacology and distribution of the glutamate-gated chloride channels and that differences between the glutamate-gated chloride channels from different nematodes may underlie species-specific variations in anthelmintic action. ------------------- Key: 6140 Medline: 13678635 Authors: Pellerone FI;Archer SK;Behm CA;Grant WN;Lacey MJ;Somerville AC Title: Trehalose metabolism genes in Caenorhabditis elegans and filarial nematodes. Citation: International Journal for Parasitology 33: 1195-1206 2003 Type: REVIEW Genes: rrf-3 tre-1 tre-2 tre-3 tre-4 tre-5 tps-1 tps-2 Abstract: The sugar trehalose is claimed to be important in the physiology of nematodes where it may function in sugar transport, energy storage and protection against environmental stresses. In this study we investigated the role of trehalose metabolism in nematodes, using Caenorhabditis elegans as a model, and also identified complementary DNA clones putatively encoding genes involved in trehalose pathways in filarial nematodes. In C. elegans two putative trehalose-6-phosphate synthase (tps) genes encode the enzymes that catalyse trehalose synthesis and five putative trehalase (tre) genes encode enzymes catalysing hydrolysis of the sugar. We showed by RT-PCR or Northern analysis that each of these genes is expressed as mRNA at all stages of the C. elegans life cycle. Database searches and sequencing of expressed sequence tag clones revealed that at least one tps gene and two tre genes are expressed in the filarial nematode Brugia malayi, while one tps gene and at least one tre gene were identified for Onchocerca volvulus. We used the feeding method of RNA interference in C. elegans to knock down temporarily the expression of each of the tps and tre genes. Semiquantitative RT-PCR analysis confirmed that expression of each gene was silenced by RNA interference. We did not observe an obvious phenotype for any of the genes silenced individually but gas-chromatographic analysis showed >90% decline in trehalose levels when both tps genes were targeted simultaneously. This decline in trehalose content did not affect viability or development of the nematodes. ------------------- Key: 6141 Medline: Authors: Navarrete-Vazquez G;Yepez L;Hernandez-Campos A;Tapia A;Hernandez-Luis F;Cedillo R;Gonzalez J;Martinez-Fernandez A;Martinez-Grueiro M;Castillo R Title: Synthesis and antiparasitic activity of albendazole and mebendazole analogues. Citation: Bioorganic & Medicinal Chemistry 11: 4615-4622 2003 Type: ARTICLE Genes: Abstract: Albendazole (Abz) and Mebendazole (Mbz) analogues have been synthesized and in vitro tested against the protozoa Giardia lamblia, Trichomonas vaginalis and the helminths Trichinella spiralis and Caenorhabditis elegans. Results indicate that compounds 4a, 4b (Abz analogues), 12b and 20 (Mbz analogues) are as active as antiprotozoal agents as Metronidazole against G. lamblia. Compound 9 was 58 times more active than Abz against T. vaginalis. Compounds 8 and 4a also shown high activity against this protozoan. Compounds 4b and 5a were as active as Abz. None of the Mbz analogues showed activity against T. vaginalis. The anthelmintic activity presented by these compounds was ------------------- Key: 6142 Medline: 14522947 Authors: Desai A;Rybina S;Muller-Reichert T;Shevchenko A;Shevchenko A;Hyman A;Oegema K Title: KNL-1 directs assembly of the microtubule-binding interface of the kinetochore in C. elegans. Citation: Genes & Development 17: 2421-2435 2003 Type: ARTICLE Genes: cls-2 hcp-1 hcp-2 hcp-3 him-10 klp-19 knl-1 ndc-80 smc-4 Abstract: Segregation of the replicated genome during cell division requires kinetochores, mechanochemical organelles that assemble on mitotic chromosomes to connect them to spindle microtubules. CENP-A, a histone H3 variant, and CENP-C, a conserved structural protein, form the DNA-proximal foundation for kinetochore assembly. Using RNA interference-based genomics in Caenorhabditis elegans, we identified KNL-1, a novel kinetochore protein whose depletion, like that of CeCENP-A or CeCENP-C, leads to a "kinetochore-null" phenotype. KNL-1 is downstream of CeCENP-A and CeCENP-C in a linear assembly hierarchy. In embryonic extracts, KNL-1 exhibits substoichiometric interactions with CeCENP-C and forms a near-stoichiometric complex with CeNDC-80 and HIM-10, the C. elegans homologs of Ndc80p/HEC1p and Nuf2p-two widely conserved outer kinetochore components. However, CeNDC-80 and HIM-10 are not functionally equivalent to KNL-1 because their inhibition, although preventing formation of a mechanically stable kinetochore-microtubule interface and causing chromosome missegregation, does not result in a kinetochore-null phenotype. The greater functional importance of KNL-1 may be due to its requirement for targeting multiple components of the outer kinetochore, including CeNDC-80 and HIM-10. Thus, KNL-1 plays a central role in translating the initiation of kinetochore assembly by CeCENP-A and CeCENP-C into the formation of a functional ------------------- Key: 6143 Medline: Authors: Boyd WA;Williams PL Title: Comparison of the sensitivity of three nematode species to copper and their utility in aquatic and soil toxicity Citation: Environmental Toxicology & Chemistry 22: 2768-2774 2003 Type: ARTICLE Genes: Abstract: Nematodes are useful organisms for aquatic and soil toxicity testing because of their abundance and diversity as well as their ease of culturing and maintenance in the laboratory. The nematode Caenorhabditis elegans has been used extensively in toxicity testing, but its sensitivity to metal exposures in relation to other nematodes remains unclear. In this study, we compare the sensitivity and ease of use of two other rhabditid nematodes, Panagrellus redivivus and Pristionchus pacificus, to C. elegans. Toxicity endpoints were chosen to investigate the effects of Cu on the survival of these nematodes after soil exposures and on the survival, reproduction, movement, and feeding behavior of nematodes after exposures in aquatic medium. In all lethality testing, P. pacificus was the most sensitive, C elegans exhibited intermediate sensitivity, and P. redivivus was the least sensitive. Reproduction and movement of C. elegans and reproduction of P. pacificus were decreased 50% by similar concentrations of Cu (EC50s similar to2 mg/L), but P. pacificus movement was less sensitive to Cu exposures (EC50 = 8 mg/L). Although all nematodes may be useful in lethality assays, using P. redivivus in toxicity tests is complicated by the presence of two sexes and difficulties in obtaining age-synchronized cultures. Pristionchus pacificus is an ideal acute toxicity-testing organism because of its sensitivity and ease of culturing. However, C. elegans appears to be more sensitive and therefore most useful in behavioral assays. Future studies of the relative sensitivities of nematodes in toxicity testing should continue to investigate additional toxicants, nematode species, and quantifications of sublethal effects after soil exposures. ------------------- Key: 6146 Medline: 14536063 Authors: Lanjuin A;VanHoven MK;Bargmann CI;Thompson JK;Sengupta P Title: Otx/otd homeobox genes specify distinct sensory neuron identities in C. elegans. Citation: Developmental Cell 4: 621-633 2003 Type: ARTICLE Genes: ceh-36 ceh-37 flp-6 gcy-5 gcy-7 gcy-8 lim-4 lim-6 odr-1 osm-6 str-1 str-2 ttx-1 Abstract: The mechanisms by which the diverse functional identities of neurons are generated are poorly understood. C. elegans responds to thermal and chemical stimuli using 12 types of sensory neurons. The Otx/otd homolog ttK-1 specifies the identities of the AFD thermosensory neurons. We show here that ceh-36 and ceh-37, the remaining two Otx-like genes in the C. elegans genome, specify the identities of AWC, ASE, and AWB chemosensory neurons, defining a role for this gene family in sensory neuron specification. All C. elegans OtK genes and rat Otx1 can substitute for ceh-37 and ceh-36, but only ceh-37 functionally substitutes for ttx-1. Functional substitution in the AWB neurons is mediated by activation of the same downstream target lim-4 by different Otx genes. Misexpression experiments indicate that although the specific identity adopted upon expression of an Otx gene may be constrained by the cellular context, individual Otx genes preferentially promote distinct neuronal ------------------- Key: 6147 Medline: 12844540 Authors: Lithgow GJ Title: Does anti-aging equal anti-microbial? Citation: Science of Aging Knowledge Environment 25: PE16- 2003 Type: REVIEW Genes: age-1 daf-2 dbl-1 Abstract: Aging is the dominant risk factor for human disease in developed countries. Could it be that a wide variety of disease states all have their origins in a common mechanism? Major signaling pathways that determine the rate of aging, such as the insulin/insulin-like growth factor 1 (IGF-1) pathway, might give clues to the nature of this major disease risk factor. It has now been shown that insulin/IGF-1 signaling influences Caenorhabditis elegans resistance to bacteria in such a way that long-lived worms are stress-resistant and slow to succumb to infection. Perhaps enhanced innate immunity is a feature of genetically determined longevity. ------------------- Key: 6148 Medline: 12844535 Authors: Larsen PL Title: Direct and indirect transcriptional targets of DAF-16. Citation: Science of Aging Knowledge Environment 17: PE9- 2003 Type: REVIEW Genes: daf-2 daf-16 hsp-90 scl-1 Abstract: Several genes involved in the determination of life span have been identified by mutation in the free-living soil nematode Caenorhabditis elegans. One of the key pathways studied in the context of life span is the DAF-2 pathway. The daf-2 gene is homologous to the insulin and insulin-like growth factor 1 receptor families. A downstream gene, daf-16, encodes a protein that is homologous to the forkhead transcription factor. A study by McElwee, Bubb, and Thomas, published in the current issue of Aging Cell, used genome-scale gene expression analysis to search for genes that are differentially expressed between long-lived daf-2(e1370) and short-lived daf-16(m27);daf-2(e1370) animals. In doing so, they identified candidate direct and indirect targets of DAF-16. In this Perspective, I discuss the results of this study. ------------------- Key: 6149 Medline: 14522875 Authors: Piekny AJ;Johnson JLF;Cham GD;Mains PE Title: The Caenorhabditis elegans nonmuscle myosin genes nmy-1 and nmy-2 function as redundant components of the let-502/Rho-binding kinase and mel-11/myosin phosphatase pathway during embryonic morphogenesi Citation: Development 130: 5695-5704 2003 Type: ARTICLE Genes: hmp-1 hmp-2 hmr-1 let-502 mel-11 mlc-4 nmy-1 nmy-2 rde-2 sma-1 spc-1 Abstract: Rho-binding kinase and the myosin phosphatase targeting subunit regulate nonmuscle contractile events in higher eukaryotes. Genetic evidence indicates that the C elegans homologs regulate embryonic morphogenesis by controlling the actin-mediated epidermal cell shape changes that transform the spherical embryo into a long, thin worm. LET-502/Rho-binding kinase triggers elongation while MEL-11/myosin phosphatase targeting subunit inhibits this contractile event. We describe mutations in the nonmuscle myosin heavy chain gene nmy-1 that were isolated as suppressors of the mel-11 hypercontraction phenotype. However, a nmy-1 null allele displays elongation defects less severe than mutations in let-502 or in the single nonmuscle myosin light chain gene mlc-4. This results because nmy-1 is partially redundant with another nonmuscle myosin heavy chain, nmy-2, which was previously known only for its role in anterior/posterior polarity and cytokinesis in the early embryo. At the onset of elongation, NMY-1 forms filamentous-like structures similar to actin, and LET-502 is interspersed with these structures, where it may trigger contraction. MEL-11, which inhibits elongation, is initially cytoplasmic. In response to LET-502 activity, MEL-11 becomes sequestered away from the contractile apparatus, to the plasma membrane, when elongation commences. Upon completion of morphogenesis, MEL-11 again appears in the cytoplasm where it may halt actin/myosin ------------------- Key: 6150 Medline: 12941269 Authors: Jungnickel MK;Sutton KA;Florman HM Title: In the beginning: lessons from fertilization in mice and worms. Citation: Cell 114: 401-404 2003 Type: REVIEW Genes: Abstract: Sexual reproduction proceeds by fertilization; formation of new individuals by the union of haploid gametes. Recent reports in Cell and in Developmental Cell may provide new insights as to how this process begins and is regulated. ------------------- Key: 6151 Medline: Authors: Fedorov A;Roy S;Fedorova L;Gilbert W Title: Mystery of intron gain. Citation: Genome Research 13: 2236-2241 2003 Type: ARTICLE Genes: Abstract: For nearly 15 years, it has been widely believed that many introns were recently acquired by the genes of multicellular organisms. However, the mechanism Of acquisition has yet to be described for a single animal intron. Here, we report a large-scale computational analysis of the human, Drosophila melanogaster, Caenorhabditis elegans, and Arabidopsis thaliana genomes. We divided 147,796 human intron sequences into batches of similar lengths and aligned them with each other. Different types of homologies between introns were found, but none showed evidence of simple intron transposition. Also, 106,902 plant, 39,624 Drosophila, and 6021 C elegans introns were examined. No single case of homologous introns in nonhomologous genes was detected. Thus, we found no example of transposition of introns in the last 50 million years in humans, in 3 million years in Drosophila and C elegans, or in 5 million years in Arabidopsis. Either new introns do not arise via transposition of other introns or intron transposition must have occurred so early in evolution that all traces of homology have been lost. ------------------- Key: 6152 Medline: 14509658 Authors: Caldwell GA;Cao S;Gelwix CC;Sexton EG;Caldwell KA Title: An animal model to discern torsin function: suppression of protein aggregation in C. elegans. Citation: Advances in Neurology 94: 79-85 2004 Type: ARTICLE Genes: ooc-5 tor-1 tor-2 Abstract: Dystonia is a movement disorder characterized by sustained muscle contractions that frequently cause twisting or repetitive movements or abnormal postures. Oppenheim's dystonia, the most severe early-onset form of this disorder, is transmitted in an autosomal-dominant manner with reduced penetrance (30% to 40%) and has been linked to specific deletions in the human DYT1 (TOR1A) gene that encodes a protein of unknown function termed torsin A. These breakthroughs have established the groundwork for subsequent investigation of the cellular mechanisms responsible for dystonia using the comparative genomics of ------------------- Key: 6153 Medline: 14576426 Authors: Arantes-Oliveira N;Berman JR;Kenyon C Title: Healthy animals with extreme longevity. Citation: Science 302: 611- 2003 Type: ARTICLE Genes: daf-2 Abstract: In the nematode Caenorhabditis elegans, mutations that inhibit insulin/IGF-1 (insulin-like growth factor 1) signaling, such as daf-2 insulin/IGF-1 receptor mutation, can double the life-span of the animal. Removing the germ-line precursor cells also extends life-span by approximately 60%. This life-span extension is not a result of sterility; it appears to be due to altered endocrine signaling. Removal of the germ line or the entire reproductive system of daf-2 mutants can further extend life-span: these animals can live four times as long as normal. ------------------- Key: 6154 Medline: Authors: Borgonie G;Link CD;Claeys M;Coomans A Title: Lysosomal and pseudocoelom routing protects Caenorhabditis elegans from ricin toxicity. Citation: Nematology 5: 339-350 2003 Type: ARTICLE Genes: Abstract: The resistance of the nematode Caenorhabditis elegans towards the highly potent toxin ricin has been studied. Incubation of C. elegans in ricin did not affect life span or progeny production. However, micro-injection of the ricin A-chain into the distal, syncitial gonad caused degeneration and sterility in test specimens, confirming that C. elegans ribosomes are sensitive. Using transmission electron microscopy, it was observed that ricin is effectively internalised into the intestinal cells. When pre-labelled with gold, the toxin reached only the lysosomes. When native toxin was used, the toxin was either routed to the lysosomes or underwent transcytosis to the pseudocoelomatic cavity and incorporation into embryos. None of the ricin reached either the trans Golgi network or the Golgi apparatus, considered essential for toxicity. The observed oral non-toxicity is therefore due to alternate sorting of the toxin, a mechanism not previously observed. The data indicate that, although ricin can opportunistically bind to, and be internalised by, cell surface receptors, these receptors are not sufficient to ------------------- Key: 6155 Medline: 12893826 Authors: Hihi AK;Kebir H;Hekimi S Title: Sensitivity of Caenorhabditis elegans clk-1 mutants to ubiquinone side-chain length reveals multiple ubiquinone-dependent processes. Citation: Journal of Biological Chemistry 278: 41013-41018 2003 Type: ARTICLE Genes: clk-1 daf-2 isp-1 Abstract: Ubiquinone ( coenzyme Q, or Q) is a membrane constituent, whose head group is capable of accepting and donating electrons and whose lipidic side chain is composed of a variable number of isoprene subunits. A possible role for Q as a dietary antioxidant for treating conditions that involve altered cellular redox states is being intensely studied. Mutations in the clk-1 gene of the nematode Caenorhabditis elegans affect numerous physiological rates including behavioral rates, developmental rates, reproduction, and life span. clk-1 encodes a protein associated with the inner mitochondrial membrane that is necessary for Q biosynthesis in C. elegans. clk-1 mutants do not synthesize Q but accumulate demethoxyubiquinone, a Q synthesis intermediate that is able to partially sustain mitochondrial respiration in worms as well as in mammals. Recently, we and others have found that exogenous Q is necessary for the fertility and development of clk-1 mutants. Here, we take advantage of the clk-1 genetic model to identify structural features of Q that are functionally important in vivo. We show that clk-1 mutants are exquisitely sensitive to the length of the side chain of the Q they consume. We also identified differential sensitivity to Q side-chain length between null alleles of clk-1 (qm30 and qm51) and the weaker allele e2519. This allows us to propose a model where we distinguish several types of Q-dependent processes in vivo: processes that are very sensitive to Q side-chain length and processes that are permissive to Q with shorter chains. ------------------- Key: 6156 Medline: 12937167 Authors: Kubiak TM;Larsen MJ;Zantello MR;Bowman JW;Nulf SC;Lowery DE Title: Functional annotation of the putative orphan Caenorhabditis elegans G-protein-coupled receptor C10C6.2 as a FLP15 peptide receptor. Citation: Journal of Biological Chemistry 278: 42115-42120 2003 Type: ARTICLE Genes: flp-15 Abstract: This report describes the cloning and functional annotation of a Caenorhabditis elegans orphan G-protein-coupled receptor (GPCR) (C10C6.2) as a receptor for the FMRFamide-related peptides (FaRPs) encoded on the flp15 precursor gene, leading to the receptor designation FLP15-R. A cDNA encoding C10C6.2 was obtained using PCR techniques, confirmed identical to the Worm-pep-predicted sequence, and cloned into a vector appropriate for eucaryotic expression. A [S-35]guanosine 5'-O-(thiotriphosphate) (GTPgammaS) assay with membranes prepared from Chinese hamster ovary (CHO) cells transiently transfected with FLP15-R was used as a read-out for receptor activation. FLP15-R was activated by putative FLP15 peptides, GGPQGPLRF-NH2 (FLP15-1), RG-PSGPLRF-NH2 (FLP15-2A), its des-Arg(1) counterpart, GPSGPLRF-NH2 (FLP15-2B), and to a lesser extent, by a tobacco hornworm Manduca sexta FaRP, GNSFLRF-NH2 (F7G) (potency ranking FLP15-2A > FLP15-1 > FLP15-2B >> F7G). FLP15-R activation was abolished in the transfected cells pretreated with pertussis toxin, suggesting a preferential receptor coupling to G(i)/G(o) proteins. The functional expression of FLP15-R in mammalian cells was temperature-dependent. Either no stimulation or significantly lower ligand-evoked [S-35]GTPgammaS binding was observed in membranes prepared from transfected FLP15-R/CHO cells cultured at 37 degreesC. However, a 37 to 28 degreesC temperature shift implemented 24 h post-transfection consistently resulted in an improved activation signal and was essential for detectable functional expression of FLP15-R in CHO cells. To our knowledge, the FLP15 receptor is only the second deorphanized C. elegans neuropeptide GPCR reported to date. ------------------- Key: 6157 Medline: 14550409 Authors: Shin TH;Mello CC Title: Chromatin regulation during C. elegans germline Citation: Current Opinion in Genetics & Development 13: 455-462 2003 Type: REVIEW Genes: hda-1 let-418 mep-1 mes-2 mes-3 mes-4 mes-6 nos-2 pie-1 skn-1 Abstract: Recent studies in Caenorhabditis elegans implicate PcG- and NuRD-like chromatin regulators in the establishment and maintenance of germline-soma distinctions. Somatic cells appear to utilize NuRD-related nucleosome-remodeling factors to overwrite germline-specific chromatin states that are specified through PcG-like activities. The germline, in turn, may rely on an asymmetrically inherited inhibitor to prevent chromatin reorganization that would otherwise erase pluripotency. ------------------- Key: 6158 Medline: 12913116 Authors: Goedert M Title: Neurodegenerative tauopathy in the worm. Citation: Proceedings of the National Academy of Sciences USA 100: 9653-9655 2003 Type: REVIEW Genes: Abstract: The most common neurodegenerative diseases are characterized by the presence of abnormal filamentous protein inclusions in nerve cells of the brain. In Alzheimer's disease, these inclusions are made of hyperphosphorylated tau protein. Together with the extracellular beta-amyloid deposits, they consitute the defining neuropathological characteristics of Alzheimer's disease. Tau inclusions, in the absence of extracellular deposits, are characteristic of progressive supranuclear palsy, corticobasal degeneration, Pick's disease, argyrophilic grain disease, and frontotemporal dementia and parkinsonism linked to chromosome 17. The identification of mutations in Tau in FTDP-17 has established that dysfunction of tau protein is central to the neurodegenerative process. At an experimental level, the expression of mutant human tau in nerve cells is leading to improved models of neurodegeneration. In this issue of PNAS, Kraemer et al. describe lines of Caenorhabditis elegans expressing transgenic wild-type and mutant human tau protein. They represent an important addition to ------------------- Key: 6159 Medline: 14573539 Authors: Rose JK;Kaun KR;Chen SH;Rankin CH Title: GLR-1, a non-NMDA glutamate receptor homolog, is critical for long-term memory in Caenorhabditis elegans. Citation: Journal of Neuroscience 23: 9595-9599 2003 Type: ARTICLE Genes: glr-1 mec-7 snb-1 Abstract: Long-term memory for habituation to tap in Caenorhabditis elegans depends on glr-1, a homolog of mammalian non-NMDA glutamate receptors; mutations in glr-1 blocked long-term memory formation. Green fluorescent protein (GFP) constructs were used to visualize glr-1 expression in the interneurons of the mechanosensory circuit and synaptobrevin in the tap sensory neurons of trained and untrained worms. Trained animals had less GLR-1::GFP expression than untrained animals; there was no difference in the vesicle marker synaptobrevin. Heat shock during training blocked both the behavioral expression of long-term memory and the change in GLR-1::GFP expression. Thus, long-term memory in C. elegans is dependent on glr-1 and likely involves changes in the expression or ------------------- Key: 6160 Medline: 14550624 Authors: Chiang SH;MacDougald OA Title: Will fatty worms help cure human obesity? Citation: Trends in Genetics 19: 523-525 2003 Type: REVIEW Genes: fat-7 Abstract: The incidence of obesity has reached epidemic proportions within industrial societies; however, research on human obesity has been hampered by our inability to control genetic and environmental factors. The control of energy homeostasis appears to be conserved among species. Recent creative research in Caenorhabditis elegans, including the application of a genome-wide RNA interference analysis, has provided insight into the genes involved in energy balance. In this article, we discuss the results of these studies and their potential importance to humans. ------------------- Key: 6161 Medline: Authors: Ge H;Walhout AJM;Vidal M Title: Integrating 'omic' information: a bridge between genomics and systems biology. Citation: Trends in Genetics 19: 551-560 2003 Type: ARTICLE Genes: Abstract: The availability of genome sequences for several organisms, including humans, and the resulting first-approximation lists of genes, have allowed a transition from molecular biology to 'modular biology'. In modular biology, biological processes of interest, or modules, are studied as complex systems of functionally interacting macromolecules. Functional genomic and proteomic ('omic') approaches can be helpful to accelerate the identification of the genes and gene products involved in particular modules, and to describe the functional relationships between them. However, the data emerging from individual omic approaches should be viewed with caution because of the occurrence of false-negative and false-positive results and because single annotations are not sufficient for an understanding of gene function. To increase the reliability of gene function annotation, multiple independent datasets need to be integrated. Here, we review the recent development of strategies for such integration and we argue that these will be important for a systems approach to ------------------- Key: 6162 Medline: 14574563 Authors: Fonseca-Salamanca F;Martinez-Grueiro MM;Martinez-Fernandez AR Title: Nematocidal activity of nitazoxanide in laboratory models. Citation: Parasitology Research 91: 321-324 2003 Type: ARTICLE Genes: Abstract: The nematocidal activity of a broad-spectrum antiparasitic agent, nitazoxanide [( N -(5-nitrothiazol-2-gammal)salicylamide; NTZ], was evaluated in both in vitro and in vivo models using Caenorhabditis elegans, Heligmosomoides polygyrus and Trichinella spiralis. In vitro, NTZ (100 muM) exhibited a low activity against C. elegans and had no effect on embryonation and hatching of H. polygyrus eggs. At concentrations of 100 and 50 muM, the inhibition of excretion/secretion of acetylcholinesterase and acid phosphatase of adult H. polygyrus by NTZ was variable. The in vitro effects of mebendazole (5 muM), albendazole (1 muM) and levamisole (10 muM) were superior to those of NTZ. In mice, NTZ at 1 g/kg proved to be inactive against preadults of T. spiralis whereas mebendazole at 10 mg/kg reduced the worm burden by up to 83%. NTZ at 1 g/kg per day for 3 consecutive days showed a low activity against adults of H. polygyrus (21% reduction). Levamisole, at a single dose of 10 mg/kg, reduced the worm burden by up to 89.9%. The results of this study suggest that NTZ would not have met criteria of a ------------------- Key: 6163 Medline: 14560015 Authors: Wang F;Yoder J;Antoshechkin I;Han M Title: Caenorhabditis elegans EVL-14/PDS-5 and SCC-3 are essential for sister chromatid cohesion in meiosis and mitosis. Citation: Molecular and Cellular Biology 23: 7698-7707 2003 Type: ARTICLE Genes: evl-14 rec-8 scc-3 spo-11 Abstract: Sister chromatid cohesion is fundamental for the faithful transmission of chromosomes during both meiosis and mitosis. Proteins involved in this process are highly conserved from yeasts to humans. In screenings for sterile animals with abnormal vulval morphology, mutations in the Caenorhabditis elegans evl-14 and scc-3 genes were isolated. Defects in cell divisions were observed in germ line as well as in vulval and somatic gonad lineages. Through positional cloning of these genes, we have shown that EVL-14 and SCC-3 are likely the only C. elegans homologs of the yeast sister chromatid cohesion proteins Pds5 and Scc3, respectively. Both evl-14 and scc-3 mutants displayed defects in the meiotic germ line. In evl-14 mutants, synaptonemal complexes (SCs) were detectable but more than the usual six DAPI (4',6'-diamidino-2-phenylindole)-positive structures were seen at diakinesis, suggesting that EVL-14/PDS-5 is important for the maintenance of sister chromatid cohesion in late prophase. In scc-3 mutant animals, normal SCs were not visible and similar to24 DAPI-positive structures were seen at diakinesis, indicating that SCC-3 is necessary for sister chromatid cohesion. Immunostaining revealed that localization of REC-8, a homolog of the yeast meiotic cohesin subunit Rec8, to the chromosomes depends on the presence of SCC-3 but not that of EVL-14/PDS-5. scc-3 RNA interference (RNAi)-treated embryos were 100% lethal and displayed defects in cell divisions. evl-14 RNAi caused a range of phenotypes. These results indicate that EVL-14/PDS-5 and SCC-3 have functions in both mitosis and ------------------- Key: 6164 Medline: 12917438 Authors: Morais VA;Crystal AS;Pijak DS;Carlin D;Costa J;Lee VMY;Doms RW Title: The transmembrane domain region of nicastrin mediates direct interactions with APH-1 and the gamma-secretase Citation: Journal of Biological Chemistry 278: 43284-43291 2003 Type: ARTICLE Genes: aph-1 Abstract: Nicastrin (NCT) is a type I integral membrane protein that is one of the four essential components of the gamma-secretase complex, a protein assembly that catalyzes the intramembranous cleavage of the amyloid precursor protein and Notch. Other gamma-secretase components include presenilin-1 (PS1), APH-1, and PEN-2, all of which span the membrane multiple times. The mechanism by which NCT associates with the gamma-secretase complex and regulates its activity is unclear. To avoid the misfolding phenotype often associated with introducing deletions or mutations into heavily glycosylated and disulfide-bonded proteins such as NCT, we produced chimeras between human (hNCT) and Caenorhabditis elegans NCT (ceNCT). Although ceNCT did not associate with human gamma-secretase components, all of the ceNCT/hNCT chimeras interacted with gamma-secretase components from human, C. elegans, or both, indicating that they folded correctly. A region at the C-terminal end of hNCT, encompassing the last 50 residues of its ectodomain, the transmembrane domain, and the cytoplasmic domain was important for mediating interactions with human PS1, APH-1, and PEN-2. This finding is consistent with the fact that the bulk of the gamma-secretase complex proteins resides within the membrane, with relatively small extramembranous domains. Finally, hNCT associated with hAPH-1 in the absence of PS, consistent with NCT and APH-1 forming a subcomplex prior to association with PS1 and PEN-2 and indicating that the interactions between NCT with PS1 may be indirect or stabilized by the presence of APH-1. ------------------- Key: 6165 Medline: 12930831 Authors: Brooks DR;Hooper NM;Isaac RE Title: The Caenorhabditis elegans orthologue of mammalian puromycin-sensitive aminopeptidase has roles in embryogenesis and reproduction. Citation: Journal of Biological Chemistry 278: 42795-42801 2003 Type: ARTICLE Genes: pam-1 rrf-3 Abstract: Mammals possess membrane-associated and cytosolic forms of the puromycin-sensitive aminopeptidase (PSA; EC 3.4.11.14). Increasing evidence suggests the membrane PSA is involved in neuromodulation within the central nervous system and in reproductive biology. The functional roles of the cytosolic PSA are less clear. The genome of the nematode Caenorhabditis elegans encodes an aminopeptidase, F49E8.3 (PAM-1), that is orthologous to PSA, and sequence analysis predicts it to be cytosolic. We have determined the spatio/temporal gene expression pattern of pam-1 by using the promoter region of F49E8.3 to control expression in the nematode of a second exon translational fusion of the aminopeptidase to green fluorescent protein. Cytosolic fluorescence was observed throughout development in the intestine and nerve cells of the head. Neuronal expression was also observed in the tail of adult males. Recombinant PAM-1, expressed and purified from Escherichia coli, hydrolyzed the N-terminal amino acid from peptide substrates. Favored substrates had positively charged or small neutral amino acids in the N-terminal position. Peptide hydrolysis was inhibited by the metal-chelating agent 1,10-phenanthroline and by the aminopeptidase inhibitors actinonin, amastatin, and leuhistin. However, the enzyme was similar to 100-fold less sensitive toward puromycin (IC50, 135 muM) than other PSA homologues. Following inactivation of the enzyme, aminopeptidase activity was recovered with Zn2+, Co2+, and Ni2+. Silencing expression of pam-1 by RNA interference resulted in 30% embryonic lethality. Surviving adult hermaphrodites deposited large numbers of oocytes throughout the self-fertile period. The overall brood size was, however, unaffected. We conclude that pam-1 encodes an aminopeptidase that clusters phylogenetically with the PSAs, despite attenuated sensitivity toward puromycin, and that it functions in embryo development and reproduction of the nematode. ------------------- Key: 6166 Medline: Authors: Tajima T;Takiguchi N;Kato J;Ikeda T;Kuroda A;Ohtake H Title: Mutants of the nematode Caenorhabditis elegans that are defective specifically in their attraction to Citation: Journal of Bioscience & Bioengineering 96: 149-153 2003 Type: ARTICLE Genes: che-2 che-3 che-5 che-7 che-10 odr-1 odr-3 odr-10 osm-3 osm-5 osm-9 tax-2 tax-4 tax-6 Abstract: The nematode Caenorhabditis elegans exhibits chemotaxis toward a wide variety of chemicals including water-soluble molecules and volatile organic compounds. We have previously discovered that C elegans wild-type strain N2 is strongly attracted by cycloheximide which has long been known as a bitter tastant for humans and other mammals. We describe here the isolation and initial characterization of the first mutants which were defective specifically in their attraction to cycloheximide. In our screenings, we selected two mutants that were defective in chemotaxis to cycloheximide but normal in their attraction to NH4Cl and histidine. These mutants also avoided quinine hydrochloride, CuSO4, and high concentrations of NaCl similar to the wild-type strain N2. Furthermore, no observable defect was detected in their attraction to volatile odorants such as isoamyl alcohol and diacetyl. Dye-filling experiments suggested that they have no morphological defect in the sensory endings of the amphid ------------------- Key: 6167 Medline: Authors: Karabinos A;Schulze E;Schunamen J;Parry DAD;Weber K Title: Automatic classification and clustering of Caenorhabditis elegans using a computer vision system. Citation: Lect N Comp 2690: 751-755 2003 Type: ARTICLE Genes: Abstract: ------------------- Key: 6168 Medline: Authors: Shimada H;Tominaga N;Kohra S;Ishibashi H;Mitsui Y;Ura K;Arizono K Title: Metallothionein gene expression in the larvae of Caenorhabditis elegans is a potential biomarker for cadmium and mercury. Citation: Trace Elements and Electrolytes 20: 240-243 2003 Type: ARTICLE Genes: Abstract: Previously, we reported that the induction of vitellogenin mRNA in the larvae of Caenorhabditis elegans (C. elegans) can be used as a biomarker for short-term screening of environmental endocrine disrupters. Therefore, the present study was designed to determine if the induction of metallothionein (MT) mRNA in the larvae of C. elegans would be a biomarker for short-term screening of heavy metals. The larvae were exposed to various concentrations of cadmium (Cd), mercury (Hg), zinc chloride (Zn), cupper chloride (Cu) or lead acetate (Pb) for 2h. Cd (1, 10 and 100 uM) and Hg (0.01, 0.1, 1 and 10 uM) exposures resulted in the marked induction of MT-I and MT-II mRNAs in the larvae of C. elegans as measured by reverse transcription polymerase chain reaction. The Cd and Hg induction of MT-II was higher than that of MT-I mRNA, and concentration-dependent increase was observed in MT-II but not in MT-I. Time course analysis for MT-I and MT-II expressions with Cd and Hg were also determined. Cd induction of MT-I and MT-II mRNAs reached a peak at 2 h after the exposure (10 uM), and the levels of MT-II were higher than that of MT-I. For Hg, an initial peak of induction of MT-II mRNA occurred 15 minutes after the exposure (0.1 uM), and the levels reached maximum by 2 h. The initial peak of induction of MT-I mRNA occurred much later (about 2 h after Hg exposure) than MT-II mRNA. These results indicate that the induction of MT-II mRNA in the larvae of C. elegans can be used as a potential biomarker ------------------- Key: 6169 Medline: 14605367 Authors: Nystul TG;Goldmark JP;Padilla PA;Roth MB Title: Suspended animation in C. elegans requires the spindle checkpoint. Citation: Science 302: 1038-1041 2003 Type: ARTICLE Genes: mdf-2 san-1 Abstract: In response to environmental signals such as anoxia, many organisms enter a state of suspended animation, an extreme form of quiescence in which microscopically visible movement ceases. We have identified a gene, san-1, that is required for suspended animation in Caenorhabditis elegans embryos. We show that san-1 functions as a spindle checkpoint component in C. elegans. During anoxia-induced suspended animation, embryos lacking functional SAN-1 or a second spindle checkpoint component, MDF-2, failed to arrest the cell cycle, exhibited chromosome missegregation, and showed reduced viability. These data provide a model for how a dynamic biological process is arrested in suspended animation. ------------------- Key: 6170 Medline: 14605370 Authors: Prahlad V;Pilgrim D;Goodwin EB Title: Roles for mating and environment in C. elegans sex determination. Citation: Science 302: 1046-1049 2003 Type: ARTICLE Genes: Abstract: In Caenorhabditis elegans the two sexes, hermaphrodites and males, are thought to be irreversibly determined at fertilization by the ratio of X chromosomes to sets of autosomes: XX embryos develop as hermaphrodites and XO embryos as males. We show instead that both sex and genotype of C. elegans can be altered postembryonically and that this. exibility requires sexual reproduction. When grown in specific bacterial metabolites, some XX larvae generated by mating males and hermaphrodites develop as males and lose one X chromosome. However, XX larvae produced by hermaphrodite self-fertilization show no such changes. We propose that sexual reproduction increases developmental. exibility of progeny, allowing for better adaptation to changing environments. ------------------- Key: 6171 Medline: 14583748 Authors: Potter CJ;Luo L Title: Food for thought: a receptor finds its ligand. Citation: Nature Neuroscience 6: 1119-1120 2003 Type: REVIEW Genes: flp-18 flp-21 npr-1 Abstract: In C. elegans, social and solitary feeding behavior can be determined by a single amino acid change in a G protein-coupled receptor. A new study identifies ligands for this receptor and suggests how changes in behavior evolve at the molecular level. ------------------- Key: 6172 Medline: 14583749 Authors: Goaillard JM;Marder E Title: Exciting guts with GABA. Citation: Nature Neuroscience 6: 1121-1122 2003 Type: REVIEW Genes: exp-1 unc-49 Abstract: A new study in this issue demonstrates that two GABAergic motor neurons in C. elegans are excitatory at target muscles because GABA activates a ligand-gated cation conductance, which is structurally similar to several other ligand-gated channels. ------------------- Key: 6173 Medline: 14555952 Authors: Beg AA;Jorgensen EM Title: EXP-1 is an excitatory GABA-gated cation channel. Citation: Nature Neuroscience 6: 1145-1152 2003 Type: ARTICLE Genes: exp-1 unc-49 Abstract: gamma-aminobutyric acid (GABA) mediates fast inhibitory neurotransmission by activating anion-selective ligand-gated ion channels. Although electrophysiological studies indicate that GABA may activate cation-selective ligand-gated ion channels in some cell types, such a channel has never been characterized at the molecular level. Here we show that GABA mediates enteric muscle contraction in the nematode Caenorhabditis elegans via the EXP-1 receptor, a cation-selective ligand-gated ion channel. The EXP-1 protein resembles ionotropic GABA receptor subunits in almost all domains. In the pore-forming domain of EXP-1, however, the residues that confer anion selectivity are exchanged for those that specify cation selectivity. When expressed in Xenopus laevis oocytes, EXP-1 forms a GABA receptor that is permeable to cations and not anions. We conclude that some of the excitatory functions assigned to GABA are mediated ------------------- Key: 6174 Medline: 14555955 Authors: Rogers C;Reale V;Kim K;Chatwin H;Li C;Evans P;de Bono M Title: Inhibition of Caenorhabditis elegans social feeding FMRFamide-related peptide activation of NPR-1. Citation: Nature Neuroscience 6: 1178-1185 2003 Type: ARTICLE Genes: flp-18 flp-21 npr-1 Abstract: Social and solitary feeding in natural Caenorhabditis elegans isolates are associated with two alleles of the orphan G-protein-coupled receptor (GPCR) NPR-1: social feeders contain NPR-1 215F, whereas solitary feeders contain NPR-1 215V. Here we identify FMRFamide-related neuropeptides (FaRPs) encoded by the flp-18 and flp-21 genes as NPR-1 ligands and show that these peptides can differentially activate the NPR-1 215F and NPR-1 215V receptors. Multicopy overexpression of flp-21 transformed wild social animals into solitary feeders. Conversely, a flp-21 deletion partially phenocopied the npr-1(null) phenotype, which is consistent with NPR-1 activation by FLP-21 in vivo but also implicates other ligands for NPR-1. Phylogenetic studies indicate that the dominant npr-1 215V allele likely arose from an ancestral npr-1 215F gene in C. elegans. Our data suggest a model in which solitary feeding evolved in an ancestral social strain of C. elegans by a gain-of-function mutation that modified the response of NPR-1 to FLP-18 and FLP-21 ligands. ------------------- Key: 6175 Medline: 14528312 Authors: Furukawa M;He YJ;Borchers C;Xiong Y Title: Targeting of protein ubiquitination by BTB-Cullin 3-Roc1 ubiquitin ligases. Citation: Nature Cell Biology 5: 1001-1007 2003 Type: ARTICLE Genes: mei-1 mei-2 mel-26 Abstract: The concentrations and functions of many cellular proteins are regulated by the ubiquitin pathway. Cullin family proteins bind with the RING-finger protein Roc1 to recruit the ubiquitin-conjugating enzyme (E2) to the ubiquitin ligase complex (E3). Cul1 and Cul7, but not other cullins, bind to an adaptor protein, Skp1. Cul1 associates with one of many F-box proteins through Skp1 to assemble various SCF-Roc1 E3 ligases that each selectively ubiquitinate one or more specific substrates. Here, we show that Cul3, but not other cullins, binds directly to multiple BTB domains through a conserved amino-terminal domain. In vitro, Cul3 promoted ubiquitination of Caenorhabditis elegans MEI-1, a katanin-like protein whose degradation requires the function of both Cul3 and BTB protein MEL-26. We suggest that in vivo there exists a potentially large number of BCR3 (BTB-Cul3-Roc1) E3 ubiquitin ligases. ------------------- Key: 6176 Medline: 14580339 Authors: Poyurovsky MV;Jacq X;Ma C;Karni-Schmidt O;Parker PJ;Chalfie M;Manley JL;Prives C Title: Nucleotide binding by the MDM2 RING domain facilitates Arf-independent MDM2 nucleolar localization. Citation: Molecular Cell 12: 875-887 2003 Type: ARTICLE Genes: Abstract: The RING domain of Mdm2 contains a conserved Walker A or P loop motif that is a characteristic of nucleotide binding proteins. We found that Mdm2 binds adenine-containing nucleotides preferentially and that nucleotide binding leads to a conformational change in the Mdm2 C terminus. Although nucleotide binding is not required for Mdm2 E3 ubiquitin ligase activity, we show that nucleotide binding-defective P loop mutants are impaired in p14(ARF)-independent nucleolar localization both in vivo and in vitro. Consistent with this, ATP-bound Mdm2 is preferentially localized to the nucleolus. Indeed, we identify a unique amino acid substitution in the P loop motif (K454A) that uncouples nucleolar localization and E3 ubiquitin ligase activity of Mdm2 and leads to upregulation of the E3 activity both in human cells and in Caenorhabditis elegans. We propose that nucleotide binding-facilitated nucleolar localization of Mdm2 is an evolutionarily conserved regulator of Mdm2 activity. ------------------- Key: 6177 Medline: 14573470 Authors: Church DL;Lambie EJ Title: The promotion of gonadal cell divisions by the Caenorhabditis elegans TRPM cation channel GON-2 is antagonized by GEM-4 copine. Citation: Genetics 165: 563-574 2003 Type: ARTICLE Genes: gem-4 gon-2 sDf7 sDf8 Abstract: The initiation of postembryonic cell divisions by the gonadal precursors of C. elegans requires the activity of gon-2. gon-2 encodes a predicted cation channel (GON-2) of the TRPM subfamily of TRP proteins and is likely to mediate the influx of Ca2+ and/or Mg2+. We report here that mutations in gem-4 (gon-2 extragenic modifier) are capable of suppressing loss-of-function alleles of gon-2. gem-4 encodes a member of the copine family of Ca2+-dependent phosphatidylserine binding proteins. Overall, our data indicate that GEM-4 antagonizes GON-2. This antagonism could be mediated by a direct inhibition of GON-2 by GEM-4, since both proteins are predicted to be localized to the plasma membrane. Alternatively, GEM-4 could affect GON-2 activity levels by either promoting endocytosis or inhibiting exocytosis of vesicles that carry GON-2. It is also possible that GEM-4 and GON-2 act in parallel to each other. Mutation of gem-4 does not suppress the gonadal defects produced by inactivation of gon-4, suggesting that gon-4 either acts downstream of gem-4 and gon-2 or acts in a parallel regulatory pathway. ------------------- Key: 6178 Medline: 14573471 Authors: Fukushige T;Goszczynski B;Tian H;McGhee JD Title: The evolutionary duplication and probable demise of an endodermal GATA factor in Caenorhabditis elegans. Citation: Genetics 165: 575-588 2003 Type: ARTICLE Genes: elt-2 elt-3 elt-4 ges-1 hsp-70 Abstract: We describe the elt-4 gene from the nematode Caenorhabditis elegans. elt-4 is predicted to encode a very small (72 residues, 8.1 kD) GATA-type zinc finger transcription factor. The elt-4 gene is located similar to5 kb upstream of the C. elegans elt-2 gene, which also encodes a GATA-type transcription factor; the zinc finger DNA-binding domains are highly conserved (24/25 residues) between the two proteins. The elt-2 gene is expressed only in the intestine and is essential for normal intestinal development. This article explores whether elt-4 also has a role in intestinal development. Reporter fusions to the elt-4 promoter or reporter insertions into the elt-4 coding regions show that elt-4 is indeed expressed in the intestine, beginning at the 1.5-fold stage of embryogenesis and continuing into adulthood. elt-4 reporter fusions are also expressed in nine cells of the posterior pharynx. Ectopic expression of elt-4 cDNA within the embryo does not cause detectable ectopic expression of biochemical markers of gut differentiation; furthermore, ectopic elt-4 expression neither inhibits nor enhances the ectopic marker expression caused by ectopic elt-2 expression. A deletion allele of elt-4 was isolated but no obvious phenotype could be detected, either in the grit or elsewhere; brood sizes, hatching efficiencies, and growth rates were indistinguishable from wild type. We found no evidence that elt-4 provided backup functions for elt-2. We used microarray analysis to search for genes that might be differentially expressed between L1 larvae of the elt-4 deletion strain and wild-type worms. Paired hybridizations were repeated seven times, allowing us to conclude, with some confidence, that no candidate target transcript could be identified as significantly up- or downregulated by loss of elt-4 function. In vitro binding experiments could not detect specific binding of ELT-4 protein to candidate binding sites (double-stranded oligonucleotides containing single or multiple WGATAR sequences); ELT-4 protein neither enhanced nor inhibited the strong sequence-specific binding of the ELT-2 protein. Whereas ELT-2 protein is a strong transcriptional activator in yeast, ELT-4 protein has no such activity tinder similar conditions, nor does it influence the transcriptional activity of coexpressed ELT-2 protein. Although an elt-2 homolog was easily identified in the genomic sequence of the related nematode C. briggsae, no elt-4 homolog could be identified. Analysis of the changes in silent third codon positions within the DNA-binding domains indicates that elt-4 arose as a duplication of (elt-2, some 25-55 MYA. Thus, elt-4 has survived far longer than the average duplicated gene in C. elegans, even though no obvious biological function Could be detected. elt-4 provides an interesting example of a tandemly duplicated gene that may originally have been the same size as elt-2 but has gradually been whittled down to its present size of little more than a zinc finger. Although elt-4 must confer (or must have conferred) some selective advantage to C. elegans, we suggest that its ------------------- Key: 6179 Medline: 14573472 Authors: Peters AD;Halligan DL;Whitlock MC;Keightley PD Title: Dominance and overdominance of mildly deleterious induced mutations for fitness traits in Caenorhabditis elegans. Citation: Genetics 165: 589-599 2003 Type: ARTICLE Genes: Abstract: We estimated the average dominance coefficient of mildly deleterious mutations ((h) over bar, the proportion by which mutations in the heterozygous state reduce fitness components relative to those in the homozygous state) in the nematode Coenorhabditis elegans. From 56 worm lines that carry mutations induced by the point mutagen ethyl methanesulfonate (EMS), we selected 19 lines that are relatively high in fitness and estimated the viabilities, productivities, and relative fitnesses of heterozygotes and homozyotes compared to the ancestral wild type. There was very little effect of homozygous or heterozygous mutations on egg-to-adult viability. For productivity and relative fitness, we found that the average dominance coefficient, (h) over bar, was similar to0.1, Suggesting that mildly deleterious mutations are on average partially recessive. These estimates were not significantly different from zero (complete recessivity) but were significantly different from 0.5 (additivity). In addition, there was a significant amount of variation in (h) over bar among lines, and analysis of average dominance coefficients of individual lines suggested that several lines showed overdominance for fitness. Further investigation of two of these lines partially confirmed this finding. ------------------- Key: 6180 Medline: 14568548 Authors: Tsalik EL;Niacaris T;Wenick AS;Pau K;Avery L;Hobert O Title: LIM homeobox gene-dependent expression of biogenic amine receptors in restricted regions of the C. elegans nervous system. Citation: Developmental Biology 263: 81-102 2003 Type: ARTICLE Genes: ceh-10 ceh-23 dop-1 dop-2 glr-1 hen-1 kal-1 lim-4 lim-6 lin-11 mec-3 ser-1 ser-2 ser-4 sra-11 unc-17 unc-25 unc-47 zig-5 Abstract: Biogenic amines regulate a variety of behaviors. Their functions are predominantly mediated through G-protein-coupled 7-transmembrane domain receptors (GPCR), 16 of which are predicted to exist in the genome sequence of the nematode Caenorhabditis elegans. We describe here the expression pattern of several of these aminergic receptors, including two serotonin receptors (ser-1 and ser-4), one tyramine receptor (ser-2), and two dopamine receptors (dop-1 and dop-2). Moreover, we describe distinct but partially overlapping expression patterns of different splice forms of the ser-2 tyramine receptor locus. We find that each of the aminergic receptor genes is expressed in restricted regions of the nervous system and that many of them reveal significant overlap with the expression of regulatory factors of the LIM homeobox (Lhx) gene family. We demonstrate that the expression of several of the biogenic amine receptors is abrogated in specific cell types in Lhx gene mutants, thus establishing a role for these Lhx genes in regulating aspects of neurotransmission. We extend these findings with other cell fate markers and show that the lim-4 Lhx gene is required for several but not all aspects of RID motor neuron differentiation and that the lim-6 Lhx gene is required for specific aspects of RIS interneuron differentiation. We also use aminergic receptor gfp reporter fusions as tools to visualize the anatomy of specific neurons in Lhx mutant backgrounds and find that the development of the elaborate dendritic branching pattern of the PVD harsh touch sensory neuron requires the rnec-3 Lhx gene. Lastly, we analyze a mutant allele of the ser-2 tyramine receptor, a target of the ttx-3 Lhx gene in the AIY intemeuron class. ser-2 mutants display none of the defects previously shown to be ------------------- Key: 6181 Medline: 14614817 Authors: Han Z;Saam JR;Adams HP;Mango SE;Schumacher JM Title: The C. elegans tousled-like kinase (TLK-1) has an essential role in transcription. Citation: Current Biology 13: 1921-1929 2003 Type: ARTICLE Genes: air-2 cdk-7 elt-2 end-3 med-1 myo-2 pes-10 tlk-1 Abstract: Background: The Tousled kinases comprise an evolutionarily conserved family of proteins that have been previously implicated in chromatin remodeling, DNA replication, and DNA repair. Here, we used RNA mediated interference (RNAi) to determine the function of the C. elegans Tousled kinase (TLK-1) during embryonic development. Results: TLK-1-deficient embryos arrested with a phenotype reminiscent of embryos that are broadly defective in transcription, and the expression of several reporter genes was dramatically reduced in tlk-1(RNAi) embryos. Furthermore, posttranslational modifications of RNA polymerase II (RNAPII) and histone H3 that have been correlated with transcription elongation, phosphorylation of the RNAPII CTD at Serine 2, and methylation of histone H3 at Lysine 36 were found at significantly reduced levels in tlk-1(RNAi) embryos as compared to wild-type. Conclusions: These results reveal a surprising requirement for a Tousled-like kinase in transcriptional regulation during development, likely during the elongation phase. In addition, our results confirm that the link between RNAPII phosphorylation and histone H3 methylation previously observed in budding yeast is functionally conserved in metazoans. ------------------- Key: 6182 Medline: 12888112 Authors: Carroll PM;Dougherty B;Ross-Macdonald P;Browman K;FitzGerald K Title: Model systems in drug discovery: chemical genetics meets genomics. Citation: Pharmacology & Therapeutics 99: 183-220 2003 Type: REVIEW Genes: glp-1 hop-1 lin-12 sel-12 Abstract: Animal model systems are an intricate part of the discovery and development of new medicines. The sequencing of not only the human genome but also those of the various pathogenic bacteria, the nematode Caenorhabditis elegans, the fruitfly Drosophila, and the mouse has enabled the discovery of new drug targets to push forward at an unprecedented pace. The knowledge and tools in these "model" systems are allowing researchers to carry out experiments more efficiently and are uncovering previously hidden biological connections. While the history of bacteria, yeast, and mice in drug discovery are long, their roles are ever evolving. In contrast, the history of Drosophila and C elegans at pharmaceutical companies is short. We will briefly review the historic role of each model organism in drug discovery and then update the readers as to the abilities and liabilities of each model within the context of drug development. ------------------- Key: 6183 Medline: 14576308 Authors: Zhang L;Luo L Title: Splice site prediction with quadratic discriminant analysis using diversity measure. Citation: Nucleic Acids Research 31: 6214-6220 2003 Type: ARTICLE Genes: Abstract: Based on the conservation of nucleotides at splicing sites and the features of base composition and base correlation around these sites we use the method of increment of diversity combined with quadratic discriminant analysis (IDQD) to study the dependence structure of splicing sites and predict the exons/introns and their boundaries for four model genomes: Caenorhabditis elegans, Arabidopsis thaliana, Drosophila melanogaster and human. The comparison of compositional features between two sequences and the comparison of base dependencies at adjacent or non-adjacent positions of two sequences can be integrated automatically in the increment of diversity (ID). Eight feature variables around a potential splice site are defined in terms of ID. They are integrated in a single formal framework given by IDQD. In our calculations 7 (8) base region around the donor (acceptor) sites have been considered in studying the conservation of nucleotides and sequences of 48 bp on either side of splice sites have been used in studying the compositional and base-correlating features. The windows are enlarged to 16 (donor), 29 (acceptor) and 80 bp (either side) to improve the prediction for human splice sites. The prediction capability of the present method is comparable with the leading splice site detector-GeneSplicer. ------------------- Key: 6184 Medline: 14529715 Authors: Grunwald ME;Kaplan JM Title: Mutations in the ligand-binding and pore domains control exit of glutamate receptors from the endoplasmic reticulum in C. elegans. Citation: Neuropharmacology 45: 768-776 2003 Type: ARTICLE Genes: eat-4 glr-1 unc-11 Abstract: The abundance of ion channels and neurotransmitter receptors in the plasma membrane is limited by the efficiency of protein folding and subunit assembly in the endoplasmic reticulum (ER). The ER has a quality-control system for monitoring nascent proteins, which prevents incompletely folded and assembled proteins from being transported from the ER. Chaperone proteins identify Unfolded and misassembled proteins in the ER via retention motifs that are normally buried at intersubunit contacts or via carbohydrate residues that are attached to misfolded domains. Here, we examined the trafficking of a C. elegalls non-NMDA glutamate receptor (GLR-1). We show that Mutations in the pore domain (predicted to block ion permeation) and mutations in the ligand-binding domain (predicted to block glutamate binding) both caused a dramatic reduction in the synaptic abundance of GLR1 and increased retention of GLR-1 in the ER. These results suggest that the structural integrity of the ligand-binding site and the pore domain of GLR-1 are monitored in the ER during the process of quality control. ------------------- Key: 6185 Medline: Authors: Araujo SJ;Tear G Title: Axon guidance mechanisms and molecules: lessons from invertebrates. Citation: Nature Reviews Neuroscience 4: 910-922 2003 Type: REVIEW Genes: ced-10 max-1 sax-3 seu-1 seu-2 seu-3 slt-1 unc-5 unc-6 unc-34 unc-40 unc-44 unc-71 unc-73 unc-115 unc-129 Abstract: Vertebrates and invertebrates share the formidable task of accurately establishing the elaborate connections that make up their nervous systems. Researchers investigating this process have the challenge of identifying the molecules and mechanisms that underlie this process. Each group of organisms offers their own advantages for piecing together the conserved constituents. Broadly speaking, the invertebrates have allowed the discovery of relevant genes through classical genetic screens for mutations that affect the process of axon guidance, whereas vertebrates provide numerous systems for the elaboration of the functional mechanisms. Here, we focus on the role of invertebrates in characterizing the molecular mechanisms of axon guidance. ------------------- Key: 6186 Medline: 12939266 Authors: Nehrke K Title: A reduction in intestinal cell pH(i) due to loss of the Caenorhabditis elegans Na+/H+ exchanger NHX-2 increases life span. Citation: Journal of Biological Chemistry 278: 44657-44666 2003 Type: ARTICLE Genes: nhx-2 opt-1 opt-2 opt-3 Abstract: Na+/H+ exchangers are involved in cell volume regulation, fluid secretion and absorption, and pH homeostasis. NHX-2 is a Caenorhabditis elegans Na+/H+ exchanger expressed exclusively at the apical membrane of intestinal epithelial cells. The inactivation of various intestinal nutrient transport proteins has been shown previously to influence aging via metabolic potential and a mechanism resembling caloric restriction. We report here a functional coupling of NHX-2 activity with nutrient uptake that results in long lived worms. Gene inactivation of nhx-2 by RNAi led to a loss of fat stores in the intestine and a 40% increase in longevity. The NHX-2 protein was coincidentally expressed with OPT-2, an oligopeptide transporter that is driven by a transmembrane proton gradient and that is also known to be involved in fat accumulation. Gene inactivation of opt-2 led to a phenotype resembling that of nhx-2, although not as severe. In order to explore this potential functional interaction, we combined RNA interference with a genetically encoded, fluorescence-based reagent to measure intestinal intracellular pH (pH(i)) in live worms under physiological conditions. Our results suggest first that OPT-2 is the main dipeptide uptake pathway in the nematode intestine, and second that dipeptide uptake results in intestinal cell acidification, and finally that recovery following dipeptide-induced acidification is normally a function of NHX-2. The loss of NHX-2 protein results in decreased steady-state intestinal cell pHi, and we hypothesize that this change perturbs proton-coupled nutrient uptake processes such as performed by OPT-2. Our data demonstrate a functional role for a Na+/H+ exchanger in nutrient absorption in vivo and lays the groundwork for examining integrated acid-base physiology in a non-mammalian model organism. ------------------- Key: 6187 Medline: 12930835 Authors: Strutz-Seebohm N;Werner M;Madsen DM;Seebohm G;Zheng Y;Walker CS;Maricq AV;Hollmann M Title: Functional analysis of Caenorhabditis elegans glutamate receptor subunits by domain transplantation. Citation: Journal of Biological Chemistry 278: 44691-44701 2003 Type: ARTICLE Genes: glr-1 glr-2 glr-3 glr-4 glr-5 glr-6 glr-7 glr-8 nmr-1 nmr-2 Abstract: Glutamate receptors are not only abundant and important mediators of fast excitatory synaptic transmission in vertebrates, but they also serve a similar function in invertebrates such as Drosophila and the nematode Caenorhabditis elegans. In C. elegans, an animal with only 302 neurons, 10 different glutamate receptor subunits have been identified and cloned. To study the ion channel properties of these receptor subunits, we recorded glutamate-gated currents from Xenopus oocytes that expressed either C. elegans glutamate receptor subunits or chimeric rat/C. elegans glutamate receptor subunits. The chimeras were constructed between the C. elegans glutamate receptor pore domains and either the rat kainate receptor subunit GluR6, the alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate ( AMPA) receptor subunit GluR1, or the N-methyl-D-aspartate ( NMDA) receptor subunit NMDAR1-1a. Although native subunits were nonfunctional, 9 of 10 ion pores were found to conduct current upon transplantation into rat receptor subunits. A provisional classification of the C. elegans glutamate receptor subunits was attempted based on functionality of the chimeras. C. elegans glutamate receptor ion pores, at a position homologous to a highly conserved site critical for ion permeation properties in vertebrate glutamate receptor pores, contain amino acids not found in vertebrate glutamate receptors. We show that the pore-constricting Q/R site, which in vertebrate receptors determines calcium permeability and rectification properties of the ion channel, in C. elegans can be occupied by other amino acids, including, surprisingly, lysine and proline, without ------------------- Key: 6188 Medline: 14525938 Authors: Strayer A;Wu Z;Christen Y;Link CD;Luo Y Title: Expression of the small heat-shock protein Hsp-16-2 in Caenorhabditis elegans is suppressed by Ginkgo biloba extract EGb 761. Citation: FASEB Journal : 2305-2307 2003 Type: ARTICLE Genes: hsp-16-2 Abstract: EGb 761, a standardized extract of Ginkgo biloba leaves, has been shown to have antioxidative properties. We have previously demonstrated that EGb 761 increases stress resistance and mean life span in the model organism Caenorhabditis elegans. In this study, the molecular mechanism of EGb 761 on alleviating effects of oxidative stress is further investigated using transgenic C. elegans expressing a jellyfish green fluorescent protein (GFP)-tagged inducible small heat-shock protein gene (hsp-16-2). The expression of hsp-16-2 induced by the pro-oxidant juglone and by heat shock was significantly suppressed by 86% and 33%, respectively, in the transgenic nematode fed with EGb 761. These effects of EGb 761 correlate with its ability to increase mean survival rate of the nematode in response to acute oxidative and thermal stresses, as well as to attenuate the basal levels of hydrogen peroxide in the organism. Thus, we interpret the suppression of hsp-16-2/GFP expression as an indication that EGb 761 decreases cellular stress resulting from exogenous treatments, therefore leading to a decreased transcriptional induction of the reporter transgene. These results support the hypothesis that EGb 761 augments the natural antistress system of C. elegans, thus increasing stress resistance and life span. ------------------- Key: 6189 Medline: 14578922 Authors: Legouis R;Jaulin-Bastard F;Schott S;Navarro C;Borg JP;Labouesse M Title: Basolateral targeting by leucine-rich repeat domains in epithelial cells. Citation: EMBO Reports 4: 1096-1102 2003 Type: ARTICLE Genes: let-413 Abstract: The asymmetric distribution of proteins to basolateral and apical membranes is an important feature of epithelial cell polarity. To investigate how basolateral LAP proteins (LRR (for leucine-rich repeats) and PDZ (for PSD-95/Discs-large/ZO-1), which play key roles in cell polarity, reach their target membrane, we carried out a structure - function study of three LAP proteins: Caenorhabditis elegans LET-413, human Erbin and human Scribble (hScrib). Deletion and point mutation analyses establish that their LRR domain is crucial for basolateral membrane targeting. This property is specific to the LRR domain of LAP proteins, as the non-LAP protein SUR-8 does not localize at the basolateral membrane of epithelial cells, despite having a closely related LRR domain. Importantly, functional studies of LET-413 in C. elegans show that although its PDZ domain is dispensable during embryogenesis, its LRR domain is essential. Our data establish a novel paradigm for protein localization by showing that a subset of LRR domains direct subcellular localization in polarized cells. ------------------- Key: 6190 Medline: 14568617 Authors: Sugahara K;Mikami T;Uyama T;Mizuguchi S;Nomura K;Kitagawa H Title: Recent advances in the structural biology of chondroitin sulfate and dermatan sulfate. Citation: Current Opinion in Structural Biology 13: 612-620 2003 Type: REVIEW Genes: rib-1 rib-2 sqv-1 sqv-2 sqv-3 sqv-4 sqv-5 sqv-6 sqv-7 sqv-8 Abstract: Recent glycobiology studies have suggested fundamental biological functions for chondroitin, chondroitin sulfate and dermatan sulfate, which are widely distributed as glycosaminoglycan sidechains of proteoglycans in the extracellular matrix and at cell surfaces. They have been implicated in the signaling functions of various heparin-binding growth factors and chemokines, and play critical roles in the development of the central nervous system. They also function as receptors for various pathogens. These functions are closely associated with the sulfation patterns of the glycosaminoglycan chains. Surprisingly, nonsulfated chondroitin is indispensable in the morphogenesis and cell division of Caenorhabditis elegans, as revealed by RNA interference experiments of the recently cloned chondroitin synthase gene and by the analysis of mutants of squashed vulva genes. ------------------- Key: 6191 Medline: Authors: van Veen JE;Hawley RS Title: Meiosis: when even two is a crowd. Citation: Current Biology 13: R831-R833 2003 Type: REVIEW Genes: Abstract: Recent studies in Caenorhabditis elegans show that crossover interference, which usually limits the number of exchanges per meiotic bivalent to just 'one', requires the continuity of both homologs. One 'function' of crossover interference may be the prevention of crossover events that might not effectively hold homologs together. ------------------- Key: 6192 Medline: 14588260 Authors: Spike CA;Strome S Title: Germ plasm: protein degradation in the soma. Citation: Current Biology 13: R837-R839 2003 Type: REVIEW Genes: cul-2 mbk-2 mex-1 mex-5 mex-6 par-1 pie-1 pos-1 zif-1 Abstract: Germ plasm is a specialized cytoplasm that is physically segregated to the germline cells during early embryogenesis. Recent results suggest that, in Caenorhabditis elegans, germ plasm is also prevented from accumulating in somatic lineages by a ubiquitin ligase that targets germ plasm proteins for degradation. ------------------- Key: 6193 Medline: 14588249 Authors: Shyn SI;Kerr R;Schafer WR Title: Serotonin and G(o) modulates functional states of neurons and muscles controlling C. elegans egg-laying behavior. Citation: Current Biology 13: 1910-1915 2003 Type: ARTICLE Genes: egl-19 egl-30 goa-1 gpa-1 gsa-7 gsa-14 unc-68 Abstract: From nematodes to humans, animals employ neuromodulators like serotonin to regulate behavioral patterns and states. In the nematode C. elegans, serotonin has been shown to act in a modulatory fashion to increase the rate and alter the temporal pattern of egg laying [1-4]. Though many candidate effectors and regulators of serotonin have been identified in genetic studies [5-16], their effects on specific neurons and muscles in the egg-laying circuitry have been difficult to determine. Using the genetically encoded Ca2+ indicator cameleon, we found that serotonin acts directly on the vulval muscles to increase the frequency of Ca2+ transients. In contrast, we found that the spontaneous activity of the egg-laying motorneurons was silenced by serotonin. Mutations in G protein a subunit genes altered the responses of both vulval muscles and egg-laying neurons to serotonin; specifically, mutations in the Gqalpha homolog egl-30 blocked serotonin stimulation of vulval muscle Ca2+ transients, while mutations in the G(o)alpha homolog goa-1 prevented the silencing of motorneuron activity by serotonin. These data indicate that serotonin stimulates egg laying by directly modulating the functional state of the vulval muscles. In addition, serotonin inhibits the activity of the motorneurons that release it, providing a feedback regulatory effect that may contribute to serotonin adaptation. ------------------- Key: 6194 Medline: Authors: Cuppen E;van der Linden AM;Jansen G;Plasterk RHA Title: Proteins interacting with Caenorhabditis elegans G(a) subunits. Citation: Comparative and Functional Genomics 4: 479-491 2003 Type: ARTICLE Genes: egl-30 goa-1 gpa-1 gpa-2 gpa-3 gpa-4 gpa-5 gpa-6 gpa-7 gpa-8 gpa-9 gpa-10 gpa-11 gpa-12 gpa-13 gpa-14 gpa-15 gpa-16 gpa-17 gsa-1 lin-8 lin-36 nhr-22 odr-3 rrf-3 Abstract: To identify novel components in heterotrimeric G-protein signaling, we performed an extensive screen for proteins interacting with Caenorhabditis elegans G-alpha subunits. The genome of C. elegans contains homologues of each of the four mammalian classes of G-alpha subunits (Gs, Gi/o, Gq and G12), and 17 other G-alpha subunits. We tested 19 of the G-alpha subunits and four constitutively activated G-alpha subunits in a large-scale yeast two-hybrid experiment. This resulted in the identification of 24 clones, representing 11 different proteins that interact with four different G-alpha subunits. This set includes C. elegans orthologues of known interactors of G-alpha subunits, such as AGS3 (LGN/PINS), CalNuc and Rap1Gap, but also novel proteins, including two members of the nuclear receptor super family and a homologue of human haspin (germ cell-specific kinase). All interactions were found to be unique for a specific G-alpha subunit but variable for the activation status of the G-alpha subunit. We used expression pattern and RNA interference analysis of the G-protein interactors in an attempt to substantiate the biological relevance of the observed interactions. Furthermore, by means of a membrane recruitment assay, we found evidence that GPA-7 and the nuclear receptor NHR-22 ------------------- Key: 6195 Medline: Authors: Choi BK;Chitwood DJ;Paik YK Title: Proteomic changes during disturbance of cholesterol metabolism by azacoprostane treatment in Caenorhabditis elegans. Citation: Molecular & Cellular Proteomics 2: 1086-1095 2003 Type: ARTICLE Genes: lrp-1 rme-2 vit-2 vit-6 Abstract: Although nematodes like Caenorhabditis elegans are incapable of the de novo cholesterol biosynthesis, they can utilize nonfunctional sterols by converting them into cholesterol and other sterols for cellular function. The results reported previously and presented here suggest that blocking of sterol conversion to cholesterol in C. elegans by 25-azacoprostane-HCL (azacoprostane) treatment causes a serious defect in germ cell development, growth, cuticle development, and motility behavior. To establish a biochemical basis for these physiological abnormalities, we performed proteomic analysis of mixed stage worms that had been treated with the drug. Our results from a differential display proteomic analysis revealed significant decreases in the levels of proteins involved in collagen and cytoskeleton organization such as protein disulfide isomerase (6.7-fold), beta-tubulin (5.41-fold), and NEX-1 protein (>30-fold). Also reduced were enzymes involved in energy production such as phosphoglycerate kinase (4.8-fold) and phosphoenolypyruvate carboxykinase (8.5-fold), a target for antifilarial drugs such as azacoprostane. In particular, reductions in the expression of lipoprotein familie4s such as vetellogenin-2 (7.7-fold) and vitellogenin-6 (5.4-fold) were prominent in the drug-treated worms, indicating that sterol metabolism disturbance caused by azacoprostane treatment is tightly coupled with suppression of the lipid transfer-related proteins at the protein level. However, competitive quantitative reverse transcriptase polymerase chain reaction showed that the transcriptional levels of vit-2, vit-6, and their receptors (e.g. rme-2 and lrp-1) in drug-treated worms were 3- to 5-fold higher than those in the untreated group, suggesting a presence of a sterol regulatory element-binding protein (SREBP)-like pathway in these genes. In fact, multiple predicted sterol regulatory elements or related regulatory sequences responding to sterols were found to be located at the 5'-flanking regions in vit-2 and lrp-1 genes, and their transcriptional activities fluctuated highly in response to changes in sterol concentration. Thus, many physiological abnormalities caused by azacoprostane-mediated sterol metabolism disturbance appear to be exerted at least in ------------------- Key: 6196 Medline: 14623435 Authors: Muller HAJ;Bossinger O Title: Molecular networks controlling epithelial cell polarity in development. Citation: Mechanisms of Development 120: 1231-1256 2003 Type: ARTICLE Genes: ajm-1 apr-1 cdc-42 ced-10 che-14 crb-1 crb-3 dlg-1 elt-2 elt-3 emb-9 end-1 end-3 epi-1 erm-1 ges-1 hmp-1 hmp-2 hmr-1 klp-18 lad-1 lam-3 let-2 let-413 let-502 lin-26 mel-11 mig-2 mlc-4 pak-1 par-1 par-2 par-3 par-6 pha-4 pkc-3 rac-1 rac-2 sdt-1 unc-73 zen-4 Abstract: During embryonic development, polarized epithelial cells are either formed during cleavage or formed from mesenchymal cells. Because the formation of epithelia during embryogenesis has to occur with high fidelity to ensure proper development, embryos allow a functional approach to study epithelial cell polarization in vivo. In particular, genetic model organisms have greatly advanced our understanding of the generation and maintenance of epithelial cell polarity. Many novel and important polarity genes have been identified and characterized in invertebrate systems, like Drosophila melanogaster and Caenorhabditis elegans. With the rapid identification of mammalian homologues of these invertebrate polarity genes, it has become clear that many important protein domains, single proteins and even entire protein complexes are evolutionarily conserved. It is to be expected that the field of epithelial cell polarity is just experiencing the 'top of the iceberg' of a large protein network that is fundamental for the specific adhesive, cell signalling and transport functions of epithelial cells. ------------------- Key: 6197 Medline: 12937278 Authors: Segbert C;Barkus R;Powers J;Strome S;Saxton WM;Bossinger O Title: KLP-18, a Klp2 kinesin, is required for assembly of acentrosomal meiotic spindles in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 14: 4458-4469 2003 Type: ARTICLE Genes: fem-2 fem-3 glp-4 klp-10 klp-18 rpp-1 Abstract: The proper segregation of chromosomes during meiosis or mitosis requires the assembly of well organized spindles. In many organisms, meiotic spindles lack centrosomes. The formation of such acentrosomal spindles seems to involve first assembly or capture of microtubules (MTs) in a random pattern around the meiotic chromosomes and then parallel bundling and bipolar organization by the action of MT motors and other proteins. Here, we describe the structure, distribution, and function of KLP-18, a Caenorhabditis elegans Klp2 kinesin. Previous reports of Klp2 kinesins agree that it concentrates in spindles, but do not provide a clear view of its function. During prometaphase, metaphase, and anaphase, KLP-18 concentrates toward the poles in both meiotic and mitotic spindles. Depletion of KLP-18 by RNA-mediated interference prevents parallel bundling/bipolar organization of the MTs that accumulate around female meiotic chromosomes. Hence, meiotic chromosome segregation fails, leading to haploid or aneuploid embryos. Subsequence assembly and function of centrosomal mitotic spindles is normal except when aberrant maternal chromatic is present. This suggests that althoughtKLP-18 is critical for organizing chromosomal-derived MTs into a parallel bipolar spindle, the order inherent in centrosome-derived astral MT arrays greatly reduces or eliminates the need for KLP-18 ------------------- Key: 6198 Medline: Authors: Castillo-Davis CI;Hartl DL Title: Conservation, relocation and duplication in genome evolution. Citation: Trends in Genetics 19: 593-597 2003 Type: REVIEW Genes: Abstract: The advent of whole-genome sequencing and genome-wide transcriptional profiling has opened up new approaches to the resolution of questions that only a few years ago seemed unanswerable. At the same time they have revealed new and sometimes unexpected patterns of gene conservation and functional compensation, chromosomal clustering of transcriptionally related genes, relocation of genes to depopulate or overpopulate the X chromosome with certain functional classes of genes, and gene duplication and functional divergence. What makes molecular evolutionary genomics different from previous approaches is the generality of the results. Choice of genes, and the uncertainties of extrapolating from a sample of genes to the entire genome, is supplanted by direct genome-wide observations. In this article we examine some key recent experiments in RNA interference that illustrate some of the strengths and limitations of evolutionary genomic analysis. ------------------- Key: 6199 Medline: 13129846 Authors: Nance J;Munro EM;Priess JR Title: C. elegans PAR-3 and PAR-6 are required for apicobasal asymmetries associated with cell adhesion and gastrulation. Citation: Development 130: 5339-5350 2003 Type: ARTICLE Genes: end-1 hmp-1 hmr-1 lad-1 nmy-1 nmy-2 par-1 par-2 par-3 par-6 pie-1 pkc-3 Abstract: PAR proteins distribute asymmetrically across the anterior-posterior axis of the 1-cell-stage C. elegans embryo, and function to establish subsequent anterior-posterior asymmetries. By the end of the 4-cell stage, anteriorly localized PAR proteins, such as PAR-3 and PAR-6, redistribute to the outer, apical Surfaces of cells, whereas posteriorly localized PAR proteins, such as PAR-1 and PAR-2, redistribute to the inner, basolateral surfaces. Because PAR proteins are provided maternally, distinguishing apicobasal from earlier anterior-posterior functions requires a method that selectively prevents PAR activity after the 1-cell stage. In the present study we generated hybrid PAR proteins that are targeted for degradation after the 1-cell stage. Embryos containing the hybrid PAR proteins had normal anterior-posterior polarity, but showed defects in apicobasal asymmetries associated with gastrulation. Ectopic separations appeared between lateral surfaces of cells that are normally tightly adherent, cells that ingress during gastrulation failed to accumulate nonmuscle myosin at their apical surfaces and ingression was slowed. Thus, PAR proteins function in both apicobasal and anterior-posterior asymmetry during the ------------------- Key: 6200 Medline: 14534142 Authors: Bergmann DC;Lee M;Robertson B;Tsou MFB;Rose LS;Wood WB Title: Embryonic handedness choice in C. elegans involves the G(alpha) protein GPA-16. Citation: Development 130: 5731-5740 2003 Type: ARTICLE Genes: emb-5 emb-8 emb-11 emb-12 emb-14 emb-18 emb-21 emb-26 emb-27 emb-34 gad-1 glp-1 gpa-16 let-99 par-2 par-3 par-4 par-6 spd-1 spd-2 spn-1 spn-2 spn-3 stu-10 stu-11 zyg-2 zyg-8 zyg-10 zyg-11 Abstract: The mechanism by which polarity of the left-right (LR) axis is initially established with the correct handedness is not understood for any embryo. C elegans embryos exhibit LR asymmetry with an invariant handedness that is first apparent at the six-cell stage and persists throughout development. We show here that a strong loss-of-function mutation in a gene originally designated spn-1 affects early spindle orientations and results in near randomization of handedness choice. This mutation interacts genetically with mutations in three par genes that encode localized cortical components. We show that the spn-1 gene encodes the Galpha protein GPA-16, which appears to be required for centrosomal association of a Gbeta protein. We will henceforth refer to this gene as gpa-16. These results demonstrate for the first time involvement of heterotrimeric G proteins in establishment of embryonic LR asymmetry and suggest how they might act. ------------------- Key: 6201 Medline: Authors: Ono S Title: Regulation of actin filament dynamics by actin depolymerizing factor/cofilin and actin-interacting protein 1: new blades for twisted filaments. Citation: Biochemistry 42: 13363-13370 2003 Type: REVIEW Genes: unc-60 unc-78 Abstract: Actin depolymerizing factor (ADF)/cofilin enhances turnover of actin filaments by severing and depolymerizing filaments. A number of proteins functionally interact with ADF/cofilin to modulate the dynamics of actin filaments. Actin-interacting protein 1 (AIP1) has emerged as a conserved WD-repeat protein that specifically enhances ADF/cofilin-induced actin dynamics. Interaction of AIP1 with actin was originally characterized by a yeast two-hybrid system. However, biochemical studies revealed its unique activity on ADF/cofilin-bound actin filaments. AIP1 alone has negligible effects on actin filament dynamics, whereas in the presence of ADF/cofilin, AIP1 enhances filament fragmentation by capping ends of severed filaments. Studies in model organisms demonstrated that AIP1 genetically interacts with ADF/cofilin and participates in several actin-dependent cellular events. The crystal structure of AIP1 revealed its unique structure with two seven-bladed beta-propeller domains. Thus, AIP1 is a new class of actin regulatory proteins that selectively enhances ADF/cofilin-dependent actin filament dynamics. ------------------- Key: 6202 Medline: 12937276 Authors: Galy V;Mattaj IW;Askjaer P Title: Caenorhabditis elegans nucleoporins Nup93 and Nup205 determine the limit of nuclear pore complex size exclusion in vivo. Citation: Molecular Biology of the Cell 14: 5104-5115 2003 Type: ARTICLE Genes: npp-1 npp-2 npp-3 npp-4 npp-5 npp-6 npp-7 npp-8 npp-9 npp-10 npp-11 npp-12 npp-13 npp-14 npp-15 npp-16 npp-17 npp-18 npp-19 npp-20 Abstract: Nuclear pore complexes (NPCs) span the nuclear envelope and mediate communication between the nucleus and the cytoplasm. To obtain insight into the structure and function of NPCs of multicellular organisms, we have initiated an extensive analysis of Caenorhabditis elegans nucleoporins. Of 20 assigned C. elegans nucleoporin genes, 17 were found to be essential for embryonic development either alone or in combination. In several cases, depletion of nucleoporins by RNAi caused severe defects in nuclear appearance. More specifically, the C. elegans homologs of vertebrate Nup93 and Nup205 were each found to be required for normal NPC distribution in the nuclear envelope in vivo. Depletion of Nup93 or Nup205 caused a failure in nuclear exclusion of nonnuclear macromolecules of similar to70 kDa without preventing active nuclear protein import or the assembly of the nuclear envelope. The defects in NPC exclusion were accompanied by abnormal chromatin condensation and early embryonic arrest. Thus, the contribution to NPC structure of Nup93 and Nup205 is essential for establishment of normal NPC function and for ------------------- Key: 6203 Medline: 14628056 Authors: Sijen T;Plasterk RHA Title: Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi. Citation: Nature 426: 310-314 2003 Type: ARTICLE Genes: mut-7 mut-14 mut-16 pie-1 rde-1 rde-4 unc-22 Abstract: Transposable elements are stretches of DNA that can move and multiply within the genome of an organism. The Caenorhabditis elegans genome contains multiple Tc1 transposons that jump in somatic cells, but are silenced in the germ line(1-3). Many mutants that have lost this silencing have also lost the ability to execute RNA interference (RNAi)(2,3), a process whereby genes are suppressed by exposure to homologous double-stranded RNA ( dsRNA). Here we show how RNAi causes transposon silencing in the nematode germ line. We find evidence for transposon-derived dsRNAs, in particular to the terminal inverted repeats, and show that these RNAs may derive from read-through transcription of entire transposable elements. Small interfering RNAs of Tc1 were detected. When a germline-expressed reporter gene is fused to a stretch of Tc1 sequence, this transgene is silenced in a manner dependent on functional mutator genes (mut-7, mut-16 and pk732). These results indicate that RNAi surveillance is triggered by fortuitous read-through transcription of dispersed Tc1 copies, which can form dsRNA as a result of 'snap-back' of the terminal inverted repeats. RNAi mediated by this dsRNA silences transposase gene expression. ------------------- Key: 6204 Medline: 12905072 Authors: Kuervers LM;Jones CL;O'Neil NJ;Baillie DL Title: The sterol modifying enzyme LET-767 is essential for growth, reproduction and development in Caenorhabditis Citation: Molecular Genetics & Genomics 270: 121-131 2003 Type: ARTICLE Genes: let-767 sDf125 Abstract: The let-767 gene encodes a protein that is similar to mammalian steroid enzymes that are responsible for the reduction of 17-beta hydroxysteroid hormones. Caenorhabditis elegans is incapable of the de novo synthesis of cholesterol. Therefore, this free-living nematode must extract cholesterol from its environment and modify it to form steroid hormones that are necessary for its survival. C. elegans is unable to survive in the absence of supplemental cholesterol, and is therefore sensitive to cholesterol limitation. We show that a mutation in let-767 results in hypersensitivity to cholesterol limitation, supporting the hypothesis that LET-767 acts on a sterol derivative. Furthermore, let-767 mutants exhibit defects in embryogenesis, female reproduction and molting. Although ecdysone is the major molting hormone in insects, there is as yet no evidence for ecdysone synthesis in C. elegans, suggesting that a different hormone is required for molting in C. elegans. Our results suggest that LET-767 modifies a sterol hormone that is required both for embryogenesis and for later ------------------- Key: 6205 Medline: Authors: Dolinski CM;Baldwin JG Title: Fine structure of the stoma of Bunonema sp. and Teratorhabditis palmarum (Nematoda) and its phylogenetic significance. Citation: Journal of Nematology 35: 244-251 2003 Type: ARTICLE Genes: Abstract: Fine structure of the stoma, including the cheilostom, gymnostom, and stegostom of Bunonema sp. and Teratorhabditis palmarum was compared with Caenorhabditis elegans to consider fine structural characters that may, be phylogenetically informative. The stegostom, enclosed by the anterior end of the pharynx, includes a triradiate lumen surrounded by radial cells (interradial or pairs of adradial cells) repeated in the dorsal and subventral sectors; in Rhabditina, typically the stegostom includes anteriorly two sets of epithelia] and posteriorly two sets of muscular radial cells. These muscle cells are anteriorly m1 and posteriorly m2. In Bunonema sp., unlike T. palmarum and C. elegans, the stegostom has a third set of interradial epithelial cells. In Bunonema sp., m1 is expressed by three interradial cells, whereas in T palmarum and C elegans m1 is three pairs of adradial muscle cells (i.e., six cells). I it all three taxa m2 is expressed as three pairs of adradial muscle cells. Posterior processes of adjacent adradial cells fuse, and closely apposed nuclei may present a figure-eight shape. However, in Bunonema the three interradial m I cells each have a long posterior process enclosing two separate round nuclei. In combination with additional characters, these diverse stoma features may prove phylogenetically informative. Specifically, the radial epithelia] cells of the stegostom appear to be a synapomorphy consistent with a bunonemid-diplogastrid-rhabditid clade, whereas a thickening in the dorsal sector of the stoma cuticle lining is interpreted as a synapomorphy supporting a ------------------- Key: 6206 Medline: Authors: Hartman P;Belmont P;Zuber S;Ishii N;Anderson J Title: Relationship between catalase and life span in recombinant inbred strains of Caenorhabditis elegans. Citation: Journal of Nematology 35: 314-319 2003 Type: ARTICLE Genes: Abstract: Johnson and Wood constructed recombinant inbred strains of Caenorhabditis elegans with life spans ranging from 10 to 31 days. Using these strains, we have demonstrated previously that hyperoxia and methyl viologen inhibited development at rates inversely correlated with life span. The growth rates of the short-lived recombinant inbred strains were more profoundly inhibited by oxidative stress than were those of the long-lived strains. Here we report a positive correlation between life span and catalase levels in these same strains. Specifically, when compared to short-lived strains at 10 days after fertilization, the long-lived strains possessed higher levels of total enzymatic catalase. Northern blots indicated a similar relationship between life span and clt-1mRNA (the cytosolic catalase). This suggests that at least some of the polygenes that influence life span are also responsible for regulating gene expression of catalase, an important defense component against oxidative stress. ------------------- Key: 6207 Medline: 14627270 Authors: Caldwell KN;Anderson GL;Williams PL;Beuchat LR Title: Attraction of a free-living nematode, Caenorhabditis elegans, to foodborne pathogenic bacteria and its potential as a vector of Salmonella Poona for preharvest contamination of cantaloupe. Citation: Journal of Food Protection 66: 1964-1971 2003 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans was studied to determine the potential role of free-living microbivorous nematodes as vectors for preharvest contamination of fruits and vegetables with foodborne pathogens. The propensity of C. elegans to be attracted to seven strains of Escherichia coli O157:H7, eight serotypes of Salmonella, six strains of Listeria monocytogenes, and cantaloupe juice was investigated. Twenty to 30 adult worms were placed on the surface of K agar midway between a 24-h bacterial colony and 10 mul of uninoculated tryptic soy broth (TSB) or cantaloupe juice positioned 1.5 cm apart. The numbers of nematodes that migrated to the colony, to the TSB, and to the cantaloupe juice within 5, 10, 15, and 20 min at 21degreesC were determined, and then the plates were incubated at 37degreesC for up to 7 days to determine the ability of C. elegans to survive and reproduce in bacterial colonies. The nematode was attracted to colonies of all test pathogens and survived and reproduced within colonies for up to 7 days. C. elegans was not attracted to cantaloupe juice. The potential of C. elegans to serve as a vector for the transport of Salmonella Poona to cantaloupe rinds was investigated. Adult worms that had been immersed in a suspension of Salmonella Poona were deposited 1 or 3 cm below the surface of soil on which a piece of cantaloupe rind was placed. The rind was analyzed for the presence of Salmonella Poona after 1, 3, 7, and 10 days at 21degreesC. The presence of Salmonella Poona was evident more quickly on rinds positioned on soil beneath which C. elegans inoculated with Salmonella Poona was initially deposited than on rinds positioned on soil beneath which Salmonella Poona alone was deposited. The time required to detect Salmonella Poona on rinds was longer when the rind was placed 3 cm above the inoculum than when the rind was placed 1 cm above the inoculum. Free-living nematodes may play a role in the preharvest dispersal of incidental human pathogens in soil to the surfaces of raw fruits and vegetables in contact with soil during development and maturation, as evidenced by the behavior of C. elegans as a ------------------- Key: 6208 Medline: 12954633 Authors: Harding A;Hsu V;Kornfeld K;Hancock JF Title: Identification of residues and domains of Raf important for function in vivo and in vitro. Citation: Journal of Biological Chemistry 278: 45519-45527 2003 Type: ARTICLE Genes: lin-45 Abstract: Random mutagenesis and genetic screens for impaired Raf function in Caenorhabditis elegans were used to identify six loss-of-function alleles of lin-45 raf that result in a substitution of a single amino acid. The mutations were classified as weak, intermediate, and strong based on phenotypic severity. We engineered these mutations into the homologous residues of vertebrate Raf-1 and analyzed the mutant proteins for their underlying biochemical defects. Surprisingly, phenotype strength did not correlate with the catalytic activity of the mutant proteins. Amino acid substitutions Val-589 and Ser-619 severely compromised Raf kinase activity, yet these mutants displayed weak phenotypes in the genetic screen. Interestingly, this is because these mutant Raf proteins efficiently activate the MAPK (mitogen-activated protein kinase) cascade in living cells, a result that may inform the analysis of knockout mice. Equally intriguing was the observation that mutant proteins with non-functional Ras-binding domains, and thereby deficient in Ras-mediated membrane recruitment, displayed only intermediate strength phenotypes. This confirms that secondary mechanisms exist to couple Ras to Raf in vivo. The strongest phenotype in the genetic screens was displayed by a S508N mutation that again did not correlate with a significant loss of kinase activity or membrane recruitment by oncogenic Ras in biochemical assays. Ser-508 lies within the Raf-1 activation loop, and mutation of this residue in Raf-1 and the equivalent Ser-615 in B-Raf revealed that this residue regulates Raf binding to MEK. Further characterization revealed that in response to activation by epidermal growth factor, the Raf-S508N mutant protein displayed both reduced catalytic activity and aberrant activation kinetics: characteristics that may explain the C. elegans phenotype. ------------------- Key: 6209 Medline: 14597199 Authors: Kostic I;Li S;Roy R Title: cki-1 links cell division and cell fate acquisition in the C. elegans somatic gonad. Citation: Developmental Biology 263: 242-252 2003 Type: ARTICLE Genes: cdh-3 cki-1 glp-1 lag-2 lin-3 Abstract: The formation of a complex multicellular organism requires the precise specification of many diverse cell types at the correct time and position throughout development. This may be achieved by coordinating cell fate specification processes with progression through the cell cycle. Here, we show that the extra distal tip cells (DTCs) associated with the loss of cki-1, a Caenorhabditis elegans homologue of the cyclin-dependent kinase inhibitor p27, do not arise from duplications of pre-existing DTCs, but that they are formed from another cell type within the somatic gonad. Results from our laser microsurgery experiments suggest that the extra DTCs are caused by aberrant somatic gonadal precursor cell divisions in the absence of cki-1, resulting in abnormal daughter cell fates. cki-1(RNAi) animals also possess extra anchor cells and ectopic gonad arms with variable sheath cell numbers and positioning. In addition, cki-1 (RNAi) animals display an endomitotic oocyte (Emo) phenotype. Our results uncover a novel role of this CKI in cell fate acquisition, either by directly influencing specification, or through a more conventional role in appropriately linking cell cycle phase with this process. ------------------- Key: 6210 Medline: 14597206 Authors: Hapiak V;Hresko MC;Schriefer LA;Saiyasisongkhram K;Bercher M;Plenefisch J Title: mua-6, a gene required for tissue integrity in Caenorhabditis elegans, encodes a cytoplasmic intermediate filament. Citation: Developmental Biology 263: 330-342 2003 Type: ARTICLE Genes: ifa-2 mua-6 mnDf4 mnDf41 Abstract: Locomotion in Caenorhabditis elegans requires force transmission through a network of proteins linking the skeletal muscle, via an intervening basal lamina and epidermis (hypodermis), to the cuticle. Mutations in mua-6 result in hypodermal rupture, muscle detachment from the bodywall, and progressive paralysis. It is shown that mua-6 encodes the cytoplasmic intermediate filament (cIF) A2 protein and that a MUA-6/IFA-2::GFP fusion protein that rescues the presumptive mua-6 null allele localizes to hypodermal hemidesmosomes. This result is consistent with what is known about the function of cIFs in vertebrates. Although MUA-6/IFA-2 is expressed embryonically, and plays an essential postembryonic role in tissue integrity, it is not required for embryonic development of muscle-cuticle linkages nor for the localization of other cIFs or hem ides mosome-associated proteins in the embryo. Finally, the molecular lesion in the mua-6(rh85) allele suggests that the head domain of the MUA-6/IFA-2 is dispensable for its function. ------------------- Key: 6211 Medline: Authors: Morck C;Axang C;Pilon M Title: Erratum to "A genetic analysis of axon guidance in the C. elegans pharynx" Citation: Developmental Biology 263: 367-368 2003 Type: CORRECT Genes: efn-2 efn-3 smp-1 smp-2 Abstract: The publisher regrets that several corrections requested by the author were not made. ------------------- Key: 6212 Medline: 14645848 Authors: Wang X;Wu YC;Fadok VA;Lee MC;Gengyo-Ando K;Cheng LC;Ledwich D;Hsu PK;Chen JY;Chou BK;Henson P;Mitani S;Xue D Title: Cell corpse engulfment mediated by C. elegans phosphatidylserine receptor through CED-5 and CED-12. Citation: Science 302: 1563-1566 2003 Type: ARTICLE Genes: ced1 ced-2 ced-5 ced-6 ced-7 ced-10 ced-12 psr-1 Abstract: During apoptosis, phosphatidylserine, which is normally restricted to the inner lea. et of the plasma membrane, is exposed on the surface of apoptotic cells and has been suggested to act as an "eat-me" signal to trigger phagocytosis. It is unclear how phagocytes recognize phosphatidylserine. Recently, a putative phosphatidylserine receptor (PSR) was identified and proposed to mediate recognition of phosphatidylserine and phagocytosis. We report that psr-1, the Caenorhabditis elegans homolog of PSR, is important for cell corpse engulfment. In vitro PSR-1 binds preferentially phosphatidylserine or cells with exposed phosphatidylserine. In C. elegans, PSR-1 acts in the same cell corpse engulfment pathway mediated by intracellular signaling molecules CED-2 ( homologous to the human CrkII protein), CED-5 (DOCK180), CED-10 (Rac GTPase), and CED-12 (ELMO), possibly through direct interaction with CED-5 and CED-12. Our findings suggest that PSR-1 is likely an upstream receptor for the signaling pathway containing CED-2, CED-5, CED-10, and CED-12 proteins and plays an important role in recognizing phosphatidylserine during phagocytosis. ------------------- Key: 6213 Medline: 14622579 Authors: Schuske KR;Richmond JE:Matthies DS;Davis WS;Runz S;Rube DA;van der Bliek AM;Jorgensen EM Title: Endophilin is required for synaptic vesicle endocytosis by localizing synaptojanin. Citation: Neuron 40: 749-762 2003 Type: ARTICLE Genes: dyn-1 unc-26 unc-57 Abstract: Endophilin is a membrane-associated protein required for endocytosis of synaptic vesicles. Two models have been proposed for endophilin: that it alters lipid composition in order to shape membranes during endocytosis, or that it binds the polyphosphoinositide phosphatase synaptojanin and recruits this phosphatase to membranes. In this study, we demonstrate that the unc-57 gene encodes the Caenorhabditis elegans ortholog of endophilin A. We demonstrate that endophilin is required in C. elegans for synaptic vesicle recycling. Furthermore, the defects observed in endophilin mutants closely resemble those observed in synaptojanin mutants. The electrophysiological phenotype of endophilin and synaptojanin double mutants are virtually identical to the single mutants, demonstrating that endophilin and synaptojanin function in the same pathway. Finally, endophilin is required to stabilize expression of synaptojanin at the synapse. These data suggest that endophilin is an adaptor protein required to localize and stabilize synaptojanin at membranes during synaptic vesicle recycling. ------------------- Key: 6214 Medline: 12885961 Authors: Ganko EW;Bhattacharjee V;Schliekelman P;McDonald JF Title: Evidence for the contribution of LTR retrotransposons to C. elegans gene evolution. Citation: Molecular Biology and Evolution 20: 1925-1931 2003 Type: ARTICLE Genes: Abstract: LTR retrotransposons may be important contributors to host gene evolution because they contain regulatory and coding signals. In an effort to assess the possible contribution of LTR retrotransposons to C. elegans gene evolution, we searched upstream and downstream of LTR retrotransposon sequences for the presence of predicted genes. Sixty-three percent of LTR retrotransposon sequences (79/124) are located within 1 kb of a gene or within gene boundaries. Most gene-retrotransposon associations were located along the chromosome arms. Our results are consistent with the hypothesis that LTR retrotransposons have contributed to the structural and/or regulatory evolution of genes in C. elegans. ------------------- Key: 6215 Medline: 14600234 Authors: Joshua GWP;Karlyshev AV;Smith MP;Isherwood KE;Titball RW;Wren BW Title: A Caenorhabditis elegans model of Yersinia infection: biofilm formation on a biotic surface. Citation: Microbiology 149: 3221-3229 2003 Type: ARTICLE Genes: Abstract: To investigate Yersinia pathogenicity and the evolutionary divergence of the genus, the effect of pathogenic yersiniae on the model organism Caenorhabditis elegans was studied. Three strains of Yersinia pestis, including a strain lacking pMT1, caused blockage and death of C. elegans; one strain, lacking the haemin storage (hms) locus, caused no effect. Similarly, 15 strains of Yersinia enterocolitica caused no effect. Strains of Yersinia pseudotuberculosis showed different levels of pathogenicity. The majority of strains (76%) caused no discernible effect; 5% caused a weak infection, 9(.)5% an intermediate infection, and 9(.)5% a severe infection. There was no consistent relationship between serotype and severity of infection; nor was there any relationship between strains causing infection of C. elegans and those able to form a biofilm on an abiotic surface. Electron microscope and cytochemical examination of infected worms indicated that the infection phenotype is a result of biofilm formation on the head of the worm. Seven transposon mutants of Y. pseudotuberculosis strain YPIII pIB1 were completely or partially attenuated; mutated genes included genes encoding proteins involved in haemin storage and lipopolysaccharide biosynthesis. A screen of 15 defined C. elegans mutants identified four where mutation caused (complete) resistance to infection by Y. pseudotuberculosis YPIII pIB1. These mutants, srf-2, srf-3, srf-5 and the dauer pathway gene daf-1, also exhibit altered binding of lectins to the nematode surface. This suggests that biofilm formation on a biotic surface is an interactive process involving both bacterial and invertebrate control mechanisms. ------------------- Key: 6216 Medline: 14610052 Authors: O'Toole ET;McDonald K;Mantler J;McIntosh JR;Hyman AA;Muller-Reichert T Title: Morphologically distinct microtubule ends in the mitotic centrosome of Caenorhabditis elegans. Citation: Journal of Cell Biology 163: 451-456 2003 Type: ARTICLE Genes: Abstract: During mitosis, the connections of microtubules (MTs) to centrosomes and kinetochores are dynamic. From in vitro studies, it is known that the dynamic behavior of MTs is related to the structure of their ends, but we know little about the structure of MT ends in spindles. Here, we use high-voltage electron tomography to study the centrosome- and kinetochore-associated ends of spindle MTs in embryonic cells of the nematode, Caenorhabditis elegans. Centrosome-associated MT ends are either closed or open. Closed MT ends are more numerous and are uniformly distributed around the centrosome, but open ends are found preferentially on kinetochore-attached MTs. These results have structural implications for models of MT interactions with centrosomes. ------------------- Key: 6217 Medline: 13129931 Authors: Guo J;Lemire BD Title: The ubiquinone-binding site of the Saccharomyces cerevisiae succinate-ubiquinone oxidoreductase is a source of superoxide. Citation: Journal of Biological Chemistry 278: 47629-47635 2003 Type: ARTICLE Genes: mev-1 Abstract: The mitochondrial succinate dehydrogenase (SDH) is a tetrameric iron-sulfur flavoprotein of the Krebs cycle and of the respiratory chain. A number of mutations in human SDH genes are responsible for the development of paragangliomas, cancers of the head and neck region. The mev-1 mutation in the Caenorhabditis elegans gene encoding the homolog of the SDHC subunit results in premature aging and hypersensitivity to oxidative stress. It also increases the production of superoxide radicals by the enzyme. In this work, we used the yeast succinate dehydrogenase to investigate the molecular and catalytic effects of paraganglioma- and mev-1-like mutations. We mutated Pro-190 of the yeast Sdh2p subunit to Gln (P190Q) and recreated the C. elegans mev-1 mutation by converting Ser-94 in the Sdh3p subunit into a glutamate residue (S94E). The P190Q and S94E mutants have reduced succinate-ubiquinone oxidoreductase activities and are hypersensitive to oxygen and paraquat. Although the mutant enzymes have lower turnover numbers for ubiquinol reduction, larger fractions of the remaining activities are diverted toward superoxide production. The P190Q and S94E mutations are located near the proximal ubiquinone-binding site, suggesting that the superoxide radicals may originate from a ubisemiquinone intermediate formed at this site during the catalytic cycle. We suggest that certain mutations in SDH can make it a significant source of superoxide production in mitochondria, which may contribute directly to disease progression. Our data also challenge the dogma that superoxide production by SDH is a flavin-mediated event rather than a quinone-mediated one. ------------------- Key: 6218 Medline: 14622138 Authors: Sasagawa Y;Urano T;Kohara Y;Takahashi H;Higashitani A Title: Caenorhabditis elegans RBX1 is essential for meiosis, mitotic chromosomal condensation and segregation, and cytokinesis. Citation: Genes to Cell 8: 857-872 2003 Type: ARTICLE Genes: glc-7 gld-1 rbx-1 Abstract: Background: The RING-H2 finger protein RBX1 (ROC1/HRT1) is a common subunit of SKP1-CDC53/CUL1-F-box (SCF), other cullins and von Hippel-Lindau (VHL) tumour suppressor E3 ubiquitin ligase complexes. RBX1 protein sequences are highly conserved in various species, including yeasts, Drosophila melanogaster, mice and humans. In Saccharomyces cerevisiae, RBX1 is essential for the G1/S transition. Results: Caenorhabditis elegans RBX1 is strongly expressed in early embryos and in the gonad, including meiotic cells. Depletion of RBX1 by RNA-mediated interference (RNAi) caused pronounced defects in the first meiotic division. Several irregular phenotypes were identified in embryos that escaped from meiotic arrest: defects in mitotic chromosomal condensation and segregation, abnormal chromosome bridges, giant nuclei, abnormal cortical protrusion, multinucleate cells and defects in germ cell proliferation. Moreover, histone H3 phosphorylation at Ser(10) and Ser(28) was significantly reduced in these embryos. The histone H3 phosphorylation defect of embryos was rescued by the additional depletion of protein phosphatase 1 (GLC7alpha/beta) by RNAi. Conclusion: These results indicate that the RBX1 protein participates in diverse functions relevant to chromosome metabolism and ------------------- Key: 6219 Medline: 14630941 Authors: Kamikura DM;Cooper JA Title: Lipoprotein receptors and a disabled family cytoplasmic adaptor protein regulate EGL-17/FGF export in C. elegans. Citation: Genes & Development 17: 2798-2811 2003 Type: ARTICLE Genes: apm-1 apt-2 apt-4 apt-5 apt-6 apt-10 dab-1 egl-17 let-23 lrp-1 lrp-2 rme-2 unc-101 Abstract: Growth factors and morphogens need to be secreted to act on distant cells during development and in response to injury. Here, we report evidence that efficient export of a fibroblast growth factor (FGF), EGL-17, from the Caenorhabditis elegans developing vulva requires the lipoprotein receptor-related proteins Ce-LRP-1 and Ce-LRP-2 and a cytoplasmic adaptor protein, Ce-DAB-1 (Disabled). Lipoprotein receptors are transmembrane proteins best known for their roles in endocytosis. Ce-LRP-1 and Ce-LRP-2 possess a conserved intraluminal domain that can bind to EGL-17, as well as a cytosolic FXNPXY motif that can bind to Ce-DAB-1. Ce-DAB-1 contains signals that confer subcellular localization to Golgi-proximal vesicles. These results suggest a model in which Ce-DAB-1 coordinates selection of receptors and cargo, including EGL-17, for transport through the secretory pathway. ------------------- Key: 6220 Medline: 14604799 Authors: Astolfi P;Bellizzi D;Sgaramella V Title: Frequencey and coverage of trinucleotide repeats in eukaryotes. Citation: Gene 317: 117-125 2003 Type: ARTICLE Genes: Abstract: In the aim to assess whether the tri-repeat shortage reported in vertebrates affects specific motifs, such as those causing neuromuscular diseases in man, we detected approximate di-, tri- and tetra-repeats (STR) longer than 25 bases in human chromosomes 21 and 22, and in some model organisms (M. musculus, D. melanogaster, C elegans, A. thaliana and S. cerevisiae). We found that overall STR are more represented in mouse and in man than in the other organisms. However, tri-repeats are less represented than di- and tetra- in man and mouse, but show intermediate values between di- and tetra- in the other organisms. In man, ACG shows the lowest both frequency and coverage, ATC the highest coverage and AAT the highest frequency. In general, coverage and frequency of tri-repeats are linearly related, except for ACC, ATC, AAG, AGG motifs in man and AAG, AGG in mouse, which exhibit unexpectedly long repeats. Often their copy numbers exceed that found responsible for the dynamic mutations, set at around 40. The shortage in frequency and coverage of tri- vs. di- and tetra-repeats observed in man and mouse can be ascribed to a subset of the remaining tri-repeat motifs, but among them those recognized as dynamically mutable (AAG, AGC and CCG) are not the least represented. Possible constraints in tri-repeat expansion seem to be structural and conserved along the evolutionary scale: a motif-specific relaxation of the relevant controls may be responsible for the occasional expansions found in mouse and man. ------------------- Key: 6221 Medline: Authors: Chen C;Dewaele S;Braeckman B;Desmyter L;Verstraelen J;Borgonie G;Vanfleteren J;Contreras R Title: A high-throughput screening system for genes extending life-span. Citation: Experimental Gerontology 38: 1051-1063 2003 Type: ARTICLE Genes: Abstract: We developed a high-throughput functional genomic screening system that allows identification of genes prolonging life-span in the baker's yeast Saccharomyces cerevisiae. The method is based on isolating yeast mother cells with extended number of cell divisions as indicated by the increased number of bud scars on their surface. Fluorescently labelled Wheat Germ Agglutinin was used for specific staining of chitin, a major component of bud scars. Screening of a human HepG2 cDNA expression library in yeast resulted in the isolation of 12 yeast transformants with a potentially prolonged life-span. The transgene in one of the lines was identified as ferritin light chain (FTL) and studied in more detail. Yeast cells containing FTL showed an enhanced iron and H2O2 resistance, a reduced cell death rate and an increased number of cell divisions. Overexpression of FTL in the nematode Caenorhabditis elegans resulted in a life-span increase of 8% confirming our yeast observations in a multicellular organism. Our data demonstrate that this method permits a fast screening of libraries for hunting genes involved in ------------------- Key: 6222 Medline: 14629117 Authors: Izeta A;Malcomber S;O'Rourke D;Hodgkin J;O'Hare P Title: A C-terminal targeting signal controls differential compartmentalisation of Caenorhabditis elegans host cell factor (HCF) to the nucleus or mitochondria. Citation: European Journal of Cell Biology 82: 495-504 2003 Type: ARTICLE Genes: Abstract: HCF-1 (host cell factor 1) is a human protein originally identified as a component of the VP16 transcription complex. A related protein HCF-2 is also present in humans and while at least HCF-1 appears to be required for normal cell growth there is currently little information on the precise cellular role(s) of these proteins. C. elegans contains a single HCF orthologue (CeHCF) which is very closely related to human HCF-2. To contribute to an understanding of the activities of these proteins here we analyse the subcellular localisation of the CeHCF protein in live transgenic worms and in mammalian cells. We constructed a green fluorescent protein (GFP) fusion of CeHCF and studied localisation after ectopic expression under the control of a heat shock protein promoter. The CeHCF-GFP protein accumulated in the cell nuclei at every stage of development and in a wide variety of cell types. Nuclear accumulation with nucleolar sparing was evident on the larvae and adult stages, but not earlier in development in which the protein accumulated diffusely in the nucleoplasm. Surprisingly the same protein accumulated in the mitochondria of a stable HeLa cell lines suggesting a differential localisation of CeHCF in mammalian cells. Furthermore, when overexpressed in transient transfection the CeHCF accumulated in both nuclear and mitochondrial compartments. We have refined the targeting determinants of CeHCF to the last 23 amino acids at the extreme C-terminus and show that they contain interdigitated amino acids involved in both nuclear and mitochondrial targeting. This novel targeting signal is sufficient to redirect HCF-2 into mitochondria. It can also be transferred to an unrelated protein, resulting in its targeting to both the ------------------- Key: 6223 Medline: 14602075 Authors: Schaner CE;Deshpande G;Schedl PD;Kelly WG Title: A conserved chromatin architecture marks and maintains the restricted germ cell lineage in worms and flies. Citation: Developmental Cell 5: 747-757 2003 Type: ARTICLE Genes: emb-4 hda-1 let-418 mep-1 mes-2 mes-3 mes-4 mes-6 mex-1 nos-1 nos-2 pie-1 Abstract: In C. elegans, mRNA production is initially repressed in the embryonic germline by a protein unique to C. elegans germ cells, PIE-1. PIE-1 is degraded upon the birth of the germ cell precursors, Z2 and Z3. We have identified a chromatin-based mechanism that succeeds PIE-1 repression in these cells. A subset of nucleosomal histone modifications, methylated lysine 4 on histone H3 (H3meK4) and acetylated lysine 8 on histone H4 (H4acetylK8), are globally lost and the DNA appears more condensed. This coincides with PIE-1 degradation and requires that germline identity is not disrupted. Drosophila pole cell chromatin also lacks H3meK4, indicating that a unique chromatin architecture is a conserved feature of embryonic germ cells. Regulation of the germline-specific chromatin architecture requires functional nanos activity in both organisms. These results indicate that genome-wide repression via a nanos-regulated, germ cell-specific chromatin organization is a conserved feature of germline maintenance during embryogenesis. ------------------- Key: 6224 Medline: 14614844 Authors: Goldstein B Title: Asymmetric division: AGS proteins position the spindle. Citation: Current Biology 13: R879-R880 2003 Type: REVIEW Genes: Abstract: Many cells divide asymmetrically by shifting their division machinery toward a specific region of the cell cortex, but little is known about how this occurs. Three recent papers have implicated activators of heterotrimeric G protein signaling in this process in Caenorhabditis elegans. ------------------- Key: 6225 Medline: Authors: Woo JS;Jung JS;Ha NC;Shin J;Kim KH;Lee W;Oh BH Title: Unique structural features of a BCL-2 family protein CED-9 and biophysical characterization of CED-9/EGL-1 interactions. Citation: Cell Death and Differentiation 10: 1310-1319 2003 Type: ARTICLE Genes: ced-9 egl-1 Abstract: The interactions between B-cell lymphoma 2 (BCL-2) family members are known to be mediated through the binding of the BH3 domain of a proapoptotic member to the BH3-binding groove of an antiapoptotic member. We determined the crystal structure of antiapoptotic CED-9, which reveals a unique C-terminal helix altering the common BH3-binding region. A coexpression system to produce CED-9 in complex with proapoptotic EGL-1 enabled us to show that the binding of EGL-1 to CED-9 is extremely stable, raising the melting temperature (T-M) of CED-9 by 25degreesC, and that the binding surface of CED-9 extends beyond the BH3-binding region and reaches the BH4 domain. Consistently, the T-M and a H-1-N-15 correlation NMR spectrum of CED-9 in complex with EGL-1 are drastically different from those of CED-9 in complex with the EGL-1 BH3 peptide. The data suggest that the recognition between other BCL-2 family members may also involve much wider protein surfaces than is previously thought. ------------------- Key: 6226 Medline: 14622602 Authors: Libina N;Berman JR;Kenyon C Title: Tissue-specific activities of C. elegans DAF-16 in the regulation of lifespan. Citation: Cell 115: 489-502 2003 Type: ARTICLE Genes: daf-2 daf-16 ges-1 mes-1 myo-3 sod-3 unc-119 Abstract: In C. elegans, the transcription factor DAF-16 promotes longevity in response to reduced insulin/IGF-1 signaling or germline ablation. In this study, we have asked how different tissues interact to specify the life-span of the animal. We find that several tissues act as signaling centers. In particular, DAF-16 activity in the intestine, which is also the animal's adipose tissue, completely restores the longevity of daf-16(-) germline-deficient animals, and increases the lifespans of daf-16(-) insulin/IGF-1-pathway mutants substantially. Our findings indicate that DAF-16 may control two types of downstream signals: DAF-16 activity in signaling cells upregulates DAF-16 in specific responding tissues, possibly via regulation of insulin-like peptides, and also evokes DAF-16-independent responses. We suggest that this network of tissue interactions and feedback regulation allows the tissues to equilibrate and fine-tune their expression of downstream genes, which, in turn, coordinates their rates of aging within the animal. ------------------- Key: 6227 Medline: 14618537 Authors: Friedenberg NA Title: Determinism in a transient assemblage: the roles of dispersal and local competition. Citation: American Naturalist 162: 586-596 2003 Type: ARTICLE Genes: Abstract: Both dispersal and local competitive ability may determine the outcome of competition among species that cannot coexist locally. I develop a spatially implicit model of two-species competition at a small spatial scale. The model predicts the relative fitness of two competitors based on local reproductive rates and regional dispersal rates in the context of the number, size, and extinction probability of habitat patches in the landscape. I test the predictions of this model experimentally using two genotypes of the bacteriophagous soil nematode Caenorhabditis elegans in patchy microcosms. One genotype has higher fecundity while the other is a better disperser. With such a fecundity-dispersal trade-off between competitors, the model predicts that relative fitness will be affected most by local population size when patches do not go extinct and by the number of patches when there is a high probability of patch extinction. The microcosm experiments support the model predictions. Both approaches suggest that competitive dominance in a patchily distributed transient assemblage will depend upon the architecture and predictability of the environment. These mechanisms, operating at a small scale with high spatial admixture, may be embedded in a larger metacommunity process. ------------------- Key: 6228 Medline: Authors: Nagai K;Sunazuka T;Shiomi K;Harder A;Turberg A;Omura S Title: Synthesis and biological activities of novel 4"-alkylidene avermectin derivatives. Citation: Bioorganic & Medicinal Chemistry Letters 13: 3943-3946 2003 Type: ARTICLE Genes: Abstract: Horner-Emmons reaction of 4"-dehydro-5-O-TBDMS-avermectin B-1a with a variety of phosphorus ylides using LHMDS gave novel 4"-alkylidene avermectin derivatives in high yields. Further modifications led to derivatives bearing diverse functional groups. The new avermectin derivatives showed potent growth inhibitory activity against Artemia salina and Caenorhabditis elegans. ------------------- Key: 6229 Medline: 12944392 Authors: Griffitts JS;Huffman DL;Whitacre JL;Barrows BD;Marroquin LD;Muller R;Brown JR;Hennet T;Esko JD;Aroian RV Title: Resistance to a bacterial toxin is mediated by removal of a conserved glycosylation pathway required for toxin-host interactions. Citation: Journal of Biological Chemistry 278: 45594-45602 2003 Type: ARTICLE Genes: bre-2 bre-3 bre-4 bre-5 Abstract: Crystal (Cry) proteins made by the bacterium Bacillus thuringiensis are pore-forming toxins that specifically target insects and nematodes and are used around the world to kill insect pests. To better understand how pore-forming toxins interact with their host, we have screened for Caenorhabditis elegans mutants that resist Cry protein intoxication. We find that Cry toxin resistance involves the loss of two glycosyltransferase genes, bre-2 and bre-4. These glycosyltransferases function in the intestine to confer susceptibility to toxin. Furthermore, they are required for the interaction of active toxin with intestinal cells, suggesting they make an oligosaccharide receptor for toxin. Similarly, the bre-3 resistance gene is also required for toxin interaction with intestinal cells. Cloning of the bre-3 gene indicates it is the C. elegans homologue of the Drosophila egghead (egh) gene. This identification is striking given that the previously identified bre-5 has homology to Drosophila brainiac (brn) and that egh-brn likely function as consecutive glycosyltransferases in Drosophila epithelial cells. We find that, like in Drosophila, bre-3 and bre-5 act in a single pathway in C. elegans. bre-2 and bre-4 are also part of this pathway, thereby extending it. Consistent with its homology to brn, we demonstrate that C. elegans bre-5 rescues the Drosophila brn mutant and that BRE-5 encodes the dominant UDP-GlcNAc:Man GlcNAc transferase activity in C. elegans. Resistance to Cry toxins has uncovered a four component glycosylation pathway that is functionally conserved between nematodes and insects and that provides the basis of the dominant mechanism of resistance in C. ------------------- Key: 6230 Medline: 14580264 Authors: Szewczyk N;Kozak E;Conley CA Title: Chemically defiend medium and Caenorhabditis elegans. Citation: BMC Biotechnology 3: - 2003 Type: ARTICLE Genes: Abstract: Background: C. elegans has been established as a powerful genetic system. Use of a chemically defined medium (C. elegans Maintenance Medium (CeMM)) now allows standardization and systematic manipulation of the nutrients that animals receive. Liquid cultivation allows automated culturing and experimentation and should be of use in large-scale growth and screening of animals. Results: We find that CeMM is versatile and culturing is simple. CeMM can be used in a solid or liquid state, it can be stored unused for at least a year, unattended actively growing cultures may be maintained longer than with standard techniques, and standard C. elegans protocols work well with animals grown in defined medium. We also find that there are caveats to using defined medium. Animals in defined medium grow more slowly than on standard medium, appear to display adaptation to the defined medium, and display altered growth rates as they change the composition of the defined medium. Conclusions: As was suggested with the introduction of C. elegans as a potential genetic system, use of defined medium with C. elegans should prove a powerful tool. ------------------- Key: 6231 Medline: 14657490 Authors: Tonkin LA;Bass BL Title: Mutations in RNAi rescue aberrant chemotaxis of ADAR mutants. Citation: Science 302: 1725- 2003 Type: ARTICLE Genes: adr-1 adr-2 rde-1 rde-4 Abstract: Adenosine deaminases that act on RNA (ADARs) are RNA editing enzymes that convert adenosine (A) to inosine (I) within double-stranded RNA (dsRNA). ADARs are found in metazoa where they are highly expressed in neuronal tissues. Drosophila melanogaster and Caenorhabditis elegans strains lacking all ADAR activity are viable but exhibit behavioral defects, whereas mice lacking ADARs die embryonically or shortly after birth. ------------------- Key: 6232 Medline: 14657502 Authors: Shibata Y;Branicky R;Landaverde IO;Hekimi S Title: Redox regulation of germline and vulval development in Caenorhabditis elegans. Citation: Science 302: 1779-1782 2003 Type: ARTICLE Genes: ark-1 clk-1 dsc-4 itr-1 let-60 lin-1 sid-1 sod-1 sod-2 sod-3 sod-4 vit-2 vit-3 vit-4 vit-5 vit-6 Abstract: In vitro studies have indicated that reactive oxygen species (ROS) and the oxidation of signaling molecules are important mediators of signal transduction. We have identified two pathways by which the altered redox chemistry of the clk-1 mutants of Caenorhabditis elegans acts in vivo on germline development. One pathway depends on the oxidation of an analog of vertebrate low density lipoprotein (LDL) and acts on the germline through the Ack-related tyrosine kinase (ARK-1) kinase and inositol trisphosphate (IP3) signaling. The other pathway is the oncogenic ras signaling pathway, whose action on germline as well as vulval development appears to be modulated by ------------------- Key: 6233 Medline: Authors: Hu JY;Fan Y;Lin YH;Zhang HB;Ong SL;Dong N;Xu JL;Ng WJ;Zhang LH Title: Microbial diversity and prevalence of virulent pathogens in biofilms developed in a water reclamation system. Citation: Research in Microbiology 154: 623-629 2003 Type: ARTICLE Genes: Abstract: Bacterial biofilm is a common phenomenon in both natural and engineered systems which often becomes a source of contamination and microbially influenced corrosion. It is thought that formation of biofilm in the monoculture of several bacterial species is regulated by acylhomoserine lactone (AHL) quorum-sensing signals. In this study, we investigated the microbial diversity and existence of AHL-producing and AHL-degrading bacterial species in the biofilm samples from a water reclamation system located in a tropical environment. 16S ribosomal DNA sequencing analysis indicated the presence of at least 11 bacterial species, including the frequently encountered bacterial pathogens Pseudomonas aeruginosa and Klebsiella pneumoniae, and several rare pathogens. We showed that only two groups of isolates, belonging to P. aertuginosa and Enterobacter agglomerans, produced AHL signals. We also found that three bacterial isolates, i.e., Agrobacterium tumefaciens XJOL Bacillus cereus XJO8, and Ralstonia sp. XJ12, expressed AHL degradation enzymes. Furthermore, we showed that P. aeruginosa isolate HL43 was virulent against animal model Caenorhabditis elegans and released 2-6-fold more pyocyanin cytotoxin than P auruginosa strains PA01 and PA14, the two commonly used laboratory strains. These data indicate the complexity and importance of biofilm research in water reclamation. ------------------- Key: 6234 Medline: 14612577 Authors: Santi CM;Yuan A;Fawcett G;Wang ZW;Butler A;Nonet ML;Wei A;Rojas P;Salkoff L Title: Dissection of K+ currents in Caenorhabditis elegans muscle cells by genetics and RNA interference. Citation: Proceedings of the National Academy of Sciences USA 100: 14391-14396 2003 Type: ARTICLE Genes: slo-2 Abstract: GFP-promoter experiments have previously shown that at least nine genes encoding potassium channel subunits are expressed in Caenorhabditis elegans muscle. By using genetic, RNA interference, and physiological techniques we revealed the molecular identity of the major components of the outward K+ currents in body wall muscle cells in culture. We found that under physiological conditions, outward current is dominated by the products of only two genes, Shaker (Kv1) and Shal (Kv4), both expressing voltage-dependent potassium channels. Other channels may be held in reserve to respond to particular circumstances. Because GFP-promoter experiments indicated that slo-2 expression is prominent, we created a deletion mutant to identify the SLO-2 current in vivo. In both whole-cell and single-channel modes, in vivo SLO-2 channels were active only when intracellular Ca2+ and Cl- were raised above normal physiological conditions, as occurs during hypoxia. Under such conditions, SLO-2 is the largest outward current, contributing up to 87% of the total current. Other channels are present in muscle, but our results suggest that they are unlikely to contribute a large outward component under physiological conditions. However, they, too, may contribute currents conditional on other factors. Hence, the picture that emerges is of a complex membrane with a small number of household conductances functioning under normal circumstances, but with additional conductances that are activated during unusual ------------------- Key: 6235 Medline: 14636565 Authors: Shi Y;Blackwell TK Title: A two-tiered transcription regulation mechanism that protects germ cell identity. Citation: Molecular Cell 12: 1062-1064 2003 Type: REVIEW Genes: pie-1 nos-1 nos-2 Abstract: In the November issue of Developmental Cell, Schaner and colleagues (2003) describe remarkable versatility in how the embryonic germ lineage blocks differentiation: in early C. elegans germ cell precursors transcription is silenced but chromatin remains open, and then after lineage restriction a conserved inhibitory chromatin architecture ------------------- Key: 6236 Medline: 14551256 Authors: Roberts B;Clucas C;Johnstone IL Title: Loss of SEC-23 in Caenorhabditis elegans causes defects in oogenesis, morphogenesis, and extracellular matrix secretion. Citation: Molecular Biology of the Cell 14: 4414-4426 2003 Type: ARTICLE Genes: col-12 dpy-7 emo-1 glp-1 rme-2 sec-23 Abstract: SEC-23 is a component of coat protein complex II (COPII)-coated vesicles involved in the endoplasmic reticulum-to-Golgi transport pathway of eukaryotes. During postembryonic life, Caenorhabditis elegans is surrounded by a collagenous exoskeleton termed the cuticle. From a screen for mutants defective in cuticle secretion, we identified and characterized a sec-23 mutant of C. elegans. By sequence homology, C. elegans has only the single sec-23 gene described herein. In addition to the cuticle secretion defect, mutants fail to complete embryonic morphogenesis. However, they progress through the earlier stages of embryogenesis, including gastrulation, and achieve substantial morphogenesis before death. We demonstrated a maternal component of SEC-23 function sufficient for progression through the earlier stages of embryogenesis and explaining the limited phenotype of the zygotic mutant. By RNA-mediated interference, we investigated the effects of perturbing COPII function during various postembryonic stages. During larval stages, major defects in cuticle synthesis and molting were observed. In the adult hermaphrodite, reduction of SEC-23 function by RNA-mediated interference caused a rapid onset of sterility, with defects in oogenesis including early maturation of the germline nuclei, probably a result of the observed loss of the GLP-1 receptor from the membrane surfaces adjacent to the developing germline nuclei. ------------------- Key: 6237 Medline: 12937270 Authors: Wright AJ;Hunter CP Title: Mutations in a beta-tubulin disrupt spindle orientation and microtubule dynamics in the early Caenorhabditis elegans embryo. Citation: Molecular Biology of the Cell 14: 4512-4525 2003 Type: ARTICLE Genes: tba-1 tba-2 tbb-1 tbb-2 nDf12 sDf121 sDf130 Abstract: The early Caenorhabditis elegans embryo contains abundant transcripts for two alpha- and two beta-tubulins, raising the question of whether each isoform performs specialized functions or simply contributes to total tubulin levels. Our identification of two recessive, complementing alleles of a beta-tubulin that disrupt nuclear-centrosome centration and rotation in the early embryo originally suggested that this tubulin, tbb-2, has specialized functions. However, embryos from tbb-2 deletion worms do not have defects in nuclear-centrosome centration and rotation suggesting that the complementing alleles are not null mutations. Both complementing alleles have distinct effects on microtubule dynamics and show allele-specific interactions with the two embryonically expressed alpha-tubulins: One of the alleles causes microtubules to be cold stable and resistant to the microtubule-depolymerizing drug benomyl, whereas the other causes cell cycle-specific defects in microtubule polymerization. Gene-specific RNA interference targeting all four embryonically expressed tubulin genes singly and in all double combinations showed that the tubulin isoforms in the early embryo are largely functionally redundant with the exception of tbb-2. tbb-2 is required for centrosome stabilization during anaphase of the first cell division, suggesting that tbb-2 may be specialized for interactions ------------------- Key: 6238 Medline: 14615205 Authors: Ruiz-Diez B;Sanchez P;Baquero F;Martinez JL;Navas A Title: Differential interactions within the Caenorhabditis elegans-Pseudomonas aeruginosa pathogenesis model. Citation: Journal of Theoretical Biology 225: 469-476 2003 Type: ARTICLE Genes: Abstract: A pathogenesis model based on the interaction between Caenorhabditis elegans and bacterial opportunistic pathogens has recently been developed. In the case of Pseudomonas aeruginosa, the model is based on three different modes of nematode killing (fast killing, slow killing and lethal paralysis) by virulent bacteria that has been incubated in different nutrient media. Using parametric statistics and Probit analysis, we test the reliability of the three different killing systems with respect to bacterial virulence. To accomplish this, we use three P. aeruginosa strains, each with a different level of virulence and one strain of non-virulent Escherichia coli. Probit function proved to be effective in quantifying the virulence of P. aeruginosa. The results of the killing curve analysis using the Probit function demonstrates that the slow-killing test is the most reliable method for quantifying virulence using the C elegans model of bacterial pathogenesis. Although the greatest virulence differences are observed after long periods of incubation, the Probit analysis clearly shows that the death kinetics of C elegans depend on the first hours of nematode/bacteria interaction. In contrast, fast killing seems to be non-specific, at least under our experimental conditions, since the killing rates of virulent P. aeruginosa and non-virulent E coli strains were indistinguishable. ------------------- Key: 6239 Medline: 14638858 Authors: Al-Bassam J;Cui Y;Klopfenstein D;Carragher BO;Vale RD;Milligan RA Title: Distinct conformations of the kinesin Unc104 neck regulate a monomer to dimer motor transition. Citation: Journal of Cell Biology 163: 743-753 2003 Type: ARTICLE Genes: unc-104 Abstract: Caenhorhabditis elegans Unc104 kinesin transports synaptic vesicles at rapid velocities. Unc104 is primarily monomeric in solution, but recent motility studies suggest that it may dimerize when concentrated on membranes. Using cryo-electron microscopy, we observe two conformations of microtubule-bound Unc104: a monomeric state in which the two neck helices form an intramolecular, parallel coiled coil; and a dimeric state in which the neck helices form an intermolecular coiled coil. The intramolecular folded conformation is abolished by deletion of a flexible hinge separating the neck helices, indicating that it acts as a spacer to accommodate the parallel coiled-coil configuration. The neck hinge deletion mutation does not alter motor velocity in vitro but produces a severe uncoordinated phenotype in transgenic C elegans, suggesting that the folded conformation plays an important role in motor regulation. We suggest that the Unc104 neck regulates motility by switching from a self-folded, repressed state to a dimerized conformation that can support fast processive movement. ------------------- Key: 6240 Medline: 14517217 Authors: Burgess J;Hihi AK;Benard CY;Branicky R;Hekimi S Title: Molecular mechanism of maternal rescue in the clk-1 mutants of Caenorhabditis elegans. Citation: Journal of Biological Chemistry 278: 49555-49562 2003 Type: ARTICLE Genes: clk-1 daf-2 Abstract: The clk-1 mutants of Caenorhabditis elegans display an average slowing down of physiological rates, including those of development, various behaviors, and aging. clk-1 encodes a hydroxylase involved in the biosynthesis of the redox-active lipid ubiquinone (co-enzyme Q), and in clk-1 mutants, ubiquinone is replaced by its biosynthetic precursor demethoxyubiquinone. Surprisingly, homozygous clk-1 mutants display a wild-type phenotype when issued from a heterozygous mother. Here, we show that this maternal effect is the result of the persistence of small amounts of maternally derived CLK-1 protein and that maternal CLK-1 is sufficient for the synthesis of considerable amounts of ubiquinone during development. However, gradual depletion of CLK-1 and ubiquinone, and expression of the mutant phenotype, can be produced experimentally by developmental arrest. We also show that the very long lifespan observed in daf-2 clk-1 double mutants is not abolished by the maternal effect. This suggests that, like developmental arrest, the increased lifespan conferred by daf-2 allows for depletion of maternal CLK-1, resulting in the expression of the synergism between clk-1 and daf-2. Thus, increased adult longevity can be uncoupled from the early mutant phenotypes, indicating that it is possible to obtain an increased adult lifespan from the late inactivation of ------------------- Key: 6241 Medline: 14623111 Authors: Im SH;Lee J Title: Identification of HMG-5 as a double-stranded telomeric DNA-binding protein in the nematode Caenorhabditis elegans. Citation: FEBS Letters 554: 455-461 2003 Type: ARTICLE Genes: ceh-37 hmg-5 Abstract: Many protein components of telomeres, the multifunctional DNA-protein complexes at the ends of eukaryotic chromosomes, have been identified in diverse species ranging from yeast to humans. In Caenorhabditis elegans, CEH-37 has been identified by a yeast one hybrid screen to be a double-stranded telomere-binding protein. However, the role of CEH-37 in telomere function is unclear because a deletion mutation in this gene does not cause severe telomere defects. This observation raises the possibility of the presence of genetic redundancy. To identify additional double-stranded telomere-binding proteins in C. elegans, we used a different approach, namely, a proteomic approach. Affinity chromatography followed by Finnigan LCQ ion trap mass spectrometer analysis allowed us to identify several candidate proteins. We further characterized one of these, HMG-5, which is encoded by F45E4.9. HMG-5 bound to double-stranded telomere in vitro as shown by competition assays. At least two telomeric DNA repeats were needed for this binding. HMG-5 was expressed in the nuclei of the oocytes and all embryonic cells, but not in the hatched larvae or adults. HMG-5 mainly localized to the chromosomal ends, indicating that HMG-5 also binds to telomeres in vivo. These observations suggest that HMG-5 may participate, together with CEH-37, in early embryogenesis by acting at the telomeres. ------------------- Key: 6242 Medline: 14659008 Authors: Gupta BP;Sternberg PW Title: The draft genome sequence of the nematode Caenorhabditis briggsae, a companion to C. elegans. Citation: Genome Biology 4: 16-19 2003 Type: ARTICLE Genes: Abstract: The publication of the draft genome sequence of Caenorhabditis briggsae improves the annotation of the genome of its close relative Caenorhabditis elegans and will facilitate comparative genomics and the study of the evolutionary changes during development. ------------------- Key: 6243 Medline: Authors: Tominaga N;Kohra S;Iguchi T;Arizono K Title: A multi-generation sublethal assay of phenols using the nematode Caenorhabditis elegans. Citation: Journal of Health Science 49: 459-463 2003 Type: ARTICLE Genes: Abstract: ------------------- Key: 6244 Medline: Authors: Page AP;Winter AD Title: Enzymes involved in the biogenesis of the nematode cuticle. Citation: Advances in Parasitology 53: 85-148 2003 Type: REVIEW Genes: bli-1 bli-2 bli-4 col-12 col-13 col-19 cut-1 cut-2 cyp-9 dpy-2 dpy-3 dpy-6 dpy-7 dpy-8 dpy-10 dpy-11 dpy-13 dpy-17 dpy-18 kpc-4 let-268 lin-29 lon-3 lrp-1 nhr-23 nhr-25 nhr-77 nhr-81 nhr-82 pdi-1 pdi-2 pdi-3 phy-1 phy-2 phy-3 phy-4 rol-6 rol-8 sqt-1 sqt-3 Abstract: Nematodes include species that are significant parasites of man, his domestic animals and crops, and cause chronic debilitating diseases in the developing world; such as lymphatic filariasis and river blindness caused by filarial species. Around one third of the World's population harbour parasitic nematodes; no vaccines exist for prevention of infection, limited effective drugs are available and drug resistance is an ever-increasing problem. A critical structure of the nematode is the protective cuticle, a collagen-rich extracellular matrix (ECM) that forms the exoskeleton, and is critical for viability. This resilient structure is synthesized sequentially five times during nematode development and offer protection from the environment, including the hosts' immune response. The detailed characterization of this complex structure; its components, and the means by which they are synthesized, modified, processed and assembled will identify targets that may be exploited in the future control of parasitic nematodes. This review will focus on the nematode cuticle. This structure is predominantly composed of collagens, a class of proteins that are modified by a range of co- and post-translational modifications prior to assembly into higher order complexes or ECMs. The collagens and their associated enzymes have been comprehensively characterized in vertebrate systems and some of these studies will be addressed in this review. Conversely, the biosynthesis of this class of essential structural proteins has not been studied in such detail in the nematodes. As with all morphogenetic, functional and developmental studies in the Nematoda phylum, the free-living species Caenorhabditis elegans has proven to be invaluable in the characterization of the cuticle and the cuticle collagen gene family, and is now proving to be an excellent model in the study of cuticle collagen biosynthetic enzymes. This model system will be the main ------------------- Key: 6245 Medline: Authors: Powell-Coffman JA Title: bHLH-PAS proteins in C. elegans. Citation: PAS Proteins: Regulators and Sensor of Development and Physiology. Kluwer Academic Publisher, Norwell. : 51-68 Type: REVIEW Genes: aha-1 ahr-1 daf-2 egl-9 hif-1 vhl-1 Abstract: During development and homeostasis, individual cells must divide, differentiate, migrate, adapt to the environment, or die at the appropriate times and places. A key to deciphering the molecular mechanisms by which cells make these decisions is to characterize the regulation and function of the proteins that regulate important changes in gene expression. The family of transcription factors that contain basic-helix-loop-helix and PAS motifs has been shown to control many critical developmental events and to mediate responses to certain environmental stimuli. For example, bHLH-PAS proteins play central roles in the development of specific neural tissues and vasculature, and they are core components of the molecular clock that govern circadian rhythms. bHLH-PAS proteins are also integral to the pathways that sense and respond to hypoxia (low oxygen) and certain xenobiotics (1). Phylogenetic analyses suggest that bHLH-PAS genes arose early in animal development, and in some cases, the functions of individual genes are largely conserved across phyla. This review describes the bHLH-PAS gene family in a genetic model organism, the nematode Caenorhabditis elegans. ------------------- Key: 6246 Medline: 14560955 Authors: Long X;Muller F;Avruch J Title: TOR action in mammalian cells and in Caenorhabditis Citation: Current Trends in Microbiology 279: 115-138 2003 Type: REVIEW Genes: Abstract: The p70 S6 kinase (p70 S6K) was the first signaling element in mammalian cells shown to be inhibited by rapamycin. The activity of the p70 S6K in mammalian cell is upregulated by extracellular amino acids (especially leucine) and by signals from receptor tyrosine kinases (RTKs), primarily through activation of the type 1A PI-3 kinase. The amino acid-/rapamycin-sensitive input and the PI-3 kinase input are co-dominant but largely independent, in that deletion of the amino-terminal and carboxy-terminal noncatalytic sequences flanking the p70 S6K catalytic domain renders the kinase insensitive to inhibition by both rapamycin and by withdrawal of amino acids, whereas this p70 S6K mutant remains responsive to activation by RTKs and to inhibition by wortmannin. At a molecular level, this dual control of p70 S6K activity is attributable to phosphorylation of the two p70 S6K sites: The Ptd Ins 3,4,5P(3)-dependent kinase1 (PDK1) phosphorylates p70 S6K at a Thr on the activation loop, whereas mTOR phosphorylates a Thr located in a hydrophobic motif carboxyterminal to the catalytic domain. Together these two phosphorylations engender a strong, positively cooperative activation of p70 S6K, so that each is indispensable for physiologic regulation. Like RTKs, the p70 S6K appears early in metazoan evolution and comes to represent an important site at which the more ancient, nutrient-responsive TOR pathway converges with the RTK/PI-3 kinase pathway in the control of cell growth. Dual regulation of p70 S6K is seen in Drosophila; however, this convergence is not yet evident in Caenorhabditis elegans, wherein nutrient activation of the insulin receptor (InsR) pathway negatively regulates dauer development and longevity, whereas the TOR pathway regulates overall mRNA translation through effectors distinct from p70 S6K, as in yeast. The C. elegans TOR and InsR pathways show none of the cross- or convergent regulation seen in mammalian cells. The nature of the elements that couple nutrient sufficiency to TOR activity remain to be discovered, and the mechanisms by which RTKs influence TOR activity in mammalian cells require further study. One pathway for RTK control involves the tuberous sclerosis complex, which is absent in C. elegans, but of major importance in Drosophila ------------------- Key: 6247 Medline: 12954713 Authors: Yu H;Pretot RF;Burglin TR;Sternberg PW Title: Distinct roles of transcription factors EGL-46 and DAF-19 in specifying the functionality of a polycystin-expressing sensory neuron necessary for C. elegans male vulva location behavior. Citation: Development 130: 5217-5227 2003 Type: ARTICLE Genes: ceh-26 daf-19 egl-44 egl-46 lov-1 nlp-8 osm-5 osm-6 pdk-2 Abstract: Caenorhabditis elegans polycystins LOV-1 and PKD-2 are expressed in the male-specific HOB neuron, and are necessary for sensation of the hermaphrodite vulva during mating. We demonstrate that male vulva location behavior and expression of lov-1 and pkd-2 in the ciliated sensory neuron HOB require the activities of transcription factor EGL-46 and to some extent also EGL-44. This EGL-46-regulated program is specific to HOB and is distinct from a general ciliogenic pathway functioning in all ciliated neurons. The ciliogenic pathway regulator DAF-19 affects downstream components of the HOB-specific program indirectly and is independent of EGL-46 activity. The sensory function of HOB requires the combined action of ------------------- Key: 6248 Medline: 14647365 Authors: Blaxter M Title: Two worms are better than one. Citation: Nature 426: 395-396 2003 Type: REVIEW Genes: Abstract: The genome of the microscopic worm Caenorhabditis briggsae has been sequenced, and show some remarkable differences from the genome of the better known - and physically similar - C. elegans. ------------------- Key: 6249 Medline: 14635135 Authors: Symersky J;Li S;Carson M;Luo D;Luan CH;Luo M Title: Structural genomics of Caenorhabditis elegans: structure of dihydropteridine reductase. Citation: Proteins: Structure, Function, and Genetics 53: 944-946 Type: ARTICLE Genes: Abstract: The biosynthesis of catecholamnes includes hydroxylation of the aromatic amino acids phenylalanin, tyrosine, and tryptophan. Corresponding hydroxylases use tetrahydrobiopterin (BH4), which is oxidized to a quinonoid form of dihydrobiopterin. ------------------- Key: 6250 Medline: 14635136 Authors: Symersky J;Lin G;Li S;Qiu S;Carson M;Schormann N;Luo M Title: Structural genomics of Caenorhabditis elegans: crystal structure of calmodulin. Citation: Proteins: Structure, Function, and Genetics 53: 947-949 Type: ARTICLE Genes: Abstract: Calmodulin (CaM), a conserved eucaryotic protein, can bind specifically to a large number of intracellular proteins and modulate their activity in response to the Ca2+ concentration. This small 17-kDa acidic protein belongs to a family of homologous calcium-binding proteins that bind Ca2+ through the EF-hand motif (e.g., parvalbumin or troponin C). A compact, calcium-free, apo form of CaM is converted to an extended dumbbell-shaped form on binding Ca2+. ------------------- Key: 6251 Medline: 14581619 Authors: Liedtke W;Tobin DM;Bargmann CI;Friedman JM Title: Mammalian TRPV4 (VR-OAC) directs behavioral responses to osmotic and mechanical stimuli in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 100: 14531-14536 2003 Type: ARTICLE Genes: elt-2 glr-1 ocr-2 odr-1 odr-3 osm-9 osm-10 sra-6 Abstract: All animals detect osmotic and mechanical stimuli, but the molecular basis for these responses is incompletely understood. The vertebrate transient receptor potential channel vanilloid subfamily 4 (TRPV4) (VR-OAC) cation channel has been suggested to be an osmo/mechanosensory channel. To assess its function in vivo, we expressed TRPV4 in Caenorhabditis elegans sensory neurons and examined its ability to generate behavioral responses to sensory stimuli. C elegans ASH neurons function as polymodal sensory neurons that generate a characteristic escape behavior in response to mechanical, osmotic, or olfactory stimuli. These behaviors require the TRPV channel OSM-9 because osm-9 mutants do not avoid nose touch, high osmolarity, or noxious odors. Expression of mammalian TRPV4 in ASH neurons of osm-9 worms restored avoidance responses to hypertonicity and nose touch, but not the response to odorant repellents. Mutations known to reduce TRPV4 channel activity also reduced its ability to direct nematode avoidance behavior. TRPV4 function in ASH required the endogenous C. elegans osmotic and nose touch avoidance genes ocr-2, odr-3, osm-10, and glr-1, indicating that TRPV4 is integrated into the normal ASH sensory apparatus. The osmotic and mechanical avoidance responses of TRPV4- expressing animals were different in their sensitivity and temperature dependence from the responses of wild-type animals, suggesting that the TRPV4 channel confers its characteristic properties on the transgenic animals' behavior. These results provide evidence that TRPV4 can function as a component of an osmotic/mechanical sensor in ------------------- Key: 6252 Medline: 14668850 Authors: Vellai T;Takacs-Vellai K;Zhang Y;Kovacs AL;Orosz L;Muller F Title: Influence of TOR kinase on lifespan in C. elegans. Citation: Nature 426: 620- 2003 Type: ARTICLE Genes: daf-2 daf-16 let-363 Abstract: The group of enzymes known as TOR (for 'target of rapamycin') kinases regulates cell growth and proliferation in response to nutrients and hormone-dependent mitogenic signals. Here we show that TOR deficiency in the nematode Caenorhabditis elegans more than doubles its natural lifespan. This new function for TOR signalling in ageing control may represent a link between nutrition, metabolism and longevity. ------------------- Key: 6253 Medline: 14656969 Authors: Cutter AD;Payseur BA;Salcedo T;Estes AM;Good JM;Wood E;Hartl T;Maughan H;Strempel J;Wang BM;Bryan AC;Dellos M Title: Molecular correlates of genes exhibiting RNAi phenotypes in Caenorhabditis elegans. Citation: Genome Research 13: 2651-2657 2003 Type: ARTICLE Genes: Abstract: Understanding genome-wide links between genotype and phenotype has generally been difficult due to both the complexity of phenotypes, and until recently, inaccessibility to large numbers of genes that might underlie a trait. To address this issue, we establish the association between particular RNAi phenotypes in Caenorhabditis elegans and sequence characteristics of the corresponding proteins and DNA. We find that genes showing RNAi phenotypes are long and highly expressed with little noncoding DNA and high rates of synonymous site substitution (K.). In addition, genes conferring RNAi phenotypes have significantly lower rates of nonsynonymous site substitution (K-A). Collectively, these sequence features explain nearly 20% of the difference between the sets of loci that display or lack a RNAi-mediated effect, and reflect aspects both of the RNA! mechanism and the biological function of the genes. For example, the particularly low rate of evolution of genes in the sterility RNAi phenotype class suggests a role of C elegans life history in shaping these patterns of sequence and expression characteristics on phenotypes. This approach also allows prediction of a set of heretofore-uncharacterized loci for which we expect future RNAi studies to reveal phenotypic effects (i.e., false ------------------- Key: 6254 Medline: 14653817 Authors: Mohrlen F;Hutter H;Zwilling R Title: The astacin protein family in Caenorhabditis elegans. Citation: European Journal of Biochemistry 270: 4909-4920 2003 Type: ARTICLE Genes: nas-1 nas-2 nas-3 nas-4 nas-5 nas-6 nas-7 nas-8 nas-9 nas-10 nas-11 nas-12 nas-13 nas-14 nas-15 nas-16 nas-17 nas-18 nas-19 nas-20 nas-21 nas-22 nas-23 nas-24 nas-25 nas-26 nas-27 nas-28 nas-29 nas-30 nas-31 nas-32 nas-33 nas-34 nas-35 nas-36 nas-37 nas-38 nas-39 nas-40 Abstract: In the nematode Caenorhabditis elegans, 40 genes code for astacin-like proteins (nematode astacins, NAS). The astacins are metalloproteases present in bacteria, invertebrates and vertebrates and serve a variety of physiological functions like digestion, hatching, peptide processing, morphogenesis and pattern formation. With the exception of one distorted pseudogene, all the other C. elegans astacins are expressed and are evidently functional. For 13 genes we found splicing patterns differing from the Genefinder predictions in WormBase, sometimes markedly. The GFP expression pattern for NAS-4 shows a specific localization in anterior pharynx cells and in the whole digestive tract (as the secreted form). In contrast, NAS-7 is found in the head of adult hermaphrodites, but not in pharynx cells or in the lumen of the digestive tract. In embryos, NAS-7 fluorescence becomes detectable just before hatching. In C. elegans astacins, three basic structural and functional moieties can be discerned: a prepro portion, the central catalytic chain and long C-terminal extensions with presumably regulatory functions. Within the regulatory moiety, EFG-like, CUB, SXC, and ISP-1 domains can be distinguished. Based on structural differences of the regulatory unit we established six NAS subgroups, which seemingly represented different functional and evolutionary clusters. This pattern deduced exclusively from the domain arrangement in the regulatory moiety is perfectly reflected in an evolutionary tree constructed solely from amino acid sequence information of the catalytic chain. Related catalytic chains tend to have related regulatory ------------------- Key: 6255 Medline: 14713049 Authors: Boyd WA;Cole RD;Anderson GL;Williams PL Title: The effects of metals and food availability on the behavior of Caenorhabditis elegans. Citation: Environmental Toxicology & Chemistry 22: 3049-3055 2003 Type: ARTICLE Genes: Abstract: Caenorhabdiris elegons, a nonparasitic soil nematode, was used to assess the combined effects of metal exposures and food availability on behavior. Movement was monitored using a computer tracking system after exposures to Cu, Pb, or Cd while feeding was measured as a change in optical density (DeltaOD) of bacteria suspensions over the exposure period. After 24-h exposures at hig and low bacteria concentrations. movement was decreased in a concentration-dependent fashion by Pb and Cd but feeding reductions were not directly proportional to exposure concentrations. Copper exposure induced concentration-dependent declines in feeding and movement regardless of bacteria concentration. The impact of 24-h metal exposures was apparently reduced by increasing food availability. Therefore, exposures were shortened to 4 It in an attempt to minimize starvation effects on movement. Although nematodes were immobilized following 24 h of food depravation, worms deprived of food during the 4-h exposure continued to feed and move after exposure. A bead-ingestion assay after 4-h exposures was also used as an additional means of assessing the effects of metals on feeding behavior. Ingestion was significantly reduced by all concentrations of metals tested, indicating its sensitivity as a sublethal assay. Feeding (AOD) during exposures exhibited similar trends as ingestion but was slightly less sensitive. while movement was the least sensitive assay of 4-h metal exposures to C. elegans. Assessment of multiple sublethal endpoints allowed for the determination of the separate and interactive effects of metals and food ------------------- Key: 6256 Medline: 14654017 Authors: Blackwell TK;Walker AK Title: Transcription elongation: TLKing to chromatin? Citation: Current Biology 13: R915-R916 2003 Type: REVIEW Genes: tlk-1 Abstract: The tousled-like kinases have been implicated in chromatin deposition, but surprising new findings in Caenorhabditis elegans indicate they have a role in transcription elongation. Are these apparently distinct functions of tousled-like kinases related? ------------------- Key: 6257 Medline: 14630038 Authors: Fostel JL;Coste LB;Jacobson LA Title: Degradation of transgene-coded and endogenous proteins in the muscles of Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 312: 173-177 2003 Type: ARTICLE Genes: Abstract: To develop reporter systems to study the regulation of protein degradation in innervated muscle, we have used strains of the nematode Caenorhabditis elegans containing transgenes that fuse lacZ or green fluorescent protein (GFP) coding regions to muscle-specific promoter/enhancer regions, such that the fusion proteins are expressed exclusively in body-wall and vulval muscle cells. The starvation-induced degradation of the beta-galactosidase reporter protein is quantitatively similar to that of two endogenous muscle proteins, arginine kinase and adenylate kinase. A soluble GFP in the muscle cytosol is degraded during starvation, but when GFP is fused to a full-length myosin heavy chain and incorporated into myofibrils, it is resistant to starvation-induced degradation. This suggests that under some conditions soluble muscle proteins may be extensively catabolized in preference to the proteins of the contractile fibers. ------------------- Key: 6258 Medline: Authors: Scholey JM Title: Intraflagellar transport. Citation: Annual Review of Cell & Developmental Biology 19: 423-443 2003 Type: REVIEW Genes: Abstract: It has been a decade since a novel form of microtubule (MT)-based motility, i.e., intraflagellar transport (IFT), was discovered in Chlamydomonas flagella. Subsequent research has supported the hypothesis that IFT is required for the assembly and maintenance of all cilia and flagella and that its underlying mechanism involves the transport of nonmembrane-bound macromolecular protein complexes (IFT particles) along axonemal MTs beneath the ciliary membrane. IFT requires the action of the anterograde kinesin-H motors and the retrograde IFT-dynein motors to transport IFT particles in opposite directions along the MT polymer lattice from the basal body to the tip of the axoneme and back again. A rich diversity of biological processes has been shown to depend upon IFT, including flagellar length control, cell swimming, mating and feeding, photoreception, animal development, sensory perception, chemosensory behavior, and lifespan control. These processes reflect the varied roles of cilia and flagella in motility and sensory signaling. ------------------- Key: 6259 Medline: Authors: Lai EC Title: microRNAs: Runts of the genome assert themselves. Citation: Current Biology 13: R925-R936 2003 Type: REVIEW Genes: let-7 lin-4 lin-14 Abstract: microRNAs form an abundant class of 21-22 nucleotide, non-coding RNA that is common to diverse species of multicellular life. Although they are currently the subject of intense, directed study, the path toward their discovery has been dominated by chance and serendipity. In this review, I examine how these tiny molecules have risen from genetic obscurity to scientific stardom, and discuss the emerging biological functions of these novel ------------------- Key: 6260 Medline: 14685240 Authors: Johnston RJ;Hobert O Title: A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Citation: Nature 426: 845-849 2003 Type: ARTICLE Genes: ceh-36 cog-2 gcy-5 gcy-6 gcy-7 lim-6 lsy-6 Abstract: How left/right functional asymmetry is layered on top of an anatomically symmetrical nervous system is poorly understood. In the nematode Caenorhabditis elegans, two morphologically bilateral taste receptor neurons, ASE left (ASEL) and ASE right (ASER), display a left/right asymmetrical expression pattern of putative chemoreceptor genes that correlates with a diversification of chemosensory specificities(1,2). Here we show that a previously undefined microRNA termed lsy-6 controls this neuronal left/right asymmetry of chemosensory receptor expression. lsy-6 mutants that we retrieved from a genetic screen for defects in neuronal left/right asymmetry display a loss of the ASEL-specific chemoreceptor expression profile with a concomitant gain of the ASER-specific profile. Alsy-6 reporter gene construct is expressed in less than ten neurons including ASEL, but not ASER. lsy-6 exerts its effects on ASEL through repression of cog-1, an Nkx-type homeobox gene, which contains a lsy-6 complementary site in its 30 untranslated region and that has been shown to control ASE-specific chemoreceptor expression profiles(3). lsy-6 is the first microRNA to our knowledge with a role in neuronal patterning, providing new insights into left/right axis formation. ------------------- Key: 6261 Medline: 14530273 Authors: Jonassen T;Davis DE;Larsen PL;Clarke CF Title: Reproductive fitness and quinone content of Caenorhabditis elegans clk-1 mutants fed coenzyme Q isoforms of varying length. Citation: Journal of Biological Chemistry 278: 51735-51742 2003 Type: ARTICLE Genes: clk-1 Abstract: Caenorhabditis elegans clk-1 mutants lack coenzyme Q(9) and accumulate the biosynthetic intermediate demethoxy-Q(9). A dietary source of ubiquinone (Q) is required for larval growth and development of the gonad and germ cells. We considered that uptake of the shorter Q(8) isoform present in the Escherichia coli food may contribute to the Clk phenotypes of slowed development and reduced brood size observed when the animals are fed Q-replete E. coli. To test the effect of isoprene tail length, N2 and clk-1 animals were fed E. coli engineered to produce Q(7), Q(8), Q(9), or Q(10). Wild-type nematodes showed no change in reproductive fitness regardless of the Q(n) isoform fed. clk-1(e2519) fed the Q(9) diet showed increased egg production; however, this diet did not improve reproductive fitness of the clk-1(qm30) animals. Furthermore, animals with the more severe clk-1(qm30) allele become sterile and their progeny inviable when fed Q(7)-containing bacteria. The content of Q(7) in the mitochondria of clk-1 animals was decreased relative to Q(8), suggesting less effective transport of Q(7) to the mitochondria, impaired retention, or decreased stability. Additionally, regardless of E. coli diet, clk-1(qm30) animals contain a dysfunctional dense form of mitochondria. The gonads of clk-1(qm30) worms fed Q(7)-containing food were severely shrunken and disordered. The differential fertility of clk-1 mutant nematodes fed Q isoforms may result from changes in Q localization, altered recognition by Q-binding proteins, and/or potential defects in mitochondrial function resulting from the mutant CLK-1 polypeptide itself. ------------------- Key: 6262 Medline: 14644423 Authors: Lee MH;Han SM;Han JW;Kim YM;Ahnn J;Koo HS Title: Caenorhabditis elegans dna-2 is involved in DNA repair and is essential for germ-line development. Citation: FEBS Letters 555: 250-256 2003 Type: ARTICLE Genes: dna-2 mre-11 Abstract: Caenorhabditis elegans germ cell proliferation and development were severely damaged in second generation dna-2 homozygotes. Even in the first generation, a much higher incidence of aberrant chromosomes in oocytes and resultantly higher embryonic lethality were found vs. wild type, when DNA breaks were induced by gamma-rays or camptothecin. The deficiency of dna-2 in combination with RNA interference on mre-11 gene expression synergistically aggravated germ-line development, especially oocyte formation. These results suggest that C. elegans Dna-2 is involved in a DNA repair pathway paralleling homologous recombination or non-homologous end joining with mre-11 ------------------- Key: 6263 Medline: 14684823 Authors: Berry KL;Bulow HE;Hall DH;Hobert O Title: A C. elegans CLIC-like protein required for intracellular tube formation and maintenance. Citation: Science 302: 2134-2137 2003 Type: ARTICLE Genes: exc-4 Abstract: The Caenorhabditis elegans excretory canal is composed of a single elongated and branched cell that is tunneled by an inner lumen of apical character. Loss of the exc-4 gene causes a cystic enlargement of this intracellular tube. exc-4 encodes a member of the chloride intracellular channel (CLIC) family of proteins. EXC-4 protein localizes to various tubular membranes in distinct cell types, including the lumenal membrane of the excretory tubes. A conserved 55 - amino acid domain enables EXC-4 translocation from the cytosol to the lumenal membrane. The tubular architecture of this membrane requires EXC-4 for both its formation and maintenance. ------------------- Key: 6264 Medline: 14677634 Authors: Sampayo JN;Olsen A;Lithgow GJ Title: Oxidative stress in Caenorhabditis elegans: protective effects of superoxide dismutase/catalase mimetics. Citation: Aging Cell 2: 319-326 2003 Type: REVIEW Genes: Abstract: The lifespan of Caenorhabditis elegans can be extended by the administration of synthetic superoxide dismutase/ catalase mimetics (SCMs) without any effects on development or fertility. Here we demonstrate that the mimetics, Euk-134 and Euk-8, confer resistance to the oxidative stress-inducing agent, paraquat and to thermal stress. The protective effects of the compounds are apparent with treatments either during development or during adulthood and are independent of an insulin/IGF-I-like signalling pathway also known to affect thermal and oxidative stress resistance. Worms exposed to the compounds do not induce a cellular stress response and no detrimental effects are observed. ------------------- Key: 6265 Medline: Authors: McElwee J;Bubb K;Thomas JH Title: Transcriptional outputs of the Caenorhabditis elegans forkhead protein DAF-16. Citation: Aging Cell 2: 341- 2003 Type: CORRECT Genes: Abstract: ------------------- Key: 6266 Medline: 14657363 Authors: Yau DM;Yokoyama N;Goshima Y;Siddiqui ZK;Siddiqui SS;Kozasa Title: Identification and molecular characterization of the Galpha12-Rho guanine nucleotide exchange factor pathway in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 100: 14748-14753 2003 Type: ARTICLE Genes: gpa-12 rrf-3 Abstract: Galpha12/13-mediated pathways have been shown to be involved in various fundamental cellular functions in mammalian cells such as axonal guidance, apoptosis, and chemotaxis. Here, we identified a homologue of Rho-guanine nucleotide exchange factor (GEF) in Caenorhabditis elegans (CeRhoGEF), which functions downstream of gpa-12, the C elegans homologue of Galpha12/13. CeRhoGEF contains a PSD-95/Dlg/ZO-1 domain and a regulator of G protein signaling (RGS) domain upstream of the Dbl hornology-pleckstrin homology region similar to mammalian RhoGEFs with RGS domains, PSD-95/Dlg/ZO-1-RhoGEF and leukemia-associated RhoGEF. It has been shown in mammalian cells that these RhoGEFs interact with activated forms of Galpha12 or Galpha13 through their RGS domains. We demonstrated by coimmunoprecipitation that the RGS domain of CeRhoGEF interacts with GPA-12 in an AIF(4)(-) activation-dependent manner and confirmed that the Dbl homologypleckstrin homology domain of CeRhoGEF was capable of Rhodependent signaling. These results proved conservation of the Galpha12-RhoGEF pathway in C elegans. Expression of DsRed or GFP under the control of the promoter of CeRhoGEF or gpa-12 revealed an overlap of their expression patterns in ventral cord motor neurons and several neurons in the head. RNA-mediated gene interference for CeRhoGEF and gpa-12 resulted in similar phenotypes such as embryonic lethality and sensory and locomotive defects in adults. Thus, the Galpha12/13-RhoGEF pathway is likely ------------------- Key: 6267 Medline: 14768892 Authors: Preclin V;Martin E;Segalat L Title: Target sequences of Tc1, Tc3 and Tc5 transposons of Caenorhabditis elegans. Citation: Genetical Research 82: 85-88 2003 Type: ARTICLE Genes: gpa-2 mut-7 Abstract: We report here the consensus target sequence of transposons Tc1, Tc3 and Tc5 of Caenorhabditis elegans. These sequences were obtained by molecular analysis of 1008 random new insertions which have not been exposed to natural selection. This analysis reveals consensus target sites slightly different from those previously reported, and confirms that the mariner elements Tc1 and Tc3 insert in sites which are not preferentially palindromic. ------------------- Key: 6268 Medline: 14642561 Authors: Jeong YS;Kang Y;Lim KH;Lee MH;Lee J;Koo HS Title: Deficiency of Caenorhabditis elegans RecQ5 homologue reduces life span and increases sensitivity to ionizing Citation: DNA Repair 2: 1309-1319 2003 Type: ARTICLE Genes: him-6 rcq-5 Abstract: Gene expression and RNA interference phenotypes were investigated for a Caenorhabditis elegans homologue (Ce-RCQ-5) of human RecQ5 protein. Expression of the mRNA was observed by in situ hybridization from earliest embryogenesis and gradually decreased during late embryogenesis. Ce-RCQ-5 was immuno-localized in the nuclei of embryos, germ cells, and oocytes and also in the nuclei of various somatic cells of larvae and adults. Despite ubiquitous expression in postembryonic cells, RCQ-5 protein expression was highest in intestinal cells, which was confirmed by tagging the gene expression with green fluorescence protein. When endogenous Ce-rcq-5 gene expression was inhibited by RNA interference, no clear phenotypes were observed during development. However, C. elegans life span was reduced by 37% due to RNA interference of rcq-5 gene, suggesting its possible role in maintenance of genomic stability, as has been ascribed to other RecQ family DNA helicases. In addition, C. elegans became significantly more sensitive to ionizing radiation after inhibition of rcq-5 gene expression, indicating an involvement of C. elegans RCQ-5 in a cellular response to DNA damage, possibly in DNA repair. ------------------- Key: 6269 Medline: 14651925 Authors: Kim C;Forrester WC Title: Functional analysis of the domains of the C. elegans Ror receptor tyrosine kinase CAM-1. Citation: Developmental Biology 264: 376-390 2003 Type: ARTICLE Genes: cam-1 Abstract: cam-1 encodes a Caenorhabditis elegans orphan receptor tyrosine kinase (RTK) of the Ror family that is required for cell migration and to orient cell polarity. Ror RTKs share a common domain structure. The predicted extracellular region contains immunoglobulin (Ig), cysteine-rich (CRD), and kringle (Kri) domains. Intracellularly are tyrosine kinase (Kin) and serine- and threonine (S/T)-rich domains. To investigate the functional requirement for CAM-1 domains in mediating cell migration, we engineered deletions that remove various domains and assessed the ability of these CAM-1 derivatives to rescue cam-1 mutant phenotypes. We find that the Ig, Kri, Kin, and S/T domains are dispensable for cell migration, but the CRD is required. Surprisingly, the entire intracellular region of CAM-1 is not required for proper cell migration. Most notably, a version of CAM-1 from which all domains besides the CRD and transmembrane domains have been deleted is able to rescue the migration of a single cell type, although not those of other cell types. Our results show that CAM-1 does not function exclusively as a canonical RTK and that it may function, at least in part, to regulate the distribution of a secreted ligand-possibly a Writ protein. ------------------- Key: 6270 Medline: 14644192 Authors: Glotzer M Title: Cytokinesis: progress on all fronts. Citation: Current Opinion in Cell Biology 15: 684-690 2003 Type: REVIEW Genes: let-21 par-2 zen-4 Abstract: Cell multiplication requires sequestration of the duplicated and segregated genome into two daughter cells. The mitotic spindle is critical for orchestrating sister chromatid separation and division plane positioning. During anaphase, spindle microtubules become bundled to form the central spindle, which is essential for completion of cytokinesis. Central spindle assembly is mediated by a microtubule-associated protein and a kinesin-RhoGAP complex, both of which are regulated by phosphorylation/dephosphorylation. The central spindle also plays a role in cleavage furrow positioning, which appears to involve activation of RhoA. New results have provided some initial clues as to how furrow positioning is achieved. Particularly notable is the discovery that a protein activated by RhoA, formin, has actin nucleation ------------------- Key: 6271 Medline: 14638320 Authors: Aboobaker A;Blaxter M Title: Hox gene evolution in nematodes: novelty conserved. Citation: Current Opinion in Genetics & Development 13: 593-598 2003 Type: REVIEW Genes: ced-3 ceh-13 egl-5 let-60 lin-3 lin-39 mab-3 mab-5 mes-2 mes-3 mes-6 nob-1 pal-1 php-3 sop-2 Abstract: The conserved homeobox (Hox) gene cluster is neither conserved nor clustered in the nematode Caenorhabditis elegans. Instead, C. elegans has a reduced and dispersed gene complement that is the result the loss of Hox genes in stages throughout its evolutionary history. The roles of Hox genes in patterning the nematode body axis are also divergent, although there are tantalising remnants of ancient regulatory systems. Hox patterning also differs greatly between C. elegans and a second "model" nematode, Pristionchus pacificus. The pattern of Hox gene evolution may be indicative of the move to deterministic developmental modes in nematodes. ------------------- Key: 6272 Medline: 14675154 Authors: Estevez M;Estevez AO;Cowie RH;Gardner KL Title: The voltage-gated calcium channel UNC-2 is involved in stress-mediated regulation of tryptophan hydroxylase. Citation: Journal of Neurochemistry 88: 102-113 2004 Type: ARTICLE Genes: bas-1 daf-1 daf-2 daf-3 daf-4 daf-5 daf-7 daf-8 daf-12 daf-14 dbl-1 sma-2 sma-3 sma-4 sma-6 tph-1 unc-2 unc-43 Abstract: Migraine is an episodic pain disorder whose pathophysiology is related to deficiency of serotonin signaling and abnormal function of the P/Q-type calcium channel, CACNA1A. Because the relationship of the CACNA1A channel to serotonin signaling is unknown and potentially of therapeutic interest we have used genetic analysis of the Caenorhabditis elegans ortholog of this calcium channel, UNC-2, to help identify candidate downstream effectors of the human channel. By genetic dissection of the lethargic mutant phenotype of unc-2, we have established an epistasis pathway showing that UNC-2 function antagonizes a transforming growth factor (TGF)-beta pathway influencing movement rate. This same UNC-2/TGF-beta pathway is required for accumulation of normal serotonin levels and stress-induced modulation of tryptophan hydroxylase (tph) expression in the serotonergic chemosensory ADF neurons, but not the NSM neurons. We also show that transgenic expression of the migraine-associated Ca2+ channel, CACNA1A, in unc-2 animals can functionally substitute for UNC-2 in stress-activated regulation of tph expression. The demonstration that these evolutionarily related channels share a conserved ability to modulate tph expression through their effects on TGF-beta signaling provides the first specific example of how CACNA1A function may influence levels of the critical migraine neurotransmitter ------------------- Key: 6273 Medline: 14641049 Authors: Sampayo JN;Gill MS;Lithgow GJ Title: Oxidative stress and aging - the use of superoxide dismutase/catalase mimetics to extend lifespan. Citation: Biochemical Society Transactions 31: 1305-1307 2003 Type: ARTICLE Genes: age-1 clk-1 daf-2 ins-1 ins-18 isp-1 lrs-2 pdk-1 sir-2.1 unc-31 unc-64 Abstract: To date, more than 40 genes have been identified in the nematode Coenorhabditis elegans, which, when mutated, lead to an increase in lifespan. Of those tested, all confer an increased resistance to oxidative stress. in addition, the lifespan of C elegans can also be extended by the administration of synthetic superoxide dismutase/catalase mimetics. These compounds also appear to confer resistance to oxidative damage, since they protect against paraquat treatment. The protective effects of these compounds are apparent with treatment during either development or adulthood. These findings have demonstrated that pharmacological intervention in the aging process is possible and that these compounds can provide important information about the underlying mechanisms. To date, such interventions have targeted known processes rather than screening compound libraries because of the limitations of assessing lifespan in nematodes. However, we have recently developed a microplate-based assay that allows for a rapid and objective score of nematode survival at rates many times higher than previously possible. This system now provides the opportunity to perform high-throughput screens for compounds that affect nematode survival in the face of acute oxidative stress and will facilitate the identification of novel drugs that extend nematode ------------------- Key: 6274 Medline: Authors: Srinivasan J;Sinz W;Jesse T;Wiggers-Perebolte L;Jansen K;Buntjer J;van der Meulen M;Sommer RJ Title: An integrated physical and genetic map of the nematode Pristionchus pacificus. Citation: Molecular Genetics & Genomics 269: 715-722 2003 Type: ARTICLE Genes: Abstract: The free-living nematode Pristionchus pacificus is one of several species that have recently been developed as a satellite system for comparative functional studies in evolutionary developmental biology. Comparisons of developmental processes between P. pacificus and the well established model organism Caenorhabditis elegans at the cellular and genetic levels provide detailed insight into the molecular changes that shape evolutionary transitions. To facilitate genetic analysis and cloning of mutations in P. pacificus, we previously generated a BAC-based genetic linkage map for this organism. Here, we describe the construction of a physical map of P. pacificus genome based on AFLP fingerprint analysis of 7747 BAC clones. Most of the SSCP markers used to generate the genetic linkage map were derived from BAC ends, so that the physical genome map and the genetic map can be integrated. The contigs that make up the physical map are evenly distributed over the genetic linkage map and no clustering is observed, indicating that the physical map provides a valid representation of the P. pacificus genome. The integrated genome map thus provides a framework for positional cloning and the study of genome evolution in nematodes. ------------------- Key: 6275 Medline: 14675531 Authors: Davies AG;Pierce-Shimomura JT;Kim H;VanHoven MK;Thiele TR;Bonci A;Bargmann CI;McIntire SL Title: A central role of the BK potassium channel in behavioral responses to ethanol in C. elegans. Citation: Cell 115: 655-666 2003 Type: ARTICLE Genes: dgk-1 goa-1 slo-1 Abstract: The activities of many neuronal proteins are modulated by ethanol, but the fundamental mechanisms underlying behavioral effects of ethanol remain unclear. To identify mechanisms responsible for intoxication, we screened for Caenorhabditis elegans mutants with altered behavioral responses to ethanol. We found that slo-1 mutants, which were previously recognized as having slightly uncoordinated movement, are highly resistant to ethanol in two behavioral assays. Numerous loss-of-function slo-1 alleles emerged from our screens, indicating that slo-1 has a central role in ethanol responses. slo-1 encodes the BK potassium channel. Electrophysiological analysis shows that ethanol activates the channel in vivo, which would inhibit neuronal activity. Moreover, behaviors of slo-1 gain-of-function mutants resemble those of ethanol-intoxicated animals. These results demonstrate that selective activation of BK channels is responsible for acute intoxicating effects of ethanol in C. elegans. BK channel activation may explain a variety of behavioral responses to ethanol in invertebrate and vertebrate systems. ------------------- Key: 6276 Medline: Authors: Herman RK Title: The tale behind the worm. Citation: Science 303: 42- 2004 Type: REVIEW Genes: Abstract: I'm one of the 2000 or so worm people who study the tiny nematode Caenorhabditis elegans. When we are asked by an outsider why we play with worms, our much-practiced answer goes something like this: In the mid-1960s, Sydney Brenner chose C. elegans as a model organism for elucidating animal development and behavior because of the roundworm's cellular simplicity and advantages for genetic studies. The analysis of mutants helps us learn what the nonmutant versions of genes do. We know the location and lineage of every cell in an adult C. elegans as well as the wiring of all the worm's 302 neurons, down to the last synapse. C. elegans was the first multicellular organism to have its DNA completely sequenced (1), and many of its genes resemble those of humans and do similar jobs. The importance of such research was highlighted when Brenner, John Sulston, and Bob Horvitz were awarded the 2002 Nobel Prize in physiology or medicine for their worm work. ------------------- Key: 6277 Medline: Authors: Labouesse M Title: Caenorhabditis elegans. Citation: M S-Medecine Sciences 19: 1171-1172 2003 Type: REVIEW Genes: Abstract: (In French.) ------------------- Key: 6278 Medline: Authors: Pujol N;Ewbank JJ Title: A worm's life. Citation: M S-Medecine Sciences 19: 1209-1217 2003 Type: REVIEW Genes: clk-1 daf-2 daf-16 dbl-1 glp-1 nsy-1 odr-10 pmk-1 sek-1 str-2 Abstract: Despite its relative anatomic simplicity, the nematode Caenorhabditis elegans (C. elegans) is a complex multicellular organism. In this review, we describe studies that have contributed to a better understanding of certain aspects of the worm's physiology. We focus on the cellular and molecular basis of the interaction between C. elegans and its environment, including its sensory capacities, the intrinsic biological clock that governs the speed of its life, and on some of the factors that control its life span. We also outline very recent findings that have demonstrated the existence of an innate immune system in C. elegans. Finally, we highlight a number of novel techniques that are transforming the worm from a largely genetic model system into an attractive organism for functional genomic ------------------- Key: 6279 Medline: Authors: Segalat L;Neri C Title: C. elegans as a model for human inherited degenerative diseases. Citation: M S-Medecine Sciences 19: 1218-1225 2003 Type: REVIEW Genes: dyc-1 dys-1 egl-19 hlh-1 mec-3 mec-7 osm-10 Abstract: C. elegans as a model for human inherited degenerative diseases. The nematode C. elegans is an established model for developmental biology. Since the early 90's, this simple model organism has been increasingly used for studying human disease pathogenesis. C. elegans models based either on the mutagenesis of human disease genes conserved in this nematode or transgenesis with disease genes not conserved in C. elegans show several features that are observed in mammalian models. These observations suggest that the genetic dissection and pharmacological manipulation of disease-like phenotypes in C. elegans will shed light on the cellular mechanisms that are altered in human diseases, and the compounds that may be used as drugs. This review illustrates these aspects by commenting on two inherited degenerative diseases, Duchenne's muscular dystrophy and Huntington's neurodegenerative disease. ------------------- Key: 6280 Medline: Authors: Weimer RM;Jorgensen EM Title: Controversies in synaptic vesicle exocytosis. Citation: Journal of Cell Science 116: 3661-3666 2003 Type: REVIEW Genes: unc-13 unc-18 Abstract: At the heart of synaptic transmission resides the synaptic vesicle cycle- a membrane trafficking pathway in which small membrane-bound vesicles mediate the release of neurotransmitter from presynaptic terminals. The cycle resembles general membrane trafficking and has three phases: vesicle filling, release and recycling. During filling, neurotransmitter is loaded into vesicles via vesicular neurotransmitter transporters. It is then released by exocytosis: vesicles dock with the plasma membrane and undergo a maturation step, termed priming; then, following influx of calcium through voltage-gated channels, a calcium sensor promotes fusion of the vesicle with the plasma membrane. Membrane fusion consumes vesicle membrane and vesicle proteins; thus, these components must be recycled to sustain neurotransmitter release. ------------------- Key: 6281 Medline: 12915588 Authors: Cram EJ;Clark SG;Schwarzbauer JE Title: Talin loss-of-function uncovers roles in cell contractility and migration in C. elegans. Citation: Journal of Cell Science 116: 3871-3878 2003 Type: ARTICLE Genes: pat-2 pat-3 Abstract: Integrin receptors for extracellular matrix transmit mechanical and biochemical information through molecular connections to the actin cytoskeleton and to several intracellular signaling pathways. In Caenorhabditis elegans, integrins are essential for embryonic development, muscle cell adhesion and contraction, and migration of nerve cell axons and gonadal distal tip cells. To identify key components involved in distal tip cell migration, we are using an RNA interference (RNAi)-based genetic screen for deformities in gonad morphogenesis. We have found that talin, a cytoskeletal-associated protein and focal adhesion component, is expressed in the distal tip cell and plays a central role in regulating its migration. Reduction of talin expression caused severe defects in gonad formation because of aberrant distal tip cell migration and also disrupted oocyte maturation and gonad sheath cell structure. Contractile muscle cells showed disorganization of the actin cytoskeleton leading to complete paralysis, a phenotype that was also observed with depletion of pat-2 and pat-3 integrins. These in vivo analyses show that talin is required not only for strong adhesion and cytoskeletal organization by contractile cells, but also for dynamic regulation of integrin signals during cell migration. In addition, induction of distal tip cell migration defects by bacterial RNAi in C. elegans provides an effective screen to identify genes involved in integrin signaling and ------------------- Key: 6282 Medline: 14625390 Authors: Lesa GM;Palfreyman M;Hall DH;Clandinin MT;Rudolph C;Jorgensen EM;Schiavo G Title: Long chain polyunsaturated fatty acids are required for efficient neurotransmission in C. elegans. Citation: Journal of Cell Science 116: 4965-4975 2003 Type: ARTICLE Genes: egl-1 elt-2 fat-3 rab-3 Abstract: The complex lipid constituents of the eukaryotic plasma membrane are precisely controlled in a cell-type-specific manner, suggesting an important, but as yet, unknown cellular function. Neuronal membranes are enriched in long-chain polyunsaturated fatty acids (LC-PUFAs) and alterations in LC-PUFA metabolism cause debilitating neuronal pathologies. However, the physiological role of LC-PUFAs in neurons is unknown. We have characterized the neuronal phenotype of C. elegans mutants depleted of LC-PUFAs. The C. elegans genome encodes a single Delta6-desaturase gene (fat-3), an essential enzyme for LC-PUFA biosynthesis. Animals lacking fat-3 function do not synthesize LC-PUFAs and show movement and egg-laying abnormalities associated with neuronal impairment. Expression of functional fat-3 in neurons, or application of exogenous LC-PUFAs to adult animals rescues these defects. Pharmacological, ultrastructural and electrophysiological analyses demonstrate that fat-3 mutant animals are depleted of synaptic vesicles and release abnormally low levels of neurotransmitter at cholinergic and serotonergic neuromuscular junctions. These data indicate that LC-PUFAs are essential for efficient neurotransmission in C. elegans and may account for the clinical conditions associated with mis-regulation of ------------------- Key: 6283 Medline: Authors: Evans CJ;Aguilera RJ Title: DNase II: genes, enzymes and function. Citation: Gene 322: 1-15 2003 Type: REVIEW Genes: cps-6 crn-1 crn-2 crn-3 crn-4 crn-5 cyp-13 nuc-1 Abstract: Deoxyribonuclease (DNase) II, which was discovered more than 50 years ago, is a mammalian endonuclease that functions optimally at acid pH in the absence of divalent cations. Its lysosomal localization and ubiquitous tissue distribution suggested that this enzyme played a role in the degradation of exogenous DNA encountered by phagocytosis, although the relative importance of such a role was unknown. Subsequent investigations also suggested that DNase II was important for DNA fragmentation and degradation during cell death. Within the last few years, our work and that of others has lead to the cloning of various mammalian DNase II genes as well as the identification and characterization of highly homologous genes in the invertebrates Caenorhabditis elegans and Drosophila melanogaster. Interestingly, studies of the C elegans DNase II homolog NUC-1 were the first to suggest that DNase II enzymes were fundamentally important in engulfment-mediated DNA degradation, particularly that associated with programmed cell death, due to the presence of persistent apoptotic-cell nuclei within phagocytic cells in nuc-1 mutants. Similarly, mutation of the Drosophila DNase II-like gene was found to result in the accumulation of low-molecular-weight DNA throughout the animals. Homozygous mutation (knockout) of the DNase II gene in mice revealed a much more complex and extensive phenotype including perinatal lethality. The lethality of DNase II-knockout mice is likely the result of multiple developmental defects, the most obvious being a loss of definitive erythropoiesis. Closer examination revealed that a defect in engulftnent-mediated DNA degradation is the primary defect in DNase II-null mice. In this review, we have compiled information from studies on DNase II from various organisms to provide a consensus model for the role ------------------- Key: 6284 Medline: 12925583 Authors: Moghal N;Garcia LR;Khan LA;Iwasaki K;Sternberg PW Title: Modulation of EGF receptor-mediated vulva development by the heterotrimeric G-protein G(alpha)q and excitable cells in C. elegans. Citation: Development 130: 4553-4566 2003 Type: ARTICLE Genes: aex-3 bar-1 dys-1 egl-19 egl-30 goa-1 let-23 let-60 lin-3 lin-15 lin-31 myo-3 phm-2 pry-1 sur-1 unc-4 unc-13 unc-18 unc-64 Abstract: The extent to which excitable cells and behavior modulate animal development has not been examined in detail. Here, we demonstrate the existence of a novel pathway for promoting vulval fates in C elegans that involves activation of the heterotrimeric Galphaq protein, EGL-30. EGL-30 acts with muscle-expressed EGL-19 L-type voltage-gated calcium channels to promote vulva development, and acts downstream or parallel to LET-60 (RAS). This pathway is not essential for vulval induction on standard Petri plates, but can be stimulated by expression of activated EGL-30 in neurons, or by an EGL-30-dependent change in behavior that occurs in a liquid environment. Our results indicate that excitable cells and animal behavior can provide modulatory inputs into the effects of growth factor signaling on cell fates, and suggest that communication between these cell populations is important for normal development to occur under certain ------------------- Key: 6285 Medline: 12952898 Authors: Yochem J;Herman RK Title: Investigating C. elegans development through mosaic analysis. Citation: Development 130: 4761-4768 2003 Type: REVIEW Genes: daf-2 glp-1 her-1 let-23 let-60 lin-12 lin-44 ncl-1 sma-3 sur-5 unc-5 unc-6 unc-36 unc-52 vab-8 Abstract: The analysis of genetically mosaic worms, in which some cells carry a wild-type gene and others are homozygous mutant, can reveal where in the animal a gene acts to prevent the appearance of a mutant phenotype. In this primer article, we describe how Caenorhabditis elegans genetic mosaics are generated, identified and analyzed, and we discuss examples in which the analysis of mosaic worms has provided important information about the development of this organism. ------------------- Key: 6286 Medline: 12944426 Authors: Ruvinsky I;Ruvkun G Title: Functional tests of enhancer conservation between distantly related species. Citation: Development 130: 5133-5142 2003 Type: ARTICLE Genes: ace-1 ric-19 sng-1 unc-25 unc-30 unc-47 unc-119 vab-3 Abstract: Expression patterns of orthologous genes are often conserved, even between distantly related organisms, suggesting that once established, developmental programs can be stably maintained over long periods of evolutionary time. Because many orthologous transcription factors are also functionally conserved, one possible model to account for homologous gene expression patterns, is conservation of specific binding sites within cis-regulatory elements of orthologous genes. If this model is correct, a cis-regulatory element from one organism would be expected to function in a distantly related organism. To test this hypothesis, we fused the green fluorescent protein gene to neuronal and muscular enhancer elements from a variety of Drosophila melanogaster genes, and tested whether these would activate expression in the homologous cell types in Caenorhabditis elegans. Regulatory elements from several genes directed appropriate expression in homologous tissue types, suggesting conservation of regulatory sites. However, enhancers of most Drosophila genes tested were not properly recognized in C elegans, implying that over this evolutionary distance enough changes occurred in cis-regulatory sequences and/or transcription factors to prevent proper recognition of heterospecific enhancers. Comparisons of enhancer elements of orthologous genes between C. elegans and C. briggsae revealed extensive conservation, as well as specific instances of functional divergence. Our results indicate that functional changes in cis-regulatory sequences accumulate on timescales much shorter than the divergence of arthropods and nematodes, and that mechanisms other than conservation of individual binding sites within enhancer elements are responsible for the conservation of expression patterns of homologous genes between distantly related species. ------------------- Key: 6288 Medline: 13129846 Authors: Hutter H Title: Extracellular cues and pioneers act together to guide axons in the ventral cord of C. elegans. Citation: Development 130: 5307-5318 2003 Type: ARTICLE Genes: glr-1 lin-11 mab-20 nid-1 odr-2 sax-3 slt-1 unc-6 unc-30 unc-47 unc-129 vab-1 Abstract: The ventral cord is the major longitudinal axon tract in C elegans containing essential components of the motor circuit. Previous studies have shown that axons grow out sequentially and that there is a single pioneer for the right axon tract which is important for the correct outgrowth of follower axons. Here, the dependencies between early and late outgrowing axons in the ventral cord were studied systematically with laser ablation experiments and a detailed analysis of mutants using multi-color GFP markers. Different classes of axon were affected to a different extent when the AVG pioneer neuron was eliminated. In the majority of the animals, axons were able to grow out normally even in the absence of the pioneer, suggesting that its presence is not absolutely essential for the correct outgrowth of follower axons. The transcription factor LIN-11 was found to be essential for the differentiation and pioneering function of the AVG neuron. UNC-30 appears to play a similar role for the PVP pioneer neurons. Later outgrowing axons typically do not simply follow earlier outgrowing ones, but subtle dependencies between certain groups of early and late outgrowing axons do exist. Different groups of axons growing in the same axon bundle apparently use different combinations of guidance cues for their navigation and can ------------------- Key: 6289 Medline: 14534135 Authors: Tsou MFB;Hayashi A;Rose LS Title: LET-99 opposes G(alpha)/GPR signaling to generate asymmetry for spindle positioning in response to PAR and MES-1/SRC-1 signaling. Citation: Development 130: 5717-5730 2003 Type: ARTICLE Genes: gpa-16 gpb-1 goa-1 gpr-1 gpr-2 let-99 mes-1 par-3 spn-1 src-1 Abstract: G-protein signaling plays important roles in asymmetric cell division. In C elegans embryos, homologs of receptor-independent G protein activators, GPR-1 and GPR-2 (GPR-1/2), function together with Galpha (GOA-1 and GPA-16) to generate asymmetric spindle pole elongation during divisions in the P lineage. Although Galpha is uniformly localized at the cell cortex, the cortical localization of GPR-1/2 is asymmetric in dividing P cells. In this report, we show that the asymmetry of GPR-1/2 localization depends on PAR-3 and its downstream intermediate LET-99. Furthermore, in addition to its involvement in spindle elongation, Galpha is required for the intrinsically programmed nuclear rotation event that orients the spindle in the one-cell. LET-99 functions antagonistically to the Galpha/GPR-1/2 signaling pathway, providing an explanation for how Galpha-dependent force is regulated asymmetrically by PAR polarity cues during both nuclear rotation and anaphase spindle elongation. In addition, Galpha and LET-99 are required for spindle orientation during the extrinsically polarized division of EMS cells. In this cell, both GPR-1/2 and LET-99 are asymmetrically localized in response to the MES-1/SRC-1 signaling pathway. Their localization patterns at the EMS/P-2 cell boundary are complementary, suggesting that LET-99 and Galpha/GPR-1/2 signaling function in opposite ways during this cell division as well. These results provide insight into how polarity cues are transmitted into specific spindle positions in both extrinsic and intrinsic pathways of asymmetric cell division. ------------------- Key: 6290 Medline: 14534136 Authors: Ding M;Goncharov A;Jin Y;Chisholm AD Title: C. elegans ankyrin repeat protein VAB-19 is a component of epidermal attachment structures and is essential for epidermal morphogenesis. Citation: Development 130: 5791-5801 2003 Type: ARTICLE Genes: let-805 mup-4 pat-3 sma-1 smg-3 vab-10 vab-19 nDf2 Abstract: Elongation of the epidermis of the nematode Caenorhabditis elegans involves both actomyosin-mediated changes in lateral epidermal cell shape and body muscle attachment to dorsal and ventral epidermal cells via intermediate-filament/hemidesmosome structures. vab-19 mutants are defective in epidermal elongation and muscle attachment to the epidermis. VAB-19 is a member of a conserved family of ankyrin repeat-containing proteins that includes the human tumor suppressor Kank. In epidermal cells, VAB-19::GFP localizes with components of epidermal attachment structures. In vab-19 mutants, epidermal attachment structures form normally but do not remain localized to muscle-adjacent regions of the epidermis. VAB-19 localization requires function of the transmembrane attachment structure component Myotactin. vab-19 mutants also display aberrant actin organization in the epidermis. Loss of function in the spectrin SMA-1 partly bypasses the requirement for VAB-19 in elongation, suggesting that VAB-19 and SMA-1/spectrin might play antagonistic roles in regulation of the actin cytoskeleton. ------------------- Key: 6291 Medline: 14623821 Authors: Vogel C;Teichmann SA;Chothia C Title: The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity. Citation: Development 130: 6317-6328 2003 Type: ARTICLE Genes: Abstract: Drosophila melanogaster is an arthropod with a much more complex anatomy and physiology than the nematode Caenorhabditis elegans. We investigated one of the protein superfamilies in the two organisms that plays a major role in development and function of cell-cell communication: the immunoglobulin superfamily (IgSF). Using hidden Markov models, we identified 142 IgSF proteins in Drosophila and 80 in C. elegans. Of these, 58 and 22, respectively, have been previously identified by experiments. On the basis of homology and the structural characterisation of the proteins, we can suggest probable types of function for most of the novel proteins. Though overall Drosophila has fewer genes than C. elegans, it has many more IgSF cell-surface and secreted proteins. Half the IgSF proteins in C. elegans and three quarters of those in Drosophila have evolved subsequent to the divergence of the two organisms. These results suggest that the expansion of this protein superfamily is one of the factors that have contributed to the formation of the more complex physiological features that are found in Drosophila. ------------------- Key: 6292 Medline: 12944400 Authors: McCracken S;Longman D;Johnstone IL;Caceres JF;Blencowe BJ Title: An evolutionarily conserved role for SRm160 in 3'-end processing that functions independently of exon junction complex formation. Citation: Journal of Biological Chemistry 278: 44153-44160 2003 Type: ARTICLE Genes: rsr-1 suf-1 Abstract: SRm160 (the SR-related nuclear matrix protein of 160 kDa) functions as a splicing coactivator and 3'-end cleavage-stimulatory factor. It is also a component of the splicing-dependent exon-junction complex (EJC), which has been implicated in coupling of pre-mRNA splicing with mRNA turnover and mRNA export. We have investigated whether the association of SRm160 with the EJC is important for efficient 3'-end cleavage. The EJC components RNPS1, REF, UAP56, and Y14 interact with SRm160. However, when these factors were tethered to transcripts, only SRm160 and RNPS1 stimulated 3'-end cleavage. Whereas SRm160 stimulated cleavage to a similar extent in the presence or absence of an active intron, stimulation of 3'-end cleavage by tethered RNPS1 is dependent on an active intron. Assembly of an EJC adjacent to the cleavage and polyadenylation signal in vitro did not significantly affect cleavage efficiency. These results suggest that SRm160 stimulates cleavage independently of its association with EJC components and that the cleavage-stimulatory activity of RNPS1 may be an indirect consequence of its ability to stimulate splicing. Using RNA interference (RNAi) in Caenorhabditis elegans, we determined whether interactions between SRm160 and the cleavage machinery are important in a whole organism context. Simultaneous RNAi of SRm160 and the cleavage factor CstF-50 (Cleavage stimulation factor 50-kDa subunit) resulted in late embryonic developmental arrest. In contrast, RNAi of CstF-50 in combination with RNPS1 or REFs did not result in an apparent phenotype. Our combined results provide evidence for an evolutionarily conserved interaction between SRm160 and the 3'-end cleavage machinery that functions independently of EJC ------------------- Key: 6293 Medline: 14559182 Authors: Nelson P;Kiriakidou M;Sharma A;Maniataki E;Mourelatos Z Title: The microRNA world: small is mighty. Citation: Trends in Biochemical Sciences 28: 534-540 2003 Type: REVIEW Genes: hbl-1 let-7 lin-4 lin-14 lin-28 Abstract: A new paradigm of RNA-directed gene expression regulation has emerged recently, profound in scope but arresting in the apparent simplicity of its core mechanism. Cells express numerous small ( approximately 22 nucleotide) RNAs that act as specificity determinants to direct destruction or translational repression of their mRNA targets. These small RNAs arise from processing of double-stranded RNA by the Dicer nuclease and incorporate with proteins that belong to the Argonaute family. Small RNAs might also target and silence homologous DNA sequences. The immense potential of small RNAs as controllers of gene networks is just beginning to unfold. ------------------- Key: 6294 Medline: 12966085 Authors: Dowell P;Otto TC;Adi S;Lane MD Title: Convergence of peroxisome proliferator-activated receptor gamma and Foxo1 signaling pathways. Citation: Journal of Biological Chemistry 278: 45485-45491 2003 Type: ARTICLE Genes: daf-12 daf-16 Abstract: The forkhead factor Foxo1 (or FKHR) was identified in a yeast two-hybrid screen as a peroxisome proliferator-activated receptor (PPAR) gamma-interacting protein. Foxo1 antagonized PPARgamma activity and vice versa indicating that these transcription factors functionally interact in a reciprocal antagonistic manner. One mechanism by which Foxo1 antagonizes PPARgamma activity is through disruption of DNA binding as Foxo1 inhibited the DNA binding activity of a PPARgamma/retinoid X receptor alpha heterodimeric complex. The Caenorhabditis elegans nuclear hormone receptor, DAF-12, interacted with the C. elegans forkhead factor, DAF-16, paralleling the interaction between PPARgamma and Foxo1. daf-12 and daf-16 have been implicated in C. elegans insulin-like signaling pathways, and PPARgamma and Foxo1 likewise have been linked to mammalian insulin signaling pathways. These results suggest a convergence of PPARgamma and Foxo1 signaling that may play a role in insulin action and the insulinomimetic properties of PPARgamma ligands. A more general convergence of nuclear hormone receptor and forkhead factor pathways may be important for multiple biological processes and this convergence may be evolutionarily conserved. ------------------- Key: 6295 Medline: 14559923 Authors: Brooks DR;Appleford PJ;Murray L;Isaac RE Title: An essential role in molting and morphogenesis of Caenorhabditis elegans for ACN-1, a novel member of the angiotensin-converting enzyme family that lacks a metallopeptidase active site. Citation: Journal of Biological Chemistry 278: 52340-52346 2003 Type: ARTICLE Genes: acn-1 ltd-1 nhr-23 nhr-25 Abstract: Genome sequence analyses predict many proteins that are structurally related to proteases but lack catalytic residues, thus making functional assignment difficult. We show that one of these proteins (ACN-1), a unique multi-domain angiotensin-converting enzyme (ACE)-like protein from Caenorhabditis elegans, is essential for larval development and adult morphogenesis. Green fluorescent protein-tagged ACN-1 is expressed in hypodermal cells, the developing vulva, and the ray papillae of the male tail. The hypodermal expression of acn-1 appears to be controlled by nhr-23 and nhr-25, two nuclear hormone receptors known to regulate molting in C. elegans. acn-1(RNAi) causes arrest of larval development because of a molting defect, a protruding vulva in adult hermaphrodites, severely disrupted alae, and an incomplete seam syncytium. Adult males also have multiple tail defects. The failure of the larval seam cells to undergo normal cell fusion is the likely reason for the severe disruption of the adult alae. We propose that alteration of the ancestral ACE during evolution, by loss of the metallopeptidase active site and the addition of new protein modules, has provided opportunities for novel molecular interactions important for post-embryonic ------------------- Key: 6296 Medline: 14668369 Authors: Geng W;Cosman P;Baek JH;Berry CC;Schafer WR Title: Quantitative classification and natural clustering of Caenorhabditis elegans behavioral phenotypes. Citation: Genetics 165: 1117-1126 2003 Type: ARTICLE Genes: egl-19 goa-1 nic-1 unc-2 unc-29 unc-36 unc-38 Abstract: Genetic analysis of nervous system function relies on the rigorous description of behavioral phenotypes. However, standard methods for classifying the behavioral patterns of mutant Caenorhabditis elegans rely on human observation and are therefore subjective and imprecise. Here we describe the application of machine learning to quantitatively define and classify the behavioral patterns of C. elegans nervous system mutants. We have used an automated tracking and image processing system to obtain measurements of a wide range of morphological and behavioral features from recordings of representative mutant types. Using principal component analysis, we represented the behavioral patterns of eight mutant types as data clouds distributed in multidimensional feature space. Cluster analysis using the k-means algorithm made it possible to quantitatively assess the relative similarities between different behavioral phenotypes and to identify natural phenotypic clusters among the data. Since the patterns of phenotypic similarity identified in this study closely paralleled the functional similarities of the mutant gene products, the complex phenotypic signatures obtained from these image data appeared to represent an effective diagnostic of the mutants' underlying molecular defects. ------------------- Key: 6297 Medline: 14668370 Authors: Rizzon C;Martin E;Marais G;Duret L;Segalat L;Biemont C Title: Patterns of selection against transposons inferred from the distribution of Tc1, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans. Citation: Genetics 165: 1127-1135 2003 Type: ARTICLE Genes: mut-7 Abstract: To identify the factors (selective or mutational) that affect the distribution of transposable elements (TEs) within a genome, it is necessary to compare the pattern of newly arising element insertions to the pattern of element insertions that have been fixed in a population. To do this, we analyzed the distribution of recent mutant insertions of the Tc1, Tc3, and Tc5 elements in a mut-7 background of the nematode Caenorhabditis elegans and compared it to the distribution of element insertions (presumably fixed) within the sequenced genome. Tc1 elements preferentially insert in regions with high recombination rates, whereas Tc3 and Tc5 do not. Although Tc1 and Tc3 both insert in TA dinucleotides, there is no clear relationship between the frequency of insertions and the TA dinucleotide density. There is a strong selection against TE insertions within coding regions: the probability that a TE will be fixed is at least 31 times lower in coding regions than in noncoding regions. Contrary to the prediction of theoretical models, We found that the selective pressure against TE insertions does not increase with the recombination rate. These findings indicate that the distribution of these three transposon families in the genome of C. elegans is determined essentially by just two factors: the pattern of insertions, which is a characteristic of each family, and the selection against ------------------- Key: 6298 Medline: 14668410 Authors: Cinar HN;Richards KL;Oommen KS;Newman AP Title: The EGL-13 SOX domain transcription factor affects the uterine pi cell lineages in Caenorhabditis elegans. Citation: Genetics 165: 1623-1628 2003 Type: ARTICLE Genes: cog-2 egl-13 lin-11 lin-12 Abstract: We isolated egl-13 mutants in which the pi cells of the Caenorhabditis elegans uterus initially appeared to develop normally but then underwent an extra round of cell division. The data suggest that egl-13 is required for maintenance of the pi cell fate. ------------------- Key: 6299 Medline: 14703012 Authors: Karabinos A;Bussing I;Schulze E;Wang J;Weber K;Schnabel R Title: Functional analysis of the single calmodulin gene in the nematode Caenorhabditis elegans by RNA interference and 4-D microscopy. Citation: European Journal of Cell Biology 82: 557-563 2003 Type: ARTICLE Genes: cal-1 cal-2 cal-3 cal-4 cmd-1 nmy-1 Abstract: Calmodulin (CaM), a small calcium-binding protein, is the key mediator of numerous calcium-induced changes in cellular activity. Its ligands include enzymes, cytoskeletal proteins and ion channels, identified in large part by biochemical and cell biological approaches. Thus far it has been difficult to assess the function of CaM genetically, because of the maternal supply in Drosophila and the presence of at least three nonallelic genes in vertebrates. Here we use the unique possibility offered by the C. elegans model system to inactivate the single CaM gene (cmd-1) through RNA interference (RNAi). We show that the RNAi microinjection approach results in a severe embryonic lethal phenotype. Embryos show disturbed morphogenesis, aberrant cell migration patterns, a striking hyperproliferation of cells and multiple defects in apoptosis. Finally, we show that RNAi delivery by the feeding protocol does not allow the efficient silencing of the CaM gene obtained by microinjection. General differences between the two delivery methods are discussed. ------------------- Key: 6300 Medline: 14680656 Authors: Hill JK;Gillespie PG Title: Seeing touch: moving closer to the worm mechanotransduction complex. Citation: Current Biology 13: R967-R969 2003 Type: REVIEW Genes: mec-4 mec-10 Abstract: In touch receptor cells of the nematode, two channel subunits of the DEG/ENaC family have long been thought to carry out mechanotransduction. New work shows that these channel subunits are responsible for events that occur within 50 milliseconds of transduction, and may be the transduction channel subunits themselves. ------------------- Key: 6301 Medline: 14662656 Authors: Grad LI;Lemire BD Title: Mitochondrial complex I mutations in Caenorhabditis elegans produce cytochrome c oxidase deficiency, oxidative stress and vitamin-responsive lactic acidosis. Citation: Human Molecular Genetics 13: 303-314 2004 Type: ARTICLE Genes: nuo-1 Abstract: Mitochondrial dysfunction, with an estimated incidence of 1 in 10 000 live births, is among the most common genetically determined conditions. Missense mutations in the human NDUFV1 gene, which encodes the 51 kDa active site subunit of the NADH-ubiquinone oxidoreductase or complex I, can lead to severe neurological disorders. Owing to the rare and often sporadic nature of mitochondrial disorders, the mechanisms of pathogenesis of most mutations remain poorly understood. We have generated transgenic strains of Caenorhabditis elegans that express disease-causing mutations in the nuo-1 gene, the C. elegans homolog of the NDUFV1 gene. The transgenic strains demonstrate hallmark features of complex I dysfunction such as lactic acidosis and decreased NADH-dependent mitochondrial respiration. They are also hypersensitive to exogenous oxidative stress, suggesting that cellular defense mechanisms against reactive oxygen species are already taxed by an endogenous stress. The lactic acidosis induced by the NDUFV1 mutations could be partially corrected with the vitamins riboflavin and thiamine or with sodium dichloroacetate, an activator of the pyruvate dehydrogenase complex, resulting in significant increases in animal fitness. Surprisingly, cytochrome c oxidase activity and protein levels were reduced, establishing a connection between complexes I and IV. Our results indicate that complex I mutations exert their pathogenic effects in multiple ways: by impeding the metabolism of NADH, by increasing the production of reactive oxygen species, and by interfering with the function or assembly of other mitochondrial respiratory chain components. ------------------- Key: 6302 Medline: 14734103 Authors: Millet ACM;Ewbank JJ Title: Immunity in Caenorhabditis elegans. Citation: Current Opinion in Immunology 16: 4-9 2004 Type: REVIEW Genes: abf-2 age-1 akt-1 akt-2 daf-2 daf-4 daf-16 dbl-1 lon-1 mab-21 mef-2 nsy-1 pdk-1 pmk-1 sek-1 skn-1 sma-2 sma-3 sma-4 sma-6 unc-43 Abstract: Until very recently it was not known whether the invertebrate Caenorhabditis elegans was capable of mounting a specific immune response to protect itself from pathogens. It has only just become clear that this simple nematode in fact possesses a complex innate immune system, involving multiple signalling pathways and an armoury of antimicrobial proteins and peptides. Genetic and microarray approaches are now revealing the molecular cross-talk that exists between the different signalling cascades. ------------------- Key: 6303 Medline: 14701877 Authors: Karp X;Greenwald I Title: Post-transcriptional regulation of the E/Daughterless ortholog HLH-2, negative feedback, and birth order bias during the AC/VU decision in C. elegans. Citation: Genes & Development 17: 3100-3111 2003 Type: ARTICLE Genes: hlh-2 lag-2 lin-12 Abstract: The anchor cell/ventral uterine precursor cell (AC/VU) decision in Caenorhabditis elegans is a canonical example of lin-12/Notch-mediated lateral specification. Two initially equivalent cells interact via the receptor LIN-12 and its ligand LAG-2, so that one becomes the AC and the other a VU. During this interaction, feedback loops amplify a small difference in lin-12 activity, limiting lin-12 transcription to the presumptive VU and lag-2 transcription to the presumptive AC. Here, we find that hlh-2 appears to be required for the VU fate and directly activates lag-2 transcription in the presumptive AC. HLH-2 appears to accumulate selectively in the presumptive AC prior to differential transcription of lin-12 or lag-2, and is therefore the earliest detectable difference between the two cells undergoing the AC/VU decision. The restricted accumulation of HLH-2 to the presumptive AC reflects post-transcriptional down-regulation of HLH-2 in the presumptive VU. Our observations suggest that hlh-2 is regulated as part of the negative feedback that down-regulates lag-2 transcription in the presumptive VU. Finally, we show that the AC/VU decision in an individual hermaphrodite is biased by the relative birth order of the two cells, so that the first-born cell is more likely to become the VU. We propose models to suggest how birth order, HLH-2 accumulation, and transcription of lag-2 may be linked during the AC/VU decision. ------------------- Key: 6304 Medline: Authors: Askjaer P;Galy V;Hannak E;Mattaj IW Title: Ran GTPase cycle and importins alpha and beta are essential for spindle formation and nuclear envelope assembly in living Caenorhabditis elegans embryos. Citation: Molecular Biology of the Cell 15: 3- 2004 Type: CORRECT Genes: npp-9 npp-10 Abstract: In the MATERIALS AND METHODS section and in Table 1 of the article "Ran GTPase Cycle and Importin alpha and beta Are Essential for Spindle Formation and Nuclear Envelope Assemble in Living Caenorhabditis elegans Embryos", by P. Askjaer, V. Galy, E. Hannak, and I.W. Mattaj, (Mol. Biol. Cell [2002] 13, 4355-4370), the C. elegans gene F59A2.1 encoding a homologue of vertebrate RanBP2 was incorrectly named npp-10. Instead, it should read npp-9. The authors apologize for this error. ------------------- Key: 6305 Medline: 14565976 Authors: Lu C;Srayko M;Mains PE Title: The Caenorhabditis elegans microtubule-severing complex MEI-1/MEI-2 katanin interacts differently with two superficially redundant beta-tubulin isotypes. Citation: Molecular Biology of the Cell 15: 142-150 2004 Type: Genes: mei-1 mei-2 tbb-1 tbb-2 sDf130 Abstract: The microtubule-severing protein complex katanin is required for a variety of important microtubule-base morphological changes in both animals and plants. Caenorhabditis elegans katanin is encoded by the mei-1 and mei-2 genes and is required for oocyte meiotic spindle formation and must be inactivated before the first mitotic cleavage. We identified a mutation, sb26, in the tbb-2 beta-tubulin gene that partially inhibits MEI-1/MEI-2 activity: sb26 rescues lethality caused by ectopic MEI-1/MEI-2 expression during mitosis, and sb26 increases meiotic defects in a genetic background where MEI-1/MEI-2 activity is lower than normal. sb26 does not interfere with MEI-1/MEI-2 microtubule localization, suggesting that this mutation likely interferes with severing. Tubulin deletion alleles and RNA-mediated interference revealed that TBB-2 and the other germline enriched beta-tubulin isotype, TBB-1, are redundant for embryonic viability. However, limiting MEI-1/MEI-2 activity in these experiments revealed that MEI-1/MEI-2 preferentially interacts with TBB-2-containing microtubules. Our results demonstrate that these two superficially redundant beta-tubulin isotypes have functionally distinct roles in vivo. ------------------- Key: 6306 Medline: 14565969 Authors: Dang H;Li Z;Skolnik EY;Fares H Title: Disease-related myotubularins functions in endocytic traffic in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 15: 189-196 2004 Type: ARTICLE Genes: arf-6 cup-6 cup-10 mtm-6 mtm-9 Abstract: MTM1, MTMR2, and SBF2 belong to a family of proteins called the myotubularins. X-linked myotubular myopathy, a severe congenital disorder characterized by hypotonia and generalized muscle weakness in newborn males, is caused by mutations in MTM1 (Laporte et al., 1996). Charcot-Marie-Tooth types 4131 and 4132 are severe demyelinating neuropathies caused by mutations in MTMR2 (Bolino et al., 2000) and SBF2/MTMR13 (Senderek et al., 2003), respectively. Although several myotubularins are known to regulate phosphoinositide-phosphate levels in cells, little is known about the actual cellular process that is defective in patients with these diseases. Mutations in worm MTM-6 and MTM-9, myotubularins belonging to two subgroups, disorganize phosphoinositide 3-phosphate localization and block endocytosis in the coelomocytes of Caenorhabditis elegans. We demonstrate that MTM-6 and MTM-9 function as part of a complex to regulate an endocytic pathway that involves the Arf6 GTPase, and we define protein domains required for MTM-6 activity. ------------------- Key: 6307 Medline: 14702046 Authors: Bean CJ;Schaner CE;Kelly WG Title: Meiotic pairing and imprinted X chromatin assembly in Caenorhabditis elegans. Citation: Nature Genetics 36: 100-105 2004 Type: ARTICLE Genes: her-1 him-3 him-8 tra-2 sDp1 sDp2 sDp3 Abstract: The genetic imprinting of individual loci or whole chromosomes, as in imprinted X-chromosome inactivation in mammals(1,2), is established and reset during gametogenesis; defects in this process in the parent can result in disease in the offspring(3). We describe a sperm-specific chromatin-based imprinting of the X chromosome in the nematode Caenorhabditis elegans that is restricted to histone H3 modifications. The epigenetic imprint is established during spermatogenesis and its stability in the offspring is affected by the presence of a pairing partner during meiosis in the parental germ line. We observed that DNA lacking a pairing partner during meiosis, the normal situation for the X chromosome in males, is targeted for methylation of histone H3 at Lys9 (H3-Lys9) and can be silenced. Targeting unpaired DNA for silencing during meiosis, a potential hallmark of genome defense, could therefore have a conserved role in imprinted X-chromosome inactivation and, ultimately, in sex ------------------- Key: 6308 Medline: 14681585 Authors: Newbury S;Woollard A Title: The 5'-3' exoribonuclease xrn-1 is essential for ventral epithelial enclosure during C. elegans embryogenesis. Citation: RNA 10: 59-65 2004 Type: ARTICLE Genes: dcr-1 xrn-1 Abstract: Ribonucleases have been studied in yeast and bacteria, but their biological significance to multicellular organisms is virtually unknown. However, there is increasing evidence that specific, timed transcript degradation is critical for regulation of many cellular processes, including early development and RNA interference. in this report we have investigated the effects of the 5'-3' exoribonuclease xrn-1 on the development of the nematode worm Caenorhabditis elegans. Silencing of xrn-1 expression using RNA interference results in embryos that fail to complete ventral enclosure, where the outer layer of cells normally closes over the mesoderm in a purse-string movement. Our data suggest that xrn-1 is involved in a critical aspect of epithelial movement and reveal an unexpected link between RNA stability and morphogenesis. Because xrn-1 is highly conserved in all eukaryotes, it is possible that it plays a role in similar morphological processes such as dorsal or thorax closure in Drosophila and wound healing in humans. In contrast to work in human tissue culture cells, where the 3'-5' pathway has been shown to be the most important for degradation of mRNAs. Our work shows that the 5'-3' degradation pathway is crucially important at a critical stage of development in C elegans. We have also investigated whether xrn-1 can influence the response of C. elegans to RNA interference. Our data indicate that xrn-1 plays a facilitating, but not crucial role in this process. ------------------- Key: 6309 Medline: 14688791 Authors: Nishiwaki K;Kubota Y;Chigira Y;Roy SK;Suzuki M;Schvarzstein M;Jigami Y;Hisamoto N;Matsumoto K Title: An NDPase links ADAM protease glycosylation with organ morphogenesis in C. elegans. Citation: Nature Cell Biology 6: 31-37 2004 Type: ARTICLE Genes: dpy-7 mec-7 mig-17 mig-23 unc-54 Abstract: In the nematode Caenorhabditis elegans, the gonad acquires two U-shaped arms through the directed migration of its distal tip cells (DTCs), which are located at the tip of the growing gonad arms(1). A member of the ADAM (a disintegrin and metalloprotease) family, MIG-17, regulates directional migration of DTCs: MIG-17 is synthesized and secreted from the muscle cells of the body wall, and diffuses to the gonad where it is required for DTC migration(2). The mig-23 mutation causes defective migration of DTCs and interacts genetically with mig-17. Here, we report that mig-23 encodes a membrane-bound nucleoside diphosphatase (NDPase) required for glycosylation and proper localization of MIG-17. Our findings indicate that an NDPase affects organ ------------------- Key: 6310 Medline: 14697201 Authors: Malone CJ;Misner L;Le Bot N;Tsai MC;Campbell JM;Ahringer J;White JG Title: The C. elegans Hook protein, ZYG-12, mediates the essential attachment between the centrosome and nucleus. Citation: Cell 115: 825-836 2003 Type: ARTICLE Genes: dhc-1 dli-1 spd-5 sun-1 tba-1 tba-2 zyg-9 zyg-12 Abstract: The centrosome and nucleus are intimately associated in most animal cells, yet the significance of this interaction is unknown. Mutations in the zyg-12 gene of Caenorhabditis elegans perturb the attachment of the centrosome to the nucleus, giving rise to aberrant spindles and ultimately, DNA segregation defects and lethality. These phenotypes indicate that the attachment is essential. ZYG-12 is a member of the Hook family of cytoskeletal linker proteins and localizes to both the nuclear envelope (via SUN-1) and centrosomes. ZYG-12 is able to bind the dynein subunit DLI-1 in a two-hybrid assay and is required for dynein localization to the nuclear envelope. Loss of dynein function causes a low percentage of defective centrosome/nuclei interactions in both Drosophila and Caenorhabditis elegans. We propose that dynein and ZYG-12 move the centrosomes toward the nucleus, followed by a ZYG-12/SUN-1-dependent anchorage. ------------------- Key: 6311 Medline: 14697358 Authors: Pang KM;Ishidate T;Nakamura K;Shirayama M;Trzepacz C;Schubert CM;Priess JR;Mello CC Title: The minibrain kinase homolog, mbk-2, is required for spindle positioning and asymmetric cell division in early C. elegans embryos. Citation: Developmental Biology 265: 127-139 2004 Type: ARTICLE Genes: mbk-2 mei-1 mel-26 mex-5 mex-6 par-1 par-2 par-3 pie-1 Abstract: In the newly fertilized Caenorhabditis elegans zygote, cytoplasmic determinants become localized asymmetrically along the anterior-posterior (A - P) axis of the embryo. The mitotic apparatus then orients so as to cleave the embryo into anterior and posterior blastomeres that differ in both size and developmental potential. Here we describe a role for MBK-2, a member of the Dyrk family of protein kinases, in asymmetric cell division in C. elegans. In mbk-2 mutants, the initial mitotic spindle is misplaced and cytoplasmic factors, including the germline-specific protein PIE-1, are mislocalized. Our findings support a model in which MBK-2 down-regulates the katanin-related protein MEI-1 to control spindle positioning and acts through distinct, as yet unknown factors, to control the localization of cytoplasmic determinants. These findings in conjunction with work from Schizosaccharomyces pombe indicate a possible conserved role for Dyrk family kinases in the regulation of spindle placement during cell ------------------- Key: 6312 Medline: 14704165 Authors: Colosimo ME;Tran S;Sengupta P Title: The divergent orphan nuclear receptor ODR-7 regulates olfactory neuron gene expression via multiple mechanisms in Caenorhabditis elegans. Citation: Genetics 165: 1779-1791 2003 Type: ARTICLE Genes: nhr-74 nsy-1 odr-1 odr-7 odr-10 str-2 Abstract: Nuclear receptors regulate numerous critical biological processes. The C. elegans genome is predicted to encode similar to270 nuclear receptors of which >250 are unique to nematodes. ODR-7 is the only member of this large divergent family whose functions have been defined genetically. ODR-7 is expressed in the AWA olfactory neurons and specifies AWA sensory identity by promoting the expression of AWA-specific signaling genes and repressing the expression of an AWC-specific olfactory receptor gene. To elucidate the molecular mechanisms of action of a divergent nuclear receptor, we have identified residues and domains required for different aspects of ODR-7 function in vivo. ODR-7 utilizes an unexpected diversity of mechanisms to regulate the expression of different sets of target genes. Moreover, these mechanisms are distinct in normal and heterologous cellular contexts. The odr-7ortholog in the closely related nematode C. briggsae can fully substitute for all ODR-7-mediated functions, indicating conservation of function across 25-120 million years of divergence. ------------------- Key: 6313 Medline: 14704166 Authors: Katju V;Lynch M Title: The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome. Citation: Genetics 165: 1793-1803 2003 Type: ARTICLE Genes: Abstract: The significance of gene duplication in provisioning raw materials for the evolution of genomic diversity is widely recognized, but the early evolutionary dynamics of duplicate genes remain obscure. To elucidate the structural characteristics of newly arisen gene duplicates at infancy and their subsequent evolutionary properties, we analyzed gene pairs with less than or equal to10% divergence at synonymous sites within the genome of Caenorhabditis elegans. Structural heterogeneity between duplicate copies is present very early in their evolutionary history and is maintained over longer evolutionary timescales, suggesting that duplications across gene boundaries in conjunction with shuffling events have at least as much potential to contribute to long-term evolution as do fully redundant (complete) duplicates. The median duplication span of 1.4 kb falls short of the average gene length in C. elegans (2.5 kb), suggesting that partial gene duplications are frequent. Most gene duplicates reside close to the parent copy at inception, often as tandem inverted loci, and appear to disperse in the genome as they age, as a result of reduced survivorship of duplicates located in proximity to the ancestral copy. We propose that illegitimate recombination events leading to inverted duplications play a disproportionately large role in gene duplication within this genome in comparison with other mechanisms. ------------------- Key: 6314 Medline: 14704167 Authors: Bastiani CA;Gharib S;Simon MI;Sternberg PW Title: Caenorhabditis elegans G(alpha)(q) regulates egg-laying behavior via a PLC(beta)-independent and serotonin-dependent signaling pathway and likely functions both in the nervous system and in muscle. Citation: Genetics 165: 1805-1822 2003 Type: ARTICLE Genes: cha-1 egl-1 egl-8 egl-30 itr-1 tpa-1 unc-13 Abstract: egl-30encodes the single C. elegans ortholog of vertebrate Got,, family members. We analyzed the expression pattern of EGL-30 and found that it is broadly expressed, with highest expression in the nervous system and in pharyngeal muscle. We isolated dominant, gain-of-function alleles of egl-30 as intragenic revertants of an egl-30 reduction-of-function mutation. Using these gain-of function mutants and existing reduction-of-function mutants, we examined the site and mode of action of EGL-30. On the basis of pharmacological analysis, it has been determined that egl-30 functions both in the nervous system and in the vulval muscles for egg-laying behavior. Genetic epistasis over mutations that eliminate detectable levels of serotonin reveals that egl-30 requires serotonin to regulate egg laying. Furthermore, pharmacological response assays strongly suggest that EGL-30 may directly couple to a serotonin receptor to mediate egg laying. We also examined genetic interactions with mutations in the gene that encodes the single C. elegans homolog of PLCbeta and mutations in genes that encode signaling molecules downstream of PLCbeta. We conclude that PLCbeta functions in parallel with egl-30 with respect to egg laying or is not the major effector of EGL-30. In contrast, PLCbeta-mediated signaling is likely downstream of EGL-30 with respect to pharyngeal-pumping behavior. Our data indicate that there are multiple signaling pathways downstream of EGL-30 and that different pathways could predominate with respect to the regulation of different behaviors. ------------------- Key: 6315 Medline: 14688212 Authors: Rostaing P;Weimer RM;Jorgensen EM;Triller A;Bessereau JL Title: Preservation of immunoreactivity and fine structure of adult C. elegans tissues using high-pressure freezing. Citation: Journal of Histochemistry & Cytochemistry 52: 1-12 2004 Type: ARTICLE Genes: acr-5 ajm-1 gap-43 lin-15 unc-17 vab-10 Abstract: The location of a protein labeled by immunogold techniques can be resolved under an electron beam to within nanometers of its epitope, a resolution that makes immunoelectron microscopy a valuable tool for studies of cell biology. However, tissues in the nematode Caenorhabditis elegans are difficult to preserve for immunoelectron microscopic studies. The animal's cuticle slows the diffusion of solutions into the animal and thus makes it difficult to preserve both immunoreactivity and cell morphology. Here we describe a protocol that circumvents these problems. Specifically, we instantly immobilized tissue in vitreous ice by freezing living adult animals under high pressure. Frozen specimens were then chemically fixed, dehydrated, and embedded at low temperatures. As a result, chemical diffusion across the cuticle could occur over an extended period without morphological deterioration. We show that this method is capable of preserving both cell morphology, including fine structures, and immunoreactivity. Therefore, it provides a means to characterize the localization of endogenous proteins and exogenous proteins, such as the green fluorescent protein (GFP), with respect to subcellular compartments in C elegans tissues by using postembedding immunogold labeling. ------------------- Key: 6316 Medline: 14740010 Authors: Lochnit G;Geyer R Title: Evidence for the presence of the Kennedy and Bremer-Greenberg pathways in Caenorhabditis elegans. Citation: Acta Biochimica Polonica 50: 1239-1243 2003 Type: ARTICLE Genes: Abstract: Nematodes were found to synthesize phosphorylcholine-containing molecules not present in higher organisms, i.e. phosphorylcholine-substituted glycosphingolipids and (glyco)proteins. Investigations on the biosynthesis of these structures provided first biochemical evidence for the presence of the Kennedy and Bremer-Greenberg pathways in the model organism Caenorhabditis elegans. ------------------- Key: 6317 Medline: 14646232 Authors: Takanami T;Zhang YZ;Aoki H;Abe T;Yoshida S;Takahashi H;Horiuchi S;Higashitani A Title: Efficient repair of DNA damage induced by heavy ion particles in meiotic prophase I nuclei of Caenorhabditis elegans. Citation: Journal of Radiation Research 44: 271-276 2003 Type: ARTICLE Genes: atl-1 ced-3 rad-51 rdh-1 Abstract: The effects of heavy ion particle irradiation on meiosis and reproductive development in the nematode Caenorhabditis elegans were studied. Meiotic pachytene nuclei are significantly resistant to particle irradiation by the heavy ions carbon and argon, as well as to X-rays, but not UV, whereas diplotene to diakinesis stage oocytes and early embryonic cells are not. Chromosomal abnormalities appear in mitotic cells and in maturing oocytes irradiated with heavy ion particles during the diplotene to the early diakinesis stages, but not in oocytes irradiated during the pachytene stage. The pachytene nuclei of ced-3 mutants, which are defective in apoptosis, are similarly resistant to ionizing radiation, but pachytene nuclei depleted for Ce-atl-1 (ataxia-telangiectasia like 1) or Ce-rdh-1/rad-51 are more sensitive. Pachytene nuclei thus appear to effectively repair heavy ion-induced DNA damage by the meiotic homologous recombination system. ------------------- Key: 6318 Medline: 14704673 Authors: Podbilewicz B Title: Sweet control of cell migration, cytokinesis and organogenesis. Citation: Nature Cell Biology 6: 9-11 2004 Type: REVIEW Genes: mig-17 mig-23 sqv-5 Abstract: Why are proteins glycosylated? On the basis of new studies, I propose two models to clarify the specific functions of glycosylation in worms. The first explains how intra- and inter-cellular trafficking of an N-glycosylated disintegrin-metalloprotease guides somatic gonadal cells through their migratory route, determining the shape of an organ. The second explains how rigid coats of secreted chondroitin proteoglycans bend membranes to drive cytokinesis and epithelial invagination. ------------------- Key: 6319 Medline: 14697357 Authors: Dichtel-Danjoy ML;Felix MA Title: The two steps of vulval induction in Oscheius tipulea CEW1 recruit common regulators including a MEK kinase. Citation: Developmental Biology 265: 113-126 2004 Type: ARTICLE Genes: Abstract: The cell interactions that specify the spatial pattern of vulval precursor cell (VPC) fates differ between the nematodes Oscheius tipulae CEW1 and Caenorhabditis elegans. In the former, the centered pattern of fates is obtained by two successive inductions from the gonadal anchor cell, whereas in the latter, a single inductive step by the anchor cell (EGF-Ras-MAP kinase pathway) can act as a morphogen and is reinforced by lateral signaling between the vulval precursors (Notch pathway). We performed a genetic screen for vulva mutants in O. tipulae CEW1. Here we present the mutants that specifically affect the vulval induction mechanisms. Phenotypic and epistatic analyses of these mutants show that both vulval induction steps share common components, one of which appears to be MEK kinase(s). Moreover, the inductive pathway (including MEK kinase) influences the competence of the vulval precursor cells and more strikingly their division pattern as well, irrespective of their vulval fate. Finally, a comparison of vulval mutant phenotypes obtained in C. elegans and O. tipulae CEW1 highlights the evolution of vulval induction mechanisms between the two species. ------------------- Key: 6320 Medline: 14616061 Authors: Schneider SQ;Bowerman B Title: Cell polarity and the cytoskeleton in the Caenorhabditis elegans zygote. Citation: Annual Review of Genetics 37: 221-249 2003 Type: REVIEW Genes: cdc-42 cyk-1 cul-3 efn-2 gld-1 glp-1 goa-1 gpa-16 gpb-1 gpc-1 gpr-1 gpr-2 ipp-5 let-23 let-99 lin-3 lin-5 lip-1 mei-1 mei-2 mex-1 mex-3 mex-5 mex-6 mlc-4 nmy-2pal-1 par-1 par-2 par-3 par-4 par-5 par-6 pfn-1 pie-1 pkc-3 plk-1 pod-1 pos-1 ric-8 spe-11 vab-1 zen-4 zif-1 Abstract: The anterior-posterior axis of the Caenorhabditis elegans zygote forms shortly after fertilization when the sperm pronucleus and its associated centrosomal asters provide a cue that establishes the anterior-posterior (AP) body axis. In response to this cue, the microfilament cytoskeleton polarizes the distribution of a group of widely conserved, cortically localized regulators called the PAR proteins, which are required for the first mitotic division to be asymmetric. These asymmetries include a posterior displacement of the first mitotic spindle and the differential segregation of cell-fate determinants to the anterior and posterior daughters produced by the first cleavage of the zygote. Here we review recent advances in our understanding of the mechanisms that polarize the one-cell zygote to generate an AP axis of asymmetry. ------------------- Key: 6321 Medline: 14688121 Authors: Tawill S;Le Goff L;Ali F;Blaxter M;Allen JE Title: Both free-living and parasitic nematodes induce a characteristic Th2 response that is dependent on the presence of intact glycans. Citation: Infection and Immunity 72: 398-407 2004 Type: ARTICLE Genes: Abstract: Infection with parasitic nematodes is characterized by the induction of a profound type 2 immune response. We have studied the role of glycans in the induction of the skewed type 2 response by antigens of the parasitic nematode Brugia malayi as well as the free-living nematode Caenorhabditis elegans. Lymph node cells from BALB/c mice immunized with soluble extracts of the two nematodes showed distinct antigen-specific proliferation and cytokine production; however, both nematodes induced antigen-specific-interleukin 4 (IL-4) production, demonstrating that the induction of a biased type 2 response is not unique to parasitic nematodes. Sodium periodate-treated soluble extracts of both nematodes consistently induced significantly less IL-4 production than the respective mock-treated extracts, indicating that glycans play a critical role in the induction of the Th2 immune response by these nematodes. The glycan-dependent induction of the Th2-potentiating cytokine IL-4 occurs by 72 h postinoculation. Our data suggest that glycan determinants common to nematodes act as ligands, displaying distinct molecular patterns that trigger the immune system to launch a biased Th2 immune response upon exposure to these organisms or their products. Further, the similarity of our findings to those for Schistosoma mansoni egg antigen is striking considering the enormous phylogenetic distance between nematodes and trematodes. These data thus have important implications for how the mammalian host responds to widely divergent metazoan invaders and suggest that the powerful C. elegans model system can be used to ------------------- Key: 6322 Medline: 14738755 Authors: Felix MA Title: Genomes: a helpful cousin for our favourite worm. Citation: Current Biology 14: R75-R77 2004 Type: REVIEW Genes: lin-48 Abstract: The recently published genome of the nematdoe Caenorhabditis briggsae provides a drastic improvement in structural annotation of the C. elegans genome, as well as a promising source of evolutionary comparisons. ------------------- Key: 6323 Medline: 14738731 Authors: Tijsterman M;May RC;Simmer F;Okihara KL;Plasterk RHA Title: Genes required for systemic RNA interference in Caenorhabditis elegans. Citation: Current Biology 14: 111-116 2004 Type: ARTICLE Genes: cav-1 cav-2 dyn-1 ehs-1 par-1 par-6 pos-1 rab-5 rme-1 rme-8 rsd-2 rsd-3 rsd-4 rsd-6 rsd-8 unc-11 unc-15 unc-22 Abstract: RNA interference (RNAi) in the nematode worm, Caenorhabditis elegans, occurs systemically. Double-stranded RNA (dsRNA) provided in the diet can be absorbed from the gut lumen and distributed throughout the body, triggering RNAi in tissues that are not exposed to the initial dsRNA trigger [1]. This is in marked contrast to other animals, in which RNAi does not spread from targeted tissues to neighboring cells [2]. Here, we report the characterization of mutants defective in the systemic aspect of RNAi, but not in the core RNAi process itself. Analysis of these mutants suggests that dsRNA uptake is a specific process involving several unique proteins. ------------------- Key: 6324 Medline: 14696039 Authors: Jones AK;Sattelle DB Title: Functional genomics of the nicotinic acetylcholine receptor gene family of the nematode, Caenorhabditis elegans. Citation: BioEssays 26: 39-49 2003 Type: REVIEW Genes: acr-2 acr-3 acr-4 acr-5 acr-6 acr-7 acr-8 acr-9 acr-10 acr-11 acr-12 acr-13 acr-14 acr-15 acr-16 acr-17 acr-18 acr-19 acr-20 acr-21 acr-23 deg-3 des-2 lev-1 lev-9 lev-10 lev-11 ric-3 tpa-1 unc-22 unc-29 unc-38 unc-50 unc-63 Abstract: Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels that bring about a diversity of fast synaptic actions. Analysis of the Caenorhabditis elegans genome has revealed one of the most-extensive and diverse nAChR gene families known, consisting of at least 27 subunits. Striking variation with possible functional implications has been observed in normally conserved motifs at the acetylcholine-binding site and in the channel-lining region. Some nAChR subunits are particular to neurons whilst others are present in both neurons and muscles. The localization of subunits in non-synaptic regions suggests novel roles for nAChRs. Genetic and heterologous expression studies have identified a subset of nAChR subunits that are important drug targets while the study of mutants has identified genes functionally-linked to nAChRs. Future studies using C. elegans offer the prospect of increasing our understanding of the functional diversity of a complex nAChR gene family as well as addressing the role of nAChRs and associated proteins in human disorders. ------------------- Key: 6325 Medline: 14715134 Authors: Alcedo J;Kenyon C Title: Regulation of C. elegans longevity by specific gustatory and olfactory neurons. Citation: Neuron 41: 45-55 2003 Type: ARTICLE Genes: daf-2 daf-16 fem-1 fer-15 odr-1 odr-2 odr-3 odr-7 odr-10 osm-3 rrf-3 srd-1 str-2 Abstract: The life span of C. elegans is extended by mutations that inhibit the function of sensory neurons. In this study, we show that specific subsets of sensory neurons influence longevity. We find that certain gustatory neurons inhibit longevity, whereas others promote longevity, most likely by influencing insulin/IGF-1 signaling. Olfactory neurons also influence life span, and they act in a distinct pathway that involves the reproductive system. In addition, we find that a putative chemosensory G protein-coupled receptor that is expressed in some of these sensory neurons inhibits longevity. Together our findings imply that the life span of C. elegans is regulated by environmental cues and that these cues are perceived and integrated in a complex and sophisticated fashion by specific chemosensory neurons. ------------------- Key: 6326 Medline: 14730154 Authors: Kawano T;Takuwa K;Ishiguro M;Nakajima T;Kimura Y Title: Cloning and characterization of a Caenorhabditis elegans cDNA encoding a new insulin/IGF-like peptide. Citation: Bioscience Biotechnology and Biochemistry 67: 2678-2682 Type: ARTICLE Genes: Abstract: A Caenorhabditis elegans cDNA encoding a new insulin/IGF-like peptide was cloned and examined. The predicted peptide shows significant sequence similarity with the peptide Ceinsulin-1 reported previously and contains a characteristic insertion consisting of three residues in the putative B domain as with the Ceinsulin-1. The gene expression pattern during development is almost identical to that of Ceinsulin-1. The predicted tertiary structure of the peptide is quite similar to that of Ceinsulin-1, and their predicted receptor-recognition surfaces also closely match. These facts suggest that both peptides could recognize the same receptor. ------------------- Key: 6327 Medline: Authors: Chen JJ;Caswell-Chen EP Title: Why Caenorhabditis elegans adults sacrifice their bodies to progeny. Citation: Nematology 5: 641-645 2003 Type: ARTICLE Genes: Abstract: We present a novel interpretation regarding the ecology and evolution of matricidal hatching ('bagging') in Caenorhabditis elegans. Subjecting young and mature adult C elegans to stress induced matricidal hatching. The process of egg retention followed by internal hatching under starvation was reversible, depending on whether adults were returned to food before internal juveniles caused irreversible harm to the adult. We surface sterilised adult C elegans and then starved them to test the hypothesis that matricidal hatching promotes progeny survival by enhancing to some degree the transition to the dauer stage. When the surface sterilisation stress time was short, the parent C elegans enclosed many progeny that competed for resources so that apparently only a few progeny obtained sufficient nutrition to support transition to the dauer stage. Longer sterilisation stress and starvation resulted in fewer, larger progeny with a higher proportion reaching the dauer stage, suggesting a direct correlation between the phenomena. In stressful environments, the production of even a single, stress-resistant, long-lived dauer, in lieu of progeny that cannot achieve the dauer, is a fitness advantage. The results are consistent with the hypothesis. We infer that intra-uterine hatch is a part of the C elegans life cycle, and complements androdioecy and the dauer stage to enhance progeny survival and dispersal under stress. This is a possible explanation of why a seemingly detrimental behaviour, matricidal hatching, has been perpetuated in C elegans through evolutionary time. ------------------- Key: 6328 Medline: 14681444 Authors: Gunsalus KC;Yueh WC;MacMenamin P;Piano F Title: RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects. Citation: Nucleic Acids Research 32: D406-D410 2004 Type: ARTICLE Genes: Abstract: RNA interference (RNAi) is being used in large-scale genomic studies as a rapid way to obtain in vivo functional information associated with specific genes. How best to archive and mine the complex data derived from these studies provides a series of challenges associated with both the methods used to elicit the RNAi response and the functional data gathered. RNAiDB (RNAi Database; http://www. rnai.org) has been created for the archival, distribution and analysis of phenotypic data from large-scale RNAi analyses in Caenorhabditis elegans. The database contains a compendium of publicly available data and provides information on experimental methods and phenotypic results, including raw data in the form of images and streaming time-lapse movies. Phenotypic summaries together with graphical displays of RNAi to gene mappings allow quick intuitive comparison of results from different RNAi assays and visualization of the gene product(s) potentially inhibited by each RNAi experiment based on multiple sequence analysis methods. RNAiDB can be searched using combinatorial queries and using the novel tool PhenoBlast, which ranks genes according to their overall phenotypic similarity. RNAiDB could serve as a model database for distributing and navigating in vivo functional information from large-scale systematic ------------------- Key: 6329 Medline: 14681445 Authors: Harris TW;Chen N;Cunningham F;Tello-Ruiz M;Antoshechkin I;Bastiani C;Bieri T;Blasiar D;Bradnam K;Chan J;Chen CK;Chen WJ;Davis P;Kenny E;Kishore R;Lawson D;Lee R;Muller HM;Nakamura C;Ozersky P;Petchers Title: WormBase: a multi-species resource for nematode biology and genomics. Citation: Nucleic Acids Research 32: D411-D417 2004 Type: ARTICLE Genes: Abstract: WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, WormBase extends beyond the genomic sequence, integrating experimental results with extensively annotated views of the genome. The WormBase Consortium continues to expand the biological scope and utility of WormBase with the inclusion of large-scale genomic analyses, through active data and literature curation, through new analysis and visualization tools, and through refinement of the user interface. Over the past year, the nearly complete genomic sequence and comparative analyses of the closely related species Caenorhabditis briggsae have been integrated into WormBase, including gene predictions, ortholog assignments and a new synteny viewer to display the relationships between the two species. Extensive site-wide refinement of the user interface now provides quick access to the most frequently accessed resources and a consistent browsing experience across the site. Unified single-page views now provide complete summaries of commonly accessed entries like genes. These advances continue to increase the utility of WormBase for C.elegans researchers, as well as for those researchers exploring problems in functional and comparative genomics in the context of a powerful genetic system. ------------------- Key: 6330 Medline: 14681448 Authors: Wylie T;Martin JC;Dante M;Mitreva MD;Clifton SW;Chinwalla A;Waterston RH;Wilson RK;McCarter JP Title: Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes. Citation: Nucleic Acids Research 32: D423-D426 2004 Type: ARTICLE Genes: Abstract: Nematode.net (www.nematode.net) is a web- accessible resource for investigating gene sequences from nematode genomes. The database is an outgrowth of the parasitic nematode EST project at Washington University's Genome Sequencing Center (GSC), St Louis. A sister project at the University of Edinburgh and the Sanger Institute is also underway. More than 295,000 ESTs have been generated from >30 nematodes other than Caenorhabditis elegans including key parasites of humans, animals and plants. Nematode.net currently provides NemaGene EST cluster consensus sequence, enhanced online BLAST search tools, functional classifications of cluster sequences and comprehensive information concerning the ongoing generation of nematode genome data. The long-term goal of nematode.net is to provide the scientific community with the highest quality sequence information and tools for studying these diverse species. ------------------- Key: 6331 Medline: 14681447 Authors: Srinivasan J;Otto GW;Kahlow U;Geisler R;Sommer RJ Title: AppaDB: an AcedB database for the nematode satellite organism Pristionchus pacificus. Citation: Nucleic Acids Research 32: D421-D422 2004 Type: ARTICLE Genes: Abstract: Pristionchus pacificus is a free-living nematode of the Diplogastridae family and was recently developed as a satellite system in evolutionary developmental biology. AppaDB, a P.pacificus database, was created (http://appadb.eb.tuebingen. mpg.de) to integrate the genomic data of P.pacificus, comprising the physical map, genetic linkage map, EST and BAC end sequence and hybridization data. This developing database serves as a repository to search and find any information regarding physical contigs or genetic markers required for mapping of mutants. Additionally, it provides a platform for the Caenorhabditis elegans community to compare nematode genetic data in an evolutionary perspective. ------------------- Key: 6332 Medline: Authors: Li S;Armstrong CM;Bertin N;Ge H;Milstein S;Boxem M;Vidalain PO;Han JDJ;Chesneau A;Hoa G;Goldberg DS;Li N;Martinez M;Rual JF;Lamesch P;Xu L;Tewari M;Wong SL;Zhang LV;Berriz GF;Jacotot L;Vaglio P;Reboul Title: A map of the interactome network of the metazoan C. Citation: Science 303: 540-543 2004 Type: ARTICLE Genes: Abstract: To initiate studies on how protein-protein interaction (or "interactome") networks relate to multicellular functions, we have mapped a large fraction of the Caenorhabditis elegans interactome network. Starting with a subset of metazoan-specific proteins, more than 4000 interactions were identified from high-throughput, yeast two-hybrid (HT=Y2H) screens. Independent coaffinity purification assays experimentally validated the overall quality of this Y2H data set. Together with already described Y2H interactions and interologs predicted in silico, the current version of the Worm Interactome (WI5) map contains similar to5500 interactions. Topological and biological features of this interactome network, as well as its integration with phenome and transcriptome data sets, lead to numerous biological hypotheses. ------------------- Key: 6333 Medline: 15002776 Authors: Conant GC;Wagner A Title: Duplicate genes and robustness to transient gene knock-downs in Caenorhabditis elegans. Citation: Proceedings of the Royal Society of London B 271: 89-96 Type: ARTICLE Genes: Abstract: We examine robustness to mutations in the nematode worm Caenorhabditis elegans and the role of single-copy and duplicate genes in it. We do so by integrating complete genome sequence and microarray gene expression data with results from a genome-scale study using RNA interference (RNAi) to temporarily eliminate the functions of more than 16 000 worm genes. We found that 89% of single-copy and 96% of duplicate genes show no detectable phenotypic effect in an RNAi knock-down experiment. We find that mutational robustness is greatest for closely related gene duplicates, large gene families and similarly expressed genes. We discuss the different causes of mutational robustness in single-copy and duplicate genes, as well as its evolutionary origin. ------------------- Key: 6335 Medline: 14715127 Authors: Antebi A Title: Long life: a matter of taste (and smell). Citation: Neuron 41: 1-6 2004 Type: REVIEW Genes: daf-2 daf-16 Abstract: Insulin/IGF signaling has emerged as a central regulator of metazoan aging. In C. elegans, insulin-like peptides are expressed predominately in neurons. Alcedo and Kenyon demonstrate that removal of specific gustatory and olfactory neurons result in longer life, suggesting that metazoan longevity is influenced by sensory perception. ------------------- Key: 6336 Medline: 12949121 Authors: Lee KZ;Sommer RJ Title: Operon structure and trans-splicing in the nematode Pristionchus pacificus. Citation: Molecular Biology and Evolution 20: 2097-2103 2003 Type: ARTICLE Genes: Abstract: In the nematode Caenorhabditis elegans, up to 15% of the genes are organized in operons. Polycistronic precursor RNAs are processed by trans-splicing at the 5' ends of genes by adding a specific trans-spliced leader. Ten different spliced leaders are known in C. elegans that differ in sequence and abundance. The SL1 leader is most abundant and is spliced to the 5' ends of monocistronic genes and to upstream genes in operons. Trans-splicing is common among nematodes and was observed in the genera Panagrellus, Ascaris, Haemonchus, Anisakis, and Brugia. However, little is known about operons in nonrhabditid nematodes. Dolichorhabditis CEW1, another rhabditid nematode that is now called Oscheius CEW1, contains operons and SL2 trans-splicing. We have studied the presence of operons and trans-splicing in Pristionchus pacificus, a species of the Diplogastridae that has recently been developed as a satellite organism in evolutionary developmental biology. We provide evidence that P. pacificus contains operons and that downstream genes are trans-spliced to SL2. Surprisingly, the one operon analyzed so far in P. pacificus is not conserved in C. elegans, ------------------- Key: 6337 Medline: 14647240 Authors: Ameisen JC Title: Looking for death at the core of life in the light of evolution. Citation: Cell Death and Differentiation 11: 4-10 2004 Type: REVIEW Genes: Abstract: 'Nothing makes sense in biology, but in the light of evolution' wrote Theodosius Dobzhansky, one of the founders of the New Synthesis that led to the unification of evolutionary theory and genetics in the midst of the 20th century. During the last 3 years, the Nobel Committee has provided strong support to this view by highlighting the importance of seminal discoveries identifying in various, early diverging model organisms, ancestral evolutionary conserved molecular mechanisms of crucial importance for our own survival and fitness. ------------------- Key: 6338 Medline: 14685167 Authors: Knudson AG Title: Of sea urchins and worms: development and cancer. Citation: Cell Death and Differentiation 11: 11-12 2004 Type: REVIEW Genes: Abstract: The award of the 2002 Nobel Prize to Brenner, Sulston, and Horvitz was one of the most satisfying I can recall, recognizing as it did the long sought meaningful conjunction of developmental biology with cancer research. Cancer is the ultimate derangement of growth and differentiation, affecting as it does the placenta, the embryo, the fetus, the infant, the child, the adolescent, and the adult of any age. Little wonder then that developmental biologists (embryologists in bygone days) have contributed so much to our understanding of cancer's origin. Indeed, the first coherent view of cancer was painted by the great embryologist Theodor Boveri in his heuristic volume of 1914 on the origin of cancer. Having observed the developmental aberrations of sea urchin embryos that can follow upon abnormalities of centrosome number and of the segregation of chromosomes, he associated causally the already known phenomenon of centrosome abnormalities of cancer with the latter's histopathology. He further posited that such pathology could be attributed to a single chromosomally aberrant cell. ------------------- Key: 6339 Medline: 14685168 Authors: Stergiou L;Hengartner MO Title: Death and more: DNA damage response pathways in the nematode C. elegans. Citation: Cell Death and Differentiation 11: 21-28 2004 Type: REVIEW Genes: atl-1 atm-1 ced-3 ced-4 ced-9 cep-1 chk-1 chk-2 clk-2 egl-1 hpr-7 hpr-17 hsr-9 hus-1 mre-11 mrt-2 rad-5 rad-51 spo-11 Abstract: Genotoxic stress is a threat to our cells' genome integrity. Failure to repair DNA lesions properly after the induction of cell proliferation arrest can lead to mutations or large-scale genomic instability. Because such changes may have tumorigenic potential, damaged cells are often eliminated via apoptosis. Loss of this apoptotic response is actually one of the hallmarks of cancer. Towards the effort to elucidate the DNA damage-induced signaling steps leading to these biological events, an easily accessible model system is required, where the acquired knowledge can reveal the mechanisms underlying more complex organisms. Accumulating evidence coming from studies in Caenorhabditis elegans point to its usefulness as such. In the worm's germline, DNA damage can induce both cell cycle arrest and apoptosis, two responses that are spatially separated. The latter is a tightly controlled process that is genetically indistinguishable from developmental programmed cell death. Upstream of the central death machinery, components of the DNA damage signaling cascade lie and act either as sensors of the lesion or as transducers of the initial signal detected. This review summarizes the findings of several studies that specify the elements of the DNA damage-induced responses, as components of the cell cycle control machinery, the repairing process or the apoptotic outcome. The validity of C. elegans as a tool to further dissect the complex signaling network of these responses and the high potential for it to reveal important links to cancer and other ------------------- Key: 6340 Medline: Authors: Boyce M;Degterev A;Yuan J Title: Caspases: an ancient cellular sword of Damocles. Citation: Cell Death and Differentiation 11: 29-37 2004 Type: REVIEW Genes: ced-3 ced-4 csp-1 csp-2 csp-3 Abstract: Caspases are a family of cysteine proteases homologous to the Caenorhabditis elegans programmed cell death gene product CED-3. Caspases and their distant relatives, meta- and paracaspases, have been found in phylogenetically distant nonmetazoan groups, including plants, fungi and prokaryotes. This review summarizes the current information on the mechanisms and functions of non-mammalian caspases and their relatives in apoptotic and nonapoptotic processes, and explores the possible evolutionary origin of the caspase family. ------------------- Key: 6341 Medline: 14647239 Authors: Putcha GV;Johnson EM Title: "Men are but worms:" neuronal cell death in C. elegans and vertebrates. Citation: Cell Death and Differentiation 11: 38-48 2004 Type: REVIEW Genes: ced-3 ced-4 ced-9 ces-1 egl-1 tra-1 Abstract: Awarding the 2002 Nobel Prize in Physiology or Medicine to Sydney Brenner, H Robert Horvitz, and John E Sulston for 'their discoveries concerning the genetic regulation of organ development and programmed cell death (PCD)' highlights the significant contribution that the study of experimental organisms, such as the nematode Caenorhabditis elegans, has made to our understanding of human physiology and pathophysiology. Their studies of lineage determination in worms established the 'central dogma' of apoptosis: The BH3-only protein EGL-1 is induced in cells destined to die, interacts with the BCL-2-like inhibitor CED-9, displacing the adaptor CED-4, which then promotes activation of the caspase CED-3. The vast majority of cells undergoing PCD during development in C. elegans, as in vertebrates, are neurons. Accordingly, the genetic regulation of apoptosis is strikingly similar in nematode and vertebrate neurons. This review summarizes these similarities - and the important differences - in the molecular mechanisms responsible for neuronal PCD in C. elegans and vertebrates, and examines the implications that our understanding of physiological neuronal apoptosis may have for the diagnosis and treatment of acute and chronic human neurodegenerative ------------------- Key: 6342 Medline: 14711411 Authors: Boulton SJ;Martin JS;Polanowska J;Hill DE;Gartner A;Vidal M Title: BRCA1/BARD1 orthologs required for DNA repair in Caenorhabditis elegans. Citation: Current Biology 14: 33-39 2004 Type: ARTICLE Genes: brc-1 brd-1 rad-51 smt-1 tac-1 ubc-9 Abstract: Inherited germline mutations in the tumor suppressor gene BRCA1 predispose individuals to early onset breast and ovarian cancer [1]. BRCA1 together with its structurally related partner BARD1 is required for homologous recombination and DNA double-strand break repair, but how they perform these functions remains elusive [2, 3]. As part of a comprehensive search for DNA repair genes in C. elegans, we identified a BARD1 ortholog. In protein interaction screens, Ce-BRD-1 was found to interact with components of the sumoylation pathway, the TACC domain protein TAC-1, and most importantly, a homolog of mammalian BRCA1. We show that animals depleted for either Ce-brc-1 or Ce-brd-1 display similar abnormalities, including a high incidence of males, elevated levels of p53-dependent germ cell death before and after irradiation, and impaired progeny survival and chromosome fragmentation after irradiation. Furthermore, depletion of ubc-9 and tac-1 leads to radiation sensitivity and a high incidence of males, respectively, potentially linking these genes to the C. elegans BRCA1 pathway. Our findings support a shared role for Ce-BRC-1 and Ce-BRD-1 in C. elegans DNA repair processes, and this role will permit studies of the BRCA1 pathway in an organism amenable to rapid genetic and biochemical analysis. ------------------- Key: 6343 Medline: 14711416 Authors: Satterlee JS;Ryu WS;Sengupta P Title: The CMK-1 CaMKI and the TAX-4 cyclic nucleotide-gated channel regulate thermosensory neuron gene expression and function in C. elegans. Citation: Current Biology 14: 62-68 2004 Type: ARTICLE Genes: ckk-1 cmk-1 crh-1 gcy-8 nhr-38 tax-2 tax-4 ttx-1 ttx-3 Abstract: The cultivation temperature (T-c) modulates the thermosensory responses exhibited by C. elegans on thermal gradients [1-5]. The AFD sensory neurons are essential for thermosensory behaviors [2], but the molecular mechanisms by which temperature is sensed and the memory of the T-c is encoded are unknown. Here, we show that the CMK-1 Ca2+/calmodulin-dependent protein kinase I (CaMKI) and the TAX-4 cyclic nucleotide-gated channel regulate gene expression, morphology, and functions of the AFD thermosensory neurons. Mutations in cmk-1 and tax-4 result in temperature-dependent defects in AFD-specific gene expression, and TAX-4 functions are required during larval stages to maintain gene expression in the adult. CMK-1 and TAX-4 act cell autonomously to regulate AFD-mediated thermosensory behaviors. The molecular requirements for CMK-1 activity in the AFD neurons appear to be distinct from those previously described [6, 7]. We propose that the activation of distinct programs of AFD-specific gene expression at different temperatures by CMK-1 and TAX-4 enables C. elegans to sense and/or encode a memory for the T-c. ------------------- Key: 6345 Medline: Authors: Abbott AL Title: Heterochronic genes. Citation: Current Biology 13: R824-R825 2003 Type: REVIEW Genes: daf-12 hbl-1 let-7 lin-4 lin-14 lin-28 lin-29 lin-41 lin-42 lin-46 lin-57 lin-58 Abstract: ------------------- Key: 6346 Medline: 14627718 Authors: Liang J;Lints R;Foehr ML;Tokarz R;Yu L;Emmons SW;Liu J;Savage-Dunn C Title: The Caenorhabditis elegans schnurri homolog sma-9 mediates stage- and cell type-specific responses to DBL-1 BMP-related signaling. Citation: Development 130: 6453-6464 2003 Type: ARTICLE Genes: cat-2 daf-4 dbl-1 lon-1 lon-3 sma-2 sma-3 sma-4 sma-6 sma-9 Abstract: In Caenorhabditis elegans, the DBL-1 pathway, a BMP/TGFbeta-related signaling cascade, regulates body size and male tail development. We have cloned a new gene, sma-9, that encodes the C elegans homolog of Schnurri, a large zinc finger transcription factor that regulates dpp target genes in Drosophila. Genetic interactions, the sma-9 loss-of-function phenotype, and the expression pattern suggest that sma-9 acts as a downstream component and is required in the DBL-1 signaling pathway, and thus provide the first evidence of a conserved role for Schnurri proteins in BMP signaling. Analysis of sma-9 mutant phenotypes demonstrates that SMA-9 activity is temporally and spatially restricted relative to known DBL-1 pathway components. In contrast with Drosophila schnurri, the presence of multiple alternatively spliced sma-9 transcripts suggests protein isoforms with potentially different cell sublocalization and molecular functions. We propose that SMA-9 isoforms function as transcriptional cofactors that confer specific responses to DBL-1 pathway ------------------- Key: 6347 Medline: 14752152 Authors: Sternberg PW Title: A pattern of precision. Citation: Science 303: 637-638 2004 Type: REVIEW Genes: ark-1 dpy-23 egl-17 lin-12 lip-1 lst-3 lst-4 Abstract: The amazing precision with which different cell types find their correct locations in developing tissues has fascinated biologists for decades. Models of cell fate patterning during development emphasize the contrast between spatial gradients of developmental signals that act at long range and cell-to-cell signaling events that act locally. Development of the vulva in the nematode Caenorhabditis elegans provides an elegant model system for examining the patterning of cell fate in an animal. There is strong evidence that two different intercellular signals contribute to the relatively simple induction of cell fate among vulval precursor cells (VPCs): a long-range spatial gradient of epidermal growth factor (EGF) mediated by the EGF receptor (1,2) and a cell-to-cell lateral signal mediated by the Notch-like receptor LIN-12 (3-5). It is well established that the combined action of the EGF receptor and LIN-12 receptor signaling pathways generate the pattern of VPCs in the developing vulva (6); however, the molecular details of this cooperative effect have remained elusive. On page 663 of this issue, Yoo et al. (7) provide the missing molecular connection. They report that VPCs activated by a low lever of EGF are blocked from adopting a particular cell fate by a LIN-12 lateral signal ------------------- Key: 6348 Medline: 14752159 Authors: Yoo AS;Bais C;Greenwald I Title: Crosstalk between the EGFR and LIN-12/Notch pathways in C. elegans vulval development. Citation: Science 303: 663-666 2004 Type: ARTICLE Genes: ark-1 dpy-23 egl-17 gap-1 lag-1 let-23 lin-12 lip-1 lst-1 lst-2 lst-3 lst-4 mpk-1 unc-101 vha-7 Abstract: The Caenorhabditis elegans vulva is an important paradigm for cell-cell interactions in animal development. The fates of six vulval precursor cells are patterned through the action of the epidermal growth factor receptor - mitogen-activated protein kinase (EGFR-MAPK) inductive signaling pathway, which specifies the 1degrees fate, and the LIN-12/Notch lateral signaling pathway, which specifies the 2degrees fate. Here, we provide evidence that the inductive signal is spatially graded and initially activates the EGFR-MAPK pathway in the prospective 2degrees cells. Subsequently, this effect is counteracted by the expression of multiple new negative regulators of the EGFR-MAPK pathway, under direct transcriptional control of the LIN-12-mediated lateral signal. ------------------- Key: 6349 Medline: 14749834 Authors: Zheng Y;Mellem JE;Brockie PJ;Madsen DM;Maricq AV Title: SOL-1 is a CUB-domain protein required for GLR-1 glutamate receptor function in C. elegans. Citation: Nature 427: 451-457 2004 Type: ARTICLE Genes: glr-1 nmr-1 sol-1 Abstract: Ionotropic glutamate receptors (iGluRs) mediate most excitatory synaptic signalling between neurons. Binding of the neurotransmitter glutamate causes a conformational change in these receptors that gates open a transmembrane pore through which ions can pass. The gating of iGluRs is crucially dependent on a conserved amino acid that was first identified in the 'lurcher' ataxic mouse(1). Through a screen for modifiers of iGluR function in a transgenic strain of Caenorhabditis elegans expressing a GLR-1 subunit containing the lurcher mutation, we identify suppressor of lurcher (sol-1). This gene encodes a transmembrane protein that is predicted to contain four extracellular beta-barrel-forming domains known as CUB domains(2,3). SOL-1 and GLR-1 are colocalized at the cell surface and can be coimmunoprecipitated. By recording from neurons expressing GLR-1, we show that SOL-1 is an accessory protein that is selectively required for glutamate-gated currents. We propose that SOL-1 participates in the gating of non-NMDA (N-methyl-D-aspartate) iGluRs, thereby providing a previously unknown mechanism of regulation for this important class of neurotransmitter receptor. ------------------- Key: 6350 Medline: 14739645 Authors: Monleon D;Chiang YW;Aramini JM:Swapna GVT;Macapagal D;Gunsalus KC;Kim S;Szyperski T;Montelione GT Title: Backbone 1H, 15N and 13C assignments for the 21 kaD Caenorhabditis elegans homologue of 'brain-specific' protein. Citation: Journal of Biomolecular NMR 28: 91-92 2004 Type: ARTICLE Genes: Abstract: The Northeast Structural Genomics Consortium (NESG) is a pilot project designed to evaluate the feasibility and value of structural genomics. The 21 kDa Caenorhabditis elegans protein coded by gene CE32E8.3 (TrEMBL protein P91127, referred to here as WR33) is one of several hundred targets identified for structural analysis by the Northeast Structural Genomics Consortium (www.nesg.org). WR33 belongs to a large protein domain family with homologues in several eukaryotic genomes, including those of Homo sapiens (TrEMBL proteins Q9Y326, O94811, and Q9Y6H0), Mus musculis (TrEMBL protein Q9CRB6), and Drosophila melanogaster (TrEMBL protein Q(VV43). The 25 kDa Bos Taurus (bovine) homologue from this family (Q27957), with 38% sequence identity with WR33 over 175 residues, is characterized as 'brain specific protein P25' (Shiratsuchi et al., 1995) and is expressed in oligodendrocytes and neutrophils of bovine brain tissue. However, none of the members of this strongly conserved protein domain family has a characterized biological function. ------------------- Key: 6351 Medline: 14723706 Authors: Nagamatsu Y;Ohshima Y Title: Mechanisms for the control of body size by a G-kinase and a downstream TGF beta signal pathway in Caenorhabditis elegans. Citation: Genes to Cells 9: 39-47 2004 Type: ARTICLE Genes: dbl-1 egl-4 lon-1 sma-1 sma-2 sma-4 sma-6 Abstract: We recently showed that egl-4 mutants in Caenorhabditis elegans have a much larger body size and that the egl-4 gene encodes cyclic GMP-dependent protein kinases (G-kinases). Cell sizes, but not cell numbers, in the major organs are increased in the mutants. Genetic interaction studies suggest that EGL-4 represses the DBL-1/TGFbeta pathway that is known to control body size. To understand the mechanisms of body size control in C. elegans, we analysed sma-2, sma-4 and sma-6 small mutants in the DBL-1 pathway. The volumes of major organs were precisely determined with the method developed by us. They are significantly decreased as compared to those of the wild-type while cell numbers are not, indicating that cell size is decreased. DNA contents in the nuclei of major organs are not significantly changed in the small mutants and in an egl-4 large mutant. Total protein contents are much decreased in the small mutants and slightly increased in the egl-4 mutant. Based on these results, we propose that decreased cell and body size of the small mutants in the DBL-1/TGFbeta pathway is mainly due to decreased levels of protein expression, and that increase in fluid content is a major reason for the increase in cell and body size in ------------------- Key: 6352 Medline: 14634695 Authors: Quintin S;Mains PE;Zinke A;Hyman AA Title: The mbk-2 kinase is required for inactivation of MEI-1/katanin in the one-cell Caenorhabditis elegans Citation: EMBO Reports 4: 1175-1181 2003 Type: ARTICLE Genes: mbk-2 mei-1 mel-26 tbb-2 zyg-9 Abstract: The Caenorhabditis elegans early embryo is widely used to study the regulation of microtubule-related processes. In a screen for mutants affecting the first cell division, we isolated a temperature-sensitive mutation affecting pronuclear migration and spindle positioning, phenotypes typically linked to microtubule or centrosome defects. In the mutant, microtubules are shorter and chromosome segregation is impaired, while centrosome organization appears normal. The mutation corresponds to a strong loss of function in mbk-2, a conserved serine/threonine kinase. The microtubule-related defects are due to the postmeiotic persistence of MEI-1, a homologue of the microtubule-severing protein katanin. In addition, P-granule distribution is abnormal in mbk-2 mutants, consistent with genetic evidence that mbk-2 has other functions and with the requirement of mbk-2 activity at the one-cell stage. We propose that mbk-2 potentiates the degradation of MEI-1 and other proteins, possibly via ------------------- Key: 6353 Medline: 14648222 Authors: Buckley MS;Chau J;Hoppe PE;Coulter DE Title: odd-skipped homologs function during gut development in C. elegans. Citation: Development Genes & Evolution 214: 10-18 2004 Type: ARTICLE Genes: odd-1 odd-2 Abstract: Genes in the odd-skipped (odd) family encode a discrete subset of C2H2 zinc finger proteins that are widely distributed among metazoan phyla. Although the initial member (odd) was identified as a Drosophila pair-rule gene, various homologs are expressed within each of the three germ layers in complex patterns that suggest roles in many pathways beyond segmentation. To further investigate the evolutionary history and extant functions of genes in this family, we have initiated a characterization of two homologs, odd-1 and odd-2, identified in the genome of the nematode, Caenorhabditis elegans. Sequence comparisons with homologs from insects (Drosophila and Anopheles) and mammals suggest that two paralogs were present within an ancestral metazoan; additional insect paralogs and both extant mammalian genes likely resulted from gene duplications that occurred after the split between the arthropods and chordates. Analyses of gene function using RNAi indicate that odd-1 and odd-2 play essential and distinct roles during gut development. Specific expression of both genes in the developing intestine and other cells in the vicinity of the gut was shown using GFP-reporters. These results indicate primary functions for both genes that are most like those of the Drosophila paralogs bowel and drumstick, and support a model in which gut specification represents the ancestral role for genes in ------------------- Key: 6354 Medline: 14627726 Authors: Frank CA;Baum FP;Garriga G Title: HLH-14 is a C. elegans Achate-Scute protein that promotes neurogenesis through asymmetric cell division. Citation: Development 130: 6507-6518 2004 Type: ARTICLE Genes: ced-3 ham-1 hlh-2 hlh-14 nlp-1 sra-6 srb-6 unc-86 ccDf5 maDf4 Abstract: Achaete-Scute basic helix-loop-helix (bHLH) proteins promote neurogenesis during metazoan development. In this study, we characterize a C elegans Achaete-Scute homolog, HLH-14. We find that a number of neuroblasts express HLH-14 in the C elegans embryo, including the PVQ/HSN/PHB neuroblast, a cell that generates the PVQ interneuron, the HSN motoneuron and the PHB; sensory neuron. hlh-14 mutants lack all three of these neurons. The fact that HLH-14 promotes all three classes of neuron indicates that C elegans proneural bHLH factors may act less specifically than their fly and mammalian homologs. Furthermore, neural loss in hlh-14 mutants results from a defect in an asymmetric cell division: the PVQ/HSN/PHB neuroblast inappropriately assumes characteristics of its sister cell, the hyp7/T blast cell. We argue that bHLH proteins, which control various aspects of metazoan development, can control cell fate choices in C. elegans by regulating asymmetric cell divisions. Finally, a reduction in the function of hlh-2, which encodes the C elegans E/Daughterless bHLH homolog, results in similar neuron loss as hlh-14 mutants and enhances the effects of partially reducing hlh-14 function. We propose that HLH-14 and HLH-2 act together to specify neuroblast lineages and promote ------------------- Key: 6355 Medline: 14660541 Authors: Yonker SA;Meyer BJ Title: Recruitment of C. elegans dosage compensation proteins for gene-specific versus chromosome-wide repression. Citation: Development 130: 6519-6532 2003 Type: ARTICLE Genes: dpy-21 dpy-26 dpy-27 dpy-28 her-1 mix-1 sdc-1 sdc-2 sdc-3 xol-1 Abstract: In C elegans, an X-chromosome-wide regulatory process compensates for the difference in X-linked gene dose between males (XO) and hermaphrodites (XX) by equalizing levels of X-chromosome transcripts between the sexes. To achieve dosage compensation, a large protein complex is targeted to the X chromosomes of hermaphrodites to reduce their expression by half. This repression complex is also targeted to a single autosomal gene, her-1. By silencing this male-specific gene, the complex induces hermaphrodite sexual development. Our analysis of the atypical dosage compensation gene dpy-21 revealed the first molecular differences in the complex that achieves gene-specific versus chromosome-wide repression. dpy-21 mutations, shown here to be null, cause elevated X-linked gene expression in XX animals, but unlike mutations in other dosage compensation genes, they do not cause extensive XX-specific lethality or disrupt the stability or targeting of the dosage compensation complex to X. Nonetheless, DPY-21 is a member of the dosage compensation complex and localizes to X chromosomes in a hermaphrodite-specific manner. However, DPY-21 is the first member of the dosage compensation complex that does not also associate with her-1. In addition to a difference in the composition of the complex at her-1 versus X, we also found differences in the targeting of the complex to these sites. Within the complex, SDC-2 plays the lead role in recognizing X-chromosome targets, while SDC-3 plays the lead in ------------------- Key: 6356 Medline: Authors: Braeckman BP;Houthoofd K;Vanfleteren J Title: Energy metabolism, anti-oxidant defense and aging in Caenorhabditis elegans. Citation: Model Systems in Aging 3: 99-144 2004 Type: REVIEW Genes: aap-1 age-1 akt-1 akt-2 atp-1 cco-1 clk-1 clk-2 clk-3 ctl-1 ctl-1 cyc-1 daf-2 daf-4 daf-7 daf-12 daf-16 daf-18 daf-23 eat-2 fer-15 gas-1 glp-4 gro-1 ins-1 ins-9 ins-18 ins-22 isp-1 ist-1 mev-5 nuo-1 old-1 pdk-1 rad-5 sir-2.1 sod-3 tkr-1 unc-31 unc-64 Abstract: Food restrictions and impaired gene function by mutation or RNAi treatment can extend the lifespan of Caenorhabditis elegans considerably. In contrast to the widespread belief, the antiaging action of these interventions is not due to a reduction of the rate of metabolism. Calorie restriction causes several alterations that are similar to those observed for the Ins/IGF mutants, but acts independently of this pathway. Life extension is associated with coordinated increases in superoxide dismutase and catalase activities in calorie-restricted worms and in mutants in the Ins/IGF transduction pathway. Mutation in any one of the clk genes does not result in a clear metabolic downregulation or upregulation of antioxidant enzymes. Lifespan extension in these mutants might by linked to their slow developmental rate during juvenile life, analogous to the effects caused by silencing of several genes with a mitochondrial function by RNAi treatment, and suggesting a regulatory system that makes various rates of juvenile life to persist during adulthood. The outcome would be slowing of a number of processes ------------------- Key: 6357 Medline: 14706351 Authors: Gravel C;Stergiou L;Gagnon SN;Desnoyers S Title: The C. elegans gene pme-5: molecular cloning and role in the DNA-damage response of a tankyrase orthologue. Citation: DNA Repair 3: 171-182 2004 Type: ARTICLE Genes: hus-1 pme-5 Abstract: Tankyrases are recently identified proteins characterized by ankyrin repeats and a poly(ADP-ribose) polymerase (PARP) signature motif. In vertebrates, tankyrases mediate protein-protein interactions via the ankyrin domain. Many partners have been identified that could function in telomere maintenance, signal transduction in vesicular transport, and cell death. To further our knowledge of tankyrases and to study their function in development, we sought and found a tankyrase-related gene in Caenorhabditis elegans that we named pine-5 (poly(ADP-ribose) metabolism enzyme-5). The protein encoded includes a large ankyrin domain and a catalytic PARP domain containing the well-conserved PARP signature sequence and the regulatory region. Unlike other tankyrases, PME-5 lacks a sterile-alpha module (SAM), but has a coiled coil domain which may mediate oligomerization. We also found that pnie-5 mRNA is alternatively spliced at the fifth exon, producing a long (PME-5L) and a short (PME-5S) transcript. Both isoforms are constitutively expressed during the life cycle of C. elegans. We also show DNA damage increases expression of pine-5, a response that requires the DNA damage checkpoint gene hus-1. Moreover, DNA damage-induced germ cell apoptosis was slightly increased in pme-5(RNAi) hermaphrodites. Altogether, these data indicate that pme-5 is part of a DNA damage response pathway which leads to apoptosis in C. elegans. ------------------- Key: 6358 Medline: 14747334 Authors: Burkeen AK;Maday SL;Rybicka KK;Sulcove JA;Ward J;Huang MM;Barstead R;Franzini-Armstrong C;Allen TStC Title: Disruption of Caenorhabditis elegans muscle structure and function caused by mutation of troponin I. Citation: Biophysical Journal 86: 991-1001 2004 Type: ARTICLE Genes: unc-27 Abstract: Caenorhabditis elegans strains mutant for the unc-27 gene show abnormal locomotion and muscle structure. Experiments revealed that unc-27 is one of four C. elegans troponin I genes and that three mutant alleles truncate the protein: recessive and presumed null allele e155 terminates after nine codons; semidominant su142sd eliminates the inhibitory and C-terminal regions; and semidominant su195sd abbreviates the extreme C-terminus. Assays of in vivo muscular performance at high and low loads indicated that su142sd is most deleterious, with e155 least and su195sd intermediate. Microscopy revealed in mutant muscle a prevalent disorder of dense body positioning and a less well defined sarcomeric structure, with small islands of thin. laments interspersed within the overlap region of A bands and even within the H zone. The mutants' rigid paralysis and sarcomeric disarray are consistent with unregulated contraction of the sarcomeres, in which small portions of each myofibril shorten irregularly and independently of one another, thereby distorting the disposition of. laments. The exacerbated deficits of su142sd worms are compatible with involvement in vivo of the N-terminal portion of troponin I in enhancing force production, and the severe impairment associated with su195sd highlights importance of the extreme C-terminus in ------------------- Key: 6359 Medline: 14698813 Authors: Johnson TE Title: Advantages and disadvantages of Caenorhabditis elegans for aging research. Citation: Experimental Gerontology 38: 1329-1332 2003 Type: REVIEW Genes: age-1 daf-16 fer-15 old-1 Abstract: 'The Worm' Caenorhabditis elegans has become the organism of choice for research in to the genetic basis of longevity and aging. There are several dozen laboratories exploring aging in this nematode species and several thousand investigators use this species to address their question of interest. Although the number of papers reporting advances in C. elegans aging is significantly less than the number published on aging in the mouse or in the fruit fly, the worm papers arguably are preeminent. For example, the Feb. 28, 2003, annual aging issue of Science carried four review; in three of these, C. elegans played a prominent role (Longo and Finch, 2003; Tatar et al., 2003; Hekimi and Guarente, 2003). The reasons for this are manifold but prominent among them are the facile genetics that has led to the identification of a hundred or more genes that prolong life over that of the wild type. The Award of the Nobel Prize to Drs Brenner, Sulston and Horvitz (Marx, 2002) has secured a place for the worm, along side of its more classical brethren: Drosophila and mice. ------------------- Key: 6360 Medline: 14695939 Authors: Rodriguez-Aguilera JC;Asencio C;Ruiz-Ferrer M;Vela J;Navas Title: Caenorhabditis elegans ubiquinone biosynthesis genes. Citation: Biofactors 18: 237-244 2003 Type: ARTICLE Genes: clk-1 coq-1 coq-2 coq03 coq-4 coq-5 coq-6 coq-7 coq-8 Abstract: Ubiquinone (coenzyme Q, Q) is an essential lipid electron carrier in the mitochondria respiratory chain, and also functions as antioxidant and participates as a cofactor of mitochondrial uncoupling proteins. Caenorhabditis elegans synthesize Q9, but both dietary Q8 and endogenous Q9 biosynthesis determine Q balance. Thus, it is of current interest to know the regulatory mechanisms of Q9 biosynthesis in this nematode. Here we review results that leaded to identification of genes involved in Q9 biosynthesis in this nematode using the RNA interference technology. C. elegans coq genes were silenced and depletion of Q content was observed, indicating that the genes related here participate in Q9 biosynthesis. Silenced populations showed an extension of adult life span, probably by the decrease of endogenous oxidative stress produced in mitochondria. We also report the heterologous complementation of C. elegans coq-5 and coq-7 genes in their homologue yeast coq null mutants, leading to restore its ability to growth in non-fermentable sugars. These complemented yeast strains accumulated Q6 but also the intermediate demethoxy-Q6. These findings support the conservative functional homology of these genes. ------------------- Key: 6361 Medline: 14698617 Authors: Myllyharju J;Kivirikko KI Title: Collagens, modifying enzymes and their mutations in humans, flies and worms. Citation: Trends in Genetics 20: 33-43 2004 Type: REVIEW Genes: bli-1 bli-2 bli-4 cle-1 dpy-2 dpy-3 dpy-5 dpy-7 dpy-8 dpy-10 dpy-11 dpy-13 dpy-18 emb-9 let-2 let-268 lon-3 pdi-2 pdi-3 phy-1 phy-2 phy-3 rol-6 sqt-1 sqt-3 Abstract: Collagens and proteins with collagen-like domains form large superfamilies in various species, and the numbers of known family members are increasing constantly. Vertebrates have at least 27 collagen types with 42 distinct polypeptide chains, >20 additional proteins with collagen-like domains and similar to20 isoenzymes of various collagen-modifying enzymes. Caenorhabditis elegans has similar to175 cuticle collagen polypeptides and two basement membrane collagens. Drosophila melanogaster has far fewer collagens than many other species but has similar to20 polypeptides similar to the catalytic subunits of prolyl 4-hydroxylase, the key enzyme of collagen synthesis. More than 1300 mutations have so far been characterized in 23 of the 42 human collagen genes in various diseases, and many mouse models and C. elegans mutants are also available to analyse the collagen gene family and their modifying ------------------- Key: 6362 Medline: Authors: Weiner A Title: Soaking up RNAi. Citation: Molecular Cell 12: 535-536 2003 Type: REVIEW Genes: sid-1 Abstract: RNA interference (RNAi) describes the ability of double-stranded RNA (dsRNA) to inhibit homologous gene expression at the RNA or DNA level. In a recent paper, Feinberg and Hunter report that a single transmembrane dsRNA transport protein may enable RNAi to spread systemically from one cell to another. ------------------- Key: 6363 Medline: 12872228 Authors: Masselon C;Pasa-Tolic L;Lee SW;Li L;Anderson GA;Harkewicz R;Smith RD Title: Identification of tryptic peptides from large databases using multiplexed tandem mass spectrometry: simulations and experimental results. Citation: Proteomics 3: 1279-1286 2003 Type: ARTICLE Genes: Abstract: Multiplexed tandem mass spectrometry (MS/MS) has recently been demonstrated as a means to increase the throughput of peptide identification in liquid chromatography (LC) MS/MS experiments. In this approach, a set of parent species is dissociated simultaneously and measured in a single spectrum (in the same manner that a single parent ion is conventionally studied), providing a gain in sensitivity and throughput proportional to the number of species that can be simultaneously addressed. In the present work, simulations performed using the Caenorhabditis elegans predicted proteins database show that multiplexed MS/MS data allow the identification of tryptic peptides from mixtures of up to ten peptides from a single dataset with only three "y" or "b" fragments per peptide and a mass accuracy of 2.5 to 5 ppm. At this level of database and data complexity, 98% of the 500 peptides considered in the simulation were correctly identified. This compares favorably with the rates obtained for classical MS/MS at more modest mass measurement accuracy. LC multiplexed Fourier transform-ion cyclotron resonance MS/MS data obtained from a 66 kDa protein (bovine serum albumin) tryptic digest sample are presented to illustrate the approach, and confirm that peptides can be effectively identified from the C. elegans database to which the ------------------- Key: 6364 Medline: 14747830 Authors: Sengupta P Title: Taking sides in the nervous system with miRNA. Citation: Nature Neuroscience 7: 100-102 2004 Type: REVIEW Genes: ceh-36 cog-1 gcy-5 gcy-5 gcy-7 lin-49 lsy-6 unc-37 Abstract: At first glance, the nervous systems of vertebrates and invertebrates seem bilaterally symmetrical, but on closer inspection left-right asymmetries become apparent. Humans, for example, show gross anatomical differences between right and left temporal lobes, and visual and language faculties are asymmetrically distributed between the two hemispheres. How these asymmetries arise during development remains something of a mystery (for review, see ref.1). In the nematode Caenorhabditis elegans, the AWC and ASE chemosensory neuron pairs are bilaterally symmetrical based on anatomical considerations, but nevertheless display asymmetrical gene expression patterns. A recent study in nature by Johnston and Hobert identifies a microRNA (miRNA) as a crucial mediator of this asymmetry in the ASE neurons. ------------------- Key: 6365 Medline: 14730301 Authors: McCarroll SA;Murphy CT;Zou S;Pletcher SD;Chin CS;Jan YN;Kenyon C;Bargmann CI;Li H Title: Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Citation: Nature Genetics 36: 197-204 2004 Type: ARTICLE Genes: Abstract: We developed a method for systematically comparing gene expression patterns across organisms using genome-wide comparative analysis of DNA microarray experiments. We identified analogous gene expression programs comprising shared patterns of regulation across orthologous genes. Biological features of these patterns could be identified as highly conserved subpatterns that correspond to Gene Ontology categories. Here, we demonstrate these methods by analyzing a specific biological process, aging, and show that similar analysis can be applied to a range of biological processes. We found that two highly diverged animals, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, implement a shared adult-onset expression program of genes involved in mitochondrial metabolism, DNA repair, catabolism, peptidolysis and cellular transport. Most of these changes were implemented early in adulthood. Using this approach to search databases of gene expression data, we found conserved transcriptional signatures in larval development, embryogenesis, gametogenesis and mRNA degradation. ------------------- Key: 6366 Medline: 14698436 Authors: Couthier A;Smith J;McGarr P;Craig B;Gilleard JS Title: Ectopic expression of a Haemonchus contortus GATA transcription factor in Caenorhabditis elegans reveals conserved function in spite of extensive sequence divergence. Citation: Molecular & Biochemical Parasitology 133: 241-253 2004 Type: ARTICLE Genes: elt-1 elt-2 elt-3 elt-4 elt-5 elt-6 elt-7 end-1 end-3 ibf-2 med-1 med-2 Abstract: Comparative analysis between Caenorhabditis elegans and other nematode species offers a powerful approach to study gene function. C. elegans also has great potential as a surrogate expression system to study the function of genes from parasitic nematode species where transgenic methodologies are unavailable. However there is little information on the extent to which the biology of C. elegans is conserved with other nematode species and very few parasitic nematode genes have yet been functionally expressed in C. elegans. We have identified and characterised a homologue of the C elegans GATA transcription factor elt-2, a central regulator of endoderm development, from the parasitic nematode Haemonchus contortus. The H. contortus ELT-2 polypeptide is present in endoderm nuclei throughout embryonic and post-embryonic development, except for in the infective L3 stage, and our experiments reveal that the development of the H. contortus endodermal lineage is strikingly similar to that of C elegans. Sequence conservation between the H. contortus and C elegans ELT-2 polypeptides broadly reflects function since the major region of sequence identity corresponds to the DNA binding domain. However, the overall level of sequence identity is remarkably low with the only other major region of identity corresponding to an unusual zinc finger domain. In spite of this, ectopic expression of the H. contortus elt-2 gene in transgenic C elegans is sufficient to activate a programme of endodermal differentiation demonstrating that function is highly conserved. This approach of ectopic expression using an inducible promoter provides an effective way in which to use C elegans for the in vivo functional analysis of ------------------- Key: 6367 Medline: 14706697 Authors: Kawano T;Kataoka N;Dreyfuss G;Sakamoto H Title: Ce-Y14 and MAG-1, components of exon-exon junction complex, are required for embyrogenesis and germline sexual switching in Caenorhabditis elegans. Citation: Mechanisms of Development 121: 27-35 2004 Type: ARTICLE Genes: mag-1 nxf-1 Abstract: Y14 is a component of the splicing-dependent exon-exon junction complex (EJC) and is involved in the mRNA quality control system called nonsense-mediated mRNA decay. It has recently been shown that together with another EJC component, Mago, the Drosophila homologue DmY14/Tsunagi is required for proper localization of oskar mRNA during oogenesis, a process critical for posterior formation in Drosophila development. Here we show that the nematode Caenorhabditis elegans Ce-Y14 and MAG-1 (Mago homologue) are required for late embryogenesis and proper germline sexual differentiation. Like in other organisms, Ce-Y14 preferentially binds to spliced mRNA and specifically interacts with MAG-1. Consistent with the evolutionarily conserved interaction between Y14 and Mago homologues, suppression of Ce-Y14 by RNAi resulted in the same phenotypes as those caused by RNAi of mag-1 lethality during late embryogenesis and masculinization of the adult hermaphrodite germline. Our results demonstrate that the evolutionarily conserved interaction between two EJC components, Ce-Y14 and MAG-1, has critical developmental roles in C. elegans. ------------------- Key: 6368 Medline: 14982397 Authors: Jonker MJ;Sweijen RAJC;Kammenga JE Title: Toxicity of simple mixtures to the nematode Caenorhabditis elegans in relation to soil sorption. Citation: Environmental Toxicology & Chemistry 23: 480-488 2004 Type: ARTICLE Genes: Abstract: Single and combined toxicity of copper-zinc, copper-cadmium, cadmium-lead, copper-carbendazim, and copper-carbendazimiprodione to the nematode Caenorhabditis elegans in soil was studied. The one-week population increase was estimated as the toxicity endpoint. The aim was to study the relationship between mixture interactions in the soil and the combined toxic effect. Soil sorption was quantified using the Freundlich adsorption constant. Joint toxicity patterns were quantified by comparing mixture effects to the effect of individual constituents and were related to total metal concentrations in the soil, water-soluble concentrations, and 0.01 M CaCl2-extractable concentrations. The metal with the highest adsorption constant influenced the sorption of metal with the lowest adsorption constant when both were combined, indicating interaction. Consequently, both the composition of the mixture as well as the relative toxicity of individual mixture constituents differed between total, water-soluble, and CaCl2-extractable concentrations, which was taken into account in the data quantification procedure that was applied. Both the additive and the independent model were generally inadequate to describe the effects of metal mixtures. Compared to the additive model, synergism was observed at dose levels higher than the median effect isobole. A general relationship between mixture interactions in the soil and the combined toxicity was not ------------------- Key: 6369 Medline: 14660440 Authors: Hansen D;Wilson-Berry L;Dang T;Schedl T Title: Control of the proliferation versus meiotic development decision in the C. elegans germline through regulation of GLD-1 protein accumulation. Citation: Development 131: 93-104 2004 Type: ARTICLE Genes: fbf-1 fbf-2 fog-3 gld-1 gld-2 glp-1 lag-1 lag-2 let-241 nos-3 Abstract: Maintenance of the stem cell population in the C elegans germline requires GLP-1/Notch signaling. We show that this signaling inhibits the accumulation of the RNA binding protein GLD-1. In a genetic screen to identify other genes involved in regulating GLD-1 activity, we identified mutations in the nos-3 gene, the protein product of which is similar to the Drosophila translational regulator Nanos. Our data demonstrate that nos-3 promotes GLD-1 accumulation redundantly with gld-2, and that nos-3 functions genetically downstream or parallel to fbf, an inhibitor of GLD-1 translation. We show that the GLD-1 accumulation pattern is important in controlling the proliferation versus meiotic development decision, with low GLD-1 levels allowing proliferation and increased levels promoting ------------------- Key: 6370 Medline: 14660442 Authors: Hwang BJ;Sternberg PW Title: A cell-specific enhancer that specifies lin-3 expression in the C. elegans anchor cell for vulval development. Citation: Development 131: 143-151 2004 Type: ARTICLE Genes: hlh-2 let-23 lin-3 nhr-25 Abstract: During C. elegans vulval development, the anchor cell (AC) in the somatic gonad expresses lin-3, activating the EGF receptor signaling pathway in vulval precursor cells (VPCs) and thereby inducing and patterning VPCs. Previous studies with lin-3 mutants and transgene expression have revealed that the level of LIN-3 in the AC must be precisely regulated for proper vulval development. To understand how lin-3 expression is achieved in the AC, we identified a 59 bp lin-3 enhancer sufficient to activate lin-3 transcription solely in the AC. The enhancer contains two E-box elements, and one FTZ-F1 nuclear hormone receptor (NHR) binding site that is mutated in a vulvaless mutant, lin-3(e1417). Mutagenesis studies show that both E-boxes and the NHR binding site are necessary to express lin-3 in the AC. In vitro DNA-binding studies and in vivo functional assays indicate that distinct trans-acting factors, including the E-protein/Daughterless homolog HLH-2 and unidentified nuclear hormone receptor(s), are necessary for lin-3 transcription in the AC and thus are involved in vulval development. ------------------- Key: 6371 Medline: 14738749 Authors: van den Heuvel S Title: Protein degradatin: CUL-3 and BTB - partners in Citation: Current Biology 14: R59-R61 2004 Type: REVIEW Genes: cul-3 cul-4 mei-1 mei-2 mel-26 Abstract: In early C. elegrans embryos, the transition from meiosis to mitosis requires degradation of the MEI-1 protein. A novel class of SCF-like ubiquitin ligases has been identified that mediates this process. These ligases contain the CUL-3 scaffold at their core and use a BTB-domain protein in substrate recognition. ------------------- Key: 6372 Medline: 14761308 Authors: Lee J;Nam S;Hwang SB;Hong M;Kwon JY;Jeong KS;Im SH;Shim J;Park MC Title: Functional genomic approaches using the nematode Caenorhabditis elegans as a model system. Citation: Journal of Biochemistry and Molecular Biology 37: 107-113 2004 Type: REVIEW Genes: rrf-3 Abstract: Since the completion of the genome project of the nematode C. elegans in 1998, functional genomic approaches have been applied to elucidate the gene and protein networks in this model organism. The recent completion of the whole genome of C. briggsae, a close sister species of C. elegans, now makes it possible to employ the comparative genomic approaches for identifying regulatory mechanisms that are conserved in these species and to make more precise annotation of the predicted genes. RNA interference (RNAi) screenings in C. elegans have been performed to screen the whole genome for the genes whose mutations give rise to specific phenotypes of interest. RNAi screens can also be used to identify genes that act genetically together with a gene of interest. Microarray experiments have been very useful in identifying genes that exhibit co-regulated expression profiles in given genetic or environmental conditions. Proteomic approaches also can be applied to the nematode, just as in other species whose genomes are known. With all these functional genomic tools, genetics will still remain an important tool for gene function studies in the post genome era. New breakthroughs in C. elegans biology, such as establishing a feasible gene knockout method, immortalized cells lines, or identifying viruses that can be used as vectors for introducing exogenous gene constructs into the worms, will augment the usage of this small organism for genome-wide biology. ------------------- Key: 6373 Medline: 14744438 Authors: Bartel DP Title: MicroRNAs: genomics, biogenesis, mechanism, and function. Citation: Cell 116: 281-297 2004 Type: REVIEW Genes: cog-1 hbl-1 let-7 lin-4 lin-14 lin-28 lsy-6 Abstract: MicroRNAs (miRNAs) are endogenous similar to22 nt RNAs that can play important regulatory roles in animals and plants by targeting mRNAs; for cleavage or translational repression. Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes. ------------------- Key: 6374 Medline: 14706236 Authors: Ishii N;Senoo-Matsuda N;Miyake K;Yasuda K;Ishii T;Hartman PS;Furukawa S Title: Coenzyme Q10 can prolong life C. elegans lifespan by lowering oxidative stress. Citation: Mechanisms of Ageing & Development 125: 41-46 2004 Type: ARTICLE Genes: mev-1 Abstract: The mev-1 gene encodes cytochrome b, a large subunit of the Complex II enzyme succinate-CoQ oxidoreductase. The mev-1(kn1) mutants are hypersensitive to oxidative stress and age precociously, probably because of elevated superoxide anion production in mitochondria. Coenzyme Q (CoQ) is essential for the mitochondrial respiratory chain. Here, we show that CoQ(10) and Vitamin E extended the life span of wild-type Caenorhabditis elegans. Conversely, only CoQ10 recovered the life shortening effects seen in mev-1. We also show that CoQ(10) but not Vitamin E reduced superoxide anion levels in wild type and mev-1. Another previously described phenotype of mev-1 animals is the presence of supernumerary apoptotic cells. We now demonstrate that CoQ(10) (but not Vitamin E) suppressed these supernumerary apoptoses. Collectively these data suggest that exogenously supplied CoQ(10) can play a significant anti-aging function. It may do so either by acting as an antioxidant to dismutate the free radical superoxide anion or by reducing the uncoupling of reactions during election transport that could otherwise result in superoxide anion production. The latter activity has not been ascribed to CoQ(10); however, it is known that conditions that uncouple electron transport reactions can lead to elevated superoxide anion production. ------------------- Key: 6375 Medline: 14762140 Authors: Hills T;Brockie PJ;Maricq AV Title: Dopamine and glutamate control area-restricted search behavior in Caenorhabditis elegans. Citation: Journal of Neuroscience 24: 1217-1225 2004 Type: ARTICLE Genes: cat-2 ced-1 dat-1 eat-4 glr-1 glr-2 Abstract: Area-restricted search (ARS) is a foraging strategy used by many animals to locate resources. The behavior is characterized by a time-dependent reduction in turning frequency after the last resource encounter. This maximizes the time spent in areas in which resources are abundant and extends the search to a larger area when resources become scarce. We demonstrate that dopaminergic and glutamatergic signaling contribute to the neural circuit controlling ARS in the nematode Caenorhabditis elegans. Ablation of dopaminergic neurons eliminated ARS behavior, as did application of the dopamine receptor antagonist raclopride. Furthermore, ARS was affected by mutations in the glutamate receptor subunits GLR-1 and GLR-2 and the EAT-4 glutamate vesicular transporter. Interestingly, preincubation on dopamine restored the behavior in worms with defective dopaminergic signaling, but not in glr-1, glr-2, or eat-4 mutants. This suggests that dopaminergic and glutamatergic signaling function in the same pathway to regulate turn frequency. Both GLR-1 and GLR-2 are expressed in the locomotory control circuit that modulates the direction of locomotion in response to sensory stimuli and the duration of forward movement during foraging. We propose a mechanism for ARS in C. elegans in which dopamine, released in response to food, modulates glutamatergic signaling in the locomotory control circuit, thus resulting in an increased turn frequency. ------------------- Key: 6376 Medline: 14729570 Authors: Vella MC;Choi EY;Lin SY;Reinert K;Slack FJ Title: The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3'UTR. Citation: Genes & Development 18: 132-137 2004 Type: ARTICLE Genes: let-7 lin-4 lin-41 Abstract: Caenorhabditis elegans let-7, a founding member of the microRNA family, is predicted to bind to six sites in the 3'UTR of the mRNA of its target gene, lin-41, to down-regulate LIN-41. Here, we demonstrate that wild-type let-7 microRNA binds in vitro to RNA from the lin-41 3'UTR. This interaction is dependent on two conserved let-7 complementary sites (LCSs). A 27-nucleotide sequence between the LCSs is also necessary for down-regulation in vivo. LCS mutations compensatory to the lesion in let-7(n2853) can partially restore lin-41 3'UTR function in a let-7(n2853) background, providing the first experimental evidence for an animal miRNA binding directly to its validated target in vivo. ------------------- Key: 6377 Medline: 14668486 Authors: Morley JF;Morimoto RI Title: Regulation of longevity in Caenorhabditis elegans by heat shock factor and molecular chaperones. Citation: Molecular Biology of the Cell 15: 657-664 2004 Type: ARTICLE Genes: age-1 daf-2 daf-16 daf-21 hsf-1 hsp-1 hsp-16 old-1 sip-1 Abstract: The correlation between longevity and stress resistance observed in long-lived mutant animals suggests that the ability to sense and respond to environmental challenges could be important for the regulation of life span. We therefore examined the role of heat shock factor (HSF-1), a master transcriptional regulator of stress-inducible gene expression and protein folding homeostasis, in the regulation of longevity. Down-regulation of hsf-1 by RNA interference suppressed longevity of mutants in an insulin-like signaling (ILS) pathway that functions in the nervous system of Caenorhabditis elegans to influence aging. hsf-1 was also required for temperature-induced dauer larvae formation in an ILS mutant. Using tissue-specific expression of wild-type or dominant negative HSF-1, we demonstrated that HSF-1 acts in multiple tissues to regulate longevity. Down-regulation of individual molecular chaperones, transcriptional targets of HSF-1, also decreased longevity of long-lived mutant but not wild-type animals. However, suppression by individual chaperones was to a lesser extent, suggesting an important role for networks of chaperones. The interaction of ILS with HSF-1 could represent an important molecular strategy to couple the regulation of longevity with an ancient genetic switch that governs the ability of cells to sense ------------------- Key: 6378 Medline: Authors: Bolm M;Jansen WTM;Schnabel R;Shhatwal GS Title: Hydrogen peroxide-mediated killing of Caenorhabditis elegans: a common feature of different Streptococcal species. Citation: Infection and Immunity 72: 1192-1194 2004 Type: ARTICLE Genes: Abstract: Recently, we reported that Streptococcus pyogenes kills Caenorhabditis elegans by the use of hydrogen peroxide (H2O2). Here we show that diverse streptococcal species cause death of C. elegans larvae in proportion to the level of H2O2 produced. H2O2 may mask the effects of other pathogenicity factors of catalase-negative bacteria in the C. elegans infection model. ------------------- Key: 6379 Medline: 14630920 Authors: Hashmi S;Zhang J;Oksov Y;Lustigman S Title: The Caenorhabditis elegans cathepsin Z-like cysteine protease, Ce-CPZ-1, has a multifunctional role during the worms' development. Citation: Journal of Biological Chemistry 279: 6035-6045 2004 Type: ARTICLE Genes: cpz-1 cpz-2 Abstract: We have analyzed the expression and function of Ce-cpz-1, a Caenorhabditis elegans cathepsin Z-like cysteine protease gene, during development of the worm. The cpz-1 gene is expressed in various hypodermal cells of all developmental stages and is specifically expressed in the gonads and the pharynx of adult worms. Disruption of cpz-1 function by RNA interference or cpz-1(ok497) deletion mutant suggests that cpz-1 has a role in the molting pathways. The presence of the native CPZ-1 protein in the hypodermis/cuticle of larval and adult stages and along the length of the pharynx of adult worms, as well as the cyclic expression of the transcript during larval development, supports such function. We hypothesize that the CPZ-1 enzyme functions directly as a proteolytic enzyme degrading cuticular proteins before ecdysis and/or indirectly by processing other proteins such as proenzymes and/or other proteins that have an essential role during molting. Notably, an impressive level of the CPZ-1 native protein is present in both the new and the old cuticles during larval molting, in particular in the regions that are degraded prior to shedding and ecdysis. The similar localization of the related Onchocerca volvulus cathepsin Z protein suggests that the function of CPZ-1 during molting might be conserved in other nematodes. Based on the cpz-1 RNA interference and cpz-1 (ok497) deletion mutant phenotypes, it appears that cpz-1 have additional roles during morphogenesis. Deletion of cpz-1 coding sequence or inhibition of cpz-1 function by RNA interference also caused morphological defects in the head or tail region of larvae, improperly developed gonad in adult worms and embryonic lethality. The CPZ-1 native protein in these affected regions may have a role in the cuticular and the basement membrane extracellular matrix assembly process. The present findings have defined a critical role for ------------------- Key: 6380 Medline: 14702387 Authors: Ellis GC;Phillips JB;O'Rourke S;Lyczak R;Bowerman B Title: Maternally expressed and partially redundant beta-tubulins in Caenorhabditis elegans are autoregulated. Citation: Journal of Cell Science 117: 457-464 2004 Type: ARTICLE Genes: tbb-2 nDf15 sDf121 sDf130 sDp3 Abstract: The mitotic spindle, which partitions replicated chromosomes to daughter cells during cell division, is composed of microtubule assemblies of alpha/beta-tubulin heterodimers. Positioning of the mitotic spindle influences the size and location of daughter cells, and can be important for the proper partitioning of developmental determinants. We describe two semi-dominant mis-sense mutations in tbb-2, one of two C. elegans beta-tubulin genes that are maternally expressed and together are required for microtubule-dependent processes in the early embryo. These mutations result in a posteriorly displaced and mis-oriented mitotic spindle during the first cell division. In contrast, a probable tbb-2 null allele is recessive, and when homozygous results in less severe spindle positioning defects and only partially penetrant embryonic lethality. Two of the tbb-2 mutations result in reduced levels of TBB-2 protein, and increased levels of a second maternally expressed beta-tubulin, TBB-1. However, levels of TBB-1 are not increased in a tbb-2 mutant with an allele that does not result in reduced levels of TBB-2 protein. We conclude that feedback regulation influences maternal beta-tubulin expression in C. elegans, but cannot fully restore normal microtubule function in the absence of one beta-tubulin isoform. ------------------- Key: 6381 Medline: 14750151 Authors: Miyahara K;Suzuki N;Ishihara T;Tsuchiya E;Katsura I Title: TBX2/TBX3 transcriptional factor homologue controls olfactory adaptation in Caenorhabditis elegans. Citation: Journal of Neurobiology 58: 392-402 2004 Type: ARTICLE Genes: sdf-13 tbx-2 Abstract: Although transcriptional factors are known to play important roles in synaptic plasticity, their role in olfactory adaptation has not been studied well. Here we report that Ce-TBX-2, the TBX2/TBX3 transcriptional factor homologue of the nematode Caenorhabditis elegans, is involved in olfactory adaptation. Two missense hypomorphic mutations in this gene confer abnormality in adaptation, but not chemotaxis, to all the odorants sensed by AWC olfactory neurons. The Ce-tbx-2 gene is expressed in AWB, AWC, ASJ, and many pharyngeal neurons, but expression in AWC neurons is sufficient for normal adaptation. Unexpectedly, the protein product is localized mostly in cytoplasm. The AWC neurons in the mutants retain their characteristic morphology and many marker gene expressions, suggesting that the mutants are abnormal in neural functions rather than neuronal differentiation. The results of this study imply that some of the mammalian T-box family proteins, which play central roles in embryonic development, may also control functions like neural ------------------- Key: 6382 Medline: 14961122 Authors: Kennedy S;Wang D;Ruvkun G Title: A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Citation: Nature 427: 645-649 2004 Type: ARTICLE Genes: dpy-13 eri-1 hmr-1 lin-1 myo-2 mut-16 rde-1 rde-4 rrf-1 rrf-3 sid-1 unc-13 unc-17 unc-22 unc-25 unc-47 Abstract: In many organisms, introducing double-stranded RNA (dsRNA) causes the degradation of messenger RNA that is homologous to the trigger dsRNA-a process known as RNA interference. The dsRNA is cleaved into short interfering RNAs (siRNAs), which hybridize to homologous mRNAs and induce their degradation(1). dsRNAs vary in their ability to trigger RNA interference: many mRNA-targeting dsRNAs show weak phenotypes, and nearly all mRNAs of the Caenorhabditis elegans nervous system are refractory to RNA interference(2-4). C. elegans eri-1 was identified in a genetic screen for mutants with enhanced sensitivity to dsRNAs. Here we show that eri-1 encodes an evolutionarily conserved protein with domains homologous to nucleic-acid-binding and exonuclease proteins. After exposure to dsRNA or siRNAs, animals with eri-1 mutations accumulate more siRNAs than do wild-type animals. C. elegans ERI-1 and its human orthologue degrade siRNAs in vitro. In the nematode worm, ERI-1 is predominantly cytoplasmic and is expressed most highly in the gonad and a subset of neurons, suggesting that ERI-1 siRNase activity suppresses RNA interference more intensely in these tissues. Thus, ERI-1 is a negative regulator that may normally function to limit the duration, cell-type specificity or endogenous functions of RNA interference. ------------------- Key: 6383 Medline: Authors: Danial NN;Korsmeyer SJ Title: Cell death: critical control points. Citation: Cell 116: 205-219 2004 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-12 egl-1 icd-1 nuc-1 Abstract: Programmed cell death is a distinct genetic and biochemical pathway essential to metazoans. An intact death pathway is required for successful embryonic development and the maintenance of normal tissue homeostasis. Apoptosis has proven to be tightly interwoven with other essential cell pathways. The identification of critical control points in the cell death pathway has yielded fundamental insights for basic biology, as well as provided rational targets for new therapeutics. ------------------- Key: 6384 Medline: 14976312 Authors: Csankovszki G;McDonel P;Meyer BJ Title: Recruitment and spreading of the C. elegans dosage compensation complex along X chromosomes. Citation: Science 303: 1182-1185 2004 Type: ARTICLE Genes: dpy-27 let-2 lin-14 lin-15 lon-2 myo-2 unc-1 unc-2 unc-6 unc-9 unc-20 uvt-4 mnDp1 mnDp10 mnDp25 mnDp30 mnDp57 mnDp66 stDp2 yDp4 yDp7 yDp11 yDp13 yDp14 Abstract: To achieve X-chromosome dosage compensation, organisms must distinguish X chromosomes from autosomes. We identified multiple, cis-acting regions that recruit the Caenorhabditis elegans dosage compensation complex (DCC) through a search for regions of X that bind the complex when detached from X. The DCC normally assembles along the entire X chromosome, but not all detached regions recruit the complex, despite having genes known to be dosage compensated on the native X. Thus, the DCC binds first to recruitment sites, then spreads to neighboring X regions to accomplish chromosome-wide gene repression. From a large chromosomal domain, we defined a 793-base pair fragment that functions in vivo as an X-recognition element to ------------------- Key: 6385 Medline: 14638695 Authors: Grimsley CM;Kinchen JM;Tosello-Trampont AC;Brugnera E;Haney LB;Lu M;Chen Q;Klingele D;Hengartner MO;Ravichandran KS Title: Dock180 and ELMO1 proteins cooperate to promote evolutionarily conserved Rac-dependent cell migration. Citation: Journal of Biological Chemistry 279: 6087-6097 2004 Type: ARTICLE Genes: ced-5 Abstract: Cell migration is essential throughout embryonic and adult life. In numerous cell systems, the small GTPase Rac is required for lamellipodia formation at the leading edge and movement ability. However, the molecular mechanisms leading to Rac activation during migration are still unclear. Recently, a mammalian superfamily of proteins related to the prototype member Dock180 has been identified with homologues in Drosophila and Caenorhabditis elegans. Here, we addressed the role of Dock180 and ELMO1 proteins, which function as a complex to mediate Rac activation, in mammalian cell migration. Using mutants of Dock180 and ELMO1 in a Transwell assay as well as transgenic rescue of a C. elegans mutant lacking CED-5 (Dock180 homologue), we identified specific regions of Dock180 and ELMO1 required for migration in vitro and in a whole animal model. In both systems, the Dock180.ELMO1 complex formation and the ability to activate Rac were required. We also found that ELMO1 regulated multiple Dock180 superfamily members to promote migration. Interestingly, deletion mutants of ELMO1 missing their first 531 or first 330 amino acids that can still bind and cooperate with Dock180 in Rac activation failed to promote migration, which correlated with the inability to localize to lamellipodia. This finding suggests that Rac activation by the ELMO.Dock180 complex at discrete intracellular locations mediated by the N-terminal 330 amino acids of ELMO1 rather than generalized Rac activation plays a role in cell migration. ------------------- Key: 6386 Medline: 14762059 Authors: Mitreva M;McCarter JP;Martin J;Dante M;Wylie T;Chiapelli B;Pape D;Clifton SW;Nutman TB;Waterston RH Title: Comparative genomics of gene expression in the parasitice and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans. Citation: Genome Research 14: 209-220 2004 Type: ARTICLE Genes: Abstract: Although developmental timing of gene expression is used to infer potential gene function, Studies have yet to correlate this information between species. We analyzed 10,921 ESTs in 3311 clusters from first- and infective third-stage larva (L1, L3i) of the parasitic nematode Strongyloides stercoralis and compared the results to Caenorhabditis elegans, a species that has an L3i-like dauer stage. In the comparison of S. stercoralis clusters with stage-specific expression to C elegans homologs expressed in either dauer or nondauer stages, matches between S. stercoralis L1 and C elegans nondauer-expressed genes dominated, suggesting conservation in the repertoire of genes expressed during growth in nutrient-rich conditions. For example, S. stercoralis collagen transcripts were abundant in L1 but not L3i, a pattern consistent with C elegans collagens. Although a greater proportion of S. stercoralis L3i than L1 genes have homologs among the C elegans dauer-specific transcripts, we did not uncover evidence of a robust conserved L3i/dauer 'expression signature.' Strikingly, in comparisons of S. stercoralis clusters to C elegans homologs with RNAi knockouts, those with significant L1-specific expression were more than twice as likely as L3i-specific clusters to match genes with phenotypes. We also provide functional ------------------- Key: 6387 Medline: 14755799 Authors: Moore R;Boyd L Title: Analysis of RING finger genes required for embryogenesis in C. elegans. Citation: Genesis 38: 1-12 2004 Type: ARTICLE Genes: act-1 act-2 act-3 act-4 act-5 arc-1 col-2 col-8 col-9 col-10 col-12 col-13 col-17 col-18 col-19 col-35 col-36 col-39 gpd-1 gpd-2 glp-4 lin-41 par-1 par-2 par-3 par-6 rnf-5 rpm-1 sli-1 sqt-1 tam-1 trf-1 vit-1 vit-2 vit-3 vit-5 Abstract: The RING finger motif exists in E3 ligases of the ubiquitination pathway. These ubiquitin ligases bind to target proteins, leading to their modification by covalent addition of ubiquitin peptides. Current databases contain hundreds of proteins with RING finger motifs. This study investigates the role of RING finger genes in embryogenesis of the nematode, Caenorhabditis elegans. We expand the previous list of RING finger-containing genes and show that there are 103 RING finger-containing genes in the C. elegans genome. DNA microarrays of these 103 genes were probed with various RNA samples to identify 16 RING finger genes whose expression is enriched in the germline. RNA interference (RNAi) analysis was then used to determine the developmental role of these genes. One RING finger gene, C32D5.10, showed a dramatic larval arrest upon RNAi. Three RING finger genes exhibited embryonic lethality after RNAi. These three genes include par-Z and two small RING finger proteins: F35G12.9 (an ortholog of APC11) and ZK287.5 (an ortholog of rbx1). Embryos from RNAi of the APC11 and rbx1 orthologs were arrested in the cell cycle, confirming the role of these particular RING finger proteins in regulation of the cell cycle. ------------------- Key: 6388 Medline: 14685271 Authors: Yoder JH;Chong H;Guan K;Han M Title: Modulation of KSR activity in Caenorhabditis elegans by Zn ions, PAR-1 kinase and PP2A phosphatase. Citation: EMBO Journal 23: 111-119 2004 Type: ARTICLE Genes: ksr-1 let-60 lin-1 lin-15 lin-31 lin-45 mek-2 mpk-1 par-1 rol-4 sur-6 sur-7 sur-8 Abstract: Vulval differentiation in Caenorhabditis elegans is controlled by a conserved signal transduction pathway mediated by Ras and a kinase cascade that includes Raf, Mek and MAPK. Activation of this cascade is positively regulated by a number of proteins such as KSR ( kinase suppressor of Ras), SUR-8/SOC-2, SUR-6/PP2A-B and CDF-1. We describe the functional characterization of sur-7 and several genes that regulate signaling downstream of ras. We identified sur-7 by isolating a mutation that suppresses an activated ras allele, and showed that SUR-7 is a divergent member of the cation diffusion facilitator family of heavy metal ion transporters that is probably localized to the endoplosmic recticulum membrane and regulates cellular Zn2+ concentrations. Genetic double mutant analyses suggest that the SUR-7-mediated effect is not a general toxic response. Instead, Zn2+ ions target a specific step of the pathway, probably regulation of the scaffolding protein KSR. Biochemical analysis in mammalian cells indicates that high Zn2+ concentration causes a dramatic increase of KSR phosphorylation. Genetic analysis also indicates that PP2A phosphatase and PAR-1 kinase act downstream of Raf to positively and negatively regulate KSR activity, respectively. ------------------- Key: 6389 Medline: 14739932 Authors: Sanyal S;Wintle RF;Kindt KS;Nuttley WM;Arvan R;Fitzmaurice P;Bigras E;Merz DC;Hebert TE;van der Kooy D;Schafer WR;Culotti JG;Van Tol HHM Title: Dopamine modulates the plasticity of mechanosensory responses in Caenorhabditis elegans. Citation: EMBO Journal 23: 473-482 2004 Type: ARTICLE Genes: cat-2 dop-1 dop-11 him-5 Abstract: Dopamine-modulated behaviors, including information processing and reward, are subject to behavioral plasticity. Disruption of these behaviors is thought to support drug addictions and psychoses. The plasticity of dopamine-mediated behaviors, for example, habituation and sensitization, are not well understood at the molecular level. We show that in the nematode Caenorhabditis elegans, a D1-like dopamine receptor gene (dop-1) modulates the plasticity of mechanosensory behaviors in which dopamine had not been implicated previously. A mutant of dop-1 displayed faster habituation to nonlocalized mechanical stimulation. This phenotype was rescued by the introduction of a wild-type copy of the gene. The dop-1 gene is expressed in mechanosensory neurons, particularly the ALM and PLM neurons. Selective expression of the dop-1 gene in mechanosensory neurons using the mec-7 promoter rescues the mechanosensory deficit in dop-1 mutant animals. The tyrosine hydroxylase-deficient C. elegans mutant (cat-2) also displays these specific behavioral deficits. These observations provide genetic evidence that dopamine signaling modulates behavioral plasticity in C. elegans. ------------------- Key: 6390 Medline: 14668411 Authors: Reinke V;San Gil I;Ward S;Kazmer K Title: Genome-wide germline-enriched and sex-biased expression profiles in Caenorhabditis elegans. Citation: Development 131: 311-323 2004 Type: ARTICLE Genes: egl-13 fem-1 fem-3 glp-4 flp-3 flp-6 flp-8 flp-9 her-1 him-5 lin-2 lov-1 mab-3 nlp-1 nlp-2 nlp-3 nlp-12 nlp-14 nlp-25 nlp-31 pkd-2 sir-2.2 Abstract: We performed a genome-wide analysis of gene expression in C. elegans to identify germline- and sex-regulated genes. Using mutants that cause defects in germ cell proliferation or gametogenesis, we identified sets of genes with germline-enriched expression in either hermaphrodites or males, or in both sexes. Additionally, we compared gene expression profiles between males and hermaphrodites lacking germline tissue to define genes with sex-biased expression in terminally differentiated somatic tissues. Cross-referencing hermaphrodite germline and somatic gene sets with in situ hybridization data demonstrates that the vast majority of these genes have appropriate spatial expression patterns. Additionally, we examined gene expression at multiple times during wild-type germline development to define temporal expression profiles for these genes. Sex- and germline-regulated genes have a non-random distribution in the genome, with especially strong biases for and against the X chromosome. Comparison with data from large-scale RNAi screens demonstrates that genes expressed in the oogenic germline display visible phenotypes more frequently than expected. ------------------- Key: 6391 Medline: 14681186 Authors: da Graca LS;Zimmerman KK;Mitchell MC;Kozhan-Gorodetska M;Sekiewicz K;Morales Y;Patterson GI Title: DAF-5 is a Ski oncoprotein homolg that functions in a neuronal TGF beta pathway to regulate C. elegans dauer development. Citation: Development 131: 435-446 2004 Type: ARTICLE Genes: cki-1 daf-1 daf-3 daf-4 daf-5 daf-7 daf-8 daf-14 dpy-7 dpy-30 ges-1 myo-2 myo-3 rnr-1 sma-2 unc-14 unc-119 Abstract: An unconventional TGFbeta superfamily pathway plays a crucial role in the decision between dauer diapause and reproductive growth. We have studied the daf-5 gene, which, along with the daf-3 Smad gene, is antagonized by upstream receptors and receptor-regulated Smads. We show that DAF-5 is a novel member of the Sno/Ski superfamily that binds to DAF-3 Smad, suggesting that DAF-5, like Sno/Ski, is a regulator of transcription in a TGFbeta superfamily signaling pathway. However, we present evidence that DAF-5 is an unconventional Sno/Ski protein, because DAF-5 acts as a co-factor, rather than an antagonist, of a Smad protein. We show that expressing DAF-5 in the nervous system rescues a daf-5 mutant, whereas muscle or hypodermal expression does not. Previous work suggested that DAF-5 and DAF-3 function in pharyngeal muscle to regulate gene expression, but our analysis of regulation of a pharynx specific promoter suggests otherwise. We present a model in which DAF-5 and DAF-3 control the production or release of a hormone from the nervous system by either regulating the expression of biosynthetic genes or by altering the connectivity or the differentiated state of neurons. ------------------- Key: 6392 Medline: 15055763 Authors: Jang SH;Park Y;Park SC;Kim PI;Lee DG;Hahm KS Title: Antinematocidal activity and the mechanism of the antimicrobial peptide, HP (2-20), against Caenorhabditis elegans. Citation: Biotechnology Letters 26: 287-291 2004 Type: ARTICLE Genes: Abstract: The peptide HP (2-20), derived from the N-terminal sequence of Helicobacter pylori ribosomal protein L1 (RPL1), has a nematicidal activity against eggs and worms of Caenorhabditis elegans. Eggs treated with HP (2-20) (69%) has a higher fluorescence intensity with propidium iodide staining, which was similar to that of melittin (82%) but higher than untreated cells (5.7%). Confocal microscopy showed that the peptides were located in the shell of the eggs and the inner and outer surfaces of the worms. HP (2-20) therefore may exert its antinematodal activity by disrupting the structure of the egg's shell and the cell membrane via pore formation or by direct interaction with the lipid bilayers in a detergent-like manner. ------------------- Key: 6393 Medline: 14758362 Authors: Wang X;Chamberlin HM Title: Evolutionary innovation of the excretory system in Caenorhabditis elegans. Citation: Nature Genetics 36: 231-232 2004 Type: ARTICLE Genes: lin-48 Abstract: The evolution of complexity relies on changes that result in new gene functions. Here we show that the unique morphological and functional features of the excretory duct cell in C. elegans result from the gain of expression of a single gene. Our results show that innovation can be achieved by altered expression of a transcription factor without coevolution of all target genes. ------------------- Key: 6394 Medline: 15095973 Authors: Koga M;Ohshima Y Title: The C. elegans ceh-36 gene encodes a putative homemodomain transcription factor involved in chemosensory functins of ASE and AWC neurons. Citation: Journal of Molecular Biology 336: 579-587 2004 Type: ARTICLE Genes: ceh-36 che-1 gcy-5 gcy-6 gcy-7 tax-2 Abstract: Chemotaxis to water-soluble chemicals such as sodium ion is an important behavior of Caenorhabditis elegans for seeking food, and ASE chemosensory neurons have a major role in this behavior. We isolated mutants defective in chemotaxis to sodium acetate. We show here that among them ks86 had a mutation in the ceh-36 gene. ceh-36 :: gfp reporter constructs were expressed in ASE and AWC neurons. In a mutant of the che-1 gene, which encodes another transcription factor and is required for specification of ASE neurons, expression of the ceh-36 :: gfp reporter in ASE is lost. This indicates that the ceh-36 gene functions downstream of the che-1 gene in ASE. In the ceh-36(ks86) mutant, expression of the tax-2 gene encoding a cyclic nucleotide-gated channel was reduced in ASE and AWC. This affords an explanation for defects of the ceh-36 mutant in the chemotaxis mediated by ASE and AWC. When a ceh-36 cDNA was expressed in an adult ceh-36 mutant by a heat shock promoter, chemotaxis to sodium acetate was recovered. These results suggest that ceh-36 is required for functions, and not for development, of ASE. ------------------- Key: 6395 Medline: Authors: Simmer F;Moorman C;van der Linden AM;Kuijk E;van den Berghe PVE;Kamath FS;Fraser AG;Ahringer J;Plasterk RHA Title: Genome-wide RNAi of C. elegans using the hypersensitive rrf-3 strain reveals novel gene functions. Citation: PLoS Biology 1: 77-84 2003 Type: ARTICLE Genes: bli-3 bli-5 dpy-4 dpy-6 dpy-9 egl-30 gpc-2 hlh-2 mes-3 mex-3 rol-3 rrf-3 unc-73 unc-87 unc-108 Abstract: RNA-mediated interference (RNAi) is a method to inhibit gene function by introduction of double-stranded RNA (dsRNA). Recently, an RNAi library was constructed that consists of bacterial clones expressing dsRNA, corresponding to nearly 90% of the 19,427 predicted genes of C. elegans. Feeding of this RNAi library to the standard wild-type laboratory strain Bristol N2 detected phenotypes for approximately 10% of the corresponding genes. To increase the number of genes for which a loss-of-function phenotype can be detected, we undertook a genome-wide RNAi screen using the rrf-3 mutant strain, which we found to be hypersensitive to RNAi. Feeding of the RNAi library to rrf-3 mutants resulted in additional loss-of -function phenotypes for 393 genes, increasing the number of genes with a phenotype by 23%. These additional phenotypes are distributed over different phenotypic classes. We also studied interexerimental variability in RNAi results and found persistent levels of false negatives. In addition, we used the RNAi phenotypes obtained with the genome-wide screens to systematically clone seven existing genetic mutants with visible phenotypes. The genome-wide RNAi screen using rrf-3 significantly increased the functional data on the C. elegans genome. The resulting dataset will be valuable in conjunction wit other functional genomics approaches, as ------------------- Key: 6396 Medline: Authors: Stein LD;Bao Z;Blasiar D;Blumenthal T;Brent MR;Chen N;Chinwalla A;Clarke L;Clee C;Coghlan A;Coulson A;D'Eustachio P;Fitch DHA;Fulton LA;Fulton RE;Griffiths-Jones S;Harris TW;Hillier LW;Kamath R;Kuwaba Title: The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. Citation: PLoS Biology 1: 166-192 2003 Type: ARTICLE Genes: Abstract: The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4 % of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will ------------------- Key: 6397 Medline: 14732394 Authors: Melkman T;Sengupta P Title: The worm's sense of smell. Development of functional diversity in the chemosensory system of Caenorhabditis elegans. Citation: Developmental Biology 265: 302-319 2004 Type: REVIEW Genes: apx-1 ceh-14 ceh-36 ceh-37 che-1 cnd-1 daf-19 gcy-5 gcy-6 gcy-7 glp-1 ham-1 hlh-2 hlh-3 lag-2 lim-4 lin-11 lin-12 lin-32 lit-1 mom-2 odr-1 odr-3 odr-7 odr-10 osm-1 osm-3 osm-6 pop-1 srd-1 str-2 ttx-1 unc-3 unc-42 unc-130 wrm-1 Abstract: Animals sense their chemical environment using multiple chemosensory neuron types, each of which exhibits characteristic response properties. The chemosensory neurons of the nematode Caenorhabditis elegans provide an excellent system in which to explore the developmental mechanisms giving rise to this functional diversity. In this review, we discuss the principles underlying the patterning, generation, differentiation, and diversification of chemosensory neuron subtypes in C. elegans. Current knowledge of the molecular mechanisms underlying each of these individual steps is derived from work in different model organisms. It is essential to describe the complete developmental pathways in each organism to determine whether functional diversification in chemosensory systems is achieved via conserved or novel mechanisms. Such a complete description may be possible in ------------------- Key: 6398 Medline: 14732404 Authors: Crowe E;Candido EPM Title: Characterization of C. elegans RING finger protein 1, a binding partner of ubiquitin-conjugating enzyme 1. Citation: Developmental Biology 265: 446-459 2004 Type: ARTICLE Genes: rfp-1 rrf-3 ubc-1 ubc-2 ubc-12 Abstract: In a yeast two-hybrid screen, RING finger protein 1 (RFP-1) and UBR1 were identified as potential binding partners of C. elegans UBC1, a ubiquitin-conjugating enzyme with a high degree of identity to S. cerevisiae UBC2/RAD6. The interaction of RFP-1 and UBC-1 was confirmed by co-immunoprecipitation experiments. Yeast interaction trap experiments mapped the region of interaction to the basic N-terminal 313 residues of RFP-1. The acidic carboxy-terminal extension of UBC-1 was not required for the interaction with RFP-1. Western blot analysis and indirect immunohistochemical staining show that RFP-1 is present in embryos, larvae, and adults, where it is found in intestinal, nerve ring, pharyngeal, gonadal, and oocyte cell nuclei. Double-stranded RNA interference experiments against rfp-1 indicate that this gene is required for L1 development, vulval development, and for egg laying. By contrast, RNA interference against ubc-1 gave no obvious phenotype, suggesting that ubc-1 is nonessential or is functionally redundant. ------------------- Key: 6399 Medline: 14732406 Authors: Landmann F;Quintin S;Labouesse M Title: Multiple regulatory elements with spatially and temporally distinct activities control the expression of the epithelial differentiation gene lin-26 in C. elegans. Citation: Developmental Biology 265: 478-490 2004 Type: ARTICLE Genes: ceh-13 elt-1 elt-3 elt-5 elt-6 lin-26 lir-1 lir-2 nhr-23 nhr-25 nob-1 pha-4 Abstract: Epithelial differentiation is a very early event during development of most species. The nematode Caenorhabditis elegans, with its well-defined and invariant lineage, offers the possibility to link cell lineage, cell fate specification and gene regulation during epithelial differentiation. Here, we focus on the regulation of the gene lin-26, which is required for proper differentiation of epithelial cells in the ectoderm and mesoderm (somatic gonad). lin-26 expression starts in early embryos and remains on throughout development, in many cell types originating from different sublineages. Using GFP reporters and mutant rescue assays, we performed a molecular dissection of the lin-26 promoter and could identify almost all elements required to establish its complex spatial and temporal expression. Most of these elements act redundantly, or synergistically once combined, to drive expression in cells related by function. We also show that lin-26 promoter elements mediate activation in the epidermis (hypodermis) by the GATA factor ELT-1, or repression in the foregut (pharynx) by the FoxA protein PHA-4. Taken together, our data indicate that lin-26 regulation is achieved to a large extent through ------------------- Key: 6400 Medline: 14729475 Authors: Segbert C;Johnson K;Theres C;van Furden D;Bossinger O Title: Molecular and functional analysis of apical junction formation in the gut epithelium of Caenorhabditis elegans. Citation: Developmental Biology 266: 17-26 2004 Type: ARTICLE Genes: ajm-1 crb-1 dlg-1 erm-1 hmp-1 hmp-2 hmr-1 let-413 Abstract: The Caenorhabditis elegans intestine is a simple and accessible model system to analyze the mechanism of junction assembly. In comparison to Drosophila and vertebrates, the C. elegans apical junction is remarkable because a single electron-dense structure is implicated in complex processes such as epithelial tightness, vectorial transport and cell adhesion. Here we present evidence in support of a heterogeneous molecular assembly of junctional proteins found in Drosophila and vertebrate epithelia associated with different junctions or regions of the plasma membrane. In addition, we show that molecularly diverse complexes participate in different aspects of epithelial maturation in the C. elegans intestine. DLG-1 (Discs large) acts synergistically with the catenin-cadherin complex (HMP-1-HMP-2-HMR-1) and the Ezrin-Radixin-Moesin homolog (ERM-1) to ensure tissue integrity of the intestinal tube. The correct localization of DLG-1 itself depends on AJM-1, a coiled-coil protein. Double depletion of HMP-1 (a-catenin) and LET-413 (C. elegans homolog of Drosophila Scribble) suggests that the catenin-cadherin complex is epistatic to LET-413, while additional depletion of subapically expressed CRB-1 (Crumbs) emphasizes a role of CRB-1 concerning apical ------------------- Key: 6401 Medline: 14729486 Authors: Smith MM;Levitan DJ Title: The Caenorhabditis elegans homolog of the putative prostate cancer susceptibility gene ELAC2, hoe-1, plays a role in germline proliferation. Citation: Developmental Biology 266: 151-160 2004 Type: ARTICLE Genes: cul-1 gld-1 glp-1 glp-3 glp-4 hoe-1 let-23 let-60 lin-1 lin-12 lin-15 lin-45 mek-2 Abstract: The potential prostate cancer susceptibility gene ELAC2 has a Caenorhabditis elegans homolog (which we call hoe-1, for homolog of ELAC2). We have explored the biological role of this gene using RNAi to reduce gene activity. We found that worms subjected to hoe-1 RNAi are slow-growing and sterile. The sterility results from a drastic reduction in germline proliferation and cell-cycle arrest of germline nuclei. We found that hoe-1 is required for hyperproliferation phenotypes seen with mutations in three different genes, suggesting hoe-1 may be generally required for germline proliferation. We also found that reduction of hoe-1 by RNAi suppresses the multivulva (Muv) phenotype resulting from activating mutations in ras and that this suppression is likely to be indirect. This is the first demonstration of a biological role for this class of proteins in a complex eukaryote and adds important information when considering the role of ELAC2 in prostate cancer. ------------------- Key: 6402 Medline: 14615488 Authors: Eichmuller S;Vezzoli V;Bazzini C;Ritter M;Furst J;Jakab M;Ravasio A;Chwatal S;Dossena S;Botta G;Meyer G;Maier B;Valenti G;Lang F;Paulmichl M Title: Using the Caenorhabditis elegans operons for identifying functinal partner proteins in human cells. Citation: Journal of Biological Chemistry 279: 7136-7146 2004 Type: ARTICLE Genes: acr-2 acr-3 acr-11 acr-12 acr-13 acr-14 acr-16 acr-17 acr-19 acr-21 avr-12 avr-15 cca-1 ccb-1 clh-3 clh-4 clh-5 clh-6 deg-1 deg-3 des-2 egl-2 egl-19 egl-36 exp-2 gab-1 glr-1 glr-3 glr-4 glr-6 glr-7 gon-2 icl-1 inx-6 irk-1 irk-2 itr-1 kqt-1 kqt-3 mec-4 mec-10 mrp-1 mrp-2 mrp-4 mrp-5 mrp-6 nmr-1 nmr-2 ocr-4 osm-9 pgp-5 pgp-7 pgp-8 pgp-9 shw-3 tax-2 tax-4 trp-1 trp-2 twk-1 twk-12 twk-23 unc-2 unc-8 unc-38 unc-49 unc-63 unc-68 unc-103 Abstract: How can a large number of different phenotypes be generated by a limited number of genotypes? Promiscuity between different, structurally related and/or unrelated proteins seems to provide a plausible explanation to this pertinent question. Strategies able to predict such functional interrelations between different proteins are important to restrict the number of putative candidate proteins, which can then be subjected to time-consuming functional tests. Here we describe the use of the operon structure of the nematode genome to identify partner proteins in human cells. In this work we focus on ion channels proteins, which build an interface between the cell and the outside world and are responsible for a growing number of diseases in humans. However, the proposed strategy for the partner protein quest is not restricted to this scientific area but can be adopted in virtually every field of human biology where protein-protein interactions are assumed. ------------------- Key: 6404 Medline: 14718919 Authors: Ryder SP;Frater LA;Abramovitz DL;Goodwin EB;Williamson JR Title: RNA target specificity of the STAR/GSG domain post-transcriptional regulatory protein GLD-1. Citation: Nature Structural & Molecular Biology 1: 20-28 2004 Type: ARTICLE Genes: apx-1 cdc-25.1 ced-7 cej-1 cgh-1 cpb-1 daz-1 emo-1 fbf-1 fbf-2 gld-1 glp-1 lad-1 lin-36 lin-45 mes-3 mes-4 nhr-23 nos-3 peb-1 pie-1 puf-5 puf-6 puf-7 puf-8 rme-2 tra-1 tra-2 unc37 unc-62 wee-1.3 Abstract: The post-transcriptional regulation of gene expression underlies several critical developmental phenomena. In metazoa, gene products that are expressed, silenced and packaged during oogenesis govern early developmental processes prior to nascent transcription activation. Furthermore, tissue-specific alternative splicing of several transcription factors controls pattern formation and organ development. A highly conserved family of proteins containing a STAR/GSG RNA-binding domain is essential to both processes. Here, we identify the consensus STAR-binding element (SBE) required for specific mRNA recognition by GLD-1, a key regulator of Caenorhabditis elegans germline development. We have identified and verified new GLD-1 repression targets containing this sequence. The results suggest additional functions of GLD-1 in X-chromosome silencing and early embryogenesis. The SBE is present in Quaking and How mRNA targets, suggesting that STAR protein specificity is highly conserved. Similarities between the SBE and the branch-site signal indicate a possible competition mechanism for STAR/GSG regulation of splicing variants. ------------------- Key: 6405 Medline: 14718911 Authors: Butcher SE;Wickens M Title: STAR-studded circuitry. Citation: Nature Structural & Molecular Biology 1: 2-3 2004 Type: REVIEW Genes: gld-1 tra-2 Abstract: A recent study reports the RNA sequences that bind to the translational repressor protein GLD-1. The data suggest that a network of developmental genes may be regulated by GLD-1 or related STAR proteins through silencing or alternative splicing. ------------------- Key: 6406 Medline: 15009089 Authors: Ogawa S;Matsubayashi Y;Nishida E Title: An evolutionarily conserved gene required for proper microtubule architecture in Caenorhabditis elegans. Citation: Genes to Cells 9: 83-93 2004 Type: ARTICLE Genes: Abstract: Microtubules are involved in many cellular events during the cell cycle and also in a variety of early embryonic developmental processes. Their architecture and properties change dramatically during the cell cycle and are properly regulated. However, these regulatory mechanisms have not been fully elucidated. C05D11.3 gene of Caenorhabditis elegans encodes a low molecular weight protein that is evolutionarily conserved from yeasts to mammals. A mouse homolog of the C05D11.3 product, APACD (ATP binding protein associated with cell differentiation), contains a thioredoxin-like domain and P-loop, and is present in both the nucleus and the cytoplasm, showing often localization to centrosomes and midbody. In C. elegans, C05D11.3 is expressed throughout development with higher levels of expression in most cells of the nervous system and in vulva. C05D11.3 RNAi-treated embryos show apparent defects in pronuclear migration or nuclear-centrosome rotation, and exhibit little astral microtubules and defective small spindles. These results indicate that C05D11.3, an evolutionarily conserved gene, is essential for proper microtubule organization and function in C. elegans. This gene family may be a conserved regulator of microtubule dynamics and function. ------------------- Key: 6407 Medline: 14757812 Authors: Hwang BJ;Muller HM;Sternberg PW Title: Genome annotation by high-throughput 5' RNA end determination. Citation: Proceedings of the National Academy of Science USA 101: 1650-1655 2004 Type: ARTICLE Genes: Abstract: Complete gene identification and annotation, including alternative transcripts, remains a challenge in understanding genome organization. Such annotation can be achieved by a combination of computational analysis and experimental confirmation. Here, we describe a high-throughput technique, trans-spliced exon coupled RNA end determination (TEC-RED), that identifies 5' ends of expressed genes in nematodes. TEC-RED can distinguish coding regions from regulatory regions and identify genes as well as their alternative transcripts that have different 5' ends. Application of TEC-RED to approximate to10% of the Caenorhabditis elegans genome yielded tags 75% of which experimentally verified predicted 5'-RNA ends and 25% of which provided previously unknown information about 5'-RNA ends, including the identification of 99 previously unknown genes and 32 previously unknown operons. This technique will be applicable in any organisms that have a trans-splicing reaction from spliced leader RNA. We also describe an efficient sequential method for concatenating short sequence tags for any serial analysis of gene expression-like techniques. ------------------- Key: 6408 Medline: 14668347 Authors: Veljkovic E;Stasiuk S;Skelly PJ;Shoemaker CB;Verrey F Title: Functional characterization of Caenorhabditis elegans heteromeric amino acid transporters. Citation: Journal of Biological Chemistry 279: 7655-7662 2004 Type: ARTICLE Genes: aat-1 aat-2 aat-3 aat-4 aat-5 aat-6 aat-7 aat-8 aat-9 atg-1 atg-2 Abstract: ammalian heteromeric amino acid transporters (HATs) are composed of a multi-transmembrane spanning catalytic protein covalently associated with a type II glycoprotein (e.g. 4F2hc, rBAT) through a disulfide bond. Caenorhabditis elegans has nine genes encoding close homologues of the HAT catalytic proteins. Three of these genes (designated AAT-1 to AAT-3) have a much higher degree of similarity to the mammalian homologues than the other six, including the presence of a cysteine residue at the position known to form a disulfide bridge to the glycoprotein partner in mammalian HATs. C. elegans also has two genes encoding homologues of the heteromeric amino acid transporter type II glycoprotein subunits (designated ATG-1 and ATG-2). Both ATG, and/or AAT-1, -2, -3 proteins were expressed in Xenopus oocytes and tested for amino acid transport function. This screen revealed that AAT-1 and AAT-3 facilitate amino acid transport when expressed together with ATG-2 but not with ATG-1 or the mammalian type II glycoproteins 4F2hc and rBAT. AAT-1 and AAT-3 covalently bind to both C. elegans ATG glycoproteins, but only the pairs with ATG-2 traffic to the oocyte surface. Both of these functional, surface-expressed C. elegans HATs transport most neutral amino acids and display the highest transport rate for L-Ala and L-Ser (apparent Km 100 muM range). Similar to their mammalian counterparts, the C. elegans HATs function as (near) obligatory amino acid exchangers. Taken together, this study demonstrates that the heteromeric structure and the amino acid exchange function of HATs have been conserved throughout the ------------------- Key: 6409 Medline: 14965353 Authors: Anson RM;Hansford RG Title: Mitochondrial influence on aging rate in Caenorhabditis elegans. Citation: Aging Cell 3: 29-34 2004 Type: REVIEW Genes: Abstract: Virtually every model of mitochondrial involvement in aging shares the underlying proposition that mitochondrial dysfunction will accelerate the rate of aging. Caenorhabditis elegans is a post-mitotic organism with limited capacity for replacement and repair, and there is a great deal of evidence that interventions which decrease the induction of damage extend lifespan in this model. However, decreased availability of ubiquinone in adulthood has also been found to promote longevity and stress resistance, and evidence tentatively supports decreased mitochondrial function under these conditions. In addition, gene silencing experiments and mutations that target mitochondrial electron transport have also been found to increase lifespan and stress resistance in C. elegans, as has treatment with the mitochondrial inhibitor antimycin A. The involvement of damage by reactive oxygen species has been suggested, and yet many of these manipulations would be expected to increase the production of reactive oxygen species. The extension of lifespan by these interventions seems paradoxical and the mechanism, when it is elucidated, promises to have far-reaching significance. ------------------- Key: 6410 Medline: 14738880 Authors: Kolotuev I;Podbilewicz B Title: Pristionchus pacificus vulva formation: polarized division, cell migration, cell fusion, and evolution of invagination. Citation: Developmental Biology 266: 322-333 2004 Type: ARTICLE Genes: Abstract: Tube formation is a widespread process during organogenesis. Specific cellular behaviors participate in the invagination of epithelial monolayers that form tubes. However, little is known about the evolutionary mechanisms of cell assembly into tubes during development. In Caenorhabditis elegans, the detailed step-to-step process of vulva formation has been studied in wild type and in several mutants. Here we show that cellular processes during vulva development, which involve toroidal cell formation and stacking of rings, are conserved between C elegans and Pristionchus pacificus, two species of nematodes that diverged approximately 100 million years ago. These cellular behaviors are divided into phases of cell proliferation, short-range migration, and cell fusion that are temporally distinct in C elegans but not in P. pacificus. Thus, we identify heterochronic changes in the cellular events of vulva development between these two species. We find that alterations in the division axes of two equivalent vulval cells from Left-Right cleavage in C. elegans to Anterior-Posterior division in P pacificus can cause the formation of an additional eighth ring. Thus, orthogonal changes in cell division axes with alterations in the number and sequence of cell fusion events result in dramatic differences in vulval shape and in the number of rings in the species studied. Our characterization of vulva formation in P. pacificus compared to C elegans provides an evolutionary-developmental foundation for molecular genetic analyses of organogenesis in different species within the ------------------- Key: 6411 Medline: 14738885 Authors: Vilimas T;Abraham A;Okkema PG Title: An early pharyngeal muscle enhancer from the Caenorhabditis elegans ceh-22 gene is targeted by the Forkhead factor PHA-4. Citation: Developmental Biology 266: 388-398 2004 Type: ARTICLE Genes: ceh-22 egl-15 pes-10 pha-4 Abstract: Caenorhabditis elegans pharyngeal muscle development involves ceh-22, an NK-2 family homeobox gene related to genes controlling heart development in other species. ceh-22 is the earliest known gene expressed in the pharyngeal muscles and is likely regulated directly by factors specifying pharyngeal muscle fate. We have previously implicated the ceh-22 distal enhancer in initiating ceh-22 expression. Here we analyze the distal enhancer using functional and comparative assays. The distal enhancer contains three subelements contributing additively to its activity, and functionally important regulatory sequences are highly conserved in Caenorhabditis briggsae. One subelement, termed DE3, is strongly active in the pharyngeal muscles, and we identified two short oligonucleotides (de199 and de209) contributing to DE3 activity. Multimerized de209 enhances transcription similarly to DE3 specifically in the pharyngeal muscles, suggesting it may be an essential site regulating ceh-22. de209 binds the pan-pharyngeal Forkhead factor PHA-4 in vitro and responds to ectopic pha-4 expression in vivo, suggesting that PHA-4 directly initiates ceh-22 expression through de209. Because de209 enhancer activity is primarily limited to the pharyngeal muscles, we hypothesize that de209 also binds factors functioning with PHA-4 to specifically activate ceh-22 expression in pharyngeal ------------------- Key: 6412 Medline: 14738886 Authors: Gissendanner CR;Crossgrove K;Kraus KA;Maina CV;Sluder AE Title: Expression and function of conserved nuclear receptor genes in Caenorhabditis elegans. Citation: Developmental Biology 266: 399-416 2004 Type: ARTICLE Genes: ama-1 daf-7 daf-12 fax-1 lin-42 nhr-6 nhr-8 nhr-23 nhr-25 nhr-41 nhr-48 nhr-49 nhr-64 nhr-67 nhr-69 nhr-85 nhr-91 rrf-3 sex-1 unc-55 Abstract: The Caenorhabditis elegans genome encodes 284 nuclear receptor (NR) genes. Among these 284 NR genes are 15 genes conserved among the Metazoa. Here, we analyze the, expression and function of eight heretofore uncharacterized conserved C elegans NR genes. Reporter gene analysis demonstrates that these genes have distinct expression patterns and that a majority of the C elegans cell types express a conserved NR gene. RNA interference with NR gene function resulted in visible phenotypes for three of the genes, revealing functions in various processes during postembryonic development. Five of the conserved NR genes are orthologs of NR genes that function during molting and metamorphosis in insects. Functional studies confirm a role for most of these 'ecdysone cascade' NR orthologs during the continuous growth and dauer molts. Transcript levels for these genes fluctuate in a reiterated pattern during the molting cycles, reminiscent of the expression hierarchy observed in the insect ecdysone response. Together, these analyses provide a foundation for further dissecting the role of NRs in nematode development as well as for evaluating conservation of NR functions among the Metazoa. ------------------- Key: 6413 Medline: Authors: Clark JW;Eggebrecht AT Title: The small world of the nobel nematode Caenorhabditis elegans. Citation: Condensed Matter Theories 18: 389-406 2003 Type: REVIEW Genes: Abstract: ------------------- Key: 6414 Medline: 14761681 Authors: Cole RD;Anderson GL;Williams PL Title: The nematode Caenorhabditis elegans as a model of organosphsphate-induced mammalian neurotoxicity. Citation: Toxicology and Applied Pharmacology 194: 248-256 2004 Type: ARTICLE Genes: Abstract: Fifteen organic phosphate pesticides were tested by computer tracking for their acute behavioral toxicity with the nematode Caenorhabditis elegans. Thirteen of these 15 chemicals are used as insecticides and are anticholesterase agents. The other two chemicals are used as herbicides. EC50 values for each chemical were compared to the corresponding LD50 acute lethality value in rats and mice. Order of toxicity was found to be significantly correlated in comparisons of C. elegans to both rats and mice. Mechanistic investigations were conducted by assaying 8 of the 15 chemicals for anticholinesterase activity in C. elegans. Significant cholinesterase inhibition was confirmed for five chemicals that had displayed high behavioral toxicity, while three chemicals of low behavioral toxicity showed no significant decrease in cholinesterase activity. Toxicity for two chemicals that do not inhibit cholinesterase in mammals was linked to pH effects. Detailed comparison of individual chemicals and metabolic issues are discussed. These results have positive implications for the use of C elegans as a mammalian neurological model and support the use of C elegans in early rounds of chemical toxicity screening. ------------------- Key: 6415 Medline: Authors: Ferguson MR;Fan X;Mukherjee M;Luo J;Khan R;Ferreon JC;Hilser VJ;Shope RE;Fox RO Title: Directed discovery of bivalent peptide ligands to an SH3 domain. Citation: Protein Science 13: 626-632 2004 Type: ARTICLE Genes: sem-5 Abstract: The Caenorhabditis elegans SEM-5 SH3 domains recognize proline-rich peptide segments with modest affinity. We developed a bivalent peptide ligand that contains a naturally occurring proline-rich binding sequence, tethered by a glycine linker to a disulfide-closed loop segment containing six variable residues. The glycine linker allows the loop segment to explore regions of greatest diversity in sequence and structure of the SH3 domain: the RT and n-Src loops. The bivalent ligand was optimized using phage display, leading to a peptide (PP-G(4)-L) with 1000-fold increased affinity for the SEM-5 C-terminal SH3 domain over that of a natural ligand. NMR analysis of the complex confirms that the peptide loop segment is targeted to the RT and n-Src loops and parts of the beta-sheet scaffold of this SH3 domain. This binding region is comparable to that targeted by a natural non-PXXP peptide to the p67(phox) SH3 domain, a region not known to be targeted in the Grb2 SH3 domain family. PP-G(4)-L may aid in the discovery of additional binding partners of Grb2 family SH3 domains. ------------------- Key: 6416 Medline: 14766299 Authors: Finley JB;Qiu SH;Luan CH;Luo M Title: Structural genomics for Caenorhabditis elegans: high throughput protein expression analysis. Citation: Protein Expression and Purification 34: 49-55 2004 Type: ARTICLE Genes: Abstract: The structural genomics initiatives have begun with the aim to create a so-called 'basic set library' of protein folds that will be used to improve protein prediction methods. Such a library is thought to require the determination of tip to 10,000 new structures, including representative structures of several sequence variants from each protein fold. To meet this goal in a reasonable time frame and cost, automated systems must be utilized to clone and to identify the soluble recombinant proteins contained in multiple genomes. This paper presents such a system, developed using the genome of Caenorhabditis elegans (19,099 genes) as a model eukaryotic organism for structural genomics. This system successfully automates nearly all aspects of recombinant protein expression analysis including subcloning, bacterial growth, recombinant protein expression, protein purification, and scoring protein solubility. ------------------- Key: 6417 Medline: 14988716 Authors: Kopp A Title: Making a better worm. Citation: Nature Genetics 36: 213-214 2004 Type: REVIEW Genes: lin-48 Abstract: The excretory systems of closely related worm species have distinct morphological and functional features. A new study now shows that evolutionary gain of lin-48 expression in the excretory duct cell in Caenorhabditis elegans is responsible for the unique excretory system innovations present in this species. ------------------- Key: 6418 Medline: 14730447 Authors: Felix MA Title: Alternative morphs and plasticity of vulval development in a rhabditid nematode species. Citation: Development Genes & Evolution 214: 55-63 2004 Type: ARTICLE Genes: Abstract: The nematode species Rhabditis sp. SB347 (Family Rhabditidae) in standard culture conditions displays two developmental morphs with distinct modes of sexual reproduction: (1) females and males that develop through four feeding juvenile ("larval") stages; (2) self-fertile protandric hermaphrodites that develop through an obligatory non-feeding third juvenile stage, the "dauer" larva. In females and males, somatic gonad development begins in the first larval stage, whereas in hermaphrodites it is delayed to the second larval stage. Vulval development also differs between females and hermaphrodites: (1) the P8.p cell divides in females but stays undivided in hermaphrodites; (2) the number, timing, and source of inductive signals from the gonad to the vulval precursor cells differ between the two morphs. These results show that discrete vulva developmental routes can be adopted by animals of the same genotype. ------------------- Key: 6419 Medline: 14977564 Authors: Herman MA;Wu M Title: Noncanonical Wnt signaling pathways in C. elegans converge on POP-1/TCF and control cell polarity. Citation: Frontiers in Bioscience 9: 1530-1539 2004 Type: REVIEW Genes: apr-1 bar-1 dsh-2 egl-20 end-1 end-3 gpa-16 goa-1 hmp-2 hmr-1 lin-17 lin-44 lit-1 mab-5 mes-1 mig-5 mom-1 mom-2 mom-3 mom-4 mom-5 pop-1 psa-1 psa-4 pry-1 sgg-1 src-1 tlp-1 unc-37 wrm-1 Abstract: In the nematode Caenorhabditis elegans, a canonical Wnt signaling pathway controls a cell migration whereas noncanonical Wnt pathways control the polarities of individual cells. Despite the differences in the identities and interactions among canonical and noncanonical Wnt pathway components, as well as the processes they regulate, almost all C. elegans Wnt pathways involve the sole Tcf homolog, POP-1. Intriguingly, POP-1 is asymmetrically distributed between the daughters of an asymmetric cell division, with the anterior sister cell usually having a higher level of nuclear POP-1 than its posterior sister. At some divisions, asymmetric distribution of POP-1 is controlled by noncanonical Wnt signaling, but at others the asymmetry is generated independently. Recent experiments suggest that despite this elaborate anterior-posterior POP-1 asymmetry, the quantity of POP-1 protein may have less to do with the subsequent determination of fate than does the quality of the POP-1 protein in the cell. In this review, we will embark on a quest to understand Quality (1), at least from the standpoint of the effect POP/Tcf quality has on the control of cell polarity in C. elegans. ------------------- Key: 6420 Medline: 14594448 Authors: Mee CJ;Tomlinson SR;Perestenko PV;de Pomerai D;Duce IR;Usherwood PNR;Bell DR Title: Latrophilin is required for toxicity of black widow spider venom in Caenorhabditis elegans. Citation: Biochemical Journal 378: 185-191 2004 Type: ARTICLE Genes: Abstract: Black widow spider venom (BWSV) kills Caenorhabditis elegans after injection owing to the presence of heat- and detergent-sensitive components, which are high-molecular-mass latrotoxins. A C. elegans homologue of latrophilin/CIRL (calcium-independent receptor for latrotoxin), B0457.1, was identified and shown to have five conserved domains. RNAi (RNA interference) of this gene rendered C. elegans resistant to BWSV, whereas RNAi for CYP37A1 or a neurexin I homologue, and a deletion mutant of the related B0286.2 gene, had no effect on BWSV toxicity. The latrophilin RNAi mutants exhibit changes in defaecation cycle and alterations in drug sensitivity. These results demonstrate that latrophilin mediates the toxicity of BWSV and provide evidence for a physiological function of this receptor. ------------------- Key: 6421 Medline: 15003118 Authors: Sheps JA;Ralph S;Zhao ZY;Baillie DL;Ling V Title: The ABC transporter gene family of Caenorhabditis elegans has implications for the evolutionary dynamics of multidrug resistance in eukaryotes. Citation: Genome Biology 5: 52-68 2004 Type: ARTICLE Genes: abt-1 abt-2 abt-3 abt-4 abt-5 ced-7 cft-1 haf-1 haf-2 haf-3 haf-4 haf-5 haf-6 haf-7 haf-8 haf-9 mrp-1 mrp-2 mrp-3 mrp-4 mrp-5 mrp-6 mrp-7 mrp-8 pgp-1 pgp-2 pgp-3 pgp-4 pgp-5 pgp-6 pgp-7 pgp-8 pgp-9 pgp-10 pgp-11 pgp-12 pgp-13 pgp-14 pgp-15 Abstract: Background: Many drugs of natural origin are hydrophobic and can pass through cell membranes. Hydrophobic molecules must be susceptible to active efflux systems if they are to be maintained at lower concentrations in cells than in their environment. Multi-drug resistance (MDR), often mediated by intrinsic membrane proteins that couple energy to drug efflux, provides this function. All eukaryotic genomes encode several gene families capable of encoding MDR functions, among which the ABC transporters are the largest. The number of candidate MDR genes means that study of the drug-resistance properties of an organism cannot be effectively carried out without taking a genomic perspective. Results: We have annotated sequences for all 60 ABC transporters from the Caenorhabditis elegans genome, and performed a phylogenetic analysis of these along with the 49 human, 30 yeast, and 57 fly ABC transporters currently available in GenBank. Classification according to a unified nomenclature is presented. Comparison between genomes reveals much gene duplication and loss, and surprisingly little orthology among analogous genes. Proteins capable of conferring MDR are found in several distinct subfamilies and are likely to have arisen independently multiple times. Conclusions: ABC transporter evolution fits a pattern expected from a process termed 'dynamic-coherence'. This is an unusual result for such a highly conserved gene family as this one, present in all domains of cellular life. Mechanistically, this may result from the broad substrate specificity of some ABC proteins, which both reduces selection against gene loss, and leads to the facile sorting of functions among paralogs following gene duplication. ------------------- Key: 6422 Medline: 14755119 Authors: Piekny AJ;Mains PE Title: Squeezing an egg into a worm: C. elegans embryonic morphogenesis. Citation: TheScientificWorld 3: 1370-1381 2003 Type: REVIEW Genes: age-1 ajm-1 ced-10 daf-2 daf-16 die-1 dlg-1 efn-1 efn-2 efn-3 efn-4 fem-2 gex-2 gex-3 hmp-1 hmp-2 hmr-1 let-413 let-502 mab-20 mel-11 mig-2 mlc-4 nmy-1 nmy-2 ptp-3 sma-1 spc-1 sqt-3 unc-73 vab-1 Abstract: We review key morphogenetic events that occur during Caenorhabditis elegans (www.wormbase.org/) embryogenesis. Morphogenesis transforms tissues from one shape into another through cell migrations and shape changes, often utilizing highly conserved actin-based contractile systems. Three major morphogenetic events occur during C. elegans embryogenesis: (1) dorsal intercalation, during which two rows of dorsal epidermal cells intercalate to form a single row; (2) ventral enclosure, where the dorsally located sheet of epidermal cells stretches to the ventral midline, encasing the embryo within a single epithelial sheet; and (3) elongation, during which actin-mediated contractions within the epithelial sheet lengthens the embryo. Here, we describe the known molecular players involved in each of these processes. ------------------- Key: 6423 Medline: 12725749 Authors: Wong C;Stearns T Title: Centrosome biology: a SAS-sy centriole in the cell cycle. Citation: Current Biology 13: R351-R352 2003 Type: REVIEW Genes: sas-4 Abstract: A novel protein in Caenorhabditis elegans, SAS-4, is a component of centrioles and is required for centriole duplication. Depletion of SAS-4 results in stunted centrioles and a smaller centrosome, suggesting a link to organelle size control. ------------------- Key: 6424 Medline: 14706854 Authors: Lener T;Burgstaller G;Gimona M Title: The role of calponin in the gene profile of metastatic cells: inhibition of metastatic cell motility by multiple calponin repeats. Citation: FEBS Letters 556: 221-226 2004 Type: ARTICLE Genes: unc-87 Abstract: Metastasis of diseased cells is the basic event leading to death in individuals with cancer. Establishment of metastasis requires that tumour cells migrate from the site of the primary tumour into the circulation system, escape from the vasculature and form secondary tumours at novel sites. These processes depend to a large degree on cytoskeletal remodeling. We show here that multiple copies of the short actin-binding module CLIK(23) from human or Caenorhabditis elegans calponin proteins effectively inhibit cell motility on two dimensional matrices and suppress soft agar colony formation of metastatic melanoma and adenocarcinoma cells of murine and human origin. Ectopic expression of CLIK(23) modules for 30 days results in the formation of multinucleated cells. The repeat displays true modular behaviour, resulting in increased cytoskeletal effects in direct correlation with the increase in number of modules. Our results demonstrate that the role of calponin in the signature profile of metastasising cells is that of a mechanical stabiliser of the actin cytoskeleton, which interferes with actin turnover by binding at a unique interface along the actin ------------------- Key: 6425 Medline: 14992718 Authors: Tewari M;Hu PJ;Ahn JS;Ayivi-Guedehoussou N;Vidalain PO;Li S;Milstein S;Armstrong CM;Boxem M;Butler MD;Busiguina S;Rual JF;Ibarrola N;Chaklos ST;Bertin N;Vaglio P;Edgley ML;King KV;Albert PS;Vandenhaut Title: Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Citation: Molecular Cell 13: 469-482 2004 Type: ARTICLE Genes: abu-1 arf-1 atp-2 daf-1 daf-3 daf-4 daf-5 daf-7 daf-8 daf-12 daf-14 daf-21 dnc-2 lap-1 lbp-6 lys-8 psa-1 Abstract: To initiate a system-level analysis of C. elegans DAF-7/TGF-beta signaling, we combined interactome mapping with single and double genetic perturbations. Yeast two-hybrid (Y2H) screens starting with known DAF-7/TGF-beta pathway components defined a network of 71 interactions among 59 proteins. Coaffinity purification (co-AP) assays in mammalian cells confirmed the overall quality of this network. Systematic perturbations of the network using RNAi, both in wild-type and daf-7/TGF-beta pathway mutant animals, identified nine DAF-7/TGF-beta signaling modifiers, seven of which are conserved in humans. We show that one of these has functional homology to human SNO/SKI oncoproteins and that mutations at the corresponding genetic locus daf-5 confer defects in DAF-7/TGF-beta signaling. Our results reveal substantial molecular complexity in DAF-7/TGF-beta signal transduction. Integrating interactome maps with systematic genetic perturbations may be useful for developing a systems ------------------- Key: 6426 Medline: 14565992 Authors: Denton J;Nehrke K;Rutledge E;Morrison R;Strange K Title: Alternative splicing of N- and C-termini of a C. elegans ClC channel alters gating and sensitivity to external Cl- and H+. Citation: Journal of Physiology 555: 97-114 2004 Type: ARTICLE Genes: clh-3 Abstract: CLH-3 is a meiotic cell cycle-regulated ClC Cl- channel that is functionally expressed in oocytes of the nematode Caenorhabditis elegans. CLH-3a and CLH-3b are alternatively spliced variants that have identical intramembrane regions, but which exhibit striking differences in their N- and C-termini. Structural and functional studies indicate that N- and C-terminal domains modulate ClC channel activity. We therefore postulated that alternative splicing of CLH-3 would alter channel gating and physiological functions. To begin testing this hypothesis, we characterized the biophysical properties of CLH-3a and CLH-3b expressed heterologously in HEK293 cells. CLH-3a activates more slowly and requires stronger hyperpolarization for activation than CLH-3b. Depolarizing conditioning voltages dramatically increase CLH-3a current amplitude and induce a slow inactivation process at hyperpolarized voltages, but have no significant effect on CLH-3b activity. CLH-3a also differs significantly in its extracellular Cl- and pH sensitivity compared to CLH-3b. Immunofluorescence microscopy demonstrated that CLH3b is translationally expressed during all stages of oocyte development, and furthermore, the biophysical properties of the native oocyte Cl- current are indistinguishable from those of heterologously expressed CLH-3b. We conclude that CLH-3b carries the oocyte Cl- current and that the channel probably functions in nonexcitable cells to depolarize membrane potential and/or mediate net Cl- transport. The unique voltage-dependent properties of CLH-3a suggest that the channel may function in muscle cells and neurones to regulate membrane excitability. We suggest that alternative splicing of CLH-3 N- and C-termini modifies the functional properties of the channel by altering the accessibility and/or function of pore-associated ion-binding sites. ------------------- Key: 6427 Medline: 14999070 Authors: Loria PM;Hodgkin J;Hobert O Title: A conserved postsynaptic transmembrane protein affecting neuromuscular signaling in Caenorhabditis elegans. Citation: Journal of Neuroscience 24: 2191-2201 2004 Type: ARTICLE Genes: cof-2 unc-17 unc-25 unc-29 unc-38 unc-122 eDf4 eDf5 eDf10 eDf11 eDf13 eDf24 Abstract: For a motor unit to function, neurons and muscle cells need to adopt their correct cell fate, form appropriate cellular contacts, and assemble a specific repertoire of signaling proteins into presynaptic and postsynaptic structures. In the nematode Caenorhabditis elegans, a disruption of any of these steps causes uncoordinated locomotory behavior (unc phenotype). We report here the positional cloning of a new unc gene, unc-122, which we show by mosaic analysis and tissue-specific rescue experiments to act in muscle to affect locomotory behavior. unc-122 codes for a phylogenetically conserved type II transmembrane protein with collagen repeats and a cysteine-rich olfactomedin domain. Together with uncharacterized proteins in C. elegans, Drosophila, and vertebrates, UNC-122 defines a novel family of proteins that we term "Colmedins." UNC-122 protein is expressed exclusively in muscle and coelomocytes and localizes to the postsynaptic surface of GABAergic and cholinergic neuromuscular junctions (NMJs). Presynaptic and postsynaptic structures are present and properly aligned in unc-122 mutant animals, yet the animals display neurotransmission defects characterized by an altered sensitivity toward drugs that interfere with cholinergic signaling. Moreover, unc-122 mutant animals display anatomical defects in motor axons that are likely a secondary consequence of neurotransmission defects. Both the neuroanatomical and locomotory defects worsen progressively during the life of an animal, consistent with a role of unc-122 in acute signaling at the NMJ. On the basis of motifs in the UNC-122 protein sequence that are characteristic of extracellular matrix proteins, we propose that UNC-122 is involved in maintaining a structural microenvironment that allows efficient neuromuscular signaling. ------------------- Key: 6428 Medline: 14975728 Authors: Woo WM;Goncharov A;Jin Y;Chisholm AD Title: Intermediate filaments are required for C. elegans epidermal elongation. Citation: Developmental Biology 267: 216-229 2004 Type: ARTICLE Genes: ifa-2 ifa-3 ifb-1 rrf-3 unc-54 maDf4 Abstract: Cytoplasmic intermediate filaments (cIFs) are thought to provide mechanical strength to vertebrate cells; however, their function in invertebrates has been largely unexplored. The Caenorhabditis elegans genome encodes multiple cIFs. The C. elegans ifb-1 locus encodes two cIF isoforms, IFB-1A and IFB-1B, that differ in their head domains. We show that both IFB-1 isoforms are expressed in epidermal cells, within which they are localized to muscle-epidermal attachment structures. Reduction in IFB-1A function by mutation or RNA interference (RNAi) causes epidermal fragility, abnormal epidermal morphogenesis, and muscle detachment, consistent with IFB-1A providing mechanical strength to epidermal attachment structures. Reduction in IFB-1B function causes morphogenetic defects and defective outgrowth of the excretory cell. Reduction in function of both IFB-1 isoforms results in embryonic arrest due to muscle detachment and failure in epidermal cell elongation at the 2-fold stage. Two other cIFs, IFA-2 and IFA-3, are expressed in epidermal cells. We show that loss of function in IFA-3 results in defects in morphogenesis indistinguishable from those of embryos lacking ifb-1. In contrast, IFA-2 is not required for embryonic morphogenesis. Our data indicate that IFB-1 and IFA-3 are likely the major cIF isoforms in embryonic epidermal ------------------- Key: 6429 Medline: 14975731 Authors: Koh K;Bernstein Y;Sundaram MV Title: The nT1 translocation separates vulval regulatory elements from the egl-18 and elt-6 GATA factor genes. Citation: Developmental Biology 267: 252-263 2004 Type: ARTICLE Genes: act-1 act-2 act-3 egl-4 egl-17 egl-18 eff-1 elt-6 lin-39 Abstract: egl-18 and elt-6 are partially redundant, adjacent genes encoding GATA factors essential for viability, seam cell development, and vulval development in Caenorhabditis elegans. The nT1 reciprocal translocation causes a strong Vulvaless phenotype, and an nT1 breakpoint was previously mapped to the left arm of LGIV, where egl-18/elt-6 are located. Here we present evidence that the nT1 vulval phenotype is due to a disruption of egl-18/elt-6 function specifically in the vulva. egl-18 mutations do not complement nT1 for vulval defects, and the nT1 breakpoint on LGIV is located within similar to800 bp upstream of a potential transcriptional start site of egl-18. In addition, we have identified a similar to350-bp cis-regulatory region sufficient for vulval expression just upstream of the nT1 breakpoint. By examining the fusion state and division patterns of the cells in the developing vulva of nT1 mutants, we demonstrate that egl-18/elt-6 prevent fusion and promote cell proliferation at multiple steps of vulval development. ------------------- Key: 6430 Medline: 14724126 Authors: Kao G;Tuck S;Baillie D;Sundaram MV Title: C. elegans SUR-5/PR55 cooperates with LET-92/protein phsophatase 2A and promotes Raf activity independently of inhibitory Akt phosphorylation sites. Citation: Development 131: 755-765 2004 Type: ARTICLE Genes: akt-1 akt-2 ksr-1 ksr-2 let-60 let-92 lin-45 mpk-1 par-1 pry-1 sur-6 sur-8 qDf8 Abstract: Protein phosphatase 2A (PP2A) can both positively and negatively influence the Ras/Raf/MEK/ERK signaling pathway, but its relevant substrates are largely unknown. In C elegans, the PR55/B regulatory subunit of PP2A, which is encoded by sur-6, positively regulates Ras-mediated vulval induction and acts at a step between Ras and Raf. We show that the catalytic subunit (C) of PP2A, which is encoded by let-92, also positively regulates vulval induction. Therefore SUR-6/PR55 and LET-92/PP2A-C probably act together to dephosphorylate a Ras pathway substrate. PP2A has been proposed to activate the Raf kinase by removing inhibitory phosphates from Ser259 from Raf-1 or from equivalent Akt phosphorylation sites in other Raf family members. However, we find that mutant forms of C. elegans LIN-45 RAF that lack these sites still require sur-6. Therefore, SUR-6 must influence Raf activity via a different mechanism. SUR-6 and KSR (kinase suppressor of Ras) function at a similar step in Raf activation but our genetic analysis suggests that KSR activity is intact in sur-6 mutants. We identify the kinase PAR-1 as a negative regulator of vulval induction and show that it acts in opposition to SUR-6 and KSR-1. In addition to their roles in Ras signaling, SUR-6/PR55 and LET-92/PP2A-C cooperate to control mitotic progression during early embryogenesis. ------------------- Key: 6431 Medline: 14757639 Authors: Huang X;Powell-Coffman JA;Jin Y Title: The AHR-1 aryl hydrocarbon receptor and its cofactor the AHA-1 aryl hydrocarbon receptor nuclear translocator specify GABAergic neuron cell fate in C. elegans. Citation: Development 131: 819-828 2004 Type: ARTICLE Genes: aha-1 ahr-1 avr-15 ceh-10 daf-21 glr-1 lim-4 lim-6 unc-25 unc-47 dxDf1 dxDf2 eDf3 mnDf111 nDf23 nDf29 qDf5 qDf7 qDf9 Abstract: The aryl hydrocarbon receptors (AHR) are bHLH-PAS domain containing transcription factors. In mammals, they mediate responses to environmental toxins such as 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin (TCDD). Such functions of AHRs require a cofactor, the aryl hydrocarbon receptor nuclear translocator (ARNT), and the cytoplasmic chaperonins RSP90 and XAP2. AHR homologs have been identified throughout the animal kingdom. We report here that the C. elegans orthologs of AHR and ARNT, ahr-1 and aha-1, regulate GABAergic motor neuron fate specification. Four C. elegans neurons known as RMED, RMEV, RMEL and RMER express the neurotransmitter GABA and control head muscle movements. ahr-1 is expressed in RMEL and RMER neurons. Loss of function in ahr-1 causes RMEL and RMER neurons to adopt a RMED/RMEV-like fate, whereas the ectopic expression of ahr-1 in RMED and RMEV neurons can transform them into RMEL/RMER-like neurons. This function of ahr-1 requires aha-1, but not daf-21/hsp90. Our results demonstrate that C. elegans ahr-1 functions as a cell-type specific determinant. This study further supports the notion that the ancestral role of the AHR proteins is in regulating ------------------- Key: 6432 Medline: 14644776 Authors: Lamitina ST;Morrison R;Moeckel GW;Strange K Title: Adaptation of the nematode Caenorhabditis elegans to extreme osmotic stress. Citation: American Journal of Physiology - Cell Physiology 286: C785-C791 2004 Type: ARTICLE Genes: Abstract: The ability to control osmotic balance is essential for cellular life. Cellular osmotic homeostasis is maintained by accumulation and loss of inorganic ions and organic osmolytes. Although osmoregulation has been studied extensively in many cell types, major gaps exist in our molecular understanding of this essential process. Because of its numerous experimental advantages, the nematode Caenorhabditis elegans provides a powerful model system to characterize the genetic basis of animal cell osmoregulation. We therefore characterized the ability of worms to adapt to extreme osmotic stress. Exposure of worms to high-salt growth agar causes rapid shrinkage. Survival is normal on agar containing up to 200 mM NaCl. When grown on 200 mM NaCl for 2 wk, worms are able to survive well on agar containing up to 500 mM NaCl. HPLC analysis demonstrated that levels of the organic osmolyte glycerol increase 15- to 20-fold in nematodes grown on 200 mM NaCl agar. Accumulation of glycerol begins 3 h after exposure to hypertonic stress and peaks by 24 h. Glycerol accumulation is mediated primarily by synthesis from metabolic precursors. Consistent with this finding, hypertonicity increases transcriptional expression of glycerol 3-phosphate dehydrogenase, an enzyme that is rate limiting for hypertonicity- induced glycerol synthesis in yeast. Worms adapted to high salt swell and then return to their initial body volume when exposed to low-salt agar. During recovery from hypertonic stress, glycerol levels fall rapidly and glycerol excretion increases approximately fivefold. Our studies provide the first description of osmotic adaptation in C. elegans and provide the foundation for genetic and functional genomic analysis of animal cell ------------------- Key: 6433 Medline: Authors: Heininger P;Plezer J;Claus E;Pfitzner S Title: Results of long-term sediment quality studies on the River Elbe. Citation: Acta Hydrochimica et Hydrobiologica 31: 356-367 2004 Type: ARTICLE Genes: Abstract: The results of long-term studies in the Upper and Middle Elbe River between 1991 and 2001 are presented and the temporal and spatial trends in sediment contamination and toxicity are studied. Although the concentrations of heavy metals and arsenic have significantly decreased in the last 10 years for most of the toxic elements they are still far from natural background values. For organic priority pollutants increasing as well as decreasing trends are observed, depending on the Elbe reach and/or the parameter under consideration. Elbe sediments have a permanent measurable toxicity. It is usually low in terms of aquatic tests as far as the persisting hot spots are not considered. Whole sediment testing with nematode Caenorhabditis elegans which was started in 1997 revealed clear toxic effects. In contrast to the priority pollution situation, no significant trend could be found in general sediment toxicity between 1992 and 2001. ------------------- Key: 6434 Medline: 14981253 Authors: Grunwald ME;Mellem JE;Strutz N;Maricq AV;Kaplan JM Title: Clathrin-mediated endocytosis is required for compensatory regulation of GLR-1 glutamate receptors after activity blockade. Citation: Proceedings of the National Academy of Sciences USA 101: 3190-3195 2004 Type: ARTICLE Genes: eat-4 glr-1 nmr-1 unc-2 unc-11 Abstract: Chronic changes in neural activity trigger a variety of compensatory homeostatic mechanisms by which neurons maintain a normal level of synaptic input. Here we show that chronic activity blockade triggers a compensatory change in the abundance of GLR-1, a Caenorhabditis elegans glutamate receptor. In mutants lacking a voltage-dependent calcium channel (unc-2) or a vesicular glutamate transporter (VGLUT; eat-4), the abundance of GLR-1 in the ventral nerve cord was increased. Similarly, the amplitude of glutamate-evoked currents in ventral cord interneurons was increased in eat-4 VGLUT mutants compared with wild-type controls. The effects of eat-4 VGLUT mutations on GLR-1 abundance in the ventral cord were eliminated in double mutants lacking both the clathrin adaptin protein unc-11 AP180 and eat-4 VGLUT. In contrast, mutations that decreased ubiquitination of GLR-1 did not prevent increased ventral cord abundance of GLR-1 in eat-4 VGLUT mutants. Taken together, our results suggest that GLR-1 is regulated in a homeostatic manner and that this effect depends on clathrin-mediated endocytosis but does not require ------------------- Key: 6435 Medline: 14993261 Authors: Yeong FM Title: Anaphase-promoting complex in Caenorhabditis elegans. Citation: Molecular and Cellular Biology 24: 2215-2225 2004 Type: REVIEW Genes: apc-5 apc-10 apc-11 cye-1 emb-27 emb-30 fzr-1 fzy-1 ify-1 lin-23 lin-35 mat-1 mat-2 mat-3 mdf-1 mdf-2 pod-3 pod-4 pod-5 pod-6 rec-8 scc-3 sep-1 smc-1 smc-3 tim-1 ubq-2 Abstract: Progression through critical events in cell division relies to a large extent on the destruction of key effectors of the cell cycle. An example can be seen in the regulation of the major cell cycle effector, the cyclin-dependent kinases (CDKs). CDKs depend upon the binding of their activators, the cyclins, to drive specific events at particular stages in the cell division cycle. As different cyclins are synthesized at different phases of the cell cycle, the CDK, when associated with cyclins, essentially exhibits distinct activities in each phase of the cell cycle. The destruction of cell cycle stage-specific cyclins therefore plays an important role in limiting the activities of the CDKs at the end of each stage so that the CDKs can associate with yet other cyclins to drive progression of the cell cycle (reviewed in reference 45). ------------------- Key: 6436 Medline: 15214724 Authors: Park JO;Hargreaves JR;McConville EJ;Stirling GR;Ghisalberti EL;Sivasithamparam K Title: Production of leucinostatins and nematocidal activity of Australian isolates of Paecilomyces lilacinus (Thom) Citation: Letters in Applied Microbiology 38: 271-276 2004 Type: ARTICLE Genes: Abstract: Aims: To evaluate the relationship between leucinostatin production by Paecilomyces lilacinus isolates and their biological activities. Methods and Results: The nematicidal, parasitic and enzymatic activity of Australian P. lilacinus isolates were investigated. Nematicidal activities of culture filtrates were measured by mortality and inhibition of reproduction of Caenorhabditis elegans, whereas egg-parasitic activity was measured by colonization on Meloidogyne javanica. Enzymatic activities (protease and chitinase) were assayed on solid media. The results suggest that leucinostatins in P. lilacinus are indicators of nematicidal activity, whereas chitinase activity might be related to parasitism. Conclusions: Nematicidal activity of culture filtrates of Paecilomyces lilacinus strains related to their ability to produce leucinostatins. Significance Impact of the Study: This is the first study describing the leucinostatins as nematicides. ------------------- Key: 6437 Medline: 15199953 Authors: Schulenburg H;Kurz CL;Ewbank JJ Title: Evolution of the innate immune system: the worm Citation: Immunological Reviews 198: 36-58 2004 Type: REVIEW Genes: abf-1 abf-2 abf-3 abf-4 abf-5 abf-6 age-1 akt-1 akt-2 bre-5 ced-3 ced-4 ced-9 ctl-1 ctl-2 daf-2 daf-4 daf-16 daf-28 dbl-1 egl-1 egl-9 gcs-1 gst-4 ikb-1 ins-1 ins-7 ins-18 ins-28 lon-1 lon-3 lys-1 lys-2 lys-3 lys-4 lys-5 lys-6 lys-7 lys-8 lys-9 lys-10 mef-2 mev-1 mtl-1 nlp-29 nsy-1 pcs-1 pdk-1 pgp-1 pgp-2 pgp-3 pgp-4 phm-2 pik-1 pmk-1 rad-8 sek-1 skn-1 sma-2 sma-3 sma-4 sma-6 sod-3 srf-2 srf-3 srf-5 tol-1 trf-1 Abstract: Simple model organisms that are amenable to comprehensive experimental analysis can be used to elucidate the molecular genetic architecture of complex traits. They can thereby enhance our understanding of these traits in other organisms, including humans. Here, we describe the use of the nematode Caenorhabditis elegans as a tractable model system to study innate immunity. We detail our current understanding of the worm's immune system, which seems to be characterized by four main signaling cascades: a p38 mitogen-activated protein kinase, a transforming growth factor-beta-like, a programed cell death, and an insulin-like receptor pathway. Many details, especially regarding pathogen recognition and immune effectors, are only poorly characterized and clearly warrant further investigation. We additionally speculate on the evolution of the C. elegans immune system, taking into special consideration the relationship between immunity, stress responses and digestion, the diversification of the different parts of the immune system in response to multiple and/or coevolving pathogens, and the trade-off between immunity and host life history traits. Using C. elegans to address these different facets of host-pathogen interactions provides a fresh perspective on our understanding of the structure and complexity of innate immune systems in animals and plants. ------------------- Key: 6438 Medline: 15020414 Authors: Chen J;Li X;Greenwald I Title: sel-7, a positive regulator of lin-12 activity, encodes a novel nuclear protein in Caenorhabditis elegans. Citation: Genetics 166: 151-160 2004 Type: ARTICLE Genes: glp-1 lag-1 lin-12 sel-4 sel-7 sel-12 Abstract: Suppressor genetics in C. elegans has identified key components of the LIN-12/Notch signaling pathway. Here, we describe a genetic and molecular characterization of the suppressor gene sel-7. We show that reducing or eliminating sel-7 activity suppresses the effects of constitutive lin-12 activity, enhances the effects of partially reduced lin-12 activity, and causes a synthetic Lin-12(0) phenotype when combined with a null mutation in the sel-12 presenilin gene. These observations suggest that sel-7 is a positive regulator of lin-12 activity. We also show that SEL-7 encodes a novel nuclear protein. Through yeast two-hybrid screening, we identified an apparent interaction partner, K08E3.8, that also interacts with SEL-8, a known component of the nuclear complex that forms upon LIN-12 activation. Our data suggest potential roles for SEL-7 in the assembly or function of this nuclear complex. ------------------- Key: 6439 Medline: 15020415 Authors: McKay JP;Raizen DM;Gottschalk A;Schafer WR;Avery L Title: eat-2 and eat-18 are required for nicotinic neurotransmission in the Caenorhabditis elegans pharynx. Citation: Genetics 166: 161-169 2004 Type: ARTICLE Genes: eat-2 eat-18 eDf3 eDf7 Abstract: Mutations in eat-2 and eat-18 cause the same defect in C. elegans feeding behaviour: the pharynx is unable to pump rapidly in the presence of food. EAT-2 is a nicotinic acetylcholine receptor subunit that functions in the pharyngeal muscle. It is localized to the synapse between pharyngeal muscle and the main pharyngeal excitatory motor neuron MC, and it is required for MC stimulation of pharyngeal muscle. eat-18 encodes a small protein that has no homology to previously characterized proteins. It has a single transmembrane domain and a short extracellular region. Allele-specific genetic interactions between eat-2 and eat-18 suggest that EAT-18 interacts physically with the EAT-2 receptor. While eat-2 appears to be required specifically for MC neurotransmission, eat-18 also appears to be required for the function of other nicotinic receptors in the pharynx. In eat-18 mutants, the gross localization of EAT-2 at the MC synapse is normal, suggesting that it is not required for trafficking. These data indicate that eat-18 could be a novel component of the pharyngeal nicotinic receptor. ------------------- Key: 6440 Medline: 15020416 Authors: Siegfried KR;Kidd AR;Chesney MA;Kimble J Title: The sys-1 and sys-3 genes cooperate with Wnt signaling to establish the proximal-distal axis of the Caenorhabditis elegans gonad. Citation: Genetics 166: 171-186 2004 Type: ARTICLE Genes: egl-20 gon-3 gon-4 gon-14 gon-15 gon-16 lin-17 lin-44 lit-1 mom-1 pop-1 sys-1 sys-3 wrm-1 ctDf1 eDf19 mDf4 mDf7 mDf8 mDf9 mDf10 nDf29 nDf31 nDf32 nDf35 nDf41 sDf2 sDf60 Abstract: To form the proximal-distal axis of the C. elegans gonad, two somatic gonadal precursor cells, Z1 and Z4, divide asymmetrically to generate one daughter with a proximal fate and one with a distal fate. Genes governing this process include the lin-17 frizzled receptor, wrm-1/beta-catenin, the pop-1/TCF transcription factor, lit-1/nemo-like kinase, and the sys-1 gene. Normally, all of these regulators promote the distal fate. Here we show that nuclear levels of a pop-1 GFP fusion protein are less abundant in the distal than in the proximal Z1/Z4 daughters. This POP-1 asymmetry is lost in mutants disrupting Wnt/MAPK regulation, but retained in sys-1 mutants. We find that sys-1 is haplo-insufficient for gonadogenesis defects and that sys-1 and pop-1 mutants display a strong genetic interaction in double heterozygotes. Therefore, sys-1 is a dose-sensitive locus and may function together with pop-1 to control Z1/Z4 asymmetry. To identify other regulatory genes in this process, we screened for mutants resembling sys-1. Four such genes were identified (gon-14, -15, -16 and sys-3) and shown to interact genetically with sys-1. However, only sys-3 promotes the distal fate at the expense of the proximal fate. We suggest that sys-3 is a new key gene in this pathway and that gon-14, gon-15 and gon-16 may cooperate with POP-1 and SYS-1 at multiple stages of gonad ------------------- Key: 6441 Medline: 14985121 Authors: Madi A;Hoffrogge R;Blasko B;Glocker MO;Fesus L Title: Amine donor protein substrates for transglutaminase activity in Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 315: 1064-1069 2004 Type: ARTICLE Genes: Abstract: Transglutaminase dependent cross-linking of proteins has been implicated in a wide range of biological phenomena occurring in both extracellular and intracellular compartments. Clarification of the physiological role of transglutaminases requires identification of substrate molecules. Here we report the detection, purification, and identification by mass spectrometry of proteins, the glutamate dehydrogenase, a protein disulfide isomerase, and aldehyde dehydrogenase as amine donor substrates for the transglutaminase activity of the nematode Caenorhabditis elegans utilizing a novel biotinylated oligoglutamine peptide as a substrate. We also purified and identified streptavidin-binding proteins of the worm. ------------------- Key: 6442 Medline: 14984742 Authors: Hazkani-Covo E;Levanon EY;Rotman G;Graur D;Novik A Title: Evolution of multicellularity in Metazoa: comparative analysis of the subcellular localization of proteins in Saccharomyces, Drosophila and Caenorhabditis. Citation: Cell Biology International 28: 171-178 2004 Type: ARTICLE Genes: Abstract: A comparison of the subcellular assignments of proteins between the unicellular Saccharomyces cerevisiae and the multicellular Drosophila melanogaster and Caenorhabditis elegans was performed using a computation tool for the prediction of subcellular localization. Nine subcellular compartments were studied: (1) extracellular domain, (2) cell membrane, (3) cytoplasm, (4) endoplasmic reticulum, (5) Golgi apparatus, (6) lysosome, (7) peroxisome, (8) mitochondria, and (9) nucleus. The transition to multicellularity was found to be characterized by an increase in the total number of proteins encoded by the genome. Interestingly, this increase is distributed unevenly among the subcellular compartments. That is, a disproportionate increase in the number of proteins in the extracellular domain, the cell membrane, and the cytoplasm is observed in multicellular organisms, while no such increase is seen in other subcellular compartments. A possible explanation involves signal transduction. In terms of protein numbers, signal transduction pathways may be roughly described as a pyramid with an expansive base in the extracellular domain (the numerous extracellular signal proteins), progressively narrowing at the cell membrane and cytoplasmic levels, and ending in a narrow tip consisting of only a handful of transcription modulators in the nucleus. Our observations suggest that extracellular signaling interactions among metazoan cells account for the uneven increase in the numbers of proteins among subcellular compartments during the transition to ------------------- Key: 6443 Medline: 14982959 Authors: Berezikov E;Bargmann CI;Plasterk RHA Title: Homologous gene targeting in Caenorhabditis elegans by biolistic transformation. Citation: Nucleic Acids Research 32: e40- 2004 Type: ARTICLE Genes: unc-22 unc-54 unc-119 Abstract: Targeted homologous recombination is a powerful approach for genome manipulation that is widely used for gene alteration and knockouts in mouse and yeast. In Caenorhabditis elegans, several methods of target-selected mutagenesis have been implemented but none of them provides the opportunity of introducing exact predefined changes into the genome. Although anecdotal cases of homologous gene targeting in C.elegans have been reported, no practical technique of gene targeting has been developed so far. In this work we demonstrate that transformation of C.elegans by microparticle bombardment (biolistic transformation) can result in homologous recombination between introduced DNA and the chromosomal locus. We describe a scaled up version of biolistic transformation that can be used as a method for homologous gene targeting ------------------- Key: 6444 Medline: 14993596 Authors: Cipollo JF;Awad A;Costello CE;Robbins PW;Hirschberg CB Title: Biosynthesis in vitro of Caenorhabditis elegans phosphorylcholine oligosaccharides. Citation: Proceedings of the National Academy of Sciences USA 101: 3404-3408 2004 Type: ARTICLE Genes: Abstract: The biosynthesis in vitro of phosphorylcholine oligosaccharides in Caenorhabditis elegans has been investigated. Here we show that extracts of C elegans' microsomes transfer phosphorylcholine from L-alpha-dipaimitoyl phosphatidylcholine to hybrid and complex type N-linked oligosaccharides containing mannose residues disubstituted with N-acetylglucosamine. The reaction products are consistent with structures reported for C elegans as well those found in the filarial nematodes Acanthocheilonema viteae, Onchocerca volvulus, and Brugia malayi, strongly supporting the concept that the phosphorylcholine oligosaccharide biosynthetic enzymes are conserved in this group of organisms. Because it is thought that phosphorylcholine substitution of oligosaccharides modulates host immune response in filarial infections, this in vitro system may help in gaining an understanding of the basis for this response. ------------------- Key: 6445 Medline: Authors: Ruvkun G Title: Regulation of C. elegans life span by insulin-like signaling. Citation: Endocrine Aspects of Successful Aging: Genes, Hormones and Lifestyles. Springer-Verlag, Berlin. : 1-17 2004 Type: REVIEW Genes: Abstract: ------------------- Key: 6446 Medline: Authors: McCarter JP;Mitreva M;Clifton SW;Bird DM;Waterston RH Title: Nematode gene sequences: Update for December 2003. Citation: Journal of Nematology 35: 465-469 2003 Type: ARTICLE Genes: Abstract: ------------------- Key: 6447 Medline: Authors: Poletti G;Orsini F;Ullschmied J;Skala J;Kralikova B;Pfeifer M;Kadlec C;Mocek T;Prag A;Cotelli F;Lamia CL;Batani D;Bernardinello A;Desai T;Zullini A Title: X-ray microscopy and imaging of Caenorhabditis elegans nematode using a laser plasma pulsed X-ray source. Citation: Laser-Generated and Other Laboratory X-Ray and EUV Sources, Optics, and Applications. SPIE-INT Society Optical Engineering, Bellingham. : 375-382 2003 Type: REVIEW Genes: Abstract: ------------------- Key: 6448 Medline: 15037100 Authors: Nisbet AJ;Cottee P;Gasser RB Title: Molecular biology of reproduction and development in parasitic nematodes: progress and opportunities. Citation: International Journal for Parasitology 34: 125-138 2004 Type: ARTICLE Genes: akt-1 akt-2 daf-2 daf-4 daf-7 fog-2 fox-1 her-1 mab-3 mab-23 sex-1 tra-1 tra-2 xol-1 Abstract: Molecular biological research on the development and reproduction of parasites is of major significance for many fundamental and applied areas of medical and veterinary parasitology. Together with knowledge of parasite biology and epidemiology, the application of molecular tools and technologies provides unique opportunities for elucidating developmental and reproductive processes in helminths. This article focuses specifically on recent progress in studying the molecular mechanisms of development, sexual differentiation and reproduction in parasitic nematodes of socio-economic importance and comparative analyses, where appropriate, with the free-living nematode Caenorhabditis elegans. It also describes the implications of such work for understanding reproduction, tissue migration, hypobiosis, signal transduction and host-parasite interactions at the molecular level, and for seeking new means of parasite intervention. ------------------- Key: 6449 Medline: Authors: Igaki T;Miura M Title: Role of Bcl-2 family members in invertebrates. Citation: Biochimica et Biophysica Acta 1644: 73-81 2004 Type: ARTICLE Genes: ced-3 ced-4 ced-9 egl-1 Abstract: Proteins belonging to the Bcl-2 family function as regulators of 'life-or-death' decisions in response to various intrinsic and extrinsic stimuli. In mammals, cell death is controlled by pro- and anti-apoptotic members of the Bcl-2 family, which function upstream of the caspase cascade. Structural and functional homologues of the Bcl-2 family proteins also exist in lower eukaryotes, such as nematodes and flies. In nematodes, an anti-apoptotic Bcl-2 family protein, CED-9, functions as a potent cell death inhibitor, and a BH3-only protein, EGL-1, acts as an inhibitor of CED-9 to facilitate the spatio-temporal regulation of programmed cell death. On the other hand, the Drosophila genome encodes two Bcl-2 family proteins, Drob-1/Debcl/dBorg-1/dBok and Buffy/dBorg-2, both of which structurally belong to the pro-apoptotic group, despite abundant similarities in the cell death mechanisms between flies and vertebrates. Drob-1 acts as a pro-apoptotic factor in vitro and in vivo, and Buffy/dBorg-2 exhibits a weak anti-apoptotic function. The ancestral role of the Bcl-2 family protein may be pro-apoptotic, and the evolution of the functions of this family of proteins may be closely linked with the contribution of mitochondria to the cell death pathway. ------------------- Key: 6450 Medline: 14960273 Authors: Chen N;Greenwald I Title: The lateral signal for LIN-12/Notch in C. elegans vulval development comprises redundant secreted and transmembrane DSL proteins. Citation: Developmental Cell 6: 183-192 2004 Type: ARTICLE Genes: apx-1 arg-1 dsl-1 dsl-2 dsl-3 dsl-4 dsl-5 dsl-6 dsl-7 egl-17 lag-2 let-60 lin-3 lin-12 lin-15 sur-2 Abstract: The vulval precursor cells (VPCs) are spatially patterned by a LET-23/EGF receptor-mediated inductive signal and a LIN-12/Notch-mediated lateral signal. The lateral signal has eluded identification, so the mechanism by which lateral signaling is activated has not been known. Here, we computationally identify ten genes that encode potential ligands for LIN-12, and show that three of these genes, apx-1, dsl-1, and lag-2, are functionally redundant components of the lateral signal. We also show that transcription of all three genes is initiated or upregulated in VPCs in response to inductive signaling, suggesting that direct transcriptional control of the lateral signal by the inductive signal is part of the mechanism by which these cell signaling events are coordinated. In addition, we show that DSL-1, which lacks a predicted transmembrane domain, is a natural secreted ligand and can substitute for the transmembrane ligand ------------------- Key: 6451 Medline: Authors: Smith JV;Luo Y Title: Elevation of oxidative free radicals in Alzheimer's disease models can be attenuated by Gingko biloba extract EGb 761. Citation: Journal of Alzheimer's Disease 5: 287-300 2003 Type: ARTICLE Genes: mev-1 Abstract: The role of amyloid beta-peptide (Abeta) in the free-radical oxidative-stress model of neurotoxicity in Alzheimer's disease (AD) has received much attention recently. In this study, we have employed both in vitro and in vivo models displaying endogenous Abeta production to study the effects of Abeta on intracellular free radical levels. We employed a neuroblastoma cell line stably expressing an AD-associated double mutation, which exhibits both increased secretion and intracellular accumulation of Abeta when stimulated, as well as transgenic Caenorhabditis elegans constitutively expressing human Abeta. A rise in levels of hydrogen peroxide (H2O2) was observed in both in vitro and in vivo AD-associated transgenic models expressing the Abeta peptide compared with the wild type controls. Treatment of the cells or C. elegans with Ginkgo biloba extract EGb 761 significantly attenuated the basal as well as the induced levels of H2O2-related reactive oxygen species (ROS). Among individual EGb 761 components tested, kaempferol and quercetin provided maximum attenuation in both models. Furthermore, an age-dependent increase in H2O2-related ROS was observed in wild type C. elegans, which is accelerated in the AD-associated C. elegans mutant. These results support the hypothesis of the involvement of Abeta and ROS in association with AD. ------------------- Key: 6452 Medline: 15044786 Authors: Bolm M;Chhatwal GS;Jansen WTM Title: Bacterial resistance in daf-2 mutants. Citation: Science 303: 1976- 2004 Type: REVIEW Genes: ctl-1 ctl-2 daf-2 daf-16 sod-3 Abstract: In their Brevia "Long-lived C. elegans daf-2 mutants are resistant to bacterial pathogens," D.A. Garsin et al. show that long-lived C. elegans daf-2 mutants are resistant to killing by bacterial pathogens. Partial loss-of-function mutations in daf-2, which encodes an insulin-like receptor, results in de-repression of the transcription factor daf-16, leading to life extension and increased resistance to bacterial pathogens Enterococcus faecalis, Staphylococcus aureus, and Pseudomonas aeruginosa. ------------------- Key: 6453 Medline: Authors: Ausubel FM;Begun J;Kim DH;Moy T;Ruvkun G;Calderwood SB;Sifri CD;Garsin DA Title: Bacterial resistance of daf-2 mutants - response. Citation: Science 303: 1976- 2004 Type: REVIEW Genes: age-1 daf-2 Abstract: Bolm et al. raise an important issue that we have considered as well. Because many streptococcal species are able to quickly kill C. elegans through the production of hydrogen peroxide, and because long-lived C. elegans daf-2 and age-1 mutants are more resistant to oxidative stress, Bolm et al. suggest that the apparent resistance of these mutants to bacterial pathogens is a consequence of their tolerance to reactive oxygen species. ------------------- Key: 6454 Medline: 14694072 Authors: Nikolaidis N;Nei M Title: Concerted and nonconcerted evolution of the Hsp70 gene superfamily in two sibling species of nematodes. Citation: Molecular Biology and Evolution 21: 498-505 2004 Type: ARTICLE Genes: Abstract: We have identified the Hsp70 gene superfamily of the nematode Caenorhabditis briggsae and investigated the evolution of these genes in comparison with Hsp70 genes from C. elegans, Drosophila, and yeast. The Hsp70 genes are classified into three monophyletic groups according to their subcellular localization, namely, cytoplasm (CYT), endoplasmic reticulum (ER), and mitochondria (MT). The Hsp110 genes can be classified into the polyphyletic CYT group and the monophyletic ER group. The different Hsp70 and Hsp110 groups appeared to evolve following the model of divergent evolution. This model can also explain the evolution of the ER and MT genes. On the other hand, the CYT genes are divided into heat-inducible and constitutively expressed genes. The constitutively expressed genes have evolved more or less following the birth-and-death process, and the rates of gene birth and gene death are different between the two nematode species. By contrast, some heat-inducible genes show an intraspecies phylogenetic clustering. This suggests that they are subject to sequence homogenization resulting from gene conversion-like events. In addition, the heat-inducible genes show high levels of sequence conservation in both intra-species and inter-species comparisons, and in most cases, amino acid sequence similarity is higher than nucleotide sequence similarity. This indicates that purifying selection also plays an important role in maintaining high sequence similarity among paralogous Hsp70 genes. Therefore, we suggest that the CYT heat-inducible genes have been subjected to a combination of purifying selection, birth-and-death process, and gene ------------------- Key: 6455 Medline: 15006138 Authors: Ellerbrock BR;Coscarelli EM;Gurney ME;Geary TG Title: Screening for presenilin inhibitors using the free-living nematode, Caenorhabditis elegans. Citation: Journal of Biomolecular Screening 9: 147-152 2004 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans contains 3 homologs of presenilin genes that are associated with Alzheimer's disease. Loss-of-function mutations in C. elegans genes cause a defect in egg laying. In humans, loss of presenilin-1 (PS1) function reduces amyloid-beta peptide processing from the amyloid protein precursor. Worms were screened for compounds that block egg laying, phenocopying, presenilin loss of function. To accommodate even relatively high throughput screening, a semiautomated method to quantify egg laying was devised by measuring the chitinase released into the culture medium. Chitinase is released by hatching eggs, but little is shed into the medium from the body cavity of a hermaphrodite with an egg laying deficient (egl) phenotype. Assay validation involved measuring chitinase release from wild-type C. elegans (N2 strain), sel-12 presenilin loss-of-function mutants, and 2 strains of C. elegans with mutations in the egl-36 K+ channel gene. Failure to find specific presenilin inhibitors in this collection likely reflects the small number of compounds tested, rather than a flaw in screening strategy. Absent defined biochemical pathways for presenilin, this screening method, which takes advantage of the genetic system available in C. elegans and its historical use for anthelminthic screening, permits an entry into mechanism-based discovery of drugs for Alzheimer's disease. ------------------- Key: 6456 Medline: 15013747 Authors: Jee C;Lee J;Lee JI;Lee WH;Park BJ;Yu JR;Park E;Kim E;Ahnn J Title: SHN-1, a Shank homologue in C. elegans, affects defecation rhythm via the inositol-1,4,5-trisphosphate receptor. Citation: FEBS Letters 561: 29-36 2004 Type: ARTICLE Genes: itr-1 shn-1 Abstract: Protein localization in the postsynaptic density (PSD) of neurons is mediated by scaffolding proteins such as PSD-95 and Shank, which ensure proper function of receptors at the membrane. The Shank family of scaffolding proteins contain PDZ (PSD-95, Dig, and ZO-1) domains and have been implicated in the localizations of many receptor proteins including glutamate receptors in mammals. We have identified and characterized shn-1, the only homologue of Shank in Caenorhahditis elegans. The shn-1 gene shows approximately 40% identity over 1000 amino acids to rat Shanks. SHN-1 protein is localized in various tissues including neurons, pharynx and intestine. RNAi suppression of SHN-1 did not cause lethality or developmental abnormality. However, suppression of SHN-1 in the itr-1 (sa73) mutant, which has a defective inositol-1,4,5-trisphosphate (IP3) receptor, resulted in animals with altered defecation rhythm. Our data suggest a possible role of SHN-1 in affecting function of IP3 ------------------- Key: 6457 Medline: 15018934 Authors: Lanjuin A;Sengupta P Title: Specification of chemosensory neuron subytpe identities in Caenorhabditis elegans. Citation: Current Opinion in Neurobiology 14: 22-30 2004 Type: REVIEW Genes: ceh-36 ceh-37 che-1 cog-1 daf-19 lim-4 lin-11 lin-49 lsy-6 odr-7 osm-5 osm-6 str-2 unc-37 unc-42 Abstract: Cellular diversity in the nervous system arises from the presence of multiple neuronal subtypes, each of which is specialized to perform a unique function. Work in Caenorhabditis elegans has begun to reveal the pathways that are essential for the specification of identities of neuronal subtypes in its chemosensory system. The functions of each chemosensory neuron subtype are specified by distinct developmental cascades, using molecules from well-conserved transcription factor families. Additional cellular complexity is generated by novel mechanisms that further diversify the identities of the left and right members of a bilateral sensory neuron pair. ------------------- Key: 6458 Medline: Authors: Shen K Title: Molecular mechanisms of target specificity during synapse formation. Citation: Current Opinion in Neurobiology 14: 83-88 2004 Type: REVIEW Genes: syg-1 syg-2 Abstract: Neurons are connected with a high degree of specificity in neuronal circuits. Axon guidance mechanisms are responsible for directing axons to their approximate target region. It is not well understood how precise synaptic connections form between specific pre- and postsynaptic neurons within the target area. Recent analysis of a group of cell surface proteins in different systems has shed light on the diverse cellular and molecular mechanisms that generate the precise patterns of connectivity. ------------------- Key: 6459 Medline: 15036152 Authors: Rual JF;Hill DE;Vidal M Title: ORFeome projects: gateway between genomics and omics. Citation: Current Opinion in Chemical Biology 8: 20-25 2004 Type: REVIEW Genes: Abstract: At all layers of the hierarchical organization of life, biological phenomena can be considered either by focusing one's attention on individual components, of by studying the underlying principles of the systems formed by these individual components (i.e. by using 'reductionist' or 'integrative' approaches, respectively) [1-3]. Since both reductionist and integrative approaches can lead to complementary information, they should ideally be used in combination. ------------------- Key: 6460 Medline: 15066285 Authors: Lo MC;Gay F;Odom R;Shi Y;Lin R Title: Phosphorylation of the beta-catenin/MAPK complex promotes 14-3-3-mediated nuclear export of TCF/POP-1 in signal-responsive cells in C. elegans. Citation: Cell 117: 95-106 2004 Type: ARTICLE Genes: crm-1 lit-1 med-1 mom-2 mom-4 mom-5 par-5 pop-1 wrm-1 Abstract: In C. elegans embryos, a Wnt/MAPK signaling pathway downregulates the TCF/LEF transcription factor POP-1, resulting in a lower nuclear level in signal-responsive cells compared to their sisters. Although the beta-catenin WRM-1 is required for POP-1 downregulation, a direct interaction between these two proteins does not seem to be required, as the beta-catenin-interacting domain of POP-1 is dispensable for both POP-1 downregulation and function in early embryos. We show here that WRM-1 downregulates POP-1 by promoting its phosphorylation by the MAP kinase LIT-1 and subsequent nuclear export via a 14-4-4 protein, PAR-5. In signal-responsive cells, we also detect a concurrent upregulation of nuclear LIT-1 that is dependent of Wnt/MAPK signaling. Our results suggest a model whereby Wnt/MAPK signaling downregulates POP-1 levels in responsive cells, in part by increasing nuclear LIT-1 levels, thereby increasing POP-1 phosphorylation and PAR-5 mediated nuclear ------------------- Key: 6461 Medline: 15034661 Authors: Viney ME;Franks NR Title: Is dauer pheromone of Caenorhabditis elegans really a pheromone? Citation: Naturwissenschaften 91: 123-124 2004 Type: REVIEW Genes: Abstract: Animals respond to signals and cues in their environment. The difference between a signal (e.g. a pheromone) and a cue (e.g. a waste product) is that the information content of a signal is subject to natural selection, whereas that of a cue is not. The model free-living nematode Caenorhabditis elegans forms an alternative developmental morph (the dauer larva) in response to a so-called 'dauer pheromone', produced by all worms. We suggest that the production of 'dauer pheromone' has no fitness advantage for an individual worm and therefore we propose that 'dauer pheromone' is not a signal, but a cue. Thus, it should not be called a pheromone. ------------------- Key: 6462 Medline: Authors: Muller HAJ;Bossinger O Title: Mechanisms of establishing cell polarity. Citation: Comments on Theoretical Biology 7: 53-76 2002 Type: REVIEW Genes: ajm-1 crb-1 dlg-1 elt-2 emb-9 end-1 end-3 hmp-1 hmr-1 let-2 let-23 let-413 lin-2 lin-7 lin-10 med-1 med-2 par-1 par-2 par-3 par-6 pkc-3 pod-1 skn-1 Abstract: Most, if not all, cells are polarized. The polarization of a cell is expressed in the asymmetric distribution of cellular compartments, organelles, or molecules within the cell of within the plasma membrane. This asymmetry allows a cell to fulfill specific tasks such as vectorial transport, directed migration, and signal transduction. In this review we give a brief summary on some of the best-studied polarized cell types and the cellular basis of their polarized organization. As specific examples we then review current progress being made in understanding the generation and maintenance of cell polarity in developing embryos of the genetically tractable model organisms Drosophila melanogaster and Caenorhabditis elegans. ------------------- Key: 6463 Medline: 15063180 Authors: Bossinger O;Fukushige T;Claeys M;Borgonie G;McGhee JD Title: The apical disposition of the Caenorhabditis elegans intestinal terminal web is maintained by LET-413. Citation: Developmental Biology 268: 448-456 2004 Type: ARTICLE Genes: ajm-1 dlg-1 hmp-1 ifb-2 let-413 Abstract: We wish to understand how organ-specific structures assemble during embryonic development. In the present paper, we consider what determines the subapical position of the terminal web in the intestinal cells of the nematode Caenorhabditis elegans. The terminal web refers to the organelle-depleted, intermediate filament-rich layer of cytoplasm that underlies the apical microvilli of polarized epithelial cells. It is generally regarded as the anchor for actin rootlets protruding from the microvillar cores. We demonstrate that: (i) the widely used monoclonal antibody MH33 reacts (only) with the gut-specific intermediate filament protein encoded by the ifb-2 gene; (ii) IFB-2 protein accumulates near the gut lumen beginning at the lima bean stage of embryogenesis and remains associated with the gut lumen into adulthood; and (iii) as revealed by immunoelectron microscopy, IFB-2 protein is confined to a discrete circumferential subapical layer within the intestinal terminal web (known in nematodes as the "endotube"); this layer joins directly to the apical junction complexes that connect adjacent gut cells. To investigate what determines the disposition of the IFB-2-containing structure as the terminal web assembles during development, RNAi was used to remove the functions of gene products previously shown to be involved in the overall apicobasal polarity of the developing gut cell. Removal of dlg-1, ajm-1, or hmp-1 function has little effect on the overall position or continuity of the terminal web IFB-2-containing layer. In contrast, removal of the function of the let-413 gene leads to a basolateral expansion of the terminal web, to the point where it can now extend around the entire circumference of the gut cell. The same treatment also leads to concordant basolateral expansion of both gut cell cortical actin and the actin-associated protein ERM-1. LET-413 has previously been shown to be basolaterally located and to prevent the basolateral expansion of several individual apical proteins. In the present context, we conclude that LET-413 is also necessary to maintain the entire terminal web or brush border assembly at the apical surface of C elegans gut cells, a dramatic example of the so-called "fence" function ascribed to epithelial cell junctions. On the other hand, LET-413 is not necessary to establish this apical location during early development. Finally, the distance at which the terminal web intermediate filament layer lies beneath the gut cell surface (both apical and basolateral) must be determined independently of apical ------------------- Key: 6464 Medline: 15003846 Authors: Liu J;Dent JA;Beech RN;Prichard RK Title: Genomic organization of an avermectin receptor subunit from Haemonchus contortus and expression of its putative promoter region in Caenorhabditis elegans. Citation: Molecular & Biochemical Parasitology 134: 267-274 2004 Type: ARTICLE Genes: Abstract: Avermectins and milbemycins are believed to exert their anthelmintic effects by binding to glutamate-gated chloride channels (GluCls). Two GluCI subunits have been localized in the pharynx in Caenorhabditis elegans, and the pharynx has been implicated as a major target for avermectins in C. elegans. However, in parasitic nematodes, the pharyngeal localization of the GluCl subunits needs to be determined. The HcGhiCla gene encoding an alpha-type GluCl subunit has been cloned from Haemonchus contortus previously. To investigate the expression site of the HcGluCla gene we have isolated a 1439bp 5'-flanking region and determined the genomic organization of this gene. The HcGluCla gene is composed of 12 exons separated by 11 introns and spans approximately 7.3 kb of genomic DNA. Analysis of the 1439 bp 5'-flanking region of the HcGluCla gene revealed that it contained TATA, CCAAT boxes, and several other consensus transcriptional factor recognition sequences. The 1439 bp 5'-flanking region and the first exon and intron and part of the second exon of the HcGluCla gene were fused to green fluorescence protein (GFP) reporter gene and microinjected into the gonads of C. elegans. After microinjection of the construct into C elegans, four stable transformed lines were established and assayed for GFP expression. The transformed animals exhibited fluorescence in the two pairs of MC and M2 pharyngeal neurons, but no expression was detected in the muscle cells. Expression of HcGluCla in pharyngeal neurons suggests a mechanism for the effects of avermectins and milbemycins on pharyngeal function in ------------------- Key: 6465 Medline: 15038283 Authors: Kwon JY;Hong M;Choi MS;Kang S;Duke K;Kim S;Lee S;Lee J Title: Ethanol-response genes and their regulation analyzed by a microarray and comparative genomic approach in the nematode Caenorhabditis elegans. Citation: Genomics 83: 600-614 2004 Type: ARTICLE Genes: alh-1 aly-2 cdc-14 col-7 col-60 col-120 crt-1 dhs-23 dnj-23 dpy-18 elo-1 far-7 fmo-15 glr-2 gpa-1 grp-1 gst-1 gst-42 hsp-12.6 hsp-16.1 hsp-16.41 hsp-16.49 hsp-70 icl-1 ins-33 ipp-5 lec-8 lec-9 lys-2 lys-5 nhr-3 nhr-68 nhr-132 nlp-4 opt-2 pab-2 pdi-2 pes-2 plp-1 prx-11 ptr-14 rab-3 rnp-3 skr-8 skr-13 spp-18 stc-1 stl-1 vhp-1 Abstract: The nematode shows responses to acute ethanol exposure that are similar to those observed in humans, mice, and Drosophila, namely hyperactivity followed by uncoordination and sedation. We used in this report the nematode Caenorhabditis elegans as a model system to identify and characterize the genes that are affected by ethanol exposure and to link those genes functionally into an ethanol-induced gene network. By analyzing the expression profiles of all C. elegans ORTs using microarrays, we identified 230 genes affected by ethanol. While the ethanol response of some of the identified genes was significant at early time points, that of the majority was at late time points, indicating that the genes in the latter case might represent the physiological consequence of the ethanol exposure. We further characterized the early response genes that may represent those involved directly in the ethanol response. These genes included many heat shock protein genes, indicating that high concentration of ethanol acts as a strong stress to the animal. Interestingly, we identified two non-heat-shock protein genes that were specifically responsive to ethanol. glr-2 was the only glutamate receptor gene to be induced by ethanol. T28C12.4, which encodes a protein with limited homology to human neuroligin, was also specific to ethanol stress. Finally, by analyzing the promoter regions of the early response genes, we identified a regulatory element, TCTGCGTCTCT, that was necessary for the expression of subsets of ethanol ------------------- Key: 6466 Medline: 15003625 Authors: Hanazawa M;Kawasaki I;Kunitomo H;Gengyo-Ando K;Bennett KL;Mitani S;Iino Y Title: The Caenorhabditis elegans eukaryotic initiation factor 5A homologue, IFF-1, is required for germ cell proliferation, gametogenesis and localization of the P-granule component of PGL-1. Citation: Mechanisms of Development 121: 213-224 2004 Type: ARTICLE Genes: gld-1 glh-1 glh-4 glp-4 iff-1 iff-2 rrf-1 Abstract: Eukaryotic initiation factor 5A (eIF-5A) was originally isolated as a translation initiation factor. However, this function has since been reconsidered, with recent studies pointing to roles for eIF-5A in mRNA metabolism and trafficking [Microbiol. Mol. Biol. Rev. 66 (2002) 460; Eur. Mol. Biol. Org. J. 17 (1998) 2914]. The Caenorhabditis elegans genome contains two eIF-5A homologues, iff-1 and iff-2, whose functions in vivo were examined in this study. The iff-2 mutation causes somatic defects that include slow larval growth and disorganized somatic gonadal structures in hermaphrodites. iff-2 males show disorganized tail sensory rays and spicules. On the other hand, iff-I mRNA is expressed in the gonad, and the lack of iff-I activity causes sterility with an underproliferated gemiline resulting from impaired mitotic proliferation in both hermaphrodites and males. In spite of underproliferation, meiotic nuclei are observed, as revealed by presence of immunoreactivity to the anti-HIM-3 antibody; however, no gametogenesis occurs in the iff-I gonads. These phenotypes are in part similar to the mutants affected in the components of P granules, which are the C. elegans counterparts of germ granules [Cuff. Top Dev. Biol. 50 (2000) 155]. We found that localization of the P-granule component PGL-I to P granules is disrupted in the iff-I mutant. In summary, the two C. elegans homologues of eIF-5A act in different tissues: IFF-2 is required in the soma, and IFF-1 is required in the germline for germ cell proliferation, for gametogenesis after entry into mciosis, and for proper PGL-I localization on P granules. ------------------- Key: 6467 Medline: Authors: Sommer RJ Title: Cells and genes as networks in nematode development and evolution. Citation: Handbook of Graphs and Networks: from the genome to the network. S Bornholdt and HG Schuster (eds). Wiley-VCH, Weinheim. : 131-144 2003 Type: REVIEW Genes: lin-39 mab-5 Abstract: During the last decades, the concept of networks became very useful in many areas of modern biology. Biological systems are organized in a hierarchical fashion, generating networks of interacting modules at many levels of organization. Not only ecosystems, populations of species and individual organisms, but also organs, tissues and cells within one organism, as well as genetic networks and signaling cascades, build networks of interacting units within a hierarchical system [26]. At each level, multiple units (modules) exist that interact with one another to form complex networks. Therefore, the concept of networks can be applied to many, if not to all biological phenomena. In the following article, I would like to describe a case study in evolutionary developmental biology that indicates how the concept of networks can be used in developmental and evolutionary biology. ------------------- Key: 6468 Medline: 14872060 Authors: Saijou E;Fujiwara T;Suzaki T;Inoue K;Sakamoto H Title: RBD-1, a nucleolar RNA-binding protein, is essential for Caenorhabditis elegans early development through 18S ribosomal RNA processing. Citation: Nucleic Acids Research 32: 1028-1036 2004 Type: ARTICLE Genes: fib-1 rbd-1 Abstract: RBD-1 is the Caenorhabditis elegans homolog of Mrd1p, which was recently shown to be required for 18S ribosomal RNA (rRNA) processing in yeast. To gain insights into the relationship between ribosome biogenesis and the development of multicellular organisms, we examined the expression and function of RBD-1. Maternal RBD-1 in the fertilized egg disappears immediately after cleavage starts, whereas zygotic RBD-1 first appears in late embryos and is localized in the nucleolus in most cells, although zygotic transcription of pre-rRNA is known to be initiated as early as the one-cell stage. RNA interference of the rbd-1gene severely inhibits the processing of 18S rRNA in association with various developmental abnormalities, indicating its essential role in pre-rRNA processing and development in C. elegans. These results provide evidence for the linkage between ribosome biogenesis and the control of development and imply unexpected uncoupling of transcription and processing of pre-rRNA in early C. ------------------- Key: 6469 Medline: 15044551 Authors: Cai T;Fukushige T;Notkins AL;Krause M Title: Insulinoma-associated protein IA-2, a vesicle transmembrane protein, genetically interacts with UNC-31/CAPS and affects neurosecretion in Caenorhabditis elegans. Citation: Journal of Neuroscience 24: 3115-3124 2004 Type: ARTICLE Genes: aex-3 daf-2 daf-7 daf-11 daf-12 daf-28 ida-1 rab-3 snb-1 snt-1 unc-18 unc-31 unc-64 unc-104 Abstract: IA-2 (insulinoma-associated protein 2), a major autoantigen in type 1 diabetes, is a receptor-tyrosine phosphatase-like protein associated with the membrane of secretory granules of neural and endocrine-specific cells. Loss of IA-2 activity in the mouse results in reduced insulin release and additional phenotypes, consistent with a general effect on neurosecretion and hormone release. To gain further insight into the cellular mechanisms of IA-2 function, we have studied the Caenorhabditis elegans homolog, CeIA-2 encoded by the ida-1 gene. Using two independent putative null alleles of ida-1, we demonstrate that animals lacking CeIA-2 activity are viable and exhibit subtle defects. Genetic studies of mutants in ida-1 and several genes involved in neurosecretory vesicle cargo release and signaling highlight two roles for CeIA-2. First, CeIA-2 has a specific and novel genetic interaction with UNC-31/CAPS, a protein that has been shown in other systems to regulate dense-core vesicle cargo release. Second, loss of CeIA-2 activity enhances weak alleles in the insulin-like signaling pathway. These results suggest that CeIA-2 may be an important factor in dense-core vesicle cargo release with parallels to insulin signaling in mammals. ------------------- Key: 6470 Medline: Authors: Rostaing P;Weimer RM;Jorgensen EM;Triller A;Bessereau JL Title: Preservation of immunoreactivity and fine structure of adult C. elegans tissues using high-pressure freezing. Citation: Journal of Histochemistry & Cytochemistry 52: 555- 2004 Type: CORRECT Genes: Abstract: The authors note that one parameter of experimental conditions was misreported. In the Materials and Methods section under the heading of Chemical Fixation and Freeze-substitution the concentration of osmium listed is 0.01% when, in fact, the concentration used was 1%. ------------------- Key: 6471 Medline: 15003172 Authors: Bulow HE;Hobert O Title: Differential sulfations and epimerization define heparan sulfate specificity in nervous system development. Citation: Neuron 41: 723-736 2004 Type: ARTICLE Genes: hse-5 hst-2 hst-6 ina-1 kal-1 sax-3 slt-1 unc-6 vab-1 Abstract: Heparan sulfate proteoglycans (HSPG) are components of the extracellular matrix through which axons navigate to reach their targets. The heparan sulfate (HS) side chains of HSPGs show complex and differentially regulated patterns of secondary modifications, including sulfations of distinct hydroxyl groups and epimerization of an asymmetric carbon atom. These modifications endow the HSPG-containing extracellular matrix with the potential to code for an enormous molecular diversity. Attempting to decode this diversity, we analyzed C. elegans animals lacking three HS-modifying enzymes, glucuronyl C5-epimerase, heparan 6O-sulfotransferase, and 2O-sulfotransferase. Each of the mutant animals exhibit distinct as well as overlapping axonal and cellular guidance defects in specific neuron classes. We have linked individual HS modifications to two specific guidance systems, the sax-3/Robo and kal-1/Anosmin-1 systems, whose activity is dependent on different HS modifications in different cellular contexts. Our results demonstrate that the molecular diversity in HS encodes information that is crucial for different aspects of neuronal development. ------------------- Key: 6472 Medline: Authors: Treusch S;Knuth S;Slaugenhaupt SA;Goldin E;Grant BD;Fares H Title: Caenorhabditis elegans functional orthologue of human protein h-mucolipin-1 is required for lysosome biogenesis. Citation: Proceedings of the National Academy of Sciences USA 101: 4483-4488 2004 Type: ARTICLE Genes: cup-5 Abstract: Mucolipidosis type IV (MLIV) is an autosomal recessive lysosomal storage disease characterized by severe psychomotor retardation, achlorhydria, and ophthalmological abnormalities. Cells from several tissues in MLIV patients accumulate large vacuoles that are presumed to be lysosomes, but whose exact nature remains to be determined. Other defects include the deterioration of neuronal integrity in the retina and the cerebellum. MCOLN1, the gene mutated in MLIV patients, encodes a protein called h-mucolipin-1 that has six predicted transmembrane domains and functions as a Ca2+-permeable channel that is modulated by changes in Ca2+ concentration. CUP-5 is the Caenorhabditis elegans functional orthologue of h-mucolipin-1. Mutations in cup-5 result in the accumulation of large vacuoles in several cells, in increased cell death, and in embryonic lethality. We demonstrate here that CUP-5 functions in the biogenesis of lysosomes originating from hybrid organelles. We also show that at least two h-mucolipin family members rescue cup-5 mutant endocytic defects, indicating that there may be functional redundancy among the human proteins. Finally, we propose a model that relates the lysosome biogenesis defect in the absence of CUP-5/h-mucolipin-1 to cellular ------------------- Key: 6473 Medline: 15041195 Authors: Matsuura T;Oikawa T;Wakabayashi T;Shingai R Title: Effect of simultaneous presentation of multiple attractants on chemotactic response of the nematode Caenorhabditis elegans. Citation: Neuroscience Research 48: 419-429 2004 Type: ARTICLE Genes: Abstract: Chemotactic behaviors of the nematode, Caenorhabditis elegans in response to chemical attractants, such as water-soluble sodium acetate and an odorant diacetyl, which were sensed by different sensory neurons, were investigated using various concentrations of these chemical attractants. In the presence of only sodium acetate attractant, the fraction of animals that were roaming around the outside of the attractant and original locations correlated negatively with the chemotaxis index for sodium acetate (P < 0.01). In contrast, the fraction of animals that remained in the original location correlated negatively with the chemotaxis index in the presence of only diacetyl attractant (P < 0.05). These results indicate that the manner of chemotaxis responses differs between sodium acetate and diacetyl. In order to investigate the effect of multiple attractants on chemotactic behaviors, the chemotactic responses to simultaneous presentation of sodium acetate and diacetyl were examined. The fraction of animals that gathered at the 0.7 M sodium acetate location was greater than that at the 0.1% diacetyl location in the presence of both attractants (P < 0.05), although the chemotaxis indexes for 0.7 M sodium acetate and 0.1% diacetyl were similar in the presence of a single attractant. On the other hand, the fraction of animals that gathered at the 0.02% diacetyl location was greater than that at the 0.1 M sodium acetate location in the presence of both attractants (P < 0.05), although the chemotaxis indexes for 0.02% diacetyl and 0.1 M sodium acetate were similar in the presence of a single attractant. These results suggest the existence of excitatory and/or inhibitory connections in the neuronal circuit for attractant selection, and that the efficacy of these connections may change according to the concentrations of both attractants. ------------------- Key: 6474 Medline: 15037255 Authors: Yamanaka K;Okubo Y;Suzaki T;Ogura T Title: Analysis of the two p97/VCP/Cdc48p proteins of Caenorhabditis elegans and their suppression of polyglutamine-induced protein aggregation. Citation: Journal of Structural Biology 146: 242-250 2004 Type: ARTICLE Genes: Abstract: A class of inherited neurodegenerative diseases including Huntington's disease is caused by polyglutamine (polyQ) expansion in the responsible proteins. Pathology is typically associated with polyQ expansions of greater than 40 residues, and the longer the length of the expansion, the earlier the onset of disease. It has been reported that p97/VCP/Cdc48p, a member of AAA family of proteins, can bind to longer polyQ tracts. In Caenorhabditis elegans, two p97/VCP/Cdc48p homologues, C41C4.8 and C06A1.1, have been identified. Our results indicate that these p97/VCP/Cdc48p homologues have essential but redundant functions in C elegans. To provide a model system for investigating the molecular basis of pathogenesis, we have expressed polyQ expansions fused to green fluorescent protein in the body wall muscle cells of C elegans. When the repeats are longer than 40, discrete cytoplasmic aggregates are formed and these appear at an early stage of embryogenesis. The formation of aggregates was partially suppressed by co-expression of either C41C4.8 or C06A1.1. These results suggest that these p97/VCP/Cdc48p homologues, AAA chaperones, may play a protective role in polyQ ------------------- Key: 6475 Medline: 14726532 Authors: Walker AK;Shi Y;Blackwell TK Title: An extensive requirement for transcription factor IID-specific TAF-1 in Caenorhabditis elegans embryonic transcription. Citation: Journal of Biological Chemistry 279: 15339-15347 2004 Type: ARTICLE Genes: cbp-1 cki-2 elt-2 elt-5 end-1 end-3 hda-1 hsp-16.2 let-858 med-1 med-2 pal-1 pes-10 pha-4 pop-1 rps-5 rps-26 rsp-5 skn-1 sur-5 tlf-1 Abstract: The general transcription factor TFIID sets the mRNA start site and consists of TATA-binding protein and associated factors (TAF(II)s), some of which are also present in SPT-ADA-GCN5 (SAGA)-related complexes. In yeast, results of multiple studies indicate that TFIID-specific TAFIIs are not required for the transcription of most genes, implying that intact TFIID may have a surprisingly specialized role in transcription. Relatively little is known about how TAFIIs contribute to metazoan transcription in vivo, especially at developmental and tissue-specific genes. Previously, we investigated functions of four shared TFIID/SAGA TAF(II)s in Caenorhabditis elegans. Whereas TAF-4 was required for essentially all embryonic transcription, TAF-5, TAF-9, and TAF-10 were dispensable at multiple developmental and other metazoan-specific promoters. Here we show evidence that in C. elegans embryos transcription of most genes requires TFIID-specific TAF-1. TAF-1 is not as universally required as TAF-4, but it is essential for a greater proportion of transcription than TAF-5, -9, or -10 and is important for transcription of many developmental and other metazoan-specific genes. TAF-2, which binds core promoters with TAF-1, appears to be required for a similarly substantial proportion of transcription. C. elegans TAF-1 overlaps functionally with the coactivator p300/CBP (CBP-1), and at some genes it is required along with the TBP-like protein TLF(TRF2). We conclude that during C. elegans embryogenesis TAF-1 and TFIID have broad roles in transcription and development and that TFIID and TLF may act together at certain promoters. Our findings imply that in metazoans TFIID may be of widespread importance for transcription and for expression ------------------- Key: 6476 Medline: 14739286 Authors: Pak SC;Kumar V;Tsu C;Luke CJ;Askew YS;Askew DJ;Mills DR;Bromme D;Silverman GA Title: SRP-2 is a cross-class inhibitor that participates in postembryonic development of the nematode Caenorhabditis elegans. Citation: Journal of Biological Chemistry 279: 15448-15459 2004 Type: ARTICLE Genes: srp-1 srp-2 srp-3 srp-4 srp-5 srp-6 srp-7 srp-8 srp-9 Abstract: High molecular weight serpins are members of a large superfamily of structurally conserved proteins that inactivate target proteinases by a suicide substrate-like mechanism. In vertebrates, different clades of serpins distribute predominantly to either the intracellular or extracellular space. Although much is known about the function, structure, and inhibitory mechanism of circulating serpins such as alpha(1)-antitrypsin (SERPINA1) and antithrombin III (SERPINC1), relatively little is known about the function of the vertebrate intracellular (clade B) serpins. To gain a better understanding of the biology of the intracellular serpins, we initiated a comparative genomics study using Caenorhabditis elegans as a model system. A screen of the C. elegans genomic and cDNA databases revealed nine serpin genes, tandemly arrayed on chromosome V. Although the C. elegans serpins represent a unique clade ( L), they share significant functional homology with members of the clade B group of intracellular serpins, since they lack typical N-terminal signal peptides and reside intracellularly. To determine whether nematode serpins function as proteinase inhibitors, one family member, srp-2, was chosen for further characterization. Biochemical analysis of recombinant SRP-2 protein revealed SRP-2 to be a dual cross-class inhibitor of the apoptosis-related serine proteinase, granzyme B, and the lysosomal cysteine proteinases, cathepsins K, L, S, and V. Analysis of temporal and spatial expression indicated that SRP-2 was present during early embryonic development and highly expressed in the intestine and hypoderm of larval and adult worms. Transgenic animals engineered to overexpress SRP-2 were slow growing and/or arrested at the first, second, or third larval stages. These data suggest that perturbations of serpin-proteinase balance are critical for correct postembryonic development in C. ------------------- Key: 6477 Medline: 15066124 Authors: Andachi Y Title: Caenorhabditis elegans T-box genes tbx-9 and tbx-8 are required for formation of hypodermis and body-wall muscle in embryogenesis. Citation: Genes to Cells 9: 331-344 2004 Type: ARTICLE Genes: dpy-17 elt-1 hlh-1 pos-1 tbx-8 tbx-9 Abstract: Transcription factors containing the DNA binding motif, T-box, play an important role in the embryonic development of metazoans. There are 20 T-box genes in the nematode Caenorhabditis elegans, three of which reportedly have postembryonic functions. We characterized two T-box genes, tbx-9 and tbx-8, that are phylogenetically related to each other. tbx-9 is expressed in a subset of embryonic cells that are precursors of the intestine, body-wall muscle, and hypodermis. The expression pattern of tbx-8 is markedly similar to that of tbx-9. Both tbx-9 mutants and tbx-8 mutants show incomplete penetrant morphogenetic defects in embryogenesis, but the malformations of the tbx-9 and tbx-8 mutants are observed in different parts of their bodies. In embryos with both tbx-9 and tbx-8 inactivated, the body structure is severely disorganized, more so than the sum of the separate mutant phenotypes. Further analysis shows that the hypodermis and body-wall muscle show abnormalities at the site of morphogenetic defects of these mutants. Together, these data indicate that tbx-9 and tbx-8 do not only contribute individually to formation of the hypodermis and body-wall muscle, but also suggests functional redundancy between tbx-9 and tbx-8 in embryonic morphogenesis. ------------------- Key: 6478 Medline: 15066188 Authors: Sugimoto A Title: High-throughput RNAi in Caenorhabditis elegans: genome-wide screens and functional genomics. Citation: Differentiation 72: 81-91 2004 Type: REVIEW Genes: cps-6 mes-3 mes-4 mes-6 mut-16 nuc-1 par-1 ppw-2 rrf-3 unc-22 zfp-1 Abstract: The phenomenon of RNA-mediated interference (RNAi) was first discovered in the nematode Caenorhabditis elegans, in which introduction of double-stranded RNA causes specific inactivation of genes with corresponding sequences. Technical advances in RNAi methodology and the availability of the complete genome sequence have enabled the high-throughput, genome-wide RNAi analysis of this organism. Several groups have used large-scale RNAi to systematically examine every C. elegans gene for knock-down phenotypes, providing basal information to be mined in more detailed studies. Now, in addition to functional genomic RNAi analyses, high-throughput RNAi is also routinely used for rapid, genome-wide screens for genes involved in specific biological processes. The integration of high-throughput RNAi experiments with other large-scale data, such as DNA microarrays and protein-protein interaction maps, enhances the speed and reliability of such screens. The accumulation of RNAi phenotype data dramatically accelerates our understanding of this organism ------------------- Key: 6479 Medline: 15043831 Authors: Blackwell TK Title: Germ cells: finding programs of mass repression. Citation: Current Biology 14: R229-R230 2004 Type: REVIEW Genes: Abstract: Transcription is globally silenced in the germline of animals. Recent studies have shown that, in Caenorhabditis elegans, this silencing is initially mediated through direct repression, but in Drosophila, the factors involved include pgc, a non-coding cytoplasmic RNA. Why are these mechanisms so diverse and complex? ------------------- Key: 6480 Medline: 15010772 Authors: Swatloski RP;Holbrey JD;Memon SB;Caldwell GA;Caldwell KA;Rogers RD Title: Using Caenorhabditis elegans to probe toxicity of 1-alkyl-3-methylimidazolium chloride based ionic liquids. Citation: Chemical Communications : 668-669 2004 Type: ARTICLE Genes: Abstract: Ionic liquids are gaining attention as new solvents within the green chemistry community; however this attention has quickly outstripped current environmental and toxicological data available. In the present communication, we establish the use of Caenorhabditis elegans as a model organism for inexpensively and quickly exploring toxicological effects of 1-alkyl-3-methylimidazolium chloride ionic liquids. ------------------- Key: 6481 Medline: 14988722 Authors: Hilliard MA;Bergamasco C;Arbucci S;Plasterk RHA;Bazzicalupo P Title: Worms taste bitter: ASH neurons, QUI-1, GPA-3 and ODR-3 mediate quinine avoidance in Caenorhabditis elegans. Citation: EMBO Journal 23: 1101-1111 2004 Type: ARTICLE Genes: eat-4 glr-1 gpa-3 gpa-13 gpa-16 odr-3 osm-6 osm-9 osm-10 qui-1 Abstract: An animal's ability to detect and avoid toxic compounds in the environment is crucial for survival. We show that the nematode Caenorhabditis elegans avoids many water-soluble substances that are toxic and that taste bitter to humans. We have used laser ablation and a genetic cell rescue strategy to identify sensory neurons involved in the avoidance of the bitter substance quinine, and found that ASH, a polymodal nociceptive neuron that senses many aversive stimuli, is the principal player in this response. Two G protein alpha subunits GPA-3 and ODR-3, expressed in ASH and in different, nonoverlapping sets of sensory neurons, are necessary for the response to quinine, although the effect of odr-3 can only be appreciated in the absence of gpa-3. We identified and cloned a new gene, qui-1, necessary for quinine and SDS avoidance. qui-1 codes for a novel protein with WD-40 domains and which is expressed in the avoidance sensory neurons ASH and ADL. ------------------- Key: 6482 Medline: 15134198 Authors: Halligan DL;Peters AD;Keightley PD Title: Estimating numbers of EMS-induced mutations affecting life history traits in Caenorhabditis elegans in crosses between inbred sublines. Citation: Genetical Research 82: 191-205 2003 Type: ARTICLE Genes: Abstract: Inbred lines of the nematode Caenorhabditis elegans containing independent EMS-induced mutations were crossed to the ancestral wild-type strain (N2). Replicated inbred sublines were generated from the F1 offspring under conditions of minimal selection and, along with the N2 and mutant progenitor lines, were assayed for several fitness correlate including relative fitness (w). A modification of the Castle-Wright estimator and a maximum-likelihood (ML) method were used to estimate the numbers and effects of detectable mutations affecting these characters. The ML method allows for variation in mutational effects by fitting either one or two classes of mutational effect, and uses a Box-Cox power transformation of residual values to account for a skewed distribution of residuals. Both the Castle-Wright and the ML analyses suggest that most of the variation among sublines was due to a few (~1.5-2.5 on average) large-effect mutations. Under ML, a model with two classes of mutational effects, including a class with small effects, fitted better than a single mutation class model, although not significantly better. Nonetheless, given that we expect there to be many mutations induced per line, our results support the hypothesis that mutations vary widely in their effects. ------------------- Key: 6483 Medline: 14985345 Authors: Kukkola L;Koivunen P;Pakkanen O;Page AP;Myllyharju J Title: Collagen prolyl 4-hydroxylase tetramers and dimers show identical decreases in Km values for peptide substrates with increasing chain length. Citation: Journal of Biological Chemistry 279: 18656-18661 2004 Type: ARTICLE Genes: phy-1 phy-2 pdi-2 Abstract: The collagen prolyl 4-hydroxylases ( collagen P4Hs, EC 1.14.11.2) play a key role in the synthesis of the extracellular matrix. The vertebrate enzymes are alpha(2)beta(2) tetramers, the beta subunit being identical to protein disulfide isomerase (PDI). The main Caenorhabditis elegans collagen P4H form is an unusual PHY-1/PHY-2/(PDI)(2) mixed tetramer consisting of two types of catalytic alpha subunit, but the PHY-1 and PHY-2 polypeptides also form active PHY/PDI dimers. The lengths of peptide substrates have a major effect on their interaction with the P4H tetramers, the K-m values decreasing markedly with increasing chain length. This phenomenon has been explained in terms of processive binding of the two catalytic subunits to long peptides. We determined here the K-m values of a collagen P4H having two catalytic sites, the C. elegans mixed tetramer, and a form having only one such site, the PHY-1/PDI dimer, for peptides of varying lengths. All the K-m values of the PHY-1/PDI dimer were found to be about 1.5-2.5 times those of the tetramer, but increasing peptide length led to identical decreases in the values of both enzyme forms. The K-m for a nonhydroxylated collagen fragment with 33-X-Y-Gly- triplets but only 11 -X-Pro-Gly-triplets was found to correspond to the number of the former rather than the latter. To study the individual roles of the two catalytic sites in a tetramer, we produced mutant PHY-1/PHY-2/(PDI)(2) tetramers in which binding of the Fe2+ ion or 2-oxoglutarate to one of the two catalytic sites was prevented. The activities of the mutant tetramers decreased to markedly less than 50% of that of the wild type, being about 5 - 10% and 20 - 30% with the enzymes having one of the two Fe2+-binding sites or 2-oxoglutarate-binding sites inactivated, respectively, while the K-m values for these cosubstrates or peptide substrates were not affected. Our data thus indicate that although collagen P4Hs do not act on peptide substrates by a processive mechanism, prevention of hydroxylation at one of the two catalytic sites in the tetramer impairs the function of the other catalytic site. ------------------- Key: 6484 Medline: 14973273 Authors: Killian DJ;Hubbard EJA Title: C. elegans pro-1 activity is required for soma/germline interactions that influence proliferation and differentiation in the germ line. Citation: Development 131: 1267-1278 2004 Type: ARTICLE Genes: fem-1 glp-1 lin-12 mpk-1 pro-1 rrf-1 mnDf58 Abstract: Strict spatial and temporal regulation of proliferation and differentiation is essential for proper germline development and often involves soma/germline interactions. In C elegans, a particularly striking outcome of defective regulation of the proliferation/differentiation pattern is the Pro phenotype in which an ectopic mass of proliferating germ cells occupies the proximal adult germ line, a region normally occupied by gametes. We describe a reduction-of-function mutation in the gene pro-1 that causes a highly penetrant Pro phenotype. The pro-1 mutant Pro phenotype stems from defects in the time and position of the first meiotic entry during early germline development. pro-1(RNAi) produces a loss of somatic gonad structures and concomitant reduction in germline proliferation and gametogenesis. pro-1 encodes a member of a highly conserved subfamily of WD-repeat proteins. pro-1(+) is required in the sheath/spermatheca lineage of the somatic gonad in its role in the proper establishment of the proliferation/differentiation pattern in the germline. Our results provide a handle for further analysis of this somato-germline interaction. ------------------- Key: 6485 Medline: 14993191 Authors: Chang W;Tilman C;Thoemke K;Markussen FH;Mathies LD;Kimble J;Zarkower D Title: A forkhead protein controls sexual identity of the C. elegans male somatic gonad. Citation: Development 131: 1425-1436 2004 Type: ARTICLE Genes: fkh-6 tra-1 tra-2 ccDf4 Abstract: In sex determination, globally acting genes control a spectrum of tissue-specific regulators to coordinate the overall development of an animal into one sex or the other. In mammals, primary sex determination initially occurs in the gonad, with the sex of other tissues specified as a secondary event. In insects and nematodes, globally acting regulatory pathways have been elucidated, but the more tissue- and organ-specific downstream effectors of these pathways remain largely unknown. We focus on the control of sexual dimorphism in the C. elegans gonad. We find that the forkhead transcription factor FKH-6 promotes male gonadal cell fates in XO animals. Loss-of-function fkh-6 mutant males have feminized gonads and often develop a vulva. In these mutant males, sex-specific cell divisions and migrations in the early gonad occur in the hermaphrodite mode, and hermaphrodite-specific gonadal markers are expressed. However, sexual transformation is not complete and the male gonad is malformed. By contrast, fkh-6 mutant hermaphrodites exhibit no sign of sex reversal. Most fkh-6 hermaphrodites form a two-armed symmetrical gonad resembling that of the wild type, but differentiation of the spermatheca and uterus is variably abnormal. The function of fkh-6 appears to be restricted to the gonad: fkh-6 mutants have no detectable defects in extra-gonadal tissues, and expression of a rescuing jkh-6 reporter is gonad-specific. Genetic and molecular analyses place fkh-6 downstream of tra-1, the terminal regulator of the global sex determination pathway, with respect to the first gonadal cell division. We conclude that jkh-6 regulates gonadogenesis in both sexes, but is male specific in establishing sexual dimorphism in the early gonad. ------------------- Key: 6486 Medline: 15119448 Authors: Cutter AD Title: Sperm-limited fecundity in nematodes: how many sperm are enough? Citation: Evolution 58: 651-655 2004 Type: ARTICLE Genes: Abstract: The Bateman principle, which holds that oocytes are the limiting gamete in reproduction, is violated in a variety of species. Self-fertilizing hermaphrodites of the nematode Caenorhabditis elegans provide an example of a system in which sperm number limits lifetime reproductive Output, in this species due to the protandrous nature of sperm production that in turn delays the onset of fertilization. This reproductive delay forms the basis of a trade-off between generation time and total fecundity, in which sperm number plays a pivotal role. I use an age-structured population model to describe the number of sperm that maximize fitness, given larval development time and rates of gamete production. The model predicts the evolution of sperm numbers that are consistent with empirical data for C. elegans provided that precocious larval sperm production is taken into account. Several testable hypotheses follow from the model regarding how natural selection and environmental variation may influence patterns of sperm production among populations or species with a similar mode ------------------- Key: 6487 Medline: 14960577 Authors: Yuan C;Kent C Title: Identification of critical residues of choline kinase A2 from Caenorhabditis elegans. Citation: Journal of Biological Chemistry 279: 17801-17809 2004 Type: ARTICLE Genes: cka-2 Abstract: Choline kinase catalyzes the phosphorylation of choline by ATP, the first committed step in the CDP-choline pathway for phosphatidylcholine biosynthesis. To begin to elucidate the mechanism of catalysis by this enzyme, choline kinase A-2 from Caenorhabditis elegans was analyzed by systematic mutagenesis of highly conserved residues followed by analysis of kinetic and structural parameters. Specifically, mutants were analyzed with respect to K-m and k(cat) values for each substrate and Mg2+, inhibitory constants for Mg2+ and Ca2+, secondary structure as monitored by circular dichroism, and sensitivity to unfolding in guanidinium hydrochloride. The most severe impairment of catalysis occurred with the modification of Asp-255 and Asn-260, which are located in the conserved Brenner's phosphotransferase motif, and Asp-301 and Glu-303, in the signature choline kinase motif. For example, mutation of Asp-255 or Asp-301 to Ala eliminated detectable catalytic activity, and mutation of Asn-260 and Glu-303 to Ala decreased k(cat) by 300- and 10-fold, respectively. Additionally, the K-m for Mg2+ for mutants N260A and E303A was approximately 30-fold higher than that of wild type. Several other residues (Ser-86, Arg-111, Glu-125, and Trp-387) were identified as being important: Catalytic efficiencies (k(cat)/K-m) for the enzymes in which these residues were mutated to Ala were reduced to 2-25% of wild type. The high degree of structural similarity among choline kinase A-2, aminoglycoside phosphotransferases, and protein kinases, together with the results from this mutational analysis, indicates it is likely that these conserved residues are located at the ------------------- Key: 6488 Medline: 15048112 Authors: Couillault C;Pujol N;Reboul J;Sabatier L;Guichou JF;Kohara Y;Ewbank J Title: TLR-independent control of innate immunity in Caenorhabditis elegans by the TIR domain adaptor protein TIR-1, an ortholog of human SARM. Citation: Nature Immunology 5: 488-494 2004 Type: ARTICLE Genes: ceh-38 cnc-2 cnc-3 cnc-4 cnc-6 nlp-29 nlp-31 nlp-33 pal-1 rab-1 tir-1 tol-1 Abstract: Both plants and animals respond to infection by synthesizing compounds that directly inhibit or kill invading pathogens. We report here the identification of infection-inducible antimicrobial peptides in Caenorhabditis elegans. Expression of two of these peptides, NLP-29 and NLP-31, was differentially regulated by fungal and bacterial infection and was controlled in part by tir-1, which encodes an ortholog of SARM, a Toll-interleukin 1 receptor (TIR) domain protein. Inactivation of tir-1 by RNA interference caused increased susceptibility to infection. We identify protein partners for TIR-1 and show that the small GTPase Rab1 and the f subunit of ATP synthase participate specifically in the control of antimicrobial peptide gene expression. As the activity of tir-1 was independent of the single nematode Toll-like receptor, TIR-1 may represent a component of a previously uncharacterized, but conserved, innate immune ------------------- Key: 6489 Medline: 15035988 Authors: Shen K;Fetter RD;Bargmann CI Title: Synaptic specificity is generated by the synaptic guidepost protein SYG-2 and its receptor, SYG-1. Citation: Cell 116: 869-881 2004 Type: ARTICLE Genes: lin-11 syg-1 syg-2 unc-104 Abstract: Synaptic connections in the nervous system are directed onto specific cellular and subcellular targets. Synaptic guidepost cells in the C. elegans vulval epithelium drive synapses from the HSNL motor neuron onto adjacent target neurons and muscles. Here, we show that the transmembrane immunoglobulin superfamily protein SYG-2 is a central component of the synaptic guidepost signal. SYG-2 is expressed transiently by primary vulval epithelial cells during synapse formation. SYG-2 binds SYG-1, the receptor on HSNL, and directs SYG-1 accumulation and synapse formation to adjacent regions of HSNL. syg-1 and syg-2 mutants have defects in synaptic specificity; the HSNL neuron forms fewer synapses onto its normal targets and forms ectopic synapses onto inappropriate targets. Misexpression of SYG-2 in secondary epithelial cells causes aberrant accumulation of SYG-1 and synaptic markers in HSNL adjacent to the SYG-2-expressing cells. Our results indicate that local interactions between immunoglobulin superfamily proteins can determine specificity during ------------------- Key: 6490 Medline: 15030761 Authors: Ikegami R;Zheng H;Ong SW;Culotti J Title: Integration of semaphorin-2A/MAB-20, ephrin-4, and UNC-129 TGF-beta signaling pathways regulates sorting of distinct sensory rays in C. elegans. Citation: Developmental Cell 6: 383-395 2004 Type: ARTICLE Genes: efn-1 erf-1 erf-2 erf-3 erf-4 erf-5 mab-20 mab-26 plx-1 plx-2 unc-129 Abstract: Semaphorins and ephrins are axon guidance cues. In C. elegans, semaphorin-2a/mab-20 and ephrin-4/efn-4/mab-26 also regulate cell sorting to form distinct rays in the male tail. Several erf (enhancer of ray fusion) mutations were identified in a mab-20 enhancer screen. Mutants of plexin-2 (plx-2) and unc-129, which encodes an axon guiding TGF-beta, were also found to be erfs. Genetic analyses show that plx-2 and mab-20 function in the same pathway, as expected if PLX-2 is a receptor for MAB-20. Surprisingly, MAB-20 also signals in a parallel pathway that requires efn-4. This signal utilizes a non-plexin receptor. The expression of plx-2, efn-4, and unc-129 in subsets of 3-cell sensory ray clusters likely mediates the ray-specific cell sorting functions of the ubiquitously expressed mab-20. We present a model for the integrated control of TGF-beta, semaphorin, and ephrin signaling in the sorting of cell clusters into distinct rays in the ------------------- Key: 6491 Medline: 15063172 Authors: Hansen D;Hubbard EJA;Schedl T Title: Multi-pathway control of the proliferation versus meiotic development decision in the Caenorhabditis elegans Citation: Developmental Biology 268: 342-357 2004 Type: ARTICLE Genes: gld-1 gld-2 glp-1 him-3 him-14 nos-1 nos-2 nos-3 rec-8 Abstract: An important event in the development of the germline is the initiation of meiotic development. In Caenorhabditis elegans, the conserved GLP-1/Notch signaling pathway regulates the proliferative versus meiotic entry decision, at least in part, by spatially inhibiting genes in the gld-1 and gld-2 parallel pathways, which are proposed to either inhibit proliferation and/or promote meiotic development. Mutations that cause constitutive activation of the GLP-1 pathway, or inactivation of both the gld-1 and gld-2 parallel pathways, result in a tumorous germline in which all cells are thought to be proliferative. Here, to analyze proliferation and meiotic entry in wild-type and mutant tumorous germlines, we use anti-REC-8 and anti-HIM-3 specific antibodies as markers, which under our fixation conditions, stain proliferative and meiotic cells, respectively. Using these makers in wild-type animals, we find that the border of the switch from proliferation to meiotic entry is staggered in late-larval and adult germlines. In wild-type adults, the switch occurs between 19 and 26 cell diameters from the distal end, on average. Our analysis of mutants reveals that tumorous germlines that form when GLP-1 is constitutively active are completely proliferative, while tumors due to inactivation of the gld-1 and gld-2 pathways show evidence of meiotic entry. Genetic and time course studies suggest that a third pathway may exist, parallel to the GLD-1 and GLD-2 pathways, that promotes meiotic development. ------------------- Key: 6492 Medline: 14960582 Authors: Smit L;Baas A;Kuipers J;Korswagen H;van de Wetering M;Clevers H Title: Wnt activates the Tak1/Nemo-like kinase pathway. Citation: Journal of Biological Chemistry 279: 17232-17240 2004 Type: ARTICLE Genes: lit-1 mom-2 mom-4 pop-1 tap-1 wrm-1 Abstract: Genetic studies on endoderm-mesoderm specification in Caenorhabditis elegans have demonstrated a role for several Wnt cascade components as well as for a MAPK-like pathway in this process. The latter pathway includes the MAPK kinase kinase-like MOM-4/Tak1, its adaptor TAP-1/Tab1, and the MAPK-like LIT-1/Nemolike kinase. A model has been proposed in which the Tak1 kinase cascade counteracts the Wnt cascade at the level of beta-catenin/TCF phosphorylation. In this model, the signal that activates the Tak1 kinase cascade is unknown. As an alternative explanation of these genetic data, we have explored whether Tak1 is directly activated by Wnt. We find that Wnt1 stimulation results in autophosphorylation and activation of MOM-4/Tak1 in a TAP-1/Tab1-dependent fashion. Wnt1-induced Tak1 stimulation activates Nemo-like kinase, resulting in the phosphorylation of TCF. Our results combined with the genetic data from C. elegans imply a mechanism whereby Wnt directly activates the MOM-4/Tak1 kinase signaling pathway. Thus, Wnt signal transduction through the canonical pathway activates beta-catenin/TCF, whereas Wnt signal transduction through the Tak1 pathway phosphorylates and inhibits TCF, which might function as a ------------------- Key: 6493 Medline: 14973340 Authors: Nakayama S;Endoh H Title: Preferential cleavage of Paramecium DNA mediated by the C. elegans Tc1 transposase in vitro. Citation: Genes & Genetic Systems 78: 391-398 2003 Type: ARTICLE Genes: Abstract: In the ciliate Paramecium aurelia complex, thousands of internal eliminated sequences (IESs) are excised from the germline micromiclear DNA during macro-nuclear differentiation. Based on the resemblance of Paramecium IES end sequences to Tel transposon termini, it has been proposed that Paramecium IESs might have degenerately evolved from Tc1 family transposons, and still be removed by an enzyme homologous to a Tel transposase. In this study, we found that transposase preferentially cleaved (or nicked) 58 sites near the IESs in Paramecium DNA, at sequences consisting of TT or TCTA. Since one excision junction of the P. primaurelia W2 IES was included in such sites, this suggests that a Tc1-like transposase is involved in the IES excision process, although it is probably not a sole factor responsible for the precise cleavage. In addition, unmethylated substrate DNA appeared to decrease the cleavage specificity, suggesting an involvement of DNA methylation in the cleavage. Although these results do not directly address the transposon origin of Paramecium IESs, it is likely that the enzymatic machinery responsible for the initial cleavage is derived from a Tc1-like transposase. The mechanism necessary for precise excision is discussed, in relation to recent knowledge of IES excision obtained in Tetrahymena and ------------------- Key: 6494 Medline: 15102906 Authors: Koushika SP;Schaefer AM;Vincent R;Willis JH;Bowerman B;Nonet ML Title: Mutations in Caenorhabditis elegans cytoplasmic dynein components reveal specificity of neuronal retrograde cargo. Citation: Journal of Neuroscience 24: 3907-3916 2004 Type: ARTICLE Genes: dhc-1 dli-1 dnc-1 dnc-2 mec-7 rab-3 sma-1 snb-1 sng-1 snt-1 unc-7 unc-104 sDf22 Abstract: We describe Caenorhabditis elegans dynein complex mutants, which misaccumulate synaptic proteins at the ends of neuronal processes. Ultrastructural analysis revealed irregularly sized vesicles that likely represent accumulation of cargo. We propose that synaptobrevin, synaptotagmin, and UNC-104 are specific cargoes of the dynein complex. Many cargoes link to dynein via interactions between dynactin and vesicle-associated spectrin. However, loss of spectrin results in only mild and occasional defects in synaptobrevin localization. Thus, the dynein-dynactin complex shows neuronal cargo selectivity without spectrin being a critical component of cargo binding. We observed parallels to progressive motor neuron disease symptoms in these animals. With age, neuronal misaccumulations increase in size and frequency; locomotion becomes progressively slower; and life span is shortened. These mutants provide a model to assess whether defects in transport of specific cargo mediate neuronal ------------------- Key: 6495 Medline: 15115160 Authors: Balaji V;Jesudason MV;Sridharan G;Subramanian K Title: Detection of virulence attributes of Burkholderia pseudomallei. Citation: Indian Journal of Medical Research 119: 101-106 2004 Type: ARTICLE Genes: Abstract: Background & objectives: Melioidosis caused by Burkholderia pseudomallei is an emerging disease in India. This study examined the toxin activity of bacteria-free culture filtrate in three different cell lines (cytotoxic assay) and its effect on Caenorhabditis elegans (nematode toxicity assay). Endotoxic activity of the viable bacteria was also studied in C elegans (co-culture killing assay). Methods: For toxin studies, serial doubling dilutions of unheated, heated crude and ultra filtrate of bacteria-free culture supernatants of B. pseudomallei were tested in 96-well microtitre plate containing confluent mono layers of McCoy, Hep-2 and HeLa cell lines. For the effects on C. elegans, the worms were exposed to heated and unheated bacteria-free culture supernatants in 24-well microtitre plate for 24 h and then transferred to OP50 Escherichia coli lawn culture. The endotoxic activity of the live bacterium was studied by feeding the worms in the lawn culture of B. pseudomallei. Results: All the clinical isolates (n=38) produced cytotoxic changes in all the cell lines. No difference was observed in the cytotoxicity of unheated, heated and ultra-filtered culture supernatant. The septicaemic isolates were observed to produce cytotoxic changes in high dilutions (1:160) of culture filtrate. None of the unheated and heated crude filtrate had deleterious effect on C. elegans, while all the live bacteria were found to be lethal to the nematode. Interpretation & conclusion: The culture supernatants, though produced cytopathic effect in various tissue cultures, failed to have any deleterious effect on the worms. However, live bacteria were lethal to the worms B. pseudomallei. Use of C elegans model to detect virulence attributes of B. pseudomallei is recommended as an alternative to tissue culture methods as this can be carried out in laboratories where a tissue culture set up is not available. ------------------- Key: 6496 Medline: 15082781 Authors: Smith MG;Des Etages SG;Snyder M Title: Microbial syngergy via an ethanol-triggered pathway. Citation: Molecular and Cellular Biology 24: 3874-3884 2004 Type: ARTICLE Genes: Abstract: We have discovered a microbial interaction between yeast, bacteria, and nematodes. Upon coculturing, Saccharomyces cerevisiae stimulated the growth of several species of Acinetobacter, including, A. baumannii, A. haemolyticus, A. johnsonii, and A. radioresistens, as well as several natural isolates of Acinetobacter. This enhanced growth was due to a diffusible factor that was shown to be ethanol by chemical assays and evaluation of strains lacking ADH1, ADH3, and ADH5, as all three genes are involved. in ethanol production by yeast. This effect is specific to ethanol: methanol, butanol, and dimethyl sulfoxide were unable to stimulate growth to any appreciable level. Low doses of ethanol not only stimulated growth to a higher cell density but also served as a signaling molecule: in the presence of ethanol, Acinetobacter species were able to withstand the toxic effects of salt, indicating that ethanol alters cell physiology. Furthermore, ethanol-fed A. baumannii displayed increased pathogenicity when confronted with a predator, Caenorhabditis elegans. Our results are consistent with the concept that ethanol can serve as a signaling molecule which can affect bacterial physiology and survival. ------------------- Key: 6497 Medline: 15082545 Authors: Mehta N;Loria PM;Hobert O Title: A genetic screen for neurite outgrowth mutants in Caenorhabditis elegans reveals a new function for the F-box ubiquitin ligase component LIN-23. Citation: Genetics 166: 1253-1267 2004 Type: ARTICLE Genes: eno-1 eno-2 eno-3 eno-4 eno-6 eno-7 eno-8 eno-9 eno-11 lim-6 lin-23 rpm-1 sax-1 sel-10 unc-30 unc-34 unc-44 unc-61 unc-71 unc-76 mnDf30 mnDf39 Abstract: ene, but does not display defects in cell cycle regulation. We have thus defined separable activities of LIN-23 in two distinct processes, cell cycle control and axon patterning. We propose that LIN-23 tat-gets distinct substrates for ubiquitination within each process.Axon pathfinding and target recognition are highly dynamic and tightly regulated cellular processes. One of the mechanisms involved in regulating protein activity levels during axonal and synaptic development is protein ubiquitination. We describe here the isolation of several Caenorhabditis elegans mutants, termed eno (ectopic/erratic neurite outgrowth) mutants, that display defects in axon outgrowth of specific neuron classes. One retrieved mutant is characterized by abnormal termination of axon outgrowth in a subset of several distinct neuron classes, including ventral nerve cord motor neurons, head motor neurons, and mechanosensory neurons. This mutant is allelic to lin-23, which codes for an F-box-containing component of an SCF E3 ubiquitin ligase complex that was previously shown to negatively regulate postembryonic cell divisions. We demonstrate that LIN-23 is a broadly expressed cytoplasmically localized protein that is required autonomously in neurons to affect axon outgrowth. Our newly isolated allele of lin-23, a point mutation in the C-terminal tail of the protein, displays axonal outgrowth defects similar to those observed in null alleles of this gene, but does not display defects in cell cycle regulation. We have thus defined separable activities of LIN-23 in two distinct processes, cell cycle control and axon patterning. We propose that LIN-23 tat-gets distinct substrates for ubiquitination within each process. ------------------- Key: 6498 Medline: 15082546 Authors: Estes S;Phillips PC;Denver DR;Thomas WK;Lynch M Title: Mutation accumulation in populations of varying size: the distribution of mutational effects for fitness correlates in Caenorhabditis elegans. Citation: Genetics 166: 1269-1279 2004 Type: ARTICLE Genes: msh-2 Abstract: The consequences of mutation for population-genetic and evolutionary processes depend on the rate and, especially, the frequency distribution of mutational effects on fitness. We sought to approximate the form of the distribution of mutational effects by conducting divergence experiments in which lines of a DNA repair-deficient strain of Caenorhabditis elegans, msh-2, were maintained at a range of population sizes. Assays of these lines conducted in parallel with the ancestral control suggest that the mutational variance is dominated by contributions from highly detrimental imitations. This was evidenced by the ability of all but the smallest population-size treatments to maintain relatively high levels of mean fitness even under the 100-fold increase in mutational pressure caused by knocking out the msh-2 gene. However, we show that the mean fitness decline experienced by larger populations is actually greater than expected on the basis of our estimates of mutational parameters, which could be consistent with the existence of a common class of initiations with small individual effects. Further, comparison of the total mutation rate estimated from direct sequencing of DNA to that detected from phenotypic analyses implies the existence of a large class of evolutionarily relevant mutations with no measurable effect on laboratory ------------------- Key: 6499 Medline: 15082572 Authors: Prachumwat A;DeVincentis L;Palopoli MF Title: Intron size correlates positively with recombination rate in Caenorhabditis elegans. Citation: Genetics 166: 1585-1590 2004 Type: ARTICLE Genes: Abstract: A negative correlation between intron size and recombination rate has been reported for the Drosophila melanogaster and human genomes. Population-genetic models suggest that this pattern could be caused by an interaction between recombination rate and the efficacy of natural selection. To test this idea, we examined variation in intron size and recombination rate across the genome of the nematode Caenorhabditis elegans. Interestingly, we found that intron size correlated positively with recombination rate in this species. ------------------- Key: 6500 Medline: 15099303 Authors: Copley RR;Aloy P;Russell RB;Telford MJ Title: Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idosyncrasies of Caenorhabditis elegans. Citation: Evolution & Development 6: 164-169 2004 Type: ARTICLE Genes: Abstract: There has been broad acceptance among evolutionary biologists of the Ecdysozoa hypothesis that, based principally on molecular phylogenetic studies of small and large subunit ribosomal RNA sequences, postulates a close relationship between molting taxa such as arthropods and nematodes. On the other hand, recent studies of as many as 100 additional genes do not support the Ecdysozoa hypothesis and instead favor the older Coelomata hypothesis that groups the coelomate arthropods with the coelomate vertebrates to the exclusion of the nematodes. Here, exploiting completely sequenced genomes, we examined this question using cladistic analyses of the phylogenetic distribution of 1712 orthologous genes and 2906 protein domain combinations; we found stronger support for the Coelomata hypothesis than for the Ecdysozoa hypothesis. However, although arrived at by considering very large data sets, we show that this conclusion is unreliable, biased toward grouping arthropods with chordates by systematic high rate of character loss in the nematode. When we addressed this problem, we found slightly more support for Ecdysozoa than for Coelomata. Our identification of this systematic bias even when using entire genomes has important implications for future phylogenetic studies. We conclude that the results from the intensively sampled ribosomal RNA genes supporting the Ecdysozoa hypothesis provide the most credible current estimates of metazoan ------------------- Key: 6501 Medline: 15062118 Authors: Gonczy P Title: Centrosomes: hooked on the nucleus. Citation: Current Biology 14: R268-R270 2004 Type: REVIEW Genes: sun-1 zyg-12 Abstract: A recent study has shown that the Hook protein ZYG-12 of Caenorhabditis elegans is essential for attachment of the centrosome to the nucleus. The results suggest a novel mechanism for the tight coupling between these two organelles, and shed new light on its biological significance. ------------------- Key: 6502 Medline: 15062099 Authors: Couteau F;Nebashima K;Villeneuve A;Zetka M Title: A component of C. elegans meiotic chromosome axes at the interface of homolog alignment, synapsis, nuclear reorganization, and recombination. Citation: Current Biology 14: 585-592 2004 Type: ARTICLE Genes: chk-2 him-3 syp-1 syp-2 nDf41 Abstract: A universal feature of meiotic prophase is the pairing of homologous chromosomes, a fundamental prerequisite for the successful completion of all subsequent meiotic events [1, 2]. HIM-3 is a Caenorhabditis elegans meiosis-specific noncohesin component of chromosome axes that is required for synapsis [3]. Our characterization of new him-3 alleles reveals previously unknown functions for the protein. HIM-3 is required for the establishment of initial contacts between homologs, for the nuclear reorganization characteristic of early meiotic prophase, and for the coordination of these events with synaptonemal complex (SC) assembly. Despite the absence of homolog alignment, we find that recombination is initiated efficiently, indicating that initial pairing is not a prerequisite for early steps of the recombination pathway. Surprisingly, RAD-51-marked recombination intermediates disappear with apparent wild-type kinetics in him-3 null mutants in which homologs are spatially unavailable for recombination, raising the possibility that HIM-3's presence at chromosome axes inhibits the use of sister chromatids as templates for repair. We propose that HIM-3 is a molecular link between multiple landmark events of meiotic prophase; it is critical for establishing chromosome identity by configuring homologs to facilitate their recognition while simultaneously imposing structural constraints that later promote the formation of the crossover essential for proper ------------------- Key: 6503 Medline: 15084301 Authors: Sundaram MV Title: Vulval development: the battle between Ras and Notch. Citation: Current Biology 14: R311-R313 2004 Type: REVIEW Genes: apx-1 dsl-1 egl-17 lag-2 let-23 lin-3 lin-12 sur-2 Abstract: Vulval patterning in Caenorhabditis elegans is controlled by both Ras-mediated 'inductive' signaling and LIN-12/Notch-mediated 'lateral' signaling. Recent studies have identified the lateral signal as well as various genes that are targets of the lateral signaling pathway, and begun to define the multiple molecular links connecting Ras and Notch. ------------------- Key: 6504 Medline: 14678010 Authors: Fei YJ;Liu JC;Inoue K;Zhuang L;Miyake K;Miyauchi S;Ganapathy V Title: Relevance of NAC-2, an Na+-coupled citrate transporter, to life span, body size and fat content in Caenorhabditis elegans. Citation: Biochemical Journal 379: 191-198 2004 Type: ARTICLE Genes: daf-2 nac-1 nac-2 nac-3 Abstract: We have cloned and functionally characterized an Na+-coupled citrate transporter from Caenorhabditis elegans (ceNAC-2). This transporter shows significant sequence homology to Drosophila Indy and the mammalian Na+-coupled citrate transporter NaCT (now known as NaC2). When heterologously expressed in a mammalian cell line or in Xenopas oocytes, the cloned ceNAC-2 mediates the Na-coupled transport of various intermediates of the citric acid cycle. However, it transports the tricarboxylate citrate more efficiently than dicarboxylates Such as succinate, a feature different from that of ceNAC-1 (formerly known as ceNaDC1) and ceNAC-3 (formerly known as ceNaDC2). The transport process is electrogenic. as evidenced from the substrate-induced inward Currents in oocytes expressing the transporter under voltage-clamp conditions. Expression studies using a reporter-gene fusion method in transgenic C. elegans show that the gene is expressed in the intestinal tract, the organ responsible for not only the digestion and absorption Of nutrients but also for the storage of energy in this organism. Functional knockdown of the transporter by RNAi (RNA interference) not only leads to a significant increase in life span, but also causes a significant decrease in body size and fat content. The substrates of ceNAC-2 play a critical role in metabolic energy production and in the biosynthesis of cholesterol and fatty acids. The present studies suggest that the knockdown of these metabolic functions by RNAi is linked to an extension of life span and a decrease in fat content and ------------------- Key: 6505 Medline: 14998926 Authors: Zhang S;Sokolchik I;Blanco G;Sze JY Title: Caenorhabditis elegans TRPV ion channel regulates 5HT biosynthesis in chemosensory neurons. Citation: Development 131: 1629-1638 2004 Type: ARTICLE Genes: cat-1 daf-2 daf-7 daf-16 gpa-3 gpa-13 lin-11 nss-1 ocr-2 odr-3 odr-7 odr-10 osm-9 oms-11 tax-2 tph-1 unc-43 Abstract: Serotonin (5HT) is a pivotal signaling molecule that modulates behavioral and endocrine responses to diverse chemical and physical stimuli. We report cell-specific regulation of 5HT biosynthesis by transient receptor potential V (TRPV) ion channels in C elegans. Mutations in the TRPV genes osm-9 or ocr-2 dramatically downregulate the expression of the gene encoding the 5HT synthesis enzyme tryptophan hydroxylase (tph-1) in the serotonergic chemosensory neurons ADF, but neither the mutation nor the double mutation of both channel genes affects other types of serotonergic neurons. The TRPV genes are expressed in the ADF neurons but not in other serotonergic neurons, and act cell-autonomously to regulate a neuron-specific transcription program. Whereas in olfactory neurons OSM-9 and OCR-2 function is dependent on ODR-3 Galpha, the activity of ODR-3 or two other Ga proteins expressed in the ADF neurons is not required for upregulating tph-1 expression, thus the TRPV ion channels in different neurons may be regulated by different mechanisms. A gain-of-function mutation in CaMKII UNC-43 partially suppresses the downregulation of tph-1 in the TRPV mutants, thus CaMKII may be an effector of the TRPV signaling. Mutations in the TP.PV genes cause worms developmentally arrest at the Dauer stage. This developmental defect is due in part to reduced 5HT inputs into daf-2/insulin ------------------- Key: 6506 Medline: 15081363 Authors: Lints R;Jia L;Kim K;Li C;Emmons SW Title: Axial patterning of C. elegans male sensilla identities by selector genes. Citation: Developmental Biology 269: 137-151 2004 Type: ARTICLE Genes: dbl-1 egl-5 flp-5 flp-6 flp-11 flp-17 mab-5 mab-18 mab-23 sma-2 sma-3 sma-4 tph-1 Abstract: The fan and rays of the C. elegans male tail constitute a compound sensory organ essential for mating. Within this organ, the individual sensilla, known as rays, have unique identities. We show that ray identities are patterned by a selector gene mechanism in a manner similar to other serially homologous axial structures. One selector gene that promotes the identities of a subset of the rays is the Hox gene egl-5. Within EGL-5-expressing rays, further patterning is provided by a Pax-6 homolog and a signal of the TGFbeta family. These genes and pathway coordinately specify multiple ray properties affecting all three terminal ray cell types. These properties include complex patterns of FMRFamide-like (FaR-P) neuropeptides, serotonin (5HT) and dopamine expression, and ray morphology. Differences in these differentiated characteristics give each sensillum a unique identity and potentially endow the compound ray organ with a higher-order information ------------------- Key: 6507 Medline: 15087124 Authors: Zagrobelny M;Jeffares DC;Arctander P Title: Differences in non-LTR retrotransposons within C. elegans and C. briggsae genomes. Citation: Gene 330: 61-66 2004 Type: ARTICLE Genes: Abstract: An exhaustive study of the Sam/Frodo family of non-LTR retrotransposons in the Caenorhabditis elegans and Caenorhabditis briggsae genomes demonstrated that C briggsae contains 60 Sam/Frodc, elements including a new subfamily designated Merry, while at least 1000 elements are present in C. elegans. In contrast to C. elegans, C. briggsae does not contain any other non-LTR retrotransposons. The Sam/ Frodo/Merry sequences in C. briggsae are shorter and less complete than the Sam/Frodo sequences in C. elegans probably because they all lack a functional first open reading frame (ORFI) and because the genome only encodes one functional reverse transcriptase gene of a non-LTR retrotransposon. Evidence of purifying selection for a functional reverse transcriptase sequence in master/leader elements was found in both nematodes in spite of low copy numbers in C. briggsae. Sam elements in C. elegans are the most abundant Sam/Frodo/Merry family members. They contain the only functional ORF1 copies and, unlike Frodo and Merry members, have a higher GC content than the genomic regions in which they reside. This may indicate a higher transcription rate within this subfamily. ------------------- Key: 6508 Medline: 15084257 Authors: Beer MA;Tavazoie S Title: Predicting gene expression from sequence. Citation: Cell 117: 185-198 2004 Type: ARTICLE Genes: Abstract: We describe a systematic genome-wide approach for learning the complex combinatorial code underlying gene expression. Our probabilistic approach identifies local DNA-sequence elements and the positional and combinatorial constraints that determine their context-dependent role in transcriptional regulation. The inferred regulatory rules correctly predict expression patterns for 73% of genes in Saccharomyces cerevisiae, utilizing microarray expression data and sequences in the 800 bp upstream of genes. Application to Caenorhabditis elegans identifies predictive regulatory elements and combinatorial rules that control the phased temporal expression of transcription factors, histones, and germline specific genes. Successful prediction requires diverse and complex rules utilizing AND, OR, and NOT logic, with significant constraints on motif strength, orientation, and relative position. This system generates a large number of mechanistic hypotheses for focused experimental validation, and establishes a predictive dynamical framework for understanding cellular behavior from genomic sequence. ------------------- Key: 6509 Medline: 15066636 Authors: Abraham MC;Shaham S Title: Death without caspases, caspases without death. Citation: Trends in Cell Biology 14: 184-193 2004 Type: REVIEW Genes: ced-3 ced-4 ced-9 csp-1 csp-2 csp-3 icd-1 Abstract: Apoptosis is a conserved cell-death process displaying characteristic morphological and molecular changes including activation of caspase proteases. Recent work challenges the accepted roles of these proteases. New investigations in mice and the nematode Caenorhabditis elegans suggest that there could be caspase-independent pathways leading to cell death. In addition, another type of cell death displaying autophagic features might depend on caspases. Recent studies also indicate that caspase activation does not always lead to cell death and, instead, might be important for cell differentiation. Here, we review recent evidence for both the expanded roles of caspases and the existence of caspase-independent cell-death processes. We suggest that cellular context plays an important role in defining the consequences of ------------------- Key: 6510 Medline: 15084750 Authors: Nollen EAA;Garcia SM;van Haaften G;Kim S;Chavez A;Morimoto RI;Plasterk RHA Title: Genome-wide RNA interference screen identifies previously undescribed regulators of polyglutamine aggregation. Citation: Proceedings of the National Academy of Sciences USA 101: 6403-6408 2004 Type: ARTICLE Genes: ama-1 cct-5 eft-2 eif-2 hsp-6 imb-3 pas-4 phi-9 phi-37 phi-44 rab-1 rme-8 rps-26 rpt-5 tbb-2 uba-1 Abstract: Protein misfolding and the formation of aggregates are increasingly recognized components of the pathology of human genetic disease and hallmarks of many neurodegenerative disorders. As exemplified by polyglutamine diseases, the propensity for protein misfolding is associated with the length of polyglutamine expansions and age-dependent changes in protein-folding homeostasis, suggesting a critical role for a protein homeostatic buffer. To identify the complement of protein factors that protects cells against the formation of protein aggregates, we tested transgenic Caenorhabditis elegans strains expressing polyglutamine expansion yellow fluorescent protein fusion proteins at the threshold length associated with the age-dependent appearance of protein aggregation. We used genome-wide RNA interference to identify genes that, when suppressed, resulted in the premature appearance of protein aggregates. Our screen identified 186 genes corresponding to five principal classes of polyglutamine regulators: genes involved in RNA metabolism, protein synthesis, protein folding, and protein degradation; and those involved in protein trafficking. We propose that each of these classes represents a molecular machine collectively comprising the protein homeostatic buffer that responds to the expression of damaged proteins ------------------- Key: 6511 Medline: 15123841 Authors: Liberati NT;Fitzgerald KA;Kim DH;Feinbaum R;Golenbock DT;Ausubel FM Title: Requirement for a conserved Toll/interleukin-1 resistance domain protein in the Caenorhabditis elegans immune response. Citation: Proceedings of the National Academy of Sciences USA 101: 6593-6598 2004 Type: ARTICLE Genes: pmk-1 tir-1 Abstract: The p38 mitogen-activated protein kinase pathway regulates innate immune responses in evolutionarily diverse species. We have previously shown that the Caenorhabditis elegans p38 mitogen-activated protein kinase, PMK-1, functions in an innate immune response pathway that mediates resistance to a variety of microbial pathogens. Here, we show that tir-1, a gene encoding a highly conserved Toll/lL-1 resistance (TIR) domain protein, is also required for C elegans resistance to microbial pathogens. RNA interference inactivation of tir-1 resulted in enhanced susceptibility to killing by pathogens and correspondingly diminished PMK-1 phosphorylation. Unlike all known TIR-domain adapter proteins, overexpression of the human TIR-1 homologue, SARM, in mammalian cells was not sufficient to induce expression of NF-kappaB or IRF3-dependent reporter genes that are activated by Toll-like receptor signaling. These data reveal the involvement of a previously uncharacterized, evolutionarily conserved TIR domain protein in innate immunity that is functionally distinct from other known TIR domain signaling adapters. ------------------- Key: 6512 Medline: 15116111 Authors: Hodgkin J Title: Dissecting worm immunity. Citation: Nature Immunology 5: 471-472 2004 Type: REVIEW Genes: ikb-1 nlp-29 nlp-31 pik-1 tir-1 tol-1 trf-1 Abstract: The function of the mammalian TIR domain adaptor protein SARM is unclear. In Caenorhabditis elegans, however, the homolog of SARM controls the induction of peptides involved in innate immunity. ------------------- Key: 6513 Medline: 14764544 Authors: Minakuchi Y;Ito M;Kohara Y Title: SPI: a tool for incorporating gene expression data into a four-dimensional database of Caenorhabditis elegans embryogenesis. Citation: Bioinformatics 20: 1097-1109 2004 Type: ARTICLE Genes: Abstract: Motivation: A comprehensive gene expression database is essential for computer modeling and simulation of biological phenomena, including development. Development is a four-dimensional (4D; 3D structure and time course) phenomenon. We are constructing a 4D database of gene expression for the early embryogenesis of the nematode Caenorhabditis elegans. As a framework of the 4D database, we have constructed computer graphics (CG), into which we will incorporate the expression data of a number of genes at the subcellular level. However, the assignment of 3D distribution of gene products (protein, mRNA), of embryos at various developmental stages, is both difficult and tedious. We need to automate this process. For this purpose, we developed a new system, named SPI after superimposing fluorescent confocal microscopic data onto a CG framework. Results: The scheme of this system comprises the following: (1) acquirement of serial sections (40 slices) of fluorescent confocal images of three colors (4',6'-diamino-2-phenylindole (DAPI) for nuclei, indodicarbocyanine (Cy-3) for the internal marker, which is a germline-specific protein POS-1 and indocarbocyanine (Cy-5) for the gene product to be examined); (2) identification of several features of the stained embryos, such as contour, developmental stage and position of the internal marker; (3) selection of CG images of the corresponding stage for template matching; (4) superimposition of serial sections onto the CG; (5) assignment of the position of superimposed gene products. The Snakes algorithm identified the embryo contour. The detection accuracy of embryo contours was 92.1% when applied to 2- to 28-cell-stage embryos. The accuracy of the developmental stage prediction method was 81.2% for 2- to 8-cell-stage embryos. We manually judged only the later stage embryos because the accuracy for embryos at the later stages was unsatisfactory due to experimental noise effects. Finally, our system chose the optimal CG and performed the superposition and assignment of gene product distribution. We established an initial 4D gene expression database with 56 maternal gene products. ------------------- Key: 6514 Medline: 15107848 Authors: Zhang H;Smolen GA;Palmer R;Christoforou A;van den Heuvel S;Haber DA Title: SUMO modification is required for in vivo Hox gene regulation by the Caenorhabditis elegans Polycombe group protein SOP-2. Citation: Nature Genetics 36: 507-511 2004 Type: ARTICLE Genes: aos-1 sop-2 uba-2 ubc-9 Abstract: Post-translational modification of proteins by the ubiquitin-like molecule SUMO (sumoylation) regulates their subcellular localization and affects their functional properties in vitro 1,2, but the physiological function of sumoylation in multicellular organisms is largely unknown. Here, we show that the C. elegans Polycomb group (PcG) protein SOP-2 interacts with the SUMO-conjugating enzyme UBC-9 through its evolutionarily conserved SAM domain. Sumoylation of SOP-2 is required for its localization to nuclear bodies in vivo and for its physiological repression of Hox genes. Global disruption of sumoylation phenocopies a sop-2 mutation by causing ectopic Hox gene expression and homeotic transformations. Chimeric constructs in which the SOP-2 SAM domain is replaced with that derived from fruit fly or mammalian PcG proteins, but not those in which the SOP-2 SAM domain is replaced with the SAM domains of non-PcG proteins, confer appropriate in vivo nuclear localization and Hox gene repression. These observations indicate that sumoylation of PcG proteins, modulated by their evolutionarily conserved SAM domain, is essential to their physiological repression of Hox genes. ------------------- Key: 6515 Medline: 14996832 Authors: Petriv OI;Rachubinski RA Title: Lack of peroxisomal catalase causes a progeric phenotype in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 279: 19996-20001 2004 Type: ARTICLE Genes: clk-1 ctl-1 ctl-2 ctl-3 Abstract: Studies using the nematode Caenorhabditis elegans as a model system to investigate the aging process have implicated the insulin/insulin-like growth factor-I signaling pathway in the regulation of organismal longevity through its action on a subset of target genes. These targets can be classified into genes that shorten or extend life-span upon their induction. Genes that shorten life-span include a variety of stress response genes, among them genes encoding catalases; however, no evidence directly implicates catalases in the aging process of nematodes or other organisms. Using genetic mutants, we show that lack of peroxisomal catalase CTL-2 causes a progeric phenotype in C. elegans. Lack of peroxisomal catalase also affects the developmental program of C. elegans, since Deltactl-2 mutants exhibit decreased egg laying capacity. In contrast, lack of cytosolic catalase CTL-1 has no effect on either nematode aging or egg laying capacity. The Deltactl-2 mutation also shortens the maximum life-span of the long lived Deltaclk-1 mutant and accelerates the onset of its egg laying period. The more rapid aging of Deltactl-2 worms is apparently not due to increased carbonylation of the major C. elegans proteins, although altered peroxisome morphology in the Deltactl-2 mutant suggests that changes in peroxisomal function, including increased production of reactive oxygen species, underlie the progeric phenotype of the Deltactl-2 mutant. Our findings support an important role for peroxisomal catalase in both the development and aging of C. elegans and suggest the utility of the Deltactl-2 mutant as a convenient model for the study of aging and the human ------------------- Key: 6516 Medline: 14982934 Authors: Fujii M;Matsumoto Y;Tanaka N;Miki K;Suzuki T;Ishii N;Ayusawa D Title: Mutations in chemosensory cilia cause resistance to paraquat in nematode Caenorhabditis elegans. Citation: Journal of Biological Chemistry 279: 20277-20282 2004 Type: ARTICLE Genes: che-1 che-2 che-3 che-5 che-6 che-7 che-9 che-10 che-11 che-12 che-13 che-14 ctl-1 ctl-2 daf-6 daf-10 daf-19 dyf-1 dyf-2 dyf-3 dyf-4 dyf-5 dyf-6 dyf-7 dyf-8 dyf-9 dyf-10 dyf-11 dyf-12 dyf-13 mec-1 mec-8 mev-4 osm-1 osm-3 osm-5 osm-6 sod-1 sod-2 sod-3 sod-4 tax-2 tax-4 Abstract: The relationship between oxidative stress and longevity is a matter of concern in various organisms. We isolated mutants resistant to paraquat from nematode Caenorhabditis elegans. One mutant named mev-4 was long-lived and showed cross-resistance to heat and Dyf phenotype (defective in dye filling). Genetic and sequence analysis revealed that mev-4 had a nonsense mutation on the che-11 gene, homologues of which are involved in formation of cilia and flagella in other organisms. The paraquat resistance was commonly observed in various Dyf mutants and did not depend on the daf-16 gene, whereas the extension of life span did depend on it. Expression of antioxidant enzyme genes seemed normal. These results suggest that chemosensory neurons are a target of oxidative stress and influence longevity dependent on the daf-16 signaling in C. elegans. ------------------- Key: 6517 Medline: 15099742 Authors: Isermann K;Liebau E;Roeder T;Bruchhaus I Title: A peroxiredoxin specifically expressed in two types of pharyngeal neurons is required for normal growth and egg production in Caenorhabditis elegans. Citation: Journal of Molecular Biology 338: 745-755 2004 Type: ARTICLE Genes: prx-1 prx-2 prx-3 Abstract: A family of antioxidant proteins, the peroxiredoxins, serve two purposes, detoxification of reactive oxygen species and cellular signaling. Among the three peroxiredoxins of Caenorhabditis elegans (CePrx1-3), CePrx2 was found to have a very unusual expression pattern, restricted to only two types of pharyngeal neurons; namely, the single pharyngeal interneuron I4 and the sensory interneuron I2. CePrx1 and CePrx3-depleted worms showed no obvious phenotypic alterations, whereas worms devoid of CePrx2 were retarded developmentally and had a significantly reduced brood size. Other features, such as lifespan, pharyngeal activity or defecation rates were indistinguishable from those of wild-type worms. Recombinant CePrx2 revealed antioxidant activity, as it was able to detoxify hydrogen peroxide and butylhydroperoxide (t-BOOH), and to protect glutamine synthetase from inactivation by thiol-dependent metal-catalyzed oxidation. In addition, the molecule was able to act as a terminal peroxidase in the thioredoxin system. Expression of ceprx2 in C. elegans was induced after short-term exposure of worms to t-BOOH but survival of ceprx2 knockout mutants in the presence of reactive oxygen or nitrogen species was not impaired. Thus, CePrx2 may protect specifically the two types of neurons from oxidative damage or, more likely, plays a critical role in peroxide signaling in this nematode. ------------------- Key: 6518 Medline: 15084461 Authors: Gerisch B;Antebi A Title: Hormonal signals produced by DAF-9/cytochrome P450 regulate C. elegans dauer diapause in response to environmental Citation: Development 131: 1765-1776 2004 Type: ARTICLE Genes: col-3 daf-2 daf-3 daf-5 daf-7 daf-9 daf-11 daf-12 daf-16 dpy-7 mec-7 ncl-1 osm-6 sdf-9 wrt-1 mgDf50 Abstract: In response to the environment, the nematode C elegans must choose between arrest at a long-lived alternate third larval stage, the dauer diapause, or reproductive development. This decision may ultimately be mediated by daf-9, a cytochrome P450 related to steroidogenic hydroxylases and its cognate nuclear receptor daf-12, implying organism-wide coordination by lipophilic hormones. Accordingly, here we show that daf-9(+) works cell non-autonomously to bypass diapause, and promote gonadal outgrowth. Among daf-9-expressing cells, the hypodermis is most visibly regulated by environmental inputs, including dietary cholesterol. On in reproductive growth, off in dauer, hypodermal daf-9 expression is strictly daf-12 dependent, suggesting feedback regulation. Expressing daf-9 constitutively in hypodermis rescues dauer phenotypes of daf-9, as well as insulin/IGF receptor and TGFbeta mutants, revealing that daf-9 is an important downstream point of control within the dauer circuits. This study illuminates how endocrine networks integrate environmental cues and transduce them into adaptive life history choices. ------------------- Key: 6519 Medline: 15084462 Authors: Mak HY;Ruvkun G Title: Intercellular signaling of reproductive development by the C. elegans DAF-9 cytochrome P450. Citation: Development 131: 1777-1786 2004 Type: ARTICLE Genes: che-2 col-12 daf-1 daf-2 daf-7 daf-9 daf-12 dpy-7 sdf-9 Abstract: Parallel pathways control C elegans reproductive development in response to environmental cues. Attenuation of daf-2 insulin-like or daf-7 TGFbeta-Iike signaling pathways cause developmental arrest at the stress resistant and long-lived dauer stage. Loss-of-function mutations in the cytochrome P450 gene daf-9 also cause dauer arrest and defects in cell migration. A rescuing daf9::GFP fusion gene driven by the daf-9 promoter is expressed in two head cells at all stages, in the hypodermis from mid-second larval stage (L2) to the fourth larval stage (L4), and in the spermatheca of the adult hermaphrodite. Although the level of daf-9::GFP expression in the head cells and spermatheca is constant, hypodermal daf-9::GFP expression is modulated by multiple inputs. In particular, daf-9::GFP expression in the hypodermis is absolutely dependent on daf-12, the nuclear receptor that is negatively regulated by daf-9 gene activity, suggesting feedback control between daf-9 and daf-12 in this tissue. daf-9 expression exclusively in the hypodermis is sufficient to restore reproductive, development in daf-9 mutant animals, suggesting that daf-9 functions in a cell nonautonomous manner. Furthermore, constitutive expression of daf-9 in the hypodermis suppresses dauer arrest of daf-7 mutant animals and inhibits dauer remodelling of some tissues in daf-2 mutant animals. Thus, daf-9 may integrate outputs from daf-2 and daf-7 signaling pathways to relay neuroendocrine signals through synthesis of a lipophilic hormone. ------------------- Key: 6520 Medline: 15030753 Authors: Antebi A Title: Tipping the balance toward longevity. Citation: Developmental Cell 6: 315-316 2004 Type: REVIEW Genes: daf-16 sir-2.1 Abstract: Genetic experiments in C. elegans suggested that SIR2, an NAD-dependent protein deacetylase, acts through FOXO/DAF-16 transcription factor to prolong life. Recent studies show that mammalian SIR2 deacetylates FOXO, and may maximize survival by tempering cell death and increasing stress resistance. ------------------- Key: 6521 Medline: Authors: Feng W;Long JF;Fan JS;Suetake T;Zhang M Title: The tetrameric L27 domain complex as an organization platform for supramolecular assemblies. Citation: Nature Structural & Molecular Biology 11: 475-480 2004 Type: ARTICLE Genes: lin-2 lin-7 lin-10 Abstract: L27 domain, initially identified in the Caenorhabditis elegans Lin-2 and Lin-7 proteins, is a protein interaction module that exists in a large family of scaffold proteins. The domain can function as an organization center of large protein assemblies required for establishment and maintenance of cell polarity. We have solved the high-resolution NMR structure of a tetrameric complex of L27 domains containing two SAP97-mLin-2 L27 domain heterodimers. Each L27 domain contains three alpha-helices. The first two helices of each domain are packed together to form a four-helical bundle in the heterodimer. The third helix of each L27 domain forms another four-helical bundle that assembles the two heterodimers into a tetramer. The structure of the complex provides a mechanistic explanation for L27 domain mediated polymerization of scaffold proteins, a process that is crucial for the assembly of supramolecular complexes in asymmetric cells. ------------------- Key: 6522 Medline: Authors: Oliver B;Parisi M Title: Battle of the Xs. Citation: BioEssays 26: 543-548 2004 Type: REVIEW Genes: Abstract: Females and males often exhibit conspicuous morphological, physiological and behavioral differences. Similarly, gene expression profiles indicate that a large portion of the genome is sex-differentially deployed, particularly in the germ line. Because males and females are so fundamentally different, each sex is likely to have a different optimal gene expression profile that is never fully achieved in either sex because of antagonistic selection in females versus males. Males are hemizygous for the X chromosome, which means that recessive male-favorable de novo mutations on the X chromosome are subject to immediate selection. In females, a recessive female-favorable mutation on one of two X chromosomes is not available for selection until it becomes frequent enough in the local population to result in homozygous individuals. Given that most mutations are recessive, one would expect that genes or alleles favoring males should accumulate on the X chromosome. Recent microarray work in Drosophila and C. elegans clearly shows the opposite. Why is the X chromosome a highly disfavored location for genes with male-biased expression in these animals? ------------------- Key: 6523 Medline: 14698964 Authors: Moulton G;Attwood TK;Parry-Smith DJ;Packer JCL Title: Phylogenomic analysis and evolution of the potassium channel gene family. Citation: Receptors & Channels 9: 363-377 2003 Type: ARTICLE Genes: Abstract: Potassium channels govern the permeability of cells to potassium ions, thereby controlling the membrane potential. In metazoa, potassium channels are encoded by a large, diverse gene family. Previous analyses of this gene family have focused on its diversity in mammals. Here we have pursued a more comprehensive study in Caenorhabditis elegans, Drosophila melanogaster, and mammalian genomes. The investigation revealed 164 potassium channel encoding genes in C. elegans, D. melanogaster, and mammals, classified into seven conserved families, which we applied to phylogenetic analysis. The trees are discussed in relation to the assignment of orthologous relationships between genes and vertebrate genome duplication. ------------------- Key: 6524 Medline: 15123580 Authors: Castillo-Davis CI;Kondrashov FA;Hartl DL;Kulathinal RJ Title: The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint. Citation: Genome Research 14: 802-811 2004 Type: ARTICLE Genes: Abstract: We compare the functional spectrum of protein evolution in two separate animal lineages with respect to two hypotheses: (1) rates of divergence are distributed similarly among functional classes within both lineages, indicating that selective pressure on the proteome is largely independent of organismic-level biological requirements; and (2) rates of divergence are distributed differently among functional classes within each lineage, indicating species-specific selective regimes impact genome-wide substitutional patterns. Integrating comparative genome sequence with data from tissue-specific expressed-sequence-tag (EST) libraries and detailed database annotations, we find a functional genomic signature of rapid evolution and selective constraint shared between mammalian and nematode lineages despite their extensive morphological and ecological differences and distant common ancestry. In both phyla, we find evidence of accelerated evolution among components of molecular systems involved in coevolutionary change. In mammals, lineage-specific fast evolving genes include those involved in reproduction, immunity, and possibly, maternal-fetal conflict. Likelihood ratio tests provide evidence for positive selection in these rapidly evolving functional categories in mammals. In contrast, slowly evolving genes, in terms of amino acid or insertion/deletion (indel) change, in both phyla are involved in core molecular processes such as transcription, translation, and protein transport. Thus, strong purifying selection appears to act on the same core cellular processes in both mammalian and nematode lineages, whereas ------------------- Key: 6525 Medline: 15338614 Authors: McKay SJ;Johnsen R;Khattra J;Asano J;Baillie DL;Chan S;Dube N;Fang L;Goszczynski B;Ha E;Halfnight E;Hollebakken R;Huang P;Hung K;Jensen V;Jones SJM;Kai H;Li D;Mah A;Marra M;McGhee J;Newbury R;Pouzyrev Title: Gene expression profiling of cells, tissues, and developmental stages of the nematode C. elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 68: 159-169 2004 Type: REVIEW Genes: Abstract: Completion of the DNA sequences of the human genome and that of the nematode Caenorhabditis elegans allows the large-scale identification and analysis of orthologs of human genes in an organism amenable to detailed genetic and molecular analyses. WE are determining gene expression profiles in specific cells, tissues, and developmental stages in C. elegans. Our ultimate goal is not only to describe detailed gene expression profiles, but also to gain a greater understanding of the organization of gene regulatory networks and to determine how they control cell function during development and differentiation. ------------------- Key: 6526 Medline: 15100407 Authors: Fridkin A;Mills E;Margalit A;Neufeld E;Lee KK;Feinstein N;Cohen M;Wilson KL;Gruenbaum Y Title: Matefin, a Caenorhabditis elegans germ line-specific SUN-domain nuclear membrane protein, is essential for early embryonic development and germ cell development. Citation: Proceedings of the National Academy of Sciences USA 101: 6987-6992 2004 Type: ARTICLE Genes: lmn-1 mes-2 mes-3 mes-6 mtf-1 unc-84 Abstract: Caenorhabditis elegans mtf-1 encodes matefin, which has a predicted SUN domain, a coiled-coil region, an anti-erbB-2 IgG domain, and two hydrophobic regions. We show that matefin is a nuclear membrane protein that colocalizes in vivo with Ce-lamin, the single nuclear lamin protein in C elegans, and binds Ce-lamin in vitro but does not require Ce-lamin for its localization. Matefin is detected in all embryonic cells until midembryogenesis and thereafter only in germ-line cells. Embryonic matefin is maternally deposited, and matefin is the first nuclear membrane protein known to have germ line-restricted expression. Animals homozygous for an mtf-1 deletion allele show that matefin is essential for germ line maturation and survival. However, matefin is also required for embryogenesis because mtf-1 (RNAi) embryos die around the approximate to300-cell stage with defects in nuclear structure, DNA content, and chromatin morphology. Down-regulating matefin in mes-3 animals only slightly enhances embryonic lethality, and elimination of UNC-84, the only other SUN-domain gene in C. elegans, has no affect on mtf-1 (RNAi) animals. Thus, mtf-1 mediates a previously uncharacterized pathway(s) required for embryogenesis as well as germ line proliferation or survival. ------------------- Key: 6527 Medline: 15066373 Authors: Platzer U;Meinzer HP Title: Genetic networks in the early development of Caenorhabditis elegans. Citation: International Review of Cytology 234: 47-100 2004 Type: ARTICLE Genes: Abstract: One of the best-studied model organisms in biology is Caenorhabditis elegans. Because of its simple architecture and other biological advantages, considerable data have been collected about the regulation of its development. In this review, currently available data concerning the early phase of embryonic development are presented in the form of genetic networks. We performed computer simulations of regulatory mechanisms in embryonic development, and the results are described and compared with experimental observations. ------------------- Key: 6528 Medline: 15096560 Authors: Jacobsen N;Nielsen PS;Jeffares DC;Eriksen J;Ohlsson H;Arctander P;Kauppinen S Title: Direct isolation of poly(A)+ RNA from 4 M guanidine thiocyante-lysed cell extracts using locked nucleic acid oligo(T) capture. Citation: Nucleic Acids Research 32: e64- 2004 Type: ARTICLE Genes: let-2 Abstract: LNA oligonucleotides constitute a class of bicyclic RNA analogues having an exceptionally high affinity for their complementary DNA and RNA target molecules. We here report a novel method for highly efficient isolation of intact poly(A)+ RNA using an LNA-substituted oligo(dT) affinity ligand, based on the increased affinity of LNA-T for complementary poly(A) tracts. Poly(A)+ RNA was isolated directly from 4 M guanidine thiocyanate-lysed Caenorhabditis elegans worm extracts as well as from lysed human K562 and vincristine-resistant K562/VCR leukemia cells using LNA_2.T oligonucleotide as an affinity probe, in which every second thymidine was substituted by LNA thymidine. In accordance with the significantly increased stability of the LNA_2.T-A duplexes in 4 M GuSCN, we obtained a 30- to 50-fold mRNA yield increase using the LNA-substituted oligo(T) affinity probe compared with DNA-oligo(dT)-selected mRNA samples. The LNA_2.T affinity probe was, furthermore, highly efficient in isolation of poly(A)+ RNA in a low salt concentration range of 50-100 mM NaCl in poly(A) binding buffer, as validated by selecting the mRNA pools from total RNA samples extracted from different Saccharomyces cerevisiae strains, followed by northern blot analysis. Finally, we demonstrated the utility of the LNA-oligo(T)-selected mRNA in quantitative real-time PCR by analysing the relative expression levels of the human mdr1 multidrug resistance gene in the two K562 cell lines employing pre-validated Taqman assays. Successful use of the NH2-modified LNA_2.T probe in isolation of human mRNA implies that the LNA-oligo(T) method could be automated for streamlined, high throughput expression profiling by real-time PCR by covalently coupling the LNA affinity probe to solid, pre-activated ------------------- Key: 6529 Medline: 15101434 Authors: Hughes AL;Friedman R Title: Differential loss of ancestral gene families as a source of genomic divergence in animals. Citation: Proceedings of the Royal Society of London B 271: S107-S109 2004 Type: ARTICLE Genes: Abstract: A phylogenetic approach was used to reconstruct the pattern of an apparent loss of 2106 ancestral gene families in four animal genomes (Caenorhabditis elegans, Drosophila melanogaster, human and fugu). Substantially higher rates of loss of ancestral gene families were found in the invertebrates than in the vertebrates. These results indicate that the differential loss of ancestral gene families can be a significant factor in the evolutionary diversification of organisms. ------------------- Key: 6530 Medline: Authors: Bourbon HM;Aguilera A;Ansari AZ;Asturias FJ;Berk AJ;Bjorklund S;Blackwell TK;Borggrefe T;Carey M;Carlson M;Conaway JW;Conaway RC;Emmons SW;Fondell JD;Freedman LP;Fukasawa T;Gustafsson CM;Han M;He X;.. Title: A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. Citation: Molecular Cell 14: 553-557 2004 Type: ARTICLE Genes: Abstract: Promoter-specific initiation of transcription of RNA polymerase II (Pol II) requires both gene-specific regulators and general transcription factors (GTFs: TFIIB, -D, -E, -F, and -H) (Woychik and Hampsey, 2002). Biochemical and genetic studies in yeast led to the discovery of a Mediator (MED) complex of 20 protein subunits, linking transcriptional regulators to Pol II and GTFs (Flanagan et al., 1991; Kelleher et al., 1990; Kim et al., 1994). In vitro, Mediator stimulates basal transcription, enables activated transcription, and relieves the interfering effect (Gill and Ptashne, 1988) of a strong transcriptional activator (Kim et al., 1994). The identification of Mediator subunits revealed that many were products of previous genetic screens (Carlson, 1997; Lee and Young, 2000; Myers and Kornberg, 2000; Nonet and Young, 1989; Suzuki et al., 1988), and some were shown to interact directly with Pol II and GTFs (Koleske et al., 1992; Myers et al., 1998; Sakurai and Fukasawa, 2000; Thompson et al., 1993). Further genetic studies demonstrated the role of Mediator in repression as well as activation (Li et al., 1995; Song et al., 1996), and established the relevance of Mediator to transcription control in vivo (Barberis et al., 1995; Holstege et al., 1998; Thompson and Young, 1995). ------------------- Key: 6531 Medline: 15170261 Authors: Denver DR;Morris K;Kewalramani A;Harris KE;Chow A;Estes S;Lynch M;Thomas WK Title: Abundance, distribution, and mutation rates of homopolymeric nucleotide runs in the genome of Citation: Journal of Molecular Evolution 58: 584-595 2004 Type: ARTICLE Genes: Abstract: Homopolymeric nucleotide runs, also called mononucleotide microsatellites, are a ubiquitous, dominant, and mutagenic feature of eukaryotic genomes. A clear understanding of the forces that shape patterns of homopolymer evolution, however, is lacking. We provide a focused investigation of the abundance, chromosomal distribution, and mutation spectra of the four strand-specific homopolymer types (A, T, G, Q greater than or equal to8 bp in the genome of Caenorhabditis elegans. A and T homopolymers vastly outnumber G and C HPs, and the run-length distributions of A and T homopolymers differ significantly from G and C homopolymers. A scanning window analysis of homopolymer chromosomal distribution reveals distinct clusters of homopolymer density in autosome arms that are regions of high recombination in C. elegans. Dramatic biases are detected among closely spaced homopolymers; for instance, we observe 994 A homopolymers immediately followed by a T homopolymer (5' to 3') and only 8 instances of T homopolymers directly followed by an A homopolymer. Empirical homopolymer mutation assays in a set of C. elegans mutation-accumulation lines reveal an similar to20-fold higher mutation rate for G and C homopolymers compared to A and T homopolymers. Nuclear A and T homopolymers are also found to mutate similar to100-fold more slowly than mitochondrial A and T homopolymers. This integrative approach yields a total nuclear genome-wide homopolymer mutation rate estimate of similar to1.6 mutations per genome per generation. ------------------- Key: 6532 Medline: Authors: Delattre M;Gonczy P Title: The arithmetic of centrosome biogenesis. Citation: Journal of Cell Science 117: 1619-1629 2004 Type: REVIEW Genes: sas-4 tac-1 zyg-1 Abstract: How do cells regulate centrosome number? A canonical duplication cycle generates two centrosomes from one in most proliferating cells. Centrioles are key to this process, and molecules such as centrins, SAS-4 and ZYG-1 govern daughter centriole formation. Cdk2 activity probably couples centrosome duplication with the S phase, and a licensing mechanism appears to limit centrosome duplication to once per cell cycle. However, such mechanisms must be altered in some cells - for example, spermatocytes - in which centrosome duplication and DNA replication are uncoupled. There are also alternative pathways of centrosome biogenesis. For example, one centrosome is reconstituted from two gametes at fertilization; in this case, the most common strategy involves differential contributions of centrioles and pericentriolar material (PCM) from each gamete. Furthermore, centrioles can sometimes form de novo from no apparent template. This occurs, for instance, in the early mouse embryo and in parthenogenetic species and might rely on a pre-existing seed that resides within PCM but is not visible by ------------------- Key: 6533 Medline: 15016808 Authors: Kuzmin EV;Karpova OV;Elthon TE;Newton KJ Title: Mitochondrial respiratory deficiencies signal up-regulation of genes for heat shock proteins. Citation: Journal of Biological Chemistry 279: 20672-20677 2004 Type: ARTICLE Genes: gst-4 hsp-16.1 hsp-16.48 hsp-17 hsp-70 hsp-70.6 pqm-1 Abstract: The consequences of mitochondrial dysfunction are not limited to the development of oxidative stress or initiation of apoptosis but can result in the establishment of stress tolerance. Using maize mitochondrial mutants, we show that permanent mitochondrial deficiencies trigger novel Ca2+-independent signaling pathways, leading to constitutive expression of genes for molecular chaperones, heat shock proteins (HSPs) of different classes. The signaling to activate hsp genes appears to originate from a reduced mitochondrial transmembrane potential. Upon depolarization of mitochondrial membranes in transient assays, gene induction for mitochondrial HSPs occurred more rapidly than that for cytosolic HSPs. We also demonstrate that in the nematode Caenorhabditis elegans transcription of hsp genes can be induced by RNA interference of nuclear respiratory genes. In both organisms, activation of hsp genes in response to mitochondrial impairment is distinct from their responses to heat shock and is not associated with oxidative stress. Thus, mitochondria-to-nucleus signaling to express a hsp gene network is apparently a widespread retrograde mechanism to facilitate cell defense ------------------- Key: 6534 Medline: 15105376 Authors: Lee MH;Schedl T Title: Translation repression of GLD-1 protects its mRNA targets from nonsense-mediated mRNA decay in C. elegans. Citation: Genes & Development 18: 1047-1059 2004 Type: ARTICLE Genes: gld-1 gna-2 lin-45 mes-3 nos-3 oma-1 oma-2 rme-2 smg-2 smg-3 smg-4 Abstract: Previously, we identified multiple in vivo mRNA targets of the maxi-KH/STAR domain protein GLD-1 by their ability to interact with GLD-1 in cytoplasmic extracts and, for all targets tested thus far, GLD-1 functions as a translational repressor. However, here we show that GLD-1 stabilizes the mRNAs of two targets, gna-2 (T23G11.2) and Y75B12B.1. gna-2 mRNA has two upstream open reading frames (uORF), resulting in two premature stop codons. We found that gna-2 mRNA is a naturally occurring mRNA target of nonsense-mediated mRNA decay (NMD) and that the binding of GLD-1 protects gna-2 mRNA from NMD, likely by repressing translation of the uORFs. Therefore, gna-2 mRNA comes under two posttranscriptional. controls: (1) translation regulation by a specific translational repressor, GLD-1; and (2) uORF elicited regulation, mainly through NMD. As a result, these two posttranscriptional controls together provide precise temporal and spatial control of gene expression. Consistent with this novel mode of regulation, when GLD-1 mRNA targets acquire premature stop codon mutations, GLD-1 protects them from NMD. Analysis of several mRNA targets containing premature stop codons suggests that in translation repression, GLD-1 either represses ribosome assembly on the target mRNA, or subsequent ribosome elongation to the premature stop codon. ------------------- Key: 6535 Medline: 15123748 Authors: Houthoofd K;Braeckman BP;Vanfleteren JR Title: The hunt for the record life span in Caenorhabditis Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 59: 408-410 2004 Type: REVIEW Genes: age-1 clk-1 daf-2 fer-15 gro-1 Abstract: Many genes regulate the aging rate of the nematode Caenorhabditis elegans (1-3). Reduced Ins/IGF-1 (insulin-like growth factor-1) signaling, which is the most intensively studied mechanism of life extension in C. elegans, also increases the life span of flies and mice (4,5). A recent report showed that daf-2 RNAi treatment and germ-line ablation of worms carrying the daf-2(e1368) hypomorphic mutation in the gene encoding the C. elegans Ins/IGF-1 receptor further increases their life span up to 6.0-fold (6). These authors claimed that this was a record life extension, missing an earlier result. ------------------- Key: 6536 Medline: 15160843 Authors: Park Y;Jang SH;Lee DG;Hahm KS Title: Antinematodal effect of antimicrobial peptide, PMAP-23, isolated from porcine myeloid against Caenorhabditis elegans. Citation: Journal of Peptide Science 10: 304-311 2004 Type: ARTICLE Genes: Abstract: The antinematodal activity and mechanism of a 23-iner antimicrobial peptide, PMAP-23, derived from pig myeloid was investigated. PMAP-23 displayed a strong antinematodal activity against the eggs and worms of Caenorhabditis elegans. To investigate the antinematodal mechanism of PMAP-23. fluorescence activated flow cytometry and confocal laser scanning microscopy were performed. C. elegans treated with PMAP-23 showed higher fluorescence intensity by propidium iodide (PI) staining than normal cells. Confocal microscopy showed that the peptide was localized in the egg's shell and cell membrane. The action of the peptide against C. elegans membranes was examined by testing the membrane disrupting activity using liposome (PC/PS: 3:1, w/w). The result suggests that PMAP-23 may exert its antinematodal activity by disrupting the structure of the cell membrane via pore formation or via direct interaction with the lipid bilayers ------------------- Key: 6537 Medline: 15135044 Authors: Khan LA;Nukina N Title: Molecular and functional analysis of Caenorhabditis elegans CHIP, a homologue of mammalian CHIP. Citation: FEBS Letters 565: 11-18 2004 Type: ARTICLE Genes: chn-1 Abstract: A recently identified molecule C-terminus of Hsc70 interacting protein (CHIP) has been reported to be an E3 ubiquitin ligase collaborating with molecular chaperones for the degradation of misfolded or unfolded proteins. The physiological roles of CHIP in animal and plant development remain largely unknown. Here, we show that the knockdown of CeCHIP by RNAi and knockout by a deletion mutation arrests the development of the animal at the larval stage. CeCHIP expresses ubiquitously in all tissues but there are tissue specific variations of expression level. CeCHIP produces dose dependent phenotypes in vivo. Over expression of CHIP causes embryonic lethality, while a comparatively lower level of over expression causes locomotion and egg laying defects, and the CHIP over expressed animals form dauers at a higher temperature. ------------------- Key: 6538 Medline: Authors: Bastiani CA;Simon MI;Sternberg PW Title: Control of Caenorhabditis elegans behavior and development by G proteins big and small. Citation: Cell Signalling in Prokaryotes and Lower Metazoa. Kluwer Academic Publ. : 195-242 2004 Type: REVIEW Genes: Abstract: ------------------- Key: 6539 Medline: 15184656 Authors: Kiontke K;Gavin NP;Raynes Y;Roehrig C;Piano F;Fitch DHA Title: Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss. Citation: Proceedings of the National Academy of Sciences USA 101: 9003-9008 2004 Type: ARTICLE Genes: Abstract: Despite the prominence of Caenorhabditis elegans as a major developmental and genetic model system, its phylogenetic relationship to its closest relatives has not been resolved. Resolution of these relationships is necessary for studying the steps that underlie life history, genomic, and morphological evolution of this important system. By using data from five different nuclear genes from 10 Caenorhabditis species currently in culture, we find a well resolved phylogeny that reveals three striking patterns in the evolution of this animal group: (i) Hermaphroditism has evolved independently in C elegans and its close relative Caenorhabditis briggsae; (ii) there is a large degree of intron turnover within Caenorhabditis, and intron losses are much more frequent than intron gains; and (iii) despite the lack of marked morphological diversity, more genetic disparity is present within this one genus than has occurred within all vertebrates. ------------------- Key: 6540 Medline: 15186741 Authors: Cheeks RJ;Canman JC;Gabriel WN;Meyer N;Strome S;Goldstein B Title: C. elegans PAR proteins function by mobilizing and stabilizing asymmetrically localized protein complexes. Citation: Current Biology 14: 851-862 2004 Type: ARTICLE Genes: mex-5 mex-6 nmy-2 par-1 par-2 par-3 par-4 par-5 par-6 pie-1 pkc-3 Abstract: Background: The PAR proteins are part of an ancient and widely conserved machinery for polarizing cells during animal development. Here we use a combination of genetics and live imaging methods in the model organism Caenorhabditis elegans to dissect the cellular mechanisms by which PAR proteins polarize cells. Results: We demonstrate two distinct mechanisms by which PAR proteins polarize the C. elegans zygote. First, we show that several components of the PAR pathway function in intracellular motility, producing a polarized movement of the cell cortex. We present evidence that this cortical motility may drive the movement of cellular components that must become asymmetrically distributed, including both germline-specific ribonucleoprotein complexes and cortical domains containing the PAR proteins themselves. Second, PAR-1 functions to refine the asymmetric localization of germline ribonucleoprotein complexes by selectively stabilizing only those complexes that reach the PAR-1-enriched posterior cell cortex during the period of cortical motility. Conclusions: These results identify two cellular mechanisms by which the PAR proteins polarize the C. elegans zygote, and they suggest mechanisms by which PAR proteins may polarize cells in diverse animal systems. ------------------- Key: 6541 Medline: Authors: Hitt R;Wolf DH Title: Der1p, a protein required for degradation of malfolded soluble proteins of the endoplasmic reticulum: topology and Der1-like proteins. Citation: FEMS Yeast Research 4: 721-729 2004 Type: ARTICLE Genes: Abstract: ------------------- Key: 6542 Medline: 15020807 Authors: Montgomery MK Title: The use of double-stranded RNA to knock down specific gene activity. Citation: Methods in Molecular Biology 260: 129-144 2004 Type: REVIEW Genes: Abstract: In many eukaryotes, the introduction of double-stranded RNA (dsRNA) into cells triggers the degradation of cognate mRNAs through a posttranscriptional gene silencing mechanism. This phenomenon has been called RNA interference or RNAi. Several methods for delivering dsRNA into the model organism C. elegans are described; these methods include (1) microinjecting dsRNA synthesized in vitro into the body cavity of the worm, (2) soaking worms in a solution of dsRNA, (3) feeding worms dsRNA-expressing bacteria, and (4) engineering transgenic worm strains to express dsRNA in vivo. Variations of these methods may be used to perform RNAi in other species as well. The choice of which delivery method to use, along with other options (region to target, length of dsRNA) are also discussed. ------------------- Key: 6543 Medline: 15109782 Authors: Dichtel-Danjoy ML;Felix MA Title: Phenotypic neighborhood and micro-evolvability. Citation: Trends in Genetics 20: 268-276 2004 Type: REVIEW Genes: Abstract: The complex relationship between the genotype and the phenotype constrains and biases phenotypic evolution. Indeed, random mutation can have non-random (anisotropic) effects on the phenotype. In this review, we propose an operational definition of the'phenotypic neighborhood' of a given genotype, as obtained after induced mutagenesis or in mutation accumulation lines, with examples of anisotropic distributions of phenotypes reached when exploring the vicinity of a genotype. We also compare the phenotypic neighborhood for a given developmental process among species, focusing on nematode vulva development. Finally, we compare the phenotypic neighborhood assessed by mutagenesis with the phenotypic spectrum of wild isolates of the same species and make inferences about the action of selection and/or drift on the same developmental process in ------------------- Key: 6544 Medline: 15134634 Authors: Bulow HE;Boulin T;Hobert O Title: Differential functions of the C. elegans FGF receptor in axon outgrowth and maintenance of axon position. Citation: Neuron 42: 367-374 2004 Type: ARTICLE Genes: egl-15 let-60 let-756 pin-2 srq-1 unc-47 zig-4 Abstract: Wiring of the nervous system requires that axons navigate to their targets and maintain their correct positions in axon fascicles after termination of axon outgrowth. We show here that the C. elegans fibroblast growth factor receptor (FGFR), EGL-15, affects both processes in fundamentally distinct manners. FGF-dependent activation of the EGL-15 tyrosine kinase and subsequently the GTPase LET-60/ras is required within epidermal cells, the substratum for most outgrowing axon, for appropriate outgrowth of specific axon classes to their target area. In contrast, genetic elimination of the FGFR isoform EGL-15(5A), defined by the inclusion of an alternative extracellular interimmunoglobulin domain, has no consequence for axon outgrowth but leads to a failure to postembryonically maintain axon position within defined axon fascicles. An engineered, secreted form of EGL-15(5A) containing only its ectodomain is sufficient for maintenance of axon position, thus providing novel insights into receptor tyrosine kinase function and the process of maintaining axon position. ------------------- Key: 6545 Medline: 15126693 Authors: Parker JA;Holbert S;Lambert E;Abderrahmane S;Neri C Title: Genetic and pharmacological suppression of polyglutamine-dependent neuronal dysfunction in Caenorhabditis elegans. Citation: Journal of Molecular Neuroscience 23: 61-67 2004 Type: ARTICLE Genes: apt-4 cbp-1 dlg-1 dnj-25 gpd-3 mlk-1 rpn-12 sem-5 ubc-20 Abstract: The identification of disease genes for several neurodegenerative illnesses has allowed for the development of disease models in experimental organisms. We discuss our approach to studying Huntington's disease, the best characterized of the polyglutamine (polyQ) expansion disorders. We have developed a system in Caenorhabditis elegans to study the effects of (polyQ)-dependent neuronal dysfunction at the resolution of two neurons in screening for genetic and pharmacological suppression. Our data suggest that C. elegans might be instructive in searching for targets and active compounds against polyglutamine neuronal toxicity. ------------------- Key: 6546 Medline: 15180374 Authors: Anderson GL;Cole RD;Williams PL Title: Assessing behavioral toxicity with Caenorhabditis elegans. Citation: Environmental Toxicology & Chemistry 23: 1235-1240 2004 Type: ARTICLE Genes: Abstract: Behavior, even in simple metazoans, depends upon integrated processes at the subcellular, cellular, and organismal level, and thus is susceptible to disruption by a broad spectrum of chemicals. Locomotor behavior (movement) of the small free-living nematode Caenorhabditis elegans has proven to be useful in assessing toxicity. Recently reported observations suggest that behavioral change (reduced movement) occurs after 4 h of exposure to heavy metals, and that with abbreviated exposure, the concentration-response relationship for Pb (a known neurotoxic metal) differs from that for Cu. In this Study, movement was evaluated after 4-h exposures for nine compounds from three chemical classes: organic pesticides, organic solvents, and heavy metals. Concentration-dependent reduction of movement was observed for all test compounds with the exception of mebendazole. for which test concentrations were limited by solubility. Within each chemical class, movement was more sensitive to the neurotoxic compounds than to substances not believed to be neurotoxic, Lis evidenced by behavioral effective concentration to reduce average worm movement to 50% of the control movement values (e.g., levamisole and chlorpyrifos < mebendazole. ethanol and acetone < dimethylsulfoxide. and Pb and Al < Cu). These observations are discussed as they relate to the Use Of acute behavioral tests in assessing general chemical toxicity, and the enhanced Value of 4-h ------------------- Key: 6547 Medline: 15152596 Authors: Polanowska J;Martin JS;Fisher R;Scopa T;Rae I;Boulton SJ Title: Tandem immunoaffinity purification of protein complexes from Caenorhabditis elegans. Citation: Biotechniques 36: 778+- 2004 Type: ARTICLE Genes: Abstract: Multiprotein complexes are the functional units of many cellular processes. Defining the components of these complexes, how they associate, and their intrinsic biochemical activities provides a wealth of information about the context in which proteins operate. The nematode Caenorhabditis elegans is a powerful organism for genetically defining cellular pathways, but how the proteins operate biochemically within such pathways has not been explored significantly due to the absence of robust systems for biochemical studies. Here we describe the first method for tandem immunoaffinity purification of native protein complexes from C. elegans that can be applied to any nematode protein of interest. ------------------- Key: 6549 Medline: 15068796 Authors: Hertweck M;Gobel C;Baumeister R Title: C. elegans SGK-1 is the critical component in the Akt/PKB kinase complex to control stress response and life span. Citation: Developmental Cell 6: 577-588 2004 Type: ARTICLE Genes: age-1 akt-1 akt-2 daf-2 daf-7 daf-11 daf-16 daf-18 pdk-1 rrf-3 sgk-1 Abstract: The DAF-2 insulin receptor-like signaling pathway controls metabolism, development, longevity, and stress response in C. elegans. Here we show that SGK-1, the C. elegans homolog of the serum- and glucocorticoid-inducible kinase SGK, acts in parallel to the AKT kinases to mediate DAF-2 signaling. Loss of sgk-1 results in defective egg-laying, extended generation time, increased stress resistance, and an extension of life span. SGK-1 forms a protein complex with the AKT kinases, and is activated by and strictly depends on PDK-1. All three kinases of this complex are able to directly phosphorylate DAF-16/FKHRL1, yet have different functions in DAF-2 signaling. Whereas AKT-1 and AKT-2 are more important for regulating dauer formation, SGK-1 is the crucial factor for the control of development, stress response, and longevity. Our data also suggest the existence of a second pathway from DAF-2 to DAF-16 that does not depend on AKT-1, AKT-2, and SGK-1. ------------------- Key: 6550 Medline: 15068795 Authors: Ceol CJ;Horvitz HR Title: A new class of C. elegans synMuv genes implicates a Tip60/NuA4-like HAT complex as a negative regulator of Ras signaling. Citation: Developmental Cell 6: 563-576 2004 Type: ARTICLE Genes: dpl-1 epc-1 let-23 let-50 lin-3 lin-8 lin-15 lin-35 lin-36 lin-37 lin-38 lin-56 mys-1 ssl-1 trr-1 Abstract: The class A and class B synMuv genes are functionally redundant negative regulators of a Ras signaling pathway that induces C. elegans vulval development. A number of class B synMuv genes encode components of an Rb and histone deacetylase complex that likely acts to repress transcription of genes required for vulval induction. We discovered a new class of synMuv genes that acts redundantly with both the A and B classes of genes in vulval cell-fate determination. These new class C synMuv genes encode TRRAP, MYST family histone acetyltransferase, and Enhancer of Polycomb homologs, which form a putative C. elegans Tip60/NuA4-like histone acetyltransferase complex. A fourth gene with partial class C synMuv properties encodes a homolog of the mammalian SWI/SNF family ATPase p400. Our findings indicate that the coordinated action of two chromatin-modifying complexes, one with histone deacetylase and the other with histone acetyltransferase activity, is important in regulating Ras signaling and specifying cell fates during C. elegans development. ------------------- Key: 6551 Medline: 15068791 Authors: Kemp CA;Kopish KR;Zipperlen P;Ahringer J;O'Connell KF Title: Centrosome maturation and duplication in C. elegans require the coiled-coil protein SPD-2. Citation: Developmental Cell 6: 511-523 2004 Type: ARTICLE Genes: air-1 dhc-1 plk-1 sas-4 spd-2 spd-5 tbg-1 zyg-1 zyg-9 Abstract: Centrosomes are major determinants of mitotic spindle structure, but the mechanisms regulating their behavior remain poorly understood. The spd-2 gene of C. elegans is required for centrosome assembly or "maturation." Here we show that spd-2 encodes a coiled-coil protein that localizes within pericentriolar material (PCM) and in the immediate vicinity of centrioles. During maturation, SPD-2 gradually accumulates at the centrosome in a manner that is partially dependent on Aurora-A kinase and cytoplasmic dynein. Interestingly, SPD-2 interacts genetically with dynein heavy chain and SPD-5, another coiled-coil protein required for centrosome maturation. SPD-2 and SPD-5 are codependent for localization to the PCM, but SPD-2 localizes to centrioles independently of SPD-5. Surprisingly, we also find that SPD-2 is required for centrosome duplication and genetically interacts with ZYG-1, a kinase required for duplication. Thus, we have identified SPD-2 as a factor critical for the two basic functions of the centrosome-microtubule organization and ------------------- Key: 6552 Medline: 15086962 Authors: Kadandale P;Singson A Title: Oocyte production and sperm utilization patterns in semi-fertile strains of Caenorhabditis elegans. Citation: BMC Developmental Biology 4:3: - 2004 Type: ARTICLE Genes: fem-1 fer-14 spe-9 spe-13 spe-40 Abstract: BACKGROUND: Caenorhabditis elegans hermaphrodites are capable of producing hundreds of progeny. However, genetic and environmental factors can keep many animals from attaining their full reproductive potential. In these situations, efficient use of any functional gametes becomes more important for reproductive success. To learn about this aspect of C. elegans reproductive biology, we examined oocyte production and sperm utilization patterns in a unique collection of semi-fertile sperm function mutants. RESULTS: In the mutants examined here, broods can be very small but sperm induced high levels of ovulation. Ovulation rates reach maximum levels between the first and second day of adulthood. Ovulations rates remain high during the reproductive period and gradually decline with age. These results further demonstrate a decoupling of the ability of sperm to fertilize oocytes and induce ovulation. We also observe that in our semi-fertile mutants the peak of successful fertilization events precedes the bulk of oocyte production. Mixing populations of functional and nonfunctional sperm under conditions without sperm competition also shows that functional sperm are utilized efficiently. Although overall brood size can be similar for different mutant strains, slight differences in the pattern of sperm utilization in these strains can lead to significant differences in resource utilization and population growth. CONCLUSIONS: This study represents the first detailed description of oocyte and progeny production patterns over the entire reproductive period for wild-type and fertility impaired strains of C. elegans. The phenotype of our mutants provide an ideal system for studying sperm utilization patterns since they only affect one major process, the ability to fertilize oocytes. In semi-fertile mutants, the nature of the reproductive process and/or specific molecular mechanisms ensures that any functional sperm are utilized quickly. Only a fraction of the sperm produced by our semi-sterile mutants are functional as opposed to every sperm having a low but equal chance of fertilizing an oocyte. In addition to the number of progeny produced, the pattern of progeny production can have an important influence on the dynamics of population growth. ------------------- Key: 6553 Medline: 15070432 Authors: Maslov S;Sneppen K;Eriksen KA;Yan KK Title: Upstream plasticity and downstream robustness in evolution of molecular networks. Citation: BMC Evolutionary Biology 4:9: - 2004 Type: ARTICLE Genes: Abstract: BACKGROUND: Gene duplication followed by the functional divergence of the resulting pair of paralogous proteins is a major force shaping molecular networks in living organisms. Recent species-wide data for protein-protein interactions and transcriptional regulations allow us to assess the effect of gene duplication on robustness and plasticity of these molecular networks. RESULTS: We demonstrate that the transcriptional regulation of duplicated genes in baker's yeast Saccharomyces cerevisiae diverges fast so that on average they lose 3% of common transcription factors for every 1% divergence of their amino acid sequences. The set of protein-protein interaction partners of their protein products changes at a slower rate exhibiting a broad plateau for amino acid sequence similarity above 70%. The stability of functional roles of duplicated genes at such relatively low sequence similarity is further corroborated by their ability to substitute for each other in single gene knockout experiments in yeast and RNAi experiments in a nematode worm Caenorhabditis elegans. We also quantified the divergence rate of physical interaction neighborhoods of paralogous proteins in a bacterium Helicobacter pylori and a fly Drosophila melanogaster. However, in the absence of system-wide data on transcription factors' binding in these organisms we could not compare this rate to that of transcriptional regulation of duplicated genes. CONCLUSIONS: For all molecular networks studied in this work we found that even the most distantly related paralogous proteins with amino acid sequence identities around 20% on average have more similar positions within a network than a randomly selected pair of proteins. For yeast we also found that the upstream regulation of genes evolves more rapidly than downstream functions of their protein products. This is in accordance with a view which puts regulatory changes as one of the main driving forces of the evolution. In this context a very important open question is to what extent our results obtained for homologous genes within a single species (paralogs) carries ------------------- Key: 6554 Medline: 15136141 Authors: Qin H;Powell-Coffman JA Title: The Caenorhabditis elegans aryl hydrocarbon receptor, AHR-1, regulates neuronal development. Citation: Developmental Biology 270: 64-75 2004 Type: ARTICLE Genes: ahr-1 egl-2 gcy-32 mec-18 npr-1 sax-3 unc-5 unc-6 unc-40 unc-86 unc-129 Abstract: The mammalian aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that mediates the toxic effects of dioxins and related compounds. Dioxins have been shown to cause a range of neurological defects, but the role of AHR during normal neuronal development is not known. Here we investigate the developmental functions of ahr-1, the Caenorhabditis elegans aryl hydrocarbon receptor homolog. We show that ahr-1:GFP is expressed in a subset of neurons, and we demonstrate that animals lacking ahr-1 function have specific defects in neuronal differentiation, as evidenced by changes in gene expression, aberrant cell migration, axon branching, or supernumerary neuronal processes. In ahr-1-deficient animals, the touch receptor neuron AVM and its sister cell, the interneuron SDQR, exhibit cell and axonal migration defects. We show that dorsal migration of SDQR is mediated by UNC-6/Netrin, SAX-3/Robo, and UNC-129/TGFbeta, and this process requires the functions of both ahr-1 and its transcription factor dimerization partner aha-1. We also document a role for ahr-1 during the differentiation of the neurons that contact th ------------------- Key: 6555 Medline: 15135534 Authors: Laws TR;Harding SV;Smith MP;Atkins TP;Titball RW Title: Age influences resistance of Caenorhabditis elegans to killing by pathogenic bacteria. Citation: FEMS Microbiology Letters 234: 281-287 2004 Type: ARTICLE Genes: age-1 age-2 Abstract: Caenorhabditis elegans has previously been proposed as an alternative host for models of infectious disease caused by human pathogens. When exposed to some human pathogenic bacteria, the life span of nematodes is significantly reduced. We have shown that mutations in the age-1, and/or age-2 genes of C elegans, that normally enhance life expectancy, can also increase resistance to killing by the bacterial pathogens Pseudomonas aeruginosa, Salmonella enterica var. Typhimurium, Burkholderia cepacia or Yersinia pseudotuberculosis. We also found that the rate at which wild-type C elegans was killed by the bacterial pathogens tested increased as nematodes aged. In the case of P. aeruginosa infection, the difference in life span of wild type and age-1 mutants of C elegans was not due to differences in the level of bacterial colonisation of the gut. ------------------- Key: 6556 Medline: 15157420 Authors: Fukuto HS;Ferkey DM;Apicella AJ;Lans H;Sharmeen T;Chen W;Lefkowitz RJ;Jansen G;Schafer WR;Hart AC Title: G protein-coupled receptor kinase function is essential for chemosensation in C. elegans. Citation: Neuron 42: 581-593 2004 Type: ARTICLE Genes: arr-1 eat-16 glr-1 grk-2 odr-3 odr-10 osm-9 srb-6 Abstract: G protein-coupled receptors (GPCRs) mediate diverse signaling processes, including olfaction. G protein-coupled receptor kinases (GRKs) are important regulators of G protein signal transduction that specifically phosphorylate activated GPCRs to terminate signaling. Despite previously described roles for GRKs in GPCR signal downregulation, animals lacking C. elegans G protein-coupled receptor kinase-2 (Ce-grk-2) function are not hypersensitive to odorants. Instead, decreased Ce-grk-2 function in adult sensory neurons profoundly disrupts chemosensation, based on both behavioral analysis and Ca2+ imaging. Although mammalian arrestin proteins cooperate with GRKs in receptor desensitization, loss of C. elegans arrestin-1 (arr-1) does not disrupt chemosensation. Either overexpression of the C. elegans Galpha. subunit odr-3 or loss of eat-16, which encodes a regulator of G protein signaling (FIGS) protein, restores chemosensation in Ce-grk-2 mutants. These results demonstrate that loss of GRK function can lead to reduced GPCR signal transduction and suggest an important role for RGS proteins in the regulation of chemosensation. ------------------- Key: 6557 Medline: 15194510 Authors: Ndegwa S;Lemire BD Title: Caenorhabditis elegans development requires mitochondrial function in the nervous system. Citation: Biochemical and Biophysical Research Communications 319: 1307-1313 2004 Type: ARTICLE Genes: atp-2 let-858 myo-2 nuo-1 pie-1 unc-54 unc-119 Abstract: The mitochondrial respiratory chain (MRC) supplies the majority of the energy requirements of most eucaryotic cells. A null mutation in the Caenorhabditis elegans nuo-1 gene encoding a subunit of complex I (NADH-ubiquinone oxidoreductase) is lethal, leading to a developmental arrest at the third larval stage. To identify the tissues that regulate development in response to mitochondrial dysfunction, we restored nuo-1 expression with tissue-specific promoters. Only expression of nuo-1 ubiquitously or in the nervous system supported development to the adult stage. Pharyngeal expression of nuo-1 allowed development to proceed to the fourth larval stage. Expression of nuo-1 in the body muscles or in the germline had no effect. Furthermore, only ubiquitous or nervous system expression of nuo-1 allowed exit from the dauer state. Our results indicate that MRC function in the nervous system is needed to send and receive signals that control larval development and exit from dauer. ------------------- Key: 6558 Medline: 15182714 Authors: Davies AG;Bettinger JC;Thiele TR;Judy ME;McIntire SL Title: Natural variation in the npr-1 gene modifies ethanol responses of wild strains of C. elegans. Citation: Neuron 42: 731-743 2004 Type: ARTICLE Genes: daf-1 daf-3 daf-7 daf-8 daf-14 dgk-1 egl-4 flp-18 flp-21 npr-1 ocr-2 odr-8 osm-9 tax-4 Abstract: Variation in the acute response to ethanol between individuals has a significant impact on determining susceptibility to alcoholism. The degree to which genetics contributes to this variation is of great interest. Here we show that allelic variation that alters the functional level of NPR-1, a neuropeptide Y (NPY) receptor-like protein, can account for natural variation in the acute response to ethanol in wild strains of Caenorhabditis elegans. NPR-1 negatively regulates the development of acute tolerance to ethanol, a neuroadaptive process that compensates for effects of ethanol. Furthermore, dynamic changes in the NPR-1 pathway provide a mechanism for ethanol tolerance in C. elegans. This suggests an explanation for the conserved function of NPY-related pathways in ethanol responses across diverse species. Moreover, these data indicate that genetic variation in the level of NPR-1 function determines much of the phenotypic variation in adaptive behavioral responses to ethanol that ------------------- Key: 6559 Medline: Authors: Davies AG;McIntire SL Title: Using C. elegans to screen for targets of ethanol and behavior-altering drugs. Citation: Biological Procedures Online 6: 113-119 2004 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans is an attractive model system for determining the targets of neuroactive compounds. Genetic screens in C. elegans provide a relatively unbiased approach to the identification of genes that are essential for behavioral effects of drugs and neuroactive compounds such as alcohol. Much work in vertebrate systems has identified multiple potential targets of ethanol but which, if any, of those candidates are responsible for the behavioral effects of alcohol in uncertain. Here we provide detailed methodology for a genetics screen for mutants of C. elegans that are resistant to the depressive effects of ethanol on locomotion and for the subsequent behavioral analysis of the mutants. The methods we describe should also be applicable for use in screening for mutants that are resistant or hypersensitive to many neuroactive compounds and for identifying the molecular targets or biochemical pathways mediating drug responses. ------------------- Key: 6560 Medline: 15141086 Authors: Huang C;Xiong C;Kornfeld K Title: Measurements of age-related changes of physiological processes that predict lifespan of Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 101: 8084-8089 2004 Type: ARTICLE Genes: age-1 clk-1 daf-2 daf-16 eat-2 Abstract: Aging is characterized by progressive, degenerative changes in many tissues. To elucidate the relationships among degenerative changes in Caenorhabditis elegans, we developed methods to measure age-related changes quantitatively and analyzed correlations among these changes by using a longitudinal study. The age-related declines of pharyngeal pumping and body movement were positively correlated with each other and lifespan. These findings suggest that the declines of pharyngeal pumping and body movement cause a decline in survival probability or that a shared regulatory system mediates the declines in pharyngeal pumping, body movement, and survival probability. Furthermore, measurements of these processes can be used to predict lifespan and detect premature aging. The declines of physiological processes were measured in daf-2, age-1, daf-16, eat-2, and clk-1 mutants that have altered lifespans. Each mutant strain displayed changes in one or more age-related declines, but the correlations among age-related changes were similar to WT. These measurements were used to generate a system of four stages that describes the aging proces ------------------- Key: 6561 Medline: 15151149 Authors: Schulenburg H;Muller S Title: Natural variation in the response of Caenorhabditis elegans toward Bacillus thruingiensis. Citation: Parasitology 128: 433-443 2004 Type: ARTICLE Genes: Abstract: Almost nothing is known about the natural ecology of the nematode Caenorhabditis elegans, including its interactions with parasites. To help rectify this discrepancy, we assessed natural variation in the response of C. elegans towards a potential parasite, the soil bacterium Bacillus thuringiensis. Our results show that 10 isolates from across the world differ significantly in survival rate and infection level when Confronted with a parasitic strain of B. thuringiensis. Furthermore, behavioural responses are identified as an important component of C. elegans defence, inducing evasion and possibly reduced ingestion of parasites. Again, the natural isolates show significant differences in these traits. In conclusion, worm defence is indicated to be complex and variable across space, implying that parasites play an important role in the ecology, of this species. Based on these results, we expect C. elegans to be a promising model host for future analysis of the evolutionary dynamics of parasite-host interactions. ------------------- Key: 6562 Medline: 15156192 Authors: Lee J;Ahnn J;Bae SC Title: Homologs of RUNX and CBF beta/PEBP2 beta in C. elegans. Citation: Oncogene 23: 4346-4352 2004 Type: ARTICLE Genes: bro-1 daf-4 dbl-1 rnt-1 sma-2 sma-3 sma-4 sma-6 Abstract: RUNX proteins are evolutionarily well-conserved transcription factors that are involved in essential aspects of the development of metazoan animals ranging from nematodes to humans. Geneticor epigenetic defects in any one of the three RUNX proteins in humans cause severe diseases. Although much is known about the functions and signaling pathways of the RUNX proteins through the use of mammalian systems, there are still gaps in our knowledge with regard to the functions of the RUNX proteins in normal development and disease states. Recently, the nematode Caenorhabditis elegans was revealed to bear one RUNX homolog (RNT-1) and one homolog of the RUNX protein partner CBFbeta/PEBP2beta (BRO-1). The expression patterns and biological functions of RNT-1 and the manner in which it is regulated are all comparable to what has been observed for the mammalian RUNX proteins. Thus, the nematode system is a promising model system for elucidating the functions and regulation of Runt proteins. In addition, it has recently emerged that the RNT-1 protein is involved in a transforming growth factor beta signaling pathway. The ------------------- Key: 6563 Medline: 15143192 Authors: Wicky C;Alpi A;Passannante M;Rose A;Gartner A;Muller F Title: Multiple genetic pathways involving the Caenorhabditis elegans Bloom's Syndrome gene him-6, rad-51, and top-3 are needed to maintain genome stability in the germ line. Citation: Molecular and Cellular Biology 24: 5016-2027 2004 Type: ARTICLE Genes: dpy-3 dpy-5 him-6 rad-51 spo-11 top-3 unc-1 unc-3 unc-54 unc-101 Abstract: Bloom's syndrome (BS) is an autosomal-recessive human disorder caused by mutations in the BS RecQ helicase and is associated with loss of genomic integrity and an increased incidence of cancer. We analyzed the mitotic and the meiotic roles of Caenorhabditis elegans him-6, which we show to encode the ortholog of the human BS gene. Mutations in him-6 result in an enhanced irradiation sensitivity, a partially defective S-phase checkpoint, and in reduced levels of DNA-damage induced apoptosis. Furthermore, him-6 mutants exhibit a decreased frequency of meiotic recombination that is probably due to a defect in the progression of crossover recombination. In mitotically proliferating germ cells, our genetic interaction studies, as well as the assessment of the number of double-strand breaks via RAD-51 foci, reveal a complex regulatory network that is different from the situation in yeast. Although the number of double-strand breaks in him-6 and top-3 single mutants is elevated, the combined depletion of him-6 and top-3 leads to mitotic catastrophe concomitant with a massive increase in the level of double-strand breaks, a ------------------- Key: 6564 Medline: 15090591 Authors: Cox EA;Tuskey C;Hardin J Title: Cell adhesion receptors in C. elegans. Citation: Journal of Cell Science 117: 1867-1870 2004 Type: REVIEW Genes: cdh-1 cdh-3 cdh-5 cdh-6 cdh-7 cdh-8 cdh-9 cdh-10 cdh-11 cdh-12 clc-1 clc-2 clc-3 clc-4 crb-1 dgn-1 eat-20 hmr-1 ina-1 mua-3 mup-4 nlr-1 pat-2 pat-3 rig-3 syg-1 wrk-1 Abstract: C. elegans has numerous putative cell adhesion receptors, many of which have vertebrate homologues. The simple body plan of C. elegans, it optical transparency and genetic tractability make it well suited for the study of adhesion receptors and their associated complexes (reviewed by Cox and Hardin in this issue, pp. 1885-1897). We focus here on receptors that are likely to directly mediate adhesion either between cells or to the extracellular matrix; for information on other cell surface receptors please refer to Hutter et al. (Hutter et al., 2000). ------------------- Key: 6565 Medline: 15090594 Authors: Cox EA;Hardin J Title: Sticky worms: adhesion complexes in C. elegans. Citation: Journal of Cell Science 117: 1885-1897 2001 Type: ARTICLE Genes: ajm-1 atn-1 clc-1 clc-2 clc-3 clc-4 crb-1 crl-1 deb-1 dgn-1 dlg-1 dyb-1 dys-1 eat-20 evl-20 gex-2 gex-3 gsk-3 hmp-2 hmr-1 let-413 mig-2 par-3 pat-3 pat-4 pes-7 unc-52 unc-70 unc-97 unc-98 unc-112 vab-10 vab-19 Abstract: Caenorhabditis elegans is a powerful model system for investigating the establishment, regulation and function of adhesive structures in vivo. C elegans has several adhesion complexes related to those in vertebrates. These include: (1) epithelial apical junctions, which have features of both adherens and tight junctions; (2) dense bodies, which are muscle-attachment structures similar to focal adhesions; (3) fibrous organelles, which resemble hemidesmosomes and mediate mechanical coupling between tissues; and (4) a putative dystrophin-glycoprotein complex that has potential roles in muscle function and embryogenesis. Recent work has increased our understanding of these structures and has given new insights into the functions of their vertebrate counterparts. ------------------- Key: 6566 Medline: 15155582 Authors: Pires-daSilva A;Sommer RJ Title: Conservation of the global sex determination gene tra-1 in distantly related nematodes. Citation: Genes & Development 18: 1198-1208 2004 Type: ARTICLE Genes: tra-1 tra-2 tra-3 Abstract: Sex determination has long intrigued evolutionists, geneticists, and developmental biologists in a similar way. Substantial evidence indicates that sex determination evolves rapidly and, therefore, can be used to study how molecular patterning processes evolve. In Caenorhabditis elegans, sex determination relies on a signaling pathway that involves a cascade of negatively acting factors, finally triggering the GLI-family zinc-finger transcription factor TRA-1. We have started to investigate sex determination in the nematode satellite species Pristionchus pacificus that is separated from C. elegans for 200-300 million years. In P. pacificus, animals with two X chromosomes develop as hermaphrodites, whereas XO animals develop as males. We used an unbiased forward genetic approach and isolated several mutants with a hermaphrodite to male transformation of the XX karyotype. We identified one complementation group as representing the P. pacificus ortholog of tra-1, providing the first evidence for the conservation of a global sex determination gene over a time period of at least 200 million years. A Ppa-tra-1 morpholino phenocopies Ppa-tra-1 mutants an ------------------- Key: 6567 Medline: 15122256 Authors: Joeng KS;Song EJ;Lee KJ;Lee J Title: Long lifespan in worms with long telomeric DNA. Citation: Nature Genetics 36: 607-611 2004 Type: ARTICLE Genes: clk-2 daf-16 hrp-1 mut-7 Abstract: Telomere length is a crucial factor in senescence(1-3), but it has not been determined whether animals with long telomeres live longer than those with normal-length telomeres in the isogenic background of a given species. Here we show the effect of long telomeres on lifespan in the nematode Caenorhabditis elegans. We examined the effect of telomere length on lifespan by overexpressing HRP-1, a telomere-binding protein, which gradually increased telomere length in worms. Worms with longer telomeres lived longer. We confirmed that the extension of lifespan was due to the increased telomere length, and not to the overexpression of HRP-1 per se, by examining the lifespans of nontransgenic progeny of the transgenic worms, who retained the longer telomeres. The lifespan-extending effect of long telomeres was dependent on daf-16. The number of germ stem cells was not affected in worms with long telomeres, indicating that the telomere effect on lifespan is independent of germ stem cell cycling. Worms with long telomeres were more resistant to heat stress. Taken together, our results suggest that signaling may be initiated in postmitotic somatic cells by telomere length ------------------- Key: 6568 Medline: 15088067 Authors: Shimozono S;Fukano T;Kimura KD;Mori I;Kirino Y;Miyawaki A Title: Slow Ca2+ dynamics in pharyngeal muscles in Caenorhabditis elegans during fast pumping. Citation: EMBO Reports 5: 521-526 2004 Type: ARTICLE Genes: unc-68 Abstract: The pharyngeal muscles of Caenorhabditis elegans are composed of the corpus, isthmus and terminal bulb from anterior to posterior. These components are excited in a coordinated fashion to facilitate proper feeding through pumping and peristalsis. We analysed the spatiotemporal pattern of intracellular calcium dynamics in the pharyngeal muscles during feeding. We used a new ratiometric fluorescent calcium indicator and a new optical system that allows simultaneous illumination and detection at any two wavelengths. Pumping was observed with fast, repetitive and synchronous spikes in calcium concentrations in the corpus and terminal bulb, indicative of electrical coupling throughout the muscles. The posterior isthmus, however, responded to only one out of several pumping spikes to produce broad calcium transients, leading to peristalsis, the slow and gradual motion needed for efficient swallows. The excitation-calcium coupling may be uniquely modulated in this region at the level of calcium channels on the plasma membrane. ------------------- Key: 6569 Medline: 15056620 Authors: Good K;Ciosk R;Nance J;Neves A;Hill RJ;Priess JR Title: The T-box transcription factors TBX-37 and TBX-38 link GLP-1/Notch signaling to mesoderm induction in C. elegans embryos. Citation: Development 131: 1967-1978 2004 Type: ARTICLE Genes: apx-1 lag-2 pha-4 spe-6 tbx-34 tbx-37 tbx-38 ctDf3 eDf20 tDf7 zuDf1 zuDf3 zuDf5 eDp6 Abstract: The four-cell C elegans embryo contains two sister cells called ABa and ABp that initially have equivalent abilities to produce ectodermal cell types. Multiple Notch-mediated interactions occur during the early cell divisions that diversify the ABa and ABp descendants. The first interaction determines the pattern of ectodermal cell types produced by ABp. The second interaction induces two ABa granddaughters to become mesodermal precursors. We show that T-box transcription factors called TBX-37 and TBX-38 are essential for mesodermal induction, and that these factors are expressed in ABa, but not ABp, descendants. We provide evidence that the first Notch interaction functions largely, if not entirely, to prevent TBX-37, TBX-38 expression in ABp descendants. Neither the second Notch interaction nor TBX-37, TBX-38 alone are sufficient for mesodermal induction, indicating that both must function together. We conclude that TBX-37, TBX-38 play a key role in distinguishing the outcomes of two sequential Notch-mediated interactions. ------------------- Key: 6570 Medline: 15073154 Authors: Pepper ASR;McCane JE;Kemper K;Yeung DA;Lee RC;Ambros V;Moss EG Title: The C. elegans heterochronic gene lin-46 affects developmental timing at two larval stages and encodes a relative of the scaffolding protein gephyrin. Citation: Development 131: 2049-2059 2004 Type: ARTICLE Genes: let-7 lin-14 lin-28 lin-41 lin-42 lin-46 lin-57 Abstract: The succession of developmental events in the C elegans larva is governed by the heterochronic genes. When mutated, these genes cause either precocious or retarded developmental phenotypes, in which stage-specific patterns of cell division and differentiation are either skipped or reiterated, respectively. We identified a new heterochronic gene, lin-46, from mutations that suppress the precocious phenotypes caused by mutations in the heterochronic genes lin-14 and lin-28. lin-46 mutants on their own display retarded phenotypes in which cell division patterns are reiterated and differentiation is prevented in certain cell lineages. Our analysis indicates that lin-46 acts at a step immediately downstream of lin-28, affecting both the regulation of the heterochronic gene pathway and execution of stage-specific developmental events at two stages: the third larval stage and adult. We also show that lin-46 is required prior to the third stage for normal adult cell fates, suggesting that it acts once to control fates at both stages, and that it affects adult fates through the let-7 branch of the heterochronic pathway. Interestingly, lin-46 encodes a protein homologous to MoeA of bacteria and the C-terminal domain of mammalian gephyrin, a multifunctional scaffolding protein. Our findings suggest that the LIN-46 protein acts as a scaffold for a multiprotein assembly that controls developmental timing, and expand the known roles of gephyrin-related proteins to ------------------- Key: 6571 Medline: 15073148 Authors: Dalpe G;Zhang LW;Zheng H;Culotti JG Title: Conversion of cell movement responses to Semaphorin-1 and Plexin-1 from attraction to repulsion by lowered levels of specific RAC GTPases in C. elegans. Citation: Development 131: 2073-2088 2004 Type: ARTICLE Genes: ced-10 let-502 mig-2 plx-1 rac-2 rho-1 smp-1 smp-2 unc-73 Abstract: Plexins are functional receptors for Semaphorin axon guidance cues. Previous studies have established that some Plexins directly bind RAC(GTP) and RHO. Recent work in C elegans showed that semaphorin 1 (smp-1 and smp-2) and plexin 1 (plx-1) are required to prevent anterior displacement of the ray 1 cells in the male tail (Fujii et al., 2002; Ginzburg et al., 2002). We show genetically that plx1 is part of the same functional pathway as smp-1 and smp2 for male ray positioning. RAC GTPase genes mig-2 and ced-10 probably function redundantly, whereas unc-73, which encodes a GEF for both of these GTPases, is required cell autonomously for preventing anterior displacement of ray 1 cells. RNAi analysis indicates that rho-1-encoded RHO GTPase, plus let-502 and K08B12.5-encoded RHO-kinases, are also required to prevent anterior displacement of ray I cells, suggesting that different kinds of RHO-family GTPases act similarly in ray 1 positioning. At low doses of wild-type mig-2 and ced-10, the Semaphorin 1 proteins no longer act through PLX-1 to prevent anterior displacements of ray 1, but have the opposite effect, acting through PLX-1 to mediate anterior displacements of ray 1. These results suggest that Plexin I senses levels of distinct RHO and RAC GTPases. At normal levels of RHO and RAC, Semaphorin 1 proteins and FLX-1 prevent a forward displacement of ray I cells, whereas at low levels of cycling RAC, Semaphorin 1 proteins and PLX-1 actively mediate their anterior displacement. Endogenously and ectopically expressed SMP-1 and SMP-2 suggest that the hook, a major source of Semaphorin 1 proteins in the male tail, normally attracts PLX-1-expressiing ray 1 cells. ------------------- Key: 6572 Medline: 15186742 Authors: Pelletier L;Ozlu N;Hannak E;Cowan C;Habermann B;Ruer M;Muller-Reichert T;Hyman AA Title: The Caenorhabditis elegans centrosomal protein SPD-2 is required for both pericentriolar material recruitment and centriole duplication. Citation: Current Biology 14: 863-873 2004 Type: ARTICLE Genes: sas-4 spd-2 spd-5 Abstract: Background: The centrosome is composed of a centriole pair and pericentriolar material (PCM). By marking the site of PCM assembly, the centrioles define the number of centrosomes present in the cell. The PCM, in turn, is responsible for the microtubule (MT) nucleation activity of centrosomes. Therefore, in order to assemble a functional bipolar mitotic spindle, a cell needs to control both centriole duplication and PCM recruitment. To date, however, the molecular mechanisms that govern these two processes still remain poorly understood. Results: Here we show that SPD-2 is a novel component of the C. elegans centrosome. SPD-2 localizes to the centriole throughout the cell cycle and accumulates on the PCM during mitosis. We show that SPD-2 requires SPD-5 for its accumulation on the PCM and that in the absence of SPD-2, centrosome assembly fails. We further show that centriole duplication is also defective in spd-2(RNAi) embryos, but not in spd-5(RNAi) embryos, where PCM recruitment is efficiently blocked. Conclusions: Taken together, our results suggest that SPD-2 may link PCM recruitment and centriole duplication in C. elegans. SPD-2 shares homology with a human centrosome protein, suggesting that this key component of the C. elegans centrosome is evolutionarily conserved. ------------------- Key: 6573 Medline: 15083533 Authors: Phillips JB;Lyczak R;Ellis GC;Bowerman B Title: Roles for two partially redundant alpha-tubulins during mitosis in early Caenorhabditis elegans embryos. Citation: Cell Motility and the Cytoskeleton 58: 112-126 2004 Type: ARTICLE Genes: tba-1 tba-2 tbb-1 tbb-2 qDf9 Abstract: The Caenorhabditis elegans genome encodes multiple isotypes of alpha-tubulin and beta-tubulin. Roles for a number of these tubulins in neuronal development have been described, but less is known about the isoforms that function during early embryonic development. Microtubules are required for multiple events after fertilization produces a one-cell zygote in C. elegans, including pronuclear migration, mitotic spindle assembly and function, and proper spindle positioning. Here we describe a conditional and dominant mis-sense mutation in the C. elegans alpha-tubulin gene tba-1 that disrupts pronuclear migration and positioning of the first mitotic spindle, and results in a highly penetrant embryonic lethality, at the restrictive temperature of 26degreesC. Our analysis of the dominant tba-1 (or346ts) allele suggests that TBA-1 assembles into microtubules in early embryonic cells. However, we also show that reduction of tba-1 function using RNA interference results in defects much less severe than those caused by the dominant or346ts mutation, due to partial redundancy of TBA-1 and another alpha-tubulin called TBA-2. Reducing the function of both TBA-1 and TBA-2 results in severe defects in microtubule-dependent processes. We conclude that microtubules in the early C. elegans embryo are composed of both TBA-1 and TBA-2, and that the dominant tba-1 (or346ts) mutation disrupts MT assembly or stability. ------------------- Key: 6574 Medline: 15376539 Authors: Jonker MJ;Piskiewicz AM;Castella NII;Kammenga JE Title: Toxicity of binary mixtures of cadmium-copper and carbendazim-copper to the nematode Caenorhabditis elegans. Citation: Environmental Toxicolgy and Chemistry 23: 1529-1537 2004 Type: ARTICLE Genes: Abstract: For ecological risk assessment, the additive model may be used to empirically predict toxic mixture effects. Detailed toxicity tests were performed to determine whether effects of mixtures of copper-cadmium and copper-carbendazim on Caenorhabditis elegans were similar to the effects of the individual compounds. Effects on the course of reproduction, the length of the juvenile period, the length of the reproductive period, and body length were analyzed. Dose-response data were compared to the additive model and tested for four deviation patterns from additivity: No deviation, synergistic/antagonistic deviation, dose ratio-dependent deviation, dose level-dependent deviation. During the exposure, the cadmium-copper effect on reproduction changed from a synergistic, to a dose ratio-dependent deviation from additivity. More cadmium in the mixture decreased the toxicity and more copper increased the toxicity. The effect of copper-carbendazim on reproduction was synergistic at low dose levels and antagonistic at high dose levels and independent of time. Mixture effects on the juvenile and reproductive period were similar to single component effects. It was concluded that the observed time-dependence of toxic interactions was small and that interactions on the timing of reproduction were not found. The additive model underestimated mixture effects on reproduction and body length. ------------------- Key: 6575 Medline: 15145337 Authors: Gaud A;Simon JM;Witzel T;Carre-Pierrat M;Wermuth CG;Segalat L Title: Prednisone reduces muscle degeneration in dystrophin-deficient Caenorhabditis elegans. Citation: Neuromuscular Disorders 14: 365-370 2004 Type: ARTICLE Genes: dys-1 Abstract: Duchenne muscular dystrophy is a degenerative muscular disease caused by mutations in the dystrophin gene. There is no curative treatment against Duchenne muscular dystrophy. In several countries, the steroid prednisone (or analogs) is prescribed as a palliative treatment. In the model animal Caenorhabditis elegans, mutations of the dys-1 dystrophin-like gene lead to a muscular degenerative phenotype when they are associated with a mild MyoD mutation. This cheap and fast-growing model of dystrophinopathy may be used to screen for molecules able to slow muscle degeneration. In a blind screen of approximately 100 compounds covering a wide spectrum of targets, we found that prednisone is beneficial to the C elegans dystrophin-deficient muscles. Prednisone reduces by 40% the number of degenerating cells in this animal. This result is a proof-of-principle for the use of C. elegans as a tool in the search for molecules active against the effects of dystrophin-deficiency. Moreover, since C. elegans is not susceptible to inflammation, this suggests that prednisone exerts a direct effect on muscle survival. ------------------- Key: 6576 Medline: Authors: Kim SY;Valencia M;Lee ES;Park D;Oh M;Xue D;Park WF Title: Identification of CED-3 substrates by a yeast-based screening method. Citation: Molecular Biotechnology 27: 1-6 2004 Type: ARTICLE Genes: Abstract: ------------------- Key: 6577 Medline: Authors: van der Linden AM;Plasterk RHA Title: Shotgun cloning of transposon insertions in the genome of Caenorhabditis elegans. Citation: Comparative and Functional Genomics 5: 225-229 2004 Type: ARTICLE Genes: mut-7 Abstract: We present a strategy to identify and map large numbers of transposon insertions in the genome of Caenorhabditis elegans. Our approach makes use of the mutator strain mut-7, which has germline-transposition activity of the Tc1/mariner family of transposons, a display protocol to detect new transposon insertions, and the availability of the genomic sequence of C. elegans. From a pilot insertional mutagenesis screen, we have obtained 351 new Tc1 transposons inserted in or near 219 predicted C. elegans genes. The strategy presented provides an approach to isolate insertions of natural transposable elements in many C. elegans genes and to create a large-scale collection of C. elegans mutants. ------------------- Key: 6578 Medline: 15217699 Authors: Yen K;Mastitis JW;Mobbs CV Title: Lifespan is not determined by metabolic rate: evidence from fishes and C. elegans. Citation: Experimental Gerontology 39: 947-949 2004 Type: ARTICLE Genes: Abstract: Roy Walford is best known for his work in the immunology of aging and mechanisms of caloric restriction, mainly in mice (and, later, humans), but interestingly, much of his early research in gerontology focused on the effects of temperature on lifespan in fishes (Walford et al., 1969; Liu and Walford, 1972, 1970, 1975; Liu et al., 1975). Although it had been known since 1916 that reducing temperature in poikilotherms would increase lifespan (Loeb and Northrop, 1916) (paper in which Drosophila was first used in gerontological research), this paper, and many papers subsequently demonstrating this effect in numerous other poikilotherms, essentially attributed the effect to physical effects, viz., a reduction in enzyme and/or metabolic rates. Under the sway of the rate-of-living theory, very few if any subsequent studies actually tested this hypothesis, which was considered so obvious as to not ------------------- Key: 6579 Medline: 15149037 Authors: Huffman DL;Bischof LJ;Griffitts JS;Aroian RV Title: Pore worms: using Caenorhabditis elegans to study how bacterial toxins interact with their target host. Citation: International Journal of Medical Microbiology 293: 599-607 2004 Type: ARTICLE Genes: bre-1 bre-2 bre-3 bre-4 bre-5 Abstract: The interaction of pathogenic bacteria with a target host is regulated both by bacterial virulence factors and by host components that either protect the host or that promote pathogenesis. The soil nematode Caenorbabditis, elegans is a host for a number of bacterial pathogens, as briefly reviewed here. Bacillus thuringiensis (Bt) is a pathogenic bacteria that C. elegans is likely to encounter naturally in the soil. The pore-forming Crystal (Cry) toxins made by Bt are recognized as the dominant virulence factor in this host-pathogen interaction. Forward genetic screens for C. elegans mutants resistant to the Cry toxin, Cry5B, have identified a host carbohydrate structure that promotes pathogenesis. Data suggest this structure is likely to be a Cry5B receptor expressed in the host intestine. This finding is discussed in light of other carbohydrate receptors for bacterial toxins. To investigate host-toxin interactions on a global level, the response of C. elegans to the pore-forming Cry5B is also being investigated by gene transcription profiling (microarrays). These data are beginning to reveal a diverse intracellular response to toxin exposure. To put these investigations in perspective, host responses to other pore-forming toxins are discussed. Investigations with Cry5B in C. elegans show a promising beginning in helping to elucidate host-toxin and host-pathogen interactions. ------------------- Key: 6580 Medline: Authors: Loidl J;Pasierbek P;Rose AM Title: Conservation and variability of meiotic processes - lessons from the unconventional meiosis of C. elegans. Citation: Chromosomes Today 14: 93-101 2004 Type: ARTICLE Genes: Abstract: ------------------- Key: 6581 Medline: 14522246 Authors: Samara C;Tavernarakis N Title: Calcium-dependent and aspartyl proteases in neurodegeneration and ageing in C. elegans. Citation: Ageing Research Reviews 2: 451-471 2004 Type: REVIEW Genes: Abstract: Proteolytic mechanisms have been implicated in the process of ageing, and in many neurodegenerative disorders such as Alzheimer's, Parkinson's and Huntington's diseases, which are most prevalent in old age. Simple model organisms such as the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, which offer the prowess of sophisticated genetic approaches, have contributed to our understanding of ageing and neurodegeneration. Intensive research in these systems has resulted in detailed models of the ageing process, and also of several neurodegenerative diseases, which recapitulate same aspects of the human pathologies. Inappropriate cell death is a major component of these and other devastating conditions such as stroke. The dissection of the molecular mechanisms underlying the process of cell degeneration in ageing is of utmost importance. Evidence from investigations in C. elegans implicates deregulated proteolysis as one major determinant of cellular destruction in neurodegeneration and ageing, and suggests that the process depends critically on the activation of calcium-dependent, calpain proteases and lysosomal aspartyl proteases. Apart from shedding light on important but inadequately understood facets of such phenomena, these discoveries hold promise for developing novel, effective intervention strategies aiming to ameliorate or even counter inappropriate cell ------------------- Key: 6582 Medline: 15180830 Authors: Zahn TR;Angleson JK;MacMorris MA;Domke E;Hutton JH;Schwartz C;Hutton JC Title: Dense core vesicle dynamics in Caenorhabditis elegans neurons and the role of kinesin UNC-104. Citation: Traffic 5: 544-559 2004 Type: ARTICLE Genes: aex-3 cab-1 egl-3 ida-1 rab-3 rme-1 rpm-1 sad-1 snb-1 snt-1 syd-2 unc-11 unc-13 unc-14 unc-31 unc-51 unc-64 unc-104 Abstract: We have developed a model system in Caenorhabditis elegans to perform genetic and molecular analysis of peptidergic neurotransmission using green fluorescent protein (GFP)-tagged IDA-1. IDA-1 represents the nematode ortholog of the transmembrane proteins ICA512 and phogrin that are localized to dense core secretory vesicles (DCVs) of mammalian neuroendocrine tissues. IDA-1::GFP was expressed in a small subset of neurons and present in both axonal and dendritic extensions, where it was localized to small mobile vesicular elements that at the ultrastructural level corresponded to 50 nm electron-dense objects in the neuronal processes. The post-translational processing of IDA-1::GFP in transgenic worms was dependent on the neuropeptide proprotein convertase EGL-3, indicating that the protein was efficiently targeted to the peptidergic secretory pathway. Time-lapse epifluorescence microscopy of IDA-1::GFP revealed that DCVs moved in a saltatory and bidirectional manner. DCV velocity profiles exhibited multiple distinct peaks, suggesting the participation of multiple molecular motors with distinct properties. Differences between velocity profiles for axonal and dendritic processes furthermore suggested a polarized distribution of the molecular transport machinery. Study of a number of candidate mutants identified the kinesin UNC-104 (KIF1A) as the microtubule motor that is specifically responsible for anterograde axonal transport of DCVs at velocities of 1.6 mum/s-2.7 mum/s. ------------------- Key: 6583 Medline: 15064356 Authors: Ono K;Ono S Title: Tropomyosin and troponin are required for ovarian contraction in the Caenorhabditis elegans reproductive system. Citation: Molecular Biology of the Cell 15: 2782-2793 2004 Type: ARTICLE Genes: lev-11 mup-2 pat-10 tmy-1 tnc-1 tnc-2 tni-1 tni-2 tni-3 tni-4 unc-27 unc-60 Abstract: Ovulation in the nematode Caenorhabditis elegans is coordinated by interactions between the somatic gonad and germ cells. Myoepithelial sheath cells of the proximal ovary are smooth muscle-like cells, but the regulatory mechanism of their contraction is unknown. We show that contraction of the ovarian muscle requires tropomyosin and troponin, which are generally major actin-linked regulators of contraction of striated muscle. RNA interference of tropomyosin or troponin C caused sterility by inhibiting ovarian contraction that is required for expelling mature oocytes into the spermatheca where fertilization takes place, thus causing accumulation of endomitotic oocytes in the ovary. Tropomyosin and troponin C were associated with actin filaments in the myoepithelial sheath, and the association of troponin C with actin was dependent on tropomyosin. A mutation in the actin depolymerizing factor/cofilin gene suppressed the ovulation defects by RNA interference of tropomyosin or troponin C. These results strongly suggest that tropomyosin and troponin are the actin-linked regulators for contraction of ovarian muscle in the C. elegans reproductive system. ------------------- Key: 6584 Medline: 15175155 Authors: Kuersten S;Segal SP;Verheyden J;LaMartina SM;Goodwin EB Title: NXF-2, REF-1, and REF-2 affect the choice of nuclear export pathway for tra-2 mRNA in C. elegans. Citation: Molecular Cell 14: 599-610 2004 Type: ARTICLE Genes: nxf-1 nxf-2 ref-1 ref-2 ref-3 tra-1 tra-2 Abstract: In C. elegans, tra-2 mRNA nuclear export is controlled by a 3'UTR element, the TRE. In the absence of TRA-1, the TRE retains tra-2 mRNA in the nucleus. The binding of TRA-1 to the XUTR overcomes this retention resulting in export of a TRA-1/tra-2 mRNA complex. Here, we find that, unlike most mRNAs, tra-2 mRNA exits the nucleus via an alternative pathway to NXF-1 that requires CRM1 activity. Inhibition of export by NXF-1 depends upon the TRE, CeNXF-2, CeREF-1, and CeREF-2. Removal of the TRE or any one of these factors results in export of tra-2 by NXF-1. NXF-2 and REF-1 specifically bind the TRE, suggesting that they directly control tra-2 mRNA export. Furthermore, choice of proper export pathway affects tra-2 translational control. Therefore, tra-2 mRNA export is highly regulated and plays an important role in development by regulating the activity of tra-2 mRNA in the cytoplasm. ------------------- Key: 6585 Medline: 15153179 Authors: Golden TR;Melov S Title: Microarray analysis of gene expression with age in individual nematodes. Citation: Aging Cell 3: 111-124 2004 Type: ARTICLE Genes: Abstract: We compare the aging of wild-type and long-lived C. elegans by gene expression profiling of individual nematodes. Using a custom cDNA array, we have characterized the gene expression of 4-5 individuals at 4 distinct ages throughout the adult lifespan of wild-type N2 nematodes, and at the same ages for individuals of the long-lived strain daf-2(e1370). Using statistical tools developed for microarray data analysis, we identify genes that differentiate aging N2 from aging daf-2, as well as classes of genes that change with age in a similar way in both genotypes. Our novel approach of studying individual nematodes provides practical advantages, since it obviates the use of mutants or drugs to block reproduction, as well as the use of stressful mass-culturing procedures, that have been required for previous microarray studies of C. elegans. In addition, this approach has the potential to uncover the molecular variability between individuals of a population, variation that is missed when studying pools of thousands of individuals. ------------------- Key: 6586 Medline: 15183729 Authors: Portman DS;Emmons SW Title: Identification of C. elegans sensory ray genes using whole-genome expression profiling. Citation: Developmental Biology 270: 499-512 2004 Type: ARTICLE Genes: cat-2 ceh-43 ces-2 cwp-1 cwp-2 cwp-3 cwp-4 dat-1 egl-2 egl-46 hlh-4 hlh-10 lin-22 lin-32 lov-1 pkd-2 ram-5 spt-3 srd-1 srj-10 srw-22 srw-85 srw-140 str-64 tbb-4 tph-1 twk-9 twk-21 Abstract: The three cells that comprise each C. elegans sensory ray (two sensory neurons and a structural cell) descend from a single neuroblast precursor cell. The atonal ortholog lin-32 and the E/daughterless otholog hlh-2 act to confer neural competence during ray development, but additional regulatory factors that control specific aspects of cell fate are largely unknown. Here, we use full-genome DNA microarrays to compare gene expression profiles in adult males Of two Mutant strains to identify new components of the regulatory network that controls ray development and function. This approach identified a large set of candidate ray genes. Using reporter genes, we confirmed ray expression for 13 of these, including a beta-tubulin, a TWK-family channel, a putative chemoreceptor and four novel genes (the cwp genes) with a potential role in sensory signaling through the C. elegans polycystins lov-1 and pk-d-2. Additionally, we have found several ray-expressed transcription factors, including the Zn-finger factor egl-46 and the bHLH gene hlh-10. The expression of many of these genes requires lin-32 function, though this requirement may not reflect direct activation by lin-32. Our strategy provides a complementary foundation for modeling the genetic network that controls the development ------------------- Key: 6587 Medline: 15166144 Authors: Solomon A;Bandhakavi S;Jabbar S;Shah R;Beitel GJ;Morimoto Title: Caenorhabditis elegans OSR-1 regulates behavioral and physiological responses to hyperosmotic environments. Citation: Genetics 167: 161-170 2004 Type: ARTICLE Genes: age-1 daf-16 jnk-1 nsy-1 ocr-2 osm-9 osm-10 osr-1 osr-2 osr-3 osr-4 pmk-1 sek-1 unc-43 Abstract: The molecular mechanisms that enable multicellular organisms to sense and modulate their responses to hyperosmotic environments are poorly understood. Here, we employ Caenorhabditis elegans to characterize the response of a multicellular organism to osmotic stress and establish a genetic screen to isolate mutants that are osmotic stress resistant (OSR). In this study, we describe the cloning of a novel gene, osr-1, and demonstrate that it regulates osmosensation, adaptation, and survival in hyperosmotic environments. Whereas wild-type animals exposed to hyperosmotic conditions rapidly lose body volume, motility, and viability, osr-1(rm1) mutant animals maintain normal body volume, motility, and viability even upon chronic exposures to high osmolarity environments. In addition, osr-1(rm1) animals are specifically resistant to osmotic stress and are distinct from previously characterized osmotic avoidance defective (OSM) and general stress resistance age-1(hx546) mutants. OSR-1 is expressed in the hypodermis and intestine, and expression of OSR-1 in hypodermal cells rescues the osr-1(rm1) phenotypes. Genetic epistasis analysis indicates that OSR-1 regulates survival under osmotic stress via CaMKII and a conserved p38 MAP kinase signaling cascade and regulates osmotic avoidance and resistance to acute dehydration likely by distinct mechanisms. We suggest that OSR-1 plays a central role in integrating stress detection and adaptation responses by invoking multiple signaling pathways to promote survival under hyperosmotic environments. ------------------- Key: 6588 Medline: Authors: Beaster-Jones L;Okkema PG Title: DNA binding and in vivo function of C. elegans PEB-1 require a conserved FLYWCH motif. Citation: Journal of Molecular Biology 339: 695-706 2004 Type: ARTICLE Genes: peb-1 Abstract: Caenorhabditis elegans PEB-1 is a novel protein containing a DNA-binding domain in its N terminus, which includes a Cys/His-rich FLYWCH motif also found in Drosophila Mod(mdg4) proteins, and a large C-terminal domain of unknown function. PEB-1 is expressed in most pharyngeal cell types, but its molecular function remains unclear. Here we describe comparative and functional analyses of PEB-1. Characterization of the PEB-1 sequence from C. briggsae indicates highest conservation in the DNA-binding domain (including the FLYWCH motif) and the C terminus, suggesting two functional domains. The PEB-1 FLYWCH motif is essential for DNA-binding and in vivo function; however, it does not bind detectable metal. Likewise, the PEB-1 C terminus is necessary for full activity in vivo, although the DNA-binding domain alone is sufficient for partial function. Both the FLYWCH motif and the C-terminal domain are required for efficient nuclear localization, suggesting PEB-1 must bind DNA and other components to remain in the nucleus. Analysis of binding sites revealed a YDTGCCRW PEB-1 consensus-binding site, and matches to this consensus are widespread in the C. elegans genome. ------------------- Key: 6589 Medline: 15135065 Authors: Banyai L;Patthy L Title: Evidence that human genes of modular proteins have retained significantly more ancestral introns than their fly or worm orthologues. Citation: FEBS Letters 565: 127-132 2004 Type: ARTICLE Genes: Abstract: Comparison of the exon-intron structures of human, fly and worm orthologues of mosaic genes assembled from class 1-1 modules by exon-shuffling has revealed that human genes retained significantly more of the original inter-module introns than their protostome orthologues. It is suggested that the much higher rate of intron loss in the worm- and insect lineages than in the chordate lineage reflects their greater tendency for genome compaction. ------------------- Key: 6590 Medline: Authors: Yu HY;Luscombe NM;Lu HX;Zhu XW;Xia Y;Han JDJ;Bertin N;Chung S;Vidal M;Gerstein M Title: Annotation transfer between genomes: protein-protein interlogs and protein-DNA regulogs. Citation: Genome Research 14: 1107-1118 2004 Type: ARTICLE Genes: Abstract: Proteins function mainly through interactions, especially with DNA and other proteins. While some large-scale interaction networks are now available for a number of model organisms, their experimental generation remains difficult. Consequently, interolog mapping-the transfer of interaction annotation from one organism to another using comparative genomics-is of significant value. Here we quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins. Using interaction information from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Helicobacter pylori, we find that protein-protein interactions can be transferred when a pair of proteins has a joint sequence identity >80% or a joint E-value <10(-70). (These "joint" quantities are the geometric means of the identities or E-values for the two pairs of interacting proteins.) We generalize Our interolog analysis to protein-DNA binding, finding such interactions are conserved at specific thresholds between 30% and 60% Sequence identity depending oil the protein family. Furthermore, we introduce the concept of a "regulog"-a conserved regulatory relationship between proteins across different species. We map interologs and regulogs from yeast to a number of genomes with limited experimental annotation (e.g., Arabidopsis thaliana) and make these available through ail online database at http://interolog.gersteinlab.org. Specifically, we are able to transfer -90,000 potential protein-protein interactions to the worm. We test a number of these in two-hybrid experiments and are able to verify 45 overlaps, which we ------------------- Key: 6591 Medline: 15230964 Authors: Wang X;Greenberg JF;Chamberlin HM Title: Evolution of regulatory elements producing a conserved gene expression pattern in Caenorhabditis. Citation: Evolution & Development 6: 237-245 2004 Type: ARTICLE Genes: egl-38 lin-48 pax-2 Abstract: Natural selection acts at the level of function, not at the logistical level of how organisms achieve a particular function. Consequently, significant DNA sequence and regulatory differences can achieve the same function, such as a particular gene expression pattern. To investigate how regulatory features underlying a conserved function can evolve, we compared the regulation of a conserved gene expression pattern in the related species Caenorhabditis elegans and C. briggsae. We find that both C. elegans and C. briggsae express the ovo-related zinc finger gene lin-48 in the same pattern in hindgut cells. However, the regulation of this gene by the Pax-2/5/8 protein EGL-38 differs in two important ways. First, specific differences in the regulatory sequences of lin-48 result in the presence of two redundant EGL-38 response elements in C. elegans, whereas the redundancy is absent in C. briggsae. Second, there is a single egl-38 gene in C. briggsae. In contrast, the gene is duplicated in C. elegans, with only one copy retaining the ability to regulate lin-48 in vivo. These results illustrate molecular changes that can occur despite maintenance of conserved gene function in different ------------------- Key: 6592 Medline: 15138003 Authors: MacDonald D;VanCrey K;Harrison P;Rangachari PK;Rosenfeld J;Warren C;Sorger G Title: Ascaridole-less infusions of Chenopodium ambrosioides contain a nematocide(s) that is(are) not toxic to mammalian smooth muscle. Citation: Journal of Ethnopharmacology 92: 214-221 2004 Type: ARTICLE Genes: Abstract: Infusions of Chenopodium ambrosioides (L.) have been used for centuries in the Americas as a popular remedy against intestinal worm infections. The essential oil of Chenopodium ambrosioides contains high levels of ascaridole, which is a potent anthelmintic, but which has also been responsible for human fatalities, leading to its disuse. Almost 90% of the nematocidal activity of Chenopodium ambrosioides infusions was due to a hydrophilic component different from ascaridole. Synthetic ascaridole and the ascaridole from infusions, extracted into hexane, caused a reduction of carbachol-induced contractions in rat gastrointestinal smooth muscle at concentrations required to kill Caenorhabditis elegans (L.). The herbal infusion and the ascaridole-free hexane-extracted aqueous residue of the above infusion, at nematocidal concentrations, had no detectable effect on smooth muscle contraction in the above system. It would appear that the traditional form of usage of Chenopodium ambrosioides infusions as a vermifuge is safer than the use of the herb's essential oil. ------------------- Key: 6593 Medline: 15159532 Authors: Nagele P;Metz LB;Crowder CM Title: Nitrous oxide (N2O) requires the N-methyl-D-aspartate receptor for its action in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 101: 8791-8796 2004 Type: ARTICLE Genes: glr-1 nmr-1 Abstract: Nitrous oxide (N2O, also known as laughing gas) and volatile anesthetics (VAs), the original and still most widely used general anesthetics, produce anesthesia by ill-defined mechanisms. Electrophysiological experiments in vertebrate neurons have suggested that N2O and VAs may act by distinct mechanisms; N2O antagonizes the N-methyl-D-aspartate (NMDA) subtype of glutamate receptors, whereas VAs alter the function of a variety of other synaptic proteins. However, no genetic or pharmacological experiments have demonstrated that any of these in vitro actions are responsible for the behavioral effects of either class of anesthetics. By using genetic tools in Caenorhabditis elegans, we tested whether the action of N2O requires the NMDA receptor in vivo and whether its mechanism is shared by VAs. Distinct from the action of VAs, N2O produced behavioral defects highly specific and characteristic of that produced by loss-of-function mutations in both NMIDA and non-NMDA glutamate receptors. A null mutant of nmr-1, which encodes a C elegans NMDA receptor, was completely resistant to the behavioral effects of N2O, whereas a non-NMDA receptor-null mutant was normally sensitive. The N2O-resistant nmr-1(null) mutant was not resistant to VAs. Likewise, VA-resistant mutants had wild-type sensitivity to N2O. Thus, the behavioral effects of N2O require the NMDA receptor NMR-1, consistent with the hypothesis formed from vertebrate electrophysiological data that a major target of N2O is the ------------------- Key: 6594 Medline: 15184665 Authors: Nystul TG;Roth MB Title: Carbon monoxide-induced suspended animation protects against hypoxic damage in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 101: 9133-9136 2004 Type: ARTICLE Genes: hif-1 Abstract: Oxygen deprivation is a major cause of cellular damage and death. Here we demonstrate that Caenorhabditis elegans embryos, which can survive both in anoxia (< 0.001 kPa O-2) by entering into suspended animation and in mild hypoxia (0.25-1 kPa O-2) through a hypoxia-inducible factor 1-mediated response, cannot survive in intermediate concentrations of oxygen, between 0.01 and 0.1 kPa O-2. Moreover, we show that carbon monoxide can protect C. elegans embryos against hypoxic damage in this sensitive range. Carbon monoxide can also rescue the hypoxia-sensitive mutant hif-1(ia04) from lethality in hypoxia. This work defines the oxygen tensions over which hypoxic damage occurs in C. elegans embryos and demonstrates that carbon monoxide can prevent this damage ------------------- Key: 6595 Medline: 15020702 Authors: Jospin M;Mariol MC;Segalat L;Allard B Title: Patch clamp study of the UNC-105 degenerin and its interaction with the LET-2 collagen in Caenorhabditis elegans muscle. Citation: Journal of Physiology 557: 379-388 2004 Type: ARTICLE Genes: let-2 unc-105 Abstract: Degenerins have emerged from genetic studies in Caenorhabditis elegans as candidate mechanically gated amiloride-sensitive ion channels for transducing mechanical stimuli into cellular responses. In C elegans muscle, the existence of a genetic interaction between the unc-105 degenerin gene and let-2, a gene encoding an alpha2(IV) collagen, raised the possibility that UNC-105 may function as a mechanically gated channel in a stretch receptor complex. However, to date, ion channel activity of UNC- 105 has only been recorded in a gain-of-function mutant form in heterologous expression systems. In this study we investigated the in situ properties of UNC-105 using the whole cell configuration of the patch clamp technique on body wall muscle cells from acutely dissected C. elegans. Amiloride was found to be without effect on membrane potential of wild-type muscle cells, suggesting that the UNC-105 degenerin is electrically silent in resting muscle. Hypo-osmotic shocks induced a reversible depolarization of muscle cells but which was not affected by amiloride. Deformation of the cells by applying tension to the filamentous complex on which muscle cells remained attached or by ejecting external solution under pressure failed to induce any change of membrane potential. In gain-of-function unc-105(n506) mutant cells, an amiloride-sensitive inward Na+ current was found to be constitutively active, leading to maintained muscle depolarization. An associated mutation in the alpha2 (IV) collagen LET-2 led to the closure of the mutant UNC-105 (n506) channel while a collagenase treatment of these double mutant cells caused it to re-open, giving evidence for a functional interaction between LET-2 collagen and ------------------- Key: 6596 Medline: 15182666 Authors: Portereiko MF;Saam J;Mango SE Title: ZEN-4/MKLP1 is required to polarize the foregut epithelium. Citation: Current Biology 14: 932-941 2004 Type: ARTICLE Genes: ajm-1 cdh-3 cyk-4 dhc-1 hmr-1 let-413 pha-4 unc-70 zen-4 Abstract: Background: Epithelial tubes are a key component of organs and are generated from cells with distinct apicobasolateral polarity. Here, we describe a novel function during tubulogenesis for ZEN-4, the Caenorhabditis elegans ortholog of mitotic kinesin-like protein 1 (MKLP1), and CYK-4, which contains a RhoGAP (GTPase-activating protein) domain. Previous studies revealed that these proteins comprise centralspindlin (a complex that functions during mitosis to bundle microtubules), construct the spindle midzone, and complete cytokinesis. Results: Our analyses demonstrate that ZEN-4/MKLP1 functions postmitotically to establish the foregut epithelium. Mutants that lack ZEN-4/MKLP1 express polarity markers but fail to target these proteins appropriately to the cell cortex. Affected proteins include PAR-3/Bazooka and PKC-3/atypical protein kinase C at the apical membrane domain, and HMR-1/cadherin and AJM-1 within C. elegans apical junctions (CeAJ). Microtubules and actin are disorganized in zen-4 mutants compared to the wild-type. Conclusion: We suggest that ZEN-4/MKLP1 and CYK-4/RhoGAP regulate an early step in epithelial polarization that is required to establish the ------------------- Key: 6597 Medline: 15182677 Authors: Tenor JL;McCormick BA;Ausubel FM;Aballay A Title: Caenorhabditis elegans-based screen identifies Salmonella virulence factors required for conserved host-pathogen interactions. Citation: Current Biology 14: 1018-1024 2004 Type: ARTICLE Genes: ced-10 mtl-2 pmk-1 Abstract: A Caenorhabditis elegans-Salmonella enterica host-pathogen model was used to identify both novel and previously known S. enterica virulence factors (HilA, HilD, InvH, SptP, RhuM, Spi4-F, PipA, VsdA, RepC, Sb25, RfaL, GmhA, LeuO, CstA, and RecC), including several related to the type III secretion system (TTSS) encoded in Salmonella pathogenicity island 1 (SPI-1). Mutants corresponding to presumptive novel virulence-related genes exhibited diminished ability to invade epithelial cells and/or to induce polymorphonuclear leukocyte migration in a tissue culture model of mammalian enteropathogenesis. When expressed in C. elegans intestinal cells, the S. enterica TTSS-exported effector protein SptP inhibited a conserved p38 MAPK signaling pathway and suppressed the diminished pathogenicity phenotype of an S. enterica sptP mutant. These results show that C. elegans is an attractive model to study the interaction between Salmonella effector proteins and components of the innate immune response, in part because there is a remarkable overlap between Salmonella virulence factors required for human and ------------------- Key: 6598 Medline: Authors: Biondi N;Piccardi R;Margheri MC;Rodolfi L;Smith GD;Tredici MR Title: Evaluation of Nostoc strain ATCC 53789 as a potential source of natural pesticides. Citation: Applied and Environmental Microbiology 70: 3313-3320 2004 Type: ARTICLE Genes: Abstract: The cyanobacterium Nostoc strain ATCC 53789, a known cryptophycin producer, was tested for its potential as a source of natural pesticides. The antibacterial, antifungal, insecticidal, nematocidal, and cytotoxic activities of methanolic extracts of the cyanobacterium were evaluated. Among the target organisms, nine fungi (Armillaria sp., Fusarium oxysporum f. sp. melonis, Penicillium expansum, Phytophthora cambivora, P. cinnamomi, Rhizoctonia solani, Rosellinia, sp., Sclerotinia sclerotiorum, and Verticillium albo-atrum) were growth inhibited and one insect (Helicoverpa armigera) was killed by the extract, as well as the two model organisms for nematocidal (Caenorhabditis elegans) and cytotoxic (Artemia salina) activity. No antibacterial activity was detected. The antifungal activity against S. sclerotiorum was further studied with both extracts and biomass of the cyanobacterium in a system involving tomato as a host plant. Finally, the herbicidal activity of Nostoc strain ATCC 53789 was evaluated against a grass mixture. To fully exploit the potential of this cyanobacterium in agriculture as a source of pesticides, suitable application methods to overcome its toxicity toward plants and nontarget organisms ------------------- Key: 6599 Medline: 15128663 Authors: Hobert O;Hutter H;Hynes RO Title: The immunoglobulin superfamily in Caenorhabditis elegans and Drosophila melanogaster. Citation: Development 131: 2237-2238 2004 Type: REVIEW Genes: unc-52 unc-73 unc-89 zig-2 zig-3 zig-4 zig-5 zig-6 zig-7 zig-8 Abstract: A recent report by Vogel et al. describes a bioinformatic analysis of immunoglobulin superfamily (IgSF) members in Caenorhabditis elegans and Drosophila melanogaster (Vogel et al., 2003). We have previously published reports presenting genome-sequence-driven analyses of worm and fly IgSF members (Hutter et al., 2000; Hynes and Zhao, 2000; Aurelio et al., 2002). In Vogel et al. (Vogel et al., 2003), these papers are either not cited (Hynes and Zhao, 2000; Aurelio et al., 2002) or their content is essentially ignored (Hutter et al., 2000), although they cover much of the same ground as the Vogel et al. paper. Furthermore, the Vogel et al. paper contains errors and misclassifications of IgSF family members. Given the high degree of interest in this superfamily, we wish to correct the errors and clarify any misconceptions caused by the conflation of structural features with functional ------------------- Key: 6600 Medline: Authors: Vogel C;Teichmann A;Chothia C Title: Response: Looking at the bigger picture. Citation: Development 131: 2238-2240 2004 Type: REVIEW Genes: unc-73 unc-89 zig-2 zig-3 zig-4 zig-5 zig-6 zig-7 zig-8 Abstract: Hobert et al. (Hobert et al., 2004) have made a number of criticisms on our paper (Vogel et al., 2003). In the following paragraphs we give our replies to these criticisms. In a number of cases, the comments do provide useful corrections to the paper. Nevertheless, the major conclusions of our paper are not affected by these corrections and they remain both novel and valid. ------------------- Key: 6601 Medline: 15102704 Authors: Pocock R;Ahringer J;Mitsch M;Maxwell S;Woollard A Title: A regulatory network of T-box genes and the even-skipped homologue vab-7 controls patterning and morphogenesis in C. elegans. Citation: Development 131: 2373-2385 2004 Type: ARTICLE Genes: ajm-1 hlh-1 hsp-16-2 hsp-16-4 mab-9 mls-1 myo-3 pal-1 rrf-3 tbx-2 tbx-7 tbx-8 tbx-9 tbx-11 tbx-18 tbx-30 tbx-31 tbx-32 tbx-33 tbx-34 tbx-35 tbx-36 tbx-37 tbx-38 tbx-39 tbx-40 tbx-41 vab-7 Abstract: T-box genes form a large family of conserved transcription factors with diverse roles in animal development, but so far functions for only a few have been studied in detail. Here we show that four Caenorhabditis elegans T-box genes and the even-skipped-like homeobox gene vab-7 function within a regulatory network to control embryonic patterning and morphogenesis. tbx-8 and tbx-9 have functionally redundant roles in the intercalation of posterior dorsal hypodermal cells, in muscle cell positioning and in intestinal development. Inhibiting tbx-9 alone using RNA interference (RNAi) produces worms that have a thickened, 'bobbed tail' phenotype, similar to that seen in mutants of vab-7, which itself has been shown to pattern posterior muscle and hypodermal cells. In support of the view that these genes function in the same pathway, we find that tbx-8 and tbx-9 are both necessary and sufficient for vab-7 expression. In addition, a third T-box gene, tbx-30, acts to repress vab-7 expression in the anterior of embryos. We further show that vab-7 itself represses the T-box gene mab-9 in posterior cells. Thus, during posterior patterning in C elegans, there are multiple interactions between T-box genes and the vab-7 homeobox gene. Evolutionary parallels in other organisms suggest that regulatory interactions between T-box genes and even-skipped homologues are ------------------- Key: 6602 Medline: 15232111 Authors: Chang C;Yu TW;Bargmann CI;Tessier-Lavigne M Title: Inhibition of netrin-mediated axon attraction by a receptor protein tyrosine phosphatase. Citation: Science 305: 103-106 2004 Type: ARTICLE Genes: ced-10 clr-1 mec-4 mec-7 odr-1 sax-3 slt-1 unc-6 unc-34 unc-40 Abstract: During axon guidance, the ventral guidance of the Caenorhabditis elegans anterior ventral microtubule axon is controlled by two cues, the UNC-6/ netrin attractant recognized by the UNC-40/DCC receptor and the SLT-1/slit repellent recognized by the SAX-3/robo receptor. We show here that loss-of-function mutations in clr-1 enhance netrin-dependent attraction, suppressing ventral guidance defects in slt-1 mutants. clr-1 encodes a transmembrane receptor protein tyrosine phosphatase ( RPTP) that functions in AVM to inhibit signaling through the DCC family receptor UNC-40 and its effector, UNC-34/enabled. The known effects of other RPTPs in axon guidance could result from modulation of guidance receptors like ------------------- Key: 6603 Medline: Authors: Ishii N Title: Life span and oxidative stress in nematode. Citation: Journal of Clinical Biochemistry and Nutrition 34: 61-68 2003 Type: REVIEW Genes: flp-1 flp-2 flp-3 flp-4 flp-5 flp-6 flp-7 flp-8 flp-9 flp-10 flp-11 flp-12 flp-13 flp-14 flp-15 flp-16 flp-17 flp-18 flp-19 flp-20 flp-21 flp-22 flp-23 gcy-7 mec-3 ttx-3 unc-47 unc-86 Abstract: ------------------- Key: 6604 Medline: 15236235 Authors: Kim K;Li C Title: Expression and regulation of an FMRFamide-related neuropeptide gene family in Caenorhabditis elegans. Citation: Journal of Comparative Neurology 475: 540-550 2004 Type: ARTICLE Genes: Abstract: FMRFamide (Phe-Met-Arg-Phe-NH2) and related peptides (FaRPs) have been found throughout the animal kingdom, where they are involved in many behaviors. We previously identified 22 genes comprising the flp gene family that encodes FaRPs in Caenorhabditis elegans; in this paper we report the identification of another flp gene, flp-23. As a first step toward determining their functional roles in C. elegans, we examined the cell-specific expression pattern of the flp gene family. Of the 19 flp genes examined, each gene is expressed in a distinct set of cells; these cells include interneurons, motor neurons, and sensory neurons that are involved in multiple behaviors, as well as supporting cells, muscle cells, and epidermal cells. Several flp genes show sex-specific expression patterns. Furthermore, we find that expression of two flp genes changes in response to the developmental state of the animal. Many neurons express multiple flp genes. To investigate how flp genes are regulated in different neuronal subtypes, we examined flp expression in a small, well-defined subset of neurons, the mechanosensory neurons. Mutations in the unc-86 and mec-3 genes, which are necessary for the production and differentiation of the mechanosensory neurons, result in the complete loss of flp-4, flp-8, and flp-20 expression in mechanosensory neurons. Collectively, these data indicate that members of the flp gene family are likely to influence multiple behaviors and that their regulation can be dependent on the ------------------- Key: 6605 Medline: 15035988 Authors: Shen K;Fetter RD;Bargmann CI Title: Synaptic specificity is generated by the synaptic guidepost protein SYG-2 and its receptor, SYG-1. Citation: Cell 117: 553- 2004 Type: CORRECT Genes: syg-1 syg-2 Abstract: We regret that a table printed in this article (Cell 116, 869-881, 19 March 2004) was missing some information. The corrected table is printed below. ------------------- Key: 6606 Medline: Authors: Sawarkar R Title: A gene involved in nematode feeding behavior. Citation: Journal of Biosciences 29: 3-5 204 Type: REVIEW Genes: flp-18 flp-21 npr-1 Abstract: Recent studies on feeding behaviour in the soil nematode Caenorhabditis elegans provide a striking illustration of how genetic and environmental influences together mould complex behaviour. ------------------- Key: 6607 Medline: 15166316 Authors: Skop AR;Liu H;Yates J;Meyer BJ;Heald R Title: Dissection of the mammalian midbody proteome reveals conserved cytokinesis mechanisms. Citation: Science 305: 61-66 2004 Type: ARTICLE Genes: Abstract: Cytokinesis is the essential process that partitions cellular contents into daughter cells. To identify and characterize cytokinesis proteins rapidly, we used a functional proteomic and comparative genomic strategy. Midbodies were isolated from mammalian cells, proteins were identified by multidimensional protein identification technology ( MudPIT), and protein function was assessed in Caenorhabditis elegans. Of 172 homologs disrupted by RNA interference, 58% displayed defects in cleavage furrow formation or completion, or germline cytokinesis. Functional dissection of the midbody demonstrated the importance of lipid rafts and vesicle trafficking pathways in cytokinesis, and the utilization of common membrane cytoskeletal components in diverse morphogenetic events in the cleavage furrow, the germline, and neurons. ------------------- Key: 6608 Medline: 15054140 Authors: Eraly SA;Monte JC;Nigam SK Title: Novel slc22 transporter homolgs in fly, worm, and human clarify the phylogeny of organic anion and cation transporters. Citation: Physiological Genomics 18: 12-24 2004 Type: ARTICLE Genes: Abstract: Slc22 family organic anion and cation transporters (OATs, OCTs, and OCTNs) are transmembrane proteins expressed predominantly in kidney and liver. These proteins mediate the uptake or excretion of numerous physiologically (and pharmacologically) important compounds, and accordingly have been the focus of intensive study. Here we investigate the molecular phylogeny of the slc22 transporters, identifying homologs in Drosophila and C. elegans, several of which are developmentally regulated, as well as reporting the cloning of a novel human family member, UST6, expressed exclusively in liver in both embryo and adult. The latter helps define a subfamily within the OATs, which appears to have human- and rodent-specific members, raising potential issues with respect to the use of rodents as models for the transport of organic anions ( which include many pharmaceuticals) in humans. Although this phylogenetic inference could not be made on the basis of sequence alignment, analysis of intron phasing suggests that the OAT, OCT, and OCTN lineages of the slc22 family formed after the divergence of vertebrates and invertebrates. Subsequently, these lineages expanded through independent tandem duplications to produce multiple gene pairs. After analyzing over 200 other transporter genes, we find such pairing to be relatively specific to vertebrate organic anion and cation transporters, suggesting selection for gene pairing operating within this family in particular. This might reflect a requirement for redundancy or broader substrate specificity in vertebrates (compared to invertebrates), due to their greater physiological complexity and thus potentially broader exposure to organic ------------------- Key: 6609 Medline: 15200961 Authors: Zhang H;Christoforou A;Aravind L;Emmons SW;van den Heuvel S;Haber DA Title: The C. elegans Polycomb gene sop-2 encodes an RNA binding protein. Citation: Molecular Cell 14: 841-847 2004 Type: ARTICLE Genes: alg-1 alg-2 dcr-1 drh-1 ego-1 mut-7 rde-1 rde-2 rde-4 sop-2 Abstract: Epigenetic silencing of Hox cluster genes by Polycomb group (PcG) proteins is thought to involve the formation of a stably inherited repressive chromatin structure. Here we show that the C. elegans-specific PcG protein SOP-2 directly binds to RNA through three nonoverlapping regions, each of which is essential for its localization to characteristic nuclear bodies and for its in vivo function in the repression of Hox genes. Functional studies indicate that the RNA involved in SOP-2 binding is distinct from either siRNA or microRNA. Remarkably, the vertebrate PcG protein Rae28, which is functionally and structurally related to SOP-2, also binds to RNA through an FCS finger domain. Substitution of the Rae28 FCS finger for the essential RNA binding region of SOP-2 partially restores localization to nuclear bodies. These observations suggest that direct binding to RNA is an evolutionarily conserved and potentially important property of PcG proteins. ------------------- Key: 6610 Medline: 15178131 Authors: Hartman P;Ponder R;Lo HH;Ishii N Title: Mitochondrial oxidative stress can lead to nuclear hypermutability. Citation: Mechansisms of Ageing & Development 125: 417-420 2004 Type: ARTICLE Genes: fem-3 mev-1 Abstract: Reactive oxygen species (ROS) are generated in mitochondria and are thought to be important in aging, carcinogenesis, and the development of other pathologies. We now provide direct experimental evidence linking mitochondrial ROS generation to the induction of nuclear DNA damage and subsequent mutagenesis of a chromosomal gene. Specifically, we demonstrate that the mev-1 mutant of Caenorhabditis elegans has elevated levels of oxidative damage in its chromosomal DNA. This mutant was shown previously to overproduce ROS in its mitochondria. We also show that mutation frequencies were higher in the mev-1 mutant under hypoxia than in the wild type strain. By extension. these data imply that mitochondrially derived ROS mutate other genes, including tumor suppressor genes and oncogenes. We propose that this three-step process (mitochondrial ROS --> nuclear DNA damage --> mutation) contributes to aging and age-associated diseases. ------------------- Key: 6611 Medline: 15178135 Authors: Kayser EB;Sedensky MM;Morgan PG Title: The effects of complex I function and oxidative damage on lifespan and anesthetic sensitivity in Caenorhabditis elegans. Citation: Mechanisms of Ageing & Development 125: 455-464 2004 Type: ARTICLE Genes: clk-1 gas-1 mev-1 seg-1 seg-2 Abstract: A mutation in a subunit of complex 1 of the mitochondrial electron transport chain (gas-1) causes Caenorhabditis elegans to be hypersensitive to volatile anesthetics and oxygen as well as shortening lifespan. We hypothesized that changes in mitochondrial respiration or reactive oxygen species production cause these changes. Therefore, we compared gas-1 to other mitochondrial mutants to identify the relative importance of these two aspects of mitochondrial function in determining longevity. Lifespans of gas-1 and mev-1 were decreased compared with N2, while that of clk-1 was increased. Rates of oxidative phosphorylation were decreased in all three mutants, but the ROS damage was decreased only in clk-1. Suppressors of gas-1 increased rates of oxidative phosphorylation, decreased oxidative damage to mitochondrial proteins and increased lifespan. Two strains containing combinations of mutations predicted to have very decreased complex I function, had unexpectedly Iona lifespans. We conclude that mitochondrial changes in lifespan appear to be mediated primarily by changes in oxidative damage rather than by changes in rates of oxidative phosphorylation. In contrast, the effects of mitochondrial changes on anesthetic sensitivity appear to be mediated by both altered ------------------- Key: 6612 Medline: 15209660 Authors: Fisher AL Title: Of worms and women: Sarcopenia and its role in disability and mortality. Citation: Journal of the American Geriatrics Society 52: 1185-1190 2004 Type: ARTICLE Genes: age-1 daf-2 Abstract: The loss of muscle mass during aging has been termed sarcopenia. Sarcopenia results in a decrease in physical strength during aging that results in important consequences for more severely affected individuals in terms of function and as a marker for disability and increased mortality. Despite the clinical importance of this condition, the pathophysiology leading to the development of sarcopenia is not well understood, and few treatments exist to prevent or reverse the condition. Recently, sarcopenia has been found to occur during aging in the nematode Caenorhabditis elegans, which is an organism increasingly used to study genetic and biochemical events involved in aging. Like in humans, sarcopenia in C. elegans leads to declines in mobility and serves as a marker for increased mortality. Interestingly, mutations affecting the age-1 gene, which slows aging of the animal, result in significant delays in the development of sarcopenia, suggesting a direct causal relationship between organismal aging and sarcopenia. These findings suggest that, in humans and worms, sarcopenia may represent a biomarker for the biological age, as opposed to chronological age, of the individual. These findings also suggest that C. elegans will develop into an important model system in which to study the biochemical and genetics events responsible for sarcopenia and to test therapeutics ------------------- Key: 6613 Medline: 15115755 Authors: Lee SJ;Yook JS;Han SM;Koo HS Title: A Werner syndrome protein homolog affects C. elegans development, growth rate, life span and sensitivity to DNA damage by acting at a DNA damage checkpoint. Citation: Development 131: 2565-2575 2004 Type: ARTICLE Genes: chk-1 div-1 wrn-1 Abstract: A Werner syndrome protein homolog in C. elegans (WRN-1) was immunolocalized to the nuclei of germ cells, embryonic cells, and many other cells of larval and adult worms. When wrn-1 expression was inhibited by RNA interference (RNAi), a slight reduction in C elegans life span was observed, with accompanying signs of premature aging, such as earlier accumulation of lipofuscin and tissue deterioration in the head. In addition, various developmental defects, including small, dumpy, ruptured, transparent body, growth arrest and bag of worms, were induced by RNAi. The frequency of these defects was accentuated by gamma-irradiation, implying that they were derived from spontaneous or induced DNA damage. wrn-1(RNAi) worms showed accelerated larval growth irrespective of gamma-irradiation, and pre-meiotic germ cells had an abnormal checkpoint response to DNA replication blockage. These observations suggest that WRN-1 acts as a checkpoint protein for DNA damage and replication blockage. This idea is also supported by an accelerated S phase in wrn-1(RNAi) embryonic cells. wrn-1(RNAi) phenotypes similar to those of Werner syndrome, such as premature aging and short stature, suggest wrn-1-deficient C. elegans as a useful model organism for Werner syndrome. ------------------- Key: 6614 Medline: 15115754 Authors: Huang P;Stern MJ Title: FGF signaling functions in the hypodermis to regulate fluid balance in C. elegans. Citation: Development 131: 2595-2604 2004 Type: ARTICLE Genes: clr-1 egl-15 let-756 mpk-1 snb-1 soc-2 unc-14 sDp3 Abstract: Signaling by the Caenorhabditis elegans fibroblast growth factor receptor EGL-15 is activated by LET-756, a fibroblast growth factor, and attenuated by CLR-1, a receptor tyrosine phosphatase. Hyperactive EGL-15 signaling results in a dramatic or phenotype characterized by the accumulation of clear fluid within the pseudocoelomic space, suggesting that regulated EGL-15 signaling is essential for fluid homeostasis in C. elegans. To determine the cellular focus of EGL-15 signaling, we identified an enhancer element (e15) within the egl-15 promoter, which is both necessary for the promoter activity and sufficient when duplicated to drive either egl-15 or clr-1 rescue activity. This enhancer drives GFP expression in hypodermal cells. Consistent with this finding, immunofluorescence studies of EGL-15 indicate that EGL-15 is expressed in hypodermal cells, and hypodermal promoters can drive full clr-1 and egl-15 rescue activity. Moreover, a mosaic analysis of mpk-1, which acts downstream of egl-15, suggests that its suppression of Clr (Soc) function is required in the hypodermis. These results suggest that EGL-15 and CLR-1 act in the hypodermis to regulate fluid ------------------- Key: 6615 Medline: 15210732 Authors: Broday L;Kolotuev I;Didier C;Bhoumik A;Podbilewicz B;Ronai Title: The LIM domain protein UNC-95 is required for the assembly of muscle attachment structures and is regulated by the RING finger protein RNF-5 in C. elegans. Citation: Journal of Cell Biology 165: 857-867 2004 Type: ARTICLE Genes: rnf-5 unc-95 Abstract: Here, we describe a new muscle LIM domain protein, UNC-95, and identify it as a novel target for the RING finger protein RNF-5 in the Caenorhabditis elegans body wall muscle. unc-95(su33) animals have disorganized muscle actin and myosin-containing filaments as a result of a failure to assemble normal muscle adhesion structures. UNC-95 is active downstream of PAT-3/beta-integrin in the assembly pathways of the muscle dense body and M-line attachments, and upstream of DEB-1/vinculin in the dense body assembly pathway. The translational UNC-95::GFP fusion construct is expressed in dense bodies, M-lines, and muscle-muscle cell boundaries as well as in muscle cell bodies. UNC-95 is partially colocalized with RNF-5 in muscle dense bodies and its expression and localization are regulated by RNF-5. rnf-5(RNAi) or a RING domain deleted mutant, rnf-5(tm794), exhibit structural defects of the muscle attachment sites. Together, our data demonstrate that UNC-95 constitutes an essential component of muscle adhesion sites that is regulated by RNF-5. ------------------- Key: 6616 Medline: 15183927 Authors: Nicholas HR;Hodgkin J Title: Responses to infection and possible recognition strategies in the innate immune system of Caenorhabditis elegans. Citation: Molecular Immunology 41: 479-493 2004 Type: REVIEW Genes: abf-1 abf-2 abf-3 abf-4 abf-5 abf-6 age-1 daf-2 daf-16 dbl-1 ikb-1 lys-1 lys-2 lys-3 lys-4 lys-5 lys-6 lys-7 lys-8 lys-9 lys-10 mef-2 nsy-1 pik-1 pmk-1 sek-1 spp-1 spp-2 spp-3 spp-4 spp-5 spp-6 spp-7 spp-8 spp-9 spp-10 spp-11 spp-12 spp-13 spp-14 spp-15 spp-16 spp-17 spp-18 spp-19 spp-20 tli-1 tol-1 trf-1 Abstract: In recent years, researchers investigating innate immunity have begun to use C. elegans as a new model system. The worm has been found to mount protective responses to a variety of fungal and bacterial pathogens. Four signalling pathways involved in such responses have been identified so far: the p38 MAP kinase pathway, the programmed cell death pathway, the TGF-beta pathway and the DAF-2 insulin/IGF-I like signalling pathway. Activation of these pathways can lead to the production of immune effector molecules such as lysozymes, lipases and saposin-like proteins, which can act directly against the invading microorganisms. The signalling pathways used and the effectors produced depend on the nature of the infection, indicating that the worm can detect and discriminate between infecting microorganisms. However, the molecules involved in recognition of pathogens have yet to be identified. The worm genome encodes Various proteins which might have this recognition function, such as numerous proteins containing C-type lectin domains. These and other candidates are ------------------- Key: 6617 Medline: 15102851 Authors: Uccelletti D;O'Callaghan C;Berninsone P;Zemtseva I;Abeijon C;Hirschberg CB Title: ire-1-dependent transcriptional up-regulation of a lumenal uridine diphosphatase from Caenorhabditis elegans. Citation: Journal of Biological Chemistry 279: 27390-27398 2004 Type: ARTICLE Genes: mig-23 ntp-1uda-1 Abstract: Lumenal ecto-nucleoside tri- and di-phosphohydrolases (ENTPDases) of the secretory pathway of eukaryotes hydrolyze nucleoside diphosphates resulting from glycosyltransferase-mediated reactions, yielding nucleoside monophosphates. The latter are weaker inhibitors of glycosyltransferases than the former and are also antiporters for the transport of nucleotide sugars from the cytosol to the endoplasmic reticulum ( ER) and Golgi apparatus (GA) lumen. Here we describe the presence of two cation-dependent nucleotide phosphohydrolase activities in membranes of Caenorhabditis elegans: one, UDA-1, is a UDP/GDPase encoded by the gene uda-1, whereas the other is an apyrase encoded by the gene ntp-1. UDA-1 shares significant amino acid sequence similarity to yeast GA Gda1p and mammalian UDP/GDPases and has a lumenal active site in vesicles displaying an intermediate density between those of the ER and GA when expressed in S. cerevisiae. NTP-1 expressed in COS-7 cells appeared to localize to the GA. The transcript of uda-1 but not those of two other C. elegans ENTPDase mRNAs (ntp-1 and mig-23) was induced up to 3.5-fold by high temperature, tunicamycin, and ethanol. The same effectors triggered the unfolded protein response as shown by the induction of expression of green fluorescent protein under the control of the BiP chaperone promoter and the UDP-glucose: glycoprotein glucosyltransferase. Up-regulation of uda-1 did not occur in ire-1-deficient mutants, demonstrating the role of this ER stress sensor in this event. We hypothesize that up-regulation of uda-1 favors hydrolysis of the glucosyltransferase inhibitory product UDP to UMP, and that the latter product then exits the lumen of the ER or pre-GA compartment in a coupled exchange with the entry of UDP-glucose, thereby further relieving ER stress by favoring protein re-glycosylation. ------------------- Key: 6618 Medline: 15220933 Authors: Gray JM;Karow DS;Lu H;Chang AJ;Chang JS;Ellis RE;Marletta MA;Bargmann CI Title: Oxygen sensation and social feeding mediated by a C. elegans guanylate cyclase homologue. Citation: Nature 430: 317-322 2004 Type: ARTICLE Genes: gcy-32 gcy-33 gcy-34 gcy-35 gcy-36 gcy-37 npr-1 tax-2 tax-4 Abstract: Specialized oxygen-sensing cells in the nervous system generate rapid behavioural responses to oxygen. We show here that the nematode Caenorhabditis elegans exhibits a strong behavioural preference for 5-12% oxygen, avoiding higher and lower oxygen levels. 3',5'-cyclic guanosine monophosphate (cGMP) is a common second messenger in sensory transduction and is implicated in oxygen sensation. Avoidance of high oxygen levels by C. elegans requires the sensory cGMP-gated channel tax-2/tax-4 and a specific soluble guanylate cyclase homologue, gcy-35. The GCY-35 haem domain binds molecular oxygen, unlike the haem domains of classical nitric-oxide-regulated guanylate cyclases. GCY-35 and TAX-4 mediate oxygen sensation in four sensory neurons that control a naturally polymorphic social feeding behaviour in C. elegans. Social feeding and related behaviours occur only when oxygen exceeds C. elegans' preferred level, and require gcy-35 activity. Our results suggest that GCY-35 is regulated by molecular oxygen, and that social feeding can be a behavioural strategy for responding to hyperoxic environments. ------------------- Key: 6619 Medline: 15208641 Authors: Liao EH;Hung W;Abrams B;Zhen M Title: An SCF-like ubiquitin ligase complex that controls presynaptic differentiation. Citation: Nature 430: 345-350 2004 Type: ARTICLE Genes: cam-1 egl-15 fsn-1 let-23 rpm-1 syd-2 vab-1 Abstract: During synapse formation, specialized subcellular structures develop at synaptic junctions in a tightly regulated fashion. Cross-signalling initiated by ephrins, Wnts and transforming growth factor-beta family members between presynaptic and postsynaptic termini are proposed to govern synapse formation(1-3). It is not well understood how multiple signals are integrated and regulated by developing synaptic termini to control synaptic differentiation. Here we report the identification of FSN-1, a novel F-box protein that is required in presynaptic neurons for the restriction and/or maturation of synapses in Caenorhabditis elegans. Many F-box proteins are target recognition subunits of SCF (Skp, Cullin, F-box) ubiquitin-ligase complexes(4-7). fsn-1 functions in the same pathway as rpm-1, a gene encoding a large protein with RING finger domains(8,9). FSN-1 physically associates with RPM-1 and the C. elegans homologues of SKP1 and Cullin to form a new type of SCF complex at presynaptic periactive zones. We provide evidence that T10H9.2, which encodes the C. elegans receptor tyrosine kinase ALK ( anaplastic lymphoma kinase(10)), may be a target or a downstream effector through which FSN-1 stabilizes synapse formation. This neuron-specific, SCF-like complex therefore provides a localized signal to attenuate presynaptic differentiation. ------------------- Key: 6620 Medline: 15133127 Authors: Walker DS;Ly S;Gower NJD;Baylis HA Title: IRI-1, a LIN-15B homologue, interacts with inositol-1,4,5-triphosphate receptors and regulates gonadogenesis, defecation, and pharyngeal pumping in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 15: 3073-3082 2004 Type: ARTICLE Genes: cnt-1 iri-1 itr-1 lin-15 Abstract: Inositol-1,4,5-triphosphate receptors (IP(3)Rs) are ligand-gated Ca2+ channels that control Ca2+ release from intracellular stores. They are central to a wide range of cellular responses. IP3Rs in Caenorhabditis elegans are encoded by a single gene, itr-1, and are widely expressed. Signaling through IP3 and IP(3)Rs is important in ovulation, control of the defecation cycle, modulation of pharyngeal pumping rate, and embryogenesis. To further elucidate the molecular basis of the diversity of IP,R function, we used a yeast two-hybrid screen to search for proteins that interact with ITR-1. We identified an interaction between ITR-1 and IRI-1, a previously uncharacterized protein with homology to LIN-15B. Iri-1 is widely expressed, and its expression overlaps significantly with that of itr-1. In agreement with this observation, iri-1 functions in known itr-1-mediated processes, namely, upregulation of pharyngeal pumping in response to food and control of the defecation cycle. Knockdown of iri-1 in an itr-1 loss-of-function mutant potentiates some of these effects and sheds light on the signaling pathways that control pharyngeal pumping rate. Knockdown of iri-1 expression also results in a sterile, evl phenotype, as a consequence of failures in early Z1/Z4 lineage divisions, such that gonadogenesis is severely disrupted. ------------------- Key: 6621 Medline: Authors: Tenuta M;Ferris H Title: Sensitivity of nematode life-history groups to ions and osmotic tensions of nitrogenous solutions. Citation: Journal of Nematology 36: 85-94 2004 Type: ARTICLE Genes: Abstract: Guild designation of nematodes of similar trophic function and life-history strategy provides a basis for Using nematode faunal analyses in all integrative assessment of soil food web condition. Omnivorous and predaceous nematodes, categorized at the upper end of a colollizer-persistcr (C-P) continuum of nematode functional guilds are generally not abundant in cropped soil. These nematodes are more sensitive to heavy metal concentrations than those in other c-p groups, but whether sensitivity to agrochemicals contributes to the observed low abundance of high c-p groups in cropped Soils is less Well Understood. An exposure assay in solution was itself to compare the sensitivity of nematodes representing various guilds obtained front field soils and front laboratory culture to several nitrogen sources. Nematodes in c-p groups 4 and 5 were more sensitive to nitrogen solutions titan nematodes representing lower c-p groups. There were both osmotic and specific ion effects-the latter most evident in exposure of nematodes to NaNO2 and (NH4)2SO(4). The RC50 (concentration resulting in nematode recovery of one half of that of distilled water) for (NH4)(2)SO1 was < 0.052 M-N for c-p groups 4 and 5 compared to much greater Values (0.34 to 0.81 M-N) for c-p groups 1 to 3. In non-ionic polyethylene glycol (PEG) solutions, osmotic tensions of 0.40 to 0.43 MPa reduced the recovery of exposed nematodes by half (RT50; water potential of solution resulting in nematode recovery of one half of that of distilled water) for c-p groups 4 and 5 compared to > 1.93 MPa for c-p groups 1 to 3. RT50 values for urea solutions, also non-ionic, were greater than for PEG. Caenorhabditis elegans N2 (c-p 1) and Meloidogyne javanica (c-p 3) reared oil solid medium and in hydroponic culture, respectively, were slightly more sensitive to specific ion and osmotic effects than nematodes of similar c-p groups obtained front soil. The greater sensitivity of c-p 4 and 5 nematodes to nitrogen solutions suggests that fertilizers may contribute to the low abundance of these nematodes in annual cropping systems. This study supports the use of nematode faunal analyses as indicators of chemical stress in soil. ------------------- Key: 6622 Medline: 15196946 Authors: Fay DS;Qiu XH;Large E;Smith CP;Mango S;Johanson BL Title: The coordinate regulation of pharyngeal development in C. elegans by lin-35/Rb, pha-1, and ubc-18. Citation: Developmental Biology 271: 11-25 2004 Type: ARTICLE Genes: efl-1 hda-1 let-418 lin-15 lin-35 lin-36 lin-37 lin-53 pha-1 pha-4 sup-36 sup-37 ubc-18 Abstract: Organ development is a complex process involving the coordination of cell proliferation, differentiation, and morphogenetic events. Using a screen to identify genes that function coordinately with lin-35/Rb during animal development, we have isolated a weak loss-of-function (LOF) mutation in pha-1, lin-35; pha-1 double mutants are defective at an early step in pharyngeal morphogenesis leading to an abnormal pharyngeal architecture. pha-1 is also synthetically lethal with other class B synthetic multivulval (SynMuv) genes including the C elegans E2F homolog, efl-1. Reporter analyses indicate that pha-1 is broadly expressed during embryonic development and that its functions reside in the cytoplasm. We also provide genetic and phenotypic evidence to support the model that PHA-1, a novel protein, and UBC-18, a ubiquitin-conjugating enzyme that we have previously shown to function with lin-35 during pharyngeal development, act in parallel pathways to regulate the activity of a common cellular target. ------------------- Key: 6623 Medline: Authors: Yu XQ;Kanost MR Title: Immulectin-2, a pattern recognition receptor that stimulates hemocyte encapsulation and melanization in the tobacco hornworm, Manduca sexta. Citation: Developmental & Comparative Immunology 28: 891-900 2004 Type: ARTICLE Genes: Abstract: In insects, encapsulation followed by melanization is a major defense mechanism against metazoan parasites. However, insects must recognize and differentiate nonself before they mount an immune response. Recognition of pathogens in insects is accomplished by a set of pattern recognition receptors (PRRs). Binding of PRRs to pathogens is linked to a variety of immune responses including phagocytosis, nodule formation, encapsulation, and prophenoloxidase activation. So far, little is known about how recognition of pathogens by PRRs triggers different immune responses. In this article, we report that immulectin-2, a C-type lectin, enhances encapsulation and melanization processes in the tobacco hornworm, Manduca sexta. Coating of agarose beads with recombinant carboxyl-terminal carbohydrate-recognition domain (CRD2-II) of immulectin-2 enhanced encapsulation of the beads in vitro by hemocytes and melanization of the beads in vivo in M. sexta larvae. Recombinant CRD2-II also directly bound to granular cells and oenocytoids, but not to plasmatocytes or spherule cells. Immulectin-2 in hemolymph of M. sexta larvae bound to the surface of a nematode, Caenorhabditis elegans, and recombinant CRD2-II directly bound to C. elegans and a human filarial nematode, Brugia malayi. Binding of CRD2-II to C. elegans enhanced melanization of the nematode in vivo. Our results suggest that binding of immulectin-2 to the surface of parasites can trigger encapsulation and melanization responses in M. sexta. ------------------- Key: 6624 Medline: 15203005 Authors: Cheung BHH;Arellano-Carbajal F;Rybicki I;de Bono M Title: Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior. Citation: Current Biology 14: 1105-1111 2004 Type: ARTICLE Genes: daf-7 flp-8 gcy-31 gcy-32 gcy-33 gcy-34 gcy-35 gcy-36 gcy-37 npr-1 Abstract: The genome of the nematode Caenorhabditis elegans encodes seven soluble guanylate cyclases (sGCs) [1]. In mammals, sGCs function as alpha/beta heterodimers activated by gaseous ligands binding to a haem prosthetic group [2, 3]. The principal activator is nitric oxide, which acts through sGCs to regulate diverse cellular events. In C. elegans the function of sGCs is mysterious: the worm genome does not appear to encode nitric oxide synthase, and all C. elegans sGC subunits are more closely related to mammalian beta than alpha subunits [1]. Here, we show that two of the seven C. Wegans sGCs, GCY-35 and GCY-36, promote aggregation behavior. gcy-35 and gcy-36 are expressed in a small number of neurons. These include the body cavity neurons AQR, PQR, and URX, which are directly exposed to the blood equivalent of C. elegans and regulate aggregation behavior [4]. We show that GCY-35 and GCY-36 act as a-like and beta-like sGC subunits and that their function in the URX sensory neurons is sufficient for strong nematode aggregation. Neither GCY-35 nor GCY-36 is absolutely required for C. elegans to aggregate. Instead, these molecules may transduce one of several pathways that induce C. elegans to aggregate or may modulate aggregation by responding to cues in C. elegans body fluid. ------------------- Key: 6625 Medline: 15116070 Authors: Mizuno T;Hisamoto N;Terada T;Kondo T;Adachi M;Nishida E;Kim DH;Ausubel FM;Matsumoto K Title: The Caenorhabditis elegans MAPK phosphatase VHP-1 mediates a novel JNK-like signaling pathway in stress response. Citation: EMBO Journal 23: 2226-2234 2004 Type: ARTICLE Genes: jnk-1 kgb-1 kgb-2 mek-1 mlk-1 pmk-1 sek-1 vhp-1 Abstract: Mitogen-activated protein kinases (MAPKs) are integral to the mechanisms by which cells respond to physiological stimuli and to a wide variety of environmental stresses. MAPK cascades can be inactivated at the MAPK activation step by members of the MAPK phosphatase (MKP) family. However, the components that act in MKP-regulated pathways have not been well characterized in the context of whole organisms. Here we characterize the Caenorhabditis elegans vhp-1 gene, encoding an MKP that acts preferentially on the c-Jun N-terminal kinase (JNK) and p38 MAPKs. We found that animals defective in vhp-1 are arrested during larval development. This vhp-1 defect is suppressed by loss-of-function mutations in the kgb-1, mek-1, and mlk-1 genes encoding a JNK-like MAPK, an MKK7-type MAPKK, and an MLK-type MAPKKK, respectively. The genetic and biochemical data presented here demonstrate a critical role for VHP-1 in the KGB-1 pathway. Loss-of-function mutations in each component in the KGB-1 pathway result in hypersensitivity to heavy metals. These results suggest that VHP-1 plays a pivotal role in the integration and fine-tuning of the stress response regulated by the KGB-1 MAPK pathway. ------------------- Key: 6626 Medline: 15211521 Authors: Lu SY;Symersky J;Li SL;Carson M;Chen LQ;Meehan E;Luo M Title: Structural genomics of Caenorhabditis elegans: crystal structure of the tropomodulin C-terminal domain. Citation: Proteins 56: 384-386 2004 Type: ARTICLE Genes: Abstract: The actin filament, an essential part of cytoskeleton, is associated with a number of functions including cellular shape and motility, cell integrity and division, endocytosis, cytokinesis, and muscle contraction. The supramolecular organization of the filament includes actin-binding proteins that regulate filament properties. The actin filament is polar, so that the barbed end is distinct from the pointed end. Tropomodulin is the pointed-end capping protein which maintains the length and dynamics of the actin filament (1). The protein was originally isolated by Fowler (2) and shown to inhibit the binding of tropomyosin to actin (3). Tropomodulin's capping activity is dependent upon its association with tropomyosin. In the absence of tropmyosin, capping activity of tropomodulin is greatly reduced. ------------------- Key: 6627 Medline: 15134588 Authors: Munoz ET;Bogarad LD;Deem MW Title: Microarray and EST database estimates of mRNA expression levels differ: the protein length versus expression curve for C. elegans. Citation: BMC Genomics 5: 1-6 2004 Type: ARTICLE Genes: Abstract: Background: Various methods for estimating protein expression levels are known. The level of correlation between these methods is only fair, and systematic biases in each of the methods cannot be ruled out. We here investigate systematic biases in the estimation of gene expression rates from microarray data and from abundance within the Expressed Sequence Tag (EST) database. We suggest that length is a significant factor in biases to measured gene expression rates. As a specific example of the importance of the bias of expression rate with length, we address the following evolutionary question: Does the average C. elegans protein length increase or decrease with expression level? Two different answers to this question have been reported in the literature, one method using expression levels estimated by abundance within the EST database and another using microarrays. We have investigated this issue by constructing the full protein length versus expression curve for C. elegans, using both methods for estimating expression levels. Results: The microarray data show a monotonic decrease of length with expression level, whereas the abundance within the EST database data show a non-monotonic behavior. Furthermore, the ratio of the expression level estimated by the EST database to that measured by microarrays is not constant, but rather systematically biased with gene length. Conclusions: It is suggested that the length bias may lie primarily in the abundance within the EST database method, being not ameliorated by internal standards as it is in the microarray data, and that this bias should be removed before data interpretation. When this is done, both the microarray and the abundance within the EST database give a monotonic decrease of spliced length with expression level, and the correlation between the EST and microarray data becomes larger. We suggest that standard RNA controls be used to normalize the length bias in any method that measures expression. ------------------- Key: 6628 Medline: 15096503 Authors: Jirakulaporn T;Muslin AJ Title: Cation diffusion facilitator proteins modulate Raf-1 activity. Citation: Journal of Biological Chemistry 279: 27807-27815 2004 Type: ARTICLE Genes: cdf-1 Abstract: The Ras-extracellular signal-regulated kinase (ERK) cascade is a critical intracellular signaling pathway that regulates growth, survival, and differentiation. Previous work established that Ras-GTP binds to, and facilitates the activation of, the protein kinase Raf-1. Recently, it was demonstrated that the cation diffusion facilitator (CDF) proteins are involved in Ras-ERK signaling by use of a Caenorhabditis elegans genetic screen that identified suppressors of activated Ras. In the current work, we demonstrate that CDF proteins may function downstream of Ras, but upstream of Raf-1 in Xenopus oocytes. We also show that the C. elegans protein CDF-1 and its mammalian homologue ZnT-1 bind to the amino-terminal regulatory portion of Raf-1 and promote the biological and enzymatic activity of Raf-1. Furthermore, we show that Zn2+ inhibits Raf-1 binding to ZnT-1. We propose a model in which CDF protein binding facilitates Raf-1 activation. ------------------- Key: 6629 Medline: 15041754 Authors: Jedrusik MA;Schulze E Title: Analysis of germline chromatin silencing by double-stranded RNA-mediated interference (RNAi) in Caenorhabditis elegans. Citation: Methods in Molecular Biology 254: 35-48 2004 Type: ARTICLE Genes: let-858 mes-2 mes-3 mes-4 mes-6 Abstract: ------------------- Key: 6630 Medline: 15103067 Authors: Hull D;Timmons L Title: Methods for delivery of double-stranded RNA into Caenorhabditis elegans. Citation: Methods in Molecular Biology 265: 23-58 2004 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans is often employed in investigations of diverse aspects of biology, including behavior, development, basic cellular processes, and disease states. The ability to utilize double-stranded RNA (dsRNA) to inhibit specific gene function in this organism has dramatically increased its value for these kinds of studies and has provided more flexibility in experimental design that include procedures. Here, we have collected a set of protocols from the C. elegans community for propagation of C. elegans, techniques for dsRNA preparation, four basic methods for delivery of dsRNA to C. elegans (injection, soaking, feeding, and in vivo delivery), and we suggest schemes that should facilitate detection of specific gene silencing. ------------------- Key: 6631 Medline: 15103066 Authors: Montgomery MK Title: RNA interference: historical overview and significance. Citation: Methods in Molecular Biology 265: 3-21 2004 Type: REVIEW Genes: Abstract: In the early 1990s, attempts to manipulate gene expression by researchers working in three different fields resulted in unanticipated gene silencing. Rather than ignoring such results, these researchers went on to document and further investigate the nature of such silencing, which was named "co-suppression" in plants, "quelling" in fungi, and "RNA interference" (RNAi) in nematodes. By the late 1990s, it was discovered that silencing could be initiated in this diverse set of organisms by exposing cells to double-stranded RNA (dsRNA), which directed the destruction of mRNAs containing similar sequences. Soon afterward, such dsRNA-mediated silencing was employed as a reverse genetic technique to analyze the functions of specific genes in a broad variety of organisms. Biochemical and genetic studies designed to uncover the components of the RNA silencing machinery identified a common core of proteins that serve to amplify the interfering RNA signal and direct endonucleolytic cleavage of target RNAs. A subset of silencing events may also direct DNA methylation of targeted genes. RNA silencing is thought to have evolved as a defense mechanism to suppress viral replication and transposon mobilization. However, additional functions involving the RNAi machinery have been uncovered, including posttranscriptional regulation of endogenous genes, and maintenance of structure and function of heterochromatin. Whereas many researchers have focused on understanding the natural biological functions of RNA silencing, others are testing its utility in antiviral and cancer therapies and in other biotechnological and biomedical applications. ------------------- Key: 6632 Medline: Authors: He L;Hannon GJ Title: MicroRNAs: small RNAs with a big role in gene regulation. Citation: Nature Reviews Genetics 5: 522-531 2004 Type: REVIEW Genes: dcr-1 hbl-1 let-7 lin-4 lin-14 lin-41 lin-57 lsy-6 Abstract: MicroRNAs are a family of small, non-coding RNAs that regulate gene expression in a sequence-specific manner. The two founding members of the microRNA family were originally identified in Caenorhabditis elegans as genes that were required for the timed regulation of developmental events. Since then, hundreds of microRNAs have been identified in almost all metazoan genomes, including worms, flies, plants and mammals. MicroRNAs have diverse expression patterns and might regulate various developmental and physiological processes. Their discovery adds a new dimension to our understanding of complex gene regulatory networks. ------------------- Key: 6633 Medline: 15232584 Authors: Nash B;Bowerman B Title: Uncoiling centriole duplication. Citation: Nature Cell Biology 6: 573-575 2004 Type: REVIEW Genes: sas-4 sas-5 spd-2 zyg-1 Abstract: The invariant duplication of the centriole once per cell cycle is critical for cell division. SAS-5 is the most recent of three coiled-coil centriolar proteins found to be required for centriole duplication in Caenorhabditis elegans. ------------------- Key: 6634 Medline: 15232593 Authors: Delattre M;Leidel S;Wani K;Baumer K;Bamat J;Schnabel H;Feichtinger R;Schnabel R;Gonczy P Title: Centriolar SAS-5 is required for centrosome duplication in C. elegans. Citation: Nature Cell Biology 6: 656-664 2004 Type: ARTICLE Genes: sas-4 sas-5 zyg-1 Abstract: Centrosomes, the major microtubule-organizing centres (MTOCs) of animal cells, are comprised of a pair of centrioles surrounded by pericentriolar material (PCM). Early in the cell cycle, there is a single centrosome, which duplicates during S-phase to direct bipolar spindle assembly during mitosis(1). Although crucial for proper cell division, the mechanisms that govern centrosome duplication are not fully understood. Here, we identify the Caenorhabditis elegans gene sas-5 as essential for daughter-centriole formation. SAS-5 is a coiled-coil protein that localizes primarily to centrioles. Fluorescence recovery after photobleaching (FRAP) experiments with green fluorescent protein (GFP) fused to SAS-5 (GFP-SAS-5) demonstrated that the protein shuttles between centrioles and the cytoplasm throughout the cell cycle. Analysis of mutant alleles revealed that the presence of SAS-5 at centrioles is crucial for daughter-centriole formation and that ZYG-1, a kinase that is also essential for this process(2), controls the distribution of SAS-5 to centrioles. Furthermore, partial RNA-interference (RNAi)-mediated inactivation experiments suggest that both sas-5 and zyg-1 are dose-dependent regulators of centrosome duplication. ------------------- Key: 6635 Medline: 15073178 Authors: Wang JC;Walker A;Blackwell TK;Yamamoto KR Title: The Caenorhabditis elegans ortholog of TRAP240, CeTRAP240/let-19, selectively modulates gene expression and is essential for embryogenesis. Citation: Journal of Biological Chemistry 279: 29270-29277 2004 Type: ARTICLE Genes: dpy-22 elt-5 end-1 hlh-1 let-19 med-1 nhr-2 pal-1 pes-10 pha-4 sop-1 sur-5 Abstract: Mediator complexes are large multiprotein assemblies that function in the regulation of eukaryotic gene transcription. In yeast, certain mediator subunits appear to comprise a subcomplex that acts in the regulation of a specific subset of genes. We investigated in a metazoan, Caenorhabditis elegans, the roles and interactions of two of those subunits, CeTRAP240/let-19 and CeTRAP230/dpy-22. We found that CeTRAP240/let-19 contains four domains that are conserved in the human TRAP240 protein and that one of those domains displays intrinsic transcriptional repression activity. Using RNA interference, we found that reduced expression of CeTRAP240/let-19 displayed a high penetrance of embryonic lethality in F1 progeny; animals that escaped embryonic arrest showed mutant phenotypes such as burst vulva and molting defects. CeTRAP240/let-19 appeared to affect specific genes, as CeTRAP240/let-19(RNAi) led to selectively reduced expression of a subset of reporter genes examined. Genetic experiments supported the view that CeTRAP240/let-19 and CeTRAP230/dpy-22, like their Drosophila and yeast counterparts, can operate on common pathways. Thus, a male tail phenotype caused by the pal-1(e2091) mutation was suppressed not only by CeTRAP230/dpy-22 mutants, as reported previously, but also by reduced expression of CeTRAP240/let-19. Additionally, CeTRAP240/let-19(RNAi) in a CeTRAP230/dpy-22 mutant background produced a strong synthetic lethal phenotype. Overall, our results establish specific roles of CeTRAP240/let-19 in C. elegans embryonic development and a functional interaction between CeTRAP240/let-19 and CeTRAP230/dpy-22. Interestingly, whereas this interaction has been conserved from yeast to mammals, the subcomplex modulates metazoan-specific genetic pathways, likely in addition to those also controlled in yeast. ------------------- Key: 6636 Medline: 15231741 Authors: Cho S;Jin SW;Cohen A;Ellis RE Title: A phylogeny of Caenorhabditis reveals frequent loss of introns during nematode evolution. Citation: Genome Research 14: 1207-1220 2004 Type: ARTICLE Genes: cpb-1 cpb-2 cpb-3 fog-1 fog-3 Abstract: Since introns were discovered 26 years ago, people have wondered how changes in intron/exon structure occur, and what role these changes play in evolution. To answer these questions, we have begun studying gene structure in nematodes related to Caenorhabditis elegans. As a first step, we cloned a set of five genes from six different Caenorhabditis species, and used their amino acid sequences to construct the first detailed phylogeny of this genus. Our data indicate that nematode introns are lost at a very high rate during evolution, almost 400-fold higher than in mammals. These losses do not occur randomly, but instead, favor some introns and do not affect others. In contrast, intron gains are far less common than losses in these genes. On the basis of the sequences at each intron site, we suggest that several distinct mechanisms can cause introns to be lost. The small size of C. elegans introns should increase the rate at which each of these types of loss can occur, and might account for the dramatic difference in loss rate between nematodes and mammals. ------------------- Key: 6637 Medline: 15194189 Authors: Wachi M;Ogawa T;Yokoyama K;Hokii Y;Shimoyama M;Muto A;Ushida C Title: Isolation of eight novel Caenorhabditis elegans small RNAs. Citation: Gene 335: 47-56 2004 Type: ARTICLE Genes: rpl-6 rpl-30 rps-12 rps-23 rps-29 Abstract: Eight novel small RNAs that were encoded in the regions corresponding to the introns of protein-coding genes were isolated from Caenorhabditis elegans. Seven of them showed a typical snoRNA secondary structure: one C/D snoRNA and six H/ACA snoRNAs. The remaining one RNA did not show any homology to other RNAs in a database. Four of the seven isolated snoRNAs could form base pairings with parts of rRNAs, suggesting that they are potential pseudouridilation sites and methylation sites. The results of our study suggest that there are more as-yet-unidentified small ncRNAs of which genes are located in the intron regions of protein-coding genes in C. elegans. ------------------- Key: 6638 Medline: 15177019 Authors: McKee AE;Silver PA Title: REF-ereeing the cytoplasmic fate of mRNA via nuclear Citation: Developmental Cell 6: 740-742 2004 Type: REVIEW Genes: nxf-1 nxf-2 ref-1 ref-2 tra-1 tra-2 Abstract: The C. elegans sex-determining gene tra-2 is subject to multiple forms of regulation. A report in the June 4 issue of Molecular Cell now shows that proteins associated with the tra-2 mRNA determine its pathway of nuclear export and influence its cytoplasmic fate. These findings demonstrate an additional level of control and link nuclear export to the regulation of sexual development. ------------------- Key: 6639 Medline: 15177025 Authors: Wenick AS;Hobert O Title: Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in C. elegans. Citation: Developmental Cell 6: 757-770 2004 Type: ARTICLE Genes: ceh-10 ceh-22 ceh-23 cha-1 des-2 dpy-7 elt-2 gar-2 glc-3 hen-1 inx-18 jnk-1 kal-1 lat-1 ldb-1 lin-14 mgl-1 mod-1 myo-3 nlp-15 nxh-1 pll-1 ser-2 snb-1 sra-6 sra-11 ttx-3 unc-17 unc-47 unc-122 wrk-1 Abstract: Gene batteries are sets of coregulated genes with common cis-regulatory elements that define the differentiated state of a cell. The nature of gene batteries for individual neuronal cellular subtypes and their linked cis-regulatory elements is poorly defined. Through molecular dissection of the highly modular cis-regulatory architecture of individual neuronally expressed genes, we have defined a conserved 16 bp cis-regulatory motif that drives gene expression in a single interneuron subtype, termed AIY, in the nematode Caenorhabditis elegans. This motif is bound and activated by the Paired- and LIM-type homeodomain proteins CEH-10 and TTX-3. Using genome-wide phylogenetic footprinting, we delineated the location, distribution, and evolution of AIY-specific cis-regulatory elements throughout the genome and thereby defined a large battery of AIY-expressed genes, all of which represent direct Paired/LIM homeodomain target genes. The identity of these homeodomain targets provides novel insights into the ------------------- Key: 6640 Medline: 15177034 Authors: Gobel V;Barrett PL;Hall DH;Fleming JT Title: Lumen morphogenesis in C. elegans requires the membrane-cytoskeleton linker erm-1. Citation: Developmental Cell 6: 865-873 2004 Type: ARTICLE Genes: act-5 erm-1 nfm-1 hDf27 hDf28 sDf4 Abstract: Epithelial tubes are basic building blocks of complex organs, but their architectural requirements are not well understood. Here we show that erm-1 is a unique C. elegans ortholog of the ERM family of cytoskeleton-membrane linkers, with an essential role in lumen morphogenesis. ERM-1 localizes to the luminal membranes of those tubular organ epithelia which lack stabilization by cuticle. RNA interference (RNAi), a germline deletion, and overexpression of erm-1 cause cystic luminal phenotypes in these epithelia. Confocal and ultrastructural analyses indicate that erm-1 functions directly in apical membrane morphogenesis, rather than in epithelial polarity and junction assembly as has been previously proposed for ERMs. We also show that act-5/cytoplasmic actin and sma-1/ P-H-spectrin are required for lumen formation and functionally interact with erm-1. Our findings suggest that there are common structural constraints on the architecture ------------------- Key: 6641 Medline: 15102610 Authors: Sedensky MM;Siefker JM;Koh JY;Miller DM;Morgan PG Title: A stomatin and a degenerin interact in lipid rafts of the nervous system of Caenorhabditis elegans. Citation: American Journal of Physiology - Cell Physiology 287: C468-C474 2004 Type: ARTICLE Genes: unc-1 unc-8 unc-24 Abstract: In Caenorhabditis elegans, the gene unc-1 controls anesthetic sensitivity and normal locomotion. The protein UNC-1 is a close homolog of the mammalian protein stomatin and is expressed primarily in the nervous system. Genetic studies in C. elegans have shown that the UNC-1 protein interacts with a sodium channel subunit, UNC-8. In humans, absence of stomatin is associated with abnormal sodium and potassium levels in red blood cells. Stomatin also has been postulated to participate in the formation of lipid rafts, which are membrane microdomains associated with protein complexes, cholesterol, and sphingolipids. In this study, we isolated a low-density, detergent-resistant fraction from cell membranes of C. elegans. This fraction contains cholesterol, sphingolipids, and protein consistent with their identification as lipid rafts. We then probed Western blots of protein from the rafts and found that the UNC-1 protein is almost totally restricted to this fraction. The UNC-8 protein is also found in rafts and coimmunoprecipitates UNC-1. A second stomatin-like protein, UNC-24, also affects anesthetic sensitivity, is found in lipid rafts, and regulates UNC-1 distribution. Mutations in the unc-24 gene alter the distribution of UNC-1 in lipid rafts. Each of these mutations alters anesthetic sensitivity in C. elegans. Because lipid rafts contain many of the putative targets of volatile anesthetics, they may represent a novel class of targets for volatile ------------------- Key: 6642 Medline: 15247331 Authors: Cheung I;Schertzer M;Baross A;Rose AM;Lansdorp PM;Baird DM Title: Strain-specific telomere length revealed by single telomere length analysis in Caenorhabditis elegans. Citation: Nucleic Acids Research 32: 3383-3391 2004 Type: ARTICLE Genes: mrt-2 Abstract: Terminal restriction fragment analysis is the only method currently available for measuring telomere length in Caenorhabditis elegans. Its limitations include low sensitivity and interference by the presence of interstitial telomeric sequences in the C.elegans genome. Here we report the adaptation of single telomere length analysis (STELA) to measure the length of telomeric repeats on the left arm of chromosome V in C. elegans. This highly sensitive PCR-based method allows telomere length measurement from as few as a single worm. The application of STELA to eight wild-type C. elegans strains revealed considerable strain-specific differences in telomere length. Within individual strains, short outlying telomeres were observed that were clearly distinct from the bulk telomere length distributions, suggesting that processes other than end-replication losses and telomerase-mediated lengthening may generate telomere length heterogeneity in C. elegans. The utility of this method was further demonstrated by the characterization of telomere shortening in mrt-2 mutants. We conclude that STELA appears to be a valuable tool for studying telomere biology in C. elegans. ------------------- Key: 6643 Medline: 15247332 Authors: Hajarnavis A;Korf I;Durbin R Title: A probabilistic model of 3' end formation in Caenorhabditis elegans. Citation: Nucleic Acids Research 32: 3392-3399 2004 Type: ARTICLE Genes: Abstract: The 3' ends of mRNAs terminate with a poly(A) tail. This post-transcriptional modification is directed by sequence features present in the 3'-untranslated region (3'-UTR). We have undertaken a computational analysis of 3' end formation in Caenorhabditis elegans. By aligning cDNAs that diverge from genomic sequence at the poly(A) tract, we accurately identified a large set of true cleavage sites. When there are many transcripts aligned to a particular locus, local variation of the cleavage site over a span of a few bases is frequently observed. We find that in addition to the well-known AAUAAA motif there are several regions with distinct nucleotide compositional biases. We propose a generalized hidden Markov model that describes sequence features in C.elegans 3'-UTRs. We find that a computer program employing this model accurately predicts experimentally observed 3' ends even when there are multiple AAUAAA motifs and multiple cleavage sites. We have made available a complete set of polyadenylation site predictions for the C.elegans genome, including a subset of 6570 supported by aligned transcripts. ------------------- Key: 6644 Medline: 15221853 Authors: Timmons L Title: Endogenous inhibitors of RNA interference in Caenorhabditis elegans. Citation: BioEssays 26: 715-718 2004 Type: REVIEW Genes: ego-1 eri-1 rrf-1 rrf-3 Abstract: In eukaryotes, double-stranded RNAs (dsRNAs) or short, interfering dsRNAs (siRNAs) can reduce the accumulation of a sequence-related mRNA, often resulting in a loss-of-function phenotype-a process termed RNA interference (RNAi). Unfortunately, some mRNAs are resistant to the effects of dsRNA. Experiments designed to unravel RNAi mechanisms in Caenorhabditis elegans have led to the identification of two worm proteins, RRF3((1,2)) and, now, ERI-1,((3)) that can inhibit RNAi responses. Animals defective in either protein can display enhanced RNAi phenotypes for mRNAs that were previously resistant to dsRNA. Since ERI-1 is a conserved protein, development of procedures to enhance RNAi effectiveness in other systems ------------------- Key: 6645 Medline: 15203185 Authors: De Castro E;De Castro SH;Johnson TE Title: Isolation of long-lived mutants in Caenorhabditis elegans using selection for resistance to juglone. Citation: Free Radical Biology & Medicine 37: 139-145 2004 Type: ARTICLE Genes: age-1 Abstract: The accumulation of molecular damage from attack by reactive oxygen species is one cause of aging. Therefore, some mutant organisms showing increased resistance to reactive oxygen species should live longer. We show that selection for Caenorhabditis elegans mutants that are resistant to juglone, a reactive oxygen species-generating compound, leads to the identification of long-lived mutants. Indeed, four of six resistant mutants isolated were also long-lived. This study illustrates once more the strong relationship between oxidative stress and the aging ------------------- Key: 6646 Medline: 15203195 Authors: Keaney M;Matthijssens F;Sharpe M;Vanfleteren J;Gems D Title: Superoxide dismutase mimetics elevate superoxide dismutase activity in vivo but do not retard aging in the nematode Caenorhabditis elegans. Citation: Free Radical Biology & Medicine 37: 239-250 2004 Type: ARTICLE Genes: daf-16 daf-18 Abstract: According to the oxidative damage theory a primary cause of aging is the accrual of molecular damage from reactive oxygen species (ROS), particularly superoxide and its derivatives. This predicts that treatments that reduce ROS levels should retard aging. Using the nematode Caenorhabditis elegans, we tested the effects on stress resistance and life span of treatment with EUK-8 and EUK-134, synthetic mimetics of the antioxidant enzyme superoxide dismutase (SOD), which neutralises superoxide. Treatment with SOD mimetics elevated in vivo SOD activity levels, particularly in mitochondria, where up to 5-fold increases in SOD activity were recorded. Treatment with exogenous SOD mimetics did not affect endogenous protein SOD levels. Where life span was reduced by the superoxide generators paraquat and plumbagin, EUK-8 treatment increased life span in a dose-dependent fashion. Yet in the absence of a superoxide generator, treatment with EUK-8 or EUK-134 did not increase life span, even at doses that were optimal for protection against pro-oxidants. Thus, an elevation of SOD activity levels sufficient to increase life span when it is limited by superoxide generators does not retard aging in the absence of superoxide generators. This suggests that C elegans life span is not normally limited by levels of superoxide and its derivatives. ------------------- Key: 6647 Medline: 15231740 Authors: Blacque OE;Reardon MJ;Li C;McCarthy J;Mahjoub MR;Ansley SJ;Badano JL;Mah AK;Beales PL;Davidson WS;Johnsen RC;Audeh M;Plasterk RHA;Baillie DL;Katsanis N;Quarmby LM;Wicks SR;Leroux MR Title: Loss of C. elegans BBS-7 and BBS-8 protein function results in cilia defects and compromised intraflagellar transport. Citation: Genes & Development 18: 1630-1642 2004 Type: ARTICLE Genes: bbs-7 bbs-8 che-11 gcy-5 osm-5 osm-11 Abstract: Bardet-Biedl syndrome (BBS) is a genetically heterogeneous developmental disorder whose molecular basis is largely unknown. Here, we show that mutations in the Caenorhabditis elegans bbs-7 and bbs-8 genes cause structural and functional defects in cilia. C. elegans BBS proteins localize predominantly at the base of cilia, and like proteins involved in intraflagellar transport (IFT), a process necessary for cilia biogenesis and maintenance, move bidirectionally along the ciliary axoneme. Importantly, we demonstrate that BBS-7 and BBS-8 are required for the normal localization/motility of the IFT proteins OSM-5/Polaris and CHE-11, and to a notably lesser extent, CHE-2. We propose that BBS proteins play important, selective roles in the assembly and/or function of IFT particle components. Our findings also suggest that some of the cardinal and secondary symptoms of BBS, such as obesity, diabetes, cardiomyopathy, and learning defects may result from cilia dysfunction. ------------------- Key: 6648 Medline: Authors: Ji YJ;Song HO;Park CS;Ahnn J Title: Isolaton and characterization of bisphenol-A resistant mutants in Caenorhabditis elegans. Citation: Korean Journal of Genetics 26: 107-114 2004 Type: ARTICLE Genes: Abstract: ------------------- Key: 6649 Medline: 15255192 Authors: Suzuki M;Sagoh N;Iwasaki H;Inoue H;Takahashi K Title: Metalloproteases with EGF, CUB, and thrombospondin-1 domains function in molting of Caenorhabditis elegans. Citation: Biological Chemistry 385: 565-568 2004 Type: ARTICLE Genes: dpy-31 nas-9 nas-10 nas-11 nas-15 nas-26 nas-32 nas-35 nas-36 nas-37 nas-38 nas-39 rde-1 toh-2 Abstract: Functional analysis using RNAi was performed on eleven genes for metalloproteases of the M12A family in Caenorhabditis elegans and the interference of the C17G1.6 gene (nas-37) was found to cause incomplete molting. The RNAi of the C26C6.3 gene (nas-36) also caused a similar molting defect but not so severely as that of the nas-37 gene. Both the genes encode an astacin-like metalloprotease with an epidermal growth factor (EGF)-like domain, a CUB domain, and a thrombospondin-1 domain, in this order. The promoter-driven green fluorescent protein (GFP) expression analysis suggested that they are expressed in hypodermal cells throughout the larval stages and in the vulva of adult animals. In the genetic background of rde-1(ne219), where RNAi does not work, the molting defect caused by the nas-37 interference was observed when the transgenic wild-type rde-1 gene was expressed under the control of the dpy-7 promoter, known to be active in the hypodermal cells, but not under the control of the myo-3 promoter, active in the muscular cells. Therefore these proteases are thought to be secreted by the hypodermal cells and to participate in shedding of old cuticles. ------------------- Key: 6650 Medline: Authors: Haag ES Title: Germline imprinting: battle of the sexes or battle of the X's? Citation: Developmental Cell 6: 157-165 2004 Type: REVIEW Genes: her-1 Abstract: The X chromosome is largely inactivated in spermatogenesis of heterogametic males, and in multiple phyla it encodes few genes specifically expressed in the male germline. Writing in Nature Genetics, Bean et al. report a parallel between male germline X inactivation in nematodes and a fungal gene-silencing mechanism that alters the way we view the evolution of both phenomena. ------------------- Key: 6651 Medline: 15138888 Authors: Fisk Green R;Lorson M;Walhout AJ;Vidal M;van den Heuvel S Title: Identification of critical domains and putative partners for the Caenorhabditis elegans spindle component LIN-5. Citation: Molecular Genetics & Genomics 271: 532-544 2004 Type: ARTICLE Genes: gei-16 gpr-1 gpr-2 lfi-1 lin-5 unc-15 mnDf100 Abstract: Successful cell division requires proper assembly, placement and functioning of the spindle apparatus that segregates the chromosomes. The Caenorhabditis elegans gene lin-5 encodes a novel coiled-coil component of the spindle required for spindle positioning and chromosome segregation. To gain further insights into lin-5 function, we screened for dominant suppressors of the partial loss-of-function phenotype associated with the mutation lin-5(ev571ts ), and isolated 68 suppressing mutations. Eight out of the ten suppressors sequenced contained intragenic missense mutations immediately upstream of the lesion in lin-5(ev571ts ). These probably help to stabilize protein-protein interactions mediated by the coiled-coil domain. This domain was found to be required for binding to several putative LIN-5 interacting (LFI) proteins identified in yeast two-hybrid screens. Interestingly, interaction with the coiled-coil protein LFI-1 was specifically reduced by the lin-5(ev571ts ) mutation and restored by a representative intragenic suppressor mutation. Immunostaining experiments showed that LIN-5 and LFI-1 may co-localize around the kinetochore microtubules during metaphase, indicating potential interaction in vivo. The coiled-coil domain of LIN-5 was also found to mediate homodimerization, while the C-terminal region of LIN-5 was sufficient for interaction with GPR-1, a recently identified component of a LIN-5 spindle-regulatory complex. A single amino-acid substitution in the N-terminal region of LIN-5, encoded by the e1457 allele, abolished all LIN-5 interactions. Taken together, our results indicate that the spindle functions of LIN-5 depend on interactions with multiple protein partners, and that these interactions are mediated through several different domains of LIN-5. ------------------- Key: 6652 Medline: 15221760 Authors: Greetham D;Morgan C;Campbell AM;van Rossum AJ;Barrett J;Brophy PM Title: Evidence of glutathione transferase complexing and signaling in the model nematode Caenorhabditis elegans using a pull-down proteomic assay. Citation: Proteomics 4: 1989-1995 2004 Type: ARTICLE Genes: Abstract: Phage display techniques using random peptide interactions have supported the role of mammalian glutathione transferase (GST) as part of a signalling pathway for both oxidative stress and an apoptosis pathway. Little is known about the interaction of nonmammalian GST with other proteins. GSTs have been implicated in the development of chronic nematode infections by neutralising cytotoxic products arising from host immune initiated reactive oxygen species (ROS) assault. In this study we attached one of the key GSTs expressed in the model nematode Caenorhabditis elegans to an affinity support matrix and directly identified major interacting proteins by two-dimensional electrophoresis and peptide mass fingerprinting before and following oxidative stress. Nematode GST does not appear to be a stand-alone enzyme and interacts with many types of proteins in both normal and ROS stress conditions. Pull-down proteomic presents a flexible, label free, rapid and economical assay without specialised ligand fishing equipment to identify protein binding partners. ------------------- Key: 6653 Medline: 15123614 Authors: Hoflich J;Berninsome P;Gobel C;Gravato-Nobre MJ;Libby BJ;Darby C;Politz SM;Hodgkin J;Hirschberg CB;Baumeister R Title: Loss of srf-3-encoded nucleotide sugar transporter activity in Caenorhabditis elegans alters surface antigenicity and prevents bacterial adherence. Citation: Journal of Biological Chemistry 279: 30440-30448 2004 Type: ARTICLE Genes: srf-3 sDf22 Abstract: During the establishment of a bacterial infection, the surface molecules of the host organism are of particular importance, since they mediate the first contact with the pathogen. In Caenorhabditis elegans, mutations in the srf-3 locus confer resistance to infection by Microbacterium nematophilum, and they also prevent biofilm formation by Yersinia pseudotuberculosis, a close relative of the bubonic plague agent Yersinia pestis. We cloned srf-3 and found that it encodes a multitransmembrane hydrophobic protein resembling nucleotide sugar transporters of the Golgi apparatus membrane. srf-3 is exclusively expressed in secretory cells, consistent with its proposed function in cuticle/surface modification. We demonstrate that SRF-3 can function as a nucleotide sugar transporter in heterologous in vitro and in vivo systems. UDP-galactose and UDP-N-acetylglucosamine are substrates for SRF-3. We propose that the inability of Yersinia biofilms and M. nematophilum to adhere to the nematode cuticle is due to an altered glycoconjugate surface composition of the srf-3 ------------------- Key: 6654 Medline: Authors: Zhen M;Jin Y Title: Presynaptic terminal differentiation: transport and assembly. Citation: Current Opinion in Neurobiology 14: 280-287 2004 Type: REVIEW Genes: syd-2 unc-10 unc-13 unc-18 Abstract: The formation of chemical synapses involves reciprocal induction and independent assembly of pre- and postsynaptic structures. The major events in presynaptic terminal differentiation are the formation of the active zone and the clustering of synaptic vesicles. A number of proteins that are present in the presynaptic active zone have been identified. Recent studies of various mutants have clarified the in vivo functions of some of the main players. Time-lapse imaging studies have captured dynamic and transient events in the transport of synaptic components, and therefore provided insight into the early stages of synaptogenesis. ------------------- Key: 6655 Medline: 15221851 Authors: Rattner BP;Meller VH Title: Worm chromosomes call for recognition! Citation: BioEssays 26: 707-710 2004 Type: REVIEW Genes: sdc-2 xol-1 Abstract: Many organisms face a dilemma rooted in the unequal numbers of X chromosomes carried by the two sexes and the need to maintain equivalent expression of X-linked genes. Several strategies have arisen to cope with this problem. All rely on accurately targeting epigenetic modifications to entire chromosomes. Targeting results from the action of recognition elements that attract modification and may rely on spreading of modification in cis along the affected chromosome. A recent report describing the first X chromosome recognition element from C. elegans opens the way to defining the relative contributions of these factors to the compensation of X-linked gene expression in worms.((1)) Extrachromosomal arrays composed of a C. elegans recognition element attract proteins that modify the C. elegans X chromosomes and interact genetically with mutations disrupting compensation. Moreover, examination of X:A translocations provides the first evidence for spreading of modification along C. elegans X chromosomes. ------------------- Key: 6656 Medline: 15340062 Authors: Jantsch V;Pasierbek P;Mueller MM;Schweizer D;Jantsch M;Loidl J Title: Targeted gene knockout reveals a role in meiotic recombination for ZHP-3, a Zip3-related protein in Caenorhabditis elegans. Citation: Molecular and Cellular Biology 24: 7998-8006 2004 Type: ARTICLE Genes: him-3 spo-11 syp-1 syp-2 zhp-3 Abstract: The meiotically expressed Zip3 protein is found conserved from Saccharomyces cerevisiae to humans. In baker's yeast, Zip3p has been implicated in synaptonemal complex (SC) formation, while little is known about the protein's function in multicellular organisms. We report here the successful targeted gene disruption of zhp-3 (K02B12.8), the ZIP3 homolog in the nematode Caenorhabditis elegans. Homozygous zhp-3 knockout worms show normal homologue pairing and SC formation. Also, the timing of appearance and the nuclear localization of the recombination protein Rad-51 seem normal in these animals, suggesting proper initiation of meiotic recombination by DNA double-strand breaks. However, the occurrence of univalents during diplotene indicated that C. elegans ZHP-3 protein is essential for reciprocal recombination between homologous chromosomes and thus chiasma formation. In the absence of ZHP-3, reciprocal recombination is abolished and double-strand breaks seem to be repaired via alternative pathways, leading to achiasmatic chromosomes and the occurrence of univalents during meiosis I. Green fluorescent protein-tagged C. elegans ZHP-3 forms lines between synapsed chromosomes and requires the SC for its proper localization. ------------------- Key: 6657 Medline: 15238517 Authors: Steger KA;Avery L Title: The GAR-3 muscarinic receptor cooperates with calcium signals to regulate muscle contraction in the Caenorhabditis elegans pharynx. Citation: Genetics 167: 633-643 2004 Type: ARTICLE Genes: avr-15 eat-2 egl-19 gar-3 gpb-2 itr-1 Abstract: Muscarinic acetylcholine receptors regulate the activity of neurons and muscle cells through G-protein-coupled cascades. Here, we identify a pathway through which the GAR-3 muscarinic receptor regulates both membrane potential and excitation-con traction coupling in the Caenorhabditis elegans pharyngeal muscle. GAR-3 signaling is enhanced in worms overexpressing gar-3 or lacking GPB-2, a G-protein P-subunit involved in RGS-mediated inhibition of G(o)alpha- and G(q)alpha-linked pathways. High levels of signaling through GAR-3 inhibit pharyngeal muscle relaxation and impair feeding-but do not block muscle repolarization-when worms are exposed to arecoline, a muscarinic agonist. Loss of gar-3 function results in shortened action potentials and brief muscle contractions in the pharyngeal terminal bulb. High levels of calcium entry through voltage-gated channels also impair terminal bulb relaxation and sensitize worms to the toxic effects of arecoline. Mutation of gar-3 reverses this sensitivity, suggesting that GAR-3 regulates calcium influx or calcium-dependent processes. Because the effects of GAR-3 signaling on membrane depolarization and muscle contraction can be separated, we conclude that GAR-3 regulates multiple calcium-dependent processes in the C. elegans pharyngeal muscle. ------------------- Key: 6658 Medline: 15238518 Authors: Kawasaki I;Amiri A;Fan Y;Meyer N;Dunkelbarger S;Motohashi T;Karashima T;Bossinger O;Strome S Title: The PGL family proteins associate with germ granules and function redundantly in Caenorhabditis elegans germline development. Citation: Genetics 167: 645-661 2004 Type: ARTICLE Genes: glh-1 glp-4 him-3 pgl-1 pgl-2 pgl-3 Abstract: PGL-1 is a constitutive protein component of C. elegans germ granules, also known as P granules. Maternally supplied PGL-1 is essential for germline development but only at elevated temperature, raising the possibility that redundant factors provide sufficient function at lower temperatures. We have identified two PGLA-related proteins, PGL-2 and PGL-3, by sequence analysis of the C. elegans genome and by a yeast two-hybrid screen for proteins that interact with PGL-1. PGL-3 is associated with P granules at all stages of development, while PGL-2 is associated with 11 granules only during postembryonic development. All three PGL proteins interact with each other in vitro. Furthermore, PGL-1 and PGL-3 are co-immuno-precipitated from embryo extracts, indicating that they are indeed in the same protein complex in vivo. Nevertheless, each PGL. protein localizes to P granules independently of the other two. pgl-2 or pgl-3 single-mutant worms do not show obvious defects in germline development. However, pgl-1; pgl-3 (but not pgl-2; pgl-1) double-mutant hermaphrodites and males show significantly enhanced sterility at all temperatures, compared to pgl-1 alone. Mutant hermaphrodites show defects in germline proliferation and in production of healthy gametes and viable embryos. Our findings demonstrate that both PGL-2 and PGL-3 are components of P granules, both interact with PGL-1, and at least PGL-3 functions redundantly with PGL-1 to ensure fertility in both sexes of ------------------- Key: 6659 Medline: 15238519 Authors: Garbe D;Doto JB;Sundaram MV Title: Caenorhabditis elegans lin-35/Rb, efl-1/E2F and other synthetic multivulva genes negatively regulate the anaphase-promoting complex gene mat-3/APC8. Citation: Genetics 167: 663-672 2004 Type: ARTICLE Genes: cki-1 dpl-1 efl-1 fzr-1 fzy-1 let-60 lin-8 lin-15 lin-35 lin-36 lin-53 mat-3 hDf35 wcDf1 Abstract: Retinoblastoma (Rb)/E2F complexes repress expression of many genes important for G(i)-to-S transition, but also appear to regulate gene expression at other stages of the cell cycle. In C. elegans, lin-35/Rb and other synthetic Multivulva (SynMuv) group B genes function redundantly with other sets of genes to regulate G(i)/S progression, vulval and pharyngeal differentiation, and other unknown processes required for viabilty. Here we show that lin-35/Rb, efl-1/E2F, and other SynMuv B genes negatively regulate a component of the anaphase-promoting complex or cyclosome (APC/C. The APC/C is a multisubunit complex that promotes metaphase-to-anaphase progression and G, arrest by targeting different substrates for ubiquitination and proteasome-mediated destruction. The C. elegans APC/C gene mai-3/APC8 has been defined by temperature-sensitive embryonic lethal alleles that strongly affect germline meiosis and mitosis but only weakly affect somatic development. We describe severe nonconditional mat-3 alleles and a hypomorphic viable allele (ku233), all of which affect postembryonic cell divisions including those of the vulval lineage. The ku23 lesion is located outside of the mat-3 coding region and reduces mat-3 mRNA expression. Loss-of-function alleles of lin-35/Rb and other SynMuv B genes Suppress mat-3(ku233) defects by restoring mat-3 mRNA to wild-type levels. Therefore, Rb/E2F complexes appear to repress mat-3 expression. ------------------- Key: 6660 Medline: 15238520 Authors: Joshi P;Eisenmann DM Title: The Caenorhabditis elegans pvl-5 gene protects hypodermal cells from ced-3-dependent, ced-4-independent cell death. Citation: Genetics 167: 673-685 2004 Type: ARTICLE Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 egl-1 pvl-5 arDp2 mnDf39 Abstract: Programmed cell death (PCD) is regulated by multiple evolutionarily conserved mechanisms to ensure by the survival of the cell. Here we describe pvl-5, a gene that likely regulates PCD in Caenorhabditis elegans. In wild-type hermaphrodites at the L2 stage there are 11 Pn.p hypodermal cells in the ventral midline arrayed along the anterior-posterior axis and 6 of these cells become the vulval precursor cells. In pvl-5(ga87) animals there are fewer Pn.p cells (average of 7.0) present at this time. Lineage analysis reveals that the missing Pn.p cells die around the time of the L1 molt in a manner that often resembles the programmed cell deaths that occur normally in C. elegans development. This Pn.p cell death is suppressed by mutations in the caspase gene ced-3 and in the bc1-2 homolog ced-9, Suggesting that the Pn.p cells are dying by PCD in pvl-5 mutants. Surprisingly, the Pn.p cell death is not suppressed by loss of ced-4 function. ced-4 (Apaf-1) is required for all previously known apoptotic cell deaths in C. elegans. This suggests that loss of pvl 5 function leads to the activation of a ced-3-dependent, ced-4-independent form of PCD and that pvl-5 may normally function to protect Cells from inappropriate activation of the apoptotic pathway. ------------------- Key: 6661 Medline: 14769996 Authors: Celotto AM;Graveley BR Title: Using single-strand conformational polymorphism gel electrophoresis to analyze mutually exclusive alternative splicing. Citation: Methods in Molecular Biology 257: 65-74 2004 Type: ARTICLE Genes: Abstract: Single-strand conformational polymorphism analysis has been used successfully to identify single nucleotide changes within sequences based on the fact that multidetection enhancement gels will separate molecules based on their conformation rather than their size. We have expanded the utility of this technique to analyze easily the alternative splicing of pre-mRNAs containing multiple mutually exclusive exons of the same size. We have used this technique to study the Caenorhabditis elegans let-2 gene containing two alternative exons and the Drosophilia melanogaster Dscam gene, which contains 12 mutually exclusive exons. The ease and the quantitative nature of this technique should be very useful. ------------------- Key: 6662 Medline: 15126679 Authors: Morton DB Title: Invertebrates yield a plethora of atypical guanylyl cyclases. Citation: Molecular Neurobiology 29: 97-116 2004 Type: REVIEW Genes: daf-11 gcy-6 gcy-11 gcy-12 gcy-15 gcy-21 gcy-25 gcy-27 gcy-31 gcy-32 gcy-33 gcy-34 gcy-35 gcy-36 gcy-37 odr-1 Abstract: Invertebrate model systems have a long history of generating new insights into neuronal signaling systems. This review focuses on cyclic GMP signaling and describes recent advances in understanding the properties and functions of guanylyl cyclases in invertebrates. The sequencing of three invertebrate genomes has provided a complete catalog of the guanylyl cyclases in C. elegans, Drosophila, and the mosquito Anopheles gambiae. Using this data and that from cloned guanylyl cyclases in Manduca sexta, C. elegans, and Drosophila, plus predictions and models from vertebrate guanylyl cyclases, evidence is presented that there is a much broader array of properties for these enzymes than previously realized. In addition to the classic homodimeric receptor guanylyl cyclases, C. elegans has at least two receptor guanylyl cyclases that are predicted to require heterodimer formation for activity. Soluble guanylyl cyclases are generally recognized as being obligate heterodimers that are activated by nitric oxide (NO). Some of the soluble guanylyl cyclases in C. elegans may heterodimeric, but all appear to be insensitive to NO. The beta2 soluble guanylyl cyclase subunit in mammals and similar ones in Manduca and Drosophila are active in the absence of additional subunits and there is evidence that Drosophila and Anopheles also express an additional subunit that enhances this activity. ------------------- Key: 6663 Medline: 15280232 Authors: Withee J;Galligan B;Hawkins N;Garriga G Title: Caenorhabditis elegans WASP and Ena/VASP proteins play compensatory roles in morphogenesis and neuronal cell migration. Citation: Genetics 167: 1165-1176 2004 Type: ARTICLE Genes: unc-34 wsp-1 wve-1 Abstract: We report here that WASP and Ena/VASP family proteins play overlapping roles in C. elegansmorphogenesis and neuronal cell migration. Specifically, these studies demonstrate that UNC-34/Ena plays a role in morphogenesis that is revealed only in the absence of WSP-1 function and that WSP-1 has a role in neuronal cell migration that is revealed only in the absence of UNC-34/Ena activity. To identify additional genes that act in parallel to unc-34/ena during morphogenesis, we performed a screen for synthetic lethals in an unc-34 null mutant background utilizing an RNAi feeding approach. To our knowledge, this is the first reported RNTAi-based screen for genetic interactors. As a result of this screen, we identified a second C. elegans WASP family protein, wve-1, that is most homologous to SCAR/WAVE proteins. Animals with impaired wve-1 function display defects in gastrulation, fail to undergo proper morphogenesis, and exhibit defects in neuronal cell migrations and axon outgrowth. Reducing wve-1 levels in either unc-34/ena or wsp-1 mutant backgrounds also leads to a significant enhancement of the gastrulation and morphogenesis defects. Thus, unc-34/ena, wsp-1, and wve-1 play overlapping roles during embryogenesis and unc-34/ena and wsp-1 play overlapping roles in neuronal cell migration. These observations show that WASP and Ena/VASP proteins can compensate for each other in vivo and provide the first demonstration of a role for Ena/VASP proteins in gastrulation and morphogenesis. In addition, our results provide the first example of an in vivo role for WASP family proteins in neuronal cell migrations and ------------------- Key: 6664 Medline: 15219696 Authors: Leapman RD:Kocsis E;Zhang G;Talbot TL;Laquerriere P Title: Three-dimensional distributions of elements in biological samples by energy-filtered electron tomography. Citation: Ultramicroscopy 100: 115-125 2004 Type: ARTICLE Genes: Abstract: By combining electron tomography with energy-filtered electron microscopy, we have shown the feasibility of determining the three-dimensional distributions of phosphorus in biological specimens. Thin sections of the nematode, Caenorhabditis elegans were prepared by high-pressure freezing,. freeze-substitution and plastic embedding. Images were recorded at energy losses above and below the phosphorus L-2,L-3 edge using a post-column imaging filter operating at a beam energy of 120 keV. The unstained specimens exhibited minimal contrast in bright-field images. After it was determined that the specimen was sufficiently thin to allow two-window ratio imaging of phosphorus, pairs of pre-edge and post-edge images were acquired in series over a tilt range of ñ55degrees at 5degrees increments for two orthogonal tilt axes. The projected phosphorus distributions were aligned using the pre-edge images that contained inelastic contrast from colloidal gold particles deposited on the specimen surface. A reconstruction and surface rendering of the phosphorus distribution clearly revealed features 15-20 nm in diameter, which were identified as ribosomes distributed along the stacked membranes of endoplasmic reticulum and in the cytoplasm. The sensitivity of the technique was estimated at <35 phosphorus atoms per voxel based on the known total ribosomal phosphorus content of approximately 7000 atoms. Although a high electron dose of approximately 10(7) e/nm(2) was required to record two-axis tilt series, specimens were sufficiently stable to allow image alignment and tomographic reconstruction. ------------------- Key: 6665 Medline: 15219396 Authors: Vastenhouw NL;Plasterk RHA Title: RNAi protects the Caenorhabditis elegans germline against transposition. Citation: Trends in Genetics 20: 314-319 2004 Type: REVIEW Genes: mut-7 mut-8 mut-14 mut-15 rde-1 rde-2 rde-4 Abstract: The availability of complete genome sequences has revealed that genomes contain numerous mobile genetic elements. The activity of these transposons results in genome instability. In the nematode Caenorhabditis elegans, transposition is silenced in the germline, protecting the genome from heritable defects that are caused by transposon jumps. The discovery of RNA interference (RNAi) has greatly increased our understanding of this genome-defense mechanism because transposon silencing and RNAi share common factors. RNAi is the post-transcriptional silencing of a gene in response to double-stranded RNA (dsRNA), which is processed into small interfering RNAs (siRNAs) that mediate sequence-specific RNA degradation. Indeed, transposon-derived dsRNA and siRNAs are detected in vivo and are capable of inducing silencing. In addition, many new genes have been identified that are required for the silencing of transposons. In this article, we discuss our current model for transposon silencing and address several unanswered questions because many aspects of this protection mechanism in C. elegans might be present in a ------------------- Key: 6666 Medline: 15295601 Authors: Denver DR;Morris K;Lynch M;Thomas WK Title: High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Citation: Nature 430: 679-682 2004 Type: ARTICLE Genes: Abstract: Mutations have pivotal functions in the onset of genetic diseases and are the fundamental substrate for evolution. However, present estimates of the spontaneous mutation rate and spectrum are derived from indirect and biased measurements. For instance, mutation rate estimates for Caenorhabditis elegans are extrapolated from observations on a few genetic loci with visible phenotypes and vary over an order of magnitude(1). Alternative approaches in mammals, relying on phylogenetic comparisons of pseudogene loci(2) and fourfold degenerate codon positions(3), suffer from uncertainties in the actual number of generations separating the compared species and the inability to exclude biases associated with natural selection. Here we provide a direct and unbiased estimate of the nuclear mutation rate and its molecular spectrum with a set of C. elegans mutation-accumulation lines that reveal a mutation rate about tenfold higher than previous indirect estimates and an excess of insertions over deletions. Because deletions dominate patterns of C. elegans pseudogene variation(4,5), our observations indicate that natural selection might be significant in promoting small genome size, and challenge the prevalent assumption that pseudogene divergence accurately reflects the spontaneous ------------------- Key: 6667 Medline: 15233996 Authors: Menzel O;Vellai T;Takacs-Vellai K;Reymond A;Mueller F;Antonarakis SE;Guipponi M Title: The Caenorhabditis elegans ortholog of C21orf80, a potential new protein O-vucosyltransferase, is required for normal development. Citation: Genomics 84: 320-330 2004 Type: ARTICLE Genes: pad-2 Abstract: Down syndrome (DS), as a phenotypic result of trisomy 2 1, is the most frequent aneuploidy at birth and the most common known genetic cause of mental retardation. DS is also characterized by other phenotypes affecting many organs, including brain, muscle, heart, limbs, gastrointestinal tract, skeleton, and blood. Any of the human chromosome 21 (Hsa21) genes may contribute to some of the DS phenotypes. To determine which of the Hsa21 genes are involved in DS, the effects of disrupting and overexpressing individual human gene orthologs in model organisms, such as the nematode Caenorhabditis elegans, can be analyzed. Here, we isolated and characterized C21orf80 (human chromosome 21 open reading frame 80), a potential novel protein O-fucosyltransferase gene that encodes three alternatively spliced transcripts. Transient expression of tagged C21orf80 proteins suggests a primary intracellular localization in the Golgi apparatus. To gain insight into the biological role of C21orf80 and its potential role in DS, we isolated its C. elegans ortholog, pad-2, and performed RNA interference (RNAi) and overexpression experiments. pad-2(RNAi) embryos showed failure to undergo normal morphogenesis. Transgenic worms with elevated dosage of pad-2 displayed severe body malformations and abnormal neuronal development. These results show that pad-2 is required for normal development and suggest potential roles for C21orf80 in the pathogenesis of DS. ------------------- Key: 6668 Medline: 15242805 Authors: van Furden D;Johnson K;Segbert C;Bossinger O Title: The C. elegans ezrin-radixin-moesin protein ERM-1 is necessary for apical junction remodelling and tubulogenesis in the intestine. Citation: Developmental Biology 272: 262-276 2004 Type: ARTICLE Genes: dlg-1 erm-1 frm-1 frm-2 frm-3 frm-4 frm-5 frm-6 frm-7 frm-8 frm-9 frm-10 hmr-1 hum-4 let-413 max-1 nfm-1 ptp-1 unc-112 Abstract: Members of the ezrin-radixin-moesin (ERM) family of proteins have been found to serve as linkers between membrane proteins and the F-actin cytoskeleton in many organisms. We used RNA interference (RNAi) approach to assay ERM proteins of the Caenorhabditis elegans genome for a possible involvement in apical junction (AJ) assembly or positioning. We identify erm-1 as the only ERM protein required for development and show, by multiple RNA interference, that additional four-point one, ezrin-radixin-moesin (FERM) domain-containing proteins cannot compensate for the depletion of ERM-1. ERNI-I is expressed in most if not all cells of the embryo at low levels but is upregulated in epithelia, like the intestine. ERM-1 protein co-localizes with F-actin and the intermediate filament protein IFB-2 at the apical cell cortex. ERM-1 depletion results in intestine-specific phenotypes like lumenal constrictions or even obstructions. This phenotype arises after epithelial polarization of intestinal cells and can be monitored using markers of the apical junction. We show that the initial steps of epithelial polarization in the intestine are not affected in erm-1(RNAi) embryos but the positioning of apical junction proteins to an apico-lateral position arrests prematurely or fails, resulting in multiple obstructions of the intestinal flow after hatching. Mechanistically, this phenotype might be due to an altered apical cytoskeleton because the apical enrichment of F-actin filaments is lost specifically in the intestine. ERM-1 is the first protein of the apical membrane domain affecting junction remodelling in C. elegans. ERM-1 interacts genetically with the catenin-cadherin system but not with the DLG-1 (Discs large)-dependent establishment of the apical junction. ------------------- Key: 6669 Medline: 15151982 Authors: Aono S;Legouis R;Hoose WA;Kemphues KJ Title: PAR-3 is required for epithelial cell polarity in the distal spermatheca of C. elegans. Citation: Development 131: 2865-2874 2004 Type: ARTICLE Genes: ajm-1 ceh-18 ipp-5 let-23 let-413 let-502 lin-3 par-3 par-6 pkc-2 rrf-1 Abstract: PAR-3 is localized asymmetrically in epithelial cells in a variety of animals from Caenorhabditis elegans to mammals. Although C. elegans PAR-3 is known to act in early blastomeres to polarize the embryo, a role for PAR-3 in epithelial cells of C. elegans has not been established. Using RNA interference to deplete PAR-3 in developing larvae, we discovered a requirement for PAR-3 in spermathecal development. Spermathecal precursor cells are born during larval development and differentiate into an epithelium that forms a tube for the storage of sperm. Eggs must enter the spermatheca to complete ovulation. PAR-3-depleted worms exhibit defects in ovulation. Consistent with this phenotype, PAR-3 is transiently expressed and localized asymmetrically in the developing somatic gonad, including the spermathecal precursor cells of L4 larvae. We found that the defect in ovulation can be partially suppressed by a mutation in IPP-5, an inositol polyphosphate 5-phosphatase, indicating that one effect of PAR-3 depletion is disruption of signaling between oocyte and spermatheca. Microscopy revealed that the distribution of AJM-1, an apical junction marker, and apical microfilaments are severely affected in the distal spermatheca of PAR-3-depleted worms. We propose that PAR-3 activity is required for the proper polarization of spermathecal cells and that defective ovulation results from defective distal spermathecal development. ------------------- Key: 6670 Medline: 15151984 Authors: Belfiore M;Pugnale P;Saudan Z;Puoti A Title: Roles of the C. elegans cyclophilin-like protein MOG-6 in MEP-1 binding and germline fates. Citation: Development 131: 2935-2945 2004 Type: ARTICLE Genes: ceh-13 cyp-3 cyp-4 cyp-7 fem-3 fbf-1 fbf-2 ges-1 gld-3 glp-1 mep-1 mog-1 mog-4 mog-5 mog-6 nos-3 mnDf29 mnDf57 mnDf62 mnDf66 mnDf87 mnDf89 mnDf90 Abstract: The switch from spermatogenesis to oogenesis in the Caenorhabditis elegans hermaphrodite requires mog-6, which post-transcriptionally represses the fem-3 RNA. In this study, we show that mog-6 codes for a divergent nuclear cyclophilin, in that a conserved domain is not required for its function in the sperm-oocyte switch. MOG-6 binds to the nuclear zinc finger protein MEP-1 through two separate domains that are essential for the role of MOG-6 in the sperm-oocyte switch. We propose that MOG-6 has a function distinct from that of prevailing cyclophilins and that its binding to MEP-1 is essential for germline sex determination. Finally, we found that gld-3 mog-6 mutants develop germline tumors, suggesting that mog-6 might function in the decision between mitosis and meiosis. ------------------- Key: 6671 Medline: 15210315 Authors: Iwasaki Y;Gomi S Title: Stochastic formulation for a partial neural circuit of C. elegans. Citation: Bulletin of Mathematical Biology 66: 727-743 2004 Type: ARTICLE Genes: Abstract: We present a stochastic formulation for a partial neural circuit of Caenorhabditis elegans. This study is concerned with how to reduce the degree of freedom in a large neural circuit. In the presented formulation, neurons in the whole neural circuit are divided into two complementary groups. One is the neurons which are mainly associated with a certain behavior, and the other is the remaining neurons of C. elegans. In an ordinary study on a partial neural circuit, the influence of the latter (the remaining neurons) on the former (the associated neurons) is completely neglected. In the presented formulation, however, the influence is expressed by a stochastic variable. The structure of the ensemble for the stochastic variable is appropriately evaluated by the neural connectivity of C. elegans since the neural connectivity of C. elegans has been completely determined. In this way, the degree of freedom is effectively reduced. We apply the presented formulation to determine the synaptic signs in the touch sensitivity circuit of C. elegans. The synaptic signs are determined to satisfy the locomotory behaviors in C. elegans. We find that the influence of the remaining neurons on the touch sensitivity circuit is important to determine the synaptic signs. ------------------- Key: 6672 Medline: 15254247 Authors: Spartz AK;Herman RK;Shaw JE Title: SMU-2 and SMU-1, Caenorhabditis elegans homologs of mammalian spliceosome-associated proteins RED and fSAP57, work together to affect splice site choice. Citation: Molecular and Cellular Biology 24: 6811-6823 2004 Type: ARTICLE Genes: mec-8 smu-1 smu-2 unc-52 ccDf11 Abstract: Mutations in the Caenorhabditis elegans gene smu-2 suppress mec-8 and unc-52 mutations. It has been proposed that MEC-8 regulates the alternative splicing of unc-52 transcripts, which encode the core protein of perlecan, a basement membrane proteoglycan. We show that mutation in smu-2 leads to enhanced accumulation of transcripts that skip exon 17, but not exon 18, of unc-52, which explains our finding that smu-2 mutations suppress the uncoordination conferred by nonsense mutations in exon P, but not in exon 18, of unc-52. We conclude that smu-2 encodes a ubiquitously expressed nuclear protein that is 40% identical to the human RED protein, a component of purified spliceosomes. The effects of smu-2 mutation on both unc-52 pre-mRNA splicing and the suppression of mec-8 and unc-52 mutant phenotypes are indistinguishable from the effects of mutation in smu-1, a gene that encodes a protein that is 62% identical to human spliceosome-associated protein fSAP57. We provide evidence that SMU-2 protects SMU-1 from degradation in vivo. In vitro and in vivo coimmunoprecipitation experiments indicate that SMU-2 and SMU-1 bind to each other. We propose that SMU-2 and SMU-1 function together to regulate splice site choice in the ------------------- Key: 6673 Medline: 15231060 Authors: Luo Y Title: Long-lived worms and aging. Citation: Redox Report 9: 65-69 2004 Type: REVIEW Genes: age-1 clk-1 daf-2 daf-12 daf-16 daf-23 eat-1 eat-2 hsp-16-2 old-1 Abstract: Several investigators have generated long-lived nematode worms (Caenorhabditis elegans) in the past decade by mutation of genes in the organism in order to study the genetics of aging and longevity. Dozens of longevity assurance genes (LAG) that dramatically increase the longevity of this organism have been identified. All long-lived mutants of C. elegans are also resistant to environmental stress, such as high temperature, reactive oxygen species (ROS), and ultraviolet irradiation. Double mutation of LAGs further extended life span up to 400%, providing more insight into cellular mechanisms that put limits on the life span of organisms. With the availability of the LAG mutants and combined DNA microarray and RNAi technology, the understanding of actual biochemical processes that determine life span is within reach: the downstream signal transduction pathway may regulate life span by up-regulating pro-longevity genes such as those that encode antioxidant enzymes and/or stress-response proteins, and down-regulating specific life-shortening genes. Furthermore, longevity could be modified through chemical manipulation. Results from these studies further support the free radical theory of aging, suggest that the molecular mechanism of aging process may be shared in all organisms, and provide insight for ------------------- Key: 6674 Medline: 15150269 Authors: Mohri K;Vorobiev S;Fedorov AA;Almo SC;Ono S Title: Identification of functional residues on Caenorhabditis elegans actin-interacting protein 1 (UNC-78) for disassembly of actin depolymerizing factor/cofilin-bound actin filaments. Citation: Journal of Biological Chemistry 279: 31697-31707 2004 Type: ARTICLE Genes: unc-60 unc-78 Abstract: Actin-interacting protein 1 (AIP1) is a WD40 repeat protein that enhances actin filament disassembly in the presence of actin-depolymerizing factor (ADF)/cofilin. AIP1 also caps the barbed end of ADF/cofilin-bound actin filament. However, the mechanism by which AIP1 interacts with ADF/cofilin and actin is not clearly understood. We determined the crystal structure of Caenorhabditis elegans AIP1 ( UNC-78), which revealed 14 WD40 modules arranged in two seven-bladed beta-propeller domains. The structure allowed for the mapping of conserved surface residues, and mutagenesis studies identified five residues that affected the ADF/cofilin-dependent actin filament disassembly activity. Mutations of these residues, which reside in blades 3 and 4 in the N-terminal propeller domain, had significant effects on the disassembly activity but did not alter the barbed end capping activity. These data support a model in which this conserved surface of AIP1 plays a direct role in enhancing fragmentation/depolymerization of ADF/cofilin-bound actin filaments but not in barbed end ------------------- Key: 6675 Medline: 15242600 Authors: Huyen Y;Jeffrey PD;Derry WB;Rothman JH;Pavletich NP;Stavridi ES;Halazonetis TD Title: Structural differences in the DNA binding domains of human p53 and its C. elegans ortholog Cep-1. Citation: Structure 12: 1237-1243 2004 Type: ARTICLE Genes: cep-1 Abstract: The DNA binding domains of human p53 and Cep-1, its C. elegans ortholog, recognize essentially identical DNA sequences despite poor sequence similarity. We solved the three-dimensional structure of the Cep-1 DNA binding domain in the absence of DNA and compared it to that of human p53. The two domains have similar overall folds. However, three loops, involved in DNA and Zn binding in human p53, contain small et helices in Cep-1. The a. helix in loop L3 of Cep-1 orients the side chains of two conserved arginines toward DNA; in human p53, both arginines are mutation hotspots, but only one contacts DNA. The a helix in loop L1 of Cep-1 repositions the entire loop, making it unlikely for residues of this loop to contact bases in the major groove of DNA, as occurs in human p53. Thus, during evolution there have been considerable changes in the structure of the p53 DNA binding domain. ------------------- Key: 6676 Medline: 15306811 Authors: Chang S;Johnston RJ;Frokjaer-Jensen C;Lockery S;Hobert O Title: MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Citation: Nature 430: 785-789 2004 Type: ARTICLE Genes: ceh-36 che-1 cog-1 die-1 gcy-5 gcy-7 lim-6 lin-49 lsy-6 mir-273 unc-37 Abstract: Animal microRNAs ( miRNAs) are gene regulatory factors that prevent the expression of specific messenger RNA targets by binding to their 3' untranslated region(1-3). The Caenorhabditis elegans lsy-6 miRNA ( for lateral symmetry defective) is required for the left/right asymmetric expression of guanyl cyclase (gcy) genes in two chemosensory neurons termed ASE left (ASEL) and ASE right (ASER)(4,5). The asymmetric expression of these putative chemoreceptors in turn correlates with the functional lateralization of the ASE neurons(6). Here we find that a mutation in the die-1 zinc-finger transcription factor disrupts both the chemosensory laterality and left/right asymmetric expression of chemoreceptor genes in the ASE neurons. die-1 controls chemosensory laterality by activating the expression of lsy-6 specifically in ASEL, but not in ASER, where die-1 expression is downregulated through two sites in its 30 untranslated region. These two sites are complementary to mir-273, a previously uncharacterized miRNA, whose expression is strongly biased towards ASER. Forced bilateral expression of mir-273 in ASEL and ASER causes a loss of asymmetric die-1 expression and ASE laterality. Thus, an inverse distribution of two sequentially acting miRNAs in two bilaterally symmetric neurons controls laterality of the nematode chemosensory ------------------- Key: 6677 Medline: 15315508 Authors: Hutter H Title: Five-colour in vivo imaging of neurons in Caenorhabditis elegans. Citation: Journal of Microscopy 215: 213-218 2004 Type: ARTICLE Genes: glr-1 odr-2 unc-47 unc-129 Abstract: In the last few years variants of the 'green fluorescent protein' (GFP) with different spectral properties have been generated. This has greatly increased the number of possible applications for these fluorochromes in cell biology. The significant overlap of the excitation and emission spectra of the different GFP variants imposes constraints on the number of variants that can be used simultaneously in a single sample. In particular, the two brightest variants, GFP and YFP, are difficult to separate spectrally. This study shows that GFP and YFP can be readily separated with little spectral overlap (cross-talk) with the use of a confocal microscope equipped with an acusto-optical beam splitter and freely adjustable emission windows. Under optimal recording conditions cross-talk is less than 10%. Together with two other fluorescent proteins and the lipophilic dye DiD, a total of five different colours can now be used simultaneously to label in vivo distinct anatomical structures such as neurons and their processes. Spatial resolution of the confocal microscope is sufficient to resolve the relative position of labelled axons within a single axon bundle. The use of five distinct marker dyes allows the in vivo analysis of the Caenorhabditis elegans nervous system at unprecedented resolution and richness in detail at the light microscopic ------------------- Key: 6678 Medline: Authors: 15262945 Title: A movable surface: formation of Yersinia sp. biofilms on motile Caenorhabditis elegans. Citation: Journal of Bacteriology 186: 5087-5092 2004 Type: ARTICLE Genes: unc-13 unc-54 Abstract: Bubonic plague is transmitted by fleas whose feeding is blocked by a mass of Yersinia pestis in the digestive tract. Y. pestis and the closely related Y. pseudotuberculosis also block the feeding of Caenorhabditis elegans by forming a biofilm on the nematode head. C. elegans mutants with severe motility defects acquire almost no biofilm, indicating that normal animals accumulate the biofilm matrix as they move through a Yersinia lawn. Using the lectin wheat germ agglutinin as a probe, we show that the matrix on C elegans contains carbohydrate produced by Yersinia. The carbohydrate is present in bacterial lawns prior to addition of nematodes, indicating that biofilm formation does not involve signaling between the two organisms. Furthermore, biofilm accumulation depends on continuous C. elegans exposure to a lawn of Yersinia ------------------- Key: 6679 Medline: 15277919 Authors: Kayser EB;Morgan PG;Sedensky MM Title: Mitochondrial complex I function affects halothane sensitivity in Caenorhabditis elegans. Citation: Anesthesiology 101: 365-372 2004 Type: ARTICLE Genes: gas-1 Abstract: Background: The gene gas-1 encodes a subunit of complex 1 of the mitochondrial electron transport chain in Caenorhabditis elegans. A mutation in gas-1 profoundly increases sensitivity of C elegans to volatile anesthetics. It is unclear which aspects of mitochondrial function account for the hypersensitivity of the mutant. Methods: Oxidative phosphorylation was determined by measuring mitochondrial oxygen consumption using electron donors specific for either complex I or complex II. Adenosine triphosphate concentrations were determined by measuring luciferase activity. Oxidative damage to mitochondrial proteins was identified using specific antibodies. Results: Halothane inhibited oxidative phosphorylation in isolated wild-type mitochondria within a concentration range that immobilizes intact worms. At equal halothane concentrations, complex I activity but not complex II activity was lower in mitochondria from mutant (gas-1) animals than from wild-type (N2) animals. The halothane concentrations needed to immobilize 50% of N2 or gas-1 animals, respectively, did not reduce oxidative phosphorylation to identical rates in the two strains. In air, adenosine triphosphate concentrations were similar for N2 and gas-1 but were decreased in the presence of halothane only in gas-1 animals. Oxygen tension changed the sensitivity of both strains to halothane. When nematodes were raised in room air, oxidative damage to nutochondrial proteins was increased in the mutant animal compared with the wild type. Conclusions: Rates of oxidative phosphorylation and changes in adenosine triphosphate concentrations by themselves do not control anesthetic-induced immobility of wild-type C. elegans. However. they may contribute to the increased sensitivity to volatile anesthetics of the gas-1 mutant. Oxidative damage to proteins may be an important contributor to ------------------- Key: 6680 Medline: 15269234 Authors: Sakaguchi A;Matsumoto K;Hisamoto N Title: Roles of MAP kinase cascades in Caenorhabditis elegans. Citation: Journal of Biochemistry 136: 7-11 2004 Type: REVIEW Genes: dlk-1 glh-1 jip-1 jkk-1 jnk-1 kgb-1 kgb-2 kin-18 lit-1 mek-1 mkk-4 mlk-1 mom-1 mom-2 mom-4 mom-5 mtk-1nsy-1 pmk-1 pmk-2 pmk-3 pop-1 sek-1 tap-1 unc-16 unc-43 wrm-1 zap-1 Abstract: Mitogen-activated protein kinases (MAPKs) are serine/threonine protein kinases that are activated by diverse stimuli such as growth factors, cytokines, neurotransmitters and various cellular stresses. MAPK cascades are generally present as three-component modules, consisting of MAPKKK, MAPKK and MAPK. The precise molecular mechanisms by which these MAPK cascades transmit signals is an area of intense research, and our evolving understanding of these signal cascades has been facilitated in great part by genetic analyses in model organisms. One organism that has been commonly used for genetic manipulation and physiological characterization is the nematode Caenorhabditis elegans. Genes sequenced in the C. elegans genome project have furthered the identification of components involved in several MAPK pathways. Genetic and biochemical studies on these components have shed light on the physiological roles of MAPK cascades in the control of cell fate decision, neuronal function and immunity in C. elegans. ------------------- Key: 6681 Medline: 15312767 Authors: Petriv OI;Tang L;Titorenko VI;Rachubinski RA Title: A new definition for the consensus sequence of the peroxisome targeting signal type 2. Citation: Journal of Molecular Biology 341: 119-134 2004 Type: ARTICLE Genes: Abstract: All organisms except the nematode Caenorhabditis elegans have been shown to possess an import system for peroxisomal proteins containing a peroxisome targeting signal type 2 (PTS2). The currently accepted consensus sequence for this amino-terminal nonapeptide is -(R/K)(L/V/I)X-5(H/Q)(L/A)-. Some C. elegans proteins contain putative PTS2 motifs, including the ortholog (CeMeK) of human mevalonate kinase, an enzyme known to be targeted by PTS2 to mammalian peroxisomes. We cloned the gene for CeMeK (open reading frame Y42G9A.4) and examined the subcellular localization of CeMeK and of two other proteins with putative PTS2s at their amino termini encoded by the open reading frames D1053.2 and W10G11.11. All three proteins localized to the cytosol, confirming and extending the finding that C. elegans lacks PTS2-dependent peroxisomal protein import. The putative PTS2s of the proteins encoded by D1053.2 and W10G11.11 did not function in targeting to peroxisomes in yeast or mammalian cells, suggesting that the current PTS2 consensus sequence is too broad. Analysis of available experimental data on both functional and nonfunctional PTS2s led to two re-evaluated PTS2 consensus sequences: -R(L/V/I/Q)XX(L/V/I/H)(L/S/G/A)X(H/Q)(L/A)-, describes the most common variants of PTS2, while -(R/K)(L/V/I/Q)XX(L/V/I/H/ Q)(L/S/G/A/K)X(H/Q)(L/A/F)-, describes essentially all variants of PTS2. These redefined PTS2 consensus sequences will facilitate the identification of proteins of unknown cellular localization as possible peroxisomal proteins. ------------------- Key: 6682 Medline: 15310838 Authors: Granger L;Martin E;Segalat L Title: Mos as a tool for genome-wide insertional mutagenesis in Caenorhabditis elegans: results of a pilot study. Citation: Nucleic Acids Research 32: e117- 2004 Type: ARTICLE Genes: Abstract: The sequence of the Caenorhabditis elegans genome contains approximately 19 000 genes. Available mutants currently exist for <20% of these genes. The existence of a Mos-based inducible transposon system in C.elegans could theoretically serve as a tool to saturate the genome with insertions. We report here the results of a pilot study aimed at assaying this strategy. We generated 914 independent random Mos insertions and determined their location by inverse PCR. The distribution of the insertions throughout the genome does not reveal any gross distortion, with the exception of a major hotspot on chromosome I (rDNA locus). Transposons are evenly distributed between the genic and intergenic regions. Within genes, transposons insert preferentially into the introns. We derived the consensus target site for Mos in C.elegans (ATATAT), which is common to Tc1, another mariner element. Finally, we assayed the mutagenic properties of insertions located in exons by comparing the phenotype of homozygous strains to that of known mutations or RNAi of the same gene. This pilot experiment shows that a Mos-based approach is a viable strategy that can contribute to the constitution of genome-wide collections of identified C.elegans mutants. ------------------- Key: 6683 Medline: 15254550 Authors: Wood JG;Rogina B;Lavu S;Howitz K;Helfand SL;Tatar M;Sinclair D Title: Sirtuin activators mimic caloric restriction and delay ageing in metazoans. Citation: Nature 430: 686-689 2004 Type: ARTICLE Genes: sir-2.1 Abstract: Caloric restriction extends lifespan in numerous species. In the budding yeast Saccharomyces cerevisiae this effect requires Sir2 (ref. 1), a member of the sirtuin family of NAD+-dependent deacetylases. Sirtuin activating compounds (STACs) can promote the survival of human cells and extend the replicative lifespan of yeast. Here we show that resveratrol and other STACs activate sirtuins from Caenorhabditis elegans and Drosophila melanogaster, and extend the lifespan of these animals without reducing fecundity. Lifespan extension is dependent on functional Sir2, and is not observed when nutrients are restricted. Together these data indicate that STACs slow metazoan ageing by mechanisms that may be related to caloric ------------------- Key: 6684 Medline: 15256594 Authors: Kim DH;Liberati NT;Mizuno T;Inoue H;Hisamoto N;Matsumoto K;Ausubel FM Title: Integration of Caenorhabditis elegans MAPK pathways mediating immunity and stress resistance by MEK-1 MAPK kinase and VHP-1 MAPK phosphatase. Citation: Proceedings of the National Academy of Sciences USA 101: 10990-10994 2004 Type: ARTICLE Genes: jnk-1 kgb-1 mek-1 nsy-1 pmk-1 sek-1 vhp-1 Abstract: The p38 and JNK classes of mitogen-activated protein kinases (MAPKs) have evolutionarily conserved roles in the control of cellular responses to microbial and abiotic stresses. The mechanisms by which crosstalk between distinct p38 and c-Jun N-terminal kinase (JNK) MAPK pathways occurs with resultant integration of signaling information have been difficult to establish, particularly in the context of whole organism physiology. In Caenorhabditis elegans a PMK-1 p38 MAPK pathway is required for resistance to bacterial infection, and a KGB-1 JNK-like MAPK pathway has recently been shown to mediate resistance to heavy metal stress. Here, we show that two components of the KGB-1 pathway, MEK-1 MAPK kinase (MAPKK), a homolog of mammalian MKK7, and VHP-1 MAPK phosphatase (MKP), a homolog of mammalian MKP7, also regulate pathogen resistance through the modulation of PMK-1 activity. The regulation of p38 and JNK-like MAPK pathways mediating immunity and heavy metal stress by common MAPKK and MKP signaling components suggests pivotal roles for MEK-1 and VHP-1 in the integration of diverse stress signals contributing to pathogen resistance in C elegans. In addition, these data point to mechanisms in multicellular organisms by which signals transduced by distinct MAPK pathways may be subject to physiological integration at the level of regulation of ------------------- Key: 6685 Medline: 15256590 Authors: Huffman DL;Abrami L;Sasik R;Corbeil J;van der Goot FG;Aroian RV Title: Mitogen-activated protein kinase pathways defend against bacterial pore-forming toxins. Citation: Proceedings of the National Academy of Sciences USA 101: 10995-11000 2004 Type: ARTICLE Genes: glp-4 jnk-1 kgb-1 kgb-2 rrf-3 sek-1 ttm-1 ttm-2 Abstract: Cytolytic pore-forming toxins are important for the virulence of many disease-causing bacteria. How target cells molecularly respond to these toxins and whether or not they can mount a defense are poorly understood. By using microarrays, we demonstrate that the nematode Caenorhabditis elegans responds robustly to Cry5B, a member of the pore-forming Crystal toxin family made by Bacillus thuringiensis. This genomic response is distinct from that seen with a different stressor, the heavy metal cadmium. A p38 mitogen-activated protein kinase (MAPK) kinase and a c-Jun N-terminal-like MAPK are both transcriptionally up-regulated by Cry5B. Moreover, both MAPK pathways are functionally important because elimination of either leads to animals that are (t) hypersensitive to a low, chronic dose of toxin and (it) hypersensitive to a high, brief dose of toxin such that the animal might naturally encounter in the wild. These results extend to mammalian cells because inhibition of p38 results in the hypersensitivity of baby hamster kidney cells to aerolysin, a pore-forming toxin that targets humans. Furthermore, we identify two downstream transcriptional targets of the p38 MAPK pathway, ttm-1 and ttm-2, that are required for defense against Cry5B. Our data demonstrate that cells defend against pore-forming toxins by means of conserved MAPK pathways. ------------------- Key: 6686 Medline: 15273685 Authors: Deng X;Hofmann ER;Villanueva A;Hobert O;Capodieci P;Veach DR;Yin X;Campodonico L;Glekas A;Cordon-Cardo C;Clarkson B;Bornmann WG;Fuks Z;Hengartner MO;Kolesnick R Title: Caenorhabditis elegans ABL-1 antagonizes p53-mediated germline apoptosis after ionizing irradiation. Citation: Nature Genetics 36: 906-912 2004 Type: ARTICLE Genes: abl-1 ced-1 ced-3 ced-4 ced-9 cep-1 clk-2 egl-1 hus-1 mek-2 mpk-1 mre-11 mrt-2 rad-51 Abstract: c-Abl, a conserved nonreceptor tyrosine kinase, integrates genotoxic stress responses, acting as a transducer of both pro- and antiapoptotic effector pathways(1). Nuclear c-Abl seems to interact with the p53 homolog p73 to elicit apoptosis(2,3). Although several observations suggest that cytoplasmic localization of c-Abl is required for antiapoptotic function(4,5), the signals that mediate its antiapoptotic effect are largely unknown. Here we show that worms carrying an abl-1 deletion allele, abl-1(ok171), are specifically hypersensitive to radiation-induced apoptosis in the Caenorhabditis elegans germ line. Our findings delineate an apoptotic pathway antagonized by ABL-1, which requires sequentially the cell cycle checkpoint genes clk-2, hus-1 and mrt-2; the C. elegans p53 homolog, cep-1; and the genes encoding the components of the conserved apoptotic machinery, ced-3, ced-9 and egl-1. ABL-1 does not antagonize germline apoptosis induced by the DNA-alkylating agent ethylnitrosourea. Furthermore, worms treated with the c-Abl inhibitor STI-571 ( Gleevec; used in human cancer therapy), two newly synthesized STI-571 variants or PD166326 had a phenotype similar to that generated by abl-1( ok171). These studies indicate that ABL-1 distinguishes proapoptotic signals triggered by two different DNA-damaging agents and suggest that C. elegans might provide tissue models for development of anticancer ------------------- Key: 6687 Medline: 15303097 Authors: Kipreos ET Title: Developmental quiescence: Cdc14 moonlighting in G1. Citation: Nature Cell Biology 6: 693-695 2004 Type: REVIEW Genes: cdc-14 cki-1 zen-4 Abstract: Cdc14 is a phosphatase that can antagonize CDK/cyclin cell-cycle functions. New insights from Caenorhabditis elegans show that CDC-14 is required to prevent cell-cycle entry during extended periods of developmentally regulated quiescence, and also clarify its role in creating the central mitotic spindle during anaphase. ------------------- Key: 6688 Medline: 15247923 Authors: Saito RM;Perreault A;Peach B;Satterlee JS;van den Heuvel S Title: The CDC-14 phosphatase controls developmental cell-cycle arrest in C. elegans. Citation: Nature Cell Biology 6: 777-783 2004 Type: ARTICLE Genes: cdc-14 cki-1 cye-1 lag-2 let-23 let-60 lin-12 lin-35 rrf-3 ccDf2 ccDf5 mnDf100 Abstract: Temporal control of cell division is critical for proper animal development. To identify mechanisms involved in developmental arrest of cell division, we screened for cell-cycle mutants that disrupt the reproducible pattern of somatic divisions in the nematode C. elegans. Here, we show that the cdc-14 phosphatase is required for the quiescent state of specific precursor cells. Whereas budding yeast Cdc14p is essential for mitotic exit, inactivation of C. elegans cdc-14 resulted in extra divisions in multiple lineages, with no apparent defects in mitosis or cell-fate determination. CDC-14 fused to the green fluorescent protein (GFP-CDC-14) localized dynamically and accumulated in the cytoplasm during G1 phase. Genetic interaction and transgene expression studies suggest that cdc-14 functions upstream of the cki-1 Cip/Kip inhibitor to promote accumulation of CKI-1 in the nucleus. Our data support a model in which CDC-14 promotes a hypophosphorylated and stable form of CKI-1 required for developmentally ------------------- Key: 6689 Medline: 15318222 Authors: Kim H;Rogers MJ;Richmond JE;McIntire SL Title: SNF-6 is an acetylcholine transporter interacting with the dystrophin complex in Caenorhabditis elegans. Citation: Nature 430: 891-896 2004 Type: ARTICLE Genes: ace-1 ace-2 dyb-1 dyc-1 dys-2 egl-19 hlh-1 snf-6 stn-1 Abstract: Muscular dystrophies are among the most common human genetic diseases and are characterized by progressive muscle degeneration. Muscular dystrophies result from genetic defects in components of the dystrophin-glycoprotein complex (DGC), a multimeric complex found in the muscle cell plasma membrane(1). The DGC links the intracellular cytoskeleton to the extracellular matrix and is thought to be important for maintaining the mechanical integrity of muscles(2) and organizing signalling molecules(3). The exact role of the DGC in the pathogenesis of disease has, however, remained uncertain(4). Mutations in Caenorhabditis elegans DGC genes lead to specific defects in coordinated movement and can also cause muscle degeneration(5-7). Here we show that mutations in the gene snf-6 result in phenotypes indistinguishable from those of the DGC mutants, and that snf-6 encodes a novel acetylcholine/choline transporter. SNF-6 mediates the uptake of acetylcholine at neuromuscular junctions during periods of increased synaptic activity. SNF-6 also interacts with the DGC, and mutations in DGC genes cause a loss of SNF-6 at neuromuscular junctions. Improper clearing of acetylcholine and prolonged excitation of muscles might contribute to the pathogenesis of muscular ------------------- Key: 6690 Medline: 15282614 Authors: Mishima M;Pavicic V;Gruneberg U;Nigg EA;Glotzer M Title: Cell cycle regulation of central spindle assembly. Citation: Nature 430: 908-913 2004 Type: ARTICLE Genes: cdc-14 let-21 zen-4 Abstract: The bipolar mitotic spindle is responsible for segregating sister chromatids at anaphase. Microtubule motor proteins generate spindle bipolarity and enable the spindle to perform mechanical work(1). A major change in spindle architecture occurs at anaphase onset when central spindle assembly begins. This structure regulates the initiation of cytokinesis and is essential for its completion(2). Central spindle assembly requires the central-spindlin complex composed of the Caenorhabditis elegans ZEN-4 (mammalian orthologue MKLP1) kinesin-like protein and the Rho family GAP CYK-4 (MgcRacGAP). Here we describe a regulatory mechanism that controls the timing of central spindle assembly. The mitotic kinase Cdk1/cyclin B phosphorylates the motor domain of ZEN-4 on a conserved site within a basic amino-terminal extension characteristic of the MKLP1 subfamily. Phosphorylation by Cdk1 diminishes the motor activity of ZEN-4 by reducing its affinity for microtubules. Preventing Cdk1 phosphorylation of ZEN-4/MKLP1 causes enhanced metaphase spindle localization and defects in chromosome segregation. Thus, phosphoregulation of the motor domain of MKLP1 kinesin ensures that central spindle assembly occurs at the appropriate time in the cell cycle and maintains genomic ------------------- Key: 6691 Medline: 15155810 Authors: Klopfenstein DR;Vale RD Title: The lipid binding pleckstrin homology domain in UNC-104 kinesin is necessary for synaptic vesicle transport in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 15: 3729-3739 2004 Type: ARTICLE Genes: unc-104 Abstract: UNC-104 (KIF1A) is a kinesin motor that transports synaptic vesicles from the neuronal cell body to the terminal. Previous in vitro studies have shown that a Dictyostelium relative of UNC-104 transports liposomes containing acidic phospholipids, but whether this interaction is needed for the recognition and transport of synaptic vesicles in metazoans remains unexplored. Here, we have introduced mutations in the nonmotor domain of UNC-104 and examined whether these mutant motors can rescue an unc-104 Caenorhabditis elegans strain. We show that a pleckstrin homology (PH) domain in UNC-104 is essential for membrane transport in living C. elegans, that this PH domain binds specifically to phosphatidylinositol-4,5-bisphosphate (PI(4,5)P-2), and that point mutants in the PH domain that interfere with PI(4,5)P, binding in vitro also interfere with UNC-104 function in vivo. Several other lipid-binding modules could not effectively substitute for the UNC-104 PH domain in this in vivo assay. Real time imaging also revealed that a lipid-binding point mutation in the PH domain reduced movement velocity and processivity of individual UNC-104::GFP punctae in neurites. These results reveal a critical role for PI(4,5)P-2 binding in UNC-104-mediated axonal transport and shows that the cargo-binding properties of the distal PH domain can affect motor output. ------------------- Key: 6692 Medline: 15194811 Authors: Yin X;Gower NJD;Baylis HA;Strange K Title: Inositol 1,4,5-trisphosphate signaling regulates rhythmic contractile activity of myoepithelial sheath cells in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 15: 3938-3949 2004 Type: ARTICLE Genes: egl-8 fog-2 itr-1 let-23 let-502 lin-3 plc-1 plc-2 plc-3 plc-4 pll-1 rrf-1 unc-4 unc-24 vab-1 Abstract: Intercellular communication between germ cells and neighboring somatic cells is essential for reproduction. Caenorhabditis elegans oocytes are surrounded by and coupled via gap junctions to smooth muscle-like myoepithelial sheath cells. Rhythmic sheath cell contraction drives ovulation and is triggered by a factor secreted from oocytes undergoing meiotic maturation. We demonstrate for the first time that signaling through the epidermal growth factor-like ligand LIN-3 and the LET-23 tyrosine kinase receptor induces ovulatory contractions of sheath cells. Reduction-of-function mutations in the inositol 1,4,5-trisphosphate (IP3) receptor gene itr-1 and knockdown of itr-1 expression by RNA interference inhibit sheath contractile activity. itr-1 gain-of-function mutations increase the rate and force of basal contractions and induce tonic sheath contraction during ovulation. Sheath contractile activity is disrupted by RNAi of plc-3, one of six phospholipase C-encoding genes in the C. elegans genome. PLC-3 is a PLC-gamma homolog and is expressed in contractile sheath cells of the proximal gonad. Maintenance of sheath contractile activity requires plasma membrane Ca2+ entry. We conclude that IP3 generated by LET-23 mediated activation of PLC-gamma induces repetitive intracellular Ca2+ release that drives rhythmic sheath cell contraction. Calcium entry may function to trigger Ca2+ release via IP3 receptors and/or refill intracellular Ca2+ ------------------- Key: 6693 Medline: 15271910 Authors: Moy TI;Mylonakis E;Calderwood SB;Ausubel FM Title: Cytotoxicity of hydrogen peroxide produced by Enterococcus faecium. Citation: Infection and Immunity 72: 4512-4520 2004 Type: ARTICLE Genes: daf-2 daf-16 Abstract: Although the opportunistic bacterial pathogen Enterococcus faecium is a leading source of nosocomial infections, it appears to lack many of the overt virulence factors produced by other bacterial pathogens, and the underlying mechanism of pathogenesis is not clear. Using E. faecium-mediated killing of the nematode worm Caenorhabditis elegans as an indicator of toxicity, we determined that E. faecium produces hydrogen peroxide at levels that cause cellular damage. We identified E. faecium transposon insertion mutants with altered C elegans killing activity, and these mutants were altered in hydrogen peroxide production. Mutation of an NADH oxidase-encoding gene eliminated nearly all NADH oxidase activity and reduced hydrogen peroxide production. Mutation of an NADH peroxidase-encoding gene resulted in the enhanced accumulation of hydrogen peroxide. E. faecium is able to produce hydrogen peroxide by using glycerol-3-phosphate oxidase, and addition of glycerol to the culture medium enhanced the killing of C elegans. Conversely, addition of glucose, which leads to the down-regulation of glycerol metabolism, prevented both C. elegans killing and hydrogen peroxide production. Lastly, detoxification of hydrogen peroxide either by exogenously added catalase or by a C. elegans transgenic strain overproducing catalase prevented E. faecium-mediated killing. These results suggest that hydrogen peroxide produced by E. faecium has cytotoxic effects and highlight the utility of C. elegans pathogenicity models for identifying bacterial virulence ------------------- Key: 6694 Medline: 15265690 Authors: Kinnaird JH;Maitland K;Walker GA;Wheatley I;Thompson FJ;Devaney E Title: HRP-2, a heterogeneous nuclear ribonucleoprotein, is essential for embryogenesis and oogenesis in Caenorhabditis elegans. Citation: Experimental Cell Research 298: 418-430 2004 Type: ARTICLE Genes: end-1 elt-2 hrp-2 med-1 myo-2 pha-4 pes-10 Abstract: Heterogeneous nuclear ribonucleoproteins (hnRNPs) have fundamental roles in the posttranscriptional control of gene expression. Here, we describe an hnRNP from Caenorhabditis elegans(HRP-2), which shares significant homology with mammalian hnRNP R, hnRNP Q and ACF, the essential complementation factor in ApoB mRNA editing. All four proteins possess a similar molecular architecture, with three closely linked RNA-binding domains and a C-terminus that contains RG/RGG repeat motifs. An HPP-2::GFP fusion protein was ubiquitously expressed in C. elegans during embryogenesis and subsequent larval development. Expression was also detected in the hermaphrodite gonad using a specific antibody, suggesting that HRP-2 is provided maternally. HRP-2 was predominantly localised to nuclei and analysis of transgenic lines expressing C-terminal deletions of HRP-2 defined a functional nuclear localisation signal. Analysis by RNAi demonstrated that HRP-2 was essential for embryogenesis and fertility. Cell divisions were slower in hrp-2(RNAi) embryos and the majority showed an early embryonic arrest phenotype. Shorter exposure to dsRNA allowed development to the twofold stage and the few embryos that hatched were abnormal. Adult worms that developed from embryos exposed to RNAi were completely sterile due to a failure in oocyte formation. These results demonstrate that HRP-2 or its RNA targets are essential for normal embryonic development and ------------------- Key: 6695 Medline: Authors: Poletti G;Orsini F;Batani D;Bernardinello A;Desai T;Ullschmied J;Skala J;Kralikova B;Krousky E;Juha L;Pfeifer M;Kadlec C;Mocek T;Prag A;Renner O;Cotelli F;Lamia CL;Zullini A Title: Soft X-ray contact microscopy of nematode Caenorhabditis elegans. Citation: European Physical Journal D 30: 235-241 2004 Type: ARTICLE Genes: Abstract: Soft X-ray Contact Microscopy (SXCM) of Caenorhabditis elegans nematodes with typical length similar to 800 mum and diameter similar to 30 mum has been performed using the PALS laser source of wavelength lambda = 1.314 mum and pulse duration tau ( FWHM) = 400 ps. Pulsed soft X-rays were generated using molybdenum and gold targets with laser intensities I greater than or equal to 10(14) W/cm(2). Images have been recorded on PMMA photo resists and analyzed using an atomic force microscope operating in contact mode. Cuticle features and several internal organs have been identified in the SXCM images including lateral field, cuticle annuli, pharynx, and hypodermal and neuronal cell nuclei. ------------------- Key: 6696 Medline: 15268855 Authors: Nicholas HR;Hodgkin J Title: The ERK MAP kinase cascade mediates tail swelling and a protective response to rectal infection in C. elegans. Citation: Current Biology 14: 1256-1261 2004 Type: ARTICLE Genes: bus-2 cdf-1 egl-5 egl-15 egl-17 eor-1 eor-2 ksr-1 ksr-2 let-23 let-60 let-756 lin-1 lin-3 lin-35 lin-31 lin-45 mab-5 mek-2 mpk-1 sem-5 soc-2 sos-1 sur-2 sur-6 Abstract: The nematode Caenorhabditis elegans is proving to be an attractive model organism for investigating innate immune responses to infection [1]. Among the known pathogens of C. elegans is the bacterium Microbacterium nematophilum, which adheres to the nematode rectum and postanal cuticle, inducing swelling of the underlying hypodermal tissue and causing mild constipation [2]. We find that on infection by M. nematophilum, an extracellular signal-regulated kinase (ERK) mitogen-activated protein (MAP) kinase cascade mediates tail swelling and protects C. elegans from severe constipation, which would otherwise arrest development and cause sterility. Involvement in pathogen defense represents a new role for ERK MAP kinase signaling in this organism. ------------------- Key: 6697 Medline: 15268860 Authors: Miller MA;Cutter AD;Yamamoto I;Ward S;Greenstein D Title: Clustered organization of reproductive genes in the C. elegans genome. Citation: Current Biology 14: 1284-1290 2004 Type: ARTICLE Genes: ark-1 cav-1 clr-1 cpb-2 efn-2 fbf-1 fbf-2 fem-1 gex-3 inx-8 inx-9 itr-1 let-23 let-60 lin-3 lin-45 lip-1 mel-11 mog-5 msp-3 msp-10 msp-19 msp-31 msp-32 msp-36 msp-38 msp-40 msp-49 msp-50 msp-51 msp-53 msp-55 msp-56 msp-57 msp-59 msp-63 msp-64 msp-65 msp-74 msp-76 msp-77 msp-78 msp-79 msp-81 smp-113 msp-142 msp-152 nmr-1 oma-1 ptc-1 ptp-2 rme-2 soc-2 tsp-12 unc-43 vab-1 Abstract: Defining the forces that sculpt genome organization is fundamental for understanding the origin, persistence, and diversification of species [1, 2]. The genomic sequences of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae provide an excellent opportunity to explore the dynamics of chromosome evolution [3, 4]. Extensive chromosomal rearrangement has accompanied divergence from their common ancestor, an event occurring roughly 100 million years ago (Mya) [4]; yet, morphologically, these species are nearly indistinguishable and both reproduce primarily by self-fertilization. Here, we show that genes expressed during spermatogenesis (sperm genes) are nonrandomly distributed across the C. elegans genome into three large clusters located on two autosomes. In addition to sperm genes, these chromosomal regions are enriched for genes involved in the hermaphrodite sperm/oocyte switch and in the reception of sperm signals that control fertilization. Most loci are present in single copy, suggesting that cluster formation is largely due to gene aggregation and not to tandem duplication. Comparative mapping indicates that the C. briggsae genome differs dramatically from the C. elegans genome in clustering. Because clustered genes have a direct role in reproduction and thus fitness, their aggregated pattern might have been shaped by natural selection, perhaps as hermaphroditism evolved. ------------------- Key: 6698 Medline: 15268861 Authors: Kimura KD;Miyawaki A;Matsumoto K;Mori I Title: The C. elegans thermosensory neuron AFD responds to Citation: Current Biology 14: 1291-1295 2004 Type: ARTICLE Genes: cmk-1 tax-2 tax-4 tax-6 Abstract: The mechanism of temperature sensation is far less understood than the sensory response to other environmental stimuli such as light, odor, and taste. Thermotaxis behavior in C. elegans requires the ability to discriminate temperature differences as small as similar to0.05degreesC and to memorize the previously cultivated temperature [1, 2]. The AFD neuron is the only major thermosensory neuron required for the thermotaxis behavior [3]. Genetic analyses have revealed several signal transduction molecules that are required for the sensation and/or memory of temperature information in the AFD neuron [4-7], but its physiological properties, such as its ability to sense absolute temperature or temperature change, have been unclear. We show here that the AFD neuron responds to warming. Calcium concentration in the cell body of AFD neuron is increased transiently in response to warming, but not to absolute temperature or to cooling. The transient response requires the activity of the TAX-4 cGMP-gated cation channel, which plays an essential role in the function of the AFD neuron [5]. Interestingly, the AFD neuron further responds to step-like warming above a threshold that is set by temperature memory. We suggest that C. elegans provides an ideal model to genetically and physiologically reveal the molecular mechanism for sensation and memory of temperature information. ------------------- Key: 6699 Medline: 15268863 Authors: Law E;Nuttley WM;van der Kooy D Title: Contextual taste cues modulate olfactory learning in C. elegans by an occasion-setting mechanism. Citation: Current Biology 14: 1303-1308 2004 Type: ARTICLE Genes: che-1 gpc-1 lrn-2 Abstract: Manipulations of context can affect learning and memory performance across species in many associative learning paradigms [1-3]. Using taste cues to create distinct contexts for olfactory adaptation assays in the nematode Caenorhabditis elegans, we now show that performance in this associative learning paradigm is sensitive to context manipulations, and we investigate the mechanism(s) used for the integration of context cues in learning. One possibility is that the taste and olfactory stimuli are perceived as a combined, blended cue that the animals then associate with the unconditioned stimulus (US) in the same manner as with any other unitary conditioned stimuli (CS) [4]. Alternatively, an occasion-setting model suggests that the taste cues only define the appropriate context for olfactory memory retrieval without directly entering into the primary association [5]. Analysis of genetic mutants demonstrated that the olfactory and context cues are sensed by distinct primary sensory neurons and that the animals' ability to use taste cues to modulate olfactory learning is independent from their ability to utilize these same taste cues for adaptation. We interpret these results as evidence for the occasion-setting mechanism [5] in which context cues modulate primary Pavlovian association by functioning in a hierarchical manner to define the appropriate setting for memory recall. ------------------- Key: 6701 Medline: 15261257 Authors: Nagai K;Shiomi K;Sunazuka T;Harder A;Turberg A;Omura S Title: Synthesis and biological evaluation of novel 4"-alkoxy avermectin derivatives. Citation: Bioorganic & Medicinal Chemistry Letters 14: 4135-4139 2004 Type: ARTICLE Genes: Abstract: Novel 4"-alkoxy avermectin derivatives were synthesized via rhodium carbenoid mediated O-H insertion reaction and tested for antiparasite activity against Artemia salina and Caenorhabditis elegans. ------------------- Key: 6702 Medline: 15219740 Authors: Schuske K;Beg AA;Jorgensen EM Title: The GABA nervous system in C. elegans. Citation: Trends in Neurosciences 27: 407-414 2004 Type: REVIEW Genes: exp-1 unc-25 unc-30 unc-46 unc-47 unc-49 Abstract: GABA neurotransmission requires a specialized set of proteins to synthesize, transport or respond to GABA. This article reviews results from a genetic strategy in the nematode Caenorhabditis elegans designed to identify the genes responsible for these activities. These studies identified mutations in genes encoding five different proteins: the biosynthetic enzyme for GABA, the vesicular GABA transporter, a transcription factor that determines GABA neuron identity, a classic inhibitory GABA receptor and a novel excitatory GABA receptor. This review discusses the strategy employed to identify these genes as well as the conclusions about GABA transmission derived from study of the mutant phenotypes. ------------------- Key: 6703 Medline: Authors: Yamashima T Title: Ca2+-dependent proteases in ischemic neuronal death. A conserved 'calpain-cathepsin cascade' from nematodes to primates. Citation: Cell Calcium 36: 285-293 2004 Type: ARTICLE Genes: Abstract: From rodents to primates, transient global brain ischemia is a well known cause of delayed neuronal death of the vulnerable neurons including cornu Ammonis 1 (CA1) pyramidal cells of the hippocampus. Previous reports using the rodent experimental paradigm indicated that apoptosis is a main contributor to such ischemic neuronal death. In primates, however, the detailed molecular mechanism of ischemic neuronal death still remains obscure. Recent data suggest that necrosis rather than apoptosis appear to be the crucial component of the damage to the nervous system during human ischemic injuries and neurodegenerative diseases. Currently, necrotic neuronal death mediated by Ca2+-dependent cysteine proteases, is becoming accepted to underlie the pathology of neurodegenerative conditions from the nematode Caenorhabditis elegans to primates. This paper reviews the role of cysteine proteases such as caspase, calpain and cathepsin in order to clarify the mechanism of ischemic neuronal death being triggered by the unspecific digestion of lysosomal proteases. ------------------- Key: 6704 Medline: 15289669 Authors: Maddox PS;Oegema K;Desai A;Cheeseman IM Title: "Holo"er than thou: chromosome segregation and kinetochore function in C. elegans. Citation: Chromosome Research 12: 641-653 2004 Type: REVIEW Genes: air-2 bir-1 bub-1 bub-3 cls-2 csc-1 czw-1 hcp-1 hcp-2 hcp-3 hcp-4 hcp-6 him-10 icp-1 klp-7 knl-1 mdf-1 mdf-2 mis-12 mix-1 ndc-80 san-1 scc-1 scc-3 smc-1 smc-3 tim-1 Abstract: Kinetochores are proteinaceous organelles that assemble on centromeric DNA to direct chromosome segregation in all eukaryotes. While many aspects of kinetochore function are conserved, the nature of the chromosomal domain upon which kinetochores assemble varies dramatically between different species. In monocentric eukaryotes, kinetochores assemble on a localized region of each chromosome. In contrast, holocentric species such as the nematode Caenorhabditis elegans have diffuse kinetochores that form along the entire length of their chromosomes. Here, we discuss the nature of chromosome segregation in C. elegans. In addition to reviewing what is known about kinetochore function, chromosome structure, and chromosome movement, we consider the consequences of the specialized holocentric architecture on chromosome segregation. ------------------- Key: 6705 Medline: 15280233 Authors: Cui M;Fay DS;Han M Title: lin-35/Rb cooperates with the SWI/SNF complex to control Caenorhabditis elegans larval development. Citation: Genetics 167: 1177-1185 2004 Type: ARTICLE Genes: hda-1 let-418 lin8 lin-9 lin-15 lin-35 lin-36 lin-37 lin-53 Abstract: Null mutations in lin-35, the Caenorhabdilis elegans ortholog of the mammalian Rb protein, cause no obvious morphological defects. Using a genetic approach to identify genes that may function redundantly with lin-35, we have isolated a mutation in the C. elegans psa-1 gene. lin-35; psa-1 double mutants display severe developmental defects leading to early larval arrest and adult sterility. The psa-1 gene has previously been shown to encode a C. elegans homolog of yeast SWI3, a critical component of the SWI/SNF complex, and has been shown to regulate asymmetric cell divisions during C. elegans development. We observed strong genetic interactions between psa-1 and lin-35 as well as a subset of the class B synMuv genes that include lin-37 and lin-9. Loss-of-function mutations in lin-35, lin-37, and lin-9 strongly enhanced the defects of asymmetric T cell division associated with a psa-1 mutation. Our results suggest that LIN-35/Rb and a certain class B synMuv proteins collaborate with the SWI/SNF protein complex to regulate the T cell division as well as other events essential for larval growth. ------------------- Key: 6706 Medline: 15215209 Authors: Liu J;Vasudevan S;Kipreos ET Title: CUL-2 and ZYG-11 promote meiotic anaphase II and the proper placement of the anterior-posterior axis in C. elegans. Citation: Development 131: 3513-3525 2004 Type: ARTICLE Genes: air-2 cul-2 cyb-1 elb-1 elc-1 emb-30 par-2 par-3 par-6 rbx-1 rec-8 tbb-2 zyg-11 Abstract: The faithful segregation of chromosomes during meiosis is vital for sexual reproduction. Currently, little is known about the molecular mechanisms regulating the initiation and completion of meiotic anaphase. We show that inactivation of CUL-2, a member of the cullin family of ubiquitin ligases, delays or abolishes meiotic anaphase 11 with no effect on anaphase 1, indicating differential regulation during the two meiotic stages. In cul-2 mutants, the cohesin REC-8 is removed from chromosomes normally during meiosis II and sister chromatids separate, suggesting that the failure to complete anaphase results from a defect in chromosome movement rather than from a failure to sever chromosome attachments. CUL-2 is required for the degradation of cyclin B1 in meiosis and inactivation of cyclin B1 partially rescued the meiotic delay in cul-2 mutants. In cul-2 mutants, the failure to degrade cyclin B1 precedes the metaphase II arrest. CUL-2 is also required for at least two aspects of embryonic polarity. The extended meiosis II in cul-2 mutants induces polarity reversals that include reversed orientation of polarity proteins, P granules, pronuclei migration and asymmetric cell division. Independently of its role in meiotic progression, CUL-2 is required to limit the initiation/ spread of the polarity protein PAR-2 in regions distant from microtubule organizing centers. Finally, we show that inactivation of the leucine-rich repeat protein ZYG-11 produces meiotic and polarity reversal defects similar to those observed in cul-2 mutants, suggesting that the two proteins function in the same pathways. ------------------- Key: 6707 Medline: 15328017 Authors: Bender AM;Wells O;Fay DS Title: lin-35/Rb and xnp-1/ATR-X function redundantly to control somatic gonad development in C. elegans. Citation: Developmental Biology 273: 335-349 2004 Type: ARTICLE Genes: lag-2 lim-7 lin-9 lin-15 lin-35 lin-36 lin-37 lin-53 slr-8 xnp-1 hDp8 Abstract: In screens for genetic modifiers of lin-35/Rb, the C. elegans retinoblastoma protein (Rb) homolog, we have identified a mutation in snp-1. Mutation in xnp-1, including a presumed null allele, are viable and, in general, appear indistinguishable from the wild type. In contrast, xnp-1 lin-35 double mutants are typically sterile and exhibit severe defects in gonadal development. Analyses of the abnormal gonads indicate a defect in the lineages that generate cells of the sheath and spermatheca, xnp-1 encodes the C. elegans homolog of ATR-X, a human disease gene associated with severe forms of mental retardation and urogenital developmental defects. xnp-1/ATR-X is a member of the Swi2/Snf2 family of ATP-dependent DEAD-DEAH box helicases, which function in nucleosome remodeling and transcriptional regulation. Expression of an xnp-1::GFP promoter fusion is detected throughout C. elegans development in several cell types including neurons and cells of the somatic gonad. Our findings demonstrate a new biological role for Rb family members in somatic gonad development and implicate lin-35 in the execution of multiple cell fates in C. elegans. In addition, our results suggest a possible conserved function for xnp-1/ATR-X in gonadal development across species. ------------------- Key: 6708 Medline: 14653860 Authors: Zannoni S;L'Hernault SW;Singson AW Title: Dynamic localization of SPE-9 in sperm: a protein required for sperm-oocyte interactions in Caenorhabditis elegans. Citation: BMC Developmental Biology 3:10: - 2004 Type: ARTICLE Genes: him-5 him-8 spe-9 spe-12 Abstract: BACKGROUND: Fertilization in Caenorhabditis elegans requires functional SPE-9 protein in sperm. SPE-9 is a transmembrane protein with a predicted extracellular domain that contains ten epidermal growth factor (EGF)-like motifs. The presence of these EGF-like motifs suggests that SPE-9 is likely to function in gamete adhesive and/or ligand-receptor interactions. RESULTS: We obtained specific antisera directed against different regions of SPE-9 in order to determine its subcellular localization. SPE-9 is segregated to spermatids with a pattern that is consistent with localization to the plasma membrane. During spermiogenesis, SPE-9 becomes localized to spiky projections that coalesce to form a pseudopod. This leads to an accumulation of SPE-9 on the pseudopod of mature sperm. CONCLUSIONS: The wild type localization patterns of SPE-9 provide further evidence that like the sperm of other species, C. elegans sperm have molecularly mosaic and dynamic regions. SPE-9 is redistributed by what is likely to be a novel mechanism that is very fast (approximately 5 minutes) and is coincident with dramatic rearrangements in the major sperm protein cytoskeleton. We conclude that SPE-9 ends up in a location on mature sperm where it can function during fertilization and this localization defines the sperm region required for these interactions. ------------------- Key: 6709 Medline: 14527340 Authors: Rappleye CA;Tagawa A;Le Bot N;Ahringer J;Aroian RV Title: Involvement of fatty acid pathways and cortical interaction of the pronuclear complex in Caenorhabditis elegans embryonic polarity. Citation: BMC Developmental Biology 3:8: - 2004 Type: ARTICLE Genes: emb-8 pod-1 pod-2 Abstract: BACKGROUND: Cell polarity is essential for many decisions made during development. While investigation of polarity-specific factors has yielded great insights into the polarization process, little is known on how these polarity-specific factors link to the basic cellular mechanisms that function in non-polarity aspects of the cell. To better understand the mechanisms that establish embryonic polarity, we investigated genes required for polarity in the one-cell C. elegans embryo that are also required for other non-polarity functions. This has led to the identification of the Pod-class of mutants that are characterized by osmosensitive embryos and defects in anterior-posterior polarity. RESULTS: Mutation in either of two loci of this class, emb-8 and pod-2, disrupts embryonic polarization and results in osmotically-sensitive embryos. Loss of emb-8, a previously uncharacterized polarity gene, causes mislocalization of PAR-3 and PAR-2 that molecularly mark the anterior and posterior cortices. emb-8 encodes NADPH-cytochrome P450 reductase, a protein supplying electrons to cytochrome P450-family enzymes, some of which catalyze fatty acid modifications. Cloning of the previously characterized polarity gene pod-2 reveals it encodes acetyl-CoA carboxylase, an enzyme that catalyzes the first step in de novo fatty acid synthesis. Depletion of fatty acid synthase, the next enzyme in the biosynthetic pathway, by RNA-interference (RNAi) also causes similar loss of one-cell polarity. Furthermore, pod-2 polarity defects can be rescued by addition of exogenous fatty acids. By following the behavior of the pronucleus in emb-8 and pod-2 mutant embryos, we demonstrate that loss of polarity correlates with impaired interaction between the pronucleus-centrosome complex and the posterior cortex. CONCLUSIONS: The characterization of emb-8 and pod-2 mutant embryos suggests that the pronucleus-centrosome complex interaction with the cortex plays a direct role in establishing polarity and that fatty acid pathways are important for this polarizing event. ------------------- Key: 6710 Medline: 15274122 Authors: Bantscheff M;Ringel B;Madi A;Schnabel R;Glocker MO;Thiesen HJ Title: Differential proteome analysis and mass spectrometric characterization of germ line development-related proteins of Caenorhabditis elegans. Citation: Proteomics 4: 2283-2295 2004 Type: ARTICLE Genes: glp-1 Abstract: Proteome maps and differences of protein patterns of the synchronized larval stage L4 of the temperature-sensitive Caenorhabditis elegans (C. elegans) glp-1 mutant (e2144ts) were investigated after cultivation at 15degreesC (developing a normal phenotype) or 25degreesC (developing a mutated phenotype) by two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry. From the 183 identified protein spots six proteins were found differently expressed. The Vit-6 vitellogenin (CE28594), the hypothetical 17.2 protein (CE25224), the hypothetical 17.4 protein (CE16999), and the heat shock protein 16 kDa (CE14249) were more abundant when growing worm cultures at 25degreesC. By contrast, the nucleoside diphosphate kinase (CE09650) was found increased at 15degreesC. Most notably, the eukariotic initiation factor 5A-1 (CE00503), highly abundant at 15degreesC, was not present in cultures grown at 25degreesC. Its absence at 25degreesC can not be attributed to lack of the enzymatic machinery that is necessary for hypusinylation. Instead, a direct downstream effect of the lack of functionality of GLP-1 may cause the expression of this protein. The yolk proteins 115 kDa and 88 kDa were attributed by mass spectrometric protein structure analysis as C-terminal and N-terminal fragments of the Vit-6 vitellogin protein (CE28594), respectively. The cleavage site between both derivatives was located between R764 and A768. A conflict in the database sequences at amino acid positions 1622 and 1623 of vitellogenin-6 was solved by mass spectrometric sequence analysis. The combination of 2-DE with mass spectrometry enabled the identification of mutation-associated differences on somatic gonadal cell and germ line cell development-associated proteins. ------------------- Key: 6711 Medline: 15256508 Authors: Castillo-Davis CI;Hartl DL;Achaz G Title: cis-Regulatory and protein evolution in orthologous and duplicate genes. Citation: Genome Research 14: 1530-1536 2004 Type: ARTICLE Genes: Abstract: The relationship between protein and regulatory sequence evolution is a central question in molecular evolution. It is currently not known to what extent changes in gene expression are coupled with the evolution of protein coding sequences, or whether these changes differ among orthologs (species homologs) and paralogs (duplicate genes). Here, we develop a method to measure the extent of functionally relevant cis-regulatory sequence change in homologous genes, and validate it using microarray data and experimentally verified regulatory elements in different eukaryotic species. By comparing the genomes of Caenorhabditis elegans and C. briggsae, we found that protein and regulatory evolution is weakly coupled in orthologs but not paralogs, suggesting that selective pressure on gene expression and protein evolution is quite similar and persists for a significant amount of time following speciation but not gene duplication. Additionally, duplicates of both species exhibit a dramatic acceleration of both regulatory and protein evolution compared to orthologs, suggesting increased directional selection and/or relaxed selection on both gene expression patterns and protein function in duplicate genes. ------------------- Key: 6712 Medline: 15282156 Authors: Yanowitz JL;Shakir MA;Hedgecock E;Hutter H;Fire AZ;Lundquist EA Title: UNC-39, the C. elegans homolog of the human myotonic dystrophy-associated homeodomain protein Six5, regulates cell motility and differentiation. Citation: Developmental Biology 272: 389-402 2004 Type: ARTICLE Genes: ced-3 ceh-35 unc-39 itDf2 nDf42 yDf8 Abstract: Mutations in the unc-39 gene of C elegans lead to migration and differentiation defects in a subset of mesodermal and ectodermal cells, including muscles and neurons. Defects include mesodermal specification and differentiation as well a neuronal migration and axon pathfinding defects. Molecular analysis revealed that unc-39 corresponds to the previously named gene ceh-35 and that the UNC-39 protein belongs to the Six4/5 family of homeodomain transcription factors and is similar to human Six5, a protein implicated in the pathogenesis of type I myotonic dystrophy (DM1). We show that human Six5 and UNC-39 are functional homologs, suggesting that further characterization of the C. elegans unc-39 gene might provide insight into the etiology of DM1. ------------------- Key: 6713 Medline: 15282157 Authors: Morck C;Rauthan M;Wagberg F;Pilon M Title: pha-2 encodes the C. elegans ortholog of the homeodomain protein HEX and is required for the formation of the pharyngeal isthmus. Citation: Developmental Biology 272: 403-418 2004 Type: ARTICLE Genes: ceh-22 pha-2 Abstract: The pha-2 mutant was isolated in 1993 by Leon Avery in a screen for worms with visible defects in pharyngeal feeding behavior. In pha-2 mutant worms, the pharyngeal isthmus is abnormally thick and short and, in contrast to wild-type worms, harbors several cell nuclei. We show here that pha-2 encodes a homeodomain protein and is homologous to the vertebrate homeobox gene, Hex (also known as Prh). Consistent with a function in pharyngeal development, the pha-2 gene is expressed in the pharyngeal primordiurn of Caenorhabditis elegans embryos, particularly in pm5 cells that form the bulk of the isthmus. We show that in the pha-2 mutant there is a failure of the pm5 cells to elongate anteriorly while keeping their nuclei within the nascent posterior bulb to form the isthmus during the 3-fold embryonic stage. We also present evidence that pha-2 regulates itself positively in pm5 cells, that it is a downstream target of the forkhead gene pha-4, and that it may also act in the isthmus as an inhibitor of the ceh-22 gene, an Nkx2.5 homolog. Finally, we have begun characterizing the regulation of the pha-2 gene and find that intronic sequences are essential for the complete pha-2 expression profile. The present report is the first to examine the expression and function of an invertebrate Hex homolog, that is, the C. elegans pha-2 gene. ------------------- Key: 6714 Medline: 15282160 Authors: Putiri E;Zannoni S;Kadandale P;Singson A Title: Functional domains and temperature-sensitive mutations in SPE-9, an EGF repeat-containing protein required for fertility in Caenorhabditis elegans. Citation: Developmental Biology 272: 448-459 2004 Type: ARTICLE Genes: fer-1 him-5 spe-9 spe-13 Abstract: The spe-9 gene is required for fertility in Caenorhabditis elegans and encodes a sperm transmembrane protein with an extracellular domain (ECD) that contains 10 epidermal growth factor (EGF) repeats. Deletion analysis reveals that the EGF repeats and the transmembrane domain are required for fertilization. In contrast, the cytoplasmic region of SPE-9 is not essential for fertilization. Individual point mutations in all 10 EGF motifs uncover a differential sensitivity of these sequences to alteration. Some EGF repeats cannot tolerate mutation leading to a complete lack of fertility. Other EGF repeats can be mutated to create animals with temperature-sensitive (ts) fertility phenotypes. All ts mutations were generated by changing either conserved cysteine or glycine residues in the EGF motifs. For two endogenous is alleles of spe-9, loss of function at nonpermissive temperatures is not due to protein mislocalization or degradation. Additionally, the proper localization of SPE-9 in sperm is not altered in a genetically interacting fertility mutant (spe-13) or a mutant that affects sperm vesicle-plasma membrane fusion (fer-1). Like the EGF repeats in the Notch/LIN-12/GLP-1 receptors and their ligands, the EGF repeats in SPE-9 may carry out different functions. Because EGF motifs are found in many proteins in different species, similar experimental strategies could be used to generate useful temperature-sensitive mutations in other EGF motif-containing molecules. ------------------- Key: 6715 Medline: 15282161 Authors: Karp X;Greenwald I Title: Multiple roles for the E/Daughterless ortholog HLH-2 during C. elegans gonadogenesis. Citation: Developmental Biology 272: 460-469 2004 Type: ARTICLE Genes: hlh-2 lag-2 lin-12 smg-1 Abstract: HLH-2 is the Caenorhabditis elegans ortholog of the Drosophila Daughterless and mammalian E basic helix- loop -helix (bHLH) transcriptional activators that function during diverse events during animal development. HLH-2 has been implicated in cell fate specification in different neural lineages and in the LIN-12/Notch-mediated anchor cell (AC)/ventral uterine precursor cell (VU) decision in the somatic gonad. Here, we show that hlh-2 plays several distinct roles during somatic gonadogenesis. Our analysis suggests that hlh-2 is required to endow specific somatic gonadal cells with the competence to undergo the ACNU decision, as well as functioning in the AC/VU decision per se; this novel "proAC" role appears to be analogous to the proneural role of Drosophila Daughterless. In addition to its two distinct roles in the specification of the AC, hlh-2 is also required for correct differentiation and function of the AC. hlh-2 also acts at an independent point in the gonadal lineage both to specify distal tip cells (DTCs) and in DTC differentiation and function. ------------------- Key: 6716 Medline: 15282167 Authors: Natarajan L;Jackson MB;Szyleyko E;Eisenmann DM Title: Identification of evolutionarily conserved promoter elements and amino acids required for function of the C. elegans beta-catenin homolog BAR-1. Citation: Developmental Biology 272: 536-557 2004 Type: ARTICLE Genes: bar-1 egl-18 pry-1 Abstract: beta-catenins are conserved transcription factors regulated posttranslationally by Wnt signaling. bar-1 encodes a Caenorhabditis elegans beta-catenin acting in multiple Wnt-mediated processes, including cell fate specification by vulval precursor cells (VPCs) and migration of the Q(L) neuroblast progeny. We took two approaches to extend our knowledge of bar-1 function. First, we undertook a bar-1 promoter analysis using transcriptional GFP reporter fusions and found that bar-1 expression is regulated in specific cells at the transcriptional level. We identified promoter elements necessary for bar-1 expression in several cell types, including a 321-bp element sufficient for expression in ventral cord neurons (VCNs) and a 1.1-kb element sufficient for expression in the developing vulva and adult seam cells. Expression of bar-l from the 321-bp element rescued the Uncoordinated (Unc) phenotype of bar-1 mutants, but not the vulval phenotype, suggesting that a Writ pathway may act in ventral cord neurons to mediate proper locomotion. By comparison of the 1.1-kb element to homologous sequences from Caenorhabditis briggsae, we identified evolutionarily conserved sequences necessary for expression in vulval or seam cells. Second, we analyzed 24 mutations in bar-1 and identified several residues required for BAR-1 activity in C. elegans. By phylogenetic comparison, we found that most of these residues are conserved and may identify amino acids necessary for beta-catenin function in all species. ------------------- Key: 6717 Medline: 15201219 Authors: Mootz D;Ho DM;Hunter CP Title: The STAR/Maxi-KH doman protein GLD-1 mediates a developmental switch in the translational control of C. elegans PAL-1. Citation: Development 131: 3263-3272 2004 Type: ARTICLE Genes: gld-1 mex-3 pal-1 pie-1 tra-2 Abstract: Translational control is an essential mechanism of gene control utilized throughout development, yet the molecular mechanisms underlying translational activation and repression are poorly understood. We have investigated the translational control of the C elegans caudal homolog, pall, and found that GLD-1, a member of the evolutionarily conserved STAR/Maxi-KH domain family, acts through a minimal pal-1 3' UTR element to repress pal-1 translation in the distal germline. We also provide data suggesting that GLD-1 may repress pal-1 translation after initiation. Finally, we show that GLD-1 represses the distal germline expression of the KH domain protein MEX-3, which was previously shown to repress PAL-1 expression in the proximal germline and which appears specialized to control PAL-1 expression patterns in the embryo. Hence, GLD-1 mediates a developmental switch in the control of PAL-1 repression, allowing MEX-3 to accumulate and take over the task of PAL-1 repression in the proximal germline, where ------------------- Key: 6718 Medline: 15449707 Authors: Luersen K;Eschbach ML;Liebau E;Walter RD Title: Functional GATA- and initiator-like-elements exhibit a similar arrangement in the promoters of Caenorhabditis elegans polyamine synthesis enzymes. Citation: Biological Chemistry 385: 711-721 2004 Type: ARTICLE Genes: pha-1 Abstract: Polyamines are essential cell constituents involved in growth processes. In Caenorhabditis elegans the polyamine synthetic pathway consists of three enzymes, ornithine decarboxylase (ODC), Sadenosylmethionine decarboxylase (AdoMetDC) and spermidine synthase. Their gene expression pattern was determined in C. elegans by microinjection of green fluorescent protein (GFP) reporter gene constructs. All transgenic animals exhibited GFP expression in their intestinal cells. For the AdoMetDC promoter, fluorescence was additionally observed in dopaminergic neurons, while the ODC promoter also drives a malespecific GFP expression in the distal part of the reproductive system. The minimal promoter regions for intestinespecific expression of the AdoMetDC and spermidine synthase genes were determined by deletion mutants. Using the Seqcomp and Family Relation programs, a similar arrangement of putative cisregulatory elements within these regions and also within the respective regions of the orthologous Caenorhabditis briggsae genes were found. The functional conservation of the latter was confirmed by heterologous transformation experiments. Moreover, the involvement of putative GATA and initiator(Inr)likeelements in gene expression was determined by mutagenesis studies. RNase protection assay revealed that the Inrlikeelement does not represent the main transcriptional start site, at least of C. elegans spermidine synthase. In conclusion, a similar minimal promoter architecture was found for C. elegans as well as C. briggsae AdoMetDC and spermidine synthase, two genes that participate in the same metabolic pathway. ------------------- Key: 6719 Medline: 15294159 Authors: Hoppe T;Cassata G;Barral JM;Springer W;Hutagalung AH;Epstein HF;Baumeister R Title: Regulation of the myosin-directed chaperone UNC-45 by a novel E3/E4-multiubiquitylation complex in C. elegans. Citation: Cell 118: 337-349 2004 Type: ARTICLE Genes: chn-1 let-70 ubc-18 ufd-2 unc-45 Abstract: The organization of the motor protein myosin into motile cellular structures requires precise temporal and spatial control. Caenorhabditis elegans UNC-45 facilitates this by functioning both as a chaperone and as a Hsp90 cochaperone for myosin during thick filament assembly. Consequently, mutations in C. elegans unc-45 result in paralyzed animals with severe myofibril disorganization in striated body wall muscles. Here, we report a new E3/E4 complex, formed by CHN-1, the C. elegans ortholog of CHIP (carboxyl terminus of Hsc70-interacting protein), and UFD-2, an enzyme known to have ubiquitin conjugating E4 activity in yeast, as necessary and sufficient to multiubiquitylate UNC-45 in vitro. The phenotype of unc-45 temperature-sensitive animals is partially suppressed by chn-1 loss of function, while UNC-45 overexpression in worms deficient for chn-1 results in severely disorganized muscle cells. These results identify CHN-1 and UFD-2 as a functional E3/E4 complex and UNC-45 as its physiologically relevant ------------------- Key: 6720 Medline: 15294151 Authors: Gonczy P Title: Myosin assembly: the power of multiubiquitylation. Citation: Cell 118: 272-274 2004 Type: REVIEW Genes: chn-1 ufd-2 unc-45 Abstract: Ubiquitylation provides a means of targeting substrate proteins for degradation by the proteasome. Novel findings in C. elegans (Hoppe et al., 2004, this issue of Cell) establish that two ubiquitin-ligases team up to multiubiquitylate the myosin chaperone UNC-45, suggesting a novel link between regulated protein degradation and myosin assembly. ------------------- Key: 6721 Medline: 15265494 Authors: Alho MAM;D'Accorso NB;Ochoa C;Castro A;Calderon F;Chana A;Reviriego F;Paez JA;Campillo NE;Martinez-Grueiro M;Lopez-Santa Cruz AM;Martinez AR Title: Synthesis and nematocide activity of S-glycopyranosyl-6,7-diarylthiolumazines. Citation: Bioorganic & Medicinal Chemistry 12: 4431-4437 2004 Type: ARTICLE Genes: Abstract: 6,7-Diaryl derivatives of mono and di-S-glycopyranosylthiolumazine derivatives 5-8 were prepared to test their nematocide activity. In vitro tests against Caenorhabditis elegans were performed and it was found that monosubstituted derivatives 5-7 showed higher activity than the corresponding unsubstituted 2-thiolumazines 1-3, whilst 2-S,4-S-di-glycopyranosylpteridine derivative 8 was inactive in contrast to unsubstituted derivative 4. In order to check whether the lack of activity of 8 was due to the two bulky substituents of the pteridine nucleus, 2-S,4-S-dimethyl derivative 9 was synthesized and assayed showing also lack of activity. A theoretical study on the stability of the different possible tautomers of compound 4 was carried out in an attempt to explain some, in appearance, anomalous C-13 NMR data of this compound. ------------------- Key: 6722 Medline: 15371014 Authors: Appleford PJ;Griffiths M;Yao SYM;Ng AML;Chomey EG;Isaac RE;Coates D;Hope IA;Cass CE;Young JD;Baldwin SA Title: Functional redundancy of the two nucleoside transporters of the ENT family (CeENT1, CeENT2) required for development of Caenorhabditis elegans. Citation: Molecular Membrane Biology 21: 247-259 2004 Type: ARTICLE Genes: ent-1 ent-2 ent-3 ent-4 ent-5 Abstract: The genome of Caenorhabditis elegans encodes multiple homologues of the two major families of mammalian equilibrative and concentrative nucleoside transporters. As part of a programme aimed at understanding the biological rationale underlying the multiplicity of eukaryote nucleoside transporters, we have now demonstrated that the nematode genes ZK809.4 (ent-1) and K09A9.3 (ent-2) encode equilibrative transporters, which we designate CeENT1 and CeENT2 respectively. These transporters resemble their human counterparts hENT1 and hENT2 in exhibiting similar broad permeant specificities for nucleosides, while differing in their permeant selectivities for nucleobases. They are insensitive to the classic inhibitors of mammalian nucleoside transport, nitrobenzylthioinosine, dilazep and draflazine, but are inhibited by the vasoactive drug dipyridamole. Use of green fluorescent protein reporter constructs indicated that the transporters are present in a limited number of locations in the adult, including intestine and pharynx. Their potential roles in these tissues were explored by using RNA interference to disrupt gene expression. Although disruption of ent-1 or ent-2 expression alone had no effect, simultaneous disruption of both genes yielded pronounced developmental defects involving the intestine and vulva. ------------------- Key: 6723 Medline: 15306736 Authors: Dunn NA;Lockery SR;Pierce-Shimomura JT;Conery JS Title: A neural network model of chemotaxis predicts function of synaptic connections in the nematode Caenorhabditis Citation: Journal of Computational Biology 17: 137-147 2004 Type: ARTICLE Genes: Abstract: The anatomical connectivity of the nervous system of the nematode Caenorhabditis elegans has been almost completely described, but determination of the neurophysiological basis of behavior in this system is just beginning. Here we used an optimization algorithm to search for patterns of connectivity sufficient to compute the sensorimotor transformation underlying C. elegans chemotaxis, a simple form of spatial orientation behavior in which turning probability is modulated by the rate of change of chemical concentration. Optimization produced differentiator networks capable of simulating chemotaxis. A surprising feature of these networks was inhibitory feedback connections on all neurons. Further analysis showed that feedback regulates the latency between sensory input and behavior. Common patterns of connectivity between the model and biological networks suggest new functions for previously identified connections in the C. elegans nervous ------------------- Key: 6724 Medline: Authors: Masler EP Title: Comparison of alanine aminopeptidase activities in Heterodera glycines and Caenorhabditis elegans. Citation: Nematology 6: 223-229 2004 Type: ARTICLE Genes: Abstract: Aminopeptidases in whole body homogenates of Caenorhabditis elegans and Heterodera glycines were detected using a colorimetric assay with a series of seven aminoacyl p-nitroanilide substrates. Enzyme properties evaluated included substrate preference and stability in response to metal salts, alcohols and storage. The preferred substrate for both species was Ala-pNA, but C. elegans had a much broader substrate range than H. glycines. All substrates were more active in C. elegans than in H. glycines homogenates, except Pro-pNA which was three times more active than in H. glycines. Ca2+, Mg2+ and Zn2+ inhibited C. elegans activity in a dose responsive manner but had little effect on H. glycines aminopeptidase, and CO2+ was mildly inhibitory in both species. Ethanol inhibited both C. elegans and H. glycines aminopeptidases but methanol inhibited only H. glycines and increased C. elegans activity. Heterodera glycines aminopeptidase was more stable at room temperature than C. elegans. ------------------- Key: 6725 Medline: 15243155 Authors: Coghlan A;Wolfe KH Title: Origins of recently gained introns in Caenorhabditis. Citation: Proceedings of the National Academy of Sciences USA 101: 11362-11367 2004 Type: ARTICLE Genes: dis-3 hsp-60 klp-20 smg-2 stc-1 tre-3 Abstract: The genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae both contain approximate to100,000 introns, of which >6,000 are unique to one or the other species. To study the origins of new introns, we used a conservative method involving phylogenetic comparisons to animal orthologs and nematode paralogs to identify cases where an intron content difference between C elegans and C briggsae was caused by intron insertion rather than deletion. We identified 81 recently gained introns in C elegrans and 41 in C briggsae. Novel introns have a stronger exon splice site consensus sequence than the general population of introns and show the same preference for phase 0 sites in codons over phases 1 and 2. More of the novel introns are inserted in genes that are expressed in the C elegans germ line than expected by chance. Thirteen of the 122 gained introns are in genes whose protein products function in premRNA processing, including three gains in the gene for spliceosomal protein SF3B1 and two in the nonsense-mediated decay gene smg-2. Twenty-eight novel introns have significant DNA sequence identity to other introns, including three that are similar to other introns in the same gene. All of these similarities involve minisatellites or palindromes in the intron sequences. Our results suggest that at least some of the intron gains were caused by reverse splicing of a preexisting intron. ------------------- Key: 6726 Medline: 15333823 Authors: Houthoofd K;Braeckman BP;Johnson TE;Vanfleteren JR Title: Extending life-span in C. elegans. Citation: Science 305: 1238-1239 2004 Type: REVIEW Genes: Abstract: The life-span of the nematode Caenorhabditis elegans can be extended by at least six different mechanisms, including calorie restriction, reduced Ins/IGF-1 signaling, germline ablation, food sensing amphid ablation, mitochondrial deficiency, and decreased temperature. Reduced Ins/IGF-1 signaling and calorie restriction can also increase the life-span of flies and mice. The Brevia "Healthy animals with extreme longevity" by N. Arantes-Oliveira et al. (24 Oct. 2003, p.611) showed that daf-2 RNAi treatment and gonad ablation of worms carrying the daf-2(e1368) hypomorphic mutation in the gene encoding the C. elegans Ins/IGF-1 receptor increases their life-span 6.0-fold. We have found that the average life-span of daf-2(e1370) mutants grown in axenic medium [sterile liquid medium based on yeast extract, soy peptone, and hemoglobin; see (1)] was 90.9 days, representing a 6.3-fold life extension relative to wild-type controls grown on plate cultures seeded with life E. coli cells (1). ------------------- Key: 6727 Medline: 15268752 Authors: Kurz CL;Tan MW Title: Regulation of aging and innate immunity in C. elegans. Citation: Aging Cell 3: 185-193 2004 Type: REVIEW Genes: Abstract: The free-living soil nematode Caenorhabditis elegans is a versatile model for the study of the genetic regulation of aging and of host-pathogen interactions. Many genes affecting multiple processes, such as neuroendocrine signalling, nutritional sensing and mitochondrial functions, have been shown to play important roles in determining the lifespan of C. elegans. The DAF-2-mediated insulin signalling pathway is the major pathway that regulates aging in this nematode and this role appears universal; neuroendrocrine signalling also affects aging in Drosophila and mice. Recent studies have shown that the innate immune function in C. elegans is modulated by signalling from the TGF-beta-like, the p38 MAPK and the DAF-2 insulin pathways. The requirement for the DAF-2 pathway in modulating aging and immunity suggests that these processes may be linked at the molecular level. It is well known that as humans age, immunosenescence occurs in which there is a general degradation of immune efficiency. However, the molecular mechanisms involved in this process remain unclear. In this review, we discuss the molecular mechanisms that modulate aging and immune response and attempt to suggest molecular links between these two ------------------- Key: 6728 Medline: 15268753 Authors: DeVeale B;Brummel T;Seroude L Title: Immunity and aging: the enemy within? Citation: Aging Cell 3: 195-208 2004 Type: REVIEW Genes: Abstract: Functional analyses of changes in the immune response indicate that aging is associated with a decline of adaptive immunity whereas innate immunity is ramped up. Gene expression studies also support age-dependent changes in immunity. Studies using a large panel of methodologies and multiple species show that some of the most dramatic transcriptional changes that occur during aging are associated with immunity. This observation leads to two fundamental questions: (1) Why is the immune response altered with age? (2) Is this a consequence of aging or does it contribute to it? The origin of these changes and the mechanistic relationship among them as well as with aging must be identified. In mammals, this task is complicated by the interdependence of the innate and adaptive immune systems. The value of invertebrates as model organisms to help answer these questions is presented. This includes a description of the immune response in invertebrate models and how it compares with vertebrates, focusing on conserved pathways. Finally, these questions are explored in light of recent reports and data from our laboratory. Experimental alterations of longevity indicate that the differential expression of immunity-related genes during aging is linked to the rate of aging. Long-lived nematodes are more resistant to pathogens and blocking the expression of immune-related genes can prevent lifespan extension. These observations suggest that the immune response has a positive effect on longevity, possibly by increasing fitness. By contrast, it has been reported that activation of the immune system can reduce longevity upon starvation. We also observed that deregulation of the immune response has drastic effects on viability and longevity in Drosophila. These data suggest that the immune response results in a trade-off between beneficial and detrimental effects that might profoundly affect the aging process. Given this, immunity may be an ally early in life, but turns out to be an enemy as we age. ------------------- Key: 6729 Medline: 15289613 Authors: Hamaoka BY;Cann CE;Geisbrecht BV;Leahy DJ Title: Crystal structure of Caenorhabditis elegans HER-1 and characterization of the interaction between HER-1 and TRA-2A. Citation: Proceedings of the National Academy of Sciences USA 101: 11673-11678 2004 Type: ARTICLE Genes: her-1 tra-2 Abstract: HER-1 is a secreted protein that promotes male development in the nematode Caenorhabditis elegans. HER-1 inhibits the function of TRA-2A, a multipass integral membrane protein thought to serve as its receptor. We report here the 1.5-Angstrom crystal structure of HER-1. The structure was solved by the multiwavelength anomalous diffraction method by using selenomethionyl-substituted HER-1 produced in Chinese hamster ovary cells. The HER-1 structure consists of two all-helical domains and is not closely homologous to any known structure. Sites of amino acid substitutions known to impair HER-1 function were mapped on the HER-1 structure and classified according to the likely mechanism by which they affect HER-1 activity. A subset of these and other amino acid substitutions on the HER-1 surface were assayed for their ability to disrupt interactions between HER-1 and TRA-2A-expressing cells, and a localized region on the HER-1 surface important for mediating this interaction was identified. ------------------- Key: 6730 Medline: 15280551 Authors: Petersen CI;McFarland TR;Stepanovic SZ;Yang P;Reiner DJ;Hayashi K;George AL;Roden DM;Thomas JH;Balser JR Title: In vivo identification of genes that modify ether-a-go-go-related gene activity in Caenorhabditis elegans may also affect human cardiac arrhythmia. Citation: Proceedings of the National Academy of Sciences USA 101: 11773-11778 2004 Type: ARTICLE Genes: egl-2 mec-14 unc-103 Abstract: Human ether-a-go-go-related gene (HERG) encodes the pore-forming subunit of I-Kr, a cardiac K+ channel. Although many commonly used drugs block I-Kr, in certain individuals, this action evokes a paradoxical life-threatening cardiac rhythm disturbance, known as the acquired long QT syndrome (aLQTS). Although aLQTS has become the leading cause of drug withdrawal by the U.S. Food and Drug Administration, DNA sequencing in aLQTS patients has revealed HERG mutations only in rare cases, suggesting that unknown HERG modulators are often responsible. By using the worm Caenorhabditis elegans, we have developed in vivo behavioral assays that identify candidate modulators of unc-103, the worm HERG orthologue. By using RNA-interference methods, we have shown that worm homologues of two HERG-interacting proteins, Hyperkinetic and K channel regulator 1 (KCR1), modify unc-103 function. Examination of the human KCR1 sequence in patients with drug-induced cardiac repolarization defects revealed a sequence variation (the substitution of isoleucine 447 by valine, I447V) that occurs at a reduced frequency (11.1%) relative to a matched control population (7.0%), suggesting that I447V may be an allele for reduced aLQTS susceptibility. This clinical result is supported by in vitro studies of H ERG dofetilide sensitivity by using coexpression of HERG with wild-type and 1447V KCR1 cDNAs. Our studies demonstrate the feasibility of using C. elegans ------------------- Key: 6731 Medline: 15343338 Authors: Cowan CR;Hyman AA Title: Centrosomes direct cell polarity independently of microtubule assembly in C. elegans embryos. Citation: Nature 431: 92-96 2004 Type: ARTICLE Genes: par-2 sas-4 spd-2 spd-5 Abstract: Polarity establishment requires a symmetry-breaking event, resulting in an axis along which determinants are segregated. In Caenorhabditis elegans, oocytes are apolar and are triggered to polarize rapidly along one axis after fertilization. The establishment of this first polarity axis is revealed by the asymmetric distribution of PAR proteins and cortical activity in the one-celled embryo. Current evidence suggests that the centrosome pronucleus complex contributed by the sperm is involved in defining the polarization axis(1-6). Here we directly assess the contribution of the centrosome to polarity establishment by laser ablating the centrosome before and during polarization. We find that the centrosome is required to initiate polarity but not to maintain it. Initiation of polarity coincides with the proximity of the centrosome to the cortex and the assembly of pericentriolar material on the immature sperm centrosome. Depletion of microtubules or the microtubule nucleator gamma-tubulin did not affect polarity establishment. These results demonstrate that the centrosome provides an initiating signal that polarizes C. elegans embryos and indicate that this signalling event might be independent of the role of the centrosome as a microtubule nucleator. ------------------- Key: 6732 Medline: Authors: Chen JJ;Caswell-Chen EP Title: Facultative vivipary is a life-history trait in Caenorhabditis elegans. Citation: Journal of Nematology 36: 107-113 2004 Type: ARTICLE Genes: Abstract: Organisms partition their resources among growth, maintenance, mid reproduction and, when resources become limiting, the allocation to one process necessitates reduced allocation to others. When starved, Caenorhabditis elegans adults retain progeny internally which then consume the parent body contents, and some of those larvae use the resources to reach the resistant, long-lived dauer stage. If starved under similarly extreme conditiotis, larvae from eggs laid outside of the body are tillable to develop into dauers. We interpret this switch from ovipary, or laying eggs, to bearing live younig as facuiltative vivipary. This switch is induced by starvation of late fourth-stage lavae, young adults, or gravid adults. In C. elegans, vivipary is the altruistic allocation of all available parental energy and nutrients to progeny, with the associated costs to adult hermaphrodites of truncated life span and fectundity. As a life-history trait, facultative vivipary is a survival-enhancing response to stress that may provide hisights into the evolution of reproduction and longevity. ------------------- Key: 6733 Medline: 15296755 Authors: Willson J;Amliwala K;Davis A;Cook A;Cuttle MF;Kriek N;Hopper NA;O'Connor V;Harder A;Walker RJ;Holden-Dye L Title: Latrotoxin receptor signaling engages the UNC-13-dependent vesicle-priming pathway in C. elegans. Citation: Current Biology 14: 1374-1379 2004 Type: ARTICLE Genes: egl-8 egl-30 goa-1 lat-1 lat-2 rrf-3 snb-1 unc-13 Abstract: alpha-latrotoxin (LTX), a 120 kDa protein in black widow spider venom, triggers massive neurotransmitter exocytosis. Previous studies have highlighted a role for both intrinsic pore-forming activity and receptor binding in the action of this toxin [1]. Intriguingly, activation of a presynaptic G protein-coupled receptor, latrophilin, may trigger release independent of pore-formation [2]. Here we have utilized a previously identified ligand of nematode latrophilin, emodepside [3], to define a latrophilin-dependent pathway for neurotransmitter release in C. elegans. In the pharyngeal nervous system of this animal, emodepside (100 nM) stimulates exocytosis and elicits pharyngeal paralysis. The pharynxes of animals with latrophilin (lat-1) gene knockouts are resistant to emodepside, indicating that emodepside exerts its high-affinity paralytic effect through LAT-1. The expression pattern of lat-1 supports the hypothesis that emodepside exerts its effect on the pharynx primarily via neuronal latrophilin. We build on these observations to show that pharynxes from animals with either reduction or loss of function mutations in Gq, phospholipaseC-beta, and UNC-13 are resistant to emodepside. The latter is a key priming molecule essential for synaptic vesicle-mediated release of neurotransmitter [4, 5]. We conclude that the small molecule ligand emodepside triggers latrophilin-mediated exocytosis via a pathway that engages UNC-13-dependent vesicle priming. ------------------- Key: 6734 Medline: 15358137 Authors: Dong KJ;Qian JX Title: Quantum algorithm for programmed cell death of Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 321: 515-516 2004 Type: ARTICLE Genes: Abstract: During the development of Caenorhabditis elegans, through cell divisions, a total of exactly 1090 cells are generated, 131 of which undergo programmed cell death (PCD) to result in an adult organism comprising 959 cells. Of those 131, exactly 113 undergo PCD during embryogenesis. subdivided across the cell lineages in the following fashion: 98 for AB lineage; 14 for MS lineage; and 1 for C lineage. Is there a law underlying these numbers, and if there is, what Could it be? Here we wish to show that the count of the cells undergoing PCD complies with the cipher laws related to the algorithms of Shor and of Grover. ------------------- Key: 6735 Medline: 15296777 Authors: Rankin CH Title: Invertebrate learning: what can't a worm learn? Citation: Current Biology 14: R617-R618 2004 Type: REVIEW Genes: gpc-1 lrn-2 Abstract: The nematode worm Caenorhabditis elegans can learn and remember the stimuli it encounters, the environment it is in, and its own physiological state. Analyses of mutations in C. elegans that affect different aspects of experience are beginning to address the nature of learning. ------------------- Key: 6736 Medline: 15328611 Authors: Swain SC;Keusekotten K;Baumeister R;Sturzenbaum SR Title: C. elegans metallothioneins: new insights into the phenotypic effects of cadmium toxicosis. Citation: Journal of Molecular Biology 341: 951-959 2004 Type: ARTICLE Genes: mtl-1 mtl-2 rrf-3 Abstract: Metallothioneins are considered to be the primary player in the detoxification of and protection from cadmium, a teratogen, mutagen and potentially lethal heavy metal. The nematode Caenorhabditis elegans has only two metallothioneins, mtl-1 and mtl-2, thus making it an ideal organism to investigate the phenotypic effects of cadmium toxicosis. The functional importance of metallothioneins in cadmium trafficking was highlighted through the generation of viable green fluorescent protein (GFP) expressing transgenes, a metallothionein null allele, as well as RNAi mediated metallothionein knock-downs. A highly sensitive dose and temporal transcriptional response to cadmium, but not copper or zinc, was shown to be equally prevalent in both isoforms. No measurable compensatory up-regulation of mtl-1 could be observed in the null allele of mtl-2, suggesting that both isoforms are independent and not synergistic in their mode of action. Exposure to cadmium affected all demographic indices measured, manifested by a reduction in body size, generation time, brood size and lifespan. These effects were magnified in the knock-out or wild-type subjected to a knock down by RNAi, however, only in the presence of cadmium. This substantiates the notion that metallothioneins play a pivotal role in the protection from cadmium toxicosis. Finally, an earthworm metallothionein-GFP construct could be activated in C. elegans upon exposure to cadmium, the results providing further evidence that the transcriptional control of metallothioneins is fundamentally divergent in lower invertebrates and not mediated via MTF-1 as in more complex organisms. ------------------- Key: 6737 Medline: 15317977 Authors: Wang L;Kimble J;Wickens M Title: Tissue-specific modification of gld-2 mRNA in C. elegans: likely C-to-U editing. Citation: RNA 10: 1444-1448 2004 Type: ARTICLE Genes: cdd-1 cdd-2 gld-2 Abstract: Seventeen years after the discovery of tissue-specific apoB mRNA editing, only three nucleus-encoded mRNAs have been shown to undergo C-to-U editing. All three mRNAs occur in mammals. apoB mRNA editing is tissue-specific and occurs normally, whereas NF1 and NAT1 mRNA editing is found largely in tumors. Here we report the first example of C-to-U RNA editing in Caenorhabditis elegans. The gld-2 gene encodes an atypical poly(A) polymerase that governs the mitosis/meiosis decision in the germ line as well as progression through meiosis and early embryogenesis. At least two of its alternatively spliced transcripts are germline-specific. We find that most and perhaps all germline-specific transcripts generated by the gld-2 gene undergo C-to-U editing, but that somatic transcripts show no detectable editing. The gld-2 C-to-U editing event changes the codon from CCG to CUG, which is predicted to cause a proline to leucine substitution in the protein sequence. Our finding suggest the presence of a sequence- and tissue-specific cytidine deaminase acting on RNA, or CDAR. This CDAR modifies a specific base in gld-2 mRNA, and acts only in the germline. ------------------- Key: 6738 Medline: 15318203 Authors: Bowerman B Title: Cell division: timing the machine. Citation: Nature 430: 840-842 2004 Type: REVIEW Genes: cdc-14 zen-4 Abstract: During cell division everything must happen at the right time, or errors occur. A common cellular control device, protein phosphorylation, is now shown to time the assembly of a key part of the division machinery. ------------------- Key: 6739 Medline: 15187259 Authors: Gartner A;MacQueen AJ;Villeneuve AM Title: Methods for analyzing checkpoint responses in Caenorhabditis elegans. Citation: Methods in Molecular Biology 280: 257-274 2004 Type: CHAPTER Genes: ced-3 ced-4 ced-9 cep-1 chk-2 egl-1 mrt-2 rad-5 Abstract: In response to genotoxic insults, cells activate DNA damage checkpoint pathways that stimulate DNA repair, lead to a transient cell cycle arrest, and/or elicit programmed cell death (apoptosis) of affected cells. The Caenorhabditis elegans germ line was recently established as a model system to study these processes in a genetically tractable, multicellular organism. The utility of this system was revealed by the finding that upon treatment with genotoxic agents, premeiotic C. elegans germ cells transiently halt cell cycle progression, whereas meiotic prophase germ cells in the late pachytene stage readily undergo apoptosis. Further, accumulation of unrepaired meiotic recombination intermediates can also lead to the apoptotic demise of affected pachytene cells. DNA damage-induced cell death requires key components of the evolutionarily conserved apoptosis machinery. Moreover, both cell cycle arrest and pachytene apoptosis responses depend on conserved DNA damage checkpoint proteins. Genetics- and genomics-based approaches that have demonstrated roles for conserved checkpoint proteins have also begun to uncover novel components of these response pathways. In this chapter, we will briefly review the C. elegans DNA damage-response field, and we will discuss in detail the methods that are being used to assay DNA damage responses in C. elegans. ------------------- Key: 6740 Medline: 15315757 Authors: Reddy KC;Villeneuve AM Title: C. elegans HIM-17 links chromatin modification and competence for initiation of meiotic recombination. Citation: Cell 118: 439-452 2004 Type: ARTICLE Genes: him-17 lin-35 rad-51 rec-8 spo-11 Abstract: Initiation of meiotic recombination by double-strand breaks (DSBs) must occur in a controlled fashion to avoid jeopardizing genome integrity. Here, we identify chromatin-associated protein HIM-17 as a link between chromatin state and DSB formation during C. elegans meiosis. Dependencies of several meiotic prophase events on HIM-17 parallel those seen for DSB-generating enzyme SPO-11. HIM-17 is essential for DSB formation but dispensable for homolog synapsis. Crossovers and chiasmata are eliminated in him-17 null mutants but are restored by artificially induced DSBs, indicating that all components required to convert DSBs into chiasmata are present. Unlike SPO-11, HIM-17 is also required for proper accumulation of histone H3 methylation at lysine 9 on meiotic prophase chromosomes. HIM-17 shares structural features with three proteins that interact genetically with LIN-35/Rb, a known component of chromatin-modifying complexes. Futhermore, DSB levels and incidence of chiasmata can be modulated by loss of LIN-35/Rb. These and other data suggest that chromatin stage governs the timing ------------------- Key: 6741 Medline: 15304642 Authors: Bae T;Banger AK;Wallace A;Glass EM;Aslund F;Schneewind O;Missiakas DM Title: Staphylococcus aureus virulence genes identified by bursa aurealis mutagenesis and nematode killing. Citation: Proceedings of the National Academy of Sciences USA 101: 12312-12317 2004 Type: ARTICLE Genes: Abstract: Staphylococcus aureus is the leading cause of wound and hospital-acquired infections worldwide. The emergence of S. aureus strains with resistance to multiple antibiotics requires the identification of bacterial virulence genes and the development of novel therapeutic strategies. Herein, bursa aurealis, a mariner-based transposon, was used for random mutagenesis and for the isolation of 10,325 S. aureus variants with defined insertion sites. By screening for loss-of-function mutants in a Caenorhabditis elegans killing assay, 71 S. aureus virulence genes were identified. Some of these genes are also required for S. aureus abscess formation in a murine infection model. ------------------- Key: 6742 Medline: 15314158 Authors: Grimson A;O'Connor S;Newman CL;Anderson P Title: SMG-1 is a phosphatidylinositol kinase-related protein kinase required for nonsense-mediated mRNA decay in Caenorhabditis elegans. Citation: Molecular and Cellular Biology 24: 7483-7490 2004 Type: ARTICLE Genes: rpl-12 smg-1 smg-2 smg-3 smg-4 smg-5 Abstract: Eukaryotic messenger RNAs containing premature stop codons are selectively and rapidly degraded, a phenomenon termed nonsense-mediated mRNA decay (NMD). Previous studies with both Caenohabditis elegans and mammalian cells indicate that SMG-2/human UPF1, a central regulator of NMD, is phosphorylated in an SMG-1-dependent manner. We report here that smg-1, which is required for NMD in C. elegans, encodes a protein kinase of the phosphatidylinositol kinase superfamily of protein kinases. We identify null alleles of smg-1 and demonstrate that SMG-1 kinase activity is required in vivo for NMD and in vitro for SMG-2 phosphorylation. SMG-1 and SMG-2 coimmunoprecipitate from crude extracts, and this interaction is maintained in smg-3 and smg-4 mutants, both of which are required for SMG-2 phosphorylation in vivo and in vitro. SMG-2 is located diffusely through the cytoplasm, and its location is unaltered in mutants that disrupt the cycle of SMG-2 phosphorylation. We discuss the role of SMG-2 ------------------- Key: 6743 Medline: 15314147 Authors: Chen Z;Eastburn DJ;Han M Title: The Caenorhabditis elegans nuclear receptor gene nhr-25 regulates epidermal cell development. Citation: Molecular and Cellular Biology 24: 7345-7358 2004 Type: ARTICLE Genes: lin-11 lin-39 nhr-25 sid-1 Abstract: The development of the epidermis of Caenorhabditis elegans involves cell fusion, migration, and differentiation events. To understand the mechanisms underlying these processes, we characterized the roles of NHR-25, a member of the nuclear receptor family of transcription factors. The NHR-25 homologs Ftz-F1 in Drosophild and SF-1 in mammals are involved in various biological processes, including regulation of patterning during development, reproduction, metabolism, metamorphosis, and homeostasis. Impairment of nhr-25 activity leads to severe phenotypes in embryos and many postembryonic tissues. Further analysis has indicated that nhr-25 activity is required for the proper development, including cell-cell fusion, of several epidermal cell types, such as the epidermal syncytial, seam, and Pn.p cells. Our results also suggest that nhr-25 is likely to regulate cell-cell junctions and/or fusion. In a subset of Pn.p cells, called vulval precursor cells, nhr-25 acts collaboratively with the lin-39 Hox gene in regulating vulval cell differentiation. Additionally, our data suggest that nhr-25 may also function with another Hox gene, nob-1, during embryogenesis. Overall, our results indicate that nhr-25 plays an integral role in regulating cellular processes of epidermal cells. ------------------- Key: 6744 Medline: 15279946 Authors: Komuniecki RW;Hobson RJ;Rex EB;Hapiak VM;Komuniecki PR Title: Biogenic amine receptors in parasitic nematodes: what can be learned from Caenorhabditis elegans. Citation: Molecular & Biochemical Parasitology 137: 1-11 2004 Type: REVIEW Genes: dop-1 egl-19 egl-30 mod-1 ser-1 ser-2 ser-4 ser-7 Abstract: The biogenic amines, serotonin, octopamine, tyramine and dopamine regulate many essential processes in parasitic nematodes, such as pharyngeal pumping, muscle contraction, and egg-laying, as well as more complex behaviors, such as mechanosensation and foraging, making biogenic amine receptors excellent targets for drug discovery. This review is designed to summarize our knowledge of nematode biogenic amine signaling and preliminarily identify some of the key receptors involved in the regulation of biogenic amine-dependent behaviors through an analysis of the free-living nematode, Caenorhabditis elegans. ------------------- Key: 6745 Medline: 15279955 Authors: Tarr DEK;Scott AL Title: MSP domain proteins show enhanced expressions in male germ line cells. Citation: Molecular & Biochemical Parasitology 137: 87-98 2004 Type: ARTICLE Genes: ssp-9 ssp-10 ssp-11 ssp-16 ssp-19 ssp-31 ssp-32 Abstract: Nematode sperm utilize a crawling motility based on polymerization-depolymerization of a nematode-specific cytoskeletal molecule - major sperm protein (MSP). While several proteins that interact with and regulate MSP filament formation have been identified using in vitro approaches, it is likely that additional molecules participate in vivo in the regulation of MSP cytoskeletal dynamics. By comparing EST data generated from an Ascaris suum testis germinal zone cDNA library with EST data from other tissue- and stage-specific A. suum cDNA libraries and with expression profile data from Caenorhabditis elegans, 42 genes were selected with exclusive or enhanced expression in male germ line cells. In addition to 11 protein kinases and seven protein phosphatases, 10 genes encoding proteins with protein-protein interaction domains were identified. These potential cytoskeletal modifiers included five novel MSP-domain proteins (As-MDPs). All five As-mdps were highly expressed in male gem line cells, but only As-mdp-2, 3 and 5 were transcribed exclusively in the testis. The prediction that As-MDP-1, 2 and 3 were cytosolic components and that As-MDP-4 and 5 were associated with the sperm cell membrane proteins was supported by the results of immunoblotting experiments. The 23 members of the MDP family of proteins from C. elegans were predicted to be transcribed in the testis. The findings provide additional candidates to the growing list of molecules that regulate MSP cytoskeletal dynamics. ------------------- Key: 6746 Medline: 15287963 Authors: Hare EE;Loer CM Title: Function and evolution of the serotonin-synthetic bas-1 gene and other aromatic amino acid decarboxylase genes in Caenorhabditis. Citation: BMC Evolutionary Biology 4: 24- 2004 Type: ARTICLE Genes: bas-1 tdc-1 unc-25 Abstract: Background: Aromatic L-amino acid decarboxylase (AADC) enzymes catalyze the synthesis of biogenic amines, including the neurotransmitters serotonin and dopamine, throughout the animal kingdom. These neurotransmitters typically perform important functions in both the nervous system and other tissues, as illustrated by the debilitating conditions that arise from their deficiency. Studying the regulation and evolution of AADC genes is therefore desirable to further our understanding of how nervous systems function and evolve. Results: In the nematode C. elegans, the bas-1 gene is required for both serotonin and dopamine synthesis, and maps genetically near two AADC-homologous sequences. We show by transformation rescue and sequencing of mutant alleles that bas-1 encodes an AADC enzyme. Expression of a reporter construct in transgenics suggests that the bas-1 gene is expressed, as expected, in identified serotonergic and dopaminergic neurons. The bas-1 gene is one of six AADC-like sequences in the C. elegans genome, including a duplicate that is immediately downstream of the bas-1 gene. Some of the six AADC genes are quite similar to known serotonin- and dopamine-synthetic AADC's from other organisms whereas others are divergent, suggesting previously unidentified functions. In comparing the AADC genes of C. elegans with those of the congeneric C. briggsae, we find only four orthologous AADC genes in C. briggsae. Two C. elegans AADC genes-those most similar to bas-1-are missing from C. briggsae. Phylogenetic analysis indicates that one or both of these bas-1-like genes were present in the common ancestor of C. elegans and C. briggsae, and were retained in the C. elegans line, but lost in the C. briggsae line. Further analysis of the two bas-1-like genes in C. elegans suggests that they are unlikely to encode functional enzymes, and may be expressed pseudogenes. Conclusions: The bas-1 gene of C. elegans encodes a serotonin- and dopamine-synthetic AADC enzyme. Two C. elegans AADC-homologous genes that are closely related to bas-1 are missing from the congeneric C. briggsae; one or more these genes was present in the common ancestor of C. elegans and C. briggsae. Despite their persistence in C. elegans, evidence suggests the bas-1-like genes do not encode functional AADC proteins. The presence of the genes in C. elegans raises questions about how many 'predicted genes' in sequenced genomes are functional, and how duplicate genes are retained or lost during evolution. This is another example of unexpected retention of duplicate genes ------------------- Key: 6747 Medline: 15155758 Authors: Meissner B;Boll M;Daniel H;Baumeister R Title: Deletion of the intestinal peptide transporter affects insulin and TOR signaling in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 279: 36739-36745 2004 Type: ARTICLE Genes: daf-2 daf-16 eat-2 let-363 pep-1 pep-2 Abstract: The mammalian intestinal peptide transporter PEPT1 mediates the uptake of di- and tripeptides from the gut lumen into intestinal epithelial cells and acts in parallel with amino acid transporters. Here we address the importance of the PEPT1 orthologue PEP-2 for the assimilation of dietary protein and for overall protein nutrition in Caenorhabditis elegans. pep-2 is expressed specifically along the apical membrane of the intestinal cells, and in pep-2 deletion mutant animals, uptake of intact peptides from the gut lumen is abolished. The consequences are a severely retarded development, reduced progeny and body size, and increased stress tolerance. We show here that pep-2 cross-talks with both the C. elegans target of rapamycin (TOR) and the DAF2/insulin-signaling pathways. The pep-2 mutant enhances the developmental and longevity phenotypes of daf-2, resulting, among other effects, in a pronounced increase in adult life span. Moreover, all aspects of a weak let-363/TOR RNA interference phenotype are intensified by pep-2 deletion, indicating that pep-2 function upstream of TOR-mediated nutrient sensing. Our findings provide evidence for a predominant role of the intestinal peptide transporter for the delivery of bulk quantities of amino acids for growth and development, which consequently affects signaling pathways that regulate metabolism and ------------------- Key: 6748 Medline: 15234973 Authors: Zhang Y;Foster JM;Kumar S;Fougere M;Carlow CKS Title: Cofactor-independent phosphoglycerate mutase has an essential role in Caenorhabditis elegans and is conserved in parasitic nematodes. Citation: Journal of Biological Chemistry 279: 37185-37190 2004 Type: ARTICLE Genes: pos-1 unc-22 Abstract: Phosphoglycerate mutases catalyze the interconversion of 2- and 3-phosphoglycerate in the glycolytic and gluconeogenic pathways. They exist in two unrelated forms that are either cofactor (2,3-diphosphoglycerate)-dependent or cofactor-independent. The two enzymes have no similarity in amino acid sequence, tertiary structure, or catalytic mechanism. Certain organisms including vertebrates have only the cofactor-dependent form, whereas other organisms can possess the independent form or both. Caenorhabditis elegans has been predicted to have only independent phosphoglycerate mutase. In this study, we have cloned and produced recombinant, independent phosphoglycerate mutases from C. elegans and the human-parasitic nematode Brugia malayi. They are 70% identical to each other and related to known bacterial, fungal, and protozoan enzymes. The nematode enzymes possess the catalytic serine, and other key amino acids proposed for catalysis and recombinant enzymes showed typical phosphoglycerate mutase activities in both the glycolytic and gluconeogenic directions. The gene is essential in C. elegans, because the reduction of its activity by RNA interference led to embryonic lethality, larval lethality, and abnormal body morphology. Promoter reporter analysis indicated widespread expression in larval and adult C. elegans with the highest levels apparent in the nerve ring, intestine, and body wall muscles. The enzyme was found in a diverse group of nematodes representing the major clades, indicating that it is conserved throughout this phylum. Our results demonstrate that nematodes, unlike vertebrates, utilize independent phosphoglycerate mutase in glycolytic and gluconeogenic pathways and that the enzyme is probably ------------------- Key: 6749 Medline: 15247908 Authors: Lu M;Kinchen JM;Rossman KL;Grimsley C;deBakker C;Brugnera E;Tosello-Trampont AC;Haney LB;Klingele D;Sondek J;Hengartner MO;Ravichandran KS Title: PH domain of ELMO functions in trans to regulate Rac activation via Dock180. Citation: Nature Structural & Molecular Biology 11: 756-762 2004 Type: ARTICLE Genes: ced-12 Abstract: The members of the Dock180 superfamily of proteins are novel guanine nucleotide exchange factors (GEF) for Rho family GTPases and are linked to multiple biological processes from worms to mammals. ELMO is a critical regulator of Dock180, and the Dock180-ELMO complex functions as a bipartite GEF for Rac. We identified a mechanism wherein the PH domain of ELMO, by binding the Dock180-Rac complex in trans, stabilizes Rac in the nucleotide-free transition state. Mutagenesis studies reveal that this ELMO PH domain-dependent regulation is essential for the Dock180-ELMO complex to function in phagocytosis and cell migration. Genetic rescue studies in Caenorhabditis elegans using ELMO and its homolog CED-12 support the above observations in vivo. These data reveal a new mode of action of PH domains and a novel, evolutionarily conserved mechanism by which a bipartite GEF ------------------- Key: 6750 Medline: 15353560 Authors: Snel B;van Noort V;Huynen MA Title: Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes. Citation: Nucleic Acids Research 32: 4725-4731 2004 Type: ARTICLE Genes: Abstract: Differences between species have been suggested to largely reside in the network of connections among the genes. Nevertheless, the rate at which these connections evolve has not been properly quantified. Here, we measure the extent to which co-regulation between pairs of genes is conserved over large phylogenetic distances; between two eukaryotes Caenorhabditis elegans and Saccharomyces cerevisiae, and between two prokaryotes Escherichia coli and Bacillus subtilis. We first construct a reliable set of co-regulated genes by combining various functional genomics data from yeast, and subsequently determine conservation of co-regulation in worm from the distribution of co-expression values. For B.subtilis and E.coli, we use known operons and regulons. We find that between 76 and 80% of the co-regulatory connections are conserved between orthologous pairs of genes, which is very high compared with previous estimates and expectations regarding network evolution. We show that in the case of gene duplication after speciation, one of the two inparalogous genes tends to retain its original co-regulatory relationship, while the other loses this link and is presumably free for differentiation or sub-functionalization. The high level of co-regulation conservation implies that reliably predicted functional relationships from functional genomics data in one species can be transferred with high accuracy to another species when that species also harbours the ------------------- Key: 6751 Medline: 15288503 Authors: Wakabayashi T;Kitagawa I;Shingai R Title: Neurons regulating the duration of forward locomotion in Caenorhabditis elegans. Citation: Neuroscience Research 50: 103-111 2004 Type: ARTICLE Genes: che-2 mec-4 odr-1 odr-3 ttx-1 ttx-3 Abstract: The locomotory behavior of Caenorhabditis elegans consists of four simple events, forward and backward movements, omega-shaped turns and rests. The wide variety of behaviors of this worm is achieved through a combination of these simple locomotions. To gain insight into the neuronal mechanisms regulating this locomotion, we analyzed the locomotory behavior of C. elegans over a long time period. By using an automatic worm tracking system, we revealed the existence of at least two distinct behavioral states - pivoting and traveling - in the forward locomotion of C. elegans in the absence of food. Pivoting is characterized by pronounced directional switching and resulting in short-duration forward movement. whereas in the traveling state forward movement is of longer duration. Pivoting occurred when we transferred a well-fed worm to an unseeded plate, and then the transition to traveling occurred, successively. We showed that, by laser ablation, antagonistic neuronal pathways consisting of nine classes of sensory neurons and four classes of interneurons were involved in this regulation. Loss of any one of these neurons altered the locomotory behavior. ------------------- Key: 6752 Medline: 15329389 Authors: Lipton J;Kleeman G;Ghosh R;Lints R;Emmons SW Title: Mate searching in Caenorhabditis elegans: a genetic model for sex drive in a simple invertebrate. Citation: Journal of Neuroscience 24: 7427-7434 2004 Type: ARTICLE Genes: daf-2 daf-16 fem-1 fem-2 fem-3 fog-1 fog-2 glp-1 him-5 mog-3 spe-26 tph-1 mgDf50 Abstract: Much of animal behavior is regulated to accomplish goals necessary for survival and reproduction. Little is known about the underlying motivational or drive states that are postulated to mediate such goal-directed behaviors. Here, we describe a mate-searching behavior of the Caenorhabditis elegans male that resembles the motivated behaviors of vertebrates. Adult C. elegans males, if isolated from mating partners, will leave the area of a food source and wander about their environment in an apparent search for a mate. When mating partners are present on the food source, males do not wander but remain with them. This behavior is sexually dimorphic for C. elegans and two additional male/hermaphrodite species studied; for these species, hermaphrodites leave food significantly slower than males. In contrast, for three male - female species examined, both males and females left food, in two cases with similar frequency, suggesting coordinate evolution of behavioral dimorphism with hermaphroditism. We use a quantitative behavioral assay to show that C. elegans male mate searching is regulated by signals from hermaphrodites and by physiological signals indicating nutritional and reproductive status. We identify genes in the serotonin, insulin, and sex determination pathways that affect the rate of mate searching. These genes may contribute to physiological and reproductive regulatory mechanisms. Our results establish C. elegans as a model genetic animal with a simple nervous system in which neural pathways leading to a motivated behavior may be genetically dissected. ------------------- Key: 6753 Medline: 15330854 Authors: Nakano Y;Nagamatsu Y;Ohshima Y Title: cGMP and a germ-line signal control body size in C. elegans through cGMP-dependent protein kinase EGL-4. Citation: Genes to Cells 9: 773-779 2004 Type: ARTICLE Genes: col-19 daf-4 daf-16 dbl-1 dss-1 egl-4 sma-2 sma-3 sma-4 sma-6 tax-2 mgDf50 Abstract: Mechanisms involved in the control of body size are largely unknown. In the nematode C. elegans, several small body size mutants were isolated, and the responsible genes were reported to encode putative components of a TGFbeta signalling pathway. Recently, mutants in the egl-4 gene encoding cGMP-dependent protein kinases were found to have a larger body size, and it was suggested that EGL-4 down-regulates the TGFbeta/DBL-1 pathway. We show that a permeable cGMP analogue 8-Br-cGMP significantly reduces body size of the wild-type but not that of an egl-4 mutant, indicating that cGMP controls body size through EGL-4. Laser ablation of germ-line cells revealed that a germ-line signal and EGL-4 function in the same pathway. Targeted expression of EGL-4 indicates that EGL-4 can function in hypodermis, neurones and intestine both cell-autonomously and cell-nonautonomously to control organ and body size. We propose a signal cascade for the control of body size that involves a germ-line signal, cGMP, G-kinase EGL-4 and DBL-1/TGFbeta pathway. It is interesting that two important pathways involving cGMP and TGFbeta, respectively, are related. Also, the results suggest a novel mechanism for the control of organ and body size in which hypodermis plays a key role. ------------------- Key: 6754 Medline: 15215208 Authors: Sonneville R;Gonczy P Title: zyg-11 and cul-2 regulate progression through meiosis II and polarity establishment in C. elegans. Citation: Development 131: 3527-3543 2004 Type: ARTICLE Genes: air-1 cdc-25.1 chk-2 cki-1 cki-2 cks-1 cul-2 cyb-1 cyb-2.2 cyb-3 elc-1 fzr-1 mat-1 ncc-1 paa-1 pas-5 pbs-2 pbs-7 puf-3 rec-8 spd-2 tba-2 zyg-11 nDf29 Abstract: The mechanisms that ensure coupling between meiotic cell cycle progression and subsequent developmental events, including specification of embryonic axes, are poorly understood. Here, we establish that zyg-11 and the cullin cul-2 promote the metaphase-to-anaphase transition and M phase exit at meiosis H in Caenorhabditis elegans. Our results indicate that ZYG-11 acts with a CUL-2-based E3 ligase that is essential at meiosis II and that functions redundantly with the anaphase-promoting complex/cyclosome at meiosis I. Our data also indicate that delayed M phase exit in zyg-11(RNAi) embryos is due to accumulation of the B type cyclin CYB-3. We demonstrate that PAR proteins and P granules become polarized in an inverted manner during the meiosis II delay resulting from zyg-11 or cul-2 inactivation, and that zyg-11 and cul-2 can regulate polarity establishment independently of a role in cell cycle progression. Furthermore, we find that microtubules appear dispensable for ectopic polarity during the meiosis II delay in zyg-11(RNAi) embryos, as well as for AP polarity during the first mitotic cell cycle in wild-type embryos. Our findings suggest a model in which a CUL-2-based E3 ligase promotes cell cycle progression and prevents polarity establishment during meiosis II, and in which the centrosome acts as a cue to polarize the embryo along the AP axis after exit from the meiotic cell cycle. ------------------- Key: 6755 Medline: 15333932 Authors: Symersky J;Zhang Y;Schormann N;Li S;Bunzel R;Pruett P;Luan CH;Luo M Title: Structural genomics of Caenorhabditis elegans: structure of the BAG domain. Citation: Acta Crystallographica Section D-Biological Crystallography 60: 1606-1610 2004 Type: ARTICLE Genes: Abstract: Binding of the BAG domain to the eukaryotic chaperone heat-shock protein (Hsp70) promotes ATP-dependent release of the protein substrate from Hsp70. Although the murine and human BAG domains have been shown to form an antiparallel three-helix bundle, the Caenorhabditis elegans BAG domain is formed by two antiparallel helices, while the third helix is extended away and stabilized by crystal-packing interactions. A small beta-sheet between helices 2 and 3 interferes with formation of the intramolecular three-helix bundle. However, intermolecular three-helix bundles are observed throughout the crystal packing and suggest that stable functional dimers and tetramers can be formed in solution. The structure may represent a new folding type of the BAG domain. ------------------- Key: 6756 Medline: 15372040 Authors: Mello CC;Conte D Title: Revealing the world of RNA interference. Citation: Nature 431: 338-342 2004 Type: REVIEW Genes: par-1 rde-1 rde-4 Abstract: The recent discoveries of RNA interference and the related RNA silencing pathways have revolutionized our understanding of gene regulation. RNA interference has been used as a research tool to control the expression of specific genes in numerous experimental organisms and has potential as a therapeutic strategy to reduce the expression of problem genes. At the heart of RNA interference lies a remarkable RNA processing mechanism that is now known to underlie many distinct biological ------------------- Key: 6757 Medline: Authors: Ambros V Title: The functions of animal microRNAs. Citation: Nature 431: 350-355 2004 Type: REVIEW Genes: ceh-36 che-1 cog-1 die-1 gcy-5 gcy-7 let-7 lim-6 lin-4 lin-14 lin-28 lin-49 lsy-6 mir-273 unc-37 Abstract: MicroRNAs (miRNAs) are small RNAs that regulate the expression of complementary messenger RNAs. Hundreds of miRNA genes have been found in diverse animals, and many of these are phylogenetically conserved. With miRNA roles identified in developmental timing, cell death, cell proliferation, haemotopoiesis and patterning of the nervous system, evidence is mounting that animal miRNAs are more numerous, and their regulatory impact more pervasive, than was previously suspected. ------------------- Key: 6758 Medline: Authors: Meister G;Tuschl T Title: Mechanisms of gene silencing by double-stranded RNA. Citation: Nature 431: 343-349 2004 Type: REVIEW Genes: alg-1 alg-2 dcr-1 drh-1 drh-2 ego-1 eri-1 mut-7 mut-14 ppw-1 rde-1 rde-4 rrf-1 rrf-3 sid-1 smg-2 Abstract: Double-stranded RNA (dsRNA) is an important regulator of gene expression in many eukaryotes. It triggers different types of gene silencing that are collectively referred to as RNA silencing or RNA interference. A key step in known silencing pathways is the processing of dsRNAs into short RNA duplexes of characteristic size and structure. These short dsRNAs guide RNA silencing by specific and distinct mechanisms. Many components of the RNA silencing machinery still need to be identified and characterized, but a more complete understanding of the process is imminent. ------------------- Key: 6759 Medline: Authors: Santander J;Robeson J Title: Bacteriophage prophylaxis against Salmonella enteritidis and Salmonella pullorum using Caenorhabditis elegans as an assay system. Citation: Electronic Journal of Biotechnology 7: 206-209 2004 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans has been used as animal model system to study bacterial pathogenesis. In this study we used C. elegans in a bacteriophage prophylaxis assay to test phage protection against infection by Salmonella enteritidis and S. pullorum. We found that pretreatment of nematodes with bacteriophage that lyse S. enteritidis and S. pullorum results in enhanced survival of C. elegans, when challenged with these bacterial pathogens. ------------------- Key: 6760 Medline: 15313609 Authors: Small TM;Gernert KM;Flaherty DB;Mercer KB;Borodovsky M;Benian GM Title: Three new isoforms of Caenorhabditis elegans UNC-89 containing MLCK-like protein kinase domains. Citation: Journal of Molecular Biology 342: 91-108 2004 Type: ARTICLE Genes: unc-54 unc-89 Abstract: In Caenorhabditis elegans, the gene unc-89 is required for A-band organization of striated muscle. In mammals, a likely homolog of UNC-89, called obscurin, has been described and found to be localized at both the M-lines and Z-discs of striated muscle. Here, we show that the coding sequence for unc-89 is larger than originally thought, and that the gene encodes at least four major isoforms: UNC-89-A (original isoform, 732 kDa), UNC-89-B (potentially 900 kDa), and UNC-89-C and UNC-89-D (each 156 kDa). UNC-89-C and UNC-89-D, except for unique N-terminal tails of eight and 11 residues, respectively, are co-linear with the C terminus of UNC-89-B. The unc-89 complex transcription unit contains at least three promoters: one directing UNC-89A and -B primarily in body-wall and pharyngeal muscle, one internal promoter directing expression of UNC-89-C primarily in body wall muscle, and one internal promoter directing expression of UNC-89-D primarily in a few muscle cells of the tail. Isoform-specific RNA interference resulted in a muscle structural phenotype similar to a typical unc-89 mutant, but with varying degrees of severity. Antibodies generated to the interkinase region shared by the UNC-89-B, -C and -D isoforms localize to the middle of A-bands, like previously-described UNC-89 antibodies, and detect proteins on immunoblots consistent with the proposed gene organization and additional isoforms. The three new UNC-89 isoforms contain two protein kinase domains, of the myosin light chain kinase (MLCK) family. UNC-89-B contains two complete protein kinase domains, designated PK1 and PK2. UNC-89-C and -D begin with partial kinase domains, PK-1C and PK1-D. Homology modeling suggests that PK2 is catalytically active, PK1 is inactive, and that PK-1C and PK-1D have similar structures at their N termini that may ------------------- Key: 6761 Medline: 15371340 Authors: Cheeseman IM;Niessen S;Anderson S;Hyndman F;Yates JR;Oegema K;Desai A Title: A conserved protein network controls assembly of the outer kinetochre and its ability to sustain tension. Citation: Genes & Development 18: 2255-2268 2004 Type: ARTICLE Genes: bub-1 hcp1- hcp-2 hcp-4 him-10 kbp-1 kbp-2 kbp-3 kbp-4 kbp-5 knl-1 knl-3 mis-12 ndc-80 Abstract: Kinetochores play an essential role in chromosome segregation by forming dynamic connections with spindle microtubules. Here, we identify a set of 10 copurifying kinetochore proteins from Caenorhabditis elegans, seven of which were previously uncharacterized. Using in vivo assays to monitor chromosome segregation, this copurifying protein network plays a central role at the kinetochore-microtubule interface. In addition, our analysis suggests that the network is comprised of three groups of proteins that contribute in distinct ways to this interface: KNL proteins act after the assembly of centromeric chromatin to generate the core of the microtubule-binding interface, MIS proteins control the rate and extent of formation of this interface, and NDC proteins are necessary to sustain tension during interactions with spindle microtubules. We also purify a similar set of associated proteins from human cells that includes four novel proteins and has recognizable homologs from each functional class. Thus, this protein network is a conserved constituent of the outer kinetochore, and the functions defined by our analysis in C. elegans are likely ------------------- Key: 6762 Medline: 15232211 Authors: Lee JI;Ahnn J Title: Calcineurin in animal behavior. Citation: Molecules & Cells 17: 390-396 2004 Type: REVIEW Genes: Abstract: The conserved Ca2+/calmodulin-dependent phosphatase calcineurin has been shown to be involved in numerous and diverse functions both at the cellular and organism level. Recent genetic and pharmacological studies in animals including C. elegans, Drosophila, Aplysia, rat and mice have also implicated calcineurin in behavior, particularly in the regulation of plasticity and modulation of behaviors. These studies have not only brought a clearer understanding of the molecular contributions to behavior, but should also give insight into roles that calcineurin may be playing in the cognitive and behavioral defects ------------------- Key: 6763 Medline: 15201454 Authors: Voisine C;Hart AC Title: Caenorhabditis elegans as a model system for triplet repeat diseases. Citation: Methods in Molecular Biology 277: 141-160 2004 Type: REVIEW Genes: Abstract: Common features underlie the generation and function of neurons in multicellular animals. It is likely that conserved pathways and genes also are involved in neuronal degeneration and malfunction. To address the molecular mechanisms of complex human neurological disorders, many investigators are choosing to study these diseases in simpler organisms. The nematode Caenorhabditis elegans provides an excellent model system to address genetically the mechanisms of triplet repeat diseases. Advantages of using C. elegans as a model system include the ease of genetic manipulation, the sequenced genome, and a short life cycle. Furthermore, researchers can precisely identify specific neurons and follow their development or survival throughout the animal's lifetime. This chapter describes the tools and approaches for modeling triplet repeat diseases in C. elegans with a specific emphasis on polyglutamine (polyQ) diseases. Although the bulk of the chapter is devoted to generating a polyQ disease model in C. elegans, it also addresses potential avenues for assessing the impact of specific candidate genes/pathways on the disease process, including cell death and aging. ------------------- Key: 6764 Medline: 15375261 Authors: Ao W;Gaudet J;Kent WJ;Muttumu S;Mango SE Title: Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR. Citation: Science 305: 1743-1746 2004 Type: ARTICLE Genes: ceh-22 daf-12 myo-2 pha-4 Abstract: Growth and development of the Caenorhabditis elegans foregut (pharynx) depends on coordinated gene expression, mediated by pharynx defective (PHA)-4/FoxA in combination with additional, largely unidentified transcription factors. Here, we used whole genome analysis to establish clusters of genes expressed in different pharyngeal cell types. We created an expectation maximization algorithm to identify cis-regulatory elements that activate expression within the pharyngeal gene clusters. One of these elements mediates the response to environmental conditions within pharyngeal muscles and is recognized by the nuclear hormone receptor (NHR) DAF-12. Our data suggest that PHA-4 and DAF-12 endow the pharynx with transcriptional plasticity to respond to diverse developmental and physiological cues. Our combination of bioinformatics and in vivo analysis has provided a powerful means for genome-wide investigation of transcriptional control. ------------------- Key: 6765 Medline: 15317971 Authors: Ohler U;Yekta S;Lim LP;Bartel DP;Burge CB Title: Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. Citation: RNA 10: 1309-1322 2004 Type: ARTICLE Genes: lys-6 mir-39 mir-62 mir-64 mir-65 mir-66 mir-72 mir-229 mir-238 mir-239 mir-259 mir-353 mir-354 mir-355 mir-356 mir-357 mir-358 mir-359 mir-360 mir-362 mir-392 Abstract: MicroRNAs are similar to22-nucleotide (nt) RNAs processed from foldback segments of endogenous transcripts. Some are known to play important gene regulatory roles during animal and plant development by pairing to the messages of protein-coding genes to direct the post-transcriptional repression of these messages. Previously, we developed a computational method called MiRscan, which scores features related to the foldbacks, and used this algorithm to identify new miRNA genes in the nematode Caenorhabditis elegans. In the present study, to identify sequences that might be involved in processing or transcriptional regulation of miRNAs, we aligned sequences upstream and downstream of orthologous nematode miRNA foldbacks. These alignments showed a pronounced peak in sequence conservation about 200 bp upstream of the miRNA foldback and revealed a highly significant sequence motif, with consensus CTCCGCCC, that is present upstream of almost all independently transcribed nematode miRNA genes. Scoring the pattern of upstream/downstream conservation, the occurrence of this sequence motif, and orthology of host genes for intronic miRNA candidates, yielded substantial improvements in the accuracy of MiRscan. Nine new C. elegans miRNA gene candidates were validated using a PCR-sequencing protocol. As previously seen for bacterial RNA genes, sequence features outside of the RNA secondary structure can therefore be very useful for the computational identification of eukaryotic noncoding RNA genes. The total number of confidently identified nematode miRNAs now approaches 100. The improved analysis supports our previous assertion that miRNA gene identification is nearing completion in C. elegans with apparently no more than 20 miRNA genes now remaining to be identified. ------------------- Key: 6766 Medline: 15306688 Authors: Jager S;Schwartz HT;Horvitz HR;Conradt B Title: The Caenorhabditis elegans F-box protein SEL-10 promotes female development and may target FEM-1 and FEM-3 for degradation by the proteasome. Citation: Proceedings of the National Academy of Sciences USA 101: 12549-12554 2004 Type: ARTICLE Genes: egl-41 fem-1 fem-2 fem-3 her-1 him-8 lin-12 sdc-1 sel-10 sel-12 tra-2 nDf42 ctDp8 Abstract: The Caenorhabditis elegans F-box protein SEL-10 and its human homolog have been proposed to regulate LIN-12 Notch signaling by targeting for ubiquitin-mediated proteasomal degradation LIN-12 Notch proteins and SEL-12 PS1 presenilins, the latter of which have been implicated in Alzheimer's disease. We found that sel-10 is the same gene as egl-41, which previously had been defined by gain-of-function mutations that semidominantly cause masculinization of the hermaphrodite soma. Our results demonstrate that mutations causing loss-of-function of sel-10 also have masculinizing activity, indicating that sel-10 functions to promote female development. Genetically, sel-10 acts upstream of the genes fern-1, fem-2, and fem-3 and downstream of her-1 and probably tra-2. When expressed in mammalian cells, SEL-10 protein coimmunoprecipitates with FEM-1, FEM-2, and FEM-3, which are required for masculinization, and FEM-1 and FEM-3 are targeted by SEL-10 for proteasomal degradation. We propose that SEL-10-mediated proteolysis of FEM-1 and FEM-3 is required for normal hermaphrodite development. ------------------- Key: 6767 Medline: 15468735 Authors: Sakata K;Shingai R Title: Neural network model to generate head swing in locomotion of Caenorhabditis elegans. Citation: Network: Computation in Neural Systems 15: 199-216 2004 Type: ARTICLE Genes: Abstract: Computer simulation of the neural network composed of the head neurons of Caenorhabditis elegans was performed to reconstruct the realistic changes in the membrane potential of motoneurons in swinging the head for coordinated forward locomotion. The model neuron had ion channels for calcium and potassium, whose parameters were obtained by fitting the experimental data. Transmission properties of the chemical synapses were set as graded. The neural network involved in forward movement was extracted by tracing the neuronal activity flow upstream from the motoneurons connected to the head muscles. Simulations were performed with datasets, which included all combinations of the excitatory and inhibitory properties of the neurons. In this model, a pulse input entered only from motoneuron VB1, and activation of the stretch receptors on SAA neurons was necessary for the periodic bending. The synaptic output property of each neuron was estimated for the alternate contraction of the dorsal and ventral muscles. The AIB neuron was excitatory, RIV and SMD neurons seemed to be excitatory and RMD and SAA neurons seemed to be inhibitory. With datasets violating Dale's principle for the SMB neuron, AM neuron was excitatory and RMD neuron was inhibitory. RIA, RIV and SMD neurons seemed to be ------------------- Key: 6768 Medline: Authors: Fan Y;Esmail MA;Ansley SJ;Blacque OE;Boroevich K;Ross AJ;Moore SJ;Badano JL;May-Simera H;Compton DS;Green JS;Lewis RA;van Haelst MM;Parfrey PS;Baillie DL;Beales PL;Katsanis N;Davidson WS;Leroux MR Title: Mutations in a member of the Ras superfamily of small GTP-binding proteins causes Bardet-Biedl syndrome. Citation: Nature Genetics 36: 989-993 2004 Type: ARTICLE Genes: arl-6 bbs-3 bbs-7 bbs-8 che-13 daf-19 Abstract: RAB, ADP-ribosylation factors (ARFs) and ARF-like (ARL) proteins belong to the Ras superfamily of small GTP-binding proteins and are essential for various membrane-associated intracellular trafficking processes(1,2). None of the similar to50 known members of this family are linked to human disease. Using a bioinformatic screen for ciliary genes in combination with mutational analyses, we identified ARL6 as the gene underlying Bardet-Biedl syndrome type 3, a multisystemic disorder characterized by obesity, blindness, polydactyly, renal abnormalities and cognitive impairment(3,4). We uncovered four different homozygous substitutions in ARL6 in four unrelated families affected with Bardet-Biedl syndrome, two of which disrupt a threonine residue important for GTP binding(5) and function(5-7) of several related small GTP-binding proteins. Analysis of the Caenorhabditis elegans ARL6 homolog indicates that it is specifically expressed in ciliated cells, and that, in addition to the postulated cytoplasmic functions of ARL proteins, it undergoes intraflagellar transport. These findings implicate a small GTP-binding protein in ciliary transport and the ------------------- Key: 6769 Medline: 15313604 Authors: Washietl S;Hofacker IL Title: Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. Citation: Journal of Molecular Biology 342: 19-30 2004 Type: ARTICLE Genes: Abstract: Facing the ever-growing list of newly discovered classes of functional RNAs, it can be expected that further types of functional RNAs are still hidden in recently completed genomes. The computational identification of such RNA genes is, therefore, of major importance. While most known functional RNAs have characteristic secondary structures, their free energies are generally not statistically significant enough to distinguish RNA genes from the genomic background. Additional information is required. Considering the wide availability of new genomic data of closely related species, comparative studies seem to be the most promising approach. Here, we show that prediction of consensus structures of aligned sequences can be a significant measure to detect functional RNAs. We report a new method to test multiple sequence alignments for the existence of an unusually structured and conserved fold. We show for alignments of six types of well-known functional RNA that an energy score consisting of free energy and a covariation term significantly improves sensitivity compared to single sequence predictions. We further test our method on a number of non-coding RNAs from Caenorhabditis elegans/Caenorhabditis briggsae and seven Saccharomyces species. Most RNAs can be detected with high significance. We provide a Perl implementation that can be used readily to score single alignments and discuss how the methods described here can be extended to allow for efficient genome-wide screens. ------------------- Key: 6770 Medline: 15302406 Authors: Brownlie JC;Whyard S Title: CemaT1 is an active transposon within the Caenorhabditis elegans genome. Citation: Gene 338: 55-64 2004 Type: ARTICLE Genes: Abstract: The maT clade of transposons is a group of transposable elements intermediate in sequence and predicted protein structure to mariner and T-C transposons, with a distribution thus far limited to a few invertebrate species. In the nematode Caenorhabditis elegans, there are eight copies of CemaT1 that are predicted to encode a functional transposase, with five copies being >99% identical. We present evidence, based on searches of publicly available databases and on PCR-based mobility assays, that the CemaT1 transposase is expressed in C. elegans and that the CemaT transposons are capable of excising in both somatic and germline tissues. We also show that the frequency of CemaT1 excisions within the genome of the N2 strain of C. elegans is comparable to that of the Tc1 transposon. However, unlike T-C transposons in mutator strains of C elegans, maT transposons do not exhibit increased frequencies of mobility, suggesting that maT is not regulated by the same factors that control T-C activity in these strains. Finally, we show that CemaT1 transposons are capable of precise transpositions as well as orientation inversions at some loci, and thereby become members of an increasing number of identified active ------------------- Key: 6771 Medline: 15321066 Authors: Whittaker AJ;Sternberg PW Title: Sensory processing by neural circuits in Caenorhabditis elegans. Citation: Current Opinion in Neurobiology 14: 450-456 2004 Type: REVIEW Genes: cat-2 eat-4 egl-19 gar-2 glr-1 glr-2 lov-1 mec-2 mec-4 nmr-1 pkd-2 unc-103 Abstract: The anatomical and developmental constancy of Caenorhabditis elegans belies the complexity of its numerically small nervous system. Indeed, there is an increased appreciation of C. elegans as an organism to study systems level questions. Many recent studies focus on the circuits that control locomotion, egg-laying, and male mating behaviors and their modulation by multiple sensory ------------------- Key: 6772 Medline: 15324682 Authors: Riedl CAL;Sokolowski MB Title: Behavioral genetics: guanylyl cyclase prompts worms to party. Citation: Current Biology 14: R657-R658 2004 Type: REVIEW Genes: daf-7 npr-1 tax-2 tax-4 Abstract: When it comes to foraging, there are two types of worm in the world: those who enjoy a party, and those who prefer to dine alone. Two recent reports describe roles for guanylyl cyclase in the neuromolecular signaling systems that effect this natural behavioral dimorphism. ------------------- Key: 6773 Medline: 15324689 Authors: Betschinger J;Knoblich JA Title: Dare to be different: asymmetric cell division in Drosophila, C. elegans and vertebrates. Citation: Current Biology 14: R674-R685 2004 Type: REVIEW Genes: glp-1 goa-1 gpa-1 gpa-16 gpb-1 gpc-2 gpr-1 gpr-2 mbk-2 mex-1 mex-5 mex-6 par-1 par-2 par-3 par-4 par-5 par-6 pie-1 pkc-3 pos-1 Abstract: One widespread mechanism for the generation of diverse cell types is the unequal inheritance of cell fate determinants. Several such determinants have been identified in the fruitfly Drosophila melanogaster and the worm Caenorhabditis elegans and the molecular machinery responsible for their asymmetric segregation is beginning to be unraveled. To divide asymmetrically, cells establish an axis of polarity, orient the mitotic spindle along this axis and localize cell fate determinants to one side of the cell. During cytokinesis, determinants are then segregated into one of the two daughter cells where they direct cell fate. Here, we outline the steps and factors that are involved in this process in Drosophila and C. elegans and discuss their potential conservation in vertebrates. ------------------- Key: 6774 Medline: 15253933 Authors: Jia K;Chen D;Riddle DL Title: The TOR pathway interacts with the insulin signaling pathway to regulate C. elegans larval development, metabollism and life span. Citation: Development 131: 3897-3906 2004 Type: ARTICLE Genes: daf-2 daf-15 daf-16 dpy-20 let-363 unc-24 unc-63 mgDf47 Abstract: The highly conserved target-of-rapamycin (TOR) protein kinases control cell growth in response to nutrients and growth factors. In mammals, TOR has been shown to interact with raptor to relay nutrient signals to downstream translation machinery. We report that in C elegans, mutations in the genes encoding CeTOR and raptor result in dauer-like larval arrest, implying that CeTOR regulates dauer diapause. The daf-15 (raptor) and let-363 (CeTOR) mutants shift metabolism to accumulate fat, and raptor mutations extend adult life span. daf-15 transcription is regulated by DAF-16, a FOXO transcription factor that is in turn regulated by daf-2 insulin/IGF signaling. This is a new mechanism that regulates the TOR pathway. Thus, DAF-2 insulin/IGF signaling and nutrient signaling converge on DAF-15 (raptor) to regulate C. elegans larval development, metabolism and life span. ------------------- Key: 6775 Medline: 15314028 Authors: Ludewig AH;Kober-Eisermann C;Weitzel C;Bethke A;Neubert K;Gerisch B;Hutter H;Antebi A Title: A novel nuclear receptor/coregulator complex controls C. elegans lipid metabolism, larval development, and aging. Citation: Genes & Development 18: 2120-2133 2004 Type: ARTICLE Genes: daf-2 daf-7 daf-9 daf-12 din-1 Abstract: Environmental cues transduced by an endocrine network converge on Caenorhabditis elegans nuclear receptor DAF-12 to mediate arrest at dauer diapause or continuous larval development. In adults, DAF-12 selects long-lived or short-lived modes. How these organismal choices are molecularly specified is unknown. Here we show that coregulator DIN-1 and DAF-12 physically and genetically interact to instruct organismal fates. Homologous to human corepressor SHARP, DIN-1 comes in long (L) and short (S) isoforms, which are nuclear localized but have distinct functions. DIN-1L, has embryonic and larval developmental roles. DIN-1S, along with DAF-12, regulates lipid metabolism, larval stage-specific programs, diapause, and longevity. Epistasis experiments reveal that din-1S acts in the dauer pathways downstream of lipophilic hormone, insulin/IGF, and TGFP signaling, the same point as daf-12. We propose that the DIN-1S/DAF-12 complex serves as a molecular switch that implements slow life history alternatives in response to diminished hormonal signals. ------------------- Key: 6776 Medline: 15355315 Authors: Bimonte M;Gianni D;Allegra D;Russo T;Zambrano N Title: Mutation of the feh-1 gene, the Caenorhabditis elegan orthologue of mammalian Fe65, decreases the expression of tow acetylcholinesterase genes. Citation: European Journal of Neuroscience 20: 1483-1488 2004 Type: ARTICLE Genes: ace-1 ace-2 ace-3 ace-4 feh-1 Abstract: The molecular adaptor Fe65 is one of the cytosolic ligands of the Alzheimer's beta-amyloid precursor protein (APP), and this complex is believed to play important roles in mammalian cells. Upon cleavage of APP by specific processing activities, the complex between Fe65 and the APP intracellular domain (AICD) translocates to the nucleus. Experimental evidence suggests that the Fe65-AICD complex regulates gene transcription. In Caenorhabditis elegans the orthologue of the Fe65 gene, feh-1, regulates pharyngeal activity. In fact, the rate of pharyngeal contraction is increased following transient or stable suppression of the feh-1 gene expression. Here we show that the increased contraction rate of the pharynx in feh-1 mutant worms is associated to decreased acetylcholinesterase activity. The decreased activity is accompanied by reduced expression of ace-1 and ace-2 transcripts, coding for the two major acetylcholinesterase activities in the nematode. These results indicate a target of the regulatory mechanisms based on the Fe65-APP complex that could be relevant for the pathogenesis of Alzheimer's disease. ------------------- Key: 6777 Medline: 15340150 Authors: Inoue T;Sugimoto A;Suzuki Y;Yamamoto M;Tsujimoto M;Inoue K;Aoki J;Arai H Title: Type II platelet-activating factor-acetylhydrolase is essential for epithelial morphogenesis in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 101: 13233-13238 2004 Type: ARTICLE Genes: eff-1 paf-1 paf-2 Abstract: Type II platelet-activating factor-acetylhydrolase [PAF-AH (II)] is an N-myristoylated enzyme that contains a lipase/esterase catalytic motif and selectively hydrolyzes the sn-2 acetyl ester of PAF and other short-chain acyl groups attached to phosphoglycerides. However, the physiological role of this enzyme remains to be elucidated. PAF-AH (II) is conserved in a variety of species ranging from a simple multicellular organism, Caenorhabditis elegans, to mammals. C. elegans possesses two homologous PAF-AH (II) genes, named paf-1 and paf-2. In this study, we generated these two loss-of-function mutants to elucidate the in vivo PAF-AH (II) function. Surprisingly, mutants of paf-2, a major isoform of C. elegans PAF-AH (II)s, exhibits gross defects in epithelial sheet formation, resulting in unsuccessful subsequent morphogenesis with complete penetrance. Moreover, paf-2 RNA interference worms show a variable abnormal morphology, including ectopic protrusions and a lumpy shape at the late embryonic and early larval stages due to epithelial organization defects. Consistent with these phenotypes, PAF-AH (II) is predominantly expressed in epithelial cells of C. elegans. This study demonstrates that PAF-AH (II) is essential for epithelial morphogenesis. ------------------- Key: 6778 Medline: 15359118 Authors: Bandyopadhyay J;Lee J;Bandyopadhyay A Title: Regulation of calcineurin, a calcium/calmodulin-dependent protein phosphatase, in C. elegans. Citation: Molecules & Cells 18: 10-16 2004 Type: REVIEW Genes: cna-1 cnb-1 eat-16 egl-10 egl-30 goa-1 rcn-1 tax-6 unc-43 Abstract: Calcineurin is a calcium/calmodulin-dependent serine/ threonine protein phosphatase. It is a heterodimeric protein consisting of a catalytic subunit calcineurin A, and a regulatory calcium-binding subunit, calcineurin B. The primary sequence of both subunits and heterodimeric structure is highly conserved from yeast to mammals. Calcineurin has long been implicated in various signaling pathways. Calcineurin genes (cna-1/tax-6 and cnb-1) have been identified in the nematode Caenorhabditis elegans, which share high homology with their Drosophila and mammalian counterparts. C. elegans calcineurin binds calcium and functions as a heterodimeric protein phosphatase establishing its biochemical conservation. Calcineurin expresses in diverse tissues implicating its important role in various physiological processes. This review will focus in brief on the expression pattern and regulation of calcineurin including its effect on growth and development, locomotion, egg-laying, and sensory ------------------- Key: 6779 Medline: Authors: Gutierrez-Zepeda A;Luo Y Title: Testing the amyloid toxicity hypothesis of Alzheimer's disease in transgenic Caenorhabditis elegans. Citation: Frontiers in Bioscience 9: 3333-3338 2004 Type: ARTICLE Genes: Abstract: Alzheimer's disease ( AD) is affecting more people every year due to the increase in elderly population. This disease is characterized by senior plaques, containing aggregated amyloid beta peptide ( A beta), and neurofibrillary tangles in the AD brains. The A beta depositions are thought to increase in cellular oxidative stress, which subsequently produces neuronal cell death in the patient's brain, causing loss of memory and, in the latter stages, dementia. Diverse models have been established to test this "Amyloid Toxicity Hypothesis of AD". Among these, the use of the nematode Caenorhabditis elegans has some advantages. This invertebrate has its entire genome known, as well as numerous gene homologues to those seen in humans. In relationship with the cell model, the nematode gives the benefit of an organismal view of the disease. The nematode's short life span proves useful, when compared with that of mice, allowing mechanistic studies of the disease and pharmacological treatments. Alongside with other laboratories, we have used this in vivo model to correlate the A expression with its toxicity through the observance of the organism's behavior to provide a better understanding of the cellular processes underlining AD. ------------------- Key: 6780 Medline: 15327944 Authors: Kim YI;Cho JH;Yoo OJ;Ahnn J Title: Transcriptional regulation and life-span modulation of cytosolic aconitase and ferritin genes in C. elegans. Citation: Journal of Molecular Biology 342: 421-433 2004 Type: ARTICLE Genes: aco-1 ftn-1 ftn-2 Abstract: Ferritin is the major iron storage protein regulating cytosolic concentration of iron by storing excess iron. Vertebrate ferritins are heteropolymeric proteins composed of heavy chain and light chain subunits. We have characterized two Caenorhabditis elegans genes (ftn-1 and ftn-2), which encode ferritin homologs showing high degree of similarity to mammalian ferritin heavy chains. Even though these two ferritins are more than 78% identical in amino acid sequence, our data show that expression patterns and responses to iron are quite different. Cytosolic aconitase (aco-1), iron regulatory protein, is known to regulate cellular iron concentration by modulating translation of the ferritin mRNA in addition to its enzymatic activity that converts citrate into iso-citrate. We have shown that the expression levels of aco-1 and ftn-1 genes are both regulated by iron treatment but in opposite ways. Interestingly, mutant animals lacking ACO-1 and FTN-1 show significantly reduced life-span upon iron stress, while N2 and ftn-2 animals show no difference. Our results suggest that ftn-1 and aco-1 are transcriptionally regulated by iron and are important for iron homeostasis affecting life-span upon iron stress conditions in C. ------------------- Key: 6781 Medline: 15327975 Authors: Mertens I;Vandingenen A;Meeusen T;Janssen T;Luyten W;Nachman RJ;De Loof A;Schoofs L Title: Functional characterization of the putative orphan neuropeptide G-protein coupled receptor C26F1.6 in Caenorhabditis elegans. Citation: FEBS Letters 573: 55-60 2004 Type: ARTICLE Genes: flp-1 flp-2 flp-3 flp-4 flp-5 flp-6 flp-7 flp-10 flp-11 flp-13 flp-14 flp-15 flp-16 flp-18 Abstract: In this study, we describe the cloning and the characterization of the third FMRFamide-related peptide (FaRP) receptor in Caenorhabditis elegans, the VRFa receptor 1. Numerous structurally different FaRPs were synthesized and used to screen the orphan C26F1.6 receptor for activation. Two peptides ending in M(orL)VRFamide elicited a calcium response in receptor expressing mammalian cells. The response is dose-dependent and appeared to be very specific, since very closely related FaRPs were less active, even the other peptides ending in M(orL)VRFamide. Pharmacological profiling of the most active peptide suggests that SMVRFa is the most active binding core. N-terminal extension decreases peptide ------------------- Key: 6782 Medline: 15326288 Authors: van Haaften G;Vastenhouw NL;Nollen EAA;Plasterk RHA;Tijsterman M Title: Gene interactions in the DNA damage-response pathway identified by genome-wide RNA-interference anaylsis of synthetic lethality. Citation: Proceedings of the National Academy of Science USA 101: 12992-12996 2004 Type: ARTICLE Genes: elb-1 mog-1 rad-51 rrf-3 skr-8 Abstract: Here, we describe a systematic search for synthetic gene interactions in a multicellular organism, the nematode Caenorhabditis elegans. We established a high-throughput method to determine synthetic gene interactions by genome-wide RNA interference and identified genes that are required to protect the germ line against DNA double-strand breaks. Besides known DNA-repair proteins such as the C elegans orthologs of TopBP1, RPA2, and RAD51, eight genes previously unassociated with a double-strand-break response were identified. Knockdown of these genes increased sensitivity to ionizing radiation and camptothecin and resulted in increased chromosomal nondisjunction. All genes have human orthologs that may play a role in human carcinogenesis. ------------------- Key: 6783 Medline: 15388799 Authors: Touchon M;Arneodo A;d'Aubenton-Carafa Y;Thermes C Title: Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes. Citation: Nucleic Acids Research 17: 4969-4978 2004 Type: ARTICLE Genes: Abstract: Under no-strand bias conditions, each genomic DNA strand should present equimolarities of A and T and of G and C. Deviations from these rules are attributed to asymmetric properties intrinsic to DNA mutation-repair processes. In bacteria, strand biases are associated with replication or transcription. In eukaryotes, recent studies demonstrate that human genes present transcription-coupled biases that might reflect transcription-coupled repair processes. Here, we study strand asymmetries in intron sequences of evolutionarily distant eukaryotes, and show that two superimposed intron biases can be distinguished. (i) Biases that are maximum at intron extremities and decrease over large distances to zero values in internal regions, possibly reflecting interactions between pre-mRNA and splicing machinery; these extend over approximately 0.5 kb in mammals and Arabidopsis thaliana, and over 1 kb in Caenorhabditis elegans and Drosophila melanogaster. (ii) Biases that are constant along introns, possibly associated with transcription. Strikingly, in C.elegans, these latter biases extend over intergenic regions that separate co-oriented genes. When appropriately examined, all genomes present transcription-coupled excess of T over A in the coding strand. On the opposite, GC skews are either positive (mammals, plants) or negative (invertebrates). These results suggest that transcription-coupled asymmetries result from mutation-repair mechanisms that differ between vertebrates and invertebrates. ------------------- Key: 6784 Medline: 15469912 Authors: Grigorenko AP;Moliaka YK;Soto MC;Mello CC;Rogaev EI Title: The Caenorhabditis elegans IMPAS gene, imp-2, is essential for develoment and is functionally distinct from related presenilins. Citation: Proceedings of the National Academy of Sciences USA 101: 14955-14960 2004 Type: ARTICLE Genes: glp-1 imp-1 imp-2 imp-3 lin-12 lrp-1 sel-12 Abstract: Presenilins (PSs) are required for Notch signaling in the development of vertebrates and invertebrates. Mutations in human PS1 and PS2 homologs are a cause of familial Alzheimer's disease (AD). The function of the recently identified ancient family of IMPAS proteins (IMP/SPP/PSH) homologous to PSs is not yet known. We show here that, unlike PSs, IMPs (orthologous C elegans Ce-imp-2 and human hIMP1/SPP) do not promote Notch (C elegans lin-12,glp-1) proteolysis or signaling. The knock-down of Ce-imp-2 leads to embryonic death and an abnormal molting phenotype in Caenorhabditis elegans. The molting defect induced by Ce-imp-2 deficiency was mimicked by depleting cholesterol or disrupting Ce-Irp-1 and suppressed, in part, by expression of the Ce-Irp-1 derivate. C elegans Irp-1 is a homolog of mammalian megalin, lipoprotein receptor-related protein (LRP) receptors essential for cholesterol and lipoprotein endocytosis and signaling. These data suggest that IMPs are functionally distinct from related PSs and implicate IMPs as critical regulators of development that may potentially interact with the lipid-lipoprotein receptor-mediated pathway. ------------------- Key: 6785 Medline: Authors: DeRenzo C;Seydoux G Title: A clean start: degradation of maternal proteins at the oocyte-to-embryo transition. Citation: Trends in Cell Biology 14: 420-426 2004 Type: REVIEW Genes: cul-2 cul-3 mbk-2 mei-1 mei-2 mel-26 mex-1 mex-5 mex-6 oma-1 par-1 pie-1 pos-1 rfl-1 zif-1 Abstract: In many organisms, the transition from oocyte to embryo occurs in the absence of mRNA transcription. Therefore, early developmental programs rely on maternal mRNAs and proteins that are synthesized during oogenesis. The regulated translation of maternal RNAs is essential for the proper deployment of regulatory factors during early embryogenesis. Recent studies suggest that the degradation of maternal proteins by the ubiquitin-proteasome pathway is also crucial for the oocyte-to-embryo transition. In this article, we explore the hypothesis that the coordinated degradation of germline proteins is essential for remodeling the oocyte into a totipotent zygote that is capable of somatic development. ------------------- Key: 6786 Medline: 15328410 Authors: Young JAT;Dillin A Title: MAPping innate immunity. Citation: Proceedings of the National Academy of Sciences USA 101: 12781-12782 2004 Type: REVIEW Genes: jnk-1 kgb-1 kgb-2 mek-1 pmk-1 sek-1 ttm-1 ttm-2 Abstract: The capacity to mount an immune response that eliminates infection of a host by a microbial pathogen is critical for species survival and propagation. Mammals have developed complex immune systems that integrate innate responses, such as phagocytosis and the production of antimicrobial peptides after Toll-like receptor activation, along with adaptive responses, such as antibody production and activation of helper and cytotoxic T cell populations. By contrast, simpler organisms have much less complex immune systems that are focused exclusively on generating innate immune defenses. Over the last few years, it has become apparent that mitogen-activated protein (MAP) kinase (MAPK)-signaling pathways play an essential and central role in the immune responses within each of these species. ------------------- Key: 6787 Medline: 15457263 Authors: Gally C;Eimer S;Richmond JE;Bessereau JL Title: A transmembrane protein required for acetylcholine receptor clustering in Caenorhabditis elegans. Citation: Nature 431: 578-582 2004 Type: ARTICLE Genes: eat-18 lev-10 unc-29 unc-38 unc-49 Abstract: Clustering neurotransmitter receptors at the synapse is crucial for efficient neurotransmission. Here we identify a Caenorhabditis elegans locus, lev-10, required for postsynaptic aggregation of ionotropic acetylcholine receptors (AChRs). lev-10 mutants were identified on the basis of weak resistance to the anthelminthic drug levamisole, a nematode-specific cholinergic agonist that activates AChRs present at neuromuscular junctions (NMJs) resulting in muscle hypercontraction and death at high concentrations(1-3). In lev-10 mutants, the density of levamisole-sensitive AChRs at NMJs is markedly reduced, yet the number of functional AChRs present at the muscle cell surface remains unchanged. LEV-10 is a transmembrane protein localized to cholinergic NMJs and required in body-wall muscles for AChR clustering. We also show that the LEV-10 extracellular region, containing five predicted CUB domains and one LDLa domain, is sufficient to rescue AChR aggregation in lev-10 mutants. This suggests a mechanism for AChR clustering that relies on extracellular protein - protein interactions. Such a mechanism is likely to be evolutionarily conserved because CUB/LDL transmembrane proteins similar to LEV-10, but lacking any assigned function, are expressed in the mammalian nervous system and might be used to cluster ionotropic receptors in vertebrates. ------------------- Key: 6788 Medline: 15226312 Authors: Sasata RJ;Reed DW;Loewen MC;Covello PS Title: Domain swapping localizes the structural determinants of regioselectivity in membrane-bound fatty acid desaturases of Caenorhabditis elegans. Citation: Journal of Biological Chemistry 279: 39296-39302 2004 Type: ARTICLE Genes: fat-1 fat-2 Abstract: Most fatty acid desaturases are members of a large superfamily of integral membrane, O-2-dependent, iron-containing enzymes that catalyze a variety of oxidative modifications to lipids. Sharing a similar primary structure and membrane topology, these enzymes are broadly categorized according to their positional specificity or regioselectivity, which designates the preferred position for substrate modification. To investigate the structural basis of regioselectivity in membrane-bound desaturases, the Caenorhabditis elegans omega-3 (FAT-1) and "Delta12" (FAT-2) desaturases were used as a model system. With the use of unnatural substrates, the regioselectivity of C. elegans FAT-2 was clearly defined as nu+3, i.e. it "measures" three carbons from an existing double bond. The structural basis for nu+3 and omega-3 regioselectivities was examined through construction and expression of chimeric DNA sequences based on FAT-1 and FAT-2. Each sequence was divided into seven domains, and chimeras were constructed in which specific domains were replaced with sequence from the other desaturase. When tested by expression in yeast using exogenously supplied substrates, chimeric sequences were found in which domain swapping resulted in a change of regioselectivity from nu+3 to omega-3 and vice versa. In this way, the structural determinants of regioselectivity in FAT-1 and FAT-2 have been localized to two interdependent regions: a relatively hydrophobic region ------------------- Key: 6789 Medline: 15254038 Authors: Gunther CV;Riddle DL Title: Alternative polyadenylation results in a truncated daf-4 BMP receptor that antagonizes DAF-7-mediated development in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 279: 39555-39564 2004 Type: ARTICLE Genes: daf-4 Abstract: The DAF-4 receptor kinase, which promotes larval development, is encoded by a 2.9 kb mRNA transcribed from the only type II TGF-beta/BMP receptor gene in Caenorhabditis elegans. Here we report that alternative polyadenylation in intron 5 of daf-4 results in a 2.0 kb mRNA that encodes an open reading frame including only the N-terminal secretion signal and ligand-binding domains, and not the transmembrane or kinase domains, of DAF-4. Northern blots and real-time RT-PCR amplifications using RNA samples from developmentally staged animals show that expression levels of both the 2.9 kb and 2.0 kb transcripts are relatively constant, and their abundances similar, except for the transition between non-dauer and dauer stages. In dauer larvae, the steady-state level of the 2.0 kb mRNA increases more than 10-fold and exceeds the 2.9 kb transcript, coincident with an absence of signaling from DAF-4. Transgenic expression of a recombinant daf-4 transgene that encodes only the 2.0 kb mRNA enhances the Daf-c phenotype of a daf-4 hypomorph, whereas the same transgene with a nonsense mutation does not. These data suggest that a polypeptide encoded by the 2.0 kb transcript can function as an antagonist of full-length DAF-4 signaling. Alternative processing of type II receptor transcripts to generate an antagonist is a novel mechanism for negative regulation of a TGF-beta signaling pathway. ------------------- Key: 6790 Medline: 15199049 Authors: Popovici C;Conchonaud F;Birnbaum D;Roubin R Title: Functional phylogeny relates LET-756 to fibroblast growth factor 9. Citation: Journal of Biological Chemistry 279: 40146-40152 2004 Type: ARTICLE Genes: egl-17 let-756 Abstract: Fibroblast growth factors (FGFs) are secreted regulatory proteins involved in various developmental processes. In vertebrates, the FGF superfamily comprises 22 members. In non-vertebrates, six FGF genes have been identified in Ciona intestinalis, three in Drosophila melanogaster, and two (let-756 and egl-17) in Caenorhabditis elegans. The core of LET-756 shares a 30-50% sequence identity with the various members of the superfamily. The relationships between vertebrate and non-vertebrate FGFs are not clear. We made chimeric FGFs by replacing the core region of LET-756 by the cores of various mammalian, fly, and worm FGFs. LET-756 deleted in its core region was no longer able to rescue the lethal phenotype of a let-756 null mutant, and only chimeras containing the cores of FGFs 9, 16, and 20 showed rescue capacity. This core contains an internal motif of six amino acid residues (EFISIA) whose deletion or mutation abolished both the rescue activity and FGF secretion in the supernatant of transfected COS-1 cells. Chimera containing the core of C. intestinalis FGF9/16/20, a potential ortholog of FGF9 lacking the complete EFISIA motif, was not able to rescue the lethal phenotype or be secreted. However, the introduction of the EFISIA motif restored both activities. The data show that the EFISIA motif in the core of LET-756 is essential for its biological activity and that FGFs 9, 16, and 20, which contain that motif, are functionally close to LET-756 and may be evolutionary related. This non-classical mode of secretion using an internal motif is conserved throughout ------------------- Key: 6791 Medline: 15342507 Authors: Lans H;Rademakers S;Jansen G Title: A network of stimulatory and inhibitory Galpha-subunits regulates olfaction in Caenorhabditis elegans. Citation: Genetics 167: 1677-1687 2004 Type: ARTICLE Genes: gpa-2 gpa-3 gpa-5 gpa-6 gpa-13 odr-1 odr-3 odr-7 Abstract: The two pairs of sensory neurons of C. elegans, AWA and AWC, that mediate odorant attraction, express six Galpha-subunits, suggesting that olfaction is regulated by a complex signaling network. Here, we describe the cellular localization and functions of the six olfactory Ga-subunits: GPA-2, GPA-3, GPA-5, GPA-6, GPA13, and ODR-3. All except GPA-6 localize to sensory cilia, suggesting a direct role in sensory transduction. GPA-2, GPA-3, GPA-5, and GPA-6 are also present in cell bodies and axons and GPA-5 specifically localizes to synaptic sites. Analysis of animals with single- to sixfold loss-of-function mutations shows that olfaction involves a balance between multiple stimulatory and inhibitory signals. ODR-3 constitutes the main stimulatory signal and is sufficient for the detection of odorants. GPA-3 forms a second stimulatory signal in the AWA and AWC neurons, also Sufficient for odorant detection. In AWA, signaling is suppressed by GPA-5. In AWC, GPA-2 and GPA-13 negatively and positively regulate signaling, respectively. Finally, we show that only ODR-3 plays a role in cilia morphogenesis. Defects in this process are, however, independent of olfactory behavior. Our findings reveal the existence of a complex signaling network that controls odorant detection by C. elegans. ------------------- Key: 6792 Medline: 15342508 Authors: Zahler AM;Tuttle JD;Chisholm AD Title: Genetic suppression of intronic +1G mutations by compensatory U1 snRNA changes in Caenorhabditis elegans. Citation: Genetics 167: 1689-1696 2004 Type: ARTICLE Genes: sup-6 sup-39 unc-13 unc-73 Abstract: Mutations to the canonical +1G of introns, which are commonly found in many human inherited disease alleles, invariably result in aberrant splicing. Here we report genetic findings in C. elegans that aberrant splicing due to +1G mutations can be suppressed by U1 snRTNA mutations. An intronic +1G-to-U mutation, e936, in the C. elegans unc-73 gene causes aberrant splicing and loss of gene function. We previously showed that mutation of the sup-39 gene promotes splicing at the mutant splice donor in e936 mutants. We demonstrate here that sup-39 is a U1 snRNA gene; Suppressor mutations in sup-39 are compensatory substitutions in the 5' end, which enhance recognition of the mutant splice donor. sup-6 (st19) is an allele-specific suppressor of unc-13(e309), which contains an intronic +1G-to-A transition. The e309 mutation activates a cryptic splice site, and sup-6(st19) restores splicing to the mutant splice donor. sup-6 also encodes a U1 snRTNA and the mutant contains a compensatory substitution at its 5' end. This is the first demonstration that U1 snRNAs can act to suppress the effects of mutations to the invariant +1G of introns. These findings are suggestive of a potential treatment of certain alleles of inherited human genetic ------------------- Key: 6793 Medline: 15342509 Authors: Miley GR;Fantz D;Glossip D;Lu X;Saito RM;Palmer RE;Inoue T;van den Heuvel S;Sternberg PW;Kornfeld K Title: Identification of residues of the Caenorhabditis elegans LIN-1 ETS domain that are necessary for DNA binding and regulation of vulval cell fates. Citation: Genetics 167: 1697-1709 2004 Type: ARTICLE Genes: let-341 lin-1 lin-12 Abstract: LIN-1 is an ETS domain protein. A receptor tyrosine kinase/Ras/mitogen-activated protein kinase signaling pathway regulates LIN-1 in the P6.p cell to induce the primary vulval cell fate during Caenorhabditis elegans development. We identified 23 lin-1 loss-of-function mutations by conducting several genetic screens. We characterized the molecular lesions in these lin-1 alleles and in several previously identified lin-1 alleles. Nine missense mutations and 10 nonsense mutations were identified. All of these lin-1 missense mutations affect highly conserved residues in the ETS domain. These missense mutations can be arranged in an allelic series; the strongest mutations eliminate most or all lin-1 functions, and the weakest mutation partially reduces lin-1 function. An electrophoretic mobility shift assay was used to demonstrate that purified LIN-1 protein has sequence-specific DNA-binding activity that required the core sequence GGAA. LIN-1 mutant proteins containing the missense substitutions had dramatically reduced DNA binding. These experiments identify eight highly conserved residues of the ETS domain that are necessary for DNA binding. The identification of multiple imitations that reduce the function of lin-1 as an inhibitor of the primary vulval cell fate and also reduce DNA binding suggest that DNA binding is essential for LIN-1 function in an animal. ------------------- Key: 6794 Medline: 15371514 Authors: Aronoff R;Mellem JE;Maricq AV;Sprengel R;Seeburg PH Title: Neuronal toxicity in Caenorhabditis elegans from an editing site mutant in glutamate receptor channels. Citation: Journal of Neuroscience 24: 8135-8140 2004 Type: ARTICLE Genes: crt-1 eat-4 glr-1 glr-2 Abstract: Ionotropic glutamate receptors (iGluRs) in Caenorhabditis elegans are predicted to have high permeability for Ca2+ because of glutamine ( Q) residues in the pore loop. This contrasts to the low Ca2+ permeability of similar iGluRs in principal neurons of mammals, because of an edited arginine ( R) at the critical pore position in at least one channel subunit. Here, we introduced the R residue into the pore loop of a glutamate receptor subunit, GLR-2, in C. elegans. GLR-2( R) participated in channel formation, as revealed by decreased rectification of kainate-evoked currents in electrophysiological recordings when GLR-2( R) and the wild-type GLR-2( Q) were coexpressed in worms. Notably, the transgenic worms exhibited, at low penetrance, strong phenotypic impairments including uncoordination, neuronal degeneration, developmental arrest, and lethality. Penetrance of adverse phenotypes could be enhanced by transgenic expression of an optimal GLR-2( Q)/(R) ratio, implicating channel activity as the cause. In direct support, a mutation in eat-4, which prevents glutamatergic transmission, suppressed adverse phenotypes. Suppression was also achieved by mutation in calreticulin, which is necessary for maintainance of intracellular Ca2+ stores in the endoplasmic reticulum. Thus, synaptically activated GLR-2(R)-containing iGluR channels appear to trigger inappropriate, neurotoxic Ca2+ release from intracellular stores. ------------------- Key: 6795 Medline: Authors: Houthoofd K;Braeckman BP;Vanfleteren JR Title: Metabolism and life span determination in C. elegans. Citation: Energy Metabolism and Lifespan Determination 14: 143-175 2003 Type: REVIEW Genes: Abstract: ------------------- Key: 6796 Medline: Authors: Ishii N;Hartman PS Title: Electron transport and life span in C. elegans. Citation: Energy Metabolism and Lifespan Determination 14: 177-195 2003 Type: REVIEW Genes: Abstract: ------------------- Key: 6797 Medline: 15242630 Authors: Labouesse M Title: Epithelium-mesenchyme: a balancing act of RhoGAP and Citation: Current Biology 14: R508-R510 2004 Type: REVIEW Genes: cyk-4 let-21 pkc-3 zen-4 Abstract: Transitions between epithelium and mesenchyme, in either direction, contribute repeatedly to animal development. Three striking papers suggest that distinct components with opposite activities, which together form a complex known for its role in cytokinesis, control these opposite ------------------- Key: 6798 Medline: 15315752 Authors: Maleki S;Keeney S Title: Modifying histones and initiating meiotic recombination: new answers to an old question. Citation: Cell 118: 404-406 2004 Type: REVIEW Genes: him-17 spo-11 Abstract: It is well documented that the formation of the DNA double-strand breaks (DSBs) that initiate meiotic recombination is influenced by chromatin and larger scale chromosome organization, but the molecular nature of this influence has remained elusive. Several recent studies, including (this issue of Cell), shed light on this issue by revealing roles for posttranslational histone modifications in promoting DSB formation. ------------------- Key: 6799 Medline: Authors: Buckingham SD;Esmaeili B;Wood M;Sattelle DB Title: RNA interference: from model organisms towards therapy for neural and neuromuscular disorders. Citation: Human Molecular Genetics 13: R275-R288 2004 Type: REVIEW Genes: dcr-1 dys-1 egl-19 ego-1 emr-1 mut-2 mut-7 rde-1 rde-2 rde-3 rde-4 rrf-1 rrf-3 sid-1 smg-2 smg-5 smg-6 vig-1 Abstract: Experimental RNA interference (RNAi) leading to the selective knockdown of gene function is induced by introducing into cells either double stranded RNA (dsRNA), or short interfering RNA (siRNA) fragments into which dsRNA is cut. The siRNA triggers degradation of homologous messenger RNA (mRNA). Widely used as a research tool in the genetic model organisms Caenorhabditis elegans, Drosophila melanogaster and mouse to investigate the function of individual genes, RNAi has also been deployed in genome-wide, specific gene-knockdown screens. Recent rapid progress in the application of RNAi to mammalian cells, including neurons and muscle cells, offers new approaches to drug target identification and validation. Advances in targeted delivery of RNAi-inducing molecules has raised the possibility of using RNAi directly as a therapy for a variety of human genetic and other neural and neuromuscular disorders. Here, we review examples of the application of RNAi to worm, fly and mouse models of such diseases aimed at understanding their pathophysiology and we address problems to be solved in developing RNAi-based therapies. ------------------- Key: 6800 Medline: 15341747 Authors: Shemer G;Suissa M;Kolotuev I;Nguyen KCQ;Hall DH;Podbilewicz B Title: EFF-1 is sufficient to initiate and execute tissue-specific cell fusion in C. elegans. Citation: Current Biology 14: 1587-1591 2004 Type: ARTICLE Genes: eff-1 Abstract: Despite the identification of essential processes in which cell fusion plays spectacular roles such as in fertilization and development of muscle, bone, and placenta [1-5], there are no identified proteins that directly mediate developmental cell fusion reactions. C. elegans has recently become among the best-characterized models to use for studying developmental cell fusion [5-15]. The eff-1 (epithelial fusion failure) gene encodes novel type I membrane proteins required for epithelial cell fusion. Analysis of eff-1 mutants showed that cell fusion normally restricts routes for cell migration and establishes body and organ shape and size [ 5, 8, 9, 11]. Here, we explored cell fusion by using time-lapse confocal and electron microscopy of different organs. We found that ectopic expression of eff-1 is sufficient to fuse epithelial cells that do not normally fuse. This ectopic fusion results in cytoplasmic content mixing and disappearance of apical junctions, starting less than 50 min after the start of eff-1 transcription. We found that eff-1 is necessary to initiate and expand multiple microfusion events between pharyngeal muscle cells. Surprisingly, eff-1 is not required to fuse the gonadal anchor cell to uterine cells. Thus, eff-1 is sufficient and essential for most but not all cell fusion events during C. elegans development. ------------------- Key: 6801 Medline: Authors: Houthoofd K;Braeckman BP;De Vreese A;Van Eygen S;Lenaerts I;Brys K;Matthijssens F;Vanfleteren JR Title: Caloric restriction, Ins/IGF-1 signalling and longevity in the nematode Caenorhabditis elegans. Citation: Belgian Journal of Zoology 134: 79-84 2004 Type: ARTICLE Genes: age-1 daf-2 daf-16 eat-2 Abstract: Several mechanisms of life span extension in C elegans have been described, including caloric restriction, reduced Ins/IGF-1 signalling, Clk mutation and germ line ablation. Here, we describe the effects of caloric restriction on metabolism and life span in C. elegans and examine whether Ins/IGF-1 signalling is involved in the life extension observed in calorically restricted worms. We show that life span extension in restricted worms is not caused by a reduced metabolic rate, but is accompanied by enhanced stress resistance. We further show that caloric restriction and Ins/IGF-1 have additive effects on life span extension and on the stress defense enzyme activities, and that caloric restriction acts independently of daf-16. Thus, caloric restriction extends life span by mechanisms distinct from those affected by the Ins/IGF-1-like pathway. ------------------- Key: 6802 Medline: 15388931 Authors: Schormann N;Symersky J;Luo M Title: Structure of sperm-specific protein SSP-19 from Caenorhabditis elegans. Citation: Acta Crystallographica Section D-Biological Crystallography 60: 1840-1845 2004 Type: ARTICLE Genes: Abstract: Structural data are reported for SSP-19, a sperm-specific protein (SSP) family member from Caenorhabditis elegans. The SSP family [ also known as the major sperm protein-like (MSP-like) family] contains proteins with only 107 - 109 amino acids, compared with 127 amino acids in the major sperm protein (MSP) family. MSP, the most abundant protein in nematode sperm, forms a dynamic actin-like cytoskeleton that provides the framework for the nematode sperm motility. In vivo, MSP dimers polymerize to form filaments that are constructed from two helical strands, which assemble into larger macromolecular structures. Little is known about the SSP family and a similar function is inferred from sequence and structural homology [Pfam ( Protein Families Database of Alignments and HMMs) and SCOP ( Structural Classification of Proteins) classification]. Despite the overall structural homology, the monomer - monomer interactions in SSP-19 are strikingly different from the interactions in the two MSP canonic domains ------------------- Key: 6803 Medline: 15331023 Authors: Feng Z;Cronin CJ;Wittig JH;Sternberg PW;Schafer WR Title: An imaging system for standardized quantitative analysis of C. elegans behavior. Citation: BMC Bioinformatics 5: 1-6 2004 Type: ARTICLE Genes: Abstract: BACKGROUND: The nematode Caenorhabditis elegans is widely used for the genetic analysis of neuronal cell biology, development, and behavior. Because traditional methods for evaluating behavioral phenotypes are qualitative and imprecise, there is a need for tools that allow quantitation and standardization of C. elegans behavioral assays. RESULTS: Here we describe a tracking and imaging system for the automated analysis of C. elegans morphology and behavior. Using this system, it is possible to record the behavior of individual nematodes over long time periods and quantify 144 specific phenotypic parameters. CONCLUSIONS: These tools for phenotypic analysis will provide reliable, comprehensive scoring of a wide range of behavioral abnormalities, and will make it possible to standardize assays such that behavioral data from different labs can readily be compared. In addition, this system will facilitate high-throughput collection of phenotypic data that can ultimately be used to generate a comprehensive database of C. elegans phenotypic information. AVAILABILITY: The hardware configuration and software for the system are available from wschafer@ucsd.edu ------------------- Key: 6807 Medline: Authors: Couteau F;Goodyer W;Zetka M Title: Finding and keeping your partner during meiosis. Citation: Cell Cycle 3: 1014-1016 2004 Type: REVIEW Genes: him-3 Abstract: HIM-3 is a meiosis-specific protein that localizes to the cores of chromosomes from the earliest stages of prophase I until the metaphase to anaphase I transition in Caenorhabditis elegans. him-3 mutations disrupt homolog alignment, synapsis, and recombination and we propose that the association of HIM-3 with chromosome axes is a critical event in meiotic chromosome morphogenesis that is required for the proper coordination of these processes. The presence of HIM-3-like proteins in other eukaryotes, some of which are known to be required for synapsis and recombination, suggests the existence of a conserved class of axis-associated proteins that function at the junction of essential meiotic processes. ------------------- Key: 6808 Medline: 15254012 Authors: Williams SN;Locke CJ;Braden AL;Caldwell KA;Caldwell GA Title: Epileptic-like convulsions associated with LIS-1 in the cytoskeletal control of neurotransmitter signaling in Caenorhabditis elegans. Citation: Human Molecular Genetics 13: 2043-2059 2004 Type: ARTICLE Genes: dhc-1 lis-1 pnm-1 unc-4 unc-25 unc-32 unc-43 unc-46 unc-47 unc-49 unc-104 Abstract: Cortical malformations are a collection of disorders affecting brain development. Mutations in the LIS1 gene lead to a disorganized and smooth cerebral cortex caused by failure in neuronal migration. Among the clinical consequences of lissencephaly are mental retardation and intractable epilepsy. It remains unclear whether the seizures result from aberrant neuronal placement, disruption of intrinsic properties of neurons, or both. The nematode Caenorhabditis elegans offers an opportunity to study such convulsions in a simple animal with a defined nervous system. Here we show that convulsions mimicking epilepsy can be induced by a mutation in a C. elegans lis-1 allele (pnm-1), in combination with a chemical antagonist of gamma-aminobutyric acid (GABA) neurotransmitter signaling. Identical convulsions were obtained using C. elegans mutants defective in GABA transmission, whereas none of these mutants or the antagonist alone caused convulsions, indicating a threshold was exceeded in response to this combination. Crosses between pnm-1 and fluorescent marker strains designed to exclusively illuminate either the processes of GABAergic neurons or synaptic vesicles surprisingly showed no deviations in neuronal architecture. Instead, presynaptic defects in GABAergic vesicle distribution were clearly evident and could be phenocopied by RNAi directed against cytoplasmic dynein, a known LIS1 interactor. Furthermore, mutations in UNC-104, a neuronal-specific kinesin, and SNB-1, a synaptic vesicle-associated protein termed synaptobrevin, exhibit similar convulsion phenotypes following chemical induction. Taken together, these studies establish C. elegans as a system to investigate subtle cytoskeletal mechanisms regulating intrinsic neuronal activity and suggest that it may be possible to dissociate the epileptic consequences of lissencephaly from the more phenotypically overt cortical defects associated with neuronal migration. ------------------- Key: 6809 Medline: 15059258 Authors: Nelson CE;Hersh BM;Carroll SB Title: The regulatory content of intergenic CNA shapes genome architecture. Citation: Genome Biology 5: R25- 2004 Type: ARTICLE Genes: ceh-6 ceh-16 ceh-17 ceh-26 ceh-43 ceh-44 cfz-2 dac-1 daf-7 dbl-1 efl-1 egl-20 fkh-7 hlh-1 let-23 let-756 lin-17 lin-44 lin-48 mig-1 mom-2 mon-5 nfi-1 num-1 pax-1 pha-4 pop-1 sax-3 tab-1 tig-2 unc-6 unc-62 unc-86 unc-129 vab-1 vab-7 vab-15 wnt-1 wnt-2 Abstract: BACKGROUND: Factors affecting the organization and spacing of functionally unrelated genes in metazoan genomes are not well understood. Because of the vast size of a typical metazoan genome compared to known regulatory and protein-coding regions, functional DNA is generally considered to have a negligible impact on gene spacing and genome organization. In particular, it has been impossible to estimate the global impact, if any, of regulatory elements on genome architecture. RESULTS: To investigate this, we examined the relationship between regulatory complexity and gene spacing in Caenorhabditis elegans and Drosophila melanogaster. We found that gene density directly reflects local regulatory complexity, such that the amount of noncoding DNA between a gene and its nearest neighbors correlates positively with that gene's regulatory complexity. Genes with complex functions are flanked by significantly more noncoding DNA than genes with simple or housekeeping functions. Genes of low regulatory complexity are associated with approximately the same amount of noncoding DNA in D. melanogaster and C. elegans, while loci of high regulatory complexity are significantly larger in the more complex animal. Complex genes in C. elegans have larger 5' than 3' noncoding intervals, whereas those in D. melanogaster have roughly equivalent 5' and 3' noncoding intervals. CONCLUSIONS: Intergenic distance, and hence genome architecture, is highly nonrandom. Rather, it is shaped by regulatory information contained in noncoding DNA. Our findings suggest that in compact genomes, the species-specific loss of nonfunctional DNA reveals a landscape of regulatory information by leaving a profile of functional DNA in its wake. ------------------- Key: 6810 Medline: 15189151 Authors: Haltiwanger RS;Lowe JB Title: Role of glycosylation in development. Citation: Annual Review of Biochemistry 73: 491-537 2004 Type: REVIEW Genes: bre-2 bre-3 bre-4 bre-5 gly-2 gly-12 gly-13 gly-14 sqv-1 sqv-2 sqv-3 sqv-4 sqv-5 sqv-6 sqv-7 sqv-8 Abstract: Researchers have long predicted that complex carbohydrates on cell surfaces would play important roles in developmental processes because of the observation that specific carbohydrate structures appear in specific spatial and temporal patterns throughout development. The astounding number and complexity of carbohydrate structures on cell surfaces added support to the concept that glycoconjugates would function in cellular communication during development. Although the structural complexity inherent in glycoconjugates has slowed advances in our understanding of their functions, the complete sequencing of the genomes of organisms classically used in developmental studies (e.g., mice, Drosophila melanogaster, and Caenorhabditis elegans) has led to demonstration of essential functions for a number of glycoconjugates in developmental processes. Here we present a review of recent studies analyzing function of a variety of glycoconjugates (O-fucose, O-mannose, N-glycans, mucin-type O-glycans, proteoglycans, glycosphingolipids), focusing on lessons learned from human disease and genetic studies in mice, D. ------------------- Key: 6811 Medline: 15331236 Authors: Ackley BD;Jin Y Title: Genetic analysis of synaptic target recognition and assembly. Citation: Trends in Neurosciences 27: 540-547 2004 Type: REVIEW Genes: fmi-1 fsn-1 him-4 hmr-1 ptp-3 rpm-1 sad-1 sax-3 smp-1 syd-2 syg-1 syg-2 unc-10 unc-11 unc-13 unc-18 unc-34 unc-73 Abstract: Formation of synapses by neurons onto specific targets is essential to the function of a nervous system. The isolation and analysis of Caenorhabditis elegans and Drosophila mutants with synaptogenesis defects has provided insight into the functions of evolutionarily conserved molecules at single-synapse resolution. Importantly, such studies have uncovered novel molecules and signaling mechanisms. Here, recent progress on synaptic target recognition and synaptic assembly are reviewed. ------------------- Key: 6812 Medline: 15383649 Authors: Syntichaki P;Tavernarakis N Title: Genetic models of mechanotransduction: the nematode Caenorhabditis elegans. Citation: Physiological Reviews 84: 1097-1153 2004 Type: REVIEW Genes: cct-1 cct-2 cct-4 ced-2 ced-3 ced-4 ced-5 ced-10 che-3 daf-11 deg-1 deg-3 del-1 eat-4 egl-5 egl-44 flr-1 glr-1 let-2 lin-14 lin-17 lin-32 lov-1 mab-5 mec-1 mec-2 mec-3 mec-4 mec-5 mec-6 mec-7 mec-8 mec-9 mec-10 mec-12 mec-14 mec-15 mec-16 mec-17 mec-18 ocr-1 ocr-2 ocr-3 ocr-4 osm-1 osm-9 osm-10 pag-3 pdk-2 sem-4 sup-40 sup-41 sup-42 sup-43 unc-1 unc-3 unc-5 unc-6 unc-8 unc13 unc-14 unc-24 unc-25 unc-27 unc-30 unc-33 unc-34 unc-40 unc-44 unc-51 unc-53 unc-55 unc-59 unc-61 unc-62 unc-69 unc-71 unc-73 unc-75 unc-76 unc-85 unc-86 unc-98 unc-104 unc-105 Abstract: Mechanotransduction, the conversion of a mechanical stimulus into a biological response, constitutes the basis for a plethora of fundamental biological processes such as the senses of touch, balance, and hearing and contributes critically to development and homeostasis in all organisms. Despite this profound importance in biology, we know remarkably little about how mechanical input forces delivered to a cell are interpreted to an extensive repertoire of output physiological responses. Recent, elegant genetic and electrophysiological studies have shown that specialized macromolecular complexes, encompassing mechanically gated ion channels, play a central role in the transformation of mechanical forces into a cellular signal, which takes place in mechanosensory organs of diverse organisms. These complexes are highly efficient sensors, closely entangled with their surrounding environment. Such association appears essential for proper channel gating and provides proximity of the mechanosensory apparatus to the source of triggering mechanical energy. Genetic and molecular evidence collected in model organisms such as the nematode worm Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the mouse highlight two distinct classes of mechanically gated ion channels: the degenerin (DEG)/epithelial Na+ channel (ENaC) family and the transient receptor potential (TRP) family of ion channels. In addition to the core channel proteins, several other potentially interacting molecules have in some cases been identified, which are likely parts of the mechanotransducing apparatus. Based on cumulative data, a model of the sensory mechanotransducer has emerged that encompasses our current understanding of the process and fulfills the structural requirements dictated by its dedicated function. It remains to be seen how general this model is and whether it will withstand the impiteous test ------------------- Key: 6813 Medline: 15452567 Authors: Jorgensen EM Title: Dopamine: should I stay or should I go now? Citation: Nature Neuroscience 7: 1019-1021 2004 Type: REVIEW Genes: dop-1 dop-3 dop-4 eat-16 egl-30 goa-1 gpb-2 unc-13 Abstract: In C. elegans, dopamine signaling regulates locomotion behavior. Chase and colleagues report that this signaling occurs through extrasynaptic and antagonistically acting receptors coexpressed in motor neurons. These results provide surprising insights into the G-protein pathways mediating this antagonism, with implications for dopamine signaling across species. ------------------- Key: 6814 Medline: 15378064 Authors: Chase DL;Pepper JS;Koelle MR Title: Mechanism of extrasynaptic dopamine signaling in Caenorhabditis elegans. Citation: Nature Neuroscience 7: 1096-1103 2004 Type: ARTICLE Genes: acr-2 cat-2 dgk-1 dop-1 dop-2 dop-3 eat-16 egl-8 egl-10 egl-30 goa-1 gpb-2 unc-47 Abstract: D1-like and D2-like dopamine receptors have synergistic and antagonistic effects on behavior. To understand the mechanisms underlying these effects, we studied dopamine signaling genetically in Caenorhabditis elegans. Knocking out a D2-like receptor, DOP-3, caused locomotion defects similar to those observed in animals lacking dopamine. Knocking out a D1-like receptor, DOP-1, reversed the defects of the DOP-3 knockout. DOP-3 and DOP-1 have their antagonistic effects on locomotion by acting in the same motor neurons, which coexpress the receptors and which are not postsynaptic to dopaminergic neurons. In a screen for mutants unable to respond to dopamine, we identified four genes that encode components of the antagonistic Galpha(o) and Galpha(q) signaling pathways, including Galpha(o) itself and two subunits of the regulator of G protein signaling (RGS) complex that inhibits Galpha(q). Our results indicate that extrasynaptic dopamine regulates C. elegans locomotion through D1- and D2-like receptors that activate the antagonistic Galpha(q) and Galpha(o) signaling pathways, respectively. ------------------- Key: 6815 Medline: 15456826 Authors: Moresco JJ;Koelle MR Title: Activation of EGL-47, a Galpha(o)-coupled receptor, inhibits function of hermaphrodite-specific motor neurons to regulate Caenorhabditis elegans egg-laying behavior. Citation: Journal of Neuroscience 24: 8522-8530 2004 Type: ARTICLE Genes: egl-47 goa-1 Abstract: Caenorhabditis elegans egg-laying behavior is inhibited by neurotransmitter signaling through the neural G-protein Galpha(o) and serves as a model for analyzing Galpha(o) signaling. Mutations that alter egg-laying frequency have identified genes encoding a number of signaling proteins that act with Galpha(o), but the receptors that activate Galpha(o) remain mostly uncharacterized. To further analyze Galpha(o) signaling, we cloned the egl-47 gene, which was identified by two dominant mutations that severely inhibit egg laying. egl-47 encodes two orphan G-protein-coupled receptor isoforms, which share all seven transmembrane domains but have different extracellular N termini. Both dominant mutations change the same alanine to valine in the sixth transmembrane domain, resulting in constitutively activated receptors. Deletion of the egl-47 gene caused no detectable egg-laying defects, suggesting that EGL-47 functions redundantly, or it inhibits egg laying under specific circumstances as yet unidentified. Using promoter:: green fluorescent protein transgenes, we found that EGL-47 is expressed in a number of neurons, including the hermaphrodite-specific neurons (HSNs) that innervate the egg-laying muscles to stimulate contraction. Transgenic expression of constitutively active EGL-47 or constitutively active Galpha(o) specifically in the HSNs was sufficient to inhibit egg-laying behavior. Our results suggest that EGL-47 regulates egg laying by activating Galpha(o) in the HSN motor neurons to inhibit their activity. Because several neurotransmitters act through Galpha(o) to inhibit HSN function, it appears that loss of any one receptor, such as EGL-47, causes only mild defects. Galpha(o) apparently integrates signaling from multiple receptors in the HSNs, including EGL-47, to set the frequency of egg-laying behavior. ------------------- Key: 6816 Medline: 15362159 Authors: Tobin DM;Bargmann CI Title: Invertebrate nociception: behaviors, neurons and molecules. Citation: Journal of Neurobiology 61: 161-174 2004 Type: REVIEW Genes: flr-1 glr-1 glr-2 mec-1 mec-4 mec-5 mec-7 mec-9 mec-10 mec-12 nmr-1 ocr-1 ocr-2 ocr-3 ocr-4 osm-9 tax-2 tax-4 unc-8 unc-105 Abstract: Genetic analysis of nociceptive behaviors in the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster has led to the discovery of conserved sensory transduction channels and signaling molecules. These are embedded in neurons and circuits that generate responses to noxious signals. This article reviews the neurons and molecular mechanisms that underlie invertebrate nociception. We begin with the neurobiology of invertebrate nociception, and then focus on molecules with conserved functions in vertebrate nociception and sensory biology. ------------------- Key: 6817 Medline: 15336632 Authors: Park HK;Suh D;Hyun M;Koo HS;Ahn B Title: A DNA repair gene of Caenorhabditis elegans: a homolog of human XPF. Citation: DNA Repair 3: 1375-1383 2004 Type: ARTICLE Genes: Abstract: The xeroderma pigmentosum complementation group F (XPF) protein is a structure-specific endonuclease in a complex with ERCC I and is essential for nucleotide excision repair (NER). We report a single cDNA of Caenorhabditis elegans (C. elegans) encoding highly similar protein to human XPF and other XPF members. We propose to name the corresponding C. elegans gene xpf. Messenger RNA for C. elegans xpf is 5'-tagged with a SL2 splice leader, suggesting an operon-like expression for xpf. Using RNAi, we showed that loss of C elegans xpf function caused hypersensitivity to ultra-violet (UV) irradiation, as observed in enhanced germ cell apoptosis and increased embryonic lethality. This study suggests that C. elegans xpf is conserved in evolution and plays a role in the repair of UV-damaged DNA ------------------- Key: 6818 Medline: 15355793 Authors: Hoeppner DJ;Spector MS;Ratliff TM;Kinchen JM;Granat S;Lin SC;Bhusri S;Conradt B;Herman MA;Hengartner MO Title: eor-1 and eor-2 are required for cell-specific apoptotic death in C. elegans. Citation: Developmental Biology 274: 125-138 2004 Type: ARTICLE Genes: ced-3 ced-4 ced-9 ces-1 ces-2 egl-1 egl-41 eor-1 eor-2 him-5 tra-1 Abstract: Programmed cell death occurs in every multicellular organism and in diverse cell types yet the genetic controls that define which cells will live and which will die remain poorly understood. During development of the nematode Caenorhabditis elegalls, the coordinated activity of four gene products, EGL-1, CED-9, CED-4 and CED-3, results in the death of essentially all cells fated to die. To identify novel upstream components of the cell death pathway, we performed a genetic screen for mutations that abolish the death of the hermaphrodite-specific neurons (HSNs), a homologous pair of cells required for egg-laying in the hermaphrodite. We identified and cloned the genes, eor-1 and eor-2, which are required to specify the fate of cell death in male HSNs. In addition to defects in HSN death, mutation of either gene leads to defects in coordinated movement, neuronal migration, male tail development, and viability; all consistent with abnormal neuronal differentiation. eor-1 encodes a putative transcription factor related to the human oncogene PLZF. eor-2 encodes a novel but conserved protein. We propose that eor-1 and eor-2 function together throughout the nervous system to promote terminal differentiation of neurons and function specifically in male HSNs to promote ------------------- Key: 6819 Medline: 15355798 Authors: Kariya K;Bui YK;Gao X;Sternberg PW;Kataoka T Title: Phospholipase C(epsilon) regulates ovulation in Caenorhabditis elegans. Citation: Developmental Biology 274: 201-210 2004 Type: ARTICLE Genes: itr-1 let-23 lfe-2 plc-1 Abstract: Phospholipase Cepsilon (PLCepsilon) is a novel class of phosphoinositide-specific PLC with unknown physiological functions. Here, we present the first genetic analysis of PLCepsilon in an intact organism, the nematode Caenorhabditis elegans. Ovulation in C. elegans is dependent on an inositol 1,4,5-trisphosphate (IP3) signaling pathway activated by the receptor tyrosine kinase LET-23. We generated deletion mutants of the gene, plc-1, encoding C. elegans PM. We observed a novel ovulation phenotype whereby oocytes are trapped in the spermatheca due to delayed dilation of the spermatheca-uterine valve. The expression of plc-1 in the adult spermatheca is consistent with its involvement in regulation of ovulation. On the other hand, we failed to observe genetic interaction of plc-1 with let-23-mediated IP3 signaling pathway genes, suggesting a complex mechanism for control of ovulation. ------------------- Key: 6820 Medline: 15369677 Authors: Inoue T;Oz HS;Wiland D;Gharib S;Deshpande R;Hill RJ;Katz WS;Sternberg PW Title: C. elegans LIN-28 is a Ryk ortholog and functions in parallel to LIN-17/Frizzled in Wnt signaling. Citation: Cell 118: 795-806 2004 Type: ARTICLE Genes: cwn-1 cwn-2 egl-20 lin-18 lin-44 mom-2 sup-5 Abstract: Wnt proteins are intercellular signals that regulate various aspects of animal development. In Caenorhabditis elegans, mutations in lin-17, a Frizzled-class Wnt receptor, and in lin-18 affect cell fate patterning in the P7.p vulval lineage. We found that lin-18 encodes a member of the Ryk/Derailed family of tyrosine kinase-related receptors, recently found to function as Wnt receptors. Members of this family have nonactive kinase domains. The LIN-18 kinase domain is dispensable for LIN-18 function, while the Wnt binding WIF domain is required. We also found that Wnt proteins LIN-44, MOM-2, and CWN-2 redundantly regulate P7.p patterning. Genetic interactions indicate that LIN-17 and LIN-18 function independently of each other in parallel pathways, and different ligands display different receptor specificities. Thus, two independent Wnt signaling pathways, one employing a Ryk receptor and the other a Frizzled receptor, function in parallel to regulate cell fate patterning in the C. elegans vulva. ------------------- Key: 6821 Medline: 15351708 Authors: Zhao Z;Fang LL;Johnsen R;Baillie DL Title: ATP-binding cassette protein E is involved in gene transcription and translation in Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 323: 104-111 2004 Type: ARTICLE Genes: eri-1 nhr-91 rpl-4 Abstract: ATP-binding cassette protein E (ABCE) gene has been annotated as an RNase L inhibitor in eukaryotes. All eukaryotic species show the ubiquitous presence and high degree of conservation of ABCEs, however, RNase L is present only in mammals. This indicates that ABCEs may function not only as RNase L inhibitors, but also may have other functions that have yet to be determined. As an initial investigation into the novel functions of ABCE, we characterized the gene (Y39E4B.1) in Caenorhabditis elegans by a combination of data mining and functional assays. ABCE promoters drove GFP expressions in hypoderm, pharynx, vulvae, head, and tail neurons at all developmental stages. Three genes, rpl-4, nhr-91, and C07B5.3, were previously found to interact with ABCE. Our expression data showed overlapping expression patterns of ABCE and rpl-4 and nhr-91, but not C07B5.3. RNAi against ABCE resulted in embryonic lethality and slow growth. These data suggest that ABCE protein might be involved in the control of translation and transcription, work as shuttle protein between cytoplasm and nucleus, and possibly as a nucleocytoplasmic transporter. In addition, RNAi data suggest that ABCE and NHR-91 may function in vulvae development and molting pathways in C elegans. Furthermore, our data suggest that ABCE, along with its interacting components, functions in a well-conserved pathway. ------------------- Key: 6822 Medline: 15363402 Authors: Seydoux G Title: Surfing the actomyosin wave: polarization of the C. elegans zygote. Citation: Developmental Cell 7: 285-286 2004 Type: REVIEW Genes: mlc-4 nmy-2 par-1 par-2 par-3 pkc-3 Abstract: Many cell types rely on asymmetrically localized PAR proteins to become polarized. New evidence reveals that cortical flows powered by actomyosin contractions can mobilize PAR complexes to create distinct cortical domains. ------------------- Key: 6823 Medline: 15363415 Authors: Munro E;Nance J;Priess JR Title: Cortical flows powered by asymmetrical contraction transport PAR proteins to establish and maintain anterior-posterior polarity in the early C. elegans embryo. Citation: Developmental Cell 7: 413-424 2004 Type: ARTICLE Genes: mlc-4 nmy-2 nop-1 par-2 par-3 par-6 spd-5 Abstract: The C. elegans PAR proteins PAR-3, PAR-6, and PKC-3 are asymmetrically localized and have essential roles in cell polarity. We show that the one-cell C. elegans embryo contains a dynamic and contractile actomyosin network that appears to be destabilized near the point of sperm entry. This asymmetry initiates a flow of cortical nonmuscle myosin (NMY-2) and F-actin toward the opposite, future anterior, pole. PAR-3, PAR-6, and PKC-3, as well as non-PAR proteins that associate with the cytoskeleton, appear to be transported to the anterior by this cortical flow. In turn, PAR-3, PAR-6, and PKC-3 modulate cortical actomyosin dynamics and promote cortical flow. PAR-2, which localizes to the posterior cortex, inhibits NMY-2 from accumulating at the posterior cortex during flow, thus maintaining asymmetry by preventing inappropriate, posterior-directed flows. Similar actomyosin flows accompany the establishment of PAR asymmetries that form after the one-cell stage, suggesting that actomyosin-mediated cortical flows have a general role in PAR asymmetry. ------------------- Key: 6824 Medline: 15490828 Authors: Geng W;Cosman P;Berry CC;Feng Z;Schafer WR Title: Automatic tracking, feature extraction and classification of C. elegans phenotypes. Citation: IEEE Transactions on Biomedical Engineering 51: 1811-1820 2004 Type: ARTICLE Genes: cat-2 dgk-1 dop-1 eat-4 egl-19 flp-1 goa-1 nic-1 tph-1 unc-2 unc-29 unc-36 unc-38 unc-43 unc-63 Abstract: This paper presents a method for automatic tracking of the head, tail, and entire body movement of the nematode Caenorhabditis elegans (C. elegans) using computer vision and digital image analysis techniques. The characteristics of the worm's movement, posture and texture information were extracted from a 5-min image sequence. A Random Forests classifier was then used to identify the worm type, and the features that best describe the data. A total of 1597 individual worm video sequences, representing wild type and 15 different mutant types, were analyzed. The average correct classification ratio, measured by out-of-bag (OOB) error rate, was 90.9%. The features that have most discrimination ability were also studied. The algorithm developed will be an essential part of a completely automated C. elegans tracking and identification ------------------- Key: 6825 Medline: 15344920 Authors: Bettinger JC;McIntire SL Title: State-dependancy in C. elegans. Citation: Genes, Brain and Behavior 3: 266-272 2004 Type: ARTICLE Genes: cat-1 cat-2 glr-1 Abstract: Memory and the expression of learned behaviors by an organism are often triggered by contextual cues that resemble those that were present when the initial learning occurred. In state-dependent learning, the cue eliciting a learned behavior is a neuroactive drug; behaviors initially learned during exposure to centrally acting compounds such as ethanol are subsequently recalled better if the drug stimulus is again present during testing. Although state-dependent learning is well documented in many vertebrate systems, the molecular mechanisms underlying state-dependent learning and other forms of contextual learning are not understood. Here we demonstrate and present a genetic analysis of state- dependent adaptation in Caenorhabditis elegans. C. elegans normally exhibits adaptation, or reduced behavioral response, to an olfactory stimulus after prior exposure to the stimulus. If the adaptation to the olfactory stimulus is acquired during ethanol administration, the adaptation is subsequently displayed only if the ethanol stimulus is again present. cat-1 and cat-2 mutant animals are defective in dopaminergic neuron signaling and are impaired in state dependency, indicating that dopamine functions in state-dependent adaptation in C. elegans. ------------------- Key: 6826 Medline: 15492042 Authors: Labbe JC;McCarthy EK;Goldstein B Title: The forces that position a mitotic spindle asymmetrically are tethered until after the time of splice assembly. Citation: Journal of Cell Biology 167: 245-256 2004 Type: ARTICLE Genes: par-2 par-3 Abstract: Regulation of the mitotic spindle's position is important for cells to divide asymmetrically. Here, we use Caenorhabditis elegans embryos to provide the first analysis of the temporal regulation of forces that asymmetrically position a mitotic spindle. We find that asymmetric pulling forces, regulated by cortical PAR proteins, begin to act as early as prophase and prometaphase, even before the spindle forms and shifts to a posterior position. The spindle does not shift asymmetrically during these early phases due to a tethering force, mediated by astral microtubules that reach the anterior cell cortex. We show that this tether is normally released after spindle assembly and independently of anaphase entry. Monitoring microtrubule dynamics by photobleaching segments of microtubules during anaphase revealed that spindle microtubules do not undergo significant poleward flux in C. elegans. Together with the known absence of anaphase A, these data suggest that the major forces contributing to chromosome separation during anaphase originate outside the spindle. We propose that the forces positioning the mitotic spindle asymmetrically are tethered until after the time of spindle assembly and that these same forces are used later to drive chromosome ------------------- Key: 6827 Medline: 15302100 Authors: Hasegawa K;Miwa S;Tsutsumiuchi K;Taniguchi H;Miwa J Title: Extremely low dose of acrylamide decreases lifespan in Caenorhabditis elegans. Citation: Toxicology Letters 152: 183-189 2004 Type: ARTICLE Genes: Abstract: The neurotoxic, genotoxic and carcinogenic effects of industrial exposure to acrylamide have been studied in animals and humans for more than 30 years. A recent search for the cause of high background levels of acrylamide in industrially unexposed people revealed that it is formed during the frying or baking of foods by means of the Maillard reaction. To evaluate the biological consequences of continuous exposure to acrylamide at levels found in common foodstuffs, we studied the effects of acrylamide on the three parameters of (1) growth, (2) fecundity and (3) lifespan in the nematode Caenorhabditis elegans. As for growth and fecundity, no deleterious consequences were observed when the animals were raised in the acrylamide concentrations of 0.5 microg/L to 5mg/L, which are commonly found in daily consumed foodstuffs. Conversely, in 500 mg/L of acrylamide, they showed retarded growth with reduced body and brood sizes. Unlike the first two parameters, however, lifespan decreased significantly even in 0.5 microg/L of acrylamide, the maximum theoretical concentration allowed in drinking water by the WHO and US EPA. Very interestingly, the acrylamide effect on lifespan is biphasic as lifespan increased to near normalcy in 5 mg/L and decreased again in 500 mg/L. ------------------- Key: 6828 Medline: 15294864 Authors: Mathies LD;Schvarzstein M;Morphy KM;Blelloch R;Spence AM;Kimble J Title: TRA-1/GLI controls development of somatic gonadal precursors in C. elegans. Citation: Development 131: 4333-4343 2004 Type: ARTICLE Genes: ced-2 ced-3 ehn-1 ehn-3 fem-3 fog-2 hnd-1 tra-1 tra-2 eDp6 mDf4 nDf41 Abstract: TRA-1/GLI is best known as a master regulator of sex determination in the nematode C elegans, but its fly and vertebrate homologs (e.g. Ci, GLI) regulate embryonic patterning and cell proliferation. In this paper, we show that TRA-1/GLI controls development of the two somatic gonadal precursors (SGPs) in both XX and XO animals, in addition to its role in sex determination. Normally, SGPs reside at the poles of the gonadal primordium and divide according to intrinsic gonadal axes. In tra-1-null mutants, however, SGPs assume non-polar positions and the polarity of one SGP is reversed. Consistent with its SGP function, TRA-1 protein is present in SGPs; during embryogenesis and early larval development. Previous studies have shown that the ehn-3 gene also affects SGP positions, and we report here that tra-1 and ehn-3 interact genetically. Whereas SGPs in tra-1 and ehn-3 single mutants are largely normal and generate many descendants, those in ehn-3 double mutants do not mature or divide. Furthermore, tra-1 is a dominant enhancer of the ehn-3 gonadal defect, which includes the enhancement of a weak sexual transformation in the gonad. We cloned ehn-3, and found that it encodes a C2H2 zinc-finger protein. A rescuing EHN-3::GFP reporter is predominantly nuclear and expressed specifically in SGPs. The EHN-3 protein is therefore likely to regulate gene expression. We propose that TRA-1/GLI and EHN-3 have overlapping roles in regulation of multiple steps of SGP development. We speculate that regulation of SGP development may be an evolutionarily ancient role of TRA-1/GLI in nematode development. ------------------- Key: 6829 Medline: 15454534 Authors: Eckmann CR;Crittenden SL;Suh N;Kimble J Title: GLD-3 and control of the mitosis/meiosis decision in the germline of Caenorhabditis elegans. Citation: Genetics 168: 147-160 2004 Type: ARTICLE Genes: fbf-1 fbf-2 gld-1 gld-2 gld-3 nos-3 Abstract: Germ cells can divide mitotically to replenish germline tissue or meiotically to produce gametes. In this article, we report that GLD-3, a Caenorhabditis elegans Bicaudal-C homolog, promotes the transition from mitosis to meiosis together with the GLD-2 poly(A) polymerase. GLD-3 binds GLD-2 via a small N-terminal region present in both GLD-3S and GLD-3L isoforms, and GLD-2 and GLD-3 can be co-immunoprecipitated from worm extracts. The FBF repressor binds specifically to elements in the gld-3S 3'-UTR, and FBF regulates gld-3 expression. Furthermore, FBF acts largely upstream of gld-3 in the mitosis/meiosis decision. By contrast, GLD-3 acts upstream of FBF in the sperm/oocyte decision, and GLD-3 protein can antagonize FBF binding to RNA regulatory elements. To address the relative importance of these two regulatory mechanisms in the mitosis/meiosis and sperm/oocyte decisions, we isolated a deletion mutant, gld-3(q741), that removes the FBF-binding site from GLD-3L, but leaves the GLD-2-binding site intact. Animals homozygous for gld-3(q741) enter meiosis, but are ferminized. Therefore, GLD-3 promotes meiosis primarily via its interaction with GLD-2, and it promotes spermatogenesis primarily via its interaction with FBF. ------------------- Key: 6830 Medline: Authors: Hobert O Title: Common logic of transcription factor and microRNA action. Citation: Trends in Biochemical Sciences 29: 462-468 2004 Type: REVIEW Genes: ceh-1 ceh-10 ceh-36 che-1 cog-1 die-1 gcy-5 gcy-7 hbl-1 let-7 lim-6 lin-4 lin-14 lin-28 lin-41 lsy-6 mir-273 ttx-3 unc-4 vab-7 Abstract: Over the past few years, microRNAs (miRNAs) have emerged as abundant regulators of gene expression. Like many transcription factors (TFs), miRNAs are important determinants of cellular fate specification. Here I provide a conceptual framework for miRNA action in the context of creating cellular diversity in a developing organism, and emphasize the conceptual similarity of TF- and miRNA-mediated control of gene expression. Both TFs and miRNAs are trans-acting factors that exert their activity through composite cis-regulatory elements that are 'hard-wired' into DNA or RNA. TFs and miRNAs act in a largely combinatorial manner - that is, many different TFs or miRNAs control one gene - and they act cooperatively on their targets - that is, there are several cis-regulatory elements for a single TF or miRNA species in a target gene. Just as the set of TFs in a given cell type has been proposed to constitute a 'code' that specifies cellular differentiation, so 'miRNA codes' are likely to have conceptually similar roles in the specification of cell types. ------------------- Key: 6831 Medline: 15486284 Authors: Goodman MB Title: Deconstructing C. elegans sensory mechanotransduction. Citation: Science 306: 427-428 2004 Type: REVIEW Genes: mec-2 mec-4 mec-6 mec-10 Abstract: ------------------- Key: 6832 Medline: Authors: Bracht J;Hunter S;Eachus R;Weeks P;Pasquinelli AE Title: Trans-splicing and polyadenylation of leet-7 microRNA primary transcripts. Citation: RNA 10: 1586-1594 2004 Type: ARTICLE Genes: alg-1 dcr-1 eft-2 let-7 lin-4 rrf-3 Abstract: Members of the microRNA (miRNA) class of 22-nucleotide RNAs regulate the expression of target genes that contain sequences of antisense complementarity. Maturation of miRNAs involves cleavage of longer primary transcripts, but little is yet understood about how miRNA genes are transcribed and enter the processing pathway. We find that relatively long, polyadenylated transcripts encoded by the Caenorhabditis elegans let-7 gene undergo trans-splicing to the spliced leader 1 (SL1) RNA. Deletions, including removal of the trans-splice site, upstream of mature let-7 sequence result in stable accumulation of primary transcripts and compromised production of mature let-7 RNA in vivo. Our data show that multiple steps of let-7 miRNA biogenesis can be uncoupled, allowing for complex regulation in the production of a functional miRNA. Finally, the observation that let-7 primary transcripts undergo splicing highlights the importance of identifying the sequence of endogenous pri-miRNA substrates recognized by the cellular processing machinery. ------------------- Key: 6833 Medline: 15383679 Authors: Cohen LS;Mikhli C;Friedman C;Jankowska-Anyszka M;Stepinski J;Darzynkiewicz E;Davis RE Title: Nematode m(7) GpppG and m(3)(2,2,7)GpppG decapping: activities in Ascaris embryos and characterization of C. elegans scavenger DcpS. Citation: RNA 10: 1609-1624 2004 Type: ARTICLE Genes: Abstract: A spliced leader contributes the mature 5' ends of many mRNAs in trans-splicing organisms. Trans-spliced metazoan mRNAs acquire an M,2,2,7 GpppN cap from the added spliced leader exon. The presence of these caps, along with the typical m(7)GpppN cap on non-trans-spliced mRNAs, requires that cellular mRNA cap-binding proteins and mRNA metabolism deal with different cap structures. We have developed and used an in vitro system to examine mRNA degradation and decapping activities in nematode embryo extracts. The predominant pathway of mRNA decay is a 3' to 5' pathway with exoribonuclease degradation of the RNA followed by hydrolysis of resulting mRNA cap by a scavenger (DcpS-like) decapping activity. Direct decapping of mRNA by a Dcp1/Dcp2-like activity does occur, but is similar to15-fold less active than the 3' to 5' pathway. The DcpS-like activity in nematode embryo extracts hydrolyzes both m(7)GpppG and m(3)(2,2,7)GpppG dinucleoside triphosphates. The Dcp1/Dcp2-like activity in extracts also hydrolyzes these two cap structures at the 5' ends of RNAs. Interestingly, recombinant nematode DcpS differs from its human ortholog in its substrate length requirement and in its capacity to hydrolyze m(3)(2,2,7)GpppG. ------------------- Key: 6834 Medline: 15383288 Authors: Yan N;Gu L;Kokel D;Chai J;Li W;Han A;Chen L;Xue D;Shi Y Title: Structural, biochemical, and functional analyses of CED-9 recognition by the proapoptotic proteins EGL-1 and CED-4. Citation: Molecular Cell 15: 999-1006 2004 Type: ARTICLE Genes: ced-4 ced-9 egl-1 Abstract: Programmed cell death in Caenorhabditis elegans is initiated by the binding of EGL-1 to CED-9, which disrupts the CED-4/CED-9 complex and allows CED-4 to activate the cell-killing caspase CED-3. Here we demonstrate that the C-terminal half of EGL-1 is necessary and sufficient for binding to CED-9 and for killing cells. Structure of the EGL-1/CED-9 complex revealed that EGL-1 adopts an extended alpha-helical conformation and induces substantial structural rearrangements in CED-9 upon binding. EGL-1 interface mutants failed to bind to CED-9 or to release CED-4 from the CED-4/CED-9 complex, and were unable to induce cell death in vivo. A surface patch on CED-9, different from that required for binding to EGL-1, was identified to be responsible for binding to QED-4. These data suggest a working mechanism for the release of CED-4 from the CED-4/ CED-9 complex upon EGL-1 binding and provide a mechanistic framework for understanding apoptosis activation in C. elegrans. ------------------- Key: 6835 Medline: 15280391 Authors: Culetto E;Baylis HA;Richmond JE;Jones AK;Fleming JT;Squire MD;Lewis JA;Sattelle DB Title: The Caenorhabditis elegans unc-63 gene encodes a levamisole-sensitive nicotinic acetylcholine receptor alpha subunit. Citation: Journal of Biological Chemistry 279: 42476-42483 2004 Type: ARTICLE Genes: lev-1 unc-29 unc-38 unc-63 Abstract: The anthelmintic drug levamisole causes hypercontraction of body wall muscles and lethality in nematode worms. In the nematode Caenorhabditis elegans, a genetic screen for levamisole resistance has identified 12 genes, three of which (unc-38, unc-29, and lev-1) encode nicotinic acetylcholine receptor (nAChR) subunits. Here we describe the molecular and functional characterization of another levamisole-resistant gene, unc-63, encoding a nAChR alpha subunit with a predicted amino acid sequence most similar to that of UNC-38. Like UNC-38 and UNC-29, UNC-63 is expressed in body wall muscles. In addition, UNC-63 is expressed in vulval muscles and neurons. We also show that LEV-1 is expressed in body wall muscle, thus overlapping the cellular localization of UNC-63, UNC-38, and UNC-29 and suggesting possible association in vivo. This is supported by electrophysiological studies on body wall muscle, which demonstrate that a levamisole-sensitive nAChR present at the C. elegans neuromuscular junction requires both UNC-63 and LEV-1 subunits. Thus, at least four subunits, two alpha types (UNC-38 and UNC-63) and two non-alpha types (UNC-29 and LEV-1), can contribute to levamisole-sensitive muscle nAChRs in nematodes. ------------------- Key: 6836 Medline: 15380065 Authors: Bender LB;Cao R;Zhang Y;Strome S Title: The MES-2/MES-3/MES-6 complex and regulation of histone H3 methylation in C. elegans. Citation: Current Biology 14: 1639-1643 2004 Type: ARTICLE Genes: mes-2 mes-3 mes-6 Abstract: The C. elegans proteins MES-2 and MES-6, orthologs of the Polycomb group (PcG) chromatin repressors E(Z) and ESC [1, 2], exist in a complex with their novel partner MES-3 [3]. The MES system participates in silencing the X chromosomes in the hermaphrodite germline [4, 5]. Loss of maternal MES function leads to germline degeneration and sterility [6]. We report here that the MES complex is responsible for di- and trimethylation of histone H3 Lys27 (H3-K27) in the adult germline and in early embryos and that MES-dependent H3-K27 marks are concentrated on the X's. Another H3-K27 HMT functions in adult somatic cells oocytes, and the PGCs of embryos. In PGCs, the ME; complex may specifically convert dimethyl to trimethyl H3-K27. The HMT activity of the MES complex appears to be dependent on the SET domain of MES-2. MES-2 thus joins its orthologs Drosophila E(Z) and human EZH2 among SET domain proteins known to function as HMTs (reviewed in [7]). Methylation of histones is important for long-term epigenetic regulation of chromatin and plays a key role in diverse processes such as X inactivation and oncogenesis [8]. Our results contribute to understanding the composition and roles of E(Z)/MES-2 complexes across species. ------------------- Key: 6837 Medline: 15466489 Authors: Broday L;Kolotuev I;Didier C;Bhoumik A;Gupta BP;Sternberg PW;Podbilewicz B;Ronai Z Title: The small ubiquitin-like modifier (SUMO) is required for gonadal and uterine-vulval morphogenesis in Caenorhabditis elegans. Citation: Genes & Development 18: 2380-2391 2004 Type: ARTICLE Genes: lin-11 smo-1 Abstract: The small ubiquitin-like modifier (SUMO) modification alters the subcellular distribution and function of its substrates. Here we show the major role of SUMO during the development of the Caenorhabditis elegans reproductive system. smo-1 deletion mutants develop into sterile adults with abnormal somatic gonad, germ line, and vulva. SMO-1:: GFP reporter is highly expressed in the somatic reproductive system. smo-1 animals lack a vulval-uterine connection as a result of impaired ventral uterine pi-cell differentiation and anchor cell fusion. Mutations in the LIN-11 LIM domain transcription factor lead to a uterine phenotype that resembles the smo-1 phenotype. LIN-11 is sumoylated, and its sumoylation is required for its activity during uterine morphogenesis. Expression of a SUMO-modified LIN-11 in the smo-1 background partially rescued pi-cell differentiation and retained LIN-11 in nuclear bodies. Thus, our results identify the reproductive system as the major SUMO target during postembryonic development and highlight LIN-11 as a physiological substrate whose sumoylation is associated with the ------------------- Key: 6838 Medline: Authors: Van Troys M;Ono K;Dewitte D;Jonckheere V;De Ruyck N;Vandekerckhove J;Ono S;Ampe C Title: TetrThymosin beta is required for actin dynamics in Caenorhabditis elegans and acts via functionally different actin-binding repeats. Citation: Molecular Biology of the Cell 15: 4735-4748 2004 Type: ARTICLE Genes: tth-1 Abstract: Generating specific actin structures via controlled actin polymerization is a prerequisite for eukaryote development and reproduction. We here report on an essential Caenorhabditis elegans protein tetraThymosinbeta expressed in developing neurons and crucial during oocyte maturation in adults. TetraThymosinbeta has four repeats, each related to the actin monomer-sequestering protein thymosinbeta4 and assists in actin filament elongation. For homologues with similar multirepeat structures, a profilin-like mechanism of ushering actin onto filament barbed ends, based on the formation of a 1:1 complex, is proposed to underlie this activity. We, however, demonstrate that tetraThymosinbeta binds multiple actin monomers via different repeats and in addition also interacts with filamentous actin. All repeats need to be functional for attaining full activity in various in vitro assays. The activities on actin are thus a direct consequence of the repeated structure. In containing both G- and F-actin interaction sites, tetraThymosinbeta may be reminiscent of nonhomologous multimodular actin regulatory proteins implicated in actin filament dynamics. A mutation that suppresses expression of tetraThymosinbeta is homozygous lethal. Mutant organisms develop into adults but display a dumpy phenotype and fail to reproduce as their oocytes lack essential actin structures. This strongly suggests that the activity of tetraThymosinbeta is of crucial importance at specific developmental stages requiring actin polymerization. ------------------- Key: 6839 Medline: 15363797 Authors: Hardin J;Lockwood C Title: Skin tight: cell adhesion in the epidermis of Caenorhabditis elegans. Citation: Current Opinion in Cell Biology 16: 486-492 2004 Type: REVIEW Genes: ajm-1 clc-1 crb-1 crl-1 dlg-1 eat-20 erm-1 hmp-1 hmp-2 hmr-1 jac-1 let-413 let-805 mua-3 mup-4 sma-1 spc-1 vab-9 vab-10 vab-19 Abstract: The powerful genetics, genomics and microscopy tools available for C. elegans make it well suited to studying how epithelial cells adhere to one another and the extracellular matrix, and how the integrated, simultaneous activities of multiple cell adhesion complexes function to shape an organism. Recent studies using forward and reverse genetics have shed light on how phylogenetically conserved cell adhesion complexes, such as the cadherin/catenin complex, claudins, the Discs large complex and hemidesmosome-like attachment structures, regulate epithelial cell adhesion, providing new insights into conserved cell adhesion mechanisms in higher eukaryotes. ------------------- Key: 6840 Medline: Authors: Kniazeva M;Crawford QT;Seiber M;Wang CY;Han M Title: Monomethyl branched-chain fatty acids play an essential role in Caenorhabditis elegans development. Citation: PLoS Biology 2: 1446-1459 2004 Type: ARTICLE Genes: acs-1 cyp-1 daf-2 daf-16 elo-1 elo-2 elo-3 elo-4 elo-5 elo-6 elo-7 elo-8 lpd-1 mxl-3 nhr-49 pnk-1 tim-13 tlf-1 Abstract: ------------------- Key: 6841 Medline: 15385167 Authors: Ji YJ;Nam S;Jin YH;Cha EJ;Lee KS;Choi KY;Song HO;Lee J;Bae SC;Ahnn J Title: RNT-1, the C. elegans homologue of mammalian RUNX transcription factors, regulates body size and mail tail development. Citation: Developmental Biology 274: 402-412 2004 Type: ARTICLE Genes: cnb-1 him-5 kin-29 lon-1 rnt-1 sma-2 sma-3 sma-4 sma-6 Abstract: The rnt-1 gene is the only Caenorhabditis elegans homologue of the mammalian RUNX genes. Several lines of molecular biological evidence have demonstrated that the RUNX proteins interact and cooperate with Smads, which are transforming growth factor-beta (TGF-beta) signal mediators. However, the involvement of RUNX in TGF-beta signaling has not yet been supported by any genetic evidence. The Sma/ Mab TGF-beta signaling pathway in C. elegans is known to regulate body length and male tail development. The rnt-1(ok351) mutants show the characteristic phenotypes observed in mutants of the Sma/Mab pathway, namely, they have a small body size and ray defects. Moreover, RNT-1 can physically interact with SMA-4 which is one of the Smads in C. elegans, and double mutant animals containing both the rnt-1(ok351) mutation and a mutation in a known Sma/Mab pathway gene displayed synergism in the aberrant phenotypes. In addition, lon-1(e185) mutants was epistatic to rnt-1(ok351) mutants in terms of long phenotype, suggesting that lon-1 is indeed downstream target of rnt-1. Our data reveal that RNT-1 functionally cooperates with the SMA-4 proteins to regulate ------------------- Key: 6842 Medline: 15254157 Authors: Jospin M;Allard B Title: An amiloride-sensitive H+-gated Na+ channel in Caenorhabditis elegans body wall muscle cells. Citation: Journal of Physiology 559: 715-720 2004 Type: ARTICLE Genes: unc-49 unc-105 Abstract: About 30 genes are predicted to encode degenerin/epithelial sodium channels (DEG/ENaCs) in Caenorhabditis elegans but the gating mode of these channels has not been determined. Using the whole-cell configuration of the patch-clamp technique in acutely dissected C. elegans, we investigated the effects of H+ as a potential activating factor of DEG/ENaCs on electrical properties of body wall muscle cells. Under current-clamp conditions, decreasing external pH from 7.2 to 6.1 led to a reversible depolarization of muscle cells associated with a decrease in input resistance which was partially inhibited by amiloride. Under voltage-clamp conditions, extracellular acidification activated an inward desensitizing current at -60 mv. In the absence of external Ca2+, H+ -gated channels were found to be slightly more permeable to Na+ than to K+ and were blocked by amiloride with a K-0.5 of 31 mum at -60 mV. An inward current could be also activated by protons in a GABA receptor null mutant in the presence of D-tubocurare and in an unc-105 null mutant. These results demonstrate that ion channels sharing common properties with mammalian acid-sensing ion channels (ASICs) are functional in C. elegans muscle which should prove useful for understanding proton sensing in animals. ------------------- Key: 6843 Medline: Authors: Kam N;Harel D;Kugler H;Marelly R;Pnueli A;Hubbard EJA;Stern MJ Title: Formal modeling of C. elegans development: a scenario-based approach. Citation: Modeling in Molecular Biology. G Ciobanu and G Rozenberg (eds). Natural Computing Series, Springer-Verlag. : 151-173 2004 Type: REVIEW Genes: Abstract: We present preliminary results of a new approach to the formal modeling of biological phenomena. The approach stems from the conceptual compatibility of the methods and logic of data collection and analysis in the field of developmental genetics with the languages, methods and tools of scenario-based reactive system design. In particular, we use the recently developed methodology consisting of the language of live sequence charts with the play-in/play-out process, to model the well-characterized process of cell fate acquisition during C. elegans vulval ------------------- Key: 6844 Medline: 15482109 Authors: Mylonakis E;Ausubel FM;Tang RJ;Calderwood SB Title: The art of serendipity: killing of Caenorhabditis elegans by human pathogens as a model of bacterial and fungal pathogenesis. Citation: Expert Review of Antiinfective Therapy 1: 167-173 2003 Type: REVIEW Genes: age-1 ced-3 ced-4 ced-9 egl-9 ikb-1 lys-1 lys-7 lys-8 pik-1 tol-1 trf-1 Abstract: The nematode worm, Caenorhabditis elegans, has been used to develop a facile model system of host-pathogen interactions to identify basic evolutionarily conserved pathways associated with microbial pathogenesis. The model involves the killing of Caenorhabditis elegans by a variety of human pathogens. Several virulence-related genes in a variety of pathogens previously shown to be involved in mammalian infection have also been shown to play a role in Caenorhabditis elegans killing. Screening of large numbers of microbial mutants for attenuation in a mammalian model would require thousands of mice, rats or rabbits. In contrast, the Caenorhabditis elegans model allows rapid identification of mutants in microbial genes associated with pathogenesis and then these phenotypes can be confirmed in a relevant mammalian model. ------------------- Key: 6845 Medline: Authors: McCarter JP Title: Genomic filtering: an approach to discovering novel antiparasitics. Citation: Trends in Parasitology 20: 462-468 2004 Type: REVIEW Genes: fat-2 Abstract: Genomic filtering is a rapid approach to identifying and prioritizing molecular targets for drug discovery. For infectious disease applications, comparative genomics filters allow the selection of pathogen-specific gene products, whereas functional genomics filters, such as RNA interference (RNAi), allow the selection of gene products essential for pathogen survival. The approach is especially applicable to antiparasitic drug discovery where the phylogenetic distance between parasite and host make the likelihood of drug cross-toxicity due to conservation of molecular targets greater than for more distantly related pathogens such as prokaryotes. This article discusses some of the inherent challenges of applying genomics to the early steps of drug discovery and describes one successful comparative and functional genomics filtering strategy that has been implemented to prioritize molecular targets and identify chemical leads for nematode control. ------------------- Key: 6846 Medline: 15351430 Authors: De Luca A Title: Letter to the editor: Prednisone in dystrophin-deficient Caenorhabditis elegans. Citation: Neuromuscular Disorders 14: 696-698 2004 Type: LETTER Genes: Abstract: I read with interest and some concern the manuscript "Prednisone reduces muscle degeneration in dystrophin-deficient Caenorhabditis elegans" by Gaud et al. dealing the the potential usefulness of the dystrophin-deficient worm in performing a large drug screening project to identify novel therapies for Duchenne muscular dystrophy. The authors base the value of the model on the evidence that, out of hundreds of compounds tested, only prednisone reduced the signs of muscular degeneration in this model. The promising event is that prednisone belongs to a unique class of drugs clinically useful in delaying the progression of the disease. My concern arises from various considerations based on the current state-of-the-art in the specific field investigated by the authors. A few of these considerations are reviewed ------------------- Key: 6847 Medline: 15469513 Authors: Mylonakis E;Idnurm A;Moreno R;El Khoury J;Rottman JB;Ausubel FM;Heitman J;Calderwood SB Title: Cryptococcus neoformans Kin1 protein kinase homologue, identified through a Caenorhabditis elegans screen, promotes virulence in mammals. Citation: Molecular Microbiology 54: 407-419 2004 Type: ARTICLE Genes: Abstract: Cryptococcal infections are a global cause of significant morbidity and mortality. Recent studies support the hypothesis that virulence of Cryptococcus neoformans may have evolved via survival selection in environmental hosts, such as amoebae and free-living nematodes. We used killing of the nematode Caenorhabditis elegans by C. neoformans as an assay to screen a library of random C. neoformans insertion mutants. Of 350 mutants tested, seven were identified with attenuated virulence that persisted after crossing the mutation back into a wild-type strain. Genetic analysis of one strain revealed an insertion in a gene homologous to Saccharomyces cerevisiae KIN1, which encodes a serine/threonine protein kinase. C. neoformans kin1 mutants exhibited significant defects in virulence in murine inhalation and haematogenous infection models and displayed increased binding to alveolar and peritoneal macrophages. The kin1 mutant phenotypes were complemented by the wild-type KIN1 gene. These findings show that the C. neoformans Kin1 kinase homologue is required for full virulence in disparate hosts and that C. elegans can be used as a substitute host to identify novel factors involved in fungal pathogenesis in mammals. ------------------- Key: 6848 Medline: 15280428 Authors: Yoneda T;Benedetti C;Urano F;Clark SG;Harding HP;Ron D Title: Compartment-specific perturbation of protein handling activates genes encoding mitochondrial chaperones. Citation: Journal of Cell Science 117: 4055-4066 2004 Type: ARTICLE Genes: aco-2 cit-1 cox-1 cts-1 fum-1 hsp-4 hps-6 hsp-60 hsp-70 lrs-2 mdh-1 myo-3 phb-2 pif-1 sod-3 spg-7 unc-32 Abstract: Protein folding in the mitochondria is assisted by nuclear-encoded compartment-specific chaperones but regulation of the expression of their encoding genes is poorly understood. We found that the mitochondrial matrix HSP70 and HSP60 chaperones, encoded by the Caenorhabditis elegans hsp-6 and hsp-60 genes, were selectively activated by perturbations that impair assembly of multi-subunit mitochondrial complexes or by RNAi of genes encoding mitochondrial. chaperones or proteases, which lead to defective protein folding and processing in the organelle. hsp-6 and hsp-60 induction was specific to perturbed mitochondrial protein handling, as neither heat-shock nor endoplasmic reticulum stress nor manipulations that impair mitochondrial steps in intermediary metabolism or ATP synthesis activated the mitochondrial chaperone genes. These observations support the existence of a mitochondrial unfolded protein response that couples mitochondrial chaperone gene expression to changes in the protein handling environment in the organelle. ------------------- Key: 6849 Medline: 15452142 Authors: Powers J;Rose DJ;Saunders A;Dunkelbarger S;Strome S;Saxton WM Title: Loss of KLP-19 polar ejection force causes misorientation and missegregation of holocentric chromosomes. Citation: Journal of Cell Biology 166: 991-1001 2004 Type: ARTICLE Genes: hcp-3 hcp-6 klp-12 klp-19 mei-1 smc-1 Abstract: Holocentric chromosomes assemble kinetochores along their length instead of at a focused spot. The elongated expanse of an individual holocentric kinetochore and its potential flexibility heighten the risk of stable attachment to microtubules from both poles of the mitotic spindle (merotelic attachment), and hence aberrant segregation of chromosomes. Little is known about the mechanisms that holocentric species have evolved to avoid this type of error. Our studies of the influence of KLP-19, an essential microtubule motor, on the behavior of holocentric Caenorhabditis elegans chromosomes suggest that it has a major role in combating merotelic attachments. Depletion of KLP-19, which associates with nonkinetochore chromatin, allows aberrant poleward chromosome motion during prometaphase, misalignment of holocentric kinetochores, and multiple anaphase chromosome bridges in all mitotic divisions. Time-lapse movies of GFP-labeled mono- and bipolar spindles demonstrate that KLP-19 generates a force on relatively stiff holocentric chromosomes that pushes them away from poles. We hypothesize that this polar ejection force minimizes merotelic misattachment by maintaining a constant tension on pole-kinetochore connections throughout prometaphase, tension that compels sister kinetochores to face directly toward opposite poles. ------------------- Key: 6850 Medline: Authors: Yurchenco PD;Wadsworth WG Title: Assembly and tissue functions of early embryonic laminins and netrins. Citation: Current Opinion in Cell Biology 15: 572-579 2004 Type: REVIEW Genes: unc-5 unc-6 unc-40 Abstract: Vertebrate laminins and netrins share IN-terminal domain structure, but appear to be only distantly related. Both families can be divided into different subfamilies on the basis of structural considerations. Recent observations suggest that specific laminin and netrin members have developmental functions that are highly conserved across species. Vertebrate laminin-1 (alpha1beta1gamma1) and laminin-10 (alpha5beta1gamma1), like the two Caenorhabditis elegans laminins, are embryonically expressed and are essential for basement membrane assembly. Basement membrane assembly is a cooperative process in which laminins polymerize through their LN domains and anchor to the cell surface through their G domains; this leads to cell signaling through integrins and dystroglycan (and possibly other receptors) recruited to the adherent laminin. Netrins may associate with this network through heterotypic LN domain interactions. Vertebrate netrin-1, like invertebrate UNIC-6/netrins, is well known as an extracellular guidance cue that directs axon migration towards or away from the ventral midline. It also regulates cell adhesions and migrations, probably as a basement membrane component. Although sharing structural features, these two vertebrate protein families are quite distinct, having both retained members that mediate the ancestral developmental functions. ------------------- Key: 6851 Medline: 15228383 Authors: Zhu S;Hanneman A;Reinhold VN;Spence AM;Schachter H Title: Caenorhabditis elegans triple null mutant lacking UDP-N-acetyl-D-glucosamine: alpha-3-D-mannoside beta1,2-N-acetylglucosaminyltransferase I. Citation: Biochemical Journal 382: 995-1001 2004 Type: ARTICLE Genes: gly-12 gly-13 gly-14 Abstract: We have previously reported, from the nematode worm Caenorhabditis elegans, three genes (gly-12, gly-13 and gly-14) encoding enzymically active UDP-N-acetyl-D-glucosamine:alpha-3-D-mannoside beta1,2-N-acetylglucosaminyltransferase I (GnT I), an enzyme essential for hybrid, paucimannose and complex N-glycan synthesis. We now describe a worm with null mutations in all three GnT I genes, gly-14 (III);gly-12 gly-13 (X) (III and X refer to the chromosome number). The triple-knock-out (TKO) worms have a normal phenotype, although they do not express GnT I activity and do not synthesize 31 paucimannose, complex and fucosylated oligomannose N-glycans present in the wildtype worm. The TKO worm has increased amounts of non-fucosylated oligomannose N-glycan structures, a finding consistent with the site of GnT I action. Five fucosylated oligomannose N-glycan structures were observed in TKO, but not wild-type, worms, indicating the presence of unusual GnT I-independent fucosyltransferases. It is concluded that wild-type C. elegans makes a large number of GnT I-dependent N-glycans that are not essential for normal worm development under laboratory conditions. The TKO worm may be more susceptible to mutations in other genes, thereby providing an approach for the identification of ------------------- Key: 6852 Medline: Authors: Segalat L Title: Reply to the Letter to the Editor: Reply to de Luca: Prednisone in dystrophin-deficient Caenorhabditis elegans. Citation: Neuromuscular Disorders 14: 698- 2004 Type: LETTER Genes: Abstract: In her commentary on our recently published paper, A. de Luca questions the approach consisting in screening random molecules on a dystrophin-deficient invertebrate model (C. elegans) in order to identify potential therapeutic clues. ------------------- Key: 6853 Medline: 15369666 Authors: He X Title: Wnt signaling went derailed again: a new track via the LIN-18 receptor? Citation: Cell 118: 668-670 2004 Type: REVIEW Genes: cwn-2 lin-17 lin-18 lin-44 mom-2 Abstract: In this issue of Cell, Inoue et al. (2004) reports that LIN-18, an atypical receptor tyrosine kinase related to mammalian Ryk and Drosophila Derailed, mediates Wnt signaling in parallel to LIN-17/Frizzled (Fz) during worm vulval development. LIN-18/Ryk and LIN-17/Fz appear to exhibit distinct Wnt specificity, and surprisingly, the LIN-18 intracellular domain may be dispensable. ------------------- Key: 6854 Medline: 15483120 Authors: Runko E;Kaprielian Z Title: Caenorhabditis elegans VEM-1, a novel membrane protein, regulates the guidance of ventral nerve cord-associated axons. Citation: Journal of Neuroscience 24: 9015-9026 2004 Type: ARTICLE Genes: glr-1 sax-3 unc-40 vem-1 Abstract: In the developing CNS, pathfinding growth cones use intermediate target- and pioneer axon-associated guidance cues to navigate along stereotypical trajectories. We previously showed that the novel membrane-associated protein Vema is localized to the floor plate and the optic chiasm, intermediate targets located at the ventral midline of the spinal cord and diencephalon in the developing rodent CNS, respectively. Here, we report that the Caenorhabditis elegans ortholog of vema, vem-1, is expressed by the AVG pioneer midline neuron and by several neurons that extend longitudinally projecting axons into the ventral nerve cord (VNC). In vem-1 mutants and vem-1( RNAi) animals, a subset of posteriorly projecting interneuron axons either fail to extend ventrally to the VNC and, instead, assume aberrant lateral positions or are inappropriately located in the left tract of the VNC. In addition, ventral motor neuron axons exhibit pathfinding errors within the VNC and along the dorsoventral body axis. The conserved UNC-40/DCC and SAX-3-/Robo receptors mediate signaling events that regulate axon guidance in a wide variety of systems. Double-mutant analyses reveal that vem-1 genetically interacts with unc-40 and is likely to function in parallel with sax-3 to regulate the guidance of a subset of VNC-associated interneuron and motor neuron axons. Consistent with these genetic data, we also show that VEM-1 is capable of physically interacting with UNC-40 ------------------- Key: 6855 Medline: 15508623 Authors: Kenney SJ;Anderson GL;Williams PL;Millner PD;Beuchat LR Title: Effectiveness of cleaners and sanitizers in killing salmonella Newport in the gut of free-living nematode, Caenorhabditis elegans. Citation: Journal of Food Protection 67: 2151-2157 2004 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans, a free-living nematode found in soil, has been shown to ingest human enteric pathogens, thereby potentially serving as a vector for preharvest contamination of fruits and vegetables. A study was undertaken to evaluate the efficacy of cleaners and sanitizers in killing Salmonella enterica serotype Newport in the gut of C elegans. Adult worms were fed nalidixic acid-adapted cells of Escherichia coli OP50 (control) or Salmonella Newport for 24 h, washed, placed on paper discs, and incubated at temperatures of 4 or 20degreesC and relative humidities of 33 or 98% for 24 h. Two commercial cleaners (Enforce and K Foam Lo) and four sanitizers (2% acetic acid, 2% lactic acid, Sanova, and chlorine [50 and 200 mug/ml]) were applied to worms for 0, 2, or 10 min. Populations of E. coli and Salmonella Newport (CFU per worm) in untreated and treated worms were determined by sonicating worms in 0.1% peptone and surface plating suspensions of released cells on tryptic soy agar containing nalidixic acid. Populations of Salmonella Newport in worms exposed to 33 or 98% relative humidity at 4degreesC or 33% relative humidity at 20degreesC were significantly (P less than or equal to 0.05) lower than the number surviving exposure to 98% relative humidity at 20degreesC. In general, treatment of desiccated worms with cleaners and sanitizers was effective in significantly (P less than or equal to 0.05) reducing the number of ingested Salmonella Newport. Results indicate that temperature and relative humidity influence the survival of Salmonella Newport in the gut of C. elegans, and cleaners and ------------------- Key: 6856 Medline: 15308663 Authors: McElwee JJ;Schuster E;Blanc E;Thomas JH;Gems D Title: Shared transcriptional signature in Caenorhabditis elegans dauer larvae and long-lived daf-2 mutants implicates detoxification system in longevity assurance. Citation: Journal of Biological Chemistry 279: 44533-44543 2004 Type: ARTICLE Genes: daf-2 daf-16 hif-1 hsp-12 hsp-16 hsp-16.1 hsp-16.48 hsp-43 nhx-2 pep-2 sip-1 Abstract: In the nematode Caenorhabditis elegans, formation of the long-lived dauer larva and adult aging are both controlled by insulin/insulin-like growth factor-1 signaling. Potentially, increased adult life span in daf-2 insulin/ insulin-like growth factor-1 receptor mutants results from mis-expression in the adult of a dauer larva longevity program. By using oligonucleotide microarray analysis, we identified a dauer transcriptional signature in daf-2 mutant adults. By means of a nonbiased statistical approach, we identified gene classes whose expression is altered similarly in dauers and daf-2 mutants, which represent potential determinants of life span. These include known determinants of longevity; the small heat shock protein/alpha-crystallins are up-regulated in both milieus. The cytochrome P450, short-chain dehydrogenase/ reductase, UDP-glucuronosyltransferase, and glutathione S-transferase ( in daf-2 mutants) gene classes were also up-regulated. These four gene classes act together in metabolism and excretion of toxic endobiotic and xenobiotic metabolites. This suggests that diverse toxic lipophilic and electrophilic metabolites, disposed of by phase 1 and phase 2 drug metabolism, may be the major determinants of the molecular damage that causes aging. In addition, we observed downregulation of genes linked to nutrient uptake, including nhx-2 and pep-2. These work together in the uptake of dipeptides in the intestine, implying dietary restriction in daf-2 mutants. Some gene groups up-regulated in dauers and/or daf-2 were enriched for certain promoter elements as follows: the daf-16-binding element, the heat shock-response element, the heat shock-associated sequence, or the hif-1-response element. By contrast, the daf-16-associated element was enriched in genes down-regulated in dauers and daf-2 mutants. Thus, particular promoter elements appear longevity-associated or ------------------- Key: 6857 Medline: 15272318 Authors: Lettre G;Kritikou EA;Jaeggi M;Calixto A;Fraser AG;Kamath RS;Ahringer J;Hengartner MO Title: Genome-wide RNAi identifies p53-dependent and -independent regulators of germ cell apoptosis in C. elegans. Citation: Cell Death and Differentiation 11: 1198-1203 2004 Type: ARTICLE Genes: ape-1 bmk-1 ced-3 ced-9 cep-1 cpb-3 gst-5 hus-1 pmk-1 pmk-2 pmk-3 pqn-60 rad-50 rad-51 ser-3 Abstract: We used genome-wide RNA interference (RNAi) to identify genes that affect apoptosis in the C. elegans germ line. RNAi-mediated knockdown of 21 genes caused a moderate to strong increase in germ cell death. Genetic epistasis studies with these RNAi candidates showed that a large subset (16/21) requires p53 to activate germ cell apoptosis. Apoptosis following knockdown of the genes in the p53-dependent class also depended on a functional DNA damage response pathway, suggesting that these genes might function in DNA repair or to maintain genome integrity. As apoptotic pathways are conserved, orthologues of the worm germline apoptosis genes presented here could be involved in the maintenance of genomic stability, p53 activation, and fertility in mammals. ------------------- Key: 6858 Medline: 15454087 Authors: Zhang S;Ma C;Chalfie M Title: Combinatorial marking of cells and organelles with reconstituted fluorescent proteins. Citation: Cell 119: 137-144 2004 Type: ARTICLE Genes: acr-5 cat-1 egl-44 hsp-16.2 mec-2 mec-3 sto-6 unc-4 unc-24 unc-37 unc-47 Abstract: Expression of GFP and other fluorescent proteins depends on cis-regulatory elements. Because these elements rarely direct expression to specific cell types, GFP production cannot always be sufficiently limited. Here we show that reconstitution of GFP, YFP, and CFP previously split into two polypeptides yields fluorescent products when coexpressed in C. elegans. Because this reconstitution involves two components, it can confirm cellular coexpression and identify cells expressing a previously uncharacterized promoter. By choosing promoters whose expression patterns overlap for a single cell type, we can produce animals with fluorescence only in those cells. Furthermore, when one partial GFP polypeptide is fused with a subcellularly localized protein or peptide, this restricted expression leads to the fluorescent marking of cellular components in a subset of cells. ------------------- Key: 6859 Medline: Authors: Bossinger O;Bachmann A Title: Ciliogenesis: polarity proteins on the move. Citation: Current Biology 14: R844-R846 2004 Type: REVIEW Genes: Abstract: ------------------- Key: 6860 Medline: 15458647 Authors: Verbrugghe KJC;White JG Title: SPD-1 is required for the formation of the spindle midzone but is not essential for the completion of cytokinesis in C. elegans embryos. Citation: Current Biology 14: 1755-1760 2004 Type: ARTICLE Genes: air-2 bir-1 cyk-4 icp-1 spd-1 zen-4 Abstract: The process of cytokinesis can be divided into two stages: the assembly and constriction of an actomyosin ring giving rise to a narrow intracellular canal and the final breaking and resealing of this canal [1]. Mutations in several genes of Caenorhabiditis elegans disrupt the spindle midzone (anti-parallel microtubules and associated proteins that form between the spindle poles) and give rise to failures in the completion of cytokinesis [2-9]. We show that loss of function of spd-1 causes midzone disruptions, although cytokinesis generally completes. SPD-1 is a conserved microtubule-bundling protein that localizes to the midzone and also to microtubule bundles in the cytoplasm. The midzone localization of SPD-1 is perturbed in embryos depleted of other midzone components, yet the cytoplasmic bundles are not affected. We found that two other midzone components also localize to the ingressing furrow in wild-type embryos; when SPD-1 is depleted, there is no visible midzone, and only this furrow localization remains. SPD-1 differs from other midzone components in that it is essential for the integrity of the midzone, yet not for cytokinesis. Also, it can localize to the midzone when other midzone components are depleted, suggesting that SPD-1 may play an early role in the pathway of midzone ------------------- Key: 6861 Medline: 15489294 Authors: Shostak Y;Van Gilst MR;Antebi A;Yamamoto KR Title: Identification of C. elegans DAF-12-binding sites, response elements, and target genes. Citation: Genes & Development 18: 2529-2544 2004 Type: ARTICLE Genes: adt-1 cav-1 col-130 daf-7 daf-12 gcy-36 gex-3 grd-8 gst-37 ifa-2 lit-1 nex-3 odc-1 pqn-89 sel-8 skr-8 Abstract: Intracellular receptor DAF-12 regulates dauer formation and developmental age and affects Caenorhabditis elegans lifespan. Genetic analyses place DAF-12 at the convergence of several signal transduction pathways; however, the downstream effectors and the molecular basis for the receptor's multiple physiological outputs are unknown. Beginning with C. elegans genomic DNA, we devised a procedure for multiple rounds of selection and amplification that yielded fragments bearing DAF-12-binding sites. These genomic fragments mediated DAF-12-dependent transcriptional regulation both in Saccharornyces cerevisiae and in C. elegans; that is, they served as functional DAF-12 response elements. We determined that most of the genomic fragments that displayed DAF-12 response element activity in yeast were linked to genes that were regulated by DAF-12 in C. elegans; indeed, the response element-containing fragments typically resided within clusters of DAF-12-regulated genes. DAF-12 target gene regulation was developmental program and stage specific, potentially predicting a fit of these targets into regulatory networks governing aspects of C. elegans ------------------- Key: 6862 Medline: 15374666 Authors: Crowder CM Title: Ethanol targets: a BK channel cocktail in C. elegans. Citation: Trends in Neurosciences 27: 579-582 2004 Type: REVIEW Genes: slo-1 Abstract: A genetic screen for resistance to ethanol intoxication in Caenorhabditis elegans isolated mutants of the gene slo-1. slo-1 encodes the pore-forming subunit of a large-conductance Ca2+-activated K+ channel previously shown to limit excitatory neurotransmitter release in C. elegans. Electrophysiological data recorded in vivo are consistent with a model in which ethanol potentiation of SLO-1 produces intoxication in C. elegans by reducing excitatoryneurotransmitter release. ------------------- Key: 6863 Medline: 15331665 Authors: Cockell MM;Baumer K;Gonczy P Title: lis-1 is required for dynein-dependent cell division processes in C. elegans embryos. Citation: Journal of Cell Science 117: 4571-4582 2004 Type: ARTICLE Genes: dhc-1 dnc-1 dnc-2 hcp-4 lis-1 pnm-1 tba-2 Abstract: We investigated the role of the evolutionarily conserved protein Lis1 in cell division processes of Caenorhabditis elegans embryos. We identified apparent null alleles of lis-1, which result in defects identical to those observed after inactivation of the dynein heavy chain dhc-1, including defects in centrosome separation and spindle assembly. We raised antibodies against LIS-1 and generated transgenic animals expressing functional GFP-LIS-1. Using indirect immunofluorescence and spinning-disk confocal microscopy, we found that LIS-1 is present throughout the cytoplasm and is enriched in discrete subcellular locations, including the cell cortex, the vicinity of microtubule asters, the nuclear periphery and kinetochores. We established that lis-1 contributes to, but is not essential for, DHC-1 enrichment at specific subcellular locations. Conversely, we found that dhc-1, as well as the dynactin components dnc-1 (p150(Glued)) and dnc-2 (p50/dynamitin), are essential for LIS-1 targeting to the nuclear periphery, but not to the cell cortex nor to kinetochores. These results suggest that dynein and Lis1, albeit functioning in identical processes, are targeted partially independently of one another. ------------------- Key: 6864 Medline: Authors: Tominaga N;Kohra S;Iguchi T;Arizono K Title: Effects of perfluoro organic compound toxicity on nematode Caenorhabditis elegans fecundity. Citation: Journal of Health Science 50: 545-550 2004 Type: ARTICLE Genes: Abstract: ------------------- Key: 6865 Medline: 15522306 Authors: Lee J;Jee C;Song HO;Bandyopadhyay J;Lee JI;Yu JR;Lee J;Park BJ;Ahnn J Title: Opposing functions of calcineurin and CaMKII regulate G-protein signaling in egg-laying behavior of C. elegans. Citation: Journal of Molecular Biology 344: 585-595 2004 Type: ARTICLE Genes: cnb-1 egl-10 egl-30 tax-6 unc-43 Abstract: Ca2+/calmodulin-dependent calcineurin has been shown to have important roles in various Ca2+ signaling pathways. We have previously reported that cnb-1(jh103) mutants, null mutants of a regulatory B subunit, displayed pleiotropic defects including uncoordinated movement and delayed egg laying in Caenorhabditis elegans. Interestingly, gain-of-function mutants of a catalytic A subunit showed exactly opposite phenotypes to those of cnb-1 (null) mutants providing an excellent genetic model to define calcium-mediated signaling pathway at the organism level. Furthermore, calcineurin is also important for normal cuticle formation, which is required for maintenance of normal body size in C. elegans. Genetic interactions between tax-6 and several mutants including egl-30 and egl-10, which are known to be involved in G-protein signaling pathways suggest that calcineurin indeed regulates locomotion and serotonin-mediated egg laying through goa-1 (Goalpha) and egl-30(Gqalpha). Our results indicate that, along with CaMKII, calcineurin regulates G-protein-coupled phosphorylation signaling pathways in C. ------------------- Key: 6866 Medline: 15539494 Authors: Davis MW;Birnie AJ;Chan AC;Page AP;Jorgensen EM Title: A conserved metalloprotease mediates ecdysis in Caenorhabditis elegans. Citation: Development 131: 6001-6008 2004 Type: ARTICLE Genes: nas-37 Abstract: Molting is required for progression between larval stages in the life cycle of nematodes. We have identified four mutant alleles of a Caenorhabditis elegans metalloprotease gene, nas-37, that cause incomplete ecdysis. At each molt the cuticle fails to open sufficiently at the anterior end and the partially shed cuticle is dragged behind the animal. The gene is expressed in hypodermal cells 4 hours before ecdysis during all larval stages. The NAS-37 protein accumulates in the anterior cuticle and is shed in the cuticle after eedysis. This pattern of protein accumulation places NAS-37 in the right place and at the right time to degrade the cuticle to facilitate ecdysis. The nas-37 gene has orthologs in other nematode species, including parasitic nematodes, and they undergo a similar shedding process. For example, Haemonchus contortus molts by digesting a ring of cuticle at the tip of the nose. Incubating Haemonchus larvae in extracted exsheathing fluids causes a refractile ring of digested cuticle to form at the tip of the nose. When Haemonchus cuticles are incubated with purified NAS-37, a similar refractile ring forms. NAS-37 degradation of the Haemonchus cuticle suggests that the metalloproteases and the cuticle substrates involved in exsheathment of parasitic nematodes ------------------- Key: 6867 Medline: 15313573 Authors: Chase DL;Koelle MR Title: Genetic analysis of RGS protein function in Caenorhabditis elegans. Citation: Methods in Enzymology 389: 305-320 2004 Type: REVIEW Genes: Abstract: Caenorhabditis elegans has close homologs or orthologs of most mammalian (RGS) and G proteins, and mutants for all the RGS and G-protein genes of C elegans have been generated. C. elegans RGS proteins can be matched to the specific Galpha proteins they regulate in vivo by comparing the defects in animals lacking or transgenically overexpressing an RGS protein with defects in a specific Galpha mutant. Transgenic expression of mutated RGS proteins or subdomains in C elegans has also been used to carry out structure/function studies of RGS proteins. We propose that similar strategies can be used to understand the function of RGS proteins from other organisms by expressing them in C elegans. This article describes general considerations regarding such experiments and provides detailed protocols for quantitatively measuring G-protein signaling phenotypes in C elegans. ------------------- Key: 6868 Medline: 15489327 Authors: Lamesch P;Milstein S;Hao T;Rosenberg J;Li N;Sequerra R;Bosak S;Doucette-Stamm L;Vandenhaute J;Hill DE;Vidal M Title: C. elegans ORFeome version 3.1: increasing the coverage of ORFeome resources with improved gene predictions. Citation: Genome Research 14: 2064-2069 2004 Type: ARTICLE Genes: Abstract: The first version of the Caenorhabditis elegans ORFeome cloning project, based on release WS9 of Wormbase (August 1999), provided experimental verifications for approximately 55% of predicted protein-encoding open reading frames (ORFs). The remaining 45% of predicted ORFs could not be cloned, possibly as a result of mispredicted gene boundaries. Since the release of WS9, gene predictions have improved continuously. To test the accuracy of evolving predictions, we attempted to PCR-amplify from a highly representative worm cDNA library and Gateway-clone approximately 4200 ORFs missed earlier and for which new predictions are available in WS100 (May 2003). In this set we successfully cloned 63% of ORFs with supporting experimental data ("touched" ORFs), and 42% of ORFs with no supporting experimental evidence ("untouched" ORFs). Approximately 2000 full-length ORFs were cloned in-frame, 13% of which were corrected in their exon/intron structure relative to WS100 predictions. In total, approximately 12,500 C. elegans ORFs are now available as Gateway Entry clones for various reverse proteomics (ORFeome v3.1). This work illustrates why the cloning of a complete C. elegans ORFeome, and likely the ORFeomes of other multicellular organisms, needs to be an iterative process that requires multiple rounds of experimental validation together with gradually improving gene predictions. ------------------- Key: 6869 Medline: 15489328 Authors: Hope IA;Stevens J;Garner A;Hayes J;Cheo DL;Brasch MA;Vidal Title: Feasibility of genome-scale construction of promoter::reporter gene fusions for expression in Caenorhabditis elegans using a Multisite Gateway recombination system. Citation: Genome Research 14: 2070-2075 2004 Type: ARTICLE Genes: Abstract: The understanding of gene function increasingly requires the characterization of DNA segments containing promoters and their associated regulatory sequences. We describe a novel approach for linking multiple DNA segments, here applied to the generation of promoter::reporter fusions. Promoters from Caenorhabditis elegans genes were cloned using the MultiSite Gateway cloning technology. The capacity for using this system for efficient construction of chimeric genes was explored by constructing promoter::reporter gene fusions with a gfp reporter. The promoters were found to provide appropriate expression of GFP upon introduction into C. elegans, demonstrating that the short Gateway recombination site between the promoter and the reporter did not interfere with transcription or translation. The recombinational cloning involved in the Gateway system, which permits the highly efficient and precise transfer of DNA segments between plasmid vectors, makes this technology ideal for genomics research programs. ------------------- Key: 6870 Medline: 15489332 Authors: Luan CH;Qiu S;Finley JB;Carson M;Gray RJ;Huang W;Johnson D;Tsao J;Reboul J;Vaglio P;Hill DE;Vidal M;DeLucas LJ;Luo M Title: High-throughput expression of C. elegans proteins. Citation: Genome Research 14: 2102-2110 2004 Type: ARTICLE Genes: Abstract: Proteome-scale studies of protein three-dimensional structures should provide valuable information for both investigating basic biology and developing therapeutics. Critical for these endeavors is the expression of recombinant proteins. We selected Caenorhabditis elegans as our model organism in a structural proteomics initiative because of the high quality of its genome sequence and the availability of its ORFeome, protein-encoding open reading frames (ORFs), in a flexible recombinational cloning format. We developed a robotic pipeline for recombinant protein expression, applying the Gateway cloning/expression technology and utilizing a stepwise automation strategy on an integrated robotic platform. Using the pipeline, we have carried out heterologous protein expression experiments on 10,167 ORFs of C. elegans. With one expression vector and one Escherichia coli strain, protein expression was observed for 4854 ORFs, and 1536 were soluble. Bioinformatics analysis of the data indicates that protein hydrophobicity is a key determining factor for an ORF to yield a soluble expression product. This protein expression effort has investigated the largest number of genes in any organism to date. The pipeline described here is applicable to high-throughput expression of recombinant proteins for other species, both prokaryotic and eukaryotic, provided that ORFeome resources become available. ------------------- Key: 6871 Medline: 15489338 Authors: Chen N;Lawson D;Bradnam K;Harris TW;Stein LD Title: WormBase as an integrated platform for the C. elegans ORFeome. Citation: Genome Research 14: 2155-2161 2004 Type: ARTICLE Genes: Abstract: The ORFeome project has validated and corrected a large number of predicted gene models in the nematode C. elegans, and has provided an enormous resource for proteome-scale studies. To make the resource useful to the research and teaching community, it needs to be integrated with other large-scale data sets, including the C. elegans genome, cell lineage, neurological wiring diagram, transcriptome, and gene expression map. This integration is also critical because the ORFeome data sets, like other 'omics' data sets, have significant false-positive and false-negative rates, and comparison to related data is necessary to make confidence judgments in any given data point. WormBase, the central data repository for information about C. elegans and related nematodes, provides such a platform for integration. In this report, we will describe how C. elegans ORFeome data are deposited in the database, how they are used to correct gene models, how they are integrated and displayed in the context of other data sets at the WormBase Web site, and how WormBase establishes connection with the reagent-based resources at the ORFeome ------------------- Key: 6872 Medline: 15489339 Authors: Rual JF;Ceron J;Koreth J;Hao T;Nicot AS;Hirozane-Kishikawa T;Vandenhaute J;Orkin SH;Hill DE;van den Heuvel S;Vidal M Title: Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Citation: Genome Research 14: 2162-2168 2004 Type: ARTICLE Genes: Abstract: The recently completed Caenorhabditis elegans genome sequence allows application of high-throughput (HT) approaches for phenotypic analyses using RNA interference (RNAi). As large phenotypic data sets become available, "phenoclustering" strategies can be used to begin understanding the complex molecular networks involved in development and other biological processes. The current HT-RNAi resources represent a great asset for phenotypic profiling but are limited by lack of flexibility. For instance, existing resources do not take advantage of the latest improvements in RNAi technology, such as inducible hairpin RNAi. Here we show that a C. elegans ORFeome resource, generated with the Gateway cloning system, can be used as a starting point to generate alternative HT-RNAi resources with enhanced flexibility. The versatility inherent to the Gateway system suggests that additional HT-RNAi libraries can now be readily generated to perform gene knockdowns under various conditions, increasing the possibilities for phenome mapping in C. elegans. ------------------- Key: 6873 Medline: 15489340 Authors: Dupuy D;Li QR;Deplancke B;Boxem M;Hao T;Lamesch P;Sequerra R;Bosak S;Doucette-Stamm L;Hope IA;Hill DE;Walhout AJM;Vidal M Title: A first version of the Caenorhabditis elegans Promoterome. Citation: Genome Research 14: 2169-2175 2004 Type: ARTICLE Genes: Abstract: |An important aspect of the development of systems biology approaches in metazoans is the characterization of expression patterns of nearly all genes predicted from genome sequences. Such "localizome" maps should provide information on where (in what cells or tissues) and when (at what stage of development or under what conditions) genes are expressed. They should also indicate in what cellular compartments the corresponding proteins are localized. Caenorhabditis elegans is particularly suited for the development of a localizome map since all its 959 adult somatic cells can be visualized by microscopy, and its cell lineage has been completely described. Here we address one of the challenges of C. elegans localizome mapping projects: that of obtaining a genome-wide resource of C. elegans promoters needed to generate transgenic animals expressing localization markers such as the green fluorescent protein (GFP). To ensure high flexibility for future uses, we utilized the newly developed MultiSite Gateway system. We generated and validated "version 1.1" of the Promoterome: a resource of approximately 6000 C. elegans promoters. These promoters can be transferred easily into various Gateway Destination vectors to drive expression of markers such as GFP, alone (promoter::GFP constructs), or in fusion with protein-encoding open reading frames available in ORFeome resources ------------------- Key: 6874 Medline: 15492222 Authors: Chao MY;Komatsu H;Fukuto HS;Dionne HM;Hart AC Title: Feeding status and serotonin rapidly and reversibly modulate a Caenorhabditis elegans chemosensory circuit. Citation: Proceedings of the National Academy of Sciences USA 101: 15512-15517 2004 Type: ARTICLE Genes: glr-1 gpa-11 mod-5 tph-1 Abstract: Serotonin (5-HT) modulates synaptic efficacy in the nervous system of vertebrates and invertebrates. In the nematode Caenorhabditis elegans, many behaviors are regulated by 5-HT levels, which are in turn regulated by the presence or absence of food. Here, we show that both food and 5-HT signaling modulate chemosensory avoidance response of octanol in C elegans, and that this modulation is both rapid and reversible. Sensitivity to octanol is decreased when animals are off food or when 5-HT levels are decreased; conversely, sensitivity is increased when animals are on food or have increased 5-HT signaling. Laser microsurgery and behavioral experiments reveal that sensory input from different subsets of octanol-sensing neurons is selectively used, depending on stimulus strength, feeding status, and 5-HT levels. 5-HT directly targets at least one pair of sensory neurons, and 5-HT signaling requires the Galpha protein GPA-11. Glutamatergic signaling is required for response to octanol, and the GLR-1 glutamate receptor plays an important role in behavioral response off food but not on food. Our results demonstrate that 5-HT modulation of neuronal activity via G protein signaling underlies behavioral plasticity by rapidly altering the functional circuitry of a chemosensory circuit. ------------------- Key: 6875 Medline: 15531879 Authors: Denli AM;Tops BBJ;Plasterk RHA;Ketting RF;Hannon GJ Title: Processing of primary microRNAs by the Microprocessor complex. Citation: Nature 432: 231-235 2004 Type: ARTICLE Genes: drsh-1 let-7 pash-1 rrf-3 Abstract: Mature microRNAs (miRNAs) are generated via a two-step processing pathway to yield similar to22-nucleotide small RNAs that regulate gene expression at the post-transcriptional level(1). Initial cleavage is catalysed by Drosha, a nuclease of the RNase III family, which acts on primary miRNA transcripts (pri-miRNAs) in the nucleus(2). Here we show that Drosha exists in a multiprotein complex, the Microprocessor, and begin the process of deconstructing that complex into its constituent components. Along with Drosha, the Microprocessor also contains Pasha (partner of Drosha), a double-stranded RNA binding protein. Suppression of Pasha expression in Drosophila cells or Caenorhabditis elegans interferes with pri-miRNA processing, leading to an accumulation of pri-miRNAs and a reduction in mature miRNAs. Finally, depletion or mutation of pash-1 in C. elegans causes de-repression of a let-7 reporter and the appearance of phenotypic defects overlapping those observed upon examination of worms with lesions in Dicer (dcr-1) or Drosha (drsh-1). Considered together, these results indicate a role for Pasha in miRNA maturation and ------------------- Key: 6876 Medline: Authors: Sadrozinski HFW;Bashkirov V;Bruzzi M;Ebrahimi M;Feldt J;Heimann J;Keeney B;Martinez-McKinney F;Menichelli D;Nelson G;Nesom G;Schulte RWM;Seiden A;Spencer E;Wray Title: The Particle Tracking Silicon Microscope PTSM. Citation: IEEE Transactions on Nuclear Science 51: 2032-2036 2004 Type: ARTICLE Genes: Abstract: A novel position- and energy-sensitive particle detector for radiobiological application is described. The aim is to support research in radiation response of biological systems, for example in the induction of mutations in C elegans, where precise knowledge of location and intensity of the radiation is crucial to understand radiation sensitivity of individual cells. The "Particle Tracking Silicon Microscope" (PTSM) consists of a silicon strip detector in direct contact with radiobiological samples (e.g., C. elegans), such that the location and intensity of particle radiation can be controlled at the 10 mum scale. The readout is performed with low-noise readout electronics, which allows the determination of the particle's position from the hit strip address and its energy from the specific energy loss. In our implementation, the energy loss is measured through the time-over-threshold (TOT). The noise rate at acceptable thresholds is so low that the single particles can be detected with 100% efficiency. The performance of the front-end ASIC is described, and the results of initial environmental tests are reported. These include placing biological samples and saline solutions in direct contact ------------------- Key: 6877 Medline: 15473957 Authors: Zinn K Title: Dendritic tiling: new insights from genetics. Citation: Neuron 44: 211-218 2004 Type: REVIEW Genes: sax-1 sax-2 Abstract: Two papers in the current issues of Neuron (Gallegos and Bargmann) and Ceff (Emoto et al.) identify a conserved kinase, SAX-1/Trc, and a large protein required for Trc activity, SAX-2/Fry, as essential elements in the control of dendritic branching and tiling in Drosophila and C. elegans. The tiling and ectopic branching phenotypes of trc mutants appear to be independently generated. Thus, this kinase is the first signaling protein to be associated specifically with tiling. ------------------- Key: 6878 Medline: 15473964 Authors: Gallegos ME;Bargmann CI Title: Mechanosensory neurite termination and tiling depend on SAX-2 and the SAX-1 kinase. Citation: Neuron 44: 239-249 2004 Type: ARTICLE Genes: cam-1 dig-1 lin-22 lin-30 lin-39 sax-1 sax-2 Abstract: Mechanosensory neurons provide accurate information about stimulus location by restricting their sensory dendrites to nonoverlapping regions, a pattern called tiling. Here, we show that C. elegans sax-1 and sax-2 regulate mechanosensory tiling by controlling the termination point of sensory dendrites. During development, the posterior PLM mechanosensory dendrite overlaps transiently with the anterior ALM mechanosensory neuron. This overlap is eliminated during a discrete period of paused or slowed PLM process growth, between an early period of rapid outgrowth and a later period of maintenance growth. In sax-2 mutants, the PLM sensory dendrite fails to slow between the active growth and maintenance growth phases, leading to sustained overlap of anterior and posterior mechanosensory processes. sax-2 encodes a large conserved protein with HEAT/Armadillo repeats that functions with sax-1, an NDR cell morphology-regulating kinase. High-level expression of sax-2 leads to premature neurite termination, suggesting that SAX-2 can directly inhibit neurite growth. ------------------- Key: 6879 Medline: 15317844 Authors: Shim J;Umemura T;Nothstein E;Rongo C Title: The unfolded protein response regulates glutamate receptor export from the endoplasmic reticulum. Citation: Molecular Biology of the Cell 15: 4818-4828 2004 Type: ARTICLE Genes: atf-6 cat-1 glr-1 glr-2 glr-5 ire-1 lin-10 pek-1 sel-1 snb-1 twk-18 xbp-1 Abstract: alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA)-type glutamate receptors mediate the majority of excitatory signaling in the CNS, and the functional properties and subcellular fate of these receptors depend on receptor subunit composition. Subunit assembly is thought to occur in the endoplasmic reticulum (ER), although we are just beginning to understand the underlying mechanism. Here we examine the trafficking of Caenorhabditis elegans glutamate receptors through the ER. Our data indicate that neurons require signaling by the unfolded protein response (UPR) to move GLR-1, GLR-2, and GLR-5 subunits out of the ER and through the secretory pathway. In contrast, other neuronal transmembrane proteins do not require UPR signaling for ER exit. The requirement for the UPR pathway is cell type and age dependent: impairment for receptor trafficking increases as animals age and does not occur in all neurons. Expression of XBP-1, a component of the UPR pathway, is elevated in neurons during development. Our results suggest that UPR signaling is a critical step in neural function that is needed for glutamate receptor assembly and secretion. ------------------- Key: 6880 Medline: 15371539 Authors: Stear JH;Roth MB Title: The Caenorhabditis elegans kinetochore reorganizes at prometaphase and in response to checkpoint stimuli. Citation: Molecular Biology of the Cell 15: 5187-5196 2004 Type: ARTICLE Genes: bub-1 hcp-1 hcp-2 hcp-3 him-10 san-1 Abstract: Previous studies of the kinetochore in mammalian systems have demonstrated that this structure undergoes reorganizations after microtubule attachment or in response to activation of the spindle checkpoint. Here, we show that the Caenorhabditis elegans kinetochore displays analogous rearrangements at prometaphase, when microtubule/chromosome interactions are being established, and after exposure to checkpoint stimuli such as nocodazole or anoxia. These reorganizations are characterized by a dissociation of several kinetochore proteins, including HCP-1/CeCENP-F, HIM-10/CeNuf2, SAN-1/CeMad3, and CeBUB-1, from the centromere. We further demonstrate that at metaphase, despite having dissociated from the centromere, these reorganized kinetochore proteins maintain their associations with the metaphase plate. After checkpoint activation, these proteins are detectable as large "flares" that project out laterally from the metaphase plate. Disrupting these gene products via RNA interference results in sensitivity to checkpoint stimuli, as well as defects in the organization of chromosomes at metaphase. These phenotypes suggest that these proteins, and by extension their reorganization during mitosis, are important for mediating the checkpoint response as well as directing the ------------------- Key: 6881 Medline: 15507120 Authors: Aoyama Y;Urushiyama S;Yamada M;Kato C;Ide H;Higuchi S;Akiyama T;Shibuya H Title: MFB-1, an F-box-type ubiquitin ligase, regulates TGF-beta signalling. Citation: Genes to Cells 9: 1093-1101 2004 Type: ARTICLE Genes: daf-1 daf-2 daf-3 daf-4 daf-7 daf-11 daf-14 mfb-1 Abstract: TGF-beta signalling regulates cell growth, differentiation, morphogenesis and apoptosis. MAFbx/Atrogin-1 has been identified as a regulator for skeletal muscle atrophy and encodes an F-box-type E3 ubiquitin ligase. However, little is known about how MAFbx/Atrogin-1 regulates cellular signalling. Here, we identify and genetically characterize MFB-1, a MAFbx/Atrogin-1 homologue from Caenorhabditis elegans. The mfb-1 deletion mutant significantly enhanced the dauer constitutive (Daf-c) phenotype caused by mutations in the DAF-7/TGF-beta-like signalling pathway, but not the DAF-2/insulin receptor-like signalling pathway. Conversely, the Daf-c phenotypes of DAF-7 pathway mutants were partially suppressed by mfb-1 cDNA transgenes. Therefore, MFB-1 acts genetically downstream in the DAF-7 pathway. A mfb-1::GFP fusion was found to be expressed in the nervous system, hypodermis and intestine and overlapped expression of many DAF-7 pathway genes. We propose that MFB-1 is a novel F-box protein that negatively regulates dauer formation in concert with the DAF-7 signalling ------------------- Key: 6882 Medline: 15475164 Authors: Yang J;Li WH Title: Developmental constraint on gene duplicability in fruit flies and nematodes. Citation: Gene 340: 237-240 2004 Type: ARTICLE Genes: Abstract: A previous study in nematodes suggested that developmental constraint reduces the duplicability of genes involved in early development. Recent large-scale gene expression studies of fly development enabled us to conduct a more detailed study of this issue. We found that the average duplicability of genes involved in embryonic development is indeed lower than that of genes involved in larval development but not significantly lower than that of genes involved in later stages of development. Moreover, in both flies and nematodes genes with multiple expression peaks do not seem to have a lower duplicability than do genes with a single expression peak. Thus, although developmental constraint does appear to reduce gene duplicability, the effect seems weak or at best moderate. ------------------- Key: 6883 Medline: 15474045 Authors: Boxem M;Tsai CW;Zhang Y;Saito RM;Liu JO Title: The C. elegans methionine aminopeptidase 2 analog map-2 is required for germ cell proliferation. Citation: FEBS Letters 576: 245-250 2004 Type: ARTICLE Genes: map-1 map-2 rrf-1 Abstract: We have investigated the physiological function of type 2 methionine aminopeptidases (MetAP2) using Caenorhabditis elegans as a model system. A homolog of human MetAP2 was found in the C. elegans genome, which we termed MAP-2. MAP-2 protein displayed methionine aminopeptidase activity and was sensitive to inhibition by fumagillin. Downregulation of map-2 expression by RNAi led to sterility, resulting from a defect in germ cell proliferation. These observations suggest that MAP-2 is essential for germ cell development in C elegans and that this ubiquitous enzyme may play important roles in a tissue ------------------- Key: 6884 Medline: 15464029 Authors: Suo S;Ishiura S;Van Tol HHM Title: Dopamine receptors in C. elegans. Citation: European Journal of Pharmacology 500: 159-166 2004 Type: REVIEW Genes: cat-2 cat-4 dop-1 dop-2 eat-4 glr-1 glr-2 mec-7 Abstract: Dopamine regulates various physiological functions in the central nervous system and the periphery. Dysfunction of the dopamine system is implicated in a wide variety of disorders and behaviors including schizophrenia, addiction, and attention-deficit hyperactivity disorder. Medications that modulate dopamine signaling have therapeutic efficacy on the treatment of these disorders. However, the causes of these disorders and the role of dopamine are still unclear. Studying the dopamine system in a model organism, such as Caenorhabditis elegans, allows the genetic analysis in a simple and well-described nervous system, which may provide new insight into the molecular mechanisms of dopamine signaling. In this review, we summarize recent findings on pharmacological and biochemical properties of the C. elegans dopamine receptors and their physiological role in the control of behavior. ------------------- Key: 6885 Medline: 15479638 Authors: Hess HA;Roper JC;Grill SW;Koelle MR Title: RGS-7 completes a receptor-independent heterotrimeric G protein cycle to asymmetrically regulate mitotic spindle positioning in C. elegans. Citation: Cell 119: 209-218 2004 Type: ARTICLE Genes: eat-16 egl-10 goa-1 gpr-1 gpr-2 lin-5 rgs-1 rgs-2 rgs-3 rgs-4 rgs-5 rgs-6 rgs-7 rgs-8 rgs-9 rgs-10 rgs-11 ric-8 Abstract: Heterotrimeric G proteins promote microtubule forces that position mitotic spindles during asymmetric cell division in C. elegans embryos. While all previously studied G protein functions require activation by seven-transmembrane receptors, this function appears to be receptor independent. We found that mutating a regulator of G protein signaling, RGS-7, resulted in hyperasymmetric spindle movements due to decreased force on one spindle pole. RGS-7 is localized at the cell cortex, and its effects require two redundant Galpha(o)-related G proteins and their nonreceptor activators RIC-8 and GPR-1/2. Using recombinant proteins, we found that RIC-8 stimulates GTP binding by Galpha(o) and that the FIGS domain of RGS-7 stimulates GTP hydrolysis by Galpha(o), demonstrating that Galpha(o) passes through the GTP bound state during its activity cycle. While GTPase activators typically inactivate G proteins, RGS-7 instead appears to promote G protein function asymmetrically in the cell, perhaps acting ------------------- Key: 6886 Medline: 15479639 Authors: Afshar K;Willard FS;Colombo K;Johnston CA;McCudden CR;Siderovski DP;Gonczy P Title: RIC-8 is required for GPR-1/2-dependent G(alpha) function during asymmetric division of C. elegans embryos. Citation: Cell 119: 219-230 2004 Type: ARTICLE Genes: goa-1 gpa-16 gpb-1 gpr-1 gpr-2 ric-8 Abstract: Heterotrimeric G proteins are crucial for asymmetric cell division, but the mechanisms of signal activation remain poorly understood. Here, we establish that the evolutionarily conserved protein RIC-8 is required for proper asymmetric division of one-cell stage C. elegans embryos. Spindle severing experiments demonstrate that RIC-8 is required for generation of substantial pulling forces on astral microtubules. RIC-8 physically interacts with GOA-1 and GPA-16, two Galpha subunits that act in a partially redundant manner in one-cell stage embryos. RIC-8 preferentially binds to GDP bound GOA-1 and is a guanine nucleotide exchange factor (GEF) for GOA-1. Our analysis suggests that RIC-8 acts before the GoLoco protein GPR-1/2 in the sequence of events leading to Galpha activation. Furthermore, coimmunoprecipitation and in vivo epistasis demonstrate that inactivation of the Gbeta subunit GPB-1 alleviates the need for RIC-8 in one-cell stage embryos. Our findings suggest a mechanism in which RIC-8 favors generation of Galpha free from Gbetagamma and enables GPR-1/2 to mediate asymmetric cell division. ------------------- Key: 6887 Medline: 15517014 Authors: Poulin G;Nandakumar R;Ahringer J Title: Genome-wide RNAi screens in Caenorhabditis elegans: impact on cancer research. Citation: Oncogene 23: 8340-8345 2004 Type: REVIEW Genes: apr-1 atm-1 brc-1 cdk-4 cep-1 cey-1 daf-1 daf-18 egl-15 erm-1 fum-1 gap-2 him-6 hmr-1 kin-2 lin-35 mev-1 mlh-1 msh-2 msh-6 par-4 pms-2 ptc-1 rib-1 rib-2 sma-4 vhl-1 wrn-1 Abstract: Genes linked to human cancers often function in evolutionary conserved pathways, and research in C. elegans has been instrumental in dissecting some of the pathways affected, such as apoptosis and Ras signalling. The advent of RNA interference (RNAi) technology has allowed high-throughput loss-of-function analyses of C. elegans gene functions. Here we review some of the most recent genome-wide RNAi screens that have been conducted and discuss their impact on cancer research and possibilities for future screens. We also show that genes causally implicated in human cancers are significantly more likely to have a C. elegans homologue than average, validating the use of C. elegans as a cancer gene discovery platform. We foresee that genome-wide RNAi screens in C. elegans will continue to be productive in identifying new cancer gene candidates and will provide further insights into cancer ------------------- Key: 6888 Medline: 15517018 Authors: van Haaften G;Plasterk RHA;Tijsterman M Title: Genomic instability and cancer: scanning the Caenorhabditis elegans genome for tumor suppressors. Citation: Oncogene 23: 8366-8375 2004 Type: REVIEW Genes: brc-1 cep-1 dog-1 mrt-2 msh-2 msh-6 mut-16 rad-5 unc-58 unc-93 Abstract: Maintaining the stability of the genome is critical to normal cell growth and development. The early notion that cancer is the result of mutations in genes controlling cellular growth implied that gene or genome integrity is vital to the prevention of oncogenesis, and many genes and pathways that prevent genomic deterioration have been identified over the past decades. Recent progress in reverse genetic approaches, principally RNA interference, now allows the systematic analysis of gene function on a genomic scale in an animal system. Here, we discuss genomic approaches in the model organism Caenorhabditis elegans, aimed to identify genes and genetic networks that contribute to genome stability and are thus potentially involved in human carcinogenesis. ------------------- Key: 6889 Medline: Authors: Colonius K Title: The dauer mutation of the Caenorhabditis elegans, simulated with the Penna and the Stauffer models. Citation: International Journal of Modern Physics C 15: 939-945 2004 Type: ARTICLE Genes: Abstract: Two aging models were analyzed on whether they can confirm the dauer mutation of the nematode helps to preserve the species. As a result the Penna model shows that populations with daver larvae survive bad environmental conditions, whereas populations without it die out. In the Stauffer model, the advantage of the dauer mutation for the survival is only given under certain conditions. ------------------- Key: 6890 Medline: 15465323 Authors: Schachter H Title: Protein glycosylation lessons from Caenorhabditis elegans. Citation: Current Opinion in Structural Biology 14: 607-616 2004 Type: REVIEW Genes: bre-2 bre-3 bre-4 bre-5 chi-1 chi-2 dad-1 fut-1 fut-2 fut-4 fut-8 gly-1 gly-2 gly-3 gly-4 gly-5 gly-6 gly-7 gly-8 gly-12 gly-13 gly-14 gly-15 gly-16 gly-17 gly-18 gly-20 hse-5 hst-1 mig-17 mig-23 ntp-1 ogt-1 ppp-1 rib-1 rib-2 spe-2 srf-3 sqv-1 sqv-2 sqv-3 sqv-4 sqv-5 sqv-6 sqv-7 sqv-8 Abstract: From observations on human diseases and mutant mice, it has become clear that glycosylation plays a major role in metazoan development. Caenorhabditis elegans provides powerful tools to study this problem that are not available in men or mice. The worm has many genes homologous to mammalian genes involved in glycosylation. Glycobiologists have, in recent years, cloned and expressed some of these genes and studied the effects of mutations on worm development. Recent studies have focused on N-glycosylation, lumenal nucleoside diphosphatases, the resistance of C. elegans to a bacterial toxin and infections, fucosylation and proteoglycans. ------------------- Key: 6891 Medline: 15489852 Authors: Snow JJ;Ou G;Gunnarson AL;Walker MRS;Zhou HM;Brust-Mascher I;Scholey JM Title: Two anterograde intraflagellar transport motors cooperate to build sensory cilia on C. elegans neurons. Citation: Nature Cell Biology 6: 1109-1113 2004 Type: ARTICLE Genes: kap-1 klp-11 klp-20 osm-3 osm-6 Abstract: Cilia have diverse roles in motility and sensory reception and their dysfunction contributes to cilia-related diseases. Assembly and maintenance of cilia depends on the intraflagellar transport (IFT) of axoneme, membrane, matrix and signalling proteins to appropriate destinations within the organelle(1-4). In the current model, these diverse cargo proteins bind to multiple sites on macromolecular IFT particles, which are moved by a single anterograde IFT motor, kinesin-II, from the ciliary base to its distal tip(5,6), where cargo-unloading occurs(1-4,7). Here, we describe the observation of fluorescent IFT motors and IFT particles moving along distinct domains within sensory cilia of wild-type and IFT-motor-mutant Caenorhabditis elegans. We show that two anterograde IFT motor holoenzymes, kinesin-II and Osm-3-kinesin(8), cooperate in a surprising way to control two pathways of IFT that build distinct parts of cilia. Instead of each motor independently moving its own specific cargo to a distinct destination, the two motors function redundantly to transport IFT particles along doublet microtubules adjacent to the transition zone to form the axoneme middle segment(9). Next, Osm-3-kinesin alone transports IFT particles along the distal singlet microtubules to stabilize the distal segment. Thus, the subtle coordinate activity of these IFT motors creates two sequential ------------------- Key: 6892 Medline: 15525531 Authors: Lamont LB;Crittenden SL:Bernstein D;Wickens M;Kimble J Title: FBF-1 and FBF-2 regulate the size of the mitotic region in the C. elegans germline. Citation: Developmental Cell 7: 697-707 2004 Type: ARTICLE Genes: fbf-1 fbf-2 gld-1 gld-2 glp-1 Abstract: In the C. elegans germline, GLIP-1/Notch signaling and two nearly identical RNA binding proteins, FBF-1 and FBF-2, promote proliferation. Here, we show that the fbf-1 and fbf-2 genes are largely redundant for promoting mitosis but that they have opposite roles in fine-tuning the size of the mitotic region. The mitotic region is smaller than normal in fbf-1 mutants but larger than normal in fbf-2 mutants. Consistent with gene-specific roles, fbf-2 expression is limited to the distal germline, while fbf-1 expression is broader. The fbf-2 gene, but apparently not fbf-1, is controlled by GLP-1/Notch signaling, and the abundance of FBF-1 and FBF-2 proteins is limited by reciprocal 3'UTR repression. We propose that the divergent fbf genes and their regulatory subnetwork enable a precise control over size of the mitotic region. Therefore, fbf-1 and fbf-2 provide a paradigm for how recently duplicated genes can diverge to fine-tune patterning during animal ------------------- Key: 6893 Medline: Authors: 15517015 Title: Towards full employment: using RNAi to find roles for the redundant. Citation: Oncogene 23: 8346-8352 2004 Type: REVIEW Genes: dpl-1 goa-1 gpa-16 Abstract: Cancer is a genetic disease that ultimately results from the failure of cells to respond correctly to diverse signals. Signal transduction and signal integration are highly complex, requiring the combinatorial interaction of multiple genes. Classical genetics in model organisms including Caenorhabditis elegans has been of immense use in identifying nonredundant components of conserved signalling pathways. However, it is likely that there is much functional redundancy in the informational processing machinery of metazoan cells; we therefore need to develop methods for uncovering such redundant functions in model organisms if we are to use them to understand complex gene interactions and oncogene cooperation. RNAi may provide a powerful tool to probe redundancy in informational networks. In this review, I set out some of the progress made so far by classical genetics in understanding redundancy in gene networks, and outline how RNAi may allow us to approach this problem more systematically in C. elegans. In particular, I discuss the use of genome-wide RNAi screens in C. elegans to identify synthetic lethal interactions and compare this with synthetic lethal interaction analysis in Saccharomyces cerevisiae. ------------------- Key: 6894 Medline: 15464131 Authors: Schafer WR Title: Addiction research in a simple animal model: the nematode Caenorhabditis elegans. Citation: Neuropharmacology 47: 123-131 2004 Type: REVIEW Genes: dop-1 mec-2 mec-4 slo-1 unc-2 unc-29 unc-36 unc-38 Abstract: Genetic analysis in the nematode C elegans has provided important insights into many aspects of neuronal cell biology, including functions related to addiction. Specifically, genetic and molecular screens to have been used to identify molecules involved in long-term responses to drugs of abuse and to analyze the mechanisms underlying their effects on nervous system development, plasticity, and behavior. This review presents a personal view of addiction-related research in C elegans, and includes a discussion of technical innovations that have facilitated neurobiological analyses in C elegans and a look at future prospects drug addiction research in simple animal models. ------------------- Key: 6895 Medline: 15314097 Authors: Merris M;Kraeft J;Tint GS;Lenard J Title: Long-term effects of sterol depletion in C. elegans: sterol content of synchronized wild-type and mutant populations. Citation: Journal of Lipid Research 45: 2044-2051 2004 Type: ARTICLE Genes: clk-1 daf-9 daf-12 daf-16 npc-1 Abstract: Three major long-term effects of sterol deprivation in Caenorhabditis elegans are described. 1) The life expectancy of sterol-deprived wild-type animals is decreased by more than 40%. Similar decreases are found in animals carrying mutations in the daf-9, daf-12, daf-16, and clk-1 genes, suggesting that previously described aging pathways involving these genes are not involved in the life-extending effects of sterols. 2) There is a premature loss of motility, measured by response to mild touch. 3) There is a rapid postreproductive onset of sarcopenia (muscle wasting) as measured by total body fluorescence in a myo3::GFP-expressing strain. We also report that five sterols (the desmethylsterols cholesterol, 7-dehydrocholesterol, and lathosterol and the 4alpha-methyl sterols lophenol and 4alpha-methyl-cholesta-Delta8(14)-en-3beta-ol) are found in significant amounts at all stages of development and aging in cholesterol-fed animals. Supplying any one of these as the sole sterol confers similar protection from the long-term effects of sterol deprivation. These findings suggest that sterols are required continuously throughout the animal's life. ------------------- Key: 6896 Medline: 15394906 Authors: Lytle BL;Peterson FC;Qiu SH;Luo M;Zhao Q;Markley JL;Volkman BF Title: Solution structure of a ubiquitin-like domain from tubulin-binding cofactor B. Citation: Journal of Biological Chemistry 279: 46787-46793 2004 Type: ARTICLE Genes: Abstract: Proper folding and assembly of tubulin alphabeta-heterodimers involves a stepwise progression mediated by a group of protein cofactors A through E. Upon release of the tubulin monomers from the chaperonin CCT, they are acted upon by each cofactor in the folding pathway through a unique combination of protein interaction domains. Three-dimensional structures have previously been reported for cofactor A and the C-terminal CAP-Gly domain of cofactor B (CoB). Here we report the NMR structure of the N-terminal domain of Caenorhabditis elegans CoB and show that it closely resembles ubiquitin as was recently postulated on the basis of bioinformatic analysis (Grynberg, M., Jaroszewski, L., and Godzik, A. (2003) BMC Bioinformatics 4, 46). CoB binds partially folded alpha-tubulin monomers, and a putative tubulin-binding motif within the N-terminal domain is identified from sequence and structure comparisons. Based on modeling of the homologous cofactor E ubiquitin-like domain, we hypothesize that cofactors B and E may associate via their beta-grasp domains in a manner analogous to the PB1 and caspase-activated deoxyribonuclease superfamily of protein ------------------- Key: 6897 Medline: 15498551 Authors: Ami D;Natalello A;Zullini A;Doglia SM Title: Fourier transform infrared microspectroscopy as a new tool for nematode studies. Citation: FEBS Letters 576: 297-300 2004 Type: ARTICLE Genes: Abstract: We report the results of a microspectroscopy study on the Fourier transform infrared (FT-IR) absorption spectra of Caenorhabditis elegans, collected from the different parts of a single intact specimen - pharynx, intestine and tail regions. The principal absorption bands were assigned to the molecular species present in C. elegans, with an excellent reproducibility for the pharynx spectrum. These results enabled us to explore if FT-IR microspectroscopy could offer a new tool for nematode identification. As an example, the discrimination among four well characterised nematode taxa is reported. The FT-IR results completely match those obtained by Blaxter and colleagues through molecular biology [Nature 392 (1998) 71]. ------------------- Key: 6898 Medline: 15342467 Authors: Ciosk R;DePalma M;Priess JR Title: ATX-2, the C. elegans ortholog of ataxin 2, functions in translational regulation in the germline. Citation: Development 131: 4831-4841 2004 Type: ARTICLE Genes: atx-2 fem-1 fem-3 fog-2 gld-1 gld-2 glp-1 mex-3 pab-1 rme-2 tra-2 Abstract: Human ataxin 2 is a protein of unknown function that is implicated in the neurodegenerative disorder spinocerebellar ataxia type 2. We found that the C. elegans ortholog of ataxin 2, ATX-2, forms a complex with PAB-1, a cytoplasmic poly(A)-binding protein, and that ATX-2 is required for development of the germline. In the absence of ATX-2, proliferation of stem cells is reduced, and the germline is abnormally masculinized. These defects appear to result from inappropriate translational regulation that normally is mediated by the conserved KH-domain protein GLD-1. We find that MEX-3, a second KH-domain protein, exhibits a novel, ATX-2-dependent role in preventing inappropriate translation in the germline stem cells. Together, our results suggest that ATX-2 functions in translational regulation that is mediated by GLD-1 and ------------------- Key: 6899 Medline: 15498497 Authors: Couwenbergs C;Spilker AC;Gotta M Title: Control of embryonic spindle positioning and G(alpha) activity by C. elegans RIC-8. Citation: Current Biology 14: 1871-1876 2004 Type: ARTICLE Genes: goa-1 gpa-16 gpr-1 gpr-2 let-99 lin-5 ric-8 Abstract: Asymmetric spindle positioning is of fundamental importance for generating cell diversity during development. In the C. elegans 1 cell embryo, spindle positioning has been shown to depend on heterotrimeric G protein signaling. Two Galpha subunits, GOA-1 and GPA-16 (hereafter Galpha), and receptor independent activators of G protein signaling GPR-1 and GPR-2 (GPR1/2) are required for proper regulation of spindle positioning [1]. However, it remains unclear whether Galpha regulates spindle positioning in its GDP or GTP bound form. Here, we investigate the role of RIC-8 in this pathway. RIC-8 was genetically shown to act in concert with goa-1 to regulate centrosome movements in C. elegans [2, 3]. Interestingly, mammalian RIC-8 was recently found to behave as a GEF for Galpha subunits in vitro [4]. We show that reduction of function of ric-8 results in a 1 cell embryo phenotype very similar to the phenotype of embryos depleted of Galpha. RIC-8 is able to directly bind to GOA-1, preferentially to GOA-1-GDP, consistent with a GEF role. RIC-8 is localized at the embryo cortex, and its activity is essential for the asymmetric localization of GPR-1/2. We suggest that RIC-8 directly modulates Galpha activity and that Galpha-GTP is the signaling molecule regulating spindle positioning in the early embryo. ------------------- Key: 6900 Medline: 15498499 Authors: Thomas-Vernig CL;Sims PA;Simske JS;Hardin J Title: The inositol 1,4,5-trisphosphate receptor regulates epidermal cell migration in Caenorhabditis elegans. Citation: Current Biology 14: 1882-1887 2004 Type: ARTICLE Genes: cmd-1 itr-1 sca-1 Abstract: Polarized migration and spreading of epithelial sheets is important during many processes in vivo, including embryogenesis and wound healing. However, the signaling pathways that regulate epithelial migrations are poorly understood. To identify molecular components that regulate the spreading of epithelial sheets, we performed a screen for mutations that perturb epidermal cell migration during embryogenesis in Caenorhabditis elegans. We identified one mutant (jc5) as a weak mutation in itr-1, which encodes the single inositol 1,4,5-trisphosphate receptor (ITR) in C. elegans. During the migration of the embryonic epidermis, jc5 embryos display defects including misdirected migration or premature cessation of migration. Cells that halt their migration have disorganized F-actin and display reduced filopodial protrusive activity at their leading edge. Furthermore, some filopodia formed by epidermal cells in itr-(jc5) embryos exhibit abnormally long lifetimes. Pharmacological studies with the inositol 1,4,5-trisphosphate antagonist xestospongin C phenocopy these defects, confirming that ITR function is important for proper epidermal migration. Our results provide the first molecular evidence that movements of embryonic epithelial cell sheets can be controlled by ITRs and suggest that such regulation may be a widespread mechanism for coordinating epithelial cell movements during ------------------- Key: 6901 Medline: 15502826 Authors: Barrett PL;Fleming JT;Gobel V Title: Targeted gene alteration in Caenorhabditis elegans by gene conversion. Citation: Nature Genetics 56: 1231-1237 2004 Type: ARTICLE Genes: frm-3 mut-2 mut-7 tkr-1 Abstract: Now that some genomes have been completely sequenced, the ability to direct specific mutations into genomes is particularly desirable. Here we present a method to create mutations in the Caenorhabditis elegans genome efficiently through transgene-directed, transposon-mediated gene conversion. Engineered deletions targeted into two genes show that the frequency of obtaining the desired mutation was higher using this approach than using standard transposon insertion-deletion approaches. We also targeted an engineered green fluorescent protein insertion-replacement cassette to one of these genes, thereby confirming that custom alleles of different types can be created in vitro to make the corresponding mutations in vivo. This approach should also be applicable to heterologous transposons in C elegans and other organisms, including vertebrates. ------------------- Key: 6902 Medline: Authors: Hirotsu T;Saeki S;Yamamoto M;Iino Y Title: The Ras-MAPK pathway is important for olfaction in Caenorhabditis elegans. Citation: Nature 432: 653- 2004 Type: CORRECT Genes: ksr-1 let-60 mek-2 mpk-1 Abstract: ------------------- Key: 6903 Medline: Authors: Bishop T;Lau KW;Epstein ACR;Kim SK;Jiang M;O'Rourke D;Pugh CW;Gleadle JM;Taylor MS;Hodgkin J;Ratcliffe PJ Title: Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans. Citation: PLoS Biology 2: 1549-1560 2004 Type: ARTICLE Genes: bli-4 cah-4 dpy-11 dpy-18 egl-9 fmo-12 gon-1 hif-1 let-268 mig-17 nhr-57 phy-2 sqt-3 unc-6 vhl-1 Abstract: ------------------- Key: 6904 Medline: Authors: Matyash V;Entchev EV;Mende F;Wilsch-Brauninger M;Thiele C;Schmidt AW;Knolker JH;Ward S;Kurzchalia TV Title: Sterol-derived hormone(s) controls entry into diapause in Caenorhabditis elegans by consecutive activation of DAF-12 and DAF-16. Citation: PLoS Biology 2: 1561-1571 2004 Type: ARTICLE Genes: daf-2 daf-3 daf-5 daf-6 daf-7 daf-9 daf-10 daf-12 daf-16 daf-22 Abstract: ------------------- Key: 6905 Medline: 10965035 Authors: Satoh A;Hazuki M;Kojima K;Hirabayashi J;Matsumoto I Title: Ligand-binding properties of annexin from Caenorhabditis elegans (annexin XVI, Nex-1). Citation: Journal of Biochemistry 136: 407- 2004 Type: ARTICLE Genes: Abstract: ------------------- Key: 6906 Medline: Authors: Goodman MB;Lumpkin EA;Ricci A;Tracey D;Kernan M;Nicolson T Title: Molecules and mechanisms of mechanotransduction. Citation: Journal of Neuroscience 24: 9220-9222 2004 Type: REVIEW Genes: Abstract: ------------------- Key: 6907 Medline: 15562624 Authors: Huamanchay O;Genzlinger L;Iglesias M;Ortega YR Title: Ingestion of Cryptosporidium oocysts by Caenorhabditis elegans. Citation: Journal of Parasitology 90: 1176-1178 2004 Type: ARTICLE Genes: Abstract: Cryptosporidium parvum has been associated with outbreaks of human illness by consumption of contaminated water, fresh fruits, and vegetables. Free-living nematodes may play a role in pathogen transmission in the environment. Caenorhabditis elegans is a free-living soil nematode that has been extensively studied and serves as a good model to study possible transmission of C. parvum oocysts that may come into contact with produce before harvest. The objective of this study was to determine whether C. elegans could serve as a potential mechanical vector for transport of infectious C parvum and Cyclospora cayetanensis in agricultural settings and whether C. elegans could ingest, excrete, and protect oocysts from desiccation. Seventy to 85% of worms ingested between 0 and 500 oocysts after 1 and 2 hr incubation with oocysts. Most of the nematodes ingested between 101 and 200 oocysts after 2 hr. Intact oocysts and empty shells were excreted by nematodes. Infectivity was determined by the neonatal assay with different treatments of worms (intact or homogenized) or oocysts or both. Adult C. elegans containing C. parvum kept in water were infective for mice. In conclusion, C. elegans adults can ingest and excrete C. parvum oocysts. Caenorhabditis elegans containing C. parvum oocysts can infect mice but does not seem to protect oocysts from extreme desiccation at 23 C incubation of a day or longer. Cyclospora oocysts were not ingested by C. elegans. The role of free-living nematodes in produce contamination ------------------- Key: 6908 Medline: 15501449 Authors: Ding M;Woo WM;Chisholm AD Title: The cytoskeleton and epidermal morphogenesis in C. elegans. Citation: Experimental Cell Research 301: 84-90 2004 Type: REVIEW Genes: ajm-1 dlg-1 hmp-1 hmp-2 hmr-1 ifa-2 ifa-3 ifb-1 let-413 let-502 mel-11 mlc-4 nmy-1 nmy-2 sma-1 spc-1 vab-9 vab-10 vab-19 Abstract: During Caenorhabditis elegans development, the process of epidermal elongation converts the bean-shaped embryo into the long thin shape of the larval worm. Epidermal elongation results from changes in the shape of epidermal cells, which in turn result from changes in the epidermal cytoskeleton, the extracellular matrix, and in cell-matrix adhesion junctions. Here, we review the roles of cytoskeletal filament systems in epidermal cell shape change during elongation. Genetic and cell biological analyses have established that all three major cytoskeletal filament systems (actin microfilaments, microtubules, and intermediate filaments (IFs)) play distinct and essential roles in epidermal cell shape change. Recent work has also highlighted the importance of communication between these systems for their integrated function in epidermal elongation. Epidermal cells undergo reciprocal interactions with underlying muscle cells, which regulate the position and function of IF-containing cell-matrix adhesion structures within the epidermis. Elongation thus exemplifies the reciprocal tissue interactions of ------------------- Key: 6909 Medline: 15530389 Authors: Zhang S;Arnadottir J;Keller C;Caldwell GA;Yao CA;Chalfie M Title: MEC-2 is recruited to the putative mechanosensory complex in C. elegans touch receptor neurons through its stomatin-like domain. Citation: Current Biology 14: 1888-1896 2004 Type: ARTICLE Genes: mec-2 mec-4 mec-6 mec-10 unc-24 Abstract: Background: The response to gentle body touch in C. elegans requires a degenerin channel complex containing four proteins (MEC-2, MEC-4, MEC-6, and MEC-10). The central portion of the integral membrane protein MEC-2 contains a stomatin-like region that is highly conserved from bacteria to mammals. The molecular function of this domain in MEC-2, however, is unknown. Results: Here, we show that MEC-2 colocalizes with the degenerin MEC-4 in regular puncta along touch receptor neuron processes. This punctate localization requires the other channel complex proteins. The stomatin-like region of MEC-2 interacts with the intracellular cytoplasmic portion of MEC-4. Missense mutations in this region that destroy the interaction also disrupt the punctate localization and degenerin-regulating function of MEC-2. Missense mutations outside this region apparently have no effect on the punctate localization but significantly reduce the regulatory effect of MEC-2 on the MEC-4 degenerin channel. A second stomatin-like protein, UNC-24, colocalizes with MEC-2 in vivo and coimmunoprecipitates with MEC-2 and MEC-4 in Xenopus oocytes; unc-24 enhances the touch insensitivity of temperature-sensitive alleles of rnec-4 and mec-6. Conclusion: Two stomatin homologs, MEC-2 and UNC-24, interact with the MEC-4 degenerin through their stomatin-like regions, which act as protein binding domains. At least in the case of MEC-2, this binding allows its nonstomatin domains to regulate channel activity. Stomatin-like regions in other proteins may serve a similar protein binding function. ------------------- Key: 6910 Medline: 15543163 Authors: Jabbour AM;Ho PK;Puryer MA;Ashley DM;Ekert PG;Hawkins CJ Title: The Caenorhabditis elegans CED-9 protein does not directly inhibit the caspase CED-3, in vitro nor in yeast. Citation: Cell Death and Differentiation 11: 1309-1316 2004 Type: ARTICLE Genes: ced-3 ced-4 ced-9 Abstract: A genetically defined pathway orchestrates the removal of 131 of the 1090 somatic cells generated during the development of the hermaphrodite nematode Caenorhabditis elegans. Regulation of apoptosis is highly evolutionarily conserved and the nematode cell death pathway is a valuable model for studying mammalian apoptotic pathways, the dysregulation of which can contribute to numerous diseases. The nematode caspase CED-3 is ultimately responsible for the destruction of worm cells in response to apoptotic signals, but it must first be activated by CED-4. CED-9 inhibits programmed cell death and considerable data have demonstrated that CED-9 can directly bind and inhibit CED-4. However, it has been suggested that CED-9 may also directly inhibit CED-3. In this study, we used a yeast-based system and biochemical approaches to explore this second potential mechanism of action. While we confirmed the ability of CED-9 to inhibit CED-4, our data argue that CED-9 can not directly inhibit CED-3. ------------------- Key: 6911 Medline: 15364921 Authors: Veljkovic E;Bacconi A;Stetak A;Hajnal A;Stasiuk S;Skelly PJ;Forster I;Shoemaker CB;Verrey F Title: Aromatic amino acid transporter AAT-9 of Caenorhabditis elegans localizes to neurons and muscle cells. Citation: Journal of Biological Chemistry 279: 49268-49273 2004 Type: ARTICLE Genes: aat-1 aat-3 aat-9 atg-1 atg-2 Abstract: The Caenorhabditis elegans genome encodes nine homologues of mammalian glycoprotein-associated amino acid transporters. Two of these C. elegans proteins (AAT-1 and AAT-3) have been shown to function as catalytic subunits (light chains) of heteromeric amino acid transporters. These proteins need to associate with a glycoprotein heavy chain subunit (ATG-2) to reach the cell surface in a manner similar to that of their mammalian homologues. AAT-1 and AAT-3 contain a cysteine residue in the second putative extracellular loop through which a disulfide bridge can form with a heavy chain. In contrast, six C. elegans members of this family (AAT-4 to AAT-9) lack such a cysteine residue. We show here that one of these transporter proteins, AAT-9, reaches the cell surface in Xenopus oocytes without an exogenous heavy chain and that it functions as an exchanger of aromatic amino acids. Two-electrode voltage clamp experiments demonstrate that AAT-9 displays a substrate-activated conductance. Immunofluorescence shows that it is expressed close to the pharyngeal bulbs within C. elegans neurons. The selective expression of an aat-9 promoter-green fluorescent protein construct in several neurons of this region and in wall muscle cells around the mouth supports and extends these localization data. Taken together, the results show that AAT-9 is expressed in excitable cells of the nematode head and pharynx in which it may provide a pathway for aromatic ------------------- Key: 6912 Medline: Authors: Hockelmann C;Moens T;Juttner F Title: Odor compounds from cyanobacterial biofilms acting as attractants and repellents for free-living nematodes. Citation: Limnology & Oceanography 49: 1809-1819 2004 Type: ARTICLE Genes: Abstract: Nematodes can both taste and smell an array of compounds, but whether and how these senses effect their capacity to locate microhabitats in aquatic environments is not known. Cyanobacterial biofilms may offer structure, shelter, and food for nematodes and are known to produce a variety of odor compounds. We studied the chemotaxis response of the freshwater nematode Bursilla monhystera (Rhabditidae) and the terrestrial model organism Caenorhabditis elegans (Rhabditidae) to odors of cyanobacterial biofilms. We used gas chromatography-mass spectometry ultra-trace analysis to identify odor compounds produced by two epilithic cyanobacterial biofilms of Lake Zurich. We also studied artificial, axenic biofilms of Plectonema sp., Calothrix sp., and Calothrix parietina, to assign these compounds to the metabolism of the cyanobacteria. The axenic cyanobacteria and epilithic biofilms had many odor compounds in common. B. monhystera was significantly attracted to Plectonema sp. and C. parietina but not to Calothrix sp. C. elegans, in contrast, was not attracted to any of these cyanobacterial biofilms. Furthermore, we applied a multicomponent mixture of odor compounds and found significant attraction for both nematodes. Although C. elegans was also attracted by a variety of single odor compounds, B. monhystera was not attracted to any of the volatiles tested. beta-ionone even repelled this species. Our experiments demonstrate that aquatic nematodes are attracted to cyanobacterial biofilms using odor compounds as chemical cues. In contrast to the model organism, C. elegans, the chemotaxis of the aquatic nematode is elicited by a multicomponent odor rather than by single compounds. ------------------- Key: 6913 Medline: 15540462 Authors: Karabinos A;Schunemann J;Weber K Title: Most genes encoding cytoplasmic intermediate filament (IF) proteins of the nematode Caenorhabditis elegans are required in late embryogenesis. Citation: European Journal of Cell Biology 83: 457-468 2004 Type: ARTICLE Genes: Abstract: Intestinal cells of C. elegans show an unexpectedly high complexity of cytoplasmic intermediate filament (IF) proteins. Of the 11 known IF genes six are coexpressed in the intestine, i.e. genes B2, C1, C2, D1, D2, and E1. Specific antibodies and GFP-promoter constructs show that genes B2, D1, D2, and E1 are exclusively expressed in intestinal cells. Using RNA interference (RNAi) by microinjection at 25 degreesC rather than at 20 degreesC we observe for the first time lethal phenotypes for C1 and D2. RNAi at 25 degreesC also shows that the known A1 phenotype occurs already in the late embryo after microinjection and is also observed by feeding which was not the case at 20 degreesC. Thus, RNAi at 25 degreesC may also be useful for the future analysis of other nematode genes. Finally, we show that triple RNAi at 20 degreesC is necessary for the combinations B2, D1, E1 and B2, D1, D2 to obtain a phenotype. Together with earlier results on genes A1, A2, A3, B1, and C2 RNAi phenotypes are now established for all 11 IF genes except for the A4 gene. RNAi phenotypes except for A2 (early larval lethality) and C2 (adult phenotype) relate to the late embryo. We conclude that in C. elegans cytoplasmic IFs are required for tissue integrity including late embryonic stages. This is in strong contrast to the mouse, where ablation IF genes apparently does not affect the embryo proper. ------------------- Key: 6914 Medline: Authors: Claeys M;Vanhecke D;Couvreur M;Tytgat T;Coomans A;Borgonie Title: High-pressure freezing and freeze substitution of gravid Caenorhabditis elegans (Nematoda: Rhabditida) for transmission electron microscopy. Citation: Nematology 6: 319-327 2004 Type: ARTICLE Genes: Abstract: Because chemical fixatives have a profound negative influence on tissue morphology and antigenicity, alternative fixation methods must be applied for some purposes. In this work we used high-pressure freezing (HPF) followed by freeze substitution to maximally preserve antigenicity and morphology. We developed a pipette method for bringing living Caenorhabditis elegans nematodes into the HPF recipient. Using cellulose tubes, it is possible to select individual nematodes for fixation. We were able to HPF complete adults and preserve the morphology in an enhanced fashion compared to chemically fixed tissue. Cellular organelles, especially mitochondria, were much better preserved. Uterine embryos protected by the intact eggshell were excellently preserved without the need for elaborate techniques. Antigenicity with MH27 and ICB4 antiscra was tested. With the MH27 serum, an adequate, reproducible, specific binding pattern with chemically fixed tissue could Only be achieved using purified antibodies, whereas with high-pressure freezing, unpurified MH27 antisera was effective. For ICB4 antisera, a reproducible specific binding pattern was achieved at a concentration of primary antiserum 1000x lower than that ------------------- Key: 6915 Medline: 15569254 Authors: Rex E;Molitor SC;Hapiak V;Xiao H;Henderson M;Komuniecki R Title: Tyramine receptor (SER-2) isoforms are involved in the regulation ofpharyngeal pumping and foraging behavior in Caenorhabditis elegans. Citation: Journal of Neurochemistry 91: 1104-1115 2004 Type: ARTICLE Genes: ser-2 Abstract: Octopamine regulates essential processes in nematodes; however, little is known about the physiological role of its precursor, tyramine. In the present study, we have characterized alternatively spliced Caenorhabditis elegans tyramine receptor isoforms (SER-2 and SER-2A) that differ by 23 amino acids within the mid-region of the third intracellular loop. Membranes prepared from cells expressing either SER-2 or SER-2A bind [H-3]lysergic acid diethylamide (LSD) in the low nanomolar range and exhibit highest affinity for tyramine. Similarly, both isoforms exhibit nearly identical K-i values for a number of antagonists. In contrast, SER-2A exhibits a significantly lower affinity than SER-2 for other physiologically relevant biogenic amines, including octopamine. Pertussis toxin treatment reduces affinity for both tyramine and octopamine, especially for octopamine in membranes from cells expressing SER-2, suggesting that the conformation of the mid-region of the third intracellular loop is dictated by G-protein interactions and is responsible for the differential tyramine/octopamine affinities of the two isoforms. Tyramine reduces forskolin-stimulated cAMP levels in HEK293 cells expressing either isoform with nearly identical IC50 values. Tyramine, but not octopamine, also elevates Ca2+ levels in cells expressing SER-2 and to a lesser extent SER-2A. Most importantly, ser-2 null mutants (pk1357) fail to suppress head movements while reversing in response to nose-touch, suggesting a role for SER-2 in the regulation of foraging behavior, and fail to respond to tyramine in assays measuring serotonin-dependent pharyngeal pumping. These are the first reported functions for SER-2. These results suggest that C. elegans contains tyramine receptors, that individual SER-2 isoforms may differ significantly in their sensitivity to other physiologically relevant biogenic amines, such as octopamine (OA), and that tyraminergic signaling may be important in the regulation of key processes in nematodes. ------------------- Key: 6916 Medline: 15522291 Authors: Hong M;Kwon JY;Shim J;Lee J Title: Differential hypoxia response of hsp-16 genes in the nematode. Citation: Journal of Molecular Biology 344: 369-381 2004 Type: ARTICLE Genes: apm-1 hif-1 hsp-16 hsp-16.1 hsp-16.2 hsp-16.41 hsp-16.48 Abstract: Small heat shock proteins are induced by various stresses. We here report the differential hypoxia responses of the hsp-16 genes in the nematode. The hsp-16.1 and hsp-16.2 genes in Caenorhabditis elegans responded to hypoxia, while hsp-16.41 and hsp-16.48, which share the promoter regions with hsp-16.1 and hsp-16.2, respectively, did not. For comparative genomic analysis, we identified ten hsp-16 genes in the nematode C. briggsae from the genome database. The comparison of the promoter sequences revealed a new conserved sequence block, CAC(A/T)CT, that was required for the orientation-dependent hypoxia. response, but not for other stress responses such as heat or ethanol. We propose a working model for the orientation-dependent promoter usage between two genes sharing the promoter region. We also discuss a possible application of the hypoxia-inducible promoter for conditional gene expression. ------------------- Key: 6917 Medline: 15522294 Authors: Zhao Z;Sheps JA;Ling V;Fang LL;Baillie DL Title: Expression analysis of ABC transporters reveals differential functions of tandemly duplicated genes in Caenorhabditis elegans. Citation: Journal of Molecular Biology 344: 409-417 2004 Type: ARTICLE Genes: abt-5 cft-1 haf-2 haf-3 haf-4 haf-5 haf-7 haf-9 mrp-1 mrp-2 mrp-5 mrp-7 pgp-1 pgp-2 pgp-3 pgp-4 pgp-5 pgp-6 pgp-7 pgp-8 pgp-9 pgp-10 pgp-11 pgp-12 pgp-13 pgp-14 pgp-15 pmp-1 pmp-2 pmp-3 pmp-4 pmp-5 rfc-1 tag-167 Abstract: We have previously identified 60 predicted ABC transporter genes in the Caenorhabditis elegans genome and classified them into eight groups. As an initial step towards understanding how these putative ABC genes work in worms, we generated promoter-fluorescent protein fusions for the entire family to address when and where these genes are turned on in vivo. Both Aequoria green fluorescent protein (GFP) and Discosoma red fluorescent protein (RFP) were used as reporters in our transgenic assay. Observable expression is more frequently seen from fusions to genes in subfamilies B, C, D and E than those in subfamilies A and G. Sixteen worm ABC genes are found in tandem duplications, forming two four-gene clusters and four two-gene clusters. Fifteen out of the 16 duplicated gene promoters drove different or partially overlapping expression patterns, suggesting active functions for these duplicated genes. Furthermore, our results suggest that an internal promoter can cause differential expression of genes within an operon. Finally, our observations suggest that it is possible for coding sequences to function as a regulatory region for a neighbouring gene. ------------------- Key: 6918 Medline: 15364955 Authors: Paschinger K;Rendic D;Lochnit G;Jantsch V;Wilson IBH Title: Molecular basis of anti-horseradish peroxidase staining in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 279: 49588-49598 2004 Type: ARTICLE Genes: fut-1 fut-3 fut-4 fut-5 fut-6 gly-12 gly-13 gly-14 Abstract: Cross-reactivity with anti-horseradish peroxidase antiserum is a feature of many glycoproteins from plants and invertebrates; indeed staining with this reagent has been used to track neurons in Drosophila melanogaster and Caenorhabditis elegans. Although in insects the evidence indicates that the cross-reaction results from the presence of core alpha1,3-fucosylated N-glycans, the molecular basis for anti-horseradish peroxidase staining in nematodes has been unresolved to date. By using Western blots of wild-type and mutant C. elegans extracts in conjunction with specific inhibitors, we show that the cross-reaction is due to core alpha1,3-fucosylation. Of the various mutants examined, one with a deletion of the fut-1 (K08F8.3) gene showed no reaction to anti-horseradish peroxidase; the molecular phenotype was rescued by injection of either the K08F8 cosmid or the fut-1 open reading frame under control of the let-858 promoter. Furthermore, expression of fut-1 cDNA in Pichia and insect cells in conjunction with antibody staining, high pressure liquid chromatography, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry analyses showed that FUT-1 is a core alpha1,3-fucosyltransferase with an unusual substrate specificity. It is the only core fucosyltransferase in plants and animals described to date that does not require the prior action of ------------------- Key: 6919 Medline: 15470638 Authors: Laugsch M;Schierenberg E Title: Differences in maternal supply and early development of closely related nematode species. Citation: International Journal of Developmental Biology 48: 655-662 2004 Type: ARTICLE Genes: mes-1 Abstract: Comparative analyses revealed considerable differences in embryonic pattern formation and cell-specification between Caenorhabditis elegans and Acrobeloides nanus, members of two neighboring nematode clades. While C. elegans develops very rapidly, A. nanus needs 4-5 times as long. To investigate whether differences during early embryogenesis could be related to developmental tempo, we studied three more slowly developing representatives of the genus Rhabditis, thus close relatives of C. elegans. Besides differences in body size and mode of reproduction, they differ from C. elegans in the order of cleavages, germline behavior and requirement for early zygotic transcription, showing evident similarities to A. nanus. The distinct variations in cell-cycle rhythms and arrest after inhibition of transcription appear to reflect a species-specific interplay in the timing between exhausting maternal supplies and making available newly transcribed gene products. Looking for the reversal of cleavage polarity in the germline present in C. elegans but not in A. nanus, two of the studied species express this distinct feature only in a later cell generation. We found that a C. elegans mutant in the mes-1 gene shows a similar deviation. Concerning specification of the gut cell lineage and the potential to compensate for lost cells, the three tested Rhabditis species behave less regulatively, like C. elegans; in contrast to A. nanus, the gut precursor EMS requires an inductive signal from the germline cell P-2 and an experimentally eliminated EMS cell is not replaced by a neighboring blastomere. In conclusion, embryogenesis of the examined Rhabditis species includes features of both the fast-developing C. elegans and the slow-developing A. ------------------- Key: 6920 Medline: 15514056 Authors: Maine EM;Hansen D;Springer D;Vought VE Title: Caenorhabditis elegans atx-2 promotes germline proliferation and the oocyte fate. Citation: Genetics 168: 817-830 2004 Type: ARTICLE Genes: atx-1 ego-4 fog-2 gld-1 gld-2 glp-1 ncc-1 nos-3 tra-2 Abstract: In the Caenorhabditis elegans germline, proliferation is induced by Notch-type signaling. Entry of germ cells into meiosis is triggered by activity of the GLD-1 and GLD-2 pathways, which function redundantly to promote meiosis and/or inhibit proliferation. Activation of the germline Notch-type receptor, GLP-1, ultimately inhibits the activities of the GLD-1 and GLD-2 pathways. We previously identified several ego (enhancer of glp-1) genes that promote germline proliferation and interact genetically with the GLP-1 signaling pathway. Here, we show that atx-2 is an ego gene. Our data suggest that ATX-2 is not a positive regulator of the GLP-1 signaling pathway and GLP-1 signaling is not the sole positive regulator of ATX-2 activity. Moreover, our data indicate that GLP-1 must have an additional function, which may be to repress activity of a third meiotic entry pathway that would work in parallel with the GLD-1 and GLD-2 pathways. In addition to its role in proliferation, ATX-2 acts downstream of FOG-2 to promote the female germline fate. ------------------- Key: 6921 Medline: 15514057 Authors: Hawasli AH;Saifee O;Liu C;Nonet ML;Crowder CM Title: Resistance to volatile anesthetics by mutations enhancing excitatory neurotransmitter release in Caenorhabditis elegans. Citation: Genetics 168: 831-843 2004 Type: ARTICLE Genes: dgk-1 egl-8 egl-30 slo-1 unc-43 unc-64 Abstract: The molecular mechanisms whereby volatile general anesthetics (VAs) disrupt behavior remain undefined. In Caenorhabditis elegans mutations in the gene unc-64, which encodes the presynaptic protein syntaxin 1A, produce large allele-specific differences in VA sensitivity. UNC-64 syntaxin normally functions to mediate fusion of neurotransinitter vesicles with the presynaptic membrane. The precise role of syntaxin in the VA mechanism is as yet unclear, but a variety of results suggests that a protein interacting with syntaxin to regulate neuro transmitter release is essential for VA action in C. elegans. To identify additional proteins that function with syntaxin to control neurotransmitter release and VA action, we screened for suppressors of the phenotypes produced by unc-64 reduction of function. Loss-of-function mutations in slo-1, which encodes a Ca2+-activated K+ channel, and in unc-43, which encodes CaM-kinase II, and a gain-of-function mutation in egl-30, which encodes Gqalpha, were isolated as syntaxin suppressors. The slo-1 and egl-30 mutations conferred resistance to VAs, but unc-43 mutations did not. The effects of slo-l and egl-30 on VA sensitivity can be explained by their actions upstream or parallel to syntaxin to increase the level of excitatory neurotransmitter release. These results strengthen the link between transmitter release and VA action. ------------------- Key: 6922 Medline: 15514058 Authors: de Jong L;Meng Y;Dent J;Hekimi S Title: Thiamine pyrophosphate biosynthesis and transport in the nematode Caenorhabditis elegans. Citation: Genetics 168: 845-854 2004 Type: ARTICLE Genes: clk-1 eat-4 eat-6 myo-2 myo-3 tpk-1 Abstract: Thiamine (vitamin B1) is required in the diet of animals, and thiamine deficiency leads to diseases such as beri-beri and the Wernicke-Korsakoff syndrome. Dietary thiamine (vitamin B1) consists mainly of thiamine pyrophosphate (TPP), which is transformed into thiamine by gastrointestinal phosphatases before absorption. It is believed that TPP itself cannot be transported across plasma membranes in significant amounts. We have identified a partial loss-of-function mutation in the Coenorhabditis elegans gene (tpk-1) that encodes thiamine pyrophosphokinase, which forms TPP from thiamine at the expense of ATP inside cells. The mutation slows physiological rhythms and the phenotype it produces can be rescued by TPP but not thiamine supplementation. tpk-1 functions cell nonautonomously, as the expression of wild-type tpk-1 in one tissue can rescue the function of other tissues that express only mutant tpk-1. These observations indicate that, in contrast to expectation from previous evidence, TPP can be transported across cell membranes. We also find that thiamine supplementation partially rescues the phenotype of partial loss-of-function mutants of the Na/K ATPase, providing genetic evidence that thiamine absorption, and/or redistribution from the absorbing cells, requires the full activity of this enzyme. ------------------- Key: 6923 Medline: 15527756 Authors: Gal TZ;Glazer I;Koltai H Title: An LEA group 3 family member is involved in survival of C. elegans during exposure to stress. Citation: FEBS Letters 577: 21-26 2004 Type: ARTICLE Genes: lea-1 unc-120 Abstract: In order to establish a functional role for late embryogenesis abundant (LEA) proteins in response to stress conditions in Caenorhabditis elegans, we silenced the expression of an LEA (Ce-lea-1) gene and determined the survival of worms under stress conditions. Ce-lea-1 transcription was induced during dehydration of C. elegans dauer juveniles. Following partial silencing of Ce-lea-1 transcription, we demonstrated a specific and significant reduction in worm survival during induction of desiccation, osmotic and heat stress. Together, these results establish a functional role for Ce-lea-1 in stress survival of C elegans and suggest that Ce-lea-1 may function as a component that is common to the responses to the examined stress conditions. ------------------- Key: 6924 Medline: 15530383 Authors: DeLuca JG;Salmon ED Title: Kinetochores: if you build it, they will come. Citation: Current Biology 14: R921-R923 2004 Type: REVIEW Genes: hcp-1 hcp-2 hcp-4 him-10 kbp-1 kbp-2 kbp-3 kbp-4 kbp-5 knl-1 knl-3 mis-12 ndc-80 Abstract: Successful mitosis depends critically on the segregation of chromosomes by kinetochore microtubules. A recent paper describes a conserved protein network from Caenorhabditis elegans that is composed of three classes of molecules, each of which contributes uniquely to the building of the kinetochore-microtubule attachment site. ------------------- Key: 6925 Medline: 15537535 Authors: Hampoelz B;Knoblich JA Title: Heterotrimeric G proteins: new tricks for an old dog. Citation: Cell 119: 453-456 2004 Type: REVIEW Genes: goa-1 gpa-16 gpb-1 gpr-1 gpr-2 lin-5 rgs-7 ric-8 Abstract: Heterotrimeric G proteins are well known for their function in signal transduction downstream of seven transmembrane receptors. More recently, however, genetic analysis in C. elegans and in Drosophila has revealed a second, essential function of these molecules in positioning the mitotic spindle and attaching microtubules to the cell cortex. Five new publications in Cell (Afshar et al., 2004; Du and Macara, 2004 [this issue of Cell]; Hess et al., 2004), Developmental Cell (Martin-McCaffrey et al., 2004), and Current Biology (Couwenbergs et al., 2004) show that this function is conserved in vertebrates and-like the classical pathway- involves cycling of G proteins between GDP and GTP bound conformations. ------------------- Key: 6926 Medline: 15493987 Authors: Scholey JM;Ou G;Snow J;Gunnarson A Title: Intraflegellar transport motors in Caenorhabditis elegans neurons. Citation: Biochemical Society Transactions 32: 682-684 2004 Type: ARTICLE Genes: avr-1 caf-1 caf-2 che-1 che-2 che-3 che-4 che-8 che-9 che-10 che-11 che-12 che-13 che-14 daf-6 daf-10 daf-11 daf-19 daf-21 daf-24 dlc-1 dyf-1 dyf-2 dyf-3 dyf-4 dyf-5 dyf-6 dyf-7 dyf-8 dyf-9 dyf-10 dyf-11 dyf-12 dyf-13 kap-1 klp-2 klp-11 klp-20 lan-5 mec-1 nss-2 osm-1 osm-2 osm-3 osm-4 osm-5 osm-6 osm-7 osm-9 osm-10 osm-13 ptd-1 ptr-7 ric-1 ric-5 tax-1 tax-3 tax-5 xbx-1 Abstract: IFT (intraflagellar transport) assembles and maintains sensory cilia on the dendritic endings of chemosensory neurons within the nematode Caenorhabditis elegans. During IFT, macromolecular protein complexes called IFT particles (which carry ciliary precursors) are moved from the base of the sensory cilium to its distal tip by anterograde IFT motors (kinesin-II and Osm-3 kinesin) and back to the base by retrograde IFT-dynein [Rosenbaum and Witman (2002) Nat. Rev. Mol. Cell Biol. 3, 813-825; Scholey (2003) Annu. Rev. Cell Dev. Biol. 19, 423-443; and Snell, Pan and Wang (2004) Cell 117, 693-697]. In the present study, we describe the protein machinery of IFT in C. elegans, which we have analysed using time-lapse fluorescence microscopy of green fluorescent protein-fusion proteins in concert with ciliary mutants. ------------------- Key: 6927 Medline: 15556862 Authors: Hesselson D;Newman C;Kim KW;Kimble J Title: GON-1 and fibulin have antagonistic roles in control of organ shape. Citation: Current Biology 14: 2005-2010 2004 Type: ARTICLE Genes: epi-1 fbl-1 gon-1 him-4 let-2 mig-17 nid-1 unc-52 Abstract: Most developing organs are surrounded by an extracellular matrix (ECM), which must be remodeled to accommodate growth and morphogenesis. In C. elegans, the GON-1 ADAMTS metalloprotease regulates both elongation and shape of the developing gonad [1]. Here, we report that either human ADAMTS-4 or ADAMTS-9 can substitute for GON-1 in transgenic worms, suggesting functional conservation between human and nematode homologs. We further identify fibulin (FBL-1), a widely conserved ECM component [2], as critical for gonadal morphogenesis. FBL-1 is expressed in nongonadal tissues but is present at the surface of the elongating gonad. A fibulin deletion mutant has a wider than normal gonad as well as body size defects. We find that GON-1 and fibulin have antagonistic roles in controlling gonadal shape. Depletion of fbl-1, but not other ECM components, rescues gon-1 elongation defects, and removal of gon-1 rescues fbl-1 width defects. Therefore, the GON-1 protease normally promotes tissue elongation and expansion, whereas the fibulin ECM protein blocks these key morphogenetic processes. We suggest that control of organ shape by GON-1 and fibulin in C. elegans may provide a model for similar cellular processes, including vasculogenesis, in humans. ------------------- Key: 6928 Medline: 15545320 Authors: Anyanful A;Ono K;Johnsen RC;Ly H;Jensen V;Baillie DL;Ono S Title: The RNA-binding protein SUP-12 controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. Citation: Journal of Cell Biology 167: 639-647 2004 Type: ARTICLE Genes: sup-12 unc-60 Abstract: Tissue-specific alternative pre-mRNA splicing is essential for increasing diversity of functionally different gene products. In Caenorhabditis elegans, UNC-60A and UNC-60B, nonmuscle and muscle isoforms of actin depolymerizing factor (ADF)/cofilin, are expressed by alternative splicing of unc-60 and regulate distinct actin-dependent developmental processes. We report that SUP-12, a member of a new family of RNA recognition motif (RRM) proteins, including SEB-4, regulates muscle-specific splicing of unc-60. In sup-12 mutants, expression of UNC-60B is decreased, whereas UNC-60A is up-regulated in muscle. sup-12 mutations strongly suppress muscle defects in unc-60B mutants by allowing expression of UNC-60A in muscle that can substitute for UNC-60B, thus unmasking their functional redundancy. SUP-12 is expressed in muscle and localized to the nuclei in a speckled pattern. The RRM domain of SUP-12 binds to several sites of the unc-60 pre-mRNA including the UG repeats near the 3'-splice site in the first intron. Our results suggest that SUP-12 is a novel tissue-specific splicing factor and regulates ------------------- Key: 6929 Medline: 15579687 Authors: Cinar HN;Chisholm AD Title: Genetic analysis of the Caenorhabditis elegans pax-6 locus: roles of paired domain-containing and nonpaired domain-containing isoforms. Citation: Genetics 168: 1307-1322 2004 Type: ARTICLE Genes: mab-18 oig-1 pax-6 vab-3 Abstract: PAX-6 proteins are involved in eye and brain development in many animals. In the nematode Caenorhabditis elegans the pax-6 locus encodes multiple PAX-6 isoforms both with and without a paired domain. Mutations in the C. elegans pax-6 locus can be grouped into three classes. Mutations that affect paired domain-containing isoforms cause defects in epidermal morphogenesis, epidermal cell fates, and gonad cell migration and define the class I (vab-3) complementation group. The class II mutation mab-18(bx23) affects nonpaired domain-containing isoforms and transforms the fate of a sensory organ in the male tail. Class III mutations affect both paired domain and nonpaired domain isoforms; the most severe class III Mutations are candidate null mutations in pax-6. Class III mutant phenotypes do not resemble a simple sum of class I and class II phenotypes. A comparison of class I and class III phenotypes indicates that PAX-6 isoforms can interact additively, synergistically, or antagonistically, depending on the cellular context. ------------------- Key: 6931 Medline: 15520385 Authors: Carvelli L;McDonald PW;Blakely RD;DeFelice LJ Title: Dopamine transporters depolarize neurons by a channel mechanism. Citation: Proceedings of the National Academy of Sciences USA 101: 16046-16051 2004 Type: ARTICLE Genes: dat-1 Abstract: Neurotransmitter transporters generate larger currents than expected if one assumes fixed stoichiometry models. It remains controversial, however, whether these depolarizing currents arise from high density and rapid turnover rates of a classical transporter, or whether transporters exhibit bona fide channel behavior. Although heterologously expressed transporters show single-channel behavior and noise analysis in native cells strongly suggests channel behavior, no directly observed single-channel events associated with transporters have been reported thus far in native cells. We describe single-channel events arising directly from the Caenorhabditis elegans cloparnine transporter (DAT-1) as evidenced by DA-induced channel activity blocked by a high-affinity DAT-1 inhibitor, increased channel activity in neurons that over-express DAT-1, and loss of channels in dat-1 knockout neurons. Our data indicate that authentic transporter channels underlie depolarizing whole-cell currents. Thus, DA transporters not only transport DA but also exhibit a channel mode of conduction that directly modulates membrane potential and neuronal function. ------------------- Key: 6932 Medline: 15543143 Authors: Bianchi L;Gerstbrein B;Frokjaer-Jensen C;Royal DC;Mukherjee G;Royal MA;Xue J;Schafer WR;Driscoll M Title: The neurotoxic MEC-4(d) DEG/ENaC sodium channel conducts calcium: implications for necrosis initiation. Citation: Nature Neuroscience 7: 1337-1344 2004 Type: ARTICLE Genes: cca-1 crt-1 egl-19 mec-2 mec-4 mec-6 mec-10 nca-1 nca-2 unc-2 unc-36 Abstract: Hyperactivation of the Caenorhabditis elegans MEC-4 Na+ channel of the DEG/ENaC superfamily (MEC-4(d)) induces neuronal necrosis through an increase in intracellular Ca2+ and calpain activation. How exacerbated Na+ channel activity elicits a toxic rise in cytoplasmic Ca2+, however, has remained unclear. We tested the hypothesis that MEC-4(d)-induced membrane depolarization activates voltage-gated Ca2+ channels (VGCCs) to initiate a toxic Ca2+ influx, and ruled out a critical requirement for VGCCs. Instead, we found that MEC-4(d) itself conducts Ca2+ both when heterologously expressed in Xenopus oocytes and in vivo in C. elegans touch neurons. Data generated using the Ca2+ sensor cameleon suggest that an induced release of endoplasmic reticulum (ER) Ca2+ is crucial for progression through necrosis. We propose a refined molecular model of necrosis initiation in which Ca2+ influx through the MEC-4(d) channel activates Ca2+- induced Ca2+ release from the ER to promote neuronal death, a mechanism that may apply to neurotoxicity associated with activation of the ASIC1a channel in mammalian ischemia. ------------------- Key: 6933 Medline: Authors: Blumenthal T;Davis RE Title: Exploring nematode diversity. Citation: Nature Genetics 36: 1246-1247 2004 Type: REVIEW Genes: Abstract: A massive study of expressed-sequence tags from both free-living and parasitic nematodes identifies tens of thousands of genes not present in Caenorhabditis elegans. Half of these are unique to nematodes and should provide new insights into the lifestyles of parasitic nematodes. ------------------- Key: 6934 Medline: 15543149 Authors: Parkinson J;Mitreva M;Whitton C;Thomson M;Daub J;Martin J;Schmid R;Hall N;Barrell B;Waterston RH;McCarter JP;Blaxter ML Title: A transcriptomic analysis of the phylum Nematoda. Citation: Nature Genetics 36: 1259-1267 2004 Type: ARTICLE Genes: Abstract: The phylum Nematoda occupies a huge range of ecological niches, from free-living microbivores to human parasites. We analyzed the genomic biology of the phylum using 265,494 expressed-sequence tag sequences, corresponding to 93,645 putative genes, from 30 species, including 28 parasites. From 35% to 70% of each species' genes had significant similarity to proteins from the model nematode Caenorhabditis elegans. More than half of the putative genes were unique to the phylum, and 23% were unique to the species from which they were derived. We have not yet come close to exhausting the genomic diversity of the phylum. We identified more than 2,600 different known protein domains, some of which had differential abundances between major taxonomic groups of nematodes. We also defined 4,228 nematode-specific protein families from nematode-restricted genes: this class of genes probably underpins species- and higher-level taxonomic disparity. Nematode-specific families are particularly interesting as drug and vaccine ------------------- Key: 6935 Medline: Authors: Dennehy JJ;Livdahl TP Title: Polymorphic foraging behavior among Caenorhabditis elegans: frequency- and density-dependent selection. Citation: Journal of Nematology 36: 276-280 2004 Type: ARTICLE Genes: Abstract: Strains of Caenorhabditis elegans obtained from their natural soil environment exhibit one of two forms of foraging behavior. Some strains forage solitarily and disperse evenly on a bacterial lawn. Other strains move rapidly until they encounter groups of conspecifics, and then slow their movement and join the group. Strains expressing these behaviors are globally widespread and have been isolated from the same location, suggesting a foraging polymorphism. We hypothesized that density-dependent selection maintains both foraging alleles in populations. Alternatively, both foraging alleles could be retained in populations through frequency-dependent selection. We tested both of these hypotheses by manipulating strain density and frequency, and observing changes in population density over nine. Our results indicated that neither density- nor frequency-dependent selection appears to be responsible for the observed polymorphism. The clumping strain consistently out-competed the solitary strain over all treatment levels. We Suggest other potential factors that may maintain both alleles in populations. ------------------- Key: 6936 Medline: 15456850 Authors: Britton C;Murray L Title: Cathepsin L protease (CPL-1) is essential for yolk processing during embryogenesis in Caenorhabditis elegans. Citation: Journal of Cell Science 117: 5133-5143 2004 Type: ARTICLE Genes: cpl-1 rab-7 rme-2 Abstract: Cysteine proteases are involved in the degradation of intracellular and extracellular proteins, although their precise roles in vivo are not well understood. Here we characterise a genetic mutant of the Caenorhabditis elegans cathepsin L protease gene cpl-1. CPL-1 is provided maternally and is essential for C. elegans embryogenesis. Immunofluorescence and electron microscopy data show that yolk endocytosis and initial yolk platelet formation occur normally in cpl-1 mutant oocytes and embryos. However, at around the 8-12 cell stage of embryogenesis, yolk platelets begin to aggregate and these enlarged yolk platelets fill the cytoplasm of cpl-1 mutant embryos. Co- incident with this aggregation is loss of fluorescence from a yolk green fluorescent protein (YP170::GFP). This suggests that loss of CPL-1 activity leads to aberrant processing and/or conformational changes in yolk proteins, resulting in abnormal platelet fusion. This study has relevance to the abnormal fusion and aggregation of lysosomes in cathepsin L-deficient mice and to other lysosomal disorders. ------------------- Key: 6937 Medline: 15456854 Authors: Minniti AN;Labarca M;Hurtado C;Brandan E Title: Caenorhabditis elegans syndecan (SDN-1) is required for normal egg laying and associates with the nervous system and the vulva. Citation: Journal of Cell Science 117: 5179-5190 2004 Type: ARTICLE Genes: gpn-1 sdn-1 Abstract: In Caenorhabditis elegans, the identification of many enzymes involved in the synthesis and modification of glycosaminoglycans (GAGs), essential components of proteoglycans, has attained special attention in recent years. Mutations in all the genes that encode for GAG biosynthetic enzymes show defects in the development of the vulva, specifically in the invagination of the vulval epithelium. Mutants for certain heparan sulfate modifying enzymes present axonal and cellular guidance defects in specific neuronal classes. Although most of the enzymes involved in the biosynthesis and modification of heparan sulfate have been characterized in C. elegans, little is known regarding the core proteins to which these GAGs covalently bind in proteoglycans. A single syndecan homologue (sdn-1) has been identified in the C elegans genome through sequence analysis. In the present study, we show that C elegans synthesizes sulfated proteoglycans, seen as three distinct species in western blot analysis. In the sdn-1 (ok449) deletion mutant allele we observed the lack of one species, which corresponds to a 50 kDa product after heparitinase treatment. The expression of sdn-1 mRNA and sequencing revealed that sdn-1 (4449) deletion mutants lack two glycosylation sites. Hence, the missing protein in the western blot analysis probably corresponds to SDN-1. In addition, we show that SDN-1 localizes to the C elegans nerve ring, nerve cords and to the vulva. SDN-1 is found specifically phosphorylated in nerve ring neurons and in the vulva, in both wild-type worms and sdn-1 (ok449) deletion mutants. These mutants show a defective egg-laying phenotype. Our results show for the first time, the identification, localization and some functional aspects of syndecan in the nematode C. elegans. ------------------- Key: 6938 Medline: 15527985 Authors: Zhang P;Min W;Li WH Title: Different age distribution patterns of human, nematode, and Arabidopsis duplicate genes. Citation: Gene 342: 263-268 2004 Type: ARTICLE Genes: Abstract: We studied the age distribution of duplicate genes in each of four eukaryotic genomes: human, Arabidopsis thaliana, Caenorhabditis elegans, and Drosophila melanogaster. The four distributions differ greatly from each other, contrary to the previous proposal of a universal L-shaped distribution in all eukaryotic genomes studied. Indeed, only the distribution in humans is L-shaped. The distribution in Arabidopsis is consistent with the hypothesis of an ancient genome duplication with no recent burst of duplication events, while the distribution in C elegans is nearly uniform. We also applied a nonparametric method to the human distribution to show that the rate of loss of duplicate genes decreases over time, contrary to the proposal of an exponential decay. One possible explanation of the decreasing rate of loss of duplicate genes over time could be rapid functional divergence between duplicate genes, providing an advantage for the ------------------- Key: 6939 Medline: 15603250 Authors: Westlund B;Stilwell G;Sluder A Title: Invertebrate disease models in neurotherapeutic discovery. Citation: Current Opinion in Drug Discovery & Development 7: 169-178 2004 Type: REVIEW Genes: Abstract: Models that reproduce many of the cellular and molecular aspects of various human neurodegenerative disorders have been developed in the fruit fly Drosophila melanogaster and the nematode Caenorhabditis elegans. An understanding of the underlying molecular and genetic mechanisms of disease pathogenesis is being gained from studies utilizing the wealth of genetic and molecular tools available for these invertebrate model organisms. This review focuses on recent studies that lay a foundation for utilizing these disease models in drug discovery and for continued genetic dissection of disease mechanisms. ------------------- Key: 6940 Medline: 15556850 Authors: Meighan CM;Cram EJ;Schwarzbauer JE Title: Organogenesis: cutting to the chase. Citation: Current Biology 14: R948-R950 2004 Type: REVIEW Genes: fbl-1 gon-1 mig-17 Abstract: Gonad morphogenesis in Caenorhabditis elegans requires two secreted proteases. Recent studies show that alterations of the extracellular matrix component fibulin-1 rescue gonadogenesis in the absence of these proteases. This finding is a critical step toward understanding the role of extracellular matrix in organogenesis. ------------------- Key: 6941 Medline: 15556863 Authors: Kubota Y;Kuroki R;Nishiwaki K Title: A fibulin-1 homolog interacts with an ADAM protease that controls cell migration in C. elegans. Citation: Current Biology 14: 2011-2018 2004 Type: ARTICLE Genes: fbl-1 mig-17 eDf19 Abstract: ADAM (a disintegrin and metalloprotease) family proteins play important roles in animal development and pathogenesis [1]. In C. elegans, a secreted ADAM protein, MIG-17, acts from outside the gonad to control the migration of gonadal distal tip cells (DTCs) that promote gonad morphogenesis [2]. Here, we report that dominant mutations in the fbl-1 gene encoding fibulin-1 spliced isoforms, which are calcium binding extracellular matrix proteins, bypass the requirement for MIG-17 activity in directing DTC migration. Specific amino acid substitutions in the third EGF-like motif of one of the two isoforms, FBL-1C, which corresponds to mammalian fibulin-1 C, suppress mig-17 mutations. FBL-1C is synthesized in the gut cells and localizes strongly to the gonadal basement membrane in a MIG-17-dependent manner. Localization of mutant FBL-1C is weaker than that of the wild-type protein and is insensitive to MIG-17 activity, suggesting that it gains a novel function that compensates for its reduced molecular density. We propose that proteolysis by MIG-17 recruits FBL-1C to the gonadal basement membrane, where it is required for the guidance of DTCs, and that mutant FBL-1C acts in a manner that mimics the downstream events of MIG-17-mediated proteolysis. ------------------- Key: 6942 Medline: 15556870 Authors: Juo P;Kaplan JM Title: The anaphase-promoting complex regulates the abundance of GLR-1 glutamate receptors in the ventral nerve cord of C. elegans. Citation: Current Biology 14: 2057-2062 2004 Type: ARTICLE Genes: emb-27 emb-30 flr-1 mat-1 mat-2 mat-3 unc-11 Abstract: The anaphase-promoting complex (APC) is a multisubunit E3 ubiquitin ligase that targets key cell cycle regulatory proteins for degradation. Blockade of APC activity causes mitotic arrest [1, 2]. Recent evidence suggests that the APC may have roles outside the cell cycle [3-6]. Several studies indicate that ubiquitin plays an important role in regulating synaptic strength [7-13]. We previously showed that ubiquitin is directly conjugated to GLR-1, a C. elegans non-NMDA (N-methyl-D-aspartate) class glutamate receptor (GluR), resulting in its removal from synapses [13]. By contrast, endocytosis of rodent AMPA GluRs is apparently regulated by ubiquitination of associated scaffolding proteins [12, 14]. Relatively little is known about the E3 ligases that mediate these effects. We examined the effects of perturbing APC function on postmitotic neurons in the nematode C. elegans. Temperature-sensitive mutations in APC subunits increased the abundance of GLR-1 in the ventral nerve cord. Mutations that block clathrin-mediated endocytosis blocked the effects of the APC mutations, suggesting that the APC regulates some aspect of GLR-1 recycling. Overexpression of ubiquitin decreased the density of GLR-1-containing synapses, and APC mutations blunted this effect. APC mutants had locomotion defects consistent with increased synaptic strength. This study defines a novel function for ------------------- Key: 6943 Medline: 15283700 Authors: Abo-Dalo B;Ndjonka D;Pinnen F;Liebau E;Luersen K Title: A novel member of the GCN5-related N-acetyltransferase superfamily from Caenorhabditis elegans preferentially catalyses the N-acetylation of thialysine [S-(2-aminoethyl)-L-cysteine]. Citation: Biochemical Journal 384: 129-137 2004 Type: ARTICLE Genes: Abstract: The putative diamine N-acetyltransferase D2023.4 has been cloned from the model nematode Caenorhabditis elegans. The 483 bp open reading frame of the cDNA encodes a deduced polypeptide of 18.6 kDa. Accordingly, the recombinantly expressed His(6)-tagged protein forms an enzymically active homodimer with a molecular mass of approx. 44000 Da. The protein belongs to the GNAT (GCN5-related N-acetyltransferase) superfamily, and its amino acid sequence exhibits considerable similarity to mammalian spermidine/spermine-N-1-acetyltransferases. However, neither the polyamines spermidine and spen-nine nor the diamines putrescine and cadaverine were efficiently acetylated by the protein. The smaller diamines diaminopropane and ethylenediamine, as well as L-lysine, represent better substrates, but, surprisingly, the enzyme most efficiently catalyses the N-acetylation of amino acids analogous with L-lysine. As determined by the k(cat)/K-m values, the C. elegans N-acetyltransferase prefers thialysine [S-(2-aminoethyl)-L-cysteine], followed by O-(2-aminoethyl)-L-serine and S-(2-aminoethyl)-D,L-homocysteine. Reversed-phase HPLC and mass spectrometric analyses revealed that N-acetylation of L-lysine and L-thialysine occurs exclusively at the amino moiety of the side chain. Remarkably, heterologous expression of C. elegans N-acetyltransferase D2023.4 in Escherichia coli, which does not possess a homologous gene, results in a pronounced resistance against the anti-metabolite thialysine. Furthermore, C. elegans N-acetyltransferase D2023.4 exhibits the highest homology with a number of GNATs found in numerous genomes from bacteria to mammals that have not been biochemically characterized so far, suggesting a novel group of GNAT enzymes closely related to spermidine/spermine-N-1-acetyltransferase, but with a distinct substrate specificity. Taken together, we propose to name the enzyme 'thialysine epsilon-acetyltransferase'. ------------------- Key: 6944 Medline: 15530417 Authors: Gudgen M;Chandrasekaran A;Frazier T;Boyd L Title: Interactions with the ubiquitin pathway of Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 325: 479-486 2004 Type: ARTICLE Genes: brc-1 nhl-1 par-2 prx-12 rfp-1 rnf-1 ubc-1 ubc-2 ubc-4 ubc-6 ubc-7 ubc-8 ubc-13 ubc-16 ubc-18 ubc-19 ubc-20 ubc-22 Abstract: The ubiquitin system is a well-conserved and pervasive process for post-synthetic modification of proteins. Three key components of the pathway are required for ubiquitination to occur: the E1 ubiquitin activating enzyme, the E2 ubiquitin conjugating enzyme, and the E3 ubiquitin ligase. There are several different E2 ubiquitin conjugating enzymes and an even greater number of E3 ubiquitin ligases. Interactions between these two groups are critical for substrate ubiquitination. This study reports a two-hybrid analysis of interactions within the ubiquitin system of Caenorhabditis elegans. Forty-three RING finger proteins (presumed E3 ubiquitin ligases) and 14 predicted E2 ubiquitin conjugating enzymes were included in the screen. A total of 31 E2-E3 interactions were uncovered. In addition, the UBC-13 conjugating enzyme was observed to interact with two different E2s, UEV-1 and UBC-1. The interaction of UBC-1 and UBC-13 was confirmed with in vitro ubiquitination reactions. Using NHL-1 as the E3 in the assays, ubiquitination was observed when both UBC- 1 and UBC-13 were present but not with either alone. These data imply that some E2s require dimerization in ------------------- Key: 6945 Medline: 15530424 Authors: Cho SW;Choi KY;Park CS Title: A new putative cyclic nucleotide-gated channel gene, cng-3, is critical for thermotolerance in Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 325: 525-531 2004 Type: ARTICLE Genes: che-1 cng-3 tax-4 Abstract: Cyclic nucleotide-gated (CNG) channels encoded by tax-4 and tax-2 genes are required for chemo- and thermo-sensation in Caenorhabditis elegans. Here we report the identification and the characterization of cng-3, a new CNG channel gene, found in C elegans. CNG-3 contains Six Putative transmembrane regions and a cyclic nucleotide-binding domain that show high homology with CNG channels of higher animals as well as TAX-4. The expression of cng-3 is detected from early stages in worm development and restricted in five sensory neurons of amphid including AFD neuron. While a cng-3 null mutant displays normal chemotaxis to volatile odorants, the mutant worms exhibit impaired thermal tolerance. These results indicate that CNG-3, a new member of CNG channel subunits, may play a critical role in sensation or response of thermal stress in ------------------- Key: 6946 Medline: 15473839 Authors: Reddien PW;Horvitz HR Title: The engulfment process of programmed cell death in Caenorhabditis elegans. Citation: Annual Review of Cell & Developmental Biology 20: 193-221 2004 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ced-12 csp-1 csp-2 csp-3 lin-24 lin-33 mec-4 mig-2 nex-1 nuc-1 psr-1 rac-2 unc-73 Abstract: Programmed cell death involves the removal of cell corpses by other cells in a process termed engulfment. Genetic studies of the nematode Caenorhabditis elegans have led to a framework not only for the killing step of programmed cell death but also for the process of cell-corpse engulfment. This work has defined two signal transduction pathways that act redundantly to control engulfment. Signals expressed by dying cells probably regulate these C. elegans pathways. Components of the cell-corpse recognition system of one of the C. elegans pathways include the CED-7 ABC transporter, which likely presents a death ligand on the surface of the dying cell; the CED-1 transmembrane receptor, which recognizes this signal; and the CED-6 adaptor protein, which may transduce a signal from CED-1. The second C. elegans pathway acts in parallel and involves a novel Rac GTPase signaling pathway, with the components CED-2 CrkII, CED-5 DOCK 180, CED-12 ELMO, and CED-10 Rac. The cell-corpse recognition system that activates this pathway remains to be characterized. In C. elegans, and possibly in mammals, the process of cell-corpse engulfment promotes the death process itself. The known mechanisms for cell-corpse engulfment leave much to be discovered concerning this fundamental aspect of metazoan biology. ------------------- Key: 6947 Medline: 15473847 Authors: Cowan CR;Hyman AA Title: Asymmetric cell division in C. elegans: cortical polarity and spindle positioning. Citation: Annual Review of Cell & Developmental Biology 20: 427-453 2004 Type: REVIEW Genes: arp-2 arp-3 cyk-1 gpr-1 gpr-2 let-99 let-502 mel-11 mlc-4 nmy-2 nop-1 par-1 par-2 par-3 par-5 par-6 pfn-1 pkc-3 rho-1 zyg-8 Abstract: The one-cell Caenorhabditis elegans embryo divides asymmetrically into a larger and smaller blastomere, each with a different fate. How does such asymmetry arise? The sperm-supplied centrosome establishes an axis of polarity in the embryo that is transduced into the establishment of anterior and posterior cortical domains. These cortical domains define the polarity of the embryo, acting upstream of the PAR proteins. The PAR proteins, in turn, determine the subsequent segregation of fate determinants and the plane of cell division. We address how cortical asymmetry could be established, relying on data from C. elegans and other polarized cells, as well as from applicable models. We discuss how cortical polarity influences spindle position to accomplish an asymmetric division, presenting the current models of spindle orientation and anaphase spindle displacement. We focus on asymmetric cell division as a function of the actin and microtubule cytoskeletons, emphasizing the cell biology of polarity. ------------------- Key: 6948 Medline: 15572111 Authors: Emtage L;Gu G;Hartwieg E;Chalfie M Title: Extracellular proteins organize the mechanosensory channel complex in C. elegans touch receptor neurons. Citation: Neuron 44: 795-807 2004 Type: ARTICLE Genes: him-4 mec-1 mec-4 mec-5 mec-6 mec-7 mec-9 mec-12 smg-5 Abstract: Specialized extracellular matrix (ECM) is associated with virtually every mechanosensory system studied. C. elegans touch receptor neurons have specialized ECM and attach to the surrounding epidermis. The mec-1 gene encodes an ECM protein with multiple EGF and Kunitz domains. MEC-1 is needed for the accumulation of the collagen MEC-5 and other ECM components, attachment, and, separately, for touch sensitivity. MEC-1 and MEC-5 bind to touch processes uniformly and in puncta. These puncta colocalize with and localize the mechanosensory channel complex in the touch neurons. In turn, the production of the MEC-1 and MEC-5 puncta appears to rely on interactions with the neighboring epidermal tissue. These and other observations lead us to propose that extracellular, but not cytoskeletal, tethering of the degenerin channel is needed for mechanosensory transduction. Additionally, our experiments demonstrate an important role of the ECM in organizing the placement of the channel complex. ------------------- Key: 6949 Medline: 15558032 Authors: Croce A;Cassata G;Disanza A;Gagliani MC;Tacchetti C;Malabarba G;Carlier MF;Scita G;Baumeister R;Di Fiore PP Title: A novel actin barbed-end-capping activity in EPS-8 regulates apical morphogenesis in intestinal cells of Caenorhabditis elegans. Citation: Nature Cell Biology 6: 1173-1179 2004 Type: ARTICLE Genes: eps-8 opt-2 Abstract: Redundant gene function frequently hampers investigations of the physiological roles of mammalian proteins. This is the case for Eps8, a receptor tyrosine kinase ( RTK) substrate(1) that participates in the activation of the Rac-specific guanine nucleotide-exchange function of Sos1 ( refs 2 - 5), thereby regulating actin remodelling by RTKs. EPS8-knockout mice, however, exhibit no evident phenotype(2), owing to the redundant function of three other EPS8-related genes(6). Here we show that in the nematode Caenorhabditis elegans, only one orthologue of the EPS8 gene exists, which gives rise to two alternatively spliced isoforms, EPS-8A and EPS-8B, differing at their carboxyl termini. In the nematode, eps-8 is essential for embryonic development. Furthermore, EPS-8A, but not EPS-8B, is specifically required for proper apical morphogenesis in the intestinal cells. This latter phenotype could be precisely correlated with a previously unknown actin barbed-end-capping activity, which is present in the C terminus of the EPS-8A isoform. Therefore, nematode genetics allowed not only the unmasking of distinct EPS-8-linked phenotypes, but also the definition of a novel function for this molecule in actin dynamics. ------------------- Key: 6950 Medline: 15454573 Authors: Moribe H;Yochem J;Yamada H;Tabuse Y;Fujimoto T;Mekada E Title: Tetraspanin protein (TSP-15) is required for epidermal integrity in Caenorhabditis elegans. Citation: Journal of Cell Science 117: 5209-5220 2004 Type: ARTICLE Genes: bli-2 dpy-5 dpy-7 sur-5 tsp-15 nDf23 nDf25 nDf29 Abstract: Epidermal integrity is essential for animal development and survival. Here, we demonstrate that TSP-15, a member of the tetraspanin protein family, is required for epithelial membrane integrity in Caenorhabditis elegans. Reduction of tsp-15 function by mutation or by RNA interference elicits abnormalities of the hypodermis, including dissociation of the cuticle and degeneration of the hypodermis. Lethality during molting often results. Examination of GFP transgenic animals, genetic mosaic analysis and rescue assays revealed that TSP-15 functions in hyp7, a large syncytium that composes most of the hypodermis. Assays with a membrane-impermeable dye or leakage analysis of a hypodermal-specific marker indicate that the barrier function of the hypodermal membrane is impaired owing to the loss or reduction of TSP-15. These results indicate that TSP-15 functions in the maintenance of epithelial cell integrity. ------------------- Key: 6951 Medline: 15454571 Authors: Kachur T;Ao W;Berger J;Pilgrim D Title: Maternal UNC-45 is involved in cytokinesis and colocalizes with non-muscle myosin in the early Caenorhabditis elegans embryo. Citation: Journal of Cell Science 117: 5313-5321 2004 Type: ARTICLE Genes: hum-2 nmy-2 unc-45 Abstract: The Caenorhabditis elegans UNC-45 protein contains tetratricopeptide repeats and a domain with similarity to fungal proteins, and it differentially colocalizes with myosin heavy chain B in the body wall muscles of adult worms. Although it is essential for normal myosin filament assembly in body wall muscle development, strong mutants show a previously unexplained maternal effect. We show here that the UNC-45 protein is maternally contributed and is present in all cells of the early embryo whereas zygotic UNC-45 expression is only detected in the developing muscle cells. Embryos produced from adults with reduced germline expression of UNC-45 exhibit cytokinesis defects suggesting that UNC-45 has a novel role in the early embryo in addition to muscle development. Yeast two-hybrid screens show that UNC-45 can directly interact with NMY-2, a non-muscle type II myosin, and UNC-45 and NMY-2 colocalize at cell boundaries in early embryos. Localization of UNC-45 at these boundaries is dependent upon the presence of NMY-2. Our results suggest that UNC-45 interacts with more than one type of myosin and functions in the embryo to regulate cytoplasmic myosin assembly and/or stability during cytokinesis. ------------------- Key: 6952 Medline: 15466891 Authors: Frazier T;Shakes D;Hota U;Boyd L Title: Caenorhabditis elegans UBC-2 functions with the anaphase-promoting complex but also has other activities. Citation: Journal of Cell Science 117: 5427-5435 2004 Type: ARTICLE Genes: apc-3 apc-11 cdc-27 emb-27 mat-1 mat-2 ubc-1 ubc-2 ubc-7 ubc-13 ubc-16 ubc-18 ubc-20 ubc-22 uev-2 Abstract: The anaphase-promoting complex or cyclosome (APC/C) is a multi-subunit ubiquitin ligase that regulates the eukaryotic cell cycle. APC/C belongs to the RING finger class, of ubiquitin ligases that function by interacting with a ubiquitin-conjugating enzyme (Ubc), thus inciting the Ubc to transfer ubiquitin onto a target protein. Extensive studies with APC/C in other organisms have identified several possible Ubcs that might function as partners for APC/C. This report presents phenotypic and biochemical evidence showing that, in Caenorhabditis elegans, UBC-2 interacts specifically with the APC/C. This conclusion is based on three lines of evidence: first, the RNAi phenotype of ubc-2 is indistinguishable from RNAi phenotypes of APC/C subunits; second, RNAi of ubc-2 but not other Ubcs enhances the phenotype of hypomorphic APC/C mutants; third, purified UBC-2 and APC-11, the RING finger subunit of the APC/C, show robust ubiquitination activity in in vitro assays. APC-11 interaction is specific for UBC-2 as ubiquitination is not seen when APC-11 is combined other C. elegans Ubcs. As expected from the Ubc that functions with the APC/C, ubc-2(RNAi) produces metaphase blocks in both mitotic germ cells and in meiotic divisions of post-fertilization oocytes. In addition, ubc-2(RNAi) results in two germline phenotypes that appear to be unrelated to the APC/C: an expanded transition zone indicative of a pre-pachytene meiotic arrest and endo-reduplicated oocytes indicative of a problem in ------------------- Key: 6953 Medline: 15557118 Authors: Chan RC;Severson AF;Meyer BJ Title: Condensin restructures chromosomes in preparation for meiotic divisions. Citation: Journal of Cell Biology 167: 613-625 2004 Type: ARTICLE Genes: air-2 dpy-26 dpy-27 dpy-28 hcp-6 mix-1 rec-8 smc-1 smc-3 smc-4 spo-11 syp-1 Abstract: T he production of haploid gametes from diploid germ cells requires two rounds of meiotic chromosome segregation after one round of replication. Accurate meiotic chromosome segregation involves the remodeling of each pair of homologous chromosomes around the site of crossover into a highly condensed and ordered structure. We showed that condensin, the protein complex needed for mitotic chromosome compaction, restructures chromosomes during melosis in Caenorhabditis elegans. In particular, condensin promotes both meiotic chromosome condensation after crossover recombination and the remodeling of sister chromatids. Condensin helps resolve cohesin-independent linkages between sister chromatids and alleviates recombination-independent linkages between homologues. The safeguarding of chromosome resolution by condensin permits chromosome segregation and is crucial for the formation of discrete, individualized bivalent chromosomes. ------------------- Key: 6954 Medline: 15557647 Authors: Huber B;Feldmann F;Kothe M;Vandamme P;Wopperer J;Riedel K;Eberl L Title: Identification of a novel virulence factor in Burkholderia cenocepacia H111 required for efficient slow killing of Caenorhabditis elegans. Citation: Infection and Immunity 72: 7220-7230 2004 Type: ARTICLE Genes: Abstract: Burkholderia cenocepacia H111, which was isolated from a cystic fibrosis patient, employs a quorum-sensing (QS) system, encoded by cep, to control the expression of virulence factors as well as the formation of biofilms. The QS system is thought to ensure that pathogenic traits are expressed only when the bacterial population density is high enough to overwhelm the host before it is able to mount an efficient response. While the wild-type strain effectively kills the nematode Caenorhabditis elegans, the pathogenicity of mutants with defective quorum sensing is attenuated. To date, very little is known about the cep-regulated virulence factors required for nematode killing. Here we report the identification of a cep-regulated gene, whose predicted amino acid sequence is highly similar to the QS-regulated protein AidA of the plant pathogen Ralstonia solanacearum. By use of polyclonal antibodies directed against AidA, it is demonstrated that the protein is expressed in the late-exponential phase and accumulates during growth arrest. We show that B. cenocepacia H111 AidA is essential for slow killing of C. elegans but has little effect on fast killing, suggesting that the protein plays a role in the accumulation of the strain in the nematode gut. Thus, AidA appears to be required for establishing an infection-like process rather than acting as a toxin. Furthermore, evidence is provided that AidA is produced not only by B. cenocepacia but also ------------------- Key: 6955 Medline: 15574824 Authors: GuhaThakurta D;Schriefer LA;Waterston RH;Stormo GD Title: Novel transcription regulatory elements in Caenorhabditis elegans muscle genes. Citation: Genome Research 14: 2457-2468 2004 Type: ARTICLE Genes: act-1 act-2 act-3 act-4 atn-1 ces-2 deb-1 egl-19 emb-9 epi-1 gei-1 gpd-2 gpd-3 hlh-1 lam-1 let-2 let-756 lev-11 lin-28mec-8 mef-2 mlc-1 mlc-2 mlc-3 mup-2 myo-1 myo-2 myo-3 pat-3 pat-4 pat-10 skn-1 sup-10 tni-1 unc-22 unc-15 unc-45 unc-52 unc-54 unc-60 unc-68 unc-87 unc-89 unc-97 unc-105 unc-112 unc-120 Abstract: We report the identification of three new transcription regulatory elements that are associated with muscle gene expression in the nematode Caenorhabditis elegans. Starting from a subset of well-characterized nematode muscle genes, we identified conserved DNA motifs in the promoter regions using computational DNA pattern-recognition algorithms. These were considered to be putative muscle transcription regulatory motifs. Using the green-fluorescent protein (GFP) as a reporter, experiments were done to determine the biological activity of these motifs in driving muscle gene expression. Prediction accuracy of muscle expression based on the presence of these three motifs was encouraging; nine of 10 previously uncharacterized genes that were predicted to have muscle expression were shown to be expressed either specifically or selectively in the muscle tissues, whereas only one of the nine that scored low for these motifs expressed in muscle. Knockouts of putative regulatory elements in the promoter of the mlc-2 and unc-89 genes show that they significantly contribute to muscle expression and act in a synergistic manner. We find that these DNA motifs are also present in the muscle promoters of C, briggsae, indicating that they are functionally conserved in the nematodes. ------------------- Key: 6956 Medline: 15469970 Authors: Sasson IE;Stern MJ Title: FGF and PI3 kinase signaling pathways antagonistically modulate sex muscle differentiation in C. elegans. Citation: Development 131: 5381-5392 2004 Type: ARTICLE Genes: aex-3 akt-1 daf-16 daf-18 egl-15 hlh-1 myo-3 pdk-1 soc-2 sur-8 unc-14 unc-54 Abstract: Myogenesis in vertebrate myocytes is promoted by activation of the phosphatidyl-inositol Y-kinase (PI3 kinase) pathway and inhibited by fibroblast growth factor (FGF) signaling. We show that hyperactivation of the Caenorhabditis elegans FGF receptor, EGL-15, similarly inhibits the differentiation of the hermaphrodite sex muscles. Activation of the P13 kinase signaling pathway can partially suppress this differentiation defect, mimicking the antagonistic relationship between these two pathways known to influence vertebrate myogenesis. When hyperactivated EGL-15 can also interfere with the proper development of the body wall musculature. Hyperactivation of EGL-15 has also revealed additional effects on a number of fundamental processes within the postembryonic muscle lineage, such as cell division polarity. These studies provide important in vivo insights into the contribution of FGF signaling events to myogenesis. ------------------- Key: 6957 Medline: Authors: Kalogeropoulos N;Christoforou C;Green AJ;Gill S;Ashcroft NR Title: chk-1 is an essential gene and is required for an S-M checkpoint during early embryogenesis. Citation: Cell Cycle 3: 1196-1200 2004 Type: ARTICLE Genes: chk-1 fem-1 fem-3 Abstract: The chk1 gene was first discovered in screens for radiation sensitive mutants in S. pombe. 1 Genetic analysis revealed that chk1 is involved in a DNA damage G(2)-M checkpoint. Chk1 becomes activated in response to DNA damage and prevents entry into mitosis by inhibiting the cell cycle machinery. This checkpoint decreases the risk of defective DNA being inherited by daughter cells, therefore reducing the risk of genetic instability. In higher eukaryotes, chk1 homologues have similar checkpoint functions. For example, an avian B-lymphoma cell line that is defective for Chk1 fails to arrest in G(2)-M after DNA damage. Nonetheless, these Chk1 defective cells are viable indicating that Chk1 is not essential for normal somatic cells to divide. 2 In spite of this, mouse and Drosophila homozygous Chk1 mutants die during embryogenesis suggesting that this is an essential gene for embryonic cell cycles. 3,4 What particular role does Chk1 have in directing embryonic cell divisions? Here we used the model organism, C. elegans, to address the role of chk-1 during development. As expected, disruption of chk-1 by RNAi eliminated the DNA damage checkpoink response in C. elegans. In addition, we revealed that chk-1 was predominantly expressed during embryogenesis and in the postembryonic germline. Indeed, we found that chk-1 had an essential role in embryo and germline development. More specifically, disruption of chk-1 expression resulted in embryo lethality, which was attributed to a defect in an intrinsic S-M checkpoint hence causing premature entry into phase. ------------------- Key: 6958 Medline: 15598130 Authors: Atkinson-Leadbeater K;Nuttley WM;van der Kooy D Title: A genetic dissociation of learning and recall in Caenorhabditis elegans. Citation: Behavioral Neuroscience 118: 1206-1213 2004 Type: ARTICLE Genes: dpy-2 Abstract: A learning event can be dissociated into 3 components: acquisition, storage, and recall. When the laboratory wild-type strain of Caenorhabditis elegans (N2 strain) is exposed to benzaldehyde in the absence of food, the worms display a reduction of their attractive response to this volatile odorant. This results from the association between benzaldehyde and a nutrient-deficient environment. Another wild-type isolate, the CB4856 strain, fails to display this decreased response to benzaldehyde after exposure to benzaldehyde in the absence of food. However, like the N2 strain, when tested to isoamyl alcohol after benzaldehyde conditioning, the CB4856 strain displays a decreased isoamyl alcohol response. Therefore, the CB4856 strain does not have an acquisition deficit, but it suffers from a recall deficit specific to benzaldehyde. ------------------- Key: 6959 Medline: 15493014 Authors: Kenning C;Kipping I;Sommer RJ Title: Isolation of mutations with Dumpy-like phenotypes and of collagen genes in the nematode Pristionchus pacificus. Citation: Genesis 40: 176-183 2004 Type: ARTICLE Genes: apm-2 col-14 col-19 col-48 col-65 col-73 col-82 col-99 col-128 col-165 dpy-1 dpy-2 dpy-3 dpy-4 dpy-5 dpy-6 dpy-7 dpy-8 dpy-9 dpy-10 dpy-11 dpy-12 dpy-13 dpy-14 dpy-15 dpy-16 dpy-17 dpy-18 dpy-19 dpy-20 dpy-21 dpy-22 dpy-23 dpy-24 dpy-25 dpy-26 dpy-27 dpy-28 dpy-29 dpy-30 emb-9 let-2 let-333 rol-1 rol-2 rol-3 rol-4 rol-5 rol-6 rol-7 rol-8 rol-9 sdc-3 sqt-1 sqt-3 Abstract: The nematode Pristionchus pacificus was developed as a satellite system in evolutionary developmental biology and forward and reverse genetic approaches allow a detailed comparison of various developmental processes between A pacificus and Caenorhabditis elegans. To facilitate map-based cloning in A pacificus, a genome map was generated including a genetic linkage map of similar to300 molecular markers and a physical map of 10,000 BAC clones. Here, we describe the isolation and characterization of more than 40 morphological mutations that can be used as genetic markers. These mutations fall into 12 Dumpy genes and one Roller gene that represent morphological markers for all six P. pacificus chromosomes. Using an in silico approach, we identified similar to150 hits of A pacificus collagen genes in the available EST, BAC-end, and fosmid-end sequences. However, 1:1 orthologs could only be identified for fewer than 20 collagen genes. ------------------- Key: 6960 Medline: Authors: Dunn NA;Conery JS;Lockery SR Title: Curcuit optimization predicts dynamic networks for chemosensory orientation in the nematode Caenorhabditis elegans. Citation: Advances in Neural Information Processing Systems 16: 1279-1286 2004 Type: ARTICLE Genes: Abstract: ------------------- Key: 6961 Medline: Authors: Dutt A;Canevascini S;Froehli-Hoier E;Hajnal A Title: EGF signal propagation during C. elegans vulval development mediated by ROM-1 Rhomboid. Citation: PLoS Biology 2: 1799-1814 2004 Type: ARTICLE Genes: bar-1 egl-17 egl-38 let-23 let-60 lin-2 lin-3 lin-12 lin-15 lin-31 mpk-1 pry-1 rom-1 rom-2 rom-3 rom-4 rom-5 sem-5 Abstract: ------------------- Key: 6962 Medline: 15485840 Authors: Curran SP;Leverich EP;Koehler CM;Larsen PL Title: Defective mitochondrial protein translocation precludes normal Caenorhabditis elegans development. Citation: Journal of Biological Chemistry 279: 54655-54662 2004 Type: ARTICLE Genes: Abstract: We demonstrate biochemically that the genes identified by sequence similarity as orthologs of the mitochondrial import machinery are functionally conserved in Caenorhabditis elegans. Specifically, tin-9.1 and tin-10 RNA interference (RNAi) treatment of nematodes impairs import of the ADP/ATP carrier into isolated mitochondria. Developmental phenotypes are associated with gene knock-down of the mitochondrial import components. RNAi of tomm-7 and ddp-1 resulted in mitochondria with an interconnected morphology in vivo, presumably due to defects in the assembly of outer membrane fission/fusion components. RNAi of the small Tim proteins TIN-9.1, TIN-9.2, and TIN-10 resulted in a small body size, reduced number of progeny produced, and partial embryonic lethality. An additional phenotype of the tin-9.2(RNAi) animals is defective formation of the somatic gonad. The biochemical demonstration that the protein import activity is reduced, under the same conditions that yield the defects in specific tissues and lethality in a later generation, suggests that the developmental abnormalities observed are a consequence of defects in mitochondrial ------------------- Key: 6963 Medline: 15576683 Authors: Gutierrez A;Sommer RJ Title: Evolution of dnmt-2 and mbd-2-like genes in the free-living nematodes Pristionchus pacificus, Caenorhabditis elegans and Caenorhabditis briggsae. Citation: Nucleic Acids Research 32: 6388-6396 2004 Type: ARTICLE Genes: mbd-2 Abstract: Whole genome sequencing of several metazoan model organisms provides a platform for studying genome evolution. How representative are the genomes of these model organisms for their respective phyla? Within nematodes, for example, the free-living soil nematode Caenorhabditis elegans is a highly derived species with unusual genomic characters, such as a reduced Hox cluster (Curr. Biol., 13, 37-40) and the absence of a Hedgehog signaling system. Here, we describe the recent loss of a DNA methyltransferase-2 gene (dnmt-2) in C.elegans. A dnmt-2-like gene is present in the satellite model organism Pristionchus pacificus, another free-living nematode that diverged from C.elegans 200-300 million years ago. In contrast, C.elegans, Caenorhabditis briggsae and P.pacificus all contain an mbd-2-like gene, which encodes another essential component of the methylation system of higher animals and fungi. Cel-mbd-2 is expressed throughout development and RNA interference (RNAi) experiments result in variable phenotypes. In contrast, Cbr-mbd-2 RNAi results in paralyzed larval or adult worms suggesting recent changes of gene function within the genus Caenorhabditis. We speculate that both genes were part of an ancestral DNA methylation system in nematodes and that gene loss and sequence divergence have abolished DNA methylation in C.elegans. ------------------- Key: 6964 Medline: 15485872 Authors: Izumikawa T;Kitagawa H;Mizuguchi S;Nomura KH;Nomura K;Tamura J;Gengyo-Ando K;Mitani S;Sugahara K Title: Nematode chondroitin polymerizing factor showing cell-/organ-specific expression is indispensable for chondroitin synthesis and embryonic cell division. Citation: Journal of Biological Chemistry 279: 53755-53761 2004 Type: ARTICLE Genes: pfc-1 sqv-5 Abstract: Chondroitin polymerization was first demonstrated in vitro when human chondroitin synthase (ChSy) was coexpressed with human chondroitin polymerizing factor (ChPF), which is homologous to ChSy but has little glycosyltransferase activity. To analyze the biological function of chondroitin, the Caenorhabditis elegans ortholog of human ChSy (sqv-5) was recently cloned, and the expression of its product was depleted by RNA-mediated interference (RNAi) and deletion mutagenesis. Blocking of chondroitin synthesis resulted in defects of cytokinesis in early embryogenesis, and eventually, cell division stopped. Here, we cloned the ortholog of human ChPF in C. elegans, PAR2.4. Despite little glycosyltransferase activity of the gene product, chondroitin polymerization was demonstrated as in the case of mammals when PAR2.4 was coexpressed with cChSy in vitro. The worm phenotypes including the reversion of cytokinesis, observed after the depletion of PAR2.4 by RNAi, were very similar to the cChSy (sqv-5)-RNAi phenotypes. Thus, PAR2.4 in addition to cChSy is indispensable for the biosynthesis of chondroitin in C. elegans, and the two cooperate to synthesize chondroitin in vivo. The expression of the PAR2.4 protein was observed in seam cells, which can act as neural stem cells in early embryonic lineages. The expression was also detected in vulva and distal tip cells of the growing gonad arms from L3 through to the young adult stage. These findings are consistent with the notion that chondroitin is involved in the organogenesis of the vulva and maturation of the gonad and also indicative of an involvement in distal tip cell migration and neural ------------------- Key: 6965 Medline: 15452127 Authors: Cipollo JF;Awad AM;Costello CE;Hirschberg CB Title: srf-3, a mutant of Caenorhabditis elegans, resistant to bacterial infection and to biofilm binding, is deficient in glycoconjugates. Citation: Journal of Biological Chemistry 279: 52893-52903 2004 Type: ARTICLE Genes: srf-3 Abstract: srf-3 is a mutant of C. elegans that is resistant to infection by Microbacterium nematophilum and to binding of the biofilm produced by Yersinia pseudotuberculosis and Yersinia pestis. Recently, SRF-3 was characterized as a nucleotide sugar transporter of the Golgi apparatus occurring exclusively in hypodermal seam cells, pharyngeal cells, and spermatheca. Based on the above observations, we hypothesized that srf-3 may have altered glyconjugates that may enable the mutant nematode to grow unaffected in the presence of the above pathogenic bacteria. Following analyses of N- and O-linked glycoconjugates of srf-3 and wild type nematodes using a combination of enzymatic degradation, permethylation, and mass spectrometry, we found in srf-3 a 65% reduction of acidic O-linked glycoconjugates containing glucuronic acid and galactose as well as a reduction of N- linked glycoconjugates containing galactose and fucose. These results are consistent with the specificity of SRF-3 for UDP-galactose and strongly suggest that the above glycoconjugates play an important role in allowing adhesion of M. nematophilum or Y. pseudotuberculosis biofilm to wild type C. elegans. Furthermore, because seam cells as well as pharyngeal cells secrete their glycoconjugates to the cuticle and surrounding surfaces, the results also demonstrate the critical role of these cells and their secreted glycoproteins in nematode-bacteria interactions and offer a mechanistic basis for strategies to block such recognition ------------------- Key: 6966 Medline: 15581640 Authors: Yakushiji Y;Yamanaka K;Ogura T Title: Identification of a cysteine residue important for the ATPase activity of C. elegans fidgetin homologue. Citation: FEBS Letters 578: 191-197 2004 Type: ARTICLE Genes: Abstract: Based on the amino acid alignment, Caenorhabditis elegans F32D1.1 was identified to be a homologue of the mammalian fidgetin. We produced and purified the F32D1.1 protein by using a baculovirus-expression system. F32D1.1 has an ATPase activity, which is sensitive to N-ethylmaleimide. K-m and V-max for the ATPase activity of F32D1.1 were estimated to be 0.44 mM and 225 nmol/mg/min, respectively. When the cysteine at the position of 368 was mutated to alanine, the ATPase activity was greatly decreased; V-max was decreased to one-sixth, while K. remained similar. These results suggest that the unique position of cysteine 368, located immediately downstream of the Walker A motif, plays an important role in the ATPhydrolysis process of C elegans F32D1.1 protein. ------------------- Key: 6967 Medline: 15572126 Authors: Walston T;Tuskey C;Edgar L;Hawkins N;Ellis G;Bowerman B;Wood W;Hardin J Title: Multiple Wnt signaling pathways converge to orient the mitotic spindle in early C. elegans embryos. Citation: Developmental Cell 7: 831-841 2004 Type: ARTICLE Genes: ama-1 apr-1 dsh-1 dsh-2 gpa-16 gsk-3 jnk-1 kin-19 let-92 lit-1 mig-5 mom-2 mom-5 pal-1 pop-1 pry-1 src-1 wrm-1 Abstract: How cells integrate the input of multiple polarizing signals during division is poorly understood. We demonstrate that two distinct Caenorhabditis elegans Wnt pathways contribute to the polarization of the ABar blastomere by differentially regulating its duplicated centrosomes. Contact with the C blastomere orients the ABar spindle through a nontranscriptional Wnt spindle alignment pathway, while a Wnt/beta-catenin pathway controls the timing of ABar spindle rotation. The three C. elegans Dishevelled homologs contribute to these processes in different ways, suggesting that functional distinctions may exist among them. We also find that CKI (KIN-19) plays a role not only in the Wnt/beta-catenin pathway, but also in the Wnt spindle orientation pathway as well. Based on these findings, we establish a model for the coordination of cell-cell interactions and distinct Wnt signaling pathways that ensures the robust timing and orientation of spindle rotation during a developmentally regulated cell division event. ------------------- Key: 6968 Medline: 15509773 Authors: Li J;Brown G;Ailion M;Lee S;Thomas JH Title: NCR-1 and NCR-2, the C. elegans homologs of the human Niemann-Pick type C1 disease protein, function upstream of DAF-9 in the dauer formation pathways. Citation: Development 131: 5741-5752 2004 Type: ARTICLE Genes: daf-2 daf-7 daf-9 daf-12 daf-16 ncr-1 ncr-2 sdf-9 Abstract: Mutations in the human NPC1 gene cause most cases of Niemann-Pick type C (NP-C) disease, a fatal autosomal recessive neurodegenerative disorder. NPC1 is implicated in intracellular trafficking of cholesterol and glycolipids, but its exact function remains unclear. The C. elegans genome contains two homologs of NPC1, ncr-1 and ncr-2, and an ncr-2; ncr-1 double deletion mutant forms dauer larvae constitutively (Daf-c). We have analyzed the phenotypes of ncr single and double mutants in detail, and determined the ncr gene expression patterns. We find that the ncr genes function in a hormonal branch of the dauer formation pathway upstream of daf-9 and daf-12, which encode a cytochrome P450 enzyme and a nuclear hormone receptor, respectively. ncr-1 is expressed broadly in tissues with high levels of cholesterol, whereas expression of ncr-2 is restricted to a few cells. Both Ncr genes are expressed in the XXX cells, which are implicated in regulating dauer formation via the daf-9 pathway. Only the ncr-1 mutant is hypersensitive to cholesterol deprivation and to progesterone, an inhibitor of intracellular cholesterol trafficking. Our results support the hypothesis that ncr-1 and ncr-2 are involved in intracellular cholesterol processing in C. elegans, and that a sterol-signaling defect is responsible for the Daf-c phenotype of the ncr-2; ------------------- Key: 6969 Medline: 15572125 Authors: Dammermann A;Muller-Reichert T;Pelletier L;Habermann B;Desai A;Oegema K Title: Centriole assembly requires both centriolar and pericentriolar material proteins. Citation: Developmental Cell 7: 815-829 2004 Type: ARTICLE Genes: air-1 sas-4 sas-5 sas-6 spd-2 spd-5 zyg-1 Abstract: Centrioles organize pericentriolar material to form centrosomes and also template the formation of cilia. Despite the importance of centrioles in dividing and differentiated cells, their assembly remains poorly understood at a molecular level. Here, we develop a fluorescence microscopy-based assay for centriole assembly in the 1-cell stage C. elegans embryo. We use this assay to characterize SAS-6, a centriolar protein that we identified based on its requirement for centrosome duplication. We show that SAS-6, a member of a conserved metazoan protein family, is specifically required for new centriole assembly, a result we confirm by electron microscopy. We further use the centriole assembly assay to examine the roles of three pericentriolar material proteins: SPD-5, the kinase aurora-A, and gamma-tubulin. Our results suggest that the pericentriolar material promotes daughter centriole formation by concentrating gamma-tubulin around the parent centriole. Thus, both centriolar and pericentriolar material proteins contribute to centriole ------------------- Key: 6970 Medline: Authors: Belair G;Cote JC Title: Screening of the nematicidal activity of the bacterium Bacillus thuringiensis Berliner on the free-living nematode Caenorhabditis elegans. Citation: Russian Journal of Nematology 12: 131-138 2004 Type: ARTICLE Genes: Abstract: The nematicidal activity of 68 Bacillus thuringiensis Berliner serotypes on Caenorhabditis elegans was investigated. Toxicity was determined by transferring a 100 mul aqueous Suspension containing twenty C. elegans juveniles onto an agar plate containing a sporulated, crystal-producing Culture of B. thuringiensis as the Source of food. The B. thuringiensis 407 Cry-, a crystal-minus strain, was included as a non-toxic control. The number of eggs, juveniles and adults was determined after 96 hours of incubation at 25degreesC. For the B. thuringiensis 407 Cry- strain, the average numbers of C. elegans juveniles and adults, and C. elegans eggs were 62/plate, and 22/plate, respectively, after the 96-hour incubation period. A total of six B. thuringiensis serovars caused significantly high nematicidal activity and a total of 13 serovars, caused a significantly high reduction in the production of eggs. Six B. thuringiensis serovars had a significant effect in both assays. These were var. thuringiensis, cameroun, tolworthi, darmstadiensis, toumanoffi and fukuokaensis. Whereas four of these synthesize the wide-spectrum P-exotoxin and one produce a Cyt protein, var. cameroun produces neither. ------------------- Key: 6971 Medline: 15572119 Authors: Zarnescu DC;Moses K Title: Born again at the synapse: a new function for the anaphase promoting complex/cyclosome. Citation: Developmental Cell 7: 777-778 2004 Type: REVIEW Genes: emb-27 glr-1 unc-11 Abstract: Currently, perhaps the most significant biological problem is to understand the mechanisms of learning and memory, and many of the answers will come from molecular explanations of synaptic plasticity. Two new papers have established a surprising connection: the Anaphase Promoting Complex/Cyclosome (APC/C) has a second function in controlling local protein stability at synapses, and hence in the control of behavior (Juo and Kaplan, 2004; van Roessel et al., 2004). ------------------- Key: 6972 Medline: 15692856 Authors: Rodger S;Griffiths BS;McNicol JW;Wheatley RW;Young IM Title: The impact of bacterial diet on the migration and navigation of Caenorhabditis elegans. Citation: Microbial Ecology 48: 358-365 2004 Type: ARTICLE Genes: Abstract: Can diet have a significant impact on the ability of organisms to sense and locate food? Focusing on the bacterial feeder Caenorhabditis elegans, we investigated what effect preconditioning on a range of bacterial substrates had on the subsequent chemotaxis process involved in the nematode locating other bacterial populations. Remarkably, we found that C. elegans, initially fed on a diet of Escherichia coli OP50, was significantly impaired in finding E. coli OP50 populations, compared to other available bacterial populations (P < 0.001). We found similar results for another bacterial feeding nematode species, suggesting that a general "substrate legacy" may operate across a wide range of organisms. We discuss this important finding with respect to the variation in response exhibited within a given nematode population, and the impact nematode migration has on bacterial dispersal in the environment. ------------------- Key: 6973 Medline: 15530573 Authors: Bettinger JC;Carnell L;Davies AG;McIntire SL Title: The use of Caenorhabditis elegans in molecular neuropharmacology. Citation: International Review of Neurobiology 62: 195-212 2004 Type: REVIEW Genes: avr-14 avr-15 gas-1 glc-1 mod-5 ndg-4 npr-1 nrf-5 nrf-6 slo-1 tph-1 unc-79 Abstract: ------------------- Key: 6974 Medline: 15371529 Authors: Haber M;Schungel M;Putz A;Muller S;Hasert B;Schulenburg H Title: Evolutionary history of Caenorhabditis elegans inferred from micorsatellites: evidence for spatial and temporal genetic differentiation and the occurrence of outbreeding. Citation: Molecular Biology and Evolution 22: 160-173 2005 Type: ARTICLE Genes: Abstract: Although diverse biological disciplines employ the nematode Caenorhabditis elegans as a highly efficient laboratory model system, little is known about its natural history. We investigated its evolutionary past using 10 polymorphic trinucleotide and tetranucleotide microsatellites, derived from across the whole genome. These microsatellites were analyzed from the 35 previously available natural isolates from different parts of the world and also 23 new strains isolated from northwest Germany. Our results highlight that C. elegans lineages differentiate genetically with respect to geographic distance and, to a lesser extent, differences in the time of strain isolation. The latter indicates some turnover of strain genotypes at specific locations. Our data also demonstrate the coexistence of highly diverse genotypes in the population from northwest Germany, which is best explained by recent migration events. Furthermore, selfing is confirmed as the primary mode of reproduction for this hermaphroditic nematode in nature. Importantly, we also find evidence for the occurrence of occasional outbreeding. Taken together, these results support the previous notion that C. elegans is a colonizer, whereby selling may permit rapid dispersal within new habitats even in the absence of potential mates, whereas occasional outcrossing may serve to compensate for the disadvantages of inbreeding. Such information about the natural history of C. elegans should be of great value for an in-depth understanding of the complexity of this organism, including its multifaceted developmental, neurological, or molecular ------------------- Key: 6975 Medline: 15371532 Authors: Cutter AD;Ward S Title: Sexual and temporal dynamics of molecular evolution in C. elegans development. Citation: Molecular Biology and Evolution 22: 178-188 2005 Type: ARTICLE Genes: Abstract: Dissection of the phenotypic and molecular details of development and differentiation is a centuries-old topic in evolutionary biology. However, an adequate understanding is missing for the molecular evolution of genes that are expressed differentially throughout development-across time, tissues, and the sexes. In this study, we investigate the dynamics of gene evolution across Caenorhabditis elegans ontogeny and among genes expressed differentially between each sex and gamete type. Using gene classes identified by genome-wide gene expression developmental time series and comparative sequence analysis with the congener C. briggsae, we demonstrate that genes expressed predominantly after reproductive maturity evolve more rapidly than genes expressed earlier in development and that genes expressed transiently during embryogenesis evolve faster than other embryonic transcripts. These results are indicative of relaxed selection on genes expressed after maturity, in accord with the mutation-accumulation model of aging. Furthermore, genes involved in spermatogenesis reveal more rapid evolution than other phenotypic classes of genes. Average rates of evolution among male soma-related genes indicates that selection acts to maintain males in these androdioecious species, despite their rarity, and the rapid evolution of sperm genes suggests that sexual selection acts on sperm ------------------- Key: 6976 Medline: 15574588 Authors: Apfeld J;O'Connor G;McDonagh T;DiStefano PS;Curtis R Title: The AMP-activated protein kinase AAK-2 links energy levels and insulin-like signals to lifespan in C. elegans. Citation: Genes & Development 18: 3004-3009 2004 Type: ARTICLE Genes: aak-2 daf-2 daf-16 par-4 Abstract: Although limiting energy availability extends lifespan in many organisms, it is not understood how lifespan is coupled to energy levels. We find that the AMP:ATP ratio, a measure of energy levels, increases with age in Caenorhabditis elegans and can be used to predict life expectancy. The C. elegans AMP-activated protein kinase alpha subunit AAK-2 is activated by AMP and functions to extend lifespan. In addition, either an environmental stressor that increases the AMP:ATP ratio or mutations that lower insulin-like signaling extend lifespan in an aak-2-dependent manner. Thus, AAK-2 is a sensor that couples lifespan to information about energy levels and ------------------- Key: 6977 Medline: 15581870 Authors: Fernandez AP;Gibbons J;Okkema PG Title: C. elegans peb-1 mutants exhibit pleiotropic defects in molting, feeding, and morphology. Citation: Developmental Biology 276: 352-366 2004 Type: ARTICLE Genes: ceh-22 lrp-1 peb-1 pha-4 Abstract: Caenorhabditis elegans PEB-1 is a novel DNA-binding protein expressed in most pharyngeal cell types and outside the pharynx in the hypodermis, hindgut, and vulva. Previous RNAi analyses indicated that PEB-1 is required for normal morphology of these tissues and growth-, however, the peb-1 null phenotype was unknown. Here we describe the deletion mutant peb-1(cu9) that not only exhibits the morphological defects observed in peb-1(RNAi) animals, but also results in penetrant larval lethality characterized by defects in pharyngeal function and molting. Consistent with a function in molting, we found that PEB-1 was detectable in all hypodermal and hindgut cells underlying the cuticle. Comparison to molting-defective lrp-1(ku156) mutants revealed that the peb-1(cu9) mutants were particularly defective in shedding the pharyngeal cuticle, and this defect likely contributed to feeding defects and lethality. Most markers of pharyngeal cell differentiation examined were expressed normally in peb-1(cu9) mutants; however, g1 gland cell expression of a kel-1::gfp reporter was reduced. As g1 gland cells have prominent functions during molting, we suggest defective gland cell differentiation contributes to peb-1(cu9) molting defects. In comparison, other peb-1 mutant phenotypes, including hindgut abnormalities, appeared independent of the molting defect. Similar phenotypes resulted from late loss of pha-4 function, suggesting that PEB-1 and PHA-4 have common functions in some tissues where they are co-expressed. ------------------- Key: 6978 Medline: 15581880 Authors: Teng Y;Girard L;Ferreira HB;Sternberg PW;Emmons SW Title: Dissection of cis-regulatory elements in the C. elegans Hox gene egl-5 promoter. Citation: Developmental Biology 276: 476-492 2004 Type: ARTICLE Genes: ceh-13 egl-5 lin-39 mab-5 nob-1 pal-1 php-3 Abstract: Hox genes are highly conserved segmental identity genes well known for their complex expression patterns and divergent targets. Here we present an analysis of cis-regulatory elements in the Caenorhabditis elegans Hox gene egl-5, which is expressed in multiple tissues in the posterior region of the nematode. We have utilized phylogenetic footprinting to efficiently identify cis-regulatory elements and have characterized these with gfp reporters and tissue-specific rescue experiments. We have found that the complex expression pattern of egl-5 is the cumulative result of the activities of multiple tissue or local region-specific activator sequences that are conserved both in sequence and near-perfect order in the related nematode Caenorhabditis briggsae. Two conserved regulatory blocks analyzed in detail contain multiple sites for both positively and negatively acting factors. One of these regions may promote activation of egl-5 in certain cells via the Wnt pathway. Positively acting regions are repressed in inappropriate tissues by additional negative pathways acting at other sites within the promoter. Our analysis has allowed us to implicate several new regulatory factors significant to the control of egl-5 expression. ------------------- Key: 6979 Medline: 15581881 Authors: Robertson SM;Shetty P;Lin R Title: Identification of lineage-specific zygotic transcripts in early Caenorhabditis elegans embryos. Citation: Developmental Biology 276: 493-507 2004 Type: ARTICLE Genes: act-2 act-4 cey-1 cey-2 cdc-42 cdk-1 daf-21 dpy-30 eft-3 end-1 end-3 glp-1 hlh-3 inf-1 ins-34 kin-33 kin-34 med-1 med-2 mex-1 mex-6 mom-2 nhr-2 nit-1 oma-1 par-5 pes-10 pie-1 pos-1 sdz-1 sdz-2 sdz-3 sdz-4 sdz-5 sdz-6 sdz-7 sdz-8 sdz-9 sdz-10 sdz-11 sdz-12 sdz-13 sdz-14 sdz-15 sdz-16 sdz-17 sdz-18 sdz-19 sdz-20 sdz-21 sdz-22 sdz-23 sdz-24 sdz-25 sdz-26 sdz-27 sdz-28 sdz-29 sdz-30 sdz-31 sdz-32 sdz-33 sdz-34 sdz-35 sdz-36 sdz-37 sdz-38 skn-1 str-125 tba-2 tbx-1 tbx-11 tbx-35 vet-1 vet-2 vet-3 vet-4 vet-6 Abstract: During Caenorhabditis elegans embryogenesis, a maternally supplied transcription factor, SKN-1, is required for the specification of the mesendodermal precursor, EMS, in the 4-cell stage embryo. When EMS divides, it gives rise to a mesoderm-restricted precursor, MS, and an endoderm-restricted precursor, E. To systematically identify genes that function as key regulators of MS and/or E-derived tissues, we identified, by microarray analyses, genes that are newly transcribed within a short developmental window (approximately 30 min) encompassing the generation and fate specification of the MS and E blastomeres. By comparing total cDNAs generated from individual, carefully staged embryos, we identified 275 genes up-regulated in 12-cell embryos compared to 4-cell embryos. Fifty of these 275 genes are down-regulated in 12-cell skn-1 mutant embryos and are designated skn-1-dependent zygotic (sdz) genes. The spatial and temporal expression patterns in C. elegans embryos of 10 randomly selected sdz genes were analyzed by a nuclear GFP reporter driven by the endogenous 5'regulatory sequence of each gene. GFP expression, although absent at the 4-cell stage, was detected at the 12- to 16-cell stage for all 10 genes and was restricted to EMS-derived lineages for 7 of the 10. Among the seven lineage-specific genes, three genes are expressed equally in both MS and E lineages, two are expressed exclusively or predominantly in the MS lineage, and two are expressed exclusively in the E lineage. Depletion of skn-1 by RNAi abolishes the expression of all seven reporter transgenes in vivo, confirming that these genes are indeed skn-1 dependent. These results demonstrate the successful combination of single-staged embryo cDNAs, genetic mutants, and whole transcriptome microarray analysis to identify stage- and lineage-specific ------------------- Key: 6980 Medline: 15579684 Authors: Novelli J;Ahmed S;Hodgkin J Title: Gene interactions in Caenorhabditis elegans define DPY-31 as a candidate procollage C-proteinase and SQT-3/ROL-4 as its predicted major target. Citation: Genetics 168: 1259-1273 2004 Type: ARTICLE Genes: dpy-4 dpy-13 dpy-31 ram-4 rol-1 rol-4 sqt-3 arDf1 ctDf1 nDf16 Abstract: Zinc metalloproteases of the BMP-1/TOLLOID family (also known as astacins) are extracellular enzymes involved in important developmental processes in metazoans. We report the characterization of the Caenorhabditis elegans gene dpy-31, which encodes the first essential astacin metalloprotease identified in this organism. Loss-of-function mutations in dpy-31 result in cuticle defects, abnormal morphology, and embryonic lethality, indicating that dpy-31 is required for formation of the collagenous exoskeleton. DPY-31 is widely expressed in the hypodermal cells, which are responsible for cuticle secretion. We have investigated the dpy31 function through reversion analysis. While complete reversion can be obtained only by intragenic suppressors, reversion of the Dpy-31 lethal phenotype also can be caused by dominant extragerlic suppressors. Nine extragenic suppressors carry mutations in the uniquely essential collagen gene sqt-3, which we show is the same gene as rol-4. Most mutations exhibit the unusual property of exclusively dominant suppression and all affect the sequence of the SQT-3 collagen C terminus. This suggests that DPY-31 is responsible for C-terminal proteolytic processing of collagen trimers and is therefore a structural and functional homolog of vertebrate BMP-1. The results also demonstrate the critical importance of the collagen C-terminal sequence, which is highly conserved among all 49 ------------------- Key: 6981 Medline: 15579685 Authors: Nabeshima K;Villeneuve AM;Hillers KJ Title: Chromosome-wide regulation of meiotic crossover formation in Caenorhabditis elegans requires properly assembled chromosome axes. Citation: Genetics 168: 1275-1292 2004 Type: ARTICLE Genes: him-3 Abstract: Most sexually reproducing organisms depend on the regulated formation of crossovers, and the consequent chiasmata, to accomplish successful segregation of homologous chromosomes at the meiosis 1 division. A robust, chromosome-wide crossover control system limits chromosome pairs to one crossover in most meioses in the nematode Caenorhabditis elegans; this system has been proposed to rely on structural integrity of meiotic chromosome axes. Here, we test this hypothesis using a mutant, him-3(me80), that assembles reduced levels of meiosis-specific axis component HIM-3 along cohesin-containing chromosome axes. Whereas pairing, synapsis, and crossing over are eliminated when HIM-3 is absent, the him-3(me80) mutant supports assembly of synaptonemal complex protein SYP-1 along some paired chromosomes, resulting in partial competence for chiasma formation. We present both genetic and cytological evidence indicating that the him-3(me80) mutation leads to an increased incidence of meiotic products with two crossovers. These results indicate that limiting the amount of a major axis component results in a reduced capacity to communicate the presence of a (nascent) crossover and/or to discourage others in response. ------------------- Key: 6982 Medline: 15579686 Authors: Yochem J;Bell LR;Herman RK Title: The identities of sym-2, sym-3 and sym-4, three genes that are synthetically lethal with mec-8 in Caenorhabditis elegans. Citation: Genetics 168: 1293-1306 2004 Type: ARTICLE Genes: mec-8 sym-1 sym-2 sym-3 sym-4 sym-5 mnDf67 mnDf68 Abstract: On the basis of synthetic lethality, five genes in Caenorhabditis elegans are known to be redundant with the mec-8 gene, which encodes a protein that contains two copies of an RNA recognition motif (RRM) and affects alternative RNA splicing. The molecular identities of two of the redundant genes, sym-1 and ym-5, were previously reported. The remaining three genes have now been cloned, and their synthetically lethal phenotypes with mec-8 are described in more detail. Animals homozygous for mec-8 and sym-2 loss-of-function mutations die during late embryogenesis. The SYM-2 predicted protein contains three RRMs; we propose that SYM-2 and MEC-8 can substitute for each other in promoting the maturation of the transcripts of a vital gene. Animals homozygous for mutations in mec-8 and in either sym-3 or sym-4 have the same striking defect: they arrest development just prior to or just after hatching with a pharynx that appears fully formed but is not properly attached to the body cuticle. sym-3 encodes a protein of unknown function with orthologs in Drosophila and mammals. sym-4 encodes a WD-repeat protein and may also have orthologs in Drosophila and mammals. We propose that SYM-3 and SYMA contribute to a common developmental pathway that is redundant with a MEC-8-dependent pathway. ------------------- Key: 6983 Medline: 15542095 Authors: Redmond DL;Geldhof P;Knox DP Title: Evaluation of Caenorhabditis elegans glycoproteins as protective immunogens against Haemonchus contortus challenge in sheep. Citation: International Journal for Parasitology 34: 1347-1353 2004 Type: ARTICLE Genes: Abstract: High levels of protection can be attained against Haemonchus contortus challenge infection in sheep using native antigens isolated from the gut of the adult parasite. However, vaccination with recombinant forms of these antigens, or components thereof, has disappointingly failed to generate similar levels of protection, suggesting that appropriate nematode glycosylation may be a prerequisite for protection. The free-living nematode, Caenorhabditis elegans is closely related to H. contortus and has been shown to share similar glycan moieties. In order to investigate the potentially protective role of these glycan moieties, a complex set of glycoproteins was isolated from C elegans using ConA-lectin chromatography and their efficacy as immunogens against H. contortus challenge infection evaluated in sheep. Despite the generation of a high titre systemic IgG antibody response to the C. elegans glycoproteins and the ability of these antibodies to bind to the microvillar surface of the gut of H. contortus, no protection against challenge infection was observed. Serum antibodies to the C. elegans glycoproteins cross-reacted with the H. contortus host-protective antigen, H-gal-GP, by ELISA, although the level of cross-reactivity was not of a magnitude considered protective. Qualitative differences were also determined between the glycan epitopes of the C. elegans ConA-binding proteins and those of H-gal-GP, suggesting the presence of ------------------- Key: 6984 Medline: 15663485 Authors: Xie J;Dernovici S;Ribeiro P Title: Mutagenesis analysis of the serotonin 5-HT2C receptor and a Caenorhabditis elegans 5-HT2 homologue: conserved residues of helix 4 and helix 7 contribute to agonist-dependent activation of 5-HT2 recept Citation: Journal of Neurochemistry 92: 375-387 2005 Type: ARTICLE Genes: Abstract: An alignment of serotonin [5-hydroxytryptamine (5-HT)] G protein-coupled receptors identified a lysine at position 4.45 (helix 4) and a small polar residue (serine or cysteine) at 7.45 (helix 7) that occur exclusively in the 5-HT2 receptor family. Other serotonin receptors have a hydrophobic amino acid, typically a methionine, at 4.45 and an invariant asparagine at 7.45. The functional significance of these class-specific substitutions was tested by site-directed mutagenesis of two distantly related 5-HT2 receptors, Caenorhabditis elegans 5-HT2ce and rat 5-HT2C. Residues 4.45 and 7.45 were each mutated to a methionine and asparagine, respectively, or an alanine and the resulting constructs were tested for activity. A K4.45M mutation decreased serotonin-dependent activity (E-max) of the rat 5-HT2C receptor by 60% and that of the C. elegans homologue by 40%, as determined by a fluorometric plate-based calcium assay. The rat mutant also exhibited nearly sixfold higher agonist binding affinity and significantly lower constitutive activity compared with wildtype. Mutagenesis of S7.45 in the C. elegans receptor increased serotonin binding affinity by up to 25-fold and decreased E-max by up to 65%. The same mutations of the cognate C7.45 in rat 5-HT2C produced a smaller fourfold change in the affinity for serotonin and decreased agonist efficacy by up to 50%. Substitutions of S/C7.45 did not produce a significant change in the basal activity of either receptor. All mutants tested exhibited levels of receptor expression similar to the corresponding wildtype based on measurements of specific [H-3]-mesulergine binding or flow cytometry analyses. Taken together, these results suggest that K4.45 and S/C7.45 play an important role in the conformational rearrangements leading to ------------------- Key: 6985 Medline: 15590605 Authors: Jenkins NL;McColl G;Lithgow GJ Title: Fitness cost of extended lifespan in Caenorhabditis Citation: Proceedings of the Royal Society of London - Series B: Biological Sciences 271: 2523-2526 2004 Type: ARTICLE Genes: daf-2 Abstract: An insulin/IGF-I-like signalling pathway determines the rate of aging of the adult nematode, Caenorhabditis elegans. Mutations in genes encoding this pathway can result in a doubling of lifespan. While such mutations may appear to have little effect on development or fertility, evolutionary theory predicts that large increases in lifespan will not be optimal for fitness. We demonstrate by laboratory natural selection that partial loss of function of the insulin receptor-like protein DAF-2 results in dramatically reduced fitness even under laboratory conditions. Despite long-lived mutants appearing healthy, they exhibit a heavy fitness cost consistent with an ------------------- Key: 6986 Medline: 15580270 Authors: O'Hagan R;Chalfie M;Goodman MB Title: The MEC-4 DEG/ENaC channel of Caenorhabditis elegans touch receptor neurons transduces mechanical signals. Citation: Nature Neuroscience 8: 43-50 2005 Type: ARTICLE Genes: mec-2 mec-4 mec-6 mec-7 mec-10 Abstract: Transformation of mechanical energy into ionic currents is essential for touch, hearing and nociception. Although DEG/ENaC proteins are believed to form sensory mechanotransduction channels, the evidence for this role remains indirect. By recording from C. elegans touch receptor neurons in vivo, we found that external force evokes rapidly activating mechanoreceptor currents (MRCs) carried mostly by Na+ and blocked by amiloride-characteristics consistent with direct mechanical gating of a DEG/ENaC channel. Like mammalian Pacinian corpuscles, these neurons depolarized with both positive and negative changes in external force but not with sustained force. Null mutations in the DEG/ENaC gene mec-4 and in the accessory ion channel subunit genes mec-2 and mec-6 eliminated MRCs. In contrast, the genetic elimination of touch neuron-specific microtubules reduced, but did not abolish, MRCs. Our findings link the application of external force to the activation of a molecularly defined metazoan sensory transduction channel. ------------------- Key: 6987 Medline: Authors: Ronan D;Gillespie P Title: Metazoan mechanotransduction mystery finally solved. Citation: Nature Neuroscience 8: 7-8 2005 Type: REVIEW Genes: mec-2 mec-4 mec-6 mec-7 mec-10 mec-12 Abstract: ------------------- Key: 6988 Medline: 15650738 Authors: Azevedo RBR;Lohaus R;Braun V;Gumbel M;Umamaheshwar M;Agapow PM;Houthoofd W;Platzer U;Borgonie G;Meinzer HP;Leroi AM Title: The simplicity of metazoan cell lineages. Citation: Nature 433: 152-156 2005 Type: ARTICLE Genes: Abstract: Developmental processes are thought to be highly complex, but there have been few attempts to measure and compare such complexity across different groups of organisms(1-5). Here we introduce a measure of biological complexity based on the similarity between developmental and computer programs(6-9). We define the algorithmic complexity of a cell lineage as the length of the shortest description of the lineage based on its constituent sublineages(9-13). We then use this measure to estimate the complexity of the embryonic lineages of four metazoan species from two different phyla. We find that these cell lineages are significantly simpler than would be expected by chance. Furthermore, evolutionary simulations show that the complexity of the embryonic lineages surveyed is near that of the simplest lineages evolvable, assuming strong developmental constraints on the spatial positions of cells and stabilizing selection on cell number. We propose that selection for decreased complexity has played a major role ------------------- Key: 6989 Medline: 15525675 Authors: Pellis-van Berkel W;Verheijen MHG;Cuppen E;Asahina M;de Rooij J;Jansen G;Plasterk RHA;Bos JL;Zwartkruis FJT Title: Requirement of the Caenorhabditis elegans RapGEF pxf-1 and rap-1 for epithelial integrity. Citation: Molecular Biology of the Cell 16: 106-116 2005 Type: ARTICLE Genes: let-53 let-73 let-658 let-659 pxf-1 rap-1 rap-2 Abstract: The Rap-pathway has been implicated in various cellular processes but its exact physiological function remains poorly defined. Here we show that the Caenorhabditis elegans homologue of the mammalian guanine nucleotide exchange factors PDZ-GEFs, PXF-1, specifically activates Rap1 and Rap2. Green fluorescent protein (GFP) reporter constructs demonstrate that sites of pxf-1 expression include the hypodermis and gut. Particularly striking is the oscillating expression of pxf-1 in the pharynx during the four larval molts. Deletion of the catalytic domain from pxf-1 leads to hypodermal defects, resulting in lethality. The cuticle secreted by pxf-1 mutants is disorganized and can often not be shed during molting. At later stages, hypodermal degeneration is seen and animals that reach adulthood frequently die with a burst vulva phenotype. Importantly, disruption of rap-1 leads to a similar, but less severe phenotype, which is enhanced by the simultaneous removal of rap-2. In addition, the lethal phenotype of pxf-1 can be rescued by expression of an activated version of rap-1. Together these results demonstrate that the pxf-1/rap pathway in C. elegans is required for maintenance of epithelial integrity, in which it probably functions in polarized secretion. ------------------- Key: 6990 Medline: 15269213 Authors: Kayser EB;Sedensky MM;Morgan PG;Hoppel CL Title: Mitochondrial oxidative phosphorylation is defective in the long-lived mutant clk-1. Citation: Journal of Biological Chemistry 279: 54479-54486 2004 Type: ARTICLE Genes: clk-1 Abstract: The long-lived mutant of Caenorhabditis elegans, clk-1, is unable to synthesize ubiquinone, CoQ(9). Instead, the mutant accumulates demethoxyubiquinone(9) and small amounts of rhodoquinone(9) as well as dietary CoQ(8). We found a profound defect in oxidative phosphorylation, a test of integrated mitochondrial function, in clk-1 mitochondria fueled by NADH-linked electron donors, i.e. complex I-dependent substrates. Electron transfer from complex I to complex III, which requires quinones, is severely depressed, whereas the individual complexes are fully active. In contrast, oxidative phosphorylation initiated through complex II, which also requires quinones, is completely normal. Here we show that complexes I and II differ in their ability to use the quinone pool in clk-1. This is the first direct demonstration of a differential interaction of complex I and complex II with the endogenous quinone pool. This study uses the combined power of molecular genetics and biochemistry to highlight the role of quinones in mitochondrial function and aging. ------------------- Key: 6991 Medline: 15572146 Authors: Maruyama R;Endo S;Sugimoto A;Yamamoto M Title: Caenorhabditis elegans DAZ-1 is expressed in proliferating germ cells and directs proper nuclear organization and cytoplasmic core formation during oogenesis. Citation: Developmental Biology 277: 142-154 2005 Type: ARTICLE Genes: daz-1 eft-3 gld-1 gld-2 glp-1 Abstract: The deleted in azoospermia (DAZ) family genes encode potential RNA-binding proteins that are expressed exclusively in germ cells in a wide range of metazoans. We have previously shown that mutations in daz-1, the only DAZ family gene in Caenorhabditis elegans, cause pachytene stage arrest of female germ cells but do not affect spermatogenesis. In this study, we report that DAZ-1 protein is most abundantly expressed in proliferating female germ cells, in a manner independent of the GLP-1 signaling pathway. DAZ-1 is dispensable in males but it is expressed also in male mitotic germ cells. Detailed phenotypic analyses with fluorescence microscopy and transmission electron microscopy have revealed that loss of daz-1 function causes multiple abnormalities as early as the onset of meiotic prophase, which include aberrant chromatin structure, small nucleoli, absence of the cytoplasmic core, and precocious cellularization. Although the reduced size of nucleoli is indicative of a low translational activity in these cells, artificial repression of general translation in the germline does not phenocopy the daz-1 mutant. Thus, we propose that DAZ-1 in C. elegans plays essential roles in female premeiotic and early meiotic germ cells, probably via regulating the translational activity of specific target genes required ------------------- Key: 6992 Medline: 15582293 Authors: Holzenberger M;Kappeler L;De Magalhaes Filho C Title: IGF-1 signaling and aging. Citation: Experimental Gerontology 39: 1761-1764 2004 Type: ARTICLE Genes: Abstract: We briefly compare calorie restriction, GHRH-R and Pit-1 mutants with knockout phenotypes of GH receptor, IGF-1 receptor and p66Shc, to make some general conclusions. Growth, fertility and longevity phenotypes may dissociate in some of these mutants, and we try to interpret this. Follows a short discussion on the importance of genetic background for aging studies in mice. We then evoke studies in C elegans showing that lifespan may be regulated in a non-cell-autonomous fashion, and that the nervous system could play a central role therein. Recent findings on DILP-2 regulation in Drosophila transpose this hypothesis of endocrine lifespan regulation to insects. Work in mice shows that inactivation of the insulin receptor specifically in the adipose tissue is sufficient to increase the mouse lifespan. In summary, exciting findings obtained in very different model organisms are rapidly converging and suggest that animal lifespan may be subject to endocrine regulation. Interestingly, the hypothalamus centralizes many age related hormonal regulations and at the same time participates in the integration of numerous nutritional signals, such that one could ask whether the hypothalamus may be at the crossroads of metabolic and ------------------- Key: 6993 Medline: 15572150 Authors: Rudel D;Riebesell M;Sommer RJ Title: Gonadogenesis in Pristionchus pacificus and organ evolution: development, adult morphology and cell-cell interactions in the hermaphrodite gonad. Citation: Developmental Biology 277: 200-221 2005 Type: ARTICLE Genes: Abstract: The nematode gonad is an exemplary system for the study of organogenesis and fundamental problems in developmental and cellular biology. Nematode gonads vary dramatically across species (Chitwood, B.G., Chitwood, M.B., 1950. Introduction to Nematology." University Park Press, Baltimore; Felix, M.A., Sternberg, P.W, 1996. Symmetry breakage in the development of one-armed gonads in nematodes. Development 122, 2129-2142). As such, comparative developmental biology of gonadogenesis offers the potential to investigate changes in developmental and cellular processes that result in novel organ morphologies and thus may give insights into how these changes can affect animal bauplane. Pristionchus pacificus is a free-living nematode that diverged from the model nematode Caenorhabditis elegans around 200-300 million years ago. The morphology and development of P. pacificus is highly homologous to that of C. elegans. However, many differences in morphology and the underlying molecular signaling networks are easy to identify, making P. pacificus ideal for a comparative approach. Here, we report a detailed description of the P. pacificus hermaphrodite gonad using electron and fluorescent microscopy that will provide a basis for both phenotypic studies of genetic mutations and in vivo molecular studies of cloned genes involved in P. pacificus gonad development. We report that the morphology of the P. pacificus gonad is distinct from that of C. elegans. Among these differences are germ line patterning differences, heterochronic differences, novel gonadal arm-migrations, novel cellular composition of some somatic tissues (e.g., the number of cells that comprise the sheath and different spermathecal regions are different), the absence of a somatic tissue (e.g., the spermathecal valve cells), a novel architecture for the sheath, and changes in the cellular and sub-cellular morphology of the individual sheath cells. Additionally, we report a set of cell ablations in P. pacificus that indicate extensive cell communication between the somatic gonadal tissues and the germ line. Individual ablation experiments in P. pacificus show significant differences in the effects of individual somatic tissues on germ line patterning in comparison to C. ------------------- Key: 6994 Medline: 15641163 Authors: Williams TR;Lee TM;Johnson CM Title: Glaucoma studies in the eyeless worm: stress responsiveness and temporal expression of the Caenorhabditis elegans myocilin-like gene, cof-2. Citation: Cellular and Molecular Biology 50: 723-731 2004 Type: ARTICLE Genes: cof-2 Abstract: Prolonged exposure to stress and the resulting over-stimulation of the HPA system are often detrimental to the homeostasis of an organism. In fact, chronic stress is believed to affect the pathology of several disease states including coronary heart disease and hypertension, diabetes and obesity. In humans, mutations in the GLC1A gene have been associated with primary open angle glaucoma. Previous studies on this gene have suggested that its expression is also affected by the same factors that mediate the stress response. With the ultimate goal of using the nematode, Caenorhabditis elegans, as an invertebrate model for glaucoma, we have measured the stress responsiveness of the cof-2 gene, one of two C. elegans proteins with significant homology to the myocilin olfactomedin domain. We show that both cof-2 mRNA and protein expression are developmentally regulated and that both are affected by heat shock stress. ------------------- Key: 6995 Medline: 15607983 Authors: Kahn-Kirby AH;Dantzker JLM;Apicella AJ;Schafer WR;Browse J;Bargmann CI;Watts JL Title: Specific polyunsaturated fatty acids drive TRPV-dependent sensory signaling in vivo. Citation: Cell 119: 889-900 2004 Type: ARTICLE Genes: egl-8 egl-30 elo-1 elo-2 fat-1 fat-3 fat-4 ocr-2 osm-9 Abstract: A variety of lipid and lipid-derived molecules can modulate TRP cation channel activity, but the identity of the lipids that affect TRP channel function in vivo is unknown. Here, we use genetic and behavioral analysis in the nematode C. elegans to implicate a subset of 20-carbon polyunsaturated fatty acids (PUFAs) in TRPV channel-dependent olfactory and nociceptive behaviors. Olfactory and nociceptive TRPV signaling are sustained by overlapping but nonidentical sets of 20-carbon PUFAs including eicosapentaenoic acid (EPA) and arachidonic acid (AA). PUFAs act upstream of TRPV family channels in sensory transduction. Shortterm dietary supplementation with PUFAs can rescue PUFA biosynthetic mutants, and exogenous PUFAs elicit rapid TRPV-dependent calcium transients in sensory neurons, bypassing the normal requirement for PUFA synthesis. These results suggest that a subset of PUFAs with omega-3 and omega-6 acyl groups act as endogenous modulators of TRPV signal transduction. ------------------- Key: 6996 Medline: Authors: Vriens J;Owsianik G;Voets T;Droogmans G;Nilius B Title: Invertebrate TRP proteins as functional models for mammalian channels. Citation: Pflugers Archiv-European Journal of Physiology 449: 213-226 2004 Type: ARTICLE Genes: ced-11 cup-5 gon-2 gtl-1 gtl-2 lov-1 ocr-1 ocr-2 ocr-3 ocr-4 osm-9 pkd-2 trp-1 trp-2 trp-3 Abstract: ------------------- Key: 6997 Medline: Authors: Yates DM;Wolstenholme AJ Title: Dirofilaria immitis: identification of a novel ligand-gated ion channel-related polypeptide. Citation: Experimental Parasitology 108: 182-185 2004 Type: ARTICLE Genes: unc-49 Abstract: We have isolated a cDNA from Dirofilaria immitis that encodes a predicted ion channel subunit, Di-LGR-1. Secondary structure predictions and database searches reveal that Di-LGR-1 is distantly related to ligand-gated anion channels, such as the GABA(A) receptors, though there are marked differences in the sequences of the putative channel forming regions. Di-LGR-1 has 52%. sequence identity to the Caenorhabditis elegans predicted polypeptide, T27A1.4: neighbour-joining trees show that these two polypeptides are the most divergent members of the nematode ligand-gated anion channel family. No close homologues are present in vertebrates, suggesting that their function may be specific to nematodes. RNAi experiments using a fragment of T27A1.4 with C elegans failed to reveal any obvious phenotype, so the function of ------------------- Key: 6998 Medline: 15601834 Authors: Dinkova TD;Keiper BD;Korneeva NL;Aamodt EJ;Rhoads RE Title: Translation of a small subset of Caenorhabditis elegans mRNAs is dependent on a specific eukaryotic translation initiation factor 4E isoform. Citation: Molecular and Cellular Biology 25: 100-113 2005 Type: ARTICLE Genes: act-5 daf-12 egl-3 egl-15 egl-21 egl-46 glr-4 gpd-3 grl-20 hbl-1 ife-4 kin-29 lam-3 myo-1 myo-2 myo-3 peb-1 rpl-27 sol-1 srh-2 trp-1 xtr-1 Abstract: The mRNA cap-binding protein eukaryotic translation initiation factor 4E (eIF4E) participates in protein synthesis initiation, translational repression of specific mRNAs, and nucleocytoplasmic shuttling. Multiple isoforms of eIF4E are expressed in a variety of organisms, but their specific roles are poorly understood. We investigated one Caenorhabditis elegans isoform, IFE-4, which has homologues in plants and mammals. IFE-4::green fluorescent protein (GFP) was expressed in pharyngeal and tail neurons, body wall muscle, spermatheca, and vulva. Knockout of ife-4 by RNA interference (RNAi) or a null mutation produced a pleiotropic phenotype that included egg-laying defects. Sedimentation analysis demonstrated that IFE-4, but not IFE-1, was present in 48S initiation complexes, indicating that it participates in protein synthesis initiation. mRNAs affected by ife-4 knockout were determined by DNA microarray analysis of polysomal distribution. Polysome shifts, in the absence of total mRNA changes, were observed for only 33 of the 18,967 C. elegans mRNAs tested, of which a disproportionate number were related to egg laying and were expressed in neurons and/or muscle. Translational regulation was confirmed by reduced levels of DAF-12, EGL-15, and KIN-29. The functions of these proteins can explain some phenotypes observed in ife-4 knockout mutants. These results indicate that translation of a limited subset of mRNAs is dependent on a specific isoform of eIF4E. ------------------- Key: 6999 Medline: Authors: Baird SE;Davidson CR;Bohrer JC Title: The genetics of ray pattern variation in Caenorhabditis briggsae. Citation: BMC Evolutionary Biology 5: 1-9 2005 Type: ARTICLE Genes: egl-5 mab-5 mip-1 Abstract: Background: How does intraspecific variation relate to macroevolutionary change in morphology? This question can be addressed in species in which derived characters are present but not fixed. In rhabditid nematodes, the arrangement of the nine bilateral pairs of peripheral sense organs ( rays) in tails of males is often the most highly divergent character between species. The development of ray pattern involves inputs from hometic gene expression patterns, TGFbeta signalling, Wnt signalling, and other genetic pathways. In Caenorhabditis briggsae, strain-specific variation in ray pattern has provided an entree into the evolution of ray pattern. Some strains were fixed for a derived pattern. Other strains were more plastic and exhibited derived and ancestral patterns at equal frequencies. Results: Recombinant inbred lines ( RILs) constructed from crosses between the variant C. briggsae AF16 and HK104 strains exhibited a wide range of phenotypes including some that were more extreme than either parental strain. Transgressive segregation was significantly associated with allelic variation in the C. briggsae homolog of abdominal B, Cb-egl-5. At least two genes that affected different elements of ray pattern, ray position and ray fusion, were linked to a second gene, mip-1. Consistent with this, the segregation of ray position and ray fusion phenotypes were only partially correlated in the RILs. Conclusions: The evolution of ray pattern has involved allelic variation at multiple loci. Some of these loci impact the specification of ray identities and simultaneously affect multiple ray pattern elements. Others impact individual characters and are not constrained by covariance with other ray pattern elements. Among the genetic pathways that may be involved in ray pattern evolution is specification of anteroposterior positional information by homeotic genes. ------------------- Key: 7000 Medline: 15602545 Authors: Yanik MF;Cinar H;Cinar JN;Chisholm AD;Jin Y;Ben-Yakar A Title: Functional regeneration after laser axotomy. Citation: Nature 432: 822- 2004 Type: ARTICLE Genes: Abstract: Understanding how nerves regenerate is an important step towards developing treatments for human neurological disease, but investigation has so far been limited to complex organisms (mouse and zebrafish) in the absence of precision techniques for severing axons (axotomy). Here we use femtosecond laser surgery for axotomy in the roundworm Caenorhabditis elegans and show that these axons functionally regenerate after the operation. Application of this precise surgical technique should enable nerve regeneration to be studied in vivo in its most evolutionarily simple form. ------------------- Key: 7001 Medline: 15163357 Authors: Astin J;Merry A;Rajan J;Kuwabara PE Title: Caenorhabditis elegans functional genomics: Omic resonance. Citation: Briefings in Functional Genomics & Proteomics 3: 26-34 2004 Type: REVIEW Genes: Abstract: The nematode Caenorhabditis elegans is widely used as a model organism for studying many fundamental aspects of development and cell biology, including processes underlying human disease. The genome of C. elegans encodes over 19,000 protein-coding genes and hundreds of non-coding RNAs. The availability of whole genome sequence has facilitated the development of high throughput techniques for elucidating the function of individual genes and gene products. Furthermore, attempts can now be made to integrate these substantial functional genomics data collections and to understand at a global level how the flow of genomic information that is at the core of the central dogma leads to the development of a multicellular ------------------- Key: 7002 Medline: 12587023 Authors: Guziewicz M;Vitullo T;Simmons B;Kohn RE Title: Analyzing defects in the Caenorhabditis elegans nervous system using organismal and cell biological approaches. Citation: Cell Biology Education 1: 18-25 2002 Type: ARTICLE Genes: Abstract: The goal of this laboratory exercise is to increase student understanding of the impact of nervous system function at both the organismal and cellular levels. This inquiry-based exercise is designed for an undergraduate course examining principles of cell biology. After observing the movement of Caenorhabditis elegans with defects in their nervous system, students examine the structure of the nervous system to categorize the type of defect. They distinguish between defects in synaptic vesicle transport and defects in synaptic vesicle fusion with membranes. The synaptic vesicles are tagged with green fluorescent protein (GFP), simplifying cellular analysis. The expected outcome of this experiment is that students will better understand the concepts of vesicle transport, neurotransmitter release, GFP, and the relation between the nervous system and behavior. ------------------- Key: 7003 Medline: 11361338 Authors: Gurvitz A;Wabnegger L;Langer S;Hamilton B;Ruis H;Hartig A Title: The tetratricopeptide repeat domains of human, tobacco, and nematode PEX5 proteins are functionally interchangeable with the analogous native domain for peroxisomal import of PTS1-terminated proteins Citation: Molecular Genetics & Genomics 265: 276-286 2001 Type: ARTICLE Genes: pex-5 Abstract: In the yeast Saccharomyces cerevisiae, beta-oxidation of fatty acids is compartmentalised in peroxisomes. Most yeast peroxisomal matrix proteins contain a type 1C-terminal peroxisomal targeting signal (PTS1) consisting of the tripeptide SKL or a conservative variant thereof. PTS1-terminated proteins are imported by Pex5p, which interacts with the targeting signal via a tetratricopeptide repeat (TPR) domain. Yeast cells devoid of Pex5p are unable to import PTS1-containing proteins and cannot degrade fatty acids. Here, the PEX5-TPR domains from human, tobacco, and nematode were inserted into a TPR-less yeast Pex5p construct to generate Pex5p chimaeras. These hybrid proteins were examined for functional complementation of the pex5delta mutant phenotype. Expression of the Pex5p chimaeras in pex5delta mutant cells restored peroxisomal import of PTS1-terminated proteins. Chimaera expression also re-established degradation of oleic acid, allowing growth on this fatty acid as a sole carbon source. We conclude that, in the context of Pex5p chimaeras, the human, tobacco, and nematode Pex5p-TPR domains are functionally interchangeable with the native domain for the peroxisomal import of yeast proteins terminating with canonical PTS1s. Non-conserved yeast PTS1s, such as HRL and HKL, did not interact with the tobacco PEX5-TPR domain in the two-hybrid system. HRL occurs at the C-terminus of the peroxisomal protein Eci1p, which is required for growth on unsaturated fatty acids. Although mutant pex5delta cells expressing a yeast/tobacco Pex5p chimaera failed to import a GFP-Eci1p reporter protein, they were able to grow on oleic acid. We reason that this is due to a cryptic PTS in native Eci1p that can function in a redundant system with ------------------- Key: 7004 Medline: 12548541 Authors: Schneider SQ;Finnerty JR;Martindale MQ Title: Protein evolution: structure-function relationships of the oncogene beta-catenin in the evolution of multicellular animals. Citation: Journal of Experimental Zoology 295B: 25-44 2003 Type: ARTICLE Genes: bar-1 hmp-2 wrm-1 Abstract: Beta-catenin functions as a cytoskeletal linker protein in cadherin-mediated adhesion and as a signal mediator in wnt-signal transduction pathways. We use a novel integrative approach, combining evolutionary, genomic, and three-dimensional structural data to analyze and trace the structural and functional evolution of beta-catenin genes. This approach also enabled us to examine the effects of gene duplication on the structure and function of beta-catenin genes in Drosophila, C. elegans, and vertebrates. By sampling a large number of different taxa, we identified both ancestral and derived motifs and residues within the different regions of the beta-catenin proteins. Projecting amino acid substitutions onto the three- dimensional structure established for mouse beta-catenin, we identified specific domains that exhibit loss and gain of selective constraints during beta catenin evolution. Structural changes, changes in the amino acid substitution rate, and the appearance of novel functional domains in beta-catenin can be mapped to specific branches on the metazoan tree. Together, our analyses suggest that a single, beta-catenin gene fulfilled both adhesion and signaling functions in the last common ancestor of metazoans some 700 million years ago. In addition, gene duplications facilitated the evolution of beta-catenins with novel functions and allowed the evolution of multiple, single-function proteins (cell adhesion or wnt-signaling) from the ancestral, dual-function protein. Integrative methods such as those we have applied here, utilizing the 'natural experiments' present in animal diversity, can be employed to identify novel and shared functional motifs and residues in virtually any protein among the proteomes of ------------------- Key: 7005 Medline: 11054566 Authors: Zhang YZ;Lindblom T;Chang A;Sudol M;Sluder AE;Golemis EA Title: Evidence that Dim1 associated with proteins involved in the pre-mRNA splicing, and delineation of residues essential for Dim1 interactions with hnRNP F and Npw38/PQBP-1. Citation: Gene 257: 33-43 2000 Type: ARTICLE Genes: apc-4 apc-8 dim-1 dml-1 Abstract: The small evolutionarily conserved protein Dim1p/hDim1/Dib1p/DML-1 was initially defined as a factor essential for progression through the G2/M transition, and shown to be required to maintain the steady state level of a component of the fission yeast anaphase promoting complex/cyclosome. More recently, Dib1p has been defined as a component of the U4/U6.U5 tri-snRNP, required for pre-mRNA splicing. To investigate the mechanism(s) of Dim1 function, reiterative two-hybrid screening was performed to identify interacting proteins. Proteins thus identified were solely those involved in pre-mRNA splicing or related functions, and one partner induced a striking synthetic phenotype when co-expressed with hDim1 in mammalian cells. Saturating alanine scanning mutagenesis of Dim1 allowed delineation of amino acids essential for its ability to interact with its defined partners: mapping these residues on the structural coordinates of hDim1 defined an interactive sector of the protein. Finally, depletion studies have recently shown that Dim1 function is essential for pre-mRNA splicing in yeast. We find that elimination of DML-1 expression in C. elegans by RNA interference leads to embryonal lethality during gastrulation, marked by a failure to correctly express early zygotic transcripts. These results parallel the arrest phenotypes associated with global disruption of zygotic gene expression, suggesting that Dim1 proteins maintain an essential ------------------- Key: 7006 Medline: 15384179 Authors: Ishida M;Yamazaki T;Houjou T;Imagawa M;Harada A;Inoue K;Taguchi R Title: High-resolution analysis by nano-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for the identification of molecular species of phospholipds and their oxidized meta Citation: Rapid Communications in Mass Spectrometry 18: 2486-2494 Type: ARTICLE Genes: Abstract: Nano-electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) was applied to identify the molecular species of phosphatidylethanolamine of Caenorhabditis elegans, which has a high concentration of phospholipids with a fatty acyl chain having an odd number of carbon atoms. The molecular species of diacyl phosphatidylethanolamine with one fatty acyl chain having an odd number of carbon atoms and one fatty acyl chain having an even number of carbon atoms was identified separately from alkyl-acyl phosphatidylethanolamine with an alkyl chain having an even number of carbon atoms and a fatty acyl chain having an even number of carbon atoms. Furthermore, nano-ESI-FTICRMS was applied to the direct identification of oxidized phosphatidylcholine from soybean. The mass peaks of individual molecular species of oxidative phosphatidylcholine, such as 34:3 diacyl phosphatidylcholine with peroxide (+2O) (m/z 788.544) or 34:2 diacyl phosphatidylcholine with peroxide (+2O) (m/z 790.560), can be separated from the peaks of the molecular species of the non-oxidative phospholipids. This suggests that the mass peaks with a difference of less than 0.1 mass units in their molecular weight can be separated and that their individual exact molecular compositions can be obtained by the FTICRMS analysis. The high resolution and high accuracy of FTICRMS are very effective in the analysis of molecular species of phospholipids and their ------------------- Key: 7007 Medline: 15653505 Authors: Evason K;Huang C;Yamben I;Covey DF;Kornfeld K Title: Anticonvulsant medications extend worm life-span. Citation: Science 307: 258-262 2005 Type: ARTICLE Genes: aex-3 daf-2 daf-16 eat-2 egl-1 osm-3 tax-4 unc-31 unc-64 Abstract: Genetic studies have elucidated mechanisms that regulate aging, but there has been little progress in identifying drugs that delay aging. Here, we report that ethosuximide, trimethadione, and 3,3-diethyl-2-pyrrolidinone increase mean and maximum life-span of Caenorhabditis elegans and delay age-related declines of physiological processes, indicating that these compounds retard the aging process. These compounds, two of which are approved for human use, are anticonvulsants that modulate neural activity. These compounds also regulated neuromuscular activity in nematodes. These findings suggest that the life-span-extending activity of these compounds is related to the anticonvulsant activity and implicate neural activity in the regulation of aging. ------------------- Key: 7008 Medline: Authors: Apfeld J;O'Connor G;McDonagh T;DiStefano PS;Curtis R Title: The AMP-activated protein kinase AAK-2 links energy levels and insulin-like signals to lifespan in C. elegans. Citation: Genes & Development 19: 1- 2005 Type: CORRECT Genes: aak-1 aak-2 Abstract: ------------------- Key: 7009 Medline: 15620690 Authors: Kim TH;Hwang SB;Jeong PY;Lee J;Cho JW Title: Requirement of tyrosylprotein sulfotransferase-A for proper cuticle formation in the nematode C. elegans. Citation: FEBS Letters 579: 53-58 2005 Type: ARTICLE Genes: rol-6 Abstract: Tyrosine O-sulfation is one of the post-translational modification processes that occur to membrane proteins and secreted proteins in eukaryotes. Tyrosylprotein sulfotransferase (TPST) is responsible for this modification, and in this report, we describe the expression pattern and the biological role of TPST-A in the nematode Caenorhabditis elegans. We found that TPST-A was mainly expressed in the hypodermis, especially in the seam cells. Reduction of TPST-A activity by RNAi caused severe defects in cuticle formation, indicating that TPST-A is involved in the cuticle formation in the nematode. We found that RNAi of TPST-A suppressed the roller phenotype caused by mutations in the rol-6 collagen gene, suggesting that sulfation of collagen proteins may be important for proper organization of the extracellular cuticle matrix. The TPST-A RNAi significantly decreased the dityrosine level in the worms, raising the possibility that the sulfation process may be a pre-requisite for the collagen tyrosine ------------------- Key: 7010 Medline: 15610845 Authors: Vella MC;Reinert K;Slack FJ Title: Architecture of a validated microRNA::target interaction. Citation: Chemistry & Biology 11: 1619-1623 2004 Type: ARTICLE Genes: let-7 lin-4 lin-14 lin-41 Abstract: MicroRNAs are small similar to22 nucleotide regulators of numerous biological processes and bind target gene messenger RNAs to control gene expression. The C. elegans microRNA let-7 and its target lin-41 were the first microRNA::target interaction to be validated in vivo. let-7 molecules form imperfect duplexes with two required let-7 complementary sites in the lin-41 3' UTR. Here, we show that base pairing at both the 5' and 3' ends of the let-7 binding site, as well as the presence of unpaired RNA residues in the predicted duplexes, are required for lin-41 downregulation. In this study, our model for microRNA::target interactions also demonstrates that the context of a microRNA binding can be critical for function, revealing an unforeseen complexity in microRNA::target ------------------- Key: 7011 Medline: 15611166 Authors: Hajdu-Cronin YM;Chen WJ;Sternberg PW Title: The L-type cyclin CYL-1 and the heat-shock-factor HSF-1 are required for heat-shock-induced protein expression in Caenorhabditis elegans. Citation: Genetics 168: 1937-1949 2004 Type: ARTICLE Genes: cyl-1 dpy-20 goa-1 hsf-1 hsp-16.2 hsp-16.41 lin-3 sup-45 arDf1 ctDf1 Abstract: In a screen for suppressors of activated GOA-1 (Galpha(o)) under the control of the hsp-16.2 heat-shock promote, we identified three genetic loci that affected heat-shock-induced GOA-1 expression. The cyl-1 mutants are essentially wild type in appearance, while hsf-1 and sup-45 mutants have egg-laying defects. The hsf-1 mutation also causes a temperature-sensitive developmental arrest, and hsf-1 mutants have decreased life span. Western analysis indicated that mutations in all three loci suppressed the activated GOA-1 transgene by decreasing its expression. Heat-shock-induced expression of hsp-16.2 mRNA was reduced in cyl-1 mutants and virtually eliminated in hsf-1 and sup-45 mutants, as compared to wild-type expression. The mutations could also suppress other transgenes under heat-shock control, cyl-1 and sup-45, but not hsf-1, mutations suppressed a defect caused by a transgene not under heat-shock control, suggesting a role in general transcription or a post-transcriptional aspect of gene expression, hsf-1 encodes the C. elegans homolog of the human heat-shock factor HSF1, and cyl-1 encodes a cyclin most similar to cyclin L. We believe HSF-1 acts in heat-shock-inducible transcription and CYL-1 acts more generally in gene expression. ------------------- Key: 7012 Medline: 15371357 Authors: Forrester WC;Kim C;Garriga G Title: The Caenorhabditis elegans Ror RTK CAM-1 inhibits EGL-20/Wnt signaling in cell migration. Citation: Genetics 168: 1951-1962 2004 Type: ARTICLE Genes: bar-1 cam-1 egl-20 lin-17 mab-5 mig-1 pry-1 vab-8 Abstract: During Caenorhabditis elegans development, the HSN neurons and the right Q neuroblast and its descendants undergo long-range anteriorly directed migrations. Both of these migrations require EGL-20, a C. elegans Wnt homolog. Through a canonical Wnt signaling pathway, EGL-20/Wnt transcriptionally activates the Hox gene mab-5 in the left Q neuroblast and its descendants, causing the cells to migrate posteriorly. In this report, we show that CAM-1, a Ror receptor tyrosine kinase (RTK) family member inhibits, EGL-20 signaling. Excess EGL-20, like loss of cam-1, caused the HSNs to migrate too far anteriorly. Excess CAM-1, like loss of egl-20, shifted the final positions of the HSNs posteriorly and caused the left Q neuroblast descendants to migrate anteriorly. The reversal in the migration of the left Q neuroblast and its descendants resulted from a failure to express mab-5, an egl-20 mutant phenotype. Our data suggest that CAM-1 negatively regulates EGL-20. ------------------- Key: 7013 Medline: 15801597 Authors: Cranfield CG;Dawe A;Karloukovski V;Dunin-Borkowski RE;de Pomerai D;Dobson J Title: Biogenic magnetite in the nematode Caenorhabditis elegans. Citation: Proceedings of the Royal Society of London B 271: S436-S439 2004 Type: ARTICLE Genes: Abstract: The nematode Caenorhabditis elegans is widely used as a model system in biological research. Recently, examination of the production of heatshock proteins in this organism in response to mobile phone-type electromagnetic field exposure produced the most robust demonstration to date of a non-thermal, deleterious biological effect. Though these results appear to be a sound demonstration of non-thermal bioeffects, to our knowledge, no mechanism has been proposed to explain them. We show, apparently for the first time, that biogenic magnetite, a ferrimagnetic iron oxide, is present in C. elegans. Its presence may have confounding effects on experiments involving electromagnetic fields as well as implications for the use of this nematode as a model system for iron biomineralization in multicellular organisms. ------------------- Key: 7014 Medline: 15539484 Authors: Tian X;Hansen D;Schedl T;Skeath JB Title: Epsin potentiates Notch pathway activity in Drosophila and C. elegans. Citation: Development 131: 5807-5815 2004 Type: ARTICLE Genes: epn-1 glp-1 rrf-1 Abstract: Endocytosis and trafficking within the endocytosis pathway are known to modulate the activity of different signaling pathways. Epsins promote endocytosis and are postulated to target specific proteins for regulated endocytosis. Here, we present a functional link between the Notch pathway and epsins. We identify the Drosophila ortholog of epsin, liquid facets (lqf), as an inhibitor of cardioblast development in a genetic screen for mutants that affect heart development. We find that lqf inhibits cardioblast development and promotes the development of fusion-competent myoblasts, suggesting a model in which lqf acts on or in fusion-competent myoblasts to prevent their acquisition of the cardioblast fate. lqf and Notch exhibit essentially identical heart phenotypes, and lqf genetically interacts with the Notch pathway during multiple Notch-dependent events in Drosophila. We extended the link between the Notch pathway and epsin function to C elegans, where the C elegans lqf ortholog acts in the signaling cell to promote the glp-1/Notch pathway activity during germline development. Our results suggest that epsins play a specific, evolutionarily conserved role to promote Notch signaling during animal development and support the idea that they do so by targeting ligands of the Notch pathway for endocytosis. ------------------- Key: 7015 Medline: 15539489 Authors: Benard CY;Kebir H;Takagi S;Hekimi S Title: mau-2 acts cell-autonomously to guide axonal migrations in Caenorhabditis elegans. Citation: Development 131: 5947-5958 2004 Type: ARTICLE Genes: mau-2 slt-1 unc-6 unc-40 nDf23 nDf24 Abstract: The gene mau-2 has been found to be required for the guidance of cellular and axonal migrations along both the anteroposterior and the dorsoventral body axes during the development of the nematode C elegans. We show that mau-2 encodes a novel, previously uncharacterized protein that is highly conserved among animals. Maternal mau-2 gene expression is sufficient for normal development until the fourth larval stage, and a MAU-2::GFP fusion protein localizes to the cytoplasm of neurones. mau-2 is ubiquitously expressed in embryos by late gastrulation and becomes predominantly expressed in the nervous system as morphogenesis progresses. Expression of mau-2 within individual neurones rescues the guidance defects of mau-2 mutants, indicating that mau-2 functions cell-autonomously. Altering the activity of both the dorsal repellent slt-1 and mau-2 leads to the abnormal dorsal projection of the AVM axon, a phenotype that is novel and specific to the interaction of these two genes, indicating that mau-2 participates in the guidance of AVM by a slt-1-independent mechanism. Taken together, mau-2 defines a novel guidance factor that might be involved in the intracellular processing of guidance cues encountered by migrating cells and axons; during development. ------------------- Key: 7016 Medline: 15539493 Authors: Lai T;Garriga G Title: The conserved kinase UNC-51 acts with VAB-8 and UNC-14 to regulate axon outgrowth in C. elegans. Citation: Development 131: 5991-6000 2004 Type: ARTICLE Genes: unc-6 unc-14 unc-51 vab-8 Abstract: Directional cues guide growth cones. While molecules like UNC-6/netrin direct migrations along the dorsoventral axis of many organisms, it is unclear how anteroposterior guidance is achieved. We describe a physical interaction between VAB-8, a protein both necessary and sufficient for posteriorly directed migrations in C. elegans, and UNC-51, a conserved serine/threonine kinase that functions generally in axon outgrowth. We show that both proteins function in the CAN neurons to direct their axons posteriorly. Expression in the CANs of peptides predicted to interfere with interactions between UNC-51 and both VAB-8 and UNC-14, a second protein that interacts physically with UNC-51, disrupts CAN axon outgrowth. We provide genetic evidence that VAB-8 functions in an UNC-51 pathway for posteriorly directed CAN axon guidance and show that VAB-8 and UNC-14 can be targets of UNC-51 kinase activity. Taken together, our results suggest that VAB-8 and UNC-14 are substrates that mediate the function of ------------------- Key: 7017 Medline: 15576487 Authors: Li Y;Kelly WG;Logsdon JM;Schurko AM;Harfe BD;Hill-Harfe KL;Kahn RA Title: Functional genomic analysis of the ADP-ribosylation factor family of GTPases: phylogeny among diverse eukaryotes and function in C. elegans. Citation: FASEB Journal 18: 1834-1850 2004 Type: ARTICLE Genes: arf-1 arf-3 arf-6 arl-1 arl-2 arl-3 arl-5 arl-6 arl-8 evl-20 sar-1 Abstract: ADP-ribosylation factor (Arf) and Arf-like (Arl) proteins are a family of highly conserved 21 kDa GTPases that emerged early in the evolution of eukaryotes. These proteins serve regulatory roles in vesicular traffic, lipid metabolism, microtubule dynamics, development, and likely other cellular processes. We found evidence for the presence of 6 Arf family members in the protist Giardia lamblia and 22 members in mammals. A phylogenetic analysis was performed to delineate the evolutionary relationships among Arf family members and to attempt to organize them by both their evolutionary origins and functions in cells and/or organisms. The similar to 100 protein sequences analyzed from animals, fungi, plants, and protists clustered into 11 groups, including Arfs, nine Arls, and Sar proteins. To begin functional analyses of the family in a metazoan model organism, we examined roles for all three C. elegans Arfs (Arf-1, Arf-3, and Arf-6) and three Arls (Arl-1, Arl-2, and Arl-3) by use of RNA-mediated interference (RNAi). Injection of double-stranded RNA (dsRNA) encoding Arf-1 or Arf-3 into N2 hermaphrodites produced embryonic lethality in their offspring and, later, sterility in the injected animals themselves. Injection of Arl-2 dsRNA resulted in a disorganized germline and sterility in early offspring, with later offspring exhibiting an early embryonic arrest. Thus, of the six Arf family members examined in C. elegans, at least three are required for embryogenesis. These data represent the first analysis of the role(s) of multiple members of this family in the development of a multicellular organism. ------------------- Key: 7018 Medline: 15637588 Authors: Solari F;Bourbon-Piffaut A;Masse I;Payrastre B;Chan AML;Billaud M Title: The human tumour suppressor PTEN regulates longevity and dauer formation in Caenorhabditis elegans. Citation: Oncogene 24: 20-27 2005 Type: ARTICLE Genes: daf-2 daf-18 Abstract: The PTEN tumour suppressor is a phosphatase that dephosphorylates phosphatidylinositol 3, 4, 5 triphosphate (PIP3) and protein substrates. PTEN function is modulated by its carboxy-terminal region, which contains several clustered phosphorylation sites and a PDZ-binding motif (PDZbm). Although PTEN growth suppression effect is well demonstrated, its additional biological roles are less well understood. DAF-18, a Caenorhabditis elegans homologue PTEN, is a component of the insulin/IGF-I signalling pathway that controls entry to the dauer larval stage and adult longevity. To further explore the role of PTEN in the insulin signalling cascade and its possible involvement in the mechanisms of ageing, we undertook a study of PTEN function in C. elegans. We now report that human PTEN can substitute for DAF-18 and restores the dauer and longevity phenotypes in worms devoid of DAF-18. Furthermore, we provide genetic and biochemical evidence that dauer and lifespan control depends on PTEN-mediated regulation of PIP3 levels. Finally, we established that phosphorylation sites in the C-terminus of PTEN and its PDZbm are necessary for PTEN control of the insulin/IGF-I pathway. These results demonstrate that PTEN negatively regulates the insulin/IGF pathway in a whole organism and raise the hypothesis that PTEN may be involved in mammalian ageing. ------------------- Key: 7019 Medline: 15620652 Authors: Park FD;Tenlen JR;Priess JR Title: C. elegans MOM-5/Frizzled functions in MOM-2/Wnt-independent cell polarity and is localized asymmetrically prior to cell division. Citation: Current Biology 14: 2252-2258 2004 Type: ARTICLE Genes: lit-1 mom-1 mom-2 mom-5 pop-1 wrm-1 Abstract: C. elegans embryonic cells have a common anterior/ posterior (a/p) polarity that is apparent in the localization of the transcription factor POP-1 [1, 2]. The level of nuclear POP-1 remains high in the anterior daughters of dividing cells but is lowered in the posterior daughters [2, 3]. To generate POP-1 asymmetry, most early embryonic cells require contact with signaling cells that express the ligand MOM-2/Wnt [4, 5]; the point of cell contact specifies the daughter with low nuclear POP-1 [6, 7]. In contrast, slightly older embryonic cells that have no apparent prior exposure to Wnt signaling can generate POP-1 asymmetry, provided these cells express MOM-5/Frizzled [7]. We show here that MOM-5::GFP is enriched at the posterior pole of cells prior to division and that a similar asymmetry is observed in cultured cells with no apparent prior exposure to Wnt signaling. While depleting these latter cells of MOM-5/Frizzled causes both daughter cells to have high levels of POP-1 [7], we show that both daughter cells have low levels of POP-1 in embryos with atypically high levels of MOM-5::GFP. These results suggest that MOM-5/Frizzled asymmetry leads to POP-1 asymmetry. In later embryogenesis, we find that MOM-5::GFP localizes to the leading edges of epidermal cells during ventral enclosure. These localization patterns suggest a parallel between MOM-5/ Frizzled and the roles of Drosophila Frizzled in planar polarity and dorsal ------------------- Key: 7020 Medline: 15555070 Authors: Schulenburg H;Ewbank JJ Title: Diversity and specificity in the interaction between Caenorhabditis elegans and the pathogen Serratia Citation: BMC Evolutionary Biology 4: 1-8 2004 Type: ARTICLE Genes: Abstract: Background: Co-evolutionary arms races between parasites and hosts are considered to be of immense importance in the evolution of living organisms, potentially leading to highly dynamic life-history changes. The outcome of such arms races is in many cases thought to be determined by frequency dependent selection, which relies on genetic variation in host susceptibility and parasite virulence, and also genotype-specific interactions between host and parasite. Empirical evidence for these two prerequisites is scarce, however, especially for invertebrate hosts. We addressed this topic by analysing the interaction between natural isolates of the soil nematode Caenorhabditis elegans and the pathogenic soil bacterium Serratia marcescens. Results: Our analysis reveals the presence of i) significant variation in host susceptibility, ii) significant variation in pathogen virulence, and iii) significant strain- and genotype-specific interactions between the two species. Conclusions: The results obtained support the previous notion that highly specific interactions between parasites and animal hosts are generally widespread. At least for C. elegans, the high specificity is observed among isolates from the same population, such that it may provide a basis for and/or represent the outcome of co-evolutionary adaptations under natural conditions. Since both C. elegans and S. marcescens permit comprehensive molecular analyses, these two species provide a promising model system for inference of the molecular basis of such highly specific interactions, which are as yet unexplored in invertebrate hosts. ------------------- Key: 7021 Medline: 15618405 Authors: Chen N;Pai S;Zhao Z;Mah A;Newbury R;Johnsen RC;Altun Z;Moerman DG;Baillie DL;Stein LD Title: Identification of a nematode chemosensory gene family. Citation: Proceedings of the National Academy of Sciences USA 102: 146-151 2005 Type: ARTICLE Genes: Abstract: Taking advantage of the recent availability of the whole genome sequence of Caenorhabditis briggsae, a closely related nematode to Caenorhabditis elegans, we have examined the chemosensory gene superfamily by using comparative genomic methods. We have identified a chemosensory gene family, serpentine receptor class ab (srab), which exists in both species with 25 members in C elegans and 14 members in C briggsae. More than 20% of these gene models are reannotated. The srab family is similar to, but distinct from, the previously described serpentine receptor class a (sra) family and shows a differential expansion in C elegans similar to that previously described for sra. The cellular expression patterns for multiple members of the srab family in both phasmid neurons in the tail and amphid neurons in the head supports the conclusion that they are chemosensory genes and suggests that they may play a role in integrating chemosensory inputs from both ends of the organism. The expansion of both the srab and sra gene families in C elegans relative to C briggsae is due to multiple rounds of ------------------- Key: 7022 Medline: Authors: Willson J;Amliwala K;Davis A;Cook A;Cuttle MF;Kriek N;Hopper NA;O'Connor V;Harder A;Walker RJ;Holden-Dye L Title: Latrotoxin recetor signaling engages the UNC-13-dependent vesicle-priming pathway in C. elegans. Citation: Current Biology 14: 2310- 2004 Type: CORRECT Genes: lat-1 Abstract: ------------------- Key: 7023 Medline: Authors: Verbrugghe KJC;White JG Title: SPD-1 is required for the formation of the spindle midzone but is not essential for the completion of cytokinesis in C. elegans embryos. Citation: Current Biology 14: 2311- 2004 Type: CORRECT Genes: spd-1 Abstract: ------------------- Key: 7024 Medline: Authors: Wickelgren I Title: As the worms ages: epilepsy drugs lengthen nematode life span. Citation: Science 307: 193- 2005 Type: REVIEW Genes: Abstract: ------------------- Key: 7025 Medline: 15621535 Authors: Myers TR;Greenwald I Title: lin-35 Rb acts in the major hypodermis to oppose Ras-mediated vulval induction in C. elegans. Citation: Developmental Cell 8: 117-123 2005 Type: ARTICLE Genes: dpy-7 let-60 lin-8 lin-31 lin-35 Abstract: Specification of vulval precursor cell (VPC) fates in C. elegans has served as an important signal transduction paradigm. Genetic studies have indicated that a large group of synthetic multivulva (SynMuv) genes, including the Rb ortholog lin-35, antagonizes the activity of the EGF receptor-Ras-MAP kinase pathway during VPC specification. A prevalent view has been that Rb-mediated transcriptional regulation and chromatin remodeling activities act in the VPCs to antagonize Ras activation through effects on promoters of target genes of the EGF receptor-Ras-MAP kinase pathway that promote vulval fates. Here, we have investigated the cellular focus of lin-35 using conventional genetic mosaic analysis and tissue-specific expression. Our results indicate that lin-35 activity is required in the major hypodermal syncytium and not in the VPCs to inhibit vulval fates. LIN-35 Rb may inhibit vulval fates by regulating a signal from hyp7 to the VPCs or the physiological state of hyp7. ------------------- Key: 7026 Medline: 15620647 Authors: de Bakker CD;Haney LB;Kinchen JM;Grimsley C;Lu M;Klingele D;Hsu PK;Chou BK;Cheng LC;Blangy A;Sondek J;Hengartner MO;Wu YC;Ravichandran KS Title: Phagocytosis of apoptotic cells is regulated by an UNC-73/TRIO-MIG-2/RhoG signaling module and armadillo repeats of CED-12/ELMO. Citation: Current Biology 14: 2208-2216 2004 Type: ARTICLE Genes: ced-2 ced-5 ced-10 ced-12 mig-2 rac-2 unc-73 Abstract: Background: Phagocytosis of cells undergoing apoptosis is essential during development, cellular turnover, and wound healing. Failure to promptly clear apoptotic cells has been linked to autoimmune disorders. C. elegans CED-12 and mammalian ELMO are evolutionarily conserved scaffolding proteins that play a critical role in engulfment from worm to human. ELMO functions together with Dock180 (a guanine nucleotide exchange factor for Rac) to mediate Rac-dependent cytoskeletal reorganization during engulfment and cell migration. However, the components upstream of ELMO and Dock180 during engulfment remain elusive. Results: Here, we define a conserved signaling module involving the small GTPase RhoG and its exchange factor TRIO, which functions upstream of ELMO/Dock180/ Rac during engulfment. Complementary studies in C. elegans show that MIG-2 (which we identify as the homolog of mammalian RhoG) and UNC-73 (the TRIO homolog) also regulate corpse clearance in vivo, upstream of CED-12. At the molecular level, we identify a novel set of evolutionarily conserved Armadillo (ARM) repeats within CED-12/ELMO that mediate an interaction with activated MIG-2/RhoG; this, in turn, promotes Dock180-mediated Rac activation and cytoskeletal reorganization. Conclusions: The combination of in vitro and in vivo studies presented here identify two evolutionarily conserved players in engulfment, TRIO/UNC73 and RhoG/ MIG-2, and the TRIO --> RhoG signaling module is linked by ELMO/CED-12 to Dock180-dependent Rac activation during engulfment. This work also identifies ARM repeats within CED-12/ELMO and their role in linking RhoG and Rac, two GTPases that function in tandem during engulfment. ------------------- Key: 7027 Medline: 15620651 Authors: Colosimo ME;Brown A;Mukhapodhyay S;Gabel C;Lanjuin AE;Samuel ADT;Sengupta P Title: Identification of thermosensory and olfactory neuron-specific genes via expression profiling of single neuron types. Citation: Current Biology 14: 2245-2251 2004 Type: ARTICLE Genes: ceh-37 dac-1 daf-11 dgk-3 gcy-8 nhr-38 nlp-3 nlp-7 odr-1 odr-3 srd-16 srd-23 sru-38 str-220 ttx-1 zyg-8 Abstract: Most C. elegans sensory neuron types consist of a single bilateral pair of neurons, and respond to a unique set of sensory stimuli. Although genes required for the development and function of individual sensory neuron types have been identified in forward genetic screens, these approaches are unlikely to identify genes that when mutated result in subtle or pleiotropic phenotypes. Here, we describe a complementary approach to identify sensory neuron type-specific genes via microarray analysis using RNA from sorted AWB olfactory and AFD thermosensory neurons. The expression patterns of subsets of these genes were further verified in vivo. Genes identified by this analysis encode 7-transmembrane receptors, kinases, and nuclearfactors including dac-1, which encodes a homolog of the highly conserved Dachshund protein [1]. dac-1 is expressed in a subset of sensory neurons including the AFD neurons and is regulated by the TTX-1 OTX homeodomain protein [2]. On thermal gradients, dac-1 mutants fail to suppress a cryophilic drive but continue to track isotherms at the cultivation temperature, representing the first genetic separation of these AFD-mediated behaviors. Expression profiling of single neuron types provides a rapid, powerful, and unbiased method for identifying neuron-specific genes whose functions can then be ------------------- Key: 7028 Medline: 15605074 Authors: Schumacher B;Schertel C;Wittenburg N;Tuck S;Mitani S;Gartner A;Conradt B;Shaham S Title: C. elegans ced-13 can promote apoptosis and is induced in response to DNA damage. Citation: Cell Death and Differentiation 12: 153-161 2005 Type: ARTICLE Genes: ced-3 ced-4 ced-9 ced-13 cep-1 egl-1 glp-4 mrt-2 Abstract: The p53 tumor suppressor promotes apoptosis in response to DNA damage. Here we describe the Caenorhabditis elegans gene ced-13, which encodes a conserved BH3-only protein. We show that ced-13 mRNA accumulates following DNA damage, and that this accumulation is dependent on an intact C. elegans cep-1/p53 gene. We demonstrate that CED-13 protein physically interacts with the antiapoptotic Bcl-2-related protein CED-9. Furthermore, overexpression of ced-13 in somatic cells leads to the death of cells that normally survive, and this death requires the core apoptotic pathway of C. elegans. Recent studies have implicated two BH3-only proteins, Noxa and PUMA, in p53-induced apoptosis in mammals. Our studies suggest that in addition to the BH3-only protein EGL-1, CED-13 might also promote apoptosis in the C. elegans germ line in response to p53 activation. We propose that an evolutionarily conserved pathway exists in which p53 promotes cell death by inducing expression of two BH3-only genes. ------------------- Key: 7029 Medline: 15639227 Authors: Lee BC;Lee YK;Lee HJ;Stadtman ER;Lee KH;Chung N Title: Cloning and characterization of antioxidant enzyme methionine sulfoxide-S-reductase from Caenorhabditis elegans. Citation: Archives of Biochemistry & Biophysics 434: 275-281 2004 Type: ARTICLE Genes: Abstract: Methionine (Met) residues in proteins are susceptible to oxidation. The resulting methionine sulfoxide can be reduced back to methionine by methionine, sulfoxide-S-reductase (MsrA). The MsrA gene, isolated front Caenorhabditis elegans was cloned and expressed in Escherichia coli. The resultant enzyme Was able to revert both free Met and Met in proteins in the presence of either NADPH or dithiothreitol (DTT). However, approximately seven times higher enzyme activity was observed in the presence of DTT than of NADPH. The enzyme had an absolute specificity for the reduction Of L-methionine-S-sulfoxide but no specificity for the R isomer. K-m and k(cat) values for the enzyme were similar to1.18 mM and 3.64 min(-1), respectively. Other kinetics properties of the enzyme were ------------------- Key: 7030 Medline: 15496475 Authors: Lamitina ST;Strange K Title: Transcriptional targets of DAF-16 insulin signaling pathway protect C. elegans from extreme hypertonic stress. Citation: American Journal of Physiology - Cell Physiology 288: C467-C474 2005 Type: ARTICLE Genes: age-1 daf-2 daf-16 fat-6 hgo-1 ifa-1 tps-1 tps-2 Abstract: All cells adapt to hypertonic stress by regulating their volume after shrinkage, by accumulating organic osmolytes, and by activating mechanisms that protect against and repair hypertonicity-induced damage. In mammals and nematodes, inhibition of signaling from the DAF-2/IGF-1 insulin receptor activates the DAF-16/FOXO transcription factor, resulting in increased life span and resistance to some types of stress. We tested the hypothesis that inhibition of insulin signaling in Caenorhabditis elegans also increases hypertonic stress resistance. Genetic inhibition of DAF-2 or its downstream target, the AGE-1 phosphatidylinositol 3-kinase, confers striking resistance to a normally lethal hypertonic shock in a DAF-16-dependent manner. However, insulin signaling is not inhibited by or required for adaptation to hypertonic conditions. Microarray studies have identified 263 genes that are transcriptionally upregulated by DAF-16 activation. We identified 14 DAF-16-upregulated genes by RNA interference screening that are required for age-1 hypertonic stress resistance. These genes encode heat shock proteins, proteins of unknown function, and trehalose synthesis enzymes. Trehalose levels were elevated approximately twofold in age-1 mutants, but this increase was insufficient to prevent rapid hypertonic shrinkage. However, age-1 animals unable to synthesize trehalose survive poorly under hypertonic conditions. We conclude that increased expression of proteins that protect eukaryotic cells against environmental stress and/or repair stress-induced molecular damage confers hypertonic stress resistance in C. elegans daf-2/ age-1 mutants. Elevated levels of solutes such as trehalose may also function in a cytoprotective manner. Our studies provide novel insights into stress resistance in animal cells and a foundation for new studies aimed at defining molecular mechanisms ------------------- Key: 7031 Medline: 15625192 Authors: Chuang CF;Bargmann CI Title: A Toll-interleukin 1 repeat protein at the synapse specifies asymmetric odorant receptor expression via ASK1 MAPKKK signaling. Citation: Genes & Development 19: 270-281 2005 Type: ARTICLE Genes: lin-10 nsy-1 nsy-2 odr-3 ofm-1 sek-1 str-2 tir-1 unc-2 unc-36 unc-43 unc-76 Abstract: A stochastic lateral signaling interaction between two developing Caenorhabditis elegans AWC olfactory neurons causes them to take on asymmetric patterns of odorant receptor expression, called AWC(OFF) and AWC(ON). Here we show that the AWC lateral signaling gene tir-1 (previously known as nsy-2) encodes a conserved post-synaptic protein that specifies the choice between AWC(OFF) and AWC(ON). Genetic evidence suggests that tir-1 acts downstream of a voltage-gated calcium channel and CaMKH (UNC-43) to regulate AWC asymmetry via the NSY-1(ASK1) p38/JNK MAP (mitogen-activated protein) kinase cascade. TIR-1 localizes NSY-1 to post-synaptic regions of AWC, and TIR-1 binds UNC-43, suggesting that it assembles a synaptic signaling complex that regulates odorant receptor expression. Temperature-shift experiments indicate that tir-1 affects AWC during a critical period late in embryogenesis, near the time of AWC synapse formation. TIR-1 is a multidomain protein with a TIR (Toll-interleukin-1 receptor) domain that activates signaling, SAM repeats that mediate localization to post-synaptic regions of axons, and an N-terminal inhibitory domain. TIR-1 and other TIR proteins are implicated in vertebrate and invertebrate innate immunity, as are NSY-1/ASK1 kinases, so this pathway may also have a conserved function in immune signaling. ------------------- Key: 7032 Medline: 15614779 Authors: Birnbaum D;Popovici C;Roubin R Title: A pair as a minimum: the two fibroblast growth factos of the nematode Caenorhabditis elegans. Citation: Developmental Dynamics 232: 247-255 2005 Type: REVIEW Genes: clr-1 dab-1 dbl-1 egl-15 egl-17 egl-20 ina-1 let-60 let-341 let-756 lin-45 mek-2 mpk-1 ptp-2 sax-3 sem-5 slt-1 soc-1 soc-2 sur-8 unc-5 unc-6 unc-40 unc-129 Abstract: Fibroblast growth factors (FGFs) regulate many important developmental and homeostatic physiological events. The FGF superfamily contains several families. In this review, we present recent findings on the two FGFs of the nematode Caenorhabditis elegans from both functional and phylogenic points of view. C. elegans has a single FGFR (EGL-15) with two functionally exclusive isoforms, and two FGFs (LET-756 and EGL-17), which play distinct roles: an essential function for the former, and guidance of the migrating sex myoblasts for the latter. Regulation of homeostasis by control of the fluid balance could be the basis for the essential function of LET-756. Phylogenetic and functional studies suggest that LET-756, like vertebrate FGF9, -16, and -20, belongs to the FGF9 family, whereas EGL-17, like vertebrate FGF8, -17, and -18, could be included in the FGF8 family. ------------------- Key: 7033 Medline: 15652154 Authors: Dong J;Song MO;Freedman JH Title: Identification and characterization of a family of Caenorhabditis elegans genes that is homologous to the cadmium-responsive gene cdr-1. Citation: Biochimica et Biophysica Acta - Gene Structure and Expression 1727: 16-26 2005 Type: ARTICLE Genes: cdr-1 cdr-2 cdr-3 cdr-4 cdr-5 cdr-6 cdr-7 Abstract: Six Caenorhabditis elegans genes that are homologous to the novel, cadmium-responsive gene cdr-1 have been identified and characterized. Nucleotide and amino acid sequence comparisons among the CDR family, which includes cdr-1, cdr-2, cdr-3, cdr-4, cdr-5, cdr-6, and cdr-7, reveals a high degree of identity among the seven members in this family. There are high levels of amino acid and nucleotide sequence similarity in the lengths of the open reading frames, predicted sizes, and protein characteristics. The seven proteins are predicted to be extremely hydrophobic, and are classified as integral membrane proteins. Structural analysis of the predicted proteins suggests that they may have similar biological functions. In response to cadmium exposure, cdr-1, cdr-2, cdr-3, and cdr-4 transcription significantly increases. In contrast, the levels of cdr-5, cdr-6, and cdr-7 transcription are not significantly affected or inhibited by cadmium exposure. Further, in non-exposed C elegans, cdr-2, cdr-4, cdr-6, and cdr-7 are constitutively expressed. When CDR-1 expression was inhibited using RNAi, numerous fluid droplets were observed throughout the nematode body cavity. This phenotype became more pronounced in the presence of hypotonic stress. This suggests that CDR-1 may function in osmoregulation to maintain salt balance in C. elegans. ------------------- Key: 7034 Medline: 15619469 Authors: Rodriguez-Aguilera JC;Gavilan A;Asencio C;Navas P Title: The role of ubiquinon in Caenorhabditis elegans longevity. Citation: Ageing Research Reviews 4: 41-53 2005 Type: REVIEW Genes: age-1 cat-5 clk-1 clk-2 clk-3 coq-1 coq-2 coq-3 coq-4 coq-5 coq-6 coq-7 coq-8 daf-2 daf-16 daf-18 gro-1 pdk-1 sod-2 Abstract: Aging is an irreversible physiological process that affects all living organisms. Different mutations in the insulin signaling pathway and caloric restriction have been shown to retard aging in Caenorhabditis elegans. In addition, mutations or RNAi silencing of components of the respiratory chain results in the modification of adult life span. Another class of genes that affect life span in C. elegans is the clock (clk) genes. Particularly interesting is clk-1, which encodes an enzyme required for ubiquinone (coenzyme Q, CoQ) biosynthesis. Down-regulation by RNAi silencing of the genes required for ubiquinone biosynthesis also extends life span in C. elegans, and CoQ supplied in the diet also affects nematode longevity in both clk-1 and wild-type strains. Although there are many aspects that can be considered in aging, we focus this review on the role of CoQ in the longevity of C. elegans. We will review the current information about the biosynthesis of CoQ and its dietary supplementation related to the extension of life span. We will also analyze the function of CoQ in the electron transport chain and reactive oxygen species production in the context of aging. We hypothesize that the role of CoQ on longevity of C. elegans supports the oxidative damage theory of aging. ------------------- Key: 7035 Medline: 15619471 Authors: Smelick C;Ahmed S Title: Achieving immortality in the C. elegans germline. Citation: Ageing Research Reviews 4: 67-82 2005 Type: REVIEW Genes: hus-1 mre-11 mrt-2 Abstract: Germline immortality is a topic that has intrigued theoretical biologists interested in aging for over a century. The germ cell lineage can be passed from one generation to the next, indefinitely. In contrast, somatic cells are typically only needed for a single generation and are then discarded. Germ cells may, therefore, harbor rejuvenation mechanisms that enable them to proliferate for eons. Such processes are thought to be either absent from or down-regulated in somatic cells, although cell non-autonomous forms of rejuvenation are formally possible. A thorough description of mechanisms that foster eternal youth in germ cells is lacking. The mysteries of germline immortality are being addressed in the nematode Caenorhabditis elegans by studying mutants that reproduce normally for several generations but eventually become sterile. The mortal germline mutants probably become sterile as a consequence of accumulating various forms of heritable cellular damage. Such mutants are abundant, indicating that several different biochemical pathways are required to rejuvenate the germline. Thus, forward genetics should help to define mechanisms that enable the germline to achieve immortality. ------------------- Key: 7036 Medline: 15642374 Authors: Xu X;Lee D;Shih HY;Seo S;Ahn J;Lee M Title: Linking integrin to IP3 signaling is important for ovulation in Caenorhabditis elegans. Citation: FEBS Letters 579: 549-553 2005 Type: ARTICLE Genes: emb-9 epi-1 ipp-5 itr-1 let-2 lfe-1 lfe-2 pat-3 pat-10 plc-3 rrf-1 Abstract: Signals from germ and myoepithelial sheath cells initiate ovulation in Caenorhabditis elegans. The coordinated dilation and contraction of spermatheca lead to subsequent fertilization of oocyte. Either the dominant negative mutant pat-3 beta integrin or disruption of talin expression block ovulation [Cram, E.J., Clark, S.G. and Schwarzbauer, J.E. (2003) Talin loss-of-function uncovers roles in cell contractility and migration in C. elegans. J. Cell. Sci. 116, 3871-3878; Lee, M., Cram, E.J., Shen, B. and Schwarzbauer, J.E. (2001) Role of beta pat-3 integrins in development and function of Caenorhabditis elegans muscles and gonads. J. Biol. Chem. 276, 36404-36410], suggesting that the interaction between the cell and the extracellular matrix (ECM) is also important for ovulation. Here, we report that integrin plays an essential role in fertility via IP3 signaling. Sterility caused by RNAi of pat-3 and ECM molecules was suppressed by increased IP3 signaling. Our data suggest that the cell-ECM interaction controls ovulation via IP3 signaling. ------------------- Key: 7037 Medline: 15621439 Authors: Wareham DW;Papakonstantinopoulou A;Curtis MA Title: The Pseudomonas aeruginosa PA14 type III secretion system is expressed but not essential to virulence in the Caenorhabditis elegans-P. aeruginosa pathogenicity model. Citation: FEMS Microbiology Letters 242: 209-216 2005 Type: ARTICLE Genes: sek-1 Abstract: The Pseudomonas aeruginosa type III secretion system (TTSS), enabling direct injection of toxins into host cells, has been shown to be crucial to virulence in several models of P. aeruginosa pathogenesis. Using the strain PA14 and its isogenic mutant, PA14exsA, we investigated the role of the TTSS during infection of the nematode Caenorhabditis elegans. Although C elegans N2 was killed by PA14 in an infection like process over 48 to 72 h the same effect was observed following infection with PA14exsA, implying that a functional TTSS was not essential for virulence. This was despite the TTSS being actively expressed during C elegans infection as demonstrated by the use of green fluorescent reporter constructs and RT-PCR. However, compared to the wild type PA14, PA14exsA did display a reduced rate of killing of C elegans strain AU1 which harbours a mutation in the sek-1 gene encoding a MAP kinase involved in nematode innate immunity. A fuller understanding of the mechanism of resistance to type III attack in C elegans may lead to the identification and development of novel therapeutic targets affording protection to TTSS products ------------------- Key: 7038 Medline: 15542610 Authors: Jiang G;Zhuang L;Miyauchi S;Miyake K;Fei YJ;Ganapathy V Title: A Na+/Cl- coupled GABA transporter, GAT-1, from Caenorhabditis elegans. Citation: Journal of Biological Chemistry 280: 2065-2077 2005 Type: ARTICLE Genes: gat-1 rrf-3 snf-11 unc-2 unc-25 unc-47 Abstract: GABA functions as an inhibitory neurotransmitter in body muscles and as an excitatory neurotransmitter in enteric muscles in Caenorhabditis elegans. Whereas many of the components of the GABA-ergic neurotransmission in this organism have been identified at the molecular and functional levels, no transporter specific for this neurotransmitter has been identified to date. Here we report on the cloning and functional characterization of a GABA transporter from C. elegans (ceGAT-1) and on the functional relevance of the transporter to the biology of body muscles and enteric muscles. ceGAT-1 is coded by snf-11 gene, a member of the sodium-dependent neurotransmitter symporter gene family in C. elegans. The cloned ceGAT-1 functions as a Na+/Cl--coupled high-affinity transporter selective for GABA with a K-t of similar to15 muM. The Na+:Cl-:GABA stoichiometry for ce-GAT-1-mediated transport process is 2:1:1. The transport process is electrogenic as evidenced from GABA-induced inward currents in Xenopus laevis oocytes that express ceGAT-1 heterologously. The transporter is expressed exclusively in GABA-ergic neurons and in two other additional neurons. We also investigated the functional relevance of ceGAT-1 to the biology of body muscles and enteric muscles by ceGAT-1-specific RNA interference (RNAi) in rrf-3 mutant, a strain of C. elegans in which neurons are not refractory to RNAi as in the wild type strain. The down-regulation of ceGAT-1 by RNAi leads to an interesting phenotype associated with altered function of body muscles ( as evident from changes in thrashing frequency) and enteric muscles ( as evident from the rates of defecation failure) and also with altered sensitivity to aldicarb-induced paralysis. These findings provide unequivocal evidence for a modulatory role of GABA and ceGAT-1 in the biology of cholinergic neurons and in the function of body muscles and ------------------- Key: 7039 Medline: 15690045 Authors: Jeong PY;Jung M;Yim YH;Kim H;Park M;Hong EM;Lee W;Kim YH;Kim K;Paik YK Title: Chemical structure and biological activity of the Caenorhabditis elegans dauer-inducing pheromone. Citation: Nature 433: 541-545 2005 Type: ARTICLE Genes: che-3 che-11 daf-3 daf-5 daf-6 daf-10 daf-11 daf-12 daf-13 daf-16 daf-18 daf-22 Abstract: Pheromones are cell type-specific signals used for communication between individuals of the same species. When faced with overcrowding or starvation, Caenorhabditis elegans secrete the pheromone daumone, which facilitates communication between individuals for adaptation to adverse environmental stimuli(1-4). Daumone signals C. elegans to enter the dauer stage, an enduring and non-ageing stage of the nematode life cycle with distinctive adaptive features and extended life. Because daumone is a key regulator of chemosensory processes in development and ageing(5,6), the chemical identification of daumone is important for elucidating features of the daumone-mediated signalling pathway. Here we report the isolation of natural daumone from C. elegans by large-scale purification, as well as the total chemical synthesis of daumone. We present the stereospecific chemical structure of purified daumone, a fatty acid derivative. We demonstrate that both natural and chemically synthesized daumones equally induce dauer larva formation in C. elegans (N2 strain) and certain dauer mutants, and also result in competition between food and daumone. These results should help to elucidate the daumone-mediated signalling pathway, which might in turn influence ageing and obesity research and the development of antinematodal drugs. ------------------- Key: 7040 Medline: 15635489 Authors: Hafen E Title: Cancer, type 2 diabetes, and ageing: news from flies and worms. Citation: Swiss Medical Weekly 134: 711-719 2004 Type: REVIEW Genes: daf-16 Abstract: The turnout suppressor gene PTEN is, next to p53, the second most frequently mutated gene in human cancers. The genes TSC1 and TSC2 are mutated in the severe human syndrome called Tuberous Sclerosis. Patients with this disease have large benign tumours composed of large cells in the brain. The genetic dissection of pathways controlling the growth of cells, organs, and the entire organism in Drosophila has contributed to the understanding of the signalling pathways that are controlled by these two turnout suppressors. Together with, studies on nutrient regulation of growth and ageing in the nematode Caenorhabditis elegans, evidence from these model organisms has moved the Insulin/IGF (IIS) and the Target Rapamycin (TOR) signalling pathway onto the centre stage of cellular growth control and made them attractive novel targets for cancer therapy. In this review, I will outline the contributions of model organism genetics to the understanding of these disease relevant pathways and highlight the evolutionary conservation of ------------------- Key: 7041 Medline: 15610759 Authors: Troulinaki K;Tavernarakis N Title: Neurodegenerative conditions associated with ageing: a molecular interplay? Citation: Mechanisms of Ageing & Development 126: 23-33 2005 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ced-12 deg-1 mec-4 Abstract: The ageing process precipitates dramatic alterations in the physiology of all organisms, including reduced cellular function, compromised resistance to stress and pathological agents, and increased likelihood of developing age-related diseases. Among the, most characteristic pathologies associated with old age are numerous late-onset neurodegenerative disorders such as Alzheimer's. Parkinson's and Huntington's diseases. In addition to stroke, which also inflicts loss of neuronal cells, these conditions account for ever-increasing debilitation among the elderly. Recent studies in model organisms such as the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster. which offer the prowess of sophisticated genetic approaches. have uncovered significant, novel aspects of the molecular mechanisms that underlie both neurodegeneration and the ageing process. These advances hold promise that the intimate link between the, aged state and the manifestation of several neurodegenerative diseases will be deciphered. Here. we discuss the mechanisms by which ageing interfaces with. and influences, the progression of neurodegeneration. ------------------- Key: 7042 Medline: 15610772 Authors: Hertweck M;Baumeister R Title: Automated assays to study longevity in C. elegans. Citation: Mechanisms of Ageing & Development 126: 139-145 2005 Type: REVIEW Genes: age-1 akt-1 akt-2 ctl-1 ctl-2 daf-2 daf-15 daf-16 daf-18 dao-1 dao-5 dao-8 dao-9 let-363 mtl-1 mtl-2 old-1 pep-2 pdk-1 sgk-1 sod-1 sod-3 Abstract: The nematode Caenorhabditis elegans is excellently suited as a model for studying the genetic and molecular genetic basis of aging, and to test chemical compounds that interfere with the aging process. Mutants of factors in both the insulin and target of rapamycin (TOR) signalling pathways have been shown to extend life span of the worm. Phenotypic similarities among those mutants suggested that, exploiting the corresponding phenotypes in a semiautomated way, may increase the speed of investigating life span and aging in C elegans. Here, we discuss several methodological approaches to automate longevity assays in the nematode. ------------------- Key: 7043 Medline: 15669958 Authors: Cutter AD Title: Mutation and the experimental evolution of outcrossing in Caenorhabditis elegans. Citation: Journal of Evolutionary Biology 18: 27-34 2005 Type: ARTICLE Genes: msh-6 spe-27 Abstract: An understanding of the forces that contribute to the phylogenetically widespread phenomenon of sexual reproduction has posed a longstanding problem in evolutionary biology. Mutational theories contend that sex can be maintained when the deleterious mutation rate is sufficiently high, although empirical evidence is equivocal and experimental studies are rare. To test the influence of mutation on the evolution of obligate outcrossing, I introduced a genetic polymorphism for breeding system into populations of the nematode Caenorhabditis elegans with high- and low-mutation rate genetic backgrounds and tracked the change in frequency of females, hermaphrodites, and males over approximately 21 generations. Hermaphrodites invaded all populations, regardless of mutational background. However, experimental populations with elevated mutation rates experienced more outcrossing and greater retention of females. This provides experimental evidence consistent with deleterious mutational explanations for the evolution of sex in principle, but the action of other processes is required to explain the evolution of sex in entirety. ------------------- Key: 7044 Medline: 15563467 Authors: Jose AM;Koelle MR Title: Domains, amino acid residues, and new isoforms of Caenorhabditis elegans diacylglycerol kinase 1 (DGK-1) important for terminating diacylglycerol signaling in vivo. Citation: Journal of Biological Chemistry 280: 2730-2736 2005 Type: ARTICLE Genes: dgk-1 goa-1 Abstract: Diacylglycerol kinases (DGKs) inhibit diacylglycerol (DAG) signaling by phosphorylating DAG. DGK-1, the Caenorhabditis elegans ortholog of human neuronal DGKtheta, inhibits neurotransmission to control behavior. DGK-1, like DGKtheta, has three cysteine-rich domains (CRDs), a pleckstrin homology domain, and a kinase domain. To identify DGK domains and amino acid residues critical for terminating DAG signaling in vivo, we analyzed 20 dgk-1 mutants defective in DGK-1-controlled behaviors. We found by sequencing that the mutations included nine amino acid substitutions and seven premature stop codons that impair the physiological functions of DGK-1. All nine amino acid substitutions are in the second CRD, the third CRD, or the kinase domain. Thus, these domains are important for the termination of DAG signaling by DGK-1 in vivo. Seven of the substituted amino acid residues are present in all human DGKs and likely define key residues required for the function of all DGKs. An ATP-binding site mutation expected to inactivate the kinase domain retained very little physiological function, but we found two stop codon mutants predicted to truncate DGK-1 before its kinase domain that retained significantly more function. We detected novel splice forms of dgk-1 that can reconcile this apparent conflict, as they skip exons containing the stop codons to produce DGK-1 isoforms that contain the kinase domain. Two of these isoforms lack an intact pleckstrin homology domain and yet appear to have significant function. Additional novel isoform(s) account for all of the DGK-1 function necessary for one behavior, dopamine response. ------------------- Key: 7045 Medline: 15666355 Authors: Nance J Title: PAR proteins and the establishment of cell polarity during C. elegans development. Citation: BioEssays 27: 126-135 2005 Type: REVIEW Genes: air-1 cdc-42 cul-2 cyk-4 gpr-1 gpr-2 let-99 let-413 mex-5 mex-6 mlc-4 nmy-2 par-1 par-2 par-3 par-4 par-5 par-6 pfn-1 pie-1 pkc-3 pod-1 spd-2 spd-5 zen-4 Abstract: Cells become polarized to develop functional specializations and to distribute developmental determinants unequally during division. Studies that began in the nematode C. elegans have identified a group of largely conserved proteins, called PAR proteins, that play key roles in the polarization of many different cell types. During initial stages of cell polarization, certain PAR proteins become distributed asymmetrically along the cell cortex and subsequently direct the localization and/or activity of other proteins. Here I discuss recent findings on how PAR proteins become and remain asymmetric in three different contexts during C. elegans development: anterior-posterior polarization of the one-cell embryo, apicobasal polarization of non-epithelial early embryonic cells, and apicobasal polarization of epithelial cells. Although polarity within each of these cell types requires PAR proteins, the cues and regulators of PAR asymmetry can ------------------- Key: 7046 Medline: 15563610 Authors: Hu J;Barr MM Title: ATP-2 interacts with the PLAT domain of LOV-1 and is involved in Caenorhabditis elegans polycystin signaling. Citation: Molecular Biology of the Cell 16: 458-469 2005 Type: ARTICLE Genes: asb-1 asg-2 atp-2 lov-1 nuo-1 odr-10 osm-5 pkd-2 Abstract: Caenorhabditis elegans is a powerful model to study the molecular basis of autosomal dominant polycystic kidney disease (ADPKD). ADPKD is caused by mutations in the polycystic kidney disease (PKD)1 or PKD2 gene, encoding polycystin (PC)-1 or PC-2, respectively. The C. elegans polycystins LOV-1 and PKD-2 are required for male mating behaviors and are localized to sensory cilia. The function of the evolutionarily conserved polycystin/lipoxygenase/alpha-toxin (PLAT) domain found in all PC-1 family members remains an enigma. Here, we report that ATP-2, the beta subunit of the ATP synthase, physically associates with the LOV-1 PLAT domain and that this interaction is evolutionarily conserved. In addition to the expected mitochondria localization, ATP-2 and other ATP synthase components colocalize with LOV-1 and PKD-2 in cilia. Disrupting the function of the ATP synthase or overexpression of atp-2 results in a male mating behavior defect. We further show that atp-2, lov-1, and pkd-2 act in the same molecular pathway. We propose that the ciliary localized ATP synthase may play a previously unsuspected role in polycystin signaling. ------------------- Key: 7047 Medline: 15563606 Authors: Sakamoto R;Byrd DT;Brown HM;Hisamoto N;Matsumoto K;Jin Y Title: The Caenorhabditis elegans UNC-14 RUN domain protein binds to the kinesin-1 and UNC-16 complex and regulates synaptic vesicle localization. Citation: Molecular Biology of the Cell 16: 483-496 2005 Type: ARTICLE Genes: klc-1 klc-2 sem-4 unc-14 unc-16 unc-116 Abstract: Kinesin-1 is a heterotetramer composed of kinesin heavy chain (KHC) and kinesin light chain (KLC). The Caenorhabditis elegans genome has a single KHC, encoded by the unc-116 gene, and two KLCs, encoded by the klc-1 and klc-2 genes. We show here that UNC-116/KHC and KLC-2 form a complex orthologous to conventionai kinesin-1. KLC-2 also binds UNC-16, the C. elegans JIP3/JSAP1 JNK-signaling scaffold protein, and the UNC-14 RUN domain protein. The localization of UNC-16 and UNC-14 depends on kinesin-1 (UNC-116 and KLC-2). Furthermore, mutations in unc-16, klc-2, unc-116, and unc-14 all alter the localization of cargos containing synaptic vesicle markers. Double mutant analysis is consistent with these four genes functioning in the same pathway. Our data support a model whereby UNC-16 and UNC-14 function together as kinesin-1 cargos and regulators for the transport or localization of synaptic vesicle components. ------------------- Key: 7048 Medline: 15548597 Authors: Bishop JD;Han Z;Schumacher JM Title: The Caenorhabditis elegans Aurora B kinase AIR-2 phophorylates and is required for the localization of a BimC kinesin to meiotic and mitotic spindles. Citation: Molecular Biology of the Cell 16: 742-756 2005 Type: ARTICLE Genes: air-1 air-2 bmk-1 icp-1 zen-4 Abstract: BimC kinesins are required for mitotic spindle assembly in a variety of organisms. These proteins are localized to centrosomes, spindle microtubules, and the spindle midzone. We have previously shown that the Caenorhabditis elegans Aurora B kinase AIR-2 is required for the localization of the ZEN-4 kinesin protein to midzone microtubules. To determine whether the association of BimC kinesins with spindle microtubules is also dependent on AIR-2, we examined the expression pattern of BMK-1, a C. elegans BimC kinesin, in wild-type and AIR-2-deficient embryos. BMK-1 is highly expressed in the hermaphrodite gonad and is localized to meiotic spindle microtubules in the newly fertilized embryo. In mitotic embryos, BMK-1 is associated with spindle microtubules from prophase through anaphase and is concentrated at the spindle midzone during anaphase and telophase. In the absence of AIR-2, BMK-1 localization to meiotic and mitotic spindles is greatly reduced. This is not a consequence of loss of ZEN-4 localization because BMK-1 is appropriately localized in ZEN-4-deficient embryos. Furthermore, AIR-2 and BMK-1 directly interact with one another and the C-terminal tail domain of BMK-1 is specifically phosphorylated by AIR-2 in vitro. Together with our previous data, these results suggest that at least one function of the Aurora B kinases is to recruit spindle-associated motor proteins to their sites of action. ------------------- Key: 7049 Medline: 15653635 Authors: Tops BBJ;Tabara H;Sijen T;Simmer F;Mello CC;Plasterk RHA;Ketting RF Title: RDE-2 interacts with MUT-7 to mediate RNA interference in Caenorhabditis elegans. Citation: Nucleic Acids Research 33: 347-355 2005 Type: ARTICLE Genes: mut-7 mut-8 mut-14 par-1 rde-1 rde-2 rde-4 Abstract: In Caenorhabditis elegans, the activity of transposable elements is repressed in the germline. One of the mechanisms involved in this repression is RNA interference (RNAi), a process in which dsRNA targets cleavage of mRNAs in a sequence-specific manner. The first gene found to be involved in RNAi and transposon silencing in C.elegans is mut-7, a gene encoding a putative exoribonuclease. Here, we show that the MUT-7 protein resides in complexes of approximately 250 kDa in the nucleus and in the cytosol. In addition, we find that upon triggering of RNAi the cytosolic MUT-7 complex increases in size. This increase is independent of the presence of target RNA, but does depend on the presence of RDE-1 and RDE-4, two proteins involved in small interfering RNA (siRNA) production. Finally, using a yeast two-hybrid screen, we identified RDE-2/MUT-8 as one of the other components of this complex. This protein is encoded by the rde-2/mut-8 locus, previously implicated in RNAi and transposon silencing. Using genetic complementation analysis, we show that the interaction between these two proteins is required for efficient RNAi in vivo. Together these data support a role for the MUT-7/RDE-2 complex downstream of siRNA formation, but upstream of siRNA mediated target RNA recognition, possibly indicating a role in the siRNA amplification step. ------------------- Key: 7050 Medline: Authors: Warner HR Title: Longevity genes: from primitive organisms to humans. Citation: Mechanisms of Ageing & Development 126: 235-242 2005 Type: ARTICLE Genes: age-1 clk-1 daf-2 eat-2 hsf-1 hsp-16 hsp-70 isp-1 old-1 sir-2 tkr-1 tor-1 Abstract: Recent results indicate that the longevity of both invertebrates and vertebrates can be altered through genetic manipulation and pharmacological intervention. Most of these interventions involve alterations of one or more of the following: insulin/IGF-I signaling pathway, caloric intake, stress resistance and nuclear structure. How longevity regulation relates to aging per se is less clear, but longevity increases are usually accompanied by extended periods of good health. How these results will translate to primate aging and longevity remains to be shown. ------------------- Key: 7051 Medline: Authors: Zhou Z;Mangahas PM;Yu X Title: The genetics of hiding the corpse: engulfment and degradation of apoptotic cells in C. elegans and D. melanogaster. Citation: Current Topics in Developmental Biology. GP Schatten (ed). Academic Press. 63: 91-143 2004 Type: CHAPTER Genes: Abstract: ------------------- Key: 7052 Medline: 15673683 Authors: Sokolchik I;Tanabe T;Baldi PF;Sze JY Title: Polymodal sensory function of the Caenorhabditis elegans OCR-2 channel arises from distinct intrinsic determinants within protein and is selectively conserved in mammalian TRPV proteins. Citation: Journal of Neuroscience 25: 1015-1023 2005 Type: ARTICLE Genes: ocr-2 ocr-4 odr-10 osm-3 osm-9 tph-1 Abstract: Caenorhabditis elegans OCR- 2 ( OSM- 9 and capsaicin receptor- related) is a TRPV ( vanilloid subfamily of transient receptor potential channel) protein that regulates serotonin ( 5- HT) biosynthesis in chemosensory neurons and also mediates olfactory and osmotic sensation. Here, we identify the molecular basis for the polymodal function of OCR- 2 in its native cellular environment. We show that OCR- 2 function in 5- HT production and osmotic sensing is governed by its N- terminal region upstream of the ankyrin repeats domain, but the diacetyl sensitivity is mediated by independent mechanisms. The ocr- 2( yz5) mutation results in a glycine- to- glutamate substitution ( G36E) within the N- terminal region. The G36E substitution causes dramatic downregulation of 5- HT synthesis in the ADF neurons, eliminates osmosensation mediated by the ASH neurons, but does not affect the response to the odorant diacetyl mediated by the AWA neurons. Conversely, wild- type sequence of the N- terminal segment confers osmotic sensitivity and upregulation of 5- HT production to a normally insensitive C. elegans homolog, OCR- 4, but this chimeric channel does not respond to diacetyl stimuli. Furthermore, expression of either the mouse or human TRPV2 gene under the ocr- 2 promoter can substantially restore 5- HT biosynthesis in ocr- 2- null mutants but cannot improve the deficits in osmotic or olfactory sensation, suggesting that TRPV2 can substitute for the role of OCR- 2 only in serotonergic neurons. Thus, different sensory functions of OCR- 2 arise from separable intrinsic determinants, and specific functional properties of TRPV channel proteins may be selectively conserved across phyla. ------------------- Key: 7053 Medline: 15664928 Authors: Begun J;Sifri CD;Goldman S;Calderwood SB;Ausubel FM Title: Staphylococcus aureus virulence factors indentified by using a high-throughput Caenorhabditis elegans-killing Citation: Infection and Immunity 73: 872-877 2005 Type: ARTICLE Genes: Abstract: Staphylococcus aureus is an important human pathogen that is also able to kill the model nematode Caenorhabditis elegans. We constructed a 2,950-member Tn917 transposon insertion library in S. aureus strain NCTC 8325. Twenty-one of these insertions exhibited attenuated C. elegans killing, and of these, 12 contained insertions in different genes or chromosomal locations. Ten of these 12 insertions showed attenuated killing phenotypes when transduced into two different S. aureus strains, and 5 of the 10 mutants correspond to genes that have not been previously identified in signature-tagged mutagenesis studies. These latter five mutants were tested in a murine renal abscess model, and one mutant harboring an insertion in nagD exhibited attenuated virulence. Interestingly, Tn917 was shown to have a very strong bias for insertions near the terminus of DNA replication. ------------------- Key: 7054 Medline: 15649460 Authors: Cardoso C;Couillault C;Mignon-Ravix C;Millet A;Ewbank JJ;Fontes M;Pujol N Title: XNP-1/ATR-X acts with RB, HP1 and the NuRD complex during larval development in C. elegans. Citation: Developmental Biology 278: 49-59 2005 Type: ARTICLE Genes: egl-27 hda-1 hpl-2 let-418 lin-9 lin-15 lin-35 lin-36 lin-37 lin-38 lin-53 xnp-1 Abstract: Mutations in the XNP/ATR-X gene cause several X-linked mental retardation syndromes in humans. The XNP/ATR-X gene encodes a DNA-helicase belonging to the SNF2 family. It has been proposed that XNP/ATR-X might be involved in chromatin remodelling. The lack of a mouse model for the ATR-X syndrome has, however, hampered functional studies of XNP/ATR-X. C. elegans possesses one homolog of the XNP/ATR-X gene, named xnp-1. By analysing a deletion mutant, we show that xnp-1 is required for the development of the embryo and the somatic gonad. Moreover, we show that abrogation of xnp-1 function in combination with inactivation of genes of the NuRD complex, as well as lin-35/Rb and hpl-2/HP1 leads to a stereotyped block of larval development with a cessation of growth but not of cell division. We also demonstrate a specific function for xnp-1 together with lin-35 or hpl-2 in the control of transgene expression, a process known to be dependent on chromatin remodelling. This study thus demonstrates that in vivo XNP-1 acts in association with RB, HP1 and the NuRD complex during development. ------------------- Key: 7055 Medline: 15649465 Authors: Deshpande R;Inoue T;Priess JR;Hill RJ Title: lin-17/Frizzled and lin-18 regulate POP-1/TCF-1 localization and cell type specification during C. elegans vulval development. Citation: Developmental Biology 278: 118-129 2005 Type: ARTICLE Genes: ajm-1 lin-17 lin-18 pop-1 Abstract: The Caenorhabditis elegans vulva is comprised of highly similar anterior and posterior halves that are arranged in a mirror symmetric pattern. The cell lineages that form each half of the vulva are identical, except that they occur in opposite orientations with respect to the anterior/posterior axis. We show that most vulval cell divisions produce sister cells that have asymmetric levels of POP-1 and that the asymmetry has opposite orientations in the two halves of the vulva. We demonstrate that lin-17 (Frizzled type Writ receptor) and lin-18 (Ryk) regulate the pattern of POP-1 localization and cell type specification in the posterior half of the vulva. In the absence of lin-17 and lin-18, posterior lineages are reversed and resemble anterior lineages. These experiments suggest that Writ signaling pathways reorient cell lineages in the posterior half of the vulva from a default orientation displayed in the anterior half of the vulva. ------------------- Key: 7056 Medline: Authors: Apfeld J;O'Connor G;McDonagh T;DiStefano PS;Curtis R Title: The AMP-activated protein kinase AAK-2 links energy levels and insulin-like signals to lifespan in C. elegans. Citation: Genes & Development 19: 411- 2005 Type: CORRECT Genes: Abstract: ------------------- Key: 7057 Medline: 15653303 Authors: Kim DH;Ausubel FM Title: Evolutionary perspectives on innate immunity from the study of Caenorhabditis elegans. Citation: Current Opinion in Immunology 17: 4-10 2005 Type: REVIEW Genes: age-1 ced-3 ced-4 daf-2 daf-16 dbl-1 kgb-1 let-60 mek-1 mom-4 mpk-1 nlp-29 nlp-31 nsy-1 pmk-1 sek-1 tir-1 tol-1 vhp-1 Abstract: Genetic and functional genomic approaches have begun to define the molecular determinants of pathogen resistance in Caenorhabditis elegans. Conserved signal transduction components are required for pathogen resistance, including a Toll/IL-1 receptor domain adaptor protein that functions upstream of a conserved p38 MAP kinase pathway. We suggest that this pathway is an ancestral innate immune signaling pathway present in the common ancestor of nematodes, arthropods and vertebrates, which is likely to predate the involvement of canonical Toll signaling pathways in innate immunity. We anticipate that the study of pathogen resistance in C. elegans will continue to provide evolutionary and mechanistic insights into the signal transduction and physiology of innate immunity. ------------------- Key: 7058 Medline: 15687288 Authors: Fernandez AG;Gunsalus KC;Huang J;Chuang LS;Ying N;Liang H;Tang C;Schetter AJ;Zegar C;Rual JF;Hill DE;Reinke V;Vidal M;Piano F Title: New genes with roles in the C. elegans embryo revealed using RNAi of overy-enriched ORFeome clones. Citation: Genome Research 15: 250-259 2005 Type: ARTICLE Genes: air-2 aph-1 aph-2 cdk-5 csc-1 cup-5 dpy-30 egl-18 hrp-1 hus-1 ife-3 inx-3 lin-3 lin-41 lrs-2 mdt-6 mex-5 mom-1 mom-4 mom-5 ooc-3 puf-8 spn-4 sqv-1 sqv-5 sqv-7 Abstract: Several RNA interference (RNAi)-based functional genomic projects have been performed in Caenorhabditis elegans to identify genes required during embryogenesis. These studies have demonstrated that the ovary is enriched for transcripts essential for the first cell divisions. However, comparing RNAi results suggests that many genes involved in embryogenesis have yet to be identified, especially those eliciting partially penetrant phenotypes. To discover additional genes required for C elegans embryonic development, we tested by RNAi II23 ORFeome clones selected to represent ovary-enriched genes not associated with an embryonic phenotype. We discovered 155 new ovary-enriched genes with roles during embryogenesis, of which 69% show partial penetrance lethality. Time-lapse microscopy revealed specific phenotypes during early embryogenesis for genes giving rise to high penetrance lethality. Together with previous studies, we now have evidence that 1843 C elegans genes have roles in embryogenesis, and that many more remain to be found. Using all available RNAi phenotypic data for the ovary-enriched genes, we re-examined the distribution of genes by chromosomal location, functional class, ovary enrichment, and conservation and found that trends are driven almost exclusively by genes eliciting high-penetrance phenotypes. Furthermore, we discovered a striking direct relationship between phylogenetic distribution and the penetrance level ------------------- Key: 7059 Medline: 15665853 Authors: Leidel S;Delattre M;Cerutti L;Baumer K;Gonczy P Title: SAS-6 defines a protein family required for centrosome duplication in C. elegans and in human cells. Citation: Nature Cell Biology 7: 115-125 2005 Type: ARTICLE Genes: sas-4 sas-5 sas-6 spd-2 zyg-1 Abstract: The mechanisms that ensure centrosome duplication are poorly understood. In Caenorhabditis elegans, ZYG-1,SAS- 4, SAS- 5 and SPD-2 are required for centriole formation. However, it is unclear whether these proteins have functional homologues in other organisms. Here, we identify SAS- 6 as a component that is required for daughter centriole formation in C. elegans. SAS- 6 is a coiled-coil protein that is recruited to centrioles at the onset of the centrosome duplication cycle. Our analysis indicates that SAS-6 and SAS- 5 associate and that this interaction, as well as ZYG-1 function, is required for SAS- 6 centriolar recruitment. SAS- 6 is the founding member of an evolutionarily conserved protein family that contains the novel PISA motif. We investigated the function of the human homologue of SAS-6. GFP - HsSAS-6 localizes to centrosomes and its overexpression results in excess foci-bearing centriolar markers. Furthermore, siRNA-mediated inactivation of HsSAS-6 in U2OS cells abrogates centrosome overduplication following aphidicolin treatment and interferes with the normal centrosome duplication cycle. Therefore, HsSAS-6 is also required for centrosome duplication, indicating that the function of SAS-6-related proteins has been widely conserved during evolution. ------------------- Key: 7060 Medline: 15489510 Authors: Schade MA;Reynolds NK;Miller KG Title: Mutations that rescue the paralysis of C. elegans ric-8 (synembryn) mutants activate the Gs pathway and define a major branch of the synaptic signaling network. Citation: Genetics 169: 631-649 2005 Type: ARTICLE Genes: acy-1 dgk-1 eat-16 egl-30 goa-1 gpb-2 gsa-1 kin-2 ric-8 Abstract: To identify hypothesized missing components of the synaptic G alpha(o)-G alpha(q), signaling network, which tightly regulates neurotransmitter release, we undertook two large for-ward genetic screens in the model organism C. elegans and focused first on mutations that strongly rescue the paralysis of ric-8(md303) reduction-of-function mutants, previously shown to be defective in G alpha(q) pathway activation. Through high-resolution mapping followed by sequence analysis, we show that these mutations affect four genes. Two activate the Gaq pathway through gain-of-function mutations in Gaq; however, all of the remaining mutations activate components of the G alpha(s) pathway, including G alpha(s), adenylyl cyclase, and protein kinase A. Pharmacological assays suggest that the Gas pathway-activating mutations increase steady-state neurotransmitter release, and the strongly impaired neurotransmitter release of ric-8(md303) mutants is rescued to greater than wild-type levels by the strongest G alpha(s) pathway activating mutations. Using transgene induction studies, we show that activating the G alpha(s) pathway in adult animals rapidly induces hyperactive locomotion and rapidly rescues the paralysis of the ric-8 mutant. Using cell-specific promoters we show that neuronal, but not muscle, G alpha(s) pathway activation is sufficient to rescue ric-8(md303)'s paralysis. Our results appear to link RIC-8 (synembryn) and a third major G alpha pathway, the G alpha(s) pathway, with the previously discovered G alpha(o) and G alpha(q) pathways of the ------------------- Key: 7061 Medline: 15489511 Authors: Reynolds NK;Schade MA;Miller KG Title: Convergent, RIC-8-dependent G alpha signaling pathways in the C. elegans synaptic signaling network. Citation: Genetics 169: 650-670 2005 Type: ARTICLE Genes: acy-1 eat-16 egl-30 goa-1 gsa-1 kin-2 ric-8 unc-13 Abstract: We used gain-of-function and null synaptic signaling network mutants to investigate the relationship of the G alpha(q) and G alpha(s), pathways to synaptic vesicle priming and to each other. Genetic epistasis studies using G alpha(q) gain-of-function and null mutations, along with a mutation that blocks synaptic vesicle priming and the synaptic vesicle priming stimulator phorbol ester, suggest that the G alpha(q) pathway generates the core, obligatory signals for synaptic vesicle priming. In contrast, the G alpha(s) pathway is not required for the core priming function, because steady-state levels of neuro transmitter release are not significantly altered in animals lacking a neuronal G alpha(s) pathway, even though these animals are strongly paralyzed as a result of functional (nondevelopmental) defects. However, our genetic analysis indicates that these two functionally distinct pathways converge and that they do so downstream of DAG production. Further linking the two pathways, our epistasis analysis of a ric-8 null mutant suggests that RIC-8 (a receptor-independent G alpha guanine nucleotide exchange factor) is required to maintain both the G alpha(q) vesicle priming pathway and the neuronal Got, pathway in a functional state. We propose that the neuronal Ga, pathway transduces critical positional information onto the core G alpha(q) pathway to stabilize the priming of selected ------------------- Key: 7062 Medline: 15671174 Authors: Kinnunen T;Huang Z;Townsend J;Gatdula MM;Brown JR;Esko JD;Turnbull JE Title: Heparan 2-O-sulfotransferase, hst-2, is essential for normal cell migration in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 102: 1507-1512 2005 Type: ARTICLE Genes: hst-2 Abstract: The importance of heparan sulfate proteoglycans has been highlighted by a number of human genetic disorders associated with mutations in genes encoding for heparan sulfate proteoglycan protein cores or blosynthetic enzymes required for heparan sulfate (HS) assembly. To study the functional role of HS in Caenorhabditis elegans development cosmid sequence C34F6.4 was identified as the C. elegans ortholog of vertebrate heparan 2-O-sulf otransferase (HS2ST) and the gene named hst-2. HS2ST activity is present in C. elegans and is completely absent in a deletion mutant of hst-2, ok595, and specifically reduced by hst-2 RNA interference. Expression of hst-2 in CHO cells deficient in HS2ST rescues enzyme activity and binding of FGF2 to cell surface HS. hst-2 expression is found in the hypodermis, muscle, distal tip cells (DTCs), and in neurons. A null mutation in hst-2 causes cell migration defects. This work demonstrates sulfotransferase activity in C. elegans and indicates that specific 2-O-sulfate modifications are critical for normal HS functions in controlling cell migration. ------------------- Key: 7063 Medline: 15608221 Authors: Chen N;Harris TW;Antoshechkin I;Bastiani C;Bieri T;Blasiar D;Bradnam K;Canaran P;Chan J;Chen CK;Chen WJ;Cunningham F;Davis P;Kenny E;Kishore R;Lawson D;Lee R;Muller HM;Nakamura C;Pai S;Ozersky P;Petch Title: WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Citation: Nucleic Acids Research 33: D383-D389 2005 Type: REVIEW Genes: Abstract: WormBase (http://www.wormbase.org), the model organism database for information about Caenorhabditis elegans and related nematodes, continues to expand in breadth and depth. Over the past year, WormBase has added multiple large-scale datasets including SAGE, interactome, 3D protein structure datasets and NCBI KOGs. To accommodate this growth, the International WormBase Consortium has improved the user interface by adding new features to aid in navigation, visualization of large-scale datasets, advanced searching and data mining. Internally, we have restructured the database models to rationalize the representation of genes and to prepare the system to accept the genome sequences of three additional Caenorhabditis species over the coming year. ------------------- Key: 7064 Medline: 15716932 Authors: Hengartner M Title: Divide and conquer. Citation: Nature 433: 692-694 2005 Type: REVIEW Genes: ced-3 ced-4 ced-9 drp-1 egl-1 Abstract: ------------------- Key: 7065 Medline: 15716954 Authors: Jagasia R;Grote P;Westermann B;Conradt B Title: DRP-1-mediated mitochondrial fragmentation during EGL-1-induced cell death in C. elegans. Citation: Nature 433: 754-760 2005 Type: ARTICLE Genes: ced-3 ced-4 ced-9 drp-1 egl-1 icd-1 Abstract: Genetic analyses in Caenorhabditis elegans have been instrumental in the elucidation of the central cell-death machinery, which is conserved from C. elegans to mammals(1,2). One possible difference that has emerged is the role of mitochondria. By releasing cytochrome c, mitochondria are involved in the activation of caspases in mammals(3,4). However, there has previously been no evidence that mitochondria are involved in caspase activation in C. elegans. Here we show that mitochondria fragment in cells that normally undergo programmed cell death during C. elegans development. Mitochondrial fragmentation is induced by the BH3-only protein EGL-1 and can be blocked by mutations in the bcl-2-like gene ced-9, indicating that members of the Bcl-2 family might function in the regulation of mitochondrial fragmentation in apoptotic cells. Mitochondrial fragmentation is independent of CED-4/Apaf-1 and CED-3/caspase, indicating that it occurs before or simultaneously with their activation. Furthermore, DRP-1/dynamin-related protein, a key component of the mitochondrial fission machinery, is required and sufficient to induce mitochondrial fragmentation and programmed cell death during C. elegans development. These results assign an important role to mitochondria in the cell-death pathway in C. elegans. ------------------- Key: 7066 Medline: 15680404 Authors: Watanabe M;Mitani N;Ishii N;Miki K Title: A mutation in a cuticle collagen causes hypersensitivity to the endocrine disrupting chemical, bisphenol A, in Caenorhabditis elegans. Citation: Mutation Research 570: 71-80 2005 Type: ARTICLE Genes: bis-1 bli-1 bli-6 col-121 dpy-1 dpy-2 dpy-4 dpy-5 dpy-7 dpy-8 dpy-9 dpy-10 dpy-13 dpy-17 dpy-18 dpy-20 lon-1 lon-2 lon-3 sqt-1 sqt-3 unc-5 unc-17 unc-22 unc-24 unc-43 unc-60 unc-129 Abstract: A novel mutant gene, bis-1 (bisphenol A sensitive) has been isolated in the nematode, Caenorhabditis elegans, that affects the response to endocrine disrupting chemicals (EDC). The bis-1 (nx3) allele is hypersensitive to bisphenol A (BPA), is allelic to a collagen gene (col-121), and is expressed in hypodermal cells. Among the collagen mutants so far studied, bis-1(nx3), dpy-2(e8), dpy-7(e88) and dpy-10(e128) showed BPA sensitivity. The isolated mutant may work as a useful tool for the assay of EDC toxicity since the physiological effect of the collagen mutation (glycine substitution) indicates an increased ------------------- Key: 7067 Medline: Authors: Gems D;McElwee JJ Title: Broad spectrum detoxification: the major longevity assurance process regulated by insulin/IGF-1 signaling? Citation: Mechanisms of Ageing & Development 126: 381-387 2005 Type: REVIEW Genes: ctl-1 daf-2 sod-1 sod-3 Abstract: Our recent survey of genes regulated by insulin/IGF-1 signaling (IIS) in Caenorhabditis elegans suggests a role for a number of gene classes in longevity assurance. Based on these findings, we propose a model for the biochemistry of longevity assurance and ageing, which is as follows. Ageing results from molecular damage from highly diverse endobiotic toxins. These are stochastic by-products of diverse metabolic processes, of which reactive oxygen species (ROS) are likely to be only one component. Our microarray analysis suggests a major role in longevity assurance of the phase 1, phase 2 detoxification system involving cytochrome P450 (CYP), short-chain dehydrogenase/ reductase (SDR) and UDP-glucuronosyltransferase (UGT) enzymes. Unlike superoxide and hydrogen peroxide detoxification, this system is energetically costly, and requires the excretion from the cell of its products. Given such costs, its activity may be selected against, as predicted by the disposable soma theory. CYP and UGT enzymes target lipophilic molecular species; insufficient activity of this system is consistent with age-pigment (lipofuscin) accumulation during ageing. We suggest that IIS-regulated longevity assurance involves: (a) energetically costly detoxification and excretion of molecular rubbish, and (b) conservation of existing proteins via molecular chaperones. Given the emphasis in this theory on investment in cellular waste disposal, and on protein conservation, we have dubbed it the green ------------------- Key: 7068 Medline: 15699524 Authors: Glenn CF;Chow DK;David L;Cooke CA;Gami MS;Iser WB;Hanselman KB;Goldberg IG;Wolkow CA Title: Behavioral deficits during early stages of aging in Caenorhabditis elegans result from locomotory deficits possibly linked to muscle frailty. Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 59: 1251-1260 2005 Type: ARTICLE Genes: Abstract: Many behavioral responses require the coordination of sensory inputs with motor outputs. Aging is associated with progressive declines in both motor function and muscle structure. However, the consequences of age-related motor deficits on behavior have not been clearly defined. Here, we examined the effects of aging on behavior in the nematode, Caenorhabditis elegans. As animals aged, mild locomotory deficits appeared that were sufficient to impair behavioral responses to sensory cues. In contrast, sensory ability appeared well maintained during aging. Age-related behavioral declines were delayed in animals with mutations in the daf-2/insulin-like pathway governing longevity. A decline in muscle tissue integrity was correlated with the onset of age-related behavioral deficits, although significant muscle deterioration was not. Treatment with a muscarinic agonist significantly improved locomotory behavior in aged animals, indicating that improved neuromuscular signaling may be one strategy for reducing the severity of age-related behavioral impairments. ------------------- Key: 7069 Medline: 15647338 Authors: Barr MM Title: Caenorhabditis elegans as a model to study renal development and disease: sexy cilia. Citation: Journal of the American Society of Nephrology 16: 305-312 2005 Type: REVIEW Genes: arl-6 kap-1 klc-1 klc-2 klp-11 klp-20 lov-1 pkd-2 osm-3 osm-5 osm-12 Abstract: The nematode Caenorhabditis elegans has no kidney per se, yet "the worm" has proved to be an excellent model to study renal-related issues, including tubulogenesis of the excretory canal, membrane transport and ion channel function, and human genetic diseases including autosomal dominant polycystic kidney disease (ADPKD). The goal of this review is to explain how C. elegans has provided insight into cilia development, cilia function, and human cystic kidney diseases. ------------------- Key: 7070 Medline: 15713455 Authors: Murayama T;Toh Y;Ohshima Y;Koga M Title: The dyf-3 gene encodes a novel protein required for sensory cilium formation in Caenorhabditis elegans. Citation: Journal of Molecular Biology 346: 677-687 2005 Type: ARTICLE Genes: cat-2 cat-4 daf-19 dgk-1 dyf-3 goa-1 Abstract: Ciliated neurons in animals are important for the reception of environmental stimuli. To understand the mechanism of cilium morphogenesis in Caenorhabditis elegans, we analyzed dyf-3 mutants that are defective in uptake of a fluorescent dye and abnormal in sensory cilium structure. Expression of green fluorescent protein in sensory neurons of a dyf-3 mutant revealed that the mutant has stunted cilia and abnormal posterior projections in some sensory neurons. The dyf-3 gene encodes three proteins with different N-terminals. The largest DYF-3 protein has 404 amino acid residues that are 38% identical with those of a predicted human protein of unknown function. Expression of a functional dyf-3::gfp fusion gene is detected in 26 chemosensory neurons, including six IL2 neurons, eight pairs of amphid neurons (ASE, ADF, ASG, ASH, ASI, ASJ, ASK and ADL) and two pairs of phasmid neurons (PHA and PHB). Expression of a dyf-3 cDNA in specific neurons of dyf-3 animals indicated that dyf-3 acts cell-autonomously for fluorescent dye uptake. Reduction of dyf-3::gfp expression in a daf-19 mutant suggests that dyf-3 expression is regulated by DAF-19 transcription factor, and DYF-3 may be involved in the intraflagellar transport system. ------------------- Key: 7071 Medline: 15615786 Authors: Silhankova M;Jindra M;Asahina M Title: Nuclear receptor NHR-25 is required for cell-shape dynamics during epidermal differentiation in Caenorhabditis elegans. Citation: Journal of Cell Science 118: 223-232 2005 Type: ARTICLE Genes: acn-1 ajm-1 cdh-3 col-19 mab-5 nhr-25 rol-6 rrf-3 Abstract: Epithelial cell shape changes underlie important events in animal development. During the postembryonic life of the nematode Caenorhabditis elegans, stem epidermal seam cells lose and actively renew mutual adherens junction contacts after each asymmetric division that separates them. The seam cell contacts are important for epidermal differentiation, but what regulates the cell-shape changes that restore them is unknown. Here, we show that NHR-25, a transcription factor of the nuclear receptor family, is expressed in the seam cells and is necessary for these cells to elongate and reach their neighbors after the asymmetric divisions. A failure to do so, caused by nhr-25 RNA interference, compromises the subsequent fate of seam-cell anterior daughters. Unexpectedly, the lack of cell-cell contacts does not prevent a unique seam cell to produce a neuroblast, even though a homeotic gene (mab-5) that normally prevents the neuroblast commitment is ectopically expressed in the absence of nhr-25 function. Seam cells lacking mutual contacts display reduced expression of a Fat-like cadherin marker cdh-3::gfp. Although some seam cells retain the ability to fuse at the final larval stage, the resulting syncytium shows gaps and bifurcations, translating into anomalies in cuticular ridges (alae) produced by the syncytium. nhr-25 RNAi markedly enhances branching of the alae caused by a mutant cuticular collagen gene rol-6. Silencing of nhr-25 also disturbs epidermal ultrastructure, which is probably the cause of compromised cuticle secretion and molting. Cell shape dynamics and molting thus represent distinct roles ------------------- Key: 7072 Medline: 15670846 Authors: Cho JH;Ko KM;Singaravelu G;Ahnn J Title: Caenorhabditis elegans PMR1, a P-type calcium ATPase, is important for calcium/manganese homeostasis and oxidative stress response. Citation: FEBS Letters 579: 778-782 2005 Type: ARTICLE Genes: daf-2 daf-16 pmr-1 Abstract: The Caenorhahditis elegans PMR1, a P-type Ca2+/Mn2+ ATPase, is expressed in hypodermal seam cells, intestinal cells and spermatheca; localized in Golgi complex. Knock down of pmr-1 as well as overexpression of truncated Caenorhabditis elegans PMR1, which mimics dominant mutations observed in human Hailey-Hailey disease, renders the worm highly sensitive to EGTA and Mn2+. Interestingly, pmr-1 knock down not only causes animals to become resistant to oxidative stress but also suppresses high reactive oxygen species sensitivity of smf-3 RNA-mediated interference and daf-16 worms. These findings suggest that C elegans PMR1 has important roles in Ca2+ and Mn2+ homeostasis and oxidative stress response. ------------------- Key: 7073 Medline: 15691769 Authors: Banerjee D;Kwok A;Lin SY;Slack FJ Title: Developmental timing in C. elegans is regulated by kin-20 and tim-1, homologs of core circadian clock genes. Citation: Developmental Cell 8: 287-295 2005 Type: ARTICLE Genes: aha-1 gsk-3 hbl-1 kin-19 kin-20 let-7 lin-41 lin-42 tim-1 Abstract: In Caenorhabditis elegans, heterochronic genes constitute a developmental timer that specifies temporal cell fate selection. The heterochronic gene lin-42 is the C. elegans homolog of Drosophila and mammalian period, key regulators of circadian rhythms, which specify changes in behavior and physiology over a 24 hr day/night cycle. We show a role for two other circadian gene homologs, tim-1 and kin-20, in the developmental timer. Along with lin-42, tim-1 and kin-20, the C. elegans homologs of the Drosophila circadian clock genes timeless and doubletime, respectively, are required to maintain late-larval identity and prevent premature expression of adult cell fates. The molecular parallels between circadian and developmental timing pathways suggest the existence of a conserved molecular mechanism that may be used for different types of biological timing. ------------------- Key: 7074 Medline: 15661512 Authors: Gunsalus KC;Piano F Title: RNAi as a tool to study cell biology: building the genome-phenome bridge. Citation: Current Opinion in Cell Biology 17: 3-8 2005 Type: REVIEW Genes: rrf-3 Abstract: In the few short years since its discovery, RNA interference (RNAi) has revolutionized the functional analysis of genomes: both technical and conceptual approaches to the investigation of gene function are being transformed as a result of this new technology. Genome-scale RNAi analyses have already been performed in the model organisms Caenorhabditis elegans (in vivo) and Drosophila melanogaster (in cell lines), ushering in a new era of RNAi-based approaches to probing the inner workings of the cell. The transformation of complex phenotypic data into mineable 'digitized' formats is fostering the emergence of a new area of bioinformatics related to the ------------------- Key: 7075 Medline: 15577941 Authors: Hilliard MA;Apicella AJ;Kerr R;Suzuki H;Bazzicalupo P;Schafer WR Title: In vivo imaging of C. elegans ASH neurons: cellular response and adaptation to chemical repellents. Citation: EMBO Journal 24: 63-72 2005 Type: ARTICLE Genes: egl-19 gpa-1 gpa-3 gpa-11 gpa-13 gpa-14 gpa-15 gpc-1 goa-1 gsa-1 lin-15 odr-3 osm-9 osm-10 unc-2 unc-13 Abstract: ASH sensory neurons are required in Caenorhabditis elegans for a wide range of avoidance behaviors in response to chemical repellents, high osmotic solutions and nose touch. The ASH neurons are therefore hypothesized to be polymodal nociceptive neurons. To understand the nature of polymodal sensory response and adaptation at the cellular level, we expressed the calcium indicator protein cameleon in ASH and analyzed intracellular Ca2+ responses following stimulation with chemical repellents, osmotic shock and nose touch. We found that a variety of noxious stimuli evoked strong responses in ASH including quinine, denatonium, detergents, heavy metals, both hyper- and hypo- osmotic shock and nose touch. We observed that repeated chemical stimulation led to a reversible reduction in the magnitude of the sensory response, indicating that adaptation occurs within the ASH sensory neuron. A key component of ASH adaptation is GPC- 1, a G- protein gamma-subunit expressed specifically in chemosensory neurons. We hypothesize that G- protein gamma- subunit heterogeneity provides a mechanism for repellent- specific adaptation, which could facilitate discrimination of a variety of repellents by these polymodal sensory neurons. ------------------- Key: 7076 Medline: 15707894 Authors: Schumacher B;Hanazawa M;Lee MH;Nayak S;Volkmann K;Hofmann R;Hengartner M;Schedl T;Gartner A Title: Translational repression of C. elegans p53 by GLD-1 regulates DNA damage-induced apoptosis. Citation: Cell 120: 357-368 2005 Type: ARTICLE Genes: ced-3 ced-4 ced-9 cep-1 egl-1 gld-1 gna-1 rad-51 rme-2 Abstract: p53 is a tumor suppressor gene whose regulation is crucial to maintaining genome stability and for the apoptotic elimination of abnormal, potentially cancer-predisposing cells. C. elegans contains a primordial p53 gene, cep-1, that acts as a transcription factor necessary for DNA damage-induced apoptosis. In a genetic screen for negative regulators of CEP-1, we identified a mutation in GLD-1, a translational repressor implicated in multiple C. elegans germ cell fate decisions and related to mammalian Quaking proteins. CEP-1-dependent transcription of proapoptotic genes is upregulated in the gld-1(op236) mutant and an elevation of p53-mediated germ cell apoptosis in response to DNA damage is observed. Further, we demonstrate that GLD-1 mediates its repressive effect by directly binding to the 3'UTR of cep-1/p53 mRNA and repressing its translation. This study reveals that the regulation of cep-1/p53 translation influences DNA damage-induced apoptosis and demonstrates the physiological importance of this ------------------- Key: 7077 Medline: Authors: Leroi AM;Bartke A;De Benedictis G;Franceschi C;Gartner A;Gonos E;Feder ME;Kivisild T;Lee S;Kartal-Ozer N;Schumacher M;Sikora E;Slagboom E;Tatar M;Yashin AI;Vijg Title: What evidence is there for the existence of individual genes with antagonistic pleitropic effects? Citation: Mechanisms of Ageing & Development 126: 421-429 2005 Type: REVIEW Genes: age-1 clk-1 daf-2 glp-1 Abstract: Classical evolutionary theory predicts the existence of genes with antagonistic effects on longevity and various components of early-life fitness. Quantitative genetic studies have provided convincing evidence that such genes exist. However, antagonistic pleiotropic effects have rarely been attributed to individual loci. We examine several classes of longevity-assurance genes: those involved in regulation of the gonad; the insulin-like growth factor pathway; free-radical scavenging; heat shock proteins and apoptosis. We find initial evidence that antagonistic pleiotropic effects are pervasive in each of these classes of genes and in various model systems-although most studies lack explicit studies of fitness components. This is particularly true of human studies. Very little is known about the early-life fitness effects of longevity loci. Given the possible medical importance of such effects we urge their future study. ------------------- Key: 7078 Medline: Authors: Goranson NC;Ebersole JP;Brault S Title: Resolving an adaptive conundrum: reproduction in Caenorhabditis elegans is not sperm-limited when food is scarce. Citation: Evolutionary Ecology Research 7: 325-333 2005 Type: ARTICLE Genes: Abstract: Question: Has the less expensive gamete (sperm) really been selected as the limiting factor in a nematode's reproduction. as laboratory studies have implied? Hypothesis: Reproductive output of the self-fertilizing hermaphroditic nematode Caenorhabditis elegans is oocyte-limited in the worm's natural environment: soil. Organism: Sperm depletion and laying of unfertilized oocytes occurs in well-fed laboratory cultures of the self-fertilizing hermaphroditic nematode, Caenorhabditis elegans. This phenomenon has been much discussed as a possible contradiction to the usual expectation of selection for maximum fertility. Methods: Caenorhabditis elegans were maintained in a variety of food regimes. not just the ad libitum Escherichia coli typical of laboratory cultures. Sperm production, oocyte production and body size were measured for nematodes cultured on agar with feeding treatments of serially diluted bacteria suspensions. before and during gamete formation. Body sizes were also measured for worms cultured in soil or compost microcosms. Results: Reproduction was sperm-limited only for nematodes in the highest food treatments (10(6) or more E. coli cells per day); lower food treatments produced smaller worms with considerable excess sperm. Caenorhabditis elegans grown ill natural soil or compost microcosms achieved the same sizes as those in treatments that showed oocyte limitation, not the large sizes of those typical of C. elegans in treatments that exhibited sperm limitation. Enriching soil or compost by adding E. coli produced appreciably larger C. elegans, but only if numbers of other invertebrates - potential predators/competitors of C. elegans - were minimized. Even with increased nutrients and reduced numbers of other invertebrates, only a few C. elegans in natural soil or compost were large enough to be consistent with sperm limitation. ------------------- Key: 7079 Medline: 15661349 Authors: Keightley PD;Charlesworth B Title: Genetics instability of C. elegans comes naturally. Citation: Trends in Genetics 21: 67-70 2005 Type: REVIEW Genes: Abstract: There have been many attempts to measure the genome-wide mutation rate for spontaneous mutations, using measurements of traits in inbred lines in which mutations have accumulated. However, these are likely to miss many small-effect mutations that are important for evolutionary processes. Recently, the genome-wide spontaneous mutation rate in inbred lines of Caenorhabditis elegans was estimated, using DNA sequencing. The results imply that the mutation rate is surprisingly high, and that insertion-deletion mutations are unexpectedly common. Phenotypic assays of the same lines detected only a small proportion of mutations that were predicted to have evolutionarily significant fitness effects. ------------------- Key: 7080 Medline: 15684055 Authors: Fisher J;Piterman N;Hubbard EJA;Stern MJ;Harel D Title: Computational insights into Caenorhabditis elegans vulval development. Citation: Proceedings of the National Academy of Sciences USA 102: 1951-1956 2005 Type: ARTICLE Genes: let-23 lin-2 lin-3 lin-7 lin-10 lin-12 lin-15 Abstract: Studies of Caenorhabditis elegans vulval development provide a paradigm for pattern formation during animal development. The fates of the six vulval precursor cells are specified by the combined action of an inductive signal that activates the EGF receptor mitogen-activated PK signaling pathway (specifying a primary fate) and a lateral signal mediated by LIN-12/Notch (specifying a secondary fate). Here we use methods devised for the engineering of complex reactive systems to model a biological system. We have chosen the visual formalism of statecharts and use it to formalize Sternberg and Horvitz's 1989 model [Sternberg, P. W. & Horvitz, H. R. (11989) Cell 58, 679-693], which forms the basis for our current understanding of the interaction between these two signaling pathways. The construction and execution of our model suggest that different levels of the inductive signal induce a temporally graded response of the EGF receptor mitogen-activated PK pathway and make explicit the importance of this temporal response. Our model also suggests the existence of an additional mechanism operating during lateral specification that prohibits neighboring ------------------- Key: 7081 Medline: 15687387 Authors: Takiya S;Ishikawa T;Ohtsuka K;Nishita Y;Suzuki Y Title: Fibroin-modulator-binding protein-1 (FMBP-1) contains a novel DNA-binding domain, repeats of the score and three amino acid peptide (STP), conserved from Caenorhabditis elegans to humans. Citation: Nucleic Acids Research 33: 786-795 2005 Type: ARTICLE Genes: Abstract: The predicted transcriptional regulatory factor for the fibroin gene of the silkworm Bombyx mori, fibroin-modulator-binding protein-1 (FMBP-1), was purified by sequential DNA affinity column chromatography, and cDNA clones corresponding to FMBP-1 were isolated from a library. The N-terminal half of FMBP-1 has a weak similarity to the DNA-binding domain of several transcriptional regulatory factors in higher plants. The C-terminal half contains four tandem repeats of a novel 23 amino acid motif, which we named the score and three amino acid peptide (STP). Other genes containing STP repeats were found in Drosophila, Caenorhabditis elegans, mouse and human. Mutational analysis of FMBP-1 showed that the STP repeats form a novel DNA-binding domain. Sequences flanking STP repeats modulated DNA-binding activity. The FMBP-1 gene was expressed during the fourth to fifth instar. FMBP-1 activity appeared to be regulated at the transcriptional level and by the post-transcriptional modification. ------------------- Key: 7082 Medline: 15704008 Authors: Franchini A;Imbriano C;Peruzzi E;Mantovani R;Ottaviani E Title: Expression of the CCAAT-binding factor NF-Y in Caenorhabditis elegans. Citation: Journal of Molecular Histology 36: 139-145 2005 Type: ARTICLE Genes: Abstract: NF-Y is a conserved trimer with histone-like subunits that binds and activates the common CCAAT promoter element. C. elegans NF-Y genes present two CeNF-YAs, a unique feature in kingdoms other than plants, one CeNF-YB and one CeNF-YC. The expression of both CeNF-YAs is restricted to the gonads and developing embryos, whereas the histone-like CeNF-YB- and CeNF-YC are also present in the pharyngeal bulb, in the neurons of ganglia surrounding the pharynx and in sensory organs of the head. Moreover, in infertile, 12-day-old worms, expression of the three subunits falls dramatically in the gonads. Our data indicate that NF-Y is not ubiquitously expressed. ------------------- Key: 7083 Medline: 15684092 Authors: Denton J;Nehrke K;Yin X;Morrison R;Strange K Title: GCK-3, a newly identified Ste20 kinase, binds to and regulates the activity of a cell cycle-dependent ClC anion channel. Citation: Journal of General Physiology 125: 113-125 2005 Type: ARTICLE Genes: clh-3 gck-3 Abstract: CLH-3b is a Caenorhabditis elegans ClC anion channel that is expressed in the worm oocyte. The channel is activated during oocyte meiotic maturation and in response to cell swelling by serine/threonine dephosphorylation events mediated by the type 1 phosphatases GLC-7alpha and GLC-7beta. We have now identified a new member of the Ste20 kinase superfamily, GCK-3, that interacts with the CLH-3b COOH terminus via a specific binding motif GCK-3 inhibits CLH-3b in a phosphorylation-dependent manner when the two proteins are coexpressed in HEK293 cells. dh-3 and gck-3 are expressed predominantly in the C. elegans oocyte and the fluid-secreting excretory cell. Knockdown of gck-3 expression constitutively activates CLH-3b in nonmaturing worm oocytes. We conclude that GCK-3 functions in cell cycle- and cell volume-regulated signaling pathways that control CLH-3b activity. GCK-3 inactivates CLH-3b by phosphorylating the channel and/or associated regulatory proteins. Our studies provide new insight into physiologically relevant signaling pathways that control ClC channel activity and suggest novel mechanisms for coupling cell volume dhanges to cell cycle events and for coodinately regulating ion channels and transporters that control cellular Cl- content, cell volume, and epithelial fluid secretion. ------------------- Key: 7084 Medline: Authors: Kunitomo H;Uesugi H;Kohara Y;Iino Y Title: Identification of ciliated sensory neuron-expressed genes in Caenorhabditis elegans using targeted pull-down of poly(A) tails. Citation: Genome Biology 6: 1-17 2005 Type: ARTICLE Genes: acr-5 che-2 che-11 daf-19 del-1 eft-3 hsp-16.48 lmn-1 odr-10 pab-1 rgs-3 snt-1 spp-5 tax-2 unc-8 unc-54 Abstract: ------------------- Key: 7085 Medline: 15708572 Authors: Yanowitz J;Fire A Title: Cyclin D involvement demarcates a late transition in C. elegans embryogenesis. Citation: Developmental Biology 279: 244-251 2005 Type: ARTICLE Genes: cyd-1 cup-5 Abstract: During development, progression through the cell cycle must be coordinately regulated with cellular differentiation. Despite significant progress in identifying genes required independently for each of these processes, the molecules which facilitate this cross talk have for the most part been elusive. Using the six macrophage-like coelomocytes of the nematode Caenorhabditis elegans as a model system to gain insight into the mesodermal differentiation pathway, we have isolated a set of mutants that alter coelomocyte numbers. One of these mutations, cc600, apparently results from a partial loss-of function in the C. elegans cyclin D gene, cyd-1. The mutant has coelomocyte-specific defects without changes in other lineages. The mutants show that cell growth, terminal differentiation and cellular function proceed in the absence of cyd-1 activity and cell division. The results suggest that certain mesodermal lineages may be uniquely affected by changes in cyd-1 activity. ------------------- Key: 7086 Medline: 15707898 Authors: Nakata K;Abrams B;Grill B;Goncharov A;Huang X;Chisholm AD;Jin Y Title: Regulation of a DLK-1 and p38 MAP kinase pathway by the ubiquitin ligase RPM-1 is required for presynaptic development. Citation: Cell 120: 407-420 2005 Type: ARTICLE Genes: dlk-1 mkk-4 pmk-3 rpm-1 syd-1 unc-10 Abstract: Synapses display a stereotyped ultrastructural organization, commonly containing a single electron-dense presynaptic density surrounded by a cluster of synaptic vesicles. The mechanism controlling subsynaptic proportion is not understood. Loss of function in the C. elegans rpm-1 gene, a putative RING finger/E3 ubiquitin ligase, causes disorganized presynaptic cytoarchitecture. RPM-1 is localized to the presynaptic periactive zone. We report that RPM-1 negatively regulates a p38 MAP kinase pathway composed of the dual leucine zipper-bearing MAPKKK DLK-1, the MAPKK MKK-4, and the p38 MAP kinase PMK-3. Inactivation of this pathway suppresses rpm-1 loss of function phenotypes, whereas overexpression or constitutive activation of this pathway causes synaptic defects resembling rpm-1(lf) mutants. DLK-1, like RPM-1, is localized to the periactive zone. DLK-1 protein levels are elevated in rpm-1 mutants. The RPM-1 RING finger can stimulate ubiquitination of DLK-1. Our data reveal a presynaptic role of a previously unknown p38 MAP kinase ------------------- Key: 7087 Medline: 15724817 Authors: Schmutz C;Spang A Title: Knockdown of the centrosomal component SAS-5 results in defects in nuclear morphology in Caenorhabditis elegans. Citation: European Journal of Cell Biology 84: 75-82 2005 Type: ARTICLE Genes: sas-5 ced-3 ced-4 egl-1 Abstract: Several different processes must be completed in order to proceed through cell division. First, the centrosomes have to be duplicated and the genomic material is replicated. The separation of the chromatin is achieved by a bipolar spindle, which in turn is organized by the two centrosomes. The last step of cell division involves the separation of cellular content and the cleavage of the cell by cytokinesis. We used RNAi to study the centrosomal component SAS-5 in the early Caenorhabditis elegans embryo. While the first cell division and the establishment of polarity of sas-5 dsRNA-treated embryos was indistinguishable from wild type, subsequent cleavages were abnormal. Time-lapse microscopy studies of worms expressing beta-tubulin::GFP revealed that the absence of SAS-5 results in a failure of mitotic spindle assembly starting at the two-cell stage embryo. Furthermore, the chromatin in at least one of the two cells in the early embryo was dispersed. Yet, this dispersion did neither trigger apoptosis nor affect nuclear envelope assembly. No intrinsic size control for the nucleus seems to exist in ------------------- Key: 7088 Medline: 15661845 Authors: Hollins C;Zorio DAR;MacMorris M;Blumenthal T Title: U2AF binding selects for the high conservation of the C. elegans 3' splice site. Citation: RNA 11: 248-253 2005 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans is unusual among animals in having a highly conserved octamer sequence at the 3' splice site: UUUU CAG/R. This sequence can bind to the essential heterodimeric splicing factor U2AF, with U2AF(65) contacting the U tract and U2AF(35) contacting the splice site itself (AG/R). Here we demonstrate a strong correspondence between binding to U2AF of RNA oligonucleotides with variant octamer sequences and the frequency with which such variations occur in splice sites. C. elegans L12AF has a strong preference for the octamer sequence and exerts much of the pressure for 3' splice sites to have the precise UUUUCAG/R sequence. At two positions the splice site has a very strong preference for U even though alternative bases can also bind tightly to U2AF, suggesting that evolution can select against sequences that may have a relatively modest reduction in binding. Although pyrimidines are frequently present at the first base in the exon, U2AF has a very strong bias against them, arguing there is a mechanism to compensate for weakened U2AF binding at this position. Finally, the C in the consensus sequence must remain adjacent to the AG/R ------------------- Key: 7089 Medline: Authors: Hujova J;Sikora J;Dobrovolny R;Poupetova H;Ledvinova J;Kostrouchova M;Hrebicek M Title: Characterization of gana-1, a Caenorhabditis elegans gene encoding a single ortholog of vertebrate alpha-galactosidase and alpha-N-acetylgalactosaminidase. Citation: BMC Cell Biology 6: 1-13 2005 Type: ARTICLE Genes: gana-1 Abstract: ------------------- Key: 7090 Medline: Authors: Cronin CJ;Mendel JE;Mukhtar S;Kim YM;Stirbl R;Bruck J;Sternberg PW Title: An automated system for measuring parameters of nematode sinusoidal movement. Citation: BMC Genetics 6: 1-19 2005 Type: ARTICLE Genes: cat-4 egl-30 goa-1 mrp-1 gpg-1 pgp-3 Abstract: ------------------- Key: 7091 Medline: 15664654 Authors: Murray J;Manoury B;Balic A;Watts C;Maizels RM Title: Bm-CPI-2, a cystatin from Brugia malayi nematode parasites, differs from Caenorhabditis elegans cystatins in a specific site mediating inhibition of the antigen-processing enzyme AEP. Citation: Molecular & Biochemical Parasitology 139: 197-203 2005 Type: ARTICLE Genes: Abstract: The filarial parasite Brugia malayi survives for many years in the human lymphatic system. One immune evasion mechanism employed by Brugia is thought to be the release of cysteine protease inhibitors (cystatins), and we have previously shown that the recombinant cystatin Bm-CPI-2 interferes with protease-dependent antigen processing in the MHC class II antigen presentation pathway. Analogy with vertebrate cystatins suggested that Bm-CPI-2 is bi-functional, with one face of the protein blocking papain-like proteases, and the other able to inhibit legumains such as asparaginyl endopeptidase (AEP). Site-directed mutagenesis was carried out on Bm-CPI-2 at Asn-77, the residue on which AEP inhibition is dependent in vertebrate homologues. Two mutations at this site (to Asp and Lys) showed 10-fold diminished and ablated activity respectively, in assays of AEP inhibition, while blocking of papain-like proteases was reduced by only a small degree. Comparison of the B. malayi cystatins with two homologues encoded by the free-living model organism, Caenorhabditis elegans, suggested that while the papain site may be intact, the AEP site would not be functional. This supposition was tested with recombinant C. elegans proteins, Ce-CPI-1 (K08B4.6) and Ce-CPI-2 (R01B10.1), both of which block cathepsins and neither of which possess the ability to block AEP. Thus, Brugia CPI-2 may have convergently evolved to inhibit an enzyme important only in the mammalian environment. ------------------- Key: 7092 Medline: Authors: Sharan R;Suthram S;Kelley RM;Kuhn T;McCuine S;Uetz P;Sittler T;Karp RM;Ideker T Title: Conserved patterns of protein interaction in multiple species. Citation: Proceedings of the National Academy of Sciences USA 102: 1974-1979 2005 Type: ARTICLE Genes: Abstract: To elucidate cellular machinery on a global scale, we performed a multiple comparison of the recently available protein-protein interaction networks of Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae. This comparison integrated protein interaction and sequence information to reveal 71 network regions that were conserved across all three species and many exclusive to the metazoans. We used this conservation, and found statistically significant support for 4,645 previously undescribed protein functions and 2,609 previously undescribed protein interactions. We tested 60 interaction predictions for yeast by two-hybrid analysis, confirming approximately half of these. Significantly, many of the predicted functions and interactions would not have been identified from sequence similarity alone, demonstrating that network comparisons provide essential biological information beyond what is gleaned from the genome. ------------------- Key: 7093 Medline: Authors: Geary TG;Kubiak TM Title: Neuropeptide G-protein-coupled receptors, their cognate ligands and behavior in Caenorhabditis elegans. Citation: Trends in Pharmacological Sciences 26: 56-58 2005 Type: REVIEW Genes: flp-7 flp-11 flp-15 flp-18 flp-21 npr-1 Abstract: Despite a simple nervous system, the free-living nematode Caenorhabditis elegans exhibits complex behaviors. The identification of peptide ligands for a G-protein-coupled receptor (GPCR) has provided insight into the neuronal circuitry involved in the regulation of feeding behavior in this worm. Progress in this regard has been accelerated by the discovery that functional expression of worm GPCRs in mammalian cells can be highly temperature dependent. Gene silencing and behavioral analysis has further identified several putative peptide GPCRs that are implicated in reproduction and locomotion. These studies suggest that these peptide GPCRs are legitimate targets for the discovery of novel anthellmintic agents. ------------------- Key: 7094 Medline: Authors: Haag ES;Doty AV Title: Sex determination across evolution: connecting the dots. Citation: PLoS Biology 3: 21-24 2005 Type: REVIEW Genes: dim-1 fem-2 fem-3 fog-2 mab-3 xol-1 Abstract: ------------------- Key: 7095 Medline: Authors: Nayak S;Goree J;Schedl T Title: fog-2 and the evolution of self-fertile hermaphroditism in Caenorhabditis. Citation: PLoS Biology 3: 57-71 2005 Type: ARTICLE Genes: atx-2 fbf-1 fbf-2 fem-1 fem-2 fem-3 fkh-6 fog-1 fog-2 fog-3 fox-1 ftr-1 gld-1 gld-3 her-1 laf-1 mab-3 mag-1 mog-1 mog-4 mog-5 mog-6 nos-1 nos-2 nos-3 psa-1 rme-2 sdc-1 sdc-2 sdc-3 sec-23 sex-1 srg-34 tra-1 tra-2 tra-3 Abstract: Somatic and germline sex determination pathways have diverged significantly in animals, making comparisons between taxa difficult. To overcome this difficulty, we compared the genes in the germline sex determination pathways of Caenorhabditis elegans and C. briggsae, two Caenorhabditis species with similar reproductive systems and sequenced genomes. We demonstrate that C. briggsae has orthologs of all known C. elegans sex determination genes with one exception: fog- 2. Hermaphroditic nematodes are essentially females that produce sperm early in life, which they use for self fertilization. In C. elegans, this brief period of spermatogenesis requires FOG- 2 and the RNA- binding protein GLD- 1, which together repress translation of the tra- 2 mRNA. FOG- 2 is part of a large C. elegans FOG- 2- related protein family defined by the presence of an F- box and Duf38/ FOG- 2 homogy domain. A fog- 2- related gene family is also present in C. briggsae, however, the branch containing fog- 2 appears to have arisen relatively recently in C. elegans, post- speciation. The C- terminus of FOG- 2 is rapidly evolving, is required for GLD- 1 interaction, and is likely critical for the role of FOG- 2 in sex determination. In addition, C. briggsae gld- 1 appears to play the opposite role in sex determination ( promoting the female fate) while maintaining conserved roles in meiotic progression during oogenesis. Our data indicate that the regulation of the hermaphrodite germline sex determination pathway at the level of FOG- 2/ GLD- 1/ tra- 2 mRNA is fundamentally different between C. elegans and C. briggsae, providing functional evidence in support of the independent evolution of self- fertile hermaphroditism. We speculate on the convergent evolution of hermaphroditism in Caenorhabditis based on the plasticity of the C. elegans germline sex determination cascade, in which multiple mutant paths yield ------------------- Key: 7096 Medline: 15696167 Authors: Zheng M;Messerschmidt D;Jungblut B;Sommer RJ Title: Conservation and diversification of Wnt signaling function during the evolution of nematode vulva development. Citation: Nature Genetics 37: 300-304 2005 Type: ARTICLE Genes: apr-1 bar-1 egl-20 lin-17 lin-44 mig-5 Abstract: Cell-fate specification and cell-cell signaling have been well studied during vulva development in Caenorhabditis elegans and provide a paradigm in evolutionary developmental biology(1,2). Pristionchus pacificus has been developed as a 'satellite' organism with an integrated physical and genetic map that allows detailed comparisons to C. elegans(3-5).A common aspect of vulva formation in both species is the polarization of the P7. p lineage, which is responsible for vulval symmetry. In C. elegans, Wnt signaling is crucial for P7. p cell-fate patterning(6); nothing is known about vulval symmetry in P. pacificus. We isolated mutations that disrupt polarization of the P7. p lineage in P. pacificus and found that the corresponding gene encodes a Frizzled-like molecule. In addition, mutations in Ppa-lin-17 (encoding Frizzled) and morpholino knock-down of Ppa-lin-44 (encoding Wnt), Ppa-egl-20 (encoding Wnt), Ppa-mig-5 (encoding Dsh), Ppa-apr-1 (encoding APC) and Ppa-bar-1 (encoding beta-catenin) results in gonad-independent vulva differentiation, indicating that these genes have a role in a negative signaling process. In contrast, in C. elegans, Wnt signaling has a positive role in vulva induction, and mutations in bar-1 result in a hypoinduced phenotype(7). Therefore, whereas the molecular mechanisms that generate vulval symmetry are conserved, the genetic control of vulva ------------------- Key: 7097 Medline: 15744306 Authors: Kinchen JM;Cabello J;Klingele D;Wong K;Feichtinger R;Schnabel H;Schnabel R;Hengartner MO Title: Two pathways converge at CED-10 to mediate actin rearrangement and corpse removal in C. elegans. Citation: Nature 434: 93-99 2005 Type: ARTICLE Genes: ced-1 ced-2 ced-3 ced-5 ced-6 ced-7 ced-10 ced-12 gla-1 mig-2 unc-69 unc-119 Abstract: The removal of apoptotic cells is essential for the physiological well being of the organism(1-3). In Caenorhabditis elegans, two conserved, partially redundant genetic pathways regulate this process(4-6). In the first pathway, the proteins CED-2, CED-5 and CED-12 ( mammalian homologues CrkII, Dock180 and ELMO, respectively) function to activate CED-10 (Rac1)(7,8). In the second group, the candidate receptor CED-1 (CD91/LRP/SREC) probably recognizes an unknown ligand on the apoptotic cell(9) and signals via its cytoplasmic tail to the adaptor protein CED-6 (hCED-6/GULP)(10,11), whereas CED-7 (ABCA1) is thought to play a role in membrane dynamics(12). Molecular understanding of how the second pathway promotes engulfment of the apoptotic cell is lacking. Here, we show that CED-1, CED-6 and CED-7 are required for actin reorganization around the apoptotic cell corpse, and that CED-1 and CED-6 colocalize with each other and with actin around the dead cell. Furthermore, we find that the CED-10( Rac) GTPase acts genetically downstream of these proteins to mediate corpse removal, functionally linking the two engulfment pathways and identifying the CED-1, - 6 and - 7 signalling module as upstream regulators of Rac activation. ------------------- Key: 7098 Medline: 15723795 Authors: Cinar H;Keles S;Jin Y Title: Expression profiling of GABAergic motor neurons in Caenorhabditis elegans. Citation: Current Biology 15: 340-346 2005 Type: ARTICLE Genes: acr-12 acr-14 ahr-1 flp-13 jkk-1 jnk-1 oig-1 rpy-1 sng-1 snn-1 snt-1 syd-1 tni-4 twk-30 unc-25 unc-30 unc-46 unc-47 Abstract: Neurons constitute the most diverse cell types and acquire their identity by the activity of particular genetic programs [1]. The GABAergic nervous system in C. elegans [2] consists of 26 neurons that fall into six classes [3, 4]. Animals that are defective in GABAergic neuron function and development display "shrinker" movement [5], abnormal foraging and defecation [4, 6]. Among the known shrinker genes, unc-25 and unc47 encode the GABA biosynthetic enzyme glutamic acid decarboxylase and vesicular transporter, respectively [7, 8]. unc-30 encodes a homeodomain protein of the Pitx family and regulates the differentiation of the D-type GABAergic neurons [9]. unc-46 probably functions in presynaptic GABA release [6], but its identity has not been reported. By cell-based microarray analysis, we identified over 250 genes with enriched expression in GABAergic neurons. The highly enriched gene set included all known genes. In vivo expression study with computational predictions further identified six new genes that are potential transcriptional targets of UNC-30. Behavioral studies of a deletion mutant implicate a function of a nicotinic receptor subunit in D-type neurons. Our analysis demonstrates the utility of neuron-specific genomics in identifying cell-specific genes and regulatory networks. ------------------- Key: 7099 Medline: 15723796 Authors: McCarroll SA;Li H;Bargmann CI Title: Identification of transcriptional regulatory elements in chemosensory receptor genes by probabilistic segmentation. Citation: Current Biology 15: 347-352 2005 Type: ARTICLE Genes: acy-2 cam-1 ceh-13 gpa-1 hlh-2 ina-1 lin-39 nlp-7 nlp-10 osm-9 pal-1 srh-132 srh-186 srh-220 sri-51 sro-1 tax-6 Abstract: Genome sequencing has allowed many gene regulatory elements to be identified through cross-species comparisons [1-5]. However, the expression of genes in multigene families can diverge rapidly between related species [6-9]. An alternative approach to characterizing multigene families utilizes the fact that genes within the group are likely to share aspects of their regulation. Here, we use a statistical approach, probabilistic segmentation [10], to identify sequences that are overrepresented in the regions upstream of C. elegans chemosensory receptor genes. Although each of these elements is present in only a subset of the genes, their distribution across and within the promoters of chemosensory receptor genes makes it possible to detect them. Many of the motifs show positional preference with respect to the translational start site and correspond to the binding sites of known families of transcription factors. We verified one motif, the E-box sequence WWYCACSTGYY, by showing that it directs expression of reporter genes to the ADL chemosensory neurons. Thus, probabilistic segmentation can be used to identify functional regulatory elements with no previous knowledge of gene expression or regulation. This approach may be of particular value for rapidly evolving genes in the immune system and the nervous system. ------------------- Key: 7100 Medline: 15723800 Authors: Lu M;Kinchen JM;Rossman KL;Grimsley C;Hall M;Sondek J;Hengartner MO;Yajnik V;Ravidhandran KS Title: A steric-inhibition model for regulation of nucleotide exchange via the Dock180 family of GEFs. Citation: Current Biology 15: 371-377 2005 Type: ARTICLE Genes: ced-5 ced-12 Abstract: CDM (CED-5, Dock180, Myoblast city) family members have been recently identified as novel, evolutionarily conserved guanine nucleotide exchange factors (GEFs) for Rho-family GTPases [1-7]. They regulate multiple processes, including embryonic development, cell migration, apoptotic-cell engulfment, tumor invasion, and HIV-1 infection, in diverse model systems [4, 6, 8-16]. However, the mechanism(s) of regulation of CDM proteins has not been well understood. Here, our studies on the prototype member Dock180 reveal a steric-inhibition model for regulating the Dock180 family of GEFs. At basal state, the N-terminal SH3 domain of Dock180 binds to the distant catalytic Docker domain and negatively regulates the function of Dock180. Further studies revealed that the SH3: Docker interaction sterically blocks Rac access to the Docker domain. Interestingly, ELMO binding to the SH3 domain of Dock180 disrupted the SH3:Docker interaction, facilitated Rac access to the Docker domain and contributed to the GEF activity of the Dock180; ELMO complex. Additional genetic rescue studies in C. elegans suggested that the regulation of the Docker-domain-mediated GEF activity by the SH3 domain and its adjoining region is evolutionarily conserved. This steric-inhibition model may be a general mechanism for regulating multiple SH3-domain-containing Dock180 family members and may have implications for a ------------------- Key: 7101 Medline: 15723801 Authors: Chen CCG;Simard MJ;Tabara H;Brownell DR;McCollough JA;Mello CC Title: A member of the polymerase beta nucleotidyltransferase superfamily is required for RNA interference in C. elegans. Citation: Current Biology 15: 378-383 2005 Type: ARTICLE Genes: let-7 lin-4 mut-7 pos-1 rde-1 rde-3 unc-22 Abstract: RNA interference (RNAi) is an ancient, highly conserved mechanism in which small RNA molecules (siRNAs) guide the sequence-specific silencing of gene expression [1]. Several silencing machinery protein components have been identified, including helicases, RNase-related proteins, double- and singlestranded RNA binding proteins, and RNA-dependent RNA polymerase-related proteins [2]. Work on these factors has led to the revelation that RNAi mechanisms intersect with cellular pathways required for development and fertility (3, 4]. Despite rapid progress in understanding key steps in the RNAi pathway, it is clear that many factors required for both RNAi and related developmental mechanisms have not yet been identified. Here, we report the characterization of the C. elegans gene rde-3. Genetic analysis of presumptive null alleles indicates that rde-3 is required for siRNA accumulation and for efficient RNAi in all tissues, and it is essential for fertility and viability at high temperatures. RDE-3 contains conserved domains found in the polymerase beta nucleotidyltransferase superfamily, which includes conventional poly(A) polymerases, 2'-5' oligoadenylate synthetase (OAS), and yeast Trf4p [5]. These findings implicate a new enzymatic modality in RNAi and suggest possible models for the role of RDE-3 in the RNAi ------------------- Key: 7102 Medline: Authors: Kenyon C Title: The plasticity of aging: insights from long-lived mutants. Citation: Cell 120: 449-460 2005 Type: REVIEW Genes: clk-1 daf-2 daf-16 ins-7 isp-1 mev-1 old-1 sir-2 Abstract: Mutations in genes affecting endocrine signaling, stress responses, metabolism, and telomeres can all increase the life spans of model organisms. These mutations have revealed evolutionarily conserved pathways for aging, some of which appear to extend life span in response to sensory cues, caloric restriction, or stress. Many mutations affecting longevity pathways delay age-related disease, and the molecular analysis of these pathways is leading to a mechanistic understanding of how these two processesaging and disease susceptibility-are linked. ------------------- Key: 7103 Medline: Authors: Partridge L;Gems D;Withers DJ Title: Sex and death: what is the connection? Citation: Cell 120: 461-472 2005 Type: REVIEW Genes: age-1 akt-1 akt-2 daf-2 daf-16 daf-18 ist-1 sgk-1 Abstract: A cost of reproduction, where lifespan and fecundity are negatively correlated, is of widespread occurrence. Mutations in insulin/IGF signaling (IIS) pathways and dietary restriction (DR) can extend lifespan in model organisms but do not always reduce fecundity, suggesting that the link between lifespan and fecundity is not inevitable. Understanding the molecular basis of the cost of reproduction will be informed by elucidation of the mechanisms by which DR and IIS affect these two traits. ------------------- Key: 7104 Medline: 15707967 Authors: Lee EY;Shim YH;Chitwood DJ;Hwang SB;Lee J;Paik YK Title: Cholesterol-producing transgenic Caenorhabditis elegans lives longer due to newly acquired enhanced stress resistance. Citation: Biochemical and Biophysical Research Communications 328: 929-936 2005 Type: ARTICLE Genes: age-1 Abstract: Because Caenorhabditis elegans lacks several components of the de novo sterol biosynthetic pathway, it requires sterol as an essential nutrient. Supplemented cholesterol undergoes extensive enzymatic modification in C elegans to form other sterols of unknown function. 7-Dehydrocholesterol reductase (DHCR) catalyzes the reduction of the A 7 double bond of sterols and is suspected to be defective in C elegans, in which the major endogenous sterol is 7-dehydrocholesterol (7DHC). We microinjected a human DHCR expression vector into C. elegans, which was then incorporated into chromosome by gamma-radiation. This transgenic C. elegans was named cholegans, i.e., cholesterol-producing C. elegans, because it was able to convert 7DHC into cholesterol. We investigated the effects of changes in sterol composition on longevity and stress resistance by examining brood size, mean life span, UV resistance, and thermotolerance. Cholegans contained 80% more cholesterol than the wild-type control. The brood size of cholegans was reduced by 40% compared to the wild-type control, although the growth rate was not significantly changed. The mean life span of cholegans was increased up to 131% in sterol-deficient medium as compared to wild-type. The biochemical basis for life span extension of cholegans appears to partly result from its acquired resistance against both UV irradiation ------------------- Key: 7105 Medline: 15655525 Authors: Bamber BA;Richmond JE;Otto JF;Jorgensen EM Title: The composition of the GABA receptor at the Caenorhabditis elegans neuromuscular junction. Citation: British Journal of Pharmacology 144: 502-509 2005 Type: ARTICLE Genes: unc-49 Abstract: 1 The unc-49 gene of the nematode Caenorhabditis elegans encodes three gamma-aminobutyric acid type A (GABA(A)) receptor subunits. Two of these, UNC-49B and UNC-49C, are expressed at high abundance and co-localize at the neuromuscular junction. 2 The UNC-49B subunit is sufficient to form a GABA(A) receptor in vitro and in vivo. Furthermore, all loss-of-function unc-49 alleles lack functional UNC-49B. No mutations specifically inactivate UNC-49C. Thus, UNC-49C appears to be dispensable for receptor function; however, UNC-49C has been conserved among different nematode species, suggesting it plays a necessary role. 3 To ascertain whether UNC-49C is part of the GABA(A) receptor in vivo, we performed patch-clamp electrophysiology on C. elegans muscle cells. Sensitivity to GABA, and to the antagonists picrotoxin and pregnenolone sulfate, matched the UNC-49B/C heteromer rather than the UNC-49B homomer, for both exogenous and synaptically-released GABA. 4 The synaptic localization of UNC-49C requires the presence of UNC-49B, indicative of a physical association between the two subunits in vivo. Thus, the in vivo receptor is an UNC-49B/C heteromer. 5 UNC-49C plays a negative modulatory role. Using the rapid ligand-exchange technique in vitro, we determined that UNC-49C causes accelerated receptor desensitization. Previously, UNC-49C was shown to reduce single-channel conductance in UNC-49B/C heteromers. Thus, the function of UNC-49B is to provide GABA responsiveness and localization to synapses, while the function of UNC-49C is to negatively modulate receptor function and precisely shape inhibitory ------------------- Key: 7106 Medline: 15579462 Authors: Putrenko I;Zakikhani M;Dent JA Title: A family of acetylcholine-gated chloride channel subunits in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 280: 6392-6398 2005 Type: ARTICLE Genes: Abstract: The genome of the nematode Caenorhabditis elegans encodes a surprisingly large and diverse superfamily of genes encoding Cys loop ligand-gated ion channels. Here we report the first cloning, expression, and pharmacological characterization of members of a family of anion-selective acetylcholine receptor subunits. Two subunits, ACC-1 and ACC-2, form homomeric channels for which acetylcholine and arecoline, but not nicotine, are efficient agonists. These channels are blocked by D-tubocurarine but not by a-bungarotoxin. We provide evidence that two additional subunits, ACC-3 and ACC-4, interact with ACC-1 and ACC-2. The acetylcholine-binding domain of these channels appears to have diverged substantially from the acetylcholine-binding domain of nicotinic receptors. ------------------- Key: 7107 Medline: 15611047 Authors: Shostak Y;Yamamoto KR Title: Overlapping but separable determinants of DNA binding and nuclear localization map to the C-terminal end of the Caenorhabditis elegans DAF-12 DNA binding domain. Citation: Journal of Biological Chemistry 280: 6554-6560 2005 Type: ARTICLE Genes: daf-12 Abstract: Proteins are commonly viewed as modular assemblies of functional domains. We analyzed a loss-of-function mutation in the Caenorhabditis elegans intracellular receptor DAF-12, a conservative substitution of an arginine to a lysine at position 197 (R197K). Arg(197) resides in region similar to a nuclear localization signal, just downstream of the receptor minimal zinc finger DNA binding domain (DBD) core. We found that the R197K, but not mutations of neighboring arginine or lysine residues, dramatically reduced DAF-12 transcriptional regulatory activity in a yeast reporter assay. This reduction in regulatory activity correlated with greatly decreased DNA binding affinity in vitro, suggesting a role for the DAF-12 DBD C-terminal region (dbdC), and specifically for Arg(197), in DNA binding. Remarkably, three basic residues immediately contiguous with Arg(197) played little role in DNA binding and rather affected nuclear localization; in contrast, Arg(197) itself was dispensable for nuclear localization. Thus, DAF-12 dbdC harbors overlapping but separable determinants of DNA binding and nuclear localization in a ------------------- Key: 7108 Medline: 15718049 Authors: Murakami S;Murakami H Title: The effects of aging and oxidative stress on learning behavior in C. elegans. Citation: Neurobiology of Aging 26: 899-905 2005 Type: ARTICLE Genes: clk-1 daf-16 gas-1 isp-1 mev-1 Abstract: Oxidative stress is associated with age-related declines of biological functions. However, the nervous system is preserved during aging in Caenorhabditis elegans and, thus, it is not well explored whether aging and oxidative stress affect nervous functions. Here we report that age-related decline can be observed in a type of associative-learning behavior, referred to as isothermal tracking. We also report the effects of mutants with altered sensitivity to oxidative stress on learning behavior and motor activity in young adults. The isp-1 and clk-1 mutants are members of the Clk class of mutants and have deficits in the function of the mitochondrial respiratory chain, leading to reduced levels of oxidative stress, increased longevity, delayed rhythmic behaviors and other phenotypes. Both the Clk mutations and pretreatment with a metabolic antioxidant, alpha-lipoic acid (LA), increased the ability to show isothermal tracking and modestly reduced motor activity. Mutants with increased oxidative stress showed severely impaired learning behavior and modestly reduced motor activity. Therefore, physiological levels of oxidative stress may be too high for learning behavior but, perhaps, not for motor activity. We discuss the relevance of oxidative stress to the aging and evolution of behaviors. ------------------- Key: 7109 Medline: 15743415 Authors: Ruksana R;Kuroda K;Terami H;Bando T;Kitaoka S;Takaya T;Sakube Y;Kagawa H Title: Tissue expression of four troponin I genes and their molecular interactions with two troponin C isoforms in Caenorhabditis elegans. Citation: Genes to Cells 10: 261-276 2005 Type: ARTICLE Genes: hlh-1 myo-2 pat-10 tni-1 tni-2 tni-3 tni-4 unc-27 Abstract: Gene duplication is a major genetic event that can produce multiple protein isoforms. Comparative sequence and functional analysis of related gene products can provide insights into protein family evolution. To characterize the Caenorhabditis elegans troponin I family, we analyzed gene structures, tissue expression patterns and RNAi phenotypes of four troponin I isoforms. Tissue expression patterns were determined using lacZ/gfp/rfp reporter gene assays. The tni-1, tni-2/unc-27 and tni-3 genes, each encoding a troponin I isoform, are uniquely expressed in body wall, vulval and anal muscles but at different levels; tni-4 was expressed solely in the pharynx. Expressing tni-1 and -2 gene RNAi caused motility defects similar to unc-27 (e155) mutant, a tni-2 null allele. The tni-3 RNAi expression produced egg laying defects while the tni-4 RNAi caused arrest at gastrulation. Overlay analyses were used to assay interactions between the troponin I and two troponin C isoforms. The three body wall troponin I isoforms interacted with body wall and pharyngeal troponin C isoforms; TNI-4 interacted only with pharyngeal troponin C. Our results suggest the body wall genes have evolved following duplication of the pharynx gene and provide important data about gene duplication and functional differentiation of nematode troponin I isoforms. ------------------- Key: 7110 Medline: Authors: Desai T;Batani D;Bernardiello A;Poletti G;Orsini F;Ullschmied J;Skala J;Kralikova B;Krousky E;Pfeifer M;Kadlec C;Mocek T;Prag A; Renner O;Juha L;Cotelli F;Donin CLL;Zullini A Title: Investigation of Caenorhabditis elegans using soft X-ray contact microscopy. Citation: Physica Medica 20: 121-125 2004 Type: ARTICLE Genes: Abstract: ------------------- Key: 7111 Medline: 15569358 Authors: Gill MS;Held JM;Fisher AL;Gibson BW;Lithgow GJ Title: Lipophilic regulator of a developmental switch in Caenorhabditis elegans. Citation: Aging Cell 3: 413-421 2004 Type: ARTICLE Genes: daf-2 daf-7 daf-9 daf-12 Abstract: In Caenorhabditis elegans, the decision to develop into a reproductive adult or arrest as a dauer larva is influenced by multiple pathways including insulin-like and transforming growth factor beta (TGFbeta)-like signalling pathways. It has been proposed that lipophilic hormones act downstream of these pathways to regulate dauer formation. One likely target for such a hormone is DAF-12, an orphan nuclear hormone receptor that mediates these developmental decisions and also influences adult lifespan. In order to find lipophilic hormones we have generated lipophilic extracts from mass cultures of C. elegans and shown that they rescue the dauer constitutive phenotype of class 1 daf-2 insulin signalling mutants and the TGFbeta signalling mutant daf-7. These extracts are also able to rescue the lethal dauer phenotype of daf-9 mutants, which lack a P450 steroid hydroxylase thought to be involved in the synthesis of the DAF-12 ligand; extracts, however, have no effect on a DAF-12 ligand binding domain mutant that is predicted to be ligand insensitive. The production of this hormone appears to be DAF-9 dependent as extracts from a daf-9;daf-12 double mutant do not exhibit this activity. Preliminary fractionation of the lipophilic extracts shows that the activity is hydrophobic with some polar properties, consistent with a small lipophilic hormone. We propose that the dauer rescuing activity is a hormone synthesized by DAF-9 that acts through DAF-12. ------------------- Key: 7112 Medline: 15646636 Authors: Fridkin A;Karabinos A;Gruenbaum Y Title: Intermediate filaments in Caenorhabditis elegans. Citation: Methods in Cell Biology 78: 703-718 2004 Type: REVIEW Genes: Abstract: ------------------- Key: 7113 Medline: 15519907 Authors: Dengg M;van Meel JC Title: Caenorhabditis elegans as model system for rapid toxicity assessment of pharmaceutical compounds. Citation: Journal of Pharmacological & Toxicological Methods 50: 209-214 2004 Type: ARTICLE Genes: hsp-16 Abstract: INTRODUCTION: The model organism Caenorhabditis elegans is widely used for genetic studies as well as a living biomonitor in ecotoxicology. In this study, we investigated whether C. elegans may represent a suitable model for rapid preliminary toxicity studies of pharmaceutical compounds. METHODS: For this purpose, we used the EGFR kinase inhibitors BIBU1361, BIBX1382, and an inactive chemical analogue BIBU1476. As a first parameter to score for toxicity, we determined lethality of the wild-type C. elegans strain N2 (Bristol) in the presence of the compounds. The transgenic C. elegans strain PC72 (lacZ, heat shock protein-16 [hsp-16] construct) was used as a report organism for toxic effects. PC72 expresses beta-Galactosidase which is induced by hsp-16 in direct response when exposed to toxic compounds. The expression of beta-Galactosidase in cells was subsequently visualized by histochemical staining with X-Gal. RESULTS: A rank order of potency with respect to lethality was established: BIBU1361>BIBX1382>>BIB1476. The induction of beta-Galactosidase was concentration-dependent for each compound and demonstrated the same order of potency as observed for lethality. Furthermore, these compounds showed the same order for lethality in rodents, the first requirement of validation. DISCUSSION: These results indicate that wild-type C. elegans and the transgenic strain PC72 are both suitable models to determine the toxicity of pharmaceutical compounds. This approach allows for an easy and fast ranking of compound toxicity, which may lead to a more rational choice for further in vivo ------------------- Key: 7114 Medline: 15745997 Authors: Kim DH;Lee KH;Kim JH;Ryu GH;Bae SH;Lee BC;Moon KY;Byun SM;Koo HS;Seo YS Title: Enzymatic properties of the Caenorhabditis elegans Dna2 endonuclease/helicase and a species-specific interaction between RPA and Dna2. Citation: Nucleic Acids Research 33: 1372-1383 2005 Type: ARTICLE Genes: Abstract: In both budding and fission yeasts, a null mutation of the DNA2 gene is lethal. In contrast, a null mutation of Caenorhabditis elegans dna2+ causes a delayed lethality, allowing survival of some mutant C.elegans adults to F2 generation. In order to understand reasons for this difference in requirement of Dna2 between these organisms, we examined the enzymatic properties of the recombinant C.elegans Dna2 (CeDna2) and its interaction with replication-protein A (RPA) from various sources. Like budding yeast Dna2, CeDna2 possesses DNA-dependent ATPase, helicase and endonuclease activities. The specific activities of both ATPase and endonuclease activities of the CeDna2 were considerably higher than the yeast Dna2 (approximately 10- and 20-fold, respectively). CeDna2 endonuclease efficiently degraded a short 5' single-stranded DNA tail (<10 nt) that was hardly cleaved by ScDna2. Both endonuclease and helicase activities of CeDna2 were stimulated by CeRPA, but not by human or yeast RPA, demonstrating a species-specific interaction between Dna2 and RPA. These and other enzymatic properties of CeDna2 described in this paper may shed light on the observation that C.elegans is less stringently dependent on Dna2 for its viability than Saccharomyces cerevisiae. We propose that flaps generated by DNA polymerase delta-mediated displacement DNA synthesis are mostly short in C.elegans eukaryotes, and hence less dependent on Dna2 ------------------- Key: 7115 Medline: 15728356 Authors: Gray JM;Hill JJ;Bargmann CI Title: A circuit for navigation in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 102: 3184-3191 2005 Type: ARTICLE Genes: cat-2 che-2 nmr-1 odr-2 osm-3 osm-6 tph-1 ttx-3 Abstract: Caenorhabditis elegans explores its environment by interrupting its forward movement with occasional turns and reversals. Turns and reversals occur at stable frequencies but irregular intervals, producing probabilistic exploratory behaviors. Here we dissect the roles of individual sensory neurons, interneurons, and motor neurons in exploratory behaviors under different conditions. After animals are removed from bacterial food, they initiate a local search behavior consisting of reversals and deep omega-shaped turns triggered by AWC olfactory neurons, ASK gustatory neurons, and AIB interneurons. Over the following 30 min, the animals disperse as reversals and omega turns are suppressed by ASI gustatory neurons and AIY interneurons. Interneurons and motor neurons downstream of AIB and AN encode specific aspects of reversal and turn frequency, amplitude, and directionality. SMD motor neurons help encode the steep amplitude of omega turns, RIV motor neurons specify the ventral bias of turns that follow a reversal, and SMB motor neurons set the amplitude of sinusoidal movement. Many of these sensory neurons, interneurons, and motor neurons are also implicated in chemotaxis and thermotaxis. Thus, this circuit may represent a common substrate for multiple navigation ------------------- Key: 7116 Medline: 15728376 Authors: Margalit A;Segura-Totten M;Gruenbaum Y;Wilson KL Title: Barrier-to-autointegration factor is requried to segregate and enclose chromosomes within the nuclear envelope and assemble the nuclear lamina. Citation: Proceedings of the National Academy of Sciences USA 102: 3290-3295 2005 Type: ARTICLE Genes: baf-1 lag-2 Abstract: Barrier-to-autointegration factor (BAF) binds dsDNA, LEM-domain proteins, and lamins. Caenorhabditis elegans BAF requires Celamin and two LEM-domain proteins (Ce-emerin and Ce-MAN1) to localize during nuclear assembly. It was unknown whether Celamin and LEM proteins, in turn, depend on Ce-BAF (mutually dependent structural roles). RNA interference-mediated downregulation of Ce-BAF caused gross defects in chromosome segregation, chromatin decondensation, and mitotic progression as early as the two-cell stage, and embryos died at the approximate to100-cell stage. Nuclear pores reassembled, whereas Ce-lamin, Ce-emerin, and Ce-MAN1 bound chromatin but remained patchy and disorganized. The nuclear membranes formed but failed to enclose anaphase-bridged chromatin. Time-lapse imaging showed two phenotypes: anaphase-bridged chromatin that eventually resolved, and segregated chromatin that returned to the midzone. Thus, the assembly of BAF, lamins, and LEM-domain proteins is mutually dependent, and is required to capture segregated chromosomes within the nascent nuclear envelope. Embryos that escaped lethality by down-regulation of Ce-BAF grew into sterile adults with misplaced distal tip cells and gonads, further suggesting that mild postembryonic ------------------- Key: 7117 Medline: Authors: Van Gilst MR;Hadjivassiliou H;Jolly A;Yamamoto KR Title: Nuclear hormone receptor NHR-49 controls fat consumption and fatty acid composition in C. elegans. Citation: Plos Biology 3: 301-312 2005 Type: ARTICLE Genes: acs-2 ctl-2 ech-1 elo-2 fat-1 fat-2 fat-3 fat-4 fat-5 fat-6 fat-7 lbp-1 lbp-2 lbp-3 lbp-4 lbp-5 lbp-6 lbp-7 lbp-8 nhr-49 Abstract: Mammalian nuclear hormone receptors (NHRs), such as liver X receptor, farnesoid X receptor, and peroxisome proliferator-activated receptors (PPARs), precisely control energy metabolism. Consequently, these receptors are important targets for the treatment of metabolic diseases, including diabetes and obesity. A thorough understanding of NHR fat regulatory networks has been limited, however, by a lack of genetically tractable experimental systems. Here we show that deletion of the Caenorhabditis elegans NHR gene nhr-49 yielded worms with elevated fat content and shortened life span. Employing a quantitative RT-PCR screen, we found that nhr-49 influenced the expression of 13 genes involved in energy metabolism. Indeed, nhr-49 served as a key regulator of fat usage, modulating pathways that control the consumption of fat and maintain a normal balance of fatty acid saturation. We found that the two phenotypes of the nhr-49 knockout were linked to distinct pathways and were separable: The high-fat phenotype was due to reduced expression of enzymes in fatty acid beta-oxidation, and the shortened adult life span resulted from impaired expression of a stearoyl-CoA desaturase. Despite its sequence relationship with the mammalian hepatocyte nuclear factor 4 receptor, the biological activities of nhr-49 were most similar to those of the mammalian PPARs, implying an evolutionarily conserved role for NHRs in modulating fat consumption and composition. Our findings in C. elegans provide novel insights into how NHR regulatory networks are coordinated to govern fat ------------------- Key: 7118 Medline: 15708444 Authors: Houthoofd K;Braeckman BP;Lenaerts I;Brys K;Matthijssens F;de Vreese A;van Eygen S;Vanfleteren JR Title: DAF-2 pathway mutations and food restriction in aging Caenorhabditis elegans differentially affect metabolism. Citation: Neurobiology of Aging 26: 689-696 2005 Type: ARTICLE Genes: daf-2 daf-16 Abstract: In Caenorhabditis elegans, metabolism and life expectancy respond to environmental cues of food availability and temperature. Several genes act in a neuroendocrine, DAF-2, insulin/IGF-1 receptor-like pathway in which reduced signaling affects metabolism and increases longevity. Here we describe the effect of reduced DAF-2 signaling on several parameters of metabolism including rates of oxygen consumption and heat output, the calorimetric/respirometric ratio, ATP levels, XTT reduction capacity and accumulation of lipofuscin. We also asked whether the DAF-2 signaling pathway mediates the metabolic and longevity effects of axenic culture medium. We show that both interventions act either antagonistically or in concert, depending on the parameter examined and that axenic culture medium, unlike DAF-2 signaling, does not need DAF-16 for generating these effects. In addition, we provide evidence that DAF-2 signaling controls mitochondrial bioenergetics by adjusting the rate of ATP synthesis to the rate of ATP utilization and by regulating the heat-producing proton leak pathway. ------------------- Key: 7119 Medline: 15750353 Authors: Cho SW;Cho JH;Song HO Park CS Title: Identification and characterization of a putative cyclic nucleotide-gated channel, CNG-1, in C. elegans. Citation: Molecules & Cells 19: 149-154 2005 Type: ARTICLE Genes: Abstract: Cyclic nucleotide-gated (CNG) channels encoded by the tax-4 and tax-2 genes are required for chemosensing and thermosensing in the nematode C. elegans. We identified a gene in the C elegans genome, which we designated cng-1, that is highly homologous to tax-4. Partial CNG-1 protein tagged with green fluorescent protein was expressed in several sensory neurons of the amphid. We created a deletion mutant of cng-1, cng-1 (jh111), to investigate its in vivo function. The mutant worms had no detectable abnormalities in terms of their basic behavior or morphology. Whereas tax-4 and tax-2 mutants failed to respond to water-soluble or volatile chemical attractants, the cng-1 null mutant exhibited normal chemotaxis to such chemicals and a tax-4;cng-1 double mutant had a similar phenotype to tax-4 single mutants. Interestingly, cng-1 and tax-4 had a synergistic effect on brood size. ------------------- Key: 7120 Medline: 15616189 Authors: Encalada SE;Willis J;Lyczak R;Bowerman B Title: A spindle checkpoint functions during mitosis in the early Caenorhabditis elegans embryo. Citation: Molecular Biology of the Cell 16: 1056-1070 2005 Type: ARTICLE Genes: apo-5 dhc-1 dnc-1 hcp-1 hcp-2 mdf-1 mdf-2 zyg-9 Abstract: During mitosis, chromosome segregation is regulated by a spindle checkpoint mechanism. This checkpoint delays anaphase until all kinetochores are captured by microtubules from both spindle poles, chromosomes congress to the metaphase plate, and the tension between kinetochores and their attached microtubules is properly sensed. Although the spindle checkpoint can be activated in many different cell types, the role of this regulatory mechanism in rapidly dividing embryonic animal cells has remained controversial. Here, using time-lapse imaging of live embryonic cells, we show that chemical or mutational disruption of the mitotic spindle in early Caenorhabditis elegans embryos delays progression through mitosis. By reducing the function of conserved checkpoint genes in mutant embryos with defective mitotic spindles, we show that these delays require the spindle checkpoint. In the absence of a functional checkpoint, more severe defects in chromosome segregation are observed in mutants with abnormal mitotic spindles. We also show that the conserved kinesin CeMCAK, the CENP-F-related proteins HCP-1 and HCP-2, and the core kinetochore protein CeCENP-C all are required for this checkpoint. Our analysis indicates that spindle checkpoint mechanisms are functional in the rapidly dividing cells of an early animal embryo and that this checkpoint can prevent chromosome segregation defects ------------------- Key: 7121 Medline: 15616192 Authors: Schmidt DJ;Rose DJ;Saxton MW;Strome S Title: Functional analysis of cytoplasmic dynein heavy chain in Caenorhabditis elegans with fast-acting temperature-sensitive mutations. Citation: Molecular Biology of the Cell 16: 1200-1212 2005 Type: ARTICLE Genes: dhc-1 let-354 hDf6 gaDp1 hDp37 Abstract: Cytoplasmic dynein, a minus-end-directed microtubule motor, has been implicated in many cellular and developmental processes. Identification of specific cellular processes that rely directly on dynein would be facilitated by a means to induce specific and rapid inhibition of its function. We have identified conditional variants of a Caenorhabditis elegans dynein heavy chain (DHC-1) that lose function within a minute of a modest temperature upshift. Mutant embryos generated at elevated temperature show defects in centrosome separation, pronuclear migration, rotation of the centrosome/nucleus complex, bipolar spindle assembly, anaphase chromosome segregation, and cytokinesis. Our analyses of mutant embryos generated at permissive temperature and then upshifted quickly just before events of interest indicate that DHC-1 is required specifically for rotation of the centrosome/nucleus complex, for chromosome congression to a well ordered metaphase plate, and for timely initiation of anaphase. Our results do not support the view that DHC-1 is required for anaphase B separation of spindle poles and chromosomes. A P-loop mutation identified in two independent dominant temperature-sensitive alleles of dhc-1, when engineered into the DHC1 gene of Saccharomyces cerevisiae, conferred a dominant temperature-sensitive dynein loss-of-function phenotype. This suggests that temperature-sensitive mutations can be created for time-resolved function analyses of dyneins and perhaps other P-loop proteins in a ------------------- Key: 7122 Medline: 15647385 Authors: Take-uchi M;Kobayashi Y;Kimura KD;Ishihara T;Katsura I Title: FLR-4, a novel serine/threonine protein kinase, regulates defecation rhythm in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 16: 1355-1365 2005 Type: ARTICLE Genes: flr-1 flr-3 flr-4 unc-3 mnDf19 mnDf20 mnDp1 mnDp25 Abstract: The defecation behavior of the nematode Caenorhabditis elegans is controlled by a 45-s ultradian rhythm. An essential component of the clock that regulates the rhythm is the inositol trisphosphate receptor in the intestine, but other components remain to be discovered. Here, we show that the flr-4 gene, whose mutants exhibit very short defecation cycle periods, encodes a novel serine/threonine protein kinase with a carboxyl terminal hydrophobic region. The expression of functional flr-4::GFP was detected in the intestine, part of pharyngeal muscles and a pair of neurons, but expression of flr-4 in the intestine was sufficient for the wild-type phenotype. Furthermore, laser killing of the flr-4-expressing neurons did not change the defecation phenotypes of wild-type and flr-4 mutant animals. Temperature-shift experiments with a temperature-sensitive flr-4 mutant suggested that FLR-4 acts in a cell-functional rather than developmental aspect in the regulation of defecation rhythms. The function of FLR-4 was impaired by missense mutations in the kinase domain and near the hydrophobic region, where the latter allele seemed to be a weak antimorph. Thus, a novel protein kinase with a unique structural feature acts in the intestine to increase the length of defecation cycle ------------------- Key: 7123 Medline: 15647374 Authors: Glodowski DR;Wright T;Martinowich K;Chang HCH;Beach D;Rongo C Title: Distinct LIN-10 domains are required for its neuronal function, its epithelial function, and its synaptic localization. Citation: Molecular Biology of the Cell 16: 1417-1426 2005 Type: ARTICLE Genes: glr-1 lin-10 lin-31 Abstract: alpha-Amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA)-type glutamate receptors (AMPARs) mediate excitatory neurotransmission at neuronal synapses, and their regulated localization plays a role in synaptic plasticity. In Caenorhabditis elegans, the PDZ and PTB domain-containing protein LIN-10 is required both for the synaptic localization of the AMPAR subunit GLR-1 and for vulval fate induction in epithelia. Here, we examine the role that different LIN-10 domains play in GLR-1 localization. We find that an amino-terminal region of LIN-10 directs LIN-10 protein localization to the Golgi and to synaptic clusters. In addition, mutations in the carboxyl-terminal PDZ domains prevent LIN-10 from regulating GLR-1 localization in neurons but do not prevent LIN-10 from functioning in the vulval epithelia. A mutation in the amino terminus prevents the protein from functioning in the vulval epithelia but does not prevent it from functioning to regulate GLR-1 localization in neurons. Finally, we show that human Mint2 can substitute for LIN-10 to facilitate GLR-1 localization in neurons and that the Mint2 amino terminus is critical for this function. Together, our data suggest that LIN-10 uses distinct modular domains for its functions in neurons and epithelial cells and that during evolution its vertebrate ortholog Mint2 has retained the ability to direct AMPAR localization in neurons. ------------------- Key: 7124 Medline: 15659564 Authors: Wolf MTF;Lee J;Panther F;Otto EA;Guan K;Hildebrandt F Title: Expression and phenotype analysis of the nephrocystin-1 and nephrocystin-4 homologs in Caenorhabditis elegans. Citation: Journal of the American Society of Nephrology 16: 676-687 2005 Type: ARTICLE Genes: him-5 lov-1 nph-1 nph-4 pkd-2 Abstract: Nephronophthisis (NPHP), an autosomal-recessive cystic kidney disease, is the most frequent genetic cause of end-stage renal failure in children. NPHP types 1 and 4 are caused by mutations in NPHP1 and NPHP4, encoding the proteins nephrocystin-1 and nephrocystin-4, respectively. Nephrocystin-1 and nephrocystin-4 are expressed in primary cilia of renal epithelial cells. NPHP1 and NPHP4 are highly conserved in Caenorhabditis elegans. However, this species does not have a kidney but an excretory system that consists of an excretory cell, an excretory gland cell, a duct cell, and a pore cell. Therefore, cell type-specific expression pattern and function of the nephrocystin homologs in C. elegans were of interest. Expression of green fluorescence protein fusion constructs that contain the C. elegans promoter regions for nph-1 and nph-4 was not found in the excretory system but in ciliated sensory neurons of the head (amphid neurons) and the tail in hermaphrodites (phasmid neurons) and males (sensory ray neurons). As the knockout phenotype for the PKD homologs lov-1 and pkd-2 shows impaired male mating behavior, RNAi knockdown animals were analyzed for this phenotype. A similar phenotype was found in the nph-1 and nph-4 RNAi knockdown animals compared with the lov-1 and pkd-2 knockout phenotype. Thus, it is suggested that renal cyst-causing genes may be part of a shared functional module, highly conserved in evolution. The NPHP homologs may be necessary for initial assembly of the cilium, whereas the polycystic kidney disease homologs may function ------------------- Key: 7125 Medline: 15672447 Authors: Porter MY;Turmaine M;Mole SE Title: Identification and characterization of Caenorhabditis elegans palmitoyl protein thioesterase 1. Citation: Journal of Neuroscience Research 79: 836-848 2005 Type: ARTICLE Genes: ppt-1 Abstract: Infantile neuronal ceroid lipofuscinosis (INCL; Batten disease) is a severe neurodegenerative disorder of childhood characterized by the accumulation of autofluorescent storage material in lysosomes. It is caused by mutation of the CLN1/PPT1 gene, which encodes the lysosomal enzyme palmitoyl protein thioesterase-1 (PPT1), but the mechanism of disease pathogenesis and substrates for the enzyme are unknown. Caenorhabditis elegans is a simple nematode worm, with a fully sequenced genome, which is easy to maintain and manipulate. It has a completely mapped cell lineage and nervous system and has already provided clues about the pathogenesis of several human neuronal and lysosomal storage disorders. We have identified and characterized a PPT1 homologue in C. elegans. We found that, although this gene was not essential for the animal's survival, its mutation resulted in a mild developmental and reproductive phenotype, affected the number and size of mitochondria, and resulted in an abnormality in mitochondrial morphology, possibly suggestive of a role for this organelle in INCL pathogenesis. This strain, deleted for ppt-1, potentially provides a model system for the study of PPT1 and the ------------------- Key: 7126 Medline: 15738262 Authors: Nabeshima K;Villeneuve AM;Colaicovo MP Title: Crossing over is coupled to late meiotic prophase bivalent differentiation through asymmetric disassembly of the SC. Citation: Journal of Cell Biology 168: 683-689 2005 Type: ARTICLE Genes: air-2 him-3 him-14 msh-4 msh-5 rad-51 rec-8 spo-11 syp-1 syp-2 Abstract: Homologous chromosome pairs (bivalents) undergo restructuring during meiotic prophase to convert a configuration that promotes crossover recombination into one that promotes bipolar spindle attachment and localized cohesion loss. We have imaged remodeling of meiotic chromosome structures after pachytene exit in Caenorhabditis elegans. Chromosome shortening during diplonema is accompanied by coiling of chromosome axes and highly asymmetric departure of synaptonemal complex (SC) central region proteins SYP-1 and SYP-2, which diminish over most. of the length of each desynapsing bivalent while becoming concentrated on axis segments distal to the single emerging chiasma. This and other manifestations of asymmetry along chromosomes are lost in synapsis-proficient crossover-defective mutants, which often retain SYP-1,2 along the full lengths of coiled diplotene axes. Moreover, a gamma-irradiation treatment that restores crossovers in the spo-11 mutant also restores asymmetry of SYP-1 localization. We propose that crossovers or crossover precursors serve as symmetry-breaking events that promote differentiation of subregions of the bivalent by triggering asymmetric disassembly of the SC. ------------------- Key: 7127 Medline: 15752362 Authors: Kuhnl J;Bobik T;Procter JB;Burmeister C;Hoppner J;Wilde I;Luersen K;Torde AE;Walter RD;Liebau E Title: Functional analysis of the methylmalonyl-CoA epimerase from Caenorhabditis elegans. Citation: FEBS Journal 272: 1465-1477 2005 Type: ARTICLE Genes: Abstract: Methylmalonyl-CoA epimerase (MCE) is an enzyme involved in the propionyl-CoA metabolism that is responsible for the degradation of branched amino acids and odd-chain fatty acids. This pathway typically functions in the reversible conversion of propionyl-CoA to succinyl-CoA. The Caenorhabditis elegans genome contains a single gene encoding MCE (mce-1) corresponding to a 15 kDa protein. This was expressed in Escherichia coli and the enzymatic activity was determined. Analysis of the protein expression pattern at both the tissue and subcellular level by microinjection of green fluorescent protein constructs revealed expression in the pharynx, hypodermis and, most prominently in body wall muscles. The subcellular pattern agrees with predictions of mitochondrial localization. The sequence similarity to an MCE of known structure was high enough to permit a three-dimensional model to be built, suggesting conservation of ligand and metal binding sites. Comparison with corresponding sequences from a variety of organisms shows more than 1/6 of the sequence is completely conserved. Mutants allelic to mce-1 showed no obvious phenotypic alterations, demonstrating that the enzyme is not essential for normal worm development under laboratory conditions. However, survival of the knockout mutants was altered when exposed to stress conditions, with mutants surprisingly showing an increased resistance to oxidative ------------------- Key: 7128 Medline: 15659483 Authors: Cassata G;Shemer G;Morandi P;Donhauser R;Podbilewicz B;Baumeister R Title: ceh-16/engrailed patterns the embryonic epidermis of Caenorhabditis elegans. Citation: Development 132: 739-749 2005 Type: ARTICLE Genes: ceh-16 ceh-20 eff-1 elt-1 elt-3 elt-5 lin-39 nhr-73 nhr-74 scm-1 wrt-2 wrt-5 Abstract: engrailed is a homeobox gene essential for developmental functions such as differentiation of cell populations and the onset of compartment boundaries in arthropods and vertebrates. We present the first functional study on engrailed in an unsegmented animal: the nematode Caenorhabditis elegans. In the developing worm embryo, ceh-16/engrailed is predominantly expressed in one bilateral row of epidermal cells (the seam cells). We show that ceh-16/engrailed primes a specification cascade through three mechanisms: (1) it suppresses fusion between seam cells and other epidermal cells by repressing eff-1/fusogen expression; (2) it triggers the differentiation of the seam cells through different factors, including the GATA factor elt-5; and (3) it segregates the seam cells into a distinct lateral cellular compartment, repressing cell migration toward dorsal and ------------------- Key: 7129 Medline: 15773900 Authors: Towers PR;Edwards B;Richmond JE;Sattelle DB Title: The Caenorhabditis elegans lev-8 gene encodes a novel type of nicotinic acetylcholine receptor alpha subunit. Citation: Journal of Neurochemistry 93: 1-9 2005 Type: ARTICLE Genes: lev-8 Abstract: We have cloned Caenorhabditis elegans lev-8 and demonstrated that it encodes a novel nicotinic acetylcholine receptor (nAChR) subunit (previously designated ACR-13), which has functional roles in body wall and uterine muscles as part of a levamisole-sensitive receptor. LEV-8 is an alpha subunit and is the first to be described from the ACR-8-like group, a new class of nAChR with atypical acetylcholine-binding site (loop C) and channel-lining motifs. A single base pair change in the first intron of lev-8 in lev-8(x15) mutants leads to alternative splicing and the introduction of a premature stop codon. lev-8(x15) worms are partially resistant to levamisole-induced egg laying and paralysis, phenotypes rescued by expression of the wild-type gene. lev-8(x15) worms also show reduced rates of pharyngeal pumping. Electrophysiological recordings from body wall muscle show that currents recorded in response to levamisole have reduced amplitude in lev-8(x15) compared with wild-type animals. Consistent with these phenotypic observations, green fluorescent protein fused to LEV-8 is expressed in body wall and uterine muscle, motor neurons and epithelial-derived socket cells. Thus, LEV-8 is a levamisole receptor subunit and exhibits the most diverse ------------------- Key: 7130 Medline: 15708304 Authors: Garcia-Lara J;Needham AJ;Foster SJ Title: Invertebrates as animal models for Staphylococcus aureus pathogenesis: a window into host-pathogen interaction. Citation: FEMS Immunology & Medical Microbiology 43: 311-323 2005 Type: REVIEW Genes: Abstract: Recently, the use of invertebrate models of infection has given exciting insights into host-pathogen interaction for a number of bacteria. In particular, this has revealed important factors of the host response with remarkable parallels in higher organisms. Here, we review the advances attained in the elucidation of virulence determinants of a major human pathogen, Staphylococcus aureus, in relation to the invertebrate models thus far applied, the silkworm (Bombyx mori), the fruit fly (Drosophila melanogaster) and the roundworm (Caenorhabditis elegans). Also, the major pathways of host defence are covered in light of the response to S. aureus and the similarities and divergences in innate immunity of vertebrates and invertebrates. Consequently, we comparatively consider pathogen recognition receptors, signal transduction pathways (including Toll, Imd and others), and the humoral and cellular antimicrobial effectors. The technically convenient and ethically acceptable invertebrates appear as a valuable first tool to discriminate molecules participating from both sides of the host-S. aureus interaction as well as a high throughput method for ------------------- Key: 7131 Medline: 15737923 Authors: Youle RJ Title: Morphology of mitochondria during apoptosis: worms-to-beetles in worms. Citation: Developmental Cell 8: 298-299 2005 Type: REVIEW Genes: ced-3 ced-4 ced-9 egl-1 Abstract: Although mitochondria are crucial for most pathways of mammalian cell apoptosis, evidence for their role in classic invertebrate models of programmed cell death has been frustratingly scant. New work showing that inhibition of mitochondrial fragmentation during C. elegans development inhibits programmed cell death bridges this gap and should advance a more detailed understanding of the role of mitochondria in caspase activation. ------------------- Key: 7132 Medline: 15737928 Authors: Grosshans H;Johnson T;Reinert KL;Gerstein M;Slack FJ Title: The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. Citation: Developmental Cell 8: 321-330 2005 Type: ARTICLE Genes: daf-12 die-1 hbl-1 let-7 let-60 lin-4 lin-14 lin-28 lin-41 lin-59 lss-4 lss-18 par-5 pha-4 smg-1 Abstract: The let-7 microRNA is phylogenetically conserved and temporally expressed in many animals. C. elegans let-7 controls terminal differentiation in a stem cell-like lineage in the hypodermis, while human let-7 has been implicated in lung cancer. To elucidate let-7s role in temporal control of nematode development, we used sequence analysis and reverse genetics to identify candidate let-7 target genes. We show that the nuclear hormone receptor daf-12 is a let-7 target in seam cells, while the forkhead transcription factor pha-4 is a target in the intestine. Additional likely targets are the zinc finger protein die-1 and the putative chromatin remodeling factor Iss-4. Together with the previous identification of the hunchback ortholog hbl-1 as a let-7 target in the ventral nerve cord, our findings show that let-7 acts in at least three tissues to regulate different transcription factors, raising the possibility of let-7 as a master temporal regulator. ------------------- Key: 7133 Medline: 15737937 Authors: Broitman-Maduro G;Maduro MF;Rothman JH Title: The noncanonical binding site of the MED-1 GATA factor defines differentially regulated target genes in the C. elegans mesendoderm. Citation: Developmental Cell 8: 427-433 2005 Type: ARTICLE Genes: ceh-20 end-1 end-3 hlh-25 hlh-27 hlh-28 hlh-29 med-1 med-2 pal-1 pop-1 skn-1 sox-1 str-243 tbx-33 tbx-35 wee-1.1 Abstract: Mesoderm and endoderm in C. elegans arise from sister cells called MS and E, respectively. The identities of both of these mesendodermal progenitors are controlled by MED-1 and -2, members of the GATA factor family. In the E lineage, these factors activate a sequential cascade of GATA factors, beginning with their immediate targets, the endoderm-specifying end genes. We report that MED-1 binds invariant noncanonical sites in the end genes, revealing that the MEDs are atypical members of the GATA factor family that do not recognize GATA sequences. By searching the genome for clusters of these MED sites, we have identified 19 candidate MED targets. Based on their expression patterns, these define three distinct classes of MED-regulated genes: MS-specific, E-specific, and E plus MS-specific. Some MED targets encode transcription factors related to those that regulate mesendoderm development in other phyla, supporting the existence of an ancient metazoan mesendoderm gene regulatory network. ------------------- Key: 7134 Medline: 15733661 Authors: Killian DJ;Hubbard EJA Title: Caenorhabditis elegans germline patterning requires coordinated development of the somatic gonadal sheath and the germ line. Citation: Developmental Biology 279: 322-335 2005 Type: ARTICLE Genes: gld-1 glp-1 hlh-12 mig-24 pro-1 puf-8 Abstract: Interactions between the somatic gonad and the genii line influence the amplification, maintenance, and differentiation of genii cells. In Caenorhabditis elegans, the distal tip cell/germline interaction promotes a mitotic fate and/or inhibits meiosis through GLP-1/Notch signaling. However, GLP-1-mediated signaling alone is not sufficient for a wild-type level of germline proliferation. Here, we provide evidence that specific cells of the somatic gonadal sheath lineage influence amplification, differentiation, and the potential for tumorigenesis of the germ line. First, an interaction between the distal-most pair of sheath cells and the proliferation zone of the germ line is required for larval germline amplification. Second, we show that insufficient larval germline amplification retards gonad elongation and thus delays meiotic entry. Third, a more severe delay in meiotic entry, as is exhibited in certain mutant backgrounds, inappropriately juxtaposes undifferentiated germ cells with cells of the proximal sheath lineage, leading to the formation of a proximal germline tumor derived front undifferentiated germ cells. Tumors derived from dedifferentiated germ cells, however, respond to the proximal interaction differently depending on the Mutant background. Our study underscores the importance of strict developmental coordination between neighboring tissues. We discuss these results in the context of mechanisms that may underlie tumorigenesis. ------------------- Key: 7135 Medline: 15733671 Authors: Fukushige T;Goszczynski B;Yan J;McGhee J Title: Transcriptional control and patterning of the pho-1 gene, an essential acid phosphatase expressed in the C. elegans intestine. Citation: Developmental Biology 279: 446-461 2005 Type: ARTICLE Genes: acn-1 elt-2 elt-7 ges-1 lit-1 pho-1 pop-1 Abstract: We have previously described an acid phosphatase enzyme, PHO-1, present at the lumenal surface of all but the anterior six cells of the Caenorhabditis elegans intestine. In the present paper, we identify the pho-1 structural gene, which encodes a histidine acid phosphatase showing highest similarity to human prostatic acid phosphatase. The pho-15'-flanking DNA is capable of directing reporter gene expression that is both gut specific, correctly timed and correctly "patterned', that is, not expressed in the gut anterior. Furthermore, this anterior-posterior patterning of pho-1 expression responds to the C. elegans Wnt pathway as if pho-1 is repressed (directly or indirectly) by high levels of the HMG effector protein POP-1. Transgenic analysis of the pho-1 promoter shows that gut expression is critically dependent oil a single WGATAR site. The gut-specific GATA factor ELT-2 binds to this site in vitro and removal of ELT-2 from the embryo destroys expression of the pho-1 reporter. Thus, all our results indicate that pho-1 is a direct downstream target of ELT-2. Finally, the pho-1 loss-of-function mutation shows an interesting and unexpected phenotype for a somatically-expressed hydrolytic enzyme: loss of pho-1 causes arrest of the majority of embryos but this lethality is a maternal effect. We suggest that pho-1 is required by the maternal intestine to assimilate some nutrient or cleavage product that is subsequently provided to the next generation of embryos. ------------------- Key: 7136 Medline: 15767665 Authors: Moore LL;Stanvitch G;Roth MB;Rosen D Title: HCP-4/CENP-C promotes the prophase timing of centromere resolution by enabling the centromere association of HCP-6 in Caenorhabditis elegans. Citation: Molecular and Cellular Biology 25: 2583-2592 2005 Type: ARTICLE Genes: air-2 coh-2 hcp-4 hcp-6 him-1 knl-1 mix-1 Abstract: Prior to microtubule capture, sister centromeres resolve from one another, coming to rest on opposite surfaces of the condensing chromosome. Subsequent assembly of sister kinetochores at each sister centromere generates a geometry favorable for equal levels of segregation of chromatids. The holocentric chromosomes of Caenorhabditis elegans are uniquely suited for the study of centromere resolution and subsequent kinetochore assembly. In C. elegans, only two proteins have been identified as being necessary for centromere resolution, the kinase AIR-2 (prophase only) and the centromere protein HCP-4/CENP-C. Here we found that the loss of proteins involved in chromosome cohesion bypassed the requirement for HCP-4/CENP-C but not for AIR-2. Interestingly, the loss of cohesin proteins also restored the localization of HCP-6 to the kinetochore. The loss of the condensin II protein HCP-6 or MIX-1/SMC2 impaired centromere resolution. Furthermore, the loss of HCP-6 or MIX-1/SMC2 resulted in no centromere resolution when either nocodazole or RNA interference (RNAi) of the kinetochore protein KNL-1 perturbed spindle-kinetochore interactions. This result suggests that normal prophase centromere resolution is mediated by condensin II proteins, which are actively recruited to sister centromeres to mediate the process of resolution. ------------------- Key: 7137 Medline: 15741313 Authors: Grishok A;Sinskey JL;Sharp PA Title: Transcriptional silencing by RNAi in the soma of a transgene C. elegans. Citation: Genes & Development 19: 683-696 2005 Type: ARTICLE Genes: alg-1 alg-2 asb-1 asg-1 cki-1 cye-1 dao-5 dcr-1 egl-27 elt-2 gfl-1 hda-2 hpl-1 hpl-2 mrg-1 mut-16 myo-2 myo-3 npp-4 pab-1 pes-10 pie-1 prg-1 prg-2 puf-6 puf-7 rad-51 rde-1 rde-4 rpl-36 rrf-1 rrf-3 rsd-3 rsd-6 set-1 set-2 smo-1 sop-2 tsn-1 uba-2 unc-54 unc-119 zfp-1 Abstract: The silencing of transgene expression at the level of transcription in the soma of Caenorhabditis elegans through an RNAi-dependent pathway has not been previously characterized. Most gene silencing due to RNAi in C. elegans occurs at the post-transcriptional level. We observed transcriptional silencing when worms containing the elt-2::gfp/LacZ transgene were fed RNA produced from the commonly used L4440 vector. The transgene and the vector share plasmid backbone sequences. This transgene silencing depends on multiple RNAi pathway genes, including dcr-1, rde-1, rde-4, and rrf-1. Unlike post-transcriptional gene silencing in worms, elt-2::gfp/LacZ silencing is dependent on the PAZ-PIWI protein Alg-1 and on the HP1 homolog Hpl-2. The latter is a chromatin silencing factor, and expression of the transgene is inhibited at the level of intron-containing precursor mRNA. This inhibition is accompanied by a decrease in the acetylation of histones associated with the transgene. This transcriptional silencing in the soma can be distinguished from transgene silencing in the germline by its inability to be transmitted across generations and its dependence on the rde-1 gene. We therefore define this type of silencing as RNAi-induced Transcriptional Gene Silencing (RNAi-TGS). Additional chromatin-modifying components affecting RNAi-TGS were identified in a candidate RNAi screen. ------------------- Key: 7138 Medline: 15799956 Authors: Walker MW;Jones KA;Tamm J;Zhong HL;Smith KE;Gerald C;Vaysse P;Branchek TA Title: Use of Caenorhabditis elegans G alpa(q) chimeras to detect G-protein-coupled receptor signals. Citation: Journal of Biomolecular Screening 10: 127-136 2005 Type: ARTICLE Genes: Abstract: G-protein-coupled receptors (GPCRs) activate heterotrimeric G-proteins (G(i)-, G(s)-, G(q)-, or G(12)-like) to generate specific intracellular responses, depending on the receptor/G-protein coupling. The aim was to enable a majority of GPCRs to generate a predetermined output by signaling through a single G-protein-supported pathway. The authors focused on calcium responses as the output, then engineered G alpha(q) to promote promiscuous receptor interactions. Starting with a human G alpha(q) containing 5 G alpha(z) residues in the C-tertninal receptor recognition domain (hG alpha(q/z5)) they evaluated agonist-stimulated calcium responses for 33 diverse GPCRs (G(i)-, G(s)-, and G(q)-coupled) and found 20 of 33 responders. In parallel, they tested Caenorhabditis elegans G alpha(q) containing 5 or 9 C-terminal G alpha(z) residues (cG alpha(q/z5), cG alpha(q/z9)). Signal detection was enhanced with cG alpha(q/z5) and cG alpha(q/z9) (yielding 25/33 and 26/33 responders, respectively). In a separate study of G alpha(s)-coupled receptors, the authors compared hG alpha(q/s5) versus hG alpha(q/s9), cG alpha(q/s9), and cG alpha(q/s21) and observed optimal function with cG alpha(q/s9). Cotransfection of an engineered G alpha(q) "cocktail" (cG alpha(q/z5) plus cG alpha(q/s9)) provided a powerful and efficient screening platform. When the chimeras included N-terminal myristoylation sites (to promote membrane localization), calcium responses were sustained or improved, depending on the receptor. This approach toward a "universal functional assay" is particularly useful for orphan GPCRs whose signaling ------------------- Key: 7139 Medline: 15734653 Authors: Behm CA;Bendig MM;McCarter JP;Sluder AE Title: RNAi-based discovery and validation of new drug targets in filarial nematodes. Citation: Trends in Parasitology 21: 97-100 2005 Type: ARTICLE Genes: Abstract: Human filarial nematodes cause river blindness and lymphatic filariasis, both of which are diseases that produce considerable morbidity. Control of these diseases relies on drug treatments that are ineffective against macrofilariae and are threatened by the development of resistance. New validated drug targets are required to allow development of new classes of antifilarial drugs. To identify and validate potential new drug targets, we propose a collaborative research strategy utilizing bioinformatic filters and assessment of gene function by RNA interference in Caenorhabditis elegans and Brugia ------------------- Key: 7140 Medline: 15734654 Authors: Foster JM;Zhang YH;Kumar S;Carlow CKS Title: Mining nematode genome data for novel drug targets. Citation: Trends in Parasitology 21: 101-104 2005 Type: ARTICLE Genes: Abstract: Expressed sequence tag projects have currently produced over 400 000 partial gene sequences from more than 30 nematode species and the full genomic sequences of selected nematodes are being determined. In addition, functional analyses in the model nematode Caenorhabditis elegans have addressed the role of almost all genes predicted by the genome sequence. This recent explosion in the amount of available nematode DNA sequences, coupled with new gene function data, provides an unprecedented opportunity to identify pre-validated drug targets through efficient mining of nematode genomic databases. This article describes the various information sources available and strategies that can expedite this process. ------------------- Key: 7141 Medline: 15791247 Authors: Sonnichsen B;Koski LB;Walsh A;Marschall P;Neumann B;Brehm M;Alleaume AM;Artelt J;Bettencourt J;Cassin E;Hewitson M;Holz C;Khan M;Lazik S;Martin C;Nitzsche B;Ruer M;Stamford J;Winzi M;Heinkel R;Roder M Title: Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Citation: Nature 434: 462-469 2005 Type: ARTICLE Genes: Abstract: A key challenge of functional genomics today is to generate well-annotated data sets that can be interpreted across different platforms and technologies. Large-scale functional genomics data often fail to connect to standard experimental approaches of gene characterization in individual laboratories. Furthermore, a lack of universal annotation standards for phenotypic data sets makes it difficult to compare different screening approaches. Here we address this problem in a screen designed to identify all genes required for the first two rounds of cell division in the Caenorhabditis elegans embryo. We used RNA-mediated interference to target 98% of all genes predicted in the C. elegans genome in combination with differential interference contrast time-lapse microscopy. Through systematic annotation of the resulting movies, we developed a phenotypic profiling system, which shows high correlation with cellular processes and biochemical pathways, thus enabling us to predict new functions for previously uncharacterized genes. ------------------- Key: 7142 Medline: Authors: Glotzer M Title: The molecular requirements for cytokinesis. Citation: Science 307: 1735-1739 2005 Type: REVIEW Genes: air-2 bir-1 csc-1 cyk-4 icp-1 klp-19 let-21 spd-1 zen-4 Abstract: After anaphase onset, animal cells build an actomyosin contractile ring that constricts the plasma membrane to generate two daughter cells connected by a cytoplasmic bridge. The bridge is ultimately severed to complete cytokinesis. Myriad techniques have been used to identify proteins that participate in cytokinesis in vertebrates, insects, and nematodes. A conserved core of about 20 proteins are individually involved with cytokinesis in most animal cells. These components are found in the contractile ring, on the central spindle, within the RhoA pathway, and on vesicles that expand the membrane and sever the bridge. Cytokinesis involves additional proteins, but they, or their requirement in cytokinesis, are not conserved among animal cells. ------------------- Key: 7143 Medline: Authors: Robins H;Li Y;Padgett RW Title: Incorporating structure to predict microRNA targets. Citation: Proceedings of the National Academy of Sciences USA 102: 4006-4009 2005 Type: ARTICLE Genes: daf-12 let-7 lin-4 lin-14 lin-28 lin-41 Abstract: MicroRNAs (miRNAs) are a recently discovered set of regulatory genes that constitute up to an estimated 1% of the total number of genes in animal genomes, including Caenorhabditis elegans, Drosophila, mouse, and humans [Lagos-Quintana, M., Rauhut, R., Lendeckel, W. M Tuschl, T. (2001) Science 294, 853-858; Lai, E. C., Tomancak, P., Williams, R. W. M Rubin, G.M. (2003) Genome Biol. 4, R42; Lau, N. C., Lim, L. P., Weinstein, E. G. M Bartel, D. P. (2001) Science 294, 858-862; Lee, R. C. M Ambros, V. (2001) Science 294, 862-8644; and Lee, R. C., Feinbaum, R. L. M Ambros, V. (1993) Cell 115, 787-798]. In animals, miRNAs regulate genes by attenuating protein translation through imperfect base pair binding to 3' UTR sequences of target genes. A major challenge in understanding the regulatory role of miRNAs is to accurately predict regulated targets. We have developed an algorithm for predicting targets that does not rely on evolutionary conservation. As one of the features of this algorithm, we incorporate the folded structure of mRNA. By using Drosophila miRNAs as a test case, we have validated our predictions in 10 of 15 genes tested. One of these validated genes is mad as a target for bantam. Furthermore, our computational and experimental data suggest that miRNAs have fewer targets than previously reported. ------------------- Key: 7144 Medline: 15753033 Authors: Peden EM;Barr MM Title: The KLP-6 kinesin is required for male mating behaviors and polycystin localization in Caenorhabditis elegans. Citation: Current Biology 15: 394-404 2005 Type: ARTICLE Genes: che-3 che-11 daf-10 kap-1 klp-6 klp-11 klp-20 lov-1 osm-3 osm-5 pkd-2 unc-104 Abstract: Background: Male mating behavior of the nematode Caenorhabditis elegans offers an intriguing model to study the genetics of sensory behavior, cilia function, and autosomal dominant polycystic kidney disease (ADPKD). The C. elegans polycystins LOV-1 and PKD-2 act in male-specific sensory cilia required for response and vulva-location mating behaviors. Results: Here, we identify and characterize a new mating mutant, sy511. sy511 behavioral phenotypes were mapped to a mutation in the klp-6 locus, a gene encoding a member of the kinesin-3 family (previously known as the UNC-104/Kif1A family). KLP-6 has a single homolog of unknown function in vertebrate genomes, including fish, chicken, mouse, rat, and human. We show that KLP-6 expresses exclusively in sensory neurons with exposed ciliated endings and colocalizes with the polycystins in cilia of male-specific neurons. Cilia of klp-6 mutants appear normal, suggesting a defect in sensory neuron function but not development. KLP-6 structure-function analysis reveals that the putative cargo binding domain directs the motor to cilia. Consistent with a motor-cargo association between KLP-6 and the polycystins, klp-6 is required for PKD-2 localization and function within cilia. Genetically, we find klp-6 regulates behavior through polycystin-dependent and -independent pathways. Conclusion: Multiple ciliary transport pathways dependent on kinesin-II, OSM-3, and KLP-6 may act sequentially to build cilia and localize sensory ciliary membrane proteins such as the polycystins. We propose that KLP-6 and the polycystins function as an evolutionarily conserved ciliary unit. KLP-6 promises new routes to understanding cilia function, behavior, and ADPKD. ------------------- Key: 7145 Medline: 15753035 Authors: del Campo JJ;Opoku-Serebuoh E;Isaacson AB;Scranton VL;Tucker M;Han M;Mohler WA Title: Fusogenic activity of EFF-1 is regulated via dynamic localization in fusing somatic cells of C. elegans. Citation: Current Biology 15: 413-423 2005 Type: ARTICLE Genes: eff-1 Abstract: Background: Many animal tissues form via fusion of cells. Yet in all instances of developmental cell fusion, the mechanism underlying fusion of plasma membranes remains poorly understood. EFF-1 is required for most somatic cell fusions in C. elegans, and misexpressed EFF-1 alters the normal pattern of fusing hypodermal cells. However, the autonomous activity of EFF-1, the rules governing its specificity, and the mechanism of its action have not been examined. Results: We show that EFF-1 acts as a cellular fusogen, capable of inducing fusion of virtually any somatic cells in C. elegans, yet targeted precisely to fusion-fated contacts during normal development. Misexpression of EFF-1 in early embryos causes fusion among groups of cells composed entirely of nonfusion-fated members. Measurements of cytoplasm diffusion in induced fusion events show that ectopic EFF-1 expression produces fusion pores similar to those in normal fusion events. GFP-labeled EFF-1 is specifically targeted to fusion-competent cell contacts via reciprocal localization to the touching membranes of EFF-1-expressing cells. EFF-1 function is also governed by intercellular barriers that prohibit cell fusion between distinct tissues. Analysis of mutant versions of EFF-1 indicates a novel mode of fusogenicity, employing neither a phospholipase active site nor hydrophobic fusion-peptide acting solely in pore formation. Conclusions: EFF-1 can confer potent fusogenic activity to nonfusing cell types. However, it is normally targeted only to fusion-fated cell borders via mutual interaction between EFF-1-expressing cells and relocalization to the plasma membrane. Because EFF-1 appears evolutionarily unique to nematodes, multiple mechanisms may have evolved for controlled plasma-membrane ------------------- Key: 7146 Medline: Authors: Jager T;Alda Alvarez O;Kammenga JE;Kooijman SALM Title: Modelling nematode life cycles using dymanic energy Citation: Functional Ecology 19: 136-144 2005 Type: ARTICLE Genes: Abstract: 1. To understand the life cycle of an organism, it is important to understand the underlying physiological mechanisms of their life histories. We here use the theory of dynamic energy budgets (DEB) to investigate the close relationships between growth, reproduction and respiration in nematodes. 2. Using a set of simplified equations based on DEB theory, we are able to accurately describe life-cycle data from the literature for the free-living bacterivorous nematodes Caenorhabditis elegans, C. briggsae and Acrobeloides nanus, under different temperature or food regimes. 3. Nematodes apparently differ from other animals, as the initial growth is slower than expected. We explain this phenomenon by food limitation in the larvae, which is supported by more detailed physiological studies. 4. Food density and temperature are shown to have predictable effects on the growth curves (temperature affects only growth rate, whereas food density also affects ultimate size), although the reproduction patterns reveal some deviations from model predictions. 5. The presented model integrates the different aspects of the life cycle into a single framework, and can be applied as such to interpret the effects of various stressors. ------------------- Key: 7147 Medline: 15771612 Authors: Houthoofd K;Fidalgo MA;Hoogewijs D;Braeckman BP;Lenaerts I;Brys K;Matthijssen F;De Vreese A;Van Eygen S;Munoz MJ;Vanfleteren JR Title: Metabolism, physiology and stress defense in three aging Ins/IGF-1 mutants of the nematode Caenorhabditis elegans. Citation: Aging Cell 4: 87-95 2005 Type: ARTICLE Genes: Abstract: The insulin/insulin-like growth factor-1 (Ins/IGF-1) pathway regulates the aging rate of the nematode Caenorhabditis elegans. We describe other features of the three Ins/IGF-1 mutants daf-2, age-1 and aap-1. We show that the investigated Ins/IGF-1 mutants all have a reduced body volume, reduced reproductive capacity, increased ATP concentrations and an elevated stress resistance. We also observed that heat production is lower in these mutants, although the respiration rate was similar or higher compared with wild-type individuals, suggesting a metabolic shift in these mutants. ------------------- Key: 7148 Medline: 15771615 Authors: Ventura N;Rea S;Henderson ST;Condo I;Johnson TE;Testi R Title: Reduced expression of frataxin extends the lifespan of Caenorhabditis elegans. Citation: Aging Cell 4: 109-112 2005 Type: ARTICLE Genes: Abstract: Defects in the expression of the mitochondrial protein frataxin cause Friedreich's ataxia, an hereditary neurodegenerative syndrome characterized by progressive ataxia and associated with reduced life expectancy in humans. Homozygous inactivation of the frataxin gene results in embryonic lethality in mice, suggesting that frataxin is required for organismic survival. Intriguingly, the inactivation of many mitochondrial genes in the nematode Caenorhabditis elegans by RNAi extends lifespan. We therefore investigated whether inactivation of frataxin by RNAi-mediated suppression of the frataxin homolog gene (frh-1) would also prolong lifespan in the nematode. Frataxin-deficient animals have a small body size, reduced fertility and altered responses to oxidative stress. Importantly, frataxin suppression by RNAi significantly extends lifespan in C. elegans. ------------------- Key: 7149 Medline: Authors: Simmer F;Plasterk RHA Title: RNAi in Caenorhabditis elegans. Citation: Gene Silencing by RNA Interference: Technolgy and Application. CRC Press, Boca Raton. : 167-182 2005 Type: REVIEW Genes: Abstract: ------------------- Key: 7150 Medline: Authors: Appleford PJ;Woollard A Title: Delivery of RNAi reagents in C. elegans by microinjection. Citation: Gene Silencing by RNA Interference: Technolgy and Application. CRC Press, Boca Raton. : 183-200 2005 Type: REVIEW Genes: Abstract: ------------------- Key: 7151 Medline: 15791235 Authors: O'Rourke SM;Bowerman B Title: Frontiers of gene function. Citation: Nature 434: 444-445 2005 Type: REVIEW Genes: Abstract: ------------------- Key: 7152 Medline: 15533247 Authors: Henricson A;Sonnhammer ELL;Baillie DL;Vaz Gomes A Title: Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs. Citation: BMC Genomics 5: 1-18 2004 Type: ARTICLE Genes: rrf-3 rsd-2 rsd-3 rsd-4 rsd-6 sft-4 sid-1 Abstract: ------------------- Key: 7153 Medline: 15642378 Authors: Kinchen JM;Hengartner MO Title: Tales of cannibalism, suicide, and murder: programmed cell death in C. elegans. Citation: Current Topics in Developmental Biology 65: 1-45 2005 Type: REVIEW Genes: Abstract: "Life is pleasant. Death is peaceful. It's the transition that's troublesome," said Isaac Asimov. Indeed, much scientific work over the last hundred years centered around attempts either to stave off or to induce the onset of death, at both the organismal and the cellular levels. In this quest, the nematode C. elegans has proven an invaluable tool, first, in the articulation of the genetic pathway by which programmed cell death proceeds, and also as a continuing source of inspiration. It is our purpose in this Chapter to familiarize the reader with the topic of programmed cell death in C. elegans and its relevance to current research in the fields of apoptosis and cell corpse clearance. ------------------- Key: 7154 Medline: 15576926 Authors: van den Heuvel S Title: The C. elegans cell cycle: overview of molecules and mechanisms. Citation: Methods in Molecular Biology 296: 51-67 2005 Type: REVIEW Genes: Abstract: The nematode C. elegans provides an animal model that allows for genetic dissection of cell cycle regulation in the context of development. Processes such as progression through meiotic prophase, spindle function, chromosome segregation, and cytokinesis are attractive topics to study in the worm, because of their relative visibility and susceptibility to RNA interference. In addition, the reproducible cell lineage greatly helps the identification and characterization of mutants that affect cell cycle entry or exit during larval development. This chapter looks at cell division as an integral part of C. elegans development, describes how it can be studied in the worm and summarizes some of the conserved cell cycle components described to date. ------------------- Key: 7155 Medline: 15769874 Authors: Bernstein D;Hook B;Hajarnavis A;Opperman L;Wickens M Title: Binding specificity and mRNA targets of a C. elegans PUF protein, FBF-1. Citation: RNA 11: 447-458 2005 Type: ARTICLE Genes: fbf-1 fbf-2 fem-3 gld-1 Abstract: Sequence-specific RNA-protein interactions underlie regulation of many mRNAs. Here we analyze the RNA sequence specificity of Caenorhabditis elegans FBF-1, a founding member of the PUF protein family. Like other PUF proteins, FRF-1 binds to the 3' UTR of target mRNAs and decreases expression of those target genes. Here, we show that FBF-1 and its close relative, FBF-2, bind with similar affinity to multiple RNA sites. We use mutagenesis and in vivo selection experiments to identify nucleotides that are essential for FBF-1 binding. The binding elements comprise a "core" central region and flanking sequences. The core region is similar but distinct from the binding sites of other PUF proteins. We combine the identification of binding elements with informatics to predict new FBF-1 binding sites in a C. elegans 3' UTR database. These data identify a set of new candidate mRNA targets of FBF-1 and ------------------- Key: 7156 Medline: 15767563 Authors: Rao AU;Carta LK:Lesuisse E;Hamza I Title: Lack of heme synthesis in a free-living eukaryote. Citation: Proceedings of the National Academy of Sciences USA 102: 4270-4275 2005 Type: ARTICLE Genes: Abstract: In most free-living eukaryotes studied thus far, heme is synthesized from a series of intermediates through a well defined evolutionarily conserved pathway. We found that free-living worms, including the model genetic organism Caenorhabditis elegans, and parasitic helminths are unable to synthesize heme de novo, even though these animals contain hemoproteins that function in key biological processes. Radioisotope, fluorescence labeling, and heme analog studies suggest that C elegans acquires heme from exogenous sources. Iron-deprived worms were unable to grow in the presence of adequate heme unless rescued by increasing heme levels in the growth medium. These data indicate that although worms use dietary heme for incorporation into hemoproteins, ingested heme is also used as an iron source when iron is limiting. Our results provide a biochemical basis for the dependence of worm growth and development on heme, and they suggest that pharmacologic targeting of heme transport pathways in worms could be an important control measure for helminthic ------------------- Key: 7157 Medline: 15761060 Authors: Thomas JH;Kelley JL;Robertson HM;Ly K;Swanson WJ Title: Adaptive evolution in the SRZ chemoreceptor families of Caenorhabditis elegans and Caenorhabditis briggsae. Citation: Proceedings of the National Academy of Sciences USA 102: 4476-4481 2005 Type: ARTICLE Genes: Abstract: We investigated the possibility of positive selection acting on members of the putative seven-pass chemoreceptor superfamily in Caenorhabditis elegans, which comprises approximate to 1,300 genes encoding seven-pass G protein-coupled receptors (GPCRs). Using a maximum-likelihood approach, we conducted statistical tests for evidence of codon sites where the ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site (d(N)/d(s)) was >1. Evidence for positive selection was found only for the srz family, about which virtually nothing specific is known. We extended the annotation of the srz gene family, establishing gene models for 60 srz genes in C elegans and 28 srz genes in Caenorhabditis briggsae. d(N)/d(s) ratios varied dramatically in different regions of the SRZ proteins, peaking in predicted extracellular regions. These regions included 23 sites where evidence of positive selection was highly significant, corresponding remarkably well with regions implicated in ligand binding in other GPCR family members. We interpret these results as indicating that the srz family is under positive selection, probably driven by ligand binding. ------------------- Key: 7158 Medline: 15767565 Authors: Oh SW;Mukhopadhyay A;Svrzikapa N;Jiang F;Davis RJ;Tissenbaum HA Title: JNK regulates lifespan in Caenorhabditis elegans by modulating nuclear translocation of forkhead transcription factor/DAF-16. Citation: Proceedings of the National Academy of Sciences USA 102: 4494-4499 2005 Type: ARTICLE Genes: aap-1 age-1 akt-1 akt-2 daf-16 ist-1 jkk-1 jnk-1 mek-1 unc-16 Abstract: DAF-16/forkhead transcription factor, the downstream target of the insulin-like signaling in Caenorhabditis elegans, is indispensable for both lifespan regulation and stress resistance. Here, we demonstrate that c-Jun N-terminal kinase (JNK) is a positive regulator of DAF-16 in both processes. Our genetic analysis suggests that the JNK pathway acts in parallel with the insulin-like signaling pathway to regulate lifespan and both pathways converge onto DAF-16. We also show that JNK-1 directly interacts with and phosphorylates DAF-16. Moreover, in response to heat stress, JNK-1 promotes the translocation of DAF-16 into the nucleus. Our findings define an interaction between two well conserved proteins, JNK-1 and DAF-16, and provide a mechanism by which JNK regulates longevity and stress resistance. ------------------- Key: 7159 Medline: 15716098 Authors: Petalcorin MIR;Joshua GW;Agapow PM;Dolphin CT Title: The fmo genes of Caenorhabditis elegans and C. briggsae: characterisation, gene expression and comparative genomic analysis. Citation: Gene 346: 83-96 2005 Type: ARTICLE Genes: fmo-1 fmo-2 fmo-3 fmo-4 fmo-5 Abstract: The flavin-containing monooxygenase (FMO) gene family is conserved and ancient with representatives present in almost all phyla so far examined. The genes encode FAD-, NADP- and O-2-dependent enzymes that catalyse oxygenation of soft-nucleophilic heteroatom centres in a range of substrates. Although usually classified as xenobiotic-metabolising enzymes, examples of FMOs exist that have evolved to metabolise specific endogenous substrates as part of a discrete physiological process. The genome of Caenorhabditis elegans contains five predicted genes encoding putative homologs of mammalian FMOs, K08C7.2, K08C7.5, Y39A1A.19, F53F4.5 and H24K24.5, which we have named fmo and numbered fmo-1 to fmo-5, respectively. As a first step towards determining their functional role(s), we have experimentally characterised these C. elegans fmo genes including analysing reporter gene expression patterns and RNAi phenotypes. Two major gene expression patterns were observed, either intestinal or hypodermal, but no gross RNAi phenotypes were found possibly due to functional redundancy. The internal structures of fmo-2, fmo-3 and fmo-4 have been compared with orthologs identified in the related nematode C. briggsae. For each orthologous pair, a global comparison of the paired upstream intergenic regions was performed and a number of conserved noncoding sequences, which may represent potential cis-regulatory elements, identified. Phylogenetic analysis reveals that several of the fmo homologs are the result of gene duplication along the ------------------- Key: 7160 Medline: 15766527 Authors: Johnson SM;Grosshans H;Shingara J;Byrom M;Jarvis R;Cheng A;Labourier E;Reinert KL;Brown D;Slack FJ Title: RAS is regulated by the let-7 microRNA family. Citation: Cell 120: 635-647 2005 Type: ARTICLE Genes: daf-12 let-7 let-60 lin-31 mir-48 mir-84 mir-241 unc-54 Abstract: MicroRNAs (miRNAs) are regulatory RNAs found in multicellular eukaryotes, including humans, where they are implicated in cancer. The let-7 miRNA times seam cell terminal differentiation in C. elegans. Here we show that the let-7 family negatively regulates let-60/RAS. Loss of let-60/RAS suppresses let-7, and the let-60/RAS 3'UTR contains multiple let-7 complementary sites (LCSs), restricting reporter gene expression in a let-7-dependent manner. mir-84, a let-7 family member, is largely absent in vulval precursor cell P6.p at the time that let-60/RAS specifies the 1 degrees vulval fate in that cell, and mir-84 overexpression suppresses the multivulva phenotype of activating let-60/ RAS mutations. The 3'UTRs of the human RAS genes contain multiple LCSs, allowing let-7 to regulate RAS expression. let-7 expression is lower in lung tumors than in normal lung tissue, while RAS protein is significantly higher in lung tumors, providing a possible mechanism for let-7 in cancer. ------------------- Key: 7161 Medline: 15737730 Authors: Sifri CD;Begun J;Ausubel FM Title: The worm has turned - microbial virulence modeled in Caenorhabditis elegans. Citation: Trends in Microbiology 13: 119-127 2005 Type: REVIEW Genes: Abstract: The nematode Caenorhabditis elegans is emerging as a facile and economical model host for the study of evolutionarily conserved mechanisms of microbial pathogenesis and innate immunity. A rapidly growing number of human and animal microbial pathogens have been shown to injure and kill nematodes. In many cases, microbial genes known to be important for full virulence in mammalian models have been shown to be similarly required for maximum pathogenicity in nematodes. C. elegans has been used in mutation-based screening systems to identify novel virulence-related microbial genes and immune-related host genes, many of which have been validated in mammalian models of disease. C. elegans-based pathogenesis systems hold the potential to simultaneously explore the molecular genetic determinants of both pathogen virulence and host defense. ------------------- Key: 7162 Medline: Authors: Myagmar BE;Umikawa M;Asato T;Taira K;Oshiro M;Hino A;Takei K;Uezato H;Kariya K Title: PARG1, a protein-tyrosine phosphatase-associated RhoGAP, as a putative Rap2 effector. Citation: Biochemical and Biophysical Research Communications 329: 1046-1052 2005 Type: ARTICLE Genes: Abstract: Rap2 belongs to the Ras family of small GTP-binding proteins, but its specific signaling role is unclear. By yeast two-hybrid screening, we have found that the Caenorhabditis elegans ortholog of Rap2 interacts with a protein containing a Rho-GTPase-activating protein (RhoGAP) domain, ZK669.1a, whose human ortholog PARG1 exhibits RhoGAP activity in vitro. ZK669.1a and PARG1 share a homology region with previously unknown function, designated the ZK669.1a and PARG1 homology (ZPH) region. Here we show that the ZPH region of PARG1 mediates interaction with Rap2. PARG1 interacted with Rap2 in a GTP-dependent manner but not with Ras or Rap1. We also show that PARG1 and its mutant lacking the ZPH region induce typical cytoskeletal changes for Rho inactivation in fibroblasts. Rap2 suppressed this in vivo action of PARG1 but not that of the mutant PARG1. These results suggest that PARG1 is a putative specific effector of Rap2 to ------------------- Key: 7163 Medline: 15803195 Authors: Jones AK;Buckingham SD;Sattelle DB Title: Chemistry-to-gene screens in Caenorhabditis elegans. Citation: Nature Reviews Drug Discovery 4: 321-330 2005 Type: REVIEW Genes: acr-13 aex-3 cha-1 egl-10 lev-1 lev-8 lev-9 lev-10 lev-11 ric-1 ric-3 ric-4 ric-8 snt-1 unc-2 unc-10 unc-11 unc-13 unc-17 unc-18 unc-22 unc-26 unc-29 unc-31 unc-32 unc-36 unc-38 unc-41 unc-50 unc-63 unc-64 unc-65 unc-68 unc-74 unc-75 unc-14 Abstract: The nematode worm Caenorhabditis elegans is a genetic model organism linked to an impressive portfolio of fundamental discoveries in biology.This free-living nematode, which can be easily and inexpensively grown in the laboratory, is also a natural vehicle for screening for drugs that are active against nematode parasites. Here, we show that chemistry-to-gene screens using this animal model can define targets of antiparasitic drugs, identify novel candidate drug targets and contribute to the discovery of new drugs for treating human diseases. ------------------- Key: 7164 Medline: 15793589 Authors: Parker JA;Arango M;Abderrahmane S;Lambert E;Tourette C;Catoire H;Neri C Title: Resveratrol rescues mutant polyglutamine cytotoxicity in nematode and mammalian neurons. Citation: Nature Genetics 37: 349-350 2005 Type: ARTICLE Genes: age-1 daf-16 sir-2.1 Abstract: We report that Sir2 activation through increased sir-2.1 dosage or treatment with the sirtuin activator resveratrol specifically rescued early neuronal dysfunction phenotypes induced by mutant polyglutamines in transgenic Caenorhabditis elegans. These effects are dependent on daf-16 (Forkhead). Additionally, resveratrol rescued mutant polyglutamine - specific cell death in neuronal cells derived from HdhQ111 knock-in mice. We conclude that Sir2 activation may protect against mutant polyglutamines. ------------------- Key: 7165 Medline: Authors: Miller AC;Thiele TR;Faumont S;Moravec ML;Lockery SR Title: Step-response analysis of chemotaxis in Caenorhabditis elegans. Citation: Journal of Neuroscience 25: 3369-3378 2005 Type: ARTICLE Genes: che-1 Abstract: The sensorimotor transformation underlying Caenorhabditis elegans chemotaxis has been difficult to measure directly under normal assay conditions. Thus, key features of this transformation remain obscure, such as its time course and dependence on stimulus amplitude. Here, we present a comprehensive characterization of the transformation as obtained by inducing stepwise temporal changes in attractant concentration within the substrate as the worm crawls across it. We found that the step response is complex, with multiple phases and a nonlinear dependence on the sign and amplitude of the stimulus. Nevertheless, the step response could be reduced to a simple kinetic model that predicted the results of chemotaxis assays. Analysis of the model showed that chemotaxis results from the combined effects of approach and avoidance responses to concentration increases and decreases, respectively. Surprisingly, ablation of the ASE chemosensory neurons, known to be necessary for chemotaxis in chemical gradient assays, eliminated avoidance responses but left approach responses intact. These results indicate that the transformation can be dissected into components to which ------------------- Key: 7167 Medline: 15773757 Authors: Margalit A;Liu J;Fridkin A;Wilson KL;Gruenbaum Y Title: A lamin-dependent pathway that regulates nuclear organization, cell cycle progression and germ cell development. Citation: Novartis Foundation Symposium 264: 231-240 2005 Type: ARTICLE Genes: baf-1 emr-1 lem-1 lmn-1 unc-83 unc-84 Abstract: The C. elegans genome encodes a single lamin protein (Ce-lamin), three LEM domain proteins (Ce-emerin, Ce-MAN1 and LEM-3) and a single BAF protein (Ce-BAF). Down-regulation of Ce-lamin causes embryonic lethality. Abnormalities include rapid changes in nuclear morphology during interphase, inability of cells to complete mitosis, abnormal condensation of chromatin, clustering of nuclear pore complexes (NPCs), and missing or abnormal germ cells. Ce-emerin and Ce-MAN1 are both embedded in the inner nuclear membrane, and both bind Ce-lamin and Ce-BAF; in addition, both require Ce-lamin for their localization. Mutations in human emerin cause X-linked recessive Emery-Dreifuss muscular dystrophy. In C. elegans, loss of Ce-emerin alone has no detectable phenotype, while loss of 90% Ce-MAN1 causes approximately 15% embryonic lethality. However in worms that lack Ce-emerin, a approximately 90% reduction of Ce-MAN1 is lethal to all embryos by the 100-cell stage, with a phenotype involving chromatin condensation and repeated cycles of anaphase chromosome bridging and cytokinesis. The anaphase-bridged chromatin retained a mitosis-specific phosphohistone H3 epitope, and failed to recruit detectable Ce-lamin or Ce-BAF. Down-regulation of Ce-BAF showed similar phenotypes. These findings suggest that lamin, LEM-domain proteins and BAF are part of a lamina network essential for chromatin organization and cell division, and that Ce-emerin and Ce-MAN1 share at least one and possibly multiple overlapping functions, which may be relevant to ------------------- Key: 7168 Medline: 15644189 Authors: May RC;Plasterk RH Title: RNA interference spreading in C. elegans. Citation: Methods in Enzymology 392: 308-315 2005 Type: REVIEW Genes: fed-1 fed-2 rde-4 rsd-2 rsd-3 rsd-4 rsd-6 sid-1 Abstract: The phenomenon of RNA interference (RNAi) occurs in eukaryotic organisms from across the boundaries of taxonomic kingdoms. In all cases, the basic mechanism of RNAi appears to be conserved--an initial trigger [double-stranded RNA (dsRNA) containing perfect homology over at least 19-21/bp with an endogenous gene] is processed into short interfering RNA (siRNA) molecules and these siRNAs stimulate degradation of the homologous mRNA. In the vast majority of species, RNAi can only be initiated following the deliberate introduction of dsRNA into a cell by microinjection, electroporation, or transfection. However, in the nematode worm Caenorhabditis elegans, RNAi can be simply initiated by supplying dsRNA in the surrounding medium or in the diet. Following uptake, this dsRNA triggers a systemic effect, initiating RNAi against the corresponding target gene in tissues that are not in direct contact with the external milieu. This phenomenon of systemic RNAi, or RNAi spreading, is notably absent from mammalian species, a fact that is likely to prove a substantial barrier to the wider use of RNAi as a clinical therapy. An understanding of the mechanism of systemic RNAi is therefore of considerable importance, and several advances of the last few years have begun to shed light on this process. Here we review our current understanding of systemic RNAi in C. elegans and draw comparisons with systemic RNAi pathways in other organisms. ------------------- Key: 7169 Medline: 15644174 Authors: Wang J;Barr M Title: RNA interferece in Caenorhabditis elegans. Citation: Methods in Enzymology 392: 36-55 2005 Type: REVIEW Genes: ego-1 eri-1 rde-1 rde-4 rrf-1 rrf-3 Abstract: RNA interference (RNAi) was first discovered in the nematode Caenorhabditis elegans (Fire et al., 1998; Guo and Kemphues, 1995). The completion of the C. elegans genome in 1998 coupled with the advent of RNAi techniques to knock down gene function ushered in a new age in the field of functional genomics. There are four methods for double-stranded RNA (dsRNA) delivery in C. elegans: (1) injection of dsRNA into any region of the animal (Fire et al., 1998), (2) feeding with bacteria producing dsRNA (Timmons et al., 2001), (3) soaking in dsRNA (Tabara et al., 1998), and (4) in vivo production of dsRNA from transgenic promoters (Tavernarakis et al., 2000). In this chapter, we discuss the molecular genetic mechanisms, techniques, and applications of RNAi in C. elegans. ------------------- Key: 7170 Medline: 15817158 Authors: Jauregui AR;Barr MM Title: Functional characterization of the C. elegans nephrocystins NPHP-1 and NPHP-4 and their role in cilia and male sensory behaviors. Citation: Experimental Cell Research 305: 333-342 2005 Type: ARTICLE Genes: lov-1 nphp-1 nphp-2 pkd-2 Abstract: Autosomal dominant polycystic kidney disease (ADPKD) and nephronophthisis (NPH) share two common features: cystic kidneys and ciliary localized gene products. Mutation in either the PKD1 or PKD2 gene accounts for 95% of all ADPKD cases. Mutation in one of four genes (NPHP1-4) results in nephronophthisis. The NPHP1, NPHP2, PKD1, and PKD2 protein products (nephrocystin-1, nephrocystin-2 or inversin, polycystin-1, and polycystin-2, respectively) localize to primary cilia of renal epithelia. However, the relationship between the nephrocystins and polycystins, if any, is unknown. In the nematode Caenorhabditis elegans, the LOV-1 and PKD-2 polycystins localize to male-specific sensory cilia and are required for male mating behaviors. To test the hypothesis that ADPKD and NPH cysts arise from a common defect in cilia, we characterized the C. elegans homologs of NPHP1 and NPHP4. C. elegans nphp-1 and nphp-4 are expressed in a subset of sensory neurons. GFP-tagged NPHP-1 and NPHP-4 proteins localize to ciliated sensory endings of dendrites and colocalize with PKD-2 in male-specific sensory cilia. The cilia of nphp-1(ok500) and nphp-4(tm925) mutants are intact. nphp-1; nphp-4 double, but not single, mutant males are response defective. We propose that NPHP-1 and NPHP-4 proteins play important and redundant roles in facilitating ciliary sensory signal transduction. ------------------- Key: 7171 Medline: 15749820 Authors: Inoue T;Wang M;Ririe TO;Fernandes JS;Sternberg PW Title: Transcriptional network underlying Caenorhabditis elegans vulval development. Citation: Proceedings of the National Academy of Sciences USA 102: 4972-4977 2005 Type: ARTICLE Genes: cdh-3 ceh-2 cog-1 egl-17 egl-38 lin-3 lin-11 lin-17 lin-18 lin-29 sqv-4 zmp-1 Abstract: The vulval development of Caenorhabditis elegans provides an opportunity to investigate genetic networks that control gene expression during organogenesis. During the fourth larval stage (L4), seven vulval cell types are produced, each of which executes a distinct gene expression program. We analyze how the expression of cell-type-specific genes is regulated. Ras and Writ signaling pathways play major roles in generating the spatial pattern of cell types and regulate gene expression through a network of transcription factors. One transcription factor (lin-29) primarily controls the temporal expression pattern. Other transcription factors (lin-11, cog-1, and egl-38) act in combination to control cell-type-specific gene expression. The complexity of the network arises in part because of the dynamic nature of gene expression, in part because of the presence of seven cell types, and also because there are multiple regulatory paths for gene expression within each ------------------- Key: 7172 Medline: 15820693 Authors: Dreier L;Burbea M;Kaplan JM Title: LIN-23-mediated degradation of beta-catenin regulates the abundance of GLR-1 glutamate receptors in the ventral nerve cord of C. elegans. Citation: Neuron 46: 51-64 2005 Type: ARTICLE Genes: bar-1 glr-1 gsk-3 lin-10 lin-23 pop-1 unc-11 Abstract: Ubiquitin-mediated protein degradation has been proposed to play an important role in regulating synaptic transmission. Here we show that LIN-23, the substrate binding subunit of a Skp1/Cullin/F Box (SCF) ubiquitin ligase, regulates the abundance of the glutamate receptor GLR-1 in the ventral nerve cord of C. elegans. Mutants lacking lin-23 had an increased abundance of GLR-1 in the ventral cord. The increase of GLR-1 was not caused by changes in the ubiquitination of GLR-1. Instead, SCFLIN-23 regulates GLR-1 through the P-catenin homolog BAR-1 and the TCF/Lef transcription factor homolog POP-1. We hypothesize that LIN-23-mediated degradation of BAR-1 P-catenin regulates the transcription of Wnt target genes, which in turn alter postsynaptic properties. ------------------- Key: 7173 Medline: 15702348 Authors: Brownlie JC;Johnson NM:Whyard S Title: The Caenorhabditis elegans genome contains active CbmaT1 and Tcb1 transposons. Citation: Molecular Genetics & Genomics 273: 92-101 2005 Type: ARTICLE Genes: unc-22 Abstract: The maT clade of transposons is a group of transposable elements intermediate in sequence and predicted protein structure to mariner and Tc transposons, with a distribution thus far limited to a few invertebrate species. We present evidence, based on searches of publicly available databases, that the nematode Caenorhabditis briggsae has several maT-like transposons, which we have designated as CbmaT elements, dispersed throughout its genome. We also describe two additional transposon sequences that probably share their evolutionary history with the CbmaT transposons. One resembles a fold back variant of a CbmaT element, with long (380-bp) inverted terminal repeats (ITRs) that show a high degree (71%) of identity to CbmaT1. The other, which shares only the 26-bp ITR sequences with one of the CbmaT variants, is present in eight nearly identical copies, but does not have a transposase gene and may therefore be cross mobilised by a CbmaT transposase. Using PCR-based mobility assays, we show that CbmaT1 transposons are capable of excising from the C. briggsae genome. CbmaT1 excised approximately 500 times less frequently than Tcb1 in the reference strain AF16, but both CbmaT1 and Tcb1 excised at extremely high frequencies in the HK105 strain. The HK105 strain also exhibited a high frequency of spontaneous induction of unc-22 mutants, suggesting that it may be a mutator strain of C. briggsae. ------------------- Key: 7174 Medline: 15659649 Authors: Jenna S;Caruso ME;Emadali A;Nguyen DT;Dominguez M;Li S;Roy R;Reboul J;Vidal M;Tzimas GN;Bosse R;Chevet E Title: Regulation of membrane trafficking by a novel Cdc42-related protein in Caenorhabditis elegans epithelial cells. Citation: Molecular Biology of the Cell 16: 1629-1639 2005 Type: ARTICLE Genes: cdc-42 ced-10 che-14 crp-1 mig-2 rab-1 rab-3 rab-6.1 rab-6.2 rab-8 rab-37 rac-2 rap-2 rho-1 unc-108 Abstract: Rho GTPases are mainly known for their implication in cytoskeleton remodeling. They have also been recently shown to regulate various aspects of membrane trafficking. Here, we report the identification and the characterization of a novel Caenorhabditis elegans Cdc42-related protein, CRP-1, that shows atypical enzymatic characteristics in vitro. Expression in mouse fibroblasts revealed that, in contrast with CDC-42, CRP-1 was unable to reorganize the actin cytoskeleton and mainly localized to trans-Golgi network and recycling endosomes. This subcellular localization, as well as its expression profile restricted to a subset of epithelial-like cells in C. elegans, suggested a potential function for this protein in polarized membrane trafficking. Consistent with this hypothesis, alteration of CRP-1 expression affected the apical trafficking of CHE-14 in vulval and rectal epithelial cells and sphingolipids (C-6-NBD-ceramide) uptake and/or trafficking in intestinal cells. However, it did not affect basolateral trafficking of myotactin in the pharynx and the targeting of IFB-2 and AJM-1, two cytosolic apical markers of intestine epithelial cells. Hence, our data demonstrate a function for CRP-1 in the regulation of membrane trafficking in a subset of cells with epithelial characteristics. ------------------- Key: 7175 Medline: 15798199 Authors: Martin JS;Winkelmann N;Petalcorin MIR;McIlwraith MJ;Boulton SJ Title: RAD-51-dependent and -independent roles of a Caenorhabditis elegans BRCA2-related protein during DNA double-strand break repair. Citation: Molecular and Cellular Biology 25: 3137-3139 2005 Type: ARTICLE Genes: brc-2 lig-4 rad-5 rad-51 spo-11 Abstract: The BRCA2 tumor suppressor is implicated in DNA double-strand break (DSB) repair by homologous recombination (HR), where it regulates the RAD51 recombinase. We describe a BRCA2-related protein of Caenorhabditis elegans (CeBRC-2) that interacts directly with RAD-51 via a single BRC motif and that binds preferentially to single-stranded DNA through an oligonucleotide-oligosaccharide binding fold. Cebrc-2 mutants fail to repair meiotic or radiation-induced DSBs by HR due to inefficient RAD-51 nuclear localization and a failure to target RAD-51 to sites of DSBs. Genetic and cytological comparisons of Cebrc-2 and rad-51 mutants revealed fundamental phenotypic differences that suggest a role for Cebrc-2 in promoting the use of an alternative repair pathway in the absence of rad-51 and independent of nonhomologous end joining (NHEJ). Unlike rad-51 mutants, Cebrc-2 mutants also accumulate RPA-1 at DSBs, and abnormal chromosome aggregates that arise during the meiotic prophase can be rescued by blocking the NHEJ pathway. CeBRC-2 also forms foci in response to DNA damage and can do so independently of rad-51. Thus, CeBRC-2 not only regulates RAD-51 during HR but can also function ------------------- Key: 7176 Medline: 15804834 Authors: Hoogewijs D;Geuens E;Dewilde S;Moens L;Vierstraete A;Vinogradov S;Vanfleteren JR Title: Genome-wide analysis of the globin gene family of C. elegans. Citation: IUBMB Life 56: 697-702 2004 Type: ARTICLE Genes: Abstract: The aim of our study was to annotate sequences for 35 putative globins from the nematode Caenorhabditis elegans. All these proteins are expressed, but seven of these differ from the gene predictions in Wormbase. The entire polypeptide sequences for 31 genes and the core globin domain of four proteins were confirmed or corrected. All core globin domains were aligned manually following a procedure that was designed to fit the putative sequences to the crystal structure based alignment of 56 known globin crystal structures. Neighbor-joining analysis of the resulting alignment showed that the majority of these globins are very divergent from each other, possibly suggesting a long evolutionary divergence. The surprisingly high number and low sequence conservation of putative globins in this small organism urges a detailed functional analysis. ------------------- Key: 7177 Medline: 15805498 Authors: Wei C;Lamesch P;Arumugam M;Rosenberg J;Hu P;Vidal M;Brent Title: Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions. Citation: Genome Research 15: 577-582 2005 Type: ARTICLE Genes: Abstract: The genome of Caenorhabditis elegans was the first animal genome to be sequenced. Although considerable effort has been devoted to annotating it, the standard WormBase annotation contains thousands of predicted genes for which there is no cDNA or EST evidence. We hypothesized that a more complete experimental annotation could be obtained by creating a more accurate gene-prediction program and then amplifying and sequencing predicted genes. Our approach was to adapt the TWINSCAN gene prediction system to C elegans and C briggsae and to improve its splice site and intron-length models. The resulting system has 60% sensitivity and 58% specificity in exact prediction of open reading frames (ORFs), and hence, proteins-the best results we are aware of any multicellular organism. We then attempted to amplify, clone, and sequence 265 TWINSCAN-predicted ORFs that did not overlap WormBase gene annotations. The success rate was 55%, adding 146 genes that were completely absent from WormBase to the ORF clone collection (ORFeome). The same procedure had a 7% success rate on 90 Worm Base "predicted" genes that do not overlap TWINSCAN predictions. These results indicate that the accuracy of WormBase could be significantly increased by replacing its partially curated predicted genes with TWINSCAN predictions. The technology described in this study will continue to drive the C elegans ORFeome toward completion and contribute to the annotation of the three Caenorhabditis species currently being sequenced. The results also suggest that this technology can significantly improve our knowledge of the "parts list" for even the best-studied model organisms. ------------------- Key: 7178 Medline: 15774721 Authors: Robert VJP;Sijen T;van Wolfswinkel J;Plasterk RHA Title: Chromatin and RNAi factors protect the C. elegans germline against repetitive sequences. Citation: Genes & Development 19: 782-787 2005 Type: ARTICLE Genes: egl-13 gfi-4 hmg-5 hpl-2 ima-1 ima-3 kbp-1 kbp-3 lsm-7 mes-4 mrg-1 mut-16 pgl-1 ppw-2 pqn-2 rde-3 rha-1 sas-4 smu-2 srh-75 vha-7 Abstract: Protection of genomes against invasion by repetitive sequences, such as transposons, viruses, and repetitive transgenes, involves strong and selective silencing of these sequences. During silencing of repetitive transgenes, a trans effect ("cosuppression") occurs that results in silencing of cognate endogenous genes. Here we report RNA interference (RNAi) screens performed to catalog genes required for cosuppression in the Caenorhabditis elegans germline. We find factors with a putative role in chromatin remodeling and factors involved in RNAi. Together with molecular data also presented in this study, these results suggest that in C. elegans repetitive sequences trigger transcriptional gene silencing using RNAi and chromatin factors. ------------------- Key: 7179 Medline: 15689373 Authors: Leight ER;Glossip D;Kornfeld K Title: Sumoylation of LIN-1 promotes transcriptional repression and inhibition of vulval cell fates. Citation: Development 132: 1047-1056 2005 Type: ARTICLE Genes: lin-1 mek-2 mep-1 mpk-1 smg-1 smo-1 ubc-9 Abstract: The LIN-1 ETS transcription factor inhibits vulval cell fates during Caenorhabditis elegans development. We demonstrate that LIN-1 interacts with UBC-9, a small ubiquitin-related modifier (SUMO) conjugating enzyme. This interaction is mediated by two consensus sumoylation motifs in LIN-1. Biochemical studies showed that LIN-1 is covalently modified by SUMO-1. ubc-9 and smo-1, the gene encoding SUMO-1, inhibit vulval cell fates and function at the level of lin-1, indicating that sumoylation promotes LIN-1 inhibition of vulval cell fates. Sumoylation of LIN-1 promoted transcriptional repression and mediated an interaction with MEP-1, a protein previously shown to associate with the nucleosome remodeling and histone deacetylation (NuRD) transcriptional repression complex. Genetic studies showed that mep-1 inhibits vulval cell fates and functions at the level of lin-1. We propose that sumoylation of LIN-1 mediates an interaction with MEP-1 that contributes to transcriptional repression of genes that promote vulval cell fates. These studies identify a molecular mechanism for SUMO-mediated transcriptional repression. ------------------- Key: 7180 Medline: 15780187 Authors: Pilon M;Morck C Title: Development of Caenorhabditis elegans pharynx, with emphasis on its nervous system. Citation: Acta Pharmacologica Sinica 26: 396-404 2005 Type: REVIEW Genes: ceh-22 lin-35 mnm-1 mnm-2 mnm-3 mnm-4 pha-1 myo-1 myo-2 pha-2 pha-3 pha-4 sax-3 slt-1 ubc-18 unc-5 unc-6 unc-49 unc-51 unc-69 unc-73 unc-115 Abstract: The Caenorhabditis elegans pharynx is a neuromuscular tube of which the function is to pump and crush bacteria, and inject them into the intestine. The 80-cell pharynx develops via the morphogenesis and differentiation of the cells that compose its semi-spherical primordium, and requires the activity of several evolutionarily conserved genes, such as pha-4 (the homolog to the Drosophila forkhead and vertebrate FoxA), ceh-22 (the homolog to the Drosophila tinman and vertebrate Nkx2.5), and pha-2 (the homolog to the vertebrate Hex). There are 20 neurons in the pharynx, each with a reproducible unique trajectory. Developmental genetic analysis of axon guidance in the pharynx indicates that some axon trajectories are in part established without growth cones, whereas other parts necessitate growth cone function and guidance. Here we provide an overview of the developmental genetics of the Caenorhabditis elegans pharynx, with an emphasis on its ------------------- Key: 7181 Medline: Authors: Fox RM;Von Stetina SE;Barlow SJ;Shaffer C;Olszewski KL;Moore JH;Dupuy D;Vidal M;Miller DM Title: A gene expression fingerprint of C. elegans embryonic motor neurons. Citation: BMC Genomics 6: 1-23 2005 Type: ARTICLE Genes: abl-1 acr-2 acr-12 acr-14 acy-1 clr-1 cwn-1 cwn-2 dgk-1 dop-1 dsh-1 dsh-2 egl-2 egl-8 egl-10 egl-16 egl-30 egl-47 flp-2 flp-4 flp-5 flp-14 gar-2 gar-3 gcy-19 glr-5 goa-1 gpa-9 gpb-2 gpc-2 gsa-1 ida-1 ins-1 ins-18 kin-2 lev-10 lin-17 lit-1 mab-9 mig-5 mig-13 mom-4 mom-5 nca-1 nlp-9 nlp-15 nlp-21npr-1 npr-2 par-1 pkc-3 ric-3 ric-8 ric-19 rgs-1 rpy-1 ser-4 snf-5 syg-1 tap-1 tig-1 trp-1 tsp-7 twk-30 unc-3 unc-4 unc-5 unc-6 unc-13 unc-14 unc-29 unc-31 unc-38 unc-40 unc-44 unc-51 unc-63 unc-76 unc-115 uvt-6 Abstract: ------------------- Key: 7182 Medline: 15796979 Authors: Oza JP;Yeh JB;Reich NO Title: DNA methylation modulates Salmonella enterica serovar Typhimurium virulence in Caenorhabditis elegans. Citation: FEMS Microbiology Letters 245: 53-59 2005 Type: ARTICLE Genes: glp-1 Abstract: Salmonella enterica serovar Typhimurium was previously shown to be virulent in Caenorhabditis elegans. Here we demonstrate that DNA adenine methyltransferase (DAM) modulates Salmonella virulence in the nematode, as it does in mice. After 5 days of continual exposure to bacteria, twice as many worms died when exposed to the wild-type than the dam-mutant strain of Salmonella. Similar trends in virulence were observed when worms were exposed to Salmonella strains for 5 h and transferred to the avirulent Escherichia coli OP50. While a 10-fold attenuation was observed in the absence of DAM, the dam-strain was still able to infect and persist in the host worm. Our results further support the use of C. elegans as an accessible and readily studied animal model of bacterial pathogenesis. However, our results suggest that crucial host responses differ between the murine and nematode models. Additionally, we carried out preliminary liquid culture based experiments with the long term goal of developing high throughput animal based screens of DAM inhibitors. ------------------- Key: 7183 Medline: 15808856 Authors: Bando T;Ikeda T;Kagawa H Title: The homeoproteins MAB-18 and CEH-14 insulate the dauer collagen gene col-43 from activation by the adjacent promoter of spermatheca gene sth-1 in Caenorhabditis elegans. Citation: Journal of Molecular Biology 348: 101-112 2005 Type: ARTICLE Genes: ceh-14 col-43 daf-11 mab-18 sth-1 Abstract: Genome searches in this study indicate that the nematode Caenorhabditis elegans genome has 2582 bidirectionally oriented genes that account for more than 25% of the total genes. We analyze the transcriptional repression system for one of these predicted bidirectional promoters, which controls the expression of the spermathecal gene sth-1 and collagen gene col-43. These two genes are separated by 1.3 kb and are transcribed bidirectionally. sth-1 is expressed in spermatheca after the L4 stage and col-43 is expressed in the hypodermal cells of the L2d dauer stage. The upstream regions required for the expression of sth-1 and col-43 shared an overlapped control sequence. Two homeoproteins, MAB-18 and CEH-14, were isolated by yeast one-hybrid screening as binding proteins of the overlapped region. MAB-18 bound to two homeodomain-binding sites and interacted with CEH-14 to repress col-43 expression in spermatheca. These results indicate that the two homeoproteins interact with each other to repress col-43 expression in sth-1-expressing tissues. This is the first report of bidirectional gene regulation analysis in the C. elegans genome. ------------------- Key: 7184 Medline: Authors: Bazopoulou MD;Troullinaki K;Tavernarakis N Title: Protein turnover and ageing. Citation: Focus on Protein Research : 19-45 2004 Type: REVIEW Genes: Abstract: ------------------- Key: 7185 Medline: 15576912 Authors: Shakir MA;Lundquist EA Title: Analysis of cell migration in Caenorhabditis elegans. Citation: Methods in Molecular Biology 294: 159-173 2005 Type: REVIEW Genes: ceh-23 him-4 hlh-8 mec-4 osm-6 unc-39 unc-73 unc-86 unc-119 Abstract: This chapter is concerned with a method of analysis and quantification of cell migration defects in mutants of the nematode worm Caenorhabditis elegans. The method takes advantage of transgenic expression of the green fluorescent protein to visualize migrating cells. By following these protocols, one will be able to analyze cell migration defects in new mutant strains for comparison to wild-type and to other mutants. Techniques described include obtaining wild-type and mutant worm strains as well as strains harboring green fluorescent protein transgenes; maintenance and manipulation of C. elegans in the laboratory; introducing transgenes into different genetic backgrounds; mounting worms for fluorescence microscopy; and scoring and analysis of cell migration defects. ------------------- Key: 7186 Medline: 15649894 Authors: Visser F;Baldwin SA;Isaac RE;Young JD;Cass CE Title: Identification and mutational analysis of amino acid residues involved in dipyridamole interactions with human and Caenorhabditis elegans equilibrative nucleoside transporters. Citation: Journal of Biological Chemistry 280: 11025-11034 2005 Type: ARTICLE Genes: Abstract: The equilibrative nucleoside transporters, hENT1 and CeENT1 from humans and Caenorhabditis elegans, respectively, are inhibited by nanomolar concentrations of dipyridamole and share a common 11-transmembrane helix (TM) topology. Random mutagenesis and screening by functional complementation in yeast for clones with reduced sensitivities to dipyridamole yielded mutations at Ile429 in TM 11 of CeENT1 and Met33 in TM 1 of hENT1. Mutational analysis of the corresponding residues of both proteins suggested important roles for these residues in competitive inhibition of hENT1 and CeENT1 by dipyridamole. To verify the roles of these residues in dipyridamole interactions, hENT2, which naturally exhibits low dipyridamole sensitivity, was mutated to contain side chains favorable for high affinity dipyridamole binding (i.e. a Met at the TM 1 and/or an Ile at the TM 11 positions). The single mutants exhibited increased hENT2 sensitivity to inhibition by dipyridamole, and the double mutant was the most sensitive, with an IC50 value that was only 2% of that of wild type. Functional analysis of the TM 1 and 11 mutants of hENT1 and CeENT1 revealed that Ala and Thr in the TM 1 and 11 positions, respectively, impaired uridine and adenosine transport and that Leu442 of hENT1 was involved in permeant selectivity. Mechanistic and structural models of dipyridamole interactions with the TM 1 and 11 residues are proposed. This study demonstrated that the corresponding residues in TMs and 11 of hENT1, hENT2, and CeENT1 are important for dipyridamole interactions and nucleoside transport. ------------------- Key: 7187 Medline: 15797828 Authors: Entchev EV;Kurzchalia TV Title: Requirement of sterols in the life cycle of the nematode Caenorhabditis elegans. Citation: Seminars in Cell & Developmental Biology 16: 175-182 2005 Type: REVIEW Genes: daf-2 daf-3 daf-5 daf-7 daf-9 daf-10 daf-12 daf-16 daf-22 lrp-1 ncr-1 ncr-2 rme-2 Abstract: The nematode Caenorhabditis elegans represents an excellent model for studying many aspects of sterol function on the level of a whole organism. Recent studies show that especially two processes in the life cycle of the worm, dauer larva formation and molting, depend on sterols. In both cases, cholesterol or its derivatives seem to act as hormones rather than being structural components of the membrane. Investigations on C elegans could provide information on the etiology of human diseases that display defects in the transport or metabolism of sterols. ------------------- Key: 7188 Medline: 15797839 Authors: Mangahas PM;Zhou Z Title: Clearance of apoptotic cells in Caenorhabditis elegans. Citation: Seminars in Cell & Developmental Biology 16: 295-306 2005 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-8 ced-10 ced-12 cps-6 crn-1 crn-2 crn-3 crn-4 crn-5 crn-6 cyp-13 egl-1 gex-2 gex-3 nuc-1 psr-1 wah-1 Abstract: MicroRNAs (miRNAs) are an endogenously encoded class of small RNAs that have been proposed to function as key posttranscriptional regulators of gene expression in a range of eukaryotic species, including humans. The small size of miRNA precursors makes them potentially ideal for use by viruses as inhibitors of host cell defense pathways. Here, we demonstrate that the pathogenic human herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV) encodes an array of 11 distinct miRNAs, all of which are expressed at readily detectable levels in latently KSHV infected cells. Individual KSHV miRNAs were expressed at up to 2,200 copies per cell. The KSHV miRNAs are expressed from what appears to be a single genetic locus that largely coincides with an approximate to 4-kb noncoding sequence located between the KSHV v-cyclin and K12/Kaposin genes, both of which are also expressed in latently infected cells. Computer analysis of potential mRNA targets for these viral miRNAs identified a number of interesting candidate genes, including several mRNAs previously shown to be down-regulated in KSHV-infected cells. We hypothesize that these viral miRNAs play a critical role in the establishment and/or maintenance of KSHV latent infection in vivo and, hence, in KSHV-induced oncogenesis. ------------------- Key: 7189 Medline: Authors: Trutschl M;Dinkova TD;Rhoads RE Title: Application of machine learning and visualization of heterogeneous datasets to uncover relationships between translation and developmental state expression of C. elegans mRNAs. Citation: Physiological Genomics 21: 264-273 2005 Type: ARTICLE Genes: ife-4 Abstract: The relationships between genes in neighboring clusters in a self-organizing map (SOM) and properties attributed to them are sometimes difficult to discern, especially when heterogeneous datasets are used. We report a novel approach to identify correlations between heterogeneous datasets. One dataset, derived from microarray analysis of polysomal distribution, contained changes in the translational efficiency of Caenorhabditis elegans mRNAs resulting from loss of specific eIF4E isoform. The other dataset contained expression patterns of mRNAs across all developmental stages. Two algorithms were applied to these datasets: a classical scatter plot and an SOM. The outputs were linked using a two-dimensional color scale. This revealed that an mRNA's eIF4E-dependent translational efficiency is strongly dependent on its expression during development. This correlation was not detectable with a traditional one-dimensional color scale. ------------------- Key: 7190 Medline: Authors: Cao S;Gelwix CC;Caldwell KA;Caldwell GA Title: Torsin-mediated protection from cellular stress in dopminergic neurons of Caenorhabditis elegans. Citation: Journal of Neuroscience 25: 3801-3812 2005 Type: ARTICLE Genes: cat-2 dat-1 tor-2 Abstract: Parkinson's disease (PD) is linked genetically to proteins that function in the management of cellular stress resulting from protein misfolding and oxidative damage. Overexpression or mutation of alpha-synuclein results in the formation of Lewy bodies and neurodegeneration of dopaminergic (DA) neurons. Human torsinA, mutations in which cause another movement disorder termed early-onset torsion dystonia, is highly expressed in DA neurons and is also a component of Lewy bodies. Previous work has established torsins as having molecular chaperone activity. Thus, we examined the ability of torsinA to manage cellular stress within DA neurons of the nematode Caenorhabditis elegans. Worm DA neurons undergo a reproducible pattern of neurodegeneration after treatment with 6-hydroxydopamine (6-OHDA), a neurotoxin commonly used to model PD. Overexpression of torsins in C. elegans DA neurons results in dramatic suppression of neurodegeneration after 6-OHDA treatment. In contrast, expression of either dystonia-associated mutant torsinA or combined overexpression of wild-type and mutant torsinA yielded greatly diminished neuroprotection against 6-OHDA. We further demonstrated that torsins seem to protect DA neurons from 6-OHDA through downregulating protein levels of the dopamine transporter (DAT-1) in vivo. Additionally, we determined that torsins protect robustly against DA neurodegeneration caused by overexpression of alpha-synuclein. Using mutant nematodes lacking DAT-1 function, we also showed that torsin neuroprotection from alpha-synuclein-induced degeneration occurs in a manner independent of this transporter. Together, these data have mechanistic implications for movement disorders, because our results demonstrate that torsin proteins have the ------------------- Key: 7191 Medline: Authors: Yeh E;Kawano T;Weimer RM;Bessereau JL;Zhen M Title: Identification of genes involved in synaptogenesis using a fluorescent active zone marker in Caenorhabditis elegans. Citation: Journal of Neuroscience 25: 3833-3841 2005 Type: ARTICLE Genes: fsn-1 goa-1 rpm-1 syd-1 syd-2 unc-3 unc-10 unc-12 unc-25 unc-30 unc47 unc-104 unc-116 Abstract: Active zones are presynaptic regions where synaptic vesicles fuse with plasma membrane to release neurotransmitters. Active zones are highly organized structurally and are functionally conserved among different species. Synapse defective-2 (SYD-2) family proteins regulate active zone morphology in Caenorhabditis elegans and Drosophila. Here, we demonstrate by immunoelectron microscopy that at C. elegans synapses, SYD-2 localizes strictly at active zones and can be used as an active zone marker when fused to green fluorescent protein (GFP). By driving expression of SYD-2::GFP fusion protein in GABAergic neurons, we are able to visualize discrete fluorescent puncta corresponding to active zones in living C. elegans. During development, the number of GABAergic synapses made by specific motoneurons increases only slightly from larvae to adult stages. In contrast, the number of SYD-2::GFP puncta doubles, suggesting that individual synapses accommodate the increasing size of their synaptic targets mainly by incorporating more active zone materials. Furthermore, we used this marker to perform a genetic screen to identify genes involved in the development of active zones. We recovered 16 mutants with altered SYD-2::GFP expression, including alleles of five genes that have been implicated previously in synapse formation or nervous-system development. Mapping of 11 additional mutants suggests that they may represent novel genes involved in active zone formation. ------------------- Key: 7192 Medline: 15654117 Authors: Dempsey CM;Mackenzie SM;Gargus A;Blanco G;Sze JY Title: Serotonin (5HT), fluoxetine, imipramine and dopamine target distinct 5HT receptor signaling to modulate Caenorhabditis elegans egg-laying behavior. Citation: Genetics 169: 1425-1436 2005 Type: ARTICLE Genes: dgk-1 egl-1 egl-8 itr-1 mod-1 mod-5 ser-1 ser-2 ser-4 tpa-1 tph-1 Abstract: Drugs that target the scrotonergic system are the most commonly prescribed therapeutic agents and are used for treatment of a wide range of behavioral and neurological disorders. However, the mechanism of the drug action remain a conjecture. Here, we dissect the genetic targets of serotonin (5HT), the selective 5HT reuptake inhibitor (SSRI) fluoxetine (Prozac), the tricyclic antidepressant imipramine, and dopamine. Using the well-established scrotonergic response in C. elegans egg-laying behavior as a paradigm, we show that action of fluoxetine and imipramine at the 5HT reuptake transporter (SERT) and at 5HT receptors are separable mechanisms. Even mutants completely lacking 5HT or SERT can partially respond to fluoxetine and imipramine. Furthermore, distinct mechanisms for each drug can be recognized to mediate these responses. Deletion of SER-1, a 5HT1 receptor, abolishes the response to 5HT but has only a minor effect on the response to imipramine and no effect on the response to fluoxerinc. In contrast, deletion of SER-4, a 5HT2 receptor, confers significant resistance to imipramine while leaving the responses to 5HT or fluoxetine intact. Further, fluoxetine can stimulate egg laying via the Gq protein EGL-30, independent of SER-1, SER-4, or 5HT. We also show that dopamine antagonizes the 5HT action via the 5HT-gated ion channel MOD-1 signaling, Suggesting that this channel activity couples 5HT and dopamine signaling. These results suggest that the actions of these drugs at specific receptor Subtypes could determine their therapeutic efficacy. SSRIs and tricyclic antidepressarus may regulate ------------------- Key: 7193 Medline: 15654086 Authors: Mohri A;Kodama E;Kimura KD;Koike M;Mizuno T;Mori I Title: Genetic control of temperature preference in the nematode Caenorhabditis elegans. Citation: Genetics 169: 1437-1450 2005 Type: ARTICLE Genes: aho-1 aho-2 aho-3 bas-1 cat-1 cat-4 goa-1 tph-1 Abstract: Animals modify behavioral outputs in response to environmental changes. C. elegans exhibits thermotaxis, where well-fed animals show attraction to their cultivation temperature on a thermal gradient without food. We show here that feeding-state-clependent modulation of thermotaxis is a powerful behavioral paradigm for elucidating the mechanism underlying neural plasticity, learning, and memory in higher animals. Starved experience alone could induce aversive response to cultivation temperature. Changing both cultivation temperature and feeding state Simultaneously evoked transient attraction to or aversion to the previous cultivation temperature: recultivation of starved animals with food immediately induced attraction to the temperature associated with starvation, although the animals eventually exhibited thermotaxis to the new temperature associated with food. These results suggest that the change in feeding state quickly stimulates the switch between attraction and aversion for the temperature in memory and that the acquisition of new temperature memory establishes more slowly. We isolated aho (abnormal hunger orientation) mutants that are defective in starvation-induced cultivation-temperature avoidance. Some aho mutants responded normally to changes in feeding state with respect to locomotory activity, implying that the primary thermosensation followed by temperature memory formation remains normal and the modulatory aspect of thermotaxis is ------------------- Key: 7194 Medline: 15654100 Authors: Holway AH;Hung C;Michael WM Title: Systematic, RNA-interference-mediated identificaiton of mus-101 modifier genes in Caenorhabditis elegans. Citation: Genetics 169: 1451-1460 2005 Type: ARTICLE Genes: arx-7 gei-17 let-49 mus-101 Abstract: The Mus101 family of chromosomal proteins, identified initially in Drosophila, is widely conserved and has been shown to function in a variety of DNA metabolic processes. Such functions include DNA replication, DNA damage repair, postreplication repair, damage checkpoint activation, chromosome stability, and chromosome condensation. Despite its conservation and widespread involvement in chromosome biogenesis, very little is known about how Mus101 is regulated and what other proteins are required for Mus101 to exert its functions. To learn more about Mus101, we have initiated an analysis of the protein in C. elegans. Here, we show that C. elegans mus-101 is an essential gene, that it is required for DNA replication, and that it also plays an important role in the DNA damage response. Furthermore, we rise RNA interference (RNAi)-mediated reverse genetics to screen for genes that modify a mus-101 partial loss-of-function RNAi phenotype. Using a systematic approach toward modifier gene discovery, we have found five chromosome I genes that modify the mus-101 RNAi phenotype, and we go on to show that one of them encodes an E3 SUMO ligase that promotes SUMO modification of MUS-101 in vitro. These results expand our understanding of MUS-101 regulation and show that genetic interactions can be uncovered rising screening strategies that rely solely on ------------------- Key: 7195 Medline: 15654093 Authors: Williams DC;Boulin T;Ruaud AF;Jorgensen EM;Bessereau JL Title: Characterization of Mos1-mediated mutagenesis in Caenorhabditis elegans: a method for the rapid identification of mutated genes. Citation: Genetics 169: 1779-1785 2005 Type: ARTICLE Genes: Abstract: Insertional mutagenesis with a heterologous transposon provides a method to rapidly determine the molecular identity of mutated genes. The Drosophila transposon Mos1 can be mobilized to cause mutations in Caenorhabditis elegans (BESSEREAU et al. 2001); however, the mutagenic rate vas initially too low for use in most forward genetic screens. To increase the effectiveness of Mos1-mediated mutagenesis we examined the conditions influencing Mos1 transposition. First, optimal transposition occurs 24 hr after expression of the transposase and is unlikely to Occur in differentiated sperm or oocytes. Second, transposition is limited to germ-cell nuclei that contain donor elements, but the transposase enzyme can diffuse throughout the gonad syncytium. Third, silencing of transposition is caused by changes in the donor array that occur over time. Finally, multiple transposition events occur in individual germ cells. By using screening techniques based on these results, Mos1 mutagenicity was increased to within an order of magnitude of chemical ------------------- Key: 7196 Medline: 15775964 Authors: Sasakura H;Inada H;Kuhara A;Fusaoka E;Takemoto D;Takeuchi K;Mori I Title: Maintenance of neuronal positions in organized ganglia by SAX-7, a Caenorhabditis elegans homologue of L1. Citation: EMBO Journal 24: 1477-1488 2005 Type: ARTICLE Genes: sax-7 Abstract: The L1 family of cell adhesion molecules is predominantly expressed in the nervous system. Mutations in human L1 cause neuronal diseases such as HSAS, MASA, and SPG1. Here we show that sax-7 gene encodes an L1 homologue in Caenorhabditis elegans. In sax-7 mutants, the organization of ganglia and positioning of neurons are abnormal in the adult stage, but these abnormalities are not observed in early larval stage. Misplacement of neurons in sax-7 mutants is triggered by mechanical force linked to body movement. Short and long forms of SAX-7 exhibited strong and weak homophilic adhesion activities in in vitro aggregation assay, respectively, which correlated with their different activities in vivo. SAX-7 was localized on plasma membranes of neurons in vivo. Expression of SAX-7 only in a single neuron in sax-7 mutants cell-autonomously restored its normal neuronal position. Expression of SAX-7 in two different head neurons in sax-7 mutants led to the forced attachment of these neurons. We propose that both homophilic and heterophilic interactions of SAX-7 are essential for maintenance of neuronal positions in ------------------- Key: 7197 Medline: 15882588 Authors: Shan G;Kim K;Li C;Walthall WW Title: Convergent genetic programs regulate related motor neuron classes similarities and differences in Caenorhabditis elegans. Citation: Developmental Biology 280: 494-503 2005 Type: ARTICLE Genes: Abstract: How do genetic programs create features common to a specific cell or tissue type while generating modifications necessary for functional diversification? We have addressed this question using the nematode Caenorhabditis elegans. The dorsal D (DD) and ventral D (VD) motorneurons (mns), referred to collectively as the D inns, compose a cross-inhibitory network that contributes to the animal's sinuous locomotion. The D inns share a number of structural and functional features, but are distinguished from one another by their synaptic patterns and the expression of a neuropepticle gene. Our findings suggest that the similarities and differences are generated at the transcriptional level. UNC-30 contains a homeodomain and activates structural and functional genes expressed in both classes. UNC-55 is a nuclear receptor expressed in the VD mns that is necessary for generating features that distinguish the two classes of D inns from one another. In unc-55 mutants, the VD mns adopt the DID mn synaptic pattern and peptide expression profile. Conversely, ectopic expression of unc-55 in the DD mns causes them to adopt VD mn features. The promoter of the neuropeptide gene expressed in the DD inns contains putative binding sites for both UNC-30 and UNC-55; alteration of these sites suggests that UNC-55 represses the ability of UNC-30 to activate a subset of genes that are expressed in the DD mns but not in the VD inns. Thus UNC-55 acts as a switch for the features that distinguish these two functionally ------------------- Key: 7198 Medline: 15716342 Authors: Dalpe G;Brown L;Culotti JG Title: Vulva morphogenesis involves attraction of plexin 1-expressing primordial vulva cells to semaphorin 1a sequentially expressed at the vulva midline. Citation: Development 132: 1387-1400 2005 Type: ARTICLE Genes: ced-10 let-60 mig-2 plx-1 smp-1 smp-2 unc-73 Abstract: Vulva development in C elegans involves cell fate specification followed by a morphogenesis phase in which homologous mirror image pairs within a linear array of primordial vulva cells form a crescent shape as they move sequentially towards a midline position within the array. The homologous pairs from opposite half vulvae in fixed sequence fuse with one another at their leading tips to form ring-shaped (toroidal) cells stacked in precise alignment one atop the other. Here, we show that the semaphorin la SMP-1, and its plexin receptor PLX-1, are required for the movement of homologous pairs of vulva cells towards this midline position. SMP-1 is upregulated on the lumen membrane of each primordial vulva cell as it enters the forming vulva and apparently attracts the next flanking homologous PLX-1-expressing vulva cells towards the lumen surface of the ring. Consequently, a new ring-shaped cell forms immediately ventral to the previously formed ring. This smp-1- and plx-1-dependent process repeats until seven rings are stacked along the dorsoventral axis, creating a common vulva lumen. Ectopic expression of SMP-1 suggests it has an instructive role in vulva cell migration. At least two parallel acting pathways are required for vulva formation: one requires SMP-1, PLX-1 and CED-10; and another requires the MIG-2 Rac GTPase and ------------------- Key: 7199 Medline: 15750187 Authors: Yang L;Sym M;Kenyon C Title: The roles of two C. elegans HOX co-factor orthologs in cell migration and vulva development. Citation: Development 132: 1413-1428 2005 Type: ARTICLE Genes: ceh-20 egl-20 lin-39 mab-5 mig-13 unc-62 nDf16 yDp1 Abstract: Anteroposterior cell migration and patterning in C elegans are governed by multiple, interacting signaling pathways and transcription factors. In this study, we have investigated the role of ceh-20, the C elegans ortholog of the HOX co-factor Extradenticle (Exd/Pbx), and unc-62, the C elegans ortholog of Homothorax (Hth/Meis/Prep), in two processes that are regulated by Hox gene lin-39: cell migration and vulva formation. As in lin-39 mutants, the anterior migrations of neuroblasts in the Q lineage are truncated in Hox co-factor mutants. Surprisingly, though, our findings suggested that the roles of ceh-20 and unc-62 are different from that of lin-39; specifically, ceh-20 and unc-62 but not lin-39 are required for the transmembrane protein MIG-13 to promote anterior migration. To our knowledge, ceh-20 and unc-62 are the only genes that have been implicated in the mig-13 pathway. We find that ceh-20 and unc-62 are also required for several steps in vulva development. Surprisingly, ceh-20 and unc-62 mutants have phenotypes that are starkly different from those of lin-39 mutants. Thus, in this process, too, ceh-20 and unc-62 are likely to have functions that are independent of lin-39. ------------------- Key: 7200 Medline: Authors: Agrafioti I;Swire J;Abbott J;Huntley D;Butcher S;Stumpf MPH Title: Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks. Citation: BMC Evolutionary Biology 5: 1-14 2005 Type: ARTICLE Genes: Abstract: Background: Protein interaction networks aim to summarize the complex interplay of proteins in an organism. Early studies suggested that the position of a protein in the network determines its evolutionary rate but there has been considerable disagreement as to what extent other factors, such as protein abundance, modify this reported dependence. Results: We compare the genomes of Saccharomyces cerevisiae and Caenorhabditis elegans with those of closely related species to elucidate the recent evolutionary history of their respective protein interaction networks. Interaction and expression data are studied in the light of a detailed phylogenetic analysis. The underlying network structure is incorporated explicitly into the statistical analysis. The increased phylogenetic resolution, paired with high-quality interaction data, allows us to resolve the way in which protein interaction network structure and abundance of proteins affect the evolutionary rate. We find that expression levels are better predictors of the evolutionary rate than a protein's connectivity. Detailed analysis of the two organisms also shows that the evolutionary rates of interacting proteins are not sufficiently similar to be mutually predictive. Conclusion: It appears that meaningful inferences about the evolution of protein interaction networks require comparative analysis of reasonably closely related species. The signature of protein evolution is shaped by a protein's abundance in the organism and its function and the biological process it is involved in. Its position in the interaction networks and its connectivity may modulate this but they appear to have only minor influence on a protein's evolutionary rate. ------------------- Key: 7201 Medline: 15809072 Authors: Suda H;Shouyama T;Yasuda K;Ishii N Title: Direct measurement of oxygen consumption rate on the nematode Caenorhabditis elegans by using an optical technique. Citation: Biochemical and Biophysical Research Communications 330: 839-843 2005 Type: ARTICLE Genes: Abstract: It is well known that aging and longevity strongly correlate with energy metabolism. The nematode Caenorhabditis elegans is widely used as an ultimate model of experimental animals. Thus, we developed a novel tool, which is constructed from an optical detector, using an indirect method that can measure simply the energy metabolism of C elegans. If we measure the oxygen consumption rate using this optical tool, we can easily evaluate the activity of mitochondria as an index in the aging process. However, a direct measurement of the oxygen consumption rate of C elegans exposed in air is thought to be impossible because of the high concentration of atmospheric oxygen and the small size of the animals. We demonstrate here that we can directly detect the oxygen consumption with a small number of animals (<= 40) and a short accumulation time (<= 30 min) at high precision by using both an optical probe and a small chamber. The metabolic rate of a 4-day-old hermaphrodite animal, for example, was approximately 80 nW. Our method using C elegans has the potential to become a useful technique for ------------------- Key: 7202 Medline: Authors: Hilliard MA;Apicella AJ;Kerr R;Suzuki H;Bazzicalupo P;Schafer WR Title: In vivo imaging of C. elegans ASH neurons: cellular response and adaptation to chemical repellents. Citation: EMBO Journal 24: 1489- 2005 Type: CORRECT Genes: Abstract: ------------------- Key: 7203 Medline: 15838512 Authors: Koreth J;van den Heuvel S Title: Cell-cycle control in Caenorhabditis elegans: how the worm moves from G1 to S. Citation: Oncogene 24: 2756-2764 2005 Type: REVIEW Genes: Abstract: The nematode Caenorhabditis elegans offers a powerful model system to study cell division control during animal development. Progress from the one- cell zygote to adult stage follows a nearly invariant pattern of divisions. This, combined with a transparent body and efficient genetics, allows for sensitive identification and quantitative analysis of cell- cycle mutants. Nearly all G1 control genes identified in C. elegans have mammalian homologs. Examples include a D- type cyclin and CDK4/ 6- related kinase, a member of the retinoblastoma protein family and CDK inhibitors of the Cip/ Kip family. Genetic studies have placed the currently known G1 regulators into pathways similar to those in mammals. Together, this validates the use of C. elegans in identifying additional regulators of cell- cycle entry and exit. For instance, we recently found that the CDC- 14 phosphatase promotes maintenance of the quiescent state. Here, we describe cell-cycle control as an integral part of C. elegans development, summarize current knowledge of G1 control genes in the worm, compare the results with those obtained in other species, and discuss the possible implications of cellcycle studies in C. elegans for higher organisms, ------------------- Key: 7204 Medline: 15809090 Authors: Mertens I;Meeusen T;Janssen T;Nachman R;Schoofs L Title: Molecular characterization of two G protein-coupled receptor splice variants as FLP2 receptors in Citation: Biochemical and Biophysical Research Communications 330: 967-974 2005 Type: ARTICLE Genes: flp-1 flp-2 flp-3 flp-4 flp-5 flp-6 flp-7 flp-9 flp-10 flp-11 flp-12 flp-13 flp-14 flp-15 flp-16 flp-18 flp-19 flp-22 nlp-1 nlp-2 nlp-3 nlp-6 nlp-7 nlp-10 nlp-11 nlp-12 nlp-13 nlp-14 nlp-17 nlp-22 nlp-23 nlp-30 Abstract: Two alternatively spliced Caenorhabditis elegans G protein-coupled receptors, T19F4.1a and T19F4.1b, were cloned and functionally characterized. The T19F4.1b receptor protein is 30 amino acids longer than T19F4.1a, and the difference in amino acid constitution is exclusively conferred to the intracellular C-terminal region, suggesting a potential difference in G protein-coupling specificity. Following cloning of the receptor cDNAs into the pcDNA3 vector and stable or transient transfection into Chinese hamster ovary cells, the aequorin bioluminescence/Ca2+ assay was used to investigate receptor activation. This is the first report of the construction of a cell line stably expressing a C elegans neuropeptide receptor. Our experiments identified both receptors as being cognate receptors for two FMRFamide-related peptides encoded by the flp-2 precursor: SPREPIRFamide (FLP2-A) and LRGEPIRFamide (FLP2-B). Pharmacological profiling using truncated forms of FLP2-A and -B revealed that the active core of both peptides is EPIRFamide. Screening of peptides encoded by other flps did not result in a significant activation of the receptor. In contrast to other C. elegans receptors tested in heterologous expression systems, the functional activation of both T19F4.1a and T19F4.1b was not temperature-dependent. Screening in cells lacking the ------------------- Key: 7205 Medline: 15775989 Authors: Hyman AA Title: Boveri revisited. Citation: EMBO Journal 24: 1104-1110 2005 Type: REVIEW Genes: Abstract: ------------------- Key: 7206 Medline: 15809433 Authors: Baer CF;Shaw F;Steding C;Baumgartner M;Hawkins A;Houppert A;Mason N;Reed M;Simonelic K;Woodard W;Lynch M Title: Comparative evolutionary genetics of spontaneous mutations affecting fitness in rhabditid nematodes. Citation: Proceedings of the National Academy of Sciences USA 102: 5785-5790 2005 Type: ARTICLE Genes: Abstract: Deleterious mutations are of fundamental importance to all aspects of organismal biology. Evolutionary geneticists have expended tremendous effort to estimate the genome-wide rate of mutation and the effects of new mutations on fitness, but the degree to which genomic mutational properties vary within and between taxa is largely unknown, particularly in multicellular organisms. Beginning with two highly inbred strains from each of three species in the nematode family Rhabditidae (Caenorhabditis briggsae, Caenorhabditis elegans, and Oscheius myriophila), we allowed mutations to accumulate in the relative absence of natural selection for 200 generations. We document significant variation in the rate of decay of fitness because of new mutations between strains and between species. Estimates of the per-generation mutational decay of fitness were very consistent within strains between assays 100 generations apart. Rate of mutational decay in fitness was positively associated with genomic mutation rate and negatively associated with average mutational effect. These results provide unambiguous experimental evidence for substantial variation in genome-wide properties of mutation both within and between species and reinforce conclusions from previous experiments that the cumulative effects on fitness of new mutations can differ ------------------- Key: 7207 Medline: Authors: Migunova VD;Byzov BA Title: Determinants of trophic modes of the nematophagous fungus Arthrobotrys oligospora interacting with bacteriovous nematode Caenorhabditis elegans. Citation: Pedobiologia 49: 101-108 2005 Type: ARTICLE Genes: Abstract: The determinants of saprotrophic or predatory modes of the nematophagous fungus Arthrobotrys oligospora were investigated in soil microcosms and on solid nutrient media. A sterilized soil amended with 1% w/w alfalfa meat (C:N = 32) and inocutated with conidia of A. oligospora, showed lower mycelium biomass and higher specific rate of conidia production in the presence of the bacterivorous nematode Caenorhabditis elegans than in its absence. As few as 10 nematodes g-1 soil. were sufficient to enhance spore formation by the vegetative mycelium. Given that the fungus was not limited by available carbon and nitrogen, this indicates that nematodes provide essential. growth factors regulating the development of A. oligospora. Carbon mineralisation by A. oligospora, measured as the rate of CO2 production, was found to be 25-35% tower in the presence of 20-60 C. elegans g(-1) soil compared to soil without nematodes. This showed that A. oligospora had tower saprotrophic activity in the predaceous phase. Trap formation and nematophagous activity of A. oligospora were observed only where conidia were inoculated on nutrient poor medium (water agar), on tow-nitrogen medium (Yeast Carbon Base agar) or on medium containing no amino-acids or vitamins (Czapek-Dox agar). A. oligospora did not form trapping structures when grown on nutrient-rich media containing three amino-acids (L-histidine monohydrocloride, DL-methionine and DL-tryptophan) and vitamins (biotin, calcium pantothenate, folic acid, inositol, niacin, p-aminobenzoic acid, pyridoxine hydrochloride, riboflavine, thiamine hydrochloride). It is concluded that predaceous behaviour of A. oligospora can be regulated either by nitrogen sources or by physiologically active compounds (amino-acids or vitamins) present in nematodes. ------------------- Key: 7208 Medline: 15800213 Authors: Qiu S;Adema CM;Lane T Title: A computational study of off-target effects of RNA interference. Citation: Nucleic Acids Research 33: 1834-1847 2005 Type: ARTICLE Genes: Abstract: RNA interference (RNAi) is an intracellular mechanism for post-transcriptional gene silencing that is frequently used to study gene function. RNAi is initiated by short interfering RNA (siRNA) of similar to 21 nt in length, either generated from the double-stranded RNA (dsRNA) by using the enzyme Dicer or introduced experimentally. Following association with an RNAi silencing complex, siRNA targets mRNA transcripts that have sequence identity for destruction. A phenotype resulting from this knockdown of expression may inform about the function of the targeted gene. However, 'off-target effects' compromise the specificity of RNAi if sequence identity between siRNA and random mRNA transcripts causes RNAi to knockdown expression of non-targeted genes. The complete off-target effects must be investigated systematically on each gene in a genome by adjusting a group of parameters, which is too expensive to conduct experimentally and motivates a study in silico. This computational study examined the potential for off-target effects of RNAi, employing the genome and transcriptome sequence data of Homo sapiens, Caenorhabditis elegans and Schizosaccharomyces pombe. The chance for RNAi off-target effects proved considerable, ranging from 5 to 80% for each of the organisms, when using as parameter the exact identity between any possible siRNA sequences (arbitrary length ranging from 17 to 28 nt) derived from a dsRNA (range 100-400 nt) representing the coding sequences of target genes and all other siRNAs within the genome. Remarkably, high-sequence specificity and low probability for off-target reactivity were optimally balanced for siRNA of 21 nt, the length observed mostly in vivo. The chance for off-target RNAi increased (although not always significantly) with greater length of the initial dsRNA sequence, inclusion into the analysis of available untranslated region sequences and allowing for mismatches between siRNA and target sequences. siRNA sequences from within 100 nt of the 5' termini of coding sequences had low chances for off-target reactivity. This may be owing to coding constraints for signal peptide-encoding regions of genes relative to regions that encode for mature proteins. Off-target distribution varied along the chromosomes of C.elegans, apparently owing to the use of more unique sequences in gene-dense regions. Finally, biological and thermodynamical descriptors of effective siRNA reduced the number of potential siRNAs compared with those identified by sequence identity alone, but off-target RNAi remained likely, with an off-target error rate of similar to 10%. These results also suggest a direction for future in vivo studies that could both help in calibrating true off-target rates in living organisms and also in contributing evidence toward the debate of whether siRNA efficacy is correlated with, or independent of, the target molecule. In summary, off-target effects present a real but not prohibitive concern that should be considered for RNAi experiments. ------------------- Key: 7209 Medline: Authors: Wei A;Yuan A;Fawcett G;Butler A;Davis T;Xu SY;Salkoff L Title: Efficient isolation of targeted Caenorhabditis elegans deletion strains using highly thermostable restriction endonucleases and PCR. Citation: Nucleic Acids Research 33: 2060- 2005 Type: CORRECT Genes: Abstract: ------------------- Key: 7210 Medline: 15710626 Authors: Lee DW;Zhao X;Scarselletta S;Schweinsberg PJ;Eisenberg E;Grant BD;Greene LE Title: ATP binding regulates oligomerization and endosome association of RME-1 family proteins. Citation: Journal of Biological Chemistry 280: 17213-17220 2005 Type: ARTICLE Genes: rme-1 Abstract: Members of the RME-1/mRme-1/EHD1 protein family have recently been shown to function in the recycling of membrane proteins from recycling endosomes to the plasma membrane. RME-1 family proteins are normally found in close association with recycling endosomes and the vesicles and tubules emanating from these endosomes, consistent with the proposal that these proteins directly participate in endosomal transport. RME-1 family proteins contain a C-terminal EH (eps15 homology) domain thought to be involved in linking RME-1 to other endocytic proteins, a coiled-coil domain thought to be involved in homo-oligomerization and an N-terminal P-loop domain thought to mediate nucleotide binding. In the present study, we show that both Caenorhabditis elegans and mouse RME-1 proteins bind and hydrolyze ATP. No significant GTP binding or hydrolysis was detected. Mutation or deletion of the ATP-binding P-loop prevented RME-1 oligomerization and at the same time dissociated RME-1 from endosomes. In addition, ATP depletion caused RME-1 to lose its endosome association in the cell, resulting in cytosolic localization. Taken together, these results indicate that ATP binding is required for oligomerization of mRme-1/EHD1, which in turn is required for its association with ------------------- Key: 7211 Medline: Authors: Schumacher B;Schertel C;Wittenburg N;Tuck S;Mitani S;Gartner A;Conradt B;Shaham S Title: C. elegans ced-13 can promote apoptosis and is induced in response to DNA damage. Citation: Cell Death and Differentiation 12: 532- 2005 Type: CORRECT Genes: ced-1 ced-3 ced-4 ced-9 ced-13 egl-1 Abstract: ------------------- Key: 7212 Medline: Authors: Pasquinelli A;Hunter S;Bracht J Title: MicroRNAs: a developing story. Citation: Current Opinion in Genetics & Development 15: 200-205 2005 Type: REVIEW Genes: die-1 gcy-5 let-7 lin-4 lin-14 lsy-6 Abstract: Caenorhabditis elegans increasingly is attractive as a toxicity test organism, particularly as a model system to study mechanisms of toxicity at a molecular level and the way that these lead to whole organism and population level effects. Inhibitions of growth, reproduction, movement, and feeding rate all have been proposed as sublethal toxicity endpoints. These endpoints are more sensitive than 24-h acute toxicity endpoints, but assays are much more time consuming, making them difficult to use in mass screening. The RNA/DNA ratio, after 48-h exposure to metals, has median effective concentration (EC50) values of 0.05, 0.6, 6. 1, and 35 mg/L for Cu, Pb, Cd, and Zn, respectively. This makes it a slightly more sensitive toxicity endpoint than reduction of individual growth after 72-h exposure to the same concentrations. This facilitates the near-simultaneous assessment of sublethal toxicity in many nematode samples. The constant cell number of C. elegans means that different stages in the life history have very different RNA/DNA ratios even in the absence of toxins. So, RNA/DNA ratios can be used only on prereproductive, age ------------------- Key: 7212 Medline: Authors: Ibiam U;Grant A Title: RNA/DNA ratios as a sublethal endpoint for large-scale toxicity tests with the nematode Caenorhabditis elegans. Citation: Environmental Toxicology and Chemistry 24: 1155-1159 2005 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans increasingly is attractive as a toxicity test organism, particularly as a model system to study mechanisms of toxicity at a molecular level and the way that these lead to whole organism and population level effects. Inhibitions of growth, reproduction, movement, and feeding rate all have been proposed as sublethal toxicity endpoints. These endpoints are more sensitive than 24-h acute toxicity endpoints, but assays are much more time consuming, making them difficult to use in mass screening. The RNA/DNA ratio, after 48-h exposure to metals, has median effective concentration (EC50) values of 0.05, 0.6, 6. 1, and 35 mg/L for Cu, Pb, Cd, and Zn, respectively. This makes it a slightly more sensitive toxicity endpoint than reduction of individual growth after 72-h exposure to the same concentrations. This facilitates the near-simultaneous assessment of sublethal toxicity in many nematode samples. The constant cell number of C. elegans means that different stages in the life history have very different RNA/DNA ratios even in the absence of toxins. So, RNA/DNA ratios can be used only on prereproductive, age synchronized cultures. Assessing the sublethal toxicity of metals to C. elegans shows that it is sensitive ------------------- Key: 7213 Medline: 15848803 Authors: Alkema MJ:Hunter-Ensor M;Ringstad N;Horvitz HR Title: Tyramine functions independently of octopamine in the Caenorhabditis elegans nervous system. Citation: Neuron 46: 247-260 2005 Type: ARTICLE Genes: bas-1 cat-1 cat-2 mec-4 mec-7 tbh-1 tdc-1 tph-1 unc-3 Abstract: Octopamine biosynthesis requires tyrosine decarboxylase to convert tyrosine into tyramine and tyramine P-hydroxylase to convert tyramine into octopamine. We identified and characterized a Caenorhabditis elegans tyrosine decarboxylase gene, tdc-1, and a tyramine P-hydroxylase gene, tbh-1. The TBH-1 protein is expressed in a subset of TDC-1 -expressing cells, indicating that C. elegans has tyraminergic cells that are distinct from its octoparninergic cells. tdc-1 mutants have behavioral defects not shared by tbh-1 mutants. We show that tyramine plays a specific role in the inhibition of egg laying, the modulation of reversal behavior, and the suppression of head oscillations in response to anterior touch. We propose a model for the neural circuit that coordinates locomotion and head oscillations in response to anterior touch. Our findings establish tyramine as a neurotransmitter in C. elegans, and we suggest that tyramine is a genuine neurotransmitter in other invertebrates and possibly in vertebrates as well. ------------------- Key: 7214 Medline: Authors: Bird DM Title: Model systems in agriculture: lessons from worms. Citation: Annals of Applied Biology 146: 147-154 2005 Type: REVIEW Genes: Abstract: Genomic tools are expanding the utility of organisms originally developed as models for biomedical research as a means to address complex agricultural problems. Conversely, agricultural pests are serving as models to help unravel questions of basic biology. Examples from C. elegans and root-knot nematode of this two-way exchange are discussed. ------------------- Key: 7215 Medline: 15813144 Authors: Szewczyk NJ;McLamb W Title: Surviving atmospheric spacecraft breakpoint. Citation: Wilderness & Environmental Medicine 16: 27-32 2005 Type: ARTICLE Genes: Abstract: Spacecraft travel higher and faster than aircraft, making breakup potentially less survivable. As with aircraft breakup, the dissipation of lethal forces via spacecraft breakup around an organism is likely to greatly increase the odds of survival. By employing a knowledge of space and aviation physiology, comparative physiology, and search-and-rescue techniques, we were able to correctly predict and execute the recovery of live animals following the breakup of the space shuttle Columbia. In this study, we make what is, to our knowledge, the first report of an animal, Caenorhabditis elegans, surviving the atmospheric breakup of the spacecraft that was supporting it and discuss both the lethal events these animals had to escape and the implications for search and rescue following spacecraft breakup. ------------------- Key: 7216 Medline: Authors: Strange K Title: The end of "naive reductionism": rise of systems biology or renaissance of physiology? Citation: American Journal of Physiology - Cell Physiology 288: C968-C974 2005 Type: ARTICLE Genes: Abstract: Systems biology is an emerging discipline focused on tackling the enormous intellectual and technical challenges associated with translating genome sequence into a comprehensive understanding of how organisms are built and run. Physiology and systems biology share the goal of understanding the integrated function of complex, multicomponent biological systems ranging from interacting proteins that carry out specific tasks to whole organisms. Despite this common ground, physiology as an academic discipline runs the real risk of fading into the background and being superseded organizationally and administratively by systems biology. My goal in this article is to discuss briefly the cornerstones of modern systems biology, specifically functional genomics, nonmammalian model organisms and computational biology, and to emphasize the need to embrace them as essential components of 21st-century physiology departments and research and ------------------- Key: 7217 Medline: 15843685 Authors: Taskov K;Chapple C;Kruykov GV;Castellano S;Lobanov AV;Korotkov KV;Guigo R;Gladyshev VN Title: Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome? Citation: Nucleic Acids Research 33: 2227-2238 2005 Type: ARTICLE Genes: Abstract: Selenocysteine (Sec) is co-translationally inserted into selenoproteins in response to codon UGA with the help of the selenocysteine insertion sequence (SECIS) element. The number of selenoproteins in animals varies, with humans having 25 and mice having 24 selenoproteins. To date, however, only one selenoprotein, thioredoxin reductase, has been detected in Caenorhabditis elegans, and this enzyme contains only one Sec. Here, we characterize the selenoproteomes of C.elegans and Caenorhabditis briggsae with three independent algorithms, one searching for pairs of homologous nematode SECIS elements, another searching for Cys- or Sec-containing homologs of potential nematode selenoprotein genes and the third identifying Sec-containing homologs of annotated nematode proteins. These methods suggest that thioredoxin reductase is the only Sec-containing protein in the C.elegans and C.briggsae genomes. In contrast, we identified additional selenoproteins in other nematodes. Assuming that Sec insertion mechanisms are conserved between nematodes and other eukaryotes, the data suggest that nematode selenoproteomes were reduced during evolution, and that in an extreme reduction case Sec insertion systems probably decode only a single UGA codon in C.elegans and C.briggsae genomes. In addition, all detected genes had a rare form of SECIS element containing a guanosine in place of a conserved adenosine present in most other SECIS structures, suggesting that in organisms with small selenoproteomes SECIS elements may change rapidly. ------------------- Key: 7218 Medline: 15765206 Authors: Yochem J;Hall DH;Bell LR;Hedgecock EM;Herman RK Title: Isopentenyl-diphosphate isomerase is essential for viability of Caenorhabditis elegans. Citation: Molecular Genetics & Genomics 273: 158-166 2005 Type: ARTICLE Genes: idi-1 sDp3 Abstract: Homozygosity for a mutation in the idi-1 gene of Caenorhabditis elegans results in paralysis during the first larval stage, followed by an arrest of growth and development late in the first larval stage. Apoptotic corpses, which are apparently the result of normal programmed cell death, persist in the arrested larvae. In genetic mosaics, an additional defect becomes evident upon examination with Nomarski optics: cells that are genotypically mutant enlarge, and their cytoplasm becomes dimpled. Electron microscopy indicates that the dimpling reflects an accumulation of many enlarged lysosomes and autophagosomes. The mosaics demonstrate that the lethal mutation acts cell autonomously with respect to this vesicular abnormality and that there is a maternal effect with respect to the time of developmental arrest of mutant progeny. Cloning of the gene reveals that it is the only gene in C. elegans for isopentenyl-diphosphate isomerase, an enzyme that is important for the synthesis of lipophilic molecules, including farnesyl and geranyl diphosphates. ------------------- Key: 7219 Medline: 15716356 Authors: Poteryaev D;Squirrell JM;Campbell JM;White JG;Spang A Title: Involvement of the actin cytoskeleton and homotypic membrane fusion in ER dynamics in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 16: 2139-2153 2005 Type: ARTICLE Genes: arf-1 cdk-1 dnj-10 hsp-1 hsp-3 hsp-4 inx-9 nmy-2 nsf-1 par-2 par-3 par-6 rab-1 ran-1 sec-23 ufd-1 Abstract: The endoplasmic reticulum (ER) is the major intracellular membrane system. The ER is essential for protein and lipid biosynthesis, transport of proteins along the secretory pathway, and calcium storage. Here, we describe our investigations into the dynamics and regulation of the ER in the early Caenorhabditis elegans embryo. Using a GFP fusion to the ER-resident signal pepticlase SP12, we observed the morphological transitions of the ER through fertilization and the early cell-cycles in living embryos. These transitions were tightly coordinated with the division cycle: upon onset of mitosis, the ER formed structured sheets that redispersed at the initiation of cleavage. Although microtubules were not required for the transition of the ER between these different states, the actin cytoskeleton facilitated the dispersal of the ER at the end of mitosis. The ER had an asymmetric distribution in the early embryo, which was dependent on the establishment of polarity by the PAR proteins. The small GTPase ARF-1 played an essential role in the ER dynamics, although this function appeared to be unrelated to the role of ARF-1 in vesicular traffic. In addition, the ER-resident heat shock protein BiP and a homologue of the AAA ATPase Cdc48/p97 were found to be crucial for the ER transitions. Both proteins have been implicated in homotypic ER membrane fusion. We provide evidence that homotypic membrane fusion is required to form the sheet structure in the early ------------------- Key: 7220 Medline: 15826655 Authors: Ayala YM;Pantano S;D'Ambrogio A;Buratti E;Brindisi A;Marchetti C;Romano M;Baralle FE Title: Human, Drosophila, and C. elegans TDP43: nucleic acid binding properties and splicing regulatory function. Citation: Journal of Molecular Biology 348: 575-588 2005 Type: ARTICLE Genes: Abstract: TAR DNA binding protein (TDP43), a highly conserved heterogeneous nuclear ribonucleoprotein, was found to down-regulate splicing of the exon 9 cystic fibrosis transmembrane conductance regulator (CFTR) through specific binding to a UG-rich polymorphic region upstream of the 3' splice site. Despite the emergence of new information regarding the protein's nuclear localization and splicing regulatory activity, TDP43's role in cells remains elusive. To investigate the function of human TDP43 and its homologues, we cloned and characterized the proteins from Drosophila melanogaster and Caenorhabditis elegans. The proteins from human, fly, and worm show striking similarities in their nucleic acid binding specificity. We found that residues at two different positions, which show a strong conservation among TDP43 family members, are linked to the tight recognition of the target sequence. Our three-dimensional model of TDP43 in complex with a (UG)(m) sequence predicts that these residues make amino acid side-chain to base contacts. Moreover, our results suggest that Drosophila TDP43 is comparable to human TDP43 in regulating exon splicing. On the other hand, C. elegans TDP43 has no effect on exon recognition. TDP43 from C. elegans lacks the glycine-rich domain found at the carboxy terminus of the other two homologues. Mutants of human and fly TDP43 devoid of the C-terminal domain are likewise unable to affect splicing. Our studies suggest that the glycine-rich domain is essential for splicing regulation by human and fly TDP43. ------------------- Key: 7221 Medline: 15849720 Authors: Thompson G;de Pomerai DI Title: Toxicity of short-chain alcohols to the nematode Caenorhabditis elegans: a comparison of endpoints. Citation: Journal of Biochemical & Molecular Toxicology 19: 87-95 Type: ARTICLE Genes: Abstract: The toxicities of 4 short-chain alcohols-namely methanol, ethanol, iso-propanol and isobutanol-were compared in the nematode Caenorhabditis elegans using several different ecotoxicological endpoints. Range-finding tests were conducted using transgenic PC161 worms carrying a double reporter construct (GFP plus lacZ) linked to the stress-inducible hsp16-1 promoter. These tests showed little response from the GFP reporter, but gave good dose-response curves for the lacZ reporter-showing clear induction at 0.5% v/v ethanol in an overnight assay, but only at 4% in a shorter 6-h assay. Comparison of the short-term dose-response curves shows a confusing pattern of differences between the four alcohols tested, although dose-dependence is evident across at least part of the concentration range. Feeding inhibition assays are somewhat inconclusive with regard to alcohol type, although iso-butanol and iso-propanol appear more toxic than ethanol, while methanol is least toxic. To resolve some of the remaining ambiguities, we also used a fecundity assay to show that iso-propanol is more toxic than ethanol, and a lethality assay to show that iso-butanol is more toxic than iso-propanol. Most of the endpoints studied are consistent with the following order of toxicity: iso-butanol iso-propanol ethanol methanol. ------------------- Key: 7222 Medline: 15780968 Authors: Haag ES;Ackerman AD Title: Intraspecific variation in fem-3 and tra-2, two rapidly coevolving nematode sex-determining genes. Citation: Gene 349: 35-42 2005 Type: ARTICLE Genes: fem-3 tra-2 Abstract: The sex determination gene fem-3 encodes one of the most divergent proteins yet described in the terrestrial nematode Caenorhabditis. Despite this rapid sequence change, however, FEM-3 is essential for male development in the three species surveyed thus far. It also participates in conserved protein-protein complexes with the transmembrane receptor TRA-2 and the phosphatase FEM-2 in these species. These interactions show strong species specificity, indicating that conserved residues are not sufficient for function and that compensatory evolution between binding partners is important. To shed further light on the nature of this coevolution, and to discern the extent of amino acid polymorphism allowed in FEM-3 and the domain of TRA-2 that binds it, we have examined intraspecific variation in the gonochoristic species Caenorhabditis remanei. Ten new complete Cr-fem-3 alleles from three regions of the United States are described. We also obtained sequences for the FEM-3-binding domain of TRA-2 for 9 of the same strains. These alleles were compared with each other, with the European founder alleles, and with the orthologous sequences from the congeners Caenorhabditis elegans and C. briggsae. We find that FEM-3 harbors abundant amino acid polymorphisms along its entire length. The majority (but not all) of these occur in nonconserved residues, and in at least one domain there is evidence for diversifying selection. The FEM-3-binding domain of TRA-2 is less polymorphic than FEM-3. Amino acids neither polymorphic nor conserved between species are candidates for residues mediating species-specific interaction of FEM-3 with its binding ------------------- Key: 7223 Medline: 15855309 Authors: Porte D;Baskin DG;Schwartz MW Title: Perspectives in diabetes - insulin signaling in the central nervous system - a critical role in metabolic homeostasis and disease from C. elegans to humans. Citation: Diabetes 54: 1264-1276 2005 Type: REVIEW Genes: Abstract: Insulin and its signaling systems are implicated in both central and peripheral mechanisms governing the ingestion, distribution, metabolism, and storage of nutrients in organisms ranging from worms to humans. Input from the environment regarding the availability and type of nutrients is sensed and integrated with humoral information (provided in part by insulin) regarding the sufficiency of body fat stores. In response to these afferent inputs, neuronal pathways are activated that influence energy flux and nutrient metabolism in the body and ensure reproductive competency. Growing evidence supports the hypothesis that reduced central nervous system insulin signaling from either defective secretion or action contributes to the pathogenesis of common metabolic disorders, including diabetes and obesity, and may therefore help to explain the close association between these two disorders. These considerations implicate insulin action in the brain, an organ previously considered to be insulin independent, as a key determinant of both glucose and energy homeostasis. ------------------- Key: 7224 Medline: Authors: Henderson ST;Johnson TE Title: daf-16 integrates developmental and environmental inputs to mediate aging in the nematode Caenorhabditis elegans. Citation: Current Biology 15: 690- 2005 Type: CORRECT Genes: daf-16 Abstract: ------------------- Key: 7225 Medline: 15823525 Authors: Kontani K;Rothman JH Title: Cell fusion: EFF is enough. Citation: Current Biology 15: R252-R254 2005 Type: REVIEW Genes: eff-1 Abstract: Developmentally programmed cell-cell fusion in Caenorhabditis elegans requires the EFF-1 protein, which is sufficient to cause normally non-fusing cells to fuse. EFF-1 localizes to fusion-fated membranes, implicating it as a direct fusogen. ------------------- Key: 7226 Medline: 15850386 Authors: Robin G;DeBonis S;Dornier A;Cappello G;Ebel C;Wade RH;Thierry-Mieg D;Kozielski F Title: Essential kinesins: characterization of Caenorhabditis elegans KLP-15. Citation: Biochemistry 44: 6526-6536 2005 Type: ARTICLE Genes: klp-15 Abstract: Kinesins form a superfamily of molecular motors involved in cell division and intracellular transport. Twenty kinesins have been found in the Caenorhabditis elegans genome, and four of these belong to the kinesin-14 subfamily, i.e., kinesins with C-terminal motor domains. Three of these kinesin-14s, KLP-15, KLP-16, and KLP-17, form a distinct subgroup in which KLP-15 and KLP-16 are more than 90% identical and appear to be related by a relatively recent gene duplication. They are essential for meiotic spindle organization and chromosome segregation, and are mostly expressed in the germline. With 587 amino acids each, they are among the smallest kinesins known. Using bacterially expressed KLP-15 constructs with different length extensions preceding the motor domain, we have determined in vitro the following characteristic properties: ATPase activity, microtubule binding, oligomeric state, microtubule gliding activity, and direction of movement. The constructs exhibit a monomer-dimer equilibrium that depends on the length of the predicted alpha-helical coiled-coil region preceding the motor domain. The longest construct with the complete coiled-coil domain is a stable dimer, and the shortest construct with only seven amino acids preceding the motor domain is a monomer. In microtubule gliding assays, the monomer is immobile whereas the fully dimeric KLP-15 construct supports gliding at 2.3 mu m/min and moves toward microtubule minus ends, like other members of the kinesin-14 subfamily studied to date. ------------------- Key: 7227 Medline: 15865318 Authors: Hasegawa K;Saigusa T;Tamai Y Title: Caenorhabditis elegans opens up new insights into circadian clock mechanisms. Citation: Chronobiology International 22: 1-19 2005 Type: REVIEW Genes: Abstract: The roundworm, Caenorhabditis elegans, is known to carry homologues of clock genes such as per (=period) and tim (=timeless), which constitute the core of the circadian clock in Drosophila and mammals: lin-42 and tim-1. Analyses using WormBase (C. elegans gene database) have identified with relatively high identity analogous of the clock genes recognized in Drosophila and mammals, with the notable exception of cry (= cryptochrome), which is lacking in C. elegans. All of these C. elegans cognates of the clock genes appear to belong to members of the PAS-superfamily and to participate in development or responsiveness to the environment but apparently are not involved in the C. elegans circadian clock. Nevertheless, C. elegans exhibits convincing circadian rhythms in locomotor behavior in the adult stage and in resistance to hyperosmotic stress in starved larvae (L1) after hatching, indicating that it has a circadian clock with a core design entirely different from that of Drosophila and mammals. Here two possibilities are considered. First, the core of the C. elegans circadian clock includes transcriptional/translational feedback loops between genes and their protein products that arc entirely different from those of Drosophila and mammals. Second, a more basic principle such as homeostasis governs the circadian cellular physiology, and was established primarily to minimize the accumulation of DNA damage in response to an environment cycling at 24 h intervals. ------------------- Key: 7228 Medline: 15817227 Authors: Walstrom KM;Schmidt D;Bean CJ:Kelly WG Title: RNA helicase A is important for germline transcriptional control, proliferation, and meiosis in C. elegans. Citation: Mechanisms of Development 122: 707-720 2005 Type: ARTICLE Genes: fem-1 glp-4 rha-1 mnDf69 Abstract: RNA helicase A (RHA) is a multifunctional protein with established roles in chromatin regulation. The protein is conserved in worms, Drosophila, and mammals, but its role in worms has not been previously studied. We found that a deletion mutant lacking rha-1 has a temperature-sensitive defect in germline transcriptional silencing, consistent with RHA-1 having a function in transcription regulation. Transcriptional desilencing in these rha-1(tm329) mutants was associated with a loss of lysine 9 methylation on histone H3 that is normally associated with silenced chromatin. Other histone modifications are also mis-localized in the germ cells in the mutants. These defects in histone modifications suggest that there is a general transcription regulation defect in the mutant worms that results in a temperature-sensitive sterile phenotype. At the restrictive temperature, the extent of germ cell mitoses is reduced, and the mutants are sterile due to defects in meiosis and gametogenesis. Our results suggest that RHA-1 is a conserved transcription regulation protein that controls germline proliferation and development in C. elegans. ------------------- Key: 7229 Medline: Authors: Paschinger K;Staudacher E;Stemmer U;Fabini G;Wilson IBH Title: Fucosyltransferase substrate specificity and the order of fucosylation in invertebrates. Citation: Glycobiology 15: 463-474 2005 Type: ARTICLE Genes: Abstract: Core alpha 1,6-fucosylation is a conserved feature of animal N-linked oligosaccharides being present in both invertebrates and vertebrates. To prove that the enzymatic basis for this modification is also evolutionarily conserved, cDNAs encoding the catalytic regions of the predicted Caenorhabditis elegans and Drosophila melanogaster homologs of vertebrate alpha 1,6-fucosyltransferases (E.C. 2.4.1.68) were engineered for expression in the yeast Pichia pastoris. Recombinant forms of both enzymes were found to display core fucosyltransferase activity as shown by a variety of methods. Unsubstituted nonreducing terminal GlcNAc residues appeared to be an obligatory feature of the substrate for the recombinant Caenorhabditis and Drosophila alpha 1,6-fucosyltransferases, as well as for native Caenorhabditis and Schistosoma mansoni core alpha 1,6-fucosyltransferases. On the other hand, these alpha 1,6-fucosyltransferases could not act on N-glycopeptides already carrying core alpha 1,3-fucose residues, whereas recombinant Drosophila and native Schistosoma core alpha 1,3-fucosyltransferases were able to use core alpha 1,6-fucosylated glycans as substrates. Lewis-type fucosylation was observed with native Schistosoma extracts and could take place after core alpha 1,3-fucosylation, whereas prior Lewis-type fucosylation precluded the action of the Schistosoma core alpha 1,3-fucosyltransferase. Overall, we conclude that the strict order of fucosylation events, previously determined for fucosyltransferases in crude extracts from insect cell lines (core alpha 1,6 before core alpha 1,3), also applies for recombinant Drosophila core alpha 1,3- and alpha ------------------- Key: 7230 Medline: Authors: Reisner K;Asikainen S;Vartiainen S;Wong G Title: Developmental and biological insights obtained from gene expression profiling of the nematode Caenorhabditis Citation: Current Genomics 6: 97-107 2005 Type: ARTICLE Genes: Abstract: ------------------- Key: 7231 Medline: Authors: Tamas I;Hodges E;Dessi P;Johnsen R;Vaz Gomes A Title: A combined approach exploring gene function based on worm-human orthology. Citation: BMC Genomics 6: 65- 2005 Type: ARTICLE Genes: rrf-3 Abstract: ------------------- Key: 7232 Medline: 15852004 Authors: Denver DR;Morris K;Streelman JT;Kim SK;Lynch M;Thomas WK Title: The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Citation: Nature Genetics 37: 544-548 2005 Type: ARTICLE Genes: Abstract: The evolutionary importance of gene-expression divergence is unclear: some studies suggest that it is an important mechanism for evolution by natural selection(1,2), whereas others claim that most between-species regulatory changes are neutral or nearly neutral(3). We examined global transcriptional divergence patterns in a set of Caenorhabditis elegans mutation-accumulation lines and natural isolate lines to provide insights into the evolutionary importance of transcriptional variation and to discriminate between the forces of mutation and natural selection in shaping the evolution of gene expression. We detected the effects of selection on transcriptional divergence patterns and characterized them with respect to coexpressed gene sets, chromosomal clustering of expression changes and functional gene categories. We directly compared observed transcriptional variation patterns in the mutation-accumulation and natural isolate lines to a neutral model of transcriptome evolution to show that strong stabilizing selection dominates the evolution of transcriptional change for thousands of C. elegans expressed sequences. ------------------- Key: 7233 Medline: 15858590 Authors: Gibson G Title: Mutation accumulation of the transcriptome. Citation: Nature Genetics 37: 458-460 2005 Type: REVIEW Genes: Abstract: A microarray-based study of the nematode Caenorhabditis elegans offers a first glimpse of the effect of mutation accumulation on transcriptional variation. One major conclusion is that stabilizing selection must constrain the divergence of gene expression profiles in natural populations. ------------------- Key: 7234 Medline: 15734735 Authors: Oskouian B;Mendel J;Shocron E;Lee MA;Fyrst H;Saba JD Title: Regulation of sphingosine-1-phosphate lyase gene expression by members of the GATA family of transcription factors. Citation: Journal of Biological Chemistry 280: 18403-18410 2005 Type: ARTICLE Genes: acn-1 elt-2 Abstract: Sphingosine-1-phosphate is a bioactive sphingolipid that regulates proliferation, differentiation, migration, and apoptosis. Sphingosine-1-phosphate is irreversibly degraded by the highly conserved enzyme sphingosine-1-phosphate lyase. Recent studies have suggested that sphingosine-1-phosphate lyase expression affects animal development and cell fate decisions. Despite its crucial role, mechanisms affecting expression of sphingosine-1- phosphate lyase remain poorly understood. In this study, regulation of sphingosine-1- phosphate lyase gene expression was investigated in Caenorhabditis elegans, where lyase expression is spatially restricted to cells of the developing and adult gut and is essential for normal development. Deletion analysis and generation of transgenic worms combined with fluorescence microscopy identified a 350-nucleotide sequence upstream of the ATG start site necessary for maximal lyase expression in adult worms. Site-specific mutagenesis of a GATA transcription factor-binding motif in the promoter led to loss of reporter expression. Knockdown of the gut-specific GATA transcription factor ELT-2 by RNA interference similarly led to loss of reporter expression. ELT-2 interacted with the GATA factor-binding motif in vitro and was also capable of driving expression of a Caenorhabditis elegans lyase promoter-beta-galactosidase reporter in a heterologous yeast system. These studies demonstrate that ELT-2 regulates sphingosine-1- phosphate lyase expression in vivo. Additionally, we demonstrate that the human sphingosine-1-phosphate lyase gene is regulated by a GATA transcription factor. Overexpression of GATA-4 led to both an increase in activity of a reporter gene as well as an increase in endogenous sphingosine-1- phosphate lyase protein. ------------------- Key: 7235 Medline: 15837805 Authors: Halaschek-Wiener J;Khattra JS;McKay S;Pouzyrev A;Stott JM;Yang GS;Holt RA;Jones SJM;Marra MA;Brooks-Wilson AR;Riddle DL Title: Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression. Citation: Genome Research 15: 603-615 2005 Type: ARTICLE Genes: act-1 act-2 act-3 act-4 act-5 asp-1 asp-2 asp-3 asp-4 asp-5 asp-6 cct-1 cct-4 cct-6 cey-1 cey-2 cey-3 cey-4 col-8 col-19 col-55 col-84 col-95 col-119 col-122 col-124 col-140 col-141 col-143 col-159 col-160 col-178 col-179 col-183 col-184 daf-2 dnj-29 eft-2 eft-3 eft-4 fat-2 gst-1 gst-7 hda-1 his-24 his-41 his-62 his-72 hsp-1 hsp-3 hsp-6 hsp-12.3 hsp-12.6 hsp-16.1 hsp-16.2 hsp-16.11 hsp-16.41 hsp-16.48 hsp-16.49 mcm-2 mcm-3 mcm-4 mcm-5 mcm-6 msp-3 msp-31 msp-33 msp-38 msp-40 msp-45 msp-64 msp-152 mtl-1 nlp-27 nlp-28 nlp-29 nlp-31 pqn-28 puf-3 puf-5 puf-6 puf-7 puf-10 rpa-1 rpl-2 rpl-4 rpl-8 rpl-10 rpl-14 rpl-17 rpl-19 rpl-20 rpl-22 rpl-23 rpl-29 rpl-27 rpl-30 rpl-31 rpl-35 rpl-43 rpn-2 rpn-8 rpn-9 rpn-11 rps-0 rps-2 rps-7 rps-8 rps-11 rps-13 rps-17 rps-22 rps-27 sip-1 sod-1 ssp-1 ssp-10 ssp-14 ssq-1 ssq-2 ssq-3 ssq-4 tba-1 tbb-1 tbb-2 tbg-1 tts-1 vit-1 vit-2 vit-3 vit-4 vit-5 vit-6 Abstract: We have identified longevity-associated genes in a long-lived Caenorhabdids elegans daf-2 (insulin/lGF receptor) mutant using serial analysis of gene expression (SAGE), a method that efficiently quantifies large numbers of mRNA transcripts by sequencing short tags. Reduction of daf-2 signaling in these Mutant worms leads to a doubling in mean lifespan. We prepared C elegans SAGE libraries from 1, 6, and 10-d-old adult daf-2 and from 1 and 6-d-old control adults. Differences in gene expression between daf-2 libraries representing different ages and between daf-2 versus control libraries identified not only single genes, but whole gene fainilies that were differentially regulated. These gene families are part of major metabolic pathways including lipid, protein, and energy metabolism, stress response, and cell structure. Similar expression patterns of closely related family members emphasize the importance of these genes in aging-related processes. Global analysis of metabolism-associated genes showed hypometabolic features in mid-life daf-2 mutants that diminish with advanced age. Comparison Of Our results to recent microarray Studies highlights sets of overlapping genes that are highly conserved throughout evolution and thus represent strong candidate genes that control aging ------------------- Key: 7236 Medline: 15854912 Authors: Cheeseman IM;MacLeod I;Yates JR;Oegema K;Desai A Title: The CENP-F-like proteins HCP-1 and HCP-2 target CLASP to kinetochores to mediate chromosome segregation. Citation: Current Biology 15: 771-777 2005 Type: ARTICLE Genes: cls-2 gpr-1 gpr-2 hcp-1 hcp-2 Abstract: During chromosome segregation, kinetochores form dynamic connections with spindle microtubules. In vertebrates, these attachments require the activities of a number of outer kinetochore proteins, including CENP-F [1, 2] and the widely conserved microtubule-associated protein CLASP [3]. Here, we investigate the functional relationship between HCP-1/2, two redundant CENP-F-like proteins, and CLASP(CLS-2) in Caenorhabditis elegans. HCP-1/2 and CLASP(CLS-2) localize transiently to mitotic C. elegans kinetochores with nearly identical kinetic profiles, and biochemical purifications demonstrate that they also associate physically. In embryos depleted of HCP-1/2, CLASP(CLS-2) no longer localizes to chromosomes, whereas CLASP(CLS-2) depletion does not prevent HCP-1/2 targeting. Consistent with the localization dependency and biochemical association, depletion of HCP-1/2 or CLASP(CLS-2) resulted in virtually identical defects in mitotic chromosome segregation characterized by a failure of sister-chromatid biorientation. This phenotype could be partially suppressed by disrupting the astral forces that pull spindle poles apart in the 1 cell embryo, indicating that CLASP(CLS-2) is required for biorientation when chromosome-spindle attachments are subjected to poleward force. Our results establish that the key role of HCP-1/2 is to target CLASP(CLS-2) to kinetochores, and they support the recently proposed model that CLASP functions to promote the ------------------- Key: 7237 Medline: 15854913 Authors: Guse A;Mishima M;Glotzer M Title: Phosphorylation of ZEN-4/MKLP1 by aurora B regulates completion of cytokinesis. Citation: Current Biology 15: 778-786 2005 Type: ARTICLE Genes: zen-4 Abstract: The central spindle regulates the formation and positioning of the contractile ring and is essential for completion of cytokinesis [1]. Central spindle assembly begins in early anaphase with the bundling of overlapping, antiparallel, nonkinetochore microtubules [2, 3], and these bundles become compacted and mature into the midbody. Prominent components of the central spindle include aurora B kinase and centralspindlin, a complex containing a Kinesin-6 protein (ZEN-4/MKLP1) and a Rho family GAP (CYK4/MgcRacGAP) that is essential for central spindle assembly [4]. Centralspindlin localization depends on aurora B kinase [5]. Aurora B concentrates in the midbody and persists between daughter cells. Here, we show that in C. elegans embryos and in cultured human cells, respectively, ZEN-4 and MKLP1 are phosphorylated by aurora B in vitro and in vivo on conserved C-terminal serine residues. In C. elegans embryos, a nonphosphorylatable mutant of ZEN-4 localizes properly but does not efficiently support completion of cytokinesis. In mammalian cells, an inhibitor of aurora kinase acutely attenuates phosphorylation of MKLP1. Inhibition of aurora B in late anaphase causes cytokinesis defects without disrupting the central spindle. These data indicate a conserved role for aurora-B-mediated phosphorylation of ZEN-4/MKLP1 in the completion of ------------------- Key: 7238 Medline: 16054058 Authors: Antebi A Title: The prepared mind of the worm. Citation: Cell Metabolism 1: 157-158 2005 Type: REVIEW Genes: Abstract: In C. elegans, dauer pheromone is an indicator of population density and influences pathways that regulate metabolism, development, and aging. In a recent publication in Nature, Paik and coworkers (Jeong et al., 2005) show the purified substance to be a pyran ring conjugated to heptanoic acid, setting the stage for dissecting downstream signaling pathways. ------------------- Key: 7239 Medline: Authors: Parker JA;Arango M;Abderrahmane S;Lambert E;Tourette C;Catoire H;Neri C Title: Resveratrol rescues mutant polyglutamine cytotoxicity in nematode and mammalian neurons. Citation: Nature Genetics 37: 555- 2005 Type: CORRECT Genes: Abstract: ------------------- Key: 7240 Medline: Authors: Baugh LR;Wen JC;Hill AA;Slonim DK;Brown EL;Hunter CP Title: Synthetic lethal analysis of Caenorhabditis elegans posterior embryonic patterning genes identifies conserved genetic interactions. Citation: Genome Biology 6: 80-87 2005 Type: ARTICLE Genes: aqp-2 ceh-40 cwn-1 elt-3 hlh-1 hnd-1 lin-26 mab-21 nhr-25 nob-1 spp-10 tbx-8 tbx-9 unc-62 unc-120 vab-7 Abstract: ------------------- Key: 7241 Medline: Authors: Geng W;Cosman P;Schafer WR Title: Detecting attached worm eggs using deformable template matching. Citation: Proceedings of the Seventh IASTED International Conference on Computer Graphics and Imaging : 309-314 2004 Type: ARTICLE Genes: Abstract: ------------------- Key: 7242 Medline: 15649349 Authors: Henson PM Title: Engulfment: ingestion and migration with Rac, Rho and TRIO. Citation: Current Biology 15: R29-R30 2005 Type: REVIEW Genes: ced-2 ced-5 ced-10 ced-12 mig-2 unc-73 Abstract: Apoptotic cells are removed from tissues by uptake mechanisms that depend on the GTPase Rac (CED-10 in C. elegans), which is activated by DOCK180/CED-5 in a trimolecular complex with ELMO/CED-12 and CrkII/CED-2. A study now identifies upstream components of this pathway in both worms and mammalian cells involving yet another GTPase, RhoG/MIG-2, and its activator TRIO/UNC-73. ------------------- Key: 7243 Medline: 15840448 Authors: Fay DS Title: The cell cycle and development: lessons from C. elegans. Citation: Seminars in Cell & Developmental Biology 16: 397-406 2005 Type: REVIEW Genes: cdc-25.1 cep-1 cki-1 cki-2 cul-1 cul-2 cul-3 cul-4 cye-1 dpl-1 efl-1 fzr-1 hyp-7 lin-9 lin-14 lin-23 lin-35 lon-1 ncc-1 Abstract: The invariant developmental cell lineage of Caenorhabditis elegans (and other similar nematodes) provides one of the best examples of how cell division patterns can be precisely coordinated with cell fates. Although the field has made substantial progress towards elucidating the many factors that control the acquisition of individual cell or tissue-specific identities, the interplay between these determinants and core regulators of the cell cycle is just beginning to be understood. This review provides an overview of the known mechanisms that govern somatic cell growth, proliferation, and differentiation in C. elegans. In particular, I will focus on those studies that have uncovered novel genes or mechanisms, and which may enhance our understanding of corresponding processes in other organisms. ------------------- Key: 7244 Medline: Authors: Saffih-Hdadi K;Bruckler L;Amichot M;Belzunces L Title: Modeling impact of parathion and its metabolite paraoxon on the nematode Caenorhabditis elegans. Citation: Environmental Toxicology & Chemistry 24: 1387-1394 2005 Type: ARTICLE Genes: Abstract: Parathion is an insecticide of a group of highly toxic organophosphorous compounds. In vivo, it is activated to the toxic metabolite paraoxon. Laboratory experiments have shown that a single relationship between the variable (concentration X time of application) and the percentage of paralyzed nematodes is relevant. Aqueous (0.01 M CaCl2) extracts from soil that had received a dose of parathion as used in practice during an incubation experiment had no effect on nematodes, because sorption and biodegradation of the pesticide decreased the pesticide concentration in the soluble phase. To predict the toxicological effects of parathion and paraoxon on nematodes under various soil conditions during a simulation period of 20 d, we used a model predicting the concentrations of parathion and paraoxon over time in the soil liquid phase. In this model, sorption and biodegradation of both parathion and paraoxon were taken into account, and the results indicated that sorption effects were dominant and determined the differential toxicological risks between soils. Variable effects were predicted for short times (typically < 5 d), and critical toxicological conditions were predicted for longer duration (typically > 10-15 d), in all cases. ------------------- Key: 7245 Medline: 15772130 Authors: Fukushige T;Krause M Title: The myogenic potency of HLH-1 reveals wide-spread develomental plasticity in early C. elegans embryos. Citation: Development 132: 1795-1805 2005 Type: ARTICLE Genes: hlh-1 lit-1 mex-1 mex-3 pal-1 pop-1 skn-1 wrm-1 Abstract: In vertebrates, striated muscle development depends on both the expression of members of the myogenic regulatory factor family (MRFs) and on extrinsic cellular cues, including Wnt signaling. The 81 embryonically born body wall muscle cells in C elegans are comparable to the striated muscle of vertebrates. These muscle cells all express the gene hlh-1, encoding HLH-1 (CeMyoD) which is the only MRF-related factor in the nematode. However, genetic studies have shown that body wall muscle development occurs in the absence of HLH-1 activity, making the role of this factor in nematode myogenesis unclear. By ectopically expressing hlh-1 in early blastomeres of the C. elegans embryo, we show that CeMyoD is a bona fide MRF that can convert almost all cells to a muscle-like fate, regardless of their lineage of origin. The window during which ectopic HLH-1 can function is surprisingly broad, spanning the first 3 hours of development when cell lineages are normally established and non-muscle cell fate markers begin to be expressed. We have begun to explore the maternal factors controlling zygotic hlh-1 expression. We find that the Caudal-related homeobox factor PAL-1 can activate hlh-1 in blastomeres that either lack POP-1/TCF or that have down-regulated POP-1/TCF in response to Wnt/MAP kinase signaling. The potent myogenic activity of HLH-1 highlights the remarkable developmental plasticity of early C. elegans blastomeres and reveals the evolutionary conservation of MyoD function. ------------------- Key: 7246 Medline: 15772128 Authors: Baugh LR;Hill AA;Claggett JM;Hill-Harfe K;Wen JC;Slonim DK;Brown EL;Hunter CP Title: The homeodomain protein PAL-1 specifies a lineage-specific regulatory network in the C. elegans embryo. Citation: Development 132: 1843-1854 2005 Type: ARTICLE Genes: ceh-16 cwn-1 elt-1 elt-3 end-1 end-3 gcy-11 ges-1 hlh-1 hmg-3 hmg-5 hnd-1 lin-26 mab-21 med-1 med-2 mex-3 nhr-25 nhr-60 nob-1 nob-2 pal-1 pie-1 plp-1 ptr-2 ptr-23 skn-1 spp-10 sqt-3 tbx-8 tbx-9 unc-120 vab-7 wrt-5 Abstract: Maternal and zygotic activities of the homeodomain protein PAL-1 specify the identity and maintain the development of the multipotent C blastomere lineage in the C. elegans embryo. To identify PAL-1 regulatory target genes, we used microarrays to compare transcript abundance in wild-type embryos with mutant embryos lacking a C blastomere and to mutant embryos with extra C blastomeres. pal-1-dependent C-lineage expression was verified for select candidate target genes by reporter gene analysis, though many of the target genes are expressed in additional lineages as well. The set of validated target genes includes 12 transcription factors, an uncharacterized wingless ligand and five uncharacterized genes. Phenotypic analysis demonstrates that the identified PAL-1 target genes affect specification, differentiation and morphogenesis of C-lineage cells. In particular, we show that cell fate-specific genes (or tissue identity genes) and a posterior HOX gene are activated in lineage-specific fashion. Transcription of targets is initiated in four temporal phases, which together with their spatial expression patterns leads to a model of the regulatory ------------------- Key: 7247 Medline: 15790964 Authors: Yoda A;Kouike H;Okano H;Sawa H Title: Components of the transcriptional Mediator complex are required for asymmetrical cell division in C. elegans. Citation: Development 132: 1885-1893 2005 Type: ARTICLE Genes: bar-1 dpy-22 let-19 let-425 lin-17 lin-39 pal-1 sop-1 sur-2 tlp-1 mnDf46 Abstract: Asymmetric cell division is a fundamental process that produces cellular diversity during development. In C elegans, the Wnt signaling pathway regulates the asymmetric divisions of a number of cells including the T blast cell. We found that the let-19 and dpy-22 mutants have defects in their T-cell lineage, and lineage analyses showed that the defects were caused by disruption in the asymmetry of the T-cell division. We found that let-19 and dpy-22 encode homologs of the human proteins MED13/TRAP240 and MED12/TRAP230, respectively, which are components of the Mediator complex. Mediator is a multicomponent complex that can regulate transcription by transducing the signals between activators and RNA polymerase in vitro. We also showed that LET-19 and DPY-22 form a complex in vivo with other components of Mediator, SUR-2/MED23 and LET-425/MED6. In the let-19 and dpy-22 mutants, tlp-1, which is normally expressed asymmetrically between the T-cell daughters through the function of the Wnt pathway, was expressed symmetrically in both daughter cells. Furthermore, we found that the let-19 and dpy-22 mutants were defective in the fusion of the Pn.p cell, a process that is regulated by bar-1/β-catenin. Ectopic cell fusion in bar-1 mutants was suppressed by the let-19 or dpy-22 mutations, while defective cell fusion in let-19 mutants was suppressed by lin-39/Hox mutations, suggesting that let-19 and dpy-22 repress the transcription of lin-39. These results suggest that LET-19 and DPY-22 in the Mediator complex repress the transcription of Wnt target genes. ------------------- Key: 7248 Medline: 15790967 Authors: Efimenko E;Bubb K;Mak HY;Holzman T;Leroux MR;Ruvkun G;Thomas JH;Swoboda P Title: Analysis of xbx genes in C. elegans. Citation: Development 132: 1923-1934 2005 Type: ARTICLE Genes: arl-3 aqp-2 bbs-1 bbs-2 bbs-5 bbs-7 bbs-8 che-2 che-11 che-13 daf-19 gpa-9 nhr-44 nud-1 odr-4 osm-1 osm-5 osm-6 srg-2 srh-74 sru-12 srx-54 str-1 str-13 str-44 str-144 tub-1 xbx-1 xbx-2 xbx-3 xbx-4 xbx-5 xbx-6 xbx-7 Abstract: Cilia and flagella are widespread eukaryotic subcellular components that are conserved from green algae to mammals. In different organisms they function in cell motility, movement of extracellular fluids and sensory reception. While the function and structural description of cilia and flagella are well established, there are many questions that remain unanswered. In particular, very little is known about the developmental mechanisms by which cilia are generated and shaped and how their components are assembled into functional machineries. To find genes involved in cilia development we used as a search tool a promoter motif, the X-box, which participates in the regulation of certain ciliary genes in the nematode Caenorhabditis elegans. By using a genome search approach for X-box promoter motif-containing genes (xbx genes) we identified a list of about 750 xbx genes (candidates). This list comprises some already known ciliary genes as well as new genes, many of which we hypothesize to be important for cilium structure and function. We derived a C elegans X-box consensus sequence by in vivo expression analysis. We found that xbx gene expression patterns were dependent on particular X-box nucleotide compositions and the distance from the respective gene start. We propose a model where DAF-19, the RFX-type transcription factor binding to the X-box, is responsible for the development of a ciliary module in C elegans, which includes genes for cilium structure, transport machinery, receptors and other ------------------- Key: 7249 Medline: 15790968 Authors: Melkman T;Sengupta P Title: Regulation of chemosensory and GABAergic motor neuron development by the C. elegans Aristaless/Arx homolog alr-1. Citation: Development 132: 1935-1949 2005 Type: ARTICLE Genes: alr-1 che-14 daf-6 flp-13 lin-11 odr-7 odr-10 ops-1 osm-6 sns-10 str-2 unc-25 unc-30 unc-47 unc-55 unc-130 Abstract: Mutations in the highly conserved Aristaless-related homeodomain protein ARX have been shown to underlie multiple forms of X-linked mental retardation. Arx knockout mice exhibit thinner cerebral cortices because of decreased neural precursor proliferation, and also exhibit defects in the differentiation and migration of GABAergic interneurons. However, the role of ARX in the observed behavioral and developmental abnormalities is unclear. The regulatory functions of individual homeodomain proteins and the networks in which they act are frequently highly conserved across species, although these networks may be deployed in different developmental contexts. In Drosophila, aristaless mutants exhibit defects in the development of terminal appendages, and Aristaless has been shown to function with the LIM-homeodomain protein LIM1 to regulate leg development. Here, we describe the role of the Aristaless/Arx homolog alr-1 in C. elegans. We show that alr-1 acts in a pathway with the LIM1 ortholog lin-11 to regulate the development of a subset of chemosensory neurons. Moreover, we demonstrate that the differentiation of a GABAergic motoneuron subtype is affected in alr-1 mutants, suggesting parallels with ARX functions in vertebrates. Investigating ALR-1 functions in C elegans may yield insights into the role of this important protein in neuronal development and the etiology of mental ------------------- Key: 7250 Medline: 15888078 Authors: Gravato-Nobre MJ;Hodgkin J Title: Caenorhabditis elegans as a model for innate immunity to pathogens. Citation: Cellular Microbiology 7: 741-751 2005 Type: REVIEW Genes: abf-1 abf-2 abf-3 abf-4 abf-5 abf-6 age-1 ced-3 ced-4 ced-9 cnc-2 cnc-4 daf-2 daf-4 daf-16 dbl-1 egl-1 jnk-1 kgb-1 lin-45 lys-1 lys-7 lys-8 mek-1 mek-2 mpk-1 nlp-29 nlp-31 nlp-33 nsy-1 nsy-2 pdk-1 phm-2 pmk-1 rab-1 sek-1 sma-2 sma-3 sma-4 sma-6 spp-1 srf-2 srf-3 srf-5 tir-1 tol-1 ttm-1 Abstract: The amenability of the nematode Caenorhabditis elegans for genetic analysis and other experimentation provides a powerful tool for studying host-pathogen interactions. Our current understanding of how C. elegans responds to pathogen challenges is in its infancy, but the discovery that the worm has inducible defence responses, which to some extent parallel those of other organisms, demonstrates the potential of this model organism for the study of innate immunity. Most progress in dissecting the C. elegans antimicrobial response has focused around signal transduction pathways and the expression of genes activated by the worm in response to microbial infections. ------------------- Key: 7251 Medline: 15866166 Authors: Kimura A;Onami S Title: Computer simulations and image processing reveal length-dependent pulling force as the primary mechanism for C. elegans male pronuclear migration. Citation: Developmental Cell 8: 765-775 2005 Type: ARTICLE Genes: dhc-1 par-3 zyg-1 zyg-9 Abstract: A male pronucleus migrates toward the center of an egg to reach the female pronucleus for zygote formation. This migration depends on microtubules growing from two centrosomes associated with the male pronucleus. Two mechanisms were previously proposed for this migration: a "pushing mechanism," which uses the pushing force resulting from microtubule polymerization, and a "pulling mechanism," which uses the length-dependent pulling force generated by minus-end-directed motors anchored throughout the cytoplasm. We combined two computer-assisted analyses to examine the relative contribution of these mechanisms to male pronuclear migration. Computer simulation revealed an intrinsic difference in migration behavior of the male pronucleus between the pushing and pulling mechanisms. In vivo measurements using image processing showed that the actual migration behavior in Caenorhabditis elegans confirms the pulling mechanism. A male pronucleus having a single centrosome migrated toward the single aster. We propose that the pulling mechanism is the primary mechanism for male pronuclear migration. ------------------- Key: 7252 Medline: 15866168 Authors: Kontani K;Moskowitz IPG;Rothman JH Title: Repression of cell-cell fusion by components of the C. elegans vacuolar ATPase complex. Citation: Developmental Cell 8: 787-794 2005 Type: ARTICLE Genes: eff-1 fus-1 vha-1 vha-2 eDf18 Abstract: Cell-cell fusion initiates fertilization, sculpts tissues during animal development, reprograms stem cells to new differentiated states, and may be a key step in cancer progression. While cell fusion is tightly regulated, the mechanisms that limit fusion to appropriate partners are unknown. Here, we report that the fus-1 gene is essential to repress fusion of epidermal cells in C. elegans: in severe fus-1 mutants, all epidermal cells, except the lateral seam cells, inappropriately fuse into a single large syncytium. This hyperfusion requires EFF-1, an integral membrane protein essential for fusion of epidermal cells into discrete syncytia. FUS-1 is localized to the apical plasma membrane in all epidermal cells potentiated to undergo fusion, whereas it is virtually undetectable in nonfusing seam cells. fus-1 encodes the e subunit of the vacuolar H+-ATPase (V-ATPase), and loss of other V-ATPase subunits also causes widespread hyperfusion. These findings raise the possibility of manipulating cell fusion by altering V-ATPase activity. ------------------- Key: 7253 Medline: Authors: Novillo A;Won SJ;Li C;Callard IP Title: Changes in nuclear receptor and vitellogenin gene expression in response to steroids and heavy metal in Caenorhabditis elegans. Citation: Integrative and Comparative Biology 45: 61-71 2005 Type: ARTICLE Genes: cdr-1 dpl-1 gst-4 hsp-4 mes-4 mtl-2 nhr-12 nhr-35 nhr-47 nhr-59 nhr-63 nhr-66 nhr-68 nhr-69 nhr-94 nhr-105 pos-1 ptr-2 sip-1 unc-55 vit-2 vit-3 vit-4 vit-5 Abstract: To gain basic understanding of the reproductive and developmental effects of endocrine disrupting chemicals in invertebrates, we have used C. elegans as an animal model. The completion of the C elegans genome sequence brings to bear microarray analysis as a tool for these studies. We previously showed that the C. elegans genome was responsive to vertebrate steroid hormones, and changes in gene expression of traditional biomarkers used in environmental studies were detected; i.e., vitellogenin (vtg), cytochrome P450 (cyp450), glutathione-S-transferase (gst) and heat shock proteins (hsp). The data were interpreted to suggest that exogenous lipophilic compounds can be metabolized via cytochrome P450 proteins, and that the resulting metabolites can bind to members of the Nuclear Receptor (NR) class of proteins and regulate gene expression. In the present study, using DNA microarrays, we examined the pattern of gene expression after progesterone (10(-5), 10(-7) M), estradiol (10-5 M), cholesterol (10(-9) M) and cadmium (0.1, 1 and 10 μ M) exposure, with special attention to the members of NRs. Of approximately 284 NRs in C. elegans, expression of 25 NR genes (representing 9% of the total NRs in C elegans) was altered after exposure to steroids. Of note, each steroid activated or inhibited different subsets of NR genes, and only estradiol regulated NR genes implicated in neurogenesis. These results suggest that NRs respond to a variety of exogenous steroids, which regulate important metabolic and developmental pathways. The response of the C elegans genome to cholesterol and cadmium was analyzed in more detail. Cholesterol is a probable precursor to signaling molecules that may interact with NRs and we focused on expression of genes related to lipid metabolism (cyp450), transport and storage (Le., vitellogenin). Worms exposed to cadmium respond principally by activating the expression of genes encoding stress-responsive proteins, such as mtl-2 and cdr-1, and no significant changes in expression of NRs or vtg genes were observed. The possible implications of these results with regard to the evolution of steroid receptors, endocrine disruption and the role of vitellogenin as a lipid ------------------- Key: 7254 Medline: 15811859 Authors: Yanagi K;Mizuno T;Tsuyama T;Tada S;Iida Y;Sugimoto A;Eki T;Enomoto T;Hanaoka F Title: Caenorhabditis elegans geminin homologue participates in cell cycle regulation and germ line development. Citation: Journal of Biological Chemistry 280: 19689-19694 2005 Type: ARTICLE Genes: cdt-1 ceh-32 cul-4 gmn-1 mcm-6 nob-1 orc-2 Abstract: Cdt1 is an essential component for the assembly of a pre-replicative complex. Cdt1 activity is inhibited by geminin, which also participates in neural development and embryonic differentiation in many eukaryotes. Although Cdt1 homologues have been identified in organisms ranging from yeast to human, geminin homologues had not been described for Caenorhabditis elegans and fungi. Here, we identify the C. elegans geminin, GMN-1. Biochemical analysis reveals that GMN-1 associates with C. elegans CDT-1, the Hox protein NOB-1, and the Six protein CEH-32. GMN-1 inhibits not only the interaction between mouse Cdt1 and Mcm6 but also licensing activity in Xenopus egg extracts. RNA interference-mediated reduction of GMN-1 is associated with enlarged germ nuclei with aberrant nucleolar morphology, severely impaired gametogenesis, and chromosome bridging in intestinal cells. We conclude that the Cdt1-geminin system is conserved throughout metazoans and that geminin has evolved in these taxa to regulate proliferation and differentiation by directly interacting with Cdt1 and homeobox proteins. ------------------- Key: 7255 Medline: 15883196 Authors: Yang H;Mains PE;McNally FJ Title: Kinesin-1 mediates translocation of the meiotic spindle to the oocyte cortex through KCA-1, a novel cargo adapter. Citation: Journal of Cell Biology 169: 447-457 2005 Type: ARTICLE Genes: dhc-1 kca-1 klc-1 klc-2 mat-2 unc-116 Abstract: In animals, female meiotic spindles are attached to the egg cortex in a perpendicular orientation at anaphase to allow the selective disposal of three haploid chromosome sets into polar bodies. We have identified a complex of interacting Caenorhabditis elegans proteins that are involved in the earliest step in asymmetric positioning of anastral meiotic spindles, translocation to the cortex. This complex is composed of the kinesin-1 heavy chain orthologue, UNC-116, the kinesin light chain orthologues, KLC-1 and-2, and a novel cargo adaptor, KCA-1. Depletion of any of these subunits by RNA interference resulted in meiosis I metaphase spindles that remained stationary at a position several micrometers from the cell cortex during the time when wild- type spindles translocated to the cortex. After this prolonged stationary period, unc-116( RNAi) spindles moved to the cortex through a partially redundant mechanism that is dependent on the anaphase-promoting complex. This study thus reveals two sequential mechanisms for translocating anastral spindles ------------------- Key: 7256 Medline: Authors: Clouaire T;Roussigne M;Ecochard V;Mathe C;Amalric F;Girard JP Title: The THAP domain of THAP1 is a large C2CH module with zinc-dependent sequence-specific DNA-binding activity. Citation: Proceedings of the National Academy of Sciences USA 102: 6907-6912 2005 Type: ARTICLE Genes: cdc-14 ctb-1 him-17 lin-15 lin-36 Abstract: ------------------- Key: 7257 Medline: 15790806 Authors: Kim JK;Gabel HW;Kamath RS;Tewari M;Pasquinelli A;Rual JF;Kennedy S;Dybbs M;Bertin N;Kaplan JM;Vidal M;Ruvkun G Title: Functional genomic analysis of RNA interference in C. elegans. Citation: Science 308: 1164-1167 2005 Type: REVIEW Genes: aco-2 cdl-1 cpf-2 dcr-1 dpy-20 drh-1 eri-1 gfl-1 haf-4 hda-3 ima-3 imb-2 imb-5 kin-10 let-7 lin-5 mes-4 mom-2 mtk-1 mut-7 mut-16 ncl-1 npp-1 npp-9 npp-16 paa-1 ppp-1 pop-1 pqn-28 pqn-70 prp-21 ran-3 rba-1 rde-1 rde-4 rde-5 rnp-2 rpl-25.2 rrf-3 rsd-2 rsp-7 skr-1 smg-2 smg-5 smg-6 snr-7 spd-5 vha-11 zfp-1 Abstract: RNA interference (RNAi) of target genes is triggered by doubte-stranded RNAs (dsRNAs) processed by conserved nucleases and accessory factors. To identify the genetic components required for RNAi, we performed a genome-wide screen using an engineered RNAi sensor strain of Caenorhabditis elegans. The RNAi screen identified 90 genes. These included Piwi/PAZ proteins, DEAH helicases, RNA binding/processing factors, chromatin-associated factors, DNA recombination proteins, nuclear import/export factors, and 11 known components of the RNAi machinery. We demonstrate that some of these genes are also required for germline and somatic transgene silencing. Moreover, the physical interactions among these potential RNAi factors suggest links to other RNA-dependent gene regulatory pathways. ------------------- Key: 7258 Medline: Authors: Ansley SJ;Badano JL;Blacque OE;Hill J;Hoskins BE;Leitch CC;Kim JC;Ross AJ:Eicher ER;Teslovich TM;Mah AK;Johnsen RC;Cavender JC;Lewis RA;Leroux MR;Beales PL;Katsanis N Title: Basal body dysfunction is a likely cause of pleiotropic Bardet-Biedl syndrome. Citation: Nature 425: 628-633 2003 Type: ARTICLE Genes: bbs-1 bbs-2 bbs-7 bbs-8 che-2 daf-19 osm-1 osm-5 osm-6 Abstract: ------------------- Key: 7259 Medline: 15905404 Authors: Essers MA;de Vries-Smits LMM;Barker N;Polderman PE;Burgering BMT;Korswagen HC Title: Functional interaction between beta-catenin and FOXO in oxidative stress signaling. Citation: Science 308: 1181-1184 2005 Type: ARTICLE Genes: bar-1 daf-2 daf-16 pop-1 pry-1 sod-3 Abstract: beta-Catenin is a multifunctional protein that mediates Writ signaling by binding to members of the T cell factor (TCF) family of transcription factors. Here, we report an evolutionarily conserved interaction of beta-catenin with FOXO transcription factors, which are regulated by insulin and oxidative stress signaling. beta-Catenin binds directly to FOXO and enhances FOXO transcriptional activity in mammalian cells. In Caenorhabditis elegans, loss of the beta-catenin BAR-1 reduces the activity of the FOXO ortholog DAF-16 in dauer formation and life span. Association of beta-catenin with FOXO was enhanced in cells exposed to oxidative stress. Furthermore, BAR-1 was required for the oxidative stress-induced expression of the DAF-16 target gene sod-3 and for resistance to oxidative damage. These results demonstrate a role for β-catenin in regulating FOXO function that is particularly important under conditions of oxidative stress. ------------------- Key: 7260 Medline: 15944127 Authors: Francis MM;Evans SP;Jensen M;Madsen DM;Mancuso J;Norman KR;Maricq AV Title: The Ror receptor tyrosine kinase CAM-1 is required for the ACR-16-mediated synaptic transmission at the C. elegans neuromuscular junction. Citation: Neuron 46: 581-594 2005 Type: ARTICLE Genes: acr-2 acr-3 acr-5 acr-7 acr-11 acr-12 acr-15 acr-16 acr-17 acr-18 acr-19 acr-20 acr-22 acr-23 cam-1 unc-29 unc-49 unc-104 Abstract: Nicotinic (cholinergic) neurotransmission plays a critical role in the vertebrate nervous system, underlies nicotine addiction, and nicotinic receptor dysfunction leads to neurological disorders. The C. elegans neuromuscular junction (NMJ) shares many characteristics with neuronal synapses, including multiple classes of postsynaptic currents. Here, we identify two genes required for the major excitatory current found at the C. elegans NMJ: acr-16, which encodes a nicotinic AChR subunit homologous to the vertebrate alpha 7 subunit, and cam-1, which encodes a Ror receptor tyrosine kinase. acr-16 mutants lack fast cholinergic current at the NMJ and exhibit synthetic behavioral deficits with other known AChR mutants. In cam-1 mutants, ACR-16 is mislocalized and ACR-16-dependent currents are disrupted. The postsynaptic deficit in cam-1 mutants is accompanied by alterations in the distribution of cholinergic vesicles and associated synaptic proteins. We hypothesize that CAM-1 contributes to the localization or stabilization of postsynaptic ACR-16 receptors and presynaptic release sites. ------------------- Key: 7261 Medline: 15893731 Authors: Whetstine JR;Ceron J;Ladd B;Dufourcq P;Reinke V;Shi Y Title: Regulation of tissue-specific and extracellular matrix-related genes by a class I histone deacetylase. Citation: Molecular Cell 18: 483-490 2005 Type: ARTICLE Genes: asp-6 cli-2 clp-4 col-10 col-12 col-13 col-14 col-33 col-34 col-40 col-8192 col-93 col-94 col-97 col-101 col-103 col-107 col-113 col-118 col-126 col-133 col-144 col-145 col-146 col-154 col-166 col-159 col-160 col-166 cpr-4 dpy-13 hda-1 lec-6 lec-8 nas-30 nex-1 ram-2 taf-1 taf-6 Abstract: Class I histone deacetylases (HDACs) repress transcription by deacetylating histones and have been shown to play crucial roles in mouse, Xenopus, zebrafish, and C. elegans development. To identify the molecular networks regulated by a class I HDAC in a multicellular organism, we carried out a global gene expression profiling study using C. elegans embryos, and identified tissue-specific and extracellular matrix (ECM)-related genes as major HDA-1 targets. Ectopic expression of HDA-1 or C. elegans cystatin, an HDA-1 target identified from the microarray, significantly perturbed mammalian cell invasion. Similarly, RNAi depletion or overexpression of human HDAC-1 also affected cell migration. These findings suggest that HDA-1/HDAC-1 may play a critical, evolutionarily conserved role in regulating the extracellular microenvironment. Because human HDACs are targets for cancer therapy, these findings have significant implications in cancer treatment. ------------------- Key: 7262 Medline: 15520260 Authors: Stewart MK;Clark NL:Merrihew G;Galloway EM;Thomas JH Title: High genetic diversity in the chemoreceptor superfamily of Caenorhabditis elegans. Citation: Genetics 169: 1985-1996 2005 Type: ARTICLE Genes: srh-13 srh-14 srh-24 srh-83 srh-86 srh-95 srh-97 srh-99 srh-100 srh-101 srh-102 srh-103 srh-104 srh-108 srh-126 srh-143 srh-176 srh-192 srh-193 srh-194 srh-195 srh-196 srh-201 srh-202 srh-204 srh-220 srh-222 srh-223 srh-226 srh-227 srh-228 srh-237 srh- srh-249 srh-263 srh-272 srh-286 srh-287 srh-288 srh-289 srh-290 srh-291 srh-292 srh-307 srj-34 str-2 str-17 str-49 str-98 str-104 str-105 str-142 str-117 str-193 str-195 str-196 str-198 str-199 str-200 str-201 str-213 str-237 Abstract: We investigated genetic polymorphism in the Caenorhabditis elegans srh and str chemoreceptor gene families, each of which consists of similar to 300 genes encoding seven-pass G-protein-coupled receptors. Almost one-third of the genes in each family are annotated as pseudogenes because of apparent functional defects in N2, the sequenced wild-type strain of C. elegans. More than half of these "pseudogenes" have only one apparent defect, usually a stop codon or deletion. We sequenced the defective region for 31 such genes in 22 wild isolates of C. elegans. For 10 of the 31 genes, we found an apparently functional allele in one or more wild isolates, suggesting that these are not pseudogenes but instead functional genes with a defective allele in N2. We suggest the term "flatliner" to describe genes whose functional vs. pseudogene status is unclear. Investigations of flatliner gene positions, d(N)/d(S) ratios, and phylogenetic trees indicate that they are not readily distinguished from functional genes in N2. We also report striking heterogeneity in the frequency of other polymorphisms among these genes. Finally, the large majority of polymorphism was found in just two strains from geographically isolated islands, Hawaii and Madeira. This suggests that our sampling of wild diversity in C. elegans is narrow and that identification of additional strains from similarly isolated regions will greatly expand the diversity available for study. ------------------- Key: 7263 Medline: 15687263 Authors: Maciejowski J;Ahn JH;Cipriani PG;Killian DJ;Chaudhary AL;Lee JI;Voutev R;Johnsen RC;Baillie DL;Gunsalus KC;Fitch DHA;Hubbard EJA Title: Autosomal genes of autosomal/X-linked duplicated gene pairs and germ-line proliferation in Caenorhabditis elegans. Citation: Genetics 169: 1997-2011 2005 Type: ARTICLE Genes: eft-3 eft-4 glp-1 glp-3 pab-1 pab-2 rpl-11 rpl-11.1 rpl-11.2 rpl-24 rpl-24.1 rpl-24.2 rpl-25 rpl-25.1 rpl-25.2 rpl-31 rrf-1 qDf7 sDf50 sDf70 Abstract: We report molecular genetic studies of three genes involved in early germ-line proliferation in Caenorhabditis elegans that lend unexpected insight into a germ-line/soma functional separation of autosomal/X-linked duplicated gene pairs. In a genetic screen for germ-line proliferation-defective mutants, we identified mutations in rpl-11.1 (L11 protein of the large ribosomal subunit), pab-1 [a poly(A)-binding protein], and glp-3/eft-3 (an elongation factor 1-alpha homolog). All three are members of autosome/X gene pairs. Consistent with a germ-line-restricted function of rpl-11.1 and pab-1, mutations in these genes extend life span and cause gigantism. We further examined the RNAi phenotypes of the three sets of rpl genes (rpl-11, rpl-24, and rpl-25) and found that for the two rpl genes with autosomal/X-linked pairs (rpl-11 and rpl-25), zygotic germ-line function is carried by the autosomal copy. Available RNAi results for highly conserved autosomal/X-linked gene pairs suggest that other duplicated genes may follow a similar trend. The three rpl and the pab-1/2 duplications predate the divergence between C. elegans and C. briggsae, while the eft-3/4 duplication appears to have occurred in the lineage to C. elegans after it diverged front C. briggsae. The duplicated C. briggsae orthologs of the three C. elegans autosomal/X-linked gene pairs also display functional differences between paralogs. We present hypotheses for evolutionary, mechanisms that may underlie germ-line/soma subfunctionalization of duplicated genes, taking into account the role of X chromosome silencing in the germ line and analogous mammalian phenomena. ------------------- Key: 7264 Medline: Authors: Lissemore JL;Lackner LL;Fedoriw GD;De Stasio EA Title: Isolation of Caenorhabditis elegans genomic DNA and detection of deletions in the unc-93 gene using PCR. Citation: Biochemistry and Molecular Biology Education 33: 219-226 2005 Type: ARTICLE Genes: Abstract: ------------------- Key: 7265 Medline: 15781453 Authors: Shen C;Nettleton D;Jiang M;Kim SK;Powell-Coffman JA Title: Roles of the HIF-1 hypoxia-inducible factor during hypoxia response in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 280: 20580-20588 2005 Type: ARTICLE Genes: bli-3 cam-1 daf-2 daf-16 dpf-6 dpy-18 efk-1 egl-9 fmo-12 fmo-14 gei-7 hif-1 ins-22 inx-2 let-75 lin-42 mod-5 mxl-3 ncr-1 nhr-57 nhr-58 npc-1 npc-2 npp-6 phy-2 pqn-43 ptr-8 pyc-1 sca-1 smg-2 srv-22 str-257 tax-6 tbx-33 tbx-38 unc-14 vab-1 vhl-1 Abstract: The human hypoxia-inducible transcription factor HIF-1 is a critical regulator of cellular and systemic responses to low oxygen levels. When oxygen levels are high, the HIF-1alpha subunit is hydroxylated and is targeted for degradation by the von Hippel-Lindau tumor suppressor protein (VHL). This regulatory pathway is evolutionarily conserved, and the Caenorhabditis elegans hif-1 and vhl-1 genes encode homologs of the HIF-1alpha subunit and VHL. To understand and describe more fully the molecular basis for hypoxia response in this important genetic model system, we compared hypoxia-induced changes in mRNA expression in wild-type, hif-1-deficient, and vhl-1-deficient C. elegans using whole genome microarrays. These studies identified 110 hypoxia-regulated gene expression changes, 63 of which require hif-1 function. Mutation of vhl-1 abrogates most hif-1-dependent changes in mRNA expression. Genes regulated by C. elegans hif-1 have predicted functions in signal transduction, metabolism, transport, and extracellular matrix remodeling. We examined the in vivo requirement for 16 HIF-1 target genes and discovered that the phy-2 prolyl 4-hydroxylase alpha subunit is critical for survival in hypoxic conditions. Some HIF-1 target genes negatively regulate formation of stress-resistant dauer larvae. The microarray data presented herein also provide clear evidence for an HIF-1-independent pathway for hypoxia response, and this pathway regulates the expression of multiple heat shock proteins and several transcription ------------------- Key: 7266 Medline: 15924569 Authors: Gerstbrein B;Stamatas G;Kollias N;Driscoll M Title: In vivo spectrofluorimetry reveals endogenous biomarkers that report healthspan and dietary restriction in Caenorhabditis elegans. Citation: Aging Cell 4: 127-137 2005 Type: ARTICLE Genes: age-1 daf-2 daf-16 eat-2 gas-1 mev-1 unc-26 Abstract: Autofluorescent lipofuscin and advanced glycation end-products (age pigments) accumulate with age across phyla, yet little is understood about their formation under physiological conditions and their specific contributions to the aging process. We used in vivo spectrofluorimetry to quantitate autofluorescence in wild-type Caenorhabditis elegans and longevity mutants disrupted for distinct aspects of the aging process. In wild-type animals, age pigments increase into adulthood, accumulating slowly during the reproductive phase and more rapidly during the post-reproductive period. As in humans, insulin signaling influences age pigment accumulation - mutations that lower efficacy of insulin signaling and extend lifespan [daf-2(e1370) insulin receptor and age-1(hx546) PI3-kinase] dramatically lower age pigment accumulation; conversely, elimination of the insulin-inhibited DAF-16/FOXO transcription factor causes a huge increase in age pigment accumulation, supporting that the short-lived daf-16 null mutant is truly progeric. By contrast, mutations that increase mitochondrial reactive oxygen species production do not affect age pigment accumulation, challenging assumptions about the role of oxidative stress in generating these species in vivo. Dietary restriction reduces age pigment levels significantly and is associated with a unique spectral shift that might serve as a rapidly scored reporter of the dietary restricted state. Unexpectedly, genetically identical siblings that age poorly (as judged by decrepit locomotory capacity) have dramatically higher levels of age pigments than their same-aged siblings that appear to have aged more gracefully and move youthfully. Thus, high age pigment levels indicate a physiologically aged state rather than simply marking chronological time, and age pigments are valid reporters of ------------------- Key: 7267 Medline: 15936276 Authors: Patton A;Knuth S;Schaheen B;Dang H;Greenwald I;Fares H Title: Endocytosis function of a ligand-gated ion channel homolog in Caenorhabditis elegans. Citation: Current Biology 15: 1045-1050 2005 Type: ARTICLE Genes: cup-4 cup-5 nDf16 Abstract: Ligand-gated ion channels are transmembrane proteins that respond to a variety of transmitters, including acetylcholine, gamma-aminobutyric acid (GABA), glycine, and glutamate [1, 2]. These proteins play key roles in neurotransmission and are typically found in the nervous system and at neuromuscular junctions [3]. Recently, acetylcholine receptor family members also have been found in nonneuronal cells, including macrophages [4], keratinocytes [5], bronchial epithelial cells [5], and endothelial cells of arteries [6]. The function of these channels in nonneuronal cells in mammals remains to be elucidated, though it has been shown that the acetylcholine receptor alpha 7 subunit is required for acetylcholine-mediated inhibition of tumor necrosis factor release by activated macrophages [4]. We show that cup-4, a gene required for efficient endocytosis of fluids by C. elegans coelomocytes, encodes a protein that is homologous to ligand-gated ion channels, with the highest degree of similarity to nicotinic acetylcholine receptors. Worms lacking CUP-4 have reduced phosphatidylinositol 4,5-bisphosphate levels at the plasma membrane, suggesting that CUP-4 regulates endocytosis through modulation of phospholipase C activity. ------------------- Key: 7268 Medline: 15907843 Authors: Kapulkin V;Hiester BG;Link CD Title: Compensatory regulation among ER chaperones in C. elegans. Citation: FEBS Letters 579: 3063-3068 2005 Type: ARTICLE Genes: crt-1 dnj-7 hsp-3 hsp-4 ire-1 sca-1 stc-1 xbp-1 Abstract: We have identified a particularly clear case of compensatory transcriptional regulation among ER chaperones in Caenorhabditis elegans using a GFP reporter transgene that is under the control of the promoter of hsp-4, a C. elegans homolog of GRP-78/BiP. Knockdown by RNA interference of 9 known or predicted ER chaperones induced hsp-4 upregulation via the ire-1lxbp-1 signaling cascade employed in the unfolded protein response. We show that this compensatory regulation is specific for ER chaperones, not dependent on RNA interference, and required for maintaining viability in worms containing a deletion of the ------------------- Key: 7269 Medline: 15862884 Authors: Kenney SJ;Anderson GL;Williams PL;Millner PD;Beuchat LR Title: Persistence of Escherichia coli O157:H7, Salmonella Newport and Salmonella Poona in the gut of a free-living nematode, Caenorhabditis elegans, and transmission to progeny and uninfected nematodes. Citation: International Journal of Food Microbiology 101: 227-236 Type: ARTICLE Genes: Abstract: A study was undertaken to determine the persistence of Escherichia coli O157:H7 and salmonellae in the gut of a free-living nematode. Caenorhabditis elegans, as affected by temperature and relative humidity and to determine if infected worms transmit Salmonella enterica serotype Newport to progeny and uninfected worms. Worms were fed cells of a non-pathogenic strain of E. coli (OP50), E. coli 0157:H7, S. enterica serotype Newport, and S. enterica scrotype Poona, followed by incubating at 4, 20, or 37 degrees C for up to 5 days. initial populations of ingested pathogens significantly increased by up to 2.93 log(10) cfu/worm within 1 day at 20 degrees C on K agar and remained constant for an additional 4 days. When worms were placed on Bacto agar, Populations of ingested pathogens remained constant at 4 T, decreased significantly at 20 T, and increased significantly at 37 degrees C within 3 days. Wortris fed E. coli OP50 or S. Newport were incubated at 4 or 20 degrees C at relative humidities of 33%. 75%, or 98% to determine survival characteristics of ingested bacteria. Fewer cells of the pathogens survived incubation at 33% relative humidity compared to higher relative humidities. Populations of ingested E. coli OP50 and S. Newport decreased by LIP to 1.65 and 3.44 log(10) cfu/worm, respectively, in worms incubated at 20 degrees C and 33% relative humidity. Placement together on K agar of adult worms, labeled with green fluorescent protein (gfp) in the pharynx area, that had ingested gfP-labeled S. Newport and uninfected wild type worms resulted in transfer of the pathogen to gut of wild type worms. S. Newport was isolated from C elegans two generations removed from exposure to the pathogen. Results of these studies show that C. elegans may serve as a temporary reservoir of foodborne pathogens, and could perhaps, be a vector for contaminating preharvest fruits and vegetables, thus potentially increasing the risk of enteric infections associated with consumption of raw ------------------- Key: 7270 Medline: 15938711 Authors: Hirotsu T;Iino Y Title: Neural circuit-dependent odor adaptation in C. elegans is regulated by the Ras-MAPK pathway. Citation: Genes to Cells 10: 517-530 2005 Type: ARTICLE Genes: let-60 mek-2 odr-4 odr-7 osm-9 ttx-3 Abstract: The molecular machinery that mediates odor adaptation in the olfactory neurons is well documented in various animal species. However, types of adaptation that depend on neural circuits are mostly unexplored. We report here that the Ras-MAPK pathway is essential for such a type of odor adaptation, called early adaptation, in C. elegans. Early adaptation requires a pair of AIY interneurons, which receive synaptic inputs from olfactory neurons. Mutants of the Ras-MAPK pathway show defects in early adaptation. Continued exposure to an odorant causes activation of MAP kinase not only in the olfactory neurons, but also in the AIY interneurons. While activity of the Ras-MAPK pathway in the olfactory neurons is important for odor perception, its activity in the AIY interneurons is important for odor adaptation. Our results thus reveal a dual role of the Ras-MAPK pathway in sensory processing in the nervous system of C. elegans. ------------------- Key: 7271 Medline: 15890626 Authors: Arkblad EL;Tuck S;Pestov NB;Dmitriev RI;Kostina MB;Stenvall J;Tranberg M;Rydstrom J Title: A Caenorhabditis elegans mutant lacking functional nicotinamide mucleotide transhydrogenase displays increased sensitivity to oxidative stress. Citation: Free Radical Biology & Medicine 38: 1518-1525 2005 Type: ARTICLE Genes: nnt-1 Abstract: Proton-translocating mitochondrial nicotinamide nucleotide transhydrogenase (NNT) was investigated regarding its physiological role in Caenorhabditis elegans. NNT catalyzes the reduction of NADP+ by NADH driven by the electrochemical proton gradient, Delta p, and is thus a potentially important source of mitochondrial NADPH. Mitochondrial detoxification of reactive oxygen species (ROS) by glutathione-dependent peroxidases depends on NADPH for regeneration of reduced glutathione. Transhydrogenase may therefore be directly involved in the defense against oxidative stress. nnt-1 deletion mutants of C elegans, nnt-1(sv34), were isolated and shown to grow essentially as wild type under normal laboratory conditions, but with a strongly lowered GSH/GSSG ratio. Under conditions of oxidative stress, caused by the superoxide-generating agent methyl viologen, growth of worms lacking nnt-1 activity was severely impaired. A similar result was obtained by using RNAi. Reintroducing nnt-1 in the nnt-1(sv34) knockout mutant led to a partial rescue of growth under oxidative stress conditions. These results provide evidence for the first time that nnt-1 is important in the defense against mitochondrial oxidative stress. ------------------- Key: 7272 Medline: 15862350 Authors: Koulen P;Duncan RS;Liu J;Cohen NE;Yannazzo JAS;McClung N;Lockhart CL;Branden M;Buechner M Title: Polycystin-2 accelerates Ca2+ release from intracellular stores in Caenorhabditis elegans. Citation: Cell Calcium 37: 593-601 2005 Type: ARTICLE Genes: pkd-2 Abstract: Polycystin-2, a member of the TRP family of calcium channels, is encoded by the human PKD2 gene. Mutations in that gene can lead to swelling of nephrons into the fluid-filled cysts of polycystic kidney disease. In addition to expression in tubular epithelial cells, human polycystin-2 is found in muscle and neuronal cells, but its cell biological function has been unclear. A homologue in Caenorhabditis elegans is necessary for male mating behavior. We compared the behavior, calcium signaling mechanisms, and electrophysiology of wild-type and pkd-2 knockout C elegans. In addition to characterizing PKD-2-mediated aggregation and mating behaviors, we found that polycystin-2 is an intracellular Ca2+ release channel that is required for the normal pattern of Ca2+ responses involving IP3 and ryanodine receptor-mediated Ca2+ release from intracellular stores. Activity of polycystin-2 creates brief cytosolic Ca2+ transients with increased amplitude and decreased duration. Polycystin-2, along with the IP3 and ryanodine receptors, acts as a major calcium-release channel in the endoplasmic reticulum in cells where rapid calcium signaling is required, and polycystin-2 activity is essential in those excitable cells for rapid responses to stimuli. ------------------- Key: 7273 Medline: 16054081 Authors: Teramoto T;Lambie EJ;Iwasaki K Title: Differential regulation of TRPM channels governs electrolyte homeostasis in the C. elegans intestine. Citation: Cell Metabolism 1: 343-354 2005 Type: ARTICLE Genes: Abstract: The transient receptor potential (TRP) channels are implicated in various cellular processes, including sensory signal transduction and electrolyte homeostasis. We show here that the GTL-1 and GON-2 TRPM channels regulate electrolyte homeostasis in the C. elegans intestine. GON-2 is responsible for a large outwardly rectifying current of intestinal cells, and its activity is tightly regulated by intracellular Mg2+ levels, while GTL-1 mainly contributes to appropriate Mg2+ responsiveness of the outwardly rectifying current. We also used nickel cytotoxicity to study the function of these channels. Both GON-2 and GTL-1 are necessary for intestinal uptake of nickel, but GTL-1 is continuously active while GON-2 is inactivated at higher Mg2+ levels. This type of differential regulation of intestinal electrolyte absorption ensures a constant supply of electrolytes through GTL-1, while occasional bursts of GON-2 activity allow rapid return to normal electrolyte concentrations following physiological perturbations. ------------------- Key: 7274 Medline: 15886897 Authors: Graves AL;Boyd WA;Williams PL Title: Using transgenic Caenorhabditis elegans in soil toxicity testing. Citation: Archives of Environmental Contamination and Toxicology 48: 490-494 2005 Type: ARTICLE Genes: Abstract: Soil bioassays are important tools for evaluating toxicological effects within the terrestrial environment. The American Society for Testing and Materials E2172-01 Standard Guide outlines a method for conducting laboratory soil toxicity tests using the nematode Caenorhabditis elegans. This method is an efficient too] for extracting C elegans from soil samples and can be carried out after a 24-h exposure period using relatively small amounts of soil. Drawbacks of this method include problems with (1) recovery of nematodes from soils containing a high percentage of organic matter, and (2) distinguishing indigenous nematode species from nematodes added for the laboratory test. Due in part to these issues, C. elegans has not been extensively accepted for use in soil testing. To address these concerns and improve upon the American Society for Testing and Materials method, this project focused on using transgenic strains of C. elegans carrying a GFP-expressing element. Lethality and behavior tests revealed that the transgenic nematodes respond similarly to the wild-type N2 strain, indicating that they can be used in the same manner in soil testing. The GFP marker is easily identifiable not only within soils containing a large amount of organic matter, but also in field-collected soils containing indigenous nematodes. These results support the use of transgenic GFP C. elegans in soil bioassays as a tool to further the reliability of ------------------- Key: 7275 Medline: Authors: Parker JA;Arango M;Abderrahmane S;Lambert E;Tourette C;Catoire H;Neri C Title: Resveratrol rescues mutant polyglutamine cytotoxicity in nematode and mammalian neurons. Citation: MS - Medecine Sciences 21: 556-557 2005 Type: ARTICLE Genes: Abstract: ------------------- Key: 7276 Medline: 15916936 Authors: Rankin CH Title: Nematode memory: now, where was I? Citation: Current Biology 15: R374-R375 2005 Type: REVIEW Genes: gcy-32 gcy-34 gcy-35 gcy-36 tax-2 tax-4 Abstract: The nematode Caenorhabditis elegans is able to use tastes, smells and temperature to locate food. New data show that worms can also detect the level of oxygen in the environment and migrate towards an oxygen level associated ------------------- Key: 7277 Medline: 15916946 Authors: Han Z;Riefler GM;Saam JR;Mango SE;Schumacher JM Title: The C. elegans Tousled-like kinase contributes to chromosome segregation as a substrate and regulator of the Aurora B kinase. Citation: Current Biology 15: 894-904 2005 Type: ARTICLE Genes: air-1 air-2 asf-1 icp-1 tlk-1 Abstract: BACKGROUND: The Aurora kinases control multiple aspects of mitosis, among them centrosome maturation, spindle assembly, chromosome segregation, and cytokinesis. Aurora activity is regulated in part by a subset of Aurora substrates that, once phosphorylated, can enhance Aurora kinase activity. Aurora A substrate activators include TPX2 and Ajuba, whereas the only known Aurora B substrate activator is the chromosomal passenger INCENP. RESULTS: We report that the C. elegans Tousled kinase TLK-1 is a second substrate activator of the Aurora B kinase AIR-2. Tousled kinase (Tlk) expression and activity have been linked to ongoing DNA replication, and Tlk can phosphorylate the chromatin assembly factor Asf. Here, we show that TLK-1 is phosphorylated by AIR-2 during prophase/prometaphase and that phosphorylation increases TLK-1 kinase activity in vitro. Phosphorylated TLK-1 increases AIR-2 kinase activity in a manner that is independent of TLK-1 kinase activity but depends on the presence of ICP-1/INCENP. In vivo, TLK-1 and AIR-2 cooperate to ensure proper mitotic chromosome segregation. CONCLUSIONS: The C. elegans Tousled kinase TLK-1 is a substrate and activator of the Aurora B kinase AIR-2. These results suggest that Tousled kinases have a previously unrecognized role in mitosis and that Aurora B associates with discrete regulatory complexes that may impart distinct substrate specificities and functions to the Aurora B kinase. ------------------- Key: 7278 Medline: 15916947 Authors: Cheung BHH;Cohen M;Rogers C;Albayram O;de Bono M Title: Experience-dependent modulation of C. elegans behavior by ambient oxygen. Citation: Current Biology 15: 905-917 2005 Type: ARTICLE Genes: gcy-32 gcy-34 gcy-35 gcy-36 npr-1 Abstract: BACKGROUND: Ambient oxygen (O2) influences the behavior of organisms from bacteria to man. In C. elegans, an atypical O2 binding soluble guanylate cyclase (sGC), GCY-35, regulates O2 responses. However, how acute and chronic changes in O2 modify behavior is poorly understood. RESULTS: Aggregating C. elegans strains can respond to a reduction in ambient O2 by a rapid, reversible, and graded inhibition of roaming behavior. This aerokinetic response is mediated by GCY-35 and GCY-36 sGCs, which appear to become activated as O2 levels drop and to depolarize the AQR, PQR, and URX neurons. Coexpression of GCY-35 and GCY-36 is sufficient to transform olfactory neurons into O2 sensors. Natural variation at the npr-1 neuropeptide receptor alters both food-sensing and O2-sensing circuits to reconfigure the salient features of the C. elegans environment. When cultivated in 1% O2 for a few hours, C. elegans reset their preferred ambient O2, seeking instead of avoiding 0%-5% O2. This plasticity involves reprogramming the AQR, PQR, and URX neurons. CONCLUSIONS: To navigate O2 gradients, C. elegans can modulate turning rates and speed of movement. Aerotaxis can be reprogrammed by experience or engineered artificially. We propose a model in which prolonged activation of the AQR, PQR, and URX neurons by low O2 switches on previously inactive O2 sensors. This enables aerotaxis to low O2 environments and may encode a "memory" of previous cultivation in low O2. ------------------- Key: 7279 Medline: 15916950 Authors: Blacque OE;Perens EA;Boroevich KA;Inglis PN;Li C;Warner A;Khattra J;Holt RA;Ou G;Mah AK;McKay SJ;Huang P;Swoboda P;Jones SJM;Marra MA;Baillie DL;Moerman DG;Shaham S;Leroux MR Title: Functional genomics of the cilium, a sensory organelle. Citation: Current Biology 15: 935-941 2005 Type: ARTICLE Genes: abu-1 amx-1 bbs-1 bbs-2 bbs-5 cat-2 che-2 che-11 che-13 daf-19 dgk-1 dli-1 dyf-13 fbl-1 gcy-34 ksr-1 mec-12 osm-1 osm-3 osm-5 osm-6 osm-12 rsp-1 sto-1 sto-2 sqv-5 tba-6 tba-9 vab-10 Abstract: Cilia and flagella play important roles in many physiological processes, including cell and fluid movement, sensory perception, and development. The biogenesis and maintenance of cilia depend on intraflagellar transport (IFT), a motility process that operates bidirectionally along the ciliary axoneme. Disruption in IFT and cilia function causes several human disorders, including polycystic kidneys, retinal dystrophy, neurosensory impairment, and Bardet-Biedl syndrome (BBS). To uncover new ciliary components, including IFT proteins, we compared C. elegans ciliated neuronal and nonciliated cells through serial analysis of gene expression (SAGE) and screened for genes potentially regulated by the ciliogenic transcription factor, DAF-19. Using these complementary approaches, we identified numerous candidate ciliary genes and confirmed the ciliated-cell-specific expression of 14 novel genes. One of these, C27H5.7a, encodes a ciliary protein that undergoes IFT. As with other IFT proteins, its ciliary localization and transport is disrupted by mutations in IFT and bbs genes. Furthermore, we demonstrate that the ciliary structural defect of C. elegans dyf-13(mn396) mutants is caused by a mutation in C27H5.7a. Together, our findings help define a ciliary transcriptome and suggest that DYF-13, an evolutionarily conserved protein, is a novel core IFT component required for cilia function. ------------------- Key: 7280 Medline: 15916954 Authors: Mitrovich QM;Anderson P Title: mRNA surveillance of expressed pseudogenes in C. elegans. Citation: Current Biology 15: 963-967 2005 Type: ARTICLE Genes: cbp-1 cbp-2 rpl-7 smg-1 smg-2 ubq-1 ubq-3 ubq-4 Abstract: Messenger RNAs (mRNAs) that contain premature translation termination codons (PTCs) are targeted for rapid degradation in all eukaryotes tested. The mechanisms of nonsense-mediated mRNA decay (NMD) have been described in considerable detail, but the biological roles of NMD in wild-type organisms are poorly understood. mRNAs of wild-type organisms known to be degraded by NMD ("natural targets" of NMD) include by-products of regulated alternative splicing, out-of-frame mRNAs derived from unproductive gene rearrangements, cytoplasmic pre-mRNAs, endogenous retroviral and transposon RNAs, and mRNAs having upstream open reading frames or other unusual sequence features. NMD may function to eliminate aberrant PTC-containing mRNAs in order to protect cells from expression of potentially deleterious truncated proteins. Pseudogenes are nonfunctional genes or gene fragments that accumulate mutations through genetic drift. Such mutations will often introduce shifts of reading frame and/or PTCs, and mRNAs of expressed pseudogenes may thus be substrates of NMD. We demonstrate that mRNAs expressed from C. elegans pseudogenes are degraded by NMD and discuss possible implications for both mRNA surveillance and protein evolution. We describe an expressed pseudogene that encodes a small nucleolar RNA (snoRNA) within an intron and suggest this represents an evolutionary intermediate between snoRNA-encoding host genes that do or do not encode proteins. ------------------- Key: 7281 Medline: 15797864 Authors: Wei AD;Butler A;Salkoff L Title: KCNQ-like potassium channels in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 280: 21337-21345 2005 Type: ARTICLE Genes: kqt-1 kqt-2 kqt-3 Abstract: The human KCNQ gene family encodes potassium channels linked to several genetic syndromes including neonatal epilepsy, cardiac arrhythmia, and progressive deafness. KCNQ channels form M-type potassium channels, which are critical regulators of neuronal excitability that mediate autonomic responses, pain, and higher brain function. Fundamental mechanisms of the normal and abnormal cellular roles for these channels may be gained from their study in simple model organisms. Here we report that a multigene family of KCNQ-like channels is present in the nematode, Caenorhabditis elegans. We show that many aspects of the functional properties, tissue expression pattern, and modulation of these C. elegans channels are conserved, including suppression by the M1 muscarinic receptor. We also describe a conserved mechanism of modulation by diacylglycerol for a subset of C. elegans and vertebrate KCNQ/KQT channels, which is dependent upon the carboxyl-terminal domains of channel subunits and activated protein kinase C. ------------------- Key: 7282 Medline: 15783531 Authors: Grill SW;Kruse K;Julicher F Title: Theory of mitotic spindle oscillations. Citation: Physical Review Letters 94: 10810-4 2005 Type: ARTICLE Genes: Abstract: During unequal cell division the mitotic spindle is positioned away from the center of the cell before cell cleavage. In many biological systems this repositioning is accompanied by oscillatory movements of the spindle. We present a theoretical description for mitotic spindle oscillations. We show that the cooperative attachment and detachment of cortical force generators to astral microtubules leads to spontaneous oscillations beyond a critical number of force generators. This mechanism can quantitatively describe the spindle oscillations observed during unequal division of the one cell stage Caenorhabditis elegans embryo. ------------------- Key: 7283 Medline: 15935762 Authors: Kidd AR;Miskowski JA;Siegfried KR;Sawa H;Kimble J Title: A beta-catenin identified by functional rather than sequence criteria and its role in Wnt/MAPK signaling. Citation: Cell 121: 761-772 2005 Type: ARTICLE Genes: apr-1 bar-2 dsh-2 lin-17 lit-1 mig-5 mom-4 pop-1 pry-1 sgg-1 sys-1 unc-37 wrm-1 Abstract: Wnt/MAPK signaling is a common variant of Wnt signaling in C. elegans and has been implicated in vertebrates. The sys-1 gene works with Wnt/MAPK signaling to control cell fates during C. elegans development. We report that the SYS-1 amino acid sequence is novel but that SYS-1 functions as beta-catenin: SYS-1 rescues a bar-1/beta-catenin null mutant, binds the POP-1/TCF beta-catenin binding domain, and coactivates POP-1-dependent transcription. Moreover, we provide genetic and molecular evidence that SYS-1 levels are crucial to POP-1 activity. Our results suggest that Wnt/MAPK signaling promotes POP-1 export from the nucleus to accommodate the limiting availability of its SYS-1/beta-catenin transcriptional coactivator. Discovery of SYS-1/beta-catenin extends our definition of beta-catenins and brings together aspects of the canonical mechanism for Wnt signaling with the noncanonical Wnt/MAPK mechanism. We discuss the idea that a similar pathway may be employed broadly in animal development. ------------------- Key: 7284 Medline: 15923631 Authors: Yang Y;Lundquist EA Title: The actin-binding protein UNC-115/abLIM controls formation of lamellipodia and filopodia and neuronal morphogenesis in Caenorhabditis elegans. Citation: Molecular and Cellular Biology 25: 5158-5170 2005 Type: ARTICLE Genes: unc-115 Abstract: The roles of actin-binding proteins in development and morphogenesis are not well understood. The actin-binding protein UNC-115 has been implicated in cytoskeletal signaling downstream of Rac in Caenorhabditis elegans axon pathfinding, but the cellular role of UNC-115 in this process remains undefined. Here we report that UNC-115 overactivity in C. elegans neurons promotes the formation of neurites and lamellipodial and filopodial extensions similar to those induced by activated Rac and normally found in C. elegans growth cones. We show that UNC-115 activity in neuronal morphogenesis is enhanced by two molecular mechanisms: when ectopically driven to the plasma membrane by the myristoylation sequence of c-Sre, and by mutation of a putative serine phosphorylation site in the actin-binding domain of UNC-115. In support of the hypothesis that UNC-115 modulates actin cytoskeletal organization, we show that UNC-115 activity in serum-starved NIH 3T3 fibroblasts results in the formation of lamellipodia and filopodia. We conclude that UNC-115 is a novel regulator of the formation of lamellipodia and filopodia in neurons, possibly in the growth cone during ------------------- Key: 7285 Medline: 15901674 Authors: Berset TA;Hoier EF;Hajnal A Title: The C. elegans homolog of the mammalian tumor suppressor Dep-1/Scc1 inhibits EGFR signaling to regulate binary cell fate decisions. Citation: Genes & Development 19: 1328-1340 2005 Type: ARTICLE Genes: bar-1 dep-1 let-23 let-60 lin-2 lin-7 lin-10 lin-12 lin-15 lip-1 pry-1 sem-5 Abstract: Protein phosphorylation by kinases and the subsequent dephosphorylation by phosphatases are key mechanisms that regulate intracellular signal transduction during development. Here, we report the identification of the receptor protein tyrosine phosphatase DEP-1 as a negative regulator of the Caenorhabditis elegans EGF receptor. DEP-1 amplifies in the developing vulva and the excretory system the small differences in the amount of EGF signal received by equivalent precursor cells to achieve binary cell fate decisions. During vulval development, DEP-1 inhibits EGFR signaling in the secondary cell lineage in parallel with the NOTCH-mediated lateral inhibition, while EGFR signaling simultaneously down-regulates DEP-1 and NOTCH expression in the primary cell lineage. This regulatory network of inhibitors results in the full activation of the EGFR/RAS/MAPK pathway in the primary vulval cells and at the same time keeps the EGFR/RAS/MAPK pathway inactive in the adjacent secondary cells. Mammalian Dep-1/Scc1 functions as a tumor-suppressor gene in the intestinal epithelium. Thus, mutations in human Dep-1 may promote tumor formation through a hyperactivation of the EGF ------------------- Key: 7286 Medline: Authors: Lange D;Storment CW;Conley CA;Kovacs GTA Title: A microfluidic shadow imaging systemf or the study of the nematode Caenorhabditis elegans in space. Citation: Sensors and Actuators B 107: 904-914 2005 Type: ARTICLE Genes: Abstract: ------------------- Key: 7287 Medline: 15863031 Authors: Huang P;Stern MJ Title: FGF signaling in flies and worms: more and more relevant to vertebrate biology. Citation: Cytokine & Growth Factor Reviews 16: 151-158 2005 Type: REVIEW Genes: egl-17 let-756 Abstract: FGF signaling in the invertebrate model systems Drosophila melanogaster and Caenorhabditis elegans was initially most obviously involved in cell motility events. More recently, however, FGFs and FGF signaling in these systems have been shown to affect many additional cellular processes. This recent work has shown that the pleiotropies of these FGF receptors resemble those of their vertebrate counterparts, and, in many cases, serve as excellent models for understanding the fundamental molecular mechanisms controlling these events. ------------------- Key: 7288 Medline: 15895077 Authors: Sato M;Sato K;Fonarev P;Huang CJ;Liou W;Grant BD Title: Caenorhabditis elegans RME-6 is a novel regulator of RAB-5 at the clathrin-coated pit. Citation: Nature Cell Biology 7: 559-569 2005 Type: ARTICLE Genes: rab-5 rme-6 Abstract: Here we identify a new regulator of endocytosis called RME-6. RME-6 is evolutionarily conserved among metazoans and contains Ras-GAP (GTPase-activating protein)-like and Vps9 domains. Consistent with the known catalytic function of Vps9 domains in Rab5 GDP/GTP exchange, we found that RME-6 binds specifically to Caenorhabditis elegans RAB-5 in the GDP-bound conformation, and rme-6 mutants have phenotypes that indicate low RAB-5 activity. However, unlike other Rab5-associated proteins, a rescuing green fluorescent protein (GFP)-RME-6 fusion protein primarily localizes to clathrin-coated pits, physically interacts with alpha-adaptin, a clathrin adaptor protein, and requires clathrin to achieve its cortical localization. In rme-6 mutants, transport from the plasma membrane to endosomes is defective, and small 110-nm endocytic vesicles accumulate just below the plasma membrane. These results suggest a mechanism for the activation of Rab5 in clathrin-coated pits or clathrin-coated vesicles that is essential for the delivery of endocytic cargo to early ------------------- Key: 7289 Medline: 15910738 Authors: Menzel R;Rodel M;Kulas J;Steinberg CEW Title: CYP35: Xenobiotically induced gene expression in the nematode Caenorhabditis elegans. Citation: Archives of Biochemistry & Biophysics 438: 93-102 2005 Type: ARTICLE Genes: cyp-35 Abstract: Although over 80 cytochrome P450 (CYP) encoding genes have been identified in the genome of the nematode Caenorhabditis elegans very little is known about their involvement in biotransformation. This paper demonstrates a concentration-dependent relationship of C. elegans CYP35A1, A2, A5, and C1 gene expression in response to four organic xenobiotics, namely atrazine, PCB52, fluoranthene, and lansoprazole. The toxicity of these xenobiotics was determined using a reproduction assay. CYP-specific messenger RNA expression was analyzed by semi-quantitative RT-PCR resulting in a strongly increasing, concentration-dependent induction well below the EC50 for reproduction. For PCB52, approximately 0.5% of the EC50 induces a 2-fold increase of CYP35 gene expression. Using a double mutant and multiple RNAi of CYP35A/C it was possible to diminish the reproduction decline caused by PCB52 and fluoranthene. ------------------- Key: 7290 Medline: 15935751 Authors: Bowerman B Title: Advocating asymmetry and the POP-1 paradox: noncanonical Wnt signaling in C. elegans. Citation: Cell 121: 662-664 2005 Type: REVIEW Genes: lit-1 pop-1 sys-1 wrm-1 Abstract: In this issue of Cell, Kidd and colleagues (Kidd et al., 2005) describe their identification of a novel beta-catenin that functions in noncanonical C. elegans Writ signaling pathways to specify the different fates of daughter cells produced by asymmetric cell division. ------------------- Key: 7291 Medline: 15799965 Authors: Park KH;Hernandez L;Cai SQ;Wang Y;Sesti F Title: A family of K+ channel ancillary subunits regulate taste sensitivity in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 280: 21893-21899 2005 Type: ARTICLE Genes: kvs-1 mps-1 mps-2 mps-3 mps-4 Abstract: We have identified a family of ancillary subunits of K(+) channels in Caenorhabditis elegans. MPS-1 and its related members MPS-2, MPS-3, and MPS-4 are detected in the nervous system of the nematode. Electrophysiological analysis in ASE neurons and mammalian cells and epigenetic inactivation by double-stranded RNA interference (RNAi) in vivo show that each MPS can associate with and functionally endow the voltage-gated K(+) channel KVS-1. In the chemosensory neuron ADF, three different MPS subunits combine with KVS-1 to form both binary (MPS-1.KVS-1) and ternary (MPS-2.MPS-3.KVS-1) complexes. RNAi of mps-2, mps-3, or both, enhance the taste of the animal for sodium without altering the susceptibility to other attractants. When sodium is introduced in the test plate as background or as antagonist attractant, the nematode loses the ability to recognize a second attractant. Thus, it appears that the chemosensory apparatus of C. elegans uses sensory thresholds and that a voltage-gated K(+) channel is ------------------- Key: 7292 Medline: 15840655 Authors: Chang HCH;Rongo C Title: Cytosolic tail sequences and subunit interactions are critical for synaptic localization of glutamate receptors. Citation: Journal of Cell Science 118: 1945-1956 2005 Type: ARTICLE Genes: glr-1 glr-2 Abstract: AMPA-type glutamate receptors mediate excitatory synaptic transmission in the nervous system. The receptor subunit composition and subcellular localization play an important role in regulating synaptic strength. GLR-1 and GLR-2 are the Caenorhabditis elegans subunits most closely related to the mammalian AMPA-type receptors. These subunits are expressed in overlapping sets of interneurons, and contain type-I PDZ binding motifs in their carboxyterminal cytosolic tail sequences. We report that GLR-1 and GLR-2 may form a heteromeric complex, the localization of which depends on either GLR-1 or GLR-2 tail sequences. Subunit interactions alone can mediate synaptic localization as endogenous GLR-1, or GLR-2 subunits can rescue the localization defects of subunits lacking tail sequences. Moreover, GLR-2 cytosolic tail sequences are sufficient to confer synaptic localization on a heterologous reporter containing a single-transmembrane domain. The localization of this GLR-2 reporter requires both a PDZ-binding motif in the GLR-2 tail sequence, and sequences outside of this motif. The PDZ protein LIN-10 regulates the localization of the reporter through the sequences outside of the PDZ-binding motif. Our results suggest that multiple synaptic localization signals reside in the cytosolic tail sequence of the receptor subunits, and that channel assembly can rescue the synaptic localization defects of individual mutant subunits as long as there are also wild-type subunits in the receptor complex. ------------------- Key: 7293 Medline: 15888316 Authors: Kondo M;Senoo-Matsuda N;Yanase S;Ishii T;Hartman PS;Ishii N Title: Effect of oxidative stress on translocation of DAF-16 in oxygen-sensitive mutants, mev-1 and gas-1 of Caenorhabditis elegans. Citation: Mechanisms of Ageing & Development 126: 637-641 2005 Type: ARTICLE Genes: daf-16 gas-1 mev-1 Abstract: Mutations in the mev-1 and gas-1 genes of the nematode Caenorhabditis elegans render animals hypersensitive to oxygen and paraquat, and lead to premature aging. We show that both mutants overproduce superoxide anion in isolated sub-mitochondrial particles, which probably explains their hypersensitivity to oxidative stress. The daf-16 gene encodes a fork-head transcription factor that is negatively regulated by an insulin-signaling pathway. In wild-type animals, the DAF-16 protein normally resides in the cytoplasm and only becomes translocated to nuclei upon activating stimuli such as oxidative stress. Conversely, DAF-16 resides constitutively in the nuclei of mev-1 and gas-1 mutants even under normal growth conditions. Supplementation of the antioxidant coenzyme Q(10) reversed this nuclear translocation of DAF-16. Since both gas-1 and mev-1 encode subunits of electron transport chain complexes, these data illustrate how mitochondrial perturbations can impact signal transduction pathways. ------------------- Key: 7294 Medline: 15888317 Authors: Kondo M;Yanase S;Ishii T;Hartman PS;Matsumoto K;Ishii N Title: The p38 signal transduction pathway participates in the oxidative stress-mediated translocation of DAF-16 to Caenorhabditis elegans nuclei. Citation: Mechanisms of Ageing & Development 126: 642-647 2005 Type: ARTICLE Genes: daf-2 daf-16 jkk-1 jnk-1 mek-1 nsy-1 pmk-1 sek-1 Abstract: Much attention has focused on the insulin-like signaling pathway in Caenorhabditis elegans because of its pivotal role in life-span determination and oxidative stress resistance. The daf-16 gene encodes a fork-head transcription factor that is negatively regulated by this insulin-signaling pathway. The DAF-16 protein is translocated to the nucleus when animals were subjected to oxidative stress in the form of paraquat. This oxidative stress-mediated translocation was blocked by mutation of the p38-related sek-1 (MAPKK) mutant and DAF-16 instead remained cytoplasmic. The fact that DAF-16 translocation by oxidative stress is epistatic to sek-1 suggests that oxidative stress mediates regulation of DAF-16 through activating the p38 signal transduction pathway upstream of daf-16 so as to mobilize DAF-16 to the nucleus and activate ------------------- Key: 7295 Medline: 15953361 Authors: Rex E;Hapiak V;Hobson R;Smith K;Xiao H;Komuniecki R Title: TYRA-2 (F01E11.5): a Caenorhabditis elegans tyramine receptor expressed in the MC and NSM pharyngeal neurons. Citation: Journal of Neurochemistry 94: 181-191 2005 Type: ARTICLE Genes: ser-2 tyra-2 Abstract: Tyramine appears to regulate key processes in nematodes, such as pharyngeal pumping, and more complex behaviors, such as foraging. Recently, a Caenorhabditis elegans tyramine receptor, SER-2, was identified that is involved in the TA-dependent regulation of these processes. In the present study, we have identified a second C. elegans gene, tyra-2 (F01E11.5) that encodes a tyramine receptor. This is the first identification of multiple tyramine receptor genes in any invertebrate. Membranes from COS-7 cells expressing TYRA-2 bind [H-3]tyramine with high affinity with a K-d of 20 ñ 5 nm. Other physiologically relevant biogenic amines, such as octopamine and dopamine, inhibit [H-3]tyramine binding with much lower affinity (K(i)s of 1.55 ñ 0.5 and 1.78 ñ 0.6 mu m, respectively), supporting the identification of TYRA-2 as a tyramine receptor. Indeed, tyramine also dramatically increases GTP gamma S binding to membranes from cells expressing TYRA-2 (EC50 of 50 ñ 13 nm) and the TA-dependent GTP gamma S binding is PTX-sensitive suggesting that TYRA-2 may couple to G alpha(i/o). Based on fluorescence from tyra::gfp fusion constructs, TYRA-2 expression appears to be exclusively neuronal in the MC and NSM pharyngeal neurons, the AS family of amphid neurons and neurons in the nerve ring, body and tail. Taken together, these results suggest that TYRA-2 encodes a second G alpha(i/o)-coupled tyramine receptor and suggests that TA-dependent neuromodulation may be mediated by multiple receptors and more complex than ------------------- Key: 7296 Medline: Authors: Denver DR; Feinberg S;Estes S;Thomas WK;Lynch M Title: Mutation rates, spectra and hotspots in mismatch repair-deficient Caenorhabditis elegans. Citation: Genetics 170: 107-113 2005 Type: ARTICLE Genes: msh-2 msh-6 Abstract: Although it is clear that postreplicative DNA mismatch repair (MMR) plays a critical role in maintaining genomic stability in nearly all forms of life surveyed, much remains to be understood about the genome-wide impact of MMR on spontaneous mutation processes and the extent to which MMR-deficient mutation patterns vary among species. We analyzed spontaneous mutation processes across multiple genomic regions using two sets of mismatch repair-deficient (msh-2 and msh-6) Caenorhabditis elegans mutation-accumulation (MA) lines and compared our observations to mutation spectra in a set of wild-type (WT), repair-proficient C. elegans MA lines. Across most sequences surveyed in the MMR-deficient MA lines, mutation rates were similar to 100-fold higher than rates in the WT MA lines, although homopolymeric nucleotide-run (HP) loci composed of A:T base pairs mutated at an similar to 500-fold greater rate. In contrast to yeast and humans where mutation spectra vary substantially with respect to different specific MMR-deficient genotypes, mutation rates and patterns were overall highly similar between the msh-2 and msh-6 C. elegans MA lines. This, along with the apparent absence of a Saccharomyces cerevisiae MSH3 ortholog in the C. elegans genome, suggests that C. elegans MMR surveillance is carried out by a single Msh-2/Msh-6 ------------------- Key: 7297 Medline: Authors: Lu C;Mains PE Title: Mutations of a redundant alpha-tubulin gene affect Caenorhabditis elegans early embryonic cleavage via MEI-1/katanin-dependent and -independent pathways. Citation: Genetics 170: 115-126 2005 Type: ARTICLE Genes: mei-1 mei-2 mel-26 mel-45 tba-1 tba-2 tbb-1 tbb-2 zyg-9 dxDf2 Abstract: The C. elegans zygote supports both meiosis and mitosis within a common cytoplasm. The meiotic spindle is small and is located anteriorly, whereas the first mitotic spindle fills the zygote. The C. elegans microtubule-severing complex, katanin, is encoded by the mei-1 and mei-2 genes and is solely required for oocyte meiotic spindle formation; ectopic mitotic katanin activity disrupts mitotic spindles. Here we characterize two mutations that rescue the lethality caused by ectopic MEI-1/MEI-2. Both mutations are gain-of-function alleles of tba-2 alpha-tubulin. These tba-2 alleles do not prevent MEI-1/MEI-2 microtubule localization but do interfere with its activity. TBA-1 and TBA-2 are redundant for viability, but when katanin activity is limiting, TBA-2 is preferred over TBA-1 by katanin. This is similar to what we previously reported for the beta-tubulins. Removing both preferred alpha- and beta-isoforms results in normal development, suggesting that the katanin isoform preferences are not absolute. We conclude that while the C. elegans embryo expresses redundant alpha- and beta-tubulin isoforms, they nevertheless have subtle functional specializations. Finally, we identified a dominant tba-2 allele that disrupts both meiotic and mitotic spindle formation independently of MEI-1/MEI-2 activity. Genetic studies suggest that this tba-2 mutation has a "poisonous" effect on microtubule function. ------------------- Key: 7298 Medline: 15716039 Authors: Lee M;Shen B;Schwarzbauer JE;Ahn J;Kwon J Title: Connections between integrins and Rac GTPase pathways control gonad formation and function in C. elegans. Citation: Biochemica et Biophysica Acta 1723: 248-255 2005 Type: ARTICLE Genes: ced-5 ced-10 mig-2 pat-3 rol-6 unc-54 unc-73 Abstract: The integnins are a family of up heterodimeric transmembrane receptors that link extracellular matrix (ECM) proteins to the cytoskeleton and orchestrate cell behaviors. It's been suggested that integrins interact with Rho family small GTPases, such as Rho and Rac. We took advantage of a C. elegans nematode line expressing HA-beta tail, a beta integrin transgene inhibiting the functions of endogenous integrins, to determine the combined effects of reducing PAT-3 beta integrin and Rac pathway activities. Double mutants of HA-beta tail and unc-73, a guanine nucleotide exchange factor GEF for MIG-2/Rac, had body wall and vulval muscle abnormalities. On the other hand, HA-beta tail combined with mutant CED-5, another Rac interacting protein, showed ovulation defects and sterility. RNA-mediated interference (RNAi) of pat-3 on Rae mutant backgrounds also affected gonad structure and function. These results show a functional link between integrins and Rac signaling in muscles and gonads. Furthermore, data showing distinct phenotypes of HA-beta tail with unc-73 versus ced-5 suggest some tissue-specificity in the usage of Rae signaling pathways. ------------------- Key: 7299 Medline: 15907773 Authors: Shatilla A;Leduc A;Yang X;Ramotar D Title: Identification of two apurinic/apyrimidinic endonucleases from Caenorhabditis elegans by cross-species complementation. Citation: DNA Repair 4: 655-670 2005 Type: ARTICLE Genes: apn-1 exo-3 Abstract: The Saccharomyces cerevisiae mutant strain YW778, which lacks apurinic/apyrimidinic (AP) endonuclease and 3'-diesterase DNA repair activities, displays high levels of spontaneous mutations and hypersensitivities to several DNA damaging agents. We searched a cDNA library derived from the nematode Caenorhabditis elegans for gene products that would rescue the DNA repair defects of this yeast mutant. We isolated two genes, apn-1 and exo-3, encoding proteins that have not been previously characterized. Both APN-1 and EXO-3 share significant identity with the functionally established Escherichia coli AP endonucleases, endonuclease IV and exonuclease III, respectively. Strain YW778 expressing either apn-1 or exo-3 shows parental levels of spontaneous mutations, as well as resistance to DNA damaging agents that produce AP sites and DNA single strand breaks with blocked 3'-ends. Using an in vitro assay, we show that the apn-1 and exo-3 genes independently express AP endonuclease activity in the yeast mutant. We further characterize the EXO-3 protein and three of its mutated variants E68A, D190A, and H279A. The E68A variant retains both AP endonuclease and 3'-diesterase repair activities in vitro, yet severely lacks the ability to protect strain YW778 from spontaneous and drug-induced DNA lesions, suggesting that this variant E68A may possess a defect that interferes with the repair process in vivo. In contrast, D190A and H279A are completely devoid of DNA repair activities and fail to rescue the genetic instability of strain YW778. Our data strongly suggest that EXO-3 and APN-1 are enzymes possessing intrinsic AP ------------------- Key: 7300 Medline: 15983867 Authors: Robinson-Rechavi M;Maina CV;Gissendanner CR;Laudet V;Sluder A Title: Explosive lineage-specific expansion of the oprhan nuclear receptor HNF4 in nematodes. Citation: Journal of Molecular Evolution 60: 577-586 2005 Type: ARTICLE Genes: daf-12 fax-1 nhr-2 nhr-6 nhr-23 nhr-25 nhr-41 nhr-67 nhr-91 unc-55 Abstract: The nuclear receptor superfamily expanded in at least two episodes: one early in metazoan evolution, the second within the vertebrate lineage. An exception to this pattern is the genome of the nematode Caenorhabditis elegans, which encodes more than 270 nuclear receptors, most of them highly divergent. We generated 128 cDNA sequences for 76 C. elegans nuclear receptors, confirming that these are active genes. Among these numerous receptors are 13 orthologues of nuclear receptors found in arthropods and/or vertebrates. We show that the supplementary nuclear receptors (supnrs) originated from an explosive burst of duplications of a unique orphan receptor, HNF4. This origin has specific implications for the role of ligand binding in the function and evolution of the nematode supplementary nuclear receptors. Moreover, the supplementary nuclear receptors include a group of very rapidly evolving genes found primarily on chromosome V. We propose a model of lineage-specific duplications from a chromosome on which duplication and substitution rates are highly increased. Our results provide a framework to study nuclear receptors in nematodes, as well as to consider the functional and evolutionary consequences of lineage-specific duplications. ------------------- Key: 7301 Medline: 15988528 Authors: Kurz T;Ozlu N;Rudolf F;O'Rourke SM;Luke B;Hofmann K;Hyman AA;Bowerman B;Peter M Title: The conserved protein DCN-1/Dcn1p is required for cullin neddylation in C. elegans and S. cerevisiae. Citation: Nature 435: 1257-1261 2005 Type: ARTICLE Genes: cul-3 dcn-1 mei-1 rfl-1 Abstract: SCF-type E3 ubiquitin ligases are multi-protein complexes required for polyubiquitination and subsequent degradation of target proteins by the 26S proteasome(1). Cullins, together with the RING-finger protein Rbx1, form the catalytic core of the ligase, and recruit the substrate-recognition module(1-4). Cycles of covalent modification of cullins by the ubiquitin-like molecule Nedd8 (neddylation)(5) and removal of Nedd8 by the COP9 signalosome (deneddylation) positively regulate E3 ligase activity(6,7). Here we report the identification and analysis of a widely conserved protein that is required for cullin neddylation in the nematode Caenorhabditis elegans and the yeast Saccharomyces cerevisiae. C. elegans DCN-1 and S. cerevisiae Dcn1p ( defective in cullin neddylation) are characterized by a novel UBA-like ubiquitin-binding domain and a DUF298 domain of unknown function. Consistent with their requirements for neddylation, DCN-1 and Dcn1p directly bind Nedd8 and physically associate with cullins in both species. Moreover, overexpression of Dcn1p in yeast results in the accumulation of Nedd8-modified cullin Cdc53p. Both in vivo and in vitro experiments indicate that Dcn1p does not inhibit deneddylation of Cdc53p by the COP9 signalosome, but greatly increases the kinetics of the ------------------- Key: 7302 Medline: Authors: Chang W;Lloyd CE;Zarkower D Title: DSH-2 regulates asymmetric cell division in the early C. elegans somatic gonad. Citation: Mechanisms of Development 122: 781-789 2005 Type: ARTICLE Genes: dsh-2 lin-17 pop-1 ccDf2 ccDf3 ccDf4 ccDf5 maDf4 nDf3 Abstract: Like other organs, the C elegans gonad develops from a simple primordium that must undergo axial patterning to generate correct adult morphology. Proximal/distal (PD) polarity in the C elegans gonad is established early during gonadogenesis by the somatic gonad precursor cells, Z1 and Z4. Z1 and Z4 each divide asymmetrically to generate one daughter with a proximal fate and one with a distal fate. PD polarity of the Z1/Z4 lineages requires the activity of a Wnt pathway that activates the TCF/LEF homolog pop-1. How the gonadal pathway controllingpop-1 is regulated by upstream factors has been unclear, as neither Wnt nor Dishevelled (Dsh) proteins have been shown to be required. Here we show that the C elegans dsh homolog dsh-2 controls gonadal polarity. As in pop-1 mutants, dsh-2 hermaphrodites have Z1 and Z4 lineage defects indicative of defective PD polarity and are missing gonadal arms. Males have an elongated but disorganized gonad, also with lineage defects. DSH-2 protein is expressed in the Z1/Z4 gonadal precursor cells. Asymmetric distribution of nuclear GFP::POP-1 in Z1 and Z4 daughter cells is reversed in dsh-2 mutants, with higher levels in distal than proximal daughters. dsh-2 and the frizzled receptor homolog lin-17 have a strong genetic interaction, suggesting that they act in a common pathway. We suggest that DSH-2 functions as an upstream regulator of POP-1 in the somatic gonad to control asymmetric cell division, thereby establishing proximal-distal polarity of the developing organ. ------------------- Key: 7303 Medline: 15972600 Authors: Olgun A;Aleksenko T;Pereira-Smith OM;Vassilatis DK Title: Functional analysis of MRG-1: the ortholog of human MRG15 in Caenorhabditis elegans. Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 60: 543-548 2005 Type: ARTICLE Genes: Abstract: Mortality Factor on Chromosome 4 (MORF4) induces senescence in several immortal human cell lines. MORF-related gene on chromosome 15 (MRG15), another expressed family member, is highly conserved and expressed in yeast to humans. To determine the biological functions of human MRG15 (hMRG15) we used RNA-mediated interference (RNAi) to silence mrg-1, the Caenorhabditis elegans ortholog, and its closest homolog Y37D8A.11. Expression of mrg-1 RNAi resulted in sterility, body wall defects, vulval protrusion, and posterior developmental defects in worms. We expressed mrg-1 under its own and the cytomegalovirus promoter in human cells. Both constructs were expressed, indicating that C. elegans promoter elements are functional in mammalian cells. Overexpression from the cytomegalovirus promoter eventually resulted in cell death, possibly due to competition with hMRG15 in endogenous nucleoprotein complexes. Recent data indicate a role for yeast and human MRG15 in transcriptional regulation via chromatin remodeling. Here we demonstrate the importance of mrg-1 in development and reproduction in C. elegans and discuss its potential to impact the aging process. ------------------- Key: 7304 Medline: Authors: Deken SL;Vincent R;Hadwiger G;Liu Q;Wang ZW;Nonet ML Title: Redundant localization mechanisms of RIM and ELKS in Caenorhabitis elegans. Citation: Journal of Neuroscience 25: 5975-5983 2005 Type: ARTICLE Genes: syd-2 unc-2 unc-10 unc-13 Abstract: Active zone proteins play a fundamental role in regulating neurotransmitter release and defining release sites. The functional roles of active zone components are beginning to be elucidated; however, the mechanisms of active zone protein localization are unknown. Studies have shown that glutamine, leucine, lysine, and serine-rich protein (ELKS), a recently defined member of the active zone complex, acts to localize the active zone protein Rab3a-interacting molecule (RIM) and regulates synaptic transmission in cultured neurons. Here, we test the function of ELKS in vivo. Like mammalian ELKS, Caenorhabditis elegans ELKS is an active zone protein that directly interacts with the postsynaptic density-25/Discs large/zona occludens (PDZ) domain of RIM. However, RIM protein localizes in the absence of ELKS and vice versa. In addition, elks mutants exhibit neither the behavioral nor the physiological defects associated with unc-10 RIM mutants, indicating that ELKS is not a critical component of the C. elegans release machinery. Interestingly, expression of the soluble PDZ domain of RIM disrupts ELKS active zone targeting, suggesting a tight association between the two proteins in vivo. RIM truncations containing only the PDZ and C2A domains target to release sites in an ELKS-dependent manner. Together, these data identify ELKS as a new member of the C. elegans active zone complex, define the role of ELKS in synaptic transmission, and characterize the relationship between ELKS and RIM in vivo. Furthermore, they demonstrate that multiple different protein-protein interactions redundantly anchor both ELKS and RIM to active zones and implicate novel proteins in the formation of the active zone. ------------------- Key: 7305 Medline: 15914661 Authors: Shtonda B;Avery L Title: CCA-1, EGL-19 and EXP-2 currents shape action potentials in the Caenorhabditis elegans pharynx. Citation: Journal of Experimental Biology 208: 2177-2190 2005 Type: ARTICLE Genes: cca-1 egl-19 exp-2 Abstract: The pharynx of Caenorhabditis elegans is a tubular muscle controlled by its own set of neurons. We developed a technique to voltage clamp the pharyngeal muscle and demonstrate by analyzing mutants that the pharyngeal action potential is regulated by three major voltage-gated currents, conducted by a T-type calcium channel CCA-1, an L-type calcium channel EGL-19 and a potassium channel EXP-2. We show that CCA-1 exhibits T-type calcium channel properties: activation at -40 mV and rapid inactivation. Our results suggest that CCA-1's role is to accelerate the action potential upstroke in the pharyngeal muscle in response to excitatory inputs. Similarly to other L-type channels, EGL-19 activates at high voltages and inactivates slowly; thus it may maintain the plateau phase of the action potential. EXP-2 is a potassium channel of the kV family that shows inward rectifier properties when expressed in Xenopus laevis oocytes. We show that endogenous EXP-2 is not a true inward rectifier - it conducts large outward currents at potentials up to +20 mV and is therefore well suited to trigger rapid repolarization at the end of the action potential plateau phase. Our results suggest that EXP-2 is a potassium channel with unusual properties that uses a hyperpolarization threshold to activate a regenerative ------------------- Key: 7306 Medline: 15914662 Authors: Steger KA;Shtonda BB;Thacker C;Snutch TP;Avery L Title: The C. elegans T-type calcium channel CCA-1 boosts neuromuscular transmission. Citation: Journal of Experimental Biology 208: 2191-2203 2005 Type: ARTICLE Genes: cca-1 eat-2 snt-1 unc-17 Abstract: Low threshold-activated or T-type calcium channels are postulated to mediate a variety of bursting and rhythmic electrical firing events. However, T-type channels' exact physiological contributions have been difficult to assess because of their incompletely defined pharmacology and the difficulty in isolating T-type currents from more robust high threshold calcium currents. A current in C elegans pharyngeal muscle displays the kinetic features of a T-type calcium channel and is absent in animals homozygous for mutations at the cca-1 locus (see accompanying paper). cca-1 is expressed in pharyngeal muscle and encodes a protein (CCA-1) with strong homology to the alpha(1) subunits of vertebrate T-type channels. We show that CCA-1 plays a critical role at the pharyngeal neuromuscular junction, permitting the efficient initiation of action potentials in response to stimulation by the MC motor neuron. Loss of cca-1 function decreases the chance that excitatory input from MC will successfully trigger an action potential, and reduces the ability of an animal to take in food. Intracellular voltage recordings demonstrate that when wild-type cca-1 is absent, the depolarizing phase of the pharyngeal action potential tends to plateau or stall near -30 mV, the voltage at which the CCA-1 channel is likely to be activated. We conclude that the CCA-1 T-type calcium channel boosts the excitatory effect of synaptic input, allowing for reliable and rapid depolarization. and contraction of the pharyngeal muscle. We also show that the pharyngeal muscle employs alternative strategies for initiating action potentials in certain cases of compromised MC motor neuron function. ------------------- Key: 7307 Medline: 15840570 Authors: Vatamaniuk OK;Bucher EA;Sundaram MV;Rea PA Title: CeHMT-1, a putative phytochelatin transporter, is required for cadmium tolerance in Caenorhabditis elegans. Citation: Journal of Biological Chemistry 280: 23684-23690 2005 Type: ARTICLE Genes: haf-7 haf-9 hmt-1 pcs-1 Abstract: Phytochelatins (PCs), (gamma-Glu-Cys) nGly polymers that were formerly considered to be restricted to plants and some fungal systems, are now known to play a critical role in heavy metal (notably Cd2+) detoxification in Caenorhabditis elegans. In view of the functional equivalence of the gene encoding C. elegans PC synthase 1, ce-pcs-1, to its homologs from plant and fungal sources, we have gone on to explore processes downstream of PC fabrication in this organism. Here we describe the identification of a half-molecule ATP-binding cassette transporter, CeHMT-1, from C. elegans with an equivalent topology to that of the putative PC transporter SpHMT-1 from Schizosaccharomyces pombe. At one level, CeHMT-1 satisfies the requirements of a Cd2+ tolerance factor involved in the sequestration and/or elimination of (CdPC)-P-. complexes. Heterologous expression of cehmt-1 in S. pombe alleviates the Cd2+-hypersensitivity of hmt(-) mutants concomitant with the localization of Ce-HMT-1 to the vacuolar membrane. Suppression of the expression of ce-hmt-1 in intact worms by RNA interference (RNAi) confers a Cd2+-hypersensitive phenotype similar to but more pronounced than that exhibited by ce-pcs-1 RNAi worms. At another level, it is evident from comparisons of the cell morphology of ce-hmt-1 and ce-pcs-1 single and double RNAi mutants that CeHMT-1 also contributes to Cd2+ tolerance in other ways. Whereas the intestinal epithelial cells of ce-pcs-1 RNAi worms undergo necrosis upon exposure to toxic levels of Cd2+, the corresponding cells of ce-hmt-1 RNAi worms instead elaborate punctate refractive inclusions within the vicinity of the nucleus. Moreover, a deficiency in Ce-HMT-1 does not interfere with the phenotype associated with CePCS-1 deficiency and vice versa. Double ce-hmt-1; ce-pcs-1 RNAi mutants exhibit both cell morphologies when exposed to Cd2+. These results and those from our previous investigations of the requirement for PC synthase for heavy metal tolerance in C. elegans demonstrate PC-dependent, HMT-1-mediated heavy metal detoxification not only in S. pombe but also in some invertebrates while at the same time indicating that the ------------------- Key: 7308 Medline: 15880508 Authors: Konwerski J;Senchuk M;Petty E;Lahaie D;Schisa JA Title: Cloning and expression analysis of pos-1 in the nematodes Caenorhabditis briggsae and Caenorhabditis remanei. Citation: Developmental Dynamics 233: 1006-1012 2005 Type: ARTICLE Genes: glh-1 glh-2 glh-3 glh-4 glp-1 pal-1 pgl-1 pos-1 Abstract: The Caenorhabditis elegans pos-1 gene encodes a zinc-finger protein that is required for germline specification during embryogenesis. The maternally provided mRNA is translationally regulated both spatially and temporally during early development. We have cloned orthologs of pos-1 from C. briggsae and C. remanei, two Caenorhabditis species that have diverged from C. elegans by approximately 20-40 million years. Two regions in the 3' untranslated region are highly conserved among all three species. We find that the pos-1 RNA is expressed in the hermaphrodite and female gonads of C. briggsae and C. remanei but POS-1 protein is not detected at high levels in C. briggsae until the 2-cell stage of embyrogenesis. The protein expression is restricted to the germline precursors of the embryo. We conclude that pos-1 appears to be translationally regulated in C. briggsae as it is in C. elegans and speculate the conserved 3' UTR sequences may be involved. ------------------- Key: 7309 Medline: 15935776 Authors: Neves A;Priess JR Title: The REF-1 family of bHLH transcription factors pattern C. elegans embryos through Notch-dependent and Notch-independent pathways. Citation: Developmental Cell 8: 867-879 2005 Type: ARTICLE Genes: glp-1 hlh-25 hlh-26 hlh-27 hlh-29 lag-2 lin-12 ref-1 skn-1 tbx-37 tbx-38 unc-37 Abstract: Much of the patterning of early C. elegans embryos involves a series of Notch interactions that occur in rapid succession and have distinct outcomes; however, none of the targets for these interactions have been identified. We show that the REF-1 family of bHLH transcription factors is a major target of Notch signaling in all these interactions and that most examples of Notch-mediated transcriptional repression can be attributed to REF-1 activities. The REF-1 family is expressed and has similar functions in both Notch-dependent and Notch-independent pathways, and this dual mode of deployment is used repeatedly to pattern the embryo. REF-1 proteins are unusual in that they contain two different bHLH domains and lack the distinguishing characteristics of Hairy/Enhancer of Split (HES) bHLH proteins that are Notch targets in other systems. Our results show that the highly divergent REF-1 proteins are nonetheless HES-like bHLH effectors of Notch signaling. ------------------- Key: 7310 Medline: 15935777 Authors: Ross JM;Kalis AK;Murphy MW;Zarkower D Title: The DM domain protein MAB-3 promotes sex-specific neurogenesis in C. elegans by regulating bHLH proteins. Citation: Developmental Cell 8: 881-892 2005 Type: ARTICLE Genes: lin-32 mab-3 mab-5 pal-1 ref-1 eDf21 mnDf16 mnDf29 mnDf59 mnDf63 mnDf66 mnDf89 Abstract: Sexual dimorphism in the nervous system is required for sexual behavior and reproduction in many metazoan species. However, little is known of how sex determination pathways impose sex specificity on nervous system development. In C. elegans, the conserved sexual regulator MAB-3 controls several aspects of male development, including formation of V rays, male-specific sense organs required for mating. Here we show that MAB-3 promotes expression of the proneural protein LIN-32 in V ray precursors by transcriptional repression of ref-1, a member of the Hes family of neurogenic factors. Mutations in ref-1 restore lin-32:gfp expression and normal V ray development to mab-3 mutants, suggesting that ref-1 is the primary target of MAB-3 in the V ray lineage. Proteins related to MAB-3 (DM domain proteins) control sexual differentiation in diverse metazoans. We therefore suggest that regulation of Hes genes by DM domain proteins may be a general mechanism for specifying sex-specific neurons. ------------------- Key: 7311 Medline: 15935778 Authors: Perens EA;Shaham S Title: C. elegans daf-6 encodes a patch-related protein required for lumen formation. Citation: Developmental Cell 8: 893-906 2005 Type: ARTICLE Genes: che-14 daf-6 ptr-7 Abstract: Sensory organs are often composed of neuronal sensory endings accommodated in a lumen formed by ensheathing epithelia or glia. Here we show that lumen formation in the C. elegans amphid sensory organ requires the gene daf-6. daf-6 encodes a Patched-related protein that localizes to the luminal surfaces of the amphid channel and other C. elegans tubes. While daf-6 mutants display only amphid lumen defects, animals defective for both daf-6 and the Dispatched gene che-14 exhibit defects in all tubular structures that express daf-6. Furthermore, DAF-6 protein is mislocalized, and lumen morphogenesis is abnormal, in mutants with defective sensory neuron endings. We propose that amphid lumen morphogenesis is coordinated by neuron-derived cues and a DAF-6/CHE-14 system that regulates vesicle dynamics during tubulogenesis. ------------------- Key: 7312 Medline: 15935771 Authors: Wiggin GR;Fawcett JP;Pawson T Title: Polarity proteins in axon specification and synaptogenesis. Citation: Developmental Cell 8: 803-816 2005 Type: REVIEW Genes: crmp-2 gsk-3 par-1 par-2 par-3 par-4 par-5 par-6 Abstract: The neuron is a prime example of a highly polarized cell. It is becoming clear that conserved protein complexes, which have been shown to regulate polarity in such diverse systems as the C. elegans zygote and mammalian epithelia, are also required for neuronal polarization. This review considers the role of these polarity proteins in axon specification and synapto-genesis. ------------------- Key: 7313 Medline: 15936327 Authors: Drabikowski K;Trzebiatowska A;Chiquet-Ehrismann R Title: ten-1, an essential gene for germ cell development, epidermal morphogenesis, gonad migration, and neuronal pathfinding in Caenorhabditis elegans. Citation: Developmental Biology 282: 27-38 2005 Type: ARTICLE Genes: rrf-1 rrf-3 ten-1 Abstract: ten-m (odz) is the only pair-rule gene discovered in Drosophila that encodes a transmembrane protein and not a transcription factor. The vertebrate Ten-m orthologues have been implicated in pattern formation and neuronal development. To investigate the role of this protein in development, we characterize here the structure and function of the Caenorhabditis elegans orthologue ten-1. We found that two promoters control the expression of two different ten-1 transcripts. This results in the expression of type II transmembrane protein variants differing in their intracellular domains. Both ten-1 transcripts show complex, but distinct, expression patterns during development and in the adult. Interference with Ten-1 expression by RNAi experiments leads to multiple phenotypes resulting in defects in hypodermal cell migration, neuronal migration, pathfinding and fasciculation, distal tip cell migration, the establishment of the somatic gonad, and gametogenesis. The RNAi phenotypes were confirmed by the analysis of a deletion mutant which revealed that Ten-1 is essential for somatic gonad formation. The intracellular domain of the long form was detected at the cell membrane and in the nucleus. We propose that Ten-1 acts as a receptor for morphogenetic cue(s) and directly signals to the nucleus by translocation of its intracellular domain to the nucleus following its proteolytic release from the cell ------------------- Key: 7314 Medline: 15936335 Authors: Liu Z;Fujii T;Nukazuka A;Kurokawa R;Suzuki M;Fujisawa H;Takagi S Title: C. elegans PlexinA PLX-1 mediates a cell contact-dependent stop signal in vulval precursor cells. Citation: Developmental Biology 282: 138-151 2005 Type: ARTICLE Genes: plx-1 smp-1 smp-2 Abstract: PLX-1 is a PlexinA transmembrane protein in Caenorhabditis elegans, and the transmembrane-type semaphorin, SMP-1, is a ligand for PLX-1. The SMP-1 /PLX-1 system has been shown to be necessary for proper epidermal morphogenesis in the male tail and seam cells. Here, we show that the SMP-1/PLX-1 system also regulates vulval morphogenesis. In ply-1 and smp-1 mutants, hermaphrodites sometimes exhibit a protruding vulva or multiple vulva-like protrusions. Throughout the vulval development of ply-1 and smp-1 mutants, the arrangement of vulval cells is often disrupted. In the initial step of vulval morphogenesis, vulval precursor cells (VPCs) are generated normally but are subsequently arranged abnormally in mutants. Continuous observation revealed that plx-1 VPC fails to terminate longitudinal extension after making contact with neighbor VPCs. The arrangement defects of VPCs in plx-1 and smp-1 mutants are rescued by expressing the respective cDNA in VPCs. plx-1::egfp and smp-1::egfP transgenes are both expressed in all vulval cells, including VPCs, throughout vulval development. We propose that the SMP-1/PLX-1 system is responsible for a cell contact-mediated stop signal for VPC extension. Analyses using cell fate-specific markers showed that the arrangement defects of VPCs also affect cell fate specification and cell lineages, but in a relatively small fraction of plx-1 mutants. ------------------- Key: 7315 Medline: 15936342 Authors: McNally KL;McNally FJ Title: Fertilization initiates the transition from anaphase I to metaphase II during female meiosis in C. elegans. Citation: Developmental Biology 282: 218-230 2005 Type: ARTICLE Genes: fer-1 spe-9 spe-11 sDp2 Abstract: Oocytes from most animals arrest twice during the meiotic cell cycle. The universally conserved prophase I arrest is released by a maturation hormone that allows progression to a second arrest point, typically metaphase I or II. This second arrest allows for short-term storage of fertilization-competent eggs and is released by signaling that occurs during fertilization. Nematodes are unique in that the maturation hormone is secreted by sperm rather than by the mother's somatic tissues. We have investigated the nature of the second arrest in matured but unfertilized Caenorhabditis elegans embryos using time-lapse imaging of GFP-tubulin or GFP-histone. Unfertilized embryos completed anaphase I but did not form polar bodies or assemble meiosis 11 spindles. Nevertheless, unfertilized embryos assembled female pronuclei at the same time as fertilized embryos. Analysis of embryos fertilized by sperm lacking the SPE-11 protein indicated that fertilization promotes meiotic cytokinesis through the SPE-11 protein but assembly of the meiosis II spindle is initiated through an SPE-11-independent pathway. ------------------- Key: 7316 Medline: 15936343 Authors: Sapio MR;Hilliard MA;Cermola M;Favre R;Bazzicalupo B Title: The Zona Pellucida domain containing proteins, CUT-1, CUT-3 and CUT-5, play essential roles in the development of the larval alae in Caenorhabditis elegans. Citation: Developmental Biology 282: 231-245 2005 Type: ARTICLE Genes: cut-1 cut-3 cut-4 cut-5 cut-6 daf-2 daf-7 daf-8 Abstract: The alae, longitudinal ridges of the lateral cuticle, are the most visible specialization of the Caenorhabditis elegans surface. They are present only in L1 and clatter larvae and in adults. Little is known about the mechanisms through which at the appropriate stages secretion of cuticle components by the seam cells results in the formation of the alae. Here we show that three proteins, each containing a Zona Pellucida domain (ZP), are components of the cuticle necessary for larval alae development: CUT-1 and CUT-5 in dauer larvae and CUT-3 and CUT-5 in L1s. Transcriptional regulation of the corresponding genes contributes to the stage-specific role of these proteins. Larvae with reduced cut-1, cut-3 or cut-5 function not only lack alae but are also larger in diameter due to an increase in the width of the lateral cuticle. We propose a model in which reduction of the body diameter, which occurs in normal L1 and dauer larvae, is the result of a dorso-ventral shrinking of the internal layer of the lateral cuticle and formation of the alae results from the folding of the external layer of the lateral cuticle over the reduced, internal one. Alae of ------------------- Key: 7317 Medline: 15960981 Authors: Sherwood DR;Butler JA;Kramer JM;Sternberg PW Title: FOS-1 promotes baement-membrane removal during anchor-cell invasion in C. elegans. Citation: Cell 121: 951-962 2005 Type: ARTICLE Genes: cdh-3 egl-17 evl-5 fos-1 him-4 lin-3 mig-2 pat-3 sel-8 Abstract: Cell invasion through basement membranes is crucial during morphogenesis and cancer metastasis. Here, we genetically dissect this process during anchor-cell invasion into the vulval epithelium in C. elegans. We have identified the fos transcription factor ortholog fos-1 as a critical regulator of basement-membrane removal. In fos-1 mutants, the gonadal anchor cell extends cellular processes normally toward vulval cells, but these processes fail to remove the basement membranes separating the gonad from the vulval epithelium. fos-1 is expressed in the anchor cell and controls invasion cell autonomously. We have identified ZMP-1, a membrane-type matrix metalloproteinase, CDH-3, a Fat-like protocadherin, and hemicentin, a fibulin family extracellular matrix protein, as transcriptional targets of FOS-1 that promote invasion. These results reveal a key genetic network that controls basement-membrane removal during cell invasion. ------------------- Key: 7318 Medline: 15935281 Authors: Goyal K;Browne JA;Burnell AM;Tunnacliffe A Title: Dehydration-induced tps gene transcripts from an anhydrobiotic nematode contain novel spliced leaders and encode atypical GT-20 family proteins. Citation: Biochimie 87: 565-574 2005 Type: ARTICLE Genes: tps-1 tps-2 Abstract: Accumulation of the non-reducing disaccharide trehalose is associated with desiccation tolerance during anhydrobiosis in a number of invertebrates, but there is little information on trehalose biosynthetic genes in these organisms. We have identified two trehalose-6-phosphate synthase (tps) genes in the anhydrobiotic nematode Aphelenchus avenae and determined full length cDNA sequences for both; for comparison, full length tps cDNAs from the model nematode, Caenorhabditis elegans, have also been obtained. The A. avenae genes encode very similar proteins containing the catalytic domain characteristic of the GT-20 family of glycosyltransferases and are most similar to tps-2 of C. elegans; no evidence was found for a gene in A. avenae corresponding to Ce-tps-1. Analysis of A. avenae tps cDNAs revealed several features of interest, including alternative trans-splicing of spliced leader sequences in Aav-tps-1, and four different, novel SL1-related trans-spliced leaders, which were different to the canonical SL1 sequence found in all other nematodes studied. The latter observation suggests that A. avenae does not comply with the strict evolutionary conservation of SL1 sequences observed in other species. Unusual features were also noted in predicted nematode TPS proteins, which distinguish them from homologues in other higher eukaryotes (plants and insects) and in micro-organisms. Phylogenetic analysis confirmed their membership of the GT-20 glycosyltransferase family, but indicated an accelerated rate of molecular evolution. Furthermore, nematode TPS proteins possess N- and C-terminal domains, which are unrelated to those of other eukaryotes: nematode C-terminal domains, for example, do not contain trehalose-6-phosphate phosphatase-like sequences, as seen in plant and insect homologues. During onset of anhydrobiosis, both tps genes in A. avenae are upregulated, but exposure to cold or increased osmolarity also results in gene induction, although to a lesser extent. Trehalose seems likely therefore to play a role in ------------------- Key: 7319 Medline: Authors: Gilleard JS Title: The use of Caenorhabditis elegans in parasitic nematode research. Citation: Parasitology 128: S49-S70 2005 Type: REVIEW Genes: apx-1 art-1 ben-1 ced-3 cpl-1 elt-2 glp-1 lag-2 lin-39 lin-48 mab-5 ppp-1 sod-1 tra-2 Abstract: There is increasing interest in the use of the free-living nematode Caenorhabditis elegans as a tool for parasitic nematode research and there are now a number of compelling examples of its successful application. C. elegans has the potential to become a standard tool for molecular helminthology researchers, just as yeast is routinely used by molecular biologists to study vertebrate biology. However, in order to exploit C. elegans in a meaningful manner, we need a detailed understanding of the extent to which different aspects of C. elegans biology have been conserved with particular groups of parasitic nematodes. This review first considers the current state of knowledge regarding the conservation of genome organisation across the nematode phylum and then discusses some recent evolutionary development studies in free-living nematodes. The aim is to provide some important concepts that are relevant to the extrapolation of information from C. elegans to parasitic nematodes and also to the interpretation of experiments that use C. elegans as a surrogate expression system. In general, examples have been specifically chosen because they highlight the importance of careful experimentation and interpretation of data. Consequently, the focus is on the differences that have been found between nematode species rather than the similarities. Finally, there is a detailed discussion of the current status of C. elegans as a heterologous expression system to study parasite gene function and regulation using successful examples from the literature. ------------------- Key: 7320 Medline: 15921654 Authors: Phelan P Title: Innexins: members of an evolutionarily conserved family of gap-junction proteins. Citation: Biochimica et Biophysica Acta 1711: 225-245 2005 Type: REVIEW Genes: eat-5 inx-3 inx-6 unc-7 unc-9 Abstract: Gap junctions are clusters of intercellular channels that provide cells, in all metazoan organisms, with a means of communicating directly with their neighbours. Surprisingly, two gene families have evolved to fulfil this fundamental, and highly conserved, function. In vertebrates, gap junctions are assembled from a large family of connexin proteins. Innexins were originally characterized as the structural components of gap junctions in Drosophila, an arthropod, and the nematode Caenorhabditis elegans. Since then, innexin homologues have been identified in representatives of the other major invertebrate phyla and in insect-associated viruses. Intriguingly, functional innexin homologues have also been found in vertebrate genomes. These studies have informed our understanding of the molecular evolution of gap junctions and have greatly expanded the numbers of model systems available for functional studies. Genetic manipulation of innexin function in relatively simple cellular systems should speed progress not only in defining the importance of gap junctions in a variety of biological processes but also in elucidating the mechanisms by which they act. ------------------- Key: 7321 Medline: Authors: Artal-Sanz M;Tavernarakis N Title: Proteolytic mechanisms in necrotic cell death and neurodegeneratin. Citation: FEBS Letters 579: 3287-3296 2005 Type: REVIEW Genes: asp-3 asp-4 clp-1 tra-3 Abstract: ------------------- Key: 7322 Medline: Authors: Kadandale P;Geldziler B;Hoffmann M;Singson A Title: Use of SNPs to determine the breakpoints of complex deficiencies, facilitating gene mapping in Caenorhabditis elegans. Citation: BMC Genetics 6: 1-7 2005 Type: ARTICLE Genes: dif-2 dpy-20 eat-1 him-8 let-59 let-64 let-68 let-70 let-71 let-73 let-91 let-97 let-98 let-99 let-100 let-309 let-311 let-655 let-656 lin-3 pha-3 rib-1 sem-3 spe-19 ozDf1 ozDf2 sDf62 Abstract: ------------------- Key: 7323 Medline: 15998324 Authors: Roudier N;Lefebvre C;Legouis R Title: CeVPS-27 is an endosomal protein required for the molting and the endocytic trafficking of the low-density lipoprotein receptor-related protein 1 in Caenorhabditis Citation: Traffic 6: 695-705 2005 Type: ARTICLE Genes: vps-4 vps-23 vps-27 vps-32 vps-36 Abstract: Class E vacuolar protein-sorting (Vps) proteins were first described in yeast as being involved in receptor-mediated endocytosis and multivesicular body formation. Inactivation by RNA interference of the class E VPS genes of the nematode Caenorhabditis elegans revealed heterogeneous phenotypes. We have further characterized the role of the essential gene Cevps-27, ortholog of human hepatocyte growth factor-regulated tyrosine kinase substrate, during the development of C. elegans. Use of green fluorescent protein fusion constructs and antibody staining revealed that Cevps-27 localizes to endosomal membranes. It is widely expressed but enriched in epithelial cells. Cevps-27 mutants presented enlarged endosomal structures and an accumulation of autophagic vesicles as revealed by electron microscopy and the analysis of the autophagic marker LGG-1. Cevps-27 animals arrested at L2-L3 molt with an inability to degrade their old cuticle. This molting phenotype was more severe when Cevps-27 worms were grown on suboptimal concentrations of cholesterol. Furthermore, defective endocytic trafficking of the low-density lipoprotein receptor-related protein 1 (LRP-1) was also observed in Cevps-27 mutants. These results indicate that CeVPS-27 is required for endosomal and autophagic pathways in C. elegans and plays a crucial role in the control of molting through LRP-1 internalization and cholesterol traffic. ------------------- Key: 7324 Medline: 15930100 Authors: Dixon SJ;Roy PR Title: Muscle arm development in Caenorhabditis elegans. Citation: Development 132: 3079-3092 2005 Type: ARTICLE Genes: act-1 act-2 act-3 dpy-5 dpy-10 egl-30 lev-11 lin-6 lon-2 sma-6 unc-15 unc-54 unc-60 unc-78 unc-104 Abstract: In several types of animals, muscle cells use membrane extensions to contact motor axons during development. To better understand the process of membrane extension in muscle cells, we investigated the development of Caenorhabditis elegans muscle arms, which extend to motor axons and form the postsynaptic element of the neuromuscular junction. We found that muscle arm development is a highly regulated process: the number of muscle arms extended by each muscle, the shape of the muscle arms and the path taken by the muscle arms to reach the motor axons are largely stereotypical. We also investigated the role of several cytoskeletal components and regulators during arm development, and found that tropomyosin (LEV-11), the actin depolymerizing activity of ADF/cofilin (UNC-60B) and, surprisingly, myosin heavy chain B (UNC-54) are each required for muscle arm extension. This is the first evidence that UNC-54, which is found in thick filaments of sarcomeres, can also play a role in membrane extension. The muscle arm phenotypes produced when these genes are mutated support a 'two-phase' model that distinguishes passive muscle arm development in embryogenesis from active muscle arm extension during ------------------- Key: 7325 Medline: 15975936 Authors: Kosinski M;McDonald K;Schwartz J;Yamamoto I;Greenstein D Title: C. elegans sperm bud vesicles to deliver a meiotic maturation signal to distant oocytes. Citation: Development 132: 3357-3369 2005 Type: ARTICLE Genes: emo-1 fem-3 fog-2 spe-8 spe-27 Abstract: The major sperm protein (MSP) is the central cytoskeletal element required for actin-independent motility of nematode spermatozoa. MSP has a dual role in Caenorhabditis elegans reproduction, functioning as a hormone for both oocyte meiotic maturation and ovarian muscle contraction. The identification of the signaling function of MSP raised the question, how do spermatozoa, which are devoid of ribosomes, ER and Golgi, release a cytoplasmic protein lacking a signal sequence? Here, we provide evidence that MSP export occurs by the budding of novel vesicles that have both inner and outer membranes with MSP sandwiched in between. MSP vesicles are apparently labile structures that generate long-range MSP gradients for signaling at the oocyte cell surface. Both spermatozoa and non-motile spermatids bud MSP vesicles, but their stability and signaling properties differ. Budding protrusions from the cell body contain MSP, but not the MSD proteins, which counteract MSP filament assembly. We propose that MSP generates the protrusive force for its own vesicular ------------------- Key: 7326 Medline: 15936091 Authors: Ahn IY;Winter CE Title: Determination of DNA base composition by small scale acrylamide-CsCl gradient centrifugation. Citation: Journal of Biochemical and Biophysical Methods 63: 155-160 2005 Type: ARTICLE Genes: Abstract: In this paper we describe a simple and rapid protocol for DNA base composition determination by CsCl gradient in the presence of acrylamide. This method permits the determination of GC content in microgram amounts of DNA, and results are easily documented in photographs or graphs. The protocol was applied to the characterization of nematode DNA, but can be used for other organisms. Analyzing several experiments the mean standard deviation observed in the calculated GC content is near 1.3%. ------------------- Key: 7327 Medline: 15998808 Authors: Hamilton B;Dong Y;Shindo M;Liu W;Odell I;Ruvkun G;Lee SS Title: A systematic RNAi screen for longevity genes in C. elegans. Citation: Genes & Development 19: 1544-1555 2005 Type: ARTICLE Genes: age-1 akt-1 atp-3 cco-1 cdh-12 ceh-18 clk-1 cyc-1 daf-2 daf-16 dpy-13 eat-1 eat-3 eat-4 eat-6 egl-3 glp-1 gcy-18 gcy-23 hmr-1 hsp-6 iff-1 ins-18 isp-1 lrs-2 pdk-1 rrf-3 sir-2.1 sgk-1 spt-4 vit-2 vit-5 Abstract: We report here the first genome-wide functional genomic screen for longevity genes. We systematically surveyed Caenorhabditis elegans genes using large-scale RNA interference (RNAi), and found that RNAi inactivation of 89 genes extend C. elegans lifespan. Components of the daf-2/insulin-like signaling pathway are recovered, as well as genes that regulate metabolism, signal transduction, protein turnover, and gene expression. Many of these candidate longevity genes are conserved across animal phylogeny. Genetic interaction analyses with the new longevity genes indicate that some act upstream of the daf-16/FOXO transcription factor or the sir2.1 protein deacetylase, and others function independently of daf-16/FOXO and sir2.1, and might define new pathways to regulate lifespan. ------------------- Key: 7328 Medline: 15920475 Authors: Okochi Y;Kimura KD;Ohta A;Mori I Title: Diverse regulation of sensory signaling by C. elegans nPKC-epsilon/eta TTX-4. Citation: EMBO Journal 24: 2127-2137 2005 Type: ARTICLE Genes: dgk-1 egl-8 kin-13 pld-1 tax-6 ttx-1 ttx-3 ttx-4 Abstract: Molecular and pharmacological studies in vitro suggest that protein kinase C (PKC) family members play important roles in intracellular signal transduction. Nevertheless, the in vivo roles of PKC are poorly understood. We show here that nPKC-epsilon/eta TTX-4 in the nematode Caenorhabditis elegans is required for the regulation of signal transduction in various sensory neurons for temperature, odor, taste, and high osmolality. Interestingly, the requirement for TTX-4 differs in different sensory neurons. In AFD thermosensory neurons, gain or loss of TTX-4 function inactivates or hyperactivates the neural activity, respectively, suggesting negative regulation of temperature sensation by TTX-4. In contrast, TTX-4 positively regulates the signal sensation of ASH nociceptive neurons. Moreover, in AWA and AWC olfactory neurons, TTX-4 plays a partially redundant role with another nPKC, TPA-1, to regulate olfactory signaling. These results suggest that C. elegans nPKCs regulate different sensory signaling in various sensory neurons. Thus, C. elegans provides an ideal model to reveal genetically novel components of nPKC-mediated molecular pathways in sensory signaling. ------------------- Key: 7329 Medline: Authors: Mustard JA;Beggs KT;Mercer AR Title: Molecular biology of the invertebrate dopamine receptor. Citation: Archives of Insect Biochemistry and Physiology 59: 103-117 2005 Type: REVIEW Genes: cat-2 dop-1 dop-2 dop-3 Abstract: Dopamine is found in the nervous systems of both vertebrates and invertebrates. However, the specific actions of dopamine depend on the dopamine receptor type that is expressed in the target cell. As in mammals, different subtypes of dopamine receptors have been cloned and characterized from invertebrates, and these receptor subtypes have different structural and functional properties. Understanding how these receptors respond to dopamine and in which cells each receptor type is expressed is key to our understanding of the role of dopamine signaling. Comparison of the amino acid sequences and experimentally determined functional properties suggest that there are at least three distinct types of dopamine receptors in invertebrates. This review focuses on invertebrate dopamine receptors for which the genes have been isolated and identified, and examines our current knowledge of the functional and structural properties of these receptors, and their pharmacology and expression. ------------------- Key: 7330 Medline: Authors: Hermann GJ;Schroeder LK;Hieb CA;Kershner AM;Rabbitts BM;Fonarev P;Grant BD;Priess JR Title: Genetic analysis of lysosomal trafficking in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 16: 3273-3288 2005 Type: ARTICLE Genes: apt-2 apt-6 apt-7 bec-1 cad-1 cup-5 daf-4 dpy-23 eea-1 flu-1 flu-2 flu-3 flu-4 glo-1 glo-2 glo-3 glo-4 let-512 mtm-6 pqn-9 rab-7 rme-1 rme-8 rrf-3 snx-1 unc-54 vac-1 vps-5 vps-16 vps-27 vps-29 vps-30 vps-34 vps-41 vps-45 vps-54 ypt-7 Abstract: The intestinal cells of Caenorhabditis elegans embryos contain prominent, birefringent gut granules that we show are lysosome-related organelles. Gut granules are labeled by lysosomal markers, and their formation is disrupted in embryos depleted of AP-3 subunits, VPS-16, and VPS-41. We define a class of gut granule loss (glo) mutants that are defective in gut granule biogenesis. We show that the glo-1 gene encodes a predicted Rab GTPase that localizes to lysosome-related gut granules in the intestine and that glo-4 encodes a possible GLO-1 guanine nucleotide exchange factor. These and other glo genes are homologous to genes implicated in the biogenesis of specialized lysosome-related organelles such as melanosomes in mammals and pigment granules in Drosophila. The glo mutants thus provide a simple model system for the analysis of lysosome-related organelle biogenesis in animal cells. ------------------- Key: 7331 Medline: Authors: Ratsch G;Sonnenburg S;Scholkopf B Title: RASE: recognition of alternatively spliced exons in C. elegans. Citation: Bioinformatics 21: i369-i377 2005 Type: ARTICLE Genes: Abstract: ------------------- Key: 7332 Medline: Authors: Mylonakis E;Aballay A Title: Worms and flies as genetically tractable animal models to study host-pathogen interactions. Citation: Infection and Immunity 73: 3833-3841 2005 Type: REVIEW Genes: age-1 bre-5 daf-2 ced-3 ced-4 ced-9 daf-16 ikb-1 nlp-29 nsy-1 pik-1 pmk-1 sek-1 tol-1 trf-1 ttm-1 ttm-2 Abstract: ------------------- Key: 7333 Medline: Authors: Samuel ADT;Sengupta P Title: Sensorimotor integration: locating locomotion in neural circuits. Citation: Current Biology 15: R341-R343 2005 Type: REVIEW Genes: Abstract: Neural components of the circuits that transform sensory cues into changes in motor activities are largely unknown. Several recent studies have now functionally mapped the sensorimotor circuits responsible for locomotion behaviors under defined environmental conditions in the nematode Caenorhabditis elegans. ------------------- Key: 7334 Medline: Authors: Link CD Title: Invertebrate models of Alzheimer's disease. Citation: Genes, Brain, & Behavior 4: 147-156 2005 Type: REVIEW Genes: Abstract: The intensely studied model organisms Caenorhabditis elegans and Drosophila melanogaster have been employed to study a number of neurodegenerative diseases, including Alzheimer's disease (AD). Although worms and flies are phylogenetically distant from humans, results of both classic genetic analyses and transgenic manipulation of these invertebrates suggest they are valid models for at least some aspects of AD. This review describes the rationale for AD-relevant studies in worms and flies and discusses both what has been learned from these studies and what may be discovered in the future. ------------------- Key: 7335 Medline: 15798396 Authors: Hamelin M;Meng X;Cuddy M;Korsun K;Ondeyka J;Simpson PB;Cully DF;Priest BT Title: A high-trhoughput assay for modulators of ligand-gated chloride channels. Citation: Assay & Drug Development Technologies 3: 59-64 2005 Type: ARTICLE Genes: Abstract: Invertebrate glutamate-gated chloride channels (GluCls) are important targets for anthelmintics and insecticides such as ivermectin. To facilitate screening for novel GluCl modulators, the Caenorhabditis elegans GluCl alpha2beta channel was chosen as a surrogate for parasite channels not yet cloned, and an inducible stable human embryonic kidney cell line was generated. Functional expression of the alpha2 and beta subunits was confirmed by whole-cell voltage clamp assays. Using this cell line, a high-throughput assay was developed that detects membrane potential changes associated with the activation of GluCls. In this assay, membrane depolarization was quantified via changes in fluorescence resonance energy transfer between two membrane-associated dyes. Robust and reproducible signals were detected in response to addition of glutamate or ivermectin. This assay was used for the screening of over 180,000 samples from natural and synthetic sources. ------------------- Key: 7336 Medline: Authors: MacQueen AJ;Baggett JJ;Perumov N;Bauer RA;Januszewski T;Schriefer L;Waddle JA Title: ACT-5 is an essential Caenorhabditis elegans actin required for intestinal microvilli formation. Citation: Molecular Biology of the Cell 16: 3247-3259 2005 Type: ARTICLE Genes: act-5 Abstract: Investigation of Caenorhabditis elegans act-5 gene function revealed that intestinal microvillus formation requires a specific actin isoform. ACT-5 is the most diverged of the five C. elegans actins, sharing only 93% identity with the other four. Green fluorescent protein reporter and immunofluorescence analysis indicated that act-5 gene expression is limited to microvillus-containing cells within the intestine and excretory systems and that ACT-5 is apically localized within intestinal cells. Animals heterozygous for a dominant act-5 mutation looked clear and thin and grew slowly. Animals homozygous for either the dominant act-5 mutation, or a recessive loss of function mutant, exhibited normal morphology and intestinal cell polarity, but died during the first larval stage. Ultrastructural analysis revealed a complete loss of intestinal microvilli in homozygous act-5 mutants. Forced expression of ACT-1 under the control of the act-5 promoter did not rescue the lethality of the act-5 mutant. Together with immuno-electron microscopy experiments that indicated ACT-5 is enriched within microvilli themselves, these results suggest a microvillus-specific function for act-5, and further, they raise the possibility that specific actins may be specialized for building microvilli and related structures. ------------------- Key: 7337 Medline: 15878875 Authors: Palmitessa A;Hess HA;Bany IA;Kim YM;Koelle MR;Benovic JL Title: Caenorhabditis elegans arrestin regulates neural G protein signaling and olfactory adaptation and recovery. Citation: Journal of Biological Chemistry 280: 24649-24662 2005 Type: ARTICLE Genes: adp-1 arr-1 egl-30 goa-1 lin-15 odr-3 osm-9 Abstract: Although regulation of G protein-coupled receptor signaling by receptor kinases and arrestins is a well established biochemical process, the physiological significance of such regulation remains poorly understood. To better understand the in vivo consequences of arrestin function, we have examined the function of the sole arrestin in Caenorhabditis elegans (ARR-1). ARR-1 is primarily expressed in the nervous system, including the HSN neuron and various chemosensory neurons involved in detecting soluble and volatile odorants. arr-1 null mutants exhibit normal chemotaxis but have significant defects in olfactory adaptation and recovery to volatile odorants. In contrast, adaptation is enhanced in animals overexpressing ARR-1. Both the adaptation and recovery defects of arr-1 mutants are rescued by transgenic expression of wild-type ARR-1, whereas expression of a C-terminally truncated ARR-1 effectively rescues only the adaptation defect. A potential mechanistic basis for these findings is revealed by in vitro studies demonstrating that wild-type ARR-1 binds proteins of the endocytic machinery and promotes receptor endocytosis, whereas C-terminally truncated ARR-1 does not. These results demonstrate that ARR-1 functions to regulate chemosensory signaling, enabling organisms to adapt to a variety of environmental cues, and provide an in vivo link between arrestin, receptor endocytosis, and temporal ------------------- Key: 7338 Medline: 15856303 Authors: Jovelin R;Phillips PC Title: Functional constraint and divergence in the G protein family in Caenorhabditis elegans and Caenorhabditis Citation: Molecular Genetics & Genomics 273: 299-310 2005 Type: ARTICLE Genes: che-13 egl-30 goa-1 gpa-1 gpa-2 gpa-3 gpa-4 gpa-5 gpa-6 gpa-7 gpa-8 gpa-9 gpa-10 gpa-11 gpa-12 gpa-13 gpa-14 gpa-15 gpa-16 gpb-1 gpb-2 gpc-1 gpc-2 gsa-1 lin-25 nlp-4 odr-3 pas-5 ubc-25 Abstract: Part of the challenge of the post-genomic world is to identify functional elements within the wide array of information generated by genome sequencing. Although cross-species comparisons and investigation of rates of sequence divergence are an efficient approach, the relationship between sequence divergence and functional conservation is not clear. Here, we use a comparative approach to examine questions of evolutionary rates and conserved function within the guanine nucleotide-binding protein (G protein) gene family in nematodes of the genus Caenorhabditis. In particular, we show that, in cases where the Caenorhabditis elegans ortholog shows a loss-of-function phenotype, G protein genes of C. elegans and Caenorhabditis briggsae diverge on average three times more slowly than G protein genes that do not exhibit any phenotype when mutated in C. elegans, suggesting that genes with loss of function phenotypes are subject to stronger selective constraints in relation to their function in both species. Our results also indicate that selection is as strong on G proteins involved in environmental perception as it is on those controlling other important processes. Finally, using phylogenetic footprinting, we identify a conserved noncoding motif present in multiple copies in the genomes of four species of Caenorhabditis. The presence of this motif in the same intron in the gpa-1 genes of C. elegans, C. briggsae and Caenorhabditis remanei suggests that it plays a role in the regulation of gpa-1, as well as ------------------- Key: 7339 Medline: 15892079 Authors: Materi W;Pilgrim D Title: Novel Caenorhabditis elegans unc-119 axon outgrowth defects correlate with behavioral phenotypes that are partially rescued by nonneural UNC-119. Citation: Genesis 42: 104-116 2005 Type: ARTICLE Genes: daf-7 mec-4 myo-3 unc-4 unc-44 unc-51 unc-104 unc-119 Abstract: UNC-119 function is necessary for the correct development of the Caenorhabditis elegans nervous system. Worms mutant for unc-119 exhibit nervous system structural defects, including supernumerary axon branches, defasciculated nerve fibers, and choice point errors. Axons of both mechanosensory (ALM) and chemosensory (ASI) neurons have elongation defects within the nerve ring. Expressing unc-119 cDNA in mechano- sensory neurons rescues the elongation defect of ALM axons, but expression in ASI neurons does not rescue ASI axon elongation defects. Neither gross movement nor dauer larva formation defects are rescued in either case. However, expressing a construct including introns under the control of the same promoters results in substantial rescue of phenotypic defects. In these cases reporter expression expands to tissues outside those specified by the promoter, notably into head muscles. Surprisingly, expressing an unc-119 cDNA construct under the control of a muscle-specific promoter fully rescues the dauer formation defect and substantially rescues movement. Thus, although UNC-119 normally acts in a cell-autonomous fashion, the cell-nonautonomous rescue of neural function suggests that it either acts at the cell surface or that it can be transported into the cell from the extracellular environment and play its normal role. ------------------- Key: 7340 Medline: 15995364 Authors: Shim J;Lee J Title: The AP-3 clathrin-associated complex is essential for embryonic and larval development in Caenorhabditis elegans. Citation: Molecules and Cells 19: 452-457 2005 Type: ARTICLE Genes: apb-3 apd-3 apm-3 aps-3 apt-5 apt-6 apt-7 apt-8 Abstract: The adaptor protein (AP) complexes are involved in membrane transport of many proteins. There are 3 AP complexes in C elegans unlike mammals that have four. To study the biological functions of the AP-3 complexes of C elegans, we sought homologues of the mouse and human genes that encode subunits of the AP-3 complexes by screening C elegans genomic and EST sequences. We identified single copies of homologues of the mu 3, sigma 3, beta 3 and delta genes. The medium chain of AP-3 is encoded by a single gene in C elegans but two different genes in mammals. Since there are no known mutations in these genes in C elegans, we performed RNAi to assess their functions in development. RNAi of each of the genes caused embryonic and larval lethal phenotypes. APM-3 is expressed in most cells, particularly strongly in spermatheca and vulva. We conclude that the products of the C elegans mu 3 sigma 3, beta 3 and delta genes are essential for embryogenesis and larval ------------------- Key: 7341 Medline: 15814591 Authors: Sherman T;Chernova MN;Clark JS;Jiang L;Alper SL;Nehrke K Title: The abts and sulp families of anion transporters from Caenorhabditis elegans. Citation: American Journal of Physiology - Cell Physiology 289: C341-C351 2005 Type: ARTICLE Genes: abts-1 abts-2 abts-3 abts-4 sulp-1 sulp-2 sulp-3 sulp-4 sulp-5 sulp-6 sulp-7 sulp-8 Abstract: The slc4 and slc26 gene families encode two distinct groups of gene products that transport HCO3- and other anions in mammalian cells. The SLC4 and SLC26 proteins are important contributors to transepithelial movement of fluids and electrolytes and to cellular pH and volume regulation. Herein we describe the cDNA cloning from the nematode Caenorhabditis elegans of four anion bicarbonate transporter (abts) homologs of slc4 cDNA and eight sulfate permease (sulp) homologs of slc26 cDNA. Analysis of transgenic nematode strains carrying promoter:: GFP fusions suggests relatively restricted expression patterns for many of these genes. At least three genes are expressed primarily in the intestine, three are expressed primarily in the excretory cell, and one is expressed in both of these polarized cell types. One of the genes is also expressed exclusively in the myoepithelium-like cells of the pharynx. Many of the sulp gene products localize to the basolateral membrane rather than to the apical membrane. Several ABTS and SULP proteins exhibited anion transport function in Xenopus oocytes. The strongest Cl- transporter among these also mediated Cl-/HCO3- exchange. These findings encourage exploitation of the genetic strengths of the nematode model system in the study of the physiological roles of anion transport by the proteins of these two ------------------- Key: 7342 Medline: Authors: Geard N;Wiles J Title: A gene network model for developing cell lineages. Citation: Artificial Life 11: 249-267 2005 Type: REVIEW Genes: Abstract: ------------------- Key: 7343 Medline: 15923155 Authors: Dequen F;Gagnon SN;Desnoyers S Title: Ionizing radiations in Caenorhabditis elegans induce poly(ADP-ribosyl)ation, a conserved DNA-damage response essential for survival. Citation: DNA Repair 4: 814-825 2005 Type: ARTICLE Genes: pme-1 pme-2 Abstract: Poly(ADP-ribosyl)ation is one of the first responses to DNA damage in mammal. Although it is involved in base excision repair, its exact role has not been ascertained yet. Poly (ADP-ribose) polymerise-1 (PARP-1) and PARP-2 mediate trios( of the poly(ADP-ribosyl)ation response in mammals and are well conserved in evolution. Their respective homologues PME-1 and PME-2 are found in the nematode Caenorhabditis elegans, a well-known genetically tractable model currently used in DNA damage response research. Here we report the functional analysis of PME-1 and PME-2 in presence of DNA damage. Worms irradiated with high doses of ionizing radiations displayed a sharp drop in their NAD(+) content immediately after treatment, and a biphasic increase in poly(ADP-ribose). The physiological importance of the poly (ADP-ribosyl)ation response was highlighted when worms were preincubated with mammalian PARP inhibitors (3AB, DHQ, PJ34) and irradiated. The embryonic survival rate of the progeny was significantly decreased in;dose-dependent manner. The inhibitor 3AB had a weak effect on embryonic survival, followed closely by DHQ. However, PJ34, a member of the phenantridinone family. was very effective even when used at low concentration (100 nM). In vitro PARP assay using recombinant PME-1 and PME-2 showed a similar pattern of inhibition where 3AB and DHQ were weak inhibitor, and PJ34 a stronger one. Inhibitors affect mostly the poly(AI)P-ribose) polymers elongation at high concentrations. These results suggest that poly(ADP-ribosyl)ation in response to DNA damage is an ancient and very important biochemical process protecting ------------------- Key: 7344 Medline: Authors: Marin I;Vallejo J Title: Parkinson disease: from cellular and animal models to genomics. Citation: Current Genomics 6: 241-250 2005 Type: REVIEW Genes: Abstract: ------------------- Key: 7345 Medline: Authors: Estes S;Ajie BC;Lynch M;Phillips PC Title: Spontaneous mutational correlations for life-history, morphological and behavioral characters in Caenorhabditis elegans. Citation: Genetics 170: 645-653 2005 Type: ARTICLE Genes: Abstract: The pattern of mutational covariance among traits plays a central, but largely untested, role in many theories in evolutionary genetics. Here we estimate the pattern of phenotypic, environmental, and mutational correlations for a set of life-history, behavioral, and morphological traits using 67 self-fertilizing lines of Caenorhabditis elegans, each having independently experienced an average of 370 generations of spontaneous mutation accumulation. Bivariate relationships of mutational effects indicate the existence of extensive pleiotropy. We find that mutations may tend to produce manifold effects on suites of functionally related traits; however, our data do not support the idea of completely parcelated pleiotropy, in which functional units are separately affected by mutations. Positive net phenotypic and mutational correlations are common for life-history traits, with environmental correlations being comparatively smaller and of the same sign for most pairs of traits. Observed mutational correlations are shown to be higher than those produced by the chance accumulation of nonpleiotropic mutations in the same lines. ------------------- Key: 7346 Medline: Authors: Ajie BC;Estes S;Lynch M;Phillips PC Title: Behavioral degradation under mutation accumulation in Caenorhabditis elegans. Citation: Genetics 170: 655-660 2005 Type: ARTICLE Genes: Abstract: Spontaneous mutations play a fundamental role in the maintenance of genetic variation in natural populations, the nature of inbreeding depression, the evolution of sexual reproduction, and the conservation of endangered species. Using long-term mutation-accumulation lines of the nematode Caenorhabditis elegans, we estimate the rate and magnitude of mutational effects for a suite of behaviors characterizing individual chemosensory responses to a repellant stimulus. In accordance with evidence that the vast majority of mutations are deleterious, we find that behavioral responses degrade over time as a result of spontaneous mutation accumulation. The rate of mutation for behavioral traits is roughly of the same order or slightly smaller than those previously estimated for reproductive traits and the average size of the mutational effects is also comparable. These results have important implications for the maintenance of genetic variation for behavior in natural populations as well as for expectations for behavioral change within endangered species and captive populations. ------------------- Key: 7347 Medline: 16049479 Authors: Sieburth D;Ch'ng Q;Dybbs M;Tavazoie M;Kennedy S;Wang D;Dupuy D;Rual JF;Hill DE;Vidal M;Ruvkun G;Kaplan JM Title: Systematic analysis of genes required for synapse structure and function. Citation: Nature 436: 510-517 2005 Type: ARTICLE Genes: acy-1 aex-3 apt-3 apt-4 arr-1 cab-1 cam-1 ccb-1 daf-15 dgk-1 dig-1 duo-2 eat-16 egl-3 egl-8 egl-10 egl-21 fer-1 fshr-1 gei-1 goa-1 ins-22 ins-31 inx-15 inx-16 let-60 nab-1 nep-1 nlp-12 opt-2 osm-9 pkc-1 prk-2 prx-2 pxn-2 rab-3 rab-5 rbf-1 ric-4 sad-1 sbt-1 ser-7 skr-3 snb-1 snn-1 sos-1 syd-1 tap-1 ulp-4 unc-2 unc-10 unc-13 unc-17 unc-18 unc-31 unc-36 unc-43 unc-57 unc-68 unc-104 unc-115 wwp-1 Abstract: Chemical synapses are complex structures that mediate rapid intercellular signalling in the nervous system. Proteomic studies suggest that several hundred proteins will be found at synaptic specializations. Here we describe a systematic screen to identify genes required for the function or development of Caenorhabditis elegans neuromuscular junctions. A total of 185 genes were identified in an RNA interference screen for decreased acetylcholine secretion; 132 of these genes had not previously been implicated in synaptic transmission. Functional profiles for these genes were determined by comparing secretion defects observed after RNA interference under a variety of conditions. Hierarchical clustering identified groups of functionally related genes, including those involved in the synaptic vesicle cycle, neuropeptide signalling and responsiveness to phorbol esters. Twenty-four genes encoded proteins that were localized to presynaptic specializations. Loss-of-function mutations in 12 genes caused defects in presynaptic structure. ------------------- Key: 7348 Medline: 15983168 Authors: Johnson TE Title: Genes, phenes, and dreams of immortality: the 2003 Kleemeier Award Lecture. Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 60: 680-687 2005 Type: REVIEW Genes: Abstract: The 2002 Kleemeier Award from the Gerontological Society of America was awarded to Thomas E. Johnson, PhD, of the University of Colorado at Boulder. Dr. Johnson was the pioneer who first applied genetic analyses to the study of the aging processes in Caenorhabditis elegans and who introduced the nematode as an aging model. Longer life span was chosen as a surrogate marker to[slowed aging. Here Dr. Johnson describes his role(s) in the isolation of age-1, the first longevity mutant, which can more than double the life span and which slows the rate of aging more than twofold. He also reviews research suggesting conservation of function and applicability to intervention by pharmacological targeting of the Age-1 pathway. Current work by biotechnology companies targets this and other basic discoveries in an attempt to postpone human aging. ------------------- Key: 7349 Medline: 15899899 Authors: Cipollo JF;Awad AM;Costello CE;Hirschberg CB Title: N-glycans of Caenorhabditis elegans are specific to developmental stages. Citation: Journal of Biological Chemistry 280: 26063-26072 2005 Type: ARTICLE Genes: Abstract: We have examined the N-glycans present during the developmental stages of Caenorhabditis elegans using two approaches, 1) a combination of permethylation followed by MALDI-TOF mass spectrometry (MS) and 2) derivatization with 2-aminobenzamide followed by separation by high-performance liquid chromatography and analyses by MALDI-TOF MS, post source decay (PSD) MS, and MALDI-QoTOF MS/MS. The N-glycan profile of each developmental stage ( Larva 1, Larva 2, Larva 3, Larva 4, and Dauer and adult) appears to be unique. The pattern of complex N-glycans was stage-specific with the general trend of number and abundance of glycans being Dauer approximate to L1 > adult approximate to L4 > L3 approximate to L2. Dauer larvae contained complex N-glycans with higher molecular masses than those seen in other stages. MALDI-QoTOF MS/MS of Hex(4)HexNAc(4) showed an N-acetyllactosamine substitution not previously observed in C. elegans. Phosphorylcholine (Pc)-substituted glycans were also found to be stage-specific. Higher molecular weight Pc-containing glycans, including fucose-containing ones such as difucosyl Pc-glycan (Pc(1)dHex(2)Hex(5)HexNAc(6)) seen in Dauer larvae, have not been observed in any organism. Pc(2)Hex(4)HexNAc(3), from Dauer larvae, when subjected to PSD MS analyses, showed Pc may substitute both core and terminally linked GlcNAc; no such structure has previously been reported in any organism. C. elegans-specific fucosyl and native methylated glycans were found in all developmental stages. Taken together, the above results demonstrate that in-depth investigation of the role of the above N-glycans during C. elegans development should lead to a better understanding of their significance and the ways that they may govern interactions, both within the organism during development and between the mobile nematode and its pathogens. ------------------- Key: 7350 Medline: 15930110 Authors: Chatterjee I;Richmond A;Putiri E;Shakes DC;Singson A Title: The Caenorhabditis elegans spe-38 gene encodes a novel four-pass integral membrane protein required for sperm function at fertilization. Citation: Development 132: 2795-2808 2005 Type: ARTICLE Genes: fem-1 fer-1 fog-2 him-5 spe-9 spe-38 spe-41 trp-3 hDf17 Abstract: A mutation in the Caenorhabditis elegans spe-38 gene results in a sperm-specific fertility defect. spe-38 sperm are indistinguishable from wild-type sperm with regards to their morphology, motility and migratory behavior. spe-38 sperm make close contact with oocytes but fail to fertilize them. spe-38 sperm can also stimulate ovulation and engage in sperm competition. The spe-38 gene is predicted to encode a novel four-pass (tetraspan) integral membrane protein. Structurally similar tetraspan molecules have been implicated in processes such as gamete adhesion/fusion in mammals, membrane adhesion/fusion during yeast mating, and the formation/function of tight-junctions in metazoa. In antibody localization experiments, SPE-38 was found to concentrate on the pseudopod of mature sperm, consistent with it playing a direct role in gamete interactions. ------------------- Key: 7351 Medline: 15930113 Authors: Maddox AS;Habermann B;Desai A;Oegema K Title: Distinct roles for two C. elegans anillins in the gonad and early embryo. Citation: Development 132: 2837-2848 2005 Type: ARTICLE Genes: ani-1 ani-2 ani-3 nmy-2 rde-1 unc-59 unc-61 Abstract: Anillins are conserved proteins that are important for stabilizing and remodeling the actin cytoskeleton. Anillins have been implicated in cytokinesis in several systems and in cellularization of the syncytial Drosophila embryo. Here, we examine the functions of three C elegans proteins with homology to anillin (ANI-1, ANI-2 and ANI-3). We show that ANI-I and ANI-2 contribute to embryonic viability by performing distinct functions in the early embryo and gonad, respectively. By contrast, ANI-3 appears to be dispensable for embryonic development. ANI-1 is essential for cortical ruffling and pseudocleavage, contractile events that occur in embryos prior to mitosis. ANI-1 is also required for the highly asymmetric cytokinetic events that extrude the two polar bodies during oocyte meiosis, but is dispensable for cytokinesis following mitotic chromosome segregation. During both meiosis and mitosis, ANI-I targets the septins, but not myosin 11, to the contractile ring and does not require either for its own targeting. In contrast to ANI-1, ANI-2 functions during oogenesis to maintain the structure of the rachis, the central core of cytoplasm that connects the developing oocytes in the syncytial gonad. In ANI-2-depleted worms, oocytes disconnect prematurely from the defective rachis, generating embryos of varying sizes. Our results highlight specialization of divergent anillin family proteins in the C elegans life cycle and reveal conserved roles for this protein family in organizing syncytial structures and ------------------- Key: 7352 Medline: Authors: Nascarella MA;Presley SM Title: Formation of Yersinia pseudotuberculosis biofilms on multiple surfaces on Caenorhabditis elegans. Citation: World Journal of Microbiology & Biotechnology 21: 229-231 2005 Type: ARTICLE Genes: Abstract: A liquid-based assay was used to evaluate the ability of Yersinia pseudotuberculosis to form a bacterial biofilm on the nematode Caenorhabditis elegans. After 3 days of incubation in the liquid assay a biofilm was clearly visible by light microscopy on both the head and vulva region of the worms. At times, the biofilm formation on the vulva appeared to prevent the laying of eggs by the adult hermaphrodite; the eggs would later hatch inside of the worm. One possible explanation for the biofilm formation observed on the vulva may be the increased motion of the cuticle surrounding the vulva when the worm is immersed in a liquid culture. This is the first report of biofilm formation on the vulva of C. elegans. ------------------- Key: 7353 Medline: 15973501 Authors: Sasagawa Y;Kikuchi K;Dazai K;Higashitani A Title: Caenorhabditis elegans Elongin BC complex is essential for cell proliferation and chromosome condensation and segregation during mitosis and meiotic division II. Citation: Chromosome Research 13: 357-375 2005 Type: ARTICLE Genes: cul-2 elb-1 elc-1 elc-2 mei-1 rbx-1 Abstract: The ubiquitin-mediated protein degradation system is involved in a wide variety of cellular functions. The RING-H2 finger protein RBX1 is a common subunit of Cullin-based ubiquitin ligases. Caenorhabditis elegans RBX1 and CUL2 are essential for regulating chromosome condensation and segregation during mitosis and meiosis and are also critical for cell proliferation. Here, we demonstrate that Elongin B (ELB1) and C (ELC1) form a stable complex, and that depletion of either gene product by RNA-mediated interference (RNAi) causes pronounced defects in the second meiotic division. Embryos and adults that escape meiotic arrest have several irregular phenotypes. These include defects in mitotic chromosomal condensation and segregation, pronuclear rotation, and germ cell proliferation, abnormal cortical protrusion, and accumulation of the cyclin-dependent kinase inhibitor CKI1. All these defects are consistent with those found after depletion of CUL2. In addition, direct interaction between ELC1 and CUL2 is revealed by bacterial two-hybrid analysis. Thus, the RBX1/CUL2/ELC1/ELB1 complex acts as an E3 ubiquitin ligase in C. elegans and is essential for diverse functions relevant to chromosomal dynamics and cell cycle control. ------------------- Key: 7354 Medline: Authors: Roudier N;Lefebvre C;Legouis R Title: CeVPS-27 is an endosomal protein required for the molting and the endocytic trafficking of the low-density lipoprotein receptor-related protein 1 in Caenorhabditis Citation: Traffic 6: 695-705 2005 Type: ARTICLE Genes: lgg-1 vps-4 vps-23 vps-27 vps-32 vps-36 Abstract: ------------------- Key: 7355 Medline: Authors: Hamahashi S;Onami S;Kitano H Title: Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking. Citation: BMC Bioinformatics 6: 1-15 2005 Type: ARTICLE Genes: Abstract: ------------------- Key: 7356 Medline: 15917232 Authors: Touroutine D;Fox RM;Von Stetina SE;Burdina A;Miller DM;Richmond JE Title: acr-16 encodes an essential subunit of the levamisole-resistant nicotinic receptor at the Caenorhabditis elegans neuromuscular junction. Citation: Journal of Biological Chemistry 280: 27013-27021 2005 Type: ARTICLE Genes: acr-8 acr-16 lev-1 lev-8 unc-29 unc-38 unc-63 Abstract: The Caenorhabditis elegans neuromuscular junction (NMJ) contains three pharmacologically distinct ionotropic receptors: gamma-aminobutyric acid receptors, levamisole-sensitive nicotinic receptors, and levamisole-insensitive nicotinic receptors. The subunit compositions of the gamma-aminobutyric acid- and levamisole-sensitive receptors have been elucidated, but the levamisole-insensitive acetylcholine receptor is uncharacterized. To determine which of the similar to 40 putative nicotinic receptor subunit genes in the C. elegans genome encodes the levamisole-resistant receptor, we utilized MAPCeL, a microarray profiling strategy. Of seven nicotinic receptor subunit transcripts found to be enriched in muscle, five encode the levamisole receptor subunits, leaving two candidates for the levamisole-insensitive receptor: acr-8 and acr-16. Electrophysiological analysis of the acr-16 deletion mutant showed that the levamisole-insensitive muscle acetylcholine current was eliminated, whereas deletion of acr-8 had no effect. These data suggest that ACR-16, like its closest vertebrate homolog, the nicotinic receptor alpha 7-subunit, may form homomeric receptors in vivo. Genetic ablation of both the levamisole-sensitive receptor and acr-16 abolished all cholinergic synaptic currents at the NMJ and severely impaired C. elegans locomotion. Therefore, ACR-16-containing receptors account for all non-levamisole-sensitive nicotinic synaptic signaling at the C. elegans NMJ. The determination of subunit composition for all three C. elegans body wall muscle ionotropic receptors provides a critical foundation for ------------------- Key: 7357 Medline: 16049494 Authors: Ou G;Blacque OE;Snow JJ;Leroux MR;Scholey JM Title: Functional coordination of intraflagellar transport motors. Citation: Nature 436: 583-587 2005 Type: ARTICLE Genes: bbs-7 bbs-8 che-2 che-11 dyf-1 dyf-2 dyf-3 dyf-4 dyf-5 dyf-6 dyf-7 dyf-8 dyf-9 dyf-10 dyf-11 dyf-12 dyf-13 kap-1 klp-11 osm-3 osm-5 osm-12 Abstract: Cilia have diverse roles in motility and sensory reception, and defects in cilia function contribute to ciliary diseases such as Bardet-Biedl syndrome (BBS). Intraflagellar transport (IFT) motors assemble and maintain cilia by transporting ciliary precursors, bound to protein complexes called IFT particles, from the base of the cilium to their site of incorporation at the distal tip. In Caenorhabditis elegans, this is accomplished by two IFT motors, kinesin-II and osmotic avoidance defective (OSM)-3 kinesin, which cooperate to form two sequential anterograde IFT pathways that build distinct parts of cilia. By observing the movement of fluorescent IFT motors and IFT particles along the cilia of numerous ciliary mutants, we identified three genes whose protein products mediate the functional coordination of these motors. The BBS proteins BBS-7 and BBS-8 are required to stabilize complexes of IFT particles containing both of the IFT motors, because IFT particles in bbs-7 and bbs-8 mutants break down into two subcomplexes, IFT-A and IFT-B, which are moved separately by kinesin-II and OSM-3 kinesin, respectively. A conserved ciliary protein, DYF-1, is specifically required for OSM-3 kinesin to dock onto and move IFT particles, because OSM-3 kinesin is inactive and intact IFT particles are moved by kinesin-II alone in dyf-1 mutants. These findings implicate BBS ciliary disease proteins and an OSM-3 kinesin activator in the formation of two IFT pathways that build functional ------------------- Key: 7358 Medline: Authors: Chao MY;Larkins-Ford J;Tucey TM;Hart AC Title: lin-12 Notch functions in the adult nervous system of C. elegans. Citation: BMC Neuroscience 6: 1-12 2005 Type: ARTICLE Genes: glr-1 grk-2 lin-12 Abstract: ------------------- Key: 7359 Medline: 16077003 Authors: Takeshita H;Sawa H Title: Asymmetric cortical and nuclear localizations of WRM-1/beta-catenin during asymmetric cell division in C. elegans. Citation: Genes & Development 19: 1743-1748 2005 Type: ARTICLE Genes: lin-44 lit-1 mom-4 wrm-1 Abstract: beta-Catenin can promote adhesion at the cell cortex and mediate Wnt signaling in the nucleus. We show that, in Caenorhabditis elegans, both WRM-1/beta-catenin and LIT-1 kinase localize to the anterior cell cortex during asymmetric cell division but to the nucleus of the posterior daughter afterward. Both the cortical and nuclear localizations are regulated by Wnts and are apparently coupled. We also found that the daughters show different nuclear export rates for LIT-1. Our results indicate that Wnt signals release cortical WRM-1 from the posterior cortex to generate cortical asymmetry that may control WRM-1 asymmetric nuclear localization by regulating cell ------------------- Key: 7360 Medline: Authors: Jackson BP;Williams PL;Lanzirotti A;Bertsch PM Title: Evidence for biogenic pyromorphite formation by the nematode Caenorhabditis elegans. Citation: Environmental Science & Technology 39: 5620-5625 2005 Type: ARTICLE Genes: Abstract: The determination of chemical speciation and spatial distribution is a prerequisite for a mechanistic understanding of contaminant bioavailability and toxicity to an organism. We have employed synchrotron X-ray techniques to study Cu and Pb speciation and spatial distribution in the soil nematode Caenorhabditis elegans. Nematodes were exposed to each metal ion singly or simultaneously in solution for 24 h and were then rinsed thoroughly and preserved in formalin for transportation to the National Synchrotron Light Source. Experiments were conducted at the microprobe beamline X26A employing a focused beam of approximately 10 mu m in diameter. Nematodes were mounted in agar gel on Kapton tape. Two-dimensional elemental maps for Cu- and Pb-exposed nematodes were collected in fluorescence mode. Copper was homogeneously distributed throughout the body of the nematode, but Pb exhibited a high degree of localization in the nematode, exclusively in the anterior pharynx region. Detectable localized concentrations of Pb in C. elegans occurred at aqueous exposure concentrations of 2.4 mu M. Micro X-ray diffraction of these Pb hotspots gave a diffraction pattern indicating a crystalline Pb solid that was consistent with the Pb phosphate, pyromorphite. Biogenic inorganic phosphate granule formation is relatively common in soil invertebrates; however, these phosphates are typically amorphous, and we believe that this is the first report of crystalline pyromorphite formed ------------------- Key: 7361 Medline: Authors: Anderson GL;Kenney SJ:Millner PD;Beuchat LR;Williams PL Title: Shedding of foodborne pathogens by Caenorhabditis elegans in compost-amended and unamended soil. Citation: Food Microbiology 23: 146-153 2006 Type: ARTICLE Genes: Abstract: A study was done to characterize the shedding of foodborne pathogenic bacteria by Caenorhabditis elegans, evaluate the persistence of worm populations cocultured with foodborne pathogens, and determine if C elegans disperses ingested pathogens in soil as a result of shedding. Escherichia. coli O157:H7, Salmonella enterica serotype Poona, and Listeria monocytogenes, as well as E coli OP50, a non-pathogenic strain, were studied. Synchronous populations of C elegans were fed for 24h on confluent lawns of nalidixic acid-adapted bacteria. C elegans shed viable cells of ingested bacteria on tryptic soy agar supplemented with nalidixic acid (50 mu g ml(-1)) (TSAN) throughout a 5-h post-feeding period. C elegans persisted for up to 10 days by feeding on bacteria that had been shed and grew on TSAN. Eggs harvested from C elegans cultured on shed foodborne pathogens had the same level of viability as those collected from C elegans grown on shed E. coli OP50. After 6-7 days, 78%, 64%, 64%, and 76% of eggs laid by C elegans that had fed on E. coli O157:H7, S. Poona, L. inonocytogenes, and E. coli OP50, respectively, were viable. Worms fed on E. coli O15TH7 were inoculated into soil and soil amended with turkey manure compost. Populations of C elegans persisted in compostamended soil for at least 7 days but declined in unamended soil. E. coli O157:H7 was detected at 4 and 6 days post inoculation in compost-amended and unamended soil, and in unamended soil inoculated with E. coli OP50. Populations of E. coli O157:H7 in soil amended with turkey manure compost were significantly(alpha = 0.05) higher than those in unamended soil. Results indicate that C elegans can act as a vector to disperse foodborne pathogens in soil, potentially resulting in increased risk of contaminating the surface of ------------------- Key: 7362 Medline: 15960969 Authors: Montell DJ Title: Anchors away! Fos fosters anchor-cell invasion. Citation: Cell 121: 816-817 2005 Type: REVIEW Genes: cdh-3 fos-1 him-4 zmp-1 Abstract: Invasion of cells through breakdown of the basement membrane is a crucial step during development and cancer metastasis. In this issue of Cell, simple and genetically tractable cellular assay in the worm for elucidating the molecular processes that underlie cell invasion in vivo is described. They demonstrate that the transcription factor Fos is required for cell invasion and identify three of its downstream target genes (encoding a matrix metalloproteinase, hemicentin, and a fat-like protocadherin). ------------------- Key: 7363 Medline: 16028834 Authors: Geanacopoulos M Title: The determinants of lifespan in the nematode Caenorhabditis elegans: a short primer. Citation: Science Progress 87: 227-247 2004 Type: REVIEW Genes: Abstract: Transparent, easily-maintained, amenable to genetic manipulation, and living for only a few weeks, the nematode Caenorhabditis elegans is a leading animal model for the study of the determinants of lifespan. The original genetic screen for increased longevity identified a mutant, age-1, with a defect in one component of a signal transduction pathway. This pathway functioned as a genetic switch and governed the decision whether to enter a specialized larval form, dauer, that enables the worm to withstand the scarcity of food or other stressful conditions. These age-1 worms had an increased tendency to become dauers, but if they did not adopt the dauer developmental pathway, they lived longer than wild type worms. age-1 and other longevity mutants with dauer phenotypes are vigorous, indicating that they do not suffer from a significant energy deficit, and stress resistant. Mutation of genes encoding mitochondrial components was found to be another means of extending the lifespan of the worm, although the associated phenotypes suggest a deficiency of available energy. While there are now many documented genetic manipulations which can extend the worm's lifespan, it has been difficult to come to definite conclusions as to the mechanism(s) by which lifespan is extended. The most carefully studied mutant strains have complex changes in gene expression and metabolism making it difficult to ascertain what changes are critical. The free radical theory of aging is the dominant biochemical theory of aging, and the phenotypes of the well-characterized longevity mutants worm can be accommodated to it. However discrete interventions to lower reactive oxygen species, or mitigate their effects, have not produced consistent easily-interpretable results in terms of lifespan extension. It has become clear that the insulin-dependent signalling mechanism that regulates lifespan in the worm functions in the context of a complex endocrine system and the hormonal control of aging is an emerging focus of ------------------- Key: 7364 Medline: 15984549 Authors: Ruvkun GB Title: The tiny RNA world. Citation: Harvey Lectures 99: 1-21 2003 Type: REVIEW Genes: Abstract: ------------------- Key: 7365 Medline: 16049496 Authors: Wang D;Kennedy S;Conte D;Kim JK;Gabel HW;Kamath RS;Mello CC;Ruvkun G Title: Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants. Citation: Nature 436: 593-597 2005 Type: ARTICLE Genes: dcr-1 dpl-1 eri-1 gfl-1 hpl-2 let-23 let-60 let-418 lin-1 lin-8 lin-9 lin-13 lin-15 lin-35 lin-36 lin-37 lin-38 lin-53 lin-56 mep-1 mes-4 mut-7 mut-14 mut-16 pqn-28 rde-1 rde-4 rrf-1 rrf-3 tam-1 unc-22 zfp-1 Abstract: Caenorhabditis elegans homologues of the retinoblastoma (Rb) tumour suppressor complex specify cell lineage during development(1,2). Here we show that mutations in Rb pathway components enhance RNA interference (RNAi) and cause somatic cells to express genes and elaborate perinuclear structures normally limited to germline-specific P granules. Furthermore, particular gene inactivations that disrupt RNAi reverse the cell lineage transformations of Rb pathway mutants. These findings suggest that mutations in Rb pathway components cause cells to revert to patterns of gene expression normally restricted to germ cells. Rb may act by a similar mechanism to transform mammalian cells. ------------------- Key: 7366 Medline: 16049464 Authors: Bargmann C Title: Genomics reaches the synapse. Citation: Nature 436: 473-474 2005 Type: REVIEW Genes: eri-1 lin-15 Abstract: ------------------- Key: 7367 Medline: Authors: Liu Q;Chen B;Yankova M;Morest DK;Maryon E;Hand AR;Nonet ML;Wang ZW Title: Presynaptic ryanodine receptors are required for normal quantal size at the Caenorhabditis elegans neuromuscular junction. Citation: Journal of Neuroscience 25: 6745-6754 2005 Type: ARTICLE Genes: itr-1 myo-3 rab-3 ric-4 ryr-1 unc-29 unc-49 unc-64 unc-68 Abstract: Analyses of the effect of ryanodine in vertebrate brain slices have led to the conclusion that presynaptic ryanodine receptors (RYRs) may have several functions in synaptic release, including causing large-amplitude miniature postsynaptic currents (mPSCs) by promoting concerted multivesicular release. However, the role of RYRs in synaptic release is controversial. To better understand the role of RYRs in synaptic release, we analyzed the effect of RYR mutation on mPSCs and evoked postsynaptic currents (ePSCs) at the Caenorhabditis elegans neuromuscular junction (NMJ). Amplitudes of mPSCs varied greatly at the C. elegans NMJ. Loss-of-function mutations of the RYR gene unc-68 (uncoordinated 68) essentially abolished large-amplitude mPSCs. The amplitude of ePSCs was also greatly suppressed. These defects were completely rescued by expressing wild-type UNC-68 specifically in neurons but not in muscle cells, suggesting that RYRs acted presynaptically. A combination of removing extracellular Ca2+ and UNC-68 function eliminated mPSCs, suggesting that influx and RYR-mediated release are likely the exclusive sources of Ca2+ for synaptic release. Large-amplitude mPSCs did not appear to be caused by multivesicular release, as has been suggested to occur at vertebrate central synapses, because the rise time of mPSCs was constant regardless of the amplitude but distinctive from that of ePSCs, and because large-amplitude mPSCs persisted under conditions that inhibit synchronized synaptic release, including elimination of extracellular Ca2+, and mutations of syntaxin and SNAP25 ( soluble N-ethylmaleimide-sensitive factor attachment protein 25). These observations suggest that RYRs are essential to normal quantal size and are potential regulators of quantal size. ------------------- Key: 7368 Medline: Authors: Bergtold M;Gunther V;Traunspurger W Title: Is there competition among ciliates and nematodes? Citation: Freshwater Biology 50: 1351-1359 2005 Type: ARTICLE Genes: Abstract: 1. Biotic interaction between the ciliate Cyclidium glaucoma and the nematode Caenorhabditis elegans was investigated by manipulating the densities of the organisms in microcosms with and without sediment. 2. After 11 days the abundance of ciliates, nematodes and bacteria as well as extracellular enzyme activity were determined. Ciliates had a negative effect on nematode abundance in microcosms without sediment and in microcosms with sandy sediment, whereas in muddy sediment the effect was less distinctive. An effect of nematodes on ciliates was not observed. 3. The common resource bacteria were not affected negatively by the activity of the grazers. Overall grazer biomass increased with the addition of sediment to the microcosms, suggesting a rise of the carrying capacity in the experimental system. Especially in muddy sediment the abundance of bacteria and extracellular enzyme activity was higher compared to the microcosms without sediment. 4. The results of the experiment suggest a strong interspecific competition between nematodes and ciliates, where nematodes are, at least temporary, strongly affected. ------------------- Key: 7369 Medline: 16015606 Authors: Felix MA Title: An inversion in the wiring of an intercellular signal: evolution of Wnt signaling in the nematode vulva. Citation: BioEssays 27: 765-769 2005 Type: REVIEW Genes: apr-1 bar-1 egl-20 lin-17 lin-39 lin-44 mab-5 mom-2 vab-7 Abstract: Signal transduction pathways are largely conserved throughout the animal kingdom. The repertoire of pathways is limited and each pathway is used in different intercellular signaling events during the development of a given animal. For example, Writ signaling is recruited, sometimes redundantly with other molecular pathways, in four cell specification events during Caenorhabditis elegans vulva development, including the activation of vulval differentiation. Strikingly,a recent study finds that Writs act to repress vulval differentiation in the nematode Pristionchus pacificus,((1)) demonstrating evolutionary flexibility in the use of intercellular ------------------- Key: 7370 Medline: 16041374 Authors: Rea SL;Wu D;Cypser JR;Vaupel JW;Johnson TE Title: A stress-sensitive reporter predicts longevity in isogenic populations of Caenorhabditis elegans. Citation: Nature Genetics 37: 894-898 2005 Type: ARTICLE Genes: gst-4 hsp-16.2 mtl-2 myo-2 Abstract: When both genotype and environment are held constant, 'chance' variation in the lifespan of individuals in a population is still quite large. Using isogenic populations of the nematode Caenorhabditis elegans, we show that, on the first day of adult life, chance variation in the level of induction of a green fluorescent protein (GFP) reporter coupled to a promoter from the gene hsp-16.2 predicts as much as a fourfold variation in subsequent survival. The same reporter is also a predictor of ability to withstand a subsequent lethal thermal stress. The level of induction of GFP is not heritable, and GFP expression levels in other reporter constructs are not associated with differences in longevity. HSP-16.2 itself is probably not responsible for the observed differences in survival but instead probably reflects a hidden, heterogeneous, but now quantifiable, physiological state that dictates the ability of an organism to deal with the rigors of living. ------------------- Key: 7371 Medline: 15986473 Authors: Navarro RE;Blackwell TK Title: Requirement for P granules and meiosis for accumulation of the germline RNA helicase CGH-1. Citation: Genesis 42: 172-180 2005 Type: ARTICLE Genes: cgh-1 gld-1 gld-2 glh-1 glh-4 pgl-1 Abstract: In Caenorhabditis elegans, lack of the conserved germline RNA helicase CGH-1 causes infertility and excessive levels of physiological germline apoptosis, a process that normally claims about half of all developing oocytes. In yeast the CGH-1 ortholog is a key component of degradative "processing (P) bodies," which may share some properties with germline protein-RNA complexes such as P granules. During oogenesis CGH-1 associates with P granules, but also accumulates to high levels in additional cytoplasmic particles. Here we show that appropriate levels and localization of CGH-1 depends on some P granule components and on mechanisms that establish meiotic development. At the same time, germ cell death is not increased by various abnormalities in P granules or meiosis. We conclude that in developing oocytes CGH-1 particles accumulate specifically in response to meiotic development and have distinct functions from P granules, and may be dynamic protein-mRNA ------------------- Key: 7372 Medline: Authors: Juang BT;Izeta A;O'Hare P;Luisi BF Title: Purification and characterization of the Caenorhabditis elegans HCF protein and domains of human HCF. Citation: Biochemistry 44: 10396-10405 2005 Type: ARTICLE Genes: Abstract: The human cellular factor (HCF) is a multidomain protein that is implicated in processes of cell cycle progression, and it is recruited into a multicomponent assembly that triggers the expression of the herpes simplex vir-us genome. The amino-terminal domain of HCF has been proposed to form a "kelch" type beta-propeller fold, and the carboxy-terminal domain contains a repeat of a fibronectin-like motif. We describe the expression, purification, and characterization of the domains from the human HCF and of the full-length HCF from Caenorhabditis elegans. The purified recombinant C. elegans HCF can substitute for the human HCF in efficiently forming a multiprotein complex on a herpes simplex virus promoter element. As noted in earlier studies, a segment of human HCF encompassing the human kelch domain forms a stable complex on a viral promoter element. The purified fibronectin domain can also be recruited into this complex, but not into the stable complex formed with the minimal kelch domain. These results suggest that the fibronectin domain can interact with HCF in the transcriptional activating complex and that the association requires a ------------------- Key: 7373 Medline: Authors: Hentschel DM;Bonventre JV Title: Novel non-rodent models of kidney disease. Citation: Current Molecular Medicine 5: 537-546 2005 Type: REVIEW Genes: Abstract: ------------------- Key: 7374 Medline: Authors: Mukhopadhyay A;Deplancke B;Walhout AJM;Tissenbaum HA Title: C. elegans tubby regulates life span and fat storage by two independent mechanisms. Citation: Cell Metabolism 2: 35-42 2005 Type: ARTICLE Genes: Abstract: In C. elegans, similar to in mammals, mutations in the tubby homolog, tub-1, promote increased fat deposition. Here, we show that mutation in tub-1 also leads to life span extension dependent on daf-16/FOXO. Interestingly, function of tub-1 in fat storage is independent of daf-16. A yeast two-hybrid screen identified a novel TUB-1 interaction partner (RBG-3); a RabGTPase-activating protein. Both TUB-1 and RBG-3 localize to overlapping neurons. Importantly, RNAi of rbg-3 decreases fat deposition in tub-1-mutants but does not affect life span. We demonstrate that TUB-1 is expressed in ciliated neurons and undergoes both dendritic and ciliary transport. Additionally, tub-1 mutants are chemotaxis defective. Thus, tub-1 may regulate fat storage either by modulating transport, sensing, or responding to signals in ciliated neurons. Taken together, we define a role for tub-1 in regulation of life span and show that tub-1 regulates life ------------------- Key: 7375 Medline: 16051801 Authors: Remy JJ;Hobert O Title: An interneuronal chemoreceptor required for olfactory imprinting in C. elegans. Citation: Science 309: 787-790 2005 Type: ARTICLE Genes: ser-2 sra-11 ttx-3 Abstract: Animals alter their behavioral patterns in an experience-dependent manner. Olfactory imprinting is a process in which the exposure of animals to olfactory cues during specific and restricted time windows leaves a permanent memory ("olfactory imprint") that shapes the animal's behavior upon encountering the olfactory cues at later times. We found that Caenorhabditis elegans displays olfactory imprinting behavior that is mediated by a single pair of interneurons. To function in olfactory imprinting, this interneuron pair must express a G protein-coupled chemoreceptor family member encoded by the Sra-11 gene. Our study provides insights into the cellular and molecular basis of olfactory imprinting and reveals a function for a chemosensory receptor family member in interneurons. ------------------- Key: 7376 Medline: 16079852 Authors: Bringmann H;Hyman AA Title: A cytokinesis furrow is positioned by two consecutive signals. Citation: Nature 436: 731-734 2005 Type: ARTICLE Genes: act-4 air-1 cyk-1 cyk-4 klp-7 let-21 mel-11 mlc-4 nmy-2 pfn-1 rho-1 spd-1 zen-4 Abstract: The position of the cytokinesis furrow in a cell determines the relative sizes of its two daughter cells as well as the distribution of their contents. In animal cells, the position of the cytokinesis furrow is specified by the position of the mitotic spindle(1). The cytokinesis furrow bisects the spindle midway between the microtubule asters, at the site of the microtubule-based midzone, producing two daughter cells. Experiments in some cell types have suggested that the midzone positions the furrow(2,3), but experiments in other cells have suggested that the asters position the furrow(4,5). One possibility is that different organisms and cell types use different mechanisms to position the cytokinesis furrow. An alternative possibility is that both asters and the midzone contribute to furrow positioning(6,7). Recent work in C. elegans has suggested that centrosome separation and the midzone are implicated in cytokinesis(8). Here we examine the relative contributions of different parts of the mitotic spindle to positioning of the cytokinesis furrow in the C. elegans zygote. By spatially separating the spindle midzone from one of the asters using an ultraviolet laser, we show that the cytokinesis furrow is first positioned by a signal determined by microtubule asters, and then by a second signal that is derived from the spindle midzone. Thus, the position of the cytokinesis furrow is specified by two consecutive furrowing activities. ------------------- Key: 7377 Medline: 16024786 Authors: Lee J;Li W;Guan KL Title: SRC-1 mediates UNC-5 signaling in Caenorhabditis elegans. Citation: Molecular and Cellular Biology 25: 6485-6495 2005 Type: ARTICLE Genes: src-1 unc-5 unc-6 unc-34 unc-40 Abstract: The secreted molecule unc-6/netrin is important for guiding axon projections and cell migrations. unc-5 and unc-40/DCC are identified as receptors for unc-6/netrin. The downstream factors of unc-6 receptors are beginning to be elucidated, and some key factors have been identified in various organisms. Here, we showed that SRC-1 interacts with the cytosolic domain of UNC-5 through its SH2 domain. This interaction also requires the intact kinase activity of SRC-1. Downregulation of src-1 by RNA interference decreases the biological processes initiated by the UNC-5 protein and decreases UNC-5 tyrosine phosphorylation. We also generated a chimeric protein consisting of the extracellular domain and transmembrane domain of UNC-5 and an intracellular domain of SRC-1. This fusion protein is able to partially rescue mutant phenotypes caused by unc-5 but not unc-6, unc-40, and unc-34. Our results support a model in which SRC-1 is required for UNC-5-induced axon repulsion and gonad migration signaling pathways and in which localizing SRC-1 activity to UNC-5 is crucial for proper signal transduction in response to unc-6/netrin. ------------------- Key: 7378 Medline: 15878844 Authors: Menard C;Horvitz HR;Cannon S Title: Chimeric mutations in the M2 segment of the 5-hydroxytryptamine-gated chloride channel MOD-1 define a minimal determinant of anion/cation permeability. Citation: Journal of Biological Chemistry 280: 27502-27507 2005 Type: ARTICLE Genes: mod-1 Abstract: The ionic selectivity of ligand-gated ion channels (LGICs) determines whether receptor activation produces an excitatory or inhibitory response. The determinants of anion/cation selectivity were investigated for a new member of the LGIC superfamily, MOD-1, a serotonin-gated chloride channel cloned from the nematode Caenorhabditis elegans. In common with other anionic LGICs ( glycine receptors and GABA(A) receptors), the selectivity triple mutant in the pore-forming M2 segment ( proline insertion, Ala -> Glu substitution at the central ring, and Thr -> Val at the hydrophobic ring) converted the selectivity of MOD-1 from anionic to cationic. Unlike other LGICs, however, this mutant in MOD-1 was highly selective for K+ over other cations. Subsets of this selectivity triple mutant were studied to define the minimal change required for conversion from anion-permeable to cation-permeable. The double mutant at the central ring of charge (Delta Pro-269/A270E) produced a non-selective cation channel. Charge reversal at the central ring alone (A270E) was sufficient to convert MOD-1 to cation-permeable. These results refine the determinants of ion-charge selectivity in LGICs and demonstrate the critical role of the central ring of charge formed by the M2 segments. ------------------- Key: 7379 Medline: 15932871 Authors: Ben-Ami HC;Yassin L;Farah H;Michaeli A;Eshel M;Treinin M Title: RIC-2 affects properties and quantity of nicotinic acetylcholine receptors via a mechanism that does not require the coiled-coil domains. Citation: Journal of Biological Chemistry 280: 28053-28060 2005 Type: ARTICLE Genes: deg-3 des-2 ric-3 Abstract: Members of the RIC-3 gene family are effectors of nicotinic acetylcholine receptor ( nAChR) expression in vertebrates and invertebrates. In Caenorhabditis elegans RIC-3 is needed for functional expression of multiple nAChRs, including the DEG-3/DES-2 nAChR. Effects of RIC-3 on DEG-3/DES-2 functional expression are found in vivo and following heterologous expression in Xenopus leavis oocytes. We now show that in X. leavis oocytes RIC-3 also affects the kinetics and agonist affinity properties of the DEG-3/DES-2 receptor. Because these effects are mimicked by increasing the ratio of DEG-3 subunits within DEG-3/DES-2 receptors, this suggests that RIC-3 may preferentially promote maturation of DEG-3-rich receptors. Indeed, effects of RIC-3 on functional expression of DEG-3/DES-2 positively correlate with the DEG-3 to DES-2 ratio. All RIC-3 family members have two transmembrane domains followed by one or two coiled-coil domains. Here we show that the effects of RIC-3 on functional expression and on receptor properties are mediated by the transmembrane domains and do not require the coiled-coil domains. In agreement with this, mammals express a RIC-3 transcript lacking the coiled-coil domain that is capable of promoting DEG-3/DES-2 functional expression. Last, we show that RIC-3 affects DEG-3 quantity, suggesting stabilization of receptors or receptor intermediates by RIC-3. Together our results suggest that subunit-specific interactions of RIC-3 with nAChR subunits, mediated by the transmembrane domains, are sufficient for the effects of RIC-3 on nAChR quantity and quality. ------------------- Key: 7380 Medline: Authors: Lochnit G;Bongaarts R;Geyer R Title: Searching new targets for anthelminthic strategies: interference with glycosphingolipid biosynthesis and phosphorylcholine metabolism affects development of Caenorhabditis elegans. Citation: International Journal for Parasitology 35: 911-923 2005 Type: ARTICLE Genes: rrf-3 Abstract: Nematode infections are amongst the most abundant diseases of man and animals. They are characterised by a low mortality but high morbidity, thus reflecting the adaptation of these parasites to their hosts. Resistance as well as severe side-effects and efficacies restricted to distinct larval stages or parasites of the anthelmithics used at present require the urgent development of new and more nematode-specific drugs, targeting enzymes of parasite restricted biosynthetic routes. Caenorhabditis elegans has been found to be a good model system for parasitic nematodes, drug screening and developmental studies. Structural analyses have revealed nematode-specific glycosphingolipid structures of the arthro-series, carrying in part, phosphorylcholine substituents. These biomolecules appear to play important roles in nematode development, fertility and survival within the host and are, therefore, good target-candidates for the development of new anthelminthic strategies. Here we show that RNAi experiments targeting enzymes of glycosphingolipid biosynthesis or choline metabolism result, in part, in a drastic reduction of fertility. We further tested various chemical inhibitors of these pathways and found significant effects on the development of the worms, resulting in developmental arrest, sterility and, in part, lethality. Such inhibitors can, therefore, help to define new classes ------------------- Key: 7381 Medline: 16005289 Authors: Barriere A;Felix MA Title: High local genetic diversity and low outcrossing rate in Caenorhabditis elegans natural populations. Citation: Current Biology 15: 1176-1184 2005 Type: ARTICLE Genes: Abstract: Background: Caenorhabditis elegans is a major model system in biology, yet very little is known about its biology outside the laboratory. In particular, its unusual mode of reproduction with self-fertile hermaphrodites and facultative males raises the question of its frequency of outcrossing in natural populations. Results: We describe the first analysis of C. elegans individuals sampled directly from natural populations. C. elegans is found predominantly in the dauer stage and with a very low frequency of males versus hermaphrodites. Whereas C. elegans was previously shown to display a low worldwide genetic diversity, we find by comparison a surprisingly high local genetic diversity of C. elegans populations; this local diversity is contributed in great part by immigration of new alleles rather than by mutation. Our results on heterozygote frequency, male frequency, and linkage disequilibrium furthermore show that selfing is the predominant mode of reproduction in C. elegans natural populations but that infrequent outcrossing events occur, at a rate of approximately 1%. Conclusions: Our results give a first insight in the biology of C. elegans in the natural populations. They demonstrate that local populations of C. elegans are genetically diverse and that a low frequency of outcrossing allows for the recombination ------------------- Key: 7382 Medline: 16005300 Authors: Syntichaki P;Samara C;Tavernarakis N Title: The vacuolar H+-ATPase mediates intracellular acidification required for neurodegeneration in C. elegans. Citation: Current Biology 15: 1249-1254 2005 Type: ARTICLE Genes: crt-1 deg-3 mec-4 spe-5 unc-32 unc-68 vha-2 vha-10 vha-12 Abstract: Numerous studies implicate necrotic cell death in devastating human pathologies such as stroke and neurodegenerative diseases [1, 2]. Investigations in both nematodes and mammals converge to implicate specific calpain and aspartyl proteases in the execution of necrotic cell death [2, 3]. It is believed that these proteases become activated under conditions that inflict necrotic cell death. However, the factors that modulate necrosis and govern the erroneous activation of these otherwise benign enzymes are largely unknown. Here we show that the function of the vacuolar H+-ATPase, a pump that acidifies lysosomes and other intracellular organelles, is essential for necrotic cell death in C. elegans. Cytoplasmic pH drops in dying cells. Intracellular acidification requires the vacuolar H+-ATPase, whereas alkalization of endosomal and lysosomal compartments by weak bases protects against necrosis. In addition, we show that vacuolar H+-ATPase activity is required downstream of cytoplasmic calcium overload during necrosis. Thus, intracellular pH is an important modulator of necrosis in C. elegans. We propose that vacuolar H+-ATPase activity is required to establish necrosis-promoting, acidic intracellular conditions that augment the function of executioner aspartyl proteases in dying cells. Similar mechanisms may contribute to necrotic cell death that follows extreme acidosis-for example, during stroke-in humans. ------------------- Key: 7383 Medline: 16005279 Authors: Joshi PM;Rothman JR Title: Nematode gastrulation: having a BLASTocoel! Citation: Current Biology 15: R495-R498 2005 Type: REVIEW Genes: gad-1 emb-5 Abstract: During gastrulation of the nematode worm Caenorhabditis elegans, individual cells ingress into a solid ball of cells. Gastrulation in a basal nematode, in contrast, has now been found to occur by invagination into a blastocoel, revealing an unanticipated embryological affinity between nematodes and all other triploblastic metazoans. ------------------- Key: 7384 Medline: 15939489 Authors: Buckingham SD;Kidd JF;Law RJ;Franks CJ;Sattelle DB Title: Structure and function of two-pore-domain K+ channels: contributions from genetic model organisms. Citation: Trends in Pharmacological Sciences 26: 361-367 2005 Type: REVIEW Genes: twk-1 twk-2 twk-3 twk-4 twk-5 twk-6 twk-7 twk-8 twk-9 twk-10 twk-11 twk-12 twk-13 twk-14 twk-16 twk-17 twk-18 twk-20 twk-21 twk-22 twk-23 twk-24 twk-25 twk-26 twk-28 twk-29 twk-30 twk-31 twk-32 twk-33 twk-34 twk-35 twk-36 twk-37 twk-39 twk-40 twk-41 twk-42 twk-43 twk-44 twk-45 Abstract: K+ channels that possess two pore domains in each channel subunit are common in many animal tissues. Such channels are generated from large families of subunits and are implicated in several functions, including temperature sensation, responses to ischaemia, K+ homeostasis and setting the resting potential of the cell. Their activity can be modulated by polyunsaturated fatty acids, pH and oxygen, and some are candidate targets of volatile anaesthetics. However, despite their potential as targets for novel drugs for human health, comparatively little is known about the molecular basis of their diverse physiological and pharmacological properties. Genetic model organisms have considerable potential for improving our understanding of these channels. In this article, we review the contributions of some of these genetic model organisms to recent advances in our knowledge of two-pore-domain K+ ------------------- Key: 7385 Medline: 16094371 Authors: Gunsalus KC;Ge H;Schetter AJ;Goldberg DS;Han JDJ;Hao T;Berriz GF;Bertin N;Huang J;Chuang LS;Li N;Mani R;Hyman AA;Sonnichsen B;Echeverri CJ;Roth FP;Vidal M;Piano F Title: Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Citation: Nature 436: 861-865 2005 Type: ARTICLE Genes: hcp-4 lig-1 mcm-2 mcm-3 mcm-4 mcm-5 mcm-6 mcm-7 npp-2 npp-10 npp-19 ran-1 rnr-1 Abstract: Although numerous fundamental aspects of development have been uncovered through the study of individual genes and proteins, system-level models are still missing for most developmental processes. The first two cell divisions of Caenorhabditis elegans embryogenesis constitute an ideal test bed for a system-level approach. Early embryogenesis, including processes such as cell division and establishment of cellular polarity, is readily amenable to large-scale functional analysis. A first step toward a system-level understanding is to provide 'first-draft' models both of the molecular assemblies involved(1) and of the functional connections between them. Here we show that such models can be derived from an integrated gene/protein network generated from three different types of functional relationship(2): protein interaction(3), expression profiling similarity(4) and phenotypic profiling similarity(5), as estimated from detailed early embryonic RNA interference phenotypes systematically recorded for hundreds of early embryogenesis genes(6). The topology of the integrated network suggests that C. elegans early embryogenesis is achieved through coordination of a limited set of molecular machines. We assessed the overall predictive value of such molecular machine models by dynamic localization of ten previously uncharacterized ------------------- Key: 7386 Medline: Authors: Anyanful A;Dolan-Livengood JM;Lewis T;Sheth S;DeZalia MN;Sherman MA;Kalman LV;Benian GM;Kalman D Title: Paralysis and killing of Caenorhabditis elegans by enteropathogenic Escherichia coli requires the bacterial tryptophanase gene. Citation: Molecular Microbiology 57: 988-1007 2005 Type: ARTICLE Genes: age-1 bre-5 ced-3 ced-4 daf-2 daf-16 egl-9 hif-1 mek-1 mev-1 nsy-1 pgp-1 pgp-3 pmk-1 rol-6 sek-1 srf-3 vhl-1 Abstract: Pathogenic Escherichia coli, including enteropathogenic E. coli (EPEC), enterohaemorrhagic E. coli (EHEC), enteroinvasive E. coli (EIEC) and enterotoxigenic E. coli (ETEC) are major causes of food and water-borne disease. We have developed a genetically tractable model of pathogenic E. coli virulence based on our observation that these bacteria paralyse and kill the nematode Caenorhabditis elegans. Paralysis and killing of C. elegans by EPEC did not require direct contact, suggesting that a secreted toxin mediates the effect. Virulence against C. elegans required tryptophan and bacterial tryptophanase, the enzyme catalysing the production of indole and other molecules from tryptophan. Thus, lack of tryptophan in growth media or deletion of tryptophanase gene failed to paralyse or kill C. elegans. While known tryptophan metabolites failed to complement an EPEC tryptophanase mutant when presented extracellularly, complementation was achieved with the enzyme itself expressed either within the pathogen or within a cocultured K12 strains. Thus, an unknown metabolite of tryptophanase, derived from EPEC or from commensal non-pathogenic strains, appears to directly or indirectly regulate toxin production within EPEC. EPEC strains containing mutations in the locus of enterocyte effacement (LEE), a pathogenicity island required for virulence in humans, also displayed attenuated capacity to paralyse and kill nematodes. Furthermore, tryptophanase activity was required for full activation of the LEE1 promoter, and for efficient formation of actin-filled membranous protrusions (attaching and effacing lesions) that form on the surface of mammalian epithelial cells following attachment and which depends on LEE genes. Finally, several C. elegans genes, including hif-1 and egl-9, rendered C. elegans less susceptible to EPEC when mutated, suggesting their involvement in mediating toxin effects. Other genes including sek-1, mek-1, mev-1, pgp-1,3 and vhl-1, rendered C. elegans more susceptible to EPEC effects when mutated, suggesting their involvement in protecting the worms. Moreover we have found that C. elegans genes controlling lifespan (daf-2, age-1 and daf-16), also mediate susceptibility to EPEC. Together, these data suggest that this C. elegans/EPEC system will be valuable in elucidating novel factors relevant to human disease that regulate virulence in the pathogen or susceptibility to infection in the host. ------------------- Key: 7387 Medline: 16001968 Authors: Sugiura M;Fuke S;Suo S;Sasagawa N;Van Tol HHM;Ishiura S Title: Characterization of a novel D2-like dopamine receptor with a truncated splice variant and a D1-like dopamine receptor unique to invertebrates from Caenorhabditis elegans. Citation: Journal of Neurochemistry 94: 1146-1157 2005 Type: ARTICLE Genes: dop-3 dop-4 Abstract: We have cloned two novel Caenorhabditis elegans dopamine receptors, DOP-3 and DOP-4. DOP-3 shows high sequence homology with other D2-like dopamine receptors. As a result of alternative splicing, a truncated splice variant of DOP-3, DOP-3nf, was produced. Because of the in-frame insertion of a stop codon in the third intracellular loop, DOP-3nf lacks the sixth and seventh transmembrane domains that are found in the full-length DOP-3 receptor. Reporter gene assay showed that DOP-3 attenuates forskolin-stimulated cAMP formation in response to dopamine stimulation, whereas DOP-3nf does not. When DOP-3 was coexpressed with DOP-3nf, the ability to inhibit forskolin-stimulated cAMP formation was reduced. DOP-4 shows high sequence homology with D1-like dopamine receptors unique to invertebrates, which are distinct from mammalian D1-like dopamine receptors. Reporter gene assay showed that DOP-4 stimulates cAMP accumulation in response to dopamine stimulation. These two receptors provide new opportunities to understand dopaminergic signaling at the ------------------- Key: 7388 Medline: 15990870 Authors: Gottschalk A;Almedom RB;Schedletzky T;Anderson SD;Yates JR;Schafer WR Title: Identification and characterization of novel nicotinic receptor-associated proteins in Caenorhabditis elegans. Citation: EMBO Journal 24: 2566-2578 2005 Type: ARTICLE Genes: acr-8 acr-12 acr-13 cam-1 clr-1 cnb-1 col-51 egl-15 gei-11 lev-1 lev-8 lev-10 plk-2 pqn-81 ptr-14 ric-3 rrf-3 sem-5 soc-1 sos-1 sra-3 srr-9 tax-6 unc-29 unc-38 unc-63 wrm-1 Abstract: Nicotinic acetylcholine receptors (nAChRs) mediate fast excitatory neurotransmission in neurons and muscles. To identify nAChR accessory proteins, which may regulate their expression or function, we performed tandem affinity purification of the levamisole-sensitive nAChR from Caenorhabditis elegans, mass spectrometry of associated components, and RNAi-based screening for effects on in vivo nicotine sensitivity. Among the proteins identified was the calcineurin A subunit TAX-6, which appeared to function as a negative regulator of nAChR activity. We also identified five proteins not previously linked to nAChR function, whose inactivation conferred nicotine resistance, implicating them as positive regulators of nAChR activity. Of these, the copine NRA-1 colocalized with the levamisole receptor at neuronal and muscle plasma membranes, and, when mutated, caused reduced synaptic nAChR expression. Loss of SOC-1, which acts in receptor tyrosine kinase (RTK) signaling, also reduced synaptic levamisole receptor levels, as did mutations in the fibroblast growth factor receptor EGL-15, and another RTK, CAM-1. Thus, tandem affinity purification is a viable approach to identify novel proteins regulating neurotransmitter receptor activity or expression in model systems like C. elegans. ------------------- Key: 7389 Medline: 15990876 Authors: Poulin G;Dong Y;Fraser AG;Hopper NA;Ahringer J Title: Chromatin regulation and sumoylation in the inhibition of Ras-induced vulval development in Caenorhabditis elegans. Citation: EMBO Journal 24: 2613-2623 2005 Type: ARTICLE Genes: ada-2 chd-3 dcp-66 dpl-1 efl-1 egr-1 epc-1 gei-2 gei-4 gon-10 hda-1 hpl-2 lag-2 let-23 let-60 let-418 lin-3 lin-9 lin-13 lin-15 lin-35 lin-36 lin-37 lin-51 lin-52 lin-61 mep-1 met-2 mys-1 pcaf-1 rba-1 rba-2 rls-1 rrf-3 ruvb-1 ruvb-2 smo-1 ssl-1 tam-1 trr-1 uba-2 ubc-9 Abstract: In Caenorhabditis elegans, numerous 'synMuv' (synthetic multivulval) genes encode for chromatin-associated proteins involved in transcriptional repression, including an orthologue of Rb and components of the NuRD histone deacetylase complex. These genes antagonize Ras signalling to prevent erroneous adoption of vulval fate. To identify new components of this mechanism, we performed a genome-wide RNA interference (RNAi) screen. After RNAi of 16757 genes, we found nine new synMuv genes. Based on predicted functions and genetic epistasis experiments, we propose that at least four post-translational modifications converge to inhibit Ras-stimulated vulval development: sumoylation, histone tail deacetylation, methylation, and acetylation. In addition, we demonstrate a novel role for sumoylation in inhibiting LIN-12/Notch signalling in the vulva. We further show that many of the synMuv genes are involved in gene regulation outside the vulva, negatively regulating the expression of the Delta homologue lag-2. As most of the genes identified in this screen are conserved in humans, we suggest that similar interactions may be relevant in mammals for control of Ras and Notch signalling, crosstalk between these pathways, and cell ------------------- Key: 7390 Medline: 15890334 Authors: Praitis V;Ciccone E;Austin J Title: SMA-1 spectrin has essential roles in epithelial cell sheet morphogenesis in C. elegans. Citation: Developmental Biology 283: 157-170 2005 Type: ARTICLE Genes: sma-1 spc-1 Abstract: During Caenorhabditis elegans development, the embryo acquires its vermiform shape due to changes in the shape of epithelial cells, a process that requires an apically localized actin cytoskeleton. We show that SMA-1, an ortholog of beta(H)-spectrin required for normal morphogenesis, localizes to the apical membrane of epithelial cells when these cells are rapidly elongating. In spc-1 alpha-spectrin mutants, SMA-1 localizes to the apical membrane but its organization is altered, consistent with the hypothesis these proteins act together to form an apically localized spectrin-based membrane skeleton (SBMS). SMA-1 is required to maintain the association between actin and the apical membrane; sma-1 mutant embryos fail to elongate because actin, which provides the driving force for cell shape change, dissociates from the apical membrane skeleton during morphogenesis. Analysis of sma-1 expression constructs and mutant strains indicates SMA-1 maintains the association between actin and the apical membrane via interactions at its N-terminus and this activity is independent of a-spectrin. SMA-1 also preserves dynamic changes in the organization of the apical membrane skeleton. Taken together, our results show the SMA-1 SBMS plays a dynamic role in converting changes in actin organization into changes in epithelial cell shape during C elegans embryogenesis. ------------------- Key: 7391 Medline: Authors: Schumacher B;Hanazawa M;Lee MH;Nayak S;Volkmann K;Hofmann ER;Hengartner M;Schedl T;Gartner A Title: Translational repression of C. elegans p53 by GLD-1 regulates DNA damage-induced apoptosis. Citation: Cell 122: 145- 2005 Type: CORRECT Genes: Abstract: ------------------- Key: 7392 Medline: 15979372 Authors: Dequen F;St. Laurent JF;Gagnon SN;Carreau M;Desnoyers S Title: The Caenorhabditis elegans FancD2 ortholog is required for survival following DNA damage. Citation: Comparative Biochemistry & Physiology B-Biochemistry & Molecular Biology 141: 453-460 2005 Type: ARTICLE Genes: Abstract: Fanconi anemia (FA) is an autosomal recessive disease characterized by bone-marrow failure, congenital abnormalities, and cancer susceptibility. There are I I FA complementation groups in human where 8 genes have been identified, We found that FancD2 is conserved in evolution and present in the genome of the nematode Caenorhabditis elegans. The gene Y41E3.9 (CeFancD2) encodes a structural ortholog of human FANCD2 and is composed of 10 predicted exons. Our analysis showed that exons 6 and 7 were absent from a CeFancD2 EST suggesting the presence of a splice variant. In an attempt to characterize its role in DNA damage, we depleted worms of CeFANCD2 using RNAi. When the CeFANCD2(RNAi) worms were treated with a crosslinking agent, a significant drop in the progeny survival was noted. These worms were also sensitive, although to a lesser extent, to ionizing radiation (IR). Therefore, these data support an important role for CeFANCD2 in DNA damage response as for its human counterpart. The data also support the usefulness of C. elegans to study the Fanconi anemia pathway, and emphasize the biological importance of FANCD2 in DNA damage response throughout evolution. ------------------- Key: 7393 Medline: Authors: Rose JK;Sangha S;Rai S;Norman KR;Rankin CH Title: Decreased sensory stimulation reduces behavioral responding, retards development, and alters neuronal connectivity in Caenorhabditis elegans. Citation: Journal of Neuroscience 25: 7159-7168 2005 Type: ARTICLE Genes: avr-14 avr-15 cat-2 daf-2 eat-4 egl-4 glr-1 mec-4 nmr-1 npr-1 osm-6 snb-1 Abstract: Activity-dependent plasticity is a critical component of nervous systems. We show that in Caenorhabditis elegans, worms raised in isolation made smaller responses to mechanosensory stimulation and were smaller and slower to begin laying eggs than age-matched group-raised worms. The glutamate receptor gene GLR-1 was critical for the observed alterations in behavior but not in size, whereas the cGMP-dependent protein kinase gene EGL-4 was critical for the observed changes in size but not the changes in behavior. Mechanosensory stimulation during development reversed the effects of isolation on behavior and began to reduce the effects of isolation on size. In C. elegans, the six mechanosensory touch neurons synapse onto the four pair of command interneurons for forward and backward movement. Touch ( mechanosensory) neurons of worms raised in isolation expressed lower levels of green fluorescent protein ( GFP)tagged synaptobrevin than touch neurons of worms raised in colonies. Command interneurons of worms raised in isolation expressed lower levels of GFP-tagged glutamate receptors than command interneurons of worms raised in groups. Brief mechanical stimulation during larval development rescued the expression of GFP-tagged glutamate receptors but not GFP-tagged synaptobrevin. Together, these results indicate that the level of stimulation experienced by C. elegans during development profoundly affects the development of neuronal connectivity and has widespread cellular and behavioral consequences. ------------------- Key: 7394 Medline: 15992384 Authors: Nass R;Hahn MK;Jessen T;McDonald PW;Carvelli L;Blakely RD Title: A genetic screen in Caenorhabditis elegans for dopamine neuron insensitivity to 6-hydroxydopamine identifies dopamine transporter mutants impacting transporter biosynthesis and trafficking. Citation: Journal of Neurochemistry 94: 774-785 2005 Type: ARTICLE Genes: dat-1 Abstract: The presynaptic dopamine (DA) transporter (DAT) is a major determinant of synaptic DA inactivation, an important target for psychostimulants including cocaine and amphetamine, and a mediator of DA neuron vulnerability to the neurotoxins 6-hydroxydopamine (6-OHDA) and 1-methyl-4-phenylpyridinium ion. To exploit genetic approaches for the study of DATs and neural degeneration, we exploited the visibility of green fluorescent protein (GFP)-tagged DA neurons in transgenic nematodes to implement a forward genetic screen for suppressors of 6-OHDA sensitivity. In our initial effort, we identified three novel dat-1 alleles conferring 6-OHDA resistance. Two of the dat-1 alleles derive from point mutations in conserved glycine residues (G55, G90) in contiguous DAT-1 transmembrane domains (TM1 and TM2, respectively), whereas the third allele results in altered translation of the transporter's COOH terminus. Our studies reveal biosynthetic, trafficking and functional defects in the DAT-1 mutants, exhibited both in vitro and in vivo. These studies validate a forward genetic approach to the isolation of DA neuronspecific toxin suppressors and point to critical contributions of the mutated residues, as well as elements of the DAT-1 COOH terminus, to functional ------------------- Key: 7395 Medline: Authors: Dmitrieva NI;Celeste A;Nussenzweig A;Burg MB Title: KU86 preserves chromatin integrity in cells adapted to high NaCl. Citation: Proceedings of the National Academy of Sciences USA 102: 10730-10735 2005 Type: ARTICLE Genes: cku-80 Abstract: ------------------- Key: 7396 Medline: 15380030 Authors: Liu T;Zimmerman KK;Patterson GI Title: Regulation of signaling genes by TBG beta during entry into dauer diapause in C. elegans. Citation: BMC Developmental Biology 4:11: - 2005 Type: ARTICLE Genes: aap-1 age-1 akt-1 akt-2 apx-1 cdk-4 clk-1 clk-2 col-2 col-36 col-40 cut-1 daf-1 daf-2 daf-3 daf-4 daf-5 daf-7 daf-8 daf-9 daf-11 daf-12 daf-14 daf-16 daf-19 daf-21 daf-28 dbl-1 gcy-22 gyc-31 gcy-34 gpa-2 gpa-3 gpa-10 grd-2 grd-6 grd-7 grd-14 hsf-1 ins-1 ins-2 ins-3 ins-4 ins-6 ins-7 ins-8 ins-9 ins-11 ins-17 ins-18 ins-22 ins-23 ins-24 ins-26 ins-30 ins-32 ins-33 ins-34 ins-35 ins-37 ist-1 kin-8 kin-29 lag-1 lim-6 lin-28 lin-28 mev-1 nhr-25 nhr-73 nhr-74 npc-1 npc-2 npp-10 old-1 pdk-1 ptc-3 ptr-6 ptr-11 ptr-16 ptr-18 tr-23 rnr-1 rol-6 sir-2.1 sod-3 slc-1 srh-75 srh-195 srg-21 srg-32 tax-2 tax-4 tph-1 unc-3 wrt-1 wrt-2 Abstract: BACKGROUND: When resources are scant, C. elegans larvae arrest as long-lived dauers under the control of insulin/IGF- and TGFbeta-related signaling pathways. However, critical questions remain regarding the regulation of this developmental event. How do three dozen insulin-like proteins regulate one tyrosine kinase receptor to control complex events in dauer, metabolism and aging? How are signals from the TGFbeta and insulin/IGF pathways integrated? What gene expression programs do these pathways regulate, and how do they control complex downstream events? RESULTS: We have identified genes that show different levels of expression in a comparison of wild-type L2 or L3 larvae (non-dauer) to TGFbeta mutants at similar developmental stages undergoing dauer formation. Many insulin/IGF pathway and other known dauer regulatory genes have changes in expression that suggest strong positive feedback by the TGFbeta pathway. In addition, many insulin-like ligand and novel genes with similarity to the extracellular domain of insulin/IGF receptors have altered expression. We have identified a large group of regulated genes with putative binding sites for the FOXO transcription factor, DAF-16. Genes with DAF-16 sites upstream of the transcription start site tend to be upregulated, whereas genes with DAF-16 sites downstream of the coding region tend to be downregulated. Finally, we also see strong regulation of many novel hedgehog- and patched-related genes, hormone biosynthetic genes, cell cycle genes, and other regulatory genes. CONCLUSIONS: The feedback regulation of insulin/IGF pathway and other dauer genes that we observe would be predicted to amplify signals from the TGFbeta pathway; this amplification may serve to ensure a decisive choice between "dauer" and "non-dauer", even if environmental cues are ambiguous. Up and down regulation of insulin-like ligands and novel genes with similarity to the extracellular domain of insulin/IGF receptors suggests opposing roles for several members of these large gene families. Unlike in adults, most genes with putative DAF-16 binding sites are upregulated during dauer entry, suggesting that DAF-16 has different activity in dauer versus adult metabolism and aging. However, our observation that the position of putative DAF-16 binding sites is correlated with the direction of regulation suggests a novel method of achieving gene-specific regulation from a single pathway. We see evidence of TGFbeta-mediated regulation of several other classes of regulatory genes, and we discuss possible functions of ------------------- Key: 7397 Medline: Authors: Tabuse Y;Nabetani T;Tsugita A Title: Proteoic analysis of protein expression profiles during Caenorhabditis elegans development using two-dimensional gel electrophoresis. Citation: Proteomics 5: 2876-2891 2005 Type: ARTICLE Genes: aco-1 aco-2 alh-1 alh-12 ard-1 asp-6 atp-2 cct-1 cct-2 cct-4 cct-5 cct-6 cpl-1 crf-1 crt-1 cyp-5 cyp-5 dhs-12 dim-1 gpd-1 gpd-2 gpd-3 gta-1 hsp-1 hsp-3 hsp-4 hsp-6 hsp-60 kat-1 lap-1 lbp-2 lec-1 lec-2 lec-3 lec-6 let-721 let-767 lev-11 lin-6 lmn-1 mcm-7 mdh-1 mel-32 pab-1 pas-1 pas-4 pas-5 pas-6 pas-7 pbs-1 pcn-1 pdi-2 pdi-3 pfn-1 rpa-0 rnp-5 rps-0 rpt-1 rpt-2 rpt-4 sdh-1 sec-1 sip-1 sod-2 srs-2 tba-2 tbb-1 tsn-1 vab-21 vha-8 vha-12 vit-6 Abstract: Coordinated protein expression is critical for the normal execution of animal development. To obtain overall proteome profiles during animal development, a small free-living soil nematode, Caenorhabditis elegans, was used as a model and the developmental changes of protein expressions were analyzed using two-dimensional difference gel electrophoresis. Protein samples from six developmental stages were prelabeled with fluorescent cyanine dyes and separated on two-dimensional electrophoresis gels. Image-to-image analysis of protein abundances together with protein identification by peptide mass fingerprinting yielded the developmental expression profiles of 231 spots representing 165 proteins. About a quarter of the identified proteins were expressed in multiple spots with different isoelectric points, suggesting a certain proportion of proteins were variously modified. This notion was supported by the observation that about a third of the multispot proteins were stained positive for a phosphoprotein specific dye. While a fairly large number of the proteins showed little alteration in their expression profiles during development, about 40 proteins were found to be significantly either up- or down-regulated between the embryos and newly hatched L1 larvae. Down-regulated proteins included those related to the cell cycle such as MCM-7, PCN-1, and the mitotic checkpoint protein, while up-regulated proteins included structural proteins such as actins, LEV-11, DIM-1, VAB-21, metabolic enzymes such as ATP synthase, ALH-12, fluctose-1,6-bisphosphate aldolase and GPD-3, and galectins. A standard proteome map was obtained where the defects in the mutations of developmental genes and the effects of reagents on the development in C. elegans were analyzed. ------------------- Key: 7398 Medline: 16107851 Authors: Lu R;Maduro M;Li F;Li HW;Broitman-Maduro G;Li WX;Ding W Title: Animal virus replication and RNAi-mediated antiviral silencing in Caenorhabditis elegans. Citation: Nature 436: 1040-1043 2005 Type: ARTICLE Genes: alg-1 alg-2 rde-1 ppw-1 ppw-2 Abstract: The worm Caenorhabditis elegans is a model system for studying many aspects of biology, including host responses to bacterial pathogens(1,2), but it is not known to support replication of any virus. Plants and insects encode multiple Dicer enzymes that recognize distinct precursors of small RNAs and may act cooperatively(3-7). However, it is not known whether the single Dicer of worms and mammals is able to initiate the small RNA-guided RNA interference (RNAi) antiviral immunity as occurs in plants(8) and insects(9). Here we show complete replication of the Flock house virus (FHV) bipartite, plus-strand RNA genome in C. elegans. We show that FHV replication in C. elegans triggers potent antiviral silencing that requires RDE-1, an Argonaute protein(10,11) essential for RNAi mediated by small interfering RNAs (siRNAs) but not by microRNAs. This immunity system is capable of rapid virus clearance in the absence of FHV B2 protein, which acts as a broad-spectrum RNAi inhibitor(9,12) upstream of rde-1 by targeting the siRNA precursor. This work establishes a C. elegans model for genetic studies of animal virus - host interactions and indicates that mammals might use a siRNA pathway as an antiviral response. ------------------- Key: 7399 Medline: 16107852 Authors: Wilkins C;Dishongh R;Moore SC;Whitt MA;Chow M;Machaca K Title: RNA interference is an antiviral defence mechanism in Caenorhabditis elegans. Citation: Nature 436: 1044-1047 2005 Type: ARTICLE Genes: eri-1 rde-1 rde-4 rrf-3 Abstract: RNA interference (RNAi) is an evolutionarily conserved sequence-specific post-transcriptional gene silencing mechanism that is well defined genetically in Caenorhabditis elegans(1-4). RNAi has been postulated to function as an adaptive antiviral immune mechanism in the worm, but there is no experimental evidence for this. Part of the limitation is that there are no known natural viral pathogens of C. elegans. Here we describe an infection model in C. elegans using the mammalian pathogen vesicular stomatitis virus (VSV) to study the role of RNAi in antiviral immunity. VSV infection is potentiated in cells derived from RNAi-defective worm mutants (rde-1; rde-4), leading to the production of infectious progeny virus, and is inhibited in mutants with an enhanced RNAi response (rrf-3; eri-1). Because the RNAi response occurs in the absence of exogenously added VSV small interfering RNAs, these results show that RNAi is activated during VSV infection and that RNAi is a genuine antiviral immune defence mechanism in the worm. ------------------- Key: 7400 Medline: Authors: Zhang G;Sleiman SF;Tseng RJ;Rajakumar V;Wang X;Chamberlin Title: Alteration of the DNA binding domain disrupts distinct functions of the C. elegans Pax protein EGL-38. Citation: Mechanisms of Development 122: 887-899 2005 Type: ARTICLE Genes: egl-38 lin-48 Abstract: The paired-domain-containing Pax transcription factors play an important role in the development of a range of organ, tissue and cell types. Although DNA binding elements and target genes for Pax proteins have been identified, how these proteins identify appropriate DNA elements and regulate different genes in different cellular contexts is not well understood. To investigate the relationship between Pax proteins and their targets, we have studied the in vivo and in vitro properties associated with wild-type and different mutant variants of the Caenorhabditis elegans Pax protein EGL-38. Here, we characterize the properties of four mutations that result in an amino acid substitution in the DNA binding domain of EGL-38. We find that animals bearing the different mutant alleles exhibit tissue-preferential defects in egl-38 function. The mutant proteins are also altered in their activity in an ectopic expression assay and in their in vitro DNA binding properties. Using in vitro selection, we have identified binding sites for EGL-38. However, we show that selected sites function poorly in vivo as EGL-38 response elements, indicating that sequence features in addition to DNA binding determine the efficacy of Pax response elements. The distinction between DNA. binding and activity is consistent with the model that other factors commonly play a role in mediating Pax protein target site selection and ------------------- Key: 7401 Medline: 16055700 Authors: Ketel CS;Andersen EF;Vargas ML;Suh J;Strome S;Simon JA Title: Subunit contributions to histone methyltransferase activities of fly and worm polycomb group complexes. Citation: Molecular and Cellular Biology 25: 6857-6868 2005 Type: ARTICLE Genes: mes-2 mes-3 mes-6 Abstract: The ESC-E(Z) complex of Drosophila melanogaster Polycomb group (PcG) repressors is a histone H3 methyltransferase (HMTase). This complex silences fly Hox genes, and related HMTases control germ line development in worms, flowering in plants, and X inactivation in mammals. The fly complex contains a catalytic SET domain subunit, E(Z), plus three noncatalytic subunits, SU(Z)12, ESC, and NURF-55. The four-subunit complex is > 1,000-fold more active than E(Z) alone. Here we show that ESC and SU(Z)12 play key roles in potentiating E(Z) HMTase activity. We also show that loss of ESC disrupts global methylation of histone H3-lysine 27 in fly embryos. Subunit mutations identify domains required for catalytic activity and/or binding to specific partners. We describe missense mutations in surface loops of ESC, in the CXC domain of E(Z), and in the conserved VEFS domain of SU(Z)12, which each disrupt HMTase activity but preserve complex assembly. Thus, the E(Z) SET domain requires multiple partner inputs to produce active HMTase. We also find that a recombinant worm complex containing the E(Z) homolog, MES-2, has robust HMTase activity, which depends upon both MES-6, an ESC homolog, and MES-3, a pioneer protein. Thus, although the fly and mammalian PcG complexes absolutely require SU(Z)12, the worm complex generates HMTase activity from a distinct partner set. ------------------- Key: 7402 Medline: 16077004 Authors: Nakamura K;Kim S;Ishidate T;Bei Y;Pang K;Shirayama M;Trzepacz C;Brownell DR;Mello CC Title: Wnt signaling drives WRM-1/beta-tatenin asymmetries in early C. elegans embryos. Citation: Genes & Development 19: 1749-1754 2005 Type: ARTICLE Genes: apr-1 crm-1 gsk-3 imb-4 lit-1 mom-2 mom-4 mom-5 par-5 pop-1 pry-1 ran-3 ran-5 wrm-1 Abstract: beta-Catenin regulates cell adhesion and cellular differentiation during development, and misregulation of beta-catenin contributes to numerous forms of cancer in humans. Here we describe Caenorhabditis elegans conditional alleles of mom-2/Wnt, mom-4/Tak1, and wrm-1/beta-catenin. We use these reagents to examine the regulation of WRM-1/beta-catenin during a Wnt-signaling-induced asymmetric cell division. While WRM-1 protein initially accumulates in the nuclei of all cells, signaling promotes the retention of WRM-1 in nuclei of responding cells. We show that both PRY-1/Axin and the nuclear exportin homolog IMB-4/CRM-1 antagonize signaling. These findings reveal how Wnt signals direct the asymmetric localization of beta-catenin during polarized cell division. ------------------- Key: 7403 Medline: Authors: Siepel A;Bejerano G;Pedersen JS;Hinrich AS;Hou M;Rosenbloom K;Clawson H;Spieth J;Hillier LW;Richard S;Weinstock GM;Wilson RK;Gibbs RA;Kent WJ;Miller W;Haussler D Title: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Citation: Genome Research 15: 1034-1050 2005 Type: ARTICLE Genes: Abstract: We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide Multiple alignments of five vertebrate species (human, Mouse, rat, chicken, and Fugu rubripes). Parallel searches have been performed with multiple alignments Of four insect species (three species of Drosophila and Anopheles gambiae), two species of Caenorhabditis, and seven species of Saccharomyces. Conserved elements were identified with a computer program called phastCons, which is based on a two-state phylogenetic hidden Markov model (phylo-HMM). PhastCons works by fitting a phylo-HMM to the data by maximum likelihood, Subject to constraints designed to calibrate the model across species groups, and then predicting conserved elements based oil this model. The predicted elements cover roughly 3%-8% of the human genome (depending on the details of the calibration procedure) and Substantially higher fractions of the more compact Drosophila melanogaster (37%-53%), Caenorhabditis elegans (18%-37%), and Saccharaomyces cerevisiae (47%-68%) genomes. From yeasts to vertebrates, in order of increasing genome size and general biological complexity, increasing fractions of conserved bases are found to lie Outside of the exons of known protein-coding genes. In all groups, the most highly conserved elements (HCEs), by log-odds score, are hundreds or thousands of bases long. These elements share certain properties With Ultraconserved elements, but they tend to be longer and less perfectly conserved, and they overlap genes of somewhat different functional categories. In vertebrates, HCEs are associated with the 3' UTRs of regulatory genes, stable gene deserts, and megabase-sized regions rich in moderately conserved noncoding sequences. Noncoding HCEs also show strong statistical evidence of ail enrichment for RNA secondary ------------------- Key: 7404 Medline: 15944183 Authors: Watanabe N;Nagamatsu Y;Gengyo-Ando K;Mitani S;Ohshima Y Title: Control of body size by SMA-5, a homolog of MAP kinase BMK1/ERK5, in C. elegans. Citation: Development 132: 3175-3184 2005 Type: ARTICLE Genes: sma-5 Abstract: We have analyzed the sma-5(n678) mutant in C. elegans to elucidate mechanisms controlling body size. The sma-5 mutant is very small, grows slowly and its intestinal granules look abnormal. We found a 15 kb deletion in the mutant that includes a 226 bp deletion of the 3' end of the W06B3.2-coding sequence. Based on this result, rescue experiments, RNAi experiments and a newly isolated deletion mutant of W06B3.2, we conclude that W06B3.2 is the sma-5 gene. The sma-5 mutant has much smaller intestine, body wall muscles and hypodermis than those of the wild type. However, the number of intestinal cells or body wall muscle cells is not changed, indicating that the sma-5 mutant has much smaller cells. In relation to the smaller cell size, the amount of total protein is drastically decreased; however, the DNA content of the intestinal nuclei is unchanged in the sma-5 mutant. The sma-5 gene is expressed in intestine, excretory cell and hypodermis, and encodes homologs of a mammalian MAP kinase BMK1/ERK5/MAPK7, which was reported to control cell cycle and cell proliferation. Expression of the sma-5 gene in hypodermis is important for body size control, and it can function both organ-autonomously and non-autonomously. We propose that the sma-5 gene functions in a MAP kinase pathway to regulate body size mainly through control of cell growth. ------------------- Key: 7405 Medline: 15958510 Authors: Putzke AP;Hikita ST;Clegg DO;Rothman JH Title: Essential kinase-independent role of a Fer-like non-receptor tyrosine kinase in Caenorhabditis elegans Citation: Development 132: 3185-3195 2005 Type: ARTICLE Genes: elt-1 emb-9 frk-1 hmp-1 hmp-2 hmr-1 let-2 pat-3 mDf7 Abstract: Morphogenesis requires coordination of cell surface activity and cytoskeletal architecture. During the initial stage of morphogenesis in Caenorhabditis elegans, the concerted movement of surface epithelial cells results in enclosure of the embryo by the epidermis. We report that Fer-related kinase-1 (FRK-1), an ortholog of the mammalian non-receptor tyrosine kinase Fer, is necessary for embryonic enclosure and morphogenesis in C. elegans. Expression of FRK-1 in epidermal cells is sufficient to rescue a chromosomal deficiency that removes the frk-1 locus, demonstrating its autonomous requirement in the epidermis. The essential function of FRK-1 is independent of its kinase domain, suggesting a non-enzymatic role in morphogenesis. Localization of FRK-1 to the plasma membrane requires beta-catenin, but not cadherin or alpha-catenin, and muscle-expressed beta-integrin is nonautonomously required for this localization; in the absence of these components FRK-1 becomes nuclear. Mouse FerT rescues the morphogenetic defects of frk-1 mutants and expression of FRK-1 in mammalian cells results in loss of adhesion, implying a conserved function for FRK-1/FerT in cell adhesion and morphogenesis. Thus, FRK-1 performs a kinase-independent function in differentiation and morphogenesis of the C. elegans epidermis during ------------------- Key: 7406 Medline: 15983401 Authors: Yabe T;Suzuki N;Furukawa T;Ishihara T;Katsura I Title: Multidrug resistance-associated protein MRP-1 regulates dauer diapause by its export activity in Caenorhabditis elegans. Citation: Development 132: 3197-3207 2005 Type: ARTICLE Genes: che-3 daf- daf-2 daf-5 daf-11 daf-16 mrp-1 sdf-14 unc-31 Abstract: Multidrug resistance-associated proteins (MRPs), when overexpressed, confer drug resistance to cancer cells by exporting anti-cancer agents through the cell membrane, but their role in animal development has not been elucidated. Here we show that an MRP homolog regulates larval development in the nematode Caenorhabdifis elegans. C. elegans forms a special third-stage larva called a dauer larva under conditions inappropriate for growth. By contrast, we found that mutants in mrp-1, an MRP homolog gene, form dauer larvae even under conditions appropriate for growth, in the background of certain mutations that partially block the insulin signaling pathway. A functional mrp-1::GFP gene was shown to be expressed in many tissues, and the wild-type mrp-1 gene must be expressed in multiple tissues for a wild-type phenotype. Human MRP1 could substitute for C. elegans MRP-1 in dauer larva regulation, and an inhibitor of the human MRP1 transport activity impaired this function, showing that export activity is required for normal dauer larva regulation. Epistasis studies revealed that MRP-1 acts in neither the TGF-beta nor the cGMP signaling pathway. mrp-1 mutations enhanced the dauer-constitutive phenotype of mutants in the insulin signaling pathway more strongly than that in other pathways. Thus, MRP-1, through its export activity, supports the induction of the normal (non-dauer) life cycle by the insulin signaling pathway. ------------------- Key: 7407 Medline: 16037210 Authors: Bachorik JL;Kimble J Title: Redundant control of the Caenorhabditis elegans sperm/oocyte switch by PUF-8 and FBF-1, two distinct PUF RNA-binding proteins. Citation: Proceedings of the National Academy of Sciences USA 102: 10893-10897 2005 Type: ARTICLE Genes: fbf-1 fbf-2 fem-1 fem-2 fem-3 fog-1 fog-2 fog-3 gld-1 puf-8 Abstract: PUF proteins control both growth and differentiation in the C elegans germ line. These conserved RNA-binding proteins inhibit expression of target mRNAs, either by repressing translation or promoting degradation. Previous studies showed that PUF-8, a PUF protein with striking similarity to human Pumilio, prevents return of primary spermatocytes to the mitotic cell cycle [Subramaniam, K. & Seydoux, G. (2003) Curr. Biol. 13, 134-139]. We now report that PUF-8 is also critical for the hermaphrodite sperm/oocyte switch. Most puf-8 mutant hermaphrodites make both sperm and oocytes and are self-fertile, but some make a vast excess of sperm and fail to switch into oogenesis. This puf-8 defect is dramatically enhanced by removal of another puf gene called fbf-1: all fbf-1 puf-8 double mutants fail in the hermaphrodite sperm/oocyte switch. Therefore, puf-8 and fbf-1 act redundantly to control this decision. Epistasis analyses place puf-8 and fbf-1 upstream of fog-2, a gene near the top of the germ-line sex determination pathway. Furthermore, the abundance of FOG-2 increases dramatically in the distal region of fbf-1 puf-8 double mutants. We suggest that PUF-8 and FBF-1 may control fog-2 expression, and that the sperm/oocyte decision occurs in the distal germ line. ------------------- Key: 7408 Medline: Authors: Vought VE;Ohmachi M;Lee MH;Maine EM Title: EGO-1, a putative RNA-directed RNA polymerase, promotes germline proliferation in parallel with GLP-1/Notch signaling and regulates the spatial organization of nuclear pore complexes and germline P... Citation: Genetics 170: 1121-1132 2005 Type: ARTICLE Genes: dcr-1 ego-1 gld-1 gld-2 glp-1 rrf-3 Abstract: Caenorhabditis elegans EGO-I, a putative cellular RNA-directed RNA polymerase, promotes several aspects of germline development, including proliferation, meiosis, and gametogenesis, and ensures a robust response to RNA interference. In C. elegans, GLP-1/Notch signaling from the somatic gonad maintains a population of proliferating germ cells, while entry of germ cells into meiosis is triggered by the GLD-1 and GLD-2 pathways. GLP-1 signaling prevents germ cells from entering meiosis by inhibiting GLD-1 and GLD-2 activity. We originally identified the ego-1 gene on the basis of a genetic interaction with glp-1. Here, we investigate the role of ego-1 in germline proliferation. Our data indicate that EGO-I does not positively regulate GLP-1 protein levels or GLP-1 signaling activity. Moreover, GLP-1 signaling does not positively regulate EGO-1 activity. EGO-I does not inhibit expression of GLD-1 protein in the distal germline. Instead, EGO-1 acts in parallel with GLP-1 signaling to influence the proliferation vs. meiosis fate choice. Moreover, EGO-1 and GLD-1 act in parallel to ensure germline health. Finally, the size and distribution of nuclear pore complexes and perinuclear P granules are altered in the absence of EGO-1, effects that disrupt germ cell biology per se and probably ------------------- Key: 7409 Medline: Authors: Jiang Y;Horner V;Liu J Title: The HMX homeodomain protein MLS-2 regulates cleavage orientation, cell proliferation and cell fate specification in the C. elegans postembryonic mesoderm. Citation: Development 132: 4119-4130 2005 Type: ARTICLE Genes: cye-1 hlh-1 hlh-8 mab-5 mls-2 Abstract: The proper formation of a complex multicellular organism requires the precise coordination of many cellular events, including cell proliferation, cell fate specification and differentiation. The C. elegans postembryonic mesodermal lineage, the M lineage, allows us to study mechanisms coordinating these events at single cell resolution. We have identified an HMX homeodomain protein MLS-2 in a screen for factors required for M lineage patterning. The MLS-2 protein is present in nuclei of undifferentiated cells in the early M lineage and in a subset of head neurons. In the M lineage, MLS-2 activity appears to be tightly regulated at the fourth round of cell division, coincident with the transition from proliferation to differentiation. A predicted null allele of mls-2, cc615, causes reduced cell proliferation in the M lineage, whereas a semi-dominant, 4119 gain-of-function allele, tm252, results in increased cell proliferation. Loss or overexpression of mls-2 also affects cleavage orientation and cell fate specification in the M lineage. We show that the increased cell proliferation in mls-2(tm252) mutants requires CYE-1, a G1 cell cycle regulator. Furthermore, the C. elegans Myod homolog HLH-1 acts downstream of mls-2 to specify M-derived coelomocyte cell fates. Thus MLS-2 functions in a cell type-specific manner to regulate both ------------------- Key: 7410 Medline: Authors: Takacs-Vellai K;Vellai T;Puoti A;Passannante M;Wicky C;Streit A;Kovacs AL;Mueller F Title: Inactivation of the autophagy gene bec-1 triggers apoptotic cell death in C. elegans. Citation: Current Biology 15: 1513-1517 2005 Type: ARTICLE Genes: bec-1 ced-3 ced-9 glp-1 let-512 Abstract: Programmed cell death (PCD) is an essential and highly orchestrated process that plays a major role in morphogenesis and tissue homeostasis during development. In humans, defects in regulation or execution of cell death lead to diabetes, neurodegenerative disorders, and cancer [1]. Two major types of PCD have been distinguished: the caspase-mediated process of apoptosis and the caspase-independent process involving autophagy [1, 2]. Although apoptosis and autophagy are often activated together in response to stress [3], the molecular mechanisms underlying their interplay remain unclear. Here we show that BEC-1, the C. elegans ortholog of the yeast and mammalian autophagy proteins Atg6Nps30 and Beclin 1, is essential for development. We demonstrate that BECA is necessary for the function of the class III P13 kinase LET-512/Vps34, an essential protein required for autophagy, membrane trafficking, and endocytosis. Furthermore, BECA forms a complex with the antiapoptotic protein CED-9/Bcl-2, and its depletion triggers CED-3/Caspase-dependent PCD. Based on our results, we propose that bec-1 represents a link between autophagy and apoptosis, thus supporting the view that the two processes act in concerted manner in the cell death machinery. ------------------- Key: 7411 Medline: 15784240 Authors: Martinez-Grueiro M;Gimenez-Pardo C;Gomez-Barrio A;Franck X;Fournet A;Hocquemiller R;Figadere B;Casado-Escribano N Title: Nematocidal and trichomonacidal activities of 2-substituted quinolines. Citation: Il Farmaco 60: 219-224 2005 Type: ARTICLE Genes: Abstract: Several quinolines were synthesized and evaluated in vitro and in vivo against the nematodes Caenorhabditis elegans, Heligmosomoides polygyrus and the protozoa Trichomonas vaginalis. If some of them have shown in vitro nematocide activity (at 10 microM), however, their trichomonacidal activity reached 50% reduction at only 100 microM. The in vivo activity on Trichinella spiralis model was evaluated for some of the most in vitro active quinolines. ------------------- Key: 7412 Medline: 15837622 Authors: Lackner MR;Kindt RM;Carroll PM;Brown K;Cancilla MR;Chen C;de Silva H;Franke Y;Guan B;Heuer T;Hung T;Keegan K;Lee JM;Manne V;O'Brien C;Parry D;Perez-Villar JJ;Reddy RK;Xiao H;Zhan H;Cockett M;Plowman G Title: Chemical genetics identifies Rab geranylgeranyl transferase as an apoptotic target of farnesly transferase inhibitors. Citation: Cancer Cell 7: 325-336 2005 Type: ARTICLE Genes: ced-1 ced-3 ced-4 ced-9 ced-10 cep-1 cpl-1 rab-5 rab-7 vps-41 Abstract: A chemical genetics approach identified a cellular target of several proapoptotic farnesyl transferase inhibitors (FTIs). Treatment with these FTIs caused p53-independent apoptosis in Caenorhabditis elegans, which was mimicked by knockdown of endosomal trafficking proteins, including Rab5, Rab7, the HOPS complex, and notably the enzyme Rab geranylgeranyl transferase (RabGGT). These FTIs were found to inhibit mammalian RabGGT with potencies that correlated with their proapoptotic activity. Knockdown of RabGGT induced apoptosis in mammalian cancer cell lines, and both RabGGT subunits were overexpressed in several tumor tissues. These findings validate RabGGT, and by extension endosomal function, as a therapeutically relevant target for modulation of apoptosis, and enhance our understanding of the mechanism of action of FTIs. ------------------- Key: 7413 Medline: Authors: Hanover JA;Forsythe ME;Hennessey PT;Brodigan TM;Love DC;Ashwell G;Krause M Title: A Caenorhabditis elegans model of insulin resistance: Altered macronutrient storage and dauer formation in an OGT-1 knockout. Citation: Proceedings of the National Academy of Sciences USA 102: 11266-11271 2005 Type: ARTICLE Genes: daf-2 elt-2 hlh-2 lin-26 ogt-1 Abstract: O-linked N-acetylglucosamine (O-GlcNAc) is an evolutionarily conserved modification of nuclear pore proteins, signaling kinases, and transcription factors. The O-GlcNAc transferase (OGT) catalyzing O-GlcNAc addition is essential in mammals and mediates the last step in a nutrient-sensing "hexosamine-signaling pathway." This pathway may be deregulated in diabetes and neurodegenerative disease. To examine the function of O-GlcNAc in a genetically amenable organism, we describe a putative null allele of OGT in Caenorhabditis elegans that is viable and fertile. We demonstrate that, whereas nuclear pore proteins of the homozygous deletion strain are devoid of O-GlcNAc, nuclear transport of transcription factors appears normal. However, the OGT mutant exhibits striking metabolic changes manifested in a approximate to 3-fold elevation in trehalose levels and glycogen stores with a concomitant approximate to 3-fold decrease in triglycericles levels. In nematodes, a highly conserved insulin-like signaling cascade regulates macronutrient storage, longevity, and dauer formation. The OGT knockout suppresses dauer larvae formation induced by a temperature-sensitive allele of the insulin-like receptor gene daf-2. Our findings demonstrate that OGT modulates macronutrient storage and dauer formation in C elegans, providing a unique genetic model for examining the role of ------------------- Key: 7414 Medline: Authors: Ackley BD;Harrington RJ;Hudson ML;Williams L;Kenyon CJ;Chisholm AD;Jin Y Title: The two isoforms of the Caenorhabditis elegans leukocyte-common antigen related tyrosine phosphatase PTP-3 function independently in axon guidance and synapse formation. Citation: Journal of Neuroscience 25: 7517-7528 2005 Type: ARTICLE Genes: cle-1 nid-1 ptp-3 snt-1 syd-2 unc-10 unc-49 unc-104 mnDf90 Abstract: Leukocyte-common antigen related (LAR)-like phosphatase receptors are conserved cell adhesion molecules that function in multiple developmental processes. The Caenorhabditis elegans ptp-3 gene encodes two LAR family isoforms that differ in the extracellular domain. We show here that the long isoform, PTP-3A, localizes specifically at synapses and that the short isoform, PTP-3B, is extrasynaptic. Mutations in ptp-3 cause defects in axon guidance that can be rescued by PTP-3B but not by PTP-3A. Mutations that specifically affect ptp-3A do not affect axon guidance but instead cause alterations in synapse morphology. Genetic double-mutant analysis is consistent with ptp-3A acting with the extracellular matrix component nidogen, nid-1, and the intracellular adaptor alpha-liprin, syd-2. nid-1 and syd-2 are required for the recruitment and stability of PTP-3A at synapses, and mutations in ptp-3 or nid-1 result in aberrant localization of SYD-2. Overexpression of PTP-3A is able to bypass the requirement for nid-1 for the localization of SYD-2 and RIM. We propose that PTP-3A acts as a molecular link between the extracellular matrix and alpha-liprin during ------------------- Key: 7415 Medline: 16103211 Authors: Sundaram MV Title: The love-hate relationship between Ras and Notch. Citation: Genes & Development 19: 1825-1839 2005 Type: REVIEW Genes: apx-1 dep-1 dsl-1 hlh-2 ksr-1 ksr-2 lag-2 let-23 let-60 lin-1 lin-3 lin-12 lin-31 lin-39 lin-45 mek-2 mep-1 mir-84 mpk-1 sem-5 smo-1 sos-1 sur-2 Abstract: The Ras and Notch signaling pathways are used over and over again during development to control many different biological processes. Frequently, these two signaling pathways intersect to influence common processes, but sometimes they cooperate and sometimes they antagonize each other. The Caenorhabditis elegans vulva and the Drosophila eye are two classic paradigms for understanding how Ras and Notch affect cell fates, and how the two pathways work together to control biological pattern. Recent advances in these systems reveal some of the mechanisms by which Ras and Notch can interact. Similar types of interactions in mammals may be important for determining whether and how alterations in Ras or Notch lead to cancer. ------------------- Key: 7416 Medline: 16054029 Authors: Srayko M;Kaya A;Stamford J;Hyman AA Title: Identification and characterization of factors required for microtubule growth and nucleation in the early C. elegans embryo. Citation: Develomental Cell 9: 223-236 2005 Type: ARTICLE Genes: air-1 dhc-1 ebp-2 gip-1 hcp-4 klp-7 mel-26 ran-1 sas-1 spd-2 spd-5 tac-1 tbg-1 tpxl-1 zyg-8 zyg-9 Abstract: Microtubules (MTs) are dynamic polymers that undergo cell cycle and position-sensitive regulation of polymerization and depolymerization. Although many different factors that regulate MT dynamics have been described, to date there has been no systematic analysis of genes required for MT dynamics in a single system. Here, we use a transgenic EB1::GFP strain, which labels the growing plus ends of MTs, to analyze the growth rate, nucleation rate, and distribution of growing MTs in the Caenorhabditis elegans embryo. We also present the results from an RNAi screen of 40 genes previously implicated in MT-based processes. Our findings suggest that fast microtubule growth is dependent on the amount of free tubulin and the ZYG-9-TAC-1 complex. Robust MT nucleation by centrosomes requires AIR-1, SPD-2, SPD-5, and 7-tubulin. However, we found that centrosomes do not nucleate MTs to saturation; rather, the depolymerizing kinesin-13 subfamily member KLP-7 is required to limit microtubule outgrowth from centrosomes. ------------------- Key: 7417 Medline: 16054030 Authors: Ozlu N;Srayko M;Kinoshita K;Habermann B;O'Toole ET;Muller-Reichert T;Schmalz N;Desai A;Hyman AA Title: An essential function of the C. elegans ortholog of TPX2 is to localize activated Aurora A kinase to mitotic spindles. Citation: Developmental Cell 9: 237-248 2005 Type: ARTICLE Genes: air-1 spd-5 tpxl-1 Abstract: In vertebrates, the microtubule binding protein TPX2 is required for meiotic and mitotic spindle assembly. TPX2 is also known to bind to and activate Aurora A kinase and target it to the spindle. However, the relationship between the TPX2-Aurora A interaction and the role of TPX2 in spindle assembly is unclear. Here, we identify TPXL-1, a C. elegans protein that is the first characterized invertebrate ortholog of TPX2. We demonstrate that an essential role of TPXL-1 during mitosis is to activate and target Aurora A to microtubules. Our data suggest that this targeting stabilizes microtubuies connecting kinetochores to the spindle poles. Thus, activation and targeting of Aurora A appears to be an ancient and conserved function of TPX2 that plays a central role in mitotic spindle assembly. ------------------- Key: 7418 Medline: 16022603 Authors: de Bono M;Maricq AV Title: Neuronal substrates of complex behaviors in C. elegans. Citation: Annual Review of Neuroscience 28: 451-501 2005 Type: REVIEW Genes: adp-1 aex-1 aex-3 aex-5 bas-1 cat-1 cha-1 che-2 clk-1 cmk-1 daf-1 daf-2 daf-3 daf-5 daf-7 daf-8 daf-14 daf-16 dec-4 dop-1 dop-3 eat-4 egl-2 egl-3 egl-8 egl-19 exp-1 flp-18 flp-21 flr-1 gcy-5 gcy-6 gcy-7 gcy-32 gcy-34 gcy-35 gcy-36 gcy-37 glr-1 glr-2 goa-1 gpa-11 gpc-1 grk-2 gui-1 hen-1 ire-1 itr-1 lin-10 lov-1 lrn-1 lrn-2 mod-1 mod-5 nmr-1 nmr-2 npr-1 ocr-2 odr-1 odr-3 odr-4 odr-10 osm-3 osm-5 osm-6 osm-9 osm-10 pkd-2 rab-3 shn-1 sol-1 tax-2 tax-4 tax-6 unc-2 unc-8 unc-11 unc-13 unc-25 unc43 unc-47 unc-68 Abstract: A current challenge in neuroscience is to bridge the gaps between genes, proteins, neurons, neural circuits, and behavior in a single animal model. The nematode Caenorhabditis elegans has unique features that facilitate this synthesis. Its nervous system includes exactly 302 neurons, and their pattern of synaptic connectivity is known. With only five olfactory neurons, C. elegans can dynamically respond to dozens of attractive and repellant odors. Thermosensory neurons enable the nematode to remember its cultivation temperature and to track narrow isotherms. Polymodal sensory neurons detect a wide range of nociceptive cues and signal robust escape responses. Pairing of sensory stimuli leads to long-lived changes in behavior consistent with associative learning. Worms exhibit social behaviors and complex ultradian rhythms driven by Ca2+ oscillators with clock-like properties. Genetic analysis has identified gene products required for nervous system function and elucidated the molecular and ------------------- Key: 7419 Medline: Authors: McCarthy EK;Goldstein B Title: Asymmetric division: a kinesin for spindle positioning. Citation: Current Biology 15: R591-R593 2005 Type: REVIEW Genes: kca-1 klc-1 klc-2 mei-1 unc-116 Abstract: The meiotic spindles of animal eggs move to extremely asymmetric positions, close to the cell cortex. A recent paper has identified a motor complex that may move the meiotic spindle toward the cortex in Caenorhabditis elegans eggs. ------------------- Key: 7420 Medline: Authors: Gal TZ;Glazer I;Koltai H Title: Stressed worms: responding to the post-genomics era. Citation: Molecular & Biochemical Parasitology 143: 1-5 2005 Type: REVIEW Genes: lea-1 osr-1 pmk-1 Abstract: Nematodes are among the most successful organisms in withstanding stress conditions associated with water loss, and viable individuals have been recovered from dry desert soils. Little is known about the biochemical and molecular events underpinning nematodes' physiological responses to dehydration. Post-genomics research in Caenorhabditis elegans may offer an opportunity to understand the stress response better. This review focuses on recent progress in understanding the molecular mechanisms of water-loss associated stress response in the model nematode C. elegans and in parasitic nematodes and discusses the scope for applying the knowledge and tools derived from a model organism for the study of wild, environmentally-adapted, parasitic nematodes, in the light of the emergence of genomics research of non-model organisms. ------------------- Key: 7421 Medline: Authors: Hawkins NC;Ellis G;Bowerman B;Garriga G Title: MOM-5 Frizzled regulates the distribution of DSH-2 to control C. elegans asymmetric neuroblast divisions. Citation: Developmental Biology 284: 246-259 2005 Type: ARTICLE Genes: cfz-2 dsh-1 dsh-2 lin-17 mig-1 mig-5 mom-5 pop-1 Abstract: Asymmetric cell divisions produce all 302 neurons of the C elegans hermaphrodite. Here, we describe a role for a C elegans Dishevelled homolog, DSH-2, in an asymmetric neuroblast division. In dsh-2 mutants, neurons normally descended from the anterior neuroblast daughter of the ABp1/rpppa blast cell were frequently duplicated, while non-neuronal cells produced by the posterior daughter cell were often missing. These observations indicate that in the absence of dsh-2 function, the posterior daughter cell was transformed into a second anterior-like cell. Loss of mom-5, a C elegans frizzled homolog, produced a similar phenotype. We also show that the DSH-2 protein localized to the cell cortex in most cells of the embryo. In the absence of MOM-5/Fz, DSH-2 was localized to the cytoplasm, suggesting that MOM-5 regulates asymmetric cell division by controlling the localization of DSH-2. Although all neurons in C elegans are produced by an invariant pattern of cell divisions, our results indicate that cell signaling may contribute to asymmetric neuroblast division during ------------------- Key: 7422 Medline: Authors: Hutter H;Wacker I;Schmid C;Hedgecock EM Title: Novel genes controlling ventral cord asymmetry and navigation of pioneer axons in C. elegans. Citation: Developmental Biology 284: 260-272 2005 Type: ARTICLE Genes: ast-1 ast-2 ast-4 ast-5 ast-6 ast-7 lin-11 unc-34 unc-71 unc-130 vab-15 zag-1 Abstract: The ventral cord in C. elegans is the major longitudinal axon tract containing essential components of the motor circuit. In genetic screens using transgenic animals expressing neuron specific GFP reporters, we identified twelve genes required for the correct outgrowth of interneuron axons of the motor circuit. In mutant animals, axons fail to navigate correctly towards the ventral cord or fail to fasciculate correctly within the ventral cord. Several of those mutants define previously uncharacterised genes. Two of the genes, ast-4 and ast-7, are involved in the generation of left-right asymmetry of the two ventral cord axon tracts. Three other genes specifically affect pioneer- follower relationships between early and late outgrowing axons, controlling either differentiation of a pioneer neuron (lin-11) or the ability of axons to follow a pioneer (ast-2, unc-130). Navigation of the ventral cord pioneer neuron AVG itself is defective in ast-4, ast-6 and unc-130 mutants. Correlation of these defects with navigation defects in different classes of follower axons revealed a true pioneer role for AVG in the guidance of interneurons in the ventral cord. Taken together, these genes provide a basis to address different aspects of axon navigation within the ventral cord of C. elegans. ------------------- Key: 7423 Medline: 15896824 Authors: Walker G;Houthoofd K;Vanfleteren JR;Gems D Title: Dietary restriction in C. elegans: from rate-of-living effects to nutrient sensing pathways. Citation: Mechanims of Ageing and Development 126: 929-937 2005 Type: ARTICLE Genes: clk-1 eat-1 eat-2 eat-6 daf-2 daf-15 daf-16 let-363 nac-1 nac-2 nac-3 nhx-2 pep-2 sir-2.1 Abstract: The nematode Caenorhabditis elegans has been subjected to dietary restriction (DR) by a number of means, with varying results in terms of fecundity and lifespan. Two possible mechanisms by which DR increases lifespan are reduction of metabolic rate and reduction of insulin/IGF-1 signalling. Experimental tests have not supported either possibility. However, interaction studies suggest that DR and insulin/IGF- I signalling may act in parallel on common regulated processes. In this review, we discuss recent developments in C. elegans DR research, including new discoveries about the biology of nutrient uptake in the gut, and the importance of invasion by the bacterial food source as a determinant of lifespan. The evidence that the effect of DR on lifespan in C. elegans is mediated by the TOR pathway is discussed. We conclude that the effect of DR on lifespan is likely to involve multiple mechanisms, which may differ according to the DR regimen used and the organism under study. ------------------- Key: 7424 Medline: 16085714 Authors: Rocheleau CE;Ronnlund A;Tuck S;Sundaram MV Title: Caenorhabditis elegans CNK-1 promotes Raf activation but is not essential for Ras/Raf signaling. Citation: Proceedings of the National Academy of Sciences USA 102: 11757-11762 2005 Type: ARTICLE Genes: cnk-1 dpy-20 ksr-1 let-23 let-60 lin-45 sur-6 sur-8 nDf40 Abstract: Connector enhancer of Ksr (CNK) is a conserved multidomain protein essential for Ras signaling in Drosophila melanogaster and thought to be involved in Raf kinase activation. However, the precise role of CNK in Ras signaling is not known, and mammalian CNKs are proposed to have distinct functions. Caenorhabditis elegans has a single CNK homologue, cnk-1. Here, we describe the role of cnk-1 in C. elegans Ras signaling and its requirements for LIN-45 Raf activation. We find that cnk-1 positively regulates multiple Ras signaling events during development, but, unlike Drosophila CNK, cnk-1 does not appear to be essential for signaling. cnk-1 mutants appear to be normal but show cell-type-specific genetic interactions with mutations in two other Ras pathway scaffolds/adaptors ksr-1 and sur-8. Genetic epistasis using various activated LIN-45 Raf transgenes shows that CNK-1 promotes LIN-45 Raf activation at a step between the dephosphorylation of inhibitory sites in the regulatory domain and activating phosphorylation in the kinase domain. Our data are consistent with a model in which CNK promotes Raf phosphorylation/activation through membrane localization, oligomerization, or association with an activating kinase. ------------------- Key: 7425 Medline: Authors: Wong K;Hengartner M Title: C. elegans as a model disease for neuroacanthocytosis. Citation: Neuroacanthocytosis Syndromes : 187-195 2004 Type: REVIEW Genes: Abstract: ------------------- Key: 7426 Medline: 16109369 Authors: Ding L;Spencer A;Morita K;Han M Title: The developmental timing regulator AIN-1 interacts with miRISCs and may target the Argonaute protein ALG-1 to cytoplasmic P bodies in C. elegans. Citation: Molecular Cell 19: 437-447 2005 Type: ARTICLE Genes: ain-1 alg-1 eff-1 hbl-1 let-60 lin-1 lin-14 lin-28 lin-31 lin-37 mnDp1 Abstract: In metazoans, microRNAs (miRNAs) carry out various regulatory functions through association with multiprotein miRNA-induced silencing complexes (miRISCs) that contain Dicer and Argonaute proteins. How miRNAs regulate the expression of their mRNA targets remains a major research question. We have identified the C. elegrans ain-1 gene through a genetic suppressor screen and shown that it functions with the heterochronic genetic pathway that regulates developmental timing. Biochemical analysis indicates that AIN-1 interacts with protein complexes containing an Argonaute protein, Dicer, and miRNAs. AIN-1 shares homology with the candidate human neurological disease protein GW182, shown to localize in cytoplasmic processing bodies that are sites of mRNA degradation and storage. A functional AIN-1::GFP also localizes at the likely worm processing bodies. When coexpressed from transgenes, AIN-1 targets ALG-1 to the foci. These results suggest a model where AIN-1 regulates a subset of miRISCs by localization to the processing bodies, facilitating degradation or translational inhibition of mRNA targets. ------------------- Key: 7427 Medline: 16109366 Authors: Karsenti E Title: TPX or not TPX? Citation: Molecular Cell 19: 431-432 2005 Type: REVIEW Genes: tpxl-1 Abstract: An Aurora A regulatory module has been identified in two different proteins: TPX2 in Xenopus laevis and TPXL-1 in C. elegans. The diverse roles of these two proteins in spindle assembly leave us to beckon the true C. elegans TPX2 ortholog to center stage. ------------------- Key: 7428 Medline: Authors: Liedtke W Title: TRPV4 plays an evolutionary conserved role in the transduction of osmotic and mechanical stimuli in living animals. Citation: Journal of Physiology 567: 53-58 2005 Type: ARTICLE Genes: ocr-2 osm-9 Abstract: The TRPV4 ion channel, previously named vanilloid receptor-related osmotically activated channel (VR-OAC), functions in vivo in the transduction of osmotic and mechanical stimuli. In trpv4 null mice, TRPV4 was found to be necessary for the maintenance of systemic osmotic equilibrium, and for normal thresholds in response to noxious mechanical stimuli. In a Caenorhabditis elegans TRPV mutant transgenic for mammalian TRPV4, the mammalian transgene was directing the osmotic and mechanical avoidance response in the context of the ASH 'nociceptive' neurone. Molecular mechanisms of gating of TRPV4 in vivo are not known at this point and have to be determined. ------------------- Key: 7429 Medline: Authors: Estevez AY;Strange K Title: Calcium feedback mechanisms regulate oscillatory activity of a TRP-like Ca2+ conductance in C. elegans intestinal Citation: Journal of Physiology 567: 239-251 2005 Type: ARTICLE Genes: Abstract: Inositol-1,4,5-trisphosphate (IP3)-dependent Ca2+ oscillations in Caenorhabditis elegans intestinal epithelial cells regulate the nematode defecation cycle. The role of plasma membrane ion channels in intestinal cell oscillatory Ca2+ signalling is unknown. We have shown previously that cultured intestinal cells express a Ca2+-selective conductance, I-ORCa, that is biophysically similar to TRPM7 currents. I-ORCa activates slowly and stabilizes when cells are patch clamped with pipette solutions containing 10 mm BAPTA and free Ca2+ concentrations of similar to 17 nm. However, when BAPTA concentration is lowered to I MM, IORCa oscillates. Oscillations in channel activity induced simultaneous oscillations in cytoplasmic Ca 21 levels. Removal of extracellular Ca2+ inhibited I-ORCa oscillations, whereas readdition of Ca2+ to the bath caused a rapid and transient reactivation of the current. Experimental manoeuvres that elevated intracellular Ca2+ blocked current oscillations. Elevation of intracellular Ca2+ in the presence of 10 mm BAPTA to block I-ORCa oscillations led to a dose-dependent increase in the rate of current activation. At intracellular Ca2+ concentrations of 250 nm, current activation was transient. Patch pipette solutions buffered with 1-4 mm of either BAPTA or EGTA gave rise to similar patterns of I-ORCa oscillations. We conclude that changes in Ca2+ concentration close to the intracellular opening of the channel pore regulate channel activity. Low concentrations of Ca2+ activate the channel. As Ca2+ enters and accumulates near the pore mouth, channel activity is inhibited. Oscillating plasma membrane Ca2+ entry may play a role in generating intracellular Ca2+ oscillations that ------------------- Key: 7430 Medline: 15910089 Authors: Filippidis G;Kouloumentas C;Kapsokalyvas D;Voglis G;Tavernarakis N;Papazoglou TG Title: Imaging of Caenorhabditis elegans samples and sub-cellular localization of new generation photosensitizers for photodynamic therapy, using non-linear microscopy. Citation: Journal of Physics D-Applied Physics 38: 2625-2632 2005 Type: ARTICLE Genes: Abstract: Two-photon excitation fluorescence (TPEF) and second-harmonic generation (SHG) are relatively new promising tools for the imaging and mapping of biological structures and processes at the microscopic level. The combination of the two image-contrast modes in a single instrument can provide unique and complementary information concerning the structure and the function of tissues and individual cells. The extended application of this novel, innovative technique by the biological community is limited due to the high price of commercial multiphoton microscopes. In this study, a compact, inexpensive and reliable setup utilizing ferntosecond pulses for excitation was developed for the TPEF and SHG imaging of biological samples. Specific cell types of the nematode Caenorhabditis elegans were imaged. Detection of the endogenous structural proteins of the worm, which are responsible for observation of SHG signals, was achieved. Additionally, the binding of different photosensitizers in the HL-60 cell line was investigated, using non-linear microscopy. The sub-cellular localization of photosensitizers of a new generation, very promising for photodynamic therapy (PDT), (Hypericum perforatum L. extracts) was achieved. The sub-cellular localization of these novel photosensitizers was linked with their photodynamic action during PDT, and the possible mechanisms for cell killing have been elucidated. ------------------- Key: 7431 Medline: 16091596 Authors: Natsuka S;Kawaguchi M;Wada Y;Ichikawa A;Ikura K;Hase S Title: Characterization of wheat germ agglutinin ligand on soluble glycoproteins in Caenorhabditis elegans. Citation: Journal of Biochemistry 138: 209-213 2005 Type: ARTICLE Genes: Abstract: Some mutants of Caenorhabditis elegans show altered patterns of ectopic binding with wheat germ agglutinin (WGA). Some of these mutants also have defects of morphogenesis and movement during development. To clarify the structures of WGA-ligands in C. elegans that may be involved in developmental events, we have analyzed glycan structures capable of binding WGA. We isolated glycoproteins from wild-type C. elegans by WGA-affinity chromatography, and analyzed their glycan structures by a combination of hydrazine degradation and fluorescent labeling. The glycoproteins had oligomannose-type and complex-type N-glycans that included agalacto-biantenna and agalacto-tetraantenna glycans. Although the complex-type glycans carried beta-GlcNAc residues at their non-reducing ends, they did not bind to the WGA-agaroseresin. Thus, it was suggested that these N-glycans were not responsible for WGA-binding of the isolated glycoproteins. Hydrazinolysis of the glycoproteins also released a considerable amount of GalNAc monosaccharide. It was surmised that N-acetylgalactosamine was derived from mucin-type O-glycans with the Tn-antigen structure (Ga1NAc alpha 1-O-Ser/Thr). WGA-blotting assay of neoglycoproteins revealed that a cluster of Tn-antigens was a good ligand for WGA. These results suggested that the WGA-ligand in C. elegans is a cluster of alpha-GalNAc monosaccharides linked to mucin-like glycoprotein(s). The observations reported in this paper emphasize the possible significance of mucin-type O-glycans in the development of a multicellular ------------------- Key: 7432 Medline: 16113247 Authors: Prithiviraj B;Bais HP;Weir T;Suresh B;Najarro EH;Dayakar BV;Schweizer HP;Vivanco JM Title: Down regulation of virulence factors of Pseudomonas aeruginosa by salicylic acid attenuates its virulence on Arabidopsis thaliana and Caenorhabditis elegans. Citation: Infection and Immunity 73: 5319-5328 2005 Type: ARTICLE Genes: Abstract: Salicylic acid (SA) is a phenolic metabolite produced by plants and is known to play an important role in several physiological processes, such as the induction of plant defense responses against pathogen attack. Here, using the Arabidopsis thaliana-Pseudomonas aeruginosa pathosystem, we provide evidence that SA acts directly on the pathogen, down regulating fitness and virulence factor production of the bacteria. Pseudomonas aeruginosa PA14 showed reduced attachment and biofilm formation on the roots of the Arabidopsis mutants lox2 and cpr5-2, which produce elevated amounts of SA, as well as on wild-type Arabidopsis plants primed with exogenous SA, a treatment known to enhance endogenous SA concentration. Salicylic acid at a concentration that did not inhibit PA14 growth was sufficient to significantly affect the ability of the bacteria to attach and form biofilm communities on abiotic surfaces. Furthermore, SA down regulated three known virulence factors of PA14: pyocyanin, protease, and elastase. Interestingly, P. aeruginosa produced more pyocyanin when infiltrated into leaves of the Arabidopsis transgenic line NahG, which accumulates less SA than wild-type plants. This finding suggests that endogenous SA plays a role in down regulating the synthesis and secretion of pyocyanin in vivo. To further test if SA directly affects the virulence of P. aeruginosa, we used the Caenorhabiditis elegans-P. aeruginosa infection model. The addition of SA to P. aeruginosa lawns significantly diminished the bacterium's ability to kill the worms, without affecting the accumulation of bacteria inside the nematodes' guts, suggesting that SA negatively affects factors that influence the virulence of P. aeruginosa. We employed microarray technology to identify SA target genes. These analyses showed that SA treatment affected expression of 331 genes. It selectively repressed transcription of exoproteins and other virulence factors, while it had no effect on expression of housekeeping genes. Our results indicate that in addition to its role as a signal molecule in plant defense responses, SA works as an anti-infective compound by affecting the physiology of P. aeruginosa and ultimately attenuating its virulence. ------------------- Key: 7433 Medline: Authors: Ning F;Delhomme D;LeCun Y;Piano F;Bottou L;Barbano PE Title: Toward automatic phenotyping of developing embryos from videos. Citation: IEEE Transactions on Image Processing 14: 1360-1371 2005 Type: ARTICLE Genes: Abstract: We describe a trainable system for analyzing videos of developing C. elegans embryos. The system automatically detects, segments, and locates cells and nuclei in microscopic images. The system was designed as the central component of a fully automated phenotyping system. The system contains three modules 1) a convolutional network trained to classify each pixel into five categories. cell wall, cytoplasm, nucleus membrane, nucleus, outside medium; 2) an energy-based model, which cleans up the output of the convolutional network by learning local consistency constraints that must be satisfied by label images; 3) a set of elastic models of the embryo at various stages of development that are matched to the label images. ------------------- Key: 7434 Medline: Authors: Alvarez OA;Jager T;Kooijman SALM;Kammenga JE Title: Responses to stress of Caenorhabditis elegans populations with different reproductive strategies. Citation: Functional Ecology 19: 656-664 2005 Type: ARTICLE Genes: Abstract: 1. Hermaphroditic and gonochoric reproduction are essentially different reproductive strategies that may lead to diverging population responses to adverse environmental conditions. Each strategy implies different physiological mechanisms, which affect life-history traits and represent different ways of dealing with stress. 2. We studied the performance of hermaphroditic vs gonochoric strains in the nematode Caenorhabditis elegans exposed to cadmium stress at the individual and population level. 3. Under control conditions, the gonochoric strain started reproduction earlier than the hermaphroditic strain at a smaller size. This was due to an earlier switch from sperm to oocyte production triggered by male sperm availability. Under cadmium stress hermaphrodites showed a decrease in the size at onset of reproduction, presumably as a strategy to maintain a high population growth rate. In contrast the body size of gonochoric nematodes was not affected. 4. A process-based model (DEBtox) was used as a tool for analysing life-history data and calculating population growth rates. The model fitted the data well using physiologically relevant parameters such as ageing, survival or reproduction related parameters. The simultaneous fit of all life-history traits was used to obtain populations growth rate estimates. 5. The differences between the two C. elegans strains were reflected at the population level. Lower population growth rates, as calculated by DEBtox, were found in the gonochoric strain, largely determined by the proportion of males in the offspring. 6. From the overall results we suggest that the differences found between both populations are due to the reproductive strategy. Under control conditions, CB strain (with gonochoric reproduction) does not favour population growth rates in the short term due to faster ageing and copulation costs on survival. Furthermore, in response to stress this strain also showed lower performance than the N2 hermaphroditic strain, mainly ------------------- Key: 7435 Medline: 16043310 Authors: Cardona ST;Wopperer J;Eberl L;Valvano MA Title: Diverse pathogenicity of Burkholderia cepacia complex strains in the Caenorhabditis elegans host model. Citation: FEMS Microbiology Letters 250: 97-104 2005 Type: ARTICLE Genes: Abstract: A fast screening method was developed to assess the pathogenicity of a diverse collection of environmental and clinical Burkholderia cepacia complex isolates in the nematode Caenorhabditis elegans. The method was validated by comparison with the standard slow-killing assay. We observed that the pathogenicity of B. cepacia complex isolates in C elegans was strain-dependent but species-independent. The wide range of observed pathogenic phenotypes agrees with the high degree of phenotypic variation among species of the R cepacia complex and suggests that the taxonomic classification of a given strain within the complex cannot predict pathogenicity. ------------------- Key: 7436 Medline: Authors: Poteryaev D;Spang A Title: A role of SAND-family proteins in endocytosis. Citation: Biochemical Society Transactions 33: 606-608 2005 Type: ARTICLE Genes: cup-5 lmp-1 rab-5 rab-7 rab-11 rme-1 rme-8 sand-1 Abstract: Caenorhabditis elegans has recently been used as an attractive model system to gain insight into mechanisms of endocytosis in multicellular organisms. A combination of forward and reverse genetics has identified a number of new membrane trafficking factors. Most of them have mammalian homologues which function in the same transport events. We describe a novel C elegans gene sand-1, whose loss of function causes profound endocytic defects in many tissues. SAND-1 belongs to a conserved family of proteins present in all eukaryotic species, whose genome is sequenced. However, SAND family has not been previously characterized in metazoa. our comparison of C elegans SAND-1 and its yeast homologue, Mon1p, showed a conserved role of the SAND-family proteins in late steps of endocytic transport. ------------------- Key: 7437 Medline: 16061202 Authors: Husson SJ;Clynen E;Baggerman G;De Loof A;Schoofs L Title: Discovering neuropeptides in Caenorhabditis elegans by two dimensional liquid chromatography and mass spectrometry. Citation: Biochemical and Biophysical Research Communications 335: 76-86 2005 Type: ARTICLE Genes: flp-1 flp-3 flp-5 flp-6 flp-9 flp-11 flp-13 flp-16 flp-18 flp-19 flp-22 flp-24 flp-25 flp-26 flp-27 flp-28 flp-31 nlp-1 nlp-4 nlp-5 nlp-6 nlp-7 nlp-8 nlp-9 nlp-1 nlp-10 nlp-11 nlp-12 nlp-13 nlp-14 nlp-15 nlp-16 nlp-17 nlp-18 nlp-19 nlp-20 nlp-21 nlp-26 nlp-27 nlp-29 nlp-31 nlp-33 nlp-34 nlp-35 nlp-36 nlp-37 nlp-38 nlp-39 nlp-40 nlp-51 Abstract: Completion of the Caenorhabditis elegans genome sequencing project in 1998 has provided more insight into the complexity of nematode neuropeptide signaling. Several C. elegans neuropeptide precursor genes, coding for approximately 250 peptides, have been predicted from the genomic database. One can, however, not deduce whether all these peptides are actually expressed, nor is it possible to predict all post-translational modifications. Using two dimensional nanoscale liquid chromatography combined with tandem mass spectrometry and database mining, we analyzed a mixed stage C elegans extract. This peptidomic setup yielded 21 peptides derived from formerly predicted neuropeptide-like protein (NLP) precursors and 28 predicted FMRFamide-related peptides. In addition, we were able to sequence 11 entirely novel peptides derived from nine peptide precursors that were not predicted or identified in any way previously. Some of the identified peptides display profound sequence similarities with neuropeptides from other invertebrates, indicating that these peptides have a long evolutionary history. ------------------- Key: 7438 Medline: 16055082 Authors: Hikita T;Qadota H;Tsuboi D;Taya S;Moerman DG;Kaibuchi K Title: Identification of a novel CDC42 GEF that is localized to the PAT-3-mediated adhesive structure. Citation: Biochemical and Biophysical Research Communications 335: 139-145 2005 Type: ARTICLE Genes: cdc-42 deb-1 pat-2 pat-3 pat-4 uig-1 unc-52 unc-112 Abstract: In the model organism Caenorhabditis elegans, UNG-112 is colocalized with PAT-3/beta-integrin and is a critical protein in the formation of PAT-3-mediated adhesive structure in body-wall muscle cells. However, the signaling pathway downstream of PAT-3/UNC-112 is largely unknown. To clarify the signaling pathway from PAT-3/UNC-112 to the actin cytoskeleton, we searched for and identified a novel Dbl homology/pleckstrin homology (DH/PH) domain containing protein, UIG-1 (UNC-112-interacting guanine nucleotide exchange factor-1). UIG-1 was colocalized with UNC-112 at dense bodies in body-wall muscle cells. UIG-1 showed CDC-42-specific GEF activity in vitro and induced filopodia formation in NIH 3T3 cells. Depletion of CDC-42 or PAT-3 in the developmental stage, by RNAi, prevented the formation of continuous actin filament in body-wall muscle cells. Taken together, these results suggest that UIG-1 links a PAT-3/UNC-112 complex to the CDC-42 signaling pathway during muscle formation. ------------------- Key: 7439 Medline: 16106407 Authors: Hong RL;Villwock A;Sommer RJ Title: Cultivation of the Rhabditid Poikilolaimus oxycercus as a laboratory nematode for genetic analyses. Citation: Journal of Experimental Zoology 303A: 742-760 2005 Type: ARTICLE Genes: Abstract: Vulva formation is a paradigm for evolutionary developmental biology in nematodes. Not only do the number of vulval precursor cells (VPCs) differ between members in the Rhabditidae and Diplogastridae, they are also sculpted via different developmental mechanisms, either by cell fusion in most Rhabditidae or by programmed cell death in the Diplogastridae. In this context, the species Poikilolaimus oxycercus is the only known species in the family Rhabditidae to have a subset of the Pn.p cells commit programmed cell death during the patterning of the VPCs. Our current study introduces P. oxycercus as a new laboratory organism. There are discrete laboratory strains that are genetically polymorphic from each other as well as heterogeneous within each strain. In order to cultivate this gonochoristic nematode into an experimental model with a tractable genetic system, we produced two inbreeding tolerant, near-isogenic strains capable of producing viable progeny with each other. We also described P. oxycera's morphology by scanning electron microscopy (SEM), basic life history traits, hybrid viability, and mating behavior. P. oxycercus females have no preference for inter- or intra-strain matings, and can mate with multiple males in a relatively short time period, suggesting a propensity for maintaining heterozygosity through promiscuity. Interestingly, all sexes from three species in the genus Poikilolaimus show five 4',6-diamidino-2-phenylindole (DAPI) staining bodies in their germ line cells. This could indicate that Poikilolaimus species possess five bivalent chromosomes in their germ lines, in contrast to the hermaphroditic Caenorhabditis elegans or Pristionchus pacificus, which have six chromosomes. ------------------- Key: 7440 Medline: 16113240 Authors: Suematsu T;Sato A;Sakurai M;Watanabe K;Ohtsuki T Title: A unique tRNA recognition machanism of Caenorhabditis elegans mitochondrial EF-Tu2. Citation: Nucleic Acids Research 33: 4683-4691 2005 Type: ARTICLE Genes: Abstract: Nematode mitochondria expresses two types of extremely truncated tRNAs that are specifically recognized by two distinct elongation factor Tu (EF-Tu) species named EF-Tu1 and EF-Tu2. This is unlike the canonical EF-Tu molecule that participates in the standard protein biosynthesis systems, which basically recognizes all elongator tRNAs. EF-Tu2 specifically recognizes Ser-tRNA(Ser) that lacks a D arm but has a short T arm. Our previous study led us to speculate the lack of the D arm may be essential for the tRNA recognition of EF-Tu2. However, here, we showed that the EF-Tu2 can bind to D arm-bearing Ser-tRNAs, in which the D-T arm interaction was weakened by the mutations. The ethylnitrosourea-modification interference assay showed that EF-Tu2 is unique, in that it interacts with the phosphate groups on the T stem on the side that is opposite to where canonical EF-Tu binds. The hydrolysis protection assay using several EF-Tu2 mutants then strongly suggests that seven C-terminal amino acid residues of EF-Tu2 are essential for its aminoacyl-tRNA-binding activity. Our results indicate that the formation of the nematode mitochondrial (mt) EF-Tu2/GTP/aminoacyl-tRNA ternary complex is probably supported by a unique interaction between the C-terminal extension of EF-Tu2 and the tRNA. ------------------- Key: 7441 Medline: Authors: Richie CT;Golden A Title: Chromosome segregation: Aurora B gets Tousled. Citation: Current Biology 15: R379-R382 2005 Type: REVIEW Genes: air-1 air-2 bir-1 csc-1 icp-1 tlk-1 Abstract: Aurora B kinases play important roles during mitosis in eukaryotic cells; new work in Caenorhabditis elegans has identified the Tousled kinase TLK-1 as a substrate activator of the model nematode's Aurora B kinase AIR-2 which acts to ensure proper chromosome segregation during ------------------- Key: 7442 Medline: Authors: Iser WB;Kim D;Bachman E;Wolkow C Title: Examination of the requirement for ucp-4, a putative homolog of mammalian uncoupling proteins, for stress tolerance and longevity in C. elegans. Citation: Mechanisms of Ageing & Development 126: 1090-1096 2005 Type: ARTICLE Genes: mev-1 ucp-4 Abstract: Reactive oxygen species (ROS) are generated by mitochondrial respiration and can react with and damage cellular components, According to the free radical theory of aging, oxidative damage from mitochondrial ROS is a major cause of cellular decline during aging, Mitochondrial uncoupling proteins (UCPs) uncouple ATP production from electron transport and can be stimulated by free radicals. suggesting UCPs may perform a cytoprotective function. The nematode, Caenorhabditis elegans. contains one UCP-like protein, encoded by the ucp-4 gene. We have investigated the genetic requirement for ucp-4 in normal aging and stress resistance. Consistent with the hypothesis that ucp-4 encodes a putative uncoupling protein, animals lacking ucp-4 function contained elevated ATP levels, However, the absence of ucp-4 function did not affect adult lifespan or survival in the presence of thermal or oxidative stress. Together, these results demonstrate that ucp-4 is a negative regulator of ATP production in C. elegans. but is not required for normal lifespan. ------------------- Key: 7443 Medline: 16145941 Authors: Winska P;Golos B;Ciesla J;Zielinski Z;Fraczyk T;Walajtys-Rode E;Rode W Title: Developmental arrest in Caenorhabditis elegans dauer larvae causes high expression of enzymes involved in thymidylate biosynthesis, similar to that found in Trichinella muscle larvae. Citation: Parasitology 131: 247-254 2005 Type: ARTICLE Genes: Abstract: Crude extract specific activities of thymidylate synthase, dUTPase, thymidine kinase and dihydrofolate reductase were high during the development of Caenorhabditis elegans, the dauer larva activities being similar to those previously determined in Trichinella spiralis and T. pseudospiralis muscle larvae (with the exception of thymidine kinase, not detected in Trichinella). High thymidylate synthase expression in developmentally arrested larvae, demonstrated also at the mRNA and protein levels, is in agreement with a global cell cycle arrest of dauer larvae and indicates this unusual cell cycle regulation pattern can be shared by developmentally arrested larvae of C. elegans and the two Trichnella species. Hence, the phenomenon may be characteristic for developmentally arrested larvae of different nematodes, rather than specific for the parasitic Trichinella muscle larvae. Endogenous C. elegans thymidylate synthase was purified and its molecular properties compared with those of the recombinant protein, expression of the latter in E. coli cells confirming the NCBI database sequence identity. ------------------- Key: 7444 Medline: Authors: Gower NJD;Walker DS;Baylis HA Title: Inositol 1,4,5-trisphosphate signaling regulates mating behavior in Caenorhabditis elegans males. Citation: Molecular Biology of the Cell 16: 3978-3986 2005 Type: ARTICLE Genes: egl-8 fer-1 him-5 him-8 itr-1 plc-1 plc-2 plc-3 plc-4 pll-1 Abstract: Complex behavior requires the coordinated action of the nervous system and nonneuronal targets. Male mating in Caenorhabditis elegans consists of a series of defined behavioral steps that lead to the physiological outcomes required for successful impregnation. We demonstrate that signaling mediated by inositol 1,4,5-trisphosphate (IP3) is required at several points during mating. Disruption of IP3 receptor (itr-1) function results in dramatic loss of male fertility, due to defects in turning behavior (during vulva location), spicule insertion and sperm transfer. To elucidate the signaling pathways responsible, we knocked down the six C. elegans genes encoding phospholipase C (PLC) family members. egl-8, which encodes PLC-beta, functions in spicule insertion and sperm transfer. itr-1 and egl-8 are widely expressed in the male reproductive system. An itr-1 gain-of-function mutation rescues infertility caused by egl-8 RNA interference, indicating that egl-8 and itr-1 function together as central components of the signaling events controlling sperm ------------------- Key: 7445 Medline: Authors: Wang H;Spang A;Sullivan MA;Hryhorenko J;Hagen FK Title: The terminal phase of cytokinesis in the Caenorhabditis elegans early embryo required protein glycosylation. Citation: Molecular Biology of the Cell 16: 4202-4213 2005 Type: ARTICLE Genes: bre-5 gly-3 gly-4 gly-5 gly-6 gly-7 gly-8 gly-9 gly-10 gly-11 sqv-2 sqv-6 Abstract: RNA interference (RNAi) was used to characterize the requirement of protein glycosylation for cell membrane stability during cytokinesis in the early embryo. This screen targeted 13 enzymes or components of polypeptide sugar transferases that initiate either N-glycosylation or three different pathways of O-glycosylation. RNAi of genes in the mucin-type and epidermal growth factor-fringe glycosylation pathways did not affect cytokinesis. However, embryos deficient in N-glycosylation exhibited a variable inability to complete cytokinesis. The most potent block in early embryonic cell division was obtained by RNAi of the polypeptide xylose transferase (ppXyl-T), which is required to initiate the proteoglycan modification pathway. Two generations of ppXyl-T RNAi-feeding treatment reduced the body size, mobility, brood size, and life span of adult animals. Embryos escaping ppXyl-T and Gal-T2 RNAi lethality develop to adulthood but have cytokinesis-deficient offspring, suggesting that glycosyltransferases in the proteoglycan pathway are maternal proteins in the early embryo. Gal-T2::GFP fusions and anti-Gal-T2 antibodies revealed a perinuclear staining pattern, consistent with the localization of the Golgi apparatus. RNAi in green fluorescent protein (GFP)-tagged strains to follow tubulin, PIE-1, and chromatin showed that deficient proteoglycan biosynthesis uncouples the stability of newly formed cell membranes from cytokinesis, whereas cleavage furrow initiation, mitotic spindle function, karyokinesis, and partitioning of intrinsic components are intact. ------------------- Key: 7446 Medline: Authors: Umemura T;Rapp P;Rongo C Title: The role of regulatory domain interactions in UNC-43 CaMKII localization and trafficking. Citation: Journal of Cell Science 118: 3327-3338 2005 Type: ARTICLE Genes: unc-2 unc-43 Abstract: Calcium and calmodulin-dependent protein kinase II (CaMKII) plays a fundamental role in the synaptic plasticity events that underlie learning and memory. Regulation of CaMKII kinase activity occurs through an autoinhibitory mechanism in which a regulatory domain of the kinase occupies the catalytic site and calcium/calmodulin activates the kinase by binding to and displacing this regulatory domain. A single putative ortholog of CaMKlI, encoded by unc-43, is present in the Caenorhabditis elegans nervous system. Here we examined UNC-43 subcellular localization in the neurons of intact animals and show that UNC-43 is localized to clusters in ventral cord neurites, as well as to an unlocalized pool within these neurites. A mutation that mimics autophosphorylation within the regulatory domain results in an increase in the levels of UNC-43 in the unlocalized neurite pool. Multiple residues of CaMKII facilitate the interaction between the catalytic domain and the regulatory domain, thereby keeping the kinase inactive. Whereas most mutations in these residues result in an increased neurite pool of UNC-43, we have identified two residues that result in the opposite effect when mutated: a decreased neurite pool of UNC-43. The activity of UNC-2, a voltage-dependent calcium channel, is also required for UNC-43 to accumulate in the neurites, suggesting that neural activity regulates the localization of UNC-43. Our results suggest that the activation of UNC-43 by calcium/calmodulin displaces the autoinhibitory domain, thereby exposing key residues of the catalytic domain that allow for protein translocation to the neurites. ------------------- Key: 7447 Medline: 16140983 Authors: Steven R;Zhang L;Culotti J;Pawson T Title: The UNC-73/Trio RhoGEF-2 domain is required in separate isoforms for the regulation of pharynx pumping and normal neurotransmission in C. elegans. Citation: Genes & Development 19: 2016-2029 2005 Type: ARTICLE Genes: bas-1 dgk-1 goa-1 rab-3 rbf-1 snb-1 snt-1 tph-1 unc-10 unc-13 unc-18 unc-31 unc-64 unc-73 Abstract: In both Caenorhabditis elegans and Drosophila, UNC-73/Trio functions in axon guidance by signaling through the Rae GTPase to regulate cytoskeletal rearrangements necessary for growth cone migrations. Here, we show that the complex C. elegans unc-73 gene encodes at least eight differentially expressed UNC-73 intracellular protein isoforms. Previously reported mutations affecting UNC-73 isoforms encoding the Rae-specific RhoGEF-1 domain cause uncoordinated movement, correlating with defects in axon guidance. Mutations in isoforms encoding the Rho-specific RhoGEF-2 domain, which we describe here, result in L1 stage larval lethality with no associated axon guidance defects. Isoform-specific rescue experiments reveal separate functions for the various RhoGEF-2-containing UNC-73 isoforms, which would not likely be discovered by conventional genetic screening. UNC-73 D1 and D2 appear to function redundantly in pharynx muscle to regulate the rate and strength of pharynx pumping, and in the HSN neurons and vulval muscles to control egg laying. Isoforms C1, C2, E, and F act redundantly within the nervous system to regulate the speed of locomotion. The multiple UNC-73 isoforms containing Rac- and Rho-specific RhoGEF domains therefore have distinct physiological functions. In addition to its previously identified role involving RhoGEF-1 in migrating cells and growth cones, our data indicate that UNC-73 signals through RhoGEF-2 to regulate pharynx and vulva musculature and to modulate synaptic neurotransmission. ------------------- Key: 7448 Medline: 16023097 Authors: Wang X;Kweon J;Larson S;Chen L Title: A role for the C. elegans L1CAM homologue lad-1/sax-7 in maintaining tissue attachment. Citation: Developmental Biology 284: 273-291 2005 Type: ARTICLE Genes: exc-9 lad-1 mau-8 sax-7 stDf7 Abstract: The L1 family of cell adhesion molecules (L1CAMs) is important for neural development. Mutations in one of the human L1 CAM genes, L1, can result in several neurological syndromes, the symptoms of which are variably penetrant. The physiological cause of these symptoms, collectively termed CRASH, is not clear. Caenorhabditis elegans animals genetically null for the L1CAM homologue LAD-1, exhibit variably penetrant pleiotropic phenotypes that are similar to the CRASH symptoms; thus the C. elegans lad-1 mutant provides an excellent model system to study how disruption of L1 leads to these abnormalities. These phenotypes include uncoordinated movements, variable embryonic lethality, and abnormal neuronal distribution and axon trajectories. Our analysis revealed that many of these phenotypes are likely a result of tissue detachment. ------------------- Key: 7449 Medline: 15979607 Authors: Frank CA;Hawkins NC;Guenther C;Horvitz HR;Garriga G Title: C. elegans HAM-1 positions the cleavage plane and regulates apoptosis in asymmetric neuroblast divisions. Citation: Developmental Biology 284: 301-310 2005 Type: ARTICLE Genes: ced-3 ham-1 stDf22 Abstract: Asymmetric cell division occurs when a mother cell divides to generate two distinct daughter cells, a process that promotes the generation of cellular diversity in metazoans. During Caenorhabditis elegans development, the asymmetric divisions of neural progenitors generate neurons, neural support cells and apoptotic cells. C elegans HAM-1 is an asymmetrically distributed cortical protein that regulates several of these asymmetric neuroblast divisions. Here, we show that HAM-1 is a novel protein and define residues important for HAM-1 function and distribution to the cell cortex. Our phenotypic analysis of ham-1 mutant embryos suggests that HAM-1 controls only neuroblast divisions that produce apoptotic cells. Moreover, ham-1 mutant embryos contain many unusually large cell-death corpses. An investigation of this corpse phenotype revealed that it results from a reversal of neuroblast polarity. A misplacement of the neuroblast cleavage plane generates daughter cells of abnormal size, with the apoptotic daughters larger than normal. Thus, HAM-1 regulates the position of the cleavage plane, apoptosis and mitotic potential in C. elegans asymmetric cell divisions. ------------------- Key: 7450 Medline: 15987632 Authors: Thoemke K;Yi W;Ross JM;Kim S;Reinke V;Zarkower D Title: Genome-wide analysis of sex-enriched gene expression during C. elegans larval development. Citation: Developmental Biology 284: 500-508 2005 Type: ARTICLE Genes: ceh-7 cwp-1 cwp-2 egl-1 egl-5 far-2 far-3 her-1 lbp-2 let-268 lov-1 mab-3 mab-9 pqn-4 ram-5 sra-1 tra-1 tra-2 wrt-10 xol-1 Abstract: Sex determination in C elegans is controlled by the TRA-1 zinc finger protein, a Ci/GLI homolog that promotes female cell fates throughout the body. The regulatory hierarchy that controls TRA-1 is well established, but the downstream effectors that establish sexual dimorphism during larval development remain largely unknown. Here, we describe the use of cDNA microarrays to identify sex-enriched transcripts expressed during three stages of C. elegans larval development. By excluding previously identified germline-enriched transcripts, we focused on somatic sexual development. This approach identified a large number of sex-enriched transcripts that are good candidates to encode regulators of somatic sexual development. We found little overlap between genes with sex-enriched expression in early versus late larval development, indicating that distinct sexual regulatory programs operate at these times. Genes with sex-enriched expression are found throughout the genome, with no strong bias between autosomes and X chromosomes. Reporter gene analysis revealed that these genes are expressed in highly specific patterns in a variety of sexually dimorphic cells. We searched for TRA-1 consensus DNA binding sites near genes with sex-enriched expression, and found that most strongly sex-enriched mRNAs are likely to be regulated indirectly by TRA-1. These results suggest that TRA-1 controls sexual dimorphism through a small number of intermediary regulators rather than by acting directly on the full constellation of genes involved in sex-specific differentiation. ------------------- Key: 7451 Medline: 15979606 Authors: Maduro MF;Hill RJ;Heid PJ;Newman-Smith ED;Zhu J;Priess JR;Rothman JH Title: Genetic redundancy in endoderm specification within the genus Caenorhabditis. Citation: Developmental Biology 284: 509-522 2005 Type: ARTICLE Genes: aip-1 cat-4 ced-1 dpr-1 elt-2 elt-7 end-1 end-2 end-3 lit-1 med-1 mom-2 pie-1 pop-1 ric-7 skn-1 src-1 itDf2 Abstract: Specification of the endoderm precursor, the E cell, in Caenorhabditis elegans requires a genomic region called the Endoderm Determining Region (EDR). We showed previously that end-1, a gene within the EDR encoding a GATA-type transcription factor, restores endoderm specification to embryos deleted for the EDR and obtained evidence for genetic redundancy in this process. Here, we report molecular identification of end-3, a nearby paralog of end-1 in the EDR, and show that end-1 and end-3 together define the endoderm-specifying properties of the EDR. Both genes are expressed in the early E lineage and each is individually sufficient to specify endodermal fate in the E cell and in non-endodermal precursors when ectopically expressed. The loss of function of both end genes, but not either one alone, eliminates endoderm in nearly all embryos and results in conversion of E into a C-like mesectodermal precursor, similar to deletions of the EDR. While two putative end-1 null mutants display no overt phenotype, a missense mutation that alters a residue in the zinc finger domain of END-3 results in misspecification of E in approximately 9% of mutant embryos. We report that the EDR in C. briggsae, which is estimated to have diverged from C elegans similar to 50-120 myr ago, contains three end-like genes, resulting from both the ancient duplication that produced end-1 and end-3 in C elegans, and a more recent duplication of end-3 in the lineage specific to C briggsae. Transgenes containing the C briggsae end homologs show E lineage-specific expression and function in C elegans, demonstrating their functional conservation. Moreover, RNAi experiments indicate that the C. briggsae end genes also function redundantly to specify endoderm. We propose that duplicated end genes have been maintained over long periods of evolution, owing in part to their synergistic function. ------------------- Key: 7452 Medline: 16122423 Authors: Bagga S;Bracht J;Hunter S;Massirer K;Holtz J;Eachus R;Pasquinelli AE Title: Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Citation: Cell 122: 553-563 2005 Type: ARTICLE Genes: col-10 eft-2 let-7 lin-4 lin-14 lin-28 lin-41 rde-1 rde-4 smg-2 unc-54 xrn-1 Abstract: MicroRNAs (miRNAs) are similar to 22 nucleotide RNAs that negatively regulate the expression of protein-coding genes. In a present model of miRNA function in animals, miRNAs that form imperfect duplexes with their targets inhibit protein expression without affecting mRNA levels. Here, we report that in C. elegans, regulation by the let-7miRNA results in degradation of its lin-41 target mRNA, despite the fact that its 3'UTR regulatory sequences can only partially base-pair with the miRNA. Furthermore, lin-14 and lin-28 are targets of the lin-4 miRNA, and we show that the mRNA levels for these protein-coding genes significantly decrease in response to lin-4 expression. This study reveals that mRNAs containing partial miRNA complementary sites can be targeted for degradation in vivo, raising the possibility that regulation at the level of mRNA stability may be more common than previously appreciated for the ------------------- Key: 7453 Medline: 16129975 Authors: Nagele P;Metz LB;Crowder CM Title: Xenon acts by inhibition on non-N-methyl-D-aspartate receptor-mediated glutamatergic neurotransmission in Caenorhabditis elegans. Citation: Anesthesiology 103: 508-513 2005 Type: ARTICLE Genes: glr-1 lin-15 nmr-1 unc-64 Abstract: Background: Electrophysiologic experiments in rodents have found that nitrous oxide and xenon inhibit N-methyl-D-aspartate (NMDA)-type glutamate receptors. These findings led to the hypothesis that xenon and nitrous oxide along with ketamine form a class of anesthetics with the identical mechanism, NMDA receptor antagonism. Here, the authors ask in Caenorhabditis elegans whether xenon, like nitrous oxide, acts by a NMDA receptor-mediated mechanism. Methods: Xenon:oxygen mixtures were delivered into sealed chambers until the desired concentration was achieved. The effects of xenon on various behaviors were measured on wildtype and mutant C elegans strains. Results: With an EC50 of 15-20 vol% depending on behavioral endpoint, xenon altered C elegans locomotion in a manner indistinguishable from that of mutants in glutamatergic transmission. Xenon reduced the frequency and duration of backward locomotion without altering its speed or other behaviors tested. Mutation of glr-1, encoding a non-NMDA glutamate receptor subunit, abolished the behavioral effects of xenon; however, mutation of nmr-1, which encodes the pore-forming subunit of an NMDA glutamate receptor previously shown to be required for nitrous oxide action, did not significantly alter xenon response. Transformation of the glr-1 mutant with the wild-type glr-1 gene partially restored xenon sensitivity, confirming that glr-1 was necessary for the full action of xenon. Conclusions: Xenon acts in C elegans to alter locomotion through a mechanism requiring the non-NMDA glutamate receptor encoded by glr-1. Unlike for the action of nitrous oxide in C elegans, the NMDA receptor encoded by nmr-1 is not essential for sensitivity to xenon. ------------------- Key: 7454 Medline: Authors: Tajsharghi H;Pilon M;Oldfors A Title: A Caenorhabditis elegans model of the myosin heavy chain IIa E706T mutation. Citation: Annals of Neurology 58: 442-448 2005 Type: ARTICLE Genes: unc-54 Abstract: Mutations in myosin heavy chain (MyHC) genes recently have been shown to be associated with various forms of congenital myopathies: myosin myopathies. The MyHC IIa E706K mutation is associated with congenital joint contractures, early-onset muscle weakness, and progressive course with moderate to severe muscle weakness later in life. To study the pathogenicity of this MyHC mutation, we investigated the effect of the corresponding mutation (E710K) in the major MyHC isoform. (MyHC B) of the body wall muscle of the nematode Caenorhabditis elegans. Worms with null mutations in the MyHC B gene (unc-54) are severely paralyzed and depleted of thick filaments in the body wall muscle sarcomeres. unc-54 null mutants with extrachromosomal arrays of a gene construct including the entire wild-type unc-54 gene were partially rescued as determined by a motility assay and by morphological analysis of the body wall muscle. Analysis of unc-54 null mutants with extrachromosomal arrays of the unc-54 gene with the E710K mutation were severely paralyzed but showed formation of thick filaments in the body wall muscle. We conclude that the MyHC E706K (E710K in C. elegans) mutation is pathogenic and that the effect is primarily functional rather than structural because thick filaments are formed. The C. elegans model may be useful to study suspected pathogenic mutations in MyHC genes associated with human ------------------- Key: 7455 Medline: 16000380 Authors: Wang J;Mohler WA;Savage-Dunn C Title: C-terminal mutants of C. elegans Smads reveal tissue-specific requirements for protein activation by TGF-beta signaling. Citation: Development 132: 3505-3513 2005 Type: ARTICLE Genes: him-5 lin-31 lon-1 sma-2 sma-3 sma-4 sma-6 Abstract: TGF-beta signaling in the nematode Caenorhabditis elegans plays multiple roles in the development of the animal. The Sma/Mab pathway controls body size, male tail sensory ray identity and spicule formation. Three Smad genes, sma-2, sma-3 and sma-4, are all required for signal transduction, suggesting that the functional complex could be a heterotrimer. Because the C termini of Smads play important roles in receptor-mediated activation and heteromeric complex formation, we generated C-terminal mutations in the C. elegans Smad genes and tested their activities in vivo in each of their distinct developmental roles. We show that pseudophosphorylated SMA-3 is dominant negative in body size, but functional in sensory ray and spicule development. Somewhat differently, pseudophosphorylated SMA-2 is active in any tissue. The C-terminal mutants of SMA-4 function like wild type, suggesting that the SMA-4 C terminus is dispensable. Using a combination of different C-terminal mutations in SMA-2 and SMA-3, we found a complex set of requirements for Smad-phosphorylation state that are specific to each outcome. Finally, we detected a physical interaction of SMA-3 with the forkhead transcription factor LIN-31, which is enhanced by SMA-3 pseudophosphorylation and reduced in an unphosphorylatable mutant. We conclude that the tissue-specific requirements for Smad phosphorylation may result, in part, from the need to interact with tissue-specific transcription co-factors that have different affinities for phosphorylated and unphosphorylated Smad protein. ------------------- Key: 7456 Medline: Authors: Fitch DHA Title: Evolution: an ecological context for C. elegans. Citation: Current Biology 15: R655-R658 2005 Type: REVIEW Genes: Abstract: Despite low global diversity among natural populations of Caenorhabditis elegans, neighboring populations can be as genetically distinct as strains from different continents, probably owing to transient bottlenecks and ongoing dispersal as a dauer larva. Selfing predominates in the wild, but rare outcrossing may also play an important role. ------------------- Key: 7457 Medline: 16099833 Authors: Johnston RJ;Chang S;Etchberger JF;Ortiz CO;Hobert O Title: MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision. Citation: Proceedings of the National Academy of Sciences USA 102: 12449-12454 2005 Type: ARTICLE Genes: ceh-36 cog-1 die-1 flp-4 flp-20 gcy-5 gcy-6 gcy-7 gcy-22 hen-1 lim-6 lsy-6 mir-273 Abstract: The elucidation of the architecture of gene regulatory networks that control cell-type specific gene expression programs represents a major challenge in developmental biology. We describe here a cell fate decision between two alternative neuronal fates and the architecture of a gene regulatory network that controls this cell fate decision. The two Caenorhabditis elegans taste receptor neurons "ASE left" (ASEL) and "ASE right" (ASER) share many bilaterally symmetric features, but each cell expresses a distinct set of chemoreceptors that endow the gustatory system with the capacity to sense and discriminate specific environmental inputs. We show that these left/right asymmetric fates develop from a precursor state in which both ASE neurons express equivalent features. This hybrid precursor state is unstable and transitions into the stable ASEL or ASER terminal end state. Although this transition is spatially stereotyped in wild-type animals, mutant analysis reveals that each cell has the potential to transition into either the ASEL or ASER stable end state. The stability and irreversibility of the terminal differentiated state is ensured by the interactions of two microRNAs (miRNAs) and their transcription factor targets in a double-negative feedback loop. Simple feedback loops are found as common motifs in many gene regulatory networks, but the loop described here is unusually complex and involves miRNAs. The interaction of miRNAs in double-negative feedback loops may not only be a means for miRNAs to regulate their own expression but may also represent a general paradigm for how terminal cell fates are selected and stabilized. ------------------- Key: 7458 Medline: Authors: Scholl EH;Bird DM Title: Resolving tylenchid evolutionary relationships through multiple gene analysis derived from EST data. Citation: Molecular Phylogenetics and Evolution 36: 536-545 2005 Type: ARTICLE Genes: Abstract: Sequence-based phylogenetic analyses typically are based on a small number of character sets and report gene trees which may not reflect the true species tree. We employed an EST mining strategy to suppress such incongruencies, and recovered the most robust phylogeny for five species of plant-parasitic nematode (Meloidogyne arenaria, M. chitwoodi, M. hapla, M. incognita, and M. javanica), three closely related tylenchid taxa (Heterodera glycines, Globodera pallida, and G. rostochiensis) and a distant taxon, Caenorhabditis elegans. Our multiple-gene approach is based on sampling more than 80,000 publicly available tylenchid EST sequences to identify phylum-wide orthologues. Bayesian inference, minimum evolution, maximum likelihood and protein distance methods were employed for phylogenetic reconstruction and hypothesis tests were constructed to elucidate differential selective pressures across the phylogeny for each gene. Our results place M. incognita and M. javanica as sister taxa, with M. arenaria as the next closely related nematode. Significant differences in selective pressure were revealed for some genes under some hypotheses, though all but one gene are exclusively under purifying selection, indicating conservation across the orthologous groups. This EST-based multi-gene analysis is a first step towards accomplishing genome-wide coverage for tylenchid evolutionary analyses. (c) 2005 Elsevier Inc. All rights reserved. ------------------- Key: 7459 Medline: Authors: Ji YJ;Singaravelu G;Ahnn J Title: RNT-1 regulation in C. elegans. Citation: Journal of Cellular Biochemistry 96: 8-15 2005 Type: ARTICLE Genes: bar-1 bro-1 daf-1 daf-3 daf-4 daf-5 daf-7 daf-8 daf-14 dbl-1 egl-20 lin-17 lin-44 lon-1mig-5 par-5 pop-1 pry-1 rnt-1 sgg-1 sma-2 sma-3 sma-4 sma-6 sma-9 tlp-1 unc-129 Abstract: RUNXs are important transcription factors, which are involved in animal development and human carcinogenesis. RNT-1, the only homologue of RUNXs, in Caenorhabditis elegans (C. elegans) has been identified and viable mutant animals of rnt-1 gene have been isolated and characterized recently. Genetic analyses using rnt-1 mutants have shown that RNT-1 is regulated by TGF beta- and Wnt-signaling pathways in the body size regulation and male tail development. Here, we review our current understanding of RNT-1 functions in these signaling pathways. Furthermore, future prospects of RNT-1 and BRO-1 studies in C. elegans are discussed in this review. ------------------- Key: 7460 Medline: 16014321 Authors: McMiller L;Johnson CM Title: Molecular characterization of HLH-17, a C. elegans bHLH protein required for normal larval development. Citation: Gene 356: 1-10 2005 Type: ARTICLE Genes: hlh-17 Abstract: The basic helix-loop-helix (bHLH) transcription factor family regulates numerous developmental events in eukaryotic cells. In the model system, C elegans, thirty-seven bHLH proteins have been identified. via genome-wide sequence analysis and fourteen have been genetically characterized to date. These proteins influence cell fate specification of neural lineages and differentiation of myogenic lineages and have distinct roles in somatic gonadogenesis. We report here on the molecular characterization of HLH-17, a protein whose putative bHLH domain is homologous to the mammalian bHLH proteins BETA3 and bHLHB5. The gene hlh-17 is transcriptionally active at all developmental stages, with the highest steady state accumulation of hlh-17 mRNA during embryogenesis. An upstream hlh-17 sequence drives expression of GFP in the sheath cells of the cephalic sensilla. Finally, animals that are defective in HLH-17 via RNAi display egglaying defects, while those carrying null mutations in hlh-17 do not develop beyond the L2 stage and are less attracted to potassium and sodium ions. We propose that hlh-17 affects the ability of C. elegans to respond to food cues, with possible downstream effects on insulin-signaling genes involved in the normal development ------------------- Key: 7461 Medline: 16000383 Authors: Thompson BE;Bernstein DS;Bachorik JL;Petcherski AG;Wickens M;Kimble J Title: Dose-dependent control of proliferation and sperm specification by FOG-1/CPEB. Citation: Development 132: 3471-3481 2005 Type: ARTICLE Genes: fbf-1 fbf-2 fem-3 fog-1 fog-3 gld-1 gld-2 gld-3 glp-1 nos-3 Abstract: RNA-binding proteins control germline development in metazoans. This work focuses on control of the C elegans germline by two RNA-binding proteins: FOG-1, a CPEB homolog; and FBF, a PUF family member. Previous studies have shown that FOG-1 specifies the sperm fate and that FBF promotes proliferation. Here, we report that FOG-1 also promotes proliferation. Whereas fbf-1 Jbf-2 double mutants make similar to 120 germ cells, fog-1; fbf-1 Jbf-2 triple mutants make only similar to 10 germ cells. The triple mutant germline divides normally until early L2, when germ cells prematurely enter meiosis and begin oogenesis. Importantly, fog-1/+; fbf-1 fbf-2 animals make more germ cells than fbf-1 fbf-2 double mutants, demonstrating that one dose of wild-type fog-1 promotes proliferation more effectively than two doses - at least in the absence of FBF. FOG-1 protein is barely detectable in proliferating germ cells, but abundant in germ cells destined for spermatogenesis. Based on fog-1 dose effects, together with the gradient of FOG-1 protein abundance, we suggest that low FOG-1 promotes proliferation and high FOG-1 specifies spermatogenesis. FBF binds specifically to regulatory elements in the fog-1 3'UTR, and FOG-1 increases in animals lacking FBF. Therefore, FBF represses fog-1 expression. We suggest that FBF promotes continued proliferation, at least in part, by maintaining FOG-1 at a low level appropriate for proliferation. The dose-dependent control of proliferation and cell fate by FOG-1 has striking parallels with Xenopus CPEB, suggesting a conserved mechanism in ------------------- Key: 7462 Medline: Authors: Higashitani A;Higashitani A;Sasagawa Y;Sugimoto T;Miyazawa Y;Szewczyk NJ;Viso M;Gasset G;Eche B;Fukui K;Shimazu T;Fujimoto N;Kuriyama K;Ishioka N Title: Checkpoint and physiological apoptosis in germ cells proceeds normally in spaceflown Caenorhabditis elegans. Citation: Apoptosis 10: 949-954 2005 Type: ARTICLE Genes: atl-1 ced-1 ced-2 ced-3 ced-4 ced-9 cep-1 egl-1 mrt-2 nuc-1 rad-5 rad-51 rdh-1 Abstract: It is important for human life in space to study the effects of environmental factors during spaceflight on a number of physiological phenomena. Apoptosis plays important roles in development and tissue homeostasis in metazoans. In this study, we have analyzed apoptotic activity in germ cells of the nematode C. elegans, following spacefight. Comparison of the number of cell corpses in wild type or ced-1 mutants, grown under either ground or spaceflight conditions, showed that both pachytene-checkpoint apoptosis and physiological apoptosis in germ cells occurred normally under spaceflight conditions. In addition, the expression levels of the checkpoint and apoptosis related genes are comparable between spaceflight and ground conditions. This is the first report documenting the occurrence of checkpoint apoptosis in the space environment and suggests that metazoans, including humans, would be able to eliminate cells that have failed to repair DNA lesions introduced by ------------------- Key: 7463 Medline: Authors: McColl G;Vantipalli MC;Lithgow GJ Title: C. elegans ortholog of mammalian Ku70 interacts with insulin-like signaling to modulate stress resistance and life span. Citation: FASEB Journal 19: 0302-0318 2005 Type: ARTICLE Genes: cku-70 cku-80 daf-2 daf-16 glp-4 Abstract: The mammalian Ku heterodimer has important roles in DNA double strand break repair, telomere maintenance, cell cycle checkpoint-arrest, tumor suppression, and cellular stress resistance. To investigate the evolutionarily conserved functions of Ku, we knocked down expression by RNA interference (RNAi) of Ku genes in C. elegans. We found that C. elegans Ku70 (CKU-70) is required for resistance to genotoxic stress, regulates cytotoxic stress responses, and influences aging. The latter effects are dependent on an IGF-1/insulin-like signaling pathway previously shown to affect life span. Reduction of CKU-70 activity amplifies the aging phenotype of long-lived insulin receptor daf-2 mutations in a daf-16-dependent manner. These observations support the view that organismal stress resistance determines life span and Ku70 modulates these effects. ------------------- Key: 7464 Medline: Authors: Eisenhut RJ;Knox D;Hermann GJ Title: Characterization of a conserved apoptotic marker expressed in Caenorhabditis elegans phagocytic cells. Citation: Biochemical and Biophysical Research Communications 335: 1231-1238 2005 Type: ARTICLE Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-10 ced-12 egl-1 nuc-1 Abstract: We have identified and characterized a monoclonal antibody, F2-P3E3, that recognizes a Caenorhabditis elegans apoptotic epitope expressed within phagocytic cells, which is conserved in four other nematode species. In C elegans, F2-P3E3 staining requires both programmed cell death and phagocytosis. We show that the F2-P3E3 epitope is expressed within embryonic intestinal cells, which act as phagocytes but do not undergo programmed cell death. F2-P3E3 staining is present within LMP-1::GFP labeled organelles in the intestinal primordium and is coincident with persistent DNA that has been phagocytosed in nuc-1(-) embryos, suggesting that it labels phagosomes. While apoptotic events are typically isolated in C elegans, F2-P3E3 staining is commonly found within adjacent cells. This observation suggests that F2-P3E3 might recognize an epitope expressed in multiple cells in response to signals from a single corpse. F2-P3E3 represents a new tool for studying cell death in C elegans. ------------------- Key: 7465 Medline: Authors: Richardson SJ;Hennebry SC;Smith BJ;Wright HM Title: Evolution of the thyroid hormone distributor protein transthyretin in microbes, C. elegans, and vertebrates. Citation: Annals of the New York Academy of Sciences 1040: 448-451 2005 Type: REVIEW Genes: Abstract: ------------------- Key: 7466 Medline: Authors: Mertens I;Vandingenen A;Clynen E;Nachman RJ;de Loof A;Schoofs L Title: Characterization of an RFamide-related peptide orphan GPCR in C. elegans. Citation: Annals of the New York Academy of Sciences 1040: 410-412 2005 Type: REVIEW Genes: flp-7 flp-11 Abstract: ------------------- Key: 7467 Medline: Authors: Nanji M;Hopper NA;Gems D Title: LET-60 RAS modulates effects of insulin/IGF-1 signaling on development and aging in Caenorhabditis elegans. Citation: Aging Cell 4: 235-245 2005 Type: ARTICLE Genes: Abstract: ------------------- Key: 7468 Medline: Authors: Ayyadevara S;Engle MR;Singh SP;Dandapat A;Lichti CF;Benes H;Reis RJS;Liebau E;Zimniak P Title: Lifespan and stress resistance of Caenorhabditis elegans are increased by the expression of glutathione transferases capable of metabolizing the lipid peroxidation product 4-hydroxynonenal. Citation: Aging Cell 4: 257-271 2005 Type: ARTICLE Genes: Abstract: ------------------- Key: 7469 Medline: Authors: Felix MA Title: Developmental biology of nematodes - What we learn from Caenorhabditis elegans. Citation: Nematology: Advances and Perspectives, Vol 1: Nematode Morphology, Physiology and Ecology. Oxford University Press, New York, NY. 1: 71-174 2004 Type: REVIEW Genes: Abstract: ------------------- Key: 7470 Medline: Authors: Pujol N;Ewbank JJ Title: Pathogen avoidance using toll signaling in C. elegans. Citation: Toll and Toll-Like Receptors: An Immunologic Perspective. Kluwer Academic/Plenum Publications, New York, NY. : 162-167 2005 Type: REVIEW Genes: Abstract: ------------------- Key: 7471 Medline: Authors: Crickmore N Title: Using worms to better understand how Bacillus thuringiensis kills insects. Citation: Trends in Microbiology 13: 347-350 2005 Type: REVIEW Genes: Abstract: Bacillus thuringiensis is widely used as a biological pesticide to control insects that either cause damage to crops or transmit disease. That it can also target the model organism Caenorhabditis elegans has not only provided exciting new insights into how the toxins produced by the bacterium target their victims but also how target insects counter the attack. Modern approaches such as reverse genetics and microarray technology have revealed novel receptors for the toxins and possible signal transduction pathways induced within the host following intoxication. This article will discuss how these findings fit in with current models and how they might influence future studies. ------------------- Key: 7472 Medline: 16084527 Authors: Lee J;Song HO;Jee C;Vanoaica L;Ahnn J Title: Calcineurin regulates enteric muscle contraction through EXP-1, excitatory GABA-gated channel, in C. elegans. Citation: Journal of Molecular Biology 352: 313-318 2005 Type: ARTICLE Genes: cnb-1 exp-1 tax-6 unc-25 Abstract: The enteric muscle contraction (EMC) is the last step of the defecation behavior which occurs every 50 s in Caenorhabditis elegans. This EMC is regulated by intestinal and anal depressor muscles, which are innervated by GABA motor neurons. Our data show that calcineurin (tax-6) is expressed in intestinal muscle and anal depressor muscle, and the gain-of-function mutant of calcineurin, tax-6(jh107), shows defects in enteric muscle contractions. In addition, the intracellular region of EXP-1, an excitatory GABA receptor, specifically binds to calcineurin A. This interaction between TAX-6 and EXP-1 appears to be independent of both calcium and CNB, which is the calcium-binding regulatory subunit. Genetic evidence of epistasis between cnb-1(jh103) and exp-1(sa6) suggests that calcineurin functions as a negative regulator of excitatory GABA receptor in GABA signaling in C. elegans. ------------------- Key: 7473 Medline: 16081104 Authors: Spanier B;Sturzenbaum SR;Holden-Dye LM;Baumeister R Title: Caenorhabditis elegans Neprilysin NEP-1: an effector of locomotion and pharyngeal pumping. Citation: Journal of Molecular Biology 352: 429-437 2005 Type: ARTICLE Genes: nep-1 Abstract: The control of signal peptide activity by cell surface proteases is one of the main factors that regulate the development and behaviour of organisms. In mammals, neprilysins (NEPs) are known to play a key role in these processes and their inactivation can initiate cellular disorganisation, which in turn may lead to prostate cancer or Hirschsprung disease. Although the proteome of the nematode Caenorhabditis elegans has been intensively studied, very little is known about the function of neprilysins. ZK20.6 (NEP-1), the C. elegans protein with highest identity to mammalian neprilysins, is a 753 amino acid residue protein that displays all neprilysin-typical characteristics, including a short intracellular domain, a transmembrane domain and a long extracellular active domain. Here we show that the expression pattern of nep-1 is limited to pharyngeal cells and a single head neuron. Compared to wild-type, the locomotion of nep-1 knockout animals is significantly impaired, a phenotype that can be rescued by the extrachromosomal re-introduction of nep-1. This suggests that this enzyme plays an important role in the regulation of nematode locomotion. Finally, electrophysiological recording of the pharyngeal activity showed a high sensitivity of the nep-1 pharynx to serotonin (5-HT) and to the neuropeptide AF1 (C. elegans FLP-8), indicating that NEP-1 is a central component that controls the neuronal innervation of pharyngeal pumping in C. ------------------- Key: 7474 Medline: Authors: Kage E;Hayashi Y;Takeuchi H;Hirotsu T;Kunitomo H;Inoue T;Arai H;Iino Y;Kubo T Title: MBR-1, a novel helix-turn-helix transcription factor, is required for pruning excessive neurites in Caenorhabditis elegans. Citation: Current Biology 15: 1554-1559 2005 Type: ARTICLE Genes: mbr-1 unc-86 zig-3 Abstract: In the developing brain, excessive neurites are actively pruned in the construction and remodeling of neural circuits. We demonstrate for the first time that the pruning of neurites occurs in the simple neural circuit of Caenorhabditis elegans and that a novel transcription factor, MBR-1, is involved in this process. We identified MBR-1 as a C. elegans ortholog of Mblk-1, a transcription factor that is expressed preferentially in the mushroom bodies of the honeybee brain [1]. Although Mblk-1 homologs are conserved among animal species, their roles in the nervous system have never been analyzed. We used C. elegans as an ideal model animal for analysis of neuronal development. mbr-1 is expressed in various neurons in the head and tail ganglia. A comparison of the morphology of mbr-1-expressing neurons revealed that excessive neurites connecting the left and right AIM interneurons are eliminated during larval stages in wild-type but are sustained through the adult stage in the mbr-1 mutant. In addition, mbr-1 expression is regulated by UNC-86, a POU domain transcription factor, and the pruning of the excessive AIM connection is impaired in the unc-86 mutant. These findings provide an important clue for further genetic dissection of neurite pruning. ------------------- Key: 7475 Medline: Authors: Sivasundar A;Hey J Title: Sampling from natural populations with RNAi reveals high outcrossing and population structure in Caenorhabditis elegans. Citation: Current Biology 15: 1598-1602 2005 Type: ARTICLE Genes: Abstract: Despite a nearly worldwide distribution in nature, Caenorhabditis elegans exhibits low levels of genetic polymorphism [1-6], possibly as an indirect consequence of low levels of outcrossing. In the laboratory, Caenorhabditis elegans males are produced at low rates and are steadily eliminated from cultures [7, 8], so that reproduction happens largely through self-fertilization in hermaphrodites. C. elegans is increasingly the focus of evolutionary research [1-4, 7, 9-12]; however, natural outcrossing rates are difficult to measure because mating tests with laboratory strains are usually required to identify C. elegans. We sampled natural populations of C. elegans with an RNA interference (RNAi) assay. Heterozygosities and polymorphism patterns revealed surprisingly high levels of population structure and outcrossing (approximately 22% of individuals are estimated to be the result of outcrossing and not self-fertilization). The finding of strong local population structure, together with low levels of diversity on local and global scales, suggests a metapopulation model of frequent extinction and recolonization of local populations. The occurrence of substantial outcrossing suggests that the extinction of local populations is probably not driven by the accumulation of harmful ------------------- Key: 7476 Medline: Authors: Schafer WR Title: Deciphering the neural and molecular mechanisms of C. elegans behavior. Citation: Current Biology 15: R723-R729 2005 Type: REVIEW Genes: Abstract: Because of its small and well-characterized nervous system and amenability to genetic manipulation, the nematode Caenorhabditis elegrans offers the promise of understanding the mechanisms underlying a whole animal's behavior at the molecular and cellular levels. In fact, this goal was a primary motivation behind the development of C. elegans as an experimental organism 40 years ago. Yet it has proven surprisingly difficult to obtain a mechanistic understanding of how the C. elegans nervous system generates behavior, despite the existence of a 'wiring diagram' that contains a degree of information about neural connectivity unparalleled in any organism. This review describes three types of information - molecular data on cellular neurochemistry, temporal information about neural activity patterns, and behavioral data on the consequences of neural ablation and manipulation - that, along with genetic analysis, may ultimately lead to a complete functional map of the C. elegans nervous system. ------------------- Key: 7477 Medline: Authors: Masuda M;Saimaru H;Takamura N;Imai K Title: An improved method for proteomics studies in C. elegans by fluorogenic derivatization, HPLC isolation, enzymatic digestion and liquid chromatography-tandem mass spectrometric identification. Citation: Biomedical Chromatography 19: 556-560 2005 Type: ARTICLE Genes: act-2 atp-2 cyp-2 cyp-5 cyp-6 cyp-7 far-2 hsp-70 lev-11 msp-32 rpl-1 rpl-7 rpl-14 rpl-20 rpl-23 rpl-30 rps-1 vit-3 vit-5 vit-6 Abstract: An improved method for proteomics studies, which includes the fluorogenic derivertization of protein mixtures with 7-chloro-4-(dimethylaminoethylaminosulfonyl)-2,1,3-benzoxad iazole (DAABD-Cl), followed by HPLC isolation, enzymatic digestion and idetification of the derivatized proteins by HPLC-electrospray ionization (ESI)-MS/MS with the probability-based protein identification algorithm, identified 103 proteins in the soluble extract (10 mu g protein) of Caenorhabditis elegans. ------------------- Key: 7478 Medline: 16033794 Authors: Ghenea S;Boudreau JR;Lague NP;Chin-Sang ID Title: The VAB-1 Eph receptor tyrosine kinase and SAX-3/Robo neuronal receptors function together during C. elegans embryonic morphogenesis. Citation: Development 132: 3679-3690 2005 Type: ARTICLE Genes: efn-4 ptp-3 rab-1 sax-3 slt-1 Abstract: Mutations that affect the single C elegans Eph receptor tyrosine kinase VAB-1 cause defects in cell movements during embryogenesis. Here, we provide genetic and molecular evidence that the VAB-1 Eph receptor functions with another neuronal receptor, SAX-3/Robo, for proper embryogenesis. Our analysis of sax-3 mutants shows that SAX-3/Robo functions with the VAB-1 Eph receptor for gastrulation cleft closure and ventral epidermal enclosure. In addition, SAX-3 functions autonomously for epidermal morphogenesis independently of VAB-1. A double-mutant combination between vab-1 and slt-1 unmasks a role for the SLT-1 ligand in embryogenesis. We provide evidence for a physical interaction between the VAB-1 tyrosine kinase domain and the juxtamembrane and CC1 region of the SAX-3/Robo receptor. Gene dosage, non-allelic non-complementation experiments and co-localization of the two receptors are consistent with a model in which these two receptors form a complex and function together during ------------------- Key: 7479 Medline: Authors: Roy PJ;Morris Q Title: Network news: functional modules revealed during early embryogenesis in C. elegans. Citation: Developmental Cell 9: 307-315 2005 Type: REVIEW Genes: Abstract: The functional module is fast becoming the operational unit of the postgenomics era. A new report in Nature by Gunsalus and colleagues describes, using a multiply supported network, functional modules within early C. elegans embryos and identifies several new components of known molecular machines. ------------------- Key: 7480 Medline: Authors: Leidel S;Gonczy P Title: Centrosome duplication and nematodes: recent insights from an old relationship. Citation: Developmental Cell 9: 317-325 2005 Type: REVIEW Genes: air-1 sas-4 sas-5 sas-6 spd-2 spd-5 zyg-1 Abstract: Centrosome duplication is required for proper cell division, and centriole formation is a key step in this process. This review discusses recent studies in C. elegans that have identified five core proteins required for centriole formation, thus shedding light into the mechanisms underlying centrosome duplication in nematodes ------------------- Key: 7481 Medline: Authors: Powell JR;Jow MM;Meyer BJ Title: The T-box transcription factor SEA-1 is an autosomal element of the X:A signal that determines C. elegans sex. Citation: Developmental Cell 9: 339-349 2005 Type: ARTICLE Genes: ceh-39 dpy-27 dpy-30 fox-1 him-8 sdc-2 sdc-3 sea-1 sex-1 sex-2 xol-1 ccDf3 yDp14 Abstract: Sex is determined in C. elegans by a chromosome-counting mechanism that tallies X chromosome dose relative to the sets of autosomes, the X:A ratio. A group of genes on X called X signal elements (XSEs) communicates X chromosome number by repressinig the activity of the master sex-determination switch gene xol-1 in a dose-dependent manner. xol-1 is repressed by transcriptional and posttranscriptional mechanisms and is inactive in XX animals (hermaphrodite) but active in XO animals (male). Prior to our work, the nature of the autosomal signal and its target(s) were unknown. Here we show the signal includes discrete, trans-acting autosomal signal elements (ASEs) that counter XSEs to coordinately control both sex determination and dosage compensation. sea-1, the first autosomal signal element, encodes a T-box transcription factor that opposes XSEs by activating transcription of xol-1. Hence, xol-1 integrates both X and autosomal signals to determine sexual fate. ------------------- Key: 7482 Medline: Authors: Abbott AL;Alvarez-Saavedra E;Miska EA;Lau NC;Bartel DP;Horvitz HR;Ambros V Title: The let-7 microRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Citation: Developmental Cell 9: 403-414 2005 Type: ARTICLE Genes: hbl-1 let-7 lin-4 lin-14 lin-28 lin-29 lin-41 lin-46 mir-48 mir-84 mir-241 Abstract: The microRNA let-7 is a critical regulator of developmental timing events at the larval-to-adult transition in C. elegans. Recently, microRNAs with sequence similarity to let-7 have been identified. We find that doubly mutant animals lacking the let-7family microRNA genes mir-48 and mir-84 exhibit retarded molting behavior and retarded adult gene expression in the hypodermis. Triply mutant animals lacking mir-48, mir-84, and mir-241 exhibit repetition of L2-stage events in addition to retarded adult-stage events. mir-48, mir-84, and mir-241 function together to control the L2-to-L3 transition, likely by base pairing to complementary sites in the hbi-13 ' UTR and downregulating hbi-1 activity. Genetic analysis indicates that mir-48, mir-84, and mir-241 specify the timing of the L2-to-L3 transition in parallel to the heterochronic genes lin-28 and lin-46. These results indicate that let-7family microRNAs function in combination to affect both early and late developmental timing decisions. ------------------- Key: 7483 Medline: Authors: Li M;Jones-Rhoades MW;Lau NC;Bartel DP;Rougvie AE Title: Regulatory mutations of mir-48, a C. elegans let-7 family microRNA, cause developmental timing defects. Citation: Developmental Cell 9: 415-422 2005 Type: ARTICLE Genes: hbl-1 let-7 lin-4 lin-41 lin-58 mir-48 mir-84 mir-241 Abstract: The C. elegans heterochronic genes program stage-specific temporal identities in multiple tissues during larval development. These genes include the first two miRNA-encoding genes discovered, lin-4 and let-7 We show that lin-58 alleles, identified as lin-4 suppressors, define another miRNA that controls developmental time. These alleles are unique in that they contain point mutations in a gene regulatory element of mir-48, a let-7 family member. mir-48 is expressed prematurely in lin-58 mutants, whereas expression of mir-241, another let-7 family member residing immediately upstream of mir-48, appears to be unaffected. A mir-48 transgene bearing a lin-58 point mutation causes strong precocious phenotypes in the hypodermis and vulva when expressed from multicopy arrays. rnir-48::gfp fusions reveal expression in these tissues, and inclusion of a lin-58 mutation causes precocious and enhanced gfp expression. These results suggest that lin-58 alleles disrupt a repressor binding site that restricts the time of miR-48 action in wildtype ------------------- Key: 7484 Medline: Authors: Gutierrez-Zepeda A;Santell R;Wu Z;Brown M;Wu Y;Khan I;Link CD;Zhao B;Luo Y Title: Soy isoflavone glycitein protects against beta amyloid-induced toxicity and oxidative stress in transgenic Caenorhabditis elegans. Citation: BMC Neuroscience 6: 28-36 2005 Type: ARTICLE Genes: Abstract: ------------------- Key: 7485 Medline: Authors: Kroft TL;Gleason EJ;L'Hernault SW Title: The spe-42 gene is required for sperm-egg interactions during C. elegans fertilization and encodes a sperm-specific transmembrane protein. Citation: Developmental Biology 286: 169-181 2005 Type: ARTICLE Genes: fem-1 fem-3 fer-15 glo-1 spe-42 sDf35 stDf4 yDf12 Abstract: Fertilization, the union of sperm and egg to form a new organism, is a critical process that bridges generations. Although the cytological and physiological aspects of fertilization are relatively well understood, little is known about the molecular interactions that occur between gametes. C. elegans has emerged as a powerful system for the identification of genes that are necessary for fertilization. C. elegans spe-42 mutants are sterile, producing cytologically normal spermatozoa that fail to fertilize oocytes. Indeed, male mating behavior, sperm transfer to hermaphrodites, sperm migration to the spermatheca, which is the site of fertilization and sperm competition are normal in spe-42 mutants. spe-42 mutant sperm make direct contact with oocytes in the spermatheca, suggesting that SPE-42 plays a role during sperm-egg interactions just prior to fertilization. No other obvious defects were observed in spe-42 mutant worms. Cloning and sequence analysis revealed that SPE-42 is a novel predicted 7-pass integral membrane protein with homologs in many metazoan species, suggesting that its mechanism of action could be conserved. ------------------- Key: 7486 Medline: 15936258 Authors: Ou G;Qin H;Rosenbaum JL;Scholey JM Title: The PKD protein qilin undergoes intraflagellar transport. Citation: Current Biology 15: R410-R411 2005 Type: REVIEW Genes: bbs-7 bbs-8 dyf-3 osm-3 Abstract: ------------------- Key: 7487 Medline: 15939418 Authors: Geldziler B;Chatterjee I;Singson A Title: The genetic and molecular analysis of spe-19, a gene required for sperm activation in Caenorhabditis elegans. Citation: Developmental Biology 283: 424-436 2005 Type: ARTICLE Genes: fem-1 fer-1 fog-2 spe-1 spe-6 spe-8 spe-19 ozDf1 ozDf2 yDf4 Abstract: During the process of spermiogenesis (sperm activation) in Caenorhabditis elegans, the dramatic morphological events that ultimately transform round sessile spermatids into polar motile spermatozoa occur without the synthesis of any new gene products. Previous studies have identified four genes (spe-8, spe-12, spe-27 and spe-29) that specifically block spermiogenesis and lead to hermaphrodite-specific fertility defects. Here, we report the cloning and characterization of a new component of the sperm activation pathway, spe-19, that is required for fertility in hermaphrodites. spe-19 is predicted to encode a novel single-pass transmembrane protein. The spe-19 mutant phenotype, genetic interactions and the molecular nature of the gene product suggest SPE-19 to be a candidate for the receptor/co-receptor necessary for the transduction of the activation signal across the sperm plasma membrane. ------------------- Key: 7488 Medline: 15990936 Authors: Dudley NR;Goldstein B Title: RNA interference in Caenorhabditis elegans. Citation: Methods in Molecular Biology 309: 29-38 2005 Type: REVIEW Genes: Abstract: ------------------- Key: 7489 Medline: Authors: Fan X;She YM;Bagshaw RD;Callahan JW;Schachter H;Mahuran DJ Title: Identification of the hydrophobic glycoproteins of Caenorhabditis elegans. Citation: Glycobiology 15: 952-964 2005 Type: ARTICLE Genes: col-43 cpl-1 cpr-6 csq-1 dig-1 dyn-1 grd-3 grd-4 ina-1 itx-1 lad-1 lam-1 lrp-1 nid-1 npp-12 pat-3 ptr-8 stc-1 str-204 tol-1 vha-5 zig-1 Abstract: Hydrophobic proteins such as integral membrane proteins are difficult to separate, and therefore to study, at a proteomics level. However, the Asn-linked (N-linked) carbohydrates (N-glycans) contained in membrane glycoproteins are important in differentiation, embryogenesis, inflammation, cancer and metastasis, and other vital cellular processes. Thus, the identification of these proteins and their sites of glycosylation in a well-characterized model organism is the first step toward understanding the mechanisms by which N-glycans and their associated proteins function in vivo. In this report, a proteomics method recently developed by our group was applied to identify 117 hydrophobic N-glycosylated proteins of Caenorhabditis elegans extracts by analysis of 195 glycopeptides containing 199 Asn-linked oligosaccharides. Most of the proteins identified are involved in cell adhesion, metabolism, or the transport of small molecules. In addition, there are 18 proteins for which no function is known or predictable by sequence homologies and two proteins which were previously predicted to exist only on the basis of genomic sequences in the C. elegans database. Because N-glycosylation is initiated in the lumen of the endoplasmic reticulum (ER), our data can be used to reassess the previously predicted subcellular localizations of these proteins. As well, the identification of N-glycosylation sites helps establish the membrane topology of the associated glycoproteins. Caenorhabditis elegans strains are presently available with mutations in 17 of the genes we have identified. The powerful genetic tools available for C. elegans can be used to make other strains with mutations in genes encoding N-glycosylated proteins and thereby determine N-glycan function. ------------------- Key: 7490 Medline: Authors: Sha K;Fire A Title: Imprinting capacity of gamete lineages in Caenorhabditis elegans. Citation: Genetics 170: 1633-1652 2005 Type: ARTICLE Genes: pha-1 unc-54 Abstract: We have observed a gamete-of-origin imprinting effect in C. elegans using a set of GFP reporter transgenes. From a single progenitor line carrying an extrachromosomal unc-54::gfp transgene array, we generated three independent autosomal integrations of the unc-54::gfp transgene. The progenitor line, two of its three integrated derivatives, and a nonrelated unc-119:gfp transgene exhibit an imprinting effect: single-generation transmission of these transgenes through the male germline results in similar to 1.5- to 2.0-fold greater expression than transmission through the female germline. There is a detectable resetting of the imprint after passage through the opposite germline for a single generation, indicating that the imprinted status of the transgenes is reversible. In cases where the transgene is maintained in either the oocyte lineage or sperm lineage for multiple, consecutive generations, a full reset requires passage through the opposite germline for several generations. Taken together, our results indicate that C. elegans has the ability to imprint chromosomes and that differences in the cell and/or molecular biology of oogenesis and spermatogenesis are manifest in an imprint that can persist in both somatic and germline gene expression for multiple generations. ------------------- Key: 7491 Medline: Authors: Anderson P Title: A place for RNAi. Citation: Developmental Cell 9: 311-312 2005 Type: REVIEW Genes: ain-1 Abstract: Processing bodies (P bodies) are discrete cytoplasmic foci to which mRNA is routed for degradation. In mammalian cells, they are also associated with miRNA-induced translational silencing and siRNA-induced mRNA degradation. In a recent issue of Molecular Cell, Ding and coworkers described an argonaute-interacting protein that appears to promote the assembly of P bodies in C. elegans. ------------------- Key: 7492 Medline: Authors: Skrdla PJ Title: Statistical kinetic approach for modeling lifespan. Citation: Biophysical Chemistry 118: 22-24 2005 Type: ARTICLE Genes: daf-2 daf-16 Abstract: Lifespan regulation through gene expression involves complex biochemical processes. Unfortunately, current mathematical models for treating lifespan data afford little insight into the mechanisms that control longevity. In this work, we demonstrate the use of a novel kinetic model to successfully fit the lifespan curves of the nematode, Caenorhabditis elegans. Our findings show that population aging may be treated analogously to a dispersive chemical process [P.J. Skrdla, R.T. Robertson, J. Phys. Chem. B 109 10611 (2005)]. Much like the Gompertz model, only two fit parameters, alpha and beta, are needed to adequately describe the entire data set for each nematode population. These parameters relate a 'global first-order time constant' and a 'global second-order rate constant', with units of (time) and (time)(-2), respectively. In C. elegans, the increased longevity resulting from DAF-16 (a transcription factor) activity in the intestinal tissue correlates with a larger a value and a smaller beta value; the opposite is true for animals with shorter lifespans. A basic physical interpretation of the two parameters is ------------------- Key: 7493 Medline: Authors: Chu KW;Chan SKW;Chow KL Title: Improvement of heavy metal stress and toxicity assays by coupling a transgenic reporter in a mutant nematode strain. Citation: Aquatic Toxicology 74: 320-332 2005 Type: ARTICLE Genes: age-1 cdf-1 clk-1 daf-2 daf-3 daf-5 daf-9 daf-10 daf-11 daf-12 daf-16 daf-18 daf-21 hif-1 mev-1 unc-4 unc-75 Abstract: Previous studies have demonstrated that wild type Caenorhabditis elegans displays high sensitivity to heavy metals in a lethality test at a level comparable to that of other bioindicator organisms. Taking advantage of the genetics of this model organism, we have tested a number of mutant strains for enhanced sensitivity in heavy metal induced lethality and stress response. These mutants are defective in genes controlling dauer formation, longevity or response to reactive oxygen species (ROS). Among the tested mutants, a double mutant daf-16 unc-75 strain was identified to have superior sensitivity. It has a 6-, 3- and 2-fold increase in sensitivity to cadmium, copper and zinc, respectively, as compared with that of wild type animals. When a fluorescent reporter transgene was coupled with this double mutant for stress detection, a 10-fold enhancement of sensitivity to cadmium over the wild type strain was observed. These transgenic animals, superior to most of the model organisms currently used in bioassays for environmental pollutants, offer a fast and economic approach to reveal the bioavailability of toxic substance in field samples. This study also demonstrates that combination of genetic mutations and transgenesis is a viable approach to identify sensitive indicator animals for environmental monitoring. ------------------- Key: 7494 Medline: Authors: Ausubel FM Title: Areinnate immune signaling pathways in plants and animals conserved? Citation: Nature Immunology 6: 973-979 2005 Type: REVIEW Genes: nsy-1 pmk-1 sek-1 tir-1 Abstract: Although adaptive immunity is unique to vertebrates, the innate immune response seems to have ancient origins. Common features of innate immunity in vertebrates, invertebrate animals and plants include defined receptors for microbe-associated molecules, conserved mitogen-associated protein kinase signaling cascades and the production of antimicrobial peptides. It is commonly reported that these similarities in innate immunity represent a process of divergent evolution from an ancient unicellular eukaryote that pre-dated the divergence of the plant and animal kingdoms. However, at present, data suggest that the seemingly analogous regulatory modules used in plant and animal innate immunity are a consequence of convergent evolution and reflect inherent constraints on how an innate immune system can be constructed. ------------------- Key: 7495 Medline: 16051528 Authors: Mooijaart SP;Brandt BW;Baldal EA;Pijpe J;Kuningas M;Beekman M;Zwaan BJ;Slagboom PE;Westendorp RGJ;van Heemst D Title: C. elegans DAF-12, nuclear hormone receptors and human longevity and disease at old age. Citation: Ageing Research Reviews 4: 351-371 2005 Type: REVIEW Genes: daf-9 daf-12 din-1 Abstract: In Caenorhabditis elegans, DAF-12 appears to be a decisive checkpoint for many life history traits including longevity. The daf-12 gene encodes a Nuclear Hormone Receptor (NHR) and is member of a superfamily that is abundantly represented throughout the animal kingdom, including humans. It is, however, unclear which of the human receptor representatives are most similar to DAF-12, and what their role is in determining human longevity and disease at old age. Using a sequence similarity search, we identified human NHRs similar to C. elegans DAF-12 and found that, based on sequence similarity, Liver X Receptor A and B are most similar to C. elegans DAF-12, followed by the Pregnane X Receptor, Vitamin D Receptor, Constitutive Andosteron Receptor and the Farnesoid X Receptor. Their biological functions include, amongst others, detoxification and immunomodulation. Both are processes that are involved in protecting the body from harmful environmental influences. Furthermore, the DAF-12 signalling systems seem to be functionally conserved and all six human NHRs have cholesterol derived compounds as their ligands. We conclude that the DAF-12 signalling system seems to be evolutionary conserved and that NHRs in man are critical for body homeostasis and survival. Genomic variations in these NHRs or their target genes are prime candidates for the regulation of human lifespan and disease ------------------- Key: 7496 Medline: Authors: Kaltenbach LS;Updike DL;Mango SE Title: Contribution of the amino and carboxyl termini for PHA-4/FoxA function in Caenorhabditis elegans. Citation: Developmental Dynamics 234: 346-354 2005 Type: ARTICLE Genes: ceh-43 pha-4 smg-1 smg-3 Abstract: ------------------- Key: 7497 Medline: Authors: Pemberton TJ;Kay JE Title: Identification and comparative analysis of the peptidyl-prolyl cis/trans isomerase repertoires of H. sapiens, D. melanogaster, C. elegans, S. cerevisiae and Sz. pombe. Citation: Comparative and Functional Genomics 6: 277-300 2005 Type: ARTICLE Genes: Abstract: ------------------- Key: 7498 Medline: Authors: Shatilla A;Ishchenko AA;Saparbaev M;Ramotar D Title: Characterization of Caenorhabditis elegans exonuclease-3 and evidence that a Mg2+-dependent variant exhibits a distinct mode of action on damaged DNA. Citation: Biochemistry 44: 12835-12848 2005 Type: ARTICLE Genes: apn-1 exo-3 Abstract: The Caenorhabditis elegans genes, exo-3 and apn-1, encode the proteins EXO-3 and APN-1, belonging to the exo III and endo IV families of apurinic/apyrimidinic (AP) endonucleases/3'-diesterases, respectively. Homologues of EXO-3 and APN-1 in E. coli and yeast have been clearly documented to repair AP sites and DNA strand breaks with blocked 3' ends to prevent genomic instability. Herein, we purified the C. elegans EXO-3, expressed as a Gst-fusion protein in yeast, and demonstrated that it possesses strong AP endonuclease and 3'-diesterase activities. However, unlike the E. coli counterpart exonuclease III, EXO-3 shows no significant level of 3' --> 5' exonuclease activity following incision at AP sites. In addition, EXO-3 lacks the ability to directly incise DNA at the 5' side of various oxidatively damaged bases, as observed for the human counterpart Ape1, suggesting that C. elegans evolved a member with tailored functions. Importantly, a variant form of EXO-3, E68A, demonstrates altered magnesium-binding properties, and although the in vitro AP endonuclease is nearly fully recovered in the presence of MgCl2, the 3'-diesterase activity is reduced when compared to the native enzyme. We suggest that Glu68 plays a role in coordinating Mg2+ binding for the enzyme catalytic mechanism. Further analysis reveals that neither purified Gst-EXO-3 nor the E68A variant forms a readily detectable DNA-protein complex with an oligonucleotide substrate containing either an AP site or an alpha,beta-unsaturated aldehyde at its 3' end. However, if the reaction is conducted in the presence of crude extracts derived from either yeast or C. elegans embryos, only E68A forms a distinct slow migrating DNA-protein complex with each of the substrates, suggesting that Glu68 may be required to facilitate the release of EXO-3 from the incised DNA to allow entry of the remaining components of the base-excision repair pathway. Thus, the slow migrating DNA-protein complex formed by the E68A variant could be indicative of a stalled repair process with associated ------------------- Key: 7499 Medline: Authors: Van Gilst MR;Hadjivassiliou H;Yamamoto KR Title: A Caenorhabditis elegans nutrient response system partially dependent on nuclear receptor NHR-49. Citation: Proceedings of the National Academy of Sciences USA 102: 13496-13501 2005 Type: ARTICLE Genes: acdh-1 acdh-2 acs-2 acs-11 cpt-3 cpt-4 ech-1 ech-6 fat-2 fat-3 fat-4 fat-7 gei-7 hacd-1 lbp-1 lbp-8 Abstract: Appropriate response to nutritional stress is critical for animal survival and metabolic health. To better understand regulatory networks that sense and respond to nutritional availability, we developed a quantitative RT-PCR strategy to monitor changes in metabolic gene expression resulting from short-term food deprivation (fasting) in Caenorhabditis elegans. Examining 97 fat and glucose metabolism genes in fed and fasted animals, we identified 18 genes significantly influenced by food withdrawal in all developmental stages. Fasting response genes fell into multiple kinetic classes, with some genes showing significant activation or repression just 1 h after food was removed. As expected, fasting stimulated the expression of genes involved in mobilizing fats for energy production, including mitochondrial beta-oxidation genes. Surprisingly, however, we found that other mitochondrial beta-oxidation genes were repressed by food deprivation. Fasting also affected genes involved in mono- and polyunsaturated fatty acid synthesis: four desaturases were induced, and one stearoyl-CoA desaturase (SCD) was strongly repressed. Accordingly, fasted animals displayed considerable changes in fatty acid composition. Finally, nuclear receptor nhr-49 played a key role in nutritional response, enabling induction of beta-oxidation genes upon food deprivation and facilitating activation of SCD in fed animals. Our characterization of a fasting response system and our finding that nhr-49 regulates a sector within this system provide insight into the mechanisms by which animals ------------------- Key: 7500 Medline: Authors: Van Voorhies WA;Fuchs J;Thomas S Title: The longevity of Caenorhabditis elegans in soil. Citation: Biology Letters 1: 247-249 2005 Type: ARTICLE Genes: daf-2 fer-1 Abstract: Relatively simple model organisms such as yeast, fruit-flies and the nematode, Caenorhabditis elegans, have proven to be invaluable resources in biological studies. An example is the widespread use of C. elegans to investigate the complex process of ageing. An important issue when interpreting results from these studies is the similarity of the observed C elegans mortality pattern in the laboratory to that expected in its natural environment. We found that the longevity of C elegans under more natural conditions is reduced up to 10-fold compared with standard laboratory culture conditions. Additionally, C. elegans mutants that live twice as long as wild-type worms in laboratory conditions typically die sooner than wild-type worms in a natural soil. These results indicate that conclusions regarding extended longevity drawn from standard laboratory assays may not extend to animals in their native environment. ------------------- Key: 7501 Medline: Authors: Espelt MV;Estevez AY;Yin XY;Strange K Title: Oscillatory Ca2+ signaling in the isolated Caenorhabditis elegans intestine: role of the inositol-1,4,5-trisphospate receptor and phospholipases C beta and gamma. Citation: Journal of General Physiology 126: 379-392 2005 Type: ARTICLE Genes: dgk-1 dgk-2 dgk-3 egl-8 glo-1 ipp-5 itr-1 lfe-2 nhx-2 plc-1 plc-2 plc-3 plc-4 pll-1 rde-1 Abstract: Defecation in the nematode Caenorhabditis elegans is a readily observable ultradian behavioral rhythm that occurs once every 45-50 s and is mediated in part by posterior body wall muscle contraction (pBoc). pBoc is not regulated by neural input but instead is likely controlled by rhythmic Ca2+ oscillations in the intestinal epithelium. We developed an isolated nematode intestine preparation that allows combined physiological, genetic, and molecular characterization of oscillatory Ca2+ signaling. Isolated intestines loaded with fluo-4 AM exhibit spontaneous rhythmic Ca2+ oscillations with a period of similar to 50 s. Oscillations were only detected in the apical cell pole of the intestinal epithelium and occur as a posterior-to-anterior moving intercellular Ca2+ wave. Loss-of-function mutations in the inositol-1,4,5-trisphosphate (IP3) receptor ITR-1 reduce pBoc and Ca2+ oscillation frequency and intercellular Ca2+ wave velocity. In contrast, gain-of-function mutations in the IP3 binding and regulatory domains of ITR-1 have no effect on pBoc or Ca2+ oscillation frequency but dramatically increase the speed of the intercellular Ca2+ wave. Systemic RNA interference (RNAi) screening of the six C. elegans phospholipase C (PLC)-encoding genes demonstrated that pBoc and Ca2+ oscillations require the combined function of PLC-gamma and PLC-beta homologues. Disruption of PLC-gamma and PLC-beta activity by mutation or RNAi induced arrhythmia in pBoc and intestinal Ca2+ oscillations. The function of the two enzymes is additive. Epistasis analysis suggests that PLC-gamma functions primarily to generate IP3 that controls ITR-1 activity. In contrast, IP3 generated by PLC-beta appears to play little or no direct role in ITR-1 regulation. PLC-beta may function instead to control PIP2 levels and/or G protein signaling events. Our findings provide new insights into intestinal cell Ca2+ signaling mechanisms and establish C. elegans as a powerful model system for defining the gene networks and molecular mechanisms that underlie the generation and regulation of Ca2+ oscillations and intercellular Ca2+ waves in nonexcitable cells. ------------------- Key: 7502 Medline: Authors: C. elegans Sequencing Consortium Title: Genome sequence of the nematode Caenorhabditis elegans: A platform for investigating biology. Citation: Science 283: 35- 1999 Type: CORRECT Genes: Abstract: ------------------- Key: 7503 Medline: Authors: C. elegans Sequencing Consortium Title: Genome sequence of the nematode Caenorhabditis elegans: A platform for investigating biology. Citation: Science 285: 1493- 1999 Type: CORRECT Genes: Abstract: ------------------- Key: 7504 Medline: 15977988 Authors: Wu Y;Luo Y Title: Transgenic C. elegans as a model in Alzheimer's research. Citation: Current Alzheimer Research 2: 37-45 2005 Type: REVIEW Genes: Abstract: Alzheimer's disease (AD) has been associated with aggregation of beta-amyloid peptide (Abeta) and cell death in the brain. Using various models, such as the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and the mouse Mus musculus, investigators have attempted to imitate the pathology process of AD for better understanding of the cellular mechanisms and for possible therapeutic intervention. Among many in vitro and in vivo models of AD, transgenic C. elegans expressing human Abeta has shown its own advantages. The transgenic C. elegans model have been used in studying AD due to its short life span, facility to maintain, ability to develop muscle-associated deposits reactive to amyloid-specific dyes and the concomitant progressive paralysis phenotype. Moreover, the transgenic C. elegans exhibits increased levels of reactive oxygen species (ROS) and protein carbonyls, similar to those observed in AD patients, supporting the current theory on Abeta-induced oxidative stress and subsequent neurodegeneration in AD. DNA microarray assays of the worm demonstrated several stress-related genes being upregulated, particularly two genes homologous to human alphaB-crystallin and tumor necrosis factor-related protein, which were also upregulated in postmortem AD brain. Studies in our laboratory along with others suggest that the transgenic C. elegans model is a suitable in vivo model to relate Abeta-expression with its toxicity, which may underlie AD pathology. It may also be used as a tool for pharmacological evaluation of novel therapeutic agents. ------------------- Key: 7505 Medline: 16208361 Authors: Yan N;Chai J;Lee ES;Gu L;Liu Q;He J;Wu JW;Kokel D;Li H;Hao Q;Xue D;Shi Y Title: Structure of the CED-4-CED-9 complex provides insights into programmed cell death in Caenorhabditis elegans. Citation: Nature 437: 831-837 2005 Type: ARTICLE Genes: ced-3 ced-4 ced-9 egl-1 Abstract: Interplay among four genes - egl-1, ced-9, ced-4 and ced-3 - controls the onset of programmed cell death in the nematode Caenorhabditis elegans. Activation of the cell-killing protease CED-3 requires CED-4. However, CED-4 is constitutively inhibited by CED-9 until its release by EGL-1. Here we report the crystal structure of the CED-4 - CED-9 complex at 2.6 angstrom resolution, and a complete reconstitution of the CED-3 activation pathway using homogeneous proteins of CED-4, CED-9 and EGL-1. One molecule of CED-9 binds to an asymmetric dimer of CED-4, but specifically recognizes only one of the two CED-4 molecules. This specific interaction prevents CED-4 from activating CED-3. EGL-1 binding induces pronounced conformational changes in CED-9 that result in the dissociation of the CED-4 dimer from CED-9. The released CED-4 dimer further dimerizes to form a tetramer, which facilitates the autoactivation of CED-3. Together, our studies provide important insights into the regulation of cell death activation in C. elegans. ------------------- Key: 7506 Medline: Authors: Szewczyk NJ;Jacobson LA Title: Signal-transduction networks and the regulation of muscle protein degradation. Citation: International Journal of Biochemistry & Cell Biology 37: 1997-2011 2005 Type: REVIEW Genes: let-23 let-756 Abstract: Protein degradation in muscle functions in maintaining normal physiological homeostasis and adapting to new homeostatic states, and is required for muscle wasting or atrophy in various pathological states. The interplay between protein synthesis and degradation to maintain homeostasis is complex and responds to a variety of autocrine and intercellular signals from neuronal inputs, hormones, cytokines, growth factors and other regulatory molecules. The intracellular events that connect extracellular signals to the molecular control of protein degradation are incompletely understood, but likely involve interacting signal-transduction networks rather than isolated pathways. We review some examples of signal-transduction systems that regulate protein degradation, including effectors of proteolysis inducing factor (PIF), insulin and insulin-like growth factor (IGF) and their receptors, and fibroblast growth factor (FGF) and its receptors. ------------------- Key: 7507 Medline: Authors: Styer KL;Hopkins GW;Bartra SS;Plano GV;Frothingham R;Aballay A Title: Yersinia pestis kills Caenorhabditis elegans by a biofilm-independent process that involves novel virulence factors. Citation: EMBO Reports 6: 992-997 2005 Type: ARTICLE Genes: Abstract: It is known that Yersinia pestis kills Caenorhabditis elegans by a biofilm-dependent mechanism that is similar to the mechanism used by the pathogen to block food intake in the flea vector. Using Y. pestis KIM5, which lacks the genes that are required for biofilm formation, we show that Y. pestis can kill C. elegans by a biofilm-independent mechanism that correlates with the accumulation of the pathogen in the intestine. We used this novel Y. pestis - C. elegans pathogenesis system to show that previously known and unknown virulence-related genes are required for full virulence in C. elegans. Six Y. pestis mutants with insertions in genes that are not related to virulence before were isolated using C. elegans. One of the six mutants carried an insertion in a novel virulence gene and showed significantly reduced virulence in a mouse model of Y. pestis pathogenesis. Our results indicate that the Y. pestis - C. elegans pathogenesis system that is described here can be used to identify and study previously uncharacterized Y. pestis gene products required for virulence in mammalian systems. ------------------- Key: 7508 Medline: Authors: Kaltenbach LS;Updike DL;Mango SE Title: Contribution of the amino and carboxyl termini for PHA-4/FoxA function in Caenorhabditis elegans. Citation: Developmental Dynamics 234: 346-354 2005 Type: ARTICLE Genes: ceh-43 pha-4 smg-1 smg-3 Abstract: FoxA transcription factors are central regulators of gut development in all animals that have been studied. Here we examine the sole Caenorhabditis elegans FoxA protein, which is called pha-4. We describe the molecular characterization of five pha-4 mutations and characterize their associated phenotypes. Two nonsense mutations are predicted to truncate PHA-4 after the DNA binding domain and remove the conserved carboxyl terminus. Surprisingly, animals harboring these mutations are viable, provided the mutant mRNAs are stabilized by inactivating the nonsense-mediated decay pathway. Two additional nonsense mutations reveal that the DNA binding domain is critical for activity. A missense mutation predicted to alter the PHA-4 amino terminus leads to a dramatic reduction in pha-4 activity even though the protein is expressed appropriately. We suggest that the PHA-4 amino terminus is essential for PHA-4 function in vivo, possibly as a transactivation domain, and can compensate for loss of the carboxyl terminus. We also provide evidence for autoregulation by ------------------- Key: 7509 Medline: Authors: Luke-Glaser S;Pintard L;Lu C;Mains PE;Peter M Title: The BTB protein MEL-26 promotes cytokinesis in C. elegans by a CUL-3-independent mechanism. Citation: Current Biology 15: 1605-1615 2005 Type: ARTICLE Genes: cul-3 mei-1 mel-26 pod-1 rfl-1 tbb-2 Abstract: Background: The initiation of a cleavage furrow is essential to separate cells during cytokinesis, but little is known about the mechanisms controlling this actin-driven process. Previous studies in C. elegans embryos revealed that inactivation of the CUL-3-based E3 ligase activator rfl-1 results in an aberrant microtubule network, ectopic furrowing during pronuclear migration, and defects during cytokinesis. Results: Here, we show that MEL-26, a substrate-specific adaptor of the CUL-3-based E3 ligase, is required for efficient cell separation and cleavage furrow ingression during the C. elegans early mitotic divisions. Loss of MEL-26 function leads to delayed onset and slow ingression of cytokinesis furrows that frequently regress. Conversely, increased levels of MEL-26 in cul-3(RNAi) and rfl-1 mutant embryos cause a hypercontractile cortex, with several simultaneously ingressing furrows during pronuclear migration. MEL-26 accumulates at cleavage furrows and binds the actin-interacting protein POD-1. Importantly, POD-1 is not a substrate of the MEL-26/CUL-3 ligase but is required to localize MEL-26 to the cortex. Conclusions: Our results suggest that MEL-26 not only acts as a substrate-specific adaptor within the MEL26/CUL-3 complex, but also promotes cytokinesis by a CUL-3- and microtubule-independent mechanism. ------------------- Key: 7510 Medline: Authors: Qin H;Burnette DT;Bae HK;Forscher P;Barr MM;Rosenbaum JL Title: Intraflagellar transport is required for the vectorial movement of TRPV channels in the ciliary membrane. Citation: Current Biology 15: 1695-1699 2005 Type: ARTICLE Genes: che-3 daf-10 kap-1 klp-11 ocr-2 osm-3 osm-5 osm-9 pkd-2 Abstract: The membranes of all eukaryotic motile (9 + 2) and immotile primary (9 + 0) cilia harbor channels and receptors involved in sensory transduction (reviewed by [1]). These membrane proteins are transported from the cytoplasm onto the ciliary membrane by vesicles targeted for exocytosis at a point adjacent to the ciliary basal body [2, 3]. Here, we use time-lapse fluorescence microscopy to demonstrate that select GFP-tagged sensory receptors undergo rapid vectorial transport along the entire length of the cilia of Caenorhabditis elegans sensory neurons. Transient receptor potential vanilloid (TRPV) channels OSM-9 and OCR-2 [4, 5] move in ciliary membranes at rates comparable to the intraflagellar transport (IFT) machinery located between the membrane and the underlying axonemal microtubules [6-8]. OSM-9 motility is disrupted in certain IFT mutant backgrounds. Surprisingly, motility of transient receptor potential polycystin (TRPP) channel PKD-2 (polycystic kidney disease-2) [9], a mechano-receptor [10], was not detected. Our study demonstrates that IFT, previously shown to be necessary for transport of axonemal components [11], is also involved in the motility of TRPV membrane protein movement along cilia of C. elegans sensory cells. ------------------- Key: 7511 Medline: Authors: Suzuki M;Tsuji T;Ohtake H Title: A model of motor control of the nematode C. elegans with neuronal circuits. Citation: Artificial Intelligence in Medicine 35: 75-86 2005 Type: ARTICLE Genes: Abstract: Objective: Living organisms have mechanisms to adapt to various conditions of external environments. If we can realize these mechanisms on the computer, it may be possible to apply methods of biological and biomimetic adaptation to the engineering of artificial machines. This paper focuses on the nematode Caenorhabditis elegans (C. elegans), which has a relatively simple structure and is one of the most studied multicellular organisms. We aim to develop its computer model, artificial C. elegans, to analyze control mechanisms with respect to motion. Although C. elegans processes many kinds of external stimuli, we focused on gentle touch stimulation. Methods: The proposed model consists of a neuronal circuit model for motor control that responds to gentle touch stimuli and a kinematic model of the body for movement. All parameters included in the neuronal circuit model are adjusted by using the real-coded genetic algorithm. Also, the neuronal oscillator model is employed in the body model to generate the sinusoidal movement. The motion velocity of the body model is controlled by the neuronal circuit model so as to correspond to the touch stimuli that are received in sensory neurons. Conclusion: The computer simulations confirmed that the proposed model is capable of realizing motor control similar to that of the actual organism qualitatively. By using the artificial organism it may be possible to clarify or predict some characteristics that cannot be measured in actual experiments. With the recent development of computer technology, such a computational analysis becomes a real possibility. The artificial C. elegans will contribute for studies in experimental biology in future, although it is stilt developing at present. ------------------- Key: 7512 Medline: Authors: Goh KI;Kahng B;Kim D Title: Graph theoretic analysis of protein interaction networks of eukaryotes. Citation: Physica A 357: 501-512 2005 Type: ARTICLE Genes: Abstract: Owing to the recent progress in high-throughput experimental techniques, the datasets of large-scale protein interactions of prototypical multicellular species, the nematode worm Caenorhabditis elegans and the fruit fly Drosophila melanogaster, have been assayed. The datasets are obtained mainly by using the yeast hybrid method, which contains false-positive and false-negative simultaneously. Accordingly, while it is desirable to test such datasets through further wet experiments, here we invoke recent developed network theory to test such high-throughput datasets in a simple way. Based on the fact that the key biological processes indispensable to maintaining life are conserved across eukaryotic species, and the comparison of structural properties of the protein interaction networks (PINs) of the two species with those of the yeast PIN, we find that while the worm and yeast PIN datasets exhibit similar structural properties, the current fly dataset, though most comprehensively screened ever, does not reflect generic structural properties correctly as it is. The modularity is suppressed and the connectivity correlation is lacking. Addition of interologs to the current fly dataset increases the modularity and enhances the occurrence of triangular motifs as well. The connectivity correlation function of the fly, however, remains distinct under such interolog additions, for which we present a possible scenario through an in silico modeling. ------------------- Key: 7513 Medline: Authors: Tucker M;Sieber M;Morphew M;Han M Title: The Caenorhabditis elegans aristaless orthologue, alr-1, is required for maintaining the functional and structural integrity of the amphid sensory organs. Citation: Molecular Biology of the Cell 16: 4695-4704 2005 Type: ARTICLE Genes: alr-1 hmp-1 hmp-2 osm-3 ctDf19 Abstract: The homeobox-containing aristaless-related protein ARX has been directly linked to the development of a number of human disorders involving mental retardation and epilepsy and clearly plays a critical role in development of the vertebrate central nervous system. In this work, we investigate the role of ALR-1, the Caenorhabditis elegans aristaless orthologue, in amphid sensory function. Our studies indicate that ALR-1 is required for maintenance of the amphid organ structure throughout larval development. Mutant analysis indicates a progressive loss in the amphid neurons' ability to fill with lipophilic dyes as well as a declining chemotactic response. The degeneration in amphid function corresponds with a failure of the glial-like amphid socket cell to maintain. its specific cell shape and cell-cell contacts. Consistent with ALR-1 expression within the amphid socket cell, our results indicate a cell autonomous role for ALR-1 in maintaining cell shape. Furthermore, we demonstrate a role for ALR-1 in the proper morphogenesis of the anterior hypodermis. Genetic interaction tests also suggest that ALR-1 may function cooperatively with the cell adhesion processes in maintaining the amphid sensory organs. ------------------- Key: 7514 Medline: Authors: Houthoofd K;Johnson TE;Vanfleteren JR Title: Dietary restriction in the nematode Caenorhabditis elegans. Citation: Journals of Gerontology Series A-Biological Sciences & Medical Sciences 60: 1125-1131 2005 Type: REVIEW Genes: Abstract: The first observation of the positive effect of reduced food intake on mammalian life span was made 70 years ago (1). In the decades that followed, researchers successfully applied this method to increase the life span of a very wide range of animals. The nematode Caenorhabditis elegans is an excellent model organism for studying the aging process. However, relatively little effort has been made to study the effects of dietary restriction in C. elegans. In this review we discuss the difficulties of subjecting C. elegans to dietary restriction, the effects of dietary restriction on metabolism and stress defense, and the potential role of different signaling pathways in DR-induced life extension. Recent experiments suggest that the TOR (target of rapamycin) pathway, rather than insulin-like signaling, might be involved in mediating the life-extending effect of dietary restriction. ------------------- Key: 7515 Medline: Authors: Skantar AM;Agama K;Meyer SLF:Carta LK;Vinyard BT Title: Effects of geldanamycis on hatching and juvenile motility in Caenorhbditis elegans and Heterodera glycines. Citation: Journal of Chemical Ecology 31: 2481-2491 2005 Type: ARTICLE Genes: Abstract: Several Streptomyces species are known to produce metabolites that inhibit plant pathogens. One such compound is geldanamycin (GA), a benzoquinone ansamycin originally isolated from Streptomyces hygroscopicus. We examined the effect of geldanamycin on egg hatch and juvenile motility in Caenorhabditis elegans and in two populations of the plant-parasitic nematode Heterodera glycines. When C. elegans eggs were exposed to geldanamycin, both hatch and motility were reduced by GA doses between 2 and 50 mu g/ml. The H. glycines inbred populations TN17 and TN18 exhibited low dose stimulation of hatch and motility, whereas levels occurring at higher GA doses were at or below control levels. These experiments represent the first demonstration of geldanamycin effects in C. elegans and H. glycines and suggest that the heat shock chaperone Hsp90, the known molecular target of geldanamycin, may be involved in nematode egg hatch and motility. This study also indicates that geldanamycin-producing strains of Streptomyces may be useful as biocontrol agents for nematodes. ------------------- Key: 7516 Medline: Authors: Molin L;Puisieux A Title: C. elegans homologue of the Caf1 gene, which encodes a subunit of the CCR-NOT complex, is essential for embryonic and larval development and for meiotic progression. Citation: Gene 358: 73-81 2005 Type: ARTICLE Genes: ccf-1 fem-1 fem-3 glp-4 lin-15 lin-35 rrf-3 ctDf3 eDf2 eDp6 Abstract: The evolutionary conserved CCR4-NOT multi subunit complex is involved in different aspects of mRNA metabolism, including mRNA synthesis initiation and mRNA deadenylation (shortening of the poly(A) tail) in yeast and higher eukaryotes. Here we report the characterization of the gene encoding the Caf1 subunit of this complex in Caenorhabditis elegans, ccf-1, and the phenotypes associated with its inactivation. Use of staged populations and of mutants strains with altered germline showed that ccf-1 is predominantly expressed in embryos and adults. Loss of ccf-1 function, by both RNAi and a deletion allele, caused early embryonic and larval lethality. It also resulted in sterility in both males and hermaphrodites by blocking germ cell development at the pachytene stage of meiosis 1. These results reveal that ccf-1 is an essential factor for both somatic and germline development in C elegans. Functional analysis of cef-1 may contribute to the understanding of the molecular role of the CCR4-NOT complex. ------------------- Key: 7517 Medline: 16117625 Authors: Meyer BJ;McDonel P;Csankovszki G;Ralston E Title: Sex and X-chromosome-wide repression in Caenorhabditis elegans. Citation: Cold Spring Harbor Symposia on Quantitative Biology 69: 71-79 2004 Type: REVIEW Genes: Abstract: ------------------- Key: 7518 Medline: 16117673 Authors: Robert VJP;Vastenhouw NL;Plasterk RHA Title: RNA interference, transposon silencing, and cosuppression in the Caenorhabditis elegans germ line: similarities and differences. Citation: Cold Spring Harbor Symposia on Quantitative Biology 69: 397-402 2004 Type: REVIEW Genes: Abstract: ------------------- Key: 7519 Medline: 16117677 Authors: Wang D;Ruvkun G Title: Regulation of Caenorhabditis elegans RNA interference by the daf-2 insulin stress and longevity signaling pathway. Citation: Cold Spring Harbor Symposia on Quantitative Biology 69: 429-431 2004 Type: REVIEW Genes: Abstract: ------------------- Key: 7520 Medline: Authors: Paschinger K;Fabini G;Schuster D;Rendic D;Wilson IBH Title: Definition of immunogenic carbohydrate epitopes. Citation: Acta Biochimica Polonica 52: 629-632 2005 Type: ARTICLE Genes: fut-1 Abstract: Carbohydrates are known as sources of immunological cross-reactivity of allergenic significance. In celery and in cypress pollen, the major allergens Api g 5 and Cup a 1 are recognised by antisera raised against anti-horseradish peroxidase and by patients' IgE which apparently bind carbohydrate epitopes; mass spectrometric analysis of the tryptic peptides and of their N-glycans showed the presence of oligosaccharides carrying both xylose and core alpha 1,3-fucose residues. Core alpha 1,3-fucose residues are also a feature of invertebrates: genetic and biochemical studies on the fruitfly Drosophila melanogaster, the parasitic trematode Schistosoma mansoni and the nematode worm Caenorhabditis elegans indicate that these organisms possess core alpha 1,3-fucosyltransferases. Various experiments have shown that fucosyltransferases from both fly and worm are responsible in vivo and in vitro for the synthesis of N-glycans which cross-react with anti-horseradish peroxidase; thus, we can consider these enzymes as useful tools in generating standard compounds for testing cross-reactive carbohydrate epitopes of ------------------- Key: 7521 Medline: Authors: Miller DJ;Ball EE;Technau U Title: Cnidarians and ancestral genetic complexity in the animal kingdom. Citation: Trends in Genetics 21: 536-539 2005 Type: REVIEW Genes: Abstract: Eleven of the twelve recognized wingless (Wnt) subfamilies are represented in the sea anemone Nematostelia vectensis, indicating that this developmentally important gene family was already fully diversified in the common ancestor of 'higher' animals. In deuterostomes, although duplications have occurred, no novel subfamilies of Wnts have evolved. By contrast, the protostomes Drosophila and Caenorhabditis have lost half of the ancestral Writs. This pattern - loss of genes from an ancestrally complex state - might be more important in animal evolution than previously recognized. ------------------- Key: 7522 Medline: Authors: Mitreva M;Blaxter ML;Bird DM;McCarter JP Title: Comparative genomics of nematodes. Citation: Trends in Genetics 21: 573-581 2005 Type: REVIEW Genes: Abstract: Recent transcriptome and genome projects have dramatically expanded the biological data available across the phylum Nematoda. Here we summarize analyses of these sequences, which have revealed multiple unexpected results. Despite a uniform body plan, nematodes are more diverse at the molecular level than was previously recognized, with many species- and group-specific novel genes. In the genus Caenorhabditis, changes in chromosome arrangement, particularly local inversions, are also rapid, with breakpoints occurring at 50-fold the rate in vertebrates. Tylenchid plant parasitic nematode genomes contain several genes closely related to genes in bacteria, implicating horizontal gene transfer events in the origins of plant parasitism. Functional genomics techniques are also moving from Caenorhabditis elegans to application throughout the phylum. Soon, eight more draft nematode genome sequences will be available. This unique resource will underpin both molecular understanding of these most abundant metazoan organisms and aid in the examination of the dynamics of genome evolution in animals. ------------------- Key: 7523 Medline: Authors: Frand AR;Russel S;Ruvkun G Title: Functional genomic analysis of C. elegans molting. Citation: PLoS Biology 3: 1719-1733 2005 Type: ARTICLE Genes: ach-1 adt-2 alg-1 bli-1 bli-3 bli-4 bli-5 fbn-1 gei-16 kin-2 let-92 lev-11 lir-1 lrp-1 lrp-23 mlt-8 mlt-9 mlt-10 mlt-11 nas-36 nas-37 nhr-23 nhr-25 noah-1 noah-2 pan-1 ptr-4 ptr-23 qua-1 rrf-3 rme-8 skp-1 unc-52 xrn-2 Abstract: Although the molting cycle is a hallmark of insects and nematodes, neither the endocrine control of molting via size, stage, and nutritional inputs nor the enzymatic mechanism for synthesis and release of the exoskeleton is well understood. Here, we identify endocrine and enzymatic regulators of molting in C. elegans through a genome-wide RNA-interference screen. Products of the 159 genes discovered include annotated transcription factors, secreted peptides, transmembrane proteins, and extracellular matrix enzymes essential for molting. Fusions between several genes and green fluorescent protein show a pulse of expression before each molt in epithelial cells that synthesize the exoskeleton, indicating that the corresponding proteins are made in the correct time and place to regulate molting. We show further that inactivation of particular genes abrogates expression of the green fluorescent protein reporter genes, revealing regulatory networks that might couple the expression of genes essential for molting to endocrine cues. Many molting genes are conserved in parasitic nematodes responsible for human disease, and thus represent attractive targets for ------------------- Key: 7524 Medline: Authors: Lipton J Title: Mating worms and the cystic kidney: Caenorhabditis elegans as a model for renal disease. Citation: Pediatric Nephrology 20: 1531-1536 2005 Type: REVIEW Genes: daf-19 egl-44 egl-46 lov-1 psm-5 pkd-2 Abstract: Polycystic kidney disease (PKD) is caused by a group of variably inherited human disorders that are major causes of end-stage renal disease in both children and adults. The genetic culprits responsible for autosomal-dominant PKD (ADPKD), the polycystins, have been identified, yet still little is known about the molecular mechanisms that result in the disease phenotype. Polycystin homologs have been isolated in the model genetic organism Caenorhabditis elegans and, interestingly, play a specific role in C. elegans male mating behavior. Despite the recruitment of the polycystins for divergent functions in worms and humans it appears that the fundamental molecular and genetic interactions of these genes are evolutionarily conserved. In addition, studies in the worm have contributed to an understanding of the emerging role for cilia in the function of the polycystin pathway, expanding a promising frontier in PKD research. C. elegans has also been used to identify a gene family which may have significance for understanding the formation and maintenance of renal ------------------- Key: 7525 Medline: Authors: Kipreos ET Title: C. elegans cell cycles: invariance and stem cell divisions. Citation: Nature Reviews Molecular Cell Biology 6: 766-776 2005 Type: REVIEW Genes: cdc-25.1 cdk-2 cdk-4 cki-1 cyd-1 cye-1 cul-1 div-1 dpl-1 efl-1 efl-2 fbf-1 fbf-2 fzr-1 gld-1 gld-2 gld-3 glp-1 lag-1 lag-2 lag-3 lin-3 lin-5 lin-12 lin-14 lin-23 lin-35 lin-59 nos-1 nos-2 wee-1.3 Abstract: The adult Caenorhabditis elegans nematode, a small roundworm, has a precisely defined number of somatic cells that create organs that are also found in larger animals, including intestine, muscles, skin, an excretory system and a primitive brain. Every cell has a defined role in this sophisticated, but tiny animal. Therefore, stringent control of the cell cycle is required to produce the almost invariant cell lineage that generates the C. elegans somatic body plan. The proliferation of germ cells is regulated differently, and occurs within a stem cell niche. ------------------- Key: 7526 Medline: Authors: Faumont S;Miller AC;Lockery SR Title: Chemosensory behavior of semi-restrained Caenorhabditis elegans. Citation: Journal of Neurobiology 65: 171-178 2005 Type: ARTICLE Genes: egl-2 Abstract: A new behavioral assay is described for studying chemosensation in the nematode Caenorhabditis elegans. This assay presents three main characteristics: (1) the worm is restrained by gluing, preserving correlates of identifiable behaviors; (2) the amplitude and time course of the stimulus are controlled by the experimenter; and (3) the behavior is recorded quantitatively. We show that restrained C. elegans display behaviors comparable to those of freely moving worms. Moreover, the chemosensory response of wild-type glued animals to changes in salt concentration is similar to that of freely moving animals. This glued-worm assay was used to reveal new chemosensory deficits of the potassium channel mutant egl-2. We conclude that the glued worm assay can be used to study the chemosensory regulation of C. elegans behavior and how it is affected by neuronal or genetic manipulations. ------------------- Key: 7527 Medline: Authors: Filippidis G;Kouloumentas C;Voglis G;Zacharopoulou F;Papazoglou TG;Tavernarakis N Title: Imaging of Caenorhabditis elegans neurons by second-harmonic generation and two-photon excitation Citation: Journal of Biomedical Optics 10: 24015- 2005 Type: ARTICLE Genes: Abstract: Second-harmonic generation (SHG) and two-photon excitation fluorescence (TPEF) are relatively new and promising tools for the detailed imaging of biological samples and processes at the microscopic level. By exploiting these nonlinear phenomena phototoxicity and photobleaching effects on the specimens are reduced dramatically. The main target of this work was the development of a compact inexpensive and reliable experimental apparatus for nonlinear microscopy measurements. Femtosecond laser pulses were utilized for excitation. We achieved high-resolution imaging and mapping of Caenorhabditis elegans (C. elegans) neurons and muscular structures of the pharynx, at the microscopic level by performing SHG and TPEF measurements. By detecting nonlinear phenomena such as SHG and TPEF it is feasible to extract valuable information concerning the structure and the function of nematode neurons. ------------------- Key: 7528 Medline: Authors: McVeigh P;Leech S;Mair GR;Marks NJ;Geary TG;Maule AG Title: Analysis of FMRFamide-like peptide (FLP) diversity in phylum Nematoda. Citation: International Journal for Parasitology 35: 1043-1060 2005 Type: ARTICLE Genes: flp-1 flp-2 flp-3 flp-4 flp-5 flp-6 flp-7 flp-8 flp-9 flp-10 flp-11 flp-12 flp-13 flp-14 flp-15 flp-16 flp-17 flp-18 flp-19 flp-20 flp-21 flp-22 flp-23 flp-24 flp-25 flp-26 flp-27 flp-28 flp-29 flp-30 Abstract: This study reports a series of systematic BLAST searches of nematode ESTs on the Genbank database, using search strings derived from known nematode FLPs (those encoded by Caenorhabditis elegans flp genes as well as those isolated from other nematodes including Ascaris situm), as well as query sequences representative of theoretical FLPs. Over 1000 putative FLP-encoding ESTs were identified from multiple nematode species. A total of 969 ESTs representing sequelogs of the 23 known C. elegans flp genes were identified in 32 species, from clades I, III, IV and V. Numerical analysis of EST numbers suggests that flp-1, flp-11 and flp-14 are amongst the most highly expressed flp genes. Speculative BLAST searches were performed using theoretical FLP C-termini as queries, in an attempt to identify putative novel FLP sequences in the EST database. These searches yielded eight multi-species sequelogs encoding FLPs with novel signatures that are believed to identify distinct flp genes. These novel genes encode 25 distinct previously unidentified FLPs, and raise the current total of known nematode flp genes to 31. Additionally, software-based analyses of the presence of signal peptides were performed, with signal peptides being identified on at least one member of each group of flp ESTs, further confirming their status as secreted peptides. The data reveal that nematode FLPs encompass the most complex neuropeptide family known within the metazoa. Moreover, individual FLPs and FLP motifs are highly conserved across the nematodes with little evidence for inter-clade or inter-lifestyle variation, supporting their fundamental role in free-living and parasitic species. ------------------- Key: 7529 Medline: Authors: Matharu BK;Manrao MR;Kaul VK Title: Synthesis and nematicidal activity of 4-thiazolidinones. Citation: Indian Journal of Heterocyclic Chemistry 15: 95-96 2005 Type: ARTICLE Genes: Abstract: Condensation of thioglycollic acid with benzal-1-napthylamine and its C-phenyl derivatives (I-VIII) resulted in the formation of 2-phenyl-3-(l-naphthyl)-4-thiazolidinone and its C-phenyl derivatives (1a-Villa). The synthesized compounds were characterized on the basis of elemental analysis and spectral studies and screened for their nematicidal activity against Ditylenchus myceliophagus and Caenorhabditis elegans. Compounds IVa and VIIa have shown promising nematicidal activity against both the test ------------------- Key: 7530 Medline: Authors: Zugasti O;Rajan J;Kuwabara PE Title: The function and expansion of the Patched- and Hedgehog-related homologs in C. elegans. Citation: Genome Research 15: 1402-1410 2005 Type: ARTICLE Genes: che-14 grd-1 grd-2 grd-3 grd-4 grd-5 grd-6 grd-7 grd-8 grd-9 grd-10 grd-11 grd-12 grd-13 grd-14 grd-15 him-8 hog-1 lrp-1 ncr-1 ncr-2 ptc-1 ptc-3 ptd-2 ptr-1 ptr-2 ptr-3 ptr-4 ptr-5 ptr-6 ptr-7 ptr-8 ptr-9 ptr-10 ptr-11 ptr-12 ptr-13 ptr-14 ptr-15 ptr-16 ptr-17 ptr-18 ptr-19 ptr-20 ptr-21 ptr-22 ptr-23 ptr-24 qua-1 rrf-3 scp-1 wrt-1 wrt-2 wrt-3 wrt-4 wrt-5 wrt-6 wrt-7 wrt-8 wrt-9 wrt-10 Abstract: The Hedgehog (Hh) signaling pathway promotes pattern formation and cell proliferation in Drosophila and vertebrates. Hh is a ligand that binds and represses the Patched (Ptc) receptor and thereby releases the latent activity of the multipass membrane protein Smoothened (Smo), which is essential for transducing the Hh signal. In Caenorhabditis elegans, the Hh signaling pathway has undergone considerable divergence. Surprisingly, obvious Smo and Hh homologs are absent whereas PTC, PTC-related (PTR), and a large family of nematode Hh-related (Hh-r) proteins are present. We find that the number of PTC-related and Hh-r proteins has expanded in C elegans, and that this expansion occurred early in Nematoda. Moreover, the function of these proteins appears to be conserved in Caenorhabditis briggsae. Given our present understanding of the Hh signaling pathway, the absence of Hh and Smo raises many questions about the evolution and the function of the PTC, PTR, and Hh-r proteins in C elegans. To gain insights into their roles, we performed a global survey of the phenotypes produced by RNA-mediated interference (RNAi). Our study reveals that these genes do not require Smo for activity and that they function in multiple aspects of C elegans development, including molting, cytokinesis, growth, and pattern formation. Moreover, a subset of the PTC, PTR, and Hh-r proteins have the same RNAi phenotypes, indicating that they have the ------------------- Key: 7531 Medline: Authors: Singh ND;Davis JC;Petrov DA Title: X-linked genes evolve higher codon bias in Drosophila and Caenorhabditis. Citation: Genetics 171: 145-155 2005 Type: ARTICLE Genes: Abstract: Comparing patterns of molecular evolution between autosomes and sex chromosomes (such as X and W chromosomes) can provide insight into the forces underlying genome evolution. Here we investigate patterns of codon bias evolution on the X chromosome and autosomes in Drosophila and Caenorhabditis. We demonstrate that X-linked genes have significantly higher codon bias compared to autosomal genes in both Drosophila and Caenorhabditis. Furthermore, genes that become X-linked evolve higher codon bias gradually, over tens of millions of years. We provide several lines of evidence that this elevation in codon bias is due exclusively to their chromosomal location and not to any other property of X-linked genes. We present-two possible explanations for these observations. One possibility is that natural selection is more efficient on the X chromosome due to effective haploidy of the X chromosomes in males and persistently low effective numbers of reproducing males compared to that of females. Alternatively, X-linked genes might experience stronger natural selection for higher codon bias as a result of maladaptive reduction of their dosage engendered by the ------------------- Key: 7532 Medline: Authors: Inoue H;Hisamoto N;An JH;Oliveira RP;Nishida E;Blackwell TK;Matsumoto K Title: The C. elegans p38 MAPK pathway regulates nuclear localization of the transcription factor SKN-1 in oxidative stress response. Citation: Genes & Development 19: 2278-2283 2005 Type: ARTICLE Genes: crm-1 gcs-1 nsy-1 pmk-1 pmk-2 sek-1 skn-1 tir-1 unc-43 Abstract: The evolutionarily conserved p38 mitogen-activated protein kinase (MAPK) cascade is an integral part of the response to a variety of environmental stresses. Here we show that the Caenorhabditis elegans PMK-1 p38 MAPK pathway regulates the oxidative stress response via the CNC transcription factor SKN-1. In response to oxidative stress, PMK-1 phosphorylates SKN-1, leading to its accumulation in intestine nuclei, where SKN-1 activates transcription of gcs-1, a phase II detoxification enzyme gene. These results delineate the C. elegans p38 MAPK signaling pathway leading to the nucleus that responds to oxidative stress. ------------------- Key: 7533 Medline: Authors: Alvarez OA;Jager T;Kooijman SALM;Kammenga JE Title: Responses to stress of Caenorhabditis elegans populations with different reproductive strategies. Citation: Functional Biology 19: 897- 2005 Type: CORRECT Genes: Abstract: ------------------- Key: 7534 Medline: Authors: Luke CJ;Pak SC;Askew DJ;Askew YS;Smith JE;Silverman GA Title: Selective conservation of the RSL-encoding, proteinase inhibitory-type, clade L serpins in Caenorhabidtis elegans. Citation: Frontiers in Bioscience 11: 581-594 2005 Type: ARTICLE Genes: Abstract: Serpins are a highly conserved superfamily of serine and papain-like cysteine proteinase inhibitors that are divided phylogenetically into clades. Serpins also can be divided anatomically into those that reside predominately outside or inside cells. While the activities of the extracellular serpins are well understood, the biological functions, as well as the overall distribution of the intracellular (serpin(IC)) serpins is less well defined. Conceivably, the biological function of the serpins(IC) might be revealed by analysis of species with genomes of lower complexity. To this end, we sought to define the clade L serpin repertoire of Caenorhabditis elegans and other nematode species. Analysis of the C. elegans genome revealed the presence of 9 serpin genes. Five genes encoded for full-length serpins with functional reactive site loops (RSL). By definition, these genes were designated proteinase inhibitory-type, RSL-encoding serpins. Four of the C. elegans genes encoded for proteins without an RSL or transcripts with premature termination codons. The high percentage of non-RSL encoding to RSL-encoding serpin genes suggested that the former served a unique biological function rather than residing in the genome as simple pseudogenes. If this hypothesis was correct, we expected these non-RSL encoding genes to be conserved precisely in other Caenorhabditis species. However, in contrast to the RSL-encoding serpins that were well conserved and segregated into 3 sub-clades, we failed to detect non-RSL encoding serpin orthologues in the genomes of Caenorhabditis briggsae and Caenorhabditis remanei. These data suggested that unlike their RSL-encoding paralogues, the relatively high percentage of non-RSL encoding serpins in C. elegans was a vestige of recent duplication events and these latter genes were unlikely to serve essential functions in Caenorhabditis ------------------- Key: 7535 Medline: Authors: Tilmann C;Kimble J Title: Cyclin D regulation of a sexually dimorphic asymmetric cell division. Citation: Developmental Cell 9: 489-499 2005 Type: ARTICLE Genes: cdk-4 cki-1 cki-2 cyd-1 cye-1 dpl-1 fkh-6 dpl-1 gon-4 lin-35 pop-1 sys-1 tra-1 Abstract: The C. elegans somatic gonadal precursor cell (SGP) divides asymmetrically to establish gonad-specific coordinates in both sexes. In addition, the SGP division is sexually dimorphic and initiates sex-specific programs of gonadogenesis. Wnt/MAPK signaling determines the gonadal axes, and the FKH-6 transcription factor specifies the male mode of SGP division. In this paper, we demonstrate that C. elegans cyclin D controls PCP-1/TCF asymmetry in the SGP daughters as well as fkh-6 and rnr expression in the SGPs. Although cyclin D mutants have delayed SGP divisions, the cyclin D defects are not mimicked by other methods of retarding the SGP division. We find that EFL-1/E2F has an antagonistic effect on fkh-6 expression and gonadogenesis, which is relieved by cyclin D activity. We propose that cyclin D and other canonical regulators of the G1/S transition coordinate key regulators of axis formation and sex determination with cell cycle progression to achieve the sexually dimorphic SGP asymmetric division. ------------------- Key: 7536 Medline: Authors: Zhang Y;Foster JM;Nelson LS;Ma D;Carlow CKS Title: The chitin synthase genes chs-1 and chs-2 are essential for C. elegans development and responsible for chitin deposition in the eggshell and pharynx, respectively. Citation: Developmental Biology 285: 330-339 2005 Type: ARTICLE Genes: chs-1 chs-2 Abstract: It is widely accepted that chitin is present in nematodes. However, its precise role in embryogenesis is unclear and it is unknown if chitin is necessary in other nematode tissues. Here, we determined the roles of chitin and the two predicted chitin synthase genes in Caenorhabditis elegans by chitin localization and gene disruption. Using a novel probe, we detected chitin in the eggshell and discovered elaborate chitin localization patterns in the pharyngeal lumen walls. Chitin deposition in these two sites is likely regulated by the activities of chs-1 (T25G3.2) and chs-2 (F48A11.1), respectively. Reducing chs-1 gene activity by RNAi led to eggs that were fragile and permeable to small molecules, and in the most severe case, absence of embryonic cell division. Complete loss of function in a chs-1 deletion resulted in embryos that lacked chitin in their eggshells and failed to divide. These results showed that eggshell chitin provides both mechanical support and chemical impermeability essential to developing embryos. Knocking down chs-2 by RNAi caused a defect in the pharynx and led to L1 larval arrest, indicating that chitin is involved in the development and ------------------- Key: 7537 Medline: Authors: Zinovyeva AY;Forrester WC Title: The C. elegans Frizzled CFZ-2 is required for cell migration and interacts with multiple Wnt signaling Citation: Developmental Biology 285: 447-461 2005 Type: ARTICLE Genes: cfz-2 cwn-1 cwn-2 egl-20 lin-44 mom-2 mom-5 Abstract: Members of the Frizzled family of integral membrane proteins are implicated in many developmental events, including specifying cell fate, orienting cell and planar polarity, and directing cell migration. Frizzleds function as cell surface receptors for secreted Writ proteins. We report here the isolation of a mutation in cfz-2, a Caenorhabditis elegans Frizzled gene. Mutation of cfz-2 causes defective cell migration, disorganization of head neurons, and can cause ectopic axon outgrowth. Analysis of mosaic animals shows that CFZ-2 functions cell nonautonomously, but does not rule out an autonomous role. CFZ-2 is expressed primarily in the anterior of embryos and in several cells in the head of adults. Our analysis of interactions between CFZ-2 and other Writ pathways reveals that three Writs, CWN-1, CWN-2 and EGL-20, and a Frizzled, MOM-5, function redundantly with one another and with CFZ-2 for specific cell migrations. In contrast, CWN-1, CWN-2, EGL-20, CFZ-2, and MOM-5 antagonize one another for other migrations. Therefore, CFZ-2 functions by collaborating with and/or antagonizing other Writ signaling pathways to regulate specific cell migrations. ------------------- Key: 7538 Medline: Authors: Maduro MF;Kasmir JJ;Zhu J;Rothman JH Title: The Wnt effector POP-1 and the PAL-1/Caudal homeoprotein collaborate with SKN-1 to activate C. elegans endoderm development. Citation: Developmental Biology 285: 510-523 2005 Type: ARTICLE Genes: end-1 end-3 med-1 med-2 mom-2 pal-1 pop-1 skn-1 sDF127 Abstract: POP-1, a Tcf/Lef-1-like target of the convergent Writ and MAP kinase (MAPK) signaling pathways, functions throughout Caenorhabditis elegans development to generate unequal daughters during asymmetric cell divisions. A particularly prominent such asymmetric division occurs when the EMS blastomere divides to produce MS, a mesoderm precursor, and E, the sole endoderm, progenitor. POP-1 allows mesoderm development in the MS lineage by repressing the endoderm-promoting end-1 and end-3 genes. This repression is relieved in the E lineage by Wnt/MAPK signaling, which results in phosphorylation and export of POP-1 from the E nucleus. Here, we report that, in addition to repressing E development in MS, POP-1 also functions positively in endoderm development, in conjunction with the well-characterized endoderm-promoting SKN-1 -> MED regulatory cascade. While removal of POP-1 alone results in derepression of endoderm development in the MS lineage, mutations in several genes that result in impenetrant loss of endoderm are strongly enhanced by loss of pop-1 function. A Lef-1-like binding site is essential for activation of an end-1 promoter fusion, suggesting that POP-1 may act directly on end-1. Thus, POP-1 may generate developmental asymmetry during many cell divisions in C elegans by reiteratively switching from repressive and activating states. Furthermore, we report that the Caudal-like homeodomain protein PAL-1, whose role in early embryogenesis was thought to be exclusive specification of mesectodermal development in the lineage of the C blastomere, can act with POP-1 to activate endoderm specification in the absence of the SKN-1 -> MED transcriptional input, accounting for the impenetrance of mutants lacking SKN-1 or MED-1,2 activity. We conclude that the combined action of several separate transcriptional regulatory inputs, including SKN-1, the MEDs, PAL-1, and the Wnt/MAPK-activated form of POP-1, are responsible for activating end gene transcription and endoderm development. ------------------- Key: 7539 Medline: Authors: Shetty P;Lo MC;Robertson SM;Lin R Title: C. elegans TCF protein, POP-1, converts from repressor to activator as a result of Wnt-induced lowering of nuclear levels. Citation: Developmental Biology 285: 584-592 2005 Type: ARTICLE Genes: end-1 end-3 pop-1 sds-23 sds-26 wrm-1 Abstract: Canonical Wnt signaling converts the TCF/LEF transcription factor from repressor to activator by increasing nuclear levels of its coactivator, beta-catenin. A striking exception had been reported for Wnt-induced endoderm formation during C. elegans embryogenesis. It has long been believed that transcriptional activation of Wnt target genes in the endoderm precursor occurred due to a lowering of nuclear levels of the worm TCF/LEF protein, POP-1, effectively alleviating POP-1 repressive activity. Contrary to this model, we demonstrate here that POP-1 directly activates Wnt target genes in the endoderm precursor. Wnt converts POP-1 from a repressor to an activator, and this conversion requires that POP-1 nuclear levels be lowered in the endoderm precursor. We propose that the balance between TCF/LEF and coactivator(s), achieved by elevating coactivator levels (the canonical pathway) and/or reducing TCF/LEF levels (worm endoderm), determines Wnt signal strength. ------------------- Key: 7540 Medline: Authors: Masse I;Molin L;Billaud M;Solari F Title: Lifespan and dauer regulation by tissue-specific activities of Caenorhabditis elegans DAF-18. Citation: Developmental Biology 286: 91-101 2005 Type: ARTICLE Genes: daf-2 daf-16 daf-18 Abstract: In Caenorhabditis elegans, the insulin/IGF-1 DAF-2 receptor controls entry into dauer and longevity. DAF-2 signaling cascade includes the PI3 kinase homolog AGE-1 and the FOXO transcription factor DAF-16. The DAF-2 pathway is downregulated by DAF-18 which is encoded by the ortholog of the human tumor suppressor gene PTEN. We have previously shown that, like PTEN, DAF-18 antagonizes the activity of PI3 kinase/AGE-1. To further explore the role of DAF-18 in the regulation of the insulin pathway, we investigated which tissue(s) DAF-18 functions in to regulate dauer formation and lifespan. Our data show that complete dauer formation requires daf-18 expression in several tissues and that the remodeling of dauer tissues depends on both cell autonomous and cell nonautonomous daf-18 function(s). Conversely, daf-18 expression increases adult lifespan in all individual tissues tested. Furthermore, we show that the role of DAF-18 in clatter and lifespan control depends on DAF-16 activation, which is regulated by both cell autonomous and cell nonautonomous DAF-18 function(s) and in a tissue-specific manner. Overall, our data strongly suggest that several tissues act as signaling centers to mediate DAF-18 function and that DAF-18 could act outside the canonical DAF-2/DAF-16 pathway to regulate dauer and lifespan. ------------------- Key: 7541 Medline: Authors: Kim K;Colosimo ME;Yeung H;Sengupta P Title: The UNC-3 Olf/EBF protein represses alternate neuronal programs to specify chemosensory neuron identity. Citation: Developmental Biology 286: 136-148 2005 Type: ARTICLE Genes: ceh-36 che-1 cog-1 daf-7 flp-3 flp-6 flp-8 flp-20 gcy-5 gcy-7 gpa-4 gpa-9 lim-4 lim-6 mec-4 myo-3 odr-1 odr-7 odr-10 sra-6 str-1 str-2 str-3 unc-3 unc-35 Abstract: Neuronal identities are specified by the combinatorial functions of activators and repressors of gene expression. Members of the well-conserved Olf/EBF (O/E) transcription factor family have been shown to play important roles in neuronal and non-neuronal development and differentiation. O/E proteins are highly expressed in the olfactory epithelium, and O/E binding sites have been identified upstream of olfactory genes. However, the roles of O/E proteins in sensory neuron development are unclear. Here we show that the O/E protein UNC-3 is required for subtype specification of the ASI chemosensory neurons in Caenorhabditis elegans. UNC-3 promotes an ASI identity by directly repressing the expression of alternate neuronal programs and by activating expression of ASI-specific genes including the daf-7 TGF-beta gene. Our results indicate that UNC-3 is a critical component of the transcription factor code that integrates cell-intrinsic developmental programs with external signals to specify sensory neuronal identity and suggest models for O/E protein functions in other systems. ------------------- Key: 7542 Medline: Authors: Tiensuu T;Larsen MK;Vernersson E;Tuck S Title: lin-1 has both positive and negative functions in specifying multiple cell fates induced by Ras/MAP kinase signaling in C. elegans. Citation: Developmental Biology 286: 338-351 2005 Type: ARTICLE Genes: egl-5 egl-17 eor-1 let-23 let-60 lin-1 lin-12 lin-15 lin-31 lin-44 lip-1 mab-5 mpk-1 Abstract: lin-1 encodes an ETS domain transcription factor that functions downstream of a Ras/MAP kinase pathway mediating induction of the 1 degrees cell fate during vulval development in the C elegans hermaphrodite. Mutants lacking lin-I activity display a phenotype similar to that caused by mutations that constitutively activate let-60 Ras consistent with a model in which lin-1 is a repressor of the 1 degrees fate whose activity is inhibited by phosphorylation by MPK-l MAP kinase. Here, we show that, contrary the current model, lin-1 is required positively for the proper expression of several genes regulated by the pathway in cells adopting the 1 degrees cell fate. We show that the positive requirement for lin-1 is downstream of let-60 Ras and mpk-1 MAP kinase, and that it has a focus in the vulval precursor cells themselves. lin-1 alleles encoding proteins lacking a docking site for MPK-l MAP kinase are defective in the positive function. We also show that lin-1 apparently has both positive and negative functions during the specification of the fates of other cells in the worm requiring Ras/MAP kinase signaling. ------------------- Key: 7543 Medline: Authors: Rougvie AE Title: Intrinsic and extrinsic regulators of developmental timing: from miRNAs to nutritional cues. Citation: Development 132: 3787-3798 2005 Type: REVIEW Genes: col-19 daf-12 hbl-1 let-7 lin-4 lin-14 lin-28 lin-29 lin-41 lin-42 lin-46 mir-48 mir-84 mir-241 Abstract: A fundamental challenge in biology is to understand the reproducibility of developmental programs between individuals of the same metazoan species. This developmental precision reflects the meticulous integration of temporal control mechanisms with those that specify other aspects of pattern formation, such as spatial and sexual information. The cues that guide these developmental events are largely intrinsic to the organism but can also include extrinsic inputs, such as nutrition or temperature. This review discusses the well-characterized developmental timing mechanism that patterns the C elegans epidermis. Components of this pathway are conserved, and their links to developmental time control in other species are considered, including the temporal patterning of the fly nervous system. Particular attention is given to the roles of miRNAs in developmental timing and to the emerging mechanisms that link developmental programs to nutritional ------------------- Key: 7544 Medline: Authors: Reichart K;Menzel R Title: Expression profiling of five different xenobiotics using a Caenorhabditis elegans whole genome microarray. Citation: Chemosphere 61: 229-237 2005 Type: ARTICLE Genes: gst-4 mtl-1 vem-1 vit-1 vit-6 Abstract: The soil nematode Caenorhabditis elegans is frequently used in ecotoxicological studies due to its wide distribution in terrestrial habitats, its easy handling in the laboratory, and its sensitivity against different kinds of stress. Since its genome has been completely sequenced, more and more studies are investigating the functional relation of gene expression and phenotypic response. For these reasons C elegans seems to be an attractive animal for the development of a new, genome based, ecotoxicological test system. In recent years, the DNA array technique has been established as a powerful tool to obtain distinct gene expression patterns in response to different experimental conditions. Using a C elegans whole genome DNA microarray in this study, the effects of five different xenobiotics on the gene expression of the nematode were investigated. The exposure time for the following five applied compounds beta-NF (5 mg/l), Fla (0.5 mg/l), atrazine (25 mg/l), clofibrate (10 mg/l) and DES (0.5 mg/l) was 48 ñ 5 h. The analysis of the data showed a clear induction of 203 genes belonging to different families like the cytochromes P450, UDP-glucoronosyltransferases (UDPGT), glutathione S-transferases (GST), carboxylesterases, collagenes, C-type lectins and others. Under the applied conditions, fluoranthene was able to induce most of the induceable genes, followed by clofibrate, atrazine, beta-naphthoflavone and diethylstilbestrol. A decreased expression could be shown for 153 genes with atrazine having the strongest effect followed by fluoranthene, diethylstilbestrol, beta-naphthoflavone and clofibrate. For upregulated genes a change ranging from approximately 2.1-till 42.3-fold and for downregulated genes from approximately 2.1 till 6.6-fold of gene expression could be affected through the applied xenobiotics. The results confirm the applicability of the gene expression for the development of an ecotoxicological test system. Compared to classical tests the main advantages of this new approach will be the increased sensitivity and it's potential for a substance class specific effect determination as well as the large numbers of genes that can be screened rapidly at the same time and the selection of well regulated marker ------------------- Key: 7545 Medline: Authors: Norman KR;Fazzio RT;Mellem JE;Espelt MV;Strange K;Beckerle MC;Maricq AV Title: The Rho/Rac-family guanine nucleotide exchange factor VAV-1 regulates rhythmic behaviors in C. elegans. Citation: Cell 123: 119-132 2005 Type: ARTICLE Genes: cdc-42 ced-10 ife-2 ipp-5 itr-1 let-23 lin-3 mig-2 pha-4 ppk-1 ppk-2 ppk-3 rac-2 rho-1 vav-1 Abstract: Rhythmic behaviors are a fundamental feature of all organisms. Pharyngeal pumping, the defecation cycle, and gonadal-sheath-cell contractions are three well-characterized rhythmic behaviors in the nematode C. elegans. The periodicities of the rhythms range from subsecond (pharynx) to seconds (gonadal sheath) to minutes (defecation). However, the molecular mechanisms underlying these rhythmic behaviors are not well understood. Here, we show that the C. elegans Rho/Rac-family guanine nucleotide exchange factor, VAV-1, which is homologous to the mammalian Vav proto-oncogene, has a crucial role in all three behaviors. vav-1 mutants die as larvae because VAV-1 function is required in the pharynx for synchronous contraction of the musculature. In addition, ovulation and the defecation cycle are abnormal and arrhythmic. We show that Rho/Rac-family GTPases and the signaling molecule inositol triphosphate (IP3) act downstream of VAV-1 signaling and that the VAV-1 pathway modulates rhythmic behaviors by dynamically regulating the concentration of intracellular Ca2+. ------------------- Key: 7546 Medline: Authors: Baylis HA Title: VAV's got rhythm. Citation: Cell 123: 5-7 2005 Type: REVIEW Genes: ced-10 itr-1 mig-2 rho-1 vav-1 Abstract: Biological rhythms with periods of less than a day are physiologically important but poorly understood. In this issue of Cell, Norman, Maricq, and colleagues (Norman et al., 2005) show that VAV-1, a guanine nucleotide exchange factor for Rho-family GTPases, is necessary for three rhythmic behaviors in the nematode Caenorhabditis elegans: feeding, defecation, and ovulation. ------------------- Key: 7547 Medline: Authors: Wakabayashi T;Osada T;Shingai R Title: Serotonin deficiency shortens the duration of forward movement in Caenorhabditis elegans. Citation: Bioscience, Biotechnology & Biochemistry 69: 1767-1770 2005 Type: ARTICLE Genes: bas-1 cat-4 egl-1 tph-1 Abstract: Serotonin has been implicated in numerous behaviors in a wide variety of animals. We examined the effect of serotonin deficiency, induced by genetic perturbations and cell ablations, on the duration of Caenorhabditis elegans forward movement. Mutants with defective serotonin biosynthesis or worms with ablated serotonergic neurons showed a markedly decreased duration of forward movement, suggesting involvement of this neuromodulator in the regulation of the duration of worm locomotion. ------------------- Key: 7548 Medline: Authors: Davis MW;Hammarlund M;Harrach T;Hullett P;Olsen S;Jorgensen EM Title: Rapid single nucleotide polymorphism mapping in C. elegans. Citation: BMC Genomics 6: 1-11 2005 Type: ARTICLE Genes: Abstract: ------------------- Key: 7549 Medline: Authors: Johnson NM:Behm CA;Trowell SC Title: Heritable and inducible gene knockdown in C. elegans using Wormgate and the ORFeome. Citation: Gene 359: 26-34 2005 Type: ARTICLE Genes: eat-2 rrf-3 unc-4 Abstract: Double-stranded RNA (dsRNA) mediated gene silencing (RNA interference; RNAi) is a powerful tool for investigating gene function. It is usually performed in Caenorhabditis elegans via the injection or oral delivery of dsRNA, but an alternative approach, the expression of RNA hairpins from introduced DNA (hairpin RNAi; hpRNAi) has several advantages: (1) it can be induced systemically or in a tissue-specific manner; (2) because it is heritable, it allows consistent RNAi silencing across a whole population of genetically identical animals; and (3) it can be applied in refractory tissue such as neurons. hpRNAi has not been widely used to investigate gene function because a number of steps are relatively inefficient and labour-intensive. We describe Wormgate, a new cloning system, which facilitates the efficient high-throughput production of hpRNAi constructs using clones from the C elegans ORFeome library. The combined use of pWormgate2 and the ORFeome library, with a recently developed particle bombardment transformation system, expedites hpRNAi gene silencing. This will be particularly useful for studying those genes that are refractory to the effects of injected or fed dsRNA, such as neural genes. We report the efficient production of hpRNAi constructs using pWormgate2 and also the knockdown of selected genes, including neurally expressed genes that have previously been refractory to RNAi. Further, when combined with the rrf-3 RNAi hypersensitive strain, the Wormgate approach delivered a highly penetrant knockdown phenotype in nearly 100% of worms for a gene that was completely refractory to other ------------------- Key: 7550 Medline: 16190471 Authors: Ning F;Delhomme D;LeCun Y;Piano F;Bottou L;Barbano PE Title: Toward automatic phenotyping of developing embryos from videos. Citation: IEEE Transactions on Image Processing 14: 1360-1371 2005 Type: ARTICLE Genes: Abstract: We describe a trainable system for analyzing videos of developing C. elegans embryos. The system automatically detects, segments, and locates cells and nuclei in microscopic images. The system was designed as the central component of a fully automated phenotyping system. The system contains three modules 1) a convolutional network trained to classify each pixel into five categories: cell wall, cytoplasm, nucleus membrane, nucleus, outside medium; 2) an energy-based model, which cleans up the output of the convolutional network by learning local consistency constraints that must be satisfied by label images; 3) a set of elastic models of the embryo at various stages of development that are matched to the label images. ------------------- Key: 7551 Medline: 16038089 Authors: Zhao Y;Johnsen R;Baillie D;Rose A Title: Worms in space? A model biological dosimeter. Citation: Gravitation & Space Biology Bulletin 18: 11-16 2005 Type: REVIEW Genes: Abstract: Although it is well known that radiation causes mutational damage, little is known about the biological effects of long-term exposure to radiation in space. Exposure to radiation can result in serious heritable defects in experimental animals, and in humans, susceptibility to cancer, radiation-sickness, and death at high dosages. It is possible to do ground controlled studies of different types of radiation on experimental animals and to physically measure radiation on the space station or on space probes. However, the actual biological affects of long-term exposure to the full range of space radiation have not been studied, and little information is available about the biological consequences of solar flares. Biological systems are not simply passive recording instruments. They respond differently under different conditions, and thus it is important to be able to collect data from a living animal. There are technical difficulties that restrict the placement of an experimental organism in a space environment for long periods of time, in a manner that allows for the recovery of genetic data. Use of the self-fertilizing hermaphroditic nematode, Caenorhabditis elegans offers potential for the design of a biological dosimeter. In this paper, we describe the advantages of this model system and review the literature of C. elegans ------------------- Key: 7552 Medline: 16038100 Authors: Rahlen T;Sunga J;Rask J;Herrera A;Lam K;Sing L;Sato K;Ramos RA;Kirven-Brooks M;Reiss-Bubenheim D Title: Methods for the culture of C. elegans and S. cerevisiae in microgravity. Citation: Gravitation & Space Biology Bulletin 18: 91-92 2005 Type: ARTICLE Genes: Abstract: To support the study of the effects of microgravity on biological systems, our group is developing and testing methods that allow the cultivation of C. elegans and S. cerevisiae in microgravity. Our aim is to develop the experimental means by which investigators may conduct peer reviewed biological experiments with C. elegans or S. cerevisiae in microgravity. Our protocols are aimed at enabling investigators to grow these organisms for extended periods during which samples may be sub-cultured, collected, preserved, frozen, and/or returned to earth for analysis. Data presented include characterization of the growth phenotype of these organisms in liquid medium in OptiCells(TM) (Biocrystal, LTD). ------------------- Key: 7553 Medline: 15896656 Authors: Oey NA;Ijlst L;van Roermund CW;Wijburg FA;Wanders RJ Title: dif-1 and colt, both implicated in early embryonic development, encode carnitine acylcarnitine translocase. Citation: Molecular Genetics & Metabolism 85: 121-124 2005 Type: ARTICLE Genes: dif-1 Abstract: It has always been assumed that during development the embryo and fetus depend only on glycolysis for energy generation and that they do not oxidize fatty acids. Recently, however, we found abundant expression and activity of fatty acid oxidation (FAO) enzymes in the human embryo and fetus. In a search for FAO gene expression during development we came across two embryonic differentiation genes: differentiation defective (dif-1) and congested-like trachea (colt) of Caenorhabditis elegans and Drosophila melanogaster, respectively. Earlier studies showed that expression of these two genes is essential during developmental stages with high energy requirements. Both dif-1 and colt encode proteins with sequence similarity to the mitochondrial carnitine acylcarnitine carrier (CACT), which suggests that the DIF-1 and COLT proteins might be functional orthologues of CACT. To investigate this, we expressed both dif-1 and colt in Saccharomyces cerevisiae. Our results show that DIF-1 and COLT can functionally complement a yeast CACT deletion strain and thus function as carnitine acylcarnitine transporters. This finding is well in line with the recent observation that embryos are capable of oxidizing fatty acids and furthermore implies that FAO is essential during early embryonic development when the energy demand is high. ------------------- Key: 7554 Medline: Authors: Milani M;Drobne D;Tatti F;Batani D;Poletti G;Orsini F;Zullini A;Zrimec A Title: Read-out of soft X-ray contact microscopy microradiographs by focused ion beam/scanning electron microscope. Citation: Scanning 27: 249-253 2005 Type: ARTICLE Genes: Abstract: A novel focused ion beam-based technique is presented for the read-out of microradiographs of Caenorhabditis elegans nematodes generated by soft x-ray contact microscopy (SXCM). In previous studies, the read-out was performed by atomic force microscopy (AFM), but in our work SXCM microradiographs were imaged by scanning ion microscopy (SIM) in a focused ion beam/scanning electron microscope (FIB/SEM). It allows an ad libitum selection of a sample region for gross morphologic to nanometric investigations, with a sequence of imaging and cutting. The FIB/SEM is less sensitive to height variation of the relief, and sectioning makes it possible to analyse the sample further. The SXCM can be coupled to SIM in a more efficient and faster way than to AFM. Scanning ion microscopy is the method of choice for the read-out of microradiographs of small multicellular organisms. ------------------- Key: 7555 Medline: Authors: Liedtke W Title: TRPV4 as osmosensor: a transgenic approach. Citation: Pflugers Arch - European Journal of Physiology 451: 176-180 2005 Type: REVIEW Genes: ocr-2 osm-9 Abstract: The transient receptor potential vanilloid 4 (TRPV4) ion channel was named initially vanilloid-receptor-related osmotically activated channel (VR-OAC). Preliminary answers to the question, "What is the function of the trpv4 gene in live animals ?" are highlighted briefly in this review. In trpv4 null mice, TRPV4 is necessary for the maintenance of osmotic equilibrium, and in Caenorhabditis elegans transgenic for mammalian TRPV4, TRPV4 directs the osmotic avoidance response in the context of the ASH "nociceptive" neuron. The molecular mechanisms of gating of TRPV4 in vivo need to be determined; in particular, whether TRPV4 in live animals is gated via phosphorylation of defined amino-acid residues or more directly through the osmotic stimulus itself. ------------------- Key: 7556 Medline: Authors: O'Neil RG;Heller S Title: The mechanosensitive nature of TRPV channels. Citation: Pflugers Arch - European Journal of Physiology 451: 193-203 2005 Type: REVIEW Genes: ocr-2 ocr-4 osm-9 Abstract: Transient receptor potential vanilloid (TRPV) channels are widely expressed in both sensory and nonsensory cells. Whereas the channels display a broad diversity to activation by chemical and physical stimuli, activation by mechanical stimuli is common to many members of this group in both lower and higher organisms. Genetic screening in Caenorhabditis elegans has demonstrated an essential role for two TRPV channels in sensory neurons. OSM-9 and OCR-2, for example, are essential for both osmosensory and mechanosensory (nose-touch) behaviors. Likewise, two Drosophila TRPV channels, NAN and IAV, have been shown to be critical for hearing by the mechanosensitive chordotonal organs located in the fly's antennae. The mechanosensitive nature of the channels appears to be conserved in higher organisms for some TRPV channels. Two vertebrate channels, TRPV2 and TRPV4, are sensitive to hypotonic cell swelling, shear stress/fluid flow (TRPV4), and membrane stretch (TRPV2). In the osmosensing neurons of the hypothalamus (circumventricular organs), TRPV4 appears to function as an osmoreceptor, or part of an osmoreceptor complex, in control of vasopressin release, whereas in inner ear hair cells and vascular baroreceptors a mechanosensory role is suggestive, but not demonstrated. Finally, in many nonsensory cells expressing TRPV4, such as vascular endothelial cells and renal tubular epithelial cells, the channel exhibits well-developed local mechanosensory transduction processes where both cell swelling and shear stress/fluid flow lead to channel activation. Hence, many TRPV channels, or combinations of TRPV channels, display a mechanosensitive nature that underlies multiple mechanosensitive processes from worms to mammals. ------------------- Key: 7557 Medline: 16101677 Authors: Morrow IC;Parton RG Title: Flotillins and the PHB domain protein family: rafts, worms and anaesthetics. Citation: Traffic 6: 725-740 2005 Type: REVIEW Genes: mec-2 unc-1 unc-24 Abstract: While our understanding of lipid microdomains has advanced in recent years, many aspects of their formation and dynamics are still unclear. In particular, the molecular determinants that facilitate the partitioning of integral membrane proteins into lipid raft domains are yet to be clarified. This review focuses on a family of raft-associated integral membrane proteins, termed flotillins, which belongs to a larger class of integral membrane proteins that carry an evolutionarily conserved domain called the prohibitin homology (PHB) domain. A number of studies now suggest that eucaryotic proteins carrying this domain have affinity for lipid raft domains. The PHB domain is carried by a diverse array of proteins including stomatin, podocin, the archetypal PHB protein, prohibitin, lower eucaryotic proteins such as the Dictyostelium discoideum proteins vacuolin A and vacuolin B and the Caenorhabditis elegans proteins unc-1, unc-24 and mec-2. The presence of this domain in some procaryotic proteins suggests that the PHB domain may constitute a primordial lipid recognition motif. Recent work has provided new insights into the trafficking and targeting of flotillin and other PHB domain proteins. While the function of this large family of proteins remains unclear, studies of the C. elegans PHB proteins suggest possible links to a class of volatile anaesthetics raising the possibility that these lipophilic agents could influence lipid raft domains. This review will discuss recent insights into the cell biology of flotillins and the large family of evolutionarily conserved PHB domain proteins. ------------------- Key: 7558 Medline: Authors: Eastburn DJ;Han M Title: A gain-of-function allele of cbp-1, the Caenorhabditis elegans ortholog of the mammalian CBP/p300 gene, causes an increase in histone acetyltransferase activity and antagonism of activated Ras. Citation: Molecular and Cellular Biology 25: 9427-9434 2005 Type: ARTICLE Genes: cbp-1 let-50 let-60 lin-1 lin-15 lin-31 pry-1 sqv-3 sur-6 tnDf2 Abstract: An RTK-Ras-mitogen-activated protein kinase (MAPK) signaling pathway plays a key role in vulval induction in Caenorhabditis elegans. We have previously carried out screens for suppressors of activated Ras to identify factors that play critical roles in the regulation of the pathway. ku258 was isolated as a semidominant allelle that suppresses the Multivulva phenotype caused by activated let-60 ras. Our genetic and molecular analyses indicate that ku258 is a gain-of-function allelle resulting from two point mutations in the C. elegans homolog of the transcriptional coactivator p300/CBP, cbp-1. Genetic data also suggest that cbp-1 may act downstream of the Ras signaling pathway, but not primarily downstream of the Wnt signaling pathway, to negatively regulate vulval cell fate specification. cbp-1 may function in concert with LIN-1, an Ets transcription factor family member that is one of the targets of MAPK. In vitro histone acetylation assays have revealed that together, the two point mutations cause a sevenfold increase in the histone acetyltransferase (RAT) activity of recombinant CBP-1. To our knowledge, this is the only such RAT activity mutation isolated in a CBP/p300 family protein, and this mutation may define a negative role of the RAT activity in antagonizing Ras function in a specific developmental event. ------------------- Key: 7559 Medline: Authors: Wadsworth WG Title: Axon pruning: C. elegans makes the cut. Citation: Current Biology 15: R796-R798 2005 Type: REVIEW Genes: mbr-1 unc-86 Abstract: Axon pruning has recently been described in the simple nervous system of the nematode Caenorhabditis elegans. Generating excess processes and pruning may be a phylogenetically conserved feature reflecting a flexibility to modify neural circuits. ------------------- Key: 7560 Medline: Authors: Cole DG Title: Intraflagellar transport: keeping the motors coordinated. Citation: Current Biology 15: R798-R781 2005 Type: REVIEW Genes: bbs-7 bbs-8 dyf-1 kap-1 klp-11 klp-20 osm-3 Abstract: Intraflagellar transport is a conserved delivery system that services eukaryotic cilia and flagella. Recent work in the nematode Caenorhabditis elegans has identified proteins required for the functional coordination of intraflagellar transport motors and their cargoes. ------------------- Key: 7561 Medline: Authors: Landsverk ML;Epstein HF Title: Genetic analysis of myosin II assembly and organization in model organisms. Citation: Cellular and Molecular Life Sciences 62: 2270-2282 2005 Type: REVIEW Genes: myo-1 myo-2 myo-3 unc-45 unc-54 Abstract: Myosins are a large family of actin-based motor proteins that are involved in a variety of cellular processes. Class II, or conventional, myosins are organized into a number of multi-component structures such as muscle thick filaments, non-muscle filaments and the actomyosin ring during cell division. A number of conditions must be met for the proper assembly and organization of myosin II-containing structures, including the correct stoichiometry of myosin and its associated proteins, and the conformation and regulation of the myosin molecule itself by molecular chaperones and protein kinases. In this review we discuss the use of model organisms in the genetic analysis of the assembly and organization of myosin-containing structures. ------------------- Key: 7562 Medline: Authors: Chandler RJ;Venditti CP Title: Genetic and genomic systems to study methylmalonic Citation: Molecular Genetics and Metabolism 86: 34-43 2005 Type: ARTICLE Genes: Abstract: ------------------- Key: 7563 Medline: Authors: Pop C;Salvesen GS Title: The nematode death machine in 3D. Citation: Cell 123: 192-193 2005 Type: REVIEW Genes: ced-3 ced-4 ced-9 egl-1 Abstract: ------------------- Key: 7564 Medline: Authors: Watanabe M;Mitani N;Ishii N;Miki K Title: Corrigendum to "A mutation in a cuticle collagen causes hypersensitivity to the endocrine disrupting chemical, bisphenol A, in Caenorhabditis elegans." Citation: Mutation Research 578: 436- 2005 Type: CORRECT Genes: bis-1 col-121 Abstract: ------------------- Key: 7565 Medline: Authors: Brownlie JC;Whyard S Title: Identification of novel non-autonomous CemaT transposable elements and evidence of their mobility within the C. elegans genome. Citation: Genetics 125: 243-251 2005 Type: ARTICLE Genes: Abstract: ------------------- Key: 7566 Medline: Authors: Tang S;Hyman BC Title: Rolling circle amplification of complete nematode mitochondrial genomes. Citation: Journal of Nematology 37: 236-241 2005 Type: ARTICLE Genes: Abstract: -------------------